#' Setting parameters used in MDRDist
#'
#' @param command calling sequence for MBMDR-4.4.1 from command line. If not set,
#' the binaries delivered with this package will be used.
#' @param p number of permutations in MBMDR's maxT-test
#' @param m number of observations that are needed for significant cell
#' @param x significance level in MBMDR-first-level test
#' @param a correction-method in MBMDR
#' @param cutting_p significance level in MBMDR-second-level test
#' @param exclude_creating_data should data used for calculating MBMDR be evaluated for distance?
#' @param fraction_of_real_data number of real observations randomly drawn,
#' where 1 equals nrow(data)
#' @param fraction_of_artificial_data number of artificial observations randomly generated,
#' where 1 equals nrow(data)
#' @param do_bootstrapping choosing real observations randomly with
#' (-> bootstrapping) or without (-> subsampling) replacement
#' @param dissimilarity_exponent The exponent used when calculating dissimilarity.
#' It is "Dissimilarity = (1 - Similarity) ** dissim_exp".
#' Most commonly it is set to 0.5 or 1.
#'
#' @return nothing, but fills R-intern "options"-list
#' @export
#'
#' @import checkmate
#'
set_options <- function(
command = NA,
p = 100,
m = 10,
x = .1,
a = "NONE",
cutting_p = .05,
fraction_of_real_data = .63,
fraction_of_artificial_data = .63,
do_bootstrapping = FALSE,
exclude_creating_data = FALSE,
dissimilarity_exponent = .5
){
# run tests, whether input data are valid
checkmate::assertCharacter(command)
checkmate::assertNumber(x = p, lower = 0, upper = 10000)
checkmate::assertNumber(x = m, lower = 0, upper = 1000)
checkmate::assertNumber(x = x, lower = 0, upper = 1)
checkmate::assertChoice(x = a, choices = c("NONE", "CODOMINANT", "ONESTEP", "ADDITIVE"))
checkmate::assertNumber(x = cutting_p, lower = 0, upper = 1)
checkmate::assertNumber(x = fraction_of_real_data, lower = 0, upper = 20)
checkmate::assertNumber(x = fraction_of_artificial_data, lower = 0, upper = 20)
checkmate::assertLogical(x = do_bootstrapping)
checkmate::assertLogical(exclude_creating_data)
checkmate::assertNumber(x = dissimilarity_exponent, lower = 0, upper = 1)
# if not given, automatically set mbmdr-path to version delivered with package
if(is.na(command)){
command <- sprintf("%s/exec/mbmdr-4.4.1-%s-64bits",
system.file(package = "MDRDist"),
tolower(Sys.info()["sysname"]))
}
# fill options-list with parameters
# del mdrdist
options("mdrdist_command" = command)
options("mdrdist_p" = p)
options("mdrdist_m" = m)
options("mdrdist_x" = as.character(x))
options("mdrdist_a" = a)
options("mdrdist_cutting_p" = cutting_p)
options("mdrdist_fraction_of_real_data" = fraction_of_real_data)
options("mdrdist_fraction_of_artificial_data" = fraction_of_artificial_data)
options("mdrdist_do_bootstrapping" = do_bootstrapping)
options("mdrdist_exclude_creating_data" = exclude_creating_data)
options("mdrdist_dissimilarity_exponent" = dissimilarity_exponent)
}
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