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diff-binom-confint-0.0.9
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مشاهده بیشتر
تبلیغات ما
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مشاهده بیشترتوضیحات
Computation of confidence intervals for binomial proportions and for difference of binomial proportions.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | diff-binom-confint-0.0.9 |
| نام | diff-binom-confint |
| نسخه کتابخانه | 0.0.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | DeepPSP |
| ایمیل نویسنده | wenh06@gmail.com |
| آدرس صفحه اصلی | https://github.com/DeepPSP/DBCI |
| آدرس اینترنتی | https://pypi.org/project/diff-binom-confint/ |
| مجوز | MIT |
# Confidence Intervals for Difference of Binomial Proportions
[](https://codecov.io/gh/DeepPSP/DBCI)
[](https://dbci.readthedocs.io/en/latest/?badge=latest)
Computation of confidence intervals for binomial proportions and for difference of binomial proportions.
\[[GitHub Pages](https://deeppsp.github.io/DBCI/)\] \[[Read the Docs](http://dbci.readthedocs.io/)\]
## Installation
Run
```bash
python -m pip install diff-binom-confint
```
or install the latest version in [GitHub](https://github.com/DeepPSP/DBCI/) using
```bash
python -m pip install git+https://github.com/DeepPSP/DBCI.git
```
or git clone this repository and install locally via
```bash
cd DBCI
python -m pip install .
```
## `Numba` accelerated version
Install using
```bash
python -m pip install diff-binom-confint[acc]
```
## Usage examples
```python
from diff_binom_confint import compute_difference_confidence_interval
n_positive, n_total = 84, 101
ref_positive, ref_total = 89, 105
confint = compute_difference_confidence_interval(
n_positive,
n_total,
ref_positive,
ref_total,
conf_level=0.95,
method="wilson",
)
```
## Implemented methods
### Confidence intervals for binomial proportions
<details>
<summary>Click to view!</summary>
| Method (type) | Implemented |
|-------------------|--------------------|
| wilson | :heavy_check_mark: |
| wilson-cc | :heavy_check_mark: |
| wald | :heavy_check_mark: |
| wald-cc | :heavy_check_mark: |
| agresti-coull | :heavy_check_mark: |
| jeffreys | :heavy_check_mark: |
| clopper-pearson | :heavy_check_mark: |
| arcsine | :heavy_check_mark: |
| logit | :heavy_check_mark: |
| pratt | :heavy_check_mark: |
| witting | :heavy_check_mark: |
| mid-p | :heavy_check_mark: |
| lik | :heavy_check_mark: |
| blaker | :heavy_check_mark: |
| modified-wilson | :heavy_check_mark: |
| modified-jeffreys | :heavy_check_mark: |
</details>
### Confidence intervals for difference of binomial proportions
<details>
<summary>Click to view!</summary>
| Method (type) | Implemented |
|-----------------------------|--------------------|
| wilson | :heavy_check_mark: |
| wilson-cc | :heavy_check_mark: |
| wald | :heavy_check_mark: |
| wald-cc | :heavy_check_mark: |
| haldane | :heavy_check_mark: |
| jeffreys-perks | :heavy_check_mark: |
| mee | :heavy_check_mark: |
| miettinen-nurminen | :heavy_check_mark: |
| true-profile | :heavy_check_mark: |
| hauck-anderson | :heavy_check_mark: |
| agresti-caffo | :heavy_check_mark: |
| carlin-louis | :heavy_check_mark: |
| brown-li | :heavy_check_mark: |
| brown-li-jeffrey | :heavy_check_mark: |
| miettinen-nurminen-brown-li | :heavy_check_mark: |
| exact | :x: |
| mid-p | :x: |
| santner-snell | :x: |
| chan-zhang | :x: |
| agresti-min | :x: |
| wang | :x: |
| pradhan-banerjee | :x: |
</details>
## References
1. <a name="ref1"></a> [SAS](https://www.lexjansen.com/wuss/2016/127_Final_Paper_PDF.pdf)
2. <a name="ref2"></a> [PASS](https://ncss-wpengine.netdna-ssl.com/wp-content/themes/ncss/pdf/Procedures/PASS/Confidence_Intervals_for_the_Difference_Between_Two_Proportions.pdf)
3. <a name="ref3"></a> [statsmodels.stats.proportion](https://www.statsmodels.org/devel/_modules/statsmodels/stats/proportion.html)
4. <a name="ref4"></a> [scipy.stats._binomtest](https://github.com/scipy/scipy/blob/main/scipy/stats/_binomtest.py)
5. <a name="ref5"></a> [corplingstats](https://corplingstats.wordpress.com/2019/04/27/correcting-for-continuity/)
6. <a name="ref6"></a> [DescTools.StatsAndCIs](https://github.com/AndriSignorell/DescTools/blob/master/R/StatsAndCIs.r)
7. <a name="ref7"></a> [Newcombee](https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0258(19980430)17:8%3C873::AID-SIM779%3E3.0.CO;2-I)
## NOTE
[Reference 1](#ref1) has errors in the description of the methods `Wilson CC`, `Mee`, `Miettinen-Nurminen`.
The correct computation of `Wilson CC` is given in [Reference 5](#ref5).
The correct computation of `Mee`, `Miettinen-Nurminen` are given in the **code blocks** in [Reference 1](#ref1)
## Test data
[Test data](test/test-data/) are
1. taken (with slight modification, e.g. the `upper_bound` of `miettinen-nurminen-brown-li` method in the [edge case file](test/test-data/example-10-10-vs-0-20.csv)) from [Reference 1](#ref1) for automatic test of the correctness of the implementation of the algorithms.
2. generated using [DescTools.StatsAndCIs](#ref6) via
```R
library("DescTools")
library("data.table")
results = data.table()
for (m in c("wilson", "wald", "waldcc", "agresti-coull", "jeffreys",
"modified wilson", "wilsoncc","modified jeffreys",
"clopper-pearson", "arcsine", "logit", "witting", "pratt",
"midp", "lik", "blaker")){
ci = BinomCI(84,101,method = m)
new_row = data.table("method" = m, "ratio"=ci[1], "lower_bound" = ci[2], "upper_bound" = ci[3])
results = rbindlist(list(results, new_row))
}
fwrite(results, "./test/test-data/example-84-101.csv") # with manual slight adjustment of method names
```
3. taken from [Reference 7](#ref7) (Table II).
The filenames has the following pattern:
```python
# for computing confidence interval for difference of binomial proportions
"example-(?P<n_positive>[\\d]+)-(?P<n_total>[\\d]+)-vs-(?P<ref_positive>[\\d]+)-(?P<ref_total>[\\d]+)\\.csv"
# for computing confidence interval for binomial proportions
"example-(?P<n_positive>[\\d]+)-(?P<n_total>[\\d]+)\\.csv"
```
Note that the out-of-range values (e.g. `> 1`) are left as empty values in the `.csv` files.
## Known Issues
1. Edge cases incorrect for the method `true-profile`.
نیازمندی
| مقدار | نام |
|---|---|
| - | numpy |
| - | scipy |
| - | deprecate-kwargs |
| - | Deprecated |
| - | dataclasses |
| - | typing-extensions |
| - | numba |
| - | pandas |
| ==22.3.0 | black |
| - | flake8 |
| - | pytest |
| - | pytest-xdist |
| - | pytest-cov |
| - | numba |
| - | pandas |
| ==22.3.0 | black |
| - | flake8 |
| - | pytest |
| - | pytest-xdist |
| - | pytest-cov |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl diff-binom-confint-0.0.9:
pip install diff-binom-confint-0.0.9.whl
نصب پکیج tar.gz diff-binom-confint-0.0.9:
pip install diff-binom-confint-0.0.9.tar.gz