Merge pull request #17 from special-uor/dev

CRAN v0.0.6

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fxTWAPLS
 Title: An Improved Version of WA-PLS
-Version: 0.0.5
+Version: 0.0.6
 Authors@R: c(
     person(given = "Mengmeng",
            family = "Liu",
@@ -37,7 +37,6 @@ Description: The goal of this package is to provide an improved version of
     pseudo-replication.
 License: GPL-3
 Encoding: UTF-8
-LazyData: true
 URL: https://github.com/special-uor/fxTWAPLS/, 
      https://special-uor.github.io/fxTWAPLS/,
      https://research.reading.ac.uk/palaeoclimate/
@@ -50,12 +49,11 @@ Imports:
     ggplot2,
     MASS,
     parallel,
-    progress,
     progressr
 Suggests:
     magrittr,
+    progress,
     scales,
-    testthat,
     tictoc
 Depends: 
     R (>= 3.6)

NEWS.md

@@ -1,3 +1,8 @@
+# fxTWAPLS 0.0.6
+
+* Removed unused benchmark functions and test.
+* Simplified the list of suggested packages.
+
 # fxTWAPLS 0.0.5
 
 * Added support for the `progressr` API (display a progress bar).

R.ignore/utils-benchmark.R

@@ -0,0 +1,85 @@
+#' Perform parallel benchmarks 
+#' 
+#' Perform parallel benchmarks on a function and generate a plot with execution 
+#' times vs CPU count.
+#'
+#' @param CPUS Vector with the number of CPUs.
+#' @param FUN Parallel function, MUST have a parameter called \code{cpus}.
+#' @param plot Boolean flag to request a plot for the results.
+#' @param quiet Boolean flag to print results of each execution.
+#' @param ... Optional arguments for \code{FUN}, must be named; e.g. 
+#'     \code{x = test_df}.
+#'
+#' @examples
+#' # Define toy function that sleeps for (2/cpus) seconds
+#' a <- function(cpus) {Sys.sleep(2/cpus)}
+#' fxTWAPLS:::par_benchmark(c(1, 2), a)
+#' \donttest{
+#' fxTWAPLS:::par_benchmark(c(1, 2), a, plot = TRUE)
+#' }
+#' 
+#' @keywords internal
+#' @noRd
+par_benchmark <- function(CPUS, FUN, plot = FALSE, quiet = FALSE, ...) {
+  cpus <- NULL # Local binding
+  tictoc::tic.clearlog()
+  for (c in CPUS) {
+    tictoc::tic(paste0("Using ", c, " CPUs"))
+    out <- FUN(..., cpus = c)
+    tictoc::toc(log = TRUE, quiet = quiet)
+  }
+  times <- unlist(tictoc::tic.log(format = TRUE))
+  times <- gsub(" sec elapsed", "", unlist(times))
+  times <- gsub(".*: ", "", unlist(times))
+  times <- as.numeric(times)
+  times_df <- data.frame(cpus = CPUS, times = times)
+
+  if(plot) {
+    print(ggplot2::qplot(cpus, times, data = times_df) + 
+            ggplot2::geom_area(alpha = 0.5) + 
+            ggplot2::geom_line() + 
+            ggplot2::labs(x = "CPUs", y = "Execution time [seconds]") +
+            ggplot2::scale_x_continuous(breaks = 1:max(CPUS)) + 
+            ggplot2::scale_y_continuous(breaks = scales::pretty_breaks(10))
+    )
+  }
+  return(times_df)
+}
+
+#' Combine results with progress bar
+#' 
+#' Combine results with progress bar, to be used in combination with 
+#'     \code{\link[foreach::foreach]{foreach::foreach}}.
+#'     
+#' @importFrom utils flush.console
+#' @importFrom utils setTxtProgressBar
+#' @importFrom utils txtProgressBar
+#' 
+#' @param iterator Number of iterations.
+#' @param FUN Function to combine the results (default: \code{rbind}).
+#' @param ... Optional parameters.
+#' 
+#' @examples
+#' \donttest{
+#' # Load binary operator for backend
+#' `%do%` <- foreach::`%do%`
+#' N <- 5
+#' out <- foreach::foreach(i = 1:N, 
+#'                         .combine = fxTWAPLS:::comb_pb(N)) %do% {
+#'                         Sys.sleep(1)
+#'                         i
+#'                        }
+#' }
+#' 
+#' @noRd
+#' @keywords internal
+comb_pb <- function(iterator, FUN = rbind, ...) {
+  pb <- txtProgressBar(min = 1, max = iterator - 1, style = 3)
+  count <- 0
+  function(...) {
+    count <- count + length(list(...)) - 1
+    setTxtProgressBar(pb, count)
+    flush.console()
+    FUN(...) # this can feed into .combine option of foreach
+  }
+}

R/utils.R

@@ -1,89 +1,3 @@
-#' Perform parallel benchmarks 
-#' 
-#' Perform parallel benchmarks on a function and generate a plot with execution 
-#' times vs CPU count.
-#'
-#' @param CPUS Vector with the number of CPUs.
-#' @param FUN Parallel function, MUST have a parameter called \code{cpus}.
-#' @param plot Boolean flag to request a plot for the results.
-#' @param quiet Boolean flag to print results of each execution.
-#' @param ... Optional arguments for \code{FUN}, must be named; e.g. 
-#'     \code{x = test_df}.
-#'
-#' @examples
-#' # Define toy function that sleeps for (2/cpus) seconds
-#' a <- function(cpus) {Sys.sleep(2/cpus)}
-#' fxTWAPLS:::par_benchmark(c(1, 2), a)
-#' \donttest{
-#' fxTWAPLS:::par_benchmark(c(1, 2), a, plot = TRUE)
-#' }
-#' 
-#' @keywords internal
-#' @noRd
-par_benchmark <- function(CPUS, FUN, plot = FALSE, quiet = FALSE, ...) {
-  cpus <- NULL # Local binding
-  tictoc::tic.clearlog()
-  for (c in CPUS) {
-    tictoc::tic(paste0("Using ", c, " CPUs"))
-    out <- FUN(..., cpus = c)
-    tictoc::toc(log = TRUE, quiet = quiet)
-  }
-  times <- unlist(tictoc::tic.log(format = TRUE))
-  times <- gsub(" sec elapsed", "", unlist(times))
-  times <- gsub(".*: ", "", unlist(times))
-  times <- as.numeric(times)
-  times_df <- data.frame(cpus = CPUS, times = times)
-
-  if(plot) {
-    print(ggplot2::qplot(cpus, times, data = times_df) + 
-            ggplot2::geom_area(alpha = 0.5) + 
-            ggplot2::geom_line() + 
-            ggplot2::labs(x = "CPUs", y = "Execution time [seconds]") +
-            ggplot2::scale_x_continuous(breaks = 1:max(CPUS)) + 
-            ggplot2::scale_y_continuous(breaks = scales::pretty_breaks(10))
-    )
-  }
-  return(times_df)
-}
-
-#' Combine results with progress bar
-#' 
-#' Combine results with progress bar, to be used in combination with 
-#'     \code{\link[foreach::foreach]{foreach::foreach}}.
-#'     
-#' @importFrom utils flush.console
-#' @importFrom utils setTxtProgressBar
-#' @importFrom utils txtProgressBar
-#' 
-#' @param iterator Number of iterations.
-#' @param FUN Function to combine the results (default: \code{rbind}).
-#' @param ... Optional parameters.
-#' 
-#' @examples
-#' \donttest{
-#' # Load binary operator for backend
-#' `%do%` <- foreach::`%do%`
-#' N <- 5
-#' out <- foreach::foreach(i = 1:N, 
-#'                         .combine = fxTWAPLS:::comb_pb(N)) %do% {
-#'                         Sys.sleep(1)
-#'                         i
-#'                        }
-#' }
-#' 
-#' @noRd
-#' @keywords internal
-comb_pb <- function(iterator, FUN = rbind, ...) {
-  pb <- txtProgressBar(min = 1, max = iterator - 1, style = 3)
-  count <- 0
-  function(...) {
-    count <- count + length(list(...)) - 1
-    setTxtProgressBar(pb, count)
-    flush.console()
-    FUN(...) # this can feed into .combine option of foreach
-  }
-}
-
 #' Show progress bar
 #'
 #' @param expr R expression.