similar to: bayesian gene network construction

Hi everyone, I'm attempting to use the bnlearn package to calculate conditional probabilities, and I'm running into a problem when the "cpquery" function is used within a loop. I've created an example, shown below, using data included with the package. When using the cpquery function in a loop, a variable created in the loop ("evi" in the example) is not

Hi all. I've recently uploaded a package (bnlearn) to CRAN. It builds fine on both Linux (32 and 64 bit) and Windows, but fails on MacOSX ix86 because of C90 vs C99 issues: http://www.r-project.org/nosvn/R.check/r-patched-macosx-ix86/bnlearn-00install.html Since I've no MacOSX machine at hand, I would like to ask you: why is C99 not the default for gcc on MacOSX ix86? Is it safe to

Hi all I have built a Bayesian network using discrete data using the bnlearn package. When I try to run the cpquery function on this data it returns NaN for some some cases. Running the cpquery in debug mode for such a case (n=10^5, method="lw") creates the following output: generated a grand total of 1e+05 samples. > event has a probability mass of 14982.37 out of

Dear Ross, This usually happen because you have parameters with a value of NaN in your network, because the data you estimate the network from are sparse and you are using maximum likelihood estimates. You should either 1) use simpler networks for which you can estimate all conditional distributions from the data or 2) use posterior estimates for the parameters. Cheers, Marco On 13 July

I'm trying to teach myself about Bayesian Networks and am working with the following data and the bnlearn package. I understand the conceptual aspects of BNs, but I'm not sure how to specify the response variables in R when constructing a dag plot. I've cecked ?hc and done numerous google searches without luck. Can anyone help? library("bnlearn")

Hello... I tried to build R-devel today on Fedora Core 1 (with gcc 3.3.2) but I am running into a couple of errors. On the same system R-1.8.1 compiles just fine, as did a previous version of R-devel. This is what I did: # change LANG as default in FC1 is UTF-8 export LANG=en_US.ISO8859-1 export LANGVAR=en_US.ISO8859-1 # get fresh sources and configure mkdir R-devel rsync -vrC

Hi, I need to classify, using Naive Bayes and Bayes Networks, and estimate their performance using cross validation. How can I do this? I tried the bnlearn package for Bayes Networks, althought I need to get more indexes, not only the error rate (precision, sensitivity, ...). I also tried the *e1071* package, but I could not find a way to do cross-validation. Thanks for everyone. Guilherme.

Hello, I start running into problems with 1.7. due to packages which are only supported by 1.8., therefore I tried to get 1.8. but synaptic only shows up with 1.7.. Are there already debian 1.8 packages? Another question would be, how I can keep all my previously installed packages. will they be kept in '/usr/local/lib/R/site-library or does the new R overwrite these addional packages?

Hi, I am interested in using a bayesian network as a predictor (machine learning); however, I can't get any of the implementations (deal, nblearn) to learn & predict stuff. Shouldn't there also be probabilites for each node after the learning phase, how can I access these? Cheers, Stephan -- View this message in context:

Hi, I'm new to R and am trying to implement a state-space model, and do some simulations looking at how well it works. Does anyone have an example I could use as a template? I'm having trouble working out where to start, and haven't been able to find anything similar in the help files or on the web. My example is a surplus production fisheries model, so something similar to that

Dear R-help list: I have two related questions regarding the functions boot.strength and custom.strength in bnlearn. 1) I am using the following commands (on a set of continuous data, the example here run on fake data): > myblacklist<-data.frame(from=c("x1", "x1", "x1", "x2", "x2", "x2")) , to=c("x2",

Hi: I have clustered microarray gene expression data and trying to map between microarray probe, gene, pathway, gene ontology, and homology for a set of (affy) microarray probes. Is there any package in R which facilitates this? I am looking at bioconductor, but till now could not find a solution. A link to some worked example would be appreciated. Thanks and regards. John [[alternative HTML

Hi Anyone have experience with very large datasets and the Bayesian Network package, bnlearn? In my experience R doesn't react well to very large datasets. Is there a way to divide up the dataset into pieces and incrementally learn the network with the pieces? This would also be helpful incase R crashes, because I could save the network after learning each piece. Thank you.

Hi every one I am working on shiny app using bnlearn for Bayesian networks and using r studio I get a fatal error and when I use R GUI I get this error ** caught segfault *** address 0xfffffffc0fcd6248, cause 'memory not mapped' Traceback: 1: .Call("mappred", node = node, fitted = fitted, data = data, n = as.integer(n), from = from, prob = prob, debug = debug) 2:

Hello, I am beginner user of R. I am trying to use GeneNet package. I started by the example on this link: http://strimmerlab.org/software/genenet/download/arabidopsis-net.R However I am getting an error at this line:system("fdp -T svg -o arthdyn.svg arthdyn.dot") # SVG format sh: fdp: command not found I tried to search how to intall the fdp command but could not find explanation. I am

Its just a simple question I guess: I have a vector with missing information like x<-c(0,1,31,131,NA,133,NA,310,NA,112,3,1,2,93) How can I make a vector like this no missing in it. I used the x[x<0] commabd and tried some more, with no success. thx Korbinian

Hi all, I have just uploaded an R syntax highlighting pattern for NEdit - for those that prefer Nedit over Emacs (like myself). NEdit: http://www.nedit.org R pattern: ftp://ftp.nedit.org/pub/contrib/highlighting/r.pats Comments welcome! Korbinian -- Korbinian Strimmer http://users.ox.ac.uk/~strimmer Dept. of Zoology, University of Oxford, South Parks Road, Oxford

i checked all my options again. could it be, that it is a problem with my compiler? does dovecot support gcc3.2 with glibc 2.2.5? korbinian

I am completely new to wine. I remember reading somewhere that the problem(.wine is not owned by you) occurs when wine is run under sudo or root. I am not familiar with the unix part of Mac os, but I do know that sudo is a command and root is a type of user/access who has control over the entire computer like an administrator.Does that mean that I can't run wine from my administrator account

Hello: I have a 4-column dataset: Crime, Education, Urbanization, Age. I want to construct a multiple linear regression to find the effect of Education, Urbanization, and Age on Crime" lm(Crime ~ Education + Urbanization + Age) If I use + in above statement, does it mean it will build a model to find the relationship between Crime and Education when Urbanization and Age are held constant?