Displaying 20 results from an estimated 7000 matches similar to: "CMD check puzzle"
2008 Apr 25
3
Use of survreg.distributions
Dear R-user:
I am using survreg(Surv()) for fitting a Tobit model of left-censored longitudinal data. For logarithmic transformation of y data, I am trying use survreg.distributions in the following way:
tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id), dist="gaussian", data=y.data, scale=0, weights=w)
my.gaussian<-survreg.distributions$gaussian
2008 Mar 03
1
Problem plotting curve on survival curve
Calum had a long question about drawing survival curves after fitting a Weibull
model, using pweibull, which I have not reproduced.
It is easier to get survival curves using the predict function. Here is a
simple example:
> library(survival)
> tfit <- survreg(Surv(time, status) ~ factor(ph.ecog), data=lung)
> table(lung$ph.ecog)
0 1 2 3 <NA>
63 113 50 1
2012 Oct 19
1
Looping survdiff
The number of recent questions from umn.edu makes me wonder if there's homework involved....
Simpler for your example is to use get and subset.
dat <- structure(..... as found below
var.to.test <- names(dat)[4:6] #variables of interest
nvar <- length(var.to.test)
chisq <- double(nvar)
for (i in 1:nvar) {
tfit <- survdiff(Surv(time, completion==2) ~
2008 Dec 02
1
Left-truncated regression
Hi.
I am looking for a function for left-truncated data.
I have one data set with 2 variables (Hours~Yrs_Ed).
I already left-censored the data at 200 and left-truncated it at the same
spot, so that I am able to make 2 estimations (one for censoring and one for
truncation).
I know how to make the linear regression for the left-censored variable
(hours) and how to plot the regression line into the
2009 Jul 28
1
Wishlist: Navigate to "Index" page of help when no topic specified (PR#13860)
Hi all,
When I install a new package, and don't yet know any function names,
I have to play the "poor man's game" to get to the standard
help system "Index" page for the package:
Poor Man's Game -=20
Load new package;=20
issue search() command;
find position (say N) of loaded package;=20
issue objects(pos =3D N) command;
get name of a random function (san
2009 Aug 05
2
Wishlist: Navigate to "Index" page of help when no topic (PR#13872)
On 04/08/2009 7:33 PM, Steven McKinney wrote:
>> -----Original Message-----
>> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca]
>> Sent: Tuesday, August 04, 2009 8:03 AM
>> To: Steven McKinney
>> Cc: r-devel at stat.math.ethz.ch; R-bugs at r-project.org
>> Subject: Re: [Rd] Wishlist: Navigate to "Index" page of help when no
>> topic
2007 Jul 24
1
Fit t distribution
Hi all, I am trying to fit t distribution using the function "tFit" in the
library(fBasics).
I am using the code tFit(datac[[2]]) and it returns the following list.
Title:
Student-t Parameter Estimation
Call:
tFit(x = datac[[2]])
Model:
Student-t Distribution
Estimated Parameter(s):
df
78.4428
I just wonder how can I refer to the estimated parameters. I tried
2006 Jan 19
2
Tobit estimation?
Folks,
Based on
http://www.biostat.wustl.edu/archives/html/s-news/1999-06/msg00125.html
I thought I should experiment with using survreg() to estimate tobit
models.
I start by simulating a data frame with 100 observations from a tobit model
> x1 <- runif(100)
> x2 <- runif(100)*3
> ystar <- 2 + 3*x1 - 4*x2 + rnorm(100)*2
> y <- ystar
> censored <- ystar <= 0
2009 Aug 13
2
CMD check error (bug?)
R version 2.9.0 running on Centos (Red Hat linux).
I have a pair of packages coxme and bdsmatrix. The latter is installed
in my local library (I don't have permission for global install at
work.) That is, it is in the location pointed to in R_LIBS_USER. In R,
the command library(bdsmatrix) works fine.
Coxme depends on bdsmatrix, in fact uses some cross-calls to it's C
routines, which
2009 Feb 09
1
One more note
There are some warnings earlier in the log about my .Rd files (missing a
description of weights and subset in a couple). The only message that I
don't completely understand is
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Error in firstlib(which.lib.loc, package) :
Tcl/Tk support is not available on this system
I'm also curious about this.
2007 Dec 05
4
coxme frailty model standard errors?
Hello,
I am running R 2.6.1 on windows xp
I am trying to fit a cox proportional hazard model with a shared
Gaussian frailty term using coxme
My model is specified as:
nofit1<-coxme(Surv(Age,cen1new)~ Sex+bo2+bo3,random=~1|isl,data=mydat)
With x1-x3 being dummy variables, and isl being the community level
variable with 4 levels.
Does anyone know if there is a way to get the standard error
2012 Oct 11
2
Question on survival
Hi,
I'm going crazy trying to plot a quite simple graph.
i need to plot estimated hazard rate from a cox model.
supposing the model i like this:
coxPhMod=coxph(Surv(TIME, EV) ~ AGE+A+B+strata(C) data=data)
with 4 level for C.
how can i obtain a graph with 4 estimated (better smoothed) hazard curve
(base-line hazard + 3 proportional) to highlight the effect of C.
thanks!!
laudan
[[alternative
2013 Jun 05
0
Survival aareg problem
On 06/05/2013 12:33 AM, r-help-request at r-project.org wrote:
> Dear friends - I'm on windows 7, R 2.15.2
>
> when I run the example for aareg in survival package I see this:
>
> plot(lfit[4], ylim=c(-4,4))
> error in xy.coords(x, y, xlabel, ylabel, log) :
> 'x' is a list, but does not have components 'x' and 'y'
>
> Is that a matter
2012 Oct 05
0
problems with printing and plotting aareg
It's a bug in summary.aareg which no one found until now.
What's wrong:
If dfbeta=TRUE then there is a second estimate of variance calculated, labeled as
test.var2. If maxtime is set, then both estimates of variance need to be recalculated by
the summary routine. An incorrect if-then-else flow led it to look for test.var2 when it
wasn't relevant. My test cases with maxtime also
2012 Oct 04
0
problems with plotting and printing aareg
Hi all,
I've ventured into the world of nonparametric survival and I would like to use the "maxtime" option for printing and plotting my aareg fit.
However, my fit does not have "test.var2" and this stops the print and plot when adding a maxtime.
My code is as follows:
Response<-Surv(Time,Event)
Model<-aareg(Response~Factor1*Factor2)
2009 Aug 04
0
Wishlist: Navigate to "Index" page of help when no topic (PR#13868)
On 7/28/2009 6:30 PM, smckinney at bccrc.ca wrote:
> Hi all,
>
> When I install a new package, and don't yet know any function names,
> I have to play the "poor man's game" to get to the standard
> help system "Index" page for the package:
You could complain to the package author or maintainer, who should have
created a help alias with the package name
2009 Aug 04
0
Wishlist: Navigate to "Index" page of help when no topic (PR#13871)
> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca]
> Sent: Tuesday, August 04, 2009 8:03 AM
> To: Steven McKinney
> Cc: r-devel at stat.math.ethz.ch; R-bugs at r-project.org
> Subject: Re: [Rd] Wishlist: Navigate to "Index" page of help when no
> topic specified (PR#13860)
>=20
> On 7/28/2009 6:30 PM, smckinney at bccrc.ca
2009 Aug 05
0
Wishlist: Navigate to "Index" page of help when no topic (PR#13873)
> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch at stats.uwo.ca]
> Sent: Tuesday, August 04, 2009 5:06 PM
> To: Steven McKinney
> Cc: 'r-devel at stat.math.ethz.ch'; 'R-bugs at r-project.org'
> Subject: Re: [Rd] Wishlist: Navigate to "Index" page of help when no
> topic specified (PR#13860)
>=20
> On 04/08/2009 7:33 PM,
2008 Aug 22
1
R CMD check problem
I have a query after finding an error running Rtools on a Windows machine.
I am trying to build an update to the R fda library using Rtools27 under
Windows XP Pro. This is the current fda library on RForge:
http://r-forge.r-project.org/projects/fda
Following R CMD build, R CMD check produces the following error in
00Install.out:
installing R.css in F:/work/RForge/fda.Rcheck
make: ***
2010 Oct 06
4
problem with abline
Hi All,
I am running a scatter plot and trying to add a best fit line. I use an abline function, but get no line drawn over the points. I also get no error. I arm using V 2.10.0 on Windows 7.
Here is my code, including the SAS transport file import:
require (foreign)
require (chron)
require (Hmisc)
require (lattice)
clin <- sasxport.get("y:\\temp\\subset.xpt")
attach(clin)