add: runtime_test demo

CVE/DESCRIPTION

@@ -6,7 +6,7 @@ Date: 2019-07-29
 Author: Loki
 Maintainer: Loki <loki@no.mail>
 Description: More about what it does (maybe more than one line)
-License: What license is it under?
+License: GPL-3
 Imports: Rcpp (>= 1.0.2)
 LinkingTo: Rcpp, RcppArmadillo
 Encoding: UTF-8

CVE/R/CVE.R

@@ -20,12 +20,22 @@
 #'      TODO: See ...
 #' @examples
 #' library(CVE)
-#' ds <- dataset("M5")
-#' X <- ds$X
-#' Y <- ds$Y
-#' dr <- cve(Y ~ X, k = 1)
 #'
-#' @references Fertl L, Bura E. Conditional Variance Estimation for Sufficient Dimension Reduction, 2019
+#' # sample dataset
+#' ds <- dataset("M5")
+#'
+#' # call ´cve´ with default method (aka "simple")
+#' dr.simple <- cve(ds$Y ~ ds$X, k = ncol(ds$B))
+#' # plot optimization history (loss via iteration)
+#' plot(dr.simple, main = "CVE M5 simple")
+#'
+#' # call ´cve´ with method "linesearch" using ´data.frame´ as data.
+#' data <- data.frame(Y = ds$Y, X = ds$X)
+#' # Note: ´Y, X´ are NOT defined, they are extracted from ´data´.
+#' dr.linesearch <- cve(Y ~ ., data, method = "linesearch", k = ncol(ds$B))
+#' plot(dr.linesearch, main = "CVE M5 linesearch")
+#'
+#' @references Fertl L., Bura E. Conditional Variance Estimation for Sufficient Dimension Reduction, 2019
 #'
 #' @import stats
 #' @importFrom stats model.frame
@@ -51,6 +61,7 @@ cve <- function(formula, data, method = "simple", ...) {
     return(dr)
 }
 
+#' @param nObs as describet in the Paper.
 #' @rdname cve
 #' @export
 cve.call <- function(X, Y, method = "simple", nObs = nrow(X)^.5, k, ...) {
@@ -101,7 +112,10 @@ cve.call <- function(X, Y, method = "simple", nObs = nrow(X)^.5, k, ...) {
 #' }
 #' @param ... Pass through parameters to [plot()] and [lines()]
 #'
-#' @seealso see \code{\link{par}} for graphical parameters to pass through.
+#' @usage ## S3 method for class 'cve'
+#' plot(x, content = "history", ...)
+#' @seealso see \code{\link{par}} for graphical parameters to pass through
+#'      as well as \code{\link{plot}} for standard plot utility.
 #' @importFrom graphics plot lines points
 #' @method plot cve
 #' @export

CVE/demo/00Index

@@ -0,0 +1 @@
+runtime_test    Runtime comparison of CVE against MAVE for M1 - M5 datasets.

CVE/demo/runtime_test.R

@@ -0,0 +1,106 @@
+# -----------------------------------------------------------------------------
+# Program: runtime_test.R
+# Author: Loki
+# Date: 2019.08.12
+#
+# Purpose:
+#      Comparing runtime of "MAVE" with "CVE".
+#
+# RevisionHistory:
+#      Loki -- 2019.08.12 initial creation
+# -----------------------------------------------------------------------------
+
+# load CVE package
+library(CVE)
+# load MAVE package for comparison
+library(MAVE)
+
+# set nr of simulations per dataset
+nr.sim <- 10
+
+# set names of datasets to run tests on
+dataset.names <- c("M1", "M2", "M3", "M4", "M5")
+
+#' Orthogonal projection to sub-space spanned by `B`
+#'
+#' @param B Matrix
+#' @return Orthogonal Projection Matrix
+proj <- function(B) {
+    B %*% solve(t(B) %*% B) %*% t(B)
+}
+
+#' Compute nObs given dataset dimension \code{n}.
+#'
+#' @param n Number of samples
+#' @return Numeric estimate of \code{nObs}
+nObs <- function (n) { n^0.5 }
+
+## prepare "logging"
+# result error, time, ... data.frame's
+error <- matrix(nrow = nr.sim, ncol = 2 * length(dataset.names))
+time <- matrix(nrow = nr.sim, ncol = 2 * length(dataset.names))
+# convert to data.frames
+error <- as.data.frame(error)
+time <- as.data.frame(time)
+# set names
+names(error) <- kronecker(c("CVE.", "MAVE."), dataset.names, paste0)
+names(time) <- kronecker(c("CVE.", "MAVE."), dataset.names, paste0)
+
+# get current time
+start.time <- Sys.time()
+## main comparison loop (iterate `nr.sim` times for each dataset)
+for (i in seq_along(dataset.names)) {
+    for (j in 1:nr.sim) {
+        name <- dataset.names[i]
+        # reporting progress
+        cat("\rRunning Test (", name, j , "):",
+            (i - 1) * nr.sim + j, "/", length(dataset.names) * nr.sim,
+            " - Time since start:", format(Sys.time() - start.time), "\033[K")
+        # sample new dataset
+        ds <- dataset(name)
+        k <- ncol(ds$B) # real dim
+        data <- data.frame(X = ds$X, Y = ds$Y)
+        # call CVE
+        cve.time <- system.time(
+            cve.res <- cve(Y ~ .,
+                           data = data,
+                           method = "simple",
+                           k = k)
+        )
+        # call MAVE
+        mave.time <- system.time(
+            mave.res <- mave(Y ~ .,
+                             data = data,
+                             method = "meanMAVE")
+        )
+        # compute real and approximated sub-space projections
+        P <- proj(ds$B) # real
+        P.cve <- proj(cve.res$B)
+        P.mave <- proj(mave.res$dir[[k]])
+        # compute (and store) errors
+        error[j, paste0("CVE.", name)] <- norm(P - P.cve, 'F') / sqrt(2 * k)
+        error[j, paste0("MAVE.", name)] <- norm(P - P.mave, 'F') / sqrt(2 * k)
+        # store run-times
+        time[j, paste0("CVE.", name)] <- cve.time["elapsed"]
+        time[j, paste0("MAVE.", name)] <- mave.time["elapsed"]
+    }
+}
+
+cat("\n\n## Time [sec] Means:\n")
+print(colMeans(time))
+cat("\n## Error Means:\n")
+print(colMeans(error))
+
+len <- length(dataset.names)
+boxplot(as.matrix(error),
+    main = paste0("Error (nr.sim = ", nr.sim, ")"),
+    ylab = expression(error == group("||", P[B] - P[hat(B)], "||")[F] / sqrt(2*k)),
+    las = 2,
+    at = c(1:len, 1:len + len + 1)
+)
+boxplot(as.matrix(time),
+    main = paste0("Time (nr.sim = ", nr.sim, ")"),
+    ylab = "time [sec]",
+    las = 2,
+    at = c(1:len, 1:len + len + 1)
+)

CVE/man/cve.Rd

@@ -26,6 +26,8 @@ See: \code{\link{formula}}.}
 
 \item{...}{Further parameters depending on the used method.
 TODO: See ...}
+
+\item{nObs}{as describet in the Paper.}
 }
 \description{
 Conditional Variance Estimator (CVE) is a novel sufficient dimension
@@ -35,12 +37,22 @@ where B'X is a lower dimensional projection of the predictors.
 }
 \examples{
 library(CVE)
+
+# sample dataset
 ds <- dataset("M5")
-X <- ds$X
+
-Y <- ds$Y
+# call ´cve´ with default method (aka "simple")
-dr <- cve(Y ~ X, k = 1)
+dr.simple <- cve(ds$Y ~ ds$X, k = ncol(ds$B))
+# plot optimization history (loss via iteration)
+plot(dr.simple, main = "CVE M5 simple")
+
+# call ´cve´ with method "linesearch" using ´data.frame´ as data.
+data <- data.frame(Y = ds$Y, X = ds$X)
+# Note: ´Y, X´ are NOT defined, they are extracted from ´data´.
+dr.linesearch <- cve(Y ~ ., data, method = "linesearch", k = ncol(ds$B))
+plot(dr.linesearch, main = "CVE M5 linesearch")
 
 }
 \references{
-Fertl L, Bura E. Conditional Variance Estimation for Sufficient Dimension Reduction, 2019
+Fertl L., Bura E. Conditional Variance Estimation for Sufficient Dimension Reduction, 2019
 }

CVE/man/plot.cve.Rd

@@ -2,24 +2,27 @@
 % Please edit documentation in R/CVE.R
 \name{plot.cve}
 \alias{plot.cve}
-\title{Ploting helper for objects of class \code{"cve"}.}
+\title{Ploting helper for objects of class \code{cve}.}
 \usage{
-\method{plot}{cve}(x, ...)
+## S3 method for class 'cve'
+plot(x, content = "history", ...)
 }
 \arguments{
-\item{x}{Object of class \code{"cve"} (result of [cve()]).}
+\item{x}{Object of class \code{cve} (result of [cve()]).}
 
 \item{...}{Pass through parameters to [plot()] and [lines()]}
 
 \item{content}{Specifies what to plot:
 \itemize{
-     \item "history" Plots the loss history from stiefel optimization.
+     \item "history" Plots the loss history from stiefel optimization
+         (default).
      \item ... TODO: add (if there are any)
 }}
 }
 \description{
-Ploting helper for objects of class \code{"cve"}.
+Ploting helper for objects of class \code{cve}.
 }
 \seealso{
-see \code{\link{par}} for graphical parameters to pass through.
+see \code{\link{par}} for graphical parameters to pass through
+     as well as \code{\link{plot}} for standard plot utility.
 }

README.md

@@ -5,3 +5,29 @@
 The `*.R` and `*.cpp` files in the root directory are _development_ and _test_ files.
 
 ## TODO: README.md
+
+# Package Structure
+
+## Demos
+A demo is an `.R` file that lives in `demo/`. Demos are like examples but tend to
+be longer. Instead of focussing on a single function, they show how to weave
+together multiple functions to solve a problem.
+
+You list and access demos with `demo()`:
+   * Show all available demos: `demo()`.
+   * Show all demos in a package: `demo(package = "CVE")`.
+   * Run a specific demo: `demo("runtime_test", package = "CVE")`.
+   * Find a demo: `system.file("demo", "runtime_test.R", package = "CVE")`.
+
+Each demo must be listed in `demo/00Index` in the following form:
+`demo-name Demo description`.
+The demo name is the name of the file without the extension,
+e.g. `demo/runtime_test.R` becomes `runtime_test`.
+
+By default the demo ask for human input for each plot: "Hit to see next plot".
+This behaviour can be overridden by adding `devAskNewPage(ask = FALSE)` to
+the demo file. You can add pauses by adding:
+`readline("press any key to continue")`.
+
+**Note**: Demos are not automatically tested by `R CMD check`. This means that they
+can easily break without your knowledge.