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###############################################################
# Chong Wu
# email: wuxx0845@umn.edu
###############################################################
# Intent:
# This function suppresses the following notes generated by "R CMD check":
# - "Note: no visible binding for global variable '.->ConfigString'"
# - "Note: no visible binding for '<<-' assignment to 'ConfigString'"
# Usage:
# Add the following right in the beginning of the .r file (before the Reference
# class is defined in the sourced .r file):
# suppressBindingNotes(c(".->ConfigString","ConfigString"))
#suppressBindingNotes <- function(variablesMentionedInNotes) {
# for(variable in variablesMentionedInNotes) {
# assign(variable,NULL, envir = .GlobalEnv)
# }
#}
#suppressBindingNotes(c(".->ConfigString","ConfigString"))
simulateData <- function(nSam=100, s=12,ncluster = 20,mu = 1000, size = 25) {
data(throat.tree,envir = environment())
data(dd,envir = environment())
tree <- get("throat.tree", envir = environment())
dd1 = get("dd",envir = environment())
tree.dist <- cophenetic(tree)
obj <- pam(as.dist(tree.dist), ncluster,diss =TRUE)
clustering <- obj$clustering
otu.ids <- tree$tip.label
p.est = dd1$pi
names(p.est) <- names(dd1$pi)
theta <- dd1$theta
gplus <- (1 - theta) / theta
p.est <- p.est[otu.ids]
g.est <- p.est * gplus
p.clus <- sort(tapply(p.est, clustering, sum), decreasing=T)
scale2 = function(x)as.numeric(scale(x))
comm <- matrix(0, nSam, length(g.est))
rownames(comm) <- 1:nrow(comm)
colnames(comm) <- names(g.est)
# comm.p hold the underlying proportions
comm.p <- comm
nSeq <- rnbinom(nSam, mu = mu, size = size)
for (i in 1:nSam) {
comm.p[i, ] <- rdirichlet(1, g.est)[1, ]
comm[i, ] <- rmultinom(1, nSeq[i], prob=comm.p[i, ])[, 1]
}
otu.ids <- names(which(clustering == s))
# No additional covariates in this case.
OTU = comm[, otu.ids]
return(list(informative.OTU = OTU,whole.OTU = OTU))
}
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