pwpop: Estimate Net Reproductive Rates Over Multiple Periods Of An...

In fishmethods: Fishery Science Methods and Models

Estimate Net Reproductive Rates Over Multiple Periods Of An Abundance Time Series Using Piecewise Regression

Description

Function estimates net reproductive rates for periods of change over a time series of abundance data.

Usage

pwpop(abund = NULL, year = NULL, periods = NULL, Cs = NULL,
 startR = NULL, upperR = NULL, lowerR = NULL, graph = TRUE)

Arguments

abund	the vector of time series of abundance data (e.g. run counts, indices of relative abundance, etc.).
year	the vector of years associated with abundance data.
periods	the number of periods over which to fit the population model.
Cs	the vector of user-specified initial starting value for year(s) of change - number of values equals periods - 1 (enclose within c()).
startR	the vector of user-specified initial starting values for R - one value for each period (enclose within c()).
upperR	the vector of user-specified upper limits for R (one for each period) used in optimization (enclose within c()).
lowerR	the vector of user-specified lower limits for R (one for each period) used in optimization (enclose within c()).
graph	Logical specifying whether a graph of observed versus predicted values is plotted. Default=TRUE.

Details

A simple population model is fitted to abundance data to estimate the net reproductive rate for specified periods of time. The model is Nt=N0*R^t where Nt is the abundance at time t, N0 is the estimated initial population size and R is the net reproductive rate. R can be used as an indication that the population is stable (R=1), is increasing (R>1) or is declining (R<1) over a specified time period. The fitted equation is the linearized form: log(Nt)=log(N0)+log(R)*t, where log is the natural-log; therefore, zeros are not allowed.

To simultaneously estimate the parameters for periods of trends in the abundance data, a piecewise regression approach is used. The linearized model is fitted separately to data for each period but models are linked so that the ending year for the preceding period is also the intercept for the current period. As an example, the models for three periods are

log(N1,t)=log(N1,0)+log(R1)*t for t<C1

log(N2,t)=log(N1,0)+C1*(log(R1)-log(R2))+log(R2)*t for t>=C1 and t<C2

log(N3,t)=log(N1,0)+C1*(log(R1)-log(R2))+C2*(log(R2)-log(R3))+log(R3)*t for t>=C2

The parameters estimated for these models are log(N1,0), log(R1), C1, log(R2), C2, and log(R3). t is time starting at 1 for the first year of abundance and ending at x for the last year of abundance(year information is still needed for plotting). Entered Cs value are converted to the same scale as t. Back-transform the log(R) values using exp to obtain the R values for each period. The function optim is used to obtain parameter estimates and associated standard errors by minimizing the sum of squares (log(N)-log(pred))^2. Add first year-1 to each C to put estimates on year scale.

Value

Estimates	list element with the parameter estimates and associated standard errors, residual sum of squares, Akaike's Information Criterion for least squares (AIC), and coefficient of determination (r2).
Data	list element with the abundance data, years, t, log predicted values, and back-transformation predicted values.

Author(s)

Gary A. Nelson, Massachusetts Division of Marine Fisheries [e-mail]

References

Neter, J. , M. H. Kutner, C. J. Nachtsheim, and W. Wasserman. 1996. Applied Linear Statistical Models. The Magraw-Hill Companies. 1408 p.

Examples

data(counts)
pwpop(abund = counts$number, year = counts$year,periods = 3, Cs = c(2000,2005), 
startR = c(0.5,0.5,0.5), 
upperR = c(10,10,10), 
lowerR = c(-10,-10,-10))

fishmethods documentation built on April 27, 2023, 9:10 a.m.