From 8c59e4e62cfaa0d39b8489c9fff17dacba1be92a Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Sat, 29 Jun 2024 23:30:43 -0400 Subject: [PATCH 01/11] Prepare for CRAN release --- DESCRIPTION | 12 ++++++++---- README.md | 54 +++++++++++++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 60 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2186183..94d3659 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,13 +1,17 @@ Package: hidradenitis Title: Calculate Clinical Scores for Hidradenitis Suppurativa (HS), a Dermatologic Disease Version: 0.0.0.9000 -Authors@R: - person("Bill", "Denney", email="wdenney@humanpredictions.com", role=c("aut", "cre"), comment=c(ORCID="0000-0002-5759-428X")) +Authors@R: + c( + person("Bill", "Denney", email="wdenney@humanpredictions.com", role=c("aut", "cre"), comment=c(ORCID="0000-0002-5759-428X")), + person("Devon", "Bartlett", email="dbartlett@humanpredictions.com", role = "aut") + ) Description: Calculate clinical scores for hidradenitis suppurativa (HS), a dermatologic disease. The scores are typically used for evaluation of efficacy in clinical trials. The scores are not commonly used in clinical - practice. The specific scores implemented are HiSQOL, HiSQOL-Adolescent, HS - PtGA, HASI-R, and HASI. + practice. The specific scores implemented are HiSCR + (), HASI-R (), HS PGA + (), and IHS4 (). License: GPL (>= 3) Encoding: UTF-8 Roxygen: list(markdown = TRUE) diff --git a/README.md b/README.md index 9426940..1c6f113 100644 --- a/README.md +++ b/README.md @@ -3,12 +3,24 @@ [![R-CMD-check](https://github.com/billdenney/hidradenitis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/billdenney/hidradenitis/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/billdenney/hidradenitis/branch/main/graph/badge.svg)](https://app.codecov.io/gh/billdenney/hidradenitis?branch=main) +[![CRAN status](https://www.r-pkg.org/badges/version/hidradenitis)](https://CRAN.R-project.org/package=hidradenitis) -The goal of hidradenitis is to ... +The goal of the `hidradenitis` package is to support use and interpretation of +clinical scores for hidradenitis suppurativa. ## Installation +### Stable version + +You can install the stable version of hidradenitis from CRAN with: + +``` r +install.packages("devtools") +``` + +### Development version + You can install the development version of hidradenitis from [GitHub](https://github.com/) with: ``` r @@ -22,5 +34,43 @@ This is a basic example which shows you how to solve a common problem: ``` r library(hidradenitis) -## basic example code + +hasi_r_num( + bsa_percent_within_site = c(0, 0, 0, 0, 5, 1, 4.3, 1.2, 6.8, 7.2), + bodysite = + c("Right Axilla", "Buttocks including Intergluteal Cleft", + "Back", "Left Thigh", "Head & Neck", "Left Axilla", + "Chest", "Pubis & Genitals", "Abdomen", "Right Thigh"), + inflam_color_chg = c(0, 0, 0, 0, 2, 3, 1, 3, 2, 0), + induration = c(0, 0, 0, 0, 2, 3, 1, 3, 2, 0), + open_skin_surface = c(0, 0, 0, 0, 2, 3, 1, 3, 2, 0), + tunnels = c(0, 0, 0, 0, 2, 3, 1, 3, 2, 0) +) + +hiscr( + baseline_abscess = c(3, 2, 4), + baseline_nodule = c(5, 4, 6), + baseline_fistula = c(2, 1, 3), + timepoint_abscess = c(1, 1, 2), + timepoint_nodule = c(2, 3, 2), + timepoint_fistula = c(2, 1, 3), + percentage = 50 +) + +hs_pga <- + hs_pga_num( + abscess_fistula = c(0, 0, 1, 0, 1, 2, 6), + inflammatory_nodule = c(0, 0, 0, 3, 5, 8, 12), + non_inflammatory_nodule = c(0, 1, 0, 0, 0, 0, 0) + ) +hs_pga_char(hs_pga) + +ihs4 <- + ihs4_num( + nodules = c(5, 3, 2), + abscesses = c(2, 1, 0), + draining_tunnels = c(1, 2, 3) + ) +ihs4_char(ihs4) + ``` From ccb7227fe7ab24d8bbfe236f42037b3876d947fa Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Sat, 29 Jun 2024 23:33:23 -0400 Subject: [PATCH 02/11] Bump version; add comments --- .Rbuildignore | 1 + DESCRIPTION | 2 +- cran-comments.md | 8 ++++++++ 3 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 cran-comments.md diff --git a/.Rbuildignore b/.Rbuildignore index b74ca4f..b63c006 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,3 +6,4 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^cran-comments\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index 94d3659..e7ca21b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: hidradenitis Title: Calculate Clinical Scores for Hidradenitis Suppurativa (HS), a Dermatologic Disease -Version: 0.0.0.9000 +Version: 1.0.0 Authors@R: c( person("Bill", "Denney", email="wdenney@humanpredictions.com", role=c("aut", "cre"), comment=c(ORCID="0000-0002-5759-428X")), diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..b5b121f --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,8 @@ +## R CMD check results + +0 errors | 0 warnings | 1 note + +* This is a new release. +* The package name is part of the disease name which the package supports + understanding of. The use of the pacakge name in the description and title in + the DESCRIPTION file is for that reason. From 5ac26b752a3ff3c3973f7684d8488e9c659bbff2 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Sat, 29 Jun 2024 23:34:45 -0400 Subject: [PATCH 03/11] Update spell check words --- inst/WORDLIST | 27 +++++++++++++++++++++++++-- 1 file changed, 25 insertions(+), 2 deletions(-) diff --git a/inst/WORDLIST b/inst/WORDLIST index db8ee98..3571c3a 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,9 +1,32 @@ +Alavi CMD Codecov +Dermatol Dermatologic +Epub +Goldfarb HASI -HiSQOL -PtGA +HIDRAscore +HiSCR +IHS +JEADV +JS +Kimball +Lowes +Marzano +PGA +PMC +PMCID +PMID Suppurativa +Venereology +Zouboulis +adalimumab +al +bjd dermatologic +doi +et +induration +jdv suppurativa From 77f350f1885361464824835c0ed9a99f49bb0f23 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Sat, 29 Jun 2024 23:36:15 -0400 Subject: [PATCH 04/11] Create NEWS.md --- NEWS.md | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 NEWS.md diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..6075c40 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,3 @@ +# hidradenitis 1.0.0 + +* Initial CRAN submission. From d13d6dabea332a499a18426afddf4cc76ec44e5d Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Sat, 29 Jun 2024 23:37:02 -0400 Subject: [PATCH 05/11] As initially submitted to CRAN --- .Rbuildignore | 1 + CRAN-SUBMISSION | 3 +++ 2 files changed, 4 insertions(+) create mode 100644 CRAN-SUBMISSION diff --git a/.Rbuildignore b/.Rbuildignore index b63c006..8ac0eaa 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -7,3 +7,4 @@ ^docs$ ^pkgdown$ ^cran-comments\.md$ +^CRAN-SUBMISSION$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..150e9df --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 1.0.0 +Date: 2024-06-30 03:36:40 UTC +SHA: 77f350f1885361464824835c0ed9a99f49bb0f23 From ad6c668c104fa12ffc46b586a0d0042bdd973dd6 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Sun, 30 Jun 2024 00:58:54 -0400 Subject: [PATCH 06/11] Add CodeFactor badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 1c6f113..ce7709b 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,7 @@ [![R-CMD-check](https://github.com/billdenney/hidradenitis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/billdenney/hidradenitis/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/billdenney/hidradenitis/branch/main/graph/badge.svg)](https://app.codecov.io/gh/billdenney/hidradenitis?branch=main) [![CRAN status](https://www.r-pkg.org/badges/version/hidradenitis)](https://CRAN.R-project.org/package=hidradenitis) +[![CodeFactor](https://www.codefactor.io/repository/github/billdenney/hidradenitis/badge)](https://www.codefactor.io/repository/github/billdenney/hidradenitis) The goal of the `hidradenitis` package is to support use and interpretation of From bd0d394a7abf2b0cc2b33c399133449382a6c03b Mon Sep 17 00:00:00 2001 From: Devon Bartlett Date: Tue, 2 Jul 2024 14:30:38 -0500 Subject: [PATCH 07/11] CRAN suggested changes --- DESCRIPTION | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e7ca21b..975cf07 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,9 +9,13 @@ Authors@R: Description: Calculate clinical scores for hidradenitis suppurativa (HS), a dermatologic disease. The scores are typically used for evaluation of efficacy in clinical trials. The scores are not commonly used in clinical - practice. The specific scores implemented are HiSCR - (), HASI-R (), HS PGA - (), and IHS4 (). + practice. The specific scores implemented are Hidradenitis Suppurativa Clinical + Response (HiSCR) (Kimball, A. B., Sobell, J. M., Zouboulis, C. C. (2015) ), + Hidradenitis Suppurativa Area and Severity Index Revised (HASI-R) (Goldfarb, N., Lowes, M. A., Butt, + M., King, T., Alavi, A., & Kirby, J. S. (2020) ), hidradenitis suppurativa Physician + Global Assessment (HS PGA) (Marzano, A. V., Chiricozzi, A., Giovanardi, G., Argenziano, G., Bettoli, + V., Bianchi, L., Rongioletti, F. (2020) ), and the International +Hidradenitis Suppurativa Severity Score System (IHS4) (CHRISTOS C. ZOUBOULIS, ATHANASSIOS KYRGIDIS (2017) ). License: GPL (>= 3) Encoding: UTF-8 Roxygen: list(markdown = TRUE) From aab3620355992b688d8d4659de991c036da54a21 Mon Sep 17 00:00:00 2001 From: Devon Bartlett Date: Tue, 2 Jul 2024 14:43:55 -0500 Subject: [PATCH 08/11] Fixing DESCRIPTION lines --- DESCRIPTION | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 975cf07..0c8ff30 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,13 +9,16 @@ Authors@R: Description: Calculate clinical scores for hidradenitis suppurativa (HS), a dermatologic disease. The scores are typically used for evaluation of efficacy in clinical trials. The scores are not commonly used in clinical - practice. The specific scores implemented are Hidradenitis Suppurativa Clinical - Response (HiSCR) (Kimball, A. B., Sobell, J. M., Zouboulis, C. C. (2015) ), - Hidradenitis Suppurativa Area and Severity Index Revised (HASI-R) (Goldfarb, N., Lowes, M. A., Butt, - M., King, T., Alavi, A., & Kirby, J. S. (2020) ), hidradenitis suppurativa Physician - Global Assessment (HS PGA) (Marzano, A. V., Chiricozzi, A., Giovanardi, G., Argenziano, G., Bettoli, - V., Bianchi, L., Rongioletti, F. (2020) ), and the International -Hidradenitis Suppurativa Severity Score System (IHS4) (CHRISTOS C. ZOUBOULIS, ATHANASSIOS KYRGIDIS (2017) ). + practice. The specific scores implemented are Hidradenitis Suppurativa + Clinical Response (HiSCR) (Kimball, A. B., Sobell, J. M., Zouboulis, C. C. + (2015) ), Hidradenitis Suppurativa Area and Severity + Index Revised (HASI-R) (Goldfarb, N., Lowes, M. A., Butt, M., King, T., + Alavi, A., & Kirby, J. S. (2020) ), hidradenitis + suppurativa Physician Global Assessment (HS PGA) (Marzano, A. V., Chiricozzi, + A., Giovanardi, G., Argenziano, G., Bettoli, V., Bianchi, L., Rongioletti, F. + (2020) ), and the International Hidradenitis Suppurativa + Severity Score System (IHS4) (CHRISTOS C. ZOUBOULIS, ATHANASSIOS KYRGIDIS (2017) + ). License: GPL (>= 3) Encoding: UTF-8 Roxygen: list(markdown = TRUE) From a3158024c38550c1a52075aac621d0b58c2d7bf2 Mon Sep 17 00:00:00 2001 From: Devon Bartlett Date: Tue, 2 Jul 2024 14:47:19 -0500 Subject: [PATCH 09/11] Fixing capitalization --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0c8ff30..748f48a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,7 +17,7 @@ Description: Calculate clinical scores for hidradenitis suppurativa (HS), a suppurativa Physician Global Assessment (HS PGA) (Marzano, A. V., Chiricozzi, A., Giovanardi, G., Argenziano, G., Bettoli, V., Bianchi, L., Rongioletti, F. (2020) ), and the International Hidradenitis Suppurativa - Severity Score System (IHS4) (CHRISTOS C. ZOUBOULIS, ATHANASSIOS KYRGIDIS (2017) + Severity Score System (IHS4) (Christos C. Zouboulis, Athanassios Kyrgidis (2017) ). License: GPL (>= 3) Encoding: UTF-8 From 0ff357caf3022bd3ae9d779e85d43499e781dfc3 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Wed, 3 Jul 2024 09:28:46 -0400 Subject: [PATCH 10/11] Change author names to "et al." format; update spell check --- DESCRIPTION | 15 ++++++--------- cran-comments.md | 1 + inst/WORDLIST | 1 + 3 files changed, 8 insertions(+), 9 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 748f48a..ba106d4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,15 +10,12 @@ Description: Calculate clinical scores for hidradenitis suppurativa (HS), a dermatologic disease. The scores are typically used for evaluation of efficacy in clinical trials. The scores are not commonly used in clinical practice. The specific scores implemented are Hidradenitis Suppurativa - Clinical Response (HiSCR) (Kimball, A. B., Sobell, J. M., Zouboulis, C. C. - (2015) ), Hidradenitis Suppurativa Area and Severity - Index Revised (HASI-R) (Goldfarb, N., Lowes, M. A., Butt, M., King, T., - Alavi, A., & Kirby, J. S. (2020) ), hidradenitis - suppurativa Physician Global Assessment (HS PGA) (Marzano, A. V., Chiricozzi, - A., Giovanardi, G., Argenziano, G., Bettoli, V., Bianchi, L., Rongioletti, F. - (2020) ), and the International Hidradenitis Suppurativa - Severity Score System (IHS4) (Christos C. Zouboulis, Athanassios Kyrgidis (2017) - ). + Clinical Response (HiSCR) (Kimball, et al. (2015) ), + Hidradenitis Suppurativa Area and Severity Index Revised (HASI-R) (Goldfarb, + et al. (2020) ), hidradenitis suppurativa Physician + Global Assessment (HS PGA) (Marzano, et al. (2020) ), + and the International Hidradenitis Suppurativa Severity Score System (IHS4) + (Zouboulis, et al. (2017) ). License: GPL (>= 3) Encoding: UTF-8 Roxygen: list(markdown = TRUE) diff --git a/cran-comments.md b/cran-comments.md index b5b121f..8dcab8a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -6,3 +6,4 @@ * The package name is part of the disease name which the package supports understanding of. The use of the pacakge name in the description and title in the DESCRIPTION file is for that reason. +* DOI authors and years have been added, as requested. diff --git a/inst/WORDLIST b/inst/WORDLIST index 3571c3a..350035a 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,5 +1,6 @@ Alavi CMD +CodeFactor Codecov Dermatol Dermatologic From 4c17678c37b175cd09ca010190b5c5ee55dc6bb1 Mon Sep 17 00:00:00 2001 From: Bill Denney Date: Wed, 3 Jul 2024 09:29:52 -0400 Subject: [PATCH 11/11] As submitted to CRAN --- CRAN-SUBMISSION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 150e9df..01d4eaa 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 1.0.0 -Date: 2024-06-30 03:36:40 UTC -SHA: 77f350f1885361464824835c0ed9a99f49bb0f23 +Date: 2024-07-03 13:29:36 UTC +SHA: 0ff357caf3022bd3ae9d779e85d43499e781dfc3