Displaying 20 results from an estimated 800 matches similar to: "Interpreting the example given by Prof Frank Harrell in {Design} validate.cph"
2011 Feb 19
0
contrasting Somer's D from Design package
Dear R help,
I am having a problem with the Design package and my problem is detailed
here.
I fit a cox model to my data and validate the Somer's Dxy using the Design
package.
(Because of computation time problem, i only try 10 bootstrap samples for
the time being)
This is the model without stratification:
> library(Design)
>
2011 Mar 01
1
which does the "S.D." returned by {Hmisc} rcorr.cens measure?
Dear R-help,
This is an example in the {Hmisc} manual under rcorr.cens function:
> set.seed(1)
> x <- round(rnorm(200))
> y <- rnorm(200)
> round(rcorr.cens(x, y, outx=F),4)
C Index Dxy S.D. n missing
uncensored Relevant Pairs Concordant Uncertain
0.4831 -0.0338 0.0462 200.0000
2009 Jul 15
0
Nagelkerkes R2N
I am interested Andrea is whether you ever established why your R2 was 1.
I have had a similar situation previously.
My main issue though, which I'd be v grateful for advice on, is why I am obtaining such negative values -0.3 for Somers Dxy using validate.cph from the Design package given my value of Nagelkerke R2 is not so low 13.2%.
I have this output when fitting 6 variables all with
2014 Jul 05
1
Predictions from "coxph" or "cph" objects
Dear R users,
My apologies for the simple question, as I'm starting to learn the concepts
behind the Cox PH model. I was just experimenting with the survival and rms
packages for this.
I'm simply trying to obtain the expected survival time (as opposed to the
probability of survival at a given time t). I can't seem to find an option
from the "type" argument in the predict
2010 Oct 01
6
Interpreting the example given by Frank Harrell in the predict.lrm {Design} help
Dear list,
I am relatively new to ordinal models and have been working through the example given by Frank Harrell in the predict.lrm {Design} help
All of this makes sense to me, except for the responses, i,e how do i interpret them? i would be extremely grateful if someone could explain the results?
First i establish the date and model -
> y <- factor(sample(1:3, 400, TRUE), 1:3,
2005 Apr 05
0
Regression Modeling Strategies Workshop by Frank Harrell in Southern California
Dr. Frank E. Harrell, Jr., Professor and Chair of the Department of
Biostatistics at Vanderbilt University is giving a one-day workshop on
Regression Modeling Strategies on Friday, April 29, 2005. Analyses of the
example datasets use R/S-Plus and make extensive use of the Hmisc library
written by Professor Harrell.The workshop is sponsored by the Southern
California Chapter of the American
2005 Sep 12
0
Trying to reach Frank Harrell
Does anyone have a valid email address for Frank Harrell of Hmisc fame? I've
tried getting in touch with him at both fharrell at virginia.edu and
f.harrell at vanderbilt.edu, but messages to either of those addresses get
bounced. Frank, if you're reading this, please email me from an account that
will accept a reply.
Jeff Hallman
2011 May 05
1
Confidence interval for difference in Harrell's c statistics (or equivalently Somers' D statistics)
Dear All,
I am trying to calculate a 95% confidence interval for the difference in two
c statistics (or equivalently D statistics). In Stata I gather that this
can be done using the lincom command. Is there anything similar in R?
As you can see below I have two datasets (that are actually two independent
subsets of the same data) and the respective c statistics for the variables
in both cases.
2009 Sep 08
1
Obtaining value of median survival for survfit function to use in calculation
Hi,
I'm sure this should be simple but I can't figure it out! I want to get the median survival calculated by the survfit function and use the value rather than just be able to print it. Something like this:
library(survival)
data(lung)
lung.byPS = survfit(Surv (time, status) ~ ph.ecog, data=lung)
# lung.byPS
Call: survfit(formula = Surv(time, status) ~ ph.ecog, data = lung)
1
2008 Apr 21
2
Trend test for survival data
Hello,
is there a R package that provides a log rank trend test
for survival data in >=3 treatment groups?
Or are there any comparable trend tests for survival data in R?
Thanks a lot
Markus
--
Dipl. Inf. Markus Kreuz
Universitaet Leipzig
Institut fuer medizinische Informatik, Statistik und Epidemiologie (IMISE)
Haertelstr. 16-18
D-04107 Leipzig
Tel. +49 341 97 16 276
Fax. +49 341 97 16
2009 Nov 13
2
survreg function in survival package
Hi,
Is it normal to get intercept in the list of covariates in the output of survreg function with standard error, z, p.value etc? Does it mean that intercept was fitted with the covariates? Does Value column represent coefficients or some thing else?
Regards,
-------------------------------------------------
tmp = survreg(Surv(futime, fustat) ~ ecog.ps + rx, ovarian,
2011 Oct 29
1
How to plot survival data from multiple trials (simulations)?
Dear all:
Could anyone please provide some R codes to plot the below survival data to compare two groups (0 vs 1) after 2 simulations (TRL)? need 95% prediction interval on the plot from these 2 trials. I would like to simulate 1000 trials later. Thanks a lot for your great help and consideration!
yan
TRL ID ECOG BASE PTR8 GROUP POP ST ind
1 1 1 1 2.2636717 0.255634126 1 1 99.4 F
3 1 2 1
2012 Jun 05
1
model.frame and predvars
I was looking at how the model.frame method for lm works and comparing
it to my own for coxph.
The big difference is that I try to retain xlevels and predvars
information for a new model frame, and lm does not.
I use a call to model.frame in predict.coxph, which is why I went that
route, but never noted the difference till now (preparing for my course
in Nashville).
Could someone shed light
2009 Aug 01
2
Cox ridge regression
Hello,
I have questions regarding penalized Cox regression using survival
package (functions coxph() and ridge()). I am using R 2.8.0 on Ubuntu
Linux and survival package version 2.35-4.
Question 1. Consider the following example from help(ridge):
> fit1 <- coxph(Surv(futime, fustat) ~ rx + ridge(age, ecog.ps, theta=1), ovarian)
As I understand, this builds a model in which `rx' is
2011 Jun 13
1
Somers Dyx
Hello R Community,
I'm continuing to work through logistic regression (thanks for all the help on score test) and have come up against a new opposition.
I'm trying to compute Somers Dyx as some suggest this is the preferred method to Somers Dxy (Demaris, 1992). I have searchered the [R] archieves to no avail for a function or code to compute Dyx (not Dxy). The overview of Hmisc has
2006 Jul 27
1
replace values in a distance matrix
Hi to everybody!
I´m just a beginner in R, and I´m trying to replace values in a distance matrix with a concret condition: replace all values (elements) lower than 4.5 with value=18.
I´ve tried this, but it doesn´t work...
Dxy would be my 117 x 117 euclidean distance matrix
M18 and M4.5 would be 117 x 117 matrices:
M18<-matrix(rep(18,13689),nrow=117)
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$ph.ecog)
0 1 2 3 <NA>
63 113 50 1
2012 Apr 08
0
Need help interpreting output from rcorrp.cens with Cox regression
Dear R-listers,
I am an MD and clinical epidemiologist developing a measure of comorbidity severity for patients with liver disease. Having developed my comorbidity score as the linear predictor from a Cox regression model I want to compare the discriminative ability of my comorbidity measure with the "old" comorbidity measure, Charlson's Comorbidity Index. I have nearly 10,000
2012 Aug 17
0
REPOST: Need help interpreting output from rcorrp.cens with Cox regression
I am reposting my message from April 8th because I never received a response to the original post:
Dear R-listers,
I am an MD and clinical epidemiologist developing a measure of comorbidity severity for patients with liver disease. Having developed my comorbidity score as the linear predictor from a Cox regression model I want to compare the discriminative ability of my comorbidity measure with
2009 Feb 06
1
Using subset in validate() in Design, what is the correct syntax?
Hi
I am trying to understand how to get the validate() function in Design
to work with the subset option. I tried this:
ovarian.cph=cph(Surv(futime, fustat) ~ age+factor(ecog.ps)+strat(rx),
time.inc=1000, x=T, y=T, data=ovarian)
validate(ovarian.cph)
#fine when no subset is used, but the following two don't work:
> validate(ovarian.cph, subset=ovarian$ecog.ps==2)
Error in