t;, log='y', type='l', yaxt='n',
main="US Death Rates")
axis(2, c(1,2,5,10,20, 50), c(1,2,5,10, 20, 50), las=2)
This code works fine on my screen. The error comes up when I put it into an
.Rmd file
and apply rmarkdown::render() to it.
Likely some font file is needed, but what one?
Terry
oss talk in my brain from the rstan library
-- Gregg's note shows such a function in purr. But I rather like having as few
dependencies as possible in a package, one usage is normally not enough, at
least for
something this simple.
Terry T.
On 12/27/22 14:38, Bert Gunter wrote:
> Well, I
. SuStaIn tends to give small variances.
Terry T.
--
Terry M Therneau, PhD
Department of Quantitative Health Sciences
Mayo Clinic
thern...@mayo.edu
"TERR-ree THUR-noh"
[[alternative HTML version deleted]]
__
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he explicit x$iter function. Am I indeed
overlooking
something? I don't expect a speed increase, just cleaner code.
Terry T.
--
Terry M Therneau, PhD
Department of Quantitative Health Sciences
Mayo Clinic
thern...@mayo.edu
"TERR-ree THUR-noh"
[[alternati
I prefer the duplicated() function, since the final code will be clear to a future reader.
(Particularly when I am that future reader).
last <- !duplicated(mydata$ID, fromLast=TRUE) # point to the last ID for each
subject
mydata$data3[last] <- NA
Terry T.
(I read the list once
1-.428)*coef.
>
Yes, the "mean" component is the reference level for predict and survfit.� If I
could go
back in time it would be labeled as "reference" instead of "mean".�� Another
opportunity
for me to make the documentation clearer.
Good questions,
� Terry T
fault survival curve would
be for a
sex of .453, say, was off-putting to many.
Terry T.
On 9/3/21 11:01 AM, Bond, Stephen wrote:
>
> Hi,
>
> Please, help me understand what is happening with the means of a Cox model?
>
> I have:
>
> R version 4.0.2 (2020-06-22) -- &qu
an approximation.
Terry T.
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and provide commented, minimal, self-contained
Is there a complement to the methods function, that will list all the defined
methods for
a class? One solution is to look directly at the NAMESPACE file, for the
package that
defines it, and parse out the entries. I was looking for something built-in,
i.e., easier.
--
Terry M
.vector?"
Nevertheless I understand Roger's confusion.
--
Terry M Therneau, PhD
Department of Quantitative Health Sciences
Mayo Clinic
thern...@mayo.edu
"TERR-ree THUR-noh"
[[alternative HTML version deleted]]
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. Perhaps add a link in
the
wilcox.test help page?
Footnote: AUC is a special case of C but not vice versa. People sometimes try
to extend
AUC to the other data types, but IMHO with only moderate success.
--
Terry M Therneau, PhD
Department of Health Science Research
Mayo Clinic
thern...@mayo
way to turn off clip
is with a
new plot.
--
Terry M Therneau, PhD
Department of Health Science Research
Mayo Clinic
thern...@mayo.edu
"TERR-ree THUR-noh"
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don't break it". Part of the testing involved running the test suits of
all 679 reverse dependencies under the new version.
Terry Therneau
thern...@mayo.edu
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93 69 60 88 88 80 77 41 59 79 31
chi-squared: 72 76 82 83 89 79 69 67 77 78 69 77 83 88 87 89 78
chi: 92 73 89 87
chi-squares: 77 83
chi-bar-square: 91
There doesn't look to be a trend over time. The 1922 Fisher reference uses the
Greek
symbol, by the way.
Terry T
[[alternative
tx))) %*% coef(fit3)[4:7] +
coef(fit3)[3]
lines(sqrt(tx), ty3, col=2)
The right tail is now better behaved. Eliminating the points >900 makes
things even
better behaved.
Terry T.
On 8/8/19 9:07 AM, Ferenci Tamas wrote:
> I was thinking of two possible ways to
> plo
John,
The text below is cut out of a "how to write a package" course I gave at the
R
conference in Vanderbilt. I need to find a home for the course notes, because
it had a
lot of tidbits that are not well explained in the R documentation.
Terry T.
Model frames:
One of
I've created a hex sticker for survival. How should that be added to the
package
directory? It's temporarily in man/figures on the github page.
Terry T.
(Actually, the idea was from Ryan Lennon. I liked it, and we found someone with
actual
graphical skills to execute
. This
might be only the second request for the feature in the 30+ years since that
date.
Terry Therneau
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nes in data0 and/or data1. Do you want to
collapse that person into a single row before the glm fits? If subject "Jones"
is represented by 15 lines in the data and "Smith" by 2, it does seem a bit
unfair to give Jones 15 observations in the glm fit. But full discussion of
this
set will have < 100 elements. Since this is
inside the survival package, and that package is on the 'recommended' list, I can't
depend on any package outside the recommended list.
Terry T.
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othing.
The CART book (Brieman, Freidman, Olshen and Stone) on which rpart is based highlights the
difference between odds-regression (for which the final prediction is a percent, and error
is Gini) and classification. For the former treat y as continuous.
Terry T.
On 05/15/2017 05:
since that would lead to an invalid time interval.
Please look at the "Asking for help" section of https://www.r-project.org/help.html, and
in particular the link on reproducable examples. You need to give an example, with data,
that reproduces the problem.
Terry T.
(PS, I agree th
o the R/ directory, then R CMD build followed by R CMD INSTALL. Macintosh is
essentially as easy, though you need to install Xcode for the compilers. The compile
toolchain for windows is outside my ken.
Let's keep talking.
Terry T.
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t found" emails.
Terry T.
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and provide commented, min
and to the next dozen who will invariably contact me directly.
Thanks,
Terry Therneau
Forwarded Message
Subject: RE: survival package
Date: Wed, 26 Apr 2017 18:05:30 +
From: sesh...@mskcc.org
To: Therneau, Terry M., Ph.D. <thern...@mayo.edu>
Thank you for the
s the kind of task for which someone, somewhere will have written routines. I just
don't know who or where.
Any hints?
Terry T.
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PLEA
than the first?
What if the single subject with ph.ecog=3 had ended up in the validation data
set; how should we judge their prediction?
This complexity is one reason that there is not a simple function for
"validation" with a new data set.
On 02/27/2017 09:48 AM, Alfredo wrote:
T
e best one, and then prune there.
How do you define "best"?
Terry Therneau
On 02/26/2017 05:00 AM, r-help-requ...@r-project.org wrote:
I'd like to use a different data ( validation) set for pruning my
classification tree. Unfortunately there aren't arguments to get this in
prune.rpart
on the new data. Caveat -- I don't know mice() well at all: the
dat1 data set below has multiple observations per subject, should the mice() command be
cognizant of this?
Terry Therneau
library(survival)
library(mice)
test1 <- data.frame (time=c(4,3,1,1,2,2,3,5,2,4,
nflection point, and b[3] is the change in slope at the inflection point.
The main downside is that k is arbitrary. I simply choose it to "look right", though it
too could be part of an optimization.
Terry Therneau
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and in the 20s for method 1
(detectCores() =80 on the box, we used mc.cores=50). Wall time for method 2
is looking to be several hours.
Any pointers to documentation/discussion at this level would be much
appreciated. I'm going to be fitting a lot of models.
Terry T.
s I've found addresses this
particular question. Both direct answers and pointers to other docs would be
welcome.
Terry T.
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s on a regular schedule. Even then you will lose a few. (In one study several
years ago, long term follow-up of cancer, there was a new Mrs Smith who refused to
acknowledge the existence of the prior wife, even to forward letters.)
Terry Therneau
it. As a consequence, the maintainer expects to get
new emails that ``we have found a bug in your code: it gives a different answer than
SAS''. (This is an actual quote.)
Terry Therneau
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Good afternoon r
http://wsitest01.com/minerals.php?france=y18m1xba0w8z
My best to you
terry minton
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PLEASE do read the posting guide
r. A bit
more background might make me more excited about extending the code to this
case.
Terry Therneau
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PLEASE do read the posting
have given us no details of your example code that "doesn't work", and I can't read
your mind. So no, we can't help. Give us a hint.
Terry T
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on the details of this.
Terry Therneau
--
On 09/06/2016 05:00 AM, r-help-requ...@r-project.org wrote:
Dear Elisabetta,
I have no direct answer to your question, but a suggestion: Use the
'coxme' function (in the package with the same name). In the help page
<- survSplit(Surv(obsT, status) ~ ., dfSurv, cut=seq(30, 90, by=30), id="ID",
zero=0)
I will fix this. I apologize for the error.
Terry Therneau
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re to
imagine a case where I would need it badly enough to wait a lifetime for the
answer. The Efron approximation is pretty darn good for cases like this, and
it is fast.
Terry Therneau
---
Dear users,
I'm trying to estimate a conditional logist
the tmerge and survSplit functions, which are useful tools to build the
requisite data sets, and to the "multi-state" vignette for model fits and plots.
Terry Therneau
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I was right that there is an easy answer!
Thanks for the 3 quick answers, all three correct and useful.
Terry Therneau
On 04/15/2016 07:15 AM, Thierry Onkelinx wrote:
Dear Terry,
Does fitting group + age:group instead of age*group solves your problem?
Best regards,
ir. Thierry Onkelinx
tion.
Yes, I can reconstruct these from the original fit, but I have a lot of variables for
several models and it would be easier to have an automatic form. I suspect that there is
an easy answer, but I don't see it.
Terry Therneau
__
R-h
On 04/02/2016 05:00 AM, r-help-requ...@r-project.org wrote:
Hello,
I'm looking for a way in which R can make my live easier.
Currently i'm using R convert data from a dataframe to json's and then sending
these json's to a rest api using a curl command in the terminal (i'm on a mac).
I've
LET you put a phrase like "log(time)" into the model statement,
so people end up doing the right thing, but by accident.
Terry T.
On 03/30/2016 05:28 PM, Göran Broström wrote:
On 2016-03-30 23:06, David Winsemius wrote:
On Mar 29, 2016, at 1:47 PM, Jennifer Wu, Miss
<jennifer..
covariates. Otherwise there is little we can do.
Terry Therneau
On 03/30/2016 05:00 AM, r-help-requ...@r-project.org wrote:
I am having convergence issues when I use coxph with a interaction term
(glarg*bca_py) and interaction term with the restricted cubic spline
(glarg*bca_time_ns). I use survival
)
In your case I'd advise an end run: fit the model using ns() instead of pspline. I like
smoothing splines better than regression splines, but the fact is that for most data sets
they result in nearly identical answers.
Terry T
__
R-help@r-pro
also curious to learn exactly what you mean by "interval
censored poisson". Exponential with interval time to first event is equivalent to
poisson, which is what I'd guess from "lognormal", but you may mean something else.
Terry Therneau
(author of survival)
On 02/14/2
it
(not an unwarranted assumption), I'm not aware of any work on what an appropriate variance
would be for the concordance in that case.
3. I need to think about the large variance issue.
Terry Therneau
On 01/20/2016 08:09 PM, r-help-requ...@r-project.org wrote:
Hi,
I'm running conditional logistic
nd and so has chosen not to make a guess.
Also, please do not post in html. As you see below it leads to a mangled
message.
Terry Therneau
On 12/22/2015 05:00 AM, r-help-requ...@r-project.org wrote:
Merry Christmas everyone:
I have the following data(mydat) and would like to fit a conditional
es missing out of both the fit and the residuals.
(Unfortunately, only a few modeling functions in R pay attention to the difference between
these two na.action options.)
Terry Therneau
On 12/04/2015 05:00 AM, r-help-requ...@r-project.org wrote:
Hi,
I am fitting an AFT model assuming a Weibull
rning cost. I
still use the latex form myself as it is not at all difficult to use --- once you learn it.
Terry Therneau
On 11/18/2015 05:00 AM, r-help-requ...@r-project.org wrote:
I am looking for a gentle introduction to SWEAVE, and would appreciate
recommendations.
I have an R program that I w
-infinity to +infinity. Or more precisely, for any value that the
maximizer might guess at some point during the iteration.
Terry T.
On 11/14/2015 05:00 AM, r-help-requ...@r-project.org wrote:
Thanks Terry but the error persists. See:
>library(foreign)> library(survival)> library(VGAM) &
ng of what
observations are in what part(s) of the tree, sorting the data, tracking missing values,
etc. If you ever do want to write your own code you are more than welcome to build off
this --- I wouldn't want to write that part again.
Terry Therneau
On 11/12/2015 05:00 AM, r-help-requ...@r-project
cale 1/a.
But even if I am correct the discontinuity at b will cause the underlying Newton-Raphson
method to fail.
Terry Therneau
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PLEASE d
in advanced,
Raoni
No one has done the theory work to see if the method used by coxme extends to random
effects models. I suspect that it does, but that is a long way from a proof. So at this
point I don't have a good suggestion, even though I have been thinking about the problem.
Terry Therneau
(0, .15),
xlab="Value", ylab="Density")
points(1:24, y/sum(y))
-
There are a half dozen ways to parameterize a Weibull distribution; the location-scale
form used by survreg is one of the less common. See help(survreg) for more information --
look at the exam
The cutpoint is on the predictor, so the interpretation is the same as it is for any other
rpart model. The subjects with predictor < cutpoint form one group and those > cutpoint
the other. The cutpoint is chosen to give the greatest difference in "average y" between
the groups. For poisson
15:17
(Preservation of the names is not important)
Terry T
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and
document TS-140 talks about IBM 360 and Dec VAX machines but no others, which should
give you an idea of its age.
Terry Therneau
On 09/27/2015 05:00 AM, r-help-requ...@r-project.org wrote:
Peter
Thanks for the explanation. One further comment ? you wrote:
>I don't think the FDA "
text/csv" field coming from an http POST request. This
is an internal service on an internal Mayo server and coded by our own IT department; this
will not be the first case where I have found that their definition of "csv" is not quite
standard.
Terry T.
On 23/09/15 10:00, T
is not one that I had considered.
You should transform it to dsCMatrix first, which is a symmetric
class. Or if it is small enough, to a simple matrix.
Terry T.
On 09/22/2015 05:00 AM, r-help-requ...@r-project.org wrote:
I have a problem with running the mixed effects Cox regression model using
read.csv call but it is not so easy to replace it with something else.
Terry T
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PLEASE do read the posting guide http://www.R-project.org/
xph does left truncation but not left (or interval) censoring
survreg does interval censoring but not left truncation (or time
dependent covariates).
Terry T
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alive at time =10, say,
is integral(S(t), from 10 to infin) / S(10), where S is the survival curve. You can also
read off quantiles of the expected remaining life.
Terry Therneau
(author of the survival package)
On 08/18/2015 05:00 AM, r-help-requ...@r-project.org wrote:
Dear All,
I would
practice. The 'equal weights' notion embedded in a fixed effects model + SAS type 3 is an
isolated backwater.
Terry T.
PS. The Devils' Drug Development Dictionary at the same source has some gems. Three
rather random choices:
Bayesian - One who, vaguely expecting a horse and catching a glimpse
, in my opinion.
3. Should you ever use it? No. There is a very strong inverse correlation between
understand what it really is and recommend its use. Stephen Senn has written very
intellgently on the issues.
Terry Therneau
On 07/22/2015 05:00 AM, r-help-requ...@r-project.org wrote
not as dense as I think.
Terry T.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal
Yes it is obvious --- once someone else pointed it out.
Thanks for the hint.
Terry T.
On 07/16/2015 12:52 PM, Peter Langfelder wrote:
Hi Terry,
maybe I'm missing something, but why not define a matrix BB = V'B;
then t(B) %*% V = t(BB), then your problem reduces to finding A such
that t(BB
for unbiased variance; I've never looked for it. I'm not
convinced that it is worthwhile though.
Terry Therneau
On 07/04/2015 05:00 AM, r-help-requ...@r-project.org wrote:
I would like help understanding why a survival regression with no censored
data-points does not give the same variance estimates
. This (or something like it) is what I was looking for.
Am I overlooking something?
Terry Therneau
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PLEASE do read the posting guide http
-- heresy!) would
have been a much better design choice. But as long as I'm in R the coxph routine tries to
be a good citizen.
Terry T.
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- terms2[-strat$terms]
X - model.matrix(terms2, mf)
X
}
tdata - data.frame(y= 1:10, zed = 1:10, grp = factor(c(1,1,1,2,2,2,1,1,3,3)))
testfun(y ~ zed*grp, tdata)
testfun(y ~ strata(grp)*zed, tdata)
Terry T.
- original message --
For building design matrices for Cox proportional
so this saved me substantial time.
Terry T.
On 06/04/2015 03:00 PM, Marc Schwartz wrote:
On Jun 4, 2015, at 12:56 PM, Therneau, Terry M., Ph.D. thern...@mayo.edu
wrote:
I'm checking the survival package and get the following error. How do I find
the offending line? (There are a LOT
I'm checking the survival package and get the following error. How do I find the offending
line? (There are a LOT of files in the man directory.)
Terry T.
--
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd
but not the repeated measures one. Statisticially you can use a
generalized estimating equations approach (package gee) or a random effect per subject
approach (lme or lmer package).
Terry T.
On 05/27/2015 05:00 AM, r-help-requ...@r-project.org wrote:
I mostly use Stata 13 for my regression analysis
or numeric.
Terry Therneau
On 05/13/2015 05:00 AM, r-help-requ...@r-project.org wrote:
Dear R-help,
I am interested in plotting some pedigrees and came across the kinship2
package. What follows is an example of the pedigrees I am working with
Now, when running
## check package availability
to the data and ask what is the predicted survival time for a low risk subject.
The answer will at best be greater than 5 years. The program cannot say if it is 6 or
10 or even 1000. A bigger data set does not help.
Terry Therneau
__
R-help@r-project.org
people would have been reading the results in a
program (like you are), I didn't want to break their code so left the internal variable
alone. It appears that I traded maybe safer for certain confusion.
Terry Therneau
On 04/09/2015 05:00 AM, r-help-requ...@r-project.org wrote:
Hi,?
I need
that it will become obvious once I
have an example.
Terry Therneau
On 03/06/2015 05:00 AM, r-help-requ...@r-project.org wrote:
I don?t understand an error message from a thielsen function call within a
dplyr do function call.
by.CaseNo - group_by(as.data.frame(MAP.dt), CaseNo)
MAP.thielsen
it needs to deal with all
of these.
Professor Ripley has pointed out that the default action of sort() for right censored
times, which I agree is reasonable.
Terry Therneau (author of the survival package)
On 02/13/2015 05:00 AM, r-help-requ...@r-project.org wrote:
It seems that Surv objects
plotting oval so of course the plotted tree is easier to grasp.
Terry T.
On 02/11/2015 05:00 AM, r-help-requ...@r-project.org wrote:
Hi all,
In the attachment or this link (http://oi58.tinypic.com/35ic9qc.jpg) you'll find the
decision tree I made. I used the Rpart package to make the tree
/technical-reports
http://www.mayo.edu/research/departments-divisions/department-health-sciences-research/division-biomedical-statistics-informatics/technical-reports
Terry Therneau
-- begin included message ---
I am looking for R example codes to compute age-standardized death
families; I don't think that your distribution can be written in that way.
Look at survival under the Task Views tab (upper left corner) of the cran.org web page
-- someone else may have already done it.
Terry T.
__
R-help@r-project.org mailing
using baseline values fails just because the covariates are out of date. So PH
might hold for the updated (time-dependent) covariates and fail when using baseline
values. This is a very study specific situation, however.
Terry T.
__
R-help@r
note implies that output was attached. Note that r-help strips away all
attachments, so none of us saw it.
Terry Therneau
On 12/19/2014 05:00 AM, r-help-requ...@r-project.org wrote:
Hi all,
I have a data set like this:
Test.cox file:
V1V2 V3Survival
Use the coxme funtion (package coxme), which has the same syntax as lme4.
The frailty() function in coxph only handles the simple case of a random
intercept.
Terry Therneau
On 12/12/2014 05:00 AM, r-help-requ...@r-project.org wrote:
Hi,
I have a very simple Cox regression model in which I
anyone?
Terry Therneau
=
tmt% R CMD build dart
* preparing 'dart':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
Terry T.
On 11/18/2014 08:47 AM, Hadley Wickham wrote:
Do you have a .Rbuildignore? If so, what's in it?
Hadley
On Tue, Nov 18, 2014 at 7:07 AM, Therneau, Terry M., Ph.D.
thern...@mayo.edu wrote:
I have a new package (local use only). R CMD check fails with a messge I
haven't seen before
This is fixed in version 2.37-8 of the survival package, which has been in my send to
CRAN real-soon-now queue for 6 months. Your note is a prod to get it done. I've been
updating and adding vignettes.
Terry Therneau
On 11/05/2014 05:00 AM, r-help-requ...@r-project.org wrote:
I am
of their use to the time dependent covariates vignette.
Terry Therneau
On 10/03/2014 05:00 AM, r-help-requ...@r-project.org wrote:
Hello! I hope someone can help me. It would save me days of work. Thanks in
advance!
I have two dataframes which look like these:
myframe - data.frame (Timestamp=c
, mistaken, or otherwise deficient,
only that my understanding is so.
Could someone illuminate?
Terry T.
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('b')).
Terry T.
On 10/03/2014 09:52 AM, peter dalgaard wrote:
S3 only has single dispatch, so in one case it dispatches to c.Date and in the
other to c.POSIXct, both of those return an object of the corresponding class.
In both cases, the arguments pass through
c(unlist(lapply(list
useful for me to see. Continuous variables go to the left of the | and categoricals to
the right of the |. Having a family id to the left makes no sense at all.
Terry Therneau
On 09/15/2014 03:20 PM, Marie Dogherty wrote:
Dr. Therneau,
I was wondering if you had a spare minute, if you
On 07/30/2014 05:00 AM, r-help-requ...@r-project.org wrote:
A while ago, I inquired about fitting excess relative risk models in R. This is
a follow-up about what I ended up doing in case the question pops up again.
While I was not successful in using standard tools, switching to Bayesian
tried running an example to see if the result is a
hazard or a cumulative hazard but the run failed and it's time to run to a meeting.
Assume it is cumulative hazard. Then exp(-fit$lambda0) will give the baseline survival curve.
Terry T
On 08/27/2014 02:47 PM, David Winsemius wrote:
On Aug
that you want Dr Therneau to respond intelligently :-)
Terry T.
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and provide commented, minimal
and the xbar at each time is
replaced with an appropriate weighted survey estimate. See various papers by Brian Langholz.
Terry T
On 08/13/2014 07:26 AM, John Pura wrote:
Hi Dr. Therneau,
The original question on the forum was:
My problem was how to build a Cox model for the matched data (1
stratum only once.
For any of the above you can add a robust variance. Required if case weights
are used.
Terry T
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with 30 years ago (because I don't remember it exaclty):
The incidence of the condition under consideration and its subsequent death rate will
both drop by 1/2 at the commencement of a study, and will not return to their former
values until the study finishes or the PI retires.
Terry T
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