require(expm) require(boot) require(MASS) require(gridBase) require(grid) require(optimParallel) #setwd("Your directory") setwd("D:/Data/Melville_2012/MS-Gradient/Scripts") #################################################################################################### #PVL10-50 #################################################################################################### if (core=="PVL") { if (model=="low-resolution") { data<-read.delim("Southern California age data in cores.txt", header=TRUE) data<-data[which(data$Station=="PVL10-50"),] data<-data[,c("Coarse.scale.unit","Age..y.")] data<-na.omit(data) names(data)<-c("X","Y") data$Y<-data$Y/1000 fdata<-data[,c("X","Y")] select=which(fdata[,"X"]<3) fdata=fdata[select,] age=fdata[,2]*1000 layer=fdata[,1] } ####################### #high-resolution model ####################### if (model=="high-resolution") { data<-read.delim("Southern California age data in cores.txt", header=TRUE) data<-data[which(data$Station=="PVL10-50"),] species=data[,"taxon"] data<-data[,c("Fine.scale.unit","Age..y.","Increment.lower.depth")] data<-na.omit(data) names(data)<-c("X","Y","Lower.depth..cm.") data$Y<-data$Y/1000 fdata<-data[,c("X","Y")] select=which(fdata[,"X"]<14) fdata=fdata[select,] species=species[select] cm.data=data[,"Lower.depth..cm."] cm.levels=as.numeric((tapply(cm.data[select], fdata[,1], mean))) fdata=fdata[,1:2] age=fdata[,2]*1000 layer=fdata[,1] } } #################################################################################################### #OC-50 #################################################################################################### if (core=="OC") { if (model=="low-resolution") { data<-read.delim("Southern California age data in cores.txt", header=TRUE) data<-data[which(data$Station=="OC-50"),] data<-data[,c("Coarse.scale.unit","Age..y.")] data<-na.omit(data) names(data)<-c("X","Y") data$Y<-data$Y/1000 fdata<-data[,c("X","Y")] select=which(fdata[,"X"]<3) fdata=fdata[select,] age=fdata[,2]*1000 layer=fdata[,1] } ####################### #high-resolution model ####################### if (model=="high-resolution") { data<-read.delim("Southern California age data in cores.txt", header=TRUE) data<-data[which(data$Station=="OC-50"),] species=data[,"taxon"] data<-data[,c("Fine.scale.unit","Age..y.","Increment.lower.depth")] data<-na.omit(data) names(data)<-c("X","Y","Lower.depth..cm.") data$Y<-data$Y/1000 fdata<-data[,c("X","Y")] select=which(fdata[,"X"]<14) fdata=fdata[select,] species=species[select] cm.data=data[,"Lower.depth..cm."] cm.levels=as.numeric((tapply(cm.data[select], fdata[,1], mean))) fdata=fdata[,1:2] age=fdata[,2]*1000 layer=fdata[,1] } } #################################################################################################### #PVL5-50# #################################################################################################### if (core == "PVL550") { ####################### #low-resolution model ####################### if (model=="low-resolution") { data<-read.delim("Southern California age data in cores.txt", header=TRUE) data<-data[which(data$Station=="PVL5-50"),] data<-data[,c("Coarse.scale.unit","Age..y.")] data<-na.omit(data) names(data)<-c("X","Y") data$Y<-data$Y/1000 fdata<-data[,c("X","Y")] select=which(fdata[,"X"]<3) fdata=fdata[select,] age=fdata[,2]*1000 layer=fdata[,1] } ####################### #high-resolution model ####################### if (model=="high-resolution") { data<-read.delim("Southern California age data in cores.txt", header=TRUE) data<-data[which(data$Station=="PVL5-50"),] species=data[,"taxon"] data<-data[,c("Fine.scale.unit","Age..y.","Increment.lower.depth")] data<-na.omit(data) names(data)<-c("X","Y","Lower.depth..cm.") data$Y<-data$Y/1000 fdata<-data[,c("X","Y")] select=which(fdata[,"X"]<14) fdata=fdata[select,] species=species[select] cm.data=data[,"Lower.depth..cm."] cm.levels=as.numeric((tapply(cm.data[select], fdata[,1], mean))) fdata=fdata[,1:2] age=fdata[,2]*1000 layer=fdata[,1] } } #################################################################################################### #PVL5-75 #################################################################################################### if (core == "PVL575") { if (model=="low-resolution") { data<-read.delim("Southern California age data in cores.txt", header=TRUE) data<-data[which(data$Station=="PVL5-75"),] data<-data[,c("Coarse.scale.unit","Age..y.")] data<-na.omit(data) names(data)<-c("X","Y") data$Y<-data$Y/1000 fdata<-data[,c("X","Y")] select=which(fdata[,"X"]<3) fdata=fdata[select,] age=fdata[,2]*1000 layer=fdata[,1] } ####################### #high-resolution model ####################### if (model=="high-resolution") { data<-read.delim("Southern California age data in cores.txt", header=TRUE) data<-data[which(data$Station=="PVL5-75"),] species=data[,"taxon"] data<-data[,c("Fine.scale.unit","Age..y.","Increment.lower.depth")] data<-na.omit(data) names(data)<-c("X","Y","Lower.depth..cm.") data$Y<-data$Y/1000 fdata<-data[,c("X","Y")] select=which(fdata[,"X"]<12) fdata=fdata[select,] species=species[select] cm.data=data[,"Lower.depth..cm."] cm.levels=as.numeric((tapply(cm.data[select], fdata[,1], mean))) fdata=fdata[,1:2] age=fdata[,2]*1000 layer=fdata[,1] } } ##############################################################################################