Package index • vaultkeepr

Connect

Open a connection to the VegVault database and explore its contents.

open_vault(): Open a vault
explore_vault(): Explore a vault

Get data

Retrieve data from the vault. Chain these after open_vault() to build a query plan.

Datasets

get_datasets(): get Datasets
get_common_dataset_type(): Get common dataset type

Samples

get_samples(): Get samples
get_age_uncertainty(): Get age uncertainties for samples

Taxa

get_taxa(): Get taxa information

Traits

get_traits(): Get trait values for the data

Abiotic data

get_abiotic_data(): Get abiotic data

Filter

Narrow the selection of datasets, samples, taxa, traits, and abiotic variables before extracting data.

Datasets

select_dataset_by_type(): get Datasets by selected type
select_dataset_by_geo(): Select dataset by geographical location

Samples

select_samples_by_age(): Select samples by age

Taxa

select_taxa_by_id(): Only select taxa by ID
select_taxa_by_name(): Only select taxa by name

Abiotic variables

select_abiotic_var_by_id(): Select abiotic variables by id
select_abiotic_var_by_name(): Select abiotic variables by name

Traits

select_traits_by_domain_name(): Select traits by domain name

Extract & process

Extract and post-process the selected data.

extract_data(): Extract data from a plan
pack_data(): Pack the data into nested tibbles
classify_taxa(): Classify taxa
get_classification_table(): Get the classification table for the data

References & citations

Retrieve data citations for the selected data.

get_references(): Get references for selected VegVault Plan

Utilities

Helper functions used in advanced workflows.

get_taxon_names(): Get taxon names from a vault plan
get_readable_column_names(): Get readable column names
stop_quietly(): Stop the script