similar to: how to permute, simulate Markov chain

Hi all, I was hoping somebody may know of a function for simulating a large binary sequence (length >10 million) using a (1st order) markov model with known (2x2) transition matrix. It needs to be reasonably fast. I have tried the following; mc<-function(sq,P){ s<-c() x<-row.names(P) n<-length(sq) p1<-sum(sq)/n s[1] <- rbinom(1,1,p1); for ( i in 2:n){ s[i]

Hi, Does anybody know a function to simulate a Markov chain given a probability transition matrix and an initial state ? Thanks. Philippe -- -------------------------------------------------- Philippe Hup? Institut Curie - Equipe Bioinformatique 26, rue d'Ulm - 75005 PARIS France +33 (0)1 42 34 65 29 Philippe.Hupe at curie.fr <mailto:Philippe.Hupe at curie.fr>

Hello, can any one point me to R-packages (if available) which include spatial Markov Chain methods? My second question is more general but hopefully not OT: Currently we are using the software TPROGS, which let people simulate property distributions in space by some Markov Chain approaches. We face some problems due to the lack of information between distances of samples along borehole path

Hello all, I am currently attempting to replicate data from a political science article that utilized a Markov chain transition model to predict voter turnout intention at time *t*; the data was separated into two different models based on whether prior intent was to vote or not to vote. The details don't really matter. Mostly I am curious how to run a Markov chain transition model in R,

Dear help group, Just fyi a markov chain is a sequence of transitions between states (say A,T,G,C - on a gene) with a given probability for each transition. In this case there'd be 16 different kinds, each with a different weight. Given a transition matrix (4x4) filled with all transition probabilities of course, how can I generate a random sequence of a given length, say 200?

Dear experts, I have to generate 1000 transitions of a discrete time Markov Chain and then give and estimation of the equilibrium distribution. I know the transition matrix. 0.3 0.7 0 0.2 0.5 0.3 0 0.4 0.6 Do you know how to do it with R? Thanks a lot! Estefania [[alternative HTML version deleted]]

Hello, my question is if anyone has any good ideas how to create a Markov Chain from ordered data. So, I have some sort of time series, and if value1 happens as time1 and value2 happens at time2 I record this as an update to the probability transition matrix. The problem is that I cannot predefine the size of the matrix (as I don't know how many states(values) I will have in the end) and

Does anyone have any "R" code for computing the entropy of a simple first or second order Markov chain, given a transition matrix something like the following (or the symbol vector from which it is computed)? AGRe ARIe CSRe DIRe DSCe eos HRMe SPTe TOBe AGRe 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000

I have the following data of continuous time Markov chain. Time - [1] 0.00000000 0.01219893 0.35903929 0.69378720 0.77247183 1.56008543 [7] 1.80607724 2.59023990 2.87196272 3.05311707 3.14737319 3.20758500 [13] 3.26668915 3.42428440 3.53324567 3.83668537 3.96784473 4.17196149 [19] 4.29982361 4.46163281 4.78519834 5.20381355 5.65441135 5.78623851 [25] 6.07602075 6.10351864 6.37001057 6.62859413

I'm testing some different formulations of pairwise interaction point processes in Spatstat (version 1.11-6) using R 2.5.0 on a Windows platform and I wish to simulate them using the Metropolis-Hastings algorithm implemented with Spatstat. Spatstat utilizes Fortran77 code with the preprocessor RatFor to do the Metropolis-Hastings MCMC, but the Makefile is more complicated than any I have

Hello, My name is Maria, MBA student in Sanfransisco, USA. In my credit scoring class, I have hard time making "transition matrix", which explains probability especially in relation to "Markov chain model". It is regarding people's monthly credit payment behavior. Does R have function to caculate it? I am actually a novice in using 'R'. Please help me!!! Maria

Could anyone tell me where can I find some examples of the applications to economics of a Markov chain? Many thanks in advance. Luis Rivera. -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not

Hi, I am trying to write a simulation of the movements of four animals between six patches. The movement between patches is based on a first-order Markov chain so that the next patch they visit depends on the patch they were in before. I have written code that allows me to simulate the movement of one animal but when I add more there seems to be a problem and all chains come back as N/A. I can

I need to find a computationally simple process for the movement of interest rates. In this simplified model, an interest rate can have 3--5 possible values, and its movement is characterized by a matrix of transition probabilities (ie, it is a Markov process). I would like to estimate this process from a given set of data. For example, let the interest rate time series be: 7 3 8 2 5 9 6

Dear R users, I am working on allocating the rows within a dataframe into some factor levels.Consider the following dataframe: Start.action Start.time 1 Start.setting 2010-12-30 17:58:00 2 Start.setting 2010-12-30 18:40:00 3 Start.setting 2010-12-31 22:39:00 4 Start.setting 2010-12-31 23:24:00 5

Good evening I often have as output from simulations a list of various values, vectors and matrices. Supposing that I then run said simulation several times, I often want to extract a particular result from each simulation for plotting and, ideally, put it in a matrix. A simple example v1 <- 1:5 v2 <- 6:10 other1 <- "stuff" other2 <- "stuff" set1 <-

Dear R users, I'd like to change the default order of colors & line types. Especially I am using ggplot2 and using color Set1. In Set1, the default color order is red, blue, green, violet,.. ect. However, I want to put red in fourth (not first). Likewise, I want to change the order of default linetype. I want to put "solid" line in fourth. How can I do thses? R code to draw the

Colleagues, (R: 2.13.0; OS X) I often receive sequential datasets in which there are new rows interposed between existing rows. For example: SET1 <- data.frame(list(LETTERS=LETTERS[c(1:4, 6:10)], NUMBERS=c(1:4, 6:10))) SET2 <- data.frame(list(LETTERS=LETTERS[1:10], NUMBERS=1:10)) > SET1 LETTERS NUMBERS 1 A 1 2 B 2 3 C 3 4 D 4 5

Slowly we are getting to the point, that we miss enough optimization opportunities as the result of our own passes. For this we need to fix AlgebraicOpt to be able to handle mods on sources without creating new issues. The last patch enables looping opts. v2: update commit author Karol Herbst (3): nv50/ir: fix AlgebraicOpt for slcts with mods nv50/ir: handle logops with NOT in AlgebraicOpt

Dear all, I have two sets of data (say set1 and set2) as follow: set1 x1 x2 x3 0.30 0.43 3.88 0.38 0.59 3.53 0.30 0.42 2.12 0.33 0.53 2.12 0.30 0.47 3.76 set2 y1 y2 y3 0.32 0.47 5.18 0.23 0.26 1.06 0.42 0.65 3.88 0.28 0.38 3.76 0.35 0.47 1.41 The "pairs" function (such as pairs(~x1+x2+x3 data=set1, main="Simple Scatterplot Matrix") ) is