R/SongZhangDicrano.R

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

#' Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
#' 
#' Character matrix and two cladograms for 13 dicranograptid
#' (and outgroup) graptoloids, taken from Song and Zhang (2014). Included
#' here for use with functions related to character change.

#' @name SongZhangDicrano
#' @rdname SongZhangDicrano
#' @aliases charMatDicrano cladogramDicranoX12 cladogramDicranoX13

#' @details
#' This example dataset is composed of a small cladistic character data for 13 taxa and 24 characters,
#' taken from Song and Zhang (2014). Note that character 22 is a biostratigraphic character, which was
#' not included in all analyses by Song and Zhang.
#' 
#' The first included cladogram \code{cladogramDicranoX12} is the
#' majority-rule consensus of a maximum-parsimony analysis on 12
#' taxa (excluding on taxa with incompletely known anatomy) with
#' 24 characters, including a biostratigraphic character. This
#' tree is included here as, among the four trees depicted,
#' it appeared to be the basis for the majority of Song and
#' Zhang's discussion of dicranograptid systematics.
#' 
#' The second cladogram \code{cladogramDicranoX13} is a maximum-parsimony tree found by a maximum-parsimony
#' analysis of 13 taxa with 24 characters, including a biostratigraphic character. This tree is much more resolved
#' than the alternative majority-rule cladogram for 12 taxa.
#' 
#' The matrix and both trees were entered by hand from their flat graphic depiction in Song and Zhang's
#' manuscript.

#' @format 
#' Loading this dataset adds two objects to the R environment.
#' \code{charMatDicrano} is a \code{data.frame} object composed of multiple factors, with \code{NA} values
#' representing missing values (states coded as '?'), read in with \code{readNexus} from package
#' \code{phylobase}. \code{cladogramDicranoX12} and 
#' \code{cladogramDicranoX13} are both cladograms, formatted as \code{phylo} class objects
#' for use with package \code{ape}, without branch-lengths (as
#' these was are, respectively, consensus tree and a maximum-parsimony tree from separate
#' maximum-parsimony analyses).

#' @source 
#' Song, Y., and Y. Zhang. 2014. A preliminary study on the relationship of the
#' early dicranograptids based on cladistic analysis. \emph{GFF} 136(1):243-248.

#' @keywords datasets

#' @docType data

#' @examples
#' 
#' data(SongZhangDicrano)
#' 
#' # Examining morphospace with a distance matrix
#' 
#' # calculate a distance matrix from the morph character data
#' char <- charMatDicrano[,-22]	# remove strat character
#' charDist <- matrix(,nrow(char),nrow(char))
#' rownames(charDist) <- colnames(charDist) <- rownames(char)
#' for(i in 1:nrow(char)){for(j in 1:nrow(char)){
#' 	charDiff <- logical()
#' 	for(k in 1:ncol(char)){
#' 		selectPair <- char[c(i,j),k]
#' 		if(all(!is.na(selectPair))){
#' 			#drop states that are missing			
#' 			isSame <- identical(selectPair[1],selectPair[2])
#' 			charDiff <- c(charDiff,isSame)
#' 			}
#' 		}
#' 	charDist[i,j] <- 1-sum(charDiff)/length(charDiff)
#' 	}}
#' 
#' #####
#' # PCO of character distance matrix
#' 
#' #can apply PCO (use lingoes correction to account for negative values
#'    #resulting from non-euclidean matrix
#' pco_res <- pcoa(charDist,correction = "lingoes")
#' 
#' #relative corrected eigenvalues
#' rel_corr_eig <- pco_res$values$Rel_corr_eig
#' layout(1:2)
#' plot(rel_corr_eig)
#' #cumulative
#' plot(cumsum(rel_corr_eig))
#' 
#' #well let's look at those PCO axes anyway
#' layout(1)
#' pco_axes <- pco_res$vectors
#' plot(pco_axes[,1],pco_axes[,2],pch = 16,
#'    xlab = paste("PCO Axis 1, Rel. Corr. Eigenvalue  = ",round(rel_corr_eig[1],3)),
#'    ylab = paste("PCO Axis 2, Rel. Corr. Eigenvalue  = ",round(rel_corr_eig[2],3)))
#' 
#' #######
#' 
#' # plot 12 taxon majority rule tree from Song and Zhang
#' plot(cladogramDicranoX12,
#' 	main = "MajRule_24charX12Taxa_wBiostratChar")
#' 
#' # plot 13 taxon MPT
#' plot(cladogramDicranoX13,
#' 	main = "MPT_24charX13Taxa_wBiostratChar")
#' 
#' ##############
#' 
#' \dontrun{
#' # Data was generated with following script:
#' require(ape)
#' require(phylobase)
#' 
#' charMatDicrano <- readNexus(file.choose(),type = "data",SYMBOLS = " 0 1 2")
#' 
#' cladogramDicranoX12 <- read.tree(file.choose())
#' cladogramDicranoX13 <- read.nexus(file.choose())
#' 
#' cladogramDicranoX13$tip.label <- rownames(
#' 	 charMatDicrano)[c(13,8,7,9,12,10,1,4,6,2,3,11,5)]
#' 
#' save(charMatDicrano,cladogramDicranoX12,file = "SongZhangDicrano.rdata")
#' }
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