Compare dietary proportions for a single source across different groups

This function takes in an object of class simmr_output and creates probabilistic comparisons for a given source and a set of at least two groups.

compare_groups(
  simmr_out,
  source_name = simmr_out$input$source_names[1],
  groups = 1:2,
  plot = TRUE
)

Arguments

simmr_out

An object of class simmr_output created from simmr_mcmc or simmr_ffvb.

source_name

The name of a source. This should match the names exactly given to simmr_load.

groups

The integer values of the group numbers to be compared. At least two groups must be specified.

plot

A logical value specifying whether plots should be produced or not.

Value

If there are two groups, a vector containing the differences between the two groups proportions for that source. If there are multiple groups, a list containing the following fields:

Ordering

The different possible orderings of the dietary proportions across groups

out_all

The dietary proportions for this source across the groups specified as columns in a matrix

Details

When two groups are specified, the function produces a direct calculation of the probability that one group is bigger than the other. When more than two groups are given, the function produces a set of most likely probabilistic orderings for each combination of groups. The function produces boxplots by default and also allows for the storage of the output for further analysis if required.

See also

See simmr_mcmc for complete examples.

Author

Andrew Parnell <andrew.parnell@mu.ie>

Examples

if (FALSE) {
data(geese_data)
simmr_in <- with(
  geese_data,
  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,
    group = groups
  )
)

# Print
simmr_in

# Plot
plot(simmr_in,
  group = 1:8, xlab = expression(paste(delta^13, "C (per mille)", sep = "")),
  ylab = expression(paste(delta^15, "N (per mille)", sep = "")),
  title = "Isospace plot of Inger et al Geese data"
)

# Run MCMC for each group
simmr_out <- simmr_ffvb(simmr_in)

# Print output
simmr_out

# Summarise output
summary(simmr_out, type = "quantiles", group = 1)
summary(simmr_out, type = "quantiles", group = c(1, 3))
summary(simmr_out, type = c("quantiles", "statistics"), group = c(1, 3))

# Plot - only a single group allowed
plot(simmr_out, type = "boxplot", group = 2, title = "simmr output group 2")
plot(simmr_out, type = c("density", "matrix"), grp = 6, title = "simmr output group 6")

# Compare groups
compare_groups(simmr_out, source = "Zostera", groups = 1:2)
compare_groups(simmr_out, source = "Zostera", groups = 1:3)
compare_groups(simmr_out, source = "U.lactuca", groups = c(4:5, 7, 2))
}