FitCoupledGrowth: FitCoupledGrowth class

In biogrowth: Modelling of Population Growth

FitCoupledGrowth class

Description

The FitCoupledGrowth class contains a Baranyi model fitted to experimental data considering the coupling between the primary and secondary models. Its constructor is fit_coupled_growth().

It is a subclass of list with the items:

• fit: object returned by FME::modFit().

• mode: fitting approach.

• weight: type of weights for the two-steps approach.

• logbase_mu: base of the logarithm used for the calculation of mu.

• data: data used for the model fitting.

Usage

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

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

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

## S3 method for class 'FitCoupledGrowth'
predict(object, newdata = NULL, ...)

## S3 method for class 'FitCoupledGrowth'
residuals(object, ...)

## S3 method for class 'FitCoupledGrowth'
vcov(object, ...)

## S3 method for class 'FitCoupledGrowth'
deviance(object, ...)

## S3 method for class 'FitCoupledGrowth'
fitted(object, ...)

## S3 method for class 'FitCoupledGrowth'
logLik(object, ...)

## S3 method for class 'FitCoupledGrowth'
AIC(object, ..., k = 2)

## S3 method for class 'FitCoupledGrowth'
plot(
  x,
  y = NULL,
  ...,
  line_col = "black",
  line_size = 1,
  line_type = 1,
  point_col = "black",
  point_size = 3,
  point_shape = 16,
  label_y = NULL,
  label_x = NULL
)

Arguments

x	The object of class FitCoupledGrowth to plot.
...	ignored.
object	an instance of FitCoupledGrowth
newdata	tibble (or data.frame) with the conditions for the prediction. If NULL (default), the fitting conditions. For two_steps fits, it must have a column named temp. For one_step, it must have a column named temp and one named time.
k	penalty for the parameters (k=2 by default)
y	ignored
line_col	colour of the line
line_size	size of the line
line_type	type of the line
point_col	colour of the points
point_size	size of the points
point_shape	shape of the point
label_y	label for the y-axis. By default, NULL (default value depending on the mode)
label_x	label for the x-axis. By default, NULL (default value depending on the mode)

Methods (by generic)

• print(FitCoupledGrowth): print of the model

• coef(FitCoupledGrowth): vector of fitted model parameters.

• summary(FitCoupledGrowth): statistical summary of the fit.

• predict(FitCoupledGrowth): vector of model predictions.

• residuals(FitCoupledGrowth): vector of model residuals.

• vcov(FitCoupledGrowth): variance-covariance matrix of the model, estimated as 1/(0.5*Hessian) for regression

• deviance(FitCoupledGrowth): deviance of the model.

• fitted(FitCoupledGrowth): vector of fitted values.

• logLik(FitCoupledGrowth): loglikelihood of the model

• AIC(FitCoupledGrowth): Akaike Information Criterion

• plot(FitCoupledGrowth): compares the fitted model against the data.

biogrowth documentation built on April 13, 2025, 5:12 p.m.