fishgrowth (version 1.0.2)

pred_band: Prediction Band

Description

Calculate a prediction band for a fitted growth curve.

Usage

pred_band(age, model, level = 0.95)

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

Arguments

age

a vector of ages to calculate the prediction band.

model

a fitted growth model.

level

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()