unit testing

NAMESPACE

@@ -1,4 +1,9 @@
+S3method(bootstrap,multiOU)
+S3method(simulate,multiOU)
+S3method(summary,multiOU)
+S3method(update,multiOU)
 export(bootstrap)
+export(convert)
 export(evaluate_likelihood)
 export(format_data)
 export(mrcaOUCH)
@@ -7,8 +12,4 @@ export(paintBranches)
 export(tip_plot)
 import(geiger)
 import(ouch)
-S3method(bootstrap,multiOU)
-S3method(simulate,multiOU)
-S3method(summary,multiOU)
-S3method(update,multiOU)
 useDynLib(wrightscape)

R/treeformats.R

@@ -3,7 +3,8 @@
 #'  toggles between ouch and ape format trees 
 #' @param ot a phylogenetic tree of class "phylo" or "ouchtree"
 #' @param regimes optional list of regimes for an ouchtree
-#' @param the 
+#' @return a phylogenetic tree in the alternative format
+#' @export
 convert <- function(ot, regimes=NULL){
 	if(is(ot, "ouchtree")){
 

demo/parrotfish_data.R

@@ -4,10 +4,8 @@ require(phytools)
 require(geiger)
 
 # This data has not been released
-path = "labrids/"
-labrid_tree <- read.nexus("labrid_tree.nex")
-diet_data <- read.csv("labriddata_parrotfish.csv")
-#fin_data <-read.csv(paste(path,"labrid.csv", sep=""))
+labrid_tree <- read.nexus("../data/labrid_tree.nex")
+diet_data <- read.csv("../data/labriddata_parrotfish.csv")
 
 corrected_data <- diet_data
 # Use the simple names from Price et al 2010

man/convert.Rd

@@ -9,8 +9,9 @@
   "ouchtree"}
 
   \item{regimes}{optional list of regimes for an ouchtree}
-
-  \item{the}{}
+}
+\value{
+  a phylogenetic tree in the alternative format
 }
 \description{
   toggles between ouch and ape format trees

man/multiOU_lik_lca.Rd

@@ -6,7 +6,8 @@
     sigma = NULL, theta = NULL, Xo = NULL, lca)
 }
 \arguments{
-  \item{data}{- ouch-style data}
+  \item{data}{- ouch-style data -- a numeric, in the same
+  order as nodes given in "tree"}
 
   \item{tree}{- ouch-tree}