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
Generalized package title and description to not be SWFSC-specific
Changed license to Apache License (== 2), based on NMFS guidance at https://nmfs-opensci.github.io/GitHub-Guide
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"
Fixed 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