GrowthPrediction: GrowthPrediction class

GrowthPredictionR Documentation

GrowthPrediction class

Description

[Stable]

The GrowthPrediction class contains the results of a growth prediction. Its constructor is predict_growth().

It is a subclass of list with the items:

  • simulation: a tibble with the model simulation

  • primary model: a list describing the primary model as in predict_growth()

  • environment: a character describing the type of environmental conditions as in predict_growth()

  • env_conditions: a named list with the functions used to approximate the (dynamic) environmental conditions. NULL if environment="constant".

  • sec_models: a named list describing the secondary models as in predict_growth(). NULL if environment="constant".

  • gammas: a tibble describing the variation of the gamma factors through the experiment. NUll if environment="constant".

  • logbase_mu: the log-base for the definition of parameter mu (see the relevant vignette)

  • logbase_logN: the log-base for the definition of the logarithm of the population size

Usage

## S3 method for class 'GrowthPrediction'
print(x, ...)

## S3 method for class 'GrowthPrediction'
summary(object, ...)

## S3 method for class 'GrowthPrediction'
plot(
  x,
  y = NULL,
  ...,
  add_factor = NULL,
  ylims = NULL,
  label_y1 = NULL,
  label_y2 = add_factor,
  line_col = "black",
  line_size = 1,
  line_type = "solid",
  line_col2 = "black",
  line_size2 = 1,
  line_type2 = "dashed",
  label_x = "time"
)

## S3 method for class 'GrowthPrediction'
coef(object, ...)

Arguments

x

The object of class GrowthPrediction to plot.

...

ignored

object

an instance of GrowthPrediction

y

ignored

add_factor

whether to plot also one environmental factor. If NULL (default), no environmental factor is plotted. If set to one character string that matches one entry of x$env_conditions, that condition is plotted in the secondary axis. Ignored for environment="constant".

ylims

A two dimensional vector with the limits of the primary y-axis.

label_y1

Label of the primary y-axis.

label_y2

Label of the secondary y-axis.

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()

line_col2

Same as lin_col, but for the environmental factor.

line_size2

Same as line_size, but for the environmental factor.

line_type2

Same as lin_type, but for the environmental factor.

label_x

Label of the x-axis.

Methods (by generic)

  • print(GrowthPrediction): print of the model

  • summary(GrowthPrediction): summary of the model

  • plot(GrowthPrediction): predicted growth curve.

  • coef(GrowthPrediction): coefficients of the model


biogrowth documentation built on Aug. 19, 2023, 1:06 a.m.