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BioSIM 10 USER'S MANUAL - Publications du gouvernement du

1. cccccccesssseeeecceeeeceaaeeeeeeeeeeeeeeaaas 20 Generation Of solar radiation sise 20 POS SCO OLTEAN i E E ccaaauescansceeceaastdees 21 ET N D i EE N T A E A T E E E EE A AA AAE 21 Consulting and modifying linked data 21 Linked Data Editor Normals Databases page ss 22 Linked Data Editor Daily Databases page Us 23 Linked Data Editor Input Maps DEMS page ccccccccccccnsssseeeeececeeeeaeeeseeeeeeeeeeaaeeenees 24 Linked Data Editor Models Pa Ge ists siencercrsvevsdraxssnnrnestasleietesncriarcdawdevecsnertuetaveiemornscavanes 25 oi BioSIM 10 User s Manual Defining Simulations serres 26 NS EAU EOE OT Diallo s E E E teseesemenesedaueBauetiecs 26 Model Inp t TS G11 OF esiseinas E EENE EEE E ETA EEE i 29 IVIG GON DOC Enor da ON ase E E ncaateeeenereeceaqtaten 29 Mo del speciHc interac dialog ecepti ea ano a ea 30 VY Cater Cre Me OE e CO an E A il ne 30 Weather Generator Input Editor dialog ss 30 Weather Generator WG Parameters dialog ss 31 COCO eee E E E E 32 Locanons INST TNC TOPMIAL ossen E E E E E 2 Locations File OO ROMA a ea a 34 Locations List HO 1A RS dd E E 34 TOC at OMS Goneritor AIO em ose EOE R RES 33 Number of points needed to obtain good mapping results 36 Creatine a locations list in ER a a 37 Paraineter Variation AO a EE E ca ete hi ce 38 MPS EE LE EE VAY SOS SR wes ees E ET EEE EU RER EU TU EEE 40 TMC AU AD cose 40 Woe Ta e E E E E tae 41 BG BUA PR E E
2. Import a File as a Component External files to be imported as components can only be added to a group component To open the Import a File as a Component dialog the user can either click on the Add Import Component button on the Project window s toolbar select Project Add Import Component from the menu bar or right click on a group in the Project window and select Add Import Component from the pop up menu The Import a File as a Component dialog allows ricname Export Gum of preapitation csv 5 the user to load external results and use them in pah C BiosmProjects pemoBiosmynput BioSIM This can be used to generate a map from Link import file column headers to BioSIM dimensions imported values The import file must be in CSV aS ee EEA format and it must be located in the Input ne j Mame e e Latitude Latitude subdirectory of the project Longitude Longitude Year TotalPrecpitation mm ere 5 Internal name field An ID assigned internally TotaPredpitation mm sum Variable by BioSIM to locate each component of a project Merge Internal name wfewya To open the Merge dialog and add a merge component to a project the user can either click on the Add Merge button on the Project window s toolbar select Nr Merad Project Add Merge from the menu bar or right arc 2 click on the approp
3. BioSIM s graphing capabilities are limited and are only intended for basic viewing Advanced graphs must be created outside of BioSIM by exporting data When the Graph tab is selected the drop down list located in the upper right corner displays graphs in two distinct sections In the upper portion graphs currently defined for the selected component are listed In the lower portion of the drop down list below the dotted line appears a list of all the graphs that were created for the other components of the project BioSIM 10 User s Manual 53 Temperature at Scott Data A Graph 4 4 b N It can be useful to copy graph definitions from one component to the other as this copies only the definition parameters of an existing graph e g variables colours etc When a graph is copied the Graph Editor dialog opens with the parameters previously set for the copied graph Buttons available in the top left corner of the main window s Graph tab are as follows Edit Graph Used to edit the selected graph Add Graph Used to open the Graph Editor dialog allowing the user to create a new graph Remove Graph Used to delete the selected graph Save Graph Used to save the graph as an image Print Graph Used to print the selected graph Defining a graph BioSIM graphs data according to row paxage ee numbers not by components such as Stage Frequencies locations or years Thus to create a sl eae
4. How BioSIM Works Required information BioSIM controls the execution of weather driven simulation models for the prediction of seasonal processes To do so the system must e provide the simulation model with geographically specific time series of weather data that include daily air temperatures minimum and maximum and optionally precipitation wind speed snowfall and snow accumulation dew point relative humidity or solar radiation e control the execution of the selected highlighted simulation model optionally varying certain model parameter values e merge all outputs in a database e examine model outputs to extract statistical features specified by the user and present this information in the form of graphs tables or maps Seven sources of input are required by BioSIM e Weather data accessible through the Linked Data Editor e Normals monthly statistics e Daily data including forecasts e Input Maps DEMs accessible through the Linked Data Editor e Models accessible through the Linked Data Editor BioSIM 10 User s Manual 9 e Model Input specific to each model and accessible through the Model Editor s Input tab e Weather Input accessible through the Weather Generator Input Editor e Locations list accessible through the Locations File Editor A specific extension is associated to each of these input files Type of data File extension Project s subdirectory in Can be stored in which the f
5. Jacques R gni re R mi Saint Amant Ariane B chard 2014 Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Information Report LAU X 137E LIBRARY AND ARCHIVES CANADA CATALOGUING IN PUBLICATION R gni re Jacques BioSIM 10 user s manual Jacques R gniere R mi Saint Amant Ariane B chard Information report LAU X 137E Issued also in French under title BioSIM 10 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 1 100 23464 9 Cat no Fol 13 3 137E PDF 1 BioSIM Computer file Handbooks manuals etc 2 Insect pests Control Computer programs Handbooks manuals etc 3 Insect pests Climatic factors Computer simulation Handbooks manuals etc 4 Insect pests Effect of temperature on Computer simulation Handbooks manuals etc I Saint Amant R mi IL B chard Ariane III Laurentian Forestry Centre IV Title V Series Information report Laurentian Forestry Centre Online LAU X 137E SB950 3 C3R44 2014 634 9 670285536 C2014 980023 1 Her Majesty the Queen in Right of Canada 2014 Catalog Number Fol 13 3 137E PDF ISBN 978 1 100 23464 9 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
6. Mb runs 0 Add Analysis Based on the output of another component simulation analysis etc this creates a subset of results for this component and or extracts information such as time transformations events or statistics Add Function Analysis Used to execute row calculations based on a formula Add Input Analysis Can only be performed in a simulation and is used to examine weather information BioSIM 10 User s Manual ao Add Mapping Used to add a mapping component to a parent component e g a simulation an analysis a function analysis etc It can perform spatial interpolations to create maps from data points on the basis of a DEM Digital Elevation Model Add Import File Used to import a simulation from an external file Add Merge Used to merge several components of a group to create a single component An unlimited number of child components can be added to parent components thus allowing users to create chains of varying length and composition within each project However depending on the nature of the parent component it is possible that only certain types of child components may be added The following table lists the possible parent child combinations it must be read by column only and it reads as follows The component of the column header child can or cannot be added to the component of the row header parent Because a group automatically takes on the type of its paren
7. to date as possible Updating such near future forecasts implies the maintenance update of daily databases All daily databases DailyStations located in one of the weather data directories whether global or in the project s Weather subdirectory are listed in the Linked Data Editor s Daily Databases page list field The project s Weather subdirectory is always searched first NOTE When available weather forecasts can be added directly in the daily data files As for daily data forecasts apply to a specific location or station Buttons specific to the Daily Databases page are as follows New Used to create a new database When the user creates 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 subdirectory or a linked 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 are used to name daily databases Edit When a database is selected highlighted in the list field clicking on the Edit button opens this database in the Daily Database Editor application Link a New File Used to add the directory in which the new file is located to the directories list Open Options dialog Used to open the Options dialog of the Directories page in which the user can add and remove links to variou
8. 1 Fichier Edition Affichage Insertion Format Outils HEMA FEI NEA NET OL Latitude Longitude Elevation 2 Springfeld 42 1005556 72 5716667 61 Tampa 27 955 82 4561111 13 Toronto 43 6730556 79 4016667 122 Vancouver 4922 123 103333 52 amp Virginia Beach 36 8561111 75 9805556 4 Washington 38 8847222 77 0366667 0 8 Winnipeg 49 9019444 97 1213889 227 When the file is ready to be saved the user must select File Save as from the menu bar and select the CSV format in the drop down list of the type field The file must then be named and saved in the Loc subdirectory of the project The user must click on Yes if the following Excel dialog opens Microsoft Excel Booki csy may contain Features that are not compatible with CS Comma delimited Do vou want to keep the workbook in this Format To keep this Format which leaves out any incompatible features click Yes To preserve the Features click Mo Then save copy in the latest Excel format To see what might be lost click Help When attempting to close Excel after having saved the file in a CSV format Excel will ask if the file should be saved The user must click on No because it is unnecessary to save the document in Excel format Example of a locations list data file in CSV format Name ID Latitude Longitude Elevation Duchesnay 1 46 869 71 64 168 St Alban 2 46 738 72 066 78 Scott 3 46 506 71 068 149 Parameter Variation dialog
9. The file format for DEM files needs to be j Weather C BOSIM Projects DemoBieSIM Weathen Input maps C BioSIM Projects DemoBioSIM Mapinput specified by typing their extension in the second DE list field on the far right BioSIM only searches for files with extensions that appear in this list Specific DEMs can also be linked to BioSIM through the Linked Data Editor accessed from the main menu Tools Linked Data Editor or when defining a mapping component When such specific links are created BioSIM automatically adds the linked DEM s extension to the DEM format list In addition to global directories BioSIM also searches for files in local project subdirectories BioSIM 10 User s Manual CE Links page It is also useful to set the paths of applications that not need to be modified i Spreadsheet C Program Files Microsoft Office OFFICE11 EXCEL EXE Text editor Notepad exe BioSIM can be linked to The paths to BioSIM s six a PLTWidget C Program Files NRCan PLT PLTWidget exe eS main peripheral programs PLTWin PLT Widget Showidap _C Progem FNAC ShwMep Showop ox ShowMap MergeFiles Normals Editor and Daily ee Se m 5 ind Normals editor NormalsEditor exe g Data Editor are set automatically and usually do En vayas mima 3 The paths to the user s favourite spreadsheet software e g Excel or text editor Notepad exe by default to which results are to
10. BioSIM offers the possibility of varying a EE any or all numerical model parameters TE ee singly or simultaneously in a controlled manner Within a single simulation series This can be used for example in sensitivity analyses When a parameter is varied the entire series of simulations locations and replicates is repeated for each new combination of parameter values T 38 BioSIM 10 User s Manual Minimum value Maximum value Parameters to be varied in the right hand side list field are chosen from the model specific parameter list appearing in the left hand side list field Constant parameters of the Parameter Variation dialog accessed by clicking on the button of the Simulation Editor dialog Each parameter selected and transferred using the button will be varied between a minimum and a maximum value that the user must specify in the Minimum value and Maximum value fields Parameter values can be varied systematically in regular steps or randomly If the Systematic variation radio button is chosen the user must specify the step size in the In steps of field If the Random variation radio button is chosen the number of different values to be generated minimum and maximum must be specified in the Number of variations field instead BioSIM 10 User s Manual ES Defining Analyses Once a component e g a simulation has been defined even before it has been run an analysis of its o
11. CSV file in the Output subdirectory To Spreadsheet Used to export the results to disk and simultaneously send them to the user s preferred spreadsheet e g Excel To ShowMap Used to export the results to the Output subdirectory as a CSV file and simultaneously open the file in the ShowMap software For ShowMap to function properly it needs to recognize the information as a locations list Therefore when the user clicks on this button the location s name latitude longitude and elevation are automatically exported whether the user selected them or not in the Export window Open Output Directory Used to open the Output subdirectory of the project In addition to exports the Output subdirectory also contains the results of analyses that are exported as CSV files Format options specific to CSV files e g column separators and decimal delimiters can be specified in the Region page of the Options dialog The variables and statistics available for export depend on the model and the subsequent choices made by the user to obtain results for the selected component The user can select a subset of variables upper list field and statistics lower list field to be exported Variables and statistics to be exported can be added or removed by selecting them but they are exported in the same order in which they appear the order cannot be changed Graphs 9 PA X FR Temperature at Scott z Temperature at Scott
12. Once one or several components have been defined the next step 1s to execute them Components simulations analyses etc must be run before their results can become available to be viewed and analyzed For a component to be run it must be checked in the Project window Checked components can be run either by selecting Execute Checked Project in the menu bar by clicking on the Execute Checked button in the main window s toolbar or by right clicking on the component in the Project window and selecting Execute Checked from the pop up menu NOTE Whenever a change is made to a component s definition e g component parameter value or in the weather databases used for a simulation it is important to re execute the component and all its child components to update its outputs When a component is updated all child components must be updated as well To run a component and all of its child components simultaneously the user must make sure that they are all checked before re executing them Once the checked components have been executed the Execute Message Log window displays information on each component s last execution This information always includes the start and end times of the component s last execution It also lets the user know if there were any errors during execution If the component was a map the window also displays statistical information and cross validation R2 BioSIM 10 User s Manual ES
13. S ee EE ae ee graph in BioSIM for a given location ini a ee rs eos a given year different months etc the 231 ietarcananss D Aa ae a CS ne a user must select the data to be DONO ae Oe ee ee ee Sek ee ee displayed by entering the appropriate 3 ar 0 ea gee amen Co oo row numbers in the Rows from and to fields which refer to rows in the Data tab way en ne i nn np pe pu Data A Graph A 4 D M To create another graph from the same results but with different parameters the user simply needs to click on the Add Graph button again To zoom in on part of the graph the user can click and drag over the area to be zoomed on from left to right To zoom back out click and drag from right to left Graph Editor dialog The Graph Editor dialog is used to create simple graphs in BioSIM To access it the user must select a component in the Project window select the Graph s tab then click on the Add Graph button in the upper left corner of BioSIM s main window Buttons and fields in this dialog are as follows Sh BioSIM 10 User s Manual Name field Name that appears in the Graph tab s drop down CE list Stage Frequendes Stage Frequencies 2 Title field Title of the graph Time Stage Frequencies X title field Title of the X axis Time Y title field Title of the Y axis Show legend eplication Replication X axis field drop d
14. This option is for advanced users who wish to install and use hxGrid hxGrid is an external grid parallel program that makes it possible to use idle computers on a local network see System Requirements and the Advanced Options page of the Options dialog WG Error Level page The WG Error Level page is for advanced users It lets the user determine how BioSIM should bn gt behave when it is unable to assemble sufficient du ee data to generate a regime for a given weather 4 st Snowgam cm _ Solar Radiation MJ m3 variable from daily data such as would be the case i if the run requires eight matched stations and a x database contains fewer than eight stations for a given variable BioSIM does not allow the user to modify error levels from normals The same applies to climatic gradients for which at least 23 normals stations are needed As snow and solar radiation variables are derived from temperature and precipitation data BioSIM does not take their absence into account For each climatic variable the user can choose one of the following options e Error If problems with the assembly of a weather regime are encountered due to insufficient data the weather generator returns an error message in the Job in Progress dialog and in the Output Message Log window BioSIM terminates the run e Warning The user receives a warning in the Job in Progress dialog and subsequently in the Output Message L
15. are displayed here when available The button opens the help file for this model when available if unavailable the button is greyed e Model input field drop down list This Se to O O field is used to specify the values of Name Exemple Use hiGiid model specific input parameters These Poesia P P P Model Climatic Daily can either be the default parameter values About the This model computes climatic daily variables a Model Help provided by the models interface model definition or a user defined set saved in the project s Model Input subdirectory Simulation inputs Model input Define Model Input To specify a new set of parameter values for the Weather generato 2008 2010 7 L_ Define we Inpa model selected or to edit an existing set the user tint Gps contort el must click on the button to the far him 1 Deterministic right of the field to open the Model Input Editor BF Reploce locations by weather stations dialog and the model s Specific Interface dialog eee ree ee SE En The identity and meaning of model parameters are Number of fles generated Slocsl x 1 params x 1 reps 13 oa Approximate duration TGTime 00 00 00 totalT ime 00 00 01 model specific Internal name ICSazb Cancel Once a new input file has been created it automatically becomes available in the Model input field s drop down list and is subsequently available whenever the model in q
16. execution of a simulation the other three are optional indicated by an asterisk The user can place the columns in whatever order However it is essential that the name of each header be spelled exactly as follows Name ID Latitude Longitude Elevation Slope Aspect The user may add additional columns in the Locations list file If there are additional columns added to the basic seven ones they are handled collectively as Others in exports by ae BioSIM 10 User s Manual BioSIM if the Others checkbox is checked in the Export window It is not possible to select a subset of these variables for export The four compulsory columns of a BioSIM Locations list file Name Latitude Longitude and Elevation must never contain empty cells This means that every location should have a value for each variable On the other hand the three optional columns ID Slope and Aspect may be left empty Latitude and Longitude In BioSIM latitude and longitude coordinates are always expressed in decimal degrees DD Latitudes located south of the equator and longitudes located west of the prime meridian are negative Coordinates in degrees minutes and seconds DMS must be transformed into decimal degrees DD by applying the following transformation DD SIGN DMS ABS D M 60 S 3600 For example DMS DMS DD Elevation Elevations are always expressed in meters m In BioSIM all L
17. exports in the export file dates It is often useful to have each element of a time representation exported as a separate column e g year and ordinal date In that case the user must replace the default separator by the list delimiter as defined in the List delimiter field For example if the list delimiter is a comma GY j outputs two columns one for the year and one for the ordinal Julian date The user must also remember to change the column header definition in order for the two headers to be exported e g Year OrdinalDate 64 BioSIM 10 User s Manual The following list contains the most common time format codes followed by their description and an example B August c Date and time representation Thu Aug 23 14 55 02 2001 j Day of the year 001 3661 Ds o o o m Month as a decimal number 01 12 08 o o o PN E first day of week one 00 53 T Sunday as 0 0 6 first day of week one 00 53 Z Remove leading zeros e g 6 instead of dE 06 Advanced Options page While these options are often adequately set up by amp default it is good to know what they are and how Cie er EG NE they are set ting Wam when a simulation point is farther than 500 km of the nearest nomal or daily station E Run simulations even if there are missing years in the daily database Run simulation even if none of the simulation points are within km of the nearest
18. hxGrid Mapping from the menu bar or right click on the component in the Proj ect Interpolation method Universal Kriging v e Input DEM Quebec30s tif X window and select Add Mapping from Sen eo v variable name the pop up menu Output map name cv M pere pese p parameter name Pre post transformation offers the possibility to transform data before and after interpolation Pre post ess transformation 5 A mapping component is used to perform a spatial interpolation on the results of a parent component e g on a simulation an analysis a function analysis etc It produces as many maps as the number of different combinations possible between temporal dimensions variables and parameters BioSIM 10 User s Manual 450 Output directory C BioSIM Projects DemoBioSIM MapOutput Cross validation only Cancel The two ingredients required for mapping in BioSIM are 1 an input DEM that has been adequately linked to BioSIM using the browse L button to the right of the Input DEM field and 2 a component usually an analysis using locations in the area covered by the input DEM Mapping components can be added to a component whose output results are either statistical or temporal dates e g to create a map of the date at which the frequency of spruce budworm fourth larval instar is at its maximum or peak L 4 for short and they can be added directly to simulations
19. if a subset is not specified the analysis uses the entire time period covered by the parent component If beginning and end dates are used they must be entered in the same format e g year month day The Use current date shifted by checkboxes can be used to specify beginning and or end dates relative to the current system clock date This is a special feature that 1s useful when BioSIM is executed to forecast events in real time on an automatic basis The units of the shift are defined by the temporal type e g annual monthly daily For example in a daily type of simulation the number entered in the edit boxes shifts the current day by that number of days When defining a subset of the time period the final step is to select the time coverage The user has two choices Continuous button l By default the When tab is set for coverage of a Continuous time period using boundaries defined by the beginning and end dates As a result data from the entire period covered between the beginning and end dates are used by BioSIM BioSIM 10 User s Manual a Year by Year button If the Year by Year time coverage is selected BioSIM uses data from the period covered between the beginning and end dates on a year by year basis Data outside the specified year by year dates is disregarded during computation NOTE If the beginning date month and day excluding the year falls after the end dat
20. in the list The right hand side panel displays the properties definitions of the selected output variable Fields in this panel are as follows 56 BioSIM 10 User s Manual Name field Internal variable name that must not contain spaces or special characters e g etc This is the name used by BioSIM to refer to this new variable The name in the Name field corresponds to the name given to the variable in the left hand side panel and must be edited there not in the right hand side panel either by double clicking on it or by using the F2 key Title field Text that appears in the result column header either in the Data tab of the main window where the results can be viewed or in export files text or spreadsheet when the results are exported using the Export Now El or To Spreadsheet 1 buttons in the Export window Precision field The number of decimal places used to display or export results Equation field Definition of the output variable equation Each new variable is defined by one equation using a combination of operators functions constants and input variables those listed in the Available variables list The name of a new variable cannot be used in the equation defining a second new variable to do that a function analysis can be created as the child of another function analysis Each equation is typed in by the user in the Value column next to the new variable s Equation field on the right hand side
21. open the Options dialog of the Directories page in which the user can add and remove links to various directories or simply see the directories paths Before a DEM can be linked to BioSIM the projection information must be specified If BioSIM does not recognize the projection of a DEM it cannot use it BioSIM itself does not perform changes in DEM projections To do this you need to use another software e g ShowMap which is provided with BioSIM at installation or Quantum GIS GDAL Translate Arc Map etc BioSIM accepts all GDAL Raster formats http www gdal org formats_list html as the DEM s extension BioSIM recommends using GeoTIFF tif formats The Arc Info export grid binary file format flt is also supported By default BioSIM generates output maps in the bil format when the input map is in flt format ee BioSIM 10 User s Manual B10SIM also supports ArcInfo ArcMap Partager avec v Diaporama Graver Nouveau dossier Nom Date Type i Taille grids but in order to use them a i A cc 99 di testl20x120F 21 04 2011 16 50 Dossier de fichiers configur ation file with an aux or test120x1201 20 04 2011 10 08 Dossier de fichiers aux xml extension 1S needed L_ test120x120 i rejog 10 54 Roc men XML 2 G 3 test1204 20130 26 04 2011 17 12 Fichier AUX 0 Ko Usually this file is created by ArcGIS but 1f it does not exist the user must create an empty text file with the same na
22. positive eal numbers Logit transformation probabilities To transform event data the user can access the Transformation dialog by clicking on the browse L button to the right of this et rn field Apply range limits checkbox Ml Used to limit map values to PEPEE a given range between Min and Max If the limit to range fo checkbox is unchecked O map values outside the range of nr values between Min and Max are set to missing values If it is Ta mane checked M map values below Min are set to Min and those above Max are set to Max Output directory field Shows the directory in which the output map will be stored The browse L button to the right of this field can be used to access the project s MapOutput directory to see what output maps it already contains for example Cross validation only checkbox Ml When this box is checked Ml only the best mapping parameters and the cross validation R goodness of fit of the interpolation are computed The map itself is not created Advanced Mapping Options dialog Fields in the Advanced Mapping Options dialog accessed by clicking on the browse button to the far right of the Interpolation method field are activated in accordance with the interpolation method selected in the Mapping dialog Number of points field Number of nearest neighbours selected to perform the interpolation Output no data field Value of the missing no data values in the
23. select Tools Options from the menu bar or click on the Options button in the main window s toolbar The Options dialog is also accessible through many of the other dialogs either as an Options or a browse J button In those cases BioSIM has been configured to redirect the user to the relevant page of the Options dialog This dialog contains six pages used to specify or modify key set up information BioSIM Options page By default BioSIM does not save the project upon execution If you want BioSIM to save the project automatically just before executing a task check the Save at execution checkbox M Directories page In this page BioSIM s global and local directories or paths are listed Two can be set by the user global Weather and Input DEM elevations while the others are set automatically when BioSIM is installed Home and Models or when a project is opened or created local Weather and Input DEM Global directories These directories apply to all projects Home C Program Files NRCan BioSIM The user can specify several global directories for Models C Program Files NRCan BioSIM Models normals and daily weather databases by adding i them to the global Weather directory list using the browse button to the right of the list field oS ee Likewise global Input DEM directories can be Local directories These directories apply to the current project added
24. to send the selected Model input file to the text editor for advanced users Copy Used to copy the selected Model input file BioSIM 10 User s Manual 2900 Set as default Used to replace the model s current default parameter values by the values currently specified in the Model Specific Interface dialog fields these become the new default parameters used whenever this model is selected F2 key Used to rename a Model input file Model Specific Interface dialog Each model in BioSIM has its own us ll Model Specific Interface dialog p Egg development The image on the left is an example 2 211 of a model interface in this case the 77 Ga Opoto date Gray Sawyer 190 Byes PE Take ovip date of previous year No me Gypsy Moth Seasonality 2012 CTIE model Each field in this dialog appi mortality No a a e contains a parameter that can be modified by the user Fields can be text integers real numbers Booleans Yes No drop down lists or file names associated with a browse L button Files that are local to the project can be specified in a file name field with the Project keyword For example Project Input Deposit dat points to the file Deposit dat in the project s Input subdirectory To specify non default parameter values the user must click on the New 3 button in the Model Input Editor dialog type in a Model input file name and change the desired parameter value s in the M
25. use in BioSIM using spreadsheet software such as Excel 3 Microsoft Excel ities OOOO AE Fichier Edition Affichage Insertion Format Outils Donn es Fen tre MEA FEIE NIA 6 4 523 8 09 gt x 51 i fe A B k D E G H 1 City Lat N Lat N Lat N Lon W Lon W Lon W Elevation 2 Springfield 42 6 2 72 34 18 61 3 Tampa 27 57 18 82 27 22 13 4 Toronto 43 40 23 79 24 6 122 5 Vancouver 49 13 12 123 6 12 52 6 Virginia Beach 36 51 22 75 58 50 4 7 Washington 38 53 5 77 2 12 0 8 Winnipeg 49 54 7 97 7 17 227 Once such a list has been created in the spreadsheet e All latitudes and longitudes must be converted into decimal degrees In the decimal degree system latitudes south of the equator and longitudes west of the prime meridian are negative e If the file does not contain elevation data a column called Elevation must be added and filled with BioSIM s missing value code 999 Elevations can subsequently be extracted from a DEM using the ShowMap application However following extraction the file must be checked to verify that all elevations were extracted correctly because BioSIM will not work properly if some locations still have elevation values of 999 e Commas or semicolons cannot appear anywhere in the file s columns e The file must contain the four compulsory columns Name Latitude Longitude Elevation spelled exactly as mentioned here BioSIM 10 User s Manual ES
26. variable that 1s to be mapped it is harder to spatially interpolate certain types of variables such as precipitation 2 the size and resolution of the input map 3 the topography of the region being mapped flat or complex and 4 the number of weather stations available in the area being mapped When an insufficient number of points is used the results of the spatial interpolation can be erratic On the other hand if an unnecessarily large number of points is used the computation time can be excessive Trial and error is the best way to achieve a good balance between these two constraints A rough estimate can be made using the following guidelines For a province or a state between 600 and 3000 points For a large country such as Canada or the United States between 10 000 and 30 000 points Aggregation factor field Used to increase the density of points in mountainous regions point density varies with topography This is a recommended setting Extract extreme checkbox 1 When checked regionally extreme elevation points low and high will be oversampled at a rate of 1 point per 1 600 cells Exposure 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 not to be included in the locations list the No exposure radio button must be selected However if exposure values are to be included t
27. variants Regional A TPS is created for each pixel This can take a long time to compute Global a global TPS is created using N points Points are selected at random Global with clustering N is used to determine the number of clusters A K mean clustering is used to regroup similar points then a global TPS is performed For more information on this interpolation method see http en wikipedia org wik1 Thin_plate_spline For a thorough discussion see www geometrictools com Documentation ThinPlateSplines pdf Displaying Mapping Results After a mapping component is executed the results for each mapped variable include e the observed results of the parent component and estimated mapped values displayed in the Data tab of BioSIM s main window e output maps in the same format as the input DEM e the cross validation goodness of fit R results for each map generated by the component displayed in the Execute Message Log window The resulting map s can be displayed by selecting the component in the Project window and choosing Project Show Output Map s from the menu bar or by right clicking on it and selecting Show Output Map s This sends the maps to ShowMap an independent application distributed with BioSIM Right clicking again on the mapping component and selecting Show Locations displays the locations list on the maps 50 BioSIM 10 User s Manual Running Components Creating the Output Database
28. 1 2010 and that years are only stochastically distinct without any particular annual ordering involved Daily Data radio button Used to run simulations using weather data from daily stations as input daily mode Normals database name field drop down list Used to select the normals database to be used in the simulation Normals are always used to fill missing values or forecasts Daily database name field drop down list Used to select the daily database to be used in the simulation Link a New File daily mode Used to add paths for daily databases to the linked paths list thereby making them available in the drop down list Nb stations field Number of nearest daily stations to match with each simulation location BioSIM 10 User s Manual ES First year and Last year fields These fields are activated when the daily mode is selected The user must enter the first and last year s for which to run the simulation inclusively Use forecast checkbox activated only in daily mode When checked the Weather Generator uses forecasts available in the daily database instead of normals Data are considered forecasts when their date is beyond the current date Exposure factor Albedo field drop down list The user can select None or Conifer canopy to calculate the overheating of daily maximum temperature caused by exposure to sunlight Random number type field drop down list The Always
29. 100x more weight because of its profound effect on temperature and precipitation d X X Y Y Pa 100 Z Z yp The number of stations of each type normals and daily matched with each location can be set by the user BioSIM recommends eight stations The stations selected from the two databases are independent After adjustment for differences in elevation latitude and longitude see below for explanation between the simulation point and the weather stations data monthly means or daily values become a weighted average with 1 2 as weight Note that daily values are weighted on a daily basis The weighting takes into account the presence of missing data in daily station records Adjustment for differences in elevation latitude and longitude 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 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 observations from the 24 nearest stations in the normals database The regression equation is Tmin Tmax or Precip a b Elev c Lat d Lon where b c and d are gradients b is in C m and mm m c is in C North and mm Nor
30. 35 148 R gni re J St Amant R Duval P 2010 Predicting insect distributions under climate change from physiological responses spruce budworm as an example Biol Invasions 14 1571 1586 Safranyik L Carroll AL R gni re J Langor D W Riel W G Shore T L Peter B Cooke B J Nealis V G Taylor S W 2010 Assessment of range expansion of the mountain pine beetle in the boreal forest Can Entomol 142 415 442 Tobin P C Sharov A A Liebhold A A Leonard D S Roberts E A Learn M R 2004 Management of the gypsy moth through a decision algorithm under the STS project Am Entomol 50 200 209 Tobin P C Van Stappen J Blackburn L M 2010 Human visitation rates to the Apostle Islands National Lakeshore and the introduction of the non native species Lymantria dispar L J Environ Manag 91 1991 1996 6 BioSIM 10 User s Manual Tran J K Ylioja T Billings R F R gni re 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 Installation Installation BioSIM is distributed on the Internet in the form of a set up file using the following link ftp ftp cfl scf mcan gc ca regniere software BioS IM BioSIM10_x_xSetup The user must download the file BioSIMxx_x_xSetup exe where xx_x_x is the most recent version e g 10_1_0 for release 10 1 0 in a tempo
31. 4397 teletype for the hearing impaired Cette publication est galement offerte en fran ais sous le titre BioSIM 10 Manuel de l utilisateur num ro de catalogue Fol 13 3 137F PDF Acknowledgements BioSIM was developed over a period of several years and benefited from the contributions of many people including users who are too numerous to name here However we wish to acknowledge the following people for their special contributions Lukas Schaubb Jesse A Logan Michael Roden Barry Cooke Vincent Bergeron and Manon Gignac The current version of BioSIM for Windows was conceived and programmed by R mi Saint Amant The development of BioSIM was made possible thanks to the financial contribution of several Canadian Forest Service partners In particular we wish to acknowledge the following members of the SERG International Committee Forest Protection Limited Quebec s SOPFIM the provincial governments of Ontario and British Columbia and the USDA Forest Service BioSIM 10 User s Manual ii Table of Contents BioSIM Overview PR 1 anodu CIO i eene a E E E E T E E E l Scientific Documentation s srcsneacencne ssasncannceanions caanresemensnene quasneiwneassnes EKNE EE E qrawaieneashisecwennwcneds 3 At the heart of BioSIM is a daily weather generator ss 3 It Was becn APPLIEd to pint CCOMO GY einen E Erare AE ose 3 lt has Deen applied to several INS COUS ne 5 Bio IN TAa a te E E E E E I SO e E eee aaseanseedeaue s
32. Biometeorol 51 295 305 R gniere 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 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 gniere J Nealis V Porter K 2007 Climate suitability and management of biological invasions gypsy moth in Canada Biol Invasions 11 1
33. E E E R E E 41 WV MOU TAI PR RP 42 RON a ae sesesdies 42 Generating Maps Spatial Interpolation 45 D PTA OG rec crac mawccnumenninn er cunasnenesuesaue cain wncusce nit EEE A E E S 45 Tons TOM OR OO aan setae 47 Advanced Mapping Options dialog ss 47 TOO M TRO a ee ee a 48 Interpolation method 1 spatial regression ss 48 Interpolation method 2 universal kriging ss 48 Interpolation method 3 inverse weighted distance 49 Interpolation method 4 thin plate splines ss 50 Displaying Mapping RSW 8 dense seems sen on ess daeelies oies 50 Running Components Creating the Output Database 51 1 LE LA PES CS 1 LL S RIE EE NE UN A 92 D E E E E E E EE 52 P rore RU e E eo es to tel one 52 CAD A E E E EE ees 53 DAS SD mer er ener Sree eer rey erent err rent aren errr 54 CDD ITO CA OR a a a a E en 54 Other Components cog cxcsa secs ssc secivvsnaeeaiceescnea bce scaeeassanieseaauieuies cana ee ea ee on 56 Fan OM AnD S ot ctor ste nasetoe E E E E E E 56 Function Analysis GIAO O c sceatcncosssasashaeaeteeedeansutaceonsccnasaasunesertncedeaneudsceaessccrenatudeasaninerieasaads 56 Analysis Function ECSU CANO useisiin conan ciecaencsecteanatecunnteasceusten 57 PT ASS 58 BioSIM 10 User s Manual po IV MCT CEE 59 D a en AE 60 Weather Station Matches for Locations Lists ccccccccssssesssececeeecea
34. E amples DemobioS Myw eather S ample 2007 201 0 0 ailyStations Daily Graph VALCARTIER AIQUE ECF0185F3 46 9 FAIVIERE VERTE OUESTIQUE EC7016675 46 98 STE CHRISTINE QUE ECY01 000 46 82 QUEBECVJEAN LESAGE INTLIGU EC701S5001 E 46 79 STE FO U LAVALIQUE ECFOIQO04 46 75 Export Report The first drop down list on the upper left corner allows the user to select the type of weather data temperature precipitation humidity or wind speed for which to view matched stations all stations do not contain the same information 60 BioSIM 10 User s Manual When a simulation is using daily data as input station matches for the type of daily weather data selected in the first drop down list can be viewed by year using the second drop down list The years available to the user correspond to the range previously specified in the Weather Generator WG Parameters dialog The button graphs the weight of data from each daily station matched on a daily basis weights can vary due to missing data The graph allows the user to see if and for which station s missing data exist in the daily data which are to be supplied for each location When a location is selected in the left hand side list field all drop down lists and other list fields of the dialog are updated with the information relevant to this location The first list field on the right hand side displays the coordinates and elevation of the selected location The second list field
35. Examining Results Data Once a component has been successfully executed Mean the results can be viewed by selecting it in the Project Loc ae TotalPrecipitation nm window The Data tab of BioSIM s main window 1 ss ais i 2 St Alban 2009 103 003 shows the results in tabular form while the Graph tab prm ET perem allows the user to create and display graphs 4 Scott 2008 134 375 5 Scott 2009 127 49 The drop down list in the upper right corner of the hE al i main window allows the user to choose the statistics T Data Graph 4 4 H to be viewed in the Data tab The Nb Values selection is particularly useful to verify that statistics were calculated as the user intended For instance the user can verify if statistics were compiled from daily values or from monthly values 1 e 365 days or 12 months The results can comprise five components locations parameters replications time and variables When viewing the results each of the first four components is displayed in a distinct column while the variables component is displayed in as many columns as there are variables Whenever a component has a single value its column is automatically hidden If the variable represents an event its values are displayed as calendar dates in daily monthly or annual format with or without the year depending on the temporal type and mode of the component in BioSIM temporal types can by annual monthl
36. Ft y aai minimum and maximum air temperatures h ae 47 C precipitation mm dew point C Real time 2 Motta wind speed km h relative humidity y h snowfall and snow depth mm of water and solar radiation MJ m for one or several years These data are assembled from stations found in each of the two weather databases normals and daily with the latter including forecasts In assembling this weather regime BioSIM goes through the following steps e Choice of the nearest daily stations for each year when used in daily mode e Choice of the nearest normals stations always e Adjustment for differences in elevation latitude and longitude e Generation of daily values from monthly normals when needed BioSIM 10 User s Manual a7 e Assembly of all weather e Temperature adjustment for heating caused by exposure slope and aspect The next section describes each of these steps in detail Choice of the nearest sources of weather data Choice of the nearest weather stations for a given simulation point is made by categories of weather information temperature precipitation humidity wind speed and for daily data by year The nearest distance is computed in Cartesian distance the nearest stations are selected on the basis of the straight line distance d between the simulation point and the weather station Differences in latitude X longitude Y and elevation 2 are all in m Elevation is given
37. Linked Data There are four types of data that can be linked to BioSIM Normals weather databases Daily weather databases Input maps DEMs Models Normals databases daily databases and input maps can reside in different directories These files can be global to all projects or they can be local to one project All of them can be stored either in local project specific or global directories Local weather data must be placed in the Weather subdirectory of the project and local input maps DEMs must be placed in the InputMap subdirectory of the project These subdirectories are always searched first by default and do not need to be specified Global directories are specified with the Directories page of the Options dialog which can also be used to modify the list of directories in which BioSIM should look for weather databases and DEMs 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 properly set before running the models The same applies to DEMs If several files share the same name in different directories BioSIM lists them all in the lists used to ess NS choose among them but can only access the first one s found which depends on the order in which directories are me Comis USA 1981200 searched Project subdirectories are always searched fi
38. Uncertainty in detecting climate change impact on the projected yield of black spruce Picea mariana For Ecol Manag 259 730 738 Girardin M P Bernier P Y Gauthier S 2011 Increasing potential NEP of eastern boreal North American forests constrained by decreasing wildlife activity Ecosphere 2 1 23 Girardin M P Wotton B M 2009 Summer moisture and wildfire risks across Canada J Appl Meteor Climatol 48 517 533 Govind A Chen J M Bernier P Margolis H Guindon L Beaudoin A 2011 Spatially distributed modeling of the long term carbon balance of a boreal landscape Ecol Model 222 2780 2795 Guillemette F B dard S Fortin M 2008 Evaluation of a tree classification system in relation to mortality risk in Qu bec northern hardwoods For Chron 84 886 899 Hamel B B langer N Par D 2004 Productivity of black spruce and jack pine stands in Qu bec as related to climate site biological features and soil properties For Ecol Manag 191 239 251 Houle D Couture S Gagnon C 2010 Relative role of decreasing precipitation sulfate and climate on recent lake recovery Glob Biogeochem Cycles 24 Le Goff H Flannigan M D Bergeron Y 2009 Potential changes in monthly fire risk in the eastern Canadian boreal forest under future climate change Can J For Res 39 2369 2380 Michaelian M Hogg E H Hall R J Arsenault E 2011 Massive mortality of aspen following severe dro
39. alled Kauffman effect and to include the occurrence of extremes in simulations 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 threshold temperatures Temperature fluctuations across 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 gniere amp Bolstad 1994 The method used in BioSIM to generate daily values from monthly statistics is described in R gniere amp St Amant 2007 Generation of daily precipitation from monthly normals 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
40. ane 7 DS LE TE ONE TE MES AEE en a da eee de cn 8 MOTTE DO AS EEEE O E te EE 8 ee sare eee A A E N na amen seme E A ane A te eee E T 8 APC CMC AIS OUE de e am ne cest ane ws ceuesaaeninaeveceees 8 RO IE ine Mere tre eer eam eee ene Oe enrnr eenre were errr ere er aoe 9 Ci DSC UST ACC os wasp tessa conc ee td de E 9 Command Hne CX CCUMOM x secerni a AE a A ANERER E EESE 9 How BIO NN ORDRES ame E EE 9 FCC CO ANG oO aor a E E E E 9 WC al Mer Gaba NOLS MMA ONG esaa E E E EE 10 BIOS M s Mam NON eo E 12 PrO EWN O a Ree ee ee ayn en nn erate mane er E E fer miter Cane tr re E 13 Bio TINE OCC RE asnucnascer sgescudeumnench soece wasnaeasaaisoecesaaahescieosseesraates 15 Weather Data WUD LOO INR as liens ee one nee nes etes ee eee 17 WG ater RE tS SNM ga og users O E E desc OE E 17 Choice of the nearest sources of weather data Us 18 Adjustment for differences in elevation latitude and longitude 2 0 0 0 eeeccccccceeeeeeeeeeeees 18 COMCC HON TOF SIO AIG As OC Cle oases ne ed a a Sn Re us 19 Generation of daily temperature from monthly normals 19 Generation of daily precipitation from monthly normals 19 Generation of daily relative humidity and dew point from monthly normals 19 Generation of daily wind speed from monthly normals 20 Generation of snowfall and snow water equivalent
41. ansen 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 Houle D Duchesne L Boutin R 2009 Effects of a spruce budworm outbreak on element export below the rooting zone a case study for a balsam fir forest Ann For Sci 66 707 Logan J A Macfarlane W W Wilcox L 2010 Whitebark pine vulnerability to climate driven mountain pine beetle disturbance in the Greater Yellowstone ecosystem Ecol Appl 20 895 902 Logan J A R gni re J Powell J A 2003 Assessing the impacts of global warming on forest pest dynamics Front Ecol Environ 1 130 137 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 10 User s Manual EN 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 IS 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 gniere J Worner S 2007 Risk assessment of the gypsy moth Lymantria dispar L in New Zealand based on phenology modelling Int J
42. be exported need to be set by the user by clicking on the browse button w De 5 Region page The Region page allows the user to modify the variable delimiters and the time format when moe exporting a file SIM Options Letdeimter Deimter between variablesto be exported een tle Dee Bangke Decimal delimiter field Used to change the default Sat are ce eme oti decimal character in variables to be exported a gt Om ns Sn Usually this character is a period but in French 3 te Fm He Foma environments a comma is often used In that case si CS SE eea a Year Month Day t Y m d h Month Day Hour m d h a list delimiter character other than a comma must be specified in the next field Advanced 5 List delimiter field Used to change the default list delimiter between variables columns to be exported This is especially important in the case of French environments where a comma is used as a decimal place delimiter A semi colon can be used as delimiter in such a case Time format field Used to edit both the header and the format of the time variables in the For Each Year and Overall Years modes Each time a variable is added to one of the format columns the corresponding header must also be added to the table The information entered in the Time format field table affects the way in which BioSIM displays in the main window s Data tab and
43. cations List Editor Once a new locations list has been created it automatically becomes available in the Locations list field s drop down list and can be selected for any subsequent simulation regardless of the model used The button opens the Parameters Variations dialog Occasionally when conducting model behaviour analyses the user can vary one or several model parameters in a simulation definition The parameters available for this type of work are model specific e Replication field This field is used to enter the number of replications the user wishes to perform for a given simulation Two things must be taken into account when assessing whether or not replication is required the source of weather input and the nature of the model If a simulation uses either normals disaggregation or a stochastic model or both it needs to be replicated Otherwise replication is unnecessary When replication is required an adequate number of replications must be estimated based on the balance between precision and processing time The following basic guidelines can be used to choose an adequate number of replications Minimum number of replications 10 Commonly used number of replications between 30 and 60 Extensive replication 150 No number of replications provides constant output The important thing to remember is to use a number of replications that provides what the user is ready to consider as close enough constancy tolerance fo
44. contact R mi Saint Amant at Remi Stamant RNCan 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 may contact BioSIM developers by e mail at the above addresses or by regular mail at Dr Jacques R gni re or R mi Saint Amant 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 O al BioSIM 10 User s Manual Running BioSIM Graphic user interface To launch BioSIM the user can either double click on the BioSIM icon located on the desktop or select it from the computer s Start menu BioSIM s interface is available in both French and English To choose a language the user must select Tools Language and then Francais or English from the menu bar For the change to take place BioSIM must be closed and restarted Command line execution BioSIM can be run from a command line in script mode using Windows Explorer s task scheduler This is very useful when setting up a scheduled task to be run automatically e g every day When BioSIM is run in command line mode only the checked components of the project are executed To execute BioSIM in script mode use the following syntax BioSIM10 exe ProjectFilePath E where ProjectFilePath is the complete path to a BioSIM project file
45. d Enter the number of lags or let BioSIM find the best one Lag distance field Enter the lag distance or let BioSIM find the best one Detrending field Usually detrending is not necessary occasionally however interpolation is improved after detrending By default BioSIM does not detrend External drift field Used to choose the external drift variable s Usually the most useful drift variable is elevation however other variables may be chosen alone or in combinations of two A useful combination may be elevation and exposure slope aspect on sufficiently small map extents when exposure is part of the locations list Apply local range limits standard deviation M checkbox When this box is checked Ml range limits are applied to the map cell being estimated local based on the minimum Min maximum Max and a multiplier specified in the corresponding field of the standard deviation of neighbourhood point values If the Limit to range checkbox is checked map values outside the range are set to the local range limits Otherwise they are set to no data Interpolation method 3 inverse weighted distance The classic inverse weighted distance IWD interpolation method computes the value of a variable u at location x y by calculating the average of N nearby values u at locations xi yi weighted by the inverse of their distance d to the point of interpolation N P u gt wu where w Ji and h x x y y
46. d from locations in Canada derived from Brown et al 2003 Brown R D Brasnett B Robinson D 2003 Gridded North American monthly snow depth and snow water equivalent for GCM evaluation Atmos Ocean 41 1 14 For locations above 30 N in North America between 180 and 50 temperatures at which precipitation falls as snow and at which snow melts are functions of longitude T 1 5814 0 021 Longitude 5 SNOW T a 3 762 0 043 Longitude 6 Longitude is expressed in decimal degrees negative in the Western Hemisphere positive in the Eastern Hemisphere For any point located outside this range Tsnow 0 519 and Tmen 8 062 are used Generation of solar radiation The amount of solar radiation is calculated by a module extracted from MTCLIM Version 4 3 Peter Thornton Numerical Terradynamic Simulation Group School of Forestry University of Montana Missoula MT USA available at http www ntsg umt edu project mtclim o 20 BioSIM 10 User s Manual Assembly of the regime Weather regimes are assembled in the following manner First adjusted and weight averaged daily randomized normals fill the daily times series of needed weather variables Then if any daily data including forecasts are used and available they are adjusted weight averaged and used to replace randomized normals Thus any missing values in the daily observations and future weather beyond forecasts are filled with randomized normals
47. d in the Where tab Additional notes The output of an analysis always depends on what is selected in the drop down list of the output time format in the How tab output For example if the time period specified in the When tab input is for May 15 to June 15 2011 and the output time format in the How tab drop down list is set to Monthly and For each year the result of the analysis consists of two values one computed for the 17 days specified for the month of May May 15 to 31 and one computed for the 15 days specified for the month of June June 1 to 15 The Input time format grayed of the How tab always represents the temporal output time format of the parent component it is always greyed and cannot be modified in the Analysis Editor dialog ag BioSIM 10 User s Manual Generating maps spatial interpolation Mapping components are used to transform punctual results into surfaces maps and produce as many maps as the number of dimension combinations specified in their parent component e g months variables This is why resizing through analysis components must be done prior to adding a mapping component When creating a map component in BioSIM the following steps must be followed Add a simulation Generate a locations list from a DEM of the area to be mapped Add an analysis of the variables of interest Add a mapping component using the DEM of the area to be mapped i LE The key to producing an ou
48. displays information on the nearest normals stations matched to the selected location s while the third list field displays information on the nearest daily stations matched to the selected location s Note that for a given location the normals and daily stations matched may differ Both the normals and the daily stations list fields contain a column that displays the weight each weather station has in generating weather data for the selected location assuming there are no missing data These weights are inversely proportional to the distance from the location assuming there are no missing data The greyed normals and daily fields display the paths to the databases used for the simulation A complete report of all stations matched for all locations all weather categories and all years can be exported by clicking on the button BioSIM 10 User s Manual 6 Models in BioSIM Simulation models that are suitable for inclusion in BioSIM s model base must e be weather driven accept daily minimum and maximum temperature in C and optionally precipitation in mm wind speed in km h snowfall and snow accumulation in mm of water dew point in C relative humidity in and solar radiation in MJ m 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 interactive requests for input e accept as their sole command line requ
49. drop down list by choosing either Regular Grid a uniform rectangular grid or At Random distributes points at random in non missing areas of ae 300 x D a the DEM At Random is the recommended method 7 2 0109 i Extectentems Next a map must be selected from the drop down list in No exposure BE AE the DEM field BioSIM reads point coordinates Use DEM exposure Sed elevations and optionally exposure slope and aspect from the DEM C Sub region boundaries The Input Maps page of the Linked Data Editor dialog can be used to link new maps to BioSIM accessed by clicking on the browse button to the right of the DEM field Number of points field Any number of points can be specified Note that for adequate map generation it is recommended to have n gt 500 When generating a regular grid point density in both directions 1s required north south east west BioSIM 10 User s Manual ES Number of points needed to obtain good mapping results In the tutorial s example a small number of simulation points is specified in the Locations Generator dialog to limit execution time However for an area of the size of the province of Quebec 300 is definitively not a sufficient number of points A number between 600 and 3000 would be more appropriate and would produce better results When trying to determine the number of points needed the most important factors to take into consideration are 1 the
50. e e Match stations normals used to obtain a list of the normals stations matched with each location of a simulation The results can be exported The information obtained is identical to the one provided by the Show Matched Stations dialog see below but is the result of a component e Match stations daily used to obtain a list of the daily stations matched with each location of a simulation The results can be exported The information obtained is identical to the one provided by the Show Matched Stations dialog see below but is the result of a component Valid only in a simulation based on daily mode e X Validation normals used to perform a jackknife cross validation of all weather stations in the normals database matched to the locations of a simulation This makes it possible to estimate the error associated with the simulation s normals input e X Validation daily only for simulations in daily mode used to perform a jackknife cross validation of all weather stations in the daily database matched to the locations of a simulation This makes it possible to estimate the error associated with the simulation s daily input Valid only in a simulation based on daily mode e Extract normals used to estimate normals using the current normals database at each location point of a simulation Internal name field An ID assigned internally by BioSIM to locate each component of a project 58 BioSIM 10 User s Manual
51. e BioSIM starts at the end date of one year and stops at the beginning date of the following year What tab The What tab allows the user to select a subset of General amp Where When What E2 How variables For example this can be done to limit the ee ae number of maps created in a mapping component PSone TM To select a subset of variables the user must check M the Sol Select variables checkbox and then select Ml the D variables of interest rs PET Cancel How tab The How tab is the most complex tab in the Analysis Editor dialog and it can be used to perform a wide i a g Statistic to work on analysing the results of a prior component Mean variety of tasks involving calculations and peine ransfomation General Where E When What 2 How transformations Osaa Mana z Event Time when variables are maximum Drop annual part of the temporal reference for mapping It is important for the user to understand that BioSIM Temporal transfomation of pe Daily gt stores results in one of two ways either in values or in mt memm gt ForEsoh Ver is image illustrates the time transformation statistics For example simulations store information as pr er enter af M values and analyses as statistics If an analysis is based me
52. ed environment that provides simulation models with geographically specific weather inputs functioning either in a historical mode or in a predictive mode forecast The software can be used anywhere in the world and for any time period as long as the necessary weather data are available It can be used to study and predict the course of any process driven by daily weather whether physical or biological provided that a simulation model for the organism or process is available The system can make predictions for specific locations points as well as for whole territories when provided with a digital elevation model DEM of the area under consideration These forecasts can form the basis of management plans aimed at the optimization of control methods as well as the efficient deployment of available resources based on timing or risk Coupled with climate change scenarios BioSIM can also be used to predict the course of these processes in a changing environment The basic functions of BioSIM are to provide geographically adjusted weather inputs control the execution of simulations and extract information from model outputs for presentation or further analysis BioSIM assembles weather data from two spatially referenced databases the normals database containing monthly long term 30 years weather statistics e g means variances correlations and the daily database containing historical daily weather records BioSIM selects the nearest weather
53. eeeesescceeeeeeaaeeeseeeeeees 60 Modeli in BioS IM a et noun eetausmasen 62 BIOS IM Options Dialog A ee id ado 63 BOS NO DOS RAR ae dns ae ii 63 DOC OS PA a 63 E E A CUS a seen A T E E E E E A 64 RO A E E E E EO E E E 64 Advanced OPHONS PANE ae no E ee aa ce 65 vi BioSIM 10 User s Manual BioSIM Overview Introduction BioSIM is a software tool originally designed to assist in the application of temperature driven simulation models in pest management Its main purpose initially was to generate forecasts of features or events in the seasonal biology of pests or their host plants Over the years its intended use has evolved as the software s capabilities have progressed in response to the needs of an increasingly diverse group of users These new capabilities have shifted the software s usage in certain regards and its applications are now rather broad All of BioSIM s simulation models are governed by weather conditions temperature precipitation humidity wind speed snow and solar radiation However recent models can now predict the effects of weather on physical processes e g forest fires in addition to biological processes growth and plant productivity development and performance of pests BioSIM can also be used as a tool in the development and analysis of such models for purposes of scientific investigation BioSIM governs the execution of daily weather driven simulation models It features an integrat
54. er can add an unlimited number of specific Name ID Latitude Longitude Elevation Slope Aspect 0 locations Duchesnay 1 46 969 71 64 166 StaAlban 2 46758 72066 78 0 E 46 506 71 068 145 0 Buttons in the dialog s toolbar are as follows ae BioSIM 10 User s Manual Add point Used to add a location to the locations list Remove point Used to remove a location from the locations list Generate points Used to generate locations from weather stations or from a DEM It opens the Locations Generator dialog NOTE If this button is selected for a locations list that already contains locations points the points generated using the Locations Generator dialog are added to the current list the list is not overwritten Show in decimal degrees Used to show locations coordinates in decimal degrees DD Show in degrees minutes seconds Used to show locations coordinates in degrees minutes seconds DMS Locations Generator dialog Generate from field BioSIM can generate locations lists from two different sources of data Digital Elevation Models DEMs or weather stations Generate from Weather type Normal Stations Generate from a Digital Elevation Model DEM To Weather DB Canada USA 1981 2010 generate a locations list from a DEM the user must vsar 0 Fite T P 5 select the desired generation method in the Generation M Generation type At Random type field s
55. es can be made to the development team For additional details on normals databases please refer to the Normals Data and Normals Data Editor document 10 BioSIM 10 User s Manual Daily database Observed daily weather data up to the current day are contained in a daily database Forecasts can also be included in the daily database and are used when short term weather predictions are needed to obtain more accurate model forecasts such as for pest control operations requiring pesticide applications Several daily databases are available at ftp ftp cfl scf mcan gc ca regniere Data Weather Daily Please note that a Canadian Daily Database containing weather data for the last two years is available and frequently updated usually daily For more details on daily data databases please refer to the Daily Data and Daily Data Editor document Each source of weather data in the databases a weather station is georeferenced latitude longitude elevation BioSIM selects the best sources of weather data for each point in the locations 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 the literature available on this process The weather time series sent to the simulation model can consist of daily data whenever available or requested forecasts for short term predictio
56. est 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 that run without requiring any interaction with the user and without generating output to display BioSIM executes each model run of a simulation task either by spawning the model as a child component through an operating system call to the model s executable file or a call to the model s dll In the most simple applications the call to the model contains a single request the name of a parameter file that the model must open and read Adapting a simulation model to meet the basic requirements of BioSIM involves some programming capabilities While a hugely practical object oriented base class called CBioSIMModelBase is available to perform all the required basic functions of models in BioSIM this class has yet to be documented It is possible to make arrangements with BioSIM developers for technical assistance in adding a model to BioSIM s model base Once a model has been adapted for use in BioSIM adding it to BioSIM s model list is a relatively simple task For additional details on how to edit existing models or for instructions on how to create new models in BioSIM please refer to the Models and model interfaces document O 62 BioSIM 10 User s Manual BioSIM Options Dialog To access BioSIM s Options dialog the user must
57. from monthly normals by BioSIM are given in R gni re amp St Amant 2007 Generation of daily relative humidity and dew point from monthly normals Relative humidity normals in BioSIM are 12 monthly averages r r is daily relative humidity 100 with O lt r lt 1 and 12 monthly o standard deviations of r Daily stochastic values of r are generated using the Beta distribution r e Beta a B 1 where BioSIM 10 User s Manual ESS er 22 1 and p 0 D 22 1 2 O O r r The physics for dew point calculations were taken from Whiteman 2000 Whiteman C D 2000 Mountain meteorology Fundamentals and applications Oxford University Press NY pp 302 305 After a few simple algebraic transformations from fundamental thermodynamics dew point temperature in C is given by r 1 Rp 3 AT L where T is air temperature C Ry 461 JZ K kg is the gas constant of water vapour L 2 5x10 J kg is the latent heat of water over water when there 1s no sublimation from vapour to ice and r is relative humidity 100 as defined above Generation of daily wind speed from monthly normals Wind speed normals in BioSIM are 12 monthly averages and standard deviations o of In daily mean wind speed in km h Stochastic daily wind speed values w km h are generated at random from the log normal distribution w e Lnorm o7 4 Generation of snowfall and snow water equivalent This module was calibrate
58. i l gt h j l Here Pis a positive exponent called the power parameter specified in the Power field typically P 2 The number of nearby values used in averaging N is specified in the Number of points field of this dialog A modified method thought to produce a superior interpolated surface uses a different weight function P w ti_ where q Aas and max 1S the maximum distance h among the N neighbours used l N bai j l in the averaging max Method field Select either Classic or Modified or let BioSIM choose the best one Power field Select a power parameter P or let BioSIM choose the best one BioSIM 10 User s Manual 490 Interpolation method 4 thin plate splines Thin plate splines TPS is an interpolation method based on neighbourhood splines Given a set of N neighbouring points the TPS surface is described by parameters that include six global affine motion parameters and two N coefficients These parameters are uniquely defined for each neighbourhood by solving a system of linear equations not by regression Other than the value of N specified in the Number of points field in the dialog there is only one user specifiable parameter in TPS The value of N has a major effect on interpolation time depending on computer speed A number of points lower than 100 is recommended for a regional TPS and lower than 2000 for a global TPS Method field Select one of the three available
59. ile is located one of BioSIM s global directories Weather Daily weather DailyStations Weather tif fit adf etc MapInput Model _ mdi Models under BioSIM Model input specific to a model ModelInput ModelInput Locations list Weather data for simulations 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 two types of weather databases normals and daily the latter includes forecasts All temperatures in BioSIM databases are in C precipitation is in mm of water relative humidity is in dew point is in C snowfall and snow accumulation are in mm of water and wind speed is in km h BioSIM assembles weather data for simulations at each point specified in the locations list supplied from two geographically referenced databases Normals database The normals database contains long term 30 year monthly statistics that are updated on a decadal basis By default BioSIM is provided with the most recent update of North American normals Canada USA 1981 2010 However several other normals databases e g Central and South America Europe World are available at ftp ftp cfl scf mcan gc ca regniere Data Weather Normals Databases taking climate change predictions into account are available at ftp ftp cfl scf mcan gc ca regniere Data Weather Normals ClimaticChange Requests for personalised databas
60. ist files It contains the names of all the Location lists found in the project s Loc subdirectory Buttons and fields in this dialog are as follows New Used to create a new locations list file that 2 BDEAPBBAE can be edited in the Locations List Editor dialog Le Specific Locations x Delete Used to delete the selected locations list file Edit Used to send the selected locations list file a text editor to C BioSIM Projects DemoBioSIM Loc Spedific Locations csv Copy Used to copy the selected locations list file Send to ShowMap Used to send the selected locations list to the ShowMap software in which locations can be viewed as points on a map Send to Spreadsheet Used to send the selected locations list file to the spreadsheet software previously specified by the user in the Links page of the Options dialog F2 Key Used to rename the selected locations list file The browse L button to the right of the read only field at the bottom of the dialog opens Windows Explorer and gives the user direct access to the project s Loc subdirectory into which locations lists can be added renamed and deleted All locations lists created using these two dialogs are saved in the project s Loc subdirectory when the user clicks on the button Locations List Editor dialog The Locations List Editor dialog is used to fx itear lie generate edit or view a locations list in which et the us
61. m 7 on a Statistical parent component e g another analysis Se ig e then the Statistic to work on field drop down list becomes available to allow the user to select statistics to eres _ work with For example if the user were to select Sum from the drop down list this would instruct BioSIM to use the sum among the results of the statistical parent component The second part of the tab is activated when the Define time transformation checkbox is checked 1 and it is used for time transformation It allows the user to transform results from one time format e g daily to another time format e g annual Each time format consists of a type daily monthly or annual and a mode for each year or over all years If the For each year mode is selected BioSIM separates values by year before working with them If the Over all years mode is selected BioSIM uses the entire time period pa BioSIM 10 User s Manual The following example is meant to illustrate the difference between the For each year and Over all years options A simulation generated daily values from 2005 to 2008 The objective of the analysis is to transform these daily values into monthly values If For each year is selected as the Temporal transformation of mode the result will be 12 monthly values per year for each of the four years of simulation outputs for a total of 48 values If O
62. m simulation points nor mals stations as input nor mals mode In Normals mode BioSIM uses monthly means from the nearest stations NE stations of the Normals database to generate daily stochastic values Weather generator parameters will control how the generator will estimate weather at the In Daily mode BioSIM uses daily data from the nearest stations Nb stations of the Daily database Gaps are filled with stochastic values generated from the Normals database Normals database name field drop down list Used to select the normals database to be used in the Weather input database Database name Nb stations simulation Normals data Canada USA 1981 2010 8 Daily data Sample 2007 2010 8 Link a New File normals mode Used to add eee paths for normals databases to the linked paths list pistes 2008 checked SIM uzes ry thereby making them available in the drop down list Lastye 2010 Use forecast Sen date Daly mode ond Exposure factor Albedo Nb stations field Number of nearest normals Pandomnumber ype Enr stations to match with each simulation location Number of years field This field is activated when the normals mode is selected because certain models require more than one year of weather data This field allows the user to enter the number of years for which to run the simulation Note that weather data are randomly generated from normals within a given SNGP 1 e 198
63. me as the original directory name with the addition of am aux or aux xml extension This step is necessary because maps are linked to BioSIM by the file extension Once this file exists the user can see and use the ArcInfo grid in BioSIM Linked Data Editor Models page gt Linked Data Editor The Models page lists the various models J CAS available for simulations they are automatically Zoa 7 installed in the software s Models JE nee subdirectory when BioSIM is installed me Orme met Degree Day Annual If a new model executable file with an exe or Q nik i dll extension is provided by the developers it E un is accompanied by a BioSIM interface file with lt a snc gs an mdl extension Copying these two files into Models Bisina the BioSIM Models subdirectory adds the Gypsy Moth Seasonality 2011 HemlockLooper new model to the model database Also the las n Jack Pine Budworm model often comes with documentation in the ReverseDegreeDay n A 7 Snnice Biidwiarm Bialanw form of a pdf file This file should also be copied into the _ BioSIM models z subdirectory C Program Files NRCan BioSIM Models Climatic Daily mdl 3 New Used to create a new model interface to link the corresponding executable file exe or dll to BioSIM x Delete Used to delete the selected model interface Edit Used to edit the selected model interface through the M
64. n when available and normals for prediction of processes under usual or normal conditions over the longer term or to fill gaps in observed weather BioSIM 10 User s Manual a BioSIM s Main Window E CABioSIM Projects DemoBioSIM DemoBioSIM biox BioSIN File Edit View Project Tools Help LE LL BA ce PE RPG TE FE Automaticaly export at execution Main window Climatology Shows the results of the selected component File name HS Example 1 Data tab table representation o i E as Subset Graph tab graphical representation D 4 Sum of precipitation Name oS Example 3 TIC 0 DD and UP Export window Latitude Project window Add a new Sends the results Filongitude D Phenology component to the project of the current p STE Example 2 component Aspect C 0 Average Output outside of Mothers BioSIM Selects Parameter Properties window the variables and Parameter Shows the properties of the the statistics to Replication Replication current component be exported Prime ur E Tme operti A X E Variable E Group Mame Execute Message Log window ge ak Sel lect eine Shows notifications concerning the last execution m Select Unselect all Description Lowest Execute Mean Export j Sum G Sum 2 araphAray Standard Deviation Standard Error Select Unselect all The main window s toolbar buttons contain the usual Bree Windows functions for editing ope
65. new project To create a new project in BioSIM the user must launch the software and select File New from the menu bar To open an existing project the user must select File Open from the menu bar BioSIM also starts and opens a project file that is double clicked on from Windows Explorer 16 BioSIM 10 User s Manual Weather Data in BioSIM Weather Regime Assembly BioSIM can function in one of two modes normals or daily Weather database used Normals Normals database only e Used to predict processes based on typical weather or climate change scenarios When a specific actual daily time series is not important Note that even if the normals database contains monthly values BioSIM automatically generates daily time series Daily database and if Used to predict processes under specific actual needed normals database conditions to fill missing values and forecast into the future When exploring the relationship between weather and the actual past or near future outcomes of processes Whether it is used in normals or daily mode BioSIM functions much in the same way only the weather databases used to provide models with input will change For each model run BioSIM assembles an input weather regime consisting of a 7 i daily time series of weather variables fat wl apy ALR ah Depending on the model one or several y ji LA she d fis of the following variables may be used Le 3 ar ii LS
66. ng on it BioSIM Projects BioSIM stores information on components simulations analyses etc locations list files input parameter files and other specifications in projects Each project is stored in a distinct project directory composed of a project definition file with the extension biox automatically associated with BioSIM upon installation and several subdirectories The user must select a location in which to store BioSIM projects for example C MyDirectory BioSIM where C MyDirectory is the user s selected path Projects can be stored at any location on the disk but it is preferable to store each project in a distinct project directory with the same name as the project itself For example if a project file is named DemoBioSIM biox the name of the directory in which it is stored should be DemoBioSIM In this case the directory structure would be as follows ii DemoBioSIM di Input External data files Loc Locations list Mapinput Project specific DEMs MapOutput Output maps Model Input Model input parameters L Output Analysis outputs graphs and export files gt Tmp Internal component results for internal BioSIM use Weather Project specific weather databases BB DemoBiosIMbiox Project file biox All biox files are XML files Because an XML file is an editable text file advanced users can edit biox files directly BioSIM 10 User s Manual ES Creating a
67. ning saving Logg MA RE EE cutting and pasting However some of the buttons s os 5 are specific to BioSIM Their use is explained in the Ve following pages The main window of BioSIM is composed of two tabs Data and Graph There are four secondary windows docked to the main window Project Hosta crapn Properties Execute Message Log and Export z EEE mn These can be moved around and closed as needed D The four secondary windows can be configured by the user When a secondary window is moved dragged using the mouse two pictograms appear on the screen one surrounding the main window and one in the main window Ei or in whichever secondary window P the user is attempting to drag the first secondary window into These pictograms highlight the area where the secondary window currently being dragged will be docked once it is released The secondary windows can also be left free undocked ee BioSIM 10 User s Manual All secondary windows can be grouped together in a single window docked to the main window and become accessible as tabs in this window Once it has been closed a secondary window can be reopened by selecting View Toolbars and Docking Windows from the menu bar The Project window lists all the components of a project It is through this window that the user can add remove and edit project components All tabs and windows in BioSIM are linked to the component selected highlighted in the Pr
68. normals or daily station checkbox l When simulation points are farther than a given distance from the nearest source of weather data 300 km by default rete hG paralel computaton Ms mors stalig nd on your compter and ao BioSIM usually aborts the simulation and sends an error message to the Output Message Log window The default distance can be changed and BioSIM can be forced to run despite this situation E Do not remove temporary files after simulation for debugging Warn when a simulation point is farther than km of the nearest normals or daily station checkbox ll BioSIM always sends a warning to the Output Message Log window when simulation points are farther than a certain distance from the nearest source of weather data 500 km by default This distance can be changed BioSIM 10 User s Manual 65 Run simulations even if there are missing years in the daily database checkbox Ml Usually when a simulation is run using daily data and the input daily database does not contain data for one of the years specified BioSIM aborts the simulation and sends a message to the Output Message Log window This function can be deactivated Do not remove temporary files after simulation for debugging checkbox I Because BioSIM usually removes temporary files after a run this option could be useful for a developer who wants to see the temporary input and output files of a run Enable hxGrid parallel computing checkbox Ml
69. o use network grid oe Css 5 parallel computing see System Requirements and e e ication 1 Deterministic the Advanced Options page of the Options J ame o e di l Replace location list by weather stations la og Ignore first nearest weather station for validation Number of files generated 3 locs x 1 params x 1 reps 3 e Model field drop down list List Approximate duration TGTime 00 00 00 totalTime 00 00 01 containing all the models available to Internal name ICsazb BioSIM The user must select one of these models NOTE If the object of the simulation is the generation of weather regimes the user can choose from the following models Weather generator temperature precipitation or Weather generatorEX temperature precipitation wind speed relative humidity solar radiation snowfall and snow depth BioSIM has several other models that can generate weather regimes and in which the user can add or remove certain climatic variables according to specific needs as for instance the Climatic xx models in which xx is the temporal output resolution daily monthly or annual Other models are also available DegreeDay FWI CCBio etc 26 BioSIM 10 User s Manual The button opens the text editor and displays information about the model currently selected e About the model selected field Information on the simulation model selected such as literature citations credits acknowledgements and other remarks
70. ocation lists must contain elevation points If these elevations are not known they can be extracted from a DEM using the ShowMap application Slope and Aspect Slope and aspect can influence temperature through their impact on incoming radiation If there are no Slope and Aspect columns if all cells are left empty or if all values are 0 BioSIM simply does not take these attributes into account when it runs a simulation If the user does not have slope and aspect values in a locations list but wishes to use them in a simulation the ShowMap application can be used to extract this information from a DEM Cells with unknown Slope and Aspect values can be filled with 0 meaning they are considered as flat terrain ID To use a locations list file in BioSIM once all the specifications mentioned above have been met it must be saved in CSV format in the Loc subdirectory of the project each project has its own Locations subdirectory BioSIM 10 User s Manual ES When BioSIM saves a locations list modified through the Locations File Editor dialog it automatically adds a column for ID if it was not already part of the file When a locations list contains Others sets of variables BioSIM places these additional columns after the five pre set columns Name ID Latitude Longitude Elevation when it saves the file Locations File Editor dialog The Locations File Editor dialog can be used to add delete and edit Location l
71. odel Editor dialog Copy Used to copy the selected model interface Additional models may be developed and added by the user For instructions on how to proceed please refer to the Models and Model Editor document BioSIM 10 User s Manual ES 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 Project Add Simulation from the menu bar by clicking on the Add Simulation button on the first row of the Project window s toolbar or by right clicking on a group in the Project window and selecting Add Simulation from the pop up menu This opens the Simulation Editor dialog in which a new simulation can be defined or an existing one can be edited Simulation Editor dialog Buttons and fields in this dialog are as follows e Name field Name of the simulation to be po oo E defined appears in the Project window Name Example 1 Use hxGrid Description e Description field Meaningful description Mode Cimatic Daiy to be used as a reminder of the object of a Aboutthe This model computes climatic daly variables aa Hodel Hee simulation or to provide additional details on the simulation l Simulation inputs z F1 F so Model input Define Model Input Use hxGrid checkbox This option is intended SS amaS for advanced users who wish t
72. odel Specific Interface dialog Clicking on in the Model Input Editor dialog saves the new parameter value s in the specified Model input file Weather Generator interface The Weather Generator interface is the interface for BioSIM s weather regime generator It consists of two dialogs the Weather Generator Input Editor and the Weather Generator WG Parameters Weather Generator Input Editor dialog Weather Generator Input Editor 2E0 The Weather Generator Input Editor dialog is paana used to add delete and edit Weather input files 2008 2010 New Used to create a new Weather input file that starts off with default parameter values that can then be edited in the Weather Generator WG Parameters dialog C BioSIM Projects DemoBioS1M Model Input 2008 2010 t9s Delete Used to delete the selected Weather input file 30 BioSIM 10 User s Manual Edit Used to send the selected Weather input file to a text editor Copy Used to copy the selected Weather input file Set as Default Used to replace the Weather Generator s current default parameter values by the values currently used in the Weather Generator WG Parameters dialog fields these become the new default weather parameters used for all simulations F2 key Used to rename the selected Weather input file Weather Generator WG Parameters dialog Normals data radio button Used to run CETTE simulations using disaggregated weather data fro
73. of the panel For the complete list of operators functions and constants available for equations the user can click on the button Internal name field An ID assigned internally by BioSIM to locate each component of a project Analysis Function Test dialog The button opens the Analysis 4nalysisfunctionTest vi Function Test dialog It allows the user to varaties values Variables Values evaluate the syntax of each new variable s equation by using numbers that are entered in the left hand side list field s Values column and clicking on the button BioSIM 10 User s Manual STO Input Analysis To open the Input Analysis dialog and add an input analysis component to a project the user can either click on the Add Input Analysis button on the Project window s toolbar select Project Add Input Analysis from the menu bar or right click on a simulation in the Project window and select Add Input Analysis from the pop up menu An input analysis can only be performed on a put analysis simulation It is used to explore the weather inputs used in the simulation and validate avs HE them There are six types of input analyses to Description choose trom in the Type held drop down iz list e Last valid day of daily data only in daily mode used to obtain the last _ available date in the daily database for name each location Provides information about the last update of a daily databas
74. og window This warning lets the user know that there are missing weather data but the model is allowed to run anyway e Ignore When the user chooses this option for a weather variable no error message is generated and no warning appears anywhere 66 BioSIM 10 User s Manual
75. oject window A project is composed of a set of components that can be grouped together in subsets When a component is selected in the Project window all other tabs and windows are updated with the information related to this component When a component is executed using the Execute Checked button on the main window s toolbar the Data tab in the main window shows the numerical results of the component in question while the Graph tab allows the user to create and display graphs of these results The Properties window shows the internal parameters of the component The Execute Message Log window shows the last execution notifications The Export window shows all the variables that were selected for export regardless of their dimension Project Window The Project window s toolbar is made up of two rows of a vax buttons hy FS Se hy ae D AT EE The first row contains buttons that allow the user to add various 558 Climatology S Eample1 Subset components to a project These are Pf ET Sum of precipitation eos Example 3 Add Group Used to group components into sub projects a ee Add Simulation Used to create weather for locations and gaea execute models to transform this weather into model specific output models are in fact external dil s or exe s For example the spruce budworm seasonality model transforms weather into spruce budworm life stage development 4 Average Output M Date of Peaks
76. on fields 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 time required to execute the task on the user s computer It does so by keeping records of the average time required to run each model by 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 e Internal name field An ID assigned internally by BioSIM to locate each component of a project These IDs are used by BioSIM for project management but are not otherwise useful to the user Model Input Editor The Model Input Editor consists of two dialogs the Model Input Editor dialog used to add delete and edit Model input files and a Model Specific Interface dialog which varies with the model selected in which model parameter values are specified Model Input Editor dialog The Model Input Editor dialog can be used to add Model Input Editor delete and edit Model input files AAC Default Buttons and fields in this dialog are as follows C New Used to create a new Model input file in which the user can change the default parameter values of the model in the Model Specific Interface dialog C BioSIM Projects DemoBioSIM Model Input 3 C dimat Delete Used to delete the selected Model input file Edit Used
77. or to any child component of a simulation The Nb of maps created field displays the total number of maps created by the mapping component e g 12 months x 2 variables 24 output maps Name field Name of the mapping component to be defined appears next to the component in the Project window Description field A complementary description can be added to provide additional details on the mapping component for the user s benefit Use hxGrid checkbox Ml Used to generate maps in network computing mode This option is intended for advanced users who wish to use network grid parallel computing see System Requirements and the Advanced Options page of the Options dialog Interpolation method field drop down list In BioSIM the user can choose one of four interpolation methods to map model output features at the landscape level Spatial Regression Universal Kriging Inverse Weighted Distance and Thin Plate Splines Once a method is selected additional options may be specified through the Advanced Mapping Options dialog accessed via the browse LJ button on the right hand side of this field see below for more detail Input DEM field drop down list Allows the user to select a DEM for the mapping component DEMs can be added using the browse button on the right hand side of this field see the Input Maps page of the Linked Data Editor dialog for more details Output map name field Allows the user to enter an output map name Becau
78. ould not change the default settings unless they are very familiar with this topic Interpolation methods Interpolation method 1 spatial regression Spatial regression fits a multiple regression between the variable latitude longitude elevation and slope aspect Interactions and second power terms are included The model is simplified by removing adding terms according to their contribution to final goodness of fit R2 A term is included if it improves the R by at least the amount specified in the R improvement to include a term field of the Advanced Mapping Options dialog Interpolation method 2 universal kriging Universal kriging with external drift is a commonly used interpolation method see Deutsch C V Journel A G 1992 GSLIB Geostatistical Software Library and User s Guide Oxford University Press New York Kriging is a powerful and flexible but rather complex interpolation method that works on a trial and error basis and that requires ample knowledge to produce satisfactory results BioSIM optimizes the choice between the several universal kriging options variogram model detrending method search radius lags etc It 1s highly recommended that the user allows BioSIM to make these choices but it is nevertheless possible to override BioSIM s selections a8 BioSIM 10 User s Manual Model field Select the desired variogram model from the drop down list or let BioSIM choose the best one Number of lags fiel
79. output map BioSIM 10 User s Manual FRS Maximum distance to simulation point km feld If the simulation point nearest to the computed pixel is farther than this maximum distance then the pixel is set to missing value 7 z es Advanced Mapping Options Apply global range limits standard deviation checkbox When this box is Universal king checked MI range limits are applied over the ae Model Auto select best entire map global based on the minimum pr Number oflags 0 0 best Min maximum Max and a multiplier ae ees ee 1 inh specified in the corresponding field of the Detrending NoDetrending standard deviation of all point values If the av E nuda iia ener ome Limit to range checkbox is checked M map values outside this range are set to global range Soe Apply local range imits standard deviation limits Otherwise they are set to no data Apply global range limits fixed checkbox a ee th ji When this box is checked Ml range limits are tt applied over the entire map global based on ml the minimum Min and maximum Max values specified If the Limit to range checkbox is checked M map values outside this range are set to range limits Otherwise they are set to no data Specifying other fields is a specialist s task that is not recommended to the average user as it requires specific knowledge of interpolation methods Users sh
80. ow at a time on Pssciption the parent component s output Available variables E Equation one equation per output variable s Variabl variables to create new variables ey o afa Propay Valos TotalPrecipitation Title g UtilPrecipitation Precision Name field Name of the function Se er analysis component to be defined TMean appears in the Project window TMax GrowingSeasonTmean JulyTmean Description field A meaningful DaysWithoutFrost description to be used as a GrowingSeasonLength reminder of the object of the a function analysis Internal name yvqndb Available variables field Used to display all the variables available for the definition of the function analysis These are the output variables of the parent component They are used in the formulation of the equations that define the output variable s of the function analysis Equation one equation per output variable field Used to create a new variable and to define it A new variable s name is entered by the user in the left hand side of the panel that lists all the function analysis output variables defined by the user Buttons at the top of the left hand side panel can be used to perform the following New Add a new output variable Delete Delete the selected output variable Move item up Move the selected output variable up in the list Move item down Move the selected output variable down
81. own list Select the column to be used as the X axis E Variable E variable1 L20 Variable L2 Y axis field drop down list Select the column s to be Sanaa represented on the axis Columns can be added and removed D a from the graph by selecting them Fi Variable7 Pupae Variables Adults Variable9 DeathAdult For the legend to appear next to the graph the user needs to Variable 10 OvipositingAdutt Variable 11 Brood check 1 the Show legend checkbox Rows from 120 to 200 Each Y variable s point line properties can be chosen by double clicking on any Y variable in the Y axis list field This opens T the Graph Series dialog and allows the user colr to modify the display attributes of the pointsymbo Point size E variable In question Line style Line width lt 2 E Smooth line BioSIM 10 User s Manual ES Other Components Function Analysis To open the Function Analysis dialog and add a function analysis component to a project the user can either click on the Add Function Analysis button on the Project window s toolbar select Project Add Function Analysis from the menu bar or right click on the component to be analyzed in the Project window and select Add Function Analysis from the pop up menu Function Analysis dialog A function analysis can be used ina T O to perform logical or arithmetic name Funcionanalysis S operations one r
82. puting power and speed and that requires knowledge of network computing For assistance interested users may contact the development team BioSIM 10 User s Manual C Utility programs Six 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 Normals Database Editor used to edit normals databases e Daily Database Editor used to edit daily databases e MergeFiles used to merge the contents of two files based on the column headers e ShowMap a map display program grids vectors e Date used for date conversions e PLTWidget a graphics package BioSIM can also export analysis outputs to your favourite Windows spreadsheet software e g Microsoft Excel Language BioSIM is available in French and English To change the language you must select Tools Language and then click on Francais or English in the menu bar For the change to take effect you must close and restart BioSIM Technical support BioSIM is distributed without charge However the Canadian Forest Service cannot offer extensive free technical support Nevertheless 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 Jacques Regniere RNCan NRCan gc ca For technical issues concerning the installation and use of the software
83. r differences between runs depends on the problem being studied and the user s need for output constancy Factors that can influence the variability between runs are 1 the variability of normals disaggregation and 2 the degree of stochasticity of the model As a general rule the relationship between inter run variability and the variability of an output variable can be estimated with D D m where Dis the inter run standard deviation and D is the standard deviation of the output variable A preliminary simulation may be useful to obtain an estimate of D Replace locations list by weather stations checkbox Ml When the user wants to perform a jackknife cross validation of the weather gradient correction location points need to be replaced by the nearest weather stations ee BioSIM 10 User s Manual This is a four step process that requires the user to 1 create a group in which two identical simulations are defined In the first simulation 2 check the checkbox and in the second simulation check the Ignore first nearest weather station for Xvalidation checkbox Afterwards both simulations must be merged together by 3 clicking on the Add Merge button located in the first row of the Project window s toolbar When both simulations have been defined the user must 4 execute these three components using the Execute Checked F button in the main window toolbar e Number of files generated and Approximate durati
84. rary location on the destination computer by double clicking on the file name or icon and following the instructions for installation BioSIMxx_x_xSetup exe is an Inno Setup 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 suggests c Program Files NRCan but a different root directory can be specified at installation This root directory contains the following tree a NRCan 4 L BioSIM BioSIM software Models Simulation models gt Examples Default location of a BioSIM project example d Layers Default location of Shapefiles Maps Default location of common DEMs d PLT PLTWin and PLTWidget program data display 4 ShowMap ShowMap program map display Palette Colour Palette files Weather Default location of common weather databases The installation program also creates a BioSIM icon on the desktop System requirements BioSIM is compatible with the Microsoft Windows XP and Windows 7 operating systems and will run on computers with at least 50 Mb of free hard disk space The BioSIM 10 software is parallel or grid computing capable It automatically makes full use of multiple core machines It can also make use of several computers linked over a local area network through a specialized grid computing utility called hxGrid This is an advanced feature of BioSIM that greatly increases com
85. riate group component in the TET bare ae ce De Project window and select Add Merge from the gree Alter dimensions must be pop up menu 6 ane T ran one T Ex ee The Merge dialog allows the user to merge the results ee ae Rae of several components of the same type e g analyses fre same ize an the temporal type must be the same to create a single component Merging two components can be useful to export the results of several components in a single file or to perform a function analysis combining variables from _ different components A merge component can only be added to memaname ven a group that already contains more than one component of the same type Only the components present in the group are available for the merge Only one component type can be joined at a time all other component types must have the same size For example if the user wants to merge the output variables from two analyses each analysis must have the same number of locations parameter values replications and must cover the same time period type and mode Internal name field An ID assigned internally by BioSIM to locate each component of a project BioSIM 10 User s Manual so Clean Up The user can delete simulation output databases output analysis files or any other files from the current project s Tmp subdirectory by selecting Tools Clean Up Internal Files from the menu bar Once this is done simulation o
86. rsal Ecography 34 488 497 Bentz B R gni re J Fettig C J Hansen E M Hayes J L Hicke J A Kelsey R G Lundquist J Negron J F Seybold S J 2010 Climate change and bark beetles of the western US and Canada direct and indirect effects BioScience 60 602 613 Bourchier R S van Herewijk B H 2010 Distribution and potential spread of Japanese knotweed Polygonum cuspidatum in Canada relative to climate tresholds Invasive Plant Sci Manag 3 32 39 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 and J E Stone eds Mountain Pine Beetle Symposium Challenges and Solutions October 30 31 2003 Kelowna BC Natural Resources Canada Canadian Forest Service Pacific Forestry Centre Victoria BC Information Report BC X 399 Cudmore T J Bj rklund N Caroll A L Lindgren B S 2010 Climate change and range expansion of an aggressive bark beetle evidence of higher beetle reproduction in na ve host tree populations J Appl Ecol 47 1036 1043 H
87. rst E i and global directories are searched in the same order as egestas they appear in the corresponding directory list Consulting and modifying linked data In the Linked Data Editor dialog each page or tab is used to select the type of data the user wants to consult or modify Normals data ae Daily data Input maps DEMs amp or Models BioSIM 10 User s Manual ao The main list field of each tab lists all the files databases found for the requested type of data If the file the user is searching for does not appear in the appropriate list it must either be linked into the Linked Data Editor or copied into a directory that is already linked to BioSIM The user can change the Weather or Input Maps DEMs directories that are linked to BioSIM via the Directories page of the Options dialog The read only field at the bottom of the Linked Data Editor dialog always shows the full name and path of the selected file database Linked Data Editor Normals Databases page In BioSIM normals are long term monthly statistics 0 i calculated over 30 year Standard Normal Generating Periods SNGP the latest being 1981 2010 These es l statistics apply to each single weather station in the Eupe 11200 World 1981 2010 database A normals database contains these monthly vaiypatavases Statistics for a number of stations along with the Q spatial coordinates of each station la
88. s gt here the output variable is summed up Over time and the sum is divided by the total sum e Last time when cumulative of variables was lt e Time when variables stabilized tolerance When an event criterion is needed the edit box to the right of the drop down list becomes available to allow the user to enter a value For example to determine the first time when BioSIM 10 User s Manual Bo o variables were equal to or greater than 50 the event type would be First time when variables gt and 50 would be the event criterion When an event is extracted to be used in mapping the Drop annual part of the time reference checkbox must be checked because it is not possible to map time references over more than one year Events or statistics are computed for all selected variables as well as all selected locations over the time period specified for the analysis When tab Final computations The How tab has a third purpose which consists in computing averages over replications parameters or locations or any combination thereof When the Over replications checkbox is checked checked by default BioSIM computes the mean over all replications When the Over parameters checkbox is checked Ml BioSIM computes the mean over all parameter values used when model parameters have been varied When the Over locations checkbox is checked Ml BioSIM computes the mean value over all locations selecte
89. s directories or simply see the directories paths For additional details on daily databases in BioSIM please refer to the Daily Data and Daily Data Editor document BioSIM 10 User s Manual cu Linked Data Editor Input Maps DEMs page In BioSIM input maps DEMs are used to perform tikes nata taitor two different tasks generate locations lists and 2 Doda Canada 120s tif perform spatial interpolations Normais Quebecasst All input maps DEMs files with extensions defined in the Options dialog located in one of the input map directories whether global or in the project s Maplnput subdirectory are listed in the list field of oe the Input Maps DEMs page of the Linked Data Editor dialog The project s MapInput subdirectory is always searched first Input Maps Buttons specific to the Input Maps DEMs page are C Program Files NRCan Maps Canada 120s tf m as follows Send to ShowMap Used to open the ShowMap application and display the map selected highlighted in the list field Show Information Used to display the selected map s detailed information in a text editor can be specified by the user e g Notepad Link a New File Used to add the directory in which the new file is located to the linked directories list If the extension of the new map is not in the extension list the extension will automatically be added LE Open Options dialog Used to
90. se a mapping component can create more than one map a wildcard format can be used to automatically assign names to maps The user can choose and combine four different wildcards c inserts the component s name Yov inserts the variable s name t inserts the temporal reference p inserts the value of a varied parameter Output maps are stored in the project s MapOutput subdirectory in the same format as the input DEM Because all maps created in BioSIM are stored in the same output directory the user must make sure that all maps generated have been given distinct names through the judicious use of wildcards in output map names In particular if the c wildcard is used the user should assign 46 BioSIM 10 User s Manual a different name to each mapping component so that no two maps end up with the same name This prevents BioSIM from overwriting an existing map Pre post transformation field An advanced feature used to transform event data before and after interpolation Transformation dialog In some cases a transformation of the output should be Transformation I performed prior to map making The transformation is carried out prior to interpolation and then reversed to produce a map at the original scale A logit transformation is useful for example es when interpolating probabilities so that values on the output D y Log map remain between 0 and 1 No transformation C Log transformation
91. stations for each simulation point from a locations list adjusts the data for differences in elevation latitude and longitude and restores stochastic variation to long term normals a process called disaggregation when needed The weather time series sent to the simulation model can be composed of historical or simulated daily data or both What distinguishes BioSIM from other software is its ability to combine actual daily weather records including short term forecasts and disaggregated normals in a single operation BioSIM 10 User s Manual to Simulation ai Monthly statistics Monthly to daily stochastic disaggregation Temperature Forecasted Observed Jan Feb Mar Apr May Jun Jul Aug Sept Oct Nov Dec Time of the year ub Simulation model ouput T External simulation k model runs gt 5 4 L x gt x CS i Spatial interpolation BioSIM provides extensive output analysis functions to summarize model output and present it in the form of tables graphs or maps With a digital elevation map DEM for the area containing the simulation locations BioSIM can perform spatial interpolations using various methods wes BioSIM 10 User s Manual kriging spatial regression inverse distance thin plate splines and generate output maps surfaces Simulations are first executed for a series of locations and outputs are interpolated to produce an output map Such a map can then be used by i
92. t component the Maybe in the first row of the table indicates that it may or may not be possible to add a certain type of component to a group The user must always keep in mind that it 1s possible to add a component to a group only if it is possible to add this same component to its parent For example if a group child is added to an analysis 1 parent it is still possible to add a group an analysis a function analysis and a mapping 4 to this group However it is no longer possible to add a simulation an input analysis or an import file It is easy to see when certain types of components cannot be added to others because the buttons on the first row of the Project window s toolbar automatically become greyed for the current highlighted component The second row of the Project window s toolbar contains the following buttons Properties Used to edit current highlighted component ar BioSIM 10 User s Manual Match Stations Used to obtain a list of weather stations matched to simulation points can only be performed in simulations Expand All Used to expand all subcomponents children of a parent component Collapse All Used to collapse all subcomponents children of a parent component Remove Remove current highlighted component and all of its subcomponents children from the project Please note that in the Project window an existing component can be modified by double clicki
93. ter 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 R gniere J St Amant R 2008 BioSIM 9 User s Manual Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre Qu bec QC Information Report LAU X 134 At the heart of BioSIM is a daily weather generator described in R gni re J Bolstad P 1994 Statistical simulation of daily air temperature 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 BioSIM 10 User s Manual ae Beaulieu J Perron M Bousquet J 2004 Multivariate patterns of adaptive genetic variation and seed source transfer in Picea mariana Can J For Res 34 531 545 Beaulieu J Rainville A 2005 Adaptation to climate change genetic variation is both a short and a long term solution For Chron 8 704 709 Coulombe S Bernier P Y Raulier F 2010
94. th and d is in C East and mm East for temperature and precipitation respectively When the elevation of the simulation point is too different from that of the nearest stations three times the standard deviation of elevation among the 23 nearest stations BioSIM blends these local gradients with regional gradients obtained by fitting the regression equation to data from the 69 stations nearest to the simulation point a BioSIM 10 User s Manual Correction for slope and aspect If the simulation point s slope and aspect coordinates 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 two weather databases are on level ground For mathematical details of this adjustment see R gni re 1996 Generation of daily temperature 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 c
95. the same seed option is used when the user wants the weather time series generated for a simulation to be identical from one execution to the next By default the simulation uses Random seeds each execution produces stochastically different weather regimes when using normals Locations lists A Locations list is a collection of simulation points for which BioSIM can run models Locations lists are managed through the Locations File Editor dialog used to create edit or delete such lists Locations lists file format The file format used by BioSIM for Locations lists is straightforward they are comma separated values CSV files that contain specific column headers CSV files are easy to generate in worksheet software e g Excel by using the Save as function Once saved CSV files can be edited using ASCII file editors such as Notepad It is important to remember that the default format of CSV files can vary between computers depending on regional settings BioSIM requires comma separated fields values Because a CSV file s columns are comma delimited commas cannot appear anywhere within the file s columns such as in location names to avoid errors when BioSIM reads these files Also decimals must be indicated by a period not a comma as 1s often done in French operating environments In each Locations list file there are seven pre set columns variables four are mandatory since they are necessary for the
96. titude longitude inputs and elevation All normals databases Normals located in one of the weather data directories whether global or in the project s Weather subdirectory are listed in the Linked Data Editor dialog s Normals Databases page list field The project s Weather subdirectory is always searched first Buttons specific to the Normals Databases page are as follows Edit When a database is selected highlighted in the list field clicking on the Edit button opens this database in the Normals Database Editor application Link a New File Used to add the directory in which the new file is located to the directory list Open Options dialog Used to open the Options dialog of the Directories page in which the user can add and remove links to various directories or simply see the directories paths For additional details on normals databases in BioSIM please refer to the Normals Data and Normals Data Editor document BioSIM 10 User s Manual Linked Data Editor Daily Databases page Daily databases are used to run BioSIM in the real z GCCE world 1 e from daily weather records rather than SS le ea from randomized normals In addition to lt a eae o simulating historical weather daily data are used in iiai short term e g seasonal forecasting planning using the most current weather records Short term forecasting requires a daily database that is as up
97. tput map in BioSIM is to generate a suitable locations list within the simulation definition In particular the locations 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 it also needs to cover as much as possible of its range of elevations BioSIM s Locations List Editor is quite useful for generating such locations lists since it allows taking slope and aspect into consideration Remember that slope and aspect are not useful mapping factors at scales beyond 1 100 000 200 m Through a chain of several components e g analysis merge the user can convert simulation outputs into an appropriate format to obtain the desired mapping results for example to map an event date the user needs to define an analysis and extract the event beforehand A mapping component is most often added as a child to an analysis component Only in rare instances can a mapping component be added directly to a simulation Mapping Dialog Mapping creates surface grids from data points Simulation points must be within or near the region defined To open the Mapping dialog and add a by the input map elevations One map is created for each variable time parameter combination mapping component to a project the user Can either click on the Add Mapping Nb of maps created 2x1x1 2 variable x time x param total button and select Project Add Ex3 Use
98. tract a specific type of information from parent results WHERE Selection of individual or groups of simulation points N ame field Name of the analysis to be defined WHEN Selection of a period within the parent period For example you may extract g information for a specific day or calculate a mean over a specific month appear S In the Proj ect window WHAT Selection of output variables on which to conduct the analysis For example a single output variable can be used for mapping HOW This page serves 3 different purposes depending on the context 1 Input statistic used when an analysis is to be performed on a parent s results Description field A meaningful description to be used as a reminder of the obj ect of an analysis ap P Cars in 3 Mean over used to compute means over replicates parameter sets or locations the Execute Message Log window Dunas oe 2 Time transformation used to compute statistics over temporal breaks For example compute monthly means from daily values Cancel Internal name field greyed An ID assigned internally by BioSIM 40 BioSIM 10 User s Manual Where tab The Where tab allows the user to spatially subset data gl wer when what 57 How from the parent component it Can be useful when V Select a subset of locations by default all location are used outputs from a particular subset of locations are S Boate St Alban examined F Sco
99. tself or in conjunction with other geographically referenced information in the development of ecological insight or pest management plans BioSIM is of interest to any organization responsible for monitoring or managing insect pest populations forestry agriculture horticulture to plan the timely deployment of sampling or surveying crews and materials e g pheromone traps without the need for extensive phenology monitoring Also it can help time the application of pest control substances to obtain optimal results Thus using BioSIM can optimize the use of pest management resources in a cost effective manner 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 gni re 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 R gniere J Cooke B Bergeron V 1995 BioSIM a compu
100. tt By default BioSIM processes all locations To select a subset of locations the user must check the Select a subset of locations checkbox This opens the locations list used in the parent component in the Where tab s list field and allows the user to select l one or more locations that are of particular interest Cancel When tab The When tab allows the user to define a time period ot mal wren wha De How within the parent component s period to restrict the T Select a period oy defaut the entire period is used period covered by the analysis Beginning 2008 04 01 Use curent date sited by 0 End 2009 08 31 E Use current date shifted by To define the time period of interest the user must check ETE A continuous period starts on the 2005 2006 2007 2008 r ends on the end the Select a period checkbox and then use the E The Year by year period is defined annually between the specified beginning and end dates When Beginning gt End date the period starts at the end date of one year and stops at the beginning date of the following year Beginning and End fields to type in the first and last dates of the period to subset Depending on the parent component s temporal mode and type the date format beginning and end may vary By default
101. uestion is selected in the Model field For more information on model parameters please refer to the Models and Model Editor document e Weather generator field drop down list This field is used to select a set of parameters for the weather generator which assembles a location specific daily weather 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 subdirectory To specify a new set of parameter values or to edit an existing one the user must click on the button to the far right of the field This opens two dialogs the Weather Generator Input Editor and the Weather Generator WG Parameters Once a new weather input file has been created it automatically becomes available in the Weather generator field s drop down list and can be selected for any subsequent simulation regardless of the model used e Locations list field drop down list Each simulation in BioSIM is run for a series of locations also called simulation points This field is used to specify the list of locations for which the simulation is to be run The drop down list contains all existing locations lists in the Loc subdirectory of the current project BioSIM 10 User s Manual ae A new list can be created or an existing list can be edited by clicking on the button to the far right of the field This opens two dialogs the Locations File Editor and the Lo
102. ught along the southern edge of the Canadian boreal forest Glob Change Biol 17 2084 2094 Pedlar J H McKenney D W Beaulieu J Colombo S J McLachlan J S O Neill G A 2011 The implementation of assisted migration in Canadian forests For Chron 87 766 777 Pinno B D Par D Guindon L B langer N 2009 Predicting productivity of trembling aspen in the Boreal Shield ecozone of Quebec using different sources of soil and site information For Ecol Manag 257 782 789 Raulier F Bernier P Y Ung C H 2000 Modeling the influence of temperature on monthly gross primary productivity of sugar maple stands Tree Physiol 20 333 345 Riopel M B gin J Ruel J C 2011 Coefficients de distribution de la r g n ration cing ans apr s des coupes avec protection des petites tiges marchandes appliqu es dans des sapini res et des pressi res noires du Qu bec For Chron 87 669 683 a BioSIM 10 User s Manual Tardif J Girardin M P Conciatori F 2011 Light rings as bioindicators of climate change in interior North America Glob Planet Change 79 134 144 Ung C H Bernier P Y Raulier F Fournier R A Lambert M C R gni re J 2001 Biophysical site indices for shade tolerant and intolerant boreal species For Sci 47 83 95 It has been applied to several insects Anderson D P Sturtevant B R 2011 Pattern analysis of eastern spruce budworm Choristoneura fumiferana dispe
103. utputs and analysis results will no longer be available Weather Station Matches for Locations List This dialog lists which weather stations BioSIM matches to locations in the simulation s locations list given the selection criteria currently defined in both the first and the second drop down lists The search algorithm looks through the relevant weather databases and reports the stations matched in the list fields on the right hand side of the dialog In normals mode only normals stations are matched In daily mode both normals and daily stations are matched to locations To open the Matches for Locations List dialog the user must select a simulation in the Project window and either click on the Show Matched Stations button on the second row of the Project window s toolbar and select Project Show Matched Stations from the menu bar or right click on it and select Show Matched Stations _ Matches for Location List specific Locations Station name ID Latitude Longitute Elev m Dist km Weight 2010 Duchesnay Duchesnay Normals C Program Files NA Can weather Canada US4 1981 2010 Normals DUCHESNAY QUE ECFOZ240 E 46 87 71 65 08 99 3 RIVIERE VERTE OUESTIQUE EC7016675 46 98 71 83 19 4 O1 STE CHRISTINEIQUE EC 01 000 46 02 71 92 21 5 0 14 QUEBEC JEAN LESAGE INTL AIG EC7016294 E 46 8 71 38 F4 21 O1 DONNACONA AQUE ECY012071 46 68 F173 45 22 1 0 1 Y Daily C Program Files MR Cans
104. utputs can be specified An analysis can only be run after or simultaneously with its parent component A new analysis of the currently selected component highlighted in the Project window is defined using the Analysis Editor dialog This dialog can be accessed by selecting Project Add Analysis from the menu bar and clicking on the Add Analysis button in the first row of the Project window s toolbar or by right clicking on the component in the Project window and selecting Add Analysis from the pop up menu The Analysis Editor dialog consists of five tabs General Where When What and How Collectively these tabs specify all the information to be extracted from the parent component s results When defining an analysis it is often not necessary to fill out all the tabs By default tabs in the analysis definition correspond to the parent component s tabs Three of the tabs Where When What are used to filter subset the results from the parent component while the fourth tab How is used for calculations or transformations of the parent component s results General tab The General tab is used to name and describe the BG analysis it also provides information on the various _ cree ver when What 32 How functions performed by the other tabs of the Analysis ne Sws 7 1 Description Editor dialog Analysis is a key function of BioSIM There are 4tabs each designed to ex
105. ver all years is selected the result will be only 12 values one for each month because the computation will be made by month over all years Two types of time transformation can be performed in BioSIM statistics or events When the Statistics radio button is selected the user can compute statistics lowest value mean standard deviation highest value etc The user can choose to compute all or only one of the Statistics at a time If all statistics are computed it is not recommended to define a final computation see the definition below because the sequence of computations is not always clear and unexpected results can be obtained There are 10 options available in the drop down list All statistics by default Lowest Mean Sum Sum Standard deviation Standard error Coefficient of variation Variance Highest When the Event radio button is selected the user can extract an event An event is a specific time period at which something occurs e g time when a variable is at its maximum In the event definitions below a criterion 1s often needed in the event s definition The choices available are e Time when variables were at their maximum default e Time when variables were at their minimum e First time when variables were gt e First time when variables were lt e Last time when variables were gt e Last time when variables were lt e First time when cumulative of variables wa
106. wo methods are available to generate exposure Use DEM exposure radio button When selected exposure values are computed from the elevations of the points in the vicinity of the location on the DEM It is not recommended that locations lists contain exposures at scales coarser than 1 100 000 Generate exposure radio button When selected exposure values are generated at random There are two distributions to choose from uniform distribution Uniform radio button or normal distribution Normal radio button 36 BioSIM 10 User s Manual Generate from a weather database To generate a locations list from a weather database the user must select the type of weather station from the Weather type field s drop down list normals or daily stations the corresponding database from the Weather DB field s drop down list and if needed the filter to be applied to the list of stations using the Filter field s browse button When using daily stations the data year e g 2000 for which the user needs weather stations must also be specified in the Year field to include all available stations regardless of the year enter O in this field Sub region boundaries checkbox W When checked Wl the user can enter the corner coordinates latitude longitude of a rectangular sub region Creating a locations list outside of BioSIM Locations lists can be generated outside of BioSIM and saved as comma delimited CSV files for
107. y or daily and mode can be year by year or over all years Exporting results vx Op The Export window contains the definition of export files to access results Ms outside of BioSIM pti ert tenet File name It is possible to export results to disk M or directly to a spreadsheet The ene user can indicate to BioSIM which spreadsheet software to use by clicking on the uron Options button or by selecting Tools Options from the menu bar This opens the Options dialog on the Links page in which the user can select the preferred spreadsheet software in the Spreadsheet field If BioSIM is unable to find the spreadsheet software on the computer a dialog appears in which the user can browse and indicate where the software can be found The Export window contains the list of exports currently defined for the selected tn component When a component contains pre defined exports the export files are i overwritten each time the component is executed Buttons and fields in the Export window are as follows NE BioSIM 10 User s Manual When the Automatically export at execution checkbox is checked BioSIM automatically exports the results each time the component is executed File name field Indicates the name of the file where the results of the export are to be stored All exports are saved as CSV files in the Output subdirectory of the project Export Now Used to export the results to a

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