Merge pull request #53 from billdenney/50-prepare-for-initial-cran-release

billdenney · web-flow · commit 18017dbbd7e6 · 2024-07-31T17:41:13.000-04:00
CRAN release 1.0
diff --git 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
@@ -0,0 +1,3 @@
+Version: 1.0.0
+Date: 2024-07-03 13:29:36 UTC
+SHA: 0ff357caf3022bd3ae9d779e85d43499e781dfc3
diff --git 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) <doi:10.1111/jdv.13216>),
+  Hidradenitis Suppurativa Area and Severity Index Revised (HASI-R) (Goldfarb,
+  et al. (2020) <doi:10.1111/bjd.19565>), hidradenitis suppurativa Physician
+  Global Assessment (HS PGA) (Marzano, et al. (2020) <doi:10.1111/jdv.16328>),
+  and the International Hidradenitis Suppurativa Severity Score System (IHS4)
+  (Zouboulis, et al. (2017) <doi:10.1111/bjd.15748>).
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,3 @@
+# hidradenitis 1.0.0
+
+* Initial CRAN submission.
diff --git a/README.md b/README.md
@@ -3,12 +3,25 @@
 <!-- badges: start -->
 [![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)
 <!-- badges: end -->
 
-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
@@ -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
@@ -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

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+Version: 1.0.0`
	`2`	`+Date: 2024-07-03 13:29:36 UTC`
	`3`	`+SHA: 0ff357caf3022bd3ae9d779e85d43499e781dfc3`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+# hidradenitis 1.0.0`
	`2`	`+`
	`3`	`+* Initial CRAN submission.`