gmane.comp.lang.r.general

Re: Help with maps

Avram Aelony — 2008-12-04T03:50:50

aha!, thanks for this. Avram On Dec 2, 2008, at 5:38 PM, Ray Brownrigg wrote: ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: Help with reading code

Steven McKinney — 2008-12-04T03:50:27

Hi Dana [mailto:r-help-bounces< at >r-project.org] the zero, * "log0". after this. The command above sets a variable to "exclude" with. Any observation with weight equal to zero will get excluded. excl will have value TRUE for all observations with weight 0. zero so the above chunk keeps only the residuals and weights for the observations with non-zero weights so now there are no more observations with w == 0 in the above equation Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney< at >bccrc.ca tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Help with reading code

Dana77 — 2008-12-03T23:24:17

I would like to give out the equation for calculating the maximum likelihood. Below is the code, but I still have problems with it. After I read the code, I found there are two cases for "w(weights)". If "w" is not zero, then the equation is given as "val <- 0.5 * (sum(log(w)) - N * (log(2 * pi) + 1 - log(N) + log(sum(w * res^2))))". However, if "w" is zero, then I do not know what equation it should be since it does not make any sense for "log0". Hope someone can help me to figure this out. Thanks! function (object, REML = FALSE, ...) { res <- object$residuals p <- object$rank N <- length(res) if (is.null(w <- object$weights)) { w <- rep.int(1, N) } else { excl <- w == 0 #####I can not understand the following lines after this. if (any(excl)) { res <- res[!excl] N <- length(res) w <- w[!excl] } } N0 <- N if (REML) N <- N - p val <- 0.5 * (sum(log(w)) - N * (log(2 * pi) + 1

Re: Static random numbers

Marc Schwartz — 2008-12-04T00:29:27

See ?set.seed, which will allow you to specify the seed for the RNG, so that you can reproduce the same sequence again in the future: set.seed(1) rn1 <- as.zoo(rnorm(1000)) HTH, Marc Schwartz ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Static random numbers

Bastian Offermann — 2008-12-04T00:10:06

Hello, can anybody help me out saving random numbers? What I am doing is to generate a series of random numbers and keep it as a zoo object. z <- 1000 rn1 <- as.zoo(rnorm(z)) The random numbers will be analyzed and described in a LaTeX document, so I have to keep them static somehow. The fact that they are kept as a zoo object should not be of too much concern here. Thanks in advance. Regards Bastian Offermann ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: reading version 9 SAS datasets in R

Frank E Harrell Jr — 2008-12-03T23:39:26

Sorry I screwed that up. See http://biostat.mc.vanderbilt.edu/SASexportHowto for the correct approach, under the heading "If You Have Access to SAS". Frank

Random Forest weighting

Raghu Naik — 2008-12-03T22:24:28

Folks, I have a query around weighting in Random Forest (RF). I know that several earlier emails in this group have raised this issue, but I did not find an answer to my query. I am working on a dataset (dataset1) that consists of 4 million records that can be reduced to a dataset (dataset2) of approximately 1500 unique records with frequency counts that add up to the 4 million records number as above. Because of size issues, I cannot work with dataset1 in R and therefore, I am working with dataset2 . Each record consists of whether or not a patient chose a particular drug based on 14 comorbidity (Yes / No) variables; I am using RF to understand the comorbidity drivers of drug adoption (yes/no) classification. At full dataset level (dataset1), the drug adoption incidence is ~11%. At the reduced dataset dataset2 level, the drug adoption incidence increases to ~38%. My question is that, if am using the reduced dataset (dataset2), how should I inform RF that the adoption incidence at the full dataset level

Re: reading version 9 SAS datasets in R

Frank E Harrell Jr — 2008-12-03T22:51:06

Try FILENAME transp SASV5XPT 'D:\CES Analysis\Data\fadata.xpt'; Frank

Re: reading version 9 SAS datasets in R

Nordlund, Dan (DSHS/RDA — 2008-12-03T22:11:06

Jude, Since it appears that you have access to SAS, I would look at using the sas.get() function in the Hmisc package. While the function appears to still be broken in the Windows version, there is an easy fix that has been posted to R-help in the past. If you want to try this, you can search the R-help archives for posts on sas.get or you can email me off-list and I will send you the fix with instructions. This will avoid any v6 limitations. Hope this is helpful, Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

applying a function to another function

Carlos Cuartas — 2008-12-03T20:51:52

Hello, I did a function (sec_conop) whose arguments are syndic, well and wellconop. sec_conop(syndic='01syndic.txt',well='well-1.csv',wellconop='well-1.dat');closeAllConnections() This function takes “well” and “syndic”, matching between them and then it does some transformations. The result is exported to “wellconop”. I will apply this function to one hundred different “wells”. Therefore, for each well I use, the “wellconop argument will change too. For intance if “well” is now well-2.csv, the function will be sec_conop(syndic='01syndic.txt',well='well-2.csv',wellconop='well-2.dat');closeAllConnections() I am trying to apply this function automatically to all “well” I have, but I do not find the way. The last I tried, for three different “wells”, was : wells<-data.frame(funct=rep('sec_conop(',3),syndic=c('01syndic.txt','01syndic.txt','01syndic.txt'),well=c('well-1.csv','well-2.csv','well-3-1.csv'),wellconop=c('well-1.dat','well-2.dat','well-3.dat')) funct_3wells<-pa

reading version 9 SAS datasets in R

2008-12-03T21:40:12

Hi, I am trying to read a SAS version 9.1.3 SAS dataset into R (to preserve the SAS labels), but am unable to do so (I have read in a CSV version). I first created a transport file using the SAS code: libname ces2 'D:\CES Analysis\Data'; filename transp 'D:\CES Analysis\Data\fadata.xpt'; /* create a transport file - R cannot read file created by proc cport */ proc cport data=ces2.fadata file=transp; run; I then tried to read it in R using: Error in lookup.xport(file) : file not in SAS transfer format Next I tried using the libname statement and the xport engine to create a transport file. The problem with this method is that variable names cannot be more than 8 characters as this method creates a SAS version 6 transport file. libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt'; data to_r.fadata2; set ces2.fadata; run; But I get an error message in the SAS log: 493 libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt'; NOTE: Libref TO_R was successfully a

Re: Strplit code

John Fox — 2008-12-03T21:04:55

Dear Brian (and original poster), My apologies -- I didn't notice the original posting. By coincidence, I have a version of strsplit() that I've used to illustrate recursion: Strsplit <- function(x, split){ if (length(x) > 1) { return(lapply(x, Strsplit, split)) # vectorization } result <- character(0) if (nchar(x) == 0) return(result) posn <- regexpr(split, x) if (posn <= 0) return(x) c(result, substring(x, 1, posn - 1), Recall(substring(x, posn+1, nchar(x)), split)) # recursion } Illustration: + "Whether t'is nobler,in the mind", + "to suffer the slings:and arrows:of outrageous fortune", + "or to take arms;against;a sea of troubles") [[1]] [1] "To be" "or not to be" "that is the question" [[2]] [1] "Whether t'is nobler" "in the mind" [[3]] [1] "to suffer the slings" "and arrows" "of outrageous fortune" [[4]] [1] "or to take arms" "against" "a sea

Re: Strplit code

Prof Brian Ripley — 2008-12-03T20:46:56

With difficulty, as it is almost entirely implemented in C code (in src/main/character.c and src/main/regex.c, as well as the PCRE library).. It is not something I would undertake lightly (and I am the author/maintainer of most of that code).

Re: changing colnames in dataframes

Prof Brian Ripley — 2008-12-03T20:41:23

See the help page. You name the arguments, e.g. JJ <- data.frame( gender= c( as.character(rep( gender,3))) , J.value -c( F76 ,6-F83, F90) ) The help says Arguments: ...: these arguments are of either the form 'value' or 'tag = value'. Component names are created based on the tag (if present) or the deparsed argument itself. On Wed, 3 Dec 2008, Wolfgang Lindner wrote:

Re: how do I eliminate excess levels in lattice contourplot key/ legend?

Deepayan Sarkar — 2008-12-03T20:37:56

contourplot(z ~ X1 * X2, data = g, region = TRUE, at = seq(0, 1, length = 6)) -Deepayan ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: date operations

Gavin Simpson — 2008-12-03T20:12:30

______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Strplit code

2008-12-03T19:52:21

Dear R-users, The strsplit function does not exist in S-plus and I would like to use it. How could I reproduce the function in Splus or access to its source code? Thank you in advance, Sebastien ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Hmisc latex() and Rcmdr numSummary() percentage issues

Liviu Andronic — 2008-12-03T19:44:27

Dear R users, I have issues regarding latex() from Hmisc and numSummary() from Rcmdr. Here's an example: The resulting LaTeX code (see below) is not compilable, because of the `%' signs present in the column headers, and that are not escaped by latex() (contrary to the behaviour of xtable()). I can solve the issue manually by escaping the percentage signs `\%'. Would there be a way to automatise this? Thank you, Liviu ######## Uncompilable LaTeX ######## % latex.default(as.table(.numSummary$table), cdec = c(2), file = "", title = "") % \begin{table}[!tbp] \begin{center} \begin{tabular}{lrrrrrrr}\hline\hline \multicolumn{1}{l}{}& \multicolumn{1}{c}{mean}& \multicolumn{1}{c}{sd}& \multicolumn{1}{c}{0%}& \multicolumn{1}{c}{25%}& \multicolumn{1}{c}{50%}& \multicolumn{1}{c}{75%}& \multicolumn{1}{c}{100%} \\ \hline &$31.37$&$20.41$&$10.6$&$16.9$&$23.7$&$39$&$84.5$\\ \hline \end{tabular} \end{center} \end{table} ######## End of LaTeX ######## ######## Compilable LaTeX ######## % latex.default(as.table(

changing colnames in dataframes

Wolfgang Lindner — 2008-12-03T19:30:56

dear all, I'm building new dataframes from bigger one's using e.g. columns F76, F83, F90: JJ<-data.frame( c( as.character(rep( gender,3))) , c( F76,6- F83, F90) ) Looking into JJ one has: c.as.character.rep.gender..8... c.6...F73..F78..F79..F82..6...F84..F94..F106..F109 1 w 2 2 w 3 3 m 1 etc. Instead of the automatic colnames 'c.as.character.rep.gender..8' I like to have the colnames 'gender' and 'J.value'. I tried levels, labels etc but without success. OK, I can fix(FF) manually, but this is bad, because it has to be done again and again .. OK, I can do gender.J<-c( as.character(rep( gender,3))) Jvalue<-c( F76,6- F83, F90) JJ<-data.frame(gender.J, J.value) but this is not optimal because 'gender' is depending on rep(.., n) and I have many dataframes KK, LL, .. using 'gender' with different size. Question: is it possible to do something

Re: date operations

Gabor Grothendieck — 2008-12-03T19:13:38

In fact what it says is that x may be numeric OR difftime. Also the above does not explain it in any case because: [1] "2009-02-15" Time difference of 14290 days Warning message: Incompatible methods ("Ops.difftime", "+.Date") for "+" His question was how to avoid using as.numeric. ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: Function output difficulties

2008-12-03T19:03:32

It's not clear what you mean by "some parts of the function output". The function output is whatever you nominate it to be, and can include any selection of whatever was computed within the function. For example: testfn <- function(x){ X <- x^2 ; Y <- cos(X) ; Z <- (X + Y)/(1 + x) c(X,Z) } testfn(1.1) # [1] 1.210000 0.744295 However, I suspect your case may be a bit more complicated than that! If you were to post the function (or something like it), explaining what you want it to return, and in what way it returns what you do not want, it would be easier to help. Ted. -------------------------------------------------------------------- E-Mail: (Ted Harding) manchester.ac.uk> Fax-to-email: +44 (0)870 094 0861 Date: 03-Dec-08 Time: 19:03:29 ------------------------------ XFMail ------------------------------ ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE