From eeb6f6dc6e875804cfbd5140fd17ecdf580449aa Mon Sep 17 00:00:00 2001 From: Karl Broman Date: Sun, 10 Mar 2019 13:28:41 -0500 Subject: [PATCH] url and href to markdown --- R/calc_errorlod.R | 2 +- R/calc_genoprob.R | 2 +- R/predict_snpgeno.R | 2 +- R/read_cross2.R | 10 ++++------ R/read_pheno.R | 4 ++-- R/write_control_file.R | 8 +++----- R/zip_datafiles.R | 2 +- man/read_cross2.Rd | 6 ++---- man/write_control_file.Rd | 6 ++---- 9 files changed, 17 insertions(+), 25 deletions(-) diff --git a/R/calc_errorlod.R b/R/calc_errorlod.R index 1f655824..41999e80 100644 --- a/R/calc_errorlod.R +++ b/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. diff --git a/R/calc_genoprob.R b/R/calc_genoprob.R index 8165706f..78b88c05 100644 --- a/R/calc_genoprob.R +++ b/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. diff --git a/R/predict_snpgeno.R b/R/predict_snpgeno.R index 91f7fdb4..4ea7c0f1 100644 --- a/R/predict_snpgeno.R +++ b/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()].) diff --git a/R/read_cross2.R b/R/read_cross2.R index f6dd70ef..952f3ee3 100644 --- a/R/read_cross2.R +++ b/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 +#' and #' #' @examples #' \dontrun{ diff --git a/R/read_pheno.R b/R/read_pheno.R index 23cba9a7..f4443a35 100644 --- a/R/read_pheno.R +++ b/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 +#' and #' #' @examples #' \dontrun{ diff --git a/R/write_control_file.R b/R/write_control_file.R index 30effcf3..259280fc 100644 --- a/R/write_control_file.R +++ b/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} +#' #' @examples #' \dontrun{ #' # Control file for the sample dataset, grav2 diff --git a/R/zip_datafiles.R b/R/zip_datafiles.R index 4c479f3d..d2307ef3 100644 --- a/R/zip_datafiles.R +++ b/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 #' @examples #' \dontrun{ #' control_file <- "~/grav2_data/grav2.yaml" diff --git a/man/read_cross2.Rd b/man/read_cross2.Rd index 78d355cc..370d1cc2 100644 --- a/man/read_cross2.Rd +++ b/man/read_cross2.Rd @@ -27,10 +27,8 @@ A control file in \href{http://www.yaml.org}{YAML} or \href{http://www.json.org/}{JSON} 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}. +\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}. } \examples{ \dontrun{ diff --git a/man/write_control_file.Rd b/man/write_control_file.Rd index 7a833c40..e5e576e1 100644 --- a/man/write_control_file.Rd +++ b/man/write_control_file.Rd @@ -115,10 +115,8 @@ This function takes a set of parameters and creates the control file (in \href{http://www.yaml.org}{YAML} format) needed for the new input data file format for \href{https://kbroman.org/qtl2}{R/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}. +\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}. } \examples{ \dontrun{