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amt (version 0.2)

Animal Movement Tools

Description

Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.

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Version

Install

install.packages('amt')

Monthly Downloads

1,101

Version

0.2

License

GPL-3

Issues

14

Pull Requests

0

Stars

44

Forks

13

Maintainer

Johannes Signer

Last Published

March 3rd, 2023

Functions in amt (0.2)

as_sf_lines

Export track to lines
append_x1

Append "_x1"
amt_fisher_covar

Environmental data for fishers
as_sf_points

Coerces a track to points
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.
boot1.glm

Single bootstrap iteration
as_track

Coerce to track
deer

Relocations of 1 red deer
diff

Difference in x and y
extent

Extent of a track
flag_duplicates

Flag Low Quality Duplicates
extract_covariates

Extract covariate values
from_to

Duration of tracks
bootstrap_logrss

Bootstrap log-RSS estimate
hr_ud

Obtain the utilization distribution of a probabilistic home-range estimate
flag_fast_steps

Flag Fast Steps
centroid

Calculate the centroid of a track.
coords

Coordinates of a track.
cum_ud

Calculate a cumulative UD
flag_roundtrips

Flag Fast Round Trips
nsd

Net squared displacement (nsd)
random_steps_simple

Simulate from an ssf model
make_start

Create an initial step for simulations
get_displacement

Calculate Expected Displacement
Extract.uhc_data

Subset a uhc_data object
check_factors

Check factor levels
transform_coords

Transform CRS
plot.uhc_envelopes

Plot simplified UHC plots
amt_fisher

GPS tracks from four fishers
check_time_unit

Calculate Speed
get_max_dist

Get the maximum distance
hr_akde

Home ranges
uhc_hsf_locs

Simulated HSF location data for demonstrating UHC plots
calc_w

Calculate w(x)
conf_envelope

Create confidence envelopes from a uhc_data_frame
convert_angles

Converts angles to radians
fit_logit

Fit logistic regression
coercion

Coerce a track to other formats.
time_of_day

Time of the day when a fix was taken
prep_test_dat

Prepares test_dat for uhc_prep()
flag_defunct_clusters

Flag Defunct Clusters
sampling_period

Extract sampling period
get_amt_fisher_covars

Helper function to get fisher covars
get_distr

Obtain the step length and/or turn angle distributions from random steps or a fitted model.
has_crs

Check for Coordinate Reference Systems (CRS)
hr_isopleths

Home-range isopleths
fit_ctmm

Fit a continuous time movement model with ctmm
plot_sl

Plot step-length distribution
fit_distr

Fit distribution to data
hr_kde_lscv

Least square cross validation bandwidth
log_rss

Calculate log-RSS for a fitted model
fit_clogit

Fit a conditional logistic regression
hr_overlaps

Methods to calculate home-range overlaps
calculate_sdr

Calculate SDR
inspect

Inspect a track
hr_to_sf

Convert home ranges to sfc
make_issf_model

Create an issf-model object from scratch
random_steps

Generate Random Steps
prep_uhc

Prepare Data for UHC Plots for a Fitted Model
od

Occurrence Distribution
range

Geographic range
sdr

Calculate SDR for an Object
reexports

Objects exported from other packages
hr_area

Home-range area
sh

Relocations of one Red Deer
track

Create a track_*
remove_capture

Removes Capture Effects
hr_kde_ref_scaled

Select a bandwidth for Kernel Density Estimation
movement_metrics

Movement metrics
get_crs

Obtains the Coordinate Reference Systems
sh_forest

Forest cover
summarize_sl

Summarize step lengths
plot.uhc_data

Plot UHC plots
plot.log_rss

Plot a log_rss object
simulate_path

Simulate a movement trajectory.
remove_incomplete_strata

Remove strata with missing values for observed steps
distr_name

Name of step-length distribution and turn-angle distribution
uhc_issf_locs

Simulated iSSF location data for demonstrating UHC plots
get_sh_forest

Helper function to get forest cover
redistribution_kernel

Create a redistribution kernel
trast

Create a template raster layer
distributions

Functions create statistical distributions
plot.hr

Plot a home-range estimate
issf_w_form

Create habitat formula from iSSF
summarize_speed

Summarize speed
steps

Functions to create and work with steps
filter_min_n_burst

Filter bursts by number of relocations
site_fidelity

Test for site fidelity of animal movement.
uhc_hab

Simulated habitat rasters for demonstrating UHC plots
params

Get parameters from a (fitted) distribution
speed

Speed
track_resample

Resample track
hr_overlap_feature

Calculate the overlap between a home-range estimate and a polygon
random_points

Generate random points
random_numbers

Sample random numbers
ua_distr

Summarize distribution of used and available
summarize_sampling_rate

Returns a summary of sampling rates
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
update_sl_distr

Update movement distributions
update_distr_man

Manually update amt_distr
tracked_from_to

Subset to tracking dates
as.data.frame.uhc_data

Coerce a uhc_data object to data.frame
available_distr

Display available distributions for step lengths and turn angles.