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https://github.com/achubaty/landr_mpb_studyarea
https://github.com/achubaty/landr_mpb_studyarea
Last synced: 12 days ago
JSON representation
- Host: GitHub
- URL: https://github.com/achubaty/landr_mpb_studyarea
- Owner: achubaty
- License: other
- Created: 2021-04-20T16:16:12.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-07-18T00:35:51.000Z (4 months ago)
- Last Synced: 2024-07-18T03:44:07.137Z (4 months ago)
- Language: R
- Size: 367 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: citation.bib
Awesome Lists containing this project
README
---
title: "MPB_SK_studyArea"
author: "achubaty"
date: "20 April 2021"
output:
html_document:
keep_md: yes
editor_options:
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
```r
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
```
```r
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'
## )
```
```r
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'.
```
```r
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.