| CSEGriskfigure | R Documentation |
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().
+
CSEGriskfigure(
+ data,
+ te = 100,
+ absolutethresh = FALSE,
+ threshold = 0.1,
+ datalogged = FALSE,
+ silent = FALSE,
+ return.model = FALSE,
+ CI.method = "hessian",
+ CI.sim = 1000
+)
+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 |
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 |
datalogged |
+
+ Are the data already logged? (T/F) + |
silent |
+
+ Suppress printed output? (T/F) + |
return.model |
+
+ Return state-space model as |
CI.method |
+
+ Confidence interval method: "hessian", "parametric", "innovations", or "none". See |
CI.sim |
+
+ Number of simulations for bootstrap confidence intervals (positive integer). + |
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). +
+If return.model=TRUE, an object of class marssMLE().
+
Eli Holmes, NOAA, Seattle, USA, and Steve Ellner, Cornell Univ. +
+ + +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. +
+ + +MARSSboot(), marssMLE(), CSEGtmufigure()
+
d <- harborSeal[, 1:2]
+kem <- CSEGriskfigure(d, datalogged = TRUE)
+
+