biogrowth: FitSecondaryGrowth – R documentation

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FitSecondaryGrowth

FitSecondaryGrowth class

Description

The FitSecondaryGrowth class contains a model fitted to a set of growth rates gathered under a variety of static conditions. Its constructor is fit_secondary_growth.

It is a subclass of list with the items:

fit_results: object returned by modFit.
secondary_model: secondary model fitted to the data.
mu_opt_fit: estimated growth rate under optimum conditions.
data: data used for the fit.
transformation: type of transformation of mu for the fit.

Usage

## S3 method for class 'FitSecondaryGrowth'
plot(x, y = NULL, ..., which = 1, add_trend = FALSE)

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

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

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

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

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

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

## S3 method for class 'FitSecondaryGrowth'
predict(object, newdata = NULL, ...)

Arguments

`x`	An instance of FitSecondaryGrowth.
`y`	ignored.
`...`	ignored
`which`	A numeric with the type of plot. 1 for obs versus predicted (default), 2 for gamma curve
`add_trend`	Whether to add a trend line (only for which=2)
`object`	an instance of `FitSecondaryGrowth`.
`newdata`	A tibble describing the environmental conditions as in `fit_secondary_growth`. If `NULL`, it uses the same conditions as for model fitting (default).

Functions

plot.FitSecondaryGrowth: plots to evaluate the goodness of the fit.
summary.FitSecondaryGrowth: statistical summary of the fit.
residuals.FitSecondaryGrowth: vector of model residuals.
coef.FitSecondaryGrowth: vector of fitted model parameters.
vcov.FitSecondaryGrowth: variance-covariance matrix of the model, estimated as 1/(0.5*Hessian)
deviance.FitSecondaryGrowth: deviance of the model.
fitted.FitSecondaryGrowth: vector of fitted values.

The fitted values are returned in the same scale as the one used for the fitting (sqrt, log or none).
predict.FitSecondaryGrowth: 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