Code in this repository aims to expand the functionality of Preseq and make it available in the R statistical computing enviroment. There are five ways this is supposed to work:
The basic functionality of the preseq
program, initially
focusing only on library complexity, is available. These functions
contain the string "rfa" as part of their names.
The mathematical routines for doing rational function approximation via continued fractions were implemented as a wrapper for existing functionality in C++. This changed since version 3.1.1, and now all functionality is in R.
Fitting a zero-truncated negative binomial distribution to the sample is available. These functions include the string "ztnb" as part of the names.
The simulation module is used to generate samples based on mixture of Poisson.
Extra functions are provided to estimate the number of species represented at least r times in a random sample.
See the preseqR package on CRAN for details
We have changed the interfaces for most of our exported functions. We add new estimators for the number of species represented by at least r individuals in a random sample.
We recommand everyone to install the package preseqR
from CRAN.
It can be easily done by in an R session by typing:
>install.packages("preseqR")
The following instructions are for installing the package from the
source. Assume the source code of preseqR
has been pulled from the
git repo and it is under the current directory. Start a session in an
R interpreter and type:
>install.packages("polynom")
>install.packages("preseqR", repos=NULL, type="source")
Note that the package polynom
is required by preseqR
.
Andrew D. Smith andrewds@usc.edu
Copyright (C) 2017-2022 Chao Deng and Andrew D. Smith
Authors: Chao Deng and Andrew D. Smith
This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.