From 9593ef45150a262881d9c58614c978145b3f4c9b Mon Sep 17 00:00:00 2001 From: naeemkh Date: Tue, 9 Apr 2024 07:26:09 -0400 Subject: [PATCH 01/10] transfer the maintainer role --- DESCRIPTION | 8 ++++---- NEWS.md | 6 ++++++ cran-comments.md | 5 ++--- 3 files changed, 12 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1ae993e..2547c35 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,12 @@ Package: GPCERF Title: Gaussian Processes for Estimating Causal Exposure Response Curves -Version: 0.2.3 +Version: 0.2.4 Authors@R: c( person("Naeem", "Khoshnevis", email = "nkhoshnevis@g.harvard.edu", - role=c("aut","cre"), + role=c("aut"), comment = c(ORCID = "0000-0003-4315-1426", AFFILIATION="HUIT")), person("Boyu", "Ren", email = "bren@partners.org", - role= c("aut"), + role= c("aut","cre"), comment = c(ORCID = "0000-0002-5300-1184", AFFILIATION="McLean Hospital")), person("Tanujit", "Dey", email = "tdey@bwh.harvard.edu", role= c("ctb"), @@ -14,7 +14,7 @@ Authors@R: c( person("Danielle","Braun", email = "dbraun@hsph.harvard.edu", role=c("aut"), comment = c(ORCID = "0000-0002-5177-8598", AFFILIATION="HSPH"))) -Maintainer: Naeem Khoshnevis +Maintainer: Boyu Ren Description: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint . License: GPL (>= 3) Language: en-US diff --git a/NEWS.md b/NEWS.md index 5cef239..f39e28a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# GPCERF 0.2.4 (2024-04-09) + +## Changed + +- Dr. Boyu Ren is now the package maintainer. + # GPCERF 0.2.3 (2024-03-02) ## Changed diff --git a/cran-comments.md b/cran-comments.md index ee13456..3c27abc 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,9 +1,8 @@ Submission (March 2, 2024): -We appreciate your efforts in reviewing the GPCERF 0.2.3 package. In this upgrade, we: +We appreciate your efforts in reviewing the GPCERF 0.2.4 package. In this upgrade, we: -- Modified the method by which the user specifies the covariate columns. -- Resolved an issue involving data that contains a single covariate. +- Transfer the maintainer role from Dr. Naeem Khoshnevis to Dr. Boyu Ren. All tests and checks have passed successfully. From d963a012fcb52e799e15b26ad9971382fe726050 Mon Sep 17 00:00:00 2001 From: naeemkh Date: Tue, 9 Apr 2024 07:43:30 -0400 Subject: [PATCH 02/10] fix cran comment date --- cran-comments.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index 3c27abc..90bb117 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,4 +1,4 @@ -Submission (March 2, 2024): +Submission (April 9, 2024): We appreciate your efforts in reviewing the GPCERF 0.2.4 package. In this upgrade, we: From dc4ab75ec64d5b4cd5d89eb8ceb4bab32d792936 Mon Sep 17 00:00:00 2001 From: boyuren158 Date: Tue, 9 Apr 2024 11:12:38 -0400 Subject: [PATCH 03/10] Updated email address --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2547c35..4f41432 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Authors@R: c( person("Naeem", "Khoshnevis", email = "nkhoshnevis@g.harvard.edu", role=c("aut"), comment = c(ORCID = "0000-0003-4315-1426", AFFILIATION="HUIT")), - person("Boyu", "Ren", email = "bren@partners.org", + person("Boyu", "Ren", email = "bren@mgb.org", role= c("aut","cre"), comment = c(ORCID = "0000-0002-5300-1184", AFFILIATION="McLean Hospital")), person("Tanujit", "Dey", email = "tdey@bwh.harvard.edu", From 2df3ee414401f7979772d9ec3abd46be86063da2 Mon Sep 17 00:00:00 2001 From: boyuren158 Date: Thu, 11 Apr 2024 19:45:52 -0400 Subject: [PATCH 04/10] Attempt to fix URI --- README.md | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 0bfb59f..09672e4 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,8 @@ +--- +output: + html_document: default + pdf_document: default +---

Cover Image

@@ -194,7 +199,7 @@ Please note that the GPCERF project is released with a [Contributor Code of Cond ## Contributing -Contributions to the package are encouraged. For detailed information on how to contribute, please refer to the [CONTRIBUTING](CONTRIBUTING.md) guidelines. +Contributions to the package are encouraged. For detailed information on how to contribute, please refer to the [CONTRIBUTING](./CONTRIBUTING.md) guidelines. ## Reporting Issues & Seeking Support @@ -203,4 +208,4 @@ If you encounter any issues with GPCERF, we kindly ask you to report them on our ## References -Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint arXiv:2105.03454. +Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint doi:10.48550/arXiv:2105.03454. From bd59f77e2b1bcd67b70399d2f1da18770e952604 Mon Sep 17 00:00:00 2001 From: boyuren158 Date: Thu, 11 Apr 2024 20:41:19 -0400 Subject: [PATCH 05/10] Updated comment to CRAN to clarify two notes --- cran-comments.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/cran-comments.md b/cran-comments.md index 90bb117..542cf6a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,19 @@ +Resubmission (April 11, 2024) + +We appreciate your efforts in reviewing the GPCERF 0.2.4 package. In this upgrade, we: + +- Refer to the arXiv e-print via its DOI directly. + +Regarding the other two notes: + +- CONTRIBUTING.md is a md file in the project folder and this URI works as intended so we didn't make any change +- Rcpp cannot be removed from LinkingTo as it will cause compilation error + +All tests and checks have passed successfully. + +Best regards, +Boyu Ren + Submission (April 9, 2024): We appreciate your efforts in reviewing the GPCERF 0.2.4 package. In this upgrade, we: From 1367f5d645b5d6ce7b33ce42800a5eee187d2d21 Mon Sep 17 00:00:00 2001 From: boyuren158 Date: Thu, 11 Apr 2024 21:19:48 -0400 Subject: [PATCH 06/10] Updated REAME and cran-comments for release --- README.md | 2 +- cran-comments.md | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 09672e4..ecba8d4 100644 --- a/README.md +++ b/README.md @@ -199,7 +199,7 @@ Please note that the GPCERF project is released with a [Contributor Code of Cond ## Contributing -Contributions to the package are encouraged. For detailed information on how to contribute, please refer to the [CONTRIBUTING](./CONTRIBUTING.md) guidelines. +Contributions to the package are encouraged. For detailed information on how to contribute, please refer to the CONTRIBUTING guidelines. ## Reporting Issues & Seeking Support diff --git a/cran-comments.md b/cran-comments.md index 542cf6a..a8203fa 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -2,12 +2,12 @@ Resubmission (April 11, 2024) We appreciate your efforts in reviewing the GPCERF 0.2.4 package. In this upgrade, we: -- Refer to the arXiv e-print via its DOI directly. +- Referred to the arXiv e-print via its DOI directly. +- Removed the URI to CONTRIBUTING.md in README.md. Regarding the other two notes: -- CONTRIBUTING.md is a md file in the project folder and this URI works as intended so we didn't make any change -- Rcpp cannot be removed from LinkingTo as it will cause compilation error +- Rcpp cannot be removed from LinkingTo as it will cause compilation error. All tests and checks have passed successfully. From 1b70b7794773393fc6c0a314bba2337510ef7ac0 Mon Sep 17 00:00:00 2001 From: boyuren158 Date: Fri, 12 Apr 2024 13:00:11 -0400 Subject: [PATCH 07/10] Updated arXiv do --- index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.md b/index.md index 8815003..2032372 100644 --- a/index.md +++ b/index.md @@ -22,4 +22,4 @@ Provides a non-parametric Bayesian framework based on Gaussian process priors fo ## References -Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint arXiv:2105.03454. +Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint doi:10.48550/arXiv:2105.03454. From 5d125dc277470ec9c9d4682633022bb17b682b92 Mon Sep 17 00:00:00 2001 From: boyuren158 Date: Sat, 13 Apr 2024 15:27:41 -0400 Subject: [PATCH 08/10] Update arXiv reference syntax --- README.md | 2 +- index.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ecba8d4..6ee4a19 100644 --- a/README.md +++ b/README.md @@ -208,4 +208,4 @@ If you encounter any issues with GPCERF, we kindly ask you to report them on our ## References -Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint doi:10.48550/arXiv:2105.03454. +Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint . diff --git a/index.md b/index.md index 2032372..2bb2ba5 100644 --- a/index.md +++ b/index.md @@ -22,4 +22,4 @@ Provides a non-parametric Bayesian framework based on Gaussian process priors fo ## References -Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint doi:10.48550/arXiv:2105.03454. +Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint . From 1df2f725a4908ad4f264b70ecbc100cf63762c23 Mon Sep 17 00:00:00 2001 From: boyuren158 Date: Sat, 13 Apr 2024 19:30:01 -0400 Subject: [PATCH 09/10] Updated arXiv link --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4f41432..a491d49 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,7 +15,7 @@ Authors@R: c( role=c("aut"), comment = c(ORCID = "0000-0002-5177-8598", AFFILIATION="HSPH"))) Maintainer: Boyu Ren -Description: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint . +Description: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint . License: GPL (>= 3) Language: en-US URL: https://github.com/NSAPH-Software/GPCERF From 017524b1841fa70562366fb1ce637a747c6d6517 Mon Sep 17 00:00:00 2001 From: boyuren158 Date: Mon, 15 Apr 2024 09:50:33 -0400 Subject: [PATCH 10/10] Update arXiv link style --- DESCRIPTION | 2 +- README.md | 2 +- index.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a491d49..415b997 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,7 +15,7 @@ Authors@R: c( role=c("aut"), comment = c(ORCID = "0000-0002-5177-8598", AFFILIATION="HSPH"))) Maintainer: Boyu Ren -Description: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint . +Description: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint . License: GPL (>= 3) Language: en-US URL: https://github.com/NSAPH-Software/GPCERF diff --git a/README.md b/README.md index 6ee4a19..2fe0388 100644 --- a/README.md +++ b/README.md @@ -208,4 +208,4 @@ If you encounter any issues with GPCERF, we kindly ask you to report them on our ## References -Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint . +Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint . diff --git a/index.md b/index.md index 2bb2ba5..00f389b 100644 --- a/index.md +++ b/index.md @@ -22,4 +22,4 @@ Provides a non-parametric Bayesian framework based on Gaussian process priors fo ## References -Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint . +Ren, B., Wu, X., Braun, D., Pillai, N. and Dominici, F., 2021. Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes. arXiv preprint .