Function reference • traits.build

Building a dataset or compilation Functions that can be used when building individual datasets and entire compilation.
`build_setup_pipeline()`	Update the `remake.yml` file with new studies
`build_combine()`	Combine all the AusTraits studies into the compiled AusTraits database
`build_add_version()`	Add version information to AusTraits
`dataset_update_taxonomy()`	Apply taxonomic updates to austraits_raw
`dataset_build()`	Build dataset
`dataset_configure()`	Configure AusTraits database object
`dataset_process()`	Load Dataset
`dataset_report()`	Build reports for listed datasets
`get_schema()`	Load schema for an traits.build data compilation (excluding traits)
`get_unit_conversions()`	Make unit conversion functions
`util_get_SHA()`	Get SHA string from Github repository for latest commit
`util_get_version()`	Retrieve version for compilation from definitions
Creating metadata files Functions that help you create metadata files.
`dataset_test()`	Test whether specified `dataset_id` has the correct setup
`metadata_create_template()`	Create a template of file `metadata.yml` for specified `dataset_id`
`metadata_check_custom_R_code()`	Check the output of running `custom_R_code` specified in the metadata for specified `dataset_id`
`metadata_add_traits()`	For specified `dataset_id`, populate columns for traits into metadata
`metadata_add_contexts()`	For specified `dataset_id` import context data from a dataframe
`metadata_add_locations()`	For specified `dataset_id` import location data from a dataframe
`metadata_add_source_bibtex()`	Adds citation details to a metadata file for given study
`metadata_add_source_doi()`	Adds citation details from a doi to a metadata file for a `dataset_id`
`metadata_add_substitution()`	Add a categorical trait value substitution into a metadata file for a `dataset_id`
`metadata_add_substitutions_list()`	Add a dataframe of trait value substitutions into a metadata file for a dataset_id
`metadata_add_substitutions_table()`	Substitutions from a dataframe
`metadata_add_taxonomic_change()`	Add a taxonomic change into the `metadata.yml` file for a `dataset_id`
`metadata_add_taxonomic_changes_list()`	Add a list of taxonomic updates into a metadata file for a `dataset_id`
`metadata_find_taxonomic_change()`	Find `dataset_id`'s with a given taxonomic change
`metadata_remove_taxonomic_change()`	Remove a taxonomic change from a yaml file for a `dataset_id`
`metadata_update_taxonomic_change()`	Update a taxonomic change into a yaml file for a `dataset_id`
`metadata_exclude_observations()`	Exclude observations in a yaml file for a `dataset_id`
`dataset_find_taxon()`	Find list of unique datasets within compilation containing specified taxa
Reading & writing files Enable reading and writing of various file types.
`read_csv_char()`	Read in a csv as a tibble with column types as characters
`read_metadata()`	Read in a `metadata.yml` file for a study
`write_metadata()`	Write `metadata.yml` for a study
`read_yaml`	Read yaml (from package yaml)
`write_yaml`	write yaml (from package yaml)
`write_plaintext()`	Export AusTraits version as plain text
Working with outputs Functions to work with compiled traits.build objects.
`plot_trait_distribution_beeswarm()`	Beeswarm Trait distribution
`check_pivot_duplicates()`	Identify duplicates preventing pivoting wider
`check_pivot_wider()`	Test whether a dataset can pivot wider
`db_traits_pivot_longer()`	Pivot wide format data into a long format
`db_traits_pivot_wider()`	Pivot long format data into a wide format
Building a compilation (private) Private functions that are called in the background when building individual datasets and entire compilation. These are only of interest to developers.
`process_add_all_columns()`	Add or remove columns of data
`process_convert_units()`	Convert units to desired type
`process_create_observation_id()`	Create entity id
`process_custom_code()`	Apply custom data manipulations
`process_flag_excluded_observations()`	Flag any excluded observations
`process_flag_out_of_range_values()`	Flag values outside of allowable range
`process_flag_unsupported_characters()`	Flag values with unsupported characters
`process_flag_unsupported_traits()`	Flag any unrecognised traits
`process_flag_unsupported_values()`	Flag disallowed trait values and disallowed characters
`process_format_contexts()`	Format context data from list to tibble
`process_format_contributors()`	Format contributors from list into tibble
`process_format_locations()`	Format location data from list to tibble
`process_generate_id()`	Function to generate sequence of integer ids from vector of names Determines number of 00s needed based on number of records
`process_generate_method_ids()`	Function to generate sequence of integer ids for methods
`process_parse_data()`	Process a single dataset
`process_standardise_names()`	Standardise species names
`process_taxonomic_updates()`	Apply taxonomic updates
`process_unit_conversion_name()`	Generate unit conversion name
`dataset_test_worker()`	Test whether specified `dataset_id` has the correct setup
`metadata_path_dataset_id()`	Path to the `metadata.yml` file for specified `dataset_id`
`metadata_user_select_column()`	Select column by user
`metadata_user_select_names()`	Select variable names by user
`read_metadata_dataset()`	Read the `metadata.yml` file for specified `dataset_id`
`write_metadata_dataset()`	Write the YAML representation of `metadata.yml` for specified `dataset_id` to file `data/dataset_id/metadata.yml`
Diverse utility functions Diverse utility functions for converting and working with various data types.
`util_append_to_list()`	Add an item to the end of a list
`bib_print()`	Format BibEntry using RefManageR
`util_bib_to_list()`	Convert BibEntry object to a list
`util_check_all_values_in()`	Check values in one vector against values in another vector
`util_check_disallowed_chars()`	Check values in a vector do not contain disallowed characters
`util_df_convert_character()`	Convert all columns in data frame to character
`util_df_to_list()`	Convert dataframe to list
`util_extract_list_element()`	Extract a trait element from the definitions$traits$elements
`util_kable_styling_html()`	Format table with kable and default styling for html
`util_list_to_bib()`	Convert a list of elements into a BibEntry object
`util_list_to_df1()`	Convert a list with single entries to dataframe
`util_list_to_df2()`	Convert a list of lists to dataframe
`util_replace_null()`	Convert NULL values to a different value
`util_separate_and_sort()`	Split and sort cells with multiple values
`util_standardise_doi()`	Standardise doi
`create_tree_branch()`	Format a tree structure from a vector
Functions used when writing reports (private) Private functions used inside the template reports. These are only of interest to developers.
`notetaker_start()`	Start note recorder (needs review?)
`notetaker_add_note()`	Add a note to the note recorder as a new row
`notetaker_as_note()`	Create a tibble with two columns with note and link
`notetaker_get_note()`	Return a specific row from notes
`notetaker_print_all()`	Print all notes
`notetaker_print_note()`	Print note (needs review?)
`notetaker_print_notes()`	Print a specific row from notes
`notes_random_string()`	Create a string of random letters

Reference

Building a dataset or compilation

Creating metadata files

Reading & writing files

Working with outputs

Building a compilation (private)

Diverse utility functions

Functions used when writing reports (private)