Re: [R] simple save question

I want to assign the value of rmean from a survfit object to a variable so that it can be used in subsequent calculations, which is also what I interpreted the original poster to want. I did not understand Dr. Therneau's answer to the original poster, so I figured I would provide a simple example a

Re: [R] simple save question

No cigar. This is what I get and my session info. Any suggestions? > > library(survival) > library(ISwR) > dat.s <- Surv(melanom$days,melanom$status==1) > fit <- survfit(dat.s~1) > print(fit, print.rmean=TRUE) Call: survfit(formula = dat.s ~ 1) records n.maxn.start events *rm

Re: [R] simple save question

Well, that took a bit of detective work! Thanks. I am still not doing something right here in my efforts to implement the "easy way". Can you point out my error? > > library(survival) > library(ISwR) > dat.s <- Surv(melanom$days,melanom$status==1) > fit <- survfit(dat.s~1) > print(fit, print.rmea

Re: [R] simple save question

Thank you for the reply Dr. Winsemius. Can you take your answer a step further and, in the context of the simple, reproducible example, illustrate how it is done? I would appreciate it. Tom -- View this message in context: http://r.789695.n4.nabble.com/simple-save-question-tp3429148p3663645.htm

Re: [R] simple save question

Here is a worked example. Can you point out to me where in temp rmean is stored? Thanks. Tom > library(survival) > library(ISwR) > > dat.s <- Surv(melanom$days,melanom$status==1) > fit <- survfit(dat.s~1) > plot(fit) > summary(fit) Call: survfit(formula = dat.s ~ 1) time n.risk n.event survi

[R] How to Extract Information from SIMEX Output

Below is a SIMEX object that was generated with the "simex" function from the "simex" package applied to a logistic regression fit. From this mountain of information I would like to extract all of the values summarized in this line: .. ..$ variance.jackknife: num [1:5, 1:4] 1.684 1.144 0.85 0.62

Re: [R] Failing to install {rggobi} on win-7 R 2.12.0

I recall that my problem on Windows was related to having a number of stray versions of GTK+ installed. I went back and deleted all versions and reinstalled the latest GTK+ and that seemed to fix things. However, when I went to do any work of substance ggobi locked up and became unresponsive. Neve

Re: [R] Tutorial Tinn-R

Seems to be a relevant and reasonable question to me. -- View this message in context: http://r.789695.n4.nabble.com/Tutorial-Tinn-R-tp2300451p2300648.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

Re: [R] Sampling with replacement

How about library(TeachingSampling) SupportWR(20,4) Tom -- View this message in context: http://r.789695.n4.nabble.com/Sampling-with-replacement-tp2257450p2257644.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.or

Re: [R] Ellipse that Contains 95% of the Observed Data

I know what "get a bigger sample means". I have no clue what "ask a more statistically meaningful question" means. Can you elaborate a bit? Tom -- View this message in context: http://n4.nabble.com/Ellipse-that-Contains-95-of-the-Observed-Data-tp1694538p1695357.html Sent from the R help mailing

Re: [R] Ellipse that Contains 95% of the Observed Data

Concisely, here is what I am trying to do: #I take a random sample of 300 measurements. After I have the measurements #I post stratify them to 80 type A measurements and 220 type B measurements. #These measurements tend to be lognormally distributed so I fit them to #determine the geometric me

[R] Ellipse that Contains 95% of the Observed Data

I can take the results of a simulation with one random variable and generate an empirical interval that contains 95% of the observations, e.g., x <- rnorm(1) quantile(x,probs=c(0.025,0.975)) Is there an R function that can take the results from two random variables and generate an empirical

[R] Design of a survey using the "survey" package

I have looked through the new "Complex Surveys" book and the documentation for the "survey" package and it appears to me that there are no functions in "survey" that help one to design a sampling scheme. For example, in the book section 2.8 discusses the design of stratified samples, but there is

Re: [R] Ubunut + Eclipse + StatET: Console terminates upon error

I don't want to hijack the thread here, but since you mentioned "hover pop-up help" can you suggest a way to turn it OFF, totally and completely? Tom LaBone -- View this message in context: http://n4.nabble.com/Ubunut-Eclipse-StatET-Console-terminates-upon-error-tp1589479p1589800.html Sent from

Re: [R] Rounding a Measurement to be Consistent with its Uncertainty

Uwe Ligges-3 wrote: > > > > Tom La Bone wrote: >> I have a measurement of 8165.666 and an uncertainty of 338.9741 (the >> units of >> both are unimportant). I can easily round the uncertainty to two >> significant >> digits with signif(338.9741,2),

[R] Rounding a Measurement to be Consistent with its Uncertainty

I have a measurement of 8165.666 and an uncertainty of 338.9741 (the units of both are unimportant). I can easily round the uncertainty to two significant digits with signif(338.9741,2), which gives 340. Is there a function in R that will take 8165.666 and round it to be consistent with its uncert

Re: [R] Comparison of Output from "dwtest" and "durbin.watson"

My concern is that the two tests give different DW statistics for the weighted fit and very different p-values for the same DW statistic for the unweighted fit. Is there a "right" answer here? -- View this message in context: http://www.nabble.com/Comparison-of-Output-from-%22dwtest%22-and-

Re: [R] Comparison of Output from "dwtest" and "durbin.watson"

Allow me to reword this question. I have performed two fits to the same set of data below: a weighted fit and an unweighted fit. I performed the Durbin-Watson tests on each fit using "dwtest" and "durbin.watson". For a given fit (weighted or unweighted), should both dwtest and durbin.watson be giv

[R] Comparison of Output from "dwtest" and "durbin.watson"

Should "dwtest" and "durbin.watson" be giving me the same DW statistic and p-value for these two fits? library(lmtest) library(car) X <- c(4.8509E-1,8.2667E-2,6.4010E-2,5.1188E-2,3.4492E-2,2.1660E-2, 3.2242E-3,1.8285E-3) Y <- c(2720,1150,1010,790,482,358,78,35) W <- 1/Y^2 fit <- lm(Y ~

[R] Character from Symbol Font on rgl Plot

I want to print characters from the symbol font (or perhaps even Wingdings) in an rgl 3d plot, but I am having no luck. So, what do I have to do in order to get this snippet to print out a character from the symbol font? library(rgl) open3d() text3d(1,1,1,"a",adj=c(0.5,0.5),cex=10,family="symbol"

[R] Selecting Bootstrap Method for Quantile Regression

The help page and vignette for summary.rq(quantreg) mention that there are three different bootstrap methods available for the se="bootstrap" argument, but I can't figure out how to select a particular method. For example, if I want to use the "xy-pair bootstrap" how do I indicate this in summary.

[R] Re placing a "+" in a string

I know this is easy, but I am stumped: > gsub("0","K","8.00+00") [1] "8.KK+KK" > gsub("+","K","8.00+00") Error in gsub("+", "K", "8.00+00") : invalid regular expression '+' In addition: Warning message: In gsub("+", "K", "8.00+00") : regcomp error: 'Invalid preceding regular expression' I d

[R] R 64-bit for Ubuntu 9.04 64-bit

I just installed Ubuntu 9.04 but there does not seem to be repository for binaries for this version. Are there going to be such repositories set up in the near future? Tom -- View this message in context: http://www.nabble.com/R-64-bit-for-Ubuntu-9.04-64-bit-tp23246229p23246229.html Sent fro

Re: [R] what is R best for; what should one learn in addition to R

What do folks think about the c/gsl/Apophenia combination as one of the other stat packages? http://modelingwithdata.org/ http://apophenia.sourceforge.net/ Tom Greg Snow-2 wrote: > > > I also recommend that people doing statistics know at least the basics of > 3 different stats packages

Re: [R] R 2.9.0 MASS package

t; Tom La Bone wrote: >> I can't seem to find MASS for the latest version of R. Is it coming or >> has >> the name of the package changed? >> >> Tom > > Where did you look? > > It is in the sources (as part of VR), and also in my (SUSE)

[R] R 2.9.0 MASS package

I can't seem to find MASS for the latest version of R. Is it coming or has the name of the package changed? Tom -- View this message in context: http://www.nabble.com/R-2.9.0-MASS-package-tp23144198p23144198.html Sent from the R help mailing list archive at Nabble.com.

[R] Physical Units in Calculations

Back in 2005 I had been doing most of my work in Mathcad for over 10 years. For a number of reasons I decided to switch over to R. After much effort and help from you folks I am finally "thinking" in R rather than thinking in Mathcad and trying to translating to R. Anyway, the only task I still us

[R] Inverse of data.ellipse function

The following code generates 85% and 95% bivariate normal confidence ellipses using the data.ellipse routine in the car package. Can anyone suggest a routine in R that will tell me the confidence ellipse that would intersect the green point, or more generally, any specified point on the plot? To

[R] Extracting Coefficients and Such from mle2 Output

The mle2 function (bbmle library) gives an example something like the following in its help page. How do I access the coefficients, standard errors, etc in the summary of "a"? > x <- 0:10 > y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8) > LL <- function(ymax=15, xhalf=6) + -sum(stats::dpois(y, l

[R] Dates in Common

I have two collections of dates and I want to figure out what dates they have in common. This is not giving me what I want (I don't know what it is giving me). What is the best way to do this? Tom > data1 [1] "1948-02-24 EST" "1949-04-12 EST" "1950-05-29 EDT" "1951-05-21 EDT" [5] "1951-12-20 E

Re: [R] text rather than html help in Windows

Duncan Murdoch-2 wrote: > > Whoops, sorry, Uwe's advice is right. Text help is only the default > when run outside a console; I use Cygwin, which doesn't look like a > console to R. > I am using eclipse with StatET to run R under Ubuntu 8.04 and Windows XP Pro. I would like both implementat

[R] text rather than html help in Windows

I would like to use Rterm in Windows XP and have the help files appear in text format in the terminal rather than in the html popup window. For example, I would like to enter help(lm) and get the text to appear in the terminal window. Can anyone suggest a way to do this? Thanks and Happy Hew Year.

Re: [R] Using transform to add a date column to a dataframe

Gavin Simpson wrote: > > > It says that the two arguments have different numbers of observations. > The reason for which should now be pretty obvious as you provided a > single Date whereas airquality has 153 observations. > Thanks. I did look at ?transform but I was a bit confused because t

[R] Using transform to add a date column to a dataframe

I would like to add a column to the airquality dataset that contains the date 1950-01-01 in each row. This method does not appear to work: > attach(airquality) > data1 <- transform(airquality,Date=as.Date("1950-01-01")) Error in data.frame(list(Ozone = c(41L, 36L, 12L, 18L, NA, 28L, 23L, 19L, :

Re: [R] Left-truncated regression

Look at the sand package, which is available at http://www.csm.ornl.gov/esh/statoed/ and the NADA package, which is available from CRAN. One or both may have items of interest. Tom Zita wrote: > > Hi. > > I am looking for a function for left-truncated data. > I have one data set with 2

[R] Kolmogorov–Smirnov Test for Left Censored Data

Can someone recommend a package in R that will perform a two-sample Kolmogorov–Smirnov test on left censored data? The package "surv2sample" appears to offer such a test for right censored data and I guess that I can use this package if I flip my data, but I figured I would first ask if there was

Re: [R] Accessing Results from cenmle function in NADA package

This is very nice also. I am going to use this approach in the future when I use lm. However, I can't seem to get to work the way I want with cenmle. I will continue to experiment. Thanks folks for the suggestions. Tom David Winsemius wrote: > > > On Nov 12, 2008, at 8:48 A

Re: [R] Accessing Results from cenmle function in NADA package

Oh, I like your answer better than mine! Thanks. Tom Richard Cotton wrote: > >> I figured it out. In case anyone else ever has this question -- given > the >> following output from cenmle: >> >> >fit.cen <- cenmle(obs, censored, groups) >> > fit.cen >>Value Std. Error

Re: [R] Accessing Results from cenmle function in NADA package

-value is (for example): p.value <- summary(fit.cen)[[9]][[11]] Tom Tom La Bone wrote: > > The cenmle function is used to fit two sets of censored data and test if > they are significantly different. I can print out the results of the > analysis on the screen but can't see

[R] Accessing Results from cenmle function in NADA package

The cenmle function is used to fit two sets of censored data and test if they are significantly different. I can print out the results of the analysis on the screen but can't seem to figure out how to access these results in R and assign them to new variables, e.g., assign the slope calculated wit

Re: [R] Doing a Task Without Using a For Loop

lines of data, assigning values from the table to the 43,000 elements of a vector took 6 seconds whereas assigning values from the table to 43,000 elements of a dataframe took 21 minutes. Why is there such a huge difference? Tom Tom La Bone wrote: > > Assume that I have the dataframe

Re: [R] Doing a Task Without Using a For Loop

ct 14, 2008 at 10:58 AM, Tom La Bone > <[EMAIL PROTECTED]>wrote: > >> >> Assume that I have the dataframe "data1", which is listed at the end of >> this >> message. I want count the number of lines that each person has for each >> year. For e

[R] Doing a Task Without Using a For Loop

Assume that I have the dataframe "data1", which is listed at the end of this message. I want count the number of lines that each person has for each year. For example, the person with ID=213 has 15 entries (NinYear) for 1953. The following bit of code calculates NinYear: for (i in 1:length(data1$

[R] How do I Convert "<1" to the number 1?

Is there an elegant way in R to change a number reported as a less-than number in text format, "<1" for example, to the numeric equivalent 1? I have been trying to use as.numeric, but have not come up with anything clever yet. Tom -- View this message in context: http://www.nabble.com/How-do-

Re: [R] Error: can not allocate vector of 117.3 Mb

To see some useful discussions of this problem in various settings search R-Help for the phrase "cannot allocate vector of size". Tom ram basnet wrote: > > Hi R users, >   > I am doing multiscale bootstrapping for clustering through pvclust > package. I have large data set (observations 182 a

[R] Upgrade to R 2.7.2 from Debian Repository

I am running R 2.7.1 on an eeepc with the standard Xandros Linux. I install/upgrade R binaries using synaptic from the http://cran.r-project.org/bin/linux/debian/etch-cran/ repository. R 2.7.2 does not appear to be available from this repository. Will it be available soon or is there another repos

Re: [R] How Can I Tell if the R Running is 64 bit or 32 bit?

>> on 08/08/2008 03:58 PM milton ruser wrote: >>> Dear Prof. B.Ripley, >>> >>> If : >>>> .Machine$sizeof.pointer >>> [1] 4 >>>> 2*2*2*2 >>> [1] 16 >>> >>> So I am running with 16 bits? >&

[R] How Can I Tell if the R Running is 64 bit or 32 bit?

I think I installed 64-bit Ubuntu 8.04 and 64-bit R on my computer. I can't seem to find anything that says "this is 64-bit Ubuntu" or "this is 64-bit R". How do I tell what version of R I am running? Tom -- View this message in context: http://www.nabble.com/How-Can-I-Tell-if-the-R-Running-is-

[R] Will This Computer Run 64 bit Ubuntu/R?

After doing some reading about 64-bit systems and software I am still somewhat uncertain about some things. I have a Dell Dimension XPS 400 with a dual core Intel Pentium D 940 (3.2 GHz) and 4 Gb of memory. I currently dual boot the system with XP Professional and Ubuntu 8.04 (32 bit). If I simply

[R] Memory Problems with a Simple Bootstrap - Part II

I have distilled my bootstrap problem down to this bit of code, which calculates an estimate of the 95th percentile of 7500 random numbers drawn from a standard normal distribution: library(boot) per95 <- function( annual.data, b.index) { sample.data <- annual.data[b.index] return(quantile(s

Re: [R] Memory Problems with a Simple Bootstrap

e objects are reasonable size and the memory size also > seems reasonable. That is what I usually go by to see if there are > large objects in my memory. If it was showing that R had 1.2GB of > memory allocated to it, I wonder if there might be a memory leak > somewhere. > > On

Re: [R] Memory Problems with a Simple Bootstrap

since that appears > to be the only variable in your loop that might be growing. > > On Fri, Aug 1, 2008 at 12:09 PM, Tom La Bone <[EMAIL PROTECTED]> > wrote: >> >> >> I have a data file called inputdata.csv that looks something like this" >> >&g

[R] Memory Problems with a Simple Bootstrap

I have a data file called inputdata.csv that looks something like this" ID YearResult Month Date 1 71741954 103 540301 2 7174195443 540322 3 20924 1967 4 2 670223 4 20924

Re: [R] re sponse surface analysis

There appears to be a very promising response surface package being discussed at useR-2008, but I have been unable to find the package on CRAN or contact the authors. www.statistik.uni-dortmund.de/useR-2008/abstracts/Sztendur+Diamond.pdf Tom Jinsong Zhao wrote: > > Hi, > > Is there a pack

Re: [R] Tutorial on rgl Graphics

On further experimentation I find that "points" (via points3d) serve my purpose well (instead of the much prettier but more troublesome spheres). The default "point" appears to be a square. Is there a way to make it a circle? Tom Duncan Murdoch-2 wrote: > > On

Re: [R] Tutorial on rgl Graphics

After looking around a bit more I found the example I was looking for -- plotlm3d, which I found on the R wiki http://wiki.r-project.org/rwiki/doku.php?id=graph_gallery:new-graphics The original author was John Fox, and it was modified by Jose Claudio Faria and Duncan Murdoch. Below is a si

[R] Tutorial on rgl Graphics

Can anyone point me towards a tutorial on using the rgl graphics package? Something with lots of examples would be nice. Thanks. Tom -- View this message in context: http://www.nabble.com/Tutorial-on-rgl-Graphics-tp18649114p18649114.html Sent from the R help mailing list archive at Nabble.com.

[R] Problem with scatterplot3d example

I tried to run the following example from section 4.1.4 of the "Scatterplot3d - an R package for Visualizing Multivariate Data" vignette and got an error on the part that plots the regression plane: > library(scatterplot3d) > data(trees) > s3d <- scatterplot3d(trees, type = "h", color = "blue", +

[R] Backgrounds in Multiple Plots made with "fig"

The following code was adapted from an example Vincent Zoonekynd gave on his web site http://zoonek2.free.fr/UNIX/48_R/03.html: n <- 1000 x <- rnorm(n) qqnorm(x) qqline(x, col="red") op <- par(fig=c(.02,.5,.5,.98), new=TRUE) hist(x, probability=T, col="light blue", xlab="", ylab="", main="",

Re: [R] Deming Regression

I believe that Deming regression also goes by the name of orthogonal regression, which can be performed in R using pca methods. If you do a search of the list for "orthogonal regression" you can see the previous discussions of this topic. Tom Dexter Riley wrote: > > Hi all. Has anyone ever do

[R] Simultaneous Confidence/Prediction Bands

Is there a built-in function in R that will generate simultaneous confidence and prediction bands for linear regression? Tom -- View this message in context: http://www.nabble.com/Simultaneous-Confidence-Prediction-Bands-tp17941537p17941537.html Sent from the R help mailing list archive at Nabb

Re: [R] R on an ASUS eee PC, continued - installing packages

I am running R in the konsole of the Kate editor on an eeePC 900 (standard Xandros OS). When a plot is generated it is initially too large to fit in the screen, but if I click on the plot it automatically resizes to fit properly. I have no idea if this is a default behavior. Tom Millo Giovann

[R] Units of Difference Between Two Dates

I would like all three of these calculations to give an answer in days (or at least the same units): > as.POSIXct("1971-08-01 00:00:00") - as.POSIXct("1971-08-01 00:00:00") Time difference of 0 secs > > as.POSIXct("1971-08-01 12:00:00") - as.POSIXct("1971-08-01 00:00:00") Time difference of 12 h

[R] Statistical Methods and Software for the Analysis of Occupational Exposure Data With Non-Detectable Values

FYI This is a nice package that is not on CRAN for some reason. You can get it at http://www.csm.ornl.gov/esh/statoed/ Tom -- View this message in context: http://www.nabble.com/Statistical-Methods-and-Software-for-the-Analysis-of-Occupational-Exposure-Data-With-Non-Detectable-Values-tp169662

[R] ARAR Time Series Analysis in R

Does R have a function for doing an ARAR analysis of a time series? Tom -- View this message in context: http://www.nabble.com/ARAR-Time-Series-Analysis-in-R-tp16722577p16722577.html Sent from the R help mailing list archive at Nabble.com. __ R-help@

Re: [R] Specifying relative position of text in a plot

Thanks for all of the suggestions. The key key here seems to be using the "par" function to change the coordinate system like so plot(rnorm(100), rnorm(100)) op <- par("usr") par(usr = c(0, 1, 0, 1)) text(0.5,0.5,"TEST") par(usr = op) Prof Ripley commented that this approach will also work on l

[R] Specifying relative position of text in a plot

What is the simplest way to specify the location of text in a scatter plot (created using the plot function) in relative terms rather than specific x-y coordinates? For example, rather than putting text at (300,49) on a plot, how do I put it 1/10 of the way over from the y axis and 1/2 of the way

Re: [R] I need to buy a book in R

This is a nice list: http://www.amazon.com/Use-R/lm/RNFBA3UHW2M73/ref=cm_lmt_srch_f_1_rsrsrs0 Tom kayj wrote: > > Hi All, > > I am a new user in R and I would like to buy a book that teaches me how > to use R. In addition, I may nees to do some advanced statistical > analysis. Does anyone

[R] Meaning of Error Message from decompose

Greetings, For the following quarterly data I did a classical decomposition by hand in a spreadsheet and got reasonably similar results using Minitab 15. x 1 36 2 44 3 45 4 106 5 38 6 46 7 47 8 112

Re: [R] best text editor for Linux?

I am in a similar situation and found that Kate combined with Konsole operates very much like Tinn-R. I actually use Kate for all interpreters like Python, R, and Octave under linux. Tom Wade Wall wrote: > > Hi all, > > I know this question has been asked in the past, but I am wondering if

Re: [R] Problems with EMACS-ESS on Ubuntu

(courtesy of Vincent Goulet) did not require me to confirm that I wanted to use R. Thanks everyone for the assistance. Tom Ben Bolker wrote: > > Tom La Bone gforcecable.com> writes: > >> >> >> I installed EMACS-ESS on Windows XP-Pro and it worked with R per

[R] Problems with EMACS-ESS on Ubuntu

I installed EMACS-ESS on Windows XP-Pro and it worked with R perfectly right out of the box. I was impressed with how easy it is to use (I normally use Tinn-R). I then switched over to Ubuntu 7.10 and installed EMACS-ESS. Everything worked the same as in Windows (which is my main reason for using

Re: [R] The R Book - great resource for R beginners

IMHO "The R Book" is far better than indicated in that review and should be near the top of the list for beginners looking for a "manual" for R. Tom Katharine Mullen wrote: > > It was reviewed in the most recent R News > (http://www.r-project.org/doc/Rnews/Rnews_2007-2.pdf). > > On Thu, 29 No

[R] Linear Regression with lm Forcing the Slope to Equal 1

Is there a way to do a linear regression with lm (having one predictor variable) and constrain the slope of the line to equal 1? Tom -- View this message in context: http://www.nabble.com/Linear-Regression-with-lm-Forcing-the-Slope-to-Equal-1-tf4828804.html#a13815432 Sent from the R help maili

[R] Bootstrap CI of Slope in a Weighted Simple Linear Regression

Greetings, I would like to use the "boot" function to generate a bootstrap confidence interval for the slope in a SLR that has a zero intercept. My attempt to do this is shown below. Is this the correct implementation of the boot function to solve this problem? In particular, should I be doing an

[R] lm.boot function gives error

When I run this calculation library(ISwR) library(simple.boot) data(thuesen) fit <- lm(thuesen$short.velocity~thuesen$blood.glucose) summary(fit) fit.sb <- lm.boot(fit,R=1000,rows=F) summary(fit.sb) I get the following error from the lm.boot routine: newdata' had 100 rows but va

Re: [R] In a SLR, Why Does the Hat Matrix Depend on the Weights?

Because it does. I should have looked ahead a few chapters in the book before I asked the question. However, I can't seem to reproduce the values of the hat matrix given by R for the weighted fit example I gave. Any suggestions (other than looking ahead a few more chapters)? Tom [[

[R] In a SLR, Why Does the Hat Matrix Depend on the Weights?

I understand that the hat matrix is a function of the predictor variable alone. So, in the following example why do the values on the diagonal of the hat matrix change when I go from an unweighted fit to a weighted fit? Is the function hatvalues giving me something other than what I think it is?

[R] Documentation for Pearson Residuals

Greetings, I have been using lm to perform weighted linear regressions and resid to extract the residuals. I happened upon some class notes on the internet that described how one can specify type="pearson" in resid to extract the weighted residuals. Where is this option documented? And if you k