[R] survreg and cluster and frailty
6 490 5920 1315 64 11 120 56 26077 6 490 5920 1415 57 11 120 56 26077 6 490 5920 1515 100 01 170 43 168 104 7 409 3090 16 8 100 01 80128 65864 8 3360 3520 17 8 29 11 80128 65864 8 3360 3520 1815 29 11 80128 65864 8 3360 3520 1915 36 11 80128 65864 8 3360 3520 20 8 100 01 170 56 152 156 9 350 6040 div nestide 1 0.6027874 1 2 0.6121574 2 3 0.8094382 3 4 0.7353479 4 5 0.7353479 4 6 0.7353479 4 7 0.7353479 4 8 0.8645524 5 9 0.8645524 5 10 0.8645524 5 11 0.8645524 5 12 0.6458459 6 13 0.6458459 6 14 0.6458459 6 15 0.2722860 7 16 0.8397355 8 17 0.8397355 8 18 0.8397355 8 19 0.8397355 8 20 0.7203888 9 ----- Dr. Andrew Beckerman Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 http://www.beckslab.staff.shef.ac.uk/ __ 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] Rscript on OSX
Ido - R for OSX generally runs via an application, called R.app, which your colleague could find in their applications directory. It can run scripts and has a rather nice script editor associated with it. You can run R as you would in linux using X11.app, found in Applications->Utilities on OSX. R is not designed to run from Terminal.app (actually, terminal does not do graphics well for R). X11 provides the behaviour that you would be used to in Linux etc. BTW - there is a R-Mac-help group as well for macintosh specific issues - [EMAIL PROTECTED] Andrew - Dr. Andrew Beckerman Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 http://www.beckslab.staff.shef.ac.uk/ -- On 9 Jan 2008, at 13:22, Ido M. Tamir wrote: > Hi, > > I directed somebody to install R (2.6.1) on his OSX computer, > following instructions from http://cran.r-project.org/bin/macosx. > She can run R from the console. > But plot(1:10) doesn't produce any output or open a window (as I am > used to from linux). > > More importantly: > Rscript is not in the path (minor problem ln -s is hopefully > doable). I tried > to put a hardcoded path to Rscript into the shebang line but this > fails. And > when I try to invoke it directly: > >> -bash: ./Rscript: cannot execute binary file > > On linux this works. > > I would like to send her some Rscripts, but how can we make them > run on her system? > > > > thank you very much, > ido > > > > imaclab3:/Library/Frameworks/R.framework/Resources/bin ru$ ls -l > > total 1008 > -rwxrwxr-x 1 root admin1654 Nov 26 17:36 BATCH > -rwxrwxr-x 1 root admin2188 Nov 26 17:36 COMPILE > -rwxrwxr-x 1 root admin 34391 Nov 26 17:36 INSTALL > -rwxrwxr-x 1 root admin1593 Nov 26 17:36 LINK > -rwxrwxr-x 1 root admin7210 Nov 26 17:37 R > -rwxrwxr-x 1 root admin7210 Nov 26 17:37 R.orig > -rw-rw-r-- 1 root admin 655 Nov 26 17:37 R.rej > -rwxrwxr-x 1 root admin2244 Nov 26 17:36 REMOVE > -rwxrwxr-x 1 root admin 928 Nov 26 17:36 Rcmd > -rwxrwxr-x 1 root admin9523 Nov 26 17:36 Rd2dvi > -rwxrwxr-x 1 root admin 842 Nov 26 17:36 Rd2txt > -rwxrwxr-x 1 root admin3237 Nov 26 17:36 Rdconv > -rwxrwxr-x 1 root admin1320 Nov 26 17:36 Rdiff > -rwxrwxr-x 1 root admin2854 Nov 26 17:36 Rprof > -rwxrwxr-x 1 root admin 18084 Nov 26 17:36 Rscript > -rwxrwxr-x 1 root admin4656 Nov 26 17:36 SHLIB > -rwxrwxr-x 1 root admin 16129 Nov 26 17:36 Sd2Rd > -rwxrwxr-x 1 root admin 730 Nov 26 17:36 Stangle > -rwxrwxr-x 1 root admin 726 Nov 26 17:36 Sweave > -rwxrwxr-x 1 root admin 21715 Nov 26 17:36 build > -rwxrwxr-x 1 root admin 78570 Nov 26 17:36 check > -rwxrwxr-x 1 root admin6927 Nov 26 17:36 config > drwxrwxr-x 4 root admin 136 Nov 26 17:36 exec > -rwxrwxr-x 1 root admin3613 Nov 26 17:36 f77_f2c > -rwxrwxr-x 1 root admin 10720 Nov 26 17:36 javareconf > -rwxrwxr-x 1 root admin 215101 Nov 26 17:36 libtool > -rwxrwxr-x 1 root admin3495 Nov 26 17:36 mkinstalldirs > -rwxrwxr-x 1 root admin 413 Nov 26 17:36 pager > > __ > 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] Omnibus main effects in summary.lme?
Adam - Without resorting to the rather rich lmer/lme4 discussion realm, you need to base anova() comparisons of lme models with different fixed effects on maximum liklihood estimates rather tham REML. anova(update(l2,method="ML"),update(l2,~.-useful:nusience,method="ML")) should avoid the error and give a conservative estimate of the significance of your interaction. see also: http://tolstoy.newcastle.edu.au/R/e2/help/06/10/3565.html and related posts. A ----- Dr. Andrew Beckerman Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 http://www.beckslab.staff.shef.ac.uk/ -- On 10 Jan 2008, at 22:32, Adam D. I. Kramer wrote: > Hello, > > I've been running some HLMs using the lme function quite happily; it > does what I want and I'm pretty sure I understand it. > > The issue is that I'm currently trying to estimate a model with a > 14-level "nusiance" factor as an independent variable...which makes > the > output quite ugly. All I'm really interested in is the question of > whether > these factor as a whole (and its interactions with other factors) are > significant. > > The summary.aov function provides this sort of aggregation for lm > objects, but does not run on lme objects. I've also tried estimating > the > full model and restricted model, leaving out a main effect or > interaction > term and then using anova.lme to compare the models, but these > models appear > to be being fit differently. Say I have l2, and then > > l3 <- update(l2, .~.-useful:nusience) > anova.lme(l3,l2) > > ...to see whether the interaction term is significant, produces the > error, > "Fitted objects with different fixed effects. REML comparisons are not > meaningful." Upon examination using summary(l3), it seems that the > fixed > factors are indeed different. > > So, my question is this: How do I estimate omnibus main effects for > multi-level factors and multi-level factor interactions in lme models? > > Many thanks, > Adam D. I. Kramer > Ph.D. Student, Social and Personality Psychology > University of Oregon > > __ > 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.
[R] survreg and pweibull
Dear all - I have followed the thread the reply to which was lead by Thomas Lumley about using pweibull to generate fitted survival curves for survreg models. http://tolstoy.newcastle.edu.au/R/help/04/11/7766.html Using the lung data set, data(lung) lung.wbs <- survreg( Surv(time, status)~ 1, data=lung, dist='weibull') curve(pweibull(x, scale=exp(coef(lung.wbs)), shape=1/lung.wbs $scale,lower.tail=FALSE),from=0, to=max(lung$time)) lines(survfit(Surv(time,status)~1, data=lung), col="red") Assuming this is correct, why does the inflection point of this curve not match up to the exp(scale parameter)? Am I wrong in assuming that the scale represents the inflection, and the shape adjusts the shape around this point? I think I am perhaps confusing the scale and the median with the inflection point calcuation? One can visualise the mismatch with: abline(v=exp(coef(lung.wbs)),lty=2) abline(h=0.5,lty=2) Many thanks for the clarification R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines datasets utils stats graphics grDevices methods base other attached packages: [1] survival_2.34-1 Hmisc_3.4-3 lattice_0.17-15 MASS_7.2-44 loaded via a namespace (and not attached): [1] cluster_1.11.11 grid_2.8.0 tools_2.8.0 Andrew --------- Dr. Andrew Beckerman Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 http://www.beckslab.staff.shef.ac.uk/ http://www.flickr.com/photos/apbeckerman/ http://www.warblefly.co.uk __ 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] survreg and pweibull solved for any distribution
Dear all - Following up my own post, having found a Terry Therneau post about the value of predict(model,type="quantile"), http://tolstoy.newcastle.edu.au/R/e4/help/08/03/5335.html the following code ammendment produces what I was intending to see. It clear that the 0.5 quantile is the inflection point. And predict() has the value of being distribution independent, and producing valid SE estimates. data(lung) lung.wbs <- survreg( Surv(time, status)~ 1, data=lung, dist='weibull') curve(pweibull(x, scale=exp(coef(lung.wbs)), shape=1/lung.wbs $scale,lower.tail=FALSE),from=0, to=max(lung$time)) lines(survfit(Surv(time,status)~1, data=lung), col="red") abline(h=0.5,lty=2) abline(v=unique(predict(lung.wbs,type="quantile",p=0.5)),lty=2,col=4) However, one last technical question. In an intercept only model, how do you specify newdata to get just a single estimate? In the above example I used unique against the model predictions evaluated at every datapoint. But with no terms on the RHS of the model, how do you (can you) specify new data? Best wishes, Andrew On 26 Nov 2008, at 16:27, Andrew Beckerman wrote: Dear all - I have followed the thread the reply to which was lead by Thomas Lumley about using pweibull to generate fitted survival curves for survreg models. http://tolstoy.newcastle.edu.au/R/help/04/11/7766.html Using the lung data set, data(lung) lung.wbs <- survreg( Surv(time, status)~ 1, data=lung, dist='weibull') curve(pweibull(x, scale=exp(coef(lung.wbs)), shape=1/lung.wbs $scale,lower.tail=FALSE),from=0, to=max(lung$time)) lines(survfit(Surv(time,status)~1, data=lung), col="red") Assuming this is correct, why does the inflection point of this curve not match up to the exp(scale parameter)? Am I wrong in assuming that the scale represents the inflection, and the shape adjusts the shape around this point? I think I am perhaps confusing the scale and the median with the inflection point calcuation? One can visualise the mismatch with: abline(v=exp(coef(lung.wbs)),lty=2) abline(h=0.5,lty=2) Many thanks for the clarification R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines datasets utils stats graphics grDevices methods base other attached packages: [1] survival_2.34-1 Hmisc_3.4-3 lattice_0.17-15 MASS_7.2-44 loaded via a namespace (and not attached): [1] cluster_1.11.11 grid_2.8.0 tools_2.8.0 Andrew ----- Dr. Andrew Beckerman Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 http://www.beckslab.staff.shef.ac.uk/ http://www.flickr.com/photos/apbeckerman/ http://www.warblefly.co.uk __ 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.
[R] lattice contourplot line types
Dear all -
I would like to adjust the line type of specific contours in
contourplot from the lattice package, but it seems like lty does not
take a list in the call.
Here is my call to contourplot:
contourplot(preds~size+trt|Size.Name,
data=pred.dat,layout=c(2,4),
at=c(0.025,0.5,0.975),
par.strip.text=list(cex=1.2),
scales=list(cex=0.5),
xlab=list("Size",cex=1.2),
ylab=list("Treatment",cex=1.2),
panel=function(x,y,z,...){
panel.contourplot(x,y,z,lwd=1,...)
panel.grid(h=-1,v=-1,col="grey",...)})
I would like to specify lty=c(2,1,2) corresponding to the
at=c(0.025,0.5,0.975), and have tried this in both the core part of
the call, and in panel.countourplot. However, it only recognises the
first type.
If there is no straightforward answer, I can provide the data.
Best wishes,
Andrew
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1
locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MASS_7.2-45 lattice_0.17-17
loaded via a namespace (and not attached):
[1] grid_2.8.1
__
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] lattice contourplot line types
Sundar -
Thanks for the help! Here is my modified code. Just what I wanted.
However, it is odd that the at= call in contourplot won't take a
single value - I have had to trick it into plotting the "0" contour
along with the 0.5 to make this work.
contourplot(preds~size+trt|Size.Name,
data=pred.dat,layout=c(2,4),
par.strip.text=list(cex=1.2),
scales=list(cex=0.5),
xlab=list("Size",cex=1.2),
ylab=list("Treatment",cex=1.2),
panel=function(at,lty,...){
at.1<-c(0,0.5)
at.2<-c(0.025,0.975)
panel.contourplot(at=at.1,lty=1,...)
panel.contourplot(at=at.2,lty=2,...)
panel.grid(h=-1,v=-1,col="grey",...)})
Andrew
On 22 Feb 2009, at 21:25, Sundar Dorai-Raj wrote:
The only way I can figure out to do this is to use two calls to
panel.contourplot:
library(lattice)
x <- seq(-2, 2, length = 20)
y <- seq(-2, 2, length = 20)
grid <- expand.grid(x=x, y=y)
grid$z <- dnorm(grid$x) * dnorm(grid$y)
contourplot(z ~ x * y, grid,
panel = function(at, lty, col, ...) {
at.o <- at[seq(1, length(at), 2)]
at.e <- at[seq(2, length(at), 2)]
panel.contourplot(at = at.o, lty = 1, col = "blue", ...)
panel.contourplot(at = at.e, lty = 4, col = "red", ...)
},
at = pretty(grid$z, 10))
HTH,
--sundar
On Sun, Feb 22, 2009 at 12:45 PM, Andrew Beckerman
wrote:
Dear all -
I would like to adjust the line type of specific contours in
contourplot
from the lattice package, but it seems like lty does not take a
list in the
call.
Here is my call to contourplot:
contourplot(preds~size+trt|Size.Name,
data=pred.dat,layout=c(2,4),
at=c(0.025,0.5,0.975),
par.strip.text=list(cex=1.2),
scales=list(cex=0.5),
xlab=list("Size",cex=1.2),
ylab=list("Treatment",cex=1.2),
panel=function(x,y,z,...){
panel.contourplot(x,y,z,lwd=1,...)
panel.grid(h=-1,v=-1,col="grey",...)})
I would like to specify lty=c(2,1,2) corresponding to the
at=c(0.025,0.5,0.975), and have tried this in both the core part of
the
call, and in panel.countourplot. However, it only recognises the
first
type.
If there is no straightforward answer, I can provide the data.
Best wishes,
Andrew
R version 2.8.1 (2008-12-22)
i386-apple-darwin8.11.1
locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MASS_7.2-45 lattice_0.17-17
loaded via a namespace (and not attached):
[1] grid_2.8.1
__
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.
Dr. Andrew Beckerman
Department of Animal and Plant Sciences
University of Sheffield
Sheffield S10 2TN
UK
a.becker...@sheffield.ac.uk
__
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.
