From c75971de558568608f9685fabf0804314126abf7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Skukies?= <57703446+ReneSkukies@users.noreply.github.com> Date: Wed, 25 Oct 2023 14:52:17 +0200 Subject: [PATCH 1/2] Update README.md Update Readme to be better --- README.md | 74 ++++++++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 62 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 89bca67a..73e67d67 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,41 @@ -# UnfoldDecode +# [![logo_UnfoldDecode jl_120px](https://github.com/unfoldtoolbox/UnfoldDecode.jl/assets/57703446/965b93aa-33e1-420e-a707-1fe8d7e3bcbe)](https://github.com/unfoldtoolbox/UnfoldDecode.jl/tree/main) + [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://behinger.github.io/UnfoldDecode.jl/dev/) [![Build Status](https://github.com/behinger/UnfoldDecode.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/behinger/UnfoldDecode.jl/actions/workflows/CI.yml?query=branch%3Amain) [![Coverage](https://codecov.io/gh/behinger/UnfoldDecode.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/behinger/UnfoldDecode.jl) -Beta-stage toolbox to decode ERPs with overlap, e.g. from eye-tracking experiments. - +|rERP|EEG visualisation|EEG Simulations|BIDS pipeline|Decode EEG data|Statistical testing| +|---|---|---|---|---|---| +| | ||||| +Beta-stage toolbox to decode ERPs with overlap, e.g. from eye-tracking experiments. Currently only the overlap corrected LDA¹ proposed by [Gal Vishne, Leon Deouell et al.](https://doi.org/10.1101/2023.06.28.546397) is implemented, but more to follow. ¹ actually any MLJ supported classification/regressoin model is already supported -## Quickstart +## Install -```julia -LDA = @load LDA pkg=MultivariateStats +### Julia +
+Click to expand -des = Dict("fixation" => (@formula(0~1+condition+continuous),firbasis((-0.1,1.),100))); -uf_lda = fit(UnfoldDecodingModel,des,evt,dat,LDA(),"fixation"=>:condition) -``` +The recommended way to install julia is [juliaup](https://github.com/JuliaLang/juliaup). +It allows you to, e.g., easily update Julia at a later point, but also test out alpha/beta versions etc. + +TL:DR; If you dont want to read the explicit instructions, just copy the following command + +#### Windows + +AppStore -> JuliaUp, or `winget install julia -s msstore` in CMD + +#### Mac & Linux + +`curl -fsSL https://install.julialang.org | sh` in any shell +
+ +### UnfoldDecode -Does the trick - you should probably do an Unfold.jl tutorial first though! -## Installation Not yet registered thus you have to do: ```julia using Pkg @@ -29,6 +43,18 @@ Pkg.add(url="https://github.com/behinger/UnfoldDecode.jl") using UnfoldDecode ``` once it is registered, this will simplify to `Pkg.add("UnfoldDecode")` + +## Quickstart + +```julia +LDA = @load LDA pkg=MultivariateStats + +des = Dict("fixation" => (@formula(0~1+condition+continuous),firbasis((-0.1,1.),100))); +uf_lda = fit(UnfoldDecodingModel,des,evt,dat,LDA(),"fixation"=>:condition) +``` + +Does the trick - you should probably do an Unfold.jl tutorial first though! + ## Loading Data have a look at PyMNE.jl to read the data. You need a data-matrix + DataFrames.jl event table (similar to EEGlabs EEG.events) @@ -36,6 +62,30 @@ have a look at PyMNE.jl to read the data. You need a data-matrix + DataFrames.jl - Not thoroughly tested, no unit-tests yet! - Missing features: e.g. No time generalization is available, but straight forward to implement with the current tooling. -## Citing +## Contributions + +Contributions are very welcome. These could be typos, bugreports, feature-requests, speed-optimization, new solvers, better code, better documentation. + +### How-to Contribute + +You are very welcome to raise issues and start pull requests! + +### Adding Documentation + +1. We recommend to write a Literate.jl document and place it in `docs/_literate/FOLDER/FILENAME.jl` with `FOLDER` being `HowTo`, `Explanation`, `Tutorial` or `Reference` ([recommended reading on the 4 categories](https://documentation.divio.com/)). +2. Literate.jl converts the `.jl` file to a `.md` automatically and places it in `doc/src/_literate/FILENAME.jl`. +3. Edit [make.jl](https://github.com/unfoldtoolbox/Unfold.jl/blob/main/docs/make.jl) with a reference to `doc/src/_literate/FILENAME.jl` + +## Contributors (alphabetically) + +- **Hannes Bonasch** +- **Benedikt Ehinger** + + +## Citation If you use this code, please cite this code + the appropriate paper/algorithm + +## Acknowledgements + +Funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy – EXC 2075 – 390740016 From 601ad53a0f58df2d7a6219c6a04dfdf121773acc Mon Sep 17 00:00:00 2001 From: Judith Schepers Date: Mon, 30 Oct 2023 11:27:26 +0100 Subject: [PATCH 2/2] Update README.md Updated/Corrected paths for adding documentation. --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 73e67d67..927a9fc8 100644 --- a/README.md +++ b/README.md @@ -72,9 +72,9 @@ You are very welcome to raise issues and start pull requests! ### Adding Documentation -1. We recommend to write a Literate.jl document and place it in `docs/_literate/FOLDER/FILENAME.jl` with `FOLDER` being `HowTo`, `Explanation`, `Tutorial` or `Reference` ([recommended reading on the 4 categories](https://documentation.divio.com/)). -2. Literate.jl converts the `.jl` file to a `.md` automatically and places it in `doc/src/_literate/FILENAME.jl`. -3. Edit [make.jl](https://github.com/unfoldtoolbox/Unfold.jl/blob/main/docs/make.jl) with a reference to `doc/src/_literate/FILENAME.jl` +1. We recommend to write a Literate.jl document and place it in `docs/literate/FOLDER/FILENAME.jl` with `FOLDER` being `HowTo`, `Explanation`, `Tutorial` or `Reference` ([recommended reading on the 4 categories](https://documentation.divio.com/)). +2. Literate.jl converts the `.jl` file to a `.md` automatically and places it in `docs/src/generated/FOLDER/FILENAME.md`. +3. Edit [make.jl](https://github.com/unfoldtoolbox/Unfold.jl/blob/main/docs/make.jl) with a reference to `docs/src/generated/FOLDER/FILENAME.md`. ## Contributors (alphabetically)