download_wastd_turtledata()
: drop logger encounters, which have been removed
from the WAStD API and migrated to LoggerObservations.filter_wastd_turtledata
: add seasonsmap_fanangles
: add misorientation and factor out mean_bearing
map_fanangles
using https://github.com/dbca-wa/leaflet.circlesector/ (#46)turtle_date_awst_text
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.download_w2_data
improved to exclude duplicate attributes, added print fn.duplicate_surveys
links to sites and dates with more than one survey.local_dir
only on
export=TRUE
like plots from summarize tracks.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.odkc_data
contains Turtle Tagging data.wastd_data
: summarise_wastd_data_per_day_site()
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. download_wastd_turtledata()
now doesn't have to merge AE/TNE/LTE details
against Observation tables.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).download_wastd_turtledata()
. This should restore behaviour of analysis
functions to 0.5.5.download_wastd_turtledata()
wastd_data
.download_wastd_turtledata()
now shows correct encounter details for
nested observations like nest tags, nest loggers etc.download_wastd_turtledata()
infers verbosity from get_wastdr_verbose()
.download_w2_data()
. (#29)wastdr_msg_*
has new parameter verbose = get_wastdr_verbose()
because we
always want to make message verbosity conditional.export_wastd_turtledata
now also exports all data to an RData file.site
also
the Locality (area
), e.g. "Ningaloo".
This allows filtering to whole monitoring programs.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
).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.Status Oct 2020
download_odkc_turtledata_2020
now includes Site Visit Start (Map)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.
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.download_w2_data
to extract and parse WAMTRAM2. Early stages with
improvements planned.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.
filter_dead()
and filter_alive()
work for WAStD and ODKC data, see
examples.wastd_GET
and wastd_POST
, add examples to man, tests, vignettes.map_sv_odkc
to map Site Visit Start/End over TSC Sites.
Extremely helpful to QA TSC sites and survey methodology.map_dist
.R>=3.5
.wastd_GET
drops response
, keeps url
, date
, and status_code
.
Results now always expected from WAStD in key features
, not results
.wastd_parse
function parses any non-GeoJSON TSC API response, while
wastd_parse_gj
will parse aparse_taxon-conservationlisting
and parse_community-conservationlisting
.parse_area
for WAStD Areas.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.parse_
functions return iso_week
and season_week
instead of week
.
season_week
is a useful grouper in combination with season
.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.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),
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
.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))
.parse_surveys
can now handle surveys without a source_id
. These surveys
are e.g. those which were reconstructed by WAStD.map_dist
to map disturbance observations.parse_nesttag_observations
for WAStD "nesttag-observations".plot_survey_effort
, plot_survey_count
.paste
replaced by glue
.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.map_tracks
popup formatted, including a link to record in WAStD.theme_light()
to theme_classic()
.parse_surveys
: hours/minutes were minutes/seconds.parse_disturbance_observations
added. upsert_geojson
added.parse_survey
, plus some data viz for Surveys, see vignette "Analysis".map_tracks
, a map of turtle tracks/nests. WIP: more data viz for tracks.maturity
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