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Changelog

Source: NEWS.md

glatos 0.9.8 (2026-05-18)

Bug fixes

  • Check time zone values in read_glatos_workbook() (columns named “GLATOS_TIMESTAMP”). Suppress timestamp creation when time zone is not recognized, with warning. Warn when timestamp is valid but required case- modification (e.g., “EASTERN” was matched to “Eastern”).

glatos 0.9.7 (2026-05-13)

Bug fixes

  • Fixed bad links to source code in ReadMe and updated links per changes invoked by devtools v. 2.5.

  • Add warnings message in read_glatos_workbook() when Recovery sheet contains records that do not match any records in Deployment sheet.

  • Add validate argument to read_otn_deployments() to suppress validation by as_glatos_receivers(). When validate = FALSE, behavior is consistent with glatos v.0.8.0 and earlier.

glatos 0.9.6 (2026-04-03)

Bug fixes

glatos 0.9.5 (2026-03-25)

Bug fixes

  • Fixed bug in crw_in_polygon() that caused failure with error with non-default initPos and missing cartesianCRS arguments when crs of input polyg is cartesian.

glatos 0.9.4 (2026-02-13)

Bug fixes and minor changes

  • Fixed bug in convert_glatos_to_att() that caused ‘Tag.ID’ column in ‘Tag.Metadata’ element of ATT object” to be lost (converted to NA) if it was not integer-compatible. The glatos analog to ‘Tag.ID’, ‘animal_id’ is character and VTrack accepts ‘Tag.ID’ as character (as well as integer). convert_glatos_to_att() now returns ‘Tag.ID’ as character.
  • Optimized convert_sex() to use data.table::fcase for text translation instad of sapply() over each row.

glatos 0.9.3 (2026-02-12)

Bug fixes

  • Fixed bug in read_glatos_workbook() that caused failure when the deployment, recovery, or locations sheets contained no records; with “Error in sort.list(bx[m$xi]) : ‘x’ must be atomic for ‘sort.list’, method”shell” and “quick”“.

glatos 0.9.2 (2026-02-11)

Bug fixes and minor changes

  • Fixed bug in read_glatos_workbook() that caused failure when read_all = TRUE and project-specific column names contained capital letters; with “Error in switch(new_class, logical = as.logical, numeric = as.numeric, : EXPR must be a length 1 vector”.
  • Updated contact information.

glatos 0.9.1 (2026-02-10)

Bug fixes

  • Fixed bug in read_glatos_workbook() that caused failure when read_all = TRUE; with “Error: The following column(s) have wrong class: utc_release_date_time (must be ‘POSIXct’).”.

glatos 0.9.0 (2026-01-20)

New features

  • Added support for GLATOS workbook version 1.4 (xlsx file) in read_glatos_workbook().
    • Excel workbooks in version 1.4 have no macros and have column headers in the first row (v. 1.3 has an empty first row and usually had macros).
    • Added new input argument simplify which allows (when simplify = TRUE) return of a list with the same structure as the input workbook (e.g., columns named “Deployment”, “Recovery”, “Tagging”, …).
    • Disallow multiple columns with the same name (returns an error). In earlier versions, a suffix was added to all but the first in each set of duplicate column names.
    • fixes issue #272
  • Added support for parquet files in read_otn_detections().

glatos 0.8.1 (2025-09-09)

New features

Bug fixes and minor changes

  • Changed case of vdat.exe and paths to vdat.exe and vue.exe in tests (new default install locations on windows).
  • Added DIAG_NEXTRAK record type to vdat_csv_schema data object.
  • Added explicit calls to data objects so that they can be accessed when the package isn’t attached.
  • Allowed read_otn_detections() to handle zipped CSVs

glatos 0.8.0 (2024-09-19)

Breaking changes

  • Changed make_transition() to use jarasterize() (see New Features) and added input arg buffer.
    • Removed dependence on gdalUtilities.
    • fixes issue #234
  • Removed make_transition2() (deprecated in 0.7) and make_transition3(). Also removed dependence on fasterize.
  • Updated example TransitionLayer object greatLakesTrLayer using new make_transition() and great_lakes_polygon (an sf object) . The new version has the same cell size (resolution) as the previous, but different extents (matches great_lakes_polygon, so returned values (with same input) will differ from earlier versions.
  • Removed ‘gganimate_handout’ (pdf and html) from ‘vignettes’.

New features

Bug fixes and minor changes

  • Add @srs slot to greatLakesTrLayer data object and rename file ‘data/greatLakesTrLayer.rda’.
  • Fix bug in read_glatos_workbook() where timestamps during daylight savings were shifted one hour on linux operating system (not an issue on windows or mac).
  • Omit data.table from class of object returned by read_glatos_detections()
    and read_glatos_receivers().
  • Fix typo in Description to Suggest ‘gifski’ (not ‘gifsky’).
  • Various changes to resolve R CMD check errors, warning, and notes (generally not user-facing).

glatos 0.7.3 (2024-04-09)

Bug fixes

glatos 0.7.2 (2024-02-25)

Bug fixes

  • Fixed bug in summarize_detections() where value in locations output column was name of input column (e.g. “glatos_array”), rather than values from that column (e.g., “AGR”, “BBI”).

glatos 0.7.1 (2024-01-19)

Bug fixes and minor changes

  • Fix bug introduced in glatos 0.7.0 where x and y limits were switched when bg_map was supplied.
    • Add test for various inputs of background_xlim, background_ylim, and bg_map to function make_frames.

glatos 0.7.0 (2024-01-04)

Bug fixes and minor changes

  • Remove dependence on rgeos and rgdal.

  • This package now requires R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘glatos/inst/testdata/flynn_island_transition.rds’ ‘glatos/inst/testdata/higgins_lake_transition.rds’ ‘glatos/inst/testdata/test-detect_transmissions-dtc_spout.rds’ ‘glatos/inst/testdata/test-transmit_along_path-tr_dfin_spout.rds’

  • Deprecate make_transition and make_transition2; suggest make_transition3 instead.

  • Deprecate data object greatLakesPoly; suggest great_lakes_polygon instead.

  • prepare_deploy_sheet:

    • Set ‘skip = header_line - 1’ and ‘col_names = TRUE’ to retain first record and column names (read_excel ignores column names, unless set, when skip is set).
    • Fix non-working example code.

  • convert_otn_to_att and convert_otn_erddap_to_att:

    • Replaced sp::CRS with sf::st_crs
    • Changed link (URL) to relevant issue from GitLab to GitHub repo.

  • Remove ffmpeg functions.

    • make defunct:
      • check_dependencies
      • install_ffmpeg
      • make_video_ffmpeg

  • Fix issues with several tests caused by changes to CRS/WKT and row.names attributes.

glatos 0.6.5 (2023-09-07)

Bug fixes

  • Fix bug in summarize_detections() where setting ‘location_col’ triggers error.

glatos 0.6.4 (2023-09-06)

Bug fixes and minor changes

  • Add support for new column named ‘record_status’ in GLATOS detection export CSV.
    • Add new glatos detection schema version 1.4 (developer use)
    • fix issue #179

glatos 0.6.3 (2023-01-25)

Bug fixes and minor changes

  • Add support for new GLATOS receiver_locations file format; with code_map and code_map_comment columns.

glatos 0.6.2 (2022-10-25)

Bug fixes and minor changes

  • Fix error in position_heat_map() function resulting in Error in zip_internal... Some files do not exist. Update documentation.

glatos 0.6.1

2022-10-11

Minor changes

  • Allow sf MUTLIPOLYGON geometry type for input polyg to crw_in_polygon().

  • Use new function check_cross_boundary() instead of check_in_polygon to prevent paths crossing land (e.g., over peninsulas) in crw_in_polygon().

glatos 0.6.0

2022-06-24

Breaking changes

  • crw_in_polygon
    • replace input arg ‘EPSG’ with ‘inputCRS’ and ‘cartesianCRS’
    • unlike previous versions, input polygon (‘polyg’) must now be in Cartesian (projected) coordinate reference system or ‘cartesianCRS’ must be specified (there is no default).
    • remove dependence on sp
      • improve speed
      • return sf object (default) or data.frame
  • transmit_along_path
    • remove dependence on sp
    • return sf object (default) or data.frame
    • calculate distances along path using geodist::geodist for geographic and simple Euclidean for Cartesian coordinates. Cartesian input results in fastest computations.
    • remove EPSG input (no longer requires transformation to Cartesian CRS for calculations); but non-Cartesian input will be slower than Cartesian.
    • add pathCRS input arg for non-spatial inputs
    • change name of column ‘et’ in output to ‘time’.
    • add input arg “colNames” for non-default coordinate column name specification.
  • detect_transmissions
    • remove dependence on sp
    • return sf object (default) or data.frame
    • calculate distances along path using geodist::geodist for geographic and simple Euclidean for Cartesian coordinates. Cartesian input results in fastest computations.
    • remove EPSG input (no longer requires transformation to Cartesian CRS for calculations); but non-Cartesian input will be slower than Cartesian.
    • add inputCRS input arg for non-spatial inputs
    • change name of column ‘et’ in output to ‘time’.
    • add input arg “colNames” for non-default coordinate column name specification.

Bug fixes and minor changes

  • position_heat_map

    • fix issue #159 where kmz output worked on mac but not windows
    • fix issue #123 when input positions object was data.table.

  • remove dependence on PBSmapping

    • replace calls to PBSmapping::convUL with local functions lonlat_to_utm and utm_to_lonlat

  • remove dependence on gdalUtils

    • use gdalUtilities::gdal_rasterize instead of gdalUtils::gdal_rasterize
    • fix issue #174
    • removed gdalUtils dependency from DESCRIPTION and added gdalUtilities

  • changes to kml_to_csv

    • read data from kml with sf::read_sf instead of rgdal::readOGR
    • allow multiple feature types to be read from kml
    • change export format from separate csv files to a single csv file
    • add feature name and type to output file

  • fix ‘greatLakesPoly’ CRS to resolve warning: “CRS object has no comment”

  • added example data ‘great_lakes_polygon’; an sf POLYGON version of ‘greatLakesPoly’ (a SpatialPolygonsDataFrame)

glatos 0.5.2

2021-12-10

Bug fixes and minor changes

  • read_glatos_workbook

    • use readr::readexcel instead of openxlsx to read xlsm file
    • fix issue #138

  • removed openxlsx and cellranger dependencies from DESCRIPTION

  • fix issue preventing vignettes from building when installed (missing space in data_loading_vignette.Rmd).

glatos 0.5.1

2021-11-09

Bug fix

  • position_heat_map
    • fix issue #121 (error when input does not contain columns X and Y)

glatos 0.5.0

2021-04-27

New features

  • functions
    • prepare_deploy_sheet
    • prepare_tag_sheet
    • convert_otn_to_att

Minor changes

  • convert_glatos_to_att,
    • added argument CRS for ATT compatibility
  • residence_index
    • replaced deprecated .dots with across in dplyr::group_by calls to fix “Warning: The .dots argument of group_by() is deprecated as of dplyr 1.0.0”
  • convert_otn_erddap_to_att
    • renamed convert_otn_to_att to convert_otn_erddap_to_att to better describe what the function does

glatos 0.4.2

2020-04-06

Minor changes

  • make_transition
    • added new argument ‘invert’ for cases where input polygon represents land
    • fixes issue #101

Bug fixes

  • read_glatos_detections
    • fix bug where animal_id was not created correctly if some but not all were missing
    • fixes issue #106

glatos 0.4.1

2020-02-18

Minor changes

  • make_video
    • overhauled to no longer require ffmpeg. now is a simple wrapper for av::av_encode_video
    • added input argument ‘duration’ to set total video duration in seconds previous version of make_video renamed ‘make_video_ffmpeg’
    • calls to new ‘make_video’ with “old” arguments are caught and redirected to ‘make_video_ffmpeg’ for backward compatibility
  • make_frames
    • modified to call revised make_video (ffmpeg not required)
    • deprecated ffmpeg input argument
  • interpolate_path

Bug fixes

  • abacus_plot
    • fix issue where optional plot args passed as expressions (e.g., panel.first and panel.last) had to be wrapped in quote
    • fixes issue #87
  • summarize_detections
    • fix error in documentation listing all three summ_type options as default
    • fixes issue #94
  • check_dependencies
    • ensure that glatos package directory is checked for ffmpeg.exe
    • fixes issue #95

glatos 0.4.0

2019-11-12

New features

  • functions
    • convert_glatos_to_att
    • convert_otn_erddap_to_att
  • example data
    • walleye_att
    • blue_shart_att

Minor changes

  • make_frames
    • add argument show_progress (default = TRUE) to optionally supress progress bars
    • issue #74
  • interpolate_path
    • add argument show_progress (default = TRUE) to optionally supress progres bars
    • issue #74
  • calc_collision_probs
    • in help examples, make separate plots for detection and collision probs
    • issue #77
  • make_video
    • issue #64
    • return output file name
    • add diagnostic_mode arg to optionally return ffmpeg output (hide by default)
    • add warning when output file exists and overwrite = FALSE
  • adjust_playback_time
    • return output file name
    • add diagnostic_mode arg to optionally return ffmpeg output (hide by default)
    • add warning when output file exists and overwrite = FALSE

glatos 0.3.2

2019-10-17

bug fixes and minor changes

  • vrl2csv
    • fixed bug where output csv file names were not returned when input
      was multiple VRL file names. A vector of output CSV file names is now returned.
    • make separate call to VUE –convert-files for each VRL file.
    • add progress bar
    • improve error messaging.
  • detect_transmissions
    • fixed bug where ‘trns_x’ and ‘trns_y’ in data slot of output was not converted to input coordinate reference system when sp_out = TRUE.
  • make_frames
    • fixed bug where receivers were not displayed near the end of the time series in the images (and videos) when some receivers were missing recovery data (issue #79).
  • abacus_plot
    • added more flexible optional plotting arguments, including ‘xlim’ to set custom x limits.
    • fixed bug where plot title (specified by main argument) was not included in plot (issue #70)
    • deprecated show_receiver_status argument. Receiver status will be shown on plot whenever ‘receiver_history’ is given.

glatos 0.3.1

2019-02-27

bug fixes

  • fix missing brackets in glatos.Rd

glatos 0.3.0

2019-02-26

New features

  • functions
    • receiver_efficiency
    • residence_index
    • read_otn_deployments
    • install_ffmpeg
    • check_dependencies
  • vignettes and documentation
    • added data-loading, data-requirements, receiver_efficency, residence_index

Minor changes

  • detection_events

    • output data.table or tibble object if input is either of those and data.frame otherwise
    • faster (e.g., 11 sec vs 31 sec for 7.2M records on wimpy laptop)
    • coerce ‘time_sep’ argument to numeric if quoted and error if it cannot be coerced to numeric

  • crw_in_polygon

    • changed sampling algorithm to mimimize stuck-at-boundary errors
    • added option to input SpatialPolygons object
    • added explicit coordinate reference system (EPSG 3175 - Great Lakes projected CRS) so that default units are in meters and simulations are done in that CRS. Other CRS can be specified for other areas (via EPSG argument).
    • added option to return spatial object or simple data frame.

  • transmit_along_path

    • added option to input SpatialPolygons object
    • added explicit coordinate reference system (EPSG 3175 - Great Lakes projected CRS) so that default units are in meters and simulations are done in that CRS. Other CRS can be specified for other areas (via EPSG argument).
    • added option to return spatial object or simple data frame.

  • detect_transmissions

    • added option to input SpatialPolygons object
    • added explicit coordinate reference system (EPSG 3175 - Great Lakes projected CRS) so that default units are in meters and simulations are done in that CRS. Other CRS can be specified for other areas (via EPSG argument).
    • added option to return spatial object or simple data frame.

  • abacus_plot

    • added optional arguments show_receiver_status and receiver_history to allow receiver history status to be added to plot (issue #36)
    • added optional arguments x_res and x_format to specify x-axis tick mark spacing and format (issue #30)
    • removed input arguments that could also be passed via ellipses (issue #35)

  • position_heat_map

    • corrected accuracy issues by converting lat-lon to UTM (issue #8)
    • added optional argument abs_or_rel to specify it output is absolute numbers of fish are relative; simplified output so that only a single output type occurs in a given call
    • Changed output to kmz instead of kml
    • new folder is only created when output is png or kmz

  • dropped fasttime as a depenedency and uses lubridates fasttime implementation instead

  • Update sysdata detection schema for OTN

glatos 0.2.7

2018-08-29

Minor changes

  • interpolate_path
    • added status bars during each of three major steps and improved messaging (2018-08-29)
  • vector_heading
    • allow input coordinates as longitude and latitude (decimal degrees) (2018-08-03)

glatos 0.2.6

2018-06-11

Minor changes and bug fixes

  • read_otn_detections
    • fix bug that indexed columns by position, meaning columns had to be orderd exactly as in spec (issue #52)
  • read_glatos_detections
    • fix bug that indexed columns by position, meaning columns had to be orderd exactly as in spec (issue #52)
  • read_glatos_receivers
    • fix bug that indexed columns by position, meaning columns had to be orderd exactly as in spec (issue #52)

glatos 0.2.5

2018-03-14

New features

  • added check_dependencies() for checking if gdal and ffmpeg can be called (issue #40)

Minor changes and bug fixes

  • adjust_playback_time()
    • allow spaces in file names and paths (issue #45)
  • interpolate_path()
    • trigger error when ‘trans’ is not a transition object (issue #42)
  • make_frames()
    • fixed “cannot allocate vector” error when optional plot arg is vector (issue #47)
  • make_transition()
    • allow polygon to be input as SpatialPolygonsDataFrame (issue #37)

glatos 0.2.4

2018-03-06

Minor changes and bug fixes

  • make_video()
    • added support for input and output directories containing spaces (issue #38)
      • check if input directory exists and error/message if not
      • create output directory if it does not exist

glatos 0.2.3

2018-02-25

Major changes

  • A complete overhaul since v0.1.3. This version is no longer compatible with previous.
    • Adopt style notation suggested by Wickham (R Packages book)
    • All previous camel-case function names are now snake-case

New features

  • Added data loading functions
    • read_glatos_detections
    • read_otn_detections
    • read_glatos_workbook
    • read_glatos_receivers
    • read_vemco_tag_specs
  • Added data processing, filtering, and summarizing functions
    • min_lag
    • real_sensor_values
    • summarize_detections
  • Added animation functions
    • adjust_playback_time
    • make_frames
    • make_video
    • make_transition

glatos 0.1.3

2017-03-01

- initial release on OTN gitlab