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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739
|
#' Ensure that the outcome is univariate
#'
#' @description
#'
#' validate - asserts the following:
#'
#' - `outcomes` must have 1 column. Atomic vectors are treated as
#' 1 column matrices.
#'
#' check - returns the following:
#'
#' - `ok` A logical. Does the check pass?
#'
#' - `n_cols` A single numeric. The actual number of columns.
#'
#' @param outcomes An object to check.
#'
#' @return
#'
#' `validate_outcomes_are_univariate()` returns `outcomes` invisibly.
#'
#' `check_outcomes_are_univariate()` returns a named list of two components,
#' `ok` and `n_cols`.
#'
#' @template section-validation
#'
#' @details
#'
#' The expected way to use this validation function is to supply it the
#' `$outcomes` element of the result of a call to [mold()].
#'
#' @examples
#' validate_outcomes_are_univariate(data.frame(x = 1))
#'
#' try(validate_outcomes_are_univariate(mtcars))
#' @family validation functions
#' @export
validate_outcomes_are_univariate <- function(outcomes) {
check <- check_outcomes_are_univariate(outcomes)
if (!check$ok) {
glubort(
"The outcome must be univariate, but {check$n_cols} columns were found."
)
}
invisible(outcomes)
}
#' @rdname validate_outcomes_are_univariate
#' @export
check_outcomes_are_univariate <- function(outcomes) {
if (!is_vector(outcomes)) {
n_cols <- 0L
} else {
n_cols <- NCOL(outcomes) %||% 0L
}
ok <- (n_cols == 1L)
check <- check_list(ok = ok, n_cols = n_cols)
check
}
# ------------------------------------------------------------------------------
#' Ensure outcomes are all numeric
#'
#' @description
#'
#' validate - asserts the following:
#'
#' - `outcomes` must have numeric columns.
#'
#' check - returns the following:
#'
#' - `ok` A logical. Does the check pass?
#'
#' - `bad_classes` A named list. The names are the names of problematic columns,
#' and the values are the classes of the matching column.
#'
#' @param outcomes An object to check.
#'
#' @return
#'
#' `validate_outcomes_are_numeric()` returns `outcomes` invisibly.
#'
#' `check_outcomes_are_numeric()` returns a named list of two components,
#' `ok` and `bad_classes`.
#'
#' @template section-validation
#'
#' @details
#'
#' The expected way to use this validation function is to supply it the
#' `$outcomes` element of the result of a call to [mold()].
#'
#' @examples
#' # All good
#' check_outcomes_are_numeric(mtcars)
#'
#' # Species is not numeric
#' check_outcomes_are_numeric(iris)
#'
#' # This gives an intelligent error message
#' try(validate_outcomes_are_numeric(iris))
#' @family validation functions
#' @export
validate_outcomes_are_numeric <- function(outcomes) {
check <- check_outcomes_are_numeric(outcomes)
if (!check$ok) {
bad_cols <- glue::single_quote(names(check$bad_classes))
bad_printable_classes <- map(check$bad_classes, glue_quote_collapse)
bad_msg <- glue::glue("{bad_cols}: {bad_printable_classes}")
bad_msg <- glue::glue_collapse(bad_msg, sep = "\n")
glubort(
"All outcomes must be numeric, but the following are not:",
"\n",
"{bad_msg}"
)
}
invisible(outcomes)
}
#' @rdname validate_outcomes_are_numeric
#' @export
check_outcomes_are_numeric <- function(outcomes) {
outcomes <- check_is_data_like(outcomes)
where_numeric <- map_lgl(outcomes, is.numeric)
ok <- all(where_numeric)
if (!ok) {
bad_classes <- get_data_classes(outcomes[, !where_numeric])
} else {
bad_classes <- list()
}
check_list(ok = ok, bad_classes = bad_classes)
}
# ------------------------------------------------------------------------------
#' Ensure that the outcome has only factor columns
#'
#' @description
#'
#' validate - asserts the following:
#'
#' - `outcomes` must have factor columns.
#'
#' check - returns the following:
#'
#' - `ok` A logical. Does the check pass?
#'
#' - `bad_classes` A named list. The names are the names of problematic columns,
#' and the values are the classes of the matching column.
#'
#' @param outcomes An object to check.
#'
#' @return
#'
#' `validate_outcomes_are_factors()` returns `outcomes` invisibly.
#'
#' `check_outcomes_are_factors()` returns a named list of two components,
#' `ok` and `bad_classes`.
#'
#' @template section-validation
#'
#' @details
#'
#' The expected way to use this validation function is to supply it the
#' `$outcomes` element of the result of a call to [mold()].
#'
#' @examples
#' # Not a factor column.
#' check_outcomes_are_factors(data.frame(x = 1))
#'
#' # All good
#' check_outcomes_are_factors(data.frame(x = factor(c("A", "B"))))
#' @family validation functions
#' @export
validate_outcomes_are_factors <- function(outcomes) {
check <- check_outcomes_are_factors(outcomes)
if (!check$ok) {
bad_cols <- glue::single_quote(names(check$bad_classes))
bad_printable_classes <- map(check$bad_classes, glue_quote_collapse)
bad_msg <- glue::glue("{bad_cols}: {bad_printable_classes}")
bad_msg <- glue::glue_collapse(bad_msg, sep = "\n")
glubort(
"All outcomes must be factors, but the following are not:",
"\n",
"{bad_msg}"
)
}
invisible(outcomes)
}
#' @rdname validate_outcomes_are_factors
#' @export
check_outcomes_are_factors <- function(outcomes) {
outcomes <- check_is_data_like(outcomes, "outcomes")
where_factor <- map_lgl(outcomes, is.factor)
ok <- all(where_factor)
if (!ok) {
bad_classes <- get_data_classes(outcomes[, !where_factor])
} else {
bad_classes <- list()
}
check_list(ok = ok, bad_classes = bad_classes)
}
# ------------------------------------------------------------------------------
#' Ensure that the outcome has binary factors
#'
#' @description
#'
#' validate - asserts the following:
#'
#' - `outcomes` must have binary factor columns.
#'
#' check - returns the following:
#'
#' - `ok` A logical. Does the check pass?
#'
#' - `bad_cols` A character vector. The names of the columns with problems.
#'
#' - `num_levels` An integer vector. The actual number of levels of the columns
#' with problems.
#'
#' @param outcomes An object to check.
#'
#' @return
#'
#' `validate_outcomes_are_binary()` returns `outcomes` invisibly.
#'
#' `check_outcomes_are_binary()` returns a named list of three components,
#' `ok`, `bad_cols`, and `num_levels`.
#'
#' @template section-validation
#'
#' @details
#'
#' The expected way to use this validation function is to supply it the
#' `$outcomes` element of the result of a call to [mold()].
#'
#' @examples
#' # Not a binary factor. 0 levels
#' check_outcomes_are_binary(data.frame(x = 1))
#'
#' # Not a binary factor. 1 level
#' check_outcomes_are_binary(data.frame(x = factor("A")))
#'
#' # All good
#' check_outcomes_are_binary(data.frame(x = factor(c("A", "B"))))
#' @family validation functions
#' @export
validate_outcomes_are_binary <- function(outcomes) {
check <- check_outcomes_are_binary(outcomes)
if (!check$ok) {
bad_cols <- glue::single_quote(check$bad_cols)
bad_msg <- glue::glue("{bad_cols}: {check$num_levels}")
bad_msg <- glue::glue_collapse(bad_msg, sep = "\n")
glubort(
"The outcome must be binary, ",
"but the following number of levels were found:",
"\n",
"{bad_msg}"
)
}
invisible(outcomes)
}
#' @rdname validate_outcomes_are_binary
#' @export
check_outcomes_are_binary <- function(outcomes) {
outcomes <- check_is_data_like(outcomes, "outcomes")
outcomes_levels <- map(outcomes, levels)
pos_binary_factors <- map_lgl(outcomes_levels, is_binary)
ok <- all(pos_binary_factors)
if (!ok) {
non_binary_levels <- outcomes_levels[!pos_binary_factors]
num_levels <- map_int(non_binary_levels, length)
bad_cols <- names(num_levels)
num_levels <- unname(num_levels)
} else {
num_levels <- integer()
bad_cols <- character()
}
check_list(ok = ok, bad_cols = bad_cols, num_levels = num_levels)
}
is_binary <- function(x) {
length(x) == 2L
}
# ------------------------------------------------------------------------------
#' Ensure predictors are all numeric
#'
#' @description
#'
#' validate - asserts the following:
#'
#' - `predictors` must have numeric columns.
#'
#' check - returns the following:
#'
#' - `ok` A logical. Does the check pass?
#'
#' - `bad_classes` A named list. The names are the names of problematic columns,
#' and the values are the classes of the matching column.
#'
#' @param predictors An object to check.
#'
#' @return
#'
#' `validate_predictors_are_numeric()` returns `predictors` invisibly.
#'
#' `check_predictors_are_numeric()` returns a named list of two components,
#' `ok`, and `bad_classes`.
#'
#' @template section-validation
#'
#' @details
#'
#' The expected way to use this validation function is to supply it the
#' `$predictors` element of the result of a call to [mold()].
#'
#' @examples
#' # All good
#' check_predictors_are_numeric(mtcars)
#'
#' # Species is not numeric
#' check_predictors_are_numeric(iris)
#'
#' # This gives an intelligent error message
#' try(validate_predictors_are_numeric(iris))
#' @family validation functions
#' @export
validate_predictors_are_numeric <- function(predictors) {
check <- check_predictors_are_numeric(predictors)
if (!check$ok) {
bad_cols <- glue::single_quote(names(check$bad_classes))
bad_printable_classes <- map(check$bad_classes, glue_quote_collapse)
bad_msg <- glue::glue("{bad_cols}: {bad_printable_classes}")
bad_msg <- glue::glue_collapse(bad_msg, sep = "\n")
glubort(
"All predictors must be numeric, but the following are not:",
"\n",
"{bad_msg}"
)
}
invisible(predictors)
}
#' @rdname validate_predictors_are_numeric
#' @export
check_predictors_are_numeric <- function(predictors) {
predictors <- check_is_data_like(predictors)
where_numeric <- map_lgl(predictors, is.numeric)
ok <- all(where_numeric)
if (!ok) {
bad_classes <- get_data_classes(predictors[, !where_numeric])
} else {
bad_classes <- list()
}
check_list(ok = ok, bad_classes = bad_classes)
}
# ------------------------------------------------------------------------------
#' Ensure that `data` contains required column names
#'
#' @description
#'
#' validate - asserts the following:
#'
#' - The column names of `data` must contain all `original_names`.
#'
#' check - returns the following:
#'
#' - `ok` A logical. Does the check pass?
#'
#' - `missing_names` A character vector. The missing column names.
#'
#' @details
#'
#' A special error is thrown if the missing column is named `".outcome"`. This
#' only happens in the case where [mold()] is called using the xy-method, and
#' a _vector_ `y` value is supplied rather than a data frame or matrix. In that
#' case, `y` is coerced to a data frame, and the automatic name `".outcome"` is
#' added, and this is what is looked for in [forge()]. If this happens, and the
#' user tries to request outcomes using `forge(..., outcomes = TRUE)` but
#' the supplied `new_data` does not contain the required `".outcome"` column,
#' a special error is thrown telling them what to do. See the examples!
#'
#' @param data A data frame to check.
#'
#' @param original_names A character vector. The original column names.
#'
#' @return
#'
#' `validate_column_names()` returns `data` invisibly.
#'
#' `check_column_names()` returns a named list of two components,
#' `ok`, and `missing_names`.
#'
#' @template section-validation
#'
#' @examples
#' # ---------------------------------------------------------------------------
#'
#' original_names <- colnames(mtcars)
#'
#' test <- mtcars
#' bad_test <- test[, -c(3, 4)]
#'
#' # All good
#' check_column_names(test, original_names)
#'
#' # Missing 2 columns
#' check_column_names(bad_test, original_names)
#'
#' # Will error
#' try(validate_column_names(bad_test, original_names))
#'
#' # ---------------------------------------------------------------------------
#' # Special error when `.outcome` is missing
#'
#' train <- iris[1:100, ]
#' test <- iris[101:150, ]
#'
#' train_x <- subset(train, select = -Species)
#' train_y <- train$Species
#'
#' # Here, y is a vector
#' processed <- mold(train_x, train_y)
#'
#' # So the default column name is `".outcome"`
#' processed$outcomes
#'
#' # It doesn't affect forge() normally
#' forge(test, processed$blueprint)
#'
#' # But if the outcome is requested, and `".outcome"`
#' # is not present in `new_data`, an error is thrown
#' # with very specific instructions
#' try(forge(test, processed$blueprint, outcomes = TRUE))
#'
#' # To get this to work, just create an .outcome column in new_data
#' test$.outcome <- test$Species
#'
#' forge(test, processed$blueprint, outcomes = TRUE)
#' @family validation functions
#' @export
validate_column_names <- function(data, original_names) {
data <- check_is_data_like(data)
check <- check_column_names(data, original_names)
if (!check$ok) {
validate_missing_name_isnt_.outcome(check$missing_names)
missing_names <- glue_quote_collapse(check$missing_names)
message <- glue("The following required columns are missing: {missing_names}.")
abort(message)
}
invisible(data)
}
#' @rdname validate_column_names
#' @export
check_column_names <- function(data, original_names) {
if (!is.character(original_names)) {
glubort("`original_names` must be a character vector.")
}
new_names <- colnames(data)
has_names <- original_names %in% new_names
ok <- all(has_names)
if (!ok) {
missing_names <- original_names[!has_names]
} else {
missing_names <- character()
}
check_list(ok = ok, missing_names = missing_names)
}
validate_missing_name_isnt_.outcome <- function(missing_names) {
not_ok <- ".outcome" %in% missing_names
if (not_ok) {
missing_names <- glue_quote_collapse(missing_names)
glubort(
"The following required columns are missing: {missing_names}.
(This indicates that `mold()` was called with a vector for `y`. ",
"When this is the case, and the outcome columns are requested ",
"in `forge()`, `new_data` must include a column with the automatically ",
"generated name, '.outcome', containing the outcome.)"
)
}
invisible(missing_names)
}
# ------------------------------------------------------------------------------
#' Ensure that predictions have the correct number of rows
#'
#' @description
#'
#' validate - asserts the following:
#'
#' - The size of `pred` must be the same as the size of `new_data`.
#'
#' check - returns the following:
#'
#' - `ok` A logical. Does the check pass?
#'
#' - `size_new_data` A single numeric. The size of `new_data`.
#'
#' - `size_pred` A single numeric. The size of `pred`.
#'
#' @param pred A tibble. The predictions to return from any prediction
#' `type`. This is often created using one of the spruce functions, like
#' [spruce_numeric()].
#'
#' @param new_data A data frame of new predictors and possibly outcomes.
#'
#' @return
#'
#' `validate_prediction_size()` returns `pred` invisibly.
#'
#' `check_prediction_size()` returns a named list of three components,
#' `ok`, `size_new_data`, and `size_pred`.
#'
#' @details
#'
#' This validation function is one that is more developer focused rather than
#' user focused. It is a final check to be used right before a value is
#' returned from your specific `predict()` method, and is mainly a "good
#' practice" sanity check to ensure that your prediction blueprint always returns
#' the same number of rows as `new_data`, which is one of the modeling
#' conventions this package tries to promote.
#'
#' @template section-validation
#'
#' @examples
#' # Say new_data has 5 rows
#' new_data <- mtcars[1:5, ]
#'
#' # And somehow you generate predictions
#' # for those 5 rows
#' pred_vec <- 1:5
#'
#' # Then you use `spruce_numeric()` to clean
#' # up these numeric predictions
#' pred <- spruce_numeric(pred_vec)
#'
#' pred
#'
#' # Use this check to ensure that
#' # the number of rows or pred match new_data
#' check_prediction_size(pred, new_data)
#'
#' # An informative error message is thrown
#' # if the rows are different
#' try(validate_prediction_size(spruce_numeric(1:4), new_data))
#' @family validation functions
#' @export
validate_prediction_size <- function(pred, new_data) {
check <- check_prediction_size(pred, new_data)
if (!check$ok) {
glubort(
"The size of `new_data` ({check$size_new_data}) must match the ",
"size of `pred` ({check$size_pred})."
)
}
invisible(pred)
}
#' @rdname validate_prediction_size
#' @export
check_prediction_size <- function(pred, new_data) {
new_data <- check_is_data_like(new_data)
size_new_data <- vec_size(new_data)
size_pred <- vec_size(pred)
ok <- size_pred == size_new_data
check_list(ok = ok, size_new_data = size_new_data, size_pred = size_pred)
}
# ------------------------------------------------------------------------------
#' Ensure no duplicate terms appear in `formula`
#'
#' @description
#'
#' validate - asserts the following:
#'
#' - `formula` must not have duplicates terms on the left and right hand
#' side of the formula.
#'
#' check - returns the following:
#'
#' - `ok` A logical. Does the check pass?
#'
#' - `duplicates` A character vector. The duplicate terms.
#'
#' @param formula A formula to check.
#'
#' @param original A logical. Should the original names be checked, or should
#' the names after processing be used? If `FALSE`, `y ~ log(y)` is allowed
#' because the names are `"y"` and `"log(y)"`, if `TRUE`, `y ~ log(y)` is not
#' allowed because the original names are both `"y"`.
#'
#' @return
#'
#' `validate_no_formula_duplication()` returns `formula` invisibly.
#'
#' `check_no_formula_duplication()` returns a named list of two components,
#' `ok` and `duplicates`.
#'
#' @template section-validation
#'
#' @examples
#' # All good
#' check_no_formula_duplication(y ~ x)
#'
#' # Not good!
#' check_no_formula_duplication(y ~ y)
#'
#' # This is generally okay
#' check_no_formula_duplication(y ~ log(y))
#'
#' # But you can be more strict
#' check_no_formula_duplication(y ~ log(y), original = TRUE)
#'
#' # This would throw an error
#' try(validate_no_formula_duplication(log(y) ~ log(y)))
#' @family validation functions
#' @export
validate_no_formula_duplication <- function(formula, original = FALSE) {
check <- check_no_formula_duplication(formula, original)
if (!check$ok) {
duplicates <- glue_quote_collapse(check$duplicates)
glubort(
"The following terms are duplicated on the left and right hand side ",
"of the `formula`: {duplicates}."
)
}
invisible(formula)
}
#' @rdname validate_no_formula_duplication
#' @export
check_no_formula_duplication <- function(formula, original = FALSE) {
validate_is_formula(formula)
validate_is_bool(original, "original")
# Only required to expand any `.` values so terms() can be called
# The `.` is designed to never contain duplicates, so we just expand
# it to this column name that we hope never exists
dummy_data <- data.frame(`...dummy...` = 1)
formula <- expand_formula_dot_notation(formula, data = dummy_data)
formula_predictors <- get_predictors_formula(formula)
formula_outcomes <- get_outcomes_formula(formula)
if (original) {
predictors <- all.vars(formula_predictors)
outcomes <- all.vars(formula_outcomes)
} else {
predictors <- attr(terms(formula_predictors), "term.labels")
outcomes <- attr(terms(formula_outcomes), "term.labels")
}
duplicates <- intersect(predictors, outcomes)
ok <- length(duplicates) == 0L
check_list(ok = ok, duplicates = duplicates)
}
# ------------------------------------------------------------------------------
# ok = bool
# ... = extra info when not ok
check_list <- function(ok = TRUE, ...) {
validate_is_bool(ok, "ok")
elems <- list2(...)
c(list(ok = ok), elems)
}
|