Spike Train Analysis with R


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Documentation for package ‘STAR’ version 0.3-7

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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