title

author

date

output

editor_options

MPB_SK_studyArea

achubaty

20 April 2021

html_document

keep_md
true

chunk_output_type
console

Overview

Provide an overview of what the module does / how to use the module.

Module documentation should be written so that others can use your module. This is a template for module documentation, and should be changed to reflect your module.

R Markdown

R Markdown syntax allows R code, outputs, and figures to be rendered in the documentation.

For help writing in R Markdown, see https://rmarkdown.rstudio.com/.

Usage

library(SpaDES.core)

## Loading required package: quickPlot

## Loading required package: reproducible

## 
## Attaching package: 'SpaDES.core'

## The following objects are masked from 'package:stats':
## 
##     end, start

## The following object is masked from 'package:utils':
## 
##     citation

setPaths(modulePath = file.path("/home/achubaty/Documents/GitHub"))

## Setting:
##   options(
##     spades.modulePath = '/home/achubaty/Documents/GitHub'
##   )

## Paths set to:
##   options(
##     rasterTmpDir = '/tmp/RtmpGV5rUw/raster'
##     reproducible.cachePath = '/tmp/RtmpGV5rUw/Require/cache'
##     spades.inputPath = '/tmp/RtmptIFHCb/SpaDES/inputs'
##     spades.outputPath = '/tmp/RtmptIFHCb/SpaDES/outputs'
##     spades.modulePath = '/home/achubaty/Documents/GitHub'
##   )

getPaths() # shows where the 4 relevant paths are

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("MPB_SK_studyArea")
objects <- list()
inputs <- list()
outputs <- list()

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

## Setting:
##   options(
##     rasterTmpDir = '/tmp/RtmpGV5rUw/raster'
##     reproducible.cachePath = '/tmp/RtmpGV5rUw/Require/cache'
##     spades.inputPath = '/tmp/RtmptIFHCb/SpaDES/inputs'
##     spades.outputPath = '/tmp/RtmptIFHCb/SpaDES/outputs'
##     spades.modulePath = '/home/achubaty/Documents/GitHub'
##   )

## MPB_SK_studyArea: module code appears clean

## Apr20 10:25:13 simInit: MPB_SK Running .inputObjects for MPB_SK_studyArea

## Apr20 10:25:13 simInit: MPB_SK MPB_SK_studyArea: using dataPath '/home/achubaty/Documents/GitHub/MPB_SK_studyArea/data'.

mySimOut <- spades(mySim)

## Apr20 10:25:13 chckpn total elpsd: 0.0018 secs | 0 checkpoint init 0

## Apr20 10:25:13 save   total elpsd: 0.0038 secs | 0 save init 0

## Apr20 10:25:13 prgrss total elpsd: 0.0053 secs | 0 progress init 0

## Apr20 10:25:13 load   total elpsd: 0.0067 secs | 0 load init 0

## Apr20 10:25:13 MPB_SK total elpsd: 0.008 secs | 0 MPB_SK_studyArea init

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

## $cachePath
## [1] "/tmp/RtmpGV5rUw/Require/cache"
## 
## $inputPath
## [1] "/tmp/RtmptIFHCb/SpaDES/inputs"
## 
## $modulePath
## [1] "/home/achubaty/Documents/GitHub"
## 
## $outputPath
## [1] "/tmp/RtmptIFHCb/SpaDES/outputs"
## 
## $rasterPath
## [1] "/tmp/RtmpGV5rUw/raster//"

Parameters

Provide a summary of user-visible parameters.

paramName	paramClass	default	min	max	paramDesc
.plotInitialTime	numeric	NA	NA	NA	Describes the simulation time at which the first plot event should occur.
.plotInterval	numeric	NA	NA	NA	Describes the simulation time interval between plot events.
.saveInitialTime	numeric	NA	NA	NA	Describes the simulation time at which the first save event should occur.
.saveInterval	numeric	NA	NA	NA	This describes the simulation time interval between save events.
.useCache	logical	FALSE	NA	NA	Should this entire module be run with caching activated? This is generally intended for data-type modules, where stochasticity and time are not relevant

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("MPB_SK_studyArea", "/home/achubaty/Documents/GitHub") may be sufficient.

objectName	objectClass	desc	sourceURL
NA	NA	NA	NA

Output data

Description of the module outputs.

objectName	objectClass	desc
NA	NA	NA

Links to other modules

Describe any anticipated linkages to other modules.

achubaty/LandR_MPB_studyArea