biogrowth (version 0.2.0)

FitDynamicGrowthMCMC: FitDynamicGrowthMCMC class

Description

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

Usage

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

Arguments

x

The object of class FitDynamicGrowthMCMC to plot.

y

ignored

...

ignored

add_factor

whether to plot also one environmental factor. If NULL (default), no environmenta 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_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

point_col

Aesthetic parameter to change the colour of the point geom, see: geom_point

point_size

Aesthetic parameter to change the size of the point geom, see: geom_point

point_shape

Aesthetic parameter to change the shape of the point geom, see: geom_point

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 FitDynamicGrowthMCMC.

newdata

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

Functions

• 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: variance-covariance 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.