R package to run chronic wasting disease (CWD) models and a Shiny app. This project has moved to https://code.usgs.gov/usgs/norock/cross_p/cwdsims

This is a repository with R code for an interactive Shiny application of CWD disease models. Currently there are deterministic and stochastic models that are intended to model hunting scenarios for a 5 to 10 year time horizon. The models are sex and age structured with direct and indirect transmission.

Installation

To use this package, you should be using R 3.4+. You can install the package from GitHub using the remotes package. To build the vignettes (long-form documentation) included with the package, you'll need the knitr and markdown libraries installed.

To install all 3 packages:

install.packages(c("remotes", "knitr", "rmarkdown"))

Then to install the stable, approved package with vignettes:

remotes::install_git("https://code.usgs.gov/usgs/norock/cross_p/cwdsims", ref = "v0.1.1", build_vignettes = TRUE, build_manual = TRUE)

Or to install the most recent development version:

remotes::install_github("https://code.usgs.gov/usgs/norock/cross_p/cwdsims", build_vignettes = TRUE, build_manual = TRUE)

Note some Mac users may need to first install xQuartz (https://www.xquartz.org).

This may prompt you to update some of the necessary packages. Press "1" to update all packages. In some cases, the compilation of the later package has failed. If this occurs, re-run the install_github command above and when prompted

Do you want to install from sources the package which needs compilation? (Yes/no/cancel)

Type "no"

Introductory material

Once "CWDsims" is installed, you can find more introductory material about the package in the vignettes.

library(CWDsims)
vignette(package = "CWDsims") # all vignettes available
vignette("CWDsimsIntroVignette") # load the introduction

For a list of the available functions:

?CWDsims

Reporting bugs

Please consider reporting bugs and asking questions on the Issues page:

https://code.usgs.gov/usgs/norock/cross_p/cwdsims/issues

Follow @USGS_R on Twitter for updates on USGS R packages:

Citing CWDsims

citation(package = "CWDsims")

># To cite CWDsims in publications, please
># use:
># 
>#   Cross, P.C. and E.S. Almberg. 2019. CWDsims: 
>#   An R package for simulating chronic wasting
>#   disease scenarios, doi.org/10.5066/P9QZTTLY
># 
># A BibTeX entry for LaTeX users is
># 
>#   @Manual{,
>#     author = {Paul C. Cross and Emily S. Almberg},
>#     title = {CWDsims: An R package for simulating chronic wasing disease
>#     scenarios},
>#     publisher = {U.S. Geological Survey},
>#     address = {Reston, VA},
>#     version = {0.1.1},
>#     institution = {U.S. Geological Survey},
>#     year = {2019},
>#     url = {https://code.usgs.gov/usgs/norock/cross_p/cwdsims},
>#   }

This R package relates to USGS IPDS #IP-108402.