merge master

analysis/plotNumDocumentsByYear.R

@@ -2,10 +2,13 @@ try(setwd("~/Documents/Bristol/CHIELD/CHIELD_Online/analysis//"))
 
 d = read.csv("../data/db/Documents.csv",stringsAsFactors = F)
 
+decades= range(floor(d$year/10)*10)
+
 pdf("../../Graphs/analysis/NumDocumentsByYear.pdf",
     width=6, height=4)
 hist(d$year,
      xlab="Year",
      ylab="Number of documents",
-     main="")
+     main="",
+     breaks=seq(decades[1],decades[2]+10,by=10))
 dev.off()

analysis/variableIncreaseCurve.R

@@ -59,8 +59,7 @@ plot(newdata$numDocuments,
      xlim=range(newdata$numDocuments),
      ylim=c(0,max(predictedCurve)),
      lty=2,col=2)
-abline(0,1,lty=2)
-
+#abline(0,1,lty=2)
 points(1:length(cumUniqueVariables.mean),
        cumUniqueVariables.mean,
      xlab="Number of documents",

app/Site/downloads/CHIELD.bib

@@ -14,6 +14,15 @@ @Article{amano2014global
   pages = {20141574},
   year = {2014},
   publisher = {The Royal Society},
+} @Article{ameel2005bilinguals,
+  title = {How bilinguals solve the naming problem},
+  author = {Eef Ameel and Gert Storms and Barbara C Malt and Steven A Sloman},
+  journal = {Journal of memory and language},
+  volume = {53},
+  number = {1},
+  pages = {60--80},
+  year = {2005},
+  publisher = {Elsevier},
 } @Article{Arbib2008PrimateVG,
   title = {Primate vocalization, gesture, and the evolution of human language.},
   author = {Michael A. Arbib and Katja Liebal and Simone Pika},
@@ -424,6 +433,15 @@ @Article{creanza2017greater
   pages = {20170171},
   year = {2017},
   publisher = {The Royal Society},
+} @Article{crespi2007sly,
+  title = {Sly FOXP2: genomic conflict in the evolution of language},
+  author = {Bernard J Crespi},
+  journal = {Trends in ecology \& evolution},
+  volume = {22},
+  number = {4},
+  pages = {174--175},
+  year = {2007},
+  publisher = {Elsevier},
 } @Article{crespi2017segregating,
   title = {Segregating polymorphisms of FOXP2 are associated with measures of inner speech, speech fluency and strength of handedness in a healthy population},
   author = {Bernard Crespi and Silven Read and Peter Hurd},
@@ -522,7 +540,7 @@ @Article{delancey_2014
   year = {2014},
   volume = {1},
   number = {1},
-  pages = {59-82},
+  pages = {59--82},
 } @Article{demille2018worldwide,
   abstract = {DCDC2 is a gene strongly associated with components of the phonological processing system in animal models and in multiple independent studies of populations and languages. We propose that it may also influence population-level variation in language component usage. To test this hypothesis, we investigated the evolution and worldwide distribution of the READ1 regulatory element within DCDC2, and compared its distribution with variation in different language properties. The mutational history of READ1 was estimated by examining primate and archaic hominin sequences. This identified duplication and expansion events, which created a large number of polymorphic alleles based on internal repeat units (RU1 and RU2). Association of READ1 alleles was studied with respect to the numbers of consonants and vowels for languages in 43 human populations distributed across five continents. Using population-based approaches with multivariate ANCOVA and linear mixed effects analyses, we found that the RU1-1 allele group of READ1 is significantly associated with the number of consonants within languages independent of genetic relatedness, geographic proximity, and language family. We propose that allelic variation in READ1 helped create a subtle cognitive bias that was amplified by cultural transmission, and ultimately shaped consonant use by different populations over time.},
   title = {Worldwide distribution of the DCDC2 READ1 regulatory element and its relationship with phoneme variation across languages},
@@ -743,6 +761,15 @@ @Article{fisher2006eloquent
   pages = {9},
   year = {2006},
   publisher = {Nature Publishing Group},
+} @Article{fisher2009foxp2,
+  title = {FOXP2 as a molecular window into speech and language},
+  author = {Simon E Fisher and Constance Scharff},
+  journal = {Trends in Genetics},
+  volume = {25},
+  number = {4},
+  pages = {166--177},
+  year = {2009},
+  publisher = {Elsevier},
 } @Article{fitch2018animals,
   title = {What animals can teach us about human language: The phonological continuity hypothesis},
   author = {W Tecumseh Fitch},
@@ -934,6 +961,15 @@ @Article{hay2007phoneme
   pages = {388--400},
   year = {2007},
   publisher = {Linguistic Society of America},
+} @Article{hayakawa2016using,
+  title = {Using a foreign language changes our choices},
+  author = {Sayuri Hayakawa and Albert Costa and Alice Foucart and Boaz Keysar},
+  journal = {Trends in Cognitive Sciences},
+  volume = {20},
+  number = {11},
+  pages = {791--793},
+  year = {2016},
+  publisher = {Elsevier},
 } @Article{hayes2009natural,
   title = {Natural and unnatural constraints in Hungarian vowel harmony},
   author = {Bruce Hayes and Péter Siptár and Kie Zuraw and Zsuzsa Londe},
@@ -1038,6 +1074,22 @@ @Article{kashima1998culture
   pages = {461--486},
   year = {1998},
   publisher = {Sage Publications Sage CA: Thousand Oaks, CA},
+} @Article{kashima2014language,
+  title = {Language and culture},
+  author = {Yoshihisa Kashima and Emiko S Kashima and Evan Kidd and {others}},
+  journal = {The Oxford handbook of language and social psychology},
+  pages = {46--51},
+  year = {2014},
+  publisher = {Oxford University Press New York, NY},
+} @Article{kemmelmeier2004language,
+  title = {Language and self-construal priming: A replication and extension in a Hong Kong sample},
+  author = {Markus Kemmelmeier and Belinda Yan-Ming Cheng},
+  journal = {Journal of Cross-Cultural Psychology},
+  volume = {35},
+  number = {6},
+  pages = {705--712},
+  year = {2004},
+  publisher = {Sage Publications Sage CA: Thousand Oaks, CA},
 } @Article{kemp2012kinship,
   title = {Kinship categories across languages reflect general communicative principles},
   author = {Charles Kemp and Terry Regier},
@@ -1099,6 +1151,15 @@ @Article{knight2017wild
   number = {4},
   year = {2017},
   publisher = {University of Chicago Press},
+} @Article{kousta2008investigating,
+  title = {Investigating linguistic relativity through bilingualism: The case of grammatical gender.},
+  author = {Stavroula-Thaleia Kousta and David P Vinson and Gabriella Vigliocco},
+  journal = {Journal of Experimental Psychology: Learning, Memory, and Cognition},
+  volume = {34},
+  number = {4},
+  pages = {843},
+  year = {2008},
+  publisher = {American Psychological Association},
 } @Article{kroll1986lexical,
   title = {Lexical access for concrete and abstract words.},
   author = {Judith F Kroll and Jill S Merves},
@@ -1315,6 +1376,15 @@ @Article{majid2004can
   pages = {108--114},
   year = {2004},
   publisher = {Elsevier},
+} @Article{majid2018differential,
+  title = {Differential coding of perception in the world’s languages},
+  author = {Asifa Majid and Seán G Roberts and Ludy Cilissen and Karen Emmorey and Brenda Nicodemus and Lucinda O’grady and Bencie Woll and Barbara LeLan and Hilário {De Sousa} and Brian L Cansler and Shakila Shayani and Connie {de Vos} and Gunter Senft and N. J. Enfield and Rogayah A. Razak and Sebastian Fedden and Sylvia Tufvesson and Mark Dingemanse and Ozge Ozturk and Penelope Brown and Clair Hill and Olivier Le Guen and Vincent Hirtzel and Rik {van Gijn} and Mark A. Sicoli and Stephen C. Levinson},
+  journal = {Proceedings of the National Academy of Sciences},
+  volume = {115},
+  number = {45},
+  pages = {11369--11376},
+  year = {2018},
+  publisher = {National Acad Sciences},
 } @Article{Marck1986,
   author = {Jeffrey C. Marck},
   journal = {Journal of the Polynesian Society},
@@ -1410,7 +1480,7 @@ @Article{monaghan2019cognitive
   date-added = {2019-02-18 11:06:51 +0000},
   date-modified = {2019-02-18 11:07:58 +0000},
   journal = {Cognition},
-  pages = {147-158},
+  pages = {147--158},
   title = {Cognitive influences in language evolution: Psycholinguistic predictors of loan word borrowing},
   volume = {186},
   year = {2019},
@@ -1538,6 +1608,18 @@ @Article{onnis2018language
   pages = {132--146},
   year = {2018},
   publisher = {Elsevier},
+} @Article{Pacheco_Coelho_2019,
+  doi = {10.1098/rspb.2019.0242},
+  url = {https://doi.org/10.1098%2Frspb.2019.0242},
+  year = {2019},
+  month = {mar},
+  publisher = {The Royal Society},
+  volume = {286},
+  number = {1899},
+  pages = {20190242},
+  author = {Marco Túlio Pacheco Coelho and Elisa Barreto Pereira and Hannah J. Haynie and Thiago F. Rangel and Patrick Kavanagh and Kathryn R. Kirby and Simon J. Greenhill and Claire Bowern and Russell D. Gray and Robert K. Colwell and Nicholas Evans and Michael C. Gavin},
+  title = {Drivers of geographical patterns of North American language diversity},
+  journal = {Proceedings of the Royal Society B: Biological Sciences},
 } @Article{pagel2013ultraconserved,
   title = {Ultraconserved words point to deep language ancestry across Eurasia},
   author = {Mark Pagel and Quentin D Atkinson and Andreea S Calude and Andrew Meade},
@@ -1585,6 +1667,15 @@ @Article{pederson1998semantic
   pages = {557--589},
   year = {1998},
   publisher = {Linguistic Society of America},
+} @Article{perez2009lost,
+  title = {Lost in translation? Item validity in bilingual political surveys},
+  author = {Efrén O Pérez},
+  journal = {The Journal of politics},
+  volume = {71},
+  number = {4},
+  pages = {1530--1548},
+  year = {2009},
+  publisher = {Cambridge University Press New York, USA},
 } @Article{perez2017language,
   title = {Language Shapes People's Time Perspective and Support for Future-Oriented Policies},
   author = {Efrén O Pérez and Margit Tavits},
@@ -1900,6 +1991,15 @@ @Article{sterelny2014paleolithic
   pages = {65--77},
   year = {2014},
   publisher = {Springer},
+} @Article{sterelny2016cumulative,
+  title = {Cumulative cultural evolution and the origins of language},
+  author = {Kim Sterelny},
+  journal = {Biological Theory},
+  volume = {11},
+  number = {3},
+  pages = {173--186},
+  year = {2016},
+  publisher = {Springer},
 } @Article{szamado2006selective,
   title = {Selective Scenarios for the Emergence of Natural Language},
   volume = {21},
@@ -2264,6 +2364,17 @@ @InBook{gentner1982nouns
   title = {Why Nouns are Learned Before Verbs: Linguistic Relativity versus Natural Partitioning},
   volume = {Language development: Language, thought and Culture},
   year = {1982},
+} @InBook{ross1996contact,
+  author = {Malcolm D Ross},
+  chapter = {8},
+  date-added = {2019-03-28 12:17:02 +0000},
+  date-modified = {2019-03-28 12:18:55 +0000},
+  editor = {Mark Durie and Malcolm D Ross},
+  pages = {180},
+  publisher = {Oxford University Press on Demand},
+  title = {Contact-induced Change and the Comparative},
+  volume = {The comparative method reviewed: Regularity and irregularity in language change},
+  year = {1996},
 } @InBook{van2005language,
   author = {George Van Driem},
   chapter = {9},
@@ -2473,6 +2584,15 @@ @InProceedings{cangelosi01howNouns
   url = {http://www.isrl.uiuc.edu/~amag/langev/paper/cangelosi01howNouns.html},
   year = {2001},
   bdsk-url-1 = {http://www.isrl.uiuc.edu/~amag/langev/paper/cangelosi01howNouns.html},
+} @InProceedings{crawford08,
+  author = {Clifford Crawford},
+  title = {An evolutionary account of loanword-induced sound change in {J}apanese},
+  booktitle = {Proceedings of the 31st Annual {P}enn {L}inguistics {C}olloquium},
+  year = {2008},
+  volume = {14},
+  number = {1},
+  series = {University of {P}ennsylvania Working Papers in Linguistics},
+  pages = {57-70},
 } @InProceedings{demolin2018acoustic,
   author = {Didier Demolin},
   booktitle = {The Evolution of Language: Proceedings of the 12th International Conference (EVOLANGXII)},

app/Site/js/visualisation/GUI_for_explore.js

@@ -72,27 +72,29 @@ function updateRecord(response,type){
 }
 
 function updateGridFromNetwork(){
-		var edges = network_edges.get();
+	var edges = network_edges.get();
 	var rows = [];
 
 	for(var i=0;i<edges.length;++i){
 		var edge = edges[i];
-		var newRow = [
-			null,
-			network_nodes.get(edge.from).label,
-			edge.causal_relation,
-			network_nodes.get(edge.to).label,
-			edge.cor,
-			edge.stage,
-			edge.studyType,
-			//'<a href="document.html?key='+ edge.bibref +'">' + edge.citation + "</a>",
-			//null,
-			//null
-			edge.citation,
-			edge.bibref,
-			edge.confirmed // Confirmed
-		];
-		rows.push(newRow);
+		if((network_nodes.get(edge.from)!=null) && (network_nodes.get(edge.to)!=null)){
+			var newRow = [
+				null,
+				network_nodes.get(edge.from).label,
+				edge.causal_relation,
+				network_nodes.get(edge.to).label,
+				edge.cor,
+				edge.stage,
+				edge.studyType,
+				//'<a href="document.html?key='+ edge.bibref +'">' + edge.citation + "</a>",
+				//null,
+				//null
+				edge.citation,
+				edge.bibref,
+				edge.confirmed // Confirmed
+			];
+			rows.push(newRow);
+		}
 	}
 	dtable.clear();
 	dtable.rows.add(rows);
@@ -176,16 +178,17 @@ function getMeanNodePositions(){
 }
 
 function removeVariableViaNetwork(){
-	var n = network.getSelectedNodes();
-	for(var i=0;i<n.length;++i){
-		removeVar(n,false);
-	}
+	network.deleteSelected();
+	//var n = network.getSelectedNodes();
+	//for(var i=0;i<n.length;++i){
+	//	removeVar(n,false);
+	//}
 	// Also remove any edges:
 	// (selecting a variable will select all connected edges, 
 	//	which should be deleted above, but edges may be selected
 	//  in addition)
-	var selectedEdges = network.getSelectedEdges();
-	network_edges.remove(selectedEdges);
+	//var selectedEdges = network.getSelectedEdges();
+	//network_edges.remove(selectedEdges);
 	updateGridFromNetwork();
 }
 

app/Site/js/visualisation/exportToDot.js

@@ -1,7 +1,7 @@
 var dotEdgeTypes = {
 		">": 'arrowhead="normal",arrowtail="none"',
-		"<=>": 'arrowhead="normal",arrowtail="normal"',
-		"<": 'arrowhead="none",arrowtail="normal"',
+		"<=>": 'dir="both"',
+		"<": 'arrowhead="none",dir="back"',
 		"~": 'arrowhead="none",arrowtail="none",style="dashed"',
 		"/>":'arrowhead="tee",arrowtail="none"',
 		"/=":'arrowhead="tee",arrowtail="none"',