Re: [R] Linker problem in installing 64-bit R
Note: configure:4041: checking whether the C compiler works configure:4059: error: cannot run C compiled programs. so your compiler installation is broken, seriously enough that configure can make no progress. Also, gcc 3.4.2 is old and has a known bug that stops some R packages using Fortran working correctly, so please avoid it. Please seek local help with your OS. On Thu, 20 Apr 2006, Min Shao wrote: Hi, I am trying to compile R-2.2.1 on Solaris 2.9 with a 64-bit build. Following the instructions in R Installation and Adminstration, I changed the Note, those are example settings that have been tested, but not `instructions'. following settings in config.site: CC=gcc -m64 F77=g77 -64 CXX=g++ -m64 LDFLAGS=-L/usr/local/lib/sparcv9 -L/usr/local/lib But I got the following error messages: configure:3987: gcc -m64 -I/usr/local/include -L/usr/local/lib/sparcv9 -L/usr/local/lib conftest.c 5 /usr/ccs/bin/ld: skipping incompatible /work/net-local-b/sparc- sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9/3.4.2/sparcv9/libgcc.a when search ing for -lgcc /usr/ccs/bin/ld: skipping incompatible /work/net-local-b/sparc- sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9/3.4.2/sparcv9/libgcc_eh.a when sea rching for -lgcc_eh /usr/ccs/bin/ld: skipping incompatible /lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /usr/lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /usr/lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /work/net-local-b/sparc- sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9/3.4.2/sparcv9/libgcc.a when search ing for -lgcc /usr/ccs/bin/ld: skipping incompatible /work/net-local-b/sparc- sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9/3.4.2/sparcv9/libgcc_eh.a when sea rching for -lgcc_eh /usr/ccs/bin/ld: skipping incompatible /lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /usr/lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /usr/lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9 /3.4.2/spar cv9/crt1.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9 /3.4.2/spar cv9/crti.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/usr/ccs/lib/sparcv9/values-Xa.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9 /3.4.2/spar cv9/crtbegin.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/var/tmp//cckWp3Sb.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9 /3.4.2/spar cv9/crtend.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9 /3.4.2/spar cv9/crtn.o' is incompatible with sparc output configure:3990: $? = 0 configure:4036: result: a.out configure:4041: checking whether the C compiler works configure:4047: ./a.out configure: line 1: 25817 Bus Error (core dumped) ./$ac_file configure:4050: $? = 138 configure:4059: error: cannot run C compiled programs. I would appreciate any help with resolving the problem. Thanks, Min [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] second try; writing user-defined GLM link function
glm.24.pred-predict(glm.24,newdata=nestday, type=response, SE.fit=T) What is SE.fit? The help says se.fit. That _may_ be a problem. However, I think the real problem is that the link function argument includes a reference to vc.apfa$days that is appropriate for fitting, not prediction. One way out might be (untested) attach(va.apfa) glm.24 - glm(formula = Success ~ NestHtZ + MeanAge + I(MeanAge^2) + I(MeanAge^3), family = logexposure(ExposureDays = days), data = vc.apfa) detach() attach(nestday) glm.24.pred-predict(glm.24,newdata=nestday, type=response, SE.fit=T) detach() so that 'days' refers to the appropriate dataset both when fitting and predicting. (This is bending glm() to do something it was not designed to do, so some hoop-jumping is needed.) On Thu, 20 Apr 2006, Jessi Brown wrote: An update for all: Using the combined contributions from Mark and Dr. Ripley, I've been (apparently) successfully formulating both GLM's and GLMM's (using the MASS function glmmPQL) analyzing my nest success data. The beta parameter estimates look reasonable and the top models resemble those from earlier analyses using a different nest survival analysis approach. However, I've now run into problems when trying to predict the daily survival rates from fitted models. For example, for a model considering nest height (NestHtZ) and nest age effects (MeanAge and related terms; there is an overall cubic time trend in this model), I tried to predict the daily survival rate for each day out of a 67 day nest cycle (so MeanAge is a vector of 1 to 67) with mean nest height (also a vector 67 rows in length; both comprise the matrix nestday). Here's what happens: summary(glm.24) Call: glm(formula = Success ~ NestHtZ + MeanAge + I(MeanAge^2) + I(MeanAge^3), family = logexposure(ExposureDays = vc.apfa$days), data = vc.apfa) Deviance Residuals: Min 1Q Median 3Q Max -3.3264 -1.2341 0.6712 0.8905 1.5569 Coefficients: Estimate Std. Error z value Pr(|z|) (Intercept) 6.5742015 1.7767487 3.700 0.000215 *** NestHtZ 0.6205444 0.2484583 2.498 0.012504 * MeanAge -0.6018978 0.2983656 -2.017 0.043662 * I(MeanAge^2) 0.0380521 0.0152053 2.503 0.012330 * I(MeanAge^3) -0.0006349 0.0002358 -2.693 0.007091 ** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 174.86 on 136 degrees of freedom Residual deviance: 233.82 on 132 degrees of freedom AIC: 243.82 Number of Fisher Scoring iterations: 13 glm.24.pred-predict(glm.24,newdata=nestday, type=response, SE.fit=T) Warning message: longer object length is not a multiple of shorter object length in: plogis(eta)^days Can anyone tell me what I'm doing wrong? cheers, Jessi Brown __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] PCA biplot question
Hi, hi all, Hi everyone, I'd like to project two pcas onto one device window. I plot my first PCA: biplot(prcomp(t(cerebdevmat)), var.axes=FALSE, cex=c(1,.1), pc.biplot=TRUE) Now I'd like to project the features of another PCA onto this graph. Any suggestions? You can used co-inertia analysis (coinertia in package ade4) or maybe procuste analysis (package vegan, ade4, shapes) these analyses are adapted to the simultaneous analyses of two tables. cheers, Pierre -- Ce message a été envoyé depuis le webmail IMP (Internet Messaging Program) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] rcorrp.cens
Hi R-users, I'm having some problems in using the Hmisc package. I'm estimating a cox ph model and want to test whether the drop in concordance index due to omitting one covariate is significant. I think (but I'm not sure) here are two ways to do that: 1) predict two cox model (the full model and model without the covariate of interest) and estimate the concordance index (i.e. area under the ROC curve) with rcorr.cens for both models, then compute the difference 2) predict the two cox models and estimate directly the difference between the two c-indices using rcorrp.cens. But it seems that the rcorrp.cens gives me the drop of Dxy index. Do you have any hint? Thanks Stefano [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Mutually Orthogonal Latin Squares
Hi Jinsong Finding even a pair of mutually orthogonal latin squares for arbitrary order is a difficult problem. For example, Euler conjectured that no orthogonal latin squares exist for order 4n+2; this was only disproved in 1960 (in 1900 it was proved that there are none of order 6). . . . evidently a complicated research topic! Now, this doesn't quite answer your question, but functions panmagic.4(), panmagic.8() and magic.8() of the magic package use Latin squares of sizes 4 and 8 for their construction. HTH Robin On 20 Apr 2006, at 16:36, Jinsong Zhao wrote: Hi all, The package crossdes could contruct a complete sets of mutually orthogonal latin squares. The construction works for prime powers only. I hope to know whether there is a way to construct a mutually orthogonal Lation square for 10 or other numbers that could not be prime powers. Thanks for any suggestions. Best wishes, Jinsong Zhao __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting- guide.html -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Histogram to compare two datasets
Dear All, I am trying to create a histogram-like plot for comparing two datasets - For each interval, I want it to draw 2 bars - one for representing the number of values in each dataset for that interval. I have looked at the help for the hist() function and also for the histogram() function that is part of the lattice package, and neither seem to support multiple datasets. Could someone please point me in the right direction? Kind regards, Johan van Niekerk __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Histogram to compare two datasets
Le 21.04.2006 10:48, Johan van Niekerk a écrit : Dear All, I am trying to create a histogram-like plot for comparing two datasets - For each interval, I want it to draw 2 bars - one for representing the number of values in each dataset for that interval. I have looked at the help for the hist() function and also for the histogram() function that is part of the lattice package, and neither seem to support multiple datasets. Could someone please point me in the right direction? Kind regards, Johan van Niekerk Look there : http://addictedtor.free.fr/graphiques/search.php?q=histogram -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php +---+ | Romain FRANCOIS - http://francoisromain.free.fr | | Doctorant INRIA Futurs / EDF | +---+ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] No Discounts for Springer books (e.g. S Programming)?
Hi, I want to buy the books Modern applied Statistics with S and S Programming. Both are Springer books and according to the Discount Info on the page books related to R (http://www.r-project.org/doc/bib/R-books.html) subject to a 20 % discount. Unfortunatley the promotion code doesn't work. I already contacted Springer but didn't get an answer. Does someone know what happened with these discounts? I didn't find anything related in the archives. Thanks and best regards, Hans-Peter -- PS: if someone has a used or redundant copy for sale, don't hesitate to contact me... ;-) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] online tutorials
I work for a Investment group with a very extensive training program and we are having our new hires take a statistics course at University of Chicago where they have to complete some assignments with R. I was wondering if there are any online tutorials that exist where we could get our participants comfortable with R before the class itself? I appreciate any help at all. Thanks, Matt Maxon Learning Development Matt Maxon Citadel Investment Group, L.L.C. 312.395.2517 - office - - CONFIDENTIALITY AND SECURITY NOTICE The contents of this message and any attachments may be privileged, confidential and proprietary and also may be covered by the Electronic Communications Privacy Act. If you are not an intended recipient, please inform the sender of the transmission error and delete this message immediately without reading, disseminating, distributing or copying the contents. Citadel makes no assurances that this e-mail and any attachments are free of viruses and other harmful code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] creating empty cells with table()
Owen, Jason wrote: Hello, Suppose I simulate 20 observations from the Poisson distribution with lambda = 4. I can summarize these values using table() and then feed that to barplot() for a graph. Problem: if there are empty categories (e.g. 0) or empty categories within the range of the data (e.g. observations for 6, 7, 9), barplot() does not include the empty cells in the x-axis of the plot. Is there any way to specify table() to have specific categories (in the above example, probably 0:12) so that zeroes are included? The integer.frequency function in the plotrix package (of which there will be a new version shortly) handles this, as I couldn't tame either tabulate or table to do what I wanted for the freq function. Note that it is _not_ a highly optimized function. Jim __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] online tutorials
Maxon, Matthew [EMAIL PROTECTED] writes: I work for a Investment group with a very extensive training program and we are having our new hires take a statistics course at University of Chicago where they have to complete some assignments with R. I was wondering if there are any online tutorials that exist where we could get our participants comfortable with R before the class itself? I appreciate any help at all. There are three major sources: (1) Manuals that ship with R, notably An Introduction to R (2) Online materials contributed to CRAN http://cran.r-project.org/other-docs.html (3) Books... Re. (2), among the shorter documents, The R Guide by Jason Owen looks quite attractive for people at a very basic level of statistical knowledge (matrix calculus is assumed in some sections, though). However, these documents cover a wide range of target audiences, so you should look at all of them and calibrate against your group. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Considering port of SAS application to R
Hi there! I am considering to port a SAS application to R and I would like to hear your opinion if you think this is possible and worthwhile. SAS is mainly used to do data management and then to do some aggregations and simple computations on the data and to output a modified data set. The main problem I see is the size of the data file. As I have no access to SAS yet I cannot give real details but the SAS data file is about 7 gigabytes large. (It's only the basic SAS system without any additional modules) What do you think, would a port to R be possible with reasonable effort? Is R able to handle that size of data? Or is R prepared to work together with some database system? Thanks for your thoughts! Best regards, Werner - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Considering port of SAS application to R
Please, read the R Data Import/Export manual provided with any version of R, and come back with more specific questions. In general, R cannot deal with datasets as large as those handled by SAS. But this is true only when you use standard R functions, like read.table(), which are not written to save memory and load very large datasets (other aspects are optimized). I would advise to put your data in a database and then access to it piece-by-piece using SQL queries. There are very little cases where you actually need the whole dataset in memory at once. A simple database system, if you just need to access those data (no complex database operations required) is SQLite. There is an R package to connect to such a database without extra software needed. Thus, very convenient. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Werner Wernersen wrote: Hi there! I am considering to port a SAS application to R and I would like to hear your opinion if you think this is possible and worthwhile. SAS is mainly used to do data management and then to do some aggregations and simple computations on the data and to output a modified data set. The main problem I see is the size of the data file. As I have no access to SAS yet I cannot give real details but the SAS data file is about 7 gigabytes large. (It's only the basic SAS system without any additional modules) What do you think, would a port to R be possible with reasonable effort? Is R able to handle that size of data? Or is R prepared to work together with some database system? Thanks for your thoughts! Best regards, Werner - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Considering port of SAS application to R
R supports a number of databases and if you only need to work with a small amount of data at once it should be readily do-able; however, R keeps objects in memory and if you need large amounts at once then you could run into problems. Note that S-Plus keeps objects on disk and has other features aimed at large data and might be an alternative if R cannot handle the size and you want something based on the S language. Since SAS was developed many years ago when optimizing computer resources was more important than it is now it might be difficult to find an alternative that matches it for performance with large data sets. You probably want to quickly develop the core of your app in such a way that it has the main performance characteristics of the full app so you can get an idea of whether it will work prior to spending the time on the full code. Also note that R typically processes matrices faster than data frames and, in general, how you write your application may affect its performance. On 4/21/06, Werner Wernersen [EMAIL PROTECTED] wrote: Hi there! I am considering to port a SAS application to R and I would like to hear your opinion if you think this is possible and worthwhile. SAS is mainly used to do data management and then to do some aggregations and simple computations on the data and to output a modified data set. The main problem I see is the size of the data file. As I have no access to SAS yet I cannot give real details but the SAS data file is about 7 gigabytes large. (It's only the basic SAS system without any additional modules) What do you think, would a port to R be possible with reasonable effort? Is R able to handle that size of data? Or is R prepared to work together with some database system? Thanks for your thoughts! Best regards, Werner - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] online tutorials
I got started with the book by Venables and Ripley 'Modern Applied Statistics with S-Plus'. If you will be working with the Windows version (unbelievably easy to install) you will also find helpful material in the help file. On Thursday 20 April 2006 09:24, Maxon, Matthew wrote: I work for a Investment group with a very extensive training program and we are having our new hires take a statistics course at University of Chicago where they have to complete some assignments with R. I was wondering if there are any online tutorials that exist where we could get our participants comfortable with R before the class itself? I appreciate any help at all. Thanks, Matt Maxon Learning Development Matt Maxon Citadel Investment Group, L.L.C. 312.395.2517 - office - - CONFIDENTIALITY AND SECURITY NOTICE The contents of this message and any attachments may be privileged, confidential and proprietary and also may be covered by the Electronic Communications Privacy Act. If you are not an intended recipient, please inform the sender of the transmission error and delete this message immediately without reading, disseminating, distributing or copying the contents. Citadel makes no assurances that this e-mail and any attachments are free of viruses and other harmful code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] rcorrp.cens
Stefano Mazzuco wrote: Hi R-users, I'm having some problems in using the Hmisc package. I'm estimating a cox ph model and want to test whether the drop in concordance index due to omitting one covariate is significant. I think (but I'm not sure) here are two ways to do that: 1) predict two cox model (the full model and model without the covariate of interest) and estimate the concordance index (i.e. area under the ROC curve) with rcorr.cens for both models, then compute the difference 2) predict the two cox models and estimate directly the difference between the two c-indices using rcorrp.cens. But it seems that the rcorrp.cens gives me the drop of Dxy index. Do you have any hint? Thanks Stefano First of all, any method based on comparing rank concordances loses powers and is discouraged. Likelihood ratio tests (e.g., by embedding a smaller model in a bigger one) are much more powerful. If you must base comparisons on rank concordance (e.g., ROC area=C, Dxy) then rcorrp.cens can work if the sample size is large enough so that uncertainty about regression coefficient estimates may be ignored. rcorrp.cens doesn't give the drop in C; it gives the probability that one model is more concordant with the outcome than another, among pairs of paired predictions. The bootcov function in the Design package has a new version that will output bootstrap replicates of C for a model, and its help file tells you how to use that to compare C for two models. This should only be done to show how low a power such a procedure has. rcporrp is likely to be more powerful than that, but likelihood ratio is what you want. You will find many cases where one model increases C by only 0.02 but it has many more useful (more extreme) predictions. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] online tutorials
If you are not afraid by exoticism, this web site http://www.kb.u-psud.fr/acces-etudiant/cours/biostat/Biostat.htm is a French speaking multimedia online tutorial to R... Best regards, Bruno Bruno Falissard INSERM U669, PSIGIAM Paris Sud Innovation Group in Adolescent Mental Health Maison de Solenn 97 Boulevard de Port Royal 75679 Paris cedex 14, France tel : (+33) 6 81 82 70 76 fax : (+33) 1 45 59 34 18 web site : http://perso.wanadoo.fr/bruno.falissard/ -Message d'origine- De : [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] De la part de Maxon, Matthew Envoyé : jeudi 20 avril 2006 18:25 À : R-help@stat.math.ethz.ch Objet : [R] online tutorials I work for a Investment group with a very extensive training program and we are having our new hires take a statistics course at University of Chicago where they have to complete some assignments with R. I was wondering if there are any online tutorials that exist where we could get our participants comfortable with R before the class itself? I appreciate any help at all. Thanks, Matt Maxon Learning Development Matt Maxon Citadel Investment Group, L.L.C. 312.395.2517 - office - - CONFIDENTIALITY AND SECURITY NOTICE The contents of this message and any attachments may be privileged, confidential and proprietary and also may be covered by the Electronic Communications Privacy Act. If you are not an intended recipient, please inform the sender of the transmission error and delete this message immediately without reading, disseminating, distributing or copying the contents. Citadel makes no assurances that this e-mail and any attachments are free of viruses and other harmful code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] No Discounts for Springer books (e.g. S Programming)?
Dear Augustin, What you have to do is to register in that web page or in Springer Alert, and when you order the books, the discount is applied to your order automatically. Thanks a lot, that worked. One has to register and then the discount token is applied. - For the record: Amazon was quite a lot cheaper, so it became a would have worked... Thanks again and best regards, Hans-Peter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Considering port of SAS application to R
Forget about R for now and port the application to MySQL/PostgreSQL etc, it is possible and worthwhile. In case you happen to use (and really need) some SAS DATA STEP looping features you might be forced to look into SQL cursors, otherwise the port should be (very) straightforward. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Werner Wernersen Sent: Friday, April 21, 2006 7:09 AM To: r-help@stat.math.ethz.ch Subject: [R] Considering port of SAS application to R Hi there! I am considering to port a SAS application to R and I would like to hear your opinion if you think this is possible and worthwhile. SAS is mainly used to do data management and then to do some aggregations and simple computations on the data and to output a modified data set. The main problem I see is the size of the data file. As I have no access to SAS yet I cannot give real details but the SAS data file is about 7 gigabytes large. (It's only the basic SAS system without any additional modules) What do you think, would a port to R be possible with reasonable effort? Is R able to handle that size of data? Or is R prepared to work together with some database system? Thanks for your thoughts! Best regards, Werner - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Considering port of SAS application to R
Good suggestion. Multiple gigabytes is stretching it with R. Use PostgreSQL Python, and Python DBI database connectivity to replace your SAS data step, then use the RODBC package to import data into R convenience stores as appropriate. Steve Miller -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of bogdan romocea Sent: Friday, April 21, 2006 7:59 AM To: [EMAIL PROTECTED] Cc: r-help Subject: Re: [R] Considering port of SAS application to R Forget about R for now and port the application to MySQL/PostgreSQL etc, it is possible and worthwhile. In case you happen to use (and really need) some SAS DATA STEP looping features you might be forced to look into SQL cursors, otherwise the port should be (very) straightforward. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Werner Wernersen Sent: Friday, April 21, 2006 7:09 AM To: r-help@stat.math.ethz.ch Subject: [R] Considering port of SAS application to R Hi there! I am considering to port a SAS application to R and I would like to hear your opinion if you think this is possible and worthwhile. SAS is mainly used to do data management and then to do some aggregations and simple computations on the data and to output a modified data set. The main problem I see is the size of the data file. As I have no access to SAS yet I cannot give real details but the SAS data file is about 7 gigabytes large. (It's only the basic SAS system without any additional modules) What do you think, would a port to R be possible with reasonable effort? Is R able to handle that size of data? Or is R prepared to work together with some database system? Thanks for your thoughts! Best regards, Werner - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] message posting
Hi, I sent two emails to the R help list and got no reply. While this may be my question, it is unlike the users of this list not to reply (thankfully!). I checked for my message using the archive for April 2006 and found the following where the text of message should have been: An embedded and charset-unspecified text was scrubbed... Does this message mean that my message wasn't posted or couldn't be viewed? If so, what did I do wrong? The only thing that comes to mind is that I set the font in outlook to courrier new so that the columns in a table would line up. Thanks for any advice, Steve [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Need R code
Here's an example.
lst - list()
for (i in 1:5) {
lst[[i]] - data.frame(v=sample(1:20,10),sample(1:5,10,replace=TRUE))
colnames(lst[[i]])[2] - paste(x,i,sep=)
}
dfr - lst[[1]]
for (i in 2:length(lst)) dfr - merge(dfr,lst[[i]],all=TRUE)
dfr - dfr[order(dfr[,1]),]
print(dfr)
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of stat stat
Sent: Thursday, April 20, 2006 1:15 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Need R code
Dear r-users,
Suppose I have three datasets:
Dataset-1:
Date x y
Jan-1,2005120 230
Jan-2,2005123 -125
Jan-3,2005-110 300
Jan-4,2005114 -21
Jan-7,200511299
Mar-5,2005200 311
Dataset-2:
Date x y
Jan-2,2005123 -125
Jan-3,2005-110 300
Jan-4,2005114 -21
Jan-5,200511299
Jan-6,2005-23 12
Mar-5,2005200 311
Dataset-3:
Date x y
Jan-3,2005-110 300
Jan-4,2005114 -21
Jan-5,200511299
Mar-5,2005200 311
Apl-23,2005 123 200
Now I want to get the common dates along with x and y from
this above three datasets keeping the same order
in date-variable as it is.
For ex. I want to get:
Datex y xy
x y
(from dataset-1) (from dataset-2)
(from dataset-3)
--
--
Jan-3,2005-110 300 -110 300
-110 300
Jan-4,2005 114 -21 114-21
114 -21
Mar-5,2005200 311 200 311
200 311
Can anyone give me any R code to implement this for any
number of datasets ?
Thanks and regards
thanks in advance
-
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Re: [R] message posting
On Fri, 2006-04-21 at 09:22 -0400, Steven Lacey wrote: Hi, I sent two emails to the R help list and got no reply. While this may be my question, it is unlike the users of this list not to reply (thankfully!). I checked for my message using the archive for April 2006 and found the following where the text of message should have been: An embedded and charset-unspecified text was scrubbed... Does this message mean that my message wasn't posted or couldn't be viewed? If so, what did I do wrong? The only thing that comes to mind is that I set the font in outlook to courrier new so that the columns in a table would line up. Thanks for any advice, Steve Hi Steve [[alternative HTML version deleted]] No idea if this has anything to do with it or not, but you are asked to configure your emailer to *not* send html mail. Configure Outlook to send plain text only (generally) or set it up to send plain text only to r-help if you really want to send html-mail to others. It's been a long while since I used Outlook/Windows, but IIRC you can set this up somewhere amongst the myriad of prefs in Outlook. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% * Note new Address, Telephone Fax numbers from 6th April 2006 * %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson ECRC ENSIS [t] +44 (0)20 7679 0522 UCL Department of Geography [f] +44 (0)20 7679 0565 Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street [w] http://www.ucl.ac.uk/~ucfagls/cv/ London, UK. [w] http://www.ucl.ac.uk/~ucfagls/ WC1E 6BT. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] message posting
This can be checked/set from the toolbar at the top via the drop-down box next to the Compose in this mail format section displayed using: Tools-Options-Mail Format HTH Regards Mike A picture may be worth a thousand words, but HTML adds far more than a thousand bytes to an email. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gavin Simpson Sent: 21 April 2006 14:32 To: Steven Lacey Cc: r-help@stat.math.ethz.ch Subject: Re: [R] message posting On Fri, 2006-04-21 at 09:22 -0400, Steven Lacey wrote: Hi, I sent two emails to the R help list and got no reply. While this may be my question, it is unlike the users of this list not to reply (thankfully!). I checked for my message using the archive for April 2006 and found the following where the text of message should have been: An embedded and charset-unspecified text was scrubbed... Does this message mean that my message wasn't posted or couldn't be viewed? If so, what did I do wrong? The only thing that comes to mind is that I set the font in outlook to courrier new so that the columns in a table would line up. Thanks for any advice, Steve Hi Steve [[alternative HTML version deleted]] No idea if this has anything to do with it or not, but you are asked to configure your emailer to *not* send html mail. Configure Outlook to send plain text only (generally) or set it up to send plain text only to r-help if you really want to send html-mail to others. It's been a long while since I used Outlook/Windows, but IIRC you can set this up somewhere amongst the myriad of prefs in Outlook. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% * Note new Address, Telephone Fax numbers from 6th April 2006 * %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson ECRC ENSIS [t] +44 (0)20 7679 0522 UCL Department of Geography [f] +44 (0)20 7679 0565 Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street [w] http://www.ucl.ac.uk/~ucfagls/cv/ London, UK. [w] http://www.ucl.ac.uk/~ucfagls/ WC1E 6BT. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] aov contrasts residual error calculation
Hi, I am using aov with an Error component to model some repeated measures data. By repeated measures I mean the data look something like this... subjABC 1 411 15 2 312 17 3 5914 4 610 18 For each subject I have 3 observations, one in each of three conditions (A, B, C). I want to test the following contrast (1, 0, -1). One solution is to apply the contrast weights at the subject level explicitly and then call t.test on the difference scores. However, I am looking for a more robust solution as I my actual design has more within-subjects factors and one or more between subjects factors. A better solution is to specify the contrast in an argument to aov. The estimated difference of the contrast is the same as that in the paired t-test, but the residual df are double. While not what I expected, it follows from the documentation, which explicitly states that these contrasts are not to be used for any error term. Even though I specify 1 contrast, there are 2 df for a 3 level factor, and I suspect internally the error term is calculated by pooling across multiple contrasts. While very useful, I am wondering if there is way to get aov to calculate the residual error term only based on the specified contrasts (i.e., not assume homogeneity of variance and sphericity) for that strata? If not, I could calculate them directly using model.matrix, but I've never done that. If that is the preferred solution, I'd also appreciate coding suggestions to do it efficiently. How would I do the same thing with a two factor anova where one factor is within-subjects and one is between... Condition Mapping SubjectABC 11 411 15 12 13 14 15 16 17 18 29 210 Mapping is a between-subject factor. Condition is a within-subject factor. There are 5 levels of mapping, 8 subjects nested in each level of mapping. For each of the 40 combinations of mapping and subject there are 3 observations, one in each level of the condition factor. I want to estimate the pooled error associated with the following set of 4 orthogonal contrasts: condition.L:mapping.L condition.L:mapping.Q condition.L:mapping.C condition.L:mapping^4 What is the best way to do this? One way is to estimate the linear contrast for condition for each subject, create a 40 row matrix where the measure for each combination of mapping and subject is the linear contrast on condition. If I pass this dataframe to aov, the mse it returns is the value I am looking for. If possible, I would like to obtain the estimate without collapsing the dataframe, but am not sure how to proceed. Suggestions? Thanks, Steve __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Need R-help
Dear r users, I was trying to fit a garch(1,1) model to my dataset. But while executing I got a warning message NaNs produced in: sqrt(pred$e). And got the estimated sd's along with five NA, but as per my best knowledge I should get only one NA i.e. corresponding to the first observation only. If anyone tell me why I got this message it will be a great advantage for me. With regards, thanks in advance - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] where is the fitted value of autoregressive AR function in R?
myAR3=ar(mytimeseries, FALSE, 3); print(myAR3); Call: ar(x = mytimeseries, aic = FALSE, order.max = 3) Coefficients: 123 0.9220 0.0039 -0.1314 names(myAR) [1] orderar var.pred x.mean aic [6] n.used order.maxpartialacf resid method [11] series frequencycall asy.var.coef But where are the fitted values? And how can I construct the AR values from those terms in myAR? Thanks a lot! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] forcing apply() to return data frame
Hi All, I am (almost) successfully using apply() to apply a function recursively on a data matrix. The function is question is as.genotype() from the library 'genetics' apply(subset(chr1, names$breed == 'lab'),2,as.genotype,sep =) Unfortuantely apply puts it's results into a matrix object rather than a data frame, tranforming my factors into numerics and making the results useless. Is there a way of forcing apply() to return a data frame rather than a matrix? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] there is no xls reader in R?
I have used the following successfully: xls = odbcConnectExcel(fname) Rawdata.temp = sqlQuery( chan, select * from [sheet1$], max=2800 ) close(xls) Presuming your data is in the Excel tab sheet1. Of course, this assumes that column headers are in the first row. Greg Johnson -Original Message- From: roger bos [mailto:[EMAIL PROTECTED] Sent: Thursday, April 20, 2006 6:14 AM To: Ko-Kang Kevin Wang Cc: R-help@stat.math.ethz.ch Subject: Re: [R] there is no xls reader in R? I like to use the RODBC package for doing this. Here is my code sample: xls - odbcConnectExcel(fname) rawdata.temp - sqlFetch(xls, rawdata, max=2800) close(xls) fname is the full path to the file and rawdata is the name of the excel sheet I want to import. I tried one other approach (I think it was read.xls()) and that approach used perl scripts to read in the xls file and was very slow. RODBC is very fast and has always worked great for me. Haven't tried any of the other ways mentioned. On 4/20/06, Ko-Kang Kevin Wang [EMAIL PROTECTED] wrote: Have a look at the read.xls() in gdata package. HTH, Kevin Michael wrote: Currently I have to convert all my xls into csv before I can read it in and process the excel data in R... Is there a way to directly read in xls data? Thanks a lot! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Ko-Kang Kevin Wang Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7471 Ph (M): +61-40-451-8301 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R and ViM
Yes, my r.vim ftplugin file is a windows only solution. It is not yet at the point, however, where it may be called a solution. :) It currently only handles single lines of code. I posted it before only as a proof of concept. I should have been clearer in my earier post. For my Linux computer I have been successfully using the R.vim script by Johannes Ranke found in the vim scripts: http://www.vim.org/scripts/script.php?script_id=1048 This also uses Perl, but depends on IO::Pty, which (although I am no expert) I do not believe is available for Windows. --Bill -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jose Quesada Sent: Thursday, April 20, 2006 9:15 PM To: r-help@stat.math.ethz.ch Subject: [R] R and ViM To: Martin Maechler [EMAIL PROTECTED] Indeed. Please do check the archives. Yep. Post is there. Now back to the subject: Jose, I think your main contribution is based on autoHotKeys and that only works on Windoze, right? Michael explicitly mentioned he's working in Mac OS X. Martin That's correct, autoHotKeys is a win-only solution. Bill West's solution uses use Win32::OLE, so I guess that means it's win-only solution. I think François Pinard's is the easiest since it uses vim and R only (no 3rd application/language requireed), and that would probably work in all platforms (not sure if the GNU readline inferface is implemented in all builds of R, though). I find autoHotKey very useful (e.g., it fires vim to fill textboxes like this one -gmail editing window-, offering syntax highlighting etc) so I use it all the time and don't mind. I can understand those who don't want to install it just to communicate R and an editor. In that case, the other two solutions are better. I'll refer to them in my Rvim page (archives). However, the new R.vim syntax file has 3-level coloring, and I'm working to get improved indentation, TODO, DEBUG, etc highlighting, and other improvements. The code templates using tSkeleton (not ready yet) may be an added advantage. Those two things you can use even if you don't use autohotkeys of course. -- Cheers, -Jose PS: it seems that google mail (as an email reader) doesn't let you see your own messages when posting to a list you are subscribed to. -- Jose Quesada, PhD. [EMAIL PROTECTED] Dept. of Psychology http://www.andrew.cmu.edu/~jquesada Sussex University Brighton, UK -- Cheers, -Jose -- Jose Quesada, PhD. [EMAIL PROTECTED] Dept. of Psychology http://www.andrew.cmu.edu/~jquesada Sussex University Brighton, UK __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] programming advice?
Dear R-helpers: I am doing some exploratory programming and am considering a routine that has several other routines defined within it, so that I can avoid a large and messy global re-programming to avoid naming conflicts. My question is this: Because it is interpreted, does R have to re-build these internal routines every time the new routine is called? I'm not overly worried right now about speed, but since my test cases currently run for several minutes (which is a long time to me) I don't want to learn a lesson the hard way that you, kind readers, might help me avoid. Thanks. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] forcing apply() to return data frame
On Fri, 21 Apr 2006, Federico Calboli wrote: Hi All, I am (almost) successfully using apply() to apply a function recursively on a data matrix. The function is question is as.genotype() from the library 'genetics' apply(subset(chr1, names$breed == 'lab'),2,as.genotype,sep =) Unfortuantely apply puts it's results into a matrix object rather than a data frame, tranforming my factors into numerics and making the results useless. Is there a way of forcing apply() to return a data frame rather than a matrix? The conversion to a matrix happens on the way in to apply, not on the way out, so no. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] programming advice?
On 4/21/2006 10:45 AM, Charles Annis, P.E. wrote: Dear R-helpers: I am doing some exploratory programming and am considering a routine that has several other routines defined within it, so that I can avoid a large and messy global re-programming to avoid naming conflicts. My question is this: Because it is interpreted, does R have to re-build these internal routines every time the new routine is called? I'm not overly worried right now about speed, but since my test cases currently run for several minutes (which is a long time to me) I don't want to learn a lesson the hard way that you, kind readers, might help me avoid. I don't know the exact breakdown of the timing, but much of the work is done only once, when the source is parsed. At that point the outer function will be created in a structure parts of which are more or less identical to the structure of the functions that it creates within it. Then when it executes, copies need to be made and wrapped up as objects of their own. Only the latter work needs to be repeated on every call. I'd say avoiding naming conflicts is probably not a good enough reason on its own to use nested functions. You're better off putting your code in a package with a NAMESPACE if that's your goal. The main reason to use nested functions is for clarity: if some part of the work of a big function is neatly encapsulated in a small nested function, then do it. Those nested functions have access to the evaluation environment of their enclosing function. There are other reasons for nested functions (e.g. to create functions with static storage), but they are less common than doing it just to make the code clear. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] programming advice?
On Fri, 21 Apr 2006, Charles Annis, P.E. wrote: Dear R-helpers: I am doing some exploratory programming and am considering a routine that has several other routines defined within it, so that I can avoid a large and messy global re-programming to avoid naming conflicts. My question is this: Because it is interpreted, does R have to re-build these internal routines every time the new routine is called? I'm not overly worried right now about speed, but since my test cases currently run for several minutes (which is a long time to me) I don't want to learn a lesson the hard way that you, kind readers, might help me avoid. Yes and no. The code will be parsed once, but the functions will be created each time the routine is called. This results in some extra memory turnover, but is almost certainly not significant in the grand scheme of things. Another approach to avoiding name conflicts is to put your code in a package with a namespace and export only the functions you want to be visible externally. You might want to run your code under the profiler (?Rprof) to find out where it is really spending all its time. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] programming advice?
Charles Annis, P.E. [EMAIL PROTECTED]
writes:
Dear R-helpers:
I am doing some exploratory programming and am considering a routine that
has several other routines defined within it, so that I can avoid a large
and messy global re-programming to avoid naming conflicts.
My question is this: Because it is interpreted, does R have to re-build
these internal routines every time the new routine is called?
If you mean:
f - function(x) {
f1 - function(y) {...}
f2 - function(y) {...}
f3 - function(y) {...}
f1(x) + f2(x) + f3(x)
}
Then, yes, as I understand it, each call to f() will include the
overhead of defining functions f1, f2, and f3. In most cases, I would
expect this overhead to be quite small in relation to the actual
computations you are doing. You can probably use Rprof() to confirm
this.
You can also look at local() which I think provides a similar local
namespace, but would not require redefinition of the helper functions.
Here is a small example:
f - local({
f1 - function(y) 2*y
f2 - function(y) y + 10
function(x) {
f1(x) + f2(x)
}
})
+ seth
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Re: [R] forcing apply() to return data frame
On Fri, 2006-04-21 at 07:37 -0700, Thomas Lumley wrote: On Fri, 21 Apr 2006, Federico Calboli wrote: Hi All, I am (almost) successfully using apply() to apply a function recursively on a data matrix. The function is question is as.genotype() from the library 'genetics' apply(subset(chr1, names$breed == 'lab'),2,as.genotype,sep =) Unfortuantely apply puts it's results into a matrix object rather than a data frame, tranforming my factors into numerics and making the results useless. Is there a way of forcing apply() to return a data frame rather than a matrix? The conversion to a matrix happens on the way in to apply, not on the way out, so no. This may be a naive example, as I don't work in this domain, but based upon reviewing the online help at: http://finzi.psych.upenn.edu/R/library/genetics/html/genotype.html and presuming that the intent of the code above is referenced by the first bullet in the Details section of the function, would the following work? This presumes that 'chr1' is a data frame or can be coerced to one as in: chr1 - as.data.frame(chr1) Thus: data.frame(lapply(subset(chr1, names$breed == 'lab'), as.genotype, sep =)) HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How does ccf() really work?
The standard estimate of cross correlation uses the same denominator for all lags AND ignores the reduction in the number of observations. Consider the following: a. - a-mean(a) b. - b-mean(b) SSa - sum(a.^2) SSb - sum(b.^2) SaSb - sqrt(SSa*SSb) sum(a.*b.)/SaSb # 0.618 = cor(a, b) sum(a.[-1]*b.[-5])/SaSb # 0.568 = cc lag 1 sum(a.[1]*b.[5])/SaSb # -0.065 sum(a.[1:2]*b.[4:5])/SaSb # -0.289 These numbers match the results you reported below. If I'm not mistaken, this also matches the definition of the cross correlation function in the original Box and Jenkins book [or the more recent Box, Jenkins, Reinsel], Time Series Analysis, Forecasting and Control. The rationale, as I recall, is to reduce the false alarm rate by biasing estimates with larger lags toward zero, thereby compensating slightly for their increased random variability. hope this helps. spencer graves p.s. Thanks for including such a simple, self-contained example. Posts that don't include examples like this are typically much more difficult to understand, which in turn increases the chances that a response will not help the questionner. Robert Lundqvist wrote: I can't understand the results from cross-correlation function ccf() even though it should be simple. Here's my short example: * a-rnorm(5);b-rnorm(5) a;b [1] 1.4429135 0.8470067 1.2263730 -1.8159190 -0.6997260 [1] -0.4227674 0.8602645 -0.6810602 -1.4858726 -0.7008563 cc-ccf(a,b,lag.max=4,type=correlation) cc Autocorrelations of series 'X', by lag -4 -3 -2 -1 0 1 2 3 4 -0.056 -0.289 -0.232 0.199 0.618 0.568 -0.517 -0.280 -0.012 ** With lag 4 and vectors of length 5 there should as far as I can see only be 2 pairs of observations. The correlation would then be 1. Guess I am missing something really simple here. Anyone who could explain what is happening? Robert __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R graph strip in Greek Letters
Hi all, I have one question on xyplot() function. I am trying to produce a graph by this code. tmp - data.frame(a=rnorm(20), b=rnorm(20), rho=factor(rep(1:2, c(10,10))), k=factor(rep(1:5,4))) tmp.lattice - xyplot(a ~ b | rho*k, data=tmp, par.strip.text=list(font=5), strip=function(...) strip.default(..., strip.names=c(TRUE,TRUE))) names(tmp.lattice$condlevels) - c(k,r) tmp.lattice You can see that on the strip, I have both k and rho in greek letters. I ONLY want rho to be greek letter and remain k as an ordinary lower case 'k'. The other question is, can I change the : into = in the strip? Thanks a lot. Zijiang [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] forcing apply() to return data frame
Hi, There is a frameApply fynction in the library gdata from the gregmisc package. The manual says it is like the function 'by', but returns a data.frame. Maybe this is something for you? /Fredrik 2006/4/21, Federico Calboli [EMAIL PROTECTED]: Hi All, I am (almost) successfully using apply() to apply a function recursively on a data matrix. The function is question is as.genotype() from the library 'genetics' apply(subset(chr1, names$breed == 'lab'),2,as.genotype,sep =) Unfortuantely apply puts it's results into a matrix object rather than a data frame, tranforming my factors into numerics and making the results useless. Is there a way of forcing apply() to return a data frame rather than a matrix? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] aov contrasts residual error calculation
why not using lme() ? first, you need transform data: dat2 - as.data.frame(lapply(subset(dat, sel=-c(A,B,C)), rep, 3)) dat2$y - unlist(subset(dat, sel=c(A,B,C)), F, F) dat2$cond - factor(rep(c(A,B,C), each=nrow(dat))) dat2$inter - factor(dat2$map):factor(dat2$cond) lme1 - lme(fixed = y ~ mapping + cond + inter + other fixed effects, random = ~ 1 |subj, data=dat2, contrast=list(inter=poly(nlevels(dat2$inter)[,1:4])) Steven Lacey a écrit : Hi, I am using aov with an Error component to model some repeated measures data. By repeated measures I mean the data look something like this... subjABC 1 411 15 2 312 17 3 5914 4 610 18 For each subject I have 3 observations, one in each of three conditions (A, B, C). I want to test the following contrast (1, 0, -1). One solution is to apply the contrast weights at the subject level explicitly and then call t.test on the difference scores. However, I am looking for a more robust solution as I my actual design has more within-subjects factors and one or more between subjects factors. A better solution is to specify the contrast in an argument to aov. The estimated difference of the contrast is the same as that in the paired t-test, but the residual df are double. While not what I expected, it follows from the documentation, which explicitly states that these contrasts are not to be used for any error term. Even though I specify 1 contrast, there are 2 df for a 3 level factor, and I suspect internally the error term is calculated by pooling across multiple contrasts. While very useful, I am wondering if there is way to get aov to calculate the residual error term only based on the specified contrasts (i.e., not assume homogeneity of variance and sphericity) for that strata? If not, I could calculate them directly using model.matrix, but I've never done that. If that is the preferred solution, I'd also appreciate coding suggestions to do it efficiently. How would I do the same thing with a two factor anova where one factor is within-subjects and one is between... Condition Mapping SubjectABC 11 411 15 12 13 14 15 16 17 18 29 210 Mapping is a between-subject factor. Condition is a within-subject factor. There are 5 levels of mapping, 8 subjects nested in each level of mapping. For each of the 40 combinations of mapping and subject there are 3 observations, one in each level of the condition factor. I want to estimate the pooled error associated with the following set of 4 orthogonal contrasts: condition.L:mapping.L condition.L:mapping.Q condition.L:mapping.C condition.L:mapping^4 What is the best way to do this? One way is to estimate the linear contrast for condition for each subject, create a 40 row matrix where the measure for each combination of mapping and subject is the linear contrast on condition. If I pass this dataframe to aov, the mse it returns is the value I am looking for. If possible, I would like to obtain the estimate without collapsing the dataframe, but am not sure how to proceed. Suggestions? Thanks, Steve __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- --- [EMAIL PROTECTED] CNRS UMR 8090 - http://www-good.ibl.fr Génomique et physiologie moléculaire des maladies métaboliques I.B.L 2eme etage - 1 rue du Pr Calmette, B.P.245, 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] programming advice?
Many thanks to Duncan Murdoch, Thomas Lumley, Patrick Burns, and Seth Falcon, for the illuminating advice, which will be found in the R-help archives. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Charles Annis, P.E. Sent: Friday, April 21, 2006 10:46 AM To: R-help@stat.math.ethz.ch Subject: [R] programming advice? Dear R-helpers: I am doing some exploratory programming and am considering a routine that has several other routines defined within it, so that I can avoid a large and messy global re-programming to avoid naming conflicts. My question is this: Because it is interpreted, does R have to re-build these internal routines every time the new routine is called? I'm not overly worried right now about speed, but since my test cases currently run for several minutes (which is a long time to me) I don't want to learn a lesson the hard way that you, kind readers, might help me avoid. Thanks. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] aov contrasts residual error calculation
Jacques, Thanks for the reply. I am not using lme because I dont have the time to understand how it works and I have a balanced design, so typcial linear modelling in aov should be sufficient for my purposes. Down the road I plan to learn lme, but I'm not there yet. So any suggestions with respect to aov would be greatly appreciated. Steve -Original Message- From: Jacques Veslot [mailto:[EMAIL PROTECTED] Sent: Friday, April 21, 2006 11:58 AM To: Steven Lacey Cc: r-help@stat.math.ethz.ch Subject: Re: [R] aov contrasts residual error calculation why not using lme() ? first, you need transform data: dat2 - as.data.frame(lapply(subset(dat, sel=-c(A,B,C)), rep, 3)) dat2$y - unlist(subset(dat, sel=c(A,B,C)), F, F) dat2$cond - factor(rep(c(A,B,C), each=nrow(dat))) dat2$inter - factor(dat2$map):factor(dat2$cond) lme1 - lme(fixed = y ~ mapping + cond + inter + other fixed effects, random = ~ 1 |subj, data=dat2, contrast=list(inter=poly(nlevels(dat2$inter)[,1:4])) Steven Lacey a écrit : Hi, I am using aov with an Error component to model some repeated measures data. By repeated measures I mean the data look something like this... subjABC 1 411 15 2 312 17 3 5914 4 610 18 For each subject I have 3 observations, one in each of three conditions (A, B, C). I want to test the following contrast (1, 0, -1). One solution is to apply the contrast weights at the subject level explicitly and then call t.test on the difference scores. However, I am looking for a more robust solution as I my actual design has more within-subjects factors and one or more between subjects factors. A better solution is to specify the contrast in an argument to aov. The estimated difference of the contrast is the same as that in the paired t-test, but the residual df are double. While not what I expected, it follows from the documentation, which explicitly states that these contrasts are not to be used for any error term. Even though I specify 1 contrast, there are 2 df for a 3 level factor, and I suspect internally the error term is calculated by pooling across multiple contrasts. While very useful, I am wondering if there is way to get aov to calculate the residual error term only based on the specified contrasts (i.e., not assume homogeneity of variance and sphericity) for that strata? If not, I could calculate them directly using model.matrix, but I've never done that. If that is the preferred solution, I'd also appreciate coding suggestions to do it efficiently. How would I do the same thing with a two factor anova where one factor is within-subjects and one is between... Condition Mapping SubjectABC 11 411 15 12 13 14 15 16 17 18 29 210 Mapping is a between-subject factor. Condition is a within-subject factor. There are 5 levels of mapping, 8 subjects nested in each level of mapping. For each of the 40 combinations of mapping and subject there are 3 observations, one in each level of the condition factor. I want to estimate the pooled error associated with the following set of 4 orthogonal contrasts: condition.L:mapping.L condition.L:mapping.Q condition.L:mapping.C condition.L:mapping^4 What is the best way to do this? One way is to estimate the linear contrast for condition for each subject, create a 40 row matrix where the measure for each combination of mapping and subject is the linear contrast on condition. If I pass this dataframe to aov, the mse it returns is the value I am looking for. If possible, I would like to obtain the estimate without collapsing the dataframe, but am not sure how to proceed. Suggestions? Thanks, Steve __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- --- [EMAIL PROTECTED] CNRS UMR 8090 - http://www-good.ibl.fr Génomique et physiologie moléculaire des maladies métaboliques I.B.L 2eme etage - 1 rue du Pr Calmette, B.P.245, 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R debugging options
Regarding a function that lists functions, have you considered
getFunctions in library(svIDE)? You need to provide the argument, as
in getFunctions(1); getFunctions() returns an error message.
Beyond this, the objects function in S-Plus (at least version 6.2)
has a classes argument, which the R 2.2.1 implementation does not
have. It doesn't look like it would be too difficult to add such an
argument to objects in R, but I have not been in a position to
volunteer to do it, and without that, I didn't feel it was appropriate
for me to suggest it.
hope this helps,
spencer graves
John Fox wrote:
Dear Larry,
I'm not aware of an existing function that lists functions, but here's a
simple solution:
listFunctions - function(all.names=FALSE, envir=.GlobalEnv){
# all.names=TRUE: include names beginning with .
# envir: environment to search
Objects - objects(envir, all.names=all.names)
if (length(Objects) == 0) Objects
else names(which(sapply(Objects,
function(object) is.function(eval(parse(text=object),
envir=envir)
}
Getting mtrace() to use the function names returned by listFunctions() is a
bit tricky, because of the way mtrace() evaluates its arguments. You could
do something like the following:
for(f in listFunctions()) mtrace(char.fname=f)
Perhaps someone else knows of an existing or better solution.
I hope this helps,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Larry Howe
Sent: Tuesday, April 18, 2006 12:46 PM
To: r-help@stat.math.ethz.ch
Subject: Re: [R] R debugging options
On Monday April 17 2006 21:08, Francisco J. Zagmutt wrote:
RSiteSearch(debug) or RSiteSearch(debugging) will give
you a lot
or relevant information. I personally use library(debug)
extensivelly
and it should do all the taks you asked about. There is a
nice article
describing the debug lilbrary in the 2003/3 issue of R News
http://cran.r-project.org/doc/Rnews/Rnews_2003-3.pdf
Cheers
Francisco
Wow! That is a great package. I think it does all I need.
Is there a way to turn on debugging for all loaded functions?
My source file contains many functions and I would prefer not
to have to mtrace() each one.
Something like
mtrace(how_do_I_get_a_list_of_all_loaded_functions)
?
Larry
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Re: [R] aov contrasts residual error calculation
with error strata, aov() becomes difficult too... a nice and brief presentation of mixed models with r by John Fox at: http://cran.r-project.org/doc/contrib/Fox-Companion/appendix.html Steven Lacey a écrit : Jacques, Thanks for the reply. I am not using lme because I don’t have the time to understand how it works and I have a balanced design, so typcial linear modelling in aov should be sufficient for my purposes. Down the road I plan to learn lme, but I'm not there yet. So any suggestions with respect to aov would be greatly appreciated. Steve -Original Message- From: Jacques Veslot [mailto:[EMAIL PROTECTED] Sent: Friday, April 21, 2006 11:58 AM To: Steven Lacey Cc: r-help@stat.math.ethz.ch Subject: Re: [R] aov contrasts residual error calculation why not using lme() ? first, you need transform data: dat2 - as.data.frame(lapply(subset(dat, sel=-c(A,B,C)), rep, 3)) dat2$y - unlist(subset(dat, sel=c(A,B,C)), F, F) dat2$cond - factor(rep(c(A,B,C), each=nrow(dat))) dat2$inter - factor(dat2$map):factor(dat2$cond) lme1 - lme(fixed = y ~ mapping + cond + inter + other fixed effects, random = ~ 1 |subj, data=dat2, contrast=list(inter=poly(nlevels(dat2$inter)[,1:4])) Steven Lacey a écrit : Hi, I am using aov with an Error component to model some repeated measures data. By repeated measures I mean the data look something like this... subjABC 1 411 15 2 312 17 3 5914 4 610 18 For each subject I have 3 observations, one in each of three conditions (A, B, C). I want to test the following contrast (1, 0, -1). One solution is to apply the contrast weights at the subject level explicitly and then call t.test on the difference scores. However, I am looking for a more robust solution as I my actual design has more within-subjects factors and one or more between subjects factors. A better solution is to specify the contrast in an argument to aov. The estimated difference of the contrast is the same as that in the paired t-test, but the residual df are double. While not what I expected, it follows from the documentation, which explicitly states that these contrasts are not to be used for any error term. Even though I specify 1 contrast, there are 2 df for a 3 level factor, and I suspect internally the error term is calculated by pooling across multiple contrasts. While very useful, I am wondering if there is way to get aov to calculate the residual error term only based on the specified contrasts (i.e., not assume homogeneity of variance and sphericity) for that strata? If not, I could calculate them directly using model.matrix, but I've never done that. If that is the preferred solution, I'd also appreciate coding suggestions to do it efficiently. How would I do the same thing with a two factor anova where one factor is within-subjects and one is between... Condition Mapping SubjectABC 11 411 15 12 13 14 15 16 17 18 29 210 Mapping is a between-subject factor. Condition is a within-subject factor. There are 5 levels of mapping, 8 subjects nested in each level of mapping. For each of the 40 combinations of mapping and subject there are 3 observations, one in each level of the condition factor. I want to estimate the pooled error associated with the following set of 4 orthogonal contrasts: condition.L:mapping.L condition.L:mapping.Q condition.L:mapping.C condition.L:mapping^4 What is the best way to do this? One way is to estimate the linear contrast for condition for each subject, create a 40 row matrix where the measure for each combination of mapping and subject is the linear contrast on condition. If I pass this dataframe to aov, the mse it returns is the value I am looking for. If possible, I would like to obtain the estimate without collapsing the dataframe, but am not sure how to proceed. Suggestions? Thanks, Steve __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- --- [EMAIL PROTECTED] CNRS UMR 8090 - http://www-good.ibl.fr Génomique et physiologie moléculaire des maladies métaboliques I.B.L 2eme etage - 1 rue du Pr Calmette, B.P.245, 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Titles in MAplots
Hi Does anyone know how to set the titles in MAplots to just show the CEL file name? So far I have; #define 'Array' as object containing CEL names Array - col.names(Data) #open bmp and make a separate bmp for each MAplot bmp(C:/MAplot%03d.bmp) #remove the annotation and minimise margins par(ann=FALSE) par(mar=c(1,1,1,1)) #MAplot MAplot(Data... Does anyone know the correct arguments? Do I need to create another parameter value? Tony [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] aov contrasts residual error calculation
Hi, Steve: I'm on the opposite extreme: I don't know aov, and given that it is largely obsolete, I'm not too eager to learn it. spencer graves Steven Lacey wrote: Jacques, Thanks for the reply. I am not using lme because I don’t have the time to understand how it works and I have a balanced design, so typcial linear modelling in aov should be sufficient for my purposes. Down the road I plan to learn lme, but I'm not there yet. So any suggestions with respect to aov would be greatly appreciated. Steve -Original Message- From: Jacques Veslot [mailto:[EMAIL PROTECTED] Sent: Friday, April 21, 2006 11:58 AM To: Steven Lacey Cc: r-help@stat.math.ethz.ch Subject: Re: [R] aov contrasts residual error calculation why not using lme() ? first, you need transform data: dat2 - as.data.frame(lapply(subset(dat, sel=-c(A,B,C)), rep, 3)) dat2$y - unlist(subset(dat, sel=c(A,B,C)), F, F) dat2$cond - factor(rep(c(A,B,C), each=nrow(dat))) dat2$inter - factor(dat2$map):factor(dat2$cond) lme1 - lme(fixed = y ~ mapping + cond + inter + other fixed effects, random = ~ 1 |subj, data=dat2, contrast=list(inter=poly(nlevels(dat2$inter)[,1:4])) Steven Lacey a écrit : Hi, I am using aov with an Error component to model some repeated measures data. By repeated measures I mean the data look something like this... subjABC 1 411 15 2 312 17 3 5914 4 610 18 For each subject I have 3 observations, one in each of three conditions (A, B, C). I want to test the following contrast (1, 0, -1). One solution is to apply the contrast weights at the subject level explicitly and then call t.test on the difference scores. However, I am looking for a more robust solution as I my actual design has more within-subjects factors and one or more between subjects factors. A better solution is to specify the contrast in an argument to aov. The estimated difference of the contrast is the same as that in the paired t-test, but the residual df are double. While not what I expected, it follows from the documentation, which explicitly states that these contrasts are not to be used for any error term. Even though I specify 1 contrast, there are 2 df for a 3 level factor, and I suspect internally the error term is calculated by pooling across multiple contrasts. While very useful, I am wondering if there is way to get aov to calculate the residual error term only based on the specified contrasts (i.e., not assume homogeneity of variance and sphericity) for that strata? If not, I could calculate them directly using model.matrix, but I've never done that. If that is the preferred solution, I'd also appreciate coding suggestions to do it efficiently. How would I do the same thing with a two factor anova where one factor is within-subjects and one is between... Condition Mapping SubjectABC 11 411 15 12 13 14 15 16 17 18 29 210 Mapping is a between-subject factor. Condition is a within-subject factor. There are 5 levels of mapping, 8 subjects nested in each level of mapping. For each of the 40 combinations of mapping and subject there are 3 observations, one in each level of the condition factor. I want to estimate the pooled error associated with the following set of 4 orthogonal contrasts: condition.L:mapping.L condition.L:mapping.Q condition.L:mapping.C condition.L:mapping^4 What is the best way to do this? One way is to estimate the linear contrast for condition for each subject, create a 40 row matrix where the measure for each combination of mapping and subject is the linear contrast on condition. If I pass this dataframe to aov, the mse it returns is the value I am looking for. If possible, I would like to obtain the estimate without collapsing the dataframe, but am not sure how to proceed. Suggestions? Thanks, Steve __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R graph strip in Greek Letters
zj yang wrote:
Hi all,
I have one question on xyplot() function.
I am trying to produce a graph by this code.
tmp - data.frame(a=rnorm(20),
b=rnorm(20),
rho=factor(rep(1:2, c(10,10))),
k=factor(rep(1:5,4)))
tmp.lattice -
xyplot(a ~ b | rho*k, data=tmp,
par.strip.text=list(font=5),
strip=function(...) strip.default(..., strip.names=c(TRUE,TRUE)))
names(tmp.lattice$condlevels) - c(k,r)
tmp.lattice
You can see that on the strip, I have both k and rho in greek letters. I
ONLY want rho to be greek letter and remain k as an ordinary lower case 'k'.
The other question is, can I change the : into = in the strip? Thanks a
lot.
Zijiang
[[alternative HTML version deleted]]
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Does this help?
library(lattice)
trellis.par.set(theme = col.whitebg())
tmp - data.frame(a = rnorm(20),
b = rnorm(20),
rho = factor(rep(1:2, c(10,10))),
k = factor(rep(1:5,4)))
strip.math - function(which.given, which.panel, var.name,
factor.levels, ...) {
vn - var.name[which.given]
fl - factor.levels
expr - paste(vn, ==, fl, collapse = ,)
expr - paste(expression(, expr, ), sep = )
fl - eval(parse(text = expr))
strip.default(which.given, which.panel, vn, fl, ...)
}
xyplot(a ~ b | rho*k, data=tmp, strip = strip.math)
The eval(parse(text = ...))) is the only way I know how to build a
valid expression for the plotmath functions. See ?plotmath for more
information.
HTH,
--sundar
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Re: [R] R and ViM
Bill West wrote: Yes, my r.vim ftplugin file is a windows only solution. It is not yet at the point, however, where it may be called a solution. :) It currently only handles single lines of code. I posted it before only as a proof of concept. I should have been clearer in my earier post. For my Linux computer I have been successfully using the R.vim script by Johannes Ranke found in the vim scripts: http://www.vim.org/scripts/script.php?script_id=1048 This also uses Perl, but depends on IO::Pty, which (although I am no expert) I do not believe is available for Windows. --Bill I've been following this thread with some interest as I use both R and VIM, but I just want to point out that we have come full circle by *not* answering the original thread creator's question: https://stat.ethz.ch/pipermail/r-help/2006-April/092554.html My question now is, whether there are already people out there knowing how to do this in a similar easy way as with Emacs, and if those would be willing to share this knowledge. I did already research on the web on this topic, but i couldn't find satisfying answers, except one good looking approach on the ViM-website with a perl-script called funnel.pl, which I couldn't make running on my mac OSX 10.3.9 so far. So this last post suggests that the VIM script (id 1048) is useful (which it is), but in fact the original thread creator already stated that it doesn't work for his platform. The real answer is: there's probably no current 'similar way as with Emacs [and ESS]' to integrate R and VIM on mac OSX 10.3.9, but I bet you might find a better answer on the R-SIG-Mac email list here: https://stat.ethz.ch/mailman/listinfo/r-sig-mac So I hope this helps, Michael. ... I point all this out to illuminate how hard it is to both convey a message in email and also to interpret a message in email, to the point that responses to questions on this list can really wander off on tangents (which is not necessarily a bad thing; I had no clue the R.vim script existed for Linux). I personally find benefit in reading both the R-help and R-devel mailing lists, and I commend and am thankful for all those email authors who convey their message in email with sincerity, honesty, etc. There was a recent Wired article here: http://www.wired.com/news/technology/0,70179-0.html that cited a Journal of Personality and Social Psychology paper titled Egocentrism over e-mail: Can we communicate as well as we think?: http://content.apa.org/journals/psp/89/6 which essentially points out the fact that determining the tone of an author's email is no better than chance, which I believe can lead to misinterpretation of message and meaning, and especially when authors use negative messages like RTFM (google it; you'll figure it out quickly). -- Jeffrey Horner Computer Systems Analyst School of Medicine 615-322-8606 Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Considering port of SAS application to R
Now it sounds like a consense that it is not advisable to do everything in R but to use a database system and scripting language instead for the rough work. Thanks for all of your suggestions! Werner Steve Miller [EMAIL PROTECTED] schrieb: Good suggestion. Multiple gigabytes is stretching it with R. Use PostgreSQL Python, and Python DBI database connectivity to replace your SAS data step, then use the RODBC package to import data into R convenience stores as appropriate. Steve Miller -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of bogdan romocea Sent: Friday, April 21, 2006 7:59 AM To: [EMAIL PROTECTED] Cc: r-help Subject: Re: [R] Considering port of SAS application to R Forget about R for now and port the application to MySQL/PostgreSQL etc, it is possible and worthwhile. In case you happen to use (and really need) some SAS DATA STEP looping features you might be forced to look into SQL cursors, otherwise the port should be (very) straightforward. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Werner Wernersen Sent: Friday, April 21, 2006 7:09 AM To: r-help@stat.math.ethz.ch Subject: [R] Considering port of SAS application to R Hi there! I am considering to port a SAS application to R and I would like to hear your opinion if you think this is possible and worthwhile. SAS is mainly used to do data management and then to do some aggregations and simple computations on the data and to output a modified data set. The main problem I see is the size of the data file. As I have no access to SAS yet I cannot give real details but the SAS data file is about 7 gigabytes large. (It's only the basic SAS system without any additional modules) What do you think, would a port to R be possible with reasonable effort? Is R able to handle that size of data? Or is R prepared to work together with some database system? Thanks for your thoughts! Best regards, Werner - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] AIC and numbers of parameters
Hi. I'm fairly new to R and have a quick question regarding AIC, logLik and numbers of parameters. I see that there has been some correspondence on this in the past but none of the threads seem to have been satisfactorily resolved. I have been trying to use R to obtain AIC for fitted models and then to extrapolate to AICc. For example, using simple x-y regression data, I fitted a linear regression [lm(y~x)] and an exponential curve [nls(y~A*exp(B*x))]. AICs reported for these models are based on degrees of freedom of 3 and 2, respectively. It seems clear to me that the number of parameters in both cases is 3 (two coefficients plus the error term). Consequently, I'm dubious about the values of AIC provided by R. Equally, however, I'm reluctant to base my own calculations on logLik and my own estimates of K, without first determining why R uses the degrees of freedom it does. If anyone can explain why R gives different dfs for two models each with two parameters, I should be very grateful. Thanks, Phil __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] lmer{lme4}, poisson family and residuals
Amelie LESCROEL lescroel_cebc at no-log.org writes: Hello, Im trying to fit the following model: Dependent variable: MAXDEPTH (the maximum depth reached by a penguin during a given dive) Fixed effects: SUCCESSMN (an index of the individual quality of a bird), STUDYDAY (the day of the study, from -5 to 20, with 0=Dec 20), and the interaction SUCCESSMN*STUDYDAY Random effect: BIRD (the bird id, as each bird is performing several dives) It isn't immediately clear to me why the maximum depth should be Poisson-distributed ... as R is trying to tell you, Poisson distributions only make sense for integer data. Your best bets are probably (1) reconsider the error distribution, (2) perhaps trying using nlme instead of lmer -- it is more polished, and you can use Pinheiro and Bates Mixed-Effects Models in S and S-PLUS as a reference. Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] second try; writing user-defined GLM link function
Ok, I persuaded predict.glm to work with the default type (link) instead of response. However, I don't think it did what I expected it to do, as the output (which should be log-odds, right?) leads to non-sensical final daily survival rates (daily survival rate = probability of surviving that particular interval). For example, for a nest of age 67 days, the log-odds of survival are -53.88, leading to a daily survival rate of essentially 0 - not at all what was observed! I see two possibilities here. Either the predict function is not working as expected (still not accounting for interval length), or possibly something is off in my nest age temporal trend modeling (predicted log-odds values are reasonable up to MeanAge=44 or so). Anyone have any thoughts here? glm.24.pred-predict(glm.24, newdata=vc.new) glm.24.pred 1 2 3 4 5 6 7 6.0097208 5.5175350 5.0938348 4.7348110 4.4366542 4.193 4.0077050 8 9 10 11 12 13 14 3.8692940 3.7765131 3.7255530 3.7126045 3.7338582 3.7855051 3.8637357 15 16 17 18 19 20 21 3.9647409 4.0847113 4.2198379 4.3663111 4.5203220 4.6780610 4.8357191 22 23 24 25 26 27 28 4.9894870 5.134 5.2701150 5.3893566 5.4894710 5.5666488 5.6170809 29 30 31 32 33 34 35 5.6369580 5.6224707 5.5698100 5.4751664 5.3347309 5.1446940 4.9012465 36 37 38 39 40 41 42 4.6005793 4.2388830 3.8123484 3.3171662 2.7495272 2.1056221 1.3816416 43 44 45 46 47 48 49 0.5737766 -0.3217823 -1.3088443 -2.3912186 -3.5727145 -4.8571413 -6.2483083 50 51 52 53 54 55 56 -7.7500246 -9.3660995 -11.1003423 -12.9565623 -14.9385687 -17.0501707 -19.2951776 57 58 59 60 61 62 63 -21.6773987 -24.2006432 -26.8687203 -29.6854394 -32.6546097 -35.7800404 -39.0655408 64 65 66 67 -42.5149201 -46.1319876 -49.9205526 -53.8844243 On 4/20/06, Prof Brian Ripley [EMAIL PROTECTED] wrote: glm.24.pred-predict(glm.24,newdata=nestday, type=response, SE.fit=T) What is SE.fit? The help says se.fit. That _may_ be a problem. However, I think the real problem is that the link function argument includes a reference to vc.apfa$days that is appropriate for fitting, not prediction. One way out might be (untested) attach(va.apfa) glm.24 - glm(formula = Success ~ NestHtZ + MeanAge + I(MeanAge^2) + I(MeanAge^3), family = logexposure(ExposureDays = days), data = vc.apfa) detach() attach(nestday) glm.24.pred-predict(glm.24,newdata=nestday, type=response, SE.fit=T) detach() so that 'days' refers to the appropriate dataset both when fitting and predicting. (This is bending glm() to do something it was not designed to do, so some hoop-jumping is needed.) On Thu, 20 Apr 2006, Jessi Brown wrote: An update for all: Using the combined contributions from Mark and Dr. Ripley, I've been (apparently) successfully formulating both GLM's and GLMM's (using the MASS function glmmPQL) analyzing my nest success data. The beta parameter estimates look reasonable and the top models resemble those from earlier analyses using a different nest survival analysis approach. However, I've now run into problems when trying to predict the daily survival rates from fitted models. For example, for a model considering nest height (NestHtZ) and nest age effects (MeanAge and related terms; there is an overall cubic time trend in this model), I tried to predict the daily survival rate for each day out of a 67 day nest cycle (so MeanAge is a vector of 1 to 67) with mean nest height (also a vector 67 rows in length; both comprise the matrix nestday). Here's what happens: summary(glm.24) Call: glm(formula = Success ~ NestHtZ + MeanAge + I(MeanAge^2) + I(MeanAge^3), family = logexposure(ExposureDays = vc.apfa$days), data = vc.apfa) Deviance Residuals: Min 1Q Median 3Q Max -3.3264 -1.2341 0.6712 0.8905 1.5569 Coefficients: Estimate Std. Error z value Pr(|z|) (Intercept) 6.5742015 1.7767487 3.700 0.000215 *** NestHtZ 0.6205444 0.2484583 2.498 0.012504 * MeanAge -0.6018978 0.2983656 -2.017 0.043662 * I(MeanAge^2) 0.0380521 0.0152053 2.503 0.012330 * I(MeanAge^3) -0.0006349 0.0002358 -2.693 0.007091 ** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be
Re: [R] Parallel computing with the snow package: external file I/O possible?
Waichler, Scott R [EMAIL PROTECTED] writes:
genoud()) should be independent. However, in the code below, the
directory created by each node has the same random number in its name.
This is probably because 'random' numbers are generated starting from
a 'seed', the seed is determined (by default) from the system time,
and the system time on the two nodes is identical. The same seed is
being used, hence the same random number sequence.
See http://www.stat.uiowa.edu/~luke/R/cluster/cluster.html
Martin
I was expecting the contents of fun() or fn() to be independent from all
other executions of the same function. What am I missing here?
# Begin code
library(snow)
setDefaultClusterOptions(outfile=/tmp/cluster1)
setDefaultClusterOptions(master=moab)
cl - makeCluster(c(moab, escalante), type=SOCK)
# Define base pathname for output from my.test()
base.dir - ~
# Define a function that is called by clusterCall()
my.test - function(base.dir) {
this.host - as.character(system(hostname, intern=T))
this.rnd - sample(1:1e6, 1)
test.file - paste(sep=, base.dir, this.host, _, this.rnd)
file.create(test.file)
} # end my.test()
clusterCall(cl, my.test, base.dir)
stopCluster(cl)
# End code
For example, the files moab_65835 and escalante_65835 are created.
Regards,
Scott Waichler
Pacific Northwest National Laboratory
[EMAIL PROTECTED]
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[R] question in fitting AR model in time series?
How to force some AR coefficients to be ZERO and only allow the function ar in R to change the other coefficients? Thanks a lot! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Hmisc + summarize + quantile: Why only quantiles for first variable in data frame?
Hi Frank Harrell, thanks for the response. I understand your comment but I wasn't able to find (or recognize) an answer on how to tell FUN explicitely to use matrix operations. Would you be so kind and give me an example? Thanks so much, Kim Please read the documentation and see the examples. The first argument to summarize is a matrix or vector and if a matrix, FUN must use matrix operations if you want column-by-column results. FH -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University Kim Milferstedt wrote: Hi, I'm working on a data set that contains a couple of factors and a number of dependent variables. From all of these dependent variables I would like to calculate mean, standard deviation and quantiles. With the function FUN I get all the means and stdev that I want but quantiles are only calculated for the first of the dependent variables (column 8 in the summarize command). What do I have to do differently in order to get all the quantiles that I want? Thanks, Kim sgldm2- read.table(E:/analysistemp/060412_test_data2.txt, header=T) attach(sgldm2) names(sgldm2) FUN - function(x)c(Mean=mean(x,na.rm=TRUE), STDEV=sd(x,na.rm=TRUE), Quantile=quantile(x, probs= c(0.25,0.50,0.75),na.rm=TRUE)) ordering- llist(time_h_f, Distance_f) resALL - summarize(sgldm2[,8:10], ordering, FUN) __ Kim Milferstedt University of Illinois at Urbana-Champaign Department of Civil and Environmental Engineering 4125 Newmark Civil Engineering Building 205 North Mathews Avenue MC 250 Urbana, IL 61801 USA phone: (001) 217 333-9663 fax: (001) 217 333-6968 email: [EMAIL PROTECTED] http://cee.uiuc.edu/research/morgenroth/index.asp ___ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] question in fitting AR model in time series?
See argument ``fixed'' in help(arima). cheers, Rolf Turner [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Creat new column based on condition
Hi, How can I accomplish this task in R? V1 10 20 30 10 10 20 Create a new column V2 such that: If V1 = 10 then V2 = 4 If V1 = 20 then V2 = 6 V1 = 30 then V2 = 10 So the O/P looks like this V1 V2 10 4 20 6 30 10 10 4 10 4 20 6 Thanks in advance. Sachin __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Creat new column based on condition
Try: V1 - matrix(c(10, 20, 30, 10, 10, 20), nc = 1) V2 - 4 * (V1 == 10) + 6 * (V1 == 20) + 10 * (V1 == 30) or V2 - matrix(c(4, 6, 10)[V1/10], nc = 1) On 4/21/06, Sachin J [EMAIL PROTECTED] wrote: Hi, How can I accomplish this task in R? V1 10 20 30 10 10 20 Create a new column V2 such that: If V1 = 10 then V2 = 4 If V1 = 20 then V2 = 6 V1 = 30 then V2 = 10 So the O/P looks like this V1 V2 10 4 20 6 30 10 10 4 10 4 20 6 Thanks in advance. Sachin __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Creat new column based on condition
Hi Gabor, The first one works fine. Just out of curiosity, in second solution: I dont want to create a matrix. I want to add a new column to the existing dataframe (i.e. V2 based on the values in V1). Is there a way to do it? TIA Sachin Gabor Grothendieck [EMAIL PROTECTED] wrote: Try: V1 - matrix(c(10, 20, 30, 10, 10, 20), nc = 1) V2 - 4 * (V1 == 10) + 6 * (V1 == 20) + 10 * (V1 == 30) or V2 - matrix(c(4, 6, 10)[V1/10], nc = 1) On 4/21/06, Sachin J wrote: Hi, How can I accomplish this task in R? V1 10 20 30 10 10 20 Create a new column V2 such that: If V1 = 10 then V2 = 4 If V1 = 20 then V2 = 6 V1 = 30 then V2 = 10 So the O/P looks like this V1 V2 10 4 20 6 30 10 10 4 10 4 20 6 Thanks in advance. Sachin __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Creat new column based on condition
DF - data.frame(V1 = c(10, 20, 30, 10, 10, 20)) DF$V2 - with(DF, 4 * (V1 == 10) + 6 * (V1 == 20) + 10 * (V1 == 30)) DF$V3 - c(4, 6, 10)[DF$V1/10] or DF - data.frame(V1 = c(10, 20, 30, 10, 10, 20)) DF - transform(DF, V2 = 4 * (V1 == 10) + 6 * (V1 == 20) + 10 * (V1 == 30), V3 = c(4, 6, 10)[V1/10]) On 4/21/06, Sachin J [EMAIL PROTECTED] wrote: Hi Gabor, The first one works fine. Just out of curiosity, in second solution: I dont want to create a matrix. I want to add a new column to the existing dataframe (i.e. V2 based on the values in V1). Is there a way to do it? TIA Sachin Gabor Grothendieck [EMAIL PROTECTED] wrote: Try: V1 - matrix(c(10, 20, 30, 10, 10, 20), nc = 1) V2 - 4 * (V1 == 10) + 6 * (V1 == 20) + 10 * (V1 == 30) or V2 - matrix(c(4, 6, 10)[V1/10], nc = 1) On 4/21/06, Sachin J wrote: Hi, How can I accomplish this task in R? V1 10 20 30 10 10 20 Create a new column V2 such that: If V1 = 10 then V2 = 4 If V1 = 20 then V2 = 6 V1 = 30 then V2 = 10 So the O/P looks like this V1 V2 10 4 20 6 30 10 10 4 10 4 20 6 Thanks in advance. Sachin __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to control the data type
You can also try: round(runif(1)*10^4)/10^4 --Brett -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dirk Eddelbuettel Sent: Thursday, April 20, 2006 8:18 PM To: zhongmiao wang Cc: r-help@stat.math.ethz.ch Subject: Re: [R] how to control the data type On 20 April 2006 at 22:00, zhongmiao wang wrote: | Hello: | I am generating a random number with rnorm(1). The generated number | has 8 decimals. I don't want so many decimals. How to control the | number of decimals in R? You must have installed the professional version of R, just downgrade to the home version which has only four digits precision. Seriously, your equating display precision with the representation -- which is not correct. Consider: a - 1/3 print(a) [1] 0.333 print(a, digits=18) [1] 0.15 where the second print statement forces a display beyond the number of significant digits. So with that, your rnorm(1) result will also have more than the eight digits you saw earlier: print(rnorm(1), digits=18) [1] -0.201840514213267291 Hope this helps, Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R debugging options
Dear Spencer,
I wasn't aware of getFunctions(), though I've now taken a look at it. It's
pretty similar to listFunctions() (from my email to the list), except that
getFunctions() uses exists() rather than is.function() to test whether an
object is a function. There must be a reason for this, but I can't think
what it is, since in both cases the vector of object names shouldn't include
nonexistent objects.
Regards,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: Spencer Graves [mailto:[EMAIL PROTECTED]
Sent: Friday, April 21, 2006 11:21 AM
To: John Fox
Cc: 'Larry Howe'; r-help@stat.math.ethz.ch; Philippe Grosjean
Subject: Re: [R] R debugging options
Regarding a function that lists functions, have you
considered getFunctions in library(svIDE)? You need to
provide the argument, as
in getFunctions(1); getFunctions() returns an error message.
Beyond this, the objects function in S-Plus (at
least version 6.2) has a classes argument, which the R
2.2.1 implementation does not have. It doesn't look like it
would be too difficult to add such an argument to objects
in R, but I have not been in a position to volunteer to do
it, and without that, I didn't feel it was appropriate for me
to suggest it.
hope this helps,
spencer graves
John Fox wrote:
Dear Larry,
I'm not aware of an existing function that lists functions,
but here's
a simple solution:
listFunctions - function(all.names=FALSE, envir=.GlobalEnv){
# all.names=TRUE: include names beginning with .
# envir: environment to search
Objects - objects(envir, all.names=all.names)
if (length(Objects) == 0) Objects
else names(which(sapply(Objects,
function(object) is.function(eval(parse(text=object),
envir=envir)
}
Getting mtrace() to use the function names returned by
listFunctions()
is a bit tricky, because of the way mtrace() evaluates its
arguments.
You could do something like the following:
for(f in listFunctions()) mtrace(char.fname=f)
Perhaps someone else knows of an existing or better solution.
I hope this helps,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Larry Howe
Sent: Tuesday, April 18, 2006 12:46 PM
To: r-help@stat.math.ethz.ch
Subject: Re: [R] R debugging options
On Monday April 17 2006 21:08, Francisco J. Zagmutt wrote:
RSiteSearch(debug) or RSiteSearch(debugging) will give
you a lot
or relevant information. I personally use library(debug)
extensivelly
and it should do all the taks you asked about. There is a
nice article
describing the debug lilbrary in the 2003/3 issue of R News
http://cran.r-project.org/doc/Rnews/Rnews_2003-3.pdf
Cheers
Francisco
Wow! That is a great package. I think it does all I need.
Is there a way to turn on debugging for all loaded functions?
My source file contains many functions and I would prefer
not to have
to mtrace() each one.
Something like
mtrace(how_do_I_get_a_list_of_all_loaded_functions)
?
Larry
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Re: [R] Creat new column based on condition
On 4/21/2006 4:05 PM, Sachin J wrote: Hi, How can I accomplish this task in R? V1 10 20 30 10 10 20 Create a new column V2 such that: If V1 = 10 then V2 = 4 If V1 = 20 then V2 = 6 V1 = 30 then V2 = 10 Gabor's solution is fine; something that looks a little bit more like your code is this: V2 - NA V2 - ifelse( V1 == 10, 4, V2) V2 - ifelse( V1 == 20, 6, V2) V2 - ifelse( V1 == 30, 10, V2) or V2 - ifelse( V1 == 10, 4, ifelse( V1 == 20, 6, ifelse( V1 == 30, 10, NA ))) (where the NA is to handle any unexpected case where V1 isn't 10, 20 or 30). My preference would be to use just one assignment, and if I was sure 10, 20 and 30 were the only possibilities, would use V2 - ifelse( V1 == 10, 4, ifelse( V1 == 20, 6, 10 )) Duncan Murdoch So the O/P looks like this V1 V2 10 4 20 6 30 10 10 4 10 4 20 6 Thanks in advance. Sachin __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Hmisc + summarize + quantile: Why only quantiles for first variable in data frame?
Kim Milferstedt wrote: Hi Frank Harrell, thanks for the response. I understand your comment but I wasn't able to find (or recognize) an answer on how to tell FUN explicitely to use matrix operations. Would you be so kind and give me an example? Thanks so much, Kim See http://biostat.mc.vanderbilt.edu/SasByMeansExample plus an example in the help file for summary.formula in Hmisc which uses the apply function. summary.formula and summarize are similar in the use of FUN (which summary.formula unfortunately calls 'fun'). Frank Please read the documentation and see the examples. The first argument to summarize is a matrix or vector and if a matrix, FUN must use matrix operations if you want column-by-column results. FH -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University Kim Milferstedt wrote: Hi, I'm working on a data set that contains a couple of factors and a number of dependent variables. From all of these dependent variables I would like to calculate mean, standard deviation and quantiles. With the function FUN I get all the means and stdev that I want but quantiles are only calculated for the first of the dependent variables (column 8 in the summarize command). What do I have to do differently in order to get all the quantiles that I want? Thanks, Kim sgldm2- read.table(E:/analysistemp/060412_test_data2.txt, header=T) attach(sgldm2) names(sgldm2) FUN - function(x)c(Mean=mean(x,na.rm=TRUE), STDEV=sd(x,na.rm=TRUE), Quantile=quantile(x, probs= c(0.25,0.50,0.75),na.rm=TRUE)) ordering- llist(time_h_f, Distance_f) resALL - summarize(sgldm2[,8:10], ordering, FUN) __ Kim Milferstedt University of Illinois at Urbana-Champaign Department of Civil and Environmental Engineering 4125 Newmark Civil Engineering Building 205 North Mathews Avenue MC 250 Urbana, IL 61801 USA phone: (001) 217 333-9663 fax: (001) 217 333-6968 email: [EMAIL PROTECTED] http://cee.uiuc.edu/research/morgenroth/index.asp ___ -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Creat new column based on condition
Duncan Murdoch [EMAIL PROTECTED] writes: On 4/21/2006 4:05 PM, Sachin J wrote: Hi, How can I accomplish this task in R? V1 10 20 30 10 10 20 Create a new column V2 such that: If V1 = 10 then V2 = 4 If V1 = 20 then V2 = 6 V1 = 30 then V2 = 10 Gabor's solution is fine; something that looks a little bit more like your code is this: V2 - NA V2 - ifelse( V1 == 10, 4, V2) V2 - ifelse( V1 == 20, 6, V2) V2 - ifelse( V1 == 30, 10, V2) or V2 - ifelse( V1 == 10, 4, ifelse( V1 == 20, 6, ifelse( V1 == 30, 10, NA ))) (where the NA is to handle any unexpected case where V1 isn't 10, 20 or 30). My preference would be to use just one assignment, and if I was sure 10, 20 and 30 were the only possibilities, would use V2 - ifelse( V1 == 10, 4, ifelse( V1 == 20, 6, 10 )) Duncan Murdoch I think I'd go for something like V2 - c(4, 6, 10)[factor(V1, levels=c(10, 20, 30))] So the O/P looks like this V1 V2 10 4 20 6 30 10 10 4 10 4 20 6 Thanks in advance. Sachin __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Creat new column based on condition
Duncan Murdoch wrote: On 4/21/2006 4:05 PM, Sachin J wrote: Hi, How can I accomplish this task in R? V1 10 20 30 10 10 20 Create a new column V2 such that: If V1 = 10 then V2 = 4 If V1 = 20 then V2 = 6 V1 = 30 then V2 = 10 Gabor's solution is fine; something that looks a little bit more like your code is this: V2 - NA V2 - ifelse( V1 == 10, 4, V2) V2 - ifelse( V1 == 20, 6, V2) V2 - ifelse( V1 == 30, 10, V2) or V2 - 4*(V1==10)+6*(V2==20)+10*(V2==30) V2[V2==0] - NA Frank or V2 - ifelse( V1 == 10, 4, ifelse( V1 == 20, 6, ifelse( V1 == 30, 10, NA ))) (where the NA is to handle any unexpected case where V1 isn't 10, 20 or 30). My preference would be to use just one assignment, and if I was sure 10, 20 and 30 were the only possibilities, would use V2 - ifelse( V1 == 10, 4, ifelse( V1 == 20, 6, 10 )) Duncan Murdoch So the O/P looks like this V1 V2 10 4 20 6 30 10 10 4 10 4 20 6 Thanks in advance. Sachin -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Creat new column based on condition
Here is a compact solution using approx: DF$V2 - approx(c(10, 20, 30), c(4,6,10), DF$V1)$y On 4/21/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: DF - data.frame(V1 = c(10, 20, 30, 10, 10, 20)) DF$V2 - with(DF, 4 * (V1 == 10) + 6 * (V1 == 20) + 10 * (V1 == 30)) DF$V3 - c(4, 6, 10)[DF$V1/10] or DF - data.frame(V1 = c(10, 20, 30, 10, 10, 20)) DF - transform(DF, V2 = 4 * (V1 == 10) + 6 * (V1 == 20) + 10 * (V1 == 30), V3 = c(4, 6, 10)[V1/10]) On 4/21/06, Sachin J [EMAIL PROTECTED] wrote: Hi Gabor, The first one works fine. Just out of curiosity, in second solution: I dont want to create a matrix. I want to add a new column to the existing dataframe (i.e. V2 based on the values in V1). Is there a way to do it? TIA Sachin Gabor Grothendieck [EMAIL PROTECTED] wrote: Try: V1 - matrix(c(10, 20, 30, 10, 10, 20), nc = 1) V2 - 4 * (V1 == 10) + 6 * (V1 == 20) + 10 * (V1 == 30) or V2 - matrix(c(4, 6, 10)[V1/10], nc = 1) On 4/21/06, Sachin J wrote: Hi, How can I accomplish this task in R? V1 10 20 30 10 10 20 Create a new column V2 such that: If V1 = 10 then V2 = 4 If V1 = 20 then V2 = 6 V1 = 30 then V2 = 10 So the O/P looks like this V1 V2 10 4 20 6 30 10 10 4 10 4 20 6 Thanks in advance. Sachin __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] online tutorials
For real newbies like myself , good tutorial are had to find, and much of the
documentation is completelly opaque at first. :) However I would recommend
http://www.math.ilstu.edu/dhkim/Rstuff/Rtutor.html as a good place to start
with real basics. It is a bit like the Sample session in the Intro to R but I
found it a bit more user friendlyl.
Another source that I have just found is
http://pj.freefaculty.org/R/Rtips.html which has some good basic stuff but it
is not a tutorial.
- Original Message
From: Maxon, Matthew [EMAIL PROTECTED]
To: R-help@stat.math.ethz.ch
Sent: Thursday, April 20, 2006 12:24:39 PM
Subject: [R] online tutorials
I work for a Investment group with a very extensive training program and
we are having our new hires take a statistics course at University of
Chicago where they have to complete some assignments with R. I was
wondering if there are any online tutorials that exist where we could
get our participants comfortable with R before the class itself? I
appreciate any help at all.
Thanks,
Matt Maxon
Learning Development
Matt Maxon
Citadel Investment Group, L.L.C.
312.395.2517 - office
-
-
CONFIDENTIALITY AND SECURITY NOTICE\ \ The contents of this ...{{dropped}}
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Re: [R] how to control the data type
Have a look at ?round for one way. - Original Message From: zhongmiao wang [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Thursday, April 20, 2006 11:00:25 PM Subject: [R] how to control the data type Hello: I am generating a random number with rnorm(1). The generated number has 8 decimals. I don't want so many decimals. How to control the number of decimals in R? Thanks! Zhongmiao Wang __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Feeding a sequence to a function
Dear all,
I have written a function that takes two arguments, and I would like to feed
it all pairs of values from -10 to 10. The following code works for all
pairs of values between 1 and 10, but given R's indexing, I can't extend it
back to cover the zeros and the negative values. I'd appreciate any
suggestions for a work-around.
Thanks! Fred
Tau - matrix(0,10,10)
S2 - matrix(0,10,10)
R2w - matrix(0,10,10)
for (i in 1:10) {
for (j in 1:10) {
out - function(i,j)
Tau[i,j] - [EMAIL PROTECTED]
S2[i,j] - [EMAIL PROTECTED]
R2w[i,j] [EMAIL PROTECTED]
}
}
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[R] plotting order in a barchart.: two problems
I am new at R and have a simple problem, I think. I have a matrix: [,1] [,2] [,3] a.5 2.4 b4 3.44 c4 4 2 I want a barchart with the [,1] column plotted as the left-most group on a vertical bar chart or as the top group on a horizontal chart. However the plotting order is , [,3] [,2] [,1]. I also am having a problem getting the rows to plot on a vertical chart in the order : a , b, c . I achieved this in a horizontal chart by doing a cbind(c,b,a) but for some reason I do not seem to be getting this to work for the vertical chart. Nothing in Sort() or Order() seem particularly appropriate ( or I don't understand what the help is telling me). Any suggestions would be appreciated. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to control the data type
print(rnorm(1),digits=3) The key is understanding the difference between the value and what is printed automatically with the default number of digits given by the options() value currently in effect. ?options for digits -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of John Kane Sent: Friday, April 21, 2006 3:59 PM To: zhongmiao wang; r-help@stat.math.ethz.ch Subject: Re: [R] how to control the data type Have a look at ?round for one way. - Original Message From: zhongmiao wang [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Thursday, April 20, 2006 11:00:25 PM Subject: [R] how to control the data type Hello: I am generating a random number with rnorm(1). The generated number has 8 decimals. I don't want so many decimals. How to control the number of decimals in R? Thanks! Zhongmiao Wang __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] a question on df of linear model
Short answer: 3=8-5. Longer answer: (1) mf4Orth.lm: The degrees of freedom for the output of lm is 5 = the 4 linear regression parameters + the estimated residual standard deviation. (2) fm2Orth.lme: The lme fit with 8 degrees of freedom adds to that model random = ~I(age-11)|Subject, which estimated 3 additional parameters: The standard deviation of the adjustments for each subject to the intercept and the I(age-11) term in the model plus the correlation between those two random adjustments. (3) The naive, traditional theory for nested hypotheses would say that 2*log(likelihood ratio) is approximately distributed as chi-square with degrees of freedom = the number of additional parameters estimated in the larger model but fixed in the smaller one. This number is 3 in this case. However, the traditional chi-square approximation to the distribution of 2*log(likelihood ratio) is known NOT to work well in this case because 2 of the 3 additional parameters estimated are fixed at a boundary in the smaller model, and the third one becomes meaningless in that case. To understand this issue better and to see how to get around it, please read ch. 2 of Pinheiro and Bates. Does this answer the question? hope this helps. spencer graves Joe Moore wrote: Dear R-users: On page 155 of Mixed-effects Models in S and S-Plus, the degree of freedoms of the anova comparison of lme and lm are 8 and 5. But when I use the following SAS code: proc glm data=ortho2; class gender; model distance = age|gender / solution ; run; The df is 3. Could you please explain this to me? Thanks Joe __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Minor documentation issue
I looked at ?seq -- -- Vivek Satsangi Rochester, NY USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Minor documentation issue
(Sorry about the last email which was incomplete. I hit 'send' accidentally). I looked at ?seq. One of the forms given under Usage is seq(from). This would be the form used if seq is called with only one argument. However, this should actually say seq(to). For example, seq(1) [1] 1 seq(3) [1] 1 2 3 Cheers, -- -- Vivek Satsangi Rochester, NY USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Minor documentation issue
It is matched by the first argument which is called from even though, as the documentation indicates under the explanation of the last form, it refers to the ending value. Note, for example, that seq(from = 3) gives 1:3 and not 3:1. Also the help file does say: The interpretation of the unnamed arguments of 'seq' is _not_ standard, ... On 4/21/06, Vivek Satsangi [EMAIL PROTECTED] wrote: (Sorry about the last email which was incomplete. I hit 'send' accidentally). I looked at ?seq. One of the forms given under Usage is seq(from). This would be the form used if seq is called with only one argument. However, this should actually say seq(to). For example, seq(1) [1] 1 seq(3) [1] 1 2 3 Cheers, -- -- Vivek Satsangi Rochester, NY USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Minor documentation issue
On 4/21/2006 9:26 PM, Vivek Satsangi wrote: (Sorry about the last email which was incomplete. I hit 'send' accidentally). I looked at ?seq. One of the forms given under Usage is seq(from). This would be the form used if seq is called with only one argument. However, this should actually say seq(to). For example, seq(1) [1] 1 seq(3) [1] 1 2 3 Try this: debug(seq.default) seq(3) You'll then drop into the browser at the start of executing the seq.default function. You can print the value of to and of from, and you'll see this: Browse[1] to [1] 1 Browse[1] from [1] 3 So the documentation is correct, even if the usage in this case is the reverse of English usage. (You'll quickly want undebug(seq.default) if you don't want to spend a lot of time in the debugger; seq() is a pretty commonly used function!) Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] problems performing bootstrap
R2.1.1
Windows XP
I have defined a function:
best-function (x)
{
xx-pmax(x[,1],x[,2])
pvalue-t.test(xx,mu=100)
pvalue$p.value
}
and then I try to bootstrap best as follows:
boot( array(rnorm(30,100,1),c(15,2)),best,R=100 )
and get the following message:
Error in statistic(data, original, ...) : unused argument(s) ( ...)
I would appreciate any help that you might offer.
Thanks,
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC and
University of Maryland School of Medicine Claude Pepper OAIC
University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
410-605-7119
[EMAIL PROTECTED]
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Re: [R] Nonlinear Regression model: Diagnostics
I don't know how to get the error message you reported. The following modification of the first 'nls' example worked for me: DNase1 - subset(DNase, Run == 1) fm1DNase1 - nls( density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1) profile(fm1DNase1) fm1DNase1.2 - nls( density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1, alg=default, trace=TRUE) profile(fm1DNase1.2) Have you made scatterplots indicating that the model you are trying to fit seems plausible? If yes, I suggest you try to produce an extremely simple, self-contained example that generates your error message, then send that to this list. Before you submit another post, however, please read the posting guide! www.R-project.org/posting-guide.html. Some people have reported that the posting guide helped them solve their own problem. Failing that, I know that at least one of the R Project's leading contributors has a policy of not responding to posts that seem inconsistent with the suggestions in that guide. Even without that, I believe that posts more consistent with that guide tend to be clearer and easier to understand. This tends to increase chances of getting (quickly) the information you most need to proceed. hope this helps, spencer graves Sachin J wrote: Hi, I am trying to run the following nonlinear regression model. nreg - nls(y ~ exp(-b*x), data = mydf, start = list(b = 0), alg = default, trace = TRUE) OUTPUT: 24619327 : 0 24593178 : 0.0001166910 24555219 : 0.0005019005 24521810 : 0.001341571 24500774 : 0.002705402 24490713 : 0.004401078 24486658 : 0.00607728 24485115 : 0.007484372 24484526 : 0.008552635 24484298 : 0.009314779 24484208 : 0.009837009 24484172 : 0.01018542 24484158 : 0.01041381 24484152 : 0.01056181 24484150 : 0.01065700 24484149 : 0.01071794 24484148 : 0.01075683 24484148 : 0.01078161 24484148 : 0.01079736 24484148 : 0.01080738 24484148 : 0.01081374 Nonlinear regression model model: y ~ exp(-b * x) data: mydf b 0.01081374 residual sum-of-squares: 24484148 My question is how do I interpret the results of this model. profile(nreg) 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : 24484156 : Error in prof$getProfile() : number of iterations exceeded maximum of 50 I am unable to understand the error cause. Any pointers would be of great help. Regards, Sachin - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] problems performing bootstrap
John,
boot requires that the function accept an index (or similar), which is
used to communicate the permutation of x to the function.
Try instead:
best - function (x,i) {
xx - pmax(x[i,1],x[i,2])
pvalue - t.test(xx,mu=100)
pvalue$p.value
}
Cheers
Andrew
On Fri, Apr 21, 2006 at 10:03:12PM -0400, John Sorkin wrote:
R2.1.1
Windows XP
I have defined a function:
best-function (x)
{
xx-pmax(x[,1],x[,2])
pvalue-t.test(xx,mu=100)
pvalue$p.value
}
and then I try to bootstrap best as follows:
boot( array(rnorm(30,100,1),c(15,2)),best,R=100 )
and get the following message:
Error in statistic(data, original, ...) : unused argument(s) ( ...)
I would appreciate any help that you might offer.
Thanks,
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC and
University of Maryland School of Medicine Claude Pepper OAIC
University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
410-605-7119
[EMAIL PROTECTED]
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--
Andrew Robinson
Department of Mathematics and StatisticsTel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599
Email: [EMAIL PROTECTED] http://www.ms.unimelb.edu.au
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