NEWS.md

In ocean-tracking-network/glatos: A package for the Great Lakes Acoustic Telemetry Observation System

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.

• 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).

glatos 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

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").
  • fixed issue #182
  • cherry-picked from commit db9d69a which was merged with dev but not main.

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.
  • fixes issue #180

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.
  • fix issue #177

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

  • 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

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

ocean-tracking-network/glatos documentation built on April 17, 2025, 10:38 p.m.