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Solow & Roberts' (2003) "Non-parametric" model

SR03F1.Rd

Equation 4 from Solow & Roberts 2003 and Equations 9-11 from Solow 2005. Estimates a p-value for testing competing hypotheses of extinction/non-extinction, and a one-sided \(1 - \alpha\) confidence interval and point estimate on the time of extinction.

Usage

SR03F1(
  records,
  alpha = 0.05,
  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.

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, point estimate, 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.

References

Key Reference

Solow, A. R., & Roberts, D. L. (2003). A nonparametric test for extinction based on a sighting record. Ecology, 84(5), 1329-1332. doi:10.1890/0012-9658(2003)084[1329:ANTFEB]2.0.CO;2

Other References

Robson, D. S., & Whitlock, J. H. (1964). Estimation of a truncation point. Biometrika, 51(1-2), 33-39. doi:10.1093/biomet/51.1-2.33

Solow, A. R. (2003). Estimation of stratigraphic ranges when fossil finds are not randomly distributed. Paleobiology, 29(2), 181-185. doi:10.1666/0094-8373(2003)029<0181:EOSRWF>2.0.CO;2

Solow, A. R. (2005). Inferring extinction from a sighting record. Mathematical Biosciences, 195(1), 47-55. doi:10.1016/j.mbs.2005.02.001

Rivadeneira, M. M., Hunt, G., & Roy, K. (2009). The use of sighting records to infer species extinctions: an evaluation of different methods. Ecology, 90(5), 1291-1300. doi:10.1890/08-0316.1

Examples

# Run the Mauritian orchid analysis from Solow & Roberts 2003
SR03F1(orchid, test.time = 1996)
#> $records
#>  [1] 1933 1941 1952 1962 1965 1966 1967 1971 1974 1976 1978
#> 
#> $alpha
#> [1] 0.05
#> 
#> $test.time
#> [1] 1996
#> 
#> $p.value
#> [1] 0.1
#> 
#> $estimate
#> [1] 1980
#> 
#> $conf.int
#> [1] 1978 2016
#> 
if (FALSE) { # \dontrun{
# Run an example analysis using the Slender-billed Curlew data
SR03F1(curlew$ccon, test.time = 2022)
} # }