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    • May 2016 FEET
HPC@UC -- Harry - Harry Mangalam AWS - phone - Comment 325 - Comments 326‎ - Comments 324
EMAIL ERIC Hi Doug, Stu and Eric (cc-ed) may be able to help Harry (who I understand will be running the gateway) with debugging. It looks like it is the gateway server at UCI that is down. These are the types of things that Harry will want to know how to fix going forward. Nancy
The Galaxy log file had grown to take up all of the disk space in /home. I moved it to /tmp, restarted the galaxy server (with “service galaxy restart”, gzipped the log, and moved it back as “galaxy-log-5-3-2016.gz”
Gateway seems to be up again after the restart. Eric
Clips / Offloads


Date: Sat, 29 Nov 2014 11:02:00 -0800 To: Ilkay Altintas <>, peter bearman <>, Scott White <>, Anthon Eff <>, Malcolm Dow <>, Michael Fischer <>, Carol Ember <>, David Rudner <>, Nancy Wilkins-Diehr <>, Tolga Oztan <>, Eleanor Wynn <>, Amber Johnson <>, Lukasz <>, Rachana Ananthakrishnan <>, Brian Foster <>, Benjamin (Nick) <>

The following addresses had permanent fatal errors ----- Doug Wallace <>, John Snarey <>,

Wesley Roberts <>, Mike Fischer <>, Victor de Munck <>

  • Crownsourcing the coding of religion in the EA. An alternative to merging SCCS with EA.
  • Moved Grueter ARTICLE to Str&Dyn... now restore Model #2: Clips v1649
  • I've got to move over to eclectic together with all its subtopics - can do with EditRocket
  • Once Eff adds Carlos A. Botero‎ Moral God variables to EA dataset, test using our AnimXBwealth and FxCmntyWage variables
DONE SAR books pertaining to roughly 107 or more additional pinpointed SCCS societies.

Wiley Off-Chapters

See discussion of Geoffrey_Hellman



  Celebrating - discussion of CoSSci at XSEDE

Model Summaries for comparison with OLS

  • Ev2007Higod4 8ABQhiGodPresentation2014final2.pptx Ev2007Higod4.xls v2007 AnimXbwealth,bio.5,FxCmtyWages,No_rain_Dry,PCsizeSq,v149,v2006,v53
out <- lm(HiGod ~ Wy + AnimXbwealth + bio.5 + FxCmtyWages + No_rain_Dry + PCsizeSq + v149 + v2006 + v53)


Suggested title for the Gateway: Anthropology and HPC for Complex Social Sciences (CoSSci)

Main list

These include any change of primary data, e.g., NA for Case 186 in SCCS (may need two such cases)
  • Do models such as Main Kinship Theory
  • How to get the word out
  • Fix Kinsources
  • Google Hangouts up to 10 people
  • UCI/Fetch/xls_csv has ContributorInformationSpreadsheetWiley.xlsx consisting of # First name Last name Email address Affiliation Address line 1
Address line 2 Address line 3 City State/Province Zip/Postal Code Country Chapter Title Submission deadline Chapter length Line drawings Half tones Notes
  • Contributor Information Spreadsheet reply to Graney, Mark - Boston <>
  • Pagel
  • Travel advance for ABQ
  • Nomadism
  • Ev2007Higod4 CoSSci2 lati -> Sqlati -> not a better depvar
  • Decide what to do with CCR and complications of cc-comparative research google group or
  • Paul Rodriguez's work with Sampling distributions, Bootstrap, AiCc, etc.
  • Add Eff's Black Maps - Lukasz - Not working for WNAI
  • HPC is Trestles 20min but no 3rd output! Jan 30'2014 Łukasz_Lacinski#Could_do In *.csv: which server? Trestles / OIT / SocSci;--how long did it take?;--date;--user name;--
Send emails each day: usage-- Trestles / OIT / SocSci;-- DO Compare GUI to VM - ask about sending usage emails each week, detailing each day
Partial success (emailed Tolga) withComments83#Comments83Oztan-White-Expanded_samples_of_SCCSplusEAwithOther.28Eff.2Cn.3D371.29_and_SCCSplusAWC.28DRW.2Cn.3D562.29
Name the AWC-EA a new database and add WNAI avoidance variables -- New Paper Title "Early Evolution of Social Complexity and Respectful Avoidance Dyads" or "Early Cooperative Complexity…
Ch6 Structure, Evolution, Function, Context, Causal Imprints and History in Cross-Cultural Research
Durkheim&Swanton/Sanderson&Winkelman/Brown&Eff&Dow/Chapter5/MoralGods (all converge) - distinct from reincarnation/Buddhism/Hinduism
v1122,v53,v54,v626,v245,v817,v154,v68 ____ v621*Supercomputer Gateway. ---

Done or Obsolete

March 18-22, 2014, Doug White and Tolga Oztan. Session Co-Chairs, SASci Meeting (jointly with the Society for Applied Anthropology), Albuquerque, New Mexico. Invited Session: "Science Gateway Analytic Modeling for Comparative Research," Invited Chapter authors, Wiley Companion for Cross-Cultural Research.
  • DID Chiro for Murray -- local guy
  • DID Peter Peregrine - Invited to SASci !!
  • Order entailments by freq -- Did with Tolga
  • DID Tom: Put Maps request above square ticks, including no h[10]
Tom: Option for no h[10]
  • DID Doug: Fix maps length of label integers to align with the map -- coordinate number of integer entries
  • DID Put Creative Commons License at Virtual Manual, CoSSci pages and SocSciComputing
  • DID: A.F.C. Wallace - Stephen K. Sanderson v2013 Religion - Do NoVA on Wallace, Reincarnation, and MoralGods. VERY SIMILAR IN MODEL RESULTS FOR THESE AND NONE OF THE BROWN-EFF VARIABLES ARE SIGNIFICANT: New *DEf Models DONE - 1) Sanderson 2) Moral Gods using Coding a wages variable‎‎ - finished in 2.5 days in May. NOW: - EduR-9_FxCmtyWages
  • Sanderson - Aronoff - Rosenblatt - Hrupka - Wages - ALL DONE and in SCCS codebook
  • Charles Ragin
  • Obsolete: ToDo INSTRUCTIONS - Letter of Invitation *.doc: include 2 pp instructions


Repairs needed to wikipages Af03 Ashanti (SCCS 013) - SCCS 029: Fur (Cb17)‎‎ - SCCS 002: !Kung‎ - SCCS 15: Nkundo Mongo (Ae15)‎ - Ng01 Huron (SCCS 144) - Mbau Fijians (SCCS 102)‎
  1. Auto Ethnography - Heather Ramey

David Rudner

Run system fit (now with Est(Wy); formerly: where No Autocorrelation Dv621.1, Dv626.1, Dv676.5 all but Dv51.5)

Revision: Use aa imputed variables with y = β0Est(Wy) + β1+ ∑i=2,n+1 (βiXi) + ε
All 4 models qualify as PROPER DEf Dv51.5 NoAutocorrelationDv621.1, Dv626.1 -- Dv676.5 -- DvHiGods
Add install R; offer of help; systemfit p4

Kin Avoidance Project

MCMCpack and MCMCregress goodness-of-fit

MCMCregress - NoVA_v626v676v621MCMCregress#MCMCpack_Model_621.1 Equality of Husband and Wife

RUN: Dv621.1 could do up to aa only (imputed variables) but more efficient to run the whole script  
model0 <- MCMCregress(aa$WHe~ aa$bio.13+aa$v1122+aa$v53+aa$v54+aa$v626+aa$v68+aa$v817, b0=0, B0=0.1, c0 =2, d0 =0.11) #, marginal.likelihood = c(Chib95))
model0 <- MCMCregress(aa$WHe~ aa$bio.13+aa$v1122+aa$v53+aa$v54+aa$v626+aa$v68+aa$v817, b0=0, B0=0.1, c0 =2, d0 =0.11) #, marginal.likelihood = c(Chib95))
model1 <- MCMCregress(aa$WHe~ aa$bio.13+aa$v1122+aa$v53+aa$v54+aa$v626+aa$v68        , b0=0, B0=0.1, c0 =2, d0 =0.11) #, marginal.likelihood = c(Chib95))
model2 <- MCMCregress(aa$WHe~ aa$bio.13+aa$v1122+aa$v53+aa$v54+aa$v626       +aa$v817, b0=0, B0=0.1, c0 =2, d0 =0.11) #, marginal.likelihood = c(Chib95))
model3 <- MCMCregress(aa$WHe~ aa$bio.13+aa$v1122+aa$v53+aa$v54        +aa$v68+aa$v817, b0=0, B0=0.1, c0 =2, d0 =0.11) #, marginal.likelihood = c(Chib95))
model4 <- MCMCregress(aa$WHe~ aa$bio.13+aa$v1122+aa$v53       +aa$v626+aa$v68+aa$v817, b0=0, B0=0.1, c0 =2, d0 =0.11) #, marginal.likelihood = c(Chib95))
model5 <- MCMCregress(aa$WHe~ aa$bio.13+aa$v1122       +aa$v54+aa$v626+aa$v68+aa$v817, b0=0, B0=0.1, c0 =2, d0 =0.11) #, marginal.likelihood = c(Chib95))
model6 <- MCMCregress(aa$WHe~ aa$bio.13         +aa$v53+aa$v54+aa$v626+aa$v68+aa$v817, b0=0, B0=0.1, c0 =2, d0 =0.11) #, marginal.likelihood = c(Chib95))
model7 <- MCMCregress(aa$WHe~           aa$v1122+aa$v53+aa$v54+aa$v626+aa$v68+aa$v817, b0=0, B0=0.1, c0 =2, d0 =0.11) #, marginal.likelihood = c(Chib95))
BF <- BayesFactor(model1,model2,model3,model4,model5,model6,model7,       model0) #
summary(BF)  #The evidence to support NA over all other models considered is worth no more than a bare mention.

The thing to do here is

  1. edit the example as in or a finished model at the wiki site with the appropriate dependent and independent variables in the riv<-c(...), and run in your R screen for Dv621.1 or modify to fit the variables of a different model
  2. or use the forthcoming VM with two other options:, run your variables in the CoSSci window for DEf models in the VM, then either
    1. click the option for MCMCregress (assuming Uram's expanded script does the substitutions) or
    2. Assuming Uram's scripts codes keeps the aa matrix of imputed variables in working memory from the VM run: substitute your dependent and independent variables for those of the MCMCregress script above, copy and paste the result into the "execute goodness-of-fit test" VM window. If the test shows that one variable should be dropped, remove that model, renumber the models ordinally starting from 0 (zero) and resubmit the test until not further removal of a variable is suggested by equality of results.


  • I am looking into R code for Bonferroni read off the h[5,4,3] functions or the *.csv (which is better?) and also the MCMCregress goodness-of-fit that pulls out the depvar and the riv. The thing to do here is to put the test on the VM with directive: sort the significance tests in myOutput.csv low to high, copy into VM windowwith directive: sort the significance tests in myOutput.csv low to high, copy into VM window: HOLM-BONFERRONI GROUP SIGNIFICANCE TEST

AAA 2013 Chicago

  • Registered for the AAA next year at Chicago Hilton November 20-24, 2013 due BEFORE April 15, 2013, Doug White and Tolga Oztan. "The Evolutionary Ladders of Kinship Behaviors." Kinship Session "THE KINSHIP PAST and THE FUTURE OF A KINSHIP PUBLIC." organized by Dwight Read and Fadwa El Guindi. 2013 American Anthropological Association Annual Meeting, Chicago.
The 2013 AAA Abstract

How the three basic dimensions in the world's ethnographic formal concept (Galois) lattice of joking, avoidance and respect are organized by a Network of Variable Analysis (NoVA) reproducible at the Complex Social Science (CoSSci)

Pgraph code

  • Pgraph code for Tolga - doesnt exist

For someone starting with DEf

Tom (Weisner), To begin to think about a chapter for the Wiley Companion to Comparative Research, whatever else you do for the chapter, all you need to start with the new inferential methods is a few dependent variable names from the SCCS codebook, listed either at or Tho there are other databases, SCCS has the variables for psychological, child training and other variables related to the Whitings' work. Including results in your chapter that control for autocorrelation as opposed to those that do not is something we want to illustrate for a good number of chapters. If you send me some variable names, I can provide you with some mostly finished models to think about in relation to the arguments you want to make in the chapter. Having your perspectives on psychological anthropology alongside new developments in data analysis is important to the volume.

As a way of presenting an initial draft to an audience that includes other Wiley authors we invite you to develop and present some of your initial ideas for the Wiley chapter at the March meeting of the SASci (Anthro Sciences society) in Albuquerque. If you send me some ideas for initial variables to analyze, I will help get you get started with hypothesis testing. Our social science Gateway for cross-cultural research, with easy access to modeling with autocorrelation controls, is now an official science gateway site at and well suited for classroom use (now underway) and use by social scientists. It takes a bit of getting used to which is why in addition to the current dozen or so users for Wiley chapters (and the initial course being given this quarter), I am helping other Wiley authors get started.

Comments welcome;

-- best Douglas R. White

Neighbor graphs - Omit

  • OMIT Comments79 Towner et al R scripts for Neighbor Graphs: Vertical and Horizontal Transmission