housekeeping

gbradburd · Oct 14, 2022 · 65e4e5e · 65e4e5e
1 parent c264245
commit 65e4e5e
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Showing 20 changed files with 277 additions and 281 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,3 +9,4 @@ License: BSD
 LazyData: true
 Suggests: knitr
 VignetteBuilder: knitr
+RoxygenNote: 6.1.1
diff --git a/R/space.mix.MCMC.R b/R/space.mix.MCMC.R
@@ -307,7 +307,8 @@ get.weighted.mean.frequency <- function(sample.frequencies,mean.sample.sizes){
 	return(sample.frequency.weighted.mean)
 }
 
-curate.count.data <- function(counts,sample.sizes,prefix){
+curate.count.data <- function(counts,sample.sizes,prefix){ #FIX WAY DATA ARE DROPPED
+	#recover()
 	k <- nrow(counts)
 	original.loci <- ncol(counts)
 	sample.frequencies <- counts/sample.sizes
@@ -1909,7 +1910,7 @@ make.spacemix.map.list <- function(MCMC.output.file,geographic.locations,name.ve
 #' make.spacemix.map(example.spacemix.map.list,source=FALSE,text=TRUE)
 #' 
 make.spacemix.map <- function(spacemix.map.list,text=FALSE,ellipses=TRUE,source.option=TRUE,xlim=NULL,ylim=NULL){
-	with(spacemix.map.list,{ 
+	with(spacemix.map.list,{
 		plot(MAPP.geogen.coords,type='n',xlim=xlim,ylim=ylim,xlab="",ylab="")
 			if(ellipses){
 				lapply(1:k,FUN=function(i){plot.credible.ellipse(pp.geogen.ellipses[[i]],color.vector[i])})

diff --git a/SpaceMix_0.13.tar.gz b/SpaceMix_0.13.tar.gz
diff --git a/data/MCN.frequencies.list.RData b/data/MCN.frequencies.list.RData
diff --git a/data/ex.output.RData b/data/ex.output.RData
diff --git a/data/example.spacemix.map.list.RData b/data/example.spacemix.map.list.RData
diff --git a/data/spacemix.example.dataset.RData b/data/spacemix.example.dataset.RData
diff --git a/data/spacemix.location.data.RData b/data/spacemix.location.data.RData
diff --git a/man/MCN.frequencies.list.Rd b/man/MCN.frequencies.list.Rd
diff --git a/man/example.spacemix.map.list.Rd b/man/example.spacemix.map.list.Rd
diff --git a/man/fade.admixture.source.points.Rd b/man/fade.admixture.source.points.Rd
diff --git a/man/get.nrmlzd.sample.covariance.Rd b/man/get.nrmlzd.sample.covariance.Rd