Nothing
conv.delta <- function(yi, vi, ni, data, include, transf, var.names, append=TRUE, replace="ifna", ...) {
mstyle <- .get.mstyle()
if (missing(yi) || missing(vi))
stop(mstyle$stop("Must specify 'yi' and 'vi' arguments."))
if (missing(transf))
stop(mstyle$stop("Must specify 'transf' argument."))
if (is.logical(replace)) {
if (isTRUE(replace)) {
replace <- "all"
} else {
replace <- "ifna"
}
}
replace <- match.arg(replace, c("ifna","all"))
#########################################################################
if (missing(data))
data <- NULL
has.data <- !is.null(data)
if (is.null(data)) {
data <- sys.frame(sys.parent())
} else {
if (!is.data.frame(data))
data <- data.frame(data)
}
x <- data
### checks on var.names argument
if (missing(var.names)) {
if (inherits(x, "escalc")) {
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 {
yi.name <- "yi"
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]
}
#########################################################################
mf <- match.call()
yi <- .getx("yi", mf=mf, data=x, checknumeric=TRUE)
vi <- .getx("vi", mf=mf, data=x, checknumeric=TRUE)
ni <- .getx("ni", mf=mf, data=x, checknumeric=TRUE)
include <- .getx("include", mf=mf, data=x)
### check length of yi and vi (and ni)
if (length(yi) != length(vi))
stop(mstyle$stop("Length of 'yi' and 'vi' is not the same."))
if (!.equal.length(yi, vi, ni)) # a bit redundant with the above, but keep
stop(mstyle$stop("Supplied data vectors are not all of the same length."))
### check 'vi' argument for potential misuse
.chkviarg(mf$vi)
k <- length(yi)
### if ni/include is NULL, set to TRUE vector
if (is.null(ni))
ni <- rep(NA_real_, k)
if (is.null(include))
include <- rep(TRUE, k)
### turn numeric include vector into logical vector
include <- .chksubset(include, k, stoponk0=FALSE)
### set inputs to NA for rows not to be included
yi[!include] <- NA_real_
vi[!include] <- NA_real_
ni[!include] <- NA_real_
### get names of arguments to transf (except the first and ... in case that is there)
transfargs <- names(formals(args(transf)))
transfargs <- transfargs[-1]
transfargs <- transfargs[transfargs != "..."]
### get ... args
args <- names(sapply(mf[-1], deparse))
rmargs <- c("yi", "vi", "data", "include", "transf", "var.names", "append", "replace")
dotargs <- args[!args %in% rmargs]
### keep arguments in dotargs that are actual arguments of 'transf'
dotargs <- dotargs[dotargs %in% transfargs]
dotarglist <- list()
for (i in seq_along(dotargs)) {
dotarglist[[i]] <- .getx(dotargs[i], mf=mf, data=x, checknumeric=TRUE)
if (length(dotarglist[[i]]) == 1L)
dotarglist[[i]] <- rep(dotarglist[[i]], k)
names(dotarglist)[i] <- dotargs[i]
}
#print(dotarglist)
argmatch <- pmatch(names(dotarglist), table=c("func","method","side"), duplicates.ok=TRUE)
if (!all(is.na(argmatch)))
stop(mstyle$stop("One or more arguments in ... (partially) match an argument from numDeriv::grad()."))
#########################################################################
#ddd <- list(c(yi), ...)
#yi.t <- unlist(.mapply(FUN=transf, dots=ddd, MoreArgs=NULL))
#deriv <- unlist(.mapply(FUN=.compgrad, dots=ddd, MoreArgs=list(func=transf)))
#vi.t <- vi * deriv^2
#dat <- data.frame(yi=yi.t, vi=vi.t)
#return(dat)
yi.t <- rep(NA_real_, k)
vi.t <- rep(NA_real_, k)
deriv <- rep(NA_real_, k)
for (i in 1:k) {
args <- c(yi[[i]], as.list(sapply(dotarglist, `[[`, i))) # use [[]] in case yi is a named vector
#print(args)
tmp <- try(suppressWarnings(do.call(transf, args)), silent=TRUE)
#tmp <- try(do.call(transf, args), silent=FALSE)
if (inherits(tmp, "try-error")) {
yi.t[i] <- NA_real_
} else {
yi.t[i] <- tmp
}
args <- c(args, func=transf)
#print(args)
tmp <- try(suppressWarnings(do.call(numDeriv::grad, args)), silent=TRUE)
#tmp <- try(do.call(numDeriv::grad, args))
if (inherits(tmp, "try-error")) {
vi.t[i] <- NA_real_
} else {
vi.t[i] <- vi[i] * tmp^2
}
#tmp <- try(suppressWarnings(numDeriv::grad(func=transf, yi[i])), silent=TRUE)
#if (inherits(tmp, "try-error")) {
# deriv[i] <- NA_real_
#} else {
# deriv[i] <- tmp
#}
#vi.t[i] <- vi[i] * deriv[i]^2
}
#########################################################################
### set up data frame if 'data' was not specified
if (!has.data) {
x <- data.frame(rep(NA_real_, k), rep(NA_real_, k))
names(x) <- c(yi.name, vi.name)
}
### replace missing x$yi values
if (replace=="ifna") {
x[[yi.name]] <- replmiss(x[[yi.name]], yi.t)
} else {
x[[yi.name]][!is.na(yi.t)] <- yi.t[!is.na(yi.t)]
}
### replace missing ni values with ni attributes values from the source and target variables
### and then add ni attribute to target variable (if at least one value is not missing)
### note: values specified via 'ni' argument in conv.delta() overrule existing attribute values
ni <- replmiss(ni, attributes(yi)$ni)
ni <- replmiss(ni, attributes(x[[yi.name]])$ni)
if (any(!is.na(ni)))
attr(x[[yi.name]], "ni") <- ni
### replace missing x$vi values
if (replace=="ifna") {
x[[vi.name]] <- replmiss(x[[vi.name]], vi.t)
} else {
x[[vi.name]][!is.na(vi.t)] <- vi.t[!is.na(vi.t)]
}
#escall <- paste0("escalc(data=x, yi=", yi.name, ", vi=", vi.name, ", var.names=c('", yi.name, "','", vi.name, "'))")
#x <- eval(str2lang(escall))
x <- escalc(data=x, yi=x[[yi.name]], vi=x[[vi.name]], var.names=c(yi.name,vi.name))
if (!append)
x <- x[,c(yi.name, vi.name)]
return(x)
}
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