Dear R users,
Please can you help me with a relatively straightforward problem that I
am struggling with? I am simply trying to plot a baseline survivor and
hazard function for a simple data set of lung cancer survival where
`futime' is follow up time in months and status is 1=dead and 0=alive.
Using the survival package:
lung.wbs <- survreg( Surv(futime, status)~ 1, data=lung,
dist='weibull')
plot (lung.wbs)
Returns the error msg:
Error in xy.coords(x, y, xlabel, ylabel, log) :
x and y lengths differ
Using the Design package:
lung.wbd <- psm (Surv (futime, status)~ 1, dist="weibull",
data=lung,
na.action=na.omit)
survplot(lung.wbd)
Returns the error msg:
Error in survplot.Design(lung.wbd) : fit does not have design
information
Using the eha package (I have not figured out how to get baseline
function only, but have used ht=0/1 hypertension as a covariate):
lung.wbe <- weibreg (Surv (futime, status)~ ht, y=T, data=audit,
na.action=na.omit)
plot (lung.wbe)
I get a plot with hazard (y) against age (x) ??? I cannot control the
axes with labeling and any other covariate gets the same plot.
I have tried using covariates in the Design and Survival packages, but
they always return the same error msgs. I realise that the former 2 are
AFT survival models, but even when I convert the object with pphsm() in
the Design package, I get the same errors.
Please can anyone enlighten me as to what I seem to be doing /
understanding wrongly?
Regards,
Eric Lim
Papworth Hospital
Cambridge, UK
futime status
[1,] 0.40000000 1
[2,] 0.80000000 1
[3,] 7.10000000 1
[4,] 3.00000000 1
[5,] 0.63333333 1
[6,] 9.93333333 1
[7,] 0.50000000 1
[8,] 6.93333333 1
[9,] 23.33333333 1
[10,] 1.73333333 1
[11,] 24.66666667 1
[12,] 0.06666667 1
[13,] 14.43333333 1
[14,] 8.83333333 0
[15,] 27.53333333 0
[[alternative HTML version deleted]]
I do not belive there is a plot method for survreg object.
#You can plot survuval using the coeficents it returns:
curve(exp(-(exp(-lung.wbs$coef[1])*x)^(1/lung.wbs$scale)))
#Here is an exemple for "lung" data from library "survival"
library(survival)
data(lung)
lung.wbs <- survreg( Surv(time, status)~1, data=lung, dist='weibull')
plot(survfit(Surv(time,status),data=lung))
curve(exp(-(exp(-lung.wbs$coef[1])*x)^(1/lung.wbs$scale)),col="red",add=T)
----- Original Message -----
From: "Eric Lim" <eric.lim at cvsnet.org>
To: <r-help at stat.math.ethz.ch>
Sent: Tuesday, November 23, 2004 7:56 AM
Subject: [R] Weibull survival regression
Dear R users,
Please can you help me with a relatively straightforward problem that I
am struggling with? I am simply trying to plot a baseline survivor and
hazard function for a simple data set of lung cancer survival where
`futime' is follow up time in months and status is 1=dead and 0=alive.
Using the survival package:
lung.wbs <- survreg( Surv(futime, status)~ 1, data=lung,
dist='weibull')
plot (lung.wbs)
Returns the error msg:
Error in xy.coords(x, y, xlabel, ylabel, log) :
x and y lengths differ
Using the Design package:
lung.wbd <- psm (Surv (futime, status)~ 1, dist="weibull",
data=lung,
na.action=na.omit)
survplot(lung.wbd)
Returns the error msg:
Error in survplot.Design(lung.wbd) : fit does not have design
information
Using the eha package (I have not figured out how to get baseline
function only, but have used ht=0/1 hypertension as a covariate):
lung.wbe <- weibreg (Surv (futime, status)~ ht, y=T, data=audit,
na.action=na.omit)
plot (lung.wbe)
I get a plot with hazard (y) against age (x) ??? I cannot control the
axes with labeling and any other covariate gets the same plot.
I have tried using covariates in the Design and Survival packages, but
they always return the same error msgs. I realise that the former 2 are
AFT survival models, but even when I convert the object with pphsm() in
the Design package, I get the same errors.
Please can anyone enlighten me as to what I seem to be doing /
understanding wrongly?
Regards,
Eric Lim
Papworth Hospital
Cambridge, UK
futime status
[1,] 0.40000000 1
[2,] 0.80000000 1
[3,] 7.10000000 1
[4,] 3.00000000 1
[5,] 0.63333333 1
[6,] 9.93333333 1
[7,] 0.50000000 1
[8,] 6.93333333 1
[9,] 23.33333333 1
[10,] 1.73333333 1
[11,] 24.66666667 1
[12,] 0.06666667 1
[13,] 14.43333333 1
[14,] 8.83333333 0
[15,] 27.53333333 0
[[alternative HTML version deleted]]
______________________________________________
R-help at stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
PS: You can plot hazard in a similar way
Best regards,
Ale. .iberna
----- Original Message -----
From: "Eric Lim" <eric.lim at cvsnet.org>
To: <r-help at stat.math.ethz.ch>
Sent: Tuesday, November 23, 2004 7:56 AM
Subject: [R] Weibull survival regression
Dear R users,
Please can you help me with a relatively straightforward problem that I
am struggling with? I am simply trying to plot a baseline survivor and
hazard function for a simple data set of lung cancer survival where
`futime' is follow up time in months and status is 1=dead and 0=alive.
Using the survival package:
lung.wbs <- survreg( Surv(futime, status)~ 1, data=lung,
dist='weibull')
plot (lung.wbs)
Returns the error msg:
Error in xy.coords(x, y, xlabel, ylabel, log) :
x and y lengths differ
Using the Design package:
lung.wbd <- psm (Surv (futime, status)~ 1, dist="weibull",
data=lung,
na.action=na.omit)
survplot(lung.wbd)
Returns the error msg:
Error in survplot.Design(lung.wbd) : fit does not have design
information
Using the eha package (I have not figured out how to get baseline
function only, but have used ht=0/1 hypertension as a covariate):
lung.wbe <- weibreg (Surv (futime, status)~ ht, y=T, data=audit,
na.action=na.omit)
plot (lung.wbe)
I get a plot with hazard (y) against age (x) ??? I cannot control the
axes with labeling and any other covariate gets the same plot.
I have tried using covariates in the Design and Survival packages, but
they always return the same error msgs. I realise that the former 2 are
AFT survival models, but even when I convert the object with pphsm() in
the Design package, I get the same errors.
Please can anyone enlighten me as to what I seem to be doing /
understanding wrongly?
Regards,
Eric Lim
Papworth Hospital
Cambridge, UK
futime status
[1,] 0.40000000 1
[2,] 0.80000000 1
[3,] 7.10000000 1
[4,] 3.00000000 1
[5,] 0.63333333 1
[6,] 9.93333333 1
[7,] 0.50000000 1
[8,] 6.93333333 1
[9,] 23.33333333 1
[10,] 1.73333333 1
[11,] 24.66666667 1
[12,] 0.06666667 1
[13,] 14.43333333 1
[14,] 8.83333333 0
[15,] 27.53333333 0
[[alternative HTML version deleted]]
______________________________________________
R-help at stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
On Tue, Nov 23, 2004 at 06:56:56AM -0000, Eric Lim wrote:> Dear R users, > > Please can you help me with a relatively straightforward problem that I > am struggling with? I am simply trying to plot a baseline survivor and > hazard function for a simple data set of lung cancer survival where > `futime' is follow up time in months and status is 1=dead and 0=alive. > > Using the survival package: > > lung.wbs <- survreg( Surv(futime, status)~ 1, data=lung, dist='weibull') > > plot (lung.wbs) > > Returns the error msg: > > Error in xy.coords(x, y, xlabel, ylabel, log) : > x and y lengths differ > > Using the Design package: > > lung.wbd <- psm (Surv (futime, status)~ 1, dist="weibull", data=lung, > na.action=na.omit) > > survplot(lung.wbd) > > Returns the error msg: > > Error in survplot.Design(lung.wbd) : fit does not have design > information > > Using the eha package (I have not figured out how to get baseline > function only, but have used ht=0/1 hypertension as a covariate): > > lung.wbe <- weibreg (Surv (futime, status)~ ht, y=T, data=audit, > na.action=na.omit) > > plot (lung.wbe) > > I get a plot with hazard (y) against age (x) ??? I cannot control the > axes with labeling and any other covariate gets the same plot.Right, plot.weibreg in eha is very poorly implemented, newdata does not work, you cannot change labels of the plot, etc. I hope to get time to do it right soon, but... Anyway, the problem is simple to solve: You get the estimates of scale and shape of the Weibull distribution (or their logarithms). Since eha uses "standard R parametrization", you can simply plot the functions "dweibull / pweibull( , lower.tail = FALSE)" with the estimated parameters inserted for the hazard function, and "pweibull( , lower.tail = FALSE)" for the survival function. [...] G??ran -- G??ran Brostr??m tel: +46 90 786 5223 Department of Statistics fax: +46 90 786 6614 Ume?? University http://www.stat.umu.se/egna/gb/ SE-90187 Ume??, Sweden e-mail: gb at stat.umu.se
Eric Lim wrote:> Dear R users, > > Please can you help me with a relatively straightforward problem that I > am struggling with? I am simply trying to plot a baseline survivor and > hazard function for a simple data set of lung cancer survival where > `futime' is follow up time in months and status is 1=dead and 0=alive. > > Using the survival package: > > lung.wbs <- survreg( Surv(futime, status)~ 1, data=lung, dist='weibull') > > plot (lung.wbs) > > Returns the error msg: > > Error in xy.coords(x, y, xlabel, ylabel, log) : > x and y lengths differ > > Using the Design package: > > lung.wbd <- psm (Surv (futime, status)~ 1, dist="weibull", data=lung, > na.action=na.omit)You don't need to specify na.action here.> > survplot(lung.wbd) > > Returns the error msg: > > Error in survplot.Design(lung.wbd) : fit does not have design > informationsurvplot only works when there is at least one covariate. Sorry. Maybe someday ... -Frank Harrell> Regards, > > Eric Lim > Papworth Hospital > Cambridge, UK-- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University
On Tue, 23 Nov 2004, Eric Lim wrote:> Dear R users, > > Please can you help me with a relatively straightforward problem that I > am struggling with? I am simply trying to plot a baseline survivor and > hazard function for a simple data set of lung cancer survival where > `futime' is follow up time in months and status is 1=dead and 0=alive. > > Using the survival package: > > lung.wbs <- survreg( Surv(futime, status)~ 1, data=lung, dist='weibull') > > plot (lung.wbs) > > Returns the error msg: > > Error in xy.coords(x, y, xlabel, ylabel, log) : > x and y lengths differYes. There isn't a plot method for survreg() (and if there were, it wouldn't do this). The right thing to try would have been plot(survfit(lung.wbs) but that doesn't work either. You can get the curve you want with curve(pweibull(x, scale=exp(coef(lung.wbs)), shape=1/lung.wbs$scale, lower.tail=FALSE),from=0, to=max(lung$futime)) where most of the complications come from the fact that survreg() and pweibull() parametrise the Weibull distribution differently. Incidentally, this works quite nicely on the built-in lung cancer example data set, showing surprisingly good fit to a Weibull. data(lung) lung.wbs <- survreg( Surv(time, status)~ 1, data=lung, dist='weibull') curve(pweibull(x, scale=1/coef(lung.wbs), shape=1/lung.wbs$scale, lower.tail=FALSE),from=0, to=max(lung$time)) lines(survfit(Surv(time,status)~1, data=lung), col="red") -thomas
A big thank you to everyone who responded... Using Ales Ziberna solution with the lung dataset, I obtained:> plot(survfit(Surv(time,status),data=lung))Error in Surv(time, status) : Time variable is not numeric In addition: Warning message: is.na() applied to non-(list or vector) in: is.na(time) Using Thomas Lumley's solution with the lung dataset, I obtained:> curve(pweibull(x, scale=1/coef(lung.wbs), shape=1/lung.wbs$scale,lower.tail=FALSE),from=0, to=max(lung$time)) A Weibull survival plot appearing as a 90 degree `L' at the extremes of the plot I managed to obtain the solution by combining the two solutions: lung.wbs <- survreg( Surv(futime, status)~ 1, data=lung, dist='weibull') plot (survfit(Surv(futime,status)~1, data=lung)) curve (exp (- (exp( lung.wbs$coef[1])*x)^(1/lung.wbs$scale)), col="black", add=T, from=0, to=30) Kind regards, Eric Lim Papworth Hospital Cambridge, UK