Merge branch 'development'

.Rbuildignore

@@ -7,6 +7,7 @@
 cran-comments.md
 LICENSE
 ^_ignore$
+^_push_vignettes.sh$
 ^travis_wait_.*\.log$
 vignettes/.*_cache$
 vignettes/.*\.log$

.travis.yml

@@ -10,10 +10,15 @@ cran: http://cran.rstudio.com/
 
 sudo: required
 
+env:
+  global:
+    - secure: "KxcKSH4TFMbNMKAj6ePl4yq6SCeYQJcDkw0PMuEdImomwxqY3mP8p+GWVmNN1PKl8k7C/rgLNPAiBoJmddXMzFvGoGRWvyeER0lDN49rzNPHANF9wnMBBYN27mp98hBZlX2Vxu48M3jbmy+wRpmKKvKxTxOa8tUkt0GVEUTPeGQ="
+
 before_install:
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"
   - echo "options(repos = c(CRAN='http://cran.rstudio.com'))" >> ~/.Rprofile
+  - "chmod 755 ./_push_vignettes.sh"
 
 r_build_args: " "
 
@@ -66,6 +71,7 @@ r_github_packages:
   - jimhester/covr
 
 after_success:
+  - ./_push_vignettes.sh
   - Rscript -e 'library(covr); coveralls(coverage = print(package_coverage(quiet = FALSE))); devtools::session_info()'
 
 notifications:

DESCRIPTION

@@ -11,12 +11,12 @@ Description: Easily implement a variety of simulation models, with a focus on
     installed with `install.packages("fastshp", repos="http://rforge.net",
     type="source")`.
 URL: https://github.com/PredictiveEcology/SpaDES
-Version: 1.0.1
-Date: 2015-08-10
+Version: 1.0.2
+Date: 2015-09-09
 Authors@R: c(
-    person(c("Alex", "M"), "Chubaty", email="[email protected].ca",
+    person(c("Alex", "M"), "Chubaty", email="alexander.chubaty@canada.ca",
     role=c("aut", "cre")),
-    person(c("Eliot", "J", "B"), "McIntire", email="[email protected].ca",
+    person(c("Eliot", "J", "B"), "McIntire", email="eliot.mcintire@canada.ca",
     role=c("aut")),
     person("Steve", "Cumming", email="[email protected]",
     role=c("ctb")),
@@ -32,6 +32,7 @@ Suggests:
     Matrix,
     RColorBrewer,
     rgdal,
+    rmarkdown,
     testthat,
     tkrplot
 Imports:

NEWS

@@ -1,5 +1,19 @@
 Known issues: https://github.com/PredictiveEcology/SpaDES/issues
 
+version 1.0.2
+=============
+* update maintainer's and authors' email addresses
+* fix bug in `.parseModule` (#215)
+* improve dependency graph & module diagram (#216)
+* `simList` accessors now work with `.simList` superclass (#217)
+* fix `%>%` bug in demo (#218)
+* use `rmarkdown::render` for vignettes (with #219)
+* improve documentation (including #219)
+* reduce sizes of built vignettes (#222)
+* add slot `documentation` to module metadata (see `?defineModule`) (#224)
+* fix `inputs` data.frame construction in `simInit` (#225)
+* various other bug fixes
+
 version 1.0.1
 =============
 * no longer `attach` the simulation environment (#212)

R/module-dependencies-class.R

@@ -42,7 +42,9 @@ removeClass("person4")
 #' @slot timeunit       Describes the time (in seconds) corresponding to 1.0 simulation time units.
 #'                      Default is \code{NA}.
 #'
-#' @slot citation       A citation for the module, as a character string. Defaults to \code{NA_character_}.
+#' @slot citation       A list of citations for the module, each as character strings. Alternatively, list of filenames of \code{.bib} or similar files. Defaults to \code{NA_character_}.
+#'
+#' @slot documentation  List of filenames refering to module documentation sources.
 #'
 #' @slot reqdPkgs       Character vector of R package names to be loaded. Defaults to \code{NA_character_}.
 #'
@@ -69,24 +71,38 @@ removeClass("person4")
 #' @author Alex Chubaty
 #'
 setClass(".moduleDeps",
-         slots=list(name="character", description="character", keywords="character",
-                    childModules="character", authors="person", version="numeric_version",
+         slots=list(name="character", description="character",
+                    keywords="character", childModules="character",
+                    authors="person", version="numeric_version",
                     spatialExtent="Extent", timeframe="POSIXt", timeunit="ANY",
-                    citation="list", reqdPkgs="list", parameters="data.frame",
+                    citation="list", documentation="list",
+                    reqdPkgs="list", parameters="data.frame",
                     inputObjects="data.frame", outputObjects="data.frame"),
          prototype=list(name=character(), description=character(),
                         keywords=character(), childModules=character(),
                         authors=person(), version=numeric_version("0.0.0"),
                         spatialExtent=extent(rep(NA_real_, 4L)),
                         timeframe=as.POSIXlt(c(NA, NA)), timeunit=NA_real_,
-                        citation=list(), reqdPkgs=list(),
-                        parameters=data.frame(paramName=character(), paramClass=character(),
-                                              default=I(list()), min=numeric(), max=numeric(),
-                                              paramDesc=character()),
-                        inputObjects=data.frame(objectName=character(), objectClass=character(),
-                                                other=character(), stringsAsFactors=FALSE),
-                        outputObjects=data.frame(objectName=character(), objectClass=character(),
-                                                 other=character(), stringsAsFactors=FALSE)),
+                        citation=list(), documentation=list(), reqdPkgs=list(),
+                        parameters = data.frame(
+                          paramName=character(),
+                          paramClass=character(),
+                          default=I(list()), min=numeric(), max=numeric(),
+                          paramDesc=character()
+                        ),
+                        inputObjects = data.frame(
+                          objectName=character(),
+                          objectClass=character(),
+                          other=character(),
+                          stringsAsFactors=FALSE
+                        ),
+                        outputObjects = data.frame(
+                          objectName=character(),
+                          objectClass=character(),
+                          other=character(),
+                          stringsAsFactors=FALSE
+                        )
+                    ),
          validity=function(object) {
            if (length(object@name)!=1L) stop("name must be a single character string.")
            if (length(object@description)!=1L) stop("description must be a single character string.")

R/module-dependencies-methods.R

@@ -116,7 +116,10 @@ setMethod("depsGraph",
             } else {
               el <- depsEdgeList(sim, plot) %>% .depsPruneEdges
             }
-            return(graph_from_data_frame(el))
+            core <- c("checkpoint", "save", "progress", "load")
+            m <- modules(sim) %>% unlist
+            v <- unique(c(el$to, el$from, m[-which(m %in% core)]))
+            return(graph_from_data_frame(el, vertices=v, directed=TRUE))
 })
 
 #' @export

R/module-template.R

@@ -20,6 +20,14 @@
 #' @return Nothing is returned. The new module file is created at \code{path/name.R}, as
 #' well as anciliary files for documentation, citation, license, and readme.
 #'
+#' @note On Windows there is currently a bug in RStudio that it doesn't know what editor
+#' to open with \code{file.edit} is called (which is what moduleName does). This will return an error:
+#'
+#' \code{Error in editor(file = file, title = title) :}
+#' \code{argument "name" is missing, with no default}
+#'
+#' You can just browse to the file and open it manually.
+#'
 #' @export
 #' @docType methods
 #' @rdname newModule
@@ -57,13 +65,17 @@ defineModule(sim, list(
   version=numeric_version(\"0.0.0\"),
   spatialExtent=raster::extent(rep(NA_real_, 4)),
   timeframe=as.POSIXlt(c(NA, NA)),
-  timeunit=NA_character_, # e.g., \"year\"
-  citation=list(),
+  timeunit=NA_character_, # e.g., \"year,\",
+  citation=list(\"citation.bib\"),
+  documentation=list(\"README.txt\", \"", name, ".Rmd\"),
   reqdPkgs=list(),
   parameters=rbind(
-    defineParameter(\".plotInitialTime\", \"numeric\", NA, NA, NA, \"This describes the simulation time at which the first plot event should occur\"),
-    defineParameter(\".saveInitialTime\", \"numeric\", NA, NA, NA, \"This describes the simulation time at which the first save event should occur\")),
     #defineParameter(\"paramName\", \"paramClass\", value, min, max, \"parameter description\")),
+    defineParameter(\".plotInitialTime\", \"numeric\", NA, NA, NA, \"This describes the simulation time at which the first plot event should occur\"),
+    defineParameter(\".plotInterval\", \"numeric\", NA, NA, NA, \"This describes the simulation time at which the first plot event should occur\"),
+    defineParameter(\".saveInitialTime\", \"numeric\", NA, NA, NA, \"This describes the simulation time at which the first save event should occur\"),
+    defineParameter(\".saveInterval\", \"numeric\", NA, NA, NA, \"This describes the simulation time at which the first save event should occur\")
+  ),
   inputObjects=data.frame(objectName=NA_character_, objectClass=NA_character_, other=NA_character_, stringsAsFactors=FALSE),
   outputObjects=data.frame(objectName=NA_character_, objectClass=NA_character_, other=NA_character_, stringsAsFactors=FALSE)
 ))
@@ -86,16 +98,27 @@ doEvent.", name, " = function(sim, eventTime, eventType, debug=FALSE) {
     # ! ----- EDIT BELOW ----- ! #
     # do stuff for this event
 
+    #Plot(objectFromModule) # uncomment this, replace with object to plot
+    # schedule future event(s)
+
+    # e.g.,
+    #sim <- scheduleEvent(sim, params(sim)$", name, "$.plotInitialTime, \"", name, "\", \"plot\")
+
+    # ! ----- STOP EDITING ----- ! #
+  } else if (eventType==\"save\") {
+    # ! ----- EDIT BELOW ----- ! #
+    # do stuff for this event
+
     # e.g., call your custom functions/methods here
     # you can define your own methods below this `doEvent` function
 
     # schedule future event(s)
 
     # e.g.,
-    # sim <- scheduleEvent(sim, time(sim) + increment, \"", name, "\", \"plot\")
+    # sim <- scheduleEvent(sim, time(sim) + increment, \"", name, "\", \"save\")
 
     # ! ----- STOP EDITING ----- ! #
-  } else if (eventType==\"save\") {
+  } else if (eventType==\"event1\") {
     # ! ----- EDIT BELOW ----- ! #
     # do stuff for this event
 
@@ -105,10 +128,10 @@ doEvent.", name, " = function(sim, eventTime, eventType, debug=FALSE) {
     # schedule future event(s)
 
     # e.g.,
-    # sim <- scheduleEvent(sim, time(sim) + increment, \"", name, "\", \"save\")
+    # sim <- scheduleEvent(sim, time(sim) + increment, \"", name, "\", \"templateEvent\")
 
     # ! ----- STOP EDITING ----- ! #
-  } else if (eventType==\"templateEvent\") {
+  } else if (eventType==\"event2\") {
     # ! ----- EDIT BELOW ----- ! #
     # do stuff for this event
 
@@ -121,10 +144,10 @@ doEvent.", name, " = function(sim, eventTime, eventType, debug=FALSE) {
     # sim <- scheduleEvent(sim, time(sim) + increment, \"", name, "\", \"templateEvent\")
 
     # ! ----- STOP EDITING ----- ! #
-    } else {
-      warning(paste(\"Undefined event type: \'\", events(sim)[1, \"eventType\", with=FALSE],
-                    \"\' in module \'\", events(sim)[1, \"moduleName\", with=FALSE], \"\'\", sep=\"\"))
-    }
+  } else {
+    warning(paste(\"Undefined event type: \'\", events(sim)[1, \"eventType\", with=FALSE],
+                  \"\' in module \'\", events(sim)[1, \"moduleName\", with=FALSE], \"\'\", sep=\"\"))
+  }
   return(invisible(sim))
 }
 
@@ -176,7 +199,7 @@ doEvent.", name, " = function(sim, eventTime, eventType, debug=FALSE) {
 }
 
 ### template for your event2
-sim$", name, "Event2 = function(sim) {
+", name, "Event2 = function(sim) {
   # ! ----- EDIT BELOW ----- ! #
 
 
@@ -389,6 +412,14 @@ setMethod("newModuleDocumentation",
 #'
 #' @return Nothing is returned. All file are open via \code{file.edit}.
 #'
+#' @note On Windows there is currently a bug in RStudio that it doesn't know what editor to
+#' open with \code{file.edit} is called (which is what moduleName does). This will return an error:
+#'
+#' \code{Error in editor(file = file, title = title) :}
+#' \code{argument "name" is missing, with no default}
+#'
+#' You can just browse to the file and open it manually.
+#'
 #' @export
 #' @docType methods
 #' @rdname openModules
@@ -485,7 +516,7 @@ definition = function(name, path, version, ...) {
   on.exit(setwd(callingWd))
   setwd(path)
   zipFileName=paste0(name, "_", version, ".zip")
-  print(paste("Zipping module into zip file"))
+  print(paste("Zipping module into zip file:", zipFileName))
   zip(zipFileName, files=file.path(name), extras=c("-x","*.zip"), ...)
   file.copy(zipFileName, to=paste0(name, "/", zipFileName), overwrite=TRUE)
   file.remove(zipFileName)
@@ -504,5 +535,15 @@ setMethod("zipModule",
 setMethod("zipModule",
           signature=c(name="character", path="missing", version="missing"),
           definition = function(name, ...) {
-            zipModule(name=name, path=".", version="0.0.0", ...)
+            vers <- moduleMetadata(name, ".")$version %>% as.character
+            zipModule(name=name, path=".", version=vers, ...)
+})
+
+#' @export
+#' @rdname zipModule
+setMethod("zipModule",
+          signature=c(name="character", path="character", version="missing"),
+          definition = function(name, path, ...) {
+            vers <- moduleMetadata(name, path)$version %>% as.character
+            zipModule(name=name, path=path, version=vers, ...)
 })

R/plotting-diagrams.R

@@ -114,8 +114,8 @@ setMethod(".sim2gantt",
 #' Each module appears in a color-coded row, within which each event for that
 #' module is displayed corresponding to the sequence of events for that module.
 #' Note that only the start time of the event is meaningful is these figures:
-#' the width of the bar associated with a particular module's event corresponds
-#' to the module's timeunit, not the event's "duration".
+#' the width of the bar associated with a particular module's event DOES NOT
+#' correspond to an event's "duration".
 #'
 #' Based on this StackOverflow answer: \url{http://stackoverflow.com/a/29999300/1380598}.
 #'
@@ -133,7 +133,7 @@ setMethod(".sim2gantt",
 #' @param ...  Additional arguments passed to \code{mermaid}.
 #'             Useful for specifying \code{height} and \code{width}.
 #'
-#' @return Plots an event diagram as Gantt Chart.
+#' @return Plots an event diagram as Gantt Chart, invisibly returning a \link{mermaid} object.
 #'
 #' @seealso \code{\link{mermaid}}.
 #'
@@ -163,30 +163,35 @@ setMethod("eventDiagram",
             }
             ll <- .sim2gantt(sim, n, startDate, dots$width)
 
-            #remove progress bar events
+            # remove progress bar events
             ll <- ll[names(ll)!="progress"]
 
-            # estimate the height of the diagram
-            dots$height <- if(any(grepl(pattern="height", names(dots)))) {
-              as.numeric(dots$height)
-            } else {
-              sapply(ll, NROW) %>% sum %>% `*`(., 26L)
-            }
+            if (length(ll)) {
+              # estimate the height of the diagram
+              dots$height <- if(any(grepl(pattern="height", names(dots)))) {
+                as.numeric(dots$height)
+              } else {
+                sapply(ll, NROW) %>% sum %>% `*`(., 26L)
+              }
 
-            diagram <- paste0(
-              # mermaid "header"
-              "gantt", "\n",
-              "dateFormat  YYYY-MM-DD", "\n",
-              "title SpaDES event diagram", "\n",
+              diagram <- paste0(
+                # mermaid "header"
+                "gantt", "\n",
+                "dateFormat  YYYY-MM-DD", "\n",
+                "title SpaDES event diagram", "\n",
 
-              # mermaid "body"
-              paste("section ", names(ll), "\n", lapply(ll, function(df) {
-                paste0(df$task, ":", df$status, ",",
-                       df$pos, ",", df$start, ",", df$end,
-                       collapse = "\n")
-              }), collapse = "\n"), "\n"
-            )
-            do.call(mermaid, args=append(diagram, dots))
+                # mermaid "body"
+                paste("section ", names(ll), "\n", lapply(ll, function(df) {
+                  paste0(df$task, ":", df$status, ",",
+                         df$pos, ",", df$start, ",", df$end,
+                         collapse = "\n")
+                }), collapse = "\n"), "\n"
+              )
+              do.call(mermaid, args=append(diagram, dots))
+            } else {
+              stop("Unable to create eventDiagram for a simulation that hasn't been run.\n",
+                   "Run your simulation using `mySim <- spades(mySim)` and try again.")
+            }
 })
 
 #' @export
@@ -210,7 +215,7 @@ setMethod("eventDiagram",
 #' @param ...  Additional arguments passed to \code{mermaid}.
 #'             Useful for specifying \code{height} and \code{width}.
 #'
-#' @return Plots a sequence diagram.
+#' @return Plots a sequence diagram, invisibly returning a \link{mermaid} object.
 #'
 #' @seealso \code{\link{mermaid}}.
 #'
@@ -258,7 +263,7 @@ setMethod("objectDiagram",
 #' or \code{"tk"} for \code{igraph::tkplot}. Default missing, which uses regular
 #' \code{plot}.
 #'
-#' @param ...  Additional arguments passed to \code{plot}.
+#' @param ...  Additional arguments passed to plotting function specfied by \code{type}.
 #'
 #' @return Plots module dependency diagram.
 #'
@@ -295,4 +300,4 @@ setMethod("moduleDiagram",
           signature=c(sim="simList", type="missing"),
           definition=function(sim, type, ...) {
               plot(depsGraph(sim, TRUE), ...)
-          })
+})