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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

# \donttest{
# Get the ITRDB records
ITRDB <- get_itrdb(template = FedData::meve, 
label = "meve")
#> Downloading file: https://www.ncei.noaa.gov/pub/data/paleo/treering/chronologies/itrdb-v713-africa-crn.zip
#> Downloading file: https://www.ncei.noaa.gov/pub/data/paleo/treering/chronologies/itrdb-v713-asia-crn.zip
#> Downloading file: https://www.ncei.noaa.gov/pub/data/paleo/treering/chronologies/itrdb-v713-australia-crn.zip
#> Downloading file: https://www.ncei.noaa.gov/pub/data/paleo/treering/chronologies/itrdb-v713-canada-crn.zip
#> Downloading file: https://www.ncei.noaa.gov/pub/data/paleo/treering/chronologies/itrdb-v713-europe-crn.zip
#> Downloading file: https://www.ncei.noaa.gov/pub/data/paleo/treering/chronologies/itrdb-v713-mexico-crn.zip
#> Downloading file: https://www.ncei.noaa.gov/pub/data/paleo/treering/chronologies/itrdb-v713-southamerica-crn.zip
#> Downloading file: https://www.ncei.noaa.gov/pub/data/paleo/treering/chronologies/itrdb-v713-usa-crn.zip
#> Extracting chronology data from ITRDB version 713 dated 2024-11-07
#> Extracting chronology data from 85 files in /tmp/RtmpYzxfyX/FedData/raw/itrdb/./itrdb-v713-africa-crn.zip
#> Extracting chronology data from 1357 files in /tmp/RtmpYzxfyX/FedData/raw/itrdb/./itrdb-v713-asia-crn.zip
#> 1 file(s) couldn't be extracted:
#> mong015.crn
#> File(s) likely malformed!
#> Extracting chronology data from 192 files in /tmp/RtmpYzxfyX/FedData/raw/itrdb/./itrdb-v713-australia-crn.zip
#> 2 file(s) couldn't be extracted:
#> newz103.crn
#> newz115.crn
#> File(s) likely malformed!
#> Extracting chronology data from 901 files in /tmp/RtmpYzxfyX/FedData/raw/itrdb/./itrdb-v713-canada-crn.zip
#> Extracting chronology data from 1994 files in /tmp/RtmpYzxfyX/FedData/raw/itrdb/./itrdb-v713-europe-crn.zip
#> 25 file(s) couldn't be extracted:
#> bulg001.crn
#> bulg001e.crn
#> bulg001l.crn
#> bulg001n.crn
#> bulg001p.crn
#> bulg001x.crn
#> gree001.crn
#> gree001e.crn
#> gree001l.crn
#> gree001n.crn
#> gree001p.crn
#> gree001x.crn
#> gree005.crn
#> gree005e.crn
#> gree005l.crn
#> gree005n.crn
#> gree005p.crn
#> gree005x.crn
#> ital015.crn
#> ital015e.crn
#> ital015l.crn
#> ital015n.crn
#> ital015p.crn
#> ital015x.crn
#> swed318.crn
#> File(s) likely malformed!
#> Extracting chronology data from 246 files in /tmp/RtmpYzxfyX/FedData/raw/itrdb/./itrdb-v713-mexico-crn.zip
#> 1 file(s) couldn't be extracted:
#> mexi037la.crn
#> File(s) likely malformed!
#> Extracting chronology data from 346 files in /tmp/RtmpYzxfyX/FedData/raw/itrdb/./itrdb-v713-southamerica-crn.zip
#> Extracting chronology data from 3172 files in /tmp/RtmpYzxfyX/FedData/raw/itrdb/./itrdb-v713-usa-crn.zip
#> 41 file(s) couldn't be extracted:
#> ar081a.crn
#> co076l.crn
#> co573e_crns.crn
#> co573l_crns.crn
#> co573n_crns.crn
#> co573p_crns.crn
#> co573w_crns.crn
#> co573x_crns.crn
#> co575e_crns.crn
#> co575l_crns.crn
#> co575n_crns.crn
#> co575p_crns.crn
#> co575w_crns.crn
#> co575x_crns.crn
#> co577e_crns.crn
#> co577l_crns.crn
#> co577n_crns.crn
#> co577p_crns.crn
#> co577w_crns.crn
#> co577x_crns.crn
#> co619.crn
#> mt115.crn
#> mt115e.crn
#> mt115ea.crn
#> mt115er.crn
#> mt115l.crn
#> mt115la.crn
#> mt115lr.crn
#> mt115n.crn
#> mt115na.crn
#> mt115nr.crn
#> mt115x.crn
#> mt115xa.crn
#> mt115xr.crn
#> or081.crn
#> or081a.crn
#> or081r.crn
#> sc004.crn
#> tx054.crn
#> tx054a.crn
#> tx054r.crn
#> File(s) likely malformed!
#> 
#> ── Column specification ────────────────────────────────────────────────────────
#> cols(
#>   SERIES = col_character(),
#>   NAME = col_character(),
#>   SPECIES = col_character(),
#>   MEASUREMENT_TYPE = col_character(),
#>   CHRONOLOGY_TYPE = col_character(),
#>   ELEVATION = col_character(),
#>   LAT = col_double(),
#>   LON = col_double(),
#>   START = col_double(),
#>   END = col_double(),
#>   CONTRIBUTOR = col_character(),
#>   FILE = col_character()
#> )
#> Warning: attribute variables are assumed to be spatially constant throughout all geometries

# 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")

# }