From dbdd9e93dfbf0de3363f191b3a86f8f9148ce2b4 Mon Sep 17 00:00:00 2001
From: Duncan Gillespie <duncan.gillespie@sheffield.ac.uk>
Date: Fri, 16 Dec 2022 11:29:15 +0000
Subject: [PATCH] remove requirement for stapmr package

---
 DESCRIPTION              |  5 +++--
 NAMESPACE                |  2 +-
 R/AlcLags.R              |  1 -
 R/RRAlc.R                |  1 -
 R/RRFunc.R               |  1 -
 R/RRtob.R                |  1 -
 R/TobAlcInt.R            |  1 -
 R/TobLags.R              |  1 -
 R/fast_match.R           | 30 ++++++++++++++++++++++++++++++
 R/subgroupRisk.R         |  1 -
 man/grapes-fin-grapes.Rd | 34 ++++++++++++++++++++++++++++++++++
 11 files changed, 68 insertions(+), 10 deletions(-)
 create mode 100644 R/fast_match.R
 create mode 100644 man/grapes-fin-grapes.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index da08f07..0d0cb6f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -49,9 +49,10 @@ Imports:
     crayon,
     TTR,
     Rfast,
-    stats
+    stats,
+    brew
 RdMacros: Rdpack, lifecycle
 VignetteBuilder: knitr
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Depends: 
     R (>= 2.10)
diff --git a/NAMESPACE b/NAMESPACE
index c60b3b2..8ae683f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%fin%")
 export(AlcBinge)
 export(AlcBinge_stapm)
 export(AlcLags)
@@ -27,5 +28,4 @@ importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
 importFrom(data.table,setnames)
 importFrom(lifecycle,deprecate_soft)
-importFrom(stapmr,"%fin%")
 importFrom(stats,ar)
diff --git a/R/AlcLags.R b/R/AlcLags.R
index a21263f..98874c3 100644
--- a/R/AlcLags.R
+++ b/R/AlcLags.R
@@ -17,7 +17,6 @@
 #' on an individual's relative risk of disease has so far emerged.
 #' 
 #' @importFrom data.table := setDT setnames data.table
-#' @importFrom stapmr %fin%
 #' 
 #' @references
 #' \insertRef{holmes2012temporal}{tobalcepi}  
diff --git a/R/RRAlc.R b/R/RRAlc.R
index d24c59f..09a2f3b 100644
--- a/R/RRAlc.R
+++ b/R/RRAlc.R
@@ -39,7 +39,6 @@
 #' @return Returns a numeric vector of each individual's relative risks for the alcohol related disease specified by "disease".
 #' 
 #' @importFrom data.table := setDT setnames fifelse
-#' @importFrom stapmr %fin%
 #' 
 #' @export
 #' 
diff --git a/R/RRFunc.R b/R/RRFunc.R
index 7bea5ab..c907180 100644
--- a/R/RRFunc.R
+++ b/R/RRFunc.R
@@ -112,7 +112,6 @@
 #' 
 #' 
 #' @importFrom data.table := setDT setnames copy rbindlist
-#' @importFrom stapmr %fin%
 #' 
 #' @export
 #' 
diff --git a/R/RRtob.R b/R/RRtob.R
index 0d53dba..3cf91bd 100644
--- a/R/RRtob.R
+++ b/R/RRtob.R
@@ -37,7 +37,6 @@
 #' specified by "disease".
 #' 
 #' @importFrom data.table := setDT setnames copy
-#' @importFrom stapmr %fin%
 #' 
 #' @export
 #' 
diff --git a/R/TobAlcInt.R b/R/TobAlcInt.R
index 055fbe6..938c994 100644
--- a/R/TobAlcInt.R
+++ b/R/TobAlcInt.R
@@ -26,7 +26,6 @@
 #' specified by "disease".
 #' 
 #' @importFrom data.table := setDT setnames copy
-#' @importFrom stapmr %fin%
 #' 
 #' @export
 #' @references
diff --git a/R/TobLags.R b/R/TobLags.R
index 755f03f..b458998 100644
--- a/R/TobLags.R
+++ b/R/TobLags.R
@@ -37,7 +37,6 @@
 #' on an individual's relative risk of disease has so far emerged.
 #' 
 #' @importFrom data.table := setDT setnames data.table
-#' @importFrom stapmr %fin%
 #' 
 #' @export
 #'
diff --git a/R/fast_match.R b/R/fast_match.R
new file mode 100644
index 0000000..938ebc1
--- /dev/null
+++ b/R/fast_match.R
@@ -0,0 +1,30 @@
+
+#' Fast matching
+#' 
+#' A faster version of `%in%`.
+#' 
+#' See [fastmatch::fmatch()]
+#'
+#' @param x values to be matched
+#' @param table values to be matched against
+#'
+#' @return Logical indicating match or not
+#' @export
+#'
+#' @keywords internal
+#'
+#' @examples
+#' 
+#' \dontrun{
+#' 
+#' x %fin% y
+#' 
+#' }
+#' 
+#' 
+#' 
+`%fin%` <- function(x, table) {
+  
+  fastmatch::fmatch(x, table, nomatch = 0L) > 0L
+  
+}
\ No newline at end of file
diff --git a/R/subgroupRisk.R b/R/subgroupRisk.R
index 0f85f7c..5257455 100644
--- a/R/subgroupRisk.R
+++ b/R/subgroupRisk.R
@@ -31,7 +31,6 @@
 #' @return Returns a data table containing the subgroup specific summaries for each disease.
 #' 
 #' @importFrom data.table := setDT setnames copy .SD .N
-#' @importFrom stapmr %fin%
 #' 
 #' @export
 #' 
diff --git a/man/grapes-fin-grapes.Rd b/man/grapes-fin-grapes.Rd
new file mode 100644
index 0000000..761642d
--- /dev/null
+++ b/man/grapes-fin-grapes.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/fast_match.R
+\name{\%fin\%}
+\alias{\%fin\%}
+\title{Fast matching}
+\usage{
+x \%fin\% table
+}
+\arguments{
+\item{x}{values to be matched}
+
+\item{table}{values to be matched against}
+}
+\value{
+Logical indicating match or not
+}
+\description{
+A faster version of `%in%`.
+}
+\details{
+See [fastmatch::fmatch()]
+}
+\examples{
+
+\dontrun{
+
+x \%fin\% y
+
+}
+
+
+
+}
+\keyword{internal}