MCMCgrowth: MCMCgrowth class

In biogrowth: Modelling of Population Growth

MCMCgrowth class

Description

The MCMCgrowth class contains the results of a growth prediction consider parameter variability based on a model fitted using an MCMC algorithm.

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%, 10%, 50%, 90% and 95%) for each time point.

• model: Instance of FitDynamicGrowthMCMC used for predictions.

• env_conditions: A tibble with the environmental conditions of the simulation.

Usage

## S3 method for class 'MCMCgrowth'
print(x, ...)

## 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.
...	ignored.
y	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).

Methods (by generic)

• print(MCMCgrowth): print of the model

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

biogrowth documentation built on Aug. 19, 2023, 1:06 a.m.