# Integrated Camera-Trap Data Management and Analysis

## Documentation for package ‘ct’ version 0.4.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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