CSEGriskfigure {MARSS}

Plot Extinction Risk Metrics

Description

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.

Author(s)

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

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.

See Also

MARSSboot, marssMLE, CSEGtmufigure

Examples

d <- harborSeal[, 1:2]
kem <- CSEGriskfigure(d, datalogged = TRUE)