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)