diff --git a/.Rbuildignore b/.Rbuildignore index b74ca4f..8ac0eaa 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,3 +6,5 @@ ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^cran-comments\.md$ +^CRAN-SUBMISSION$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..01d4eaa --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 1.0.0 +Date: 2024-07-03 13:29:36 UTC +SHA: 0ff357caf3022bd3ae9d779e85d43499e781dfc3 diff --git a/DESCRIPTION b/DESCRIPTION index ccea289..c18d45d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,13 +1,21 @@ 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")) +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")), + 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 Hidradenitis Suppurativa + 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/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. diff --git a/README.md b/README.md index 9426940..ce7709b 100644 --- a/README.md +++ b/README.md @@ -3,12 +3,25 @@ [![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 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 +35,43 @@ 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) + ``` diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..8dcab8a --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,9 @@ +## 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. +* DOI authors and years have been added, as requested. diff --git a/inst/WORDLIST b/inst/WORDLIST index db8ee98..350035a 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,9 +1,33 @@ +Alavi CMD +CodeFactor 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