Updated documentation to address CRAN check notes

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: statgenQTLxT
 Type: Package
 Title: Multi-Trait and Multi-Trial Genome Wide Association Studies
-Version: 1.0.0
-Date: 2023-02-22
+Version: 1.0.2
+Date: 2024-01-23
 Authors@R: c(person(given = "Bart-Jan", 
                     family = "van Rossum", 
                     email = "bart-jan.vanrossum@wur.nl", 
@@ -52,7 +52,7 @@ Description: Fast multi-trait and multi-trail Genome Wide Association Studies
     developed by Biometris.
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends: R (>= 3.5)
 Imports: data.table,
     foreach,

NEWS.md

@@ -1,3 +1,11 @@
+# statgenQTLxT 1.0.2
+
+* Improved documentation to address CRAN check notes
+
+# statgenQTLxT 1.0.1
+
+* Minor internal changes to allow for new submission of dependency package sommer
+
 # statgenQTLxT 1.0.0
 
 * Initial CRAN version

R/RcppExports.R

@@ -22,10 +22,10 @@ updateFAHomVar <- function(s, wNew, pNew, m, maxDiag = 1e4) {
 #'
 #' Update W and P used in the iteration process in the EMFA algorithm.
 #'
-#' @param Y An n x p matrix or data.frame.
-#' @param WStart A p x p matrix or data.frame containing starting values for W.
-#' @param m An integer. The order of the model.
-#' @param PStart A p x p matrix or data.frame containing starting values for P.
+#' @param y An n x p matrix or data.frame.
+#' @param wStart A p x p matrix or data.frame containing starting values for W.
+#' @param m0 An integer. The order of the model.
+#' @param pStart A p x p matrix or data.frame containing starting values for P.
 #' @param hetVar Should an extra diagonal part be added in the model for the
 #' precision matrix?
 #' @param maxDiag A numerical value for the maximum value of the diagonal of P.
@@ -174,19 +174,19 @@ LLQuadFormDiagCPP <- function(y, vInv, size_param_x = NULL) {
 #' Compute the estimates and standard errors for the covariates in the input
 #' matrix W.
 #'
-#' @param y An n x p matrix of observed phenotypes, on p traits or environments
+#' @param y0 An n x p matrix of observed phenotypes, on p traits or environments
 #' for n genotypes. No missing values are allowed.
-#' @param w An n x c covariate matrix, c being the number of covariates and n
+#' @param w0 An n x c covariate matrix, c being the number of covariates and n
 #' being the number of genotypes. c has to be at least one (typically an
 #' intercept). No missing values are allowed.
-#' @param x An n x ns matrix of marker scores. Neither missing values nor
+#' @param x0 An n x ns matrix of marker scores. Neither missing values nor
 #' non-segregating markers are allowed.
 #' @param vg A p x p matrix of genetic covariances.
 #' @param ve A p x p matrix of environmental covariances.
 #' @param k An n x n genetic relatedness matrix.
 #' @param returnSe Should standard errors and p-values be returned?
 #' @param estCom Should the common SNP-effect model be fitted?
-#' @param ncores An integer indicating the number of cores used for parallel
+#' @param nCores An integer indicating the number of cores used for parallel
 #' computation.
 #'
 #' @return A list containing the estimates, optionally the standard errors of

R/statgenQTLxT.R

@@ -1,7 +1,5 @@
+#' @useDynLib statgenQTLxT, .registration = TRUE
+#' @importFrom Rcpp sourceCpp
 #' @keywords internal
 "_PACKAGE"
 
-#' @docType package
-#' @useDynLib statgenQTLxT, .registration = TRUE
-#' @importFrom Rcpp sourceCpp
-NULL

cran-comments.md

@@ -1,24 +1,11 @@
-Initial release. Replaced dontrun by donttest after comments on first release attempt.
+Addressed CRAN check notes.
 
 ## Test environments
-* local Windows 10 install, R 4.2.2
+* local Windows 10 install, R 4.3.2
 * winbuilder
 * macbuilder
 * R-hub (devel and release)
 
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
-
-checking CRAN incoming feasibility ... [11s] NOTE
-Maintainer: 'Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>'
-
-New submission
-
-Possibly misspelled words in DESCRIPTION:
-  Biometris (52:18)
-  GWAS (49:6)
-  Zhou (49:46)
-
-* These names and abbreviations are spelled correctly.
-
+0 errors | 0 warnings | 0 notes

src/EMFA.cpp

@@ -55,10 +55,10 @@ void updateFAHomVar(arma::mat s,
 //'
 //' Update W and P used in the iteration process in the EMFA algorithm.
 //'
-//' @param Y An n x p matrix or data.frame.
-//' @param WStart A p x p matrix or data.frame containing starting values for W.
-//' @param m An integer. The order of the model.
-//' @param PStart A p x p matrix or data.frame containing starting values for P.
+//' @param y An n x p matrix or data.frame.
+//' @param wStart A p x p matrix or data.frame containing starting values for W.
+//' @param m0 An integer. The order of the model.
+//' @param pStart A p x p matrix or data.frame containing starting values for P.
 //' @param hetVar Should an extra diagonal part be added in the model for the
 //' precision matrix?
 //' @param maxDiag A numerical value for the maximum value of the diagonal of P.

src/estEffsCPP.cpp

@@ -84,19 +84,19 @@ double LLQuadFormDiagCPP(const arma::mat &y,
 //' Compute the estimates and standard errors for the covariates in the input
 //' matrix W.
 //'
-//' @param y An n x p matrix of observed phenotypes, on p traits or environments
+//' @param y0 An n x p matrix of observed phenotypes, on p traits or environments
 //' for n genotypes. No missing values are allowed.
-//' @param w An n x c covariate matrix, c being the number of covariates and n
+//' @param w0 An n x c covariate matrix, c being the number of covariates and n
 //' being the number of genotypes. c has to be at least one (typically an
 //' intercept). No missing values are allowed.
-//' @param x An n x ns matrix of marker scores. Neither missing values nor
+//' @param x0 An n x ns matrix of marker scores. Neither missing values nor
 //' non-segregating markers are allowed.
 //' @param vg A p x p matrix of genetic covariances.
 //' @param ve A p x p matrix of environmental covariances.
 //' @param k An n x n genetic relatedness matrix.
 //' @param returnSe Should standard errors and p-values be returned?
 //' @param estCom Should the common SNP-effect model be fitted?
-//' @param ncores An integer indicating the number of cores used for parallel
+//' @param nCores An integer indicating the number of cores used for parallel
 //' computation.
 //'
 //' @return A list containing the estimates, optionally the standard errors of