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biogrowth (version 0.2.0)

FitIsoGrowth: FitIsoGrowth class

Description

The FitIsoGrowth class contains a growth model fitted to data under static conditions. Its constructor is fit_isothermal_growth.

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 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 FitIsoGrowth
summary(object, ...)
# S3 method for FitIsoGrowth
residuals(object, ...)
# S3 method for FitIsoGrowth
coef(object, ...)
# S3 method for FitIsoGrowth
vcov(object, ...)
# S3 method for FitIsoGrowth
deviance(object, ...)
# S3 method for FitIsoGrowth
fitted(object, ...)
# S3 method for FitIsoGrowth
predict(object, times = NULL, ...)

Arguments

x

The object of class FitIsoGrowth to plot.

y

ignored

...

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.

Functions

  • 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.