MCMCcoupled: MCMCcoupled class

Description

The MCMCcoupled class contains the results of a growth prediction consider parameter variability based on a model fitted using fit_coupled_growth()

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.

Usage

# S3 method for MCMCcoupled
plot(
  x,
  y = NULL,
  ...,
  add_factor = NULL,
  alpha_conf = 0.5,
  fill_conf = "grey",
  linetype_conf = 2,
  linecol_conf = "grey45",
  linetype_pred = 1,
  alpha_pred = 0.5,
  fill_pred = "grey",
  linecol_pred = "grey45",
  line_col = "black",
  line_type = 1,
  line_size = 0.5,
  label_y = "logN",
  label_x = "time"
)

Arguments

x: The object of class MCMCcoupled 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_conf: transparency of the ribbon for the confidence interval. .5 by default.
fill_conf: fill colour of the ribbon for the confidence interval. "grey" by default.
linetype_conf: linetype for the line of the confidence interval. solid by default.
linecol_conf: colour of the line for the confidence interval. "black" by default.
linetype_pred: linetype for the line of the prediction interval. solid by default.
alpha_pred: transparency of the ribbon for the prediction interval. .5 by default.
fill_pred: fill colour of the ribbon for the prediction interval. "grey" by default.
linecol_pred: colour of the line for the prediction interval. "grey45" by default.
line_col: color of the line representing the median ("black" by default).
line_type: type for the line representing the median (solid by default).
line_size: size of the line representing the median. 1 by default.
label_y: label of the y axis. "logN" by default.
label_x: label for the x-label ("time" by default).

Methods (by generic)

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