add modif to do

.Rproj.user/9DAE6990/pcs/source-pane.pper

 {
-    "activeTab" : 0
+    "activeTab" : 6
 }
\ No newline at end of file

.Rproj.user/9DAE6990/rmd-outputs

 /private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/Rtmp3VMULh/preview-1ced414f7aab.dir/stuaRt.html
 /private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/Rtmp3VMULh/preview-1ced48fe920c.dir/stuaRt.html
-
 /private/var/folders/dn/j71yz2tn5_gdffs8fqxhddrr0000gn/T/RtmpNme5vw/preview-4c4321234d03.dir/stuaRt.html
 
 
 
+
+

.Rproj.user/9DAE6990/sources/s-39B546A6/1656F55 → .Rproj.user/9DAE6990/sources/per/t/1656F55

@@ -9,11 +9,11 @@
     "id" : "1656F55",
     "lastKnownWriteTime" : 1622640147,
     "last_content_update" : 1622640147,
-    "path" : "~/stuart_package/stuart/R/geno_strains.R",
+    "path" : "~/Documents/PhD/stuart_R/stuart/R/geno_strains.R",
     "project_path" : "R/geno_strains.R",
     "properties" : {
         "cursorPosition" : "22,39",
-        "scrollLine" : "7"
+        "scrollLine" : "0"
     },
     "read_only" : false,
     "read_only_alternatives" : [

.Rproj.user/9DAE6990/sources/s-39B546A6/42D37312 → .Rproj.user/9DAE6990/sources/per/t/42D37312

@@ -5,14 +5,14 @@
     "dirty" : false,
     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "0",
+    "hash" : "3094972460",
     "id" : "42D37312",
-    "lastKnownWriteTime" : 1622465534,
-    "last_content_update" : 1622465534,
-    "path" : "~/stuart_package/stuart/R/mark_prop.R",
+    "lastKnownWriteTime" : 1623061718,
+    "last_content_update" : 1623061718577,
+    "path" : "~/Documents/PhD/stuart_R/stuart/R/mark_prop.R",
     "project_path" : "R/mark_prop.R",
     "properties" : {
-        "cursorPosition" : "2,104",
+        "cursorPosition" : "16,28",
         "scrollLine" : "0"
     },
     "read_only" : false,

.Rproj.user/9DAE6990/sources/s-39B546A6/42D37312-contents → .Rproj.user/9DAE6990/sources/per/t/42D37312-contents

@@ -14,6 +14,7 @@
 
 #### mark_prop ####
 ## excludes markers depending on proportions of homo/hetorozygous
+## to modify with chisq.test
 mark_prop <- function(tab,cross,homo=NA,hetero=NA,na=0.5){
   #calculate total number of individuals genotyped for each marker
   tab <- tab %>% mutate(n_geno = tab %>% select(n_HM1,n_HM2,n_HT) %>% rowSums(na.rm=TRUE))

.Rproj.user/9DAE6990/sources/s-39B546A6/45D91D58 → .Rproj.user/9DAE6990/sources/per/t/45D91D58

@@ -9,11 +9,11 @@
     "id" : "45D91D58",
     "lastKnownWriteTime" : 1622648301,
     "last_content_update" : 1622648301329,
-    "path" : "~/stuart_package/stuart/R/write_rqtl.R",
+    "path" : "~/Documents/PhD/stuart_R/stuart/R/write_rqtl.R",
     "project_path" : "R/write_rqtl.R",
     "properties" : {
         "cursorPosition" : "84,18",
-        "scrollLine" : "94"
+        "scrollLine" : "0"
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     "read_only" : false,
     "read_only_alternatives" : [

.Rproj.user/9DAE6990/sources/s-39B546A6/65C9B72B → .Rproj.user/9DAE6990/sources/per/t/65C9B72B

@@ -9,11 +9,11 @@
     "id" : "65C9B72B",
     "lastKnownWriteTime" : 1622642120,
     "last_content_update" : 1622642120783,
-    "path" : "~/stuart_package/stuart/R/tab_mark.R",
+    "path" : "~/Documents/PhD/stuart_R/stuart/R/tab_mark.R",
     "project_path" : "R/tab_mark.R",
     "properties" : {
         "cursorPosition" : "43,27",
-        "scrollLine" : "29",
+        "scrollLine" : "0",
         "source_window_id" : ""
     },
     "read_only" : false,

.Rproj.user/9DAE6990/sources/s-39B546A6/76AC3EC → .Rproj.user/9DAE6990/sources/per/t/76AC3EC

@@ -5,11 +5,11 @@
     "dirty" : false,
     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "0",
+    "hash" : "143869640",
     "id" : "76AC3EC",
-    "lastKnownWriteTime" : 1622644628,
-    "last_content_update" : 1622644628349,
-    "path" : "~/stuart_package/stuart/R/mark_match.R",
+    "lastKnownWriteTime" : 1623060553,
+    "last_content_update" : 1623060553,
+    "path" : "~/Documents/PhD/stuart_R/stuart/R/mark_match.R",
     "project_path" : "R/mark_match.R",
     "properties" : {
         "cursorPosition" : "20,46",

.Rproj.user/9DAE6990/sources/s-39B546A6/96AB3736 → .Rproj.user/9DAE6990/sources/per/t/96AB3736

@@ -7,14 +7,14 @@
     "folds" : "",
     "hash" : "2014255563",
     "id" : "96AB3736",
-    "lastKnownWriteTime" : 1622648726,
-    "last_content_update" : 1622648726992,
-    "path" : "~/stuart_package/stuart/vignettes/stuaRt.Rmd",
+    "lastKnownWriteTime" : 1623060592,
+    "last_content_update" : 1623060592,
+    "path" : "~/Documents/PhD/stuart_R/stuart/vignettes/stuaRt.Rmd",
     "project_path" : "vignettes/stuaRt.Rmd",
     "properties" : {
         "cursorPosition" : "135,15",
-        "last_setup_crc32" : "39B546A65bfca283",
-        "scrollLine" : "130"
+        "last_setup_crc32" : "",
+        "scrollLine" : "111"
     },
     "read_only" : false,
     "read_only_alternatives" : [

.Rproj.user/9DAE6990/sources/s-39B546A6/A6A5703A → .Rproj.user/9DAE6990/sources/per/t/A6A5703A

@@ -9,7 +9,7 @@
     "id" : "A6A5703A",
     "lastKnownWriteTime" : 1622641746,
     "last_content_update" : 1622641746302,
-    "path" : "~/stuart_package/stuart/R/stuart_tab-data.R",
+    "path" : "~/Documents/PhD/stuart_R/stuart/R/stuart_tab-data.R",
     "project_path" : "R/stuart_tab-data.R",
     "properties" : {
         "cursorPosition" : "8,12",

.Rproj.user/9DAE6990/sources/s-39B546A6/B86C81D8 → .Rproj.user/9DAE6990/sources/per/t/B86C81D8

@@ -5,11 +5,11 @@
     "dirty" : false,
     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "0",
+    "hash" : "4129306061",
     "id" : "B86C81D8",
     "lastKnownWriteTime" : 1622646597,
     "last_content_update" : 1622646597951,
-    "path" : "~/stuart_package/stuart/R/mark_allele.R",
+    "path" : "~/Documents/PhD/stuart_R/stuart/R/mark_allele.R",
     "project_path" : "R/mark_allele.R",
     "properties" : {
         "cursorPosition" : "23,55",

.Rproj.user/9DAE6990/sources/s-39B546A6/C5228C18 → .Rproj.user/9DAE6990/sources/per/t/C5228C18

@@ -5,11 +5,11 @@
     "dirty" : false,
     "encoding" : "UTF-8",
     "folds" : "",
-    "hash" : "0",
+    "hash" : "1417555270",
     "id" : "C5228C18",
     "lastKnownWriteTime" : 1622645200,
     "last_content_update" : 1622645200474,
-    "path" : "~/stuart_package/stuart/R/mark_poly.R",
+    "path" : "~/Documents/PhD/stuart_R/stuart/R/mark_poly.R",
     "project_path" : "R/mark_poly.R",
     "properties" : {
         "cursorPosition" : "9,51",