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Merge pull request #117 from cbeleites/issue/96-Consistent-code-style
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standardize/style code formatting
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@eoduniyi
eoduniyi authored May 25, 2020
2 parents 67ec09f + 232bc87 commit 9b3fd94
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209 changes: 112 additions & 97 deletions hyperSpec/R/Arith.R
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Original file line number Diff line number Diff line change
Expand Up @@ -76,74 +76,78 @@
##' flu / flu$c


setMethod ("Arith", signature (e1 = "hyperSpec", e2 = "hyperSpec"),
function (e1, e2){
validObject (e1)
validObject (e2)
setMethod(
"Arith", signature(e1 = "hyperSpec", e2 = "hyperSpec"),
function(e1, e2) {
validObject(e1)
validObject(e2)

e1 <- .expand (e1, dim (e2) [c (1, 3)])
e2 <- .expand (e2, dim (e1) [c (1, 3)])
e1 <- .expand(e1, dim(e2) [c(1, 3)])
e2 <- .expand(e2, dim(e1) [c(1, 3)])

e1 [[]] <- callGeneric (e1[[]], e2[[]])
e1
}
)
e1 [[]] <- callGeneric(e1[[]], e2[[]])
e1
}
)

.arithx <- function (e1, e2){
validObject (e1)
.arithx <- function(e1, e2) {
validObject(e1)

if (missing (e2)){
e1 [[]] <- callGeneric (e1 [[]])
if (missing(e2)) {
e1 [[]] <- callGeneric(e1 [[]])
e1
} else {
e2 <- as.matrix (e2)
e2 <- as.matrix(e2)

## called /only/ with e1 hyperSpec but e2 matrix-like
e1 <- .expand (e1, dim (e2))
e2 <- .expand (e2, dim (e1) [c (1, 3)])
e1 <- .expand(e1, dim(e2))
e2 <- .expand(e2, dim(e1) [c(1, 3)])

e1 [[]] <- callGeneric (e1 [[]], e2)
e1 [[]] <- callGeneric(e1 [[]], e2)
e1
}
}
##' @rdname Arith
setMethod ("Arith", signature (e1 = "hyperSpec", e2 = "numeric"), .arithx)
setMethod("Arith", signature(e1 = "hyperSpec", e2 = "numeric"), .arithx)
##' @rdname Arith
setMethod ("Arith", signature (e1 = "hyperSpec", e2 = "matrix"), .arithx)
setMethod("Arith", signature(e1 = "hyperSpec", e2 = "matrix"), .arithx)
##' @rdname Arith
setMethod ("Arith", signature (e1 = "hyperSpec", e2 = "missing"), .arithx)
setMethod("Arith", signature(e1 = "hyperSpec", e2 = "missing"), .arithx)

.arithy <- function (e1, e2){
e1 <- as.matrix (e1)
validObject (e2)
.arithy <- function(e1, e2) {
e1 <- as.matrix(e1)
validObject(e2)

## called /only/ with e2 hyperSpec but e1 matrix-like
e1 <- .expand (e1, dim (e2) [c (1, 3)])
e2 <- .expand (e2, dim (e1))
e1 <- .expand(e1, dim(e2) [c(1, 3)])
e2 <- .expand(e2, dim(e1))

e2 [[]] <- callGeneric (e1, e2 [[]])
e2 [[]] <- callGeneric(e1, e2 [[]])
e2
}
##' @rdname Arith
setMethod ("Arith", signature (e1 = "numeric", e2 = "hyperSpec"), .arithy)
setMethod("Arith", signature(e1 = "numeric", e2 = "hyperSpec"), .arithy)
##' @rdname Arith
setMethod ("Arith", signature (e1 = "matrix", e2 = "hyperSpec"), .arithy)
setMethod("Arith", signature(e1 = "matrix", e2 = "hyperSpec"), .arithy)

##' @param m matrix
##' @param target.dim target size to expand the vector to for the sweep-shortcuts
##' @noRd
.expand <- function (m, target.dim) {
m.dim = dim (m)
.expand <- function(m, target.dim) {
m.dim <- dim(m)

if (m.dim [1] == 1L & target.dim [1] > 1L)
m <- m [rep (1, target.dim [1]),, drop = FALSE]
if (m.dim [1] == 1L & target.dim [1] > 1L) {
m <- m [rep(1, target.dim [1]), , drop = FALSE]
}

if (is (m, "hyperSpec")) {
if (m.dim [3] == 1L & target.dim [2] > 1L)
m <- m [,, rep (1, target.dim [2]), wl.index = TRUE]
if (is(m, "hyperSpec")) {
if (m.dim [3] == 1L & target.dim [2] > 1L) {
m <- m [, , rep(1, target.dim [2]), wl.index = TRUE]
}
} else {
if (m.dim [2] == 1L & target.dim [2] > 1L)
m <- m [, rep (1, target.dim [2]), drop = FALSE]
if (m.dim [2] == 1L & target.dim [2] > 1L) {
m <- m [, rep(1, target.dim [2]), drop = FALSE]
}
}

m
Expand All @@ -156,79 +160,90 @@ setMethod ("Arith", signature (e1 = "matrix", e2 = "hyperSpec"), .arithy)
##' %*%,hyperSpec,matrix-method
##' @export
##' @seealso \code{\link[base]{matmult}} for matrix multiplications with \code{\%*\%}.
setMethod ("%*%", signature (x = "hyperSpec", y = "hyperSpec"),
function (x, y){
validObject (x)
validObject (y)

if (ncol(y) > 1)
warning(paste("Dropping column(s) of y:", paste(colnames(y$..),
collapse = ", ")))

x@data$spc <- x@data$spc %*% y@data$spc
.wl (x) <- y@wavelength
x@label$.wavelength = y@label$.wavelength

x
}
)
setMethod(
"%*%", signature(x = "hyperSpec", y = "hyperSpec"),
function(x, y) {
validObject(x)
validObject(y)

if (ncol(y) > 1) {
warning(paste("Dropping column(s) of y:", paste(colnames(y$..),
collapse = ", "
)))
}

x@data$spc <- x@data$spc %*% y@data$spc
.wl(x) <- y@wavelength
x@label$.wavelength <- y@label$.wavelength

x
}
)

##' @rdname Arith
setMethod ("%*%", signature (x = "hyperSpec", y = "matrix"),
function (x, y){
validObject (x)
x@data$spc <- x@data$spc %*% y
.wl (x) <- seq_len (ncol (y))
x@label$.wavelength = NA
x
}
)
setMethod(
"%*%", signature(x = "hyperSpec", y = "matrix"),
function(x, y) {
validObject(x)
x@data$spc <- x@data$spc %*% y
.wl(x) <- seq_len(ncol(y))
x@label$.wavelength <- NA
x
}
)

##' @rdname Arith
setMethod ("%*%", signature (x = "matrix", y = "hyperSpec"),
function (x, y){
validObject (y)

if (ncol(y) > 1)
warning(paste("Dropping column(s) of y:", paste(colnames(y$..),
collapse = ", ")))
y <- new ("hyperSpec",
wavelength = y@wavelength,
spc = x %*% y@data$spc,
log = y@log
)

y
}
)

.test (.arithx) <- function (){
context ("Arith")
setMethod(
"%*%", signature(x = "matrix", y = "hyperSpec"),
function(x, y) {
validObject(y)

if (ncol(y) > 1) {
warning(paste("Dropping column(s) of y:", paste(colnames(y$..),
collapse = ", "
)))
}
y <- new("hyperSpec",
wavelength = y@wavelength,
spc = x %*% y@data$spc,
log = y@log
)

y
}
)

.test(.arithx) <- function() {
context("Arith")

test_that("binary -", {
expect_equal (as.matrix (flu - flu),
matrix (0, nrow = nrow (flu), ncol = nwl (flu), dimnames = dimnames (flu [[]])))

expect_equal (as.matrix (flu - flu [1]), as.matrix (sweep (flu, 2, flu [1], `-`)))

expect_equal (as.matrix (flu - flu [,, 450]), as.matrix (sweep (flu, 1, flu [,, 450], `-`)))
expect_equal(
as.matrix(flu - flu),
matrix(0, nrow = nrow(flu), ncol = nwl(flu), dimnames = dimnames(flu [[]]))
)

expect_equal(as.matrix(flu - flu [1]), as.matrix(sweep(flu, 2, flu [1], `-`)))

expect_equal(as.matrix(flu - flu [, , 450]), as.matrix(sweep(flu, 1, flu [, , 450], `-`)))
})

test_that("binary /", {
expect_equal (as.matrix (flu / flu),
matrix (1, nrow = nrow (flu), ncol = nwl (flu), dimnames = dimnames (flu [[]])))

expect_equal (as.matrix (flu / flu [1]), as.matrix (sweep (flu, 2, flu [1], `/`)))

expect_equal (as.matrix (flu / flu [,, 450]), as.matrix (sweep (flu, 1, flu [,, 450], `/`)))
expect_equal(
as.matrix(flu / flu),
matrix(1, nrow = nrow(flu), ncol = nwl(flu), dimnames = dimnames(flu [[]]))
)

expect_equal(as.matrix(flu / flu [1]), as.matrix(sweep(flu, 2, flu [1], `/`)))

expect_equal(as.matrix(flu / flu [, , 450]), as.matrix(sweep(flu, 1, flu [, , 450], `/`)))
})

test_that("binary + with scalar", {
expect_equal (as.matrix (flu + 1), as.matrix (flu) + 1)
expect_equal (as.matrix (1 + flu), as.matrix (flu) + 1)
expect_equal(as.matrix(flu + 1), as.matrix(flu) + 1)
expect_equal(as.matrix(1 + flu), as.matrix(flu) + 1)
})

test_that("unary -", {
expect_equal (as.matrix (-flu), - as.matrix (flu))
expect_equal(as.matrix(-flu), -as.matrix(flu))
})
}
59 changes: 29 additions & 30 deletions hyperSpec/R/Compare.R
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Original file line number Diff line number Diff line change
@@ -1,18 +1,18 @@
##' The comparison operators \code{>}, \code{<}, \code{>=}, \code{<=},
##' \code{==}, and \code{!=} for \code{hyperSpec} objects.
##'
##'
##' \code{all.equal} checks the equality of two hyperSpec objects.
##'
##'
##' The comparison operators \code{>}, \code{<}, \code{>=}, \code{<=},
##' \code{==}, and \code{!=} work on the spectra matrix of the \code{hyperSpec}
##' object. They have their usual meaning (see \code{\link[base]{Comparison}}).
##' The operators work also with one \code{hyperSpec} object and a numeric
##' (scalar) object or a matrices of the same size as the spectra matrix of the
##' \code{hyperSpec} object.
##'
##'
##' With numeric vectors \code{\link[hyperSpec]{sweep}} might be more
##' appropriate.
##'
##'
##' If you want to calculate on the \code{data.frame} \code{hyperSpec@@data},
##' you have to do this directly on \code{hyperSpec@@data}.
##'
Expand All @@ -29,56 +29,55 @@
##' @param e1,e2 Either two \code{hyperSpec} objects or one \code{hyperSpec}
##' object and matrix of same size as \code{hyperSpec[[]]} or a scalar
##' (numeric of length 1).
##'
##'
##' As \code{hyperSpec} objects must have numeric spectra matrices, the
##' resulting matrix of the comparison is returned directly.
##' @return a logical matrix for the comparison operators.
##' @seealso \code{\link[hyperSpec]{sweep-methods}} for calculations involving
##' a vector and the spectral matrix.
##'
##'
##' \code{\link[methods]{S4groupGeneric}} for group generic methods.
##'
##'
##' \code{\link[base]{Comparison}} for the base comparison functions.
##'
##'
##' \code{\link[hyperSpec]{Arith}} for arithmetic operators,
##' \code{\link[hyperSpec]{Math}} for mathematical group generic functions
##' (groups Math and Math2) working on \code{hyperSpec} objects.
##' @keywords methods arith
##' @export
##' @examples
##'
##'
##' flu [,,445 ~ 450] > 300
##'
##'
##' all (flu == flu[[]])
##'
##'

setMethod ("Compare", signature (e1 = "hyperSpec", e2 = "hyperSpec"),
function (e1, e2){
validObject (e1)
validObject (e2)
setMethod(
"Compare", signature(e1 = "hyperSpec", e2 = "hyperSpec"),
function(e1, e2) {
validObject(e1)
validObject(e2)

callGeneric (e1[[]], e2[[]])
}
)
callGeneric(e1[[]], e2[[]])
}
)

.compx <- function (e1, e2){
validObject (e1)
callGeneric (e1 [[]], e2)
.compx <- function(e1, e2) {
validObject(e1)
callGeneric(e1 [[]], e2)
}

.compy <- function (e1, e2){
validObject (e2)
callGeneric (e1, e2 [[]])
.compy <- function(e1, e2) {
validObject(e2)
callGeneric(e1, e2 [[]])
}

##' @rdname Comparison
setMethod ("Compare", signature (e1 = "hyperSpec", e2 = "numeric"), .compx)
setMethod("Compare", signature(e1 = "hyperSpec", e2 = "numeric"), .compx)
##' @rdname Comparison
setMethod ("Compare", signature (e1 = "hyperSpec", e2 = "matrix"), .compx)
setMethod("Compare", signature(e1 = "hyperSpec", e2 = "matrix"), .compx)

##' @rdname Comparison
setMethod ("Compare", signature (e1 = "numeric", e2 = "hyperSpec"), .compy)
setMethod("Compare", signature(e1 = "numeric", e2 = "hyperSpec"), .compy)
##' @rdname Comparison
setMethod ("Compare", signature (e1 = "matrix", e2 = "hyperSpec"), .compy)


setMethod("Compare", signature(e1 = "matrix", e2 = "hyperSpec"), .compy)
16 changes: 8 additions & 8 deletions hyperSpec/R/DollarNames.R
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Original file line number Diff line number Diff line change
Expand Up @@ -11,19 +11,19 @@
##' @param pattern pattern to look for
##' @return the name of the extra data slot
##' @importFrom utils .DollarNames
.DollarNames.hyperSpec <- function (x, pattern = "")
grep (pattern, colnames (x@data), value = TRUE)
.DollarNames.hyperSpec <- function(x, pattern = "") {
grep(pattern, colnames(x@data), value = TRUE)
}

.test (.DollarNames.hyperSpec) <- function(){
context (".DollarNames")
.test(.DollarNames.hyperSpec) <- function() {
context(".DollarNames")

test_that("expansion on missing pattern", {
expect_equal(.DollarNames (flu), colnames (flu))
expect_equal(.DollarNames(flu), colnames(flu))
})

test_that("expansion on missing pattern", {
expect_equal(.DollarNames (flu, "f"), "filename")
expect_equal(.DollarNames (flu, "c"), c ("spc", "c"))
expect_equal(.DollarNames(flu, "f"), "filename")
expect_equal(.DollarNames(flu, "c"), c("spc", "c"))
})

}
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