Man pages for robschick/tangled
Creates data objects and plots for Knowlton, Schick et al. manuscript on entanglement

anomHealth anomaly between individual health and population...
anomSPHealth anomaly between individual health and population...
calcAnomReturn the differences in health between individuals and pop...
calckdpaSurvdatPrepare the data needed to calculate survivorship for...
calcKMCurvesReturn lists to be used in plotting Kaplan-Meier survival...
calcKMCurvesSevGenReturn lists to be used in plotting Kaplan-Meier survival...
calcKMUncertaintyData frame of 95% uncertainty quantiles for survivorship.
calcpresdSurvdatPrepare the data needed to calculate survivorship for...
calfTableTable describing all of the calving events in the right whale...
cleanMergeClean up the entanglement time data for geary-carrying...
dcutScalar noting when the sightings data are complete through
deadTableData frame of known deaths of individual right whales
deathyrEstimated death months of individual animals
entvecEntanglement class definitions
estStartDatesInformation about estimated start data of entanglement events
etimeInformation about gear carrying time on entangled right...
firstSightVector denoting the first month (in integer form) of animal...
genderGender of each individual right whale
getDeathsMatrix of imputed death times
healthmeanEstimated health of individual animals
healthmeanSPEstimated health of individual animals for slope plot
healthsdEstimated standard deviation health of individual animals
IDID vector of EGNo's for all individual right whales in the...
lastSightVector denoting the last month (in integer form) of animal...
makeEventsReturn 'events' data frame of last entanglement event
makeTangleCreate valid and usable variables describing the start/stop...
makeYearmonto make a year format from monYr for the right whale plotting
myNameMonth-year vector used to mark time in the model
ngNumber of Gibbs steps used in the input rda file
ntLength of the modelling
plotBoxplotHealthPlot boxplots of health during entanglement and compare to...
plotHealthThresholdMake barplot of number of months below health threshold
plotSlopeHealthReturn the slope health plot as a 'gridExtra' grob
plotSurvPlot of Kaplan-Meier survival curve for all entangled whales.
plotSurvGenderSeverityPlot of Kaplan-Meier survival curve for all entangled whales.
pophealthPopulation level health of right whales
prepBoxplotHealthDataPrepare data for making the boxplots of health during...
prepHealthThresholdPlotDataAssemble the data for plotting the barplot of % below...
prephThreshDataReproAssemble health of impacted reproductively active females
prephThreshDataUnImpPrepare data frame of health in unimpacted females for %...
prepSlopeHealthDataPrepare the individual line data for slope health plot
prepSlopeHealthDataAnnotationPrepare the data for annotating the slope health plot
prepSlopeHealthDataBarplotPrepare the data for barplot portion of the slope health plot
prepSlopeHealthDataMedianPrepare the median line data for slope health plot
presDeadsurvdatData frame of survival information for presumed dead animals
returnhealthAnomReturn the right whale population level health Anomaly as a...
returnPophealthReturn the right whale population level health as a data...
returnSurvdfReturn survival data frame for testing differences in the...
returnUnimpactedHealthReturn the health data for unimpacted whales (reproductively...
tangleAllInformation about entanglement events - raw
tangledtangled: a package for analysis and plotting of effects of...
tangleOutInformation about entanglement events - filtered and modified...
tangNonReproInformation about entanglement events of non-reproductively...
tangReproInformation about entanglement events of reproductively...
winDiagramCreate a diagram showing how we extract health anomaly...
robschick/tangled documentation built on May 25, 2017, 7:39 a.m.