InterSci wiki R Paper Examples: Using R to replicate a published study
From InterSciWiki
"Replicability by independent observers is the only reliable way to test the validity of scientific claims." -- Steven Dutch, Natural and Applied Sciences, University of Wisconsin - Green Bay
This is the list of "Target" replications - ALL UNDER DEVELOPMENT
[edit] Causality and Autocorrelation: Female Contribution to Subsistence (Eff)
Eff, E. Anthon. 2004. Does Mr. Galton Still Have a Problem? Autocorrelation in the Standard Cross-Cultural Sample. World Cultures 15(2):153-170. download
Run: Comparative research tools#Correlation_and_Regression_Using_Autocorrelation_in_model_specification\
These R results replicate Table 4 (Explaining SCCS Var#826 (Average Female Contribution to Subsistence) in Eff, E. Anthon. 2004. Does Mr. Galton Still Have a Problem? Autocorrelation in the Standard Cross-Cultural Sample. World Cultures 15(2):153-170. download with no residual autocorrelation and R-Square=.3121 variance accounted for.
[edit] Causality and Autocorrelation: Polygyny (Dow)
Causes of polygyny - being replicated by Malcolm Dow, 2008
- 1988 "Causes of Polygyny: Ecology, Economy, Kinship and Warfare" Douglas R. White & M.L. Burton. American Anthropologist 90:871-887. Reprinted 1992/1993 in Culture and Human Sexuality, Ch 15, pp. 195-212, edited by David N. Suggs and Andrew W. Miracle. Pacific Grove, CA: Brooks/Cole Publishing Co. JSTOR Author pdf - all rights reserved by JSTOR.
For replication instructions see Comparative research tools#Anthon_Eff.27s_SAR_Procedures
[edit] Gender Division of Labor and Entailment or Implicational Structures (White, Butts)
Entailment analysis - software by Carter Butts
- 2000. Douglas R. White, Manual for Statistical Entailment Analysis. World Cultures 11(1):77-90. http://eclectic.ss.uci.edu/~drwhite/entail/11-1white-SEA.pdf
[edit] Networks and Cohesion (Moody, White, McMahan)
Structural cohesion and embeddedness - software by Peter McMahan
- 2003, James Moody and Douglas R. White, Social Cohesion and Embeddedness: A Hierarchical Concept of Social Groups. American Sociological Review 68(1):1-25. Outstanding Article Publication Award from the ASA Mathematical Sociology Section, 2004.
[edit] Complex networks (Handcock)
Running the simple model for complex networks with arbitrary degree distribution and clustering in R
- 2007 Mark S. Handcock, with application to Heider vs Simmel: Emergent Features in Dynamic Structures David Krackhardt and Mark S. Handcock
Generative Model for Feedback Networks
- 2006 "Generative Model for Feedback Networks." Douglas R. White, Natasa Kejzar, Constantino Tsallis, Doyne Farmer, Scott White. Physical Review E, 016119 11pp. Reprinted in the February 1, 2006 issue of the Virtual Journal of Biological Physics Research, an edited compilation of links to articles from participating publishers that focuses on frontier research and is published by the American Physical Society and the American Institute of Physics in cooperation with numerous other societies and publishers.
Blockmodel analysis
- 2005 "Multiple Measures of Alyawarra Kinship," Woodrow W. Denham and Douglas R. White. Field Methods 17(1):70-101.
[edit] Social-circles as complex networks: Generative feedback model
Preview of outcome as movie in Pajek (right click to download, Pajek menu to open: File/Pajek project file. Then Draw/Draw-Partition-Vector, then Options/Previous-Next/Apply to:Networks-Partitions-Vectors then click Previous many times till you get back to the start : begin here
http://eclectic.ss.uci.edu/~drwhite/pub/paj/1250-0-2-0.paj
You can also use Export/2D/SVG and set options for a color edition in high quality graphics. To see evolution step by step rather than 10 new links at a time, see Natasa's slides and explication of the model.
reviewed 2005 in Europhysicsnews 36(6):218-220 by Stefan Thurner:
- 2006 Douglas R. White, Nataša Kejžar, Constantino Tsallis, Doyne Farmer, and Scott D. White. PDF: A Generative Model for Feedback Networks (including trade, biotech, kinship) Physical Review E 73, 016119 (8 pages) abstract - doi:10.1103/PhysRevE.73.016119
- Santa Fe Institute Working Paper 2005
Reprinted: Virtual Journal of Biological Physics Research February 1, 2006 issue. The Virtual Journal, which is published by the American Physical Society and the American Institute of Physics in cooperation with numerous other societies and publishers, is an edited compilation of links to articles from participating publishers, covering a focused area of frontier research. The implications of this type of model are carried further in Thurner, Kyriakopoulos and Tsallis, 2007, Unified Model for Network Dynamics Exhibiting Nonextensive Statistics Phys. Rev. E 76, 036111 (2007) (8 pages).
paj file 1250-0-2-0 | R code | Edge Based Model simulation for alpha = 0 (start), beta=1.9 (distance decay), gamma = 0 (route), N=500, steps of 15 shown in figures with black lines as tree-like links to new nodes, red lines are feedback links at various (clickable) distances. See Working Papers Series for the Social Dynamics and Evolution group for full color preprint as well as an interactive conference PDF by Kejzar.
Abstract. We investigate a simple generative model for network formation. The model is designed to describe the growth of networks of kinship, trading, corporate alliances, or autocatalytic chemical reactions, where feedback is an essential element of network growth. The underlying graphs in these situations grow via a competition between cycle formation and node addition. After choosing a given node, a search is made for another node at a suitable distance. If such a node is found, a link is added connecting this to the original node, and increasing the number of cycles in the graph; if such a node cannot be found, a new node is added, which is linked to the original node. We simulate this algorithm and find that we cannot reject the hypothesis that the empirical degree distribution is a q-exponential function, which has been used to model long-range processes in nonequilibrium statistical mechanics.
[edit] Controlled kinship simulation (White)
Kinship simulation - under development
- 1999 "Controlled Simulation of Marriage Systems." Douglas R. White. Journal of Artificial Societies and Social Simulation. http://jasss.soc.surrey.ac.uk/2/3/5.html - http://ideas.repec.org/a/jas/jasssj/1999-12-1.html
[edit] High-Order Statistical Interaction and the Fisher Test (White)
3-Way Fisher exact
- 1983 Douglas R. White, Robert Pesner, Kark Reitz, An Exact Significance Test for Three-Way Interaction Cross Cultural Research 18:103-122. http://ccr.sagepub.com/cgi/content/abstract/18/2/103
This has not yet been programmed in R.
[edit] Single factor test (White)
Father-child interaction in the SCCS
- 1990 Doug White: Single Factor Analysis Reliability in Comparative and Ethnographic Observations: The Example of High Inference Father-Child Interaction Measures, Journal of of Quantitative Anthropology 2: 109-150.
