CVS commit: pkgsrc/math/R-dplyr

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Sun Feb 12 04:09:37 UTC 2023

Modified Files:
        pkgsrc/math/R-dplyr: Makefile distinfo

Log Message:
(math/R-dplyr)  Updated 1.0.1 to 1.1.0

# dplyr 1.1.0

## New features

* [`.by`/`by`](https://dplyr.tidyverse.org/dev/reference/dplyr_by.html) is an
  experimental alternative to `group_by()` that supports per-operation grouping
  for `mutate()`, `summarise()`, `filter()`, and the `slice()` family (#6528).

  Rather than:

  ```
  starwars %>%
    group_by(species, homeworld) %>%
    summarise(mean_height = mean(height))
  ```

  You can now write:

  ```
  starwars %>%
    summarise(
      mean_height = mean(height),
      .by = c(species, homeworld)
    )
  ```

  The most useful reason to do this is because `.by` only affects a single
  operation. In the example above, an ungrouped data frame went into the
  `summarise()` call, so an ungrouped data frame will come out; with `.by`, you
  never need to remember to `ungroup()` afterwards and you never need to use
  the `.groups` argument.

  Additionally, using `summarise()` with `.by` will never sort the results by
  the group key, unlike with `group_by()`. Instead, the results are returned
  using the existing ordering of the groups from the original data. We feel this
  is more predictable, better maintains any ordering you might have already
  applied with a previous call to `arrange()`, and provides a way to maintain
  the current ordering without having to resort to factors.

  This feature was inspired by
  [data.table](https://CRAN.R-project.org/package=data.table), where the
  equivalent syntax looks like:

  ```
  starwars[, .(mean_height = mean(height)), by = .(species, homeworld)]
  ```

  `with_groups()` is superseded in favor of `.by` (#6582).

* `reframe()` is a new experimental verb that creates a new data frame by
  applying functions to columns of an existing data frame. It is very similar to
  `summarise()`, with two big differences:

  * `reframe()` can return an arbitrary number of rows per group, while
    `summarise()` reduces each group down to a single row.

  * `reframe()` always returns an ungrouped data frame, while `summarise()`
    might return a grouped or rowwise data frame, depending on the scenario.

  `reframe()` has been added in response to valid concern from the community
  that allowing `summarise()` to return any number of rows per group increases
  the chance for accidental bugs. We still feel that this is a powerful
  technique, and is a principled replacement for `do()`, so we have moved these
  features to `reframe()` (#6382).

* `group_by()` now uses a new algorithm for computing groups. It is often faster
  than the previous approach (especially when there are many groups), and in
  most cases there should be no changes. The one exception is with character
  vectors, see the C locale news bullet below for more details (#4406, #6297).

* `arrange()` now uses a faster algorithm for sorting character vectors, which
  is heavily inspired by data.table's `forder()`. See the C locale news bullet
  below for more details (#4962).

* Joins have been completely overhauled to enable more flexible join operations
  and provide more tools for quality control. Many of these changes are inspired
  by data.table's join syntax (#5914, #5661, #5413, #2240).

  * A _join specification_ can now be created through `join_by()`. This allows
    you to specify both the left and right hand side of a join using unquoted
    column names, such as `join_by(sale_date == commercial_date)`. Join
    specifications can be supplied to any `*_join()` function as the `by`
    argument.

  * Join specifications allow for new types of joins:

    * Equality joins: The most common join, specified by `==`. For example,
      `join_by(sale_date == commercial_date)`.

    * Inequality joins: For joining on inequalities, i.e.`>=`, `>`, `<`, and
      `<=`. For example, use `join_by(sale_date >= commercial_date)` to find
      every commercial that aired before a particular sale.

    * Rolling joins: For "rolling" the closest match forward or backwards when
      there isn't an exact match, specified by using the rolling helper,
      `closest()`. For example,
      `join_by(closest(sale_date >= commercial_date))` to find only the most
      recent commercial that aired before a particular sale.

    * Overlap joins: For detecting overlaps between sets of columns, specified
      by using one of the overlap helpers: `between()`, `within()`, or
      `overlaps()`. For example, use
      `join_by(between(commercial_date, sale_date_lower, sale_date))` to
      find commercials that aired before a particular sale, as long as they
      occurred after some lower bound, such as 40 days before the sale was made.

    Note that you cannot use arbitrary expressions in the join conditions, like
    `join_by(sale_date - 40 >= commercial_date)`. Instead, use `mutate()` to
    create a new column containing the result of `sale_date - 40` and refer
    to that by name in `join_by()`.

  * `multiple` is a new argument for controlling what happens when a row
    in `x` matches multiple rows in `y`. For equality joins and rolling joins,
    where this is usually surprising, this defaults to signalling a `"warning"`,
    but still returns all of the matches. For inequality joins, where multiple
    matches are usually expected, this defaults to returning `"all"` of the
    matches. You can also return only the `"first"` or `"last"` match, `"any"`
    of the matches, or you can `"error"`.

  * `keep` now defaults to `NULL` rather than `FALSE`. `NULL` implies
    `keep = FALSE` for equality conditions, but `keep = TRUE` for inequality
    conditions, since you generally want to preserve both sides of an
    inequality join.

  * `unmatched` is a new argument for controlling what happens when a row
    would be dropped because it doesn't have a match. For backwards
    compatibility, the default is `"drop"`, but you can also choose to
    `"error"` if dropped rows would be surprising.

* `across()` gains an experimental `.unpack` argument to optionally unpack
  (as in, `tidyr::unpack()`) data frames returned by functions in `.fns`
  (#6360).

* `consecutive_id()` for creating groups based on contiguous runs of the
  same values, like `data.table::rleid()` (#1534).

* `case_match()` is a "vectorised switch" variant of `case_when()` that matches
  on values rather than logical expressions. It is like a SQL "simple"
  `CASE WHEN` statement, whereas `case_when()` is like a SQL "searched"
  `CASE WHEN` statement (#6328).

* `cross_join()` is a more explicit and slightly more correct replacement for
  using `by = character()` during a join (#6604).

* `pick()` makes it easy to access a subset of columns from the current group.
  `pick()` is intended as a replacement for `across(.fns = NULL)`, `cur_data()`,
  and `cur_data_all()`. We feel that `pick()` is a much more evocative name when
  you are just trying to select a subset of columns from your data (#6204).

* `symdiff()` computes the symmetric difference (#4811).

## Lifecycle changes

### Breaking changes

* `arrange()` and `group_by()` now use the C locale, not the system locale,
  when ordering or grouping character vectors. This brings _substantial_
  performance improvements, increases reproducibility across R sessions, makes
  dplyr more consistent with data.table, and we believe it should affect little
  existing code. If it does affect your code, you can use
  `options(dplyr.legacy_locale = TRUE)` to quickly revert to the previous
  behavior. However, in general, we instead recommend that you use the new
  `.locale` argument to precisely specify the desired locale. For a full
  explanation please read the associated
  [grouping](https://github.com/tidyverse/tidyups/blob/main/006-dplyr-group-by-ordering.md)
  and [ordering](https://github.com/tidyverse/tidyups/blob/main/003-dplyr-radix-ordering.md)
  tidyups.

* `bench_tbls()`, `compare_tbls()`, `compare_tbls2()`, `eval_tbls()`,
  `eval_tbls2()`, `location()` and `changes()`, deprecated in 1.0.0, are now
  defunct (#6387).

* `frame_data()`, `data_frame_()`, `lst_()` and `tbl_sum()` are no longer
  re-exported from tibble (#6276, #6277, #6278, #6284).

* `select_vars()`, `rename_vars()`, `select_var()` and `current_vars()`,
  deprecated in 0.8.4, are now defunct (#6387).

### Newly deprecated

* `across()`, `c_across()`, `if_any()`, and `if_all()` now require the
  `.cols` and `.fns` arguments. In general, we now recommend that you use
  `pick()` instead of an empty `across()` call or `across()` with no `.fns`
  (e.g. `across(c(x, y))`. (#6523).

  * Relying on the previous default of `.cols = everything()` is deprecated.
    We have skipped the soft-deprecation stage in this case, because indirect
    usage of `across()` and friends in this way is rare.

  * Relying on the previous default of `.fns = NULL` is not yet formally
    soft-deprecated, because there was no good alternative until now, but it is
    discouraged and will be soft-deprecated in the next minor release.

* Passing `...` to `across()` is soft-deprecated because it's ambiguous when
  those arguments are evaluated. Now, instead of (e.g.)
  `across(a:b, mean, na.rm = TRUE)` you should write
  `across(a:b, ~ mean(.x, na.rm = TRUE))` (#6073).

* `all_equal()` is deprecated. We've advised against it for some time, and
  we explicitly recommend you use `all.equal()`, manually reordering the rows
  and columns as needed (#6324).

* `cur_data()` and `cur_data_all()` are soft-deprecated in favour of
  `pick()` (#6204).

* Using `by = character()` to perform a cross join is now soft-deprecated in
  favor of `cross_join()` (#6604).

* `filter()`ing with a 1-column matrix is deprecated (#6091).

* `progress_estimate()` is deprecated for all uses (#6387).

* Using `summarise()` to produce a 0 or >1 row "summary" is deprecated in favor
  of the new `reframe()`. See the NEWS bullet about `reframe()` for more details
  (#6382).

* All functions deprecated in 1.0.0 (released April 2020) and earlier now warn
  every time you  use them (#6387). This includes `combine()`, `src_local()`,
  `src_mysql()`, `src_postgres()`, `src_sqlite()`, `rename_vars_()`,
  `select_vars_()`, `summarise_each_()`, `mutate_each_()`, `as.tbl()`,
  `tbl_df()`, and a handful of older arguments. They are likely to be made
  defunct in the next major version (but not before mid 2024).

* `slice()`ing with a 1-column matrix is deprecated.

### Newly superseded

* `recode()` is superseded in favour of `case_match()` (#6433).

* `recode_factor()` is superseded. We don't have a direct replacement for it
  yet, but we plan to add one to forcats. In the meantime you can often use
`case_match(.ptype = factor(levels = ))` instead (#6433).

* `transmute()` is superseded in favour of `mutate(.keep = "none")` (#6414).

### Newly stable

* The `.keep`, `.before`, and `.after` arguments to `mutate()` have moved
  from experimental to stable.

* The `rows_*()` family of functions have moved from experimental to stable.

## vctrs

Many of dplyr's vector functions have been rewritten to make use of the vctrs
package, bringing greater consistency and improved performance.

* `between()` can now work with all vector types, not just numeric and
  date-time. Additionally, `left` and `right` can now also be vectors (with the
  same length as `x`), and `x`, `left`, and `right` are cast to the common type
  before the comparison is made (#6183, #6260, #6478).

* `case_when()` (#5106):

  * Has a new `.default` argument that is intended to replace usage of
    `TRUE ~ default_value` as a more explicit and readable way to specify
    a default value. In the future, we will deprecate the unsafe recycling of
    the LHS inputs that allows `TRUE ~` to work, so we encourage you to switch
    to using `.default`.

  * No longer requires exact matching of the types of RHS values. For example,
    the following no longer requires you to use `NA_character_`.

    ```
    x <- c("little", "unknown", "small", "missing", "large")

    case_when(
      x %in% c("little", "small") ~ "one",
      x %in% c("big", "large") ~ "two",
      x %in% c("missing", "unknown") ~ NA
    )
    ```

  * Supports a larger variety of RHS value types. For example, you can use a
    data frame to create multiple columns at once.

  * Has new `.ptype` and `.size` arguments which allow you to enforce
    a particular output type and size.

  * Has a better error when types or lengths were incompatible (#6261, #6206).

* `coalesce()` (#6265):

  * Discards `NULL` inputs up front.

  * No longer iterates over the columns of data frame input. Instead, a row is
    now only coalesced if it is entirely missing, which is consistent with
    `vctrs::vec_detect_missing()` and greatly simplifies the implementation.

  * Has new `.ptype` and `.size` arguments which allow you to enforce
    a particular output type and size.

* `first()`, `last()`, and `nth()` (#6331):

  * When used on a data frame, these functions now return a single row rather
    than a single column. This is more consistent with the vctrs principle that
    a data frame is generally treated as a vector of rows.

  * The `default` is no longer "guessed", and will always automatically be set
    to a missing value appropriate for the type of `x`.

  * Error if `n` is not an integer. `nth(x, n = 2)` is fine, but
    `nth(x, n = 2.5)` is now an error.

  Additionally, they have all gained an `na_rm` argument since they
  are summary functions (#6242, with contributions from @tnederlof).

* `if_else()` gains most of the same benefits as `case_when()`. In particular,
  `if_else()` now takes the common type of `true`, `false`, and `missing` to
  determine the output type, meaning that you can now reliably use `NA`,
  rather than `NA_character_` and friends (#6243).

* `na_if()` (#6329) now casts `y` to the type of `x` before comparison, which
  makes it clearer that this function is type and size stable on `x`. In
  particular, this means that you can no longer do `na_if(<tibble>, 0)`, which
  previously accidentally allowed you to replace any instance of `0` across
  every column of the tibble with `NA`. `na_if()` was never intended to work
  this way, and this is considered off-label usage.

  You can also now replace `NaN` values in `x` with `na_if(x, NaN)`.

* `lag()` and `lead()` now cast `default` to the type of `x`, rather than taking
  the common type. This ensures that these functions are type stable on `x`
  (#6330).

* `row_number()`, `min_rank()`, `dense_rank()`, `ntile()`, `cume_dist()`, and
  `percent_rank()` are faster and work for more types. You can now rank by
  multiple columns by supplying a data frame (#6428).

* `with_order()` now checks that the size of `order_by` is the same size as `x`,
  and now works correctly when `order_by` is a data frame (#6334).

## Minor improvements and bug fixes

* Fixed an issue with latest rlang that caused internal tools (such as
  `mask$eval_all_summarise()`) to be mentioned in error messages (#6308).

* Warnings are enriched with contextualised information in `summarise()` and
  `filter()` just like they have been in `mutate()` and `arrange()`.

* Joins now reference the correct column in `y` when a type error is thrown
  while joining on two columns with different names (#6465).

* Joins on very wide tables are no longer bottlenecked by the application of
  `suffix` (#6642).

* `*_join()` now error if you supply them with additional arguments that
  aren't used (#6228).

* `across()` used without functions inside a rowwise-data frame no longer
   generates an invalid data frame (#6264).

* Anonymous functions supplied with `function()` and `\()` are now inlined by
  `across()` if possible, which slightly improves performance and makes possible
  further optimisations in the future.

* Functions supplied to `across()` are no longer masked by columns (#6545). For
  instance, `across(1:2, mean)` will now work as expected even if there is a
  column called `mean`.

* `across()` will now error when supplied `...` without a `.fns` argument
  (#6638).

* `arrange()` now correctly ignores `NULL` inputs (#6193).

* `arrange()` now works correctly when `across()` calls are used as the 2nd
  (or more) ordering expression (#6495).

* `arrange(df, mydesc::desc(x))` works correctly when mydesc re-exports
   `dplyr::desc()` (#6231).

* `c_across()` now evaluates `all_of()` correctly and no longer allows you to
  accidentally select grouping variables (#6522).

* `c_across()` now throws a more informative error if you try to rename during
  column selection (#6522).

* dplyr no longer provides `count()` and `tally()` methods for `tbl_sql`.
  These methods have been accidentally overriding the `tbl_lazy` methods that
  dbplyr provides, which has resulted in issues with the grouping structure of
  the output (#6338, tidyverse/dbplyr#940).

* `cur_group()` now works correctly with zero row grouped data frames (#6304).

* `desc()` gives a useful error message if you give it a non-vector (#6028).

* `distinct()` now retains attributes of bare data frames (#6318).

* `distinct()` returns columns ordered the way you request, not the same
  as the input data (#6156).

* Error messages in `group_by()`, `distinct()`, `tally()`, and `count()` are now
  more relevant (#6139).

* `group_by_prepare()` loses the `caller_env` argument. It was rarely used
  and it is no longer needed (#6444).

* `group_walk()` gains an explict `.keep` argument (#6530).

* Warnings emitted inside `mutate()` and variants are now collected and stashed
  away. Run the new `last_dplyr_warnings()` function to see the warnings emitted
  within dplyr verbs during the last top-level command.

  This fixes performance issues when thousands of warnings are emitted with
  rowwise and grouped data frames (#6005, #6236).

* `mutate()` behaves a little better with 0-row rowwise inputs (#6303).

* A rowwise `mutate()` now automatically unlists list-columns containing
  length 1 vectors (#6302).

* `nest_join()` has gained the `na_matches` argument that all other joins have.

* `nest_join()` now preserves the type of `y` (#6295).

* `n_distinct()` now errors if you don't give it any input (#6535).

* `nth()`, `first()`, `last()`, and `with_order()` now sort character `order_by`
  vectors in the C locale. Using character vectors for `order_by` is rare, so we
  expect this to have little practical impact (#6451).

* `ntile()` now requires `n` to be a single positive integer.

* `relocate()` now works correctly with empty data frames and when `.before` or
  `.after` result in empty selections (#6167).

* `relocate()` no longer drops attributes of bare data frames (#6341).

* `relocate()` now retains the last name change when a single column is renamed
  multiple times while it is being moved. This better matches the behavior of
  `rename()` (#6209, with help from @eutwt).

* `rename()` now contains examples of using `all_of()` and `any_of()` to rename
  using a named character vector (#6644).

* `rename_with()` now disallows renaming in the `.cols` tidy-selection (#6561).

* `rename_with()` now checks that the result of `.fn` is the right type and size
  (#6561).

* `rows_insert()` now checks that `y` contains the `by` columns (#6652).

* `setequal()` ignores differences between freely coercible types (e.g. integer
  and double) (#6114) and ignores duplicated rows (#6057).

* `slice()` helpers again produce output equivalent to `slice(.data, 0)` when
  the `n` or `prop` argument is 0, fixing a bug introduced in the previous
  version (@eutwt, #6184).

* `slice()` with no inputs now returns 0 rows. This is mostly for theoretical
  consistency (#6573).

* `slice()` now errors if any expressions in `...` are named. This helps avoid
  accidentally misspelling an optional argument, such as `.by` (#6554).

* `slice_*()` now requires `n` to be an integer.

* `slice_*()` generics now perform argument validation. This should make
  methods more consistent and simpler to implement (#6361).

* `slice_min()` and `slice_max()` can `order_by` multiple variables if you
  supply them as a data.frame or tibble (#6176).

* `slice_min()` and `slice_max()` now consistently include missing values in
  the result if necessary (i.e. there aren't enough non-missing values to
  reach the `n` or `prop` you have selected). If you don't want missing values
  to be included at all, set `na_rm = TRUE` (#6177).

* `slice_sample()` now accepts negative `n` and `prop` values (#6402).

* `slice_sample()` returns a data frame or group with the same number of rows as
  the input when `replace = FALSE` and `n` is larger than the number of rows or
  `prop` is larger than 1. This reverts a change made in 1.0.8, returning to the
  behavior of 1.0.7 (#6185)

* `slice_sample()` now gives a more informative error when `replace = FALSE` and
  the number of rows requested in the sample exceeds the number of rows in the
  data (#6271).

* `storms` has been updated to include 2021 data and some missing storms that
   were omitted due to an error (@steveharoz, #6320).

* `summarise()` now correctly recycles named 0-column data frames (#6509).

* `union_all()`, like `union()`, now requires that data frames be compatible:
  i.e. they have the same columns, and the columns have compatible types.

* `where()` is re-exported from tidyselect (#6597).


To generate a diff of this commit:
cvs rdiff -u -r1.7 -r1.8 pkgsrc/math/R-dplyr/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/math/R-dplyr/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R-dplyr/Makefile
diff -u pkgsrc/math/R-dplyr/Makefile:1.7 pkgsrc/math/R-dplyr/Makefile:1.8
--- pkgsrc/math/R-dplyr/Makefile:1.7    Sun Dec 18 05:38:37 2022
+++ pkgsrc/math/R-dplyr/Makefile        Sun Feb 12 04:09:37 2023
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.7 2022/12/18 05:38:37 mef Exp $
+# $NetBSD: Makefile,v 1.8 2023/02/12 04:09:37 mef Exp $
 
 R_PKGNAME=     dplyr
-R_PKGVER=      1.0.10
+R_PKGVER=      1.1.0
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Grammar of data manipulation

Index: pkgsrc/math/R-dplyr/distinfo
diff -u pkgsrc/math/R-dplyr/distinfo:1.8 pkgsrc/math/R-dplyr/distinfo:1.9
--- pkgsrc/math/R-dplyr/distinfo:1.8    Sun Dec 18 05:38:37 2022
+++ pkgsrc/math/R-dplyr/distinfo        Sun Feb 12 04:09:37 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.8 2022/12/18 05:38:37 mef Exp $
+$NetBSD: distinfo,v 1.9 2023/02/12 04:09:37 mef Exp $
 
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