diff --git a/stuart/.Rhistory b/stuart/.Rhistory
index 2d33e644c30342b0c912ad1f1b9377543a78a7c7..9efc66b96a38d11ea414aae6e0f311e8792b738c 100755
--- a/stuart/.Rhistory
+++ b/stuart/.Rhistory
@@ -146,3 +146,11 @@ strains <- geno_strains(ref=annot_mini,geno=genos,par1=c("StrainsA_1","StrainsA_
 head(strains)
 genos <- genos %>% filter(!Sample.ID %in% c("StrainsA_1", "StrainsA_2", "StrainsB_1","StrainsB_2"))
 data(stuart_tab)
+devtools::build(vignettes=TRUE)
+devtools::install(build_vignettes=TRUE)
+browseVignettes(stuart)
+browseVignettes("stuart")
+use_readme_rmd()
+usethis::use_readme_rmd()
+build_readme()
+devtools::build_readme()
diff --git a/stuart/R/.DS_Store b/stuart/R/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/stuart/R/.DS_Store differ
diff --git a/stuart/R/annot_giga-data.R b/stuart/R/annot_giga-data.R
deleted file mode 100755
index 35dc35fb2343dfc7167d990f0c616661c61f2e83..0000000000000000000000000000000000000000
--- a/stuart/R/annot_giga-data.R
+++ /dev/null
@@ -1,18 +0,0 @@
-#' Data frame with gigaMUGA markers annotation
-#'
-#' A dataset containing gigaMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/new_annotations.html).
-#'
-#' @format A data frame with 143259 rows and 8 variables
-#' \describe{
-#'   \item{marker}{name of the marker}
-#'   \item{chr}{chromosome}
-#'   \item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
-#'   \item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
-#'   \item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
-#'   \item{snp}{marker alleles}
-#'   \item{unique}{indicates if the marker maps uniquely on mm10}
-#'   \item{unmapped}{indicates if the marker does not map perfectly on mm10}
-#' }
-
-
-"annot_giga"
diff --git a/stuart/R/annot_mega-data.R b/stuart/R/annot_mega-data.R
deleted file mode 100755
index f2996f8b10536149df2446c97f89766227e876f4..0000000000000000000000000000000000000000
--- a/stuart/R/annot_mega-data.R
+++ /dev/null
@@ -1,18 +0,0 @@
-#' Data frame with megaMUGA markers annotation
-#'
-#' A dataset containing megaMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/new_annotations.html).
-#'
-#' @format A data frame with 77808 rows and 8 variables
-#' \describe{
-#'   \item{marker}{name of the marker}
-#'   \item{chr}{chromosome}
-#'   \item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
-#'   \item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
-#'   \item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
-#'   \item{snp}{marker alleles}
-#'   \item{unique}{indicates if the marker maps uniquely on mm10}
-#'   \item{unmapped}{indicates if the marker does not map perfectly on mm10}
-#' }
-
-
-"annot_mega"
diff --git a/stuart/R/annot_mini-data.R b/stuart/R/annot_mini-data.R
deleted file mode 100755
index a0bc7917001a951b955da3bba16229f0cb253517..0000000000000000000000000000000000000000
--- a/stuart/R/annot_mini-data.R
+++ /dev/null
@@ -1,18 +0,0 @@
-#' Data frame with miniMUGA markers annotation
-#'
-#' A dataset containing miniMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/mini_revisited.html).
-#'
-#' @format A data frame with 11125 rows and 8 variables
-#' \describe{
-#'   \item{marker}{name of the marker}
-#'   \item{chr}{chromosome}
-#'   \item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
-#'   \item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
-#'   \item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
-#'   \item{snp}{marker alleles}
-#'   \item{unique}{indicates if the marker maps uniquely on mm10}
-#'   \item{unmapped}{indicates if the marker does not map perfectly on mm10}
-#' }
-
-
-"annot_mini"
diff --git a/stuart/R/annot_muga-data.R b/stuart/R/annot_muga-data.R
deleted file mode 100755
index e7061267231d1edfb0cf65a47994927adab2c84e..0000000000000000000000000000000000000000
--- a/stuart/R/annot_muga-data.R
+++ /dev/null
@@ -1,18 +0,0 @@
-#' Data frame with MUGA markers annotation
-#'
-#' A dataset containing MUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/muga_annotations.html).
-#'
-#' @format A data frame with 7854 rows and 8 variables
-#' \describe{
-#'   \item{marker}{name of the marker}
-#'   \item{chr}{chromosome}
-#'   \item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
-#'   \item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
-#'   \item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
-#'   \item{snp}{marker alleles}
-#'   \item{unique}{indicates if the marker maps uniquely on mm10}
-#'   \item{unmapped}{indicates if the marker does not map perfectly on mm10}
-#' }
-
-
-"annot_muga"
diff --git a/stuart/R/stuart_tab.R b/stuart/R/stuart_tab-data.R
similarity index 100%
rename from stuart/R/stuart_tab.R
rename to stuart/R/stuart_tab-data.R
diff --git a/stuart/data/.DS_Store b/stuart/data/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/stuart/data/.DS_Store differ
diff --git a/stuart/man/.DS_Store b/stuart/man/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/stuart/man/.DS_Store differ
diff --git a/stuart/man/annot_giga.Rd b/stuart/man/annot_giga.Rd
deleted file mode 100755
index 3494c3cb7d330711ac659415f698537d77fc8d47..0000000000000000000000000000000000000000
--- a/stuart/man/annot_giga.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/annot_giga-data.R
-\docType{data}
-\name{annot_giga}
-\alias{annot_giga}
-\title{Data frame with gigaMUGA markers annotation}
-\format{
-A data frame with 143259 rows and 8 variables
-\describe{
-\item{marker}{name of the marker}
-\item{chr}{chromosome}
-\item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
-\item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
-\item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
-\item{snp}{marker alleles}
-\item{unique}{indicates if the marker maps uniquely on mm10}
-\item{unmapped}{indicates if the marker does not map perfectly on mm10}
-}
-}
-\usage{
-annot_giga
-}
-\description{
-A dataset containing gigaMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/new_annotations.html).
-}
-\keyword{datasets}
diff --git a/stuart/man/annot_mega.Rd b/stuart/man/annot_mega.Rd
deleted file mode 100755
index 7f822f1a23f490d987ff55d1036e0461fdf8d468..0000000000000000000000000000000000000000
--- a/stuart/man/annot_mega.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/annot_mega-data.R
-\docType{data}
-\name{annot_mega}
-\alias{annot_mega}
-\title{Data frame with megaMUGA markers annotation}
-\format{
-A data frame with 77808 rows and 8 variables
-\describe{
-\item{marker}{name of the marker}
-\item{chr}{chromosome}
-\item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
-\item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
-\item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
-\item{snp}{marker alleles}
-\item{unique}{indicates if the marker maps uniquely on mm10}
-\item{unmapped}{indicates if the marker does not map perfectly on mm10}
-}
-}
-\usage{
-annot_mega
-}
-\description{
-A dataset containing megaMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/new_annotations.html).
-}
-\keyword{datasets}
diff --git a/stuart/man/annot_mini.Rd b/stuart/man/annot_mini.Rd
deleted file mode 100755
index 298bbd5b3dd508f11a764adb14741bb77fc8beef..0000000000000000000000000000000000000000
--- a/stuart/man/annot_mini.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/annot_mini-data.R
-\docType{data}
-\name{annot_mini}
-\alias{annot_mini}
-\title{Data frame with miniMUGA markers annotation}
-\format{
-A data frame with 11125 rows and 8 variables
-\describe{
-\item{marker}{name of the marker}
-\item{chr}{chromosome}
-\item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
-\item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
-\item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
-\item{snp}{marker alleles}
-\item{unique}{indicates if the marker maps uniquely on mm10}
-\item{unmapped}{indicates if the marker does not map perfectly on mm10}
-}
-}
-\usage{
-annot_mini
-}
-\description{
-A dataset containing miniMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/mini_revisited.html).
-}
-\keyword{datasets}
diff --git a/stuart/man/annot_muga.Rd b/stuart/man/annot_muga.Rd
deleted file mode 100755
index 718693531c480c358bd15629b6b2d5872db85cf3..0000000000000000000000000000000000000000
--- a/stuart/man/annot_muga.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/annot_muga-data.R
-\docType{data}
-\name{annot_muga}
-\alias{annot_muga}
-\title{Data frame with MUGA markers annotation}
-\format{
-A data frame with 7854 rows and 8 variables
-\describe{
-\item{marker}{name of the marker}
-\item{chr}{chromosome}
-\item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
-\item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
-\item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
-\item{snp}{marker alleles}
-\item{unique}{indicates if the marker maps uniquely on mm10}
-\item{unmapped}{indicates if the marker does not map perfectly on mm10}
-}
-}
-\usage{
-annot_muga
-}
-\description{
-A dataset containing MUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/muga_annotations.html).
-}
-\keyword{datasets}
diff --git a/stuart/man/stuart_tab.Rd b/stuart/man/stuart_tab.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..ebe357ac22fecfe7fca149db36df30412e4d55ea
--- /dev/null
+++ b/stuart/man/stuart_tab.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stuart_tab-data.R
+\docType{data}
+\name{stuart_tab}
+\alias{stuart_tab}
+\title{Output of tab_mark function}
+\format{
+A data frame with 11125 rows and 7 variables
+\describe{
+\item{SNP.Name}{name of the marker}
+\item{Allele_1}{first allele of the marker}
+\item{Allele_2}{second allele of the marker}
+\item{n_HM1}{number of homozygous individuals for the first allele}
+\item{n_HM2}{number of homozygous individuals for the second allele}
+\item{n_HT}{number of heterozygous individuals}
+\item{n_NA}{number of non genotyped individuals}
+}
+}
+\usage{
+stuart_tab
+}
+\description{
+A dataset with the output of tab_mark() function.
+}
+\keyword{datasets}
diff --git a/stuart_0.1.0.tar.gz b/stuart_0.1.0.tar.gz
index 8a516856bcf3878b16a13cec9af28e7d5ff8fc66..a534a922312f02c2196b9b0bdd6cba09a0019b3c 100644
Binary files a/stuart_0.1.0.tar.gz and b/stuart_0.1.0.tar.gz differ