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Update README.md #82

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38 changes: 17 additions & 21 deletions README.md
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Expand Up @@ -42,39 +42,35 @@ AppStore -> JuliaUp, or `winget install julia -s msstore` in CMD

```julia
using Pkg
Pkg.add("https://github.com/unfoldtoolbox/UnfoldBIDS.jl")
Pkg.add("UnfoldBIDS")
```

> **Note:** The package is currently not registered. Once it is registered the above add command will change to ```Pkg.add("UnfoldBIDS")```

## Current Functionality
## Quickstart

```julia
using UnfoldBIDS


# To look up the paths of all subjects and store in a Dataframe:
layout_df = bidsLayout(bidsPath::AbstractString; # Path to BIDS root folder
derivative::Bool=true, # Do you want to us the derivative/ processed data? Default = true
specificFolder::Union{Nothing,AbstractString}=nothing, # If you want a specific folder in derivatives or root specify here
excludeFolder::Union{Nothing,AbstractString}=nothing, # You can exclude specific folders when not looking for a specific sub-folder
task::Union{Nothing,AbstractString}=nothing, # Specify task; will load all tasks if not specified
run::Union{Nothing,AbstractString}=nothing) # Specify run; will load all runs if not specified

layout_df = bids_layout(bidsPath::AbstractString; # Path to BIDS root folder
derivatives::Bool=true, # Do you want to us the derivative/ processed data? Default = true
specificFolder::Union{Nothing,AbstractString}=nothing, # If you want a specific folder in derivatives or root specify here
excludeFolder::Union{Nothing,AbstractString}=nothing, # You can exclude specific folders when not looking for a specific sub-folder
ses::Union{Nothing,AbstractString}=nothing, # Specify session; will load all sessions if not specified
task::Union{Nothing,AbstractString}=nothing, # Specify task; will load all tasks if not specified
run::Union{Nothing,AbstractString}=nothing) # Specify run; will load all runs if not specified

# To load all data into memory/ one dataframe:
eeg_df = load_bids_eeg_data(layout_df::DataFrame)
eeg_df = load_bids_eeg_data(layout_df; verbose::Bool=true, kwargs...)

3×2 DataFrame
Row │ subject data
│ SubStrin… Py
─────┼──────────────────────────────────────────────
1 │ 005 <RawEEGLAB | sub-005_ses-001_tas…
2 │ 006 <RawEEGLAB | sub-006_ses-001_tas…
3 │ 007 <RawEEGLAB | sub-007_ses-001_tas…
# To run Unfold model:
models_df = run_unfold(dataDF, bfDict; eventcolumn="event",removeTimeexpandedXs=true, extract_data = raw_to_data, verbose::Bool=true, kwargs...)

# For dataframe containing tidy results
results_df = bids_coeftable(models_df)

# To run Unfold model:
resultsAll = runUnfold(dataDF, eventsDF, bfDict; channels::Union{Nothing, String, Integer}=nothing, eventcolumn="event")
# To unpack results into one big tidy DataFrame, with subject information
results = unpack_results(results_df)

```

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