biogrowth: FitDynamicGrowthMCMC – R documentation

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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 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, 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.

biogrowth

Modelling of Population Growth

v0.2.0

GPL-3

Authors

Alberto Garre [aut, cre] (<https://orcid.org/0000-0002-4404-3550>), Jeroen Koomen [aut], Heidy den Besten [aut], Marcel Zwietering [aut]

Initial release