Description Usage Arguments Functions
The FitMultipleGrowthMCMC
class contains a model fitted to a set of dynamic
experiments using an MCMC algorithm. Its constructor is
fit_multiple_growth_MCMC
.
It is a subclass of list with the items:
fit_results: the object returned by modFit
.
best_prediction: a list with the models predictions for each condition.
data: a list with the 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 41  ## S3 method for class 'FitMultipleGrowthMCMC'
plot(
x,
y = NULL,
...,
add_factor = NULL,
ylims = NULL,
label_x = "time",
label_y1 = "logN",
label_y2 = add_factor,
line_col = "black",
line_size = 1,
line_type = "solid",
line_col2 = "black",
line_size2 = 1,
line_type2 = "dashed",
point_size = 3,
point_shape = 16,
subplot_labels = "AUTO"
)
## S3 method for class 'FitMultipleGrowthMCMC'
summary(object, ...)
## S3 method for class 'FitMultipleGrowthMCMC'
residuals(object, ...)
## S3 method for class 'FitMultipleGrowthMCMC'
coef(object, ...)
## S3 method for class 'FitMultipleGrowthMCMC'
vcov(object, ...)
## S3 method for class 'FitMultipleGrowthMCMC'
deviance(object, ...)
## S3 method for class 'FitMultipleGrowthMCMC'
fitted(object, ...)
## S3 method for class 'FitMultipleGrowthMCMC'
predict(object, times = NULL, newdata = NULL, ...)

x 
an instance of FitMultipleGrowthMCMC. 
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_x 
label of the xaxis 
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: 
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. 
point_size 
Size of the data points 
point_shape 
shape of the data points 
subplot_labels 
labels of the subplots according to 
object 
Instance of 
times 
A numeric vector with the time points for the simulations. 
newdata 
a tibble describing the environmental conditions (as 
plot.FitMultipleGrowthMCMC
: comparison between the model fitted and the
data.
summary.FitMultipleGrowthMCMC
: statistical summary of the fit.
residuals.FitMultipleGrowthMCMC
: model residuals. They are returned as a tibble
with 4 columns: time (storage time), logN (observed count),
exp (name of the experiment) and res (residual).
coef.FitMultipleGrowthMCMC
: vector of fitted model parameters.
vcov.FitMultipleGrowthMCMC
: variancecovariance matrix of the model,
estimated as the variance of the samples from the Markov chain.
deviance.FitMultipleGrowthMCMC
: deviance of the model, calculated as the sum of
squared residuals of the prediction with the lowest standard error.
fitted.FitMultipleGrowthMCMC
: fitted values of the model. They are returned
as a tibble with 3 columns: time (storage time), exp (experiment
identifier) and fitted (fitted value).
predict.FitMultipleGrowthMCMC
: model predictions. They are returned as a tibble
with 3 columns: time (storage time), logN (observed count),
and exp (name of the experiment).
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