snd_niche {StratPal} | R Documentation |
simple niche model
Description
Defines niche model based in the "Probability of collection" model by Holland and Patzkowsky (1999).
The collection probability follows the shape of a bell curve across a gradient, where opt
determines the peak (mean) of the bell curve, and tol
the standard deviation. "snd" stands for "scaled normal distribution", as the collection probability has the shape of the probability density of the normal distribution.
Usage
snd_niche(opt, tol, prob_modifier = 1, cutoff_val = NULL)
Arguments
opt |
optimum value, gradient value where collection probability is highest |
tol |
tolerance to changes in gradient. For large values, collection probability drops off slower away from |
prob_modifier |
collection probability modifier, collection probability at |
cutoff_val |
NULL or a number. If a number, all collection probabilities at gradient values below |
Value
a function for usage with apply_niche
.
References
Holland, Steven M. and Patzkowsky, Mark E. 1999. "Models for simulating the fossil record." Geology. https://doi.org/10.1130/0091-7613(1999)027%3C0491:MFSTFR%3E2.3.CO;2
See Also
-
apply_niche()
for usage of the returned function -
bounded_niche()
for another niche model -
discrete_niche()
anddiscrete_gradient()
to define niches based on discrete categories -
vignette("advenced_functionality")
for details on how to create user defined niche models
Examples
# using water depth as niche
wd = seq(-3, 40, by = 0.5)
f = snd_niche(opt = 10, tol = 5)
plot(wd, f(wd), xlab = "Water depth", ylab = "Prob. of collection")
# set cutoff value at to 0 to model non-terrestrial species.
f = snd_niche(opt = 10, tol = 5, cutoff_val = 0)
plot(wd, f(wd), xlab = "Water depth", ylab = "Prob. of collection")
# see also
#vignette("event_data")
#for examples how to use it for niche modeling