Inference Model Output

(This section describes the location and contents of the additional output files produced during an inference model run)

Updates to other files

\LLIK (inference runs only)

During inference runs, an additional file type, llik, is created, which is described in the Inference Model Output section ;

These files contain the log-likelihoods of the model simulation for each subpopulation, as well as some diagnostics on acceptance.

The meanings of the columns are:

ll - These values are the log-likelihoods of data given the model and parameter values for a single subpopulation (in subpop column) ;

filename - ...

subpop - The values of this column are the names of the nodes from the geodata file.

accept - Either 0 or 1, depending on whether the parameters during this iteration of the simulation were accepted (1) or rejected (0) in that subpopulation ;

accept_avg ;

accept_prob ;

For inference runs, ... flepiMoP produces one file per parallel slot, for both global and chimeric outputs...

flepimop_sample
├── model_output
│   ├── seir
│   ├── spar
│   ├── snpi
│   └── llik
│       └── sample_2pop
│           └── None
│               └── 2023.05.24.02/12/48.
│                   ├── chimeric
│                   └── global
│                       ├── final
│                       │   └── 000000001.2023.05.24.02/12/48..llik.parquet
│                       └── intermediate
│                           └── 000000001.000000001.2023.05.24.02/12/48..llik.parquet