All data files now uploaded

Meta-Paleo · Aug 2, 2019 · e3f9888e2828cbbcb2d17ab462987a5a0647d09c · e3f9888
1 parent f5c030a
commit e3f9888e2828cbbcb2d17ab462987a5a0647d09c
diff --git a/README.md b/README.md
@@ -1,34 +1,50 @@
 # TetraTime
 Project to map growth of tetrapod clades through time
+  
+Potential title: Tracking the growth of the fossil record
+  
+
 This has already been done for [dinosaurs](https://peerj.com/articles/4417/) - now let's see what happens if we examine this for all tetrapod clades! 
+  
+Key research questions:
+  
+
 1. Do all clades show the same growth patterns?
 2. Are any clades 'stable'?
 3. What implications does this have on their diversity/extinction patterns?
 4. What is the structure of growth in terms of geography?
 Data sources: [Fossilworks](http://fossilworks.org/bridge.pl?user=Guest&action=displayDownloadForm)
-  
-Notes on data selction:
+  
+Notes on data selection:
 * Restricted to Mesozoic groups as the data are most complete
 * Downloaded occurences from [here](http://fossilworks.org/bridge.pl?user=Guest&action=displayDownloadForm) using the 'full form' option
 * Basic options: Set taxonomic level to species; set time span as 'Mesozoic'
 * Included collections: Keep all default options set
 * Included occurrences: Remove ichnofossils and form taxa; keep all other default options set
 * Colletion fields: basic fields, check all; geography fields, check all; time fields, check all; stratigraphy fields, check all; lithology fields, check all; no taphonomy or collection methods required
 * Occurence fields: check ocurence no, reference no, year published, taxon no, type specimen, type locality
-  
-
+  
+* Date downloaded: 02/08/2019
 Groups:
 * Dinosauria (minus Aves)
 * Aves
 * Testudinata
 * Choristodera
 * Crocodyliformes
-  
-* Ichythyosauria
+  
+* Ichythyopterygia
 * Lepidosauromorpha
 * Lissamphibia
 * Mammaliaformes
 * Pterosauria
 * Sauropterygia
+  
+
+  
+Major data contributors:
+  
+Matthew Carrano
+  
+John Alroy
+  
+Philip Mannion
+  
+Roger Benson
+  
+
+  
+Visualisation ideas:
+  
+
+  
+* Create a gif/video/dynamic figure showing how, for each clade, diversity patterns have changed through publication history.
+  
+
+  
+* Create a gif/video/dynamic figure showing how, for each clade, the geographic distribution/discovery has changed through publication history 
diff --git a/data/choristodera-refs.csv b/data/choristodera-refs.csv
diff --git a/data/crocodyliformes-occs.csv b/data/crocodyliformes-occs.csv
diff --git a/data/crocodyliformes-ranges.csv b/data/crocodyliformes-ranges.csv
diff --git a/data/crocodyliformes-refs.csv b/data/crocodyliformes-refs.csv
diff --git a/data/ichthyopterygia-occs.csv b/data/ichthyopterygia-occs.csv
diff --git a/data/ichthyopterygia-ranges.csv b/data/ichthyopterygia-ranges.csv
@@ -0,0 +1,210 @@
+  
+genus,species,"base of range (Ma)","top of range (Ma)",collections,"with abundances","geometric mean abundance"
+  
+Acamptonectes,densus,136.400,130.000,3,0,NaN
+  
+Aegirosaurus,leptospondylus,150.800,145.500,2,2,1.0000
+  
+Aegirosaurus,sp.,140.200,136.400,1,1,1.0000
+  
+Ancanamunia,sp.,161.200,145.500,1,1,1.0000
+  
+Apatodonosaurus,grayi,161.200,155.700,1,1,1.0000
+  
+Arthropterygius,chrisorum,161.200,150.800,2,2,1.0000
+  
+Arthropterygius,sp.,150.800,145.500,2,1,1.0000
+  
+Athabascasaurus,bitumineus,112.600,109.000,1,1,1.0000
+  
+Baptanodon,discus,161.200,155.700,2,1,1.0000
+  
+Baptanodon,reedi,164.700,155.700,1,1,1.0000
+  
+Baptanodon,robustus,167.700,155.700,1,1,1.0000
+  
+Barracudasauroides,panxianensis,247.200,242.000,8,0,NaN
+  
+Barracudasaurus,maotaiensis,247.200,242.000,2,2,1.0000
+  
+Besanosaurus,leptorhynchus,247.200,235.000,1,0,NaN
+  
+Brachypterygius,extremus,155.700,145.500,3,2,1.0000
+  
+Brachypterygius,pseudoscythicus,150.800,145.500,1,1,1.0000
+  
+Brachypterygius,sp.,150.800,145.500,1,0,NaN
+  
+Brachypterygius,zhuravlevi,150.800,145.500,1,0,NaN
+  
+Californosaurus,perrini,235.000,221.500,1,0,NaN
+  
+Californosaurus,sp.,235.000,221.500,1,0,NaN
+  
+Callawayia,neoscapularis,221.500,205.600,1,0,NaN
+  
+Callawayia,sp.,215.560,212.000,1,0,NaN
+  
+Callawayia,wolonggangense,235.000,221.500,1,0,NaN
+  
+Caypullisaurus,bonapartei,150.800,140.200,3,0,NaN
+  
+Cetarthrosaurus,walkeri,105.300,99.700,1,1,0.0241
+  
+Chacaicosaurus,cayi,171.600,168.400,1,0,NaN
+  
+Chaohusaurus,chaoxianensis,251.300,247.200,1,1,1.0000
+  
+Chaohusaurus,geishanensis,251.300,247.200,5,2,1.0000
+  
+Chaohusaurus,sp.,251.300,247.200,1,1,1.0000
+  
+Chaohusaurus,zhangjiawanensis,247.200,235.000,1,0,NaN
+  
+Chonespondylus,grandis,252.300,201.600,1,1,0.2500
+  
+Contectopalatus,sp.,247.200,235.000,1,0,NaN
+  
+Cryopterygius,kielanae,150.800,145.500,1,1,1.0000
+  
+Cryopterygius,kristiansenae,150.800,145.500,1,1,1.0000
+  
+Cymbospondylus,buchseri,247.200,242.000,1,1,1.0000
+  
+Cymbospondylus,natans,247.200,235.000,1,1,0.0833
+  
+Cymbospondylus,nevadanus,247.200,242.000,1,1,1.0000
+  
+Cymbospondylus,nichollsi,247.200,242.000,1,0,NaN
+  
+Cymbospondylus,petrinus,247.200,235.000,3,3,0.5000
+  
+Cymbospondylus,piscosus,247.200,242.000,1,0,NaN
+  
+Cymbospondylus,sp.,251.300,235.000,6,5,0.6988
+  
+Dearcmhara,shawcrossi,183.000,168.400,1,1,1.0000
+  
+Eurhinosaurus,longirostris,201.600,182.000,2,0,NaN
+  
+Eurhinosaurus,sp.,183.000,182.000,1,0,NaN
+  
+Excalibosaurus,costini,196.500,189.600,2,0,NaN
+  
+Gengasaurus,nicosiai,155.700,145.500,1,1,1.0000
+  
+Grippia,longirostris,251.300,247.200,3,1,1.0000
+  
+Guanlingsaurus,liangae,232.000,221.500,2,0,NaN
+  
+Guizhouichthyosaurus,sp.,242.000,235.000,2,0,NaN
+  
+Guizhouichthyosaurus,tangae,232.000,221.500,4,2,1.0000
+  
+Gulosaurus,helmi,251.300,247.200,1,1,1.0000
+  
+Hauffiopteryx,typicus,183.000,182.000,1,1,0.6000
+  
+Himalayasaurus,tibetensis,215.560,212.000,1,0,NaN
+  
+Hudsonelpidia,brevirostris,235.000,201.600,1,0,NaN
+  
+Hudsonelpidia,sp.,221.500,205.600,1,0,NaN
+  
+Ichthyosaurus,acutirostris,183.000,182.000,2,0,NaN
+  
+Ichthyosaurus,anningae,189.600,183.000,1,1,1.0000
+  
+Ichthyosaurus,breviceps,196.500,189.600,2,1,0.4615
+  
+Ichthyosaurus,brunsvicensis,145.500,130.000,1,0,NaN
+  
+Ichthyosaurus,californicus,189.600,94.300,1,1,1.0000
+  
+Ichthyosaurus,carinatus,205.600,201.600,1,1,1.0000
+  
+Ichthyosaurus,chiroligostinus,201.600,196.500,1,1,1.0000
+  
+Ichthyosaurus,comminis,201.600,183.000,1,0,NaN
+  
+Ichthyosaurus,communis,201.600,183.000,19,9,0.5646
+  
+Ichthyosaurus,conununis,201.600,196.500,1,1,1.0000
+  
+Ichthyosaurus,conybeari,196.500,189.600,1,1,0.1538
+  
+Ichthyosaurus,costatus,205.600,201.600,1,0,NaN
+  
+Ichthyosaurus,dilatatus,164.700,155.700,3,2,1.0000
+  
+Ichthyosaurus,entheciodon,150.800,145.500,1,1,0.5000
+  
+Ichthyosaurus,enthekiodon,155.700,150.800,1,0,NaN
+  
+Ichthyosaurus,franciscanus,189.600,94.300,1,1,1.0000
+  
+Ichthyosaurus,larkini,201.600,196.500,2,2,0.2462
+  
+Ichthyosaurus,longipes,183.000,182.000,1,0,NaN
+  
+Ichthyosaurus,platyodon,201.600,189.600,2,1,1.0000
+  
+Ichthyosaurus,polyptychodon,136.400,130.000,1,1,1.0000
+  
+Ichthyosaurus,quenstedti,164.700,161.200,1,0,NaN
+  
+Ichthyosaurus,rhaeticus,205.600,201.600,1,1,1.0000
+  
+Ichthyosaurus,rheticus,205.600,201.600,3,2,1.0000
+  
+Ichthyosaurus,somersetensis,201.600,196.500,1,1,0.2727
+  
+Ichthyosaurus,sp.,221.500,112.600,31,4,1.0000
+  
+Ichthyosaurus,steleodon,136.400,130.000,1,1,1.0000
+  
+Ichthyosaurus,tenuirostris,201.600,196.500,7,4,0.6389
+  
+Ichthyosaurus,thyreospondylus,150.800,145.500,2,1,0.5000
+  
+Ichthyosaurus,trigonus,150.800,145.500,2,0,NaN
+  
+Isfjordosaurus,minor,251.300,247.200,1,0,NaN
+  
+Janusaurus,lundi,150.800,145.500,1,1,1.0000
+  
+Keilhauia,nui,145.500,140.200,1,1,1.0000
+  
+Khudiakovia,calloviensis,164.700,161.200,1,0,NaN
+  
+Leninia,stellans,125.450,122.460,1,1,1.0000
+  
+Leptonectes,acutirostris,183.000,182.000,4,0,NaN
+  
+Leptonectes,disinteger,183.000,182.000,1,0,NaN
+  
+Leptonectes,moorei,189.600,183.000,1,0,NaN
+  
+Leptonectes,solei,196.500,189.600,2,2,1.0000
+  
+Leptonectes,sp.,205.600,201.600,1,0,NaN
+  
+Leptonectes,tenuirostris,201.600,183.000,7,4,0.9036
+  
+Macgowania,janiceps,221.500,205.600,1,0,NaN
+  
+Macgowania,sp.,215.560,212.000,1,0,NaN
+  
+Macropterygius,sp.,150.800,145.500,1,0,NaN
+  
+Maiaspondylus,lindoei,112.600,99.700,1,1,1.0000
+  
+Malawania,anachronus,136.400,125.450,1,0,NaN
+  
+Merriamosaurus,hulkei,251.300,247.200,1,0,NaN
+  
+Metashastasaurus,neoscapularis,221.500,205.600,2,0,NaN
+  
+Mikadocephalus,gracilirostris,242.000,235.000,1,0,NaN
+  
+Mikadocephalus,sp.,247.200,235.000,1,0,NaN
+  
+Mixosaurus,cornalianus,247.200,242.000,2,0,NaN
+  
+Mixosaurus,kuhnschnyderi,247.200,242.000,1,0,NaN
+  
+Mixosaurus,natans,247.200,242.000,1,1,1.0000
+  
+Mixosaurus,sp.,247.200,235.000,5,2,1.0000
+  
+Mixosaurus,xindianensis,247.200,242.000,1,0,NaN
+  
+Mollesaurus,periallus,171.600,168.400,1,1,1.0000
+  
+Mollesaurus,perihallus,171.600,168.400,1,0,NaN
+  
+Muiscasaurus,catheti,130.000,112.600,1,1,1.0000
+  
+Nannopterygius,enthekiodo,155.700,150.800,1,0,NaN
+  
+Omphalosaurus,merriami,252.300,247.200,1,0,NaN
+  
+Omphalosaurus,nettarhynchus,251.300,247.200,1,0,NaN
+  
+Omphalosaurus,nevadanus,247.200,235.000,1,1,0.0556
+  
+Omphalosaurus,sp.,247.200,235.000,2,1,1.0000
+  
+Omphalosaurus,wolfi,242.000,235.000,1,0,NaN
+  
+Ophthalmosaurus,cuvieri,155.700,150.800,1,1,1.0000
+  
+Ophthalmosaurus,icenicus,164.700,145.500,6,3,1.0000
+  
+Ophthalmosaurus,monocharactus,164.700,145.500,2,0,NaN
+  
+Ophthalmosaurus,natans,161.200,155.700,2,0,NaN
+  
+Ophthalmosaurus,sp.,201.600,136.400,12,5,1.0000
+  
+Ophthalmosaurus,undorensis,155.700,150.800,1,1,1.0000
+  
+Ophthalmosaurus,yasykovi,150.800,145.500,1,1,1.0000
+  
+Palvennia,hoybergeti,150.800,145.500,1,1,1.0000
+  
+Paraophthalmosaurus,saratoviensis,150.800,145.500,1,0,NaN
+  
+Paraophthalmosaurus,saveljeviensis,150.800,145.500,1,1,1.0000
+  
+Parvinatator,wapitiensis,251.300,235.000,1,0,NaN
+  
+Pervushovisaurus,bannovkensis,99.700,94.300,1,1,1.0000
+  
+Pessopteryx,nisseri,251.300,242.000,2,0,NaN
+  
+Pessosaurus,polaris,251.300,247.200,1,0,NaN
+  
+Phalarodon,atavus,247.200,242.000,4,4,0.5000
+  
+Phalarodon,callawayi,247.200,242.000,1,0,NaN
+  
+Phalarodon,fraasi,251.300,242.000,3,2,0.1667
+  
+Phalarodon,major,247.200,242.000,1,0,NaN
+  
+Phalarodon,nordenskioeldii,251.300,235.000,3,0,NaN
+  
+Phantomosaurus,neubigi,247.200,242.000,1,0,NaN
+  
+Platypterygius,americanus,105.300,94.300,4,3,1.0000
+  
+Platypterygius,australis,105.300,99.700,15,2,1.0000
+  
+Platypterygius,bedengensis,136.400,130.000,1,1,1.0000
+  
+Platypterygius,campylodon,112.600,94.300,10,1,1.0000
+  
+Platypterygius,hauthali,140.200,125.450,3,1,1.0000
+  
+Platypterygius,hercynicus,122.460,99.700,3,2,0.5000
+  
+Platypterygius,kiprijanoffi,99.700,94.300,1,0,NaN
+  
+Platypterygius,ochevi,112.600,94.300,1,0,NaN
+  
+Platypterygius,platydactylus,125.450,122.460,1,0,NaN
+  
+Platypterygius,sachicarum,125.450,122.460,1,0,NaN
+  
+Platypterygius,sp.,136.400,94.300,20,4,0.7050
+  
+Protoichthyosaurus,prosostealis,201.600,196.500,1,1,0.0909
+  
+Protoichthyosaurus,prostaxalis,201.600,196.500,2,2,0.3482
+  
+Qianichthyosaurus,sp.,242.000,235.000,2,0,NaN
+  
+Qianichthyosaurus,xingyiensis,242.000,235.000,1,0,NaN
+  
+Qianichthyosaurus,zhoui,232.000,221.500,3,1,1.0000
+  
+Quasianosteosaurus,vikinghoegdai,251.300,247.200,1,0,NaN
+  
+Shastasaurus,alexandrae,252.300,201.600,1,0,NaN
+  
+Shastasaurus,careyi,235.000,205.600,1,0,NaN
+  
+Shastasaurus,pacificus,235.000,205.600,5,1,1.0000
+  
+Shastasaurus,sp.,242.000,221.500,2,1,1.0000
+  
+Shonisaurus,mulleri,221.500,215.560,1,0,NaN
+  
+Shonisaurus,popularis,232.000,215.560,2,2,1.0000
+  
+Shonisaurus,sikanniensis,215.560,212.000,1,0,NaN
+  
+Shonisaurus,silberlingi,221.500,215.560,1,0,NaN
+  
+Simbirskiasaurus,birjukovi,130.000,125.450,1,1,1.0000
+  
+Sisteronia,seeleyi,109.000,94.300,6,3,0.6223
+  
+Sphaerodontes,caroli,161.200,155.700,1,0,NaN
+  
+Stenopterygius,aaleniensis,175.600,171.600,1,1,1.0000
+  
+Stenopterygius,cuneiceps,183.000,182.000,3,0,NaN
+  
+Stenopterygius,eos,183.000,182.000,2,0,NaN
+  
+Stenopterygius,grandis,171.600,168.400,1,0,NaN
+  
+Stenopterygius,hauffianus,183.000,171.600,8,1,1.0000
+  
+Stenopterygius,incessus,183.000,182.000,2,0,NaN
+  
+Stenopterygius,intercedens,183.000,182.000,1,0,NaN
+  
+Stenopterygius,longifrons,183.000,182.000,3,0,NaN
+  
+Stenopterygius,macrophasma,183.000,182.000,1,0,NaN
+  
+Stenopterygius,megacephalus,183.000,182.000,4,0,NaN
+  
+Stenopterygius,megalorhinus,183.000,182.000,5,0,NaN
+  
+Stenopterygius,promegacephalus,183.000,182.000,1,0,NaN
+  
+Stenopterygius,quadriscissus,183.000,182.000,5,1,1.0000
+  
+Stenopterygius,sp.,183.000,171.600,8,1,1.0000
+  
+Stenopterygius,triscissus,183.000,182.000,2,1,0.4000
+  
+Stenopterygius,uniter,183.000,182.000,1,0,NaN
+  
+Suevoleviathan,disinteger,183.000,182.000,1,1,0.5000
+  
+Suevoleviathan,integer,183.000,175.600,3,3,0.7937
+  
+Suevoleviathan,sp.,183.000,182.000,2,1,1.0000
+  
+Sveltonectes,insolitus,130.000,125.450,1,1,1.0000
+  
+Temnodontosaurus,azerguensis,182.000,175.600,1,1,1.0000
+  
+Temnodontosaurus,burgundiae,201.600,175.600,1,0,NaN
+  
+Temnodontosaurus,crassimanus,183.000,175.600,1,0,NaN
+  
+Temnodontosaurus,eurycephalus,196.500,189.600,1,0,NaN
+  
+Temnodontosaurus,longirostris,201.600,175.600,3,0,NaN
+  
+Temnodontosaurus,nuertingensis,189.600,183.000,1,1,1.0000
+  
+Temnodontosaurus,platyodon,196.500,189.600,3,3,1.0000
+  
+Temnodontosaurus,sp.,201.600,175.600,2,2,1.0000
+  
+Temnodontosaurus,trigonodon,183.000,182.000,2,2,1.0000
+  
+Thaisaurus,chonglakmanii,252.300,247.200,1,0,NaN
+  
+Thalattoarchon,saurophagis,247.200,242.000,1,1,1.0000
+  
+Tholodus,schmidi,247.200,242.000,4,1,0.2500
+  
+Toretocnemus,californicus,235.000,221.500,2,0,NaN
+  
+Toretocnemus,zitteli,252.300,201.600,1,0,NaN
+  
+Undorosaurus,gorodischensis,150.800,145.500,2,2,1.0000
+  
+Undorosaurus,khorlovensis,161.200,145.500,2,2,1.0000
+  
+Undorosaurus,nessovi,161.200,145.500,1,1,1.0000
+  
+Undorosaurus,trautscholdi,150.800,145.500,1,1,1.0000
+  
+Utatsusaurus,hataii,251.300,247.200,2,0,NaN
+  
+Utatsusaurus,sp.,251.300,247.200,3,0,NaN
+  
+Wahlisaurus,massarae,201.600,196.500,1,1,1.0000
+  
+Wimanius,odontopalatus,247.200,235.000,1,0,NaN
+  
+Xinminosaurus,catactes,247.200,242.000,1,1,1.0000