fishmethods (version 1.10-2)

growth: Fitting Growth Curves to Length- or Weight-at-Age Data

Description

Fits various growth models to length and weight-at-age data.

Usage

growth(intype=1,unit=1,size=NULL,age=NULL,calctype=1,wgtby=1,s2=NULL,error=1,
         Sinf=NULL,K=NULL,t0=NULL,B=3,graph=TRUE,
         control=list(maxiter=10000,minFactor=1/1024,tol=1e-5))

Arguments

intype

the input format: 1= individual size data; 2 = mean size data. Default intype=1.

unit

the size unit: 1= length; 2 = weight. Default unit=1.

size

the vector of size (length or weight) data.

age

the vector of ages associated with the size vector.

calctype

if intype=1, 1 = use individual size data; 2 = calculate mean size from individual size data. Default calctype=1.

wgtby

weighting scheme: 1 = no weighting; 2 = weight means by inverse variance. Weighting of individual data points is not allowed. Default wgtby=1.

s2

if intype=2 and wgtby=2, specify vector of sample variances associated with mean size-at-age data.

error

the error structure: 1 = additive; 2 = multiplicative. Default error=1.

Sinf

the starting value for L-infinity or W-infinity of the growth models. Required.

K

the starting value for K of the growth models.

t0

the starting value for t0 of the growth models.

B

the length-weight equation exponent used in the von Bertalanffy growth model for weight. Default B=3.

graph

logical value specifying if fit and residual plots should be drawn. Default graph = TRUE.

control

see function nls.

Value

List containing list elements of the equation/structure and nls output for each model. Information from nls output can be extracted using standard functions (e.g., summary()).

Details

If unit is length, a standard von Bertalanffy growth curve is fitted to length-at-age data using nonlinear least-squares (function nls). If individual data are provided, mean size data can be calculated by specifying calctype=2. When fitting mean size data, observations can be weighted by the inverse sample variance(wgtby=2), resulting in weighted nonlinear least squares. Additive or multiplicative error structures are specified via error. See page 135 in Quinn and Deriso (1999) for more information on error structures.

If unit is weight, three growth models (von Bertalanffy, Gompert and logistic) are fitted to weight-at-age data. The exponent for the von Bertalanffy growth in weight model is not estimated and must be specified (B). Individual and mean weight data can be used. When fitting mean size data, observations can be weighted by the inverse sample variance (wgtby=2), resulting in weighted nonlinear least squares. Additive or multiplicative error structures are specified via error.

Plots of model fit and residuals are generated unless graph=FALSE.

References

Quinn, T. J. and R. B. Deriso. 1999. Quantitative fish dynamics. Oxford University Press. 542 pages.

Examples

# NOT RUN {
data(pinfish)
growth(intype=1,unit=1,size=pinfish$sl,age=pinfish$age,
        calctype=1,wgtby=1,error=1,Sinf=200,K=0.3,t0=-1)
# }