Dear R-user:
I am using survreg(Surv()) for fitting a Tobit model of left-censored
longitudinal data. For logarithmic transformation of y data, I am trying use
survreg.distributions in the following way:
tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id),
dist="gaussian", data=y.data, scale=0, weights=w)
my.gaussian<-survreg.distributions$gaussian
my.gaussian$name="lognormal"
my.gaussian$dist<-my.gaussian
tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id),
dist=my.gaussian, data=y.data, scale=0, weights=w)
If I run these codes then I got the following error message,
Error in survreg(Surv(y, y >= -5, type = "left") ~ x + :
Invalid distribution object
Does anybody can help me in identifying the error(s) in these code please?
Advance thanks for your time.
Abdus Sattar
upsattar@yahoo.com
____________________________________________________________________________________
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--begin included message --- I am using survreg(Surv()) for fitting a Tobit model of left-censored longitudinal data. For logarithmic transformation of y data, I am trying use survreg.distributions in the following way: tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id), dist="gaussian", data=y.data, scale=0, weights=w) my.gaussian<-survreg.distributions$gaussian my.gaussian$name="lognormal" my.gaussian$dist<-my.gaussian tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id), dist=my.gaussian, data=y.data, scale=0, weights=w) If I run these codes then I got the following error message, Error in survreg(Surv(y, y >= -5, type = "left") ~ x + : Invalid distribution object Does anybody can help me in identifying the error(s) in these code please? --- end include ---- Can you tell us what you are trying to do? Your first model was a fit of y ~ x + eps, eps ~ Gaussian. If what you want is log(y) ~ x + eps, then all that you need do is use dist="loggaussian" in the survreg call. (Or 'lognormal'; which is the same distribution.) Terry Therneau
Hello Dr. Therneau:
Thank you for your response. Let me explain to you want I want. My y
variable(time) is normal and would like to fit the model on logarithmic
transformation of y (log(y)). I tried to run codes according to your suggestion:
tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id),
dist="lognormal", data=y.data, scale=0, weights=w)
The following error message is giving:
Error in survreg(Surv(y, y >= -5, type = "left") ~ x + :
Invalid survival times for this distribution
In addition: Warning messages:
1: In log(dlist$dtrans(Y[exactsurv, 1])) : NaNs produced
2: In log(y) : NaNs produced
Note, the data file y.data does not contain any missing data! Do you know why it
is giving me such an error message please?
Thank you again for your helpful comment/suggestion.
Best Regards,
Abdus Sattar
upsattar@yahoo.com
----- Original Message ----
From: Terry Therneau <therneau@mayo.edu>
To: upsattar@yahoo.com
Cc: r-help@R-project.org
Sent: Friday, April 25, 2008 8:46:45 AM
Subject: Re: [R] Use of survreg.distributions
--begin included message ---
I am using survreg(Surv()) for fitting a Tobit model of left-censored
longitudinal data. For logarithmic transformation of y data, I am trying use
survreg.distributions in the following way:
tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id),
dist="gaussian",
data=y.data, scale=0, weights=w)
my.gaussian<-survreg.distributions$gaussian
my.gaussian$name="lognormal"
my.gaussian$dist<-my.gaussian
tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id),
dist=my.gaussian,
data=y.data, scale=0, weights=w)
If I run these codes then I got the following error message,
Error in survreg(Surv(y, y >= -5, type = "left") ~ x + :
Invalid distribution object
Does anybody can help me in identifying the error(s) in these code please?
--- end include ----
Can you tell us what you are trying to do?
Your first model was a fit of y ~ x + eps, eps ~ Gaussian. If what you want
is log(y) ~ x + eps, then all that you need do is use
dist="loggaussian" in the
survreg call. (Or 'lognormal'; which is the same distribution.)
Terry Therneau
____________________________________________________________________________________
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=Ahu06i62sR8HDtDypao8Wcj9tAcJ
[[alternative HTML version deleted]]
It would seem to me that your problem is in your data. For survreg, you have to have positive durations, and if your data have y>=-5 as seen in>Error in survreg(Surv(y, y >= -5, type = "left") ~ x + : > Invalid survival times for this distribution >In addition: Warning messages: >1: In log(dlist$dtrans(Y[exactsurv, 1])) : NaNs produced >2: In log(y) : NaNs producedthen you have negative durations in the data. I would suggest truncating your data at y>0, as that would avoid taking natural logs of negative numbers. Corey Sparks Corey S. Sparks, Ph.D. Assistant Professor Department of Demography and Organization Studies University of Texas San Antonio One UTSA Circle San Antonio, TX 78249 email:corey.sparks at utsa.edu Date: Fri, 25 Apr 2008 10:02:21 -0700 (PDT) From: Abdus Sattar <upsattar at yahoo.com> Subject: Re: [R] Use of survreg.distributions To: Terry Therneau <therneau at mayo.edu> Cc: r-help at R-project.org Message-ID: <920678.32263.qm at web58104.mail.re3.yahoo.com> Content-Type: text/plain Hello Dr. Therneau: Thank you for your response. Let me explain to you want I want. My y variable(time) is normal and would like to fit the model on logarithmic transformation of y (log(y)). I tried to run codes according to your suggestion: tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id), dist="lognormal", data=y.data, scale=0, weights=w) The following error message is giving: Error in survreg(Surv(y, y >= -5, type = "left") ~ x + : Invalid survival times for this distribution In addition: Warning messages: 1: In log(dlist$dtrans(Y[exactsurv, 1])) : NaNs produced 2: In log(y) : NaNs produced Note, the data file y.data does not contain any missing data! Do you know why it is giving me such an error message please? Thank you again for your helpful comment/suggestion. Best Regards, Abdus Sattar upsattar at yahoo.com ----- Original Message ---- From: Terry Therneau <therneau at mayo.edu> To: upsattar at yahoo.com Cc: r-help at R-project.org Sent: Friday, April 25, 2008 8:46:45 AM Subject: Re: [R] Use of survreg.distributions --begin included message --- I am using survreg(Surv()) for fitting a Tobit model of left-censored longitudinal data. For logarithmic transformation of y data, I am trying use survreg.distributions in the following way: tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id), dist="gaussian", data=y.data, scale=0, weights=w) my.gaussian<-survreg.distributions$gaussian my.gaussian$name="lognormal" my.gaussian$dist<-my.gaussian tfit=survreg(Surv(y, y>=-5, type="left")~x + cluster(id), dist=my.gaussian, data=y.data, scale=0, weights=w) If I run these codes then I got the following error message, Error in survreg(Surv(y, y >= -5, type = "left") ~ x + : Invalid distribution object Does anybody can help me in identifying the error(s) in these code please? --- end include ---- Can you tell us what you are trying to do? Your first model was a fit of y ~ x + eps, eps ~ Gaussian. If what you want is log(y) ~ x + eps, then all that you need do is use dist="loggaussian" in the survreg call. (Or 'lognormal'; which is the same distribution.) Terry Therneau
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