MCMCgrowth: 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 MCMCgrowth
print(x, ...)
# S3 method for 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).