diff --git a/README.Rmd b/README.Rmd index 3ef61427..85317b59 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,7 +1,7 @@ --- title: "tourr: tour methods for multivariate data visualisation" author: "Hadley Wickham, Di Cook, Nick Spyrison, Ursula Laa, H. Sherry Zhang, Stuart Lee" -date: "`r format(Sys.time(), '%B %d, %Y')`" +date: "
`r format(Sys.time(), '%B %d, %Y')`" output: github_document --- diff --git a/README.md b/README.md index 7905ac2f..7671e2ba 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ tourr: tour methods for multivariate data visualisation ================ Hadley Wickham, Di Cook, Nick Spyrison, Ursula Laa, H. Sherry Zhang, Stuart Lee -March 10, 2023 +
June 20, 2023 @@ -24,8 +24,8 @@ install.packages("tourr") You can install the development version of tourr from github with: ``` r -# install.packages("devtools") -devtools::install_github("ggobi/tourr") +# install.packages("remotes") +remotes::install_github("ggobi/tourr") ``` ## Example diff --git a/docs/articles/edges.html b/docs/articles/edges.html index 88313c1f..40238eba 100644 --- a/docs/articles/edges.html +++ b/docs/articles/edges.html @@ -157,13 +157,17 @@

Ursula Laa

clustering the flea dataset:

 # get centroids of 3 clusters of the flea data
-n <- nrow(flea)
-flea_centroids <- stats::kmeans((flea[,-7]), 3)$centers
-flea_aug <- rbind(flea[,-7], flea_centroids)
+f <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
+n <- nrow(f)
+set.seed(1019)
+flea_centroids <- stats::kmeans((f), 3)$centers
+flea_aug <- rbind(f, flea_centroids)
+col <- c(rep("black", n), rep("orange", 3))
 flea_edges <- matrix(c(n+1, n+2, n+1, n+3, n+2, n+3), ncol=2, byrow = TRUE)
-animate_xy(flea_aug, edges = flea_edges)
-#> Converting input data to the required matrix format.
-#> Using half_range 66
+animate_xy(flea_aug, edges = flea_edges, + col = col, edges.col = "orange", + edges.width = 3) +#> Using half_range 4.4

diff --git a/docs/articles/edges_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/edges_files/figure-html/unnamed-chunk-2-1.png index f3a76819..3793607f 100644 Binary files a/docs/articles/edges_files/figure-html/unnamed-chunk-2-1.png and b/docs/articles/edges_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/docs/articles/edges_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/edges_files/figure-html/unnamed-chunk-3-1.png index 8690dd2c..9c29ff28 100644 Binary files a/docs/articles/edges_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/edges_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/docs/articles/edges_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/edges_files/figure-html/unnamed-chunk-4-1.png index f1eab81b..7d2f2044 100644 Binary files a/docs/articles/edges_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/edges_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/tourr.html b/docs/articles/tourr.html index cd28a6cc..65fac379 100644 --- a/docs/articles/tourr.html +++ b/docs/articles/tourr.html @@ -149,13 +149,26 @@

Tour typesTour typesanimate(f, tour_path = guided_tour(holes()), display = display_xy()) -#> Value 0.970 48.1 % better - NEW BASIS +#> Value 1.032 18.0 % better - NEW BASIS #> Using half_range 4.4

When running the full guided tour for this example, the final view @@ -180,7 +193,7 @@

Tour typesanimate(f, tour_path = guided_tour(holes()), display = display_xy(col = flea$species)) -#> Value 1.043 9.5 % better - NEW BASIS +#> Value 1.048 32.0 % better - NEW BASIS #> Using half_range 4.4

Alternatively, a colour vector can be created manually and passed @@ -195,7 +208,7 @@

Tour typesanimate(f, tour_path = guided_tour(holes()), display = display_xy(col = flea_col)) -#> Value 1.063 29.9 % better - NEW BASIS +#> Value 1.076 5.7 % better - NEW BASIS #> Using half_range 4.4

@@ -204,14 +217,14 @@

Display types\(d\)), we can choose different +display types. For example, we could look at 1D projections in a density +display, a 3D projection using depth cues, or higher dimensional +projections in a parallel coordinate or scatterplot matrix display.

When changing the display type via the display argument, we need to make sure that the basis generation is matching the -corresponding number of dimensions d. We can pass in this information -when generating the tour path. To work with 1D projections and a density +corresponding number of dimensions \(d\). We can pass in this information when +generating the tour path. To work with 1D projections and a density display, we can launch the animation as

 animate(f,
diff --git a/docs/articles/tourr_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/tourr_files/figure-html/unnamed-chunk-2-1.png
index 55e6bd19..0ba764d5 100644
Binary files a/docs/articles/tourr_files/figure-html/unnamed-chunk-2-1.png and b/docs/articles/tourr_files/figure-html/unnamed-chunk-2-1.png differ
diff --git a/docs/articles/tourr_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/tourr_files/figure-html/unnamed-chunk-3-1.png
index d2b3f0bb..47017722 100644
Binary files a/docs/articles/tourr_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/tourr_files/figure-html/unnamed-chunk-3-1.png differ
diff --git a/docs/articles/tourr_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/tourr_files/figure-html/unnamed-chunk-4-1.png
index ffad2dc9..96c104d6 100644
Binary files a/docs/articles/tourr_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/tourr_files/figure-html/unnamed-chunk-4-1.png differ
diff --git a/docs/articles/tourr_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/tourr_files/figure-html/unnamed-chunk-5-1.png
index 78301619..288bd171 100644
Binary files a/docs/articles/tourr_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/tourr_files/figure-html/unnamed-chunk-5-1.png differ
diff --git a/docs/articles/tourr_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/tourr_files/figure-html/unnamed-chunk-6-1.png
index 3183b968..96a3345a 100644
Binary files a/docs/articles/tourr_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/tourr_files/figure-html/unnamed-chunk-6-1.png differ
diff --git a/docs/articles/tourr_files/figure-html/unnamed-chunk-7-2.png b/docs/articles/tourr_files/figure-html/unnamed-chunk-7-2.png
index 86209886..aa5c6163 100644
Binary files a/docs/articles/tourr_files/figure-html/unnamed-chunk-7-2.png and b/docs/articles/tourr_files/figure-html/unnamed-chunk-7-2.png differ
diff --git a/docs/articles/tourr_files/figure-html/unnamed-chunk-8-2.png b/docs/articles/tourr_files/figure-html/unnamed-chunk-8-2.png
index e4afb5d4..05ca0efc 100644
Binary files a/docs/articles/tourr_files/figure-html/unnamed-chunk-8-2.png and b/docs/articles/tourr_files/figure-html/unnamed-chunk-8-2.png differ
diff --git a/docs/articles/tourr_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/tourr_files/figure-html/unnamed-chunk-9-1.png
index 875307b5..536ca99b 100644
Binary files a/docs/articles/tourr_files/figure-html/unnamed-chunk-9-1.png and b/docs/articles/tourr_files/figure-html/unnamed-chunk-9-1.png differ
diff --git a/docs/index.html b/docs/index.html
index ca288d99..b9aa614f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -93,7 +93,7 @@
 

 
tourr: tour methods for multivariate data visualisation
 

-
Hadley Wickham, Di Cook, Nick Spyrison, Ursula Laa, H. Sherry Zhang, Stuart Lee March 10, 2023

+
Hadley Wickham, Di Cook, Nick Spyrison, Ursula Laa, H. Sherry Zhang, Stuart Lee 
 June 20, 2023

 
 

 

@@ -108,8 +108,8 @@ 
Installationinstall.packages("tourr")

You can install the development version of tourr from github with:

-# install.packages("devtools")
-devtools::install_github("ggobi/tourr")
+# install.packages("remotes") +remotes::install_github("ggobi/tourr")

Example diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index d8110efe..7eea737c 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -4,5 +4,5 @@ pkgdown_sha: ~ articles: edges: edges.html tourr: tourr.html -last_built: 2023-06-19T02:21Z +last_built: 2023-06-20T00:25Z diff --git a/docs/reference/Flea-measurements-1.png b/docs/reference/Flea-measurements-1.png index ff92148c..29139d03 100644 Binary files a/docs/reference/Flea-measurements-1.png and b/docs/reference/Flea-measurements-1.png differ diff --git a/docs/reference/Flea-measurements-2.png b/docs/reference/Flea-measurements-2.png index 7ddc966b..b04f2f2b 100644 Binary files a/docs/reference/Flea-measurements-2.png and b/docs/reference/Flea-measurements-2.png differ diff --git a/docs/reference/Laser-measurements-1.png b/docs/reference/Laser-measurements-1.png index c339a482..cd7887ca 100644 Binary files a/docs/reference/Laser-measurements-1.png and b/docs/reference/Laser-measurements-1.png differ diff --git a/docs/reference/Olive-oil-measurements-1.png b/docs/reference/Olive-oil-measurements-1.png index 687b6e50..a32f32f7 100644 Binary files a/docs/reference/Olive-oil-measurements-1.png and b/docs/reference/Olive-oil-measurements-1.png differ diff --git a/docs/reference/Olive-oil-measurements-2.png b/docs/reference/Olive-oil-measurements-2.png index 5fdd15fc..3ce44158 100644 Binary files a/docs/reference/Olive-oil-measurements-2.png and b/docs/reference/Olive-oil-measurements-2.png differ diff --git a/docs/reference/Places-Ratings-1.png b/docs/reference/Places-Ratings-1.png index 6cb48db9..1e52a7c5 100644 Binary files a/docs/reference/Places-Ratings-1.png and b/docs/reference/Places-Ratings-1.png differ diff --git a/docs/reference/Rat-CNS-1.png b/docs/reference/Rat-CNS-1.png index cff4707b..f8bbbfbd 100644 Binary files a/docs/reference/Rat-CNS-1.png and b/docs/reference/Rat-CNS-1.png differ diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index 6fd9111f..4a4f978f 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index 15cf2967..96240dae 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png index 8b79a5a1..196a1fb7 100644 Binary files a/docs/reference/Rplot004.png and b/docs/reference/Rplot004.png differ diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png index 1188d2e8..74ccaddc 100644 Binary files a/docs/reference/Rplot005.png and b/docs/reference/Rplot005.png differ diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png index 717d7fb5..ae96577a 100644 Binary files a/docs/reference/Rplot006.png and b/docs/reference/Rplot006.png differ diff --git a/docs/reference/Rplot007.png b/docs/reference/Rplot007.png index 5d357b3b..1c1aa8dd 100644 Binary files a/docs/reference/Rplot007.png and b/docs/reference/Rplot007.png differ diff --git a/docs/reference/Rplot008.png b/docs/reference/Rplot008.png index 8b30a926..1c523e09 100644 Binary files a/docs/reference/Rplot008.png and b/docs/reference/Rplot008.png differ diff --git a/docs/reference/Rplot009.png b/docs/reference/Rplot009.png index ff243233..e40769ac 100644 Binary files a/docs/reference/Rplot009.png and b/docs/reference/Rplot009.png differ diff --git a/docs/reference/Rplot010.png b/docs/reference/Rplot010.png index 832d2691..974c7b7e 100644 Binary files a/docs/reference/Rplot010.png and b/docs/reference/Rplot010.png differ diff --git a/docs/reference/Rplot011.png b/docs/reference/Rplot011.png index 889f0bab..e3a539f9 100644 Binary files a/docs/reference/Rplot011.png and b/docs/reference/Rplot011.png differ diff --git a/docs/reference/Rplot012.png b/docs/reference/Rplot012.png index 60c01a7d..ac2efaf4 100644 Binary files a/docs/reference/Rplot012.png and b/docs/reference/Rplot012.png differ diff --git a/docs/reference/Rplot013.png b/docs/reference/Rplot013.png index 1c6b0df3..aaca69d5 100644 Binary files a/docs/reference/Rplot013.png and b/docs/reference/Rplot013.png differ diff --git a/docs/reference/Rplot014.png b/docs/reference/Rplot014.png index 104bef48..ae33b7c1 100644 Binary files a/docs/reference/Rplot014.png and b/docs/reference/Rplot014.png differ diff --git a/docs/reference/Rplot015.png b/docs/reference/Rplot015.png index 91541753..794cef6e 100644 Binary files a/docs/reference/Rplot015.png and b/docs/reference/Rplot015.png differ diff --git a/docs/reference/Rplot016.png b/docs/reference/Rplot016.png index e6e0521e..b808d031 100644 Binary files a/docs/reference/Rplot016.png and b/docs/reference/Rplot016.png differ diff --git a/docs/reference/Rplot017.png b/docs/reference/Rplot017.png index dd012f1a..90404fc2 100644 Binary files a/docs/reference/Rplot017.png and b/docs/reference/Rplot017.png differ diff --git a/docs/reference/Rplot018.png b/docs/reference/Rplot018.png index d9694fc9..1610672b 100644 Binary files a/docs/reference/Rplot018.png and b/docs/reference/Rplot018.png differ diff --git a/docs/reference/Rplot021.png b/docs/reference/Rplot021.png index 359e86d6..aff65a9f 100644 Binary files a/docs/reference/Rplot021.png and b/docs/reference/Rplot021.png differ diff --git a/docs/reference/Rplot024.png b/docs/reference/Rplot024.png index 253bd467..40a611e7 100644 Binary files a/docs/reference/Rplot024.png and b/docs/reference/Rplot024.png differ diff --git a/docs/reference/Rplot027.png b/docs/reference/Rplot027.png index 88639c75..afe92d8a 100644 Binary files a/docs/reference/Rplot027.png and b/docs/reference/Rplot027.png differ diff --git a/docs/reference/Rplot030.png b/docs/reference/Rplot030.png index ff265a02..88f525d9 100644 Binary files a/docs/reference/Rplot030.png and b/docs/reference/Rplot030.png differ diff --git a/docs/reference/Rplot031.png b/docs/reference/Rplot031.png index df68fb44..5260c970 100644 Binary files a/docs/reference/Rplot031.png and b/docs/reference/Rplot031.png differ diff --git a/docs/reference/Rplot034.png b/docs/reference/Rplot034.png index 1fa30ab6..e710b3b6 100644 Binary files a/docs/reference/Rplot034.png and b/docs/reference/Rplot034.png differ diff --git a/docs/reference/andrews-2.png b/docs/reference/andrews-2.png index 2d54ee2c..a29dd895 100644 Binary files a/docs/reference/andrews-2.png and b/docs/reference/andrews-2.png differ diff --git a/docs/reference/animate-1.png b/docs/reference/animate-1.png index 77947508..660fa219 100644 Binary files a/docs/reference/animate-1.png and b/docs/reference/animate-1.png differ diff --git a/docs/reference/animate-2.png b/docs/reference/animate-2.png index 93af5879..a2c1d9a7 100644 Binary files a/docs/reference/animate-2.png and b/docs/reference/animate-2.png differ diff --git a/docs/reference/animate-3.png b/docs/reference/animate-3.png index 14002e8f..f9b1866e 100644 Binary files a/docs/reference/animate-3.png and b/docs/reference/animate-3.png differ diff --git a/docs/reference/animate-4.png b/docs/reference/animate-4.png index 9025009e..eb86d473 100644 Binary files a/docs/reference/animate-4.png and b/docs/reference/animate-4.png differ diff --git a/docs/reference/dependence_tour-1.png b/docs/reference/dependence_tour-1.png index caefb52a..9b4ae85e 100644 Binary files a/docs/reference/dependence_tour-1.png and b/docs/reference/dependence_tour-1.png differ diff --git a/docs/reference/dependence_tour-2.png b/docs/reference/dependence_tour-2.png index 6f781652..aa026371 100644 Binary files a/docs/reference/dependence_tour-2.png and b/docs/reference/dependence_tour-2.png differ diff --git a/docs/reference/dependence_tour-3.png b/docs/reference/dependence_tour-3.png index 8b1be71f..276ac96f 100644 Binary files a/docs/reference/dependence_tour-3.png and b/docs/reference/dependence_tour-3.png differ diff --git a/docs/reference/display_andrews-11.png b/docs/reference/display_andrews-11.png index 35afe579..d10ab5bb 100644 Binary files a/docs/reference/display_andrews-11.png and b/docs/reference/display_andrews-11.png differ diff --git a/docs/reference/display_andrews-12.png b/docs/reference/display_andrews-12.png index 35afe579..d10ab5bb 100644 Binary files a/docs/reference/display_andrews-12.png and b/docs/reference/display_andrews-12.png differ diff --git a/docs/reference/display_andrews-3.png b/docs/reference/display_andrews-3.png index d84255ac..ea83dc91 100644 Binary files a/docs/reference/display_andrews-3.png and b/docs/reference/display_andrews-3.png differ diff --git a/docs/reference/display_andrews-6.png b/docs/reference/display_andrews-6.png index 00ec5f12..48e73716 100644 Binary files a/docs/reference/display_andrews-6.png and b/docs/reference/display_andrews-6.png differ diff --git a/docs/reference/display_andrews-9.png b/docs/reference/display_andrews-9.png index a250d900..eede2775 100644 Binary files a/docs/reference/display_andrews-9.png and b/docs/reference/display_andrews-9.png differ diff --git a/docs/reference/display_andrews.html b/docs/reference/display_andrews.html index 5c769937..dbfbfb97 100644 --- a/docs/reference/display_andrews.html +++ b/docs/reference/display_andrews.html @@ -121,38 +121,38 @@

Examples

# It's easy to experiment with different tour paths: animate_andrews(flea[, 1:6], guided_tour(cmass())) #> Converting input data to the required matrix format. +#> Value -0.579 -0.5 % better +#> Value -0.582 -0.1 % better #> Value -0.582 -0.0 % better +#> Value -0.578 -0.6 % better #> Value -0.582 -0.0 % better +#> Value -0.568 -2.4 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better +#> Value -0.522 -10.3 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better +#> Value -0.579 -0.5 % better +#> Value -0.556 -4.4 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better -#> Value -0.582 -0.0 % better -#> Value -0.582 -0.0 % better -#> Value -0.582 -0.0 % better -#> Value -0.582 -0.0 % better -#> Value -0.582 -0.0 % better -#> Value -0.582 -0.0 % better -#> Value -0.582 -0.0 % better -#> Value -0.582 -0.0 % better +#> Value -0.581 -0.1 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better #> Value -0.582 -0.0 % better #> No better bases found after 25 tries. Giving up. #> Final projection: -#> 0.233 0.669 -#> -0.044 -0.027 -#> -0.313 -0.146 -#> 0.088 0.597 -#> 0.750 -0.049 -#> -0.525 0.415 +#> -0.658 0.209 +#> 0.336 -0.745 +#> 0.425 0.335 +#> 0.092 0.295 +#> -0.514 -0.426 +#> -0.008 0.141 diff --git a/docs/reference/display_density2d-11.png b/docs/reference/display_density2d-11.png index 5507e0e1..6a9e985c 100644 Binary files a/docs/reference/display_density2d-11.png and b/docs/reference/display_density2d-11.png differ diff --git a/docs/reference/display_density2d-12.png b/docs/reference/display_density2d-12.png index 57489cd9..769db494 100644 Binary files a/docs/reference/display_density2d-12.png and b/docs/reference/display_density2d-12.png differ diff --git a/docs/reference/display_density2d-13.png b/docs/reference/display_density2d-13.png index 5bb0804e..178a731c 100644 Binary files a/docs/reference/display_density2d-13.png and b/docs/reference/display_density2d-13.png differ diff --git a/docs/reference/display_density2d-14.png b/docs/reference/display_density2d-14.png index f1a54676..2b2e0d66 100644 Binary files a/docs/reference/display_density2d-14.png and b/docs/reference/display_density2d-14.png differ diff --git a/docs/reference/display_density2d-15.png b/docs/reference/display_density2d-15.png index 742380ae..b34af3c7 100644 Binary files a/docs/reference/display_density2d-15.png and b/docs/reference/display_density2d-15.png differ diff --git a/docs/reference/display_density2d-16.png b/docs/reference/display_density2d-16.png index f6a60823..4666c173 100644 Binary files a/docs/reference/display_density2d-16.png and b/docs/reference/display_density2d-16.png differ diff --git a/docs/reference/display_density2d-17.png b/docs/reference/display_density2d-17.png index df824bf5..5f829649 100644 Binary files a/docs/reference/display_density2d-17.png and b/docs/reference/display_density2d-17.png differ diff --git a/docs/reference/display_density2d-18.png b/docs/reference/display_density2d-18.png index 2b55a9c0..87fc1bf9 100644 Binary files a/docs/reference/display_density2d-18.png and b/docs/reference/display_density2d-18.png differ diff --git a/docs/reference/display_density2d-2.png b/docs/reference/display_density2d-2.png index 7e4ba505..bf45525e 100644 Binary files a/docs/reference/display_density2d-2.png and b/docs/reference/display_density2d-2.png differ diff --git a/docs/reference/display_density2d-21.png b/docs/reference/display_density2d-21.png index be8b4fde..fa2bb696 100644 Binary files a/docs/reference/display_density2d-21.png and b/docs/reference/display_density2d-21.png differ diff --git a/docs/reference/display_density2d-24.png b/docs/reference/display_density2d-24.png index 7f0e147a..7a1b05ce 100644 Binary files a/docs/reference/display_density2d-24.png and b/docs/reference/display_density2d-24.png differ diff --git a/docs/reference/display_density2d-27.png b/docs/reference/display_density2d-27.png index ac1bd55b..8facfcb8 100644 Binary files a/docs/reference/display_density2d-27.png and b/docs/reference/display_density2d-27.png differ diff --git a/docs/reference/display_density2d-3.png b/docs/reference/display_density2d-3.png index 0ea0f8ea..6c4abeb6 100644 Binary files a/docs/reference/display_density2d-3.png and b/docs/reference/display_density2d-3.png differ diff --git a/docs/reference/display_density2d-30.png b/docs/reference/display_density2d-30.png index af24c9eb..d9045a24 100644 Binary files a/docs/reference/display_density2d-30.png and b/docs/reference/display_density2d-30.png differ diff --git a/docs/reference/display_density2d-31.png b/docs/reference/display_density2d-31.png index 22aeecd0..b278d0d3 100644 Binary files a/docs/reference/display_density2d-31.png and b/docs/reference/display_density2d-31.png differ diff --git a/docs/reference/display_density2d-34.png b/docs/reference/display_density2d-34.png index 0322a0e9..c8b3c63b 100644 Binary files a/docs/reference/display_density2d-34.png and b/docs/reference/display_density2d-34.png differ diff --git a/docs/reference/display_density2d-5.png b/docs/reference/display_density2d-5.png index 07dd9e42..d93735ee 100644 Binary files a/docs/reference/display_density2d-5.png and b/docs/reference/display_density2d-5.png differ diff --git a/docs/reference/display_density2d-6.png b/docs/reference/display_density2d-6.png index f4c6ab8f..72c4aa75 100644 Binary files a/docs/reference/display_density2d-6.png and b/docs/reference/display_density2d-6.png differ diff --git a/docs/reference/display_density2d-9.png b/docs/reference/display_density2d-9.png index 571f5ef6..b7cb3b80 100644 Binary files a/docs/reference/display_density2d-9.png and b/docs/reference/display_density2d-9.png differ diff --git a/docs/reference/display_density2d.html b/docs/reference/display_density2d.html index 0a9294a0..a7b9365e 100644 --- a/docs/reference/display_density2d.html +++ b/docs/reference/display_density2d.html @@ -203,9 +203,9 @@

Examples

#> Value 1.582 0.0 % better #> No better bases found after 25 tries. Giving up. #> Final projection: -#> 0.199 0.601 -#> -0.828 -0.320 -#> 0.525 -0.732 +#> 0.322 0.227 +#> 0.791 -0.598 +#> 0.520 0.769 #> Using half_range 65 diff --git a/docs/reference/display_depth-1.png b/docs/reference/display_depth-1.png index f88c9a00..1182f279 100644 Binary files a/docs/reference/display_depth-1.png and b/docs/reference/display_depth-1.png differ diff --git a/docs/reference/display_dist-10.png b/docs/reference/display_dist-10.png index 111962b5..340ee440 100644 Binary files a/docs/reference/display_dist-10.png and b/docs/reference/display_dist-10.png differ diff --git a/docs/reference/display_dist-12.png b/docs/reference/display_dist-12.png index 1119c334..ddb37c23 100644 Binary files a/docs/reference/display_dist-12.png and b/docs/reference/display_dist-12.png differ diff --git a/docs/reference/display_dist-2.png b/docs/reference/display_dist-2.png index 97b3b83f..33ef743e 100644 Binary files a/docs/reference/display_dist-2.png and b/docs/reference/display_dist-2.png differ diff --git a/docs/reference/display_dist-4.png b/docs/reference/display_dist-4.png index c73fe589..14b5c11f 100644 Binary files a/docs/reference/display_dist-4.png and b/docs/reference/display_dist-4.png differ diff --git a/docs/reference/display_dist-6.png b/docs/reference/display_dist-6.png index 0bf8b380..0dcf87dd 100644 Binary files a/docs/reference/display_dist-6.png and b/docs/reference/display_dist-6.png differ diff --git a/docs/reference/display_dist-8.png b/docs/reference/display_dist-8.png index 8688385a..e253c3b4 100644 Binary files a/docs/reference/display_dist-8.png and b/docs/reference/display_dist-8.png differ diff --git a/docs/reference/display_faces-2.png b/docs/reference/display_faces-2.png index 209642be..63ba6881 100644 Binary files a/docs/reference/display_faces-2.png and b/docs/reference/display_faces-2.png differ diff --git a/docs/reference/display_faces-4.png b/docs/reference/display_faces-4.png index fd785193..c49ad51b 100644 Binary files a/docs/reference/display_faces-4.png and b/docs/reference/display_faces-4.png differ diff --git a/docs/reference/display_faces-6.png b/docs/reference/display_faces-6.png index 5bfa37c5..c30ed00d 100644 Binary files a/docs/reference/display_faces-6.png and b/docs/reference/display_faces-6.png differ diff --git a/docs/reference/display_groupxy-2.png b/docs/reference/display_groupxy-2.png index 7432d0b6..e5751c2c 100644 Binary files a/docs/reference/display_groupxy-2.png and b/docs/reference/display_groupxy-2.png differ diff --git a/docs/reference/display_groupxy-4.png b/docs/reference/display_groupxy-4.png index b29fa161..90157ea7 100644 Binary files a/docs/reference/display_groupxy-4.png and b/docs/reference/display_groupxy-4.png differ diff --git a/docs/reference/display_pca-1.png b/docs/reference/display_pca-1.png index 40306e7d..a4d1935d 100644 Binary files a/docs/reference/display_pca-1.png and b/docs/reference/display_pca-1.png differ diff --git a/docs/reference/display_pcp-1.png b/docs/reference/display_pcp-1.png index 2d67d937..d243d32a 100644 Binary files a/docs/reference/display_pcp-1.png and b/docs/reference/display_pcp-1.png differ diff --git a/docs/reference/display_pcp-2.png b/docs/reference/display_pcp-2.png index d00d3fba..69a83f2e 100644 Binary files a/docs/reference/display_pcp-2.png and b/docs/reference/display_pcp-2.png differ diff --git a/docs/reference/display_sage-1.png b/docs/reference/display_sage-1.png index 262a005d..ebca9ed7 100644 Binary files a/docs/reference/display_sage-1.png and b/docs/reference/display_sage-1.png differ diff --git a/docs/reference/display_sage-2.png b/docs/reference/display_sage-2.png index bea80eff..95871ac5 100644 Binary files a/docs/reference/display_sage-2.png and b/docs/reference/display_sage-2.png differ diff --git a/docs/reference/display_scatmat-2.png b/docs/reference/display_scatmat-2.png index 11e4cbfb..e0529526 100644 Binary files a/docs/reference/display_scatmat-2.png and b/docs/reference/display_scatmat-2.png differ diff --git a/docs/reference/display_scatmat-4.png b/docs/reference/display_scatmat-4.png index b00f110e..bdd4e4a1 100644 Binary files a/docs/reference/display_scatmat-4.png and b/docs/reference/display_scatmat-4.png differ diff --git a/docs/reference/display_slice-1.png b/docs/reference/display_slice-1.png index f1422106..83834dda 100644 Binary files a/docs/reference/display_slice-1.png and b/docs/reference/display_slice-1.png differ diff --git a/docs/reference/display_slice-2.png b/docs/reference/display_slice-2.png index e655b477..1e801bd7 100644 Binary files a/docs/reference/display_slice-2.png and b/docs/reference/display_slice-2.png differ diff --git a/docs/reference/display_slice-3.png b/docs/reference/display_slice-3.png index 0c3eda8b..5306c950 100644 Binary files a/docs/reference/display_slice-3.png and b/docs/reference/display_slice-3.png differ diff --git a/docs/reference/display_slice-4.png b/docs/reference/display_slice-4.png index ce90c807..68f3eb65 100644 Binary files a/docs/reference/display_slice-4.png and b/docs/reference/display_slice-4.png differ diff --git a/docs/reference/display_slice.html b/docs/reference/display_slice.html index 7703332a..c3429430 100644 --- a/docs/reference/display_slice.html +++ b/docs/reference/display_slice.html @@ -187,7 +187,7 @@

Examples

animate_slice(sphere5) #> Using half_range 1 -#> Using v_rel=0.1, corresponding to a cutoff h=0.47 +#> Using v_rel=0.11, corresponding to a cutoff h=0.48 # Animate with off-center anchoring diff --git a/docs/reference/display_stars-2.png b/docs/reference/display_stars-2.png index 79d452a5..c21c31f2 100644 Binary files a/docs/reference/display_stars-2.png and b/docs/reference/display_stars-2.png differ diff --git a/docs/reference/display_stars-4.png b/docs/reference/display_stars-4.png index ae40e169..b71fc482 100644 Binary files a/docs/reference/display_stars-4.png and b/docs/reference/display_stars-4.png differ diff --git a/docs/reference/display_stars-6.png b/docs/reference/display_stars-6.png index d18c56a5..a7142202 100644 Binary files a/docs/reference/display_stars-6.png and b/docs/reference/display_stars-6.png differ diff --git a/docs/reference/display_stars-8.png b/docs/reference/display_stars-8.png index 4c8a83c5..cbaaabb1 100644 Binary files a/docs/reference/display_stars-8.png and b/docs/reference/display_stars-8.png differ diff --git a/docs/reference/display_stereo-3.png b/docs/reference/display_stereo-3.png index ccaa9b3e..0f2f9f49 100644 Binary files a/docs/reference/display_stereo-3.png and b/docs/reference/display_stereo-3.png differ diff --git a/docs/reference/display_trails-1.png b/docs/reference/display_trails-1.png index 50eaad59..47722dc1 100644 Binary files a/docs/reference/display_trails-1.png and b/docs/reference/display_trails-1.png differ diff --git a/docs/reference/display_xy-1.png b/docs/reference/display_xy-1.png index 6322a9bf..17bb8f87 100644 Binary files a/docs/reference/display_xy-1.png and b/docs/reference/display_xy-1.png differ diff --git a/docs/reference/display_xy-10.png b/docs/reference/display_xy-10.png index d5cba7f9..99f96646 100644 Binary files a/docs/reference/display_xy-10.png and b/docs/reference/display_xy-10.png differ diff --git a/docs/reference/display_xy-11.png b/docs/reference/display_xy-11.png index eab36d3d..1743f989 100644 Binary files a/docs/reference/display_xy-11.png and b/docs/reference/display_xy-11.png differ diff --git a/docs/reference/display_xy-12.png b/docs/reference/display_xy-12.png index 4537ddca..0ef5c269 100644 Binary files a/docs/reference/display_xy-12.png and b/docs/reference/display_xy-12.png differ diff --git a/docs/reference/display_xy-13.png b/docs/reference/display_xy-13.png index 81cd08a3..288260e5 100644 Binary files a/docs/reference/display_xy-13.png and b/docs/reference/display_xy-13.png differ diff --git a/docs/reference/display_xy-14.png b/docs/reference/display_xy-14.png index 3270694f..a6a75230 100644 Binary files a/docs/reference/display_xy-14.png and b/docs/reference/display_xy-14.png differ diff --git a/docs/reference/display_xy-2.png b/docs/reference/display_xy-2.png index a638d870..2d9c2f31 100644 Binary files a/docs/reference/display_xy-2.png and b/docs/reference/display_xy-2.png differ diff --git a/docs/reference/display_xy-3.png b/docs/reference/display_xy-3.png index 6fb49e5a..7ca86687 100644 Binary files a/docs/reference/display_xy-3.png and b/docs/reference/display_xy-3.png differ diff --git a/docs/reference/display_xy-4.png b/docs/reference/display_xy-4.png index bbf6d81e..9e0d92bd 100644 Binary files a/docs/reference/display_xy-4.png and b/docs/reference/display_xy-4.png differ diff --git a/docs/reference/display_xy-5.png b/docs/reference/display_xy-5.png index 20d7e337..0728c85a 100644 Binary files a/docs/reference/display_xy-5.png and b/docs/reference/display_xy-5.png differ diff --git a/docs/reference/display_xy-6.png b/docs/reference/display_xy-6.png index 34bbc625..d5c3838b 100644 Binary files a/docs/reference/display_xy-6.png and b/docs/reference/display_xy-6.png differ diff --git a/docs/reference/display_xy-7.png b/docs/reference/display_xy-7.png index 0291786b..339ba399 100644 Binary files a/docs/reference/display_xy-7.png and b/docs/reference/display_xy-7.png differ diff --git a/docs/reference/display_xy-8.png b/docs/reference/display_xy-8.png index f549f9df..559e9912 100644 Binary files a/docs/reference/display_xy-8.png and b/docs/reference/display_xy-8.png differ diff --git a/docs/reference/display_xy-9.png b/docs/reference/display_xy-9.png index 20ceecaa..087f0d89 100644 Binary files a/docs/reference/display_xy-9.png and b/docs/reference/display_xy-9.png differ diff --git a/docs/reference/display_xy.html b/docs/reference/display_xy.html index 5f411947..6dc7c47f 100644 --- a/docs/reference/display_xy.html +++ b/docs/reference/display_xy.html @@ -177,7 +177,8 @@

Examples

animate_xy(flea[, 1:3], tour_path = guided_tour(holes()), sphere = TRUE) #> Converting input data to the required matrix format. -#> Value 0.858 4.2 % better - NEW BASIS +#> Value 0.869 0.1 % better +#> Value 0.869 0.1 % better - NEW BASIS #> Using half_range 3.2 animate_xy(flea[, 1:6], center = FALSE) diff --git a/docs/reference/draw_tour_axes-1.png b/docs/reference/draw_tour_axes-1.png index 4f54e75c..8b7b4000 100644 Binary files a/docs/reference/draw_tour_axes-1.png and b/docs/reference/draw_tour_axes-1.png differ diff --git a/docs/reference/draw_tour_axes-2.png b/docs/reference/draw_tour_axes-2.png index ddbb3dba..dff5bb47 100644 Binary files a/docs/reference/draw_tour_axes-2.png and b/docs/reference/draw_tour_axes-2.png differ diff --git a/docs/reference/freeze.html b/docs/reference/freeze.html index a1a0ab75..94f27ac2 100644 --- a/docs/reference/freeze.html +++ b/docs/reference/freeze.html @@ -89,23 +89,23 @@

Examples

input <- basis_random(4, 2) freeze(input, frozen) -#> [,1] [,2] -#> [1,] 0.1805913 0.5180353 -#> [2,] 0.1388004 -0.2229295 -#> [3,] 0.0000000 0.0000000 -#> [4,] -0.8236207 -0.3847669 +#> [,1] [,2] +#> [1,] -0.423664397 -0.2308976 +#> [2,] 0.006597133 -0.1150380 +#> [3,] 0.000000000 0.0000000 +#> [4,] 0.555484808 -0.8241565 thaw(input, frozen) -#> [,1] [,2] -#> [1,] 0.1563966 0.4486317 -#> [2,] 0.1202047 -0.1930626 -#> [3,] 0.5000000 0.5000000 -#> [4,] -0.7132764 -0.3332179 +#> [,1] [,2] +#> [1,] -0.366904131 -0.19996320 +#> [2,] 0.005713285 -0.09962583 +#> [3,] 0.500000000 0.50000000 +#> [4,] 0.481063955 -0.71374043 freeze(basis_random(4, 2), frozen) #> [,1] [,2] -#> [1,] 0.01420098 0.75484763 -#> [2,] 0.13410974 -0.52329523 +#> [1,] 0.42027216 0.41234374 +#> [2,] 0.88373028 -0.08785718 #> [3,] 0.00000000 0.00000000 -#> [4,] -0.95820572 0.04149124 +#> [4,] -0.06833198 0.88877633
diff --git a/docs/reference/frozen_tour-1.png b/docs/reference/frozen_tour-1.png index fb39abab..5140099c 100644 Binary files a/docs/reference/frozen_tour-1.png and b/docs/reference/frozen_tour-1.png differ diff --git a/docs/reference/frozen_tour-2.png b/docs/reference/frozen_tour-2.png index 42b65cc6..b1fce1d7 100644 Binary files a/docs/reference/frozen_tour-2.png and b/docs/reference/frozen_tour-2.png differ diff --git a/docs/reference/frozen_tour-3.png b/docs/reference/frozen_tour-3.png index cf3fc9d6..04ab57d6 100644 Binary files a/docs/reference/frozen_tour-3.png and b/docs/reference/frozen_tour-3.png differ diff --git a/docs/reference/frozen_tour-4.png b/docs/reference/frozen_tour-4.png index 9f1e5bf6..bda0c329 100644 Binary files a/docs/reference/frozen_tour-4.png and b/docs/reference/frozen_tour-4.png differ diff --git a/docs/reference/geodesic_path.html b/docs/reference/geodesic_path.html index 86432f21..5a1b8452 100644 --- a/docs/reference/geodesic_path.html +++ b/docs/reference/geodesic_path.html @@ -121,12 +121,12 @@

Examples

path <- geodesic_path(a, b) path$dist -#> [1] 1.202971 +#> [1] 1.503865 all.equal(a, path$interpolate(0)) #> [1] TRUE # Not true generally - a rotated into plane of b all.equal(b, path$interpolate(1)) -#> [1] "Mean relative difference: 1.179555" +#> [1] "Mean relative difference: 1.619657" diff --git a/docs/reference/grand_tour-2.png b/docs/reference/grand_tour-2.png index 6ab59187..d56eee0a 100644 Binary files a/docs/reference/grand_tour-2.png and b/docs/reference/grand_tour-2.png differ diff --git a/docs/reference/grand_tour-3.png b/docs/reference/grand_tour-3.png index 3788506c..17629a8f 100644 Binary files a/docs/reference/grand_tour-3.png and b/docs/reference/grand_tour-3.png differ diff --git a/docs/reference/grand_tour-4.png b/docs/reference/grand_tour-4.png index 20838bfa..5bed5603 100644 Binary files a/docs/reference/grand_tour-4.png and b/docs/reference/grand_tour-4.png differ diff --git a/docs/reference/guided_tour-1.png b/docs/reference/guided_tour-1.png index 0670a267..cd00fa7a 100644 Binary files a/docs/reference/guided_tour-1.png and b/docs/reference/guided_tour-1.png differ diff --git a/docs/reference/guided_tour-2.png b/docs/reference/guided_tour-2.png index 32623544..a99874b2 100644 Binary files a/docs/reference/guided_tour-2.png and b/docs/reference/guided_tour-2.png differ diff --git a/docs/reference/guided_tour-3.png b/docs/reference/guided_tour-3.png index c55616bd..630e0e99 100644 Binary files a/docs/reference/guided_tour-3.png and b/docs/reference/guided_tour-3.png differ diff --git a/docs/reference/guided_tour-4.png b/docs/reference/guided_tour-4.png index 322dc0f1..75104c32 100644 Binary files a/docs/reference/guided_tour-4.png and b/docs/reference/guided_tour-4.png differ diff --git a/docs/reference/guided_tour-5.png b/docs/reference/guided_tour-5.png index 0933792c..7db9c403 100644 Binary files a/docs/reference/guided_tour-5.png and b/docs/reference/guided_tour-5.png differ diff --git a/docs/reference/guided_tour.html b/docs/reference/guided_tour.html index c1b7fcaf..54879ba8 100644 --- a/docs/reference/guided_tour.html +++ b/docs/reference/guided_tour.html @@ -144,23 +144,23 @@

See also

Examples

flea_std <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
 animate_xy(flea_std, guided_tour(holes()), sphere = TRUE)
-#> Value  0.878   2.6 % better  - NEW BASIS
+#> Value  0.806   0.7 % better  - NEW BASIS
 #> Using half_range 3.8
 
 # \donttest{
 animate_xy(flea_std, guided_tour(holes(), search_f = search_better_random), sphere = TRUE)
-#> Old 0.8214868 
-#> New 0.8117052 try 2 
-#> Accept with probability, prob = 0.3414302 
+#> Old 0.7954998 
+#> New 0.8025468 try 1 
+#> Accept 
 #> Using half_range 3.8
 
 animate_dist(flea_std, guided_tour(holes(), 1), sphere = TRUE)
-#> Value  0.736   3.4 % better  - NEW BASIS
+#> Value  0.828   6.3 % better  - NEW BASIS
 #> Using half_range 3.8
 
 
 animate_xy(flea_std, guided_tour(lda_pp(flea$species)), sphere = TRUE, col = flea$species)
-#> Value  0.962   6.4 % better  - NEW BASIS
+#> Value  0.855   15.0 % better  - NEW BASIS
 #> Using half_range 3.8
 
 # save_history is particularly useful in conjunction with the
@@ -168,8 +168,8 @@ 
Examples

 # ways
 f <- flea_std[, 1:3]
 tries <- replicate(5, save_history(f, guided_tour(holes())), simplify = FALSE)
-#> Value  0.967   5.0 % better  - NEW BASIS
-#> Value  0.972   0.6 % better  - NEW BASIS
+#> Value  0.909   24.4 % better  - NEW BASIS
+#> Value  0.972   6.9 % better  - NEW BASIS
 #> Value  0.972   0.0 % better 
 #> Value  0.972   0.0 % better 
 #> Value  0.972   0.0 % better 
@@ -196,11 +196,13 @@ 
Examples

 #> Value  0.972   0.0 % better 
 #> No better bases found after 25 tries.  Giving up.
 #> Final projection: 
-#> -0.673  -0.705  
-#> -0.657  0.433  
-#> -0.338  0.562  
-#> Value  0.937   19.6 % better  - NEW BASIS
-#> Value  0.972   3.7 % better  - NEW BASIS
+#> -0.975  -0.012  
+#> -0.146  0.793  
+#> 0.171  0.609  
+#> Value  0.853   28.4 % better  - NEW BASIS
+#> Value  0.946   10.8 % better  - NEW BASIS
+#> Value  0.970   2.6 % better  - NEW BASIS
+#> Value  0.972   0.2 % better  - NEW BASIS
 #> Value  0.972   0.0 % better 
 #> Value  0.972   0.0 % better 
 #> Value  0.972   0.0 % better 
@@ -227,11 +229,13 @@ 
Examples

 #> Value  0.972   0.0 % better 
 #> No better bases found after 25 tries.  Giving up.
 #> Final projection: 
-#> 0.876  0.434  
-#> -0.222  0.750  
-#> -0.429  0.499  
-#> Value  0.944   34.0 % better  - NEW BASIS
-#> Value  0.972   3.0 % better  - NEW BASIS
+#> -0.868  -0.444  
+#> -0.479  0.626  
+#> -0.134  0.641  
+#> Value  0.896   18.5 % better  - NEW BASIS
+#> Value  0.948   5.8 % better  - NEW BASIS
+#> Value  0.967   2.0 % better  - NEW BASIS
+#> Value  0.972   0.5 % better  - NEW BASIS
 #> Value  0.972   0.0 % better 
 #> Value  0.972   0.0 % better 
 #> Value  0.972   0.0 % better 
@@ -258,12 +262,13 @@ 
Examples

 #> Value  0.972   0.0 % better 
 #> No better bases found after 25 tries.  Giving up.
 #> Final projection: 
-#> -0.937  -0.283  
-#> 0.097  -0.776  
-#> 0.336  -0.563  
-#> Value  0.864   25.2 % better  - NEW BASIS
-#> Value  0.964   11.6 % better  - NEW BASIS
-#> Value  0.972   0.8 % better  - NEW BASIS
+#> -0.712  0.669  
+#> 0.404  0.639  
+#> 0.574  0.380  
+#> Value  0.762   3.2 % better  - NEW BASIS
+#> Value  0.887   16.4 % better  - NEW BASIS
+#> Value  0.969   9.2 % better  - NEW BASIS
+#> Value  0.972   0.4 % better  - NEW BASIS
 #> Value  0.972   0.0 % better 
 #> Value  0.972   0.0 % better 
 #> Value  0.972   0.0 % better 
@@ -290,39 +295,41 @@ 
Examples

 #> Value  0.972   0.0 % better 
 #> No better bases found after 25 tries.  Giving up.
 #> Final projection: 
-#> -0.764  0.610  
-#> -0.580  -0.509  
-#> -0.281  -0.607  
-#> Value  0.971   8.2 % better  - NEW BASIS
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.0 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.0 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.0 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
-#> Value  0.972   0.1 % better 
+#> -0.415  0.879  
+#> -0.766  -0.198  
+#> -0.491  -0.434  
+#> Value  0.883   18.0 % better  - NEW BASIS
+#> Value  0.970   9.8 % better  - NEW BASIS
+#> Value  0.972   0.2 % better  - NEW BASIS
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
+#> Value  0.972   0.0 % better 
 #> No better bases found after 25 tries.  Giving up.
 #> Final projection: 
-#> -0.743  -0.649  
-#> 0.409  -0.632  
-#> 0.530  -0.423  
+#> -0.878  0.447  
+#> -0.442  -0.620  
+#> -0.183  -0.645  
 # }
diff --git a/docs/reference/interpolate.html b/docs/reference/interpolate.html index 8859fc3f..a57aad70 100644 --- a/docs/reference/interpolate.html +++ b/docs/reference/interpolate.html @@ -93,11 +93,11 @@

Examples

dim(t1) #> [1] 6 1 10 dim(interpolate(t1, 0.01)) -#> [1] 6 1 1155 +#> [1] 6 1 1160 dim(interpolate(t1, 0.05)) -#> [1] 6 1 237 +#> [1] 6 1 236 dim(interpolate(t1, 0.1)) -#> [1] 6 1 120 +#> [1] 6 1 121 diff --git a/docs/reference/little_tour-1.png b/docs/reference/little_tour-1.png index 1c1f2bbf..bd0bb6df 100644 Binary files a/docs/reference/little_tour-1.png and b/docs/reference/little_tour-1.png differ diff --git a/docs/reference/little_tour-2.png b/docs/reference/little_tour-2.png index 6cdbbd27..e7b8d4a5 100644 Binary files a/docs/reference/little_tour-2.png and b/docs/reference/little_tour-2.png differ diff --git a/docs/reference/little_tour-3.png b/docs/reference/little_tour-3.png index dbd43158..fa3bef8f 100644 Binary files a/docs/reference/little_tour-3.png and b/docs/reference/little_tour-3.png differ diff --git a/docs/reference/little_tour-4.png b/docs/reference/little_tour-4.png index 093a5641..db9fd044 100644 Binary files a/docs/reference/little_tour-4.png and b/docs/reference/little_tour-4.png differ diff --git a/docs/reference/little_tour-5.png b/docs/reference/little_tour-5.png index 9af2126e..a901b138 100644 Binary files a/docs/reference/little_tour-5.png and b/docs/reference/little_tour-5.png differ diff --git a/docs/reference/local_tour-1.png b/docs/reference/local_tour-1.png index abc97b84..a57b8678 100644 Binary files a/docs/reference/local_tour-1.png and b/docs/reference/local_tour-1.png differ diff --git a/docs/reference/local_tour-2.png b/docs/reference/local_tour-2.png index 81d8e5ec..bff6af8a 100644 Binary files a/docs/reference/local_tour-2.png and b/docs/reference/local_tour-2.png differ diff --git a/docs/reference/local_tour-3.png b/docs/reference/local_tour-3.png index d1949d9b..3c024dad 100644 Binary files a/docs/reference/local_tour-3.png and b/docs/reference/local_tour-3.png differ diff --git a/docs/reference/manual_slice-1.png b/docs/reference/manual_slice-1.png index 47796c07..b4b4ee37 100644 Binary files a/docs/reference/manual_slice-1.png and b/docs/reference/manual_slice-1.png differ diff --git a/docs/reference/path_index-1.png b/docs/reference/path_index-1.png index 5def7766..cdc0e006 100644 Binary files a/docs/reference/path_index-1.png and b/docs/reference/path_index-1.png differ diff --git a/docs/reference/path_index-2.png b/docs/reference/path_index-2.png index 15d364c5..666eb10a 100644 Binary files a/docs/reference/path_index-2.png and b/docs/reference/path_index-2.png differ diff --git a/docs/reference/path_index.html b/docs/reference/path_index.html index c44d658d..e65e1f44 100644 --- a/docs/reference/path_index.html +++ b/docs/reference/path_index.html @@ -93,92 +93,95 @@

See also

Examples

fl_holes <- save_history(flea[, 1:6], guided_tour(holes()), sphere = TRUE)
 #> Converting input data to the required matrix format.
-#> Value  0.845   1.3 % better  - NEW BASIS
-#> Value  0.867   2.6 % better  - NEW BASIS
-#> Value  0.875   1.0 % better  - NEW BASIS
-#> Value  0.880   0.5 % better  - NEW BASIS
-#> Value  0.901   2.4 % better  - NEW BASIS
-#> Value  0.902   0.1 % better 
-#> Value  0.902   0.1 % better  - NEW BASIS
-#> Value  0.904   0.2 % better  - NEW BASIS
-#> Value  0.904   0.0 % better 
-#> Value  0.904   0.0 % better 
-#> Value  0.904   0.0 % better 
+#> Value  0.856   5.2 % better  - NEW BASIS
+#> Value  0.883   3.2 % better  - NEW BASIS
+#> Value  0.890   0.8 % better  - NEW BASIS
+#> Value  0.892   0.3 % better  - NEW BASIS
+#> Value  0.899   0.7 % better  - NEW BASIS
+#> Value  0.903   0.4 % better  - NEW BASIS
 #> Value  0.904   0.1 % better 
-#> Value  0.905   0.1 % better 
-#> Value  0.905   0.1 % better 
-#> Value  0.905   0.1 % better  - NEW BASIS
-#> Value  0.906   0.1 % better 
-#> Value  0.906   0.1 % better  - NEW BASIS
-#> Value  0.906   0.0 % better 
+#> Value  0.906   0.4 % better  - NEW BASIS
+#> Value  0.907   0.1 % better 
 #> Value  0.908   0.2 % better  - NEW BASIS
-#> Value  0.908   0.0 % better 
-#> Value  0.908   0.0 % better 
-#> Value  0.909   0.2 % better  - NEW BASIS
-#> Value  0.910   0.0 % better 
+#> Value  0.909   0.1 % better  - NEW BASIS
 #> Value  0.911   0.2 % better  - NEW BASIS
-#> Value  0.912   0.1 % better  - NEW BASIS
-#> Value  0.913   0.1 % better  - NEW BASIS
-#> Value  0.914   0.1 % better 
-#> Value  0.914   0.1 % better 
-#> Value  0.916   0.3 % better  - NEW BASIS
-#> Value  0.917   0.1 % better  - NEW BASIS
-#> Value  0.917   0.0 % better 
-#> Value  0.918   0.1 % better  - NEW BASIS
+#> Value  0.915   0.4 % better  - NEW BASIS
+#> Value  0.918   0.4 % better  - NEW BASIS
+#> Value  0.919   0.1 % better 
 #> Value  0.919   0.1 % better  - NEW BASIS
-#> Value  0.921   0.2 % better  - NEW BASIS
-#> Value  0.921   0.1 % better 
-#> Value  0.922   0.2 % better  - NEW BASIS
-#> Value  0.927   0.5 % better  - NEW BASIS
-#> Value  0.929   0.2 % better  - NEW BASIS
-#> Value  0.931   0.3 % better  - NEW BASIS
-#> Value  0.932   0.1 % better 
-#> Value  0.932   0.1 % better 
-#> Value  0.932   0.1 % better 
-#> Value  0.932   0.0 % better 
-#> Value  0.932   0.1 % better 
-#> Value  0.932   0.1 % better  - NEW BASIS
-#> Value  0.933   0.0 % better 
+#> Value  0.920   0.1 % better 
+#> Value  0.920   0.1 % better  - NEW BASIS
+#> Value  0.922   0.1 % better  - NEW BASIS
+#> Value  0.922   0.0 % better 
+#> Value  0.922   0.0 % better 
+#> Value  0.923   0.1 % better  - NEW BASIS
+#> Value  0.924   0.1 % better 
+#> Value  0.923   0.0 % better 
+#> Value  0.924   0.1 % better  - NEW BASIS
+#> Value  0.924   0.0 % better 
+#> Value  0.925   0.1 % better  - NEW BASIS
+#> Value  0.925   0.0 % better 
+#> Value  0.926   0.1 % better  - NEW BASIS
+#> Value  0.927   0.1 % better  - NEW BASIS
+#> Value  0.930   0.3 % better  - NEW BASIS
+#> Value  0.931   0.1 % better 
+#> Value  0.931   0.1 % better 
+#> Value  0.932   0.2 % better  - NEW BASIS
 #> Value  0.933   0.1 % better 
-#> Value  0.933   0.0 % better 
-#> Value  0.934   0.1 % better  - NEW BASIS
-#> Value  0.934   0.0 % better 
-#> Value  0.935   0.1 % better 
+#> Value  0.933   0.2 % better  - NEW BASIS
 #> Value  0.934   0.0 % better 
 #> Value  0.934   0.1 % better 
-#> Value  0.934   0.1 % better 
 #> Value  0.934   0.0 % better 
 #> Value  0.934   0.1 % better 
 #> Value  0.934   0.1 % better 
-#> Value  0.934   0.1 % better 
-#> Value  0.934   0.1 % better 
 #> Value  0.934   0.0 % better 
 #> Value  0.934   0.0 % better 
-#> Value  0.934   0.1 % better 
 #> Value  0.934   0.0 % better 
-#> Value  0.934   0.1 % better 
-#> Value  0.934   0.1 % better 
 #> Value  0.934   0.0 % better 
-#> Value  0.934   0.1 % better 
 #> Value  0.934   0.0 % better 
 #> Value  0.934   0.0 % better 
-#> Value  0.934   0.1 % better 
-#> Value  0.934   0.1 % better 
+#> Value  0.934   0.0 % better 
+#> Value  0.934   0.0 % better 
 #> Value  0.934   0.1 % better 
 #> Value  0.934   0.0 % better 
+#> Value  0.935   0.1 % better  - NEW BASIS
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.0 % better 
+#> Value  0.935   0.1 % better 
+#> Value  0.935   0.0 % better 
 #> No better bases found after 25 tries.  Giving up.
 #> Final projection: 
-#> -0.774  0.580  
-#> 0.351  0.692  
-#> -0.108  -0.005  
-#> 0.101  0.229  
-#> -0.494  -0.346  
-#> -0.106  -0.110  
+#> -0.102  0.960  
+#> -0.836  0.031  
+#> 0.085  0.121  
+#> -0.181  0.039  
+#> -0.455  -0.245  
+#> -0.210  -0.046  
 path_index(fl_holes, holes())
-#>  [1] 0.8337691 0.8448838 0.8666414 0.8753518 0.8797158 0.9011892 0.9023293
-#>  [8] 0.9037842 0.9047929 0.9058242 0.9076701 0.9092279 0.9112091 0.9122437
-#> [15] 0.9132170 0.9156420 0.9166765 0.9177388 0.9187142 0.9206339 0.9220459
-#> [22] 0.9267844 0.9287189 0.9312699 0.9323319 0.9336372 0.9336372
+#>  [1] 0.8131522 0.8555257 0.8826982 0.8899170 0.8924648 0.8990949 0.9028726
+#>  [8] 0.9064484 0.9080788 0.9094344 0.9110685 0.9146181 0.9179657 0.9191304
+#> [15] 0.9203588 0.9216977 0.9227311 0.9238004 0.9248211 0.9259350 0.9269204
+#> [22] 0.9301253 0.9320167 0.9334850 0.9345782 0.9345782
 #> attr(,"class")
 #> [1] "path_index"
 ## path_index(fl_holes, cmass())
@@ -191,23 +194,24 @@ 
Examples

 # Use interpolate to show all intermediate bases as well
 hi <- path_index(interpolate(fl_holes), holes())
 hi
-#>   [1] 0.8337691 0.8362300 0.8384916 0.8404956 0.8421847 0.8435047 0.8444061
-#>   [8] 0.8448456 0.8448456 0.8484745 0.8517684 0.8547151 0.8573090 0.8595506
-#>  [15] 0.8614466 0.8630094 0.8642565 0.8652099 0.8658955 0.8663419 0.8665798
-#>  [22] 0.8665798 0.8691415 0.8712785 0.8729754 0.8742225 0.8750158 0.8750158
-#>  [29] 0.8767385 0.8781081 0.8790930 0.8796671 0.8796671 0.8825587 0.8853671
-#>  [36] 0.8880557 0.8905874 0.8929256 0.8950345 0.8968800 0.8984308 0.8996586
-#>  [43] 0.9005391 0.9010526 0.9010526 0.9018927 0.9023032 0.9023032 0.9032015
-#>  [50] 0.9036907 0.9036907 0.9042889 0.9046688 0.9046688 0.9052987 0.9056885
-#>  [57] 0.9058242 0.9058242 0.9066236 0.9071882 0.9075307 0.9076663 0.9076663
-#>  [64] 0.9084136 0.9089197 0.9091859 0.9091859 0.9101246 0.9107744 0.9111402
-#>  [71] 0.9111402 0.9120046 0.9120046 0.9128105 0.9131994 0.9131994 0.9141399
-#>  [78] 0.9148684 0.9153664 0.9156157 0.9156157 0.9163493 0.9166644 0.9166644
-#>  [85] 0.9174183 0.9177302 0.9177302 0.9183520 0.9186724 0.9186724 0.9196046
-#>  [92] 0.9202444 0.9205920 0.9205920 0.9213346 0.9218169 0.9220345 0.9220345
-#>  [99] 0.9233451 0.9244748 0.9254011 0.9261039 0.9265660 0.9267735 0.9267735
-#> [106] 0.9280138 0.9286401 0.9286401 0.9300199 0.9308983 0.9312624 0.9312624
-#> [113] 0.9319944 0.9323151 0.9323151 0.9332274 0.9336253 0.9336253
+#>   [1] 0.8131522 0.8180359 0.8228032 0.8273943 0.8317546 0.8358345 0.8395915
+#>   [8] 0.8429897 0.8460011 0.8486053 0.8507900 0.8525507 0.8538907 0.8548205
+#>  [15] 0.8553576 0.8555259 0.8555259 0.8575681 0.8596498 0.8617691 0.8639200
+#>  [22] 0.8660911 0.8682651 0.8704185 0.8725216 0.8745389 0.8764306 0.8781532
+#>  [29] 0.8796618 0.8809112 0.8818586 0.8824649 0.8826968 0.8826968 0.8847952
+#>  [36] 0.8865466 0.8879408 0.8889694 0.8896259 0.8899063 0.8899063 0.8911684
+#>  [43] 0.8920235 0.8924330 0.8924330 0.8941960 0.8956927 0.8969181 0.8978701
+#>  [50] 0.8985486 0.8989561 0.8989561 0.9000044 0.9009182 0.9016846 0.9022900
+#>  [57] 0.9027195 0.9027195 0.9036957 0.9045356 0.9052335 0.9057834 0.9061793
+#>  [64] 0.9064148 0.9064148 0.9074074 0.9079579 0.9079579 0.9088738 0.9093613
+#>  [71] 0.9093613 0.9102143 0.9107787 0.9110488 0.9110488 0.9126182 0.9137416
+#>  [78] 0.9144099 0.9144099 0.9159265 0.9170375 0.9177227 0.9179664 0.9179664
+#>  [85] 0.9188410 0.9191306 0.9191306 0.9198860 0.9202874 0.9202874 0.9210446
+#>  [92] 0.9215150 0.9217010 0.9217010 0.9224725 0.9224725 0.9232069 0.9236574
+#>  [99] 0.9236574 0.9243554 0.9247389 0.9247389 0.9255973 0.9255973 0.9264214
+#> [106] 0.9268766 0.9268766 0.9279664 0.9288524 0.9295190 0.9299495 0.9299495
+#> [113] 0.9310215 0.9317312 0.9317312 0.9325846 0.9331879 0.9331879 0.9339400
+#> [120] 0.9344104 0.9344104 0.9344104
 #> attr(,"class")
 #> [1] "path_index"
 plot(hi)
diff --git a/docs/reference/paths_index-1.png b/docs/reference/paths_index-1.png
index 534b465a..7cccfdce 100644
Binary files a/docs/reference/paths_index-1.png and b/docs/reference/paths_index-1.png differ
diff --git a/docs/reference/paths_index.html b/docs/reference/paths_index.html
index ff622124..29edd306 100644
--- a/docs/reference/paths_index.html
+++ b/docs/reference/paths_index.html
@@ -93,40 +93,41 @@ 
Examples

 #> Value  2.541   0.0 % better 
 #> No better bases found after 2 tries.  Giving up.
 #> Final projection: 
-#> 0.649  -0.621  -0.285  0.199  0.240  0.124  
+#> 0.517  -0.420  0.661  -0.330  0.059  0.079  
 #> Converting input data to the required matrix format.
+#> Value  2.541   5.8 % better  - NEW BASIS
 #> Value  2.541   0.0 % better 
 #> No better bases found after 2 tries.  Giving up.
 #> Final projection: 
-#> -0.275  -0.278  0.462  -0.680  -0.124  -0.395  
+#> -0.212  -0.208  0.333  0.551  0.084  0.700  
 #> Converting input data to the required matrix format.
 #> Value  2.541   0.0 % better 
 #> No better bases found after 2 tries.  Giving up.
 #> Final projection: 
-#> -0.232  0.440  0.463  0.660  -0.026  -0.321  
+#> 0.585  0.689  0.190  0.124  -0.318  0.173  
 #> Converting input data to the required matrix format.
+#> Value  2.541   7.5 % better  - NEW BASIS
 #> Value  2.541   0.0 % better 
 #> No better bases found after 2 tries.  Giving up.
 #> Final projection: 
-#> -0.663  -0.017  -0.015  -0.118  -0.549  0.495  
+#> 0.411  -0.201  -0.550  0.145  -0.683  -0.010  
 #> Converting input data to the required matrix format.
-#> Value  2.541   3.4 % better  - NEW BASIS
 #> Value  2.541   0.0 % better 
 #> No better bases found after 2 tries.  Giving up.
 #> Final projection: 
-#> -0.053  -0.615  -0.336  0.624  -0.317  -0.130  
+#> 0.254  0.533  0.631  0.458  -0.168  -0.123  
 # Interpolate between target bases
 itries <- lapply(tries, interpolate)
 
 paths <- paths_index(itries, holes())
 head(paths)
-#>   try step    value improvement
-#> 1   1    1 2.541494  0.00000000
-#> 2   2    1 2.541494  0.00000000
-#> 3   3    1 2.541494  0.00000000
-#> 4   4    1 2.541494  0.00000000
-#> 5   5    1 2.456985  0.00000000
-#> 6   5    2 2.526657  0.06967194
+#>   try step    value  improvement
+#> 1   1    1 2.541494  0.000000000
+#> 2   2    1 2.401972  0.000000000
+#> 3   2    2 2.492944  0.090971575
+#> 4   2    3 2.442931 -0.050012650
+#> 5   2    4 2.434656 -0.008275526
+#> 6   2    5 2.541494  0.106838499
 
 if (require(ggplot2)) {
   ggplot(data = paths, aes(x=step, y=value, group = try)) + geom_line()
diff --git a/docs/reference/planned_tour-1.png b/docs/reference/planned_tour-1.png
index d0aa0f0c..ccffe1f6 100644
Binary files a/docs/reference/planned_tour-1.png and b/docs/reference/planned_tour-1.png differ
diff --git a/docs/reference/planned_tour-3.png b/docs/reference/planned_tour-3.png
index 114e0125..65b54697 100644
Binary files a/docs/reference/planned_tour-3.png and b/docs/reference/planned_tour-3.png differ
diff --git a/docs/reference/radial_tour-1.png b/docs/reference/radial_tour-1.png
index 2be66787..a8922256 100644
Binary files a/docs/reference/radial_tour-1.png and b/docs/reference/radial_tour-1.png differ
diff --git a/docs/reference/radial_tour-2.png b/docs/reference/radial_tour-2.png
index 052b5b51..a3ec2bca 100644
Binary files a/docs/reference/radial_tour-2.png and b/docs/reference/radial_tour-2.png differ
diff --git a/docs/reference/radial_tour-3.png b/docs/reference/radial_tour-3.png
index 698567be..f68b86f4 100644
Binary files a/docs/reference/radial_tour-3.png and b/docs/reference/radial_tour-3.png differ
diff --git a/docs/reference/radial_tour-4.png b/docs/reference/radial_tour-4.png
index 8ccf10aa..27784f0a 100644
Binary files a/docs/reference/radial_tour-4.png and b/docs/reference/radial_tour-4.png differ
diff --git a/docs/reference/radial_tour-5.png b/docs/reference/radial_tour-5.png
index 17581ab0..072f7ffd 100644
Binary files a/docs/reference/radial_tour-5.png and b/docs/reference/radial_tour-5.png differ
diff --git a/docs/reference/radial_tour-6.png b/docs/reference/radial_tour-6.png
index 476cbb8e..32ebfef6 100644
Binary files a/docs/reference/radial_tour-6.png and b/docs/reference/radial_tour-6.png differ
diff --git a/docs/reference/render_proj-1.png b/docs/reference/render_proj-1.png
index a0d873cc..885448ff 100644
Binary files a/docs/reference/render_proj-1.png and b/docs/reference/render_proj-1.png differ
diff --git a/docs/reference/save_history-1.png b/docs/reference/save_history-1.png
index 0bb27bd5..32cf62b0 100644
Binary files a/docs/reference/save_history-1.png and b/docs/reference/save_history-1.png differ
diff --git a/docs/reference/save_history-2.png b/docs/reference/save_history-2.png
index d6b11ac1..c5bd6d56 100644
Binary files a/docs/reference/save_history-2.png and b/docs/reference/save_history-2.png differ
diff --git a/docs/reference/save_history-3.png b/docs/reference/save_history-3.png
index f26c529c..f15e3bec 100644
Binary files a/docs/reference/save_history-3.png and b/docs/reference/save_history-3.png differ
diff --git a/docs/reference/save_history.html b/docs/reference/save_history.html
index 52b596d7..cbb4470f 100644
--- a/docs/reference/save_history.html
+++ b/docs/reference/save_history.html
@@ -141,24 +141,25 @@ 
Examples

 t2 <- save_history(testdata, guided_tour(holes(), max.tries = 10),
   max = 5
 )
-#> Value  0.886   0.8 % better  - NEW BASIS
-#> Value  0.888   0.3 % better  - NEW BASIS
-#> Value  0.889   0.0 % better 
-#> Value  0.889   0.0 % better 
-#> Value  0.889   0.0 % better 
-#> Value  0.889   0.0 % better 
-#> Value  0.889   0.0 % better 
-#> Value  0.889   0.0 % better 
-#> Value  0.889   0.0 % better 
-#> Value  0.889   0.0 % better 
-#> Value  0.889   0.0 % better 
+#> Value  0.902   6.8 % better  - NEW BASIS
+#> Value  0.906   0.4 % better  - NEW BASIS
+#> Value  0.907   0.1 % better  - NEW BASIS
+#> Value  0.908   0.1 % better 
+#> Value  0.907   0.0 % better 
+#> Value  0.907   0.0 % better 
+#> Value  0.908   0.0 % better 
+#> Value  0.907   0.0 % better 
+#> Value  0.907   0.0 % better 
+#> Value  0.907   0.0 % better 
+#> Value  0.907   0.0 % better 
+#> Value  0.907   0.0 % better 
 #> No better bases found after 10 tries.  Giving up.
 #> Final projection: 
-#> -0.805  -0.592  
-#> 0.333  -0.507  
-#> 0.491  -0.627  
+#> -0.677  0.736  
+#> -0.507  -0.483  
+#> 0.533  0.475  
 animate_xy(testdata, planned_tour(t2))
-#> Using half_range 3.5
+#> Using half_range 3.1
 
 
 # Or you can use saved histories to visualise the path that the tour took.
diff --git a/docs/reference/search_better-1.png b/docs/reference/search_better-1.png
index d23f687a..8e9c7d6a 100644
Binary files a/docs/reference/search_better-1.png and b/docs/reference/search_better-1.png differ
diff --git a/docs/reference/search_better.html b/docs/reference/search_better.html
index b7e765bf..1e0f244b 100644
--- a/docs/reference/search_better.html
+++ b/docs/reference/search_better.html
@@ -120,12 +120,12 @@ 
Examples

 #> Old 1.581977 
 #> No better bases found after 25 tries.  Giving up.
 #> Final projection: 
-#> -0.220  -0.443  
-#> 0.450  -0.320  
-#> 0.312  0.613  
-#> -0.435  0.077  
-#> -0.546  -0.191  
-#> 0.405  -0.531  
+#> -0.269  0.767  
+#> 0.064  0.484  
+#> 0.337  0.277  
+#> 0.826  -0.034  
+#> 0.067  0.128  
+#> -0.350  -0.290  
 #> Using half_range 66
diff --git a/docs/reference/search_better_random-1.png b/docs/reference/search_better_random-1.png index 431d14c8..e3615742 100644 Binary files a/docs/reference/search_better_random-1.png and b/docs/reference/search_better_random-1.png differ diff --git a/docs/reference/search_geodesic-1.png b/docs/reference/search_geodesic-1.png index 5638d989..d09d9556 100644 Binary files a/docs/reference/search_geodesic-1.png and b/docs/reference/search_geodesic-1.png differ diff --git a/docs/reference/search_geodesic.html b/docs/reference/search_geodesic.html index 7ded6590..d5e7400e 100644 --- a/docs/reference/search_geodesic.html +++ b/docs/reference/search_geodesic.html @@ -164,12 +164,12 @@

Examples

#> Value 1.582 0.0 % better #> No better bases found after 25 tries. Giving up. #> Final projection: -#> -0.056 -0.746 -#> 0.340 0.332 -#> 0.435 -0.186 -#> 0.742 0.162 -#> 0.369 -0.499 -#> 0.067 -0.152 +#> -0.452 0.123 +#> 0.370 -0.028 +#> 0.571 -0.069 +#> 0.085 -0.932 +#> 0.472 0.311 +#> -0.320 -0.119 #> Using half_range 66 diff --git a/vignettes/edges.Rmd b/vignettes/edges.Rmd index eeff8771..aa2d7a9a 100644 --- a/vignettes/edges.Rmd +++ b/vignettes/edges.Rmd @@ -46,9 +46,14 @@ It can often be useful to connect points with edges, for example sequential poin ```{r} # get centroids of 3 clusters of the flea data -n <- nrow(flea) -flea_centroids <- stats::kmeans((flea[,-7]), 3)$centers -flea_aug <- rbind(flea[,-7], flea_centroids) +f <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x)) +n <- nrow(f) +set.seed(1019) +flea_centroids <- stats::kmeans((f), 3)$centers +flea_aug <- rbind(f, flea_centroids) +col <- c(rep("black", n), rep("orange", 3)) flea_edges <- matrix(c(n+1, n+2, n+1, n+3, n+2, n+3), ncol=2, byrow = TRUE) -animate_xy(flea_aug, edges = flea_edges) +animate_xy(flea_aug, edges = flea_edges, + col = col, edges.col = "orange", + edges.width = 3) ``` diff --git a/vignettes/tourr.Rmd b/vignettes/tourr.Rmd index 68dce5fa..1b01be6c 100644 --- a/vignettes/tourr.Rmd +++ b/vignettes/tourr.Rmd @@ -53,11 +53,13 @@ The most common application is to use a grand tour, which means that the project As we have seen, the default tour type is a grand tour. By selecting the second argument, `tour_path`, in the animate function we can change this, choosing from the tour types that have been implemented in the package. The most relevant options are: -- grand tour: randomly selected bases -- guided tour: basis selection is optimising an index function -- planned tour: interpolates between a set of input bases -- little tour: a planned tour between all axis parallel projections -- local tour: alternating between the starting projection and randomly selected nearby projections +- *grand tour*: randomly selected bases +- *guided tour*: basis selection is optimising an index function +- *planned tour*: interpolates between a set of input bases +- *little tour*: a planned tour between all axis parallel projections +- *local tour*: alternating between the starting projection and randomly selected nearby projections +- *slice tour*: points outside a given orthogonal distance of the projection plane appear smaller. +- *sage tour*: reverse the curse of dimensionalityt piling, in the 2D projection For example, the guided tour can be used to move towards more interesting views of the distribution as the animation progresses. To measure the interestingness of each projection we need to define an index function which will get maximised along the tour path. You can define your own index function, or use one of those available in the `tourr` package. For our example flea data we can use the holes index which is looking for projections with low densities near the center, and can often find views that reveal clustering. @@ -93,9 +95,9 @@ animate(f, ## Display types -The default display is showing a scatterplot of the data projected to 2D. Depending on the number of dimensions we project onto (this is called d), we can choose different display types. For example, we could look at 1D projections in a density display, a 3D projection using depth cues, or higher dimensional projections in a parallel coordinate or scatterplot matrix display. +The default display is showing a scatterplot of the data projected to 2D. Depending on the number of dimensions we project onto (this is called $d$), we can choose different display types. For example, we could look at 1D projections in a density display, a 3D projection using depth cues, or higher dimensional projections in a parallel coordinate or scatterplot matrix display. -When changing the display type via the `display` argument, we need to make sure that the basis generation is matching the corresponding number of dimensions d. We can pass in this information when generating the tour path. To work with 1D projections and a density display, we can launch the animation as +When changing the display type via the `display` argument, we need to make sure that the basis generation is matching the corresponding number of dimensions $d$. We can pass in this information when generating the tour path. To work with 1D projections and a density display, we can launch the animation as ```{r} animate(f,