Merge branch 'issue-3' into develop

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rBAPS
 Title: Bayesian Analysis of Population Structure
-Version: 0.0.0.9015
+Version: 0.0.0.9016
 Date: 2020-11-09
 Authors@R:
     c(

R/dec2bitv.R

@@ -10,7 +10,7 @@ dec2bitv <- function(d, n) {
   d <- d[]
 
   f <- e <- NA
-  c(f, e) <- matlab2r::log2(max(d)) # How many digits do we need to represent the numbers?
+  c(f, e) %<-% matlab2r::log2(max(d)) # How many digits do we need to represent the numbers?
-    bits <- floor(d * 2 ^ (seq(1 - max(n, e), 0))) %% 2
+  bits <- floor(d * 2 ^ (seq(1 - max(n, e), 0))) %% 2
   return(bits)
 }

R/testFastaData.R

@@ -0,0 +1,19 @@
+testFastaData <- function(inFile) {
+  #  added by Lu Cheng, 11.11.2012
+  if (!exists(inFile, 'file')) {
+    stop('Fasta file ', inFile, ' does not exist!')
+  }
+
+  seqs <- load_fasta(inFile)
+  heds <- colnames(seqs)
+  ninds <- length(seqs)
+
+  data <- as.matrix(seqs)
+  newData <- ones(size(data)) * -9
+  newData[toupper(data) == 'A'] <- 1
+  newData[toupper(data) == 'C'] <- 2
+  newData[toupper(data) == 'G'] <- 3
+  newData[toupper(data) == 'T'] <- 4
+  data <- c(newData, t(1:ninds))
+  return(list("ninds" = ninds, "data" = data, "heds" = heds))
+}