ct_plot_inext: Plot diversity interploation and extrapolation

In ct: Camera Trap Data Management and Multi-Method Ecological Analysis

Plot diversity interploation and extrapolation

Description

plot sample-size-based and coverage-based rarefaction/extrapolation curves along with a bridging sample completeness curve

Usage

ct_plot_inext(
  inext_object,
  type = 1,
  se = TRUE,
  facet_var = "None",
  color_var = "Assemblage",
  grey = FALSE
)

Arguments

inext_object	an object as outputed by ct_inext()
type	three types of plots: type = 1: sample-size-based rarefaction/extrapolation curve type = 2: sample completeness curve type = 3: coverage-based rarefaction/extrapolation curve
se	a logical variable to display confidence interval around the estimated sampling curve.
facet_var	create a separate plot for each value of a specified variable: facet_var = "None": no separation facet_var = "Order.q": a separate plot for each diversity order facet_var = "Assemblage": a separate plot for each assemblage facet_var = "Both": a separate plot for each combination of order x assemblage
color_var	create curves in different colors for values of a specified variable: color_var = "None": all curves are in the same color color_var = "Order.q": use different colors for diversity orders color_var = "Assemblage": use different colors for sites color_var = "Both": use different colors for combinations of order x assemblage
grey	a logical variable to display grey and white ggplot2 theme

Value

a ggplot2 object

Examples

if (requireNamespace("iNEXT", quietly = TRUE)) {
## Import example data
data(penessoulou)
camdata1 <- penessoulou %>%
  dplyr::filter(project == "Last") %>%
  dplyr::mutate(site = "pene") %>%
  # remove consecutive entry of the same species at the same location within 60s
  ct_independence(species_column = species,
                  site_column = camera,
                  datetime = datetimes,
                  threshold = 60, format = "%Y-%m-%d %H:%M:%S"
                  )
head(camdata1)

# Prepare sampling data (camera-day)
camday <- ct_camera_day(
  data = camdata1,
  deployment_column = camera,
  datetime_column = datetime,
  species_column = species,
  size_column = number
)

# RAREFACTION/EXTRAPOLATION
int_ext <- ct_inext(data = camday,
                    diversity_order = c(0, 1, 2),
                    species_column = species,
                    site_column = sampling_unit,
                    size_column = number,
                    n_bootstrap = 50)
int_ext

# plot with curves colored by order
ct_plot_inext(int_ext, type = 1, color_var = "Order.q")

# plot with curves faceted by order
ct_plot_inext(int_ext, type = 1, facet_var = "Order.q")
 }

ct documentation built on Oct. 22, 2026, 1:07 a.m.