This package is considered a duplicate. The official version of this package is found at:https://rodrigosqrt3.r-universe.dev/EDE

Package: EDE 0.3.0

Rodrigo Fonseca Villa

EDE: Extinction Date Estimation from Sighting Records

Infers the extinction of a species from a time-ordered record of sightings, collecting methods from the sighting-record and stratigraphic-range literature under one interface. Includes endpoint estimators (Robson & Whitlock, 1964; Strauss & Sadler, 1989; Roberts & Solow, 2003), frequentist persistence tests (Solow, 1993a, 1993b; Burgman, Grimson & Ferson, 1995; Solow & Roberts, 2003; Solow, 2005; McInerny, Roberts, Davy & Cribb, 2006; Jarić & Ebenhard, 2010), Bayesian models (Rout, Salomon & McCarthy, 2009; Caley & Barry, 2014), methods for sightings of uncertain reliability (Thompson et al., 2013; Jarić & Roberts, 2014; Lee et al., 2014; Brook, Buettel & Jarić, 2019; Kodikara et al., 2020, 2021), models combining records and surveys (Thompson et al., 2017, 2019), and confidence intervals on the end-points of fossil ranges (Marshall, 1994, 1997; Weiss & Marshall, 1999). Every method is tested against the published examples of its source paper and returns a common result class; persistence tests are inverted to give one-sided upper confidence bounds.

Authors:Rodrigo Fonseca Villa [aut, cre]

EDE_0.3.0.tar.gz
EDE_0.3.0.zip(r-4.7-any)EDE_0.3.0.zip(r-4.6-any)
EDE_0.3.0.tar.gz(r-4.7-any)EDE_0.3.0.tar.gz(r-4.6-any)
EDE_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EDE/json (API)

# Install 'EDE' in R:

install.packages('EDE', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rodrigosqrt3/ede/issues

Datasets:

dodo - Sighting record of the dodo
extinct_birds - Sighting records of four possibly extinct birds, by evidence quality
ferret - Sighting record of the black-footed ferret
monk_seal - Sighting record of the Caribbean monk seal
orchid - Collection record of a Mauritian orchid

On CRAN:

3.18 score 3 scripts 247 downloads 31 exports 0 dependencies

Last updated from:d529244c66. Checks:6 OK. Indexed: no.

Target	Result	Time
linux-devel	OK	123
source / vignettes	OK	202
linux-release	OK	133
windows-devel	OK	74
windows-release	OK	98
wasm-release	OK	96

Exports:brook2019 burgman1995 caley_barry2014 ede_compare jaric_roberts2014 jaric2010 kodikara2020 kodikara2021 lee2014 marshall1994 marshall1994_trend marshall1997 mcinerny2006 ole robson1964 rout2009 rout2009_absences sighting_data solow_roberts2003 solow1993 solow1993_bayes solow1993b solow2005 strauss1989 strauss1989_bayes strauss1989_curve thompson2013 thompson2017 thompson2019 weiss_marshall1999 weiss_marshall1999_prior

Dependencies:

Estimating extinction dates from sighting records

Rendered fromEDE.Rmdusingknitr::rmarkdown

Last update: 2026-10-31
Started: 2026-08-07

Help page	Topics
Reliability-weighted resampling of a sighting record (Brook et al., 2019)	brook2019
Burgman, Grimson & Ferson (1995) tests for frequency sighting data	burgman1995
Caley & Barry (2014) Bayesian extinction probability from a detection record	caley_barry2014
Sighting record of the dodo	dodo
Apply every applicable method to one sighting record	ede_compare
Extinction date estimate	ede_estimate
Sighting records of four possibly extinct birds, by evidence quality	extinct_birds
Sighting record of the black-footed ferret	ferret
Reliability-adjusted extinction inference	jaric_roberts2014
Jaric & Ebenhard (2010) sighting-trend index	jaric2010
Kodikara et al. (2020) Bayesian extinction year from yearly sighting records	kodikara2020
Kodikara et al. (2021) extinction time with non-homogeneous Poisson sightings	kodikara2021
Lee et al. (2014) Bayesian extinction probability with certain and uncertain sightings	lee2014
Marshall (1994) distribution-free confidence intervals on a range end-point	marshall1994
Marshall (1994) transposition test for a trend in gap size	marshall1994_trend
Marshall (1997) generalized confidence interval for a range end-point	marshall1997
McInerny, Roberts, Davy & Cribb (2006) sighting-rate persistence test	mcinerny2006
Sighting record of the Caribbean monk seal	monk_seal
Optimal Linear Estimation of extinction date	ole
Collection record of a Mauritian orchid	orchid
Robson & Whitlock (1964) truncation point estimator	robson1964
Rout et al. (2009) Bayes factor with a declining sighting rate	rout2009
Optimal number of absent surveys before declaring eradication	rout2009_absences
Construct a validated sighting record	sighting_data
Solow & Roberts (2003) nonparametric persistence test	solow_roberts2003
Solow (1993a) constant-rate persistence test	solow1993
Solow (1993a) Bayes factor for persistence	solow1993_bayes
Solow (1993b) declining-population persistence test	solow1993b
Solow (2005) Weibull extreme-value persistence test	solow2005
Strauss & Sadler (1989) confidence interval for the end of a range	strauss1989
Strauss & Sadler (1989) Bayesian estimate of the end of a range	strauss1989_bayes
Confidence curve for the Strauss & Sadler (1989) upper bound	strauss1989_curve
Thompson et al. (2013) probability of persistence with uncertain sightings	thompson2013
Thompson et al. (2017) iterative probability that a taxon is extant	thompson2017
Thompson et al. (2019) Bayesian updating of the probability of persistence	thompson2019
Weiss & Marshall (1999) Bayesian end point for discretely sampled sections	weiss_marshall1999
Beta prior for p pooled from related records (Weiss & Marshall, 1999)	weiss_marshall1999_prior

Package: EDE 0.3.0

EDE: Extinction Date Estimation from Sighting Records

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)