diff --git a/README.md b/README.md index 7abbb7d..a934196 100644 --- a/README.md +++ b/README.md @@ -23,18 +23,18 @@ For the complete documentation of the API and modules, visit: *Individual Pipeline* -- [How to prepare your data for the individual pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/1.individual_data_preparation.ipynb) -- [Preprocess your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/2.individual_data_preprocessing.ipynb) -- [Analyze your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/3.individual_data_analysis.ipynb) -- [Plot your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/4.individual_data_plotting.ipynb) -- [Learn more about the compatibility of wearablehrv with other platforms (Labfront, VU-AMS, Empatica)](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/individual_compatibility.ipynb) +- [How to prepare your data for the individual pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/1.individual_data_preparation.ipynb) +- [Preprocess your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/2.individual_data_preprocessing.ipynb) +- [Analyze your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/3.individual_data_analysis.ipynb) +- [Plot your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/4.individual_data_plotting.ipynb) +- [Learn more about the compatibility of wearablehrv with other platforms (Labfront, VU-AMS, Empatica)](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/individual_compatibility.ipynb) *Group Pipeline* -- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/1.group_data_preparation.ipynb) -- [Determine the signal quality of your wearables](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/2.group_signal_quality.ipynb) -- [Perform four major statistical analyses to determine validity](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/3.group_data_analysis.ipynb) -- [Descriptive plots for your group data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/4.group_data_plotting.ipynb) +- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/1.group_data_preparation.ipynb) +- [Determine the signal quality of your wearables](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/2.group_signal_quality.ipynb) +- [Perform four major statistical analyses to determine validity](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/3.group_data_analysis.ipynb) +- [Descriptive plots for your group data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/4.group_data_plotting.ipynb) # User Installation @@ -119,7 +119,7 @@ With a user-friendly GUI, correct the lag between devices, align data by croppin wearablehrv.individual.visual_inspection (data_chopped, devices, conditions,criterion) ``` -![visual_inspection](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/visual_inspection.png) +![visual_inspection](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/visual_inspection.PNG) **Detect Outliers and Ectopic Beats** @@ -137,7 +137,7 @@ Check how well you performed the preprocessing by comparing the detected outlier wearablehrv.individual.ibi_comparison_plot(data_chopped, data_pp, devices, conditions, criterion, width=20, height=10) ``` -![comparison_plot](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/comparison_plot.png) +![comparison_plot](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/comparison_plot.PNG) ### 1.3 Analyze and Plot @@ -148,7 +148,7 @@ time_domain_features, frequency_domain_features = wearablehrv.individual.data_an wearablehrv.individual.bar_plot(time_domain_features, frequency_domain_features, devices, conditions, width=20, height=25, bar_width = 0.15) ``` -![bar_plot](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/bar_plot.png) +![bar_plot](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/bar_plot.PNG) ## 2. Group Pipeline @@ -176,7 +176,7 @@ data, features, summary_df, quality_df = wearablehrv.group.signal_quality(data, wearablehrv.group.signal_quality_plot2(summary_df, condition_selection=False, condition=None) ``` -![signal_quality](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/signal_quality.png) +![signal_quality](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/signal_quality.PNG) ### 2.3 Statistical Analysis @@ -189,7 +189,7 @@ mape_data = wearablehrv.group.mape_analysis(data, criterion, devices, conditions wearablehrv.group.mape_plot(mape_data, features, conditions, devices) ``` -![mape](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/mape.png) +![mape](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/mape.PNG) **Regression Analysis** @@ -198,7 +198,7 @@ regression_data = wearablehrv.group.regression_analysis(data, criterion, conditi wearablehrv.group.regression_plot(regression_data, data, criterion, conditions, devices, features, marker_color='red', width=10, height_per_condition=4) ``` -![regression](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/regression.png) +![regression](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/regression.PNG) **Intraclass Correlation Coefficient** @@ -207,7 +207,7 @@ icc_data = wearablehrv.group.icc_analysis(data, criterion, devices, conditions, wearablehrv.group.icc_plot(icc_data, conditions, devices, features) ``` -![icc](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/icc.png) +![icc](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/icc.PNG) **Bland-Altman Analysis** @@ -216,7 +216,7 @@ blandaltman_data = wearablehrv.group.blandaltman_analysis(data, criterion, devic wearablehrv.group.blandaltman_plot(data, criterion, conditions, devices, features) ``` -![bland_altman](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/bland_altman.png) +![bland_altman](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/img/bland_altman.PNG) ### 2.4 Descriptive Plots diff --git a/docs/examples/getting_started/overview.ipynb b/docs/examples/getting_started/overview.ipynb index 67da32d..5c387a3 100644 --- a/docs/examples/getting_started/overview.ipynb +++ b/docs/examples/getting_started/overview.ipynb @@ -374,7 +374,7 @@ "\n", "Continue by consulting: \n", "\n", - "- [How to prepare your data for the individual pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/1.individual_data_preparation.ipynb)" + "- [How to prepare your data for the individual pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/1.individual_data_preparation.ipynb)" ] } ], diff --git a/docs/examples/group_pipeline/1.group_data_preparation.ipynb b/docs/examples/group_pipeline/1.group_data_preparation.ipynb index ca41c2a..4f0ddb5 100644 --- a/docs/examples/group_pipeline/1.group_data_preparation.ipynb +++ b/docs/examples/group_pipeline/1.group_data_preparation.ipynb @@ -31,10 +31,10 @@ "\n", "If you have not done so, first take a look at the following notebooks:\n", "\n", - "- [How to prepare your data for the individual pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/1.individual_data_preparation.ipynb)\n", - "- [Preprocess your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/2.individual_data_preprocessing.ipynb)\n", - "- [Analyze your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/3.individual_data_analysis.ipynb)\n", - "- [Plot your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/4.individual_data_plotting.ipynb)\n" + "- [How to prepare your data for the individual pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/1.individual_data_preparation.ipynb)\n", + "- [Preprocess your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/2.individual_data_preprocessing.ipynb)\n", + "- [Analyze your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/3.individual_data_analysis.ipynb)\n", + "- [Plot your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/4.individual_data_plotting.ipynb)\n" ] }, { @@ -215,7 +215,7 @@ "\n", "Continue by consulting: \n", "\n", - "- [Determine the signal quality of your wearables](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/2.group_signal_quality.ipynb)" + "- [Determine the signal quality of your wearables](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/2.group_signal_quality.ipynb)" ] } ], diff --git a/docs/examples/group_pipeline/2.group_signal_quality.ipynb b/docs/examples/group_pipeline/2.group_signal_quality.ipynb index be89b61..8b6318b 100644 --- a/docs/examples/group_pipeline/2.group_signal_quality.ipynb +++ b/docs/examples/group_pipeline/2.group_signal_quality.ipynb @@ -33,7 +33,7 @@ "\n", "If you have not done so, first take a look at the following notebooks:\n", "\n", - "- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/1.group_data_preparation.ipynb)" + "- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/1.group_data_preparation.ipynb)" ] }, { @@ -313,7 +313,7 @@ "\n", "Continue by consulting: \n", "\n", - "- [Perform four major statistical analyses to determine validity](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/3.group_data_analysis.ipynb)" + "- [Perform four major statistical analyses to determine validity](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/3.group_data_analysis.ipynb)" ] } ], diff --git a/docs/examples/group_pipeline/3.group_data_analysis.ipynb b/docs/examples/group_pipeline/3.group_data_analysis.ipynb index 986fb74..4453061 100644 --- a/docs/examples/group_pipeline/3.group_data_analysis.ipynb +++ b/docs/examples/group_pipeline/3.group_data_analysis.ipynb @@ -40,7 +40,7 @@ "\n", "If you have not done so, first take a look at the following notebooks:\n", "\n", - "- [Determine the signal quality of your wearables](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/2.group_signal_quality.ipynb)" + "- [Determine the signal quality of your wearables](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/2.group_signal_quality.ipynb)" ] }, { @@ -516,7 +516,7 @@ "\n", "Continue by consulting: \n", "\n", - "- [Descriptive plots for your group data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/4.group_data_plotting.ipynb)\n" + "- [Descriptive plots for your group data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/4.group_data_plotting.ipynb)\n" ] } ], diff --git a/docs/examples/group_pipeline/4.group_data_plotting.ipynb b/docs/examples/group_pipeline/4.group_data_plotting.ipynb index aa9f658..799ea75 100644 --- a/docs/examples/group_pipeline/4.group_data_plotting.ipynb +++ b/docs/examples/group_pipeline/4.group_data_plotting.ipynb @@ -31,8 +31,8 @@ "\n", "If you have not done so, first take a look at the following notebooks:\n", "\n", - "- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/1.group_data_preparation.ipynb)\n", - "- [Determine the signal quality of your wearables](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/2.group_signal_quality.ipynb)\n" + "- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/1.group_data_preparation.ipynb)\n", + "- [Determine the signal quality of your wearables](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/2.group_signal_quality.ipynb)\n" ] }, { diff --git a/docs/examples/individual_pipeline/1.individual_data_preparation.ipynb b/docs/examples/individual_pipeline/1.individual_data_preparation.ipynb index 244fd3b..5d6edbd 100644 --- a/docs/examples/individual_pipeline/1.individual_data_preparation.ipynb +++ b/docs/examples/individual_pipeline/1.individual_data_preparation.ipynb @@ -22,7 +22,7 @@ "\n", "If you have not done so, first take a look at the following notebooks:\n", "\n", - "- [Installation guide for wearablehrv](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/installation.ipynb)" + "- [Installation guide for wearablehrv](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/installation.ipynb)" ] }, { @@ -281,7 +281,7 @@ "\n", "Continue by consulting: \n", "\n", - "- [Preprocess your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/2.individual_data_preprocessing.ipynb)" + "- [Preprocess your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/2.individual_data_preprocessing.ipynb)" ] } ], diff --git a/docs/examples/individual_pipeline/2.individual_data_preprocessing.ipynb b/docs/examples/individual_pipeline/2.individual_data_preprocessing.ipynb index 0db07d8..cef829f 100644 --- a/docs/examples/individual_pipeline/2.individual_data_preprocessing.ipynb +++ b/docs/examples/individual_pipeline/2.individual_data_preprocessing.ipynb @@ -38,7 +38,7 @@ "\n", "If you have not done so, first take a look at the following notebooks:\n", "\n", - "- [How to prepare your data for the individual pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/1.individual_data_preparation.ipynb)\n" + "- [How to prepare your data for the individual pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/1.individual_data_preparation.ipynb)\n" ] }, { @@ -324,7 +324,7 @@ "\n", "Continue by consulting:\n", "\n", - "- [Analyze your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/3.individual_data_analysis.ipynb)" + "- [Analyze your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/3.individual_data_analysis.ipynb)" ] } ], diff --git a/docs/examples/individual_pipeline/3.individual_data_analysis.ipynb b/docs/examples/individual_pipeline/3.individual_data_analysis.ipynb index 7626052..10d596c 100644 --- a/docs/examples/individual_pipeline/3.individual_data_analysis.ipynb +++ b/docs/examples/individual_pipeline/3.individual_data_analysis.ipynb @@ -31,7 +31,7 @@ "\n", "If you have not done so, first take a look at the following notebooks:\n", "\n", - "- [Preprocess your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/2.individual_data_preprocessing.ipynb)" + "- [Preprocess your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/2.individual_data_preprocessing.ipynb)" ] }, { @@ -175,11 +175,11 @@ "\n", "Continue by consulting:\n", "\n", - "- [Plot your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/4.individual_data_plotting.ipynb)\n", + "- [Plot your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/4.individual_data_plotting.ipynb)\n", "\n", "Or\n", "\n", - "- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/1.group_data_preparation.ipynb)" + "- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/1.group_data_preparation.ipynb)" ] } ], diff --git a/docs/examples/individual_pipeline/4.individual_data_plotting.ipynb b/docs/examples/individual_pipeline/4.individual_data_plotting.ipynb index be42d4c..9b83d28 100644 --- a/docs/examples/individual_pipeline/4.individual_data_plotting.ipynb +++ b/docs/examples/individual_pipeline/4.individual_data_plotting.ipynb @@ -31,7 +31,7 @@ "\n", "If you have not done so, first take a look at the following notebooks:\n", "\n", - "- [Analyze your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/3.individual_data_analysis.ipynb)\n" + "- [Analyze your data](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/individual_pipeline/3.individual_data_analysis.ipynb)\n" ] }, { @@ -209,7 +209,7 @@ "\n", "Continue by consulting:\n", "\n", - "- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/getting_started/1.group_data_preparation.ipynb)\n" + "- [How to prepare your data for the group pipeline](https://github.com/Aminsinichi/wearable-hrv/blob/master/docs/examples/group_pipeline/1.group_data_preparation.ipynb)\n" ] } ],