From 72ef221369df14a527c2751c002b5cf3db29520d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 9 Mar 2022 09:51:06 +0100 Subject: Fix link to saem.mmkin from README Thanks to Uwe Ligges for spotting this inmidst of a lot of ambiguous URL check results. --- docs/index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'docs/index.html') diff --git a/docs/index.html b/docs/index.html index 02b4011c..9b5b34a1 100644 --- a/docs/index.html +++ b/docs/index.html @@ -163,7 +163,7 @@
  • By default, kinetic rate constants and kinetic formation fractions are transformed internally using transform_odeparms so their estimators can more reasonably be expected to follow a normal distribution.
  • When parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which cannot occur in a single experiment with a single defined radiolabel position.
  • When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite. Mathematically, the SFORB model is equivalent to the DFOP model used by other tools for biphasic metabolite curves. However, the SFORB model has the advantage that there is a mechanistic interpretation of the model parameters.
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  • Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the nlme.mmkin and saem.mmkin and methods. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils). The saem method uses the saemix package as a backend. Analytical solutions suitable for use with this package have been implemented for parent only models and the most important models including one metabolite (SFO-SFO and DFOP-SFO). Fitting other models with saem.mmkin, while it makes use of the compiled ODE models that mkin provides, has longer run times (at least six minutes on my system).
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  • Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the nlme.mmkin and saem.mmkin and methods. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils). The saem method uses the saemix package as a backend. Analytical solutions suitable for use with this package have been implemented for parent only models and the most important models including one metabolite (SFO-SFO and DFOP-SFO). Fitting other models with saem.mmkin, while it makes use of the compiled ODE models that mkin provides, has longer run times (at least six minutes on my system).
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