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CBM Spades Manual: v. 0.1

2 CBM_defaults

2.1 Overview

This module can run independently by running the global script below. Its main task is to read-in all the default values in SpaDES-CBM which is akin to the ArchiveIndex in CBM-CFS3 runs.

2.2 Usage 

if (!require("remotes")) {
  install.packages("remotes")
}
remotes::install_github("PredictiveEcology/Require@development")
remotes::install_github("PredictiveEcology/CBMutils@development")
library(Require)
Require("PredictiveEcology/SpaDES.project@transition", require = FALSE)
Require(c("SpaDES.core (>=1.1.0)", "SpaDES.tools (>= 1.0.0)",
          "googledrive", 'RCurl', 'XML'),
          #unlist(unname(packagesNeededInModules))),
        require = "SpaDES.core", # call `require` only on this package (same as `library`)
        verbose = 1)

cacheDir <- reproducible::checkPath("cache", create = TRUE)
moduleDir <- "modules"
inputDir <- reproducible::checkPath("inputs", create = TRUE)
outputDir <- reproducible::checkPath("outputs", create = TRUE)
setPaths(inputPath = inputDir, 
         modulePath = moduleDir, 
         outputPath = outputDir, 
         cachePath = cacheDir)

times <- list(start = 0, end = 10)
parameters <- list(
  #.progress = list(type = "text", interval = 1), # for a progress bar
  ## If there are further modules, each can have its own set of parameters:
  #module1 = list(param1 = value1, param2 = value2),
  #module2 = list(param1 = value1, param2 = value2)
)
modules <- list("CBM_defaults")
objects <- list()
paths <- list(
  cachePath = cacheDir,
  modulePath = moduleDir,
  inputPath = inputDir,
  outputPath = outputDir
)

myDefaults <- simInit(times = times, params = parameters, modules = modules,
                      objects = objects, paths = paths)

outDefaults <- spades(myDefaults)
# The spades call should make a "dataset" class object
testthat::expect_true(is(outSim@.envir$cbmData, "dataset"))

2.3 Events

Describe what happens for each event type.

2.3.1 Plotting

Write what is plotted.

2.3.2 Saving

Write what is saved.

2.4 Data dependencies

2.4.1 Input data

How to obtain input data, and a description of the data required by the module. If sourceURL is specified, downloadData("CBM_defaults", "path/to/modules/dir") may be sufficient.

2.4.2 Output data

Description of the module outputs.