Merge pull request #241 from kbroman/cran

Add plot_ci; bump version for CRAN

Author: kbroman

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: qtl2
-Version: 0.39-4
+Version: 0.40
 Date: 2026-05-04
 Title: Quantitative Trait Locus Mapping in Experimental Crosses
 Description: Provides a set of tools to perform quantitative

NEWS.md

@@ -1,4 +1,4 @@
-## qtl2 0.39-4 (2026-05-04)
+## qtl2 0.40 (2026-05-04)
 
 ### New features
 
@@ -7,15 +7,15 @@
 
 ### Minor changes
 
-- In `src/matrix.cpp`, change `Rf_error()` to `Rcpp:stop()`. Issue #239
+- In `src/matrix.cpp`, change `Rf_error()` to `Rcpp:stop()`. (Issue #239)
 
 - Fixed a mistake in the documentation for `est_herit()` and
   `scan1()`. The model we use has covariance matrix
   sigma^2 [h^2 (2K) + (1-h^2)I] where K is the kinship matrix, I is
   the identity matrix, h^2 is the residual heritability, and sigma^2
   is the residual SD.
 
-- Export dim.calc_genoprob and dimnames.calc_genoprob to avoid some
+- Export `dim.calc_genoprob` and `dimnames.calc_genoprob` to avoid some
   warnings.
 
 - Small tweaks to tests of scan1coef with kinship matrix, to avoid

R/fit1.R

@@ -113,7 +113,11 @@
 #' # fit QTL model just at that position
 #' out_fit1 <- fit1(pr_max, pheno, addcovar=covar)
 #'
-#' @seealso [pull_genoprobpos()], [find_marker()]
+#' # plot estimated effects
+#' plot_ci(out_fit1$coef[1:3], out_fit1$SE[1:3],
+#'         xlab="Genotype", ylab="QTL effects")
+#'
+#' @seealso [pull_genoprobpos()], [find_marker()], [plot_ci()]
 #'
 #' @importFrom stats setNames
 #' @export

R/qtl2_grayplot.R R/grayplot.RR/qtl2_grayplot.R renamed to R/grayplot.R

@@ -1,4 +1,4 @@
-#  grayplot
+#  grayplot (internal function taken from github.com/kbroman/broman)
 #
 # Scatterplot with a gray background
 #

R/plot_ci.R

@@ -1,4 +1,4 @@
-#  plot_ci
+#  plot_ci (taken from broman::ciplot)
 #'
 #' Effect plot with multiple CIs for different groups
 #'
@@ -43,7 +43,7 @@
 #' plot_ci(out_fit1$coef[1:3], out_fit1$SE[1:3],
 #'         xlab="Genotype chr 9 @ 56.6 cM", ylab="Spleen phenotype")
 #'
-#' @seealso [plot_coef()], [plot_pxg()]
+#' @seealso [plot_coef()], [plot_pxg()], [fit1()], [pull_genoprobpos()]
 #'
 #' @keywords
 #' graphics