Merge pull request #191 from DoubleML/p-citation

PhilippBach · web-flow · commit dcedb8b26c42 · 2024-02-15T12:13:04.000+01:00
Update Citation, increment version
diff --git a/.github/workflows/check_styler.yml b/.github/workflows/check_styler.yml
@@ -30,7 +30,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
 
diff --git a/.github/workflows/deploy_docu.yml b/.github/workflows/deploy_docu.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         persist-credentials: false
     - name: Install SSH Client
@@ -40,7 +40,7 @@ jobs:
       shell: Rscript {0}
 
     - name: Cache R packages
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_LIBS_USER }}
         key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
diff --git a/.github/workflows/deploy_docu_dev.yml b/.github/workflows/deploy_docu_dev.yml
@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         persist-credentials: false
     - name: Install SSH Client
@@ -39,7 +39,7 @@ jobs:
       shell: Rscript {0}
 
     - name: Cache R packages
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_LIBS_USER }}
         key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
diff --git a/.github/workflows/deploy_pkg.yml b/.github/workflows/deploy_pkg.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -28,7 +28,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -50,7 +50,7 @@ jobs:
         run: |
           R CMD build .
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: DoubleML-pkg
           path: DoubleML_*.tar.gz
diff --git a/.github/workflows/rcheck.yml b/.github/workflows/rcheck.yml
@@ -35,7 +35,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
 
@@ -54,7 +54,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-${{ matrix.config.mlr3 }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -112,7 +112,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-${{ matrix.config.mlr3 }}-results
           path: check
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DoubleML
 Type: Package
 Title: Double Machine Learning in R
-Version: 0.5.0.9000
+Version: 1.0.0
 Authors@R: c(
     person("Philipp", "Bach", email = "philipp.bach@uni-hamburg.de", role=c("aut", "cre")),
     person("Victor", "Chernozhukov", role="aut"),
@@ -16,7 +16,8 @@ Description: Implementation of the double/debiased machine learning framework of
     these models by machine learning methods and computation of the Neyman
     orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the
     'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on
-    the 'R6' package is very flexible. 
+    the 'R6' package is very flexible. More information available in the
+    publication in the Journal of Statistical Software: <10.18637/jss.v108.i03>.
 License: MIT + file LICENSE
 URL: https://docs.doubleml.org/stable/index.html, https://github.com/DoubleML/doubleml-for-r/
 BugReports: https://github.com/DoubleML/doubleml-for-r/issues
@@ -37,7 +38,7 @@ Imports:
     mlr3learners (>= 0.3.0),
     mlr3misc
 Roxygen: list(markdown = TRUE, r6 = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     knitr,
     rmarkdown,
diff --git a/DoubleML.Rproj b/DoubleML.Rproj
@@ -15,4 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageCheckArgs: --no-tests --run-donttest
+PackageCheckArgs: --as-cran --no-tests --run-donttest
diff --git a/R/datasets.R b/R/datasets.R
@@ -170,7 +170,7 @@ fetch_401k = function(return_type = "DoubleMLData", polynomial_features = FALSE,
 #' available at [https://academic.oup.com/ectj/article/21/1/C1/5056401#supplementary-data](https://academic.oup.com/ectj/article/21/1/C1/5056401#supplementary-data).
 #'
 #' The supplementary data of the study by Bilias (2000) is available at
-#' [http://qed.econ.queensu.ca/jae/2000-v15.6/bilias/](http://qed.econ.queensu.ca/jae/2000-v15.6/bilias/).
+#' [https://www.journaldata.zbw.eu/dataset/sequential-testing-of-duration-data-the-case-of-the-pennsylvania-reemployment-bonus-experiment](https://www.journaldata.zbw.eu/dataset/sequential-testing-of-duration-data-the-case-of-the-pennsylvania-reemployment-bonus-experiment).
 #'
 #'
 #' @references Bilias Y. (2000), Sequential Testing of Duration Data:
@@ -386,7 +386,7 @@ make_plr_CCDDHNR2018 = function(n_obs = 500, dim_x = 20, alpha = 0.5,
 #' @references Turrell, A. (2018), Econometrics in Python part I - Double
 #' machine learning, Markov Wanderer: A blog on economics, science, coding and
 #' data.
-#' [http://aeturrell.com/2018/02/10/econometrics-in-python-partI-ML/](http://aeturrell.com/2018/02/10/econometrics-in-python-partI-ML/).
+#' [https://aeturrell.com/blog/posts/econometrics-in-python-parti-ml/](https://aeturrell.com/blog/posts/econometrics-in-python-parti-ml/).
 #'
 #' @param n_obs (`integer(1)`) \cr
 #' The number of observations to simulate.
diff --git a/R/double_ml.R b/R/double_ml.R
@@ -950,7 +950,7 @@ DoubleML = R6Class("DoubleML",
       if (joint == FALSE) {
         a = (1 - level) / 2
         a = c(a, 1 - a)
-        pct = format.perc(a, 3)
+        pct = format_perc(a, 3)
         fac = qnorm(a)
         ci = array(NA_real_,
           dim = c(length(parm), 2L),
@@ -962,7 +962,7 @@ DoubleML = R6Class("DoubleML",
 
         a = (1 - level)
         ab = c(a / 2, 1 - a / 2)
-        pct = format.perc(ab, 3)
+        pct = format_perc(ab, 3)
         ci = array(NA_real_,
           dim = c(length(parm), 2L),
           dimnames = list(parm, pct))
diff --git a/R/double_ml_plr.R b/R/double_ml_plr.R
@@ -278,7 +278,7 @@ DoubleMLPLR = R6Class("DoubleMLPLR",
     #' in the [mlr3tuning](https://mlr3tuning.mlr-org.com/) package. For more
     #' information on tuning in [mlr3](https://mlr3.mlr-org.com/), we refer to
     #' the section on parameter tuning in the
-    #' [mlr3 book](https://mlr3book.mlr-org.com/optimization.html#tuning).
+    #' [mlr3 book](https://mlr3book.mlr-org.com/chapters/chapter4/hyperparameter_optimization.html).
     #'
     #' @param param_set (named `list()`) \cr
     #' A named `list` with a parameter grid for each nuisance model/learner
diff --git a/R/helper.R b/R/helper.R
@@ -334,7 +334,7 @@ set_default_measure = function(measure_in = NA, task_type) {
 }
 
 
-format.perc = function(probs, digits) {
+format_perc = function(probs, digits) {
   paste(
     format(100 * probs, trim = TRUE, scientific = FALSE, digits = digits),
     "%")
@@ -425,7 +425,7 @@ check_smpl_split = function(smpl, n_obs, check_intersect = FALSE) {
     assert_subset(test_ids, seq(n_obs))
   })
   if (check_intersect) {
-    for (i_fold in seq(length(length(smpl$train_ids))))
+    for (i_fold in seq_along(length(length(smpl$train_ids))))
     {
       assert_disjunct(smpl$train_ids[[i_fold]], smpl$test_ids[[i_fold]])
     }
diff --git a/README.Rmd b/README.Rmd
@@ -101,11 +101,13 @@ Bibtex-entry:
 ```
 @misc{DoubleML2020,
       title={{DoubleML} -- {A}n Object-Oriented Implementation of Double Machine Learning in {R}}, 
-      author={P. Bach and V. Chernozhukov and M. S. Kurz and M. Spindler},
-      year={2021},
-      eprint={2103.09603},
-      archivePrefix={arXiv},
-      primaryClass={stat.ML},
+      author={P. Bach and V. Chernozhukov and M. S. Kurz and M. Spindler and Sven Klaassen},
+      year={2024},
+      journal={Journal of Statistical Software},
+      volume={108},
+      number={3},
+      pages= {1-56},
+      doi={10.18637/jss.v108.i03},
       note={arXiv:\href{https://arxiv.org/abs/2103.09603}{2103.09603} [stat.ML]}
 }
 ```
@@ -117,7 +119,7 @@ Foundation) is acknowledged – Project Number 431701914.
 
 ## References
 
-* Bach, P., Chernozhukov, V., Kurz, M. S., and Spindler, M. (2021), DoubleML - An Object-Oriented Implementation of Double Machine Learning in R, arXiv:[2103.09603](https://arxiv.org/abs/2103.09603). 
+* Bach, P., Chernozhukov, V., Kurz, M. S., Spindler, M. and Klaassen, S. (2024), DoubleML - An Object-Oriented Implementation of Double Machine Learning in R, Journal of Statistical Software, 108(3): 1-56, <doi:10.18637/jss.v108.i03>, arXiv:[2103.09603](https://arxiv.org/abs/2103.09603).
 
 * Chernozhukov, V., Chetverikov, D., Demirer, M., Duflo, E., Hansen, C., Newey, W. and Robins, J. (2018), Double/debiased machine learning for treatment and structural parameters. The Econometrics Journal, 21: C1-C68, <https://doi.org/10.1111/ectj.12097>.
 
diff --git a/README.md b/README.md
@@ -70,7 +70,12 @@ It further can be readily extended with regards to
 - … alternative resampling schemes,
 - …
 
-![OOP structure of the DoubleML package](man/figures/oop.svg?raw=true)
+<figure>
+<img src="man/figures/oop.svg?raw=true"
+alt="OOP structure of the DoubleML package" />
+<figcaption aria-hidden="true">OOP structure of the DoubleML
+package</figcaption>
+</figure>
 
 ## Installation
 
@@ -122,11 +127,13 @@ Bibtex-entry:
 
     @misc{DoubleML2020,
           title={{DoubleML} -- {A}n Object-Oriented Implementation of Double Machine Learning in {R}}, 
-          author={P. Bach and V. Chernozhukov and M. S. Kurz and M. Spindler},
-          year={2021},
-          eprint={2103.09603},
-          archivePrefix={arXiv},
-          primaryClass={stat.ML},
+          author={P. Bach and V. Chernozhukov and M. S. Kurz and M. Spindler and Sven Klaassen},
+          year={2024},
+          journal={Journal of Statistical Software},
+          volume={108},
+          number={3},
+          pages= {1-56},
+          doi={10.18637/jss.v108.i03},
           note={arXiv:\href{https://arxiv.org/abs/2103.09603}{2103.09603} [stat.ML]}
     }
 
@@ -137,9 +144,11 @@ Foundation) is acknowledged – Project Number 431701914.
 
 ## References
 
-- Bach, P., Chernozhukov, V., Kurz, M. S., and Spindler, M. (2021),
-  DoubleML - An Object-Oriented Implementation of Double Machine
-  Learning in R, arXiv:[2103.09603](https://arxiv.org/abs/2103.09603).
+- Bach, P., Chernozhukov, V., Kurz, M. S., Spindler, M. and Klaassen, S.
+  (2024), DoubleML - An Object-Oriented Implementation of Double Machine
+  Learning in R, Journal of Statistical Software, 108(3): 1-56,
+  <doi:10.18637/jss.v108.i03>,
+  arXiv:[2103.09603](https://arxiv.org/abs/2103.09603).
 
 - Chernozhukov, V., Chetverikov, D., Demirer, M., Duflo, E., Hansen, C.,
   Newey, W. and Robins, J. (2018), Double/debiased machine learning for
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,17 +1,25 @@
-bibentry(
-  bibtype = "misc",
-  key = "DoubleML2021",
-  title = "{DoubleML} -- {A}n Object-Oriented Implementation of Double Machine Learning in {R}",
-  author = c(
-    person(given = "P.", family = "Bach"),
-    person(given = "V.", family = "Chernozhukov"),
-    person(given = "M. S.", family = "Kurz"),
-    person(given = "M.", family = "Spindler")
-  ),
-  year = 2021,
-  eprint = "2103.09603",
-  archivePrefix = "arXiv",
-  primaryClass = "stat.ML",
-  note= "arXiv:\\href{https://arxiv.org/abs/2103.09603}{2103.09603} [stat.ML]",
-  textVersion = "Bach, P., Chernozhukov, V., Kurz, M. S., and Spindler, M. (2021), DoubleML - An Object-Oriented Implementation of Double Machine Learning in R, arXiv:2103.09603."
-)
+bibentry(bibtype = "Article",
+  title        = "{DoubleML}: An Object-Oriented Implementation of Double Machine Learning in {R}",
+  author       = c(person(given = "Philipp",
+                          family = "Bach",
+                          email = "philipp.bach@uni-hamburg.de"),
+                   person(given = c("Malte", "S."),
+                          family = "Kurz",
+                          email = "malte.kurz@tum.de"),
+                   person(given = "Victor",
+                          family = "Chernozhukov",
+                          email = "vchern@mit.edu"),
+                   person(given = "Martin",
+                          family = "Spindler",
+                          email = "martin.spindler@uni-hamburg.de"),
+                   person(given = "Sven",
+                          family = "Klaassen",
+                          email = "sven.klaassen@uni-hamburg.de")),
+  journal      = "Journal of Statistical Software",
+  year         = "2024",
+  volume       = "108",
+  number       = "3",
+  pages        = "1--56",
+  doi          = "10.18637/jss.v108.i03",
+  header       = "To cite DoubleML in publications use:"
+)
diff --git a/man/DoubleMLIIVM.Rd b/man/DoubleMLIIVM.Rd
diff --git a/man/DoubleMLIRM.Rd b/man/DoubleMLIRM.Rd
diff --git a/man/DoubleMLPLIV.Rd b/man/DoubleMLPLIV.Rd
diff --git a/man/DoubleMLPLR.Rd b/man/DoubleMLPLR.Rd
diff --git a/man/fetch_bonus.Rd b/man/fetch_bonus.Rd
diff --git a/man/make_plr_turrell2018.Rd b/man/make_plr_turrell2018.Rd
diff --git a/vignettes/Introduction_to_DoubleML.Rmd b/vignettes/Introduction_to_DoubleML.Rmd
