Merge pull request #331 from cmu-delphi/djm/deprecate

Djm/deprecate

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: epipredict
 Title: Basic epidemiology forecasting methods
-Version: 0.0.14
+Version: 0.0.15
 Authors@R: c(
     person("Daniel", "McDonald", , "[email protected]", role = c("aut", "cre")),
     person("Ryan", "Tibshirani", , "[email protected]", role = "aut"),
@@ -38,7 +38,7 @@ Imports:
     magrittr,
     quantreg,
     recipes (>= 1.0.4),
-    rlang,
+    rlang (>= 1.0.0),
     smoothqr,
     stats,
     tibble,

NAMESPACE

@@ -240,10 +240,11 @@ importFrom(rlang,"%@%")
 importFrom(rlang,"%||%")
 importFrom(rlang,":=")
 importFrom(rlang,abort)
+importFrom(rlang,as_function)
 importFrom(rlang,caller_env)
-importFrom(rlang,is_empty)
+importFrom(rlang,global_env)
 importFrom(rlang,is_null)
-importFrom(rlang,quos)
+importFrom(rlang,set_names)
 importFrom(smoothqr,smooth_qr)
 importFrom(stats,as.formula)
 importFrom(stats,family)
@@ -255,8 +256,6 @@ importFrom(stats,predict)
 importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,residuals)
-importFrom(tibble,as_tibble)
-importFrom(tibble,is_tibble)
 importFrom(tibble,tibble)
 importFrom(tidyr,drop_na)
 importFrom(vctrs,as_list_of)

NEWS.md

@@ -43,3 +43,6 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.0.x will indicat
 - `arx_fcast_epi_workflow()` and `arx_class_epi_workflow()` now default to
   `trainer = parsnip::logistic_reg()` to match their more canned versions.
 - add a `forecast()` method simplify generating forecasts
+- refactor `bake.epi_recipe()` and remove `epi_juice()`. 
+- Revise `compat-purrr` to use the r-lang `standalone-*` version (via 
+  `{usethis}`)

R/compat-purrr.R

@@ -1,37 +1,8 @@
-# See https://github.com/r-lib/rlang/blob/main/R/compat-purrr.R
-
-
-map <- function(.x, .f, ...) {
-  .f <- rlang::as_function(.f, env = rlang::global_env())
-  lapply(.x, .f, ...)
-}
-
-walk <- function(.x, .f, ...) {
-  map(.x, .f, ...)
-  invisible(.x)
-}
-
 walk2 <- function(.x, .y, .f, ...) {
   map2(.x, .y, .f, ...)
   invisible(.x)
 }
 
-map_lgl <- function(.x, .f, ...) {
-  .rlang_purrr_map_mold(.x, .f, logical(1), ...)
-}
-
-map_int <- function(.x, .f, ...) {
-  .rlang_purrr_map_mold(.x, .f, integer(1), ...)
-}
-
-map_dbl <- function(.x, .f, ...) {
-  .rlang_purrr_map_mold(.x, .f, double(1), ...)
-}
-
-map_chr <- function(.x, .f, ...) {
-  .rlang_purrr_map_mold(.x, .f, character(1), ...)
-}
-
 map_vec <- function(.x, .f, ...) {
   out <- map(.x, .f, ...)
   vctrs::list_unchop(out)
@@ -48,61 +19,3 @@ map2_dfr <- function(.x, .y, .f, ..., .id = NULL) {
   res <- map2(.x, .y, .f, ...)
   dplyr::bind_rows(res, .id = .id)
 }
-
-.rlang_purrr_map_mold <- function(.x, .f, .mold, ...) {
-  .f <- rlang::as_function(.f, env = rlang::global_env())
-  out <- vapply(.x, .f, .mold, ..., USE.NAMES = FALSE)
-  names(out) <- names(.x)
-  out
-}
-
-.rlang_purrr_args_recycle <- function(args) {
-  lengths <- map_int(args, length)
-  n <- max(lengths)
-
-  stopifnot(all(lengths == 1L | lengths == n))
-  to_recycle <- lengths == 1L
-  args[to_recycle] <- map(args[to_recycle], function(x) rep.int(x, n))
-
-  args
-}
-
-map2 <- function(.x, .y, .f, ...) {
-  .f <- rlang::as_function(.f, env = rlang::global_env())
-  out <- mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
-  if (length(out) == length(.x)) {
-    rlang::set_names(out, names(.x))
-  } else {
-    rlang::set_names(out, NULL)
-  }
-}
-map2_lgl <- function(.x, .y, .f, ...) {
-  as.vector(map2(.x, .y, .f, ...), "logical")
-}
-map2_int <- function(.x, .y, .f, ...) {
-  as.vector(map2(.x, .y, .f, ...), "integer")
-}
-map2_dbl <- function(.x, .y, .f, ...) {
-  as.vector(map2(.x, .y, .f, ...), "double")
-}
-map2_chr <- function(.x, .y, .f, ...) {
-  as.vector(map2(.x, .y, .f, ...), "character")
-}
-imap <- function(.x, .f, ...) {
-  map2(.x, names(.x) %||% seq_along(.x), .f, ...)
-}
-
-pmap <- function(.l, .f, ...) {
-  .f <- as.function(.f)
-  args <- .rlang_purrr_args_recycle(.l)
-  do.call("mapply", c(
-    FUN = list(quote(.f)),
-    args, MoreArgs = quote(list(...)),
-    SIMPLIFY = FALSE, USE.NAMES = FALSE
-  ))
-}
-
-reduce <- function(.x, .f, ..., .init) {
-  f <- function(x, y) .f(x, y, ...)
-  Reduce(f, .x, init = .init)
-}

R/epi_recipe.R

@@ -557,6 +557,28 @@ prep.epi_recipe <- function(
   x
 }
 
+#' @export
+bake.epi_recipe <- function(object, new_data, ..., composition = "epi_df") {
+  meta <- NULL
+  if (composition == "epi_df") {
+    if (is_epi_df(new_data)) {
+      meta <- attr(new_data, "metadata")
+    } else if (is_epi_df(object$template)) {
+      meta <- attr(object$template, "metadata")
+    }
+    composition <- "tibble"
+  }
+  new_data <- NextMethod("bake")
+  if (!is.null(meta)) {
+    new_data <- as_epi_df(
+      new_data, meta$geo_type, meta$time_type, meta$as_of,
+      meta$additional_metadata %||% list()
+    )
+  }
+  new_data
+}
+
+
 kill_levels <- function(x, keys) {
   for (i in which(names(x) %in% keys)) x[[i]] <- list(values = NA, ordered = NA)
   x

R/epipredict-package.R

@@ -1,6 +1,6 @@
 ## usethis namespace: start
 #' @importFrom tibble tibble
-#' @importFrom rlang := !! %||%
+#' @importFrom rlang := !! %||% as_function global_env set_names
 #' @importFrom stats poly predict lm residuals quantile
 #' @importFrom cli cli_abort
 #' @importFrom checkmate assert assert_character assert_int assert_scalar

R/standalone-lifecycle.R → R/import-standalone-lifecycle.R

@@ -1,3 +1,7 @@
+# Standalone file: do not edit by hand
+# Source: <https://github.com/r-lib/rlang/blob/main/R/standalone-lifecycle.R>
+# ----------------------------------------------------------------------
+#
 # ---
 # repo: r-lib/rlang
 # file: standalone-lifecycle.R
@@ -94,7 +98,8 @@ deprecate_soft <- function(msg,
   id <- paste(id, collapse = "\n")
   verbosity <- .rlang_lifecycle_verbosity()
 
-  invisible(switch(verbosity,
+  invisible(switch(
+    verbosity,
     quiet = NULL,
     warning = ,
     default =
@@ -121,7 +126,8 @@ deprecate_warn <- function(msg,
   id <- paste(id, collapse = "\n")
   verbosity <- .rlang_lifecycle_verbosity()
 
-  invisible(switch(verbosity,
+  invisible(switch(
+    verbosity,
     quiet = NULL,
     warning = ,
     default = {