1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
|
#' (Signed) rank transformation
#'
#' Transform numeric values with the integers of their rank (i.e., 1st smallest,
#' 2nd smallest, 3rd smallest, etc.). Setting the `sign` argument to `TRUE` will
#' give you signed ranks, where the ranking is done according to absolute size
#' but where the sign is preserved (i.e., 2, 1, -3, 4).
#'
#' @param x Object.
#' @param sign Logical, if `TRUE`, return signed ranks.
#' @param method Treatment of ties. Can be one of `"average"` (default),
#' `"first"`, `"last"`, `"random"`, `"max"` or `"min"`. See [rank()] for
#' details.
#' @param zeros How to handle zeros. If `"na"` (default), they are marked as
#' `NA`. If `"signrank"`, they are kept during the ranking and marked as zeros.
#' This is only used when `sign = TRUE`.
#' @param ... Arguments passed to or from other methods.
#' @inheritParams extract_column_names
#' @inheritParams standardize.data.frame
#'
#' @inheritSection center Selection of variables - the `select` argument
#'
#' @examples
#' ranktransform(c(0, 1, 5, -5, -2))
#'
#' # By default, zeros are converted to NA
#' suppressWarnings(
#' ranktransform(c(0, 1, 5, -5, -2), sign = TRUE)
#' )
#' ranktransform(c(0, 1, 5, -5, -2), sign = TRUE, zeros = "signrank")
#'
#' head(ranktransform(trees))
#' @return A rank-transformed object.
#'
#' @family transform utilities
#'
#' @export
ranktransform <- function(x, ...) {
UseMethod("ranktransform")
}
#' @rdname ranktransform
#' @export
ranktransform.numeric <- function(x,
sign = FALSE,
method = "average",
zeros = "na",
verbose = TRUE,
...) {
# no change if all values are `NA`s
if (all(is.na(x))) {
return(x)
}
zeros <- match.arg(zeros, c("na", "signrank"))
method <- match.arg(
method,
c("average", "first", "last", "random", "max", "min")
)
# Warning if only one value and return early
if (insight::has_single_value(x)) {
if (is.null(names(x))) {
name <- deparse(substitute(x))
} else {
name <- names(x)
}
if (verbose) {
insight::format_warning(
paste0(
"Variable `",
name,
"` contains only one unique value and will not be normalized."
)
)
}
return(x)
}
# Warning if only two values present but don't return early
if (length(unique(x)) == 2L) {
if (is.null(names(x))) {
name <- deparse(substitute(x))
} else {
name <- names(x)
}
if (verbose) {
# nolint
insight::format_warning(
paste0(
"Variable `",
name,
"` contains only two different values. Consider converting it to a factor."
)
)
}
}
if (sign) {
if (zeros == "na") {
out <- rep(NA, length(x))
ZEROES <- x == 0
if (any(ZEROES) && verbose) {
insight::format_warning("Zeros detected. These cannot be sign-rank transformed.") # nolint
}
out[!ZEROES] <- sign(x[!ZEROES]) * rank(abs(x[!ZEROES]),
ties.method = method,
na.last = "keep"
)
} else if (zeros == "signrank") {
out <- sign(x) * rank(abs(x), ties.method = method, na.last = "keep")
}
} else {
out <- rank(x, ties.method = method, na.last = "keep")
}
out
}
#' @export
ranktransform.factor <- function(x, ...) {
x
}
#' @export
ranktransform.grouped_df <- function(x,
select = NULL,
exclude = NULL,
sign = FALSE,
method = "average",
ignore_case = FALSE,
regex = FALSE,
zeros = "na",
verbose = TRUE,
...) {
info <- attributes(x)
grps <- attr(x, "groups", exact = TRUE)[[".rows"]]
# evaluate arguments
select <- .select_nse(select,
x,
exclude,
ignore_case,
regex = regex,
verbose = verbose
)
x <- as.data.frame(x)
for (rows in grps) {
x[rows, ] <- ranktransform(
x[rows, , drop = FALSE],
select = select,
exclude = exclude,
sign = sign,
method = method,
...
)
}
# set back class, so data frame still works with dplyr
attributes(x) <- info
x
}
#' @rdname ranktransform
#' @export
ranktransform.data.frame <- function(x,
select = NULL,
exclude = NULL,
sign = FALSE,
method = "average",
ignore_case = FALSE,
regex = FALSE,
zeros = "na",
verbose = TRUE,
...) {
# evaluate arguments
select <- .select_nse(select,
x,
exclude,
ignore_case,
regex = regex,
verbose = verbose
)
x[select] <- lapply(x[select], ranktransform, sign = sign, method = method)
x
}
|
