st.acr <- function(sim, diag=FALSE, upper = FALSE) { library(vegan) dis <- 1 - sim #use "shortest" or "extended" edis <- as.matrix(stepacross(dis.yu, path = "shortest", toolong = 1)) sim <- 1 - edis amax <- max(sim) amin <- min(sim) sim <- (sim-amin)/(amax-amin) sim2 <- sim[row(sim) > col(sim)] attr(sim2, "Size") <- nrow(sim) attr(sim2, "Labels") <- dimnames(sim)[[1]] attr(sim2, "Diag") <- diag attr(sim2, "Upper") <- upper attr(sim2, "call") <- match.call() class(sim2) <- "dist" return(sim2) }