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BioSIM 9 - User's Manual - Canadian Forest Service

1. e Event mapping analyses are event extraction analyses where a map of the event is to be generated by transforming a DEM of the area containing the points in the simulation s location list see Mapping Analysis Editor Description In this field the user may enter a meaningful title to use as a reminder of the object of the analysis Other fields of the Analysis Editor dialog depend on the type of analysis being defined 5 1 1 Average output analyses When an average output analysis is selected the Se x Analysis Editor adopts the form of a location list Summary type Average Output OF box In an average output analysis model output oe 3 Description t Cancel is averaged over replicates for selected locations 7 pea generating average time series for all model SEE E EEO output variables for all selected locations pasar SUEREC individually or lumped together when the VP ol Average over selected locations checkbox is checked This is the simplest form of model output analysis available NOTE BioSIM also offers the possibility of graphing the results of several average output analyses on the same graph select Project Export Multiple Analyses Average Output Analyses see Multiple Analysis dialog 40 Defining and Running Analyses 5 1 2 Event extraction analyses When an event extraction analysis is selected Beer this group of fields is used to define the statistical Summ
2. y amp H Natural Resources Ressources naturelles Canada Canada FL A i J AE i Cr i t Cd CRE h TER N r et Eo Er m EEF s Ss Fe EX P HAE Fe Cu MCE E a kik L THR i EE Th wy Re EOIS E mT i Tamia i T Le a NiE Jacques R gni re and R mi Saint Amant Information Report LAU X 134 2008 Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Canada BioSIM 9 User s Manual Jacques R gni re and R mi Saint Amant Information Report LAU X 134 2008 Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre LIBRARY AND ARCHIVES CANADA CATALOGUING IN PUBLICATION R gni re Jacques BioSIM 9 user s manual Jacques R gni re R mi Saint Amant Information report LAU X 134 Issued also in French under title BioSIM 9 manuel de l utilisateur Includes bibliographical references Type of computer file Electronic monograph in PDF format Mode of access World Wide Web Issued by Laurentian Forestry Centre ISBN 978 0 662 479 19 2 Cat no Fol 13 3 134E PDF 1 BioSIM Computer file Handbooks manuals etc 2 Insect pests Control Computer programs Handbooks manuals etc I Saint Amant R mi II Laurentian Forestry Centre II Title IV Series Information report Laurentian Forestry Centre Online LAU X 134 SB950 3 C3R43 2008 634 9 6702855369 C2008 980065 6 Her Majesty the Queen i
3. 2003 Daily Stations Define Location List must select one of these models The z Weather Station Matches selection made here determines the choices available in the remaining fields of the Replication 1 Advanced Simulation Editor Number of files generated 4 lacs 1 params x 1 reps 4 Approximate duration ri seconds If the obj ect of the simulation 1S the About the model selected generation of temperature re gimes choose R gni re s process oriented model of spruce budworm seasonal biology Fe ae Thi oriented model developed by R gni re 1982 Vanability in devel t Temperature generator as the model When renee the mathe of Aaa 1284 D p ion eh ccoding R gni re 1983 Additional refi de by F gni re 1987 1990 The feedi this model is selected the Model field of the Ia Er ed es To a far better iki Simulation inputs panel is de activated Cancel Model Help Shows the help file for this model if available Simulation inputs group This group of fields is used to specify model and temperature generator parameter values for the simulation as well as the list of locations for which the model will be run Model This field is used to specify values of model specific input parameters These can either be the default parameter values provided by the model s interface definition or a user defined set saved in the project s Model Input sub directory To specify a new set of para
4. and 20 BioSIM recommends 4 The stations selected from the 11 BioSIM 9 User s Manual three databases are independent If precipitation is used a second search is made to find stations with precipitation information After adjustment for differences in elevation latitude and longitude between the simulation point and weathers stations data monthly means or daily values are averaged using a weighted average procedure with 1 d as weight where d is distance in m 2 1 2 Adjustment for climatic gradients Whenever a difference in elevation latitude or longitude exists between the simulation point and the sources of weather data weather stations BioSIM adjusts data by applying climatic gradients Climatic gradients monthly values for minimum and maximum temperatures and precipitation are computed for each simulation point Local monthly gradients are obtained from a multiple linear regression equation fitted to the monthly minimum and maximum temperature and precipitation when needed observations from the 24 nearest stations in the Normals Database The regression equation 1s Tmin Tmax or Precip a b Elev c Lat d Lon where b c and d are gradients b is in C m c in C North and d in C East for temperature mm m mm North and mm East for precipitation When the elevation of the simulation point is too different from that of the nearest station BioSIM blends these local gradients with regional grad
5. z be used in this simulation Exposure factor Albeda Conifer canopy Number of normal stations to match Number of normals stations to match with each simulation location 32 Defining and Running Simulations Number of daily stations to match Number of daily stations to match with each simulation location activated only when the Daily Data radio button is checked Temperature Generator Parameters Exposure factor Albedo select None or Conifer canopy to calculate the overheating of Input Database and Time C Normals data Humber of pears 2 daily maximum temperature caused by exposure to Daily data aie po sunli ht Single year simulation a 6 Multiple year simulation Tr Normals Database used Canada U 54 1971 2000 Daily Database used Sample 2002 2003 Stations Match When the simulation model selected can use several years of weather input the TempGen interface has the following form Temperature Humber of normal stations to match First Year Last Year First and last year of simulation inclusive Number of daily stations to match Exposure factor Albedo Conifer canopy bl Other fields are as defined earlier 4 3 Location Lists Location lists are lists of simulation x locations for which a model needs Location Lists 2003 Daily Stations es to be Tun They are managed Random Locations Cancel through the Location
6. Bios IN nn RD uen bi tenus meme ouioui 11 2 1 Weather Reine ASSIS nn Ur M ace mens mia 11 2 11 Choice of the best sources of weather data Rs 11 21 2 Adjustment for climatic gradients ss 12 2 1 3 COF CUORIOrSIOpD and ASPECT nn NA NM nil 12 2 1 4 Generation of daily values from monthly normals 12 Pam Day DE 1p CA LON ps oie lia a en io nl do eects 13 2 1 6 AXSSEIMDLY Ol NG POSING end ne nn de nette 13 Dede Weather Data DASES 2 nee nero ln eme os A 13 2 2 1 Consulting and modifying the weather databases ccccccccccccceeeeesseeeeeeeeeeeeeaas 14 23 Normals Database se Ra ane in tan tale 14 2 3 1 Consulting and modifying the Normals Database 15 2 32 Nomas ETORMAIOS RE Re ame inde ea tie 16 23 3 Record structure of the Normals Database 16 2 4 D HAVE OLE CAS ALAA Coie ties aztec ales gn aes leah elec ea ea nO eee awaken 18 2 4 1 Consulting and modifying the 5 day Forecast Database 18 2 4 2 Forecast Editor CAO nement aa NEERA ba ai E 19 2 4 3 Record structure of a station s forecast data in a forecast file ceeeeeeeeeeeeeeees 19 2 5 Dany Database nerean a a A eat 20 2 51 Consulting and modifying the Daily Database ee ccccccccccceeeeseeeseeeeeeeeeeaes 20 252 Day Database FOr NN De de le anis 21 253 Consulting and modifying linked data files wea cseccceseccececeeeeeeeeeeeeeeeeeeaas 22 2 5 4 B PUR AS roe AA a CS ONE OP E T 22 259 ID EUR ADS ata RU
7. Daily Database 5 day Forecast Database Normals Forecasts Daily Data Models Database Forecast Stations List Data Type Filter No filter DESCHAMBAULT each 5 day forecast applies to a specific location or station the coordinates of which are also in the 5 day Forecast Database This database is contained in a file with the extension forecasts The file must have the same name and must reside in the same directory as the Daily Database to which it applies If this directory 1s different from the project s Weather sub directory it is specified via the Options dialog Default Daily Directory C Program Files SCF QuebecBioSlM Projects 4 0 ang E Options C Program Files SCF Quebec weather L Ecosyestemes Foreshiers BoSim weather weather Fath C Program Files S CF Quebec BioSlM Projects Demo iW eather S am 2 4 1 Consulting and modifying the 5 day Forecast Database The 5 day Forecast Database is accessible in BioSIM through the Database Editor dialog Forecasts tab The first field 1s a combo box that lists all the databases found in the set of current directories applicable to the 5 day Forecast Database type If the desired database does not appear in the list the corresponding Daily Database must either be copied into one of these directories or the appropriate directory must be added to the directory list by clicking on Sions Buttons and fields available in this p
8. Database Sample 2002 2003 and click on Jin the Model Input Editor dialog to accept these new parameter values Location List Editor Location Lists Location list Click on the Define LocationList button to the right of this field This opens the Location List Editor Click on type in the name of a new location list 2003 Daily Stations then click on _ addline and specify the name and coordinates for each of the four daily weather stations in the sample Daily Database provided with the BioSIM installation see figure below Once this is done click on L to save the new location list 2003 Daily Stations Random Locations File format DESCHAMBALULT VILLEROY QUEBEC VALCAR TIER Tutorial Model Input Editor Ea Model name tg Temperature Generation Hew Import Rename Set as default Model Input Directory C Program Files SCF Quebec Bio M Proects Oemo hdodel Input Temperature Generator Parameters Input Database and Time Normals data Daily data fear 2003 Canada USA 1971 2000 T Sample 2002 2003 g Normals Database used Daily Database used Stations Match Temperature Humber of normal stations to match Number of daily stations to match Conifer canopy Exposure factor Albedo Ix 0 Cancel di Mew Delete Edit Import Degrees Minute
9. O0 Shoot density 500 Shage speciic survival rates 0 73 TE i E alsam Fir end O79 and 0 62 oth Eth 0 66 pupae Tree species The reference output type species the number and type of reference of each model output line 6 0 year day This reference can be temporal or rot Delete TE 2nd Emergence Type Precision fe Specify the name and type of each model output variable Output reference type Models in BioSIM usually output in time steps Each output line usually contains a time reference such as a date often a Julian day This field defines the type of output line reference used by the model In particular it is important for BioSIM to know how many output columns constitute the output reference Reference columns are used in output analyses Here is a list of output reference types available 55 BioSIM 9 User s Manual Name Nb of reference columns Description Hourly year day hour 3 Multiple year hourly 1 Daily1 Julian day 1 Single year mean daily Daily2 year Julian day 2 Multiple year daily Weekly 1 week 1 Single year mean weekly Weekly2 year week 2 Multiple year weekly Monthly 1 month l Single year mean monthly Monthly2 year month 2 Multiple year monthly Mean annual ref l Mean of all year Annual year l Annual 1 Other ref Model output variable definitions Other reference type non temporal Type Choose one of the following for each output variabl
10. We E precipitation in mm for one or several years the number of years is limited by the availability of weather data These data are Mii oie AWE Real time 5 forecast normals assembled from up to 20 stations in each of Past Future the three weather databases Normals 5 day Forecast and Daily Databases In assembling this weather regime BioSIM goes through the following steps Choice of the best sources of weather data Adjustment for differences in elevation latitude and longitude Correction for slope and aspect Generation of daily values from monthly normals Generation of daily precipitation Assembly of the regime Each step is described in detail below 2 1 1 Choice of the best sources of weather data The choice of the most appropriate sources of weather data stations for a given simulation point is based on two criteria Cartesian distance the nearest station s are selected on the basis of the straight line distance d between simulation point and weather station Differences in elevation Z are also used in assessing this distance X X P Y Y 100 Z Z Data year in selecting daily weather data sources the choice of a station 1s made from the subset of stations for which daily data are available for the specified year s of the simulation The number of stations of each type Normals Daily 5 day Forecast matched with each location can be set by the user between
11. definition line in the Analysis view of BioSIM s main window is selected then click on the 4 blue nails buttons on the toolbar or select Project and then Execute selected analyses from the menu loj x Individual Date Elevation The BioSIM progress task bar will appear briefly fase Graph Results To view the analysis results click on Bet This Station Name Latitude Longitude will open the Result window In the case of an 1 DESCHAMBAULT 46 6800 71 9600 3 June A 2 VILLEROY 46 4300 71 9300 108 24 May event extraction analysis the Results table is 3 QUEBEC 468000 713800 73 31 May 4 VALCARTIER 46 9000 71 5000 168 4 June somewhat different from an average output analysis Results table The same Graphs and Exports functions are available 64 Tutorial 8 3 Example 2 8 3 1 Step 1 Defining and running a simulation Click on 4 Ito the right of the x Simulations view of BioSIM s main window Description C ES cone ene ATE or select Project and then Add simulation Mot Degree Day Summation x ModeHep from the menu bar This activates the Simulation Inputs 3 F Model Simulation Editor dialog with which a new ee riers eee TE T t tor T Define TG Input simulation can be added or an existing EE Fe FRERE Te i A Location list Random Locations Define Location List simulation can be edited Weather Station Matches 1 Descripti
12. dialog e They can be in one of several common formats such as USGS DEM ArcInfo native or export grid ASCII or Binary or Idrisi 16 or 32 bit and in one of several projections e g geographic Lambert Albers UTM State Plane Double stereographic etc Defining and running a simulation for mapping The key to producing a TEM in BioSIM is the generation of a suitable location list within the simulation definition In particular the location list must contain a sufficiently large number of simulation points gt 100 distributed more or less evenly over the entire extent of the input DEM and covering as much as possible of its range of elevations BioSIM s Location List Editor 1s quite useful in generating such location lists offering a range of methods and allowing to take slope and aspect into consideration not recommended at scales beyond 1 100 000 Defining and running an event mapping analysis Once an appropriate simulation has been run its output can be analyzed for mapping by defining and running an event mapping analysis The results of an event mapping analysis include 25 BioSIM 9 User s Manual e an event extraction output table summarizing the event values obtained for all locations e across validation analysis comparing the event values in the event extraction table with values estimated for each location by the interpolation mapping algorithm and e a TEM in the same format as the original DEM T
13. event I e Type in a useful description of the analysis to Main Event be performed e g End of year DD gt 5C oo Za Event type Maximum value of daily sum Select Daily sum as output variable and Event date range 995 to 21 O0 Event cnteror K a Maximum value of daily sum as event type Transformation one al Map Transformation e In the Map transformation group select Interpolation method Regression x Val Quebec30_as as the input map elevation and MP t map etevation Qusbec30_as Ella Output map ewent ddabove Bit type in DD_above_S as the name of the output map No data flag 9999 Precision if possible jo Wap director C Program Files S CF Guebec Bo Projects Demo M ap utp Click on ICK On To run the analysis Make sure that the new analysis definition line in the Analysis view of BioSIM s main window is selected then click on the 4 blue nails button on the toolbar or select Project and then Execute selected analyses from the menu The BioSIM progress task bar will report task progression 67 BioSIM 9 User s Manual To view the analysis results Click on Est Results of mapping analyses include cross validation verification of the goodness of fit between model output and map To view the event map Click on Me to the right of the analysis view of BioSIM s main window This will send the event map to
14. flight in the northeastern US with BioSIM Pages 99 103 in Integrating Spatial Information Technologies for Tomorrow GIS 97 Conference Proceedings February 18 1997 Vancouver BC R gni re J Sharov A 1999 Simulating temperature dependent processes at the sub continental scale male gypsy moth flight phenology as an example Int J Biometeorol 42 146 152 R gni re J Lavigne D Dickison R Staples A 1995 Performance analysis of BioSIM a seasonal pest management planning tool in New Brunswick in 1992 and 1993 Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Sainte Foy QC Information Report LAU X 115 R gni re J Lavigne D Dupont A Carter N 2007 Predicting the seasonal development of the yellowheaded spruce sawfly Pikonema alaskensis Hymenoptera Tenthredinidae in Eastern Canada Can Entomol 139 365 377 R gni re J Nealis V Porter K 2007 Climate suitability and management of biological invasions gypsy moth in Canada Biol Invasions in press Tran J K Ylioja T Billings R F R gniere J Ayres M P 2007 Impact of minimum winter temperatures on the population dynamics of Dendroctonus frontalis Coleoptera Scolytinae Ecol Appl 17 882 899 BioSIM Overview 1 2 BioSIM Installation 1 2 1 Technical support BioSIM is distributed without charge However the Canadian Forest Service cannot offer extensive free technical support Neverthel
15. in a distinct project directory composed of a project file extension BIO automatically associated with BioSIM at installation and several sub directories Assuming that a user has created a project named MyProject the directory structure of MyProject would be as follows C Program Files SCF Quebec BioSIM Projects is the default location for BioSIM s project directories but projects can be stored at any location on the disk E LD MyProject D Loc Location lists 2 MapInput Project specific DEM 2 MapOutput Output event maps O Model Input Model input parameters CD Output Analysis outputs graphs and export files CD Tmp Simulation and analysis results usually for internal BioSIM use d weather Local weather databases BioSIM Overview In this example the file MyProject bio is the project file and it contains the definitions of simulations and output analyses All BIO files are binary files accessible only through BioSIM 1 3 6 Preliminary set up These directories apply to all projects Horne C Program Files SCF Quebec Bios Models C Program Files SCF Quebec Bios Models Show directories for Normals data C Program Files SCF Quebec weather Once weather databases have been obtained running BioSIM is relatively simple First however it is important to make sure that BioSIM global directories are set to the appropriate locations with the Directories page of the Options dialog s
16. list box This list is used in the Advanced Simulations dialog to vary parameter values Caption Text appearing in the Model Interface dialog next to the parameter s field Default Default parameter value Min Minimum allowable value for numerical parameters Max Maximum allowable value for numerical parameters List List of choices for list parameters Hide Fom Show Form Show or hide the Model Interface window __tet_ Display how the model interface will appear in BioSIM Liste Delete a parameter and the associated fields in the model interface Parameter types Boolean True False parameter Integer Integer parameter _ Real Real decimal parameter _ Sting String text entry parameter _ Header Header free text to appear in the model interface File File name parameter the model will receive a string containing the file name it List parameter the model will receive a 0 based index of the selection _Lne Horizontal line to appear in the model interface To add new parameter click on one of the buttons above and click on the Model Interface window You can change the parameter order by dragging parameter names to the desired position in the list Model Interface window The Model Interface window is used to change the appearance of the Model Input dialog By clicking and dragging you can change the size the dimension and the position of all interface elements in the form To add a
17. minima Ist order autoregressive term for maxima 2nd order autoregressive term for maxima Cross correlation of daily minima and maxima Finally two values describe monthly precipitation Average monthly total precipitation Standard deviation of the ratio of observed monthly total to normal precipitation Example of an entry in the Normals file EDMONTON INT L A ALTA 53 3167 113 5667 723 1 1 1 19 7 9 0 8841 9 5393 9 7516 0 8722 0 1204 0 9628 0 1967 22 8 0 834 16 3 4 6 0 8743 8 73 8 939 0 8087 0 0299 0 9522 0 1477 12 9 0 624 9 9 1 0 8171 7 3356 6 5616 0 8534 0 0792 0 8812 0 1159 16 1 0 598 2 2 10 7 0 6188 4 1671 6 187 0 6865 0 0115 0 8102 0 1262 26 1 0 625 3 4 17 4 0 4717 3 3303 5 404 0 4963 0 0416 0 6779 0 0548 50 1 0 531 7 1 20 5 0 2991 3 0297 4 1751 0 4592 0 0013 0 6355 0 0904 87 7 0 473 9 5 22 2 0 3634 2 6492 3 7983 0 4719 0 0226 0 6293 0 0953 95 2 0 415 8 3 21 7 0 4689 3 1516 4 6102 0 4991 0 098 0 7032 0 0936 70 3 0 575 3 3 16 8 0 4479 3 4832 5 8635 0 5925 0 002 0 8191 0 1633 47 2 0 638 2 4 10 9 0 6072 4 1208 6 2504 0 5893 0 0434 0 7762 0 1072 19 8 0 745 10 9 0 4 0 7963 6 6897 7 2236 0 7588 0 0195 0 8696 0 083 17 5 0 778 16 7 5 8 0 8722 8 8328 902 0 8252 0 0813 0 8574 0 0949 17 2 0 588 17 BioSIM 9 User s Manual 2 4 5 day Forecast Database contains weather forecasts for the present day and following four days Le minimum and maximum air temperature and precipitation when used As in the
18. outdated Lei Add a new analysis relating to the highlighted simulation in the Simulation list view Access the Results frame Available once the analysis has been executed _ Stow Map Show the resulting TEM with the ShowMap utility Applies only to event mapping analyses Lts Delete the selected analysis The definition of an existing analysis can be viewed or modified by double clicking on it 39 BioSIM 9 User s Manual 5 1 Defining an Analysis An analysis is defined with the Analysis Editor FETE xl dialog There are three forms for this dialog summan tpe Evert Extraction ok depending on the type of analysis being defined in fomen Cae Summary type BioSIM can perform three types of analyses e Average output analyses are used to average model output variables over replicates and selected locations in the location list Hence the results are time series that are similar to the original model s regular output but averaged over a number of model runs see Average Output Analysis Editor e Event extraction analyses are used to extract some statistical features from one of the model s output variables e g its value on a given date or the date on which it is at its maximum This feature is referred to as an event The analysis generates one event value for each location and replicate in the simulation These values can be presented individually or averaged over replicates see Event Extraction Editor
19. patterns in eastern North America to forecast events in insect pest management Environ Entomol 23 1368 1380 R gni re J St Amant R 2007 Stochastic simulation of daily air temperature and precipitation from monthly normals in North America north of Mexico Int J Biometeorol 51 415 430 It has been applied to plant ecology Andalou C Beaulieu J Bousquet J 2005 The impact of climate change on growth of local white spruce populations in Qu bec Canada For Ecol Manag 205 169 182 Ung C H Bernier P Y Raulier F Fournier R A Lambert M C R gniere J 2001 Biophysical site indices for shade tolerant and intolerant boreal species For Sci 47 83 95 It has been applied to several insects including spruce budworm gypsy moth bark beetles and sawflies Carroll A R gni re J Logan J A Taylor S W Bentz B J Powell J A 2006 Impacts of climate change on range expansion by the mountain pine beetle Natural Resources Canada Canadian Forest Service Pacific Forestry Centre Victoria BC Mountain Pine Beetle Initiative Working Paper No 2006 14 Carroll A L Taylor S W R gni re J Safranyik L 2004 Effects of climate change on range expansion by the mountain pine beetle in British Columbia 2004 Pages 223 232 in T L Shore J E Brooks et J E Stone eds Mountain Pine Beetle Symposium Challenges and Solutions October 30 31 2003 Kelowna BC Natural Resources Canada Canadia
20. the ShowMap utility PER inix File Edit View Layers Tools Help Cea S Ble to Z me BE BR AOLE me A View Bar 7 Laver View bel I ameriquenord shp Geographic el fh BS Random Locations loc Geographic dd_above_5 flt Geographic E 1100 1250 MN 1250 1400 M 1400 1550 MN 1550 1700 M 1700 1850 M 1850 2000 M 2000 2150 iE 2150 2300 20 50 42 sate ae bi 4 Geographic Ready 68
21. threshold temperatures Fluctuations of temperature across 12 Weather Data in BioSIM thresholds result in a net acceleration of development warm temperature accelerates development more than cool temperature decreases it Thus simulations based on normals mean temperatures underestimate development compared with actual fluctuating temperatures The need for stochastic variation in normals was discussed in R gni re amp Bolstad 1994 The method used in BioSIM to generate daily values from monthly statistics is described in R gniere amp St Amant 2007 2 1 5 Daily precipitation Monthly precipitation normals average and variance are used to generate simulated daily precipitation which is distributed stochastically within each month according to the daily range of temperature The higher the range the less likely it is that precipitation will occur If the simulator predicts precipitation on a given day the amount is also inversely proportional to the day s temperature range Total simulated monthly precipitation is also a random variable determined from the mean total normal and its variance also contained in BioSIM s Normals Databases The details of daily precipitation generation from monthly normals by BioSIM are given in R gni re amp St Amant 2007 2 1 6 Assembly of the regime Temperature regimes are assembled in the following manner First adjusted and weight averaged daily randomized normals fill t
22. tin OU 46 6 3 1 Denmns a graphes nee ae diese 46 6 3 2 AVers ODU STAPS dense nee eee ien 47 6 3 3 E V nte lt tachon2D S Raph DR E 47 6 3 4 Eventextracion o D iA Ons ee E A 47 oA DZS BDU OSA EPON iena a E a ne deu Re 48 6 4 1 Expor Malol ea iles 48 6 5 Multiple Analysis DIO oegi r ne a a 49 0 0 Validation Commandin a E A 49 6 7 Clean UP ecenin a a E E 49 F MOIS UE BIOS IMG ere de 51 7 1 Adding a New Model or Modifying the Model Base 52 7 1 1 Moder Etraon eane das a naine dire 52 4152 SA 06 ere as D a D dd 53 7 1 3 Model parame lets SR Re AN EN Pen et 54 7 1 4 Output Yalta DIOS 05 nee eme Mehdi diet indie ie 55 7 1 5 Mode ESOC E sn a A entente Sac 56 7 1 6 Mode ldocumentat OMe csiis E A E E dees 37 O TUONA e E tat ae Guo aan deere esse 59 8 1 Initial Set up Directories Links and Projects ecseri iki cuitonnees 59 oT RAD Sn a ne de ee on ene 60 8 2 1 Step 1 Defining and running a simulation 60 8 2 2 Step 2 Defining and running an average output analysis 62 8 2 3 Step 3 Defining and running an event extraction analysis 64 8 3 D Re a ne ci Da 65 8 3 1 Step 1 Defining and running a simulation 65 8 3 2 Step 2 Defining and running an event mapping analysis 67 VI 1 BioSIM Overview 1 1 Introduction BioSIM is a software tool designed to assist in the application of temperature driven simulation models in pest management It can also be used as a tool in the dev
23. which can also 13 BioSIM 9 User s Manual be used to modify the list of directories in which BioSIM should look for weather databases and maps NOTE The global weather directories apply to all BioSIM projects and changing them will affect the source of weather data used in all subsequent simulations The user should verify that the weather directories are set properly before running models 2 2 1 Consulting and modifying the weather databases The Database Editor interface is a property sheet CET xl each page or tab of the property sheet is used tO Normals Forecasts Daily Data Models select the type of database you want to consult or modify Normals 5 day Forecast Daily Data or Models BioSIM s model base The first field of each page is a combo box that lists all databases found in the project s weather sub directory or in the set of global directories applicable to that database type modified through the Options dialog If the desired database does not appear in the list it must either be copied into one of these directories or the appropriate directory must be added to the directory list NOTE If the combo box is empty BioSIM is probably unable to find the selected database Verify that the relevant directory is properly set You can change the weather directory by clicking on __ Stins Each page of the Database Editor s property sheet presents different dialog elements buttons and fields For an ex
24. 03 9 4564 VALCARTIER 21 mai 475256 29 2470 VALCARTIER z22mai 37 7063 37 0571 LMI CAOTICO a ee le a7 CiO Eesults SF ee io 00 OO SO oo le 200 oO oo So oo oo DS SOS SOS IS SOS IS IE OOo SOS ooo OOo SOS ooo 6 2 Event Extraction and Event Mapping Results The event extraction or mapping Paie results panel shows the table of analysis Station Name Latitude SI 0 fad results location coordinates including 5 ESME DELNE TaI Aae e go p 2 3 ST GEQRGES 46 1500 70 7000 166 i 0 152 elevation slope and orientation and Jfa ST PROSPER 46 2167 705000 282 0 0 0 156 1 VUE VALLEE JONCTION 46 3633 70 9333 152 0 I 0 152 any varied parameter values when B HONFLEUR 46 6833 r0 8500 175 0 I 0 156 1 1 i ST CAMILLE 46 4653 70 216 396 0 0 0 160 applicable along with event values a STE GERMAINE 46 4167 0 4667 4517 0 I 0 155 J STE LUCIE 46 7333 00167 343 0 0 0 153 10 SAINT MICHEL 46 666 f0 6833 69 0 a 0 155 Menpan z In event extraction analyses and event mapping analyses results can be listed by Individual event values or Means If the Means format is selected mean event values averaged over replicates standard deviation and number of replicates with non missing event values are 45 BioSIM 9 User s Manual listed If the event is a date values can be displayed as calendar dates by selecting Individual date or Mean date Xvalidation Applicable to event mapping analyses to view the cros
25. 46 43 71 93 108 0 0 QUEBEC CITY 46 8 71 38 73 0 0 VALCARTIER 46 9 71 5 168 0 0 4 3 3 Matched Stations dialog Matches for location list 2003 Daily Stations E x This dialo g lists which Temperature Generator TG Input 2003 v Define TG Input Apply to simulation weather stations BioSIM ee Year of match 2003 yi Cancel matches to locations in the tareticcation s Name Lat La lon lon Eev Dit Weigh simulation s location list DESCHAMBAULT 460 40 71 57 given the selection criteria currently defined in the simulation s temperature generator input Normals c Program Files SCF Quebec Weather Canada USA 1971 2000 Normals DESCHAMBAULT QUE 55 15 ST ALBAN QUE 4 STE CHRISTINE QUE 55 152 STE CROIX QUE 46 70 The search algorithm looks through the three weather databases Normals Daily and 5 day Forecast and reports the stations matched in the panels on the right side of the dialog window Daily c Program Files SCF Quebec BioS IM Projects D emo Weather S ample 2 Daily Graph DESCHAMBAULT 46 40 71 57 61 0 100 VILLEROY 46 25 71 55 108 28 0 Forecasts D berett i and L Arsbtosmusin The dialog allows the user to change the temperature generator input used in the matching and to apply these changes to the simulation Data Type Filter Matching can be done for temperature and precipitation Year of match When a multi year simulation is using daily data as input stat
26. 7 0 21 0 10 0 1990 131 3 5 8 0 0 0 1990 132 1 5 17 0 0 5 1990 133 7 0 13 5 0 0 1990 134 1 0 20 0 1 0 1990 135 9 0 20 0 0 0 1990 136 6 5 17 5 0 0 1990 137 5 0 12 0 0 0 23 3 Maps in BioSIM BioSIM maps model output features events at the landscape level using one of two methods universal kriging with elevation as drift variable or spatial regression The latter is a simple algebraic transformation of an input DEM of the area to be mapped The transformation is performed during an event mapping analysis of simulation output The resulting map is called a target event map or TEM in BioSIM terminology The two ingredients required for mapping an event with BioSIM are 1 an input DEM that has been adequately linked to BioSIM and 2 a simulation conducted in several locations on the territory covered by the input DEM The map resulting from an event mapping analysis is stored in the project s MapOutput sub directory in the same format as the input DEM Input DEM e are stored in the MapInput sub directory of a specific project which is always searched first or in one of the global map directories specified by the Options Directories property page or e are associated with BioSIM through their projection information contained in a INFO file called a map association that can be created with the Map Editor dialog e An associated PRJ file contains the DEM s projection information It can be modified using the Map Editor
27. Define TG Input from the drop down list This 1s the e R g Location list 2003 Daily Stations Define Location List simulation model that will be used for this Weather Station Matches example Replication fi Adyanced 3 Simulation Inputs Number of files generated 4 locs 1 params x 1 reps 4 Approximate duration Diseconds Model We will use the default values for aboutthe model selected the parameters of the n Spruce Budworm R gni re s process oriented model of spruce budworm seasonal biology Biology model therefore we can leave this This process oriented model was developed by R gni re 1992 Variability in development rates is handled by the method of R gri re 1984 Oviposition ts simulated accoding to 1 se 9 R gni re 1983 Additional refinements were made by R gni re 1987 1990 The feeding field to Default and defoliation components were described by R gni re amp ou 1991 To provide for better OF Cancel 60 Temperature generator Click on the L Dereta button to the right of this field to define temperature regime assembly parameters Two dialogs will appear In the Model Input Editor click on land type 2003 as the name of the new set of parameter values to be defined then click on This will activate the temperature generator s model interface Select Daily Data and type 2003 in the Year field Select the Daily
28. E Cold Tolerance annual MFE Cold Tolerance daily the BioSIM models directory and then access the Model Editor dialog Tools Database Editor Models tab Default Models Directory Ci proectBioSIM Release Models Path D project BioSIM R lease Models The list panel contains all models currently linked to BioSIM on the user s system This property page of the Database Editor offers the standard and Et buttons used to add a new model or to edit the model base s information about an existing model through the Model Editor dialog The __ _ button is used to create a new model interface from an existing one 7 1 1 Model Editor dialog Model Category Population_ dynamics Model Hame SafranyikLogan The Model Editor dialog is accessed from the Tools Database Editor menu selections g letters or digits Models tab This editor is used to create E E or DLL Name SafranyikLogan dl new model interfaces or to edit existing Language Engin interfaces The Model Editor is composed of six panels The first called the General panel contains information on six topics Description 52 Models in BioSIM Model Category A general classification of models Model name Name of the model Model ID The model s 8 character ID code must be unique in the model base EXE or DLL Name Name of the model s executable file exe or dll Language Language of
29. List Editor dialog The Location List Editor is used to Fie foma Desses Minutes ex 45301 f Decimals Degrees ex 45 5 create modify or delete location Longitude lists A location list is a collection DESCHAMBAULT 71 96 6 R VILLEROY 71 933 108 of simulation points for which faueeec 73 73 VALCAR TIER 1 5 168 BioSIM should run simulations Upper panel Contains the names of all location lists currently r e Default LOC Directory sub directory Create a new location list Delete Delete a location list Edit Edit a location list with the notepad make sure you respect the format Import Import a Location list file from anywhere into the LOC sub directory it File format selector radio button e Degree minutes Enter display and save latitude and longitude in degree minute format e Decimal degrees Enter display and save latitude and longitude in decimal degrees 33 BioSIM 9 User s Manual Lower panel contains the locations found in the currently highlighted location list Add Line Add a new empty line at the bottom of the list Generate Generate a series of points and add them to the list Delete Line Delete the line containing the cursor _ Show Show the location list in ShowMap 4 3 1 Location List Generation dialog The Location List Generation dialog is used to generate a location list D xX Generate From Digital Elevation Map DEM al
30. MyExport csv Cancel existing file click on _ to the right of the field If no path is specified the file is written in the Default path the project s output sub directory File format BioSIM three formats e ASCII text files Space Tab or comma delimited csv exports in File format asc witth comal ce Fields to be exported Fields not exported Station No Exposure Station Mame Latitude Longitude Elevation Slope Up Orientation The selection of variables to be exported is contained in the right side panel Variables can be removed by highlighting and transferring them from the right to the left panel with and vice versa with gt Their order can be altered with the 4 and 2 buttons 48 Examining Analysis Results 6 5 Multiple Analysis Dialog Use the Multiple Analysis dialog to display variables from several average output or event extraction analyses on the same graph or in the same export file This dialog is available from BioSIM s menu Project Export Multiple Analyses There are two types of multiple analyses average output and event extraction Top list box Select the analyses from memea xl which you want to include variables Analyses Analjses selected Bottom list box Select the variables you want in the graph or export Note For average output analyses dates or temporal references are exported only once as the results are m
31. Random Locations __Define Location List normals defined in Temperature generation _Weather Station Matches input there is a need to replicate the runs pepicaion o the Replication field in the Simulation Editor dialog should be set to 10 Number of files generated 200 locs 1 params 10 reps 2 O00 Approximate duration 02 minutes 24 seconds About the model selected BioSiM s Degree day model This i general purpose degree day accumulator It calculates DD t DD t 1 ddit where t is in days and ddft is computed by two methods El cence _ To run the simulation make sure the new simulation definition line in the Simulations view of BioSIM s main window is selected then click on the 2 red nails button on the toolbar or make select Project and then Execute selected simulations from the menu The BioSIM progress task bar will report the progress of the simulation task a total of 200 locations x 10 replicates 2000 simulations 66 Tutorial Step 2 Defining and running an event mapping analysis Click on 4 to the right of the Analysis view of BioSIM s main window or select Project and then Add analysis from the menu bar e In the Summary type pop down field select Event mapping The dialog will change and summay ype FRET will take on the form illustrated here Description EndofyerDD gt 5C and Validiy range 1e 007 To le 007 Compound
32. SSE aa a E 23 IVA AOS iir B105 LIV arenas asc ore Rd nada nant idee ii du aie 25 3A Map Editor Dralo tisi a a e a A 26 Si Projection diiloni RS RAR nn ie 27 Defining and Running Simulations sie 29 4 1 Creatine a NCW PLO CC ices A Ad nt ie init 29 BioSIM9 User s Manual AD Demmin SIMULATIONS asses de SSSR nt is nie tie nt E 29 4 2 1 Sim l ton Editor AIO deoedswsadndsvendentsensudesdivendvanduynadnd e aiT 30 4 2 2 Mode kInput Edilio saa das teres rece a a nenes annie nee 31 4 3 Locion ASS RS Sr ne ohare ee die 33 4 3 1 Location List Generation MAO RES M RAR NN a 34 4 3 2 Locanon List Catan lS SR E a nd ee 35 4 3 3 Matehed SAUOnS dalog aesa AESA EENS 36 Ae AdyancedSimulinon Dial 8 evies haticceecerdsaveching ies sashsbetbigetuceras suateeade wens attiies ss 3T 4 5 Running Simulations Creating the Output Database sossssseeenssssssseoeresssssssssserssssss 37 3 WDetmins and RUNMIiS Analy SCS SRE Re rm dresse entente done 39 5 1 De Home A Anay S18 ii ceases a le ice a arene ees 40 oy AVerace output analyse Serrie i a CM RS CNE Se 40 5152 Event extraction analyses ss mintaniomeiinehammblaniunnebsitnelesetintan til 41 5 1 3 Eyentinappine ANALY SOS En En an einen 42 2 RONDE AMAR VS clo gern nai de eue nt ae ae Re it rset tm 43 O EX AMIS ANAVSIS RoS sca nctas eas ec tales ean a a toesacawes 45 6 1 Average OUMU RESUMES siparo o ee douane dun inde 45 6 2 Event Extraction and Event Mapping Results 45 6 3 GAP VIEN Ra RE Sec ae tn
33. a forecast becomes outdated it is disregarded by BioSIM Forecasts are only used in actual forecast simulations when the year being simulated matches the year on the system clock Example of a 5 day forecast record QUEBEC Que 46 800000 71 216667 90 1 105 2 0 7 0 0 0 2 0 6 0 0 0 6 0 6 0 0 0 1 0 9 0 0 0 4 0 10 0 0 0 19 BioSIM 9 User s Manual 2 5 Daily Database Normals Forecasts Daily Data Models The Daily Database is composed of an index file Database Sample 20022003 listing the available daily weather stations and references to the files of a sub directory containing Data Type Fiter MEIA Daily Stations List the actual daily weather records The sub directory YeaFiter romte x _ New containing Daily data files all with wea extensions Tia Edt bears the same name as the index file which has the Show extension dailyStations The index file must be vers located in one of the daily data directories set via the Delete Options dialog Add Forecast Import stations rep 2 5 1 Consulting and modifying the Daily Database l Default Daily Directory C Program igs eE Options C Program Files SCF Quebec weather U SEcosystemes Foreshers BoSin weather weather The Daily Database is accessible in BioSIM through the Database Editor dialog Daily Data tab Fath C Program Files SCF Guebec Bio M Proects Demo tw eather S am The first field 1s a combo box that
34. abases models model input and location lists and compares them with the output database files created by simulations or analyses 43 6 Examining Analysis Results Analysis results can be viewed once an analysis has been successfully executed by clicking on the button on the right of the Analysis panel of BioSIM s main window This opens the Analysis Results frame which contains three panels Results Graphs and Export The Results panel presents results in tabular form There are two variants of the Results panel the first for average output analyses and the second for event extraction and event mapping analyses The Graphs panel contains graph definitions to be applied to the results in the Results panel The Export panel contains the definition of export files to access analysis results outside of BioSIM 6 1 Average Output Results The average output results panel shows the date and the mean value of each model output variable on each date averaged over replicates either by location or averaged over locations Gf more than one location was chosen for averaging and depending on whether the Average over selected locations checkbox in the Analysis Editor dialog has been checked or not VALCARTIER 14mai VALCARTIER Tomar 39 944 3 9414 VALCARTIER 16mai 9 9011 19 5633 VALCARTIER Tima 245653 433459 VALCARTIER 18 mat 29 3549 70 46 VALCARTIER 19mai 14 6298 80 6966 VALCARTIER 20 mat 4 6772 1 07
35. active requests for input and print no run time information on the computer s display e accept as their sole command line argument the name of an input parameter specification file In BioSIM models are independent applications called executable files with EXE or DLL extensions that have no user interface and run without requiring interaction with the user and without output to the display BioSIM executes each model run of a simulation task either by spawning the model as a child process through an operating system call to the model s executable file or as a call to the model s DLL In the simplest applications the call to the model contains a single argument the name of a parameter file that the model s executable must open and read The input parameter file is created and managed by BioSIM It contains at least two records the path of an input weather data file named and created by BioSIM and the path of an output file named by BioSIM but created by the model Models may have a series of additional parameter values specified in this file and controlled either by the user or by BioSIM as defined in the model s Inputs definition part of BioSIM s Database Editor utility The model must read these input parameter values in the same order as they are defined in the model s input interface The output files thus created by the model s executable are processed by BioSIM s Analysis module Adapting a simula
36. age of the Database Editor are as follows This button has no actual function for 5 day Forecast Databases Because a 5 day Forecast Database is in fact an extension of a Daily Database the 5 day Forecast Database is created automatically as soon as a new Daily Database is created x Delete a database For 5 day Forecast Databases this button deletes the forecasts in the Daily Database but does not delete the Daily Database itself L Nw Add a new station to the database This opens the Forecast Editor dialog __ Et Access the information contained in the database about the station selected in the list left of the button This opens the Forecast Editor dialog bete Delete the currently selected station from the database 18 Weather Data in BioSIM L sow Show all stations listed in ShowMap This is useful for visualizing the spatial distribution of weather stations 2 4 2 Forecast Editor dialog Forecast Editor x Definition When the or Et button is clicked in Name JDESCHAMBAULT Cancel the Forecasts page of the Database Editor dialog Degrees Minutes Seconds the Forecast Editor dialog appears for entry or ttu e ao fe eee modification of data on a weather station Longitude 7 457 5 pee current date for it to be used in a Elevation Et meters simulation Disable this station This dialog is used to modify or add a station in the 5 day Forecast Database First Day BioSIM only uses fo
37. alue of Y e Mean value of Y e Last time when Y lt K e Time when Y stabilizes tolerance K Event criterion This is the critical value K in the definition of the output feature to be extracted For example to determine the value of a variable on day 152 June 1 the event type is value of Y at time K and K 152 is the event criterion Event date range The analysis module searches model outputs in a time sequential fashion These two fields specify the output dates between which the analysis module is to search for the defined event By default this range is 999 2100 to cover multiple year outputs However any valid date range is accepted provided that start day lt end day Transformation The event value can be transformed e g log square root 41 BioSIM 9 User s Manual Compound events A compound event is one where two output features are related to each other through some relational operator For example the time between two events could provide the duration of a process When this checkbox is checked a secondary event group of fields appears in the Analysis Editor dialog The result of a compound event analysis is a relationship between two events Relationship This field is used to specify the relationship between the first E1 and the second E2 event E1 E2 Difference E1 E2 Sum E1 E2 Ratio E1 E2 Product Min E1 E2 Smallest Max E1 E2 Largest Mean E1 E2 Mean NOTE BioSIM als
38. anada USA Map projections can be changed easily with _ Otons the ShowMap application provided with BioSIM at installation The upper panel lists the existing map associations info files found in the current map directories If several INFO files bear the same name in the project s MapInput sub directory or in the various global map directories BioSIM lists them all but can only access the first one found The project s MapInput sub directory is always searched first To add or remove map directories use the _ Brion button _ 44 Add a new map association to the list If the DEM is not in one of the global map directories BioSIM asks if you to want to add the DEM s directory to the list The DEM must have a standard extension 26 Maps in BioSIM asc Arc Info export grid ASCII files Alt Arc Info export grid Binary files must have an accompanying fls file dem USGS format DEM mg Idrisi image files must have an accompanying doc file bil BIL files mosaic Mosaic map grouping files adf aux ESRI native grids hgt HGT files _Show Map Display the map with the ShowMap application Format Shows the format of the DEM DEM file Shows the full name of the DEM file _4eview_ Provides access to BioSIM s Arcview scripts for map modifications This requires that Arcview and the Spatial Analyst extension be installed on the user s computer Title Title used when showing the map with ShowM
39. ap Eresin Access to the Projection dialog No Data The NoData flag value used in ASCH Idrisi and USGS formats for missing data Map directories Shows the list of directories where BioSIM will search for map associations The current project s MapInput sub directory is always searched first 3 1 1 Projection dialog The Projection dialog lets the user g File Hame C Program Files SCF Quebec M aps Quebec Quebec30 as nfo consult or specify map projection parameters This information is used by m aed BioSIM to transform DEM into TEM or Geographic ef Unita Degree to display maps BioSIM does not perform map re proj ection but First standard parallel Latitude FIPS zone Second standard parallel Latitude Alabama East 101 ShowMap does ne ne nigin or centre latitude UK gone E 20 174 1 Drign for centre mendian File Name Name of the map s INFO False casting Scale factor fo file Ealse northing Azimuth jo Spheroid Same as To copy projection Type WGS 84 v Semimajor axis 6378137 information from another PRJ file Semiminor avis E356752 314245 Cancel which can be selected with the _ button 27 BioSIM 9 User s Manual Projection group Type BioSIM offers a wide range of projection types The most common are Albers Lambert UTM Stereographic and State Plane If the map is unprojected degrees latitude longitude select Geographic XY units Spec
40. applicable to the Normals Database type If the desired database does not appear in the list it must either be copied into one of these directories or the appropriate directory must be added to the directory list by clicking on _ Satins Buttons and fields available in this page of the Database Editor are as follows Create a new database When you create a new database BioSIM asks for the location in which to place the new database This location can either be the current project s Weather sub directory or a global directory Next BioSIM asks for the name of the new database Usually the name must be meaningful As a rule the location and period e g Canada USA 1971 2000 are used for the Normals Database x Delete a database This button deletes the Normals file itself use with caution Data type filter Select a filter to apply to the list of stations There are four possibilities e No filter show all stations available in the database e With temperature show only stations that have temperature data e With precipitation show only stations that have precipitation data e With temperature and precipitation show only stations that have both L Nw Add a new station to the database This opens the Normals Editor dialog _ Et Access the information contained in the database about the station selected in the list left of the button This opens the Normals Editor dialog iste Delete the currently selected station fr
41. atched and merged by temporal reference In the case of event extraction analyses the first eight columns location definition are exported 45 Sooke El only once Results are always matched and mie z Export Graph To PLT merged by location f es aw ere Output variable selection Variables selected defoliation And Emergence d Analyse 3 4th gt gt Up Down tik 6 6 Validation command The Tools Validation sequence is used to check the current validity of all simulations and analyses The validation algorithm compares the dates of weather databases models model input and location lists with the output database files created by simulations or analyses When a simulation is found to be outdated the related analyses are automatically outdated 6 7 Clean Up The Clean Up dialog is used to delete simulation output databases output analysis files and any other files from the current project s Tmp sub directory Once this is done simulation outputs and analysis results are no longer available 49 7 Models in BioSIM Simulation models that are suitable for incorporation into BioSIM s model base must e be weather driven accept daily minimum and maximum temperature in C and optionally precipitation in mm as input and output a series 1 2 n of lines containing the time output line reference and an arbitrary number of output variables e make no inter
42. aw ye ETES feature to be extracted called an event because Desctiption Date of Peak ath 4 sites 2003 Cancel it is often the date of occurrence of SOME Validiyrange 6007 Tofle 007 Compoundevent I significant event from model outputs by the ee analysis module Event extraction or Event outputvarable an Map ping analyses 5 Event type Time When 4h i maximum Event date range 999 to 21 o Event cntenon K E Validity range Range of event values Tanstoimation None E considered valid Any event value outside of this range is set to a missing value Event variable This field contains a list of the model s output variables The user selects which of these is to be examined for the desired feature Event type This field offers a list of statistical features that can be extracted from model outputs by the analysis module In the event definitions below Y stands for the output variable chosen and K for the event criterion when applicable The choices available are e Time when Y is maximum default e Time when Y is minimum e First time when Y gt K e First time when Y lt K e Last time when Y gt K e Last time when Y lt K e First time when cumulative of Y gt K here the output variable is summed up over tme and the cumulative sum is divided by its last value or maximum before extraction of the event date e Value of Y at time K e Maximum value of Y e Minimum v
43. be generated at random there are two distributions to choose from uniform or O centered normal Values generated are in the range 90 90 4 3 2 Location list data files Location list data files consist of lists of geographical locations These are space delimited ASCI text files There are two formats of location lists depending on whether the coordinates are in decimal degrees or degrees minutes Format 1 old format Coordinates in degrees minutes Each line of the file contains the following space separated fields e Name no space allowed e Latitude degrees e Latitude minutes e Longitude degrees e Longitude minutes e Elevation meters e Slope e Aspect degrees Example of an old format location list CHICOUTIMI 48 25 71 5 15 00 DRUMMONDVILLE 45 53 72 29 82 0 0 GASPE 48 46 64 29 33 0 0 LAVAL 45 32 73 42 3700 Format 2 new format Coordinates in decimal degrees space separated numerical values The first line of this file contains LOC_FILE 2 to indicate the file s format Each of the following lines refers to a location e Name spaces in location names can be kept by putting the name between e Latitude decimal degrees 35 BioSIM 9 User s Manual e Longitude decimal degrees e Elevation meters e Slope e g 100 45 degrees e Aspect degrees e g 90 East Example of a location list data file LOC_FILE 2 DESCHAMBAULT 46 68 71 966100 VILLEROY
44. can be specified by the user Graph title Title line for the graph 46 Examining Analysis Results X axis title Title of the X axis Y axis title Title of the Y axis The remainder of the dialog depends on the type of analysis results being graphed 6 3 2 Average output graphs The X variable is always the date or the Lo aurec 7 ariable s to be illustrated temporal reference of the model s output e g day month year etc and Emergence and adults ard male moths Ath average instar eqgs L1 EE population density defoliation Bth Graphs can only be done one location at a time in an analysis with distinct locations Variables can be added and removed from the oK Cancel graph by selecting them in the left or right panel and clicking on Bl or E The order in which variables appear in the right panel is their order of appearance in the graph 6 3 3 Event extraction 2D graphs X Pull down list of possible X variables b w 20 3D a scissa a Elevation o Value Precision Select a precision interval around ve A each mean none standard deviation or standard F Fit regression Degrees ine 2 error of the mean Fit polynomial Check this box to fit a regression line simple or polynomial Degree in X Degree of regression equation 1 simple 2 3 4 polynomial 6 3 4 Event extraction 3D graphs X Pull down list of possible X variables 2 2 5 aD widt
45. ce Budworm Biology Delete Import Rename Set as default met Import a Model input file from a location Re oer _ 5 C Program Files SCF Quebec BioSIM Projects D emoiM odel Input other than the project s Model input sub directory L Sew Create a new Model input file starts with model specific default parameter values iste Delete an existing Model input file L erae Rename the input file _Set as defaut Replace the model s current default parameter values by the values currently used in the dialog s fields 31 BioSIM 9 User s Manual Model interface example Each model in BioSIM has its own Stating population 100 Egg hatch model ae arn Model interface This is an example ied e of a Model interface Each field in A A m a a this dialog contains a parameter that mae oes jsa Jos fae foo can be modified by the user Some me oes fps fast Ps fos fix are real numbers some are integers sss some are Booleans true false some Oviposition date Gray Sawyer Mao Sawyer model version Tauberetal x are pull down lists and some are file names associated with a 2 browse numberof generations T Output cumulative frequencies No button Files that are local to the project can be specified in a file name field with the Project keyword For example Project Data Deposit dat points to file Deposit dat in the project s Data sub directory To speci
46. ch year M Modeluses 20 pears 1 750 of daily weather input Model uses year s of daily weather input The model may require a fixed number of weather data as input for example two for the gypsy moth phenology model never less never more In that case the Model uses x years box should be checked This is determined by the model s programmer When this box is checked the Temperature generator input interface is of the single year type The year specified then is the last year of data in the weather input Model uses precipitation Some models in BioSIM require precipitation radiation or vapour pressure deficit as input along with daily minimum and maximum temperature This requirement is fulfilled when this box is checked 53 BioSIM 9 User s Manual 7 1 3 Model parameters Add Boolean Inte er Real Striri This panel is used to define the input pen era TA parameters used by the model It is Variable type Integer Properties Caption Nb Generations n_ge Delete Default jig composed of two windows the Input Parameter window 1s used to define model interface elements while the Model Interface window described below is used to design the model s interface window as it will appear in BioSIM when the model is used in the definition of a simulation T Hide Farm NbGeneration Input Parameter window Parameter name Internal parameter name appears in the field above the
47. de longitude of a rectangular region in which to search for stations in the Region boundaries group Then select the weather station type either Normals or Daily Data the database and the filter 1f needed For daily stations the data year e g 2000 must also be specified specify 0 to get all available stations e Generating a random or a regular grid of locations Enter the corner coordinates latitude longitude of a rectangular region in which to locate simulation points in the Region boundaries group Specify the generation method regular or random grid then the elevation range elevations are generated at random the ideal method to avoid spatial autocorrelations when interpolating with multiple regression 34 Defining and Running Simulations Number of points Any number of points can be specified Note that for an adequate event mapping exercise it is recommended that n gt 100 When generating a regular grid point density in both directions is required north south east west Exposure This is a combination of slope and aspect as it relates to sunlight exposure which in turn affects daily temperature regimes overheating of the daily maximum If exposure values are to be included in the location list check the Generate exposure radio button Exposures are either calculated from the DEM available only when a DEM is used to generate the location list or generated at random Distribution When exposures are to
48. e Boolean Integer 16 bits Long Integer 32 bits Real 32 bits Long Real 64 bits Date or Text L nw Add a new variable to the list iste Delete a variable from the list This list is used in the Analysis Editor dialog 7 1 5 Model source The Model Source page provides information on the intellectual property and sources of the simulation model Intellectual property This line appears each time the model is run It is limited to 128 characters It can list authors or other intellectual property liabilities attached to the model Source This panel is used to list literature references credits for development acknowledgements and _ other useful information about the model BioSIM displays the credits for the currently selected model in the Simulation Editor dialog 56 Intellectual Property Source Models in BioSIM 7 1 6 Model documentation HelpFile Baai SSS The Model Documentation page provides a TestFormat Help link between the model and the model documentation in the form of a PDF or other type of file or in the form of simple text The Help file in the present example SafranyikLogan pdf must be placed in the B10SIM Models directory where the model executable and interface reside 57 8 Tutorial This tutorial s objectives are 1 to give the BioSIM user a general overview of the software s main capabilities and 2 to illustrate the sequence of actio
49. egative Precision This field determines the number of decimal places with which output is written in the output map 0 by default For example if the analysis result Event being mapped is a date it is likely that decimal places are not needed and this field would be left at 0 Map directory Shows the directory in which the output map will be written 5 2 Running Analyses Once an analysis has been defined and the simulation it refers to has been run the next step is to execute the analysis or analyses defined For the analysis to be executed it must be selected or checked when this type of interface is used The selected analyses can be run either by selecting Execute Analyses in the Project pull down menu or by clicking on blue nails in the main window s toolbar NOTE Whenever a change is made in a simulation s definition e g model parameter value or in the weather databases used as input for the model runs it 1s important to re execute the simulation to update its outputs database When a simulation is updated all the related analyses must be updated as well To run both selected simulations and analyses in one operation either select Execute All in the Project pull down menu or click on a red and blue nails in the main window s toolbar To verify the validity of all simulations and analyses use the validation tool Tools Validation The validation algorithm compares the update dates of weather dat
50. elect Tools Options Note that the user can specify several global directories for Normals Daily weather databases and Map directories by changing the target value in the Show directories for field These directories apply to the current project Weather DB C Program Files SCF Quebec Bios Proects D emor eat Input maps C Program Files SCF Quebec Bios Proects D emoh apl It is also useful to set the paths of applications hr C Program Files SCF Cuebec PI that BioSIM Can be linked to The paths to Showh ap D project ShowMap Release ae BioSIM s two main peripheral programs PLT p ShowMap are set automatically and usually do Spreadsheet C Program Files Microsoft Office OFFICE T1 ze9 not need review Others especially Arcview and ea the user s favourite spreadsheet software should be set by the user in the Links page of the Options dialog Another useful set of options can be found in the Advanced Options page of the Options dialog While these options are often adequately set up by default it 1S good to know what they are and Run simulations even if none of the simulation points is within how they are set 300 km of the nearest normals or daily station Wam when simulation point i farther than 500 km of the nearest normals or daily station e When simulation points are farther than a given distance from the nearest source of Run simulations even if there are
51. elopment and analysis of such models for purposes of scientific investigation However BioSIM s main purpose is to generate forecasts of features or events in the seasonal biology of pests or their host plants Forecasts are made by simulation models provided by the system and are based on regional air temperature and precipitation interpolated from nearby weather stations adjusted for elevation and location differentials with regional gradients BioSIM is of interest to any organization responsible for monitoring or managing insect pest populations in outdoor situations forestry agriculture horticulture BioSIM can be used to plan the timely deployment of sampling surveying crews and materials e g pheromone traps without the need for extensive phenology monitoring Also it helps time the application of pest control substances for optimal results Thus the use of BioSIM helps optimize the use of pest management resources in a cost effective manner The package is generic in the sense that it can predict the development of populations of any plant insect or plant pathogen provided that a simulation model for the organism is available The system can make forecasts or predictions for individual point locations but can also generate maps of phenological or other events when provided with a digital elevation model or DEM of the area under consideration These forecasts can form the basis of management plans aimed at the efficient de
52. ess questions may be directed to the developers at the following electronic addresses For general questions about the usefulness and approach of BioSIM contact Jacques R gni re at jregniere nrcan gc ca For more technical issues concerning the installation and use of the software contact R mi Saint Amant at rstamant nrcan gc ca Arrangements concerning major support needs may also be made through a mutual agreement between the user the Canadian Forest Service and the developers of BioSIM You can contact BioSIM developers by e mail at the above addresses or by regular mail Dr Jacques R gni re Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 du P E P S P O Box 10380 Stn Sainte Foy Qu bec QC GIV 4C7 Canada 1 2 2 Installation BioSIM is distributed on the Internet in the form of a set up file using the link ftp ftp cfl forestry ca regniere software BioSIM Download the file BioSIMxxx_set up exe where xxx is the most recent version e g 9_04 for release 9 04 in a temporary location on the destination computer Double click on the file s icon and follow the installation process BioSIMxxx_set up exe is an InstallShield application that will safely install BioSIM and other accessory programs developed at the Laurentian Forestry Centre in a directory tree specified by the user the installation program will suggest c Program Files SCF Quebec but a different root directory can be s
53. esults can be exported to a disk or to the user s spreadsheet software most simple in CSV format Try sending this export to your spreadsheet software now using to Spreadsheet Fields not exported L1 population density defoliation male maths X o Fields to be exported 8 2 3 Step 3 Defining and running an event extraction analysis Click on to the right of the Analysis view of BioSIM s main window or select Project and then Add analysis from the menu bar This activates the Analysis Editor dialog Set the Summary type field to Event extraction e Type in a useful description of the analysis to be performed e g Date of Peak of 4th Instar 4 sites 2003 Analysis Editor Simulation 1 Event Extraction Summary type Description Date of Peak 4th 4 sites 2003 Cancel Validity range E e 007 To f e 007 Compound event D Main Event Output variable Ath Time when Hh maximum to 21 O Event crternon K a Event type Event date range 999 None Transformation e In the Main Event group define the event to be extracted from model output Select the output variable to be analyzed 4 instar from the drop down list then select the event type from the drop down list In this analysis we want BioSIM to study the day when the 4th instar is at a maximum e Click on __ Run the analysis Make sure that the new analysis
54. everal simulations have been defined the next step is to execute them Simulations must be run before their results can be viewed or analyzed For a simulation to be run it must be selected in the Simulations view of BioSIM s main window or checked when that type of display is used Selected or checked simulations can be run either by selecting Execute Simulations of the Project pull down menu or by clicking on Al red nails in the main window s toolbar NOTE Whenever a change is made in a simulation s definition e g model parameter value or in the weather databases used as input for the model runs it 1s important to re execute the simulation to update its outputs When a simulation is updated all the related analyses must be updated as well To run both checked simulations and analyses in one operation select Execute All in the Project pull down menu or click on a red and blue nails in the main window s toolbar To verify the validity of all simulations and analyses use the validation tool Tools Validation The validation algorithm compares the update dates of weather databases models model input and location lists and compares them with the output database files created by simulations or analyses When a simulation is found to be outdated the related analyses are automatically invalidated When a simulation and or analysis task is launched a progress bar display appears to report on the progress of the task and gi
55. fy non default parameter values click on L new in the Model Input Editor window specify a Model input file name in the box and type the desired parameter values in the appropriate fields of the Model interface Then click on OK in the Model Input Editor window This saves the new parameter values in the specified Model input file TempGen temperature generator interface The TempGen interface is the interface for BioSIM s temperature regime generator TempGen The definition of the various parameters in this dialog is given below Most models in BioSIM require a single year of input weather data However some models support multiple year simulations For this reason the TempGen interface has two forms a single year and a multiple year form The single year TempGen interface includes the following fields Normals Daily Data radio button The user has the choice to run simulations from normals or from daily records Temperature Generat Input Database and Time C Normals data Daily data ley 2003 Year Year of simulation This field is activated if the Daily Data radio button is checked Normals Database used Canada U 54 1971 2000 Daily Database used Sample 2002 2003 Normals Database used Select the Normals se Database to be used in this simulation Fe Humber of normal stations bo match 4 Daily Database used Select the Daily Database to Number of daily stations to match
56. g g g Elevation Map Specification Three location list generation methods are available Use the P ile Quebec30_as Generate from field to specify which method is to be ae used Degrees Minutes 150 fo e Generating a location list from a DEM Generation method Random Grid ME of points f n Select a map in the Elevation Map Specification field from the list of existing map associations input DEM Use the Map Association Editor to add new maps to BioSIM accessed with the button Then select the desired generation method Regular rectangular grid or ae Random the random method locates points at random in amp Use DEM exposure non missing areas of the DEM Random is the as recommended method BioSIM reads point coordinates and Ses elevations from the DEM If exposure values are to be used as well check the Generate exposure or Use DEM exposure radio button When Generate exposure is selected exposure values are generated at random When Use DEM exposure is selected exposures are computed from the elevations of the point s neighbourhood on the DEM It is not recommended that location lists contain exposures at scales coarser than 1 100 000 Exposure 0 No exposure Uniform Hormel e Generating a location list from the weather databases Select Weather stations in the Generation method field Enter the corner coordinates latitu
57. gni re 1996 and is applied in a case study in R gniere and Sharov 1999 It has also been the object of an M Sc thesis by Manon Gignac 2000 Department of Forestry and Geomatics Universit Laval Quebec Canada Universal kriging with elevation as external drift variable is an alternative interpolation method see Deutsch C V Journel A G 1992 GSLIB Geostatistical Software Library and User s Guide Oxford University Press NY With kriging exposure slope and aspect is not taken into 42 Defining and Running Analyses consideration in the mapping BioSIM automates the choice of the many options of universal kriging choice of variogram model detrending methods search radius lags etc Input map elevation In this field the input elevation map DEM to be transformed into an event map is specified This map must be a previously defined map association in BioSIM s map directories A new map association can be added by clicking on to the right of this field Output map event The name of the output TEM to be generated This output map will be stored in the project mapOutput sub directory and will be in the same format as the input DEM Pre post transformation This is an advanced feature used to transform event data before and after interpolation e g for linearizing probabilities No Data Value of the NODATA flag in the output Map if needed Usually it 1s 9999 unless output values can be zero or n
58. h Biase f Elevaton o Z Value Y Pull down list of possible Y variables depth 47 BioSIM 9 User s Manual 6 4 Defining Exports It is possible to export analysis results as displayed in the Results panel to a disk or directly to a spreadsheet the spreadsheet software link is defined in the Links page of the Options dialog Add The Exports window contains the list MyE sport dE D MravailhMyProject Outputs of exports currently defined for this to Spreadsheet analysis When an analysis contains i Delete pre defined exports the export files Export Now are re written each time the analysis is run ed Export all or part of the Results table in a file for treatment by software other than BioSIM An export dialog appears to help with this task jo spreadsheet Send the selected export to your spreadsheet defined in the Links page of the Options P y p dialog This action is immediate bs Delete the selected export s _EwortNow Create the export file immediately rather than by running the analysis again 6 4 1 Export dialog The Export dialog is the same for all analysis result exports whether they are from average output event extraction or event mapping analyses File name This field contains the name of a file where the results of the export are to be Default path D SCF Quebec BioSIM Projects Demo Output OK stored To browse for a directory or an Fiename
59. he daily times series of minimum and maximum temperatures and precipitation Then if any valid 5 day forecast 1s available it is adjusted and supersedes normals Finally any daily data available supersede normals Thus any missing values in the daily observations and future weather beyond 5 day forecasts are filled with randomized normals Valid 5 day forecasts must start on the current date and are used only in simulations for the current year based on the system clock 22 Weather Databases One of the most crucial and time consuming steps in implementing BioSIM is the development of the weather databases used by the system There are three types of weather databases Normals 5 day Forecast and Daily Data All temperatures in BioSIM databases are in C Precipitation is in mm of water The Daily Database and the associated 5 day Forecast Database must reside in the same directory Normals and Daily Databases can reside in different directories There can be several sets of weather databases residing in the same or in different directories These files can be global to all projects or can be local to one project All of them can be stored either in local project specific or in global directories Local project weather data must be placed in the weather sub directory of the project These sub directories are always searched by default and do not need to be specified Global directories are specified with the Options menu selection
60. he first two results are accessible by clicking on the button on the right of the Analysis panel of BioSIM s main window Displaying output event maps Once a mapping analysis has been executed the resulting map can be displayed by clicking _ Showa on the right hand side of the Analysis panel of BioSIM s main window This sends the map to ShowMap an independent application distributed with BioSIM ShowMap displays the location list overlaid on the output map 3 1 Map Editor Dialog The Map Editor is used to create links between DEM and BioSIM INFO files ER also called map associations Cancel Association List into Add _ Show Map s Ane VIEW After the DEM 1s linked to BioSIM the projection information must be specified If Format BINARY BioSIM does not recognize the projection of DEM file C Program Files SCF Quebec Maps GQuebec Guebec30_asft C Program Files SCF Quebec Maps GQuebec Guebec30_asft Quebec Maps Quebec Quebhec30 as fit a map it cannot transform it into a TEM nor s can it display the cursor s position in familiar prjecion ype Esse SSCS let degrees and minutes Hence only maps that yona pt have been adequately associated are Map directories available within BioSIM Projections can be C Program Files SCF Quebec BioSIMProjects DemosM aplnput bed C Program Files SCF Quebec Maps Quebec specified after a map has been associated C Program Files SCF Cusebec maps C
61. ients obtained by fitting the regression equation to data from the 100 stations nearest to the simulation point Once the adjustment is made data are averaged with an inverse distance square algorithm among stations of each type if the number of stations matched gt 1 2 1 3 Correction for slope and aspect If the simulation point s slope and aspect are non zero an overheating factor is applied to maximum daily temperatures This overheating factor depends on the type of surface being modeled its albedo By default BioSIM uses a conifer canopy where overheating by sunlight leads to maximum temperatures exceeding observed maxima by at most 4 C with a summertime daily range of 20 C corresponding to the effect of bright sunlight on a forested canopy It is assumed that all weather stations in the three weather databases are on level ground For mathematical details of this adjustment see R gniere 1996 2 1 4 Generation of daily values from monthly normals BioSIM interpolates linearly between monthly mean temperatures to produce expected daily normal mean minimum and maximum temperatures Addition of daily fluctuations to input temperature regimes is necessary to simulate the development of cold blooded animals and plants because of the so called Kauffman effect Biological responses to temperature are notoriously non linear That is true even with so called linear degree day models as the main source of non linearity occurs around
62. ify the horizontal spatial reference units of the maps e g m or arc degrees For projections other than Geographic unprojected additional parameters must be specified For example Lambert and Albers require six projection parameters UTM requires only the UTM zone The dialog will activate the parameter fields associated with the projection type selected Datum By default BioSIM uses the WGS84 datum estimate of the earth s radius but it also offers a wide selection 28 4 Defining and Running Simulations 4 1 Creating a New Project BioSIM stores information pertaining to simulations and analyses in projects Each project is stored in a distinct project directory composed of a project file extension BIO and several sub directories see Project directories for information on project directory structure To create a new project use File New To open an existing project use File Open 4 2 Defining Simulations Once suitable weather databases have been obtained and a project has been created the next step in using BioSIM is to define at least one simulation either by selecting Add Simulation in the Project pull down menu or by clicking on the Lau button on the right of the Simulations view of BioSIM s main window The Simulations view lists the 7 N Description LM Locationlist_ Model Input_ TG In v Add simulations currently defined in 1 Demonstration of BioSIM Examp
63. influence maritime Several experienced users especially Mr Dan Lavigne New Brunswick Department of Natural Resources and Energy Mr Paul Brouillette Minist re des Ressources naturelles et de la Faune du Qu bec and Pierre Duval Canadian Forest Service contributed greatly to the development of user friendly features and usability of the software The development of BioSIM has been made possible thanks to the financial contribution of several Canadian Forest Service partners The following members of the SERG International committee are particularly acknowledged Forest Protection Limited Quebec s Soci t de protection des arbres contre les insectes et maladies the provincial governments of Ontario and British Columbia and the USDA Forest Service l NO Table of Contents BOO LIVI Oy ON yah ahaa A En de in te id ob die l 1 1 INTOMCHONESS diet din annees l 1 1 1 D CIC COC UINE NLATION e den een 2 t2 BOSIN SaNa e EE 5 1241 ECHOS DO RS Rae ne dan dE et nan 5 122 LS AO E E A E P E A EA A Se nt E 5 1 25 SSEM QUE MEMS Fii A teens 6 1 2 4 UON DrOS ASS RS E Den a a nt SN 6 1 3 How BIOS IM WORKS RL in tere eee 6 1 3 1 ReEQUmred 111 OF MATION RASE Ne E adie teste nt 6 1 3 2 Weather data for simulations 7 1 3 3 SUMIUL AION AOC AU ONS esis EE ee te oder dits 7 1 3 4 BiSS MS man VNAO W an drain tou nent ten bartels ile 7 1 3 5 BOSIM POE Saaana A a a D de 8 1 3 6 Prelimanary Set Up snisetot aver a a tne See en ets 9 Weather Data m
64. ing its name Example of an entry in a daily weather data index file 22 Weather Data in BioSIM QUEBEC Que 46 8000000000 71 2166666667 90 1 QUEBEC Que empty line 2 5 5 Daily data files Daily weather data from different years for a given station indexed in a Daily Database can be stored in a single or in several separate files as the user chooses BioSIM provides a tool to create and edit these files but they can also be provided by the user through some other set of tools as long as they are in an appropriate format In many cases daily temperature data are generated by automatic weather stations and are updated through telecommunications hardware and software independently of BioSIM Daily temperature data files consist of daily minimum and maximum temperatures and optionally precipitation stored in space delimited ASCII files containing on each record Year Julian date day of the year starting at 1 and ending at 365 Minimum temperature Maximum temperature Precipitation optional There are a few restrictions on the format of these files e nonon numerical characters can appear among the data fields e individual values on a record must be separated by at least one space or tab e minimum and maximum daily air temperatures are in C Missing data can be identified by 999 and days for which no data exist can be omitted altogether Example of a daily weather data file 1990 129 8 0 21 0 0 0 1990 130
65. ion matches can be viewed by year Daily graph this button graphs the weight of data from each daily station matched on a daily basis weights can vary due to missing data 36 Defining and Running Simulations 44 Advanced Simulation Dialog BioSIM offers the possibility of varying up to three model parameters simultaneously in a controlled manner within a single simulation series This can be used for example to study model behaviour When a parameter is varied the entire series of simulations locations and replicates is repeated for each new combination of parameter values Model parameters to be vared Random variation Number ak values f initial larval density last sample date Observed Al IDE 36 Systematic variation shoot density subpopulation TreeKind Minimum value fo Maximum value f jo In steps of Parameters to be varied are chosen from the model specific parameter list appearing in the left panel Each parameter selected is varied between a minimum and a maximum value Parameter values can be varied systematically in regular steps or randomly If systematic variation is chosen the user must specify the step size If __K __ Cancel random variation 1s chosen the number of different values to be generated between minimum and maximum must be specified instead 45 Running Simulations Creating the Output Database Once one or s
66. ition Of Average Day of pear Number of insects QUEBEC 2rd 3rd 4th Sth Eth aah graphs and the Exports view er e e e e a containing the definition of Delete exports Regression Export Mow To add a graph Click on 5 to the right of the Graphs view of the Results window The Graph Editor dialog appears Using the gt button select a Sa yee the variables to be graphed In the Title field type athe oo t lt tsOOOC Import in the appropriate graph and axis titles then click ON Graph Tite NearQuebes 2003 sS CST a X Avis Title Day of year t Asis Tithe Number of insects The gra h can then be viewed by clicking on Loc QUEBEC Variables to be illustrated Graph or To PLT inix Fie Annotation Help elal EaR A 7 880 OS mj qaj population density defoliation Negr Quebec 2003 a o D co man Cancel Numbar af Insgecis 180 June Doy of year In Neutral mode Left Click move object 63 BioSIM 9 User s Manual To export the results Click on _ to he Default path DASCF A vebec BioS IMProjects D emo Output File name demo csv ie Cancel File format asc witth comal cs right of the Exports view of the Results window The Export Editor dialog appears Specify and export the file s name and format and select the output variables to be exported using the gt button R
67. le 1 of 2003 Daily Stat Default 2003 No TE 2 Degree day in Quebec Example 2 dd Random Locati SC Threshold normals No the project The fields in this 4 view are 5 Check boxes Selection Determines which simulations are to be run check boxes only appear when this mode of operation is in effect No Simulation number used in defining analyses Description A user supplied description reminder Model The 8 character ID of the model used in the simulation Location Name of the Location list for the simulation Model input Name of the Model input file used in the simulation TG input Name of the temperature generator input file used in the simulation Validity YES if the simulation is current NO if the simulation needs updating An existing simulation can be modified by double clicking on it __ amp Add a new simulation by opening the Simulation Editor dialog iste Delete a simulation and all analyses based on this simulation 29 BioSIM 9 User s Manual 4 2 1 Simulation Editor dialog Description In this field the user may enter E a meaningful title to be used as a reminder of _ Description FERRER the object of a simulation Model Spruce Budworm Biology Model Help Simulation Inputs so oa Model Defaut Define Model Input Model This is a pull down list containing all Temperature generator 2003 Define TG Input the models available to BioSIM The user Location list
68. lex database in BioSIM It is important to understand the distinction between the index file dailyStations and weather data files linked to the database wea A station is a location where weather data are recorded Each weather data file wea contains fiene AUEBECARPORT Canada WEA one or more years of data from a single station One station in the index file dailyStations may be linked to one or more data files wea in the database A data file wea must be linked to a station in the index file dailyStations to be used in BioSIM L Eredi Show the Links dialog Lenye Add a new year to the database When activated BioSIM looks for the new year Then BioSIM looks for the name of a data file in which to store the new year You can select an existing linked file or select New to create a new data file L amh Show the data graphically 21 BioSIM 9 User s Manual Years This combo box lists and allows you to select from all years for which the database contains data from the specified station File name Name of the file wea where the daily data are stored This field is greyed it cannot be modified To change the link to a data file use __ Linked fles 2 5 3 Consulting and modifying linked data files wea DO metw Tf a file containing daily data exists but is not located in the database directory this button is used to copy the file into the database directory Later modifications
69. lists all the databases found in the project s Weather sub directory or in the set of global directories applicable to the Daily Database type If the desired database does not appear in the list 1t must either be copied into one of these directories or the appropriate directory must be added to the directory list by clicking on _ Satins Buttons and fields available in this page of the Database Editor are as follows ay Bread Create a new database When you create a new database BioSIM asks for the location in which to place the new database This location can either be the current project s Weather sub directory or a global directory Next BioSIM asks for the name of the new database Usually the name must be meaningful As a rule the area and period e g UtahArea_1921 2001 is used for the Daily Database x Delete a database For Daily Databases this button deletes the index file but the directory containing the data files or the data files themselves are not deleted Data type filter Select a filter to apply to the list of items There are four possibilities e No filter show all stations available in the database e With temperature show only stations that have temperature data e With precipitation show only stations that have precipitation data e With temperature and precipitation show only stations that have both Year filter Show only the stations that have data for the specified year L New Add a new s
70. mation in the development of ecological insight or of pest management plans see section 3 Maps in BioSIM Output interpreter F Event a b ytc A Map brensicemation Digital slevathon moda Target event map 1 1 1 Scientific documentation BioSIM has been extensively documented in the scientific literature A general description of the approach and of the issues surrounding its use can be found in R gni re J 1996 A generalized approach to landscape wide seasonal forecasting with temperature driven simulation models Environ Entomol 25 869 881 R gniere J Logan J A 1996 Landscape wide projection of temperature driven processes for seasonal pest management decision support a generalized approach Pages 43 55 in T L Shore and D A MacLean eds Decision Support Systems in Forest Pest Management Proc Entomological Society of Canada Annual Meeting October 17 1995 Canadian Forest Service Victoria BC Canada BC Forest Research Development Agreement Report No 260 BioSIM Overview R gni re J Cooke B Bergeron V 1995 BioSIM a computer based decision support tool for seasonal planning of pest management activities User s manual Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Sainte Foy QC Information Report LAU X 116 At the heart of BioSIM is a daily weather generator described in R gniere J Bolstad P 1994 Statistical simulation of daily air temperature
71. meter values for the model selected or to edit an existing set click on the __DsfneModelineut_ button to the right of the field to open the Model Input Editor dialog and the model s specific interface dialog see Model Input Editor and Model interface example The identity and meaning of model parameters are model specific Consult model documentation for information on model parameters Temperature generator This field is used to select a set of parameters for the temperature generator which assembles a location specific temperature and precipitation time series for input into the simulation model Parameter values can be the default ones or a user defined set saved in the project s Model Input sub directory To specify a new set of parameter values or to edit an existing set click on the Dereta mt button to the right of the field This opens the Model Input Editor dialog and the TempGen interface Location list Each simulation in BioSIM is run for a series at least one of locations also called simulation points or target sites in this document This field is used to specify the list of locations for which the simulations are to be run The pull down menu contains all existing location lists in the Loc sub directory of the 30 Defining and Running Simulations current project new list can be created or an existing list can be edited by clicking on the Dsnel sinlit button to the right of the field This opens
72. missing years in the daily database weather data 300 km by default sseatevesution BioSIM normally aborts the simulation and sends an error message to the Type offie fomatto store model output BioSIM DB bsimDB x Messages view of the main window The default distance can be changed and BioSIM can be forced to run despite this situation e BioSIM sends a warning to the Messages view of the main window when simulation points are farther than a certain distance to the nearest source of weather data 500 km by default This distance can be changed FF improvement to include a term in the map interpolation regression 0 0008 BioSIM 9 User s Manual 10 Normally when a simulation is run using multiple years of observed daily data and the input daily database contains no data for one of the years required BioSIM aborts the simulation and sends a message to the Messages view of the main window This function can be deactivated By default BioSIM does not save the current project definition when a simulation or an analysis is run This can be overridden BioSIM normally places all model output in a proprietary BioSIM database Other formats are available ASCII file or ACCESS 2 Weather Data in BioSIM 2 1 Weather Regime Assembly For each model run BioSIM assembles an input weather regime consisting of a series of daily values of minimum and maximum fi air temperatures in C and optionally fa A ie eA fig AN kl MAN
73. n Forest Service Pacific Forestry Centre Victoria BC Information Report BC X 399 Hansen E M Bentz B J Turner D L 2001 Temperature based model for predicting univoltine brood proportions in spruce beetle Coleoptera Scolytidae Can Entomol 133 827 841 Logan J A R gni re J Gray D R Munson A S 2007 Risk assessment in the face of a changing environment gypsy moth and climate change in Utah Ecol Appl 17 101 117 BioSIM 9 User s Manual Nealis V G R gni re J Gray D R 2001 Modeling seasonal development of gypsy moth in a novel environment for decision support of an eradication program Pages 124 132 in A M Liebhold M L McManus I S Otvos and S L C Fosbroke eds Proc Integrated Management and Dynamics of Forest Defoliating Insects August 15 19 1999 Victoria BC USDA Forest Service General Technical Report NE 277 Pitt J P R gni re J Worner S 2007 Risk assessment of the gypsy moth Lymantria dispar L in New Zealand based on phenology modelling Int J Biometeorol 51 295 305 R gni re J Bentz B 2007 Modelling cold tolerance in the mountain pine beetle Dendroctonus ponderosae J Insect Physiol 53 559 572 R gni re J Nealis V 2002 Modelling seasonality of gypsy moth Lymantria dispar Lepidoptera Lymantriidae to evaluate probability of its persistence in novel environments Can Entomol 134 805 824 R gni re J Sharov A 1997 Forecasting gypsy moth
74. n Right of Canada 2008 Catalog Number Fol 13 3 134E PDF ISBN 978 0 662 479 19 2 ISSN 0835 1570 This publication is available in PDF at no charge from the Canadian Forest Service Bookstore at http bookstore cfs nrcan gc ca TTY 613 996 4397 teletype for the hearing impaired Cette publication est galement offerte en fran ais sous le titre BioSIM 9 Manuel de l utilisateur num ro de catalogue Fol 13 3 134F PDF Acknowledgements BioSIM was developed over a period of several years and benefited from the contributions of several people Drs Lukas Schaubb and J A Logan contributed the original concept of T functions as an approach to landscape wide projection of seasonality Some of the earlier concepts were developed in collaboration with Mr Michael Roden Dr Barry Cooke played a considerable role in developing concepts and programming of the earlier MS DOS based version of BioSIM Programming expertise was also provided by Mr Vincent Bergeron The current version of BioSIM for Windows 95 98 NT was conceived and programmed by Mr R mi Saint Amant Ms Manon Gignac played a key role in refining the map transformation currently used by BioSIM Her work on BioSIM is the subject of an M Sc thesis entitled Comparaison de la r gression spatiale et du krigeage avec d rive pour interpoler des extrants de modeles de simulation de d veloppement d insectes au Qu bec en fonction de l chelle de la topographie et de l
75. n database Canada USA 1971 2000 However several other Normals Databases are available upon request to the development team e g world climate change in North America etc e Observed daily weather data up to the current day are contained in a Daily Database e 5 day forecasts are located into Daily Databases and are used only under real time conditions when short term weather predictions are needed to obtain more accurate model forecasts such as during pest control operations using pesticide applications Each source of weather data in these databases a weather station 1s georeferenced latitude longitude elevation BioSIM selects the best sources of weather data for each point in the location list adjusts the data for differences in elevation latitude and longitude and generates daily values by restoring stochastic variation to long term monthly averages on the basis of local normals see literature on this process The weather time series sent to the simulation model can be composed of daily data whenever available or requested 5 day forecast for short term prediction when available and normals for prediction of processes under usual or normal conditions over the longer term or to fill gaps in observed weather 1 3 3 Simulation locations BioSIM runs simulations for a user specified list of geographical locations These lists are managed by the Location List Editor They can be provided by the user in files
76. nd can export analysis outputs to your favourite Windows spreadsheet e g Excel 1 3 How BioSIM Works 1 3 1 Required information BioSIM controls the execution of temperature driven simulation models for real time or historical prediction of seasonal processes To do so the system must e Provide the simulation model with geographically specific time series of daily air temperatures minimum and maximum and optionally precipitation e Control the execution of the selected simulation model optionally varying certain model parameter values e Merge all outputs in a database e Examine model outputs to extract user specified statistical features and present this information in the form of graphs tables or maps Three main sources of input are required by BioSIM e Weather information accessible through the Database Editor e Normals monthly statistics e Daily data e 5 day forecast optional BioSIM Overview e Climatic zones and thermal gradients under certain optional circumstances e Location lists see the Location List Editor e Input DEM see section 3 Maps in BioSIM 1 3 2 Weather data for simulations BioSIM assembles weather data for simulations at each point in the supplied location list from three geographically referenced databases e The Normals Database contains long term mean and extreme monthly minimum and maximum temperatures and precipitation By default BioSIM is provided with a North America
77. new parameter click on the type of parameter to be added in the Input window and click on the form A new rectangle appears You can move and resize the rectangle You can also change the size of the caption and entry fields in each rectangle by dragging the dividing sash The form becomes the model interface used by the Model Input Editor dialog This Model Interface window would then link to the Model Input Editor 7 1 4 Output variables The Output panel is used to list name the model s output variables other than the time reference date Variables must be listed in the order in which they appear in the model s main output file The order of the output variables in the list can be changed by dragging the names to the desired position in the list The number of variables in this list must be equal to the number of output variables other than time generated by the model Output Reference Type Dailyt Julian Day Model Output Variable 2nd Emergence Hew Models in BioSIM Edit your interface here Murober of subpopulations Integer Last sample date Integer Observed Al Real Initial larval density R eal Shoot density Real Shage speciic survival rates 2nd Real 3nd Feal 4th Real Sth Feal Eth Real pup e R eal BalsamFir F Tree species 20 fa Observed Al umber of subpopulations fo Last sample date Initial larval density fi
78. ns normally involved in using the software NOTE In this tutorial it is assumed that BioSIM was installed in the default directory C Program Files SCF Quebec BioSIM If this is not the case replace the default directory by the actual directory where BioSIM was installed on your computer 8 1 Initial Set up Directories Links and Projects Click on the menu bar Tools then on Options 1 In the Directories page These directories apply to all projects Home C Program Files S CF Quebec8ioS Ma Models C Program Files S CF Quebec BioS M Models e Select Normals Data in the field Show directories for Click on to select the main weather directory C Program File S S CF Show directores for Normals data hi Quebec We ather C Program Files SCF Quebec weather e Select Daily Data in the field Show directories for Click on _ to select the Daily Database directory C Program Files SFC Quebec Weather These directories apply to the current project Weather DB C Program Files SCF Quebec Bios ProectsNOemoti eat Input maps C Program Files S CF Quebec Bold Projects Demos apl e Select Input maps in the field Show directories for Click on _ 444 to select the DEM map directory C Program Files SCF Quebec Maps Quebec 2 In the Links page e Use the browse button to the right of the SpreadSheet field to find the locati
79. o offers the possibility of graphing the results of several event extraction analyses on the same graph select Project Export Multiple Analyses Event Extraction Analyses see Multiple Analysis dialog 5 1 3 Event mapping analyses Map Transformation i Se Interpolation method Regression Wal When an event mapping analysis is selected the Input map elevation Quebec30_as sos Analysis Editor adds to the standard Event ne leveni dace Extraction Analysis dialog a group of fields related to the mapping functions Nodetatlag E ee Map directory C Program Files SCF Guebec B05 M Proects Demo hd apl utp Interpolation method BioSIM offers two spatial interpolation methods spatial regression and kriging A cross validation jack knife coefficient of determination R is a good criterion for choosing between these two BioSIM can provide this cross validation comparison when a mapping analysis is defined by clicking on the butting at the right of the Interpolation Method field Note that for this function to be available the simulation for which the mapping analysis is being defined must have been run and must be valid Spatial regression is a multivariate regression relationship fitted between latitude longitude elevation and exposure if this was non zero for any point in the location list and the output feature event The spatial regression technique used in BioSIM is discussed in R
80. om the database __ ste Show all stations listed in ShowMap This is useful for visualizing the spatial distribution of weather stations 15 BioSIM 9 User s Manual 2 3 2 Normals Editor dialog When the te or __ _ button x is clicked in the Normals page of the Definition Database Editor dialog the Normals Mame AUEBECJEAN LESAGE INTL AIQUE Cancel Editor dialog appears for entry or Degrees Minutes Seconds modification of data on a weather Latitude o rh 46 E po station lraucs E 22 a 74 Elevation meters The Normals Editor dialog is used to f Disable this station modify or add a station in the n Umax Tmin i 176 7 9 0 8097 7 7149 6 8705 0 7321 0 1278 0 6723 0 1746 Normals Database All fields in the 16 6 1 0 8291 7 0536 5 7656 0 719 0 1148 0 6664 0 0689 34 0107616 6 3858 4 8402 0 7558 0 0995 0 6241 0 0536 Normals Database are editable Data i 1 3 78 0 508 36251 4 5986 0 7602 0 1008 0 5515 0 0279 can be viewed with the Graph 3 171 0388 31282 5 4012 0 5858 0 1257 0 5836 0 0481 22 2 0 4894 3 3252 4 5186 0 6817 0 1831 0 512 0 0206 button 4 25 0 5094 31606 3 6333 0 7039 0 1506 0 486 0 0166 23 4 0 4955 3 4708 3 6262 0 7367 0 7912 0 4999 0 0467 17 6 0 5409 3 9552 3 6366 0 6929 0 17313 0 5295 0 0709 D on 7 10 7 0 5864 36997 4 2622 0 7067 0 2087 0 6322 0 0812 When the Disable this station November 43 29 0724 47426 4 2197 0 741 01771 0 6066 0 0306 checkbox is checked the data from Decembe
81. on Type in the description of the Pepica po Advanced simulation being defined e g Map of degree Humber of files generated 200 locs x 1 params 10 reps 2 000 days in Quebec Example 2 Approximate duration 02 minutes 24 seconds About the model selected 2 Model Select Degree day summation Bicsi s Degree day mode from the drop down list This 1S the This ig general purpose degree day accumulator f It calculates DD t DD t 1 ddit where t is simulation model that will be used for this fin days and daft is computed by two methods example El cence 3 Simulation inputs Model click on _DeineMedelint then click on Jin the Model Input renpsiatuetmetot E Editor and type 5 C threshold as model input name Type in 5 in the Temperature threshold field of the model s interface window Temperature generator Click on Parets Inout to ean the right of this field In the Model Input Editor s anetm click on and type in Normals In the Temperature generator s interface window check the Normals data button Select the Normals Database to be used in the Normals Database used field Leave other fields to their default values f Normals data Daily data veer fo Normals Database used Canada U 54 1971 2000 Daly Database used Stations Match Temperature Humber of normal station
82. on of your favourite spreadsheet software as for example C Program Files Microsoft Office Office Excel exe 3 Create a new project 59 BioSIM 9 User s Manual x Return to BioSIM s main window Click on the menu Project Name ok bar File and then on New Project k Pens Cancel Directory C Program Files S CF Guebec BioSIM Proiects Dema m In the Project Name field of the New Project dialog type Demo and then click on x An empty project file demo bio is created and added to the new project directory D Program Files SCF Quebec BioSIM Projects Demo It is in this project directory that all information related to this tutorial will now be stored 8 2 Example 1 8 2 1 Step 1 Defining and running a simulation Click on the Add button to the right MSW Ss 10 xi of the Simulations view of BioSIM s EE F main window or select Project then DS Talaan This activates the Simulation Editor dialog with which a new simulation can be added or an existing simulation can be edited Add Delete 1 Description Type in your description of x the simulation being defined e g description CREER Demonstration of BioSIM Example 1 Model Spruce Budworm Biology Model Help Simulation Inputs c 99 odel efau efine Model Inpu 2 Model Select Spruce Budworm Biology oe Defaut Z __Define Model input Temperature generator 2003
83. ormation from model output and present it in the form of tables graphs or maps With a DEM for the area Location koop T Weather data Le Source selection t Thermal Gradients Regional Gradients F Mormals randomization containing the simulation locations BioSIM can sani oi generate a map of the event Two spatial interpolation methods are available in BioSIM to _ FA eee aime produce such maps With both approaches wha W o duties ee 0 simulations are first executed for a series of ar iz locations and results are interpolated Universal kriging with elevation as external drift variable is one of the interpolation methods proposed The second is based on a generalization of the target function approach developed by Schaub et al Schaub L P Ravlin F W Gray D R Logan J A 1995 Landscape framework to predict phenological events for gypsy moth Lepidoptera Lymantriidae management programs Environ Entomol 24 10 18 Here spatial regression is used where a relationship is estimated between model output latitude longitude elevation and exposure slope aspect From this model response surface a multivariate target function the DEM can be transformed into a landscape wide representation of model output also called a target event map or TEM Whether obtained by kriging or spatial regression such a map can then be used by itself or in conjunction with other geographically referenced infor
84. pecified at installation This root directory will contain the following tree E SCF Quebec El Li BioSIM BioSIM software LD rcview Arcview macros Models Simulation models L Projects Default location of BioSIM project directories Ci Maps Default location of common DEM Co PLT PLT Win and PLTWidget program data display 4 ShowMap ShowMap program map display L Weather Default location of common weather databases BioSIM 9 User s Manual The installation program will also create BioSIM ShowMap and PLT icons on the desktop ShowMap is a general purpose map display program grids vectors PLT is a graphics package used by BioSIM to display simulation results 1 2 3 System requirements BioSIM is compatible with the Microsoft Windows operating system and will run on microcomputers with Intel compatible processors with at least 40 Mb of free hard disk space 1 2 4 Utility programs Three separate programs are provided with BioSIM to make the system s capabilities more complete see each utility s help system for more information on its use e PLTWidget a scriptable Windows graphics widget that BioSIM uses to display analysis output graphs e PLTWin a general purpose Windows graphics program using PLTWidget linked to BioSIM to provide added flexibility in the preparation of publication quality graphics and e ShowMap a map display and query program BioSIM also provides access to Arcview through macros a
85. planation of these functions see the appropriate weather database s or model base s documentation 2 3 Normals Database Normals Forecasts Daily Data Models In BioSIM normals are long term monthly statistics Pa Canada usA 1971 2000 calculated over 30 year Standard Normal Generating Momas stations Hst Periods SNGP the latest being 1971 2000 These ss 1 E Sars zl statistics apply to each single weather station in the TEE e eaaeeae database A Normals Database contains these eee E monthly statistics for a number of stations along with the spatial coordinates of each station latitude longitude and elevation A Normals Database is contained in a file with the extension normals located in the project s Weather sub directory or in one of the global weather directories set via the Options dialog ABBEVILLE LA ABBEVILLE MS ABBEVILLE 45 GA ABBEY SASK Delete ADCODCERAI ale Poot 10776 Default Weather Directory C Program Files SCF Quebec Biol Proects D emo Options C SCF Quebec eathernversionS s C travai Fath PA CF Quebec y eather versionS Canada U54 1971 2000 Normals 14 Weather Data in BioSIM 2 3 1 Consulting and modifying the Normals Database The Normals Database is accessible in BioSIM through the Database Editor dialog Normals tab The first field 1s a combo box that lists all the databases found in the set of current directories
86. ployment of available resources based on timing or risk as well as the optimization of control efficacy BioSIM is an integrated environment that provides seasonal simulation models with geographically specific temperature input either historical or forecast BioSIM controls the execution of simulations and can extract information from model outputs for presentation or further analysis BioSIM assembles weather data for p7 cn eee oe ei mens simulations at each of a large set of i ee i r PEER Eo od locations from spatially referenced A b ue 2 oo si databases The Normals Database Pe Skee ae f contains long term mean and extreme 4 ET ao Le monthly minimum and maximum A d ey o go o j S mM o E p temperatures and precipitation Current mei Cs act 0 a observed daily weather data are oho o 4 contained in a Daily Database BioSIM selects the best sources of weather data for each point in the location list adjusts the data for differences in BioSIM 9 User s Manual elevation latitude and longitude and restores stochastic variation to long term averages normals The weather time series sent to the simulation model is composed of real time data whenever available or requested 5 day forecast for short term prediction when available and normals for prediction over the longer term or to fill gaps in observed weather BioSIM provides extensive event extraction functions to collect inf
87. r 134 4 8 0 9295 7 3023 5 9033 0 7672 0 1596 0 5939 0 0659 this station are not used by BioSIM 2 3 3 Record structure of the Normals Database The first line in the Normals file contains the date Year Month Day of the creation of the Normals Database the first and the last year of the period of data and the version of the database Then come the data themselves Data from one normals generating weather station constitute one record in the Normals Database and each station s record consists of 15 lines in the Normals file pb Weather station name 2 Georeference and switches Latitude decimal degrees Longitude decimal degrees Elevation m Use Switch No 0 Yes 1 Contains Temperatures No 0 Yes 1 Contains Precipitation No 0 Yes 1 3 Blank line 4 15 12 months of data compiled over a standard period of 30 years Each line of data is comprised of 11 variables e Monthly mean minima e Monthly mean maxima From these normal daily minimum and maximum temperatures are obtained by linear interpolation between the means of successive months adjusted to correspond to the values occurring at mid month Seven additional monthly normals are calculated from the differences between observed daily minimum and maximum temperatures and these daily normals 16 Weather Data in BioSIM Standard deviation for minima Standard deviation for maxima Ist order autoregressive term for minima 2nd order autoregressive term for
88. r dialog In the Summary type pop 66 29 down field select Average Output The dialog will amp sis ios by loc E E TTR change to the form illustrated here DESCHAMBAULT VILLEROY Type in a useful description of the analysis to be performed e g Average output near South Shore sites Highlight Valcartier and Quebec in the left panel and transfer them to the right panel of the site selection list box using the gt button This will average model output from these two locations Click on o 1 To run the analysis Make sure that the new analysis definition line in the Analysis view of BioSIM s main window is selected then click on the 4 blue nails button on the toolbar or select Project and then Execute selected analyses from the menu The BioSIM progress task bar will appear briefly 62 Tutorial 2 To view the analysis results FEU O x Graph Results Click on L amp I to open the Results window The Results VALCARTIER O6 ao t 0 0 0 0 0 VALCARTIER OF ao t 0 0 0 0 0 window has three views the QUEBEC 08 mai i 0 i 0 0 i QUEBEC 09 mai 4 582 0 0 a 0 Results table in this case the QUEBEC 10 mai 4956 0 i QUEBEC 11 mai 14 7523 0 0 0 0 date and value of all model QUEBEC 12 mai 4919 O 0 0 0 A n n n OIE RET 1 resi JA ADAD output variables averaged over sites the Graphs view os ses Description containing the defin
89. recasts in this database when BS 1 the simulation is run for the current calendar CI x year and 2 the first day of the forecast is the le el a current day Use to set the first day to the 24 25 25 27 28 29 30 1 2 3 4 5 6 7 current date using the Julian calendar tool 15 e 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 1 2 3 4 Cancel NOTE BioSIM always uses the nearest forecast station 2 4 3 Record structure of a station s forecast data in a forecast file The 5 day Forecast Database is a space delimited ASCII file with the same name as the Daily Database and in the same directory 5 day Forecast Database is an extension of a Daily Database The first line is FORECAST FILE 2 The second line is the number of stations in the database Each 5 day weather forecast entry in this file is composed of seven lines The first consists of the station s name The second line contains the station s latitude and longitude decimal degrees elevation m the use switch 0 no 1 yes and the starting date day of the year The next five lines contain the forecast itself a series of air temperature minima maxima and precipitations for 5 days Formatting details are unimportant as long as each day s forecast appears on a single line with numerical values separated by at least one space or tab A forecast is valid as long as its first day of applicability is equal to the date on the computer system s clock Whenever
90. s e 45 30 Decimals Degrees es 45 5 Longitude Add Line Generate Delete Line RENE Show Nb points C Program Files S CF Cuebec Bold Proects Demos LOCA Default LOC Directory This ends the simulation definition step Because these simulations are based on daily data 2003 and because the Spruce Budworm Biology model is deterministic there 1s no need to replicate the runs the Replication field can be left at 1 61 BioSIM 9 User s Manual To run the simulation make sure that the simulation E alala definition line in the 5 imulat ions VIEW Of BioSIM s on a Simulation 1 Demonstration of BioSIM Example 1 main window is selected then click on the 4 red nails button on the toolbar or select Project and Execute A Selected Simulations from the menu Start of simulation at 08 06 2004 13 09 31 Simulation task 1 normals DB used C Program Files SCF Quebec Weather Canada US4 1971 2000 N Daily data used C Program Files SCF Quebec BioSIM Projects Demo w eather S an Creation of output database Simulation mdb LA The BioSIM progress task bar will appear briefly Cancel 8 2 2 Step 2 Defining and running an average output analysis Click on _4 Ito the right of the Analysis view Off z i l l i i BioSIM s main window or select Project and then n O Add Analysis from the menu bar This activates the Analysis Edito
91. s to match Humber of daly stations to match Exposure factor Albedo Conifer canopy T 65 BioSIM 9 User s Manual Click on _ l in the Model Input Editor dialog to accept these new parameter values Location list Click on __D fineLocationList to the right of this field asena pa Click on and type in the name of a new location list e g Generate From Digtal Elevation Map DEM E Random locations then click on Generate This opens the Location a Map spectication List Generation dialog Check the Generate from an elevation DEM fie Quebec3_as EE map box In the DEM file field select Quebec30_as DEM of Region boundaries Degrees Minutes Quebec that comes with BioSIM In the Generation method fo fo field select Random grid In the Nb of points field type in fis p Fe fo O00 ao p Generation method Random Grid OF Click on E Nb of points 200 Exposure Ho exposure p f Uniform Generate exposure f Hormal Use DEM exposure To accept this new location list click on __ in the Location List Editor dialog Simulation Editor X Description WEE ae E E EE E TEEN TE LE Model Degree Day Summation Model Help Simulation Inputs Model 5 C Threshold Define Model Input This ends the simulation definition step Tempersture generator E z __ Define TE Inout Because these simulations are based on tenis
92. s validation results relationship between actual and mapped event values see Event mapping analyses 6 3 Graph View D Description Add Graph Contains the list of graphs currently a RENEM AEE eara Graph defined for the analysis These graphs ToPLT can be edited by double clicking on Delete their description in the Graph panel Regression Options Graphs _Add Greet Click on this button to add a new graph A Graph Editor dialog appears to assist with this task L Sieh To view the selected graph annotate and print it through the PLT Widget utility _ MAT To view the graph through the PLTWin graphics software package which offers extensive graph formatting capabilities Liste To delete the selected graph _feaession To view the results of regression analyses included in the graphs parameter values and fit statistics 6 3 1 Defining a graph There are three variants of the Graph Editor fg dialog All three share the same first few fields x Use an existing PLT graph NU impor Use a PLT file as template If this button is checked an existing PLT graph will be used asa 7 DES template for the graph the same graph options 7 evi contained in the PLT file will be applied to the 7 s Ve SSS graph being created File name The name of a PLT graph that is to be applied as a template for the graph If the Template option is not being used the remaining fields
93. stored on a disk entered directly into BioSIM or generated in a variety of ways including from a DEM of the area of interest to the user C Program Files SCF Quebec 5 x Fils Edit wiew Project Tools Help Deal talala gl de ON Descipion e Modem rom v add 1 Demonstration of BioSIM Example 1 cf 2003 Daily Stat Default 2003 No 2 Degree day in Quebec Example 2 dd FRandomLocat SC Threshold normals No Delete 1 3 4 BioSIM s main window BioSIM s main window is composed of a standard menu and tool bar as well as three panels or views Simulations Add 1 Average Output cf Average output Mo 1 Date of Peak dth d sites 20035 ch Event Extraction Time when 4th is maximum Mo Delete Result Show map The Simulations view contains the definition of simulations in the current project See Defining Simulations for more information on this view Analysis y Blok ging Delete output files m kd 4 k For Help press Fl Simulation 04 seconds BioSIM 9 User s Manual The Analysis view contains the definition of the analyses defined for the simulation s currently highlighted in the Simulations view See Defining and Running Analyses for more information on this view The third view located in the bottom part of the window contains BioSIM messages about the execution of simulation and analysis tasks such as success error message and other
94. tation to the database This opens the Daily Data Editor dialog 20 Weather Data in BioSIM _ Et Access the information contained in the database about the item selected in the items list left of the button This opens the Daily Data Editor dialog t t Delete the currently selected station from the database In the Daily Data page only the link between the station and the data file is deleted The data file itself 1s not deleted L se Show all stations listed in ShowMap This is useful for visualizing the spatial distribution of weather stations L Yew Verifies the validity of the Daily Database checks by year and station for the presence of data in the files referenced in the Daily Database index file AddForesset dd the selected daily station to the 5 day Forecast Database Import stations rep This button is used to import an earlier version of the Daily Database index prior to version 8 0 of BioSIM 2 5 2 Daily Database Editor When the or LE button is clicked in i Definition the Daily Data page of the Database Editor dialog a the Daily Data Editor dialog appears for entry or e Cancel modification of data on a weather station OC Em ie cs Longitude F1 22 E This dialog is used to modify or add a daily m w station or to add or remove a link to daily weather __tinked fies Disable this station data in a Daily Database The Daily Database is the most comp
95. the Location List Editor Weather Station Matches Access the Match Stations dialog _ Advanced Access the Advanced Simulation dialog Occasionally for model behaviour analysis the user can vary simultaneously up to three model parameters in a simulation definition Parameters available for this type of work are model specific Simulation task size and time requirements BioSIM calculates the number of model runs that will be generated by a simulation task from the number of replicates locations and distinct parameter values when applicable It also computes the approximate amount of time required to execute the task on the user s computer It does this by keeping records of the average time required to run each model with the computer it is installed on The results of these calculations appear in the read only fields at the bottom of the Simulation Editor dialog About the model Information on the simulation model selected such as literature citations credits acknowledgements and other remarks are displayed in this view when available 4 2 2 Model Input Editor The Model Input Editor is composed of two windows the Model Input Editor window and the Model interface The Model Input Editor window is used to add delete and import Model input files The Model interface is where model parameter values are specified Model Input Editor window Used to add delete and import Model input files Tx Model name cf Spru
96. the interface English French Description General description of the model L To browse for the model s executable file The other five pages of the Model Editor dialog are TG input to match the set type of weather data sent by BioSIM to the model Input parameters to design a user interface for the user to set various model parameter values Output variables to define the nature and number of model outputs including the time and other record references Model source to allow the display of intellectual property or credits and Documentation to define the source of model documentation 7 1 2 TG input This page of the Model Editor dialog defines the type of weather input required by the model Model uses the CBioSIMModelBase class This box must be checked when the model exe or dil uses is programmed within the nn C class CBioSIMModelBase Under this oe environment BioSIM automatically oo generates a full year 365 days 366 for leap years of weather data beginning with day 1 for each year When the model is not programmed within the CBioSIMModelBase framework this check box must be left FF Model uses precipitation unchecked When this is the case the model interface must specify the first and last day of weather input it requires 1 and 365 by default and whether the first day of each year should be day 1 r Temperature Generator Input M Model uses the CBioSIMModelBase class IY Begin with dapi ea
97. tion model to meet the basic requirements of BioSIM involves some programming capabilities and is documented in a document entitled CBioSIMModelBase Aa base class for BioSIM models Also it may be possible to make arrangements with BioSIM developers for technical assistance when adding a model to BioSIM s model base Once a model has been adapted for use in BioSIM adding it to BioSIM s model base is a relatively simple task 5I BioSIM 9 User s Manual 7 1 Adding a New Model or Modifying the Model Base If a model an executable file with a EXE or DLL extension 1s provided by the developers with a previously defined BioSIM interface file with a MDL extension it can be added to the model base by copying both files into the BioSIM models sub directory Often the model also comes with documentation in the form of a PDF file This file should also be copied into the BioSIM models sub directory If a model interface has not been developed the first thing to do is to copy the model s executable EXE or DLL and documentation if it exists PDF into Hormals Forecasts Daily Data Models Models List Language Filter No filter Cooke s bt efficacy model DavidPareModel Deqree Day Export Degree Day Summation G n rateur de temp rature GM Lavigne Gypsy Moth Cooke Gypsy Moth Seasonality Gypsy Moth Stability Hemlock looper INS Jack pine budworr JeanBeaulieu Make BioSIM normals MF
98. to the original data file will therefore not be accessible to BioSIM For modifications to be useful in BioSIM they must be applied to files in the Daily Database directory It is therefore ___Iport Weare recommended that daily data files be stored in the daily directory See Daily data files for a _ Gr description of the structure of wea daily weather data files Unlinked wea Files Linked wea Files AMQUI Que Unlink a data file from this station The data file is not removed it is simply unlinked gt Link a data file to this station Data files wea are not deleted by BioSIM This can be done through the Windows operating system 2 5 4 Daily data index file An index to the daily weather data is contained in a file stored in the daily weather directory either in the project s weather sub directory or in a global directory set via the Options dialog that links weather station coordinates with one or more daily weather data files Each entry in the Daily Database index file consists of at least four lines e Station name e Latitude decimal N Longitude decimal E Elevation m Use Switch No 0 Yes 1 e Name of weather data file e Additional lines such as the one above referring to other data files if applicable e Empty line end of the record Daily data files wea are most conveniently grouped in a sub directory under the location of the daily weather data index file and bear
99. useful system information The main window can have a second appearance obtained when the toolbar button is clicked This form of the BioSIM main window 4 offers the same functions with a slightly different approach to the selection of simulation and analysis tasks to be executed checked instead of selected 1 Demonstration of BioSIM Example 1 cf 2003 Daily Stat Default 2003 es Delete 2 Degree day in Quebec Example2 dd Random Local OSC Threshold normals No Simulations M1 1 Average Output cf Average output Tes pue 2 1 Date of Peak dth 4 sites 2003 cf Event Extraction Time when the mas Mo __ Delete es 3 2 Endofyear OD 5C dd Event Mapping Maximum value of dail Mo The advantage of this form of interface is that it allows BioSIM to be run from a command line in script mode This is very useful when setting up a scheduled task to be run automatically at a preset time When BioSIM runs in this script command line mode only the checked simulations and analyses are executed To execute BioSIM in script mode use the following syntax Result Biokriging BioSIM9 exe ProjectFilePath EXEC where ProjectFilePath is the complete path to a BioSIM project file e g C Program Files SCF Quebec BioSIM Projects Demo Demo bio 1 3 5 BioSIM projects BioSIM stores information on the location lists simulations and analysis specifications in projects Each project is stored
100. ve information on the steps executed so far 37 5 Defining and Running Analyses The Analysis view lists the ns Tmesnpion m summamy event Vai aa 1 1 Average Output cf Average output Ho currently defined analyses for A2 1 Date of Peak 4th 4 sites 2003 ch Event Estrachon Time when Hh is masimum No Delete the selected simulations in the Simulation list view Result Show map Analysis Blok nging Once a simulation has been defined even before it has been run an analysis of its outputs can be defined an analysis can only be run after the simulation has been carried out BioSIM provides three types of output analyses A new analysis of the currently selected simulation highlighted in the Simulation list view is defined with the Analysis Editor dialog This dialog appears when the user either selects Add Analysis in the Project pull down menu or clicks on the _ button to the right of the Analysis view of BioSIM s main window The fields in the Analysis view are Check boxes selection Only checked or selected analyses are performed No Analysis number Simulation No Simulation to which the analysis applies Description A user supplied description as memento Model 8 character model ID of the simulation analyzed Summary Type of analysis Average output Event extraction or Event mapping Event Event type when applicable Validity YES if results are current NO if results are

BioSIM 9 - User's Manual - Canadian Forest Service

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