Function reference • wastdr

API access
`build_auth()`	Build token or basic authentication based on given credentials
`download_minimal_wastd_turtledata()`	Download a minimal dataset of turtle observations from WAStD
`download_wastd_sites()`	Download Areas of type Site from WAStD
`download_wastd_turtledata()`	Download all turtle data from WAStD
`download_wastd_users()`	Download a minimal dataset of turtle observations from WAStD
`export_wastd_turtledata()`	Export all WAStD turtledata to CSV and GeoJSON files
`filter_wastd_turtledata()`	Filter WAStD turtledata to an area_name
`filter_wastd_turtledata_area()`	Filter WAStD turtledata to an area_name
`filter_wastd_turtledata_seasons()`	Filter WAStD turtledata to a season range
`handle_http_status()`	Emit a specific warning messages depending on HTTP status
`wastd_GET()`	Return GeoJSON features from a WAStD API endpoint
`wastd_POST()`	Send a POST request to WAStD's API
`wastd_bulk_post()`	Post a list of records to a WAStD or TSC API endpoint
`wastd_chunk_post()`	POST data to a WAStD API serializer in chunks
`wastd_create_update_skip()`	Create, update, skip records to a WAStD serializer.
`wastd_parse()`	Parse a `wastd_api_response` into a tibble
`wastd_post_one()`	Post a one record to a WAStD / TSC API endpoint
WA Sea Turtles DB
`add_nest_labels()`	Add labels for species and nest/track type to parsed `turtle-nest-encounters`.
`disturbance_by_season()`	Tally WAStD disturbances by season, cause, and encounter type
`filter_alive()`	Filter animal encounters to live outcomes: tagging, in water, and rescues
`filter_dead()`	Filter animal encounters to mortalities: strandings
`filter_disturbance()`	Filter disturbance data to disturbances
`filter_predation()`	Filter disturbance data to predator presences
`ggplot_disturbance_by_season()`	Plot disturbance by season
`ggplot_emergence_success()`	Plot Emergence Success for excavations of hatched nests
`ggplot_hatching_success()`	Plot HS for excavations of hatched nests
`ggplot_hatchling_misorientation()`	Return a ggplot violin plot of hatchling emergence misorientation
`ggplot_nesting_success_per_area_season_species()`	Return a stacked ggplot barchart of emergences
`ggplot_nesting_success_per_area_season_species_pct()`	Return a ggplot of nesting success
`ggplot_sighting_status_per_area_season_species()`	Return a stacked ggplot barchart of processed emergences by recapture status
`ggplot_total_emergences_per_area_season_species()`	Return a stacked ggplot barchart of emergences by processing status
`ggplot_track_success_by_date()`	Plot the track success (absolute numbers) of a given species as time series
`ggplot_track_successrate_by_date()`	Plot the track success rate (relative numbers) of a given species as time series
`hatching_emergence_success()`	Summarize HS and ES for Nest excavations
`hatching_emergence_success_area()`	Summarize HS for excavations of hatched nests grouped by `area_name`
`hatching_emergence_success_site()`	Summarize HS and ES for excavations of hatched nests grouped by `site_name`
`map_dist()`	Map nest and general disturbance observations interactively.
`map_fanangles()`	Map turtle hatchling emergence orientation from wastd_data
`map_mwi()`	Map Marine Wildlife Incident 0.6
`map_nests()`	Map tagged Turtle Nests interactively.
`map_tracks()`	Map TurtleNestEncounters interactively.
`map_wastd()`	Map Marine Wildlife Incident 0.6
`map_wastd_wamtram_sites()`	Map WAStD and WAMTRAM sites
`nesting_success_per_area_day_species()`	Calculate nesting success for emergences per area, day (turtle_date), species
`nesting_success_per_area_season_species()`	Calculate nesting success for emergences per area, season, species
`nesting_type_by_area_season_age_species()`	Pivot table of nesting type by area, season, track age, and species
`nesting_type_by_area_season_species()`	Pivot table of nesting type by area, season, and species
`nesting_type_by_season_age_species()`	Pivot table of nesting type by season, track age and species
`nesting_type_by_season_calendarday_age_species()`	Pivot table of nesting type by season, calendardate, and track age, and species
`nesting_type_by_season_calendarday_species()`	Pivot table of nesting type by season, calendardate, and species
`nesting_type_by_season_day_species()`	Pivot table of nesting type by season, turtle date. and species
`nesting_type_by_season_species()`	Pivot table of nesting type by season and species
`nesting_type_by_season_week_age_species()`	Pivot table of nesting type by season, season_week, iso_week, track age, and species
`nesting_type_by_season_week_site_species()`	Pivot table of nesting type by season, season_week, iso_week, and species
`nesting_type_by_season_week_species()`	Pivot table of nesting type by season, season_week, iso_week, and species
`nesting_type_by_site_season_age_species()`	Pivot table of nesting type by site, season, track age, and species
`nesting_type_by_site_season_species()`	Pivot table of nesting type by site, season, and species
`parse_animal_encounters()`	Parse a `wastd_api_response` of `animal-encounters` to tbl_df
`parse_area()`	Parse a `wastd_api_response` of `area` to tbl_df
`parse_area_sf()`	Parse a `wastd_api_response` of `area` to tbl_df and sf
`parse_encounterobservations()`	Parse a `wastd_api_response` of Encounter observations to tbl_df
`parse_surveys()`	Parse a `wastd_api_response` of `surveys` to tbl_df
`parse_turtle_nest_encounters()`	Parse a `wastd_api_response` of `turtle-nest-encounters` to tbl_df
`print(<wastd_api_response>)`	S3 print method for 'wastd_api_response'.
`sighting_status_per_area_season_species()`	Calculate sighting status for emergences per area, season, species
`sighting_status_per_site_season_species()`	Calculate sighting status for emergences per site, season, species
`summarise_hatching_and_emergence_success()`
`summarise_wastd_data_per_day_site()`	Summarise WAStD data per day and site
`total_emergences_per_area_season_species()`	Calculate processing success for emergences per area, season, species
`total_emergences_per_site_season_species()`	Calculate processing success for emergences per site, season, species
`track_success()`	Calculate nesting success as number of tracks with nests vs other tracks
`track_success_by_species()`	The nesting success grouped by season and species
`tracks_ts()`	Plot of nesting_type_by_season_day_species over time
WA Sea Turtles DB - Surveys
`duplicate_surveys()`	List sites with more than one production survey on a given date
`list_survey_count()`	Create a table of survey counts from the output of `parse_surveys`
`list_survey_effort()`	Create a table from the surveyed hours from the output of `parse_surveys`
`plot_survey_count()`	Plot the surveyed hours from the output of `parse_surveys`
`plot_survey_effort()`	Plot the surveyed hours from the output of `parse_surveys`
`survey_count()`	Return the number of surveys for a given site_id and season
`survey_count_heatmap()`	Plot the survey count from the output of `parse_surveys` as heatmap
`survey_ground_covered()`	Return the number of surveys for a given site_id and season
`survey_hours_heatmap()`	Plot the surveyed hours from the output of `parse_surveys` as heatmap
`survey_hours_per_person()`	Sum the hours surveyed per person by season from the output of `parse_surveys`
`survey_hours_per_site_name_and_date()`	Sum the hours surveyed per site_name and turtle date from the output of `parse_surveys`
`survey_season_site_stats()`	Generate a season by site summary from the output of `parse_surveys`
`survey_season_stats()`	Generate a season summary from the output of `parse_surveys`
`survey_show_detail()`	Select main survey attributes
`surveys_per_site_name_and_date()`	Count number of surveys per season, turtle date and site_name from the output of `parse_surveys`
ODK Central Turtle Data
`add_hatching_emergence_success_odkc()`	Add calculated egg count, hatching and emergence success to `odkc_data$tracks_egg`.
`add_nest_labels_odkc()`	Add labels for species and nest/track type to parsed `turtle-nest-encounters` from ODK Central.
`download_odkc_turtledata_2020()`	Download all turtle data from DBCA's ODK Central 2020
`exclude_training_species_odkc()`	Exclude ODKC records with `species` "corolla-corolla".
`filter_odkc_turtledata()`	Filter odkc_data to a given area_name.
`general_disturbance_by_season_odkc()`	Tally ODKC General disturbances by season, cause, and encounter type
`hatching_emergence_success_odkc()`	Summarize HS and ES for Nest excavations
`map_dist_odkc()`	Map Disturbance observations interactively from ODK Central data.
`map_mwi_odkc()`	Map Marine Wildlife Incident 0.6 parsed with ruODK from ODK Central.
`map_sv_odkc()`	Map Site Visit Start and End from ODK Central data over WAStD Sites.
`map_tracks_odkc()`	Map tracks directly from ODK data
`map_tt_odkc()`	Map Turtle Tagging 3.0 parsed with ruODK from ODK Central.
`nest_disturbance_by_season_odkc()`	Tally ODKC Nest disturbances by season, cause, and encounter type
`nesting_type_by_area_season_age_species_odkc()`	Pivot table of nesting type by area, season, track age, and species for ODKC data
`nesting_type_by_area_season_species_odkc()`	Pivot table of nesting type by area, season, and species for ODKC data
`nesting_type_by_season_age_species_odkc()`	Pivot table of nesting type by season, track age and species for ODKC data
`nesting_type_by_season_calendarday_age_species_odkc()`	Pivot table of nesting type by season, calendardate, and track age, and species for ODKC data
`nesting_type_by_season_calendarday_species_odkc()`	Pivot table of nesting type by season, calendardate, and species for ODKC data
`nesting_type_by_season_day_species_odkc()`	Pivot table of nesting type by season, turtle date. and species for ODKC data
`nesting_type_by_season_species_odkc()`	Pivot table of nesting type by season and species for ODKC data
`nesting_type_by_season_week_age_species_odkc()`	Pivot table of nesting type by season, season_week, iso_week, track age, and species for ODKC data
`nesting_type_by_season_week_site_species_odkc()`	Pivot table of nesting type by season, season_week, iso_week, and species for ODKC data
`nesting_type_by_season_week_species_odkc()`	Pivot table of nesting type by season, season_week, iso_week, and species for ODKC data
`nesting_type_by_site_season_age_species_odkc()`	Pivot table of nesting type by site, season, track age, and species for ODKC data
`nesting_type_by_site_season_species_odkc()`	Pivot table of nesting type by site, season, and species for ODKC data
Turtle Nesting Census import
Turtle Tagging DB import
`download_w2_data()`	Download Turtle Tagging data from WAMTRAM2.
`map_wamtram()`	Map WAMTRAM data
`w2_online()`	Test whether the Turtle Tagging Database WAMTRAM2 is accessible and online
WACensus access
Helpers
`absolute_angle()`	Return the smallest possible angle between two compass bearings
`add_dates()`	Add turtle dates to a dataframe with datetime col `observation_start_time`.
`datetime_as_isoweek()`	Calculate the isoweek from a given datetime
`datetime_as_season()`	Calculate the "turtle season" (FY) from a given datetime
`datetime_as_seasonweek()`	Calculate the isoweek from a given datetime
`datetime_as_turtle_date()`	Calculate the "turtle date" from a given datetime
`exclude_training_species()` `filter_realspecies()`	Exclude records with `species` "corolla-corolla".
`exclude_training_surveys()` `filter_realsurveys()`	Exclude training surveys.
`extract_possibly()`	Wrap magrittr::extract to return field value or -1
`fdate_as_tdate()`	Days since fiscal year start as true date
`filter_missing_site()` `filter_nosite()`	Filter records with missing `site_id`
`filter_missing_survey()` `filter_nosurvey()`	Filter records with missing `survey_id`
`filter_surveys_missing_end()`	Filter surveys with a missing `end_source_id`.
`filter_surveys_requiring_qa()`	Filter surveys with "NEEDS QA" in `start_comments` or `end_comments`.
`filter_wastd_season()`	Filter a dataframe of tracks, disturbance, incidents, or surveys to season
`get_more()`	Decide whether the given download limit has been reached
`gj_linestring_to_st_linestring()`	Convert a GeoJSON linestring into an st_linestring
`httpdate_as_gmt08()`	Return a UTC HTTP date string as POSIXct object in GMT+08
`httpdate_as_gmt08_turtle_date()`	Calculate the "turtle date" from a given datetime
`httpdate_as_season()`	Calculate the "turtle season" (FY) from a given UTC HTTP datestring
`humanize()`	Convert between url-safe dash-separated-strings and Human Readable Title Case
`join_tsc_sites()`	Join a dataframe with lat/lon to sf objects of sites and areas.
`leaflet_basemap()`	Create a Leaflet basemap for Western Australia
`map_chr_hack()`	Map given function, handle null as NA and flatten_chr()
`mean_bearing()`	Calculate the mean bearing of two bearings (from, to)
`mis_bearing()`	Return the smallest possible angle for a sector's mean bearing and a given direction
`odkc_works()`	Check whether ODKC is online
`read_table()`	Read a table from a SQL connection using either RODBC or DBI
`sentencecase()`	Convert between url-safe dash-separated-strings and Human readable sentence case
`sf_as_tbl()`	Convert a SimpleFeatures object to a non-spatial dataframe
`tdate_as_fdate()`	True date as days since fiscal year start
`tracks_as_geojson()`	Convert tracks to a GeoJSON string
`tun()`	A wrapper for `tidyr::unnest_wider`
`urlize()`	Convert between url-safe dash-separated-names and Human Readable Title Case
`verify_odkc_turtledata()`	Abort if the parameter x is not of class `wastd_data`
`verify_wamtram_data()`	Abort if the parameter x is not of class `wastd_data`
`verify_wastd_data()`	Abort if the parameter x is not of class `wastd_data`
`wastd_works()`	Check whether API token is set and WAStD is online
`wastdr_msg_abort()`	rlang::abort() with a red error message with a cross symbol.
`wastdr_msg_info()`	Print a blue info message with an info symbol if verbose.
`wastdr_msg_noop()`	Print a green noop message with a filled circle symbol if verbose.
`wastdr_msg_success()`	Print a green success message with a tick symbol if verbose.
`wastdr_msg_warn()`	rlang::warn() with a yellow warning message with a warning symbol if verbose.
`wastdr_settings()` `get_wastd_url()` `get_wastdr_api_url()` `get_wastdr_api_token()` `get_wastdr_api_un()` `get_wastdr_api_pw()` `get_wastdr_verbose()`	Get or set wastdr WAStD settings
`wastdr_setup()`	Configure default WAStD settings
Example data
`odkc_data`	Turtle Nesting Census data from ODK Central.
`print(<odkc_turtledata>)`	S3 print method for 'odkc_turtledata'.
`print(<wamtram_data>)`	S3 print method for 'wamtram_data'.
`print(<wastd_data>)`	S3 print method for 'wastd_data'.
`tsc_data`	TSC data, parsed, first ten records each
`wastd_ae`	WAStD AnimalEncounters, parsed, test data captured by author
`wastd_ae_raw`	WAStD AnimalEncounters, unparsed, test data captured by author
`wastd_area_raw`	WAStD Areas, unparsed
`wastd_data`	Turtle Nesting Census data from WAStD
`wastd_surveys_raw`	WAStD Surveys, unparsed, test data captured by author
`wastd_tne`	WAStD TurtleNestEncounters, parsed, test data captured by author
`wastd_tne_raw`	WAStD TurtleNestEncounters, unparsed, test data captured by author

Reference

API access

WA Sea Turtles DB

WA Sea Turtles DB - Surveys

ODK Central Turtle Data

Turtle Nesting Census import

Turtle Tagging DB import

WACensus access

Helpers

Example data