1.17.0 Uptick very to match new BioC release

Also update readme.

.travis.yml

@@ -1,4 +1,4 @@
-# Sample .travis.yml for R projects
+# Adapted from sample .travis.yml for R projects
 
 language: r
 bioc_required: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: phyloseq
-Version: 1.15.14
-Date: 2016-04-16
+Version: 1.17.0
+Date: 2016-05-05
 Title: Handling and analysis of high-throughput microbiome
     census data
 Description: phyloseq provides a set of classes and tools
@@ -15,7 +15,7 @@ Imports:
     BiocGenerics (>= 0.14.0),
     ade4 (>= 1.7.2),
     ape (>= 3.1.1),
-    biomformat (>= 0.4.0),
+    biomformat (>= 1.0.0),
     Biostrings (>= 2.28.0),
     cluster (>= 1.14.4),
     data.table (>= 1.9.6),

README.md

@@ -8,19 +8,47 @@
 
 McMurdie and Holmes (2014)
 [Waste Not, Want Not: Why Rarefying Microbiome Data is Statistically Inadmissible](http://dx.plos.org/10.1371/journal.pcbi.1003531)
-PLoS Computational Biology 10(4): e1003531
+*PLoS Computational Biology*
+10(4): e1003531
 
 Presubmission versions ahead of acceptance (2013):
 [PDF version 2](http://arxiv.org/pdf/1310.0424v2.pdf),
 [PDF version 1](http://arxiv.org/pdf/1310.0424v1.pdf)
 
 
-## Latest peer-reviewed article about phyloseq
+## Peer-reviewed articles about phyloseq
 
-[phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data](http://dx.plos.org/10.1371/journal.pone.0061217) (2013) PLoS ONE 8(4):e61217
+McMurdie and Holmes (2014) [Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking](http://bioinformatics.oxfordjournals.org/content/early/2014/10/02/bioinformatics.btu616).
+*Bioinformatics (Oxford, England)*
+31(2), 282–283.
+
+McMurdie and Holmes (2013)
+[phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data](http://dx.plos.org/10.1371/journal.pone.0061217)
+*PLoS ONE* 
+8(4):e61217
 
 ## Other resources
 
-The phyloseq project also has a number of supporting online resources, most of which can by found at [the phyloseq home page](http://joey711.github.com/phyloseq/), or from the phyloseq stable release [page on Bioconductor](http://bioconductor.org/packages/release/bioc/html/phyloseq.html).
+The phyloseq project also has a number of supporting online resources,
+including (but probably not limited to)
+
+### [the phyloseq home page](http://joey711.github.com/phyloseq/)
+
+### [the phyloseq FAQ](https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-FAQ.html)
+I recommend checking this page, and the issues tracker,
+before posting new issues.
+
+### [Bioconductor stable release](http://bioconductor.org/packages/release/bioc/html/phyloseq.html).
+
+### [the phyloseq Issue Tracker](https://github.com/joey711/phyloseq/issues)
+This is the recommended location to post
+
+(1) feature requests
+(2) bug reports
+(3) theoretical considerations
+(4) other issues, feedback
+(5) ask for help
 
-To post feature requests or ask for help, try [the phyloseq Issue Tracker](https://github.com/joey711/phyloseq/issues).
+Search previous posts,
+and check [the phyloseq FAQ](https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-FAQ.html)
+before posting a new issue.