[R] drc results differ for different versions

[Hans Vermeiren]

Hello
Thanks a lot Marc, for the suggestion to explore the issue a bit more
systematically
So I did and the conclusion is that with the old drc 1.4-2, I get a
SE=0.003, with the new drc 1.5-2, I get a SE=0.4
irrespective of the R version or the version of the packages drc depends
on

I hope somebody can help me further, I still have the feeling that a SE
of 0.003 on an IC50 of 1.2, for a reasonable good fit is more realistic
than a SE of 0.4 on an IC50 of 1.2

Regards,
Hans

Here are the results of the following test script:
d<-data.frame(dose=c(2.00e-05,4.00e-06,8.00e-07,1.60e-07,3.20e-08,6.40e-
09,1.28e-09,2.56e-10,5.10e-11,1.00e-11,2.00e-05,4.00e-06,8.00e-07,1.60e-
07,3.20e-08,6.40e-09,1.28e-09,2.56e-10,5.10e-11,1.00e-11),response=c(97.
202,81.670,47.292,16.924, 16.832,  6.832,  11.118,   1.319,   5.495,
-3.352, 102.464,  83.114,  50.631,  22.792,  18.348,  19.066,  27.794,
14.682,  11.992,  12.868))

m<- drm(response ~ (log10(dose*1e6)), data = d, fct = l4(fixed =
c(NA,NA,NA,NA), names = c("hs", "bottom", "top", "ec50")), logDose = 10,
control = drmc(useD = T))

summary(m)
RESULTS:
sessionInfo()
R version 2.7.0 (2008-04-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=Dutch_Belgium.1252;LC_CTYPE=Dutch_Belgium.1252;LC_MONETARY=Du
tch_Belgium.1252;LC_NUMERIC=C;LC_TIME=Dutch_Belgium.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


other attached packages:
[1] drc_1.5-2      plotrix_2.4-2  nlme_3.1-89    MASS_7.2-41
lattice_0.17-6
[6] alr3_1.1.7    

loaded via a namespace (and not attached):
[1] grid_2.7.0  tools_2.7.0

RESULT: ec50:(Intercept)=1.27447   SE=0.43541
CONCLUSION: R 2.7.0 with recent drc 1.5-2 (older dependencies) gives
SE=0.43541
========================================================================
=======
R version 2.9.0 (2009-04-17) 
i386-pc-mingw32 

locale:
LC_COLLATE=Dutch_Belgium.1252;LC_CTYPE=Dutch_Belgium.1252;LC_MONETARY=Du
tch_Belgium.1252;LC_NUMERIC=C;LC_TIME=Dutch_Belgium.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


other attached packages:
[1] drc_1.4-2       plotrix_2.5-5   nlme_3.1-90     MASS_7.2-46    
[5] lattice_0.17-22 alr3_1.1.7     

loaded via a namespace (and not attached):
[1] grid_2.9.0  tools_2.9.0
RESULT: ec50:(Intercept)    SE=1.2039e+00
CONCLUSION: R 2.9.0 with old drc 1.4-2 (newer dependencies) gives
SE=0.003


Hans,

You have three important factors changing here. The version of R, the  
version of drc and the versions of any relevant drc dependencies  
(alr3, lattice, magic, MASS, nlme, plotrix).

I would first try to install the newer version of drc on the older R  
system (all else staying the same) and see what you get. Don't run  
update.packages() here, lest you change other things. Just install the  
newer version of drc.

If you get the same results as the older version, then it might lead  
you to something in R or one of the package dependencies changing.

If you get a different result, then it would lead to something in drc  
changing.


You can also install the old version of drc on your more recent R  
system to see what you get, which might help to confirm behavior.

The old source version of drc would be available from:

   http://cran.r-project.org/src/contrib/Archive/drc/

I also found a Windows binary of the old package here:

   http://cran.r-project.org/bin/windows/contrib/2.6/drc_1.4-2.zip


I have also copied Christian Ritz, the drc package author/maintainer,  
so that he may be able to assist you further with the problem.

HTH,

Marc Schwartz

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