Generates a Report in HTML Format from a STAR gam Object

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Description

Writes the result of a gam fit in an html file.

Usage

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## S3 method for class 'gam'
reportHTML(object, filename, extension = "html",
           directory = getwd(), Title,
           neuron, neuronEvts, ...)

Arguments

object

an object returned by gam.

filename

a character string. The generic name of all the files (html, png as well as R data files which will be generated. See also HTMLInitFile.

extension

see HTMLInitFile.

directory

the full or relative path to the directory where the results are going to be stored. See also HTMLInitFile.

Title

See HTMLInitFile. If missing a default value baed on filename is provided.

neuron

a character string describing to which the analysis refers and used for the titles of the interaction plots (see plot.frt).

neuronEvts

a named list with the event variable from the data frame returned by mkGLMdf and corresponding to the other neurons recorded simultaneously. One list element per neuron.

...

Not used, only there for compatibilty with the generic method definition.

Details

A summary (summary.gam) of object is added to the report. A plot of the spike train after time transformation transformedTrain comes next followed by a renewal test plot (renewalTestPlot) of the spike train on the time transformed scale. The "usual" Ogata's tests plots (plot.transformedTrain) are added. Then if other trains are provided as a named list via argument neuronEvts, interactions plots (plot.frt) are built showing both the survivor function and the Berman's test. The report ends with the call which generated object.

Value

Nothing is returned, an html file and figures in png format are written to disk.

Author(s)

Christophe Pouzat christophe.pouzat@gmail.com

See Also

mkGLMdf, gam, gam.check, frt, transformedTrain, plot.transformedTrain, summary.transformedTrain

Examples

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## Not run: 
## load e070528spont data set
data(e070528spont)
## make a data frame for gam using a 2 ms bin width 
spontDF <- mkGLMdf(e070528spont,0.002,0,60)
## make data frames specific of each neuron
n1.spontDF <- spontDF[spontDF$neuron=="1",]
n2.spontDF <- spontDF[spontDF$neuron=="2",]
n3.spontDF <- spontDF[spontDF$neuron=="3",]
n4.spontDF <- spontDF[spontDF$neuron=="4",]
## save space by removing the now redundant spontDF
rm(spontDF)
## fit neuron 1 using the gam representation of a
## renewal process and a binomial model
n1.spontFit1 <- gam(event ~ s(lN.1,k=25,bs="cr"),data=n1.spontDF,family=binomial())
## create a list with the discretized spike times of the 3 other neurons
preN1 <- list(n2=with(n2.spontDF,event),n3=with(n3.spontDF,event),n4=with(n4.spontDF,event))
## generate the report
reportHTML(n1.spontFit1,"e070528spontN1gFit",neuron="1",neuronEvts=preN1)

## End(Not run)

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