Skip to content

Commit

Permalink
save progress
Browse files Browse the repository at this point in the history
  • Loading branch information
TorkelE committed May 30, 2024
1 parent c52a55d commit 67da997
Show file tree
Hide file tree
Showing 2 changed files with 280 additions and 7 deletions.
2 changes: 1 addition & 1 deletion docs/old_files/petab_ode_param_fitting.md
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ Generally, PEtab takes five different inputs to define an optimisation problem (
4. **Experimental (or simulation) conditions**: The simulations (each corresponding to a potential experiment) carried out during each step of the optimisation process (a `Dict{String,Dict{Symbol,Float64}}`).
5. **Measurements**: The measurements to which the model is fitted (a `DataFrame`).

### Observables
### [Observables](@id petab_parameter_fitting_intro_observables)
The observables define the quantities that we may measure in our experiments. Typically, each corresponds to a single species, however, [more complicated observables are possible](@ref petab_observables_observables). For each observable, we also need a noise formula, defining the uncertainty in its measurements. By default, PEtab assumes normally distributed noise, with a mean equal to the true value and a standard deviation which we have to define. It is also possible to use [more advanced noise formulas](@ref petab_observables_noise_formula).

In our example, we only have a single possible observable, the `P` species. We will assume that the noise is normally distributed with a standard deviation `0.5` (in our case this is not true, however, typically the noise distribution is unknown and a guess must be made). We combine this information in a `PEtabObservable` struct (to access the `P` species we must use [`@unpack`](@ref simulation_structure_interfacing_symbolic_representation)). Finally, we store all our observables in a dictionary, giving each an id tag (which is later used in the measurements input).
Expand Down
Loading

0 comments on commit 67da997

Please sign in to comment.