FitIsoGrowth: FitIsoGrowth class
In biogrowth: Modelling of Population Growth

FitIsoGrowth

R Documentation

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The class FitIsoGrowth has been superseded by the top-level class GrowthFit, which provides a unified approach for growth modelling.

Still, it is still returned if the superseded fit_isothermal_growth() is called.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