apply_taphonomy: model taphonomic effects

In StratPal: Stratigraphic Paleobiology Modeling Pipelines

model taphonomic effects

Description

Models taphonomy by combining the change in taphonomic conditions with the preservation potential as a function of taphonomic conditions to determine how preservation potential changes. This is then used to systematically remove (thin) the event data using thin/ remove specimens from the pre_paleoTS object using prob_remove.

Usage

apply_taphonomy(x, pres_potential, ctc)

Arguments

x	event type data, e.g. times/ages of fossil occurrences or their stratigraphic position, or a pre_paleoTS, fossils, or char_mat object.
pres_potential	function. Takes taphonomic conditions as input and returns the preservation potential (a number between 0 and 1). Must be vectorized, meaning if given a vector, it must return a vector of equal length.
ctc	function, change in taphonomic conditions (ctc) with time or stratigraphic position. . Must be vectorized, meaning if given a vector, it must return a vector of equal length.

Value

if given event type data, a numeric vector, location/timing of events (e.g. fossil occurrences) after the taphonomic filter is applied. If given a pre_paleoTS object, returns another pre_paleoTS object with reduced number of specimens. If given a fossils object as created by the FossilSim package, returns another fossils object with some occurrences removed according to preservation potential.

See Also

• apply_niche() for modeling niche preferences based on the same principle. Internally, these functions are structured identically.

• thin() and prob_remove() for the underlying mathematical procedures.

• perfect_preservation() and all_preserved() to model perfect preservation of fossils

• strat_filter() for simple stratigraphic filtering in the time domain as taphonomic effect

• as_char_mat() to construct character matrices associated with stratigraphic information

Examples

# see
#vignette("advanced_functionality")
# for details on usage
# or the documentation of apply_ecology for equivalent application to ecology

StratPal documentation built on Dec. 6, 2025, 5:08 p.m.