deal with some CRAN notes and warnings

R/plot_alpha_estimates.R

@@ -60,17 +60,18 @@ plot.alpha_estimates <- function(x, physeq = NULL, measure = NULL, color = NULL,
     df$sample_names <- rownames(df)
   }
 
-  aes_map <- ggplot2::aes_string(colour = color, shape = shape)
+  aes_map <- ggplot2::aes_string(color = "color", shape = "shape")
   my_gg <- ggplot2::ggplot(df, aes_map) +
-    ggplot2::geom_point(ggplot2::aes(x = sample_names, y = estimate)) + 
+    ggplot2::geom_point(ggplot2::aes_string(x = "sample_names", y = "estimate")) + 
     ggplot2::ylab(paste(yname1, "estimate of", yname2)) +
     ggplot2::xlab("") +
     ggplot2::labs(title = title) +
     ggplot2::theme_bw() + 
     ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1))
 
   if (!(all(is.na(df$lower)) || all(is.na(df$upper)))) {
-    my_gg <- my_gg + ggplot2::geom_segment(ggplot2::aes(x = sample_names, xend = sample_names, y = lower, yend = upper))
+    my_gg <- my_gg + 
+      ggplot2::geom_segment(ggplot2::aes_string(x = "sample_names", xend = "sample_names", y = "lower", yend = "upper"))
   }
 
   if (!trim_plot) {

R/shannon_good_turing.R

@@ -16,7 +16,7 @@ good_turing  <- function(input_data) {
     } else {
       return(input_data %>% 
                otu_table %>%
-               apply(1, function(x) good_turin(make_frequency_count_table(x))) %>%
+               apply(1, function(x) good_turing(make_frequency_count_table(x))) %>%
                alpha_estimates)
     }
   }

README.Rmd

@@ -22,7 +22,7 @@ knitr::opts_chunk$set(
 
 
 `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. 
+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!
 
@@ -53,7 +53,7 @@ devtools::install_github("adw96/breakaway")
 
 ### 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/package=breakaway) or with
 ```R
 install.packages("breakaway")
 ```
@@ -73,4 +73,4 @@ Authors: [Amy Willis](http://faculty.washington.edu/adwillis/), [Bryan Martin](h
 - ~~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.
+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.

README.md

@@ -1,27 +1,49 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-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)
-
-`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)!
+# 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)
+
+`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:
+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.
+  - `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
-------------
+## Installation
 
 ### Development version
 
@@ -32,31 +54,38 @@ 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/package=breakaway) or
+with
 
 ``` r
 install.packages("breakaway")
 ```
 
-Humans
-------
+## Humans
 
 Maintainer: [Amy Willis](http://faculty.washington.edu/adwillis/)
 
-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)
+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
------------------
+## Upcoming features
 
--   extended tutorials
--   ~~phyloseq integration~~
--   ~~better unit testing~~
--   ~~better graphics~~
--   ~~automated estimator selection based on data structure~~
--   ~~new format for modelling functions~~
+  - extended tutorials
+  - ~~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.
+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.