From 03e8624e32f3f8ecf44fba832a7cb666138214b5 Mon Sep 17 00:00:00 2001 From: Takaya Saito Date: Tue, 6 Apr 2021 13:37:32 +0200 Subject: [PATCH 1/3] Update citation --- inst/CITATION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/inst/CITATION b/inst/CITATION index 29f2adc..5e8f4d2 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -14,5 +14,5 @@ citEntry(entry = "Article", paste("Takaya Saito and Marc Rehmsmeier (2017).", "Precrec: fast and accurate precision-recall and ROC curve calculations in R.", "Bioinformatics (2017) 33 (1): 145-147.", - "doi: 10.1093/bioinformatics/btw570") -) + "https://doi.org/10.1093/bioinformatics/btw570") +) \ No newline at end of file From b2664cb48ea2706b3690755835d4c5812da00a0e Mon Sep 17 00:00:00 2001 From: Takaya Saito Date: Tue, 6 Apr 2021 13:37:51 +0200 Subject: [PATCH 2/3] Update relase docs for v1.0.1 --- DESCRIPTION | 4 ++-- NEWS.md | 4 ++++ cran-comments.md | 8 +++++--- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5f92e17..0feb664 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: prcbench Type: Package Title: Testing Workbench for Precision-Recall Curves -Version: 1.0.0 -Date: 2021-04-05 +Version: 1.0.1 +Date: 2021-04-06 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"))) diff --git a/NEWS.md b/NEWS.md index 21b1393..98f671f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# prcbench 1.0.1 + +* Update citation + # prcbench 1.0.0 * Transfer the GitHub repository to evalclass/prcbench diff --git a/cran-comments.md b/cran-comments.md index 733f7ab..87d1b26 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,12 +1,14 @@ -## Version 1.0.0 +## Version 1.0.1 This is a submission for updating the already published package - prcbench. In this version I have: -* Transferred the GitHub repository to an organization GitHub account, and +* Transferred the GitHub repository to an organization GitHub account, + +* Updated citation, and * Updated the version. - * 0.9.1 -> 1.0.0 + * 0.9.1 -> 1.0.1 ## Test environments * local Ubuntu 20.04 High Sierra, R 4.0.5 From 732647b85f77b9c4c2b615b7d2e6c8b4dbe39050 Mon Sep 17 00:00:00 2001 From: Takaya Saito Date: Tue, 6 Apr 2021 13:38:06 +0200 Subject: [PATCH 3/3] Update website for v1.0.1 --- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/articles/introduction.html | 22 +++++++++++----------- docs/authors.html | 4 ++-- docs/index.html | 2 +- docs/news/index.html | 10 +++++++++- docs/pkgdown.yml | 2 +- docs/reference/C1DATA.html | 2 +- docs/reference/C2DATA.html | 2 +- docs/reference/C3DATA.html | 2 +- docs/reference/C4DATA.html | 2 +- docs/reference/TestDataB.html | 2 +- docs/reference/TestDataC.html | 2 +- docs/reference/ToolAUCCalculator.html | 2 +- docs/reference/ToolIFBase.html | 2 +- docs/reference/ToolPRROC.html | 2 +- docs/reference/ToolPerfMeas.html | 2 +- docs/reference/ToolROCR.html | 2 +- docs/reference/Toolprecrec.html | 2 +- docs/reference/autoplot.html | 2 +- docs/reference/create_example_func.html | 6 +++--- docs/reference/create_testset.html | 2 +- docs/reference/create_toolset.html | 2 +- docs/reference/create_usrdata.html | 2 +- docs/reference/create_usrtool.html | 2 +- docs/reference/index.html | 2 +- docs/reference/prcbench.html | 2 +- docs/reference/run_benchmark.html | 2 +- docs/reference/run_evalcurve.html | 2 +- 30 files changed, 51 insertions(+), 43 deletions(-) diff --git a/docs/404.html b/docs/404.html index 0da0d12..a03a9e8 100644 --- a/docs/404.html +++ b/docs/404.html @@ -79,7 +79,7 @@ prcbench - 1.0.0 + 1.0.1 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f98f386..6ddc0ba 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -79,7 +79,7 @@ prcbench - 1.0.0 + 1.0.1 diff --git a/docs/articles/index.html b/docs/articles/index.html index 9c49b8a..84395bf 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -79,7 +79,7 @@ prcbench - 1.0.0 + 1.0.1 diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html index ffd5dde..d4d7339 100644 --- a/docs/articles/introduction.html +++ b/docs/articles/introduction.html @@ -38,7 +38,7 @@ prcbench - 1.0.0 + 1.0.1 @@ -73,7 +73,7 @@

Introduction to prcbench

-

2021-04-05

+

2021-04-06

Source: vignettes/introduction.Rmd @@ -266,11 +266,11 @@

res <- run_benchmark(testset, toolset) res

##   testset toolset      toolname   min    lq  mean median     uq   max neval
-## 1     b10    auc5 AUCCalculator 1.570 1.989  4.96  3.041  4.213  14.0     5
-## 2     b10    auc5      PerfMeas 0.059 0.063 55.37  0.066  0.085 276.6     5
-## 3     b10    auc5       precrec 5.022 5.425 24.49  5.732  9.492  96.8     5
-## 4     b10    auc5         PRROC 0.134 0.149  0.66  0.149  0.161   2.7     5
-## 5     b10    auc5          ROCR 1.491 1.517  7.76  1.631 11.996  22.2     5
+## 1 b10 auc5 AUCCalculator 1.595 2.170 4.85 2.804 3.744 14.0 5 +## 2 b10 auc5 PerfMeas 0.057 0.062 55.04 0.064 0.081 274.9 5 +## 3 b10 auc5 precrec 5.153 5.165 24.23 5.359 9.474 96.0 5 +## 4 b10 auc5 PRROC 0.133 0.134 0.68 0.140 0.151 2.9 5 +## 5 b10 auc5 ROCR 1.459 1.461 7.68 1.569 12.142 21.8 5

@@ -389,8 +389,8 @@

## pred <- list(x = seq(0, 1, 1/length(scores)), y = seq(0, ## 1, 1/length(scores)), auc = 0.5) ## } -## <bytecode: 0x5653992e95b0> -## <environment: 0x56539920e828> +## <bytecode: 0x562e3843a998> +## <environment: 0x562e383002f0>

The create_testset function produces a testset as either TestDataB or TestDataC object. See the help files of the R6 classes - help(TestDataB) and help(TestDataC) - for the methods that can be used with the Precision-Recall calculation.

@@ -413,8 +413,8 @@

res <- run_benchmark(testsetB, toolset) res 
##   testset toolset toolname min  lq mean median  uq max neval
-## 1      b5 precrec  precrec 3.8 3.8  4.0    3.9 4.0 4.5     5
-## 2      b5    ROCR     ROCR 1.5 1.6  1.7    1.7 1.9 1.9     5
+## 1 b5 precrec precrec 3.9 3.9 4.2 3.9 4.1 5.2 5 +## 2 b5 ROCR ROCR 1.5 1.5 1.5 1.5 1.5 1.7 5

diff --git a/docs/authors.html b/docs/authors.html index c626cfd..eb52d18 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -79,7 +79,7 @@ prcbench - 1.0.0 + 1.0.1

@@ -116,7 +116,7 @@

Citation

Source: inst/CITATION -

Takaya Saito and Marc Rehmsmeier (2017). Precrec: fast and accurate precision-recall and ROC curve calculations in R. Bioinformatics (2017) 33 (1): 145-147. doi: 10.1093/bioinformatics/btw570

+

Takaya Saito and Marc Rehmsmeier (2017). Precrec: fast and accurate precision-recall and ROC curve calculations in R. Bioinformatics (2017) 33 (1): 145-147. https://doi.org/10.1093/bioinformatics/btw570

@Article{,
   title = {Precrec: fast and accurate precision-recall and ROC curve calculations in R},
   author = {Takaya Saito and Marc Rehmsmeier},
diff --git a/docs/index.html b/docs/index.html
index 4c6d127..782efb1 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -38,7 +38,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/news/index.html b/docs/news/index.html
index caac420..507ac2d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -79,7 +79,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
@@ -116,6 +116,14 @@ 
Changelog 

       Source: NEWS.md
     
 
+    

+

+prcbench 1.0.1 Unreleased 
+

+
    
+
  • Update citation
    • 
+

+

     

 

 prcbench 1.0.0 Unreleased 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 04b4505..ed0b66e 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
   introduction: introduction.html
-last_built: 2021-04-05T19:25Z
+last_built: 2021-04-06T00:13Z
 urls:
   reference: https://evalclass.github.io/prcbench/reference
   article: https://evalclass.github.io/prcbench/articles
diff --git a/docs/reference/C1DATA.html b/docs/reference/C1DATA.html
index 95092f8..7e85ba5 100644
--- a/docs/reference/C1DATA.html
+++ b/docs/reference/C1DATA.html
@@ -81,7 +81,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     

 
diff --git a/docs/reference/C2DATA.html b/docs/reference/C2DATA.html
index 7d9d1d9..8b1148e 100644
--- a/docs/reference/C2DATA.html
+++ b/docs/reference/C2DATA.html
@@ -81,7 +81,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/C3DATA.html b/docs/reference/C3DATA.html
index f8960b9..ef19976 100644
--- a/docs/reference/C3DATA.html
+++ b/docs/reference/C3DATA.html
@@ -81,7 +81,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/C4DATA.html b/docs/reference/C4DATA.html
index 3309ba0..6b694e3 100644
--- a/docs/reference/C4DATA.html
+++ b/docs/reference/C4DATA.html
@@ -81,7 +81,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/TestDataB.html b/docs/reference/TestDataB.html
index 6c16535..6c751a6 100644
--- a/docs/reference/TestDataB.html
+++ b/docs/reference/TestDataB.html
@@ -80,7 +80,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/TestDataC.html b/docs/reference/TestDataC.html
index da93637..10cb02b 100644
--- a/docs/reference/TestDataC.html
+++ b/docs/reference/TestDataC.html
@@ -80,7 +80,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/ToolAUCCalculator.html b/docs/reference/ToolAUCCalculator.html
index b28ddea..ee87b14 100644
--- a/docs/reference/ToolAUCCalculator.html
+++ b/docs/reference/ToolAUCCalculator.html
@@ -80,7 +80,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/ToolIFBase.html b/docs/reference/ToolIFBase.html
index 84b925d..807e681 100644
--- a/docs/reference/ToolIFBase.html
+++ b/docs/reference/ToolIFBase.html
@@ -80,7 +80,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/ToolPRROC.html b/docs/reference/ToolPRROC.html
index 6b4f107..2e1f99b 100644
--- a/docs/reference/ToolPRROC.html
+++ b/docs/reference/ToolPRROC.html
@@ -80,7 +80,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/ToolPerfMeas.html b/docs/reference/ToolPerfMeas.html
index 66040a2..735dd3d 100644
--- a/docs/reference/ToolPerfMeas.html
+++ b/docs/reference/ToolPerfMeas.html
@@ -80,7 +80,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/ToolROCR.html b/docs/reference/ToolROCR.html
index a83c581..68bd923 100644
--- a/docs/reference/ToolROCR.html
+++ b/docs/reference/ToolROCR.html
@@ -80,7 +80,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/Toolprecrec.html b/docs/reference/Toolprecrec.html
index 182ac2f..1ce8ddc 100644
--- a/docs/reference/Toolprecrec.html
+++ b/docs/reference/Toolprecrec.html
@@ -80,7 +80,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/autoplot.html b/docs/reference/autoplot.html
index 89bcd95..34b6a05 100644
--- a/docs/reference/autoplot.html
+++ b/docs/reference/autoplot.html
@@ -81,7 +81,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
diff --git a/docs/reference/create_example_func.html b/docs/reference/create_example_func.html
index fca29e0..124ad6f 100644
--- a/docs/reference/create_example_func.html
+++ b/docs/reference/create_example_func.html
@@ -81,7 +81,7 @@
       
       
         prcbench
-        1.0.0
+        1.0.1
       
     
 
@@ -146,8 +146,8 @@ 
Examp
 #>     pred <- list(x = seq(0, 1, 1/length(scores)), y = seq(0, 
 #>         1, 1/length(scores)), auc = 0.5)
 #> }
-#> <bytecode: 0x564f5f017040>
-#> <environment: 0x564f5f01a348>

+#> <bytecode: 0x55acc2d9deb0>
+#> <environment: 0x55acc2da0d20>
diff --git a/docs/reference/create_toolset.html b/docs/reference/create_toolset.html index a275fb6..38e6c37 100644 --- a/docs/reference/create_toolset.html +++ b/docs/reference/create_toolset.html @@ -82,7 +82,7 @@ prcbench - 1.0.0 + 1.0.1 diff --git a/docs/reference/create_usrdata.html b/docs/reference/create_usrdata.html index 9f91f4b..a98601d 100644 --- a/docs/reference/create_usrdata.html +++ b/docs/reference/create_usrdata.html @@ -80,7 +80,7 @@ prcbench - 1.0.0 + 1.0.1 diff --git a/docs/reference/create_usrtool.html b/docs/reference/create_usrtool.html index 1a493e3..0fdd7b4 100644 --- a/docs/reference/create_usrtool.html +++ b/docs/reference/create_usrtool.html @@ -82,7 +82,7 @@ prcbench - 1.0.0 + 1.0.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index df2fef8..29f55c2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -79,7 +79,7 @@ prcbench - 1.0.0 + 1.0.1 diff --git a/docs/reference/prcbench.html b/docs/reference/prcbench.html index 10fc316..8e9b4ca 100644 --- a/docs/reference/prcbench.html +++ b/docs/reference/prcbench.html @@ -81,7 +81,7 @@ prcbench - 1.0.0 + 1.0.1 diff --git a/docs/reference/run_benchmark.html b/docs/reference/run_benchmark.html index d1ffa79..6eb6619 100644 --- a/docs/reference/run_benchmark.html +++ b/docs/reference/run_benchmark.html @@ -82,7 +82,7 @@ prcbench - 1.0.0 + 1.0.1 diff --git a/docs/reference/run_evalcurve.html b/docs/reference/run_evalcurve.html index 6edcf3d..07b2d77 100644 --- a/docs/reference/run_evalcurve.html +++ b/docs/reference/run_evalcurve.html @@ -81,7 +81,7 @@ prcbench - 1.0.0 + 1.0.1