biodyn-package: Biomass Dynamic Stock Assessment Model
In laurieKell/biodyn: Biomass Dynamic Model

Description Details Author(s) References See Also Examples

A package for running biomass dynamic stock fish assessments. The biodyn class can be used to fit catch and catch per unit effort to estimate stock abundance. It also has methods for evaluating the goodness of fit, estimating reference points and for modelling harvest control rules as part of Management Strategy Evaluation.

Package:	biodyn
Version:	0.0.1
Depends:	R(>=3.1.0), FLCore, ggplot2
Collate:	'biodyn-class.R' 'biodyn-generic.R' 'biodyn-control.R' 'biodyn-accessors.R' 'biodyn-constructors.R' 'biodyn-OEM.R' 'biodyn-admb.R' 'biodyn-coerce.R' 'biodyn-methods.R' 'biodyn-diags.R' 'biodyn-fwd.R' 'biodyn-hcr.R' 'biodyn-kobe.R' 'biodyn-mng.R' 'biodyn-mse.R' 'biodyn-msy.R' 'biodyn-pella.R' 'biodyn-plots.R' 'biodyn-profile.R' 'biodyns.R' 'combine.R' 'biodyn-cpp.R'
License:	GPL-2
LazyLoad:	Yes
LazyData:	No
Built:	R 2.15.3; ; 2013-03-25 16:42:17 UTC; unix

Index:

  
biodyn              Biomass Dynamic Model Class
biodyn-class        Class '"biodyn"'
biodyn-package      Implements a Biomass Dynamic Stock Assessment Model 
biodyns             List of biodyn objects
is.biodyn   
    
sim   

msy                 Maximum Sustainable Yield.
fmsy                Fishing Mortality at Maximum Sustainable Yield.
bmsy                Biomass at Maximum Sustainable Yield.
refpts              MSY, BMSY and FMSY

plot                Time series
plotEql             Equilibrium values
plotJack            Time series with uncertainty estimated by Jack Knife
plotMSE             Plots summary from MSE
plotPrd             Production function

K                   Calculate Carrying Capacity from msy and r
computePrd   
    
fit   
setControl<-   
setParams<-   
priorFn   
profile   
    
fwd   
hcr   
hcrParam   
tac   

kobe   
    
powerAnalysis   
    
mvn   
psuedo   
runMSE   
controlFn

Laurence Kell

Maintainer: Laurence Kell <laurie.kell@iccat.int>

Fletcher, R.I. 1978. On the restructuring of the Pella-Tomlinson system. Fish. Bull. 76:515–521.

Fox, W.W., Jr. 1970. An exponential surplus-yield model for optimizing exploited fish populations. Trans. Am. Fish. Soc. 99:80–88.

Garrod, D.J. 1969. Empirical assessments of catch effort relationships in the North Atlantic cod stock. ICNAF Res. Bull. 6:26–34.

Gilpin, M.E. and F.J. Ayala. 1973. Global models of growth and competition. Proc. Natl. Acad. Sci. USA 70:3590–3593.

Gompertz, B. 1825. On the nature of the function expressive of the law of human mortality, and on a new mode of determining the value of life contingencies. Phil. Trans. R. Soc. Lond. 115:513–583.

Hilborn, R. and C.J. Walters. 1992. Quantitative fisheries stock assessment: Choice, dynamics and uncertainty. New York: Chapman and Hall.

Kingsland, S. 1982. The refractory model: The logistic curve and the history of population ecology. Q. Rev. Biol. 57:29–52.

Laloe, F. 1995. Should surplus production models be fishery description tools rather than biological models? Aquat. Living Resour. 8:1–16.

Pella, J.J. and P.K. Tomlinson. 1969. A generalized stock production model. IATTC Bull. 13:421–496.

Polacheck, T., R. Hilborn, and A.E. Punt. 1993. Fitting surplus production models: Comparing methods and measuring uncertainty. Can. J. Fish. Aquat. Sci. 50:2597–2607.

Prager, M.H. 2002. Comparison of logistic and generalized surplus-production models applied to swordfish, Xiphias gladius, in the north Atlantic Ocean. Fish. Res. 58:41–57.

Quinn, T.J., II and R.B. Deriso. 1999. Quantitative fish dynamics. New York: Oxford University Press.

Schaefer, M.B. 1954. Some aspects of the dynamics of populations important to the management of the commercial marine fisheries. IATTC Bull. 1:27–56.

~~ Optional links to other man pages, e.g. ~~ FLCore ~~