# cmprsk - Competing Risks Regression
Regression modeling of sub-distribution functions in competing risks.
A python wrapper around the [cmprsk](https://cran.r-project.org/web/packages/cmprsk/index.html) R package.
*Description*: Estimation, testing and regression modeling of
subdistribution functions in competing risks, as described in Gray
(1988), A class of K-sample tests for comparing the cumulative
incidence of a competing risk, **Ann. Stat. 16:1141-1154, and Fine JP and
Gray RJ (1999), A proportional hazards model for the subdistribution
of a competing risk, JASA, 94:496-509**.
[Original Package documentation](https://cran.r-project.org/web/packages/cmprsk/cmprsk.pdf)
## Requirements
### python
* Only python 3 is now supported. Recommended python version >= 3.8
###
* The original version of this package was written with `rpy2` version 2.9.4. Since then, `rpy2` had many breaking changes.
Therefore `cmprsk` version **0.X.Y** only works with `rpy2` version 2.9.X.
* The `cmprsk` package v **1.X.Y** is now up-to-date and is using `rpy2` 3.4.5.
### Installation steps
* install `R`
* install `cmprsk` R package: open R terminal and run `install.packages("cmprsk")`
* create a virtual environment (recommended)
* install`rpy2` - if using `conda` for creating the virtual environment on MacOS M1 (apple silicon) install `rpy2` using pip (tested on version 3.5.9)
* install `pandas` (tested on version 1.5.3)
* install `scipy` (tested on version 1.10.1)
* install `pytest` and `pytest-cov` for running unit tests (dev) only
This package is using `rpy2` in order to use import the cmprsk R packge and therefore the [requirements for rpy2](https://rpy2.readthedocs.io/en/version_2.8.x/overview.html?highlight=readline#requirements) must be met.
TL;DR
* Unix like OS: Linux, MacOS, BSD. (May work on Windows, look at [rpy2 binaries])(https://rpy2.readthedocs.io/en/version_2.8.x/overview.html#microsoft-s-windows-precompiled-binaries).
* python >= 3.5
* R >= 3.3 [how to install R](https://www.datacamp.com/community/tutorials/installing-R-windows-mac-ubuntu)
* readline 7.0 - Should be installed as part of `rpy2`. [how to install on MacOS](http://blogs.perl.org/users/aristotle/2013/07/easy-osx-termreadlinegnu.html) see also the following [issue](https://github.com/conda-forge/rpy2-feedstock/issues/1)
* The`cmprsk` R library (open the R consule and run `install.packages('cmprsk')`)
## Quickstart
For example usage consult the tutorial notebook in this repo: `package_usage.ipynb`
### Example: crr
```python
import pandas as pd
import cmprsk.cmprsk as cmprsk
from cmprsk import utils
data = pd.read_csv('my_data_file.csv')
# assuming that x1,x2,x3, x4 are covatiates.
# x1 are x4 are categorical with baseline 'd' for x1 and 5 for x2
static_covariates = utils.as_indicators(data[['x1', 'x2', 'x3', 'x4']], ['x1', 'x4'], bases=['d', 5])
crr_result = cmprsk.crr(data['ftime'], data['fstatus'], static_covariates)
report = crr_result.summary
print(report)
```
`ftime` and `fstatus` can be numpy array or pandas series, and `static_covariates` is a pandas DataFrame.
The `report` is a pandas `DataFrame` as well.
### Example: cuminc
```python
import matplotlib.plt
import numpy as np
import pandas as pd
from cmprsk import cmprsk
data = pd.read_csv('cmprsk/cmprsk/tests/example_dataset.csv')
cuminc_res = cmprsk.cuminc(data.ss, data.cc, group=data.gg, strata=data.strt)
# print
cuminc_res.print
# plot using matplotlib
_, ax = plt.subplots()
for name, group in cuminc_res.groups.items():
ax.plot(group.time, group.est, label=name)
ax.fill_between(group.time, group.low_ci, group.high_ci, alpha=0.4)
ax.set_ylim([0, 1])
ax.legend()
ax.set_title('foo bar')
plt.show()
```
## Development
For running the unit tests run
pytest --cov=cmprsk cmprsk/tests/
from the project root. Note: you'll need to install [pytest-cov](https://pypi.org/project/pytest-cov/).
Current coverage
```buildoutcfg
---------- coverage: platform darwin, python 3.9.7-final-0 -----------
Name Stmts Miss Cover
----------------------------------------------------
cmprsk/__init__.py 0 0 100%
cmprsk/cmprsk.py 128 22 83%
cmprsk/rpy_utils.py 44 10 77%
cmprsk/tests/__init__.py 0 0 100%
cmprsk/tests/test_cmprsk.py 30 0 100%
cmprsk/tests/test_rpy_utils.py 27 1 96%
cmprsk/tests/test_utils.py 37 0 100%
cmprsk/utils.py 23 1 96%
----------------------------------------------------
TOTAL 289 34 88%
```
### How to update package:
0. update version in setup.py
1. rm -fr dist directory
2. python setup.py sdist bdist_wheel
3. twine upload dist/* --verbose
Raw data
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"description": "# cmprsk - Competing Risks Regression\nRegression modeling of sub-distribution functions in competing risks.\n\nA python wrapper around the [cmprsk](https://cran.r-project.org/web/packages/cmprsk/index.html) R package.\n\n*Description*: Estimation, testing and regression modeling of\nsubdistribution functions in competing risks, as described in Gray\n(1988), A class of K-sample tests for comparing the cumulative\nincidence of a competing risk, **Ann. Stat. 16:1141-1154, and Fine JP and\nGray RJ (1999), A proportional hazards model for the subdistribution\nof a competing risk, JASA, 94:496-509**.\n\n[Original Package documentation](https://cran.r-project.org/web/packages/cmprsk/cmprsk.pdf)\n\n## Requirements\n\n### python\n* Only python 3 is now supported. Recommended python version >= 3.8 \n\n###\n* The original version of this package was written with `rpy2` version 2.9.4. Since then, `rpy2` had many breaking changes. \nTherefore `cmprsk` version **0.X.Y** only works with `rpy2` version 2.9.X.\n* The `cmprsk` package v **1.X.Y** is now up-to-date and is using `rpy2` 3.4.5. \n\n### Installation steps\n\n* install `R`\n* install `cmprsk` R package: open R terminal and run `install.packages(\"cmprsk\")`\n* create a virtual environment (recommended)\n* install`rpy2` - if using `conda` for creating the virtual environment on MacOS M1 (apple silicon) install `rpy2` using pip (tested on version 3.5.9) \n* install `pandas` (tested on version 1.5.3)\n* install `scipy` (tested on version 1.10.1)\n* install `pytest` and `pytest-cov` for running unit tests (dev) only\n\nThis package is using `rpy2` in order to use import the cmprsk R packge and therefore the [requirements for rpy2](https://rpy2.readthedocs.io/en/version_2.8.x/overview.html?highlight=readline#requirements) must be met.\n\nTL;DR\n* Unix like OS: Linux, MacOS, BSD. (May work on Windows, look at [rpy2 binaries])(https://rpy2.readthedocs.io/en/version_2.8.x/overview.html#microsoft-s-windows-precompiled-binaries). \n* python >= 3.5\n* R >= 3.3 [how to install R](https://www.datacamp.com/community/tutorials/installing-R-windows-mac-ubuntu)\n* readline 7.0 - Should be installed as part of `rpy2`. [how to install on MacOS](http://blogs.perl.org/users/aristotle/2013/07/easy-osx-termreadlinegnu.html) see also the following [issue](https://github.com/conda-forge/rpy2-feedstock/issues/1)\n* The`cmprsk` R library (open the R consule and run `install.packages('cmprsk')`)\n\n## Quickstart\n\nFor example usage consult the tutorial notebook in this repo: `package_usage.ipynb`\n\n### Example: crr\n\n```python\n\nimport pandas as pd\n\nimport cmprsk.cmprsk as cmprsk\n\nfrom cmprsk import utils\n\ndata = pd.read_csv('my_data_file.csv')\n# assuming that x1,x2,x3, x4 are covatiates. \n# x1 are x4 are categorical with baseline 'd' for x1 and 5 for x2 \nstatic_covariates = utils.as_indicators(data[['x1', 'x2', 'x3', 'x4']], ['x1', 'x4'], bases=['d', 5])\n\ncrr_result = cmprsk.crr(data['ftime'], data['fstatus'], static_covariates)\nreport = crr_result.summary\n\nprint(report)\n\n```\n`ftime` and `fstatus` can be numpy array or pandas series, and `static_covariates` is a pandas DataFrame.\nThe `report` is a pandas `DataFrame` as well. \n\n### Example: cuminc\n\n```python\nimport matplotlib.plt\nimport numpy as np\nimport pandas as pd\n\n\nfrom cmprsk import cmprsk\n\ndata = pd.read_csv('cmprsk/cmprsk/tests/example_dataset.csv')\ncuminc_res = cmprsk.cuminc(data.ss, data.cc, group=data.gg, strata=data.strt)\n\n# print\ncuminc_res.print\n\n# plot using matplotlib\n\n_, ax = plt.subplots()\nfor name, group in cuminc_res.groups.items():\n ax.plot(group.time, group.est, label=name)\n ax.fill_between(group.time, group.low_ci, group.high_ci, alpha=0.4)\n \nax.set_ylim([0, 1])\nax.legend()\nax.set_title('foo bar')\nplt.show()\n\n```\n## Development\nFor running the unit tests run \n\n pytest --cov=cmprsk cmprsk/tests/\n\nfrom the project root. Note: you'll need to install [pytest-cov](https://pypi.org/project/pytest-cov/).\n\nCurrent coverage\n```buildoutcfg\n---------- coverage: platform darwin, python 3.9.7-final-0 -----------\nName Stmts Miss Cover\n----------------------------------------------------\ncmprsk/__init__.py 0 0 100%\ncmprsk/cmprsk.py 128 22 83%\ncmprsk/rpy_utils.py 44 10 77%\ncmprsk/tests/__init__.py 0 0 100%\ncmprsk/tests/test_cmprsk.py 30 0 100%\ncmprsk/tests/test_rpy_utils.py 27 1 96%\ncmprsk/tests/test_utils.py 37 0 100%\ncmprsk/utils.py 23 1 96%\n----------------------------------------------------\nTOTAL 289 34 88%\n```\n\n### How to update package:\n0. update version in setup.py\n1. rm -fr dist directory\n2. python setup.py sdist bdist_wheel \n3. twine upload dist/* --verbose\n",
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