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#' @describeIn bootCor Bootstrap the correlation of two numeric variables.
#' @export
bootCor.default <-
function(x, y, conf.level = 0.95, B = 10000, plot.hist = TRUE,
xlab = NULL, ylab = NULL, title = NULL,
plot.qq = FALSE, x.name = deparse(substitute(x)),
y.name = deparse(substitute(y)), seed = NULL, ...)
{
if (B %% 1 != 0 || B < 2) stop("B must be a positive integer")
if(!is.null(seed)) set.seed(seed)
alpha <- 1 - conf.level
if (!is.numeric(x) || !is.numeric(y)) stop("Both variables must be numeric.")
comCases <- complete.cases(x, y)
nmiss <- length(x) - sum(comCases)
if (nmiss > 0)
cat("\n ", nmiss, "observation(s) removed due to missing values.\n")
x2 <- x[comCases]
y2 <- y[comCases]
observed <- cor(x2, y2)
n <- length(x2)
#Boot
temp <- numeric(B)
for (i in 1:B)
{
index <- sample(1:n, n, replace = TRUE)
newx <- x2[index]
newy <- y2[index]
temp[i] <- cor(newx, newy)
} #end for
bootstrap.mean <- mean(temp)
# if (plot.hist){
#
# if (is.null(hist.title))
# hist.title <- paste("Bootstrap distribution of correlation\n", x.name," and ", y.name, sep=" ")
# #hist in R gives counts
# out <- hist(temp, plot=FALSE)
# out$density <- 100*(out$counts)/sum(out$counts)
# plot(out, freq = FALSE, ylab = "Percent", main = hist.title, xlab = "Correlation", cex.main = .9, cex.lab = .9)
#
# points(observed, 0, pch = 2, col = "red")
# points(bootstrap.mean, 0, pch = 4, col = "blue")
# legend(legend.loc, legend = c("Observed","Bootstrap"), pch = c(2,4),
# col = c("red", "blue"), cex = 0.8)
#
# } #end if plot.hist
#
# if (plot.qq){
# if (Sys.getenv("RSTUDIO_USER_IDENTITY") == "")
# grDevices::dev.new()
# qqnorm(temp, ylab = "Bootstrap")
# qqline(temp)
# } #end if plot.qq
# invisible(temp)
class(temp) <- "carlboot"
attr(temp, "observed") <- observed
attr(temp, "statistic") <- "correlation"
attr(temp, "groups") <- NULL
attr(temp, "x.name") <- x.name
attr(temp, "y.name") <- y.name
attr(temp, "level") <- conf.level
attr(temp, "xlab") <- xlab
attr(temp, "ylab") <- ylab
attr(temp, "title") <- title
attr(temp, "plot.hist") <- plot.hist
attr(temp, "plot.qq") <- plot.qq
temp
}
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