Re: [R] How to preserve the numeric format and digits ?
paste(A, format(m, scientific=FALSE, trim=TRUE), B, sep=) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Daren Tan Sent: Thursday, July 24, 2008 5:47 PM To: [EMAIL PROTECTED] Subject: [R] How to preserve the numeric format and digits ? Instead of m - c(4, 500) paste(A, m, B, sep=) [1] A4e+08B A5e+10B I want A4 and A500 __ R-help@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. __ R-help@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: [R] Using PrettyR to produce LaTeX output
You might look at the summary method in Dr. Harrell's Hmisc package, I believe this would give you almost exactly what you want. latex(summary(gender ~ age + bmi, data=yourdata, method='reverse')) This will get you quartiles, but if you read the documentation (?summary.formula) you can see how to create custom summaries. --Matt Matt Austin Global Statistical Leader, denosumab PMO Director, Biostatistics Amgen, Inc -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of jcarmichael Sent: Wednesday, July 23, 2008 12:46 PM To: r-help@r-project.org Subject: [R] Using PrettyR to produce LaTeX output Hello everyone. I am new to R, so please bear with me. I am trying to find an easy way to export descriptive statistics and other information about my data frame to a LaTeX format. I have found the describe function in PrettyR to be very helpful in producing results in the exact format I'm looking for. However, the value of the describe function is a LIST (rather than a data frame) which I am then unable to convert to LaTeX using the xtable package or the latex function of Hmisc. When I try to convert the list to a data frame, I get an error that says arguments imply differing number of rows. If that didn't make any sense...ultimately, here is what I'm trying (and failing) to produce as a LaTeX document... MALES FEMALES Q10 MedQ90Q10Med Q90 AGE xxxx xx xx xx xx BMI xxxxxx xxxx xx etc. xxxxxx xxxx xx Any help or guidance would be appreciated! Thank you in advanced! J. -- View this message in context: http://www.nabble.com/Using-PrettyR-to-produce-LaTeX-output-tp18618195p18618195.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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. __ R-help@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: [R] Labelling curves on graphs
Dr. Harrell's Hmisc package has labcurve. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ted Harding Sent: Wednesday, July 16, 2008 1:17 PM To: [EMAIL PROTECTED] Subject: [R] Labelling curves on graphs Hi Folks, I'd be grateful for good suggestions about the following. I'm plotting a family of (X,Y) curves (for different levels of another variable, Z): say 6 curves in all but could be more or less -- it's a rather variables situation. I'd like to label each curve with the value of Z that it corresponds to. The problem is that the layout (shapes, spacings, ranges of X over which non-NA values of Y get plotted) of the curves are very variable, and somewhat unpredictable beforehand. Of course one could simply wait until the graph was done, and then by hand position one's labels to the best effect. That, given time, is on a certain sense the optimum solution. But I'd like to be able to do a satisfactory job automatically, and quickly! This is the sort of problem already solved, in one particular way, in contour(). But here the curves are broken at the labels and the labels are centred on the curves (though nicely aligned with the curves). It might be satisfactory for me to place each label so that its baseline is on its curve, thus without overlaying the curve with the text. So maybe a displaced analogue of the way contour() does it (including alignment of the text) may be OK. Anothe possibility, for instance, is to draw lines from the ends of the curves to antries in a plotted table of Z-values. This could end up looking very untidym, though. I grant that this is a vague query. I'm still trying to form a clear view of how it ought to be approached; and I don't have R code to refer to and experiment with (that of contour() is hidden in its method). But people out there must have faced it, and I'd be grateful for their own feedback from the coal-face! With thanks, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 16-Jul-08 Time: 21:17:13 -- XFMail -- __ R-help@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. __ R-help@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: [R] linear model in the repeated data type~
allFits - lmList(y ~ t|id, data=table1, pool=FALSE) allCoefs - sapply(allFits, coef) ## preferred by me or allCoefs - list(length(allFits)) for(i in 1:length(allFits)) allCoef[[i]] - coef(allFits[[i]]) --Matt From: Manli Yan [mailto:[EMAIL PROTECTED] Sent: Wednesday, June 04, 2008 9:12 PM To: Austin, Matt Cc: r-help@r-project.org Subject: Re: [R] linear model in the repeated data type~ hi:lot thanks,how to use list to extract,I type allFit$coefficents,it came to nothing, such as I need to extract the estimates,how to do it by using list 2008/6/3 Austin, Matt [EMAIL PROTECTED]mailto:[EMAIL PROTECTED]: How about library(nlme) allFits - lmList(y ~ t|id, data=table1, pool=FALSE) or allFits - by(table1, table1$id, function(x) lm(y ~ t, data=x)) Both ways store the results as a list, so you can access individual results using list extraction. --Matt -Original Message- From: [EMAIL PROTECTED]mailto:[EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]mailto:[EMAIL PROTECTED]] On Behalf Of Manli Yan Sent: Tuesday, June 03, 2008 9:07 PM To: r-help@r-project.orgmailto:r-help@r-project.org Subject: [R] linear model in the repeated data type~ here is the data: y-c(5,2,3,7,9,0,1,4,5) id-c(1,1,6,6,7,8,15,15,19) t-c(50,56,50,56,50,50,50,60,50) table1-data.frame(y,id,t)//longitudinal data what I want to do is to use the linear model for each id ,then get the estimate value,like: fit1-lm(y~t,data=table1,subset=(id==1)) but ,you can see the variable id is quite irregular,they are not arranaged in order and many number missing,if I write a loop by using for,it will give me a lot NA, and for sure ,I dont want to type id=## for about 500 times,any one know how to deal with it? [[alternative HTML version deleted]] __ R-help@r-project.orgmailto:R-help@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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@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: [R] linear model in the repeated data type~
Apologies, the second method should have been allCoefs - vector(list, length(allFits)) for(i in 1:length(allFits)) allCoefs[[i]] - coef(allFits[[i]]) --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Austin, Matt Sent: Thursday, June 05, 2008 3:03 PM To: Manli Yan Cc: r-help@r-project.org Subject: Re: [R] linear model in the repeated data type~ allFits - lmList(y ~ t|id, data=table1, pool=FALSE) allCoefs - sapply(allFits, coef) ## preferred by me or allCoefs - list(length(allFits)) for(i in 1:length(allFits)) allCoef[[i]] - coef(allFits[[i]]) --Matt From: Manli Yan [mailto:[EMAIL PROTECTED] Sent: Wednesday, June 04, 2008 9:12 PM To: Austin, Matt Cc: r-help@r-project.org Subject: Re: [R] linear model in the repeated data type~ hi:lot thanks,how to use list to extract,I type allFit$coefficents,it came to nothing, such as I need to extract the estimates,how to do it by using list 2008/6/3 Austin, Matt [EMAIL PROTECTED]mailto:[EMAIL PROTECTED]: How about library(nlme) allFits - lmList(y ~ t|id, data=table1, pool=FALSE) or allFits - by(table1, table1$id, function(x) lm(y ~ t, data=x)) Both ways store the results as a list, so you can access individual results using list extraction. --Matt -Original Message- From: [EMAIL PROTECTED]mailto:[EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]mailto:[EMAIL PROTECTED]] On Behalf Of Manli Yan Sent: Tuesday, June 03, 2008 9:07 PM To: r-help@r-project.orgmailto:r-help@r-project.org Subject: [R] linear model in the repeated data type~ here is the data: y-c(5,2,3,7,9,0,1,4,5) id-c(1,1,6,6,7,8,15,15,19) t-c(50,56,50,56,50,50,50,60,50) table1-data.frame(y,id,t)//longitudinal data what I want to do is to use the linear model for each id ,then get the estimate value,like: fit1-lm(y~t,data=table1,subset=(id==1)) but ,you can see the variable id is quite irregular,they are not arranaged in order and many number missing,if I write a loop by using for,it will give me a lot NA, and for sure ,I dont want to type id=## for about 500 times,any one know how to deal with it? [[alternative HTML version deleted]] __ R-help@r-project.orgmailto:R-help@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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@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. __ R-help@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: [R] linear model in the repeated data type~
How about library(nlme) allFits - lmList(y ~ t|id, data=table1, pool=FALSE) or allFits - by(table1, table1$id, function(x) lm(y ~ t, data=x)) Both ways store the results as a list, so you can access individual results using list extraction. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Manli Yan Sent: Tuesday, June 03, 2008 9:07 PM To: r-help@r-project.org Subject: [R] linear model in the repeated data type~ here is the data: y-c(5,2,3,7,9,0,1,4,5) id-c(1,1,6,6,7,8,15,15,19) t-c(50,56,50,56,50,50,50,60,50) table1-data.frame(y,id,t)//longitudinal data what I want to do is to use the linear model for each id ,then get the estimate value,like: fit1-lm(y~t,data=table1,subset=(id==1)) but ,you can see the variable id is quite irregular,they are not arranaged in order and many number missing,if I write a loop by using for,it will give me a lot NA, and for sure ,I dont want to type id=## for about 500 times,any one know how to deal with it? [[alternative HTML version deleted]] __ R-help@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. __ R-help@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: [R] Row mean scores differ association
There is a R companion to Agresti's text at the following site, I believe the answer to your question is there: http://www.stat.ufl.edu/~aa/cda/cda.html --Matt Matt Austin Biostatistics Director Amgen, Inc -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of dt Excellent Sent: Thursday, April 10, 2008 1:18 PM To: R-Help Subject: [R] Row mean scores differ association Suppose that we have o 2-D contingency table where the row variable is nominal and the column one is ordinal. In SAS it is possible to compute the statistic named as row mean scores differ. How can we programmed it in R? (See also Aggresti (2002), Categorical Data Analysis, p. 302) With regards - [[alternative HTML version deleted]] __ R-help@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. __ R-help@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: [R] basehaz and newdata
I don't believe basehaz takes a newdata argument. args(basehaz) function (fit, centered = TRUE) NULL It simply extracts info from the fitted object. I think you want to use survfit method for coxph objects and then derive/extract what you need. --Matt Matt Austin Global Statistical Leader, denosumab PMO Biostatistics Director Amgen, Inc -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of mah Sent: Monday, April 07, 2008 10:01 AM To: r-help@r-project.org Subject: Re: [R] basehaz and newdata Thanks Roland, but using data frames does not resolve the issue. See revised code and output below: test1 - data.frame( + time= c(4, 3,1,1,2,2,3), + status=c(1,NA,1,0,1,1,0), + x= c(0, 2,1,1,1,0,0), + sex= c(0, 0,0,0,1,1,1) + ) f1 - coxph( Surv(time, status) ~ x + strata(sex), data=test1) #stratified model test2 - data.frame( + time= c(4, 3,1,1,2,2,3), + status=c(1,NA,1,0,1,1,0), + x= c(1, 2,1,1,1,0,0), + sex= c(0, 0,0,0,1,1,1) + ) f2 - coxph( Surv(time, status) ~ x + strata(sex), data=test2) #stratified model f1 Call: coxph(formula = Surv(time, status) ~ x + strata(sex), data = test1) coef exp(coef) se(coef) zp x 1.17 3.22 1.29 0.907 0.36 Likelihood ratio test=0.87 on 1 df, p=0.351 n=6 (1 observation deleted due to missingness) f2 Call: coxph(formula = Surv(time, status) ~ x + strata(sex), data = test2) coef exp(coef) se(coef)zp x 0.896 2.45 1.42 0.63 0.53 Likelihood ratio test=0.38 on 1 df, p=0.535 n=6 (1 observation deleted due to missingness) basehaz(f1, newdata=test2) Error in basehaz(f1, newdata = test2) : unused argument(s) (newdata = list(time = c(4, 3, 1, 1, 2, 2, 3), status = c(1, NA, 1, 0, 1, 1, 0), x = c(1, 2, 1, 1, 1, 0, 0), sex = c(0, 0, 0, 0, 1, 1, 1))) Mike On Apr 7, 11:43 am, Roland Rau [EMAIL PROTECTED] wrote: Hi, just looked at it briefly and I don't know if it is the real cause for your problems. But 'data' as well as 'newdata' require a data.frame and not a list as input. Does this help? Best, Roland mah wrote: I am unable to get thebasehazfunction to apply a proportional hazards model to a new data frame. I replicated my specific situation with the example for coxph in the help, where I changed the x value of the first record from 0 to 1. Is there something incorrect in the syntax that I am using? Thanks in advance! test1 - list(time= c(4, 3,1,1,2,2,3), status=c(1,NA,1,0,1,1,0), x= c(0, 2,1,1,1,0,0), sex= c(0, 0,0,0,1,1,1)) test2 - list(time= c(4, 3,1,1,2,2,3), status=c(1,NA,1,0,1,1,0), x= c(1, 2,1,1,1,0,0), sex= c(0, 0,0,0,1,1,1)) f1 - coxph( Surv(time, status) ~ x + strata(sex), data=test1) #stratified model f2 - coxph( Surv(time, status) ~ x + strata(sex), data=test2) #stratified model f1 Call: coxph(formula = Surv(time, status) ~ x + strata(sex), data = test1) coef exp(coef) se(coef) zp x 1.17 3.22 1.29 0.907 0.36 Likelihood ratio test=0.87 on 1 df, p=0.351 n=6 (1 observation deleted due to missingness) f2 Call: coxph(formula = Surv(time, status) ~ x + strata(sex), data = test2) coef exp(coef) se(coef)zp x 0.896 2.45 1.42 0.63 0.53 Likelihood ratio test=0.38 on 1 df, p=0.535 n=6 (1 observation deleted due to missingness) basehaz(f1, newdata=test2) Error inbasehaz(f1, newdata = test2) : unused argument(s) (newdata = list(time = c(4, 3, 1, 1, 2, 2, 3), status = c(1, NA, 1, 0, 1, 1, 0), x = c(1, 2, 1, 1, 1, 0, 0), sex = c(0, 0, 0, 0, 1, 1, 1))) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ [EMAIL PROTECTED] mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.- Hide quoted text - - Show quoted text - __ R-help@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. __ R-help@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: [R] format numbers using 1000 separator
format(10, big.mark=,, scientific=FALSE) [1] 1,000,000,000 --Matt Matt Austin Biostatistics Director Amgen, Inc -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of tom soyer Sent: Friday, April 04, 2008 2:41 PM To: r-help@r-project.org Subject: [R] format numbers using 1000 separator Hi, Does anyone know how one could format numbers using 1000 separator in R? For example, format 1000 as 1,000 and 10 as 100,000, etc. Thanks, -- Tom [[alternative HTML version deleted]] __ R-help@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. __ R-help@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: [R] Graphics and LaTeX documents with the same font
I find them helpful for displaying the differences in coupled biomarkers between therapies with different therapeutic targets. You can quickly see/show which marker is affected quicker and then the other compensating in response and how they can be reversed depending on target. Having each measure on its own actual scale and not having to do something like percent change over time is very helpful (for many biomarkers it's hard to judge the clinical relavence of scaled values). I believe in looking at the data in numerous ways, to help myself from confusing or misleading myself--which is not my intent. --Matt Austin Statistician, Amgen Inc. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of hadley wickham Sent: Friday, September 28, 2007 10:14 AM To: Frank E Harrell Jr Cc: R-help Subject: Re: [R] Graphics and LaTeX documents with the same font Yes there is harm. But to make bold lines, easy to read titles is fine. See the spar function in http://biostat.mc.vanderbilt.edu/SgraphicsHints for a starter. Also see the setps, ps.slide, and setpdf functions in the Hmisc package. I was interested to see that you have code for drawing scatterplots with multiple y-axes. As far as I know the only legitimate use for a double-axis plot is to confuse or mislead the reader (and this is not a very ethical use case). Perhaps you have a counter-example? Hadley __ R-help@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. [[alternative HTML version deleted]] __ R-help@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.
