Man pages for edwardlavender/flapper
Routines for the Analysis of Passive Acoustic Telemetry Data
| ac | The acoustic-container (AC) algorithm |
| acdc | The acoustic-container depth-contour (ACDC) algorithm |
| acdc_access | Short-cuts to elements of an '"acdc_record"' object |
| acdc_animate_record | Create a html animation of the AC/DC algorithm(s) |
| acdc_archive-class | "acdc-archive" class |
| acdc_plot_record | Plot time-specific maps from the AC/DC algorithm(s) |
| acdc_plot_trace | Plot AC* container dynamics |
| acdc_record-class | "acdc_record" class |
| acdc_simplify | Simplify the outputs of the AC/DC algorithms |
| acs_setup_containers | Setup the detection containers required for the AC*... |
| acs_setup_detection_kernels | Setup detection probability kernels for the AC* algorithm(s) |
| acs_setup_mobility | Examine the constant 'mobility' assumption of the AC*... |
| assemble_sentinel_counts | Assemble counts of transmissions/detections from sentinel... |
| buffer_and_crop | Buffer and crop a spatial object |
| cells_from_val | Obtain a RasterLayer or the cells of RasterLayer that are... |
| check... | Check that arguments supplied via '...' are allowed |
| check_class | Check the class of a function input to a parent function |
| check_class_acdc_record | Check an object is of class '"acdc_record"' |
| check_crs | Check coordinate reference systems match |
| check_dir | Check a directory exists |
| check_named_list | Check that a list is named |
| check_names | Check the names of an object contain required names |
| check_tz | Check the time zone of an object and force UTC if absent |
| check_value | Check the input value to a parent function argument |
| cl | Parallelisation helpers |
| coa | The centres of activity (COA) algorithm |
| coa_setup_delta_t | Suggest time intervals over which to calculate centres of... |
| compact | Compact a list |
| crop_from_click | Interactively crop a 'raster' |
| dat_acdc | Example ACDC algorithm output |
| dat_acoustics | Example passive acoustic telemetry detections dataset |
| dat_archival | Example archival dataset |
| dat_coast | The coastline around the MEFS Firth of Lorn acoustic array |
| dat_containers | Example detection containers from 'acs_setup_containers' |
| dat_dc | Example DC algorithm output |
| dat_dcpf_histories | Example DCPF algorithm output: particle histories |
| dat_dcpf_paths | Example DCPF algorithm output: reconstructed paths |
| dat_gebco | The bathymetry around the MEFS Firth of Lorn acoustic array |
| dat_ids | Example tagged individuals dataset |
| dat_moorings | Example passive acoustic telemetry receiver moorings dataset |
| dat_sentinel | Example sentinel tag range testing dataset |
| dc | The depth-contour (DC) algorithm |
| dcq | The 'quick' depth-contour (DCQ) algorithm |
| dist_btw_clicks | Calculate the distance between sequential mouse clicks on a... |
| dist_btw_points_3d | Calculate the Euclidean distance(s) between points in... |
| dist_btw_receivers | Compute Euclidean distances between receivers |
| dist_over_surface | Calculate the total distance of a path over a... |
| dot-acs | Back-end implementation of the AC and ACDC algorithms |
| dot-acs_pl | Intermediate wrapper for '.acs' that supports parallelisation |
| dot-planedist2 | Calculate a matrix of Euclidean distances between points |
| eval_by_kud | Evaluate movement path estimates using kernel utilisation... |
| flapper | 'flapper': Routines for the analysis of passive acoustic... |
| flapper_opts | Global example controls |
| flapper-tips-parallel | Parallelisation in 'flapper' |
| get_detection_area_sum | Calculate the total area sampled by acoustic receivers |
| get_detection_area_ts | Calculate the area sampled by receivers through time |
| get_detection_clumps | Get detection clumps |
| get_detection_containers | Define detection containers around receivers |
| get_detection_containers_envir | Sample environmental conditions around receivers |
| get_detection_containers_overlap | Get detection container overlaps |
| get_detection_days | Calculate detection days |
| get_detection_overlaps | Get 'overlapping' detections |
| get_detection_pr | A detection probability function based on distance |
| get_hr | Get animal 'home ranges' |
| get_id_rec_overlap | Calculate the overlap between individuals' time at liberty... |
| get_intersection | Spatial intersections with one or more geometries |
| get_mvt_mobility | Estimate individual swimming speeds from acoustic and... |
| get_mvt_resting | Identify resting behaviour within depth time series |
| get_n_operational_ts | Calculate the number of operational units through time |
| get_residents | Identify 'resident' individuals in a passive acoustic... |
| invert_poly | Invert a (spatial) polygon |
| kud_around_coastline | Process a kernel utilisation distribution around a barrier |
| kud_habitat | Define a 'habitat' grid for kernel smoothing |
| lcp_comp | Compare Euclidean and shortest distances |
| lcp_costs | Calculate the distances between connected cells in a Raster* |
| lcp_from_point | Create a Raster* of the least-cost distances around a point |
| lcp_graph_surface | Construct a graph for least-cost paths analysis of movement... |
| lcp_interp | Interpolate shortest (least-cost) paths between locations... |
| lcp_over_surface | Calculate shortest path(s) and/or distance(s) over a surface... |
| make_df_detections | Convert a detection matrix into a dataframe |
| make_matrix_cooccurence | Compute a detection history similarity matrix |
| make_matrix_detections | Matricise detection time series |
| make_matrix_ids | Matricise individual deployment time series |
| make_matrix_receivers | Matricise receiver deployment time series |
| mask_io | Implement 'mask' using the inside or outside of the mask |
| pf | The particle filtering routine |
| pf_access_history | Access the 'history' element of a 'pf_archive-class' object |
| pf_access_history_files | List 'history' files from a PF algorithm |
| pf_access_particles_unique | Access the cells sampled by PF |
| pf_animate_history | Create a html animation of the PF algorithm(s) |
| pf_archive-class | "pf_archive" class |
| pf_kud | Smooth POU maps |
| pf_kud_ | (Experimental) Alternative kernel smoothing routines for... |
| pf_loglik | Calculate the log-probability of movement paths from a PF... |
| pf_path-class | "pf" class |
| pf_plot_1d | Plot one-dimensional depth time series from a PF algorithm |
| pf_plot_2d | Map two-dimensional paths from a PF algorithm |
| pf_plot_3d | Map three-dimensional paths from a PF algorithm |
| pf_plot_history | Plot particle histories from a PF algorithm |
| pf_plot_map | Plot 'probability of use' from a PF algorithm |
| pf_setup_movement_pr | A simple movement model dependent on distance |
| pf_setup_optimisers | Optimisation settings for 'pf' |
| pf_setup_record | List 'record' files from an AC/DC algorithm for PF |
| pf_simplify | Convert particle histories from 'pf' into movement paths |
| pipe | Pipe operator |
| process_false_detections_sf | Pass putative false detections through a spatial filter |
| process_quality_check | Basic quality checks of passive acoustic telemetry datasets |
| process_receiver_id | Add unique receiver IDs to passive acoustic telemetry time... |
| process_surface | Process a Raster* by aggregation and quantify the error... |
| query_open_topo | Query the Open Topo Data API for elevation data |
| round_any | Round to multiple of any number |
| segments_cross_barrier | Determine if Euclidean path segments cross a barrier |
| sim_array | Simulate (marine) monitoring arrays |
| sim_detections | Simulate detections |
| sim_path_ou_1 | Simulate discrete-time movement paths under a... |
| sim_path_sa | Simulate discrete-time movement paths from step lengths and... |
| sim_path_-times | Functions for the simulation of movement paths |
| sim_surface | Populate a raster with simulated values |
| split_raster_equally | Split a raster into equal-area parts |
| summarise_along_walk | Summarise every n numbers in a vector |
| update_extent | Shrink or expand an 'extent' object |
| xy_from_click | Get location coordinates from mouse click(s) |
