Here are the analysis RmD files for reproducing the figures from our paper. To run these scripts, first clone the source directory

`git clone https://github.com/kkdey/CorShrink-pages.git`

Then go to the `analysis`

directory

`cd CorShrink-pages/analysis`

The paths of the data files in the scripts below (under Figures and Supplementary Figures) are relative to this directory.

**Figures** :

Figure 3: FLASH and softImpute imputation on PLIN1 gene expression

Figure 6: Corshrink on word2vec similarity estimates from Ebony magazine 1968 issues

**Supplementary Figures** :

We review additional methods and analysis RmD files that did not make it to the final draft of the paper.

- Simulation settings for testing CorShrink
- Example study 1 : banded structure
- Example study 2 : banded structure
- Example study 3 : banded structure
- Example study 4 : banded structure
- Example study 5 : alternate banded structure
- Example study 6 : similar banded structure
- Example study 7 : Toeplitz structure
- Example study 8 : Hub structure
- Example study 9 : Hub structure
- Example study 10 : Diagonal covariance matrix-DSC
- Example study 11 : Toeplitz covariance matrix-DSC
- Example study 12 : Graph based covariance matrix-DSC

Combined GLASSO and CorShrink for correlation/partial correlation estimation

- Model Write up: Adaptive shrinkage of partial correlations
- Comparison of ISEE and pCorShrink : Banded precision matrix example 1
- Why ISEE for N > P? :: Comparsion of ISEE and pCorShrink with standard method
- Frobenius norm comparisons of ISEE, pCorShrink and standard methods for N > P
- Why ISEE for N < P? :: Comparsion of ISEE and pCorShrink with standard method
- Frobenius norm comparisons of ISEE, pCorShrink and standard methods for N < P
- Frobenius norm comparisons of ISEE, pCorShrink and standard methods for Hub, Toeplitz and Banded precision matrices
- Testing pCorShrink and ISEE with CLIME
- Illustration of Network analysis using ISEE, pCorShrink and GLASSO
- Illustration of pCorShrink on Himalayan bird abundance data
- Illustration of pCorShrink on cellula signaling pathway data from Sachs and others (2005)
- Illustration of pCorShrink on stock market price data from huge package

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