From 12dbeda97d793c74ee0723fc9ac63a023b2327e2 Mon Sep 17 00:00:00 2001
From: Marcelo Mollinari <mmollina@gmail.com>
Date: Tue, 13 Feb 2024 09:32:05 -0500
Subject: [PATCH] updating documentation

---
 R/make_seq.R            | 14 +++++++-------
 man/make_seq_mappoly.Rd | 14 +++++++-------
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/R/make_seq.R b/R/make_seq.R
index 0357a1e8..2743065e 100755
--- a/R/make_seq.R
+++ b/R/make_seq.R
@@ -28,14 +28,14 @@
 #'
 #' @param ... Currently ignored.
 #'
-#' @return Returns an object of class \code{mappoly.sequence}, comprising:
+#' @return Returns an object of class `mappoly.sequence`, comprising:
 #' \itemize{
-#'   \item{seq.num}{Ordered vector of marker indices according to the input.}
-#'   \item{seq.phases}{List of linkage phases between markers; \code{-1} for undefined phases.}
-#'   \item{seq.rf}{Vector of recombination frequencies; \code{-1} for not estimated frequencies.}
-#'   \item{loglike}{Log-likelihood of the linkage map.}
-#'   \item{data.name}{Name of the \code{mappoly.data} object with raw data.}
-#'   \item{twopt}{Name of the \code{mappoly.twopt} object with 2-point analyses; \code{-1} if not computed.}
+#'   \item{"seq.num"}{Ordered vector of marker indices according to the input.}
+#'   \item{"seq.phases"}{List of linkage phases between markers; -1 for undefined phases.}
+#'   \item{"seq.rf"}{Vector of recombination frequencies; -1 for not estimated frequencies.}
+#'   \item{"loglike"}{Log-likelihood of the linkage map.}
+#'   \item{"data.name"}{Name of the `mappoly.data` object with raw data.}
+#'   \item{"twopt"}{Name of the `mappoly.twopt` object with 2-point analyses; -1 if not computed.}
 #' }
 #'
 #' @examples
diff --git a/man/make_seq_mappoly.Rd b/man/make_seq_mappoly.Rd
index 68003ef3..42d9a3ea 100644
--- a/man/make_seq_mappoly.Rd
+++ b/man/make_seq_mappoly.Rd
@@ -45,14 +45,14 @@ maximum number of markers with the group. Supports single values or vectors for
 \item{...}{Currently ignored.}
 }
 \value{
-Returns an object of class \code{mappoly.sequence}, comprising:
+Returns an object of class `mappoly.sequence`, comprising:
 \itemize{
-  \item{seq.num}{Ordered vector of marker indices according to the input.}
-  \item{seq.phases}{List of linkage phases between markers; \code{-1} for undefined phases.}
-  \item{seq.rf}{Vector of recombination frequencies; \code{-1} for not estimated frequencies.}
-  \item{loglike}{Log-likelihood of the linkage map.}
-  \item{data.name}{Name of the \code{mappoly.data} object with raw data.}
-  \item{twopt}{Name of the \code{mappoly.twopt} object with 2-point analyses; \code{-1} if not computed.}
+  \item{"seq.num"}{Ordered vector of marker indices according to the input.}
+  \item{"seq.phases"}{List of linkage phases between markers; -1 for undefined phases.}
+  \item{"seq.rf"}{Vector of recombination frequencies; -1 for not estimated frequencies.}
+  \item{"loglike"}{Log-likelihood of the linkage map.}
+  \item{"data.name"}{Name of the `mappoly.data` object with raw data.}
+  \item{"twopt"}{Name of the `mappoly.twopt` object with 2-point analyses; -1 if not computed.}
 }
 }
 \description{