[R] drc results differ for different versions

[Hans Vermeiren]

Hello,

We use drc to fit dose-response curves, recently we discovered that
there are quite different standard error values returned for the same
dataset depending on the drc-version / R-version that was used (not
clear which factor is important)
On R 2.9.0 using drc_1.6-3 we get an IC50 of 1.27447 and a standard
error on the IC50 of 0.43540   
Whereas on R 2.7.0 using drc_1.4-2  the IC50 is 1.2039e+00 and the
standard error is 3.7752e-03  
Normally I would use the most recent version (both R and drc library)
but it seems to me that a standard error of 0.4 on a mean of 1.2 is too
big, so I trust the values we get with the older versions more
Has anyone suggestions on 
- how to solve these discrepancies, if possible
- how to calculate which one of the 2 solutions is the correct one?

Thanks a lot,
Hans Vermeiren

Demo (on a windows machine, while the issue was actually discovered on
our ubuntu linux server):
1)
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_1.4-2      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

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 in:
Model fitted: Log-logistic (ED50 as parameter) (4 parms)

Parameter estimates:

                      Estimate  Std. Error     t-value   p-value
hs:(Intercept)     -9.8065e-01  2.5821e-03 -3.7979e+02 2.248e-33
bottom:(Intercept)  1.0955e+01  2.2546e-02  4.8591e+02 4.364e-35
top:(Intercept)     1.0502e+02  9.0935e-02  1.1549e+03 4.210e-41
ec50:(Intercept)    1.2039e+00  3.7752e-03  3.1890e+02 3.681e-32

Residual standard error: 7.026655 (16 degrees of freedom)
========================================================================
===========================================
2)
sessionInfo()
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_1.6-3       plotrix_2.5-5   nlme_3.1-90     MASS_7.2-46
magic_1.4-4     abind_1.1-0     lattice_0.17-22 alr3_1.1.7     

loaded via a namespace (and not attached):
[1] grid_2.9.0  tools_2.9.0

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)

gives:
Model fitted: Log-logistic (ED50 as parameter) (4 parms)

Parameter estimates:

                    Estimate Std. Error   t-value   p-value
hs:(Intercept)      -0.95266    0.25778  -3.69564    0.0020
bottom:(Intercept)  10.97437    2.24421   4.89009    0.0002
top:(Intercept)    106.38373    9.98378  10.65565 1.127e-08
ec50:(Intercept)     1.27447    0.43540   2.92712    0.0099

Residual standard error:

 7.020175 (16 degrees of freedom)





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