Package: amt 0.3.0.0
Johannes Signer
amt: Animal Movement Tools
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.
Authors:
amt_0.3.0.0.tar.gz
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amt.pdf |amt.html✨
amt/json (API)
NEWS
| # Install 'amt' in R: |
| install.packages('amt', repos = c('https://jmsigner.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jmsigner/amt/issues
- amt_fisher - GPS tracks from four fishers
- amt_fisher_covar - Environmental data for fishers
- deer - Relocations of 1 red deer
- sh - Relocations of one Red Deer
- sh_forest - Forest cover
- 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
Last updated 20 days agofrom:d7ffc4ef1e. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 29 2024 |
| R-4.5-win | OK | Aug 29 2024 |
| R-4.5-linux | OK | Aug 29 2024 |
| R-4.4-win | OK | Aug 29 2024 |
| R-4.4-mac | OK | Aug 29 2024 |
| R-4.3-win | OK | Aug 29 2024 |
| R-4.3-mac | OK | Aug 29 2024 |
Exports:add_nsdarrangeas_degreeas_ltrajas_moveHMMas_radas_sfas_sf_linesas_sf_pointsas_spas_telemetryas_trackavailable_distrbboxcalculate_sdrcentroidclogitconf_envelopecoordscum_distdaysdiff_xdiff_ydirection_absdirection_reldistinctextent_bothextent_maxextent_xextent_yextract_covariatesextract_covariates_alongextract_covariates_var_timefilterfilter_min_n_burstfit_clogitfit_ctmmfit_distrfit_issffit_logitfit_rsffit_ssfflag_defunct_clustersflag_duplicatesflag_fast_stepsflag_roundtripsfromfrom_toget_amt_fisher_covarsget_crsget_displacementget_max_distget_sh_forestgroup_byhas_crshourshr_akdehr_areahr_cudhr_isoplethshr_kdehr_kde_lscvhr_kde_pihr_kde_refhr_kde_ref_scaledhr_locohhr_mcphr_odhr_overlaphr_overlap_featurehr_to_sfhr_udinspectintensity_uselog_rssmake_distributionmake_exp_distrmake_gamma_distrmake_hnorm_distrmake_issf_modelmake_lnorm_distrmake_startmake_trackmake_trastmake_unif_distrmake_vonmises_distrmapmap_intminutesmk_trackmsdmutateNA_crs_nestnsdodplot_slprep_uhcpullrandom_numbersrandom_pointsrandom_stepsrandom_steps_simplerange_bothrange_xrange_yredistribution_kernelremove_capture_effectremove_incomplete_stratarolling_odsampling_periodsdrsecondsselectsimulate_pathsinuositysite_fidelitysl_distrsl_distr_namesl_distr_paramsspeedssf_formulastep_lengthsstepssteps_by_burststraightnessstratasummarisesummarizesummarize_sampling_ratesummarize_sampling_rate_manysummarize_slsummarize_speedSurvta_distrta_distr_nameta_distr_paramstactibbletime_of_daytotot_disttracktrack_aligntrack_resampletracked_from_totransform_coordsungroupunnestupdate_expupdate_gammaupdate_hnormupdate_lnormupdate_sl_distrupdate_ta_distrupdate_vonmisesweeks
Dependencies:backportsBesselbootcheckmatecircularclassclassIntclicpp11ctmmdata.tableDBIDEoptimRdigestdplyre1071expmfansifasttimefitdistrplusFNNgenericsgeometriesglueGmediangmpgslKernSmoothlatticelifecyclelubridatemagrittrmanipulateMASSMatrixmvtnormnumDerivparsedatepbivnormpillarpkgconfigpracmaproxypurrrR6rasterrbibutilsRcppRcppArmadilloRcppEigenRdpackrlangRmpfrrobustbaseRSpectras2sfsfheadersshapespstatmodstringistringrsurvivalterratibbletidyrtidyselecttimechangeunitsutf8vctrswithrwk
Calculating home-range overlaps with amt
Rendered fromp2_hr.Rmdusingknitr::rmarkdownon Aug 29 2024.Last update: 2023-03-02
Started: 2021-01-05
Fitting Step-Selection Functions with amt
Rendered fromp4_SSF.Rmdusingknitr::rmarkdownon Aug 29 2024.Last update: 2023-03-02
Started: 2017-08-16
Getting started with amt
Rendered fromp1_getting_started.Rmdusingknitr::rmarkdownon Aug 29 2024.Last update: 2023-03-02
Started: 2017-08-16
Interface to other packages with amt
Rendered fromp5_other_packages.Rmdusingknitr::rmarkdownon Aug 29 2024.Last update: 2023-07-03
Started: 2020-03-20
Resource Selection Functions (RSF) with amt
Rendered fromp3_rsf.Rmdusingknitr::rmarkdownon Aug 29 2024.Last update: 2023-03-02
Started: 2020-03-20
UHC Plots
Rendered fromp6_uhc_plots.Rmdusingknitr::rmarkdownon Aug 29 2024.Last update: 2023-03-02
Started: 2022-05-24
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GPS tracks from four fishers | amt_fisher |
| Environmental data for fishers | amt_fisher_covar |
| Export track to lines | as_sf_lines |
| Coerces a track to points | as_sf_points as_sf_points.steps_xy |
| Coerce to track | as_track as_track.data.frame as_track.sfc_POINT as_track.steps_xyt |
| Coerce a 'uhc_data' object to 'data.frame' | as.data.frame.uhc_data |
| Display available distributions for step lengths and turn angles. | available_distr |
| 'hr_kde_pi' wraps 'KernSmooth::dpik' to select bandwidth for kernel density estimation the plug-in-the-equation method in two dimensions. | bandwidth_pi hr_kde_pi hr_kde_pi.track_xy |
| Reference bandwidth | bandwidth_ref hr_kde_ref hr_kde_ref.track_xy |
| Get bounding box of a track. | bbox bbox.steps_xy bbox.track_xy |
| Calculate 'w(x)' | calc_w |
| Calculate SDR | calculate_sdr |
| Calculate the centroid of a track. | centroid centroid.track_xy |
| Calculate Speed | check_time_unit |
| Coerce a track to other formats. | as_ltraj as_ltraj.track_xy as_ltraj.track_xyt as_moveHMM as_moveHMM.track_xy as_sf as_sf.steps_xy as_sp as_telemetry as_telemetry.track_xyt coercion |
| Create confidence envelopes from a 'uhc_data_frame' | conf_envelope |
| Converts angles to radians | as_degree as_rad convert_angles |
| Coordinates of a track. | coords |
| Calculate a cumulative UD | cum_ud hr_cud hr_cud.SpatRaster |
| Relocations of 1 red deer | deer |
| Difference in x and y | diff diff_x diff_y |
| Name of step-length distribution and turn-angle distribution | distr_name sl_distr_name sl_distr_name.fit_clogit sl_distr_name.random_steps ta_distr_name ta_distr_name.fit_clogit ta_distr_name.random_steps |
| Functions create statistical distributions | distributions make_distribution make_exp_distr make_gamma_distr make_hnorm_distr make_lnorm_distr make_unif_distr make_vonmises_distr |
| Extent of a track | extent extent_both extent_max extent_x extent_y |
| Extract covariate values | extract_covariates extract_covariates.random_points extract_covariates.steps_xy extract_covariates.track_xy extract_covariates_along extract_covariates_along.steps_xy extract_covariates_var_time extract_covariates_var_time.steps_xyt extract_covariates_var_time.track_xyt |
| Subset a 'uhc_data' object | Extract.uhc_data [.uhc_data |
| Filter bursts by number of relocations | filter_min_n_burst filter_min_n_burst.track_xy |
| Fit a conditional logistic regression | fit_clogit fit_issf fit_ssf |
| Fit a continuous time movement model with 'ctmm' | fit_ctmm |
| Fit distribution to data | fit_distr |
| Fit logistic regression | fit_logit fit_rsf |
| Flag Defunct Clusters | flag_defunct_clusters flag_defunct_clusters.track_xyt |
| Flag Low Quality Duplicates | flag_duplicates flag_duplicates.track_xyt |
| Flag Fast Steps | flag_fast_steps flag_fast_steps.track_xyt |
| Flag Fast Round Trips | flag_roundtrips flag_roundtrips.track_xyt |
| Duration of tracks | from from.track_xyt from_to from_to.track_xyt to to.track_xyt |
| Helper function to get fisher covars | get_amt_fisher_covars |
| Obtains the Coordinate Reference Systems | get_crs |
| Calculate Expected Displacement | get_displacement |
| Obtain the step length and/or turn angle distributions from random steps or a fitted model. | get_distr sl_distr sl_distr.fit_clogit sl_distr.random_steps ta_distr ta_distr.fit_clogit ta_distr.random_steps |
| Get the maximum distance | get_max_dist get_max_dist.fit_clogit |
| Helper function to get forest cover | get_sh_forest |
| Check for Coordinate Reference Systems (CRS) | has_crs |
| Home ranges | hrest hr_akde hr_akde.track_xyt hr_kde hr_kde.track_xy hr_locoh hr_locoh.track_xy hr_mcp hr_od |
| Home-range area | hr_area hr_area.akde hr_area.hr hr_area.SpatRaster |
| Home-range isopleths | hr_isopleths hr_isopleths.akde hr_isopleths.hr_prob hr_isopleths.locoh hr_isopleths.mcp hr_isopleths.PackedSpatRaster hr_isopleths.SpatRaster |
| Least square cross validation bandwidth | hr_kde_lscv |
| Select a bandwidth for Kernel Density Estimation | hr_kde_ref_scaled |
| Calculate the overlap between a home-range estimate and a polygon | hr_overlap_feature |
| Methods to calculate home-range overlaps | hr_overlap hr_overlap.hr hr_overlap.list hr_overlaps |
| Convert home ranges to 'sfc' | hr_to_sf hr_to_sf.tbl_df |
| Obtain the utilization distribution of a probabilistic home-range estimate | hr_ud |
| Inspect a track | inspect inspect.track_xy |
| Create formula without stratum from iSSF | issf_drop_stratum |
| Create habitat formula from iSSF | issf_w_form |
| Calculate log-RSS for a fitted model | log_rss log_rss.fit_clogit log_rss.glm |
| Create an 'issf'-model object from scratch | make_issf_model |
| Create an initial step for simulations | make_start make_start.numeric make_start.steps_xyt make_start.track_xyt |
| Movement metrics | cum_dist intensity_use movement_metrics msd sinuosity straightness tac tot_dist |
| Net squared displacement (nsd) | add_nsd add_nsd.steps_xy add_nsd.track_xy nsd nsd.track_xy |
| Occurrence Distribution | od od.track_xyt rolling_od rolling_od.track_xyt |
| Get parameters from a (fitted) distribution | params sl_distr_params sl_distr_params.fit_clogit sl_distr_params.random_steps ta_distr_params ta_distr_params.fit_clogit ta_distr_params.random_steps |
| Plot step-length distribution | plot_sl plot_sl.fit_clogit plot_sl.random_steps |
| Plot a home-range estimate | plot.hr |
| Plot a 'log_rss' object | plot.log_rss |
| Plot UHC plots | plot.uhc_data |
| Plot simplified UHC plots | plot.uhc_envelopes |
| Prepare Data for UHC Plots for a Fitted Model | prep_uhc prep_uhc.fit_clogit prep_uhc.fit_logit prep_uhc.glm |
| Sample random numbers | random_numbers |
| Generate random points | random_points random_points.hr random_points.sf random_points.track_xy |
| Generate Random Steps | random_steps random_steps.bursted_steps_xyt random_steps.numeric random_steps.steps_xy |
| Simulate from an ssf model | random_steps_simple |
| Geographic range | range range_both range_both.track_xy range_x range_x.track_xy range_y range_y.track_xy |
| Create a redistribution kernel | redistribution_kernel |
| Removes Capture Effects | remove_capture remove_capture_effect remove_capture_effect.track_xyt |
| Remove strata with missing values for observed steps | remove_incomplete_strata remove_incomplete_strata.random_steps |
| Extract sampling period | sampling_period |
| Calculate SDR for an Object | sdr sdr.track_xyt |
| Relocations of one Red Deer | sh |
| Forest cover | sh_forest |
| Simulate a movement trajectory. | simulate_path simulate_path.default simulate_path.redistribution_kernel |
| Test for site fidelity of animal movement. | site_fidelity site_fidelity.steps_xy |
| Speed | speed speed.track_xyt |
| Takes a 'clogit' formula and returns a formula without the 'strata' and the left-hand side | ssf_formula |
| Given a fitted ssf, and new location the weights for each location is calculated | ssf_weights |
| Functions to create and work with steps | direction_abs direction_abs.track_xy direction_rel direction_rel.track_xy steps steps.track_xy steps.track_xyt steps_by_burst steps_by_burst.track_xyt step_lengths step_lengths.track_xy |
| Returns a summary of sampling rates | summarize_sampling_rate summarize_sampling_rate.track_xyt summarize_sampling_rate_many summarize_sampling_rate_many.track_xyt |
| Summarize step lengths | summarize_sl |
| Summarize speed | summarize_speed |
| Time of the day when a fix was taken | time_of_day time_of_day.steps_xyt time_of_day.track_xyt |
| Create a track_* | make_track mk_track track |
| Selects relocations that fit a new time series | track_align track_align.track_xyt |
| Resample track | track_resample track_resample.track_xyt |
| Subset to tracking dates | tracked_from_to |
| Transform CRS | transform_coords transform_coords.track_xy transform_crs |
| Create a template raster layer | make_trast make_trast.track_xy trast |
| Summarize distribution of used and available | ua_distr |
| Simulated habitat rasters for demonstrating UHC plots | uhc_hab |
| Simulated HSF location data for demonstrating UHC plots | uhc_hsf_locs |
| Simulated iSSF location data for demonstrating UHC plots | uhc_issf_locs |
| Manually update 'amt_distr' | update_distr_man update_exp update_gamma update_hnorm update_lnorm update_vonmises |
| Update movement distributions | update_sl_distr update_ta_distr |