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### =========================================================================
### Summarization methods for SparseArray objects
### -------------------------------------------------------------------------
###
### Summarization methods:
### - anyNA()
### - 'Summary' group: any(), all(), min(), max(), range(), sum(), prod()
### - mean()
### - Unary var(), sd()
###
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Workhorse behind all the summarization methods for SVT_SparseArray
### and NaArray objects
###
### 'center' ignored by all ops except "centered_X2_sum".
### Returns an integer or numeric vector of length 1 or 2.
summarize_SVT <- function(op, x, na.rm=FALSE, center=NULL)
{
stopifnot(isSingleString(op), is(x, "SVT_SparseArray") || is(x, "NaArray"))
check_svt_version(x)
## Check 'na.rm'.
if (!isTRUEorFALSE(na.rm))
stop(wmsg("'na.rm' must be TRUE or FALSE"))
## Check and normalize 'center'.
if (is.null(center)) {
center <- NA_real_
} else {
if (!isSingleNumberOrNA(center))
stop(wmsg("'center' must be NULL, or a single number"))
if (!is.double(center))
center <- as.double(center)
}
if (is(x, "NaArray")) {
SparseArray.Call("C_summarize_SVT",
x@dim, x@type, x@NaSVT, TRUE, op, na.rm, center)
} else {
SparseArray.Call("C_summarize_SVT",
x@dim, x@type, x@SVT, FALSE, op, na.rm, center)
}
}
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### anyNA(), countNAs()
###
.anyNA_SparseArray <- function(x, recursive=FALSE)
{
if (!identical(recursive, FALSE))
stop(wmsg("the anyNA() method for SparseArray objects ",
"does not support the 'recursive' argument"))
if (is(x, "COO_SparseArray"))
return(anyNA(x@nzdata))
if (is(x, "SVT_SparseArray"))
return(summarize_SVT("anyNA", x))
stop(wmsg(class(x)[[1L]], " objects are not supported"))
}
setMethod("anyNA", "SparseArray", .anyNA_SparseArray)
### NOT USED! There's no countNAs() generic yet!
### TODO: Define the countNAs() in BiocGenerics, and the colCountNAs() and
### rowCountNAs() generics in MatrixGenerics.
.countNAs_SparseArray <- function(x, recursive=FALSE)
{
if (!identical(recursive, FALSE))
stop(wmsg("the countNAs() method for SparseArray objects ",
"does not support the 'recursive' argument"))
if (is(x, "COO_SparseArray"))
return(sum(is.na(x@nzdata))) # or do 'countNAs(x@nzdata)' when it
# becomes available
if (is(x, "SVT_SparseArray"))
return(summarize_SVT("countNAs", x))
stop(wmsg(class(x)[[1L]], " objects are not supported"))
}
#setMethod("countNAs", "SparseArray", .countNAs_SparseArray)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### 'Summary' group
###
.summarize_COO <- function(op, x, na.rm=FALSE)
{
stopifnot(isSingleString(op), is(x, "COO_SparseArray"))
GENERIC <- match.fun(op)
## Whether 'x' contains zeros or not doesn't make a difference for
## sum() and any().
if (op %in% c("sum", "any"))
return(GENERIC(x@nzdata, na.rm=na.rm))
## Of course a typical COO_SparseArray object "contains" zeros
## (i.e. it would contain zeros if we converted it to a dense
## representation with as.array()). However, this is not guaranteed
## so we need to make sure to properly handle the case where it
## doesn't (admittedly unusual and definitely an inefficient way
## to represent dense data!)
x_has_zeros <- length(x@nzdata) < length(x)
if (!x_has_zeros)
return(GENERIC(x@nzdata, na.rm=na.rm))
x_type <- typeof(x@nzdata)
if (op == "all") {
## Mimic what 'all(as.array(x))' would do.
if (x_type == "double")
warning("coercing argument of type 'double' to logical")
return(FALSE)
}
zero <- vector_of_zeros(x_type, length=1L)
GENERIC(zero, x@nzdata, na.rm=na.rm)
}
setMethod("Summary", "COO_SparseArray",
function(x, ..., na.rm=FALSE)
{
if (length(list(...)) != 0L)
stop(wmsg("the ", .Generic, "() method for COO_SparseArray ",
"objects only accepts a single object"))
.summarize_COO(.Generic, x, na.rm=na.rm)
}
)
setMethod("Summary", "SVT_SparseArray",
function(x, ..., na.rm=FALSE)
{
if (length(list(...)) != 0L)
stop(wmsg("the ", .Generic, "() method for SVT_SparseArray ",
"objects only accepts a single object"))
summarize_SVT(.Generic, x, na.rm=na.rm)
}
)
### We override the range() methods defined via the Summary() methods
### above because we want to support the 'finite' argument like S3 method
### base::range.default() does. One might wonder why base::range.default()
### supports the 'finite' argument but min() and max() don't. Or more
### precisely, they seem to take it but they don't do exactly the same thing
### with it:
###
### > max(c(0, -Inf), finite=TRUE)
### [1] 1
###
### Another story for another day...
### S3/S4 combo for range.COO_SparseArray
range.COO_SparseArray <- function(..., na.rm=FALSE, finite=FALSE)
{
objects <- list(...)
if (length(objects) != 1L)
stop(wmsg("the range() method for COO_SparseArray objects ",
"only accepts a single object"))
x <- objects[[1L]]
x_has_zeros <- length(x@nzdata) < length(x)
if (!x_has_zeros)
return(range(x@nzdata, na.rm=na.rm, finite=finite))
zero <- vector_of_zeros(typeof(x@nzdata), length=1L)
range(zero, x@nzdata, na.rm=na.rm, finite=finite)
}
### The signature of all the members in the 'Summary' group generic is
### 'x, ..., na.rm' (see getGeneric("range")) which means that methods
### cannot add arguments after 'na.rm'. So we add the 'finite' argument
### before.
setMethod("range", "COO_SparseArray",
function(x, ..., finite=FALSE, na.rm=FALSE)
range.COO_SparseArray(x, ..., na.rm=na.rm, finite=finite)
)
### S3/S4 combo for range.SVT_SparseArray
range.SVT_SparseArray <- function(..., na.rm=FALSE, finite=FALSE)
{
if (!identical(finite, FALSE))
stop(wmsg("the range() method for SVT_SparseArray objects ",
"does not support the 'finite' argument"))
objects <- list(...)
if (length(objects) != 1L)
stop(wmsg("the range() method for SVT_SparseArray objects ",
"only accepts a single object"))
x <- objects[[1L]]
summarize_SVT("range", x, na.rm=na.rm)
}
### The signature of all the members in the 'Summary' group generic is
### 'x, ..., na.rm' (see getGeneric("range")) which means that methods
### cannot add arguments after 'na.rm'. So we add the 'finite' argument
### before.
setMethod("range", "SVT_SparseArray",
function(x, ..., finite=FALSE, na.rm=FALSE)
range.SVT_SparseArray(x, ..., na.rm=na.rm, finite=finite)
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### mean()
###
.mean_SparseArray <- function(x, na.rm=FALSE)
{
summarize_SVT("mean", x, na.rm=na.rm)
}
### S3/S4 combo for mean.SparseArray
mean.SparseArray <- function(x, na.rm=FALSE, ...)
.mean_SparseArray(x, na.rm=na.rm, ...)
setMethod("mean", "SparseArray", .mean_SparseArray)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### var(), sd()
###
setMethod("var", c("SparseArray", "ANY"),
function(x, y=NULL, na.rm=FALSE, use)
{
if (!is.null(y))
stop(wmsg("the var() method for SparseArray objects ",
"does not support the 'y' argument"))
if (!missing(use))
stop(wmsg("the var() method for SparseArray objects ",
"does not support the 'use' argument"))
summarize_SVT("var1", x, na.rm=na.rm)
}
)
setMethod("sd", "SparseArray",
function(x, na.rm=FALSE) summarize_SVT("sd1", x, na.rm=na.rm)
)
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