get_annotation_completeness

Screen Data Package for Demographic Annotation Coverage. Identifies time periods and deployment windows where demographic attributes (lifeStage, sex, or custom fields) are actively annotated (non-NA).

Usage

get_annotation_completeness(
  package,
  fields = c("lifeStage", "sex"),
  mode = c("any", "all"),
  species = "all",
  by = "deploymentID"
)

Arguments

package

Camera trap data package object (as returned by read_camtrap_dp()).

fields

Character vector of column names in package$data$observations to evaluate. Defaults to c("lifeStage", "sex").

mode

Character string ("any" or "all"). "any" flags observations where at least one field is annotated; "all" requires all specified fields to be non-NA. Defaults to "any".

species

Scientific or vernacular species name(s) to filter on. Defaults to "all".

by

Character vector of column name(s) in package$data$deployments to group by (e.g., "deploymentID", "locationName"). Use "all" or NULL to screen the entire dataset. Defaults to "deploymentID".

Value

A tibble detailing observation counts, percentage annotated, first and last annotated timestamps, and total annotated duration (in days) per group.

Author

Martijn Bollen

Examples

if (FALSE) { # \dontrun{
# Data paths
zipfile <- "../fis-grofwild/Projecten/Drongengoed/Input/Agouti/drongengoed.zip"
exdir <- "../fis-grofwild/Projecten/Drongengoed/Input/Agouti/filesDRG"

# Download and unzip files
download_gdrive_if_missing("1F7mCj-Wm0Ggq1evz1HusxZBgX-1ttx-S", destfile = zipfile)
unzip(zipfile, exdir = exdir)

# Import as Camtrap DP
drg <- camtraptor::read_camtrap_dp(file.path(exdir, "datapackage.json"))

# Check deployments where EITHER lifeStage OR sex is annotated
drg$data$deployments <- drg$data$deployments %>%
mutate(year = year(start), month = month(start),
       year_month = floor_date(start, unit = "month"))

coverage_dep <- get_annotation_completeness(
package = drg,
fields = c("lifeStage", "sex"),
mode = "any",
species = "Capreolus capreolus",
by = "year_month"
)
} # }