For Review: add more than 2 levels in commercial rank, and select tre…

…es in this ascending order

R/SpeciesCriteria.R

@@ -8,12 +8,14 @@
 #' \describe{
 #'   \item{CommercialName}{Vernacular/economic name (character)}
 #'   \item{Genus}{Genus associated to the vernacular name (character)}
-#'   \item{Species}{Species (without genus part) associated to the vernacular name (character)}
-#'   \item{CommercialLevel}{Economic interest level ("1" principal economic species,
-#'   "2" species logged in a objective of diversification, "0" species
-#'   whose genus is covered by a commercial name, but which are not logged) (factor)}
+#'   \item{Species}{Species (without genus part) associated to the vernacular
+#'   name (character)}
+#'   \item{CommercialLevel}{Economic interest level (1: principal economic species,
+#'   2 or more: species logged in a objective of diversification, 0: species
+#'   whose genus is covered by a commercial name, but which are not logged) (numeric)}
 #'   \item{MinFD}{Minimum Felling Diameter, in centimeter (numeric)}
-#'   \item{UpMinFD}{Enhanced Minimum Felling Diameter (over-rich stand case), in centimeter (numeric)}
+#'   \item{UpMinFD}{Enhanced Minimum Felling Diameter (over-rich stand case), in
+#'   centimeter (numeric)}
 #'   \item{MaxFD}{Maximum Felling Diameter, in centimeter (numeric)}
 #'   \item{Aggregative}{Aggregative character of the species (logical)}
 #'   ...

R/commercialcriteriajoin.R

@@ -84,8 +84,8 @@ commercialcriteriajoin <- function(
     mutate(CommercialName = ifelse(is.na(CommercialName.species), CommercialName.genus, CommercialName.species)) %>%
     dplyr::select(-CommercialName.species, -CommercialName.genus) %>%
 
-    mutate(CommercialLevel.species = as.character(CommercialLevel.species)) %>%
-    mutate(CommercialLevel.genus = as.character(CommercialLevel.genus)) %>%
+    # mutate(CommercialLevel.species = as.character(CommercialLevel.species)) %>% # remove for reviewer
+    # mutate(CommercialLevel.genus = as.character(CommercialLevel.genus)) %>% # remove for reviewer
 
     mutate(CommercialLevel = ifelse(is.na(CommercialLevel.species), CommercialLevel.genus, CommercialLevel.species)) %>%
     mutate(MinFD = ifelse(is.na(MinFD.species), MinFD.genus, MinFD.species)) %>%
@@ -97,19 +97,19 @@ commercialcriteriajoin <- function(
     dplyr::select(-CommercialLevel.species, -CommercialLevel.genus, -MinFD.species, -MinFD.genus,
                   -UpMinFD.species, -UpMinFD.genus, -MaxFD.species, -MaxFD.genus,
                   -Aggregative.species, -Aggregative.genus) %>%
-    mutate(CommercialLevel = as.character(CommercialLevel)) %>%
+    # mutate(CommercialLevel = as.character(CommercialLevel)) %>% # remove for reviewer
 
     # Exceptions management (CommercialLevel == "0" in speciescriteria)
-    mutate(CommercialName = ifelse(CommercialLevel == "0", NA, CommercialName)) %>%
-    mutate(MinFD = ifelse(CommercialLevel == "0", NA, MinFD)) %>%
-    mutate(UpMinFD = ifelse(CommercialLevel == "0", NA, UpMinFD)) %>%
-    mutate(MaxFD = ifelse(CommercialLevel == "0", NA, MaxFD)) %>%
-    mutate(Aggregative = ifelse(CommercialLevel == "0", NA, Aggregative))
+    mutate(CommercialName = ifelse(CommercialLevel == 0, NA, CommercialName)) %>% # in numeric for reviewer
+    mutate(MinFD = ifelse(CommercialLevel == 0, NA, MinFD)) %>%
+    mutate(UpMinFD = ifelse(CommercialLevel == 0, NA, UpMinFD)) %>%
+    mutate(MaxFD = ifelse(CommercialLevel == 0, NA, MaxFD)) %>%
+    mutate(Aggregative = ifelse(CommercialLevel == 0, NA, Aggregative))
 
 
   inventory <- inventory %>%
-    mutate(CommercialLevel = ifelse(is.na(CommercialLevel), "0", CommercialLevel)) %>%
-    mutate(CommercialLevel = factor(as.character(CommercialLevel)))
+    mutate(CommercialLevel = ifelse(is.na(CommercialLevel), 0, CommercialLevel)) # %>%
+    # mutate(CommercialLevel = factor(as.character(CommercialLevel))) # remove for reviewer
 
   if(nrow(inventory) != nrow(inventory0))
     stop("The number of rows between the input inventory and the output inventory

R/futurereserve.R

@@ -111,7 +111,7 @@ futurereserve <- function(
   #Future: select essence and diameters
 
   inventory <- inventory %>%
-    mutate(LoggingStatus = ifelse(CommercialLevel == "1" & Selected != "1" & HarvestableZone == TRUE &
+    mutate(LoggingStatus = ifelse(CommercialLevel == 1 & Selected != "1" & HarvestableZone == TRUE &
                                     ((Up == "0" &
                                         (DBH >= advancedloggingparameters$FutureTreesMinDiameter & DBH < MinFD))
                                      | (Up == "1" &

R/harvestable.R

@@ -162,7 +162,7 @@ harvestable <- function(
 
   # Calculation of spatial information (distance and slope)
   SpatInventory <- inventory %>%
-    dplyr::filter(CommercialLevel!= "0") %>%  # only take commercial sp, the calculation time is long enough
+    dplyr::filter(CommercialLevel!= 0) %>%  # only take commercial sp, the calculation time is long enough
     dplyr::filter(DBH >= MinFD & DBH <= MaxFD) # already selected commercial DBHs
 
   coordinates(SpatInventory) <- ~ Xutm + Yutm # transform the inventory into a spatial object by informing the coordinates
@@ -263,9 +263,9 @@ harvestable <- function(
   # Essences selection
   HarverstableConditions <- # = 1 boolean vector
     if (diversification || (!diversification && specieslax)) {
-      inventory$CommercialLevel =="1"| inventory$CommercialLevel == "2" # now or maybe after we will diversify
+      inventory$CommercialLevel >0 # now or maybe after we will diversify
     } else if (!diversification && !specieslax) {
-      inventory$CommercialLevel == "1" # We will never diversify
+      inventory$CommercialLevel == 1 # We will never diversify
     }
 
 
@@ -286,14 +286,14 @@ harvestable <- function(
   inventory <- inventory %>%
     mutate(LoggingStatus = ifelse(HarverstableConditions, #Under the above criteria, designate the harvestable species
                                   "harvestable", "non-harvestable")) %>%
-    mutate(LoggingStatus = ifelse(CommercialLevel == "0", #The non-commercial species are non-harvestable.
+    mutate(LoggingStatus = ifelse(CommercialLevel == 0, #The non-commercial species are non-harvestable.
                                   "non-harvestable", LoggingStatus)) %>%
 
     mutate(LoggingStatus = ifelse(
       !diversification &
         specieslax & #designate the secondarily harvestable species, because diversification only if necessary
         LoggingStatus == "harvestable" &
-        CommercialLevel == "2",
+        CommercialLevel >1,
       "harvestable2nd", LoggingStatus))
 
 

R/selected.R

@@ -84,16 +84,18 @@
 #' @examples
 #' data(Paracou6_2016)
 #' data(DTMParacou)
+#' data(PlotMask)
 #' data(HarvestableAreaOutputsCable)
 #' data(MainTrails)
+#' data(ForestZoneVolumeParametersTable)
 #'
 #' inventory <- addtreedim(cleaninventory(Paracou6_2016, PlotMask),
 #' volumeparameters = ForestZoneVolumeParametersTable)
 #'
 #' inventory <- commercialcriteriajoin(inventory, SpeciesCriteria)
 #'
 #' harvestableOutputs <- harvestable(inventory, topography = DTMParacou,
-#' diversification = TRUE, specieslax = FALSE,
+#' diversification = F, specieslax = T,
 #' plotslope = HarvestableAreaOutputsCable$PlotSlope,
 #' maintrails = MainTrails,
 #' harvestablepolygons = HarvestableAreaOutputsCable$HarvestablePolygons,
@@ -104,8 +106,8 @@
 #' HVinit <- harvestableOutputs$HVinit
 #'
 #' selecInventory <- selected(inventory, topography = DTMParacou,
-#' scenario = "manual", fuel = "2", diversification = TRUE,
-#' VO = 125, HVinit = HVinit, specieslax = FALSE, objectivelax = TRUE,
+#' scenario = "manual", fuel = "2", diversification = T,
+#' VO = 20, HVinit = HVinit, specieslax = T, objectivelax = T,
 #' advancedloggingparameters = loggingparameters())$inventory
 #'
 selected <- function(
@@ -213,6 +215,7 @@ selected <- function(
       inventory <- inventory %>%
         mutate(Condition = ifelse(LoggingStatus == "harvestable2nd"|LoggingStatus == "harvestable",TRUE, FALSE)) %>%
         group_by(Condition) %>%
+        arrange(CommercialLevel) %>% # add for reviewer
         arrange(desc(TreeHarvestableVolume)) %>%
         mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
         ungroup() %>%
@@ -250,6 +253,7 @@ selected <- function(
       inventory <- inventory %>%
         mutate(Condition = ifelse(LoggingStatus == "harvestable",TRUE, FALSE)) %>%
         group_by(Condition) %>%
+        arrange(CommercialLevel) %>% # add for reviewer
         arrange(desc(TreeHarvestableVolume)) %>%
         mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
         ungroup() %>%
@@ -283,7 +287,7 @@ selected <- function(
 
     inventory <- inventory %>%
       mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" &
-                                      CommercialLevel == "1" & (DBH >= UpMinFD & DBH <= MaxFD), #designate the bigger individuals, when the plot is species-rich.
+                                      CommercialLevel == 1 & (DBH >= UpMinFD & DBH <= MaxFD), #designate the bigger individuals, when the plot is species-rich.
                                     "harvestableUp", LoggingStatus))
 
     if (!diversification) {
@@ -309,6 +313,7 @@ selected <- function(
         inventory <- inventory %>%
           mutate(Condition = ifelse(LoggingStatus == "harvestableUp", TRUE, FALSE)) %>%
           group_by(Condition) %>%
+          arrange(CommercialLevel) %>% # add for reviewer
           arrange(desc(TreeHarvestableVolume)) %>%
           mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
           ungroup() %>%
@@ -331,6 +336,7 @@ selected <- function(
         inventory <- inventory %>%
           mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
           group_by(Condition) %>%
+          arrange(CommercialLevel) %>% # add for reviewer
           arrange(desc(TreeHarvestableVolume)) %>%
           mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
           ungroup() %>%
@@ -353,7 +359,7 @@ selected <- function(
 
       # Increase the MinFD of the other economic species
       inventory <- inventory %>%
-        mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" & CommercialLevel == "2" &
+        mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" & CommercialLevel >1 &
                                         (DBH >= UpMinFD & DBH <= MaxFD), #designate preferred individuals of 2nd economic rank species too, when the plot is species-rich.
                                       "harvestableUp", LoggingStatus))
 
@@ -377,6 +383,7 @@ selected <- function(
         inventory <- inventory %>%
           mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
           group_by(Condition) %>%
+          arrange(CommercialLevel) %>% # add for reviewer
           arrange(desc(TreeHarvestableVolume)) %>%
           mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
           ungroup() %>%
@@ -413,6 +420,7 @@ selected <- function(
     inventory <- inventory %>%
       mutate(Condition = ifelse(LoggingStatus == "harvestable", TRUE, FALSE)) %>%
       group_by(Condition) %>%
+      arrange(CommercialLevel) %>% # add for reviewer
       arrange(desc(TreeHarvestableVolume)) %>%
       mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
       ungroup() %>%
@@ -435,6 +443,7 @@ selected <- function(
                              (TreeHarvestableVolume > min & TreeHarvestableVolume <= MissingVolume),
                            TRUE, FALSE)) %>%
     group_by(Crumbs) %>%
+    arrange(CommercialLevel) %>% # add for reviewer
     arrange(desc(TreeHarvestableVolume))
 
   if(any(inventory$Crumbs)){

tests/testthat/test-commercialcriteriajoin.R

@@ -40,11 +40,11 @@ test_that("commercialcriteriajoin", {
          function(element) expect_type(element, "double"))
 
   expect_type(testinventory$CommercialName, "character")
-  expect_s3_class(testinventory$CommercialLevel, "factor")
+  expect_type(testinventory$CommercialLevel, "double")
 
   # Check that commercial sp have logging info, and non-commercial have not:
   TestCommercial <- testinventory %>%
-    filter(CommercialLevel == "0")
+    filter(CommercialLevel == 0)
 
   TestList <- list( # list the variables to check
     TestCommercial$CommercialName,
@@ -56,7 +56,7 @@ test_that("commercialcriteriajoin", {
          function(element) expect_true(all(is.na(element))))
 
   TestCommercial <- testinventory %>%
-    filter(CommercialLevel != "0")
+    filter(CommercialLevel != 0)
 
   TestList <- list( # list the variables to check
     TestCommercial$CommercialName,
@@ -91,8 +91,8 @@ test_that("commercialcriteriajoin", {
 
 
 # check colonnes présentes et classe:
-# CommercialName(character), CommercialLevel(factor), MinFD(numeric), UpMinFD(numeric), MaxFD(numeric)
-# Quand CommercialLevel diff de "0" : CommercialName, MinFD, UpMinFD, MaxFD dif de NA
+# CommercialName(character), CommercialLevel(numeric), MinFD(numeric), UpMinFD(numeric), MaxFD(numeric)
+# Quand CommercialLevel diff de 0 : CommercialName, MinFD, UpMinFD, MaxFD dif de NA
 # Check species attribution exceptions
 
-# Quand CommercialLevel == "0" : CommercialName, MinFD, UpMinFD, MaxFD == NA
+# Quand CommercialLevel == 0 : CommercialName, MinFD, UpMinFD, MaxFD == NA

tests/testthat/test-futurereserve.R

@@ -29,12 +29,12 @@ test_that("futurereserve", {
 
   advancedloggingparameters = loggingparameters()
 
-  # Future = CommercialLevel == "1"
+  # Future = CommercialLevel == 1
   FutureTrees <- testinventory %>%
     filter(LoggingStatus == "future")
 
 
-  expect_true(all(FutureTrees$CommercialLevel == "1"
+  expect_true(all(FutureTrees$CommercialLevel == 1
                   & (
                     (FutureTrees$Up == "0" &
                        (FutureTrees$DBH >= advancedloggingparameters$FutureTreesMinDiameter & FutureTrees$DBH < FutureTrees$MinFD))
@@ -45,7 +45,7 @@ test_that("futurereserve", {
   ReserveTrees <- testinventory %>%
     filter(LoggingStatus =="reserve")
 
-  expect_true(all(ReserveTrees$CommercialLevel == "1"
+  expect_true(all(ReserveTrees$CommercialLevel == 1
                   & (
                     (ReserveTrees$Up == "0" &
                        (ReserveTrees$DBH >= advancedloggingparameters$FutureTreesMinDiameter & ReserveTrees$DBH < ReserveTrees$MinFD))

tests/testthat/test-harvestable.R

@@ -55,32 +55,32 @@ test_that("harvestable", {
   expect_false(any(is.na(testinventory1$LoggingStatus)))
   expect_false(any(is.na(testinventory2$LoggingStatus)))
 
-  # CommercialLevel == "0" are  LoggingStatus =="non-harvestable"
+  # CommercialLevel == 0 are  LoggingStatus =="non-harvestable"
   TestCommercial <- testinventory1 %>%
-    dplyr::filter(CommercialLevel == "0")
+    dplyr::filter(CommercialLevel == 0)
 
   expect_true(all(TestCommercial$LoggingStatus =="non-harvestable"))
 
   TestCommercial <- testinventory2 %>%
-    dplyr::filter(CommercialLevel == "0")
+    dplyr::filter(CommercialLevel == 0)
 
   expect_true(all(TestCommercial$LoggingStatus =="non-harvestable"))
 
   # "harvestable": DBH >= MinFD & DBH <= MaxFD
 
-  # "harvestable": CommercialLevel == "1" ou "2" if diversification=T, or  diversification=F & specieslax=T
+  # "harvestable": CommercialLevel == 1 ou 2 if diversification=T, or  diversification=F & specieslax=T
   testinventory1a <- testinventory1 %>%
-    dplyr::filter(CommercialLevel == "2")
+    dplyr::filter(CommercialLevel == 2)
   testinventory2a <- testinventory2 %>%
-    dplyr::filter(CommercialLevel == "2")
+    dplyr::filter(CommercialLevel == 2)
 
   expect_true(any(testinventory1a$LoggingStatus =="harvestable"))
   expect_true(any(testinventory2a$LoggingStatus =="harvestable2nd"))
 
 
-  # "harvestable": CommercialLevel == "1"  diversification=F & specieslax=F
+  # "harvestable": CommercialLevel == 1  diversification=F & specieslax=F
   testinventory3a <- testinventory3 %>%
-    dplyr::filter(CommercialLevel != "1")
+    dplyr::filter(CommercialLevel != 1)
   expect_true(all(testinventory3a$LoggingStatus == "non-harvestable"))
 
 

tests/testthat/test-selected.R

@@ -182,7 +182,7 @@ test_that("selected", {
                                              VO = VO, HVinit = HVinit))$inventory
 
   TestUp <- testinventory %>%
-    dplyr::filter(CommercialLevel == "1") %>%
+    dplyr::filter(CommercialLevel == 1) %>%
     dplyr::filter(DBH >= UpMinFD & DBH <= MaxFD) %>%
     dplyr::filter(LoggingStatus != "non-harvestable") %>%
     dplyr::filter(ProbedHollow == "0")
@@ -192,13 +192,13 @@ test_that("selected", {
     dplyr::filter(LoggingStatus == "harvestableUp")
 
   if(nrow(TestUp)>0){
-    expect_true(all(TestUp$LoggingStatus == "harvestableUp")) # There are harvestableUp among the CommercialLevel = "1"
+    expect_true(all(TestUp$LoggingStatus == "harvestableUp")) # There are harvestableUp among the CommercialLevel = 1
     expect_true(all(TestDBHUp$DBH >= TestDBHUp$UpMinFD)) # DBH >= UpMinFD
     expect_true(all(TestDBHUp$Up =="1")) #  Up = "1"
   }
 
   ## if (!diversification)
-  expect_false(any(TestDBHUp$CommercialLevel == "2")) # no CommercialLevel = "2" among the harvestableUp
+  expect_false(any(TestDBHUp$CommercialLevel == 2)) # no CommercialLevel = 2 among the harvestableUp
   ### if (HVupCommercial1 == VO)
   ### if (HVupCommercial1 > VO)
   ### if (HVupCommercial1 < VO)