annotate lifelines_tool/README.md @ 2:dd5e65893cb8 draft default tip

add survival and collapsed life table outputs suggested by Wolfgang

# lifelines_tool - lifelines statistical package wrapped as a Galaxy tool.

A Galaxy tool for right censored failure time data.

Provides Kaplan-Meier plots with confidence intervals, and optional Cox proportional hazards models

Uses the [lifelines](https://lifelines.readthedocs.io/en/latest/index.html) package.

### Install to your Galaxy server from the toolshed - search for lifelines_km_cph_tool owned by fubar2

More at https://lazarus.name/demo/

#### Using the Rossi sample recidivism data from lifelines:

Runs Kaplan-Meier and generates a plot. Optional grouping variable.

Plots show confidence intervals

![KM plot sample](lifelines_rossi_km.png)

If 2 groups, runs a log-rank test for difference.

![KM plot sample](lifelines_report.png)

If a comma separated list (for example: prio, age, race, mar, fin) of covariate column names is provided,
a Cox proportional hazards model is run, the assumption of proportionality is tested, and
recommendations made.
![KM plot sample](lifelines_rossi_schoenfeld.png)

Also included are partial plots for each covariate like these from the Rossi recidivism lifelines sample data
used in the tool test.

![C-PH partial plot samples](agepartialrossi.png)

![C-PH partial plot samples](parolepartialrossi.png)

Uses pandas read_csv with tabular delimiters so should work with any tabular data with the required columns - time and status for observations.

Issues to https://github.com/fubar2/lifelines_tool please.
Autogenerated so pull requests are possibly meaningless but regeneration of a new version should work.

## Tool made with the Galaxy ToolFactory: https://github.com/fubar2/galaxy_tf_overlay
The current release includes this and a generic tabular version, and a java .jar wrapper in a history where the generating
ToolFactory form can be recreated using the redo button. Editing the tool id will make a new tool, so all other edits to parameters can be
made and the new tool generated without destroying the original sample.