Performs Basic Spike Train Analysis and Generates a Report in HTML Format from a repeatedTrain Object

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Description

Performs a "standard" analysis on a repatedTrain object, writes results to disk and generates a report in html format.

Usage

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## S3 method for class 'repeatedTrain'
reportHTML(object, filename, extension = "html",
           directory = getwd(), Title, binSize = 0.025,
           k = 100, bs = "tp", stimTimeCourse = NULL,
           colCI = 2, doGamCheck = TRUE,
           doTimeTransformation = TRUE, ...)

Arguments

object

a repeatedTrain object.

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.

binSize, k, bs

See spsth.

stimTimeCourse

See plot.repeatedTrain and plot.spsth.

colCI

See plot.spsth.

doGamCheck

Should function gam.check be used on the inhomogenous Poisson fit performed to obtain the smooth PSTH?

doTimeTransformation

Should the estimated integrated intensity be used to perform a time transformation and generate Ogata's test plots?

...

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

Details

A raster plot is added first to the report (plot.transformedTrain) with a smooth PSTH (spsth) superposed. The summary of the inhomogenous Poisson fit leading the smooth PSTH is added next together with a short summary describing how accurate the hypothesis of constant intensity/rate made during the pre-processing of the repeatedTrain was in view of the estimated rate. Check spsth for details. A plot of the smooth PSTH with approximate 95% CI is added. If doGamCheck is set to TRUE a diagnostic plot for the fitted inhomogenous Poisson model is added. If doTimeTransformation is set to TRUE the estimated integrated intensity is used to perform a time transformation and Ogata's test plots are generated.

A R data file (filename.rda) is also generated with the following objects:

  • PoissonF: the gamObject containing the result of the gam fit with the inhomogenous Poisson model.

  • Lambda: the integrated intensity of repeatedTrain under the inhomogenous Poisson model hypothesis. If doTimeTransformation was set to TRUE.

  • fct: the matched call.

Value

Nothing is returned, an html file and figures in png format are written to disk together with the R variables generated during the analysis.

Author(s)

Christophe Pouzat christophe.pouzat@gmail.com

See Also

as.repeatedTrain, plot.repeatedTrain, summary.repeatedTrain, spsth, transformedTrain, plot.transformedTrain, summary.transformedTrain, gam, gam.check, frt

Examples

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## load e070528citronellal data set
data(e070528citronellal)
## make a standard analysis on the first neuron
reportHTML(e070528citronellal[["neuron 1"]],"e070528citronellalN1",stim=c(6.14,6.64))

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