GrowthUncertainty {biogrowth}

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 class 'GrowthUncertainty'
print(x, ...)

## S3 method for class '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: geom_line()

line_size

Aesthetic parameter to change the thickness of the line geom in the plot, see: 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: geom_line()

ribbon80_fill

fill colour for the space between the 10th and 90th quantile, see: geom_ribbon()

ribbon90_fill

fill colour for the space between the 5th and 95th quantile, see: 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.