Displaying 20 results from an estimated 1000 matches similar to: "AFT-model with time-varying covariates and left-truncation"
2010 Feb 05
3
AFTREG with ID argument
Dear all,
I have some trouble using the "id"-argument with aftreg (accelerated
failure time regression analysis from the eha library).
As far as I understand it, the id argument is used to group
individuals together if there are time-varying covariates and the
data is arranged in counting process style.
Unfortunately, i cannot figure out how to use the "id"-argument. The
2010 Nov 25
2
aftreg vs survreg loglogistic aft model (different intercept term)
Hi, I'm estimating a loglogistic aft (accelerated failure time) model, just a
simple plain vanilla one (without time dependent covariates), I'm comparing
the results that I obtain between aftreg (eha package) and survreg(surv
package). If I don't use any covariate the results are identical , if I add
covariates all the coefficients are the same until a precision of 10^4 or
10^-5 except
2010 Feb 19
1
eha aftreg performance
G?ran, thanks for the update, I'm just about to install it!
Just wanted to drop you a short line about performance (as you once
requested):
aftreg takes ages on my windows machine to calculate a small set of
7 observations which are not even grouped together by "id". To be a
bit more precise, it takes 2:40 mins on my Intel T9300 Core2 Duo @
2.5 GHz. Bigger samples with about 700
2010 Feb 18
2
Extract p-value from aftreg object
Dear all,
does anyone know how I can extract specific p-values for covariates
from an aftreg object? After fitting a model with aftreg I can find
all different variables by using str(), but there's no place where
p-values are kept. The odd thing is that print() displays them
correctly.
EXAMPLE:
> testdata
start stop censor groupvar var1 var2
1 0 1 0
2011 May 02
3
ID parameter in model
Hello,
I am apparently confused about the use of an id parameter for an event
history/survival model, and why the EHA documentation for aftreg does
not specify one. All assistance and insights are appreciated.
Attempting to specifiy an id variable with the documentation example
generates an "overlapping intervals" error, so I sorted the original
mort dataframe and set subsequent entry
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
2009 May 12
1
AFT-model with time-dependent covariates
Dear R-community,
Dear Prof. Therneau,
I would like to fit an AFT-model with time-dependent covariates and right-censored data.
Searching the mailing list for information on the subject, I found some old posts which said it didn't work back then.
My questions:
(1) Has this kind of fitting already been implemented in the survival library in R?
(2) If not: Are there any alternatives/
2011 Nov 16
1
"Non-finite finite-difference value" error in eha's aftreg
Hi list!
I'm getting an error message when trying to fit an accelerated failure
time parametric model using the aftreg() function from package eha:
> Error in optim(beta, Fmin, method = "BFGS", control = list(trace =
> as.integer(printlevel)), :
> non-finite finite-difference value [2]
This only happens when adding four specific covariates at the same time
in the
2011 May 21
1
predict 'expected' with eha package
I am unsure what is being returned, and what is supposed to be
returned, when using 'predict' with "type='expected'" for an aftreg
survival model. The code below first generates a weibull model, then
uses predict to create a vector of the linear predictors, then
attempts to create the 'expected' vector, which is empty. The final
two steps in the code generate a
2010 Dec 10
1
survreg vs. aftreg (eha) - the relationship between fitted coefficients?
Dear R-users,
I need to use the aftreg function in package 'eha' to estimate failure times for left truncated survival data. Apparently, survreg still cannot fit such models. Both functions should be fitting the accelerated failure time (Weibull) model. However, as G?ran Brostr?m points out in the help file for aftreg, the parameterisation is different giving rise to different
2011 Aug 21
3
pooled hazard model with aftreg and time-dependent variables
Dear R-users,
I have two samples with individuals that are in more than one of the samples
and individuals that are only in one sample. I have been trying to do a
pooled hazard model, stacking one sample below the other, with aftreg and
time-dependent covariates. The idea behind is to see aggregate effects of
covariates, but need to control for ther effects of same individuals in both
samples
2010 Feb 23
1
Accelerated failure time interpretation of coefficients
I have one more conceptual question though, it would be fantastic if
someone could graciously help out:
I am using an accelerated failure time model with time-varying
covariates because I assume that my independent variables have a
different impact on the chance for a failure at different points in
lifetime. For example: High temperature has a different impact on
failure in earlier years
2009 Mar 17
1
AFT model
Hi,
In the package survival, using the function survreg for AFT model, I
only see 4 distributions for the response y: weibull, gaussian,
logistic, lognormal and log-logistic, which correspond to certain
distributions for the error terms. I'm wondering if there is a package
or how to obtain the parameter estimates (the beta's are of great
interest) from the AFT model (maximizing
2009 Feb 24
2
Configuring chan_dahdi.conf for Sangoma A200/Remora FXO/FXS Analog AFT card
Hi I have been having a rough time getting a Sangoma A200/Remora FXO/
FXS Analog AFT card set up properly.
The main issue is that the card has four ports and as far as I can
tell Asterisk is only seeing two. On the two that it recognizes the
"Green" FXS ports are not green, they just are not lit. The "RED" FXO
ports are indeed red, but from what I have read your not
2005 May 23
0
Left truncation in shared frailty models with time-varying covariates
Hi!
I want to estimate a shared gamma frailty model with left truncated data. I use a parametric baseline hazard so that I can use
simple ML estimation. As I have a big data set it is ok to assume piecewise constant baseline hazards.
As my data are left truncated I have modified the definition of the risk set.
Do I also have to modifiy the frailty distribution if I have left truncated data?
2010 Oct 01
2
Small p-value good or bad?
Dear R-community,
I have a short question: How do I interpret the result of a
likelihood ratio test correctly?
I am fitting a parametric survival model (with aftreg {eha}) and the
output tells me the overall p-value of my model is < 0.001. My
simple question is: Does the result mean my model fits the data well
OR does it mean my model DOES NOT fit the data well?
Some side information how the
2011 Oct 01
4
Is the output of survfit.coxph survival or baseline survival?
Dear all,
I am confused with the output of survfit.coxph.
Someone said that the survival given by summary(survfit.coxph) is the
baseline survival S_0, but some said that is the survival S=S_0^exp{beta*x}.
Which one is correct?
By the way, if I use "newdata=" in the survfit, does that mean the survival
is estimated by the value of covariates in the new data frame?
Thank you very much!
2011 Oct 06
1
non-cumulative hazard in Cox model with time-dependent covariates
Dear all,
Is there a way to calculate the non-cumulative hazard (instantaneous
hazard), which is the product of baseline hazard and exp{beta*covariate} ?
I knew in survfit, we can get the estimator of cumulative baseline hazard,
but how can we get the non-cumulative one?
Thank you very much!
Koshihaku
--
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2010 Jul 28
1
Time-dependent covariates in survreg function
Dear all,
I'm asking this question again as I didn't get a reply last time:
I'm doing a survival analysis with time-dependent covariates. Until now,
I have used a simple Cox model for this, specifically the coxph function
from the survival library. Now, I would like to try out an accelerated
failure time model with a parametric specification as implemented for
example in the survreg
2011 Nov 17
0
Non-finite finite-difference value" error in eha's, aftreg
This kind of error seems to surprise R users. It surprises me that it doesn't happen much
more frequently. The "BFGS" method of optim() from the 1990 Pascal version of my book was
called the Variable Metric method as per Fletcher's 1970 paper it was drawn from. It
really works much better with analytic gradients, and the Rvmmin package which is an all-R
version that adds bounds