Merge branch 'master' into master

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+ workflow_dispatch:
+ inputs:
+ config:
+ description: 'A comma separated list of R-hub platforms to use.'
+ type: string
+ default: 'linux,windows,macos'
+ name:
+ description: 'Run name. You can leave this empty now.'
+ type: string
+ id:
+ description: 'Unique ID. You can leave this empty now.'
+ type: string
+
+jobs:
+
+ setup:
+ runs-on: ubuntu-latest
+ outputs:
+ containers: ${{ steps.rhub-setup.outputs.containers }}
+ platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+ steps:
+ # NO NEED TO CHECKOUT HERE
+ - uses: r-hub/actions/setup@v1
+ with:
+ config: ${{ github.event.inputs.config }}
+ id: rhub-setup
+
+ linux-containers:
+ needs: setup
+ if: ${{ needs.setup.outputs.containers != '[]' }}
+ runs-on: ubuntu-latest
+ name: ${{ matrix.config.label }}
+ strategy:
+ fail-fast: false
+ matrix:
+ config: ${{ fromJson(needs.setup.outputs.containers) }}
+ container:
+ image: ${{ matrix.config.container }}
+
+ steps:
+ - uses: r-hub/actions/checkout@v1
+ - uses: r-hub/actions/platform-info@v1
+ with:
+ token: ${{ secrets.RHUB_TOKEN }}
+ job-config: ${{ matrix.config.job-config }}
+ - uses: r-hub/actions/setup-deps@v1
+ with:
+ token: ${{ secrets.RHUB_TOKEN }}
+ job-config: ${{ matrix.config.job-config }}
+ - uses: r-hub/actions/run-check@v1
+ with:
+ token: ${{ secrets.RHUB_TOKEN }}
+ job-config: ${{ matrix.config.job-config }}
+
+ other-platforms:
+ needs: setup
+ if: ${{ needs.setup.outputs.platforms != '[]' }}
+ runs-on: ${{ matrix.config.os }}
+ name: ${{ matrix.config.label }}
+ strategy:
+ fail-fast: false
+ matrix:
+ config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+ steps:
+ - uses: r-hub/actions/checkout@v1
+ - uses: r-hub/actions/setup-r@v1
+ with:
+ job-config: ${{ matrix.config.job-config }}
+ token: ${{ secrets.RHUB_TOKEN }}
+ - uses: r-hub/actions/platform-info@v1
+ with:
+ token: ${{ secrets.RHUB_TOKEN }}
+ job-config: ${{ matrix.config.job-config }}
+ - uses: r-hub/actions/setup-deps@v1
+ with:
+ job-config: ${{ matrix.config.job-config }}
+ token: ${{ secrets.RHUB_TOKEN }}
+ - uses: r-hub/actions/run-check@v1
+ with:
+ job-config: ${{ matrix.config.job-config }}
+ token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,20 +1,13 @@
 Package: tourr
 Title: Tour Methods for Multivariate Data Visualisation
-Version: 1.0.2
+Version: 1.2.0
 Authors@R: c(
  person("Hadley", "Wickham", email = "h.wickham@gmail.com", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-4757-117X")),
  person("Dianne", "Cook", email = "dicook@monash.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3813-7155")),
  person("Nick", "Spyrison", email = "nicholas.spyrison@monash.edu", role = "ctb", comment = c(ORCID = "0000-0002-8417-0212")),
  person("Ursula", "Laa", email = "ursula.laa@boku.ac.at", role = "ctb", comment = c(ORCID = "0000-0002-0249-6439")), 
  person("H. Sherry","Zhang", email = "huizezhangsh@gmail.com", role = "ctb", comment = c(ORCID = "0000-0002-7122-1463")),
  person("Stuart", "Lee", email = "stuart.lee1@monash.edu", role = "ctb", comment = c(ORCID = "0000-0003-1179-8436")))
-Author: Hadley Wickham ["aut", "ctb"],
- Dianne Cook ["aut", "cre"],
- Nick Spyrison ["ctb"],
- Ursula Laa ["ctb"],
- H. Sherry Zhang ["ctb"],
- Stuart Lee ["ctb"]
-Maintainer: Dianne Cook <dicook@monash.edu>
 Description: Implements geodesic interpolation and basis
  generation functions that allow you to create new tour
  methods from R.
@@ -28,7 +21,7 @@ Imports:
  utils,
  grDevices
 Suggests:
- TeachingDemos,
+ aplpack,
  ash,
  energy,
  testthat,

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2010-2021
+YEAR: 2010-2024
 COPYRIGHT HOLDER: Hadley Wickham, Di Cook

NAMESPACE

@@ -35,6 +35,7 @@ export(animate_stars)
 export(animate_stereo)
 export(animate_trails)
 export(animate_xy)
+export(anomaly_index)
 export(areColors)
 export(basis_init)
 export(basis_random)
@@ -69,6 +70,7 @@ export(frozen_guided_tour)
 export(frozen_tour)
 export(geodesic_path)
 export(grand_tour)
+export(guided_anomaly_tour)
 export(guided_section_tour)
 export(guided_tour)
 export(holes)
@@ -79,6 +81,7 @@ export(linear_breaks)
 export(little_tour)
 export(local_tour)
 export(loess2d)
+export(mahal_dist)
 export(manual_slice)
 export(mapColors)
 export(mapShapes)
@@ -139,7 +142,9 @@ importFrom(graphics,rect)
 importFrom(graphics,segments)
 importFrom(graphics,stars)
 importFrom(graphics,text)
+importFrom(stats,mahalanobis)
 importFrom(stats,na.omit)
+importFrom(stats,qchisq)
 importFrom(stats,quantile)
 importFrom(stats,residuals)
 importFrom(stats,rnorm)

NEWS.md

@@ -1,3 +1,17 @@
+# tourr 1.2.0 
+
+* major change: rescale is now FALSE by default.
+* flea is now standardised measurements, and flea_raw is the original units.
+* TeachingDemos removed as a Suggests, and replaced with aplpack for drawing Chernoff faces.
+* addition of a pre-specified ellipse can be added to the 2D display.
+* palette can now be a vector of values.
+* a new projection pursuit index for finding anomalies relative to a null variance-covariance matrix. May still need more work.
+* point shapes can now be specified like palettes
+
+# tourr 1.1.0 
+
+* Updated version to indicate some nice new additions for the package
+
 # tourr 1.0.2
 
 * Fix to duplicating bases during interpolate

R/anomaly-pursuit.r

@@ -0,0 +1,15 @@
+#' Anomaly index.
+#'
+#' Calculates an index that looks for the best projection of
+#' observations that are outside a pre-determined p-D ellipse.
+#'
+#' @export
+anomaly_index <- function() {
+
+ function(mat, ell2d, ellmu2d) {
+
+ mat_tab <- #mean(mahal_dist(mat, ell2d))
+ mean(mahalanobis(mat, center=ellmu2d, cov=ell2d))
+ }
+}
+

R/data.r

@@ -1,7 +1,8 @@
 #' Flea beatle measurements
 #'
 #' This data is from a paper by A. A. Lubischew, "On the Use of Discriminant
-#' Functions in Taxonomy", Biometrics, Dec 1962, pp.455-477.
+#' Functions in Taxonomy", Biometrics, Dec 1962, pp.455-477. Data is
+#' standardized, and original units are in flea_raw.
 #'
 #' \itemize{
 #' \item tars1, width of the first joint of the first tarsus in microns
@@ -16,7 +17,7 @@
 #' }
 #'
 #' @name Flea measurements
-#' @aliases flea
+#' @aliases flea, flea_raw
 #' @docType data
 #' @format A 74 x 7 numeric array
 #' @keywords datasets
@@ -25,7 +26,7 @@
 #' head(flea)
 #' animate_xy(flea[, -7])
 #' animate_xy(flea[, -7], col = flea[, 7])
-NULL
+"flea"
 
 #' Turnable laser measurements from Bellcore
 #'

R/display-faces.r

@@ -14,19 +14,19 @@
 #' # The drawing code is fairly slow, so this animation works best with a
 #' # limited number of cases
 #' flea_s <- rescale(flea[,1:6])
-#' animate_faces(flea_s[1:2, 1:6])
-#' animate_faces(flea_s[1:4, 1:6])
+#' animate_faces(flea_s[19:24, 1:6])
 #'
-#' animate_faces(flea_s[1:2, 1:6], grand_tour(5))
+#' animate_faces(flea_s[19:24, 1:6], grand_tour(5))
 display_faces <- function(...) {
- if (!requireNamespace("TeachingDemos", quietly = TRUE)) {
- stop("Please install the TeachingDemos package", call. = FALSE)
+ if (!requireNamespace("aplpack", quietly = TRUE)) {
+ stop("Please install the aplpack package", call. = FALSE)
  }
 
  render_data <- function(data, proj, geodesic) {
  x <- data %*% proj
  x <- (x + 2) / 4
- TeachingDemos::faces2(x, scale = "none")
+ aplpack::faces(x, scale = TRUE, face.type = 0,
+ cex = 0.1, print.info = FALSE)
  }
 
  list(

R/display-groupxy.r

@@ -20,6 +20,8 @@
 #' @param edges.col colour of edges to be plotted, Defaults to "black"
 #' @param edges.width line width for edges, default 1
 #' @param palette name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"
+#' @param shapeset numbers corresponding to shapes in base R points, to use for mapping
+#' categorical variable to shapes, default=c(15:17, 23:25)
 #' @param ... other arguments passed on to \code{\link{animate}} and
 #' \code{\link{display_groupxy}}
 #' @export
@@ -39,7 +41,7 @@ display_groupxy <- function(centr = TRUE, axes = "center", half_range = NULL,
  col = "black", pch = 20, cex = 1,
  edges = NULL, edges.col = "black", edges.width=1,
  group_by = NULL, plot_xgp = TRUE,
- palette = "Zissou 1", ...) {
+ palette = "Zissou 1", shapeset=c(15:17, 23:25), ...) {
  labels <- NULL
 
  # If colors are a variable, convert to colors
@@ -53,7 +55,7 @@ display_groupxy <- function(centr = TRUE, axes = "center", half_range = NULL,
  }
  # If shapes are a variable, convert shapes
  if (is.factor(pch)) {
- shapes <- mapShapes(pch)
+ shapes <- mapShapes(pch, shapeset)
  } else {
  shapes <- pch
  }