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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")).
pre_paleoTSRepresents 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").
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.
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
pre_paleoTS can be modified using
apply_niche
apply_taphonomy
time_to_strat
strat_to_time
pre_paleoTS can be transformed into paleoTS
format using reduce_to_paleoTS
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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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