pacmacro_ranges {fossilbrush}

pacmacro_ranges

Description

Function to apply a modification of Pacman trimming to macrofossil data. The function generates a densified occurrence record using the same methods as densify then trim the upper and lower ranges by a user-defined percentage. The full and trimmed ranges are then compared against each other to test if the FAD and the LAD for a taxon form a long tail in its distribution. Multiple tail thresholds can be supplied, but all test to see if the sum of the FAD and LAD which exceeds the trimmed range constitute the threshold proportion of the total range for than taxon, e.g. does the FAD and the LAD outside of the trimmed range comprise a quarter (tail.flag = 0.25) of the taxon range?

Usage

pacmacro_ranges(
  x,
  rank = "genus",
  srt = "max_ma",
  end = "min_ma",
  step = 1,
  density = 0.1,
  top = 5,
  bottom = 5,
  tail.flag = 0.35,
  method = c("histogram", "kernel")
)

Arguments

x

A stratigraphic occurrence dataset

rank

The column name in x containing the taxon names for which trimmed ranges will be calculated

srt

A column name in x denoting the occurrence FADs

end

A column name in x denoting the occurrence LADs

step

A positive integer specifying the time window size (i.e. the duration represented by each row in the output matrix)

density

A positive numeric specifying the step size for densifying records. This should ideally be smaller than step

top

The percentage by which the top of the range will be trimmed

bottom

The percentage by which the bottom of the range will be trimmed

tail.flag

a numeric vector of proportions in the range 0 > x > 1 which will be used to test for long tails

method

The method for quantifying occurrence density. By default both histogram and kernel density will be used

Value

If the user specifies a specific method (e.g. method = "kernel"), the returned value will be a data.frame containing the taxa as row names, the original taxon ranges (FAD, LAD), their ranges as trimmed by the specified value (default FAD95, LAD95), and the tail status (0 = none, 1 = tail) at the user-specified tail proportions. If method is not specified, the result will be a list of 2 data.frames, one for each method

Source

Pacman procedure modified from https://rdrr.io/github/plannapus/CONOP9companion/src/R/pacman.R.

References

Lazarus et al (2012) Paleobiology

Examples

# load dataset
data("brachios")
# subsample brachios to make for a short example runtime
set.seed(1)
brachios <- brachios[sample(1:nrow(brachios), 1000),]
# run pacmacro
pacm <- pacmacro_ranges(brachios, tail.flag = c(0.3, 0.35, 0.4),
                        rank = "genus", srt = "max_ma", end = "min_ma")