GrowthUncertainty: GrowthUncertainty class

Description

The GrowthUncertainty class contains the results of a growth prediction under isothermal conditions considering parameter uncertainty. Its constructor is predict_growth_uncertainty().

It is a subclass of list with the items:

sample: parameter sample used for the calculations.
simulations: growth curves predicted for each parameter.
quantiles: limits of the credible intervals (5%, 10%, 50%, 90%, 95%) for each time point.
model: Model used for the calculations.
mus: Mean parameter values used for the simulations.
sigma: Variance-covariance matrix used for the simulations.
logbase_mu: base of the logarithm for the definition of parameter mu (check the relevant vignette)
logbase_logN: base of the logarithm for the definition of the population size (check the relevant vignette)

Usage

# S3 method for GrowthUncertainty
print(x, ...)
# S3 method for GrowthUncertainty
plot(
  x,
  y = NULL,
  ...,
  line_col = "black",
  line_size = 0.5,
  line_type = "solid",
  ribbon80_fill = "grey",
  ribbon90_fill = "grey",
  alpha80 = 0.5,
  alpha90 = 0.4
)

Arguments

x: The object of class GrowthUncertainty to plot.
...: ignored.
y: ignored
line_col: Aesthetic parameter to change the colour of the line geom in the plot, see: ggplot2::geom_line()
line_size: Aesthetic parameter to change the thickness of the line geom in the plot, see: ggplot2::geom_line()
line_type: Aesthetic parameter to change the type of the line geom in the plot, takes numbers (1-6) or strings ("solid") see: ggplot2::geom_line()
ribbon80_fill: fill colour for the space between the 10th and 90th quantile, see: ggplot2::geom_ribbon()
ribbon90_fill: fill colour for the space between the 5th and 95th quantile, see: ggplot2::geom_ribbon()
alpha80: transparency of the ribbon aesthetic for the space between the 10th and 90th quantile. Takes a value between 0 (fully transparant) and 1 (fully opaque)
alpha90: transparency of the ribbon aesthetic for the space between the 5th and 95th quantile. Takes a value between 0 (fully transparant) and 1 (fully opaque).

Methods (by generic)

print(GrowthUncertainty): print of the model
plot(GrowthUncertainty): Growth prediction (prediction band) considering parameter uncertainty.