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Extinction date estimation from sighting records.
Given a time-ordered table of sighting counts, EDE estimates when a species most likely went extinct, or tests whether it can still be considered extant. Eleven procedures from the sighting-record literature are implemented under one interface, including endpoint estimators and constant-rate, declining-rate, sighting-rate, Weibull and combinatorial persistence tests, a sighting-trend index, and reliability-adjusted inference.
You can install the released version of EDE from CRAN with:
install.packages("EDE")And the development version from GitHub with:
# install.packages("remotes")
remotes::install_github("rodrigosqrt3/EDE")Every estimator takes a sighting_data object: a table
with one row per time unit and the number of sightings recorded in
it.
The earliest supplied time defines the observation origin. If monitoring began before the first sighting, include an initial row with count zero. Methods differ in their treatment of multiple sightings in one time unit: OLE and the Weibull test treat them as independent events, Solow’s 1993 constant-rate test uses occupied times, and Burgman’s discrete method uses the full frequencies.
library(EDE)
years <- c(1900, 1902, 1903, 1905, 1907, 1908, 1910, 1912, 1915, 1918,
1920, 1923, 1925, 1928, 1930, 1933, 1936)
sightings <- c(4, 3, 5, 2, 3, 4, 2, 1, 2, 1, 1, 2, 1, 1, 1, 1, 1)
sd <- sighting_data(data.frame(year = years, sightings = sightings))The last confirmed sighting is 1936. No sightings were recorded afterward.
ole(sd)
#> <OLE (Roberts & Solow 2003)>
#> estimate: 1941.97
#> 95% CI: [1937.48, 1956.75]
robson1964(sd)
#> <Robson & Whitlock (1964)>
#> estimate: 1939
#> 95% one-sided CI: [1936, 1993]
strauss1989(sd)
#> <Strauss & Sadler (1989)>
#> estimate: 1938.25
#> 95% one-sided CI: [1936, 1943.41]
solow1993(sd, test_year = 2000)
#> <Solow (1993)>
#> estimate: 1944
solow1993b(sd, test_year = 2000)
#> <Solow (1993b)>
#> estimate: NA
#> Warning message:
#> p-value never falls to alpha before `test_year`.
solow2005(sd, test_year = 2000)
#> <Solow (2005) Weibull test>
#> estimate: 1954
mcinerny2006(sd, test_year = 2000)
#> <McInerny, Roberts, Davy & Cribb (2006)>
#> estimate: 1942
burgman1995(sd, test_year = 1945)
#> <Burgman, Grimson & Ferson (1995)>
#> estimate: 1944
solow_roberts2003(sd, test_year = 2000)
jaric2010(sd, test_year = 2000)solow1993(), solow1993b(),
solow2005(), mcinerny2006(), and
burgman1995(), solow_roberts2003(), and
jaric2010() test a grid of candidate years up to
test_year and return the first year at which the p-value
drops to or below alpha. Pass data_out = TRUE
to get the full curve instead of the first crossing. For compatibility
with version 0.1.0, that p-value is stored in a column currently named
chance.
curve_1993 <- solow1993(sd, test_year = 2000, data_out = TRUE)
curve_2005 <- solow2005(sd, test_year = 2000, data_out = TRUE)
plot(curve_1993$time, curve_1993$chance, type = "l",
xlab = "candidate extinction year", ylab = "p-value")
lines(curve_2005$time, curve_2005$chance, col = "firebrick")The two curves diverge because they encode different models.
solow1993() assumes a stationary Poisson process and uses
the number of distinct sighting times after the observation origin.
solow2005() instead uses the spacing of the most recent
sightings under a Weibull extreme-value model, the same model used by
ole().
For uncertain records, supply one reliability per occupied time (or one per row):
uncertain <- sighting_data(data.frame(
year = c(1900, 1910, 1920, 1930),
sightings = c(1, 1, 1, 1)
))
jaric_roberts2014(uncertain, reliability = c(1, 0.9, 0.6, 0.3))| Function | Reference | Output |
|---|---|---|
ole() |
Roberts & Solow (2003) | point estimate + CI |
robson1964() |
Robson & Whitlock (1964) | point estimate + one-sided CI |
strauss1989(), strauss1989_curve() |
Strauss & Sadler (1989) | point estimate + one-sided CI / curve |
solow1993() |
Solow (1993) | first rejection time or p-value curve |
solow1993b() |
Solow (1993b) | first rejection time or p-value curve |
solow2005() |
Solow (2005) | first rejection time or p-value curve |
mcinerny2006() |
McInerny, Roberts, Davy & Cribb (2006) | first rejection time or p-value curve |
burgman1995() |
Burgman, Grimson & Ferson (1995) | first rejection time or p-value curve |
solow_roberts2003() |
Solow & Roberts (2003) | first rejection time or p-value curve |
jaric2010() |
Jarić & Ebenhard (2010) | first rejection time or p-value curve |
jaric_roberts2014() |
Jarić & Roberts (2014) | reliability-adjusted estimate + upper bound |
See vignette("EDE") for the statistical background and a
worked comparison across all eleven procedures.
GPL (>= 3)
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.