This package makes several methods used for analyzing variability in ecological data available. Currently, it supports fitting a neutral herbivory model to data using Maximum Likelihood Estimation (MLE). It also contains several helper functions for comparing distributions and assessing model fit. In addition, using the imager infrastructure, the package also supports automatic processing of leaf images, mostly in the context of leaf scans, that can retrieve rich within-leaf herbivory data. The package is integrated with the spatstat packages that allows for spatial analysis of these data.
Currently work in progress. Proceed with caution :) That said, stable versions with full documentations are available in the past_versions folder.
Report any bugs to vsbpan@gmail.com Thanks!
To use the herbivar package, you'll need to first use the install_github() function from the devtools package to install the latest version of herbivar from github. You can just run the code chunk below on your machine to install the packages. The herbivar package depends on EBImage, which can be installed via BiocManager::install(). If you are not using Windows, you might have a problem with the file libX11.6.dylib, which the dependent package imager uses. You'll need to install XQuartz (https://www.xquartz.org/) to fix the error. You can set build_vignettes = TRUE in install_github() if you want to have the vignette.
#install.packages("devtools")
#install.packages("BiocManager")
#BiocManager::install("EBImage")
devtools::install_github("vsbpan/herbivar", build_vignettes = FALSE, dependencies = TRUE, force = TRUE)
You can access the vignette via the command below. Alternatively, you can find the knitted HTML file in the vignettes folder by first downloading the ZIP file of the repository.
browseVignettes("herbivar")