FitDynamicGrowth {biogrowth} | R Documentation |
The class FitDynamicGrowth has been superseded by the top-level class GrowthFit, which provides a unified approach for growth modelling.
Still, it is still returned if the superseded fit_dynamic_growth()
is called.
It is a subclass of list with the items:
fit_results: the object returned by modFit
.
best_prediction: the model prediction for the fitted parameters.
env_conditions: environmental conditions for the fit.
data: data used for the fit.
starting: starting values for model fitting
known: parameter values set as known.
sec_models: a named vector with the secondary model for each environmental factor
## S3 method for class 'FitDynamicGrowth'
print(x, ...)
## S3 method for class 'FitDynamicGrowth'
plot(
x,
y = NULL,
...,
add_factor = NULL,
ylims = NULL,
label_y1 = "logN",
label_y2 = add_factor,
line_col = "black",
line_size = 1,
line_type = 1,
point_col = "black",
point_size = 3,
point_shape = 16,
line_col2 = "black",
line_size2 = 1,
line_type2 = "dashed"
)
## S3 method for class 'FitDynamicGrowth'
summary(object, ...)
## S3 method for class 'FitDynamicGrowth'
residuals(object, ...)
## S3 method for class 'FitDynamicGrowth'
coef(object, ...)
## S3 method for class 'FitDynamicGrowth'
vcov(object, ...)
## S3 method for class 'FitDynamicGrowth'
deviance(object, ...)
## S3 method for class 'FitDynamicGrowth'
fitted(object, ...)
## S3 method for class 'FitDynamicGrowth'
predict(object, times = NULL, newdata = NULL, ...)
## S3 method for class 'FitDynamicGrowth'
logLik(object, ...)
## S3 method for class 'FitDynamicGrowth'
AIC(object, ..., k = 2)
x |
The object of class |
... |
ignored |
y |
ignored |
add_factor |
whether to plot also one environmental factor.
If |
ylims |
A two dimensional vector with the limits of the primary y-axis. |
label_y1 |
Label of the primary y-axis. |
label_y2 |
Label of the secondary y-axis. |
line_col |
Aesthetic parameter to change the colour of the line geom in the plot, see: |
line_size |
Aesthetic parameter to change the thickness of the line geom in the plot, see: |
line_type |
Aesthetic parameter to change the type of the line geom in the plot, takes numbers (1-6) or strings ("solid") see: |
point_col |
Aesthetic parameter to change the colour of the point geom, see: |
point_size |
Aesthetic parameter to change the size of the point geom, see: |
point_shape |
Aesthetic parameter to change the shape of the point geom, see: |
line_col2 |
Same as lin_col, but for the environmental factor. |
line_size2 |
Same as line_size, but for the environmental factor. |
line_type2 |
Same as lin_type, but for the environmental factor. |
object |
an instance of FitDynamicGrowth |
times |
A numeric vector with the time points for the simulations. |
newdata |
a tibble describing the environmental conditions (as |
k |
penalty for the parameters (k=2 by default) |
print(FitDynamicGrowth)
: comparison between the fitted model and the data.
plot(FitDynamicGrowth)
: comparison between the fitted model and the data.
summary(FitDynamicGrowth)
: statistical summary of the fit.
residuals(FitDynamicGrowth)
: residuals of the model.
coef(FitDynamicGrowth)
: vector of fitted parameters.
vcov(FitDynamicGrowth)
: (unscaled) variance-covariance matrix of the model,
calculated as 1/(0.5*Hessian)
deviance(FitDynamicGrowth)
: deviance of the model.
fitted(FitDynamicGrowth)
: fitted values.
predict(FitDynamicGrowth)
: model predictions.
logLik(FitDynamicGrowth)
: loglikelihood of the model
AIC(FitDynamicGrowth)
: Akaike Information Criterion