fixed_data

Fixed data

Description

The table below contains a list of some of the datasets that are available. However, to use other datasets, you can simply place them in your local resources/data/mydatasets along with the others. The files should be on the csv format specified in Dataset.

Filename	p	n	Type	Graph
2005_sachs/	11		cont	sachs.csv
2005_sachs_1_cd3cd28_log.csv	11	992	cont	sachs.csv
2005_sachs_2_cd3cd28icam2_log.csv	11	992	cont	sachs.csv
2005_sachs_2_cd3cd28icam2_log_std.csv	11	992	cont	sachs.csv
2013_green_thomas_p50_n1000.csv	50	1000	cont	greenthomas2013_ar2.csv
2019_olsson_pavlenko_rios_p15_n1000.csv	15	1000	bin	jonesp15.csv
czech_autoworkers.csv	6	1841	bin	unknown
gmint.csv	8	5000	cont, interv	gmint.csv

2005_sachs/

File: 2005_sachs/

Directory with all the datasets from Sachs et al.[1]

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2005_sachs_1_cd3cd28_log.csv

File: 2005_sachs_1_cd3cd28_log.csv

The logged version of the 1st dataset from Sachs et al.[1].

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2005_sachs_2_cd3cd28icam2_log.csv

File: 2005_sachs_2_cd3cd28icam2_log.csv

The logged version of the 2nd dataset from Sachs et al.[1].

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2005_sachs_2_cd3cd28icam2_log_std.csv

File: 2005_sachs_2_cd3cd28icam2_log_std.csv

The logged and standardized version of the 2nd dataset from Sachs et al.[1].

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2013_green_thomas_p50_n1000.csv

File: 2013_green_thomas_p50_n1000.csv

Synthetic decomposable Gaussian graphical AR-2 (intra-class) model dataset from section 4.3 in Green and Thomas[2].

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2019_olsson_pavlenko_rios_p15_n1000.csv

File: 2019_olsson_pavlenko_rios_p15_n1000.csv

The binary decomposable dataset from section 6.2 in Olsson et al.[3].

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czech_autoworkers.csv

File: czech_autoworkers.csv

Czech autoworkers dataset from Edwards and Toma[4].

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gmint.csv

File: gmint.csv

Synthetic interventional dataset gmInt from the pcalg package Kalisch et al.[5] (see the documentation of pcalg).

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References

[1] (1,2,3,4)

Karen Sachs, Omar Perez, Dana Pe’er, Douglas A. Lauffenburger, and Garry P. Nolan. Causal protein-signaling networks derived from multiparameter single-cell data. Science, 308(5721):523–529, 2005. URL: https://www.science.org/doi/abs/10.1126/science.1105809.

[2]

Peter J. Green and Alun Thomas. Sampling decomposable graphs using a Markov chain on junction trees. Biometrika, 100(1):91–110, 2013.

[3]

Jimmy Olsson, Tatjana Pavlenko, and Felix L. Rios. Bayesian learning of weakly structural Markov graph laws using sequential Monte Carlo methods. Electronic Journal of Statistics, 13(2):2865 – 2897, 2019. URL: https://doi.org/10.1214/19-EJS1585.

[4]

David Edwards and Havranek Toma. A fast procedure for model search in multidimensional contingency tables. Biometrika, 72(2):339–351, 1985. URL: https://academic.oup.com/biomet/article-abstract/72/2/339/229687.

[5]

Markus Kalisch, Martin Mächler, Diego Colombo, Marloes H Maathuis, and Peter Bühlmann. Causal inference using graphical models with the \proglang R package \pkg pcalg. Journal of Statistical Software, 47(11):1–26, 2012.