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Updated documentation (#24)

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Waldir Leoncio 2024-04-08 13:29:03 +02:00
parent 6209bb33fa
commit f676042a17
7 changed files with 24 additions and 9 deletions
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2
DESCRIPTION
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@ -36,7 +36,7 @@ Description: Partial R implementation of the BAPS software
License: GPL-3
BugReports: https://github.com/ocbe-uio/rBAPS/issues
Encoding: UTF-8
RoxygenNote: 7.2.3
RoxygenNote: 7.3.1
Suggests:
testthat (>= 2.1.0)
Imports:

1
NAMESPACE
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@ -38,5 +38,6 @@ importFrom(methods,is)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(vcfR,read.vcfR)
importFrom(zeallot,"%<-%")

4
R/greedyMix.R
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@ -19,8 +19,8 @@
#' with high-throughput sequencing data. <http://www.htslib.org/>
#' @export
#' @examples
#' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
#' greedyMix(data, "fasta")
#' data <- system.file("extdata", "BAPS_format_clustering_diploid.txt", package = "rBAPS")
#' greedyMix(data, "baps")
greedyMix <- function(
data, format = gsub("^.*\\.", "", data), partitionCompare = NULL, npops = 1L,
counts = NULL, sumcounts = NULL, max_iter = 100L, alleleCodes = NULL,

1
R/logml2String.R
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@ -1,7 +1,6 @@
#' @title Logml to string
#' @description Returns a string representation of a logml
#' @param logml input Logml
#' @param
#' @param leading_zeros_replacement string to replace leading zeros with
#' @return String version of logml
logml2String <- function(logml, leading_zeros_replacement = " ") {

4
R/rBAPS-package.R
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@ -1,6 +1,5 @@
#' @title Bayesian Analysis of Population Structure
#' @description This is a partial implementation of the BAPS software
#' @docType package
#' @name rBAPS
#' @note Found a bug? Want to suggest a feature? Contribute to the scientific
#' and open source communities by opening an issue on our home page.
@ -11,4 +10,5 @@
#' @importFrom stats runif
#' @importFrom zeallot %<-%
#' @importFrom matlab2r nargin log2
NULL
#' @importFrom utils read.table
"_PACKAGE"

3
man/greedyMix.Rd
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@ -8,7 +8,6 @@ greedyMix(
data,
format = gsub("^.*\\\\.", "", data),
partitionCompare = NULL,
ninds = 1L,
npops = 1L,
counts = NULL,
sumcounts = NULL,
@ -27,8 +26,6 @@ greedyMix(
\item{partitionCompare}{a list of partitions to compare}
\item{ninds}{number of individuals}
\item{npops}{number of populations}
\item{counts}{counts}

18
man/rBAPS.Rd
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@ -2,6 +2,7 @@
% Please edit documentation in R/rBAPS-package.R
\docType{package}
\name{rBAPS}
\alias{rBAPS-package}
\alias{rBAPS}
\title{Bayesian Analysis of Population Structure}
\description{
@ -12,3 +13,20 @@ Found a bug? Want to suggest a feature? Contribute to the scientific
and open source communities by opening an issue on our home page.
Check the "BugReports" field on the package description for the URL.
}
\seealso{
Useful links:
\itemize{
\item Report bugs at \url{https://github.com/ocbe-uio/rBAPS/issues}
}
}
\author{
\strong{Maintainer}: Waldir Leoncio \email{w.l.netto@medisin.uio.no}
Authors:
\itemize{
\item Jukka Corander \email{jukka.corander@medisin.uio.no}
\item Gerry Tonkin-Hill \email{jukka.corander@medisin.uio.no}
}
}