Rarefaction Tool Kit

Rarefy data, calculate diversity and plot the results.


This R module is a wrapper for the rtk program.

Dependencies

This package depends on the R package RCPP, which enables using Cpp-Code easily in R packages.

How to install

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

Running the package

require("rtk")
# generate semi sparse example data
data            <- matrix(sample(x = c(rep(0, 1500),rep(1:10, 500),1:1000),size = 120, replace = T), 10)
# find the column with the lowest aboundance
samplesize      <- min(colSums(data))
# rarefy the dataset, so each column contains the same number of samples
data.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 man/.

Development

To develop this package it is recommended to install the packages Rcpp and 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.

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("rtk")

0.2.5.7 by Paul Saary, a month ago


Browse source code at https://github.com/cran/rtk


Authors: Paul Saary , Falk Hildebrand


Documentation:   PDF Manual  


GPL (>= 2) license


Imports Rcpp

Suggests testthat

Linking to Rcpp

System requirements: C++11


See at CRAN