biogrowth: FitIsoGrowth – R documentation

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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 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, ...)

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.

biogrowth

Modelling of Population Growth

v0.2.0

GPL-3

Authors

Alberto Garre [aut, cre] (<https://orcid.org/0000-0002-4404-3550>), Jeroen Koomen [aut], Heidy den Besten [aut], Marcel Zwietering [aut]

Initial release