| Name | interva JSON |
| Version |
1.0.0
JSON |
| download |
| home_page | None |
| Summary | Python implementation of the InterVA Algorithm. |
| upload_time | 2024-04-17 17:28:46 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | GPLv3 |
| keywords |
verbal
autopsy
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# interva
[](https://pypi.org/project/interva/)
[](https://github.com/verbal-autopsy-software/interva/actions)
Python implementation of the InterVA (version 5) algorithm for assigning causes of death to verbal autopsy data. This package replicates the R
version [InterVA5](https://github.com/verbal-autopsy-software/InterVA5).
## Importing package and installing dependencies
To install all package dependencies, run:
```python
pip install interva
```
To import this package's functions:
```python
from interva.interva5 import InterVA5
```
## Example data
To access example data from the package:
```python
from interva.interva5 import get_example_input
va_data = get_example_input()
```
```python
va_data
ID i004a i004b i019a i019b i022a ... i454o i455o i456o i457o i458o i459o
0 d1 . . y . y ... n n n n n n
1 d2 . . . y y ... n n n n n n
2 d3 . . y . . ... n n n n n n
3 d4 . . . y . ... n n n n n n
4 d5 . . y . . ... n n n n n n
.. ... ... ... ... ... ... ... ... ... ... ... ... ...
195 d196 . . . y . ... n n n n n n
196 d197 . . y . y ... n n n n n n
197 d198 . . y . y ... n n n n n n
198 d199 . . . y y ... n n n n n n
199 d200 . . . y y ... n n n n n n
[200 rows x 354 columns]
```
## Creating and running an InterVA5 object
To initialize an InterVA5 object (results will be written to `VA_outpt/VA5_results.csv`):
```python
iv5out = InterVA5(va_data, hiv="h", malaria="l", write=True, directory="VA_output", filename="VA5_result", output="extended", append=False, return_checked_data=True)
```
To run the InterVA5 algorithm on the InterVA5 object:
```python
iv5out.run()
```
```python
Using Probbase version: probbase v19 20210720
..........10% completed
..........20% completed
..........30% completed
..........40% completed
..........50% completed
..........60% completed
..........70% completed
..........80% completed
..........90% completed
..........100% completed
100% completed
```
Get cause-specific mortality fractions (CSMFs) for the top 8 causes:
```python
iv5out.get_csmf(top=8)
```
```python
HIV/AIDS related death 0.194408
Undetermined 0.136583
Digestive neoplasms 0.083285
Other and unspecified infect dis 0.063096
Renal failure 0.061253
Reproductive neoplasms MF 0.053655
Other and unspecified cardiac dis 0.047557
Stroke 0.045583
dtype: float64
```
getters for InterVA5 parameters:
```python
iv5out.get_hiv()
iv5out.get_malaria()
iv5out.get_ids()
```
```python
HIV parameter is h
Malaria parameter is l
ids
0 d1
1 d2
2 d3
3 d4
4 d5
...
195 d196
196 d197
197 d198
198 d199
199 d200
Name: ID, Length: 200, dtype: object
```
To change the parameters, use setters and re-run.
```python
iv5out.set_hiv("v")
iv5out.set_malaria("v")
iv5out.run()
```
Raw data
{
"_id": null,
"home_page": null,
"name": "interva",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": "openVA Team <help@openva.net>",
"keywords": "verbal autopsy",
"author": null,
"author_email": "Sherry Zhao <zhao.3248@buckeyemail.osu.edu>, Jason Thomas <jarathomas@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/52/2c/f27e85683e5076db0b4f6f2e64409bbcb6a8b0165ab717c3765c3ff5d281/interva-1.0.0.tar.gz",
"platform": null,
"description": "# interva\n\n[](https://pypi.org/project/interva/)\n[](https://github.com/verbal-autopsy-software/interva/actions)\n\nPython implementation of the InterVA (version 5) algorithm for assigning causes of death to verbal autopsy data. This package replicates the R\nversion [InterVA5](https://github.com/verbal-autopsy-software/InterVA5).\n\n\n## Importing package and installing dependencies\n\nTo install all package dependencies, run: \n\n```python\npip install interva\n```\n\nTo import this package's functions: \n\n```python\nfrom interva.interva5 import InterVA5\n```\n## Example data\n\nTo access example data from the package: \n\n```python\nfrom interva.interva5 import get_example_input\nva_data = get_example_input()\n```\n\n```python\nva_data\n ID i004a i004b i019a i019b i022a ... i454o i455o i456o i457o i458o i459o\n0 d1 . . y . y ... n n n n n n\n1 d2 . . . y y ... n n n n n n\n2 d3 . . y . . ... n n n n n n\n3 d4 . . . y . ... n n n n n n\n4 d5 . . y . . ... n n n n n n\n.. ... ... ... ... ... ... ... ... ... ... ... ... ...\n195 d196 . . . y . ... n n n n n n\n196 d197 . . y . y ... n n n n n n\n197 d198 . . y . y ... n n n n n n\n198 d199 . . . y y ... n n n n n n\n199 d200 . . . y y ... n n n n n n\n\n[200 rows x 354 columns]\n```\n \n## Creating and running an InterVA5 object\n\nTo initialize an InterVA5 object (results will be written to `VA_outpt/VA5_results.csv`):\n\n```python\niv5out = InterVA5(va_data, hiv=\"h\", malaria=\"l\", write=True, directory=\"VA_output\", filename=\"VA5_result\", output=\"extended\", append=False, return_checked_data=True)\n```\n \nTo run the InterVA5 algorithm on the InterVA5 object: \n\n```python\niv5out.run()\n```\n\n```python\nUsing Probbase version: probbase v19 20210720\n..........10% completed\n..........20% completed\n..........30% completed\n..........40% completed\n..........50% completed\n..........60% completed\n..........70% completed\n..........80% completed\n..........90% completed\n..........100% completed\n100% completed\n```\n\nGet cause-specific mortality fractions (CSMFs) for the top 8 causes:\n\n```python\niv5out.get_csmf(top=8)\n```\n\n```python\nHIV/AIDS related death 0.194408\nUndetermined 0.136583\nDigestive neoplasms 0.083285\nOther and unspecified infect dis 0.063096\nRenal failure 0.061253\nReproductive neoplasms MF 0.053655\nOther and unspecified cardiac dis 0.047557\nStroke 0.045583\ndtype: float64\n```\n\ngetters for InterVA5 parameters: \n\n```python\niv5out.get_hiv()\niv5out.get_malaria()\niv5out.get_ids()\n```\n\n```python\nHIV parameter is h\nMalaria parameter is l\nids\n0 d1\n1 d2\n2 d3\n3 d4\n4 d5\n ...\n195 d196\n196 d197\n197 d198\n198 d199\n199 d200\nName: ID, Length: 200, dtype: object\n```\n\nTo change the parameters, use setters and re-run. \n\n```python\niv5out.set_hiv(\"v\")\niv5out.set_malaria(\"v\")\niv5out.run()\n```\n",
"bugtrack_url": null,
"license": "GPLv3",
"summary": "Python implementation of the InterVA Algorithm.",
"version": "1.0.0",
"project_urls": {
"Bug Tracker": "https://github.com/verbal-autopsy-software/interva/issues",
"Homepage": "https://github.com/verbal-autopsy-software/interva"
},
"split_keywords": [
"verbal",
"autopsy"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "91b4f6d43d3e09ca106f2b3137805847bd6f5808d78d72ee4047511490d2c50a",
"md5": "5f0ed9f082a358480367b38bfc27e543",
"sha256": "47008e6c0225f60f387e788097f0fe8f28ff4b4669d6cf7874f30b30536cbef9"
},
"downloads": -1,
"filename": "interva-1.0.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "5f0ed9f082a358480367b38bfc27e543",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 182990,
"upload_time": "2024-04-17T17:28:44",
"upload_time_iso_8601": "2024-04-17T17:28:44.266234Z",
"url": "https://files.pythonhosted.org/packages/91/b4/f6d43d3e09ca106f2b3137805847bd6f5808d78d72ee4047511490d2c50a/interva-1.0.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "522cf27e85683e5076db0b4f6f2e64409bbcb6a8b0165ab717c3765c3ff5d281",
"md5": "5059b959498f3792cf2421f9e3f05f89",
"sha256": "365f4df958ce61a52b2146a5c8b2a874ac2d7972caa6b08e2311ebcff3378494"
},
"downloads": -1,
"filename": "interva-1.0.0.tar.gz",
"has_sig": false,
"md5_digest": "5059b959498f3792cf2421f9e3f05f89",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 178683,
"upload_time": "2024-04-17T17:28:46",
"upload_time_iso_8601": "2024-04-17T17:28:46.156187Z",
"url": "https://files.pythonhosted.org/packages/52/2c/f27e85683e5076db0b4f6f2e64409bbcb6a8b0165ab717c3765c3ff5d281/interva-1.0.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-04-17 17:28:46",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "verbal-autopsy-software",
"github_project": "interva",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"tox": true,
"lcname": "interva"
}
