Displaying 20 results from an estimated 4000 matches similar to: "survplot invert number at risk labels"
2012 Dec 03
1
Confidence bands with function survplot
Dear all,
I am trying to plot KM curves with confidence bands with function survplot under package rms.
However, the following codes do not seem to work. The KM curves are produced, but the confidence bands are not there.
Any insights? Thanks in advance.
library(rms)
########data generation############
n <- 1000
set.seed(731)
age <- 50 + 12*rnorm(n)
label(age) <- "Age"
2006 May 30
1
position of number at risk in survplot() graphs
Dear R-help
How can one get survplot() to place the number at risk just below the
survival curve as opposed to the default which is just above the x-axis?
I tried the code bellow but the result is not satisfactory as some numbers
are repeated several times at different y coordinates and the position of
the n.risk numbers corresponds to the x-axis tick marks not the survival
curve time of
2012 Nov 06
3
Survplot, Y-axis in percent
Hi
I am a new fan of R after getting mad with the graphical functional in SPSS.
I have been able to create a nice looking Kaplan Meyer graph using Survplot
function.
However I have difficulties in turning the y axis to percent instead of the
default 0-1 scale.
Further I have tried the function yaxt="n" without any results. Any help in
this matter will be appreciated.
The code is
2012 Mar 27
1
survplot function
Dear R-helpers
I am wondering if there is an option to the survplot function in the design
package that allows for drawing Kaplan-Meier plots starting from 0 instead of
1, similar like fun = 'event' in the standard plotting function used on a
survfit object.
I apologize in advance for having missed any obvious informational sources but
I really didn't find anything in the
2012 Sep 05
1
showing ticks for censored data in survfit() in the rms package
The answer to this may be obvious, but I was wondering in the rms
package and the survfit(), how you can plot the censored time points
as ticks.
Take for example,
library(survival)
library(rms)
foo <- data.frame(Time=c(1,2,3,4,5,6,10), Status=c(1,1,0,0,1,1,1))
answer <- survfit(Surv(foo$Time, foo$Status==1) ~1)
# this shows the censored time points as ticks at Time = 3 and 4
plot(answer)
2016 Nov 04
0
Major Update to rms package: 5.0-0
A major new version of the rms package is now on CRAN. The most
user-visible changes are:
- interactive plotly graphic methods for model fits. The best example of
this is survplot for npsurv (Kaplan-Meier) estimates where the number of
risk pop up as you hover over the curves, and you can click to bring up
confidence bands for differences in survival curves
- html methods for model fit
2016 Nov 04
0
Major Update to rms package: 5.0-0
A major new version of the rms package is now on CRAN. The most
user-visible changes are:
- interactive plotly graphic methods for model fits. The best example of
this is survplot for npsurv (Kaplan-Meier) estimates where the number of
risk pop up as you hover over the curves, and you can click to bring up
confidence bands for differences in survival curves
- html methods for model fit
2009 Oct 26
1
Unable to get Legend with survplot rms package
Hello,
I apologize for the post as I am certainly overlooking a simple
solution to my difficulties with getting a legend to print on a
survplot from the rms package.
I am plotting the following:
survplot(survest(fita), n.risk=T, conf='none', cex.n.risk=.85, dots=T,
col='gray10', lty=2)
survplot(survest(fit), n.risk=F, conf='none', add=T)
survplot(survest(fitb), n.risk=F,
2011 Aug 25
1
survplot() for cph(): Design vs rms
Hi, in Design package, a plot of survival probability vs. a covariate can be generated by survplot() on a cph object using the folliowing code:
n <- 1000
set.seed(731)
age <- 50 + 12*rnorm(n)
label(age) <- "Age"
sex <- factor(sample(c('male','female'), n, TRUE))
cens <- 15*runif(n)
h <- .02*exp(.04*(age-50)+.8*(sex=='Female'))
dt <-
2011 Mar 01
0
Major update to rms package
A new version of rms is now available on CRAN for Linux and Windows (Mac
will probably be available very soon). Largest changes include latex
methods for validate.* and adding the capability to force a subset of
variables to be included in all backwards stepdown models (single model or
validation by resampling).
Recent updates:
* In survplot.rms, fixed bug (curves were undefined if
2011 Mar 01
0
Major update to rms package
A new version of rms is now available on CRAN for Linux and Windows (Mac
will probably be available very soon). Largest changes include latex
methods for validate.* and adding the capability to force a subset of
variables to be included in all backwards stepdown models (single model or
validation by resampling).
Recent updates:
* In survplot.rms, fixed bug (curves were undefined if
2009 Feb 02
1
survfit using quantiles to group age
I am using the package Design for survival analysis. I want to plot a
simple Kaplan-Meier fit of survival vs. age, with age grouped as
quantiles. I can do this:
survplot(survfit(Surv(time,status) ~ cut(age,3), data=veteran)
but I would like to do something like this:
survplot(survfit(Surv(time,status) ~ quantile(age,3), data=veteran)
#will not work
ideally I would like to superimpose
2010 Sep 13
0
New version of rms package on CRAN
CRAN has a significant update to rms. Windows and unix/linux versions
are available and I expect the Mac version to be available soon.
The most significant improvement is addition of latex=TRUE
arguments to model fitting print methods, made especially for use
with Sweave.
Here is a summary of changes since the previous version.
Changes in version 3.1-0 (2010-09-12)
* Fixed gIndex to not
2010 Sep 13
0
New version of rms package on CRAN
CRAN has a significant update to rms. Windows and unix/linux versions
are available and I expect the Mac version to be available soon.
The most significant improvement is addition of latex=TRUE
arguments to model fitting print methods, made especially for use
with Sweave.
Here is a summary of changes since the previous version.
Changes in version 3.1-0 (2010-09-12)
* Fixed gIndex to not
2005 Feb 04
2
no. at risk in survfit()
Hi,
when I generated a survfit() object, I can get number
of patients at risk at various time points by using
summary():
fit<-survfit(Surv(time,status)~class,data=mtdata)
summary(fit)
class=1
time n.risk n.event survival std.err lower 95% CI
upper 95% CI
9.9 78 1 0.987 0.0127 0.963 1
41.5 77 1 0.974 0.0179 0.940 1
54.0 76
2012 Mar 08
1
Extended Survival Plot Lines
I've obtained a survival plot from the following code:
s = Surv(outcome.[,1], outcome.[,2])
survplot= (survfit(s ~ person.list[,1]))
plot(survplot, mark.time = FALSE)
person.list is just a list of 15 people.
When I plot this, the lines on my plot all end at different time points. Is
there a way to extend all the lines to make them end at a certain time
point? (i.e outcome.[,1]
2011 Jul 21
1
Design Survplot performance
Hi,
I have a Cox PH model that's large for my server, 120K rows, ~300 factors
with 3 levels each, so about 1000 columns. The 300 factors all pass a
preliminary test of association with the outcome. Solving this with cph from
Design takes about 3 hours. I have created the fit with x=T, y=T to save the
model data.
I want to validate the PH assumption by calling survplot(fit, gender=NA,
2008 Dec 16
2
"Dotted lines at the end of the KM-curve"
R-ers!
Referees demand that the line in the KM-curve should be changed to
dotted at the point where standarerror is <= 10 %. I don't think it's
a good habit but I urgently need to implement such a thing in R with
survfit, survplot or another program. They also want numbers at risk
below the curve
Some help, please....
Fredrik
########################
Fredrik Lundgren
2012 Jul 18
0
Building a web risk calculator based on Cox, PH--definitive method for calculating probability?
Here is an example of how to do it.
> library(survival)
> vfit <- coxph(Surv(time, status) ~ celltype + trt, data=veteran)
> userinput <- data.frame(celltype="smallcell", trt = 1)
> usercurve <- survfit(vfit, newdata=userinput) #the entire predicted
survival curve
> user2 <- summary(usercurve, time= 2*365.25) # 2 year time point
> user2$surv
[1]
2009 Feb 05
4
See source code for survplot function in Design package
Dear R users,
I know one way to see the code for a hidden function, say function_x,
is using default.function_x (e.g. summary.default). But how can I see
the code for imported packages that have no namespace (in this case
Design)?
Many Thanks
Eleni