Package: remora 0.8-03

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_0.8-03.tar.gz
remora_0.8-03.zip(r-4.5)remora_0.8-03.zip(r-4.4)remora_0.8-03.zip(r-4.3)
remora_0.8-03.tgz(r-4.4-any)remora_0.8-03.tgz(r-4.3-any)
remora_0.8-03.tar.gz(r-4.5-noble)remora_0.8-03.tar.gz(r-4.4-noble)
remora_0.8-03.tgz(r-4.4-emscripten)remora_0.8-03.tgz(r-4.3-emscripten)
remora.pdf |remora.html✨
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'))

Peer review:

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

Datasets:

On CRAN:

5.87 score 13 stars 16 scripts 30 exports 132 dependencies

Last updated 5 days agofrom:a51fbeecdb. Checks:OK: 1 ERROR: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winERRORNov 18 2024
R-4.5-linuxERRORNov 18 2024
R-4.4-winERRORNov 18 2024
R-4.4-macERRORNov 18 2024
R-4.3-winERRORNov 18 2024
R-4.3-macERRORNov 18 2024

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_tagsplotDTplotQCremoteNCDFrunQCseishinyReportwindDirwindSpdwriteQC

Dependencies:askpassbase64encbitbit64bslibcachemCFtimeclassclassIntclicliprcodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdigestdoParalleldplyre1071evaluatefansifarverfastmapfasttimefontawesomeforcatsforeachfsfurrrfuturegdistancegenericsgeodistggplot2globalsgluegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphisobanditeratorsjquerylibjsonlitekableExtraKernSmoothknitrlabelinglaterlatticelazyevalleafletleaflet.providerslifecyclelistenvlubridatemagrittrMASSMatrixmemoisemgcvmimemunsellncdf4ncmetanlmeopensslparallellypillarpkgconfigplotlypngprettyunitsprogresspromisesproxypurrrR.methodsS3R.ooR.utilsR6rappdirsrasterRColorBrewerRcppreadrrlangrmarkdownRNetCDFrstudioapis2sassscalessfshinysourcetoolsspstringistringrsvglitesyssystemfontsterratibbletidynctidyrtidyselecttimechangetinytextzdbunitsutf8vctrsviridisviridisLitevroomwithrwkxfunxml2xtableyaml

extractBlue

Rendered fromextractBlue.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

extractEnv

Rendered fromextractEnv.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

extractMoor

Rendered fromextractMoor.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2021-11-16
Started: 2021-10-13

runQC

Rendered fromrunQC.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

shinyReport_receivers

Rendered fromshinyReport_receivers.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

shinyReport_transmitters

Rendered fromshinyReport_transmitters.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Readme and manuals

Help Manual

Help pageTopics
'remora'remora-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
Remotely open BRAN netCDF filesremoteNCDF
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