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✨
DESCRIPTION |NEWS
card.svg |card.png
remora/json (API)

# 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_64WARNING865
source / vignettesOK423
linux-release-x86_64WARNING721
macos-release-arm64WARNING591
macos-oldrel-arm64WARNING538
windows-develWARNING1175
windows-releaseWARNING760
windows-oldrelWARNING1281
wasm-releaseOK240

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

extractMoor
Types of environmental data | Usage of the extractMoor() function | Load example dataset | Moorings data source | Find closest mooring to our animal detections | Moorings data download | Creating a depth-time plot using moorings data, and adding detections | Moorings data extraction | Examining the appended environmental data
Rendered fromextractMoor.Rmdusingknitr::rmarkdown

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

extractBlue
Types of environmental data | Usage of the extractBlue() function | Load example dataset | Bluelink (BRAN) environmental data extraction | Running the function with full_timeperiod = TRUE | Water temperature at depth (30 m) | Surface 3D current speeds
Rendered fromextractBlue.Rmdusingknitr::rmarkdown

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

runQC
Required data | What if my tags are detected across many reciever array projects? | Usage of the runQC() function | Accessing the QC'd data and metadata | Visualising the QC'd detections
Rendered fromrunQC.Rmdusingknitr::rmarkdown

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

extractEnv
Types of environmental data | Usage of the extractEnv() function | Load example dataset | Environmental data extraction | Gap filling functionality | Interpolated sea surface temperature | Modeled ocean surface currents | Examining the appended environmental data
Rendered fromextractEnv.Rmdusingknitr::rmarkdown

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

shinyReport_receivers
Receiver Array Report | Run Shiny App | Detections map | Detections overview | Transmitters overview | Detections over time | Detections per station | Detections per hour | Array performance | References
Rendered fromshinyReport_receivers.Rmdusingknitr::rmarkdown

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

shinyReport_transmitters
Tagging Project | Run Shiny App | Transmitter deployments | Transmitter detections | Detections over time | Abacus plot | Connectivity plot | Detections network map | References
Rendered fromshinyReport_transmitters.Rmdusingknitr::rmarkdown

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