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https://github.com/KevCaz/monitoringOutcomes
:book: Wheeler et al. (2019) DOI: 10.1111/cobi.13257 -- research compendium
https://github.com/KevCaz/monitoringOutcomes
Last synced: 3 months ago
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:book: Wheeler et al. (2019) DOI: 10.1111/cobi.13257 -- research compendium
- Host: GitHub
- URL: https://github.com/KevCaz/monitoringOutcomes
- Owner: KevCaz
- License: gpl-2.0
- Created: 2017-06-17T16:56:32.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2019-08-19T00:53:25.000Z (about 5 years ago)
- Last Synced: 2024-05-21T02:12:27.158Z (6 months ago)
- Language: R
- Homepage:
- Size: 9.3 MB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# monitoringOutcomes
[](https://travis-ci.org/KevCaz/monitoringOutcomes)
[](https://ci.appveyor.com/project/KevCaz/monitoringoutcomes)
[](https://zenodo.org/badge/latestdoi/94637265)
## Overview
R functions to reproduce the analysis carried out in : "Identifying key needs for the integration of social–ecological outcomes in arctic wildlife monitoring" (DOI: 10.1111/cobi.13257).
The following R functions (see `R/`) relate to the following figures.
- **Fig 1**: `dartdiag.R`
- **Fig 2a-b**: `walktrapdendro4.R`
- **Fig 2c**: `edge_clustering.R`
- **Fig 3**: `connectivity2a.R`
- **Fig S3**: `3netscomp2a.R`
The sets of links and nodes required to create the figures are included in the
`data` folder (basically the data associated with the paper); three versions are
furnished. See the [How to](#how-to) section to reproduce the figures of the
manuscript. Note that for some figures, the nodes coordinates are randomized to
avoid such behavior, we used `set.seed()` below.
## An R package?
We have used a standard R package to:
1. efficiently assess the quality of our code (here we simply used `R CMD check`);
2. readily share our code.
We however acknowledge that despite the form of a standard R package, the code
presented is more a organized script than a package (*i.e.* functions included
are not general).
To install this package, one very convenient way is to use [`devtools`](https://cran.r-project.org/web/packages/devtools/index.html).
Note that one of the packages required, `graphicsutils`, is not available on
the CRAN, so it should be installed with `devtools` too. So one way to
install this package is to type the following line in your R console:
```R
install.packages("devtools")
devtools::install_github("inSileco/graphicsutils")
devtools::install_github("KevCaz/monitoringOutcomes")
```
## How to
Before calling any function, load the package:
```R
devtools::load_all()
```
### Figure 1
```R
library(Cairo)
vec_col <- c("#f1bf5f", "#058544", "#27ade3")
data(nodes)
data(links)
## PNG
png("inst/fig/fig1.png", width=8, height=10, units="in", res=300)
dartdiag(nodes, links, vec_col, arrowPNG = TRUE)
dev.off()
## SVG
CairoSVG("inst/fig/fig1.svg", width=8, height=10)
dartdiag(nodes, links, vec_col)
dev.off()
```
### Figure 2 a and b
```R
data(nodes2)
data(links2)
## PNG
set.seed(3466)
png("inst/fig/fig2ab.png", units="in", res=300, width=8.5, heigh=6)
walktrap_dendro(links2, nodes2, vec_col)
dev.off()
## SVG
set.seed(3466)
CairoSVG("inst/fig/fig2ab.svg", width=8.5, heigh=6)
walktrap_dendro(links2, nodes2, vec_col)
dev.off()
```
### Figure 2c
```R
data(nodes3)
data(links3)
## PNG
png("inst/fig/fig2c.png", units="in", res=300, width=8.5, heigh=6)
connectivity2a(links3, nodes3, cex_crl = 1.5)
dev.off()
## SVG
CairoSVG("inst/fig/fig2c.svg", width = 8.5, height = 6)
connectivity2a(links3, nodes3, vec_col, cex_crl = 1.5)
dev.off()
```
### Figure 3
```R
set.seed(2)
data(links2)
data(nodes2)
vec_names <- sort(gsub(paste0(nodes2[,1L], " ", nodes2[,2L]), pattern= "^n", replacement = ""))
png("inst/fig/fig3.png", units = "in", res = 300, width = 8, height = 4.5)
edge_clustering(links2, vec_names, vec_col)
dev.off()
## SVG
set.seed(2)
CairoSVG("inst/fig/fig3.svg", width = 8, height = 4.5)
edge_clustering(links2, vec_names, vec_col)
dev.off()
```
### Figure S3
```R
set.seed(81932)
data(nodes2)
data(links2)
png("inst/fig/figS3.png", units="in", res=300, width = 8, height = 5)
netcomp2a(links2, nodes2, vec_col)
dev.off()
## SVG
set.seed(81932)
CairoSVG("inst/fig/figS3.svg", width = 8, height = 5)
netcomp2a(links2, nodes2, vec_col)
dev.off()
```
