biogrowth: FitMultipleGrowthMCMC – R documentation

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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 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, 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).

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