Replaced setDT(copy()) by data.table()

R/getTaxonomy.R

@@ -32,7 +32,7 @@ getTaxonomy <- function(genus, findOrder = FALSE) {
   ################## 1. Retrieve the Family
 
   # Load taxonomical data (sourced from Angiosperm Phylogeny Website, http://www.mobot.org/MOBOT/research/APweb/)
-  genusFamily <- setDT(copy(BIOMASS::genusFamily))
+  genusFamily <- data.table(BIOMASS::genusFamily)
   setkey(genusFamily, genus)
 
   # Create ids
@@ -48,7 +48,7 @@ getTaxonomy <- function(genus, findOrder = FALSE) {
   ################## 2. Retrieve the Order
 
   if (findOrder == TRUE) {
-    apgFamilies <- setDT(copy(BIOMASS::apgFamilies))
+    apgFamilies <- data.table(BIOMASS::apgFamilies)
 
     genusFam <- merge(genusFam, apgFamilies, by.x = "family", by.y = "famAPG", all.x = TRUE)
     genusFam <- genusFam[, .(id, inputGenus, family, order)]

R/getWoodDensity.R

@@ -111,7 +111,7 @@ if (getRversion() >= "2.15.1") {
 #' }
 #' @seealso [wdData], [sd_10]
 #' @keywords Wood density
-#' @importFrom data.table data.table := setDF setDT setkey copy chmatch %chin%
+#' @importFrom data.table data.table := setDF setDT setkey chmatch %chin%
 #'
 getWoodDensity <- function(genus, species, stand = NULL, family = NULL, region = "World",
                            addWoodDensityData = NULL, verbose = TRUE) {
@@ -148,11 +148,11 @@ getWoodDensity <- function(genus, species, stand = NULL, family = NULL, region =
   # Data processing ---------------------------------------------------------
 
   # Load global wood density database downloaded from http://datadryad.org/handle/10255/dryad.235
-  wdData <- setDT(copy(BIOMASS::wdData))
+  wdData <- data.table(BIOMASS::wdData)
 
   # Load the mean standard deviation observed at the species, Genus or Family level
   # in the Dryad dataset when at least 10 individuals are considered
-  sd_10 <- setDT(copy(BIOMASS::sd_10))
+  sd_10 <- data.table(BIOMASS::sd_10)
   sd_tot <- sd(wdData$wd)
 
   Region <- tolower(region)
@@ -175,7 +175,7 @@ getWoodDensity <- function(genus, species, stand = NULL, family = NULL, region =
   if (!is.null(addWoodDensityData)) {
     setDT(addWoodDensityData)
     if (!("family" %in% names(addWoodDensityData))) {
-      genusFamily <- setDT(copy(BIOMASS::genusFamily))
+      genusFamily <- data.table(BIOMASS::genusFamily)
       addWoodDensityData[genusFamily, on = "genus", family := i.family]
     }
     addWoodDensityData <- addWoodDensityData[!is.na(wd), ]
@@ -195,7 +195,7 @@ getWoodDensity <- function(genus, species, stand = NULL, family = NULL, region =
     inputData[, family := as.character(family)]
   } else {
     if (!exists("genusFamily", inherits = FALSE)) {
-      genusFamily <- setDT(copy(BIOMASS::genusFamily))
+      genusFamily <- data.table(BIOMASS::genusFamily)
     }
     inputData[genusFamily, on = "genus", family := i.family]
   }

data-raw/apgfamily.R

@@ -22,7 +22,7 @@ setDF(apgFamilies)
 usethis::use_data(apgFamilies, compress = "xz", overwrite = FALSE)
 
 
-apgFamiliesOrg <- setDT(copy(BIOMASS::apgFamilies))
+apgFamiliesOrg <- data.table(BIOMASS::apgFamilies)
 apgFamiliesOrg <- apgFamiliesOrg[base::order(order)]
 apgFamilies <- apgFamilies[base::order(order)]
 

data-raw/genusFamily.R

@@ -261,7 +261,7 @@ usethis::use_data(genusFamily, compress = "xz")
 
 
 genusFamily <- genusFamily[base::order(family)]
-genusFamilyOrg <- setDT(copy(BIOMASS::genusFamily))
+genusFamilyOrg <- data.table(BIOMASS::genusFamily)
 genusFamilyOrg <- genusFamilyOrg[base::order(family)]
 
 result <- merge(genusFamilyOrg, genusFamily, all = T, by = "genus")

data-raw/sd_10.R

@@ -7,7 +7,7 @@ require(data.table)
 # )
 # data_wd[, c("genus", "species") := tstrsplit(Binomial, " ", keep = 1:2)]
 
-data_wd <- setDT(copy(BIOMASS::wdData))
+data_wd <- data.table(BIOMASS::wdData)
 
 
 species <- data_wd[, .(family, genus, wd, .N), by = species][N >= 10][, .(sd = sd(wd)), by = species][, mean(sd)]