Species Accumulation Curves for Camera Trap Data

Generates species accumulation, rarefaction and extrapolation curves from camera trap data using the iNEXT package (Chao et al. 2014). The function creates sampling effort-based accumulation curves with sampling units being either camera trap stations or days.

Note that these curves are based on observed detections only and do not account for imperfect detection. Species may be present but not detected, leading to underestimation of true species richness. For analyses that explicitly account for imperfect detection, consider using occupancy-based approaches (see communityModel).

speciesAccum(
  CTtable,
  recordTable,
  speciesCol,
  recordDateTimeCol,
  recordDateTimeFormat = "ymd HMS",
  setupCol,
  dateFormat = "ymd",
  stationCol,
  assemblageCol = NULL,
  q = 0,
  x_unit = c("station", "survey_day", "station_day"),
  knots = 40,
  conf = 0.95,
  nboot = 50,
  endpoint = NULL
)

Arguments

CTtable: data.frame containing the camera trap deployment information.
recordTable: data.frame containing the camera trap records.
speciesCol: character. Name of the column specifying species names in recordTable
recordDateTimeCol: character. Name of the column containing date and time information in recordTable
recordDateTimeFormat: character. Format of column recordDateTimeCol in recordTable
setupCol: character. Name of the column containing camera setup dates in CTtable
dateFormat: character. Format of column setupCol in CTtable
stationCol: character. Name of the column containing station IDs in both tables
assemblageCol: character. Optional. Name of column in recordTable for grouping data into separate assemblages
q: numeric. The order of diversity measure. Default is 0 (species richness)
x_unit: character. Whether to use "station" or "day" as sampling unit. Default is "station"
knots: numeric. number of values along x axis for which values are computed
conf: numeric. confidence interval
nboot: numeric. number of replications
endpoint: integer. Sample size used as endpoint for rarefaction/extrapolation (in iNEXT)

Value

An object of class "iNEXT" containing:

DataInfo - data information
iNextEst - diversity estimates for rarefied and extrapolated samples
AsyEst - asymptotic diversity estimates

Details

The function provides three types of curves:

Sample-size-based rarefaction/extrapolation curve
Sample completeness curve
Coverage-based rarefaction/extrapolation curve

While these curves provide useful insights into sampling completeness and species richness patterns, they should be interpreted with caution in camera trap studies. Unlike occupancy models, they do not account for:

Imperfect detection (species present but not detected)
Variation in detection probability among species
Spatial variation in species occurrence
Temporal variation in species activity

Note

Requires package iNEXT.

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(1), 45-67.

Author

Juergen Niedballa

Examples

if (FALSE) { # \dontrun{
# Basic usage with stations as sampling units
result <- speciesAccum(
  CTtable = cams,
  recordTable = recs,
  speciesCol = "Species",
  recordDateTimeCol = "DateTime", 
  setupCol = "Setup_date",
  stationCol = "Station",
  q = 0,
  x_unit = "station"
)

# Plot results
ggiNEXT(result, type = 1)  # Sample-size-based R/E curve
ggiNEXT(result, type = 2)  # Sample completeness curve
ggiNEXT(result, type = 3)  # Coverage-based R/E curve

# With assemblage grouping and days as sampling units
result_by_assemblage <- speciesAccum(
  CTtable = cams,
  recordTable = recs,
  speciesCol = "Species",
  recordDateTimeCol = "DateTime",
  setupCol = "Setup_date",
  stationCol = "Station",
  assemblageCol = "Season",
  q = 0,
  x_unit = "day"
)
} # }