Documentation of defined S3 classes"

In StratPal: Stratigraphic Paleobiology Modeling Pipelines

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This vignette documents the S3 classes defined by the StratPal package.
For documentation of functionality, see the help page of individual functions (available via ?functionname), for working examples see the vignettes (available via browseVignettes("StratPal")).

S3 class pre_paleoTS

Represents trait values of individual specimens of a lineage sampled along time or stratigraphic position. For the motivation of this class, see the vignette on usage with the paleoTS package via vignette("paleoTS_functionality").

Structure

pre-paleoTS is a list with two elements:

• the first element is named t or h: a numeric vector, corresponding to sampling heights or times

• the second element is named vals: a list with the same number of elements as the vector h/t. Each element of the list contains the trait values of specimens sampled at that time/height.

Construction

pre_paleoTS is constructed by functions to simulate trait evolution on a specimen level/in pre-paleoTS format. These functions have suffix _sl for "specimen level". This is

• stasis_sl

• strict_stasis_sl

• random_walk_sl

• ornstein_uhlenbeck_sl

Modification

pre_paleoTS can be modified using

• apply_niche

• apply_taphonomy

• time_to_strat

• strat_to_time

Transformation into other S3 classes

pre_paleoTS can be transformed into paleoTS format using reduce_to_paleoTS

Plotting

No standalone plotting procedure is implemented for pre_paleoTS. For plotting, first use reduce_to_paleoTS and plot the results via plot after loading the paleoTS package.

S3 class char_mat

Describes a character matrix associated with positional information (time/height) for application of taphonomic and stratigraphic effects.

Structure

List with two elements:

• mat: The matrix, with taxon names as column names
• pos: named vector containing positional information (time or height) for the taxa

Construction

char_mat is constructed using as_char_mat.

Modification

Modified by apply_taphonomy. For logical reasons, apply_niche.char_mat throws an error.

Transformation into other S3 classes

None

Plotting

None

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