Jarić & Ebenhard's (2010) "Stationary" model

Equation 4 from Jarić & Ebenhard 2010. Estimates a p-value for testing competing hypotheses of extinction/non-extinction and a one-sided \(1 - \alpha\) confidence interval on the time of extinction.

Usage

JE10F1(
  records,
  alpha = 0.05,
  init.time = min(records),
  test.time = as.numeric(format(Sys.Date(), "%Y"))
)

Arguments

records: sighting records in ccon format (see convert_dodo for details).
alpha: desired significance level (defaults to \(\alpha = 0.05\)) of the \(1 - \alpha\) confidence interval.
init.time: start of the observation period. Defaults to the time of the first sighting, in which case this sighting is removed from the record.
test.time: end of the observation period, typically the present day (defaults to the current year).

Value

a list object with the original parameters and the p-value and confidence interval included as elements. The confidence interval is a two-element numeric vector called conf.int.

Note

All sighting records are assumed to be certain and sampling effort is assumed to be constant.

References

Key Reference

Jarić, I., & Ebenhard, T. (2010). A method for inferring extinction based on sighting records that change in frequency over time. Wildlife Biology, 16(3), 267-275. doi:10.2981/09-044

Other References

McCrea, R. S., Cheale, T., Campillo-Funollet, E., & Roberts, D. L. (2024). Inferring species extinction from sighting data. *Cambridge Prisms: * Extinction, 2, e19. doi:10.1017/ext.2024.18

Examples

# Run the Black-footed Ferret analysis from Jarić & Ebenhard 2010
JE10F1(ferret$ccon - 5, test.time = 223) # shift dates to align with paper
#> $records
#>  [1]   2   3   5  12  13  14  15  16  17  25  26  36  39  41  48  52  53  61  85
#> [20] 112 113 117 118 122 134 146 148
#> 
#> $alpha
#> [1] 0.05
#> 
#> $init.time
#> [1] 1
#> 
#> $test.time
#> [1] 223
#> 
#> $p.value
#> [1] 0.06965649
#> 
#> $conf.int
#> [1] 148.0000 254.6923
#> 
if (FALSE) { # \dontrun{
# Run an example analysis using the Slender-billed Curlew data
JE10F1(curlew$ccon, init.time = 1817, test.time = 2022)
} # }