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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.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.