Merge 3e89bef into c6b0af6

DESCRIPTION

@@ -1,21 +1,22 @@
 Type: Package
 Package: broomExtra
 Title: Enhancements for 'broom' Package Family
-Version: 0.0.3
+Version: 0.0.3.9000
 Authors@R: 
     person(given = "Indrajeet",
            family = "Patil",
-           role = c("aut", "cre"),
+           role = c("aut", "cre", "ctb"),
            email = "patilindrajeet.science@gmail.com",
            comment = c(ORCID = "0000-0003-1995-6531"))
 Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
 Description: Collection of functions to assist 'broom' and
     'broom.mixed' package-related data analysis workflows. In particular,
     the generic functions tidy(), glance(), and augment() choose
     appropriate S3 methods from these two packages depending on which
-    package exports the needed method. Additionally, 'grouped_' variants
-    of the generics provides a convenient way to execute functions across
-    a combination of grouping variable(s) in a dataframe.
+    package exports the needed method. Additionally, 'grouped_' and
+    'boot_' variants of the generics provides a convenient way to execute
+    functions across a combination of grouping variable(s) in a dataframe
+    or bootstrap them.
 License: GPL-3 | file LICENSE
 URL: https://indrajeetpatil.github.io/broomExtra/,
     https://github.com/IndrajeetPatil/broomExtra
@@ -27,7 +28,10 @@ Imports:
     broom.mixed (>= 0.2.4),
     dplyr (>= 0.8.1),
     magrittr (>= 1.5),
-    rlang (>= 0.3.4)
+    purrr (>= 0.3.2),
+    rlang (>= 0.3.4),
+    rsample (>= 0.0.4),
+    tidyr (>= 0.8.3)
 Suggests: 
     covr,
     gapminder,
@@ -39,9 +43,7 @@ Suggests:
     spelling,
     stringr,
     testthat,
-    tibble,
-    tidyr,
-    utils
+    tibble
 VignetteBuilder: 
     knitr
 Encoding: UTF-8

NAMESPACE

@@ -1,7 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%<>%")
 export("%>%")
 export(augment)
+export(boot_augment)
+export(boot_glance)
+export(boot_tidy)
 export(glance)
 export(grouped_augment)
 export(grouped_glance)
@@ -18,10 +22,13 @@ importFrom(dplyr,group_map)
 importFrom(dplyr,group_modify)
 importFrom(dplyr,mutate)
 importFrom(dplyr,ungroup)
+importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
+importFrom(purrr,map)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
 importFrom(rlang,enquo)
 importFrom(rlang,exec)
 importFrom(rlang,quo_squash)
-importFrom(utils,packageVersion)
+importFrom(rsample,bootstraps)
+importFrom(tidyr,unnest)

NEWS.md

@@ -1,3 +1,8 @@
+# broomExtra 0.0.4
+
+* Adds new functions for bootstrapping: `boot_tidy`, `boot_glance`,
+`boot_augment`.
+
 # broomExtra 0.0.3
 
 * This is maintenance release to make the package compatible with `R 3.6.0`.

R/boot_augment.R

@@ -0,0 +1,81 @@
+#' @title Bootstrapped dataframe with augmented predictions from each sample.
+#' @name boot_augment
+#' @author Indrajeet Patil
+#'
+#' @inheritParams grouped_augment
+#' @inheritParams rsample::bootstraps
+#'
+#' @inherit augment return value
+#' @inheritSection augment Methods
+#'
+#' @importFrom rlang !! !!! exec
+#' @importFrom dplyr mutate
+#' @importFrom purrr map
+#' @importFrom tidyr unnest
+#' @importFrom rsample bootstraps
+#'
+#' @examples
+#' set.seed(123)
+#'
+#' # example-1: linear model
+#' broomExtra::boot_augment(
+#'   data = mtcars,
+#'   times = 10,
+#'   ..f = stats::lm,
+#'   formula = mpg ~ wt,
+#'   na.action = na.omit
+#' )
+#'
+#' # example-2: linear mixed-effects model
+#' library(lme4)
+#'
+#' broomExtra::boot_augment(
+#'   data = sleepstudy,
+#'   times = 25,
+#'   ..f = lme4::lmer,
+#'   formula = Reaction ~ Days + (Days | Subject)
+#' )
+#' @export
+
+# function
+boot_augment <- function(data,
+                         times = 25,
+                         strata = NULL,
+                         apparent = FALSE,
+                         ..f,
+                         ...,
+                         augment.args = list()) {
+
+  # create a bootstrapped dataframe
+  boots <-
+    rsample::bootstraps(
+      data = data,
+      times = times,
+      strata = strata,
+      apparent = apparent
+    )
+
+  # `.x` and `.y` arguments, where `.x` is the data
+  augment_group <- function(.x, .y) {
+
+    # presumes `..f` will work with these args
+    model <- ..f(.y = ..., data = .x)
+
+    # variation on `do.call` to call function with list of arguments
+    rlang::exec(.fn = broomExtra::augment, model, !!!augment.args)
+  }
+
+  # execute function for each bootstrapped sample and tidy output
+  boots_fits <- boots %>%
+    dplyr::mutate(
+      .data = .,
+      augment_df = purrr::map(
+        .x = splits,
+        .f = augment_group
+      )
+    ) %>%
+    tidyr::unnest(data = ., augment_df)
+
+  # return the final dataframe
+  return(boots_fits)
+}

R/boot_glance.R

@@ -0,0 +1,80 @@
+#' @title Bootstrapped dataframe with model summaries from each sample.
+#' @name boot_glance
+#' @author Indrajeet Patil
+#'
+#' @inheritParams grouped_glance
+#' @inheritParams rsample::bootstraps
+#'
+#' @inherit glance return value
+#' @inheritSection glance Methods
+#'
+#' @importFrom rlang !! !!! exec
+#' @importFrom dplyr mutate
+#' @importFrom purrr map
+#' @importFrom tidyr unnest
+#' @importFrom rsample bootstraps
+#'
+#' @examples
+#' set.seed(123)
+#'
+#' # example-1: linear model
+#' broomExtra::boot_glance(
+#'   data = mtcars,
+#'   times = 500,
+#'   ..f = stats::lm,
+#'   formula = mpg ~ wt,
+#'   na.action = na.omit
+#' )
+#'
+#' # example-2: linear mixed-effects model
+#' library(lme4)
+#'
+#' broomExtra::boot_glance(
+#'   data = sleepstudy,
+#'   times = 25,
+#'   ..f = lme4::lmer,
+#'   formula = Reaction ~ Days + (Days | Subject)
+#' )
+#' @export
+
+# function
+boot_glance <- function(data,
+                        times = 25,
+                        strata = NULL,
+                        apparent = FALSE,
+                        ..f,
+                        ...) {
+
+  # create a bootstrapped dataframe
+  boots <-
+    rsample::bootstraps(
+      data = data,
+      times = times,
+      strata = strata,
+      apparent = apparent
+    )
+
+  # `.x` and `.y` arguments, where `.x` is the data
+  glance_group <- function(.x, .y) {
+
+    # presumes `..f` will work with these args
+    model <- ..f(.y = ..., data = .x)
+
+    # variation on `do.call` to call function with list of arguments
+    rlang::exec(.fn = broomExtra::glance, model)
+  }
+
+  # execute function for each bootstrapped sample and tidy output
+  boots_fits <- boots %>%
+    dplyr::mutate(
+      .data = .,
+      glance_df = purrr::map(
+        .x = splits,
+        .f = glance_group
+      )
+    ) %>%
+    tidyr::unnest(data = ., glance_df)
+
+  # return the final dataframe
+  return(boots_fits)
+}

R/boot_tidy.R

@@ -0,0 +1,83 @@
+#' @title Bootstrapped dataframe with estimates from each sample.
+#' @name boot_tidy
+#' @author Indrajeet Patil
+#'
+#' @inheritParams grouped_tidy
+#' @inheritParams rsample::bootstraps
+#'
+#' @inherit tidy return value
+#' @inheritSection tidy Methods
+#'
+#' @importFrom rlang !! !!! exec
+#' @importFrom dplyr mutate
+#' @importFrom purrr map
+#' @importFrom tidyr unnest
+#' @importFrom rsample bootstraps
+#'
+#' @examples
+#' set.seed(123)
+#'
+#' # example-1: linear model
+#' broomExtra::boot_tidy(
+#'   data = mtcars,
+#'   times = 500,
+#'   ..f = stats::lm,
+#'   formula = mpg ~ wt,
+#'   na.action = na.omit,
+#'   tidy.args = list(conf.int = TRUE, conf.level = 0.50)
+#' )
+#'
+#' # example-2: linear mixed-effects model
+#' library(lme4)
+#'
+#' broomExtra::boot_tidy(
+#'   data = sleepstudy,
+#'   times = 25,
+#'   ..f = lme4::lmer,
+#'   formula = Reaction ~ Days + (Days | Subject),
+#'   tidy.args = list(effects = "fixed")
+#' )
+#' @export
+
+# function
+boot_tidy <- function(data,
+                      times = 25,
+                      strata = NULL,
+                      apparent = FALSE,
+                      ..f,
+                      ...,
+                      tidy.args = list()) {
+
+  # create a bootstrapped dataframe
+  boots <-
+    rsample::bootstraps(
+      data = data,
+      times = times,
+      strata = strata,
+      apparent = apparent
+    )
+
+  # `.x` and `.y` arguments, where `.x` is the data
+  tidy_group <- function(.x, .y) {
+
+    # presumes `..f` will work with these args
+    model <- ..f(.y = ..., data = .x)
+
+    # variation on `do.call` to call function with list of arguments
+    rlang::exec(.fn = broomExtra::tidy, model, !!!tidy.args)
+  }
+
+  # execute function for each bootstrapped sample and tidy output
+  boots_fits <- boots %>%
+    dplyr::mutate(
+      .data = .,
+      tidy_df = purrr::map(
+        .x = splits,
+        .f = tidy_group
+      )
+    ) %>%
+    tidyr::unnest(data = ., tidy_df)
+
+  # return the final dataframe
+  return(boots_fits)
+}

R/global_vars.R

@@ -182,7 +182,11 @@ utils::globalVariables(
     "Q",
     "tau",
     "tau2",
-    "id"
+    "id",
+    "splits",
+    "augment_df",
+    "glance_df",
+    "tidy_df"
   ),
   package = "broomExtra",
   add = FALSE

R/grouped_augment.R

@@ -22,7 +22,8 @@
 #'   grouping.vars = c(cut, color),
 #'   formula = price ~ carat - 1,
 #'   ..f = stats::lm,
-#'   na.action = na.omit
+#'   na.action = na.omit,
+#'   augment.args = list(se_fit = TRUE)
 #' )
 #'
 #' # linear mixed effects model

R/grouped_glance.R

@@ -7,7 +7,6 @@
 #'
 #' @importFrom rlang !! !!! exec quo_squash enquo
 #' @importFrom dplyr group_by ungroup mutate group_map group_modify
-#' @importFrom utils packageVersion
 #'
 #' @inherit glance return value
 #' @inheritSection glance Methods

R/reexports.R

@@ -0,0 +1,7 @@
+#' @export
+#' @importFrom magrittr "%>%"
+magrittr::`%>%`
+
+#' @export
+#' @importFrom magrittr "%<>%"
+magrittr::`%<>%`