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'))

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

Datasets:

TownsvilleReefQC - Quality-controlled bull shark detections
data_with_sst_and_current - ??
imos_variables_table - ??

On CRAN:

30 exports 13 stars 2.00 score 132 dependencies 16 scripts

Last updated 20 days agofrom:71b90e6150. Checks:OK: 1 ERROR: 6. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 27 2024
R-4.5-win	ERROR	Aug 27 2024
R-4.5-linux	ERROR	Aug 27 2024
R-4.4-win	ERROR	Aug 27 2024
R-4.4-mac	ERROR	Aug 27 2024
R-4.3-win	ERROR	Aug 27 2024
R-4.3-mac	ERROR	Aug 27 2024

Exports:choose_file det_per_receiver_location det_per_species det_per_station det_per_tag det_per_tag_location det_species_station extractBlue extractEnv extractMoor get_expert_distribution_shp_CAAB getDistance getOverlap grabQC imos_variables mooringDownload mooringTable n_detections n_receivers n_species n_tags plotDT plotQC remoteNCDF runQC sei shinyReport windDir windSpd writeQC

Dependencies:askpass base64enc bit bit64 bslib cachem CFtime class classInt cli clipr codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI digest doParallel dplyr e1071 evaluate fansi farver fastmap fasttime fontawesome forcats foreach fs furrr future gdistance generics geodist ggplot2 globals glue gridExtra gtable highr hms htmltools htmlwidgets httpuv httr igraph isoband iterators jquerylib jsonlite kableExtra KernSmooth knitr labeling later lattice lazyeval leaflet leaflet.providers lifecycle listenv lubridate magrittr MASS Matrix memoise mgcv mime munsell ncdf4 ncmeta nlme openssl parallelly pillar pkgconfig plotly png prettyunits progress promises proxy purrr R.methodsS3 R.oo R.utils R6 rappdirs raster RColorBrewer Rcpp readr rlang rmarkdown RNetCDF rstudioapi s2 sass scales sf shiny sourcetools sp stringi stringr svglite sys systemfonts terra tibble tidync tidyr tidyselect timechange tinytex tzdb units utf8 vctrs viridis viridisLite vroom withr wk xfun xml2 xtable yaml

extractBlue

Rendered fromextractBlue.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2024-07-03
Started: 2023-08-16

extractEnv

Rendered fromextractEnv.Rmdusingknitr::rmarkdownon Aug 27 2024.

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

extractMoor

Rendered fromextractMoor.Rmdusingknitr::rmarkdownon Aug 27 2024.

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

runQC

Rendered fromrunQC.Rmdusingknitr::rmarkdownon Aug 27 2024.

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

shinyReport_receivers

Rendered fromshinyReport_receivers.Rmdusingknitr::rmarkdownon Aug 27 2024.

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

shinyReport_transmitters

Rendered fromshinyReport_transmitters.Rmdusingknitr::rmarkdownon Aug 27 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'remora'	remora-package remora
Choose a file interactively	choose_file
??	data_with_sst_and_current
Receiver location summary	det_per_receiver_location
Detections per species	det_per_species
Detections per station	det_per_station
Number of detections per transmitter	det_per_tag
Number of detections per tag, tag deployment coordinates and datetime	det_per_tag_location
Detections per station per species	det_species_station
Extract and append Bluelink Reanalysis (BRAN) environmental data to detection data	extractBlue
Extract and append remote sensing environmental data to detection data	extractEnv
Link the QC Detection Dataset to the Sensor Value obtained by the Nearest IMOS Mooring	extractMoor
match species CAAB code with CSIRO expert distribution shapefiles	get_expert_distribution_shp_CAAB
Find closest mooring	getDistance
Extract number of tag detections that fall within the duration of sensor coverage at each mooring	getOverlap
grab subsets of the QC output	grabQC
Table of all available IMOS variables accessible from 'remora' package	imos_variables
??	imos_variables_table
Download the IMOS Mooring Data for a Single Mooring Site	mooringDownload
Pull the Latest IMOS Moorings Dataset from the Server	mooringTable
Number of total detections per transmitter	n_detections
Number of total receivers	n_receivers
Number of total species	n_species
Number of total transmitters	n_tags
Depth-time plot	plotDT
produce interactive leaflet maps showing the occurrence of QC'd detections per species	plotQC
Remotely open BRAN netCDF files	remoteNCDF
run IMOS-ATF acoustic detections quality control process	runQC
Station Efficiency Index	sei
Render Shiny report	shinyReport
Quality-controlled bull shark detections (5 individuals, subsampled for efficiency)	TownsvilleReefQC
Calculate wind direction	windDir
Calculate wind speed	windSpd
write a QCsummary.csv file and/or QC processed '.csv' files for each tag deployment	writeQC

Package: remora 0.8-03

remora: Rapid Extraction of Marine Observations for Roving Animals

extractBlue

extractEnv

extractMoor

runQC

shinyReport_receivers

shinyReport_transmitters

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)