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Download the latest version of the ITRDB, and extract given parameters.

Source: R/ITRDB_FUNCTIONS.R
get_itrdb.Rd

get_itrdb returns a named list of length 3:

  1. 'metadata': A data frame or Simple Feature (if makeSpatial==TRUE) of the locations and names of extracted ITRDB chronologies,

  2. 'widths': A matrix of tree-ring widths/densities given user selection, and

  3. 'depths': A matrix of tree-ring sample depths.

Usage

get_itrdb(
  template = NULL,
  label = NULL,
  recon.years = NULL,
  calib.years = NULL,
  species = NULL,
  measurement.type = NULL,
  chronology.type = NULL,
  raw.dir = paste0(tempdir(), "/FedData/raw/itrdb"),
  extraction.dir = ifelse(!is.null(label), paste0(tempdir(),
    "/FedData/extractions/itrdb/", label, "/"), paste0(tempdir(),
    "/FedData/extractions/itrdb")),
  force.redo = FALSE
)

Arguments

template

An Simple Feature or SpatRaster object to serve as a template for cropping. If missing, all available global chronologies are returned.

label

A character string naming the study area.

recon.years

A numeric vector of years over which reconstructions are needed; if missing, the union of all years in the available chronologies are given.

calib.years

A numeric vector of all required years—chronologies without these years will be discarded; if missing, all available chronologies are given.

species

A character vector of 4-letter tree species identifiers; if missing, all available chronologies are given.

measurement.type

A character vector of measurement type identifiers. Options include:

  • 'Total Ring Density'

  • 'Earlywood Width'

  • 'Earlywood Density'

  • 'Latewood Width'

  • 'Minimum Density'

  • 'Ring Width'

  • 'Latewood Density'

  • 'Maximum Density'

  • 'Latewood Percent'

if missing, all available chronologies are given.

chronology.type

A character vector of chronology type identifiers. Options include:

  • 'ARSTND'

  • 'Low Pass Filter'

  • 'Residual'

  • 'Standard'

  • 'Re-Whitened Residual'

  • 'Measurements Only'

if missing, all available chronologies are given.

raw.dir

A character string indicating where raw downloaded files should be put. The directory will be created if missing.

extraction.dir

A character string indicating where the extracted and cropped ITRDB dataset should be put. The directory will be created if missing.

force.redo

If an extraction already exists, should a new one be created? Defaults to FALSE.

Value

A named list containing the 'metadata', 'widths', and 'depths' data.

Examples

if (FALSE) { # \dontrun{
# Get the ITRDB records
ITRDB <- get_itrdb(
  template = FedData::meve,
  label = "meve"
)

# Plot the VEP polygon
plot(meve)

# Map the locations of the tree ring chronologies
plot(ITRDB$metadata$geometry, pch = 1, add = TRUE)
legend("bottomleft", pch = 1, legend = "ITRDB chronologies")
} # }