Skip to contents

Interpolation and extrapolation of Hill number

Source: R/ct_inext.R
ct_inext.Rd

Computes incidence-based species diversity estimates (Hill numbers) from camera trap data. This is a wrapper around iNEXT package (Chao et al., 2014; Hsieh, Ma, & Chao, 2016).

Usage

ct_inext(
  data,
  species_column,
  site_column,
  size_column,
  strata_column = NULL,
  diversity_order = 0,
  sample_size = NULL,
  endpoint = NULL,
  knots = 40,
  n_bootstrap = 100
)

Arguments

data

A data frame, preferably the output of ct_camera_day().

species_column

The column in the data frame representing species identifiers. Can be specified as a string or unquoted column name.

site_column

The column in the data frame representing site identifiers. Can be specified as a string or unquoted column name.

size_column

(Optional) The column representing the size or abundance of the species at each site. If not provided, counts of species occurrences are calculated.

strata_column

Optional column name for a grouping variable (e.g. habitat, treatment). If provided, estimates are computed separately for each stratum.

diversity_order

Numeric specifying the order of diversity (q) for Hill numbers. Common values:

  • 0 = species richness,

  • 1 = Shannon diversity (exponential of Shannon entropy),

  • 2 = Simpson diversity (inverse of Simpson index). Defaults to 0.

sample_size

Optional numeric vector specifying sample sizes for interpolation/extrapolation.

endpoint

Optional numeric specifying the maximum sample size for extrapolation. If NULL, endpoint is the double of the current sample size

knots

Integer specifying the number of equally spaced knots for rarefaction/extrapolation. Default is 40.

n_bootstrap

Number of bootstrap replications for estimating confidence intervals. Default is 100.

Value

A list containing:

  • DataInfo: Summary statistics of input data.

  • iNextEst: Rarefaction/extrapolation results for specified diversity order.

  • AsyEst: Asymptotic diversity estimates.

Details

This function converts the input data into an incidence-frequency vector. The first element of the vector is the number of sampling units, followed by species frequencies. If strata_column is provided, the conversion is done separately for each stratum.

References

Chao, A., Gotelli, N. J., Hsieh, T. C., Sander, E. L., Ma, K. H., Colwell, R. K., & Ellison, A. M. (2014). Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecological Monographs, 84, 45–67. doi:https://doi.org/10.1890/13-0133.1

Hsieh, T. C., Ma, K. H., & Chao, A. (2016). iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods in Ecology and Evolution, 7(12), 1451–1456. doi:10.1111/2041-210X.12613

See also

ct_camera_day() for preparing sampling data (camera-day).

Examples

if (requireNamespace("iNEXT", quietly = TRUE)) {
## Import example data
camdata1 <- read.csv(ct:::table_files()[1]) %>%
  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")
 }
#> Warning: Insufficient data to provide reliable estimators and associated s.e.
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the iNEXT package.
#>   Please report the issue at <https://github.com/AnneChao/iNEXT/issues>.
#> Warning: invalid color.var setting, the iNEXT object do not consist multiple assemblages, change setting as Order.q