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PBS Mapping 2: user's guide

1. 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 density NA angle NULL bg 6el 9 bg 0 main Map xkab NULE 249 tckMinor 0 5 plotPolys polys xlim NULL ylim NULL axes TRUE tckLab TRUE tck 0 014 projection FALSE plt c 0 11 0 98 0 12 0 88 polyProps NULL border NULL lty NULL col NULL density NA angle NULL bg el 0 bg 0 main Map ylab NULL tckMinor 0 5 CCR ce In addition to the above argument changes plotMap p Ww Ww x a b NUT I r r axes TRUE tckLab TRUE tck 0 014 otPolys plotLines addPolys and addLines now invisibly return the polyProps object used for plotting rather than NULL The high level functions plotMap plotPol accept the same par parameters in their argument as plot Lys and plotLines now All functions that return PBS Mapping objects i e EventData LocationSet PolyData or PolySet objects set their class attributes appropriately We introduce the new data set bcBathymet ry in PBS Mapping version 2 00 It contains ocean bathymetry as raster data where depths are positive and it has a list structure suitably formatted for the contour and contourLines functions Appendix C Finally PBS Mapping version 2 00 includes numerous bu improvements g fixes and othe
2. 9 ol zA gt t LTS Survey Tracks J 00 800 m L 800 1200 m r 1200 1600 m N 275 127 1265 126 Longitude Figure 7 Tracks for 45 tows performed during the 2001 longspine thornyhead Sebastolobus altivelis survey along the west coast of Vancouver Island Starr et al 2002 Each tow track is colour coded by depth stratum Data come from the PolySet towTracks and PolyData towData Figure 8 illustrates the use of our software to calculate polygon areas 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 figure shows _18 areas for six selected islands highlighted in yellow based on the calcArea function Island centroids derived using calcCentroid give reference coordinates for printing island names and areas 5 Strait of Georgia UTM Northing km 5400 5410 5420 L 1 L 5390 Vancouver Island 5380 1 900 910 920 930 940 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
3. calcConvexHull calcDist createlDs rollupPolys validatePolySet validateXYData calcConvexHull C is PolyData is PolySet calcMidRange validatePolySet calcSummary is PolyData calcSummary createIDs rollupPolys validatePolySet is PolyData clipLines 2CLTR validatePolySet is PolySet clipPolys CTP validatePolySet is PolySet closePolys validatePolySet closePolys C is PolySet combineEvents validateEventData is PolyData contourLines findPolys fixBound convCP is PolyDat is PolySet ct ct convDP validatePolyData is PolySet convLP validatePolySet is PolySet convUL validateXYData convUL C extractPolyData createlDs validatePolySet is PolyData validateEventData validatePolySet findPolys C is LocationSet validatePolySet is PolySet fixPOS rollupPolys validatePolySet is PolySet is EventData validateEventData is LocationSet validateLocationSet is PolyData is PolySet validatePolyData validatePolySet isConvex validatePolySet is PolyData isConvex C isIntersecting validatePolySet is PolyData isIntersecting C joinPolys validatePolySet is PolySet joinPolys C locateEvent
4. nepacLL actually contains no convex polygons print p p convex isIntersecting Determine Whether Polygons are Self Intersecting Description Determines 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 Details When numericResult TRUE this function counts intersections as the algorithm pro cesses 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 unique PID SID regardless of whether a contour represents a hole Value PolyData with columns PID SID may be missing and intersecting If numericResult is TRUE intersecting contains the number of intersections Otherwise it contains a Boolean value See Also isConvex PolySet 78 Examples load the data if using R if is null version language amp amp version language R data nepacLL calculate then print the polygons that are self intersecting p lt isIntersecting nepacLL numericResult FALSE print p p intersecting joinPolys Join One or Two PolySets using a Logic Operation Description Joins one or two PolySets using a logic operation Usage joinPolys polys
5. 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 egual 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 create sample data for the contourLines function x lt seg 0 5 0 8 length 50 y lt Xx 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 convDP Convert EventData PolyData into a PolySet Description Converts EventData PolyData into a PolySet 68 Usage convDP data xColumns yColumns Arguments data PolyData or EventData xColumns vector of X column names yColumns vector of Y column names Details This function expects data to contain several X and Y columns For example con sider data with columns x1 y1 x2 and y2 Suppose xColumns c x1 x2 and yColumns c yi y2 The result will contain nrow data polygons Each one wil
6. c 1 1 ylim lt c 0 radius 1 2 c 2 1 width lt ifelse isR 5 6 5 polyA lt list for i in l length radius polyA i lt as PolySet data frame PID rep 1 pts POS l 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 l c X Y radius i centre B within A polyA 2 c X Y lt polyA 2 c X Y radius l radius 2 f shift B right polyA 2 1 X lt polyA 2 X size f create polysA and polysB polyA lt as PolySet joinPolys polyA 1 polyA 2 operation DIFF proj l polyB lt polyA polyB X lt abs polyB X radius 1 2 shiftB landscape adjust outer margin to ensure panels are not separated by a gap parOmi lt vector parOmi c 1 3 lt round par din 2 width 3 diff ylim 2 diff xlim 2 2 parOmi c 2 4 lt round par din 1 width 2 2 par mfrow c 3 2 mai c 0 0 0 0 omi parOmi Plot the figur lab lt list lab text lt c Polygon A Polygon B A INT B A UNION B A DIFF BY A NFXORNT B labScex lt rep cex 6 lab x lt rep mean xlim 6 lab y lt rep 0 8 6 f panel A polyA plotMap polyA xlim xlim ylim ylim xlab ylab axes F col clr red plt NULL 37 text lab text 1 x lab x 1 y labSy 1 cex lab cex 1 text xlim 1l off ylim 2 off A cex 1 6 box panel B polyB p
7. outside the identified localities Another code 0 denotes an unknown locality rather than 9 Simplified majors cover the BC coast so do minors but localities do not References Schnute J T R Haigh B A Krishka and P Starr 2001 Pacific ocean perch assessment for the west coast of Canada in 2001 Canadian Science Advisory Secretariat Research Document 2001 138 90 p Tagart J V 1991 Population dynamics of yellowtail rockfish Sebastes flavidus stocks in the northern California to southwest Vancouver Island region Ph D thesis University of Washington 323 p 114 See Also major minor and pfma ltea Longspine Thornyhead Exploratory Management Areas Description PolySet of polygons describing management areas for longspine thornyheads during the 2000 and 2001 fishing years Apr Mar Format Data frame consisting of 4 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinates and Y latitude coordinates Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting the two longspine thornyhead management regions during fishing years 2000 and 2001 Schnute et al 2004 Fishing years start April 1 and end March 31 The division between the traditional west coast of Vancouver Island fishery and the no
8. Examples 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 O 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 addPoints Add EventData PolyData to an Existing Plot as Points Description Adds EventData PolyData to an existing 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 required xlim range of X coordinates ylim range of Y coordinates polyProps PolyData specifying which points to plot and their properties par param eters 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 con taining 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 See Also 50 combineEvents convDP findPolys locat
9. In the S PLUS version of PBS Mapping we provide a contourLines function to mimic the native R contourLines function however our software does not solve the S PLUS problem of several polylines for a continuous contour In both R and S PLUS 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 PBS Data package includes a data set i sobaths of bathymetric contours for Canada s Pacific coast In addition several functions ease the manual procedure of converting polylines into polygons including convLP to convert two polylines into a single polygon 17 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 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 1 Da T MS IN 9dJ gt o 2 YN z oO OO N x N
10. TRUE plt c 0 11 0 98 0 12 0 88 polyProps NULL border NULL lty NULL col NULL density NA angle NULL bg 0 axes TRUE tckLab TRUE tck 0 014 tckMinor 0 5 tck PolySet to plot required range of X coordinates range of Y coordinates n desired projection when PolySet lacks a projection attribute one of LL UTM or a numeric value If Boolean specifies whether to check polys for a projection attribute four element numeric vector x1 x2 y1 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 polygons to plot and their properties par pa rameters 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 shading line densities lines per inch cycled by PID vector describing shading line angles degrees cycled by PID background colour of the plot Boolean value if TRUE plot axes 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 92 tck numeric vector length 1 or 2 describing the length of tick marks as a fraction of the smallest dimension If tckLab TRU
11. Arguments polys PolySet to close Details 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 end ing 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 64 Examples 4 corners 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 1 2 3 0 1 2 3 Y c 1 0 0 1 2 3 3 2 plotPolys closePolys polys col 2 2 corners and 1 opposite polys lt data frame PID c 1 1 2 2 3 3 3 POS c 1 2 1 2 1 2 3
12. Introductionn esee e et a E ss tn FAI I Y sn 1 ALSO Le Ware Installations iesen e a CC FU Ne S 2 2 PBS Mapping 2 Functions and DAS ne te ne t 3 2 LE Date Structures fot MAPS ac tis chen ceca tetat e u t e Fydd DUO 3 Polysetae Gu GU WU GYG A R E RA ag naan nent ste 3 POP A A A EE E T 4 Eyentl at ae ee ns heater le nu ae eect a teen A cite en a 5 Location sel ae eC Gyd GO ae ela FED GL FL UF Qiao 5 2 2 Map Projections sen ieis aera e e iee En RE nn re 5 2 3 PBS Mapping Functions and Algorithms sseesseeseesesesessessrssresresstseresressessrerresseesresressresee 8 Grapes Pie oni an GY GN GY Y O een 8 Computational Functions sin ee a ne ne ets e eves GU de 10 Associating Points with Polygons ses 12 Set Lnheorcne Operations a RC GG A R 13 ZS MOTE ne DAU EE a ido ect ue ti 14 2 5 Bathymetry Datsun nn anni AGY TN GROG ini ad Fo 15 2 0 Examples and Applications sisinio asins ae er aa a Er yd DF 17 2 7 Strengths Limitations and AIernatty Sess eidd ances NC 20 3 Command line Utiliti amp S s used ee Reed ddu gg ns EL NU GELLID Manet ieee 21 er o ce CID olyg ns es Y Re A ic A en NN ee 21 3 2 convUL exe Convert between UTM and LL o Au ie 22 Jor findPolkys sexe Pomts in POlVEONS sau ns CO O COC 22 3 4 gshhs2r p1 Convert GSHHS Data to PBS Mapping Format 23 INI SORAA a E EE E O Re E ten ee een ees 23 IR Clerc noe inorse a CU Ne sn Ed nt ne 24 Appendix Distribution CD eie GW FRY
13. See Also combineEvents locateEvents locatePolys LocationSet makeGrid TA Examples 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 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 boundary If tol has two elements the first specifies the 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
14. 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 D T Sandwell Global seafloor topography from satellite altimetry and ship depth soundings Science v 277 p 1957 1962 26 Sept 1997 http topex ucsd edu WWW_html mar_topo html See Also contour contourLines convCP nepacLL nepacLLhigh 55 calcArea Calculate the Areas of Polygons Description Calculates 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 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 i
15. X c 0 1 0 1 5 6 1 5 Y c t 0 2 3 0 1 5 3 plotPolys closePolys polys col 2 combineEvents Combine Measurements of Events Description Combines 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 bdry0K Boolean value if TRUE include boundary points Details This function combines measurements associated with events that occur in the same poly gon 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 65 See Also findPolys locateEvents locatePolys makeGrid makeProps Examples create an EventData data frame let each event have Z 1 events lt data frame EID 1 10 X 1 10 Y 1 10 Z rep 1 10 example output from findPolys where 1 event occurred in the first f polygon 3 in the second and 6 in the third locs lt data frame EID 1 10 PID c r
16. axis of zone 6 vertical dotted line at x 500 km corresponds to the central meridian shown in Figure 2 2 3 PBS Mapping Functions and Algorithms Our software produces maps from the data structures defined in Section 2 1 Following typical design concepts in R S it uses functions to generate plots implement algorithms and perform other tasks Where possible function arguments often have explicit default values PBS Mapping includes many functions not mentioned in this section We encourage readers to examine Appendix H which gives detailed technical descriptions of all our software s functions and other components Table H1 provides a concise summary for easy reference Graphics Functions In the R S 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 pl
17. 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 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 locateEvents Locate Events on the Current Plot Description Locates events on the current plot using the locator function 80 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 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 EID m 1 n The na omit function can remove rows with NAs Value EventData with columns EID X and Y and projection attribute egual to the map s projection The function does no
18. pch and angle to adjust properties of labels lines points and polygons where applicable e axes to disable plotting axes e tck to control major tick mark lengths e tckMinor a counterpart of tck to set a different length for minor tick marks e 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 _10 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 as their high level counterparts e g plot Lines However they do not accept parameters that affect the overall plot such as x1im ylim projection plt axes or any of the tck arguments The par parameter p1t plays a special role in PBS Mapping because we use it to set the aspect ratio required for a particular projection Recall that in R S the plot region lies inside the figure region which similarly lies inside the overall device region The parameter plt 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
19. tain unique values for each PID SID Where they do the PID SID will appear in the PolyData output with that unique 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 73 Examples create a PolySet with an extra column polys lt data frame PID c rep 1 10 rep 2 10 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 findPolys Find the Polygons that Contain Events Description Find the polygons in a PolySet that contain events specified in EventData Usage findPolys 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 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 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
20. 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 S 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 S functions Lines and polygon column names can specify graphical properties e ity 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 lt y and col have meaning EventData We define EventData as a data frame with at least three f
21. x lt 360 to produce a convenient cut in the eastern Atlantic Ocean Red vertical lines 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 6i lt x lt 180 6i UTM zone i The mid longitude in 2 2 2 3 x 183 6i 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 gt l lt x lt 126 UTM zone 9 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 40 T T T T T T T 180 160 140 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
22. 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 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 quickly 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
23. 262 add labels 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 clr black text 1 43 2 21 b 262 cex l 2 col clr black text 0 87 2 46 c 262 cex 1 2 col clr black Run command file PBSfigs r while is null dev list dev off dev cur initPBS for a im e l 10 get paste PBSfig ifelse i lt 10 0 i sep O 40 APPENDIX F Changes in PBS Mapping v 2 00 PBS Mapping version 2 00 incorporates many improvements over the previous version 1 00 described by Schnute et al 2003 We have updated functions in all three distinct layers user accessible R S functions hidden R S functions and C functions This appendix documents only the changes to user accessible R S functions These include 38 new functions Table F1 where some of them relate directly to the introduction of class attributes Appendix H gives detailed documentation for all functions and data in version 2 Table F1 New user accessible functions in PBS Mapping v 2 00 Function Description addLabels Add labels to an existing plot addPoints Add EventData PolyData to an existing plot as points addStipples Add st
24. 366 p 27 APPENDIX A Distribution CD This appendix lists the contents of the distribution CD Its directory structure reflects the contents of this report with folders for the PBS Mapping package the PBS Data package command line utilities and related software We also provide links to web sites for downloading free software and for archival purposes we include the version of R used in making the current version of PBS Mapping Each directory on the CD contains a file named 00ReadMe txt that describes the directory s contents Table A1 Directories on the distribution CD with brief descriptions of their contents Path Description PBSmapping PBS Mapping software R PBS Mapping R package for distribution S PLUS_6 PBS Mapping S PLUS 6 library for distribution S PLUS_2000 PBS Mapping S PLUS 2000 library for distribution sre Source code for PBS Mapping PBSdata PBS Data expansion for PBS Mapping R PBS Data R package for distribution S PLUS_6 PBS Data S PLUS 6 library for distribution S PLUS_2000 PBS Data S PLUS 2000 library for distribution CommandLineUtilities Utilities programmed at the Pacific Biological Station PBS clipPolys Clip PolySets convUL Convert between UTM and Longitude Latitude coordinates findPolys Find the polygons containing events gshhs2r Convert the GSHHS ASCII data format to our ASCII data format RelatedSoftware Software related
25. Commission Minor Areas Description PolySet of polygons for the PMFC minor areas Format Data frame consisting of 6 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates minor PMFC minor area numeric code and pmfc PMFC minor area designation Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting Pacific Marine Fisheries Commission PMFC minor areas The international PFMC established areas along the North American Pacific coast from California to Alaska Tagart 1991 These correspond roughly to reporting regions for the U S triennial surveys They also fit into a Canadian scheme of dividing the coast into major areas where Canadian areas 3 9 correspond to PFMC areas 3C 3D 5A 5B 5C 5D and 5E The major areas have hierarchical breakdowns into minor areas and localities Table 3 2 Fig 3 2a Schnute et al 2001 The major areas cover the BC coast and the minor areas simply cover the coast with a larger number of subdivisions Based on historic fishing grounds each minor area contains localities These typically leave holes so that a minor area can consist of various defined localities plus other regions Each locality has a code number within the minor area where 9 always me
26. Description Thins a PolySet where each unique PID SID describes a polygon Usage thinPolys polys tol 1 filter 3 Arguments polys PolySet to thin tol tolerance in kilometers 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 106 Value PolySet containing the thinned data The function recalculates the POS values for each polygon See Also thickenPolys Examples load the data if using R if is null version language amp amp version language R data nepacLL 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 towData Tow Track Data Description PolyData of tow information for a longspine thornyhead survey 2001 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 proj
27. For additional help on the arguments border lty 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 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 O 1 1 polys lt as PolySet polys projection 1 f 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 3 addStipples Add Stipples to an Existing Plot Description Adds 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 side density distance Details 52 PolyData specifying which polygons to stipple and their properties par parameters passed as direct arguments supersede these data one of 1 O or 1 corresponding to outside both sides or inside respec tively density of points relative to the default distance to offset points measured as a percentage of the absolute difference in xlim addit
28. Gulf Islands if isR data nepacLLhigh xlim lt c 123 6 122 95 ylim lt c 48 4 49 zone lt 9 PIDs and labels for Gulf Islands labelData lt data frame PID c 663 855 1271 2864 2285 2657 label c Saltspring San Juan Galiano Saturna N Pender Mayne assign nepacLLhigh to nepacUTMhigh S62 and change to UTM coordinates nepacUTMhigh lt nepacLLhigh attr nepacUTMhigh zone lt zone nepacUTMhigh lt convUL nepacUTMhigh ff 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 tempSX ylim lt range temp Y prepare areas isles lt clipPolys nepacUTMhigh xlim ylim areas lt calcArea isles labelData lt merge labelData areas all x TRUE use as character to squash factors labelDataSlabel lt paste as character labelData label round labelDataSarea sep n par mfrow c 1 1 omi c 0 0 0 0 Plot the figur 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 addPolys isles is element isles PID labelData PID col clr yellow add the labels labXY lt calcCentroid isles labXYSY lt labXYSY 2 centre vertically labelData lt merge labelData labXY all x TRUE addLabels labelData placement DATA cex 1 25 text 898 5385 Vancouver Isl
29. 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 CPUE catch effort Code for this figure includes the following key function calls e plotMap to draw a coastal map of this region clipped from nepacLL e makeGrid to create a grid in the region of interest e findPolys to associate tows with the appropriate grid cells e combineEvents to calculate the mean CPUE within each cell e addPolys to draw cells with colours in the polyProps argument scaled to the CPUE e points the native R S function to plot events on the map _19 Q uw N LO D TD ED Sb CPUE kg h 0 50 Y 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 catch per unit effort CPUE within each grid cell 0 1 by 0 19 Circles show locations of individual tows PBS Mapping can also display non geographical data such as technical drawings network diagrams and transportation schematics For example we use a PolySet to
30. Pacific region for delimiting five longspine thornyhead management regions effective since the 2002 fishing year Schnute et al 2004 The five regions from south to north are WCVI 48 5 to 50 5 Triangle 50 5 to 51 Tidemarks 51 to 51 56 Flamingo 51 56 to 53 5 and Rennell 53 5 to 54 40 Currently Flamingo is closed to directed fishing on longspine thornyheads Sebastolobus altivelis References Schnute J R Haigh B Krishka A Sinclair and P Starr 2004 The British Columbia longspine thornyhead fishery analysis of survey and commercial data 1996 2003 Cana dian Science Advisory Secretariat Research Document 2004 059 75 p See Also ltea ltsa and pl230 118 major Pacific Marine Fisheries Commission Major Areas Description PolySet of polygons for the PMFC major areas Format Data frame consisting of 6 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates major PMFC major area numeric code and pmfc PMFC major area designation Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting Pacific Marine Fisheries Commission PMFC major areas The international PFMC established areas along the North American Pacif
31. Pacific region for delimiting the boundaries of sponge bioherms found on the continental shelf in Hecate Strait and Oueen Charlotte Sound The reefs HSN Hecate Strait North HSS Hecate Strait South OCN Queen Charlotte Sound North OCS Queen Charlotte Sound South The discovery of hexactinellid sponge reefs was a result of a binational scientific project between the Institut fuer Geologie und Palaeontologie University of Stuttgart Germany and the Geological Survey of Canada Pacific Geoscience Centre Sidney BC References In Germany http www porifera org a cifi htm In Canada http www pgc nrcan gc ca marine sponge index_e htm See Also gcssa minor and local 125 srfa Slope Rockfish Assessment Areas Description PolySet of polygons for areal boundaries used in slope rockfish assessments Format Data frame consisting of 5 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates and srfa slope rockfish assessment area name Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting the boundaries in slope rockfish assessments Slope rockfish assessment boundaries were originally set up to delimit the two main fish ing grounds Goose Island and Moresby Gulli
32. PolyData a PolySet Bathymetry data spanning British Columbia s coast Northeast Pacific shoreline normal resolution Northeast Pacific shoreline high resolution Pythagoras theorem diagram PolySet Survey data Tow data Tow track polyline data World ocean shoreline normal resolution worldLLhigh World ocean shoreline high resolution 48 addLines Add a PolySet to an Existing Plot as Polylines Description Adds 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 Arguments 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 pa rameters passed as direct arguments supersede these data lty vector of line types cycled by PID col vector of colours cycled by PID 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 See Also calcLength clipLines closePolys convLP fixBound fixP0S locatePolys plotLines thinPolys thickenPolys 49
33. PolyData x projection NULL zone NULL is PolyData x fullValidation TRUE 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 exist ing 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 where the data correspond to additional fields in the data frame The R S 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 graph
34. SID secondary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates local compilation numeric code where first two digits specify PFMC minor area code and last two digits specify local area code and area local area numeric code Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting ground fish fishing localities within Pacific Marine Fisheries Commission PMFC minor areas The international PFMC established areas along the North American Pacific coast from California to Alaska Tagart 1991 These correspond roughly to reporting regions for the U S triennial surveys They also fit into a Canadian scheme of dividing the coast into major areas where Canadian areas 3 9 correspond to PFMC areas 3C 3D 5A 5B 5C 5D and 5E The major areas have hierarchical breakdowns into minor areas and localities Table 3 2 Fig 3 2a Schnute et al 2001 The major areas cover the BC coast and the minor areas simply cover the coast with a larger number of subdivisions Based on historic fishing grounds each minor area contains localities These typically leave holes so that a minor area can consist of various defined localities plus other regions Each locality has a code number within the minor area where 9 always means other i e
35. UTM zones cutm lt diff utms 2 nzon lt length cutm cutm lt cutm utms 1 nzon text cutm rep 50 75 nzon c 60 1 nzon 1 cex 1 3 col clr red box f add a box to ensure solid border Figure 3 PBSfig03 lt function clr PBSval PBSclr isR PBSval PBSisR dot PBSvalSPBSdot nepacLL UTM Zones in UTM Space if isR data nepacLL zone lt 6 xlim lt range nepacLL X ylim lt range nepacLL Y utms lt seq 186 110 6 utms vector for creating PolySet and EventData below create UTM zones lutms lt data frame PID rep l 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 lutms tol 25 close FALSE uutms lt convUL lutms create label locations central meridians lems lt data frame EID l length diff utms 2 X utms 1 length utms 1 diff utms 2 Y rep 50 75 length diff utms 2 lems 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 figur 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 ucm
36. and data sets defined in PBS Mapping arranged alphabetically within categories Category Object Description User constant PBSprint Specify whether to print summaries Plotting addLabels Add labels to an existing plot functions 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 clipLines Clip a PolySet as polylines clipPolys Clip a PolySet as polygons closePolys Close a PolySet combineEvents Combine measurements of events contourLines Pseudo simulation of R s contourLines function convCP Convert contour lines into a PolySet convDP Convert EventData PolyData into a PolySet convLP Convert polylines into a polygon convUL Convert coordinates between UTM LL projections extractPolyData Extract PolyData from a PolySet fi
37. 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 xlim and ylim before plotting It only adds PolyData con taining X and Y columns The function creates a blank plot when polys eguals 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 Conseguently 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 load the data if using R if is null version language amp amp version language R data nepacLL data surveyData plot a map plotMap nepacLL xli
38. bug Under certain conditions it fails to produce contour lines If this happens the function will produce an error message that explains a work around Value List of contours Each contour is a list with three elements level x and y level identifies the contour level and x and y provide the coordinates of the contour convCP creates a PolySet from a list in this format References R 1 9 1 s contourLines function and associated documentation http www r project org See Also contour convCP makeTopography Examples produce some data x lt seg 0 5 0 8 length 50 y lt x z lt outer x y FUN function x y sin 2 pi x 2ry2 72 calculate contour lines zc lt contourLines x y z levels c 2 8 convert contours to a PolySet and plot the result p lt convCP zc attr p PolySet projection lt 1 plotMap NULL xlim range p PolySet X ylim range p PolySet Y projection 1 addLines p PolySet convCP Convert Contour Lines into a PolySet Description Converts contour lines into a PolySet Usage convCP data projection NULL zone NULL 67 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 Details data contains a list as described below The contourLines function create a list suitable for the data argument
39. 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 file underground pdf at the web site http www europrail net maps 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 I 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 PBS Mapping works with data exported from database tables where records may not have a definite order The POS field in our PolySet definition imposes the reguired 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 correspond
40. contains the string data frame Inserting the string PolySet as the class vector s first element alters the behaviour of some functions 100 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 References Environmental Systems Research Institute ESRI 1996 ArcView GIS the geographic information system for everyone ESRI Press Redlands California See Also EventData LocationSet PolyData print Print PBS Mapping Objects Description This function 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 SS method for class LocationSet print x o S3 method for class PolyData print x S3 method for class PolySet print x SS method for class summary PBS print xX Arguments X a PBS Mapping object of appropriate class additional arguments to print 101 See Also EventData LocationSet PBSprint PolyData PolySet summary Examples load the data if using R if is null version language amp amp version language R
41. coordinates We also present a number of convenient utilities for Microsoft Windows operating systems that support computational geometry outside the framework of R or S PLUS Our results which depend significantly on the work of students illustrate the convergence of goals between academic training and applied research R SUM Schnute J T Boers N M et Haigh R 2004 PBS Mapping 2 Guide de l utilisateur Can Tech Rep Fish Aquat Sci 2549 126 viii p Le pr sent rapport d crit la seconde version du logiciel con u 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 l aide de donn es sur les p ches des poissons d mersaux le long du littoral Pacifique du Canada donn es compil es la Station biologique du Pacifique SBP Bien que con u initialement pour l analyse de donn es halieutiques notre logiciel peut s appliquer toute une vari t de domaines La biblioth que PBS Mapping Cartographie de la SBP tend le langage R et S PLUS pour inclure une capacit d impression en deux dimensions semblable celle habituellement disponible dans les syst mes d information g ographiques SIG Des modules en C permettent d acc l rer les algorithmes gr ce la g om trie num rique en trouvant par exemple les polygones qui contiennent des v
42. 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 n points x y with 1 n where 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 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 bou
43. exe and gshhs exe respectively Using a Perl script gshhs2r pl we then converted this ASCII format to ours and removed the lakes islands in lakes and ponds in islands We then clipped the data to 170 lt x lt 250 and 34 lt y lt 72 the GSHHS coordinates roughly span 0 to 360 Finally we subtracted 360 from all of the remaining x coordinates so that the Greenwich meridian becomes 0 and the northeast Pacific Ocean has negative 2 coordinates corresponding to longitudes west of 0 References Wessel P and W H F Smith 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 addPolys bcBathymetry clipPolys nepacLL plotPolys plotMap PolySet thickenPolys thinPolys 88 PBSmapping PBS Mapping Draws Maps and Implements Other GIS Procedures Description This software has evolved from fisheries research conducted at the Pacific Biological Sta tion PBS in Nanaimo British Columbia Canada It extends the R 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 ge ometry such as finding polygons that contain specified point events or converting between longitude latitude and Universal Transverse Mercator UTM coordinates I
44. 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 Locat ionSet 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 egual distances for each degree of longitude and latitude this projection exaggerates the size of objects near the earth s poles as illustrated in Figure 1 For points near the latitude y a more realistic map uses the aspect ratio 2 1 r COS y where r degrees of longitude x should occupy the same distance as 1 degree of latitude y Latitude Longitude Figure 1 Map of the world projected in longitude latitude coordinates This image based on our PolySet worldLL uses the longitude range 20 lt
45. meaning in this function and if specified will be reset to 3 close Boolean value if TRUE include the distance between each polygon s last and first vertex if necessary Details 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 com pute 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 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 59 Examples load the data if using R if is null version language amp amp version language R data nepacLL calculate the perimeter of Vancouver Island print calcLength nepacLL nepacLL PID 33 calcMidRange Calculate the Midpoint of the X Y Ranges of Polygons Description Calculates the midpoint of the X Y ranges of polygons found in a PolySet Usage calcMidRange polys rollup 3 Arguments polys PolySet to use rollup level of detail in the results 1 PIDs only 2
46. 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 et S PLUS 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 _vi 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 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 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 and 2004 Starting in
47. of portraying and understanding such complex information Maps with statistical information proved especially useful and we found ourselves facing guestions commonly addressed by Geographic Information Systems GIS Commercial GIS packages can be expensive with an additional reguirement for specialised 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 www insightful com available commercially we began by writing bilingual functions for these languages to produce the maps reguired Schnute et al 2003 describe the package PBS Mapping Version 1 which evolved from these early experiences After another year of development we have extensively revised the software and this current report serves primarily as a user s manual for PBS Mapping Version 2 The Preface explains the relationship between this document and its predecessor Schnute et al 2003 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 sampl
48. operate in different environments We built PBS Mapping for the R S 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 sguares where each sguare 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 usually preferred over raster formats Unlike R S 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 Mic
49. 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 numeric value If Boolean specifies whether to check polys for a projection attribute four element numeric vector x1 x2 y1 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 param eters 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 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 94 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 frac tion of the smallest dimension These tick marks can not
50. 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 questions 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 questions 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 for using either language Although written originally for Unix R has also been implemented for vii 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 S Nick Bo
51. produced regionally but are numbered nationally Reguests for individual reports will be filled by the issuing establishment listed on the front cover and title page Out of stock reports will be supplied for a fee by commercial agents Rapport technigue canadien des sciences halieutigues et aguatigues Les rapports technigues contiennent des renseignements scientifigues et technigues gui constituent une contribution aux connaissances actuelles mais gue ne sont pas normalement appropri s pour la publication dans un journal scientifigue Les rapports technigues sont destin s essentiellement un public international et ils sont distribu s a cet chelon Il ny a aucune restriction quant au sujet de fait la s rie refl te la vaste gamme des int r ts et des politiques du minist re des P ches et des Oc ans c est dire les scences halieutiques et aquatiques Les rapports techniques peuvent tre cit s comme des publications compl tes Le titre exact para t au dessus du r sum de chaque rapport Les rapports techniques sont r sum s dans la revue R sum s des sciences aquatiques et halieutiques et ils sont class s dans l index annual des publications scientifiques et techniques du Minist re Les num ros 1 456 de cette s rie ont t publi s titre de rapports techniques de l Office des recherches sur les p cheries du Canada Les num ros 457 a 714 sont parus titre de rapports techniques de la Direction g n rale de l
52. 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 plt 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 S like plot do not allow layout parameters like plt 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 PBS Mapping actually alter the margins so we adopt a different approach in which p1t is reset with each high 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 pltNULL Computational Functions PBS Mapping contains many functions that perform computations on PolySets and other data structures Appendix H lists them all but we give further details for some of them here 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 1 n l A bn xii i l for the area A of a polygon with vertices x y i 1 n where vertices 1 and n correspond to
53. 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 PBS Mapping 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 Vili This page has been left intentionally blank for printing purposes a 1 INTRODUCTION This report describes software written to facilitate the compilation and analysis of fishery data particularly data referenced by spatial coordinates Our 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
54. survey and the Queen Charlotte Sound survey References Schnute J R Haigh B Krishka A Sinclair and P Starr 2004 The British Columbia longspine thornyhead fishery analysis of survey and commercial data 1996 2003 Cana dian Science Advisory Secretariat Research Document 2004 059 75 p Stanley R D P Starr N Olsen and R Haigh 2003 Summary of results of the 2003 Queen Charlotte Sound bottom trawl survey Canadian Science Advisory Secretariat Research Document In Press 48 p See Also ltsa and qcssa
55. the input except for possible changes in the X and Y columns 75 See Also closePolys fixPOS isConvex isIntersecting PolySet Examples set up a long horizontal and long vertical line to extend the plot s f 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 fixPOS Fix the POS Column of a PolySet Description Fixes the POS column of a PolySet by recalculating it using sequential 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 1 to N or N to 1 de pending on the 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 2and POS 3 If exteriorCCW NA all other columns remain unchanged Otherwise it orders the X and Y col
56. 800 m 800 1200 m 1200 1600 m Survey details can be found in Starr et al 2002 2004 References Schnute J R Haigh B Krishka A Sinclair and P Starr 2004 The British Columbia longspine thornyhead fishery analysis of survey and commercial data 1996 2003 Cana dian Science Advisory Secretariat Research Document 2004 059 75 p Starr P J B A Krishka and E M Choromanski 2002 Trawl survey for thornyhead biomass estimation off the west coast of Vancouver Island September 15 to October 2 2001 Canadian Technical Report of Fisheries and Aquatic Sciences 2421 55 p Starr P J B A Krishka and E M Choromanski 2004 Longspine thornyhead random stratified trawl survey off the west coast of Vancouver Island September 6 23 2002 Cana dian Technical Report of Fisheries and Aguatic Sciences In Preparation See Also ltsa 117 ltxa Longspine Thornyhead Experimental Management Areas Description PolySet of polygons describing management areas for longspine thornyheads in effect since the 2002 fishing year Format Data frame consisting of 5 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates and name name of management region Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada
57. A 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 intersec tion union and exclusive or respectively Details This function interfaces with the General Polygon Clipper library http www cs man ac uk aig staff alan software produced by Alan Murta at the University of Manch ester Consequently we adopt some of his terminology in the details below Murta 2004 defines a generic polygon or polygon set as zero or more disjoint boundaries of arbitrary configuration He relates a boundary to a contour where each may be con vex 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 polys
58. B contains two generic polygons C D The function s output 79 is the concatenation of A op C B op C A op D B op D with PIDs 1 to 4 respectively Generally there are 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 Value If polysB is NULL the resulting PolySet contains a single generic polygon one PID possibly with several components 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 several 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 load the data if using R if is null version language amp amp version language R data nepacLL create a triangle to use in clipping polysB lt
59. D may be missing X and Y See Also calcArea calcLength calcMidRange calcSummary locateEvents locatePolys 57 Examples load the data if using R if is null version language amp amp version language R data nepacLL calculate and print the centroids for several polygons print calcCentroid nepacLL is element nepacLL PID c 33 39 47 calcConvexHull Calculate the Convex Hull for a Set of Points Description Calculates the convex hull for a set of points Usage calcConvexHull xydata Arguments xydata points to use Details This routine ignores all columns other than X and Y Value PolySet with columns PID POS X and Y See Also addPoints addPolys calcArea calcCentroid calcMidRange calcSummary locateEvents plotMap plotPoints plotPolys Examples load the data if using R if is null version language amp amp version language R data surveyData plot the convex hull and then plot the points plotMap calcConvexHull surveyData addPoints surveyData 58 calcLength Calculate the Length of Polylines Description Calculates the length of polylines found in a PolySet Usage calcLength polys rollup 3 close FALSE Arguments polys PolySet to use rollup 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
60. E u 1 z ZONE has the arguments e i IFILE ASCII input file containing the X and Y data required e o OFILE ASCI output file defaults to standard output e u or 1 convert to UTM longitude latitude coordinates required 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 findPolys 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 c EVENT FILE ASCII input file containing EventData reguired e o OFILE ASCII output file defaults to standard output Y The header line in both input files must contain field names and subseguent 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 ha
61. E 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 frac tion 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 polygon It con nects each polygon s last vertex to its first The function supports both borders border lty 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 eguals 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 bo
62. P and O For example if P contains A 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 seguentially 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 represented as one PID with possibly many SIDs _14 Polygon A Polygon B F A 3 7 ee P e s E 4 MES o MV YH ra 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 We began with a polyline of the British Columbia coast digitise
63. PBS Mapping 2 User s Guide Jon T Schnute Nicholas M Boers and Rowan Haigh Fisheries and Oceans Canada Science Branch Pacific Region Pacific Biological Station 3190 Hammond Bay Road Nanaimo British Columbia VOT 6N7 2004 Canadian Technical Report of Fisheries and Aquatic Sciences 2549 lt Fisheries and Oceans P ches et Oc ans lel I i Canada Canada Canada Canadian Technical Report of Fisheries and Aquatic Sciences Technical reports contain scientific and technical information that contributes to existing knowledge but which is not normally appropriate for primary literature Technical reports are directed primarily toward a worldwide audience and have an international distribution No restriction is placed on subject matter and the series reflects the broad interests and policies of the Department of Fisheries and Oceans namely fisheries and aquatic sciences Technical reports may be cited as full publications The correct citation appears above the abstract of each report Each report is abstracted in Aquatic Sciences and Fisheries Abstracts and indexed in the Department s annual index to scientific and technical publications Numbers 1 456 in this series were issued as Technical Reports of the Fisheries Research Board of Canada Numbers 457 714 were issued as Department of the Environment Fisheries and Marine Service Technical Reports The current series name was changed with report number 925 Technical reports are
64. PolyData lwd 3 box Figure 7 PBSfig07 lt function clr PBSval PBSclr isR PBSval PBSisR towTracks from Longspine Thornyhead Survey if isR data nepacLL data towTracks data towData add a colour column col to towData pdata lt towData pdataSZ lt pdataSdep pdata lt makeProps pdata breaks c 500 800 1200 1600 col c clr black clr red clrSblue par mfrow c 1 1 omi c 0 0 0 0 Plot the figur 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 if isR 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 black clr red clr blue text tempSrect leftt tempSrectSw temp text y c 500 800 m 800 1200 m 1200 1600 m pos 2 text tempSrectSleft tempSrectSw 2 tempSrectStop pos 3 LTS Survey Tracks else key 127 6 48 4 title LTS Survey Tracks cex title l adj 5 39 between 1 transparent T lines list col sort unique pdata col lwd 3 text list c 500 800 m 800 1200 m 1200 1600 m cex 8 adj l text 125 6 49 7 Vancouver nIsland cex 1 2 adj 1 box Figure 8 PBSfig08 lt function clr PBSval PBSclr isR PBSvalSPBSisR calcArea of the Southern
65. Sprint PolyData PolySet Examples load the data if using R if is null version language amp amp version language R data surveyData print summary surveyData 103 surveyData Survey Data Description EventData of Pacific ocean perch POP tow information 1966 89 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 min utes depth fishing depth m and year year of survey trip Attributes projection LL zone 9 Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand 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 com mercial groundfish fishing trips and research 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 biologica
66. a recherche et du d veloppement Service des p ches et de la mer minist re de l Environnement Les num ros 715 924 ont t publi s titre de rapports techniques du Service des p ches et de la mer minist re des P ches et de l Environnement Le nom actuel de la s rie a t tabli lors de la parution du num ro 925 Les rapports techniques sont produits l chelon regional mais num rot s l chelon national Les demandes de rapports seront satisfaites par l tablissement auteur dont le nom figure sur la couverture et la page du titre Les rapports puis s seront fournis contre r tribution par des agents commerciaux Canadian Technical Report of Fisheries and Aquatic Sciences 2549 2004 PBS Mapping 2 User s Guide by Jon T Schnute Nicholas M Boers and Rowan Haigh Fisheries and Oceans Canada Science Branch Pacific Region Pacific Biological Station 3190 Hammond Bay Road Nanaimo British Columbia V9T 6N7 CANADA lt Her Majesty the Queen in Right of Canada 2004 Cat No Fs97 6 2549E ISSN 0706 6457 98765 4 3 2 1 First printing September 16 2004 Correct citation for this publication Schnute J T Boers N M and Haigh R 2004 PBS Mapping 2 user s guide Can Tech Rep Fish Aguat Sci 2549 126 viii p ill TABLE OF CONTENTS ADSHAC ES ae Y Y O CF A eee et FN MO v RESUME oe in alc E a Re RH HR alsa cn v Preface nersini ER a A GNU FF ES AEE Ria dedi vi l
67. ages and choose the option Install package s from local zip files Find and select the file PBSmapping_2 00 zip then click on the button Open Alternatively it may also be possible to choose the option Install package s from CRAN and then select PBSmapping To install PBSmapping in S PLUS 2000 decompress the file PBSmapping_2 00_Splus2000 zip into the S PLUS library directory e g C Program Files SP2000 library Make sure to invoke the option of using complete folder names This creates the subdirectory tree library PBSmapping Similar instructions apply to S PLUS 6 using the file PBSmapping_2 00_Splus6 zip To remove PBSmapping from R or S PLUS open the library 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 2 00 an 2 PBS MAPPING 2 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 PBS Mapping begins with data structures that embody two essential concepts First polygons define boundaries such as shorelines and fishery management areas Second fishing events occur at specific locations defined by two geographical coordin
68. almonid data Revision 1 Canadian Technical Report of Fisheries and Aguatic 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 Aguatic Sciences 2617 91 p Sipser M 1997 Introduction to the theory of computation PWS Publishing Company Boston 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 Aguatic Sciences 2421 60 p Venables W N and Ripley B D 1999 Modern applied statistics with S PLUS GB 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 pwessel_pubs html 26 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
69. ample in a fishery context what is the total catch from all fishing events within each management region Our function combineEvent s 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 General Polygon Clipper GPC library developed by Alan Murta 2004 at the University of Manchester We adopt some of his terminology in the discussion here He defines a generic polygon or polygon set as zero or more disjoint polygonal contours that define boundaries of the polygon region Some contours can represent 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 unigue P ID 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 reguire 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
70. and adj 0 cex 1 25 text 925 5435 Strait of Georgia adj 0 cex 1 25 Figure 9 PBSfig09 lt function clr PBSval PBSclr isR PBSvalSPBSisR combineEvents in Queen Charlotte Sound if isR data nepacLL data surveyData vents lt surveyData xl lt 131 8 127 2 yl lt c 50 5 52 7 prepare EventData clip it omit NA entries and calculate CPUE vents lt vents events X gt xl 1 amp events X lt xl 2 amp eventsSY gt yl 1 amp eventsSY lt yl 2 events lt na omit events eventsScpue lt events catch eventsSeffort 60 make a grid for the Queen Charlotte Sound grid lt makeGrid x seq 131 6 127 6 1 y seq 50 6 52 6 1 projection LL zone 9 locate EventData in grid locData lt findPolys events grid events Z lt events cpue 39 pdata lt combineEvents events locData FUN mean brks lt c 0 50 300 750 1500 25000 lbrks lt length brks cols lt c clr lettuce clr moss clrSirish clr forest clr black pdata lt makeProps pdata brks col cols par mfrow c 1 1 omi c 0 0 0 0 Plot the figur plotMap nepacLL col clr land bg clr sea xlim xl ylim yl tck 0 015 mgp c 2 5 0 cex l 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 SY i pch 16 cex 0 50 col clr white points events X i event
71. and they contain an entry for each unique 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 colums X1 X2 Xn and Y1 Y2 Yn See Also calcArea calcCentroid calcConvexHull calcLength calcMidRange combineEvents findPolys locateEvents locatePolys makeGrid makeProps Examples load the data if using R if is null version language amp amp version language R data nepacLL calculate and print the centroids for several polygons print calcSummary nepacLL is element nepacLL PID c 33 39 47 rollup 3 FUN mean 61 clipLines Clip a PolySet as Polylines Description Clips a PolySet where each unique 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 clipPoly
72. ands and filtered out any islands with fewer than 15 vertices References Wessel P and W H F Smith 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 addPolys clipPolys plotPolys plotMap PolySet thickenPolys thinPolys worldLL 110 APPENDIX I PBS Data This appendix documents the objects available in PBS Data as summarised in Table I1 Subseguent pages give complete technical documentation for every object listed in alphabetic order These descriptions come from Rd files written for the R documentation system which generates corresponding LaTeX files that typeset the pages included here Table I1 Data sets defined in PBS Data Object Description bcnames British Columbia geographic names data hsgrid Hecate Strait survey grid isobath Isobaths 100 1800 m at 100 m intervals locality Localities in Pacific Marine Fisheries Commission minor areas ltea Longspine thornyhead exploratory management areas ltsa Longspine thornyhead survey strata WCVI ltsa dat Longspine thornyhead survey strata PolyData ltxa Longspine thornyhead experimental management areas major Pacific Marine Fisheries Commission major areas minor Pacific Marine Fisheries Commission minor areas pfma Pacific fishery management areas pfma dat Pacific fishery management areas PolyData pl230 230 T
73. ans other i e outside the identified localities Another code 0 denotes an unknown locality rather than 9 Simplified majors cover the BC coast so do minors but localities do not References Schnute J T R Haigh B A Krishka and P Starr 2001 Pacific ocean perch assessment for the west coast of Canada in 2001 Canadian Science Advisory Secretariat Research Document 2001 138 90 p 120 Tagart J V 1991 Population dynamics of yellowtail rockfish Sebastes flavidus stocks in the northern California to southwest Vancouver Island region Ph D thesis University of Washington 323 p See Also major local and pfma pfma Pacific Fishery Management Areas Description PolySet of polygons describing the Pacific fishery management areas PFMA Format Data frame consisting of 5 columns PID primary polygon ID SID secondary polygon ID POS position of each vertex within a given polygon X longitude coordinates and Y latitude coordinates Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source The Pacific fishery management areas divide Canada s Pacific fisheries waters into areas and subareas Notices that describe fishery openings and closures often reference them We created this data set through several steps Our source data contained too many vertices and incorrectly represented holes We eliminated its holes t
74. arch 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 Jul Calculating the area and centroid of a polygon URL http astronomy swin edu au pbourke geometry polyarea Accessed Aug 3 2004 Chamberlain R 2001 Feb O5 1 what is the best way to calculate the distance between 2 points URL http www census gov cgi bin geo gisfag O5 1 Accessed Aug 3 2004 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 P
75. are gshhs dp exe and gshhs exe respectively Using a Perl script gshhs2r pl we then converted this ASCII format to ours removed the lakes islands in lakes and ponds in islands and filtered out any islands with fewer than 15 vertices References Wessel P and W H F Smith 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 addPolys clipPolys plotPolys plotMap PolySet thickenPolys thinPolys worldLLhigh 00 worldLLhigh Shorelines of the World High Resolution Description PolySet of polygons for the global shorelines 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 In S the data are loaded auto matically on demand Source Polygon data from the GSHHS Global Self consistent Hierarchical High resolution Shore line database We thinned the full resolution GSHHS binary data with a tolerance of 1 0 km and then converted it to ASCII data using the supplied software gshhs dp exe and gshhs exe respectively Using a Perl script gshhs2r pl we then converted this ASCII format to ours removed the lakes islands in lakes and ponds in isl
76. atePo lyData validateDa ta lyProps validatePo validateDa validatePo ta lySet validateDa ta validateXYData validateData 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 appendPolys validatePolySet is PolySet as EventData validateEventData is EventData as LocationSet validateLocat is LocationSet ionSet tic as PolyData validatePolyData is PolyData as PolySet validatePolySet is PolySet calcArea rollupPolys validatePolySet calcArea C convUL is PolyData 44 calcCentroid rollupPolys validatePolySet calcCentroid C is PolyData
77. ates such as longitude and latitude The languages R and S conveniently support 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 S 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 PBS Mapping 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 reguires 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 P ID 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 verte
78. d manually from a marine map To convert this object to a meaningful closed polygon we devised the functions fixBound 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 database for the entire planet They make this available via the Internet as binary files in five different resolutions full high intermediate low and crude 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 _15 Their thinning software uses an algorithm devised by Douglas and Peucker 1973 whose initials dp appear in the file name The dp is also an abbreviation of decimate polygons We compiled both programs with a free GNU compiler as described in Appendix B Table 2 PolySets derived from the full resolution GSHHS database PolySet Thinning Longitude Latitude Vertices Polygons nepacLL 02km 190 lt x lt 110 34 lt y lt 729 75 929 536 nepacLLhigh 0 1 km 190 lt x lt 110 34 lt y lt 72 199 914 9 961 worldLL 5 0 km 20 lt x lt 360 90 lt y lt 84 30 797 210 worldLLhigh 1 0km 20 lt x lt 3609 90 lt y lt 84 191 268 1 502 Excludes polygons with fewer than 15 v
79. data nepacLL change to summary printing style PBSprint lt TRUE print the PolySet print nepacLL pythagoras Pythagoras Theorem Diagram PolySet Description PolySet of shapes to prove Pythagoras Theorem a b 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 In S the data are loaded auto matically on demand Source An artifical construct to illustrate the proof of Pythagoras Theorem using trigonometry See Also addPolys plotPolys plotMap PolySet 2 summary Summarize PBS Mapping Objects Description summary method for PBS Mapping classes Usage S3 method for class EventData summary object S3 method for class LocationSet summary object S3 method for class PolyData summary object 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 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 Value A list of summary statistics See Also EventData LocationSet PB
80. de coordinates Y latitude coordinates and popa proposed POP assessment area names Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting the proposed boundaries in Pacific ocean perch POP assessments Existing slope rockfish assessment boundaries cut right through the logical POP population units based on catch and CPUE patterns Schnute et al 2001 The new regions delimit six populations QCI Queen Charlotte Islands west and north MR Moresby Gully including Hecate Strait MI Mitchell s Gully GS Goose Islad Gully NVI west coast of Vancouver Island north of Brooks Peninsula and SVI west coast of Vancouver Island south of Brooks Peninsula 123 References Schnute J T R Haigh B A Krishka and P Starr 2001 Pacific ocean perch assessment for the west coast of Canada in 2001 Canadian Science Advisory Secretariat Research Document 2001 138 90 p See Also major minor local pfma and srfa qcssa Queen Charlotte Sound Survey Strata Description PolySet of polygons describing the survey strata for the Queen Charlotte Sound synoptic groundfish survey Format Data frame consisting of 5 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates and st
81. dinar y gd ddn nd evans 27 Appendix B Global Self consistent Hierarchical High resolution Shoreline GSHHS 28 Appendix C Bathymetry Dates ar et a E REES Sia Nee E A net 29 Appendix D Generic Mapping Tools GMT 30 Appendix E Source Code for Pi91ires Lee es GN A tn Re eases tases 34 Appendix F Changes in PBS Mapping v 2 00 40 Appendix G PBS Mapping Function Dependencies ss 43 Appendix H PBS Mapping Functions and Data ss 46 Appendix I PBS DAT eu eU RSR GB Pen Ud E 110 iy LIST OF TABLES Table 1 Principal graphics functions in the PBS Mapping package 9 Table 2 PolySets derived from the GSHHS database 15 Table A1 Directories on the distribution CDau uu eae ee dw Cyw 27 Table F1 New user accessible functions in PBS Mapping v 2 00 40 Table H1 Functions and data sets defined in PBS Mapping 46 Table I1 Data sets defined in PBS Dates and ON A y Dd Mess 110 LIST OF FIGURES Figure 1 Map of the world uu cent net ele Geeta ee ED antenne 6 Figure 2 Map of the northeastern Pacific Ocean longitude latitude eee ee eeeeeeseeeseeeeeeeees 7 Figure 3 Map of the northeastern Pacific Ocean UTM easting northing 8 Figure 4 Illustration of the thinPolys function es eL HN GYN ond ne nt man dent 12 Figure 5 Example of the JoinPolys logic operations sssesesessesresseseresressesererresserererreeseese 14 Figure 6 Several polyline
82. e algorithms Executable programs appear on our distribution CD in the directory CommandLineUtilities 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 MINX X MAX X y MIN Y Y MAX Y 99 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 MINX 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 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 OFIL
83. e 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 PBS Mapping package These make it possible to perform some of the polygon functions outside the framework of R or S Appendices provide additional information about various topics related to PBS Mapping including the contents of the distribution CD for this software an Internet source for global shoreline data an Internet source for global bathymetry data alternative Generic Mapping Tools GMT source code for the figures in this report changes in PBS Mapping from Version 1 to Version 2 function dependencies in PBS Mapping documentation for PBS Mapping functions and data a package of supplementary data for PBS Mapping of interest to local users at PBS EOmHmHUOUW oe We anticipate that our software will continue to change for the better due to bug fixes and other improvements This report documents version 2 00 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 Our distribution CD which may eventually be posted on the Internet includes the equival
84. e version language Initialization Function initPBS lt function Function initPBS Sets up colour table for the demo figures and determines R S environment PBSnam lt c PBSclr PBSisR PBSdot PBSdash PBSclr lt 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 PBSisR lt is null versionSlanguage amp amp version language R PBSdot lt ifelse PBSisR 3 7 PBSdash lt ifelse PBSisR 2 8 if PBSisR R specific initialization require PBSmapping PBSclr lt lapply PBSclr function v rgb v 1 v 2 v 3 maxColorValue 255 else S PLUS specific initialization graphsheet color table paste unlist lapply PBSclr paste collapse use names FALSE collapse pages TRUE suppress graphics warnings T for i in 1 length names PBSclr PBSclr i lt i library PBSmapping PBSval lt as list PBSnam names PBSval lt PBSnam for i in PBSnam PBSval i lt get i if PBSisR assign PBSval PBSval pos 1 else assign PBSval PBSval where 1 Figure 1 PBSfig01 lt function clr PBSval PBSclr isR PBSvalSPBSisR World UTM Zones
85. eEvents plotPoints Examples load the data if using R if is null version language amp amp version language R data nepacLL data surveyData plot a map plotMap nepacLL xlim c 136 125 ylim c 48 57 f add events addPoints surveyData col 1 7 addPolys Add a PolySet to an Existing Plot as Polygons Description Adds a PolySet to an existing plot where each unique PID SID describes a polygon Usage addPolys polys xlim NULL ylim NULL polyProps NULL border NULL lty NULL col NULL density NA angle NULL Arguments polys PolySet to add required xlim range of X coordinates ylim range of Y coordinates polyProps PolyData specifying which polygons to plot and their properties par pa rameters 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 density vector describing shading line densities lines per inch cycled by PID angle vector describing shading line angles degrees cycled by PID additional par parameters for the polygon function 51 Details The plotting routine connects the last vertex of each discrete polygon to the first vertex of that polygon It supports both borders border lty and fills col density angle It clips polys to xlim and ylim before plotting
86. ection LL zone 9 Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand 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 com mercial groundfish fishing trips and research assessment cruises off the west coast of British Columbia BC The longspine thornyhead Sebastolobus altivelis survey data were ex tracted from GFBio Information 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 lf References Starr P J B A Krishka and E M Choromanski 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 Aguatic Sciences 2421 60 p See Also makeProps PolyData towTracks towTracks Tow Track Polyline Data Description PolySet of geo referenced polyline tow track data from a longspine thornyhead survey 2001 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 In S the data are loaded auto ma
87. ent package for S PLUS A developer s guide Boers et al 2004 describes the process of building PBS Mapping from source materials for R and S and lists all required software Except for the commercial product S PLUS all software required to develop and use PBS Mapping is freely available from the Internet 1 1 Software Installation Our distribution CD Appendix A includes two subdirectories PBSmapping and PBSdata that provide everything necessary to install two packages e PBSmapping the mapping software discussed in Section 1 e PBSdata various additional data sets relevant to fisheries investigated at PBS Appendix I Each package can be installed in three software environments R version 1 90 or higher S PLUS 2000 and S PLUS 6 In the discussion below we describe the installation procedure for PBSmapping where a similar procedure applies to PBSdata Our software appears in four files e PBSmapping R PBSmapping_2 00 tar gz source code for the R distribution which can be used to build a binary package e APBSmappingARNPBSmapping_2 00 zip binary package ready for installation into R e PBSmapping S PLUS 2000APBSmapping_2 00_Splus2000 zip source code and binary package ready for installation into S PLUS 2000 e APBSmappingAS PLUS_ 6APBSmapping_2 00_Splus6 zip source code and binary package ready for installation into S PLUS 6 To install PBSmapping in R start the R GUI Click on the menu Pack
88. ents 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 PBS Mapping Dr Alan Murta through Toby Howard has generously given us permission to use his General Polygon Clipper GPC library implemented in our joinPolys function Similarly 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 PBS Mapping package 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 A 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 Rese
89. ep 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 contourLines Pseudo Simulation of R s contourLines Function S PLUS only Description Returns contour lines in a format similar to R s contourLines function Usage ncol z TRUE nlevels contourLines x seq 0 1 len nrow z y seq 0 1 len z nlevels 10 levels pretty range z na rm Arguments x y locations of grid lines at which the values in z are measured These must be in ascending order By default equally spaced values from 0 to 1 are used If x is a list its components x x and x y are used for x and y respectively If the list has component z this is used for z Zz a matrix containing the values to be plotted NAs are allowed Note that x can be used instead of z for convenience nlevels number of contour levels desired if and only if levels is not supplied levels numeric vector of levels at which to produce contour lines Details This function captures the output from the S PLUS contour function and reformats it to imitate R s contourLines function The S PLUS contour function produces significantly different contours than the corre sponding R function S PLUS may return several polylines for one continuous contour This function does not correct this behaviour 66 The S PLUS contour function contains a
90. ers has used such linkages intelligently to bring fast computational geometry into our package PBS Mapping written for both R and S PLUS 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 PBS Mapping 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 PBS Mapping Version 2 First 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
91. ertices after thinning PBS Mapping includes four data sets derived from the full resolution GSHHS database 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 meridian We generated each data set from the full resolution GSHHS database by following a consistent seguence e thin the database with a specified distance tolerance as listed in the above table using GSHHS software e convert the result to an ASCII file with GSHHS software e use our own Perl script gshhs2r p1 on this file to remove the lakes islands in lakes and ponds in islands eliminate small polygons if desired such as those with fewer than 15 vertices transform this file to another ASCII file with the structure of a PolySet e clip the data to the desired coordinate range with our own stand alone program clipPolys exe e import the ASCII table to a data frame in R S e extend the Antarctic polygon data to longitude 20 and latitude 90 with the hidden function ixGSHHSWorld world data sets only 2 5 Bathymetry Data Smith and Sandwell 1997 have produced global seafloor topography from satellite altimetry a
92. es for the slope complex of species Con sequently the boundaries do not follow those of the PFMC areas even though the names are similar 3C 3D 5AB 5CD 5EN 5ES Schnute et al 2001 attempt to clarify the various groundfish boundaries References Schnute J T R Haigh B A Krishka and P Starr 2001 Pacific ocean perch assessment for the west coast of Canada in 2001 Canadian Science Advisory Secretariat Research Document 2001 138 90 p See Also major minor local pfma and popa 126 wcvisa West Coast of Vancouver Island Survey Strata Description PolySet of polygons describing the survey strata for the west coast of Vancouver Island synoptic groundfish survey Format Data frame consisting of 8 columns PID primary polygon ID SID secondary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates ID polygon ID from ArcView dump grid unique depth identifier and index index used to identify SIDs in PIDs Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting 4 depth strata for the west coast of Vancouver Island synoptic groundfish survey The four depth zones are 50 125 m 125 200 m 200 330 m and 330 500 m This survey is complementary to both the deeper longspine thornyhead
93. escribing isobaths from 100 m to 1800 m at 100 m increments Format Data frame consisting of 6 columns PID primary polygon ID SID secondary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates and isobath isobath value m Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polyline data in use at Fisheries and Oceans Canada Pacific region for describing isobaths from 100 m to 1800 m at 100 m increments off the British Columbia coast Isobaths are an inerpolation from a bathymetry grid in ArcView The grid was created from a triangular irregular network TIN that was created from Canadian Hydrographic Service digital natural resource maps Section 3 6 Schnute et al 1999 References Environmental Systems Research Institute 1996 ArcView GIS the geographic informa tion system for everyone ESRI Press Redlands California Schnute J T N Olsen and R Haigh 1999 Slope rockfish assessment for the west coast of Canada in 1999 Canadian Stock Assessment Secretariat Research Document 99 184 104 p See Also ltsa gcssa and wcvisa 113 locality Localities in Pacific Marine Fisheries Commission Minor Areas Description PolySet of polygons for fishing ground localities within PFMC minor areas Format Data frame consisting of 7 columns PID primary polygon ID
94. et Details This function makes a grid of polygons labeling them according to byrow and addSID e byrow TRUE and addSID FALSE implies PID j 1 x m e byrow FALSE and addSID FALSE implies PID j i 1 xn e byrow TRUE and addSID TRUE implies PID 4 SID j e byrow FALSE and addSID TRUE implies PID 7 SID i Value PolySet with columns PID SID if addSID TRUE POS X and Y The PolySet is a set of rectangular grid cells with vertices i Yi Vers Yj Vera Yj 1 Ti Yj 1 See Also addPolys clipPolys combineEvents findPolys PolySet thickenPolys Examples make a 10 x 10 grid polyGrid lt makeGrid x 0 10 y 0 10 plot the grid plotPolys polyGrid density 0 projection 1 84 makeProps Make Polygon Properties Description Appends a column for a polygon property e g border or lty 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 vector 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 addStipple
95. he PolySet nepacLL and B the result of applying thinPolys to this polygon with a tolerance of ten kilometres 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 sequential 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 subsequent 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 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 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 pol
96. hree 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 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 See Also EventData PolyData PolySet 83 makeGrid Make a Grid of Polygons Description Makes 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 PolyS
97. hy 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 a region from this database The form returns an ASCII file containing X Y and Z coordinates To use this data file with PBS Mapping first load it into R S 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 aleutian lt read table aleutian txt header F col names c x y z aleutian x lt aleutian x 360 aleutian z lt aleutian z alBathy lt makeTopography aleutian alCL lt contourLines alBathy levels c 100 500 1000 2500 5000 alCP lt convCP alCL alPoly lt alCPSPolySet attr alPoly projection lt LL plotMap alPoly type n addLines alPoly col 1 5 30 APPENDIX D Generic Mapping Tools GMT Generic Mapping Tools GMT and PBS Mapping have many similar features although they
98. ic coast from California to Alaska Tagart 1991 These correspond roughly to reporting regions for the U S triennial surveys They also fit into a Canadian scheme of dividing the coast into major areas where Canadian areas 3 9 correspond to PFMC areas 3C 3D 5A 5B 5C 5D and 5E The major areas have hierarchical breakdowns into minor areas and localities Table 3 2 Fig 3 2a Schnute et al 2001 The major areas cover the BC coast and the minor areas simply cover the coast with a larger number of subdivisions Based on historic fishing grounds each minor area contains localities These typically leave holes so that a minor area can consist of various defined localities plus other regions Each locality has a code number within the minor area where 9 always means other i e outside the identified localities Another code 0 denotes an unknown locality rather than 9 Simplified majors cover the BC coast so do minors but localities do not References Schnute J T R Haigh B A Krishka and P Starr 2001 Pacific ocean perch assessment for the west coast of Canada in 2001 Canadian Science Advisory Secretariat Research Document 2001 138 90 p Tagart J V 1991 Population dynamics of yellowtail rockfish Sebastes flavidus stocks in the northern California to southwest Vancouver Island region Ph D thesis University of Washington 323 p 119 See Also minor local and pfma minor Pacific Marine Fisheries
99. ical parameters used by the R S functions lines and polygon column names can specify graphical properties 98 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 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 Details as 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 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 99 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
100. ields named EID X Y 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 STD refers to an inner polygon boundary then EID occurs in PID SID only if Bdry T An event may occur
101. if isR data worldLL data nepacLL par mfrow c 1 1 omi c 0 0 0 0 Plot the figur 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 seq 18 360 by 6 lty 1 col clr red add prime meridian abline v 0 lty 1 lwd 2 col clrSblack 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 39 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 add labels for some UTM zones text x seq 183 2 by 6 length 9 y rep 85 9 adj 0 5 cex 0 65 label 1 9 box f add a box to ensure solid border Figure 2 PBSfig02 lt function clr PBSval PBSclr isR PBSval PBSisR dot PBSvalSPBSdot nepacLL UTM Zones in LL Space if isR data nepacLL par mfrow c 1 1 omi c 0 0 0 0 Plot the figur 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 add the central meridian of zone 6 abline v 147 lty dot col clr black create and then add labels for the
102. im before plotting The function creates a blank plot when polys eguals 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 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 Conseguently 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 fixPO8 locatePolys thinPolys thickenPolys Examples 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 O 1 1 plot the PolySet plotLines polys xlim c 5 1 5 ylim c 5 1 5 91 plotMap Plot a PolySet as a Map Description Plots a PolySet as a map using the correct aspect ratio Usage plotMap Arguments polys xlim ylim projectio plt polyProps border lty col density angle bg axes tckLab polys xlim NULL ylim NULL projection
103. ing 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 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 21 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 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 PBS Mapping They also store po
104. ion 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 33 uo oe 49 30 4 S 4 Os oP ey o 49 00 5 2 a w 7 TE _ w J i 4 NO LO Ol 07 A 48 30 lt r SN We a g 48 00 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 D2 Tow tracks off the west coast of Vancouver Island drawn by A PBS Mapping B GMT produced B Format of GMT tow txt gt ffa gt signifies the start of each polyline 126 26545 48 523133 vertices follow X coordinate white space Y coordinate 126 265233 48 523716 126 265183 48 524283 126 385483 48 532567 126 3861 48 5327 126 3868 48 53285 _34 APPENDIX E Source Code for Figures To help beginners use PBS Mapping we include source code for all figures in this report An intialization function handles most compatibility issues for R and S PLUS For example it creates a global list PBSval of colours dots and dashes with appropriate values for each environment The Boolean variable PBSval PBSisR is true in the R language environment but false in the S PLUS environment as detected by the R variabl
105. ional par parameters for the points function 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 load the data if using R if is null version language amp amp version language R data nepacLL plot a map plotMap nepacLL xlim c 128 66 122 83 ylim c 48 00 51 16 f add stippling addStipples nepacLL col 2 pch 19 cex 0 25 appendPolys Append a Two Column Matrix to a PolySet Description Appends a two column matrix to a PolySet assigning PID and possibly SID values auto matically or as specified in its arguments Usage appendPolys polys mat PID NULL SID NULL isHole FALSE Arguments polys mat PID SID isHole Details 53 existing PolySet if NULL creates a new PolySet required two column matrix to append reguired new polygon s PID new polygon s SID Boolean value if TRUE mat represents a hole If polys contains an SID column and the SID argument eguals NULL this function uses the next available SID 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 appr
106. ipples to an existing plot appendPolys Append a two column matrix to a PolySet as Coerce a data frame to an object with class EventData EventData LocationSet LocationSet PolyData PolyData PolySet PolySet 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 contourLines Pseudo simulation of R s contourLines function convCP Convert contour lines into a PolySet convDP Convert EventData PolyData into a PolySet convLP Convert polylines into a polygon extractPolyData Extract PolyData from a PolySet is Determine whether an object is EventData EventData LocationSet a LocationSet PolyData PolyData PolySet 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 makeTopography Make topography data from freely available online data plotPcints Plot EventData PolyData as points print Print EventData an EventData object LocationSet a LocationSet object PolyData a PolyData object Only our S PLUS library includes our version of this function R includes a native version 4A1 PolySet a PolySet object summary PBS the summary of a PBS Mapping object summary Summarize E
107. l have two vertices x1 y1 and x2 y2 and POS values 1 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 create sample PolyData polyData lt data frame PID c 1 2 3 xt c 1 3 5 yi 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 f make a PolySet from PolyData polys lt convDP polyData xColumns c x1 x2 x3 yColumns c y1 y2 y3 f print and plot the PolySet print polys plotLines polys xlim c 0 7 ylim c 0 5 col 2 69 convLP Convert Polylines into a Polygon Description Converts two polylines 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 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 thei
108. l samples Schnute et al 2001 provide a more comprehensive history of POP surveys including the subset of data presented here References Schnute J T R Haigh B A Krishka and P Starr 2001 Pacific ocean perch assessment for the west coast of Canada in 2001 Canadian Science Advisory Secretariat Research Document 2001 138 90 p See Also addPoints combineEvents EventData findPolys makeGrid plotPoints 104 thickenPolys Thicken a PolySet of Polygons Description Thickens a PolySet where each unique PID SID describes a polygon Usage thickenPolys polys tol 1 filter 3 keepO0rig TRUE close TRUE Arguments polys PolySet to thicken tol tolerance in kilometers 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 clo
109. lotMap polyB xlim xlim ylim ylim xlab ylab axes F col clr blue plt NULL text lab text 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 clr purple panel lt c NA NA TEM AE are FER bit for i in 3 6 plotMap NULL xlim xlim ylim ylim proj 1 xlab ylab axes F p1t NULL addPolys polyA border clr red lty dash addPolys polyB border clr blue lty dash addPolys joinPolys polyA polyB operation ops i col cols i text lab text i x lab x i y lab y i cex lab cex i text xlim 1l off ylim 2 off panel i cex l 6 box Figure 6 PBSfig06 lt function clr PBSval PBSclr isR PBSval PBSisR contourLines in Queen Charlotte Sound if isR data nepacLL data bcBathymetry isob lt contourLines bcBathymetry levels c 250 1000 p lt convCP isob p PolyData col lt rep c clr red clr green clr blue clrSyellow 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 Plot the figur 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
110. lumbia longspine thornyhead fishery analysis of survey and commercial data 1996 2003 Cana dian Science Advisory Secretariat Research Document 2004 059 75 p Starr P J B A Krishka and E M Choromanski 2002 Trawl survey for thornyhead biomass estimation off the west coast of Vancouver Island September 15 to October 2 2001 Canadian Technical Report of Fisheries and Aquatic Sciences 2421 55 p Starr P J B A Krishka and E M Choromanski 2004 Longspine thornyhead random stratified trawl survey off the west coast of Vancouver Island September 6 23 2002 Cana dian Technical Report of Fisheries and Aquatic Sciences In Preparation See Also ltea ltsa dat ltxa gcssa and wcvisa 116 ltsa dat Longspine Thornyhead Survey Strata PolyData Description Support PolyData for the PolySet 1tsa Gives zonation information for the PIDs Format Data frame consisting of 4 columns PID primary polygon ID dep shallowest depth of depth strata azone areal zone A G and dzone depth zone 1 3 Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source PolyData for the PolySet 1tsa that provide zonation information for each of the 21 strata The strata comprise 7 areal zones A Barkley B Loudon Clayoquot C Clayoquot Estevan D Nootka 500 Line E Esperanza Kyuquot F Cape Cook Winter Harbour G Quatsino and three depth zones 500
111. lygons in a more efficient file format than our PolySet data frames We designed PBS Mapping for the R S 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 PBS Mapping Appendix D shows some comparative examples of code written in both environments Because PBS Mapping 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 summarises the current status of free GIS programs and data Their listings receive freguent updates and show a pattern of steady growth 3 COMMAND LINE UTILITIES The PBS Mapping package for R S 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 S working environment Furthermore some users may wish to implement computational geometry calculations without reference to the R S 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 S For each utility a corresponding c file provides a front end to shared code for th
112. m c 136 125 ylim c 48 57 95 f add events addPoints surveyData col 1 7 plotPolys Plot a PolySet as Polygons Description Plots a PolySet as polygons Usage plotPolys polys xlim Arguments polys xlim ylim projection plt polyProps border lty col density angle bg axes tckLab NULL ylim NULL projection FALSE plt c 0 11 0 98 0 12 0 88 polyProps NULL border NULL lty NULL col NULL density NA angle NULL bg O axes TRUE tckLab TRUE tck 0 014 tckMinor 0 5 tck PolySet 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 numeric value If Boolean specifies whether to check polys for a projection attribute four element numeric vector x1 x2 y1 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 polygons to plot and their properties par pa rameters 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 shading line densities lines per inch cycled by PID vector describing shading line angles degrees cycled by PID background colour of the plot Boolean val
113. mit function can remove rows with NAs If a pdata object does not exist the output contains only one polygon with a PID egual to 1 One inner boundary polygon POS goes from n to 1 can be generated by supplying a negative n If type o or type 1 the function draws a line connecting the last and first vertices Value PolySet with projection attribute egual to the map s projection The function does not set the zone attribute See Also addPolys appendPolys clipPolys closePolys fixP0S joinPolys plotMap plotPolys thickenPolys thinPolys Examples f define one polygon with up to 5 vertices on the current plot Not run polys lt locatePolys n 5 82 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 t
114. n 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 7 is 186 67 lt x lt 180 62 Value PolyData with columns PID SID may be missing and area If the proejction equals LL or UTM the units of area are square kilometres See Also calcCentroid calcLength calcMidRange calcSummary locatePolys 56 Examples load the data if using R if is null version language amp amp version language R data nepacLL 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 Calculates 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 equals 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 unique PID SID Value PolyData with columns PID SI
115. nd ship depth soundings Their database appears on the Internet at http topex ucsd edu cgi bin get data cgi A web based data acguisition form allows users to extract a region after entering longitude and latitude coordinate ranges Appendix C documents how to import their data for use with PBS Mapping 16 R and S PLUS each provide a contour function to plot contour lines The two languages however implement this function differently as itemized below In S PLUS contour returns a list with coordinates of the contour lines when the save argument is TRUE Unfortunately this list sometimes represents each continuous contour with several polylines as illustrated in Figure 6A In R contour lacks a save argument and does not return contour coordinates Instead the contourLines function accomplishes this task giving a list with somewhat different format than the list produced by the S PLUS contour function with the save TRUE The R algorithm appears better than the one used by S PLUS because it tends to capture continuous contours as single polylines Figure 6B 52 5 DN o LO TD Tig to to LO S LO 131 130 129 131 130 129 Longitude Longitude Figure 6 A The S PLUS contour function with save TRUE often returns several polylines for a single continuous contour illustrated here by cycling colours through SIDs B The R contourLines function returns a single polyline for each continuous contour
116. ndPolys Find the polygons that contain events fixBound Fix the boundary points of a PolySet fixPOS Fix the POS column of a PolySet isConvex Determine whether polygons are convex Only our S PLUS library includes our version of this function R includes a native version Object related functions Data sets isIntersecting joinPolys locateEvents locatePolys makeGrid makeProps makeTopography thickenPolys thinPolys as EventData LocationSet PolyData PolySet is EventData LocationSet PolyData PolySet print EventData LocationSet PolyData PolySet summary PBS summary EventData LocationSet PolyData PolySet bcBathymetry nepacLL nepacLLhigh pythagoras surveyData towData towTracks worldLL _47 Determine whether polygons are self intersecting Join one or two PolySets using a set theoretic operation Locate events on the current plot Locate polygons on the current plot Make a grid of polygons Make polygon properties Make topography data from freely available online data Thicken a PolySet of polygons Thin a PolySet of polygons Coerce a data frame to an object with class EventData LocationSet PolyData PolySet Determine whether an object is EventData a LocationSet PolyData a PolySet Print an EventData object a LocationSet object a PolyData object a PolySet object the summary of a PBS Mapping object Summarize EventData a LocationSet
117. ndary regardless of rotational direction This 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 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 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 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
118. o create one polygon for each sub area We manually processed a couple of cases where multiple polygons still represented a sub area We then subtracted nepacLLhigh from each polygon to simplify their boundaries and reintroduce holes This pfma data set lacks multiple sub areas and misrepresents some others The resolution of the source data exceeded nepacLLhigh As such it included rivers not described in nepacLLhigh Some sub areas lie completely in rivers The subtraction consequently removed sub areas where corresponding water did not exist in nepacLLhigh In particular the processing removed the following sub areas 8 9 8 11 8 12 10 11 12 34 25 1 25 16 28 11 28 12 28 13 28 14 29 15 29 16 and 29 17 See Also ltea ltsa ltsa dat pfma dat ltxa gcssa and wcvisa pfma dat Pacific Fishery Management Areas PolyData Description Support PolyData for the PolySet pfma Gives area information for the polygons Format Data frame consisting of 4 columns PID primary polygon ID SID secondary polygon ID area area and subarea sub area Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source PolyData for the PolySet pfma that link each of its 2917 polygons of which 1952 represent holes with 593 sub areas See Also ltea ltsa ltsa dat pfma ltxa gcssa and wcvisa pl230 230 Degree True Line from Lookout Island Descrip
119. o plot and their properties par pa rameters 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 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 90 tckMinor numeric vector length 1 or 2 describing the length of tick marks as a frac tion 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 yl
120. olorValue 255 bg rgb 224 253 254 maxColorValue 255 tck c 0 03 cex 1 8 mgp c 1 9 0 7 0 data towTracks addLines co towTracks l rgb 255 0 O maxColorValue 255 lwd 0 5 GMT Panel B gmtset ANOT_FONT_SIZE 20p pscoast Dh R 127 89 125 68 47 85 49 97 JM5i G255 255 195 S224 253 254 Ba0 5 a0 5WSne W0 5p K gt GMT Tow ps psxy R 127 89 125 68 47 85 49 97 JM5i W0 5p 255 0 0 M H0 0 lt GMT Tow txt gt gt GMT Tow ps load the nepacLL data set plot the nepacLL data set ff limit the region horizontally ff limit the region vertically ff specify the plot region size set the foreground colour set the background colour set the tick mark length ff adjust the font size ff 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 ff plot the high resolution data set ff 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 ff portrait mode allow for appending more plot code output to the postscript file GMT Tow ps limit the region add using the Mercator project
121. opriately 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 fixP0S joinPolys plotMap plotPolys Examples create two simple matrices a lt matrix data c 0 0 1 0 1 1 O 1 ncol 2 byrow TRUE b lt matrix data c 2 2 3 2 3 3 2 3 ncol 2 byrow TRUE f build a PolySet from them polys lt appendPolys NULL a polys lt appendPolys polys b print the result print polys 54 bcBathymetry Bathymetry Data Spanning British Columbia s Coast Description Bathymetry data spanning British Columbia s coast 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 level 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 In S the data are loaded auto matically on demand Source Bathymetry data acquired from the Scripps Institution of Oceanography at the University of San Diego
122. or decreasing order for outer and inner boundaries respectively If the POS field erroneously contains floating point numbers f i xPOS 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 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 PolyData We define PolyData as a data frame with a first column named PID and optionally a second column named SID Unlike a PolySet
123. orValue 255 bg rgb 224 253 254 maxColorValue 255 tck c 0 03 cex mgp c x 122 2 21 5 0 97 1 8 1 9 0 7 O GMT Panel B gmtset ANOT_FONT_ SIZE 26p pscoast Dh A0 0 1 R 129 3 122 2 47 5 51 5 A JM7i G255 255 195 S224 253 254 Ba2 alWSne W0 5p P gt GMT VI ps Latitude 50 51 49 48 128 126 Longitude 124 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 ff output to the postscript file GMT VI ps 232 234 Figure D1 A Vancouver Island as plotted in PBS Mapping compared with B the same region as output from GMT 34 Code for Figure D2 R Panel A data nepacLL plotMap nepacLL xlim c 127 89 125 68 ylim c 47 85 49 97 pltzc 0 16 0 97 0 16 0 97 col rgb 255 255 195 maxC
124. otPolys behave similarly except that pl otMap s default behaviour guarantees the correct aspect ratio as defined by either the PolySet s projection attribute or the functions projection argument If both are specified the attribute supersedes the argument When this attribute is missing pl otMap 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 pl otMap function However plotPolys plotLines andplotPoints can also set the correct aspect ratio when passed a suitable projection argument Table 1 Behaviour of the principal graphics functions in the PBS Mapping software package Function Creates a Graph Plots as Polygons Sets Aspect Ratio by Default addLabels No 2 addLines No No addPoints No addPolys No Yes 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 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 e lty cex col border density
125. outer contours only and 3 no roll up 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 load the data if using R if is null version language amp amp version language R data nepacLL calculate and print the centroids for several polygons print calcMidRange nepacLL is element nepacLL PID c 33 39 47 60 calcSummary Apply Functions to Polygons in a PolySet Description Applies 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 equal 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
126. r original order The PID column eguals 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 create two polylines polylinei 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 polylinel polyline2 reverse FALSE col 3 70 convUL Convert Coordinates between UTM and Lon Lat Description Converts coordinates between UTM and Lon Lat Usage convUL xydata Arguments xydata data frame with columns X and Y Details 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 egual to a number between 1 and 60 inclusive If it contains longitude latitude coordinates and the
127. r stability 43 APPENDIX G PBS Mapping Function Dependencies This appendix documents function dependencies within PBS Mapping 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 S working environment but functions designated C are implemented in C source code and compiled in the DLL for the mapping package R S invokes these functions with the call C addAxis addFeature addProps validatePolyProps addLabels addProps calcDist calcOrientation calcOrientation C checkProjection slip clip extractPolyData createFastIDdig createIDs createFastIDdig fixGSHHSWorld findPolys fixPOS initPlotRegion rollupPolys addLines addPoints addPolys rollupPolys C plotMaps addAxis addLabels initPlotRegion validateXYData preparePolyProps createlDs validatePolyData validateData createlDs validateEventData validateDa validateLocationSet validateDa valid
128. rat stratum descriptor Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting 2 areal strata for the Queen Charlotte Sound synoptic groundfish survey Stanley et al 2003 The two areal strata divide the central BC coast region into a northern and southern component Four depth zones 50 125 m 125 200 m 200 330 m 330 500 m are used in the survey but not delimited in this PolySet References Stanley R D P Starr N Olsen and R Haigh 2003 Summary of results of the 2003 Queen Charlotte Sound bottom trawl survey Canadian Science Advisory Secretariat Research Document In Press 48 p See Also ltsa and wcvisa 124 spongeReefs Sponge Reef Bioherms on the BC Continental Shelf Description PolySet of polygons for sponge bioherms in Hecate Strait and Queen Charlotte Sound central British Columbia coast Format Data frame consisting of 7 columns PID primary polygon ID SID secondary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates reef reef designation and type continuous or discontinuous Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada
129. ress 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 25 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 aig staff alan software Accessed Aug 3 2004 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 Aguatic 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 Aguatic Sciences 2496 82 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 CSAS Research Document 2001 138 90 p Schnute J T Wallace C G and Boxwell T A 1996 A relational database shell for marked Pacific s
130. rosoft Word On the other hand PBS Mapping inherits support from the R S environment for common raster e g BMP JPG and vector e g WMF file formats Users of Windows operating systems may find PBS Mapping 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 Figures D1 and D2 compare PBS Mapping with GMT We show the code used to produce these images in both environments where we use R code rather than S PLUS code to simplify colour handling To use the R code in S PLUS remove the call to data and replace the call to rgb with the appropriate S PLUS colour 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 A Code for Figure D1 R Panel A data nepacLL plotMap nepacLL lim c 129 3 ylim c 47 5 plt c 0 16 0 97 0 16 col rgb 255 255 195 maxCol
131. rthern exploratory area is defined by a line 230 True from Lookout Island p1230 References Schnute J R Haigh B Krishka A Sinclair and P Starr 2004 The British Columbia longspine thornyhead fishery analysis of survey and commercial data 1996 2003 Cana dian Science Advisory Secretariat Research Document 2004 059 75 p See Also ltsa ltxa and p1230 115 ltsa Longspine Thornyhead Survey Strata WCVI Description PolySet of polygons describing the survey strata for longspine thornyheads off the west coast of Vancouver Island WCVI Format Data frame consisting of 5 columns PID primary polygon ID SID secondary polygon ID POS position of each vertex within a given polygon X longitude coordinates and Y latitude coordinates Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting 21 strata for the WCVI longspine thornyhead survey Schnute et al 2004 The strata comprise 7 areal zones A Barkley B Loudon Clayoquot C Clayoquot Estevan D Nootka 500 Line E Esperanza Kyuquot F Cape Cook Winter Harbour G Quatsino and three depth zones 500 800 m 800 1200 m 1200 1600 m Survey details can be found in Starr et al 2002 2004 References Schnute J R Haigh B Krishka A Sinclair and P Starr 2004 The British Co
132. rue line from Lookout Island 49 59 52 2 N 127926 57 3 W popa Pacific ocean perch POP proposed assessment areas gcssa Oueen Charlotte Sound survey strata spongeReefs Sponge reef bioherms on the BC continental shelf srfa Slope rockfish assessment areas wcvisa West coast of Vancouver Island survey strata 111 hsgrid Hecate Strait Survey Grid Description PolySet of polygons for the Hecate Strait survey grid Format Data frame consisting of 5 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinates Y latitude coordinates cell cell designation within survey grid where rows span A L and columns span 1 6 Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand Source Polygon data in use at Fisheries and Oceans Canada Pacific region for delimiting the Hecate Strait survey grid Each grid cell is 10 nm by 10 nm The grid extent spans 131 48 30 to 130 6 30 of longitude and 52 30 to 54 30 of latitude The 12 rows are designated A L The 6 columns are designated 1 6 References Fargo J and A V Tyler 1992 Statistical testing of research trawl data with implications for survey design Neterlands Journal of Sea Research 29 97 108 See Also ltsa qcssa and wcvisa 112 isobath Isobaths 100 1800 m at 100 m intervals Description PolySet of polylines d
133. s locatePolys is EventData validatePolyData is PolySet makeGrid is PolySet makeProps validatePolyData is PolyData makeTopography plotLines plotMaps is PolyData plotMap plotMaps is PolyData plotPoints plotMaps is PolyData plotPolys plotMaps is PolyData print _45 Even tData summary EventData print LocationSet summary LocationSet print Pol y Data summary PolyData print Po ly Set summary PolySet print summary PBS summary m EV entData summary LocationSet createl summary Ds PO lyData createl summary Ds PO lySet createl Ds thickenPolys calcDis createI Ds validatePolySet is Polys thinPoly et S thickenPolys C validatePolySet is Polys et thinPolys C _ 46 APPENDIX H PBS Mapping Functions and Data This appendix documents the objects functions and data available in PBS Mapping as summarised in Table H1 Subsequent pages give complete technical documentation for every object listed in alphabetic order These descriptions come from Rd files written for the R documentation system which generates corresponding LaTeX files that typeset the pages included here Table H1 Functions
134. s fixBound Examples 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 62 clipPolys Clip a PolySet as Polygons Description Clips a PolySet where each unique 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 create a triangle that will be clipped polys lt data frame PID rep 1 3 POS 1 3 X c 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 63 closePolys Close a PolySet Description Closes a PolySet of polylines to form polygons Usage closePolys polys
135. s plotLines plotMap plotPoints and plotPolys The Z column of pdata is eguivalent 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 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 85 makeTopography Make Topography Data From Freely Available Online Data Description Makes topography data suitable for the contour and contourLines functions using freely available global seafloor topography data Usage makeTopography data Arguments data data frame with three optionally named columns X Y and Z The columns must appear in that order Each X Y combination must appear exactly once Details Data obtained 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 sub tracting 360 from the result s X coordinates x When creating bathymetry data consider negating the result s eleva
136. s SY i pch l cex 0 55 col clr black add title yrtxt lt paste min eventsSyear substring max eventsSyear 3 sep text xl 1 7 5 yl 2 l paste POP Surveys yrtxt cex 1 2 adj 0 add a key if isR right justify the legend labels temp lt legend x xl 1 3 y yl 1 7 legend rep 5 text width strwidth 1500 25000 bty n fill cols text temp rect left temp rect w tempStext y pos 2 paste brks 1 lbrks 1 brks 2 lbrks sep text temp rect leftrtemp rect w 2 temp rectStop pos 3 CPUE kg h cex 1 else key x1 1 3 y1 1 7 between 5 title CPUE kg h cex title 8 transparent T adj l rectangles list col cols border 1 size 1 Al text list paste brks 1 lbrks 1 brks 2 lbrks sep cex 7 Figure 10 PBSfigl0 lt function clr PBSval PBSclr isR PBSvalSPBSisR Pythagoras Theorem Visualized if isR data pythagoras create properties for colouring the polygons pythProps lt data frame PID c l 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 blue clr red clr yellow clr green par mfrow c 1 1 omi c 0 0 0 0 Plot the figur plotMap pythagoras plt c 01 99 01 95 lwd 2 xlim c 09 1 91 ylim c 0 19 2 86 polyProps pythProps axes F xlab ylab main Pythagoras Theorem a 262 b 262 c
137. s X ucms Y c 60 1 length utms 2 cex 1 3 col clr red box add a box to ensure solid border Cc Cc Figure 4 PBSfig04 lt function clr PBSvalSPBSclr 36 isR PBSvalSPBSisR thinPolys on Vancouver Island if isR data nepacLL par mfrow c 1 2 omi c 0 0 0 0 Plot the figur 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 add panel label text x xlim 2 0 5 y ylim 2 0 3 A cex l 6 f plot right figure thinned Vancouver Island plotMap thinPolys vi tol 10 xlim ylim col clr land bg 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 f add panel label text x xlim 2 0 5 y ylim 2 0 3 B cex l 6 box Figure 5 PBSfig05 lt function clr PBSvalSPBSclr isR PBSval PBSisR dash PBSvalSPBSdash joinPolys on Crescents radius lt c 5 4 two radii of the circles size lt abs diff radius 0 1 size of crescent SHLEEB lt 3305 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
138. s in a continuous S PLUS contour eeseseessesesesessersresseseresresseseresreses 16 Figure 7 Tow tracks from a longspine thornyhead survey in 2001 17 Figure 8 Areas of islands in the southern Strait of Georgia 18 Figure 9 Pacific ocean perch survey data 1966 89 19 Figure 10 Proof of Pythagoras Lheorenii eia ie TRS ne MR ne they wicca elena eas 20 Figure D1 PBS Mapping compared with GMT Vancouver Island 31 Figure D2 PBS Mapping compared with GMT tow tracks 0 eee eeeceeeeeereecseeceneeeeeenseeeeaees 33 ABSTRACT Schnute J T Boers N M and Haigh R 2004 PBS Mapping 2 user s guide Can Tech Rep Fish Aguat Sci 2549 126 viii p 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 the Pacific Biological Station PBS Despite its origins in fishery data analysis our software has broad applicability The library PBS Mapping extends the languages R and S PLUS 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
139. se 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 105 See Also thinPolys Examples load the data if using R if is null version language amp amp version language R data nepacLL plot Vancouver Island plotMap nepacLL nepacLL PID 33 calculate a thickened version using a 30 kilometers tolerance without keeping the original points p lt thickenPolys nepacLL nepacLL PID 33 tol 30 keepUrig FALSE convert the PolySet to EventData by dropping the PID column and renaming POS to EID p lt p 1 names p 1 lt EID convert the now invalid PolySet into a data frame and then into f EventData p lt as EventData as data frame p projection LL plot the results addPoints p col 2 pch 19 thinPolys Thin a PolySet of Polygons
140. statistics for a PolySet given a user defined function 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 closePolys adds corners from the bounding rectangle if needed to close polylines into polygons convUL converts between UTM and longitude latitude coordinates using the extensive formulas presented in Anonymous 1998 findPolys finds the polygons in a PolySet that contain events specified in EventData using the crossings test algorithm described later in this section isConvex determines which polygons in a PolySet are convex using an algorithm described below isIntersecting finds polygons that self intersect by comparing each edge pairwise with every other edge joinPolys performs set theoretic operations union intersection difference and exclusive or on polygons using the General Polygon Clipper GPC library by Murta 2004 thickenPolys adds vertices to polygons using an algorithm described below thinPolys thins the number of polygon vertices based on the Douglas Peuker line simplification algorithm Douglas and Peucker 1973 as illustrated in Figure 4 _12 Latitude 48 5 49 49 5 50 50 5 51 a 7 EEE 128 127 126 125 124 128 127 126 125 124 Longitude Longitude Figure 4 A Vancouver Island clipped from t
141. t includes data for a global shoreline and other data sets in the public domain PBSprint Specify Whether to Print Summaries Description Specifies 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 89 plotLines Plot a PolySet as Polylines Description Plots 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 numeric value If Boolean specifies whether to check polys for a projection attribute plt four element numeric vector x1 x2 y1 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 t
142. t set the zone attribute See Also addPoints combineEvents convDP EventData findPolys plotPoints Examples define five events on the current plot numbering them 10 to 14 H Not run events lt locateEvents EID 10 14 locatePolys Locate Polygons on the Current Plot Description Locates polygons on the current plot using the locator function 81 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 hasn 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 o
143. th 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 lty 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 clipPolys closePolys fixBound fixP0S locatePolys plotLines plotMap plotPoints thinPolys thickenPolys Examples 93 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 O 1 1 plot the PolySet plotMap polys xlim c 5 1 5 ylim c 5 1 5 density 0 projection 1 plotPoints Plot EventData PolyData as Points Description Plots EventData PolyData where each unique EID or PID SID describes a point Usage plotPoints data xlim NULL ylim NULL projection FALSE Arguments data xlim ylim projection plt polyProps cex col pch axes tckLab 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
144. the same point x y 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 _11 2 Xi eae Lay y y Cae Huy i l for a polygon with vertices x y i 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 attribute calcConvexHull calculates the convex hull for a given set of points using an algorithm presented by de Berg et al 2000 the incremental algorithm on p 6 7 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 fax 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 ss sin 5 cos y cos DE where R 6371 3 km denotes the earth s mean radius Wikipedia 2004 calcMidRange calculates midpoints of the X and Y ranges for each given polygon calcSummary calculates summary
145. tically on demand Source The longspine thornyhead Sebastolobus altivelis tow track spatial coordinates are avail able at the Pacific Biological 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 B A Krishka and E M Choromanski 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 See Also addLines calcLength clipLines plotLines PolySet towData 108 worldLL Shorelines of the World Normal Resolution Description PolySet of polygons for the global shorelines 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 In S the data are loaded auto matically on demand Source Polygon data from the GSHHS Global Self consistent Hierarchical High resolution Shore line database We thinned the full resolution GSHHS binary data with a tolerance of 5 0 km and then converted it to ASCII data using the supplied softw
146. tion PolySet of one polyline describing the boundary between the longspine thornyhead man agement regions in fishing years 2000 and 2001 Format Data frame consisting of 4 columns PID primary polygon ID POS position of each vertex within a given polygon X longitude coordinates and Y latitude coordinates Note In R the data must be loaded using the data function In S the data are loaded auto matically on demand 422 Source Polyline data in use at Fisheries and Oceans Canada Pacific region for describing the line 230 True from Lookout Island 127 26 57 3 W 49 59 52 2 N that formed the boundary between the traditional west coast Vancouver Island longspine thornyhead fishing ground and the northern exploratory fishing grounds during the 2000 and 2001 fishing years Schnute et al 2004 References Schnute J R Haigh B Krishka A Sinclair and P Starr 2004 The British Columbia longspine thornyhead fishery analysis of survey and commercial data 1996 2003 Cana dian Science Advisory Secretariat Research Document 2004 059 75 p See Also ltea ltsa and ltxa popa Pacific Ocean Perch POP Proposed Assessment Areas Description PolySet of polygons for areal boundaries proposed for POP assessments based on POP catch CPUE patterns Format Data frame consisting of 5 columns PID primary polygon ID POS position of each vertex within a given polygon X longitu
147. tions z to give depths positive values Value List with elements x y and z x and y are vectors while z is a matrix contour and contourLines expect data conforming to this list format See Also contour contourLines convCP read table Examples create a sample data frame file lt data frame X c 1 1 2 2 Y c 3 4 3 4 Z c 5 6 7 8 convert that data frame to the output format and print the results print makeTopography file 86 nepacLL Shoreline of the Northeast Pacific Ocean Normal Resolution Description PolySet of polygons for the northeast Pacific Ocean shoreline 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 In S the data are loaded auto matically on demand Source Polygon data from the GSHHS Global Self consistent Hierarchical High resolution Shore line database We thinned the full resolution GSHHS binary data with a tolerance of 0 2 km and then converted it to ASCII data using the supplied software gshhs dp exe and gshhs exe respectively Using a Perl script gshhs2r pl we then converted this ASCII format to ours removed the lakes islands in lakes and ponds in islands and filtered out any islands with fewer than 15
148. to PBS Mapping or the command line utilities Perl Link to ActivePerl R R 1 9 1 for Windows APPENDIX B Global Self consistent Hierarchical High resolution Shoreline GSHHS The GSHHS distribution http www ngdc noaa gov mgg shorelines gshhs html includes two programs that we use for manipulating data sets The first gshhs exe extracts ASCII data from binary files The second gshhs_dp exe thins binary files by reducing the number of points sensibly Wessel and Smith distribute both programs as C source code For technical reasons related to the binary data file format each program can be compiled in two distinct ways with or without defining a variable FLIP on the command line We compiled two versions of each program with the commands gcc 03 o gshhs exe gshhs c gcc DFLIP 03 o gshhs flip exe gshhs c gcc 03 o gshhs_dp exe gshhs_dp c gcc DFLIP O3 o gshhs_dp flip exe gshhs_dp c where the string flip in executable file names indicates that FLIP was defined by the argument DFLIP during compilation Working with Windows on an Intel platform we used gshhs flip exe and gshhs_dp flip exe to process original binary data files With binary data files previously thinned by us we used gshhs exe and gshhs_dp exe For additional details please refer to the GSHHS README file I APPENDIX C Bathymetry Data Smith and Sandwell 1997 have produced a global seafloor topograp
149. to bottom Each relatively narrow section can be 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 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 2000 1000 0 1000 2000 3000 UTM Easting km 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 boundaries The central
150. ue if TRUE plot axes 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 96 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 frac tion 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 polygon It con nects each polygon s last vertex to its first The function supports both borders border lty 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 eguals NULL In this case the user m
151. umns according to exteriorCCW Value PolySet with the same columns as the input except for possible changes to the POS X and Y columns 76 See Also closePolys fixBound isConvex isIntersecting PolySet Examples create a PolySet with broken POS numbering polys lt data frame PID c rep 1 10 rep 2 10 POS c seg 2 10 length 10 seg 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 isConvex Determine Whether Polygons are Convex Description Determines 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 Value PolyData with columns PID SID may be missing and convex Column convex contains Boolean values See Also isIntersecting PolySet TT Examples load the data if using R if is null version language amp amp version language R data nepacLL calculate then print the polygons that are convex p lt isConvex nepacLL
152. ust 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 border lty 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 Conseguently 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 clipPolys closePolys fixBound fixPOS locatePolys plotLines plotMap plotPoints thinPolys thickenPolys Examples 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 O 1 1 97 plot the PolySet plotPolys polys xlim c 5 1 5 ylim c 5 1 5 density 0 PolyData PolyData Objects Description PBS Mapping functions that expect PolyData will accept properly formatted data frames in their place see Details 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
153. ve 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 3 4 gshhs2r pl Convert GSHHS Data to PBS Mapping Format As discussed earlier in Section 2 4 our Perl script gshhs2r p1 converts data from the Global Self consistent Hierarchical High resolution Shoreline GSHHS database to a PolySet for use with PBS Mapping We first reguire an ASCII file created by gshhs exe the program supplied by the GSHHS project to convert binary to ASCII data Binary data may have been thinned with gshhs_dp exe Our utility removes non ocean shorelines such as lakes and islands within lakes as well as small polygons with N vertices or fewer The command gshhs2r pl i IFILE o OFILE n N has arguments e i IFILE ASCII input file created by gshhs exe required e o OFILE ASCII output file for a PolySet defaults to standard output e n N minimum number of vertices for an output polygon If the n parameter is not specified no filtering on the number of vertices takes place 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 stud
154. ventData EventData LocationSet a LocationSet PolyData PolyData PolySet a PolySet thickenPolys Thicken a PolySet of polygons thinPolys Thin a PolySet of polygons In addition to the new functions listed in Table F1 we have updated the interface to eleven functions in version 1 00 We made these changes to increase consistency between the new and existing functions In most cases they should not break existing code but we caution our readers to take them into account when moving to version 2 00 In the list below changes appear in bold underlined text and removed arguments appear in grey text with a strikethrough addLines polys xlim NULL ylim NULL polyProps NULL lty NULL col NULL addPolys polys xlim NULL ylim NULL polyProps NULL border NULL lty NULL col NULL density NA angle NULL calcArea polys sumPID FALSE rollup 3 clipLines polys xlim ylim keepExtra FALSE clipPolys polys xlim ylim keepExtra FALSE combineEvents events locs FUN mean bdryOK TRUE fixPOS polys exteriorCCW NA makeGrid x y byrow TRUE addSID TRUE projection NULL zone NULL 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 main Map xlab NULL yiab NULL axes TRUE tckLab TRUE tck 0 014 tckMinor 0 5 tck
155. vertices We then clipped the data to 170 lt x lt 250 and 34 lt y lt 72 the GSHHS coordinates roughly span 0 to 360 Finally we subtracted 360 from all of the remaining x coordinates so that the Greenwich meridian becomes 0 and the northeast Pacific Ocean has negative x coordinates corresponding to longitudes west of 0 References Wessel P and W H F Smith 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 addPolys bcBathymetry clipPolys nepacLLhigh plotPolys plotMap PolySet thickenPolys thinPolys 87 nepacLLhigh Shoreline of the Northeast Pacific Ocean High Resolution Description PolySet of polygons for the northeast Pacific Ocean shoreline 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 In S the data are loaded auto matically on demand Source Polygon data from the GSHHS Global Self consistent Hierarchical High resolution Shore line database We thinned the full resolution GSHHS binary data with a tolerance of 0 1 km and then converted it to ASCII data using the supplied software gshhs dp
156. x Thus in familiar mathematical notation a contour consists of n points x y with i 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 P ID 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 n to 1 along an inner boundary regardless of rotational direction This 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 P ID 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
157. y overwriting an ex isting attribute fullValidation Boolean value if TRUE fully test x Details We define EventData as a data frame with at least three fields named EID X Y Con ceptually 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 events associ ated 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 ab sent 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 72 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 Extracts 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 con
158. ygon 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 angle summation or winding number test Sum the angles swept by a ray from the trial point to seguential 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 traces a full circle and the angles do not sum to zero 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 We use the crossings test because it performs faster than angle summation Hains 1994 p 26 27 The latter reguires 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 ex
159. zone attribute is missing the function computes the mean longitude and uses that value to determine the zone The longitude range of zone 7 is 186 62 lt x lt 180 6 This function converts the X and Y columns of xydata from LL to UTM or vice versa After the conversion it adjusts the data frame s attributes accordingly Value 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 See Also closePolys fixBound Examples load the data if using R if is null version language amp amp version language R data nepacLL set the zone attribute attr nepacLL zone lt 9 convert and plot the result nepacUTM lt convUL nepacLL plotMap nepacUTM AR 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 possibl

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