diff --git a/README.md b/README.md index 02fcc36..2668edc 100644 --- a/README.md +++ b/README.md @@ -50,10 +50,10 @@ It must be a **tabular file** in one of these formats: #### Required columns -| Column | Type | Description | -| -------------- | --------------- | ----------------------------------------------------------------------------------------------------------- | -| `MIC` | float or string | MIC dilution (e.g., `0.125`, `0.25`, `1`, `2`, …). Can include censored values such as `<=0.125` or `>=64`. | -| `observations` | integer | Number of isolates observed at that MIC dilution. | +| Column | Type | Description | +| -------------- | --------------- | ---------------------------------------------------------------------------------------------------------- | +| `MIC` | float or string | MIC dilution (e.g., `0.125`, `0.25`, `1`, `2`, …). Can include censored values such as `<=0.125` or `>64`. | +| `observations` | integer | Number of isolates observed at that MIC dilution. | or @@ -75,7 +75,7 @@ MIC observations >8 2196 ``` -- censored balues (e.g >=16) are automatically detected and handled +- censored values (e.g >16) are automatically detected and handled ### 2. Parameter File (`--params`) @@ -83,12 +83,12 @@ This is an **optional** configuration file (YAML, TXT, or `key=value` list) that Typical fields include: -| Key | Description | -| ------------------ | --------------------------------------------------------------- | -| `dilution_factor` | Fold-change between MIC dilutions (e.g., `2`). | -| `distributions` | Number of Gaussian mixture components. | -| `boundary_support` | How many dilution steps to extend upper tail for censored data. | -| `percentile` | Percentile used to compute the ECOFF (e.g., `99`). | +| Key | Description | +| ------------------ | ----------------------------------------------------------------------------- | +| `dilution_factor` | Fold-change between MIC dilutions (e.g., `2`). | +| `distributions` | Number of Gaussian mixture components. | +| `boundary_support` | How many dilution steps to extend upper and/or lower tails for censored data. | +| `percentile` | Percentile used to compute the ECOFF (e.g., `99`). | #### Example (`demo_files/params.txt`) @@ -166,7 +166,7 @@ ecoff-fitter [-h] --input INPUT [--params PARAMS] | `--params` | `PARAMS` | Optional parameter file (`YAML`, `TXT`, or `key=value` list). Defines `dilution_factor`, `distributions`, and `boundary_support`. Overrides CLI flags if provided. | `None` | | `--dilution_factor` | `DILUTION_FACTOR` | Dilution factor | `2` | | `--distributions` | `DISTRIBUTIONS` | Number of Gaussian mixture components to fit. | `1` | -| `--boundary_support` | `boundary_support` | Extra upper-dilution steps for censored MICs (set to `None` to disable). | `1` | +| `--boundary_support` | `boundary_support` | Extra upper- and lower-dilution steps for censored MICs (set to `None` to disable). | `1` | | `--percentile` | `PERCENTILE` | Percentile used to compute the ECOFF (0–100). | `99.0` | | `--outfile` | `OUTFILE` | Path to save ECOFF results (`.txt` or `.pdf`). | `None` | | `--verbose` | — | Print detailed model information and parameters. | `False` |