| reportHTML.repeatedTrain {STAR} | R Documentation |
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
## 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))