diff --git a/.gitignore b/.gitignore
index c7a2117..8963550 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@ vagrantDNA/.Rproj.user*/*
 .Rproj.user
 vagrantDNA.Rcheck
 *zarr
+
diff --git a/vagrantDNA/.Rproj.user/7A513094/build_options b/vagrantDNA/.Rproj.user/7A513094/build_options
deleted file mode 100644
index 4089afd..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/build_options
+++ /dev/null
@@ -1,7 +0,0 @@
-auto_roxygenize_for_build_and_reload="0"
-auto_roxygenize_for_build_package="1"
-auto_roxygenize_for_check="1"
-live_preview_website="0"
-makefile_args=""
-preview_website="1"
-website_output_format="all"
diff --git a/vagrantDNA/.Rproj.user/7A513094/cpp-definition-cache b/vagrantDNA/.Rproj.user/7A513094/cpp-definition-cache
deleted file mode 100644
index 0637a08..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/cpp-definition-cache
+++ /dev/null
@@ -1 +0,0 @@
-[]
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/pcs/debug-breakpoints.pper b/vagrantDNA/.Rproj.user/7A513094/pcs/debug-breakpoints.pper
deleted file mode 100644
index 4893a8a..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/pcs/debug-breakpoints.pper
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "debugBreakpointsState": {
-        "breakpoints": []
-    }
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/pcs/files-pane.pper b/vagrantDNA/.Rproj.user/7A513094/pcs/files-pane.pper
deleted file mode 100644
index 345cb45..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/pcs/files-pane.pper
+++ /dev/null
@@ -1,9 +0,0 @@
-{
-    "sortOrder": [
-        {
-            "columnIndex": 2,
-            "ascending": true
-        }
-    ],
-    "path": "~/Documents/GitHub/pseudogene_quantification/vagrantDNA/man"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/pcs/source-pane.pper b/vagrantDNA/.Rproj.user/7A513094/pcs/source-pane.pper
deleted file mode 100644
index a528f3b..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/pcs/source-pane.pper
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-    "activeTab": -1
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/pcs/windowlayoutstate.pper b/vagrantDNA/.Rproj.user/7A513094/pcs/windowlayoutstate.pper
deleted file mode 100644
index 83b56bb..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/pcs/windowlayoutstate.pper
+++ /dev/null
@@ -1,14 +0,0 @@
-{
-    "left": {
-        "splitterpos": 326,
-        "topwindowstate": "HIDE",
-        "panelheight": 780,
-        "windowheight": 818
-    },
-    "right": {
-        "splitterpos": 512,
-        "topwindowstate": "NORMAL",
-        "panelheight": 818,
-        "windowheight": 856
-    }
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/pcs/workbench-pane.pper b/vagrantDNA/.Rproj.user/7A513094/pcs/workbench-pane.pper
deleted file mode 100644
index f398270..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/pcs/workbench-pane.pper
+++ /dev/null
@@ -1,5 +0,0 @@
-{
-    "TabSet1": 3,
-    "TabSet2": 3,
-    "TabZoom": {}
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/rmd-outputs b/vagrantDNA/.Rproj.user/7A513094/rmd-outputs
deleted file mode 100644
index 3f2ff2d..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/rmd-outputs
+++ /dev/null
@@ -1,5 +0,0 @@
-
-
-
-
-
diff --git a/vagrantDNA/.Rproj.user/7A513094/saved_source_markers b/vagrantDNA/.Rproj.user/7A513094/saved_source_markers
deleted file mode 100644
index 2b1bef1..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/saved_source_markers
+++ /dev/null
@@ -1 +0,0 @@
-{"active_set":"","sets":[]}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/11029130 b/vagrantDNA/.Rproj.user/7A513094/sources/prop/11029130
deleted file mode 100644
index 9fc5e93..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/11029130
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-    "tempName": "Untitled1",
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "0,0",
-    "scrollLine": "0"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/226D24EC b/vagrantDNA/.Rproj.user/7A513094/sources/prop/226D24EC
deleted file mode 100644
index 3fa202b..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/226D24EC
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "2,14",
-    "scrollLine": "0"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/2A7477B2 b/vagrantDNA/.Rproj.user/7A513094/sources/prop/2A7477B2
deleted file mode 100644
index 26bb3b8..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/2A7477B2
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "1,0",
-    "scrollLine": "0"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/34134B3A b/vagrantDNA/.Rproj.user/7A513094/sources/prop/34134B3A
deleted file mode 100644
index 867a219..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/34134B3A
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "26,55",
-    "scrollLine": "19"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/3A25F4D4 b/vagrantDNA/.Rproj.user/7A513094/sources/prop/3A25F4D4
deleted file mode 100644
index d886a6a..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/3A25F4D4
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-    "tempName": "Untitled1",
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "6,70",
-    "scrollLine": "0"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/4A6A260D b/vagrantDNA/.Rproj.user/7A513094/sources/prop/4A6A260D
deleted file mode 100644
index bb27690..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/4A6A260D
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/6EF926F2 b/vagrantDNA/.Rproj.user/7A513094/sources/prop/6EF926F2
deleted file mode 100644
index 3fe2168..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/6EF926F2
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "0,46",
-    "scrollLine": "0"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/7405AB0C b/vagrantDNA/.Rproj.user/7A513094/sources/prop/7405AB0C
deleted file mode 100644
index 6dbe7bd..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/7405AB0C
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "10,0",
-    "scrollLine": "0"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/78A8D4E0 b/vagrantDNA/.Rproj.user/7A513094/sources/prop/78A8D4E0
deleted file mode 100644
index bba92df..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/78A8D4E0
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "76,44",
-    "scrollLine": "58"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/85B4FDB3 b/vagrantDNA/.Rproj.user/7A513094/sources/prop/85B4FDB3
deleted file mode 100644
index 968cd8a..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/85B4FDB3
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "29,101",
-    "scrollLine": "21"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/B16DB1CA b/vagrantDNA/.Rproj.user/7A513094/sources/prop/B16DB1CA
deleted file mode 100644
index 7beb6c0..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/B16DB1CA
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "31,0",
-    "scrollLine": "23"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/C5CE1899 b/vagrantDNA/.Rproj.user/7A513094/sources/prop/C5CE1899
deleted file mode 100644
index 6aedcb1..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/C5CE1899
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "10,36",
-    "scrollLine": "0"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/E473D4B6 b/vagrantDNA/.Rproj.user/7A513094/sources/prop/E473D4B6
deleted file mode 100644
index e1b2f2f..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/E473D4B6
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "13,49",
-    "scrollLine": "0"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/EAFBB325 b/vagrantDNA/.Rproj.user/7A513094/sources/prop/EAFBB325
deleted file mode 100644
index a78b1b9..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/EAFBB325
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-    "source_window_id": "",
-    "Source": "Source",
-    "cursorPosition": "49,0",
-    "scrollLine": "34"
-}
\ No newline at end of file
diff --git a/vagrantDNA/.Rproj.user/7A513094/sources/prop/INDEX b/vagrantDNA/.Rproj.user/7A513094/sources/prop/INDEX
deleted file mode 100644
index 4b99359..0000000
--- a/vagrantDNA/.Rproj.user/7A513094/sources/prop/INDEX
+++ /dev/null
@@ -1,17 +0,0 @@
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FLICENSE="6EF926F2"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2FDESCRIPTION="7405AB0C"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2FNAMESPACE="226D24EC"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2FR%2FDivergence_Estimate.R="E473D4B6"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2FR%2FGet%20raw%20data.R="11029130"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2FR%2FRainbow_Plot.R="78A8D4E0"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Fdata-raw%2FDATASET.R="C5CE1899"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Fdata-raw%2FhopperDF.Rd="4FB6B84A"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Fman%2FdivEst.Rd="EAFBB325"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Fman%2FhopperDF.Rd="34134B3A"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Fman%2FhopperFX.Rd="368C6292"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Fman%2FhumanDF.Rd="B16DB1CA"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Fman%2FparrotDF.Rd="85B4FDB3"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Fman%2FparrotFX.Rd="FCF222AA"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Fman%2FrainbowPlot.Rd="4A6A260D"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Ftests%2Ftestthat%2Ftest_rainbowPlot.R="3A25F4D4"
-~%2FDocuments%2FGitHub%2Fpseudogene_quantification%2FvagrantDNA%2Ftests%2Ftestthat.R="2A7477B2"
diff --git a/vagrantDNA/.Rproj.user/shared/notebooks/patch-chunk-names b/vagrantDNA/.Rproj.user/shared/notebooks/patch-chunk-names
deleted file mode 100644
index e69de29..0000000
diff --git a/vagrantDNA/.Rproj.user/shared/notebooks/paths b/vagrantDNA/.Rproj.user/shared/notebooks/paths
deleted file mode 100644
index 16af313..0000000
--- a/vagrantDNA/.Rproj.user/shared/notebooks/paths
+++ /dev/null
@@ -1,11 +0,0 @@
-/home/hbecher/git_repos/2211-ctnnb1-project/code/01exploreData.R="AA0E783C"
-/home/hbecher/git_repos/high-dimensional-stats-r/_episodes_rmd/04-principal-component-analysis.Rmd="8A47267B"
-/home/hbecher/git_repos/pseudogene_quantification/vagrantDNA/DESCRIPTION="945CB5B9"
-/home/hbecher/git_repos/pseudogene_quantification/vagrantDNA/R/Rainbow_Plot.R="809289D1"
-/home/hbecher/git_repos/pseudogene_quantification/vagrantDNA/R/interceptPositionPlot.R="38AB3092"
-/home/hbecher/git_repos/pseudogene_quantification/vagrantDNA/R/selAllPlot.R="CB217457"
-/home/hbecher/git_repos/stat_rethinking_2022/scripts_animation/08_MCMC.r="A17BF693"
-/home/hbecher/temp/numtSim/01sim.R="6BA3B498"
-/home/hbecher/temp/numtSim/07transformData.R="6691BFB8"
-/home/hbecher/temp/numtSim/10runRainbow.R="786925B5"
-/home/hbecher/temp/numtSim/11runRainbow2.R="2898F751"
diff --git a/vagrantDNA/DESCRIPTION b/vagrantDNA/DESCRIPTION
index 3a34fa5..58d3d5c 100644
--- a/vagrantDNA/DESCRIPTION
+++ b/vagrantDNA/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: vagrantDNA
 Type: Package
 Title: Estimating the proportion of vagrant DNA in a genome
-Version: 1.1.0
+Version: 1.1.1
 Author: Richard Nichols and Hannes Becher
 Maintainer: The package maintainer <r.a.nichols@qmul.ac.uk>
 Description: The package two functions rainbowPlot and divEst. They produce two different estimates of the proportion of DNA from a particular vagrant genome. They exploit low coverge data from multiple individuals in which the vagrant DNA has taken residence (see Becher and Nichols 2022).
diff --git a/vagrantDNA/R/Rainbow_Plot.R b/vagrantDNA/R/Rainbow_Plot.R
index eed3da5..0f62eb1 100644
--- a/vagrantDNA/R/Rainbow_Plot.R
+++ b/vagrantDNA/R/Rainbow_Plot.R
@@ -82,12 +82,13 @@
 #' ## plot and printout (by default) the results of running rainbowPlot on the parrot data.
 #' rainbowPlot(parrotDF, seed = 12345, title = "Parrot")
 #' ##
-#' ## plot without printing the results and store results in res1.
-#' res1 <- rainbowPlot(parrotDF, seed = 12345, printout = FALSE, title = "Parrot")
-#' ## print just the stored estimates (the first two elements of the list)
-#' print(res1[1:2])
-#' ## Inspect the residuals of the lmer model
-#' plot(res1$lmer.model)
+#' ## plot without printing the results and store results in parrotFit
+#' parrotFit <- rainbowPlot(parrotDF, seed = 12345, printout = FALSE, title = "Parrot")
+#' ## Inspect relationship between intercepts and SNP location
+#' interceptPositionPlot(parrotFit)
+#' ## Inspect mapping depth of nuclear insert allele across samples
+#' selAllPlot(parrotDF, parrotFit)
+#'
 #' @export
 rainbowPlot <- function(data,
                       nloci = 400,
@@ -322,7 +323,7 @@ rainbowPlot <- function(data,
   if (printout) {
     cat('Intercept based on ', numgoodloci, 'SNP loci \n')
     cat('Estimate: ', signif(intercepts[1],3), '\n')
-    cat('Confindence Interval: ',
+    cat('Confidence Interval: ',
                 signif(intercepts[2],3),
                 '-',
                 signif(intercepts[3],3),
diff --git a/vagrantDNA/R/selAllPlot.R b/vagrantDNA/R/selAllPlot.R
index ad52f8c..0144e79 100644
--- a/vagrantDNA/R/selAllPlot.R
+++ b/vagrantDNA/R/selAllPlot.R
@@ -16,7 +16,7 @@
 #'  selAllPlot(humanDF) # overall alt allele counts
 #'  selAllPlot(humanDF, humanFit) # alt allele count at loci selected for fit
 #'  }
-selAllPlot <- function(dd,ff,ylim=c(0, 10),...){
+selAllPlot <- function(dd,ff,ylim=c(0, 10),ylab="Allele count",...){
   if(hasArg(ff)){
     posString <- rownames(coef(summary(ff$lmer.model)))
     sites <- substr(posString, 9, 20)
@@ -24,6 +24,7 @@ selAllPlot <- function(dd,ff,ylim=c(0, 10),...){
     boxplot(pDat$DP * exp(pDat$ylog) ~ pDat$Sample,
             main="Alt. allele count at selected loci",
             ylim=ylim,
+            ylab=ylab,
             ...)
     goodDatMeds <- round(as.numeric(tapply(pDat$DP * exp(pDat$ylog), pDat$Sample, function(x) boxplot.stats(x)$stats[3])))
     if(sum(goodDatMeds < 2) > length(goodDatMeds)/2) warning("The majority of individuals have a median alternate allele depth of 1. This suggests that vagrant DNA proportion or the sequencing depth may be insufficient for an accurate estimate. Consider using more WGS data if possible.")
@@ -31,6 +32,7 @@ selAllPlot <- function(dd,ff,ylim=c(0, 10),...){
     boxplot(dd$DP * exp(dd$ylog) ~ dd$Sample,
             main="Alt. allele count at all loci",
             ylim=ylim,
+            ylab=ylab,
             ...)
     cat("Plot shows alt allels counts for all loci. Supply rainbowPlot object to show only selected loci.\n")
     goodDatMeds <- round(as.numeric(tapply(dd$DP * exp(dd$ylog), dd$Sample, function(x) boxplot.stats(x)$stats[3])))
diff --git a/vagrantDNA/man/rainbowPlot.Rd b/vagrantDNA/man/rainbowPlot.Rd
index 2a7569f..e83b421 100644
--- a/vagrantDNA/man/rainbowPlot.Rd
+++ b/vagrantDNA/man/rainbowPlot.Rd
@@ -100,10 +100,11 @@ data(parrotDF)
 ## plot and printout (by default) the results of running rainbowPlot on the parrot data.
 rainbowPlot(parrotDF, seed = 12345, title = "Parrot")
 ##
-## plot without printing the results and store results in res1.
-res1 <- rainbowPlot(parrotDF, seed = 12345, printout = FALSE, title = "Parrot")
-## print just the stored estimates (the first two elements of the list)
-print(res1[1:2])
-## Inspect the residuals of the lmer model
-plot(res1$lmer.model)
+## plot without printing the results and store results in parrotFit
+parrotFit <- rainbowPlot(parrotDF, seed = 12345, printout = FALSE, title = "Parrot")
+## Inspect relationship between intercepts and SNP location
+interceptPositionPlot(parrotFit)
+## Inspect mapping depth of nuclear insert allele across samples
+selAllPlot(parrotDF, parrotFit)
+
 }
diff --git a/vagrantDNA/man/selAllPlot.Rd b/vagrantDNA/man/selAllPlot.Rd
index 25ae3e6..ee05e84 100644
--- a/vagrantDNA/man/selAllPlot.Rd
+++ b/vagrantDNA/man/selAllPlot.Rd
@@ -4,7 +4,7 @@
 \alias{selAllPlot}
 \title{Boxplot of alternate (vagrant) allele counts per sample}
 \usage{
-selAllPlot(dd, ff, ylim = c(0, 10), ...)
+selAllPlot(dd, ff, ylim = c(0, 10), ylab = "Allele count", ...)
 }
 \arguments{
 \item{dd}{A dataframe, such as used to run `rainbowPlot()`}
diff --git a/vagrantDNA_1.1.0.tar.gz b/vagrantDNA_1.1.1.tar.gz
similarity index 69%
rename from vagrantDNA_1.1.0.tar.gz
rename to vagrantDNA_1.1.1.tar.gz
index 84ddd18..7182698 100644
Binary files a/vagrantDNA_1.1.0.tar.gz and b/vagrantDNA_1.1.1.tar.gz differ