```
#' Time Resolved paired differences test (TPDT)
#'
#' Main function to perform a TPDT for a given dataset.
#' @param data either a [data.frame] with columns named "data", "group", "time" and "id" analogously to
#' the use of \code{TPDT.numeric}. If using \code{TPDT.numeric}, a vector with same order as group, time and id vector.
#' @param group [numeric/factor] vector with grouping variable. A character vector will be
#' converted in to numeric 1/2 internally.
#' @param time [numeric] vector of time points, has to be the same order as data, group and id.
#' @param id [numeric] vector of pairings. Each unique value of id should be present in both groups.
#' @param deriv [integer] If 1, test is conducted on first derivative of functional data. If 2, tests second derivative and so on.
#' @param lambda [numeric] Smoothing parameter to use, if known in advance. If NULL, it is computed by cross validation.
#' @param ncores [integer] Number of CPUs to use for parallization.
#' @export
#' @example demo/example.R
#' @import checkmate
TPDT <- function(x, ...) UseMethod("TPDT")
#' @describeIn TPDT Method for column wise input
#' @inheritParams TPDT
#' @export
TPDT.numeric <- function(data, group, time, id, deriv = 0, B = 100, lambda = NULL, ncores = 1, ...){
datframe <- data.frame(data = data, group = group, time = time, id = id)
# call next method
TPDT.data.frame(data = datframe, deriv = deriv, B = B, lambda = lambda, ncores = ncores, ...)
}
#' @describeIn TPDT Method for data.frame input
#' @inheritParams TPDT
#' @export
TPDT.data.frame <- function(data, deriv = 0, B = 100, lambda = NULL, ncores = 1, nbas = NULL, ...) {
# TODO:
# convert character to factor/numeric
stopifnot(all(names(data) %in% c("data", "group", "time", "id")))
# check types:
checkmate::assertIntegerish(x = deriv)
checkmate::assertIntegerish(x = ncores)
checkmate::assertIntegerish(x = B)
checkmate::assertDataFrame(data, types = "numeric", min.rows = 8, min.cols = 4,
all.missing = FALSE, col.names = "named")
if(!is.null(nbas))
checkmate::assertIntegerish(x = nbas)
if(!is.null(lambda))
checkmate::assertNumber(x = lambda, na.ok = TRUE)
# make functional data from the raw data, find lamba if not provided etc.
comptime1 <- system.time(funcdata <- prep_data(data, nbas = nbas, lambda = lambda, deriv = deriv))
# funcdata <- list(func1 = funcdata$func1, func2 = funcdata$func2,
# basis = funcdata$func1$basis)
# do test
comptime2 <- system.time(rval <-
functional.difftest(funcdata = funcdata,
B = B, deriv = deriv, ncores = ncores))
# build return object
rval <- list(comptime = comptime1[3] + comptime2[3],
data = data,
funcdata = funcdata,
columns = list(data.col = which(names(data) == "data"),
group.col = which(names(data) == "group"),
pairing.col = which(names(data) == "id"),
time.col = which(names(data) == "time")),
test = rval,
p = rval$pval)
class(rval) <- "TPDT"
return(rval)
}
```

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