R/treeselection.R
In thomasgaquiere/Maria: Simulate Different Forms of Logging on a Forest
Defines functions
treeselection
Documented in
treeselection
#'Tree selection (trees to be exploited, future and reserve trees)
#'
#'@param inventory input inventory (see the inputs formats and metadata in the
#' \code{\link{vignette}}) (data.frame)
#'
#'@param topography Digital terrain model (DTM) of the inventoried plot (LiDAR
#' or SRTM) (\code{\link{DTMParacou}}) (RasterLayer)
#'
#'@param plotslope Slopes (in radians) of the inventoried plot (with a
#' neighbourhood of 8 cells) (default: \code{\link{PlotSlope}}) (RasterLayer)
#'
#'@param harvestablepolygons Accessible area of the inventoried plot
#' (default: \code{\link{HarvestableAreaDefinition}}) (sf polygons data.frame)
#'
#'@param maintrails Main trails defined at the entire harvestable area (sf polylines)
#'
#'@param speciescriteria Table of species exploitability criteria : species
#' names, economic interest level, minimum and maximum felling diameter, in the
#' same format as \code{\link{SpeciesCriteria}} (data.frame)
#'
#'@param scenario Logging scenario: "RIL1", "RIL2broken", "RIL2", "RIL3",
#' "RIL3fuel", "RIL3fuelhollow" or "manual"(character) (see the
#' \code{\link{vignette}})
#'
#'@param objective Objective volume (m^3/ha) (numeric)
#'
#'@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 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 A list with:
#' - input inventory with new columns:
#' - The exploitability criteria ("DistCrit", "Slope" (in radians), "SlopeCrit"), and if
#' they are validated for each of the trees ("LoggingStatus").
#' - The probability of a tree having visible defects ("VisibleDefectProba")
#' and the visible defect trees ("VisibleDefect").
#' - The trees selected for harvesting ("Selected"), if the Minimum
#' Felling Diameter (MinFD) of their species has been raised ("Up").
#' The cumulative harvestable volume of harvestable trees("VolumeCumSum").
#' - The probability of a tree being probed hollow ("ProbedHollowProba")
#' and the probed hollow trees ("ProbedHollow").
#' - Future and reserve trees (LoggingStatus = "future"/"reserve")
#' (see the outputs metadata in the \code{\link{vignette}})
#' - the objective volume (VO) for the entire plot
#' - the harvestable volume with the initial
#' criteria (HVinit) for the entire plot
#' - 6 layers of spatial points: harvestable, selected, future and
#' reserve, hollow and fuel wood trees
#'
#'@details Trees will be designated as "**harvestable**" if they:
#' - belong to species of 1st economic level (if no diversification) or 1st and
#' 2nd level if (diversification)
#' - have a DBH between MinFD and MaxFD.
#' - not isolated ( >100m ('IsolateTreeMinDistance' in
#' \code{\link{loggingparameters}})) from other individuals of the same
#' species in the aggregative species case (\code{\link{SpeciesCriteria}},
#' 'Aggregative' column).
#' - on slopes < 22% ('TreeMaxSlope'in \code{\link{loggingparameters}})
#' - off the main trails.
#'
#'Trees with visible defects are identified ('VisiblyDefectModel' in
#''advancedloggingparameters' argument) among the trees with harvestable
#'criteria and are therefore considered 'non-harvestable'.
#'
#' If fuel = 2, the hollow trees (identified with the "RottenModel"
#' (\code{\link{loggingparameters}})) 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, MinFD of
#' the 1st economic rank species is increased. If this is not enough and if
#' diversification is allowed, MinFD of 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')
#'
#' **Future** trees are all trees satisfying the following conditions:
#' - species of 1st economic rank
#' - DBH between 35cm (default) ('FutureTreesMinDiameter') and the species MinFD
#' or UpMinFD if it has been raised for its species.
#'
#' **Reserve** trees are randomly chosen among future trees so that
#' the number of reserve trees is equal to the number of harvested trees.
#'
#'@seealso \code{\link{Paracou6_2016}}, \code{\link{SpeciesCriteria}},
#' \code{\link{DTMParacou}}, \code{\link{PlotSlope}},
#' \code{\link{loggingparameters}}
#'
#'
#'@export
#'
#'@importFrom dplyr filter mutate select left_join bind_rows
#'@importFrom sf st_as_sf st_point
#'@importFrom raster crs extract
#'@importFrom methods as
#'
#'
#' @examples
#' \dontrun{
#' data(Paracou6_2016)
#' data(DTMParacou)
#' data(PlotSlope)
#' data(MainTrails)
#' data(HarvestablePolygons)
#'
#' inventory <- addtreedim(inventorycheckformat(Paracou6_2016),
#' volumeparameters = ForestZoneVolumeParametersTable)
#'
#' treeselectionoutputs <- treeselection(inventory,
#' maintrails = MainTrails,
#' topography = DTMParacou, plotslope = PlotSlope,
#' harvestablepolygons = HarvestablePolygons,
#' speciescriteria = SpeciesCriteria, objective = 20,
#' scenario ="manual", fuel = "2", diversification = TRUE, specieslax = FALSE,
#' objectivelax = TRUE,
#' advancedloggingparameters = loggingparameters())
#'
#' NewInventory <- treeselectionoutputs$inventory
#'
#' NonHarvestable <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "non-harvestable"),
#' coords = c("Xutm", "Yutm"))
#'
#' Harvestable <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "harvestable"),
#' coords = c("Xutm", "Yutm"))
#'
#' HarvestableUp <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "harvestableUp"),
#' coords = c("Xutm", "Yutm"))
#'
#' Selected <- sf::st_as_sf(
#' dplyr::filter(NewInventory, Selected == "1"), coords = c("Xutm", "Yutm"))
#'
#' Reserve <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "reserve"),
#' coords = c("Xutm", "Yutm"))
#'
#' Future <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "future"),
#' coords = c("Xutm", "Yutm"))
#'
#' ProbedHollow <- sf::st_as_sf(
#' dplyr::filter(NewInventory, ProbedHollow == "1"), coords = c("Xutm", "Yutm"))
#'
#' VisibleDefect <- sf::st_as_sf(
#' dplyr::filter(NewInventory, VisibleDefect == "1"), coords = c("Xutm", "Yutm"))
#'
#' library(ggplot2)
#' ggplot() +
#' geom_sf(data = NonHarvestable,
#' aes(colour = "Non-harvestable"), show.legend = "point") +
#' geom_sf(data = VisibleDefect,
#' aes(colour = "Visible defect"), show.legend = "point") +
#' geom_sf(data = Future,
#' aes(colour = "Future"), show.legend = "point", size = 4) +
#' geom_sf(data = Reserve,
#' aes(colour = "Reserve"), show.legend = "point", size = 4) +
#' geom_sf(data = Harvestable,
#' aes(colour = "Harvestable"), show.legend = "point", size = 4) +
#' geom_sf(data = HarvestableUp,
#' aes(colour = "HarvestableUp"), show.legend = "point", size = 4) +
#' geom_sf(data = Selected,
#' aes(colour = "Selected"), show.legend = "point") +
#' geom_sf(data = ProbedHollow,
#' aes(colour = "Probed hollow"), show.legend = "point") +
#'
#' scale_colour_manual(values = c("Non-harvestable" = "grey",
#' "Visible defect" = "pink", "Harvestable" = "skyblue",
#' "HarvestableUp" = "blue", "Selected" = "red", "Future" = "orange",
#' "Reserve" = "purple", "Probed hollow" = "forestgreen")) +
#' labs(color = "Logging status")
#'}
treeselection <- function(
inventory,
topography,
plotslope,
harvestablepolygons,
maintrails,
speciescriteria,
scenario,
objective = NULL,
fuel = NULL,
diversification = NULL,
specieslax = FALSE,
objectivelax = FALSE,
advancedloggingparameters = loggingparameters()
){
# Arguments check
if(!all(unlist(lapply(list(inventory, speciescriteria), inherits, "data.frame"))))
stop("The 'inventory' and 'speciescriteria' arguments of the 'treeselection' function must be data.frames")
if(!any(inherits(objective, "numeric") || is.null(objective)))
stop("The 'objective' argument of the 'treeselection' function must be numeric or NULL")
if(!any(inherits(diversification, "logical") || is.null(diversification)))
stop("The 'diversification' argument of the 'treeselection' function must be logical or NULL")
if(!all(unlist(lapply(list(specieslax, objectivelax), inherits, "logical"))))
stop("The 'specieslax' and 'objectivelax' arguments of the 'treeselection' function must be logicals")
if (!any(scenario == "RIL1" || scenario == "RIL2broken"|| scenario == "RIL2"||
scenario == "RIL3"|| scenario == "RIL3fuel"|| scenario == "RIL3fuelhollow"|| scenario =="manual"))
stop("The 'scenario' argument of the 'treeselection' 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 'treeselection' function must be '0', '1', or '2'")
if(!all(unlist(lapply(list(topography, plotslope), inherits, "RasterLayer"))))
stop("The 'topography' and 'plotslope' arguments of the 'treeselection' function must be RasterLayer")
if(!inherits(advancedloggingparameters, "list"))
stop("The 'advancedloggingparameters' argument of the 'treeselection' function must be a list")
if(scenario == "manual" &&
(is.null(objective) || is.null(fuel) || is.null(diversification)))
stop("If you choose the 'manual' mode,
you must fill in the arguments 'objective', 'fuel' and 'diversification'")
# Global variables
Accessible <- Circ <- CircCorr <- CodeAlive <- Commercial <- NULL
Commercial.genus <- Commercial.species <- Condition <- DBH <- NULL
DeathCause <- DistCrit <- Family <- LogDBH <- NULL
ForestZoneVolumeParametersTable <- Genus <- Logged <- NULL
TimberLoggedVolume <- LoggingStatus <- MaxFD <- MaxFD.genus <- NULL
MaxFD.species <- MinFD <- MinFD.genus <- MinFD.species <- NULL
NoHollowTimberLoggedVolume <- ParamCrownDiameterAllometry <- PlotSlope <- NULL
PlotTopo <- ProbedHollow <- ProbedHollowProba <- ScientificName <- NULL
Selected <- Slope <- SlopeCrit <- 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 <- VernName.genus <- VernName.genus.genus <- NULL
VernName.species <- VolumeCumSum <- Xutm <- Yutm <- aCoef <- NULL
alpha <- alpha.family <- alpha.genus <- alpha.species <- bCoef <- NULL
beta.family <- beta.genus <- beta.species <- geometry <- idTree <- NULL
# Redefinition of the parameters according to the chosen scenario
scenariosparameters <- scenariosparameters(scenario = scenario, objective = objective, fuel = fuel,
diversification = diversification)
objective <- scenariosparameters$objective
fuel <- scenariosparameters$fuel
diversification <- scenariosparameters$diversification
# Function
if ("DeathCause" %in% names(inventory)) filter(inventory, is.null(DeathCause)) #select only still alived trees (after MainTrails) NULL ou NA
# Compute the objective volume for the entire surface of the plot
VO <- objective * unique(inventory$PlotArea)
# Joins commercial criteria to the inventory
inventory <- ONFGuyafortaxojoin(inventory, speciescriteria = speciescriteria)
# Harvestable trees identification
harvestableOutputs <- harvestable(inventory,
topography = topography, plotslope = plotslope,
harvestablepolygons = harvestablepolygons,
maintrails = maintrails,
diversification = diversification, specieslax = specieslax,
advancedloggingparameters = advancedloggingparameters)
inventory <- harvestableOutputs$inventory # new inventory
HVinit <- harvestableOutputs$HVinit # initial harvestable volume
# Trees to be exploited selection
selectedOutputs <- selected(inventory,
topography = topography,
scenario = scenario, fuel = fuel, diversification = diversification,
VO = VO, HVinit = HVinit,
specieslax = specieslax, objectivelax = objectivelax,
advancedloggingparameters = advancedloggingparameters)
inventory <- selectedOutputs$inventory # extract inventory of the selected outputs
HollowTreesPoints <- selectedOutputs$HollowTreesPoints # extract a pts vector of the selected outputs
EnergywoodTreesPoints <- selectedOutputs$EnergywoodTreesPoints # extract a pts vector of the selected outputs
# Future & reserve trees designation
inventory <- futurereserve(inventory,
speciescriteria = speciescriteria,
advancedloggingparameters = advancedloggingparameters)
# Points vector with coordinates of the harvestable trees:
HarvestableTreesPoints <- inventory %>%
filter(LoggingStatus == "harvestable"|LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable2nd") # harvestableUp = DBH > MinFD individuals, harvestable2nd = eco2 individuals is specieslax
if (dim(HarvestableTreesPoints)[1] != 0) {
HarvestableTreesPoints <- st_as_sf(HarvestableTreesPoints, coords = c("Xutm", "Yutm")) # sp::coordinates(HarvestableTreesPoints) <- ~ Xutm + Yutm
# sp::proj4string(HarvestableTreesPoints) <- raster::crs(topography)
} else {HarvestableTreesPoints = st_point(x = c(NA_real_, NA_real_))} # empty
# Points vector with coordinates of the selected trees:
SelectedTreesPoints <- inventory %>%
filter(Selected == "1")
if (dim(SelectedTreesPoints)[1] != 0) {
SelectedTreesPoints <- st_as_sf(SelectedTreesPoints, coords = c("Xutm", "Yutm")) # sp::coordinates(SelectedTreesPoints) <- ~ Xutm + Yutm
# sp::proj4string(SelectedTreesPoints) <- raster::crs(topography)
} else {SelectedTreesPoints = st_point(x = c(NA_real_, NA_real_))} # empty
# Points vector with coordinates of the future trees:
FutureTreesPoints <- inventory %>%
filter(LoggingStatus == "future")
if (dim(FutureTreesPoints)[1] != 0) {
st_as_sf(FutureTreesPoints, coords = c("Xutm", "Yutm")) # sp::coordinates(FutureTreesPoints) <- ~ Xutm + Yutm
# sp::proj4string(FutureTreesPoints) <- raster::crs(topography)
} else {FutureTreesPoints = st_point(x = c(NA_real_, NA_real_))} # empty
# Points vector with coordinates of the reserve trees:
ReserveTreesPoints <- inventory %>%
filter(LoggingStatus == "reserve")
if (dim(ReserveTreesPoints)[1] != 0) {
st_as_sf(ReserveTreesPoints, coords = c("Xutm", "Yutm")) # sp::coordinates(ReserveTreesPoints) <- ~ Xutm + Yutm
# sp::proj4string(ReserveTreesPoints) <- raster::crs(topography)
} else {ReserveTreesPoints = st_point(x = c(NA_real_, NA_real_))} # empty
# Points vector with coordinates of the big trees (DBH >= 50 cm):
BigTreesPoints <- inventory %>%
filter(DBH >= advancedloggingparameters$BigTrees & ( Selected != "1"& LoggingStatus != "harvestable" & LoggingStatus != "harvestableUp" & LoggingStatus != "harvestable2nd" ))
if (dim(BigTreesPoints)[1] != 0) {
sp::coordinates(BigTreesPoints) <- ~ Xutm + Yutm
sp::proj4string(BigTreesPoints) <- crs(topography)
BigTreesPoints <- BigTreesPoints %>% st_as_sf()
} else {BigTreesPoints = st_point(x = c(NA_real_, NA_real_))}
# where specieslax was not necessary, consider eco2s as non-exploitable:
inventory <- inventory %>%
mutate(LoggingStatus = ifelse(HVinit > VO & LoggingStatus == "harvestable2nd", "non-harvestable",
LoggingStatus))
# OUTPUTS list
treeselectionOutputs <- list(inventory = inventory,
VO = VO,
HVinit = HVinit,
HarvestableTreesPoints = HarvestableTreesPoints,
SelectedTreesPoints = SelectedTreesPoints,
FutureTreesPoints = FutureTreesPoints,
ReserveTreesPoints = ReserveTreesPoints,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = EnergywoodTreesPoints,
BigTreesPoints = BigTreesPoints)
return(treeselectionOutputs) # return the new inventory, the objective volume,
# and the 4 points vectors (Harvestable, Selected, Future and Reserve,
# Hollow and Energywood Trees)
}
thomasgaquiere/Maria documentation built on Dec. 24, 2021, 1:20 a.m.
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Defines functions treeselection
Documented in treeselection
#'Tree selection (trees to be exploited, future and reserve trees)
#'
#'@param inventory input inventory (see the inputs formats and metadata in the
#' \code{\link{vignette}}) (data.frame)
#'
#'@param topography Digital terrain model (DTM) of the inventoried plot (LiDAR
#' or SRTM) (\code{\link{DTMParacou}}) (RasterLayer)
#'
#'@param plotslope Slopes (in radians) of the inventoried plot (with a
#' neighbourhood of 8 cells) (default: \code{\link{PlotSlope}}) (RasterLayer)
#'
#'@param harvestablepolygons Accessible area of the inventoried plot
#' (default: \code{\link{HarvestableAreaDefinition}}) (sf polygons data.frame)
#'
#'@param maintrails Main trails defined at the entire harvestable area (sf polylines)
#'
#'@param speciescriteria Table of species exploitability criteria : species
#' names, economic interest level, minimum and maximum felling diameter, in the
#' same format as \code{\link{SpeciesCriteria}} (data.frame)
#'
#'@param scenario Logging scenario: "RIL1", "RIL2broken", "RIL2", "RIL3",
#' "RIL3fuel", "RIL3fuelhollow" or "manual"(character) (see the
#' \code{\link{vignette}})
#'
#'@param objective Objective volume (m^3/ha) (numeric)
#'
#'@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 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 A list with:
#' - input inventory with new columns:
#' - The exploitability criteria ("DistCrit", "Slope" (in radians), "SlopeCrit"), and if
#' they are validated for each of the trees ("LoggingStatus").
#' - The probability of a tree having visible defects ("VisibleDefectProba")
#' and the visible defect trees ("VisibleDefect").
#' - The trees selected for harvesting ("Selected"), if the Minimum
#' Felling Diameter (MinFD) of their species has been raised ("Up").
#' The cumulative harvestable volume of harvestable trees("VolumeCumSum").
#' - The probability of a tree being probed hollow ("ProbedHollowProba")
#' and the probed hollow trees ("ProbedHollow").
#' - Future and reserve trees (LoggingStatus = "future"/"reserve")
#' (see the outputs metadata in the \code{\link{vignette}})
#' - the objective volume (VO) for the entire plot
#' - the harvestable volume with the initial
#' criteria (HVinit) for the entire plot
#' - 6 layers of spatial points: harvestable, selected, future and
#' reserve, hollow and fuel wood trees
#'
#'@details Trees will be designated as "**harvestable**" if they:
#' - belong to species of 1st economic level (if no diversification) or 1st and
#' 2nd level if (diversification)
#' - have a DBH between MinFD and MaxFD.
#' - not isolated ( >100m ('IsolateTreeMinDistance' in
#' \code{\link{loggingparameters}})) from other individuals of the same
#' species in the aggregative species case (\code{\link{SpeciesCriteria}},
#' 'Aggregative' column).
#' - on slopes < 22% ('TreeMaxSlope'in \code{\link{loggingparameters}})
#' - off the main trails.
#'
#'Trees with visible defects are identified ('VisiblyDefectModel' in
#''advancedloggingparameters' argument) among the trees with harvestable
#'criteria and are therefore considered 'non-harvestable'.
#'
#' If fuel = 2, the hollow trees (identified with the "RottenModel"
#' (\code{\link{loggingparameters}})) 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, MinFD of
#' the 1st economic rank species is increased. If this is not enough and if
#' diversification is allowed, MinFD of 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')
#'
#' **Future** trees are all trees satisfying the following conditions:
#' - species of 1st economic rank
#' - DBH between 35cm (default) ('FutureTreesMinDiameter') and the species MinFD
#' or UpMinFD if it has been raised for its species.
#'
#' **Reserve** trees are randomly chosen among future trees so that
#' the number of reserve trees is equal to the number of harvested trees.
#'
#'@seealso \code{\link{Paracou6_2016}}, \code{\link{SpeciesCriteria}},
#' \code{\link{DTMParacou}}, \code{\link{PlotSlope}},
#' \code{\link{loggingparameters}}
#'
#'
#'@export
#'
#'@importFrom dplyr filter mutate select left_join bind_rows
#'@importFrom sf st_as_sf st_point
#'@importFrom raster crs extract
#'@importFrom methods as
#'
#'
#' @examples
#' \dontrun{
#' data(Paracou6_2016)
#' data(DTMParacou)
#' data(PlotSlope)
#' data(MainTrails)
#' data(HarvestablePolygons)
#'
#' inventory <- addtreedim(inventorycheckformat(Paracou6_2016),
#' volumeparameters = ForestZoneVolumeParametersTable)
#'
#' treeselectionoutputs <- treeselection(inventory,
#' maintrails = MainTrails,
#' topography = DTMParacou, plotslope = PlotSlope,
#' harvestablepolygons = HarvestablePolygons,
#' speciescriteria = SpeciesCriteria, objective = 20,
#' scenario ="manual", fuel = "2", diversification = TRUE, specieslax = FALSE,
#' objectivelax = TRUE,
#' advancedloggingparameters = loggingparameters())
#'
#' NewInventory <- treeselectionoutputs$inventory
#'
#' NonHarvestable <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "non-harvestable"),
#' coords = c("Xutm", "Yutm"))
#'
#' Harvestable <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "harvestable"),
#' coords = c("Xutm", "Yutm"))
#'
#' HarvestableUp <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "harvestableUp"),
#' coords = c("Xutm", "Yutm"))
#'
#' Selected <- sf::st_as_sf(
#' dplyr::filter(NewInventory, Selected == "1"), coords = c("Xutm", "Yutm"))
#'
#' Reserve <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "reserve"),
#' coords = c("Xutm", "Yutm"))
#'
#' Future <- sf::st_as_sf(
#' dplyr::filter(NewInventory, LoggingStatus == "future"),
#' coords = c("Xutm", "Yutm"))
#'
#' ProbedHollow <- sf::st_as_sf(
#' dplyr::filter(NewInventory, ProbedHollow == "1"), coords = c("Xutm", "Yutm"))
#'
#' VisibleDefect <- sf::st_as_sf(
#' dplyr::filter(NewInventory, VisibleDefect == "1"), coords = c("Xutm", "Yutm"))
#'
#' library(ggplot2)
#' ggplot() +
#' geom_sf(data = NonHarvestable,
#' aes(colour = "Non-harvestable"), show.legend = "point") +
#' geom_sf(data = VisibleDefect,
#' aes(colour = "Visible defect"), show.legend = "point") +
#' geom_sf(data = Future,
#' aes(colour = "Future"), show.legend = "point", size = 4) +
#' geom_sf(data = Reserve,
#' aes(colour = "Reserve"), show.legend = "point", size = 4) +
#' geom_sf(data = Harvestable,
#' aes(colour = "Harvestable"), show.legend = "point", size = 4) +
#' geom_sf(data = HarvestableUp,
#' aes(colour = "HarvestableUp"), show.legend = "point", size = 4) +
#' geom_sf(data = Selected,
#' aes(colour = "Selected"), show.legend = "point") +
#' geom_sf(data = ProbedHollow,
#' aes(colour = "Probed hollow"), show.legend = "point") +
#'
#' scale_colour_manual(values = c("Non-harvestable" = "grey",
#' "Visible defect" = "pink", "Harvestable" = "skyblue",
#' "HarvestableUp" = "blue", "Selected" = "red", "Future" = "orange",
#' "Reserve" = "purple", "Probed hollow" = "forestgreen")) +
#' labs(color = "Logging status")
#'}
treeselection <- function(
inventory,
topography,
plotslope,
harvestablepolygons,
maintrails,
speciescriteria,
scenario,
objective = NULL,
fuel = NULL,
diversification = NULL,
specieslax = FALSE,
objectivelax = FALSE,
advancedloggingparameters = loggingparameters()
){
# Arguments check
if(!all(unlist(lapply(list(inventory, speciescriteria), inherits, "data.frame"))))
stop("The 'inventory' and 'speciescriteria' arguments of the 'treeselection' function must be data.frames")
if(!any(inherits(objective, "numeric") || is.null(objective)))
stop("The 'objective' argument of the 'treeselection' function must be numeric or NULL")
if(!any(inherits(diversification, "logical") || is.null(diversification)))
stop("The 'diversification' argument of the 'treeselection' function must be logical or NULL")
if(!all(unlist(lapply(list(specieslax, objectivelax), inherits, "logical"))))
stop("The 'specieslax' and 'objectivelax' arguments of the 'treeselection' function must be logicals")
if (!any(scenario == "RIL1" || scenario == "RIL2broken"|| scenario == "RIL2"||
scenario == "RIL3"|| scenario == "RIL3fuel"|| scenario == "RIL3fuelhollow"|| scenario =="manual"))
stop("The 'scenario' argument of the 'treeselection' 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 'treeselection' function must be '0', '1', or '2'")
if(!all(unlist(lapply(list(topography, plotslope), inherits, "RasterLayer"))))
stop("The 'topography' and 'plotslope' arguments of the 'treeselection' function must be RasterLayer")
if(!inherits(advancedloggingparameters, "list"))
stop("The 'advancedloggingparameters' argument of the 'treeselection' function must be a list")
if(scenario == "manual" &&
(is.null(objective) || is.null(fuel) || is.null(diversification)))
stop("If you choose the 'manual' mode,
you must fill in the arguments 'objective', 'fuel' and 'diversification'")
# Global variables
Accessible <- Circ <- CircCorr <- CodeAlive <- Commercial <- NULL
Commercial.genus <- Commercial.species <- Condition <- DBH <- NULL
DeathCause <- DistCrit <- Family <- LogDBH <- NULL
ForestZoneVolumeParametersTable <- Genus <- Logged <- NULL
TimberLoggedVolume <- LoggingStatus <- MaxFD <- MaxFD.genus <- NULL
MaxFD.species <- MinFD <- MinFD.genus <- MinFD.species <- NULL
NoHollowTimberLoggedVolume <- ParamCrownDiameterAllometry <- PlotSlope <- NULL
PlotTopo <- ProbedHollow <- ProbedHollowProba <- ScientificName <- NULL
Selected <- Slope <- SlopeCrit <- 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 <- VernName.genus <- VernName.genus.genus <- NULL
VernName.species <- VolumeCumSum <- Xutm <- Yutm <- aCoef <- NULL
alpha <- alpha.family <- alpha.genus <- alpha.species <- bCoef <- NULL
beta.family <- beta.genus <- beta.species <- geometry <- idTree <- NULL
# Redefinition of the parameters according to the chosen scenario
scenariosparameters <- scenariosparameters(scenario = scenario, objective = objective, fuel = fuel,
diversification = diversification)
objective <- scenariosparameters$objective
fuel <- scenariosparameters$fuel
diversification <- scenariosparameters$diversification
# Function
if ("DeathCause" %in% names(inventory)) filter(inventory, is.null(DeathCause)) #select only still alived trees (after MainTrails) NULL ou NA
# Compute the objective volume for the entire surface of the plot
VO <- objective * unique(inventory$PlotArea)
# Joins commercial criteria to the inventory
inventory <- ONFGuyafortaxojoin(inventory, speciescriteria = speciescriteria)
# Harvestable trees identification
harvestableOutputs <- harvestable(inventory,
topography = topography, plotslope = plotslope,
harvestablepolygons = harvestablepolygons,
maintrails = maintrails,
diversification = diversification, specieslax = specieslax,
advancedloggingparameters = advancedloggingparameters)
inventory <- harvestableOutputs$inventory # new inventory
HVinit <- harvestableOutputs$HVinit # initial harvestable volume
# Trees to be exploited selection
selectedOutputs <- selected(inventory,
topography = topography,
scenario = scenario, fuel = fuel, diversification = diversification,
VO = VO, HVinit = HVinit,
specieslax = specieslax, objectivelax = objectivelax,
advancedloggingparameters = advancedloggingparameters)
inventory <- selectedOutputs$inventory # extract inventory of the selected outputs
HollowTreesPoints <- selectedOutputs$HollowTreesPoints # extract a pts vector of the selected outputs
EnergywoodTreesPoints <- selectedOutputs$EnergywoodTreesPoints # extract a pts vector of the selected outputs
# Future & reserve trees designation
inventory <- futurereserve(inventory,
speciescriteria = speciescriteria,
advancedloggingparameters = advancedloggingparameters)
# Points vector with coordinates of the harvestable trees:
HarvestableTreesPoints <- inventory %>%
filter(LoggingStatus == "harvestable"|LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable2nd") # harvestableUp = DBH > MinFD individuals, harvestable2nd = eco2 individuals is specieslax
if (dim(HarvestableTreesPoints)[1] != 0) {
HarvestableTreesPoints <- st_as_sf(HarvestableTreesPoints, coords = c("Xutm", "Yutm")) # sp::coordinates(HarvestableTreesPoints) <- ~ Xutm + Yutm
# sp::proj4string(HarvestableTreesPoints) <- raster::crs(topography)
} else {HarvestableTreesPoints = st_point(x = c(NA_real_, NA_real_))} # empty
# Points vector with coordinates of the selected trees:
SelectedTreesPoints <- inventory %>%
filter(Selected == "1")
if (dim(SelectedTreesPoints)[1] != 0) {
SelectedTreesPoints <- st_as_sf(SelectedTreesPoints, coords = c("Xutm", "Yutm")) # sp::coordinates(SelectedTreesPoints) <- ~ Xutm + Yutm
# sp::proj4string(SelectedTreesPoints) <- raster::crs(topography)
} else {SelectedTreesPoints = st_point(x = c(NA_real_, NA_real_))} # empty
# Points vector with coordinates of the future trees:
FutureTreesPoints <- inventory %>%
filter(LoggingStatus == "future")
if (dim(FutureTreesPoints)[1] != 0) {
st_as_sf(FutureTreesPoints, coords = c("Xutm", "Yutm")) # sp::coordinates(FutureTreesPoints) <- ~ Xutm + Yutm
# sp::proj4string(FutureTreesPoints) <- raster::crs(topography)
} else {FutureTreesPoints = st_point(x = c(NA_real_, NA_real_))} # empty
# Points vector with coordinates of the reserve trees:
ReserveTreesPoints <- inventory %>%
filter(LoggingStatus == "reserve")
if (dim(ReserveTreesPoints)[1] != 0) {
st_as_sf(ReserveTreesPoints, coords = c("Xutm", "Yutm")) # sp::coordinates(ReserveTreesPoints) <- ~ Xutm + Yutm
# sp::proj4string(ReserveTreesPoints) <- raster::crs(topography)
} else {ReserveTreesPoints = st_point(x = c(NA_real_, NA_real_))} # empty
# Points vector with coordinates of the big trees (DBH >= 50 cm):
BigTreesPoints <- inventory %>%
filter(DBH >= advancedloggingparameters$BigTrees & ( Selected != "1"& LoggingStatus != "harvestable" & LoggingStatus != "harvestableUp" & LoggingStatus != "harvestable2nd" ))
if (dim(BigTreesPoints)[1] != 0) {
sp::coordinates(BigTreesPoints) <- ~ Xutm + Yutm
sp::proj4string(BigTreesPoints) <- crs(topography)
BigTreesPoints <- BigTreesPoints %>% st_as_sf()
} else {BigTreesPoints = st_point(x = c(NA_real_, NA_real_))}
# where specieslax was not necessary, consider eco2s as non-exploitable:
inventory <- inventory %>%
mutate(LoggingStatus = ifelse(HVinit > VO & LoggingStatus == "harvestable2nd", "non-harvestable",
LoggingStatus))
# OUTPUTS list
treeselectionOutputs <- list(inventory = inventory,
VO = VO,
HVinit = HVinit,
HarvestableTreesPoints = HarvestableTreesPoints,
SelectedTreesPoints = SelectedTreesPoints,
FutureTreesPoints = FutureTreesPoints,
ReserveTreesPoints = ReserveTreesPoints,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = EnergywoodTreesPoints,
BigTreesPoints = BigTreesPoints)
return(treeselectionOutputs) # return the new inventory, the objective volume,
# and the 4 points vectors (Harvestable, Selected, Future and Reserve,
# Hollow and Energywood Trees)
}
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