fix URLs, update NEWS

jakobbossek · Mar 8, 2023 · 3cdc8a5 · 3cdc8a5
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diff --git a/NEWS b/NEWS
@@ -1,3 +1,12 @@
+ecr 2.2.1
+=========
+
+Fixes
+
+* Fixed warnings raised by r-devel versions
+* Fixed typo in the docs of approximateRefSets yielding the function not being exported
+
+
 ecr 2.2.0
 =========
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,34 @@
-# ecr 2.1.1 (upcoming)
+# ecr 2.2.1
+
+## Fixes
+
+* Fixed warnings raised by r-devel versions
+* Fixed typo in the docs of approximateRefSets yielding the function not being exported
+
+
+# ecr 2.2.0
+
+## Fixes
+
+* Fixed bug in mutPolynomial where parameter lower was sanity-checked twice and upper not at all
+* Fixed some typos in function documentations
+* Fixed bug in updateParetoArchive: optimization direction, e.g., minimize first, maximize second objective are now respected
+
+## Added
+
+* More literature references in documentation
+
+## New features
+
+* Performance assessment for stochastic multi-objective optimization algorithms (very powerful tool)
+  * Flexible scatterplots in 2D and 3D
+  * Function to calculate a set of unary and binary performance indicators for a set of problems and algorithms
+  * Function to visualize indicator distrbutions
+  * Functions to perform statistical tests and output results as well-formatted LaTeX tables
+* Exported helper functions getNumberOfChildren, getNumberOfParentsNeededForMating and generatesMultipleChildren
+
+
+# ecr 2.1.1
 
 ## Fixes
 

diff --git a/R/docs.parallelization.R b/R/docs.parallelization.R
@@ -4,7 +4,7 @@
 #' In ecr it is possible to parallelize the fitness function evaluation
 #' to make use, e.g., of multiple CP cores or nodes in a HPC cluster.
 #' For maximal flexibility this is realized by means of the \pkg{parallelMap} package
-#' (see the \href{https://github.com/berndbischl/parallelMap}{official
+#' (see the \href{https://github.com/mlr-org/parallelMap}{official
 #' GitHub page} for instructions on how to set up parallelization).
 #' The different levels of parallelization can be specified in the
 #' \code{parallelStart*} function. At them moment only the level

diff --git a/README.Rmd b/README.Rmd
@@ -4,12 +4,11 @@ output: github_document
 # ecr: Evolutionary Computation in R
 
 <!-- badges: start -->
-[![CRAN Status Badge](http://www.r-pkg.org/badges/version/ecr)](http://cran.r-project.org/web/packages/ecr)
-[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/ecr)](http://cran.rstudio.com/web/packages/ecr/index.html)
-[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/grand-total/ecr?color=orange)](http://cran.rstudio.com/web/packages/ecr/index.html)
+[![CRAN Status Badge](http://www.r-pkg.org/badges/version/ecr)](https://cran.r-project.org/package=ecr)
+[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/ecr)](https://cran.r-project.org/package=ecr)
+[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/grand-total/ecr?color=orange)](https://cran.r-project.org/package=ecr)
 [![R-CMD-check](https://github.com/jakobbossek/ecr2/workflows/R-CMD-check/badge.svg)](https://github.com/jakobbossek/ecr2/actions)
-[![Codecov test coverage](https://codecov.io/gh/jakobbossek/ecr2/branch/master/graph/badge.svg)](https://codecov.io/gh/jakobbossek/ecr2?branch=master)
-[![Research software impact](http://depsy.org/api/package/cran/ecr/badge.svg)](http://depsy.org/package/r/ecr)
+[![Codecov test coverage](https://codecov.io/gh/jakobbossek/ecr2/branch/master/graph/badge.svg)](https://app.codecov.io/gh/jakobbossek/ecr2?branch=master)
 <!-- badges: end -->
 
 **NOTE:** The **ecr package v2** is the official follow-up package to my package [ecr v1](https://github.com/jakobbossek/ecr). I was unsatisfied with some design choices and thus decided to restructure and rewrite a lot. Changes are that manifold and fundamental, that I decided to set up a new repository, since most of the **ecr v1** functions are either deprecated, renamed, deleted or underlie substantial interface changes.
@@ -31,13 +30,13 @@ The **ecr** package (version 2), *Evolutionary Computation in R*, is conceived a
 * Powerful logging mechanism.
 * Possibility to use custom representations/genotypes.
 * Possibility to define custom EA operators, i.e., mutation, variation and selection operators.
-* Easy parallelization via [parallelMap](https://cran.r-project.org/web/packages/parallelMap/index.html)
+* Easy parallelization via [parallelMap](https://cran.r-project.org/package=parallelMap)
 * Black-box approach for standard tasks.
 * Single- and multi-objective optimization.
 * Implementations of some popular performance indicators in Evolutionary Multi-Objective Optimization (EMOA), e.g., hyper-volume-indicator, epsilon indicator as well as R1, R2 and R3 indicator.
 * Predefined state-of-the-art EMOA algorithms NSGA-II, SMS-EMOA and AS-EMOA.
 
-The best way to illustrate the process of algorithm design in **ecr** is by example. Assume we aim to find the global minimum of the highly multimodal one-dimensional Ackley-Function. The function is available in the R package [smoof](https://cran.r-project.org/web/packages/smoof/index.html) and may be initialized as follows:
+The best way to illustrate the process of algorithm design in **ecr** is by example. Assume we aim to find the global minimum of the highly multimodal one-dimensional Ackley-Function. The function is available in the R package [smoof](https://cran.r-project.org/package=smoof) and may be initialized as follows:
 ```r
 library(ecr)
 library(ggplot2)
@@ -106,11 +105,11 @@ print(res$best.x)
 
 ## Installation Instructions
 
-The package will be available at [CRAN](http://cran.r-project.org) soon. Install the release version via:
+The package is available at [CRAN](https://cran.r-project.org/package=ecr). Install the release version via:
 ```r
 install.packages("ecr")
 ```
-If you are interested in trying out and playing around with the current github developer version use the [devtools](https://github.com/hadley/devtools) package and type the following command in R:
+If you are interested in trying out and playing around with the current github developer version use the [devtools](https://github.com/r-lib/devtools) package and type the following command in R:
 
 ```r
 devtools::install_github("jakobbossek/ecr2")
@@ -122,13 +121,13 @@ To cite **ecr** please use:
 > Bossek, J. (2017). Ecr 2.0: A Modular Framework for Evolutionary Computation
 > in R. In Proceedings of the Genetic and Evolutionary Computation Conference
 > (GECCO) Companion (pp. 1187–1193). Berlin, Germany:
-> ACM. http://doi.org/10.1145/3067695.3082470
+> ACM. https://doi.org/10.1145/3067695.3082470
 
 In case you made use of **ecr**'s performance assessment tools please cite:
 > Bossek, J. (2018). Performance Assessment of Multi-objective Evolutionary
 > Algorithms with the R Package Ecr. In Proceedings of the Genetic and
 > Evolutionary Computation Conference Companion (pp. 1350–1356). Kyoto, Japan:
-> ACM. http://doi.org/10.1145/3205651.3208312
+> ACM. https://doi.org/10.1145/3205651.3208312
 
 BibTeX entries for LaTeX users:
 ```
@@ -141,7 +140,7 @@ BibTeX entries for LaTeX users:
   address = {Kyoto, Japan},
   series = {GECCO '18},
   title = {{Performance Assessment of Multi-objective Evolutionary Algorithms with the R Package Ecr}},
-  url = {http://doi.acm.org/10.1145/3205651.3208312},
+  url = {https://doi.acm.org/10.1145/3205651.3208312},
   year = {2018}
 }
 @inproceedings{B2017ecr,
@@ -153,7 +152,7 @@ BibTeX entries for LaTeX users:
   series = {GECCO '18},
   address = {Berlin, Germany},
   title = {{Ecr 2.0: A Modular Framework for Evolutionary Computation in R}},
-  url = {http://doi.acm.org/10.1145/3067695.3082470},
+  url = {https://doi.acm.org/10.1145/3067695.3082470},
   year = {2017}
 }
 ```

diff --git a/README.md b/README.md
@@ -4,16 +4,14 @@
 <!-- badges: start -->
 
 [![CRAN Status
-Badge](http://www.r-pkg.org/badges/version/ecr)](http://cran.r-project.org/web/packages/ecr)
+Badge](http://www.r-pkg.org/badges/version/ecr)](https://cran.r-project.org/package=ecr)
 [![CRAN
-Downloads](http://cranlogs.r-pkg.org/badges/ecr)](http://cran.rstudio.com/web/packages/ecr/index.html)
+Downloads](http://cranlogs.r-pkg.org/badges/ecr)](https://cran.r-project.org/package=ecr)
 [![CRAN
-Downloads](http://cranlogs.r-pkg.org/badges/grand-total/ecr?color=orange)](http://cran.rstudio.com/web/packages/ecr/index.html)
+Downloads](http://cranlogs.r-pkg.org/badges/grand-total/ecr?color=orange)](https://cran.r-project.org/package=ecr)
 [![R-CMD-check](https://github.com/jakobbossek/ecr2/workflows/R-CMD-check/badge.svg)](https://github.com/jakobbossek/ecr2/actions)
 [![Codecov test
-coverage](https://codecov.io/gh/jakobbossek/ecr2/branch/master/graph/badge.svg)](https://codecov.io/gh/jakobbossek/ecr2?branch=master)
-[![Research software
-impact](http://depsy.org/api/package/cran/ecr/badge.svg)](http://depsy.org/package/r/ecr)
+coverage](https://codecov.io/gh/jakobbossek/ecr2/branch/master/graph/badge.svg)](https://app.codecov.io/gh/jakobbossek/ecr2?branch=master)
 <!-- badges: end -->
 
 **NOTE:** The **ecr package v2** is the official follow-up package to my
@@ -67,7 +65,7 @@ of ecr are the following
 -   Possibility to define custom EA operators, i.e., mutation, variation
     and selection operators.
 -   Easy parallelization via
-    [parallelMap](https://cran.r-project.org/web/packages/parallelMap/index.html)
+    [parallelMap](https://cran.r-project.org/package=parallelMap)
 -   Black-box approach for standard tasks.
 -   Single- and multi-objective optimization.
 -   Implementations of some popular performance indicators in
@@ -80,9 +78,8 @@ of ecr are the following
 The best way to illustrate the process of algorithm design in **ecr** is
 by example. Assume we aim to find the global minimum of the highly
 multimodal one-dimensional Ackley-Function. The function is available in
-the R package
-[smoof](https://cran.r-project.org/web/packages/smoof/index.html) and
-may be initialized as follows:
+the R package [smoof](https://cran.r-project.org/package=smoof) and may
+be initialized as follows:
 
 ``` r
 library(ecr)
@@ -171,16 +168,17 @@ print(res$best.x)
 
 ## Installation Instructions
 
-The package will be available at [CRAN](http://cran.r-project.org) soon.
-Install the release version via:
+The package is available at
+[CRAN](https://cran.r-project.org/package=ecr). Install the release
+version via:
 
 ``` r
 install.packages("ecr")
 ```
 
 If you are interested in trying out and playing around with the current
 github developer version use the
-[devtools](https://github.com/hadley/devtools) package and type the
+[devtools](https://github.com/r-lib/devtools) package and type the
 following command in R:
 
 ``` r
@@ -193,14 +191,14 @@ To cite **ecr** please use: \> Bossek, J. (2017). Ecr 2.0: A Modular
 Framework for Evolutionary Computation \> in R. In Proceedings of the
 Genetic and Evolutionary Computation Conference \> (GECCO) Companion
 (pp. 1187–1193). Berlin, Germany: \> ACM.
-<http://doi.org/10.1145/3067695.3082470>
+<https://doi.org/10.1145/3067695.3082470>
 
 In case you made use of **ecr**’s performance assessment tools please
 cite: \> Bossek, J. (2018). Performance Assessment of Multi-objective
 Evolutionary \> Algorithms with the R Package Ecr. In Proceedings of the
 Genetic and \> Evolutionary Computation Conference Companion
 (pp. 1350–1356). Kyoto, Japan: \> ACM.
-<http://doi.org/10.1145/3205651.3208312>
+<https://doi.org/10.1145/3205651.3208312>
 
 BibTeX entries for LaTeX users:
 
@@ -213,7 +211,7 @@ BibTeX entries for LaTeX users:
       address = {Kyoto, Japan},
       series = {GECCO '18},
       title = {{Performance Assessment of Multi-objective Evolutionary Algorithms with the R Package Ecr}},
-      url = {http://doi.acm.org/10.1145/3205651.3208312},
+      url = {https://doi.acm.org/10.1145/3205651.3208312},
       year = {2018}
     }
     @inproceedings{B2017ecr,
@@ -225,7 +223,7 @@ BibTeX entries for LaTeX users:
       series = {GECCO '18},
       address = {Berlin, Germany},
       title = {{Ecr 2.0: A Modular Framework for Evolutionary Computation in R}},
-      url = {http://doi.acm.org/10.1145/3067695.3082470},
+      url = {https://doi.acm.org/10.1145/3067695.3082470},
       year = {2017}
     }
 

diff --git a/man/ecr_parallelization.Rd b/man/ecr_parallelization.Rd