Displaying 20 results from an estimated 700 matches similar to: "Hazard plot"
2009 Apr 03
2
Schoenfeld Residuals
Dear All,
Sorry to bother you again.
I have a model:
coxfita=coxph(Surv(rem.Remtime/365,rem.Rcens)~all.sex,data=nearma)
and I'm trying to do a plot of Schoenfeld residuals using the code:
plot(cox.zph(coxfita))
abline(h=0,lty=3)
The error message I get is:
Error in plot.window(...) : need finite 'ylim' values
In addition: Warning messages:
1: In sqrt(x$var[i, i] * seval) : NaNs
2009 May 22
1
Forcing a variableinto a model using stepAIC
Dear All,
I am attempting to use forward and/or backward selection to determine
the best model for the variables I have. Unfortunately, because I am
dealing with patients and every patient is receiving treatment I need
to force the variable for treatment into the model. Is there a way to
do this using R? (Additionally, the model is stratified by
randomisation period). I know that SAS can be
2009 Jun 09
2
Isolating a single plot from plots produced simultaneously
Dear R-Help,
I am using the 'mfp' package. It produces three plots (as I am using
the Cox model) simultaneously which can be viewed together using the
following code:
fit <- mfp(Surv(rem.Remtime,rem.Rcens)~fp(age)+strata(rpa),family=cox,data=nearma,select=0.05,verbose=TRUE)
par(mfrow=c(2,2))
plot(fit)
They can be viewed separately but the return key must be pressed after
each graph
2008 Sep 30
0
Hazard curves
-- begin included message -----
I am looking at a continuous variable, age. I am looking at time to
12-month remission and can calculate the HR and 95% confidence interval are
follows:
coxfita = coxph(Surv(rem.Remtime,rem.Rcens)~nearma$all.age,data=nearma)
exp(coxfita$coefficients)
exp(confint(coxfita))
However, because I am looking at age as a continuous variable I cannot draw
a Kaplan-Meier
2009 Oct 05
0
Unusual error while using coxph
Hi all,
I'm very confused! I've been using the same code for many weeks without any
bother for various covariates. I'm now looking at another covaraite and
whenever I run the code you can see below I get an error message: "Error in
rep(0, nrow(data)) : invalid 'times' argument"
This code works:
# remove 'missing' cases from data #
snearma <-
2009 Mar 26
1
Centring variables in Cox Proportional Hazards Model
Dear All,
I am contemplating centering the covariates in my Cox model to reduce
multicollinearity between the predictors and the interaction term and
to render a more meaningful interpretation of the regression
coefficient. Suppose I have two indicator variables, x1 and x2 which
represent age categories (x1 is patients less than 16 while x2 is for
patients older than 65). If I use the following
2010 May 25
2
Relative Risk/Hazard Ratio plots for continuous variables
Dear all,
I am using Windows and R 2.9.2 for my analyses. I have a large dataset and
I am particularly interested in looking at time to an event for a continuous
variable. I would like to produce a plot of log(relative risk) or relative
risk (also known as hazard ratio) against the continuous variable.
I have spent a long time looking for advice on how to do this but my search
has proved
2012 Feb 07
2
Actual vs. predicted survival times
Dear R-help,
I am using R 2.14.1 on Windows 7.
I would like to produce a plot like the attached - although simplified to actual vs. Predicted survival time with distinguishing marks for censored and observed points. I have a dataset and have fitted a Cox model to it. In an attempt to visualise how accurate the model is it would be ideal if I could plot the actual survival times against the
2013 Feb 05
1
Calculating Cumulative Incidence Function
Hello,
I have a problem regarding calculation of Cumulative Incidence Function.
The event of interest is failure of bone-marrow transplantation, which may
occur due to relapse or death in remission. The data set that I have
consists of- lifetime variable, two indicator variables-one for relapse and
one for death in remission, and the other variables are donor type (having
3 categories), disease
2012 Mar 27
0
Standard error terms from gfcure
Dear R-help,
I am using R 2.14.1 on Windows 7 with the 'gfcure' package (cure rate model).
I have included the treatment variable in the cure part of the model as shown below:
Ø ref_treat <- gfcure(Surv(rem.Remtime,rem.Rcens)~1,~1+strata(drpa)+factor(treat(delcure)),data=delcure,dist="loglogistic")
>From that I can obtain the coefficients, standard errors etc as per
2005 Jun 04
6
New HTB-derived qdisc for accounting?
Hi,
at my local university network, I have to make sure no student
uploads more than x GB/day. So far, I give them unlimited bandwidth
until they have more than y GB (y<x) upload. After that, I use the
u32 filter to associate the affected IP address with a HTB class
limited to the rate (remainingtraffic/remainingtime).
Since the accounting is done with ipt_ACCOUNT right now and the
netfilter
2009 Jun 23
0
Fractional Polynomials in Competing Risks setting
Dear All,
I have analysed time to event data for continuous variables by
considering the multivariable fractional polynomial (MFP) model and
comparing this to the untransformed and log transformed model to
determine which transformation, if any, is best. This was possible as
the Cox model was the underlying model. However, I am now at the
situation where the assumption that the competing risks
2008 Oct 15
0
R-help Digest, Vol 67, Issue 31
V;
Sent via BlackBerry from T-Mobile
-----Original Message-----
From: r-help-request at r-project.org
Date: Tue, 30 Sep 2008 12:00:06
To: <r-help at r-project.org>
Subject: R-help Digest, Vol 67, Issue 31
Send R-help mailing list submissions to
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or, via email,
2011 Aug 22
0
Multiple forest plots with the same x-axis and colour coded estimates and lines
Dear all,
I would like to draw three forest plots to represent results at years 1, 2
and 3. I have the data as point estimates and 95% confidence intervals.
Using the following code I can get three basic forest plots - the first
which has the table of results. I have to plot each separately as the usual
par(mfrow=c(3,1)) does not work with the function forestplot within rmeta.
I can easily put
2017 Sep 14
3
Help understanding why glm and lrm.fit runs with my data, but lrm does not
Dear all,
I am using the publically available GustoW dataset. The exact version I am using is available here: https://drive.google.com/open?id=0B4oZ2TQA0PAoUm85UzBFNjZ0Ulk
I would like to produce a nomogram for 5 covariates - AGE, HYP, KILLIP, HRT and ANT. I have successfully fitted a logistic regression model using the "glm" function as shown below.
library(rms)
gusto <-
2017 Sep 14
1
Help understanding why glm and lrm.fit runs with my data, but lrm does not
Fixed 'maxiter' in the help file. Thanks.
Please give the original source of that dataset.
That dataset is a tiny sample of GUSTO-I and not large enough to fit this
model very reliably.
A nomogram using the full dataset (not publicly available to my knowledge)
is already available in http://biostat.mc.vanderbilt.edu/tmp/bbr.pdf
Use lrm, not lrm.fit for this. Adding maxit=20 will
2010 Nov 30
3
repeat write.table with the same code many times
Dear all,
I am using R version 2.9.2 in Windows.
I would like to output the results of a function I have written to a .txt
file. I know that I can do this by using the code
write.table(boothd(10),"boothd10.txt",sep="\t",append=TRUE) etc. However, I
would like to bootstrap my function 'boothd' several times and get each
vector of results as a new line in my text
2017 Sep 14
0
Help understanding why glm and lrm.fit runs with my data, but lrm does not
> On Sep 14, 2017, at 12:30 AM, Bonnett, Laura <L.J.Bonnett at liverpool.ac.uk> wrote:
>
> Dear all,
>
> I am using the publically available GustoW dataset. The exact version I am using is available here: https://drive.google.com/open?id=0B4oZ2TQA0PAoUm85UzBFNjZ0Ulk
>
> I would like to produce a nomogram for 5 covariates - AGE, HYP, KILLIP, HRT and ANT. I have
2012 Nov 26
1
A problem subsetting a data frame
Hi all,
I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows
> testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4"))
>> Error in
2008 Oct 28
3
Dose Profile
Hi Everyone,
I have data in a long format e.g. there is one row per patient but each
follow-up appointment is included in the row. So, a snippet of the data
looks like this:
TrialNo Drug Sex Rand Adate1 Date1 Dose1 Time1 Adate2 Date2 Dose2
Time2 B1001029 LTG M 15719 30/04/2003 15825 150 106 29/08/2003 15946 200
227 B1117003 LTG M 15734 30/04/2003 15825 200 91 03/09/2003 15951 250 217