biogrowth: MCMCgrowth – R documentation

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MCMCgrowth

MCMCgrowth class

Description

The MCMCgrowth class contains the results of a growth prediction consider parameter variability based on a model fitted using fit_MCMC_growth or fit_multiple_growth_MCMC.

It is a subclass of list with items:

sample: Parameter sample used for the calculations.
simulations: Individual growth curves calculated based on the parameter sample.
quantiles: Tibble with the limits of the credible intervals (5
model: Instance of FitDynamicGrowthMCMC used for predictions.
env_conditions: A tibble with the environmental conditions of the simulation.

Usage

## S3 method for class 'MCMCgrowth'
plot(
  x,
  y = NULL,
  ...,
  add_factor = NULL,
  alpha_80 = 0.5,
  fill_80 = "grey",
  alpha_90 = 0.5,
  fill_90 = "grey",
  label_y1 = "logN",
  label_y2 = add_factor,
  line_col = "black",
  line_type = 1,
  line_size = 1,
  line_type2 = 2,
  line_col2 = "black",
  line_size2 = 1,
  ylims = NULL
)

Arguments

`x`	The object of class `MCMCgrowth` to plot.
`y`	ignored
`...`	ignored.
`add_factor`	Includes the variation of one environmental factor in the plot. It must be one of the column names in x$env_conditions.
`alpha_80`	transparency of the ribbon for the 80th posterior. .5 by default.
`fill_80`	fill colour of the ribbon for the 80th posterior. "grey" by default.
`alpha_90`	transparency of the ribbon for the 90th posterior. .5 by default.
`fill_90`	fill colour of the ribbon for the 90th posterior. "grey" by default.
`label_y1`	label of the primary y axis. "logN" by default.
`label_y2`	label of the secondary y axis. The name of the environmental factor by default.
`line_col`	colour of the line representing the median. "black" by default.
`line_type`	linetype for the line representing the median. solid by default.
`line_size`	size of the line representing the median. 1 by default.
`line_type2`	linetype for the line representing the environmental condition. Dashed by default.
`line_col2`	colour of the line representing the environmental condition. "black" by default.
`line_size2`	size of the line representing the environmental condition. 1 by default.
`ylims`	limits of the primary y-axis. `NULL` by default (let ggplot choose).

Functions

plot.MCMCgrowth: plot of predicted growth (prediction band).

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