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Plot a literal interpretation of a fossil record

Source: R/plotRawFossilOccs.R
plotRawFossilOccs.Rd

plotRawFossilOccs calculates and plots the early and late boundaries associated with each taxa in a dataset.

Usage

plotRawFossilOccs(
  data,
  tax.lvl = NULL,
  sort = TRUE,
  use.midpoint = TRUE,
  return.ranges = FALSE,
  knitr = FALSE
)

Arguments

data

A data.frame containing fossil data on the age (early and late bounds of rock layer, respectively labeled as max_ma and min_ma) and the taxonomic level asked in tax_lv.

tax.lvl

A character giving the taxonomic in which calculations will be based on, which must refer to the column names in data. If NULL (default value), the function plots every individual occurrences in data.

sort

logical indicating if taxa should be sorted by their max_ma values (default value is TRUE). Otherwise (i.e., if FALSE), function will follow the order of taxa (or occurrences) inputted in data.

use.midpoint

logical indicating if function should use occurrence midpoints (between max_ma and min_ma) as occurrence temporal boundaries, a method commonly employed in paleobiology to remove noise related to extremely coarse temporal resolution due to stratification. This argument is only used if a tax.lvl is provided.

return.ranges

logical indicating if ranges calculated by function should be return as a data.frame. If tax.lvl is NULL, the function don't calculate ranges and so it has nothing to return.

knitr

Logical indicating if plot is intended to show up in RMarkdown files made by the Knitr R package.

Value

Plots a pile of the max-min temporal ranges of the chosen tax.lvl. This usually will be stratigraphic ranges for occurrences (so there is no attempt to estimate "true" ranges), and if tax.lvl = NULL (the default), occurrences are drawn as ranges of stratigraphic resolution (= the fossil dating imprecision). If return.ranges = TRUE, it returns a data.frame containing the diversity (column div) of the chosen taxonomic level, through time.

See also

Other macroevolution: calcFossilDivTT(), checkAndFixUltrametric(), countSeqDiffs(), estimateSpeciation(), fitCRBD(), lttPlot(), plotPaintedWhales(), plotProteinSeq(), simulateBirthDeathRich(), simulateTree()

Author

Matheus Januario, Jennifer Auler

Examples


data("dinos_fossil")
oldpar <- par(no.readonly = TRUE) 
par(mfrow=c(1,2))
plotRawFossilOccs(dinos_fossil, tax.lvl = "species", knitr = TRUE)
plotRawFossilOccs(dinos_fossil, tax.lvl = "genus", knitr = TRUE)

par(oldpar)