NEWS.md

wastdr 0.9.4

wastdr 0.9.2

wastdr 0.9.1

wastdr 0.9.0

wastdr 0.8.42

wastdr 0.8.40

wastdr 0.8.39

wastdr 0.8.38

wastdr 0.8.37

wastdr 0.8.36

wastdr 0.8.35

• download_wastd_turtledata(): drop logger encounters, which have been removed from the WAStD API and migrated to LoggerObservations.

wastdr 0.8.34

wastdr 0.8.33

wastdr 0.8.32

wastdr 0.8.31

wastdr 0.8.30

wastdr 0.8.29

wastdr 0.8.28

wastdr 0.8.27

wastdr 0.8.26

• Improve filter_wastd_turtledata: add seasons

wastdr 0.8.25

• Fix map_fanangles: add misorientation and factor out mean_bearing

wastdr 0.8.24

• New: map_fanangles using https://github.com/dbca-wa/leaflet.circlesector/ (#46)

wastdr 0.8.23

wastdr 0.8.22

wastdr 0.8.21

wastdr 0.8.20

wastdr 0.8.19

wastdr 0.8.18

• add_dates: add new field turtle_date_awst_text
• summarise wastd turtledata: summarise by turtle date, not calendar date

wastdr 0.8.17

wastdr 0.8.16

wastdr 0.8.15

wastdr 0.8.14

wastdr 0.8.13

wastdr 0.8.12

wastdr 0.8.11

wastdr 0.8.9

wastdr 0.8.8

wastdr 0.8.7

Major fixes

Minor fixes

• Add scalebar to all maps

Docs

Data

Maintenance

wastdr 0.8.2

Major fixes

Minor fixes

• filter_odkc_turtledata now accepts a username, which filters data by the ODK Collect Username of each submission. Some components, such as tagging data, have hand typed names in additional fields. These are also filtered by.

Docs

Data

Maintenance

wastdr 0.7.3

Major fixes

Minor fixes

• download_w2_data improved to exclude duplicate attributes, added print fn.

Docs

Data

Maintenance

wastdr 0.7.1

Major fixes

• New: duplicate_surveys links to sites and dates with more than one survey.
• Plots from summarize surveys now save to a given local_dir only on export=TRUE like plots from summarize tracks.

Minor fixes

Docs

Data

Maintenance

• Dependency versions updated

wastdr 0.7.0

Major fixes

Minor fixes

• download_odkc_turtledata2020() now includes Turtle Tagging data (4 tables), download_odkc_turtledata2019() contains NULL as placeholder in these four tables, and will be sunset after season 2020-21.

Docs

Data

• odkc_data contains Turtle Tagging data.

wastdr 0.6.1

Major fixes

Minor fixes

• New summary for wastd_data: summarise_wastd_data_per_day_site()

Docs

Data

wastdr 0.6.0

Major fixes

• WAStD API changes:
  • Observation serializers now include the most detailed feasible Encounter class. Those Observations which only ever are recorded against AnimalEncounter, TurtleNestEncounter, or LineTransectEncounter, will show now their details in the encounter group. This simply adds more fields.
    • parse_encounterobservations() now includes these details.
    • Mapping and summary helpers use the changed names (prefixed encounter_).
    • download_wastd_turtledata() now doesn't have to merge AE/TNE/LTE details against Observation tables.
    • Some observations, namely TurtleTagObservation and TurtleNestDisturbanceObservation, could also happen when not associated with an animal or turtle nest, and therefore only include the Encounter details in the WAStD API.
• TurtleNestObservation.nest_position has been replaced and merged with the already existing TurtleNestEncounter.habitat in WAStD. This simplifies the contents of the WAStD table TurtleNestObservation, which is aptly named turtle-nest-excavation in the API to include only excavation data (egg counts, HS/ES, nest depth, ambient temperatures). "Nest habitat-only" records have been deleted from TurtleNestObservation. The calculation of HS and ES is also rectified to now exclude a false 0 for "Nest habitat-only" records (which are deleted and not coming back anyways).

Minor fixes

Docs

Data

wastdr 0.5.7

Major fixes

Minor fixes

• Join essential Encounter details to nested tables in download_wastd_turtledata(). This should restore behaviour of analysis functions to 0.5.5.

Docs

Datadownload_wastd_turtledata()

• Rebuild wastd_data.

wastdr 0.5.6

Major fixes

• Bugfix: download_wastd_turtledata() now shows correct encounter details for nested observations like nest tags, nest loggers etc.

Minor fixes

• download_wastd_turtledata() infers verbosity from get_wastdr_verbose().

Docs

Data

wastdr 0.5.5

Major fixes

• Updated turtle tagging database extractor download_w2_data(). (#29)

Minor fixes

• wastdr_msg_* has new parameter verbose = get_wastdr_verbose() because we always want to make message verbosity conditional.

Docs

Data

wastdr 0.5.4

Major fixes

• Improved parsing of WAStD data

Minor fixes

Docs

Data

wastdr 0.5.3

Major fixes

Minor fixes

Docs

Data

• export_wastd_turtledata now also exports all data to an RData file.

wastdr 0.5.2

Data

• WAStD API changes: Surveys now contain in addition to the surveyed site also the Locality (area), e.g. "Ningaloo". This allows filtering to whole monitoring programs.
• WAStD API changes: Users now include is_active to indicate whether they are a closed duplicate profile or an active one. This is useful to exclude duplicate profiles from user name mapping (e.g. in etlTurtleNesting).

Docs

• All functions are now shown in Reference sorted by function family.
• Reference docs now support Markdown. Bullet point lists are easier to write now.

wastdr 0.5.1

Data

• odkc_data is not generated from wastdr::download_odkc_turtledata2020(). The first 100 records of each element are retained and sanitised of PII (names).
• download_wastd_turtledata() was extended to include LoggerObservations as nest_loggers in addition to the superseded LoggerEncounters. This prepares etlTurtleNesting to migrate the reports from using LoggerEnc to LoggerObs.

wastdr 0.5.0

Status Oct 2020

Minor fixes

• download_odkc_turtledata_2020 now includes Site Visit Start (Map)

Documentation

All ODK forms used to capture data for WAStD are included in inst/ as ODK Build savefiles, XForm XML (form ID changed to drop build_ prefix and version postfix to allow updating deployed forms on ODK Central 1.0), and XlsForm XLSX.

wastdr 0.4.0

Major changes

• The WA Sea Turtles DB (WAStD) has been separated from the Threatened Species and Communities DB (TSC). This version begins the migration of TSC functionality to a dedicated R package (tscr).
• TSC can be used with this version of wastdr.
• Renaming and rebranding will be ongoing.

wastdr 0.3.2

• Bugfix: download_wastd_turtledata called parse_encounterobservations which called add_dates incorrectly. Dates are now preserved and value-added with season, calendar and turtle date and local datetime.

wastdr 0.3.0

• Add download_w2_data to extract and parse WAMTRAM2. Early stages with improvements planned.

wastdr 0.2.19

• Upgrade map_tracks_odkc and map_mwi_odkc to Bootstrap4 image carousels to work in the Shiny app turtleviewer.

wastdr 0.2.18

• Adapted wastdr to new WAStD API (#3)
  • include example data,
  • use example data in code examples,
  • use example data in tests,
  • use example data in vignettes,
  • automate example data refresh from WAStD,
  • update docs, man, vignettes,
  • propagate updates to turtleviewer.
• Increased test coverage to near 100% (#3)
• Set up CI on GitHub Actions for Windows and Ubuntu - TODO MacOS (#3)
• Improve WAStD summarize_* methods (#5).
• Improve map popups for ODKC tracks and mwi (#6).

wastdr 0.2.11

• Start work on ODKC to WAStD data ingest via ruODK, odkc_data, wastd_post_one and wastd_bulk_post. The hard bits are:

  • Data mapping ODKC to WAStD.
  • Guess users (re-implement PostGIS's trigram fuzzy search).
  • Determine create / update / skip based on source/sourceID already present in WAStD.

wastdr 0.2.8

• Test coverage 99.9%
• filter_dead() and filter_alive() work for WAStD and ODKC data, see examples.

wastdr 0.2.6

• Test coverage increased.
• Test data included (WAStD, TSC, ODKC) and used in tests and examples.

wastdr 0.2.0

• Refactor wastd_GET and wastd_POST, add examples to man, tests, vignettes.

wastdr 0.1.33

• Add opt-in timelines to maps.

wastdr 0.1.31

• Refactor maps: humanize layer names (tracks: species, dist: causes), make map_mwi robust against null records.

wastdr 0.1.29

Minor changes

• Add map_sv_odkc to map Site Visit Start/End over TSC Sites. Extremely helpful to QA TSC sites and survey methodology.

wastdr 0.1.28

Minor changes

• Add disturbed nests and sites, both optional, to map_dist.

wastdr 0.1.27

Major changes

• Add ODK Central data wrangling.
• Bump to R>=3.5.

Minor changes

wastdr 0.1.23

Major changes

• wastd_GET drops response, keeps url, date, and status_code. Results now always expected from WAStD in key features, not results.
• Turtle parsing functions add now additional calendar date in AWST for clarity.
• Generic wastd_parse function parses any non-GeoJSON TSC API response, while wastd_parse_gj will parse a

Minor changes

wastdr 0.1.22

Minor changes

• Add parse_taxon-conservationlisting and parse_community-conservationlisting.

wastdr 0.1.21

Major changes

Minor changes

• Added parse_area for WAStD Areas.

wastdr 0.1.20

Major changes

Minor changes

• map_tracks(), map_nests(), map_dist() accept new parameters: wastd_url (default get_wastd_url()), and cluster (whether to cluster markers).
• parse_surveys() now includes an HTML link to the admin change_url in the data curation portal.
• Filters added:
  • \code{exclude_training_surveys}
  • \code{filter_surveys_requiring_qa}
  • \code{filter_surveys_missing_end}
  • \code{exclude_training_species}
  • \code{filter_missing_survey}
  • \code{filter_missing_site}
• Summaries added:
  • \code{disturbance_by_season}
  • \code{surveys_per_site_name_and_date}
  • \code{survey_hours_per_site_name_and_date}
  • \code{survey_hours_per_person}
  • \code{list_survey_count}
  • \code{list_survey_effort}
• Plots added:
  • \code{plot_survey_count}
  • \code{plot_survey_effort}
  • \code{ggplot_track_success_by_date}
  • \code{ggplot_track_successrate_by_date}
• Some refactoring of documentation templates.

wastdr 0.1.19

Major changes

• All parse_ functions return iso_week and season_week instead of week. season_week is a useful grouper in combination with season.

wastdr 0.1.18

Minor changes

• Added clutch_size_fresh to parse_turtle_nest_encounters as the number of eggs directly observed during a nesting/tagging event as opposed to clutch_size, which is reconstructed from egg remnants after a hatched nest excavation.

wastdr 0.1.17

Minor changes

• Added datetime_as_season, datetime_as_isoweek, datetime_as_turtledate. This speeds up the parsers by re-using the costly string-to-date conversion from datetime.

• Added isoweek to parsers. The parsers now provide for each record:

  • timezone-aware datetime (actual time of observation),
  • "turtle date" (nesting night start date),
  • season start year,
  • week number.

wastdr 0.1.16

Major changes

• All parse_ functions changed the column date to the more descriptive turtle_date, as in the date (ymd) of "the night before". Using turtle_date groups turtle tagging (nightfall to sunrise) and tracks (made same night but observed the next morning) under the same date. This change requires code depending on the column date to be updated to turtle_date.

Minor changes

• All parse_ functions now include season, as in the earlier year of the fiscal year. This cleanly groups the (Australian) summer nesters (nesting Oct-Mar) under the same season number. E.g., any observations made between 01/07/2017 and 30/06/2018 (AWST for the sticklers) will come up as season 2017. Note, the season for (Australian) winter nesters can be grouped by the calendar year, which can itself be derived trivially from the datetime as dplyr::mutate(year = lubridate::year(datetime)). The same goes for the calendar week, dplyr::mutate(week = lubridate::isoweek(datetime)).

wastdr 0.1.15

Bug fixes

• parse_surveys can now handle surveys without a source_id. These surveys are e.g. those which were reconstructed by WAStD.

wastdr 0.1.14

Minor changes

• Add map_nests to create a map of tagged nests from WAStD "nesttag-observations".

wastdr 0.1.13

Minor changes

• Added map_dist to map disturbance observations.
• Added parse_nesttag_observations for WAStD "nesttag-observations".

wastdr 0.1.12

Minor changes

• Survey helpers writing files accept an optional prefix for the filename they save the outputs to" plot_survey_effort, plot_survey_count.
• Survey helpers: placename and prefix are optional.
• Usage of paste replaced by glue.

wastdr 0.1.11

Minor changes

• parse_surveys now includes WAStD survey ID and absolute admin URL. The latter can be used to construct a direct link to update a survey in WAStD.

wastdr 0.1.10

Minor changes

• map_tracks popup formatted, including a link to record in WAStD.

wastdr 0.1.9

Minor changes

• Change example plot theme from theme_light() to theme_classic().

Bug fixes

• Bugfix: parse_animalencounter and parse_turtlenestencounter now correctly parse survey ID. Re-generated example data.

wastdr 0.1.8

Minor changes

• Cut down on size of vignette "analysis"

wastdr 0.1.7

Bug fixes

• patch release: fix parse_surveys: hours/minutes were minutes/seconds.

wastdr 0.1.6

Minor changes

• parse_disturbance_observations added.

wastdr 0.1.5

Minor changes

• upsert_geojson added.

wastdr 0.1.4

Minor changes

• AnimalEncounters and TurtleNestEncounters now include survey information.
• Surveys: parse_survey, plus some data viz for Surveys, see vignette "Analysis".
• wastd_POST can be used to update users and taxomony in WAStD.
• Changed example dataset names to "tne" and "nests".
• Added map_tracks, a map of turtle tracks/nests. WIP: more data viz for tracks.

wastdr 0.1.3

Minor changes

• AnimalEncounters: add maturity