R变量未找到,但具体定义

Question

我编写了一个函数来运行系统发育的广义最小二乘法,一切看起来应该可以正常工作,但由于某种原因,在脚本(W)中定义的特定变量不断变为未定义.我已经盯着这段代码好几个小时了,无法弄清楚问题出在哪里.

有任何想法吗？

myou <- function(alpha, datax, datay, tree){
    data.frame(datax[tree$tip.label,],datay[tree$tip.label,],row.names=tree$tip.label)->dat
    colnames(dat)<-c("Trait1","Trait2")
    W<-diag(vcv.phylo(tree)) # Weights
    fm <- gls(Trait1 ~ Trait2, data=dat, correlation = corMartins(alpha, tree, fixed = TRUE),weights = ~ W,method = "REML")
    return(as.numeric(fm$logLik))
}

corMartins2<-function(datax, datay, tree){
    data.frame(datax[tree$tip.label,],datay[tree$tip.label,],row.names=tree$tip.label)->dat
    colnames(dat)<-c("Trait1","Trait2")
    result <- optimize(f = myou, interval = c(0, 4), datax=datax,datay=datay, tree = tree, maximum = TRUE)
    W<-diag(vcv.phylo(tree)) # Weights
    fm <- gls(Trait1 ~ Trait2, data = dat, correlation = corMartins(result$maximum, tree, fixed =T),weights = ~ W,method = "REML")
    list(fm, result$maximum)}




#test


require(nlme)
require(phytools)
simtree<-rcoal(50)
as.data.frame(fastBM(simtree))->dat1
as.data.frame(fastBM(simtree))->dat2

corMartins2(dat1,dat2,tree=simtree)

返回"eval中的错误(expr,envir,enclos):找不到对象'W'"

即使W是专门定义的!

谢谢!

Answer 1

在错误的发生的历史gls中调用myou和corMatrins2:你必须通过W在列dat,因为gls正在寻找它存在(当你把weights = ~W像它看起来的公式dat$W并不能找到它).

只需更改data=dat为data=cbind(dat,W=W)两个功能.

Answer 2

该示例对我来说是不可重现的,因为lowerB并且upperB没有定义,但是,以下可能对您有用,cbinding dat具有W:

myou <- function(alpha, datax, datay, tree){
    data.frame(datax[tree$tip.label,],datay[tree$tip.label,],row.names=tree$tip.label)->dat
    colnames(dat)<-c("Trait1","Trait2")
    W<-diag(vcv.phylo(tree)) # Weights
            ### cbind W to dat
            dat <- cbind(dat, W = W)
    fm <- gls(Trait1 ~ Trait2, data=dat, correlation = corMartins(alpha, tree, fixed = TRUE),weights = ~ W,method = "REML")
    return(as.numeric(fm$logLik))
}

corMartins2<-function(datax, datay, tree){
    data.frame(datax[tree$tip.label,],datay[tree$tip.label,],row.names=tree$tip.label)->dat
    colnames(dat)<-c("Trait1","Trait2")
    result <- optimize(f = myou, interval = c(lowerB, upperB), datax=datax,datay=datay, tree = tree, maximum = TRUE)
    W<-diag(vcv.phylo(tree)) # Weights
    ### cbind W to dat
    dat <- cbind(dat, W = W)
    fm <- gls(Trait1 ~ Trait2, data = dat, correlation = corMartins(result$maximum, tree, fixed =T),weights = ~ W,method = "REML")
    list(fm, result$maximum)}




#test
require(phytools)
simtree<-rcoal(50)
as.data.frame(fastBM(simtree))->dat1
as.data.frame(fastBM(simtree))->dat2

corMartins2(dat1,dat2,tree=simtree)