biogrowth (version 0.2.0)

FitMultipleGrowthMCMC: FitMultipleGrowthMCMC class

Description

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.

Usage

# S3 method for 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 FitMultipleGrowthMCMC
summary(object, ...)
# S3 method for FitMultipleGrowthMCMC
residuals(object, ...)
# S3 method for FitMultipleGrowthMCMC
coef(object, ...)
# S3 method for FitMultipleGrowthMCMC
vcov(object, ...)
# S3 method for FitMultipleGrowthMCMC
deviance(object, ...)
# S3 method for FitMultipleGrowthMCMC
fitted(object, ...)
# S3 method for FitMultipleGrowthMCMC
predict(object, newdata = NULL, ...)

Arguments

x

an instance of FitMultipleGrowthMCMC.

y

ignored

...

ignored

add_factor

whether to plot also one environmental factor. If NULL (default), no environmental factor is plotted. If set to one character string that matches one entry of x$env_conditions, that condition is plotted in the secondary axis

ylims

A two dimensional vector with the limits of the primary y-axis.

label_x

label of the x-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: geom_line

line_size

Aesthetic parameter to change the thickness of the line geom in the plot, see: geom_line

line_type

Aesthetic parameter to change the type of the line geom in the plot, takes numbers (1-6) or strings ("solid") see: geom_line

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 plot_grid.

object

Instance of FitMultipleGrowthMCMC.

newdata

a tibble describing the environmental conditions (as env_conditions) in fit_multiple_growth. If NULL (default), uses the same conditions as those for fitting.

Functions

• 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: variance-covariance 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).