Nothing
jt.test <-
function (..., data = NULL,
method=c("asymptotic","simulated","exact"),
dist=FALSE,Nsim=10000)
{
#############################################################################
# This function "jt.test" tests whether k samples (k>1) come from a common
# continuous distribution, using the Jonckheere-Terpstra rank test. See Lehmann (2006),
# Nonparametrics, Statistical Methods Based on Ranks.
# The test rejects the null hypothesis of no effect when JT is too large,
# i.e., a positive trend in the samples (in the order given) seems indicated.
#
# Ties are handled by using midranks.
# While the asymptotic P-value is always returned, there is the option
# to get a P-value estimate based on Nsim simulations or an exact value based
# on the full enumeration distribution, provided method = "exact" is chosen
# and the number of full enumerations is <= the Nsim specified.
# If the latter is not the case, simulation is used with the indicated Nsim.
# These simulated or exact P-values are appropriate under the continuity
# assumption or, when ties are present, they are still appropriate
# conditionally on the tied rank pattern, provided randomization took
# place in allocating subjects to the respective samples, i.e., also
# under random sampling from a common discrete parent population.
# However, under ties the results are only meaningful conditionally given
# the observed tie pattern.
#
#
#
# Inputs:
# ...: can either be a sequence of k (>1) sample vectors,
#
# or a list of k (>1) sample vectors,
#
# or y, g, where y contains the concatenated
# samples and g is a factor which by its levels
# identifies the samples in y,
#
# or a formula y ~ g with y and g as in previous case.
#
#
# data: data frame with variables usable in formula input, default = NULL.
#
#
# method: takes values "asymptotic", "simulated", or "exact".
# The value "asymptotic" causes calculation of P-values
# using the asymptotic normal approximation, always done.
#
# The value "simulated" causes estimation of P-values
# by randomly splitting the pooled data into
# samples of sizes ns[1], ..., ns[k], where
# ns[i] is the size of the i-th sample vector,
# and n = ns[1] + ... + ns[k] is the pooled sample size.
# For each such random split the JT statistic is
# computed. This is repeated Nsim times and the proportions
# of simulated values >= the actually observed JT value
# is reported as P-value estimate.
#
# The value "exact" enumerates all n!/(ns[1]! * ... * ns[k])
# splits of the pooled sample and computes the JT statistic
# for each such split.
# The proportion of all enumerated JT statistics
# that are >= the actually observed JT value
# is reported as exact (conditional) P-value.
#
# dist: = FALSE (default) or TRUE, TRUE causes the simulated
# or fully enumerated vector of the QN statstic to be returned
# as null.dist. The length of this vector should not exceed 1e8.
#
# Nsim: number of simulations to perform,
# for method = "exact" to take hold, it needs to be >=
# the number of all possible splits of the pooled
# data into samples of sizes ns[1], ..., ns[k], where
# ns[i] is the size of the i-th sample vector.
#
# When there are NA's among the sample values they are removed,
# with a warning message indicating the number of NA's.
# It is up to the user to judge whether such removals make sense.
#
# An example:
# x1 <- c(1,2)
# x2 <- c(1.5,2.1)
# x3 <- c(1.9,3.1)
# jt.test(x1,x2,x3,method="exact",Nsim=90)
# or
# jt.test(list(x1,x2,x3),method="exact",Nsim=90)
# which produces the output below.
#############################################################################
# Jonckheere-Terpstra k-sample test.
#
# Number of samples: 3
# Sample sizes: 2, 2, 2
# Number of ties: 0
#
# Null Hypothesis: All samples come from a common population.
# Alternative: Samples indicate a positive trend.
#
# test statistic mu sig asympt. P-value
# 9.0000000 6.0000000 2.5166115 0.1166151
# exact P-Value
# 0.1666667
#
#
# Warning: At least one sample size is less than 5,
# asymptotic p-values may not be very accurate.
#############################################################################
# In order to get the output list, call
# JT.out <- jt.test(list(x1,x2,x3),method="exact",dist=T,Nsim=100000)
# then JT.out is of class "kSamples" and has components
# > names(JT.out)
# [1] "test.name" "k" "ns" "N" "n.ties" "JT"
# [7] "warning" "null.dist" "method" "Nsim"
#
# where
# test.name = "Jonckheere-Terpstra"
# k = number of samples being compared
# ns = vector of the k sample sizes ns[1],...,ns[k]
# N = ns[1] + ... + ns[k] total sample size
# n.ties = number of ties in the combined set of all n observations
# JT = 4 (or 5) vector containing the JT statistics, its mean and standard
# deviation, its asymptotic P-value, (and its exact or simulated P-value).
# warning = logical indicator, warning = TRUE indicates that at least
# one of the sample sizes is < 5.
# null.dist is a vector of simulated values of the JT statistic
# or the full enumeration of such values.
# This vector is given when dist = TRUE is specified,
# otherwise null.dist = NULL is returned.
# method = one of the following values: "asymptotic", "simulated", "exact"
# as it was ultimately used.
# Nsim = number of simulations used, when applicable.
#
# The class "kSamples" causes JT.out to be printed in a special output
# format when invoked simply as: > JT.out
# An example was shown above.
#
# Fritz Scholz, August 2015
#
#################################################################################
JTmusig <- function (rx,ns)
{
# this function computes the mean and standard deviation of the
# JT statistic when ties are present.
N <- length(rx)
dvec <- as.vector(table(rx))
X1 <- N*(N-1)*(2*N+5)
X2 <- sum(ns*(ns-1)*(2*ns+5))
X3 <- sum(dvec*(dvec-1)*(2*dvec+5))
A1 <- (X1-X2-X3)/72
A2 <- sum(ns*(ns-1)*(ns-2))*sum(dvec*(dvec-1)*(dvec-2))
A2 <- A2/(36*N*(N-1)*(N-2))
A3 <- sum(ns*(ns-1))*sum(dvec*(dvec-1))/(8*N*(N-1))
sig <- sqrt(A1+A2+A3)
nmat <- outer(ns,ns,"*")
mu <- sum(nmat[upper.tri(nmat)])/2
list(mu=mu,sig=sig)
}
##############################################################
samples <- io(..., data = data)
method <- match.arg(method)
out <- na.remove(samples)
na.t <- out$na.total
if( na.t > 1) print(paste("\n",na.t," NAs were removed!\n\n"))
if( na.t == 1) print(paste("\n",na.t," NA was removed!\n\n"))
samples <- out$x.new
k <- length(samples)
if (k < 2) stop("Must have at least two samples.")
ns <- sapply(samples, length)
n <- sum(ns)
if (any(ns == 0)) stop("One or more samples have no observations.")
rx <- rank(unlist(samples))
JTobs <- 0
pval <- 0
L <- length(unique(rx)) # to count ties
if(dist == TRUE) Nsim <- min(Nsim,1e8)
# limits the size of null.dist
ncomb <- 1
np <- n
for(i in 1:(k-1)){
ncomb <- ncomb * choose(np,ns[i])
np <- np-ns[i]
}
# it is possible that ncomb overflows to Inf
if( method == "exact" & Nsim < ncomb ) {
method <- "simulated"
}
if( method == "exact" & dist == TRUE ) nrow <- ncomb
if( method == "simulated" & dist == TRUE ) nrow <- Nsim
if( method == "simulated" ) ncomb <- 1 # don't need ncomb anymore
if(method == "asymptotic"){
Nsim <- 1
dist <- FALSE
}
useExact <- FALSE
if(method == "exact") useExact <- TRUE
if(dist == TRUE){
JTvec <- numeric(nrow)
}else{
JTvec <- 0
}
out <- .C("JTtest", pval=as.double(pval),
Nsim=as.integer(Nsim), k=as.integer(k),
rx=as.double(rx), ns=as.integer(ns),
useExact=as.integer(useExact),
getJTdist=as.integer(dist),
ncomb=as.double(ncomb),JTobs=as.double(JTobs),
JTvec = as.double(JTvec), PACKAGE = "kSamples")
JTobs <- out$JTobs
musig <- JTmusig(rx,ns)
mu <- musig$mu
sig <- musig$sig
pval <- out$pval
if(dist){
JTvec <- round(out$JTvec,8)
}else{
JTvec <- NULL
}
pval.asympt <- 1-pnorm((JTobs - mu)/sig)
if(method=="asymptotic"){
JT <- c(JTobs,mu,sig,pval.asympt)
}else{
JT <- c(JTobs,mu,sig,pval.asympt,pval)
}
if(method=="asymptotic"){
names(JT) <- c("test statistic","mu","sig"," asympt. P-value")
}
if(method=="exact"){
names(JT) <- c("test statistic","mu","sig"," asympt. P-value","exact P-Value")
}
if(method=="simulated"){
names(JT) <- c("test statistic","mu","sig"," asympt. P-value","sim. P-Value")
}
warning <- FALSE
if(min(ns) < 5) warning <- TRUE
if(dist == FALSE) null.dist <- NULL
test.name <- "Jonckheere-Terpstra"
object <- list(test.name = test.name,
k = k, ns = ns, N = n, n.ties = n - L,
JT = JT, warning = warning, null.dist = JTvec,
method=method, Nsim=Nsim)
class(object) <- "kSamples"
object
}
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