diff --git a/DESCRIPTION b/DESCRIPTION
index 0cf65ef..73d02e2 100644
--- a/DESCRIPTION
+++ b/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 <broman@wisc.edu>
@@ -25,4 +25,5 @@ LazyData: true
 Encoding: UTF-8
 ByteCompile: true
 RoxygenNote: 6.1.1
+Roxygen: list(markdown=TRUE)
 Remotes: rqtl/qtl2
diff --git a/NEWS.md b/NEWS.md
index 1bcd57c..6463183 100644
--- a/NEWS.md
+++ b/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
diff --git a/R/cbind_smother.R b/R/cbind_smother.R
index 672f1a1..2bf7d2d 100644
--- a/R/cbind_smother.R
+++ b/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`.
 #'
diff --git a/R/count_unique_geno.R b/R/count_unique_geno.R
index db83253..fa71c56 100644
--- a/R/count_unique_geno.R
+++ b/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.
diff --git a/R/encode_geno.R b/R/encode_geno.R
index 35a55b9..eb04bc5 100644
--- a/R/encode_geno.R
+++ b/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
diff --git a/R/find_consensus_geno.R b/R/find_consensus_geno.R
index 030256b..c673724 100644
--- a/R/find_consensus_geno.R
+++ b/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.
diff --git a/R/find_unique_geno.R b/R/find_unique_geno.R
index e591409..ad65a0b 100644
--- a/R/find_unique_geno.R
+++ b/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.
diff --git a/R/map_df_to_list.R b/R/map_df_to_list.R
index 84d979e..b475c3b 100644
--- a/R/map_df_to_list.R
+++ b/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.
diff --git a/R/map_list_to_df.R b/R/map_list_to_df.R
index cdd27bd..0e08110 100644
--- a/R/map_list_to_df.R
+++ b/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
diff --git a/R/probs_doqtl_to_qtl2.R b/R/probs_doqtl_to_qtl2.R
index 926ee6b..211bbd8 100644
--- a/R/probs_doqtl_to_qtl2.R
+++ b/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)
 #'
diff --git a/R/probs_qtl2_to_array.R b/R/probs_qtl2_to_array.R
index 7398f05..38389b7 100644
--- a/R/probs_qtl2_to_array.R
+++ b/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()].
 #'
diff --git a/R/probs_qtl2_to_doqtl.R b/R/probs_qtl2_to_doqtl.R
index afbb6ce..21b50a9 100644
--- a/R/probs_qtl2_to_doqtl.R
+++ b/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()].
 #'
diff --git a/R/probs_qtl_to_qtl2.R b/R/probs_qtl_to_qtl2.R
index fcef300..3477f24 100644
--- a/R/probs_qtl_to_qtl2.R
+++ b/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
diff --git a/R/qtl2convert-package.R b/R/qtl2convert-package.R
index 6bde9b5..184845d 100644
--- a/R/qtl2convert-package.R
+++ b/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)
diff --git a/R/scan_qtl2_to_qtl.R b/R/scan_qtl2_to_qtl.R
index 3095f39..e847f63 100644
--- a/R/scan_qtl2_to_qtl.R
+++ b/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).
diff --git a/R/scan_qtl_to_qtl2.R b/R/scan_qtl_to_qtl2.R
index b2cb90a..c988f4f 100644
--- a/R/scan_qtl_to_qtl2.R
+++ b/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()]
diff --git a/R/write2csv.R b/R/write2csv.R
index af465e7..8860a55 100644
--- a/R/write2csv.R
+++ b/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