File: recode_values.R

package info (click to toggle)
r-cran-datawizard 1.0.1%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid, trixie
  • size: 2,300 kB
  • sloc: sh: 13; makefile: 2
file content (529 lines) | stat: -rw-r--r-- 16,113 bytes parent folder | download
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
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
#' @title Recode old values of variables into new values
#' @name recode_values
#'
#' @description
#' This functions recodes old values into new values and can be used to to
#' recode numeric or character vectors, or factors.
#'
#' @param x A data frame, numeric or character vector, or factor.
#' @param recode A list of named vectors, which indicate the recode pairs.
#'   The _names_ of the list-elements (i.e. the left-hand side) represent the
#'   _new_ values, while the values of the list-elements indicate the original
#'   (old) values that should be replaced. When recoding numeric vectors,
#'   element names have to be surrounded in backticks. For example,
#'   ``recode=list(`0`=1)`` would recode all `1` into `0` in a numeric
#'   vector. See also 'Examples' and 'Details'.
#' @param default Defines the default value for all values that have
#'   no match in the recode-pairs. Note that, if `preserve_na=FALSE`, missing
#'   values (`NA`) are also captured by the `default` argument, and thus will
#'   also be recoded into the specified value. See 'Examples' and 'Details'.
#' @param preserve_na Logical, if `TRUE`, `NA` (missing values) are preserved.
#'   This overrides any other arguments, including `default`. Hence, if
#'   `preserve_na=TRUE`, `default` will no longer convert `NA` into the specified
#'   default value.
#' @param ... not used.
#' @inheritParams extract_column_names
#' @inheritParams categorize
#'
#' @return `x`, where old values are replaced by new values.
#'
#' @inheritSection center Selection of variables - the `select` argument
#'
#' @inherit data_rename seealso
#'
#' @note You can use `options(data_recode_pattern = "old=new")` to switch the
#' behaviour of the `recode`-argument, i.e. recode-pairs are now following the
#' pattern `old values = new values`, e.g. if `getOption("data_recode_pattern")`
#' is set to `"old=new"`, then ``recode(`1`=0)`` would recode all 1 into 0.
#' The default for ``recode(`1`=0)`` is to recode all 0 into 1.
#'
#' @details
#' This section describes the pattern of the `recode` arguments, which also
#' provides some shortcuts, in particular when recoding numeric values.
#'
#' - Single values
#'
#'   Single values either need to be wrapped in backticks (in case of numeric
#'   values) or "as is" (for character or factor levels). Example:
#'   ``recode=list(`0`=1,`1`=2)`` would recode 1 into 0, and 2 into 1.
#'   For factors or character vectors, an example is:
#'   `recode=list(x="a",y="b")` (recode "a" into "x" and "b" into "y").
#'
#' - Multiple values
#'
#'   Multiple values that should be recoded into a new value can be separated
#'   with comma. Example: ``recode=list(`1`=c(1,4),`2`=c(2,3))`` would recode the
#'   values 1 and 4 into 1, and 2 and 3 into 2. It is also possible to define  the
#'   old values as a character string, like:  ``recode=list(`1`="1,4",`2`="2,3")``
#'   For factors or character vectors, an example is:
#'   ``recode=list(x=c("a","b"),y=c("c","d"))``.
#'
#' - Value range
#'
#'   Numeric value ranges can be defined using the `:`. Example:
#'   ``recode=list(`1`=1:3,`2`=4:6)`` would recode all values from 1 to 3 into
#'   1, and 4 to 6 into 2.
#'
#' - `min` and `max`
#'
#'   placeholder to use the minimum or maximum value of the
#'   (numeric) variable. Useful, e.g., when recoding ranges of values.
#'   Example: ``recode=list(`1`="min:10",`2`="11:max")``.
#'
#' - `default` values
#'
#'   The `default` argument defines the default value for all values that have
#'   no match in the recode-pairs. For example,
#'   ``recode=list(`1`=c(1,2),`2`=c(3,4)), default=9`` would
#'   recode values 1 and 2 into 1, 3 and 4 into 2, and all other values into 9.
#'   If `preserve_na` is set to `FALSE`, `NA` (missing values) will also be
#'   recoded into the specified default value.
#'
#' - Reversing and rescaling
#'
#'   See [reverse()] and [rescale()].
#'
#' @examples
#' # numeric ----------
#' set.seed(123)
#' x <- sample(c(1:4, NA), 15, TRUE)
#' table(x, useNA = "always")
#'
#' out <- recode_values(x, list(`0` = 1, `1` = 2:3, `2` = 4))
#' out
#' table(out, useNA = "always")
#'
#' # to recode NA values, set preserve_na to FALSE
#' out <- recode_values(
#'   x,
#'   list(`0` = 1, `1` = 2:3, `2` = 4, `9` = NA),
#'   preserve_na = FALSE
#' )
#' out
#' table(out, useNA = "always")
#'
#' # preserve na ----------
#' out <- recode_values(x, list(`0` = 1, `1` = 2:3), default = 77)
#' out
#' table(out, useNA = "always")
#'
#' # recode na into default ----------
#' out <- recode_values(
#'   x,
#'   list(`0` = 1, `1` = 2:3),
#'   default = 77,
#'   preserve_na = FALSE
#' )
#' out
#' table(out, useNA = "always")
#'
#'
#' # factors (character vectors are similar) ----------
#' set.seed(123)
#' x <- as.factor(sample(c("a", "b", "c"), 15, TRUE))
#' table(x)
#'
#' out <- recode_values(x, list(x = "a", y = c("b", "c")))
#' out
#' table(out)
#'
#' out <- recode_values(x, list(x = "a", y = "b", z = "c"))
#' out
#' table(out)
#'
#' out <- recode_values(x, list(y = "b,c"), default = 77)
#' # same as
#' # recode_values(x, list(y = c("b", "c")), default = 77)
#' out
#' table(out)
#'
#'
#' # data frames ----------
#' set.seed(123)
#' d <- data.frame(
#'   x = sample(c(1:4, NA), 12, TRUE),
#'   y = as.factor(sample(c("a", "b", "c"), 12, TRUE)),
#'   stringsAsFactors = FALSE
#' )
#'
#' recode_values(
#'   d,
#'   recode = list(`0` = 1, `1` = 2:3, `2` = 4, x = "a", y = c("b", "c")),
#'   append = TRUE
#' )
#'
#'
#' # switch recode pattern to "old=new" ----------
#' options(data_recode_pattern = "old=new")
#'
#' # numeric
#' set.seed(123)
#' x <- sample(c(1:4, NA), 15, TRUE)
#' table(x, useNA = "always")
#'
#' out <- recode_values(x, list(`1` = 0, `2:3` = 1, `4` = 2))
#' table(out, useNA = "always")
#'
#' # factors (character vectors are similar)
#' set.seed(123)
#' x <- as.factor(sample(c("a", "b", "c"), 15, TRUE))
#' table(x)
#'
#' out <- recode_values(x, list(a = "x", `b, c` = "y"))
#' table(out)
#'
#' # reset options
#' options(data_recode_pattern = NULL)
#' @export
recode_values <- function(x, ...) {
  UseMethod("recode_values")
}


#' @export
recode_values.default <- function(x, verbose = TRUE, ...) {
  if (isTRUE(verbose)) {
    insight::format_alert(
      paste0("Variables of class `", class(x)[1], "` can't be recoded and remain unchanged.")
    )
  }
  return(x)
}


#' @rdname recode_values
#' @export
recode_values.numeric <- function(x,
                                  recode = NULL,
                                  default = NULL,
                                  preserve_na = TRUE,
                                  verbose = TRUE,
                                  ...) {
  # save
  original_x <- x

  # check arguments
  if (!.recode_args_ok(x, recode, verbose)) {
    return(x)
  }

  # recode-pattern option
  pattern <- getOption("data_recode_pattern")

  # make sure NAs are preserved after recoding
  missing_values <- NULL
  if (preserve_na) {
    missing_values <- is.na(x)
  }

  # check for "default" token
  if (!is.null(default)) {
    # set the default value for all values that have no match
    # (i.e. that should not be recoded)
    x <- rep(as.numeric(default), length = length(x))
  }

  for (i in names(recode)) {
    # based on option-settings, the recode-argument can either follow the
    # pattern "new=old", or "old=new"

    if (identical(pattern, "old=new")) {
      # pattern: old = new, name of list element is old value
      old_values <- i
      new_values <- recode[[i]]
    } else {
      # pattern: new = old, name of list element is new value
      old_values <- recode[[i]]
      new_values <- i
    }

    if (is.character(old_values)) {
      # replace placeholder
      old_values <- gsub("min", min(x, na.rm = TRUE), old_values, fixed = TRUE)
      old_values <- gsub("max", max(x, na.rm = TRUE), old_values, fixed = TRUE)

      # mimic vector
      if (length(old_values) == 1 && !grepl("c(", old_values, fixed = TRUE)) {
        old_values <- paste0("c(", old_values, ")")
      }

      # parse old values, which are strings (names of element), but which should
      # contain values, like "1:10" or "1, 2, 3, 4". These should now be in the
      # format "c(1, 2, 3, 4)" or "c(1:10)", and it should be possible to parse
      # and evaluate these strings into a numeric vector
      old_values <- tryCatch(eval(parse(text = old_values)), error = function(e) NULL)
    }

    if (!is.null(old_values) && (is.numeric(old_values) || is.na(old_values))) {
      x[which(original_x %in% old_values)] <- as.numeric(new_values)
    }
  }

  # set back variable labels, remove value labels
  # (these are most likely not matching anymore)
  attr(x, "label") <- attr(original_x, "label", exact = TRUE)
  attr(x, "labels") <- NULL

  # set back missing values
  if (!is.null(missing_values)) {
    x[missing_values] <- NA
  }

  x
}


#' @export
recode_values.factor <- function(x,
                                 recode = NULL,
                                 default = NULL,
                                 preserve_na = TRUE,
                                 verbose = TRUE,
                                 ...) {
  # save
  original_x <- x

  # check arguments
  if (!.recode_args_ok(x, recode, verbose)) {
    return(x)
  }

  # recode-pattern option
  pattern <- getOption("data_recode_pattern")

  # make sure NAs are preserved after recoding
  missing_values <- NULL
  if (preserve_na) {
    missing_values <- is.na(x)
  }

  # as character, so recoding works
  x <- as.character(x)

  # check for "default" token
  if (!is.null(default)) {
    # set the default value for all values that have no match
    # (i.e. that should not be recoded)
    x <- rep(as.character(default), length = length(x))
  }

  for (i in names(recode)) {
    # based on option-settings, the recode-argument can either follow the
    # pattern "new=old", or "old=new"

    if (identical(pattern, "old=new")) {
      # pattern: old = new
      # name of list element is old value

      old_values <- paste(
        deparse(insight::trim_ws(unlist(strsplit(i, ",", fixed = TRUE), use.names = FALSE))),
        collapse = ","
      )

      # parse old values, which are strings (names of element), but which should
      # contain values, like "a" or "a, b, c". These should now be in the
      # format "c("a", "b", "c")" and it should be possible to parse
      # and evaluate these strings into a numeric vector
      old_values <- tryCatch(eval(parse(text = old_values)), error = function(e) NULL)

      # recode
      x[which(original_x %in% old_values)] <- recode[[i]]
    } else {
      # pattern: new = old
      # name of list element is new value

      old_values <- as.character(recode[[i]])
      # check input style: "a, b, c"
      if (length(old_values) == 1 && grepl(",", old_values, fixed = TRUE)) {
        # split and make character vector
        old_values <- insight::trim_ws(unlist(strsplit(old_values, ",", fixed = TRUE), use.names = FALSE))
      }
      # recode
      if (identical(i, "NA")) {
        x[which(original_x %in% old_values)] <- NA_character_
      } else {
        x[which(original_x %in% old_values)] <- as.character(i)
      }
    }
  }

  # set back missing values
  if (!is.null(missing_values)) {
    x[missing_values] <- NA_character_
  }

  # make sure we have correct new levels
  x <- droplevels(as.factor(x))

  # set back variable labels, remove value labels
  # (these are most likely not matching anymore)
  attr(x, "label") <- attr(original_x, "label", exact = TRUE)
  attr(x, "labels") <- NULL

  x
}


#' @export
recode_values.character <- function(x,
                                    recode = NULL,
                                    default = NULL,
                                    preserve_na = TRUE,
                                    verbose = TRUE,
                                    ...) {
  # save
  original_x <- x

  # check arguments
  if (!.recode_args_ok(x, recode, verbose)) {
    return(x)
  }

  # recode-pattern option
  pattern <- getOption("data_recode_pattern")

  # make sure NAs are preserved after recoding
  missing_values <- NULL
  if (preserve_na) {
    missing_values <- is.na(x)
  }

  # check for "default" token
  if (!is.null(default)) {
    # set the default value for all values that have no match
    # (i.e. that should not be recoded)
    x <- rep(as.character(default), length = length(x))
  }

  for (i in names(recode)) {
    # based on option-settings, the recode-argument can either follow the
    # pattern "new=old", or "old=new"

    if (identical(pattern, "old=new")) {
      # pattern: old = new
      # name of list element is old value

      # name of list element is old value
      value_string <- paste(
        deparse(insight::trim_ws(unlist(strsplit(i, ",", fixed = TRUE), use.names = FALSE))),
        collapse = ","
      )

      # parse old values, which are strings (names of element), but which should
      # contain values, like "a" or "a, b, c". These should now be in the
      # format "c("a", "b", "c")" and it should be possible to parse
      # and evaluate these strings into a numeric vector
      old_values <- tryCatch(eval(parse(text = value_string)), error = function(e) NULL)

      # recode
      x[which(original_x %in% old_values)] <- recode[[i]]
    } else {
      # pattern: new = old
      # name of list element is new value

      old_values <- as.character(recode[[i]])
      # check input style: "a, b, c"
      if (length(old_values) == 1 && grepl(",", old_values, fixed = TRUE)) {
        # split and make character vector
        old_values <- insight::trim_ws(unlist(strsplit(old_values, ",", fixed = TRUE), use.names = FALSE))
      }
      # recode
      if (identical(i, "NA")) {
        x[which(original_x %in% old_values)] <- NA_character_
      } else {
        x[which(original_x %in% old_values)] <- as.character(i)
      }
    }
  }

  # set back variable labels, remove value labels
  # (these are most likely not matching anymore)
  attr(x, "label") <- attr(original_x, "label", exact = TRUE)
  attr(x, "labels") <- NULL

  # set back missing values
  if (!is.null(missing_values)) {
    x[missing_values] <- NA_character_
  }

  x
}


#' @rdname recode_values
#' @export
recode_values.data.frame <- function(x,
                                     select = NULL,
                                     exclude = NULL,
                                     recode = NULL,
                                     default = NULL,
                                     preserve_na = TRUE,
                                     append = FALSE,
                                     ignore_case = FALSE,
                                     regex = FALSE,
                                     verbose = TRUE,
                                     ...) {
  # evaluate arguments
  select <- .select_nse(select,
    x,
    exclude,
    ignore_case,
    regex = regex,
    verbose = verbose
  )

  # when we append variables, we call ".process_append()", which will
  # create the new variables and updates "select", so new variables are processed
  if (!isFALSE(append)) {
    # process arguments
    my_args <- .process_append(
      x,
      select,
      append,
      append_suffix = "_r",
      preserve_value_labels = TRUE
    )
    # update processed arguments
    x <- my_args$x
    select <- my_args$select
  }

  x[select] <- lapply(
    x[select],
    recode_values,
    recode = recode,
    default = default,
    preserve_na = preserve_na,
    verbose = verbose,
    ...
  )

  x
}


# utils --------------------------

.recode_args_ok <- function(x, recode, verbose) {
  ok <- TRUE
  # no missings
  valid <- stats::na.omit(x)

  # skip if all NA
  if (!length(valid)) {
    if (isTRUE(verbose)) {
      insight::format_warning("Variable contains only missing values. No recoding carried out.")
    }
    ok <- FALSE
  }

  # warn if not a list
  if (!is.list(recode) || is.null(names(recode))) {
    if (isTRUE(verbose)) {
      insight::format_warning("`recode` needs to be a (named) list. No recoding carried out.")
    }
    ok <- FALSE
  }

  ok
}