R/selected.R
In VincyaneBadouard/LoggingLab: An R Package to Simulate Forest Logging
Defines functions
selected
Documented in
selected
#'Selection of trees to log
#'
#'@description Selection of trees to log among the exploitable trees, according
#' to the objective volume and the exploitable volume on the plot.
#'
#'@param inventory Input inventory (see the inputs formats and metadata in the
#' vignette) (data.frame)
#'
#'@param topography Digital terrain model (DTM) of the inventoried plot (LiDAR
#' or SRTM) (\code{\link{DTMParacou}}) (RasterLayer **with a crs in UTM**)
#' We advise you to generate your raster with Qgis rather than with the
#' 'raster' package on R.
#'
#'@param scenario Logging scenario: "RIL1", "RIL2broken", "RIL2", "RIL3",
#' "RIL3fuel", "RIL3fuelhollow" or "manual"(character) (see the
#' vignette)
#'
#'@param fuel Fuel wood exploitation: no exploitation = "0", exploitation of
#' damage and unused part of logged trees for fuel = "1", exploitation of
#' hollow trees, damage and and unused part of the log for fuel = "2"
#'
#'@param diversification Possibility to log other species in addition to the
#' main commercial species (species with a value of 2 for commercial in the
#' \code{\link{SpeciesCriteria}} table) (logical)
#'
#'@param specieslax Allow diversification if the stand is too poor to reach the
#' objective volume without diversification, = FALSE by default (logical)
#'
#'@param VO Objective volume for the entire area of the plot (m3) (numeric
#' value)
#'
#'@param HVinit Harvestable volume(m3) in the plot for the chosen scenario
#' (\code{\link{SpeciesCriteria}}) (numeric value)
#'
#'@param objectivelax Allow exploitation in case of non-achievement of the
#' objective volume (if stand too poor), = FALSE by default (logical)
#'
#'@param advancedloggingparameters Other parameters of the logging simulator
#' \code{\link{loggingparameters}} (list)
#'
#'@return Input inventory with:
#' - The trees selected for harvesting (*Selected*)
#' - if the Minimum Felling Diameter (*MinFD*) of their species has been raised
#' (*Up*)
#' - The probability of a tree being probed hollow (*ProbedHollowProba*) and
#' the probed hollow trees (*ProbedHollow*).
#'See the outputs metadata in the vignette.
#'
#'2 sets of spatial points: (*HollowTrees* and *EnergywoodTrees*)
#'
#'@details This function allows the selection of trees to be exploited among the
#' exploitable trees. It also informs about the trees that were finally found
#' to be hollow during the probe. If fuel = 2, the hollow trees will be
#' harvested and are therefore included in the objective volume. If fuel = 0 or
#' 1, the hollow trees will not be exploited, so the function looks for other
#' trees to reach the objective volume (if possible).
#'
#' If the harvestable volume is higher than the objective volume, and that
#' diversification was not chosen, *MinFD* of the 1st economic rank species
#' only is increased.
#' If the diversification is allowed, *MinFD* of 1st and 2nd economic level
#' species is increased.
#' Then, the trees to be harvested are chosen in
#' decreasing order of volume, until the objective volume is reached.
#'
#' If the harvestable volume is lower than the objective volume,
#' diversification can be applied if it was not already applied ('specieslax')
#' (trees of all commercial ranks are selected in decreasing order of volume
#' until the objective volume is reached), or harvesting can continue despite
#' an unreached objective volume, or be abandoned ('objectivelax')
#'
#'@seealso \code{\link{Paracou6_2016}}, \code{\link{SpeciesCriteria}},
#' \code{\link{DTMParacou}}, \code{\link{loggingparameters}}
#'
#'@export
#'
#'@importFrom dplyr arrange desc ungroup rowwise mutate group_by select filter
#'@importFrom tibble add_column
#'@importFrom sp coordinates proj4string
#'@importFrom sf st_as_sf
#'@importFrom raster crs
#'
#'
#' @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 = FALSE, specieslax = TRUE,
#' plotslope = HarvestableAreaOutputsCable$PlotSlope,
#' maintrails = MainTrails,
#' harvestablepolygons = HarvestableAreaOutputsCable$HarvestablePolygons,
#' scenario = "manual", winching = "2",
#' advancedloggingparameters = loggingparameters())
#'
#' inventory <- harvestableOutputs$inventory
#' HVinit <- harvestableOutputs$HVinit
#'
#' selecInventory <- selected(inventory, topography = DTMParacou,
#' scenario = "manual", fuel = "2", diversification = TRUE,
#' VO = 20, HVinit = HVinit, specieslax = TRUE, objectivelax = TRUE,
#' advancedloggingparameters = loggingparameters())$inventory
#'
selected <- function(
inventory,
topography,
scenario,
fuel = NULL,
diversification = NULL,
VO, # objective volume for the entire surface of the plot
HVinit, # initial Harvestable Volume
specieslax = FALSE,
objectivelax = FALSE,
advancedloggingparameters = loggingparameters()
){
# Arguments check
if(!inherits(inventory, "data.frame"))
stop("Argument 'inventory' of the 'selected' function must be a data.frame")
if(!all(unlist(lapply(list(diversification, specieslax, objectivelax), inherits, "logical")))
&& !is.null(diversification))
stop("Arguments 'diversification', 'specieslax' and 'objectivelax'
of the 'selected' function must be logical")
# if (!any(scenario == "RIL1" | scenario == "RIL2broken"| scenario == "RIL2"| scenario == "RIL3"| scenario == "RIL3fuel"|
# scenario == "RIL3fuelhollow"| scenario == "manual"))
# stop("The 'scenario' argument of the 'selected' function must be 'RIL1', 'RIL2broken', 'RIL2', 'RIL3', 'RIL3fuel', 'RIL3fuelhollow' or 'manual'")
# if (!any(fuel == "0" | fuel == "1"| fuel == "2" | is.null(fuel)))
# stop("The 'fuel' argument of the 'selected' function must be '0', '1', or '2'")
if(!inherits(advancedloggingparameters, "list"))
stop("Argument 'advancedloggingparameters' of the 'selected' function must be a list")
if(scenario == "manual" &&
(is.null(fuel) || is.null(diversification)))
stop("If you choose the 'manual' mode,
you must fill in the arguments 'fuel' and 'diversification'")
if(!all(unlist(lapply(list(VO, HVinit), inherits, "numeric"))))
stop("Arguments 'VO' and 'HVinit' of the 'selected' function must be numeric")
# initial inventory
inventory0 <- inventory
# Redefinition of the parameters according to the chosen scenario
scenariosparameters <- scenariosparameters(scenario = scenario,
fuel = fuel, diversification = diversification)
fuel <- scenariosparameters$fuel
diversification <- scenariosparameters$diversification
# Global variables
Accessible <- CircCorr <- CodeAlive <- CommercialLevel <- NULL
Condition <- DBH <- NULL
DeathCause <- DistCriteria <- Family <- CommercialName <- Crumbs <- NULL
ForestZoneVolumeParametersTable <- Genus <- Logged <- NULL
TimberLoggedVolume <- LoggingStatus <- MaxFD <- MaxFD.genus <- NULL
MaxFD.species <- MinFD <- MinFD.genus <- MinFD.species <- NULL
NoHollowTimberLoggedVolume <- ParamCrownDiameterAllometry <- PlotSlope <- NULL
ProbedHollow <- ProbedHollowProba <- ScientificName <- NULL
Selected <- Slope <- SlopeCriteria <- Species <- Species.genus <- NULL
SpeciesCriteria <- Taxo <- Taxo.family <- Taxo.genus <- Taxo.species <- NULL
TreeFellingOrientationSuccess <- TreeHarvestableVolume <- NULL
TreeHeight <- TrunkHeight <- Up <- UpMinFD <- UpMinFD.genus <- NULL
UpMinFD.species <- NULL
VolumeCumSum <- Xutm <- Yutm <- aCoef <- NULL
alpha <- alpha.family <- alpha.genus <- alpha.species <- bCoef <- NULL
beta.family <- beta.genus <- beta.species <- geometry <- idTree <- NULL
# Apply S. Schmitt's "Rotten" predictive model to identify probed hollow trees.
inventory <- inventory %>%
# Estimates the probability of being probed hollow
mutate(ProbedHollowProba = ifelse(LoggingStatus == "harvestable" | LoggingStatus == "harvestable2nd",
advancedloggingparameters$RottenModel(DBH), NA)) %>%
# generate either "1" or "0" randomly for each line, depending on the proba associated with the line:
rowwise() %>%
mutate(ProbedHollow = ifelse(!is.na(ProbedHollowProba),
sample(c(1,0), size = 1, replace = F, # 1 = hollow tree, 0 = not hollow
prob = c(ProbedHollowProba, 1-ProbedHollowProba)), NA)) %>%
mutate(ProbedHollow = factor(as.numeric(ProbedHollow)))
if(fuel != "2"){
HollowTable <- filter(inventory, ProbedHollow == "1"| is.na(ProbedHollow))
inventory <- filter(inventory, ProbedHollow == "0") # we continue with just healthy trees in fuel != "2" case
}
# if objective achieved at the first attempt
inventory <- inventory %>%
mutate(Selected = ifelse(HVinit == VO & LoggingStatus == "harvestable",
"1", NA))# if we have our volume, harvestable sp = selected sp
# Create a column to indicate Which sp is FD uped. "0" = no uped, "1"= uped
inventory <- add_column(inventory, Up = "0")
if (HVinit < VO){ #diversification is necessary, designate the secondary-economic-rank species too
if (!diversification && specieslax){
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() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVlax <- sum(HarvestableTable$TreeHarvestableVolume) # Harvestable volume, with specieslax permission
if (HVlax < VO && objectivelax)
message("The exploitable volume (= ",paste(round(HVlax, digits = 1)),"m^3) is still lower
(by ",paste(round(VO- HVlax, digits = 1)),"m^3) than your objective volume
despite the diversification
(without the diversification HVinit= ",paste(round(HVinit, digits = 1)),"m^3).
You have chosen to continue harvesting with a volume lower than your objective in this case.")
if (HVlax < VO && !objectivelax)
stop("The harvestable volume = ",paste(round(HVlax, digits = 1)),"m^3)
is still lower (by ",paste(round(VO- HVlax, digits = 1)),"m^3)
than your objective volume despite the diversification
(without the diversification HVinit= ",paste(round(HVinit, digits = 1)),"m^3).
By default or because of your choice, the simulation stops.
If you wish to continue the exploitation with of an exploitable volume lower
than your objective volume, you can use the argument 'objectivelax'.")
if (!HVlax == VO)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to diversify your species selection in this case.
The exploitation was therefore carried out on this diversified selection of species.")
} else {
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() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
}
if (!diversification && !specieslax && objectivelax)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to continue logging without diversifying in this case.")
if (diversification && objectivelax)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to continue logging in this case.")
if ((!specieslax & !objectivelax) | (diversification && !objectivelax))
stop("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) is lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
By default or because of your choice, the simulation stops.
If you wish to continue the exploitation with of a harvestable volume lower
than your objective volume, you can use the argument 'objectivelax'
or the diversification of species (if not already done).")
}
if (HVinit > VO) {
inventory <- inventory %>%
mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" &
CommercialLevel == 1 & (DBH >= UpMinFD & DBH <= MaxFD), #designate the bigger individuals, when the plot is species-rich.
"harvestableUp", LoggingStatus))
if (!diversification) {
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp")
HVupCommercial1 <- sum(HarvestableTable$TreeHarvestableVolume) #Compute the harvestable volume with upgraded FD individuals
if (HVupCommercial1 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(HVupCommercial1 == VO & LoggingStatus == "harvestableUp", "1", NA))# if harvestableUp individuals are sufficient to have our volume, harvestableUp ind = selected ind
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was higher
(by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameter (MinFD) of 1st economic rank species were increased.
The objective volume has now been reached.")
}
if (HVupCommercial1 > VO){
# only individuals with DBH > FD are taken, but not all because their volumes > VO
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() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with "1" rank species and upgraded FD individuals only
message("The harvestable volume (= ",paste(round(HVupCommercial1, digits = 1)),"m^3) was higher
(by ",paste(round(HVupCommercial1-VO, digits = 1)),"m^3) than your objective volume
despite the increase in Minimum Falling Diameter (MinFD)
(Initial harvestable volume = ",paste(round(HVinit, digits = 1)),"m^3).
Trees were selected by decreasing order of volume
until the objective volume was reached.")
}
if (HVupCommercial1 < VO){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
group_by(Condition) %>%
arrange(CommercialLevel) %>% # add for reviewer
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with "1" rank species and upgraded FD individuals
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameters (MinFD) of the 1st economic rank species were increased to UpMinFD.
Some trees with DBH lower than the UpMinFD were however selected
to ensure that the objective volume was reached.")
}
}
if (diversification) {
# Increase the MinFD of the other economic species
inventory <- inventory %>%
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))
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp") #the upgraded 1st & 2nd ranks
HVupCommercial12 <- sum(HarvestableTable$TreeHarvestableVolume)
if (HVupCommercial12 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(LoggingStatus == "harvestableUp",
"1", NA))# if we have our volume, harvestable ind = selected ind
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was higher
(by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameter (MinFD) of the 1st and 2nd economic ranks species were increased to UpMinFD.
The objective volume has now been reached.")
} else if (HVupCommercial12 != VO){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
group_by(Condition) %>%
arrange(CommercialLevel) %>% # add for reviewer
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial12adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with upgraded FD individuals
if (HVupCommercial12 < VO){
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameters (MinFD) of the 1st and 2nd economic ranks species were increased to UpMinFD.
Some trees with DBH lower than the UpMinFD were however selected to ensure that the objective
volume was reached.")
}
if (HVupCommercial12 > VO){
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3)
than the objective volume, the Minimum Falling Diameter (MinFD) of the 1st and 2nd economic ranks species
were increased to UpMinFD. The objective volume has now been reached.")
}
} # end : HVupCommercial12 != VO
}
}
# if at this step there are no selected trees
if(!any(inventory$Selected == "1") & any(inventory$ProbedHollow == "0")){
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() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
}
# No NA in Selected colomn
inventory <- mutate(inventory, Selected = ifelse(is.na(Selected) , "0", Selected))
# Complete to reach the objective volume 'with crumbs'
HarvestableTable <- inventory %>%
filter(Selected == "1")
MissingVolume <- VO - sum(HarvestableTable$TreeHarvestableVolume)
min <- MissingVolume - 1
inventory <- inventory %>%
mutate(Crumbs = ifelse((LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable") & Selected != "1" &
(TreeHarvestableVolume > min & TreeHarvestableVolume <= MissingVolume),
TRUE, FALSE)) %>%
group_by(Crumbs) %>%
arrange(CommercialLevel) %>% # add for reviewer
arrange(desc(TreeHarvestableVolume))
if(any(inventory$Crumbs)){
Crumbsdf <- inventory %>%
filter(Crumbs %in% TRUE)
MaxCrumbsV <- max(Crumbsdf$TreeHarvestableVolume) # the most important remaining volume able to reach the objective
inventory <- inventory %>%
mutate(Selected = ifelse(Crumbs %in% TRUE & TreeHarvestableVolume == MaxCrumbsV, "1", Selected))
}
inventory <- inventory %>%
ungroup() %>%
select(-Crumbs)
# Add the probed hollow trees removed until now in fuel != 2 case
if(fuel != "2"){
inventory <- bind_rows(inventory, HollowTable)
}
# No NA in Selected colomn
inventory <- mutate(inventory, Selected = ifelse(is.na(Selected) , "0", Selected))
# Upgraded MinFD species:
# to inform for each individual if its species have been FD upgraded
inventory <- inventory %>%
group_by(CommercialName) %>%
mutate(Up = ifelse(any(LoggingStatus == "harvestableUp"), "1", Up)) %>%
ungroup()
if (!any(inventory$Selected == "1")) { # no selected trees
# if there are "deselected" trees and not of 'selected = 1'
if (any(inventory$ProbedHollow == "1")){ # probed hollow trees and no selected trees
stop("No trees were selected because they were all probed hollow
(",paste(round(sum(as.numeric(inventory$ProbedHollow == "1"), na.rm = TRUE), digits = 1)),
" probed hollow trees). Your objective volume may be too low (the few trees selected were found to be
hollow).")
}else if (all(inventory$LoggingStatus == "non-harvestable")) {
stop("No trees selected, you have no harvestable trees (according to your criteria (SpeciesCriteria))
in your inventory.")
}
}
# Create a POINTS VECTOR with coordinates of the probed hollow trees:
if (any(inventory$ProbedHollow == "1", na.rm = TRUE)) {
HollowTreesPoints <- inventory %>%
filter(ProbedHollow == "1")
sp::coordinates(HollowTreesPoints) <- ~ Xutm + Yutm
sp::proj4string(HollowTreesPoints) <- raster::crs(topography)
HollowTreesPoints <- st_as_sf(as(HollowTreesPoints,"SpatialPoints"))
# OUTPUTS list
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = st_point(x = c(NA_real_, NA_real_))) # empty point
} else {
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = st_point(x = c(NA_real_, NA_real_)), # empty point
EnergywoodTreesPoints = st_point(x = c(NA_real_, NA_real_)))
}
if ((fuel == "2") & any(inventory$ProbedHollow == "1", na.rm = TRUE)) {
# Hollow trees = fuel wood:
inventory <- inventory %>%
mutate(DeathCause = ifelse(Selected == "1" & ProbedHollow == "1", "hollowfuel", NA))# replace "NA" par "DeathCause" in this code line in the ONF simulator
# Create a POINTS VECTOR with coordinates of the energywood trees:
EnergywoodTreesPoints <- HollowTreesPoints
# OUTPUTS list
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = EnergywoodTreesPoints)
}
if(nrow(inventory) != nrow(inventory0))
stop("The number of rows between the input inventory and the output inventory
of the function selected() is not the same.The function must be corrected.")
return(selectedOutputs) # return the new inventory and the 2 points vectors (HollowTrees and EnergywoodTrees)
}
VincyaneBadouard/LoggingLab documentation built on Oct. 16, 2024, 9:42 p.m.
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Defines functions selected
Documented in selected
#'Selection of trees to log
#'
#'@description Selection of trees to log among the exploitable trees, according
#' to the objective volume and the exploitable volume on the plot.
#'
#'@param inventory Input inventory (see the inputs formats and metadata in the
#' vignette) (data.frame)
#'
#'@param topography Digital terrain model (DTM) of the inventoried plot (LiDAR
#' or SRTM) (\code{\link{DTMParacou}}) (RasterLayer **with a crs in UTM**)
#' We advise you to generate your raster with Qgis rather than with the
#' 'raster' package on R.
#'
#'@param scenario Logging scenario: "RIL1", "RIL2broken", "RIL2", "RIL3",
#' "RIL3fuel", "RIL3fuelhollow" or "manual"(character) (see the
#' vignette)
#'
#'@param fuel Fuel wood exploitation: no exploitation = "0", exploitation of
#' damage and unused part of logged trees for fuel = "1", exploitation of
#' hollow trees, damage and and unused part of the log for fuel = "2"
#'
#'@param diversification Possibility to log other species in addition to the
#' main commercial species (species with a value of 2 for commercial in the
#' \code{\link{SpeciesCriteria}} table) (logical)
#'
#'@param specieslax Allow diversification if the stand is too poor to reach the
#' objective volume without diversification, = FALSE by default (logical)
#'
#'@param VO Objective volume for the entire area of the plot (m3) (numeric
#' value)
#'
#'@param HVinit Harvestable volume(m3) in the plot for the chosen scenario
#' (\code{\link{SpeciesCriteria}}) (numeric value)
#'
#'@param objectivelax Allow exploitation in case of non-achievement of the
#' objective volume (if stand too poor), = FALSE by default (logical)
#'
#'@param advancedloggingparameters Other parameters of the logging simulator
#' \code{\link{loggingparameters}} (list)
#'
#'@return Input inventory with:
#' - The trees selected for harvesting (*Selected*)
#' - if the Minimum Felling Diameter (*MinFD*) of their species has been raised
#' (*Up*)
#' - The probability of a tree being probed hollow (*ProbedHollowProba*) and
#' the probed hollow trees (*ProbedHollow*).
#'See the outputs metadata in the vignette.
#'
#'2 sets of spatial points: (*HollowTrees* and *EnergywoodTrees*)
#'
#'@details This function allows the selection of trees to be exploited among the
#' exploitable trees. It also informs about the trees that were finally found
#' to be hollow during the probe. If fuel = 2, the hollow trees will be
#' harvested and are therefore included in the objective volume. If fuel = 0 or
#' 1, the hollow trees will not be exploited, so the function looks for other
#' trees to reach the objective volume (if possible).
#'
#' If the harvestable volume is higher than the objective volume, and that
#' diversification was not chosen, *MinFD* of the 1st economic rank species
#' only is increased.
#' If the diversification is allowed, *MinFD* of 1st and 2nd economic level
#' species is increased.
#' Then, the trees to be harvested are chosen in
#' decreasing order of volume, until the objective volume is reached.
#'
#' If the harvestable volume is lower than the objective volume,
#' diversification can be applied if it was not already applied ('specieslax')
#' (trees of all commercial ranks are selected in decreasing order of volume
#' until the objective volume is reached), or harvesting can continue despite
#' an unreached objective volume, or be abandoned ('objectivelax')
#'
#'@seealso \code{\link{Paracou6_2016}}, \code{\link{SpeciesCriteria}},
#' \code{\link{DTMParacou}}, \code{\link{loggingparameters}}
#'
#'@export
#'
#'@importFrom dplyr arrange desc ungroup rowwise mutate group_by select filter
#'@importFrom tibble add_column
#'@importFrom sp coordinates proj4string
#'@importFrom sf st_as_sf
#'@importFrom raster crs
#'
#'
#' @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 = FALSE, specieslax = TRUE,
#' plotslope = HarvestableAreaOutputsCable$PlotSlope,
#' maintrails = MainTrails,
#' harvestablepolygons = HarvestableAreaOutputsCable$HarvestablePolygons,
#' scenario = "manual", winching = "2",
#' advancedloggingparameters = loggingparameters())
#'
#' inventory <- harvestableOutputs$inventory
#' HVinit <- harvestableOutputs$HVinit
#'
#' selecInventory <- selected(inventory, topography = DTMParacou,
#' scenario = "manual", fuel = "2", diversification = TRUE,
#' VO = 20, HVinit = HVinit, specieslax = TRUE, objectivelax = TRUE,
#' advancedloggingparameters = loggingparameters())$inventory
#'
selected <- function(
inventory,
topography,
scenario,
fuel = NULL,
diversification = NULL,
VO, # objective volume for the entire surface of the plot
HVinit, # initial Harvestable Volume
specieslax = FALSE,
objectivelax = FALSE,
advancedloggingparameters = loggingparameters()
){
# Arguments check
if(!inherits(inventory, "data.frame"))
stop("Argument 'inventory' of the 'selected' function must be a data.frame")
if(!all(unlist(lapply(list(diversification, specieslax, objectivelax), inherits, "logical")))
&& !is.null(diversification))
stop("Arguments 'diversification', 'specieslax' and 'objectivelax'
of the 'selected' function must be logical")
# if (!any(scenario == "RIL1" | scenario == "RIL2broken"| scenario == "RIL2"| scenario == "RIL3"| scenario == "RIL3fuel"|
# scenario == "RIL3fuelhollow"| scenario == "manual"))
# stop("The 'scenario' argument of the 'selected' function must be 'RIL1', 'RIL2broken', 'RIL2', 'RIL3', 'RIL3fuel', 'RIL3fuelhollow' or 'manual'")
# if (!any(fuel == "0" | fuel == "1"| fuel == "2" | is.null(fuel)))
# stop("The 'fuel' argument of the 'selected' function must be '0', '1', or '2'")
if(!inherits(advancedloggingparameters, "list"))
stop("Argument 'advancedloggingparameters' of the 'selected' function must be a list")
if(scenario == "manual" &&
(is.null(fuel) || is.null(diversification)))
stop("If you choose the 'manual' mode,
you must fill in the arguments 'fuel' and 'diversification'")
if(!all(unlist(lapply(list(VO, HVinit), inherits, "numeric"))))
stop("Arguments 'VO' and 'HVinit' of the 'selected' function must be numeric")
# initial inventory
inventory0 <- inventory
# Redefinition of the parameters according to the chosen scenario
scenariosparameters <- scenariosparameters(scenario = scenario,
fuel = fuel, diversification = diversification)
fuel <- scenariosparameters$fuel
diversification <- scenariosparameters$diversification
# Global variables
Accessible <- CircCorr <- CodeAlive <- CommercialLevel <- NULL
Condition <- DBH <- NULL
DeathCause <- DistCriteria <- Family <- CommercialName <- Crumbs <- NULL
ForestZoneVolumeParametersTable <- Genus <- Logged <- NULL
TimberLoggedVolume <- LoggingStatus <- MaxFD <- MaxFD.genus <- NULL
MaxFD.species <- MinFD <- MinFD.genus <- MinFD.species <- NULL
NoHollowTimberLoggedVolume <- ParamCrownDiameterAllometry <- PlotSlope <- NULL
ProbedHollow <- ProbedHollowProba <- ScientificName <- NULL
Selected <- Slope <- SlopeCriteria <- Species <- Species.genus <- NULL
SpeciesCriteria <- Taxo <- Taxo.family <- Taxo.genus <- Taxo.species <- NULL
TreeFellingOrientationSuccess <- TreeHarvestableVolume <- NULL
TreeHeight <- TrunkHeight <- Up <- UpMinFD <- UpMinFD.genus <- NULL
UpMinFD.species <- NULL
VolumeCumSum <- Xutm <- Yutm <- aCoef <- NULL
alpha <- alpha.family <- alpha.genus <- alpha.species <- bCoef <- NULL
beta.family <- beta.genus <- beta.species <- geometry <- idTree <- NULL
# Apply S. Schmitt's "Rotten" predictive model to identify probed hollow trees.
inventory <- inventory %>%
# Estimates the probability of being probed hollow
mutate(ProbedHollowProba = ifelse(LoggingStatus == "harvestable" | LoggingStatus == "harvestable2nd",
advancedloggingparameters$RottenModel(DBH), NA)) %>%
# generate either "1" or "0" randomly for each line, depending on the proba associated with the line:
rowwise() %>%
mutate(ProbedHollow = ifelse(!is.na(ProbedHollowProba),
sample(c(1,0), size = 1, replace = F, # 1 = hollow tree, 0 = not hollow
prob = c(ProbedHollowProba, 1-ProbedHollowProba)), NA)) %>%
mutate(ProbedHollow = factor(as.numeric(ProbedHollow)))
if(fuel != "2"){
HollowTable <- filter(inventory, ProbedHollow == "1"| is.na(ProbedHollow))
inventory <- filter(inventory, ProbedHollow == "0") # we continue with just healthy trees in fuel != "2" case
}
# if objective achieved at the first attempt
inventory <- inventory %>%
mutate(Selected = ifelse(HVinit == VO & LoggingStatus == "harvestable",
"1", NA))# if we have our volume, harvestable sp = selected sp
# Create a column to indicate Which sp is FD uped. "0" = no uped, "1"= uped
inventory <- add_column(inventory, Up = "0")
if (HVinit < VO){ #diversification is necessary, designate the secondary-economic-rank species too
if (!diversification && specieslax){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestable2nd"|LoggingStatus == "harvestable",TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(CommercialLevel) %>% # add for reviewer
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVlax <- sum(HarvestableTable$TreeHarvestableVolume) # Harvestable volume, with specieslax permission
if (HVlax < VO && objectivelax)
message("The exploitable volume (= ",paste(round(HVlax, digits = 1)),"m^3) is still lower
(by ",paste(round(VO- HVlax, digits = 1)),"m^3) than your objective volume
despite the diversification
(without the diversification HVinit= ",paste(round(HVinit, digits = 1)),"m^3).
You have chosen to continue harvesting with a volume lower than your objective in this case.")
if (HVlax < VO && !objectivelax)
stop("The harvestable volume = ",paste(round(HVlax, digits = 1)),"m^3)
is still lower (by ",paste(round(VO- HVlax, digits = 1)),"m^3)
than your objective volume despite the diversification
(without the diversification HVinit= ",paste(round(HVinit, digits = 1)),"m^3).
By default or because of your choice, the simulation stops.
If you wish to continue the exploitation with of an exploitable volume lower
than your objective volume, you can use the argument 'objectivelax'.")
if (!HVlax == VO)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to diversify your species selection in this case.
The exploitation was therefore carried out on this diversified selection of species.")
} else {
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() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
}
if (!diversification && !specieslax && objectivelax)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to continue logging without diversifying in this case.")
if (diversification && objectivelax)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to continue logging in this case.")
if ((!specieslax & !objectivelax) | (diversification && !objectivelax))
stop("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) is lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
By default or because of your choice, the simulation stops.
If you wish to continue the exploitation with of a harvestable volume lower
than your objective volume, you can use the argument 'objectivelax'
or the diversification of species (if not already done).")
}
if (HVinit > VO) {
inventory <- inventory %>%
mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" &
CommercialLevel == 1 & (DBH >= UpMinFD & DBH <= MaxFD), #designate the bigger individuals, when the plot is species-rich.
"harvestableUp", LoggingStatus))
if (!diversification) {
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp")
HVupCommercial1 <- sum(HarvestableTable$TreeHarvestableVolume) #Compute the harvestable volume with upgraded FD individuals
if (HVupCommercial1 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(HVupCommercial1 == VO & LoggingStatus == "harvestableUp", "1", NA))# if harvestableUp individuals are sufficient to have our volume, harvestableUp ind = selected ind
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was higher
(by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameter (MinFD) of 1st economic rank species were increased.
The objective volume has now been reached.")
}
if (HVupCommercial1 > VO){
# only individuals with DBH > FD are taken, but not all because their volumes > VO
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp", TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(CommercialLevel) %>% # add for reviewer
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with "1" rank species and upgraded FD individuals only
message("The harvestable volume (= ",paste(round(HVupCommercial1, digits = 1)),"m^3) was higher
(by ",paste(round(HVupCommercial1-VO, digits = 1)),"m^3) than your objective volume
despite the increase in Minimum Falling Diameter (MinFD)
(Initial harvestable volume = ",paste(round(HVinit, digits = 1)),"m^3).
Trees were selected by decreasing order of volume
until the objective volume was reached.")
}
if (HVupCommercial1 < VO){
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() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with "1" rank species and upgraded FD individuals
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameters (MinFD) of the 1st economic rank species were increased to UpMinFD.
Some trees with DBH lower than the UpMinFD were however selected
to ensure that the objective volume was reached.")
}
}
if (diversification) {
# Increase the MinFD of the other economic species
inventory <- inventory %>%
mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" & CommercialLevel >1 &
(DBH >= UpMinFD & DBH <= MaxFD), #designate preferred individuals of 2nd economic rank species too, when the plot is species-rich.
"harvestableUp", LoggingStatus))
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp") #the upgraded 1st & 2nd ranks
HVupCommercial12 <- sum(HarvestableTable$TreeHarvestableVolume)
if (HVupCommercial12 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(LoggingStatus == "harvestableUp",
"1", NA))# if we have our volume, harvestable ind = selected ind
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was higher
(by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameter (MinFD) of the 1st and 2nd economic ranks species were increased to UpMinFD.
The objective volume has now been reached.")
} else if (HVupCommercial12 != VO){
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() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial12adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with upgraded FD individuals
if (HVupCommercial12 < VO){
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameters (MinFD) of the 1st and 2nd economic ranks species were increased to UpMinFD.
Some trees with DBH lower than the UpMinFD were however selected to ensure that the objective
volume was reached.")
}
if (HVupCommercial12 > VO){
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3)
than the objective volume, the Minimum Falling Diameter (MinFD) of the 1st and 2nd economic ranks species
were increased to UpMinFD. The objective volume has now been reached.")
}
} # end : HVupCommercial12 != VO
}
}
# if at this step there are no selected trees
if(!any(inventory$Selected == "1") & any(inventory$ProbedHollow == "0")){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestable", TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(CommercialLevel) %>% # add for reviewer
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
}
# No NA in Selected colomn
inventory <- mutate(inventory, Selected = ifelse(is.na(Selected) , "0", Selected))
# Complete to reach the objective volume 'with crumbs'
HarvestableTable <- inventory %>%
filter(Selected == "1")
MissingVolume <- VO - sum(HarvestableTable$TreeHarvestableVolume)
min <- MissingVolume - 1
inventory <- inventory %>%
mutate(Crumbs = ifelse((LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable") & Selected != "1" &
(TreeHarvestableVolume > min & TreeHarvestableVolume <= MissingVolume),
TRUE, FALSE)) %>%
group_by(Crumbs) %>%
arrange(CommercialLevel) %>% # add for reviewer
arrange(desc(TreeHarvestableVolume))
if(any(inventory$Crumbs)){
Crumbsdf <- inventory %>%
filter(Crumbs %in% TRUE)
MaxCrumbsV <- max(Crumbsdf$TreeHarvestableVolume) # the most important remaining volume able to reach the objective
inventory <- inventory %>%
mutate(Selected = ifelse(Crumbs %in% TRUE & TreeHarvestableVolume == MaxCrumbsV, "1", Selected))
}
inventory <- inventory %>%
ungroup() %>%
select(-Crumbs)
# Add the probed hollow trees removed until now in fuel != 2 case
if(fuel != "2"){
inventory <- bind_rows(inventory, HollowTable)
}
# No NA in Selected colomn
inventory <- mutate(inventory, Selected = ifelse(is.na(Selected) , "0", Selected))
# Upgraded MinFD species:
# to inform for each individual if its species have been FD upgraded
inventory <- inventory %>%
group_by(CommercialName) %>%
mutate(Up = ifelse(any(LoggingStatus == "harvestableUp"), "1", Up)) %>%
ungroup()
if (!any(inventory$Selected == "1")) { # no selected trees
# if there are "deselected" trees and not of 'selected = 1'
if (any(inventory$ProbedHollow == "1")){ # probed hollow trees and no selected trees
stop("No trees were selected because they were all probed hollow
(",paste(round(sum(as.numeric(inventory$ProbedHollow == "1"), na.rm = TRUE), digits = 1)),
" probed hollow trees). Your objective volume may be too low (the few trees selected were found to be
hollow).")
}else if (all(inventory$LoggingStatus == "non-harvestable")) {
stop("No trees selected, you have no harvestable trees (according to your criteria (SpeciesCriteria))
in your inventory.")
}
}
# Create a POINTS VECTOR with coordinates of the probed hollow trees:
if (any(inventory$ProbedHollow == "1", na.rm = TRUE)) {
HollowTreesPoints <- inventory %>%
filter(ProbedHollow == "1")
sp::coordinates(HollowTreesPoints) <- ~ Xutm + Yutm
sp::proj4string(HollowTreesPoints) <- raster::crs(topography)
HollowTreesPoints <- st_as_sf(as(HollowTreesPoints,"SpatialPoints"))
# OUTPUTS list
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = st_point(x = c(NA_real_, NA_real_))) # empty point
} else {
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = st_point(x = c(NA_real_, NA_real_)), # empty point
EnergywoodTreesPoints = st_point(x = c(NA_real_, NA_real_)))
}
if ((fuel == "2") & any(inventory$ProbedHollow == "1", na.rm = TRUE)) {
# Hollow trees = fuel wood:
inventory <- inventory %>%
mutate(DeathCause = ifelse(Selected == "1" & ProbedHollow == "1", "hollowfuel", NA))# replace "NA" par "DeathCause" in this code line in the ONF simulator
# Create a POINTS VECTOR with coordinates of the energywood trees:
EnergywoodTreesPoints <- HollowTreesPoints
# OUTPUTS list
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = EnergywoodTreesPoints)
}
if(nrow(inventory) != nrow(inventory0))
stop("The number of rows between the input inventory and the output inventory
of the function selected() is not the same.The function must be corrected.")
return(selectedOutputs) # return the new inventory and the 2 points vectors (HollowTrees and EnergywoodTrees)
}
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