mixtree-analysis-data

This is the data folder for the mixtree-analysis (https://doi.org/10.5281/zenodo.17704759). It is uploaded as a separate files as these are too heavy for GitHub. ## Dataframe Documentation ### `param_grid.rds`- **Description:** Contains all combinations of simulation (`sim_config`) and test (`test_config`) parameters. - **Columns:** - `param_id`: unique identifier for each parameter combination - `params`: list of parameters used for tree and forest generation ### `tree_grid.rds`- **Description:** Reference transmission trees generated for each `param_id` in `param_grid`. - **Columns:** - `tree_id`: `<param_id>_<replicate_id>` identifier - `tree`: transmission tree object ### `forest_grid.rds`- **Description:** Forests generated from each reference tree in `tree_grid` using parameter sets from `param_grid` with matching epidemic size. - **Columns:** - `forest_id`: `<tree_id>_<param_id>` identifier - `forest`: list of transmission trees forming the forest ### `test_grid.rds`- **Description:** Unique pairs of forests derived from the same reference tree for statistical testing. - **Columns:** - `forest_id_A`: identifier of the first forest - `forest_id_B`: identifier of the second forest ### `results.rds`- **Description:** Statistical test results applied to each forest pair in `test_grid`. - **Columns:** - `forest_id_A`, `forest_id_B`: identifiers of compared forests - `method`: test applied (`permanova` or `chisq`) - `forest_size`: number of trees per forest - `p_value`: resulting p-value ### `results_grid.rds`- **Description:** Combines `results` with simulation parameters from `param_grid` for each forest pair. - **Columns:** - `tree_id`: reference tree identifier - `forest_id_*`: identifiers of compared forests - `param_id_*`: parameter set identifiers used to generate forests - `off_R_*`: basic reproduction number (R0) of offspring distribution - `off_k_*`: dispersion parameter (k) of offspring distribution - `forest_size`: number of trees per forest - `epidemic_size`: number of vertices per tree - `method`: statistical test applied - `p_value`: resulting p-value