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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 License: GPL-3
BugReports: https://github.com/ocbe-uio/rBAPS/issues BugReports: https://github.com/ocbe-uio/rBAPS/issues
Encoding: UTF-8 Encoding: UTF-8
RoxygenNote: 7.2.3 RoxygenNote: 7.3.1
Suggests: Suggests:
testthat (>= 2.1.0) testthat (>= 2.1.0)
Imports: Imports:

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

4
R/greedyMix.R
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@ -19,8 +19,8 @@
#' with high-throughput sequencing data. <http://www.htslib.org/> #' with high-throughput sequencing data. <http://www.htslib.org/>
#' @export #' @export
#' @examples #' @examples
#' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS") #' data <- system.file("extdata", "BAPS_format_clustering_diploid.txt", package = "rBAPS")
#' greedyMix(data, "fasta") #' greedyMix(data, "baps")
greedyMix <- function( greedyMix <- function(
data, format = gsub("^.*\\.", "", data), partitionCompare = NULL, npops = 1L, data, format = gsub("^.*\\.", "", data), partitionCompare = NULL, npops = 1L,
counts = NULL, sumcounts = NULL, max_iter = 100L, alleleCodes = NULL, 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 #' @title Logml to string
#' @description Returns a string representation of a logml #' @description Returns a string representation of a logml
#' @param logml input Logml #' @param logml input Logml
#' @param
#' @param leading_zeros_replacement string to replace leading zeros with #' @param leading_zeros_replacement string to replace leading zeros with
#' @return String version of logml #' @return String version of logml
logml2String <- function(logml, leading_zeros_replacement = " ") { 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 #' @title Bayesian Analysis of Population Structure
#' @description This is a partial implementation of the BAPS software #' @description This is a partial implementation of the BAPS software
#' @docType package
#' @name rBAPS #' @name rBAPS
#' @note Found a bug? Want to suggest a feature? Contribute to the scientific #' @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. #' and open source communities by opening an issue on our home page.
@ -11,4 +10,5 @@
#' @importFrom stats runif #' @importFrom stats runif
#' @importFrom zeallot %<-% #' @importFrom zeallot %<-%
#' @importFrom matlab2r nargin log2 #' @importFrom matlab2r nargin log2
NULL #' @importFrom utils read.table
"_PACKAGE"

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

18
man/rBAPS.Rd
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@ -2,6 +2,7 @@
% Please edit documentation in R/rBAPS-package.R % Please edit documentation in R/rBAPS-package.R
\docType{package} \docType{package}
\name{rBAPS} \name{rBAPS}
\alias{rBAPS-package}
\alias{rBAPS} \alias{rBAPS}
\title{Bayesian Analysis of Population Structure} \title{Bayesian Analysis of Population Structure}
\description{ \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. and open source communities by opening an issue on our home page.
Check the "BugReports" field on the package description for the URL. 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}
}
}