From a61ea0e868f585e69c85da363e5ea8c4651ac0c9 Mon Sep 17 00:00:00 2001 From: Bart-Jan van Rossum Date: Tue, 17 Sep 2024 16:21:58 +0200 Subject: [PATCH] Fixed links to statgenSTA in documentation --- DESCRIPTION | 2 +- R/createFW.R | 4 ++-- R/gxeAmmi.R | 2 +- man/FW.Rd | 4 ++-- man/gxeAmmi.Rd | 2 +- man/gxeFw.Rd | 2 +- man/gxeGGE.Rd | 2 +- man/gxeMegaEnv.Rd | 2 +- man/gxeStability.Rd | 2 +- man/gxeVarComp.Rd | 2 +- man/gxeVarCov.Rd | 2 +- man/statgenGxE-package.Rd | 2 +- 12 files changed, 14 insertions(+), 14 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5f7a142d..ee540218 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -54,7 +54,7 @@ Description: Analysis of multi environment data of plant breeding experiments typical plant breeding experiments developed by Biometris. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon - purchase from 'VSN' international (). + purchase from 'VSN' international (). License: GPL Encoding: UTF-8 LazyData: true diff --git a/R/createFW.R b/R/createFW.R index 3bb49beb..ded088f1 100644 --- a/R/createFW.R +++ b/R/createFW.R @@ -7,8 +7,8 @@ #' @param estimates A data.frame containing the estimated values. #' @param anova A data.frame containing anova scores of the FW analysis. #' @param envEffs A data.frame containing the environmental effects. -#' @param TD The object of class \code{\link{TD}} on which the analysis was -#' performed. +#' @param TD The object of class \code{\link[statgenSTA]{TD}} on which the +#' analysis was performed. #' @param fittedGeno The fitted values for the genotypes. #' @param trait A character value indicating the analysed trait. #' @param nGeno A numerical value containing the number of genotypes in the diff --git a/R/gxeAmmi.R b/R/gxeAmmi.R index b3fbdb5b..6f883872 100644 --- a/R/gxeAmmi.R +++ b/R/gxeAmmi.R @@ -29,7 +29,7 @@ #' added component is significant in the analysis.\cr #' AMMI estimates are then computed using the results of the PCA.\cr #' -#' @param TD An object of class \code{\link{TD}}. +#' @param TD An object of class \code{\link[statgenSTA]{TD}}. #' @param trials A character string specifying the trials to be analyzed. If #' not supplied, all trials are used in the analysis. #' @param trait A character string specifying the trait to be analyzed. diff --git a/man/FW.Rd b/man/FW.Rd index 63cece8d..c7c4e8cc 100644 --- a/man/FW.Rd +++ b/man/FW.Rd @@ -33,8 +33,8 @@ analysis.} \item{nEnv}{A numerical value containing the number of environments in the analysis.} -\item{TD}{The object of class \code{\link{TD}} on which the analysis was -performed.} +\item{TD}{The object of class \code{\link[statgenSTA]{TD}} on which the +analysis was performed.} \item{fittedGeno}{The fitted values for the genotypes.} diff --git a/man/gxeAmmi.Rd b/man/gxeAmmi.Rd index 441b6762..a5e9b004 100644 --- a/man/gxeAmmi.Rd +++ b/man/gxeAmmi.Rd @@ -16,7 +16,7 @@ gxeAmmi( ) } \arguments{ -\item{TD}{An object of class \code{\link{TD}}.} +\item{TD}{An object of class \code{\link[statgenSTA]{TD}}.} \item{trials}{A character string specifying the trials to be analyzed. If not supplied, all trials are used in the analysis.} diff --git a/man/gxeFw.Rd b/man/gxeFw.Rd index 173d9e53..08285a5f 100644 --- a/man/gxeFw.Rd +++ b/man/gxeFw.Rd @@ -16,7 +16,7 @@ gxeFw( ) } \arguments{ -\item{TD}{An object of class \code{\link{TD}}.} +\item{TD}{An object of class \code{\link[statgenSTA]{TD}}.} \item{trials}{A character string specifying the trials to be analyzed. If not supplied, all trials are used in the analysis.} diff --git a/man/gxeGGE.Rd b/man/gxeGGE.Rd index 80761a14..7b2b05ae 100644 --- a/man/gxeGGE.Rd +++ b/man/gxeGGE.Rd @@ -16,7 +16,7 @@ gxeGGE( ) } \arguments{ -\item{TD}{An object of class \code{\link{TD}}.} +\item{TD}{An object of class \code{\link[statgenSTA]{TD}}.} \item{trials}{A character string specifying the trials to be analyzed. If not supplied, all trials are used in the analysis.} diff --git a/man/gxeMegaEnv.Rd b/man/gxeMegaEnv.Rd index 3c9ab1bc..177f2127 100644 --- a/man/gxeMegaEnv.Rd +++ b/man/gxeMegaEnv.Rd @@ -13,7 +13,7 @@ gxeMegaEnv( ) } \arguments{ -\item{TD}{An object of class \code{\link{TD}}.} +\item{TD}{An object of class \code{\link[statgenSTA]{TD}}.} \item{trials}{A character string specifying the trials to be analyzed. If not supplied, all trials are used in the analysis.} diff --git a/man/gxeStability.Rd b/man/gxeStability.Rd index e3fa4fa0..28eabf4e 100644 --- a/man/gxeStability.Rd +++ b/man/gxeStability.Rd @@ -14,7 +14,7 @@ gxeStability( ) } \arguments{ -\item{TD}{An object of class \code{\link{TD}}.} +\item{TD}{An object of class \code{\link[statgenSTA]{TD}}.} \item{trials}{A character string specifying the trials to be analyzed. If not supplied, all trials are used in the analysis.} diff --git a/man/gxeVarComp.Rd b/man/gxeVarComp.Rd index bccea435..8f3eb699 100644 --- a/man/gxeVarComp.Rd +++ b/man/gxeVarComp.Rd @@ -17,7 +17,7 @@ gxeVarComp( ) } \arguments{ -\item{TD}{An object of class \code{\link{TD}}.} +\item{TD}{An object of class \code{\link[statgenSTA]{TD}}.} \item{trials}{A character string specifying the trials to be analyzed. If not supplied, all trials are used in the analysis.} diff --git a/man/gxeVarCov.Rd b/man/gxeVarCov.Rd index a767c150..4d070977 100644 --- a/man/gxeVarCov.Rd +++ b/man/gxeVarCov.Rd @@ -15,7 +15,7 @@ gxeVarCov( ) } \arguments{ -\item{TD}{An object of class \code{\link{TD}}.} +\item{TD}{An object of class \code{\link[statgenSTA]{TD}}.} \item{trials}{A character string specifying the trials to be analyzed. If not supplied, all trials are used in the analysis.} diff --git a/man/statgenGxE-package.Rd b/man/statgenGxE-package.Rd index 9fac14a8..5de7b235 100644 --- a/man/statgenGxE-package.Rd +++ b/man/statgenGxE-package.Rd @@ -6,7 +6,7 @@ \alias{statgenGxE-package} \title{statgenGxE: Genotype by Environment (GxE) Analysis} \description{ -Analysis of multi environment data of plant breeding experiments following the analyses described in Malosetti, Ribaut, and van Eeuwijk (2013), \doi{10.3389/fphys.2013.00044}. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (\url{https://vsni.co.uk/software/asreml-r}). +Analysis of multi environment data of plant breeding experiments following the analyses described in Malosetti, Ribaut, and van Eeuwijk (2013), \doi{10.3389/fphys.2013.00044}. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (\url{https://vsni.co.uk/software/asreml-r/}). } \seealso{ Useful links: