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Merge pull request #2 from yufongpeng/df.jl
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Release v0.1.0
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@yufongpeng
yufongpeng authored Apr 15, 2024
2 parents 9fd0cd5 + a147dfb commit a20ba35
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/Manifest.toml
/test/result
16 changes: 10 additions & 6 deletions Project.toml
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name = "Validation"
name = "AnalyticalMethodValidation"
uuid = "b401a7b7-5953-49f1-86ca-9d186498acee"
authors = ["Yu-Fong Peng <[email protected]>"]
version = "0.2.1"
version = "0.1.0"

[deps]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
Chain = "8be319e6-bccf-4806-a6f7-6fae938471bc"
ChemistryQuantitativeAnalysis = "3ed48883-6809-43ec-b77a-d23b0650d8c4"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DataPipes = "02685ad9-2d12-40c3-9f73-c6aeda6a7ff5"
SplitApplyCombine = "03a91e81-4c3e-53e1-a0a4-9c0c8f19dd66"
Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9"

[compat]
CSV = "0.10"
Chain = "0.5"
ChemistryQuantitativeAnalysis = "0.7"
Dictionaries = "0.3"
DataFrames = "1.5.0"
DataPipes = "0.3"
SplitApplyCombine = "1"
TypedTables = "1"
julia = "1"

[extras]
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66 changes: 43 additions & 23 deletions README.md
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# Validation
# AnalyticalMethodValidation

|CI status|Coverage|
|:-------:|:------:|
[![][ci-img]][ci-url]| [![][codecov-img]][codecov-url]|

[ci-img]: https://github.com/yufongpeng/Validation.jl/actions/workflows/CI.yml/badge.svg?branch=main
[ci-url]: https://github.com/yufongpeng/Validation.jl/actions/workflows/CI.yml?query=branch%3Amain
[codecov-img]: https://codecov.io/gh/yufongpeng/Validation.jl/branch/main/graph/badge.svg
[codecov-url]: https://codecov.io/gh/yufongpeng/Validation.jl
[ci-img]: https://github.com/yufongpeng/AnalyticalMethodValidation.jl/actions/workflows/CI.yml/badge.svg?branch=main
[ci-url]: https://github.com/yufongpeng/AnalyticalMethodValidation.jl/actions/workflows/CI.yml?query=branch%3Amain
[codecov-img]: https://codecov.io/gh/yufongpeng/AnalyticalMethodValidation.jl/branch/main/graph/badge.svg
[codecov-url]: https://codecov.io/gh/yufongpeng/AnalyticalMethodValidation.jl

A small package for analyzing method validation data. It only accepts csv data from Agilent MassHunter Quantitative analysis and the table needs to be flat.
A small package for analytical method validation, and sample analysis.

For command line interfaces, see [`juliaquant`](https://github.com/yufongpeng/juliaquant).

## Function
1. `read_data`: read the data with some transformation.
2. `QCReport`: calculate accuracy and rsd of QC samples.
3. `APData`: calculate accuracy, repeatability and reproducibility.
4. `RecoveryData`: calculate recovery by prespiked/postspiked.
5. `MEData`: calculate matrix effect by with_matrix/std_solution.
6. `StabilityData`: calculate accuracy and rsd of QC samples in different tempearture and restoration days.
7. `SampleReport`: average each sample.
8. `Report`: flatten nested `Data` object for CSV output.

## Scripts
See "/scipt" for command line interfaces.
1. `read`: read csv file(s) into `AnalysisTable` (See [`ChemistryQuantitativeAnalysis.jl`](https://github.com/yufongpeng/ChemistryQuantitativeAnalysis.jl)). Currently, only data from MassHunter Software in wide format is supported.

### Report functions
These function accept `AnalysisTable` or `Batch`.
1. `qc_report`: calculate accuracy and rsd of QC samples.
2. `ap_report`: calculate accuracy, repeatability and reproducibility.
3. `recovery_report`: calculate recovery by prespiked/postspiked.
4. `me_report`: calculate matrix effect by with_matrix/std_solution.
5. `stability_report`: calculate accuracy and rsd of QC samples in different tempearture and restoration days.
6. `sample_report`: average each sample.

### Util functions
1. `pivot`: transform dataframe into wide format.
2. `unpivot`: transform dataframe into long format.
3. `selectby`: select values by specific column, and apply `select!` as if the values are columns. This function is useful to merge multiple statistical values into specific formats.
4. `mean_plus_minus_std`: round and merge mean values and standard deviations with "±".
5. `add_percentage`: add "%".
6. `normalize`: normalize dataframe by the given normalizer.
7. `qualify`: replace data out of acceptable range.
8. `qualify!`: replace data out of acceptable range.

## Computation
### Intra-day

$$\mu_{d} = \sum_{j=1}^{n_d} \dfrac{c_{d, j}}{n_d}$$
$$a_{d,j } = \dfrac{c_{d, j}}{conc.}$$

$$\mu_{d} = \sum_{j=1}^{n_d} \dfrac{a_{d, j}}{n_d}$$

$$s_{intra}^2 = \dfrac{1}{p}\sum_{i = 1}^{p}\sum_{j = 1}^{n_i} \dfrac{(c_{i, j} - \mu_i)^2}{n_i - 1}$$
$$s_{intra}^2 = \dfrac{1}{p}\sum_{i = 1}^{p}\sum_{j = 1}^{n_i} \dfrac{(a_{i, j} - \mu_i)^2}{n_i - 1}$$

$$accuracy_{intra, d} = \dfrac{\mu_{d}}{conc.}$$
$$accuracy_{intra, d} = \mu_{d}$$

$$rsd_{intra, d} = \dfrac{s_{intra}}{accuracy_{intra, d}}$$

$p$: number of days, $n_i$: number of repeats of $i$ th day, $c_{i, j}$: measured concentration of $i$ th day and $j$ th repeat, $conc.$: reference concentration
### Inter-day
$$\mu = \dfrac{1}{p}\sum_{i = 1}^{p}\sum_{j = 1}^{n_i} \dfrac{c_{i, j}}{n_i}$$

$$accuracy_{inter} = \sum_{i = 1}^{p} \dfrac{accuracy_{intra, i}}{p} = \dfrac{\mu}{conc.}$$
$$\mu = \dfrac{1}{p}\sum_{i = 1}^{p}\sum_{j = 1}^{n_i} \dfrac{a_{i, j}}{n_i}$$

$$accuracy_{inter} = \sum_{i = 1}^{p} \dfrac{accuracy_{intra, i}}{p} = \mu$$

$$repeatability = rsd_{intra} = \dfrac{s_{intra}}{accuracy_{inter}}$$

Expand All @@ -49,4 +63,10 @@ $$s_{inter}^2 = max\ \{0, s_{between}^2 - \dfrac{s_{intra}^2}{\hat{n}}\ \}$$

$$\hat{n}=\dfrac{p}{\sum_{i=1}^p\dfrac{1}{n_i}}$$

$$reproducibility = rsd_{total} = \dfrac{\sqrt{s_{inter}^2+s_{intra}^2}}{accuracy_{inter}}$$
$$reproducibility = rsd_{total} = \dfrac{\sqrt{s_{inter}^2+s_{intra}^2}}{accuracy_{inter}}$$

## Reference
[Guidelines and Recommendations of the GTFCh](https://www.gtfch.org/cms/index.php/en/guidelines)

[Appendix B - Requirements for the validation of analytical methods](https://www.gtfch.org/cms/images/stories/files/Appendix%20B%20GTFCh%2020090601.pdf)
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Registration pull request created: JuliaRegistries/General/104913

Tip: Release Notes

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Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.1.0 -m "<description of version>" a20ba3566288473010655dab47837a30e575362d
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