From 002d758f79c74d896c97932162c26cf28638e3ce Mon Sep 17 00:00:00 2001
From: Alessandro Gasparini <git@ellessenne.xyz>
Date: Sat, 25 May 2024 14:04:57 +0200
Subject: [PATCH] Updated documentation following deprecation of "@docType
 package"

---
 NAMESPACE                  |  5 +++++
 R/comorbidity-package.R    | 25 +++++++++----------------
 man/comorbidity-package.Rd | 22 +++++++++++++---------
 3 files changed, 27 insertions(+), 25 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 0c66321..7139947 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,3 +4,8 @@ export(available_algorithms)
 export(comorbidity)
 export(sample_diag)
 export(score)
+import(checkmate)
+import(data.table)
+import(stats)
+import(stringi)
+import(utils)
diff --git a/R/comorbidity-package.R b/R/comorbidity-package.R
index af4c5bb..5ebe1d3 100644
--- a/R/comorbidity-package.R
+++ b/R/comorbidity-package.R
@@ -1,20 +1,13 @@
-#' @title Computing Comorbidity Scores
-#'
-#' @description Computing comorbidity indices and scores such as the weighted Charlson
-#' score (Charlson, 1987 \doi{10.1016/0021-9681(87)90171-8}) and the Elixhauser
-#' comorbidity score (Elixhauser, 1998 \doi{10.1097/00005650-199801000-00004})
-#' using ICD-9-CM or ICD-10 codes (Quan, 2005 \doi{10.1097/01.mlr.0000182534.19832.83}).
-#' Australian and Swedish modifications of the Charlson Comorbidity Index are available
-#' as well (Sundararajan, 2004 \doi{10.1016/j.jclinepi.2004.03.012} and Ludvigsson, 2021
-#' \doi{10.2147/CLEP.S282475}).
-#'
-#' @name comorbidity-package
-#' @docType package
-#' @author Alessandro Gasparini (alessandro.gasparini@@ki.se)
-NULL
-
+#' @import checkmate data.table stats stringi utils
 #' @keywords internal
-.datatable.aware <- TRUE
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL
 
 # Quiets concerns of R CMD check re: variable names used internally
 if (getRversion() >= "2.15.1") utils::globalVariables(c(":=", "..mv", "..mvb", "NA", "canc", "diab", "diabc", "diabunc", "diabwc", "hypc", "hypunc", "metacanc", "mld", "msld", "solidtum", "value"))
+
+#' @keywords internal
+.datatable.aware <- TRUE
diff --git a/man/comorbidity-package.Rd b/man/comorbidity-package.Rd
index dc2ec19..5e72eb3 100644
--- a/man/comorbidity-package.Rd
+++ b/man/comorbidity-package.Rd
@@ -3,15 +3,9 @@
 \docType{package}
 \name{comorbidity-package}
 \alias{comorbidity-package}
-\title{Computing Comorbidity Scores}
+\title{comorbidity: Computing Comorbidity Scores}
 \description{
-Computing comorbidity indices and scores such as the weighted Charlson
-score (Charlson, 1987 \doi{10.1016/0021-9681(87)90171-8}) and the Elixhauser
-comorbidity score (Elixhauser, 1998 \doi{10.1097/00005650-199801000-00004})
-using ICD-9-CM or ICD-10 codes (Quan, 2005 \doi{10.1097/01.mlr.0000182534.19832.83}).
-Australian and Swedish modifications of the Charlson Comorbidity Index are available
-as well (Sundararajan, 2004 \doi{10.1016/j.jclinepi.2004.03.012} and Ludvigsson, 2021
-\doi{10.2147/CLEP.S282475}).
+Computing comorbidity indices and scores such as the weighted Charlson score (Charlson, 1987 \doi{10.1016/0021-9681(87)90171-8}) and the Elixhauser comorbidity score (Elixhauser, 1998 \doi{10.1097/00005650-199801000-00004}) using ICD-9-CM or ICD-10 codes (Quan, 2005 \doi{10.1097/01.mlr.0000182534.19832.83}). Australian and Swedish modifications of the Charlson Comorbidity Index are available as well (Sundararajan, 2004 \doi{10.1016/j.jclinepi.2004.03.012} and Ludvigsson, 2021 \doi{10.2147/CLEP.S282475}), together with different weighting algorithms for both the Charlson and Elixhauser comorbidity scores.
 }
 \seealso{
 Useful links:
@@ -23,5 +17,15 @@ Useful links:
 
 }
 \author{
-Alessandro Gasparini (alessandro.gasparini@ki.se)
+\strong{Maintainer}: Alessandro Gasparini \email{alessandro@ellessenne.xyz} (\href{https://orcid.org/0000-0002-8319-7624}{ORCID})
+
+Other contributors:
+\itemize{
+  \item Hojjat Salmasian \email{hsalmasian@bwh.harvard.edu} (ICD-9-CM scores) [contributor]
+  \item Jonathan Williman \email{jonathan.williman@otago.ac.nz} (\href{https://orcid.org/0000-0001-5080-4435}{ORCID}) [contributor]
+  \item Sing Yi Chia \email{cxycsy@hotmail.com} (\href{https://orcid.org/0000-0002-7591-3141}{ORCID}) [contributor]
+  \item Edmund Teo \email{ed_teo8@yahoo.com.sg} (\href{https://orcid.org/0000-0003-3936-4082}{ORCID}) [contributor]
+}
+
 }
+\keyword{internal}