Use markdown for all function documentation

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qtl2convert
-Version: 0.18
-Date: 2019-02-08
+Version: 0.19-1
+Date: 2019-03-10
 Title: Convert Data among R/qtl2, R/qtl, and DOQTL
 Description: Functions to convert data structures among the R/qtl2, R/qtl, and DOQTL packages.
 Author: Karl W Broman <[email protected]>
@@ -25,4 +25,5 @@ LazyData: true
 Encoding: UTF-8
 ByteCompile: true
 RoxygenNote: 6.1.1
+Roxygen: list(markdown=TRUE)
 Remotes: rqtl/qtl2

NEWS.md

@@ -1,3 +1,8 @@
+## qtl2convert 0.19-1 (2019-03-10)
+
+- Use Markdown for function documentation, throughout
+
+
 ## qtl2convert 0.18 (2019-02-08)
 
 - Added `scan_qtl_to_qtl2()` to convert `scanone()` output from R/qtl

R/cbind_smother.R

@@ -5,8 +5,6 @@
 #' the first matrix is deleted and that in the second matrix is used
 #' in its place.
 #'
-#' @md
-#'
 #' @param mat1 A matrix
 #' @param mat2 Another matrix, with the same number of rows as `mat`.
 #'

R/count_unique_geno.R

@@ -4,8 +4,6 @@
 #' For genotype data (markers x individuals) on a set of individuals,
 #' count the unique genotypes for each marker
 #'
-#' @md
-#'
 #' @param genotypes Matrix of genotypes (markers x individuals)
 #' @param na.strings Genotypes to be considered as missing values.
 #' @param cores Number of CPU cores to use, for parallel calculations.

R/encode_geno.R

@@ -3,8 +3,6 @@
 #'
 #' Encode a matrix of genotypes using a set of allele codes.
 #'
-#' @md
-#'
 #' @param geno Character matrix of genotypes (rows as markers, columns as individuals)
 #' @param allele_codes Two-column matrix of alleles (rows as markers)
 #' @param output_codes Vector of length four, with missing, AA, AB, BB codes

R/find_consensus_geno.R

@@ -5,8 +5,6 @@
 #' from a single inbred line, find the consensus genotype at each
 #' marker.
 #'
-#' @md
-#'
 #' @param genotypes Matrix of genotypes (markers x individuals)
 #' @param na.strings Genotypes to be considered as missing values.
 #' @param cores Number of CPU cores to use, for parallel calculations.

R/find_unique_geno.R

@@ -5,8 +5,6 @@
 #' find the unique genotypes for each marker, provided that there are exactly two.
 #' (If more than two or fewer than two, return NAs.)
 #'
-#' @md
-#'
 #' @param genotypes Matrix of genotypes (markers x individuals)
 #' @param na.strings Genotypes to be considered as missing values.
 #' @param cores Number of CPU cores to use, for parallel calculations.

R/map_df_to_list.R

@@ -2,8 +2,6 @@
 #'
 #' Convert a marker map organized as data frame to a list
 #'
-#' @md
-#'
 #' @param map Data frame with marker map
 #'
 #' @param chr_column Name of the column in `map` that contains the chromosome IDs.

R/map_list_to_df.R

@@ -2,8 +2,6 @@
 #'
 #' Convert a marker map organized as a list to a data frame
 #'
-#' @md
-#'
 #' @param map_list List of vectors containing marker positions
 #'
 #' @param chr_column Name of the chromosome column in the output

R/probs_doqtl_to_qtl2.R

@@ -2,8 +2,6 @@
 #'
 #' Convert DOQTL genotype probabilities to R/qtl2 format
 #'
-#' @md
-#'
 #' @param probs 3d array of genotype probabilities as calculated from DOQTL
 #' (individuals x genotypes x positions)
 #'

R/probs_qtl2_to_array.R

@@ -2,8 +2,6 @@
 #'
 #' Convert R/qtl2 genotype probabilities to a 3d array
 #'
-#' @md
-#'
 #' @param probs A `"calc_genoprob"` object (a list of 3d arrays of
 #' genotype probabilities), as calculated by [qtl2::calc_genoprob()].
 #'

R/probs_qtl2_to_doqtl.R

@@ -2,8 +2,6 @@
 #'
 #' Convert R/qtl2 genotype probabilities to DOQTL format
 #'
-#' @md
-#'
 #' @param probs A `"calc_genoprob"` object (a list of 3d arrays of
 #' genotype probabilities), as calculated by [qtl2::calc_genoprob()].
 #'

R/probs_qtl_to_qtl2.R

@@ -2,8 +2,6 @@
 #'
 #' Convert R/qtl genotype probabilities to R/qtl2 format
 #'
-#' @md
-#'
 #' @param cross An R/qtl `"cross"` object (see
 #'     [qtl::read.cross()] for details.) Must contain
 #'     genotype probabilities as calculated by

R/qtl2convert-package.R

@@ -2,8 +2,6 @@
 #' @importFrom Rcpp sourceCpp
 #' @useDynLib qtl2convert, .registration=TRUE
 #'
-#' @md
-#'
 #' @section Vignettes:
 #' * [user guide](http://kbroman.org/qtl2/assets/vignettes/user_guide.html)
 #' * [input file formats](http://kbroman.org/qtl2/assets/vignettes/input_files.html)

R/scan_qtl2_to_qtl.R

@@ -6,8 +6,6 @@
 #' to the form used by the R/qtl function
 #' [qtl::scanone()].
 #'
-#' @md
-#'
 #' @param scan1_output Matrix of LOD scores, as calculated by
 #' [qtl2::scan1()].
 #' @param map Map of markers/pseudomarkers (as a list of vectors).

R/scan_qtl_to_qtl2.R

@@ -2,8 +2,6 @@
 #'
 #' Convert the results of R/qtl1 [qtl::scanone()] to the form used by the R/qtl2 [qtl2::scan1()].
 #'
-#' @md
-#'
 #' @param scanone_output Data frame as output by the R/qtl1 function [qtl::scanone()].
 #'
 #' @return List with two objects: the LOD scores in [qtl2::scan1()]

R/write2csv.R

@@ -3,8 +3,6 @@
 #'
 #' Write a data frame to a CSV file in a special form, with info about the number of rows and columns.
 #'
-#' @md
-#'
 #' @param df A data frame (or matrix)
 #' @param filename File name to write
 #' @param comment Comment to place on the first line