Package: diveMove 1.6.2
Sebastian P. Luque
diveMove: Dive Analysis and Calibration
Utilities to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. Miscellaneous functions for handling location data are also provided.
Authors:
diveMove_1.6.2.tar.gz
diveMove_1.6.2.zip(r-4.5)diveMove_1.6.2.zip(r-4.4)diveMove_1.6.2.zip(r-4.3)
diveMove_1.6.2.tgz(r-4.4-x86_64)diveMove_1.6.2.tgz(r-4.4-arm64)diveMove_1.6.2.tgz(r-4.3-x86_64)diveMove_1.6.2.tgz(r-4.3-arm64)
diveMove_1.6.2.tar.gz(r-4.5-noble)diveMove_1.6.2.tar.gz(r-4.4-noble)
diveMove_1.6.2.tgz(r-4.4-emscripten)diveMove_1.6.2.tgz(r-4.3-emscripten)
diveMove.pdf |diveMove.html✨
diveMove/json (API)
NEWS
| # Install 'diveMove' in R: |
| install.packages('diveMove', repos = c('https://ocean-tracking-network.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/spluque/divemove/issues
- dives - Sample of TDR data from a fur seal
- divesTDR - Sample of TDR data from a fur seal
- divesTDRzoc - Sample of TDR data from a fur seal
- sealLocs - Ringed and Gray Seal ARGOS Satellite Location Data
animal-behaviorbehavioural-ecologybiologydivingscience
Last updated 8 months agofrom:c4eb56e7a7. Checks:OK: 7 NOTE: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 26 2024 |
| R-4.5-win-x86_64 | NOTE | Aug 26 2024 |
| R-4.5-linux-x86_64 | NOTE | Aug 26 2024 |
| R-4.4-win-x86_64 | OK | Aug 26 2024 |
| R-4.4-mac-x86_64 | OK | Aug 26 2024 |
| R-4.4-mac-aarch64 | OK | Aug 26 2024 |
| R-4.3-win-x86_64 | OK | Aug 26 2024 |
| R-4.3-mac-x86_64 | OK | Aug 26 2024 |
| R-4.3-mac-aarch64 | OK | Aug 26 2024 |
Exports:as.data.frameas.TDRspeedaustFilterbecbec2bec3boutfreqsboutinitbouts.mlebouts2.llbouts2.LLbouts2.mleFUNbouts2.nlsbouts2.nlsFUNbouts3.nlsbouts3.nlsFUNcalibrateDepthcalibrateSpeedccData<-coercecreateTDRdepth<-distSpeeddiveStatsextractDivefitMLEboutsfitNLSboutsgetCCDatagetDActgetDepthgetDiveDerivgetDiveModelgetDPhaseLabgetDtimegetFileNamegetGActgetSpeedgetSpeedCoefgetTDRgetTimegrpSpeedFilterlabelBoutslogitoneDiveStatsplotBoutsplotBoutsCDFplotDiveModelplotTDRplotZOCreadLocsreadTDRrmixexprmsDistFilterrqPlotshowspeed<-stampDivetimeBudgetunLogit
Dependencies:askpassbase64encbslibcachemclicolorspacecpp11crosstalkcurldata.tabledigestDoseFindingdplyrevaluatefansifarverfastmapfontawesomefsgenericsgeosphereggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixModelsmemoisemgcvmimemunsellmvtnormnlmeopensslpillarpkgconfigplotlypromisespurrrquadprogquantregR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalesSELspSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytexuniRegutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Dive Analysis and Calibration | diveMove-package diveMove |
| Quantile of Moving Window | .runquantile |
| Filter satellite locations | austFilter grpSpeedFilter rmsDistFilter |
| Calculate bout ending criteria from model coefficients | bec bec,mle-method bec,nls-method |
| Histogram of log-transformed frequencies | boutfreqs |
| Fit "broken stick" model to log frequency data for identification of bouts of behaviour | boutinit boutinit,Bouts-method boutinit,data.frame-method |
| Class "Bouts" for representing Poisson mixtures for identification of behavioural bouts | Bouts Bouts-class |
| Estimated cumulative frequency for two- or three-process Poisson mixture models | boutsCDF |
| Generalized log likelihood function taking any number of Poisson processes in a "broken-stick" model | boutsNLSll boutsNLSll,Bouts-method boutsNLSll,numeric-method |
| Calibrate Depth and Generate a "TDRcalibrate" object | calibrateDepth |
| Calibrate and build a "TDRcalibrate" object | calibrateSpeed |
| Read comma-delimited file with "TDR" data | createTDR readTDR |
| Calculate distance and speed between locations | distSpeed |
| Class "diveModel" for representing a model for identifying dive phases | diveModel diveModel-class |
| Sample of TDR data from a fur seal | dives divesTDR divesTDRzoc |
| Per-dive statistics | diveStats oneDiveStats stampDive |
| Extract Dives from "TDR" or "TDRcalibrate" Objects | extractDive extractDive,TDR,numeric,numeric-method extractDive,TDRcalibrate,numeric,missing-method |
| Maximum Likelihood Model of mixtures of 2 or 3 Poisson Processes | fitMLEbouts fitMLEbouts,Bouts-method fitMLEbouts,numeric-method |
| Fit mixture of Poisson Processes to Log Frequency data via Non-linear Least Squares regression | fitNLSbouts fitNLSbouts,Bouts-method fitNLSbouts,data.frame-method |
| Label each vector element or matrix row with bout membership number | labelBouts labelBouts,Bouts-method labelBouts,numeric-method |
| Plot fitted Poisson mixture model and data | plotBouts plotBouts,mle,Bouts-method plotBouts,mle,numeric-method plotBouts,nls,Bouts-method plotBouts,nls,data.frame-method |
| Plot empirical and deterministic cumulative frequency distribution Poisson mixture data and model | plotBoutsCDF plotBoutsCDF,mle,Bouts-method plotBoutsCDF,mle,numeric-method plotBoutsCDF,nls,Bouts-method plotBoutsCDF,nls,numeric-method |
| Methods for plotting models of dive phases | plotDiveModel plotDiveModel,diveModel,missing-method plotDiveModel,numeric,numeric-method plotDiveModel,TDRcalibrate,missing-method |
| Methods for plotting objects of class "TDR" and "TDRcalibrate" | plotTDR plotTDR,POSIXt,numeric-method plotTDR,TDR,missing-method plotTDR,TDRcalibrate,missing-method |
| Methods for visually assessing results of ZOC procedure | plotZOC plotZOC,TDR,matrix-method plotZOC,TDR,TDRcalibrate-method |
| Read comma-delimited file with location data | readLocs |
| Generate samples from a mixture of exponential distributions | rmixexp |
| Plot of quantile regression for speed calibrations | rqPlot |
| Ringed and Gray Seal ARGOS Satellite Location Data | sealLocs |
| Coerce, Extractor, and Replacement methods for class "TDR" objects | as.data.frame,TDR-method as.TDRspeed as.TDRspeed,TDR-method ccData<- ccData<-,TDR,data.frame-method coerce,TDR,data.frame-method coerce,TDR,TDRspeed-method depth<- depth<-,TDR,numeric-method getCCData getCCData,TDR,character-method getCCData,TDR,missing-method getDepth getDepth,TDR-method getDtime getDtime,TDR-method getFileName getFileName,TDR-method getSpeed getSpeed,TDRspeed-method getTime getTime,TDR-method show,TDR-method speed<- speed<-,TDRspeed,numeric-method TDR-accessors TDR-methods [,TDR,numeric,missing,missing-method |
| Classes "TDR" and "TDRspeed" for representing TDR information | TDR TDR-class TDRspeed TDRspeed-class |
| Methods to Show and Extract Basic Information from "TDRcalibrate" Objects | getDAct getDAct,TDRcalibrate,character-method getDAct,TDRcalibrate,missing-method getDiveDeriv getDiveDeriv,diveModel-method getDiveDeriv,TDRcalibrate-method getDiveModel getDiveModel,TDRcalibrate,missing-method getDiveModel,TDRcalibrate,numeric-method getDPhaseLab getDPhaseLab,TDRcalibrate,missing-method getDPhaseLab,TDRcalibrate,numeric-method getGAct getGAct,TDRcalibrate,character-method getGAct,TDRcalibrate,missing-method getSpeedCoef getSpeedCoef,TDRcalibrate-method getTDR getTDR,TDRcalibrate-method show,diveModel-method show,TDRcalibrate-method TDRcalibrate-accessors TDRcalibrate-methods |
| Class "TDRcalibrate" for dive analysis | TDRcalibrate TDRcalibrate-class |
| Describe the Time Budget of Major Activities from "TDRcalibrate" object. | timeBudget timeBudget,TDRcalibrate,logical-method |
