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biogrowth (version 1.0.6)

FitCoupledGrowth: 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 FitCoupledGrowth
print(x, ...)
# S3 method for FitCoupledGrowth
coef(object, ...)
# S3 method for FitCoupledGrowth
summary(object, ...)
# S3 method for FitCoupledGrowth
predict(object, newdata = NULL, ...)
# S3 method for FitCoupledGrowth
residuals(object, ...)
# S3 method for FitCoupledGrowth
vcov(object, ...)
# S3 method for FitCoupledGrowth
deviance(object, ...)
# S3 method for FitCoupledGrowth
fitted(object, ...)
# S3 method for FitCoupledGrowth
logLik(object, ...)
# S3 method for FitCoupledGrowth
AIC(object, ..., k = 2)
# S3 method for 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.