Merge branch 'release/v1.0.0' into main

evalclass · Apr 5, 2021 · df3e1a7 · df3e1a7
2 parents a0d18b5 + badcc84
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diff --git a/.travis.yml b/.travis.yml
@@ -3,7 +3,7 @@
 branches:
   only:
     - main
-    - develop
+#    - develop
 
 os:
  - linux

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,14 @@
 Package: prcbench
 Type: Package
 Title: Testing Workbench for Precision-Recall Curves
-Version: 0.9.2
+Version: 1.0.0
 Date: 2021-04-05
 Authors@R: c(
     person("Takaya", "Saito", email = "takaya.saito@outlook.com", role = c("aut", "cre")),
     person("Marc", "Rehmsmeier", email = "marc.rehmsmeier@ii.uib.no", role = c("aut")))
 Description: A testing workbench for evaluating precision-recall curves under various conditions.
-URL: https://takayasaito.github.io/prcbench/, https://github.com/takayasaito/prcbench
-BugReports: https://github.com/takayasaito/prcbench/issues
+URL: https://evalclass.github.io/prcbench/, https://github.com/evalclass/prcbench
+BugReports: https://github.com/evalclass/prcbench/issues
 Depends:
     R (>= 3.2.3)
 License: GPL-3

diff --git a/NEWS.md b/NEWS.md
@@ -1,32 +1,36 @@
-# precrec 0.9.1
+# prcbench 1.0.0
+
+* Transfer the GitHub repository to evalclass/prcbench
+
+# prcbench 0.9.1
 
 * Update Travis configurations for rJava
 
-# precrec 0.9
+# prcbench 0.9
 
 * Improve code quality using the results from lintr and CodeFactor.io
 
-# precrec 0.8.2
+# prcbench 0.8.2
 
 * Avoid data.frame() factor conversion in unit tests
 
-# precrec 0.8
+# prcbench 0.8
 
 * Fix hard-coded JAR file path issue
 
-# precrec 0.7.3
+# prcbench 0.7.3
 
 * Update curve evaluation for PRROC version 1.2
 
-# precrec 0.6.2
+# prcbench 0.6.2
 
 * Create github pages with pkgdown
 
-# precrec 0.5.2
+# prcbench 0.5.2
 
 * Update README
 
-* Update wrapper functions so that precrec works when PerfMeas is not available
+* Update wrapper functions so that prcbench works when PerfMeas is not available
 
 # prcbench 0.5
 

diff --git a/README.Rmd b/README.Rmd
@@ -5,10 +5,10 @@ output:
 
 # prcbench  <img src="man/figures/logo.png" align="right" alt="" width="100" />
 
-[![Travis](https://travis-ci.org/takayasaito/prcbench.svg?branch=main)](https://travis-ci.org/takayasaito/prcbench/)
-[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/takayasaito/prcbench?branch=main&svg=true)](https://ci.appveyor.com/project/takayasaito/prcbench/)
-[![codecov.io](https://codecov.io/github/takayasaito/prcbench/coverage.svg?branch=main)](https://codecov.io/github/takayasaito/prcbench?branch=main)
-[![CodeFactor](https://www.codefactor.io/repository/github/takayasaito/prcbench/badge)](https://www.codefactor.io/repository/github/takayasaito/prcbench/)
+[![Travis](https://travis-ci.org/evalclass/prcbench.svg?branch=main)](https://travis-ci.org/evalclass/prcbench/)
+[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/evalclass/prcbench?branch=main&svg=true)](https://ci.appveyor.com/project/takayasaito/prcbench/)
+[![codecov.io](https://codecov.io/github/evalclass/prcbench/coverage.svg?branch=main)](https://codecov.io/github/evalclass/prcbench?branch=main)
+[![CodeFactor](https://www.codefactor.io/repository/github/evalclass/prcbench/badge)](https://www.codefactor.io/repository/github/evalclass/prcbench/)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version-ago/prcbench)](https://cran.r-project.org/package=prcbench)
 [![CRAN_Logs_Badge](https://cranlogs.r-pkg.org/badges/grand-total/prcbench)](https://cran.r-project.org/package=prcbench)
 
@@ -22,12 +22,12 @@ interfaces for the following five tools. It also contains predefined test data s
 | AUCCalculator | [Tool web site](http://mark.goadrich.com/programs/AUC/)    |
 | PerfMeas      | [CRAN](https://cran.r-project.org/package=PerfMeas)      |
 | PRROC         | [CRAN](https://cran.r-project.org/package=PRROC)         |
-| precrec       | [Tool web site](https://takayasaito.github.io/precrec/), [CRAN](https://cran.r-project.org/package=precrec)       |
+| precrec       | [Tool web site](https://evalclass.github.io/precrec/), [CRAN](https://cran.r-project.org/package=precrec)       |
 
 ## Documentation
-- [Introduction to prcbench](https://takayasaito.github.io/prcbench/articles/introduction.html) -- a package vignette that contains the descriptions of the functions with several useful examples. View the vignette with `vignette("introduction", package = "prcbench")` in R. The HTML version is also available on the [GitPages](https://takayasaito.github.io/prcbench/articles/introduction.html).
+- [Introduction to prcbench](https://evalclass.github.io/prcbench/articles/introduction.html) -- a package vignette that contains the descriptions of the functions with several useful examples. View the vignette with `vignette("introduction", package = "prcbench")` in R. The HTML version is also available on the [GitHub Pages](https://evalclass.github.io/prcbench/articles/introduction.html).
 
-- [Help pages](https://takayasaito.github.io/prcbench/reference/) -- all the functions including the S3 generics have their own help pages with plenty of examples. View the main help page with `help(package = "prcbench")` in R. The HTML version is also available on the [GitPages](https://takayasaito.github.io/prcbench/reference/).
+- [Help pages](https://evalclass.github.io/prcbench/reference/) -- all the functions including the S3 generics have their own help pages with plenty of examples. View the main help page with `help(package = "prcbench")` in R. The HTML version is also available on the [GitHub Pages](https://evalclass.github.io/prcbench/reference/).
 
 ## Dependencies
 ### Java
@@ -43,7 +43,7 @@ interfaces for the following five tools. It also contains predefined test data s
 ## Installation
 * Install the release version of `prcbench` from CRAN with `install.packages("prcbench")`.
 
-* Alternatively, you can install a development version of `prcbench` from [our GitHub repository](https://github.com/takayasaito/prcbench). To install it:
+* Alternatively, you can install a development version of `prcbench` from [our GitHub repository](https://github.com/evalclass/prcbench). To install it:
 
     1. Make sure you have a working development environment.
         * **Windows**: Install Rtools (available on the CRAN website).
@@ -52,7 +52,7 @@ interfaces for the following five tools. It also contains predefined test data s
 
     2. Install `devtools` from CRAN with `install.packages("devtools")`.
 
-    3. Install `prcbench` from the GitHub repository with `devtools::install_github("takayasaito/prcbench")`.
+    3. Install `prcbench` from the GitHub repository with `devtools::install_github("evalclass/prcbench")`.
 
 ## Troubleshooting
 ### Bioconductor libraries
@@ -123,7 +123,7 @@ scores1 <- run_evalcurve(testset, toolset)
 autoplot(scores1)
 ```
 
-![](https://rawgit.com/takayasaito/prcbench/main/README_files/figure-markdown_github/unnamed-chunk-5-1.png)
+![](https://raw.githubusercontent.com/evalclass/prcbench/main/README_files/figure-gfm/unnamed-chunk-4-1.png)
 
 ```{r, warning=FALSE, fig.show='hide'}
 ## Plot the results of PerfMeas and PRROC on c1, c2, and c3 test sets
@@ -132,7 +132,7 @@ scores2 <- run_evalcurve(testset, toolset)
 autoplot(scores2, base_plot = FALSE)
 ```
 
-![](https://rawgit.com/takayasaito/prcbench/main/README_files/figure-markdown_github/unnamed-chunk-6-1.png)
+![](https://raw.githubusercontent.com/evalclass/prcbench/main/README_files/figure-gfm/unnamed-chunk-5-1.png)
 
 ```{r, echo = FALSE}
 knitr::opts_chunk$set(

diff --git a/README.md b/README.md
@@ -1,11 +1,11 @@
 
 # prcbench <img src="man/figures/logo.png" align="right" alt="" width="100" />
 
-[![Travis](https://travis-ci.org/takayasaito/prcbench.svg?branch=main)](https://travis-ci.org/takayasaito/prcbench/)
+[![Travis](https://travis-ci.org/evalclass/prcbench.svg?branch=main)](https://travis-ci.org/evalclass/prcbench/)
 [![AppVeyor Build
-Status](https://ci.appveyor.com/api/projects/status/github/takayasaito/prcbench?branch=main&svg=true)](https://ci.appveyor.com/project/takayasaito/prcbench/)
-[![codecov.io](https://codecov.io/github/takayasaito/prcbench/coverage.svg?branch=main)](https://codecov.io/github/takayasaito/prcbench?branch=main)
-[![CodeFactor](https://www.codefactor.io/repository/github/takayasaito/prcbench/badge)](https://www.codefactor.io/repository/github/takayasaito/prcbench/)
+Status](https://ci.appveyor.com/api/projects/status/github/evalclass/prcbench?branch=main&svg=true)](https://ci.appveyor.com/project/takayasaito/prcbench/)
+[![codecov.io](https://codecov.io/github/evalclass/prcbench/coverage.svg?branch=main)](https://codecov.io/github/evalclass/prcbench?branch=main)
+[![CodeFactor](https://www.codefactor.io/repository/github/evalclass/prcbench/badge)](https://www.codefactor.io/repository/github/evalclass/prcbench/)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version-ago/prcbench)](https://cran.r-project.org/package=prcbench)
 [![CRAN\_Logs\_Badge](https://cranlogs.r-pkg.org/badges/grand-total/prcbench)](https://cran.r-project.org/package=prcbench)
 
@@ -14,66 +14,66 @@ evaluating precision-recall curves under various conditions. It contains
 integrated interfaces for the following five tools. It also contains
 predefined test data sets.
 
-| Tool          | Link                                                                                                        |
-| ------------- | ----------------------------------------------------------------------------------------------------------- |
-| ROCR          | [Tool web site](https://ipa-tys.github.io/ROCR/), [CRAN](https://cran.r-project.org/package=ROCR)           |
-| AUCCalculator | [Tool web site](http://mark.goadrich.com/programs/AUC/)                                                     |
-| PerfMeas      | [CRAN](https://cran.r-project.org/package=PerfMeas)                                                         |
-| PRROC         | [CRAN](https://cran.r-project.org/package=PRROC)                                                            |
-| precrec       | [Tool web site](https://takayasaito.github.io/precrec/), [CRAN](https://cran.r-project.org/package=precrec) |
+| Tool          | Link                                                                                                      |
+|---------------|-----------------------------------------------------------------------------------------------------------|
+| ROCR          | [Tool web site](https://ipa-tys.github.io/ROCR/), [CRAN](https://cran.r-project.org/package=ROCR)         |
+| AUCCalculator | [Tool web site](http://mark.goadrich.com/programs/AUC/)                                                   |
+| PerfMeas      | [CRAN](https://cran.r-project.org/package=PerfMeas)                                                       |
+| PRROC         | [CRAN](https://cran.r-project.org/package=PRROC)                                                          |
+| precrec       | [Tool web site](https://evalclass.github.io/precrec/), [CRAN](https://cran.r-project.org/package=precrec) |
 
 ## Documentation
 
-  - [Introduction to
-    prcbench](https://takayasaito.github.io/prcbench/articles/introduction.html)
+-   [Introduction to
+    prcbench](https://evalclass.github.io/prcbench/articles/introduction.html)
     – a package vignette that contains the descriptions of the functions
     with several useful examples. View the vignette with
     `vignette("introduction", package = "prcbench")` in R. The HTML
-    version is also available on the
-    [GitPages](https://takayasaito.github.io/prcbench/articles/introduction.html).
+    version is also available on the [GitHub
+    Pages](https://evalclass.github.io/prcbench/articles/introduction.html).
 
-  - [Help pages](https://takayasaito.github.io/prcbench/reference/) –
-    all the functions including the S3 generics have their own help
-    pages with plenty of examples. View the main help page with
+-   [Help pages](https://evalclass.github.io/prcbench/reference/) – all
+    the functions including the S3 generics have their own help pages
+    with plenty of examples. View the main help page with
     `help(package = "prcbench")` in R. The HTML version is also
-    available on the
-    [GitPages](https://takayasaito.github.io/prcbench/reference/).
+    available on the [GitHub
+    Pages](https://evalclass.github.io/prcbench/reference/).
 
 ## Dependencies
 
 ### Java
 
-`AUCCalculator` requires a Java runtime (\>= 6).
+`AUCCalculator` requires a Java runtime (&gt;= 6).
 
 ### Bioconductor libraries
 
 `PerfMeas` requires Bioconductor libraries.
 
-  - [limma](https://bioconductor.org/packages/limma/)
-  - [graph](https://bioconductor.org/packages/graph/)
-  - [RBGL](https://bioconductor.org/packages/RBGL/)
+-   [limma](https://bioconductor.org/packages/limma/)
+-   [graph](https://bioconductor.org/packages/graph/)
+-   [RBGL](https://bioconductor.org/packages/RBGL/)
 
 ## Installation
 
-  - Install the release version of `prcbench` from CRAN with
+-   Install the release version of `prcbench` from CRAN with
     `install.packages("prcbench")`.
 
-  - Alternatively, you can install a development version of `prcbench`
-    from [our GitHub
-    repository](https://github.com/takayasaito/prcbench). To install it:
-    
+-   Alternatively, you can install a development version of `prcbench`
+    from [our GitHub repository](https://github.com/evalclass/prcbench).
+    To install it:
+
     1.  Make sure you have a working development environment.
-        
-          - **Windows**: Install Rtools (available on the CRAN website).
-          - **Mac**: Install Xcode from the Mac App Store.
-          - **Linux**: Install a compiler and various development
+
+        -   **Windows**: Install Rtools (available on the CRAN website).
+        -   **Mac**: Install Xcode from the Mac App Store.
+        -   **Linux**: Install a compiler and various development
             libraries (details vary across different flavors of Linux).
-    
+
     2.  Install `devtools` from CRAN with
         `install.packages("devtools")`.
-    
+
     3.  Install `prcbench` from the GitHub repository with
-        `devtools::install_github("takayasaito/prcbench")`.
+        `devtools::install_github("evalclass/prcbench")`.
 
 ## Troubleshooting
 
@@ -99,28 +99,22 @@ not work on some OSs. `prcbench` uses `system.time` when
 
 ### rJava
 
-  - Some OSs require further configuration for rJava.
+-   Some OSs require further configuration for rJava.
 
-<!-- end list -->
+<!-- -->
 
     sudo R CMD javareconf
 
-  - JDKs for macOS Big Sur.
-
-<!-- end list -->
+-   JDKs for macOS Big Sur.
 
 1.  [AdoptOpenJDK](https://adoptopenjdk.net/)
 2.  [AdoptOpenJDK with
     homebrew](https://github.com/AdoptOpenJDK/homebrew-openjdk/)
 3.  [Oracle JDK](https://www.oracle.com/java/)
 
-<!-- end list -->
-
-  - JRI support on macOS Big Sur – see this [Stack Overflow
+-   JRI support on macOS Big Sur – see this [Stack Overflow
     thread](https://stackoverflow.com/questions/65278552/cannot-install-rjava-on-big-sur).
 
-<!-- end list -->
-
 ``` r
 install.packages("rJava", configure.args="--disable-jri")
 ```
@@ -143,18 +137,23 @@ library(prcbench)
 testset <- create_testset("bench", "b10")
 toolset <- create_toolset(set_names = "auc5")
 res <- run_benchmark(testset, toolset)
+```
+
+    ## [1] "microbenchmark is not available. system.time will be used instead."
+    ## [1] "PerfMeas is not available."
 
+``` r
 ## Use knitr::kable to show the result in a table format
 knitr::kable(res$tab, digits = 2)
 ```
 
-| testset | toolset | toolname      |  min |   lq |  mean | median |    uq |    max | neval |
-| :------ | :------ | :------------ | ---: | ---: | ----: | -----: | ----: | -----: | ----: |
-| b10     | auc5    | AUCCalculator | 1.62 | 1.98 |  4.73 |   3.32 |  3.33 |  13.37 |     5 |
-| b10     | auc5    | PerfMeas      | 0.06 | 0.06 | 55.29 |   0.07 |  0.08 | 276.20 |     5 |
-| b10     | auc5    | precrec       | 4.33 | 5.23 | 24.24 |   5.24 | 10.16 |  96.26 |     5 |
-| b10     | auc5    | PRROC         | 0.13 | 0.13 |  0.64 |   0.13 |  0.15 |   2.68 |     5 |
-| b10     | auc5    | ROCR          | 1.49 | 1.52 |  7.86 |   1.63 | 12.56 |  22.11 |     5 |
+| testset | toolset | toolname      | min |  lq | mean | median |  uq | max | neval |
+|:--------|:--------|:--------------|----:|----:|-----:|-------:|----:|----:|------:|
+| b10     | auc5    | AUCCalculator |   4 |   5 |    7 |   11.2 |   9 |  31 |     5 |
+| b10     | auc5    | PerfMeas      |   0 |   0 |    0 |    0.2 |   0 |   1 |     5 |
+| b10     | auc5    | precrec       |   7 |   8 |    9 |   42.4 |  11 | 177 |     5 |
+| b10     | auc5    | PRROC         |   0 |   1 |    1 |    2.6 |   1 |  10 |     5 |
+| b10     | auc5    | ROCR          |   3 |   3 |    4 |   16.6 |  24 |  49 |     5 |
 
 ### Evaluation of precision-recall curves
 
@@ -173,16 +172,21 @@ scores1 <- run_evalcurve(testset, toolset)
 autoplot(scores1)
 ```
 
-![](https://rawgit.com/takayasaito/prcbench/main/README_files/figure-markdown_github/unnamed-chunk-5-1.png)
+![](https://raw.githubusercontent.com/evalclass/prcbench/main/README_files/figure-gfm/unnamed-chunk-4-1.png)
 
 ``` r
 ## Plot the results of PerfMeas and PRROC on c1, c2, and c3 test sets
 toolset <- create_toolset(c("PerfMeas", "PRROC"))
 scores2 <- run_evalcurve(testset, toolset)
+```
+
+    ## [1] "PerfMeas is not available."
+
+``` r
 autoplot(scores2, base_plot = FALSE)
 ```
 
-![](https://rawgit.com/takayasaito/prcbench/main/README_files/figure-markdown_github/unnamed-chunk-6-1.png)
+![](https://raw.githubusercontent.com/evalclass/prcbench/main/README_files/figure-gfm/unnamed-chunk-5-1.png)
 
 ## Citation
 
@@ -198,12 +202,12 @@ doi:
 
 ## External links
 
-  - [Classifier evaluation with imbalanced
+-   [Classifier evaluation with imbalanced
     datasets](https://classeval.wordpress.com/) – our web site that
     contains several pages with useful tips for performance evaluation
     on binary classifiers.
 
-  - [The Precision-Recall Plot Is More Informative than the ROC Plot
+-   [The Precision-Recall Plot Is More Informative than the ROC Plot
     When Evaluating Binary Classifiers on Imbalanced
     Datasets](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118432)
     – our paper that summarized potential pitfalls of ROC plots with

diff --git a/README_files/figure-gfm/unnamed-chunk-4-1.png b/README_files/figure-gfm/unnamed-chunk-4-1.png
diff --git a/README_files/figure-gfm/unnamed-chunk-5-1.png b/README_files/figure-gfm/unnamed-chunk-5-1.png
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,10 +1,12 @@
-templates:
-  params:
-    bootswatch: cerulean
+url: https://evalclass.github.io/prcbench
 
 repo:
   branch: main
 
+templates:
+  params:
+    bootswatch: cerulean
+
 reference:
   - title: Package
     contents:

diff --git a/appveyor.yml b/appveyor.yml
@@ -25,7 +25,7 @@ install:
 branches:
   only:
     - main
-    - develop
+#    - develop
 
 skip_tags: true