Displaying 20 results from an estimated 1000 matches similar to: "Reporting Kaplan-Meier / Cox-Proportional Hazard Standard Error, km.coxph.plot, survfit.object"
2008 Dec 06
1
Kaplan-Meier function from survfit
Hi All,
Please pardon me if I am missing something obvious here. How do I get
the Kaplan-Meier estimate function that is created by survfit and
plotted by the code.
fit <- survfit(Surv(time, status) , data=aml)
plot(fit)
That is, I need a function that will give me the survival estimate at
a given time: \hat{S}(t).
Thanks in advance.
Ritwik Sinha
ritwik.sinha at gmail.com | +12033042111 |
2010 Apr 19
2
Kaplan-Meier survfit problem
When I try to the code from library(survival) of library(ISwR),
the following code
survfit(Surv(days,status==1))
that could produce Kaplan-Meier estimates shows the following error
"Error in survfit(Surv(days, status == 1)) :
Survfit requires a formula or a coxph fit as the first argument"
How it can be done in R.2.10
--
View this message in context:
2008 Mar 08
1
analysing mixed effects/poisson/correlated data
I am attempting to model data with the following variables:
timepoint - n=48, monthly over 4 years
hospital - n=3
opsn1 - no of outcomes
total.patients
skillmixpc - skill mix percentage
nurse.hours.per.day
Aims
To determine if skillmix affects rate (i.e. no.of.outcomes/total.patients).
To determine if nurse.hours.per.day affects rate.
To determine if rates vary between
2009 Oct 25
3
Importing data from text file with mixed format
Hi,
I'm having difficulty importing my textfile that looks something like this:
#begin text file
Timepoint 1
ObjectNumber Volume SurfaceArea
1 5.3 9.7
2 4.9 8.3
3 5.0 9.1
4 3.5 7.8
Timepoint 2
ObjectNumber Volume SurfaceArea
1 5.1
2008 Apr 28
2
F values from a Repeated Measures aov
Hi Folks,
I have repeated measures for data on association time (under 2
acoustic condtions) in male and female frogs as they grow to adulthood
(6 timepoints). Thus, two within-subject variables (Acoustic
Condition: 2 levels, Timepoint: 6 levels) and one between-subject
variable (Sex:male or female).
I am pretty sure my distributions depart from normality but I would
first like to simply run a
2007 May 17
1
Stratified Cox proportional Hazard Model
Hello everyone,
I am a new user of R. Does anybody know how hazard ratios are extracted
for each factor level in a stratified Cox proportional hazard
regression model? I have a cancer data set where the variable
?differentiation? is a factor with three levels: poor, intermediate and
good. I would like to extract the hazard ratio for each grade level and
relate it to another prognostic factor.
2005 Jun 09
1
Prediction in Cox Proportional-Hazard Regression
He,
I used the "coxph" function, with four covariates.
Let's say something like that
> model.1 <- coxph(Surv(Time,Event)~X1+X2+X3+X4,data=DATA)
So I obtain the 4 coefficients B1,B2,B3,B4 such that
h(t) = h0(t) exp(B1*X1+ B2*X2 + B3*X3 + B4*X4).
When I use the function on the same data
> predict.coxph(model.1,type="lp")
how it works in making the prediction?
2006 Apr 03
2
testing proportional hazard in a Cox model including a time-varying covariate
I am using a syntax like coxph(Surv(start, stop, event) ~ X, data) to estimate the effect of X, which may change at each measurement (every 6 months). Is there anyone who knows a way to test the proportional hazard assumption in that case?
Thank you in advance
Jean-François Boudreau
Sherbrooke University
[[alternative HTML version deleted]]
2012 Jul 12
1
Cox proportional hazard model and coefficients
Hi,
Here is the summary-output of the Coxph-model I used (the output is based on
the best final model i.e. all significant explanatory variables and their
interactions are included):
coxph(formula = Y ~ LT + Food + Temp2 + LT:Food + LT:Temp2 +
Food:Temp2 + LT:Food:Temp2)
n= 555
coef exp(coef)
se(coef) z
2006 Mar 24
1
Clustering over strata using a Cox proportional hazard model
Hi all,
I wish to do build discrete choice model to analyse habitat selection of
wolverines.
This can be done with a 'tricked' stratified Cox proportional hazard
model.
For each individual animal each selected position, and possible
alternative non-used available positions are combined into strata.
This means that one stratum contains a set of 1 used position and
several positions which
2010 Nov 24
2
Is there an equivalent to predict(..., type="linear") of a Proportional hazard model for a Cox model instead?
Hi all,
Is there an equivalent to predict(...,type="linear") of a Proportional hazard
model for a Cox model instead?
For example, the Figure 13.12 in MASS (p384) is produced by:
(aids.ps <- survreg(Surv(survtime + 0.9, status) ~ state + T.categ +
pspline(age, df=6), data = Aidsp))
zz <- predict(aids.ps, data.frame(state = factor(rep("NSW", 83), levels =
2011 Dec 10
2
p-value for hazard ratio in Cox proportional hazards regression?
Hi,
I'm new to R and using it for Cox survival analysis. Thanks to this great forum I learned how to compute the HR with its confidence interval.
My question would be: Is there any way to get the p-value for a hazard ratio in addition to the confidence interval?
Thanks,
Thierry
--
Thierry Panje Visiting Student Researcher
Department of Psychology Stanford
2007 Jul 09
2
ANOVA: Does a Between-Subjects Factor belong in the Error Term?
I am executing a Repeated Measures Analysis of Variance with 1 DV (LOCOMOTOR
RESPONSE), 2 Within-Subjects Factors (AGE, ACOUSTIC CONDITION), and 1
Between-Subjects Factor (SEX).
Does anyone know whether the between-subjects factor (SEX) belongs in the
Error Term of the aov or not? And if it does belong, where in the Error Term
does it go? The 3 possible scenarios are listed below:
e.g.,
1.
2009 May 05
3
Cox Proportional Hazard with missing covariate data
Dear friends,
I have used R for some time now and have a tricky question about the coxph-function: To sum it up, I am not sure whether I can use coxph in conjunction with missing covariate data in a model with time-variant covariates. The point is: I know how "old" every piece that I oberserve is, but do not have fully historical information about the corresponding covariates. Maybe you
2010 Sep 16
1
ANOVA - more sophisticated contrasts
dear list,
i am using a multifactorial design with two treatments (factor A: drugs,
three levels; factor B: theraphy, two levels) and a time factor (three
levels, different timepoint). hypothetically, i measured the same subjects
for all treatements and timepoints, so its a repeated measurement design.
now i ran an anova in R and also some Tukey post-hoc tests using glht. but
what i am actually
2009 Sep 02
2
Average over data sets
Hello,
I have a number of files output1.dat, output2.dat, ... , output20.dat,
each of which monitors several variables over a fixed number of
timepoints. From this I want to create a data frame which contains the
mean value between all files, for each timepoint and each variable.
The code below works, but it seems like I should be able to do the
second part without a for loop. I played
2010 Sep 19
1
boyplots nearly identical but still highly significant effect?
dear list,
i am running a within-design ANOVA with 4 factors (4,4,2 and 2 levels each).
the last one is a time factor comprising two different treatment timepoints.
i fit a mixed-effects model using lme and apply the anova function to the
outcome. according to this analysis, there are highly significant main
effect on the first and the time factor. i then checked the boxplots for the
two 4-level
2013 Apr 01
1
Help Please, ggplot2
library(ggplot2)
a<- read.table("data", header=T)
b = na.omit(a)
ggplot(data=b) + geom_line(aes(x=timepoint, y=value,group=sample, colour= factor(sample))) +? geom_point(aes(x=timepoint, y=value, group=s
ample)) + facet_wrap(~bio, scales = "free",ncol = 5) +theme_bw() + opts(legend.direction = "horizontal",??? legend.position = "top",????
2006 Sep 20
1
Stats question - cox proportional hazards adjustments
Hi useRs,
Many studies of the link between red meat and colorectal cancer use
Cox proportional
hazards with (among other things) a gender covariate.
If it is true that men eat more red meat, drink more alcohol and smoke more than
women, and if it is also true that alcohol and tobacco are known risk
factors then why does
it make sense to "adjust" for gender? I would think that in this
2003 Feb 20
1
Variable selection in Cox proportional hazards model?
Hello,
I need to implement variable selection procedures (such as stepwise and
backward selection) in Cox proportional hazards model, but can't seem to
find an R or S-plus command for these procedures. I am aware that these
can be done in SAS.
I would appreciate help from anyone who knows how to implement these
procedures in Cox models using S-plus or (preferably) R.
Thanks!
Regards,