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krandtest.R
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"as.krandtest" <- function (sim, obs, alter="greater", call = match.call(), names = colnames(sim), p.adjust.method = "none", output = c("light", "full")) {
output <- match.arg(output)
if(output == "full")
res <- list(sim = sim, obs = obs)
else
res <- list(obs = obs)
if(length(obs)!=length(alter))
alter <- rep(alter, length = length(obs))
res$alter <- alter
## Invalid permutations are stored as NA
res$rep <- apply(sim, 2, function(x) length(stats::na.omit(x)))
res$ntest <- length(obs)
res$expvar <- data.frame(matrix(0, res$ntest, 3))
if(!is.null(names)){
res$names <- names
} else {
res$names <- paste("test", 1:res$ntest, sep="")
}
names(res$expvar) <- c("Std.Obs","Expectation","Variance")
res$pvalue <- rep(0,length(obs))
for(i in 1:length(obs)){
vec.sim <- stats::na.omit(sim[,i])
if(length(vec.sim > 0)){
## compute histogram (mainly used for 'light' randtest)
r0 <- c(vec.sim, obs[i])
l0 <- max(vec.sim) - min(vec.sim)
w0 <- l0/(log(length(vec.sim), base = 2) + 1)
xlim0 <- range(r0) + c(-w0, w0)
h0 <- graphics::hist(vec.sim, plot = FALSE, nclass = 10)
res$plot[[i]] <- list(hist = h0, xlim = xlim0)
}
res$alter[i] <- match.arg(res$alter[i], c("greater", "less", "two-sided"))
res$expvar[i,1] <- (obs[i] - mean(vec.sim)) / stats::sd(vec.sim)
res$expvar[i,2] <- mean(vec.sim)
res$expvar[i,3] <- stats::sd(vec.sim)
if(res$alter[i]=="greater"){
res$pvalue[i] <- (sum(vec.sim >= obs[i]) + 1)/(res$rep[i] + 1)
}
else if(res$alter[i]=="less"){
res$pvalue[i] <- (sum(vec.sim <= obs[i]) + 1)/(res$rep[i] + 1)
}
else if(res$alter[i]=="two-sided") {
sim0 <- abs(vec.sim - mean(vec.sim))
obs0 <- abs(obs[i] - mean(vec.sim))
res$pvalue[i] <- (sum(sim0 >= obs0) + 1) / (res$rep[i] +1)
}
}
p.adjust.method <- match.arg(p.adjust.method, p.adjust.methods)
res$adj.pvalue <- stats::p.adjust(res$pvalue, method = p.adjust.method)
res$adj.method <- p.adjust.method
res$call <- call
class(res) <- "krandtest"
if(output == "light")
class(res) <- c(class(res), "lightkrandtest")
return(res)
}
"plot.krandtest" <- function (x, mfrow = NULL, nclass = 10, main.title = x$names, ...) {
if (!inherits(x, "krandtest"))
stop("to be used with 'krandtest' object")
if (is.null(mfrow))
mfrow = grDevices::n2mfrow(x$ntest)
def.par <- graphics::par(no.readonly = TRUE)
on.exit(graphics::par(def.par))
graphics::par(mfrow = mfrow)
graphics::par(mar = c(3.1, 2.5, 2.1, 2.1))
if (length(main.title)!=length(x$names))
main.title <- x$names
if(inherits(x, "lightkrandtest")) {
for (k in 1:x$ntest) {
y0 <- max(x$plot[[k]]$hist$counts)
graphics::plot(x$plot[[k]]$hist, xlim = x$plot[[k]]$xlim, col = grDevices::grey(0.8), main = main.title[k], ...)
graphics::lines(c(x$obs[k], x$obs[k]), c(y0/2, 0))
graphics::points(x$obs[k], y0/2, pch = 18, cex = 2)
}
} else {
for (k in 1:x$ntest) {
plot.randtest(as.randtest(x$sim[,k], x$obs[k], call = match.call()), main = main.title[k], nclass = nclass)
}
}
}
"print.krandtest" <- function (x, ...) {
if (!inherits(x, "krandtest"))
stop("to be used with 'krandtest' object")
cat("class:", class(x), "\n")
## dig0 <- ceiling (log(x$rep)/log(10))
cat("Monte-Carlo tests\n")
cat("Call: ")
print(x$call)
cat("\nNumber of tests: ", x$ntest, "\n")
cat("\nAdjustment method for multiple comparisons: ", x$adj.method, "\n")
sumry <- list(Test = x$names, Obs = x$obs, Std.Obs = x$expvar[,1], Alter = x$alter)
sumry <- as.data.frame(sumry)
row.names(sumry) <- 1:x$ntest
if(any(x$rep[1] != x$rep)){
sumry <- cbind(sumry[,1:4], N.perm = x$rep)
} else {
cat("Permutation number: ", x$rep[1], "\n")
}
sumry <- cbind(sumry, Pvalue = x$pvalue)
if(x$adj.method != "none")
sumry <- cbind(sumry, Pvalue.adj = x$adj.pvalue)
print(sumry)
cat("\n")
}
"[.krandtest" <- function(x, i) {
res <- list()
if (!inherits(x, "lightkrandtest"))
if(length(i) == 1)
res$sim <- x$sim[, i, drop = FALSE]
else
res$sim <- x$sim[, i]
res$obs <- x$obs[i]
res$alter <- x$alter[i]
res$rep <- x$rep[i]
res$ntest <- length(i)
res$expvar <- x$expvar[i, ]
res$names <- x$names[i]
res$pvalue <- x$pvalue[i]
res$plot <- x$plot[i]
res$adj.pvalue <- x$adj.pvalue[i]
res$adj.method <- x$adj.method
res$call <- match.call()
class(res) <- class(x)
return(res)
}
"[[.krandtest" <- function(x, i) {
if(length(i) != 1)
stop("Only one element can be selected: 'i' must be an index of length at 1.")
obj <- x[i]
res <- list()
if (!inherits(x, "lightkrandtest"))
res$sim <- obj$sim
res$obs <- obj$obs
res$alter <- obj$alter
res$rep <- obj$rep
res$expvar <- obj$expvar
res$pvalue <- obj$pvalue
res$plot <- obj$plot
res$call <- match.call()
class(res) <- "randtest"
if (inherits(x, "lightkrandtest"))
class(res) <- c(class(res), "lightrandtest")
return(res)
}