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dist <-
function(x, y = NULL, method = NULL, ...,
diag = FALSE, upper = FALSE, pairwise = FALSE,
by_rows = TRUE, convert_similarities = TRUE,
auto_convert_data_frames = TRUE)
{
### PARAMETER HANDLING
## convenience hack to allow dist(x, "method")
if ((is.function(y) || is.character(y)) && is.null(method)) {
method <- y
y <- NULL
}
## transform data frame into matrix iff all columns are atomic and either numeric (integer or double) or logical or complex
is.n_l_c <- function(x)
all(sapply(x, is.numeric)) ||
all(sapply(x, is.logical)) ||
all(sapply(x, is.complex))
if (is.data.frame(x) && auto_convert_data_frames && is.n_l_c(x))
x <- as.matrix(x)
if (is.data.frame(y) && !is.null(y) && auto_convert_data_frames && is.n_l_c(y))
y <- as.matrix(y)
## vector handling
if (is.vector(x) && is.atomic(x))
x <- as.matrix(x)
if (!is.null(y) && is.vector(y) && is.atomic(y))
y <- as.matrix(y)
## method lookup
reg_entry <- NULL
if (is.null(method))
method <- if (is.data.frame(x))
"Gower"
else if (is.logical(x))
"Jaccard"
else
"Euclidean"
if (!is.function(method))
reg_entry <- if (inherits(method, "proxy_registry_entry"))
method
else
pr_DB$get_entry(method)
## some checks
if (!is.data.frame(x) && !is.matrix(x) && !is.list(x))
stop("Can only handle data frames, vectors, matrices, and lists!")
if ( is.data.frame(x) && !by_rows)
stop("Cannot transpose mixed data frames")
if (!is.null(y)) {
if (is.data.frame(x) && !is.data.frame(y)
|| is.matrix(x) && !is.matrix(y)
|| is.list(x) && !is.list(y))
stop("x and y must be of same type.")
if (is.matrix(x) && is.matrix(y) || is.data.frame(x) && is.data.frame(y))
if (by_rows && (ncol(x) != ncol(y)))
stop("x and y must be conform in columns.")
else if (!by_rows && (nrow(x) != nrow(y)))
stop("x and y must be conform in rows.")
}
### PREPROCESS
params <- list(...)
if (!is.null(reg_entry)) {
if(is.function(reg_entry$PREFUN) || is.character(reg_entry$PREFUN)) {
tmp <- do.call(reg_entry$PREFUN,
c(list(x, y, pairwise, params, reg_entry)))
if (!is.null(tmp)) {
x <- tmp$x
y <- tmp$y
pairwise <- tmp$pairwise
params <- tmp$p
reg_entry <- tmp$reg_entry
}
}
method <- reg_entry$FUN
}
## helper function for calling the C-level loops
.proxy_external <- function(CFUN, x, y)
do.call(".External",
c(list(CFUN, x, y, pairwise,
if (!is.function(method)) get(method) else method),
params
)
)
result <-
### PASS-THROUGH-cases
if (!is.null(reg_entry) && !reg_entry$loop) {
if (!by_rows && !is.list(x)) {
x <- t(x)
if (!is.null(y))
y <- t(y)
}
if (reg_entry$C_FUN) {
do.call(".Call", c(list(method), list(x), list(y), pairwise, params, list(PACKAGE = reg_entry$PACKAGE)))
} else ## user functions need not implement pairwise
do.call(method, c(list(x), list(y), params), envir = asNamespace(reg_entry$PACKAGE))
} else if (is.null(y)) {
### LOOP WORKHORSE for auto-proximities
## transpose data for column-wise loop
if (!by_rows && !is.list(x))
x <- t(x)
if (is.list(x) && !is.null(reg_entry) && reg_entry$abcd)
x <- do.call("rbind", x)
if (is.matrix(x) && !is.null(reg_entry) && reg_entry$abcd)
## binary matrix
.proxy_external(R_apply_dist_binary_matrix, x != 0, NULL)
else if (is.matrix(x))
## real, integer matrix
.proxy_external(R_apply_dist_matrix, x, NULL)
else if (is.list(x) && !(is.data.frame(x) && by_rows))
## list
.proxy_external(R_apply_dist_list, x, NULL)
else ## data frame (by rows)
.proxy_external(R_apply_dist_data_frame, x, NULL)
} else {
### LOOP WORKHORSE for cross-proximities
## transpose data for column-wise loop
if (!by_rows && !is.list(x)) {
x <- t(x)
y <- t(y)
}
if (is.list(x) && !is.null(reg_entry) && reg_entry$abcd)
{
x <- do.call("rbind", x)
y <- do.call("rbind", x)
}
if (is.matrix(x) && !is.null(reg_entry) && reg_entry$abcd)
## binary matrices
.proxy_external(R_apply_dist_binary_matrix, x != 0, y != 0)
else if (is.matrix(x))
## real, integer matrices
.proxy_external(R_apply_dist_matrix, x, y)
else if (is.list(x) && !(is.data.frame(x) && by_rows))
## lists
.proxy_external(R_apply_dist_list, x, y)
else ## data frames (by rows)
.proxy_external(R_apply_dist_data_frame, x, y)
}
### set col/rownames for cross-proximity-objects (if needed)
if (is.matrix(result) && is.null(dimnames(result)))
if (is.list(x) && !is.data.frame(x)) {
rownames(result) <- names(x)
colnames(result) <- names(y)
} else if (by_rows) {
rownames(result) <- rownames(x)
colnames(result) <- rownames(y)
} else {
rownames(result) <- colnames(x)
colnames(result) <- colnames(y)
}
### POSTPROCESS
if (!is.null(reg_entry)) {
if (is.function(reg_entry$POSTFUN) || is.character(reg_entry$POSTFUN))
result <- do.call(reg_entry$POSTFUN, c(list(result, params)))
if (!reg_entry$distance &&
!(is.logical(convert_similarities) && !convert_similarities)) {
result <- if (is.function(convert_similarities) ||
is.character(convert_similarities))
do.call(convert_similarities, list(result))
else if (is.null(reg_entry$convert))
pr_simil2dist(result)
else
do.call(reg_entry$convert, list(result))
}
method <- reg_entry$names[1]
}
### RETURN DIST-OBJECT
result <-
if (is.matrix(result))
structure(result, class = "crossdist")
else
if (inherits(result, "dist"))
structure(result, Diag = diag, Upper = upper)
else
structure(result, class = "pairdist")
structure(result,
method = if (is.character(method))
method
else
if (missing(method))
deparse(substitute(y))
else deparse(substitute(method)),
call = match.call())
}
simil <-
function(x, y = NULL, method = NULL, ...,
diag = FALSE, upper = FALSE, pairwise = FALSE,
by_rows = TRUE, convert_distances = TRUE,
auto_convert_data_frames = TRUE)
{
## convenience to allow dists(x, "method")
if ((is.function(y) || is.character(y)) && is.null(method)) {
method <- y
y <- NULL
}
if (is.null(method))
method <- if (is.data.frame(x))
"Gower"
else if (is.logical(x))
"Jaccard"
else
"correlation"
ret <- dist(x, y, method, ..., diag = diag, upper = upper, pairwise = pairwise,
by_rows = by_rows, convert_similarities = FALSE,
auto_convert_data_frames = auto_convert_data_frames)
## possibly convert to similarity
reg_entry <- pr_DB$get_entry(attr(ret, "method"), stop_if_missing = FALSE)
if (!is.null(reg_entry)) {
if (reg_entry$distance &&
!(is.logical(convert_distances) && !convert_distances)) {
ret <- if (is.function(convert_distances) ||
is.character(convert_distances))
do.call(convert_distances, list(ret))
else if (is.null(reg_entry$convert))
pr_dist2simil(ret)
else
do.call(reg_entry$convert, list(ret))
}
}
class(ret) <- unique(c(if (inherits(ret, "crossdist")) "crosssimil" else "simil",
class(ret)))
ret
}
# note that a simil object must always also be a dist
# object for method dispatch
as.simil <-
function(x, FUN = NULL)
{
if (inherits(x, c("simil", "crosssimil")))
x
else if (inherits(x, c("dist", "crossdist"))) {
class(x) <- if (inherits(x, "dist"))
c("simil", class(x))
else
c("crosssimil", setdiff(class(x), "crossdist"))
if (!is.null(FUN))
FUN(x)
else {
reg_entry <- NULL
if (!is.null(attr(x, "method")))
reg_entry <- pr_DB$get_entry(attr(x, "method"),
stop_if_missing = FALSE)
if (!is.null(reg_entry) && !is.null(reg_entry$convert))
do.call(reg_entry$convert, list(x))
else
pr_dist2simil(x)
}
} else
structure(stats::as.dist(x), class = c("simil", "dist"))
}
as.dist <-
function(x, FUN = NULL)
{
if (inherits(x, c("simil", "crosssimil"))) {
class(x) <- if (inherits(x, "simil"))
setdiff(class(x), "simil")
else
c("crossdist", setdiff(class(x), "crosssimil"))
if (!is.null(FUN))
FUN(x)
else {
reg_entry <- NULL
if (!is.null(attr(x, "method")))
reg_entry <- pr_DB$get_entry(attr(x, "method"),
stop_if_missing = FALSE)
if (!is.null(reg_entry) && !is.null(reg_entry$convert))
do.call(reg_entry$convert, list(x))
else
pr_simil2dist(x)
}
} else if (inherits(x, c("dist", "crossdist")))
x
else
stats::as.dist(x)
}
## as we do not know if the object is the result of some
## user-defined transformation the values of
## s(x,x) are not defined.
## we need to copy stats::as.matrix.dist() since the use of ::: is deprecated:
as.matrix <-
function(x, ...)
base::as.matrix(x, ...)
as_matrix_dist <-
function (x, ...)
{
size <- attr(x, "Size")
df <- matrix(0, size, size)
df[row(df) > col(df)] <- x
df <- df + t(df)
labels <- attr(x, "Labels")
dimnames(df) <- if (is.null(labels))
list(seq_len(size), seq_len(size))
else list(labels, labels)
df
}
as.matrix.simil <-
function(x, diag = NA, ...) {
x <- as_matrix_dist(x)
diag(x) <- diag
x
}
## however, it seems reasonable to assume that d(x,x)=0,
## which is also the default in stats.
as.matrix.dist <-
function(x, diag = 0, ...) {
x <- as_matrix_dist(x)
diag(x) <- diag
x
}
print.crossdist <-
print.crosssimil <-
function (x, digits = getOption("digits"),
justify = "none", right = TRUE, ...)
{
if (length(x) > 0) {
m <- as.matrix(x)
cf <- format(m, digits = digits, justify = justify)
print(cf, quote = FALSE, right = right, ...)
} else {
cat(data.class(x), "(0)\n", sep = "")
}
invisible(x)
}
print.pairdist <-
function(x, ...)
{
print(as.vector(x), ...)
invisible(x)
}
print.simil <-
function (x, diag = NULL, upper = NULL, digits = getOption("digits"),
justify = "none", right = TRUE, ...)
{
if (length(x)) {
if (is.null(diag))
diag <- if (is.null(a <- attr(x, "Diag")))
FALSE
else a
if (is.null(upper))
upper <- if (is.null(a <- attr(x, "Upper")))
FALSE
else a
m <- as.matrix(x)
if (diag) diag(m) <- NA
cf <- format(m, digits = digits, justify = justify)
if (!upper)
cf[row(cf) < col(cf)] <- ""
if (!diag)
cf[row(cf) == col(cf)] <- ""
print(if (diag || upper)
cf
else cf[-1, -attr(x, "Size"), drop = FALSE], quote = FALSE,
right = right, ...)
}
else {
cat(data.class(x), "(0)\n", sep = "")
}
invisible(x)
}
pr_simil2dist <-
function(x)
1 - abs(x)
pr_dist2simil <-
function(x)
1 / (1 + x)
###
|
