search for: bickel

...39;) Error in library("Biobase") : There is no package called `Biobase' I think I need to somehow install the new library like I did with the Mac UNIX version of R, but I don't know how to do this with the Carbon version. I would appreciate any help with this. Sincerely, David Bickel http://www.mcg.edu/research/biostat/bickel.html David R. Bickel, PhD Assistant Professor Medical College of Georgia Office of Biostatistics and Bioinformatics 1120 Fifteenth St., AE-3037 Augusta, GA 30912-4900 Tel.: 706-721-4697; Fax: 706-721-6294 E-mail: dbickel at mail.mcg.edu or bickel at pru...

Does anyone know how to use the equivalent of debug() on an S4 method? I would like R to enter the browser not for the generic function, but for the method of the class that I specify. Thanks, David _____________________________ David Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International Bioinformatics & Exploratory Research 7250 NW 62nd Ave., PO Box 552 Johnston, Iowa 50131-0552 515-334-4739 Tel 515-334-6634 Fax david.bickel at pioneer.com, bickel at prueba.info This communication is for use by the int...

...matrix elements of the value returned by glm. (I'm particularly interested in logistic regression.) If not, what is a good way to use R to compute Hessians or other partial derivatives of log likelihoods? I would appreciate any guidance. David _______________________________________ David R. Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International (DuPont) Bioinformatics 7200 NW 62nd Ave.; PO Box 184 Johnston, IA 50131-0184 515-334-4739 Tel 515-334-4473 Fax david.bickel at pioneer.com This communication is for use by the intended recipient and ...{{dropped}}

...any value of q and for any positive integer n? I need to perform the integration within a function with q and n as arguments. The function integrate() is giving me this message: "evaluation of function gave a result of wrong length" David _______________________________________ David R. Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International (DuPont) Bioinformatics and Exploratory Research 7200 NW 62nd Ave.; PO Box 184 Johnston, IA 50131-0184 515-334-4739 Tel 515-334-4473 Fax david.bickel at pioneer.com, bickel at prueba.info This communication is for use by the...

Given a numeric vector of observations, does R have any generic way to estimate the parameters of commonly used distributions (exponential, gamma, etc.) without numerically optimizing the likelihood function? Thanks, David _______________________________________ David R. Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International Bioinformatics & Exploratory Research 7250 NW 62nd Ave., PO Box 552 Johnston, Iowa 50131-0552 515-334-4739 Tel 515-334-6634 Fax david.bickel at pioneer.com, bickel at prueba.info This communication is for use by the int...

Does anyone know how to interrupt R in RedHat? Neither control-c nor Esc is working. What I don't want to do is close the window or kill the entire R process. Thanks, David This communication is for use by the intended recipient and ...{{dropped}}

...}) On detection of the error, I would like browser() to be called at the level of numeric.sapply(), so that I can examine x. I'm wondering if this can be done by modifying the default error handling. Using try() with browser() didn't work. Thanks, David _____________________________ David Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International Bioinformatics & Exploratory Research 7250 NW 62nd Ave., PO Box 552 Johnston, Iowa 50131-0552 515-334-4739 Tel 515-334-6634 Fax david.bickel at pioneer.com, bickel at prueba.info This communication is for use by the int...

Could anyone recommend a package for visualizing a likelihood function of two scalar parameters? I would prefer a three-dimensional plot similar to the kind Mathematica is known for, perhaps generated by a package not specific to likelihood. David ______________________________ David R. Bickel Ottawa Institute of Systems Biology BMI Dept., University of Ottawa http://www.oisb.ca/members.htm

...<- sapply(f.list, function(x){x[1]}) vec2 <- sapply(f.list, function(x){x[2]}) The values of vec1 should be as iid as possible and the values of vec2 should be as iid as possible. Any help with what I need to add to f would be greatly appreciated. David _____________________________ David Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International Bioinformatics & Exploratory Research 7250 NW 62nd Ave., PO Box 552 Johnston, Iowa 50131-0552 515-334-4739 Tel 515-334-6634 Fax david.bickel at pioneer.com, bickel at prueba.info This communication is for use by the int...

What are some reliable R functions that can compute the value of a convergent series? David -- David R. Bickel, PhD Associate Professor Ottawa Institute of Systems Biology Biochem., Micro. and I. Department Mathematics and Statistics Department University of Ottawa 451 Smyth Road Ottawa, Ontario K1H 8M5 http://www.statomics.com Office Tel: (613) 562-5800 ext. 8670 Office Fax: (613) 562-5185

...can assist with any of the following? 1. Calling an R function from Mathematica. 2. Calling a Mathematica function from R. 3. Using XML or another reliable data format to pass vectors, matrices, and/or lists from one environment to the other. Any advice would be appreciated. David -- David R. Bickel, PhD Associate Professor Ottawa Institute of Systems Biology Biochem., Micro. and I. Department Mathematics and Statistics Department University of Ottawa 451 Smyth Road Ottawa, Ontario K1H 8M5 http://www.statomics.com Office Tel: (613) 562-5800 ext. 8670 Office Fax: (613) 562-5185

...arch powerpc os darwin6.6 system powerpc, darwin6.6 status Patched major 1 minor 7.1 year 2003 month 06 day 21 language R Thanks, David _______________________________________ http://www.mcg.edu/research/biostat/bickel.html David R. Bickel, Assistant Professor Medical College of Georgia Office of Biostatistics and Bioinformatics (706) 721-4697, 721-3785; Fax: 721-6294 dbickel at mcg.edu or bickel at prueba.info

...t; that would better accommodate such extraction of distributions or likelihoods? I would also appreciate any suggestions for strategies or contributed packages that may facilitate automation. For example, would the "distrTEst" package help? David ______________________________ David R. Bickel Ottawa Institute of Systems Biology http://www.oisb.ca/members.htm

...process an intensive command while I execute other R commands. I want to do this in the same R session, rather than with multiple calls to R, so that all my modified objects will stay in the same workspace. I would appreciate any help with this. Thanks, David ______________________________ David Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International Bioinformatics & Discovery Research 7250 NW 62nd Ave., PO Box 552 Johnston, Iowa 50131-0552 706-736-9151 Home 515-334-4739 Work 515-334-6634 Fax david.bickel at pioneer.com, bickel at prueba.info This communication is f...

...something like this: > plot.postscript.file(file = 'graph.ps') If no such function exists, I'd be interested in a way to use existing R functions to do this under UNIX or Windows, preferably without a system call to GhostView (gv). Thanks, David _____________________________ David Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International Bioinformatics & Exploratory Research 7250 NW 62nd Ave., PO Box 552 Johnston, Iowa 50131-0552 515-334-4739 Work 515-334-6634 Fax david.bickel at pioneer.com, bickel at prueba.info This communication is for use by the in...

...order statistics (or sample quantiles or extreme values) for a given distribution such as a normal distribution? Both exact and asymptotic calculations are of interest. I am already aware of the 'quantile' function of 'stats'. David _______________________________________ David R. Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International (DuPont) Bioinformatics and Exploratory Research 7200 NW 62nd Ave.; PO Box 184 Johnston, IA 50131-0184 515-334-4739 Tel 515-334-4473 Fax david.bickel at pioneer.com, bickel at prueba.info This communication is for use by the...

...nt-end has encountered a problem and needs to close. We are sorry for the inconvenience." I downloaded 1.9.0 and installed it, but when I launch it, I get this message: "Fatal error: Invalid HOMEDRIVE." I would appreciate any assistance. -Dave ______________________________ David Bickel http://davidbickel.com This communication is for use by the intended recipient and ...{{dropped}}

...arallel. An alternative may be to have R and an R package behave as a stand-alone application that can be called from the UNIX command line. Is there any documentation on this? S-PLUS can do something like this. I will be using Red Hat Linux. Thank you, David ______________________________ David Bickel http://davidbickel.com Research Scientist Pioneer Hi-Bred International Bioinformatics & Discovery Research 7250 NW 62nd Ave., PO Box 552 Johnston, Iowa 50131-0552 706-736-9151 Home 515-334-4739 Work 515-334-6634 Fax david.bickel at pioneer.com, bickel at prueba.info This communication is f...

...xis="blue",lwd.ticks=0.5,col.ticks ="gray3") lines(NN,McG,pch=18,col="green") lines(NN,PBJD,pch=20,col="magenta1") points(NN,GRPR,pch=18,col="cyan") abline(h=1,pch= 1,lty=1,col="black") legend("topright",legend = c("Levina-Bickel","MacKay-Ghahramani","Pettis-Bailey-Jain-Dubes","Grassberger-Procaccia","Helix Dimension"), text.width = strwidth("Pettis-Bailey-Jain-Dubes"),pch = c(19,18,20,18,1), col = c("red4","green","magenta1",&qu...

...ion? For example, could it make use of 16 GB in one session given the right processor/OS platform? 3. Is there anything else I should consider before choosing a processor and OS? If there is a better list for these kinds of questions, please advise. David ______________________________ David R. Bickel Ottawa Institute of Systems Biology BMI Dept., University of Ottawa 451 Smyth Road Ottawa, Ontario K1H 8M5 http://www.oisb.ca/members.htm Tel: (613) 562-5800 ext. 8670 Fax: (613) 562-5185 Roger Guindon Hall, Room 1317