R/LANDIS-II-tables.R
In PredictiveEcology/LandR: Landscape Ecosystem Modelling in R
Defines functions
speciesTableUpdate
prepSpeciesTable
getSpeciesTable
Documented in
getSpeciesTable
prepSpeciesTable
speciesTableUpdate
utils::globalVariables(c(
":=", ".SD", "Area", "col1", "growthcurve", "leafLignin", "leaflongevity", "mortalityshape",
"seeddistance_eff", "seeddistance_max", "species", "species1", "species2", "wooddecayrate"
))
#' Default LANDIS-II project repo url
#'
#' @keywords internal
landisIIrepo <- paste0("https://raw.githubusercontent.com/LANDIS-II-Foundation/",
"Extensions-Succession/master/biomass-succession-archive/",
"trunk/tests/v6.0-2.0/")
#' Download and prepare a species traits table for use with \code{Biomass_core} module
#'
#' TODO: add detailed description
#'
#' @note This one is tailored to Canadian forests (?)
#'
#' @param url If NULL (the default), uses one from D. Cyr's LANDIS-II files:
#' \url{https://github.com/dcyr/LANDIS-II_IA_generalUseFiles/master/speciesTraits.csv}).
#'
#' @param dPath The destination path.
#'
#' @param cacheTags User tags to pass to \code{Cache}.
#'
#' @export
#' @importFrom data.table data.table
#' @importFrom magrittr %>%
#' @importFrom reproducible asPath Cache prepInputs
#' @rdname speciesTable
getSpeciesTable <- function(url = NULL, dPath = tempdir(), cacheTags = NULL) {
if (is.null(url))
url <- paste0("https://raw.githubusercontent.com/",
"dcyr/LANDIS-II_IA_generalUseFiles/",
"master/speciesTraits.csv")
speciesTable <- Cache(prepInputs, "speciesTraits.csv",
destinationPath = asPath(dPath),
url = url,
fun = "utils::read.csv",
header = TRUE, stringsAsFactors = FALSE,
userTags = c(cacheTags, "speciesTable")) %>%
data.table()
return(speciesTable)
}
#' Species Table Column Names
#'
#' @keywords internal
.speciesTableColNames <- c("species", "Area", "longevity", "sexualmature", "shadetolerance",
"firetolerance", "seeddistance_eff", "seeddistance_max", "resproutprob",
"resproutage_min", "resproutage_max", "postfireregen", "leaflongevity",
"wooddecayrate", "mortalityshape", "growthcurve", "leafLignin",
"hardsoft")
#' @param speciesTable A raw species traits table
#'
#' @param speciesLayers stack of species layers rasters
#'
#' @template sppEquiv
#'
#' @template sppEquivCol
#'
#' @return A \code{data.table} with columns ... TODO
#'
#' @export
#' @rdname speciesTable
prepSpeciesTable <- function(speciesTable, speciesLayers, sppEquiv = NULL, sppEquivCol = "LandR") {
if (is.null(sppEquiv))
sppEquiv <- data.table(utils::data("sppEquivalencies_CA", package = "LandR", envir = environment()))
names(speciesTable) <- .speciesTableColNames
speciesTable[, growthcurve := as.numeric(growthcurve)]
sppEquiv <- sppEquiv[!is.na(sppEquiv[[sppEquivCol]]), ]
sppNameVector <- unique(sppEquiv[[sppEquivCol]])
speciesTable <- speciesTable[species %in% equivalentName(sppNameVector, sppEquiv, "LANDIS_traits", multi = TRUE) &
Area %in% c("BSW", "BP", "MC")]
speciesTable[, species := equivalentName(speciesTable$species, sppEquiv, sppEquivCol)]
speciesTable <- speciesTable[, lapply(.SD, function(x) {
if (is.numeric(x)) min(x, na.rm = TRUE) else x[1]
}), by = "species"]
return(speciesTable)
}
#' Change species table of parameters/traits
#'
#' Changes longevity values in the species table according to Burton & Cumming (1995).
#' Only the species and values present in Boreal Shield West (BSW), Boreal Plains (BP) and
#' Montane Cordillera (MC) \code{speciesTable$Area} are being changed.
#' All others follow Dominic Cyr and Yan Boulanger's trait values
#' (\url{https://raw.githubusercontent.com/dcyr/LANDIS-II_IA_generalUseFiles/master/speciesTraits.csv}).
#' Note that BSW and BP areas correspond more closely to the region considered in Table 2 of
#' Burton & Cumming (1995), while MC will correspond to both tables.
#'
#' @param species a \code{data.table} that has species traits such as longevity, shade tolerance, etc.
#'
#' @param speciesTable TODO: DESCRIPTION NEEDED
#'
#' @template sppEquiv
#'
#' @template sppEquivCol
#'
#' @return An updated species \code{data.table}
#'
#' @export
#' @importFrom data.table data.table
#' @rdname speciesTableUpdate
speciesTableUpdate <- function(species, speciesTable, sppEquiv, sppEquivCol) {
if (is.null(sppEquiv))
sppEquiv <- data.table(utils::data("sppEquivalencies_CA", package = "LandR", envir = environment()))
if (is.null(sppEquivCol))
stop("Please provide sppEquivCol")
names(speciesTable) <- .speciesTableColNames
## make temporary table that will have new parameters for Boreal spp.
speciesTableShort <- speciesTable[Area %in% c("BSW", "BP", "MC"), .(species, longevity, shadetolerance)]
speciesTableShort[species == "ABIE.BAL", c('longevity', 'shadetolerance') := .(200, 3)] #default 150, 5
speciesTableShort[species == "ABIE.LAS", c('longevity', 'shadetolerance') := .(240, 3)] #default 250, 4
speciesTableShort[species == "BETU.PAP", longevity := 140] #default 150
speciesTableShort[species == "LARI.LAR", longevity := 350] #default 150
speciesTableShort[species == "LARI.OCC", longevity := 450] #default 900!
speciesTableShort[species == "PICE.ENG", c('longevity', 'shadetolerance') := .(460, 3)] #default 450, 4
speciesTableShort[species == "PICE.GLA", c('longevity', 'shadetolerance') := .(400, 2)] #default 250, 3
speciesTableShort[species == "PICE.MAR", c('longevity', 'shadetolerance') := .(250, 3)] #default 200, 4
speciesTableShort[species == "PINU.BAN", longevity := 150]
speciesTableShort[species == "PINU.CON.LAT", longevity := 335] #default 300
speciesTableShort[species == "PINU.PON", longevity := 575] #default 500
speciesTableShort[species == "POPU.BAL", longevity := 200] #default 130
speciesTableShort[species == "POPU.TRE", longevity := 200] #default 150
speciesTableShort[species == "PSEU.MEN", longevity := 525] ## default 600, only in MC area, corresponding to var. glauca
speciesTableShort[species == "THUJ.PLI", longevity := 1500] ##default 700, 1500 may be incorrect for MC
speciesTableShort[species == "TSUG.HET", c('longevity', 'shadetolerance') := .(500, 4)] #default 475, 5
speciesTableShort[species == "TSUG.MER", c('longevity', 'shadetolerance') := .(800, 3)] #default 700, 4
## subset, rename and "merge" species by using the minimum value
sppEquiv <- sppEquiv[!is.na(sppEquiv[[sppEquivCol]]), ]
sppNameVector <- species$species
speciesTableShort <- speciesTableShort[species %in% equivalentName(sppNameVector, sppEquiv,
"LANDIS_traits", multi = TRUE)]
speciesTableShort[, species := equivalentName(speciesTableShort$species, sppEquiv, sppEquivCol)]
speciesTableShort <- speciesTableShort[, .(longevity = min(longevity), shadetolerance = min(shadetolerance)), by = "species"]
## join and replace
species <- species[, c("longevity", "shadetolerance") := .(speciesTableShort[, longevity], speciesTableShort[, shadetolerance])]
return(species)
}
#' Download and prepare a species traits table for use with \code{Biomass_core} module
#'
#' TODO: add detailed description
#'
#' @note This one is tailored to Canadian forests (?)
#'
#' @param url If NULL (the default), uses one from the LANDIS-II project:
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/biomass-succession_test.txt"}).
#'
#' @param dPath The destination path.
#'
#' @param cacheTags User tags to pass to \code{Cache}.
#'
#' @export
#' @importFrom data.table data.table setcolorder
#' @importFrom reproducible asPath Cache prepInputs
#'
#' @return A \code{data.table} with columns ... TODO
#'
#' @export
#' @rdname prepInputsSpecies
prepInputsSpecies <- function(url = NULL, dPath, cacheTags = NULL) {
if (is.null(url))
url <- paste0(landisIIrepo, "species.txt")
mainInput <- prepInputsMainInput(url = NULL, dPath, cacheTags) ## uses default URL
maxcol <- 13 #max(count.fields(file.path(dPath, "species.txt"), sep = ""))
species <- Cache(prepInputs,
url = url,
targetFile = "species.txt",
destinationPath = dPath,
fun = "utils::read.table",
fill = TRUE, row.names = NULL, #purge = 7,
sep = "",
header = FALSE,
blank.lines.skip = TRUE,
col.names = c(paste("col", 1:maxcol, sep = "")),
stringsAsFactors = FALSE,
overwrite = TRUE)
species <- data.table(species[, 1:11])
species <- species[col1 != "LandisData", ]
species <- species[col1 != ">>", ]
colNames <- c("species", "longevity", "sexualmature", "shadetolerance",
"firetolerance", "seeddistance_eff", "seeddistance_max",
"resproutprob", "resproutage_min", "resproutage_max",
"postfireregen")
names(species) <- colNames
species[, ':='(seeddistance_eff = gsub(",", "", seeddistance_eff),
seeddistance_max = gsub(",", "", seeddistance_max))]
# change all columns to integer
species <- species[, lapply(.SD, as.integer), .SDcols = names(species)[-c(1, NCOL(species))],
by = "species,postfireregen"]
setcolorder(species, colNames)
# get additional species traits
speciesAddon <- mainInput
startRow <- which(speciesAddon$col1 == "SpeciesParameters")
speciesAddon <- speciesAddon[(startRow + 1):(startRow + nrow(species)), 1:6, with = FALSE]
names(speciesAddon) <- c("species", "leaflongevity", "wooddecayrate",
"mortalityshape", "growthcurve", "leafLignin")
speciesAddon[, ':='(leaflongevity = as.numeric(leaflongevity),
wooddecayrate = as.numeric(wooddecayrate),
mortalityshape = as.numeric(mortalityshape),
growthcurve = as.numeric(growthcurve),
leafLignin = as.numeric(leafLignin))]
species <- setkey(species, species)[setkey(speciesAddon, species), nomatch = 0]
## TODO: use species equivalency table here
## rename species for compatibility across modules (Genu_spe)
species$species1 <- as.character(substring(species$species, 1, 4))
species$species2 <- as.character(substring(species$species, 5, 7))
species[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
substring(species1, 2, 4), "_",
species2))]
species[, ':='(species1 = NULL, species2 = NULL)]
return(species)
}
#' @export
#' @rdname prepInputsSpecies
prepInputsMainInput <- function(url = NULL, dPath, cacheTags) {
if (is.null(url))
url <- paste0("https://raw.githubusercontent.com/LANDIS-II-Foundation/",
"Extensions-Succession/master/biomass-succession-archive/",
"trunk/tests/v6.0-2.0/biomass-succession_test.txt")
maxcol <- 7L
mainInput <- Cache(prepInputs,
url = url,
targetFile = "biomass-succession_test.txt",
destinationPath = dPath,
userTags = cacheTags,
fun = "utils::read.table",
fill = TRUE, #purge = 7,
sep = "",
header = FALSE,
col.names = c(paste("col", 1:maxcol, sep = "")),
blank.lines.skip = TRUE,
stringsAsFactors = FALSE)
mainInput <- data.table(mainInput)
mainInput <- mainInput[col1 != ">>",]
return(mainInput)
}
#' Prepare ecoregion table
#'
#' Get the dummy ecoregion table from LANDIS-II examples.
#'
#' @param url If NULL (the default), uses one from the LANDIS-II project:
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/ecoregion.txt"}).
#'
#' @param dPath The destination path.
#'
#' @param cacheTags User tags to pass to \code{Cache}.
#'
#' @return A \code{data.table}
#'
#' @export
#' @importFrom data.table data.table
#' @importFrom reproducible Cache prepInputs
#' @importFrom utils count.fields
#' @rdname prepInputsEcoregion
prepInputsEcoregion <- function(url = NULL, dPath, cacheTags = NULL) {
if (is.null(url))
url <- paste0(landisIIrepo, "ecoregions.txt")
maxcol <- 5 #max(count.fields(file.path(dPath, "ecoregions.txt"), sep = ""))
ecoregion <- Cache(prepInputs,
url = url,
targetFile = "ecoregions.txt",
destinationPath = dPath,
fun = "utils::read.table",
fill = TRUE,
sep = "",
# purge = 7,
header = FALSE,
blank.lines.skip = TRUE,
stringsAsFactors = FALSE,
userTags = cacheTags)
maxcol <- max(count.fields(file.path(dPath, "ecoregions.txt"), sep = ""))
colnames(ecoregion) <- c(paste("col", 1:maxcol, sep = ""))
ecoregion <- data.table(ecoregion)
ecoregion <- ecoregion[col1 != "LandisData",]
ecoregion <- ecoregion[col1 != ">>",]
names(ecoregion)[1:4] <- c("active", "mapcode", "ecoregion", "description")
ecoregion$mapcode <- as.integer(ecoregion$mapcode)
return(ecoregion)
}
#' Prepare species ecoregion table
#'
#' Get the dummy ecoregion table from LANDIS-II examples.
#'
#' @param url If NULL (the default), uses one from the LANDIS-II project:
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/biomass-succession-dynamic-inputs_test.txt"}).
#'
#' @param dPath The destination path.
#'
#' @param cacheTags User tags to pass to \code{Cache}.
#'
#' @return A \code{data.table}
#'
#' @export
#' @importFrom data.table data.table
#' @importFrom reproducible Cache prepInputs
#' @importFrom utils count.fields
#' @rdname prepInputsSpeciesEcoregion
prepInputsSpeciesEcoregion <- function(url = NULL, dPath, cacheTags = NULL) {
if (is.null(url))
url <- paste0(landisIIrepo, "biomass-succession-dynamic-inputs_test.txt")
speciesEcoregion <- Cache(prepInputs,
url = url,
fun = "utils::read.table",
destinationPath = dPath,
targetFile = "biomass-succession-dynamic-inputs_test.txt",
fill = TRUE,
sep = "",
header = FALSE,
blank.lines.skip = TRUE,
stringsAsFactors = FALSE,
userTags = cacheTags)
maxcol <- max(count.fields(file.path(dPath, "biomass-succession-dynamic-inputs_test.txt"),
sep = ""))
colnames(speciesEcoregion) <- paste("col", 1:maxcol, sep = "")
speciesEcoregion <- data.table(speciesEcoregion)
speciesEcoregion <- speciesEcoregion[col1 != "LandisData",]
speciesEcoregion <- speciesEcoregion[col1 != ">>",]
keepColNames <- c("year", "ecoregion", "species", "establishprob", "maxANPP", "maxB")
names(speciesEcoregion)[1:6] <- keepColNames
speciesEcoregion <- speciesEcoregion[, keepColNames, with = FALSE]
integerCols <- c("year", "establishprob", "maxANPP", "maxB")
speciesEcoregion[, (integerCols) := lapply(.SD, as.integer), .SDcols = integerCols]
## TODO: use species equivalency table here
## rename species for compatibility across modules (Genu_spe)
speciesEcoregion$species1 <- as.character(substring(speciesEcoregion$species, 1, 4))
speciesEcoregion$species2 <- as.character(substring(speciesEcoregion$species, 5, 7))
speciesEcoregion[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
substring(species1, 2, 4), "_", species2))]
speciesEcoregion[, ':='(species1 = NULL, species2 = NULL)]
return(speciesEcoregion)
}
PredictiveEcology/LandR documentation built on Jan. 24, 2021, 12:52 a.m.
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Defines functions speciesTableUpdate prepSpeciesTable getSpeciesTable
Documented in getSpeciesTable prepSpeciesTable speciesTableUpdate
utils::globalVariables(c(
":=", ".SD", "Area", "col1", "growthcurve", "leafLignin", "leaflongevity", "mortalityshape",
"seeddistance_eff", "seeddistance_max", "species", "species1", "species2", "wooddecayrate"
))
#' Default LANDIS-II project repo url
#'
#' @keywords internal
landisIIrepo <- paste0("https://raw.githubusercontent.com/LANDIS-II-Foundation/",
"Extensions-Succession/master/biomass-succession-archive/",
"trunk/tests/v6.0-2.0/")
#' Download and prepare a species traits table for use with \code{Biomass_core} module
#'
#' TODO: add detailed description
#'
#' @note This one is tailored to Canadian forests (?)
#'
#' @param url If NULL (the default), uses one from D. Cyr's LANDIS-II files:
#' \url{https://github.com/dcyr/LANDIS-II_IA_generalUseFiles/master/speciesTraits.csv}).
#'
#' @param dPath The destination path.
#'
#' @param cacheTags User tags to pass to \code{Cache}.
#'
#' @export
#' @importFrom data.table data.table
#' @importFrom magrittr %>%
#' @importFrom reproducible asPath Cache prepInputs
#' @rdname speciesTable
getSpeciesTable <- function(url = NULL, dPath = tempdir(), cacheTags = NULL) {
if (is.null(url))
url <- paste0("https://raw.githubusercontent.com/",
"dcyr/LANDIS-II_IA_generalUseFiles/",
"master/speciesTraits.csv")
speciesTable <- Cache(prepInputs, "speciesTraits.csv",
destinationPath = asPath(dPath),
url = url,
fun = "utils::read.csv",
header = TRUE, stringsAsFactors = FALSE,
userTags = c(cacheTags, "speciesTable")) %>%
data.table()
return(speciesTable)
}
#' Species Table Column Names
#'
#' @keywords internal
.speciesTableColNames <- c("species", "Area", "longevity", "sexualmature", "shadetolerance",
"firetolerance", "seeddistance_eff", "seeddistance_max", "resproutprob",
"resproutage_min", "resproutage_max", "postfireregen", "leaflongevity",
"wooddecayrate", "mortalityshape", "growthcurve", "leafLignin",
"hardsoft")
#' @param speciesTable A raw species traits table
#'
#' @param speciesLayers stack of species layers rasters
#'
#' @template sppEquiv
#'
#' @template sppEquivCol
#'
#' @return A \code{data.table} with columns ... TODO
#'
#' @export
#' @rdname speciesTable
prepSpeciesTable <- function(speciesTable, speciesLayers, sppEquiv = NULL, sppEquivCol = "LandR") {
if (is.null(sppEquiv))
sppEquiv <- data.table(utils::data("sppEquivalencies_CA", package = "LandR", envir = environment()))
names(speciesTable) <- .speciesTableColNames
speciesTable[, growthcurve := as.numeric(growthcurve)]
sppEquiv <- sppEquiv[!is.na(sppEquiv[[sppEquivCol]]), ]
sppNameVector <- unique(sppEquiv[[sppEquivCol]])
speciesTable <- speciesTable[species %in% equivalentName(sppNameVector, sppEquiv, "LANDIS_traits", multi = TRUE) &
Area %in% c("BSW", "BP", "MC")]
speciesTable[, species := equivalentName(speciesTable$species, sppEquiv, sppEquivCol)]
speciesTable <- speciesTable[, lapply(.SD, function(x) {
if (is.numeric(x)) min(x, na.rm = TRUE) else x[1]
}), by = "species"]
return(speciesTable)
}
#' Change species table of parameters/traits
#'
#' Changes longevity values in the species table according to Burton & Cumming (1995).
#' Only the species and values present in Boreal Shield West (BSW), Boreal Plains (BP) and
#' Montane Cordillera (MC) \code{speciesTable$Area} are being changed.
#' All others follow Dominic Cyr and Yan Boulanger's trait values
#' (\url{https://raw.githubusercontent.com/dcyr/LANDIS-II_IA_generalUseFiles/master/speciesTraits.csv}).
#' Note that BSW and BP areas correspond more closely to the region considered in Table 2 of
#' Burton & Cumming (1995), while MC will correspond to both tables.
#'
#' @param species a \code{data.table} that has species traits such as longevity, shade tolerance, etc.
#'
#' @param speciesTable TODO: DESCRIPTION NEEDED
#'
#' @template sppEquiv
#'
#' @template sppEquivCol
#'
#' @return An updated species \code{data.table}
#'
#' @export
#' @importFrom data.table data.table
#' @rdname speciesTableUpdate
speciesTableUpdate <- function(species, speciesTable, sppEquiv, sppEquivCol) {
if (is.null(sppEquiv))
sppEquiv <- data.table(utils::data("sppEquivalencies_CA", package = "LandR", envir = environment()))
if (is.null(sppEquivCol))
stop("Please provide sppEquivCol")
names(speciesTable) <- .speciesTableColNames
## make temporary table that will have new parameters for Boreal spp.
speciesTableShort <- speciesTable[Area %in% c("BSW", "BP", "MC"), .(species, longevity, shadetolerance)]
speciesTableShort[species == "ABIE.BAL", c('longevity', 'shadetolerance') := .(200, 3)] #default 150, 5
speciesTableShort[species == "ABIE.LAS", c('longevity', 'shadetolerance') := .(240, 3)] #default 250, 4
speciesTableShort[species == "BETU.PAP", longevity := 140] #default 150
speciesTableShort[species == "LARI.LAR", longevity := 350] #default 150
speciesTableShort[species == "LARI.OCC", longevity := 450] #default 900!
speciesTableShort[species == "PICE.ENG", c('longevity', 'shadetolerance') := .(460, 3)] #default 450, 4
speciesTableShort[species == "PICE.GLA", c('longevity', 'shadetolerance') := .(400, 2)] #default 250, 3
speciesTableShort[species == "PICE.MAR", c('longevity', 'shadetolerance') := .(250, 3)] #default 200, 4
speciesTableShort[species == "PINU.BAN", longevity := 150]
speciesTableShort[species == "PINU.CON.LAT", longevity := 335] #default 300
speciesTableShort[species == "PINU.PON", longevity := 575] #default 500
speciesTableShort[species == "POPU.BAL", longevity := 200] #default 130
speciesTableShort[species == "POPU.TRE", longevity := 200] #default 150
speciesTableShort[species == "PSEU.MEN", longevity := 525] ## default 600, only in MC area, corresponding to var. glauca
speciesTableShort[species == "THUJ.PLI", longevity := 1500] ##default 700, 1500 may be incorrect for MC
speciesTableShort[species == "TSUG.HET", c('longevity', 'shadetolerance') := .(500, 4)] #default 475, 5
speciesTableShort[species == "TSUG.MER", c('longevity', 'shadetolerance') := .(800, 3)] #default 700, 4
## subset, rename and "merge" species by using the minimum value
sppEquiv <- sppEquiv[!is.na(sppEquiv[[sppEquivCol]]), ]
sppNameVector <- species$species
speciesTableShort <- speciesTableShort[species %in% equivalentName(sppNameVector, sppEquiv,
"LANDIS_traits", multi = TRUE)]
speciesTableShort[, species := equivalentName(speciesTableShort$species, sppEquiv, sppEquivCol)]
speciesTableShort <- speciesTableShort[, .(longevity = min(longevity), shadetolerance = min(shadetolerance)), by = "species"]
## join and replace
species <- species[, c("longevity", "shadetolerance") := .(speciesTableShort[, longevity], speciesTableShort[, shadetolerance])]
return(species)
}
#' Download and prepare a species traits table for use with \code{Biomass_core} module
#'
#' TODO: add detailed description
#'
#' @note This one is tailored to Canadian forests (?)
#'
#' @param url If NULL (the default), uses one from the LANDIS-II project:
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/biomass-succession_test.txt"}).
#'
#' @param dPath The destination path.
#'
#' @param cacheTags User tags to pass to \code{Cache}.
#'
#' @export
#' @importFrom data.table data.table setcolorder
#' @importFrom reproducible asPath Cache prepInputs
#'
#' @return A \code{data.table} with columns ... TODO
#'
#' @export
#' @rdname prepInputsSpecies
prepInputsSpecies <- function(url = NULL, dPath, cacheTags = NULL) {
if (is.null(url))
url <- paste0(landisIIrepo, "species.txt")
mainInput <- prepInputsMainInput(url = NULL, dPath, cacheTags) ## uses default URL
maxcol <- 13 #max(count.fields(file.path(dPath, "species.txt"), sep = ""))
species <- Cache(prepInputs,
url = url,
targetFile = "species.txt",
destinationPath = dPath,
fun = "utils::read.table",
fill = TRUE, row.names = NULL, #purge = 7,
sep = "",
header = FALSE,
blank.lines.skip = TRUE,
col.names = c(paste("col", 1:maxcol, sep = "")),
stringsAsFactors = FALSE,
overwrite = TRUE)
species <- data.table(species[, 1:11])
species <- species[col1 != "LandisData", ]
species <- species[col1 != ">>", ]
colNames <- c("species", "longevity", "sexualmature", "shadetolerance",
"firetolerance", "seeddistance_eff", "seeddistance_max",
"resproutprob", "resproutage_min", "resproutage_max",
"postfireregen")
names(species) <- colNames
species[, ':='(seeddistance_eff = gsub(",", "", seeddistance_eff),
seeddistance_max = gsub(",", "", seeddistance_max))]
# change all columns to integer
species <- species[, lapply(.SD, as.integer), .SDcols = names(species)[-c(1, NCOL(species))],
by = "species,postfireregen"]
setcolorder(species, colNames)
# get additional species traits
speciesAddon <- mainInput
startRow <- which(speciesAddon$col1 == "SpeciesParameters")
speciesAddon <- speciesAddon[(startRow + 1):(startRow + nrow(species)), 1:6, with = FALSE]
names(speciesAddon) <- c("species", "leaflongevity", "wooddecayrate",
"mortalityshape", "growthcurve", "leafLignin")
speciesAddon[, ':='(leaflongevity = as.numeric(leaflongevity),
wooddecayrate = as.numeric(wooddecayrate),
mortalityshape = as.numeric(mortalityshape),
growthcurve = as.numeric(growthcurve),
leafLignin = as.numeric(leafLignin))]
species <- setkey(species, species)[setkey(speciesAddon, species), nomatch = 0]
## TODO: use species equivalency table here
## rename species for compatibility across modules (Genu_spe)
species$species1 <- as.character(substring(species$species, 1, 4))
species$species2 <- as.character(substring(species$species, 5, 7))
species[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
substring(species1, 2, 4), "_",
species2))]
species[, ':='(species1 = NULL, species2 = NULL)]
return(species)
}
#' @export
#' @rdname prepInputsSpecies
prepInputsMainInput <- function(url = NULL, dPath, cacheTags) {
if (is.null(url))
url <- paste0("https://raw.githubusercontent.com/LANDIS-II-Foundation/",
"Extensions-Succession/master/biomass-succession-archive/",
"trunk/tests/v6.0-2.0/biomass-succession_test.txt")
maxcol <- 7L
mainInput <- Cache(prepInputs,
url = url,
targetFile = "biomass-succession_test.txt",
destinationPath = dPath,
userTags = cacheTags,
fun = "utils::read.table",
fill = TRUE, #purge = 7,
sep = "",
header = FALSE,
col.names = c(paste("col", 1:maxcol, sep = "")),
blank.lines.skip = TRUE,
stringsAsFactors = FALSE)
mainInput <- data.table(mainInput)
mainInput <- mainInput[col1 != ">>",]
return(mainInput)
}
#' Prepare ecoregion table
#'
#' Get the dummy ecoregion table from LANDIS-II examples.
#'
#' @param url If NULL (the default), uses one from the LANDIS-II project:
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/ecoregion.txt"}).
#'
#' @param dPath The destination path.
#'
#' @param cacheTags User tags to pass to \code{Cache}.
#'
#' @return A \code{data.table}
#'
#' @export
#' @importFrom data.table data.table
#' @importFrom reproducible Cache prepInputs
#' @importFrom utils count.fields
#' @rdname prepInputsEcoregion
prepInputsEcoregion <- function(url = NULL, dPath, cacheTags = NULL) {
if (is.null(url))
url <- paste0(landisIIrepo, "ecoregions.txt")
maxcol <- 5 #max(count.fields(file.path(dPath, "ecoregions.txt"), sep = ""))
ecoregion <- Cache(prepInputs,
url = url,
targetFile = "ecoregions.txt",
destinationPath = dPath,
fun = "utils::read.table",
fill = TRUE,
sep = "",
# purge = 7,
header = FALSE,
blank.lines.skip = TRUE,
stringsAsFactors = FALSE,
userTags = cacheTags)
maxcol <- max(count.fields(file.path(dPath, "ecoregions.txt"), sep = ""))
colnames(ecoregion) <- c(paste("col", 1:maxcol, sep = ""))
ecoregion <- data.table(ecoregion)
ecoregion <- ecoregion[col1 != "LandisData",]
ecoregion <- ecoregion[col1 != ">>",]
names(ecoregion)[1:4] <- c("active", "mapcode", "ecoregion", "description")
ecoregion$mapcode <- as.integer(ecoregion$mapcode)
return(ecoregion)
}
#' Prepare species ecoregion table
#'
#' Get the dummy ecoregion table from LANDIS-II examples.
#'
#' @param url If NULL (the default), uses one from the LANDIS-II project:
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/biomass-succession-dynamic-inputs_test.txt"}).
#'
#' @param dPath The destination path.
#'
#' @param cacheTags User tags to pass to \code{Cache}.
#'
#' @return A \code{data.table}
#'
#' @export
#' @importFrom data.table data.table
#' @importFrom reproducible Cache prepInputs
#' @importFrom utils count.fields
#' @rdname prepInputsSpeciesEcoregion
prepInputsSpeciesEcoregion <- function(url = NULL, dPath, cacheTags = NULL) {
if (is.null(url))
url <- paste0(landisIIrepo, "biomass-succession-dynamic-inputs_test.txt")
speciesEcoregion <- Cache(prepInputs,
url = url,
fun = "utils::read.table",
destinationPath = dPath,
targetFile = "biomass-succession-dynamic-inputs_test.txt",
fill = TRUE,
sep = "",
header = FALSE,
blank.lines.skip = TRUE,
stringsAsFactors = FALSE,
userTags = cacheTags)
maxcol <- max(count.fields(file.path(dPath, "biomass-succession-dynamic-inputs_test.txt"),
sep = ""))
colnames(speciesEcoregion) <- paste("col", 1:maxcol, sep = "")
speciesEcoregion <- data.table(speciesEcoregion)
speciesEcoregion <- speciesEcoregion[col1 != "LandisData",]
speciesEcoregion <- speciesEcoregion[col1 != ">>",]
keepColNames <- c("year", "ecoregion", "species", "establishprob", "maxANPP", "maxB")
names(speciesEcoregion)[1:6] <- keepColNames
speciesEcoregion <- speciesEcoregion[, keepColNames, with = FALSE]
integerCols <- c("year", "establishprob", "maxANPP", "maxB")
speciesEcoregion[, (integerCols) := lapply(.SD, as.integer), .SDcols = integerCols]
## TODO: use species equivalency table here
## rename species for compatibility across modules (Genu_spe)
speciesEcoregion$species1 <- as.character(substring(speciesEcoregion$species, 1, 4))
speciesEcoregion$species2 <- as.character(substring(speciesEcoregion$species, 5, 7))
speciesEcoregion[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
substring(species1, 2, 4), "_", species2))]
speciesEcoregion[, ':='(species1 = NULL, species2 = NULL)]
return(speciesEcoregion)
}
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