Assign fossil occurrences to time bins — bin

A function to assign fossil occurrences to specified time bins based on different approaches commonly applied in palaeobiology.

Usage

bin_time(
  occdf,
  min_ma = "min_ma",
  max_ma = "max_ma",
  bins,
  method = "mid",
  reps = 100,
  fun = dunif,
  ...
)

Arguments

occdf: dataframe. A dataframe of the fossil occurrences you wish to bin. This dataframe should contain at least two columns with numeric values: maximum age of occurrence and minimum age of occurrence (see max_ma, min_ma). If required, numeric ages can be generated from interval names via the look_up() function.
min_ma: character. The name of the column you wish to be treated as the minimum age for occdf and bins, e.g. "min_ma" (default).
max_ma: character. The name of the column you wish to be treated as the maximum age for occdf and bins, e.g. "max_ma" (default).
bins: dataframe. A dataframe of the bins that you wish to allocate fossil occurrences to such as that returned by time_bins(). This dataframe must contain at least the following named columns: "bin" and those specified to max_ma (default: "max_ma") and min_ma (default: "min_ma"). Columns max_ma and min_ma must be numeric values.
method: character. The method desired for binning fossil occurrences. Currently, five methods exist in this function: "mid", "majority", "all", "random", and "point". See Details for a description of each.
reps: numeric. A non-negative numeric specifying the number of replications for sampling. This argument is only useful in the case of the "random" or "point" method being specified in the method argument. Defaults to 100.
fun: function. A probability density function from the stats package such as dunif or dnorm. This argument is only useful if the "point" method is specified in the method argument.
...: Additional arguments available in the called function (fun). These arguments may be required for function arguments without default values, or if you wish to overwrite the default argument value (see example). x input values are generated internally based on the age range of the fossil occurrence and should not be manually provided. Note that x input values range between 0 and 1, and function arguments should therefore be scaled to be within these bounds.

Value

For methods "mid", "majority" and "all", a dataframe of the original input occdf with the following appended columns is returned: occurrence id (id), number of bins that the occurrence age range covers (n_bins), bin assignment (bin_assignment), and bin midpoint (bin_midpoint). In the case of the "majority" method, an additional column of the majority percentage overlap (overlap_percentage) is also appended. For the "random" and "point" method, a list is returned (of length reps) with each element a copy of the occdf and appended columns (random: bin_assignment and bin_midpoint; point: bin_assignment and point_estimates).

Details

Five approaches (methods) exist in the bin_time() function for assigning occurrences to time bins:

Midpoint: The "mid" method is the simplest approach and uses the midpoint of the fossil occurrence age range to bin the occurrence.
Majority: The "majority" method bins an occurrence into the bin which it most overlaps with. As part of this implementation, the majority percentage overlap of the occurrence is also calculated and returned as an additional column in occdf. If desired, these percentages can be used to further filter an occurrence dataset.
All: The "all" method bins an occurrence into every bin its age range covers. For occurrences with age ranges of more than one bin, the occurrence row is duplicated. Each occurrence is assigned an ID in the column occdf$id so that duplicates can be tracked. Additionally, occdf$n_bins records the number of bins each occurrence appears within.
Random: The "random" method randomly samples X amount of bins (with replacement) from the bins that the fossil occurrence age range covers with equal probability regardless of bin length. The reps argument determines the number of times the sample process is repeated. All replications are stored as individual elements within the returned list with an appended bin_assignment and bin_midpoint column to the original input occdf. If desired, users can easily bind this list using do.call(rbind, x).
Point: The "point" method randomly samples X (reps) amount of point age estimates from the age range of the fossil occurrence. Sampling follows a user-input probability density function such as dnorm (see example 5). Users should also provide any additional arguments for the probability density function (see ...). However, x (vector of quantiles) values should not be provided as these values are input from the age range of each occurrence. These values range between 0 and 1, and therefore function arguments should be scaled to be within these bounds. The reps argument determines the number of times the sample process is repeated. All replications are stored as individual elements within the returned list with an appended bin_assignment and point_estimates column to the original input occdf. If desired, users can easily bind this list using do.call(rbind, x).

Developer(s)

Christopher D. Dean & Lewis A. Jones

Reviewer(s)

William Gearty

Examples

#Grab internal tetrapod data
occdf <- tetrapods[1:100, ]
bins <- time_bins()

#Assign via midpoint age of fossil occurrence data
ex1 <- bin_time(occdf = occdf, bins = bins, method = "mid")
#> Warning: One or more occurrences have a midpoint age equivalent to a bin boundary. Binning skipped for these occurrences. Hint: `which(is.na(occdf$bin_assignment))`.

#Assign to all bins that age range covers
ex2 <- bin_time(occdf = occdf, bins = bins, method = "all")

#Assign via majority overlap based on fossil occurrence age range
ex3 <- bin_time(occdf = occdf, bins = bins, method = "majority")

#Assign randomly to overlapping bins based on fossil occurrence age range
ex4 <- bin_time(occdf = occdf, bins = bins, method = "random", reps = 5)

#Assign point estimates following a normal distribution
ex5 <- bin_time(occdf = occdf, bins = bins, method = "point", reps = 5,
                fun = dnorm, mean = 0.5, sd = 0.25)