biogrowth: StochasticGrowth – R documentation

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StochasticGrowth

StochasticGrowth class

Description

The StochasticGrowth class contains the results of a growth prediction under isothermal conditions considering parameter unceratinty. Its constructor is predict_stochastic_growth.

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 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.

Usage

## S3 method for class 'StochasticGrowth'
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 `StochasticGrowth` to plot.
`y`	ignored
`...`	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).

Functions

plot.StochasticGrowth: Growth prediction (prediction band) considering parameter uncertainty.

biogrowth

Modelling of Population Growth

v0.2.0

GPL-3

Authors

Alberto Garre [aut, cre] (<https://orcid.org/0000-0002-4404-3550>), Jeroen Koomen [aut], Heidy den Besten [aut], Marcel Zwietering [aut]

Initial release