reportHTML.spikeTrain {STAR} | R Documentation |
Performs a "standard" analysis on a spikeTrain
object, computing some
cross-correlation statistics if additional spikeTrain
objects
are provided, writes results to disk and generates a report in html format.
## S3 method for class 'spikeTrain': reportHTML(object, filename, extension = "html", directory = getwd(), Title, forceTT = TRUE, digits = 3, timeUnit = "s", otherST, laglim = c(-0.1, 0.1), cch = c("both", "scch", "cch"), method = c("gsslockedTrain0", "gsslockedTrain", "gamlockedTrain"), doGamCheck = FALSE, k = 100, bs = "tp", nbEvtPerBin = 10, ...)
object |
a spikeTrain 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. |
forceTT |
Should a time transformation be performed and the
compModels plots be generated even if none of the six
renewal models fits the data? |
timeUnit, digits |
see summary.spikeTrain . |
otherST |
a named list of spikeTrain objects from
simultaneously recorded neurons or nothing. |
laglim |
see lockedTrain . |
cch |
if otherST is given (ie, not missing)
cross-intensity plots will be made using the neuron of
spikeTrain as a reference. Should smooth version of the
cross-intensity be computed ("scch" ), a "classical" one
("cch" ) or both ("both" ). Only the first element of
cch is used. |
method |
A character string, the name of the function used to
generate the smooth cross-correlation histograms, one of:
gsslockedTrain ,
gsslockedTrain0 ,
gamlockedTrain . |
doGamCheck |
if smooth estimates are requested and method
is set to gamlockedTrain , should function
gam.check be used on them? |
k |
see gamlockedTrain . |
bs |
see gamlockedTrain . |
nbEvtPerBin |
a number of event per bin used in a way similar to
the argument with the same name in jpsth when a bining
is used for pre-processing. |
... |
Passed to gsslockedTrain ,
gsslockedTrain0 ,
gamlockedTrain . |
A spike train plot (plot.spikeTrain
) is performed
first. The summary (summary.spikeTrain
) is computed next
and part of its output is written to the html file. The renewal tests
are then carried out and their results added
(renewalTestPlot
). The six duration distributions are
fitted (compModels
with argument plot
set to
FALSE
) and the best one is used to apply a time transformation
to spikeTrain
. The Ogata's tests are applied
(summary.transformedTrain
) and if they are all within
the 99% confidence interval, the result of the transformation is
plotted (plot.transformedTrain
) as well as all the Q-Q
plots of compModels
. If forceTT
is set to
TRUE
(default), then these last two plots are added even if the
best model does not pass the tests.
If other spikeTrain
objects are provided as a named list via
argument otherST
, then cross-correlation/cross-intensity
functions are estimated; Two estimations methods are available, the
classical histogram and a smooth version of it. Argument cch
controls if a single estimation is performed or if both are
performed. If the smooth version is requested a summary of the
gssanova
, gssanova0
or
gam
fit is printed (depending on the chosen value
for argument method
). Moreover if argument
doGamCheck
is set to TRUE
(and if method
is set
to gamlockedTrain
) then check plots
(gam.check
) are added to the report.
A R
data file (filename.rda
) is also generated with the
following objects:
cm
: the result of compModels
.
bestFit
: the durationDistribution
object
returned obtained by fitting the best model among the 6.
Lambda
: the integrated intensity of spikeTrain
with the best model.
fct
: the matched call.
cchL
: if other trains were provided and if argument
cch
was set to "both"
or to "cch"
. A list with
as many components as the otherST
argument. Each component is
the a hist.lockedTrain
object.
scchL
: if other trains were provided and if argument
cch
was set to "both"
or to "scch"
. A list with
as many components as the otherST
argument. Each component is
the a gsslockedTrain
, gsslockedTrain0
or
gamlockedTrain
object.
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.spikeTrain
,
plot.spikeTrain
,
summary.spikeTrain
,
renewalTestPlot
,
plot.spikeTrain
,
compModels
,
transformedTrain
,
plot.transformedTrain
,
summary.transformedTrain
,
gssanova
,
gssanova0
,
gam
,
gam.check
,
lockedTrain
,
gsslockedTrain
,
gsslockedTrain0
,
gamlockedTrain
## load e070528spont data set data(e070528spont) ## perform a standard analysis on neuron 1, looking for cross-correlations ## with the 3 other neurons up to lag +/- 250 ms. ## Store the results under the generic name: e070528spontN1 reportHTML(e070528spont[["neuron 1"]],"e070528spontN1",otherST=e070528spont[-1],laglim=c(-1,1)*0.25,forceTT=FALSE) ## Neuron 1 of e070528spont is exceptional in that it can be well ## described by a renewal process...