A consistency review of every method against its source paper.
Every new method reproduces the published examples of its source paper; where a paper's own numbers are inconsistent, the help page says so.
solow1993_bayes(): Bayes factor and posterior probability of persistence
of Solow (1993a), equation 3.rout2009() and rout2009_absences(): Bayes factor under a declining
sighting rate and the number of absent surveys needed to declare
eradication (Rout, Salomon & McCarthy 2009).caley_barry2014(): probability of persistence from yearly detections
(Caley & Barry 2014). The constant model is computed exactly; the
non-constant model ports the authors' MCMC sampler.strauss1989_bayes(): Bayesian posterior for the end of a range (Strauss &
Sadler 1989, equations 22-27).thompson2013(): probability of persistence with several observation types
of uncertain detection probability (Thompson et al. 2013), with the
annealed and quenched averages computed exactly.lee2014(): probability of persistence from certain and uncertain sightings
with false positives (Lee et al. 2014), following the authors' OpenBUGS
model but computed exactly.kodikara2020(): posterior of the extinction year from yearly certain and
uncertain sightings, Models 1-3 of Kodikara et al. (2020), computed exactly
instead of by MCMC.kodikara2021(): extinction time when sightings follow non-homogeneous
Poisson processes with Weibull rates and a change point (Kodikara et al.
2021), by numerical integration. The default reproduces the paper with the
authors' likelihood; equation 9 as printed is available as an option.brook2019(): resampling with sighting reliabilities as inclusion
probabilities, around any estimator (Brook, Buettel & Jarić 2019).thompson2017(): the iterative model of records and surveys behind the
IUCN Red List extinction-probability tool (Thompson et al. 2017).thompson2019(): Bayesian year-by-year updating (Thompson et al. 2019).jaric_roberts2014() gains test_year and data_out for the
reliability-adjusted p-value of equations 7-8.marshall1994() and marshall1994_trend(): distribution-free confidence
intervals on a range end-point and the test for a trend in gap size.marshall1997(): confidence intervals under a non-uniform fossil recovery
potential.weiss_marshall1999() and weiss_marshall1999_prior(): Bayesian end-point
for sections sampled at discrete horizons.solow1993b() returns the minimum variance unbiased estimate of the
extinction time (Solow 2005, equation 8) in estimate.burgman1995(equation = 3): the runs test on occupied and empty periods.ede_compare() applies every method that needs only the sighting record
and returns one table.dodo, monk_seal, ferret,
orchid and extinct_birds.solow1993(), solow1993b(), solow2005(),
mcinerny2006(), burgman1995(), solow_roberts2003() and jaric2010())
no longer report the year of first rejection as a point estimate, which
none of the source papers define. They return estimate = NA and the
one-sided upper confidence bound from inverting the test in upper. For
continuous-time methods the bound is now exact rather than rounded up to a
whole year: equation 5 of Solow (2005) for solow1993(), equation 17 of
Solow (2005) for solow2005(), equations 7-8 of Jarić & Ebenhard (2010)
for jaric2010(), the Robson-Whitlock bound for solow_roberts2003(), and
a numerical root for solow1993b().burgman1995() now applies equation 2 of Burgman et al. (1995), the test
for extinction, by default. The former calculation, equation 4, tests for a
change in conservation status using the longest empty run anywhere in the
record; it remains available as equation = 4.solow1993() and solow1993b() count every sighting event, as in Solow
(1993a), instead of distinct sighting times (solow1993()) or dropping all
sightings in the origin time unit (both). Only the sighting that defines the
origin is omitted.solow1993() is now labelled Solow (1993a).ole() returned an upper confidence limit earlier than the last sighting
when -log(alpha / 2) >= k. The limit does not exist in that case and is
now returned as Inf with a warning.mcinerny2006() ignored a zero-count first row. It now uses it as the known
start date and counts every sighting time, as the source paper allows.burgman1995(equation = 4) returned NaN for large numbers of sightings.
The inclusion-exclusion sum is now computed on the log scale.test_year when it is less than one
time unit after the last sighting.jaric_roberts2014() and stated that
its binary-count requirement is a package restriction.ole() and
solow2005(), and that jaric2010() is an index rather than a p-value.k for the
most recent sighting events.solow2005() calculation with the Weibull
extreme-value p-value from equation 16 of Solow (2005).solow_roberts2003() for the nonparametric two-endpoint persistence
test.jaric2010() for average-interval and sighting-trend inference.jaric_roberts2014() for records with individual sighting
reliabilities.