Correction to 'CarnivoreCode.R in supplement of A dynamic global equilibrium in carnivoran diversification over 20 million years'.

Abstract

You have accessMoreSectionsView PDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmail Cite this article Liow Lee Hsiang and Finarelli John A. 2017Correction to ‘CarnivoreCode.R in supplement of A dynamic global equilibrium in carnivoran diversification over 20 million years’Proc. R. Soc. B.2842017121320171213http://doi.org/10.1098/rspb.2017.1213SectionYou have accessCorrectionCorrection to ‘CarnivoreCode.R in supplement of A dynamic global equilibrium in carnivoran diversification over 20 million years’ Lee Hsiang Liow Lee Hsiang Liow http://orcid.org/0000-0002-3732-6069 Google Scholar Find this author on PubMed Search for more papers by this author and John A. Finarelli John A. Finarelli Google Scholar Find this author on PubMed Search for more papers by this author Lee Hsiang Liow Lee Hsiang Liow http://orcid.org/0000-0002-3732-6069 Google Scholar Find this author on PubMed Search for more papers by this author and John A. Finarelli John A. Finarelli Google Scholar Find this author on PubMed Search for more papers by this author Published:05 July 2017https://doi.org/10.1098/rspb.2017.1213This article corrects the followingResearch ArticleA dynamic global equilibrium in carnivoran diversification over 20 million yearshttps://doi.org/10.1098/rspb.2013.2312 Lee Hsiang Liow and John A. Finarelli volume 281issue 1778Proceedings of the Royal Society B: Biological Sciences07 March 2014Proc. R. Soc. B281, 20132312. (7 March 2014; Published online 22 January 2014) (doi:10.1098/rspb.2013.2312)The corrections are (i) Foote's 2000 terminology of boundary crossers (ii) the inclusion of the time boundary in boundary crosser tabulations. The output values are now in-line with Foote's own tabulations (M. Foote 2017, personal communication).Note that the correlation values between the two estimates (Pradel and Foote) are worse than reported in the electronic supplementary material, figure S12 of the paper. New plots for the comparisons are supplied. These errors do not contribute to any changes in inferences in the main text. Download figureOpen in new tabDownload PowerPointFA=function(x){min(which(x==1))}LA=function(x){max(which(x==1))}#Foote functionfooterates <- function(FA, LA, timeint){da=cbind(FA, LA)NFt=NA #number of top crosser (this was previously misnamed re Foote 2000)Nbt=NA #number of double crosser (this was previously misnamed re Foote 2000)NbL=NA #number of bottom crosserq=NA#per capita extinction ratep=NA#per capita origination ratefor (i in 1:(length(timeint)-1)){Ft= da[which(da[,1]<=timeint[i] & da[,1] > timeint[i+1] & da[,2] <= timeint[i+1]),]#top crosserbt=da[which(da[,1]>timeint[i] & da[,2]<=timeint[i+1]),]#double crosserbL=da[which(da[,1]> timeint[i] & da[,2]<= timeint[i] & da[,2]>timeint[i+1]),]#bottom crosser#Ft=da[which(da[,1]>timeint[i] & da[,2]>timeint[i+1] & da[,2]<=timeint[i]),] #old code#bt= da[which(da[,1]>timeint[i] & da[,2]<timeint[i+1]),] #old code#bL=da[which(da[,1]<timeint[i] & da[,1]>=timeint[i+1] & da[,2]<timeint[i+1]),] #old codeif (!is.null(nrow(Ft))){NFt[i]=nrow(Ft)} else{NFt[i]=1}if (!is.null(nrow(bt))){Nbt[i]=nrow(bt)}else{Nbt[i]=1}if (!is.null(nrow(bL))){NbL[i]=nrow(bL)}else{NbL[i]=1}}footeq=-log(Nbt/(NbL+ Nbt))#extinctionfootep=-log(Nbt/(NFt+ Nbt))#originationres=cbind(footeq, footep)colnames(res)=c("q","p")rownames(res)=timeint[1:(length(timeint)-1)]#return(res)return(list(NFt=NFt,NbL=NbL,Nbt=Nbt,Nb= Nbt+NbL,Nt=Nbt+NFt,p=footep,q=footeq))}#read in species filedata<-read.csv("rspb20132312supp4.csv",header=FALSE)######################prepare data in correct format for function "foote"FAD=apply(data[,2:25],1, FA)LAD=apply(data[,2:25],1, LA)times=seq(24,1,-1)FA=times[FAD]LA=times[LAD]FA<-as.integer(FA)LA<-as.integer(LA)foote=footerates(FA,LA,(times))foote=as.data.frame(foote) #Foote rates ready for usepradel.time=seq(-22,-3, 1)pradel.est.p=c(0.000, 0.580, 0.000, 0.470, 0.304, 0.107, 0.179, 0.109, 0.262, 0.393, 0.118,0.175, 0.236, 0.112, 0.161, 0.190, 0.318,0.175, 0.373, 0.136)pradel.est.q=c(0.000, 0.405, 0.095, 0.286, 0.100, 0.143, 0.000, 0.266, 0.182, 0.082,0.162, 0.195, 0.204, 0.202, 0.159, 0.057, 0.318, 0.339, 0.058, 0.293)pradel.est.d=c(0.130, 0.131, 0.158, 0.313, 0.292, -0.040, 0.219, -0.177, 0.108, 0.512,-0.050, -0.025, 0.042, -0.101, 0.003, 0.165, 0.001, -0.199, 0.504, -0.182)par(mfrow=c(2,1), mar=c(4,2,2,2))plot(pradel.time,pradel.est.p, axes=F, xlim=c(-23,-3),ylim=c(0,1),pch=20,col="red", main="speciation", xlab="")lines(pradel.time,pradel.est.p, col="red")axis(1, at=pradel.time, labels=seq(22,3,-1))axis(2)points(-times[2:22],foote$p[2:22], pch=20)lines(-times[2:22],foote$p[2:22], lwd=1)legend("topright", c("pradel", "foote"), col=c("red", "black"),lty=c(1,1), bty="n", text.col=c("red","black"))box()cor.test(pradel.est.p, foote$p[3:22])#cor= 0.3741679, p-value=0.1041plot(pradel.time,pradel.est.q, axes=F, xlim=c(-23,-3),ylim=c(0,1),pch=20, main="extinction", col="blue", xlab="Ma")lines(pradel.time,pradel.est.q, col="blue")axis(1, at=pradel.time, labels=seq(22,3,-1))axis(2)points(-times[2:22],foote$q[2:22], pch=20)lines(-times[2:22],foote$q[2:22], lwd=1)legend("topright", c("pradel", "foote"), col=c("blue", "black"),lty=c(1,1), bty="n", text.col=c("blue","black"))box()cor.test(pradel.est.q, foote$q[3:22]) #cor= -0.2798411, p-value=0.2321 Previous ArticleNext Article VIEW FULL TEXT DOWNLOAD PDF FiguresRelatedReferencesDetailsRelated articlesA dynamic global equilibrium in carnivoran diversification over 20 million years07 March 2014Proceedings of the Royal Society B: Biological Sciences This Issue12 July 2017Volume 284Issue 1858 Article InformationDOI:https://doi.org/10.1098/rspb.2017.1213PubMed:28679733Published by:Royal SocietyOnline ISSN:1471-2954History: Published online05/07/2017Published in print12/07/2017 License:© 2017 The Author(s)Published by the Royal Society. 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