fc_estimate_RoC: RRatepol: Estimate rate of change

In HOPE-UIB-BIO/R-Ratepol-package: R-Ratepol: Estimating Rate of Change in Temporal Sequences

RRatepol: Estimate rate of change

Description

This function was deprecated, please use estimate_roc().

Usage

fc_estimate_RoC(
  data_source_community,
  data_source_age,
  age_uncertainty = NULL,
  smooth_method = c("none", "m.avg", "grim", "age.w", "shep"),
  smooth_n_points = 5,
  smooth_N_points = lifecycle::deprecated(),
  smooth_age_range = 500,
  smooth_n_max = 9,
  smooth_N_max = lifecycle::deprecated(),
  working_units = c("levels", "bins", "MW"),
  Working_Units = lifecycle::deprecated(),
  bin_size = 500,
  number_of_shifts = 5,
  Number_of_shifts = lifecycle::deprecated(),
  bin_selection = c("random", "first"),
  standardise = FALSE,
  n_individuals = 150,
  N_individuals = lifecycle::deprecated(),
  dissimilarity_coefficient = c("euc", "euc.sd", "chord", "chisq", "gower", "bray"),
  DC = lifecycle::deprecated(),
  tranform_to_proportions = TRUE,
  rand = NULL,
  use_parallel = FALSE,
  interest_threshold = NULL,
  time_standardisation = NULL,
  verbose = FALSE
)

Arguments

data_source_community	Data.frame. Community data with species as columns and levels (samples) as rows. First column should be sample_id (character).
data_source_age	Data.frame with two columns: sample_id - unique ID of each level (character) age - age of level (numeric)
age_uncertainty	Usage of age uncertainty form Age-depth models. Either: matrix with number of columns as number of samples. Each column is one sample, each row is one age sequence from age-depth model. Age sequence is randomly sampled from age-depth model uncertainties at the beginning of each run. NULL - Age uncertainties are not available and, therefore, will not be used.
smooth_method	Character. type of smoothing applied for the each of the pollen type "none" - Pollen data is not smoothed "m.avg" - Moving average "grim" - Grimm's smoothing ⁠"age.w""⁠ - Age-weighted average "shep" - Shepard's 5-term filter
smooth_n_points	Numeric. Number of points for used for moving average, Grimm and Age-Weighted smoothing (odd number)
smooth_N_points	smooth_N_points is no longer supported; please use smooth_n_points
smooth_age_range	Numeric. Maximal age range for both Grimm and Age-weight smoothing
smooth_n_max	Numeric. Maximal number of samples to look in Grimm smoothing
smooth_N_max	smooth_N_max is no longer supported; please use smooth_n_max
working_units	Character. Selection of units that the dissimilarity_coefficient will be calculated between. "levels" - individual levels are going to be used "bins" - samples in predefined bins will be pooled together and one sample will be selected from each time bin as a representation. "MW" - Bins of selected size are created, starting from the beginning of the core. This is repeated many times, with each time bin (window) shifting by Z years forward. This is repeated X times, where X = bin size / Z.
Working_Units	Working_Units is no longer supported; please use working_units
bin_size	Numeric. Size of the time bin (in years)
number_of_shifts	Numeric. Value determining the number of shifts of window used in Moving window method
Number_of_shifts	Number_of_shifts is no longer supported; please use number_of_shifts
bin_selection	Character. Setting determining the the process of selection of samples from bins. "first" - sample closest to the beginning of the bin is selected as a representation. "random" - a random sample is selected as a representation.
standardise	Logical. If standardise == TRUE, then standardise each Working Unit to certain number of individuals (using random resampling without repetition)
n_individuals	Numeric. Number of grain to perform standardisation to. The N_individual is automatically adjusted to the smallest number of pollen grains in sequence.
N_individuals	N_individuals is no longer supported; please use n_individuals
dissimilarity_coefficient	Character. Dissimilarity coefficient. Type of calculation of differences between Working Units. See vegan::vegdist for more details. "euc" - Euclidean distance "euc.sd" - Standardised Euclidean distance "chord" - Chord distance "chisq" - Chi-squared coefficient "gower" - Gower's distance "bray" - Bray-Curtis distance
DC	DC is no longer supported; please use dissimilarity_coefficient
tranform_to_proportions	Logical. Should the community data be transformed to a proportion during calculations?
rand	Numeric. Number of runs used in randomisation.
use_parallel	Preference of usage of parallel computation of randomisation ⁠[value]⁠ - selected number of cores TRUE - automatically selected number of cores FALSE - does not use parallel computation (only single core)
interest_threshold	Numeric. Optional. Age, after which all results of RoC are excluded.
time_standardisation	Numeric. Units scaling for result RoC values. For example, if time_standardisation = 100, the RoC will be reported as dissimilarity per 100 yr.
verbose	Logical. If TRUE, function will output messages about internal processes

See Also

estimate_roc()

HOPE-UIB-BIO/R-Ratepol-package documentation built on March 6, 2024, 7:10 a.m.