Representative and Adequate Prioritization Toolkit in R

Biodiversity is in crisis. The overarching aim of conservation is to preserve biodiversity patterns and processes. To this end, protected areas are established to buffer species and preserve biodiversity processes. But resources are limited and so protected areas must be cost-effective. This package contains tools to generate plans for protected areas (prioritizations), using spatially explicit targets for biodiversity patterns and processes. To obtain solutions in a feasible amount of time, this package uses the commercial 'Gurobi' software package (obtained from < http://www.gurobi.com/>). Additionally, the 'rgurobi' package can also be installed to provide extra functionality (obtained from < http://github.com/jeffreyhanson/rgurobi>). For more information on using this package, see Hanson et al. (2017) .


Project Status: Active - The project has reached a stable, usable state and is being actively developed. Travis Build Status AppVeyor Build Status Coverage Status CRAN_Status_Badge

Biodiversity is in crisis. The overarching aim of conservation is to preserve biodiversity patterns and processes. To this end, protected areas are established to buffer species and preserve biodiversity processes. But resources are limited and so protected areas must be cost-effective. This package contains tools to generate plans for protected areas (prioritizations), using spatially explicit targets for biodiversity patterns and processes. To obtain solutions in a feasible amount of time, this package uses the commercial 'Gurobi' software package (obtained from http://www.gurobi.com/). Additionally, the 'rgurobi' package can also be installed to provide extra functionality (obtained from http://github.com/jeffreyhanson/rgurobi). For more information on using this package, see our paper published in Methods in Ecology and Evolution (http://dx.doi.org/doi:10.1111/2041-210X.12862).

Installation

This package depends on several packages which can be difficult to install under Linux and Mac operating systems.

Linux (Ubuntu) users can install them typing the following code into the terminal:

sudo apt-get update
sudo apt-get install libgdal-dev
sudo apt-get install libproj-dev
sudo apt-get build-dep r-cran-rgl

Mac OSX users can install them using the code below.

brew install Caskroom/cask/xquartz
brew install gdal
Rscript -e "setRepositories(ind = 1:2); install.packages(c('rgdal', 'rgeos'))"

To install the latest official version on CRAN, use the following R code:

install.packages("raptr")

To install the development version on GitHub, use this R code:

if (!require("devtools"))
  install.packages("devtools")
devtools:::install_github("jeffreyhanson/raptr")

Once this package has been installed, you can read through the vignette for a tutorial on how to use it.

View it here, or by running this R code:

vignette("raptr", package = "raptr")

Citation

citation("raptr")
## 
## To cite the raptr package in publications, use:
## 
##   Hanson JO, Rhodes JR, Possingham HP & Fuller RA raptr:
##   Representative and Adequate Prioritization Toolkit in R. Methods
##   in Ecology & Evolution, In press. DOI: 10.1111/2041-210X.12862
## 
## A BibTeX entry for LaTeX users is
## 
##   @Article{,
##     author = {Jeffrey O Hanson and Jonathan R Rhodes and Hugh P Possingham and Richard A Fuller},
##     title = {raptr: Representative and adequate prioritization toolkit in R},
##     journal = {Methods in Ecology and Evolution},
##     year = {2017},
##     volume = {In press},
##     url = {https://dx.doi.org/10.1111/2041-210X.12862},
##   }
## 
## You may also want to cite the package version. Find it with
## "help(package=raptr)".

News

raptr 0.1.1 (released)

  • vignette size has been reduced.
  • updated DOI in readme.

raptr 0.1.0 (unreleased)

  • unit tests now compatible with testthat R package (version 1.0.2.9000).
  • assertthat R package is now used for validating function arguments.
  • vignette now uses knitr::rmarkdown_notangle engine to avoid running the code during package checks, and placeholder vignette file has been removed.
  • code has been linted.
  • functions from other packages are now called explicitly using pkg::function.
  • messages are now displayed using message following best practices.
  • updated readme.
  • added citation for Methods in Ecology and Evolution paper.
  • strip debugging symbols from compiled files to reduce installation size.
  • is.GurobiInstalled now does not run gurobi to avoid spurious notes during CRAN checks on academic license.

raptr 0.0.5 (released)

  • fix documentation in make.DemandPoints.
  • \donttest instead of \dontrun for examples.
  • fix broken example code.

raptr 0.0.4 (unreleased)

  • find out which suggested packages are installed using requireNamespace.
  • add more links to package documentation.
  • register Rcpp functions.

raptr 0.0.3 (released)

  • reduce memory consumption using external pointers.
  • fix memory leaks.
  • fix bug in tests for calcSpeciesAverageInPus.

raptr 0.0.2 (unreleased)

  • reduce installation size.
  • fix typo in README.

raptr 0.0.1.1 (unreleased)

  • fixed authorship typo.
  • updated README.md with instructions for installing from CRAN.

raptr 0.0.1 (unreleased)

  • Initial package version.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("raptr")

0.1.1 by Jeffrey O Hanson, 7 months ago


https://github.com/jeffreyhanson/raptr


Report a bug at https://github.com/jeffreyhanson/raptr/issues


Browse source code at https://github.com/cran/raptr


Authors: Jeffrey O Hanson [aut, cre], Jonathan R Rhodes [aut], Hugh P Possingham [aut], Richard A Fuller [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports utils, methods, assertthat, Matrix, boot, grDevices, PBSmapping, graphics, stats, scales, shape, adehabitatHR, RgoogleMaps, RandomFields, RColorBrewer, plyr, parallel, doParallel, rgeos, rgdal, hypervolume, ks, gdalUtils, mvtnorm, ggplot2

Depends on sp, raster

Suggests knitr, roxygen2, dplyr, vegan, gurobi, rgurobi, gridExtra, rgl, testthat

Linking to Rcpp, RcppEigen, BH

System requirements: C++11


See at CRAN