Function reference • positionR

🎯 Array Design Functions

Generate receiver arrays and calculate detection coverage

generate_absences_available_habitat(): Generate absences from available habitat (whole study area minus space use areas)

generate_absences_buffer_zone(): Generate absences in buffer zone around space use area

generate_absences_random_cells(): Generate random absence points from any valid raster cells

generate_absences_system_wide(): Generate absences using system-wide detection efficiency

generate_points_bounding_box_method(): Generate points within bounding box

generate_points_constrained_hull(): Generate points within constrained convex hull

generate_points_convex_hull(): Generate points within convex hull polygon

generate_points_ellipse(): Generate points within 95% confidence ellipse

generate_points_grid_cells(): Generate points within grid cells occupied by track

generate_random_points(): Generate random points within spatial boundaries

generate_random_points_in_space_use(): Generate random points within space use estimates from calculate_space_use

generate_regular_points() generate_exact_regular_points(): Generate regular points within spatial boundaries

generate_simple_raster_absences(): Simple absence generation function that ONLY uses the raster - no other inputs

generate_space_use_absences(): Generate absence points across the entire reference raster (simplified version)

generate_space_use_absences_simple(): Wrapper to generate absences with fish/time info using simple raster logic

generate_spaced_points(): Generate points with specified spacing within spatial boundaries

calculate_station_de_characteristics(): Calculate Station Detection Efficiency Characteristics

calculate_station_distances(): Calculate cost distances from receiver stations to all raster cells (Enhanced)

calculate_detection_summaries(): Calculate detection rate summaries from fish track simulations

calculate_detection_system(): Calculate detection system probabilities and create visualization

🐟 Movement & Positioning Functions

Simulate movements and calculate WADE positions

simulate_fish_tracks(): Simulate fish tracks with correlated random walks and detection events

prepare_detection_data_for_wade(): Prepare real fish detection data for WADE positioning

calculate_fish_positions(): Calculate fish positions from acoustic telemetry data

📊 Analysis Functions

Space use, habitat selection, and performance analysis

calculate_space_use(): Calculate Space Use Estimates from Track Data

calculate_space_use_zoom(): Calculate zoom extent for map considering both track data and space use area

analyze_behavioral_temperature(): Analyze behavioral state patterns by temperature bins

analyze_comparative_habitat_selection(): Comparative habitat selection analysis using positioning and/or space use data

analyze_depth_selection(): Analyze depth selection patterns

analyze_detection_performance(): Comprehensive detection performance analysis with summary and plots

analyze_positioning_performance(): Analyze positioning performance from acoustic telemetry

analyze_single_dataset(): Analyze a single presence-absence dataset

compare_space_use_methods(): Compare multiple space use methods by generating points for each

compare_space_use_thresholds(): Compare Space Use Results Across Multiple Probability Thresholds

🎨 Visualization Functions

Publication-ready plots and visualizations

plot_behavioral_states(): Plot behavioral states over time with temperature coloring

plot_comparative_results(): Plot comparative habitat selection results

plot_depth_comparison(): Create comparison plots for multiple fish or time periods

plot_depth_selection(): Plot depth selection patterns

plot_depth_spatial(): Create spatial plot of presence/absence points colored by depth

plot_detection_rates(): Create visualization plots of detection rate performance

plot_fish_positions(): Plot fish position estimates from acoustic telemetry

plot_fish_tracks(): Plot simulated fish tracks with detection events

plot_points_on_input(): Plot generated points on spatial input object

plot_presence_absence_space_use(): Plot presence and absence points together

plot_space_use(): Plot space use estimates

plot_space_use_map(): Updated plot function with proper raster cell visualization

plot_space_use_method_comparison(): Plot comparison of multiple space use methods

plot_space_use_points(): Plot space use areas with generated random points

⚙️ Utility Functions

Data preparation and helper functions

apply_information_weighting(): Apply Information-Theoretic Weighting

create_comparison_analysis(): Create comparison analysis between positioning and space use results

create_constrained_grid_raster_data(): Create constrained hull by finding which depth_raster cells are within convex hull polygon

create_ellipse_polygon(): Create ellipse polygon for 95% confidence ellipse

create_ellipse_polygon_data(): Create ellipse polygon data with method label

create_grid_cell_polygons(): Create grid cell polygons for plotting

create_grid_polygon(): Create grid cell polygon

create_grid_raster_data(): Create grid raster data using actual raster cell boundaries

create_logistic_curve_depth(): generate detection range models Create logistic curve for detection efficiency with depth extrapolation

create_presence_absence_dataset(): Create combined presence-absence dataset for habitat selection analysis

create_space_use_polygon(): Create space use polygon for visualization

create_space_use_polygon_data(): Create space use polygon data for direct plotting

create_space_use_summary(): Create summary statistics for space use estimates

create_threshold_comparison_plots(): Create visualization plots for threshold comparison

standardize_track_data_for_points(): Standardize track data for point generation to match space_use_results time binning

standardize_track_data_space(): Standardize track data for space use analysis

sample_points_from_probabilities(): Sample points from position probability surfaces

sample_points_from_system_de(): Sample points from system detection efficiency surfaces

sample_points_from_track_grid(): Sample points from track data grid cell usage

extract_absence_time_info(): Extract time binning information from space_use_points and space_use_results

extract_space_use_time_info(): Extract time binning information from space_use_results

get_raster_cells_as_polygons(): Get raster cells as proper polygon data for accurate visualization This function creates the actual cell boundaries for each raster cell

get_space_use_exclusion_cells(): Get cells to exclude based on space use method

print_comparative_summary(): Print comparative habitat selection summary

print_detection_summary(): Print detection summary report in readable format

print_station_characteristics(): Print Station Characteristics Summary

summarize_space_use_points(): Summary function for space use points

run_array_design(): Launch Interactive Array Design Shiny Application

🔧 Internal Functions

Internal calculation and helper functions

calculate_95_ellipse_area(): Calculate 95% confidence ellipse area

calculate_constrained_convex_hull_area(): Updated constrained convex hull calculation to work with reference raster

calculate_constrained_convex_hull_area_with_data(): Calculate constrained convex hull with spatial data

calculate_convex_hull_area(): Calculate convex hull area

calculate_grid_cell_usage(): Updated grid cell usage calculation to work with reference raster

calculate_grid_cell_usage_with_data(): Calculate grid cell usage with spatial data

calculate_group_space_use(): Calculate space use metrics for a single group

calculate_threshold_summary_stats(): Calculate summary statistics for threshold comparison

calculate_track_overlap(): Calculate track overlap for spatial data

line_intersects_box(): Check if a line segment intersects with a box Uses basic line-box intersection algorithm

point_in_polygon(): Point-in-polygon test using ray casting algorithm

test_cells_in_polygon(): Test if raster cells intersect with a polygon using simple corner test Include cell if ANY of its 4 corners are inside the polygon

test_cells_in_polygon_full(): Alias for test_cells_in_polygon_simple for backward compatibility

test_cells_in_polygon_simple(): Test if raster cells intersect with a polygon using cell centers (original working version) This is the original simple method that was working

test_raster_absence_generation(): Test function to validate raster and absence generation

stoney_fish_detections: Fish Detection Data from Stoney Lake

stoney_rx_deploy: Acoustic Receiver Deployment Data from Stoney Lake