Inference Model Output

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