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_get_metadata(): Extract image metadata

ct_get_hs(): Retrieve hierarchical subject values from image metadata

ct_create_hs(): Create or add hierarchical subject values in image metadata

ct_remove_hs(): Remove specific or all hierarchical subject values from image metadata

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

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_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