solowbeet2: Solow & Beet's extinction date model

In cjcarlson/spatExtinct: A Package for Spatial Interpolation of Extinction Dates from Sighting Data

Description

The Solow & Beet method uses a Bayesian model to evaluate the extinction date of a species, using mixed certainty datsets. The solowbeet function can be used to implement model 1 (which assumes invalid sightings aren't generated until after a species is extinct) or model 2 (which assumes that valid and invalid sightings could be mixed before the true extinction date). Both models treat valid and invalid sightings as separate processes, and make inference on the likelihood of the extinction date based on what sighting rates would have generated the dataset in hand.

The solowbeet function runs a full panel including plots, exporting plotable data (for use in a preferred graphics package) and two objects in $Results that allow hypothesis testing for extinction by the specified year T.bound. First is the Bayes factor which is calculated as p(t|E)/p(t|E') where t is the data and E is the hypothesis the species is extinct. Second is the posterior probability of extinction P(E|t), which (if the prior P(E)=P(E')=0.5 for simplicity's sake) is given as P(t|E)/P(t|E)+P(t|E'). The two are connected but the Bayes factor requires no prior probability of extinction. Both use a prior on P(T_E). See Carlson et al. manuscript for details.

Usage

solowbeet2(data, inputs, modelnumber, gamma = 6, plots = FALSE,
  increment = 0.01, increment2 = 0.05, verbose = FALSE, testyear = NA)

Arguments

inputs	Should be an argument formatted as: list(dataStr = "Vini vidivici", T = 1969, posteriorPrior = "Unif"). The argument sets, in order: the name of the species, the T.bound (the outer bound the model runs to; MUST be later than (T_last + increment2*(T_last-T_first)), and the posterior prior. Options are uniform ("Unif"), linear ("Tri"), or negative exponential ("Exp")
modelnumber	Which model do you want to implement - 1 or 2?
gamma	Gamma sets the slope of the exponential decline if the exponential prior is selected. It defaults to six, from the original implementation with ivory-billed woodpeckers.
plots	Four panel plot of sightings by certainty, estimated sighting rates over time, priors, and likelihood of extinction date.
increment	Used in numerical integration over omega.
increment2	Used to estimate posterior pdf. A smaller increment2 allows finer resolution likelihood plots and more precise estimates. We suggest 0.01 for single-species, non-spatial sightings; but the argument defaults to 0.05 for spatExtinct.
verbose	Leave it turned off. Don't turn it on.
DATA	Input data should be a data frame with two columns: year and sighting. Year records the date of a sighting (though it could be any continuous units of time) and sighting records the quality of the sighting. A "1" is a certain sighting (guaranteed valid) while a "2" or anything higher is uncertain. Uncertain sightings are not necessarily invalid, and researchers may want to differentiate within uncertain sightings by quality. We typically use three categories: 1 is physical evidence or certain expert sightings, 2 are plausible expert sightings, and 3 are dubious or novice sightings without strong evidence.

References

Solow, A., Smith, W., Burgman, M., Rout, T., Wintle, B. and Roberts, D., 2012. Uncertain Sightings and the Extinction of the Ivory-Billed Woodpecker. Conservation Biology, 26(1), pp.180-184.

Solow, A.R. and Beet, A.R., 2014. On uncertain sightings and inference about extinction. Conservation biology, 28(4), pp.1119-1123.

Examples

data(thylacine)
solowbeet(thylacine,inputs=list(dataStr = 'Thylacinus cynocephalus', T=c(2017), posteriorPrior='Unif'),
         modelnumber=2,plots=TRUE)

cjcarlson/spatExtinct documentation built on May 25, 2019, 3:26 p.m.