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_pkgdown.yml
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url: http://traitecoevo.github.io/traits.build/
template:
bootswatch: cosmo
assets: "ontology/output"
home:
links:
- text: AusTraits
href: https://github.com/traitecoevo/austraits.build
navbar:
type: default
left:
- text: home
icon: fas fa-home fa-lg
href: index.html
- text: Functions
icon: fa-list
href: reference/index.html
- text: Manual
icon: fa-book
href: https://traitecoevo.github.io/traits.build-book/
- text: Ontology
icon: fa-book
href: ontology/index.html
- text: News
href: news/index.html
right:
- icon: fa-github fa-lg
href: https://github.com/traitecoevo/traits.build
reference:
- title: Building a dataset or compilation
desc: Functions that can be used when building individual datasets and entire compilation.
contents:
- '`build_setup_pipeline`'
- '`build_add_version`'
- '`dataset_update_taxonomy`'
- '`dataset_build`'
- '`dataset_configure`'
- '`dataset_process`'
- '`dataset_report`'
- '`get_schema`'
- '`get_unit_conversions`'
- '`util_get_SHA`'
- '`util_get_version`'
- title: Creating metadata files
desc: Functions that help you create metadata files.
contents:
- '`dataset_test`'
- '`metadata_create_template`'
- '`metadata_check_custom_R_code`'
- '`metadata_add_traits`'
- '`metadata_add_contexts`'
- '`metadata_add_locations`'
- '`metadata_add_source_bibtex`'
- '`metadata_add_source_doi`'
- '`metadata_add_substitution`'
- '`metadata_add_substitutions_list`'
- '`metadata_add_substitutions_table`'
- '`metadata_add_taxonomic_change`'
- '`metadata_add_taxonomic_changes_list`'
- '`metadata_find_taxonomic_change`'
- '`metadata_remove_taxonomic_change`'
- '`metadata_update_taxonomic_change`'
- '`metadata_exclude_observations`'
- '`dataset_find_taxon`'
- title: Reading & writing files
desc: Enable reading and writing of various file types.
contents:
- '`read_csv_char`'
- '`read_metadata`'
- '`write_metadata`'
- '`read_yaml`'
- '`write_yaml`'
- '`write_plaintext`'
- title: Working with outputs
desc: Functions to work with compiled traits.build objects.
contents:
- '`check_pivot_duplicates`'
- '`check_pivot_wider`'
- title: Building a compilation (private)
desc: Private functions that are called in the background when building individual datasets and entire compilation. These are only of interest to developers.
contents:
- '`process_add_all_columns`'
- '`process_convert_units`'
- '`process_create_observation_id`'
- '`process_custom_code`'
- '`process_flag_excluded_observations`'
- '`process_flag_out_of_range_values`'
- '`process_flag_unsupported_characters`'
- '`process_flag_unsupported_traits`'
- '`process_flag_unsupported_values`'
- '`process_format_contexts`'
- '`process_format_contributors`'
- '`process_format_locations`'
- '`process_generate_id`'
- '`process_generate_method_ids`'
- '`process_parse_data`'
- '`process_standardise_names`'
- '`process_taxonomic_updates`'
- '`process_unit_conversion_name`'
- '`dataset_test_worker`'
- '`metadata_path_dataset_id`'
- '`metadata_user_select_column`'
- '`metadata_user_select_names`'
- '`read_metadata_dataset`'
- '`write_metadata_dataset`'
- title: Diverse utility functions
desc: Diverse utility functions for converting and working with various data types.
contents:
- '`util_append_to_list`'
- '`bib_print`'
- '`util_append_to_list`'
- '`util_bib_to_list`'
- '`util_check_all_values_in`'
- '`util_check_disallowed_chars`'
- '`util_df_convert_character`'
- '`util_extract_list_element`'
- '`util_kable_styling_html`'
- '`util_list_to_bib`'
- '`util_replace_null`'
- '`util_separate_and_sort`'
- '`util_standardise_doi`'
- '`create_tree_branch`'
- title: Functions used when writing reports (private)
desc: Private functions used inside the template reports. These are only of interest to developers.
contents:
- '`notetaker_start`'
- '`notetaker_add_note`'
- '`notetaker_as_note`'
- '`notetaker_get_note`'
- '`notetaker_print_all`'
- '`notetaker_print_note`'
- '`notetaker_print_notes`'
- '`notes_random_string`'
- title: Deprecated function names
desc: Functions that have been moved from traits.build to austraits and renamed. Deprecated names still work.
contents:
- '`build_combine`'
- '`util_df_to_list`'
- '`util_list_to_df1`'
- '`util_list_to_df2`'