Integrated Camera-Trap Data Management and Analysis

Documentation for package ‘ct’ version 0.4.0

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ACBR	Camera trap dataset from Agbogon Community Biological Reserve (ACBR), Benin
ctdp	Camera trap data package example
ct_alpha_diversity	Alpha diversity index
ct_availability	Temporal availability adjustment
ct_bootstrap	Generate bootstrap estimates of overlap
ct_boot_ci	Bootstrap confidence intervals
ct_boot_estimates	Generate bootstrap estimates of overlap
ct_camera_day	Calculate daily camera trap captures
ct_camtrap_animal_distance	Estimate distance from camera trap to animal
ct_check_location	Interactive camera trap location adjustment
ct_check_name	Check species name and retrieve Taxonomic Serial Number (TSN) from ITIS
ct_chi2_select	Select best detection function model by Chi-squared Goodness-of-fit
ct_ci	Calculate confidence interval
ct_clone_dir	Clone directory structure
ct_convert_unit	Convert values between different units
ct_correct_datetime	Correct camera trap datetime records
ct_create_hs	Create or add hierarchical subject (hs) values in image metadata
ct_describe_df	Descriptive statistic on dataset
ct_dissimilarity	Calculate dissimilarity between communities
ct_dp_example	Read the Camtrap DP example dataset
ct_dp_filter	Filter camera trap data package
ct_dp_read	Read camera trap data package
ct_dp_table	Get core tables
ct_dp_version	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_exiftool_call	Call ExifTool
ct_find_break	Detect time gaps in a datetime series
ct_fit_activity	Fit activity model to time-of-day data
ct_fit_detmodel	Fit animal detection
ct_fit_distribution	Fit a count distribution by maximum likelihood
ct_fit_ds	Fit detection functions and estimate density/abundance
ct_fit_ise	Estimate abundance from Instantaneous Sampling (ISE) Data
ct_fit_rem	Fit Random Encounter Model (REM)
ct_fit_rest	Fit the Random Encounter and Staying Time (REST / RAD-REST) model
ct_fit_speedmodel	Fit animal speed model
ct_fit_ste	Estimate abundance from Space-To-Event (STE) Data
ct_fit_tte	Estimate abundance from Time-To-Event (TTE) Data
ct_get_effort	Calculate camera trap deployment effort
ct_get_hs	Retrieve hierarchical subject (hs) values from image metadata
ct_independence	Evaluate independent detections
ct_inext	Interpolation and extrapolation of Hill number
ct_install_exiftool	Install ExifTool, downloading (by default) the current version
ct_overlap_estimates	Estimates of coefficient of overlapping
ct_overlap_matrix	Estimate overlap coefficients for multiple species
ct_plot_calendar	Plot a calendar heatmap of daily camera trap activity
ct_plot_camtrap_activity	Plot camera trap activity over time
ct_plot_density	Plot species' activity patterns
ct_plot_inext	Plot diversity interploation and extrapolation
ct_plot_overlap	Plot overlap between two species' activity patterns
ct_plot_overlap_coef	Plot overlap coefficient matrix
ct_plot_rose_diagram	Plot a 24-hour rose diagram of daily activity
ct_QAIC	Compute QAIC for a set of detection function models
ct_read	Read a delimited file into a tibble
ct_read_metadata	Read Image Metadata
ct_remove_hs	Remove hierarchical subject (hs) values from image metadata
ct_resample	Generate bootstrap estimates of overlap
ct_rest_activity	Prepare activity (time-of-day) data for REST
ct_rest_effort	Add camera-trapping effort (days) to formatted station data
ct_rest_passes	Aggregate the number of animal passes per station for REST / RAD-REST
ct_rest_select_stay	Choose a staying-time distribution for REST by WAIC
ct_rest_stay	Prepare staying-time data for REST
ct_select_model	Model selection for Distance Sampling detection functions
ct_solartime	Transform time to solar time anchored to sunrise and sunset
ct_spatial_coverage	Estimate species spatial coverage from camera trap detections
ct_stack_df	Stack a list of data frame
ct_standardize	Standardize community data matrix
ct_summarise_camtrap_activity	Create activity summary statistics
ct_survey_design	Create a survey design for camera trap deployment
ct_temporal_shift	Calculate the temporal shift of one species' activity over two periods
ct_to_community	Convert data to a community matrix
ct_to_occupancy	Convert camera trap data to occupancy format
ct_to_radian	Convert time to radians
ct_to_time	Convert radian to time
ct_traprate_data	Prepare data for trap rate estimation
ct_traprate_estimate	Estimate trap rate
duikers	Maxwell's duiker camera-trap distance & video-start data
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