upgrade to v0.0.8

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: cardelino
 Type: Package
-Title: Clonal Analysis of Cells Using Single Cell Data
-Version: 0.0.7
-Date: 2018-07-27
+Title: Clone and Donor Identification from Single Cell Data
+Version: 0.0.8
+Date: 2018-07-31
 Authors@R: c(person("Davis", "McCarthy", role=c("aut", "cre"),
         email="davis@ebi.ac.uk"), person("Yuanhua", "Huang", 
         role=c("aut"), email="yuanhua@ebi.ac.uk"))
@@ -21,5 +21,5 @@ biocViews: SingleCell, RNASeq, Visualization, Transcriptomics, GeneExpression,
     Sequencing, Software
 RoxygenNote: 6.0.1
 NeedsCompilation: yes
-URL: https://github.com/davismcc/cardelino
-BugReports: https://github.com/davismcc/cardelino/issues
+URL: https://github.com/PMBio/cardelino
+BugReports: https://github.com/PMBio/cardelino/issues

NAMESPACE

@@ -9,7 +9,7 @@ export(cell_assign_Gibbs)
 export(clone_id)
 export(confusion_heatmap)
 export(donor_id)
-export(donor_id_GT)
+export(donor_id_EM)
 export(donor_id_Gibbs)
 export(get_prob_gap)
 export(get_prob_label)

R/plotting.R

@@ -187,7 +187,6 @@ heatmap.theme <- function(legend.position="bottom", size=12) {
 #' @references
 #' This function makes use of the \code{\link{pheatmap}} packages
 #'
-#' @examples
 vc_heatmap <- function(mat, prob, Config, show_legend=FALSE){
     # sort variants
     mut_label <- Config %*% (2**seq(ncol(Config),1))
@@ -246,7 +245,6 @@ vc_heatmap <- function(mat, prob, Config, show_legend=FALSE){
 #' Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
 #' ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
 #'
-#' @examples
 plot_tree <- function(tree, orient="h") {
     node_total <- max(tree$edge)
     node_shown <- ncol(tree$Z)