Merge pull request #276 from alan-turing-institute/fix_rcmdcheck

Update rcmdcheck.yml

.github/workflows/rcmdcheck.yml

@@ -17,12 +17,11 @@ jobs:
       matrix:
         config:
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel'}
+          - {os: ubuntu-20.04, r: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
@@ -102,20 +101,3 @@ jobs:
           install.packages('covr')
           covr::codecov()
         shell: Rscript {0}
-
-      - name: Render rmd
-        if: ${{ github.event_name == 'pull_request' && runner.os == 'Linux' && matrix.config.r == 'release'}}
-        run: |
-          pak::local_install()
-          pak::pkg_install("rmarkdown")
-          rmarkdown::render('README.Rmd')
-        shell: Rscript {0}
-
-      - name: Commit changes
-        if: ${{ github.event_name == 'pull_request' && runner.os == 'Linux' && matrix.config.r == 'release'}}
-        uses: EndBug/add-and-commit@v7
-        with:
-          author_name: github-actions
-          author_email: 41898282+github-actions[bot]@users.noreply.github.com
-          message: 'Update README.md'
-          add: 'README.md'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: distr6
 Title: The Complete R6 Probability Distributions Interface
-Version: 1.6.10
+Version: 1.6.11
 Authors@R:
     c(person(given = "Raphael",
              family = "Sonabend",

README.Rmd

@@ -11,30 +11,44 @@ set.seed(42)
 
 <img src="man/figures/logo.png" align="right" alt="" width="120" />
 
-[![CRAN Status Badge](https://www.r-pkg.org/badges/version-ago/distr6)](https://cran.r-project.org/package=distr6)
-[![CRAN Checks](https://cranchecks.info/badges/worst/distr6)](https://cran.r-project.org/web/checks/check_results_distr6.html)
+[![distr6 status badge](https://raphaels1.r-universe.dev/badges/distr6)](https://raphaels1.r-universe.dev)
 [![tic](https://github.com/alan-turing-institute/distr6/workflows/tic/badge.svg)](https://github.com/alan-turing-institute/distr6/actions)
 
-
 [![Repo Status](https://www.repostatus.org/badges/latest/active.svg)](https://github.com/alan-turing-institute/distr6)
 [![Lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://alan-turing-institute.github.io/distr6/articles/webs/api_lifecycle.html)
 
-[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/grand-total/distr6)](https://cran.r-project.org/package=distr6)
 [![codecov](https://app.codecov.io/gh/alan-turing-institute/distr6/branch/master/graph/badge.svg)](https://app.codecov.io/gh/alan-turing-institute/distr6)
 [![dependencies](https://tinyverse.netlify.com/badge/distr6)](https://CRAN.R-project.org/package=distr6)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
-[![arXiv](https://img.shields.io/badge/arXiv-2009.02993-brightgreen.svg)](https://arxiv.org/abs/2009.02993)
-[![DOI](https://zenodo.org/badge/177962537.svg)](https://zenodo.org/badge/latestdoi/177962537)
-[![Gitter chat](https://badges.gitter.im/xoopR/distr6.png)](https://gitter.im/xoopR/distr6)
-
+[![Article](https://img.shields.io/badge/Article-10.32614/RJ-2021-055-brightgreen)]([[https://doi.org/10.1093/bioinformatics/btab039](https://journal.r-project.org/archive/2021/RJ-2021-055/index.html)](https://journal.r-project.org/archive/2021/RJ-2021-055/index.html))
+[![Software DOI](https://zenodo.org/badge/177962537.svg)](https://zenodo.org/badge/latestdoi/177962537)
 
 ## What is distr6?
 
 distr6 is a unified and clean interface to organise the probability distributions implemented in R into one R6 object oriented package, as well as adding distributions yet to implemented in R, currently we have 42 probability distributions as well as 11 kernels. Building the package from the ground up and making use of tried and tested design patterns (as per Gamma et al. 1994), distr6 aims to make probability distributions easy to use, understand and analyse.
 
 distr6 extends the work of Peter Ruckdeschel, Matthias Kohl et al. who created the first object-oriented (OO) interface for distributions using S4. Their [distr package](http://distr.r-forge.r-project.org/) is currently the gold-standard in R for OO distribution handling. Using R6 we aim to take this even further and to create a scalable interface that can continue to grow with the community. Full details of the API and class structure can be seen in the [distr6 website](https://alan-turing-institute.github.io/distr6/).
 
+## Citation
+
+If you use distr6 in your research please cite as
+
+```
+@article{RJ-2021-055,
+  author = {Raphael Sonabend and Franz J. Király},
+  title = {{distr6: R6 Object-Oriented Probability Distributions
+          Interface in R}},
+  year = {2021},
+  journal = {{The R Journal}},
+  doi = {10.32614/RJ-2021-055},
+  url = {https://doi.org/10.32614/RJ-2021-055},
+  pages = {444--466},
+  volume = {13},
+  number = {1}
+}
+```
+
 ## Main Features
 
 distr6 is not intended to replace the base R distributions function but instead to give an alternative that focuses on distributions as objects that can be manipulated and accessed as required. The main features therefore centre on OOP practices, design patterns and API design. Of particular note:

README.md

@@ -15,7 +15,7 @@ Status](https://www.repostatus.org/badges/latest/active.svg)](https://github.com
 
 [![CRAN
 Downloads](https://cranlogs.r-pkg.org/badges/grand-total/distr6)](https://cran.r-project.org/package=distr6)
-[![codecov](https://app.codecov.io/gh/alan-turing-institute/distr6/branch/master/graph/badge.svg)](https://app.codecov.io/gh/alan-turing-institute/distr6))
+[![codecov](https://app.codecov.io/gh/alan-turing-institute/distr6/branch/master/graph/badge.svg)](https://app.codecov.io/gh/alan-turing-institute/distr6)
 [![dependencies](https://tinyverse.netlify.com/badge/distr6)](https://CRAN.R-project.org/package=distr6)
 [![License:
 MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
@@ -66,36 +66,42 @@ B$kurtosis()
 B$rand(5)
 #> [1] 7 7 4 7 6
 summary(B)
-#> Binomial Probability Distribution. Parameterised with:
-#>   prob = 0.5, qprob = 0.5, size = 10
-#>
-#>   Quick Statistics
+#> Binomial Probability Distribution. 
+#> Parameterised with:
+#> 
+#>       Id Support Value            Tags
+#> 1:  prob   [0,1]   0.5 linked,required
+#> 2: qprob   [0,1]       linked,required
+#> 3:  size      ℕ+    10        required
+#> 
+#> 
+#> Quick Statistics
 #>  Mean:       5
 #>  Variance:   2.5
 #>  Skewness:   0
 #>  Ex. Kurtosis:   -0.2
-#>
-#>  Support: {0, 1,...,9, 10}   Scientific Type: ℕ0
-#>
-#>  Traits: discrete; univariate
-#>  Properties: symmetric; platykurtic; no skew
+#> 
+#> Support: {0, 1,...,9, 10}    Scientific Type: ℕ0 
+#> 
+#> Traits:      discrete; univariate
+#> Properties:  symmetric; platykurtic; no skew
 ```
 
 Flexible construction of distributions for common parameterisations
 
 ``` r
 Exponential$new(rate = 2)
-#> Exp(rate = 2, scale = 0.5)
+#> Exp(rate = 2)
 Exponential$new(scale = 2)
-#> Exp(rate = 0.5, scale = 2)
+#> Exp(scale = 2)
 Normal$new(mean = 0, prec = 2)
-#> Norm(mean = 0, var = 0.5, sd = 0.707106781186548, prec = 2)
+#> Norm(mean = 0, prec = 2)
 Normal$new(mean = 0, sd = 3)$parameters()
-#>      id     value support                                 description
-#> 1: mean         0       ℝ                   Mean - Location Parameter
-#> 2:  var         9      ℝ+          Variance - Squared Scale Parameter
-#> 3:   sd         3      ℝ+        Standard Deviation - Scale Parameter
-#> 4: prec 0.1111111      ℝ+ Precision - Inverse Squared Scale Parameter
+#>      Id Support Value            Tags
+#> 1: mean       ℝ     0        required
+#> 2: prec      ℝ+       linked,required
+#> 3:   sd      ℝ+     3 linked,required
+#> 4:  var      ℝ+       linked,required
 ```
 
 Decorators for extending functionality of distributions to more complex
@@ -105,37 +111,24 @@ modelling methods
 B <- Binomial$new()
 decorate(B, "ExoticStatistics")
 #> Binomial is now decorated with ExoticStatistics
-#> Binom(prob = 0.5, qprob = 0.5, size = 10)
+#> Binom(prob = 0.5, size = 10)
 B$survival(2)
 #> [1] 0.9453125
 decorate(B, "CoreStatistics")
 #> Binomial is now decorated with CoreStatistics
-#> Binom(prob = 0.5, qprob = 0.5, size = 10)
+#> Binom(prob = 0.5, size = 10)
 B$kthmoment(6)
 #> Results from numeric calculations are approximate only. Better results may be available.
 #> [1] 190
 ```
 
-S3 compatibility to make the interface more flexible for users who are
-less familiar with OOP
-
-``` r
-B <- Binomial$new()
-mean(B) # B$mean()
-#> [1] 5
-variance(B) # B$variance()
-#> [1] 2.5
-cdf(B, 2:5) # B$cdf(2:5)
-#> [1] 0.0546875 0.1718750 0.3769531 0.6230469
-```
-
 Wrappers including truncation, huberization and product distributions
 for manipulation and composition of distributions.
 
 ``` r
 B <- Binomial$new()
 TruncatedDistribution$new(B, lower = 2, upper = 5) #Or: truncate(B,2,5)
-#> TruncBinom(Binom__prob = 0.5, Binom__qprob = 0.5,...,trunc__lower = 2, trunc__upper = 5)
+#> TruncBinom(Binom__prob = 0.5, Binom__size = 10, trunc__lower = 2, trunc__upper = 5)
 N <- Normal$new()
 MixtureDistribution$new(list(B,N), weights = c(0.1, 0.9))
 #> Binom wX Norm
@@ -172,18 +165,28 @@ distr6 has three primary use-cases:
 
 ## Installation
 
-For the latest release on CRAN, install with
+distr6 can be installed from
+[R-Universe](https://raphaels1.r-universe.dev/ui#package:distr6)
 
 ``` r
-install.packages("distr6")
+# Enable repository from raphaels1
+options(repos = c(
+  raphaels1 = 'https://raphaels1.r-universe.dev',
+  CRAN = 'https://cloud.r-project.org'))
+# Download and install distr6 in R
+install.packages('distr6')
 ```
 
-Otherwise for the latest stable build
+And GitHub
 
 ``` r
 remotes::install_github("alan-turing-institute/distr6")
 ```
 
+distr6 [will not be on
+CRAN](https://twitter.com/RaphaelS101/status/1506321623250571265) for
+the forseeable future.
+
 ## Future Plans
 
 Our plans for the next update include