Plot Extinction Risk Metrics

Generates a six-panel plot of extinction risk metrics used in Population Viability Analysis (PVA). This is a function used by one of the vignettes in the MARSS-package.

Usage

CSEGriskfigure(data, te = 100, absolutethresh = FALSE, threshold = 0.1, 
  datalogged = FALSE, silent = FALSE, return.model = FALSE, 
  CI.method = "hessian", CI.sim = 1000)

Arguments

data: A data matrix with 2 columns; time in first column and counts in second column. Note time is down rows, which is different than the base MARSS-package functions.
te: Length of forecast period (positive integer)
absolutethresh: Is extinction threshold an absolute number? (T/F)
threshold: Extinction threshold either as an absolute number, if absolutethresh=TRUE, or as a fraction of current population count, if absolutethresh=FALSE.
datalogged: Are the data already logged? (T/F)
silent: Suppress printed output? (T/F)
return.model: Return state-space model as marssMLE object? (T/F)
CI.method: Confidence interval method: "hessian", "parametrc", "innovations", or "none". See MARSSparamCIs.
CI.sim: Number of simulations for bootstrap confidence intervals (positive integer).

Details

Panel 1: Time-series plot of the data. Panel 2: CDF of extinction risk. Panel 3: PDF of time to reach threshold. Panel 4: Probability of reaching different thresholds during forecast period. Panel 5: Sample projections. Panel 6: TMU plot (uncertainty as a function of the forecast).

Value

If return.model=TRUE, an object of class marssMLE.

References

Holmes, E. E., E. J. Ward, and M. D. Scheuerell (2012) Analysis of multivariate time-series using the MARSS package. NOAA Fisheries, Northwest Fisheries Science Center, 2725 Montlake Blvd E., Seattle, WA 98112 Type RShowDoc("UserGuide",package="MARSS") to open a copy.

(theory behind the figure) Holmes, E. E., J. L. Sabo, S. V. Viscido, and W. F. Fagan. (2007) A statistical approach to quasi-extinction forecasting. Ecology Letters 10:1182-1198.

(CDF and PDF calculations) Dennis, B., P. L. Munholland, and J. M. Scott. (1991) Estimation of growth and extinction parameters for endangered species. Ecological Monographs 61:115-143.

(TMU figure) Ellner, S. P. and E. E. Holmes. (2008) Resolving the debate on when extinction risk is predictable. Ecology Letters 11:E1-E5.

Author

Eli Holmes, NOAA, Seattle, USA, and Steve Ellner, Cornell Univ.

Examples

d <- harborSeal[, 1:2]
kem <- CSEGriskfigure(d, datalogged = TRUE)
#> Analysis assumes that data and threshold are already logged
#> Using an percentage threshold for the extinction threshold
#> Threshold is 90 percent decline