Animal Movement Tools


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Documentation for package ‘amt’ version 0.1.4

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amt-package amt: Animal Movement Tools

-- A --

amt amt: Animal Movement Tools
amt_fisher GPS tracks from four fishers
amt_fisher_covar Environmental data for fishers
append_x1 Append "_x1"
as_bcpa Coerce a track to other formats.
as_bcpa.track_xyt Coerce a track to other formats.
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_move Coerce a track to other formats.
as_move.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_lines Export track to lines
as_sf_points Export track to points
as_sp Coerce a track to other formats.
as_sp.steps_xy 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.sfc_POINT Coerce to track
as_track.SpatialPoints Coerce to track
as_track.steps_xyt Coerce to track
available_distr Display available distributions for step lengths and turn angles.

-- B --

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 --

centroid Calculate the centroid of a track.
centroid.track_xy Calculate the centroid of a track.
coercion Coerce a track to other formats.
convert_angles Converts angles to radians
coords Coordinates of a track.
coords.track_xy Coordinates of a track.
crs Coordinate References System (CRS)
cum_dist Movement metrics
cum_ud Calculate a cumulative UD

-- D --

deer Relocations of 1 red deer
diff_x Track Methods
diff_x.track_xy Track Methods
diff_y Track Methods
diff_y.track_xy Track Methods
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
dispersal_kernel Create a dispersal kernel
distance_to_center Distance to center
distance_to_center.numeric Distance to center
distance_to_center.track_xy Distance to center
distance_to_centers Distance to center
distance_to_centers.track_xy Distance to center
distributions Functions to work with distributions as objects
distr_name Name of step-length distribution and turn-angle distribution
dist_cent Distance to center

-- E --

extent_both Coordinates of a track.
extent_both.track_xy Coordinates of a track.
extent_max Coordinates of a track.
extent_max.track_xy Coordinates of a track.
extent_x Coordinates of a track.
extent_x.track_xy Coordinates of a track.
extent_y Coordinates of a track.
extent_y.track_xy Coordinates of a track.
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
from Duration of tracks
from.track_xyt Duration of tracks
from_to Duration of tracks
from_to.track_xyt Duration of tracks

-- G --

get_crs Coordinate References System (CRS)
get_distr Get distribution and parameters

-- H --

habitat_kernel Simulate UD from fitted SSF
has_crs Coordinate References System (CRS)
helper Coordinates of a track.
hr Home ranges
hr_akde Home ranges
hr_akde.track_xyt Home ranges
hr_area Home ranges
hr_area.akde Home ranges
hr_area.hr Home ranges
hr_cud Calculate a cumulative UD
hr_cud.RasterLayer Calculate a cumulative UD
hr_isopleths Home ranges
hr_kde Home ranges
hr_kde.track_xy Home ranges
hr_kde_lscv Home ranges
hr_kde_pi Home ranges
hr_kde_pi.track_xy Home ranges
hr_kde_ref Home ranges
hr_kde_ref.track_xy Home ranges
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_mcp.track_xy Home ranges
hr_od Home ranges
hr_od.track_xyt Home ranges
hr_overlap Different Methods to calculate home-range overlaps
hr_overlap.hr Different Methods to calculate home-range overlaps
hr_overlap.list Different Methods to calculate home-range overlaps
hr_overlaps Different Methods to calculate home-range overlaps
hr_overlap_feature Calculate the overlap between a home-range estimate and a polygon
hr_to_sf Convert
hr_to_sf.tbl_df Convert
hr_ud Obtain the utilization distribution of a probabilistic home range

-- I --

inspect Inspect a track
inspect.track_xy Inspect a track
intensity_use Movement metrics

-- 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 to work with distributions as objects
make_exp_distr Functions to work with distributions as objects
make_gamma_distr Functions to work with distributions as objects
make_track Create a track_*
make_trast Coordinates of a track.
make_trast.track_xy Coordinates of a track.
make_unif_distr Functions to work with distributions as objects
make_vonmises_distr Functions to work with distributions as objects
mk_track Create a track_*
movement_kernel Simulate UD from fitted SSF
movement_metrics Movement metrics
msd Movement metrics

-- N --

nsd Track Methods
nsd.track_xy Track Methods

-- O --

od Occurrence Distribution
od.track_xyt Occurrence Distribution

-- P --

params Get parameters from a (fitted) distribution
plot.log_rss Plot a 'log_rss' object
plot_sl Plot step-length distribution
plot_sl.fit_clogit Plot step-length distribution
plot_sl.random_steps Plot step-length distribution

-- R --

random_numbers Functions to work with distributions as objects
random_numbers.amt_distr Functions to work with distributions as objects
random_numbers.vonmises_distr Functions to work with distributions as objects
random_points Generate random points
random_points.hr Generate random points
random_points.sf Generate random points
random_points.SpatialPolygons Generate random points
random_points.track_xy Generate random points
random_steps Generate Random Steps
random_steps.numeric Generate Random Steps
random_steps.steps_xy Generate Random Steps
range_both Coordinates of a track.
range_both.track_xy Coordinates of a track.
range_x Coordinates of a track.
range_x.track_xy Coordinates of a track.
range_y Coordinates of a track.
range_y.track_xy Coordinates of a track.
remove_capture Removes Capture Effects
remove_capture_effect Removes Capture Effects
remove_capture_effect.track_xyt Removes Capture Effects
rolling_od Occurrence Distribution
rolling_od.track_xyt Occurrence Distribution

-- S --

sh Relocations of 1 red deer
sh_forest Forest cover
simulate_tud Simulate UD from fitted SSF
simulate_ud Simulate UD from fitted SSF
simulate_ud_from_dk Simulate a UD from a dispersal kernel
simulate_xy Simulate a trajectory
sim_ud Simulate UD from fitted SSF
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 Get distribution and parameters
sl_distr.fit_clogit Get distribution and parameters
sl_distr.random_steps Get distribution and parameters
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
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

-- T --

tac Movement metrics
ta_distr Get distribution and parameters
ta_distr.fit_clogit Get distribution and parameters
ta_distr.random_steps Get distribution and parameters
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_*
track_align Selects relocations that fit a new time series
track_align.track_xyt Selects relocations that fit a new time series
track_methods Track Methods
track_resample Resample track
track_resample.track_xyt Resample track
transform_coords Transform CRS
transform_coords.track_xy Transform CRS
transform_crs Transform CRS

-- U --

update_distr_man Manually update 'amt_distr'
update_exp Manually update 'amt_distr'
update_gamma Manually update 'amt_distr'
update_sl_distr Update movement distributions
update_ta_distr Update movement distributions
update_vonmises Manually update 'amt_distr'

-- V --

velocity Track Methods
velocity.track_xyt Track Methods