reportHTML.repeatedTrain: Performs Basic Spike Train Analysis and Generates a Report in...
In STAR: Spike Train Analysis with R

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/reportHTML.repeatedTrain.R

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

## S3 method for class 'repeatedTrain'
reportHTML(object, filename, extension = "html",
           directory = getwd(), Title, binSize = 0.025,
           method = c("gsspsth0", "gsspsth", "gampsth"),
           stimTimeCourse = NULL, colCI = 2,
           doTimeTransformation = TRUE, k = 100, bs = "tp",
           doGamCheck = FALSE, ...)

`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`	See `gsspsth`, `gsspsth0`, `gampsth`.
`method`	A character string, the name of the function used to generate the smooth psth, one of: `gsspsth`, `gsspsth0`, `gampsth`.
`stimTimeCourse`	See `plot.repeatedTrain` and `plot.gsspsth`, `plot.gsspsth0`, `plot.gampsth`.
`colCI`	See `plot.gsspsth`, `plot.gsspsth0`, `plot.gampsth`.
`doGamCheck`	Should function `gam.check` be used on the inhomogenous Poisson fit performed to obtain the smooth PSTH if `method` was set to `gampsth`?
`doTimeTransformation`	Should the estimated integrated intensity be used to perform a time transformation and generate Ogata's test plots?
`k, bs`	See `gampsth`.
`...`	Passed to `gsspsth`, `gsspsth0`, `gampsth`.

A raster plot is added first to the report (plot.transformedTrain) with a smooth PSTH (gsspsth, gsspsth0, gampsth.) 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 gsspsth, gsspsth0, gampsth for details. A plot of the smooth PSTH with 95% CI (approximate in the case of gampsth) is added. If doGamCheck is set to TRUE and if method is set to gampsth 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 gssanova, gssanova0 or gamObject object containing the result of the gssanova, gssanova0 or 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.

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

Christophe Pouzat christophe.pouzat@gmail.com

as.repeatedTrain, plot.repeatedTrain, summary.repeatedTrain, gsspsth, gsspsth0, gampsth, transformedTrain, plot.transformedTrain, summary.transformedTrain, gssanova, gssanova0, gam, gam.check, frt

## Not run: 
## 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))

## End(Not run)