Fractionation estimation in R package
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README.md

Build Status DOI codecov Project Status: Active – The project has reached a stable, usable state and is being actively developed.

SIDER

Stable Isotope Discrimination Estimation in R

This package allows users to estimate Trophic Discrimination Factors (TDF) for species with no current measured TDF values using Bayesian imputation. This package is based on the MCMCglmm package and runs a MCMCglmm analysis on multiple trees using mulTree.

Installing SIDER (latest stable release)

If you want the vignettes installed along with SIDER you will need to first download and install the JAGS software which is required for the package MixSIAR that is called in the SIDER-to-MixSIAR-pipeline vignette. Please note also that these vignettes take some time to run as there are several real calls made to SIDER, and it will probably take about 15 minutes on a 2.7 GHz i5 with 16 GB RAM to install.

# Install devtools if you dont already have it
if(!require(devtools)) install.packages("devtools")
devtools::install_github("healyke/SIDER@v1.0.0.0", build_vignettes = TRUE, dependencies = "suggests")
library(SIDER)

If you want to skip the vignette installation then you can run the following.

# Install devtools if you dont already have it
if(!require(devtools)) install.packages("devtools")
devtools::install_github("healyke/SIDER@v1.0.0.0", build_vignettes = FALSE)
library(SIDER)

Installing SIDER (development - not guaranteed stable)

if(!require(devtools)) install.packages("devtools")
devtools::install_github("healyke/SIDER@master", build_vignettes = TRUE, dependencies = "suggests")
library(SIDER)

Authors

Kevin Healy, Seán B.A Kelly, Thomas Guillerme, Andrew Jackson

Citation

If you are using this package, please cite:

Healy, K., Guillerme, T., Kelly, S. B. A., Inger, R., Bearhop, S. and Jackson, A. L. (2017), SIDER: an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness. Ecography. doi:10.1111/ecog.03371

This paper also has a pre-print in PeerJ which can be found here: https://doi.org/10.7287/peerj.preprints.1950v1