Package: ct 0.5.0

ct: Camera Trap Data Management and Multi-Method Ecological Analysis

Tools for the complete camera trap data workflow in wildlife monitoring and ecological research. Reads and edits media metadata, filters independent detections, and standardises records for analysis. Measures diel activity and overlap (Ridout and Linkie (2009) <doi:10.1198/jabes.2009.08038>), directed short-term association between species with an encounter-response model (Hawkes (1971) <doi:10.1093/biomet/58.1.83>), seasonal shifts in activity, spatial coverage of detections, and species diversity. Estimates density or abundance of unmarked populations with several methods, including the random encounter model, camera trap distance sampling, time-to-event, space-to-event, instantaneous sampling, and the random encounter and staying-time model (see Rowcliffe et al. (2008) <doi:10.1111/j.1365-2664.2008.01473.x>, Howe et al. (2017) <doi:10.1111/2041-210X.12790>, Moeller et al. (2018) <doi:10.1002/ecs2.2331>, and Nakashima et al. (2018) <doi:10.1111/1365-2664.13059>).

Authors:Stanislas Mahussi Gandaho [aut, cre], Pablo Palencia [ctb, rev], R Consortium [fnd]

ct_0.5.0.tar.gz
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ct_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ct/json (API)

# Install 'ct' in R:
install.packages('ct', repos = c('https://stangandaho.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stangandaho/ct/issues

Pkgdown/docs site:https://stangandaho.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ACBR - Camera trap dataset from Agbogon Community Biological Reserve (ACBR), Benin
  • ctdp - Camera trap data package example
  • duikers - Maxwell's duiker camera-trap distance & video-start data
  • lama - Camera trap survey of the Lama Classified Forest
  • pendjari - Pendjari national park and surrounding areas
  • penessoulou - Camera-trap detections from the Penessoulou Classified Forest
  • rest_detection - Simulated camera-trap detections for the REST / RAD-REST workflow
  • rest_station - Camera-station table for the REST / RAD-REST example

On CRAN:

Conda:

camera-trapcamera-trap-data-packagecamera-trapsctct-r-packagedensity-estimationdistance-samplingecological-modellingecologyrandom-encounter-modelwildlife-monitoringcpp

5.10 score 4 stars 52 scripts 364 downloads 75 exports 118 dependencies

Last updated from:046e3849fe. Checks:15 OK. Indexed: yes.

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source / vignettesOK294
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linux-release-x86_64OK271
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macos-release-x86_64OK415
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windows-release-x86_64OK215
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wasm-releaseOK170

Exports:%<>%%>%ct_alpha_diversityct_availabilityct_boot_cict_boot_estimatesct_bootstrapct_camera_dayct_camtrap_animal_distancect_check_locationct_check_namect_chi2_selectct_cict_clone_dirct_convert_unitct_correct_datetimect_create_hsct_describe_dfct_dissimilarityct_dp_examplect_dp_filterct_dp_readct_dp_tablect_dp_versionct_exiftool_callct_find_breakct_fit_activityct_fit_detmodelct_fit_distributionct_fit_dsct_fit_encounter_responsect_fit_isect_fit_remct_fit_restct_fit_speedmodelct_fit_stect_fit_ttect_get_effortct_get_hsct_independencect_inextct_install_exiftoolct_overlap_estimatesct_overlap_matrixct_plot_calendarct_plot_camtrap_activityct_plot_densityct_plot_inextct_plot_overlapct_plot_overlap_coefct_plot_rose_diagramct_QAICct_readct_read_metadatact_remove_hsct_resamplect_rest_activityct_rest_effortct_rest_passesct_rest_select_stayct_rest_stayct_select_modelct_solartimect_spatial_coveragect_stack_dfct_standardizect_summarise_camtrap_activityct_survey_designct_temporal_shiftct_to_communityct_to_occupancyct_to_radianct_to_timect_traprate_datact_traprate_estimate

Dependencies:activityaskpassbase64encbbmlebdsmatrixbitbit64bslibcachemcamtrapdpclassclassIntclicliprcodetoolscpp11crayoncurlDBIdigestDistancedplyre1071EMLemldevaluatefarverfastmapfontawesomefrictionlessfsfuturefuture.applygenericsggplot2globalsgluegtablehighrhmshtmltoolshttrisobandjqrjquerylibjsonldjsonliteKernSmoothknitrlabelinglatticelazyevallifecyclelistenvlubridatemagrittrMASSMatrixmemoisemgcvmimemrdsmvtnormnlmenloptrnumDerivopenssloptimxoverlapparallellypbapplypillarpkgconfigpracmaprettyunitsprogressproxypurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRdpackreadrrlangrmarkdownRsolnps2S7sasssbdscalessfstringistringrsuntoolssystibbletidyrtidyselecttimechangetinytextruncnormtzdbunitsutf8uuidV8vctrsviridisLitevroomwithrwkxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Camera trap dataset from Agbogon Community Biological Reserve (ACBR), BeninACBR
Alpha diversity indexct_alpha_diversity
Temporal availability adjustmentct_availability
Bootstrap confidence intervalsct_boot_ci
Generate bootstrap estimates of overlapct_bootstrap ct_boot_estimates ct_resample
Calculate daily camera trap capturesct_camera_day
Estimate distance from camera trap to animalct_camtrap_animal_distance
Interactive camera trap location adjustmentct_check_location
Check species name and retrieve Taxonomic Serial Number (TSN) from ITISct_check_name
Select best detection function model by Chi-squared Goodness-of-fitct_chi2_select
Calculate confidence intervalct_ci
Clone directory structurect_clone_dir
Convert values between different unitsct_convert_unit
Correct camera trap datetime recordsct_correct_datetime
Create or add hierarchical subject (hs) values in image metadatact_create_hs
Descriptive statistic on datasetct_describe_df
Calculate dissimilarity between communitiesct_dissimilarity
Read the Camtrap DP example datasetct_dp_example
Filter camera trap data packagect_dp_filter
Read camera trap data packagect_dp_read
Get core tablesct_dp_table
Get Camtrap DP version Extracts the version number used by a Camera Trap Data Package object. This version number indicates what version of the Camtrap DP standard was used.ct_dp_version
Call ExifToolct_exiftool_call
Detect time gaps in a datetime seriesct_find_break
Fit activity model to time-of-day datact_fit_activity
Fit animal detectionct_fit_detmodel
Fit a count distribution by maximum likelihoodct_fit_distribution
Fit detection functions and estimate density/abundancect_fit_ds
Fit a conditional encounter-response model for camera-trap eventsct_fit_encounter_response
Estimate abundance from Instantaneous Sampling (ISE) Datact_fit_ise
Fit Random Encounter Model (REM)ct_fit_rem
Fit the Random Encounter and Staying Time (REST / RAD-REST) modelct_fit_rest
Fit animal speed modelct_fit_speedmodel
Estimate abundance from Space-To-Event (STE) Datact_fit_ste
Estimate abundance from Time-To-Event (TTE) Datact_fit_tte
Calculate camera trap deployment effortct_get_effort
Retrieve hierarchical subject (hs) values from image metadatact_get_hs
Evaluate independent detectionsct_independence
Interpolation and extrapolation of Hill numberct_inext
Install ExifTool, downloading (by default) the current versionct_install_exiftool
Estimates of coefficient of overlappingct_overlap_estimates
Estimate overlap coefficients for multiple speciesct_overlap_matrix
Plot a calendar heatmap of daily camera trap activityct_plot_calendar
Plot camera trap activity over timect_plot_camtrap_activity
Plot species' activity patternsct_plot_density
Plot diversity interploation and extrapolationct_plot_inext
Plot overlap between two species' activity patternsct_plot_overlap
Plot overlap coefficient matrixct_plot_overlap_coef
Plot a 24-hour rose diagram of daily activityct_plot_rose_diagram
Compute QAIC for a set of detection function modelsct_QAIC
Read a delimited file into a tibblect_read
Read Image Metadatact_read_metadata
Remove hierarchical subject (hs) values from image metadatact_remove_hs
Prepare activity (time-of-day) data for RESTct_rest_activity
Add camera-trapping effort (days) to formatted station datact_rest_effort
Aggregate the number of animal passes per station for REST / RAD-RESTct_rest_passes
Choose a staying-time distribution for REST by WAICct_rest_select_stay
Prepare staying-time data for RESTct_rest_stay
Model selection for Distance Sampling detection functionsct_select_model
Transform time to solar time anchored to sunrise and sunsetct_solartime
Estimate species spatial coverage from camera trap detectionsct_spatial_coverage
Stack a list of data framect_stack_df
Standardize community data matrixct_standardize
Create activity summary statisticsct_summarise_camtrap_activity
Create a survey design for camera trap deploymentct_survey_design
Calculate the temporal shift of one species' activity over two periodsct_temporal_shift
Convert data to a community matrixct_to_community
Convert camera trap data to occupancy formatct_to_occupancy
Convert time to radiansct_to_radian
Convert radian to timect_to_time
Prepare data for trap rate estimationct_traprate_data
Estimate trap ratect_traprate_estimate
Camera trap data package examplectdp
Maxwell's duiker camera-trap distance & video-start dataduikers
Camera trap survey of the Lama Classified Forestlama
Pendjari national park and surrounding areaspendjari
Camera-trap detections from the Penessoulou Classified Forestpenessoulou
Simulated camera-trap detections for the REST / RAD-REST workflowrest_detection
Camera-station table for the REST / RAD-REST examplerest_station