run_iteration: Run a single interation of RoC estimation

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

Run a single interation of RoC estimation

Description

A single run is computed following the simple steps:

• Subsetting levels in each bin: Here the working units (WU) are defined

• Standardisation of assemblage data in each WU

• Calculation of calculated as the dissimilarity coefficient (dissimilarity_coefficient)

• Calculation of RoC between WUs: RoC is calculated as (dissimilarity_coefficient) standardised by age differences between WUs.

Usage

run_iteration(
  data_source_run,
  bin_selection = "first",
  standardise = FALSE,
  n_individuals = 150,
  tranform_to_proportions = TRUE,
  dissimilarity_coefficient = "euc",
  time_standardisation = 500,
  verbose = FALSE
)

Arguments

data_source_run	List with data and bins prepared by prepare_data
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.
tranform_to_proportions	Logical. Should the community data be transformed to a proportion during calculations?
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
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.