Add readme and delete old notebooks

KnowledgeCaptureAndDiscovery · Feb 14, 2022 · f0ed212 · f0ed212
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diff --git a/notebooks/Data/02.gen_test_data.ipynb → notebooks/Data/01.gen_test_data.ipynb b/notebooks/Data/02.gen_test_data.ipynb → notebooks/Data/01.gen_test_data.ipynb
diff --git a/notebooks/Data/README.MD b/notebooks/Data/README.MD
@@ -0,0 +1,5 @@
+Methods to generate pseudo-data to test algorithms
+
+The notebooks contain the following information:
+
+* 01.gen_test_data: The notebook generate various timeseries with specific degrees of noise/frequencies/missing values. This was used to generate [test_data.csv](https://github.com/KnowledgeCaptureAndDiscovery/autoTS/blob/master/test_data/test_data.csv)
diff --git a/notebooks/Methods/04.analytical_spec_lomb_scargle_DEPRECATED.ipynb b/notebooks/Methods/04.analytical_spec_lomb_scargle_DEPRECATED.ipynb
diff --git a/...oks/Methods/benchmarking_detrending.ipynb → .../Detrending/benchmarking_detrending.ipynb b/...oks/Methods/benchmarking_detrending.ipynb → .../Detrending/benchmarking_detrending.ipynb
diff --git a/notebooks/Methods/trend.ipynb → notebooks/Methods/Detrending/trend.ipynb b/notebooks/Methods/trend.ipynb → notebooks/Methods/Detrending/trend.ipynb
diff --git a/notebooks/Methods/trend_modes.ipynb → ...ooks/Methods/Detrending/trend_modes.ipynb b/notebooks/Methods/trend_modes.ipynb → ...ooks/Methods/Detrending/trend_modes.ipynb
diff --git a/notebooks/Methods/Other methods_test_graphs.ipynb b/notebooks/Methods/Other methods_test_graphs.ipynb
diff --git a/notebooks/Methods/DBSCAN Tuning.ipynb → ...books/Methods/Outlier/DBSCAN Tuning.ipynb b/notebooks/Methods/DBSCAN Tuning.ipynb → ...books/Methods/Outlier/DBSCAN Tuning.ipynb
diff --git a/notebooks/Methods/Outlier_Detection.ipynb → ...s/Methods/Outlier/Outlier_Detection.ipynb b/notebooks/Methods/Outlier_Detection.ipynb → ...s/Methods/Outlier/Outlier_Detection.ipynb
diff --git a/notebooks/Methods/Outlier/README.md b/notebooks/Methods/Outlier/README.md
@@ -0,0 +1,6 @@
+Outlier detection
+
+Pyleoclim relies on outlier detection through clustering.
+
+* DBSCAN tuning: Understanding how to use DBSCAN for this particular application
+* Outlier_Dectection: Testing the use of the method on various signals. 
diff --git a/...Performance on Evenly Spaced Signal.ipynb → ...Performance on Evenly Spaced Signal.ipynb b/...Performance on Evenly Spaced Signal.ipynb → ...Performance on Evenly Spaced Signal.ipynb
diff --git a/.../Lomb-Scargle Performance_RvsPython.ipynb → .../Lomb-Scargle Performance_RvsPython.ipynb b/.../Lomb-Scargle Performance_RvsPython.ipynb → .../Lomb-Scargle Performance_RvsPython.ipynb
diff --git a/notebooks/Methods/Spectral Analysis/README.md b/notebooks/Methods/Spectral Analysis/README.md
@@ -0,0 +1,17 @@
+Spectral Analysis
+
+The following notebooks were used for the development of the spectral method incorporated into Pyleoclim:
+
+Completed work:
+
+* analytical_spec: computes the analytical spectral for specific timeseries and compare to the method available in Pyleoclim
+* astropy: Looks at the various algorithm available in the [astropy](https://www.astropy.org) package. Very basic testing didn't show a difference for our application and we proceeded with Scipy for Lomb-Scargle.
+* Lomb Scargle Performance on Evenly Spaced Signal.ipynb: Looks at the implementation of Lomb-Scargle in Pyleoclim with respect to WOSA implementation and use.
+* lomb_scargle_vs_wwz_analytical_benchmarks.ipynb: Evaluates the performance of the Lomb-Scargle periodogram with respect to analytical solution on specific signals.
+* Lomb-Scargle Performance_RvsPython.ipynb: Benchmarks the Lomb-Scargle algorithm as implemtented in GeochronR vs Pyleoclim
+*
+
+In Progress
+
+* gap_spectral: Notebook to look at the effect of gaps on the analysis.
+* run_algs.py (note: not a Notebook): runs various algorithms and test accuracy for the peaks
diff --git a/notebooks/Methods/analytical_spec.ipynb → ...s/Spectral Analysis/analytical_spec.ipynb b/notebooks/Methods/analytical_spec.ipynb → ...s/Spectral Analysis/analytical_spec.ipynb
diff --git a/notebooks/Methods/astropy.ipynb → ...s/Methods/Spectral Analysis/astropy.ipynb b/notebooks/Methods/astropy.ipynb → ...s/Methods/Spectral Analysis/astropy.ipynb
diff --git a/notebooks/Methods/gap_wwz_segment.ipynb → ...hods/Spectral Analysis/gap_spectral.ipynb b/notebooks/Methods/gap_wwz_segment.ipynb → ...hods/Spectral Analysis/gap_spectral.ipynb
diff --git a/...cargle_vs_wwz_analytical_benchmarks.ipynb → ...cargle_vs_wwz_analytical_benchmarks.ipynb b/...cargle_vs_wwz_analytical_benchmarks.ipynb → ...cargle_vs_wwz_analytical_benchmarks.ipynb
diff --git a/notebooks/Methods/run_algs.py → ...oks/Methods/Spectral Analysis/run_algs.py b/notebooks/Methods/run_algs.py → ...oks/Methods/Spectral Analysis/run_algs.py
diff --git a/notebooks/Methods/StackPlot.ipynb b/notebooks/Methods/StackPlot.ipynb
diff --git a/notebooks/Methods/Wavelet Analysis/README.md b/notebooks/Methods/Wavelet Analysis/README.md
@@ -0,0 +1,5 @@
+These notebooks test wavelet analysis code for various applications.
+
+* Wavelet analysis - Pywavelets: Looks at using [Pywavelets](https://pywavelets.readthedocs.io/en/latest/) for wavelet analysis of evenly-spaced data.
+* Torrence and Compo: The wavelet analysis of Torrence and Compo; its implementation in pyleoclim and comparison to WWZ
+* cross-wavelet: cross-wavelet based on WWZ. 
diff --git a/...Pywavelet CWT vs Torrence and Compo.ipynb → ...Wavelet Analysis/Torrence and Compo.ipynb b/...Pywavelet CWT vs Torrence and Compo.ipynb → ...Wavelet Analysis/Torrence and Compo.ipynb
diff --git a/...thods/Wavelet analysis - Pywavelets.ipynb → ...lysis/Wavelet analysis - Pywavelets.ipynb b/...thods/Wavelet analysis - Pywavelets.ipynb → ...lysis/Wavelet analysis - Pywavelets.ipynb
diff --git a/notebooks/Methods/cross_wavelet.ipynb → ...hods/Wavelet Analysis/cross_wavelet.ipynb b/notebooks/Methods/cross_wavelet.ipynb → ...hods/Wavelet Analysis/cross_wavelet.ipynb
diff --git a/notebooks/Methods/Welch hyperparemeters.ipynb b/notebooks/Methods/Welch hyperparemeters.ipynb
diff --git a/notebooks/Methods/gap_wwz_segment b/notebooks/Methods/gap_wwz_segment
diff --git a/notebooks/Methods/test_gap.ipynb b/notebooks/Methods/test_gap.ipynb
diff --git a/notebooks/Methods/test_gap_mtm.ipynb b/notebooks/Methods/test_gap_mtm.ipynb
diff --git a/notebooks/Methods/test_gap_wwz.ipynb b/notebooks/Methods/test_gap_wwz.ipynb
diff --git a/notebooks/Methods/test_mtm.ipynb b/notebooks/Methods/test_mtm.ipynb
diff --git a/notebooks/Methods/test_periodogram.ipynb b/notebooks/Methods/test_periodogram.ipynb
diff --git a/notebooks/Methods/test_spectrum.ipynb b/notebooks/Methods/test_spectrum.ipynb
diff --git a/notebooks/Methods/test_wavelet.ipynb b/notebooks/Methods/test_wavelet.ipynb
diff --git a/notebooks/Methods/test_wwz.ipynb b/notebooks/Methods/test_wwz.ipynb
diff --git a/notebooks/Methods/welch_method_test.ipynb b/notebooks/Methods/welch_method_test.ipynb
diff --git a/notebooks/StackPlot.ipynb b/notebooks/StackPlot.ipynb
diff --git a/notebooks/Workflows/readme.md b/notebooks/Workflows/readme.md
@@ -4,6 +4,5 @@ This folder contains a collection of notebooks describing workflows that will be
 implemented in WINGS.
 
 * Spectral Workflow: describes the steps for workflow analysis, including saving in JSON format. Each cell in the notebook is meant to emulate a workflow component for WINGS [Ready to use]
-* Spectral Workflow Test: Add a cost function to spectral workflow to characterize how well the workflow is able to capture the original periodocoties [beta]
+* Spectral Workflow Test: Add a cost function to spectral workflow to characterize how well the workflow is able to capture the original periodicities [beta]
 * Wavelet workflow: workflow for wavelet analysis [in prep]
-* Wavelet workflow Test: workflow for wavelet analysis with various methods [depricated 02/14/2022]