diff --git a/DESCRIPTION b/DESCRIPTION index 4a28dcf..f889315 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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: diff --git a/NAMESPACE b/NAMESPACE index a0b3bf9..09db974 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -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,"%<-%") diff --git a/R/greedyMix.R b/R/greedyMix.R index 38aeb8f..5df5606 100644 --- a/R/greedyMix.R +++ b/R/greedyMix.R @@ -19,8 +19,8 @@ #' with high-throughput sequencing data. #' @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, diff --git a/R/logml2String.R b/R/logml2String.R index 09ef88b..784812a 100644 --- a/R/logml2String.R +++ b/R/logml2String.R @@ -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 = " ") { diff --git a/R/rBAPS-package.R b/R/rBAPS-package.R index 810a2f1..c58245a 100644 --- a/R/rBAPS-package.R +++ b/R/rBAPS-package.R @@ -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" diff --git a/man/greedyMix.Rd b/man/greedyMix.Rd index e10fa87..db888d1 100644 --- a/man/greedyMix.Rd +++ b/man/greedyMix.Rd @@ -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} diff --git a/man/rBAPS.Rd b/man/rBAPS.Rd index cd92bd6..89040f3 100644 --- a/man/rBAPS.Rd +++ b/man/rBAPS.Rd @@ -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} +} + +}