Package index • ct

Data examples

pendjari: Pendjari national park and surrounding areas
ctdp: Camera trap data package example
duikers: Maxwell's duiker camera-trap distance & video-start data

Process media (images) file

Functions reading and writing metadata

ct_app(): Run App
ct_install_exiftool(): Install ExifTool, downloading (by default) the current version
ct_read_metadata(): Read Image Metadata
ct_exiftool_call(): Call ExifTool
ct_get_hs(): Retrieve hierarchical subject (hs) values from image metadata
ct_create_hs(): Create or add hierarchical subject (hs) values in image metadata
ct_remove_hs(): Remove hierarchical subject (hs) values from image metadata
ct_clone_dir(): Clone directory structure

Data processing

Functions for preparing and tansforming camera trap data

ct_read(): Read a delimited file into a tibble
ct_stack_df(): Stack a list of data frame
ct_check_location(): Interactive camera trap location adjustment
ct_survey_design(): Create a survey design for camera trap deployment
ct_independence(): Evaluate independent detections
ct_to_radian(): Convert time to radians
ct_solartime(): Transform time to solar time anchored to sunrise and sunset
ct_to_time(): Convert radian to time
ct_to_community(): Convert data to a community matrix
ct_standardize(): Standardize community data matrix
ct_check_name(): Check species name and retrieve Taxonomic Serial Number (TSN) from ITIS
ct_to_occupancy(): Convert camera trap data to occupancy format
ct_find_break(): Detect time gaps in a datetime series
ct_correct_datetime(): Correct camera trap datetime records
ct_get_effort(): Calculate camera trap deployment effort
ct_traprate_data(): Prepare data for trap rate estimation
ct_dp_read(): Read camera trap data package
ct_dp_table(): Get core tables
ct_dp_example(): Read the Camtrap DP example dataset
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_dp_filter(): Filter camera trap data package
ct_convert_unit(): Convert values between different units
ct_camera_day(): Calculate daily camera trap captures
ct_camtrap_animal_distance(): Estimate distance from camera trap to animal

Data analysis

Functions to run common camera trap data analysis

ct_describe_df(): Descriptive statistic on dataset
ct_plot_density(): Plot species' activity patterns
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_plot_camtrap_activity(): Plot camera trap activity over time
ct_plot_inext(): Plot diversity interploation and extrapolation
ct_overlap_estimates(): Estimates of coefficient of overlapping
ct_bootstrap() ct_resample() ct_boot_estimates(): Generate bootstrap estimates of overlap
ct_boot_ci(): Bootstrap confidence intervals
ct_ci(): Calculate confidence interval
ct_overlap_matrix(): Estimate overlap coefficients for multiple species
ct_temporal_shift(): Calculate the temporal shift of one species' activity over two periods
ct_alpha_diversity(): Alpha diversity index
ct_dissimilarity(): Calculate dissimilarity between communities
ct_spatial_coverage(): Calculate observed spatial coverage of species
ct_summarise_camtrap_activity(): Create activity summary statistics
ct_traprate_estimate(): Estimate trap rate
ct_fit_activity(): Fit activity model to time-of-day data
ct_fit_speedmodel(): Fit animal speed model
ct_fit_detmodel(): Fit animal detection
ct_fit_rem(): Fit Random Encounter Model (REM)
ct_availability(): Temporal availability adjustment
ct_select_model(): Model selection for Distance Sampling detection functions
ct_QAIC(): Compute QAIC for a set of detection function models
ct_chi2_select(): Select best detection function model by Chi-squared Goodness-of-fit
ct_fit_ds(): Fit detection functions and estimate density/abundance
ct_inext(): Interpolation and extrapolation of Hill number