Rename to babette again, thanks TECE

CONTRIBUTING.md

@@ -9,7 +9,7 @@ This GitHub follows the [Contributor Covenant Code of Conduct](code_of_conduct.m
 
 ## Which package to contribute to?
 
-`rbeast2` consists out of three packages.
+`babette` consists out of three packages.
 
 If you want to contribute to the creation of BEAST2 XML input file,
 go to [beautier](https://github.com/richelbilderbeek/beautier/blob/master/CONTRIBUTING.md).
@@ -52,15 +52,15 @@ Pull Requests should follow the same guidelines as 'Submitting code'.
 
 ## git usage
 
-To get started working on `rbeast2` do:
+To get started working on `babette` do:
 
 ```
-git clone https://github.com/richelbilderbeek/rbeast2
+git clone https://github.com/richelbilderbeek/babette
 ```
 
 Development is done on the `develop` branch. 
 To download and checkout the `develop` branch, 
-first go into the `beautier` folder (`cd rbeast2`), then do:
+first go into the `beautier` folder (`cd babette`), then do:
 
 ```
 git checkout -b develop origin/develop

DESCRIPTION

@@ -1,18 +1,18 @@
-Package: rbeast2
+Package: babette
 Title: control BEAST2 from R
 Version: 0.9.0
 Author: Richel J.C. Bilderbeek <richel@richelbilderbeek.nl>
 Maintainer: Richel J.C. Bilderbeek <richel@richelbilderbeek.nl>
-Description: rbeast2 gives full control of BEAST2 from R.
-  rbeast2 can create BEAST2 XML input files. 
-  rbeast2 can run BEAST2 with those input file.
-  rbeast2 can parse the results of that BEAST2 run.
+Description: babette gives full control of BEAST2 from R.
+  babette can create BEAST2 XML input files. 
+  babette can run BEAST2 with those input file.
+  babette can parse the results of that BEAST2 run.
 License: file LICENSE
 LazyData: true
 RoxygenNote: 6.0.1
 VignetteBuilder: knitr
-URL: https://github.com/richelbilderbeek/rbeast2
-BugReports: https://github.com/richelbilderbeek/rbeast2/issues
+URL: https://github.com/richelbilderbeek/babette
+BugReports: https://github.com/richelbilderbeek/babette/issues
 Imports:
     beautier,
     beastier,

R/get_path.R

@@ -9,7 +9,7 @@
 #' @export
 get_path <- function(filename) {
 
-  full <- system.file("extdata", filename, package = "rbeast2")
+  full <- system.file("extdata", filename, package = "babette")
   if (!file.exists(full)) {
     stop("'filename' must be the name of a file in 'inst/extdata'")
   }

README.md

@@ -1,17 +1,17 @@
-# rbeast2
+# babette
 
 Branch|[![Travis CI logo](pics/TravisCI.png)](https://travis-ci.org)|[![Codecov logo](pics/Codecov.png)](https://www.codecov.io)
 ---|---|---
-master|[![Build Status](https://travis-ci.org/richelbilderbeek/rbeast2.svg?branch=master)](https://travis-ci.org/richelbilderbeek/rbeast2)|[![codecov.io](https://codecov.io/github/richelbilderbeek/rbeast2/coverage.svg?branch=master)](https://codecov.io/github/richelbilderbeek/rbeast2/branch/master)
-develop|[![Build Status](https://travis-ci.org/richelbilderbeek/rbeast2.svg?branch=develop)](https://travis-ci.org/richelbilderbeek/rbeast2)|[![codecov.io](https://codecov.io/github/richelbilderbeek/rbeast2/coverage.svg?branch=develop)](https://codecov.io/github/richelbilderbeek/rbeast2/branch/develop)
+master|[![Build Status](https://travis-ci.org/richelbilderbeek/babette.svg?branch=master)](https://travis-ci.org/richelbilderbeek/babette)|[![codecov.io](https://codecov.io/github/richelbilderbeek/babette/coverage.svg?branch=master)](https://codecov.io/github/richelbilderbeek/babette/branch/master)
+develop|[![Build Status](https://travis-ci.org/richelbilderbeek/babette.svg?branch=develop)](https://travis-ci.org/richelbilderbeek/babette)|[![codecov.io](https://codecov.io/github/richelbilderbeek/babette/coverage.svg?branch=develop)](https://codecov.io/github/richelbilderbeek/babette/branch/develop)
 
-`rbeast2` is an R package that combines:
+`babette` is an R package that combines:
 
  * [beautier](https://github.com/richelbilderbeek/beautier) creates BEAST2 input (`.xml`) files.
  * [beastier](https://github.com/richelbilderbeek/beastier) runs BEAST2
  * [tracerer](https://github.com/richelbilderbeek/tracerer) parses BEAST2 output (`.log`, `.trees`, etc) files.
 
-![rbeast2 logo](pics/rbeast2_logo.png)
+![babette logo](pics/babette_logo.png)
 
 ## Examples
 
@@ -22,7 +22,7 @@ See [examples](examples.md).
 If you use the `devtools` R package, this is easy:
 
 ```
-devtools::install_github("richelbilderbeek/rbeast2")
+devtools::install_github("richelbilderbeek/babette")
 ```
 
 ## FAQ
@@ -31,7 +31,7 @@ See [FAQ](faq.md)
 
 ## Missing features/unsupported
 
-`rbeast2` cannot do everything `BEAUti` and `BEAST2` and `Tracer` can.
+`babette` cannot do everything `BEAUti` and `BEAST2` and `Tracer` can.
 
 See [beautier](https://github.com/richelbilderbeek/beautier) 
 for missing features in creating a BEAST2 input (`.xml`) file.

examples.md

@@ -1,9 +1,9 @@
 # Examples
 
-For all examples, do load `rbeast2`:
+For all examples, do load `babette`:
 
 ```
-library(rbeast2)
+library(babette)
 ```
 
 All examples read the alignment from a FASTA file (usually `my_fasta.fas`) 
@@ -135,7 +135,7 @@ Thanks to Paul van Els for this use case and supplying these FASTA files.
 ![Example 10: Two alignments, different site models](pics/aco_hky_nd2_tn93.png)
 
 ```{r example_10}
-rbeast2::posterior <- run_beast2(
+babette::posterior <- run_beast2(
   c("anthus_aco.fas", "anthus_nd2.fas"),
   site_models = list(
     create_hky_site_model(), 
@@ -153,7 +153,7 @@ Thanks to Paul van Els for this use case.
 [Example 11: shared clock model](aco_nd2_same_clock_model.png)
 
 ```{r example_10}
-rbeast2::posterior <- run_beast2(
+babette::posterior <- run_beast2(
   c("anthus_aco.fas", "anthus_nd2.fas"),
   clock_models = list(
     create_strict_clock_model(id = "anthus_aco"), 

faq.md

@@ -6,7 +6,7 @@ Version 2.4.7.
 
 ## What's the road map?
 
-Currently, `rbeast2` does not have a road map itself, but `beautier` does:
+Currently, `babette` does not have a road map itself, but `beautier` does:
 
  * [beautier road map](https://github.com/richelbilderbeek/beautier/blob/master/road_map.md)
 

scripts/push

@@ -1,27 +1,27 @@
 #!/bin/bash
 
-# Push all GitHubs under rbeast2
+# Push all GitHubs under babette
 
 cd ..
 git add --all :/
-git commit -m "rbeast2 update"
+git commit -m "babette update"
 git push
 cd ..
 
 cd beautier
 git add --all :/
-git commit -m "rbeast2 update"
+git commit -m "babette update"
 git push
 cd ..
 
 cd beastier
 git add --all :/
-git commit -m "rbeast2 update"
+git commit -m "babette update"
 git push
 cd ..
 
 cd tracerer
 git add --all :/
-git commit -m "rbeast2 update"
+git commit -m "babette update"
 git push
 cd ..

tests/testthat.R

@@ -1,4 +1,4 @@
 library(testthat)
-library(rbeast2)
+library(babette)
 
-test_check("rbeast2")
+test_check("babette")

tests/testthat/test-get_alignment_ids.R

@@ -3,11 +3,11 @@ context("get_alignment_ids")
 test_that("use", {
 
   testthat::expect_equal(
-    rbeast2:::get_alignment_ids(get_path("2_4.xml")),
+    babette:::get_alignment_ids(get_path("2_4.xml")),
     c("test_output_0")
   )
   testthat::expect_equal(
-    rbeast2:::get_alignment_ids(xml_filename = get_path("anthus_2_4.xml")),
+    babette:::get_alignment_ids(xml_filename = get_path("anthus_2_4.xml")),
     c("Anthus_nd2", "Anthus_aco")
   )
 
@@ -16,7 +16,7 @@ test_that("use", {
 test_that("use", {
 
   testthat::expect_error(
-    rbeast2:::get_alignment_ids("abs.ent"),
+    babette:::get_alignment_ids("abs.ent"),
     "'xml_filename' must be the name of an existing file"
   )
 

tests/testthat/test-get_path.R

@@ -3,21 +3,21 @@ context("get_path")
 test_that("use", {
 
   testthat::expect_equal(
-    system.file("extdata", "anthus_nd2.fas", package = "rbeast2"),
-    rbeast2::get_path("anthus_nd2.fas")
+    system.file("extdata", "anthus_nd2.fas", package = "babette"),
+    babette::get_path("anthus_nd2.fas")
   )
 
   testthat::expect_equal(
-    system.file("extdata", "anthus_aco.fas", package = "rbeast2"),
-    rbeast2::get_path("anthus_aco.fas")
+    system.file("extdata", "anthus_aco.fas", package = "babette"),
+    babette::get_path("anthus_aco.fas")
   )
 
 })
 
 test_that("abuse", {
 
   testthat::expect_error(
-    rbeast2::get_path("abs.ent"),
+    babette::get_path("abs.ent"),
     "'filename' must be the name of a file in 'inst/extdata'"
   )
 

tests/testthat/test-get_paths.R

@@ -4,10 +4,10 @@ test_that("use", {
 
   testthat::expect_equal(
     c(
-      rbeast2::get_path("anthus_aco.fas"),
-      rbeast2::get_path("anthus_nd2.fas")
+      babette::get_path("anthus_aco.fas"),
+      babette::get_path("anthus_nd2.fas")
     ),
-    rbeast2::get_paths(c("anthus_aco.fas", "anthus_nd2.fas"))
+    babette::get_paths(c("anthus_aco.fas", "anthus_nd2.fas"))
   )
 
 })

tests/testthat/test-onLoad.R

@@ -2,6 +2,6 @@ context("onLoad")
 
 test_that("use", {
 
-  rbeast2:::.onLoad()
+  babette:::.onLoad()
 
 })

vignettes/article.R

@@ -5,14 +5,14 @@ knitr::opts_chunk$set(
 )
 
 ## ----create_files, include = FALSE---------------------------------------
-file.copy(rbeast2::get_path("anthus_aco.fas"), "test_output_0.fas")
-file.copy(rbeast2::get_path("anthus_aco.fas"), "my_fasta.fas")
-file.copy(rbeast2::get_path("anthus_aco.fas"), "my_alignment.fas")
-file.copy(rbeast2::get_path("anthus_aco.fas"), "anthus_aco.fas")
-file.copy(rbeast2::get_path("anthus_nd2.fas"), "anthus_nd2.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "test_output_0.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "my_fasta.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "my_alignment.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "anthus_aco.fas")
+file.copy(babette::get_path("anthus_nd2.fas"), "anthus_nd2.fas")
 
 ## ------------------------------------------------------------------------
-library(rbeast2)
+library(babette)
 mcmc <- create_mcmc(chain_length = 2000, store_every = 1000)
 
 ## ----cache=TRUE----------------------------------------------------------

vignettes/article.Rmd

@@ -1,10 +1,10 @@
 ---
-title: "rbeast2: BEAUti 2, BEAST2 and Tracer for R"
+title: "babette: BEAUti 2, BEAST2 and Tracer for R"
 author: "Richel J.C. Bilderbeek"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{rbeast2: BEAUti 2, BEAST2 and Tracer for R}
+  %\VignetteIndexEntry{babette: BEAUti 2, BEAST2 and Tracer for R}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -17,17 +17,17 @@ knitr::opts_chunk$set(
 ```
 
 ```{r create_files, include = FALSE}
-file.copy(rbeast2::get_path("anthus_aco.fas"), "test_output_0.fas")
-file.copy(rbeast2::get_path("anthus_aco.fas"), "my_fasta.fas")
-file.copy(rbeast2::get_path("anthus_aco.fas"), "my_alignment.fas")
-file.copy(rbeast2::get_path("anthus_aco.fas"), "anthus_aco.fas")
-file.copy(rbeast2::get_path("anthus_nd2.fas"), "anthus_nd2.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "test_output_0.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "my_fasta.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "my_alignment.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "anthus_aco.fas")
+file.copy(babette::get_path("anthus_nd2.fas"), "anthus_nd2.fas")
 ```
 
 This vignette does the same as the code in the article.
 
 ```{r}
-library(rbeast2)
+library(babette)
 mcmc <- create_mcmc(chain_length = 2000, store_every = 1000)
 ```
 

vignettes/demo.R

@@ -4,8 +4,8 @@ knitr::opts_chunk$set(
   comment = "#>"
 )
 
-## ----load_rbeast2, results='hide', warning=FALSE, error=FALSE, message=FALSE----
-library(rbeast2)
+## ----load_babette, results='hide', warning=FALSE, error=FALSE, message=FALSE----
+library(babette)
 
 ## ------------------------------------------------------------------------
 sample_interval <- 1000

vignettes/demo.Rmd

@@ -1,10 +1,10 @@
 ---
-title: "rbeast2 demo"
+title: "babette demo"
 author: "Richel J.C. Bilderbeek"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{rbeast2 demo}
+  %\VignetteIndexEntry{babette demo}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -18,12 +18,12 @@ knitr::opts_chunk$set(
 
 ## Introduction
 
-This vignette demonstrates how to use `rbeast2`.
+This vignette demonstrates how to use `babette`.
 
 First, load the library:
 
-```{r load_rbeast2, results='hide', warning=FALSE, error=FALSE, message=FALSE}
-library(rbeast2)
+```{r load_babette, results='hide', warning=FALSE, error=FALSE, message=FALSE}
+library(babette)
 ```
 
 The following examples show:
@@ -34,7 +34,7 @@ The following examples show:
 
 Of each example, it is shown:
 
- * How to let `rbeast2` run BEAST2
+ * How to let `babette` run BEAST2
  * How the plot the posterior estimates
  * How to show the effective sample sizes (ESS)
 

vignettes/examples.R

@@ -5,12 +5,12 @@ knitr::opts_chunk$set(
 )
 
 ## ----create_files, include = FALSE---------------------------------------
-file.copy(rbeast2::get_path("anthus_aco.fas"), "test_output_0.fas")
-file.copy(rbeast2::get_path("anthus_aco.fas"), "my_fasta.fas")
-file.copy(rbeast2::get_path("anthus_aco.fas"), "my_alignment.fas")
-file.copy(rbeast2::get_path("anthus_aco.fas"), "anthus_aco.fas")
-file.copy(rbeast2::get_path("anthus_nd2.fas"), "anthus_nd2.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "test_output_0.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "my_fasta.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "my_alignment.fas")
+file.copy(babette::get_path("anthus_aco.fas"), "anthus_aco.fas")
+file.copy(babette::get_path("anthus_nd2.fas"), "anthus_nd2.fas")
 
-## ----load_rbeast2, results='hide', warning=FALSE, error=FALSE, message=FALSE----
-library(rbeast2)
+## ----load_babette, results='hide', warning=FALSE, error=FALSE, message=FALSE----
+library(babette)