Changes in version 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"). Changes in version 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. - partly fixes issue #269 - 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. - related to issue #202 Changes in version 0.9.6 (2026-04-03) Bug fixes - Fixed bug in read_glatos_workbook() that caused failure when GLATOS workbook file contains project-specific sheets and read_all = TRUE. - fixes issue #278 Changes in version 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. - fixes issue #277 Changes in version 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. - fixes issue #276 - Optimized convert_sex() to use data.table::fcase for text translation instad of sapply() over each row. Changes in version 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"". - fixes issue #275 Changes in version 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". - fixes issue #274 - Updated contact information. Changes in version 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').". - fixes issue #274 Changes in version 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(). - fixes issue #254 Changes in version 0.8.1 (2025-09-09) New features - Changed read_otn_detections() to support new OTN detection extract format. - fixes issue #254 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). - fixes issue #253 - Added DIAG_NEXTRAK record type to vdat_csv_schema data object. - fixes issue #265 - Added explicit calls to data objects so that they can be accessed when the package isn't attached. - fixes issue #261 - Allowed read_otn_detections() to handle zipped CSVs - fixes issue #262 Changes in version 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. - fixes issue #67 - 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. - fixes issue #219 - Removed 'gganimate_handout' (pdf and html) from 'vignettes'. New features - Add new function vue_convert() to convert VRL file to CSV file (detection records only; receiver event log records are not supported). - replaces vrl2csv() (deprecated). - Add new function vdat_convert() to convert VRL or VDAT files to Fathom/VDAT CSV. - Add new functions for reading data exported from VRL with VUE software. - read_vue_detection_csv() to read data from detection file exported from VUE or created using vue_convert() or vrl2csv(). - read_vue_event_csv() to read data from receiver event log file exported from VUE. - Add new function read_vdat_csv() to read data exported from VRL or VDAT using VDAT.exe (e.g., using vdat_convert()). - Add new functions to create, check, and validate glatos_animals objects: - glatos_animals() to construct a glatos_animals object from individual vectors (one for each column) and optionally check for required column names and classes using validate_glatos_animals(). - as_glatos_animals() to coerce a data.frame, or object that inherits from data.frame, to glatos_animals and optionally check for required column names and classes using validate_glatos_animals(). - is_glatos_animals() to check class attribute for "glatos_animals". - validate_glatos_animals() to check for existence of required column names and classes. - fixes issue #126 - fixes issue #78 - Add new functions to create, check, and validate glatos_detections objects: - glatos_detections() to construct a glatos_detections object from individual vectors (one for each column) and optionally check for required column names and classes using validate_glatos_detections(). - as_glatos_detections() to coerce a data.frame, or object that inherits from data.frame, to glatos_detections and optionally check for required column names and classes using validate_glatos_detections(). - is_glatos_detections() to check class attribute for "glatos_detections". - validate_glatos_detections() to check for existence of required column names and classes. - fixes issue #126 - fixes issue #78 - Add new functions to create, check, and validate glatos_recievers objects: - glatos_receivers() to construct a glatos_receivers object from individual vectors (one for each column) and optionally check for required column names and classes using validate_glatos_receivers(). - as_glatos_receivers() to coerce a data.frame, or object that inherits from data.frame, to glatos_receivers and optionally check for required column names and classes using validate_glatos_receivers(). - is_glatos_receivers() to check class attribute for "glatos_receivers". - validate_glatos_receivers() to check for existence of required column names and classes. - fixes issue #126 - fixes issue #78 - Add new function jarasterize() to allow rasterization (esp. with all_touched = TRUE) using only sf and raster. Used by make_transition(). - Add new function scale_meters_to_degrees() to inform selection of res argument to make_transition(). - In make_frames(), allow terra::SpatVector input for background map (bg_map arg). - add test for terra::SpatVector input - Add new function detection_range_model() for estimating detection range at which a certain detection efficiency is expected, using output from Innovasea's range testing software. Bug fixes and minor changes - Add @srs slot to greatLakesTrLayer data object and rename file 'data/greatLakesTrLayer.rda'. - fixes issue #213 - 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). - fixes issue #208 - Omit data.table from class of object returned by read_glatos_detections() and read_glatos_receivers(). - fixes issue #200 - Fix typo in Description to Suggest 'gifski' (not 'gifsky'). - fixes issue #185 - Various changes to resolve R CMD check errors, warning, and notes (generally not user-facing). Changes in version 0.7.3 (2024-04-09) Bug fixes - Fixed bug in summarize_detections() where values in num_locs and locations columns were incorrect. - Likely a side effect of commit 3f0a2ee which aimed to fix issue #182 Changes in version 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"). - fixed issue #182 - cherry-picked from commit db9d69a which was merged with dev but not main. Changes in version 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. Changes in version 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. Changes in version 0.6.5 (2023-09-07) Bug fixes - Fix bug in summarize_detections() where setting 'location_col' triggers error. - fixes issue #180 Changes in version 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 Changes in version 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. - fix issue #177 Changes in version 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. Changes in version 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(). Changes in version 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) Changes in version 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). Changes in version 0.5.1 2021-11-09 Bug fix - position_heat_map - fix issue #121 (error when input does not contain columns X and Y) Changes in version 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 Changes in version 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 Changes in version 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 - set ties = "ordered" for all calls to stats::approx - fixes issue #93 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 Changes in version 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 Changes in version 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. Changes in version 0.3.1 2019-02-27 bug fixes - fix missing brackets in glatos.Rd Changes in version 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 Changes in version 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) Changes in version 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) Changes in version 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) Changes in version 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 Changes in version 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 Changes in version 0.1.3 2017-03-01 - initial release on OTN gitlab