Run a single iteration of RoC estimation

A single run is computed following these steps:

Subset levels into each bin to define Working Units.
Optionally standardise assemblage counts in each WU.
Calculate dissimilarity between consecutive WUs.
Standardise dissimilarity by age difference 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,
  silent = FALSE
)

Arguments

data_source_run

list with data and bins prepared by prepare_data().

bin_selection

character. Rule for selecting one level from each bin.

"random" (default) - a level is selected at random.
"first" - the level closest to the start of the bin is selected.

standardise

logical. If TRUE, assemblage counts in each WU are rarefied to n_individuals before dissimilarity is computed.

n_individuals

numeric. Number of individuals to rarefy to when standardise = TRUE. Automatically reduced to the smallest count in the sequence if any WU has fewer individuals.

tranform_to_proportions

logical. If TRUE (default), community data are converted to proportions before dissimilarity is computed.

dissimilarity_coefficient

character. Dissimilarity coefficient used to compare consecutive WUs. See vegan::vegdist() for details.

"euc" - Euclidean distance
"euc.sd" - standardised Euclidean distance
"chord" - Chord distance
"chisq" - Chi-squared coefficient
"gower" - Gower's distance
"bray" - Bray-Curtis dissimilarity

time_standardisation

numeric. Time unit for RoC values. RoC is reported as dissimilarity per time_standardisation years. Defaults to bin_size when NULL.

verbose

logical. If TRUE, print progress messages during computation.

silent

logical. If TRUE, suppress all console output (overrides verbose).

Value

A tibble with one row per WU pair containing columns Age, ROC, ROC_up, ROC_dw, and Working_Unit.

Usage

Arguments

Value

See also