# Spike Train Analysis with R

## Documentation for package ‘STAR’ version 0.3-4

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Code demos. Use demo() to run them.

## Help Pages

A B C D E F G H I J L M P Q R S T V W misc

STAR-package | Spike Train Analysis with R

## -- A --

acf.spikeTrain | Auto- Covariance and -Correlation Function Estimation for Spike Train ISIs
as.CPSP | Counting Process Sample Paths
as.repeatedTrain | Coerce and Test repeatedTrain Objects
as.spikeTrain | Coerce, Test and Extract from spikeTrain Objects

## -- B --

brt4df | Get Backward Recurrence Times from Data Frames Generated by mkGLMdf

## -- C --

CAL1S | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
CAL1V | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
CAL2C | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
CAL2S | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
changeScale | Change the Scales of a quickPredict Object for an Interaction Term
coef.durationFit | Utility Functions for durationFit Objects
compModels | Compare Duration Models on a Specific Data Set
contour.jpsth | Related Functions and Methods for Joint-PSTHs and Joint Scatter Diagrams
contour.quickPredict | Graphical Methods for quickPredict Objects
crossGeneral | Computations of Boundary Crossing Probabilities for the Wiener Process
crossTight | Computations of Boundary Crossing Probabilities for the Wiener Process

## -- D --

df4counts | Generates a Data Frame from a repeatedTrain Object After Time Binning
diff.spikeTrain | diff method for spikeTrain objects
dinvgauss | The Inverse Gaussian Distribution
dllogis | The Log Logistic Distribution
drexp | The Refractory Exponential Distribution

## -- E --

e060517ionon | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
e060517spont | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
e060817citron | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
e060817mix | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
e060817spont | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
e060817terpi | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
e060824citral | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
e060824spont | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
e070528citronellal | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals
e070528spont | Spike Trains of several Cockroach Antennal Lobe Neurons Recorded from Six Animals

## -- F --

frt | Computes Forward Recurrence Times from Two transformedTrain Objects

## -- G --

gamlockedTrain | Function to Smooth a lockedTrain Object and Related Methods: The Penalized Regression Spline Approach
gammaMLE | Maximum Likelihood Parameter Estimation of a Gamma Model with Possibly Censored Data
gamObj | Generic Function and Methods for Extracting a gamObject
gamObj.gamlockedTrain | Generic Function and Methods for Extracting a gamObject
gamObj.gampsth | Generic Function and Methods for Extracting a gamObject
gampsth | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Penalized Regression Spline Approach
gsslockedTrain | Function to Smooth a lockedTrain Object and Related Methods: The Smoothing Spline Approach
gsslockedTrain0 | Function to Smooth a lockedTrain Object and Related Methods: The Smoothing Spline Approach
gssObj | Generic Function and Methods for Extracting a gss object
gssObj.gsslockedTrain | Generic Function and Methods for Extracting a gss object
gssObj.gsslockedTrain0 | Generic Function and Methods for Extracting a gss object
gssObj.gsspsth | Generic Function and Methods for Extracting a gss object
gssObj.gsspsth0 | Generic Function and Methods for Extracting a gss object
gsspsth | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach
gsspsth0 | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach

## -- H --

hgamma | Hazard Functions for Some Common Duration Distributions
hinvgauss | Hazard Functions for Some Common Duration Distributions
hist.lockedTrain | Auto- and Cross-Intensity Function Estimate for Spike Trains
hllogis | Hazard Functions for Some Common Duration Distributions
hlnorm | Hazard Functions for Some Common Duration Distributions
hrexp | Hazard Functions for Some Common Duration Distributions
hweibull | Hazard Functions for Some Common Duration Distributions

## -- I --

image.jpsth | Related Functions and Methods for Joint-PSTHs and Joint Scatter Diagrams
image.quickPredict | Graphical Methods for quickPredict Objects
invgaussMLE | Maximum Likelihood Parameter Estimation of an Inverse Gaussian Model with Possibly Censored Data
is.durationFit | Utility Functions for durationFit Objects
is.repeatedTrain | Coerce and Test repeatedTrain Objects
is.spikeTrain | Coerce, Test and Extract from spikeTrain Objects
is.varianceTime | Variance-Time Analysis for Spike Trains
isi | Get Lagged Inter Spike Intervals (ISIs) From Data Frames Generated by mkGLMdf
isiHistFit | ISI Histogram With Fitted Model and CI

## -- J --

jpsth | Related Functions and Methods for Joint-PSTHs and Joint Scatter Diagrams
jpsth2df | Related Functions and Methods for Joint-PSTHs and Joint Scatter Diagrams
jsd | Related Functions and Methods for Joint-PSTHs and Joint Scatter Diagrams

## -- L --

lines.CountingProcessSamplePath | Counting Process Sample Paths
lines.FirstPassageTime | Computations of Boundary Crossing Probabilities for the Wiener Process
lines.quickPredict | Graphical Methods for quickPredict Objects
llogisMLE | Maximum Likelihood Parameter Estimation of a Log Logistic Model with Possibly Censored Data
lnormMLE | Maximum Likelihood Parameter Estimation of a Log Normal Model with Possibly Censored Data
lockedTrain | Construct and Plot Time-Dependent Cross-correlation Diagram
logLik.durationFit | Utility Functions for durationFit Objects

## -- M --

maxIntensity | Simulate and Analyse Data From a Model Fitted With gss
mkAR | Generate a Data Frame With Variables Suitable For an AR Like Model
mkCPSP | Counting Process Sample Paths
mkDummy | Generates a Data Frame of Dummy Variables for Use in gam
mkGLMdf | Formats (lists of) spikeTrain and repeatedTrain Objects into Data Frame for use in glm, mgcv and gam
mkM2U | Makes a Smooth Function Mapping a Data Frame Variable Onto a Variable Uniform on Its Definition Domain
mkMappedI | Simulate and Analyse Data From a Model Fitted With gss
mkPostSimAnalysis | Simulate and Analyse Data From a Model Fitted With gss
mkREdf | Evaluates RateEvolutions for spikeTrain Lists and Returns Data Frame
mkSelf | Simulate and Analyse Data From a Model Fitted With gss
mkSimFct | Simulate and Analyse Data From a Model Fitted With gss
mkTightBMtargetFct | Computations of Boundary Crossing Probabilities for the Wiener Process
mPK | Spike Trains of a Purkinje Cells (PC) Recorded in Control Conditions and With Bath Applied Bicuculline

## -- P --

persp.jpsth | Related Functions and Methods for Joint-PSTHs and Joint Scatter Diagrams
persp.quickPredict | Graphical Methods for quickPredict Objects
pinvgauss | The Inverse Gaussian Distribution
pllogis | The Log Logistic Distribution
plot.CountingProcessSamplePath | Counting Process Sample Paths
plot.CountingProcessSamplePath.summary | Create and Explore Counting Process Sample Path Summaries
plot.FirstPassageTime | Computations of Boundary Crossing Probabilities for the Wiener Process
plot.frt | Plots and Summarizes frt Objects.
plot.gamlockedTrain | Function to Smooth a lockedTrain Object and Related Methods: The Penalized Regression Spline Approach
plot.gampsth | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Penalized Regression Spline Approach
plot.gsslockedTrain | Function to Smooth a lockedTrain Object and Related Methods: The Smoothing Spline Approach
plot.gsslockedTrain0 | Function to Smooth a lockedTrain Object and Related Methods: The Smoothing Spline Approach
plot.gsspsth | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach
plot.gsspsth0 | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach
plot.hist.lockedTrain | Auto- and Cross-Intensity Function Estimate for Spike Trains
plot.lockedTrain | Construct and Plot Time-Dependent Cross-correlation Diagram
plot.psth | Compute and Plot Peri-Stimulus Time Histogram
plot.quickPredict | Graphical Methods for quickPredict Objects
plot.rateEvolution | Evaluates and Plots a Spike Train Firing Rate's Evolution
plot.repeatedTrain | Generate a Raster Plot
plot.spikeTrain | Display Counting Process Associated with Single Spike Train
plot.ssanova | A Plot Method for ssanova and ssanvoa0 Objects Tailored to Their Use in STAR
plot.ssanova0 | A Plot Method for ssanova and ssanvoa0 Objects Tailored to Their Use in STAR
plot.transformedTrain | Plot Diagnostics for an transformedTrain Object
plot.varianceTime | Variance-Time Analysis for Spike Trains
predictLogProb | Compute the Log Probability of a "New" Data Set Using a Fitted Model Prediction
prexp | The Refractory Exponential Distribution
print.CountingProcessSamplePath | Counting Process Sample Paths
print.CountingProcessSamplePath.summary | Create and Explore Counting Process Sample Path Summaries
print.FirstPassageTime | Computations of Boundary Crossing Probabilities for the Wiener Process
print.gamlockedTrain | Function to Smooth a lockedTrain Object and Related Methods: The Penalized Regression Spline Approach
print.gampsth | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Penalized Regression Spline Approach
print.gsslockedTrain | Function to Smooth a lockedTrain Object and Related Methods: The Smoothing Spline Approach
print.gsslockedTrain0 | Function to Smooth a lockedTrain Object and Related Methods: The Smoothing Spline Approach
print.gsspsth | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach
print.gsspsth0 | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach
print.lockedTrain | Construct and Plot Time-Dependent Cross-correlation Diagram
print.repeatedTrain | Print and Summary Methods for repeatedTrain Objects
print.spikeTrain | Print and Summary Methods for spikeTrain Objects
print.summary.repeatedTrain | Print and Summary Methods for repeatedTrain Objects
psth | Compute and Plot Peri-Stimulus Time Histogram

## -- Q --

qinvgauss | The Inverse Gaussian Distribution
qllogis | The Log Logistic Distribution
qqDuration | Quantile-Quantile Plot For Fitted Duration Distributions
qrexp | The Refractory Exponential Distribution
quickPredict | A Simple Interface to predict method for ssanova and ssanova0 objects

## -- R --

raster | Generate a Raster Plot
rateEvolution | Evaluates and Plots a Spike Train Firing Rate's Evolution
renewalTestPlot | Non-Parametric Tests for Renewal Processes
reportHTML | Generic Function for Automatic HTML Report Generation
reportHTML.gam | Generates a Report in HTML Format from a STAR gam Object
reportHTML.repeatedTrain | Performs Basic Spike Train Analysis and Generates a Report in HTML Format from a repeatedTrain Object
reportHTML.spikeTrain | Performs Basic Spike Train Analysis and Generates a Report in HTML Format from a spikeTrain Object
rexpMLE | Maximum Likelihood Parameter Estimation of a Refractory Exponential Model with Possibly Censored Data
rinvgauss | The Inverse Gaussian Distribution
rllogis | The Log Logistic Distribution
rrexp | The Refractory Exponential Distribution

## -- S --

ShallowShocks | Shallow Shocks (M >= 6.0) in OFF Tohoku Area for 1885-1980
simulate.gsspsth | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach
simulate.gsspsth0 | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach
sPK | Spike Trains of a Purkinje Cells (PC) Recorded in Control Conditions and With Bath Applied Bicuculline
STAR | Spike Train Analysis with R
summary.CountingProcessSamplePath | Create and Explore Counting Process Sample Path Summaries
summary.FirstPassageTime | Computations of Boundary Crossing Probabilities for the Wiener Process
summary.frt | Plots and Summarizes frt Objects.
summary.gamlockedTrain | Function to Smooth a lockedTrain Object and Related Methods: The Penalized Regression Spline Approach
summary.gampsth | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Penalized Regression Spline Approach
summary.gsslockedTrain | Function to Smooth a lockedTrain Object and Related Methods: The Smoothing Spline Approach
summary.gsslockedTrain0 | Function to Smooth a lockedTrain Object and Related Methods: The Smoothing Spline Approach
summary.gsspsth | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach
summary.gsspsth0 | Smooth Peri Stimulus Time Histogram Related Functions and Methods: The Smoothing Spline Approach
summary.repeatedTrain | Print and Summary Methods for repeatedTrain Objects
summary.spikeTrain | Print and Summary Methods for spikeTrain Objects
summary.transformedTrain | Summary of transformedTrain Objects

## -- T --

thinProcess | Simulate and Analyse Data From a Model Fitted With gss
transformedTrain | Performs Time Transformation of Spike Trains Fitted with glm or gam

## -- V --

varianceTime | Variance-Time Analysis for Spike Trains

## -- W --

weibullMLE | Maximum Likelihood Parameter Estimation of a Weibull Model with Possibly Censored Data

## -- misc --

%frt% | Computes Forward Recurrence Times from Two transformedTrain Objects
%qp% | A Simple Interface to predict method for ssanova and ssanova0 objects
%tt% | Time Transformation Using a gssanova Objet
[.spikeTrain | Coerce, Test and Extract from spikeTrain Objects