RatePhylo.allCI <-
function(rateData, MLrate=NULL, fixed=NULL, rateMIN = 0.001, rateMAX = 50, common.mean=FALSE, lambda.est=TRUE) {
if(is.null(MLrate)) { MLrate <- c(rep(1,length(rateData$Vmat))) } else { MLrate <- MLrate }
if(is.null(fixed)) { fixed <- c(rep(FALSE,length(rateData$Vmat) - 1), FALSE) } else { op <- fixed }
n.rate <- length(MLrate)
all.CIs <- matrix(nrow=n.rate, ncol=2, dimnames=list(c(1:n.rate), c("Lci", "Uci")))
for(i in 1:n.rate) {
fix.now <- c(rep(TRUE, n.rate))
fix.now[i] <- FALSE
if(fixed[i] == FALSE) {
CI <- RatePhylo.CI(rateData, MLrate, fix.now, common.mean=common.mean, lambda.est=lambda.est)
all.CIs[i,1] <- CI[1]
all.CIs[i,2] <- CI[2]
} else { all.CIs[i,1] <- NA
all.CIs[i,2] <- NA }
}
return(all.CIs)
}
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