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amt (version 0.2.2.0)

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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Install

install.packages('amt')

Monthly Downloads

2,824

Version

0.2.2.0

License

GPL-3

Issues

Pull Requests

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Repository

https://github.com/jmsigner/amt

Maintainer

Johannes Signer

Last Published

April 1st, 2024

Functions in amt (0.2.2.0)

Reference bandwidth

Check factor levels

Calculate the centroid of a track.

Calculate w(x)

Functions create statistical distributions

Name of step-length distribution and turn-angle distribution

Extent of a track

extract_covariates

Extract covariate values

Fit logistic regression

flag_defunct_clusters

Flag Defunct Clusters

flag_duplicates

Flag Low Quality Duplicates

flag_fast_steps

Flag Fast Steps

get_amt_fisher_covars

Helper function to get fisher covars

Obtains the Coordinate Reference Systems

Home-range isopleths

Least square cross validation bandwidth

Coordinates of a track.

check_time_unit

Calculate Speed

Calculate a cumulative UD

Coerce a track to other formats.

Get the maximum distance

Fit a conditional logistic regression

filter_min_n_burst

Filter bursts by number of relocations

Helper function to get forest cover

Create habitat formula from iSSF

Calculate log-RSS for a fitted model

Obtain the utilization distribution of a probabilistic home-range estimate

Single bootstrap iteration

movement_metrics

Movement metrics

Plot a home-range estimate

Plot a log_rss object

Check for Coordinate Reference Systems (CRS)

Home-range area

Methods to calculate home-range overlaps

Convert home ranges to sfc

Net squared displacement (nsd)

Coerce to track

Relocations of 1 red deer

get_displacement

Calculate Expected Displacement

Inspect a track

Difference in x and y

Duration of tracks

flag_roundtrips

Flag Fast Round Trips

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

Get parameters from a (fitted) distribution

Generate random points

Occurrence Distribution

Generate Random Steps

issf_drop_stratum

Create formula without stratum from iSSF

Create an initial step for simulations

make_issf_model

Create an issf-model object from scratch

sampling_period

Extract sampling period

bootstrap_logrss

Bootstrap log-RSS estimate

Create confidence envelopes from a uhc_data_frame

redistribution_kernel

Create a redistribution kernel

Create a track_*

Calculate SDR for an Object

Relocations of one Red Deer

Objects exported from other packages

Test for site fidelity of animal movement.

Converts angles to radians

Prepare Data for UHC Plots for a Fitted Model

Fit distribution to data

Simulate a movement trajectory.

summarize_sampling_rate

Returns a summary of sampling rates

Summarize step lengths

Plot step-length distribution

Fit a continuous time movement model with ctmm

hr_kde_ref_scaled

Select a bandwidth for Kernel Density Estimation

hr_overlap_feature

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

update_distr_man

Manually update amt_distr

update_sl_distr

Update movement distributions

Simulated iSSF location data for demonstrating UHC plots

plot.uhc_envelopes

Plot simplified UHC plots

Geographic range

tracked_from_to

Subset to tracking dates

remove_incomplete_strata

Remove strata with missing values for observed steps

Time of the day when a fix was taken

random_steps_simple

Simulate from an ssf model

Prepares test_dat for uhc_prep()

Removes Capture Effects

summarize_speed

Summarize speed

Given a fitted ssf, and new location the weights for each location is calculated

Create a template raster layer

Functions to create and work with steps

transform_coords

Summarize distribution of used and available

Sample random numbers

Takes a clogit formula and returns a formula without the strata and the left-hand side

Simulated habitat rasters for demonstrating UHC plots

Simulated HSF location data for demonstrating UHC plots

amt_fisher_covar

Environmental data for fishers

Coerces a track to points

Extract.uhc_data

Subset a uhc_data object

as.data.frame.uhc_data

Coerce a uhc_data object to data.frame

available_distr

Display available distributions for step lengths and turn angles.

hr_kde_pi wraps KernSmooth::dpik to select bandwidth for kernel density estimation the plug-in-the-equation method in two dimensions.

GPS tracks from four fishers

Get bounding box of a track.

Export track to lines