Description Usage Arguments Functions
The FitDynamicGrowthMCMC
a model fitted based on a dynamic growth experiment
using an MCMC algorithm. Its constructor is fit_MCMC_growth
.
It is a subclass of list with the items:
fit_results: the object returned by modMCMC
.
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40  ## S3 method for class 'FitDynamicGrowthMCMC'
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 'FitDynamicGrowthMCMC'
summary(object, ...)
## S3 method for class 'FitDynamicGrowthMCMC'
residuals(object, ...)
## S3 method for class 'FitDynamicGrowthMCMC'
coef(object, ...)
## S3 method for class 'FitDynamicGrowthMCMC'
vcov(object, ...)
## S3 method for class 'FitDynamicGrowthMCMC'
deviance(object, ...)
## S3 method for class 'FitDynamicGrowthMCMC'
fitted(object, ...)
## S3 method for class 'FitDynamicGrowthMCMC'
predict(object, times = NULL, newdata = NULL, ...)

x 
The object of class 
y 
ignored 
... 
ignored 
add_factor 
whether to plot also one environmental factor.
If 
ylims 
A two dimensional vector with the limits of the primary yaxis. 
label_y1 
Label of the primary yaxis. 
label_y2 
Label of the secondary yaxis. 
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 (16) 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 
times 
A numeric vector with the time points for the simulations. 
newdata 
a tibble describing the environmental conditions (as 
plot.FitDynamicGrowthMCMC
: compares the model fitted against the data.
summary.FitDynamicGrowthMCMC
: statistical summary of the fit.
residuals.FitDynamicGrowthMCMC
: model residuals.
coef.FitDynamicGrowthMCMC
: vector of fitted model parameters.
vcov.FitDynamicGrowthMCMC
: variancecovariance matrix of the model,
estimated as the variance of the samples from the Markov chain.
deviance.FitDynamicGrowthMCMC
: deviance of the model, calculated as the sum
of squared residuals for the parameter values resulting in the best fit.
fitted.FitDynamicGrowthMCMC
: vector of fitted values.
predict.FitDynamicGrowthMCMC
: vector of model predictions.
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