summary.escalc <- function(object, out.names=c("sei","zi","pval","ci.lb","ci.ub"), var.names,
H0=0, append=TRUE, replace=TRUE, level=95, olim, digits, transf, ...) {
mstyle <- .get.mstyle()
.chkclass(class(object), must="escalc")
x <- object
level <- .level(level)
crit <- qnorm(level/2, lower.tail=FALSE)
if (length(out.names) != 5L)
stop(mstyle$stop("Argument 'out.names' must be of length 5."))
if (any(out.names != make.names(out.names, unique=TRUE))) {
out.names <- make.names(out.names, unique=TRUE)
warning(mstyle$warning(paste0("Argument 'out.names' does not contain syntactically valid variable names.\nVariable names adjusted to: out.names = c('", out.names[1], "','", out.names[2], "','", out.names[3], "','", out.names[4], "','", out.names[5], "').")), call.=FALSE)
}
if (missing(transf))
transf <- FALSE
#########################################################################
### figure out names of yi and vi variables (if possible) and extract the values (if possible)
if (missing(var.names)) { # if var.names not specified, take from object if possible
if (!is.null(attr(x, "yi.names"))) { # if yi.names attributes is available
yi.name <- attr(x, "yi.names")[1] # take the first entry to be the yi variable
} else { # if not, see if 'yi' is in the object and assume that is the yi variable
if (!is.element("yi", names(x)))
stop(mstyle$stop("Cannot determine name of the 'yi' variable."))
yi.name <- "yi"
}
if (!is.null(attr(x, "vi.names"))) { # if vi.names attributes is available
vi.name <- attr(x, "vi.names")[1] # take the first entry to be the vi variable
} else { # if not, see if 'vi' is in the object and assume that is the vi variable
if (!is.element("vi", names(x)))
stop(mstyle$stop("Cannot determine name of the 'vi' variable."))
vi.name <- "vi"
}
} else {
if (length(var.names) != 2L)
stop(mstyle$stop("Argument 'var.names' must be of length 2."))
if (any(var.names != make.names(var.names, unique=TRUE))) {
var.names <- make.names(var.names, unique=TRUE)
warning(mstyle$warning(paste0("Argument 'var.names' does not contain syntactically valid variable names.\nVariable names adjusted to: var.names = c('", var.names[1], "','", var.names[2], "').")), call.=FALSE)
}
yi.name <- var.names[1]
vi.name <- var.names[2]
}
yi <- x[[yi.name]]
vi <- x[[vi.name]]
if (is.null(yi))
stop(mstyle$stop(paste0("Cannot find variable '", yi.name, "' in the data frame.")))
if (is.null(vi))
stop(mstyle$stop(paste0("Cannot find variable '", vi.name, "' in the data frame.")))
#########################################################################
k <- length(yi)
if (length(H0) == 1L)
H0 <- rep(H0, k)
### compute sei, zi, and lower/upper CI bounds; when applying a transformation, compute the transformed outcome and CI bounds
sei <- sqrt(vi)
zi <- c(yi - H0) / sei
pval <- 2*pnorm(abs(zi), lower.tail=FALSE)
if (is.function(transf)) {
ci.lb <- mapply(transf, yi - crit * sei, ...)
ci.ub <- mapply(transf, yi + crit * sei, ...)
yi <- mapply(transf, yi, ...)
attr(x, "transf") <- TRUE
vi <- NULL
sei <- NULL
zi <- NULL
pval <- NULL
} else {
ci.lb <- yi - crit * sei
ci.ub <- yi + crit * sei
attr(x, "transf") <- FALSE
}
### make sure order of intervals is always increasing
tmp <- .psort(ci.lb, ci.ub)
ci.lb <- tmp[,1]
ci.ub <- tmp[,2]
### apply observation/outcome limits if specified
if (!missing(olim)) {
if (length(olim) != 2L)
stop(mstyle$stop("Argument 'olim' must be of length 2."))
olim <- sort(olim)
yi <- .applyolim(yi, olim) # note: zi and pval are based on unconstrained yi
ci.lb <- .applyolim(ci.lb, olim)
ci.ub <- .applyolim(ci.ub, olim)
}
x[[yi.name]] <- yi
x[[vi.name]] <- vi
#return(cbind(yi, vi, sei, zi, ci.lb, ci.ub))
### put together dataset
if (append) {
### if user wants to append
dat <- data.frame(x)
if (replace) {
### and wants to replace all values
dat[[out.names[1]]] <- sei # if variable does not exists in dat, it will be added
dat[[out.names[2]]] <- zi # if variable does not exists in dat, it will be added
dat[[out.names[3]]] <- pval # if variable does not exists in dat, it will be added
dat[[out.names[4]]] <- ci.lb # if variable does not exists in dat, it will be added
dat[[out.names[5]]] <- ci.ub # if variable does not exists in dat, it will be added
} else {
### and only wants to replace any NA values
if (is.element(out.names[1], names(dat))) { # if sei variable is in data frame, replace NA values with newly calculated values
is.na.sei <- is.na(dat[[out.names[1]]])
dat[[out.names[1]]][is.na.sei] <- sei[is.na.sei]
} else {
dat[[out.names[1]]] <- sei # if sei variable does not exist in dat, just add as new variable
}
if (is.element(out.names[2], names(dat))) { # if zi variable is in data frame, replace NA values with newly calculated values
is.na.zi <- is.na(dat[[out.names[2]]])
dat[[out.names[2]]][is.na.zi] <- zi[is.na.zi]
} else {
dat[[out.names[2]]] <- zi # if zi variable does not exist in dat, just add as new variable
}
if (is.element(out.names[3], names(dat))) { # if pval variable is in data frame, replace NA values with newly calculated values
is.na.pval <- is.na(dat[[out.names[3]]])
dat[[out.names[3]]][is.na.pval] <- pval[is.na.pval]
} else {
dat[[out.names[3]]] <- pval # if pval variable does not exist in dat, just add as new variable
}
if (is.element(out.names[4], names(dat))) { # if ci.lb variable is in data frame, replace NA values with newly calculated values
is.na.ci.lb <- is.na(dat[[out.names[4]]])
dat[[out.names[4]]][is.na.ci.lb] <- ci.lb[is.na.ci.lb]
} else {
dat[[out.names[4]]] <- ci.lb # if ci.lb variable does not exist in dat, just add as new variable
}
if (is.element(out.names[5], names(dat))) { # if ci.ub variable is in data frame, replace NA values with newly calculated values
is.na.ci.ub <- is.na(dat[[out.names[5]]])
dat[[out.names[5]]][is.na.ci.ub] <- ci.ub[is.na.ci.ub]
} else {
dat[[out.names[5]]] <- ci.ub # if ci.ub variable does not exist in dat, just add as new variable
}
}
} else {
### if user does not want to append
if (is.function(transf)) {
dat <- data.frame(yi, ci.lb, ci.ub)
names(dat) <- c(yi.name, out.names[4:5])
} else {
dat <- data.frame(yi, vi, sei, zi, pval, ci.lb, ci.ub)
names(dat) <- c(yi.name, vi.name, out.names)
}
}
### update existing digits attribute if digits is specified
if (!missing(digits)) {
attr(dat, "digits") <- .get.digits(digits=digits, xdigits=attr(x, "digits"), dmiss=FALSE)
} else {
attr(dat, "digits") <- attr(x, "digits")
}
if (is.null(attr(dat, "digits"))) # in case x no longer has a 'digits' attribute
attr(dat, "digits") <- 4
### update existing var.names attribute if var.names is specified
### and make sure all other yi.names and vi.names are added back in
if (!missing(var.names)) {
attr(dat, "yi.names") <- union(var.names[1], attr(object, "yi.names"))
} else {
attr(dat, "yi.names") <- union(yi.name, attr(object, "yi.names"))
}
if (!missing(var.names)) {
attr(dat, "vi.names") <- union(var.names[2], attr(object, "vi.names"))
} else {
attr(dat, "vi.names") <- union(vi.name, attr(object, "vi.names"))
}
### add 'sei.names', 'zi.names', 'pval.names', 'ci.lb.names', and 'ci.ub.names' to the first position of the corresponding attributes
### note: if "xyz" is not an attribute of the object, attr(object, "xyz") returns NULL, so this works fine
attr(dat, "sei.names") <- union(out.names[1], attr(object, "sei.names"))
attr(dat, "zi.names") <- union(out.names[2], attr(object, "zi.names"))
attr(dat, "pval.names") <- union(out.names[3], attr(object, "pval.names"))
attr(dat, "ci.lb.names") <- union(out.names[4], attr(object, "ci.lb.names"))
attr(dat, "ci.ub.names") <- union(out.names[5], attr(object, "ci.ub.names"))
### TODO: clean up attribute elements that are no longer actually part of the object
class(dat) <- c("escalc", "data.frame")
return(dat)
}
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