Skip to content

minor #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
DylanAdlard merged 1 commit into from
Jan 4, 2026
Merged

minor #8

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 12 additions & 12 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -75,20 +75,20 @@ 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`)

This is an **optional** configuration file (YAML, TXT, or `key=value` list) that overrides CLI arguments.

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`)

Expand Down Expand Up @@ -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` |
Expand Down
Loading