Animal Movement Tools


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Documentation for package ‘amt’ version 0.2.1.0

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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_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 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_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_test_dat Prepares 'test_dat' for 'uhc_prep()'
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