url and href to markdown

R/calc_errorlod.R

@@ -7,7 +7,7 @@
 #' markers and/or individuals).
 #'
 #' @param cross Object of class `"cross2"`. For details, see the
-#' \href{https://kbroman.org/qtl2/assets/vignettes/developer_guide.html}{R/qtl2 developer guide}.
+#' [R/qtl2 developer guide](https://kbroman.org/qtl2/assets/vignettes/developer_guide.html).
 #' @param probs Genotype probabilities as calculated from [calc_genoprob()].
 #' @param quiet If `FALSE`, print progress messages.
 #' @param cores Number of CPU cores to use, for parallel calculations.

R/calc_genoprob.R

@@ -6,7 +6,7 @@
 #' data, with possible allowance for genotyping errors.
 #'
 #' @param cross Object of class `"cross2"`. For details, see the
-#' \href{https://kbroman.org/qtl2/assets/vignettes/developer_guide.html}{R/qtl2 developer guide}.
+#' [R/qtl2 developer guide](https://kbroman.org/qtl2/assets/vignettes/developer_guide.html).
 #' @param map Genetic map of markers. May include pseudomarker
 #' locations (that is, locations that are not within the marker
 #' genotype data). If NULL, the genetic map in `cross` is used.

R/predict_snpgeno.R

@@ -3,7 +3,7 @@
 #' Predict SNP genotypes in a multiparent population from inferred genotypes plus founder strains' SNP alleles.
 #'
 #' @param cross Object of class `"cross2"`. For details, see the
-#' \href{https://kbroman.org/qtl2/assets/vignettes/developer_guide.html}{R/qtl2 developer guide}.
+#' [R/qtl2 developer guide](https://kbroman.org/qtl2/assets/vignettes/developer_guide.html).
 #' @param geno Imputed genotypes, as a list of matrices, as from [maxmarg()].
 #' @param cores Number of CPU cores to use, for parallel calculations.
 #' (If `0`, use [parallel::detectCores()].)

R/read_cross2.R

@@ -18,16 +18,14 @@
 #' [JSON](http://www.json.org/) format contains information
 #' about basic parameters as well as the names of the series of
 #' data files to be read. See the
-#' \href{https://kbroman.org/qtl2/pages/sampledata.html}{sample
-#' data files} and the
-#' \href{https://kbroman.org/qtl2/assets/vignettes/input_files.html}{vignette
-#' describing the input file format}.
+#' [sample data files](https://kbroman.org/qtl2/pages/sampledata.html) and the
+#' [vignette describing the input file format](https://kbroman.org/qtl2/assets/vignettes/input_files.html).
 #'
 #' @export
 #' @keywords IO
 #' @seealso [read_pheno()], [write_control_file()],
-#' sample data files at \url{https://kbroman.org/qtl2/pages/sampledata.html}
-#' and \url{https://github.com/rqtl/qtl2data}
+#' sample data files at <https://kbroman.org/qtl2/pages/sampledata.html>
+#' and <https://github.com/rqtl/qtl2data>
 #'
 #' @examples
 #' \dontrun{

R/read_pheno.R

@@ -30,8 +30,8 @@
 #' @export
 #' @keywords IO
 #' @seealso [read_cross2()],
-#' sample data files at \url{https://kbroman.org/qtl2/pages/sampledata.html}
-#' and \url{https://github.com/rqtl/qtl2data}
+#' sample data files at <https://kbroman.org/qtl2/pages/sampledata.html>
+#' and <https://github.com/rqtl/qtl2data>
 #'
 #' @examples
 #' \dontrun{

R/write_control_file.R

@@ -69,15 +69,13 @@
 #' control file (in [YAML](http://www.yaml.org) format) needed
 #' for the new input data file format for
 #' [R/qtl2](https://kbroman.org/qtl2).  See the
-#' \href{https://kbroman.org/qtl2/pages/sampledata.html}{sample data
-#' files} and the
-#' \href{https://kbroman.org/qtl2/assets/vignettes/input_files.html}{vignette
-#' describing the input file format}.
+#' [sample data files](https://kbroman.org/qtl2/pages/sampledata.html) and the
+#' [vignette describing the input file format](https://kbroman.org/qtl2/assets/vignettes/input_files.html).
 #'
 #' @export
 #' @keywords utilities
 #' @seealso [read_cross2()], sample data files at
-#' \url{https://kbroman.org/qtl2/pages/sampledata.html}
+#' <https://kbroman.org/qtl2/pages/sampledata.html>
 #' @examples
 #' \dontrun{
 #' # Control file for the sample dataset, grav2

R/zip_datafiles.R

@@ -30,7 +30,7 @@
 #'
 #' @export
 #' @keywords IO
-#' @seealso [read_cross2()], sample data files at \url{https://kbroman.org/qtl2/pages/sampledata.html}
+#' @seealso [read_cross2()], sample data files at <https://kbroman.org/qtl2/pages/sampledata.html>
 #' @examples
 #' \dontrun{
 #' control_file <- "~/grav2_data/grav2.yaml"