Merge pull request #1 from edahelsinki/update

Update to match the journal version

.Rbuildignore

@@ -1,4 +1,10 @@
-^.*\.Rproj$
-^\.Rproj\.user$
-^\.vscode
-^experiments$
+^.*\.Rproj$
+^\.Rproj\.user$
+^.*\.Rcheck$
+^\.vscode$
+^experiments$
+^.*.zip
+^.*.tar.gz
+^\.lintr$
+^CITATIONS.bib$
+^\.github$

.github/workflows/r_check.yml

@@ -0,0 +1,44 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,    r: 'release'}
+          - {os: windows-latest,  r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: '3.6'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

.gitignore

@@ -1,54 +1,61 @@
-.env/
-env/
-__pycache__
-*.so
-*.o
-*.pcm
-*.d
-*.root
-.vscode
-*.cxx_tmp_*
-*.rds
-*ACLiC*
-.Rproj.user
-r/*.html
-*.RData
-*.aux
-*.log
-*.fls
-*.fdb_latexmk
-*.pdf
-*.synctex.*
-*.nb.html
-.Rhistory
-.Rapp.history
-.RData
-*-Ex.R
-/*.tar.gz
-/*.Rcheck/
-vignettes/*.html
-vignettes/*.pdf
-.httr-oauth
-/*_cache/
-/cache/
-*.utf8.md
-*.knit.md
-rsconnect/
-experiments/results/*
-!experiments/results/*.jpg
-experiments/data/*
-!experiments/data/*.r
-!experiments/data/*.R
-!experiments/data/*.py
-!experiments/data/*.cpp
-!experiments/data/*.h
-tmp
-*.html
-*.zip
-*~
-*.~
-todo.md
-.lintr
-!vignettes/paper.pdf
-!vignettes/presentation.pdf
-!vignettes/poster.pdf
+.env/
+env/
+__pycache__
+*.so
+*.o
+*.pcm
+*.d
+*.root
+.vscode
+*.cxx_tmp_*
+*.rds
+*ACLiC*
+.Rproj.user
+*Rproj
+r/*.html
+*.RData
+*.Rcheck
+*.aux
+*.log
+*.fls
+*.fdb_latexmk
+*.pdf
+*.synctex.*
+*.nb.html
+.Rhistory
+.Rapp.history
+.RData
+*-Ex.R
+/*.tar.gz
+/*.Rcheck/
+vignettes/*.html
+vignettes/*.pdf
+.httr-oauth
+/*_cache/
+/cache/
+*.utf8.md
+*.knit.md
+rsconnect/
+experiments/results/*
+!experiments/results/*.png
+!experiments/results/*.jpg
+experiments/data/*
+!experiments/data/*.r
+!experiments/data/*.R
+!experiments/data/*.py
+!experiments/data/*.cpp
+!experiments/data/*.h
+tmp
+*.html
+*.zip
+*.tar.gz
+
+*~
+*.~
+todo.md
+*.dll
+data/*
+log*.txt
+!vignettes/paper.pdf
+!vignettes/presentation.pdf
+!vignettes/poster.pdf

.lintr

@@ -0,0 +1,7 @@
+linters: with_defaults(
+  line_length_linter(120),
+  commented_code_linter = NULL,
+  object_name_linter = NULL,
+  object_usage_linter = NULL
+  )
+encoding: "utf-8"

CITATIONS.bib

@@ -0,0 +1,22 @@
+@article{bjorklund2022robust,
+  title   = {Robust regression via error tolerance},
+  author  = {Bj{\"o}rklund, Anton and Henelius, Andreas and Oikarinen, Emilia and Kallonen, Kimmo and Puolam{\"a}ki, Kai},
+  year    = {2022},
+  month   = jan,
+  journal = {Data Mining and Knowledge Discovery},
+  issn    = {1384-5810, 1573-756X},
+  doi     = {10.1007/s10618-022-00819-2}
+}
+
+@inproceedings{bjorklund2019sparse,
+  title     = {Sparse Robust Regression for Explaining Classifiers},
+  booktitle = {Discovery Science},
+  author    = {Bj{\"o}rklund, Anton and Henelius, Andreas and Oikarinen, Emilia and Kallonen, Kimmo and Puolam{\"a}ki, Kai},
+  year      = {2019},
+  series    = {Lecture Notes in Computer Science},
+  volume    = {11828},
+  pages     = {351--366},
+  publisher = {Springer International Publishing},
+  doi       = {10.1007/978-3-030-33778-0_27},
+  isbn      = {978-3-030-33777-3 978-3-030-33778-0}
+}

DESCRIPTION

@@ -1,17 +1,18 @@
-Package: slise
-Title: Sparse Linear Subset Explanations
-Version: 1.0.0
-Authors@R: person("Anton", "Björklund", email = "anton.bjorklund@helsinki.fi", role = c("aut", "cre"))
-Description: An implementation of the SLISE
-    algorithm for robust regression and
-    explaining outcomes from black box models.
-Depends: R (>= 3.5), Rcpp
-License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-Imports: lbfgs, RcppArmadillo, ggplot2, stats, utils, methods, graphics, grDevices
-Suggests: scatterplot3d, grid, gridExtra, reshape2, crayon, wordcloud, testthat, stringr, numDeriv, R.rsp
-URL: https://github.com/edahelsinki/slise
-LinkingTo: Rcpp, RcppArmadillo
-RoxygenNote: 6.1.1.9000
-VignetteBuilder: R.rsp
+Package: slise
+Title: Sparse Linear Subset Explanations
+Version: 2.0.0
+Authors@R: c(
+    person("Anton", "Björklund", email = "anton.bjorklund@helsinki.fi", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7749-2918")),
+    person("Andreas", "Henelius", role = "aut", comment = c(ORCID = "0000-0002-4040-6967")),
+    person("Kai", "Puolamäki", role = "aut", comment = c(ORCID = "0000-0003-1819-1047")))
+Description: An implementation of the SLISE algorithm (for robust regression and explaining outcomes from black box models).
+Depends: R (>= 3.5), Rcpp
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Imports: lbfgs, stats, utils, methods, graphics, base
+Suggests: ggplot2, grid, gridExtra, reshape2, wordcloud, testthat, numDeriv, R.rsp
+URL: https://github.com/edahelsinki/slise
+LinkingTo: Rcpp, RcppArmadillo
+RoxygenNote: 7.1.1
+VignetteBuilder: R.rsp

LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2019 Anton Björklund, University of Helsinki
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+MIT License
+
+Copyright (c) 2022 Anton Björklund, University of Helsinki
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.

NAMESPACE

@@ -1,14 +1,29 @@
-# Generated by roxygen2: do not edit by hand
-
-S3method(explain,slise)
-S3method(plot,slise)
-S3method(predict,slise)
-S3method(print,slise)
-export(explain)
-export(slise.explain)
-export(slise.explain_comb)
-export(slise.explain_find)
-export(slise.fit)
-export(slise.raw)
-importFrom(Rcpp,sourceCpp)
-useDynLib(slise)
+# Generated by roxygen2: do not edit by hand
+
+S3method(plot,slise)
+S3method(predict,slise)
+S3method(print,slise)
+export(graduated_optimisation)
+export(scale_robust)
+export(simple_pca)
+export(slise.explain)
+export(slise.explain_comb)
+export(slise.explain_find)
+export(slise.fit)
+export(slise_initialisation_candidates)
+export(slise_initialisation_candidates2)
+export(slise_initialisation_lasso)
+export(slise_initialisation_ols)
+export(slise_initialisation_zeros)
+importFrom(Rcpp,sourceCpp)
+importFrom(graphics,legend)
+importFrom(stats,.lm.fit)
+importFrom(stats,lm.wfit)
+importFrom(stats,mad)
+importFrom(stats,median)
+importFrom(stats,predict)
+importFrom(stats,quantile)
+importFrom(stats,sd)
+importFrom(stats,uniroot)
+importFrom(utils,combn)
+useDynLib(slise)