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Plot Extinction Risk Metrics
CSEGriskfigure.Rd
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, ifabsolutethresh=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.