R: Summarises the output created with 'cosimmr

summary.cosimmr_pred_out {cosimmr}

R Documentation

Summarises the output created with `cosimmr_ffvb`

Description

Produces textual summaries and convergence diagnostics for an object created with cosimmr_ffvb. The different options are: 'quantiles' which produces credible intervals for the parameters, 'statistics' which produces means and standard deviations, and 'correlations' which produces correlations between the parameters.

Usage

## S3 method for class 'cosimmr_pred_out'
summary(
  object,
  type = c("quantiles", "statistics", "correlations"),
  obs = 1,
  ...
)

Arguments

`object`	An object of class `cosimmr_pred_output` produced by the function `predict.cosimmr_output`
`type`	The type of output required. At least none of quantiles', 'statistics', or 'correlations'.
`obs`	The observation to generate a summary for. Defaults to 1.
`...`	Not used

Details

The quantile output allows easy calculation of 95 per cent credible intervals of the posterior dietary proportions. The correlations allow the user to judge which sources are non-identifiable.

Value

A list containing the following components:

`quantiles`	The quantiles of each parameter from the posterior distribution
`statistics`	The means and standard deviations of each parameter
`correlations`	The posterior correlations between the parameters

Note that this object is reported silently so will be discarded unless the function is called with an object as in the example below.

Author(s)

Emma Govan <emmagovan@gmail.com> Andrew Parnell

Examples


# A simple example with 10 observations, 2 tracers and 4 sources

# The data
data(geese_data_day1)
cosimmr_1 <- with(
  geese_data_day1,
  cosimmr_load(
    formula = mixtures ~ c(1,2,3,3,2,3,1,2,1),
    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(cosimmr_1)


# FFVB run
cosimmr_1_out <- cosimmr_ffvb(cosimmr_1)

# Summarise
summary(cosimmr_1_out) # This outputs all the summaries
summary(cosimmr_1_out, type = "quantiles") # Just the diagnostics
# Store the output in ans
ans <- summary(cosimmr_1_out,
  type = c("quantiles", "statistics")
)

[Package cosimmr version 1.0.12 Index]

Summarises the output created with cosimmr_ffvb