FitSecondaryGrowth {biogrowth}  R Documentation 
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'
print(x, ...)
## S3 method for class 'FitSecondaryGrowth'
plot(x, y = NULL, ..., which = 1, add_trend = FALSE, add_segment = 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, ...)
## S3 method for class 'FitSecondaryGrowth'
logLik(object, ...)
## S3 method for class 'FitSecondaryGrowth'
AIC(object, ..., k = 2)
Arguments
x 
An instance of FitSecondaryGrowth. 
... 
ignored 
y 
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) 
add_segment 
Whether to join the observed and fitted points (only for which=2) 
object 
an instance of FitSecondaryGrowth 
newdata 
A tibble describing the environmental conditions as in

k 
penalty for the parameters (k=2 by default) 
Methods (by generic)

print(FitSecondaryGrowth)
: print of the model 
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)
: variancecovariance 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. 
logLik(FitSecondaryGrowth)
: loglikelihood of the model 
AIC(FitSecondaryGrowth)
: Akaike Information Criterion