For Review

DESCRIPTION

@@ -43,27 +43,27 @@ Depends:
     R (>= 4.1)
 Config/testthat/edition: 3
 Imports: 
-    magrittr (>= 2.0.1),
-    dplyr (>= 1.0.7),
-    tibble (>= 3.1.0),
-    tidyr (>= 1.1.2),
-    BIOMASS (>= 2.1.7),
-    rlang (>= 0.4.10),
-    raster (>= 3.5.29),
-    sp (>= 1.4.6),
-    sf (>= 1.0.5),
-    nngeo (>= 0.4.5),
-    fasterize (>= 1.0.3), 
-    terra (>= 1.4-22),
-    methods (>= 3.6.1),
-    utils (>= 3.6.1),
-    matlib (>= 0.9.4),
-    gdistance(>= 1.3-6),
-    smoothr (>= 0.2.2),
-    lwgeom (>= 0.2-8),
-    units (>= 0.7.2),
-    stats (>= 3.6.1),
-    parallel (>= 3.6),
+    magrittr (>= 2.0.3),
+    dplyr (>= 1.1.2),
+    tibble (>= 3.2.1),
+    tidyr (>= 1.3.0),
+    BIOMASS (>= 2.1.8),
+    rlang (>= 1.1.1),
+    raster (>= 3.6.20),
+    sp (>= 1.6.0),
+    sf (>= 1.0.12),
+    nngeo (>= 0.4.7),
+    fasterize (>= 1.0.4), 
+    terra (>= 1.7-29),
+    methods (>= 4.3.0),
+    utils (>= 4.3.0),
+    matlib (>= 0.9.6),
+    gdistance(>= 1.6.4),
+    smoothr (>= 1.0.1),
+    lwgeom (>= 0.2-11),
+    units (>= 0.8-2),
+    stats (>= 4.3.0),
+    parallel (>= 4.3.0),
     doSNOW (>= 1.0.20),
     foreach (>= 1.5.2),
     tryCatchLog (>= 1.3.1)

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/addtreedim.R

@@ -1,6 +1,10 @@
 #'Compute tree dimensions (tree, trunk and crown height, crown diameter,
 #'harvestable volume, wood density, and AGB)
 #'
+#'@description Compute tree dimensions (tree, trunk and crown height, crown
+#'  diameter, harvestable volume, wood density, and AGB) from its Diameter at
+#'  Breast Height (DBH)
+#'
 #'@param inventory Input inventory (see the inputs formats and metadata in the
 #'  vignette) (data.frame)
 #'
@@ -26,10 +30,10 @@
 #'@details 'addtreedim' compute some tree dimensions with the
 #'  'advancedloggingparameters' argument:
 #'  - Tree height (in m) ('TreeHeightAllometry')
-#'  - Tree harvestable volume (m3) ('TreeHarvestableVolumeAllometry')
+#'  - Tree harvestable volume (m3) ('TreeHarvestableVolumeAllometry')(French Guiana ONF)
 #'  - Trunk height (in m) ('TrunkHeightAllometry')
 #'  - Crown height (in m)
-#'  - Crown diameter (in m) ('CrownDiameterAllometry')
+#'  - Crown diameter (in m) ('CrownDiameterAllometry') (Aubry-Kientz et al.2019)
 #'  - Wood density (g/cm3) (by the BIOMASS package)
 #'  - Tree above-ground biomass (AGB) (in ton) (by the BIOMASS package)
 #'

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/loggingparameters.R

@@ -70,7 +70,7 @@
 #'@param CrownPartForFuel Proportion of the tree crown biomass used as fuel wood.
 #'  Default = 2/3 (double) (Branches diameter >= 5 cm) (Eleotério et al. 2019)
 #'
-#'@param Purge Part of the harvested log no used for timber, can be used for fuel
+#'@param Purge Part of the harvested log not used for timber, can be used for fuel
 #'  wood. Default = 0.14, in m3 of purge/m3 of volume of timber harvested.
 #'  (double)
 #'
@@ -94,8 +94,8 @@
 #'    - "SecondTrails" (default = 0.1)
 #'
 #'@param TreeHarvestableVolumeAllometry By default, allometry of tree
-#'  harvestable volume, French Guiana ONF formula: aCoef + bCoef * (DBH/100)^2,
-#'  aCoef and bCoef depend on the forest location, stored in
+#'  harvestable volume, French Guiana ONF formula: aCoef + bCoef * (DBH/100)^2.
+#'  With aCoef and bCoef depending on the forest location, stored in
 #'  \code{\link{ForestZoneVolumeParametersTable}}, DBH in cm. (function)
 #'
 #'@param TrunkHeightAllometry Allometry of trunk height, based on the cylinder

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 = FALSE, specieslax = TRUE,
 #' plotslope = HarvestableAreaOutputsCable$PlotSlope,
 #' maintrails = MainTrails,
 #' harvestablepolygons = HarvestableAreaOutputsCable$HarvestablePolygons,
@@ -105,7 +107,7 @@
 #'
 #' selecInventory <- selected(inventory, topography = DTMParacou,
 #' scenario = "manual", fuel = "2", diversification = TRUE,
-#' VO = 125, HVinit = HVinit, specieslax = FALSE, objectivelax = TRUE,
+#' VO = 20, HVinit = HVinit, specieslax = TRUE, objectivelax = TRUE,
 #' 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