GrowthPrediction {biogrowth}

GrowthPrediction class

Description

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