simmr: plot.simmr_output – R documentation

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plot.simmr_output

Plot different features of an object created from simmr_mcmc.

Description

This function allows for 4 different types of plots of the simmr output created from simmr_mcmc. The types are: histogram, kernel density plot, matrix plot (most useful) and boxplot. There are some minor customisation options.

Usage

## S3 method for class 'simmr_output'
plot(
  x,
  type = c("isospace", "histogram", "density", "matrix", "boxplot"),
  group = 1,
  binwidth = 0.05,
  alpha = 0.5,
  title = if (length(group) == 1) {     "simmr output plot" } else {    
    paste("simmr output plot: group", group) },
  ggargs = NULL,
  ...
)

Arguments

`x`	An object of class `simmr_output` created via `simmr_mcmc`
`type`	The type of plot required. Can be one or more of 'histogram', 'density', 'matrix', or 'boxplot'
`group`	Which group(s) to plot.
`binwidth`	The width of the bins for the histogram. Defaults to 0.05
`alpha`	The degree of transparency of the plots. Not relevant for matrix plots
`title`	The title of the plot.
`ggargs`	Extra arguments to be included in the ggplot (e.g. axis limits)
`...`	Currently not used

Details

The matrix plot should form a necessary part of any SIMM analysis since it allows the user to judge which sources are identifiable by the model. Further detail about these plots is provided in the vignette.

Author(s)

Andrew Parnell <andrew.parnell@mu.ie>

Examples

## Not run: 
# A simple example with 10 observations, 2 tracers and 4 sources

# The data
data(geese_data)

# Load into simmr
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)


# MCMC run
simmr_1_out <- simmr_mcmc(simmr_1)

# Plot
plot(simmr_1_out) # Creates all 4 plots
plot(simmr_1_out, type = "boxplot")
plot(simmr_1_out, type = "histogram")
plot(simmr_1_out, type = "density")
plot(simmr_1_out, type = "matrix")

## End(Not run)

simmr

A Stable Isotope Mixing Model

v0.4.5

GPL (>= 2)

Authors

Andrew Parnell

Initial release

2021-02-28