> On Oct 26, 2017, at 9:42 AM, Annalisa VanderWyden via R-help
> wrote:
>
>
> Hi R-help,
>
>
>
> I have fit a cox ph model to my data, but have beenreceiving an error when
> trying to fit a model to the nomogram. Here is the codeand corresponding
> error:
>
>
>
>
>
>> nomogramCF =
Hi R-help,
I have fit a cox ph model to my data, but have beenreceiving an error when
trying to fit a model to the nomogram. Here is the codeand corresponding error:
>nomogramCF = nomogram(cph_age6_40avp4,
+lp.at= seq(-10,10,by =0.5),lp = TRUE,
+
On Jun 24, 2013, at 12:00 PM, Sander van Kuijk wrote:
> Dear R-users,
>
> I have used the nomogram function from the rms package for a logistic
> regresison model made with lrm(). Everything works perfectly (r version
> 2.15.1 on a mac). My question is this: if my final model is not the one
> cr
You are using an informal shrinkage method. It is much better to use
penalized maximum likelihood estimation, built in to lrm.
If you really want to go the informal route, compute the linear
predictor from your final estimates and use ols( ) to predict that from
the component variables (you'l
Dear R-users,
I have used the nomogram function from the rms package for a logistic
regresison model made with lrm(). Everything works perfectly (r version
2.15.1 on a mac). My question is this: if my final model is not the one
created by lrm, but I internally validated the model and 'shrunk' the
This can't be done directly, but if you can output predicted values from
coxme and fit an rms ols model that predicts these predicted values with an
R^2 of 1.0 you can use nomogram() on the ols fit to get what you want.
Frank
george boul wrote
> Dear R-users,
> I am a novice R-user with some exper
Dear R-users,
I am a novice R-user with some experience in using the RMS package for taking
nomograms after various survival models.
This time, I am trying to plot a nomogram after a Random Effects Cox,
implemented by the "coxme" package. My questions are:
1. Is it possible to take a nomogram di
Got it.
Thank you so much for the help!
Min Yi MD, PhD
Department of Surgical Oncology - Unit 1484
1400 Pressler Street, #FCT17.6061
University of Texas M.D. Anderson Cancer Center
P.O. Box 301402
Houston, TX 77230-1402
Phone: 713-563-1874
Fax: 713-792-4689
From: Frank Harrell [via R] [mailto:
Hazard() is not implemented except for parametric survival models.
You are not calling nomogram() correctly; in rms the plotting step is
separated from the nomogram computations.
To plot cumulative event rates do something like:
mort10 <- function(lp) 1 - surv(10,lp)
and tell nomogram about mor
Hello,
I am using Dr. Harrell's rms package to make a nomogram. I was able to make
a beautiful one. However, I want to change 5-year survival probability to
5-year failure probability.
I couldn’t get hazard rate from Hazard(f1) because I used cph for the model.
Here is my code:
library(rms)
f1
Hello,
I am using Dr. Harrell's design package to make a nomogram. I was able to
make a beautiful one. However, I want to change 5-year survival probability
to 5-year failure probability.
I couldn’t get hazard rate from Hazard(f1) because I used cph for the model.
Here is my code:
f1 <- cph
sorry the code for nomogram
par(cex=0.8)
nom<- nomogram(f1, conf.int=F,
fun=list(surv5, surv10), funlabel=c('5-Year Survival Probability', '10-Year
Survival Probability' ), lp=F,
fun.at=c(at.surv, at.surv),label.every=1, force.label=FALSE, cex.axis=0.8,
verbose=TRUE, cex.var=0.8)
Thanks
Min
Please convert to rms. Design is no longer supported. See
http://biostat.mc.vanderbilt.edu/Rrms
Frank
min wrote
>
> sorry the code for nomogram
>
> par(cex=0.8)
> nom<- nomogram(f1, conf.int=F,
> fun=list(surv5, surv10), funlabel=c('5-Year Survival Probability',
> '10-Year Survival Probabilit
On 05/19/2010 03:17 PM, Marc Carpentier wrote:
Dear list, I'm facing the following problem : A cox model with my sex
variable interacting with several continuous variables :
cph(S~sex*(x1+x2+x3)) And I'd like to make a nomogram. I know it's a
bit tricky and one mights argue that nomogram is not a
Dear list,
I'm facing the following problem :
A cox model with my sex variable interacting with several continuous variables
: cph(S~sex*(x1+x2+x3))
And I'd like to make a nomogram. I know it's a bit tricky and one mights argue
that nomogram is not a good a choice...
I could use the parameter int
"Surv Oth","Med surv pap",
"Med surv Fol","Med Surv Oth"),
fun.at=list(at.surv, at.surv, at.surv,
at.med, at.med, at.med), varname.label=FALSE, maxscale=100)
title("stratified nomogram")
-Original Message
David Winsemius wrote:
On Apr 25, 2009, at 6:57 PM, reneepark wrote:
Hello,
I am using Dr. Harrell's design package to make a nomogram. I was able to
make a beautiful one without stratifying, however, I will need to
stratify
to meet PH assumptions. This is where I go wrong, but I'm not sure
I'm sorry - I meant a "median survival" estimate, not a median "risk."
I see - I didn't realize that by stratifying it would pool the levels of the
stratified variable. Hm, that is unfortunate, considering the stratified
variable is one that I would like to keep in the nomogram.
Thank you for yo
On Apr 25, 2009, at 6:57 PM, reneepark wrote:
Hello,
I am using Dr. Harrell's design package to make a nomogram. I was
able to
make a beautiful one without stratifying, however, I will need to
stratify
to meet PH assumptions. This is where I go wrong, but I'm not sure
where.
Non-Stra
Hello,
I am using Dr. Harrell's design package to make a nomogram. I was able to
make a beautiful one without stratifying, however, I will need to stratify
to meet PH assumptions. This is where I go wrong, but I'm not sure where.
Dear colleagues,
I hope someone can help me with my problem.
I have fitted a cox model with the following syntax:
# cox01def <-cph(Surv(TEVENT,EVENT) ~ ifelse(AGE>50, (AGE-50)^2,0) +
BMI +
# HDL+DIABETES +HISTCAR2 + log(CREAT)+
as.factor(ALBUMIN)+STENOSIS+IMT,data # = XC, x=T, y=T, surv=T) *
[EMAIL PROTECTED] wrote:
> Hi R users.
>
> I have a model of cox that already it is estimated (I have only the
> model estimated, I haven't data), how can I determine a nomogram with
> R? Is it posible to do nomograms in Design package? I think that's
> only when the model (Cox Regression i
Hi R users.
I have a model of cox that already it is estimated (I have only the
model estimated, I haven't data), how can I determine a nomogram with
R? Is it posible to do nomograms in Design package? I think that's
only when the model (Cox Regression in this case) is before estimated
i
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