Re: [R] Data frames questions

-Original Message- From: X.H Chen [mailto:[EMAIL PROTECTED] Sent: Sunday, September 24, 2006 12:16 AM To: [EMAIL PROTECTED]; r-help@stat.math.ethz.ch Subject: Re: [R] Data frames questions 1) Is there a way to build an empty data frame, containing nothing but the data frame

RE: [R] deleting specified NA values

How about: all.nas - apply( old, 1, function(x) sum( is.na( x ) ) ) new - old[all.nas dim( old )[2], ] -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06

[R] Building a package under WIN2000 / rw2.0

I have an odd problem in building a package with only R-code in it. I have a package mainly used by myself which I last build under R 1.9.0. The operation system is Win2000 5.00.2195, Service Pack 3 When I do: c:\stat\r\rw2000\bin\Rcmd install --docs=normal --build

RE: [R] sub- and superscript in plot labels

try: plot(1:10, xlab = substitute( expression(paste(nm SO[4]^{2-x}, , mu, eq cm^{-2}, yr^{-1})), list(x=) ) ) I have no understanding of why it works, formula fidgeting usually requires use of subtitute(). Btw. I started out

RE: [R] survSplit: further exploration and related topics

To Danardonos concern of splitting time for records with delayed entry: This can fairly easily be accomodated, by simply splitting time in small intervals of time since entry into the study, and then compute the value of the other timescales for each of these e.g.: current.age - time.from.entry

RE: [R] SAS or R software

Two major advantages of SAS that seems to have been overlooked in the previous replies are: 1) The data-set language is SAS for data manipulation is more human-readable than R-code in general. R is not a definite write-only laguage as APL, but in particular in datamanipulation it is

RE: [R] About ROC curves

There is a package, Lexis, not officil though, which contains a function ROC (and some other stuff for epidemiology). You can find it in: http://biostat.ku.dk/~bxc/SPE/library/ Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens

RE: [R] Unable to understand strptime() behaviour

Try to say: class(x) unclass(x) and it will dawn on you what goes on. -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED]

RE: [R] Modyfing PATH in Windows Installer for R

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Henrik Andersson Sent: Monday, December 06, 2004 2:44 PM To: [EMAIL PROTECTED] Subject: [R] Modyfing PATH in Windows Installer for R Just a small suggestion since Windows have a file system not

RE: [R] test multiple objects for being equal length

not that its much shorter: length( table( sapply( list(x,y,z), length ) ) ) == 1 Bendix -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL

RE: [R] Percentages in contingency tables *warning trivial question*

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Rachel Pearce Sent: Monday, December 13, 2004 10:37 AM To: [EMAIL PROTECTED] Subject: [R] Percentages in contingency tables *warning trivial question* I hesitate to post this question in the

RE: [R] How can I take anti log of log base 2 values in R

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Saurin Jani Sent: Friday, December 17, 2004 3:59 PM To: [EMAIL PROTECTED] Subject: [R] How can I take anti log of log base 2 values in R Hi, I am using R for microarray data anlaysis. When I

RE: [R] ordering levels

In: http://biostat.ku.dk/~bxc/SPE/library/ you will find a zip of the Lexis package that contains the function Relevel, which has precise this (and other) features. Bendix -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte

RE: [R] ordering levels: I was wrong

I was wrong about needing the Relevel from the Lexis package. The default verson of relevel does the job of reshuffling levels in any desired order, albeit with a warning (which comes from the fact that apparently only a single number had been anticipated by the designer): testf - factor(

RE: [R] Make a table

try: tapply( Z, list( X, Y ), mean ) -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc --

RE: [R] vector

If you have all your vectors in a list vl - list( p1, p2, p3) the the following should do the trick: res - numeric(0) for( i in 1:length(vl) ) res - c( res, vl[[i]] ) Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2

RE: [R] plots

For exact contol of height and width, you may want to have a look at: ?win.metafile Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06

RE: [R] numeric(0)

You would probably be better off without the loop, for example: ns - length( sequence ) num.seq - match( sequence, names ) scores - mscore[cbind(num.seq[-1],num.seq[-ns])] sum( scores ) I have used the fact that if you index a matrix with a two-column,matrix ( here, cbind( , ) ), you select the

RE: [R] output from table() in matrix form

You probably want something like: t1 - table( x ) t1 x 1 2 20 3 2 1 t2 - rbind( as.numeric( names( t1 ) ), t1 ) t2 1 2 20 1 2 20 t1 3 2 1 dimnames( t2 ) - NULL t2 [,1] [,2] [,3] [1,]12 20 [2,]321 Bendix -- Bendix Carstensen

RE: [R] plotting percent of incidents within different 'bins'

You want: tapply( Outcome, predictor, mean ) Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc

[R] arrays emerging from tapply

The code below illustrates some points about results from tapply that I find strange. I wonder if they are intended and if so why it is so. 1) When you make a table the dimnames is a *named* list, tapply returns an unnamed list. 2) data.frame behaves differently on an array and a table. Is

RE: [R] hist function to give each cell equal area

how about: x - rnorm(400) nbin-7 hist(x,breaks=quantile(x,prob=seq(0,1,length=nbin+1))) Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07

RE: [R] coxph() and intervening events

Unless you have repeated events per person, you do not need to keep tack of which follow-up belongs to whom. The likelihood contribution from the two parts is a product. See any textbook on survival anlysis or p. 50 ff. of: http://staff.pubhealth.ku.dk/~bxc/Melbourne/Staff/foils.pdf or another

RE: [R] summing subsets of rows matrices

What you need is matrix multiplication: rbind( c(1,1,0,0,0,0), c(0,0,1,1,0,0), c(0,0,0,0,1,1) ) %*% M Bendix -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38

RE: [R] glm and percentage data with many zero values

The ZIP model can be fitted with Jim Lindsey's function fmr from his gnlm library, see: http://popgen0146uns50.unimaas.nl/~jlindsey/rcode.html Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel:

[R] COURSE: Statistical practice in Epidemiology with R

Course in STATISTICAL PRACTICE IN EPIDEMIOLOGY USING R Tartu, Estonia, 26 - 31 May 2005 The course is aimed at epidemiologists and statisticians who wish to use R for statistical modelling and analysis of epidemiological data. The course

RE: [R] GLM function with poisson distribution

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Florian Menzel Sent: Tuesday, January 25, 2005 3:22 PM To: r-help@stat.math.ethz.ch; r-help@stat.math.ethz.ch Subject: [R] GLM function with poisson distribution Hello all, I found a weird

RE: [R] GLM fitting

You have a perfect separtaion of y by x, i.e. y == (x30) is true for all units. Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06

[R] How to get interction terms first in a model

Consider the following two specifications of a model: library( splines ) x - 1:100 y - rnorm( 100 ) w - rep( 1, 100 ) A - factor( sample( 1:2, 100, replace=T ) ) B - factor( sample( letters[1:4], 100, replace=T ) ) summary( lm( y ~ ns( x, knots=c(30, 50, 70 ), intercept=T ):A - 1 + B ) ) summary(

RE: [R] Barplot - Can't figure it out

What you want is probably: cxy - c(x,y) xy - rep( c(x,y), c(length(x),length(y)) ) ( txy - table(xy, cxy ) ) cxy xy 2 3 4 5 x 0 6 4 0 y 4 0 1 5 barplot( txy, beside=T ) Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels

RE: [R] save plot as jpg/gif

?Devices -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Liu, Jane Sent: Monday, February 21, 2005 10:14 AM To: RHELP Subject: [R] save plot as jpg/gif I am generating multiple plots and would like to save them as jpg or gif files. Could

[R] What file did R read?

When I run in BATCH mode I use a script (win2000): c:\stat\r\%R_VERS%\bin\Rcmd BATCH -q --no-restore --no-save %1 Now I want to be able to print the filename of the program, i.e. the value if the %1 argument, in the .Rout file. (Basically I want to write a piece of code in .First() which

RE: [R] how do I get means by factor?

tapply( x, f, mean ) maybe with tapply( x, f, mean, na.rm=T ) -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc

RE: [R] averaging within columns

?tapply Bendix Carstensen -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of thomas hills Sent: Saturday, February 26, 2005 6:17 PM To: r-help@stat.math.ethz.ch Subject: [R] averaging within columns I have a dataframe with names in the first

[R] zero.print in print.table after adding margins

The function addmargins() adds margins to a table, but returns a matrix. But even after converted to a table the print.zero=. option of print.table() does not work: x - sample( 1:7, 20, replace=T ) y - sample( 1:7, 20, replace=T ) tt - table( x, y ) tx - as.table( addmargins( table( x, y ) )

[R] Course reminder: Statistical practise in Epidemiology with R

STATISTICAL PRACTICE IN EPIDEMIOLOGY USING R Tartu, Estonia, Thursday 8 - Tuesday 13 June 2006 Application deadline: 15 April 2006. The course is aimed at epidemiologists and statisticians who wish to use R for statistical modelling and analysis of

RE: [R] Setting up contrasts

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David J. Netherway Sent: Monday, May 03, 2004 10:25 AM To: [EMAIL PROTECTED] Subject: [R] Setting up contrasts I am using the following model: lm - lm(mydata[[variableName]] ~ Age + Gender +

[R] Month names

This is how I get the month names from within R: mon - rep(strptime(01/01/1952, format = %d/%m/%Y), 12) mon$mon - mon$mon + 0:11 mnam - months(mon, abbreviate = F) mnam [1] januarfebruar marts april maj juni juli augustseptember [10] oktober november december

[R] coef and vcoc for polr inconsistent??

Is the following an inconsistency, programming glitch or a feature? One would expect that vcov(obj) was the variance-covariance of coef(obj), but apparently this is not the case for polr objects: x - rnorm( 100 ) y - rnorm( 100 ) ff - factor( sample( 1:4, 100, replace=T ) ) pm - polr( ff ~

[R] latex function in Hmisc

Is there a way to prevent latex.default() from starting LaTeX and JUST create the file requested? I generate a number of LaTeX tables for inclusion in a document running R in batch, and I don't want a lot of calls to LaTeX. I cannot find any arguments for that task in the documentation. It seems

RE: [R] frequencies

You want the function cut(), followed by table(). Bendix -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc

RE: [R] Flip rows and columns of a table?

t( my.table ) -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc -- -Original

RE: [R] Reading Numeric Data -- Trivial Question

You (and the mailing list) would defintely benefit from cliking on: Help - Manuals - An introduction to R and spend a few hours in frot of R while reading that. Bendix -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte

[R] print format for difftime

Has anyone written a function that will print a difftime in the form: hh:mm:ss or yy-mm-dd hh:mm:ss depending on the actual size. (sloppy notation for months/minutes, but surely you get the point). Bendix -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels

RE: [R] plots from batchfile on windows

Just open a device before you plot: pdf( plotfile.pdf ) plot( x, y ) dev.off() also have a look at: ?Devices Best Bendix -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38

Re: [R] assignment of inidividual variables from spss save files

The key to solving your problem is that read.spss per default gives you a *list* and not a *dataframe* (can anyone explain this choice of default?). So most likely wou want: children = read.spss(filename,to.data.frame=TRUE) attach(children) or to get things a little more handy: children -

[R] [R-pkgs] Epi package

There is now an Epi-package on CRAN. It is intended for epidemiological analysis in R. It has its own homepage, http://www.pubhealth.ku.dk/~bxc/Epi The package has been used at the course Statistical practise in Epidemiology with R, see http://www.pubhealth.ku.dk/~bxc/SPE. A mailing list for

[R] Strange parametrization in polr

In Venables \ Ripley 3rd edition (p. 231) the proportional odds model is described as: logit(p=k) = zeta_k + eta but polr apparently thinks there is a minus in front of eta, as is apprent below. Is this a bug og a feature I have overlooked? Here is the naked code for reproduction, below the

RE: [R] converting data to date format

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mike Hollegger Sent: Saturday, February 14, 2004 12:03 PM To: [EMAIL PROTECTED] Subject: [R] converting data to date format Dear all, ...snip I've tried to bring it in character-format

[R] A course in using R for Epidemiology

Course in STATISTICAL PRACTICE IN EPIDEMIOLOGY USING R Tartu, Estonia, 29 May - 4 June 2004. Aimed at young statisticians and epidemiologists wishing to broaden their epidemiological skills, in particular with respect to practical statistical

RE: [R] read.spss and time/date information

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, March 03, 2004 6:27 PM To: Peter Dalgaard Cc: [EMAIL PROTECTED] Subject: Re: [R] read.spss and time/date information On Wed, 3 Mar 2004, Peter Dalgaard

RE: [R] help

I guess what you want is: a - abs(a) floor( a / 10^floor( log10( a ) ) ) Bendix -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED]

RE: [R] creating a ps. file

paste is the function you need. Bendix C. -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc

RE: [R] glm questions --- saturated model

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David Firth Sent: Tuesday, March 16, 2004 1:12 PM To: Paul Johnson Cc: [EMAIL PROTECTED] Subject: Re: [R] glm questions Dear Paul Here are some attempts at your questions. I hope it's of some

RE: [R] Q: Odds Ratio

lr.mod - glm( y ~ x + w, family=binomial ) exp( summary( lr.mod )$coef[,1:2] %*% rbind( c(1,1,1), 1.96*c(0,-1,-1) ) ) should do the job. Pack it in a function if you like, see e.g. the (so far) undocumented function ci.lin in: http://www.biostat.ku.dk/~bxc/R/ci.lin.R (depends on)

RE: [R] Confidence Intervals for slopes

You may want: lm( y ~ x:z ) This is the same model you fitted, but prametrized differently. But please check that what you REALLY want is not lm( y ~ z + x:z ) This is the model with different intercepts as well. Bendix Carstensen -- Bendix Carstensen Senior Statistician

[R] predict.gl( ..., type=terms )

When I do: apc - glm( D ~ ns( Ax, knots=seq(50,80,10), Bo=c(40,90) ) + + ns( Cx, knots=seq(1880,1940,20), Bo=c(1840,1960) ) + + ns( Px, knots=seq(1960,1980,10), Bo=c(1940,2000) ) + + offset( log( Y ) ), + family=poisson ) pterm -

RE: [R] predict( ..., type=terms)

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Thomas Lumley Sent: Wednesday, April 07, 2004 5:44 PM To: Giovanni Petris On Wed, 7 Apr 2004, Giovanni Petris wrote: Hello, After reading the help for predict.lm and predict.glm, it is not

RE: [R] Question (on matrix indexes)

I am not sure what you mean but you might be interested in the functions row() and col(). Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43

[R] pretty for a log-axis

Is there a function that does the same as pretty but on a log-scale? Suppose you have x - exp( runif( 100, 0, 6 ) ) (which will between 1 and 403), then I would like to have a result like: log.pretty( x ) [1] 1 5 10 50 100 500 Bendix C. -- Bendix Carstensen Senior

RE: [R] Size of R user base

I wonder if there is a count of the number of downloads of each version of the R installations (for example rw1090.exe)? Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob:

[R] Course in Statistical Practise in Epidemiology using R

Course in STATISTICAL PRACTICE IN EPIDEMIOLOGY USING R Tartu, Estonia, Thursday 8 - Tuesday 13 June 2006 The course is aimed at epidemiologists and statisticians who wish to use R for statistical modelling and analysis of epidemiological data. The

[R] How to extract the variance componets from lme

Here is a piece of code fitting a model to a (part) of a dataset, just for illustration. I can extract the random interaction and the residual variance in group meth==1 using VarCorr, but how do I get the other residual variance? Is there any way to get the other variances in numerical form

[R] Course announcement: STATISTICAL PRACTICE IN EPIDEMIOLOGY USING R

Course in STATISTICAL PRACTICE IN EPIDEMIOLOGY USING R Tartu, Estonia, 25 to 30 May 2007 The course is aimed at epidemiologists and statisticians who wish to use R for statistical modelling and analysis of epidemiological data. The course requires

Re: [R] dimensions of a all objects

Generally it is difficult to get an overview of what's there. But the following function I acquired from (???) ages ago does a nice job: lls - function (pos = 1, pat = ) { dimx - function(dd) if (is.null(dim(dd))) length(dd) else dim(dd) lll - ls(pos = pos, pat = pat)

Re: [R] how to join two arrays using their column names intersection

Here is a workable solution: df1 - data.frame(ar1) df2 - data.frame(ar2) cmn - intersect(names(df1),names(df2)) rbind(df1[,cmn],df2[,cmn]) Best Bendix __ Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2-4 DK-2820

[R] Compilation of source package.

I have a samll package that works well and complies nicly on WinXP, using R-2.4.1 Now I want to add a document so i make a folder inst\doc and put the .tex and .pdf in there. But the complation then crashes. Is this because the installin expects some file to be present in inst if an inst folder

[R] Rounding?

I was a bit puzzed by: formatC(6.65,format=f,digits=1) [1] 6.6 So I experimented and found: formatC(6.6501,format=f,digits=1) [1] 6.6 formatC(6.651,format=f,digits=1) [1] 6.7 round(6.6501,1) [1] 6.7 round(6.651,1) [1] 6.7 version