inst/options.R

In PredictiveEcology/SpaDES.project: Project Templates Using 'SpaDES'

# This is an example 'options' file that can be called from `setupOptions` and `setupProject`.

# Any named list will be appended to any subsequent named list, sequentially: if there

# are >1 named list with the same element, the final one will be used.

# There are several types of approaches that can be used, but because this file is used

# for "options" only, nothing will be returned to the user or functions; this should

# only be used to create named lists.



# If R packages are needed, it is likely wise to prefix the function with the package name;

# any package that is needed can be added to the `require` argument in `setupProject`.



# This file will have access to the arguments passed into `setupParams` and `setupProject`,

# such as `paths`, `times`, or any other named argument passed to the `...`.



# Example -- local object that can be defined and used below

maxMemory <- 5e+9 # if (grepl("LandWeb", runName)) 5e+12 else 5e+9



# Example -- Use any arbitrary object that can be passed in the `...` of `setupOptions`

#   or `setupProject`

if (.mode == "development") {

  list(test = 2)

}



# Can use

if (.mode == "batch") {

  list(test = 1)

}



if (nodes == "batch") {

  list(test = 3)

}





# Example -- large named list of options

opts <- list(

  "fftempdir" = paths$scratchPath,

  "future.globals.maxSize" = 1000*1024^2,

  "LandR.assertions" = FALSE,

  "LandR.verbose" = 1,

  "map.dataPath" = normPath(paths$inputPath), # not used yet

  "map.overwrite" = TRUE,

  "map.tilePath" = paths$tilePath,

  "map.maxNumCores" = 2,

  # "map.useParallel" = mapParallel,

  "rasterMaxMemory" = maxMemory,

  # "rasterTmpDir" = scratchDir,

  "reproducible.destinationPath" = normPath(paths$inputPath),

  "reproducible.futurePlan" = FALSE,

  "reproducible.overwrite" = TRUE,

  "reproducible.quick" = FALSE,

  "reproducible.showSimilar" = TRUE,

  "reproducible.useCache" = TRUE,

  "reproducible.useCloud" = TRUE,

  "reproducible.useGDAL" = FALSE, ## NOTE: gdal is faster, but mixing gdal with raster causes inconsistencies

  # "reproducible.useMemoise" = ifelse(isTRUE(batchMode), FALSE, if (user("emcintir")) FALSE else TRUE),

  "reproducible.useGDAL" = FALSE,

  "reproducible.useNewDigestAlgorithm" = TRUE,

  "spades.inputPath" = normPath(paths$outputPath),

  "spades.moduleCodeChecks" = FALSE,

  "spades.recoveryMode" = FALSE,

  "spades.useRequire" = FALSE # Don't use Require... meaning assume all pkgs installed

)



opts <- list(

  "map.overwrite" = FALSE

)



# Example -- conditional using `if`. This example is "user" specific.

#   These statements must be simple as the parsing

#   cannot understand if this `if` is too complicated

if (user("emcintir"))

  list(

    "reproducible.showSimilar" = FALSE

  )



if (user("emcintir") && requireNamespace("Require")) {

  list(

    "reproducible.inputPaths" = Require::checkPath("~/data", create = TRUE),

    "reproducible.devMode" = TRUE

  )

}



# Example -- this will be ignored because it is not part of a named list --> pass this

#   to `sideEffects` in `setupProject`

if (requireNamespace("googledrive", quietly = TRUE))

  googledrive::drive_auth(email = "eliotmcintire@gmail.com", cache = "~/.secret")



# Example -- machine specific

if (machine("A127")) {

  list(Ncpus = 2)

}





# Example -- this will be ignored because it is not part of a named list --> pass this

#   to `sideEffects` in `setupProject`

if (requireNamespace("httr"))

  httr::set_config(httr::config(http_version = 0)) # not run b/c not named list