Package: diveMove 1.6.4

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:Sebastian P. Luque [aut, cre]

diveMove_1.6.4.tar.gz
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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

Datasets:

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

On CRAN:

animal-behavior behavioural-ecology biology diving science

6.75 score 6 stars 54 scripts 1.2k downloads 35 mentions 59 exports 82 dependencies

Last updated 1 months agofrom:cb24903fcd. Checks:OK: 9. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 14 2024
R-4.5-win-x86_64	OK	Nov 14 2024
R-4.5-linux-x86_64	OK	Nov 14 2024
R-4.4-win-x86_64	OK	Nov 14 2024
R-4.4-mac-x86_64	OK	Nov 14 2024
R-4.4-mac-aarch64	OK	Nov 14 2024
R-4.3-win-x86_64	OK	Oct 11 2024
R-4.3-mac-x86_64	OK	Oct 11 2024
R-4.3-mac-aarch64	OK	Oct 11 2024

Exports:as.data.frame as.TDRspeed austFilter bec bec2 bec3 boutfreqs boutinit bouts.mle bouts2.ll bouts2.LL bouts2.mleFUN bouts2.nls bouts2.nlsFUN bouts3.nls bouts3.nlsFUN calibrateDepth calibrateSpeed ccData<-coerce createTDR depth<-distSpeed diveStats extractDive fitMLEbouts fitNLSbouts getCCData getDAct getDepth getDiveDeriv getDiveModel getDPhaseLab getDtime getFileName getGAct getSpeed getSpeedCoef getTDR getTime grpSpeedFilter labelBouts logit oneDiveStats plotBouts plotBoutsCDF plotDiveModel plotTDR plotZOC readLocs readTDR rmixexp rmsDistFilter rqPlot show speed<-stampDive timeBudget unLogit

Dependencies:askpass base64enc bslib cachem cli colorspace cpp11 crosstalk curl data.table digest DoseFinding dplyr evaluate fansi farver fastmap fontawesome fs generics geosphere ggplot2 glue gtable highr htmltools htmlwidgets httr isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix MatrixModels memoise mgcv mime munsell mvtnorm nlme openssl pillar pkgconfig plotly promises purrr quadprog quantreg R6 rappdirs RColorBrewer Rcpp rlang rmarkdown sass scales SEL sp SparseM stringi stringr survival sys tibble tidyr tidyselect tinytex uniReg utf8 vctrs viridisLite withr xfun yaml

Diving Behaviour Analysis in R

Sebastián P. Luque

Rendered fromdiveMove.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2021-02-22
Started: 2020-09-08

Citation

Development and contributors

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