Estimate rate of change (deprecated)

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 taxa as columns and samples as rows. The first column must be named sample_id (character).

data_source_age

data.frame with two columns:

sample_id - unique identifier of each level (character)
age - age of the level (numeric)

age_uncertainty

Optional age-uncertainty matrix from an age-depth model. Either:

A matrix with one column per sample and one row per age sequence drawn from a posterior age-depth model. One row is randomly selected at the start of each randomisation run.
NULL (default) - age uncertainties are not used.

smooth_method

character. Smoothing method applied to each taxon before RoC is computed.

"none" - no smoothing (default)
"shep" - Shepard's 5-term filter (Davis, 1986; Wilkinson, 2005)
"m.avg" - moving average
"age.w" - age-weighted average
"grim" - Grimm's smoothing (Grimm & Jacobson, 1992)

smooth_n_points

numeric. Number of points used for moving average, Grimm, and age-weighted smoothing. Must be an odd number.

smooth_N_points

smooth_N_points is no longer supported; please use smooth_n_points

smooth_age_range

numeric. Maximum age range (in years) for Grimm and age-weighted smoothing windows.

smooth_n_max

numeric. Maximum number of samples included in a Grimm smoothing window.

smooth_N_max

smooth_N_max is no longer supported; please use smooth_n_max

working_units

character. Strategy used to define Working Units between which dissimilarity is calculated.

"levels" - each stratigraphical level is its own WU.
"bins" - one representative level is selected from each time bin of width bin_size.
"MW" - moving-window binning: selective binning is repeated number_of_shifts times, shifting the window by bin_size / number_of_shifts years each time. All results are retained and summarised together.

Working_Units

Working_Units is no longer supported; please use working_units

bin_size

numeric. Width of each time bin in years. Used when working_units is "bins" or "MW".

number_of_shifts

numeric. Number of window shifts in moving-window binning (working_units = "MW").

Number_of_shifts

Number_of_shifts is no longer supported; please use number_of_shifts

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.

N_individuals

N_individuals is no longer supported; please use n_individuals

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

DC

DC is no longer supported; please use dissimilarity_coefficient

tranform_to_proportions

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

rand

numeric. Number of randomisation runs. Set to NULL (default) to skip randomisation and use a single deterministic run.

use_parallel

Controls parallel computation of randomisation runs.

FALSE (default) - single core only.
TRUE - number of cores detected automatically.
A positive numeric - use that many cores.

interest_threshold

numeric. Optional. Samples older than this age are excluded from the output.

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.

Usage

Arguments

See also