passes check(), with 2 NOTES. citation() still not parsing inst/CITATION

caseywdunn · Jun 3, 2015 · ad99044 · ad99044
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Showing 7 changed files with 14 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,7 +4,7 @@ Version: 0.0.0.9000
 Authors@R: person("Casey", "Dunn", email = "[email protected]", role = c("aut", "cre"))
 Description: A collection of tools for phylogenetic tree manipulation. It is named after the Indonesian word for forest.
 Depends: R (>= 3.1.0)
-License: GPLv3 (https://www.gnu.org/copyleft/gpl.html)
+License: MIT + file LICENSE
 LazyData: true
 Collate: 
     'utility_functions.R'

diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2015
+COPYRIGHT HOLDER: Casey Dunn
diff --git a/R/utility_functions.R b/R/utility_functions.R
@@ -4,11 +4,14 @@
 #' @param phy_resolved A fully resolved phylogeny stored as a phylo object, e.g. an ML 
 #' tree.
 #' @param phy_constraint A partially resolved constraint tree.
-#' @param epsilon 
+#' @param epsilon The value to replace the branch length with
 #' @return A phylo object containing a tree that is the same as phy_resolved, except that 
 #' the length of edges that are incompatible with phy_constraint are replaced with epsilon.
 #' @examples
-#' zc <- zero_constrained( ml, constraint )
+#' data( siphonophore_ml )
+#' data( siphonophore_constraint )
+#' zc <- zero_constrained( siphonophore_ml, siphonophore_constraint )
+
 zero_constrained <- function ( phy_resolved, phy_constraint, epsilon=0.000001 ){
 	phy_resolved$edge.length[ ! compatible_edges(  phy_resolved, phy_constraint ) ] <- epsilon
 	return( phy_resolved )

diff --git a/README.md b/README.md
@@ -59,6 +59,7 @@ and running some combination of the following:
     load_all()
     test()
     document()
+    check() # A wrapper for R CMD check
 
 To regenerate the pdf manual, run the following shell command in the package directory:
 

diff --git a/hutan_manual.pdf b/hutan_manual.pdf
diff --git a/inst/CITATION b/inst/CITATION
@@ -13,7 +13,4 @@ citEntry(entry = "Article",
         "Automation and Evaluation of the SOWH Test of Phylogenetic Topologies with SOWHAT.",
         "bioRxiv",
         "URL http://dx.doi.org/10.1101/005264.")
-)
-
-
-Church, SH, JF Ryan, CW Dunn (preprint) Automation and Evaluation of the SOWH Test of Phylogenetic Topologies with SOWHAT. bioRxiv. doi:10.1101/005264.
+)
diff --git a/man/zero_constrained.Rd b/man/zero_constrained.Rd
@@ -13,7 +13,7 @@ tree.}
 
 \item{phy_constraint}{A partially resolved constraint tree.}
 
-\item{epsilon}{}
+\item{epsilon}{The value to replace the branch length with}
 }
 \value{
 A phylo object containing a tree that is the same as phy_resolved, except that
@@ -24,6 +24,8 @@ Generates the "zero-constrained" tree described by Susko 2014
 (http://dx.doi.org/10.1093/molbev/msu039)
 }
 \examples{
-zc <- zero_constrained( ml, constraint )
+data( siphonophore_ml )
+data( siphonophore_constraint )
+zc <- zero_constrained( siphonophore_ml, siphonophore_constraint )
 }