Importing new studies

Functions that can be used when importing new studies

austraits_rebuild_remake_setup()

Update the remake.yml file with new studies

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_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_sites()

For specified `dataset_id` import site data from a dataframe

metadata_add_substitution()

Add a categorical trait value substitution into a metadata file for a dataset_id

metadata_check_taxa()

Check taxa against list of known species

Helpers to use in custom R code

separate_range()

Separate cells with a range to min and max

format_flowering_months()

Create flowering times from start to end pair

convert_month_range_string_to_binary()

Convert month range to 12 element binary string

convert_month_range_vec_to_binary()

Convert vectors of month range to 12 element character strings of binary data

Reports & quality checks

add_all_columns()

Add or remove columns of data

add_note()

Add a note to the note recorder as a new row

add_version_info()

Add version information to AusTraits

append_to_list()

Add an item to the end of a list

apply_taxonomic_updates()

Apply taxonomic updates

as_link()

Generate hyperlink for markdown and html

as_note()

Create a tibble with two columns with note and link

austraits_find_species()

Find list of all unique species within AusTraits

austraits_rebuild_remake_setup()

Update the remake.yml file with new studies

austraits_rebuild_taxon_list()

Builds list of potential species from the Australian Plant Census (APC) and Australian Plant Names Index (APNI)

bib_print()

Format BibEntry using RefManageR

bind_trait_values()

Title

build_study_report()

Build report for a specific study

build_study_reports()

Build reports for all studies

build_website()

Build website

check_all_values_in()

Check values in one vector against values in another vector

clean_NA()

Ensure NA appears as a real NA and not character

combine_austraits()

Combine all the AusTraits studies into the compiled AusTraits database

compare_versions()

<brief desc>

convert_01_ny()

Convert 0/1 to n/y

convert_bib_to_list()

Convert BibEntry object to a list

convert_list_to_bib()

Convert a list of elements into a BibEntry object

convert_month_range_string_to_binary()

Convert month range to 12 element binary string

convert_month_range_string_to_binary_worker()

Convert month range to binary

convert_month_range_vec_to_binary()

Convert vectors of month range to 12 element character strings of binary data

convert_units()

Convert units to desired type

create_release()

Create release

create_tree_branch()

Format a tree structure from a vector

custom_manipulation()

Apply custom data manipulations

df_to_list()

Convert dataframe to list

export_version_plaintext()

Export AusTraits version as plain text

extract_dataset()

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extract_list_element()

Extract a trait element from the definitions$traits$elements

extract_trait()

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find_names_distance_to_neighbours()

Find the distance for nearby species (needs review)

flag_excluded_observations()

Flag any excluded observations

flag_unsupported_traits()

Remove any disallowed traits

flag_unsupported_values()

Flag values outside of allowable range

format_flowering_months()

Create flowering times from start to end pair

format_sites()

Format sites (needs review)

gather_trait_data()

Title

get_SHA()

Get SHA string from Github repository for latest commit

get_SHA_link()

Get SHA link from Github

get_month()

Return month for given indices

get_note()

Return a specific row from notes

list1_to_df()

Convert a list with single entries to dataframe

list_to_df()

Convert a list of lists to dataframe

load_study()

Load Study

load_taxonomic_resources()

Load taxonomic resources from the APC and APNI

make_unit_conversion_functions()

Make unit conversion functions

metadata_add_contexts()

For specified `dataset_id` import context data from a dataframe

metadata_add_sites()

For specified `dataset_id` import site 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_taxonomic_change()

Add a taxonomic change into the metadata yaml file for a dataset_id

metadata_add_taxonomic_changes_list()

Add a dataframe of taxonomic updates into a metadata file for a dataset_id

metadata_add_traits()

For specified `dataset_id`, populate columns for traits into metadata

metadata_check_custom_R_code()

Check the output of running `custom_R_code` specified in the metadata for specified `dataset_id`

metadata_check_taxa()

Check taxa against list of known species

metadata_create_template()

Create a template of file `metadata.yml` for specified `dataset_id`

metadata_exclude_observations()

Exclude observations in a yaml file for a dataset_id

metadata_find_taxonomic_change()

Find taxonomic changes within the metadata yml files

metadata_path_dataset_id()

Path to the `metadata.yml` file for specified `dataset_id`

metadata_read_dataset_id()

Read the `metadata.yml` file for specified `dataset_id`

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_write_dataset_id()

Write the YAML representation of metadata.yml for specified `dataset_id` to file data/dataset_id/metadata.yml

my_kable_styling_html()

Format table with kable and default styling for html

my_kable_styling_markdown()

Format table with kable and default styling for markdown

my_kable_styling_pdf()

Format table with kable and default styling for pdf

null_as()

Swap a null value to something else

parse_data()

Process a single dataset

print_all_notes()

Print all notes

print_note()

Print note (needs review?)

print_notes()

Print a specific row from notes

random_string()

Create a string of random letters

read_csv_char()

Read in a csv as a tibble with column types as characters

rename_columns()

Rename columns

replace_duplicates_with_NA()

Replace duplicate values with NA

run_benchmark()

Check performance on current system using package bench

separate_range()

Separate cells with a range to min and max

separate_trait_values()

Title

split_then_sort()

Split and sort cells with multiple values

spread_trait_data()

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standardise_names()

Standardise species names

start_notetaker()

Start note recorder (needs review?)

subset_config()

Configure AusTraits database object (needs review)

test_data_setup()

Test AusTraits studies have the correct format

trait_distribution_plot_numerical()

Title

unit_conversion_name()

Generate unit conversion name

update_taxonomy()

Update taxonomy

user_select_column()

Select column by user

user_select_names()

Select variable names by user

write_yaml()

Write yaml to filename with preferred defaults, Designed so that read_yaml(write_yaml(y)) == y

Manipulating compiled AusTraits object

extract_dataset()

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extract_trait()

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bind_trait_values()

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separate_trait_values()

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gather_trait_data()

Title

spread_trait_data()

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trait_distribution_plot_numerical()

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Make changes to all studies

Misc support

append_to_list()

Add an item to the end of a list

as_link()

Generate hyperlink for markdown and html

create_tree_branch()

Format a tree structure from a vector

df_to_list()

Convert dataframe to list

extract_list_element()

Extract a trait element from the definitions$traits$elements

find_names_distance_to_neighbours()

Find the distance for nearby species (needs review)

get_SHA()

Get SHA string from Github repository for latest commit

get_SHA_link()

Get SHA link from Github

list1_to_df()

Convert a list with single entries to dataframe

list_to_df()

Convert a list of lists to dataframe

metadata_path_dataset_id()

Path to the `metadata.yml` file for specified `dataset_id`

metadata_read_dataset_id()

Read the `metadata.yml` file for specified `dataset_id`

metadata_write_dataset_id()

Write the YAML representation of metadata.yml for specified `dataset_id` to file data/dataset_id/metadata.yml

my_kable_styling_html()

Format table with kable and default styling for html

my_kable_styling_markdown()

Format table with kable and default styling for markdown

my_kable_styling_pdf()

Format table with kable and default styling for pdf

null_as()

Swap a null value to something else

rename_columns()

Rename columns

split_then_sort()

Split and sort cells with multiple values

write_yaml()

Write yaml to filename with preferred defaults, Designed so that read_yaml(write_yaml(y)) == y