Upload data to VegBank — vb_upload • vegbankr

Upload data to VegBank via the REST API. vb_upload() is the core function that can upload to any of the supported POST endpoints. Resource-specific functions like vb_upload_plot_observations() are convenience wrappers that apply resource-specific validation. For typical usage, the resource-specific functions should be preferred.

Usage

vb_upload(resource, ..., query_params = NULL, dry_run = FALSE)

vb_upload_plot_observations(
  plot_observations,
  projects = NULL,
  parties = NULL,
  references = NULL,
  soils = NULL,
  disturbances = NULL,
  community_classifications = NULL,
  strata = NULL,
  strata_cover_data = NULL,
  stem_data = NULL,
  taxon_interpretations = NULL,
  contributors = NULL,
  dry_run = FALSE
)

vb_upload_plant_concepts(
  plant_concepts,
  plant_names = NULL,
  plant_correlations = NULL,
  parties = NULL,
  references = NULL,
  what_to_deactivate = NULL,
  dry_run = FALSE
)

vb_upload_community_concepts(
  community_concepts,
  community_names = NULL,
  community_correlations = NULL,
  parties = NULL,
  references = NULL,
  what_to_deactivate = NULL,
  dry_run = FALSE
)

vb_upload_taxon_interpretations(
  taxon_interpretations,
  parties = NULL,
  references = NULL,
  dry_run = FALSE
)

vb_upload_community_classifications(
  community_classifications,
  parties = NULL,
  references = NULL,
  contributors = NULL,
  dry_run = FALSE
)

vb_upload_cover_methods(cover_methods, references = NULL, dry_run = FALSE)

vb_upload_stratum_methods(stratum_methods, references = NULL, dry_run = FALSE)

Arguments

resource: Available only for vb_upload(). Character string specifying the VegBank resource type to upload (e.g., "plot-observations", "projects").
...: Named data frames to upload. Each data frame should correspond to a table expected by the VegBank API for the specified resource. All arguments must be named, and at least one data frame must be provided.
query_params: A named list of parameter names and values to pass to the API as query parameters. For example, list(foo="bar") will be treated as ?foo=bar in the request URL.
dry_run: Logical indicating whether to perform a dry run. If TRUE, the API will validate the data without committing changes to the database. Default is FALSE.
plot_observations: A data frame containing details about plot observations
projects: A data frame containing details about new projects
parties: A data frame containing details about new parties
references: A data frame containing details about new references
soils: A data frame containing details about observed soils
disturbances: A data frame containing details about observed disturbances
community_classifications: A data frame containing community classifications of observed plots
strata: A data frame containing details about strata defined for plot observations
strata_cover_data: A data frame containing details about plant cover as observed in different strata of a plot
stem_data: A data frame containing details about counts and/or other details about stems observed on a plot
taxon_interpretations: A data frame containing taxon interpretations of plants observed on a plot
contributors: A data frame associating parties with their contributions to plot observations, projects, and/or community classifications
plant_concepts: A data frame containing plant concepts as plant names associated with references, along with with status details and taxonomic parents
plant_names: A data frame containing plant name usages associated with specific classification systems for new plant concepts
plant_correlations: A data frame defining correlations between plant concepts
what_to_deactivate: Available only for vb_upload_plant_concepts() and vb_upload_community_concepts(). Character string specifying what existing concepts to deactivate in VegBank. Supported values are "none" and "by_party", along with "by_party_below_order" for plant uploads only. VegBank default is none.
community_concepts: A data frame containing community concepts as community names associated with references, along with with status details and taxonomic parents
community_names: A data frame containing community name usages associated with specific classification systems for new community concepts
community_correlations: A data frame defining correlations between community concepts
cover_methods: A data frame containing cover methods and their associated component cover indexes
stratum_methods: A data frame containing stratum methods and their associated component stratum types

Value

The processed response object from the VegBank API documenting what (if anything) was successfully uploaded to VegBank.

Details

The vb_upload*() family of functions can all be used to upload data to VegBank queries, with each one differing in terms of what input dataframes are expected (and, in some case, required).

Available resource-specific functions:

vb_upload_plot_observations() - Plot observational data, including soil and disturbance observations, plant taxon observations and importance assessments (potentially including stem-level details) within any defined strata, and both individual plant taxon and overall vegetation community interpretation.
vb_upload_plant_concepts() - Plant concepts linked to plant names through usages, with some status designation
vb_upload_community_concepts() - Community concepts linked to community names through usages, with some status designation
vb_upload_taxon_interpretations() - Re-interpretation of existing observation), associating them with one or more VegBank plant concepts
vb_upload_community_classifications() - Re-interpretation of existing VegBank plot observations, associating them with one or more VegBank community concepts as part of a classification activity
vb_upload_cover_methods() - New cover methods, including all component cover indexes defined by the method
vb_upload_stratum_methods() - New stratum methods, including all component stratum types defined by the method

If vb_debug() is enabled, additional debugging details will be reported to the console, primarily focused on the data being uploaded.