Merge pull request #128 from grunwaldlab/dev

merge dev before CRAN submission

Author: zachary-foster

.gitignore

@@ -12,3 +12,4 @@ inst/doc/vignettes_info.*
 big_data/**
 scratch/*.pdf
 scratch/*.svg
+inst/doc

.travis.yml

@@ -1,12 +1,20 @@
 language: r
+r:
+  - release
+  - devel
 
 sudo: required
+cran: http://cran.at.r-project.org
+
+cache: packages
 
 os:
 - linux
 
-r_github_packages:
-  - jimhester/covr
-
 after_success:
-  - Rscript -e 'library(covr);codecov()'
+  - Rscript -e 'library(covr);codecov()'
+  
+notifications:
+  email:
+    on_success: change
+    on_failure: always

DESCRIPTION

@@ -1,26 +1,20 @@
 Package: metacoder
-Title: Tools for metabarcoding experiment planning
-Version: 0.1.1.9579
+Title: Tools for Parsing, Manipulating, and Graphing Hierarchical Data
+Version: 0.1.1.710
 Authors@R: c( person("Zachary", "Foster", email =
         "zacharyfoster1989@gmail.com", role = c("aut", "cre")),
         person("Niklaus", "Grunwald", email =
         "grunwaln@science.oregonstate.edu", role = c("aut")))
-Description: A set of tools for metabarcoding (i.e. amplicon
-        metagenomics) experiment planning and analysis. Has functions
-        for parseing out taxonomic information from diverse metadata
-        (e.g. sequence headers), for taxonomically- balanced
-        subsampling of items with associated taxonomy information (e.g.
-        sequences), and for making publication-quality graphics showing
-        distributions of taxon statistics over taxonomic/phylogenetic
-        trees.
+Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
+Description: A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).  
 Depends: R (>= 3.0.2)
-License: GPL-2
+License: GPL-2 | GPL-3
 LazyData: true
 Imports: stringr, ggplot2, igraph, scales, grid, taxize, seqinr,
         reshape2, zoo, traits, RColorBrewer, RCurl, ape, reshape,
         stats, grDevices, utils, lazyeval, dplyr, magrittr, readr
 Suggests: knitr, rmarkdown, testthat
 VignetteBuilder: knitr
 RoxygenNote: 5.0.1
-Date: 2016-07-01
-Encoding: latin1
+Date: 2016-08-01
+Encoding: UTF-8

NAMESPACE

@@ -3,7 +3,7 @@
 S3method(extract_taxonomy,DNAbin)
 S3method(extract_taxonomy,default)
 S3method(extract_taxonomy,list)
-S3method(plot,taxmap)
+S3method(heat_tree,taxmap)
 S3method(primersearch,character)
 S3method(primersearch,taxmap)
 S3method(print,taxmap)
@@ -18,6 +18,7 @@ export(everything)
 export(extract_taxonomy)
 export(filter_obs)
 export(filter_taxa)
+export(heat_tree)
 export(hierarchies)
 export(layout_functions)
 export(matches)

R/dataset_documentation.R

@@ -140,7 +140,6 @@
 #' }
 #'
 #' @format An object of type \code{\link{taxmap}}
-#' @source \url{http://5.196.17.195/pr2/index.html}
 "pr2_ex_data"
 
 
@@ -182,7 +181,6 @@
 #' }
 #'
 #' @format An object of type \code{\link{taxmap}}
-#' @source \url{http://itsonedb.ba.itb.cnr.it:8080/ITS1}
 "its1_ex_data"