agesurv: Age-based Survival Estimators

Description Usage Arguments Details Value Author(s) References Examples

Description

Calculates annual survival (S) and instantaneous total mortality rates (Z) from age frequency by using linear regression (standard and weighted), Heincke, Chapman-Robson, Poisson GLM and GLMER methods.

Usage

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agesurv(age = NULL, full = NULL, last = NULL, 
estimate = c("s", "z"), method = c("lr", "he", "cr", "crcb","ripois","wlr","pois"))

Arguments

age

the vector of ages. Each row represents the age of an individual.

full

the fully-recruited age

last

the maximum age to include in the calculation. If not specified, the oldest age is used.

estimate

argument to select estimate type: "s" for annual survival, "z" for instantaneous total mortality. Default is both.

method

argument to select the estimation method: "lr" for standard linear regression, "he" for Heincke, "cr" for Chapman-Robson, "crcb" for Chapman-Robson Z estimate with bias-correction (Seber p. 418) and over-dispersion correction (Smith et al., 2012), "ripois" for Millar (2015) random-intercept Poisson mixed model estimator, "wlr" for Maceine-Bettoli weighted regression, "pois" for Poisson generalized linear model with overdispersion correction. Default is all.

Details

The individual age data are tabulated and subsetted based on the full and last arguments. Most calculations follow descriptions in Seber(1982), pages 414-418. If only two ages are present, a warning message is generated and the catch curve method is not calculated. Plus groups are not allowed.

Value

results

list element containing table of parameters and standard errors.

data

list element containing the age frequency data used in the analysis.

Author(s)

Gary A. Nelson, Massachusetts Division of Marine Fisheries gary.nelson@state.ma.us

References

Seber, G. A. F. 1982. The Estimation of Animal Abundance and Related Parameters, Second Edition. The Blackburn Press, Caldwell, New Jersey. 654 pages.

Maceina, M. J. and P. W. Bettoli. 1998. Variation in largemouth bass recruitment in four mainstream impoundments of the Tennessee River. N. Am. J. Fish. Manage. 18: 990-1003.

Millar, R. B. 2015. A better estimator of mortality rate from age-frequency data. Can. J. Fish. Aquat. Sci. 72: 364-375.

Quinn, T. J. and R. B. Deriso. 1999. Quantitative Fish Dynamics. Oxford University Press, New York, New York. 542 pages.

Smith, M. W. and 5 others. 2012. Recommendations for catch-curve analysis. N. Am. J. Fish. Manage. 32: 956-967.

Examples

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data(rockbass)
agesurv(age=rockbass$age,full=6)


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