R/modified.t.R
In Garylikai/PMLi-1.0-R-Package: AMS 597 Project Partially Matched Samples R Package
Defines functions
modified.t
Documented in
modified.t
#' @title Kim et al.'s Modified t-Statistic
#' @description \code{modified.t} is used to calculate Kim et al.'s modified
#' t-statistic for partially matched samples, specified by giving a data frame
#' or matrix, testing hypothesis, true mean and confidence level.
#' @param data a 2-by-n or n-by-2 partially matched samples data frame or
#' matrix.
#' @param alternative a character string specifying the alternative hypothesis,
#' must be one of "two.sided" (default), "greater" or "less". You can specify
#' just the initial letter.
#' @param mu a number indicating the true difference in means.
#' @param conf.level confidence level for the returned confidence interval.
#' @param ... further arguments to be passed to or from methods.
#' @details Whether the dataset input is partially matched samples will be
#' checked. If not, appropriate hypothesis tests, such as one and two sample
#' t-tests, will be performed instead.
#' @return A list with class "htest" containing the following components:
#' \item{\code{statistic}}{the value of the test statistic.}
#' \item{\code{parameter}}{the degrees of freedom of the test statistic or
#' NA.} \item{\code{p.value}}{the p-value of the test.}
#' \item{\code{conf.int}}{a confidence interval for the mean appropriate to
#' the specified alternative hypothesis.} \item{\code{estimate}}{the estimated
#' mean or difference in means.} \item{\code{null.value}}{the specified
#' hypothesized value of the mean or mean difference.}
#' \item{\code{stderr}}{the standard error of the mean (difference).}
#' \item{\code{alternative}}{a character string describing the alternative
#' hypothesis.} \item{\code{method}}{a character string indicating what type
#' of test was performed.} \item{\code{data.name}}{a character string giving
#' the name(s) of the data.}
#' @import stats
#' @author Kai Li \email{kai.li@stonybrook.edu}
#' @references Kuan P F, Huang B. A simple and robust method for partially
#' matched samples using the p-values pooling approach. \emph{Statistics in
#' medicine}. 2013; 32(19): 3247-3259.
#'
#' Kim B, Kim I, Lee S, Kim S, Rha S, Chung H. Statistical methods of
#' translating microarray data into clinically relevant diagnostic information
#' in colorectal cancer. \emph{Bioinformatics}. 2004; 21(4): 517-528. [PubMed:
#' 15374865]
#' @seealso \code{\link[stats]{t.test}} for the one and two-sample t-tests.
#'
#' \code{\link[stats]{var.test}} for the F test to compare two variances.
#'
#' \code{\link[stats]{shapiro.test}} for the Shapiro-Wilk test of normality.
#'
#' \code{\link[stats]{wilcox.test}} for the one and two-sample Wilcoxon tests.
#'
#' \code{\link{weighted.z}}, \code{\link{corrected.z}},
#' \code{\link{mle.hetero}}, and \code{\link{mle.homo}} for other statistical
#' approaches for partially matched samples.
#' @examples
#' # pm is a sample dataset for the PMLi package
#'
#' # Kim et al.'s modified t-statistic formula interface
#' modified.t(pm, "less", conf.level = 0.99)
#'
#' # p-value of Kim et al.'s modified t-statistic
#' p.value1 <- modified.t(pm)$p.value
#' @export
modified.t <- function(data, alternative = c("two.sided", "less", "greater"),
mu = 0, conf.level = 0.95, ...){
DNAME <- paste(deparse(substitute(data)))
alternative <- match.arg(alternative)
if(length(data) == 0){
stop("The data is empty. Please input a nonempty dataset to begin.\n")
}else if(is.vector(data)){
stop("The data is a vector. Please input a nonempty dataset to begin.\n")
}else if(length(data[1, ]) == 2){
data <- as.data.frame(t(data))
}else if(length(data[, 1]) == 2){
data <- as.data.frame(data)
}else{
stop("The data input is not partially matched.\n")
}
data1 <- data[which(is.na(data[1, ]) == FALSE & is.na(data[2, ]) == FALSE)]
data2 <- data[which(is.na(data[1, ]) == FALSE & is.na(data[2, ]))]
data3 <- data[which(is.na(data[1, ]) & is.na(data[2, ]) == FALSE)]
n1 <- length(data1)
n2 <- length(data2)
n3 <- length(data3)
if(n1 == 0 & n2 == 0 & n3 == 0){
stop("The data only contains missing values. Please input a valid dataset
to begin.\n")
}else if(n1 == 0 & n2 > 0 & n3 == 0){
if(shapiro.test(unlist(data2[1, ]))$p.value <= 0.05){
test <- wilcox.test(unlist(data2[1, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and only the first sample is given. Because the
Shapiro-Wilk test is significant, the p-value for the given
sample will be outputted using the one-sample Wilcoxon signed
rank test method.\n")
}else{
test <- t.test(data2[1, ], alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and only the first sample is given. Because the
Shapiro-Wilk test is not significant, the p-value for the given
sample will be outputted using the one-sample t-test method.\n")
}
STATISTIC <- test$statistic
PARAMETER <- test$parameter
PVAL <- test$p.value
CINT <- c(test$conf.int[1], test$conf.int[2])
ESTIMATE <- test$estimate
STDERR <- test$stderr
METHOD <- test$method
DNAME <- "data2"
names(STATISTIC) <- names(test$statistic)
names(ESTIMATE) <- names(test$estimate)
names(mu) <- names(test$null.value)
attr(CINT, "conf.level") <- conf.level
}else if(n1 == 0 & n2 == 0 & n3 > 0){
if(shapiro.test(unlist(data3[2, ]))$p.value <= 0.05){
test <- wilcox.test(unlist(data3[2, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and only the second sample is given. Because the
Shapiro-Wilk test is significant, the p-value for the given
sample will be outputted using the one-sample Wilcoxon signed
rank test method.\n")
}else{
test <- t.test(data3[2, ], alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and only the second sample is given. Because the
Shapiro-Wilk test is not significant, the p-value for the given
sample will be outputted using the one-sample t-test method.\n")
}
STATISTIC <- test$statistic
PARAMETER <- test$parameter
PVAL <- test$p.value
CINT <- c(test$conf.int[1], test$conf.int[2])
ESTIMATE <- test$estimate
STDERR <- test$stderr
METHOD <- test$method
DNAME <- "data3"
names(STATISTIC) <- names(test$statistic)
names(ESTIMATE) <- names(test$estimate)
names(mu) <- names(test$null.value)
attr(CINT, "conf.level") <- conf.level
}else if(n1 == 0 & n2 > 0 & n3 > 0){
if(shapiro.test(unlist(data2[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data3[2, ]))$p.value <= 0.05){
test <- wilcox.test(unlist(data2[1, ]), unlist(data3[2, ]),
alternative = alternative, mu = mu, paired = FALSE,
conf.int = TRUE, conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and two independent samples are given. Because the
Shapiro-Wilk test is significant for at least for one of the
samples, the p-value for the given independent samples will be
outputted using the two-sample Wilcoxon rank sum test method.\n")
}else{
if(var.test(unlist(data2[1, ]), unlist(data3[2, ]))$p.value <= 0.05){
test <- t.test(data2[1, ], data3[2, ], alternative = alternative,
mu = mu, conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and two independent samples are given. Because
the Shapiro-Wilk test is not significant for both independent
samples, and the F test to compare the variances of the
independent samples is significant, the p-value for the given
independent samples will be outputted using the two-sample
t-test method with unequal variance assumption.\n")
}else{
test <- t.test(data2[1, ], data3[2, ], alternative = alternative,
mu = mu, conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and two independent samples are given. Because
the Shapiro-Wilk test is not significant for both independent
samples, and the F test to compare the variances of the
independent samples is not significant, the p-value for the
given independent samples will be outputted using the
two-sample t-test method with equal variance assumption.\n")
}
}
STATISTIC <- test$statistic
PARAMETER <- test$parameter
PVAL <- test$p.value
CINT <- c(test$conf.int[1], test$conf.int[2])
ESTIMATE <- test$estimate
STDERR <- test$stderr
METHOD <- test$method
DNAME <- "data2 + data3"
names(STATISTIC) <- names(test$statistic)
names(ESTIMATE) <- names(test$estimate)
names(mu) <- names(test$null.value)
attr(CINT, "conf.level") <- conf.level
}else if(n1 > 0 & n2 == 0 & n3 == 0){
if(shapiro.test(unlist(data1[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test <- wilcox.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu, paired = TRUE,
conf.int = TRUE, conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data is completly
matched. Because the Shapiro-Wilk test is significant for at
least one of the samples, the p-value for the given data will
be outputted using Wilcoxon signed rank test method for matched
pairs.\n")
}else{
test <- t.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu,
conf.level = conf.level, paired = TRUE, var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data is completly
matched. Because the Shapiro-Wilk test is not significant for
both independent samples, the p-value for the given data will
be outputted using the matched t-test method.\n")
}
STATISTIC <- test$statistic
PARAMETER <- test$parameter
PVAL <- test$p.value
CINT <- c(test$conf.int[1], test$conf.int[2])
ESTIMATE <- test$estimate
STDERR <- test$stderr
METHOD <- test$method
DNAME <- "data1"
names(STATISTIC) <- names(test$statistic)
names(ESTIMATE) <- names(test$estimate)
names(mu) <- names(test$null.value)
attr(CINT, "conf.level") <- conf.level
}else if(n1 > 0 & n2 > 0 & n3 == 0){
if(shapiro.test(unlist(data1[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test1 <- wilcox.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu, paired = TRUE,
conf.int = TRUE, conf.level = conf.level)
if(shapiro.test(unlist(cbind(data1, data2)[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test2 <- wilcox.test(unlist(cbind(data1, data2)[1, ]),
unlist(data1[2, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired samples
is significant, the p-value for the complete matched pairs
using the Wilcoxon signed rank test method for matched pairs
will be outputted. Because the Shapiro-Wilk test for the two
independent samples is significant, the two independent
samples using the two-sample Wilcoxon rank sum test method
will also be outputted.\n")
}else{
if(var.test(unlist(cbind(data1, data2)[1, ]), unlist(data1[2, ]))$
p.value <= 0.05){
test2 <- t.test(cbind(data1, data2)[1, ], data1[2, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is significant, the p-value for the complete
matched pairs using the Wilcoxon signed rank test method
for matched pairs will be outputted. Because the
Shapiro-Wilk test for the two independent samples is not
significant and the F test to compare the variances of the
independent samples is significant, the two independent
samples using the two-sample t-test method with unequal
variance assumption will also be outputted.\n")
}else{
test2 <- t.test(cbind(data1, data2)[1, ], data1[2, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is significant, the p-value for the complete
matched pairs using the Wilcoxon signed rank test method
for matched pairs will be outputted. Because the
Shapiro-Wilk test for the two independent samples is not
significant and the F test to compare the variances of the
independent samples is not significant, the two independent
samples using the two-sample t-test method with equal
variance assumption will also be outputted.\n")
}
}
}else{
test1 <- t.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu,
conf.level = conf.level, paired = TRUE, var.equal = FALSE)
if(shapiro.test(unlist(cbind(data1, data2)[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test2 <- wilcox.test(unlist(cbind(data1, data2)[1, ]),
unlist(data1[2, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired samples
is not significant, the p-value for the complete matched
pairs using the matched t-test method for matched pairs will
be outputted. Because the Shapiro-Wilk test for the two
independent samples is significant, the two independent
samples using the two-sample Wilcoxon rank sum test method
will also be outputted.\n")
}else{
if(var.test(unlist(cbind(data1, data2)[1, ]), unlist(data1[2, ]))$
p.value <= 0.05){
test2 <- t.test(cbind(data1, data2)[1, ], data1[2, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is not significant, the p-value for the complete
matched pairs using the matched t-test method for matched
pairs will be outputted. Because the Shapiro-Wilk test for
the two independent samples is not significant and the F
test to compare the variances of the independent samples is
significant, the two independent samples using the
two-sample t-test method with unequal variance assumption
will also be outputted.\n")
}else{
test2 <- t.test(cbind(data1, data2)[1, ], data1[2, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is not significant, the p-value for the complete
matched pairs using the matched t-test method for matched
pairs will be outputted. Because the Shapiro-Wilk test for
the two independent samples is not significant and the F
test to compare the variances of the independent samples is
not significant, the two independent samples using the
two-sample t-test method with equal variance assumption
will also be outputted.\n")
}
}
}
STATISTIC <- c(test1$statistic, test2$statistic)
PARAMETER <- c(test1$parameter, test2$parameter)
PVAL <- c(test1$p.value, test2$p.value)
CINT <- c(paste(test1$conf.int[1], test1$conf.int[2], "and"),
paste(test2$conf.int[1], test2$conf.int[2]))
ESTIMATE <- c(test1$estimate, test2$estimate)
STDERR <- c(test1$stderr, test2$stderr)
METHOD <- paste(test1$method, "and", test2$method)
DNAME <- "data1 and data1 + data2"
names(STATISTIC) <- c(names(test1$statistic), names(test2$statistic))
names(ESTIMATE) <- c(names(test1$estimate), names(test2$estimate))
names(mu) <- paste(names(test1$null.value), "and",
names(test2$null.value))
attr(CINT, "conf.level") <- conf.level
}else if(n1 > 0 & n2 == 0 & n3 > 0){
if(shapiro.test(unlist(data1[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test1 <- wilcox.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu, paired = TRUE,
conf.int = TRUE, conf.level = conf.level)
if(shapiro.test(unlist(cbind(data1, data3)[2, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[1, ]))$p.value <= 0.05){
test2 <- wilcox.test(unlist(cbind(data1, data3)[2, ]),
unlist(data1[1, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired samples
is significant, the p-value for the complete matched pairs
using the Wilcoxon signed rank test method for matched pairs
will be outputted. Because the Shapiro-Wilk test for the two
independent samples is significant, the two independent
samples using the two-sample Wilcoxon rank sum test method
will also be outputted.\n")
}else{
if(var.test(unlist(cbind(data1, data3)[2, ]), unlist(data1[1, ]))$
p.value <= 0.05){
test2 <- t.test(cbind(data1, data3)[2, ], data1[1, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is significant, the p-value for the complete
matched pairs using the Wilcoxon signed rank test method
for matched pairs will be outputted. Because the
Shapiro-Wilk test for the two independent samples is not
significant and the F test to compare the variances of the
independent samples is significant, the two independent
samples using the two-sample t-test method with unequal
variance assumption will also be outputted.\n")
}else{
test2 <- t.test(cbind(data1, data3)[2, ], data1[1, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is significant, the p-value for the complete
matched pairs using the Wilcoxon signed rank test method
for matched pairs will be outputted. Because the
Shapiro-Wilk test for the two independent samples is not
significant and the F test to compare the variances of the
independent samples is not significant, the two independent
samples using the two-sample t-test method with equal
variance assumption will also be outputted.\n")
}
}
}else{
test1 <- t.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu,
conf.level = conf.level, paired = TRUE, var.equal = FALSE)
if(shapiro.test(unlist(cbind(data1, data3)[2, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[1, ]))$p.value <= 0.05){
test2 <- wilcox.test(unlist(cbind(data1, data3)[2, ]),
unlist(data1[1, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired samples
is not significant, the p-value for the complete matched
pairs using the matched t-test method for matched pairs will
be outputted. Because the Shapiro-Wilk test for the two
independent samples is significant, the two independent
samples using the two-sample Wilcoxon rank sum test method
will also be outputted.\n")
}else{
if(var.test(unlist(cbind(data1, data3)[2, ]), unlist(data1[1, ]))$
p.value <= 0.05){
test2 <- t.test(cbind(data1, data3)[2, ], data1[1, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is not significant, the p-value for the complete
matched pairs using the matched t-test method for matched
pairs will be outputted. Because the Shapiro-Wilk test for
the two independent samples is not significant and the F
test to compare the variances of the independent samples is
significant, the two independent samples using the
two-sample t-test method with unequal variance assumption
will also be outputted.\n")
}else{
test2 <- t.test(cbind(data1, data3)[2, ], data1[1, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is not significant, the p-value for the complete
matched pairs using the matched t-test method for matched
pairs will be outputted. Because the Shapiro-Wilk test for
the two independent samples is not significant and the F
test to compare the variances of the independent samples is
not significant, the two independent samples using the
two-sample t-test method with equal variance assumption
will also be outputted.\n")
}
}
}
STATISTIC <- c(test1$statistic, test2$statistic)
PARAMETER <- c(test1$parameter, test2$parameter)
PVAL <- c(test1$p.value, test2$p.value)
CINT <- c(paste(test1$conf.int[1], test1$conf.int[2], "and"),
paste(test2$conf.int[1], test2$conf.int[2]))
ESTIMATE <- c(test1$estimate, test2$estimate)
STDERR <- c(test1$stderr, test2$stderr)
METHOD <- paste(test1$method, "and", test2$method)
DNAME <- "data1 and data1 + data3"
names(STATISTIC) <- c(names(test1$statistic),
names(test2$statistic))
names(ESTIMATE) <- c(names(test1$estimate), names(test2$estimate))
names(mu) <- paste(names(test1$null.value), "and",
names(test2$null.value))
attr(CINT, "conf.level") <- conf.level
}else{
d_bar <- mean(unlist(data1[1,])-unlist(data1[2,]))
t_bar <- mean(unlist(data2[1,]))
n_bar <- mean(unlist(data3[2,]))
s_d <- sd(unlist(data1[1,])-unlist(data1[2,]))
s_t <- sd(unlist(data2[1,]))
s_n <- sd(unlist(data3[2,]))
n_h <- 2/(1/n2+1/n3)
t3 <- (n1*d_bar+n_h*(t_bar-n_bar)-mu)/
sqrt(n1*s_d^2+n_h^2*(s_t^2/n2+s_n^2/n3))
if(alternative == "two.sided"){
p_value <- 2*(1- pnorm(abs(t3)))
cint <- qnorm(1-(1-conf.level)/2)
cint <- t3 + c(-cint, cint)
}else if(alternative == "less"){
p_value <- pnorm(t3)
cint <- c(-Inf, t3+qnorm(conf.level))
}else{
p_value <- 1-pnorm(t3)
cint <- c(t3-qnorm(conf.level), Inf)
}
STATISTIC <- t3
names(STATISTIC) <- "t_3"
PARAMETER <- NULL
PVAL <- p_value
CINT <- mu+cint*sqrt(n1*s_d^2+n_h^2*(s_t^2/n2+s_n^2/n3))
attr(CINT, "conf.level") <- conf.level
ESTIMATE <- mu+t3*sqrt(n1*s_d^2+n_h^2*(s_t^2/n2+s_n^2/n3))
names(ESTIMATE) <- names(mu) <- "difference in means"
STDERR <- sqrt(n1*s_d^2+n_h^2*(s_t^2/n2+s_n^2/n3))
METHOD = "Kim et al.'s modified t-statistic"
}
result <- list(statistic = STATISTIC, parameter = PARAMETER, p.value = PVAL,
conf.int = CINT, estimate = ESTIMATE, null.value = mu,
stderr = STDERR, alternative = alternative, method = METHOD,
data.name = DNAME)
attr(result, "class") <- "htest"
return(result)
}
Garylikai/PMLi-1.0-R-Package documentation built on Dec. 28, 2021, 12:12 a.m.
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Defines functions modified.t
Documented in modified.t
#' @title Kim et al.'s Modified t-Statistic
#' @description \code{modified.t} is used to calculate Kim et al.'s modified
#' t-statistic for partially matched samples, specified by giving a data frame
#' or matrix, testing hypothesis, true mean and confidence level.
#' @param data a 2-by-n or n-by-2 partially matched samples data frame or
#' matrix.
#' @param alternative a character string specifying the alternative hypothesis,
#' must be one of "two.sided" (default), "greater" or "less". You can specify
#' just the initial letter.
#' @param mu a number indicating the true difference in means.
#' @param conf.level confidence level for the returned confidence interval.
#' @param ... further arguments to be passed to or from methods.
#' @details Whether the dataset input is partially matched samples will be
#' checked. If not, appropriate hypothesis tests, such as one and two sample
#' t-tests, will be performed instead.
#' @return A list with class "htest" containing the following components:
#' \item{\code{statistic}}{the value of the test statistic.}
#' \item{\code{parameter}}{the degrees of freedom of the test statistic or
#' NA.} \item{\code{p.value}}{the p-value of the test.}
#' \item{\code{conf.int}}{a confidence interval for the mean appropriate to
#' the specified alternative hypothesis.} \item{\code{estimate}}{the estimated
#' mean or difference in means.} \item{\code{null.value}}{the specified
#' hypothesized value of the mean or mean difference.}
#' \item{\code{stderr}}{the standard error of the mean (difference).}
#' \item{\code{alternative}}{a character string describing the alternative
#' hypothesis.} \item{\code{method}}{a character string indicating what type
#' of test was performed.} \item{\code{data.name}}{a character string giving
#' the name(s) of the data.}
#' @import stats
#' @author Kai Li \email{kai.li@stonybrook.edu}
#' @references Kuan P F, Huang B. A simple and robust method for partially
#' matched samples using the p-values pooling approach. \emph{Statistics in
#' medicine}. 2013; 32(19): 3247-3259.
#'
#' Kim B, Kim I, Lee S, Kim S, Rha S, Chung H. Statistical methods of
#' translating microarray data into clinically relevant diagnostic information
#' in colorectal cancer. \emph{Bioinformatics}. 2004; 21(4): 517-528. [PubMed:
#' 15374865]
#' @seealso \code{\link[stats]{t.test}} for the one and two-sample t-tests.
#'
#' \code{\link[stats]{var.test}} for the F test to compare two variances.
#'
#' \code{\link[stats]{shapiro.test}} for the Shapiro-Wilk test of normality.
#'
#' \code{\link[stats]{wilcox.test}} for the one and two-sample Wilcoxon tests.
#'
#' \code{\link{weighted.z}}, \code{\link{corrected.z}},
#' \code{\link{mle.hetero}}, and \code{\link{mle.homo}} for other statistical
#' approaches for partially matched samples.
#' @examples
#' # pm is a sample dataset for the PMLi package
#'
#' # Kim et al.'s modified t-statistic formula interface
#' modified.t(pm, "less", conf.level = 0.99)
#'
#' # p-value of Kim et al.'s modified t-statistic
#' p.value1 <- modified.t(pm)$p.value
#' @export
modified.t <- function(data, alternative = c("two.sided", "less", "greater"),
mu = 0, conf.level = 0.95, ...){
DNAME <- paste(deparse(substitute(data)))
alternative <- match.arg(alternative)
if(length(data) == 0){
stop("The data is empty. Please input a nonempty dataset to begin.\n")
}else if(is.vector(data)){
stop("The data is a vector. Please input a nonempty dataset to begin.\n")
}else if(length(data[1, ]) == 2){
data <- as.data.frame(t(data))
}else if(length(data[, 1]) == 2){
data <- as.data.frame(data)
}else{
stop("The data input is not partially matched.\n")
}
data1 <- data[which(is.na(data[1, ]) == FALSE & is.na(data[2, ]) == FALSE)]
data2 <- data[which(is.na(data[1, ]) == FALSE & is.na(data[2, ]))]
data3 <- data[which(is.na(data[1, ]) & is.na(data[2, ]) == FALSE)]
n1 <- length(data1)
n2 <- length(data2)
n3 <- length(data3)
if(n1 == 0 & n2 == 0 & n3 == 0){
stop("The data only contains missing values. Please input a valid dataset
to begin.\n")
}else if(n1 == 0 & n2 > 0 & n3 == 0){
if(shapiro.test(unlist(data2[1, ]))$p.value <= 0.05){
test <- wilcox.test(unlist(data2[1, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and only the first sample is given. Because the
Shapiro-Wilk test is significant, the p-value for the given
sample will be outputted using the one-sample Wilcoxon signed
rank test method.\n")
}else{
test <- t.test(data2[1, ], alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and only the first sample is given. Because the
Shapiro-Wilk test is not significant, the p-value for the given
sample will be outputted using the one-sample t-test method.\n")
}
STATISTIC <- test$statistic
PARAMETER <- test$parameter
PVAL <- test$p.value
CINT <- c(test$conf.int[1], test$conf.int[2])
ESTIMATE <- test$estimate
STDERR <- test$stderr
METHOD <- test$method
DNAME <- "data2"
names(STATISTIC) <- names(test$statistic)
names(ESTIMATE) <- names(test$estimate)
names(mu) <- names(test$null.value)
attr(CINT, "conf.level") <- conf.level
}else if(n1 == 0 & n2 == 0 & n3 > 0){
if(shapiro.test(unlist(data3[2, ]))$p.value <= 0.05){
test <- wilcox.test(unlist(data3[2, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and only the second sample is given. Because the
Shapiro-Wilk test is significant, the p-value for the given
sample will be outputted using the one-sample Wilcoxon signed
rank test method.\n")
}else{
test <- t.test(data3[2, ], alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and only the second sample is given. Because the
Shapiro-Wilk test is not significant, the p-value for the given
sample will be outputted using the one-sample t-test method.\n")
}
STATISTIC <- test$statistic
PARAMETER <- test$parameter
PVAL <- test$p.value
CINT <- c(test$conf.int[1], test$conf.int[2])
ESTIMATE <- test$estimate
STDERR <- test$stderr
METHOD <- test$method
DNAME <- "data3"
names(STATISTIC) <- names(test$statistic)
names(ESTIMATE) <- names(test$estimate)
names(mu) <- names(test$null.value)
attr(CINT, "conf.level") <- conf.level
}else if(n1 == 0 & n2 > 0 & n3 > 0){
if(shapiro.test(unlist(data2[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data3[2, ]))$p.value <= 0.05){
test <- wilcox.test(unlist(data2[1, ]), unlist(data3[2, ]),
alternative = alternative, mu = mu, paired = FALSE,
conf.int = TRUE, conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and two independent samples are given. Because the
Shapiro-Wilk test is significant for at least for one of the
samples, the p-value for the given independent samples will be
outputted using the two-sample Wilcoxon rank sum test method.\n")
}else{
if(var.test(unlist(data2[1, ]), unlist(data3[2, ]))$p.value <= 0.05){
test <- t.test(data2[1, ], data3[2, ], alternative = alternative,
mu = mu, conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and two independent samples are given. Because
the Shapiro-Wilk test is not significant for both independent
samples, and the F test to compare the variances of the
independent samples is significant, the p-value for the given
independent samples will be outputted using the two-sample
t-test method with unequal variance assumption.\n")
}else{
test <- t.test(data2[1, ], data3[2, ], alternative = alternative,
mu = mu, conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data does not have any
matched pairs, and two independent samples are given. Because
the Shapiro-Wilk test is not significant for both independent
samples, and the F test to compare the variances of the
independent samples is not significant, the p-value for the
given independent samples will be outputted using the
two-sample t-test method with equal variance assumption.\n")
}
}
STATISTIC <- test$statistic
PARAMETER <- test$parameter
PVAL <- test$p.value
CINT <- c(test$conf.int[1], test$conf.int[2])
ESTIMATE <- test$estimate
STDERR <- test$stderr
METHOD <- test$method
DNAME <- "data2 + data3"
names(STATISTIC) <- names(test$statistic)
names(ESTIMATE) <- names(test$estimate)
names(mu) <- names(test$null.value)
attr(CINT, "conf.level") <- conf.level
}else if(n1 > 0 & n2 == 0 & n3 == 0){
if(shapiro.test(unlist(data1[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test <- wilcox.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu, paired = TRUE,
conf.int = TRUE, conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data is completly
matched. Because the Shapiro-Wilk test is significant for at
least one of the samples, the p-value for the given data will
be outputted using Wilcoxon signed rank test method for matched
pairs.\n")
}else{
test <- t.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu,
conf.level = conf.level, paired = TRUE, var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data is completly
matched. Because the Shapiro-Wilk test is not significant for
both independent samples, the p-value for the given data will
be outputted using the matched t-test method.\n")
}
STATISTIC <- test$statistic
PARAMETER <- test$parameter
PVAL <- test$p.value
CINT <- c(test$conf.int[1], test$conf.int[2])
ESTIMATE <- test$estimate
STDERR <- test$stderr
METHOD <- test$method
DNAME <- "data1"
names(STATISTIC) <- names(test$statistic)
names(ESTIMATE) <- names(test$estimate)
names(mu) <- names(test$null.value)
attr(CINT, "conf.level") <- conf.level
}else if(n1 > 0 & n2 > 0 & n3 == 0){
if(shapiro.test(unlist(data1[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test1 <- wilcox.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu, paired = TRUE,
conf.int = TRUE, conf.level = conf.level)
if(shapiro.test(unlist(cbind(data1, data2)[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test2 <- wilcox.test(unlist(cbind(data1, data2)[1, ]),
unlist(data1[2, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired samples
is significant, the p-value for the complete matched pairs
using the Wilcoxon signed rank test method for matched pairs
will be outputted. Because the Shapiro-Wilk test for the two
independent samples is significant, the two independent
samples using the two-sample Wilcoxon rank sum test method
will also be outputted.\n")
}else{
if(var.test(unlist(cbind(data1, data2)[1, ]), unlist(data1[2, ]))$
p.value <= 0.05){
test2 <- t.test(cbind(data1, data2)[1, ], data1[2, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is significant, the p-value for the complete
matched pairs using the Wilcoxon signed rank test method
for matched pairs will be outputted. Because the
Shapiro-Wilk test for the two independent samples is not
significant and the F test to compare the variances of the
independent samples is significant, the two independent
samples using the two-sample t-test method with unequal
variance assumption will also be outputted.\n")
}else{
test2 <- t.test(cbind(data1, data2)[1, ], data1[2, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is significant, the p-value for the complete
matched pairs using the Wilcoxon signed rank test method
for matched pairs will be outputted. Because the
Shapiro-Wilk test for the two independent samples is not
significant and the F test to compare the variances of the
independent samples is not significant, the two independent
samples using the two-sample t-test method with equal
variance assumption will also be outputted.\n")
}
}
}else{
test1 <- t.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu,
conf.level = conf.level, paired = TRUE, var.equal = FALSE)
if(shapiro.test(unlist(cbind(data1, data2)[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test2 <- wilcox.test(unlist(cbind(data1, data2)[1, ]),
unlist(data1[2, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired samples
is not significant, the p-value for the complete matched
pairs using the matched t-test method for matched pairs will
be outputted. Because the Shapiro-Wilk test for the two
independent samples is significant, the two independent
samples using the two-sample Wilcoxon rank sum test method
will also be outputted.\n")
}else{
if(var.test(unlist(cbind(data1, data2)[1, ]), unlist(data1[2, ]))$
p.value <= 0.05){
test2 <- t.test(cbind(data1, data2)[1, ], data1[2, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is not significant, the p-value for the complete
matched pairs using the matched t-test method for matched
pairs will be outputted. Because the Shapiro-Wilk test for
the two independent samples is not significant and the F
test to compare the variances of the independent samples is
significant, the two independent samples using the
two-sample t-test method with unequal variance assumption
will also be outputted.\n")
}else{
test2 <- t.test(cbind(data1, data2)[1, ], data1[2, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the first sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is not significant, the p-value for the complete
matched pairs using the matched t-test method for matched
pairs will be outputted. Because the Shapiro-Wilk test for
the two independent samples is not significant and the F
test to compare the variances of the independent samples is
not significant, the two independent samples using the
two-sample t-test method with equal variance assumption
will also be outputted.\n")
}
}
}
STATISTIC <- c(test1$statistic, test2$statistic)
PARAMETER <- c(test1$parameter, test2$parameter)
PVAL <- c(test1$p.value, test2$p.value)
CINT <- c(paste(test1$conf.int[1], test1$conf.int[2], "and"),
paste(test2$conf.int[1], test2$conf.int[2]))
ESTIMATE <- c(test1$estimate, test2$estimate)
STDERR <- c(test1$stderr, test2$stderr)
METHOD <- paste(test1$method, "and", test2$method)
DNAME <- "data1 and data1 + data2"
names(STATISTIC) <- c(names(test1$statistic), names(test2$statistic))
names(ESTIMATE) <- c(names(test1$estimate), names(test2$estimate))
names(mu) <- paste(names(test1$null.value), "and",
names(test2$null.value))
attr(CINT, "conf.level") <- conf.level
}else if(n1 > 0 & n2 == 0 & n3 > 0){
if(shapiro.test(unlist(data1[1, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[2, ]))$p.value <= 0.05){
test1 <- wilcox.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu, paired = TRUE,
conf.int = TRUE, conf.level = conf.level)
if(shapiro.test(unlist(cbind(data1, data3)[2, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[1, ]))$p.value <= 0.05){
test2 <- wilcox.test(unlist(cbind(data1, data3)[2, ]),
unlist(data1[1, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired samples
is significant, the p-value for the complete matched pairs
using the Wilcoxon signed rank test method for matched pairs
will be outputted. Because the Shapiro-Wilk test for the two
independent samples is significant, the two independent
samples using the two-sample Wilcoxon rank sum test method
will also be outputted.\n")
}else{
if(var.test(unlist(cbind(data1, data3)[2, ]), unlist(data1[1, ]))$
p.value <= 0.05){
test2 <- t.test(cbind(data1, data3)[2, ], data1[1, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is significant, the p-value for the complete
matched pairs using the Wilcoxon signed rank test method
for matched pairs will be outputted. Because the
Shapiro-Wilk test for the two independent samples is not
significant and the F test to compare the variances of the
independent samples is significant, the two independent
samples using the two-sample t-test method with unequal
variance assumption will also be outputted.\n")
}else{
test2 <- t.test(cbind(data1, data3)[2, ], data1[1, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is significant, the p-value for the complete
matched pairs using the Wilcoxon signed rank test method
for matched pairs will be outputted. Because the
Shapiro-Wilk test for the two independent samples is not
significant and the F test to compare the variances of the
independent samples is not significant, the two independent
samples using the two-sample t-test method with equal
variance assumption will also be outputted.\n")
}
}
}else{
test1 <- t.test(unlist(data1[1, ]), unlist(data1[2, ]),
alternative = alternative, mu = mu,
conf.level = conf.level, paired = TRUE, var.equal = FALSE)
if(shapiro.test(unlist(cbind(data1, data3)[2, ]))$p.value <= 0.05 |
shapiro.test(unlist(data1[1, ]))$p.value <= 0.05){
test2 <- wilcox.test(unlist(cbind(data1, data3)[2, ]),
unlist(data1[1, ]), alternative = alternative,
mu = mu, paired = FALSE, conf.int = TRUE,
conf.level = conf.level)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired samples
is not significant, the p-value for the complete matched
pairs using the matched t-test method for matched pairs will
be outputted. Because the Shapiro-Wilk test for the two
independent samples is significant, the two independent
samples using the two-sample Wilcoxon rank sum test method
will also be outputted.\n")
}else{
if(var.test(unlist(cbind(data1, data3)[2, ]), unlist(data1[1, ]))$
p.value <= 0.05){
test2 <- t.test(cbind(data1, data3)[2, ], data1[1, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = FALSE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is not significant, the p-value for the complete
matched pairs using the matched t-test method for matched
pairs will be outputted. Because the Shapiro-Wilk test for
the two independent samples is not significant and the F
test to compare the variances of the independent samples is
significant, the two independent samples using the
two-sample t-test method with unequal variance assumption
will also be outputted.\n")
}else{
test2 <- t.test(cbind(data1, data3)[2, ], data1[1, ],
alternative = alternative, mu = mu,
conf.level = conf.level, paired = FALSE,
var.equal = TRUE)
warning("Kim et al.'s modified t-statistic assumes the data contains
partially matched samples. The inputted data contains
complete matched pairs but only the second sample is given.
Because the Shapiro-Wilk test for the matched paired
samples is not significant, the p-value for the complete
matched pairs using the matched t-test method for matched
pairs will be outputted. Because the Shapiro-Wilk test for
the two independent samples is not significant and the F
test to compare the variances of the independent samples is
not significant, the two independent samples using the
two-sample t-test method with equal variance assumption
will also be outputted.\n")
}
}
}
STATISTIC <- c(test1$statistic, test2$statistic)
PARAMETER <- c(test1$parameter, test2$parameter)
PVAL <- c(test1$p.value, test2$p.value)
CINT <- c(paste(test1$conf.int[1], test1$conf.int[2], "and"),
paste(test2$conf.int[1], test2$conf.int[2]))
ESTIMATE <- c(test1$estimate, test2$estimate)
STDERR <- c(test1$stderr, test2$stderr)
METHOD <- paste(test1$method, "and", test2$method)
DNAME <- "data1 and data1 + data3"
names(STATISTIC) <- c(names(test1$statistic),
names(test2$statistic))
names(ESTIMATE) <- c(names(test1$estimate), names(test2$estimate))
names(mu) <- paste(names(test1$null.value), "and",
names(test2$null.value))
attr(CINT, "conf.level") <- conf.level
}else{
d_bar <- mean(unlist(data1[1,])-unlist(data1[2,]))
t_bar <- mean(unlist(data2[1,]))
n_bar <- mean(unlist(data3[2,]))
s_d <- sd(unlist(data1[1,])-unlist(data1[2,]))
s_t <- sd(unlist(data2[1,]))
s_n <- sd(unlist(data3[2,]))
n_h <- 2/(1/n2+1/n3)
t3 <- (n1*d_bar+n_h*(t_bar-n_bar)-mu)/
sqrt(n1*s_d^2+n_h^2*(s_t^2/n2+s_n^2/n3))
if(alternative == "two.sided"){
p_value <- 2*(1- pnorm(abs(t3)))
cint <- qnorm(1-(1-conf.level)/2)
cint <- t3 + c(-cint, cint)
}else if(alternative == "less"){
p_value <- pnorm(t3)
cint <- c(-Inf, t3+qnorm(conf.level))
}else{
p_value <- 1-pnorm(t3)
cint <- c(t3-qnorm(conf.level), Inf)
}
STATISTIC <- t3
names(STATISTIC) <- "t_3"
PARAMETER <- NULL
PVAL <- p_value
CINT <- mu+cint*sqrt(n1*s_d^2+n_h^2*(s_t^2/n2+s_n^2/n3))
attr(CINT, "conf.level") <- conf.level
ESTIMATE <- mu+t3*sqrt(n1*s_d^2+n_h^2*(s_t^2/n2+s_n^2/n3))
names(ESTIMATE) <- names(mu) <- "difference in means"
STDERR <- sqrt(n1*s_d^2+n_h^2*(s_t^2/n2+s_n^2/n3))
METHOD = "Kim et al.'s modified t-statistic"
}
result <- list(statistic = STATISTIC, parameter = PARAMETER, p.value = PVAL,
conf.int = CINT, estimate = ESTIMATE, null.value = mu,
stderr = STDERR, alternative = alternative, method = METHOD,
data.name = DNAME)
attr(result, "class") <- "htest"
return(result)
}
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