Displaying 20 results from an estimated 300 matches similar to: "drawing hmms"
2013 Sep 02
1
Multivariate discrete HMMs
Hi r-help,
I have been using your RHmm package for some time and have recently
had to try using the package for a new dataset.
Basically I have a dataset with a number of discrete observation
variables that change over time, and I would love to try modeling them
using a HMM.
Basically I was wondering if RHmm can be used to model a multivariate
discrete HMM, i.e., the observations are a vector
2011 Dec 19
1
Training parameters for a HMM
Hi,
I'm a newbie to the world of HMMs and HMMs in R. I've had a look at
the hmm package and the RHmm package but I couldn't see anything
straightforward on how a labelled sequential dataset with observed
values and underlying states might be used to construct and train a
HMM based on that data and no pre-computed values for the transition,
emission or initial state distributions. Does
2013 Apr 16
1
HMM Package parameter estimation
Hi,
I am having difficulties estimating the parameters of a HMM using the HMM
package. I have simulated a sequence of observations from a known HMM. When
I estimate the parameters of a HMM using these simulated observations the
parameters are not at all close to the known ones. I realise the estimated
parameters are not going to be exactly the same as the known/true
parameters, but these are
2009 Aug 06
2
Convert dataframe to table with counts where column names become row names
Can anyone explain how best to go from a dataframe to a table (or better yet
a new dataframe) of counts, where the row names in the new table (or
dataframe) are the column names of the original df.
start w/
DF1 =
Pos1 Pos2 Pos3 ....
oligo1 G C A
oligo2 U U A
oligo3 G C C
oligo4 C G U
oligo5 A A G
.....
End with
DF2 =
2012 Feb 17
5
How to change the order of columns in a data frame?
Dear all,
I have a data frame in which the columns need to be ordered. The first column X is at the right position, but the remaining columns X1-Xn should be ordered like this: X1, X2, X3 etc instead of like below.
> colnames(pos1)
[1] "X" "X1" "X10" "X11" "X12" "X13" "X14" "X15" "X16"
2001 Nov 29
2
plotting (a) confidence intervals (b) standard error
Hi all,
I'm building a plot of the values in tmeant (below) against positions 1 to
5, using matplot.
tmeant looks like this:
case1 case2
pos1 861.8466 818.5909
pos2 961.2841 976.3466
pos3 878.6080 1262.8523
pos4 950.8011 1129.6080
pos5 968.1080 1063.3920
I also have lower (object tl) and upper (object tu) bounds on the
confidence intervals as follows:
tl:
pos1
2011 Apr 19
0
RHmm, mixture of gaussians, memory could not be "read" error
Hi,
I'm trying to fit a hidden Markov model (mixture of Gaussians) to stock prices (Open, High, Low, Close) data.
Here's my code:
#First download the data with package TTR
library(TTR)
n <- 200
data <- getYahooData("GOOG", strftime(as.POSIXlt(Sys.time() - n*24*3600),format="%Y%m%d"))
keep <-
2009 Sep 04
3
Applying qqmath using gamma distribution...
Hello ALL!
Can anyone tell me how to specify qqmath() function with distribution
qgamma?
In help it is bit vague how to pass shape and scale parameters for gamma.
Thank you in advance. Best,
PM
2009 Sep 17
2
QQ plotting of various distributions...
Hello!
I am trying with this question again:
I would like to test few distributional assumptions for some behavioral
response data. There are few theories about true distribution of those
data, like: normal, lognormal, gamma, ex-Gaussian
(exponential-Gaussian), Wald (inverse Gaussian) etc. The best way would
be via qq-plot, to show to students differences. First two are trivial:
qqnorm(dat$X)
2010 Dec 02
1
Hmm Topology restriction
Dear List,
We are using RHmm to cluster data through HMM. We would like to
restrict the transition matrix of HMM, to get hierarchical connections
between clusters. But, RHmm doesn't seem to support these
restrictions. Can any one suggest a library to do that.
Thanks,
Kishor
2010 Jan 17
1
packages built against upcoming releases
I admire package-builders being proactive and having their facilities
ready for upcoming R releases. However, if the publicly released
version of R is 2.10.1 and a package is built for R 2.11.0, users get
the embarrassing notice about a disconnect, and cannot do much about it.
If it is tedious to roll out a new package on time, perhaps there's a
possibility for automation here.
Thanks. I
2010 Jul 06
1
plotmath vector problem; full program enclosed
Here's another example of my plotmath whipping boy, the Normal distribution.
A colleague asks for a Normal plotted above a series of axes that
represent various other distributions (T, etc).
I want to use vectors of equations in plotmath to do this, but have
run into trouble. Now I've isolated the problem down to a relatively
small piece of working example code (below). If you would
2008 Oct 22
1
plotting matrix
a <- c(1:26)
b <- rnorm(25)
e <- rnorm(25)
f <- rnorm(25)
g <- data.frame(b,e, a,f)
I would like to plot a agianst all possibilities and then shoot it out
to a pdf one graph per page. I think it would be okay to have this as
a lattice plot or a ggplot with many graphs per page. I can figure
all of that out I think, but I need something like
r <- as.matrix(g)
plot(.~a, data=r)
2002 Sep 10
2
Traceroute
How do I allow traceroute to reach my server? Pings work fine but
traceroute stops at the last hop before my server. If I shut off the
firewall it reaches it fine.
PING danicar.net (24.222.246.120): 56 data bytes
64 bytes from 24.222.246.120: icmp_seq=0 ttl=237 time=104.0 ms
64 bytes from 24.222.246.120: icmp_seq=1 ttl=237 time=74.9 ms
64 bytes from 24.222.246.120: icmp_seq=2 ttl=237 time=90.6
2011 Jan 14
9
Selecting the first occurrence of a value after an occurrence of a different value
Hello everyone,
I am currently working with some data where I need to select the first
occurrence of a value after the occurrence of another value.
The data has two columns, one with a time and one with occurence of certain
events.
The column of data I want to select from looks like this (and each of these
events have a corresponding time in another column).
Stat71
OutMag
FirstResp
InMag
2019 Jul 24
1
[PATCH] mm/hmm: replace hmm_update with mmu_notifier_range
On Wed, Jul 24, 2019 at 04:21:55PM -0300, Jason Gunthorpe wrote:
> If we change the register to keep the hlist sorted by address then we
> can do a targetted 'undo' of past starts terminated by address
> less-than comparison of the first failing struct mmu_notifier.
>
> It relies on the fact that rcu is only used to remove items, the list
> adds are all protected by mm
2009 Jun 30
1
Windowing issue with diagram package & R 9.1
I had strange windowing behavior with R 9.1 on Windows XP when executing code from the diagram package. Perhaps it is even normal behavior that I don't understand as it was an unintentional discovery. I don't even know if it is a package issue or a windowing issue.
Reproducing it. Execute the code fragment below from vignette(diagram) that uses par() to draw a four panel
2006 Apr 04
2
ogg + theora + seeking
Hi all,
I'm actually learning how to use ogg, theora and vorbis. My idea is to create
a small program running, that is able to concatenate ogg video+audio files.
However I have some small questions. Here I will start with the first one:
I read the following for seeking in ogg for a theora key-frame:
---- snipp (http://www.xiph.org/ogg/doc/ogg-multiplex.html) ----
[...]The third point
2009 May 25
3
Interpolating variables within (RODBC library) SQL statements for MySQL
Hi everyone,
I am desperately looking for a method to interpolate strings within an SQL
statement as follows:
I get a lot of rows out of a database (in my example POSITION_to_ZIPCODE
Database with holds records for German ZIP Code <--> Gauss-Krueger
Coordinate System ) and want this to be selected and computed individually
row by row as follows:
library(RODBC)
channel <-
2008 Nov 11
1
R: R: Hidden Markov Models
Thank you for your prompt answer.
The breathing signal observations are the amplitude values as a function of time and phase.
According to our model the hidden states are the different breathing types.
Subjects, whose respiratiion process is regular, are likely to breathe, keeping the same cycle pattern/type,
for many consecutive cycles. therefore dwelling in the same hidden state.
The more