Move data.table to Imports

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/test-coverage.yaml

@@ -44,7 +44,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: coverage-test-failures
+          name: coverage-test-failures-${{ runner.temp }}
           path: ${{ runner.temp }}/package

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

@@ -23,9 +23,8 @@ Imports:
     lubridate,
     R6,
     ggplot2,
-    ggraph
-Depends: 
-  data.table
+    ggraph,
+    data.table
 RoxygenNote: 7.3.2
 Suggests:
     knitr,

NAMESPACE

@@ -18,4 +18,13 @@ import(ggplot2)
 import(ggraph)
 import(igraph)
 importFrom(R6,R6Class)
+importFrom(data.table,":=")
+importFrom(data.table,.BY)
+importFrom(data.table,.EACHI)
+importFrom(data.table,.GRP)
+importFrom(data.table,.I)
+importFrom(data.table,.N)
+importFrom(data.table,.NGRP)
+importFrom(data.table,.SD)
+importFrom(data.table,data.table)
 importFrom(stats,rnorm)

R/DataManagement.R

@@ -40,7 +40,8 @@
 #' @examples
 #' ## create a "fake and custom" data base
 #' mydb = create_fake_subjectDB(n_subjects = 100, n_facilities = 100)
-#' setnames(mydb, 1:4, c("myPatientId", "myHealthCareCenterID", "DateOfAdmission", "DateOfDischarge"))
+#' data.table::setnames(mydb, 1:4, 
+#'      c("myPatientId", "myHealthCareCenterID", "DateOfAdmission", "DateOfDischarge"))
 #' mydb[,DateOfAdmission:= as.character(DateOfAdmission)]
 #' mydb[,DateOfDischarge:= as.character(DateOfDischarge)]
 #' 
@@ -122,7 +123,7 @@ checkBase <- function(base,
       stop("Column(s) ", paste(notfound, collapse = ", "), " provided as argument were not found in the database.")
     }
     # Set column names to default
-    setnames(report$base,
+    data.table::setnames(report$base,
              old = c(subjectID, facilityID, admDate, disDate),
              new = c("sID", "fID", "Adate", "Ddate"))
 
@@ -455,15 +456,15 @@ adjust_overlapping_stays = function(report,
                    probBase[Nprob,..extraCols])
       b=b[(b[, Adate] < b[, Ddate]),]
       probBase=rbind(a,b,c,d)
-      setnames(probBase,c("sID","fID","Adate","Ddate",extraCols)) #might not be needed here
+      data.table::setnames(probBase,c("sID","fID","Adate","Ddate",extraCols)) #might not be needed here
     }else{
       a=data.table(sID=probBase[-Nprob][(C1&C2), sID],fID=probBase[-Nprob][(C1&C2), fID],Adate=probBase[-Nprob][(C1&C2), Adate],Ddate=probBase[-1][(C1&C2), Adate])
       b=data.table(sID=probBase[-Nprob][(C1&C2), sID],fID=probBase[-Nprob][(C1&C2), fID],Adate=probBase[-1][(C1&C2), Ddate],Ddate=probBase[-Nprob][(C1&C2), Ddate])
       c=data.table(sID=probBase[-Nprob][!(C1&C2), sID],fID=probBase[-Nprob][!(C1&C2), fID],Adate=probBase[-Nprob][!(C1&C2), Adate],Ddate=probBase[-Nprob][!(C1&C2), Ddate])
       d=data.table(sID=probBase[Nprob, sID],fID=probBase[Nprob, fID],Adate=probBase[Nprob, Adate],Ddate=probBase[Nprob, Ddate])
       b=b[(b[, Adate] < b[, Ddate]),]
       probBase=rbind(a,b,c,d)
-      setnames(probBase,c("sID","fID","Adate","Ddate")) #might not be needed here
+      data.table::setnames(probBase,c("sID","fID","Adate","Ddate")) #might not be needed here
     }
     if (verbose) message("Combining and sorting")
 

R/DataSummary.R

@@ -98,15 +98,15 @@ per_facility_summary <- function(base,
   losPerHosp <- (base[, .(mean(difftime(Ddate, Adate, units = "days"))), by = fID])
   # losPerHosp<-as.numeric(losPerHosp,units="days")
 
-  setnames(losPerHosp, c("node", "LOS"))
+  data.table::setnames(losPerHosp, c("node", "LOS"))
   data.table::setkey(losPerHosp, node)
 
   subjectsPerHosp <- base[, uniqueN(.SD), .SDcols = "sID", by = fID]
-  setnames(subjectsPerHosp, c("node", "subjects"))
+  data.table::setnames(subjectsPerHosp, c("node", "subjects"))
   data.table::setkey(subjectsPerHosp, node)
 
   admissionsPerHosp <- (base[, .N, by = fID])
-  setnames(admissionsPerHosp, c("node", "admissions"))
+  data.table::setnames(admissionsPerHosp, c("node", "admissions"))
   data.table::setkey(admissionsPerHosp, node)
 
   sumStats <- Reduce(

R/HospiNet.R

@@ -603,7 +603,7 @@ HospiNet <- R6::R6Class("HospiNet",
         private$.hist_degrees <- merge(private$.hist_degrees, d_t, by.x = "degree", by.y = "degree_total", all.x = TRUE)
         private$.hist_degrees <- merge(private$.hist_degrees, d_i, by.x = "degree", by.y = "degree_in", all.x = TRUE)
         private$.hist_degrees <- merge(private$.hist_degrees, d_o, by.x = "degree", by.y = "degree_out", all.x = TRUE)
-        setnames(private$.hist_degrees, 2:4, c("total_degree", "in_degree", "out_degree"))
+        data.table::setnames(private$.hist_degrees, 2:4, c("total_degree", "in_degree", "out_degree"))
         private$.hist_degrees
       } else {
         stop("`$hist_degrees` is read only", call. = FALSE)

R/HospitalNetwork-package.R

@@ -0,0 +1,15 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom data.table :=
+#' @importFrom data.table .BY
+#' @importFrom data.table .EACHI
+#' @importFrom data.table .GRP
+#' @importFrom data.table .I
+#' @importFrom data.table .N
+#' @importFrom data.table .NGRP
+#' @importFrom data.table .SD
+#' @importFrom data.table data.table
+## usethis namespace: end
+NULL

R/NetworkBuilding.R

@@ -66,9 +66,9 @@ matrix_from_edgelist <- function(edgelist,
         edgelist <- edgelist[, .N, by = c(origin_name, target_name)] # group identical couples
     }
     if (!format_long) {
-        setnames(edgelist, old = count, new = "N")
+        data.table::setnames(edgelist, old = count, new = "N")
     }
-    setnames(edgelist,
+    data.table::setnames(edgelist,
         old = c(origin_name, target_name),
         new = c("origin", "target")
     )

inst/app/mod_database.R

@@ -69,7 +69,7 @@ mod_database_server <- function(input, output, session, base)
     byfacil = reactive({
         tmp = HospitalNetwork::per_facility_summary(base()) 
         tmp[, LOS := as.difftime(tim = round(LOS, digits = 2), units = "days")]
-        setnames(tmp,
+        data.table::setnames(tmp,
                  old = c("node", "LOS", "admissions", "subjects"),
                  new = c("Facility ID", "Mean LOS", "Total number of admissions", "Distinct subjects admitted")
                  )

tests/testthat/test-adjust_overlaps.R

@@ -205,9 +205,9 @@ baseCorrDis[, `:=`(adm = as.Date(adm),
                 dis = as.Date(dis))]
 setkey(baseCorrDis, sID, adm)
 
-setnames(baseCorrDis, c("adm", "dis"), c("Adate", "Ddate"))
-setnames(baseOver, c("adm", "dis"), c("Adate", "Ddate"))
-setnames(baseCorrAdm, c("adm", "dis"), c("Adate", "Ddate"))
+data.table::setnames(baseCorrDis, c("adm", "dis"), c("Adate", "Ddate"))
+data.table::setnames(baseOver, c("adm", "dis"), c("Adate", "Ddate"))
+data.table::setnames(baseCorrAdm, c("adm", "dis"), c("Adate", "Ddate"))
 
 #=== TESTS ==========================================================
 report = list()