pred_band: Prediction Band

In fishgrowth: Fit Growth Curves to Fish Data

Prediction Band

Description

Calculate a prediction band for a fitted growth curve.

Usage

pred_band(age, model, level = 0.95)

Arguments

age	a vector of ages to calculate the prediction band.
model	a fitted growth model.
level	significance level.

Value

A data frame containing five columns:

age	age
Lhat	predicted length
sigma	growth variability
lower	lower limit of prediction band
upper	upper limit of prediction band

Note

The variability of length at age (sigma) increases linearly with length:

\sigma_L ~=~ \alpha \,+\, \beta \hat L

This calculation of sigma is demonstrated in the example below.

The lower and upper limits of the prediction band are calculated as \hat L \pm 1.96\sigma_L at the 95% significance level.

See Also

gcm, gompertz, gompertzo, richards, richardso, schnute3, vonbert, and vonberto are alternative growth models.

fishgrowth-package gives an overview of the package.

Examples

# Fit a model
init <- list(log_L1=log(20), log_L2=log(70), log_k=log(0.1),
             log_sigma_min=log(3), log_sigma_max=log(3))
dat <- list(Aoto=otoliths_had$age, Loto=otoliths_had$len, t1=1, t2=10)
model <- vonbert(init, dat)
fit <- nlminb(model$par, model$fn, model$gr,
              control=list(eval.max=1e4, iter.max=1e4))

# Calculate 95% prediction band
x <- seq(1, 18, 0.5)
band <- pred_band(x, model)

# Plot 95% prediction band
areaplot::confplot(cbind(lower,upper)~age, band, xlim=c(0,18), ylim=c(0,100),
         ylab="len", col="mistyrose")
points(len~age, otoliths_had, xlim=c(0,18), ylim=c(0,100),
       pch=16, col="#0080a010")
lines(Lhat~age, band, lwd=2, col=2)
lines(lower~age, band, lty=1, lwd=0.5, col=2)
lines(upper~age, band, lty=1, lwd=0.5, col=2)

# Calculate sigma by hand
report <- model$report()
alpha <- report$sigma_intercept
beta <- report$sigma_slope
Lhat <- band$Lhat
alpha + beta * Lhat  # same values as band$sigma calculated by pred_band()

fishgrowth documentation built on April 11, 2025, 5:52 p.m.