Code for 'Incorporating biophysical gradients and uncertainty into burn severity maps in a temperate fire-prone forested region'
This repository contains code associated with the paper:
Harvey, B.J., R.A. Andrus, S.C. Anderson. 2019. Incorporating biophysical gradients and uncertainty into burn severity maps in a temperate fire-prone forested region. In press at Ecosphere. https://doi.org/10.1002/ecs2.2600
|- DESCRIPTION # project metadata
|- README.md # this file
|- LICENSE.md # specifies the conditions of use and reuse of the code
|- burn-severity.Rproj # RStudio project file
|
|- data/ # data folder
| +- README.md # description of data columns in `BurnSeverity.csv`
| +- BurnSeverity.csv # main raw data file
| +- VariableNames.csv # lookup table of raw data columns to 'pretty' labels
|- +- generated/ # data that gets generated by code
|
|- analysis/ # the main analysis files
| +- 01-burn-severity.Rmd # analysis for Q1 portion of paper
| +- 02-burn-severity.Rmd # analysis for Q2 portion of paper
| +- 03-burn-severity.Rmd # analysis for Q3 portion of paper
| +- 04-burn-maps.Rmd # code to generate the map figures
| +- zoib-functions.R # helper R functions for the analysis
| +- zoib1re.stan # Stan ZOIB model
| +- oib1re.stan # Stan OIB model (model without the zero component)
| +- figs/ # figures get generated here
| +- make-map-data/ # Code for generating predictor data going into the
| # map predictions. Note that the various spatial files
| # are not included in this repository. They were
| # processed with the R file in this repository to generate the
| # data that are cached in the `data/generated` folder.
In order to run the included code the following R packages are required:
pkgs <- c("dplyr", "ggplot2", "plyr", "reshape2", "readr", "forcats", "here",
"purrr", "scales", "rstan", "broom", "viridis", "RColorBrewer", "devtools",
"doParallel", "cowplot", "rmarkdown")
install.packages(pkgs)
devtools::install_github("seananderson/ggsidekick")You will also need to have a C++ toolchain setup to build the Stan models. See https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started.
The spatial data extraction (for which the raw data is not included here), also required raster, rgdal, dismo, and sp.
The .Rmd files can be run by clicking the 'Knit' button in RStudio for each one or by running in a fresh R session:
rmarkdown::render("analysis/01-burn-severity.Rmd")
rmarkdown::render("analysis/02-burn-severity.Rmd")
rmarkdown::render("analysis/03-burn-severity.Rmd")
rmarkdown::render("analysis/04-burn-maps.Rmd")The analysis was run with the following computational environment:
─ Session info ──────────────────────────────────────────────────────────
setting value
version R version 3.5.2 (2018-12-20)
os macOS Mojave 10.14.2
system x86_64, darwin15.6.0
language (EN)
collate en_CA.UTF-8
ctype en_CA.UTF-8
─ Packages ──────────────────────────────────────────────────────────────
package version date source
broom 0.5.1 2018-12-05 CRAN (R 3.5.0)
cowplot 0.9.4 2019-01-08 CRAN (R 3.5.2)
doParallel 1.0.14 2018-09-24 CRAN (R 3.5.0)
dplyr 0.7.8 2018-11-10 CRAN (R 3.5.0)
forcats 0.3.0 2018-02-19 CRAN (R 3.5.0)
ggplot2 3.1.0 2018-10-25 CRAN (R 3.5.0)
here 0.1 2017-05-28 CRAN (R 3.5.0)
loo 2.0.0 2018-04-11 CRAN (R 3.5.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.5.0)
purrr 0.3.0 2019-01-27 CRAN (R 3.5.2)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.5.0)
Rcpp 1.0.0 2018-11-07 CRAN (R 3.5.0)
readr 1.3.1 2018-12-21 CRAN (R 3.5.0)
reshape2 1.4.3 2017-12-11 CRAN (R 3.5.0)
rstan 2.18.2 2018-11-07 CRAN (R 3.5.0)
scales 1.0.0 2018-08-09 CRAN (R 3.5.0)
tidyr 0.8.2 2018-10-28 CRAN (R 3.5.0)
viridis 0.5.1 2018-03-29 CRAN (R 3.5.0)
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