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#' @title iterator for nearest neighbor subsets
#' @param x a reference matrix
#' @param xu a second matrix
#' @param y a matrix of side information
#' @param kindx a matrix of nearest neighbor indices
#' @param na_rm logical indicating whether NAs must be removed.
#' @description internal
#' @keywords internal
ith_subsets_ortho_diss <- function(x,
xu = NULL,
y,
kindx,
na_rm = FALSE) {
it_kindx <- iter(kindx, by = "column")
it_xu <- iter(xu, by = "row")
nextEl <- function() {
knns <- nextElem(it_kindx)
if (na_rm) {
knns <- knns[!is.na(knns)]
}
lsubst <- list(x = x[knns, ])
if (!is.null(y)) {
lsubst$y <- y[knns, , drop = FALSE]
}
if (!is.null(xu)) {
lsubst$xu <- nextElem(it_xu)
}
return(lsubst)
}
obj <- list(nextElem = nextEl)
class(obj) <- c("isubset", "abstractiter", "iter")
obj
}
#' @title local ortho dissimilarity matrices initialized by a global
#' dissimilarity matrix
#' @param k_index_matrix a matrix of nearest neighnbor indices
#' @param Xr argument passed to ortho_projection
#' @param Yr argument passed to ortho_projection
#' @param Xu argument passed to ortho_projection
#' @param diss_method argument passed to ortho_projection
#' @param pc_selection argument passed to ortho_projection
#' @param center argument passed to ortho_projection
#' @param scale argument passed to ortho_projection
#' @description internal
#' @keywords internal
local_ortho_diss <- function(k_index_matrix, Xr, Yr, Xu,
diss_method, pc_selection, center, scale,
allow_parallel, ...) {
"%mydo%" <- get("%do%")
if (allow_parallel & getDoParRegistered()) {
"%mydo%" <- get("%dopar%")
}
if (!is.null(Xu)) {
n_xu <- nrow(Xu)
} else {
n_xu <- 0
}
n_xr <- nrow(Xr)
if (diss_method %in% c("pca", "pca.nipals")) {
use_distance_method <- "euclid"
} else {
use_distance_method <- "mahalanobis"
}
if (n_xr + n_xu == ncol(k_index_matrix)) {
## squared matrix for all possible pair-wise dissimilarities
distnc <- matrix(NA, ncol(k_index_matrix), ncol(k_index_matrix))
diag(distnc) <- 0
ith_subsets <- ith_subsets_ortho_diss(
x = Xr, y = Yr,
kindx = k_index_matrix
)
n_rows_d <- ncol(k_index_matrix)
# neighbors (excluding target sample )
n_neighbors <- nrow(k_index_matrix) - 1
has_target_indices <- TRUE
} else {
## matrix for dissimilarities between Xr and Xu
distnc <- matrix(NA, n_xr, ncol(k_index_matrix))
ith_subsets <- ith_subsets_ortho_diss(
x = Xr, xu = Xu, y = Yr,
kindx = k_index_matrix,
na_rm = TRUE
)
n_rows_d <- n_xr
n_neighbors <- nrow(k_index_matrix)
has_target_indices <- FALSE
}
dist_vec <- rep(NA, n_neighbors + 2)
ith_local_subset <- NULL
## for each computations
i <- NULL
local_d <- foreach(
i = 1:ncol(k_index_matrix),
ith_local_subset = ith_subsets,
.combine = cbind,
.inorder = FALSE,
.export = c(
"ortho_projection",
"pc_projection",
"pls_projection",
"sim_eval",
"dist_vec"
),
.packages = c("resemble")
) %mydo% { # Parallel
ith_projection <- ortho_projection(
Xr = ith_local_subset$x,
Yr = ith_local_subset$y,
Xu = ith_local_subset$xu,
method = diss_method,
pc_selection = pc_selection,
center = center,
scale = scale,
...
)
if (diss_method %in% c("pca", "pca.nipals")) {
scores <- sweep(ith_projection$scores,
MARGIN = 2,
STATS = ith_projection$scores_sd,
FUN = "/"
)
} else {
scores <- ith_projection$scores
}
ith_dist <- dist_vec
ith_dist[3:length(ith_dist)] <- f_diss(
Xr = scores[1, , drop = FALSE],
Xu = scores[-1, , drop = FALSE],
diss_method = use_distance_method,
center = FALSE,
scale = FALSE
)
ith_dist[1] <- i
ith_dist[2] <- ith_projection$n_components
ith_dist
}
## end of foreach computations
local_d <- local_d[-1, order(local_d[1, ])]
local_n_components <- local_d[1, ]
local_d <- local_d[-1, ]
add_row_indices <- ((0:(ncol(k_index_matrix) - 1)) * n_rows_d)
# necessary to remove the xi-to-xi from the indices of nearest neighnbors
if (has_target_indices) {
k_index_matrix <- k_index_matrix[-1, ]
}
vec_positions <- sweep(k_index_matrix,
MARGIN = 2,
STATS = add_row_indices, FUN = "+"
)
distnc[vec_positions] <- as.vector(local_d)
return(list(
dissimilarity_m = distnc,
local_n_components = data.table(local_n_components)
))
}
#' @title format internal messages
#' @param xr_xu_names the names of Xr and Xu
#' @description internal
#' @keywords internal
format_xr_xu_indices <- function(xr_xu_names) {
xu_insufficient <- gsub("Xu_", "", xr_xu_names[grep("^Xu_", xr_xu_names)])
xr_insufficient <- gsub("Xr_", "", xr_xu_names[grep("^Xr_", xr_xu_names)])
xu_mss <- paste0(c(
ifelse(length(xu_insufficient) > 0,
"\nXu: ", ""
),
paste(xu_insufficient, collapse = ", ")
),
collapse = " "
)
xr_mss <- paste0(c(
ifelse(length(xr_insufficient) > 0,
"\nXr: ", ""
),
paste(xr_insufficient, collapse = ", ")
),
collapse = " "
)
return(list(
xr_mss = xr_mss,
xu_mss = xu_mss
))
}
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