Create new module from template

Generate a skeleton for a new SpaDES module, a template for a documentation file, a citation file, a license file, a README.md file, and a folder that contains unit tests information. newModule is largely a wrapper around newModuleCode and newModuleDocumentation. newModuleCode will not generate the module code. newModuleDocumentation will create the other files.

newModule(name, path, ..., events = NULL, envir = parent.frame())

# S4 method for class 'character,character'
newModule(name, path, ..., events = NULL, envir = parent.frame())

# S4 method for class 'character,missing'
newModule(name, path, ..., events = NULL, envir = parent.frame())

newModuleCode(name, path, ..., events)

# S4 method for class 'character,character'
newModuleCode(name, path, ..., events)

newModuleDocumentation(name, path, ...)

# S4 method for class 'character,character'
newModuleDocumentation(name, path, ...)

# S4 method for class 'character,missing'
newModuleDocumentation(name, path, ...)

Arguments

name

Character string specifying the name of the new module.

path

Character string. Subdirectory in which to place the new module code file. The default is the current working directory.

...

Additional arguments. Currently, these can be either named function definitions (which will be added to the simList) or one or more of the following:

children: Required when type = "parent". A character vector specifying the names of child modules.
open: Logical. Should the new module file be opened after creation? Default TRUE.
type: Character string specifying one of "child" (default), or "parent".

For newModule can also be:

unitTests: Logical. Should the new module include unit test files? Default TRUE. Unit testing relies on the testthat package.
useGitHub: Logical. Is module development happening on GitHub? Default TRUE.

events

A list of named expressions, each of which is surrounded by { }. A user can specify events here, instead of accepting the default doEvent function that comes with the module template. If this is specified, all events must be specified, i.e., it will not inherit partially from the template doEvent.<moduleName>. See example.

envir

An environment where objects being passed to newModule can be found. Default parent.frame(), which should be fine for most cases.

Value

NULL (invisibly). The new module file is created at path/name.R, as well as ancillary files for documentation, citation, LICENSE, README, and tests directory.

newModuleCode is invoked for its side effect of creating new module code files.

newModuleDocumentation is nvoked for its side effect of creating new module documentation files.

Details

All files will be created within a subdirectory named name within the path:

  <path>/
    |_ <name>/
    |_ R/               # contains additional module R scripts
    |_ data/            # directory for all included data
      |_ CHECKSUMS.txt  # contains checksums for data files
    |_ tests/           # contains unit tests for module code
    |_ citation.bib     # bibtex citation for the module
    |_ LICENSE          # describes module's legal usage
    |_ README.md        # provide overview of key aspects
    |_ <name>.R         # module code file (incl. metadata)
    |_ <name>.Rmd       # documentation, usage info, etc.

Note

On Windows there is currently a bug in RStudio that prevents the editor from opening when file.edit is called. Similarly, in RStudio on macOS, there is an issue opening files where they are opened in an overlaid window rather than a new tab. file.edit does work if the user types it at the command prompt. A message with the correct lines to copy and paste is provided.

Author

Alex Chubaty and Eliot McIntire

Eliot McIntire and Alex Chubaty

Examples

# \donttest{
  tmpdir <- tempdir2("exampleNewModule")
  ## create a "myModule" module in the "modules" subdirectory.
  newModule("myModule", tmpdir)
#> New module myModule created at /tmp/Rtmp45trFG/reproducible/exampleNewModule
#> * edit module code in myModule.R
#> * write tests for your module code in tests/
#> * describe and document your module in myModule.Rmd
#> * tell others how to cite your module by editing citation.bib
#> * choose a license for your module; see LICENSE.md
#> Main module file is: /tmp/Rtmp45trFG/reproducible/exampleNewModule/myModule/myModule.R
#> Main documentation file is: /tmp/Rtmp45trFG/reproducible/exampleNewModule/myModule/myModule.Rmd

  ## create a new parent module in the "modules" subdirectory.
  newModule("myParentModule", tmpdir, type = "parent", children = c("child1", "child2"))
#> New module myParentModule created at /tmp/Rtmp45trFG/reproducible/exampleNewModule
#> * edit module code in myParentModule.R
#> * write tests for your module code in tests/
#> * describe and document your module in myParentModule.Rmd
#> * tell others how to cite your module by editing citation.bib
#> * choose a license for your module; see LICENSE.md
#> Main module file is: /tmp/Rtmp45trFG/reproducible/exampleNewModule/myParentModule/myParentModule.R
#> Main documentation file is: /tmp/Rtmp45trFG/reproducible/exampleNewModule/myParentModule/myParentModule.Rmd
  unlink(tmpdir, recursive = TRUE)
# }

if (requireNamespace("ggplot2")) {
  # We can also specify events and functions in `newModule`; it will still get all
  #   functions that are not specified from the module template (e.g., plotFun below)
  nm <- "test"
  modulePath <- Require::tempdir2()
  newModule(nm, path = modulePath, open = FALSE,
            events = list(
              init = {
                  sim <- Init(sim)                            # finds definition below
                  sim <- scheduleEvent(sim, start(sim) + 1,
                                       eventType = "plot")
                },
              plot = {
                  plotFun(sim)                                # finds the templated plotFun
                  sim <- scheduleEvent(sim, time(sim) + 1,
                                       eventType = "plot")
                }
              ,
            ),
            Init = function(sim) { # replaces Init definition from template
              sim$a <- 1
              return(sim)
            }
  )
  out <- simInitAndSpades(module = nm, paths = list(modulePath = modulePath))
  # clean up
  unlink(dir(modulePath, pattern = nm, full.names = TRUE), recursive = TRUE)
}
#> New module test created at /tmp/Rtmp45trFG/Require
#> * edit module code in test.R
#> * write tests for your module code in tests/
#> * describe and document your module in test.Rmd
#> * tell others how to cite your module by editing citation.bib
#> * choose a license for your module; see LICENSE.md
#> Main module file is: /tmp/Rtmp45trFG/Require/test/test.R
#> Main documentation file is: /tmp/Rtmp45trFG/Require/test/test.Rmd
#> Setting:
#>   options(
#>     spades.modulePath = '/tmp/Rtmp45trFG/Require'
#>   )
#> Paths set to:
#>   options(
#>     rasterTmpDir = '/tmp/Rtmp45trFG/SpaDES/scratch/raster'
#>     reproducible.cachePath = '/tmp/Rtmp45trFG/reproducible/cache'
#>     spades.inputPath = '/tmp/Rtmp45trFG/SpaDES/inputs'
#>     spades.outputPath = '/tmp/Rtmp45trFG/SpaDES/outputs'
#>     spades.modulePath = '/tmp/Rtmp45trFG/Require'
#>     spades.scratchPath = '/tmp/Rtmp45trFG/SpaDES/scratch'
#>   )
#>   terra::terraOptions(tempdir = '/tmp/Rtmp45trFG/SpaDES/scratch/terra'
#> Nov21 04:22:38 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Nov21 04:22:38 simInit test: outputObjects: a is assigned to sim inside Init, but is not declared in metadata outputObjects
#> Nov21 04:22:38 test  :.inputObjects Running .inputObjects for test
#> Nov21 04:22:38 test  :.inputObjects test: using dataPath '/tmp/Rtmp45trFG/Require/test/data'.
#> Elpsed time for simInit: 0.07399797 secs
#> Nov21 04:22:38 simInit Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Nov21 04:22:38 chckpn:init total elpsd: 0.076 secs | 0 checkpoint init 0
#> Nov21 04:22:38 save  :init total elpsd: 0.078 secs | 0 save init 0
#> Nov21 04:22:38 prgrss:init total elpsd: 0.08 secs | 0 progress init 0
#> Nov21 04:22:38 load  :init total elpsd: 0.082 secs | 0 load init 0
#> Nov21 04:22:38 test  :init total elpsd: 0.085 secs | 0 test init 1
#> Nov21 04:22:38 test  :init test
#> Nov21 04:22:38 test  :init New objects created:
#> Nov21 04:22:38 test  :init        <char>
#> Nov21 04:22:38 test  :init 1:          a
#> Nov21 04:22:38 test  :plot total elpsd: 0.095 secs | 1 test plot 5
#> Nov21 04:22:38 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> Nov21 04:22:39 test  :plot total elpsd: 0.2 secs | 2 test plot 5
#> Nov21 04:22:39 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> Nov21 04:22:39 test  :plot total elpsd: 0.28 secs | 3 test plot 5
#> Nov21 04:22:39 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> Nov21 04:22:39 test  :plot total elpsd: 0.35 secs | 4 test plot 5
#> Nov21 04:22:39 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> Nov21 04:22:39 test  :plot total elpsd: 0.43 secs | 5 test plot 5
#> Nov21 04:22:39 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> Nov21 04:22:39 test  :plot total elpsd: 0.53 secs | 6 test plot 5
#> Nov21 04:22:39 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> Nov21 04:22:39 test  :plot total elpsd: 0.61 secs | 7 test plot 5
#> Nov21 04:22:39 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> Nov21 04:22:39 test  :plot total elpsd: 0.69 secs | 8 test plot 5
#> Nov21 04:22:39 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> Nov21 04:22:39 test  :plot total elpsd: 0.79 secs | 9 test plot 5
#> Nov21 04:22:39 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> Nov21 04:22:39 test  :plot total elpsd: 0.87 secs | 10 test plot 5
#> Nov21 04:22:39 test  :plot `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

#> simList saved in
#> SpaDES.core:::savedSimEnv()$.sim
#> It will be deleted at next spades() call.