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#' @title Download the files of an example `drake` project.
#' `r lifecycle::badge("stable")`
#' @description The `drake_example()` function downloads a
#' folder from `https://github.com/wlandau/drake-examples`.
#' By default, it creates a new folder with the example name
#' in your current working directory. After the files are written,
#' have a look at the enclosed `README` file.
#' Other instructions are available in the files at
#' `https://github.com/wlandau/drake-examples`.
#' @seealso [drake_examples()], [make()]
#' @export
#' @return `NULL`
#' @param example Name of the example.
#' The possible values are the names of the folders at
#' `https://github.com/wlandau/drake-examples`.
#' @param to Character scalar,
#' the folder containing the code files for the example.
#' passed to the `exdir` argument of `utils::unzip()`.
#' @param destination Deprecated; use `to` instead.
#' @param overwrite Logical, whether to overwrite an existing folder
#' with the same name as the drake example.
#' @param quiet Logical, passed to `downloader::download()`
#' and thus `utils::download.file()`. Whether
#' to download quietly or print progress.
#' @examples
#' \dontrun{
#' isolate_example("Quarantine side effects.", {
#' if (requireNamespace("downloader")) {
#' drake_examples() # List all the drake examples.
#' # Sets up the same example from load_mtcars_example()
#' drake_example("mtcars")
#' # Sets up the SLURM example.
#' drake_example("slurm")
#' }
#' })
#' }
drake_example <- function(
example = "main",
to = getwd(),
destination = NULL,
overwrite = FALSE,
quiet = TRUE
) {
assert_pkg("downloader")
if (!is.null(destination)) {
warning(
"The 'destination' argument of drake_example() is deprecated. ",
"Use 'to' instead."
)
to <- destination
}
url <- file.path(
"https://wlandau.github.io/drake-examples",
paste0(example, ".zip")
)
zip <- paste0(tempfile(), ".zip")
downloader::download(url = url, destfile = zip, quiet = quiet)
utils::unzip(zip, exdir = to, overwrite = overwrite)
invisible()
}
#' @title List the names of all the drake examples.
#' `r lifecycle::badge("stable")`
#' @description You can find the code files of the examples at
#' `https://github.com/wlandau/drake-examples`.
#' The `drake_examples()` function downloads the list of examples
#' from `https://wlandau.github.io/drake-examples/examples.md`,
#' so you need an internet connection.
#' @export
#' @seealso [drake_example()], [make()]
#' @return Names of all the drake examples.
#' @param quiet Logical, passed to `downloader::download()`
#' and thus `utils::download.file()`. Whether
#' to download quietly or print progress.
#' @examples
#' \dontrun{
#' isolate_example("Quarantine side effects.", {
#' if (requireNamespace("downloader")) {
#' drake_examples() # List all the drake examples.
#' # Sets up the example from load_mtcars_example()
#' drake_example("mtcars")
#' # Sets up the SLURM example.
#' drake_example("slurm")
#' }
#' })
#' }
drake_examples <- function(quiet = TRUE) {
assert_pkg("downloader")
destfile <- tempfile()
downloader::download(
url = "https://wlandau.github.io/drake-examples/examples.md",
destfile = destfile,
quiet = quiet
)
out <- scan(destfile, what = character(1), quiet = TRUE)
out <- gsub(pattern = "\\.zip$", replacement = "", x = out)
sort(out)
}
#' @title Load the mtcars example.
#' `r lifecycle::badge("stable")`
#' @description Is there an association between
#' the weight and the fuel efficiency of cars?
#' To find out, we use the mtcars example from `drake_example("mtcars")`.
#' The mtcars dataset itself only has 32 rows,
#' so we generate two larger bootstrapped datasets
#' and then analyze them with regression models.
#' Finally, we summarize the regression models
#' to see if there is an association.
#' @details Use `drake_example("mtcars")` to get the code
#' for the mtcars example.
#' This function also writes/overwrites
#' the file, `report.Rmd`.
#' @export
#' @seealso [clean_mtcars_example()] [drake_examples()]
#' @return Nothing.
#' @param envir The environment to load the example into.
#' Defaults to your workspace.
#' For an insulated workspace,
#' set `envir = new.env(parent = globalenv())`.
#' @param report_file Where to write the report file. Deprecated.
#' In a future release, the report file will always be
#' `report.Rmd` and will always be written to your
#' working directory (current default).
#' @param overwrite Logical, whether to overwrite an
#' existing file `report.Rmd`.
#' @param force Deprecated.
#' @examples
#' \dontrun{
#' isolate_example("Quarantine side effects.", {
#' if (suppressWarnings(require("knitr"))) {
#' # Populate your workspace and write 'report.Rmd'.
#' load_mtcars_example() # Get the code: drake_example("mtcars")
#' # Check the dependencies of an imported function.
#' deps_code(reg1)
#' # Check the dependencies of commands in the workflow plan.
#' deps_code(my_plan$command[1])
#' deps_code(my_plan$command[4])
#' # Plot the interactive network visualization of the workflow.
#' outdated(my_plan) # Which targets are out of date?
#' # Run the workflow to build all the targets in the plan.
#' make(my_plan)
#' outdated(my_plan) # Everything should be up to date.
#' # For the reg2() model on the small dataset,
#' # the p-value is so small that there may be an association
#' # between weight and fuel efficiency after all.
#' readd(coef_regression2_small)
#' # Clean up the example.
#' clean_mtcars_example()
#' }
#' })
#' }
load_mtcars_example <- function(
envir = parent.frame(),
report_file = NULL,
overwrite = FALSE,
force = FALSE
) {
force(envir)
deprecate_force(force)
if (!is.null(report_file)) {
warn0(
"The `report_file` argument of load_mtcars_example() ",
"is deprecated and will be removed in a future release."
)
}
if (is.null(report_file)) {
report_file <- "report.Rmd"
}
populate_mtcars_example_envir(envir = envir)
if (file.exists(report_file) && overwrite) {
warn0("Overwriting file ", report_file)
}
report_path <- system.file(
file.path("rmarkdown", "examples", "mtcars", "report.Rmd"),
package = "drake",
mustWork = TRUE
)
file.copy(from = report_path, to = report_file, overwrite = overwrite)
invisible()
}
populate_mtcars_example_envir <- function(envir) {
assert_pkg("datasets")
force(envir)
mtcars <- lm <- NULL
local(envir = envir, {
random_rows <- function(data, n) {
data[sample.int(n = nrow(data), size = n, replace = TRUE), ]
}
simulate <- function(n) {
data <- random_rows(data = datasets::mtcars, n = n)
data.frame(
x = data$wt,
y = data$mpg
)
}
reg1 <- function(d) {
lm(y ~ + x, data = d)
}
reg2 <- function(d) {
d$x2 <- d$x ^ 2
lm(y ~ x2, data = d)
}
})
envir$my_plan <- mtcars_plan()
invisible()
}
mtcars_plan <- function() {
report <- small <- large <- regression1_small <- regression1_large <-
regression2_small <- regression2_large <- summ_regression1_small <-
summ_regression1_large <- summ_regression2_small <-
summ_regression2_large <- coef_regression1_small <-
coef_regression1_large <- coef_regression2_small <-
coef_regression2_large <- knit <- simulate <- reg1 <- reg2 <- NULL
drake::drake_plan(
report = knitr::knit(
drake::knitr_in("report.Rmd"),
drake::file_out("report.md"),
quiet = TRUE
),
small = simulate(48),
large = simulate(64),
regression1_small = reg1(small),
regression1_large = reg1(large),
regression2_small = reg2(small),
regression2_large = reg2(large),
summ_regression1_small =
suppressWarnings(summary(regression1_small$residuals)),
summ_regression1_large =
suppressWarnings(summary(regression1_large$residuals)),
summ_regression2_small =
suppressWarnings(summary(regression2_small$residuals)),
summ_regression2_large =
suppressWarnings(summary(regression2_large$residuals)),
coef_regression1_small =
suppressWarnings(summary(regression1_small))$coefficients,
coef_regression1_large =
suppressWarnings(summary(regression1_large))$coefficients,
coef_regression2_small =
suppressWarnings(summary(regression2_small))$coefficients,
coef_regression2_large =
suppressWarnings(summary(regression2_large))$coefficients
)
}
#' @title Clean the mtcars example from `drake_example("mtcars")`
#' `r lifecycle::badge("stable")`
#' @description This function deletes files. Use at your own risk.
#' Destroys the `.drake/` cache and the `report.Rmd` file
#' in the current working directory. Your working directory
#' (`getcwd()`) must be the folder from which you first ran
#' `load_mtcars_example()` and `make(my_plan)`.
#' @export
#' @return nothing
#' @seealso [load_mtcars_example()], [clean()]
#' @examples
#' \dontrun{
#' isolate_example("Quarantine side effects.", {
#' if (suppressWarnings(require("knitr"))) {
#' # Populate your workspace and write 'report.Rmd'.
#' load_mtcars_example() # Get the code: drake_example("mtcars")
#' # Check the dependencies of an imported function.
#' deps_code(reg1)
#' # Check the dependencies of commands in the workflow plan.
#' deps_code(my_plan$command[1])
#' deps_code(my_plan$command[4])
#' # Plot the interactive network visualization of the workflow.
#' outdated(my_plan) # Which targets are out of date?
#' # Run the workflow to build all the targets in the plan.
#' make(my_plan)
#' outdated(my_plan) # Everything should be up to date.
#' # For the reg2() model on the small dataset,
#' # the p-value is so small that there may be an association
#' # between weight and fuel efficiency after all.
#' readd(coef_regression2_small)
#' # Clean up the example.
#' clean_mtcars_example()
#' }
#' })
#' }
clean_mtcars_example <- function() {
clean(destroy = TRUE)
unlink("report.Rmd")
invisible()
}
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