search for: davidd

...1) { cat(nlevels(newtab[,1]," ") } cat("\nlab ") for(i in seq(1, ncol(newtab)-1) { cat(letters[i], " ") } cat("\ndat [", newtab[,"Freq"], " ]\n") -- | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v

A bit late, but you might like to look at http://www.qimr.edu.au/davidD/polyr.R Regarding the original posters queries: You can analyse polychoric correlations as if they were Pearson correlations using standard software (eg sem), and this usually doesn't do too badly, or go to AWLS (Browne) in LISREL etc, or ML analysis of the full multidimensional contingency t...

Hi there, If I do an lm, I get p-vlues as p-value: < 2.2e-16 Suppose am interested in exact value such as p-value = 1.6e-16 (note = and not <) How do I go about it? stephen

This is a bit late, but: > About two years ago there was a thread about this which suggested that at > that time nobody had these coefficients ready to go. > (a) has anyone in the meanwhile programmed them? http://www.qimr.edu.au/davidD/R/polyr.R > (d) I appreciate this last item is not strictly an R question, but my > intention is to use these as input into the sem package for structural > equation models. If anyone thinks that is misguided I would be intersted to > here. > > Michael Dewey > m.dewey at iop.k...

...> requires the pedigree to be coded as integers, increasing > with date of birth (therefore sire and dam always have > lower identifiers than their offspring) and with missing > values coded as 0. > > How would I go about doing this? > You might look at http://www.qimr.edu.au/davidD/sib-pair.R, specifically the read.pedigree() and wrlink() functions. The former is not very impressive speedwise -- I usually perform these tasks in the my Sib-pair (Fortran) program, which is on the same webpage. It will order the pedigree by generational position, so a DOB is not required to do...

...en correlation test, but I'm not able to find this function in any package. Perhaps it isn't in a package, but sometimes anybody have program this function or create a routine to estimate it. I found it in google and I hope what I found it's in this page, http://genepi.qimr.edu.au/staff/davidD/R/filliben.R but i can't open it. Anybody can help me? simply trying to open the page and copy the routine if it's in. Thanks in advance ----- Mario Garrido Escudero PhD student Dpto. de Biolog?a Animal, Ecolog?a, Parasitolog?a, Edafolog?a y Qca. Agr?cola Universidad de Salamanca -- V...

...ul 17 12:04:50 2000 from orpheus.qimr.edu.au -bash: ?oe90: command not found -bash: glorious: command not found -bash: ?]r90: command not found -bash: marshall4: command not found Connection to orpheus.qimr.edu.au closed. log: Jul 17 11:55:44 orpheus PAM_pwdb[14041]: (sshd) session opened for user davidD by (uid=0) Jul 17 11:55:45 orpheus sshd[14041]: syslogin_perform_logout: logout() returned an error The junk includes names of hosts on our local network who engage in ftp or telnet with my machine. There is no proble...

...expected covariance matrix O=observed covariance matrix where in your example, E will be the observed covariance matrix for the pooled groups. There are GLS etc alternatives - see eg Bollen's book on SEM. | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v

...ted code is under http://www.ece.northwestern.edu/~nocedal/lbfgsb.html released under the New BSD License. Has this already been made available in R, perhaps in other packages such as optimx? Cheers, David Duffy. | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v

...<- function(x) { chars <- unlist(strsplit(deparse(x),"")) chars <- chars[-c(1,length(chars))] paste(gsub("\\\\","/",chars),collapse="") } unback("\n") | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v

...<- function(x) { chars <- unlist(strsplit(deparse(x),"")) chars <- chars[-c(1,length(chars))] paste(gsub("\\\\","/",chars),collapse="") } unback("\n") | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v

...installed the MySQL client and ran it from my OS X system prefs. I double checked my gems and mysql (2.8.1) and mysql2 (0.3.6, 0.2.11) are BOTH listed in my local gems list in terminal. I can launch MySQL in terminal as well. Problem: So, the issue is that when launching WEBrick via the ''davidd$ rails server'' command I get: davidd$ rails server /Library/Ruby/Gems/1.8/gems/mysql2-0.2.11/lib/mysql2/mysql2.bundle: dlopen(/Library/Ruby/Gems/1.8/gems/mysql2-0.2.11/lib/mysql2/ mysql2.bundle, 9): Library not loaded: libmysqlclient.18.dylib (LoadError) Referenced from: /Library/Ruby/G...

If I run an analysis which generates statistical tests on many SNPs I would naturally want to get more details on the most significant SNPs. Directly from within R one can get the information by loading RSNPer (from Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately, the command cannot handle a vector and therefore only wants to do one at a time. I tried the lapply and

...t; David Clayton has a couple of little functions on his website, one for sequential analysis IIRC. I have some on my website for genetic association (TDT and case-control) and linkage (variance components) analysis. | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v

...) says: FEXACT ERROR: 30 Stack length exceeded in f3xact. This problem should not occur. The integer hash key is bigger than the largest allowable integer, and so appears as a negative number. Table is too big. | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v

If I do not make a mistake,the partial association model is an extension of log-linear model.I read a papers which gives an example of it.(Sloane and Morgan,1996,An Introduction to Categorical Data Analysis,Annual Review of Sociology.22:351-375) Can R fit such partial association model? ps:Another somewhat off-topic question.What's the motivations to use log-linear model?Or why use

Does anyone know if the sib TDT has been implemented in R 1. Spielman, R.S., and Ewens, W.J. (1998) A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am J Hum Genet 62, 450-458 -- Farrel Buchinsky, MD Pediatric Otolaryngologist Allegheny General Hospital Pittsburgh, PA

Hi, I am looking to do some quantitative genetic analyses using animal models and was wondering if someone could suggest an appropriate package in R. It would help if it was similar to the ASReml genetic analyses software. Thanks, Deepa Senapathi Deepa Senapathi Centre for Agri-Environmental Research (CAER) School of Agriculture, Policy & Developement. University of Reading

Hi all, I've been looking in R for an EM algorithm adjusted for multiple-locus haplotypes frequencies, but failed in 100%. Has anyone heard of anything of this kind in R? Thanks in advance, Marcin

...by Jing hua Zhao, Beth Atkinson and others could also then be used for linkage analysis of survival data (http://www.ucl.ac.uk/~rmjdjhz/r-progs.htm) (I haven't any experience with these programs yet). David Duffy. | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v