Circular Mixed Effect Mixture Models of Animal Activity Patterns

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Documentation for package ‘activityGCMM’ version 1.1.1

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activityHPD Activity highest posterior density interval estimates (activityHPD)
activityHPDmean Activity highest posterior density interval from mean activity curve
APDatPeak Activity Probability Density at Peak Time of Another
APDpointplot Activity Probability Density Point Plot
calcAPD Calculate activity probability density
calcprop Calculate proportions of circular variable within an interval
circaxis Axis labels for circular temporal data plots
circplotHPD Circular plot of activity HPD intervals
circplotmeans Circular plot of GCMM means
circplotREs Random Effects Circular Plot
combineMCMC Combine MCMC chains for posterior simulations
comboplot GCMM Combined Plot
compareGCMM Compare GCMM parameters or estimates
compareGCMMfit Compare fit of GCMM models based on circular residuals
componentsplot GCMM Components Plot
convertRad Convert Radians Scale
exampleGCMM Executable example of GCMM function
extractparam Extract parameters for posterior simulations
GCMM Generalized circular mixed effect mixture (GCMM) model
GCMMpdens Predict activity probability density at a time point
GCMMpeaksplot Plot estimated time of activity peaks
GCMMppc Posterior predictive check of GCMM model
GCMMprob Probability of Activity during Time Period
GCMMsims Create GCMM simulations
GCMMsimsparams Extract GCMM parameters for running GCMM simulations
HDI Calculate highest density interval
HPDoverlap Activity HPD Overlap
humanssample Sample data of camera trap observations of humans
mixtureplot GCMM Mixture Plot
mode Mode
multiplot Plot multiple GCMM activity curves
PDS Posterior distribution summaries and support
peaksPDplot Plot estimated number of activity peaks
plotactivityHPD Plot activity curve with activityHPDs
plotGCMMsamples Plot GCMM Activity Curve Posterior Samples
plotREs Plot GCMM activity curve with random intercepts
posteriorhistplot Plot histogram of posterior distribution
progress Report function progress
redfoxsample Sample data of camera trap observations of red fox
samplerows Sample rows of dataframe
sumCircResids Calculate sum of absolute circular residuals
updateGCMM Extend GCMM analysis
xaxis Axis labels for temporal activity plots
yMax Calculate y-axis limit for plotting multiple activity curves