Rarefy data, calculate diversity and plot the results.
This R module is a wrapper for the rtk program.
This package depends on the R package RCPP, which enables using Cpp-Code easily in R packages.
To build and install this package from source, just run these commands in a directory above the directory containing the source files.
R CMD build rtk R CMD check rtk*.tar.gz R CMD install rtk*.tar.gz
Or directly via
git clone https://github.com/hildebra/Rarefaction/ cd Rarefaction cd r-package R CMD INSTALL rtk
require("rtk")# generate semi sparse example datadata <- matrix(sample(x = c(rep(0, 1500),rep(1:10, 500),1:1000),size = 120, replace = T), 10)# find the column with the lowest aboundancesamplesize <- min(colSums(data))# rarefy the dataset, so each column contains the same number of samplesdata.rarefied <- rtk(input = data, rareDepth = samplesize, NoOfMatrices = 1)path <- "/path/to/a/file.csv"data.rarefied <- rtk(input = path, rareDepth = 1000)
More documentation if provided inside of the R package. Please look into
To develop this package it is recommended to install the packages
testthat for R.
Clone the git repo. The main software
rtk is located in
Rarefaction/rtk. The files used in the r-package are link via symbolic links. This might not work on your system, so please bear in mind, that changes on those files should always committed so that this structure is preserved, even if your system might not support this.
Unit tests are performed using testthat in the
test/testthat/ location. Read up on unit tests before adding new one.