Package: DEPONS2R 1.2.8

DEPONS2R: Read, Plot and Analyse Output from the DEPONS Model

Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.

Authors:Jacob Nabe-Nielsen [aut, cre], Caitlin K. Frankish [aut], Axelle Cordier [aut], Florian G. Weller [aut]

DEPONS2R_1.2.8.tar.gz
DEPONS2R_1.2.8.zip(r-4.7-any)DEPONS2R_1.2.8.zip(r-4.6-any)DEPONS2R_1.2.8.zip(r-4.5-any)
DEPONS2R_1.2.8.tgz(r-4.6-any)DEPONS2R_1.2.8.tgz(r-4.5-any)
DEPONS2R_1.2.8.tar.gz(r-4.7-any)DEPONS2R_1.2.8.tar.gz(r-4.6-any)
DEPONS2R_1.2.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DEPONS2R/json (API)

# Install 'DEPONS2R' in R:
install.packages('DEPONS2R', repos = c('https://jacobnabe.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jacobnabe/depons2r/issues

Datasets:
  • aisdata - Position for three ships in the inner Danish waters
  • argosmetrics - Fine and Large-scale metrics of Argos data
  • bathymetry - Bathymetry of the Kattegat area
  • coastline - Coastline of Northern Europe
  • geminidata - Observed and simulated data from Gemini windfarm construction
  • porpoisebdyn - Simulated porpoise population dynamics
  • porpoisedyn - Simulated porpoise population dynamics
  • porpoisetrack - Simulated porpoise track
  • shipdata - Ships on example routes through the Kattegat

On CRAN:

Conda:

agent-based-modelingenvironmental-modellingmarine-biology

2.90 score 1 stars 4 scripts 516 downloads 52 exports 26 dependencies

Last updated from:8ed643623f. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK283
source / vignettesOK239
linux-releaseOK287
macos-releaseOK269
macos-oldrelOK288
windows-develOK195
windows-releaseOK234
windows-oldrelOK250
wasm-releaseOK138

Exports:aggregate.dpm.sim.datais.to.DeponsShipsas.data.frameas.DeponsRasteras.rasterbboxcalib_01calib_02calib_03_make_sim_dpmcalib_03_ssdcheck.DeponsShipscrscrs<-dynfind.nearest.pilingget.latest.simget.pods.at.dist.sim.datget.simtimeinterpolate.ais.datainterpolate.mapslandscapelandscape<-make.blocksrastermake.clip.polymake.construction.trafficmake.DeponsDynmake.stationary.shipsmake.windfarmsplotplot_calib02read.DeponsBlockdynread.DeponsDynread.DeponsDynBatchread.DeponsParamread.DeponsRasterread.DeponsShipsread.DeponsTrackread.DeponsTrackBatchroutesroutes<-set.ship.typeshipsships<-startdaystartday<-summarise.aggregated.dpm.datsummarytick.to.timetime.to.ticktitletitle<-write

Dependencies:ade4adehabitatHRadehabitatLTadehabitatMAclassclassIntcliDBIe1071jsonliteKernSmoothlatticeMASSpixmapproxyrasterRcppRcppArmadillorlangs2sfspterraunitswkxml2

Readme and manuals

Help Manual

Help pageTopics
Aggregate simulated porpoise detections by piling event and houraggregate.dpm.sim.dat
Convert ship tracks to DeponsShips objectais.to.DeponsShips
Position for three ships in the inner Danish watersaisdata
Fine and Large-scale metrics of Argos dataargosmetrics
Convert DeponsDyn object to data frameas.data.frame,DeponsDyn-method
Convert DeponsTrack to data frameas.data.frame,DeponsTrack-method
Convert a RasterLayer into a DeponsRasteras.DeponsRaster as.DeponsRaster,RasterLayer-method
Convert a DeponsRaster into a RasterLayeras.raster as.raster,DeponsRaster-method
Bathymetry of the Kattegat areabathymetry
Get bbox from Depons* objectbbox bbox,DeponsRaster-method bbox,DeponsTrack-method
Plot distribution of turning angles, step lengths and speed of tracked simulated porpoises.calib_01
Calculate calibration metrics of previously filtered tracks (fine-scale or large-scale)calib_02
Create piling-response table from simulated porpoise countscalib_03_make_sim_dpm
Compute SSD for one response to piling simulationcalib_03_ssd
Check if ships move at unrealistic speeds or are outside the map boundarycheck.DeponsShips
Coastline of Northern Europecoastline
Get or set map projection in Depons* objectscrs crs,DeponsRaster-method crs,DeponsShips-method crs,DeponsTrack-method crs<- crs<-,DeponsRaster-method crs<-,DeponsShips-method crs<-,DeponsTrack-method
Package for analyzing DEPONS simulation outputDEPONS2R
DeponsBlockdyn-classDeponsBlockdyn-class
DeponsDyn-classDeponsDyn-class
DeponsRaster-classDeponsRaster-class
DeponsShips-classDeponsShips-class
DeponsTrack-classDeponsTrack-class
Extract population dynamics from objectsdyn dyn,DeponsBlockdyn-method dyn,DeponsDyn-method
Find nearest active piling from simulated CPOD blocksfind.nearest.piling
Observed and simulated data from Gemini windfarm constructiongeminidata
Get name of newest fileget.latest.sim
Assign hours since piling for detections within a distance intervalget.pods.at.dist.sim.dat
Get simulation dateget.simtime
Interpolate AIS datainterpolate.ais.data
Interpolate missing entries in a series of mapsinterpolate.maps
Get or set the landscape namelandscape landscape,DeponsBlockdyn-method landscape,DeponsDyn-method landscape,DeponsTrack-method landscape<- landscape<-,DeponsBlockdyn-method landscape<-,DeponsDyn-method landscape<-,DeponsTrack-method
Makes new file with blocksmake.blocksraster make.blocksraster,DeponsRaster-method
Make clipping polygon from bboxmake.clip.poly make.clip.poly,matrix-method
Generate artificial AIS data representing ship traffic during wind farm constructionmake.construction.traffic
Make DeponsDyn object from data stored in data framemake.DeponsDyn
Identify and parameterize stationary active ships in a DeponsShips objectmake.stationary.ships
Make wind farm construction scenariomake.windfarms
Plotting of simulated fine or large-scale metrics against argos dataplot_calib02
Plot a DeponsBlockdyn objectplot,DeponsBlockdyn,missing-method plot.DeponsBlockdyn
Plot a DeponsDyn objectplot,DeponsDyn,missing-method plot.DeponsDyn
Plot a DeponsRaster objectplot,DeponsRaster,ANY-method plot,DeponsRaster,DeponsTrack-method plot.DeponsRaster
Plot a DeponsShips objectplot,DeponsShips,missing-method plot.DeponsShips
Plot a DeponsTrack objectplot,DeponsTrack,missing-method plot.DeponsTrack
Simulated porpoise population dynamicsporpoisebdyn
Simulated porpoise population dynamicsporpoisedyn
Simulated porpoise trackporpoisetrack
Reading simulated population count for blocksread.DeponsBlockdyn
Reading DEPONS simulation outputread.DeponsDyn
Read and merges DEPONS Batchmap and Statistics Filesread.DeponsDynBatch
Read simulation parametersread.DeponsParam
Reading DEPONS raster filesread.DeponsRaster
Read DEPONS ship filesread.DeponsShips
Reading DEPONS track filesread.DeponsTrack
Read and Process DEPONS Batchmap and Statistics Filesread.DeponsTrackBatch
Get or define routes in DeponsShips objectsroutes routes,DeponsShips-method routes<- routes<-,DeponsShips-method
Convert AIS vessel type identifiers into the ship types recognized by DEPONSset.ship.type
Ships on example routes through the Kattegatshipdata
Get or define ships in DeponsShips objectsships ships,DeponsShips-method ships<- ships<-,DeponsShips-method
Get or set start date for simulationstartday startday,DeponsBlockdyn-method startday,DeponsDyn-method startday<- startday<-,DeponsBlockdyn-method startday<-,DeponsDyn-method
Summarises aggregated simulated detections before and after pilingsummarise.aggregated.dpm.dat
Summarysummary summary,DeponsBlockdyn-method summary,DeponsDyn-method summary,DeponsRaster-method summary,DeponsShips-method summary,DeponsTrack-method Summary-methods
Convert tick number to time objecttick.to.time
Convert date to tick numbertime.to.tick
Get or set the title of Depons* objectstitle title,DeponsDyn-method title,DeponsShips-method title,DeponsTrack-method title<- title<-,DeponsDyn-method title<-,DeponsShips-method title<-,DeponsTrack-method
Write DEPONS ship fileswrite,DeponsShips-method write.DeponsShips