Animal Movement Tools
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘amt’ version 0.2.2.0
Help Pages
A B C D E F G H I L M N O P R S T U misc
-- A --
| add_nsd | Net squared displacement (nsd) |
| add_nsd.steps_xy | Net squared displacement (nsd) |
| add_nsd.track_xy | Net squared displacement (nsd) |
| amt_fisher | GPS tracks from four fishers |
| amt_fisher_covar | Environmental data for fishers |
| as.data.frame.uhc_data | Coerce a 'uhc_data' object to 'data.frame' |
| as_degree | Converts angles to radians |
| as_ltraj | Coerce a track to other formats. |
| as_ltraj.track_xy | Coerce a track to other formats. |
| as_ltraj.track_xyt | Coerce a track to other formats. |
| as_moveHMM | Coerce a track to other formats. |
| as_moveHMM.track_xy | Coerce a track to other formats. |
| as_rad | Converts angles to radians |
| as_sf | Coerce a track to other formats. |
| as_sf.steps_xy | Coerce a track to other formats. |
| as_sf_lines | Export track to lines |
| as_sf_points | Coerces a track to points |
| as_sf_points.steps_xy | Coerces a track to points |
| as_sp | Coerce a track to other formats. |
| as_telemetry | Coerce a track to other formats. |
| as_telemetry.track_xyt | Coerce a track to other formats. |
| as_track | Coerce to track |
| as_track.data.frame | Coerce to track |
| as_track.sfc_POINT | Coerce to track |
| as_track.steps_xyt | Coerce to track |
| available_distr | Display available distributions for step lengths and turn angles. |
-- B --
| bandwidth_pi | 'hr_kde_pi' wraps 'KernSmooth::dpik' to select bandwidth for kernel density estimation the plug-in-the-equation method in two dimensions. |
| bandwidth_ref | Reference bandwidth |
| bbox | Get bounding box of a track. |
| bbox.steps_xy | Get bounding box of a track. |
| bbox.track_xy | Get bounding box of a track. |
-- C --
| calculate_sdr | Calculate SDR |
| calc_w | Calculate 'w(x)' |
| centroid | Calculate the centroid of a track. |
| centroid.track_xy | Calculate the centroid of a track. |
| check_time_unit | Calculate Speed |
| coercion | Coerce a track to other formats. |
| conf_envelope | Create confidence envelopes from a 'uhc_data_frame' |
| convert_angles | Converts angles to radians |
| coords | Coordinates of a track. |
| cum_dist | Movement metrics |
| cum_ud | Calculate a cumulative UD |
-- D --
| deer | Relocations of 1 red deer |
| diff | Difference in x and y |
| diff_x | Difference in x and y |
| diff_y | Difference in x and y |
| direction_abs | Functions to create and work with steps |
| direction_abs.track_xy | Functions to create and work with steps |
| direction_rel | Functions to create and work with steps |
| direction_rel.track_xy | Functions to create and work with steps |
| distributions | Functions create statistical distributions |
| distr_name | Name of step-length distribution and turn-angle distribution |
-- E --
| extent | Extent of a track |
| extent_both | Extent of a track |
| extent_max | Extent of a track |
| extent_x | Extent of a track |
| extent_y | Extent of a track |
| Extract.uhc_data | Subset a 'uhc_data' object |
| extract_covariates | Extract covariate values |
| extract_covariates.random_points | Extract covariate values |
| extract_covariates.steps_xy | Extract covariate values |
| extract_covariates.track_xy | Extract covariate values |
| extract_covariates_along | Extract covariate values |
| extract_covariates_along.steps_xy | Extract covariate values |
| extract_covariates_var_time | Extract covariate values |
| extract_covariates_var_time.steps_xyt | Extract covariate values |
| extract_covariates_var_time.track_xyt | Extract covariate values |
-- F --
| filter_min_n_burst | Filter bursts by number of relocations |
| filter_min_n_burst.track_xy | Filter bursts by number of relocations |
| fit_clogit | Fit a conditional logistic regression |
| fit_ctmm | Fit a continuous time movement model with 'ctmm' |
| fit_distr | Fit distribution to data |
| fit_issf | Fit a conditional logistic regression |
| fit_logit | Fit logistic regression |
| fit_rsf | Fit logistic regression |
| fit_ssf | Fit a conditional logistic regression |
| flag_defunct_clusters | Flag Defunct Clusters |
| flag_defunct_clusters.track_xyt | Flag Defunct Clusters |
| flag_duplicates | Flag Low Quality Duplicates |
| flag_duplicates.track_xyt | Flag Low Quality Duplicates |
| flag_fast_steps | Flag Fast Steps |
| flag_fast_steps.track_xyt | Flag Fast Steps |
| flag_roundtrips | Flag Fast Round Trips |
| flag_roundtrips.track_xyt | Flag Fast Round Trips |
| from | Duration of tracks |
| from.track_xyt | Duration of tracks |
| from_to | Duration of tracks |
| from_to.track_xyt | Duration of tracks |
-- G --
| get_amt_fisher_covars | Helper function to get fisher covars |
| get_crs | Obtains the Coordinate Reference Systems |
| get_displacement | Calculate Expected Displacement |
| get_distr | Obtain the step length and/or turn angle distributions from random steps or a fitted model. |
| get_max_dist | Get the maximum distance |
| get_max_dist.fit_clogit | Get the maximum distance |
| get_sh_forest | Helper function to get forest cover |
-- H --
| has_crs | Check for Coordinate Reference Systems (CRS) |
| hrest | Home ranges |
| hr_akde | Home ranges |
| hr_akde.track_xyt | Home ranges |
| hr_area | Home-range area |
| hr_area.akde | Home-range area |
| hr_area.hr | Home-range area |
| hr_area.RasterLayer | Home-range area |
| hr_cud | Calculate a cumulative UD |
| hr_cud.SpatRaster | Calculate a cumulative UD |
| hr_isopleths | Home-range isopleths |
| hr_isopleths.akde | Home-range isopleths |
| hr_isopleths.hr_prob | Home-range isopleths |
| hr_isopleths.locoh | Home-range isopleths |
| hr_isopleths.mcp | Home-range isopleths |
| hr_isopleths.PackedSpatRaster | Home-range isopleths |
| hr_isopleths.SpatRaster | Home-range isopleths |
| hr_kde | Home ranges |
| hr_kde.track_xy | Home ranges |
| hr_kde_lscv | Least square cross validation bandwidth |
| hr_kde_pi | 'hr_kde_pi' wraps 'KernSmooth::dpik' to select bandwidth for kernel density estimation the plug-in-the-equation method in two dimensions. |
| hr_kde_pi.track_xy | 'hr_kde_pi' wraps 'KernSmooth::dpik' to select bandwidth for kernel density estimation the plug-in-the-equation method in two dimensions. |
| hr_kde_ref | Reference bandwidth |
| hr_kde_ref.track_xy | Reference bandwidth |
| hr_kde_ref_scaled | Select a bandwidth for Kernel Density Estimation |
| hr_locoh | Home ranges |
| hr_locoh.track_xy | Home ranges |
| hr_mcp | Home ranges |
| hr_od | Home ranges |
| hr_overlap | Methods to calculate home-range overlaps |
| hr_overlap.hr | Methods to calculate home-range overlaps |
| hr_overlap.list | Methods to calculate home-range overlaps |
| hr_overlaps | Methods to calculate home-range overlaps |
| hr_overlap_feature | Calculate the overlap between a home-range estimate and a polygon |
| hr_to_sf | Convert home ranges to 'sfc' |
| hr_to_sf.tbl_df | Convert home ranges to 'sfc' |
| hr_ud | Obtain the utilization distribution of a probabilistic home-range estimate |
-- I --
| inspect | Inspect a track |
| inspect.track_xy | Inspect a track |
| intensity_use | Movement metrics |
| issf_drop_stratum | Create formula without stratum from iSSF |
| issf_w_form | Create habitat formula from iSSF |
-- L --
| log_rss | Calculate log-RSS for a fitted model |
| log_rss.fit_clogit | Calculate log-RSS for a fitted model |
| log_rss.glm | Calculate log-RSS for a fitted model |
-- M --
| make_distribution | Functions create statistical distributions |
| make_exp_distr | Functions create statistical distributions |
| make_gamma_distr | Functions create statistical distributions |
| make_hnorm_distr | Functions create statistical distributions |
| make_issf_model | Create an 'issf'-model object from scratch |
| make_lnorm_distr | Functions create statistical distributions |
| make_start | Create an initial step for simulations |
| make_start.numeric | Create an initial step for simulations |
| make_start.steps_xyt | Create an initial step for simulations |
| make_start.track_xyt | Create an initial step for simulations |
| make_track | Create a track_* |
| make_trast | Create a template raster layer |
| make_trast.track_xy | Create a template raster layer |
| make_unif_distr | Functions create statistical distributions |
| make_vonmises_distr | Functions create statistical distributions |
| mk_track | Create a track_* |
| movement_metrics | Movement metrics |
| msd | Movement metrics |
-- N --
| nsd | Net squared displacement (nsd) |
| nsd.track_xy | Net squared displacement (nsd) |
-- O --
| od | Occurrence Distribution |
| od.track_xyt | Occurrence Distribution |
-- P --
| params | Get parameters from a (fitted) distribution |
| plot.hr | Plot a home-range estimate |
| plot.log_rss | Plot a 'log_rss' object |
| plot.uhc_data | Plot UHC plots |
| plot.uhc_envelopes | Plot simplified UHC plots |
| plot_sl | Plot step-length distribution |
| plot_sl.fit_clogit | Plot step-length distribution |
| plot_sl.random_steps | Plot step-length distribution |
| prep_uhc | Prepare Data for UHC Plots for a Fitted Model |
| prep_uhc.fit_clogit | Prepare Data for UHC Plots for a Fitted Model |
| prep_uhc.fit_logit | Prepare Data for UHC Plots for a Fitted Model |
| prep_uhc.glm | Prepare Data for UHC Plots for a Fitted Model |
-- R --
| random_numbers | Sample random numbers |
| random_points | Generate random points |
| random_points.hr | Generate random points |
| random_points.sf | Generate random points |
| random_points.track_xy | Generate random points |
| random_steps | Generate Random Steps |
| random_steps.bursted_steps_xyt | Generate Random Steps |
| random_steps.numeric | Generate Random Steps |
| random_steps.steps_xy | Generate Random Steps |
| random_steps_simple | Simulate from an ssf model |
| range | Geographic range |
| range_both | Geographic range |
| range_both.track_xy | Geographic range |
| range_x | Geographic range |
| range_x.track_xy | Geographic range |
| range_y | Geographic range |
| range_y.track_xy | Geographic range |
| redistribution_kernel | Create a redistribution kernel |
| remove_capture | Removes Capture Effects |
| remove_capture_effect | Removes Capture Effects |
| remove_capture_effect.track_xyt | Removes Capture Effects |
| remove_incomplete_strata | Remove strata with missing values for observed steps |
| remove_incomplete_strata.random_steps | Remove strata with missing values for observed steps |
| rolling_od | Occurrence Distribution |
| rolling_od.track_xyt | Occurrence Distribution |
-- S --
| sampling_period | Extract sampling period |
| sdr | Calculate SDR for an Object |
| sdr.track_xyt | Calculate SDR for an Object |
| sh | Relocations of one Red Deer |
| sh_forest | Forest cover |
| simulate_path | Simulate a movement trajectory. |
| simulate_path.default | Simulate a movement trajectory. |
| simulate_path.redistribution_kernel | Simulate a movement trajectory. |
| sinuosity | Movement metrics |
| site_fidelity | Test for site fidelity of animal movement. |
| site_fidelity.steps_xy | Test for site fidelity of animal movement. |
| sl_distr | Obtain the step length and/or turn angle distributions from random steps or a fitted model. |
| sl_distr.fit_clogit | Obtain the step length and/or turn angle distributions from random steps or a fitted model. |
| sl_distr.random_steps | Obtain the step length and/or turn angle distributions from random steps or a fitted model. |
| sl_distr_name | Name of step-length distribution and turn-angle distribution |
| sl_distr_name.fit_clogit | Name of step-length distribution and turn-angle distribution |
| sl_distr_name.random_steps | Name of step-length distribution and turn-angle distribution |
| sl_distr_params | Get parameters from a (fitted) distribution |
| sl_distr_params.fit_clogit | Get parameters from a (fitted) distribution |
| sl_distr_params.random_steps | Get parameters from a (fitted) distribution |
| speed | Speed |
| speed.track_xyt | Speed |
| ssf_formula | Takes a 'clogit' formula and returns a formula without the 'strata' and the left-hand side |
| ssf_weights | Given a fitted ssf, and new location the weights for each location is calculated |
| steps | Functions to create and work with steps |
| steps.track_xy | Functions to create and work with steps |
| steps.track_xyt | Functions to create and work with steps |
| steps_by_burst | Functions to create and work with steps |
| steps_by_burst.track_xyt | Functions to create and work with steps |
| step_lengths | Functions to create and work with steps |
| step_lengths.track_xy | Functions to create and work with steps |
| straightness | Movement metrics |
| summarize_sampling_rate | Returns a summary of sampling rates |
| summarize_sampling_rate.track_xyt | Returns a summary of sampling rates |
| summarize_sampling_rate_many | Returns a summary of sampling rates |
| summarize_sampling_rate_many.track_xyt | Returns a summary of sampling rates |
| summarize_sl | Summarize step lengths |
| summarize_speed | Summarize speed |
-- T --
| tac | Movement metrics |
| ta_distr | Obtain the step length and/or turn angle distributions from random steps or a fitted model. |
| ta_distr.fit_clogit | Obtain the step length and/or turn angle distributions from random steps or a fitted model. |
| ta_distr.random_steps | Obtain the step length and/or turn angle distributions from random steps or a fitted model. |
| ta_distr_name | Name of step-length distribution and turn-angle distribution |
| ta_distr_name.fit_clogit | Name of step-length distribution and turn-angle distribution |
| ta_distr_name.random_steps | Name of step-length distribution and turn-angle distribution |
| ta_distr_params | Get parameters from a (fitted) distribution |
| ta_distr_params.fit_clogit | Get parameters from a (fitted) distribution |
| ta_distr_params.random_steps | Get parameters from a (fitted) distribution |
| time_of_day | Time of the day when a fix was taken |
| time_of_day.steps_xyt | Time of the day when a fix was taken |
| time_of_day.track_xyt | Time of the day when a fix was taken |
| to | Duration of tracks |
| to.track_xyt | Duration of tracks |
| tot_dist | Movement metrics |
| track | Create a track_* |
| tracked_from_to | Subset to tracking dates |
| track_resample | Resample track |
| track_resample.track_xyt | Resample track |
| transform_coords | Transform CRS |
| transform_coords.track_xy | Transform CRS |
| transform_crs | Transform CRS |
| trast | Create a template raster layer |
-- U --
| ua_distr | Summarize distribution of used and available |
| uhc_hab | Simulated habitat rasters for demonstrating UHC plots |
| uhc_hsf_locs | Simulated HSF location data for demonstrating UHC plots |
| uhc_issf_locs | Simulated iSSF location data for demonstrating UHC plots |
| update_distr_man | Manually update 'amt_distr' |
| update_exp | Manually update 'amt_distr' |
| update_gamma | Manually update 'amt_distr' |
| update_hnorm | Manually update 'amt_distr' |
| update_lnorm | Manually update 'amt_distr' |
| update_sl_distr | Update movement distributions |
| update_ta_distr | Update movement distributions |
| update_vonmises | Manually update 'amt_distr' |
-- misc --
| [.uhc_data | Subset a 'uhc_data' object |