R/RaiaCopesRule.R

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

#' Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
#' 
#' Dated phylogenetic trees for fossil ammonite genera, fossil ceratopsian species and (both extinct and extant) cervid
#' species, as well as trait data (shell diameter and fractal complexity of the first suture) for the ammonite dataset,
#' taken from the recent publication by Raia et al. (2015) in The American Naturalist. The goal of this paper was to
#' examine the relationship between ornamental complexity and body size in three very different groups, but
#' the datasets are very relatively large and useful for demonstrating application of comparative methods to fossil trees.
#' 

#' @name RaiaCopesRule

#' @rdname RaiaCopesRule

#' @aliases RaiaCopesRule ceratopsianTreeRaia cervidTreeRaia ammoniteTreeRaia sutureComplexity shellSize ammoniteTraitsRaia

#' @details
#' It appears that the trees were dated with tips at the last appearances, although this doesn't appear to be
#' explicitly stated in Raia et al.

#' @format 
#' The attached datasets consist of three phylogenetic trees as \code{phylo} objects, a \code{data.frame} consisting of
#' three traits for ammonites (the third trait is the log of stratigraphic duration), and the two physical traits (shell
#' size and suture complexity) as separate vectors, with taxon names.
#' 

#' @source 
#' These datasets were taken from the following study:
#' Raia, P., F. Passaro, F. Carotenuto, L. Maiorino, P. Piras, L. Teresi, S. Meiri,
#' Y. Itescu, M. Novosolov, M. A. Baiano, R. Martinez, and M. Fortelius. 2015. Cope's
#' Rule and the Universal Scaling Law of Ornament Complexity. \emph{The American Naturalist}.
#' 186(2):165-175.
#' 
#' And the corresponding Dryad repository:
#' Raia P, Passaro F, Carotenuto F, Maiorino L, Piras P, Teresi L, Meiri S, Itescu Y, Novosolov
#' M, Baiano MA, Martinez R, Fortelius M (2015) Data from: Cope's rule and the universal
#' scaling law of ornament complexity. \emph{Dryad Digital Repository}. 
#' (\doi{10.5061/dryad.50dr8})
#' 

#' @seealso
#' \code{\link{retiolitinae}}, \code{\link{macroperforateForam}}

#' @keywords datasets

#' @docType data

#' @examples
#' data(RaiaCopesRule)
#' 
#' # plotting trees
#' plot(ladderize(ammoniteTreeRaia));axisPhylo()
#' 
#' plot(ceratopsianTreeRaia);axisPhylo()
#' 
#' plot(cervidTreeRaia);axisPhylo()
#' 
#' # plotting traitgrams for ammonites
#' plotTraitgram(tree = multi2di(ammoniteTreeRaia), trait = sutureComplexity,
#' 	 conf.int = FALSE, main = "Ammonite Suture Complexity")
#' 
#' plotTraitgram(tree = multi2di(ammoniteTreeRaia), trait = shellSize,
#' 	 conf.int = FALSE, main = "Ammonite Shell Diameter")
#' 
#' ##############################################################################################
#' 
#' # The data set was generated by sourcing the following script:
#' 	 
#' \donttest{
#' 
#' library(paleotree)
#' 
#' # Let's read in the trees from Raia et al 2015, AmNat
#' 	# following is taken from their supplemental appendix, available at AmNat
#' # they all appear to be trees dated to the last appearance times
#' 	# *and* specifically the end-boundary of the interval containing the last appearance
#' 
#' #########################################
#' # ammonite genera
#' 
#' ammoniteTreeRaia <- paste0("(((((Araxoceras:4,Eoaraxoceras:4)Araxoceratidae:26.5,Pseudasp",
#'  "idites:33.199997,Dieneroceras:37.300003,(Tardicolumbites:13.000015,Cowboyiceras:13.000023)",
#'  "Dinaritaceae:24.299988,Grambergia:42.5,(Amphipopanoceras:6, Megaphyllites:46.399994)Megaph",
#'  "yllitaceae:36.5,(Proteusites:11,Nathorstites:21)Nathorstitaceae:31.5,(Inyoites:7,Lanceolit",
#'  "es:7,Parussuria:7)Noritaceae:30.300003,(((Placites:66.700012,((Acrochordiceras:10.199997, ",
#'  "Bradyia:10.199997,Globacrochordiceras:5,Paracrochordiceras:10.199997)Acrochordiceratidae:9",
#'  ".000015,Balatonites:19.200012,(Favreticeras:10,Guexites:10,Gymnotoceras:10)Beyrichitidae:9",
#'  ".200012, Eogymnotoceras:19.200012,Goricanites:14.000015)Ceratitaceae:7.100006)clade_16:7.0",
#'  "99976, (((Gaudemerites:13.000015,(Owenites:9.000015,Prosphingites:9.000015)Paranannitidae:",
#'  "4,Meekoceras:13.000015, Arctoceras:13.000015)Meekoceratoidea:5.06665,(((Riedelites:85.6000",
#'  "06,((((Berriasella:15.399994, (Polyptychites:20.399994,Surites:14)Polyptychitidae:1.399994",
#'  ")clade_32:1.400002,Bodrakiceras:20.300003, Busnardoites:16.800003,Campylotoxia:20.300003,K",
#'  "arakaschiceras:23.199997,Luppovella:16.800003,Malbosiceras:13, Pomeliceras:13.399994)Neoco",
#'  "mitidae:21.199997,(Otohoplites:8.199997,Sonneratia:4.5,Anadesmoceras:4.5, Anahoplites:20,A",
#'  "rcthoplites:8.199997,Cleoniceras:8.199997,Dimorphoplites:8.199997,Epihoplites:20, Gastropl",
#'  "ites:13.900002,Grycia:13.900002,Hoplites:13.900002)Hoplitidae:60.899994)clade_29:20.200005",
#'  ", (Engonoceras:20.400002,(Knemiceras:16.400002,Parengonoceras:7,Platiknemiceras:7)Knemicer",
#'  "atidae:4) Engonoceratoidea:74.600006,(((Glochiceras:11,(Aconeceras:36.799995,Falciferella:3",
#'  "5.899994,Protaconeceras:7, Sanmartinoceras:24.369995)Oppeliidae:25.400009)Haplocerataceae:",
#'  "15.775009,(((Mortoniceras:16.300003, Oxytropidoceras:14)Brancoceratidae:27.633331,((Parado",
#'  "lphia:12.700005,Stoliczkaia:18.800003,Tegoceras:7) Lyelliceratidae:7.566666,((Borissiakoce",
#'  "ras:10.5,Mammites:7,Mantelliceras:12.800003)Acanthoceratidae:11.783333, (Neoptychites:6,Va",
#'  "scoceras:6)Vascoceratidae:12.783333)clade_49:11.783333)clade_47:7.566666)clade_45:7.566666",
#'  ", (Epileymeriella:5,Leymeriella:11.099998)Leymeriellidae:30.400002,(Beudanticeras:44.03332",
#'  "5, Burckhardtites:21.303329,(Barremites:1.666672,Desmoceras:48.166672)clade_55:1.666656, P",
#'  "seudohaploceras:21.303329,Pseudosaynella:21.303329,Pseudosilesites:21.303329,(Puzosia:56.6",
#'  "50002, (Forbesiceras:27.666664,(Melchiorites:6.083328,Uhligella:15.48333)clade_58:6.083336",
#'  ")clade_57:6.083336) clade_56:6.083328,Valdedorsella:33.633331,Zuercherella:33.73333)Desmoc",
#'  "eratidae:1.666667) Acanthocerataceae:42.575012)clade_39:15.774994,((Coroniceras:1.25,(Mega",
#'  "tyloceras:76.203336, (Zugodactylites:10.016663,Amaltheus:2.616669)Eoderocerataceae:2.61666",
#'  "9)clade_61:2.616669)clade_60:1.25, Oxynoticeras:9.100006)Psilocerataceae:1.25)clade_38:1.2",
#'  "5)Ammonitina:4,((Saghalinites:14,Tetragonites:14) Tetragonitidae:22,(Eogaudryceras:4,Gaudr",
#'  "yceras:32,Zelandites:32)Gaudryceratidae:4)Tetragonitoidea:97.100006, (Costidiscus:12.00000",
#'  "8,Macroscaphites:34.860008)Macroscaphitidae:64.139999)Ammonitida:30.222214, (Ammonitoceras",
#'  ":98.570007,Argonauticeras:98.570007,Audaxlytoceras:27.600006,Holcolytoceras:21, (Eulytocer",
#'  "as:65.713333,Jaubertella:78.043335)clade_84:32.85667,(Ectocentrites:9.433334,(Adnethiceras",
#'  ":8.166656, Galaticeras:14.766663)clade_87:8.166672,((Protetragonites:56.933334,Lytoceras:5",
#'  "0.833336)clade_89:50.833344, Pleuroacanthites:4.666672)clade_88:4.666656)Pleuroacanthitida",
#'  "e:4.666667,Pterolytoceras:65.100006) Psiloceratida:18.222214)clade_26:18.222229,((Juraphyl",
#'  "lites:6,Nevadaphyllites:6,Togaticeras:6, Tragophylloceras:12.600006)Juraphyllitidae:6,Hypo",
#'  "rbulites:107.300003,(Adabofoloceras:25.400009, Hypophylloceras:121.100006,Ptychophyllocera",
#'  "s:56.600006,Salfeldiella:56.600006,Holcophylloceras:61.150009, Phylloceras:121.100006,Leio",
#'  "phylloceras:46.800003)Phylloceratidae:15)Phylloceratida:45.444443)clade_25:18.222214) clad",
#'  "e_22:5.066681,(Paranannites:11.566666,(Proarcestes:8.383331,Ptychites:8.383331)clade_94:8.",
#'  "383331) clade_93:11.566681)clade_21:5.06665)clade_15:7.100006,(Deweveria:33.300003,Juvenit",
#'  "es:33.300003,(Cibolites:11.5, Kingoceras:22.5,Meitianoceras:24.199997,Paraceltites:4)Parac",
#'  "eltitidae:4,Preflorianites:33.300003, Xenodiscus:33.300003)Xenodiscoidea:2)clade_14:2,Cart",
#'  "eria:37.300003,Courtilloticeras:37.300003, Eschericeratites:37.300003,Tapponnierites:37.30",
#'  "0003)Ceratitida:101.025024,(((Daraelites:76.399994, Epicanites:23.299988,Praedaraelites:15",
#'  ")Daraelitidae:28.300018,(Becanites:19.900024,Dombarocanites:47.100006, Eocanites:19.900024",
#'  ",Merocanites:22.400024,Prolecanites:4.5)Prolecanitidae:4.5)Prolecanitina:1,((Neopronorites",
#'  ":7, Sakmarites:14)Pronoritidae:17.5,(Artinskia:4.5,Bamyaniceras:34.5,Medlicottia:40.5,Prop",
#'  "inacoceras:31.5,Synartinskia:20, Uddenites:4.5)Medlicottiidae:4.5)Medlicottiina:66.700012)",
#'  "Prolecanitida:14.825012)clade_3:14.824982, (((Raymondiceras:6,(Dimeroceras:5,Paratornocera",
#'  "s:5)Dimeroceratidae:5)Dimerocerataceae:10,((Acrocanites:7, Jdaidites:7)Acrocanitidae:16.40",
#'  "0024,Kazakhstania:25.900024,Praeglyphiloceras:8,(Imitoceras:10.900024,Prionoceras:4, Triim",
#'  "itoceras:19.400024)Prionoceratidae:4,(Maeneceras:1,Sporadoceras:4)Sporadoceratidae:4)Prion",
#'  "ocerataceae:12, (Pseudoclymenia:5,(Discoclymenia:4.5,Posttornoceras:4.5)Posttornoceratidae",
#'  ":4.5)Tornocerataceae:11)Tornoceratina:10, (Popanoceras:117.533356,((Epitornoceras:28,Falci",
#'  "tornoceras:28,Lobotornoceras:6.300018,Protornoceras:5, Tornoceras:18.100006)Tornoceratidae",
#'  ":0.666656,(Cheiloceras:13,Torleyoceras:13)Cheiloceratidae:15.666656, Polonoceras:28.666656",
#'  ")Cheilocerataceae:0.666687,((((Kargalites:30.344452,(Adrianites:22.5,Nevadoceras:11, Veruz",
#'  "hites:11)Adrianitidae:19.344452)clade_122:19.344452,Pintoceras:25.78891)clade_121:25.78887",
#'  "9, ((Waagenoceras:53.14447,((Metalegoceras:9,Pericycloceras:12)Metalegoceratidae:9.5,Uralo",
#'  "ceras:14) Neoicoceratoidea:25.64447)clade_125:25.64444,((Branneroceras:3,Diaboloceras:10.6",
#'  "49994,Paralegoceras:63.600006, Schistoceras:38.100006)Schistoceratidae:3,(Wellerites:10.64",
#'  "9994,Winslowoceras:3)Welleritidae:3) Schistocerataceae:17.188904)clade_124:17.188873)clade",
#'  "_120:17.188904,(Antegoniatites:9,Habadraites:9, Primogoniatites:9,Progoniatites:9)Goniatit",
#'  "idae:17.866699)clade_119:17.866669,(Dzhaprakoceras:23,(Follotites:18.5, Muensteroceras:10,",
#'  "Xinjiangites:10)Muensteroceratidae:2,(Ammonellipsites:12.5,Helicocyclus:10,Nodopericyclus:",
#'  "10, Ouaoufilalites:10,Pericyclus:10)Pericyclidae:10.5,(Eurites:10.25,Mouydiria:10.25,Rotop",
#'  "ericyclus:10.25) Rotopericlydae:10.25,(Jerania:6,Kusinia:6,Temertassetia:6)Temertassetiida",
#'  "e:14.5)Pericyclaceae:24.233368, Stacheoceras:136.033356)Goniatitina:0.666667)Goniatitida:9",
#'  ".649994)clade_2:9.649994,(Gyroceratites:14.799988, ((Teicherticeras:8.93335,((((Probelocer",
#'  "as:36,(Timanites:12.600006,(Darkaoceras:2.5,Keuppites:2.5)Taouzitidae:2.5, (Gogoceras:10.1",
#'  "00006,Pseudoprobeloceras:2.5)Ponticeratidae:2.5,(Beloceras:9,Mesobeloceras:9) Beloceratida",
#'  "e:3.600006,(Archoceras:23.399994,Manticoceras:8,Mixomanticoceras:8,Sphaeromanticoceras:8) ",
#'  "Gephuroceratidae:4.600006)Gephurocerataceae:8)Gephuroceratatina:1.033325,Agoniatites:14.03",
#'  "3325) clade_144:1.033325,Celaeceras:6.866669)clade_143:1.033325,((Werneroceras:0.399994,(S",
#'  "obolewia:0.200012, (((Cyrtoclymenia:2.5,Clymenia:2.5)Clymeniina:2.5,Protoxyclymenia:5,Plat",
#'  "yclymenia:5)Clymeniida:21.066681, (Lunupharciceras:1.533325,Pharciceras:9.133331,Stenophar",
#'  "ciceras:1.533325,Synpharciceras:1.533325) Pharciceratatina:1.533356)clade_154:1.533325)cla",
#'  "de_153:0.199982)clade_152:0.200002,Anarcestes:5) Anarcestina:11.099976)clade_142:1.033356)",
#'  "clade_141:1.033325,Anetoceras:9.966675)clade_140:1.03333) Agoniatitida:7.100006)clade_1;")
#' 
#' ammoniteTreeRaia <- read.tree(text = ammoniteTreeRaia)
#' 
#' # what about the root age?
#' # Raia et al. are unclear
#'  # however... ahandful of taxa are known to last occur at the end-Cretaceous mass ext
#'  # Phylloceras
#' #
#' # Latest occurring tips are:
#' ammoniteTreeRaia$tip.label[
#'  which(node.depth.edgelength(ammoniteTreeRaia) == max(node.depth.edgelength(ammoniteTreeRaia)))]
#' #
#' # so we can treat distance of Phylloceras from root + end Cretaceous (66.043 Ma) as $root.time
#' (ammoniteTreeRaia$root.time <- 66.043+
#'  node.depth.edgelength(ammoniteTreeRaia)[which(ammoniteTreeRaia$tip.label == "Phylloceras")])
#' 
#' # now let's plot it
#' plot(ladderize(ammoniteTreeRaia));axisPhylo()
#' 
#' }
#' \dontrun{
#' 
#' # and let's load trait data from Raia et al. Appendix B:
#'  # FD = fractal dimension of first suture (suture complexity)
#'  # Log D = log of the mean shell diameter per genus (body size)
#'  # log dur = log of the stratigraphic duration in million years.
#' ammoniteTraitsRaia <- read.table("ammoniteTraitsRaia.txt",row.names = 1,header = TRUE)
#' 
#' sutureComplexity <- ammoniteTraitsRaia$FD
#' shellSize <- ammoniteTraitsRaia$Log_D
#' names(shellSize) <- names(sutureComplexity) <- rownames(ammoniteTraitsRaia)
#' 
#' plotTraitgram(tree = multi2di(ammoniteTreeRaia), trait = sutureComplexity,
#'   conf.int = FALSE, main = "Ammonite Suture Complexity")
#' 
#' plotTraitgram(tree = multi2di(ammoniteTreeRaia), trait = shellSize,
#'   conf.int = FALSE, main = "Ammonite Shell Diameter")
#' 
#' }
#' \donttest{
#' ########################################
#' # ceratopsian species
#' 
#' ceratopsianTreeRaia <- paste0("((((((((((((Centrosaurus_apertus:5.1,Styracosaurus_alberte",
#'  "nsis:5.9):1,(((Pachyrhinosaurus_perotorum:10.5,Pachyrhinosaurus_lakustai:7):0.5,Achelousau",
#'  "rus_horneri:6.3):0.5,Einiosaurus_procurvicornis:6.5):1):0.5, Avaceratops_lammersi:5.5):0.5",
#'  ",Diabloceratops_eatoni:3):1.1,((Chasmosaurus_russelli:1.4,Chasmosaurus_belli:1.6):2.5, (Mo",
#'  "joceratops_perifania:3.7,(Agujaceratops_mariscalensis:1.9,((Pentaceratops_sternbergii:3.5,",
#'  " Utahceratops_gettyi:1):1.5,((Vagaceratops_irvinensis:1.3,Kosmoceratops_richardsoni:1):0.4",
#'  ",(Anchiceratops_ornatus:3.9, (Arrhinoceratops_brachyops:3.9,(Torosaurus_latus:3,(Tricerato",
#'  "ps_horridus:2, Triceratops_prorsus:2):1):6):0.5):1.7):1):0.5):0.5):0.5):3.8):12.9,(Bagacer",
#'  "atops_rozhdestvenskyi:17, (Protoceratops_hellenikorhinus:9.5,Protoceratops_andrewsi:9.5):1",
#'  "2):4.5):6,(Prenoceratops_pieganensis:21, Leptoceratops_gracilis:31.6):4.5):7.5,Archaeocera",
#'  "tops_oshimai:6):5,Auroraceratops_rugosus:15):21, Liaoceratops_yanzigouensis:6):4,(Hongshan",
#'  "osaurus_houi:9,(Psittacosaurus_mongoliensis:33.5, (Psittacosaurus_meileyingensis:20,(Psitt",
#'  "acosaurus_major:7.5,(Psittacosaurus_gobiensis:21,(Psittacosaurus_sinensis:24, Psittacosaur",
#'  "us_neimongoliensis:18):1):1.5):0.5):0.5):0.5):1):23,Yinlong_downsi:6):3;")
#' 
#' ceratopsianTreeRaia <- read.tree(text = ceratopsianTreeRaia)
#' 
#' # Raia et al. placed origin of ceratopsians at ~163 Ma, base of Oxfordian
#' ceratopsianTreeRaia$root.time <- 163
#' 
#' plot(ceratopsianTreeRaia);axisPhylo()
#' 
#' ###############################################
#' # cervid species
#' 
#' cervidTreeRaia <- paste0("((((Lagomeryx_parvulus:9.925998,Lagomeryx_pumilio:10.775998):3.",
#'  "25,(Procervulus_flerovi:11.425998,Procervulus_dichotomus:7.025998,Procervulus_praelucidus:",
#'  "5.675998):3.25,(Stephanocemas_aralensis:6.925998, Stephanocemas_thomsoni:11.175998):2):2,(",
#'  "((Euprox_furcatus:14.440997,Euprox_minimus:12.590997, Euprox_dicranoceros:14.190997):2.185",
#'  "001,Heteroprox_larteti:12.175998):1.5,Muntiacus_muntjak:25.531498):1.5):1.5, (((((Alces_la",
#'  "tifrons:7.151589758,Alces_alces:7.245998):2.29,Cervalces_scotti:9.525768):6.64, Rangifer_t",
#'  "arandus:16.175998):4.35,(Procapreolus_loczyi:17.840998,Capreolus_capreolus:17.905998):2.62",
#'  "5):5.25, (((Cervavitus_novorossiae:9.109332,Cervavitus_variabilis:9.379332):7.149999, Plio",
#'  "cervus_pentelici:13.069331):2.966667,(((((Dama_clactoniana:5.133775345,Dama_dama:5.199332)",
#'  ":2.903333, (Pseudodama_farnetensis:5.860846548,Pseudodama_lyra:4.242887928, Pseudodama_nes",
#'  "tii:5.762011259):2.083333):4.166667,(Eucladoceros_ctenoides:6.892665, Eucladoceros_dicrani",
#'  "os:7.692563015):4.166667):2.083333,((Cervus_elaphus:5.734332,Cervus_nippon:5.744332, Rusa_",
#'  "timorensis:5.740332,Rusa_unicolor:5.744332,Cervus_duvaucelii:5.671332):3.4, Croizetoceros_",
#'  "ramosus:7.834332):5.208333):2.083333,((Praemegaceros_verticornis:9.610727017, (Megaceroide",
#'  "s_obscurus:6.084504245,Megaceroides_solilhacus:6.725161676):2.883334):2.883333, (Megalocer",
#' 	"os_savini:7.349060017,Megaloceros_giganteus:7.430999):5.145):3.849999):6.6):2.75):2.75);")
#' 
#' cervidTreeRaia <- read.tree(text = cervidTreeRaia)
#' 
#' # Many of the latest-occurring tips are still extant, like Rusa unicolor and Dama dama:
#' cervidTreeRaia$tip.label[
#' 	which(node.depth.edgelength(cervidTreeRaia) == max(node.depth.edgelength(cervidTreeRaia)))]
#' 
#' # note!
#' # if you plot the tree there seem to be a lot more taxa that are *almost* as late-occurring
#' 	# unclear if this is recently extinct taxa, computational rounding error, or what
#' 
#' # so we can treat distance of Dama dama to root as $root.time
#' (cervidTreeRaia$root.time <- 
#' 	node.depth.edgelength(cervidTreeRaia)[which(cervidTreeRaia$tip.label == "Dama_dama")])
#' 
#' plot(cervidTreeRaia);axisPhylo()
#' 
#' }
#' \dontrun{
#' 
#' save.image("RaiaCopesRule.rdata")
#' 
#' }
#' 
NULL