# COHEND = UNIVARIATE or BIVARIATE #####################
#' @export
roundMP.cohen.d <- function(deltax = NULL, mu0 = NULL, assumptions = TRUE, verbose = FALSE, fromStatistics = NULL, fromData = NULL) {
# validation and conversion
if (is.null(deltax)||(length(deltax)>1)) stop("deltax must be a single real value")
if ((is.null(fromData))&&(is.null(fromStatistics))) stop("you must use fromStatistics or fromData")
if (is.null(fromStatistics)) {
dta <- MP.getData(fromData, "1or2")
if(MP.rowLengths(dta) == 1) {
if(is.null(mu0)) stop ("for one-sample d_1, you must provide a value to mu0")
ngrp <- 1
x1 <- dta[[1]]
y1 <- mu0
y2 <- NULL
} else {
ngrp <- 2
x1 <- dta[[1]]
y1 <- y2 <- dta[[2]]
}
dmn <- mean(x1)-mean(y1)
args <- list(x1,y2)
args[sapply(args, is.null)] <- NULL # removing nulls
sds <- unlist(lapply(args, sd))
ns <- unlist(lapply(args, length))
} else {
if (is.null(mu0)) {
sts <- MP.vfyStat(fromStatistics, c("mean1","sd1","n1","mean2","sd2","n2"))
ngrp <- 2
dmn <- sts[["mean1"]]-sts[["mean2"]]
sds <- c(sts[["sd1"]],sts[["sd2"]])
ns <- c(sts[["n1"]],sts[["n2"]])
} else {
sts <- MP.vfyStat(fromStatistics, c("mean","sd","n"))
ngrp <- 1
dmn <- sts[["mean"]]-mu0
sds <- sts[["sd"]]
ns <- sts[["n"]]
}
}
# additional statistic computations
sdp <- sqrt(sum((ns - 1) * sds^2)/(sum(ns) - length(ns)))
nh <- 1/mean(1/ns)
d <- abs(dmn)/sdp # cohen's d
nu <- sum(ns) - length(ns)
J <- if (nu>300) 1 else gamma(nu/2) / (sqrt(nu/2) * gamma((nu-1)/2) )
g <- d * J # this is unbiased Cohen's d (Goulet-Pelletier & Cousineau, 2018)
# precision computations
# a. Extrinsinc precision
prEP <- sqrt(nu/(nu-2)*2/nh * (1+ g^2 *nh/2)- g^2/J^2)
rdEP <- round(g, -log10(prEP * 1.0001)+0.5)
# b. Systematic (worst-case) intrinsinc precision
if (assumptions) {
prWC <- ngrp * deltax / sdp
assumptext <- "based on the normality assumption, an absence of effect and the homogeneity of variance if two groups"
} else {
dta <- list(x,y)
fsum <- 1:ngrp
for (i in 1:ngrp)
fsum[i]<- sum(abs(1/ns[i] -1/(sum(ns)-ngrp) * (unlist(dta[i])-mean(unlist(dta[i])))/sd(unlist(dta[i]))*d))
tsum <- sum(fsum)
prWC <- tsum * deltax / sdp
assumptext <- "assumption-free"
}
rdWC <- round(g, -log10(prWC * 1.0001 )+0.5)
# c. Non-systematic (best-case) instrinsinc precision
prBC <- sqrt(ngrp)/sqrt(nh) *deltax / sdp
rdBC <- round(g, -log10(prBC * 1.0001)+0.5)
# output results
if (verbose) MP.showVerbose("cohen.d(unbs'd)", g, deltax, prEP, rdEP, prWC, rdWC, prBC, rdBC, assumptext)
res <- setNames( c(g, rdEP, rdWC, rdBC),
c("machine.precision","extrinsic","systematic","non.systematic") )
return(as.data.frame(t(res))[getOption("roundMP.selectedScenario")])
}
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