Feature/negative predictive value

[arshiaar]

Issues

Implements issue #750

Docstrings

• [x ] Docstrings complete and follow Napoleon (google) style
• [ x] Maths equation added
• [ x] Reference to paper/webpage is in docstring. The preferred referencing style for journal articles is APA (7th edition)

Documentation

• [ x] Add the score to the API documentation
• [x ] Add the score to the included list of metrics and tools

[Steph-Chong]

I haven't looked at your code as yet, but I wanted to provide some extra information.

Negative predictive value will also need to be added to the binary categorical score tutorial - specifically, the tutorial includes a list of binary categorical scores included in scores. "negative predictive value" should be added to this list.

[Screenshot below is taken from https://scores.readthedocs.io/en/stable/tutorials/Binary_Contingency_Scores.html]

Also, I have also just realised that the "success ratio (precision)" entry will also need to be updated to "success ratio (precision, positive predictive value)" - sorry I didn't think of that before.

[arshiaar]

name: Arshia Sharma :)

[Steph-Chong]

name: Arshia Sharma :)

Thanks Arshia. When I next update the release notes I will include you as "Arshia Sharma (@arshiaar)".

[Steph-Chong]

Thanks for this pull request @arshiaar.

I have some very minor feedback on included.md and the docstring.

I don't have the domain expertise to review the functional code and the tests, so I will leave the review of those to others.

[tennlee]

@nicholasloveday FYI, I will re-add you once I've had a chance to review tomorrow, I need to check some things. Feel free to take a look, but also feel free to wait until I've had a look.

[tennlee]

@nicholasloveday okay, feel free to review this now. Sorry! :)

[nicholasloveday]

Thanks for this update @arshiaar . The equation and tests look correct to me.

[tennlee]

In addition to the wikipedia link, can you please add this article/citation to the references: https://www.mdpi.com/1648-9144/57/5/503 . I'll wonder if it would actually be worth adding this to each of: PPV, NPV, sensitivity and specificity. The citation to use is:

Monaghan, T. F., Rahman, S. N., Agudelo, C. W., Wein, A. J., Lazar, J. M., Everaert, K., & Dmochowski, R. R. (2021). Foundational Statistical Principles in Medical Research: Sensitivity, Specificity, Positive Predictive Value, and Negative Predictive Value. Medicina, 57(5), 503. https://doi.org/10.3390/medicina57050503

For the other scores that NPV, I would suggest opening a new PR to address those, so that this score can be added sooner than later.

[tennlee]

I will merge this PR as-is, then add the additional reference afterwards.

[tennlee]

Thanks so much for all of this work! :). I have merged this, and also added the Monaghan et al. (2021) reference in to the relevant spots (NPV, PPV, specificity, sensitivity).

Here is a link to negative predictive value in the 'latest' (development) build of the docs: https://scores.readthedocs.io/en/latest/api.html#scores.categorical.BasicContingencyManager.negative_predictive_value