Package: birdscanR 0.3.0.9029

Birgen Haest

birdscanR: Migration Traffic Rate Calculation Package for 'Birdscan MR1' Radars

Extract data from 'Birdscan MR1' 'SQL' vertical-looking radar databases, filter, and process them to Migration Traffic Rates (# objects per hour and km) or density (# objects per km3) of, for example birds, and insects. Object classifications in the 'Birdscan MR1' databases are based on the dataset of Haest et al. (2021) <doi:10.5281/zenodo.5734960>). Migration Traffic Rates and densities can be calculated separately for different height bins (with a height resolution of choice) as well as over time periods of choice (e.g., 1/2 hour, 1 hour, 1 day, day/night, the full time period of observation, and anything in between). Two plotting functions are also included to explore the data in the 'SQL' databases and the resulting Migration Traffic Rate results. For details on the Migration Traffic Rate calculation procedures, see Schmid et al. (2019) <doi:10.1111/ecog.04025>.

Authors:Birgen Haest [aut, cre], Fabian Hertner [aut], Baptiste Schmid [ctb], Peter Desmet [ctb], Bart Kranstauber [ctb], Damiano Preatoni [ctb], Johannes De Groeve [ctb], Felix Liechti [ctb], Swiss Ornithological Institute [cph], Swiss Birdradar Solution AG [cph]

birdscanR_0.3.0.9029.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
birdscanR/json (API)

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

Bug tracker:https://github.com/birdscancommunity/birdscanr/issues

Pkgdown/docs site:https://birdscancommunity.github.io

Datasets:
  • classAbbreviations - Default class abbreviations table of the birdscanR package
  • manualBlindTimes - Example file on how to include manual blind times for your 'Birdscan MR1' database.

On CRAN:

Conda:

6.21 score 3 stars 10 scripts 292 downloads 33 exports 62 dependencies

Last updated from:c5a4b12a52. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK171
source / vignettesOK232
linux-release-x86_64OK168
macos-release-arm64OK127
macos-oldrel-arm64OK133
windows-develOK103
windows-releaseOK119
windows-oldrelOK125
wasm-releaseOK332

Exports:addDayNightInfoPerEchocompileDatacomputeDensitycomputeMTRconvertTimeZonecreateTimeRangeForPlotcreateVPTSdbConnectBirdscanSQLextractDbDatafilterDatafilterEchoDatafilterProtocolDatafilterSpeedFeature37getBatClassificationgetCollectionTablegetEchoFeaturesgetEchoValidationTablegetManualVisibilityTablegetProtocolTablegetRadarTablegetRfClassificationgetSiteTablegetTimeBinsTablegetVisibilityTableloadManualBlindTimesmergeVisibilityAndManualBlindTimesplotExplorationplotLongitudinalMTRQUERYreclassToBatssaveMTRsavePlotToFiletwilight

Dependencies:bitbit64classclassIntclicliprcpp11crayonDBIdplyre1071farvergenericsggplot2gluegtablehmsisobandKernSmoothlabelinglatticelifecyclemagrittrMASSmodinormpillarpkgconfigplyrprettyunitsprogressproxypurrrR6RColorBrewerRcppreadrreshape2rlangRODBCRPostgreSQLrstudioapis2S7scalessfspstringistringrsuntoolstibbletidyrtidyselecttzdbunitsutf8vctrsviridisLitevroomwithrwkyaml

create and read VPTS
Summary | Before we get started | Step 1: Create VPTS from the BirdScan MR1 example dataset | Step 2: Read the CSV-file and convert to VPTS with BioRad::as.vpts() | Step 3: Visualise
Rendered fromcreateVPTS.Rmdusingknitr::rmarkdown

Last update: 2026-06-23
Started: 2026-06-23

Guide to extracting specific tables from a Birdscan MR1 SQL database
Summary | Before we get started | Examples | Extracting the bat classification table | Extracting the echo collection table | Extracting specific echo features form the echo_rffeature_map table | Extracting information on the study site
Rendered fromextractingSingleTableFromTheSqlDatabase.Rmdusingknitr::rmarkdown

Last update: 2026-06-23
Started: 2025-07-03

Introduction to birdscanR
Summary | Before we get started | Step 1: Extract the relevant data from the SQL database (or load it from a ) | Step 2: (optional) Join the bat classification with the base MR1 classification output | Step 3: Filter the extracted data to what you are interested in | Step 4: Calculate the activity or migration traffic rates | Create some plots to explore the calculated activity / migration traffic rates
Rendered frombirdscanR.Rmdusingknitr::rmarkdown

Last update: 2026-06-23
Started: 2025-05-13

Readme and manuals

Help Manual

Help pageTopics
addDayNightInfoPerEchoaddDayNightInfoPerEcho
Example Birdscan MR1 data extract from Sempach, SwitzerlandCH_Sempach_2024_SEP24_25_DataExtract
Default class abbreviations table of the birdscanR packageclassAbbreviations
compileDatacompileData
computeDensitycomputeDensity
computeMTRcomputeMTR
Converts timestamps from radar time zone to an user-defined time zoneconvertTimeZone
Create Time Range for PlotcreateTimeRangeForPlot
createVPTScreateVPTS
Connect to a Birdscan SQL databasedbConnectBirdscanSQL
Extract DB DataextractDbData
filterDatafilterData
filterEchoDatafilterEchoData
filterProtocolDatafilterProtocolData
Filter outliers in Speed feature (collection.feature37)filterSpeedFeature37
Get a BirdScan 'batClassification' tablegetBatClassification
Get BirdScan collection tablegetCollectionTable
Get BirdScan echo featuresgetEchoFeatures
Get a BirdScan echo validation tablegetEchoValidationTable
Get manual visibility tablegetManualVisibilityTable
Get BirdScan protocol tablegetProtocolTable
Get a BirdScan radar tablegetRadarTable
Get a BirdScan 'rfClassification' tablegetRfClassification
Get BirdScan site tablegetSiteTable
Get BirdScan time bins tablegetTimeBinsTable
Get BirdScan visibility tablegetVisibilityTable
loadManualBlindTimesloadManualBlindTimes
Example file on how to include manual blind times for your 'Birdscan MR1' database.manualBlindTimes
mergeVisibilityAndManualBlindTimesmergeVisibilityAndManualBlindTimes
plotExplorationplotExploration
plotLongitudinalMTRplotLongitudinalMTR
Query 'SQL' databaseQUERY
integrate bat classificationreclassToBats
saveMTRsaveMTR
savePlotToFilesavePlotToFile
Get the nautical, civil, and solar dawn and dusk for a given timerange and locations.twilight