calculateImplicitParameters {paleoAM}R Documentation

Calculate Implicit Parameters for Modeling Time-Series of Fossil Assemblages

Description

Given a sufficient set of parameters for simulating fossil assemblages as a time-series, this function calculates the full set of parameters necessary for running each component model.

Usage

calculateImplicitParameters(
  eventChangeScale,
  bgGradientValue,
  fullGradientRange,
  eventSampleWidthRatio = NULL,
  sampleWidth = NULL,
  eventDuration = NULL,
  sedRatePerTimestep = NULL,
  maxSampleTimeStep = 500,
  minSampleTimeStep = 3,
  samplingCompleteness,
  transitionDurationRatio,
  bioturbDepthRatio
)

Arguments

eventChangeScale

A value indicating the amount relative to the background value (bgGradientValue) and the maximum possible change as indicated by fullGradientRange (in other words, simulated change must be within observed gradient, so eventChangeScale is a proportional multiplier of the total possible change).

bgGradientValue

The gradient value expected during background intervals during which no notable excursion is occurring on that environmental gradient.

fullGradientRange

A vector of two values giving the minimum and maximum gradient values observed in the empirical data.

eventSampleWidthRatio

How long should an event be relative to the amount of time (or sediment) captured within a sedimentary sample? This parameter is used for simulating event duration, sample width and sedimentation rate where any two of these three are defined and the third is not defined. This value is referred to as Resolution Potential in Belanger & Bapst (2023).

sampleWidth

The 'width' of a sample relative to core depth or outcrop height, usually given in linear units (usually centimeters). For taking sediment samples from a core, this is straightforward (how thick is each sediment sample taken?) but for outcrops this may be more difficult to determine (what is the thickness of a horizon in a shale unit?).

eventDuration

The duration (in time-units) of a simulated event during which the environmental gradient is at an excursion 'peak' level.

sedRatePerTimestep

The rate of sedimentation, given as a ratio of sediment thickness (given in linear dimensions, in the same units as sampleWidth), over time (given in the same time units as eventDuration.

maxSampleTimeStep

The maximum number of individual time-steps used for simulating a sample.

minSampleTimeStep

The minimum number of individual time-steps used for simulating a sample.

samplingCompleteness

The relative completeness of stratigraphic sampling. For example, if two-centimeter wide samples of sediment are taken from a sediment core, every ten centimeters, then the samplingCompleteness is two over 10, or that samplingCompleteness = 1/5. A simulation with a sampling completeness of 1 would be comparable to exhaustively sampling a core that recorded no gaps in sedimentation over its history. Rocky outcrops are more complicated, as fossil-bearing horizons may be relatively thin compared to the thickness of the section, such that outcrop-based fossil records should be simulated as having very low samplingCompleteness.

transitionDurationRatio

The ratio of how long the transition between peak and background intervals should be, relative to the length of the peak 'event' duration (eventDuration). The longer this transition interval, the more chances of an assemblage being sampled that represents transitional gradient values.

bioturbDepthRatio

The ratio of the sediment depth to which bioturbation occurs, made relative to the width of a sediment sample (sampleWidth). A sampleWidth of 3 cm and a biotubDepthRatio of 5 implies a bioturbation depth of 15 cm (3 * 5). Bioturbation depth varies considerably in the modern ocean, but is often the depth of active bioturbation is about 10 cm, such that the top ten centimeters of sediment (and the organic remains in those ten centimeters of sediment) are being regularly moved up and down by organism activity. For the purposes of this model, a bioturbation zone depth of 10 centimeters means that sampling a centimeter of sediment at location X, the apparent fossil assemblage that would be recovered is just as likely to include specimens that were deposited five centimeters away as those deposited at location X.

Details

Under the models considered in paleoAM, some parameterizations may be equivalent, even though the a particular analysis might be better simulated using a particular set of parameters. Allowing various different parameterizations is a useful generalization, but requires translating those equivalent parameters from one set to another (e.g. specifying parameters A, C & D, but running a simulation that requires parameters A, B & C).

This function mainly exists to calculate unspecified parameters for simulateFossilAssemblageSeries and also to identify conflicting parameter specifications.

Value

Returns a list giving the full set of parameters necessary for running simulateFossilAssemblageSeries.

References

Belanger, Christina L., and David W. Bapst. 2023. "Simulating our ability to accurately detect abrupt changes in assemblage-based paleoenvironmental proxies." Palaeontologia Electronica 26 (2), 1-32

See Also

simulateFossilAssemblageSeries


[Package paleoAM version 1.0.1 Index]