Plot the cosimmr_input data created from cosimmr_load

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.

# S3 method for cosimmr_input
plot(
  x,
  tracers = c(1, 2),
  title = "Tracers plot",
  xlab = colnames(x$mixtures)[tracers[1]],
  ylab = colnames(x$mixtures)[tracers[2]],
  sigmas = 1,
  mix_name = "Mixtures",
  colour = TRUE,
  colour_by_cov = FALSE,
  cov_name = NULL,
  ggargs = NULL,
  ...
)

Arguments

x

An object created via the function cosimmr_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.

mix_name

A optional string containing the name of the mixture objects, e.g. Geese.

colour

If TRUE (default) creates a plot. If not, puts the plot in black and white

colour_by_cov

if TRUE this allows users to colour the mixtures on the isospace plot by a specified covariate. Defaults to FALSE

cov_name

The name of the covariate the user wishes to colour the mixture points on the plot by

ggargs

Extra arguments to be included in the ggplot (e.g. axis limits)

...

Not used

Value

isospace plot

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.

See also

See plot.cosimmr_output for plotting the output of a simmr run. See cosimmr_ffvb for running a cosimmr object once the iso-space is deemed acceptable.

Author

Emma Govan <emmagovan@gmail.com>, Andrew Parnell

Examples

# \donttest{
# A simple example with 10 observations, 4 food sources and 2 tracers
data(geese_data_day1)
cosimmr_1 <- with(
  geese_data_day1,
  cosimmr_load(
    formula = mixtures ~ c(1,2,3,2,3,1,2,3,1),
    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)


### A more complicated example with 30 obs, 3 tracers and 4 sources
data(simmr_data_2)
cosimmr_3 <- with(
  simmr_data_2,
  cosimmr_load(
    formula = mixtures ~ 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
  )
)
#> Cannot scale when using mixtures ~1

# Plot 3 times - first default d13C vs d15N
plot(cosimmr_3)

# Now plot d15N vs d34S
plot(cosimmr_3, tracers = c(2, 3))

# and finally d13C vs d34S
plot(cosimmr_3, tracers = c(1, 3))

# }