surveyDashboard: Shiny dashboard for summarizing and analyzing
camera trap survey data
filterRecordTable: filter existing record table for temporal
independence between records
addToPath: replacement for exiftoolPath with identical
functionality
New features
communityModel: new argument “model” allows Royle-Nichols
models
fit, predict, plot_effects, plot_coef also support Royle-Nichols
models
predict: now accepts type = “pao” (for percentage of area occupied,
by species), “psi_array” (raw occupancy probabilities), “abundance”
(abundance statistics, for Royle-Nichols model) and “lambda_array” (raw
abundances from Royle-Nichols model)
predict: new argument “batch” to allow memory-friendly processing in
batches
communityModel: returns species richness at sampling locations (only
in JAGS models)
Bugfixes
cameraOperation: last occasions is 0 (not NA) when occasionStartTime
= 12 and retrieval time is 12 noon (to prevent dropping of records on
last day)
cameraOperation: allows any number of ProblemX_from/to columns (was
previously limited to 9). Reported by Nicolas Deere.
predict / plot_effects: fixed wrong assignment of intercept
estimates to posterior draws
Other changes
migrated functions from raster/sp to terra/sf, removed rgdal
modified plot titles in activityRadial().
package “overlap” in Suggests, not Depends
camtrapR 2.2.0
New functions
communityModel: create community occupancy models for JAGS and
Nimble. Comes with summary(), fit(), and predict() methods
plot_effects(): for plotting marginal effect plots (response curves)
from community models
plot_coef(): for plotting coefficient estimates from community
models
Bugfixes
reading digiKam database now works for Mac + Linux systems
Other changes
cameraOperation: warning instead of error if problem columns are
empty and hasProblems = TRUE
camtrapR 2.1.0
New functions
OCRdataFields: allows automatic reading of text from data fields in
images via optical character recognition (OCR), requires magick and
tesseract packages
writeDateTimeOriginal: Write values to DateTimeOriginal tag to image
metadata
New features
cameraOperation: setup/ retrieval / problem columns can be
interpreted as date-time format, then computes effort as fraction of
day. (Thank you to Zoe Siegel for the suggestion, Fridolin Zimmermann
and the Department of Ecology & Evolution from the University of
Lausanne for funding the development of the feature)
cameraOperation: gained argument occasionStartTime (deprecated in
detectionHistory / spatialDetectionHistory)
function camopPlot is now accessible via camtrapR:::camopPlot(). It
also gained an argument “lattice”, which can be TRUE or FALSE (if TRUE,
it uses levelplot() from lattice)
surveyReport: new argument camOp (for a camera operation matrix),
argument CTHasProblems is deprecated. Improved calculation of survey
effort.
timeShiftImages / addCopyrightTag: added argument
“ignoreMinorErrors”, set it to TRUE if functions fails due to bad
MakerNotes (reported by An Nguyen)
detectionMaps uses package sf instead of sp and rgdal
Bugfixes
cameraOperation now works when Problem columns are of class date or
POSIX. Now being converted to character (reported by David
Nicholls)
recordTable: supports extraction of metadata tags from video files
in camera subdirectories, and allows duplicate video file names in
different camera subdirectories (reported by Sian Green)
recordTable: fix bug that assigned Albums to wrong AlbumRoots in the
digiKam database (when reading video metadata, reported by Sian
Green)
imageRename: fixed error when hasCameraFolders is TRUE, but a
station has only 1 camera (reported by Camille Coudrat and Ezekiel
Gading)
detectionHistory: fixed a bug that caused errors when using multiple
sessions and non-standard date/time formats (reported by Daniele
Barcelos)
checkSpeciesNames: fixed error due to change in taxize::get_tsn
(reported by Ivonne Oddoy)
Other changes
lubridate is a dependency now (for cameraOperation)
additional Suggests: magick and tesseract (for OCRdataFields),
lattice (for camopPlot)
roxygen2 documentation
camtrapR 2.0.3
Bugfixes
fixed error messages if date or date/time columns contain blank
values or NA
fixed DH_error2 in detectionHistory() with output = “count”
(reported by Maddy Uetrecht)
cameraOperation failed if setupCol or retrievalCol were of class
“Date”. Now being converted to character.
imageRename: fixed camera IDs being assigned incorrectly in very
rare cases on Mac (reported by Camille Coudrat)
recordTable: fixed error when videos had metadata tags that were not
in tag groups
Other changes
recordTable / recordTableIndividual: users can specify 1-character
Exiftool arguments in additionalMetadataTags (only tested with “L” for
Latin character set, everything else will most likely break the code,
suggested by Saloni Salaria)
improved error messages in recordTable/recordTableIndividual and
detectionHistory/spatialDetectionHistory functions
camtrapR 2.0.2
Bugfixes
vignette creation conditional on availability of Exiftool (for CRAN
checks)
tests with testthat conditional on availability of Exiftool (for
CRAN checks)
appendSpeciesNames / getSpeciesImages: error message if exiftool is
not available
camtrapR 2.0.1
Bugfixes
exifTagNames: doesn’t return tag description, it caused an error on
some systems
Other changes
included tests with testthat
camtrapR 2.0.0
New features
recordTable / recordTableIndividual: video support via new argument
“video” (requires package “RSQLite”, thanks to Ana Gracanin for a
crucial tip that made date/time extraction possible)
exifTagNames returns a data frame containing all relevant
information at once: tag group names, tag descriptions, tag names and
values. Arguments returnMetadata and returnTagGroup are ignored
now.
surveyReport: reliable creation of zip files via package “zip” (if
installed)
added sample images with species tags
cameraOperation: detailed error messages if duplicate station /
camera / session names
Bugfixes
detectionHistory: when recordDateTimeCol is a date without time,
function assigns a time to avoid calculating occasion 0 for records
taken on the camera setup day (with a warning)
error message in functions that call Exiftool when inDir is empty
(no subdirectories)
surveyReport: error message when zip file can’t be created
special characters in directory names now supported (but still best
avoided; requires ExifTool 9.79 or later)
detectionMaps: fixed error when trying to plot backgroundPolygon
(reported by Oliver Wearn)
Other changes
vignette filenames changed, document type changed to html_document,
added floating table of contents
added ORCID for authors
packages “RSQLite” and “zip” in Suggests
renamed sample picture folders
camtrapR 1.2.3
Other changes
checkSpeciesNames: no error when ITIS server is not available
minor fixes in vignettes
detectionHistory: no error if occasionLength is greater than half
the number of columns in camera operation matrix, as long as it is
smaller than the total number of columns
camtrapR 1.2.2
Bugfixes
recordTable: fixed error: cameraID must be of class ‘character’ when
it is character
recordTable: fixed error: metadataSpeciesTag must be of class
‘character’ when it is character
Other changes
cameraOperation: warning if date can be interpreted but is likely
wrong (due to incorrectly set dateFormat argument)
camtrapR 1.2.1
Bugfixes
recordTable: fixed error: metadataSpeciesTag must be of class
‘character’ when it is character and IDfrom = “metadata”
recordTable: fixed: ‘Error in [.data.frame(intable, ,
match(colnames(record.table), colnames(intable))) : undefined columns
selected’ (when additionalMetadataTags are defined)
New features
multi-season sample data sets: camtrapsMultiSeason,
recordTableSampleMultiSeason,
recordTableIndividualSampleMultiSeason
Other changes
package “data.table” is a dependency now (for more reliable assembly
of record table when additionalMetadataTags are defined, see ##
Bugfixes)
camtrapR 1.2
Bugfixes
imageRename: fixed bug where fileExistsAlready in output table was
FALSE when it should be TRUE
New features
detectionHistory: support multi-season input and create detection
histories for unmarkedFrameMult (from where users can create
multi-season occupancy models with unmarked::colext), new argument
“unmarkedFrameMultInput” (developed with support from Kirsten
Weingarth)
cameraOperation: new argument: sessionCol, to specify trapping
sessions / seasons (with some changes to the row names in camera
operation matrices if there are session and / or camera
information)
spatialDetectionHistory: supports camera operation matrices with
session information
tibbles (tidyverse) or data.tables support: all functions that
require input data frames don’t throw errors if these are are tibbles or
data.tables, instead they automatically convert them to data.frames with
a message
lubridate support: date and date-time formats as defined by
lubridate are now supported (e.g. “ymd” instead of “%Y-%m-%d” or “ymd
HMS” instead of “%Y-%m-%d %H:%M:%S”)
activityOverlap: main plot title contains species names by default
without being specified
recordTable / recordTableIndividual: 2 new arguments,
“eventSummaryColumn”” and “eventSummaryFunction” for statistics by event
(e.g. max count)
recordTable / recordTableIndividual: return additional column
“n_images” indicating the number of images in an event
progress bar in console for all functions that extract image
metadata
exifTagNames: more flexible, users can define subdirectories by name
and give desired file names
Other changes
detectionHistory / spatialDetectionHistory: improved error message
if date/time values are not readable (correct row in original
recordTable is returned)
detectionMaps: new error message when XCol or YCol are not
numeric
package “rgdal” is no longer a dependency. Function “detectionMaps”
will throw an error if user tries to write shapefile but package is
missing
packages “taxize” and “ritis” are no longer dependencies. Function
“checkSpeciesNames” will throw an error if either is missing
simplified data format of sample data: only character and
numeric/integer in camtraps, recordTableSample,
recordTableIndividualSample and timeShiftTable
camtrapR 1.1
Bugfixes
appendSpeciesNames / checkSpeciesIdentification / getSpeciesImages:
fixed error ‘argument “returnFileNamesMissingTags” is missing, with no
default’
recordTableIndividual: fixed multiple individuals from same image
being removed (except for one) when removeDuplicates = TRUE
New features
detectionHistory can return counts of records per occasion (new
argument “output”)
activityOverlap can return different overlap estimators (new
argument “overlapEstimator”)
detectionHistory / spatialDetectionHistory: improved error messages
when records fall outside camera trap operation range
Other changes
added citation (see: citation(“camtrapR”))
added URLs to description
camtrapR 1.0
Bugfixes
activityDensity: fixed problem with argument allSpecies = TRUE that
caused output list to return values for one species only (reported by
Sally Soo).
appendSpeciesNames, checkSpeciesIdentification,getSpeciesImages,
recordTableIndividual: fixed error in extracting species IDs from image
metadata in directories in which no images are tagged. These stations
are now skipped with a warning.
detectionHistory / spatialDetectionHistory: fixed error with
detection histories and effort matrix full of NAs arising if camera
operation matrix had values > 2 (after argument camerasIndependent =
TRUE in cameraOperation)
Other changes
imageRename: meaningful error message if no DateTimeOriginal tag was
readable (e.g. all cameras were Reconyx HC500)
recordTable/ recordTableIndividual: new argument:
returnFileNamesMissingTags: file name of images with missing species tag
are returned if TRUE (default = FALSE)
surveyReport: in sample R script enclosed in survey report zip file,
object cameraOperation was renamed to camOp (to avoid the clash with the
function name cameraOperation)
detectionHistory: the detection history output csv was renamed from
record_history… to detection_history…
camtrapR 0.99.9
Bugfixes
camera operation: fixed bug with empty entries in cameraCol when
cameraCol is defined (reported by Partha Sarathi Ghose)
recordTable / recordTableIndividual: verbose warnings and better
handling of situations in which date/time is unreadable (empty
Exif:DateTimeOriginal metadata tag)
New features
detectionHistory / activity plot functions: if date/time is
unreadable function returns row IDs to facilitate checks
activityDensity: warning instead of error if bandwidth estimation
fails and argument allSpecies = TRUE (problem occurred with single
records, or few records at similar time of day)
Other changes
exifTagNames: returns name of image from which metadata were
extracted as a message
camtrapR 0.99.8
Bugfixes
recordTable / recordTableIndividual: column “HierarchicalSubject”
(containing digiKam metadata tags in their native format) was called
“record.table3[, col_to_move]” by mistake (thanks to Ross Pitman for
reporting)
Other changes
improved checks that function input has correct class (to make sure
data.frames are provided where the functions expect them)
camtrapR 0.99.7
Bugfixes
recordTable: returned station ID as camera ID if IDfrom = “metadata”
and cameraID = “directory”
New features
detectionMaps: gained argument ‘backgroundPolgygon’ for plotting a
SpatialPolygon object in the background of the maps
imageRename: new argument ‘createEmptyDirectories’ to control
whether empty directories should be copied or not
imageRename: if outDir contains images already, the function will
not stop with an error, but asks you whether or not to copy new images
(useful if data come in over time)
Other changes
recordTable / recordTableIndividual: improved handling and reporting
of stations without images (warning instead of error)
recordTable / recordTableIndividual: improved handling and reporting
of stations where all images lack species/individual metadata tags (only
if using metadata ID, functions will throw warning instead of error,
reported by Aditya Malgaonkar)
camtrapR 0.99.6
Bugfixes
fixed crash in cameraOperation function caused by underscores in
station / camera IDs (reported by Wyatt Petersen)
New functions
fixDateTimeOriginal: Makes DateTimeOriginal Exif metadata tag in
Reconyx Hyperfire cameras readable
New features
spatialDetectionHistory: argument ‘sessionCol’ can now create
multi-session capthist objects by either assigning individuals to
different sessions or assigning stations to different sessions
exifTagNames: gained argument ‘returnTagGroup’, and now by default
returns metadata tag group in addition to metadata tag names (to
unambiguously address specific metadata tags)
Other changes
new dependency: “ritis” - this is because parts of package taxize
(used internally by function “checkSpeciesNames”) were migrated to
ritis
detectionHistory / spatialDetectionHistory: occasionLength can be
any value between 1 and the number of columns in camOp (not half the
number of columns in camOp as before)
functions check for spaces in user-provided column names and report
them as errors
camtrapR 0.99.5
Bugfixes
recordTable/recordTableIndividual: give warning if Exif
DateTimeOriginal tag of images is unreadable (error if all tags of a
station are unreadable). May happen if images files are corrupted due to
camera malfunctioning.
recordTable/recordTableIndividual: 2 records of the same species at
the same station and same time by different cameras are not collapsed
into one record if camerasIndependent = TRUE
all functions using Exiftool: JPG files beginning with “._” are now
ignored with a warning (these are hidden, uninformative system files
created on Macs and were quite capable of messing up function
calls)
New features
getSpeciesImages can now also read image file paths from a record
table provided by the user instead of reading species IDs anew in every
function call. It gained 3 new arguments for that purpose.
recordTable and recordTableIndividual both gained an argument
(removeDuplicateRecords) to control whether duplicate records (same
station, same species, exactly same time) should be collapsed into one
record (former versions did that without asking)
Other changes
imageRename will first check all directories before actually
renaming anything. So the function won’t break halfway through, leaving
you with a half-full directory of renamed images if something goes wrong
(e.g. unreadable date/time tags).
camtrapR 0.99.4
Bugfixes
spatialDetectionHistory: trap usage now codes malfunctioning cameras
and cameras that were not set up as 0 instead of NA (as expected by the
secr package)
spatialDetectionHistory: argument “scaleEffort” can only be FALSE
now (to avoid negative trapping effort values, which secr does not
accept)
New features
spatialDetectionHistory gained argument “sessionCol”. It can be used
to split data (i.e., create a list with multiple capthist objects) if
captures come from different sessions).
Other changes
package shows startup message and checks automatically if local
package version is up to date
camtrapR 0.99.3
New functions
addCopyrightTag: Write a copyright tag into image Exif metadata
Bugfixes
detectionHistory: malfunctioning cameras (0 in camera operation
matrix) did not cause detection history matrix cells to be NA (even if
includeEffort = FALSE; reported by Hsiang Ling Chen)
detectionHistory: if the last occasion is shorter than
occasionLength, the corresponding detection history matrix cells will
now be NA if includeEffort = FALSE
surveyReport: species column names other than “Species” are now
supported, i.e. argument “speciesCol” is now respected (thanks to
Valentine Herrmann and Stefano Anile for reporting)
New features
detectionHistory gained argument “minActiveDaysPerOccasion”. It can
be used to define the minimum number of active trap days per occasion
for that occasion be included (0/1 instead of NA)
camtrapR 0.99.2
Bugfixes
recordTable: fixed problem with appending camera IDs
cameraOperation: improved messages to user
Other changes
added section about defining date formats in camera station table to
vignette 1 (Image Organisation)
camtrapR 0.99.1
Bugfixes
detectionHistory and spatialDetectionHistory did not run correctly
under some rare circumstances (combinations of input arguments)
column names of detection histories were incorrect if
occasionStartTime != 0 and datesAsOccasionNames = TRUE
argument maxNumberDays in detectionHistory / spatialDetectionHistory
works on each station individually if day1 = “survey” or “station”; and
from the specified date if day1 is a date
Other changes
additional checks for consistency of input in a number of
functions
code simplification invisible to the user
camtrapR 0.99.0
New functions
checkSpeciesNames: checks a vector of species names (common or
scientific) against the ITIS taxonomic database via package
‘taxize’
checkSpeciesIdentification: expanded from former function
checkSpeciesFolders (now defunct). Can check identification if metadata
tags were used for species identification.
createStationFolders: Create camera trap station directories,
possibly with camera subdirectories, for storing raw images (was not
included in NAMESPACE of version 0.98.0, therefore invisible. Thanks to
Patrick Lorch and Brent Pease for notification)
detection histories can begin on any specified date,
station-specific setup date or day the first station was set up (to that
end argument “beginWithDay1” was changed to “day1”)
a buffer between setup and the first occasion can be applied
(argument “buffer”).
spatialDetectionHistory:
output can be given as counts or binary (argument “output”)
an RMark data frame can be created using argument
makeRMarkInput
extended support for identification via metadata tags (in functions
appendSpeciesNames, getSpeciesImages)
exifTagNames: can return metadata, not only metadata tag names (new
argument “returnMetadata”)
createStationFolders: new argument “createinDir”.
detecionMaps: new argument “speciesToShow” to make maps for certain
species only
activity plot functions show number of records that were used
Bugfixes
surveyReport returned an error when there were stations without
records.
detecionMaps: Xcol and Ycol have arbitrary names now.
Other changes
arguments “customMetadataTags” and hasSpeciesFolders/
hasIndividualFolders was removed and replaced with argument
“IDfrom”
metadata tags assigned in image management software are always
extracted and tabulated in recordTable functions (making argument
“customMetadataTags” obsolete)
some functions changed the user’s working directory. Fixed. Thanks
to Patrick Lorch for notification.
argument “hasCameraSubfolders” was renamed to “hasCameraFolders”
(functions appendSpeciesNames, checkSpeciesIdentification,
createSpeciesFolders, imageRename, timeShiftImages)
in all 4 activity plot functions, argument “all.species” was renamed
to “allSpecies”
argument “recordTable” in spatialDetectionHistory was renamed to
“recordTableIndividual” to make the difference from “recordTable” in
“detectionHistory” clearer
camtrapR 0.98.0
New functions
createStationFolders: Create camera trap station directories,
possibly with camera subdirectories, for storing raw images
recordDatabaseIndividual: Single-species record databases from
camera trap images with custom metadata tags
spatialDetectionHistory: prepare a capthist object for spatial
capture-recapture analyses
New features
support for camera subdirectories in species identification:
Station/Camera/Species in the following function:
appendSpeciesFolders
createSpeciesFolders
checkSpeciesFolders
createStationFolders
getSpeciesImages
imageRename
recordDatabase
recordDatabaseIndividual
recordDatabase: can handle different types of directory structures
and metadata tags (both custom and manufacturer-specific) and has gained
new arguments:
hasSpeciesFolders
cameraID (expanded from includeCameras)
camerasIndependent
stationCol
customMetadataTags
metadataHierarchyDelimitor
metadataSpeciesTag
additionalMetadataTags (renamed from metadataTags)
detectionMaps: shapefile export using packages sp and rgdal