MCMCgrowth {biogrowth} R Documentation

## 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,
...,
alpha_80 = 0.5,
fill_80 = "grey",
alpha_90 = 0.5,
fill_90 = "grey",
label_y1 = "logN",
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).

[Package biogrowth version 1.0.1 Index]