Better docstrings

Better docstrings for all functions

src/io.jl

@@ -7,7 +7,9 @@
 Function to save unfold models in your BIDS root folder. Automatically creates a derivatives_subfolder (default = "Unfold") in the derivatives and subsequentely safes each model in results according to BIDS.
 Example of path so saved file: bids_root/derivatives/Unfold/sub-XXX/eeg/sub-XXX_ses-XX_task-XXX_run-XX_unfold.jld2
 
-If overwrite is false the function will check for already saved results in the same folder and with the same name i.e. same subject/session/task/run.
+# Keywords
+derivatives_subfolder (String::"Unfold"): Creates the named subfolder and saves Unfold models according to BIDS.
+overwrite (Bool::false): Does not overwrite existing datasets; can be set to true.
 """
 function save_results(results::DataFrame, bids_root::String;
     derivatives_subfolder::String="Unfold",
@@ -64,8 +66,16 @@ end
         task::Union{Nothing,AbstractString}=nothing,
         run::Union{Nothing,AbstractString}=nothing)
 
-Load Unfold models existing in a derivatives_subfolder in your BIDS root folder. If lazy is true (default) then data will not be loaded and a DataFrame containing all file paths + information will be returned (similar to bids_layout output).
-generate_Xs reconstructs the designmatrix, can be set to false for faster loading times.
+Load Unfold models existing in a derivatives_subfolder in your BIDS root folder. 
+
+# Keywords
+derivatives_subfolder (String::"Unfold"): Defines in which subfolder of bids_root/derivatives to look for Unfold models.
+lazy (Bool::false): Do not actually load the dataset into memore if true, only return a dataframe with paths
+generate_Xs (Bool::true): Do not recreate the designmatrix; improves loading time.
+ses (Union{Nothing,AbstractString}::nothing): Which session to load; loads all if nothing
+task (Union{Nothing,AbstractString}::nothing): Which task to load; loads all if nothing
+run (Union{Nothing,AbstractString}::nothing): Which run to load; loads all if nothing
+
 """
 function load_results(bids_root::String;
     derivatives_subfolder::String="Unfold",
@@ -123,7 +133,7 @@ end
 """
     _load_results(files_df; generate_Xs::Bool = true)
 
-Internal functino to load Unfold models into memory. Can also be used to load data after file information was loaded lazily (lazy=true) using load_results()
+Internal function to load Unfold models into memory. Can also be used to load data after file information was loaded lazily (lazy=true) using load_results()
 """
 function _load_results(files_df, generate_Xs::Bool = true)
 

src/load.jl

@@ -1,3 +1,23 @@
+"""
+    bids_layout(bidsPath::AbstractString;
+        derivatives::Bool=true,
+        specificFolder::Union{Nothing,AbstractString}=nothing,
+        excludeFolder::Union{Nothing,AbstractString}=nothing,
+        ses::Union{Nothing,AbstractString}=nothing,
+        task::Union{Nothing,AbstractString}=nothing,
+        run::Union{Nothing,AbstractString}=nothing)
+
+Main function to load paths of all subjects in one bids_root folder. Will return a DataFrame containing all found paths with specific subject information. Used before loading data into memore using @Ref(`load_bids_eeg_data`)
+
+# Keywords
+derivatives (Bool::true): Look for data in the derivatives folder
+specificFolder (Union{Nothing,AbstractString}::nothing): Specify a specific folder name in either derivatives or bids_root to look for data.
+excludeFolder (Union{Nothing,AbstractString}::nothing): Exclude a specific folder from data detection.
+ses (Union{Nothing,AbstractString}::nothing): Which session to load; loads all if nothing
+task (Union{Nothing,AbstractString}::nothing): Which task to load; loads all if nothing
+run (Union{Nothing,AbstractString}::nothing): Which run to load; loads all if nothing
+"""
+
 function bids_layout(bidsPath::AbstractString;
     derivatives::Bool=true,
     specificFolder::Union{Nothing,AbstractString}=nothing,
@@ -69,7 +89,12 @@ function bids_layout(bidsPath::AbstractString;
     return files_df
 end
 
-#
+"""
+    get_info!(files_df, file)
+
+Internal function to get subject information from dataframe.
+"""
+
 # get subject and file information
 function get_info!(files_df, file)
 
@@ -114,6 +139,15 @@ function check_df(files_df, ses, task, run)
 end
 #-----------------------------------------------------------------------------------------------
 # Function loading BIDS data given bidsLayout DataFrame
+"""
+    load_bids_eeg_data(layout_df; verbose::Bool=true, kwargs...)
+
+Load data found with @Ref('bids_layout') into memory.
+
+verbose (Bool::true): Show ProgressBar
+kwargs... : kwargs for CSV.read to load events from .tsv file; e.g. to specify delimeter
+"""
+
 function load_bids_eeg_data(layout_df; verbose::Bool=true, kwargs...)
 
     # Initialize an empty dataframe
@@ -220,6 +254,12 @@ end
 
 # Function to find and load all events files into a DataFrame
 
+"""
+load_events(layoutDF::DataFrame; kwargs...)
+
+Internal function to load events based on paths in the layout Df
+"""
+
 function load_events(layoutDF::DataFrame; kwargs...)
 
     all_events = DataFrame()

src/utils.jl

@@ -1,10 +1,18 @@
 """
-	run_unfold(dataDF, bfDict; eventcolumn="event",removeTimeexpandedXs=true, extract_data = raw_to_data, verbose::Bool=true, kwargs...)
-
-
-- removeTimeexpandedXs (true): Removes the timeexpanded designmatrix which significantly reduces the memory-consumption. This Xs is rarely needed, but can be recovered (look into the Unfold.load function)
-
-extractData (function) - specify the function that translate the MNE Raw object to an data array. Default is `rawToData` which uses get_data and allows to pick `channels` - see @Ref(`raw_to_data`). The optional kw- arguments (e.g. channels) need to be specified directly in the `run_unfold` function as kw-args
+	run_unfold(dataDF, bfDict; 
+		eventcolumn="event",
+		removeTimeexpandedXs=true, 
+		extract_data = raw_to_data, 
+		verbose::Bool=true, 
+		kwargs...)
+
+Run Unfold analysis on all data in dataDF.
+
+# Keywords
+eventcolumn (String::"event"): Which collumn Unfold should use during the analysis.
+removeTimeexpandedXs (Bool::true): Removes the timeexpanded designmatrix which significantly reduces the memory-consumption. This Xs is rarely needed, but can be recovered (look into the Unfold.load function)
+extractData (functionraw_to_data): Specify the function that translate the MNE Raw object to an data array. Default is `rawToData` which uses get_data and allows to pick `channels` - see @Ref(`raw_to_data`). The optional kw- arguments (e.g. channels) need to be specified directly in the `run_unfold` function as kw-args
+verbose (Bool::true): Show ProgressBar or not.
 """
 
 function run_unfold(dataDF, bfDict; eventcolumn="event",removeTimeexpandedXs=true, extract_data = raw_to_data, verbose::Bool=true, kwargs...)
@@ -40,6 +48,13 @@ function run_unfold(dataDF, bfDict; eventcolumn="event",removeTimeexpandedXs=tru
     return resultsDF
 end
 
+"""
+	raw_to_data(raw; channels::AbstractVector{<:Union{String,Integer}}=[])
+
+
+Function to get data from MNE raw object. Can choose specific channels; default loads all channels.
+"""
+
 # Function to run Preprocessing functions on data
 function raw_to_data(raw; channels::AbstractVector{<:Union{String,Integer}}=[])
     return pyconvert(Array, raw.get_data(picks=pylist(channels), units="uV"))
@@ -69,6 +84,12 @@ function unpack_events(df::DataFrame)
 	return all_events
 end
 
+"""
+	bids_coeftable(model_df)
+
+Turns all models found in model_df into tydy DataFrames and aggregates them in a new DataFrame.
+"""
+
 function bids_coeftable(model_df)
 
 	all_results = DataFrame()
@@ -116,7 +137,7 @@ end
 """
 	list_all_paths(path)
 
-Internal functino to find pathfiles
+Internal function to find pathfiles
 """
 list_all_paths(path, file_ending, file_pattern; exclude=nothing) = @cont begin
 	if isfile(path)