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  GenStat  ~  Genstat: Non-linear models

james brown (JIC)
Posted: Mon Feb 18, 2019 2:52 pm Reply with quote
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Good afternoon Genstatters,

I’m fitting logistic curves to dose-response data: Z = A+C/(1+EXP(-B(X-M)))
Z = observed growth of parasite, A = lower asymptote of logistic curve (normally growth = 0), C = estimate of growth without pesticide, M = ED50 & B = slope parameter.

I have data for a set of fungal strains. I can do most of what I want to do except that I want to fit curves with a common value of B but different values of M for different strains. The problem is that these are both non-linear parameters and Genstat seems to want to estimate either common values of B and M for all strains or separate values of both B and M for each strain.

In the menus, Stats > Regression > Standard Curves gives me the option of setting Group = Strain. Step-by-step, this:
  • Gives common estimates of A, C, B and M for all strains,
  • Gives separate estimates of A and C with common estimates of B and M (first A estimated separately, then A and C both separately),
  • Then estimates both non-linear parameters separately, which isn’t really what I want.


The commands in the input window are:
TERMS log10Dose*Strain
FITCURVE [PRINT=model,summary,estimates,accumulated; CURVE=logistic; CONSTANT=estimate; FPROB=yes] log10Dose
ADD [PRINT=model,summary,estimates,accumulated; FPROB=yes] Strain
ADD [PRINT=model,summary,estimates,accumulated; FPROB=yes] Strain.log10Dose
ADD [PRINT=model,summary,estimates,accumulated; NONLINEAR=separate; FPROB=yes]

And the parameters estimates from the last two commands are:

Estimates of parameters
-----------------------
Parameter estimate s.e.
B -6.144 0.287
M 0.86170 0.00968
C Strain V295L-1 1.545
A Strain V295L-1 0.09750
C Strain V295L-2 1.657
A Strain V295L-2 -0.04056
C Strain V295L-3 1.599
A Strain V295L-3 -0.008739
C Strain WT 1.634
A Strain WT -0.04959

Then

Estimates of parameters
-----------------------
Parameter estimate s.e.
B Strain V295L-1 -5.205 0.587
M Strain V295L-1 0.9747 0.0361
C Strain V295L-1 1.829 0.135
A Strain V295L-1 -0.197 0.129
B Strain V295L-2 -7.488 0.761
M Strain V295L-2 0.8344 0.0162
C Strain V295L-2 1.5521 0.0545
A Strain V295L-2 0.0557 0.0495
B Strain V295L-3 -8.074 0.872
M Strain V295L-3 0.8454 0.0155
C Strain V295L-3 1.4915 0.0522
A Strain V295L-3 0.0820 0.0475
B Strain WT -4.692 0.476
M Strain WT 0.8160 0.0299
C Strain WT 1.6943 0.0906
A Strain WT -0.0597 0.0832

Can anyone suggest a way of tweaking the commands so I can get separate estimates of A, C and M but a common estimate of B?

Thanks and best wishes,

James Brown

Prof James Brown
Crop Genetics Dept, John Innes Centre
Norwich NR4 7UH, England

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