Query plots from database — query_plots • plotsdatabase

This function queries a PostgreSQL inventory database to return a list of forest plots or individuals, with options to include associated traits and metadata, and to generate interactive maps.

Usage

query_plots(
  plot_name = NULL,
  tag = NULL,
  country = NULL,
  locality_name = NULL,
  method = NULL,
  extract_individuals = FALSE,
  map = FALSE,
  id_individual = NULL,
  id_plot = NULL,
  id_tax = NULL,
  id_specimen = NULL,
  show_multiple_census = FALSE,
  show_all_coordinates = FALSE,
  remove_ids = TRUE,
  collapse_multiple_val = FALSE,
  extract_traits = TRUE,
  extract_individual_features = TRUE,
  traits_to_genera = FALSE,
  wd_fam_level = FALSE,
  include_liana = FALSE,
  extract_subplot_features = TRUE,
  concatenate_stem = FALSE,
  remove_obs_with_issue = TRUE,
  include_issue = FALSE,
  include_measurement_ids = FALSE,
  output_style = c("auto", "minimal", "standard", "permanent_plot", "transect", "full")
)

Arguments

plot_name: Optional. A single string specifying plot name.
tag: Optional. Tag identifier.
country: Optional. A single string specifying country.
locality_name: Optional. A single string specifying locality name.
method: Optional. Method identifier.
extract_individuals: Logical. Whether to extract individuals. Optional.
map: Logical. Whether to generate map. Optional.
id_individual: Optional. Individual identifiers.
id_plot: Optional. Plot identifiers.
id_tax: Optional. Taxonomic identifiers.
id_specimen: Optional. Specimen identifiers.
show_multiple_census: Logical. Whether to show multiple census data. Optional.
show_all_coordinates: Logical. Whether to show all coordinates. Optional.
remove_ids: Logical. Whether to remove ID columns from output. Optional.
collapse_multiple_val: Logical. Whether to collapse multiple values. Optional.
extract_traits: Logical. Whether to extract taxonomic traits. Optional.
extract_individual_features: Logical. Whether to extract individual-level features. Optional.
traits_to_genera: Logical. Whether to aggregate traits to genus level. Optional.
wd_fam_level: Logical. Whether to use family-level wood density. Optional.
include_liana: Logical. Whether to include lianas. Optional.
extract_subplot_features: Logical. Whether to extract subplot features. Optional.
concatenate_stem: Logical. Whether to concatenate multiple stems. Optional.
remove_obs_with_issue: Logical. Whether to remove observations with issues. Optional.

Value

A list or data frame containing plot data and associated information. When multiple components are requested, returns a list with elements like `extract`, `census_features`, `coordinates`, and `coordinates_sf`. If only one component is available, returns that component directly. Returns `NA` if no plots are found matching the criteria.

Examples

if (FALSE) { # \dontrun{
  query_plots(country = "Gabon", extract_individuals = FALSE)
  
  query_plots(country = "Cameroon")
  
  query_plots(plot_name = "mbalmayo001")
} # }