Merge pull request #244 from NSAPH-Software/release_v0.4.2

Release v0.4.2
NSAPH-Software · Apr 13, 2024 · 8851c7d · 8851c7d
2 parents e41be8e + 5b40951
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,14 @@
 Package: CausalGPS
 Type: Package
 Title: Matching on Generalized Propensity Scores with Continuous Exposures
-Version: 0.4.1
+Version: 0.4.2
 Authors@R: c(
     person("Naeem", "Khoshnevis", email = "nkhoshnevis@g.harvard.edu",
            role=c("aut","cre"), 
            comment = c(ORCID = "0000-0003-4315-1426", AFFILIATION="HUIT")),
-    person("Xiao", "Wu", email = "wuxiao@g.harvard.edu",
+    person("Xiao", "Wu", email = "xw2892@cumc.columbia.edu",
            role= c("aut"),            
-           comment = c(ORCID = "0000-0002-4884-657X", AFFILIATION="HSPH")),
+           comment = c(ORCID = "0000-0002-4884-657X", AFFILIATION="CUMC")),
     person("Danielle","Braun", email = "dbraun@hsph.harvard.edu",
            role=c("aut"),     
            comment = c(ORCID = "0000-0002-5177-8598", AFFILIATION="HSPH")))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+## CausalGPS 0.4.2 (2024-04-13)
+
+### Added
+
+* heads-up message about changes in the software design that will be implemented in CausalGPS version 0.5.x.
+
+
 ## CausalGPS 0.4.1 (2023-09-29)
 
 ### Added

diff --git a/R/zzz.R b/R/zzz.R
@@ -7,6 +7,14 @@
                                                    sep = ""))
 
   logger::log_layout(flogger, index = 1)
-  # RNGkind(kind = "L'Ecuyer-CMRG")
+}
 
+.onAttach <- function(libname, pkgname){
+  packageStartupMessage(paste0(
+    "              ****                 \n"
+    ,"The CausalGPS version 0.5.x will undergo significant design changes. "
+    ,"Please be prepared to update your code accordingly, or consider "
+    ,"continuing with version 0.4.x until you are ready to update.\n"
+    ,"              ****                 \n"
+  ))
 }
diff --git a/README.md b/README.md
@@ -197,4 +197,30 @@ Please note that the CausalGPS project is released with a [Contributor Code of C
 
 ## References
 
-1. Wu, X., Mealli, F., Kioumourtzoglou, M.A., Dominici, F. and Braun, D., 2022. Matching on generalized propensity scores with continuous exposures. Journal of the American Statistical Association, pp.1-29.
+- CausalGPS method paper
+
+```
+@article{wu2022matching,
+  title={Matching on generalized propensity scores with continuous exposures},
+  author={Wu, Xiao and Mealli, Fabrizia and Kioumourtzoglou, Marianthi-Anna and Dominici, Francesca and Braun, Danielle},
+  journal={Journal of the American Statistical Association},
+  pages={1--29},
+  year={2022},
+  publisher={Taylor \& Francis}
+}
+```
+
+- CausalGPS software paper
+
+```
+@misc{khoshnevis2023causalgps,
+      title={CausalGPS: An R Package for Causal Inference With Continuous Exposures}, 
+      author={Naeem Khoshnevis and Xiao Wu and Danielle Braun},
+      year={2023},
+      eprint={2310.00561},
+      archivePrefix={arXiv},
+      primaryClass={stat.CO},
+      DOI={h10.48550/arXiv.2310.00561}
+}
+```
+
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,68 +1,15 @@
-Re-Submission (September 29, 2023)
+Submission (April 13, 2024)
 
-Thank you for your insightful feedback. We've carefully reviewed the discussions on R-package-devel and recognize that one of our dependencies, wCorr, may potentially utilize multiple cores. To address this, we've constrained the tests associated with that dependency. It’s important to note, however, that we conduct thorough testing of the package both locally and via rhub, all of which have been successful.
-
-Best regards, 
-Naeem Khoshnevis 
-Research Computing and Data Services 
-Harvard University
+Thank you so much for taking the time and reviewing the CausalGPS 0.4.2 package. In this version upgrade we:
 
+- Provided a heads-up message about changes in the software design that will be implemented in CausalGPS version 0.5.x. Since the package has no reverse dependencies, the transition is expected to be smooth. 
 
-Re-Submission (September 29, 2023)
 
-Thank you for your feedback. We have reviewed the discussions on R-package-devel and acknowledge that data.table may utilize multiple threads at certain instances. To address this, we have incorporated additional code to constrain data.table to a single thread during CRAN tests. We hope that this modification resolves the issue.
-
-Best regards, 
-Naeem Khoshnevis 
-Research Computing and Data Services 
-Harvard University
+The package tested locally and on rhub and passed all tests and checks successfully.
 
-
-Re-Submission (September 29, 2023)
-
-Thank you for your feedback. We have adjusted the package to skip the computationally intensive tests during CRAN checks due to the issues observed in one of the operating systems. We would like to kindly request acceptance of the package with this note, as the noted concern is specific to a single OS.
-
 Best regards, 
-Naeem Khoshnevis 
-Research Computing and Data Services 
-Harvard University
+Naeem Khoshnevis
 
-
-Re-Submission (September 29, 2023)
-
-Thank you for your feedback and observations. In response, and as part of this revised submission, we have instituted several modifications to address the raised concerns:
-- We have eliminated an additional vignette that required extensive computation.
-- We have relocated several examples to the `\donttest{}` block to avoid their execution during CRAN checks.
-- Some of the more computationally demanding tests have been configured to skip execution during CRAN checks.
-
-We are optimistic that these alterations will rectify the identified issues. Regrettably, we encounter limitations in verifying the resolutions directly, as attempts to reproduce the said issues both locally and during an `rhub` check were unsuccessful – all tests and checks passed without discrepancies. We appreciate your understanding and look forward to any further guidance or suggestions you might have.
-
-Best regards, 
-Naeem Khoshnevis 
-Research Computing and Data Services 
-Harvard University
-
-
-Re-Submission (September 29, 2023)
-
-Thank you for the notes. We have removed the computationally intensive vignette and also moved examples to the donttest block. We hope these changes resolve the issues. Unfortunately, we are unable to reproduce them locally or during an rhub check (as they pass successfully), so we could not verify the resolution directly.
-
-Best regards, 
-Naeem Khoshnevis 
-Research Computing and Data Services 
-Harvard University
-
-Submission (September 29, 2023)
-
-Thank you so much for taking the time and reviewing the CausalGPS 0.4.1 package. In this version upgrade we:
-
-- Added more details to the plots.
-- Removed unnecessary outcome input in the design stage. 
-- Addressed raised notes from CRAN on v0.4.0.
-
-The package tested locally and on rhub and passed all tests and checks successfully. 
-
-Best regards, 
-Naeem Khoshnevis 
-Research Computing and Data Services 
+Senior ML Research Engineer
+Kempner Institute
 Harvard University
diff --git a/docker_singularity/Dockerfile b/docker_singularity/Dockerfile
@@ -27,7 +27,6 @@ RUN R -e "install.packages(c( \
     'MASS', \
     'polycor', \
     'wCorr', \
-    'locpol', \
     'Ecume', \
     'logger', \
     'gnm'), repos='https://cloud.r-project.org')"
@@ -36,7 +35,5 @@ ENV RENV_VERSION 0.17.3
 RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
 RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
 
-
-
-
-#
+# R package installation from GitHub
+RUN R -e "remotes::install_github('NSAPH-Software/locpol', reference='master')"
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/articles/CausalGPS.html b/docs/articles/CausalGPS.html
diff --git a/docs/articles/Developers-Guide.html b/docs/articles/Developers-Guide.html
diff --git a/docs/articles/Estimating-GPS.html b/docs/articles/Estimating-GPS.html
diff --git a/docs/articles/Frequently-Asked-Questions.html b/docs/articles/Frequently-Asked-Questions.html
diff --git a/docs/articles/Generating-Pseudo-Population.html b/docs/articles/Generating-Pseudo-Population.html
diff --git a/docs/articles/Generating-Synthetic-Data.html b/docs/articles/Generating-Synthetic-Data.html
diff --git a/docs/articles/Notes-on-SL-Wrapper.html b/docs/articles/Notes-on-SL-Wrapper.html
diff --git a/docs/articles/Outcome-Models.html b/docs/articles/Outcome-Models.html
diff --git a/docs/articles/Singularity-Image.html b/docs/articles/Singularity-Image.html
diff --git a/docs/articles/Testing-the-Package.html b/docs/articles/Testing-the-Package.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
   Outcome-Models: Outcome-Models.html
   Singularity-Image: Singularity-Image.html
   Testing-the-Package: Testing-the-Package.html
-last_built: 2023-09-29T13:38Z
+last_built: 2023-10-04T15:55Z
 urls:
   reference: https://NSAPH-Software.github.io/CausalGPS/reference
   article: https://NSAPH-Software.github.io/CausalGPS/articles

diff --git a/docs/reference/CausalGPS-package.html b/docs/reference/CausalGPS-package.html
diff --git a/docs/reference/absolute_corr_fun.html b/docs/reference/absolute_corr_fun.html