Package: LTabundR 1.75

Amanda Bradford

LTabundR: Development Version

Development version

Authors:Amanda Bradford [aut, cre]

LTabundR_1.75.tar.gz
LTabundR_1.75.zip(r-4.7-any)LTabundR_1.75.zip(r-4.6-any)LTabundR_1.75.zip(r-4.5-any)
LTabundR_1.75.tgz(r-4.6-any)LTabundR_1.75.tgz(r-4.5-any)
LTabundR_1.75.tar.gz(r-4.7-any)LTabundR_1.75.tar.gz(r-4.6-any)
LTabundR_1.75.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
LTabundR/json (API)

# Install 'LTabundR' in R:
install.packages('LTabundR', repos = c('https://pifsc-protected-species-division.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pifsc-protected-species-division/ltabundr/issues

Datasets:

On CRAN:

Conda:

3.86 score 2 stars 40 scripts 82 exports 223 dependencies

Last updated from:5f00b83c41. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develWARNING384
source / vignettesOK378
linux-releaseWARNING460
macos-releaseWARNING524
macos-oldrelWARNING446
windows-develWARNING435
windows-releaseWARNING427
windows-oldrelWARNING384
wasm-releaseOK356

Exports:%>%abundancebcacoordinates_in_stratacruz_combinecruz_explorercruz_structuredas_editordas_editor_tofiledas_formatdas_inspectordas_interpolatedas_loaddas_readtextdas_timedf_curvedf_fitdf_ploter_simulatorfilter_cohortfilter_cruzg0_combineg0_modelg0_optimizeg0_plotg0_tableg0_weightedgg_effortgg_geostratumgg_sightingsggplot_idlgrp_calibrate_abundgrp_recalibrategrp_sizeidl_coerceload_cohort_settingsload_settingsload_survey_settingsltalta_checkslta_cilta_combinelta_delta_methodlta_destratifylta_diagnosticslta_enlistlta_estimateslta_plotlta_poollta_reportlta_subgroupmap_cruzmixed_group_affiliatespoints_to_lineprep_bootstrap_datasetsprocess_kmprocess_polygonprocess_sightingsprocess_strataprocess_subgroupsprocess_surveysread_polygonregion_dasregion_segmentssegmentizespecies_translatorstrata_areastrata_explorestrata_segmentsstrata_selectsubgroup_editssubgroup_eventssubgroup_explorersubgroup_phasessubgroup_populationssubgroup_sightingssubgroup_subgroupssummarize_bftsummarize_distancessummarize_effortsummarize_sightingssummarize_species

Dependencies:abindantiwordaplotaskpassassertthatbackportsbase64encbitbit64bitopsbootbroombslibcachemcarcarDatacellrangerclassclassIntclicliprcodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdeldirDerivdigestdoBydplyrDTe1071evaluatefarverfastmapfontawesomeforcatsforeachforecastFormulafracdifffsfuturefuture.applygenericsgeosphereggbreakggfunggplot2ggplotifyggpubrggrepelggsciggsignifglmnetglobalsgluegridExtragridGraphicsgtablehavenHDIntervalhexbinhighrhmshtmltoolshtmlwidgetshttpuvhttrigraphinsightinterpisobanditeratorsjomojpegjquerylibjsonliteKernSmoothkknnknitrlabelinglaterlatticelatticeExtralazyevalleafletleaflet.providerslifecyclelistenvlme4lmtestlubridatelutzlwgeommagrittrMASSMatrixMatrixModelsmemoisemgcvmicemiceaddsmimeminqamintymitmlmitoolsmodelrmrdsMuMInndjsonnlmenloptrnnetnumDerivopenssloptimxordinalotelpanparallellypatchworkpbkrtestpdftoolspillarpkgcondpkgconfigpngpolyclippolynompracmaprettyunitsprogresspromisesproxypurrrqpdfquantregR6rappdirsrasterrasterVisrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadODSreadrreadtextreadxlreformulasrematchremotesrintrojsrjsonrlangrmarkdownrnaturalearthrpartRsolnprstatixs2S7sassscalesscamsfshapeshinyshinydashboardshinyjsshinythemessourcetoolsspSparseMspatstat.dataspatstat.geomspatstat.univarspatstat.utilsstreamRstringistringrstriprtfsurvivalswfscDASswfscMiscsysterratibbletidyrtidyselecttimechangetimeDatetinytextruncnormtzdbucminfunitsurcautf8vctrsviridisLitevroomwithrwkxfunxml2xtableyamlyulab.utilszipzoo

Readme and manuals

Help Manual

Help pageTopics
Estimate density & abundanceabundance
Relative trackline detection probabilities from Barlow (2015).barlow_2015
BCA method functionbca
Cruise data processed for the CNP, 1986 - 2020 (150 km segment lengths)cnp_150km_1986_2020
Example of coded edits to 'cruz' objectcnp_1986_2020_edits
Coastlinecoastline
Determine whether coordinates occur inside a stratum polygoncoordinates_in_strata
Combine several 'cruz' objectscruz_combine
Launch a data explorer app for WinCruz surveyscruz_explorer
Review of 'cruz' object structurecruz_structure
Apply edits to a 'DAS' file...das_editor
Edit 'DAS' files and save edited versionsdas_editor_tofile
Finalize formatting of a 'DAS' objectdas_format
Use a 'Shiny' app to explore a 'DAS' file and build up a list of edits. Those edits will be saved as a list of instructions, which can subsequently be provided as an argument to 'LTabundR::process_surveys()', which will apply your list of edits before processing the data. This framework allows you to record details of required edits reproducibly without ever modifying the original dataset or producing modified versions of the original.das_inspector
Interpolate DAS datadas_interpolate
Read in and process a 'DAS' filedas_load
Read DAS file without parsing columnsdas_readtext
Adjust the timestamp within a 'DAS' filedas_time
Get detection function curvedf_curve
Fit a detection function to 'WinCruz' datadf_fit
Plot the best-fit detection function model(s)df_plot
EEZ (all US EEZ boundaries)eez
EEZ - California Current System (formatted for 'sf' mapping)eez_ccs
EEZ - Hawaii (formatted for 'sf' mapping)eez_hawaii
Encounter Rate simulator tester_simulator
Example cruz object (WHICEAS 2020)example_cruz
Example settings used in 'LTabundR' vignette (WHICEAS 2020)example_settings
Filter segments & sightings for a single cohort by species/region/year, etc.filter_cohort
Filter 'cruz' objects by species/region/year, etc.filter_cruz
Combine estimates of weighted g(0) and its CVg0_combine
Estimate relative g(0) in different survey conditionsg0_model
Find g0 values Nelder-Mead using optimizationg0_optimize
Plot Rg(0) curvesg0_plot
Relative trackline detection probabilities, _Rg(0)_g0_results
Compile table of Relative g(0) estimates by Beaufort stateg0_table
Find a single weighted g(0) estimate (and CV) from a set of Beaufort-specific estimates.g0_weighted
Add 'cruz' effort to a base 'ggplot2' map.gg_effort
Add 'cruz' geostrata to a base 'ggplot2' map.gg_geostratum
Add 'cruz' sightings to a base 'ggplot2' map.gg_sightings
Modify a 'ggplot' object to handle the International Date Line (IDL)ggplot_idl
Group size calibrationgrp_calibrate_abund
Group size coefficients for the ABUND calibration approachgrp_coeff_abund
Group size coefficients for the Gerrodette calibration approachgrp_coeff_gerrodette
Calibration options for ABUND approachgrp_ops_abund
Calibration options for Gerrodette approachgrp_ops_gerrodette
Recalibrate processed sightingsgrp_recalibrate
Group size estimationgrp_size
Coerce eastern longitudes to western (i.e., less than - 180)idl_coerce
Landland
Load cohort-specific settingsload_cohort_settings
Load settings for processing 'WinCruz' surveysload_settings
Load survey settingsload_survey_settings
Line transect analysislta
Check for missing data before running 'lta()'.lta_checks
Compute confidence intervals of a bootstrapped LTA estimatelta_ci
Combine LTA estimates from separate regionslta_combine
Estimate CV and 95% confidence intervals with the delta methodlta_delta_method
Pool stratified LTA resultslta_destratify
Run diagnostics on a LTA resultlta_diagnostics
Compile a directory of LTA results into a listlta_enlist
Build a function that creates 'estimates' sub-lists for 'lta()'lta_estimates
Plot LTA resultslta_plot
Pool bootstraps from multiple 'lta()' outputslta_pool
Build LTA tables for standard reportslta_report
Example of LTA results for three delphinids in 2010 and 2017lta_result
Subgroup-based line transect analysislta_subgroup
Interactive map for 'Wincruz' surveymap_cruz
Find affiliated species from mixed-species groupsmixed_group_affiliates
Cruise data processed for all NOAA SWFSC and PIFSC surveys, 1986 - 2020 (10 km segment lengths)noaa_10km_1986_2020
Convert coordinates to a 'sf' linepoints_to_line
Prepare bootstrapped versions of datasetsprep_bootstrap_datasets
Calculate distances between rows in a DAS fileprocess_km
Format a CSV into a polygon for mappingprocess_polygon
Process survey sightingsprocess_sightings
Process geo-strataprocess_strata
Analyze subgroup detections for false killer whalesprocess_subgroups
Process & prepare 'Wincruz' survey data for analysis.process_surveys
Read in a DAT file with polygon(s)read_polygon
Find DAS rows occurring within a region / regionsregion_das
Find segments occurring within a region / regionsregion_segments
Segmentize survey effortsegmentize
Ship codesships
Species codes used in WinCRUZspecies_codes
Species name/code search enginespecies_translator
Combine geostrata and compute areastrata_area
Strata CCSstrata_ccs
Strata CNPstrata_cnp
Strata ETPstrata_etp
Explore the package's strata polygon gallerystrata_explore
Display/map stratum assignments for segmentsstrata_segments
Select strata polygons for standard survey regionsstrata_select
Stage edits to subgroups (e.g., phase and population assignments)subgroup_edits
Find subgroup size estimates within a DAS filesubgroup_events
Simple explorer for subgroups datasubgroup_explorer
Review & stage edits to subgroup phase assignmentssubgroup_phases
Assign subgroups to populations based on polygonssubgroup_populations
Summarize sightings (for subgroup species) based on subgroupssubgroup_sightings
Summarize subgroups based on subgroup eventssubgroup_subgroups
Summarize 'Wincruz' by Beaufort Sea Statesummarize_bft
Summarize sighting distances in a tablesummarize_distances
Summarize 'Wincruz' survey effortsummarize_effort
Inventory sightings and species counts from a 'Wincruz' surveysummarize_sightings
Summarize sightings for a species (or several)summarize_species