FitIsoGrowth {biogrowth}

FitIsoGrowth class

Description

The class FitIsoGrowth has been superseded by the top-level class GrowthFit, which provides a unified approach for growth modelling.

Still, it is still returned if the superseded fit_isothermal_growth() is called.

It is a subclass of list with the items:

• data: data used for model fitting

• model: name of the primary inactivation model

• starting_point: initial value of the model parameters

• known: fixed model parameters

• fit: object returned by modFit()

• best_prediction: model prediction for the model fitted.

Usage

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

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

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

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

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

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

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

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

## S3 method for class 'FitIsoGrowth'
predict(object, times = NULL, ...)

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

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

Arguments

x

The object of class FitIsoGrowth to plot.

...

ignored

y

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()

point_col

Aesthetic parameter to change the colour of the point geom, see: geom_point()

point_size

Aesthetic parameter to change the size of the point geom, see: geom_point()

point_shape

Aesthetic parameter to change the shape of the point geom, see: geom_point()

object

an instance of FitIsoGrowth

times

numeric vector describing the time points for the prediction. If NULL (default), uses the same points as those used for fitting.

k

penalty for the parameters (k=2 by default)

Methods (by generic)

• print(FitIsoGrowth): print of the model

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

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

• residuals(FitIsoGrowth): vector of model residuals.

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

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

• deviance(FitIsoGrowth): deviance of the model.

• fitted(FitIsoGrowth): vector of fitted values.

• predict(FitIsoGrowth): vector of model predictions.

• logLik(FitIsoGrowth): loglikelihood of the model

• AIC(FitIsoGrowth): Akaike Information Criterion