Package: Distance 1.0.9

Laura Marshall

Distance: Distance Sampling Detection Function and Abundance Estimation

A simple way of fitting detection functions to distance sampling data for both line and point transects. Adjustment term selection, left and right truncation as well as monotonicity constraints and binning are supported. Abundance and density estimates can also be calculated (via a Horvitz-Thompson-like estimator) if survey area information is provided. See Miller et al. (2019) <doi:10.18637/jss.v089.i01> for more information on methods and <https://examples.distancesampling.org/> for example analyses.

Authors:David Lawrence Miller, T.J. Clark-Wolf

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Distance.pdf |Distance.html✨
Distance/json (API)
NEWS

# Install 'Distance' in R:
install.packages('Distance', repos = c('https://distancedevelopment.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/distancedevelopment/distance/issues

Datasets:

On CRAN:

17 exports 9 stars 6.33 score 27 dependencies 2 dependents 108 mentions 299 scripts 1.3k downloads

Last updated 9 months agofrom:5427008203. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-winNOTESep 17 2024
R-4.5-linuxNOTESep 17 2024
R-4.4-winOKSep 17 2024
R-4.4-macOKSep 17 2024
R-4.3-winOKSep 17 2024
R-4.3-macOKSep 17 2024

Exports:bootdhtbootdht_Dhat_summarizebootdht_Nhat_summarizechi2_selectconvert_unitscreate_binscreate.binsdht2dsds.gofdummy_ddfgof_dsmake_activity_fnQAICsummarize_ds_modelsunflattenunits_table

Dependencies:clidplyrfansigenericsgluelatticelifecyclemagrittrMatrixmgcvmrdsnlmenloptrnumDerivoptimxpillarpkgconfigpracmaR6rlangRsolnptibbletidyselecttruncnormutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Distance samplingDistance-package Distance
Add covariate levels detection function plotsadd_df_covar_line
Akaike's An Information Criterion for detection functionsAIC.dsmodel
Hawaiian amakihi point transect dataamakihi amakihi_units
Bootstrap uncertainty estimation for distance sampling modelsbootdht
Simple summary of density results for bootstrap modelbootdht_Dhat_summarize
Simple summary of abundance results for bootstrap modelbootdht_Nhat_summarize
Capercaillie in Monaughty Forestcapercaillie capercaillie_units
Check that the data supplied to 'ds' is correctcheckdata
Simulated minke whale data with cluster sizeClusterExercise ClusterExercise_units
Convert units for abundance estimationconvert_units
Create bins from a set of binned distances and a set of cutpoints.create_bins
Create bins from a set of binned distances and a set of cutpoints.create.bins
Cue counts of whale blowsCueCountingExample CueCountingExample_units
Abundance estimation for distance sampling modelsdht2
Fit detection functions and calculate abundance from line or point transect datads
Goodness of fit tests for distance sampling modelsds.gof
Ducknest line transect survey dataducknest ducknests_units ducknest_units
Duiker camera trap surveyDuikerCameraTraps DuikerCameraTraps_units
Detection function objects when detection is certaindummy_ddf
Eastern Tropical Pacific spotted dolphin surveyETP_Dolphin ETP_Dolphin_units
The flatfile data formatflatfile
Goodness of fit testing and quantile-quantile plotsgof_ds
Golf tee datagolftees golftees_units
log-likelihood value for a fitted detection functionlogLik.dsmodel
Simulated line transect survey dataLTExercise LTExercise_units
Multiplier bootstrap helper functionsmake_activity_fn
Simulated minke whale dataminke
Distribution of probabilities of detectionp_dist_table
Plot a fitted detection functionplot.dsmodel
Predictions from a fitted detection functionpredict.dsmodel
Prediction for fake detection functionspredict.fake_ddf
Print abundance estimatesprint.dht_result
Simple pretty printer for distance sampling analysesprint.dsmodel
Print summary of distance detection function model objectprint.summary.dsmodel
Simulated point transect survey dataPTExercise PTExercise_units
Tools for model selection when distance sampling data are overdispersedchi2_select QAIC
Savanna sparrow point transectsSavannah_sparrow_1980 Savannah_sparrow_1980_units Savannah_sparrow_1981 Savannah_sparrow_1981_units
Sika deer pellet data from southern Scotlandsikadeer sikadeer_units
Simulated minke whale dataStratify_example Stratify_example_units
Make a table of summary statistics for detection function modelssummarize_ds_models
Summarize bootstrap abundance uncertainty estimate outputsummary.dht_bootstrap
Summary of distance sampling analysissummary.dsmodel
Simulation of encounter rate varianceSystematic_variance_1 Systematic_variance_1_units Systematic_variance_2 Systematic_variance_2_units
Unflatten flatfile data.framesunflatten
Simulated line transect survey data with covariatesunimak unimak_units
Generate table of unit conversionsunits_table
Steve Buckland's winter wren surveyswren wren_5min wren_5min_units wren_cuecount wren_cuecount_units wren_lt wren_lt_units wren_snapshot wren_snapshot_units