calculateImplicitParameters {paleoAM} | R Documentation |
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.
calculateImplicitParameters(
eventChangeScale,
bgGradientValue,
fullGradientRange,
eventSampleWidthRatio = NULL,
sampleWidth = NULL,
eventDuration = NULL,
sedRatePerTimestep = NULL,
maxSampleTimeStep = 500,
minSampleTimeStep = 3,
samplingCompleteness,
transitionDurationRatio,
bioturbDepthRatio
)
eventChangeScale |
A value indicating the amount relative to
the background value ( |
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 |
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
|
transitionDurationRatio |
The ratio of how long the transition
between peak and background intervals should be, relative to the
length of the peak 'event' duration ( |
bioturbDepthRatio |
The ratio of the sediment depth to which
bioturbation occurs, made relative to the width of a
sediment sample ( |
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.
Returns a list giving the full set of parameters necessary for running simulateFossilAssemblageSeries
.
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
simulateFossilAssemblageSeries