CBM_defaults.Rmd

---
title: "CBM_defaults"
author: ""
date: "19 January 2018"
output: pdf_document
editor_options: 
  chunk_output_type: console
---
# CBM_defaults

## 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.

## Usage

```{r module_deafults_usage, eval=FALSE}
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)
```

```{r tests, eval=FALSE}
# The spades call should make a "dataset" class object
testthat::expect_true(is(outSim@.envir$cbmData, "dataset"))
```

## Events

Describe what happens for each event type.

### Plotting

Write what is plotted.

### Saving

Write what is saved.

## Data dependencies

### 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.

### Output data

Description of the module outputs.

## Links to other modules

Describe any anticipated linkages to other modules.