done and we are confident about the
robustness of this new functionality we will post the package to CRAN.
Happy mixing, Ingmar Visser & Maarten Speekenbrink
Ingmar Visser
Universitair Hoofddocent ontwikkelingspsychologie | Directeur College
Psychologie
Afdeling Psychologie | Faculteit Maatsch
There are several packages that allow fitting hidden Markov models
(assuming that that is what you mean by HMM ...), which you can find here:
https://cran.r-project.org/web/packages/
Best, Ingmar
Ingmar Visser
Universitair Hoofddocent ontwikkelingspsychologie | Directeur College
Psychologie
gamlss.mx can fit these I believe (although no experience with these myself)
flexmix may be (relatively easily) adaptable to accomplish this as well
hth, Ingmar
Ingmar Visser
Universitair Hoofddocent ontwikkelingspsychologie | Directeur College
Psychologie
Afdeling Psychologie | Faculteit
Searching on r-project for bayesian hidden Markov model gives several
potentially useful links:
https://www.google.com/search?q=bayesian+hidden+markov+modeldomains=r-project.orgsitesearch=r-project.orgbtnG=Google+Search
hth, Ingmar
On Fri, May 23, 2014 at 12:09 PM, Bukar Alhaji
Hi Johannes,
Below code gives good results for me; note that trying multiple
starting is often important in fitting mixture models, even in simple
cases like this.
Note also that the sigma and nu parameters in gamlssMX are fitted on a
log scale, hence the possible occurrence of negative results.
I get this error below, there seems to be hidden character in your
input instead of a parenthesis:
for(ity in 1:4)
+ {
+ if (ity==1）
Error: unexpected input in:
{
if (ity==1Ô
{
+ print(ity)
+ }
Error in print(ity) : object 'ity' not found
}
Error: unexpected '}' in }
hth, Ingmar
On Thu,
On Wed, Oct 16, 2013 at 8:30 PM, Curtis Burkhalter
curtisburkhal...@gmail.com wrote:
I try to use the mle2 function written for R. The error message states
that the argument minuslog1 is missing with no default, but I've
The argument is minuslogl
Note: l instead of 1
hth, Ingmar
Package news (see below for general description of functionality)
depmixS4 version 1.3-0 has been released on CRAN. See the NEWS file
for an overview of all changes. The most important user-visible
changes are:
1) more compact pretty-printing of parameters in print/summary of
(dep)mix objects
Robin,
On Wed, Apr 24, 2013 at 11:24 AM, Robin Tviet robintv...@outlook.comwrote:
I am trying to understand how to use the flexmix package, I have read the
Leisch paper but am very unclear what is needed for the M-step driver. I
am just fitting a simple linear regression model. The
It seems that indeed providing other starting values initiates iterations
to take place. However, more worrisome is that the does not seem to
converge, even when upping the number of iterations. Below I run a 2 state
model on the same as well for comparison (I have added set.seed statements
to
It's hard to answer these questions without knowing what the errors are and
how they can be reproduced.
Best, Ingmar
On Thu, Nov 22, 2012 at 1:03 AM, KitKat katherinewri...@trentu.ca wrote:
Thanks, I have been trying that site and another one
(http://www.statmethods.net/advstats/cluster.html)
Dear KitKat,
After installing R and reading some introductory material on getting
started with R you may want to check the CRAN task view on cluster analysis:
http://cran.r-project.org/web/views/Cluster.html
which has many useful references to all kinds and flavors of clustering
techniques,
Dear EJ,
The depmixS4 package has no forecasting or predict functions, but as you
note, the forecast distribution is a relatively straightforward function of
the parameters. The posterior function provides you with the probability
distribution over the states at the end of your sequence and the
R-site search with 'forward backward' returns references to packages for
fitting hidden Markov models.
hth, Ingmar
https://www.google.com/search?q=forward+backwarddomains=r-project.orgsitesearch=r-project.orgbtnG=Google+Search
On Wed, Oct 31, 2012 at 3:50 PM, quantum quan...@live.dk wrote:
Hi John,
I don't have access to R right now but do remember that some of the
parametersin gamlss have log and/or logit link functions which would give the
possibility for negative values.
Hth, Ingmar
Department of Psychology
University of Amsterdam
Op 11 Sep 2012 om 21:01 heeft John Kerpel
use str(dentistry.lca2) to see all values of the output; among them a value
np for number of parameters, in this case 5*2 for the 5 binary items of 2
classes + 1 for the class proportions, total 11.
hth, Ingmar
On Mon, Aug 27, 2012 at 6:05 PM, Gabriele Accetta
gabriele.acce...@gmail.com wrote:
It's fine. Just interpret them as you would any other (lower is better).
And it is the printed logLik that is out of step here. log-likelihoods
_should_ be negative.
That is not quite the case; in models with small variances log-likelihoods
can easily become positive, consider eg:
Lee,
A working, or in this case failing, example is necessary to detect what the
problem is.
This would include a statement loading the package that you use to run your
mlogit models; the latter is necessary because there are various packages
with functions that are called mlgoit.
Best, Ingmar
On
hard to judge what the problem is without an example and without the actual
error message that mlogit (which one? there are several functions with that
name in various packages) gives you.
best, Ingmar
On Mon, Jul 30, 2012 at 11:30 AM, Lee van Cleef l.van.cl...@gmx.net wrote:
Dear all,
does
this (untested):
x[x23.65] - 0
x[x23.65] - 1
will give you the markov state sequence and the transition matrix follows
from that.
hth, Ingmar Visser
On Fri, Jul 27, 2012 at 8:52 PM, cesare orsini cast...@hotmail.it wrote:
Dear Users,
i have this time series, the tree lines means different level, i
[plug to follow]
depmixS4 fits hidden/latent Markov models on (mixed mode) multivariate
longitudinal data (and it can be found on the cluster task view).
hth, Ingmar
On Thu, Jun 14, 2012 at 1:12 PM, ya xinxi...@163.com wrote:
Hi all,
I have a question, is there any R package dealing with
Deepak,
On Wed, May 2, 2012 at 7:53 AM, deepakw deepakwarr...@gmail.com wrote:
Hi I am trying to use depmixS4 package. Based on the documentation, it
seems
that depmix allows one to fit an HMM model based on a training data with
time-varying co-variates. However, I did not find any routines
(rt~1,corr~1),data=speed,transition=~Pacc+x2,nstates=2,
family=list(gaussian(),multinomial(identity)),ntimes=c(168,134,137))
set.seed(3)
fmod1 - fit(mod1)
Above code produces sensible results.
Hth, Ingmar Visser
On Fri, Apr 20, 2012 at 5:14 AM, nglthu ngl...@gmail.com wrote:
Dear helpers
Look into Sweave or knitr to combine R and LaTeX for producing reports.
hth, Ingmar
http://www.statistik.lmu.de/~leisch/Sweave/
https://github.com/yihui/knitr
On Sun, Apr 1, 2012 at 4:48 PM, Manish Gupta mandecent.gu...@gmail.comwrote:
Hi,
I am newbie in Latex and R. I am working on one
?strptime is a good place to start
hth, Ingmar
On Wed, Feb 22, 2012 at 2:09 PM, arunkumar akpbond...@gmail.com wrote:
Hi
My data looks like this
startDate=2008-06-01
dateRange =c( 2008-10-01,2008-12-01)
Is there any method to find the week number from the startDate range
-
?clusters tells you how to get class membership for new data
(and the appropriate way of getting cluster membership is to use
clusters(newModel) rather newModel@clusters)
hth, Ingmar
On Tue, Feb 7, 2012 at 8:48 AM, loyolite270 loyolite...@gmail.com wrote:
Hi
I built a flexmix GLM binomial
binomial coeffecients can be computed using ?choose
hth, Ingmar
On Wed, Dec 28, 2011 at 10:42 AM, Jason J. Pitt pit...@uchicago.edu wrote:
Hi Matilda,
My ignorance of the mathematical properties of Pascal's
Triangle might make me overlook a much easier way to do this,
but my first brute
Claus,
Given that you have observed the hidden states they are not really hidden
anymore ... so maybe an HMM is not what you are looking for.
Assuming that you had such super observation powers using something like:
by(obs,hid,table)
will get you the state dependent counts of the categories of
I did not quite get what the problem was from your description ...
However, I did search on CRAN and found at least two packages that can fit
markov switching ar models so that may be an easier way to go.
Hth, Ingmar
On Thu, Dec 1, 2011 at 5:58 PM, napps22 n.j.app...@gmail.com wrote:
Dear R
Searching: time series forecasting
on the R website gives quite a few potentially useful options.
hth, Ingmar
On Wed, Nov 16, 2011 at 1:55 PM, Aher ajit.a...@cedar-consulting.comwrote:
I have a data with the sequence of events with millions records and more
than
24 time stamped variables.
Th CRAN taskview on clustering has many clustering and mixture packages
which
may be useful for your precise situation:
http://cran.r-project.org/web/views/Cluster.html
hth, Ingmar
On Thu, Nov 10, 2011 at 7:41 PM, Dan Abner dan.abne...@gmail.com wrote:
Hello everyone,
Can anyone suggest a
Dear Edward,
Without knowing what you want exactly, it is basically impossible to help
you out.
The following code (with simulated data) works just fine. In what sense did
you not have success with HMM and/or depmixS4?
Best, Ingmar
library(HMM)
dat -
something like this:
sapply(strsplit(as.character(
f1$keyword), ), function(x){sum(nchar(x))})
hth, Ingmar
On Fri, Jun 10, 2011 at 6:48 PM, Abraham Mathew abra...@thisorthat.comwrote:
I'm trying to find the total number of letters in a row of a data frame.
Let's say I have the following
function ?stepFlexmix in the flexmix package may be what you're looking for
hth, Ingmar
On Mon, May 23, 2011 at 11:21 PM, Daniel Malter dan...@umd.edu wrote:
Hi,
I perform latent class analysis on a matrix of dichotomous variables to
create an indicator of class/category membership for each
depmixS4 can fit equality constraints in latent class and latent markov
models, best, Ingmar
On Wed, May 11, 2011 at 1:04 PM, David Duffy dav...@qimr.edu.au wrote:
I don't know of any R package that can match all the functionality of LEM
eg fitting equality constraints to model parameters a la
poLCA is an option, as is randomLCA, flexmix, and depmixS4, and there are
likely to be more
What specific models are you interested in?
Best, Ingmar
On Fri, May 6, 2011 at 6:13 AM, Wincent ronggui.hu...@gmail.com wrote:
I guess LEM is a software for latent class analysis. If so, you may
want
Michael,
It's not entirely clear what you are doing from the text (and the code is
incompplete), so just a few remarks.
I assume you are after the log likelihood rather than the likelihood
(otherwise the issue of positive/negative would not show up, dnorm always
returns positive numbers).
Taking
package msm has some examples with this type of type, ie modeling disease
state transitions in continuous time, using multi-state markov models.
hth, Ingmar
On Thu, Mar 24, 2011 at 6:22 PM, Rasanga Ruwanthi ruwanthi_...@yahoo.comwrote:
Dear List,
I have some longitudinal data, each patient
lavaan, sem, openMx all do this (there may be others)
hth, Ingmar
On Fri, Mar 11, 2011 at 8:26 AM, rvohen bingbingzhan...@126.com wrote:
In R software,does it have packages about confirmatory factor analysis in R
software? 3Q
--
View this message in context:
FWIW, the style for JSS now enforces (via Achimitization) the use of quotes
as you show above.
An excellent candidate for the fortunes package!
best, Ingmar
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
typing 'markov switching' into the R site search box gives 127 results,
certainly a few of which on the first page are possibly of interest to you.
among them packages MSBVAR and bayesGARCH
hth, best, Ingmar
On Sat, Feb 12, 2011 at 12:53 PM, Nanda Mendez nand...@hotmail.com wrote:
I'm looking
The ML estimate of lambda is the mean, so no need for (iterative)
optimization. See eg:
http://mathworld.wolfram.com/MaximumLikelihood.html
hth, Ingmar
On Fri, Feb 11, 2011 at 8:52 AM, Antje Niederlein niederlein-rs...@yahoo.de
wrote:
Hello,
I tried to fit a poisson distribution but looking
Daniel,
searching for 'latent class analysis' on
http://www.r-project.org/search.html
gives many results: the CRAN taskviews on psychometrics and the one on
clustering both contain relevant links to packages that may do what you are
looking for.
In particular, for general LCA there is package
Sebastian,
There is a number of packages that fit hidden (or latent) Markov models
which are in most regards identical to latent transition analysis.
Best, Ingmar
2011/1/24 Sebastián Daza sebastian.d...@gmail.com
Hi everyone,
Does anyone know if there is a package to run Latent Transitional
Steffen,
Consider the input you have given to range:
1e-9:1
[1] 1e-09 1e+00
versus
1e-9:1e-3
[1] 1e-09
hth, Ingmar
On Wed, Nov 10, 2010 at 10:00 AM, Steffen Uhlig
steffen.uh...@htw-saarland.de wrote:
Dear mailing list readers!
Using R and the plot function I stumbled over this little
Penny,
The ?makeDepmix page has an example of how to add your own response
distribution model.
hth, Ingmar
On Fri, Oct 22, 2010 at 3:08 PM, Penny Adversario pen...@yahoo.com wrote:
I am running a latent class regression with 3 nominal and 2 ordinal
variables using depmixS4 but the available
Software http://www.jstatsoft.org/v36/i07 which is also included as a
vignette http://cran.r-project.org/web/packages/depmixS4/index.html
The development version of depmixS4 can be found on the R-forge site:
https://r-forge.r-project.org/projects/depmix/
best, Ingmar Visser Maarten Speekenbrink
The sem package may be what you are looking for, hth, Ingmar
On Thu, Aug 26, 2010 at 9:24 PM, David Joubert jo...@hotmail.com wrote:
Hello all-
Just wondering if anyone has heard of a package performing latent factor
analysis, similar to what is done with LatentGold. I know that PoLCA does
Martin,
On Wed, Aug 25, 2010 at 10:17 AM, Loos, Martin martin.l...@eawag.ch wrote:
Good afternoon!
It may seem trivial to some/most of You, but I found it difficult to
properly include a C++-based .dll into a package that I want to build for
usage in R. I read through the Writing R
Donald,
Mixed types are handled in flexmix and in depmixS4, not sure about ordinal
in flexmix (depmixS4 does not handle ordinal but does handle multinomial,
constraints may be an
option to deal with ordinal); both have glm distributions, ie gaussian,
binary and many
others.
Best, Ingmar
On Sat,
depmixS4 can fit such models as a constrained latent markov mdoel,
best, Ingmar
On Fri, Jul 9, 2010 at 7:52 PM, Katherine Sanders
sanders@buckeyemail.osu.edu wrote:
Does anyone know how to program mover stayer models in R? They are a type
of Markov chain model where there is a group of
The objective function, scarti, needs a vector as input and not 4 separate
arguments.
constrOptim will call
pp- c(0.0088,0.3339,0.3092,1.7530)
scarti(pp)
which produces the error
hth, Ingmar
On Thu, Mar 4, 2010 at 10:27 AM, barbara.r...@uniroma1.it wrote:
I have to calculate the value of a
Samor,
A somewhat indirect answer: you could fit a mixture distribution to your
data and test
how many components are needed to best describe your data.
hth, Ingmar
On Wed, Feb 24, 2010 at 1:22 PM, Samor Gandhi samorgan...@yahoo.com wrote:
Hello,
Is there any test for bimodality in R that
Dear Mark,
I don't know whether it has ... But there are some packages that provide
functionality for
specifying mixtures of user-defined distributions, in your case a factor
model. package
flexmix has an example of how to fit mixtures of user-defined models and so
does
my own package depmixS4
Jon,
There are packages that fit mixtures of multivariate normals (mclust) and in
flexmix
one can also model multiple measures (with local independence assumption).
hth, Ingmar
On Fri, Jan 15, 2010 at 11:08 AM, Jon Toledo tintin...@hotmail.com wrote:
Iæe several packages for latent class
Dear Susanne Dave,
The gamlss package family has an enormous variety of distributions and
a function to combine
them into mixtures. In particular, the 3 parameter student's t and the
4 parameter generalized t
distribution.
Hth, Ingmar
On 15 Jun 2009, at 17:12, David Hunter wrote:
Hi
try issueing this before calling R CMD check
export _R_CHECK_CODOC_S4_METHODS_=true
hth, Ingmar
On 9 Jun 2009, at 16:17, Christophe Genolini wrote:
Hi the list,
I build a package. They was a mistake in it, but R CMD check did not
find it. Is that normal ?
Here is what Kurt gets (which
Dear Rita,
The depmixS4 package handles such models. It is still in beta testing
so I would
appreciate it if you share your experiences with it. Also let me know
if you have
further questions.
Best, Ingmar
On 16 Mar 2009, at 10:19, Rita Gaio wrote:
Dear R users,
I want to apply latent
dependencies over time into account by specifying a
transition matrix.
Similarly, there are other packages that fit similar models, searching
for hidden markov model provides a number of them.
hth, Ingmar Visser
On 12 Mar 2009, at 23:39, Prew, Paul wrote:
Hello All,
Does anyone know of a package
not match the length of object [100]
In addition: Warning message:
In resid * wt^0.5 :
longer object length is not a multiple of shorter object length
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
, Prof Brian Ripley wrote:
Weights are not supported: multistratum aov is designed for
balanced designs and uses projection for which weighting is
inappropriate.
On Wed, 17 Dec 2008, Ingmar Visser wrote:
Dear R-help,
I'm facing a problem with defining a repeated measures anova
originale-
Da: [EMAIL PROTECTED] per conto di Ingmar Visser
Inviato: mer 12/11/2008 15.10
A: Maura E Monville
Cc: r-help@r-project.org
Oggetto: Re: [R] choice of an HMM package
Dear Maura,
On 9 Nov 2008, at 02:24, Maura E Monville wrote:
We are trying to build a human respiration model
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
?by may be helpful here
eg if dat is your data.frame and yf is a factor (created using ifelse)
use by(dat,yf,mean) to compute the means for each level of yf
hth, Ingmar
On Jun 3, 2008, at 8:37 PM, Marvin Lists wrote:
Hi,
I have a data frame that I want to split into two based on the
values
://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
[[alternative HTML version deleted
rle(diff(sq)) could be helpful here,
best, Ingmar
On May 13, 2008, at 11:19 PM, Marko Milicic wrote:
Hi all R helpers,
I'm trying to comeup with nice and elegant way of detecting
consecutive
increases/decreases in the sequence of numbers. I'm trying with
combination
of which() and diff()
, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
[[alternative HTML version deleted]]
__
R
/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
The CRAN task view on cluster and mixture models likely has what you
need.
hth, Ingmar
http://cran.r-project.org/web/views/Cluster.html
On Apr 10, 2008, at 11:20 PM, Antonio Olinto wrote:
Hello,
I'm analyzing some fish length-frequency data to access relative
age and growth
information
I have a problem concerning discrepances between R (which I use) and
Statistica (which uses my supervisor).
---
can this be submitted as a fortune?
any other programs around that use supervisors, it's always good to
have a couple of
those around
ingmar
:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] spatial_7.2-40 RUnit_0.4.17 MASS_7.2-40 robustbase_0.2-8
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20
, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
[[alternative HTML version deleted]]
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8819 4402
Home Phone: +61 7 3286 7700
mailto:[EMAIL PROTECTED]
http://www.cmis.csiro.au/bill.venables/
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org]
On Behalf Of Ingmar Visser
Sent: Thursday, 27 March 2008 7:58 AM
To: R-help@r
Hi,
I need to compute an array from a matrix and an array:
A - array(1:20,c(2,2,5))
B - matrix(1:10,5)
And I would like the result to be an array consisting of the following:
rbind(A[1,,1]*B[1,],
A[2,,1]*B[1,])
rbind(A[1,,2]*B[2,],
A[2,,2]*B[2,])
rbind(A[1,,3]*B[2,],
A[2,,3]*B[2,])
etc.
Hi,
I've been searching CRAN and the web for a recursive multivariate
filter with time-varying coefficients.
What I mean is the following:
I have a series of square matrices A_t
an initial value vector y_0
and I need to compute
y_t =A_t%*%y_t-1
As these y_t may diverge quickly and/or lead
-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
[[alternative HTML version deleted
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat
PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
[[alternative HTML version
read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
Ingmar Visser
Department of Psychology, University of Amsterdam
Roetersstraat 15
1018 WB Amsterdam
The Netherlands
t: +31-20-5256723
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