[ADMB Users] Log transformation correction

[Sylvain Bonhommeau]

Dear group,

To estimate the parameters of a von Bertalanffy model (length <-
(Linf-(Linf-Lo)*exp(k*age))), i log-transform the data and the prediction
of L (L=length). There is however an offset in L_inf estimates and this can
be due to the log-transformation. I try to correct the estimates using a
bias correction method where you multiply the estimates by
10^(Mean_Square_Error/2) but it's seems that it doesn't work. (
http://www.vims.edu/people/newman_mc/pubs/Newman1993.pdf)

Anyway, i have done a simulation framework to generate data of
length-at-age with a small noise (5%) and I boostrap this and estimate the
parameters using ADMB, nls and STAN for comparison purposes. I then
estimates the estimation errors for each bootstrap without correction
(without_corr.pdf). ADMB and STAN are very similar (although STAN is way
longer) while nls is clearly not good. with_corr.pdf is the same with the
correction factor...

Does anyone have an idea how to correct the bias of parameter estimation?

Thanks!

Sylvain

PS: simulation_VB.R is the code to simulate the data and fit the VB
vb.stan is the STAN code
vb_simu.tpl is the ADMB code
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.admb-project.org/pipermail/users/attachments/20130823/ef38ea44/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: with_corr.pdf
Type: application/pdf
Size: 21779 bytes
Desc: not available
URL: <http://lists.admb-project.org/pipermail/users/attachments/20130823/ef38ea44/attachment.pdf>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: without_corr.pdf
Type: application/pdf
Size: 22120 bytes
Desc: not available
URL: <http://lists.admb-project.org/pipermail/users/attachments/20130823/ef38ea44/attachment-0001.pdf>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: simulation_VB.R
Type: application/octet-stream
Size: 7614 bytes
Desc: not available
URL: <http://lists.admb-project.org/pipermail/users/attachments/20130823/ef38ea44/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: vb.stan
Type: application/octet-stream
Size: 224 bytes
Desc: not available
URL: <http://lists.admb-project.org/pipermail/users/attachments/20130823/ef38ea44/attachment-0001.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: vb_simu.tpl
Type: application/octet-stream
Size: 734 bytes
Desc: not available
URL: <http://lists.admb-project.org/pipermail/users/attachments/20130823/ef38ea44/attachment-0002.obj>