Package: remora 0.9.10

Ian Jonsen

remora: Rapid Extraction of Marine Observations for Roving Animals

R Package to access and integrate animal tracking data from the IMOS Animal Tracking Facility database and web-app, and environmental data from the AODN database.

Authors:Fabrice Jaine [aut, ctb], Ian Jonsen [aut, ctb, cre], Vinay Udyawer [aut, ctb], Ross Dwyer [aut, ctb], Kylie Scales [aut, ctb], Francisca Maron [aut, ctb], Xavier Hoenner [aut, ctb], Charlie Huveneers [aut, ctb], Yuri Niella [aut, ctb]

remora_0.9.10.tar.gz
remora_0.9.10.zip(r-4.7)remora_0.9.10.zip(r-4.6)remora_0.9.10.zip(r-4.5)
remora_0.9.10.tgz(r-4.6-any)remora_0.9.10.tgz(r-4.5-any)
remora_0.9.10.tar.gz(r-4.7-any)remora_0.9.10.tar.gz(r-4.6-any)
remora_0.9.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
remora/json (API)
NEWS

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

Bug tracker:https://github.com/imos-animaltracking/remora/issues

Pkgdown/docs site:https://imos-animaltracking.github.io

Datasets:

On CRAN:

Conda:

6.24 score 15 stars 24 scripts 29 exports 141 dependencies

Last updated from:4bf03f7436. Checks:7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING987
source / vignettesOK419
linux-release-x86_64WARNING892
macos-release-arm64WARNING647
macos-oldrel-arm64WARNING817
windows-develWARNING1377
windows-releaseWARNING1082
windows-oldrelWARNING948
wasm-releaseOK263

Exports:choose_filedet_per_receiver_locationdet_per_speciesdet_per_stationdet_per_tagdet_per_tag_locationdet_species_stationextractBlueextractEnvextractMoorget_expert_distribution_shp_CAABgetDistancegetOverlapgrabQCimos_variablesmooringDownloadmooringTablen_detectionsn_receiversn_speciesn_tagsplotDTplotQCrunQCseishinyReportwindDirwindSpdwriteQC

Dependencies:abindaskpassbase64encbitbit64bslibcachemCFtimeclassclassIntclicliprcodetoolscommonmarkcpp11crayoncrosstalkcurldata.tableDBIdigestdoParalleldplyre1071evaluatefarverfastmapfasttimeFNNfontawesomeforcatsforeachfsfurrrfuturegdistancegenericsgeodistgeosphereggplot2globalsgluegridExtragstatgtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphintervalsisobanditeratorsjquerylibjsonlitekableExtraKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelistenvlubridatemagrittrMASSMatrixmemoisemimencdf4ncmetaopensslotelparallellypillarpkgconfigplotlypngprettyunitsprogresspromisesproxypurrrR.methodsS3R.ooR.utilsR6rappdirsrasterRColorBrewerRcppreadrrlangrmarkdownRNetCDFrstudioapis2S7sassscalessfsftimeshinysourcetoolsspspacetimestarsstringistringrsvglitesyssystemfontsterratextshapingtibbletidynctidyrtidyselecttidyterratimechangetinytextzdbunitsutf8vctrsviridisviridisLitevroomwithrwkxfunxml2xtablextsyamlzoo

extractBlue

Rendered fromextractBlue.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2024-11-18
Started: 2023-08-16

extractEnv

Rendered fromextractEnv.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2021-11-10
Started: 2021-10-13

extractMoor

Rendered fromextractMoor.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2025-10-16
Started: 2021-10-13

runQC

Rendered fromrunQC.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2023-11-10
Started: 2021-10-13

shinyReport_receivers

Rendered fromshinyReport_receivers.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2021-11-10
Started: 2021-10-13

shinyReport_transmitters

Rendered fromshinyReport_transmitters.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2021-11-10
Started: 2021-10-13

Readme and manuals

Help Manual

Help pageTopics
'remora'remora-package "_PACKAGE" remora
Choose a file interactivelychoose_file
??data_with_sst_and_current
Receiver location summarydet_per_receiver_location
Detections per speciesdet_per_species
Detections per stationdet_per_station
Number of detections per transmitterdet_per_tag
Number of detections per tag, tag deployment coordinates and datetimedet_per_tag_location
Detections per station per speciesdet_species_station
Extract and append Bluelink Reanalysis (BRAN) environmental data to detection dataextractBlue
Extract and append remote sensing environmental data to detection dataextractEnv
Link the QC Detection Dataset to the Sensor Value obtained by the Nearest IMOS MooringextractMoor
match species CAAB code with CSIRO expert distribution shapefilesget_expert_distribution_shp_CAAB
Find closest mooringgetDistance
Extract number of tag detections that fall within the duration of sensor coverage at each mooringgetOverlap
grab subsets of the QC outputgrabQC
Table of all available IMOS variables accessible from 'remora' packageimos_variables
??imos_variables_table
Download the IMOS Mooring Data for a Single Mooring SitemooringDownload
Pull the Latest IMOS Moorings Dataset from the ServermooringTable
Number of total detections per transmittern_detections
Number of total receiversn_receivers
Number of total speciesn_species
Number of total transmittersn_tags
Depth-time plotplotDT
produce interactive leaflet maps showing the occurrence of QC'd detections per speciesplotQC
run IMOS-ATF acoustic detections quality control processrunQC
Station Efficiency Indexsei
Render Shiny reportshinyReport
Quality-controlled bull shark detections (5 individuals, subsampled for efficiency)TownsvilleReefQC
Calculate wind directionwindDir
Calculate wind speedwindSpd
write a QCsummary.csv file and/or QC processed '.csv' files for each tag deploymentwriteQC