OK - I'll see if I can spare some time on the weekend to dig a bit
deeper and maybe find the issue.
(Unfortunately I cannot use a phreg model because I cannot assume a
proportional hazards assumption.)
Göran Broström wrote:
Philipp Rappold wrote:
Göran, 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 observations and 6 dependent
variables are in the 10 minutes range.
I just fired up my linux console (ubuntu) and calculation takes not
even 2 seconds here.
On my laptop (ubuntu):
system.time(fit1 <- aftreg(Surv(start, stop, censor)~var1, data=td))
user system elapsed
0.030 0.000 0.039
But on Windows I can see what you see: It takes 2.5 minutes! I don't
understand it. I can see that the time is spent in the C code (with
Rprof), but that's all I can do on a windows machine.
phreg doesn't seem to have this problem. Have you considered a
proportional hazards model instead of an aft model?
Göran
I've attached a screenshot of my system performance during
calculation, maybe that could already be a first hint (interestingly
I'm seeing some kind of sawtooth profile on physical memory history).
Generally it's not a problem for me as I can use the linux version,
but maybe you have an idea what makes it so slow. If I can provide
you with more details or help on fixing it, let me know.
Here's the dump for reconstruction:
library(eha)
testdata
start stop censor groupvar var1 var2
1 0 1 0 1 0.91663902 0.0847912
2 1 2 0 1 0.60470753 0.6487798
3 2 3 0 1 0.09599891 0.2195178
4 3 4 1 1 0.86384189 0.6667897
5 0 1 0 2 0.07747445 0.8782836
6 1 2 0 2 0.44608030 0.2218685
7 2 3 1 2 0.77317152 0.3813840
fit1 <- aftreg(Surv(start, stop, censor)~var1, data=testdata)
sessionInfo()
R version 2.9.2 (2009-08-24)
i386-pc-mingw32
locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
attached base packages:
[1] splines stats graphics grDevices datasets utils
methods base
other attached packages:
[1] eha_1.2-13 survival_2.35-8 rcom_2.2-1 rscproxy_1.3-1
loaded via a namespace (and not attached):
[1] tools_2.9.2
All the best
Philipp
------------------------------------------------------------------------
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
