R/manifoldtransform.R

In scorematchingad: Score Matching Estimation by Automatic Differentiation

#' @name tape_smd
# Build an object specifying the transformation from the natural domain of log-likelihood to another manifold.
#' @param start The starting manifold. Used for checking that `tran` and `man` match.
#' @param tran The name of a transformation. Available transformations are
#'  + ``sqrt''
#'  + ``alr''
#'  + ``clr''
#'  + ``none'' or `identity'
#' @param end The name of the manifold that `tran` maps `start` to. Available manifolds are:
#'  + ``sph'' unit sphere
#'  + ``Hn111'' hyperplane normal to the vector \eqn{1, 1, 1, 1, ...}
#'  + ``sim'' simplex
#'  + ``Euc'' Euclidean space
#' @details
#' Only some combinations of `start`, `tran` and `end` are available because `tran` must map between `start` and `end`.
#' These combinations of `start`-`tran`-`end` are currently available:
#'
#' ```{r mantrans, results = "asis", echo = FALSE}
#' cat(paste(" +", mantrancombos), sep = "\n")
#' ```
NULL

manifoldtransform <- function(start, tran = "identity", end = start){
  if (tran == "none"){tran <- "identity"}
  stopifnot(paste(start, tran, end, sep = "-") %in% mantrancombos)
  out <- list(tran = methods::new(transform_ad, tran),
       man = methods::new(man_ad, end))
  return(out)
}

Rcpp::loadModule("manifolds", TRUE)
# documentation can be found in: transform_ad$help("toM"), but it is pretty poor.
# also transform_ad@methods will list all the methods of the transform class
# documenting these classes looks like a major headache at the moment and they are only used internally

mantrancombos <- c(
  "sim-sqrt-sph",
  "sim-identity-sim",
  "sim-alr-Euc",
  "sim-clr-Hn111",
  "sph-identity-sph",
  "Euc-identity-Euc"
)