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))