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amt (version 0.2.1.0)

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

1,870

Version

0.2.1.0

License

GPL-3

Issues

Pull Requests

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Repository

https://github.com/jmsigner/amt

Maintainer

Johannes Signer

Last Published

March 28th, 2023

Functions in amt (0.2.1.0)

Calculate the centroid of a track.

Export track to lines

Reference bandwidth

Check factor levels

check_time_unit

Calculate Speed

Coerce a track to other formats.

GPS tracks from four fishers

Calculate w(x)

Difference in x and y

Relocations of 1 red deer

Single bootstrap iteration

Coordinates of a track.

extract_covariates

Extract covariate values

Extent of a track

Get bounding box of a track.

Fit a continuous time movement model with ctmm

Fit distribution to data

bootstrap_logrss

Bootstrap log-RSS estimate

Check for Coordinate Reference Systems (CRS)

Fit a conditional logistic regression

filter_min_n_burst

Filter bursts by number of relocations

Home-range isopleths

Duration of tracks

Least square cross validation bandwidth

flag_roundtrips

Flag Fast Round Trips

Create confidence envelopes from a uhc_data_frame

Home-range area

Calculate a cumulative UD

flag_duplicates

Flag Low Quality Duplicates

Methods to calculate home-range overlaps

Converts angles to radians

Inspect a track

Fit logistic regression

flag_defunct_clusters

Flag Defunct Clusters

Name of step-length distribution and turn-angle distribution

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

Functions create statistical distributions

get_displacement

Calculate Expected Displacement

Create an initial step for simulations

get_amt_fisher_covars

Helper function to get fisher covars

Obtains the Coordinate Reference Systems

Convert home ranges to sfc

Net squared displacement (nsd)

movement_metrics

Movement metrics

Create habitat formula from iSSF

random_steps_simple

Simulate from an ssf model

Generate Random Steps

Plot a log_rss object

flag_fast_steps

Flag Fast Steps

Get the maximum distance

Obtain the utilization distribution of a probabilistic home-range estimate

Helper function to get forest cover

Calculate log-RSS for a fitted model

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

Calculate SDR for an Object

make_issf_model

Create an issf-model object from scratch

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

plot.uhc_envelopes

Plot simplified UHC plots

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

Get parameters from a (fitted) distribution

Summarize step lengths

summarize_speed

Summarize speed

Occurrence Distribution

Plot a home-range estimate

Prepares test_dat for uhc_prep()

Relocations of one Red Deer

Prepare Data for UHC Plots for a Fitted Model

Geographic range

Simulate a movement trajectory.

Objects exported from other packages

redistribution_kernel

Create a redistribution kernel

Create a template raster layer

transform_coords

tracked_from_to

Subset to tracking dates

Removes Capture Effects

update_sl_distr

Update movement distributions

Test for site fidelity of animal movement.

update_distr_man

Manually update amt_distr

Simulated habitat rasters for demonstrating UHC plots

Summarize distribution of used and available

Time of the day when a fix was taken

Create a track_*

Plot step-length distribution

Generate random points

Simulated HSF location data for demonstrating UHC plots

Sample random numbers

sampling_period

Extract sampling period

remove_incomplete_strata

Remove strata with missing values for observed steps

Simulated iSSF location data for demonstrating UHC plots

summarize_sampling_rate

Returns a summary of sampling rates

Functions to create and work with steps

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.

amt_fisher_covar

Environmental data for fishers

Coerces a track to points

Coerce to track

Extract.uhc_data

Subset a uhc_data object

as.data.frame.uhc_data

Coerce a uhc_data object to data.frame