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PBSmapping User's Guide

1. intersect nepacLL with the single polygon and plot the result plotMap joinPolys nepacLL polysB col 5 add nepacLL in a different line type to emphasize the intersection addPolys nepacLL border 2 lty 8 density 0 par oldpar locateEvents Locate Events on the Current Plot Description Locate events on the current plot using the locator function Usage locateEvents EID n 512 type p Arguments EID vector of event IDs optional n maximum number of events to locate type one of n p 1 or o If p or o then the points are plotted if 1 or o then the points are joined by lines additional par parameters for the locator function locatePolys 85 Details This function allows its user to define events with mouse clicks on the current plot via the Locator function The arguments n and type are the usual parameters of the locator function If EID is not missing then n length EID On exit from locator suppose the user defined m events If EID was missing then the output data frame will contain m events However if EID exists then the output data frame will contain length EID events and both X and Y will be NA for events EIDE m 1 n The na omit function can remove rows with NAs Value EventData with columns EID X and Y and projection attribute equal to the map s projection The function does not set the zone attribute See Also addPoints combineEvents
2. calculate and print the centroids for several polygons print calcSummary nepacLL is element nepacLL PID c 33 39 47 rollup 3 FUNzmean calcVoronoi Calculate the Voronoi Dirichlet Tesselation for a Set of Points Description Calculate the Voronoi Dirichlet tesselation for a set of points Usage calcVoronoi xydata xlim NULL ylim NULL eps 1e 09 frac 0 0001 Arguments xydata a data frame with columns X and Y containing the points xlim range of X coordinates a bounding box for the coordinates ylim range of Y coordinates a bounding box for the coordinates eps the value of epsilon used in testing whether a quantity is zero frac used to detect duplicate input points which meet the condition a1 x2 lt frac x xmax xmin and yl y2 lt frac x ymax ymin Details This routine ignores all columns other than X and Y If the user leaves xlim and ylim unspecified the function defaults to the range of the data with each extent expanded by ten percent of the range This function sets the attribute projection to 1 and the attribute zone to NULL as it assumes this projection in its calculations Value PolySet with columns PID POS X and Y See Also addPoints addPolys calcArea calcCentroid calcConvexHull calcMidRange calcSummary locateEvents plotMap plotPoints plotPolys 62 clipLines Examples local envir PBSmapEnv expr oldpar par no readonly TRUE creat
3. Details When numericResult TRUE this function counts intersections as the algorithm processes them It counts certain types i e those involving vertices and those where an edge retraces over an edge more than once The function does not give special consideration to holes It returns a value for each unigue PID SID regardless of whether a contour represents a hole Value PolyData with columns PID SID may be missing and intersecting If numericResultis TRUE intersecting contains the number of intersections Otherwise it contains a Boolean value See Also isConvex PolySet joinPolys 83 Examples local envir PBSmapEnv expr load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv calculate then print the polygons that are self intersecting p lt isIntersecting nepacLL numericResult FALSE print plp intersecting joinPolys Join One or Two PolySets using a Logic Operation Description Join one or two PolySets using a logic operation Usage joinPolys polysA polysB NULL operation INT Arguments polysA PolySet to join polysB optional second PolySet with which to join operation one of DIFF INT UNION or XOR representing difference intersection union and exclusive or respectively Details This function now Mar 2013 interfaces with the Clipper library http www angusj com delphi cli
4. Value PolyData with columns PID SID may be missing and length If projection equals UTM or LL lengths are in kilometres Otherwise lengths are in the same unit as the input PolySet See Also calcArea calcCentroid calcMidRange calcSummary locatePolys Examples local envir PBSmapEnv expr load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv calculate the perimeter of Vancouver Island print calcLength nepacLL nepacLL PID 33 calcMidRange Description Calculate the Midpoint of the X Y Ranges of Polygons Calculate the midpoint of the X Y ranges of polygons found in a PolySet Usage calcMidRange polys rollup 3 Arguments polys rollup PolySet to use level of detail in the results 1 PIDs only 2 outer contours only and 3 no roll up 60 calcSummary Details If rollup equals 1 the results contain a mean range for each unique PID only When it equals 2 they contain entries for outer contours only Finally setting it to 3 prevents roll up and they contain a mean range for each unique PID SID Value PolyData with columns PID SID may be missing X and Y See Also calcArea calcCentroid calcLength calcSummary Examples local envir PBSmapEnv expr load the data if using R if is null version language 88 version language R data nepacLL envir PBSmap
5. Author s Rowan Haigh Pacific Biological Station Fisheries and Oceans Canada Nanaimo BC References See copyright notice in point in polygon See Also importShapefile point in polygon 94 plotLines Description plotLines Plot a PolySet as Polylines Plot a PolySet as polylines Usage plotLines polys xlim NULL ylim NULL projection FALSE plt c 0 11 0 98 0 12 0 88 polyProps NULL lty NULL col NULL bg 0 axes TRUE tckLab TRUE tck 0 014 tckMinor 0 5 tck Arguments polys PolySet to plot required xlim range of X coordinates ylim range of Y coordinates projection desired projection when PolySet lacks a projection attribute one of LL UTM or a nu meric value If Boolean specifies whether to check polys for a projection attribute plt four element numeric vector x1 x2 yl y2 giving the coordinates of the plot region measured as a fraction of the figure region Set to NULL if mai in par is desired polyProps PolyData specifying which polylines to plot and their properties par parameters passed as direct arguments supersede these data lty vector describing line types cycled by PID col vector describing colours cycled by PID bg background colour of the plot axes Boolean value if TRUE plot axes tckLab Boolean vector length 1 or 2 if TRUE label the major tick marks If given a two element vector the first element describes the tick marks on the x axis
6. Usage data worldLLhigh Format Data frame consisting of 4 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinate and Y latitude coordinate Attributes projection LL Note In R the data must be loaded using the data function Source Polygon data from the GSHHS Global Self consistent Hierarchical High resolution Shoreline database gshhs_i b Download from http www soest hawaii edu wessel gshhs gshhs html worldLLhigh lt importGSHHS gshhs_i b xlim c 20 360 ylim c 90 90 level 1 n 15 xoff 0 worldLLhigh lt fixGSHHSWorld worldLLhigh 112 worldLL high References Wessel P and Smith W H F 1996 A global self consistent hierarchical high resolution shoreline database Journal of Geophysical Research 101 8741 8743 http www soest hawaii edu pwessel pwessel_pubs html See Also Data worldLL nepacLL nepacLLhigh importGSHHS addPolys clipPolys plotPolys plotMap thickenPolys thinPolys Index Topic IO print 103 Topic aplot addBubbles 47 addLabels 48 addLines 50 addPoints 5l addPolys 52 addStipples 53 plotPoints 97 Topic classes EventData 71 LocationSet 86 PolyData 100 PolySet 101 Topic datasets bcBathymetry 55 nepacLL 90 nepacLLhigh 91 pythagoras 104 surveyData 106 towData 109 towTracks 110 worldLL 110 worldLLhigh 111 Topic documentation EventData 71 LocationSet 86 PBSmappi
7. close the output file dev off Jot EXAMPLE 2 clip out Manitoulin Island area which includes all four levels polys lt importGSHHS gshhg bin 2 2 2 gshhs_f b xlim c 276 279 ylim c 45 3 46 5 maxLevel 4 plot the map and add a label plotMap polys col beige bg lightblue text 82 08 45 706 Manitoulin Isl invisible pbsfun 1 pbsfun 2 End Not run importLocs Import LocationSet from a text file Description Import a text file and convert into a LocationSet Usage importLocs LocationSet Arguments LocationSet filename of LocationSet text file Value An imported LocationSet See Also importPolys importEvents importGSHHS importShapefile 80 importShapefile importPolys Import PolySet from a text file Description Import a text file and convert into a PolySet with optional PolyData attribute Usage importPolys PolySet PolyData NULL projection NULL zone NULL Arguments PolySet filename of PolySet text file PolyData optional filename of PolyData text file projection optional projection attribute to add to EventData zone optional zone attribute to add to EventData Value An imported PolySet with optional PolyData attribute See Also importEvents importLocs importGSHHS importShapefile importShapefile Import an ESRI Shapefile Description Import an ESRI shapefile shp into either a PolySet or EventData Usage importShap
8. local envir PBSmapEnv expr oldpar par no readonly TRUE load the data if using R if is null version language 88 version language R data nepacLL surveyData envir PBSmapEnv plot a map plotMap nepacLL xlim c 136 125 ylim c 48 57 add events addPoints surveyData col 1 7 par oldpar plotPolys plotPolys Plot a PolySet as Polygons Description Plot a PolySet as polygons Usage plotPolys polys xlim NULL ylim NULL projection FALSE plt c 0 11 0 98 0 12 0 88 polyProps NULL border NULL lty NULL col NULL colHoles NULL density NA angle NULL bg 0 axes TRUE 99 tckLab TRUE tck 0 014 tckMinor 0 5 tck Arguments polys PolySet to plot required xlim range of X coordinates ylim range of Y coordinates projection desired projection when PolySet lacks a projection attribute one of LL UTM or a nu meric value If Boolean specifies whether to check polys for a projection attribute plt four element numeric vector x1 x2 yl y2 giving the coordinates of the plot region measured as a fraction of the figure region Set to NULL if mai in par is desired polyProps PolyData specifying which polygons to plot and their properties par parameters passed as direct arguments supersede these data border vector describing edge colours cycled by PID lty vector describing line types cycled by PID col vector describing
9. 5380 900 910 920 930 940 UTM Easting km Figure 8 Areas km of selected islands in the southern Strait of Georgia Shoreline data have been clipped from nepacLLhigh after conversion to UTM coordinates Figure 9 portrays data from Pacific ocean perch Sebastes alutus surveys conducted along the central BC coast during the years 1966 1989 The EventData object surveyData contains information from each tow including the longitude latitude depth catch and effort tow duration These data also imply the computed value of catch per unit effort 20 CPUE catch effort Code for this figure includes the following key function calls plotMap to draw a coastal map of this region clipped from nepacLL makeGrid to create a grid in the region of interest findCells to associate tows with the appropriate grid cells combineEvents to calculate the mean CPUE within each cell addPolys to draw cells with colours in the polyProps argument scaled to the CPUE points the native R function to plot events on the map i 88 POP Surveys 1966 89 iS at j rs g YN 52 5 52 Latitude 51 5 CPUE kg h 0 50 50 300 300 750 750 1500 1500 25000 131 130 129 128 Longitude Figure 9 Portrayal of surveyData from Pacific ocean perch Sebastes alutus surveys in the central coast region of British Columbia from 1966 89 with shoreline data clipped from nepacLL Colours portray the mean
10. MA 396 p Smith W H F and Sandwell D T 1997 Global seafloor topography from satellite altimetry and ship depth soundings Science 277 1957 1962 Starr P J Krishka B A and Choromanski E M 2002 Trawl survey for thornyhead biomass estimation off the west coast of Vancouver Island September 15 October 2 2001 Canadian Technical Report of Fisheries and Aquatic Sciences 2421 60 p Venables W N and Ripley B D 1999 Modern applied statistics with S PLUS 3 Edition Springer Verlag New York NY 501 p Venables W N and Ripley B D 2000 S programming Springer Verlag New York 264 p Wessel P and Smith W H F 1996 A global self consistent hierarchical high resolution shoreline database Journal of Geophysical Research 101 8741 8743 URL http www soest hawaii edu pwessel Wikipedia 2004 Earth radius URL http en wikipedia org wiki Earth radius Accessed Aug 19 2004 Wirth N 1975 Algorithms data structures programs Prentice Hall Englewood Cliffs NJ 366 p E y Appendix A PBSdata package This appendix documents the objects available in the R package PBSdata which is not distributed on CRAN but remains available on Google Code http code google com p pbs data Fisheries and Oceans personnel can also obtain the package from the PBS Intranet website http svbcepbsgfiis sgl Look for a link on the left entitled Most recent PBS R Packages Table Al Data sets
11. createIDs extractPolyData validatePolyData closestPoint rollupPolys rollupPolys C createFastIDdig validateData createGridIDs createIDs createIDs validateEventData createFastIDdig validateData addBubbles addBubblesLegend validateEventData addLabels addFeature checkProjection validateEventData validatePolyData validatePolySet calcCentroid calcMidRange calcSummary is EventData is PolyData addLines addProps checkProjection clip createFastIDdig createIDs preparePolyProps validatePolyProps validatePolySet is PolyData addPoints addFeature checkProjection validateEventData validatePolyData is PolyData addPolys addProps checkProjection clip createFastIDdig createIDs preparePolyProps rollupPolys validatePolyProps validatePolySet is PolyData addStipples addFeature checkProjection clip validatePolySet findPolys is PolyData thickenPolys 4 appendPolys validatePolySet is PolySet as EventData validateEventData is EventData as LocationSet validateLocationSet is LocationSet as PolyData validatePolyData is PolyData as PolySet validatePolySet is PolySet calcArea rollupPolys validatePolySet calcArea C convUL is PolyData calcCentroid rollupPolys validatePolySet calcCentroid C is PolyData calcConvexHull validateXYData grDevices chull is PolySet calcLength validatePol
12. e o OFILE ASCII output file defaults to standard output The header line in both input files must contain field names and subsequent lines must contain the relevant fields of data delimited by white space The PolySet must have field names PID SID POS X Y where SID is optional The EventData must have fields EID X Y The program writes a properly formatted LocationSet with three or four columns EID PID SID Bdry where SID may be missing Section 2 1 The default standard output can be redirected to a text file ACKNOWLEDGEMENTS We thank Dr Jim Uhl and Dr Peter Walsh in the Computing Science Department Malaspina University College for encouraging and facilitating the role of students in applied fisheries research Without the dedicated work of these students named in the Preface we could not have produced the software described here We also acknowledge the valuable shoreline and bathymetry databases compiled by Dr Paul Wessel Dr Walter Smith and Dr D T Sandwell Wessel and Smith 1996 Smith and Sandwell 1997 In particular we thank Dr Paul Wessel for permission to redistribute data from the GSHHS database Code from other authors seriously enhances this version of PBSmapping Dr Gary Robinson has kindly allowed us to use his code for a stack based Douglas Peuker line simplification routine implemented in our thinPolys function Our colleague Brian Krishka helped prepare various data objects The PBSmapping pa
13. 88 109 makeTopography 67 89 mean 65 na omit 85 nepacLL 55 56 90 91 111 112 nepacLLhigh 56 90 91 111 112 par 49 53 84 85 94 100 PBSmapping 92 PBSmapping package PBSmapping 92 PBSprint 72 86 92 101 103 106 placeHoles 81 93 plot 95 96 98 100 plotLines 50 53 69 88 94 96 97 100 110 plotMap 53 55 58 61 84 86 88 90 91 94 95 100 104 111 112 plotPoints 49 51 53 54 58 61 68 84 85 88 97 97 100 107 plotPolys 53 55 58 61 86 88 90 91 96 99 104 fi 212 point in polygon 81 93 points 51 53 54 PolyData 49 54 56 57 59 60 65 67 68 72 81 82 85 87 88 94 100 100 103 106 109 polygon 52 96 100 101 PolySet 49 50 52 64 66 69 71 76 80 84 86 88 90 91 94 101 101 103 108 110 111 print 72 86 101 103 103 print summary PBS 105 pythagoras 104 read table 89 refocusWorld 104 sum 65 summary 72 86 92 101 103 105 summary EventData 103 summary LocationSet 103 INDEX summary PolyData 103 summary PolySet 103 surveyData 48 106 text 49 thickenPolys 50 53 84 86 87 90 91 95 97 100 107 108 111 112 thinPolys 50 53 84 86 90 91 95 97 100 107 108 111 112 title 94 96 98 99 towData 109 710 towTracks 109 110 worldLL 90 91 110 112 worldLLhigh 90 91 111 111 115
14. Appendix B documents how to import their data for use with PBSmapping R provides a contour function to plot contour lines This function lacks a save argument and does not return contour coordinates Instead the contourLines function accomplishes this task giving a list that captures continuous contours as single polylines Figure 6 Latitude 131 130 129 Longitude Figure 6 The R contourLines function returns a single polyline for each continuous contour Our function convCP converts the list output from contourLines into a list object that has two components a PolySet with contour coordinates and PolyData with the depth of each contour The package PBSdata includes a data set isobaths of bathymetric contours for Canada s Pacific coast In addition several functions ease the manual procedure of converting polylines into polygons including 18 e convLP to convert two polylines into a single polygon e closePolys to close the polygons in a PolySet e fixBound to fix the boundary points of a PolySet 2 6 Examples and Applications Our library includes an illustrative PolySet towTracks containing the longitude latitude coordinates of 45 tow tracks from a longspine thornyhead Sebastolobus altivelis survey in 2001 Figure 7 portrays these data relative to the west coast of Vancouver Island drawn with shoreline data clipped from the PolySet nepacLL The PolyData object towData specifies the depth of each
15. Historical values for compatibilityy with S Plus defunct PBSdot lt 3 PBSdash lt 2 PBSclr lt function PBSclr list black c 0 0 0 sea c 224 253 254 land c 255 255 195 red c 255 0 0 green c 0 255 0 blue c 0 0 255 yellow c 255 255 0 cyan c 0 255 255 magenta c 255 0 255 purple c 150 0 150 lettuce c 205 241 203 moss c 132 221 124 irish c 54 182 48 forest c 29 98 27 white c 255 255 255 fog c 223 223 223 PBSclr lt lapply PBSclr function v rgb v 1 v 2 v 3 maxColorValue 255 return PBSclr Figure 1 World UTM Zones PBSfig01 lt function World UTM Zones clr lt PBSclr data worldLL nepacLL envir sys frame sys nframe par mfrow c 1 1 omi c 0 0 0 0 Plot the figure plotMap worldLL ylim c 90 90 bg clr sea col clr land tck 0 023 mgp c 1 9 0 7 0 cex 1 2 plt c 08 98 08 98 add UTM zone boundaries abline v seg 18 360 by 6 lty 1 col clr red add prime meridian abline v 0 lty 1 lwd 2 col clr black calculate the limits of the nepacLL PolySet xlim lt range nepacLL X 360 ylim lt range nepacLL Y create and then add the nepacLL rectangle region lt data frame PID rep 1 4 POS 1 4 X c xlim 1 xlim 2 xlim 2 xlim 1 Y c ylim 1 ylim 1 ylim 2 ylim 2 region lt as PolySet region projection LL addPolys region lwd 2 border clr blue density 0 H add labels for some UTM zones text
16. Plot the figure plotMap nepacLL col clr land bg clr sea xlim c 127 8 125 5 ylim c 48 49 8 tck 0 01 mgp c 2 5 0 cex 1 2 plt c 08 1 08 98 addLines towTracks polyProps pdata lwd 3 right justify the legend labels temp lt legend x 127 6 y 48 4 legend c lwd 3 bty n text width strwidth 1200 1600 m col c clr Sblack clr red clr blue text temp rectSleft temp rect w tempStextSy c 500 800 m 800 1200 m 1200 1600 m pos 2 text tempSrectSleft temp rect w 2 tempSrectS top pos 3 LTS Survey Tracks text 125 6 49 7 Vancouver nIsland cex 1 2 adj 1 box Figure 8 calcArea of the Southern Gulf Islands PBSfig08 lt function calcArea of the Southern Gulf Islands clr lt PBSclr data nepacLLhigh envir sys frame sys nframe xlim lt c 123 6 122 95 ylim lt c 48 4 49 zone lt 9 assign nepacLLhigh to nepacUTMhigh S62 and change to UTM coordinates nepacUTMhigh lt nepacLLhigh attr nepacUTMhigh zone lt zone nepacUTMhigh lt convUL nepacUTMhigh convert limits to UTM temp lt data frame PID 1 4 POS rep 1 4 X c xlim xlim Y c ylim rev ylim temp lt convUL as PolySet temp projection LL zone zone xlim lt range temp X ylim lt range temp Y prepare areas isles lt clipPolys nepacUTMhigh xlim ylim areas lt calcArea isles PIDs and labels for Gulf Islands bigPID lt areas
17. Y 1 10 Z rep 1 10 example output from findPolys where 1 event occurred in the first polygon 3 in the second and 6 in the third locs lt data frame EID 1 10 PID c rep 1 1 rep 2 3 rep 3 6 Bdry rep 0 10 sum the Z column of the events in each polygon and print the result print combineEvents events events locs locs FUN sum 66 convCP combinePolys Combine Several Polygons into a Single Polygon Description Combine several polygons into a single polygon by modifying the PID and SID indices Usage combinePolys polys Arguments polys PolySet with one or more polygons each with possibly several components holes Details This function accepts a PolySet containing one or more polygons PIDs each with one or more components or holes SIDs The SID column need not exist in the input The function combines these polygons into a single polygon by simply renumbering the PID and SID indices The resulting PolySet contains a single PID with the value 1 and uses the SID value to differentiate between polygons their components and holes Value PolySet possibly with the addition of an SID column if it did not already exist The function may also reorder columns such that PID SID POS X and Y appear first in that order See Also dividePolys convCP Convert Contour Lines into a PolySet Description Convert output from contourLines into a PolySet Usage convCP data projection NUL
18. by making z max equal to the largest z value from all maps that will be plotted The user can also add a legend in one of four corners see legend or at a specific c X Y position If legend pos 1s NULL no legend is drawn Author s Denis Chabot Maurice Lamontagne Institute Fisheries and Oceans Canada Mont Joli QC References Tanimura S Kuroiwa C and Mizota T 2006 Proportional symbol mapping in R Journal of Statistical Software 15 5 See Also addPolys surveyData Examples local envir PBSmapEnv expr oldpar par no readonly TRUE common code for both examples below data nepacLL surveyData envir PBSmapEnv surveyData Z lt surveyData catch plot a version that only varies the size plotMap nepacLL xlim c 131 8 127 2 ylim c 50 5 52 7 col gainsboro plt c 08 99 08 99 addBubbles surveyData symbol bg rgb 9 5 0 6 legend type nested symbol zero col grey plot a version that uses different symbol colours plotMap nepacLL xlim c 131 8 127 2 ylim c 50 5 52 7 col gainsboro plt c 08 99 08 99 subset lt surveyData surveyData Z lt 1000 addBubbles subset symbol bg c red yellow green legend type horiz legend breaks pretty range subset Z n 11 symbol zero FALSE col grey min size 0 1 max size 0 4 par oldpar addLabels 49 addLabels Add Labels to an Existing Plot Description Add the label colum
19. expr oldpar par no readonly TRUE create a triangle to clip polys lt data frame PID rep 1 3 POS 1 3 X c 0 1 0 Y c 0 0 5 1 clip the triangle in the X direction and plot the results plotLines clipLines polys xlim c 0 75 ylim range polys Y par oldpar clipPolys Clip a PolySet as Polygons Description Clip a PolySet where each unigue PID SID describes a polygon Usage clipPolys polys xlim ylim keepExtra FALSE Arguments polys PolySet to clip xlim range of X coordinates ylim range of Y coordinates keepExtra Boolean value if TRUE tries to carry forward any non standard columns into the result Details For each discrete polygon the function connects vertices 1 and N It recalculates the POS values for each vertex saving the old values in a column named oldPOS For new vertices it sets oldPOS to NA Value PolySet containing the input data with some points added or removed A new column oldPOS records the original POS value for each vertex See Also clipLines fixBound Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create a triangle that will be clipped polys lt data frame PID rep 1 3 POS 1 3 Xzc 0 1 5 Y c 0 0 1 clip the triangle in the X direction and plot the results plotPolys clipPolys polys xlim c 0 75 ylim range polys Y col 2 par oldpar 64 closePolys Close a PolySet Description
20. represented as one PID with possibly many SIDs 15 Polygon A Polygon B A UNION B A DIFF B A XOR B Figure 5 Example of the joinPolys logic operations Panels A and B display the first and second PolySets respectively Panels C to F illustrate the intersection union difference and exclusive or operations respectively 2 4 Shoreline Data To portray fishery data along Canada s Pacific coast we need a PolySet that defines the relevant shoreline Originally we began with a polyline of the British Columbia coast digitized manually from a marine map To convert this object to a meaningful closed polygon we devised the functions ixBound and closePolys Satellite imagery and other sources however make our initial coastline obsolete For example Wessel and Smith 1996 have used information from the public domain to assemble a Global Self consistent Hierarchical High resolution Shoreline GSHHS http www soest hawaii edu pwessel gshhg database for the entire planet They make this available via the Internet as binary files in five different resolutions full gshhs_ b high gshhs_h b intermediate gshhs_i b low gshhs_1 b and crude gshhs_c b They also supply software as C source code for e converting the data to an ASCII plain text format gshhs c e thinning the data by reducing the number of points sensibly gshhs_dp c 16 Their thinning software uses an algorithm devised by Douglas an
21. the Pacific Biological Station PBS Despite its origins in fishery data analysis our software has broad applicability The library PBSmapping extends the R statistical language to include two dimensional plotting features similar to those commonly available in a Geographic Information System GIS Embedded C code speeds algorithms from computational geometry such as finding polygons that contain specified point events or converting between longitude latitude and Universal Transverse Mercator UTM coordinates We also present a number of convenient utilities for Microsoft Windows operating systems that support computational geometry outside the framework of R Our results which depend significantly on the work of students illustrate the convergence of goals between academic training and applied research RESUME Schnute J T Boers N M Haigh R et Couture Beil A 2013 PBSmapping 2 66 Guide de Putilisateur r vis de Canadian Technical Report of Fisheries and Aquatic Sciences 2549 vi 115 p Dernier mis a jour May 3 2013 Le pr sent rapport d crit la seconde version du logiciel congu pour faciliter la compilation et l analyse de donn es halieutiques en particulier les donn es r f renc es par des coordonn es spatiales Nos travaux de recherche ont capitalis sur des exp riences men es Paide de donn es sur les p ches des poissons d mersaux le long du littoral Pacifique du Canada donn es compil es la Station bi
22. 1 If polys contains an SID column and the SID argument equals NULL this function uses the next available SID for the corresponding PID If polys does not contain an SID column and the caller passes an SID argument all existing polygons will receive an SID of 1 The new polygon s SID will match the SID argument If isHole TRUE the polygon s POS values will appropriately represent a hole reverse order of POS If PID SID already exists in the PolySet the function will issue a warning and duplicate those identifiers Value PolySet containing mat appended to polys The function retains attributes from polys See Also addPolys clipPolys closePolys convLP fixBound fixPOS joinPolys plotMap plotPolys Examples local envir PBSmapEnv expr create two simple matrices a lt matrix data c 0 0 1 0 1 1 0 1 ncol 2 byrow TRUE b lt matrix data c 2 2 3 2 3 3 2 3 ncol 2 byrow TRUE build a PolySet from them polys lt appendPolys NULL a polys lt appendPolys polys b print the result print polys bcBathymetry Data Bathymetry Spanning British Columbia s Coast Description Bathymetry data spanning British Columbia s coast Usage data bcBathymetry Format Three element list x vector of horizontal grid line locations y vector of vertical grid line locations z x by y matrix containing water depths measured in meters Positive values indicate distance below sea l
23. 11 Y seq 0 2 length 11 events lt as EventData events projection 1 74 findPolys create a PolySet a grid polys lt makeGrid x seq 0 2 by 0 50 y seq 0 2 by 0 50 projection 1 show a picture plotPolys polys xlim range polys X c 0 1 0 1 ylim range polys Y c 0 1 0 1 projection 1 addPoints events col 2 run findCells and print the results fc lt findCells events polys fc lt fc order fc EID fc PID fc SID fc label lt paste fc PID fc SID sep print fc add labels to the graph addLabels as PolyData fc duplicated paste fc PID fc SID 1 projection 1 placement CENTROID polys as PolySet polys projection 1 col 4 par oldpar findPolys Find the Polygons that Contain Events Description Find the polygons in a PolySet that contain events specified in EventData Usage findPolys events polys maxRows 1e 05 Arguments events EventData to use polys PolySet to use maxRows estimated maximum number of rows in the output LocationSet Details The resulting data frame a LocationSet contains the columns EID PID SID if in polys and Bdry where an event EID occurs in a polygon PID SID and SID does not correspond to an inner boundary The Boolean variable Bdry indicates whether an event lies on a polygon s edge Note that if an event lies properly outside of all the polygons then a record with EID PID SID does not occur
24. GU dB 80 IMportShapeble je ni 0b RR RE nee Ge a Ra ESS 80 ISCOMVEX ora ic a a a de Be ala a ee ee ee ia 81 islntersectinr eu wo Pew a ee Be he be ee ee ee hee ees 82 JOIMPOLYS saci eh ir BR a a ae Ra de eh ok BU a a A ae a 83 locate Events se si CR RO Go RPS VAS Sd eee Se eee AR 84 locatePOlyS see oe dee Vag ee dee OR O Ay eee RO EE e Bae e 85 Location set pto y Hah en ees A Re a AG Mh Pook OS E e 86 Mak cos Goe ae ye gk PME AS OA eS a e wes 87 makeProps 2 34 ha Heb dhbd dey ott sae de dh et Phot SEARS GE ee beds 88 maKeTopopraphy lt lt msi ee eR eS OR a eR ES EE we Ee GS 89 nepac lul arun aod ee Oe ee oy A SO RS Ae Se COD ME Ue 90 nepacLLhigh euog ge O RG UL ea RA 91 PBSMappINS nb a e ea Bebe BE Re eed Dede Oe ee Dee OS ed GA y Cyd la 92 PBSpmnte een at Rae de PO BAS ee ee A ee oe Re ee E 92 placeHoles 5 25 ae8G4 50 e084 sob eb Oh oped ROB GR DU NG balk Oo wR 5 93 plothines 2 n446 83 445 o EDL Dee Se EEG e EEG REDE ESS 94 plotMap ae ara hee a he EW Sole Be ee ER es En OH a 95 plotPomts oia ns Pe EE a EA babe Deke a es 97 PIOtPO YS eee apn EN NN a a ARA 99 PolyData 223 s oras eta Y da dy ide id E DW d 100 Polys t as ti e EA A A ER RO Ro ewe SS 101 PANE deene eee RAO DO A Add e te ide 103 PYUMASOTAS as bo ls A A AN A A PE ari 104 TELOCUS World s es ia ra a ee OS eG AWG RG we 104 SUMMA Ged a Hr AS a Be ee FFR FN A ewe ais 105 survey Data coi es ea Bs ak Re ee REE oe a ee Be RO a eA PO ee A 106 thickenP
25. POS c 1 10 1 10 X c rep 1 10 rep 1 10 Y c rep 1 10 rep 1 10 colour c rep green 10 rep red 10 extract the PolyData print extractPolyData polys findCells Find the Grid Cells that Contain Events Description Find the grid cells in a PolySet that contain events specified in EventData Similar to findPolys except this function reguires a PolySet resulting from makeGrid This restriction allows this function to calculate the result with greater efficiency Usage findCells events polys Arguments events EventData to use polys PolySet to use Details The resulting data frame a LocationSet contains the columns EID PID SID if in polys and Bdry where an event EID occurs in a polygon PID SID The Boolean variable Bdry indicates whether an event lies on a polygon s edge Note that if an event lies properly outside of all the polygons then a record with EID PID SID does not occur in the output It may happen however that an event occurs in multiple polygons i e on two or more boundaries Thus the same EID can occur more than once in the output Value LocationSet that links events with polygons See Also combineEvents findPolys locateEvents locatePolys LocationSet makeGrid Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create some EventData points in a diagonal line events lt data frame EID 1 11 X seq 0 2 length
26. PolySet attempts to coerce a data frame to an object with class PolySet is PolySet returns TRUE if its argument is of class PolySet Usage as PolySet x projection NULL zone NULL is PolySet x fullValidation TRUE 102 PolySet Arguments x data frame to be coerced or tested projection optional projection attribute to add to the PolySet possibly overwriting an existing attribute zone optional zone attribute to add to the PolySet possibly overwriting an existing attribute fullValidation Boolean value if TRUE fully test x Details In our software a PolySet data frame defines a collection of polygonal contours i e line segments joined at vertices based on four or five numerical fields e PID the primary identification number for a contour e SID optional the secondary identification number for a contour e POS the position number associated with a vertex e X the horizontal coordinate at a vertex e Y the vertical coordinate at a vertex The simplest PolySet lacks an SID column and each PID corresponds to a different contour By analogy with a child s follow the dots game the POS field enumerates the vertices to be connected by straight lines Coordinates X Y specify the location of each vertex Thus in familiar mathematical notation a contour consists of points xi yi with 2 1 n where i corresponds to the POS index A PolySet has two potential interpretations The first associa
27. See Also importGSHHS importEvents importLocs importPolys placeHoles In the package sp see the function point in polygon isConvex Determine Whether Polygons are Convex Description Determine whether polygons found in a PolySet are convex Usage isConvex polys Arguments polys PolySet to use Details Convex polygons do not self intersect In a convex polygon only the first and last vertices may share the same coordinates i e the polygons are optionally closed The function does not give special consideration to holes It returns a value for each unique PID SID regardless of whether a contour represents a hole 82 isIntersecting Value PolyData with columns PID SID may be missing and convex Column convex contains Boolean values See Also isIntersecting PolySet Examples local envir PBSmapEnv expr load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv calculate then print the polygons that are convex p lt isConvex nepacLL nepacLL actually contains no convex polygons print pLlp convex isIntersecting Determine Whether Polygons are Self Intersecting Description Determine whether polygons found in a PolySet are self intersecting Usage isIntersecting polys numericResult FALSE Arguments polys PolySet to use numericResult Boolean value if TRUE returns the number of intersections
28. a text file e g gt file txt 3 2 convUL exe Convert between UTM and LL The application convUL exe reads an ASCII file containing two fields named x and Y as described further below The command convUL exe i IFILE o OFILE u 1 m z ZONE has the arguments e i IFILE ASCII input file containing the X and Y data required e o OFILE ASCII output file defaults to standard output e u or 1 convert to UTM longitude latitude coordinates required 24 e m use metres instead of kilometres as UTM measurement e z ZONE source or destination zone for the UTM coordinates required The input file must have an initial header line with field names including X and Y Subsequent lines contain the data with all fields separated by white space The program converts each x Y pair to a new pair x2 Y2 The output file matches the input file with the fields x2 Y2 appended to the end of each line The default standard output can be redirected to a text file 3 3 findPolys exe Points in Polygons The application indPolys exe reads two ASCII files one containing a PolySet and the other containing EventData The program then determines which events fall inside the available polygons The command findPolys exe p POLY FILE e EVENT FILE o OFILE has the arguments e p POLY FILE ASCII input file containing the PolySet required e e EVENT FILE ASCII input file containing EventData required
29. convDP EventData findCells findPolys plotPoints Examples define five events on the current plot numbering them 10 to 14 Not run events lt locateEvents EID 10 14 locatePolys Locate Polygons on the Current Plot Description Locate polygons on the current plot using the locator function Usage locatePolys pdata n 512 type o Arguments pdata PolyData optional with columns PID and SID optional with two more optional columns n and type n maximum number of points to locate type one of n p 1 or o If p or o then the points are plotted if 1 or o then the points are joined by lines additional par parameters for the locator function Details This function allows its user to define polygons with mouse clicks on the current plot via the locator function The arguments n and type are the usual parameters for the locator function but the user can specify them for each individual PID SID in a pdata object If a pdata object exists the function ignores columns other than PID SID n and type If pdata includes n then an outer boundary has n gt 0 and an inner boundary has n lt 0 On exit from locator suppose the user defined m vertices for a given polygon For that polygon the X and Y columns will contain NAs where POS m 1 n for outer boundaries and POS n m 1 for inner boundaries The na omit function can remove rows with NAs 86 LocationSet I
30. each edge Thus if the distance between two sequential original vertices exceeds the specified tolerance tol it adds enough vertices spaced evenly between them so that sequential vertices lie at most the distance tol apart When keepOrig FALSE the algorithm guarantees only that the first vertex of each polygon appears in the result Starting at that vertex the algorithm walks through the polygon while summing distances between vertices When the cumulative distance exceeds tol it adds a vertex on the line segment under inspection It then resets the distance sum and continues walking the polygon from this new vertex Associating Points with Polygons As discussed in the definition of LocationSet Section 2 1 our function findPolys solves the points in polygons problem Given a set of points EventData and a collection of polygons a PolySet which points lie in which polygons Several algorithms solve this problem including e The crossings test Draw a ray from the trial point in a fixed direction e g upward If the ray crosses an even number of polygon edges the point must be outside For an inside point the number of crossings must be odd e The angle summation or winding number test Sum the angles swept by a ray from the trial point to sequential vertices of the polygon For a point outside the polygon the angles sum to 0 because the ray sweeps back and forth returning to the starting point For an inside point the ray
31. eeeeeceteceteeneeeneees 7 Figure 3 Map of the northeastern Pacific Ocean UTM easting northing 9 999 99 8 Figure 4 Illustration of the thinPolys function A 13 Figure 5 Example ofthe joinPolys logic operations ooooooccnncccnoccconncconacono nnr nnr nr I IH 15 Figure 6 Polylines created by contourLines and CONVCP ee cescsseeseeeneeeeeeeeceeenseeaeeees 17 Figure 7 Tow tracks from a longspine thornyhead survey in 2001 ooooncccnnccincccooccconcconnnonnnnn 18 Figure 8 Areas of islands in the southern Strait of GeOrgla ooonconncnncnonnocononcocnnnncnncconcnnonnnonos 19 Figure 9 Pacific ocean perch survey data 1960 89 0c id min denon inci adios 20 Figure 10 Proof of Pythagoras Theorem ads 21 Figure C1 PBSmapping compared with GMT Vancouver Island ooononncnincnnnnncnnccnonccononnnonos 31 Figure C2 PBSmapping compared with GMT tow tracKS oooonncnnnnnnccnncnoncconcnonononcnncconanononnnonos 33 i ABSTRACT Schnute J T Boers N M Haigh R and Couture Beil A 2013 PBSmapping 2 66 user s guide revised from Canadian Technical Report of Fisheries and Aquatic Sciences 2549 vit 115 p Last updated May 3 2013 This report describes a second version of software designed to facilitate the compilation and analysis of fishery data particularly data referenced by spatial coordinates Our research stems from experiences with information on Canada s Pacific groundfish fisheries compiled at
32. flattened without too much distortion to give coordinates X Y measured as actual distances as illustrated by zone 6 in Figure 3 Complex formulas compiled in detail by the UK Ordnance Survey Anonymous 1998 Ordnance Survey 2010 allow conversion between two projections the UTM easting northing coordinates X Y and the usual longitude latitude coordinates x y These take account of the earth s ellipsoidal shape with a wider diameter at the equator than the poles The UTM projection scales distances exactly along two great circles the equator and the central meridian which act as X and Y axes respectively Along the equator Y 0 km by definition elsewhere Y indicates the distance north positive Y or south negative Y of the equator The central meridian is assigned a standard easting X 500 km rather than the usual X 0 km This ensures that X gt 0 km throughout the zone In effect the difference X 500 km represents the distance east of the central meridian where a negative distance corresponds to a westward displacement These interpretations are exact along the equator and central meridian but approximate elsewhere 6000 7000 8000 UTM Northing km 5000 T T T T T T T T T T T T T T 2000 1000 0 1000 UTM Easting km T T 2000 3000 Figure 3 Shoreline data for the northeastern Pacific Ocean projected in UTM coordinates zone 6 from our PolySet nepacLL Vertical red lines show UTM zone boundari
33. grid of polygons labeling them according to byrow and addSTD In the following descrip tion the variables and 7 indicate column and row numbers respectively where the lower left cell of the grid is 1 1 e byrow TRUE and addSID FALSE implies PID i j 1 x m 1 e byrow FALSE and addSID FALSE implies PID j i 1 x n 1 byrow TRUE and addSID TRUE implies PID 7 SID 7 e byrow FALSE and addSID TRUE implies PID 7 SID 1 Value PolySet with columns PID SID if addSID TRUE POS X and Y The PolySet is a set of rectangular grid cells with vertices Ti yj Titi Yj ma ura zi Yj 1 See Also addPolys clipPolys combineEvents findCells findPolys PolySet thickenPolys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE make a 10 x 10 grid polyGrid lt makeGrid x 0 10 y 0 10 plot the grid plotPolys polyGrid density 0 projection 1 par oldpar 88 makeProps makeProps Make Polygon Properties Description Append a column for a polygon property e g border or 1ty to PolyData based on measurements in the PolyData s Z column Usage makeProps pdata breaks propName col propVals 1 length breaks 1 Arguments pdata PolyData with a Z column breaks either a vector of cut points or a scalar denoting the number of intervals that Z is to be cut into propName name of the new column to append to pdata propVals v
34. level command Advanced users wishing to set the plot region using the par parameters mai or mar can disable the default initial size with the argument p1t NULL Computational Functions PBSmapping contains many functions that perform computations on PolySets and other data structures Appendix F lists them all but we give further details for some of them here a y me including formulas or algorithms for implementation and references for further reading In alphabetic order this list below highlights key features of selected functions in the package e calcArea computes polygon areas by the formula Rokne 1996 n 1 1 A Sih X 1194 gt i l for the area A of a polygon with vertices x y i 1 n where vertices 1 and n correspond to the same point x y1 x y This formula assumes identical units for x and y an aspect ratio 1 as in UTM coordinates The function automatically converts longitude latitude coordinates to UTM before calculating the area e calcCentroid computes polygon centroid coordinates x y by the formulas Bourke 1988 gt x Xi Mx Y ia dy i l y Yin LESA z Hav i l for a polygon with vertices x y 1 n where vertices 1 and n correspond to the same point x y x y and A is computed by the formula shown above in the definition of calcArea These formulas scale automatically to the units of x and y and consequently do not depend on the projection attrib
35. meridian Table 2 PolySets derived from various resolution GSHHS databases PolySet Wessel DB Thin Longitude Latitude Vertices Polygons nepacLL gshhs_h b 0 2km 190 lt x lt 110 34 SyS72 75 305 495 nepacLLhigh gshhs f b 0 1km 190 x lt 1104 34 lt y lt 72 192 762 9 986 worldLL gshhs_1 b 5 0km 209 lt x lt 3609 90 Sy lt 84 30 129 190 worldLLhigh gshhs_i b 1 0km 209 lt x lt 3604 909 lt y lt 849 187 101 1 367 Excludes polygons with fewer than 15 vertices after thinning Explicitly the commands to create the above PolySets are worldLL lt importGSHHS gshhs_ 1 b xlim c 20 360 ylim c 90 90 level 1 n 15 xoff 0 worldLL lt fixGSHHSWorld worldLL worldLLhigh lt importGSHHS gshhs_i b xlim c 20 360 ylim c 90 90 level 1 n 15 xoff 0 worldLLhigh lt fixGSHHSWorld worldLLhigh nepacLL lt importGSHHS gshhs_h b xlim c 190 110 ylim c 34 72 level 1 n 15 xoff 360 nepacLLhigh lt importGSHHS gshhs f b xlim c 190 110 ylim c 34 72 level 1 n 0 xoff 360 nepacLLhigh lt thinPolys nepacLLhigh tol 0 1 filter 3 2 5 Bathymetry Data Smith and Sandwell 1997 have produced global seafloor topography from satellite altimetry and ship depth soundings Their database appears on the Internet at http topex ucsd edu cgi bin get data cgi A web based data acquisition form allows users to extract a region after entering longitude and latitude coordinate ranges
36. oldpar par no readonly TRUE load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv plot a thinned version of Vancouver Island 3 km tolerance plotMap thinPolys nepacLL nepacLL PID 33 tol 3 add the original Vancouver Island in a different line type to emphasize the difference addPolys nepacLL nepacLL PID 33 border 2 lty 8 density 0 par oldpar towData Data Tow Information from Longspine Thornyhead Survey Description PolyData of tow information for a longspine thornyhead survey 2001 Usage data towData Format Data frame consisting of 8 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinate Y latitude coordinate depth fishing depth m effort tow effort minutes distance tow track distance km catch catch of longspine thornyhead kg and year year of survey Attributes projection LL zone 9 Note In R the data must be loaded using the data function Source The GFBio database maintained at the Pacific Biological Station Fisheries and Oceans Canada Nanaimo BC V9T 6N7 archives catches and related biological data from commercial groundfish fishing trips and re search assessment cruises off the west coast of British Columbia BC The longspine thornyhead Sebastolobus altivelis survey data were extracted from GFBio Inform
37. projection lt LL plotMap alPoly type n addLines alPoly col icol data nepacLL addPolys nepacLL col gold legend x topleft bty n col icol lwd 2 legend as character isob 3 Appendix C Generic Mapping Tools GMT Generic Mapping Tools GMT and PBSmapping have many similar features although they operate in different environments We built PBSmapping for the R statistical platform whereas Wessel and Smith developed GMT to run as commands for the UNIX operating system Each environment imposes limitations on its respective tools The following discussion focuses on image types one of the fundamental areas where the programs differ Images are commonly stored in two basic formats raster and vector The raster or bit map format uses a grid of squares where each square is assigned characteristics like colour and transparency The image s resolution often measured in dots per inch determines the density of the grid When this density is less than the resolution of the output device the image may appear jagged because distinct squares are visible Choosing a sufficiently high resolution image for an output device may result in a large file size The vector format stores coordinates for control points of lines curves and other shapes Scaling algorithms use these coordinates to produce an image at any specified size with a consistently smooth appearance In a mapping context vector formats are usual
38. region add using the Mercator projection 5 inches wide set the pen width to 0 5 points and set the colour ASCII file contains multiple polylines ASCII file does not contain a header overlay lay plot on top of earlier one input ASCII file GMT Tow txt append output to the postscript file GMT Tow ps 2 a 49 30 v L E 49 00 Jo 2 i a 1 Yi a ES Pe pa 48 30 Y 4 g 48 00 33 T T T T T T T T T T T T T T T T T T 127 5 127 126 5 126 Longitude 232 30 233 00 233 30 234 00 Figure C2 Tow tracks off the west coast of Vancouver Island drawn by A PBSmapping B GMT produced B Format of GMT tow txt gt 126 126 126 126 26545 48 523133 265233 48 523716 265183 48 524283 385483 48 532567 126 126 3861 48 5327 3868 48 53285 ff a gt signifies the start of each polyline vertices follow X coordinate white space Y coordinate 34 Appendix D Source Code for Figures To help beginners use PBSmapping we include source code for all figures in this report A global function PBSc1r provides the colours for the examples and default dots and dashes are provided by PBSdot and PBSdash respectively These objects are exported from the NAMESPACE and are globally available once PBSmapping is loaded Global colours dots and dashes Figures for PBSmapping examples last modified 2013 04 10
39. rev order areasgarea c 2 4 6 8 PID 38 labelData lt data frame PID bigPID label c Saltspring San Juan Galiano Saturna N Pender Mayne labelData lt merge labelData areas all x TRUE labelData label lt paste as character labelData label round labelDatagarea sep n par mfrow c 1 1 omi c 0 0 0 0 H Plot the figure plotMap isles col clr land bg clr sea tck 010 mgp c 1 9 7 0 cex 1 plt c 07 98 07 98 add the highlighted Gulf Islands bigisles lt isles is element isles PID labelData PID addPolys bigisles col clr yellow labXY lt calcCentroid isles labXYSY lt labXYSY 2 centre vertically labelData lt merge labelData labXY all x TRUE attr labelData projection lt UTM addLabels labelData placement DATA cex 1 25 text 898 5385 Vancouver Island adj 0 cex 1 25 text 925 5435 Strait of Georgia adj 0 cex 1 25 Figure 9 combineEvents in Queen Charlotte Sound PBSfig09 lt function combineEvents in Queen Charlotte Sound clr lt PBSclr data nepacLL surveyData envir sys frame sys nframe events lt surveyData xl lt c 131 8 127 2 yl lt c 50 5 52 7 prepare EventData clip it omit NA entries and calculate CPUE events lt events events X gt xl 1 amp events X lt xl 2 amp events Y gt yl 1 amp events SY lt yl 2 events lt na omit events events cpue lt e
40. shoreline database Wessel and Smith have designed and released a free collection of Generic Mapping Tools GMT http gmt soest hawaii edu that provide a serious alternative to our software These tools operate in the DOS UNIX environment and support many more projections than PBSmapping They also store polygons in a more efficient file format than our PolySet data frames We designed PBSmapping for the R environment with its rich support for statistical and mathematical analysis We have also included numerous algorithms from computational geometry such as findPolys and joinPolys Readers may however find GMT more useful for map formats not supported in PBSmapping Appendix C shows some comparative examples of code written in both environments Because PBSmapping includes features often supported by a Geographic Information System GIS a free GIS package might also provide an alternative to the software described here The FreeGIS web site http www freegis org summarizes the current status of free GIS programs and data Their listings receive frequent updates and show a pattern of steady growth OG 3 COMMAND LINE UTILITIES The PBSmapping package for R includes several algorithms that we have also implemented as stand alone command line utilities These can handle very large data sets that may be too large for the R working environment Furthermore some users may wish to implement computational geometry calculations without refer
41. to offset points measured as a percentage of the absolute difference in xlim additional par parameters for the points function 54 appendPolys Details This function locates stipples based on the PolySet polys and does not stipple degenerate lines Value PolyData consisting of the PolyProps used to create the plot See Also addPoints addPolys plotMap plotPoints plotPolys points PolySet Examples local envir PBSmapEnv expr oldpar par no readonly TRUE load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv plot a map plotMap nepacLL xlim c 128 66 122 83 ylim c 48 00 51 16 add stippling addStipples nepacLL col purple pch 20 cex 0 25 distance 2 par oldpar appendPolys Append a Two Column Matrix to a PolySet Description Append a two column matrix to a PolySet assigning PID and possibly SID values automatically or as specified in 1ts arguments Usage appendPolys polys mat PID NULL SID NULL isHole FALSE Arguments polys existing PolySet if NULL creates a new PolySet required mat two column matrix to append required PID new polygon s PID SID new polygon s SID isHole Boolean value if TRUE mat represents a hole bcBathymetry 55 Details If the PID argument is NULL the appended polygon s PID will be one greater than the maximum within polys if defined otherwise it will be
42. tolerance for the x axis and the second the y axis If it has only one element the function uses the same tolerance for both axes Details When moving vertices to a boundary the function moves them strictly horizontally or vertically as appropriate Value PolySet identical to the input except for possible changes in the X and Y columns See Also closePolys fixPOS isConvex isIntersecting PolySet 76 fixPOS Examples local envir PBSmapEnv expr oldpar par no readonly TRUE set up a long horizontal and long vertical line to extend the plot s limits and then try fixing the bounds of a line in the top left corner and a line in the bottom right corner polys lt data frame PID c 1 1 2 2 3 3 4 4 POS c 1 2 1 2 1 2 1 2 X c 0 10 5 5 0 1 4 9 5 1 9 9 Y c 5 5 0 10 5 1 9 9 0 1 4 9 polys lt fixBound polys tol 0 0100001 plotLines polys par oldpar fixPOS Fix the POS Column of a PolySet Description Fix the POS column of a PolySet by recalculating it using seguential integers Usage fixPOS polys exteriorCCW NA Arguments polys PolySet to fix exteriorCCW Boolean value if TRUE orders exterior polygon vertices in a counter clockwise direction If FALSE orders them in a clockwise direction If NA maintains their original order Details This function recalculates the POS values of each PID SID as either I to N or N to 1 depending on th
43. website now defunct de Berg M van Kreveld M Overmars M and Schwarzkopf O 2000 Computational geometry algorithms and applications second edition Springer Berlin Devlin K J 1998 The language of mathematics making the invisible visible W H Freeman and Company New York NY 344 p Reference taken from the first paperback printing 2000 Douglas D H and Peucker T K 1973 Algorithms for the reduction of the number of points reguired to represent a digitized line or its caricature Canadian Cartographer 10 112 22 Environmental Systems Research Institute ESRI 1996 ArcView GIS the geographic information system for everyone ESRI Press Redlands CA Foley J D van Dam A Feiner S K and Hughes J F 1996 Computer graphics principles and practice second edition in C Addison Wesley Publishing Co Boston MA Haigh R and Schnute J 1999 A relational database for climatological data Canadian Manuscript Report of Fisheries and Aguatic Sciences 2472 26 p Hains E 1994 Point in polygon strategies Chapter 1 4 p 24 46 in Heckbert P S 1994 Graphics Gems IV Academic Press San Diego CA 575 p Murta A 2004 Jul 15 General polygon clipper homepage URL http www cs man ac uk toby alan software Accessed Aug 3 2004 26 Ordnance Survey 2010 A guide to coordinate systems in Great Britain Report D00659 v2 1 Southampton UK URL http www ordnancesurvey co uk oswebs
44. who can learn new languages quickly investigate software possibilities answer technical questions and design programs that assist scientific analysis I m particularly grateful for contributions from the following students e Robert Swan University of Victoria 1996 e Mike Jensen Malaspina University College and Simon Fraser University 1997 and 1999 Chris Grandin Malaspina University College 2000 and 2001 Nick Henderson Malaspina University College 2002 Nick Boers Malaspina University College 2003 2006 Alex Couture Beil Malaspina University College 2005 2007 Starting in 1998 I began a formal connection with the Computing Science Department at Malaspina University College MUC My discussions with faculty members particularly Dr Peter Walsh and Dr Jim Uhl highlighted the convergence of goals between academic training and scientific research Projects designed for fish stock assessment give students an opportunity to further their computing science careers while producing useful software Both MUC and the Pacific Biological Station PBS where I work are located in Nanaimo British Columbia Canada This happy juxtaposition makes it easy to engage students in the exchange of ideas between academia and applied research For example Jim Uhl participated directly in Nick Boers PBS work term during the summer of 2003 Nick had completed a course in computer graphics taught by Jim in the fall of 2002 Algorithms in the
45. x seq 183 2 by 6 length 9 y rep 85 9 adj 0 5 cex 0 65 label 1 9 box Figure 2 nepacLL UTM Zones in LL Space PBSfig02 lt function nepacLL UTM Zones in LL Space clr lt PBSclr dot lt PBSdot data nepacLL envir sys frame sys nframe par mfrow c 1 1 omi c 0 0 0 0 Plot the figure plotMap nepacLL col clr land bg clr sea tck 0 014 mgp c 1 9 0 7 0 cex 1 2 plt c 08 98 08 98 add lines separating UTM zones utms lt seq 186 110 6 abline v utms col clr red H add the central meridian of zone 6 abline v 147 lty dot col clr black create and then add labels for the UTM zones 35 cutm lt diff utms 2 nzon lt length cutm cutm lt cutm utms l nzon text cutm rep 50 75 nzon c 60 1 mzon 1 cex 1 3 col clr red box Figure 3 nepacLL UTM Zones in UTM Space PBSfig03 lt function nepacLL UTM Zones in UTM Space clr lt PBSclr dot lt PBSdot data nepacLL envir sys frame sys nframe zone lt 6 xlim lt range nepacLL X ylim lt range nepacLLSY utms lt seq 186 110 6 H utms vector for creating PolySet and EventData below H create UTM zones lutms lt data frame PID rep 1 length utms each 2 POS rep c 1 2 times length utms X rep utms each 2 Y rep c ylim 1 ylim 2 times length utms lutms lt as PolySet lutms projection LL zone zone lutms lt thickenPolys lu
46. 9 61 calcSummary 49 56 60 60 61 calcVoronoi 61 clipLines 50 62 63 95 110 clipPolys 53 55 62 63 84 86 87 90 91 97 100 111 112 closePolys 50 53 55 64 69 70 75 76 84 86 95 97 100 combineEvents 51 61 65 73 74 85 87 98 107 combinePolys 66 71 contour 55 56 67 89 contourLines 55 56 66 67 89 convCP 55 56 66 69 89 convDP 51 67 85 98 convLP 50 55 67 68 95 convUL 69 cut 88 data 55 90 91 104 106 109 111 dividePolys 66 70 EventData 47 49 51 65 67 11 73 74 80 85 87 97 101 103 106 107 extractPolyData 72 findCells 65 73 74 85 87 findPolys 51 61 65 73 74 85 87 98 107 fixBound 50 53 55 62 64 70 75 76 84 95 97 100 FixPOS 50 53 55 64 75 76 84 86 95 97 100 102 importEvents 77 78 81 importGSHHS 77 77 79 81 90 91 111 112 importLocs 77 78 79 80 81 importPolys 77 79 80 81 importShapefile 77 80 80 93 is EventData EventData 71 is LocationSet LocationSet 86 INDEX is PolyData PolyData 100 is PolySet PolySet 101 isConvex 75 76 81 82 isIntersecting 75 76 82 82 joinPolys 55 69 83 83 86 105 legend 48 lines 50 101 locateEvents 5 57 58 61 65 73 74 84 98 locatePolys 50 53 56 57 59 61 65 73 74 84 85 95 97 100 LocationSet 65 72 74 86 101 103 106 locator 84 85 makeGrid 61 65 73 74 87 107 makeProps 61 65 72
47. Close a PolySet of polylines to form polygons Usage closePolys polys Arguments polys PolySet to close Details closePolys Generally run fixBound before this function The ranges of a PolySet s X and Y columns define the boundary For each discrete polygon this function determines if the first and last points lie on a boundary If both points lie on the same boundary it adds no points However if they lie on different boundaries it may add one or two corners to the polygon When the boundaries are adjacent one corner will be added as follows e top boundary left boundary implies add top left corner e top boundary right boundary implies add top right corner e bottom boundary left boundary implies add bottom left corner e bottom boundary right boundary implies add bottom right corner When the boundaries are opposite it first adds the corner closest to a starting or ending polygon vertex This determines a side left right or bottom top that connects the opposite boundaries Then it adds the other corner of that side to close the polygon Value PolySet identical to polys except for possible additional corner points See Also fixBound fixPOS Examples local envir PBSmapEnv expr oldpar par no readonly TRUE 4 corners polys lt data frame PID c 1 1 2 2 3 3 4 4 POS Eil 2 1 2 15 23 1 2 X c 0 1 2 3 0 15 25 3 Y cl 0 0 1 25 35 3 2 plotPolys clos
48. Columns yColumns Arguments data PolyData or EventData xColumns vector of X column names yColumns vector of Y column names 68 convLP Details This function expects data to contain several X and Y columns For example consider data with columns x1 yl x2 and y2 Suppose xColumns c x1 x2 and yColumns c y1 y2 The result will contain nrow data polygons Each one will have two vertices x1 y1 and x2 y2 and POS values and 2 respectively If data includes an SID column so will the result If data contains an EID and not a PID column the function uses the EIDs as PIDs If data contains both PID and EID columns the function assumes it is PolyData and ignores the EID column Value PolySet with the same PIDs as those given in data If data has an SID column the result will include it See Also addPoints plotPoints Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create sample PolyData polyData lt data frame PID c 1 2 3 xl c 1 3 5 yl c 1 3 2 x2 c 1 4 5 y2 c 2 4 1 x3 c 2 4 6 y3 c 2 3 1 print PolyData print polyData make a PolySet from PolyData polys lt convDP polyData xColumns c x1 x2 x3 yColumns c y1 y2 y3 print and plot the PolySet print polys plotLines polys xlim c 0 7 ylim c 0 5 col 2 par oldpar convLP Convert Polylines into a Polygon Description Convert two polyl
49. Conceptually an EventData object describes events EID that take place at specific points X Y in two dimensional space Additional fields specify measurements associated with these events For example in a fishery context EventData could describe fishing events associated with trawl tows based on the fields e EID fishing event tow identification number e x Y fishing location e Duration length of time for the tow e Depth average depth of the tow e Catch biomass captured Like PolyData EventData can have attributes projection and zone which may be absent Inserting the string EventData as the class attribute s first element alters the behaviour of some functions including print if PBSprint is TRUE and summary LocationSet A PolySet can define regional boundaries for drawing a map and EventData can give event points on the map Which events occur in which regions Our function findPolys discussed in Section 2 3 below solves this problem The output lies in a LocationSet a data frame with three or four columns EID PID SID Bdry where SID may be missing One row in a LocationSet means that the event EID occurs in the polygon PID SID The boundary Bdry field specifies whether Bdry T or not Bdry F the event lies on the polygon boundary If SID refers to an inner polygon boundary then EID occurs in PID SID only if Bdry T An event may occur in multiple polygons Thus the same EID can occur in mult
50. D Unlike a PolySet where each contour has many records corresponding to the vertices a PolyData object must have only one record for each PID or each PID SID combination Conceptually this object associates data with contours where the data correspond to additional fields in the data frame The R language conveniently allows data frames to contain fields of various atomic modes logical numeric complex character and null For example PolyData with the fields PID PName might assign character names to a set of primary polygons Additionally if fields X and Y exist perhaps representing locations for placing labels consider adding attributes zone and projection Inserting the string PolyData as the class attribute s first element alters the behaviour of some functions including print if PBSprint is TRUE and summary Our software particularly uses PolyData to set various plotting characteristics Consistent with graphical parameters used by the R functions lines and polygon column names can specify graphical properties e lty line type in drawing the border and or shading lines e col line or fill colour e border border colour e density density of shading lines e angle angle of shading lines When drawing polylines as opposed to closed polygons only 1ty and col have meaning EventData We define EventData as a data frame with at least three fields named EID X Y
51. Env calculate and print the centroids for several polygons print calcMidRange nepacLLLis element nepacLL PID c 33 39 47 1 calcSummary Apply Functions to Polygons in a PolySet Description Apply functions to polygons in a PolySet Usage calcSummary polys rollup 3 FUN Arguments polys PolySet to use rollup level of detail in the results 1 PIDs only by removing the SID column and then passing each PID into FUN 2 outer contours only by making hole SIDs egual to their parent s SID and then passing each PID SID into FUN and 3 no roll up FUN the function to apply it must accept a vector and return a vector or scalar optional arguments for FUN Details If rollup equals 1 the results contain an entry for each unique PID only When it equals 2 they contain entries for outer contours only Finally setting it to 3 prevents roll up and they contain an entry for each unigue PID SID Value PolyData with columns PID SID may be missing X and Y If FUN returns a vector of length greater than 1 say n names the columns X1 X2 Xn and Y1 Y2 Yn calc Voronoi 61 See Also calcArea calcCentroid calcConvexHull calcLength calcMidRange combineEvents findPolys locateEvents locatePolys makeGrid makeProps Examples local envir PBSmapEnv expr load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv
52. Extra TRUE See Also addPoints addPolys calcArea calcCentroid calcMidRange calcSummary locateEvents plotMap plotPoints plotPolys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE data surveyData envir PBSmapEnv plot the convex hull and then plot the points plotMap calcConvexHull surveyData col moccasin addPoints surveyData col blue pch 17 cex 6 par oldpar calcLength Calculate the Length of Polylines Description Calculate the length of polylines found in a PolySet Usage calcLength polys rollup 3 close FALSE calcMidRange Arguments polys rollup close Details 59 PolySet to use level of detail in the results 1 PIDs only summing the lengths of each SID within each PID and 3 no roll up Note rollup 2 has no meaning in this function and if specified will be reset to 3 Boolean value if TRUE include the distance between each polygon s last and first vertex if necessary If rollup equals 1 the results contain an entry for each unique PID only Setting it to 3 prevents roll up and they contain an entry for each unique PID SID If the projection attribute equals LL this routine uses Great Circle distances to compute the surface length of each polyline In doing so the algorithm simplifies Earth to a sphere If the projection attribute equals UTM or 1 this routine uses Pythagoras Theorem to calculate lengths
53. ID SID Bdry where SID may be missing One row in a LocationSet means that the event EID occurs in the polygon PID SID The boundary Bdry field specifies whether Bdry T or not Bdry F the event lies on the polygon boundary If SID refers to an inner polygon boundary then EID occurs in PID SID only if Bdry T An event may occur in multiple polygons Thus the same EID can occur in multiple records If an EID does not fall in any PID SID or if it falls within a hole it does not occur in the output LocationSet Inserting the string LocationSet as the first element of a LocationSet s class attribute alters the behaviour of some functions including print if PBSprint is TRUE and summary Value The as LocationSet method returns an object with classes LocationSet and data frame in that order makeGrid 87 See Also EventData PolyData PolySet makeGrid Make a Grid of Polygons Description Make a grid of polygons using PIDs and SIDs according to the input arguments Usage makeGrid x y byrow TRUE addSID TRUE projection NULL zone NULL Arguments x vector of X coordinates of length m y vector of Y coordinates of length n byrow Boolean value if TRUE increment PID along X addSID Boolean value if TRUE include an SID column in the resulting PolySet projection optional projection attribute to add to the PolySet zone optional zone attribute to add to the PolySet Details This function makes a
54. ID must similarly appear as integers in strictly increasing or decreasing order for outer and inner boundaries respectively If the Pos field erroneously contains floating point numbers f ixPOS can renumber them as sequential integers thus simplifying the insertion of a new point such as point 3 5 between points 3 and 4 A PolySet can have a projection attribute which may be missing that specifies a map projection In the current version of PBSmapping projection can have character values LL or UTM referring to Longitude Latitude and Universal Transverse Mercator We explain these projections more completely below If projection is numeric it specifies the aspect ratio r the number of x units per y unit Thus r units of x on the graph occupy the same distance as one unit of y Another optional attribute zone specifies the UTM zone ifprojection UTM or the preferred zone for conversion from Longitude Latitude if projection LL A data frame s class attribute by default contains the string data frame Inserting the string PolySet as the class vector s first element alters the behaviour of some functions For example the summary function will print details specific to a PolySet Also when PBSprint is TRUE the print function will display a PolySet s summary rather than the contents of the data frame PolyData We define PolyData as a data frame with a first column named PID and optionally a second column named SI
55. In the R language high level commands like plot create new graphs lower level commands like points and lines add features to an existing graph Similarly we provide functions plotLines plotMap plotPoints plotPolys that create graphs and others addLabels addLines addPoints addPolys addStipples that add graphical features Some of these plotting functions draw objects defined by a PolySet while others expect EventData a LocationSet or PolyData Both plotLines and addLines treat their input PolySet as polylines with no connection between the last and first vertices By contrast plotMap plotPolys and addPolys regard their input as polygons where a final line segment connects the last vertex to the first The functions plotMap and plot Polys behave similarly except that plotMap s default behaviour guarantees the correct aspect ratio as defined by either the PolySet s projection attribute or the function s projection argument If both are specified the attribute supersedes the argument When this attribute is missing plotMap uses a 1 1 projection Table 1 summarises the default behaviour of our principal graphics commands A user concerned with drawing maps where the correct aspect ratio plays a key role would likely initiate a graph with the plotMap function However plot Polys plotLines and plotPoints can also set the correct aspect ratio when passed a suitable projection argument Table 1 Behaviour of the principal g
56. L xlim c 127 89 125 68 ylim c 47 85 49 97 plt c 0 16 0 97 0 16 col rgb 255 255 195 maxColorValue 255 bg rgb 224 253 254 maxColorValue 255 tck c 0 03 cex 1 8 mgp c 1 9 0 7 data towTracks addLines towTracks col rgb 255 0 O maxColorValue 255 lwd 0 5 0 97 0 GMT Panel B gmtset ANOT FONT SIZE pscoast Dh Y R 127 89 125 68 47 85 49 97 JM5i G255 255 195 8224 253 254 Ba0 5 a0 5WSne W0 5p P K gt GMT Tow ps psxy R 127 89 125 68 47 85 49 97 JM5i W0 5p 255 0 0 M HO O lt GMT Tow txt gt gt GMT Tow ps 20p ff load the nepacLL data set plot the nepacLL data set limit the region horizontally limit the region vertically specify the plot region size set the foreground colour set the background colour set the tick mark length adjust the font size adjust the axis label locations load the towTracks data set add the towTracks data set set the colour set the line width set the annotation font size plot the high resolution data set limit the region horizontally and vertically use the Mercator projection 5 inches wide set the foreground colour set the background colour mark every 0 5 X and 0 5 Y degrees on W amp S axes set the pen width to 0 5 points portrait mode allow for appending more plot code output to the postscript file GMT Tow ps limit the
57. L zone NULL Arguments data contour line data often from the contourLines function projection optional projection attribute to add to the PolySet zone optional zone attribute to add to the PolySet convDP 67 Details data contains a list as described below The contourLines function create a list suitable for the data argument A three element list describes each contour The named elements in this list include the scalar level the vector x and the vector y Vectors x and y must have equal lengths A higher level list data contains one or more of these contours lists Value A list with two named elements PolySet and PolyData The PolySet element contains a PolySet representation of the contour lines The PolyData element links each contour line PID SID with a level See Also contour contourLines convLP makeTopography Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create sample data for the contourLines function x lt seq 0 5 0 8 length 50 y lt x z lt outer x y FUN function x y sin 2 pi x 2 y 2 2 data lt contourLines x y z levels c 0 2 0 8 pass that sample data into convCP result lt convCP data plot the result plotLines result PolySet projection 1 print result PolyData par oldpar convDP Convert EventData PolyData into a PolySet Description Convert EventData PolyData into a PolySet Usage convDP data x
58. PBSmapping 2 66 User s Guide Jon T Schnute Nicholas M Boers Rowan Haigh and Alex Couture Beil Fisheries and Oceans Canada Science Branch Pacific Region Pacific Biological Station 3190 Hammond Bay Road Nanaimo British Columbia V9T 6N7 2013 User s Guide Revised from Canadian Technical Report of Fisheries and Aquatic Sciences 2549 Fisheries and Oceans P ches et Oc ans lvl el Canada Canada Canada O Her Majesty the Queen in Right of Canada 2013 Revisions to Cat No Fs97 6 2549E ISSN 0706 6457 Last update May 3 2013 Correct citation for this publication Schnute J T Boers N M Haigh R and Couture Beil A 2013 PBSmapping 2 66 user s guide revised from Canadian Technical Report of Fisheries and Aquatic Sciences 2549 vit 115 p Last updated May 3 2013 TABLE OF CONTENTS NO iii RI NN Y e e dd y iii PRETACE a A Y YF iV l Tt duc oT RY O Cd A YY GO ADO 1 1 l Software SIA GR OW a GC O GY toda 2 2 PBSmapping Functions O e AR GO 3 ZL Data struetures Tor Maps artist lcd 3 PO Si Ai 3 Fol DIO O NN A a a a ae 4 EventData a E AE 5 Locationset SA aa ctu od DG GYFAN Gi 5 Dads Map PLO EOS ia a A EEG 5 2 3 PBSmapping Functions and Alo orithins Ai 8 Import a LLST YW Ha NW NN HR HN 8 Graphics Pune ddiaa ra GG DAL 9 Computational Functions ew ee Y A tias 10 Associating Points with Polygom cccccesccesscessceesseceseceeceeceeeseecsaecesecseeeeeaeecsaeceaeeneneeeneees 13 Sel PNSOren
59. S 57 calcConvex ull a s amp ee oe eR eee SSS ee Ea A ee Sb WL la 58 calclength seca cora a ee Mae Be OS SY ewe Ee SS Pe Gee RA 4 a 58 CalcMidRange 4 o62c4b che Shwe een ae ed bh eee bee Gad oleh bu a a 59 CaleSuUMMAaLy io bee ooo ee ee oe Eee Bh DF we bbe Lee eee 8 60 CALC VOTODOL 300 e sed Sd ee RM awe he oa ee eR BEY we a GS 61 Clipless 4 242 ate god ey y GN y Nr y y Oa ae ae th ho o A GR Se A A oe DU Ue 62 CHPPOWS osorno eee ee ea a Eee Pee Me eee See Oe Pees 63 closePolyS 2 4 pue sosa tse eh id MO de did da es a DF dued 64 COMDINEEVEN S fe gk bee A A ER e eee 65 combinePolys eo yt ri e ds dd a 66 CONVEP os crearse AAA aa 66 CONVDP iru aiia e e A od Myd od de id bdo tb id 67 COMVEP 2a eae Se ee bh oe ew Se Ae ee he oe ew Vee eee 68 convUl ec dos wR aR A we Ba os eds Be Re ae SR doe Bee HOS 69 dividePOolys a corri ee SRO EGA LE CRO Re ewe Hea eee Eee Pe bw eo 70 PyentData o 2k ek bee BA ae GR Beha ek Gy BL do ee de AAG Ree Sle ao be eR 71 extractPoly Data a vv ovas ee Bd Ye eR we Ea ee Oe AAA ae A a a 72 ImdCellS oviedo a RW UYD EG PRE a RAR Ee RS 73 IMAPOIYS 26 8 oh ieee e dae id ee Ss ea dd de iS SE ee eed 74 OXBOUNG 4 o hag dee ada ee eee ER a he aay ad AR DIE GO YW bes 75 APOS 40 278 ao ds Ga dete we we GON O eRe Son te See os Meee yg 76 IMPOHEVENtS oc on ee rete ee ee A AA TI 1MpPOnGSHAS o eg o o euw A Y IOG FT Y FU da bead TT IMPOREOCS ice Eos aA Ew A IC A A we 8 UG 79 IMpoOrtPOlYS 042 ras os dod A a A ia GA
60. Summarize PBS Mapping Objects summary method for PBS Mapping classes Usage S3 method for class EventData summary object 5 S3 method for class LocationSet summary object S3 method for class PolyData summary object z S3 method for class PolySet summary object Arguments object a PBS Mapping object such as EventData a LocationSet PolyData or a PolySet further arguments passed to or from other methods Details 105 After creating a list of summary statistics this function assigns the class summary PBS to the output in order to accomplish formatted printing via print summary PBS 106 surveyData Value A list of summary statistics See Also EventData LocationSet PBSprint PolyData PolySet Examples local envir PBSmapEnv expr load the data if using R if is null version language 88 version language R data surveyData envir PBSmapEnv print summary surveyData surveyData Data Tow Information from Pacific Ocean Perch Survey Description EventData of Pacific ocean perch POP tow information 1966 89 Usage data surveyData Format Data frame consisting of 9 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinate Y latitude coordinate trip trip ID tow tow number in trip catch catch of POP kg effort tow effort minutes depth fishing dep
61. a PolyData PolySet PolySet is Determine whether an object is EventData EventData LocationSet a LocationSet PolyData PolyData PolySet a PolySet print Print EventData an EventData object LocationSet a LocationSet object PolyData a PolyData object PolySet a PolySet object summary PBS the summary of a PBSmapping object summary Summarize EventData EventData LocationSet a LocationSet PolyData PolyData PolySet a PolySet Data sets bcBathymetry Bathymetry data spanning British Columbia s coast nepacLL Northeast Pacific shoreline normal resolution nepacLLhigh Northeast Pacific shoreline high resolution pythagoras Pythagoras theorem diagram PolySet surveyData Survey data towData Tow data towTracks Tow track polyline data worldLL World ocean shoreline normal resolution worldLLhigh World ocean shoreline high resolution Package PBSmapping May 3 2013 Version 2 66 Date 2013 05 03 Title Mapping Fisheries Data and Spatial Analysis Tools Author Jon T Schnute lt schnutej dfo shaw ca gt Nicholas Boers lt boersn macewan ca gt Rowan Haigh lt rowan haighedfo mpo gc c son Paul Wessel Franklin Antonio Maintainer Jon T Schnute lt schnutej dfo shaw ca gt Depends R gt 2 15 0 Suggests foreign maptools deldir Description This software has evolved from fisheries research conducted at the Pacific Biological Station PBS in Nanaimo British Columbia Canada It extends the R language to include two dimension
62. a PolySet In both cases the function s behaviour changes slightly To resemble the plot function it plots the border labels and other parts according to par parameters such as col For additional help on the arguments border 1ty col density and angle please see polygon and par Value PolyData consisting of the PolyProps used to create the plot Note To satisfy the aspect ratio this plotting routine resizes the plot region Consequently par parameters such as plt mai and mar will change When the function terminates these changes persist to allow for additions to the plot plotPoints Author s 97 Nicholas Boers Dept of Computer Science Grant MacEwan University Edmonton AB See Also addLabels addPolys addStipples clipPolys closePolys fixBound FixPOS locatePolys plotLines plotPoints thinPolys thickenPolys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create a PolySet to plot polys lt data frame PID rep 1 4 P0S 1 4 X c 0 1 1 0 Y c 0 0 1 1 plot the PolySet plotMap polys xlim c 5 1 5 ylim c 5 1 5 density 0 projection 1 par oldpar plotPoints Description Plot EventData PolyData as Points Plot EventData PolyData where each unique EID or PID SID describes a point Usage plotPoints data xlim Arguments data xlim ylim projection plt polyProps cex col pch axes tckLab NULL ylim NULL proj
63. a region from this database The form returns an ASCII file containing X Y and Z coordinates To use this data file with PBSmapping first load it into R with the native function read table which creates a data frame with three fields Our function makeTopography can convert this data frame to a list object with vectors x and y and an outer product matrix z ready for use by the functions contour or contourLines In particular contourLines produces a list object that can be easily converted to a PolySet using convCP which in turn produces a list object consisting of a PolySet with contour coordinates and PolyData with the depth of each contour Example Bathymetry for a small section of the Aleutian Islands Alaska where a user would specify coordinates xlim c 162 158 and ylim c 53 57 in the web based acquisition form referenced above and save Topography to a file called aleutian txt also provided in the library directory PBSmapping extra require PBSmapping isob lt c 100 500 1000 2500 5000 icol lt rgb 0 0 seg 255 100 len length isob max 255 afile lt paste system file package PBSmapping extra aleutian txt sep aleutian lt read table afile header F col names c x y z aleutian x lt aleutian x 360 aleutian z lt aleutianSz alBathy lt makeTopography aleutian alCL lt contourLines alBathy levels isob alCP lt convCP alCL alPoly lt alCP PolySet attr alPoly
64. ady for installation into R The package PBSdata can be found on the Google Code website https code google com p pbs data To remove PBSmapping from R open the 1ibrary directory and delete the associated subdirectory PBSmapping Before loading a new version of a package we recommend the removal of any previous version Eventually the installation files may have names that reflect a version number later than the current version Additionally three other PBS packages are available from CRAN that facilitate fisheries analysis and research e PBSmodelling http cran r project org web packages PBSmodelling index html e PBSddesolve http cran r project org web packages PBSddesolve index html e PBSadmb http cran r project org web packages PBSadmb index html The PBSmodelling library includes a directory called PBStools that contains useful batch files for building R packages and generating an indexed manual based on the Rd files This is not to be confused with another PBS package called PBStools at https code google com p pbs tools i 2 PBSmapping FUNCTIONS AND DATA Niklaus Wirth the author of Pascal and Modula 2 summarises the essence of software design in the title of his book Algorithms Data Structures Programs Wirth 1975 Our software package PBSmapping begins with data structures that embody two essential concepts First polygons define boundaries such as shorelines and fishery mana
65. al plotting features similar to those commonly available in a Geographic Information System GIS Embedded C code speeds algorithms from computational geometry such as finding polygons that contain specified point events or converting between longitude latitude and Universal Transverse Mercator UTM coordinates Additionally we include C code developed by Angus Johnson for the Clipper library PBSmapping also includes data for a global shoreline and other data sets in the public domain The R directory library PBSmapping doc offers a complete user s guide PBSmapping UG pdf which should be consulted to use all functions in the package effectively License GPL gt 2 URL http code google com p pbs mapping http code google com p pbs mapx http www angusj com delphi clipper php R topics documented addBubbles 2 bos ee ee we EO GE wh ee ee bee ae ee SEE eee ao 47 addabels sona nas ese Red Ss Re dy eae es a Be A RD GU Ny UWCH A 49 addlin6S a rr RDO a ERED EASE RES ERE Ee 50 addPointS 22 ei e RS ELE Sa hs ea eee RD ii od da e ea x 51 addPOlyS o s oia ad e g O A a E a T FE 52 add SUpples a cits oy SiGe kita dk Bare Bie bog do AR AA Seo eee OR od CG WN 53 appendPol ysu ee aia bea ew dee Ge SM BER ale WR Eee Se a ame Soe DE O WR Pere SG 54 beBathymetty so o 5 esc ad did di AU amp a5 A 4 a be ene E eR eho be ew Ee Ae ANA 56 46 R topics documented calcCentroid es eae ge a e A RD FR a Ee AW RW UR Y
66. als 1 and 2 the function appropriately adjusts for polygons with holes Details If rollup equals 1 the results contain a centroid for each unique PID only When it equals 2 they contain entries for outer contours only Finally setting it to 3 prevents roll up and they contain a centroid for each unigue PID SID Value PolyData with columns PID SID may be missing X and Y See Also calcArea calcLength calcMidRange calcSummary locateEvents locatePolys Examples local envir PBSmapEnv expr load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv calculate and print the centroids for several polygons print calcCentroid nepacLLLis element nepacLL PID c 33 39 47 1 58 calcLength calcConvexHull Calculate the Convex Hull for a Set of Points Description Calculate the convex hull for a set of points Usage calcConvexHull xydata keepExtra FALSE Arguments xydata a data frame with columns X and Y containing spatial coordinates keepExtra logical if TRUE retain any additional columns from the input data frame xydata Details This routine uses the function chul1 in the package grDevices By default it ignores all columns other than X and Y however the user can choose to retain additional columns in xydata by specifying keepExtra TRUE Value PolySet with columns PID POS X Y and additional columns in xydata if keep
67. and the second element describes those on the y axis tck numeric vector length 1 or 2 describing the length of tick marks as a fraction of the smallest dimension If tckLab TRUE these tick marks will be automatically labelled If given a two element vector the first element describes the tick marks on the x axis and the second element describes those on the y axis tckMinor numeric vector length 1 or 2 describing the length of tick marks as a fraction of the smallest dimension These tick marks can not be automatically labelled If given a two element vector the first element describes the tick marks on the x axis and the second element describes those on the y axis additional par parameters or the arguments main sub xlab or ylab for the title function Details This function plots a PolySet where each unigue PID SID describes a polyline It does not connect each polyline s last vertex to its first Unlike plotMap the function ignores the aspect ratio It clips polys to xlim and ylim before plotting The function creates a blank plot when polys eguals NULL In this case the user must supply both xlimand ylim arguments Alternatively it accepts the argument type n as part of which is equivalent to specifying plotMap 95 polys NULL but requires a PolySet In both cases the function s behaviour changes slightly To resemble the plot function it plots the border labels and other parts according to par parameters
68. ation on the first 45 tows from the 2001 survey Starr et al 2002 are included here Effort is time minutes from winch lock up to winch release References Starr P J Krishka B A and Choromanski E M 2002 Trawl survey for thornyhead biomass estimation off the west coast of Vancouver Island September 15 October 2 2001 Canadian Technical Report of Fisheries and Aquatic Sciences 2421 60 pp See Also makeProps PolyData towTracks 110 worldLL towTracks Data Tow Track Polylines from Longspine Thornyhead Survey Description PolySet of geo referenced polyline tow track data from a longspine thornyhead survey 2001 Usage data towTracks Format Data frame consisting of 4 columns PID primary polygon ID POS position of each vertex within a given polyline X longitude coordinate and Y latitude coordinate Attributes projection LL zone 9 Note In R the data must be loaded using the data function Source The longspine thornyhead Sebastolobus altivelis tow track spatial coordinates are available at the Pacific Bio logical Station Fisheries and Oceans Canada Nanaimo BC V9T 6N7 The geo referenced coordinates of the first 45 tows from the 2001 survey Starr et al 2002 are included here Coordinates are recorded once per minute between winch lock up and winch release References Starr P J Krishka B A and Choromanski E M 2002 Trawl survey for thornyhead biomass estimation off the w
69. ative Generic Mapping Tools GMT source code for the figures in this report function dependencies in PBSmapping documentation for PBSmapping functions and data including an indexed manual based on the Rd files HuHmUow We anticipate that our software will continue to change for the better due to bug fixes and other improvements This report documents version 2 66 which currently appears as a contributed package on the R archive http cran r project org We will post subsequent versions as they become available All software required to develop and use PBSmapping is freely available from the Internet 1 1 Software Installation We provide two mapping packages e PBSmapping the mapping software discussed in Section 1 e PBSdata various additional data sets relevant to fisheries investigated at PBS Appendix A Installation of PBSmapping can be achieved in two ways 1 navigate to http cran r project ore web packages PBSmapping index html download the appropriate binary and install from R using the menu lt Packages gt lt Install package s from local zip files gt or 2 in R use the menu lt Packages gt lt Install package s gt choose a CRAN mirror near you highlight PBSmapping and press OK Note that the software is available in two forms e PBSmapping 2 65 tar gz source code for the R distribution which can be used to build a binary package e PBSmapping _2 65 zip binary package re
70. available in PBSdata Object Description bctopo Topo British Columbia Sea Floor Topography bgcp Topo Biogeochemical Provinces claradat Data Tow Catches of Species in Oueen Charlotte Sound dbr rem Data Annual Catches of Rockfish by Sector eez bc Topo Exclusive Economic Zone for BC Coast fos fid Code Fishery Codes in GFFOS gear Code Gear Codes for Various DFO Databases hsgrid Topo Hecate Strait Assemblage Survey Grid hsisob Topo Hecate Strait Isobaths hssa Topo Hecate Strait Survey Area iphc rbr Data Longline Indices of Rockfish Catch from the IPHC SSA iphc rer Data Longline Indices of Rockfish Catch from the IPHC SSA iphc yyr Data Longline Indices of Rockfish Catch from the IPHC SSA isobath Topo Isobaths 100 to 1800 m at 100 m intervals locality Topo Localities in Pacific Marine Fisheries Commission Minor Areas ltea Topo Longspine Thornyhead Exploratory Management Areas Itmose07 Topo Longspine Thornyhead Fishing Grounds WCVI ltmosel2 Topo Longspine Thornyhead Fishing Grounds WCVI Itsa Topo Longspine Thornyhead Survey Strata WCVI Itsa bad Topo No Trawl Zones in Longspine Thornyhead Survey Area Itxa Topo Longspine Thornyhead Experimental Management Areas major Topo Pacific Marine Fisheries Commission Major Areas minor Topo Pacific Marine Fisheries Commission Minor Areas nage394 Data Age Frequency by Year for Rougheye Rockfish orfhistory Data Historic Landings of Rockfish in BC parVec Data Init
71. bubble may exceed this size when show actual is FALSE on accountof using pretty symbol to represent z values egual to 0 bubble outline border colour bubble interior fill colour If a vector the first element represents min legend breaks and the last element represents max legend breaks colours are interpolated for values of events Z between those boundaries For values outside of those boundaries interiors remain unfilled position for the legend break values for categorizing the z values The automatic method should work if zeroes are present otherwise you can specify your own break values for the legend If a single number specifies the number of breaks if a vector specifies the breaks logical if FALSE legend values are obtained using pretty and consequently the largest bubble may be larger than z max If TRUE the largest bubble in the legend will correspond to Z max display format for legend 48 addBubbles legend title title for legend legend cex size Of legend text additional arguments for points function that plots zero value symbols Details Modified from and for the legend strongly inspired by Tanimura et al 2006 by Denis Chabot to work with PBSmapping Furthermore Chabot s modifications make it possible to draw several maps with bubbles that all have the same scale instead of each bubble plot having a scale that depends on the maximum z value for that plot This is done
72. catch per unit effort CPUE within each grid cell 0 1 by 0 19 Circles show locations of individual tows PBSmapping can also display non geographical data such as technical drawings network diagrams and transportation schematics For example we use a PolySet to construct the proof of Pythagoras Theorem in Figure 10 where the caption explains the logic leading to the famous result a b c Incidentally Devlin 1998 chapter 6 p 221 mentions an historical incident that nicely distinguishes maps from network diagrams A now familiar drawing of the London Underground see the PDF file marked Standard Tube map at the web site 21 http www tfl gov uk gettingaround 1106 aspx fails to represent geography correctly but contains exactly the information passengers need to navigate the system It took two years for the designer Henry C Beck to persuade his superiors that his drawing would prove useful to the public Pythagoras Theorem a b c Proof a b 4 triangles a b 4 triangles c Figure 10 Proof of Pythagoras Theorem A PolySet defines all geometric objects in this figure and PolyData determine the colours for plotting Four blue triangles plus the yellow square a and the green square b equal four blue triangles plus the red square c consequently a b c 2 7 Strengths Limitations and Alternatives PBSmapping works with data exported from database tab
73. ckage could not exist without R and GCC We express admiration and gratitude to the remarkable teams that build document and distribute such outstanding free software En REFERENCES Anonymous 1998 The ellipsoid and the Transverse Mercator projection Geodetic Information Paper No 1 version 2 2 Ordnance Survey Southampton UK 20 p URL http Www ordsvy gov uk Becker R A Chambers J M and Wilks A R 1988 The new S language a programming environment for data analysis and graphics Wadsworth and Books Cole Pacific Grove CA Becker R A and Wilks A R 1993 Maps in S Statistics Research Report 93 2 AT amp T Bell Laboratories Murray Hill NJ 21 p URL http www research att com areas stat doc Becker R A and Wilks A R 1995 rev 1997 Constructing a geographical database Statistics Research Report 95 2 AT amp T Bell Laboratories Murray Hill NJ 23 p URL http www research att com areas stat doc Boers N M Haigh R and Schnute J T 2004 PBS Mapping 2 developer s guide Canadian Technical Report of Fisheries and Aguatic Sciences 2550 Bourke P 1988 July Calculating the area and centroid of a polygon URL http astronomy swin edu au pbourke geometry polyarea Accessed Aug 3 2004 website now defunct Chamberlain R 2001 Feb Q5 1 what is the best way to calculate the distance between 2 points URL http www census gov cgi bin geo gisfag Q5 1 Accessed Aug 3 2004
74. clipPolys closePolys fixBound fixPOS locatePolys plotLines plotMap plotPoints thinPolys thickenPolys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create a PolySet to plot polys lt data frame PID rep 1 4 POS 1 4 X c 0 1 1 0 Y c 0 0 1 1 plot the PolySet plotPolys polys xlim c 5 1 5 ylim c 5 1 5 density 0 par oldpar PolyData PolyData Objects Description PBS Mapping functions that expect PolyData will accept properly formatted data frames in their place see De tails as PolyData attempts to coerce a data frame to an object with class PolyData is PolyData returns TRUE if its argument is of class PolyData Usage as PolyData x projection NULL zone NULL is PolyData x fullValidation TRUE PolySet 101 Arguments x data frame to be coerced or tested projection optional projection attribute to add to PolyData possibly overwriting an existing attribute zone optional zone attribute to add to PolyData possibly overwriting an existing attribute fullValidation Boolean value if TRUE fully test x Details We define PolyData as a data frame with a first column named PID and optionally a second column named SID Unlike a PolySet where each contour has many records corresponding to the vertices a PolyData object must have only one record for each PID or each PID SID combination Conceptually this object associates data with contours wher
75. d Peucker 1973 whose initials dp appear in the file name The dp is also an abbreviation of decimate polygons We have created a function called importGSHHS that works directly on a specified binary data file from Wessel resolution choice left to the user to create a PBSmapping PolySet The user can choose to further alter the resolution of the newly created PolySet using our function thinPolys Alternatively the user can thin Wessel s full resolution database gshhs_f b directly using gshhs_dp c after compilation to an executable file to a desired resolution then use PBSmapping s importGSHHS on the modified binary database At the time of writing importGSHHS supports Wessel s format for data files version 2 2 0 created July 15 2011 Wessel s database gshhs wdbii_2 2 0 zip contains geographical coordinates for shorelines gshhs rivers wbd_rivers and borders wdb_ borders The latter two come from World DataBank II WDBII with the five resolutions mentioned above PBSmapping includes four data sets derived from the GSHHS databases Table 2 These all use longitude latitude LL coordinates The nepac data sets contain the northeastern Pacific Ocean shoreline in a region that extends roughly from California to Alaska Figure 2 and the world data sets cover the planet Figure 1 As discussed in section 2 2 longitude coordinates x take continuous values meaningful for the intended map with x 0 on the Greenwich prime
76. dencies This appendix documents function dependencies within PBSmapping All functions appear as underlined entries in the alphabetic list If a function depends on others the list of dependencies appears below the underlined name Following a standard in UNIX and R functions whose name begins with a period dot functions are considered hidden from the user who would normally use only the non hidden functions that call them The names here apply primarily to the R working environment but functions designated C are implemented in C source code and compiled in the DLL for the mapping package R invokes these functions with the call c Functions designated S exist as subfunctions only within the R function addAxis expandEdges validateLocationSet closestPoint validateData addAxis2 calcConvexHull validatePolyData addBubblesLegend ixGSHHSWorld validateData findPolys addCorners fixPOS validatePolyProps calcConvexHull validateData getBasename addFeature validatePolySet addProps getGridPars validateData validatePolyProps makeGrid validateXYData addLabels initPlotRegion validateData addProps insertNAs calcDist mat2df calcOrientation plotMaps calcOrientation C addAxis addLabels checkClipLimits initPlotRegion validateXYData checkProjection addLines addPoints checkRDeps addPolys clip preparePolyProps clip C
77. e Opel atl ONS zee san aly hae A tats ae arc O GR aoa eae A cs 14 DA Shoreline Dat aseosu gn YU i rd CM YD sh A Y dd a 15 2 9 Bathymecty Data AS EA O Yd A slag 17 2 6 Examples and AppleatOnss ed Y Y Ud GO 18 2 7 Strengths Limitations and Alternatives cccccccsscsseceseceseceeeeeeseeceseceseeseeeeseeeeeaeecaeees 21 d Command line Usadas ds daa 23 3 1 clipPolys exe Clip Poly Mons A 23 3 2 convUL exe Convert between UTM and LEI ad 23 3 3 findPolys exe Points in Polygons ooooconnocononocoocnononconccconocnnn conc ccon coco no conc Ynn Ynn Fon 24 ACA e 24 A A A 25 Appendix A PBSdata package iiinis FFF A Ud 27 Appendix B Bathymetry DR ee Od 29 Appendix C Generic Mapping Tools Mii a 30 Appendix D Source Code for Fig ares nana ais 34 Appendix E PBSmapping Function Dependencies ss sesessessesesssesseseesseesesressesresressresseseess 40 Appendix F PBSmapping Functions and Data a is 43 e LIST OF TABLES Table 1 Principal graphics functions in the PBSmapping package ooooooconnncninccnoccconccconncconocnnos 9 Table 2 PolySets derived from GSHHS databases ooonoccnocccooccconccooncconccconoconoconnccon coco nocnnnconnnos 16 Table A ba sets available Pda ei 27 Table F1 Functions and data sets defined in PBSmapping cooocnnoccnonoconoconcnonnnconncconacnnncnnncconncnns 43 LIST OF FIGURES FURL Mapof the wold loas 6 Figure 2 Map of the northeastern Pacific Ocean longitude latitude 00 ee
78. e dropped the bilingual R S PLUS nature of PBSmapping producing revisions solely for R and now refer to the package as PBSmapping rather than PBS Mapping used in earlier documents Additionally we maintain most of our PBS packages including PBSmapping at http code google com p pbs software Section 2 covers the mapping software itself which contains functions that perform numerous calculations on polygons These include standard set theoretic operations union intersection difference exclusive or clipping thinning thickening testing convexity forming the convex hull and calculating various statistics such as mean centroid and area We discuss public data that represent shorelines and ocean bathymetry and the package includes sample data sets drawn from these sources We also discuss the Universal Transverse Mercator UTM projection that gives a particularly accurate flat projection of the earth s surface Our software can convert between longitude latitude and UTM coordinates Section 3 documents a number of convenient command line utilities compiled separately from C code written for the PBSmapping package These make it possible to perform some of the polygon functions outside the framework of R Appendices provide additional information about various topics related to PBSmapping including a package PBSdata of supplementary information for PBSmapping an Internet source for global bathymetry data altern
79. e for Figure C1 R Panel A data nepacLL plotMap nepacLL xlim c 129 3 122 2 ylim c 47 5 51 5 plt c 0 16 0 97 0 16 0 97 col rgb 255 255 195 maxColorValue 255 bg rgb 224 253 254 maxColorValue 255 tck c 0 03 cex 1 8 mgp c 1 9 0 7 0 GMT Panel B gmtset ANOT FONT SIZE 26p pscoast Dh A0 0 1 R 129 3 122 2 47 5 51 5 JM7i G255 255 195 8224 253 254 Ba2 alWSne W0 5p A p gt GMT VI ps ff load the nepacLL data set plot the nepacLL data set limit the region horizontally limit the region vertically specify the plot region size set the foreground colour set the background colour set the tick mark length adjust the font size adjust the axis label locations set the annotation font size plot the high resolution data set skip inner polygons holes limit the region horizontally and vertically use the Mercator projection 7 inches wide set the foreground colour set the background colour mark every 2 X and 1 Y degrees on W amp S axes set the pen width to 0 5 points portrait mode output to the postscript file GMT VI ps A Latitude 50 51 49 48 128 126 Longitude 232 234 236 Figure C1 A Vancouver Island as plotted in PBSmapping compared with B the same region as output from GMT E Code for Figure C2 R Panel A data nepacLL plotMap nepacL
80. e order of POS ascending or descending in the input data POS values in the input must be properly ordered ascending or descending but they may contain fractional values For example POS 2 5 might correspond to a point manually added between POS 2 and POS 3 If exteriorCCW NA all other columns remain unchanged Otherwise it orders the X and Y columns according to exteriorCCW Value PolySet with the same columns as the input except for possible changes to the POS X and Y columns See Also closePolys fixBound isConvex isIntersecting PolySet importEvents Examples local envir PBSmapEnv expr create a PolySet with broken POS numbering polys lt data frame PID c rep 1 10 rep 2 10 POS c seq 2 10 length 10 seq 10 2 length 10 X c rep 1 10 rep 1 10 Y c rep 1 10 rep 1 10 fix the POS numbering polys lt fixPOS polys print the results print polys importEvents Import EventData from a Text File Description Import a text file and convert into EventData Usage importEvents EventData projection NULL zone NULL Arguments EventData filename of EventData text file projection optional projection attribute to add to EventData zone optional zone attribute to add to EventData Value An imported EventData See Also importPolys importLocs importGSHHS importShapefile importGSHHS Import Data from a GSHHS Database Description Impor
81. e some EventData events lt as EventData data frame EID 1 200 X rnorm 200 Y rnorm 200 projection 1 calculate the Voronoi tesselation polys lt calcVoronoi events create PolyData to color it based on area polyData lt calcArea polys names polyData Lis element names polyData area lt Z colSeg lt seg 0 4 0 95 length 4 polyData lt makeProps polyData breaks quantile polyData Z c 0 25 5 75 1 propName col propVals rgb colSeq colSeq colSeq plot the tesselation plotMap polys polyProps polyData plot the points addPoints events pch 19 par oldpar clipLines Clip a PolySet as Polylines Description Clip a PolySet where each unigue PID SID describes a polyline Usage clipLines polys xlim ylim keepExtra FALSE Arguments polys PolySet to clip xlim range of X coordinates ylim range of Y coordinates keepExtra Boolean value if TRUE tries to carry forward any non standard columns into the result Details For each discrete polyline the function does not connect vertices 1 and N It recalculates the POS values for each vertex saving the old values in a column named oldPOS For new vertices it sets oldPOS to NA Value PolySet containing the input data with some points added or removed A new column oldPOS records the original POS value for each vertex See Also clipPolys fixBound clipPolys 63 Examples local envir PBSmapEnv
82. e the data correspond to additional fields in the data frame The R S language conveniently allows non non data frames to contain fields of various atomic modes logical numeric complex character and null For example PolyData with the fields PID PName might assign character names to a set of primary polygons Additionally if fields X and Y exist perhaps representing locations for placing labels consider adding attributes zone and projection Inserting the string PolyData as the class attribute s first element alters the behaviour of some functions including print if PBSprint is TRUE and summary Our software particularly uses PolyData to set various plotting characteristics Consistent with graphical parame ters used by the R S functions lines and polygon column names can specify graphical properties e lty line type in drawing the border and or shading lines e col line or fill colour border border colour density density of shading lines angle angle of shading lines When drawing polylines as opposed to closed polygons only 1ty and col have meaning Value The as PolyData method returns an object with classes PolyData and data frame in that order See Also EventData LocationSet PolySet PolySet PolySet Objects Description PBS Mapping functions that expect PolySet s will accept properly formatted data frames in their place see De tails as
83. ePolySet is PolyData isConvex C isIntersecting validatePolySet is PolyData isIntersecting C joinPolys validatePolySet is PolySet joinPolys C locateEvents is EventData locatePolys validatePolyData is PolySet makeGrid is PolySet makeProps validatePolyData is PolyData makeTopography placeHoles calcOrientation checkRDeps plotLines plotMaps is PolyData plotMap plotMaps is PolyData plotPoints plotMaps is PolyData plotPolys plotMaps is PolyData print EventData summary EventData print LocationSet summary LocationSet print PolyData summary PolyData print PolySet summary PolySet print summary PBS refocusWorld createIDs shiftRegion S validatePolySet summary EventData summary LocationSet CreatelDs summary PolyData createIDs summary PolysSet createIDs thickenPolys calcDist createIDs validatePolySet is PolySet thickenPolys C thinPolys validatePolySet is PolySet thinPolys C 43 Appendix F PBSmapping Functions and Data This appendix documents the objects functions and data available in PBSmapping Subsequent pages give indexed technical documentation for every object generated from Rd files written for the R documentation system The package PBSmodelling includes a directory called PBStools that contains useful batch files for building R packages including the c
84. ePolys polys col 2 2 corners and 1 opposite polys lt data frame combineEvents 65 PID c 1 2 2 8 3 3 POS c 1 ls 25 25S 5 X c 0 0 1 5 6 1 5 Y c 1 0 2 3 0 1 5 3 plotPolys closePolys polys col 2 par oldpar combineEvents Combine Measurements of Events Description Combine measurements associated with events that occur in the same polygon Usage combineEvents events locs FUN bdryOK TRUE Arguments events EventData with at least four columns EID X Y Z locs LocationSet usually resulting from a call to findPolys FUN a function that produces a scalar from a vector e g mean sum optional arguments for FUN bdryOK Boolean value if TRUE include boundary points Details This function combines measurements associated with events that occur in the same polygon Each event EID has a corresponding measurement Z The locs data frame usually output from findPolys places events within polygons Thus each polygon PID SID determines a set of events within it and a corresponding vector of measurements Zv The function returns FUN Zv a summary of measurements within each polygon Value PolyData with columns PID SID if in locs and Z See Also findCells findPolys locateEvents locatePolys makeGrid makeProps Examples local envir PBSmapEnv expr create an EventData data frame let each event have Z 1 events lt data frame EID 1 10 X 1 10
85. ection FALSE plt c 0 11 0 98 0 12 0 88 polyProps NULL cex NULL col NULL pch NULL axes TRUE tckLab TRUE tck 0 014 tckMinor 0 5 tck EventData or PolyData to plot required range of X coordinates range of Y coordinates desired projection when PolySet lacks a projection attribute one of LL UTM or a nu meric value If Boolean specifies whether to check polys for a projection attribute four element numeric vector x1 x2 yl y2 giving the coordinates of the plot region measured as a fraction of the figure region Set to NULL if mai in par is desired PolyData specifying which points to plot and their properties par parameters passed as direct arguments supersede these data vector describing character expansion factors cycled by EID or PID vector describing colours cycled by EID or PID vector describing plotting characters cycled by EID or PID Boolean value if TRUE plot axes Boolean vector length or 2 if TRUE label the major tick marks If given a two element vector the first element describes the tick marks on the x axis and the second element describes those on the y axis 98 plotPoints tck numeric vector length 1 or 2 describing the length of tick marks as a fraction of the smallest dimension If tckLab TRUE these tick marks will be automatically labelled If given a two element vector the first element describes the tick marks on the x axis and the second
86. ector of values to associate with Z breaks Details This function acts like the cut function to produce PolyData suitable for the polyProps plotting argument see addLabels addLines addPoints addPolys addStipples plotLines plotMap plotPoints and plotPolys The Z column of pdata is equivalent to the data vector x of the cut function Value PolyData with the same columns as pdata plus an additional column propName See Also addLabels addLines addPoints addPolys addStipples plotLines plotMap plotPoints plotPolys PolyData PolySet Examples local envir PBSmapEnv expr create a PolyData object pd lt data frame PID 1 10 Z 1 10 using 3 intervals create a column named col and populate it with the supplied values makeProps pdata pd breaks 3 propName col propVals c 1 3 jp makeTopography 89 makeTopography Make Topography Data From Freely Available Online Data Description Make topography data suitable for the contour and contourLines functions using freely available global seafloor topography data Usage makeTopography dat digits 2 func NULL Arguments dat data frame with three optionally named columns X Y and Z The columns must appear in that order digits integer indicating the precision to be used by the function round on X Y values func function to summarize Z if X Y points are duplicated Defaults to mean if no function is specified Details Data obtain
87. ed by straight lines Coordinates X Y specify the location of each vertex Thus in familiar mathematical notation a contour consists of n points x y with 1 n where i corresponds to the Pos index A PolySet has two potential interpretations The first associates a line segment with each successive pair of points from 1 to n giving a polyline in GIS terminology composed of the sequential segments The second includes a final line segment joining points n and 1 thus giving a polygon The secondary ID field allows us to define regions as composites of polygons From this point of view each primary ID identifies a collection of polygons distinguished by secondary IDs For example a single management area PID might consist of two fishing areas each associated with a different SID A secondary polygon can also correspond to an inner boundary like the hole in a doughnut We adopt the convention that POS goes from 1 to n along an outer boundary but from 7 to along an inner boundary regardless of rotational direction This a contrasts with other GIS software such as ArcView ESRI 1996 in which outer and inner boundaries correspond to clockwise and counter clockwise directions respectively The SID field in a PolySet with secondary IDs must have integer values that appear in ascending order for a given PID Furthermore inner boundaries must follow the outer boundary that encloses them The Pos field for each contour PID S
88. ed through the acquisition form at http topex ucsd edu cgi bin get_data cgi is suitable for this function read table will import its ASCII files into R S creating the data argument for this function When creating data for regions with longitude values spanning 180 to 0 consider subtracting 360 from the result s X coordinates x When creating bathymetry data consider negating the result s elevations z to give depths positive values Combinations of X Y do not need to be complete z x y 1 NA or unique z x y zfunc Z x y Value List with elements x y and z x and y are vectors while z is a matrix with rownames x and colnames y contour and contourLines expect data conforming to this list format See Also graphics contour grDevices contourLines convCP Examples local envir PBSmapEnv expr oldpar par no readonly TRUE Example 1 Sample data frame and conversion file lt data frame X c 1 1 2 2 Y c 3 4 3 4 Z c 5 6 7 8 print makeTopography file Example 2 Aleutian Islands bathymetry isob lt c 100 500 1000 2500 5000 icol lt rgb 0 0 seq 255 100 len length isob max 255 afile lt paste system file package PBSmapping Extra aleutian txt sep aleutian lt read table afile header FALSE col names rc x y z aleutian x lt aleutian x 360 90 nepacLL aleutian z lt aleutian z alBathy lt makeTopography aleutian alCL lt c
89. efile fn readDBF TRUE projection NULL zone NULL placeholes FALSE minverts 3 Arguments fn file name of the shapefile to import specifying the extension is optional readDBF Boolean value if TRUE it also imports the dbf a database containing the feature attributes associated with the shapefile projection optional projection attribute to override the internally derived value zone optional zone attribute to override the default value of NULL placeholes logical if TRUE then for every PID identify solids and holes and place holes under appropriate solids minverts minimum number of vertices required for a polygon representing a hole to be retained does not affect solids isConvex 81 Details This routine imports an ESRI shapefile shp into either a PolySet or EventData depending on the type of shapefile It supports types 1 Point 3 PolyLine and 5 Polygon and imports type 1 into EventData and types 3 and 5 into a PolySet In addition to the shapefile shp it requires the related index file shx If a database containing feature attributes dbf exists it also imports this database by default For EventData it binds the database columns to the EventData object For a PolySet it saves the database in a PolyData object and attaches that object to the PolySet in an attribute named PolyData If a prj file exists this information is attached as an attribute If the first 3 characters are GEO
90. element describes those on the y axis tckMinor numeric vector length or 2 describing the length of tick marks as a fraction of the smallest dimension These tick marks can not be automatically labelled If given a two element vector the first element describes the tick marks on the x axis and the second element describes those on the y axis additional par parameters or the arguments main sub xlab or ylab for the title function Details This function clips data to x1im and ylim before plotting It only adds PolyData containing X and Y columns The function creates a blank plot when polys equals NULL In this case the user must supply both xlim and ylim arguments Alternatively it accepts the argument type n as part of which is equivalent to specifying polys NULL but requires a PolySet In both cases the function s behaviour changes slightly To resemble the plot function it plots the border labels and other parts according to par parameters such as col For additional help on the arguments cex col and pch please see par Value PolyData consisting of the PolyProps used to create the plot Note To satisfy the aspect ratio this plotting routine resizes the plot region Consequently par parameters such as plt mai and mar will change When the function terminates these changes persist to allow for additions to the plot See Also addPoints combineEvents convDP findPolys locateEvents Examples
91. ence to the R language Our utilities make this possible by directly processing text files with the appropriate data format They have been compiled with the same C code used for the dynamically linked library DLL in R For each utility a corresponding c file provides a front end to shared code for the algorithms Source code appears in the R library directory PBSmapping Utils 3 1 clipPolys exe Clip Polygons The application clipPolys exe reads an ASCII file containing a PolySet explained further below and then clips it The command clipPolys exe i IFILE o OFILE x MIN_X X MAX_X y MIN Y Y MAX Y has five arguments as follows e i IFILE ASCII input file containing a PolySet required e o OFILE ASCII output file defaults to standard output e x MIN X lower X limit defaults to minimum X in the PolySet e X MAXX upper X limit defaults to maximum X in the PolySet e y MIN Y lower Y limit defaults to minimum Y in the PolySet e Y MAX Y upper Y limit defaults to maximum Y in the PolySet The first line of the PolySet input file must contain the field names PID SID POS X Y where SID is optional Subsequent lines must contain the data with the same number of fields per row as in the header line All fields must be delimited by white space The program generates a properly formatted PolySet By default unless otherwise specified by o this result goes to standard output which can be redirected to
92. er clockwise rotation under SIDs identified as solids clockwise rotation if the vertices of the holes lie completely within the vertices of the solids This operation is performed for each primary polygon PID Usage placeHoles polyset minVerts 3 Arguments polyset a valid PBSmapping PolySet minVerts minimum number of vertices required for a polygon representing a hole to be retained does not affect solids Details The algorith identifies the rotation of each polygon down to the SID level using the PBSmapping function calcOrientation where output values of 1 solids clockwise rotation and 1 holes counter clockwise rotation Then for each solid the function tests whether each hole occurs within the solid To facilitate computa tion the algorithm assumes that once a hole is located in a solid it will not occur in any other solid This means that for each successive solid the number of candidate holes will either decrease or stay the same This function makes use of the point in polygon function contained in the package sp For each hole vertex the latter algorithm returns a numeric value 0 hole vertex is strictly exterior to the solid 1 hole vertex is strictly interior to the solid 2 hole vertex lies on the relative interior of an edge of the solid 3 hole vertex coincides with a solid vertex Value Returns the input PolySet where SID holes have been arranged beneath appropriate SID solids for each PID
93. erse FALSE col 3 par oldpar convUL Convert Coordinates between UTM and Lon Lat Description Convert coordinates between UTM and Lon Lat Usage convUL xydata km TRUE southern NULL Arguments xydata data frame with columns X and Y km Boolean value if TRUE UTM coordinates within xydata are in kilometres otherwise metres southern Boolean value if TRUE forces conversions from UTM to longitude latitude to produce coordi nates within the southern hemisphere For conversions from UTM this argument defaults to FALSE For conversions from LL the function determines southern from xydata 70 dividePolys Details The object xydata must possess a projection attribute that identifies the current projection If the data frame contains UTM coordinates it must also have a zone attribute equal to a number between 1 and 60 inclusive If it contains geographic longitude latitude coordinates and the zone attribute is missing the function computes the mean longitude and uses that value to determine the zone The longitude range of zone i is 186 67 lt x lt 180 67 This function converts the X and Y columns of xydata from LL to UTM or vice versa If the data span more than one zone to the right or left of the intended central zone the underlying algorithm may produce erroneous results This limitation means that the user should use the most central zone of the mapped region or allow the function to dete
94. es The central axis of zone 6 vertical dotted line at x 500 km corresponds to the central meridian shown in Figure 2 2 3 PBSmapping Functions and Algorithms Our software produces maps from the data structures defined in Section 2 1 Following typical design concepts in R it uses functions to generate plots implement algorithms and perform other tasks Where possible function arguments often have explicit default values PBSmapping includes many functions not mentioned in this section We encourage readers to examine Appendix F which gives detailed technical descriptions of all our software s functions and other components Import Functions The following functions provide some support for importing GIS data from other users and other mapping platforms e importEvents import a text file and convert into EventData e importLocs import a text file and convert into a LocationSet _9_ e importPolys import a text file and convert into a PolySet with optional PolyData attribute e importGSHHS import data from a GSHHS database and convert data into a PolySet with a PolyData attribute GSHHS A Global Self consistent Hierarchical High resolution Shoreline Database http www soest hawaii edu pwessel gshhg See Section 2 4 below for more details e importShapefile imports an ESRI shapefile shp into either a PolySet or EventData The function relies on C code provided by Roger Bivand s package maptools Graphics Functions
95. est coast of Vancouver Island September 15 October 2 2001 Canadian Technical Report of Fisheries and Aquatic Sciences 2421 60 pp See Also addLines calcLength clipLines plotLines PolySet towData worldLL Data Shorelines of the World Normal Resolution Description PolySet of polygons for the global shorelines Usage data worldLL Format Data frame consisting of 4 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinate and Y latitude coordinate Attributes projection LL worldLL high 111 Note In R the data must be loaded using the data function Source Polygon data from the GSHHS Global Self consistent Hierarchical High resolution Shoreline database gshhs_1 b Download from http www soest hawaii edu wessel gshhs gshhs html worldLL lt importGSHHS gshhs_1 b xlim c 20 360 ylim c 90 90 level 1 n 15 xoff 0 worldLL lt fixGSHHSWorld worldLL References Wessel P and Smith W H F 1996 A global self consistent hierarchical high resolution shoreline database Journal of Geophysical Research 101 8741 8743 http www soest hawaii edu pwessel pwessel_pubs html See Also Data worldLLhigh nepacLL nepacLLhigh importGSHHS addPolys clipPolys plotPolys plotMap thickenPolys thinPolys worldLLhigh Data Shorelines of the World High Resolution Description PolySet of polygons for the global shorelines
96. et polys Using this PolySet the function calculates a centroid mean range or mean X Y coordinate for each polygon and then links those PolyData with data by PID SID to determine label coordinates If data contains both PID and EID columns the function assumes it is PolyData and ignores the EID column For additional help on the arguments cex col and font please see par Value EventData or PolyData with X and Y columns that can subsequently reproduce the labels on the plot Modify this data frame to tweak label positions See Also addPoints calcCentroid calcMidRange calcSummary EventData plotPoints PolyData 50 Examples addLines local envir PBSmapEnv expr oldpar par no readonly TRUE create sample PolyData to label Vancouver Island labelData lt data frame PID 33 label Vancouver Island load data if is null version language 88 version language R data nepacLL envir PBSmapEnv plot the map plotMap nepacLL xlim c 129 122 6 ylim c 48 51 1 col lemonchiffon add the labels addLabels labelData placement CENTROID polys nepacLL cex 1 2 col 2 font 2 par oldpar addLines Description Add a PolySet to an Existing Plot as Polylines Add a PolySet to an existing plot where each unique PID SID describes a polyline Usage addLines polys xlim NULL ylim NULL polyProps NULL lty NULL col NULL arrows FALSE Argume
97. evel and negative values above it contour and contourLines expect data in this format convCP converts the output from contourLines into a PolySet Note In R the data must be loaded using the data function calcArea Source Bathymetry data acquired from the Scripps Institution of Oceanography at the University of San Diego Using their online form we requested bathymetry data for the complete nepacLL region At forty megabytes the data were not suitable for distribution in our mapping package Therefore we reduced the data to the range 140 lt x lt 122 and 47 lt y lt 61 References Smith W H F and Sandwell D T 1997 Global seafloor topography from satellite altimetry and ship depth soundings Science 277 1957 1962 http topex ucsd edu WWW_html mar_topo html See Also contour contourLines convCP nepacLL nepacLLhi gh calcArea Calculate the Areas of Polygons Description Calculate the areas of polygons found in a PolySet Usage calcArea polys rollup 3 Arguments polys PolySet to use rollup level of detail in the results 1 PIDs only by summing all the polygons with the same PID 2 outer contours only by subtracting holes from their parent and 3 no roll up Details If rollup equals 1 the results contain an area for each unique PID only When it equals 2 they contain entries for outer contours only Finally setting it to 3 prevents roll up and they contain areas
98. f a pdata object does not exist the output contains only one polygon with a PID equal to 1 One inner boundary polygon POS goes from n to 1 can be generated by supplying a negative n nan If type o or type 1 the function draws a line connecting the last and first vertices Value PolySet with projection attribute equal to the map s projection The function does not set the zone attribute See Also addPolys appendPolys clipPolys closePolys findCells findPolys FixPOS joinPolys plotMap plotPolys thickenPolys thinPolys Examples define one polygon with up to 5 vertices on the current plot Not run polys lt locatePolys n 5 LocationSet LocationSet Objects Description PBS Mapping functions that expect LocationSet s will accept properly formatted data frames in their place see Details as LocationSet attempts to coerce a data frame to an object with class LocationSet is LocationSet returns TRUE if its argument is of class LocationSet Usage as LocationSet x is LocationSet x fullValidation TRUE Arguments x data frame to be coerced or tested fullValidation Boolean value if TRUE fully test x Details A PolySet can define regional boundaries for drawing a map and EventData can give event points on the map Which events occur in which regions Our function findPolys resolves this problem The output lies in a LocationSet a data frame with three or four columns EID P
99. fill colours cycled by PID colHoles vector describing hole colours cycled by PID The default NULL should be used in most cases as it renders holes transparent colHoles is designed solely to eliminate retrace lines when images are converted to PDF format If colHoles is specified underlying information i e previously plotted shapes will be obliterated If NA is specified only outer polygons are drawn conseguently filling holes density vector describing shading line densities lines per inch cycled by PID angle vector describing shading line angles degrees cycled by PID bg background colour of the plot axes Boolean value if TRUE plot axes tckLab Boolean vector length 1 or 2 if TRUE label the major tick marks If given a two element vector the first element describes the tick marks on the x axis and the second element describes those on the y axis tck numeric vector length 1 or 2 describing the length of tick marks as a fraction of the smallest dimension If tckLab TRUE these tick marks will be automatically labelled If given a two element vector the first element describes the tick marks on the x axis and the second element describes those on the y axis tckMinor numeric vector length 1 or 2 describing the length of tick marks as a fraction of the smallest dimension These tick marks can not be automatically labelled If given a two element vector the first element describes the tick marks on the x axis a
100. for each unique PID SID Outer polygons have positive areas and inner polygons negative areas When polygons are rolled up the routine sums the positive and negative areas and consequently accounts for holes If the PolySet s projection attribute equals LL the function projects the PolySet in UTM first If the PolySet s zone attribute exists it uses it for the conversion Otherwise it computes the mean longitude and uses that value to determine the zone The longitude range of zone i is 186 67 lt x lt 180 67 Value PolyData with columns PID SID may be missing and area If the projection equals LL or UTM the units of area are square kilometres See Also calcCentroid calcLength calcMidRange calcSummary locatePolys calcCentroid 57 Examples local envir PBSmapEnv expr load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv convert LL to UTM so calculation makes sense attr nepacLL zone lt 9 nepacUTM lt convUL nepacLL calculate and print the areas print calcArea nepacUTM calcCentroid Calculate the Centroids of Polygons Description Calculate the centroids of polygons found in a PolySet Usage calcCentroid polys rollup 3 Arguments polys PolySet to use rollup level of detail in the results 1 PIDs only 2 outer contours only and 3 no roll up When rollup egu
101. fying the PID and SID indices e convCP converts results from contourlines into a PolySet e convDP converts EventData PolyData into a PolySet e convLP converts two polylines into a polygon e convUL converts between UTM and longitude latitude coordinates using the extensive formulas presented in Ordnance Survey 2010 e dividePolys divides a single polygon with several outer contour components into several polygons a polygon for each outer contour by modifying the PID and SID indices e findCells finds the cells in a grid PolySet that contain events specified in EventData using the crossings test algorithm described later in this section e findPolys finds the polygons in a PolySet that contain events specified in EventData using the crossings test algorithm described later in this section e isConvex determines which polygons in a PolySet are convex using an algorithm described below e isIntersecting finds polygons that self intersect by comparing each edge pairwise with every other edge e joinPolys performs set theoretic operations union intersection difference and exclusive or on polygons using the Clipper library developed by Angus Johnson http www angusj com delphi clipper php See Figure 13 of the PBSmodelling user s guide Schnute ef al 2006 for an example called FishTows Fig 14 in most recent version e thickenPolys adds vertices to polygons using an algorithm described below e thinPolys thins t
102. g clr sea tck c 0 028 0 tckLab c TRUE FALSE mgp c 1 9 0 7 0 cex 1 0 plt c 0 00 0 86 0 07 0 97 text x xlim 2 0 5 y ylim 2 0 3 B cex 1 6 box 36 Figure 5 joinPolys on Crescents PBSfig05 lt function joinPolys on Crescents clr lt PBSclr dash lt PBSdash radius lt c 5 4 two radii of the circles size lt abs diff radius 0 1 size of crescent shiftB lt 3 5 distance to shift second crescent pts lt 120 points in outer circle cex lt 1 0 character expansion for labels off lt 1 2 panel label offset xlim lt c 0 radius 1 2 shiftB c 1 1 ylim lt c 0 radius 1 2 c 2 1 Mmin lt 10 minimum OMI Rdin lt par din 2 par din 1 Rfig lt 3 diff ylim 2 diff xlim if Rdin gt Rfig width lt par din 1 2 Mmin height lt width 3 diff ylim 2 diff xlim Mmax lt par Sdin 2 height 2 parOmi lt c Mmax Mmin Mmax Mmin else height lt par Sdin 2 2 Mmin width lt height 2 diff xlim 3 diff ylim Mmax lt par din 1 width 2 parOmi lt c Mmin Mmax Mmin Mmax polyA lt list for i in 1 length radius polyA i lt as PolySet data frame PID rep 1 pts POS 1 pts X radius i cos seq 0 2 pi len pts Y radius i sin seq 0 2 pi len pts projection 1 polyA i c X Y lt polyA i c X Y radius i centre B wit
103. gement areas Second fishing events occur at specific locations defined by two geographical coordinates such as longitude and latitude The R language conveniently supports such structures through the concept of a data frame essentially a database table in which rows and columns define records and fields respectively Objects like data frames in R can also have attributes that store additional properties such as the projection used in defining a geographic coordinate system 2 1 Data Structures for Maps PBSmapping introduces four data structures each stored as a data frame Field names attributes and other properties of these objects implicitly dictate their type An object may also identify its type explicitly in the class attribute Each type requires a particular structure as outlined below PolySet In our software a PolySet data frame defines a collection of polygonal contours i e line segments joined at vertices based on four or five numerical fields e PID the primary identification number for a contour e SID optional the secondary identification number for a contour e POS the position number associated with a vertex e x the horizontal coordinate at a vertex e Y the vertical coordinate at a vertex The simplest PolySet lacks an SID column and each PID corresponds to a different contour By analogy with a child s follow the dots game the POS field enumerates the vertices to be connect
104. he number of polygon vertices based on the Douglas Peuker line simplification algorithm Douglas and Peucker 1973 as illustrated in Figure 4 Our function isConvex first calls isIntersecting to determine whether or not a polygon self intersects If it does it cannot be convex and the result is FALSE Otherwise the function proceeds Three seguential points in a non self intersecting polygon describe a left turn a straight line or a right turn The function locates the first non straight turn left or right in a polygon and checks that all subseguent turns are either the same or straight If so the polygon is convex otherwise it is not Like calcLength thickenPolys also supports the longitude latitude projection In this case tol is measured in kilometres and distances are computed along great circles Chamberlain 2001 a je JU Latitude 48 5 49 495 50 50 5 51 EW T e e En R T I Se SO lo a I a SEE E TA EXE NAAA AE AR T TTTT 128 127 126 125 124 128 127 126 125 124 Longitude Longitude Figure 4 A Vancouver Island clipped from the PolySet nepacLL and B the result of applying thinPolys to this polygon with a tolerance of ten kilometres When the projection is UTM or 1 our function thickenPolys accepts a tolerance specified in X or Y units kilometres in the UTM case It operates in two distinct modes When keepOrig TRUE it retains all original vertices and adds vertices as required along
105. hin A polyA 2 c X Y lt polyA 2 c X Y radius 1 radius 2 shift B right polyA 2 11 X lt polyA 2 X size create polysA and polysB polyA lt as PolySet joinPolys polyA 111 polyA 2 operation DIFF projection 1 polyB lt polyA polyB X lt abs polyB X radius 1 2 shiftB par mfrow c 3 2 mai c 0 0 0 0 omi parOmi Plot the figure lab lt list lab text lt c Polygon A Polygon B A INT B A UNION B A DIFF B A XOR B lab cex lt rep cex 6 lab x lt rep mean xlim 6 lab y lt rep 0 8 6 panel A polyA plotMap polyA xlim xlim ylim y1lim xlab ylab axes FALSE col clr red plt NULL text labStext 1 x lab x 1 y lab y 1 cex lab cex 1 text xlim 1 off ylim 2 off A cex 1 6 box panel B polyB plotMap polyB xlim xlim ylim ylim xlab ylab axes FALSE col clr blue plt NULL text labStext 2 x lab x 2 y lab y 2 cex lab cex 2 text xlim 1 off ylim 2 off B cex 1 6 box panels C to F ops lt c NA NA INT UNION DIFF XOR cols lt c NA NA clr red clr purple clr purple clrSpurple panel lt C NA NA C D E WE for i in 3 6 plotMap NULL x1lim x1im ylim ylim projection 1 xlab ylab axes FALSE plt NULL addPolys polyA border clr red lty dash addPolys polyB border clr blue lty dash addPolys joi
106. ial Parameter Vector for Model Fits pcoda Topo Hecate Strait Pacific Cod Monitoring Survey Areas pjsa Code Paul J Starr Locality Codes pl230 Topo 230 Degree True Line from Lookout Island pmfc Code Pacific Marine Fisheries Commission Areas pop age Data Pacific Ocean Perch Age Data 5AB 5CD pop pmr qcss Data Pacific Ocean Perch p mu rho for OCS Synoptic Survey popa Topo Pacific Ocean Perch Population Areas gcb Topo Oueen Charlotte Basin Surficial Geology qessa Topo Queen Charlotte Sound Survey Strata rca Topo Rockfish Conservation Areas 28 Object Description species Code Species Codes and Names primarily for marine fisheries spn Code Species Code Vector srfa Topo Slope Rockfish Assessment Areas srfs Topo Slope Rockfish Assessment Subareas testdatC Data Fisheries Catch Data with Species by Column testdatR Data Fisheries Catch Data with Species by Row trawlability Topo Fisher Knowledge of Towable Bottom utilize Code Utilization Codes for Various DFO Databases wchgsa Topo West Coast Haida Gwaii Survey Area wcvisa Topo West Coast of Vancouver Island Survey Strata ymr rem Data Annual Catches of Rockfish by Sector 29 Appendix B Bathymetry Data Smith and Sandwell 1997 have produced a global seafloor topography database from satellite altimetry and ship depth soundings Using the web based data acquisition form at http topex ucsd edu cgi bin get data cgi users can extract
107. in the output It may happen however that an event occurs in multiple polygons Thus the same EID can occur more than once in the output Value LocationSet that links events with polygons See Also combineEvents findCells locateEvents locatePolys LocationSet makeGrid fixBound 75 Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create some EventData a column of points at X 0 5 events lt data frame EID 1 10 X 5 Y seq 0 2 length 10 events lt as EventData events projection 1 create a PolySet two squares with the second above the first polys lt data frame PID c rep 1 4 rep 2 4 POS c 1 4 1 4 X c 0 1 1 0 0 1 1 0 Y c 0 0 1 1 1 1 2 2 polys lt as PolySet polys projection 1 show a picture plotPolys polys xlim range polys X c 0 1 0 1 ylim range polys Y c 0 1 0 1 projection 1 addPoints events col 2 run findPolys and print the results print findPolys events polys par oldpar fixBound Fix the Boundary Points of a PolySet Description The ranges of a PolySet s X and Y columns define its boundary This function fixes a PolySet s vertices by moving vertices near a boundary to the actual boundary Usage fixBound polys tol Arguments polys PolySet to fix tol vector length 1 or 2 specifying a percentage of the ranges to use in defining near to a bound ary If tol has two elements the first specifies the
108. ines clipPolys Clip a PolySet as polygons closePolys Close a PolySet combineEvents Combine measurements of events in same polygon combinePolys Combine several polygons into a single polygon convCP Convert results from contourlines into PolySet convDP Convert EventData PolyData into a PolySet convLP Convert polylines into a polygon convUL Convert coordinates between UTM LL projections dividePolys Divide a single polygon into several polygons extractPolyData Extract PolyData from a PolySet findCells Find cells in a grid that contain events in EventData A4 Category Obpjct_____ Description gt findPolys Find polygons that contain events in EventData fixBound Fix the boundary points of a PolySet fixPOS Fix the POS column of a PolySet isConvex Determine whether polygons are convex isIntersecting Determine whether polygons are self intersecting joinPolys Join one or two PolySets using a set theoretic operation locateEvents Locate events on the current plot locatePolys Locate polygons on the current plot makeGrid Make a grid of polygons makeProps Make polygon properties makeTopography Make topography data from freely available online data placeHoles Place holes under correct solids refocusWorld Refocus the worldLL worldLLhigh data sets thickenPolys Thicken a PolySet of polygons thinPolys Thin a PolySet of polygons Object related as Coerce a data frame to an object with class functions EventData EventData LocationSet LocationSet PolyDat
109. ines into a polygon Usage convLP polyA polyB reverse TRUE Arguments polyA PolySet containing a polyline polyB PolySet containing a polyline reverse Boolean value if TRUE reverse polyB s vertices convUL 69 Details The resulting PolySet contains all the vertices from polyA in their original order If reverse TRUE this function appends the vertices from polyB in the reverse order nrow polyB 1 Otherwise it appends them in their original order The PID column equals the PID of polyA No SID column appears in the result The resulting polygon is an exterior boundary Value PolySet with a single PID that is the same as polyA The result contains all the vertices in polyA and polyB It has the same projection and zone attributes as those in the input PolySets If an input PolySet s attributes equal NULL the function uses the other PolySet s If the PolySet attributes conflict the result s attribute equals NULL See Also addLines appendPolys closePolys convCP joinPolys plotLines Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create two polylines polylinel lt data frame PID rep 1 2 POS 1 2 X c 1 4 Y c 1 4 polyline2 lt data frame PID rep 1 2 POS 1 2 X c 2 5 Y c 1 4 create two plots to demonstrate the effect of reverse par mfrow c 2 1 plotPolys convLP polylinel polyline2 reverse TRUE col 2 plotPolys convLP polyline1 polyline2 rev
110. iple records If an EID does not fall in any PID SID or if it falls within a hole it does not occur in the output LocationSet Inserting the string Locationset as the first element of a LocationSet s class attribute alters the behaviour of some functions including print if PBSprint is TRUE and summary 2 2 Map Projections The simplest projection associates each point on the earth s surface with a longitude x 360 lt x lt 360 and latitude y 90 lt y lt 90 where x 0 on the Greenwich prime meridian The chosen range of x depends on the region of interest where negative longitudes refer to displacements west of the prime meridian When plotted on a rectangular grid with equal distances for each degree of longitude and latitude this projection exaggerates the size of objects ba near the earth s poles as illustrated in Figure 1 For points near the latitude y a more realistic map uses the aspect ratio 1 2 1 r COS y where r degrees of longitude x should occupy the same distance as 1 degree of latitude y gt TE HEL Te A Hh gt AW THIR A K y x a 5 Longitude Latitude Figure 1 Map of the world projected in longitude latitude coordinates This image based on our PolySet worl dLL uses the longitude range 20 lt x lt 360 to produce a convenient cut in the eastern Atlantic Ocean Red vertical li
111. irst we have posted the current software as a contributed package on the Comprehensive R Archive Network CRAN http cran r project org Thanks to a remarkable collection of Perl scripts developed for the R project source code in both C and R along with suitable documentation files can be tested and compiled automatically for distribution as both source and binary packages Nick Boers ensured that our source materials met the necessary standards and after we made minor changes in the C code to avoid compiler warnings the authors of the CRAN web site in Vienna Austria accepted our contribution Second Nick applied to the Canadian Natural Sciences and Engineering Research Council NSERC for a grant to support graduate studies in computing science His application cited his successful experience developing PBSmapping Version 1 as documented in Schnute et al 2003 To the delight of Nick s supporters at PBS and MUC he won a substantial award in fact the only NSERC grant given to a student from MUC this year Congratulations Nick from your colleagues at PBS and professors at MUC We ll follow your career at the University of Alberta in Edmonton with great interest Jon Schnute vi This page has been left intentionally blank for printing purposes 1 1 INTRODUCTION This report describes software written to facilitate the compilation and analysis of fishery data particularly data referenced by spatial coordinates Our
112. ite docs support guide coordinate systems great britain pdf Rokne J 1996 The area of a simple polygon p 5 6 in Arvo J 1996 Graphics Gems II Academic Press San Diego CA 672 p Rutherford K L 1999 A brief history GFCATCH 1954 1995 the groundfish catch and effort database at the Pacific Biological Station Canadian Technical Report of Fisheries and Aquatic Sciences 2299 66 p Schnute J T Boers N M and Haigh R 2003 PBS Software maps spatial analysis and other utilities Canadian Technical Report of Fisheries and Aquatic Sciences 2496 82 p Schnute J T Couture Beil A and Haigh R 2006 PBS Modelling 1 user s guide Canadian Technical Report of Fisheries and Aquatic Sciences 2674 viii 114 p Schnute J T Haigh R Krishka B A and Starr P 2001 Pacific ocean perch assessment for the west coast of Canada in 2001 Canadian Science Advisory Secretariat Research Document 2001 138 90 p Schnute J T Wallace C G and Boxwell T A 1996 A relational database shell for marked Pacific salmonid data Revision 1 Canadian Technical Report of Fisheries and Aquatic Sciences 2090A 28 p Sinclair C A and Olsen N 2002 Groundfish research cruises conducted by the Pacific Biological Station Fisheries and Oceans Canada 1944 2002 Canadian Manuscript Report of Fisheries and Aquatic Sciences 2617 91 p Sipser M 1997 Introduction to the theory of computation PWS Publishing Company Boston
113. le It clips polys to xlim and ylim before plotting For additional help on the arguments border 1ty col density and angle please see polygon and par Value PolyData consisting of the PolyProps used to create the plot See Also addLabels addStipples clipPolys closePolys fixBound FixPOS locatePolys plotLines plotMap plotPoints plotPolys thinPolys thickenPolys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create a PolySet to plot polys lt data frame PID rep 1 4 POS 1 4 X c 0 1 1 0 Y c 0 0 1 1 polys lt as PolySet polys projection 1 plot the PolySet plotPolys polys xlim c 5 1 5 ylim c 5 1 5 density 0 projection 1 add the PolySet to the plot in a different style addPolys polys col green border blue lwd 3 par oldpar addStipples Add Stipples to an Existing Plot Description Add stipples to an existing plot Usage addStipples polys xlim NULL ylim NULL polyProps NULL side 1 density 1 distance 4 Arguments polys PolySet that provides the stipple boundaries required xlim range of X coordinates ylim range of Y coordinates polyProps PolyData specifying which polygons to stipple and their properties par parameters passed as direct arguments supersede these data side one of 1 0 or 1 corresponding to outside both sides or inside respectively density density of points relative to the default distance distance
114. les where records may not have a definite order The Pos field in our PolySet definition imposes the required order for polylines and polygons This field also provides a convenient means of distinguishing inner and outer boundaries Our PolySets have a flat structure with at most two levels corresponding to primary and secondary IDs We have found these limitations acceptable in the context of our work Sceptical readers might challenge our choices and prefer more complex hierarchical 22 structures For example Becker and Wilks 1993 1995 define polygons as composites of polylines so that a common boundary between two regions need be defined only once and then referenced in each regional definition In our approach all vertices of a common boundary must be repeated in each regional definition We designed our software explicitly to address a few key issues in the spatial representation of fishery data e easy importation from databases Geographic Information Systems and other sources such as the shoreline data compiled by Wessel and Smith 1996 precise control over the boundaries chosen for clipping from a larger map support for longitude latitude and UTM easting northing coordinates computational ability to associate events with polygons in which they lie flexible plotting tools that summarise events within grids and other polygons Different purposes could well lead to other designs In addition to their comprehensive
115. ly preferred over raster formats Unlike R the UNIX environment does not have native support for generating images Wessel and Smith decided that GMT programs would output optionally encapsulated postscript files This vector based format is more popular in UNIX than Windows and is poorly supported by some word processors such as Microsoft Word On the other hand PBSmapping inherits support from the R environment for common raster e g BMP JPG and vector e g WMF file formats Users of Windows operating systems may find PBSmapping s output somewhat more convenient than that from GMT Converting GMT s postscript output to a better supported graphics format can be achieved through the Ghostscript graphical user interface GSview http www cs wisc edu ghost gsview Through an option in GSview s Edit menu the program converts PS files to the popular EMF and WMF vector formats However we obtained somewhat erratic results from this process and had greater success with raster images produced with the convert option in the File menu Figure C1 and Figure C2 compare PBSmapping with GMT We show the code used to produce these images in both environments Although one R command can span multiple lines one GMT command cannot For clarity however we span GMT commands across multiple lines in the listing below In familiar UNIX notation we indicate spanning by escaping the new line character with a backslash Cod
116. n of data to the existing plot Usage addLabels data xlim NULL ylim NULL polyProps NULL placement DATA polys NULL rollup 3 cex NULL col NULL font NULL Arguments data EventData or PolyData to add required xlim range of X coordinates ylim range of Y coordinates polyProps PolyData specifying which labels to plot and their properties par parameters passed as direct arguments supersede these data placement one of DATA CENTROID MEAN_RANGE or MEAN_XY polys PolySet to use for calculating label placement rollup level of detail at which to process polys and it should match that in data 1 PIDs only 2 outer contours only and 3 no roll up cex vector describing character expansion factors cycled by EID or PID col vector describing colours cycled by EID or PID font vector describing fonts cycled by EID or PID additional par parameters for the text function Details If data is EventData it must minimally contain the columns EID X Y and label Since the EID column does not match a column in polys set placement DATA The function plots each label at its corresponding X Y coordinate If data is PolyData it must minimally contain the columns PID and label If it also contains X and Y columns set placement DATA to plot labels at those coordinates Otherwise set placement to one of CENTROID MEAN_RANGE or MEAN_XY When placement DATA supply a PolyS
117. nPolys polyA polyB operation ops i col cols i g text lab text i x lab x i y lab y i cex labScex i text xlim 1 off ylim 2 off panel i cex 1 6 box Figure 6 contourLines in Queen Charlotte Sound PBSfig06 lt function contourLines in Queen Charlotte Sound clr lt PBSclr data nepacLL bcBathymetry envir sys frame sys nframe isob lt contourLines bcBathymetry levels c 250 1000 p lt convCP isob attr p PolySet projection lt LL p PolyData col lt rep c clr red clr green clr blue clr Syellow clr cyan clr magenta clr fog length nrow p PolyData xlim lt c 131 8382 128 2188 ylim lt c 50 42407 53 232476 region lt clipPolys nepacLL xlim xlim ylim ylim par mfrow c 1 1 omi c 0 0 0 0 H Plot the figure plotMap region xlim xlim ylim ylim col clr land bg clr sea tck 0 02 mgp c 2 75 0 cex 1 2 plt c 08 98 08 98 addLines p PolySet polyProps p PolyData lwd 3 box di Figure 7 towTracks from Longspine Thornyhead Survey PBSfig07 lt function towTracks from Longspine Thornyhead Survey clr lt PBSclr data nepacLL towTracks towData envir sys frame sys nframe add a colour column col to towData pdata lt towData pdata Z lt pdata dep pdata lt makeProps pdata breaks c 500 800 1200 1600 col c clr black clr red clr blue par mfrow c 1 1 omi c 0 0 0 0 H
118. nd the second element describes those on the y axis additional par parameters or the arguments main sub xlab or ylab for the title function 100 PolyData Details This function plots a PolySet where each unique PID SID describes a polygon It connects each polygon s last vertex to its first The function supports both borders border 1ty and fills col density angle When supplied with the appropriate arguments it can draw only borders or only fills Unlike plotMap it ignores the aspect ratio It clips polys to xlim and ylim before plotting This function creates a blank plot when polys equals NULL In this case the user must supply both xlimand ylim arguments Alternatively it accepts the argument type n as part of which is equivalent to specifying polys NULL but requires a PolySet In both cases the function s behaviour changes slightly To resemble the plot function it plots the border labels and other parts according to par parameters such as col For additional help on the arguments border 1ty col density and angle please see polygon and par Value PolyData consisting of the PolyProps used to create the plot Note To satisfy the aspect ratio this plotting routine resizes the plot region Consequently par parameters such as plt mai and mar will change When the function terminates these changes persist to allow for additions to the plot See Also addLabels addPolys addStipples
119. nes show boundaries for the 60 Universal Transverse Mercator UTM zones with explicit labels for zones 1 to 9 A black line indicates the prime meridian x 0 Our PolySet nepacLL lies within the clipping boundary shown as a blue rectangle The Universal Transverse Mercator UTM projection gives a more realistic portrayal of the earth s surface within 60 standardized longitude zones Each zone spans 6 and zone i includes points with longitude x in the range 2 2 186 67 lt x lt 180 6i UTM zone i The mid longitude in 2 2 2 3 x 183 67 Central meridian zone i defines the central meridian of zone i In particular zone 9 has central meridian 129 and covers the range 2 3 132 lt x lt 126 UTM zone 9 Eo Canada s Pacific coast lies in zones 8 to 10 Figure 2 and the projection to zone 9 gives a reasonably accurate map for fisheries in this region Latitude O 11 T T T i T T T 180 160 140 120 Longitude Figure 2 Shoreline data in longitude latitude coordinates for the northeastern Pacific Ocean as captured in our PolySet nepacLL Vertical red lines display UTM boundaries for zones 60 1 2 11 A vertical dotted line indicates the central meridian of zone 6 near the centre of this figure Visually UTM zones look like sections of orange peel cut from top to bottom Each relatively narrow section can be
120. ng 92 PolyData 100 PolySet 101 Topic file importEvents 77 importGSHHS 77 importLocs 79 importPolys 80 importShapefile 80 Topic hplot plotLines 94 plotMap 95 plotPolys 99 Topic iplot locateEvents 84 locatePolys 85 Topic logic 113 joinPolys 83 Topic manip appendPolys 54 calcArea 56 calcCentroid 57 calcConvexHull 58 calcLength 58 calcMidRange 59 calcSummary 60 calcVoronoi 61 clipLines 62 clipPolys 63 closePolys 64 combineEvents 65 combinePolys 66 convCP 66 convDP 67 convLP 68 convUL 69 dividePolys 70 extractPolyData 72 findCells 73 findPolys 74 fixBound 75 fixPOS 76 isConvex 81 isIntersecting 82 joinPolys 83 makeGrid 87 makeProps 88 makeTopography 89 placeHoles 93 refocusWorld 104 thickenPolys 107 thinPolys 108 Topic methods summary 105 Topic sysdata PBSprint 92 addBubbles 47 addLabels 48 53 88 97 100 addLines 50 69 88 95 110 addPoints 49 51 54 58 61 68 85 88 98 107 114 addPolys 48 52 54 55 58 61 84 86 88 90 91 97 100 104 111 112 addStipples 53 53 88 97 100 appendPolys 54 69 84 86 arrows 50 as EventData EventData 71 as LocationSet LocationSet 86 as PolyData PolyData 100 as PolySet PolySet 101 bcBathymetry 55 90 9 calcArea 56 57 61 calcCentroid 49 56 57 58 61 calcConvexHull 58 6 calcLength 50 56 57 58 60 61 95 110 calcMidRange 49 56 59 5
121. nts polys PolySet to add required xlim range of X coordinates ylim range of Y coordinates polyProps PolyData specifying which polylines to plot and their properties par parameters passed as direct arguments supersede these data lty vector of line types cycled by PID col vector of colours cycled by PID arrows Boolean value if TRUE add arrows using the arrows function and consider the arguments angle length and code additional par parameters for the lines function Details The plotting routine does not connect the last vertex of each discrete polyline to the first vertex of that polyline It clips polys to xlim and ylim before plotting For additional help on the arguments 1ty and col please see par Value PolyData consisting of the PolyProps used to create the plot addPoints 51 See Also calcLength clipLines closePolys convLP fixBound fixPOS locatePolys plotLines thinPolys thickenPolys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create a PolySet to plot polys lt data frame PID rep 1 4 POS 1 4 X c 0 1 1 0 Y c 0 0 1 1 polys lt as PolySet polys projection 1 plot the PolySet plotLines polys xlim c 5 1 5 ylim c 5 1 5 projection 1 add the PolySet to the plot in a different style addLines polys lwd 5 col 3 par oldpar addPoints Add EventData PolyData to an Existing Plot as Points Description Add EventData PolyData to an e
122. o thicken tol tolerance in kilometres when proj is LL and UTM otherwise same units as polys filter minimum number of vertices per result polygon keepOrig Boolean value if TRUE keep the original points in the PolySet close Boolean value if TRUE create intermediate vertices between each polygon s last and first vertex if necessary Details This function thickens each polygon within polys according to the input arguments If keepOrig TRUE all of the original vertices appear in the result It calculates the distance between two sequential original vertices and if that distance exceeds tol it adds a sufficient number of vertices spaced evenly between the two original vertices so that the distance between vertices no longer exceeds tol If close TRUE it adds intermediate vertices between the last and first vertices when necessary If keepOrig FALSE only the first vertex of each polygon is guaranteed to appear in the results From this first vertex the algorithm walks the polygon summing the distance between vertices When this cumulative distance exceeds tol it adds a vertex on the line segment under inspection After doing so it resets the distance sum and walks the polygon from this new vertex If close TRUE it will walk the line segment from the last vertex to the first Value PolySet containing the thickened data The function recalculates the POS values for each polygon See Also thinPolys 108 thinPol
123. oint 3 5 between points 3 and 4 A PolySet can have a projection attribute which may be missing that specifies a map projection In the current version of PBS Mapping projection can have character values LL or UTM referring to Longitude Latitude and Universal Transverse Mercator We explain these projections more completely below If projection is numeric it specifies the aspect ratio r the number of x units per y unit Thus r units of x on the graph occupy the same distance as one unit of y Another optional attribute zone specifies the UTM zone if projection UTM or the preferred zone for conversion from Longitude Latitude if projection LL A data frame s class attribute by default contains the string data frame Inserting the string PolySet as the class vector s first element alters the behaviour of some functions For example the summary function will print details specific to a PolySet Also when PBSprint is TRUE the print function will display a PolySet s summary rather than the contents of the data frame Value The as PolySet method returns an object with classes PolySet and data frame in that order print 103 References Environmental Systems Research Institute ESRI 1996 ArcView GIS The Geographic Information System for Everyone ESRI Press Redlands California 340 pp See Also EventData LocationSet PolyData print Print PBS Mapping Objects Description This func
124. ologique du Pacifique SBP Bien que congu initialement pour Panalyse de donn es halieutiques notre logiciel peut s appliquer a toute une vari t de domaines La biblioth gue PBSmapping Cartographie de la SBP tend le langage R pour inclure une capacit d impression en deux dimensions semblable a celle habituellement disponible dans les syst mes d information g ographiques SIG Des modules en C permettent d acc l rer les algorithmes grace la g om trie num rique en trouvant par exemple les polygones qui contiennent des v nements ponctuels sp cifiques ou en convertissant les longitudes et les latitudes en coordonn es de la projection transversale universelle UTM Nous pr sentons galement un certain nombre d applications int ressantes pour les syst mes d exploitation Microsoft Windows qui peuvent effectuer des op rations de g om trie num rique en dehors du cadre de travail R Nos r sultats auxquels plusieurs tudiants ont grandement contribu illustrent la convergence des objectifs de la formation acad mique et de la recherche appliqu e iyv PREFACE During the last decade I ve had the pleasure of directing work by computer science students from various local universities My research as a mathematician in fish stock assessment requires an extensive software toolkit including statistical languages compilers and operating system utilities It helps greatly to have bright adaptive students
125. olySs lt 6 eet OSPR PAV CH ee hee wee BASE Hee be bee 107 thinPOlyS 4 246 ae See MRE ee Pe RS Ey RR Saeed Oe ER ROW HU Ee 108 addBubbles towData towTracks worldLL worldLLhigh Index addBubbles Description Add Bubbles to Maps Add bubbles proportional to some EventData s Z column e g catch or effort to an existing plot where each unique EID describes a bubble Usage addBubbles events type c perceptual surface mon volume z max NULL min size 0 max size 0 8 symbol zero symbol fg rgb 0 0 0 0 6 symbol bg rgb 0 0 0 0 3 legend pos bottomleft legend breaks NULL symbol zero symbol fg symbol bg legend pos legend breaks show actual legend type show actual FALSE legend type c nested horiz vert legend title Abundance legend cex 0 8 Arguments events EventData to use required type scaling option for bubbles where perceptual emphasizes large z values volume empha sizes small z values and surface lies in between z max maximum value for z default max events Z determines the largest bubble keeps the same legend for different maps min size minimum size inches for a bubble representing min events Z The legend may not actu ally include a bubble of this size because the calculated legend breaks does not include the min events Z max size maximum size inches for a bubble representing z max A legend
126. on If tckLab TRUE these tick marks will be automatically labelled If given a two element vector the first element describes the tick marks on the x axis and the second element describes those on the y axis tckMinor numeric vector length or 2 describing the length of tick marks as a fraction of the smallest dimension These tick marks can not be automatically labelled If given a two element vector the first element describes the tick marks on the x axis and the second element describes those on the y axis additional par parameters or the arguments main sub xlab or ylab for the title function Details This function plots a PolySet where each unique PID SID describes a polygon It connects each polygon s last vertex to its first The function supports both borders border 1ty and fills col density angle When supplied with the appropriate arguments it can draw only borders or only fills Unlike plotLines and plotPolys it uses the aspect ratio supplied in the projection attribute of polys If this attribute is missing it attempts to use its projection argument In the absence of both it uses a default aspect ratio of 1 1 It clips polys to xlim and ylim before plotting The function creates a blank plot when polys equals NULL In this case the user must supply both xlim and ylim arguments Alternatively it accepts the argument type n as part of which is equivalent to specifying polys NULL but requires
127. ontourLines alBathy levels isob alCP lt convCP alCL alPoly lt alCP PolySet attr alPoly projection lt LL plotMap alPoly type n addLines alPoly col icol data nepacLL envir PBSmapEnv addPolys nepacLL col gold legend x topleft bty n col icol lwd 2 legend as character isob par oldpar nepacLL Data Shoreline of the NE Pacific Ocean Normal Resolution Description PolySet of polygons for the northeast Pacific Ocean shoreline Usage data nepacLL Format Data frame consisting of 4 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinate and Y latitude coordinate Attributes projection LL Note In R the data must be loaded using the data function Source Polygon data from the GSHHS Global Self consistent Hierarchical High resolution Shoreline database gshhs_h b Download from http www soest hawaii edu wessel gshhs gshhs html nepacLL lt importGSHHS gshhs_h b xlimzc 190 110 ylim c 34 72 level 1 n 15 xoff 360 References Wessel P and Smith W H F 1996 A global self consistent hierarchical high resolution shoreline database Journal of Geophysical Research 101 8741 8743 http www soest hawaii edu pwessel pwessel_pubs html See Also Data nepacLLhigh worldLL wor1dLLhigh bcBathymetry importGSHHS addPolys clipPolys plotPolys plotMap thickenPolys thinPolys nepacLL high 91 ne
128. or using either language Although written originally for Unix R has also been implemented for Microsoft s Windows operating systems The web site http cran r project org describes R as GNU S a freely available language and environment for statistical computing and graphics The GNU project http www gnu org where the recursive acronym GNU means GNU s Not Unix offers a wealth of free software including compilers for C C Fortran and Pascal Code can be written in these compiled languages to speed computations that would otherwise run more slowly in R Nick Boers has used such linkages intelligently to bring fast computational geometry into our R package PBSmapping To some extent this report constitutes a second edition of an earlier report Schnute et al 2003 that describes a suite of software utilities developed at PBS In particular the package PBSmapping has undergone extensive renovations and improvements and this document provides a definitive manual for using version 2 To accommodate the new material presented here my co authors and I have decided to remove sections of the earlier report that discuss other PBS software utilities free software available on the Internet and related technical information Readers of this current report may also wish to acquire the earlier version for additional material not included here I want to mention two milestones achieved during the production of PBSmapping Version 2 F
129. orem Visualized PBSfigl0 lt function Pythagoras Theorem Visualized clr lt PBSclr data pythagoras envir sys frame sys nframe H create properties for colouring the polygons pythProps lt data frame PID c 1 6 13 4 15 3 5 2 14 Z c rep l 9 rep 2 2 rep 3 2 rep 4 2 pythProps lt makeProps pythProps c 0 1 1 2 1 3 1 4 1 col c clr Sblue clr red clr yellow clr green par mfrow c 1 1 omi c 0 0 0 0 Plot the figure plotMap pythagoras plt c 01 99 01 95 lwd 2 xlim c 09 1 91 ylim c 0 19 2 86 polyProps pythProps axes FALSE xlab ylab main Pythagoras Theorem a 262 b 262 c 262 text x 0 1 y 1 19 adj 0 Proof text x 0 1 y 1 10 adj 0 a b 262 4 triangles a 262 b 262 4 triangles c 262 labels lt data frame X c 1 02 1 66 0 65 Y c 1 50 2 20 2 76 label c a b c text labels X labels Y as character labels label cex 1 2 text 1 03 1 81 a 262 cex 1 2 col clrSblack text 1 43 2 21 b 262 cex 1 2 col clr black text 0 87 2 46 c 262 cex 1 2 col clr black Run command file PBSfigs r PBSfigs lt function nfigs 1 10 Draw all figures with numbers in nfigs while is null dev list dev off dev cur for i in nfigs figStr lt paste PBSfig ifelse i lt 10 0 1 sep get figStr cat figStr readline 40 Appendix E PBSmapping Function Depen
130. pacLLhigh Data Shoreline of the NE Pacific Ocean High Resolution Description PolySet of polygons for the northeast Pacific Ocean shoreline Usage data nepacLLhigh Format Data frame consisting of 4 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinate and Y latitude coordinate Attributes projection LL Note In R the data must be loaded using the data function Source Polygon data from the GSHHS Global Self consistent Hierarchical High resolution Shoreline database gshhs_f b Download from http www soest hawaii edu wessel gshhs gshhs html nepacLLhigh lt importGSHHS gshhs_f b xlim c 190 110 ylim c 34 72 level 1 n 0 xoff 360 nepacLLhigh lt thinPolys nepacLLhigh tol 0 1 filter 3 References Wessel P and Smith W H F 1996 A global self consistent hierarchical high resolution shoreline database Journal of Geophysical Research 101 8741 8743 http www soest hawaii edu pwessel pwessel_pubs html See Also Data nepacLL worldLL worldLLhigh bcBathymetry importGSHHS addPolys clipPolys plotPolys plotMap thickenPolys thinPolys 92 PBSprint PBSmapping PBS Mapping Draw Maps and Implement Other GIS Procedures Description This software has evolved from fisheries research conducted at the Pacific Biological Station PBS in Nanaimo British Columbia Canada It extends the R language to include two dimen
131. pper php developed by Angus Johnson Previously it interfaced with the General Polygon Clipper library http www cs man ac uk aig staff alan software by Alan Murta at the University of Manchester We keep this historic reference to GPC because joinPolys remains faithful to Murta s definition of a generic polygon which we describe below Murta 2004 defines a generic polygon or polygon set as zero or more disjoint boundaries of arbitrary configu ration He relates a boundary to a contour where each may be convex concave or self intersecting In a PolySet the polygons associated with each unique PID loosely correspond to a generic polygon as they can represent both inner and outer boundaries Our use of the term generic polygon includes the restrictions imposed by a PolySet For example the polygons for a given PID cannot be arranged arbitrarily If polysB is NULL this function sequentially applies the operation between the generic polygons in polysA For example suppose polysA contains three generic polygons A B C The function outputs the PolySet containing A op B op C If polysB is not NULL this function applies operation between each generic polygon in polysA and each one in polysB For example suppose polysA contains two generic polygons A B and polysB contains two generic polygons C D The function s output is the concatenation of A op C B op C A op D B op D with PIDs 1 to 4 respectively Generally there a
132. raphics functions in the PBSmapping software package Function Creates a Graph Plots as Polygons Sets Aspect Ratio by Default addLabels No a 5 addLines No No E addPoints No a addPolys No Yes 5 addStipples No plotLines Yes No No plotMap Yes Yes Yes plotPoints Yes No plotPolys Yes Yes No Our high level graphics functions accept a common set of arguments consistent with existing par parameters where possible These include 10 e xlimand ylim to specify horizontal and vertical coordinate ranges e projection to specify the projection used in drawing the map or graph e plt to define the plot region relative to the figure region e polyProps to support plotting properties for individual contours Section 2 1 lty cex col border density pch and angle to adjust properties of labels lines points and polygons where applicable axes to disable plotting axes tck to control major tick mark lengths tckMinor a counterpart of tck to set a different length for minor tick marks tckLab with Boolean values to determine whether to include numeric tick labels We introduce tckMinor and tckLab to give finer control over the appearance of tick marks Each of tck tckLab and tckMinor can have length one or two A single value pertains to both axes and two values specify distinct parameters for the horizontal and vertical axes respectively Our low level graphics functions e g addLines use many of the same arguments a
133. re n times m comparisons where n number of polygons in polysA and m number of polygons in polysB If polysB contains only one generic polygon the function maintains the PIDs from polysA It also maintains them when polysA contains only one generic polygon and the operation is difference Otherwise if polysA contains only one generic polygon it maintains the PIDs from polysB 84 locateEvents Value If polysB is NULL the resulting PolySet contains a single generic polygon one PID possibly with several com ponents SIDs The function recalculates the PID and SID columns If polysB is not NULL the resulting PolySet contains one or more generic polygons PIDs each with possibly sev eral components SIDs The function recalculates the SID column and depending on the input it may recalculate the PID column References Murta A 2004 A General Polygon Clipping Library Accessed July 29 2004 http www cs man ac uk aig staff alan software gpc html See Also addPolys appendPolys clipPolys closePolys fixBound fixPOS locatePolys plotMap plotPoints thickenPolys thinPolys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv create a triangle to use in clipping polysB lt data frame PID rep 1 3 POS 1 3 X c 127 5 124 5 125 6 Y c 49 2 50 3 48 6
134. reation of the indexed manual included after Table F1 Table F1 Functions and data sets in PBSmapping arranged alphabetically within categories Category Object Description User constant PBSprint Specify whether to print summaries Import importEvents Import a text file and convert into EventData functions importLocs Import a text file and convert into a LocationSet importPolys Import a text file and convert into a PolySet importGSHHS Import data from a GSHHS database importShapefile Import an ESRI shapefile Plotting addBubbles Add bubbles to maps functions addLabels Add labels to an existing plot addLines Add a PolySet to an existing plot as polylines addPoints Add EventData PolyData to an existing plot as points addPolys Add a PolySet to an existing plot as polygons addStipples Add stipples to an existing plot plotLines Plot a PolySet as polylines plotMap Plot a PolySet as a map plotPoints Plot EventData PolyData as points plotPolys Plot a PolySet as polygons Computational appendPolys Append a two column matrix to a PolySet functions calcArea Calculate the areas of polygons calcCentroid Calculate the centroids of polygons calcConvexHull Calculate the convex hull for a set of points calcLength Calculate the length of polylines calcMidRange Calculate midpoints of the X and Y ranges for polygons calcSummary Apply functions to polygons in a PolySet calcVoronoi Calculate Voronoi tesselation for a set of points clipLines Clip a PolySet as polyl
135. renumbers the PID and SID indices so that each outer contour has a unique PID and is followed by all of its holes identifying them with SIDs greater than one Value PolySet possibly with the addition of an SID column if it did not already exist The function may also reorder columns such that PID SID POS X and Y appear first in that order See Also combinePolys EventData EventData Objects Description PBS Mapping functions that expect EventData will accept properly formatted data frames in their place see Details as EventData attempts to coerce a data frame to an object with class EventData is EventData returns TRUE if its argument is of class EventData Usage as EventData x projection NULL zone NULL is EventData x fullValidation TRUE Arguments X data frame to be coerced or tested projection optional projection attribute to add to EventData possibly overwriting an existing attribute zone optional zone attribute to add to EventData possibly overwriting an existing attribute fullValidation Boolean value if TRUE fully test x 72 extractPolyData Details We define EventData as a data frame with at least three fields named EID X Y Conceptually an EventData object describes events that take place at specific points X Y in two dimensional space Additional fields specify measurements associated with these events For example in a fishery context EventData could describe fishing even
136. ribute plt four element numeric vector x1 x2 yl y2 giving the coordinates of the plot region measured as a fraction of the figure region Set to NULL if mai in par is desired 96 plotMap polyProps PolyData specifying which polygons to plot and their properties par parameters passed as direct arguments supersede these data border vector describing edge colours cycled by PID lty vector describing line types cycled by PID col vector describing fill colours cycled by PID colHoles vector describing hole colours cycled by PID The default NULL should be used in most cases as it renders holes transparent colHoles is designed solely to eliminate retrace lines when images are converted to PDF format If colHoles is specified underlying information i e previously plotted shapes will be obliterated If NA is specified only outer polygons are drawn consequently filling holes density vector describing shading line densities lines per inch cycled by PID angle vector describing shading line angles degrees cycled by PID bg background colour of the plot axes Boolean value if TRUE plot axes tckLab Boolean vector length 1 or 2 if TRUE label the major tick marks If given a two element vector the first element describes the tick marks on the x axis and the second element describes those on the y axis tck numeric vector length 1 or 2 describing the length of tick marks as a fraction of the smallest dimensi
137. rmine the central zone when converting from geographic to UTM coordinates After the conversion this routine adjusts the data frame s attributes accordingly Value A data frame identical to xydata except that the X and Y columns contain the results of the conversion and the projection attribute matches the new projection Author s Nicholas Boers Dept of Computer Science Grant MacEwan University Edmonton AB References Ordnance Survey 2010 A guide to coordinate systems in Great Britain Report D00659 v2 1 Southampton UK http www ordnancesurvey co uk oswebsite gps docs A_Guide_to_Coordinate_Systems_in_Great_Britain pdf See Also closePolys fixBound Examples local envir PBSmapEnv expr oldpar par no readonly TRUE load the data data nepacLL envir PBSmapEnv set the zone attribute use a zone that is most central to the mapped region attr nepacLL zone lt 6 convert and plot the result nepacUTM lt convUL nepacLL plotMap nepacUTM par oldpar dividePolys Divide a Single Polygon into Several Polygons Description Divide a single polygon with several outer contour components into several polygons a polygon for each outer contour by modifying the PID and SID indices EventData 71 Usage dividePolys polys Arguments polys PolySet with one or more polygons each with possibly several components holes Details Given the input PolySet this function
138. s their high level counterparts e g plotLines However they do not accept parameters that affect the overall plot such as xlim ylim projection plt axes or any of the tck arguments The par parameter p1t plays a special role in PBSmapping because we use it to set the aspect ratio required for a particular projection Recall that in R the plot region lies inside the figure region which similarly lies inside the overall device region The parameter p1t specifies the plot region boundaries as fractions left right bottom top of the current figure region Our high level plotting functions use the initial default value plt c 0 11 0 98 0 12 0 88 but then alter p1t by shrinking the width or height to achieve the required aspect ratio In the function call the argument p1t can set a different default value but again this may be changed by the graphics function to set the aspect ratio In effect the argument p1t sets minimum margins for the plot within the figure region but the aspect ratio may force the plot to shrink in width or height giving wider margins in one direction Standard high level commands in R like plot do not allow layout parameters like p1t to be passed as arguments Instead users normally use par to set these parameters before invoking a graphics command However unlike normal graphics commands those in PBSmapping actually alter the margins so we adopt a different approach in which p1t is reset with each high
139. sWorld Refocus the worldLL worldLLhigh Data Sets Description Refocus the worldLL worldLLhigh data sets e g refocus them so that Eastern Canada appears to the west of Western Europe Usage refocusWorld polys xlim NULL ylim NULL Arguments polys PolySet with one or more polygons typically worldLL or wor1dLLhi gh required xlim range of X coordinates ylim range of Y coordinates Details This function accepts a PolySet containing one or more polygons with X coordinates that collectively span ap proximately 360 degrees The function effectively joins the PolySet into a cylinder and then splits it at an arbitrary longitude according to the user specified limits Modifications in the resulting PolySet are restricted to shifting X coordinates by multiples of 360 degrees and instead of clipping polygons the return value simply omits out of range polygons summary Value PolySet likely a subset of the input PolySet which retains the same PID SID values Author s Nicholas Boers Dept of Computer Science Grant MacEwan University Edmonton AB See Also joinPolys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE load appropriate data data worldLL envir PBSmapEnv set limits xlim lt c 100 25 ylim lt c 0 90 refocus and plot the world polys lt refocusWorld worldLL xlim ylim plotMap polys xlim ylim par oldpar summary Description
140. sent inner boundaries that define holes in the region Each contour can be convex concave or self intersecting In our PolySet the polygons associated with each unique PID correspond to a generic polygon with some restrictions Some of our functions do not support self intersecting polygons Furthermore the SID contours cannot be arranged in arbitrary order because we require that hole contours follow the outer contours in which they lie The function joinPolys can also accept two PolySet arguments P and O In this case the function returns a PolySet with all possible pairwise applications of op between generic polygons in P and O For example if P contains 4 B C and O contains D E then joinPolys returns a PolySet with six PIDs corresponding to the six generic polygons A op D B op D C op D A op E B op E and C op E More generally if P and O include m and n generic polygons respectively then the function returns a PolySet with mxn generic polygons If m 1 or n 1 the output preserves PIDs from the PolySet with more than one generic polygon Figure 5 illustrates the four supported set theoretic operations applied to crescent shaped polygons A and B Applied to one PolySet P our function joinPolys applies the set theoretic operation op sequentially to the generic polygons in P For example suppose that P contains three generic polygons A B C Then the function returns a PolySet containing the generic polygon A op B op C
141. sional plotting features similar to those commonly available in a Geographic Information System GIS Embedded C code speeds algorithms from com putational geometry such as finding polygons that contain specified point events or converting between longitude latitude and Universal Transverse Mercator UTM coordinates It includes data for a global shoreline and other data sets in the public domain For a complete user s guide see the file PBSmapping UG pdf in the R directory library PBSmapping doc PBSmapping includes 10 demos that appear as figures in the User s Guide To see them run the function PBSfigs More generally a user can view all demos available from locally installed packages with the function runDemos gt in our related and recommended package PBSmodelling PBSprint Specify Whether to Print Summaries Description Specify whether PBS Mapping should print object summaries or not If not data objects are displayed as normal Usage PBSprint Details If PBSprint TRUE the mapping software will print summaries rather than the data frames for EventData LocationSet PolyData and PolySet objects If PBSprint FALSE it will print the data frames This variable s default value is FALSE Value TRUE or FALSE depending on the user s preference See Also summary placeHoles 93 placeHoles Place Holes Under Correct Solids Description Place secondary polygons SIDs identified as holes count
142. such as col For additional help on the arguments 1ty and col please see par Value PolyData consisting of the PolyProps used to create the plot Note To satisfy the aspect ratio this plotting routine resizes the plot region Consequently par parameters such as plt mai and mar will change When the function terminates these changes persist to allow for additions to the plot See Also addLines calcLength clipLines closePolys convLP fixBound fixPOS locatePolys thinPolys thickenPolys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE create a PolySet to plot polys lt data frame PID rep 1 4 POS 1 4 X c 0 1 1 0 Y c 0 0 1 1 plot the PolySet plotLines polys xlim c 5 1 5 ylim c 5 1 5 par oldpar plotMap Plot a PolySet as a Map Description Plot a PolySet as a map using the correct aspect ratio Usage plotMap polys xlim NULL ylim NULL projection TRUE plt c 0 11 0 98 0 12 0 88 polyProps NULL border NULL lty NULL col NULL colHoles NULL density NA angle NULL bg 0 axes TRUE tckLab TRUE tck 0 014 tckMinor 0 5 tck Arguments polys PolySet to plot required xlim range of X coordinates ylim range of Y coordinates projection desired projection when PolySet lacks a projection attribute one of LL UTM or a nu meric value If Boolean specifies whether to check polys for a projection att
143. t data from a GSHHS database and convert data into a PolySet with a PolyData attribute Usage importGSHHS gshhsDB xlim ylim maxLevel 4 n 0 77 78 importGSHHS Arguments gshhsDB path name to binary GSHHS database If unspecified looks for gshhs_f b in the root of the PBSmapping library directory xlim range of X coordinates for clipping The range should be between 0 and 360 ylim range of Y coordinates for clipping maxLevel maximum level of polygons to import 1 land 2 lakes on land 3 islands in lakes or 4 ponds on islands ignored when importing lines n minimum number of vertices that must exist in a line polygon in order for it to be imported Details This routine reguires a binary GSHHS Global Self consistent Hierarchical High resolution Shoreline database file The GSHHS database has been released in the public domain and may be downloaded from http www soest hawaii edu pwessel gshhg At the time of writing the most recent databaseis gshhg bin 2 2 2 zip The database gshhg bin 2 2 2 zipcontains geographical coordinates for shorelines gshhs rivers wbd_rivers and borders wdb_borders The latter two come from World DataBank IT WDBII http meta wikimedia org wiki Geographical_datafCIA_World_DataBank_II_ and derivates The five resolutions available are full f high h intermediate i low 1 and coarse c This routine returns a PolySet object with an associated PolyData attribute The a
144. tes a line segment with each successive pair of points from to n giving a polyline in GIS terminology composed of the sequential segments The second includes a final line segment joining points n and 1 thus giving a polygon The secondary ID field allows us to define regions as composites of polygons From this point of view each primary ID identifies a collection of polygons distinguished by secondary IDs For example a single management area PID might consist of two fishing areas each defined by a unique SID A secondary polygon can also correspond to an inner boundary like the hole in a doughnut We adopt the convention that POS goes from 1 to n along an outer boundary but from n to 1 along an inner boundary regardless of rotational direction This contrasts with other GIS software such as Arc View ESRI 1996 in which outer and inner boundaries correspond to clockwise and counter clockwise directions respectively The SID field in a PolySet with secondary IDs must have integer values that appear in ascending order for a given PID Furthermore inner boundaries must follow the outer boundary that encloses them The POS field for each contour PID SID must similarly appear as integers in strictly increasing or decreasing order for outer and inner boundaries respectively If the POS field erroneously contains floating point numbers FixPOS can renumber them as sequential integers thus simplifying the insertion of a new point such as p
145. textbook Foley et al 1996 proved invaluable for writing software to produce maps of the British Columbia coast with related fishery information Quantitative fishery science requires a strong connection between theory and practice In his book on computing theory Michael Sipser 1997 p xii tells students that theory is good for you because studying it expands your mind Computer technology changes guickly Specific technical knowledge though useful today becomes outdated in just a few years Consider instead the abilities to think to express yourself clearly and precisely to solve problems and to Know when you haven t solved a problem These abilities have lasting value Studying theory trains you in these areas While dealing with the issues addressed here I found myself asking simple guestions that have numerically interesting answers How do you locate fishing events within management areas or other polygons How should regional boundaries on maps be clipped to lie within a smaller rectangle I soon realised that I had touched upon the emerging field of computational geometry where people have devised clever and efficient algorithms for addressing such guestions Remarkably effective software can now be obtained freely from the Internet I m particularly fond of R a version of the powerful statistical language S and later S PLUS devised by Becker et al 1988 Venables and Ripley 1999 2000 give excellent guidance f
146. th m and year year of survey trip Attributes projection LL zone 9 Note In R the data must be loaded using the data function Source The GFBio database maintained at the Pacific Biological Station Fisheries and Oceans Canada Nanaimo BC V9T 6N7 archives catches and related biological data from commercial groundfish fishing trips and re search assessment cruises off the west coast of British Columbia BC The POP Sebastes alutus survey data were extracted from GFBio The data extraction covers bottom trawl surveys that focus primarily on POP biomass estimation 1966 89 for the central BC coast and 1970 85 for the west coast of Vancouver Island Additionally a 1989 cruise along the entire BC coast concentrated on the collection of biological samples Schnute et al 2001 provide a more comprehensive history of POP surveys including the subset of data presented here References Schnute J T Haigh R Krishka B A and Starr P 2001 Pacific ocean perch assessment for the west coast of Canada in 2001 Canadian Science Advisory Secretariat Research Document 2001 138 90 pp thickenPolys 107 See Also addPoints combineEvents EventData findPolys makeGrid plotPoints thickenPolys Thicken a PolySet of Polygons Description Thicken a PolySet where each unique PID SID describes a polygon Usage thickenPolys polys tol 1 filter 3 keepOrig TRUE close TRUE Arguments polys PolySet t
147. then a geographic projection is assumed and projection LL If the first 4 characters are PROJ and UTM occurs elsewhere in the string then the Universal Transverse Mercator projection is assumed and projection UTM Otherwise projection 1 If an xml file exists this information is attached as an attribute Shapes of numeric shape type 5 exported from ArcView in geographic projection identify solids as polygons with vertices following a clockwise path and holes as polygons that follow a counter clockwise path Unfortuantely either the export from ArcView or the import using a C routine from the package maptools often does not report solids followed by their holes We employ a new R function placeHoles to do this for us Ideally this routine should be rendered in C but for now we use this function if the user sets the argument placeholes TRUE Depending on the size and complexity of your shapefile the computation may take a while Value For points EventData with columns EID X and Y possibly with other columns from the attribute database For polylines and polygons a PolySet with columns PID SID POS X Y and attribute projection Other attributes that may or may not be attached parent child boolean vector from original input shpType numeric shape type 1 3 or 5 prj projection information from prj file xml metadata from an xml file PolyData data from the attribute database dbf and zone UTM zone
148. ting plot where each unique PID SID describes a polygon Usage addPolys polys xlim NULL ylim NULL polyProps NULL Arguments polys xlim ylim polyProps border lty col colHoles density angle border NULL lty NULL col NULL colHoles NULL density NA angle NULL PolySet to add required range of X coordinates range of Y coordinates PolyData specifying which polygons to plot and their properties par parameters passed as direct arguments supersede these data vector describing edge colours cycled by PID vector describing line types cycled by PID vector describing fill colours cycled by PID vector describing hole colours cycled by PID The default NULL should be used in most cases as it renders holes transparent colHoles is designed solely to eliminate retrace lines when images are converted to PDF format If colHoles is specified underlying information i e previously plotted shapes will be obliterated If NA is specified only outer polygons are drawn consequently filling holes vector describing shading line densities lines per inch cycled by PID vector describing shading line angles degrees cycled by PID additional par parameters for the polygon function addStipples 53 Details The plotting routine connects the last vertex of each discrete polygon to the first vertex of that polygon It supports both borders border 1ty and fills col density ang
149. tion displays information about a PBS Mapping object summary EventData summary LocationSet summary PolyData and summary PolySet produce an object with class summary PBS Usage S3 method for class EventData print x S3 method for class LocationSet print x S3 method for class PolyData print x S3 method for class PolySet print x S3 method for class summary PBS print x Arguments x a PBS Mapping object of appropriate class additional arguments to print See Also EventData LocationSet PBSprint PolyData PolySet summary Examples local envir PBSmapEnv expr load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv change to summary printing style PBSprint lt TRUE print the PolySet print nepacLL 104 refocus World pythagoras Data Pythagoras Theorem Diagram PolySet Description PolySet of shapes to prove Pythagoras Theorem a b c Usage data pythagoras Format 4 column data frame PID primary polygon ID POS position of each vertex within a given polyline X X coordinate and Y Y coordinate Attributes projection 1 Note In R the data must be loaded using the data function Source An artificial construct to illustrate the proof of Pythagoras Theorem using trigonometry See Also addPolys plotPolys plotMap PolySet refocu
150. tms tol 25 close FALSE uutms lt convUL lutms H create label locations central meridians lems lt data frame EID 1 length diff utms 2 X utms 1 length utms 1 diff utms 2 Y rep 50 75 length diff utms 2 lcms lt as EventData lcms projection LL zone zone ucms lt convUL lcms nepacUTM lt nepacLL attr nepacUTM zone lt zone convert to correct zone nepacUTM lt convUL nepacUTM par mfrow c 1 1 omi c 0 0 0 0 Plot the figure plotMap nepacUTM col clr land bg clr sea tck 0 017 mgp c 1 9 0 7 0 cex 1 0 plt c 0 07 0 97 0 07 0 98 addLines uutms col clr red lines x c 500 500 y c 4100 7940 lty dot col clr black text ucms X ucms Y c 60 1 length utms 2 cex 1 3 col clr red box Figure 4 thinPolys on Vancouver Island PBSfig04 lt function thinPolys on Vancouver Island clr lt PBSclr data nepacLL envir sys frame sys nframe par mfrow c 1 2 omi c 0 0 0 0 H Plot the figure vi lt nepacLL nepacLL PID 33 xlim lt range vi X c 0 25 0 25 ylim lt range viSY c 0 25 0 25 plot left figure normal Vancouver Island plotMap vi xlim ylim col clr land bg clr sea tck 0 028 mgp c 1 9 0 7 0 cex 1 0 plt c 0 14 1 00 0 07 0 97 text x xlim 2 0 5 y ylim 2 0 3 A cex 1 6 plot right figure thinned Vancouver Island plotMap thinPolys vi tol 10 xlim ylim col clr land b
151. tow represented in the figure by colours corresponding to depth intervals black 500 800 m red 800 1200 m dark blue 1200 1600 m Vancouver Island 9 4 Latitude LTS Survey Tracks A 500 800 m t 800 1200 m 1200 1600 m ARA 285 420 Longitude Figure 7 Tracks for 45 tows performed during the 2001 longspine thornyhead Sebastolobus altivelis survey along the west coast of Vancouver Island Starr ef al 2002 Each tow track is colour coded by depth stratum Data PolySet towTracks and PolyData towData 19 Figure 8 illustrates the use of our software to calculate polygon areas using the function calcArea We examine a region along the south west British Columbia coast that includes a cluster of islands in the Strait of Georgia Shoreline data come from the PolySet nepacLLhigh Because area calculations do not make sense in the longitude latitude projection we convert the PolySet to UTM coordinates with comparable x and Y coordinates km and then clip to the desired region The calcArea function will also automatically convert PolySets with projection LL to UTM before calculation The figure shows areas for six selected islands highlighted in yellow Island centroids derived using calcCentroid give reference coordinates for printing island names and areas m Strait of Georgia 5420 UTM Northing km 5400 5410 5390 Vancouver Island
152. traces a full circle and the angles do not sum to zero We use the crossings test because it performs faster than angle summation Hains 1994 p 26 27 The latter requires large numbers of trigonometric function calls After finding the polygons that contain various events an analyst often wants to compute statistics associated with the events that occur inside each polygon For example in a fishery 14 context what is the total catch from all fishing events within each management region Our function combineEvents supports such calculations The function makeProps can then relate polygon properties such as colour used for plotting to these computed statistical values Set Theoretic Operations We include the function joinPolys to apply set theoretic operations difference intersection union and exclusive or to one or two PolySets Our joinPolys function interfaces with the Clipper library http www angusj com delphi clipper php developed by Angus Johnson Previously it interfaced with the General Polygon Clipper library http www cs man ac uk aig staff alan software by Alan Murta at the University of Manchester We keep this historic reference to GPC because joinPolys remains faithful to Murta s definition of a generic polygon which we describe below Murta 2004 defines a generic polygon or polygon set as zero or more disjoint polygonal contours that define boundaries of the polygon region Some contours can repre
153. ts associated with trawl tows based on the fields e EID fishing event tow identification number X Y fishing location Duration length of time for the tow Depth average depth of the tow Catch biomass captured Like PolyData EventData can have attributes projection and zone which may be absent Inserting the string EventData as the class attribute s first element alters the behaviour of some functions including print if PBSprint is TRUE and summary Value The as EventData method returns an object with classes EventData and data frame in that order See Also LocationSet PolyData PolySet extractPolyData Extract PolyData from a PolySet Description Extract PolyData from a PolySet Columns for the PolyData include those other than PID SID POS oldPOS X and Y Usage extractPolyData polys Arguments polys PolySet to use Details This function identifies the PolySet s extra columns and determines if those columns contain unigue values for each PID SID Where they do the PID SID will appear in the PolyData output with that unigue value Where they do not the extra column will contain NAs for that PID SID Value PolyData with columns PID SID and any extra columns See Also makeProps PolyData PolySet findCells 73 Examples local envir PBSmapEnv expr create a PolySet with an extra column polys lt data frame PID c rep 1 10 rep 2 10
154. ttribute contains four fields a PID b SID c Level and d Source Each record corresponds to a line polygon in the PolySet The Level indicates the line s polygon s level 1 land 2 lake 3 island 4 pond The Source identifies the data source 1 WVS 0 CIA WDBID Value A PolySet with a PolyData attribute Author s Nicholas Boers Dept of Computer Science Grant MacEwan University Edmonton AB See Also importEvents importLocs importPolys importShapefile Examples Not run pbsfun function ex 1 switch ex EXAMPLE 1 set some limits appropriate for a map of Canada limits lt list x c 216 0486 307 1274 y c 42 87209 77 35183 extract data from the GSHHS binary files you will need to download these files from http www soest hawaii edu pwessel gshhg and place them in an appropriate location polys lt importGSHHS gshhg bin 2 2 2 gshhs_l b xlim limits x limits y maxLevel 4 rivers lt importGSHHS gshhg bin 2 2 2 wdb_rivers_i b xlim limits x limits y borders lt importGSHHS gshhg bin 2 2 2 wdb_borders_i b xlim limits x limits y importLocs 79 create a PNG for the output png Canada png width 1600 height 1200 pointsize 24 plot the polygons river and then borders plotMap polys plt c 05 99 075 99 col moccasin bg skyblue addLines rivers col lightblue addLines borders col red gt
155. ute e calcConvexHull calculates the convex hull for a given set of points using the function chull in R s package grDevices e calcLength calculates polyline lengths using Pythagoras Theorem when the projection is UTM or 1 Thus the distance d between points x y and x y is d a y y The function also supports longitude latitude coordinates x y by calculating great circle distances between polygon vertices In this case the distance d between two points is Chamberlain 2001 d 2R arcsin fo 22 cos y cos y sin E where R 6371 3 km denotes the earth s mean radius Wikipedia 2004 e calcMidRange calculates midpoints of the x and Y ranges for each given polygon e calcSummary calculates summary statistics for a PolySet given a user defined function e calcVoronoi calculates the Voronoi Dirichlet tesselation for a set of points using the deldir function from the package deldir and creates a PolySet See Figure 8 of the PBSmodelling user s guide Schnute ef al 2006 for an example called CalcVor il e clipLines and clipPolys clips polylines and polygons within a specified rectangle possibly smaller than the bounding rectangle using the Sutherland Hodgman clipping algorithm Foley et al 1996 p 124 127 e closePolys adds corners from the bounding rectangle if needed to close polylines into polygons e combinePolys combines several polygons into a single polygon by modi
156. vents catch events effort 60 make a grid for the Queen Charlotte Sound grid lt makeGrid x seg 131 6 127 6 1 y seg 50 6 52 6 1 projection LL zone 9 locate EventData in grid locData lt findCells events grid events Z lt events cpue pdata lt combineEvents events locData FUN mean brks lt c 0 50 300 750 1500 25000 lbrks lt length brks cols lt c clr Slettuce clr moss clr irish clr forest clr black pdata lt makeProps pdata brks col cols par mfrow c 1 1 omi c 0 0 0 0 Plot the figure plotMap nepacLL col clr land bg clr sea xlim xl ylim yl tck 0 015 mgp c 2 5 0 cex 1 2 plt c 08 98 08 98 addPolys grid polyProps pdata for i in l nrow events plot one point at a time for clarity points events X i events Y il pch 16 cex 0 50 col clr white points events X il events Y i pch 1 cex 0 55 col clr black yrtxt lt paste min events year substring max events year 3 sep text x1 1 1 5 y1 2 1 paste POP Surveys yrtxt cex 1 2 adj 0 add a legend right justify the legend labels temp lt legend x x1 1 3 y y1 11 7 legend rep 5 text width strwidth 1500 25000 bty n fill cols text temp rectSleft tempSrect w temp text y pos 2 paste brks 1 lbrks 1 brks 2 lbrks sep text temp rect left temp rect w 2 temp rect top pos 3 CPUE kg h cex 1 39 Figure 10 Pythagoras The
157. work developed from experiences constructing databases that capture information from Canada s Pacific groundfish fisheries Fishing events take place across a broad range of coastal waters and result in the capture of many species Initially we focused on issues related to database design and development as described in previous reports by Schnute et al 1996 Haigh and Schnute 1999 Rutherford 1999 Schnute et al 2001 Section 2 and Appendix A and Sinclair and Olsen 2002 Analyses of these databases shifted our attention to the problem of portraying and understanding such complex information Maps with statistical information proved especially useful and we found ourselves facing questions commonly addressed by Geographic Information Systems GIS Commercial GIS packages can be expensive with an additional requirement for specialized training Because analysts who deal with Pacific groundfish data often have experience using the statistical languages R http cran r project org available for free or S PLUS http en wikipedia org wiki S PLUS available commercially we began by writing bilingual functions for these languages to produce the maps required Schnute et al 2003 describe the package PBSmapping Version 1 which evolved from these early experiences After another year of development we extensively revised the software and Schnute et al 2004 presented a user s manual for PBSmapping Version 2 Subsequently we hav
158. xisting plot where each unigue EID describes a point Usage addPoints data xlim NULL ylim NULL polyProps NULL cex NULL col NULL pch NULL Arguments data EventData or PolyData to add reguired xlim range of X coordinates ylim range of Y coordinates polyProps PolyData specifying which points to plot and their properties par parameters passed as direct arguments supersede these data cex vector describing character expansion factors cycled by EID or PID col vector describing colours cycled by EID or PID pch vector describing plotting characters cycled by EID or PID additional par parameters for the points function Details This function clips data to xlim and ylim before plotting It only adds PolyData containing X and Y columns For additional help on the arguments cex col and pch please see par Value PolyData consisting of the PolyProps used to create the plot 52 See Also addPolys combineEvents convDP findPolys locateEvents plotPoints Examples local envir PBSmapEnv expr oldpar par no readonly TRUE load the data if using R if is null version language 88 version language R data nepacLL surveyData envir PBSmapEnv plot a map plotMap nepacLL xlim c 136 125 ylim c 48 57 add events addPoints surveyData col 1 7 par oldpar addPolys Add a PolySet to an Existing Plot as Polygons Description Add a PolySet to an exis
159. ySet rollupPolys calcDist createIDs calcMidRange validatePolySet calcSummary is PolyData calcSummary createIDs rollupPolys validatePolySet is PolyData calcVoronoi checkRDeps validateXYData deldir deldir addCorners expandEdges clipLines clip validatePolySet is PolySet clipPolys clip validatePolySet is PolySet closePolys validatePolySet closePolys C is PolySet combineEvents validateEventData is PolyData combinePolys validatePolySet createIDs convCP is PolyData convDP validatePolyData is PolySet convLP validatePolySet is PolySet convUL validateXYData convUL C dividePolys validatePolySet createIDs extractPolyData createIDs validatePolySet is PolyData findCells validateEventData validatePolySet findCells C is LocationSet findPolys validateEventData validatePolySet findPolys C is LocationSet fixBound validatePolySet is PolySet ixPOS rollupPolys validatePolySet is PolySet importEvents as EventData importGSHHS checkClipLimits importGSHHS C importLocs as LocationSet importPolys as PolySet as PolyData importShapefile checkRDeps getBasename maptools Rshapeget C calcOrientation foreign read dbf is EventData validateEventData is LocationSet validateLocationSet is PolyData validatePolyData is PolySet validatePolySet AD isConvex validat
160. ys Examples local envir PBSmapEnv expr oldpar par no readonly TRUE load the data if using R if is null version language 88 version language R data nepacLL envir PBSmapEnv plot Vancouver Island plotMap nepacLL nepacLL PID 33 calculate a thickened version using a 30 kilometres tolerance without keeping the original points p lt thickenPolys nepacLL nepacLL PID 33 tol 30 keepOrig FALSE convert the PolySet to EventData by dropping the PID column and renaming POS to EID p lt pl 1 names p 1 lt EID convert the now invalid PolySet into a data frame and then into EventData p lt as EventData as data frame p projection LL plot the results addPoints p col 2 pch 19 par oldpar thinPolys Thin a PolySet of Polygons Description Thin a PolySet where each unigue PID SID describes a polygon Usage thinPolys polys tol 1 filter 3 Arguments polys PolySet to thin tol tolerance in kilometres when proj is LL and UTM otherwise same units as polys filter minimum number of vertices per result polygon Details This function executes the Douglas Peuker line simplification algorithm on each polygon within polys Value PolySet containing the thinned data The function recalculates the POS values for each polygon See Also thickenPolys towData 109 Examples local envir PBSmapEnv expr

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