update readme and version

adw96 · Aug 6, 2018 · 4f4af61 · 4f4af61
1 parent 2184728
commit 4f4af61
Show file tree

Hide file tree

Showing 35 changed files with 242 additions and 64 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: breakaway
 Title: Species Richness Estimation and Modeling
-Version: 4.6.2
+Version: 4.6.3
 Date: 2018-07-08
 Authors@R: as.person(c(
     "Amy Willis <adwillis@uw.edu> [aut, cre]",

diff --git a/README.Rmd b/README.Rmd
@@ -19,44 +19,58 @@ knitr::opts_chunk$set(
 [![Coverage status](https://codecov.io/gh/adw96/breakaway/branch/master/graph/badge.svg)](https://codecov.io/github/adw96/breakaway?branch=master)
 [![CRAN version](http://www.r-pkg.org/badges/version/breakaway)](https://cran.r-project.org/package=breakaway)
 
-Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. breakaway is the premier package for statistical analysis of microbial diversity. breakaway implements the latest and greatest estimates of different alpha diversity metrics, as well as the most commonly used estimates.
 
-breakaway is undergoing substantial renovations. Please submit an issue if it is interfering with your work!
+
+`breakaway` is the premier package for statistical analysis of microbial diversity. `breakaway` implements the latest and greatest estimates of richness, as well as the most commonly used estimates.
+Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 
+
+[`DivNet`](https://github.com/adw96/DivNet) is a new package by the same authors for estimating Shannon diversity, and other diversity indices. `breakaway` focuses on richness while `DivNet` focuses on Shannon, Simpson, and other alpha diversities as well as some beta diversity indices. Check it out!
+
+`breakaway` has undergone substantial renovations to make it more modern, easy-to-use, and robust. If functionality that you previously enjoyed in `breakaway` no longer exists, please submit an [issue](https://github.com/adw96/breakaway/issues)!
+
+
+### Citing breakaway
+
+The `R` package `breakaway` implements a number of different richness estimates. Please cite the following if you use them:
+
+- `breakaway()` and `kemp()`: Willis, A. & Bunge, J. (2015). Estimating diversity via frequency ratios. Biometrics.
+- `betta()`: Willis, A., Bunge, J., & Whitman, T. (2017). Improved detection of changes in species richness in high diversity microbial communities. JRSS-C.
+- `breakaway_nof1()`: Willis, A. (2016+). Species richness estimation with high diversity but spurious singletons. arXiv.
+- `objective_bayes_*()`: Barger, K. & Bunge, J. (2010). Objective Bayesian estimation for the number of species. Bayesian Analysis.
+
 
 ## Installation
 
 ### Development version
-You can install breakaway from github with:
+You can install `breakaway` from github with:
 
 ```R
 install.packages("devtools")
 devtools::install_github("adw96/breakaway")
 ```
 
-breakaway is actively maintained and continually expanding and developing its scope! Is there a method you would like to have implemented in breakaway? Submit a pull request or contact the [maintainer](http://faculty.washington.edu/adwillis/)!
+`breakaway` is actively maintained and continually expanding and developing its scope! Is there a method you would like to have implemented in breakaway? Submit a pull request or contact the [maintainer](http://faculty.washington.edu/adwillis/)!
 
 ### CRAN
 
-For now, breakaway is no longer being updated on CRAN. You can access v3.0 on CRAN [here](https://cran.r-project.org/web/packages/breakaway/index.html) or with
+For now, `breakaway` is no longer being updated on CRAN. You can access v3.0 on CRAN [here](https://cran.r-project.org/web/packages/breakaway/index.html) or with
 ```R
 install.packages("breakaway")
 ```
 
 ## Humans
 Maintainer: [Amy Willis](http://faculty.washington.edu/adwillis/)
 
-Authors: [Amy Willis](http://faculty.washington.edu/adwillis/), [Kathryn Barger](http://hnrca.tufts.edu/kathryn-barger-ph-d/) and [John Bunge](https://stat.cornell.edu/people/faculty/john-bunge)
+Authors: [Amy Willis](http://faculty.washington.edu/adwillis/), [Bryan Martin](https://bryandmartin.github.io/), [Kathryn Barger](http://hnrca.tufts.edu/kathryn-barger-ph-d/) and [John Bunge](https://stat.cornell.edu/people/faculty/john-bunge)
 
 
 ## Upcoming features
 
 - extended tutorials
-- phyloseq integration
-- CatchAll in R
-- better unit testing
-- longitudinal models for the microbiome
-- better graphics
-- automated estimator selection based on data structure
-- new format for modelling functions
-
-Do you have a request for us? Let us know!
+- ~~phyloseq integration~~
+- ~~better unit testing~~
+- ~~better graphics~~
+- ~~automated estimator selection based on data structure~~
+- ~~new format for modelling functions~~
+
+Do you have a request for us? Let us know! We want folks to use `breakaway` and are committed to making it as easy to use as possible.
diff --git a/README.md b/README.md
@@ -5,27 +5,38 @@ breakaway <img src="docs/breakaway-logo.png" align="right" width="165px"/>
 
 [![Travis-CI Build Status](https://travis-ci.org/adw96/breakaway.svg?branch=master)](https://travis-ci.org/adw96/breakaway) [![Coverage status](https://codecov.io/gh/adw96/breakaway/branch/master/graph/badge.svg)](https://codecov.io/github/adw96/breakaway?branch=master) [![CRAN version](http://www.r-pkg.org/badges/version/breakaway)](https://cran.r-project.org/package=breakaway)
 
-Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. breakaway is the premier package for statistical analysis of microbial diversity. breakaway implements the latest and greatest estimates of different alpha diversity metrics, as well as the most commonly used estimates.
+`breakaway` is the premier package for statistical analysis of microbial diversity. `breakaway` implements the latest and greatest estimates of richness, as well as the most commonly used estimates. Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis.
 
-breakaway is undergoing substantial renovations. Please submit an issue if it is interfering with your work!
+[`DivNet`](https://github.com/adw96/DivNet) is a new package by the same authors for estimating Shannon diversity, and other diversity indices. `breakaway` focuses on richness while `DivNet` focuses on Shannon, Simpson, and other alpha diversities as well as some beta diversity indices. Check it out!
+
+`breakaway` has undergone substantial renovations to make it more modern, easy-to-use, and robust. If functionality that you previously enjoyed in `breakaway` no longer exists, please submit an [issue](https://github.com/adw96/breakaway/issues)!
+
+### Citing breakaway
+
+The `R` package `breakaway` implements a number of different richness estimates. Please cite the following if you use them:
+
+-   `breakaway()` and `kemp()`: Willis, A. & Bunge, J. (2015). Estimating diversity via frequency ratios. Biometrics.
+-   `betta()`: Willis, A., Bunge, J., & Whitman, T. (2017). Improved detection of changes in species richness in high diversity microbial communities. JRSS-C.
+-   `breakaway_nof1()`: Willis, A. (2016+). Species richness estimation with high diversity but spurious singletons. arXiv.
+-   `objective_bayes_*()`: Barger, K. & Bunge, J. (2010). Objective Bayesian estimation for the number of species. Bayesian Analysis.
 
 Installation
 ------------
 
 ### Development version
 
-You can install breakaway from github with:
+You can install `breakaway` from github with:
 
 ``` r
 install.packages("devtools")
 devtools::install_github("adw96/breakaway")
 ```
 
-breakaway is actively maintained and continually expanding and developing its scope! Is there a method you would like to have implemented in breakaway? Submit a pull request or contact the [maintainer](http://faculty.washington.edu/adwillis/)!
+`breakaway` is actively maintained and continually expanding and developing its scope! Is there a method you would like to have implemented in breakaway? Submit a pull request or contact the [maintainer](http://faculty.washington.edu/adwillis/)!
 
 ### CRAN
 
-For now, breakaway is no longer being updated on CRAN. You can access v3.0 on CRAN [here](https://cran.r-project.org/web/packages/breakaway/index.html) or with
+For now, `breakaway` is no longer being updated on CRAN. You can access v3.0 on CRAN [here](https://cran.r-project.org/web/packages/breakaway/index.html) or with
 
 ``` r
 install.packages("breakaway")
@@ -36,18 +47,16 @@ Humans
 
 Maintainer: [Amy Willis](http://faculty.washington.edu/adwillis/)
 
-Authors: [Amy Willis](http://faculty.washington.edu/adwillis/), [Kathryn Barger](http://hnrca.tufts.edu/kathryn-barger-ph-d/) and [John Bunge](https://stat.cornell.edu/people/faculty/john-bunge)
+Authors: [Amy Willis](http://faculty.washington.edu/adwillis/), [Bryan Martin](https://bryandmartin.github.io/), [Kathryn Barger](http://hnrca.tufts.edu/kathryn-barger-ph-d/) and [John Bunge](https://stat.cornell.edu/people/faculty/john-bunge)
 
 Upcoming features
 -----------------
 
 -   extended tutorials
--   phyloseq integration
--   CatchAll in R
--   better unit testing
--   longitudinal models for the microbiome
--   better graphics
--   automated estimator selection based on data structure
--   new format for modelling functions
-
-Do you have a request for us? Let us know!
+-   ~~phyloseq integration~~
+-   ~~better unit testing~~
+-   ~~better graphics~~
+-   ~~automated estimator selection based on data structure~~
+-   ~~new format for modelling functions~~
+
+Do you have a request for us? Let us know! We want folks to use `breakaway` and are committed to making it as easy to use as possible.
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,11 +1,15 @@
 pandoc: 1.17.2
 pkgdown: 1.1.0.9000
 pkgdown_sha: b2798656f04ce282edea3e12734ba5588c6acd6e
+<<<<<<< Updated upstream
 articles:
   breakaway: breakaway.html
   extended-tutorial: extended-tutorial.html
   resample-estimates: resample-estimates.html
   sample-size-calculations: sample-size-calculations.html
+=======
+articles: []
+>>>>>>> Stashed changes
 urls:
   reference: http://adw96.github.io/breakaway/reference
   article: http://adw96.github.io/breakaway/articles

diff --git a/docs/reference/alpha_estimate.html b/docs/reference/alpha_estimate.html
diff --git a/docs/reference/alpha_estimates.html b/docs/reference/alpha_estimates.html
diff --git a/docs/reference/apples.html b/docs/reference/apples.html