R: Animal Movement Tools

# Animal Movement Tools

## Documentation for package ‘amt’ version 0.3.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## 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.SpatRaster | 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_align | Selects relocations that fit a new time series
track_align.track_xyt | Selects relocations that fit a new time series
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