User Guide¶

The likelihood \(L\) of a sequence of observed open and shut events \(\{t_{oi}, t_{si}\}\) can be computed as a series over the missed-events likelihoods for open events, \({}^e\mathcal{G}_{AF}(t_{oi})\) and the missed-events likelihoods for shut events, \({}^e\mathcal{G}_{FA}(t_{oi})\) [CHS96]:

\[L(Q, \{t_{oi}, t_{si}\}) = \phi_A \left[\prod_i^{n-1}{}^e\mathcal{G}_{AF}(t_{oi}){}^e\mathcal{G}_{AF}(t_{si})\right] {}^e\mathcal{G}_{AF}(t_{on}) \phi_e\]

where \(Q\) is the transition rate matrix, and \(\phi_A\) and \(\phi_e\) are the initial and final occupancies. All these objects – as well as their components – can be accessed both from python and from c++. In the following, we try and show how they can be created and manipulated from either language.

How to read this manual¶

Each topic below is illustrated by an example in c++, and another in python. These examples can be found in the source code of the package within the directory documentation/code. In any case, one can copy paste.

The user guide should read using the left eye only, and keeping the right eye on the api, or vice-versa. Most of the c++ functions and python bindings offer more functionality or parameters than mentioned in the manual.