Moved repo to https://github.com/swfsc, and updated all associated documentation. Also generalized documentation to not be as SWFSC-focused, and thus speak to more general uses of DAS files
Changed license to Apache License (== 2), based on NMFS guidance at https://nmfs-opensci.github.io/GitHub-Guide
Generalized package title and description to not be SWFSC-specific
Use reframe in grouping summaries in
das_sight for when none of a certain event are in the data
(#8)
Ensure that sum(GsSpx) equals
GsSchoolx, for all of Best, High and Low (#9)
Fix bug in das_sight and das_effort
when the DAS file contains no sightings
Changed license based on https://github.com/NOAAGov
Fix das_check index math error (#5)
Removed the tz argument from das_read, and added
‘OffsetGMT’ to the output of das_process
Link fixes - no functionality changes
swfscDAS now depends on R >= 4.0.0 for consistency across package dependencies
Added ‘strata.files’ argument to das_effort to allow
users to split effort by strata
The ‘segdata’ output of das_effort now includes
DateTime1 and DateTime2, the date/time of the start and end points of
each segment. The column order of the segdata data frame was also
slightly changed for consistency
Using the ‘continuous’ method of das_effort, effort
can now also be chopped using ‘Course’ and ‘SptKt’
Changed the name of the strata argument of
das_intersects_strata to ‘strata.files’ for
consistency
Fixed a bug in das_check where multiple files could
not be checked at once
das_check now checks for valid longitude and
latitude values
Fixed an issue where the sample stratum file did not overlap with any of the sample data
Added documentation describing how das_sight handles
additional sperm whale group size estimates
das_chop_condition,
das_chop_equallength, das_chop_section, and
das_segdata are now exported for documentation purposes
only
Changed das_within_strata to
das_intersects_strata because it uses the geometric binary
predicate st_intersects rather than
st_within
In das_effort_sight, users can now use
gs.columns to specify secondary group size columns in case
of an NA group size value
das_process now lets the user add the DateTime, Lat,
and Lon information to “?” and numeric (1:8) events using the
‘add.dtll.sight’ argument. This enables the user to filter the processed
DAS data by date/time or coordinates, if desired
For consistency with species code columns, the column name
‘SpProb’ is now ‘SpCodeProb’ in das_sight output
In das_sight, species-specific group sizes are now
calculated as the mean of the product of the school estimate and the
corresponding species percentage (for each estimate), rather than the
product of the mean of the school estimate and the mean of the
corresponding species percentage.
das_effort_sight now has an argument that lets the
user use the low group size estimate in place of an NA best
group size estimate
Changed das_chop_equal to
das_chop_equallength for naming consistency. This change
should not affect users, as it does not affect any of the syntax
required when using das_effort
Added das_within_strata for checking if individual
points, such as event points or segment midpoints, are within
user-provided strata
The “DAS_data_join” vignette demonstrates how to join external data, such as from DAT files, to processed DAS data
Where applicable, error, warning, and informational messages now report both the file name and line number. This makes the messages more useful when working with concatenated DAS objects with multiple DAS files.
Added ‘Data9’, ‘Data10’, and ‘Data12’ columns to the output of
das_read and das_process to account for all
recorded sighting information. These data are now extracted as
‘CalibSchool’, ‘PhotosAerial’, and ‘Biopsy’ from “S” events in
das_sight, and checked in das_check
Added ‘SpdKt’ (ship speed in knots) and ‘WindSpdKt’ (wind speed
in knots) to the output of das_process. The sources for
these data are also checked in das_check
Renamed items in effort list output of das_effort
and das_effort_sight: ‘siteinfo’ is now ‘sightinfo’, and
segdata columns indicating the number of sightings or animals on a
segment are now formatted as ‘description’_‘species code’,
e.g. “nSI_075”
das_sight changesFixed a bug when processing “G” and “g” events
Added columns for high and low (in addition to best) estimates of school size
Renamed columns to follow a consistent format - see
das_sight documentation for a complete description of the
various return format outputs
Added a “complete” return format, which has a row for every observer estimate for each sighting
Users can now use a das_sight argument to provide
the event code(s) by which they wish to filter the function
output