isocat

isocat: Isotope Clustering and Assignment Tools

The isocat package provides multiple tools in R for creating and quantitatively analyzing and summarizing probability-of-origin surfaces generated from stable isotope analyses of animal tissue. The package includes functions to create probability-of-origin surfaces, quantitatively compare and summarize the origins of individuals, and create and validate post-processing surfaces useful for interpreting individual origins.

Overview

isocat relates the stable isotope ratios of animal tissues to environmental isotope data to create probability-of-origin maps for individuals.

Probability-of-origin maps can be quantitatively compared, and individual origins compared and clustered.

Probability-of-origin surfaces can also be transformed to several common post-processing surfaces to facilitate interpretation of individual origins, including cumulative-sum, odds-ratio, probability quantile, and quantile-simulation surfaces. Functions are also available to find untransformed and post-processing probability-of-origin values at specific sampling sites.

For more information, and for reproducible examples, please see isocat’s vignette.

Installation

isocat is currently available on GitHub. To install without a vignette, use the following code: devtools::install_github("cjcampbell/isocat")

The isocat package provides multiple tools in R for creating and quantitatively analyzing and summarizing probability-of-origin surfaces generated from stable isotope analyses of animal tissue.

Vignette

To install isocat and its vignette directly from github, use the following code in R when using devtools >= 2.0.0:

devtools::install_github("cjcampbell/isocat", build = TRUE, force = TRUE, build_opts = c("--no-resave-data", "--no-manual"))

The vignette requires the certain packages to be installed in order to compile. The code chunk below will automatically check for and install packages needed to form the vignette.

vignettePackages <- c("kableExtra", "pvclust", "rasterVis", "ggplot2", "viridisLite", "gridExtra", "dplyr", "dendextend", "isocat")

lapply(vignettePackages, function(pckg) {
    if (!require(pckg, character.only = TRUE, quietly = FALSE)) {
      install.packages(x, dependencies = TRUE)
      require(pckg)
    }
  })
}