Displaying 20 results from an estimated 1000 matches similar to: "Cumulative Incidence : Gray's test"
2008 Dec 08
0
Query in Cuminc - stratification
Hello everyone,
I am a very new user of R and I have a query about the cuminc function in the package cmprsk. In particular I would like to verify that I am interpreting the output correctly when we have a stratification variable.
Hypothetical example:
group : fair hair, dark hair
fstatus: 1=Relapse, 2=TRM, 0=censored
strata: sex (M or F)
Our data would be split into:
Fair, male,
2011 Aug 16
0
cuminc() in cmprsk package for cumulative incidence
Hi,
To use cuminc() from cmprsk package, if a subject has 2
events (both the event of interest and the event of competing risk),
should I create 2 observations for this subject in the dataset, one for
each event with different fstatus (1 and 2), or just 1 observation with
whatever event that happened first? My analysis objective is calculate
cumulative incidence for the event of interest.
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
2010 Mar 26
2
how to make stacked plot?
Dear friends:
I'm interested to make a stacked plot of cumulative incidence. that's, the cuminc model is fitted [fit=cuminc(time, relapse)] and cumulative incidence is in place. I'd like to stack the cuminc plots (relapse of luekemia and death free from leukemia, for example) , then the constituent ratio of leukemia relapse and treatment related mortality is very clear. Can
2009 May 15
1
Plotting question re. cuminc
Hello everyone,
(This is my second question posted today on the R list).
I am carrying out a competing risks analysis using the cuminc function...this takes the form:
cuminc(ftime,fstatus,group)
In my study, fstatus has 3 different causes of failure (1,2,3) there are also censored cases (0). "group" has two levels (0 and 1).
I therefore have 6 different cumulative incidence curves:
2012 Nov 28
0
Numbers at risk below cumulative incidence function plot (plot.cuminc, cmprsk-package)
Dear R-community,
I would like to plot the numbers at risk for the different causes of failure at specific timepoints below a cumulative incidence function plot (plot.cuminc-function, cmprsk-package). For a Kaplan-Meier plot I know this is possible with the n.risk-argument in the survplot-function (rms-package), but to my knowledge no such readily-available functions are available for competing
2008 Dec 09
1
controlling axes in plot.cuminc (cmprsk library)
Dear R-help list members,
I am trying to create my own axes when plotting a cumulative incidence
curve using the plot.cuminc function in the CMPRSK library. The default
x-axis places tick marks and labels at 0, 20, 40, 60, and 80 (my data has
an upper limit of 96), whereas I want them at my own specified locations.
Here is my example code:
library(cmprsk)
attach(MYDATA)
MYCUMINC <-
2011 Jun 27
7
cumulative incidence plot vs survival plot
Hi, I am wondering if anyone can explain to me if cumulative incidence (CI) is
just "1 minus kaplan-Meier survival"? Under what circumstance, you should use
cumulative incidence vs KM survival? If the relationship is just CI =
1-survival, then what difference it makes to use one vs. the other?
And in R how I can draw a cumulative incidence plot. I know I can make a
Kaplan-Meier
2013 Feb 01
0
Cumulative Incidence Function and Pseudovalue
Hi,
I want to write own R functions for cumulative incidence function and also
for the pseudovalue of the cumulative incidence function.
Can you help me?
Tas.
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2004 Feb 26
1
variance estimator for the cumulative incidence function
Hi everyone,
I am using the package cmprsk in R to estimate the cumulative incidence
function and its variance. In the manual it is mentioned that the variance
is calculated based on Dr. Aalen's paper (1978, Nonparametric estimation of
partial transition probabilities in multiple decrement models).
I would appreciate if someone could provide me with a source where the
variance is expressed
2008 Aug 20
0
cmprsk and a time dependent covariate in the model
Dear R users,
I d like to assess the effect of "treatment" covariate on a disease relapse risk with the package cmprsk.
However, the effect of this covariate on survival is time-dependent
(assessed with cox.zph): no significant effect during the first year of follow-up,
then after 1 year a favorable effect is observed on survival (step
function might be the correct way to say that
2008 Aug 22
1
Help on competing risk package cmprsk with time dependent covariate
Dear R users,
I d like to assess the effect of "treatment" covariate on a disease relapse risk with the package cmprsk.
However, the effect of this covariate on survival is time-dependent
(assessed with cox.zph): no significant effect during the first year of follow-up,
then after 1 year a favorable effect is observed on survival (step
function might be the correct way to say that ?).
2008 Aug 22
0
Re : Help on competing risk package cmprsk with time dependent covariate
Hello again,
I m trying to use timereg package as you suggested (R2.7.1 on XP Pro).
here is my script based on the example from timereg for a fine & gray model in which
relt = time to event, rels = status 0/1/2 2=competing, 1=event of interest, 0=censored
random = covariate I want to test
library(timereg)
rel<-read.csv("relapse2.csv", header = TRUE, sep = ",",
2009 Feb 23
1
predicting cumulative hazard for coxph using predict
Hi
I am estimating the following coxph function with stratification and frailty?where each person had multiple events.
m<-coxph(Surv(dtime1,status1)~gender+cage+uplf+strata(enum)+frailty(id),xmodel)
?
> head(xmodel)
id enum dtime status gender cage uplf
1 1008666 1 2259.1412037 1 MA 0.000 0
2 1008666 2 36.7495023 1 MA 2259.141 0
3 1008666
2009 Aug 02
1
Competing Risks Regression with qualitative predictor with more than 2 categories
Hello,
I have a question regarding competing risk regression using cmprsk package (function crr()). I am using R2.9.1. How can I do to assess the effect of qualitative predictor (gg) with more than two categories (a,b,c) categorie c is the reference category. See above results, gg is considered like a ordered predictor !
Thank you for your help
Jan
> # simulated data to test
> set.seed(10)
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 <-
2010 Mar 05
1
How to parse the arguments from a function call and evaluate them in a dataframe?
Hi,
I would like to write a function which has the following syntax:
myfn <- function(formula, ftime, fstatus, data) {
# step 1: obtain terms in `formula' from dataframe `data'
# step 2: obtain ftime from `data'
# step 3: obtain fstatus from `data'
# step 4: do model estimation
# step 5: return results
}
The user would call this function as:
myfn(formula=myform,
2006 Aug 17
1
putting the mark for censored time on 1-KM curve or competing risk curve
Hi All,
I'm trying to figure out the cumulative incidence curve in R in some
limited time. I found in package "cmprsk", the command "plot.cuminc" can
get this curve. But I noticed that there is no mark for the censored
time there, comparing with the KM curve by "plot.survfit". Here are my
codes (attached is the data):
----------------
2008 Feb 12
2
Cox model
Hello R-community,
It's been a week now that I am struggling with the implementation of a cox
model in R. I have 80 cancer patients, so 80 time measurements and 80
relapse or no measurements (respective to censor, 1 if relapsed over the
examined period, 0 if not). My microarray data contain around 18000 genes.
So I have the expressions of 18000 genes in each of the 80 tumors (matrix
2010 May 06
1
Understanding of survfit.formula output
Dear list,
I am not familiar with survival analysis and I would need your help to
understand a result I have obtained.
I have used the following command line to look at number of events and
probability of survival at the first 5 years:
> su = summary(survfit(Surv(a[, Date], a[, Event]) ~ strata(a[,Prediction]),
data = a), times=c(0,1,2,3,4,5))
I have studied two kind of events (disease-free