simmr: prior_viz – R documentation

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prior_viz

Plot the prior distribution for a simmr run

Description

This function takes the output from simmr_mcmc and plots the prior distribution to enable visual inspection. This can be used by itself or as part of posterior_predictive to visually evaluate the influence of the prior on the posterior distribution.

Usage

prior_viz(
  simmr_out,
  group = 1,
  plot = TRUE,
  include_posterior = TRUE,
  n_sims = 10000,
  ggargs = NULL
)

Arguments

`simmr_out`	A run of the simmr model from `simmr_mcmc`
`group`	Which group to run it for (currently only numeric rather than group names)
`plot`	Whether to create a density plot of the prior or not. The simulated prior values are returned as part of the object
`include_posterior`	Whether to include the posterior distribution on top of the priors. Defaults to TRUE
`n_sims`	The number of simulations from the prior distribution
`ggargs`	Extra arguments to be included in the ggplot (e.g. axis limits)

Examples

## Not run: 
data(geese_data_day1)
simmr_1 <- with(
  geese_data_day1,
  simmr_load(
    mixtures = mixtures,
    source_names = source_names,
    source_means = source_means,
    source_sds = source_sds,
    correction_means = correction_means,
    correction_sds = correction_sds,
    concentration_means = concentration_means
  )
)

# Plot
plot(simmr_1)

# Print
simmr_1

# MCMC run
simmr_1_out <- simmr_mcmc(simmr_1)

# Prior predictive
prior <- prior_viz(simmr_1_out)
head(prior)
summary(prior)

## End(Not run)

simmr

A Stable Isotope Mixing Model

v0.4.5

GPL (>= 2)

Authors

Andrew Parnell

Initial release

2021-02-28