crestObj: Create a 'crestObj' object.

In mchevalier2/crestr: A Probabilistic Approach to Reconstruct Past Climates Using Palaeoecological Datasets

Create a crestObj object.

Description

Creates a crestObj object with all default parameters.

Usage

crestObj(
  taxa.name,
  taxaType,
  climate,
  pse = NA,
  dbname = NA,
  continents = NA,
  countries = NA,
  basins = NA,
  sectors = NA,
  realms = NA,
  biomes = NA,
  ecoregions = NA,
  xmn = NA,
  xmx = NA,
  ymn = NA,
  ymx = NA,
  elev_min = NA,
  elev_max = NA,
  elev_range = NA,
  year_min = 1900,
  year_max = 2021,
  nodate = TRUE,
  type_of_obs = c(1, 2, 3, 8, 9),
  df = NA,
  x = NA,
  x.name = "",
  minGridCells = 20,
  weightedPresences = FALSE,
  bin_width = NA,
  shape = NA,
  npoints = 200,
  geoWeighting = TRUE,
  climateSpaceWeighting = TRUE,
  climateSpaceWeighting.type = "linear",
  climateWithObs = FALSE,
  selectedTaxa = NA,
  distributions = NA,
  presenceThreshold = 0,
  taxWeight = "normalisation",
  uncertainties = c(0.5, 0.95)
)

Arguments

taxa.name	A vector that contains the names of the taxa to study.
taxaType	A numerical index (between 1 and 6) to define the type of palaeoproxy used: 1 for plants, 2 for beetles, 3 for chironomids, 4 for foraminifers, 5 for diatoms and 6 for rodents. The example dataset uses taxaType=0 (pseudo-data). Default is 1.
climate	A vector of the climate variables to extract. See accClimateVariables for the list of accepted values.
pse	A pollen-Species equivalency table. See createPSE for details.
dbname	The name of the data source database.
continents	A vector of the continent names defining the study area.
countries	A vector of the country names defining the study area.
basins	A vector of the ocean names defining the study area.
sectors	A vector of the marine sector names defining the study area.
realms	A vector of the studied botanical realms defining the study area.
biomes	A vector of the studied botanical biomes defining the study area.
ecoregions	A vector of the studied botanical ecoregions defining the study area.
xmn, xmx, ymn, ymx	The coordinates defining the study area.
elev_min, elev_max	Parameters to only selected grid cells with an elevation higher than elev_min or lower than elev_max (default is 'NA ).
elev_range	Parameters discard the grid cell with a high elevation range (default is NA).
year_min, year_max	The oldest and youngest occurrences accepted (default is 1900-2021).
nodate	A boolean to accept occurrences without a date (can overlap with occurrences with a date; default TRUE).
type_of_obs	The type of observation to use in the study. 1: human observation, 2: observation, 3: preserved specimen, 4: living specimen, 5: fossil specimen, 6: material sample, 7: machine observation, 8: literature, 9: unknown (Default c(1, 2, 3, 8, 9))
df	A data frame containing the data to reconstruct (counts, percentages or presence/absence data).
x	The name, age or depth of the rows of df (the samples).
x.name	A string describing the x axis (e.g. 'Sample Name', 'Age', 'Depth').
minGridCells	The minimum number of unique presence data necessary to estimate a species' climate response. Default is 20.
weightedPresences	A boolean to indicate whether the presence records should be weighted. Default is FALSE.
bin_width	The width of the bins used to correct for unbalanced climate state. Use values that split the studied climate gradient in 15-25 classes (e.g. 2°C for temperature variables). Default is 1.
shape	The imposed shape of the species pdfs. We recommend using 'normal' for temperature variables and 'lognormal' for the variables that can only take positive values, such as precipitation or aridity. Default is 'normal' for all.
npoints	The number of points to be used to fit the pdfs. Default 200.
geoWeighting	A boolean to indicate if the species should be weighting by the square root of their extension when estimating a genus/family level taxon-climate relationships.
climateSpaceWeighting	A boolean to indicate if the species pdfs should be corrected for the modern distribution of the climate space (default TRUE).
climateSpaceWeighting.type	A correction factor for the clame space weighting correction to limit the edge effects. Either 'linear' (default), 'sqrt' or 'log'.
climateWithObs	A boolean to indicate whether all climate values from the calibration dataset be included (FALSE, default) or only the climate values that corresponds to proxy observations (TRUE). Only useful in if the climate space weighting is activated.
selectedTaxa	A data frame assigns which taxa should be used for each variable (1 if the taxon should be used, 0 otherwise). The colnames should be the climate variables' names and the rownames the taxa names. Default is 1 for all taxa and all variables.
distributions	A dataframe containing the presence records of the studied proxies and their associated climate values.
presenceThreshold	All values above that threshold will be used in the reconstruction (e.g. if set at 1, all percentages below 1 will be set to 0 and the associated presences discarded). Default is 0.
taxWeight	One value among the following: 'originalData', 'presence/absence', 'percentages' or 'normalisation' (default).
uncertainties	A (vector of) threshold value(s) indicating the error bars that should be calculated (default both 50 and 95% ranges).

Value

A crestObj object that is used to store data and information for reconstructing climate

See Also

See vignette('technicalities') for details about the structure of the object. See also https://gbif.github.io/parsers/apidocs/org/gbif/api/vocabulary/BasisOfRecord.html for a detailed explanation of the types of observation.

mchevalier2/crestr documentation built on Feb. 14, 2025, 6:31 p.m.