Remove export of with_progress and format vignette.

DESCRIPTION

@@ -30,7 +30,7 @@ Description: A flexible permutation framework for making
     data or density-valued data.
 License: GPL (>= 3)
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Imports: 
     cli,

NAMESPACE

@@ -37,6 +37,5 @@ importFrom(furrr,future_map)
 importFrom(furrr,future_map_dbl)
 importFrom(magrittr,"%>%")
 importFrom(progressr,progressor)
-importFrom(progressr,with_progress)
 importFrom(tibble,tibble)
 useDynLib(flipr, .registration = TRUE)

R/flipr-package.R

@@ -9,7 +9,7 @@
 #' @useDynLib flipr, .registration = TRUE
 #' @importFrom furrr future_map future_map_dbl
 #' @import ggplot2
-#' @importFrom progressr with_progress progressor
+#' @importFrom progressr progressor
 #' @importFrom R6 R6Class
 #' @importFrom Rcpp sourceCpp
 #' @import rlang

flipr.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: bf8dffc9-fb15-4cc1-b2cb-51260a920c79
 
 RestoreWorkspace: No
 SaveWorkspace: No

vignettes/exactness.Rmd

@@ -259,7 +259,6 @@ stat_assignments <- list(delta = 1)
 nperms <- 20
 alpha <- 0.05
 
-
 progressr::with_progress({
   p <- progressr::progressor(steps = length(sim) / 10) # progress bar set up
   ii <- 1

vignettes/parallelization.Rmd

@@ -18,11 +18,28 @@ time_without_parallelization <- df_parallelization$time_without_par
 time_with_parallelization <- df_parallelization$time_par
 ```
 
-The [**flipr**](https://lmjl-alea.github.io/flipr/) package uses functions contained in the [**furrr**](https://future.futureverse.org/index.html) package for parallel processing. The setting of parallelization has to be done on the user side. We illustrate here how to achieve asynchronous evaluation. We use the [**future**](https://future.futureverse.org/index.html) package to set the plan, the **parallel** package to define a default cluster, and the [**progressr**](https://progressr.futureverse.org/index.html) package to report progress updates.
-
-## Computation without parallel processing
-
-To show the benefit of parallel processing, we compare here the processing times necessary to evaluate a grid with a plausibility function. First, here is the computation without parallelization.
+The [**flipr**](https://lmjl-alea.github.io/flipr/) package uses functions
+contained in the [**furrr**](https://future.futureverse.org/index.html) package
+for parallel processing. The setting of parallelization has to be done on the
+user side. We illustrate here how to achieve asynchronous evaluation. We use the
+[**future**](https://future.futureverse.org/index.html) package to set the plan,
+the **parallel** package to define a default cluster, and the
+[**progressr**](https://progressr.futureverse.org/index.html) package to report
+progress updates.
+
+By setting the desired number of cores, we define the number of background R
+sessions that will be used to evaluate expressions in parallel. This number is
+used to set the multisession plan with the function `future::plan()` and to
+define a default cluster with `parallel::setDefaultCluster()`. Then, to enable
+the visualization of evaluation progress, we can put the code in the
+`progressr::with_progress()` function, or more simply set it for all the
+following code with the `progressr::handlers()` function. After these settings,
+[**flipr**](https://lmjl-alea.github.io/flipr/) functions can be used, as shown
+in this example.
+
+To show the benefit of parallel processing, we compare here the processing times
+necessary to evaluate a grid with a plausibility function. First, here is the
+computation without parallelization.
 
 ```{r, eval=FALSE}
 set.seed(1234)
@@ -63,7 +80,15 @@ time_without_parallelization
 
 ## Computation with parallel processing
 
-By setting the desired number of cores, we define the number of background R sessions that will be used to evaluate expressions in parallel. This number is used to set the multisession plan with the function `future::plan()` and to define a default cluster with `parallel::setDefaultCluster()`. Then, to enable the visualization of evaluation progress, we can put the code in the `progressr::with_progress()` function, or more simply set it for all the following code with the `progressr::handlers()` function. After these settings, [**flipr**](https://lmjl-alea.github.io/flipr/) functions can be used, as shown in this example.
+By setting the desired number of cores, we define the number of background R
+sessions that will be used to evaluate expressions in parallel. This number is
+used to set the multisession plan with the function `future::plan()` and to
+define a default cluster with `parallel::setDefaultCluster()`. Then, to enable
+the visualization of evaluation progress, we can put the code in the
+`progressr::with_progress()` function, or more simply set it for all the
+following code with the `progressr::handlers()` function. After these settings,
+[**flipr**](https://lmjl-alea.github.io/flipr/) functions can be used, as shown
+in this example.
 
 ```{r, eval=FALSE}
 ncores <- 4
@@ -106,21 +131,22 @@ time_with_parallelization <- tictoc::toc()
 parallel::stopCluster(cl)
 ```
 
-It is good practice to shut down the workers with the `parallel::stopCluster()` function at the end of the code.
+It is good practice to shut down the workers with the `parallel::stopCluster()`
+function at the end of the code.
 
 ```{r}
 time_with_parallelization
 ```
 
-This experiment proves that we can save a lot of computation time when using parallel processing, as we gained approximately 33 seconds in this example to evaluate the plausibility function.
+This experiment proves that we can save a lot of computation time when using
+parallel processing, as we gained approximately 33 seconds in this example to
+evaluate the plausibility function.
 
-Finally, to return to a sequential plan with no progress updates, the following code can be used.
+Finally, to return to a sequential plan with no progress updates, the following
+code can be used.
 
 ```{r, eval=FALSE}
 future::plan(sequential)
 parallel::setDefaultCluster(NULL)
 progressr::handlers(global = FALSE)
 ```
-
-
-