R/RcppExports.R

Defines functions tracemp repmat quadform qdiag pairwise_Schur_product onemargintest mfastLmCpp ks_cumtest filldown cumsumbinning cmd

Documented in cmd cumsumbinning filldown ks_cumtest mfastLmCpp onemargintest pairwise_Schur_product qdiag quadform repmat tracemp

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#' Correlation matrix distance
#'
#' @description Computes the correlation matrix distance between two correlation matrices
#' @param x First correlation matrix
#' @param y Second correlation matrix
#' @return Returns the correlation matrix distance, which is a value between 0 and 1. The correlation matrix distance becomes
#' zero for equal correlation matrices and unity if they differ to a maximum extent.
#' @author Claus Ekstrom \email{[email protected]@rprimer.dk}
#' @references Herdin, M., and Czink, N., and Ozcelik, H., and Bonek, E. (2005). \emph{Correlation matrix distance, a meaningful measure for
#' evaluation of non-stationary mimo channels}. IEEE VTC.
#' @keywords univar
#' @examples
#'
#' m1 <- matrix(rep(1, 16), 4)
#' m2 <- matrix(c(1, 0, .5, .5, 0, 1, .5, .5, .5, .5, 1, .5, .5, .5, .5, 1), 4)
#' m3 <- matrix(c(1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1), 4)
#' cmd(m1, m1)
#' cmd(m1, m2)
#' cmd(m2, m3)
#'
#' @export cmd
cmd <- function(x, y) {
    .Call(`_MESS_cmd`, x, y)
}

#' Binning based on cumulative sum with reset above threshold
#' 
#' Fast binning of cumulative vector sum with new groups when the sum passes a threshold or the group size becomes too large
#'
#' Missing values (NA, Inf, NaN) are completely disregarded and pairwise complete cases are used f
#' 
#' @param x A matrix of regressor variables. Must have the same number of rows as the length of y.
#' @param cutoff The value of the threshold that the cumulative group sum must not cross. 
#' @param maxgroupsize An integer that defines the maximum number of elements in each group. NULL (the default) corresponds to no group size.
#' @return An integer vector giving the group indices
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @examples
#'
#' set.seed(1)
#' x <- sample(10, 20, replace = TRUE)
#' cumsumbinning(x, 15)
#' cumsumbinning(x, 15, 3)
#' 
#' @export
cumsumbinning <- function(x, cutoff, maxgroupsize = NULL) {
    .Call(`_MESS_cumsumbinning`, x, cutoff, maxgroupsize)
}

#' Fill down NA with the last observed observation
#'
#' @description Fill down missing values with the latest non-missing value
#' @param x A vector
#' @return A vector or list with the NA's replaced by the last observed value.
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @examples
#'
#' a <- c(1:5, "Howdy", NA, NA, 2:3, NA)
#' filldown(a)
#' filldown(c(NA, NA, NA, 3:5))
#'
#' @export
filldown <- function(x) {
    .Call(`_MESS_filldown`, x)
}

#' Kolmogorov-Smirnov goodness of fit test for cumulative discrete data
#'
#' The name of the function might change in the future so keep that in mind!
#'
#' @description Kolmogorov-Smirnov goodness of fit test for cumulative discrete data. 
#' @param x A vector representing the contingency table.
#' @param B The number of simulations used to compute the p-value.
#' @param prob A positive vector of the same length as x representing the distribution under the null hypothesis. It will be scaled to sum to 1. If NULL (the default) then a uniform distribution is assumed.
#' @details Simulation is done by random sampling from the null hypothesis.
#' @return A list of class "htest" giving the simulation results.
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @examples
#'
#' x <- 1:6
#' ks_cumtest(x)
#'
#' @export
ks_cumtest <- function(x, B = 10000L, prob = NULL) {
    .Call(`_MESS_ks_cumtest`, x, B, prob)
}

#' Fast marginal simple regresion analyses
#' 
#' Fast computation of simple regression slopes for each predictor represented by a column in a matrix
#'
#' Missing values (NA, Inf, NaN) are completely disregarded and pairwise complete cases are used for the analysis.
#' 
#' @param y A vector of outcomes.
#' @param x A matrix of regressor variables. Must have the same number of rows as the length of y. 
#' @param addintercept A logical that determines if the intercept should be included in all analyses (TRUE) or not (FALSE)
#' @return A data frame with three variables: coefficients, stderr, and tstat that gives the slope estimate, the corresponding standard error, and their ratio for each column in x.
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @examples
#' \dontrun{
#'   // Generate 100000 predictors and 100 observations
#'   x <- matrix(rnorm(100*100000), nrow=100)
#'   y <- rnorm(100, mean=x[,1])
#'   mfastLmCpp(y, x)
#'
#' }
#' @export
mfastLmCpp <- function(y, x, addintercept = TRUE) {
    .Call(`_MESS_mfastLmCpp`, y, x, addintercept)
}

#' Two-sided table test with fixed margins
#'
#' @description Test in a two-way contingency table with the row margin fixed. 
#' @param x A matrix representing the contingency table.
#' @param B The number of simulations used to compute the p-value.
#' @details Simulation is done by random sampling from the set of all tables with given row marginals, and works only if the marginals are strictly positive. Continuity correction is never used, and the statistic is quoted without it.
#' @return A list of class "htest" giving the simulation results.
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @examples
#'
#' m <- matrix(c(12, 4, 8, 6), 2)
#' chisq.test(m)
#' chisq.test(m, correct=FALSE)
#' fisher.test(m)
#' onemargintest(m)
#'
#' m2 <- matrix(c(9, 3, 3, 7), 2)
#' chisq.test(m2, simulate.p.value=TRUE)
#' fisher.test(m2)
#' onemargintest(m2)
#'
#' @export
onemargintest <- function(x, B = 10000L) {
    .Call(`_MESS_onemargintest`, x, B)
}

#' Compute Schur products (element-wise) of all pairwise combinations of columns in matrix
#'
#' Fast computation of all pairwise element-wise column products of a matrix.
#'
#' Note that the output order of columns corresponds to the order of the columns in x. First column 1 is multiplied with each of the other columns, then column 2 with the remaining columns etc. 
#'
#' @param x A matrix with dimensions r*c.
#' @param self A logical that determines whether a column should also be multiplied by itself.
#' @return A matrix with the same number of rows as x and a number of columns corresponding to c choose 2 (+ c if self is TRUE), where c is the number of columns of x. 
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @examples
#'
#' X <- cbind(rep(1, 4), 1:4, 4:1)
#' pairwise_Schur_product(X)
#' pairwise_Schur_product(X, self=TRUE)
#'
#' @export
pairwise_Schur_product <- function(x, self = FALSE) {
    .Call(`_MESS_pairwise_Schur_product`, x, self)
}

#' Fast extraction of matrix diagonal
#'
#' @description Fast extraction of matrix diagonal
#' @param x The matrix to extract the diagonal from
#' @return A vector with the diagonal elements
#' @details Note this function can only be used for extraction
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @export qdiag
qdiag <- function(x) {
    .Call(`_MESS_qdiag`, x)
}

#' Fast quadratic form computation
#'
#' @description Fast computation of a quadratic form  t(x) %*% M %*% x
#' @param x A matrix with dimensions n*k.
#' @param M A matrix with dimenions n*n. If it is to be inverted then the matrix should be symmetric and positive difinite (no check is done for this)
#' @param invertM A logical. If set to TRUE then M will be inverted before computations (defaults to FALSE)
#' @param transposex A logical. Should the matrix be transposed before computations (defaults to FALSE).
#' @return A matrix with dimensions k * k giving the quadratic form
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @export
quadform <- function(x, M, invertM = FALSE, transposex = FALSE) {
    .Call(`_MESS_quadform`, x, M, invertM, transposex)
}

#' Fast replication of a matrix
#'
#' @description Fast generation of a matrix by replicating a matrix row- and column-wise in a block-like fashion
#' @param x A matrix with dimensions r*c.
#' @param nrow An integer giving the number of times the matrix is replicated row-wise
#' @param ncol An integer giving the number of times the matrix is replicated column-wise
#' @return A matrix with dimensions (r*nrow) x (c*ncol)
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @examples
#'
#' m <- matrix(1:6, ncol=3)
#' repmat(m, 2)     # Stack two copies of m on top of each other
#' repmat(m, 2, 3)  # Replicate m with two copies on top and three copies side-by-side 
#'
#' @export
repmat <- function(x, nrow = 1L, ncol = 1L) {
    .Call(`_MESS_repmat`, x, nrow, ncol)
}

#' Fast computation of trace of matrix product
#'
#' @description Fast computation of the trace of the matrix product trace(t(A) %*% B)
#' @param A A matrix with dimensions n*k.
#' @param B A matrix with dimenions n*k.
#' @return The trace of the matrix product
#' @author Claus Ekstrom <[email protected]@rprimer.dk>
#' @examples
#'
#' A <- matrix(1:12, ncol=3)
#' tracemp(A, A)
#'
#' @export
tracemp <- function(A, B) {
    .Call(`_MESS_tracemp`, A, B)
}

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MESS documentation built on Jan. 4, 2018, 4:07 a.m.