From fb6981c0b02d80f7cb91b99027959ae28f781bbb Mon Sep 17 00:00:00 2001 From: diegobilski Date: Fri, 6 Dec 2024 15:20:17 -0500 Subject: [PATCH 1/6] vignette addition and dependency help update Adds vignette on updating scripts to rsyncrosim v2. Change on dependency function help. --- R/dependency.R | 32 +-- .../a01_rsyncrosim_vignette_basic.html | 106 ++++----- .../a02_rsyncrosim_vignette_uncertainty.html | 56 ++--- .../a03_rsyncrosim_vignette_pipelines.html | 56 ++--- .../a04_rsyncrosim_vignette_spatial.html | 58 ++--- .../figure-html/view results raster-1.png | Bin 16137 -> 15607 bytes .../a05_rsyncrosim_stsim_vignette.html | 30 +-- .../figure-html/view myRastersTimestep5-1.png | Bin 11253 -> 11232 bytes .../a06_rsyncrosim_install_github.html | 18 +- ...a07_updating_rsyncrosim_scripts_to_v2.html | 209 ++++++++++++++++++ docs/articles/index.html | 28 +-- docs/reference/Scenario-class.html | 6 +- docs/reference/addPackage.html | 34 +-- docs/reference/backup.html | 6 +- docs/reference/chartCriteria.html | 6 +- docs/reference/chartId.html | 12 +- docs/reference/chartOptionsFormat.html | 6 +- docs/reference/chartOptionsLegend.html | 6 +- docs/reference/chartOptionsXAxis.html | 6 +- docs/reference/chartOptionsYAxis.html | 6 +- docs/reference/command.html | 6 +- docs/reference/datasheet.html | 10 +- docs/reference/datasheetSpatRaster.html | 6 +- docs/reference/delete.html | 12 +- docs/reference/deleteLibrary.html | 44 +++- docs/reference/dependency.html | 13 +- docs/reference/description.html | 6 +- docs/reference/filepath.html | 6 +- docs/reference/folderId.html | 8 +- docs/reference/ignoreDependencies.html | 6 +- docs/reference/index.html | 6 +- docs/reference/mergeDependencies.html | 6 +- docs/reference/name.html | 8 +- docs/reference/owner.html | 6 +- docs/reference/packages.html | 144 ++++++------ docs/reference/parentId.html | 6 +- docs/reference/printCmd.html | 6 +- docs/reference/projectId.html | 6 +- docs/reference/readOnly.html | 6 +- docs/reference/removePackage.html | 10 +- docs/reference/rsyncrosim.html | 8 +- docs/reference/run.html | 6 +- docs/reference/runLog.html | 6 +- docs/reference/saveDatasheet.html | 6 +- docs/reference/scenarioId.html | 6 +- docs/reference/silent.html | 6 +- docs/reference/sqlStatement.html | 6 +- docs/reference/tempfilepath.html | 6 +- docs/reference/uninstallPackage.html | 9 +- docs/reference/version.html | 6 +- man/addPackage.Rd | 2 +- man/backup.Rd | 2 +- man/chart.Rd | 2 +- man/chartId.Rd | 2 +- man/delete.Rd | 2 +- man/deleteLibrary.Rd | 2 +- man/dependency.Rd | 23 +- man/description.Rd | 2 +- man/filepath.Rd | 2 +- man/folder.Rd | 2 +- man/folderId.Rd | 2 +- man/ignoreDependencies.Rd | 2 +- man/mergeDependencies.Rd | 2 +- man/name.Rd | 2 +- man/packages.Rd | 2 +- man/printCmd.Rd | 2 +- man/project.Rd | 2 +- man/projectId.Rd | 2 +- man/readOnly.Rd | 2 +- man/removePackage.Rd | 2 +- man/scenario.Rd | 2 +- man/scenarioId.Rd | 2 +- man/session.Rd | 2 +- man/silent.Rd | 2 +- man/sqlStatement.Rd | 2 +- man/ssimLibrary.Rd | 2 +- man/tempfilepath.Rd | 2 +- man/uninstallPackage.Rd | 2 +- man/version.Rd | 2 +- vignettes/a01_rsyncrosim_vignette_basic.Rmd | 4 +- .../a02_rsyncrosim_vignette_uncertainty.Rmd | 4 +- .../a03_rsyncrosim_vignette_pipelines.Rmd | 4 +- vignettes/a04_rsyncrosim_vignette_spatial.Rmd | 4 +- vignettes/a05_rsyncrosim_stsim_vignette.Rmd | 4 +- .../a07_updating_rsyncrosim_scripts_to_v2.Rmd | 106 +++++++++ 85 files changed, 796 insertions(+), 476 deletions(-) create mode 100644 docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html create mode 100644 vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd diff --git a/R/dependency.R b/R/dependency.R index 5c46fa39..edfea84e 100644 --- a/R/dependency.R +++ b/R/dependency.R @@ -17,19 +17,13 @@ NULL #' Otherwise, returns list of saved or error messages for each dependency of each #' scenario. #' -#' Note that the order of dependencies can be important - dependencies added most -#' recently take precedence over existing dependencies. So, dependencies included -#' in the dependency argument take precedence over any other existing dependencies. -#' If the dependency argument includes more than one element, elements are ordered -#' from lowest to highest precedence. +#' Note that the order of dependencies can be important. If the dependency argument +#' includes more than one element, elements are ordered from highest to lowest precedence. #' -#' @param ssimObject \code{\link{Scenario}} object, character string, integer, or +#' @param scenario \code{\link{Scenario}} object, character string, integer, or #' vector of these. The Scenario object, name, or ID to which a dependency is to #' be added (or has already been added if \code{remove=TRUE}). Note that integer ids -#' are slightly faster. -#' @param value \code{\link{Scenario}} object, character string, integer, or -#' vector of these. The Scenario object, name, or ID to be used as the -#' dependency. If an empty vector is provided, all dependencies are removed. +#' are slightly faster #' #' @return #' A data.frame: all dependencies for a given Scenario @@ -58,18 +52,18 @@ NULL #' } #' #' @export -setGeneric("dependency", function(ssimObject) standardGeneric("dependency")) +setGeneric("dependency", function(scenario) standardGeneric("dependency")) #' @rdname dependency -setMethod("dependency", signature(ssimObject = "character"), function(ssimObject) { - return(SyncroSimNotFound(ssimObject)) +setMethod("dependency", signature(scenario = "character"), function(scenario) { + return(SyncroSimNotFound(scenario)) }) #' @rdname dependency -setMethod("dependency", signature(ssimObject = "Scenario"), function(ssimObject) { +setMethod("dependency", signature(scenario = "Scenario"), function(scenario) { - # Rename variable - s <- ssimObject + # Rename variable so it's not the same as the rsyncrosim::scenario() function + s <- scenario # get set of existing dependencies args <- list(list = NULL, dependencies = NULL, lib = .filepath(s), @@ -124,11 +118,9 @@ setReplaceMethod( cDep <- allScns$ScenarioId[allScns$Name == v] if (length(cDep) == 0) { - stop("Could not find dependency scenario ", v) + stop("Could not find dependency scenario ", cDepRaw) } else if (length(cDep) > 1) { - stop("Found more than one scenario named ", v, - ". Please specify a dependency scenario id:", - paste0(v, collapse = ",")) + stop("Found more than one scenario named ", v, ". Please specify a dependency scenario id:", paste0(v, collapse = ",")) } else { valueList <- c(valueList, cDep) } diff --git a/docs/articles/a01_rsyncrosim_vignette_basic.html b/docs/articles/a01_rsyncrosim_vignette_basic.html index 475210e4..1973186b 100644 --- a/docs/articles/a01_rsyncrosim_vignette_basic.html +++ b/docs/articles/a01_rsyncrosim_vignette_basic.html @@ -5,7 +5,7 @@ -Introduction to `rsyncrosim` • rsyncrosim +Introduction to rsyncrosim • rsyncrosim @@ -16,7 +16,7 @@ - + Skip to contents @@ -26,7 +26,7 @@ rsyncrosim - 2.0.1 + 2.0.2
  • Changelog
    • @@ -67,7 +67,7 @@
    -

    Introduction to `rsyncrosim`

    +

    Introduction to rsyncrosim

    Source: vignettes/a01_rsyncrosim_vignette_basic.Rmd @@ -165,7 +165,7 @@

    Installing and loading R packagesIn a new R script, load the rsyncrosim package.

     +library(rsyncrosim)

    Connecting R to SyncroSim using session() @@ -214,27 +214,20 @@

    Installing SyncroSim 
     availablePackages <- packages(installed = FALSE)
 head(availablePackages)
    -
    ##                   name version
-## 1           burnP3Plus   2.0.0
-## 2  burnP3PlusCell2Fire   2.0.0
-## 3 burnP3PlusPrometheus   2.0.0
-## 4            demosales   2.0.0
-## 5                dgsim   3.0.0
-## 6           helloworld   2.0.0
-##                                               description
-## 1          Burn-P3+ package for burn probability modeling
-## 2         Cell2Fire fire growth model package for BurnP3+
-## 3        Prometheus fire growth model package for BurnP3+
-## 4                            Demo Sales SyncroSim Package
-## 5          Simulates demographics of wildlife populations
-## 6 Example demonstrating how to create a SyncroSim package
-##                                     url
-## 1  https://burnp3.github.io/BurnP3Plus/
-## 2  https://burnp3.github.io/BurnP3Plus/
-## 3  https://burnp3.github.io/BurnP3Plus/
-## 4  https://apexrms.github.io/demosales/
-## 5      https://apexrms.github.io/dgsim/
-## 6 https://apexrms.github.io/helloworld/
    +
    ##                   name version                                      description
+## 1           burnP3Plus   2.0.0   Burn-P3+ package for burn probability modeling
+## 2  burnP3PlusCell2Fire   2.0.0  Cell2Fire fire growth model package for BurnP3+
+## 3 burnP3PlusPrometheus   2.0.0 Prometheus fire growth model package for BurnP3+
+## 4            demosales   2.0.0                     Demo Sales SyncroSim Package
+## 5                dgsim   3.0.0   Simulates demographics of wildlife populations
+## 6          ecoClassify   1.0.1     ecoClassify package for image classification
+##                                      url
+## 1   https://burnp3.github.io/BurnP3Plus/
+## 2   https://burnp3.github.io/BurnP3Plus/
+## 3   https://burnp3.github.io/BurnP3Plus/
+## 4   https://apexrms.github.io/demosales/
+## 5       https://apexrms.github.io/dgsim/
+## 6 https://apexrms.github.io/ecoClassify/

    Install helloworldTime using the rynscrosim function installPackage(). This function takes a package name as input and then queries the SyncroSim package server for the @@ -260,8 +253,8 @@

    Installing SyncroSim ## 1 helloworldTime 2.0.0 ## description ## 1 Example demonstrating how to use timesteps with an R model -## location -## 1 C:\\Users\\birch\\AppData\\Local\\SyncroSim Studio\\Packages\\helloworldTime\\2.0.0 +## location +## 1 C:\\Users\\DiegoBilski\\AppData\\Local\\SyncroSim Studio\\Packages\\helloworldTime\\2.0.0 ## status ## 1 OK

    Note: you can install multiple versions of the same package @@ -387,7 +380,6 @@

    Create a new scenario using ## scenarioId [numeric] : 1 ## parentId [numeric] : 0 ## folderId [numeric] : 0 -## breakpoints [list] : ## session [Session] : C:/Program Files/SyncroSim Studio, printCmd=FALSE ## filepath [character] : path/to/helloworldLibrary.ssim ## datasheetNames [data.frame]: scope,package,name,displayName,isSingle,displayMember @@ -650,7 +642,7 @@

    Checking the run log with runLog 
     # Get run details for the first result scenario
 runLog(myResultScenario)
    -
    ## RunLog                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
+
    ## RunLog                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
 ## SyncroSim Version: 3.0.9.0
 ## Operating System: Microsoft Windows NT 6.2.9200.0
 ## 
@@ -659,19 +651,19 @@ 
    Checking the run log with runLog
 ## helloworldTime -> 2.0.0
 ## 
 ## Parent Scenario is: [1] My first scenario
-## Result scenario is: [2] My first scenario ([1] @ 13-Oct-2024 10:00 AM)
+## Result scenario is: [2] My first scenario ([1] @ 06-Dec-2024 1:46 PM)
 ## 
 ## --------------------------------------------
-## STARTING SIMULATION: 2024-10-13 : 10:00:59 AM
+## STARTING SIMULATION: 2024-12-06 : 1:47:00 PM
 ## --------------------------------------------
 ## 
-## Hello World Time (R) => Total time: 00:00:09
+## Hello World Time (R) => Total time: 00:00:17
 ## 
 ## --------------------------------------------
-## SIMULATION COMPLETE: 2024-10-13 : 10:01:08 AM
+## SIMULATION COMPLETE: 2024-12-06 : 1:47:17 PM
 ## --------------------------------------------
-## Total simulation time: 00:00:09
    
-
    ## [1] "RunLog                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  \nSyncroSim Version: 3.0.9.0\nOperating System: Microsoft Windows NT 6.2.9200.0\n\nPackages:\ncore -> 3.0.9\nhelloworldTime -> 2.0.0\n\nParent Scenario is: [1] My first scenario\nResult scenario is: [2] My first scenario ([1] @ 13-Oct-2024 10:00 AM)\n\n--------------------------------------------\nSTARTING SIMULATION: 2024-10-13 : 10:00:59 AM\n--------------------------------------------\n\nHello World Time (R) => Total time: 00:00:09\n\n--------------------------------------------\nSIMULATION COMPLETE: 2024-10-13 : 10:01:08 AM\n--------------------------------------------\nTotal simulation time: 00:00:09      "
    
+## Total simulation time: 00:00:17
    +
    ## [1] "RunLog                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               \nSyncroSim Version: 3.0.9.0\nOperating System: Microsoft Windows NT 6.2.9200.0\n\nPackages:\ncore -> 3.0.9\nhelloworldTime -> 2.0.0\n\nParent Scenario is: [1] My first scenario\nResult scenario is: [2] My first scenario ([1] @ 06-Dec-2024 1:46 PM)\n\n--------------------------------------------\nSTARTING SIMULATION: 2024-12-06 : 1:47:00 PM\n--------------------------------------------\n\nHello World Time (R) => Total time: 00:00:17\n\n--------------------------------------------\nSIMULATION COMPLETE: 2024-12-06 : 1:47:17 PM\n--------------------------------------------\nTotal simulation time: 00:00:17      "

    Note: if your scenario fails to run, it will still produce a result scenario that you can use the runLog() function on to see more information about why the run failed.

    @@ -696,15 +688,15 @@

    Result scenarios
     # Check scenarios that currently exist in your library
 scenario(myLibrary)

    -
    ##   ScenarioId ProjectId ParentId                                           Name
-## 1          1         1       NA                              My first scenario
-## 2          2         1        1 My first scenario ([1] @ 13-Oct-2024 10:00 AM)
+
    ##   ScenarioId ProjectId ParentId                                          Name
+## 1          1         1       NA                             My first scenario
+## 2          2         1        1 My first scenario ([1] @ 06-Dec-2024 1:46 PM)
 ##   Owner MergeDependencies IgnoreDependencies IsResult IsReadOnly
 ## 1   N/A                No                 NA       No         No
 ## 2   N/A                No                 NA      Yes         No
-##         DateLastModified
-## 1 2024-10-13 at 10:00 AM
-## 2 2024-10-13 at 10:01 AM
    
+##        DateLastModified
+## 1 2024-12-06 at 1:46 PM
+## 2 2024-12-06 at 1:47 PM

    The first scenario is our original scenario, and the second is the result scenario with a time and date stamp of when it was run. We can also see some other information about these scenarios, such as whether @@ -791,9 +783,9 @@

    Working with multiple scenarios
     # Check which scenarios you currently have in your library
 scenario(myLibrary)['Name']
    -
    ##                                             Name
-## 1                              My first scenario
-## 2 My first scenario ([1] @ 13-Oct-2024 10:00 AM)
    +
    ##                                            Name
+## 1                             My first scenario
+## 2 My first scenario ([1] @ 06-Dec-2024 1:46 PM)
     # Create a new scenario as a copy of an existing scenario
 myNewScenario <- scenario(ssimObject = myProject,
@@ -802,10 +794,10 @@ 
    Working with multiple scenarios
 # Make sure this new scenario has been added to the library
 scenario(myLibrary)['Name']
    -
    ##                                             Name
-## 1                              My first scenario
-## 2 My first scenario ([1] @ 13-Oct-2024 10:00 AM)
-## 3                             My second scenario
    +
    ##                                            Name
+## 1                             My first scenario
+## 2 My first scenario ([1] @ 06-Dec-2024 1:46 PM)
+## 3                            My second scenario

    To edit the new scenario, we must first load the contents of the Inputs datasheet and assign it to a new R data frame using the datasheet() function. We will set the @@ -909,7 +901,7 @@

    Getting library information usin ## 1 Name: helloworldLibrary ## 2 Owner: N/A ## 3 Read Only: No -## 4 Last Modified: 2024-10-13 at 10:01 AM +## 4 Last Modified: 2024-12-06 at 1:48 PM ## 5 Size: 204 KB (208,896 B) ## 6 Data files: helloworldLibrary.ssim.data ## 7 Publish files: helloworldLibrary.ssim.publish @@ -1026,7 +1018,7 @@

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.1.1.

    diff --git a/docs/articles/a02_rsyncrosim_vignette_uncertainty.html b/docs/articles/a02_rsyncrosim_vignette_uncertainty.html index 72ad3339..63dd2331 100644 --- a/docs/articles/a02_rsyncrosim_vignette_uncertainty.html +++ b/docs/articles/a02_rsyncrosim_vignette_uncertainty.html @@ -5,7 +5,7 @@ -`rsyncrosim`: introduction to uncertainty • rsyncrosim +rsyncrosim: introduction to uncertainty • rsyncrosim @@ -16,7 +16,7 @@ - + Skip to contents @@ -26,7 +26,7 @@ rsyncrosim - 2.0.1 + 2.0.2
  • Changelog
    • @@ -67,7 +67,7 @@
    -

    `rsyncrosim`: introduction to uncertainty

    +

    rsyncrosim: introduction to uncertainty

    Source: vignettes/a02_rsyncrosim_vignette_uncertainty.Rmd @@ -141,7 +141,7 @@

    Installing and loading R packagesIn a new R script, load the rsyncrosim package.

     +library(rsyncrosim)

    Connecting R to SyncroSim using session() @@ -186,8 +186,8 @@

    Installing SyncroSim ## 1 helloworldUncertainty 2.0.1 ## description ## 1 Example demonstrating how to use iterations with an R model -## location -## 1 C:\\Users\\birch\\AppData\\Local\\SyncroSim Studio\\Packages\\helloworldUncertainty\\2.0.1 +## location +## 1 C:\\Users\\DiegoBilski\\AppData\\Local\\SyncroSim Studio\\Packages\\helloworldUncertainty\\2.0.1 ## status ## 1 OK

    @@ -438,7 +438,7 @@

    Setting run parameters with run() str(multiprocess) 
    ## 'data.frame':    1 obs. of  4 variables:
 ##  $ EnableMultiprocessing  : logi FALSE
-##  $ MaximumJobs            : num 7
+##  $ MaximumJobs            : num 15
 ##  $ EnableMultiScenario    : logi FALSE
 ##  $ EnableCopyExternalFiles: logi NA
    @@ -468,15 +468,15 @@ 
    Setting run parameters with run()
 
     # Check that we have two scenarios, and one is a result scenario
 scenario(myLibrary)
    
-
    ##   ScenarioId ProjectId ParentId                                           Name
-## 1          1         1       NA                              My first scenario
-## 2          2         1        1 My first scenario ([1] @ 13-Oct-2024 10:02 AM)
+
    ##   ScenarioId ProjectId ParentId                                          Name
+## 1          1         1       NA                             My first scenario
+## 2          2         1        1 My first scenario ([1] @ 06-Dec-2024 1:49 PM)
 ##   Owner MergeDependencies IgnoreDependencies IsResult IsReadOnly
 ## 1   N/A                No                 NA       No         No
 ## 2   N/A                No                 NA      Yes         No
-##         DateLastModified
-## 1 2024-10-13 at 10:02 AM
-## 2 2024-10-13 at 10:02 AM
    
+##        DateLastModified
+## 1 2024-12-06 at 1:49 PM
+## 2 2024-12-06 at 1:49 PM
    @@ -496,13 +496,13 @@

    Viewing results with datasheet() # View results table head(resultsSummary)

    -
    ##   Iteration Timestep        y
-## 1         1        1  7.10001
-## 2         1        2 11.20002
-## 3         1        3 15.30003
-## 4         1        4 19.40004
-## 5         1        5 23.50005
-## 6         1        6 27.60006
    +
    ##   Iteration Timestep         y
+## 1         1        1  8.219943
+## 2         1        2 13.439887
+## 3         1        3 18.659830
+## 4         1        4 23.879774
+## 5         1        5 29.099717
+## 6         1        6 34.319661

    Plotting uncertainty in SyncroSim Studio @@ -539,7 +539,7 @@

    Plotting uncertainty in Syncro

    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.1.1.

    diff --git a/docs/articles/a03_rsyncrosim_vignette_pipelines.html b/docs/articles/a03_rsyncrosim_vignette_pipelines.html index 2e448289..2d43c05f 100644 --- a/docs/articles/a03_rsyncrosim_vignette_pipelines.html +++ b/docs/articles/a03_rsyncrosim_vignette_pipelines.html @@ -5,7 +5,7 @@ -`rsyncrosim`: introduction to pipelines • rsyncrosim +rsyncrosim: introduction to pipelines • rsyncrosim @@ -16,7 +16,7 @@ - + Skip to contents @@ -26,7 +26,7 @@ rsyncrosim - 2.0.1 + 2.0.2
  • Changelog
    • @@ -67,7 +67,7 @@
    -

    `rsyncrosim`: introduction to pipelines

    +

    rsyncrosim: introduction to pipelines

    Source: vignettes/a03_rsyncrosim_vignette_pipelines.Rmd @@ -146,7 +146,7 @@

    Installing and loading R packagesIn a new R script, load the rsyncrosim package.

     +library(rsyncrosim)

    Connecting R to SyncroSim using session() @@ -192,8 +192,8 @@

    Installing SyncroSim ## 1 helloworldPipeline 2.0.0 ## description ## 1 Example demonstrating how to use pipelines with an R model -## location -## 1 C:\\Users\\birch\\AppData\\Local\\SyncroSim Studio\\Packages\\helloworldPipeline\\2.0.0 +## location +## 1 C:\\Users\\DiegoBilski\\AppData\\Local\\SyncroSim Studio\\Packages\\helloworldPipeline\\2.0.0 ## status ## 1 OK

    @@ -446,7 +446,7 @@

    Setting run parameters with run() str(multiprocess) 
    ## 'data.frame':    1 obs. of  4 variables:
 ##  $ EnableMultiprocessing  : logi FALSE
-##  $ MaximumJobs            : num 7
+##  $ MaximumJobs            : num 15
 ##  $ EnableMultiScenario    : logi FALSE
 ##  $ EnableCopyExternalFiles: logi NA
    @@ -538,13 +538,13 @@ 
    Viewing intermediate result
 
 # View results table
 head(resultsSummary)
    -
    ##   Iteration Timestep         y
-## 1         1        1  6.423785
-## 2         1        2  9.847570
-## 3         1        3 13.271354
-## 4         1        4 16.695139
-## 5         1        5 20.118924
-## 6         1        6 23.542709
    +
    ##   Iteration Timestep        y
+## 1         1        1 10.24614
+## 2         1        2 17.49229
+## 3         1        3 24.73843
+## 4         1        4 31.98457
+## 5         1        5 39.23071
+## 6         1        6 46.47686

    We can see that for every timestep in an iteration we have a new value of y corresponding to y=mt+b.

    @@ -563,12 +563,12 @@

    Viewing final results with d # View results table head(resultsSummary) 
    ##   Iteration Timestep      yCum
-## 1         1        1  6.423785
-## 2         1        2 16.271354
-## 3         1        3 29.542709
-## 4         1        4 46.237848
-## 5         1        5 66.356771
-## 6         1        6 89.899480
    +## 1 1 1 10.24614 +## 2 1 2 27.73843 +## 3 1 3 52.47686 +## 4 1 4 84.46143 +## 5 1 5 123.69214 +## 6 1 6 170.16900

    We can see for each timestep in an iteration, we have a new value of yCum, representing the cumulative value of y over time.

    @@ -585,7 +585,7 @@

    Viewing final results with d
    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.1.1.

    diff --git a/docs/articles/a04_rsyncrosim_vignette_spatial.html b/docs/articles/a04_rsyncrosim_vignette_spatial.html index f982406b..67b2e0fe 100644 --- a/docs/articles/a04_rsyncrosim_vignette_spatial.html +++ b/docs/articles/a04_rsyncrosim_vignette_spatial.html @@ -5,7 +5,7 @@ -`rsyncrosim`: introduction to spatial data • rsyncrosim +rsyncrosim: introduction to spatial data • rsyncrosim @@ -16,7 +16,7 @@ - + Skip to contents @@ -26,7 +26,7 @@ rsyncrosim - 2.0.1 + 2.0.2
  • Changelog
    • @@ -67,7 +67,7 @@
    -

    `rsyncrosim`: introduction to spatial data

    +

    rsyncrosim: introduction to spatial data

    Source: vignettes/a04_rsyncrosim_vignette_spatial.Rmd @@ -144,7 +144,7 @@

    Installing and loading R packagesrsyncrosim and terra R packages.

     # Load R packages
-library(rsyncrosim)  # package for working with SyncroSim
+library(rsyncrosim)  # package for working with SyncroSim
 library(terra)       # package for working with spatial data

    @@ -191,8 +191,8 @@

    Installing SyncroSim ## 1 helloworldSpatial 2.0.0 ## description ## 1 Example demonstrating how to use spatial data with an R model -## location -## 1 C:\\Users\\birch\\AppData\\Local\\SyncroSim Studio\\Packages\\helloworldSpatial\\2.0.0 +## location +## 1 C:\\Users\\DiegoBilski\\AppData\\Local\\SyncroSim Studio\\Packages\\helloworldSpatial\\2.0.0 ## status ## 1 OK

    @@ -451,7 +451,7 @@

    Setting run parameters with run() str(multiprocess)

    ## 'data.frame':    1 obs. of  4 variables:
 ##  $ EnableMultiprocessing  : logi FALSE
-##  $ MaximumJobs            : num 7
+##  $ MaximumJobs            : num 15
 ##  $ EnableMultiScenario    : logi FALSE
 ##  $ EnableCopyExternalFiles: logi NA
    @@ -495,12 +495,12 @@ 
    Viewing non-spatial results
 # View results table of first transformer in the pipeline
 head(resultsSummary)
    ##   Iteration Timestep         y        OutputRasterFile
-## 1         1        1  67.68919 rasterMap_iter1_ts1.tif
-## 2         1        2 139.71237 rasterMap_iter1_ts2.tif
-## 3         1        3 211.73555 rasterMap_iter1_ts3.tif
-## 4         1        4 283.75874 rasterMap_iter1_ts4.tif
-## 5         1        5 355.78192 rasterMap_iter1_ts5.tif
-## 6         1        6 427.80510 rasterMap_iter1_ts6.tif
    +## 1 1 1 -18.39475 rasterMap_iter1_ts1.tif +## 2 1 2 -32.45549 rasterMap_iter1_ts2.tif +## 3 1 3 -46.51624 rasterMap_iter1_ts3.tif +## 4 1 4 -60.57699 rasterMap_iter1_ts4.tif +## 5 1 5 -74.63774 rasterMap_iter1_ts5.tif +## 6 1 6 -88.69849 rasterMap_iter1_ts6.tif 
     # Load results of second transformer in the pipeline
 resultsSummary2 <- datasheet(myResultScenario,
@@ -509,12 +509,12 @@ 
    Viewing non-spatial results
 # View results table of second transformer in the pipeline
 head(resultsSummary2)
    ##   Iteration Timestep       yCum
-## 1         1        1   67.68919
-## 2         1        2  207.40156
-## 3         1        3  419.13711
-## 4         1        4  702.89585
-## 5         1        5 1058.67777
-## 6         1        6 1486.48287
    +## 1 1 1 -18.39475 +## 2 1 2 -50.85024 +## 3 1 3 -97.36648 +## 4 1 4 -157.94348 +## 5 1 5 -232.58122 +## 6 1 6 -321.27971

    From viewing these datasheets, we can see that the spatial output is contained within the IntermediateDatasheet, in the column called OutputRasterFile.

    @@ -551,8 +551,8 @@

    Viewing spatial result ## coord. ref. : lon/lat WGS 84 (EPSG:4326) ## source : rasterMap_iter1_ts5.tif ## name : rasterMap_iter1_ts5 -## min value : 11.77882 -## max value : 16.52308 +## min value : -5.4379683 +## max value : -0.6937107 
     plot(rasterMaps[[1]])

    @@ -588,7 +588,7 @@

    Viewing spatial results in
    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.1.1.

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  • Changelog
    • @@ -67,7 +67,7 @@
    -

    `rsyncrosim`: introduction to `ST-Sim`

    +

    rsyncrosim: introduction to ST-Sim

    Source: vignettes/a05_rsyncrosim_stsim_vignette.Rmd @@ -141,7 +141,7 @@

    Installing and loading R packagesrsyncrosim and terra R packages.

     # Load R packages
-library(rsyncrosim)  # package for working with SyncroSim
+library(rsyncrosim)  # package for working with SyncroSim
 library(terra)       # package for working with spatial data

    @@ -186,8 +186,8 @@

    Installing SyncroSim packages()

    ##    name version                                      description
 ## 1 stsim   4.0.1 The ST-Sim state-and-transition simulation model
-##                                                                     location
-## 1 C:\\Users\\birch\\AppData\\Local\\SyncroSim Studio\\Packages\\stsim\\4.0.1
+##                                                                           location
+## 1 C:\\Users\\DiegoBilski\\AppData\\Local\\SyncroSim Studio\\Packages\\stsim\\4.0.1
 ##   status
 ## 1     OK
    @@ -767,7 +767,7 @@

    Setting run parameters with run() str(multiprocess) 
    ## 'data.frame':    1 obs. of  4 variables:
 ##  $ EnableMultiprocessing  : logi FALSE
-##  $ MaximumJobs            : num 7
+##  $ MaximumJobs            : num 15
 ##  $ EnableMultiScenario    : logi FALSE
 ##  $ EnableCopyExternalFiles: logi NA
    @@ -854,7 +854,7 @@ 
    View results
-  
    Site built with pkgdown 2.1.0.
    
+  
    Site built with pkgdown 2.1.1.
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    1iD diff --git a/docs/articles/a06_rsyncrosim_install_github.html b/docs/articles/a06_rsyncrosim_install_github.html index 68b259f6..ab9e5498 100644 --- a/docs/articles/a06_rsyncrosim_install_github.html +++ b/docs/articles/a06_rsyncrosim_install_github.html @@ -26,7 +26,7 @@ rsyncrosim - 2.0.1 + 2.0.2

  • Changelog
    • @@ -114,7 +114,7 @@
  • Load the rsyncrosim library.
    • -library(rsyncrosim)
    +library(rsyncrosim) @@ -125,7 +125,7 @@
    -

    Site built with pkgdown 2.1.0.

    +

    Site built with pkgdown 2.1.1.

    diff --git a/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html new file mode 100644 index 00000000..935a0d10 --- /dev/null +++ b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html @@ -0,0 +1,209 @@ + + + + + + + +Updating rsyncrosim scripts to version 2 • rsyncrosim + + + + + + + + + + + + + + Skip to contents + + +
    + + + + +
    +
    +

    Updating rsyncrosim scripts to version 2

    + + + Source: vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd +
    a07_updating_rsyncrosim_scripts_to_v2.Rmd
    +
    + + + +

    The introduction of +SyncroSim +Studio brought some structural changes and new functionalities, +which get reflected in the rsyncrosim package. Use the +guide below to update your rsyncrosim v1 scripts to +rsyncrosim v2.

    +

    Note: +SyncroSim +v3.0.9 or higher is required to use rsyncrosim v2.0.1 +or higher.

    +
    +

    Updated functions +

    +

    To install and uninstall packages from your SyncroSim installation, +use:

    +
    +installPackage() # Installs the selected package(s) to SyncroSim
+uninstallPackage() # Uninstalls the selected package(s)
    +

    Now you can use multiple SyncroSim packages in a single library. To +add and remove packages from your library, use:

    +
    +addPackage() # Adds package(s) to the library
+removePackage() # Removes package(s) from the library. Note that any associated datasheets will be removed as well.
    +

    And also for that reason, the package addons have been converted to +standalone packages, or incorporated into the base packages. Therefore, +the following functions no longer exist:

    +
    +addon()
+disableAddon()
+enableAddon()
    +
    +
    +

    Library +

    +

    info(ssimLibrary) no longer shows the Package +name, Current package version and Minimum package +version, and the Input and Output folder paths have been combined +into the Data folder.

    +

    the package argument in the +ssimLibrary(package) function has been renamed to +packages

    +
    +myLibrary <- ssimLibrary(packages = c())
    +

    The addon and template arguments have also +been removed.

    +
    +
    +

    Dependencies +

    +

    To view the existing dependencies for a scenario, use:

    +
    +dependency(myScenario)
    +

    To set dependedncies for a scenario, use:

    +
    +dependency(myScenario) <- c("Scenario 1", "Scenario 2")
    +

    Note that this will remove any previously set dependencies. Also, the +order in which the dependencies are listed can be important. In this +example, Scenario 1 takes precedence over +Scenario 2.

    +
    +
    +

    Multiprocessing +

    +

    The run() function no longer has the jobs +argument. Use the core_Multiprocessing datasheet to set the +number of cores to use. Note that this will affect every scenario +run.

    +
    +
    +

    Variable naming +

    +

    The ID in variable names have been changed to +Id. It is generally safe to substitute ID +for Id throughout your script, unless that affects any +variables not related to SyncroSim.

    +
    +
    +

    stsimsf +

    +

    The ST-Sim Stock & Flow package, stsimsf have been +incorporated into ST-Sim. Substitute all stsimsf_ +datasheets throghout your script for stsim_. The only +exception is the stsimsf_OutputOptions that is now called +stsim_OutputOptionsStockFlow.

    +
    +
    +

    Other removed functions +

    +
    +datasheetRaster() # previously deprecated function. Use datasheetSpatRaster() instead.
+
+addBreakpoint()
+breakpoint()
+deleteBreakpoint()
+
+ssimUpdate()
+updatePackage()
    +
    +
    +

    Other NEW functions +

    +
    +createCondaEnv(pkgs = c()) # creates the conda environment for the selecte package(s)
+
+deleteLibrary() # Note this is irreversible
+
+chart() # Create or load a SyncroSim chart. Explore other charting functions with ?chart
    +
    +
    +
    + + + +
    +

    Developed by Colin Daniel, Josie Hughes, Valentin Lucet, Alex Embrey, Katie Birchard, Leonardo Frid, Tabitha Kennedy, Shreeram Senthivasan.

    +
    + +
    +

    Site built with pkgdown 2.1.1.

    +
    + +
    +
    + + + + + + + diff --git a/docs/articles/index.html b/docs/articles/index.html index aedc46ff..8dcdd435 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -7,7 +7,7 @@ rsyncrosim - 2.0.1 + 2.0.2 -
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    • @@ -95,7 +95,7 @@

      Examples -

      Site built with pkgdown 2.1.0.

      +

      Site built with pkgdown 2.1.1.

      diff --git a/man/addPackage.Rd b/man/addPackage.Rd index ec99e1d3..9ca34d1f 100644 --- a/man/addPackage.Rd +++ b/man/addPackage.Rd @@ -32,7 +32,7 @@ of the package) or \code{FALSE} upon failure. Adds package(s) to a \code{\link{SsimLibrary}}. } \examples{ -\dontrun{ +\donttest{ # Install "stsim" and "stsimecodep" SyncroSim packages installPackage(packages = c("stsim", "stsim"), versions = c("4.0.0", "4.0.1")) diff --git a/man/backup.Rd b/man/backup.Rd index 3b77c62c..2a61cc9d 100644 --- a/man/backup.Rd +++ b/man/backup.Rd @@ -26,7 +26,7 @@ SyncroSim User Interface, but is by default at the same level as the SsimLibrary file, and is called libraryName.backup. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/chart.Rd b/man/chart.Rd index ff935fb3..1cf26577 100644 --- a/man/chart.Rd +++ b/man/chart.Rd @@ -34,7 +34,7 @@ Create or open a \code{\link{Chart}} from a SyncroSim \code{\link{Project}}. } \examples{ -\dontrun{ +\donttest{ # Set the file path and name of the new SsimLibrary myLibraryName <- file.path(tempdir(),"testlib") diff --git a/man/chartId.Rd b/man/chartId.Rd index b653e271..5606c63f 100644 --- a/man/chartId.Rd +++ b/man/chartId.Rd @@ -22,7 +22,7 @@ An integer: chart id. Retrieves the Chart Id of a SyncroSim \code{\link{Chart}}. } \examples{ -\dontrun{ +\donttest{ # Set the file path and name of the new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/delete.Rd b/man/delete.Rd index c0117970..33adb0c3 100644 --- a/man/delete.Rd +++ b/man/delete.Rd @@ -89,7 +89,7 @@ input: \code{TRUE} upon success (i.e.successful deletion) and \code{FALSE} upon Deletes one or more items. Note that this is irreversible. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/deleteLibrary.Rd b/man/deleteLibrary.Rd index 81e57f05..d5b9f2a4 100644 --- a/man/deleteLibrary.Rd +++ b/man/deleteLibrary.Rd @@ -53,7 +53,7 @@ is FALSE.} Deletes a SyncroSim library. Note this is irreversable. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/dependency.Rd b/man/dependency.Rd index d6188bc1..5e48ab52 100644 --- a/man/dependency.Rd +++ b/man/dependency.Rd @@ -8,25 +8,21 @@ \alias{dependency<-,Scenario-method} \title{Get, set or remove Scenario dependency(s)} \usage{ -dependency(ssimObject) +dependency(scenario) -\S4method{dependency}{character}(ssimObject) +\S4method{dependency}{character}(scenario) -\S4method{dependency}{Scenario}(ssimObject) +\S4method{dependency}{Scenario}(scenario) dependency(ssimObject) <- value \S4method{dependency}{Scenario}(ssimObject) <- value } \arguments{ -\item{ssimObject}{\code{\link{Scenario}} object, character string, integer, or +\item{scenario}{\code{\link{Scenario}} object, character string, integer, or vector of these. The Scenario object, name, or ID to which a dependency is to be added (or has already been added if \code{remove=TRUE}). Note that integer ids -are slightly faster.} - -\item{value}{\code{\link{Scenario}} object, character string, integer, or -vector of these. The Scenario object, name, or ID to be used as the -dependency. If an empty vector is provided, all dependencies are removed.} +are slightly faster} } \value{ A data.frame: all dependencies for a given Scenario @@ -43,14 +39,11 @@ is returned in order of precedence (from highest to lowest precedence). Otherwise, returns list of saved or error messages for each dependency of each scenario. -Note that the order of dependencies can be important - dependencies added most -recently take precedence over existing dependencies. So, dependencies included -in the dependency argument take precedence over any other existing dependencies. -If the dependency argument includes more than one element, elements are ordered -from lowest to highest precedence. +Note that the order of dependencies can be important. If the dependency argument +includes more than one element, elements are ordered from highest to lowest precedence. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/description.Rd b/man/description.Rd index 0bb268db..ec4441ea 100644 --- a/man/description.Rd +++ b/man/description.Rd @@ -35,7 +35,7 @@ Get or set the description of a \code{\link{SsimLibrary}}, \code{\link{Project}} or \code{\link{Scenario}}. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/filepath.Rd b/man/filepath.Rd index d30076a0..67a71253 100644 --- a/man/filepath.Rd +++ b/man/filepath.Rd @@ -31,7 +31,7 @@ Retrieves the path to a SyncroSim \code{\link{Session}}, of \code{\link{Folder}} on disk. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/folder.Rd b/man/folder.Rd index 1b0b07c3..121c09c3 100644 --- a/man/folder.Rd +++ b/man/folder.Rd @@ -43,7 +43,7 @@ Create or open a \code{\link{Folder}} from a SyncroSim \code{\link{Project}}. } \examples{ -\dontrun{ +\donttest{ # Set the file path and name of the new SsimLibrary myLibraryName <- file.path(tempdir(),"testlib") diff --git a/man/folderId.Rd b/man/folderId.Rd index 4980379e..52edf346 100644 --- a/man/folderId.Rd +++ b/man/folderId.Rd @@ -37,7 +37,7 @@ Retrieves the Folder Id of a SyncroSim \code{\link{Folder}} or desired folder in the SyncroSim User Interface. } \examples{ -\dontrun{ +\donttest{ # Set the file path and name of the new SsimLibrary myLibraryName <- file.path(tempdir(),"testlib") diff --git a/man/ignoreDependencies.Rd b/man/ignoreDependencies.Rd index f1db34fc..a1b249e9 100644 --- a/man/ignoreDependencies.Rd +++ b/man/ignoreDependencies.Rd @@ -34,7 +34,7 @@ A character string: Scenario Datafeeds that will be ignored. Retrieves or sets the Datafeeds to ignore for a \code{\link{Scenario}}. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/mergeDependencies.Rd b/man/mergeDependencies.Rd index c8a9d1fa..a135a921 100644 --- a/man/mergeDependencies.Rd +++ b/man/mergeDependencies.Rd @@ -36,7 +36,7 @@ Retrieves or sets whether or not a \code{\link{Scenario}} is configured to merge dependencies at run time. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(),"testlib") diff --git a/man/name.Rd b/man/name.Rd index d5aebdf2..60565656 100644 --- a/man/name.Rd +++ b/man/name.Rd @@ -59,7 +59,7 @@ Retrieves or sets the name of a \code{\link{SsimLibrary}}, \code{\link{Project}}, \code{\link{Scenario}}, or \code{\link{Folder}}. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/packages.Rd b/man/packages.Rd index 086b62e5..3777945e 100644 --- a/man/packages.Rd +++ b/man/packages.Rd @@ -36,7 +36,7 @@ called on a \code{\link{Session}} object, or the packages added to a SyncroSim Library if called on a \code{\link{SsimLibrary}} object. } \examples{ -\dontrun{ +\donttest{ # Set the file path and name of the new SsimLibrary myLibraryName <- file.path(tempdir(),"testlib") diff --git a/man/printCmd.Rd b/man/printCmd.Rd index 333018c6..af2a73b2 100644 --- a/man/printCmd.Rd +++ b/man/printCmd.Rd @@ -26,7 +26,7 @@ Retrieves a printCmd setting of a \code{\link{Session}} object. The printCmd setting configures a Session for printing commands sent to the console. } \examples{ -\dontrun{ +\donttest{ # Set SyncroSim Session mySession <- session() diff --git a/man/project.Rd b/man/project.Rd index d05f099d..9f372d49 100644 --- a/man/project.Rd +++ b/man/project.Rd @@ -54,7 +54,7 @@ named element. Note that SyncroSim automatically assigns an id to a new Project. } } \examples{ -\dontrun{ +\donttest{ # Set the file path and name of the new SsimLibrary myLibraryName <- file.path(tempdir(),"testlib_project") diff --git a/man/projectId.Rd b/man/projectId.Rd index 887233fa..05a0b5f8 100644 --- a/man/projectId.Rd +++ b/man/projectId.Rd @@ -33,7 +33,7 @@ Retrieves the projectId of a SyncroSim \code{\link{Project}}, \code{\link{Scenario}}, \code{\link{Folder}} or \code{\link{Chart}}. } \examples{ -\dontrun{ +\donttest{ # Set the file path and name of the new SsimLibrary myLibraryName <- file.path(tempdir(),"testlib") diff --git a/man/readOnly.Rd b/man/readOnly.Rd index 4ecc10b3..f3b90fe7 100644 --- a/man/readOnly.Rd +++ b/man/readOnly.Rd @@ -56,7 +56,7 @@ Retrieves or sets whether or not a \code{\link{SsimLibrary}}, read-only. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/removePackage.Rd b/man/removePackage.Rd index b58c069f..9ed219e0 100644 --- a/man/removePackage.Rd +++ b/man/removePackage.Rd @@ -25,7 +25,7 @@ removal of the package) or \code{FALSE} upon failure. Removes package(s) from a \code{\link{SsimLibrary}}. } \examples{ -\dontrun{ +\donttest{ # Install "stsim" and "stsimecodep" SyncroSim packages installPackage("stsim") installPackage("stsimecodep") diff --git a/man/scenario.Rd b/man/scenario.Rd index bc128ba4..08f02d68 100644 --- a/man/scenario.Rd +++ b/man/scenario.Rd @@ -75,7 +75,7 @@ a copy of sourceScenario. } } \examples{ -\dontrun{ +\donttest{ # Set the file path and name of the new SsimLibrary myLibraryName <- file.path(tempdir(),"testlib") diff --git a/man/scenarioId.Rd b/man/scenarioId.Rd index 5be36f6e..b1762056 100644 --- a/man/scenarioId.Rd +++ b/man/scenarioId.Rd @@ -22,7 +22,7 @@ Integer id of the input Scenario. Retrieves the scenarioId of a \code{\link{Scenario}}. } \examples{ -\dontrun{ +\donttest{ # Set the file path and name of the new SsimLibrary myLibraryName <- file.path(tempdir(),"testlib") diff --git a/man/session.Rd b/man/session.Rd index e16dcd14..987508a8 100644 --- a/man/session.Rd +++ b/man/session.Rd @@ -55,7 +55,7 @@ have updated the SyncroSim software and want to update an existing SsimObject to use the new software. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/silent.Rd b/man/silent.Rd index db96dfc5..54ad8435 100644 --- a/man/silent.Rd +++ b/man/silent.Rd @@ -36,7 +36,7 @@ Checks or sets whether a SyncroSim \code{\link{Session}} is silent or not. In a silent session, warnings from the console are ignored. } \examples{ -\dontrun{ +\donttest{ # Set up a SyncroSim Session mySession <- session() diff --git a/man/sqlStatement.Rd b/man/sqlStatement.Rd index 6f9089e0..13642723 100644 --- a/man/sqlStatement.Rd +++ b/man/sqlStatement.Rd @@ -40,7 +40,7 @@ Note that it is not possible to construct a complete SQL query at this stage, because the \code{\link{datasheet}} function may add ScenarioId and/or ProjectId to the query. } \examples{ -\dontrun{ +\donttest{ # Query total Amount for each combination of ScenarioId, Iteration, Timestep and StateLabelXID, # including only Timesteps 0,1 and 2, and Iterations 3 and 4. mySQL <- sqlStatement( diff --git a/man/ssimLibrary.Rd b/man/ssimLibrary.Rd index 746b00e2..ba4ba9bc 100644 --- a/man/ssimLibrary.Rd +++ b/man/ssimLibrary.Rd @@ -86,7 +86,7 @@ of package. } } \examples{ -\dontrun{ +\donttest{ # Make sure packages are installed installPackage("stsim") diff --git a/man/tempfilepath.Rd b/man/tempfilepath.Rd index 5dbfebf0..f5547413 100644 --- a/man/tempfilepath.Rd +++ b/man/tempfilepath.Rd @@ -28,7 +28,7 @@ Retrieves the temporary file path to a SyncroSim \code{\link{Session}}, on disk. } \examples{ -\dontrun{ +\donttest{ # Specify file path and name of new SsimLibrary myLibraryName <- file.path(tempdir(), "testlib") diff --git a/man/uninstallPackage.Rd b/man/uninstallPackage.Rd index 764aad83..87f7ade3 100644 --- a/man/uninstallPackage.Rd +++ b/man/uninstallPackage.Rd @@ -34,7 +34,7 @@ removal) and \code{FALSE} upon failure. Removes a package from SyncroSim installation } \examples{ -\dontrun{ +\donttest{ # Set SyncroSim session mySession <- session() diff --git a/man/version.Rd b/man/version.Rd index 716da168..3946cce9 100644 --- a/man/version.Rd +++ b/man/version.Rd @@ -25,7 +25,7 @@ A character string e.g. "2.2.13". Retrieves the version of a SyncroSim Session. } \examples{ -\dontrun{ +\donttest{ # Set SyncroSim Session mySession <- session() diff --git a/vignettes/a01_rsyncrosim_vignette_basic.Rmd b/vignettes/a01_rsyncrosim_vignette_basic.Rmd index eae06e61..ffbb62b6 100644 --- a/vignettes/a01_rsyncrosim_vignette_basic.Rmd +++ b/vignettes/a01_rsyncrosim_vignette_basic.Rmd @@ -1,9 +1,9 @@ --- -title: "Introduction to `rsyncrosim`" +title: "Introduction to rsyncrosim" output: rmarkdown::html_vignette # output: pdf_document vignette: > - %\VignetteIndexEntry{Introduction to `rsyncrosim`} + %\VignetteIndexEntry{Introduction to rsyncrosim} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc} params: diff --git a/vignettes/a02_rsyncrosim_vignette_uncertainty.Rmd b/vignettes/a02_rsyncrosim_vignette_uncertainty.Rmd index 48ffa04a..6516f908 100644 --- a/vignettes/a02_rsyncrosim_vignette_uncertainty.Rmd +++ b/vignettes/a02_rsyncrosim_vignette_uncertainty.Rmd @@ -1,9 +1,9 @@ --- -title: '`rsyncrosim`: introduction to uncertainty' +title: 'rsyncrosim: introduction to uncertainty' output: rmarkdown::html_vignette #output: pdf_document vignette: > - %\VignetteIndexEntry{`rsyncrosim`: introduction to uncertainty} + %\VignetteIndexEntry{rsyncrosim: introduction to uncertainty} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc} params: diff --git a/vignettes/a03_rsyncrosim_vignette_pipelines.Rmd b/vignettes/a03_rsyncrosim_vignette_pipelines.Rmd index 299e0bca..42810a53 100644 --- a/vignettes/a03_rsyncrosim_vignette_pipelines.Rmd +++ b/vignettes/a03_rsyncrosim_vignette_pipelines.Rmd @@ -1,9 +1,9 @@ --- -title: '`rsyncrosim`: introduction to pipelines' +title: 'rsyncrosim: introduction to pipelines' output: rmarkdown::html_vignette #output: pdf_document vignette: > - %\VignetteIndexEntry{`rsyncrosim`: introduction to pipelines} + %\VignetteIndexEntry{rsyncrosim: introduction to pipelines} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc} params: diff --git a/vignettes/a04_rsyncrosim_vignette_spatial.Rmd b/vignettes/a04_rsyncrosim_vignette_spatial.Rmd index 84fbfd09..81f0531b 100644 --- a/vignettes/a04_rsyncrosim_vignette_spatial.Rmd +++ b/vignettes/a04_rsyncrosim_vignette_spatial.Rmd @@ -1,9 +1,9 @@ --- -title: "`rsyncrosim`: introduction to spatial data" +title: "rsyncrosim: introduction to spatial data" output: rmarkdown::html_vignette # output: pdf_document # uncomment when releasing to CRAN vignette: > - %\VignetteIndexEntry{`rsyncrosim`: introduction to spatial data} + %\VignetteIndexEntry{rsyncrosim: introduction to spatial data} %\VignetteEngine{knitr::rmarkdown} %\usepackage[utf8]{inputenc} params: diff --git a/vignettes/a05_rsyncrosim_stsim_vignette.Rmd b/vignettes/a05_rsyncrosim_stsim_vignette.Rmd index 04721d20..08e2ff70 100644 --- a/vignettes/a05_rsyncrosim_stsim_vignette.Rmd +++ b/vignettes/a05_rsyncrosim_stsim_vignette.Rmd @@ -1,9 +1,9 @@ --- -title: "`rsyncrosim`: introduction to `ST-Sim`" +title: "rsyncrosim: introduction to ST-Sim" output: rmarkdown::html_vignette # output: pdf_document vignette: > - %\VignetteIndexEntry{`rsyncrosim`: introduction to `ST-Sim`} + %\VignetteIndexEntry{rsyncrosim: introduction to ST-Sim} %\VignetteEngine{knitr::rmarkdown} %\usepackage[utf8]{inputenc} params: diff --git a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd new file mode 100644 index 00000000..96d237fe --- /dev/null +++ b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd @@ -0,0 +1,106 @@ +--- +title: "Updating rsyncrosim scripts to version 2" + +output: rmarkdown::html_vignette +vignette: > + %\VignetteIndexEntry{Updating rsyncrosim scripts to version 2} + %\VignetteEngine{knitr::rmarkdown} + \usepackage[utf8]{inputenc} +params: + EVAL: !r identical(Sys.getenv("NOT_CRAN"), "true") +--- + +The introduction of SyncroSim Studio brought some structural changes and new functionalities, which get reflected in the `rsyncrosim` package. Use the guide below to update your `rsyncrosim v1` scripts to `rsyncrosim v2`. + +*Note*: SyncroSim v3.0.9 or higher is required to use `rsyncrosim v2.0.1` or higher. + +## Updated functions + +To install and uninstall packages from your SyncroSim installation, use: + +```{r install packages, eval=FALSE} +installPackage() # Installs the selected package(s) to SyncroSim +uninstallPackage() # Uninstalls the selected package(s) +``` + +Now you can use multiple SyncroSim packages in a single library. To add and remove packages from your library, use: + +```{r add package, eval=FALSE} +addPackage() # Adds package(s) to the library +removePackage() # Removes package(s) from the library. Note that any associated datasheets will be removed as well. +``` + +And also for that reason, the package addons have been converted to standalone packages, or incorporated into the base packages. Therefore, the following functions no longer exist: + +```{r deprecated, eval=FALSE} +addon() +disableAddon() +enableAddon() +``` + +## Library + +`info(ssimLibrary)` no longer shows the *Package name*, *Current package version* and *Minimum package version*, and the Input and Output folder paths have been combined into the *Data folder*. + +the `package` argument in the `ssimLibrary(package)` function has been renamed to `packages` + +```{r library, eval=FALSE} +myLibrary <- ssimLibrary(packages = c()) +``` + +The `addon` and `template` arguments have also been removed. + +## Dependencies + +To view the existing dependencies for a scenario, use: + +```{r view dependencies, eval=FALSE} +dependency(myScenario) +``` + +To set dependedncies for a scenario, use: + +```{r set dependencies, eval=FALSE} +dependency(myScenario) <- c("Scenario 1", "Scenario 2") +``` + +Note that this will remove any previously set dependencies. +Also, the order in which the dependencies are listed can be important. In this example, `Scenario 1` takes precedence over `Scenario 2`. + + +## Multiprocessing + +The `run()` function no longer has the `jobs` argument. Use the `core_Multiprocessing` datasheet to set the number of cores to use. Note that this will affect every scenario run. + + +## Variable naming + +The **ID** in variable names have been changed to **Id**. It is generally safe to substitute `ID` for `Id` throughout your script, unless that affects any variables not related to SyncroSim. + +## stsimsf + +The ST-Sim Stock & Flow package, `stsimsf` have been incorporated into ST-Sim. Substitute all `stsimsf_` datasheets throghout your script for `stsim_`. +The only exception is the `stsimsf_OutputOptions` that is now called `stsim_OutputOptionsStockFlow`. + +## Other removed functions + +```{r other removed, eval=FALSE} +datasheetRaster() # previously deprecated function. Use datasheetSpatRaster() instead. + +addBreakpoint() +breakpoint() +deleteBreakpoint() + +ssimUpdate() +updatePackage() +``` + +## Other NEW functions +```{r new functions, eval=FALSE} +createCondaEnv(pkgs = c()) # creates the conda environment for the selecte package(s) + +deleteLibrary() # Note this is irreversible + +chart() # Create or load a SyncroSim chart. Explore other charting functions with ?chart +``` + From 4543cc21f501f90e30f31cdc9a28bee4ac817fc5 Mon Sep 17 00:00:00 2001 From: diegobilski Date: Mon, 9 Dec 2024 07:16:16 -0500 Subject: [PATCH 2/6] a07 vignette update Added core_ datasheets name change --- docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html | 6 ++++++ vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd | 4 ++++ 2 files changed, 10 insertions(+) diff --git a/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html index 935a0d10..42f39d76 100644 --- a/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html +++ b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html @@ -153,6 +153,12 @@

      Variable naming
      +

      Core datasheets +

      +

      The corestime_ datasheets are now simply called +core_.

      +
      +

      stsimsf

      The ST-Sim Stock & Flow package, stsimsf have been diff --git a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd index 96d237fe..b1153bee 100644 --- a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd +++ b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd @@ -77,6 +77,10 @@ The `run()` function no longer has the `jobs` argument. Use the `core_Multiproce The **ID** in variable names have been changed to **Id**. It is generally safe to substitute `ID` for `Id` throughout your script, unless that affects any variables not related to SyncroSim. +## Core datasheets + +The `corestime_` datasheets are now simply called `core_`. + ## stsimsf The ST-Sim Stock & Flow package, `stsimsf` have been incorporated into ST-Sim. Substitute all `stsimsf_` datasheets throghout your script for `stsim_`. From 6d9dcf922bd56995d073b56905859faeaa9d9d18 Mon Sep 17 00:00:00 2001 From: Katie Birchard <33553358+katieb1@users.noreply.github.com> Date: Mon, 9 Dec 2024 12:44:31 -0800 Subject: [PATCH 3/6] Update a07_updating_rsyncrosim_scripts_to_v2.Rmd Add some headers and some edits for clarity --- .../a07_updating_rsyncrosim_scripts_to_v2.Rmd | 27 ++++++++++++------- 1 file changed, 17 insertions(+), 10 deletions(-) diff --git a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd index b1153bee..ea1b80e3 100644 --- a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd +++ b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd @@ -10,27 +10,34 @@ params: EVAL: !r identical(Sys.getenv("NOT_CRAN"), "true") --- -The introduction of SyncroSim Studio brought some structural changes and new functionalities, which get reflected in the `rsyncrosim` package. Use the guide below to update your `rsyncrosim v1` scripts to `rsyncrosim v2`. +The introduction of SyncroSim Studio brought some structural changes and new functionalities, which are reflected in the `rsyncrosim` package. Use the guide below to update your `rsyncrosim` version 1 scripts to be compatible with version 2. -*Note*: SyncroSim v3.0.9 or higher is required to use `rsyncrosim v2.0.1` or higher. +*Note*: SyncroSim v3.0.9 or higher is required to use `rsyncrosim v2.0.0` or higher. ## Updated functions -To install and uninstall packages from your SyncroSim installation, use: +### Installing/uninstalling packages + +Previously, the `addPackage` and `removePackage` functions were used to install and uninstall packages from SyncroSim. Now to install and uninstall packages from SyncroSim, use: ```{r install packages, eval=FALSE} -installPackage() # Installs the selected package(s) to SyncroSim -uninstallPackage() # Uninstalls the selected package(s) +installPackage() # Installs the selected package(s) to SyncroSim +uninstallPackage() # Uninstalls the selected package(s) from SyncroSim ``` +### Adding/removing packages + Now you can use multiple SyncroSim packages in a single library. To add and remove packages from your library, use: ```{r add package, eval=FALSE} -addPackage() # Adds package(s) to the library -removePackage() # Removes package(s) from the library. Note that any associated datasheets will be removed as well. +addPackage() # Adds package(s) to the library +removePackage() # Removes package(s) from the library. ``` +Note that when you remove a package from your library any associated datasheets will be removed as well. + +## Deprecated functions -And also for that reason, the package addons have been converted to standalone packages, or incorporated into the base packages. Therefore, the following functions no longer exist: +In SyncroSim 3, the concept of addon packages no longer exists. All addon packages have either been converted to standalone packages (e.g., `burnP3PlusPrometheus`) and can be added to a library without having to load a base package first, or incorporated directly into the base packages (e.g., `stsimsf` is now part of `stsim`). Therefore, the following functions have been removed: ```{r deprecated, eval=FALSE} addon() @@ -42,7 +49,7 @@ enableAddon() `info(ssimLibrary)` no longer shows the *Package name*, *Current package version* and *Minimum package version*, and the Input and Output folder paths have been combined into the *Data folder*. -the `package` argument in the `ssimLibrary(package)` function has been renamed to `packages` +The `package` argument in the `ssimLibrary(package)` function has been renamed to `packages` ```{r library, eval=FALSE} myLibrary <- ssimLibrary(packages = c()) @@ -58,7 +65,7 @@ To view the existing dependencies for a scenario, use: dependency(myScenario) ``` -To set dependedncies for a scenario, use: +To set dependencies for a scenario, use: ```{r set dependencies, eval=FALSE} dependency(myScenario) <- c("Scenario 1", "Scenario 2") From d6b7b1e2c4290a953b1aae4332f00737068bc70a Mon Sep 17 00:00:00 2001 From: diegobilski Date: Tue, 17 Dec 2024 12:12:22 -0500 Subject: [PATCH 4/6] changes to vignette and dependency additions to the Updating rsyncrosim scripts vignette. changes to dependency function desctription --- R/dependency.R | 39 ++-- ...a07_updating_rsyncrosim_scripts_to_v2.html | 184 ++++++++++++------ .../a07_updating_rsyncrosim_scripts_to_v2.Rmd | 93 ++++++--- 3 files changed, 205 insertions(+), 111 deletions(-) diff --git a/R/dependency.R b/R/dependency.R index edfea84e..7373a5da 100644 --- a/R/dependency.R +++ b/R/dependency.R @@ -3,7 +3,7 @@ #' @include AAAClassDefinitions.R NULL -#' Get, set or remove Scenario dependency(s) +#' Get, set or remove Scenario dependencies #' #' List dependencies, set dependencies, or remove dependencies from a SyncroSim #' \code{\link{Scenario}}. Setting dependencies is a way of linking together @@ -16,14 +16,21 @@ NULL #' is returned in order of precedence (from highest to lowest precedence). #' Otherwise, returns list of saved or error messages for each dependency of each #' scenario. +#' +#' Note that pre-existing dependencies will be removed when adding new dependencies unless +#' those elements are included in the vector of new dependencies. #' -#' Note that the order of dependencies can be important. If the dependency argument -#' includes more than one element, elements are ordered from highest to lowest precedence. #' -#' @param scenario \code{\link{Scenario}} object, character string, integer, or +#' @param ssimObject \code{\link{Scenario}} object, character string, integer, or #' vector of these. The Scenario object, name, or ID to which a dependency is to #' be added (or has already been added if \code{remove=TRUE}). Note that integer ids -#' are slightly faster +#' are slightly faster. +#' +#' @param value \code{\link{Scenario}} object, character string, integer, or +#' vector of these. The Scenario object, name, or ID to be used as the +#' dependency. If an empty vector is provided, all dependencies are removed. If +#' multiple elements are provided, elements should be ordered from highest to lowest +#' precedence. #' #' @return #' A data.frame: all dependencies for a given Scenario @@ -52,18 +59,18 @@ NULL #' } #' #' @export -setGeneric("dependency", function(scenario) standardGeneric("dependency")) +setGeneric("dependency", function(ssimObject) standardGeneric("dependency")) #' @rdname dependency -setMethod("dependency", signature(scenario = "character"), function(scenario) { - return(SyncroSimNotFound(scenario)) +setMethod("dependency", signature(ssimObject = "character"), function(ssimObject) { + return(SyncroSimNotFound(ssimObject)) }) #' @rdname dependency -setMethod("dependency", signature(scenario = "Scenario"), function(scenario) { +setMethod("dependency", signature(ssimObject = "Scenario"), function(ssimObject) { - # Rename variable so it's not the same as the rsyncrosim::scenario() function - s <- scenario + # Rename variable + s <- ssimObject # get set of existing dependencies args <- list(list = NULL, dependencies = NULL, lib = .filepath(s), @@ -78,7 +85,7 @@ setMethod("dependency", signature(scenario = "Scenario"), function(scenario) { names(dependencySet)[names(dependencySet) == "Id"] <- "ScenarioId" return(dependencySet) - } +} ) #' @rdname dependency @@ -118,9 +125,11 @@ setReplaceMethod( cDep <- allScns$ScenarioId[allScns$Name == v] if (length(cDep) == 0) { - stop("Could not find dependency scenario ", cDepRaw) + stop("Could not find dependency scenario ", v) } else if (length(cDep) > 1) { - stop("Found more than one scenario named ", v, ". Please specify a dependency scenario id:", paste0(v, collapse = ",")) + stop("Found more than one scenario named ", v, + ". Please specify a dependency scenario id:", + paste0(v, collapse = ",")) } else { valueList <- c(valueList, cDep) } @@ -164,7 +173,7 @@ setReplaceMethod( stop(tt) } } - + return(ssimObject) } ) \ No newline at end of file diff --git a/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html index 42f39d76..355aedfa 100644 --- a/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html +++ b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html @@ -78,113 +78,169 @@

      The introduction of SyncroSim -Studio brought some structural changes and new functionalities, -which get reflected in the rsyncrosim package. Use the -guide below to update your rsyncrosim v1 scripts to -rsyncrosim v2.

      +Studio brought some structural changes and new features, which are +reflected in the rsyncrosim package. Use the guide below to +update your rsyncrosim version 1 scripts to be compatible +with version 2.

      Note: SyncroSim -v3.0.9 or higher is required to use rsyncrosim v2.0.1 +v3.0.9 or higher is required to use rsyncrosim v2.0.0 or higher.

      Updated functions

      -

      To install and uninstall packages from your SyncroSim installation, -use:

      +
      +

      Installing/uninstalling packages +

      +

      Previously, the addPackage and +removePackage functions were used to install and uninstall +packages from SyncroSim. Now to install and uninstall packages from +SyncroSim, use:

      -installPackage() # Installs the selected package(s) to SyncroSim
-uninstallPackage() # Uninstalls the selected package(s)
      +installPackage() # Installs the selected package(s) to SyncroSim +uninstallPackage() # Uninstalls the selected package(s) from SyncroSim
      +
      +
      +

      Adding/removing packages +

      Now you can use multiple SyncroSim packages in a single library. To add and remove packages from your library, use:

      -addPackage() # Adds package(s) to the library
-removePackage() # Removes package(s) from the library. Note that any associated datasheets will be removed as well.
      -

      And also for that reason, the package addons have been converted to -standalone packages, or incorporated into the base packages. Therefore, -the following functions no longer exist:

      +addPackage() # Adds package(s) to the library +removePackage() # Removes package(s) from the library.
      +

      Note that when you remove a package from your library any associated +datasheets will be removed as well.

      +
      + +
      +

      Deprecated functions +

      +

      In SyncroSim 3, the concept of addon packages no longer exists. All +addon packages have either been converted to standalone packages (e.g., +burnP3PlusPrometheus), and can be added to a library +without having to load a base package first, or incorporated directly +into the base packages (e.g., stsimsf is now part of +stsim). Therefore, the following functions have been +removed:

       addon()
 disableAddon()
-enableAddon()
      +enableAddon() + +datasheetRaster() # previously deprecated function. Use datasheetSpatRaster() instead. + +addBreakpoint() +breakpoint() +deleteBreakpoint() + +ssimUpdate() +updatePackage()

      Library

      +

      Given this added flexibility, the addon argument has +been removed from the ssimLibrary() function, and the +package argument has been renamed to +packages.

      +
      +# instead of using
+myLibrary <- ssimLibrary(package = "PackageName", addon = "AddonName")
+
+# use
+myLibrary <- ssimLibrary(packages = c("stsim", "helloworldSpatial"))
      +
      ## Package <stsim v4.0.1> added
      +
      ## Package <helloworldSpatial v2.0.0> added

      info(ssimLibrary) no longer shows the Package name, Current package version and Minimum package version, and the Input and Output folder paths have been combined -into the Data folder.

      -

      the package argument in the -ssimLibrary(package) function has been renamed to -packages

      -
      -myLibrary <- ssimLibrary(packages = c())
      -

      The addon and template arguments have also -been removed.

      +into the Data folder. See the +Introduction +to rsyncrosim for details.

      +

      The template and addon arguments have also +been removed. You can download template libraries from +SyncroSim +Cloud.

      Dependencies

      To view the existing dependencies for a scenario, use:

      -
      +
       dependency(myScenario)
      
-
      To set dependedncies for a scenario, use:
      
-
      -dependency(myScenario) <- c("Scenario 1", "Scenario 2")
      
-
      Note that this will remove any previously set dependencies. Also, the
-order in which the dependencies are listed can be important. In this
-example, Scenario 1 takes precedence over
-Scenario 2.
      
+
      ##   ScenarioId       Name Priority
+## 1          1 Scenario 1        1
      
+
      To set dependencies for a scenario:
      
+
      +# Change from:
+dependency(myScenario, dependency = c("Scenario 2", "Scenario 3"))
      
+
      +# To:
+dependency(myScenario) <- c("Scenario 2", "Scenario 3")
+
+dependency(myScenario)
      
+
      ##   ScenarioId       Name Priority
+## 1          2 Scenario 2        1
+## 2          3 Scenario 3        2
      
+
      Note that this will remove any previously set dependencies unless the
+existing dependencies are also included in the vector. Also, the order
+in which the dependencies are listed can be important. In this example,
+Scenario 2 takes precedence over
+Scenario 3.

      Multiprocessing

      The run() function no longer has the jobs -argument. Use the core_Multiprocessing datasheet to set the -number of cores to use. Note that this will affect every scenario -run.

      +argument. Use the core_Multiprocessing library datasheet to +set the number of cores to use. Note that this will affect every +scenario run.

      +
      +multiprocessing <-
+    data.frame(EnableMultiprocessing = TRUE,
+               MaximumJobs = 6,
+               EnableMultiScenario = TRUE) # optional, to run multiple scenarios in parallel
+  
+saveDatasheet(myLibrary, multiprocessing, "core_Multiprocessing")

      Variable naming

      -

      The ID in variable names have been changed to -Id. It is generally safe to substitute ID -for Id throughout your script, unless that affects any -variables not related to SyncroSim.

      +

      The ID in the primary key changed to +Id for all datasheets. That also means that the column +names for variables depending on higher-level datasheets also changed +their suffixes to Id. It is generally safe to +substitute ID for Id throughout your script, +but it’s recommended to check the datasheet’s variable names.

      +
      +datasheet(myScenario, "stsim_FlowPathway", includeKey = TRUE, optional = TRUE, empty = TRUE)
      +
      ##  [1] FlowPathwayId                Iteration                   
+##  [3] Timestep                     FromStratumId               
+##  [5] FromSecondaryStratumId       FromTertiaryStratumId       
+##  [7] FromStateClassId             FromAgeMin                  
+##  [9] FromStockTypeId              ToStratumId                 
+## [11] ToStateClassId               ToAgeMin                    
+## [13] ToStockTypeId                TransitionGroupId           
+## [15] StateAttributeTypeId         FlowTypeId                  
+## [17] TargetType                   Multiplier                  
+## [19] TransferToStratumId          TransferToSecondaryStratumId
+## [21] TransferToTertiaryStratumId  TransferToStateClassId      
+## [23] TransferToAgeMin            
+## <0 rows> (or 0-length row.names)

      Core datasheets

      -

      The corestime_ datasheets are now simply called -core_.

      -
      -
      -

      stsimsf -

      -

      The ST-Sim Stock & Flow package, stsimsf have been -incorporated into ST-Sim. Substitute all stsimsf_ -datasheets throghout your script for stsim_. The only -exception is the stsimsf_OutputOptions that is now called -stsim_OutputOptionsStockFlow.

      -
      -
      -

      Other removed functions -

      -
      -datasheetRaster() # previously deprecated function. Use datasheetSpatRaster() instead.
-
-addBreakpoint()
-breakpoint()
-deleteBreakpoint()
-
-ssimUpdate()
-updatePackage()
      +

      The +system +datasheets, previously identified by corestime_, are +now simply called core_.

      Other NEW functions

      -
      -createCondaEnv(pkgs = c()) # creates the conda environment for the selecte package(s)
+
      +createCondaEnv(pkgs = c()) # creates the conda environment for the selected package(s)
 
 deleteLibrary() # Note this is irreversible
 
diff --git a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd
index ea1b80e3..94323546 100644
--- a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd
+++ b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd
@@ -10,7 +10,7 @@ params:
   EVAL: !r identical(Sys.getenv("NOT_CRAN"), "true")
 ---
 
-The introduction of SyncroSim Studio brought some structural changes and new functionalities, which are reflected in the `rsyncrosim` package. Use the guide below to update your `rsyncrosim` version 1 scripts to be compatible with version 2.
+The introduction of SyncroSim Studio brought some structural changes and new features, which are reflected in the `rsyncrosim` package. Use the guide below to update your `rsyncrosim` version 1 scripts to be compatible with version 2.
 
 *Note*: SyncroSim v3.0.9 or higher is required to use `rsyncrosim v2.0.0` or higher. 
 
@@ -37,78 +37,107 @@ Note that when you remove a package from your library any associated datasheets
 
 ## Deprecated functions
 
-In SyncroSim 3, the concept of addon packages no longer exists. All addon packages have either been converted to standalone packages (e.g., `burnP3PlusPrometheus`) and can be added to a library without having to load a base package first, or incorporated directly into the base packages (e.g., `stsimsf` is now part of `stsim`). Therefore, the following functions have been removed:
+In SyncroSim 3, the concept of addon packages no longer exists. All addon packages have either been converted to standalone packages (e.g., `burnP3PlusPrometheus`), and can be added to a library without having to load a base package first, or incorporated directly into the base packages (e.g., `stsimsf` is now part of `stsim`). Therefore, the following functions have been removed:
 
 ```{r deprecated, eval=FALSE}
 addon()
 disableAddon()
 enableAddon()
+
+datasheetRaster() # previously deprecated function. Use datasheetSpatRaster() instead.
+
+addBreakpoint()
+breakpoint()
+deleteBreakpoint()
+
+ssimUpdate()
+updatePackage()
 ```
 
 ## Library
 
-`info(ssimLibrary)` no longer shows the *Package name*, *Current package version* and *Minimum package version*, and the Input and Output folder paths have been combined into the *Data folder*.
-
-The `package` argument in the `ssimLibrary(package)` function has been renamed to `packages`
+Given this added flexibility, the `addon` argument has been removed from the `ssimLibrary()` function, and the `package` argument has been renamed to `packages`.
 
 ```{r library, eval=FALSE}
-myLibrary <- ssimLibrary(packages = c())
+# instead of using
+myLibrary <- ssimLibrary(package = "PackageName", addon = "AddonName")
+
+# use
+myLibrary <- ssimLibrary(packages = c("stsim", "helloworldSpatial"))
+```
+```{r load session run, warning = FALSE, echo = FALSE}
+# results for the section above
+library(rsyncrosim)
+mySession <- session()
+myLibrary <- ssimLibrary("Changes to rsyncrosim v2.ssim", packages=c("stsim", "helloworldSpatial"))
+scenario1 <- scenario(myLibrary, scenario = "Scenario 1")
+scenario2 <- scenario(myLibrary, scenario = "Scenario 2")
+scenario3 <- scenario(myLibrary, scenario = "Scenario 3")
+myScenario <- scenario(myLibrary, "my Scenario")
+dependency(myScenario) <- "Scenario 1"
 ```
 
-The `addon` and `template` arguments have also been removed.
+`info(ssimLibrary)` no longer shows the *Package name*, *Current package version* and *Minimum package version*, and the Input and Output folder paths have been combined into the *Data folder*. See the Introduction to rsyncrosim for details.
+
+The `template` and `addon` arguments have also been removed. You can download template libraries from SyncroSim Cloud.
 
 ## Dependencies
 
 To view the existing dependencies for a scenario, use:
 
-```{r view dependencies, eval=FALSE}
+```{r view dependencies}
 dependency(myScenario)
 ```
 
-To set dependencies for a scenario, use:
+To set dependencies for a scenario:
 
 ```{r set dependencies, eval=FALSE}
-dependency(myScenario) <- c("Scenario 1", "Scenario 2")
-```
+# Change from:
+dependency(myScenario, dependency = c("Scenario 2", "Scenario 3"))
 
-Note that this will remove any previously set dependencies.
-Also, the order in which the dependencies are listed can be important. In this example, `Scenario 1` takes precedence over `Scenario 2`.
+```
+```{r dependencies, warning=FALSE}
+# To:
+dependency(myScenario) <- c("Scenario 2", "Scenario 3")
 
+dependency(myScenario)
 
-## Multiprocessing
+```
 
-The `run()` function no longer has the `jobs` argument. Use the `core_Multiprocessing` datasheet to set the number of cores to use. Note that this will affect every scenario run.
+Note that this will remove any previously set dependencies unless the existing dependencies are also included in the vector.
+Also, the order in which the dependencies are listed can be important. In this example, `Scenario 2` takes precedence over `Scenario 3`.
 
 
-## Variable naming
+## Multiprocessing
 
-The **ID** in variable names have been changed to **Id**. It is generally safe to substitute `ID` for `Id` throughout your script, unless that affects any variables not related to SyncroSim.
+The `run()` function no longer has the `jobs` argument. Use the `core_Multiprocessing` library datasheet to set the number of cores to use. Note that this will affect every scenario run.
 
-## Core datasheets
+```{r multiprocessing, eval=FALSE}
+multiprocessing <-
+    data.frame(EnableMultiprocessing = TRUE,
+               MaximumJobs = 6,
+               EnableMultiScenario = TRUE) # optional, to run multiple scenarios in parallel
+  
+saveDatasheet(myLibrary, multiprocessing, "core_Multiprocessing")
+```
 
-The `corestime_` datasheets are now simply called `core_`.
 
-## stsimsf
+## Variable naming
 
-The ST-Sim Stock & Flow package, `stsimsf` have been incorporated into ST-Sim. Substitute all `stsimsf_` datasheets throghout your script for `stsim_`.
-The only exception is the `stsimsf_OutputOptions` that is now called `stsim_OutputOptionsStockFlow`.
+The **ID** in the primary key changed to **Id** for all datasheets. That also means that the column names for variables depending on higher-level datasheets also changed their suffixes to **Id**. It is generally safe to substitute `ID` for `Id` throughout your script, but it's recommended to check the datasheet's variable names.
 
-## Other removed functions
+```{r IDs, warning=FALSE}
+datasheet(myScenario, "stsim_FlowPathway", includeKey = TRUE, optional = TRUE, empty = TRUE)
+```
 
-```{r other removed, eval=FALSE}
-datasheetRaster() # previously deprecated function. Use datasheetSpatRaster() instead.
+## Core datasheets
 
-addBreakpoint()
-breakpoint()
-deleteBreakpoint()
+The system datasheets, previously identified by `corestime_`, are now simply called `core_`.
 
-ssimUpdate()
-updatePackage()
-```
 
 ## Other NEW functions
 ```{r new functions, eval=FALSE}
-createCondaEnv(pkgs = c()) # creates the conda environment for the selecte package(s)
+createCondaEnv(pkgs = c()) # creates the conda environment for the selected package(s)
 
 deleteLibrary() # Note this is irreversible
 

From 53ab97b6f25bde5f9d107b41000228b49133933e Mon Sep 17 00:00:00 2001
From: diegobilski 
Date: Thu, 19 Dec 2024 11:52:18 -0500
Subject: [PATCH 5/6] a07 vignette changes

incorporating suggested changes
---
 ...a07_updating_rsyncrosim_scripts_to_v2.html | 77 ++++++++++++-------
 .../a07_updating_rsyncrosim_scripts_to_v2.Rmd | 38 ++++++---
 2 files changed, 76 insertions(+), 39 deletions(-)

diff --git a/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html
index 355aedfa..147b47f2 100644
--- a/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html
+++ b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html
@@ -110,6 +110,10 @@ 
      Adding/removing packagesremovePackage() # Removes package(s) from the library.
      
 
      Note that when you remove a package from your library any associated
 datasheets will be removed as well.
      
+
      You can also have multiple versions of a package installed, and
+choose which package version to use within a library. Use the
+versions argument in the installPackage() and
+addPackage() functions.
      @@ -125,29 +129,48 @@

      Deprecated functions
       addon()
 disableAddon()
-enableAddon()
-
-datasheetRaster() # previously deprecated function. Use datasheetSpatRaster() instead.
-
-addBreakpoint()
+enableAddon()

      +

      Since you can install multiple versions of a package, the +updatePackage() function has been removed. To update (or +downgrade) the package version on a library, use the +versions argument in the addPackages() +function:

      +
      +# Change package version
+addPackage(myLibrary, packages = "stsim", versions = "4.0.0")
+addPackage(myLibrary, packages = "stsim", versions = "4.0.1")
      +

      Any functions depending on the deprecated raster package +have been removed, including the datasheetRaster() +function. Use datasheetSpatRaster() instead.

      +

      Other deprecated functions include:

      +
      +addBreakpoint()
 breakpoint()
 deleteBreakpoint()
 
-ssimUpdate()
-updatePackage()
      +ssimUpdate()

      Library

      -

      Given this added flexibility, the addon argument has -been removed from the ssimLibrary() function, and the -package argument has been renamed to -packages.

      -
      -# instead of using
+
      Now that addon packages no longer exist and SyncroSim libraries can
+support multiple packages, the following changes have been made to the
+ssimLibrary() function:
      
+
        
+
      • The addon argument has been removed.
        • 
+
      • The template argument has been removed. This is a
+temporary change, but in the meantime you can download template
+libraries from
+SyncroSim
+Cloud.
        • 
+
      • The package argument has been renamed to
+packages (plural).
        • 
+
      
+
      +# rsyncrosim version 1:
 myLibrary <- ssimLibrary(package = "PackageName", addon = "AddonName")
 
-# use
+# rsyncrosim version 2:
 myLibrary <- ssimLibrary(packages = c("stsim", "helloworldSpatial"))
      
 
      ## Package <stsim v4.0.1> added
      
 
      ## Package <helloworldSpatial v2.0.0> added
      
@@ -157,25 +180,24 @@ 
      LibraryData folder. See the
 Introduction
 to rsyncrosim for details.
      
-
      The template and addon arguments have also
-been removed. You can download template libraries from
-SyncroSim
-Cloud.

      Dependencies

      +

      Scenario dependencies are now set using the <- +operator in rsyncrosim. See below for examples on how the +usage of the dependency() function has changed.

      To view the existing dependencies for a scenario, use:

      -
      +
       dependency(myScenario)
      
 
      ##   ScenarioId       Name Priority
 ## 1          1 Scenario 1        1
      
 
      To set dependencies for a scenario:
      
-
      -# Change from:
+
      +# rsyncrosim version 1:
 dependency(myScenario, dependency = c("Scenario 2", "Scenario 3"))
      
-
      -# To:
+
      +# rsyncrosim version 2:
 dependency(myScenario) <- c("Scenario 2", "Scenario 3")
 
 dependency(myScenario)
      
@@ -195,11 +217,10 @@ 
      Multiprocessingcore_Multiprocessing library datasheet to
 set the number of cores to use. Note that this will affect every
 scenario run.
      
-
      +
       multiprocessing <-
     data.frame(EnableMultiprocessing = TRUE,
-               MaximumJobs = 6,
-               EnableMultiScenario = TRUE) # optional, to run multiple scenarios in parallel
+               MaximumJobs = 6)
   
 saveDatasheet(myLibrary, multiprocessing, "core_Multiprocessing")
      
 
      
@@ -212,7 +233,7 @@ 
      Variable namingId. It is generally safe to
 substitute ID for Id throughout your script,
 but it’s recommended to check the datasheet’s variable names.
      
-
      +
       datasheet(myScenario, "stsim_FlowPathway", includeKey = TRUE, optional = TRUE, empty = TRUE)
      
 
      ##  [1] FlowPathwayId                Iteration                   
 ##  [3] Timestep                     FromStratumId               
@@ -239,7 +260,7 @@ 
      Core datasheets
 
      Other NEW functions
 
      
-
      +
       createCondaEnv(pkgs = c()) # creates the conda environment for the selected package(s)
 
 deleteLibrary() # Note this is irreversible
diff --git a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd
index 94323546..0616a4e5 100644
--- a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd
+++ b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd
@@ -35,6 +35,8 @@ removePackage() # Removes package(s) from the library.
 ```
 Note that when you remove a package from your library any associated datasheets will be removed as well.
 
+You can also have multiple versions of a package installed, and choose which package version to use within a library. Use the `versions` argument in the `installPackage()` and `addPackage()` functions.
+
 ## Deprecated functions
 
 In SyncroSim 3, the concept of addon packages no longer exists. All addon packages have either been converted to standalone packages (e.g., `burnP3PlusPrometheus`), and can be added to a library without having to load a base package first, or incorporated directly into the base packages (e.g., `stsimsf` is now part of `stsim`). Therefore, the following functions have been removed:
@@ -43,30 +45,44 @@ In SyncroSim 3, the concept of addon packages no longer exists. All addon packag
 addon()
 disableAddon()
 enableAddon()
+```
+
+Since you can install multiple versions of a package, the `updatePackage()` function has been removed. To update (or downgrade) the package version on a library, use the `versions` argument in the `addPackages()` function:
+```{r changeVersion, eval=FALSE}
+# Change package version
+addPackage(myLibrary, packages = "stsim", versions = "4.0.0")
+addPackage(myLibrary, packages = "stsim", versions = "4.0.1")
+```
 
-datasheetRaster() # previously deprecated function. Use datasheetSpatRaster() instead.
+Any functions depending on the deprecated `raster` package have been removed, including the `datasheetRaster()` function. Use `datasheetSpatRaster()` instead.
 
+Other deprecated functions include:
+
+```{r otherDeprecated, eval=FALSE}
 addBreakpoint()
 breakpoint()
 deleteBreakpoint()
 
 ssimUpdate()
-updatePackage()
 ```
 
 ## Library
 
-Given this added flexibility, the `addon` argument has been removed from the `ssimLibrary()` function, and the `package` argument has been renamed to `packages`.
+Now that addon packages no longer exist and SyncroSim libraries can support multiple packages, the following changes have been made to the `ssimLibrary()` function:
+
+* The `addon` argument has been removed.
+* The `template` argument has been removed. This is a temporary change, but in the meantime you can download template libraries from SyncroSim Cloud.
+* The `package` argument has been renamed to `packages` (plural).
 
 ```{r library, eval=FALSE}
-# instead of using
+# rsyncrosim version 1:
 myLibrary <- ssimLibrary(package = "PackageName", addon = "AddonName")
 
-# use
+# rsyncrosim version 2:
 myLibrary <- ssimLibrary(packages = c("stsim", "helloworldSpatial"))
 ```
 ```{r load session run, warning = FALSE, echo = FALSE}
-# results for the section above
+# to show the packages added, plus create scenarios to show below
 library(rsyncrosim)
 mySession <- session()
 myLibrary <- ssimLibrary("Changes to rsyncrosim v2.ssim", packages=c("stsim", "helloworldSpatial"))
@@ -79,10 +95,11 @@ dependency(myScenario) <- "Scenario 1"
 
 `info(ssimLibrary)` no longer shows the *Package name*, *Current package version* and *Minimum package version*, and the Input and Output folder paths have been combined into the *Data folder*. See the Introduction to rsyncrosim for details.
 
-The `template` and `addon` arguments have also been removed. You can download template libraries from SyncroSim Cloud.
 
 ## Dependencies
 
+Scenario dependencies are now set using the `<-` operator in `rsyncrosim`. See below for examples on how the usage of the `dependency()` function has changed.
+
 To view the existing dependencies for a scenario, use:
 
 ```{r view dependencies}
@@ -92,12 +109,12 @@ dependency(myScenario)
 To set dependencies for a scenario:
 
 ```{r set dependencies, eval=FALSE}
-# Change from:
+# rsyncrosim version 1:
 dependency(myScenario, dependency = c("Scenario 2", "Scenario 3"))
 
 ```
 ```{r dependencies, warning=FALSE}
-# To:
+# rsyncrosim version 2:
 dependency(myScenario) <- c("Scenario 2", "Scenario 3")
 
 dependency(myScenario)
@@ -115,8 +132,7 @@ The `run()` function no longer has the `jobs` argument. Use the `core_Multiproce
 ```{r multiprocessing, eval=FALSE}
 multiprocessing <-
     data.frame(EnableMultiprocessing = TRUE,
-               MaximumJobs = 6,
-               EnableMultiScenario = TRUE) # optional, to run multiple scenarios in parallel
+               MaximumJobs = 6)
   
 saveDatasheet(myLibrary, multiprocessing, "core_Multiprocessing")
 ```

From 8a85adc5002a0b95e951e3ac0a4272ea32777d32 Mon Sep 17 00:00:00 2001
From: katieb1 
Date: Thu, 19 Dec 2024 10:20:05 -0800
Subject: [PATCH 6/6] Clean up / reorganization of update vignette

---
 ...a07_updating_rsyncrosim_scripts_to_v2.html | 286 +++++++++++-------
 .../a07_updating_rsyncrosim_scripts_to_v2.Rmd | 174 +++++++----
 2 files changed, 297 insertions(+), 163 deletions(-)

diff --git a/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html
index 147b47f2..41ea3e8e 100644
--- a/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html
+++ b/docs/articles/a07_updating_rsyncrosim_scripts_to_v2.html
@@ -80,9 +80,9 @@
 SyncroSim
 Studio brought some structural changes and new features, which are
 reflected in the rsyncrosim package. Use the guide below to
-update your rsyncrosim version 1 scripts to be compatible
-with version 2.
      
-
      Note:
+update your rsyncrosim v1 scripts to be compatible with
+rsyncrosim v2.
      
+
      Note:
 SyncroSim
 v3.0.9 or higher is required to use rsyncrosim v2.0.0
 or higher.
      
@@ -97,62 +97,63 @@ 
      Installing/uninstalling packages
 
      -installPackage()   # Installs the selected package(s) to SyncroSim
-uninstallPackage() # Uninstalls the selected package(s) from SyncroSim
      
+# Installs the selected package(s) to SyncroSim
+installPackage()  
+
+# Uninstalls the selected package(s) from SyncroSim
+uninstallPackage() 
      
+
      You can also have multiple versions of a package installed. Use the
+versions argument in the installPackage()
+function to specify which version of the package you would like to
+install. If you do not specify a version, then the latest version of the
+package will be installed.
      
+
      +# Install ST-Sim version 4.0.0
+installPackage(myLibrary, packages = "stsim", versions = "4.0.0")
+
+# Install the latest version of ST-Sim on the package server
+installPackage(myLibrary, packages = "stsim")
      
+
      You can also use the versions argument in the
+uninstallPackage() function to specify which version you
+would like to uninstall. If you do not specify a version, then all
+versions of that package will be uninstalled.
      
+
      +# Uninstall ST-Sim version 4.0.0
+uninstallPackage(myLibrary, packages = "stsim", versions = "4.0.0")
+
+# Uninstall all installed versions of ST-Sim
+uninstallPackage(myLibrary, packages = "stsim")
      
 
      
 
      
 
      Adding/removing packages
 
      
 
      Now you can use multiple SyncroSim packages in a single library. To
 add and remove packages from your library, use:
      
-
      -addPackage()    # Adds package(s) to the library
-removePackage() # Removes package(s) from the library.
      
-
      Note that when you remove a package from your library any associated
-datasheets will be removed as well.
      
-
      You can also have multiple versions of a package installed, and
-choose which package version to use within a library. Use the
-versions argument in the installPackage() and
-addPackage() functions.
      
-
      
-
      
-
      
-
      Deprecated functions
-
      
-
      In SyncroSim 3, the concept of addon packages no longer exists. All
-addon packages have either been converted to standalone packages (e.g.,
-burnP3PlusPrometheus), and can be added to a library
-without having to load a base package first, or incorporated directly
-into the base packages (e.g., stsimsf is now part of
-stsim). Therefore, the following functions have been
-removed:
      
-
      -addon()
-disableAddon()
-enableAddon()
      
-
      Since you can install multiple versions of a package, the
-updatePackage() function has been removed. To update (or
-downgrade) the package version on a library, use the
-versions argument in the addPackages()
-function:
      
 
      -# Change package version
-addPackage(myLibrary, packages = "stsim", versions = "4.0.0")
-addPackage(myLibrary, packages = "stsim", versions = "4.0.1")
      
-
      Any functions depending on the deprecated raster package
-have been removed, including the datasheetRaster()
-function. Use datasheetSpatRaster() instead.
      
-
      Other deprecated functions include:
      
+# Adds package(s) to the library
+addPackage()    
+
+# Removes package(s) from the library
+removePackage() 
      
+
      Note: when you remove a package from your library
+any associated datasheets will be removed as well.
      
+
      You can also choose which package version to use within a library.
+Use the versions argument in the addPackage()
+function to load a specific version of a package in a library, or to
+change the version of a package that the library uses.
      
 
      -addBreakpoint()
-breakpoint()
-deleteBreakpoint()
+# Add ST-Sim version 4.0.0 to your library
+addPackage(myLibrary, packages = "stsim", versions = "4.0.0")
 
-ssimUpdate()
      
+# Update the version of ST-Sim that your library uses
+addPackage(myLibrary, packages = "stsim", versions = "4.0.1")
      
+
      You do not need to specify a version when removing a package using
+removePackage() because only one version of a package can
+be loaded in a library at a time.
      -
      -

      Library -

      +
      +

      Creating libraries +

      Now that addon packages no longer exist and SyncroSim libraries can support multiple packages, the following changes have been made to the ssimLibrary() function:

      @@ -172,31 +173,41 @@

      Library # rsyncrosim version 2: myLibrary <- ssimLibrary(packages = c("stsim", "helloworldSpatial"))

      -
      ## Package <stsim v4.0.1> added
      -
      ## Package <helloworldSpatial v2.0.0> added
      -

      info(ssimLibrary) no longer shows the Package -name, Current package version and Minimum package -version, and the Input and Output folder paths have been combined -into the Data folder. See the +

      +
      +

      Library information +

      +

      Since multiple packages can be loaded in a library, the +info(ssimLibrary) no longer returns the following library +attributes:

      +
        +
      • Package name
        • +
      • Current package version
        • +
      • Minimum package version
        • +
      +

      In addition, now that you can link models from various packages in a +pipeline, and outputs from one transformer can be inputs to the next +transformer in a pipeline, the Input and Output +folders have been combined into a single Data folder. See the Introduction to rsyncrosim for details.

      -
      -

      Dependencies -

      +
      +

      Dependencies +

      Scenario dependencies are now set using the <- operator in rsyncrosim. See below for examples on how the usage of the dependency() function has changed.

      -

      To view the existing dependencies for a scenario, use:

      -
      +
      To view the existing dependencies for a scenario:
      
+
       dependency(myScenario)
      
 
      ##   ScenarioId       Name Priority
 ## 1          1 Scenario 1        1
      
 
      To set dependencies for a scenario:
      
-
      +
       # rsyncrosim version 1:
 dependency(myScenario, dependency = c("Scenario 2", "Scenario 3"))
      
-
      +
-
      
-
      Multiprocessing
-
      
-
      The run() function no longer has the jobs
-argument. Use the core_Multiprocessing library datasheet to
-set the number of cores to use. Note that this will affect every
-scenario run.
      
-
      -multiprocessing <-
-    data.frame(EnableMultiprocessing = TRUE,
-               MaximumJobs = 6)
+
      
+
      Multiprocessing
+
      
+
      The run() function no longer contains the
+jobs argument for setting the number of cores to use during
+a multiprocessing run. Instead, use the
+core_Multiprocessing library datasheet to set the number of
+cores.
      
+
      +multiprocessing <- data.frame(EnableMultiprocessing = TRUE,
+                              MaximumJobs = 6)
   
 saveDatasheet(myLibrary, multiprocessing, "core_Multiprocessing")
      
+
      Note: because the core_Multiprocessing
+datasheet is library-scoped, modifying this datasheet will affect every
+scenario run.
      
+
      
+
      
+
      
+
      Deprecated functions
+
      
+
      
+
      Addon functions
+
      
+
      In SyncroSim 3, the concept of addon packages no longer
+exists. All addon packages have either been converted to standalone
+packages (e.g., burnP3PlusPrometheus), and can be added to
+a library without having to load a base package first, or incorporated
+directly into its base package (e.g., stsimsf is now part
+of stsim). Therefore, the following functions have been
+removed:
      
+
        
+
      • addon()
        • 
+
      • disableAddon()
        • 
+
      • enableAddon()
        • 
+
      
+
      
+
      
+
      Update functions
+
      
+
      The following update functions have been removed:
      
+
        
+
      • 
+updatePackage(): You no longer need to update the
+installed versions of packages in your SyncroSim session because you can
+have multiple versions installed at the same time. To install or
+uninstall versions of a package from your SyncroSim session, use the
+versions argument in the installPackage()
+function instead.
        • 
+
      • 
+ssimUpdate(): To update (or downgrade) the package
+version on a library, use the versions argument in the
+addPackages() function instead.
        • 
+
      
+
      
+
      
+
      Raster functions
+
      
+
      The following deprecated raster function has been removed:
      
+
        
+
      • 
+datasheetRaster(): This function depended on the
+deprecated raster package and has now been completely
+removed from rsyncrosim. Use
+datasheetSpatRaster() instead.
        • 
+
      
+
      
+
      
+
      Breakpoint functions
+
      
+
      Setting, catching, and removing breakpoints in
+rsyncrosim scripts in no longer supported, so the following
+breakpoint functions have been removed:
      
+
        
+
      • addBreakpoint()
        • 
+
      • breakpoint()
        • 
+
      • deleteBreakpoint()
        • 
+
      
+
      
 
      
 
      
 
      Variable naming
 
      
-
      The ID in the primary key changed to
-Id for all datasheets. That also means that the column
-names for variables depending on higher-level datasheets also changed
-their suffixes to Id. It is generally safe to
-substitute ID for Id throughout your script,
-but it’s recommended to check the datasheet’s variable names.
      
-
      -datasheet(myScenario, "stsim_FlowPathway", includeKey = TRUE, optional = TRUE, empty = TRUE)
      
-
      ##  [1] FlowPathwayId                Iteration                   
-##  [3] Timestep                     FromStratumId               
-##  [5] FromSecondaryStratumId       FromTertiaryStratumId       
-##  [7] FromStateClassId             FromAgeMin                  
-##  [9] FromStockTypeId              ToStratumId                 
-## [11] ToStateClassId               ToAgeMin                    
-## [13] ToStockTypeId                TransitionGroupId           
-## [15] StateAttributeTypeId         FlowTypeId                  
-## [17] TargetType                   Multiplier                  
-## [19] TransferToStratumId          TransferToSecondaryStratumId
-## [21] TransferToTertiaryStratumId  TransferToStateClassId      
-## [23] TransferToAgeMin            
+
      The primary key column for all SyncroSim datasheets has been modified
+slightly. The ID in the primary key is now
+Id for all datasheets. This also applies to column
+names in scenario-scoped datasheets that reference values taken from
+project-scoped datasheets. It is generally safe to substitute
+ID for Id throughout your script, but it’s
+recommended to check the datasheet’s variable names.
      
+
      Below is an example of a datasheet with the new naming convention for
+primary keys:
      
+
      +datasheet(myScenario, "stsim_FlowPathway", includeKey = TRUE)
      
+
      ## [1] FlowPathwayId   FromStockTypeId ToStockTypeId   FlowTypeId     
+## [5] Multiplier     
 ## <0 rows> (or 0-length row.names)
      
 
      
 
      
@@ -254,18 +322,26 @@ 
      Core datasheets
 
      The
 system
-datasheets, previously identified by corestime_, are
-now simply called core_.
      
+datasheets, previously identified by the prefix
+corestime_, are now prefixed by core_.
      
 
      
 
      
 
      Other NEW functions
 
      
-
      -createCondaEnv(pkgs = c()) # creates the conda environment for the selected package(s)
+
      Below is a list of other new functions that have been added to
+rsyncrosim v2. For more information, on these new
+functions, refer to the
+reference
+guide.
      
+
      +# creates the conda environment for the selected package(s)
+createCondaEnv()
 
-deleteLibrary() # Note this is irreversible
+# deletes a SyncroSim library (IRREVERSIBLE)
+deleteLibrary() 
 
-chart() # Create or load a SyncroSim chart. Explore other charting functions with ?chart
      
+# Create, load, or modify SyncroSim charts using the new Chart class
+chart() 
      
 
      
   
@@ -278,7 +354,7 @@ 
      Other NEW functions
-  
      Site built with pkgdown 2.1.1.
      
+  
      Site built with pkgdown 2.1.0.
      
 
      
 
     
diff --git a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd
index 0616a4e5..7e9b2a76 100644
--- a/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd
+++ b/vignettes/a07_updating_rsyncrosim_scripts_to_v2.Rmd
@@ -10,9 +10,23 @@ params:
   EVAL: !r identical(Sys.getenv("NOT_CRAN"), "true")
 ---
 
-The introduction of SyncroSim Studio brought some structural changes and new features, which are reflected in the `rsyncrosim` package. Use the guide below to update your `rsyncrosim` version 1 scripts to be compatible with version 2.
+```{r setup, warning = FALSE, echo = FALSE, results = 'hide'}
+# to show the packages added, plus create scenarios to show below
+library(rsyncrosim)
+mySession <- session()
+myLibrary <- ssimLibrary("Changes to rsyncrosim v2.ssim")
+addPackage(myLibrary, packages = c("stsim", "helloworldSpatial"),
+            versions = c("4.0.1", "2.0.0"))
+scenario1 <- scenario(myLibrary, scenario = "Scenario 1")
+scenario2 <- scenario(myLibrary, scenario = "Scenario 2")
+scenario3 <- scenario(myLibrary, scenario = "Scenario 3")
+myScenario <- scenario(myLibrary, "my Scenario")
+dependency(myScenario) <- "Scenario 1"
+```
+
+The introduction of SyncroSim Studio brought some structural changes and new features, which are reflected in the `rsyncrosim` package. Use the guide below to update your `rsyncrosim v1` scripts to be compatible with `rsyncrosim v2`.
 
-*Note*: SyncroSim v3.0.9 or higher is required to use `rsyncrosim v2.0.0` or higher. 
+**Note:** SyncroSim v3.0.9 or higher is required to use `rsyncrosim v2.0.0` or higher. 
 
 ## Updated functions
 
@@ -21,52 +35,59 @@ The introduction of Sync
 Previously, the `addPackage` and `removePackage` functions were used to install and uninstall packages from SyncroSim. Now to install and uninstall packages from SyncroSim, use:
 
 ```{r install packages, eval=FALSE}
-installPackage()   # Installs the selected package(s) to SyncroSim
-uninstallPackage() # Uninstalls the selected package(s) from SyncroSim
+# Installs the selected package(s) to SyncroSim
+installPackage()  
+
+# Uninstalls the selected package(s) from SyncroSim
+uninstallPackage() 
 ```
 
-### Adding/removing packages
+You can also have multiple versions of a package installed. Use the `versions` argument in the `installPackage()` function to specify which version of the package you would like to install. If you do not specify a version, then the latest version of the package will be installed.
 
-Now you can use multiple SyncroSim packages in a single library. To add and remove packages from your library, use:
+```{r install package version, eval=FALSE}
+# Install ST-Sim version 4.0.0
+installPackage(myLibrary, packages = "stsim", versions = "4.0.0")
 
-```{r add package, eval=FALSE}
-addPackage()    # Adds package(s) to the library
-removePackage() # Removes package(s) from the library.
+# Install the latest version of ST-Sim on the package server
+installPackage(myLibrary, packages = "stsim")
 ```
-Note that when you remove a package from your library any associated datasheets will be removed as well.
 
-You can also have multiple versions of a package installed, and choose which package version to use within a library. Use the `versions` argument in the `installPackage()` and `addPackage()` functions.
+You can also use the `versions` argument in the `uninstallPackage()` function to specify which version you would like to uninstall. If you do not specify a version, then all versions of that package will be uninstalled.
 
-## Deprecated functions
+```{r uninstall package version, eval=FALSE}
+# Uninstall ST-Sim version 4.0.0
+uninstallPackage(myLibrary, packages = "stsim", versions = "4.0.0")
 
-In SyncroSim 3, the concept of addon packages no longer exists. All addon packages have either been converted to standalone packages (e.g., `burnP3PlusPrometheus`), and can be added to a library without having to load a base package first, or incorporated directly into the base packages (e.g., `stsimsf` is now part of `stsim`). Therefore, the following functions have been removed:
+# Uninstall all installed versions of ST-Sim
+uninstallPackage(myLibrary, packages = "stsim")
+```
+
+### Adding/removing packages
+
+Now you can use multiple SyncroSim packages in a single library. To add and remove packages from your library, use:
+
+```{r add package, eval=FALSE}
+# Adds package(s) to the library
+addPackage()    
 
-```{r deprecated, eval=FALSE}
-addon()
-disableAddon()
-enableAddon()
+# Removes package(s) from the library
+removePackage() 
 ```
+**Note:** when you remove a package from your library any associated datasheets will be removed as well.
+
+You can also choose which package version to use within a library. Use the `versions` argument in the `addPackage()` function to load a specific version of a package in a library, or to change the version of a package that the library uses.
 
-Since you can install multiple versions of a package, the `updatePackage()` function has been removed. To update (or downgrade) the package version on a library, use the `versions` argument in the `addPackages()` function:
 ```{r changeVersion, eval=FALSE}
-# Change package version
+# Add ST-Sim version 4.0.0 to your library
 addPackage(myLibrary, packages = "stsim", versions = "4.0.0")
+
+# Update the version of ST-Sim that your library uses
 addPackage(myLibrary, packages = "stsim", versions = "4.0.1")
 ```
 
-Any functions depending on the deprecated `raster` package have been removed, including the `datasheetRaster()` function. Use `datasheetSpatRaster()` instead.
-
-Other deprecated functions include:
+You do not need to specify a version when removing a package using `removePackage()` because only one version of a package can be loaded in a library at a time.
 
-```{r otherDeprecated, eval=FALSE}
-addBreakpoint()
-breakpoint()
-deleteBreakpoint()
-
-ssimUpdate()
-```
-
-## Library
+### Creating libraries
 
 Now that addon packages no longer exist and SyncroSim libraries can support multiple packages, the following changes have been made to the `ssimLibrary()` function:
 
@@ -81,26 +102,23 @@ myLibrary <- ssimLibrary(package = "PackageName", addon = "AddonName")
 # rsyncrosim version 2:
 myLibrary <- ssimLibrary(packages = c("stsim", "helloworldSpatial"))
 ```
-```{r load session run, warning = FALSE, echo = FALSE}
-# to show the packages added, plus create scenarios to show below
-library(rsyncrosim)
-mySession <- session()
-myLibrary <- ssimLibrary("Changes to rsyncrosim v2.ssim", packages=c("stsim", "helloworldSpatial"))
-scenario1 <- scenario(myLibrary, scenario = "Scenario 1")
-scenario2 <- scenario(myLibrary, scenario = "Scenario 2")
-scenario3 <- scenario(myLibrary, scenario = "Scenario 3")
-myScenario <- scenario(myLibrary, "my Scenario")
-dependency(myScenario) <- "Scenario 1"
-```
 
-`info(ssimLibrary)` no longer shows the *Package name*, *Current package version* and *Minimum package version*, and the Input and Output folder paths have been combined into the *Data folder*. See the Introduction to rsyncrosim for details.
+### Library information
+
+Since multiple packages can be loaded in a library, the `info(ssimLibrary)` no longer returns the following library attributes:
 
+* *Package name*
+* *Current package version* 
+* *Minimum package version*
 
-## Dependencies
+In addition, now that you can link models from various packages in a pipeline, and outputs from one transformer can be inputs to the next transformer in a pipeline, the *Input* and *Output* folders have been combined into a single *Data* folder. See the Introduction to rsyncrosim for details.
+
+
+### Dependencies
 
 Scenario dependencies are now set using the `<-` operator in `rsyncrosim`. See below for examples on how the usage of the `dependency()` function has changed.
 
-To view the existing dependencies for a scenario, use:
+To view the existing dependencies for a scenario:
 
 ```{r view dependencies}
 dependency(myScenario)
@@ -121,42 +139,82 @@ dependency(myScenario)
 
 ```
 
-Note that this will remove any previously set dependencies unless the existing dependencies are also included in the vector.
-Also, the order in which the dependencies are listed can be important. In this example, `Scenario 2` takes precedence over `Scenario 3`.
+**Note:** this will remove any previously set dependencies unless the existing dependencies are also included in the vector.
 
 
-## Multiprocessing
+### Multiprocessing
 
-The `run()` function no longer has the `jobs` argument. Use the `core_Multiprocessing` library datasheet to set the number of cores to use. Note that this will affect every scenario run.
+The `run()` function no longer contains the `jobs` argument for setting the number of cores to use during a multiprocessing run. Instead, use the `core_Multiprocessing` library datasheet to set the number of cores.
 
 ```{r multiprocessing, eval=FALSE}
-multiprocessing <-
-    data.frame(EnableMultiprocessing = TRUE,
-               MaximumJobs = 6)
+multiprocessing <- data.frame(EnableMultiprocessing = TRUE,
+                              MaximumJobs = 6)
   
 saveDatasheet(myLibrary, multiprocessing, "core_Multiprocessing")
 ```
 
+**Note:** because the `core_Multiprocessing` datasheet is library-scoped, modifying this datasheet will affect every scenario run.
+
+## Deprecated functions
+
+### Addon functions
+In SyncroSim 3, the concept of *addon* packages no longer exists. All addon packages have either been converted to standalone packages (e.g., `burnP3PlusPrometheus`), and can be added to a library without having to load a base package first, or incorporated directly into its base package (e.g., `stsimsf` is now part of `stsim`). Therefore, the following functions have been removed:
+
+* `addon()`
+* `disableAddon()`
+* `enableAddon()`
+
+### Update functions
+
+The following update functions have been removed:
+
+* `updatePackage()`: You no longer need to update the installed versions of packages in your SyncroSim session because you can have multiple versions installed at the same time. To install or uninstall versions of a package from your SyncroSim session, use the `versions` argument in the `installPackage()` function instead.
+* `ssimUpdate()`: To update (or downgrade) the package version on a library, use the `versions` argument in the `addPackages()` function instead.
+
+
+### Raster functions
+
+The following deprecated raster function has been removed:
+
+* `datasheetRaster()`: This function depended on the deprecated `raster` package and has now been completely removed from `rsyncrosim`. Use `datasheetSpatRaster()` instead.
+
+
+### Breakpoint functions
+
+Setting, catching, and removing breakpoints in `rsyncrosim` scripts in no longer supported, so the following breakpoint functions have been removed:
+
+* `addBreakpoint()`
+* `breakpoint()`
+* `deleteBreakpoint()`
+
 
 ## Variable naming
 
-The **ID** in the primary key changed to **Id** for all datasheets. That also means that the column names for variables depending on higher-level datasheets also changed their suffixes to **Id**. It is generally safe to substitute `ID` for `Id` throughout your script, but it's recommended to check the datasheet's variable names.
+The primary key column for all SyncroSim datasheets has been modified slightly. The **ID** in the primary key is now **Id** for all datasheets. This also applies to column names in scenario-scoped datasheets that reference values taken from project-scoped datasheets. It is generally safe to substitute `ID` for `Id` throughout your script, but it's recommended to check the datasheet's variable names.
+
+Below is an example of a datasheet with the new naming convention for primary keys:
 
 ```{r IDs, warning=FALSE}
-datasheet(myScenario, "stsim_FlowPathway", includeKey = TRUE, optional = TRUE, empty = TRUE)
+datasheet(myScenario, "stsim_FlowPathway", includeKey = TRUE)
 ```
 
 ## Core datasheets
 
-The system datasheets, previously identified by `corestime_`, are now simply called `core_`.
+The system datasheets, previously identified by the prefix `corestime_`, are now prefixed by `core_`.
 
 
 ## Other NEW functions
+
+Below is a list of other new functions that have been added to `rsyncrosim v2`. For more information, on these new functions, refer to the reference guide. 
+
 ```{r new functions, eval=FALSE}
-createCondaEnv(pkgs = c()) # creates the conda environment for the selected package(s)
+# creates the conda environment for the selected package(s)
+createCondaEnv()
 
-deleteLibrary() # Note this is irreversible
+# deletes a SyncroSim library (IRREVERSIBLE)
+deleteLibrary() 
 
-chart() # Create or load a SyncroSim chart. Explore other charting functions with ?chart
+# Create, load, or modify SyncroSim charts using the new Chart class
+chart() 
 ```