R: Plot the 'simmr_input' data created from 'simmr

plot.simmr_input {simmr}

R Documentation

Plot the `simmr_input` data created from `simmr_load`

Description

This function creates iso-space (AKA tracer-space or delta-space) plots. They are vital in determining whether the data are suitable for running in a SIMM.

Usage

## S3 method for class 'simmr_input'
plot(
  x,
  tracers = c(1, 2),
  title = "Tracers plot",
  xlab = colnames(x$mixtures)[tracers[1]],
  ylab = colnames(x$mixtures)[tracers[2]],
  sigmas = 1,
  group = 1:x$n_groups,
  mix_name = "Mixtures",
  ggargs = NULL,
  colour = TRUE,
  ...
)

Arguments

`x`	An object of class `simmr_input` created via the function `simmr_load`
`tracers`	The choice of tracers to plot. If there are more than two tracers, it is recommended to plot every pair of tracers to determine whether the mixtures lie in the mixing polygon defined by the sources
`title`	A title for the graph
`xlab`	The x-axis label. By default this is assumed to be delta-13C but can be made richer if required. See examples below.
`ylab`	The y-axis label. By default this is assumed to be delta-15N in per mil but can be changed as with the x-axis label
`sigmas`	The number of standard deviations to plot on the source values. Defaults to 1.
`group`	Which groups to plot. Can be a single group or multiple groups
`mix_name`	A optional string containing the name of the mixture objects, e.g. Geese.
`ggargs`	Extra arguments to be included in the ggplot (e.g. axis limits)
`colour`	If TRUE (default) creates a plot. If not, puts the plot in black and white
`...`	Not used

Details

It is desirable to have the vast majority of the mixture observations to be inside the convex hull defined by the food sources. When there are more than two tracers (as in one of the examples below) it is recommended to plot all the different pairs of the food sources. See the vignette for further details of richer plots.

Value

isospace plot

Author(s)

Andrew Parnell <andrew.parnell@mu.ie>

Examples


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

### A more complicated example with 30 obs, 3 tracers and 4 sources
data(simmr_data_2)
simmr_3 <- with(
  simmr_data_2,
  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 3 times - first default d13C vs d15N
plot(simmr_3)
# Now plot d15N vs d34S
plot(simmr_3, tracers = c(2, 3))
# and finally d13C vs d34S
plot(simmr_3, tracers = c(1, 3))
# See vignette('simmr') for fancier x-axis labels

# An example with multiple groups - the Geese data from Inger et al 2006
data(geese_data)
simmr_4 <- 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_4

# Plot
plot(simmr_4,
  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"
) #'

[Package simmr version 0.5.1.216 Index]

Plot the simmr_input data created from simmr_load