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").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.
read_glatos_workbook() that caused failure when GLATOS workbook
file contains project-specific sheets and read_all = TRUE.
crw_in_polygon() that caused failure with error with
non-default initPos and missing cartesianCRS arguments when crs of input
polyg is cartesian.
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.
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"".
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.
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').".
Added support for GLATOS workbook version 1.4 (xlsx file) in
read_glatos_workbook().
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", ...).Added support for parquet files in read_otn_detections().
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
Changed make_transition() to use jarasterize() (see New Features) and
added input arg buffer.
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'.
Add new function vue_convert() to convert VRL file to CSV file (detection
records only; receiver event log records are not supported).
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.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.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.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).
terra::SpatVector inputAdd 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.
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).
summarize_detections() where values in num_locs and
locations columns were incorrect.
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").
bg_map was supplied.
background_xlim, background_ylim, and
bg_map to function make_frames.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:
convert_otn_to_att and convert_otn_erddap_to_att:
sp::CRS with sf::st_crsRemove ffmpeg functions.
check_dependenciesinstall_ffmpegmake_video_ffmpegFix issues with several tests caused by changes to CRS/WKT and row.names attributes.
position_heat_map() function resulting in Error in zip_internal... Some files do not exist. Update documentation.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().
crw_in_polygon
transmit_along_path
detect_transmissions
position_heat_map
remove dependence on PBSmapping
remove dependence on gdalUtils
changes to kml_to_csv
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)
read_glatos_workbook
removed openxlsx and cellranger dependencies from DESCRIPTION
fix issue preventing vignettes from building when installed (missing space in data_loading_vignette.Rmd).
convert_glatos_to_att,
CRS for ATT compatibilityresidence_index
.dots argument of group_by() is deprecated as
of dplyr 1.0.0"convert_otn_erddap_to_att
make_video
make_frames
interpolate_path
ties = "ordered" for all calls to stats::approxabacus_plot
panel.first and panel.last) had to be wrapped in quotesummarize_detections
check_dependencies
functions
example data
make_frames
interpolate_path
calc_collision_probs
make_video
adjust_playback_time
vrl2csv
detect_transmissions
make_frames
abacus_plot
functions
vignettes and documentation
detection_events
crw_in_polygon
transmit_along_path
detect_transmissions
abacus_plot
position_heat_map
dropped fasttime as a depenedency and uses lubridates fasttime implementation instead
Update sysdata detection schema for OTN
interpolate_path
vector_heading