Displaying 20 results from an estimated 1000 matches similar to: "predict 'expected' with eha package"
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
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
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
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
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 Sep 29
0
eha aftreg overall p-value
Dear useRs,
I am currently fitting an advanced failure time model using G?ran
Brostr?m's excellent "eha" library with the "aftreg" command.
My question: How do I interpret the "Overall p-value", that is
reported at the very bottom of the output? I already figured out it
must be a chi-square test, but I am wondering what a p-value < 0.01
means:
Does it mean
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
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
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
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 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 Jan 28
1
AFT-model with time-varying covariates and left-truncation
Dear Prof. Brostr?m,
Dear R-mailinglist,
first of all thanks a lot for your great effort to incorporate
time-varying covariates into aftreg. It works like a charm so far
and I'll update you with detailled benchmarks as soon as I have them.
I have one more questions regarding Accelerated Failure Time models
(with aftreg):
You mention that left truncation in combination with time-varying
2011 Jun 03
0
predict witht he eha package
"Error in predict.coxph(f.ph.eha, newdata = mort, type = "lp") : Data
is not the same size as it was in the original fit"
This error message was added in a recent update to predict.coxph. If it
needs to reconstruct some aspects from the original fit, such as the X
matrix or strata vector, it makes sure that the data set is the same
size. It was to stop
fit <-
2005 May 07
3
converting NA/non-NA's to a binary variable
Dear R colleagues,
I am trying to create a new column in a data frame, which converts values
and NA's from another column into binary format. Essentially I need the
NA's to become 1 and the rest to be 0. The code I wrote is returning the
following error message:
Error in if (mort[i, 4] != NA) mort[i, 8] <- 0 else if (mort[i, 4] == :
missing value where TRUE/FALSE needed
2012 Apr 13
1
Coding columns for survival analysis
Hello Folks,
I have 5 columns for thousands of tree records that record whether that
tree was alive or dead. I want to recode the columns such that the cell
reads "found" when a live tree is first observed, "alive" for when a
tree is found alive and is not just found, and "mort" when it was
previously alive but is now dead.
Given the following:
> tree_live
2012 Sep 04
0
AFTREG weights
On Wed, Aug 1, 2012 at 3:08 PM, <fra.meucci@hotmail.it> wrote:
> Dear Göran Broström,
> I am trying to use AFTREG function for R to estimate a loglogistic
> survival function, including time dependent covariates.
> Actually, my Subset includes some partial events; the idea is to model
> this kind of events using something similar to “weights” in the SURVREG
> function.
2010 Jul 27
1
xYplot error
Hi,
I'm trying to plot a graph with error bars using xYplot in the Hmisc
package. My data looks like this.
mort stand site type
0.042512776 0.017854525 Plot A ST
0.010459803 0.005573305 PF ST
0.005188321 0.006842107 MSF ST
0.004276068 0.011592129 YSF ST
0.044586495 0.035225266 Plot A LD
0.038810662 0.037355408 PF
2003 Jun 16
0
new package: eha
A few days ago I uploaded to CRAN a new package called 'eha', which
stands for 'Event History Analysis'. Its main focus is on proportional
hazards modeling in survival analysis, and in that respect eha can
be regarded as a complement and an extension to the 'survival'
package. In fact eha requires survival. Eha contains three functions
for proportional hazards
2003 Jun 16
0
new package: eha
A few days ago I uploaded to CRAN a new package called 'eha', which
stands for 'Event History Analysis'. Its main focus is on proportional
hazards modeling in survival analysis, and in that respect eha can
be regarded as a complement and an extension to the 'survival'
package. In fact eha requires survival. Eha contains three functions
for proportional hazards
2008 Oct 22
2
Weibull parameter estimation
Dear R-users
I would like to fit weibull parameters using "Method of moments" in order to
provide the inital values of the parameter to de function 'fitdistr' . I
don`t have much experience with maths and I don't know how to do it.
Can anyone please put me in the rigth direction?
Borja
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