plot_quantums

Plot simulation envelopes

Usage

plot_quantums(
  input,
  labels = NULL,
  color_scale = NULL,
  legend_position = "bottom",
  quantum_position = NULL,
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  line_size = 0.5,
  base_size = 15,
  full_fun = TRUE,
  quantum = TRUE,
  standarized = FALSE
)

Arguments

input

envelope.

labels

Name of the labels. See details for more information.

color_scale

Colors used with labels.

legend_position

The position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector)

quantum_position

Vector with minimum and maximum y value of the quantum bar.

title

Plot title.

xlab, ylab

axis labels.

line_size

Size of the lines.

base_size

Base font size.

full_fun

If true observed value and envelope is plotted.

quantum

If true quantums bars are plotted.

standarized

If true observed value is standardized. See details for more details.

Value

ggplot

Details

This functions provides a plotting style for envelope objects of the spatstat package (for more information please see spatstat.explore::envelope). The location of the observed value in relation to the simulation envelope of the null model input is indicated by an additional colour bar at the bottom of the plot. If standarized = TRUE, all values are standarized by subtracting the theoretical value for CSR

Labels must be a vector including labels for the following three cases. The color scale vector is used in the same order.
1 = observed > high
2 = low < observed < high
3 = observed < low

To adjust the position of the quantum bar, use quantum_position.

Returns a ggplot object.

References

Esser, D.S., Leveau, J.H.J., Meyer, K.M., Wiegand, K., 2015. Spatial scales of interactions among bacteria and between bacteria and the leaf surface. FEMS Microbiology Ecology 91, 1–13. <https://doi.org/10.1093/femsec/fiu034>

See also

envelope

Examples

set.seed(42)
pattern <- spatstat.random::rThomas(kappa = 50, scale = 0.025, mu = 5)
csr_envelope <- spatstat.explore::envelope(pattern, fun = spatstat.explore::pcf, nsim = 19)
#> Generating 19 simulations of CSR  ...
#> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 
#> 19.
#> 
#> Done.
plot_quantums(csr_envelope, ylab = "g(r)")