animate(f,
tour_path = guided_tour(holes()),
display = display_xy(col = flea$species))
-#> Converting input data to the required matrix format.
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> No better bases found after 25 tries. Giving up.
-#> Final projection:
-#> -0.402 -0.321
-#> -0.732 -0.191
-#> -0.244 0.163
-#> -0.392 0.820
-#> -0.183 -0.393
-#> 0.235 0.087
-#> Using half_range 66
+#> Value 1.043 9.5 % better - NEW BASIS
+#> Using half_range 4.4
Alternatively, a colour vector can be created manually and passed
into the guided tour.
@@ -261,40 +195,8 @@ Tour typesanimate(f,
tour_path = guided_tour(holes()),
display = display_xy(col = flea_col))
-#> Converting input data to the required matrix format.
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> No better bases found after 25 tries. Giving up.
-#> Final projection:
-#> 0.039 0.230
-#> -0.061 -0.532
-#> -0.369 -0.398
-#> 0.054 -0.216
-#> 0.919 -0.113
-#> -0.109 0.668
-#> Using half_range 66
+#> Value 1.063 29.9 % better - NEW BASIS
+#> Using half_range 4.4
+#> Using half_range 4.4
but there is also a shortcut available
animate_dist(f)
-#> Converting input data to the required matrix format.
-#> Using half_range 66
+#> Using half_range 4.4
+#> Using half_range 4.4
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 4245ea1d..55e6bd19 100644
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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 199ea675..875307b5 100644
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diff --git a/docs/authors.html b/docs/authors.html
index d33304c2..d8c85432 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/index.html b/docs/index.html
index 253eb6d8..ca288d99 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -42,7 +42,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/news/index.html b/docs/news/index.html
index a7dbe698..d3f48ec6 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -60,6 +60,11 @@ Changelog
Source: NEWS.md
+
+
+
- Small changes in prep for CRAN
+- Time for it to be a full version number
+
- Changed line colours to take a factor, and be handled the same as points.
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index f81b88c0..d8110efe 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
articles:
edges: edges.html
tourr: tourr.html
-last_built: 2023-06-15T01:44Z
+last_built: 2023-06-19T02:21Z
diff --git a/docs/reference/Flea-measurements-1.png b/docs/reference/Flea-measurements-1.png
index 275c5c09..ff92148c 100644
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diff --git a/docs/reference/Flea-measurements-2.png b/docs/reference/Flea-measurements-2.png
index 01ab4c7a..7ddc966b 100644
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diff --git a/docs/reference/Flea-measurements.html b/docs/reference/Flea-measurements.html
index 62122f97..0dcd3514 100644
--- a/docs/reference/Flea-measurements.html
+++ b/docs/reference/Flea-measurements.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/Laser-measurements-1.png b/docs/reference/Laser-measurements-1.png
index c28dae87..c339a482 100644
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diff --git a/docs/reference/Laser-measurements.html b/docs/reference/Laser-measurements.html
index 97b41f2c..55587d5f 100644
--- a/docs/reference/Laser-measurements.html
+++ b/docs/reference/Laser-measurements.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/Olive-oil-measurements-1.png b/docs/reference/Olive-oil-measurements-1.png
index 48b56831..687b6e50 100644
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diff --git a/docs/reference/Olive-oil-measurements-2.png b/docs/reference/Olive-oil-measurements-2.png
index c88b86cb..5fdd15fc 100644
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diff --git a/docs/reference/Olive-oil-measurements.html b/docs/reference/Olive-oil-measurements.html
index 289a26db..766ff7e1 100644
--- a/docs/reference/Olive-oil-measurements.html
+++ b/docs/reference/Olive-oil-measurements.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/Ozone-measurements.html b/docs/reference/Ozone-measurements.html
index 49a68954..94c31ac8 100644
--- a/docs/reference/Ozone-measurements.html
+++ b/docs/reference/Ozone-measurements.html
@@ -22,7 +22,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/Places-Ratings-1.png b/docs/reference/Places-Ratings-1.png
index 7bb93548..6cb48db9 100644
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diff --git a/docs/reference/Places-Ratings.html b/docs/reference/Places-Ratings.html
index 2f17010f..62520caf 100644
--- a/docs/reference/Places-Ratings.html
+++ b/docs/reference/Places-Ratings.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/Rat-CNS-1.png b/docs/reference/Rat-CNS-1.png
index f8e5a85b..cff4707b 100644
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diff --git a/docs/reference/Rat-CNS.html b/docs/reference/Rat-CNS.html
index 1bfbb2b2..10cfa030 100644
--- a/docs/reference/Rat-CNS.html
+++ b/docs/reference/Rat-CNS.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
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index ad962fc0..1fa30ab6 100644
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diff --git a/docs/reference/Tropical-Atmosphere-Ocean.html b/docs/reference/Tropical-Atmosphere-Ocean.html
index 15498805..a25e408d 100644
--- a/docs/reference/Tropical-Atmosphere-Ocean.html
+++ b/docs/reference/Tropical-Atmosphere-Ocean.html
@@ -24,7 +24,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/anaglyph.html b/docs/reference/anaglyph.html
index 83f0d6af..8d0ea794 100644
--- a/docs/reference/anaglyph.html
+++ b/docs/reference/anaglyph.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/anchored_orthogonal_distance.html b/docs/reference/anchored_orthogonal_distance.html
index e9bdc068..0cbc7c35 100644
--- a/docs/reference/anchored_orthogonal_distance.html
+++ b/docs/reference/anchored_orthogonal_distance.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/andrews-2.png b/docs/reference/andrews-2.png
index 0fc64005..2d54ee2c 100644
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diff --git a/docs/reference/andrews.html b/docs/reference/andrews.html
index bc54245b..b684bc9f 100644
--- a/docs/reference/andrews.html
+++ b/docs/reference/andrews.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/angular_breaks.html b/docs/reference/angular_breaks.html
index ba5795a5..9da14f1c 100644
--- a/docs/reference/angular_breaks.html
+++ b/docs/reference/angular_breaks.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/animate-1.png b/docs/reference/animate-1.png
index 72744527..77947508 100644
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diff --git a/docs/reference/animate-2.png b/docs/reference/animate-2.png
index 305951fe..93af5879 100644
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diff --git a/docs/reference/animate-3.png b/docs/reference/animate-3.png
index 95de4db7..14002e8f 100644
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diff --git a/docs/reference/animate-4.png b/docs/reference/animate-4.png
index fb285863..9025009e 100644
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diff --git a/docs/reference/animate.html b/docs/reference/animate.html
index 8e95eb74..f60d20aa 100644
--- a/docs/reference/animate.html
+++ b/docs/reference/animate.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/areColors.html b/docs/reference/areColors.html
index 5c96e00c..e6bac5e0 100644
--- a/docs/reference/areColors.html
+++ b/docs/reference/areColors.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/bases_little.html b/docs/reference/bases_little.html
index c0f0c984..5d3fa203 100644
--- a/docs/reference/bases_little.html
+++ b/docs/reference/bases_little.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/basis_init.html b/docs/reference/basis_init.html
index f3562eb0..3ecba096 100644
--- a/docs/reference/basis_init.html
+++ b/docs/reference/basis_init.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/basis_nearby.html b/docs/reference/basis_nearby.html
index 6f521353..50aef365 100644
--- a/docs/reference/basis_nearby.html
+++ b/docs/reference/basis_nearby.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/basis_random.html b/docs/reference/basis_random.html
index ad354cc4..e0812145 100644
--- a/docs/reference/basis_random.html
+++ b/docs/reference/basis_random.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/blank_plot.html b/docs/reference/blank_plot.html
index acc8d52b..bfc43330 100644
--- a/docs/reference/blank_plot.html
+++ b/docs/reference/blank_plot.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/center.html b/docs/reference/center.html
index 24f0af85..226b372e 100644
--- a/docs/reference/center.html
+++ b/docs/reference/center.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/check_freezer_safe.html b/docs/reference/check_freezer_safe.html
index c9d25e8d..09e2dc33 100644
--- a/docs/reference/check_freezer_safe.html
+++ b/docs/reference/check_freezer_safe.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/cmass.html b/docs/reference/cmass.html
index 4604bfd9..828ac50e 100644
--- a/docs/reference/cmass.html
+++ b/docs/reference/cmass.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/compute_v_rel.html b/docs/reference/compute_v_rel.html
index 814c329d..f5eaf62c 100644
--- a/docs/reference/compute_v_rel.html
+++ b/docs/reference/compute_v_rel.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/correct_orientation.html b/docs/reference/correct_orientation.html
index 6bba22a5..a5a0b8d5 100644
--- a/docs/reference/correct_orientation.html
+++ b/docs/reference/correct_orientation.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/cumulative_radial.html b/docs/reference/cumulative_radial.html
index 5e7cb769..d81f4d65 100644
--- a/docs/reference/cumulative_radial.html
+++ b/docs/reference/cumulative_radial.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/dcor2d.html b/docs/reference/dcor2d.html
index 1b931945..5d8bf837 100644
--- a/docs/reference/dcor2d.html
+++ b/docs/reference/dcor2d.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/dependence_tour-1.png b/docs/reference/dependence_tour-1.png
index 77238473..caefb52a 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 ac27b15c..6f781652 100644
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diff --git a/docs/reference/dependence_tour-3.png b/docs/reference/dependence_tour-3.png
index d03fe2d7..8b1be71f 100644
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diff --git a/docs/reference/dependence_tour.html b/docs/reference/dependence_tour.html
index 701fa825..fe339334 100644
--- a/docs/reference/dependence_tour.html
+++ b/docs/reference/dependence_tour.html
@@ -21,7 +21,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/display_andrews-11.png b/docs/reference/display_andrews-11.png
index e8028654..35afe579 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 e8028654..35afe579 100644
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diff --git a/docs/reference/display_andrews-3.png b/docs/reference/display_andrews-3.png
index 1c81c1f9..d84255ac 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 01a3e5bc..00ec5f12 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 0d7519d2..a250d900 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 8a726ecb..5c769937 100644
--- a/docs/reference/display_andrews.html
+++ b/docs/reference/display_andrews.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -68,7 +68,7 @@ Andrews' curves tour path animation.
-
display_andrews(col = "black", ...)
+ display_andrews(col = "black", palette = "Zissou 1", ...)
animate_andrews(data, tour_path = grand_tour(3), col = "black", ...)
@@ -79,6 +79,10 @@
Arguments
color to be plotted. Defaults to "black"
+
palette
+
name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
+
+
...
other arguments passed on to animate
@@ -124,31 +128,31 @@
Examples
#> Value -0.582 -0.0 % better
#> Value -0.582 -0.0 % better
#> Value -0.582 -0.0 % better
-
#> Value -0.565 -2.9 % 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 -0.577 -0.9 % better
#> Value -0.582 -0.0 % better
#> Value -0.582 -0.0 % better
-
#> Value -0.574 -1.3 % 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
#> No better bases found after 25 tries. Giving up.
#> Final projection:
-
#> 0.151 -0.594
-
#> -0.600 -0.344
-
#> -0.104 0.395
-
#> -0.039 0.573
-
#> 0.489 -0.198
-
#> -0.605 -0.071
+
#> 0.233 0.669
+
#> -0.044 -0.027
+
#> -0.313 -0.146
+
#> 0.088 0.597
+
#> 0.750 -0.049
+
#> -0.525 0.415
diff --git a/docs/reference/display_density2d-11.png b/docs/reference/display_density2d-11.png
index 5918582f..5507e0e1 100644
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index 31eeb124..57489cd9 100644
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diff --git a/docs/reference/display_density2d-13.png b/docs/reference/display_density2d-13.png
index 0d6f0e44..5bb0804e 100644
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diff --git a/docs/reference/display_density2d-14.png b/docs/reference/display_density2d-14.png
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diff --git a/docs/reference/display_density2d-15.png b/docs/reference/display_density2d-15.png
index 3de7b319..742380ae 100644
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diff --git a/docs/reference/display_density2d-16.png b/docs/reference/display_density2d-16.png
index d85e7c26..f6a60823 100644
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index ba24557c..df824bf5 100644
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diff --git a/docs/reference/display_density2d-18.png b/docs/reference/display_density2d-18.png
index 58d3f111..2b55a9c0 100644
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diff --git a/docs/reference/display_density2d-2.png b/docs/reference/display_density2d-2.png
index 859d4aac..7e4ba505 100644
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diff --git a/docs/reference/display_density2d-21.png b/docs/reference/display_density2d-21.png
index cad879d5..be8b4fde 100644
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diff --git a/docs/reference/display_density2d-24.png b/docs/reference/display_density2d-24.png
index 8ef36eec..7f0e147a 100644
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index d00e3077..ac1bd55b 100644
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diff --git a/docs/reference/display_density2d-3.png b/docs/reference/display_density2d-3.png
index 0eaff62b..0ea0f8ea 100644
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diff --git a/docs/reference/display_density2d-30.png b/docs/reference/display_density2d-30.png
index 6df662bd..af24c9eb 100644
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diff --git a/docs/reference/display_density2d-31.png b/docs/reference/display_density2d-31.png
index 7925ee51..22aeecd0 100644
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diff --git a/docs/reference/display_density2d-34.png b/docs/reference/display_density2d-34.png
index 41c5a577..0322a0e9 100644
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diff --git a/docs/reference/display_density2d-5.png b/docs/reference/display_density2d-5.png
index b230af5e..07dd9e42 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 9efc9062..f4c6ab8f 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 347cb33e..571f5ef6 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 484e281d..0a9294a0 100644
--- a/docs/reference/display_density2d.html
+++ b/docs/reference/display_density2d.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -120,7 +120,7 @@ Arguments
palette
-name of color palette for point colour, used by grDevices::hcl.colors
, default "Zissou 1"
+name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
...
@@ -203,9 +203,9 @@ Examples
#> Value 1.582 0.0 % better
#> No better bases found after 25 tries. Giving up.
#> Final projection:
-#> -0.871 0.427
-#> -0.473 -0.863
-#> -0.133 0.270
+#> 0.199 0.601
+#> -0.828 -0.320
+#> 0.525 -0.732
#> Using half_range 65
diff --git a/docs/reference/display_depth-1.png b/docs/reference/display_depth-1.png
index c2e47f14..f88c9a00 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_depth.html b/docs/reference/display_depth.html
index bb84d8de..ae09a759 100644
--- a/docs/reference/display_depth.html
+++ b/docs/reference/display_depth.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/display_dist-10.png b/docs/reference/display_dist-10.png
index 1d59dc5e..111962b5 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 7ce68f4e..1119c334 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 54bfca47..97b3b83f 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 c514278a..c73fe589 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 3d1f0989..0bf8b380 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 af24e107..8688385a 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_dist.html b/docs/reference/display_dist.html
index e90062a6..6709861f 100644
--- a/docs/reference/display_dist.html
+++ b/docs/reference/display_dist.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -108,7 +108,7 @@ Arguments
palette
-name of color palette for point colour, used by grDevices::hcl.colors
, default "Zissou 1"
+name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
density_max
diff --git a/docs/reference/display_faces-1.png b/docs/reference/display_faces-1.png
index be9f68bc..9b8ac731 100644
Binary files a/docs/reference/display_faces-1.png and b/docs/reference/display_faces-1.png differ
diff --git a/docs/reference/display_faces-2.png b/docs/reference/display_faces-2.png
index c82c68e8..209642be 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-3.png b/docs/reference/display_faces-3.png
index aea1486f..5eda4054 100644
Binary files a/docs/reference/display_faces-3.png and b/docs/reference/display_faces-3.png differ
diff --git a/docs/reference/display_faces-4.png b/docs/reference/display_faces-4.png
index 7daa2306..fd785193 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-5.png b/docs/reference/display_faces-5.png
index 6bd67cf3..691a464e 100644
Binary files a/docs/reference/display_faces-5.png and b/docs/reference/display_faces-5.png differ
diff --git a/docs/reference/display_faces-6.png b/docs/reference/display_faces-6.png
index ac3fb082..5bfa37c5 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_faces.html b/docs/reference/display_faces.html
index f322c1a9..65dd61cc 100644
--- a/docs/reference/display_faces.html
+++ b/docs/reference/display_faces.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -101,25 +101,17 @@ See also
Examples
# The drawing code is fairly slow, so this animation works best with a
# limited number of cases
-animate_faces(flea[1:2, 1:6])
-#> Converting input data to the required matrix format.
-#> Warning: NaNs produced
+flea_s <- rescale(flea[,1:6])
+animate_faces(flea_s[1:2, 1:6])
-#> Warning: NaNs produced
-#> Error in 1:(k - 1): NA/NaN argument
-animate_faces(flea[1:4, 1:6])
-#> Converting input data to the required matrix format.
-#> Warning: NaNs produced
-#> Warning: NaNs produced
-#> Error in 1:(k - 1): NA/NaN argument
+animate_faces(flea_s[1:4, 1:6])
-
-animate_faces(flea[1:2, 1:6], grand_tour(5))
-#> Converting input data to the required matrix format.
-#> Warning: NaNs produced
-#> Error in 1:(k - 1): NA/NaN argument
+
+animate_faces(flea_s[1:2, 1:6], grand_tour(5))
+
+
diff --git a/docs/reference/display_groupxy-1.png b/docs/reference/display_groupxy-1.png
index 74ee8d4e..f57c05d9 100644
Binary files a/docs/reference/display_groupxy-1.png and b/docs/reference/display_groupxy-1.png differ
diff --git a/docs/reference/display_groupxy-2.png b/docs/reference/display_groupxy-2.png
index eb39a168..7432d0b6 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-3.png b/docs/reference/display_groupxy-3.png
index 4fd08826..e0c865ae 100644
Binary files a/docs/reference/display_groupxy-3.png and b/docs/reference/display_groupxy-3.png differ
diff --git a/docs/reference/display_groupxy-4.png b/docs/reference/display_groupxy-4.png
index 3c0b0f07..b29fa161 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_groupxy.html b/docs/reference/display_groupxy.html
index c6b6b7c2..52cb4a47 100644
--- a/docs/reference/display_groupxy.html
+++ b/docs/reference/display_groupxy.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -80,6 +80,8 @@ Display 2D tour projections displayed separately by groups
pch = 20,
cex = 1,
edges = NULL,
+ edges.col = "black",
+ edges.width = 1,
group_by = NULL,
plot_xgp = TRUE,
palette = "Zissou 1",
@@ -122,6 +124,14 @@ Arguments
A two column integer matrix giving indices of ends of lines.
+edges.col
+colour of edges to be plotted, Defaults to "black"
+
+
+edges.width
+line width for edges, default 1
+
+
group_by
variable to group by. Must have less than 25 unique values.
@@ -131,7 +141,7 @@ Arguments
palette
-name of color palette for point colour, used by grDevices::hcl.colors
, default "Zissou 1"
+name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
...
@@ -150,16 +160,25 @@ Arguments
Examples
-
f <- flea[, 1:6]
-col <- rainbow(length(unique(flea$species)))[as.numeric(as.factor(flea$species))]
-pch <- as.numeric(flea$species) + 14
-
-animate_groupxy(f, col = col, pch = pch, group_by = flea$species)
+ animate_groupxy(flea[, 1:6], col = flea$species,
+ pch = flea$species, group_by = flea$species)
#> Converting input data to the required matrix format.
-#> Error in is.factor(edges.col): object 'edges.col' not found
-animate_groupxy(f, col = col, pch = pch, group_by = flea$species, plot_xgp = FALSE)
+#> Using half_range 66
+#> Warning: "shapes" is not a graphical parameter
+#> Warning: "shapes" is not a graphical parameter
+#> Warning: "shapes" is not a graphical parameter
+
+#> Warning: "shapes" is not a graphical parameter
+#> Warning: "shapes" is not a graphical parameter
+#> Warning: "shapes" is not a graphical parameter
+
+animate_groupxy(flea[, 1:6], col = flea$species,
+ pch = flea$species, group_by = flea$species,
+ plot_xgp = FALSE)
#> Converting input data to the required matrix format.
-#> Error in is.factor(edges.col): object 'edges.col' not found
+#> Using half_range 66
+
+
diff --git a/docs/reference/display_image.html b/docs/reference/display_image.html
index a1675618..eac87f58 100644
--- a/docs/reference/display_image.html
+++ b/docs/reference/display_image.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/display_pca-1.png b/docs/reference/display_pca-1.png
index d9e31527..40306e7d 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_pca.html b/docs/reference/display_pca.html
index 0c874f00..a5bf9ce6 100644
--- a/docs/reference/display_pca.html
+++ b/docs/reference/display_pca.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -128,7 +128,7 @@ Arguments
palette
-name of color palette for point colour, used by grDevices::hcl.colors
, default "Zissou 1"
+name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
...
@@ -151,7 +151,7 @@ Arguments
Examples
-
flea_std <- scale(flea[, 1:6])
+ flea_std <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
flea_pca <- prcomp(flea_std, center = FALSE, )
flea_coefs <- flea_pca$rotation[, 1:3]
flea_scores <- flea_pca$x[, 1:3]
diff --git a/docs/reference/display_pcp-1.png b/docs/reference/display_pcp-1.png
index b4f7ff53..2d67d937 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 285585c6..d00d3fba 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_pcp.html b/docs/reference/display_pcp.html
index 4e23634b..2876b482 100644
--- a/docs/reference/display_pcp.html
+++ b/docs/reference/display_pcp.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/display_sage-1.png b/docs/reference/display_sage-1.png
index 1ca97c3f..262a005d 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 7df50458..bea80eff 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_sage.html b/docs/reference/display_sage.html
index 2f2e0ba9..18541919 100644
--- a/docs/reference/display_sage.html
+++ b/docs/reference/display_sage.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -113,7 +113,7 @@
Arguments
palette
-
name of color palette for point colour, used by grDevices::hcl.colors
, default "Zissou 1"
+
name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
...
diff --git a/docs/reference/display_scatmat-2.png b/docs/reference/display_scatmat-2.png
index 9817e86b..11e4cbfb 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 aacc3dac..b00f110e 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_scatmat.html b/docs/reference/display_scatmat.html
index fad672c1..c9a4c665 100644
--- a/docs/reference/display_scatmat.html
+++ b/docs/reference/display_scatmat.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/display_slice-1.png b/docs/reference/display_slice-1.png
index a765b4d6..f1422106 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 64535465..e655b477 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 0155bea8..0c3eda8b 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 934bc93c..ce90c807 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 5eec6580..7703332a 100644
--- a/docs/reference/display_slice.html
+++ b/docs/reference/display_slice.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -149,7 +149,7 @@ Arguments
palette
-name of color palette for point colour, used by grDevices::hcl.colors
, default "Zissou 1"
+name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
...
diff --git a/docs/reference/display_stars-2.png b/docs/reference/display_stars-2.png
index aa7ab7da..79d452a5 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 3673e497..ae40e169 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 c7f14b85..d18c56a5 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 4211dc47..4c8a83c5 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_stars.html b/docs/reference/display_stars.html
index 7e2ac1d2..4308f586 100644
--- a/docs/reference/display_stars.html
+++ b/docs/reference/display_stars.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/display_stereo-3.png b/docs/reference/display_stereo-3.png
index f924cb75..ccaa9b3e 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_stereo.html b/docs/reference/display_stereo.html
index 0f30c180..d7b7669b 100644
--- a/docs/reference/display_stereo.html
+++ b/docs/reference/display_stereo.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/display_trails-1.png b/docs/reference/display_trails-1.png
new file mode 100644
index 00000000..50eaad59
Binary files /dev/null and b/docs/reference/display_trails-1.png differ
diff --git a/docs/reference/display_trails.html b/docs/reference/display_trails.html
index baba05e2..3789a483 100644
--- a/docs/reference/display_trails.html
+++ b/docs/reference/display_trails.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -128,6 +128,15 @@ Arguments
+
+
Examples
+
animate_trails(flea[,1:6], col=flea$species)
+#> Converting input data to the required matrix format.
+#> Using half_range 66
+
+
+
+
@@ -130,7 +130,7 @@ Arguments
palette
-name of color palette for point colour, used by grDevices::hcl.colors
, default "Zissou 1"
+name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
...
@@ -159,7 +159,8 @@ Examples
animate(flea[, 1:6],
tour_path = grand_tour(),
- display = display_xy(axes = "bottomleft")
+ display = display_xy(),
+ scale = TRUE
)
#> Converting input data to the required matrix format.
#> Using half_range 66
@@ -176,7 +177,7 @@ Examples
animate_xy(flea[, 1:3], tour_path = guided_tour(holes()), sphere = TRUE)
#> Converting input data to the required matrix format.
-#> Value 0.869 1.5 % better - NEW BASIS
+#> Value 0.858 4.2 % better - NEW BASIS
#> Using half_range 3.2
animate_xy(flea[, 1:6], center = FALSE)
@@ -205,7 +206,7 @@ Examples
#> Using half_range 66
animate_xy(flea[, -7], col = flea$species,
- pch = as.numeric(flea$species))
+ pch = flea$species)
#> Converting input data to the required matrix format.
#> Using half_range 66
diff --git a/docs/reference/draw_slice_center.html b/docs/reference/draw_slice_center.html
index 97a15f16..894a3df3 100644
--- a/docs/reference/draw_slice_center.html
+++ b/docs/reference/draw_slice_center.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/draw_tour_axes-1.png b/docs/reference/draw_tour_axes-1.png
index 9af8fbf5..4f54e75c 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 4b2388f9..ddbb3dba 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/draw_tour_axes.html b/docs/reference/draw_tour_axes.html
index 2369448f..2955301c 100644
--- a/docs/reference/draw_tour_axes.html
+++ b/docs/reference/draw_tour_axes.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/estimate_eps.html b/docs/reference/estimate_eps.html
index 3accf3a2..e9f9eae9 100644
--- a/docs/reference/estimate_eps.html
+++ b/docs/reference/estimate_eps.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/eucl_norm_sq.html b/docs/reference/eucl_norm_sq.html
index 843afa30..5d22232d 100644
--- a/docs/reference/eucl_norm_sq.html
+++ b/docs/reference/eucl_norm_sq.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/find_best_dir.html b/docs/reference/find_best_dir.html
index 93e39406..857af837 100644
--- a/docs/reference/find_best_dir.html
+++ b/docs/reference/find_best_dir.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/find_best_frozen_dir.html b/docs/reference/find_best_frozen_dir.html
index 4c02bd57..330bfbab 100644
--- a/docs/reference/find_best_frozen_dir.html
+++ b/docs/reference/find_best_frozen_dir.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/find_frozen_path_peak.html b/docs/reference/find_frozen_path_peak.html
index b87693ad..a731cf11 100644
--- a/docs/reference/find_frozen_path_peak.html
+++ b/docs/reference/find_frozen_path_peak.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/find_path_peak.html b/docs/reference/find_path_peak.html
index d9434d7a..47c282f3 100644
--- a/docs/reference/find_path_peak.html
+++ b/docs/reference/find_path_peak.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/find_platform.html b/docs/reference/find_platform.html
index bb9a660c..77462c21 100644
--- a/docs/reference/find_platform.html
+++ b/docs/reference/find_platform.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/freeze.html b/docs/reference/freeze.html
index 45f43f64..a1a0ab75 100644
--- a/docs/reference/freeze.html
+++ b/docs/reference/freeze.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -89,23 +89,23 @@ Examples
input <- basis_random(4, 2)
freeze(input, frozen)
-#> [,1] [,2]
-#> [1,] 0.2013621 0.92760715
-#> [2,] -0.6285967 0.31497121
-#> [3,] 0.0000000 0.00000000
-#> [4,] -0.7501527 -0.02552751
+#> [,1] [,2]
+#> [1,] 0.1805913 0.5180353
+#> [2,] 0.1388004 -0.2229295
+#> [3,] 0.0000000 0.0000000
+#> [4,] -0.8236207 -0.3847669
thaw(input, frozen)
-#> [,1] [,2]
-#> [1,] 0.1743847 0.80333136
-#> [2,] -0.5443807 0.27277307
-#> [3,] 0.5000000 0.50000000
-#> [4,] -0.6496513 -0.02210747
+#> [,1] [,2]
+#> [1,] 0.1563966 0.4486317
+#> [2,] 0.1202047 -0.1930626
+#> [3,] 0.5000000 0.5000000
+#> [4,] -0.7132764 -0.3332179
freeze(basis_random(4, 2), frozen)
-#> [,1] [,2]
-#> [1,] 0.8050244 -0.08426066
-#> [2,] 0.5089694 -0.27067294
-#> [3,] 0.0000000 0.00000000
-#> [4,] -0.2805265 -0.88733492
+#> [,1] [,2]
+#> [1,] 0.01420098 0.75484763
+#> [2,] 0.13410974 -0.52329523
+#> [3,] 0.00000000 0.00000000
+#> [4,] -0.95820572 0.04149124
diff --git a/docs/reference/frozen_guided_tour.html b/docs/reference/frozen_guided_tour.html
index fdf6aae6..afc1a5d3 100644
--- a/docs/reference/frozen_guided_tour.html
+++ b/docs/reference/frozen_guided_tour.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/frozen_tour-1.png b/docs/reference/frozen_tour-1.png
index 8d530cbf..fb39abab 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 05b91344..42b65cc6 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 91f2b6d3..cf3fc9d6 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 ca1bb02c..9f1e5bf6 100644
Binary files a/docs/reference/frozen_tour-4.png and b/docs/reference/frozen_tour-4.png differ
diff --git a/docs/reference/frozen_tour.html b/docs/reference/frozen_tour.html
index 00e55bab..042d1493 100644
--- a/docs/reference/frozen_tour.html
+++ b/docs/reference/frozen_tour.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/geodesic_info.html b/docs/reference/geodesic_info.html
index 8ce28931..a696f9d9 100644
--- a/docs/reference/geodesic_info.html
+++ b/docs/reference/geodesic_info.html
@@ -23,7 +23,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/geodesic_path.html b/docs/reference/geodesic_path.html
index 75de3e37..86432f21 100644
--- a/docs/reference/geodesic_path.html
+++ b/docs/reference/geodesic_path.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -121,12 +121,12 @@ Examples
path <- geodesic_path(a, b)
path$dist
-#> [1] 1.881076
+#> [1] 1.202971
all.equal(a, path$interpolate(0))
#> [1] TRUE
# Not true generally - a rotated into plane of b
all.equal(b, path$interpolate(1))
-#> [1] "Mean relative difference: 1.105405"
+#> [1] "Mean relative difference: 1.179555"
diff --git a/docs/reference/grand_tour-1.png b/docs/reference/grand_tour-1.png
index b10a35a3..60321b02 100644
Binary files a/docs/reference/grand_tour-1.png and b/docs/reference/grand_tour-1.png differ
diff --git a/docs/reference/grand_tour-2.png b/docs/reference/grand_tour-2.png
index e0de05f8..6ab59187 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 3643280e..3788506c 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 668bd714..20838bfa 100644
Binary files a/docs/reference/grand_tour-4.png and b/docs/reference/grand_tour-4.png differ
diff --git a/docs/reference/grand_tour.html b/docs/reference/grand_tour.html
index fb2c35c3..e1747d9b 100644
--- a/docs/reference/grand_tour.html
+++ b/docs/reference/grand_tour.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/guided_section_tour.html b/docs/reference/guided_section_tour.html
index 60d13348..27cb5549 100644
--- a/docs/reference/guided_section_tour.html
+++ b/docs/reference/guided_section_tour.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/guided_tour-1.png b/docs/reference/guided_tour-1.png
index 1afd64ff..0670a267 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 00e689a7..32623544 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 2a52934f..c55616bd 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 b37d2a44..322dc0f1 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 bd9ea111..0933792c 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 5f1adf1b..c1b7fcaf 100644
--- a/docs/reference/guided_tour.html
+++ b/docs/reference/guided_tour.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -142,185 +142,187 @@ See also
Examples
-
animate_xy(flea[, 1:6], guided_tour(holes()), sphere = TRUE)
-#> Converting input data to the required matrix format.
-#> Value 0.811 2.7 % better - NEW BASIS
+ 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
#> Using half_range 3.8
# \donttest{
-animate_xy(flea[, 1:6], guided_tour(holes(), search_f = search_better_random), sphere = TRUE)
-#> Converting input data to the required matrix format.
-#> Old 0.8061676
-#> New 0.8021759 try 1
-#> Accept with probability, prob = 0.7582966
+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
#> Using half_range 3.8
-animate_dist(flea[, 1:6], guided_tour(holes(), 1), sphere = TRUE)
-#> Converting input data to the required matrix format.
-#> Value 0.752 9.7 % better - NEW BASIS
+animate_dist(flea_std, guided_tour(holes(), 1), sphere = TRUE)
+#> Value 0.736 3.4 % better - NEW BASIS
#> Using half_range 3.8
-animate_xy(flea[, 1:6], guided_tour(lda_pp(flea$species)), sphere = TRUE, col = flea$species)
-#> Converting input data to the required matrix format.
-#> Value 0.889 11.9 % better - NEW BASIS
+animate_xy(flea_std, guided_tour(lda_pp(flea$species)), sphere = TRUE, col = flea$species)
+#> Value 0.962 6.4 % better - NEW BASIS
#> Using half_range 3.8
# save_history is particularly useful in conjunction with the
# guided tour as it allows us to look at the tour path in many different
# ways
-f <- flea[, 1:3]
+f <- flea_std[, 1:3]
tries <- replicate(5, save_history(f, guided_tour(holes())), simplify = FALSE)
-#> Converting input data to the required matrix format.
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
+#> Value 0.967 5.0 % better - NEW BASIS
+#> Value 0.972 0.6 % 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:
-#> -0.834 0.161
-#> 0.512 0.580
-#> 0.204 -0.799
-#> Converting input data to the required matrix format.
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
+#> -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
+#> 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:
-#> -0.724 -0.026
-#> -0.676 0.221
-#> 0.134 0.975
-#> Converting input data to the required matrix format.
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
+#> 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
+#> 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:
-#> 0.171 -0.959
-#> 0.738 -0.026
-#> 0.653 0.281
-#> Converting input data to the required matrix format.
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
+#> -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
+#> 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:
-#> -0.284 -0.932
-#> -0.811 0.108
-#> 0.512 -0.346
-#> Converting input data to the required matrix format.
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
-#> Value 1.582 0.0 % better
+#> -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
#> No better bases found after 25 tries. Giving up.
#> Final projection:
-#> 0.308 -0.032
-#> -0.539 0.818
-#> 0.784 0.574
+#> -0.743 -0.649
+#> 0.409 -0.632
+#> 0.530 -0.423
# }
diff --git a/docs/reference/holes.html b/docs/reference/holes.html
index e0858d07..b9db9e3e 100644
--- a/docs/reference/holes.html
+++ b/docs/reference/holes.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/index.html b/docs/reference/index.html
index e374cb57..f003b833 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/interpolate.html b/docs/reference/interpolate.html
index d62f9002..8859fc3f 100644
--- a/docs/reference/interpolate.html
+++ b/docs/reference/interpolate.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -93,11 +93,11 @@ Examples
dim(t1)
#> [1] 6 1 10
dim(interpolate(t1, 0.01))
-#> [1] 6 1 1117
+#> [1] 6 1 1155
dim(interpolate(t1, 0.05))
-#> [1] 6 1 228
+#> [1] 6 1 237
dim(interpolate(t1, 0.1))
-#> [1] 6 1 117
+#> [1] 6 1 120
diff --git a/docs/reference/is_orthonormal.html b/docs/reference/is_orthonormal.html
index fafeb16e..0c6367b1 100644
--- a/docs/reference/is_orthonormal.html
+++ b/docs/reference/is_orthonormal.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/lda_pp.html b/docs/reference/lda_pp.html
index 302bdef1..40edeff6 100644
--- a/docs/reference/lda_pp.html
+++ b/docs/reference/lda_pp.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/linear_breaks.html b/docs/reference/linear_breaks.html
index 3120f6f7..17cbae21 100644
--- a/docs/reference/linear_breaks.html
+++ b/docs/reference/linear_breaks.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/little_tour-1.png b/docs/reference/little_tour-1.png
index fe16a902..1c1f2bbf 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 fd49d5ef..6cdbbd27 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 09f114d2..dbd43158 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 ff2cc298..093a5641 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 3472300e..9af2126e 100644
Binary files a/docs/reference/little_tour-5.png and b/docs/reference/little_tour-5.png differ
diff --git a/docs/reference/little_tour.html b/docs/reference/little_tour.html
index 5014c8a8..a9832bba 100644
--- a/docs/reference/little_tour.html
+++ b/docs/reference/little_tour.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/local_tour-1.png b/docs/reference/local_tour-1.png
index e6d9d885..abc97b84 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 5177179d..81d8e5ec 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 19232c6b..d1949d9b 100644
Binary files a/docs/reference/local_tour-3.png and b/docs/reference/local_tour-3.png differ
diff --git a/docs/reference/local_tour.html b/docs/reference/local_tour.html
index ca35f55c..46253a01 100644
--- a/docs/reference/local_tour.html
+++ b/docs/reference/local_tour.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/manual_slice-1.png b/docs/reference/manual_slice-1.png
index d9a58877..47796c07 100644
Binary files a/docs/reference/manual_slice-1.png and b/docs/reference/manual_slice-1.png differ
diff --git a/docs/reference/manual_slice.html b/docs/reference/manual_slice.html
index 155ac489..e33f1f46 100644
--- a/docs/reference/manual_slice.html
+++ b/docs/reference/manual_slice.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -129,7 +129,7 @@ Arguments
palette
-name of color palette for point colour, used by grDevices::hcl.colors
, default "Zissou 1"
+name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
...
diff --git a/docs/reference/mapColors.html b/docs/reference/mapColors.html
index 5aafefae..42c756e4 100644
--- a/docs/reference/mapColors.html
+++ b/docs/reference/mapColors.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -76,7 +76,7 @@ Arguments
palette
-name of color palette for point colour, used by grDevices::hcl.colors
, default "Zissou 1"
+name of color palette for point colour, used by hcl.colors
, default "Zissou 1"
diff --git a/docs/reference/mapShapes.html b/docs/reference/mapShapes.html
index c5f96c84..a3b77eb8 100644
--- a/docs/reference/mapShapes.html
+++ b/docs/reference/mapShapes.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/new_geodesic_path.html b/docs/reference/new_geodesic_path.html
index 4a7a32d4..585d19fa 100644
--- a/docs/reference/new_geodesic_path.html
+++ b/docs/reference/new_geodesic_path.html
@@ -21,7 +21,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/new_tour.html b/docs/reference/new_tour.html
index 53e4addc..aebe8a0f 100644
--- a/docs/reference/new_tour.html
+++ b/docs/reference/new_tour.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/norm_bin.html b/docs/reference/norm_bin.html
index 0eb154c9..d49c8e33 100644
--- a/docs/reference/norm_bin.html
+++ b/docs/reference/norm_bin.html
@@ -21,7 +21,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/normalise.html b/docs/reference/normalise.html
index 880358ad..24843ee0 100644
--- a/docs/reference/normalise.html
+++ b/docs/reference/normalise.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/orthonormalise.html b/docs/reference/orthonormalise.html
index 4ee59fb1..29bb8d41 100644
--- a/docs/reference/orthonormalise.html
+++ b/docs/reference/orthonormalise.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/orthonormalise_by.html b/docs/reference/orthonormalise_by.html
index a4c8b7af..632858af 100644
--- a/docs/reference/orthonormalise_by.html
+++ b/docs/reference/orthonormalise_by.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/path_curves.html b/docs/reference/path_curves.html
index e2c9baa1..d871fd8e 100644
--- a/docs/reference/path_curves.html
+++ b/docs/reference/path_curves.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/path_dist.html b/docs/reference/path_dist.html
index 455f4de8..71208415 100644
--- a/docs/reference/path_dist.html
+++ b/docs/reference/path_dist.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -80,8 +80,8 @@ Arguments
Examples
# This code is to be used as an example but you should increase
# the max from 2 to 50, say, to check tour coverage.
-grand <- interpolate(save_history(flea[, 1:6], max = 2), 0.2)
-#> Converting input data to the required matrix format.
+flea_std <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
+grand <- interpolate(save_history(flea_std, max = 2), 0.2)
# The grand tour -----------------------------
# Look at the tour path in a tour, how well does it cover a sphere
# Using MDS to summarise the high-d space of projections
@@ -100,149 +100,14 @@ Examples
# Compare five guided tours -----------------------------
holes1d <- guided_tour(holes(), 1)
-tour_reps <- replicate(5, save_history(flea[, 1:6], holes1d, max = 2),
+tour_reps <- replicate(5, save_history(flea_std, holes1d, max = 2),
simplify = FALSE
)
-#> Converting input data to the required matrix format.
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> No better bases found after 25 tries. Giving up.
-#> Final projection:
-#> -0.240 -0.125 0.901 -0.318 0.115 0.038
-#> Converting input data to the required matrix format.
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> No better bases found after 25 tries. Giving up.
-#> Final projection:
-#> 0.701 -0.013 0.244 -0.042 0.441 -0.502
-#> Converting input data to the required matrix format.
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> No better bases found after 25 tries. Giving up.
-#> Final projection:
-#> -0.844 0.436 0.102 0.110 -0.023 -0.272
-#> Converting input data to the required matrix format.
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> No better bases found after 25 tries. Giving up.
-#> Final projection:
-#> 0.142 -0.126 0.021 0.281 -0.529 0.777
-#> Converting input data to the required matrix format.
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> Value 2.541 0.0 % better
-#> No better bases found after 25 tries. Giving up.
-#> Final projection:
-#> -0.512 -0.683 0.019 0.203 -0.239 -0.417
+#> Value 1.175 161.5 % better - NEW BASIS
+#> Value 1.256 124.2 % better - NEW BASIS
+#> Value 1.099 161.1 % better - NEW BASIS
+#> Value 1.191 8.7 % better - NEW BASIS
+#> Value 0.969 72.9 % better - NEW BASIS
tour_reps2 <- lapply(tour_reps, interpolate, 0.2)
bases <- unlist(lapply(tour_reps2, as.list), recursive = FALSE)
@@ -253,15 +118,8 @@ Examples
ord <- as.data.frame(cmdscale(d, 2))
info <- cbind(ord, index_values)
-if (require("ggplot2")) {
- ggplot(data = info, aes(x = step, y = value, group = try)) +
- geom_line()
- ##ggplot(data = info, aes(x = V1, y = V2, group = try)) +
- ## geom_path() +
- ## geom_point(aes(size = value)) +
- ## coord_equal()
- ##last_plot() + facet_wrap(~try)
-}
+ggplot(data = info, aes(x = step, y = value, group = try)) +
+ geom_line()
#> Don't know how to automatically pick scale for object of type <function>.
#> Defaulting to continuous.
#> Error in geom_line(): Problem while computing aesthetics.
@@ -271,6 +129,11 @@ Examples
#> ✖ The following aesthetics are invalid:
#> ✖ `x = step`
#> ℹ Did you mistype the name of a data column or forget to add `after_stat()`?
+##ggplot(data = info, aes(x = V1, y = V2, group = try)) +
+## geom_path() +
+## geom_point(aes(size = value)) +
+## coord_equal()
+##last_plot() + facet_wrap(~try)
diff --git a/docs/reference/path_index-1.png b/docs/reference/path_index-1.png
index df91c494..5def7766 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 62c9da38..15d364c5 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 696cd608..c44d658d 100644
--- a/docs/reference/path_index.html
+++ b/docs/reference/path_index.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -93,87 +93,92 @@ See also
Examples
fl_holes <- save_history(flea[, 1:6], guided_tour(holes()), sphere = TRUE)
#> Converting input data to the required matrix format.
-#> Value 0.817 6.0 % better - NEW BASIS
-#> Value 0.853 4.4 % better - NEW BASIS
-#> Value 0.862 1.0 % better - NEW BASIS
-#> Value 0.862 0.1 % better
-#> Value 0.863 0.2 % better - NEW BASIS
-#> Value 0.866 0.4 % better - NEW BASIS
-#> Value 0.867 0.1 % better - NEW BASIS
-#> Value 0.869 0.2 % better - NEW BASIS
-#> Value 0.871 0.2 % better - NEW BASIS
-#> Value 0.873 0.2 % better - NEW BASIS
-#> Value 0.876 0.4 % better - NEW BASIS
-#> Value 0.876 0.0 % better
-#> Value 0.877 0.0 % better
-#> Value 0.877 0.1 % better
-#> Value 0.877 0.1 % better
-#> Value 0.876 0.0 % better
-#> Value 0.877 0.1 % better - NEW BASIS
-#> Value 0.878 0.1 % better
-#> Value 0.881 0.4 % better - NEW BASIS
-#> Value 0.882 0.2 % better - NEW BASIS
-#> Value 0.883 0.0 % better
-#> Value 0.883 0.1 % better
-#> Value 0.883 0.0 % better
-#> Value 0.883 0.1 % better - NEW BASIS
-#> Value 0.884 0.1 % better - NEW BASIS
-#> Value 0.885 0.1 % better - NEW BASIS
-#> Value 0.894 1.0 % better - NEW BASIS
-#> Value 0.898 0.4 % better - NEW BASIS
-#> Value 0.903 0.6 % better - NEW BASIS
-#> Value 0.906 0.3 % better - NEW BASIS
-#> Value 0.910 0.5 % better - NEW BASIS
-#> Value 0.914 0.3 % better - NEW BASIS
+#> 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 0.904 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 0.908 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 0.911 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 0.919 0.3 % better - NEW BASIS
-#> Value 0.924 0.5 % better - NEW BASIS
-#> Value 0.925 0.2 % better - NEW BASIS
-#> Value 0.926 0.1 % better
-#> Value 0.927 0.2 % better - NEW BASIS
-#> Value 0.928 0.1 % 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 0.919 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 0.932 0.3 % better - NEW BASIS
-#> Value 0.934 0.2 % better - NEW BASIS
-#> Value 0.935 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 0.0 % better
+#> 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 0.933 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 0.934 0.0 % 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 0.1 % 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 0.0 % 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 0.1 % better
#> Value 0.934 0.0 % better
#> No better bases found after 25 tries. Giving up.
#> Final projection:
-#> 0.706 0.645
-#> -0.416 0.666
-#> 0.139 0.021
-#> -0.129 0.239
-#> 0.537 -0.267
-#> 0.061 -0.109
+#> -0.774 0.580
+#> 0.351 0.692
+#> -0.108 -0.005
+#> 0.101 0.229
+#> -0.494 -0.346
+#> -0.106 -0.110
path_index(fl_holes, holes())
-#> [1] 0.7709381 0.8170550 0.8532431 0.8616238 0.8630056 0.8661705 0.8671572
-#> [8] 0.8686687 0.8705462 0.8725480 0.8762733 0.8771689 0.8806417 0.8824408
-#> [15] 0.8834002 0.8843186 0.8852353 0.8944692 0.8983732 0.9033724 0.9062098
-#> [22] 0.9104019 0.9135817 0.9163340 0.9193837 0.9236878 0.9251671 0.9268696
-#> [29] 0.9278338 0.9294604 0.9318559 0.9338224 0.9338224
+#> [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
#> attr(,"class")
#> [1] "path_index"
## path_index(fl_holes, cmass())
@@ -186,33 +191,23 @@ Examples
# Use interpolate to show all intermediate bases as well
hi <- path_index(interpolate(fl_holes), holes())
hi
-#> [1] 0.7709381 0.7736229 0.7764434 0.7793693 0.7823699 0.7854136 0.7884687
-#> [8] 0.7915035 0.7944869 0.7973881 0.8001775 0.8028268 0.8053094 0.8076009
-#> [15] 0.8096793 0.8115258 0.8131246 0.8144635 0.8155341 0.8163314 0.8168546
-#> [22] 0.8168546 0.8201506 0.8233946 0.8265518 0.8295920 0.8324894 0.8352235
-#> [29] 0.8377786 0.8401436 0.8423113 0.8442781 0.8460431 0.8476074 0.8489733
-#> [36] 0.8501442 0.8511234 0.8519144 0.8525202 0.8529433 0.8531855 0.8532481
-#> [43] 0.8532481 0.8551340 0.8568056 0.8582467 0.8594440 0.8603867 0.8610669
-#> [50] 0.8614798 0.8614798 0.8621798 0.8626708 0.8629524 0.8630263 0.8630263
-#> [57] 0.8640675 0.8649049 0.8655327 0.8659476 0.8661492 0.8661492 0.8667605
-#> [64] 0.8670901 0.8670901 0.8680146 0.8685820 0.8685820 0.8694905 0.8701159
-#> [71] 0.8704629 0.8704629 0.8714745 0.8721513 0.8724990 0.8724990 0.8738662
-#> [78] 0.8749202 0.8756672 0.8761154 0.8761154 0.8765997 0.8769340 0.8771508
-#> [85] 0.8771508 0.8777680 0.8783658 0.8789292 0.8794411 0.8798836 0.8802388
-#> [92] 0.8804902 0.8806233 0.8806233 0.8814770 0.8820561 0.8823715 0.8823715
-#> [99] 0.8828272 0.8831594 0.8833784 0.8833784 0.8839756 0.8842788 0.8842788
-#> [106] 0.8848921 0.8852019 0.8852019 0.8860485 0.8868730 0.8876812 0.8884740
-#> [113] 0.8892479 0.8899959 0.8907093 0.8913783 0.8919939 0.8925479 0.8930346
-#> [120] 0.8934501 0.8937930 0.8940636 0.8942637 0.8943955 0.8944610 0.8944610
-#> [127] 0.8959439 0.8970745 0.8978523 0.8982808 0.8982808 0.8995696 0.9006689
-#> [134] 0.9015808 0.9023062 0.9028453 0.9031972 0.9033603 0.9033603 0.9047206
-#> [141] 0.9056518 0.9061375 0.9061375 0.9078724 0.9091764 0.9100226 0.9103918
-#> [148] 0.9103918 0.9114133 0.9122521 0.9128952 0.9133323 0.9135557 0.9135557
-#> [155] 0.9148939 0.9158076 0.9162857 0.9162857 0.9177096 0.9186995 0.9192552
-#> [162] 0.9192552 0.9206049 0.9217163 0.9225891 0.9232211 0.9236083 0.9236083
-#> [169] 0.9245834 0.9250921 0.9250921 0.9261805 0.9267646 0.9267646 0.9275178
-#> [176] 0.9278264 0.9278264 0.9287383 0.9292865 0.9292865 0.9303541 0.9311616
-#> [183] 0.9316874 0.9316874 0.9328044 0.9335164 0.9335164 0.9335164
+#> [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
#> attr(,"class")
#> [1] "path_index"
plot(hi)
diff --git a/docs/reference/paths_index-1.png b/docs/reference/paths_index-1.png
index 64794b21..534b465a 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 5367e868..ff622124 100644
--- a/docs/reference/paths_index.html
+++ b/docs/reference/paths_index.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -93,45 +93,45 @@ Examples
#> Value 2.541 0.0 % better
#> No better bases found after 2 tries. Giving up.
#> Final projection:
-#> -0.152 0.640 0.469 -0.017 -0.588 0.034
+#> 0.649 -0.621 -0.285 0.199 0.240 0.124
#> 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:
-#> -0.010 -0.890 -0.378 -0.194 0.092 0.139
+#> -0.275 -0.278 0.462 -0.680 -0.124 -0.395
#> 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:
-#> 0.797 -0.239 0.068 -0.414 -0.036 -0.362
+#> -0.232 0.440 0.463 0.660 -0.026 -0.321
#> 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:
-#> 0.036 0.036 -0.082 -0.979 0.133 -0.124
+#> -0.663 -0.017 -0.015 -0.118 -0.549 0.495
#> 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:
-#> -0.018 -0.780 0.182 0.055 0.295 -0.517
+#> -0.053 -0.615 -0.336 0.624 -0.317 -0.130
# 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
-#> 2 2 1 2.541494 0
-#> 3 3 1 2.541009 0
-#> 4 4 1 2.541494 0
-#> 5 5 1 2.541494 0
+#> 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
if (require(ggplot2)) {
ggplot(data = paths, aes(x=step, y=value, group = try)) + geom_line()
## ggplot(data = paths, aes(x=step, y=improvement, group = try)) + geom_line()
}
-#> `geom_line()`: Each group consists of only one observation.
-#> ℹ Do you need to adjust the group aesthetic?
diff --git a/docs/reference/pda_pp.html b/docs/reference/pda_pp.html
index cca5ea2a..4d2a0131 100644
--- a/docs/reference/pda_pp.html
+++ b/docs/reference/pda_pp.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/planned_tour-1.png b/docs/reference/planned_tour-1.png
index 95bd48f5..d0aa0f0c 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 cfde271b..114e0125 100644
Binary files a/docs/reference/planned_tour-3.png and b/docs/reference/planned_tour-3.png differ
diff --git a/docs/reference/planned_tour.html b/docs/reference/planned_tour.html
index a4ca89db..ed4fd613 100644
--- a/docs/reference/planned_tour.html
+++ b/docs/reference/planned_tour.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/plot.path_curve.html b/docs/reference/plot.path_curve.html
index 54e3c286..8205f7bd 100644
--- a/docs/reference/plot.path_curve.html
+++ b/docs/reference/plot.path_curve.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/plot.path_index.html b/docs/reference/plot.path_index.html
index d532c97c..3adccccb 100644
--- a/docs/reference/plot.path_index.html
+++ b/docs/reference/plot.path_index.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/proj_dist.html b/docs/reference/proj_dist.html
index 8d282341..e5385683 100644
--- a/docs/reference/proj_dist.html
+++ b/docs/reference/proj_dist.html
@@ -19,7 +19,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/project3d.html b/docs/reference/project3d.html
index 672e42f4..5f94b1a9 100644
--- a/docs/reference/project3d.html
+++ b/docs/reference/project3d.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/radial_bin_weight_inv.html b/docs/reference/radial_bin_weight_inv.html
index b76810b3..8bf226a5 100644
--- a/docs/reference/radial_bin_weight_inv.html
+++ b/docs/reference/radial_bin_weight_inv.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/radial_tour-1.png b/docs/reference/radial_tour-1.png
index a440f56f..2be66787 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 843cb6cf..052b5b51 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 5b7d482c..698567be 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 45a0b5c7..8ccf10aa 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 e606e90d..17581ab0 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 d17a6851..476cbb8e 100644
Binary files a/docs/reference/radial_tour-6.png and b/docs/reference/radial_tour-6.png differ
diff --git a/docs/reference/radial_tour.html b/docs/reference/radial_tour.html
index 12d01a28..196ce25c 100644
--- a/docs/reference/radial_tour.html
+++ b/docs/reference/radial_tour.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/render.html b/docs/reference/render.html
index 9a112ba6..f8702a80 100644
--- a/docs/reference/render.html
+++ b/docs/reference/render.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/render_anim.html b/docs/reference/render_anim.html
index fa80a45b..08639aaa 100644
--- a/docs/reference/render_anim.html
+++ b/docs/reference/render_anim.html
@@ -22,7 +22,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/render_gif.html b/docs/reference/render_gif.html
index 55ea355f..42e20bb0 100644
--- a/docs/reference/render_gif.html
+++ b/docs/reference/render_gif.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/render_proj-1.png b/docs/reference/render_proj-1.png
index 95b96558..a0d873cc 100644
Binary files a/docs/reference/render_proj-1.png and b/docs/reference/render_proj-1.png differ
diff --git a/docs/reference/render_proj.html b/docs/reference/render_proj.html
index b7c24f0b..0e93b807 100644
--- a/docs/reference/render_proj.html
+++ b/docs/reference/render_proj.html
@@ -21,7 +21,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/rescale.html b/docs/reference/rescale.html
index eebd51b2..05f002b5 100644
--- a/docs/reference/rescale.html
+++ b/docs/reference/rescale.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/save_history-1.png b/docs/reference/save_history-1.png
index 2f11e578..0bb27bd5 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 a9125872..d6b11ac1 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 e5f2b4a4..f26c529c 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 085a245a..52b596d7 100644
--- a/docs/reference/save_history.html
+++ b/docs/reference/save_history.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -141,12 +141,24 @@ Examples
t2 <- save_history(testdata, guided_tour(holes(), max.tries = 10),
max = 5
)
-#> Value 0.881 9.0 % better - NEW BASIS
-#> Value 0.882 0.2 % better - NEW BASIS
-#> Value 0.896 1.6 % better - NEW BASIS
-#> Value 0.897 0.1 % better - NEW BASIS
+#> 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
+#> No better bases found after 10 tries. Giving up.
+#> Final projection:
+#> -0.805 -0.592
+#> 0.333 -0.507
+#> 0.491 -0.627
animate_xy(testdata, planned_tour(t2))
-#> Using half_range 3
+#> Using half_range 3.5
# 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 d4ca6ebe..d23f687a 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 744ae84b..b7e765bf 100644
--- a/docs/reference/search_better.html
+++ b/docs/reference/search_better.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -120,12 +120,12 @@ Examples
#> Old 1.581977
#> No better bases found after 25 tries. Giving up.
#> Final projection:
-#> -0.251 -0.212
-#> -0.611 0.610
-#> 0.293 -0.090
-#> 0.337 0.186
-#> 0.538 0.163
-#> 0.273 0.716
+#> -0.220 -0.443
+#> 0.450 -0.320
+#> 0.312 0.613
+#> -0.435 0.077
+#> -0.546 -0.191
+#> 0.405 -0.531
#> Using half_range 66
diff --git a/docs/reference/search_better_random-1.png b/docs/reference/search_better_random-1.png
index a8ac7f55..431d14c8 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_better_random.html b/docs/reference/search_better_random.html
index 4096e04d..31b51c76 100644
--- a/docs/reference/search_better_random.html
+++ b/docs/reference/search_better_random.html
@@ -21,7 +21,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/search_frozen_geodesic.html b/docs/reference/search_frozen_geodesic.html
index 76388ef4..49397ed6 100644
--- a/docs/reference/search_frozen_geodesic.html
+++ b/docs/reference/search_frozen_geodesic.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/search_geodesic-1.png b/docs/reference/search_geodesic-1.png
index 52eca77b..5638d989 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 6da3f23b..7ded6590 100644
--- a/docs/reference/search_geodesic.html
+++ b/docs/reference/search_geodesic.html
@@ -22,7 +22,7 @@
tourr
- 0.6.18
+ 1.0.0
@@ -164,12 +164,12 @@ Examples
#> Value 1.582 0.0 % better
#> No better bases found after 25 tries. Giving up.
#> Final projection:
-#> -0.332 -0.121
-#> 0.594 0.087
-#> 0.503 -0.024
-#> 0.351 0.524
-#> 0.400 -0.613
-#> -0.032 0.572
+#> -0.056 -0.746
+#> 0.340 0.332
+#> 0.435 -0.186
+#> 0.742 0.162
+#> 0.369 -0.499
+#> 0.067 -0.152
#> Using half_range 66
diff --git a/docs/reference/search_polish.html b/docs/reference/search_polish.html
index 56ef33f3..373f18b9 100644
--- a/docs/reference/search_polish.html
+++ b/docs/reference/search_polish.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/search_posse.html b/docs/reference/search_posse.html
index 5bf1da10..da158668 100644
--- a/docs/reference/search_posse.html
+++ b/docs/reference/search_posse.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/slice_binning.html b/docs/reference/slice_binning.html
index eb081725..1ee5fee1 100644
--- a/docs/reference/slice_binning.html
+++ b/docs/reference/slice_binning.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/slice_index.html b/docs/reference/slice_index.html
index 73485b14..e9690b91 100644
--- a/docs/reference/slice_index.html
+++ b/docs/reference/slice_index.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/sphere_data.html b/docs/reference/sphere_data.html
index c79a73b8..c6b6de34 100644
--- a/docs/reference/sphere_data.html
+++ b/docs/reference/sphere_data.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/splines2d.html b/docs/reference/splines2d.html
index 761f40cb..df28e13d 100644
--- a/docs/reference/splines2d.html
+++ b/docs/reference/splines2d.html
@@ -20,7 +20,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/step_angle.html b/docs/reference/step_angle.html
index e4de1086..5c570633 100644
--- a/docs/reference/step_angle.html
+++ b/docs/reference/step_angle.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/step_fraction.html b/docs/reference/step_fraction.html
index c53aea32..b65b79a5 100644
--- a/docs/reference/step_fraction.html
+++ b/docs/reference/step_fraction.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/t1.html b/docs/reference/t1.html
index e5b8a788..625c0f04 100644
--- a/docs/reference/t1.html
+++ b/docs/reference/t1.html
@@ -23,7 +23,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/to_stop.html b/docs/reference/to_stop.html
index 21f23ab1..d43b7fde 100644
--- a/docs/reference/to_stop.html
+++ b/docs/reference/to_stop.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/tourr-package.html b/docs/reference/tourr-package.html
index 331c3d2d..49d294ae 100644
--- a/docs/reference/tourr-package.html
+++ b/docs/reference/tourr-package.html
@@ -18,7 +18,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/weights_bincount_radial.html b/docs/reference/weights_bincount_radial.html
index 84a778f7..12e1127c 100644
--- a/docs/reference/weights_bincount_radial.html
+++ b/docs/reference/weights_bincount_radial.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/docs/reference/xnul.html b/docs/reference/xnul.html
index e5de9c31..a64e0d34 100644
--- a/docs/reference/xnul.html
+++ b/docs/reference/xnul.html
@@ -17,7 +17,7 @@
tourr
- 0.6.18
+ 1.0.0
diff --git a/inst/CITATION b/inst/CITATION
index b168b96e..bcad5fdb 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -1,17 +1,14 @@
citHeader("To cite tourr in publications use:")
-citEntry(entry = "Article",
- title = "{tourr}: An {R} Package for Exploring Multivariate Data with Projections",
- author = personList(as.person("Hadley Wickham"),
- as.person("Dianne Cook"),
- as.person("Heike Hofmann"),
- as.person("Andreas Buja")),
- journal = "Journal of Statistical Software",
- year = "2011",
- volume = "40",
- number = "2",
- pages = "1--18",
- url = "https://doi.org/10.18637/jss.v040.i02",
+bibentry("Article",
+ title = "{tourr}: An {R} Package for Exploring Multivariate Data with Projections",
+ author = "Hadley Wickham, Dianne Cook, Heike Hofmann, Andreas Buja",
+ journal = "Journal of Statistical Software",
+ year = "2011",
+ volume = "40",
+ number = "2",
+ pages = "1--18",
+ url = "https://doi.org/10.18637/jss.v040.i02",
textVersion =
paste("Hadley Wickham, Dianne Cook, Heike Hofmann, Andreas Buja (2011).",
@@ -20,17 +17,15 @@ citEntry(entry = "Article",
"URL http://www.jstatsoft.org/v40/i02/.")
)
-citEntry(entry = "Article",
- title = "A slice tour for finding hollowness in high-dimensional data",
- author = personList(as.person("Ursula Laa"),
- as.person("Dianne Cook"),
- as.person("German Valencia")),
- journal = "Journal of Computational and Graphical Statistics",
- year = "2020",
- volume = "29",
- number = "3",
- pages = "681--687",
- url = "https://doi.org/10.1080/10618600.2020.1777140",
+bibentry("Article",
+ title = "A slice tour for finding hollowness in high-dimensional data",
+ author = "Ursula Laa, Dianne Cook, German Valencia",
+ journal = "Journal of Computational and Graphical Statistics",
+ year = "2020",
+ volume = "29",
+ number = "3",
+ pages = "681--687",
+ url = "https://doi.org/10.1080/10618600.2020.1777140",
textVersion =
paste("Ursula Laa, Dianne Cook, German Valencia (2020).",
diff --git a/man/display_andrews.Rd b/man/display_andrews.Rd
index c8a8d184..f9839a4c 100644
--- a/man/display_andrews.Rd
+++ b/man/display_andrews.Rd
@@ -5,13 +5,15 @@
\alias{animate_andrews}
\title{Andrews' curves tour path animation.}
\usage{
-display_andrews(col = "black", ...)
+display_andrews(col = "black", palette = "Zissou 1", ...)
animate_andrews(data, tour_path = grand_tour(3), col = "black", ...)
}
\arguments{
\item{col}{color to be plotted. Defaults to "black"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
+
\item{...}{other arguments passed on to \code{\link{animate}}}
\item{data}{matrix, or data frame containing numeric columns}
diff --git a/man/display_density2d.Rd b/man/display_density2d.Rd
index caded43b..1f6a5ac4 100644
--- a/man/display_density2d.Rd
+++ b/man/display_density2d.Rd
@@ -40,7 +40,7 @@ If not set, defaults to maximum distance from origin to each row of data.}
\item{edges}{A two column integer matrix giving indices of ends of lines.}
-\item{palette}{name of color palette for point colour, used by \code{\link{grDevices::hcl.colors}}, default "Zissou 1"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
\item{...}{other arguments passed on to \code{\link{animate}} and
\code{\link{display_density2d}}}
diff --git a/man/display_dist.Rd b/man/display_dist.Rd
index 2c452c64..4eafd21f 100644
--- a/man/display_dist.Rd
+++ b/man/display_dist.Rd
@@ -34,7 +34,7 @@ If not set, defaults to maximum distance from origin to each row of data.}
\item{rug}{draw rug plot showing position of actual data points?}
-\item{palette}{name of color palette for point colour, used by \code{\link{grDevices::hcl.colors}}, default "Zissou 1"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
\item{density_max}{allow control of the y range for density plot}
diff --git a/man/display_faces.Rd b/man/display_faces.Rd
index c0f4a14f..e7e04eab 100644
--- a/man/display_faces.Rd
+++ b/man/display_faces.Rd
@@ -27,10 +27,11 @@ Chernoff faces. See \code{\link[TeachingDemos]{faces2}} for more details.
\examples{
# The drawing code is fairly slow, so this animation works best with a
# limited number of cases
-animate_faces(flea[1:2, 1:6])
-animate_faces(flea[1:4, 1:6])
+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[1:2, 1:6], grand_tour(5))
+animate_faces(flea_s[1:2, 1:6], grand_tour(5))
}
\seealso{
\code{\link{animate}} for options that apply to all animations
diff --git a/man/display_groupxy.Rd b/man/display_groupxy.Rd
index a959b959..101021a9 100644
--- a/man/display_groupxy.Rd
+++ b/man/display_groupxy.Rd
@@ -13,6 +13,8 @@ display_groupxy(
pch = 20,
cex = 1,
edges = NULL,
+ edges.col = "black",
+ edges.width = 1,
group_by = NULL,
plot_xgp = TRUE,
palette = "Zissou 1",
@@ -39,11 +41,15 @@ If not set, defaults to maximum distance from origin to each row of data.}
\item{edges}{A two column integer matrix giving indices of ends of lines.}
+\item{edges.col}{colour of edges to be plotted, Defaults to "black"}
+
+\item{edges.width}{line width for edges, default 1}
+
\item{group_by}{variable to group by. Must have less than 25 unique values.}
\item{plot_xgp}{if TRUE, plots points from other groups in light grey}
-\item{palette}{name of color palette for point colour, used by \code{\link{grDevices::hcl.colors}}, default "Zissou 1"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
\item{...}{other arguments passed on to \code{\link{animate}} and
\code{\link{display_groupxy}}}
@@ -59,10 +65,9 @@ This function is designed to allow comparisons across multiple groups,
contours overlaid.
}
\examples{
-f <- flea[, 1:6]
-col <- rainbow(length(unique(flea$species)))[as.numeric(as.factor(flea$species))]
-pch <- as.numeric(flea$species) + 14
-
-animate_groupxy(f, col = col, pch = pch, group_by = flea$species)
-animate_groupxy(f, col = col, pch = pch, group_by = flea$species, plot_xgp = FALSE)
+animate_groupxy(flea[, 1:6], col = flea$species,
+ pch = flea$species, group_by = flea$species)
+animate_groupxy(flea[, 1:6], col = flea$species,
+ pch = flea$species, group_by = flea$species,
+ plot_xgp = FALSE)
}
diff --git a/man/display_pca.Rd b/man/display_pca.Rd
index 3c422f4c..d6a40958 100644
--- a/man/display_pca.Rd
+++ b/man/display_pca.Rd
@@ -44,7 +44,7 @@ principal components. This is required.}
\item{edges.col}{colour of edges to be plotted, Defaults to "black.}
-\item{palette}{name of color palette for point colour, used by \code{\link{grDevices::hcl.colors}}, default "Zissou 1"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
\item{...}{other arguments passed on to \code{\link{animate}} and
\code{\link{display_slice}}}
@@ -60,7 +60,7 @@ Animate a 2D tour path on data that has been transformed into
principal components, and also show the original variable axes.
}
\examples{
-flea_std <- scale(flea[, 1:6])
+flea_std <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
flea_pca <- prcomp(flea_std, center = FALSE, )
flea_coefs <- flea_pca$rotation[, 1:3]
flea_scores <- flea_pca$x[, 1:3]
diff --git a/man/display_sage.Rd b/man/display_sage.Rd
index 8dcb866c..66202f94 100644
--- a/man/display_sage.Rd
+++ b/man/display_sage.Rd
@@ -33,7 +33,7 @@ If not set, defaults to maximum distance from origin to each row of data.}
\item{R}{scale for the radial transformation.
If not set, defaults to maximum distance from origin to each row of data.}
-\item{palette}{name of color palette for point colour, used by \code{\link{grDevices::hcl.colors}}, default "Zissou 1"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
\item{...}{other arguments passed on to \code{\link{animate}} and
\code{\link{display_sage}}}
diff --git a/man/display_slice.Rd b/man/display_slice.Rd
index aae45011..b9574c94 100644
--- a/man/display_slice.Rd
+++ b/man/display_slice.Rd
@@ -59,7 +59,7 @@ If NULL (default) the slice will be anchored at the data center.}
\item{edges.col}{colour of edges to be plotted, Defaults to "black.}
-\item{palette}{name of color palette for point colour, used by \code{\link{grDevices::hcl.colors}}, default "Zissou 1"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
\item{...}{other arguments passed on to \code{\link{animate}} and
\code{\link{display_slice}}}
diff --git a/man/display_trails.Rd b/man/display_trails.Rd
index b4ec5be2..2670b56d 100644
--- a/man/display_trails.Rd
+++ b/man/display_trails.Rd
@@ -47,3 +47,7 @@ steps ago}
\description{
Animate a 2D tour path with a point trails
}
+\examples{
+animate_trails(flea[,1:6], col=flea$species)
+
+}
diff --git a/man/display_xy.Rd b/man/display_xy.Rd
index 4a0350cf..11490182 100644
--- a/man/display_xy.Rd
+++ b/man/display_xy.Rd
@@ -46,7 +46,7 @@ If not set, defaults to maximum distance from origin to each row of data.}
\item{obs_labels}{vector of text labels to display}
-\item{palette}{name of color palette for point colour, used by \code{\link{grDevices::hcl.colors}}, default "Zissou 1"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
\item{...}{other arguments passed on to \code{\link{animate}} and
\code{\link{display_xy}}}
@@ -63,7 +63,8 @@ animate_xy(flea[, 1:6])
animate(flea[, 1:6], tour_path = grand_tour(), display = display_xy())
animate(flea[, 1:6],
tour_path = grand_tour(),
- display = display_xy(axes = "bottomleft")
+ display = display_xy(),
+ scale = TRUE
)
animate(flea[, 1:6],
tour_path = grand_tour(),
@@ -82,7 +83,7 @@ animate_xy(flea[, 1:6], dependence_tour(c(1, 2, 1, 2, 1, 2)),
animate_xy(flea[, -7], col = flea$species)
animate_xy(flea[, -7], col = flea$species,
- pch = as.numeric(flea$species))
+ pch = flea$species)
animate_xy(flea[, -7], col = flea$species,
obs_labels=as.character(1:nrow(flea)), axes="off")
diff --git a/man/guided_tour.Rd b/man/guided_tour.Rd
index aad934cb..43bff085 100644
--- a/man/guided_tour.Rd
+++ b/man/guided_tour.Rd
@@ -51,16 +51,17 @@ a method that works with tour paths like \code{\link{animate}},
\code{\link{save_history}} or \code{\link{render}}.
}
\examples{
-animate_xy(flea[, 1:6], guided_tour(holes()), sphere = TRUE)
+flea_std <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
+animate_xy(flea_std, guided_tour(holes()), sphere = TRUE)
\donttest{
-animate_xy(flea[, 1:6], guided_tour(holes(), search_f = search_better_random), sphere = TRUE)
-animate_dist(flea[, 1:6], guided_tour(holes(), 1), sphere = TRUE)
-animate_xy(flea[, 1:6], guided_tour(lda_pp(flea$species)), sphere = TRUE, col = flea$species)
+animate_xy(flea_std, guided_tour(holes(), search_f = search_better_random), sphere = TRUE)
+animate_dist(flea_std, guided_tour(holes(), 1), sphere = TRUE)
+animate_xy(flea_std, guided_tour(lda_pp(flea$species)), sphere = TRUE, col = flea$species)
# save_history is particularly useful in conjunction with the
# guided tour as it allows us to look at the tour path in many different
# ways
-f <- flea[, 1:3]
+f <- flea_std[, 1:3]
tries <- replicate(5, save_history(f, guided_tour(holes())), simplify = FALSE)
}
}
diff --git a/man/manual_slice.Rd b/man/manual_slice.Rd
index 0c06d571..56138389 100644
--- a/man/manual_slice.Rd
+++ b/man/manual_slice.Rd
@@ -42,7 +42,7 @@ If not set, defaults to maximum distance from origin to each row of data.}
\item{anchor_nav}{position of the anchor: center, topright or off}
-\item{palette}{name of color palette for point colour, used by \code{\link{grDevices::hcl.colors}}, default "Zissou 1"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
\item{...}{other options passed to output device}
}
diff --git a/man/mapColors.Rd b/man/mapColors.Rd
index 93f56e37..0f9a6604 100644
--- a/man/mapColors.Rd
+++ b/man/mapColors.Rd
@@ -9,7 +9,7 @@ mapColors(x, palette)
\arguments{
\item{x}{vector}
-\item{palette}{name of color palette for point colour, used by \code{\link{grDevices::hcl.colors}}, default "Zissou 1"}
+\item{palette}{name of color palette for point colour, used by \code{\link{hcl.colors}}, default "Zissou 1"}
}
\description{
Map vector of factors to color
diff --git a/man/path_dist.Rd b/man/path_dist.Rd
index 6dd261b0..8f7b837e 100644
--- a/man/path_dist.Rd
+++ b/man/path_dist.Rd
@@ -15,7 +15,8 @@ Compute distance matrix from bases.
\examples{
# This code is to be used as an example but you should increase
# the max from 2 to 50, say, to check tour coverage.
-grand <- interpolate(save_history(flea[, 1:6], max = 2), 0.2)
+flea_std <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
+grand <- interpolate(save_history(flea_std, max = 2), 0.2)
# The grand tour -----------------------------
# Look at the tour path in a tour, how well does it cover a sphere
# Using MDS to summarise the high-d space of projections
@@ -30,7 +31,7 @@ ggplot(data = ord, aes(x=V1, y=V2)) +
# Compare five guided tours -----------------------------
holes1d <- guided_tour(holes(), 1)
-tour_reps <- replicate(5, save_history(flea[, 1:6], holes1d, max = 2),
+tour_reps <- replicate(5, save_history(flea_std, holes1d, max = 2),
simplify = FALSE
)
tour_reps2 <- lapply(tour_reps, interpolate, 0.2)
@@ -43,13 +44,11 @@ d <- path_dist(bases)
ord <- as.data.frame(cmdscale(d, 2))
info <- cbind(ord, index_values)
-if (require("ggplot2")) {
- ggplot(data = info, aes(x = step, y = value, group = try)) +
- geom_line()
- ##ggplot(data = info, aes(x = V1, y = V2, group = try)) +
- ## geom_path() +
- ## geom_point(aes(size = value)) +
- ## coord_equal()
- ##last_plot() + facet_wrap(~try)
-}
+ggplot(data = info, aes(x = step, y = value, group = try)) +
+ geom_line()
+##ggplot(data = info, aes(x = V1, y = V2, group = try)) +
+## geom_path() +
+## geom_point(aes(size = value)) +
+## coord_equal()
+##last_plot() + facet_wrap(~try)
}
diff --git a/test/Flea-measurements.r b/test/Flea-measurements.r
deleted file mode 100644
index 5bd74e5c..00000000
--- a/test/Flea-measurements.r
+++ /dev/null
@@ -1,14 +0,0 @@
-### Name: Flea measurements
-### Title: Flea beatle measurements
-### Aliases: 'Flea measurements' flea
-### Keywords: datasets
-
-### ** Examples
-
-
-head(flea)
-animate_xy(flea[, -7])
-animate_xy(flea[, -7], col = flea[, 7])
-
-
-
diff --git a/test/Laser-measurements.r b/test/Laser-measurements.r
deleted file mode 100644
index a75d2a49..00000000
--- a/test/Laser-measurements.r
+++ /dev/null
@@ -1,13 +0,0 @@
-### Name: Laser measurements
-### Title: Turnable laser measurements from Bellcore
-### Aliases: 'Laser measurements' laser
-### Keywords: datasets
-
-### ** Examples
-
-
-head(laser)
-animate_xy(laser[, -4])
-
-
-
diff --git a/test/Olive-oil-measurements.r b/test/Olive-oil-measurements.r
deleted file mode 100644
index 579694fd..00000000
--- a/test/Olive-oil-measurements.r
+++ /dev/null
@@ -1,14 +0,0 @@
-### Name: Olive oil measurements
-### Title: Olive oil samples from Italy
-### Aliases: 'Olive oil measurements' olive
-### Keywords: datasets
-
-### ** Examples
-
-
-head(olive)
-animate_xy(olive[, c(7, 9, 10)])
-animate_xy(olive[, c(7, 9, 10)], col = olive[, 1])
-
-
-
diff --git a/test/Ozone-measurements.r b/test/Ozone-measurements.r
deleted file mode 100644
index 0ebe2fba..00000000
--- a/test/Ozone-measurements.r
+++ /dev/null
@@ -1,12 +0,0 @@
-### Name: Ozone measurements
-### Title: Monthly ozone measurements over Central America
-### Aliases: 'Ozone measurements' ozone
-### Keywords: datasets
-
-### ** Examples
-
-
-example(display_image)
-
-
-
diff --git a/test/Places-Ratings.r b/test/Places-Ratings.r
deleted file mode 100644
index c82822b4..00000000
--- a/test/Places-Ratings.r
+++ /dev/null
@@ -1,13 +0,0 @@
-### Name: Places Ratings
-### Title: Ratings of different locations across North America
-### Aliases: 'Places Ratings' places
-### Keywords: datasets
-
-### ** Examples
-
-
-head(places)
-animate_xy(places[, 1:9])
-
-
-
diff --git a/test/Rat-CNS.r b/test/Rat-CNS.r
deleted file mode 100644
index 4dca25dd..00000000
--- a/test/Rat-CNS.r
+++ /dev/null
@@ -1,13 +0,0 @@
-### Name: Rat CNS
-### Title: Rat CNS Gene Expression
-### Aliases: 'Rat CNS' ratcns
-### Keywords: datasets
-
-### ** Examples
-
-
-head(ratcns)
-animate_xy(ratcns[, 1:8], col = ratcns[, 10])
-
-
-
diff --git a/test/andrews.r b/test/andrews.r
deleted file mode 100644
index 6348a713..00000000
--- a/test/andrews.r
+++ /dev/null
@@ -1,17 +0,0 @@
-### Name: andrews
-### Title: Compute Andrews' curves
-### Aliases: andrews
-
-### ** Examples
-
-a <- andrews(1:2)
-a(0)
-a(-pi)
-grid <- seq(-pi, pi, length = 50)
-a(grid)
-
-plot(grid, andrews(1:2)(grid), type = "l")
-plot(grid, andrews(runif(5))(grid), type = "l")
-
-
-
diff --git a/test/animate.r b/test/animate.r
deleted file mode 100644
index 7061a5c7..00000000
--- a/test/animate.r
+++ /dev/null
@@ -1,17 +0,0 @@
-### Name: animate
-### Title: Animate a tour path.
-### Aliases: animate
-
-### ** Examples
-
-f <- flea[, 1:6]
-animate(f, grand_tour(), display_xy())
-# or in short
-animate(f)
-animate(f, max_frames = 30)
-## Not run:
-##D animate(f, max_frames = 10, fps = 1, aps = 0.1)
-## End(Not run)
-
-
-
diff --git a/test/dependence_tour.r b/test/dependence_tour.r
deleted file mode 100644
index b6cd4bf7..00000000
--- a/test/dependence_tour.r
+++ /dev/null
@@ -1,12 +0,0 @@
-### Name: dependence_tour
-### Title: A dependence tour path.
-### Aliases: dependence_tour
-
-### ** Examples
-
-animate_xy(flea[, 1:3], dependence_tour(c(1, 2, 2)))
-animate_xy(flea[, 1:4], dependence_tour(c(1, 2, 1, 2)))
-animate_pcp(flea[, 1:6], dependence_tour(c(1, 2, 3, 2, 1, 3)))
-
-
-
diff --git a/test/display_andrews.r b/test/display_andrews.r
deleted file mode 100644
index 9fb6ec10..00000000
--- a/test/display_andrews.r
+++ /dev/null
@@ -1,16 +0,0 @@
-### Name: display_andrews
-### Title: Andrews' curves tour path animation.
-### Aliases: display_andrews animate_andrews
-### Keywords: hplot
-
-### ** Examples
-
-animate_andrews(flea[, 1:6])
-animate_andrews(flea[, 1:6], grand_tour(d = 3))
-animate_andrews(flea[, 1:6], grand_tour(d = 6))
-
-# It's easy to experiment with different tour paths:
-animate_andrews(flea[, 1:6], guided_tour(cmass()))
-
-
-
diff --git a/test/display_density2d.r b/test/display_density2d.r
deleted file mode 100644
index e5e9ef45..00000000
--- a/test/display_density2d.r
+++ /dev/null
@@ -1,39 +0,0 @@
-### Name: display_density2d
-### Title: Display tour path with a density and scatterplot
-### Aliases: display_density2d animate_density2d
-
-### ** Examples
-
-animate_density2d(flea[, 1:6])
-animate(flea[, 1:6], tour_path = grand_tour(), display = display_density2d())
-animate(flea[, 1:6],
- tour_path = grand_tour(),
- display = display_density2d(axes = "bottomleft")
-)
-animate(flea[, 1:6],
- tour_path = grand_tour(),
- display = display_density2d(half_range = 0.5)
-)
-animate_density2d(flea[, 1:6], tour_path = little_tour())
-
-animate_density2d(flea[, 1:3], tour_path = guided_tour(holes()), sphere = TRUE)
-animate_density2d(flea[, 1:6], center = FALSE)
-
-# The default axes are centered, like a biplot, but there are other options
-animate_density2d(flea[, 1:6], axes = "bottomleft")
-animate_density2d(flea[, 1:6], axes = "off")
-animate_density2d(flea[, 1:6], dependence_tour(c(1, 2, 1, 2, 1, 2)),
- axes = "bottomleft"
-)
-
-animate_density2d(flea[, -7], col = flea$species)
-
-# You can also draw lines
-edges <- matrix(c(1:5, 2:6), ncol = 2)
-animate(
- flea[, 1:6], grand_tour(),
- display_density2d(axes = "bottomleft", edges = edges)
-)
-
-
-
diff --git a/test/display_depth.r b/test/display_depth.r
deleted file mode 100644
index a6425e54..00000000
--- a/test/display_depth.r
+++ /dev/null
@@ -1,11 +0,0 @@
-### Name: display_depth
-### Title: Display 3d projection with depth cues
-### Aliases: display_depth animate_depth
-### Keywords: hplot
-
-### ** Examples
-
-animate_depth(flea[, 1:6])
-
-
-
diff --git a/test/display_dist.r b/test/display_dist.r
deleted file mode 100644
index b68cb8fb..00000000
--- a/test/display_dist.r
+++ /dev/null
@@ -1,18 +0,0 @@
-### Name: display_dist
-### Title: 1d distribution tour path animation.
-### Aliases: display_dist animate_dist
-### Keywords: hplot
-
-### ** Examples
-
-animate_dist(flea[, 1:6])
-
-# When the distribution is not centred, it tends to wander around in a
-# distracting manner
-animate_dist(flea[, 1:6], center = FALSE)
-
-# Alternatively, you can display the distribution with a histogram
-animate_dist(flea[, 1:6], method = "hist")
-
-
-
diff --git a/test/display_faces.r b/test/display_faces.r
deleted file mode 100644
index 33053528..00000000
--- a/test/display_faces.r
+++ /dev/null
@@ -1,16 +0,0 @@
-### Name: display_faces
-### Title: Chernoff faces tour path animation.
-### Aliases: display_faces animate_faces
-### Keywords: hplot
-
-### ** Examples
-
-# The drawing code is fairly slow, so this animation works best with a
-# limited number of cases
-animate_faces(flea[1:2, 1:6])
-animate_faces(flea[1:4, 1:6])
-
-animate_faces(flea[1:2, 1:6], grand_tour(5))
-
-
-
diff --git a/test/display_groupxy.r b/test/display_groupxy.r
deleted file mode 100644
index 92e2b0c8..00000000
--- a/test/display_groupxy.r
+++ /dev/null
@@ -1,15 +0,0 @@
-### Name: display_groupxy
-### Title: Display 2D tour projections displayed separately by groups
-### Aliases: display_groupxy animate_groupxy
-
-### ** Examples
-
-f <- flea[, 1:6]
-col <- rainbow(length(unique(flea$species)))[as.numeric(as.factor(flea$species))]
-pch <- as.numeric(flea$species) + 14
-
-animate_groupxy(f, col = col, pch = pch, group_by = flea$species)
-animate_groupxy(f, col = col, pch = pch, group_by = flea$species, plot_xgp = FALSE)
-
-
-
diff --git a/test/display_image.r b/test/display_image.r
deleted file mode 100644
index 5637c8ed..00000000
--- a/test/display_image.r
+++ /dev/null
@@ -1,12 +0,0 @@
-### Name: display_image
-### Title: Image tour path animation.
-### Aliases: display_image animate_image
-### Keywords: hplot
-
-### ** Examples
-
-str(ozone)
-animate_image(ozone)
-
-
-
diff --git a/test/display_pca.r b/test/display_pca.r
deleted file mode 100644
index 23d2af93..00000000
--- a/test/display_pca.r
+++ /dev/null
@@ -1,15 +0,0 @@
-### Name: display_pca
-### Title: Display tour path with principal component scores with original
-### axes
-### Aliases: display_pca animate_pca
-
-### ** Examples
-
-flea_std <- scale(flea[, 1:6])
-flea_pca <- prcomp(flea_std, center = FALSE, )
-flea_coefs <- flea_pca$rotation[, 1:3]
-flea_scores <- flea_pca$x[, 1:3]
-animate_pca(flea_scores, pc_coefs = flea_coefs)
-
-
-
diff --git a/test/display_pcp.r b/test/display_pcp.r
deleted file mode 100644
index c91cb62c..00000000
--- a/test/display_pcp.r
+++ /dev/null
@@ -1,12 +0,0 @@
-### Name: display_pcp
-### Title: Parallel coordinates tour path animation.
-### Aliases: display_pcp animate_pcp
-### Keywords: hplot
-
-### ** Examples
-
-animate_pcp(flea[, 1:6], grand_tour(3))
-animate_pcp(flea[, 1:6], grand_tour(5))
-
-
-
diff --git a/test/display_sage.r b/test/display_sage.r
deleted file mode 100644
index e11f98cf..00000000
--- a/test/display_sage.r
+++ /dev/null
@@ -1,17 +0,0 @@
-### Name: display_sage
-### Title: Display tour path with a sage scatterplot
-### Aliases: display_sage animate_sage
-
-### ** Examples
-
-# Generate uniform samples in a 10d sphere using the geozoo package
-sphere10 <- geozoo::sphere.solid.random(10)$points
-# Columns need to be named before launching the tour
-colnames(sphere10) <- paste0("x", 1:10)
-# Standard grand tour display, points cluster near center
-animate_xy(sphere10)
-# Sage display, points are uniformly distributed across the disk
-animate_sage(sphere10)
-
-
-
diff --git a/test/display_scatmat.r b/test/display_scatmat.r
deleted file mode 100644
index dfec1292..00000000
--- a/test/display_scatmat.r
+++ /dev/null
@@ -1,12 +0,0 @@
-### Name: display_scatmat
-### Title: Scatterplot matrix tour path animation.
-### Aliases: display_scatmat animate_scatmat
-### Keywords: hplot
-
-### ** Examples
-
-animate_scatmat(flea[, 1:6], grand_tour(2))
-animate_scatmat(flea[, 1:6], grand_tour(6))
-
-
-
diff --git a/test/display_slice.r b/test/display_slice.r
deleted file mode 100644
index 09bee7f4..00000000
--- a/test/display_slice.r
+++ /dev/null
@@ -1,27 +0,0 @@
-### Name: display_slice
-### Title: Display tour path with a sliced scatterplot
-### Aliases: display_slice animate_slice
-
-### ** Examples
-
-# Generate samples on a 3d and 5d hollow sphere using the geozoo package
-sphere3 <- geozoo::sphere.hollow(3)$points
-sphere5 <- geozoo::sphere.hollow(5)$points
-
-# Columns need to be named before launching the tour
-colnames(sphere3) <- c("x1", "x2", "x3")
-colnames(sphere5) <- c("x1", "x2", "x3", "x4", "x5")
-
-# Animate with the slice display using the default parameters
-animate_slice(sphere3)
-animate_slice(sphere5)
-
-# Animate with off-center anchoring
-anchor3 <- rep(0.7, 3)
-anchor5 <- rep(0.3, 5)
-animate_slice(sphere3, anchor = anchor3)
-# Animate with thicker slice to capture more points in each view
-animate_slice(sphere5, anchor = anchor5, v_rel = 0.02)
-
-
-
diff --git a/test/display_stars.r b/test/display_stars.r
deleted file mode 100644
index efde0342..00000000
--- a/test/display_stars.r
+++ /dev/null
@@ -1,16 +0,0 @@
-### Name: display_stars
-### Title: Star glyph tour path animation.
-### Aliases: display_stars animate_stars
-### Keywords: hplot
-
-### ** Examples
-
-animate_stars(flea[1:10, 1:6])
-animate_stars(flea[1:10, 1:6], grand_tour(5))
-animate_stars(flea[, 1:6], grand_tour(5))
-animate_stars(flea[1:10, 1:6], grand_tour(5),
- col.stars = rep("grey50", 10), radius = FALSE
-)
-
-
-
diff --git a/test/display_stereo.r b/test/display_stereo.r
deleted file mode 100644
index 990aed3f..00000000
--- a/test/display_stereo.r
+++ /dev/null
@@ -1,11 +0,0 @@
-### Name: display_stereo
-### Title: Anaglpyh tour path animation.
-### Aliases: display_stereo animate_stereo
-### Keywords: hplot
-
-### ** Examples
-
-animate_stereo(flea[, 1:6])
-
-
-
diff --git a/test/display_xy.r b/test/display_xy.r
deleted file mode 100644
index 459e7dd6..00000000
--- a/test/display_xy.r
+++ /dev/null
@@ -1,38 +0,0 @@
-### Name: display_xy
-### Title: Display tour path with a scatterplot
-### Aliases: display_xy animate_xy
-
-### ** Examples
-
-animate_xy(flea[, 1:6])
-animate(flea[, 1:6], tour_path = grand_tour(), display = display_xy())
-animate(flea[, 1:6],
- tour_path = grand_tour(),
- display = display_xy(axes = "bottomleft")
-)
-animate(flea[, 1:6],
- tour_path = grand_tour(),
- display = display_xy(half_range = 0.5)
-)
-animate_xy(flea[, 1:6], tour_path = little_tour())
-animate_xy(flea[, 1:3], tour_path = guided_tour(holes()), sphere = TRUE)
-animate_xy(flea[, 1:6], center = FALSE)
-
-# The default axes are centered, like a biplot, but there are other options
-animate_xy(flea[, 1:6], axes = "bottomleft")
-animate_xy(flea[, 1:6], axes = "off")
-animate_xy(flea[, 1:6], dependence_tour(c(1, 2, 1, 2, 1, 2)),
- axes = "bottomleft"
-)
-
-animate_xy(flea[, -7], col = flea$species)
-
-# You can also draw lines
-edges <- matrix(c(1:5, 2:6), ncol = 2)
-animate(
- flea[, 1:6], grand_tour(),
- display_xy(axes = "bottomleft", edges = edges)
-)
-
-
-
diff --git a/test/freeze.r b/test/freeze.r
deleted file mode 100644
index a52df356..00000000
--- a/test/freeze.r
+++ /dev/null
@@ -1,17 +0,0 @@
-### Name: freeze
-### Title: Freeze and thaw matrices
-### Aliases: freeze thaw
-### Keywords: internal
-
-### ** Examples
-
-frozen <- matrix(NA, nrow = 4, ncol = 2)
-frozen[3, ] <- .5
-
-input <- basis_random(4, 2)
-freeze(input, frozen)
-thaw(input, frozen)
-freeze(basis_random(4, 2), frozen)
-
-
-
diff --git a/test/frozen_guided_tour.r b/test/frozen_guided_tour.r
deleted file mode 100644
index e9508951..00000000
--- a/test/frozen_guided_tour.r
+++ /dev/null
@@ -1,12 +0,0 @@
-### Name: frozen_guided_tour
-### Title: The frozen guided tour
-### Aliases: frozen_guided_tour
-
-### ** Examples
-
-frozen <- matrix(NA, nrow = 4, ncol = 2)
-frozen[3, ] <- .5
-animate_xy(flea[, 1:4], frozen_guided_tour(frozen, holes()))
-
-
-
diff --git a/test/frozen_tour.r b/test/frozen_tour.r
deleted file mode 100644
index 579943c8..00000000
--- a/test/frozen_tour.r
+++ /dev/null
@@ -1,41 +0,0 @@
-### Name: frozen_tour
-### Title: A frozen tour path.
-### Aliases: frozen_tour
-
-### ** Examples
-
-frozen <- matrix(NA, nrow = 4, ncol = 2)
-frozen[3, ] <- .5
-animate_xy(flea[, 1:4], frozen_tour(2, frozen))
-## Not run:
-##D # Doesn't work - a bug?
-##D frozen <- matrix(NA, nrow = 4, ncol = 2)
-##D frozen[1, 1] <- 0.5
-##D animate_xy(flea[, 1:4], frozen_tour(2, frozen))
-##D
-##D # Doesn't work - a bug?
-##D frozen <- matrix(NA, nrow = 4, ncol = 2)
-##D frozen[, 1] <- 1 / 2
-##D animate_xy(flea[, 1:4], frozen_tour(2, frozen))
-##D
-##D # Doesn't work - a bug?
-##D frozen[3, ] <- c(0, 1)
-##D animate_xy(flea[, 1:4], frozen_tour(2, frozen))
-##D
-##D # Doesn't move, which is correct - no free variables
-##D frozen[4, ] <- .2
-##D animate_xy(flea[, 1:4], frozen_tour(2, frozen))
-##D
-##D # Doesn't work - a bug?
-##D frozen <- matrix(NA, nrow = 4, ncol = 2)
-##D frozen[, 1] <- 1 / 2
-##D animate_xy(flea[, 1:4], frozen_tour(2, frozen))
-## End(Not run)
-# Two frozen variables in five 5.
-frozen <- matrix(NA, nrow = 5, ncol = 2)
-frozen[3, ] <- .5
-frozen[4, ] <- c(-.2, .2)
-animate_xy(flea[, 1:5], frozen_tour(2, frozen))
-
-
-
diff --git a/test/geodesic_path.r b/test/geodesic_path.r
deleted file mode 100644
index 320a8a28..00000000
--- a/test/geodesic_path.r
+++ /dev/null
@@ -1,18 +0,0 @@
-### Name: geodesic_path
-### Title: Generate geodesic path.
-### Aliases: geodesic_path
-### Keywords: internal
-
-### ** Examples
-
-a <- basis_random(4, 2)
-b <- basis_random(4, 2)
-path <- geodesic_path(a, b)
-
-path$dist
-all.equal(a, path$interpolate(0))
-# Not true generally - a rotated into plane of b
-all.equal(b, path$interpolate(1))
-
-
-
diff --git a/test/grand_tour.r b/test/grand_tour.r
deleted file mode 100644
index ef1e96cc..00000000
--- a/test/grand_tour.r
+++ /dev/null
@@ -1,27 +0,0 @@
-### Name: grand_tour
-### Title: A grand tour path.
-### Aliases: grand_tour
-
-### ** Examples
-
-# All animation methods use the grand tour path by default
-animate_dist(flea[, 1:6])
-animate_xy(flea[, 1:6])
-animate_pcp(flea[, 1:6])
-animate_pcp(flea[, 1:6], grand_tour(4))
-
-# The grand tour is a function:
-tour2d <- grand_tour(2)
-is.function(tour2d)
-
-# with two parameters, the previous projection and the data set
-args(tour2d)
-# if the previous projection is null, it will generate a starting
-# basis, otherwise the argument is ignored
-tour2d(NULL, mtcars)
-# the data argument is just used to determine the correct dimensionality
-# of the output matrix
-tour2d(NULL, mtcars[, 1:2])
-
-
-
diff --git a/test/guided_section_tour.r b/test/guided_section_tour.r
deleted file mode 100644
index 28bb11d9..00000000
--- a/test/guided_section_tour.r
+++ /dev/null
@@ -1,25 +0,0 @@
-### Name: guided_section_tour
-### Title: A guided section tour path.
-### Aliases: guided_section_tour
-
-### ** Examples
-
-# Generate samples on a 3d hollow sphere using the geozoo package
-set.seed(12345)
-sphere3 <- geozoo::sphere.hollow(3)$points
-# Columns need to be named before launching the tour
-colnames(sphere3) <- c("x1", "x2", "x3")
-# Off-center anchoring
-anchor3 <- rep(0.75, 3)
-# Index setup
-r_breaks <- linear_breaks(5, 0, 1)
-a_breaks <- angular_breaks(10)
-eps <- estimate_eps(nrow(sphere3), ncol(sphere3), 0.1 / 1, 5 * 10, 10, r_breaks)
-idx <- slice_index(r_breaks, a_breaks, eps, bintype = "polar", power = 1, reweight = TRUE, p = 3)
-# Running the guided section tour select sections showing a big hole in the center
-animate_slice(sphere3, guided_section_tour(idx, v_rel = 0.1, anchor = anchor3, max.tries = 5),
- v_rel = 0.1, anchor = anchor3
-)
-
-
-
diff --git a/test/guided_tour.r b/test/guided_tour.r
deleted file mode 100644
index 473584c6..00000000
--- a/test/guided_tour.r
+++ /dev/null
@@ -1,19 +0,0 @@
-### Name: guided_tour
-### Title: A guided tour path.
-### Aliases: guided_tour
-
-### ** Examples
-
-animate_xy(flea[, 1:6], guided_tour(holes()), sphere = TRUE)
-animate_xy(flea[, 1:6], guided_tour(holes(), search_f = search_better_random), sphere = TRUE)
-animate_dist(flea[, 1:6], guided_tour(holes(), 1), sphere = TRUE)
-animate_xy(flea[, 1:6], guided_tour(lda_pp(flea[, 7])), sphere = TRUE, col = flea$species)
-
-# save_history is particularly useful in conjunction with the
-# guided tour as it allows us to look at the tour path in many different
-# ways
-f <- flea[, 1:3]
-tries <- replicate(5, save_history(f, guided_tour(holes())), simplify = FALSE)
-
-
-
diff --git a/test/interpolate.r b/test/interpolate.r
deleted file mode 100644
index 0d62d9e9..00000000
--- a/test/interpolate.r
+++ /dev/null
@@ -1,15 +0,0 @@
-### Name: interpolate
-### Title: Interpolate geodesically between bases.
-### Aliases: interpolate
-### Keywords: hplot
-
-### ** Examples
-
-t1 <- save_history(flea[, 1:6], grand_tour(1), max = 10)
-dim(t1)
-dim(interpolate(t1, 0.01))
-dim(interpolate(t1, 0.05))
-dim(interpolate(t1, 0.1))
-
-
-
diff --git a/test/little_tour.r b/test/little_tour.r
deleted file mode 100644
index 9b5ef753..00000000
--- a/test/little_tour.r
+++ /dev/null
@@ -1,13 +0,0 @@
-### Name: little_tour
-### Title: A little tour path.
-### Aliases: little_tour
-
-### ** Examples
-
-animate_xy(flea[, 1:6], little_tour())
-animate_pcp(flea[, 1:6], little_tour(3))
-animate_scatmat(flea[, 1:6], little_tour(3))
-animate_pcp(flea[, 1:6], little_tour(4))
-
-
-
diff --git a/test/local_tour.r b/test/local_tour.r
deleted file mode 100644
index 8077361a..00000000
--- a/test/local_tour.r
+++ /dev/null
@@ -1,12 +0,0 @@
-### Name: local_tour
-### Title: A local tour path.
-### Aliases: local_tour
-
-### ** Examples
-
-animate_xy(flea[, 1:3], local_tour(basis_init(3, 2)))
-animate_xy(flea[, 1:3], local_tour(basis_init(3, 2), 0.2))
-animate_xy(flea[, 1:3], local_tour(basis_random(3, 2), 0.2))
-
-
-
diff --git a/test/norm_bin.r b/test/norm_bin.r
deleted file mode 100644
index 5edf1571..00000000
--- a/test/norm_bin.r
+++ /dev/null
@@ -1,20 +0,0 @@
-### Name: norm_bin
-### Title: Normality index.
-### Aliases: norm_bin norm_kol
-### Keywords: hplot
-
-### ** Examples
-
-# manually compute the norm_kol index
-# create the index function
-set.seed(123)
-index <- norm_kol(nrow(flea[, 1:3]))
-# create the projection
-proj <- matrix(c(1, 0, 0), nrow = 3)
-# pre-process the example data
-flea_s <- sphere_data(flea[, 1:3])
-# produce the index value
-index(flea_s %*% proj)
-
-
-
diff --git a/test/path_curves.r b/test/path_curves.r
deleted file mode 100644
index ea9034ea..00000000
--- a/test/path_curves.r
+++ /dev/null
@@ -1,40 +0,0 @@
-### Name: path_curves
-### Title: Draw the path that the geodesics took.
-### Aliases: path_curves
-
-### ** Examples
-
-path1d <- save_history(flea[, 1:6], grand_tour(1), 10)
-path2d <- save_history(flea[, 1:6], grand_tour(2), 10)
-
-if (require("ggplot2")) {
- plot(path_curves(path1d))
- plot(path_curves(interpolate(path1d)))
-
- plot(path_curves(path2d))
- plot(path_curves(interpolate(path2d)))
-
- # Instead of relying on the built in plot method, you might want to
- # generate your own. Here are few examples of alternative displays:
-
- df <- path_curves(path2d)
- ggplot(data = df, aes(x = step, y = value, group = obs:var, colour = var)) +
- geom_line() +
- facet_wrap(~obs)
-
- library(tidyr)
- ggplot(
- data = pivot_wider(df,
- id_cols = c(obs, step),
- names_from = var, names_prefix = "Var",
- values_from = value
- ),
- aes(x = Var1, y = Var2)
- ) +
- geom_point() +
- facet_wrap(~step) +
- coord_equal()
-}
-
-
-
diff --git a/test/path_dist.r b/test/path_dist.r
deleted file mode 100644
index e541b610..00000000
--- a/test/path_dist.r
+++ /dev/null
@@ -1,43 +0,0 @@
-### Name: path_dist
-### Title: Compute distance matrix from bases.
-### Aliases: path_dist
-
-### ** Examples
-
-## Not run:
-##D grand <- interpolate(save_history(flea[, 1:6], max = 50), 0.2)
-##D # The grand tour -----------------------------
-##D # Look at the tour path in a tour, how well does it cover a sphere
-##D # Using MDS
-##D d <- path_dist(grand)
-##D ord <- as.data.frame(MASS::isoMDS(d)$points)
-##D qplot(V1, V2, data = ord, geom = "path") +
-##D coord_equal() + labs(x = NULL, y = NULL)
-## End(Not run)
-
-# 5 guided tours -----------------------------
-holes1d <- guided_tour(holes(), 1)
-tour_reps <- replicate(5, save_history(flea[, 1:6], holes1d, max = 10),
- simplify = FALSE
-)
-tour_reps2 <- lapply(tour_reps, interpolate, 0.2)
-
-bases <- unlist(lapply(tour_reps2, as.list), recursive = FALSE)
-class(bases) <- "history_list"
-index_values <- paths_index(tour_reps2, holes())
-d <- path_dist(bases)
-ord <- as.data.frame(cmdscale(d, 2))
-
-info <- cbind(ord, index_values)
-if (require("ggplot2")) {
- ggplot(data = info, aes(x = step, y = value, group = try)) +
- geom_line()
- ggplot(data = info, aes(x = V1, y = V2, group = try)) +
- geom_path() +
- geom_point(aes(size = value)) +
- coord_equal()
- last_plot() + facet_wrap(~try)
-}
-
-
-
diff --git a/test/path_index.r b/test/path_index.r
deleted file mode 100644
index 8ef10036..00000000
--- a/test/path_index.r
+++ /dev/null
@@ -1,23 +0,0 @@
-### Name: path_index
-### Title: Compute index values for a tour history.
-### Aliases: path_index
-### Keywords: hplot
-
-### ** Examples
-
-fl_holes <- save_history(flea[, 1:6], guided_tour(holes()), sphere = TRUE)
-path_index(fl_holes, holes())
-path_index(fl_holes, cmass())
-
-plot(path_index(fl_holes, holes()), type = "l")
-plot(path_index(fl_holes, cmass()), type = "l")
-
-# Use interpolate to show all intermediate bases as well
-## Not run:
-##D hi <- path_index(interpolate(fl_holes), holes())
-##D hi
-##D plot(hi)
-## End(Not run)
-
-
-
diff --git a/test/paths_index.r b/test/paths_index.r
deleted file mode 100644
index 905a0833..00000000
--- a/test/paths_index.r
+++ /dev/null
@@ -1,23 +0,0 @@
-### Name: paths_index
-### Title: Compute index value for many histories.
-### Aliases: paths_index
-### Keywords: internal
-
-### ** Examples
-
-holes1d <- guided_tour(holes(), 1)
-# Perform guided tour 5 times, saving results
-tries <- replicate(5, save_history(flea[, 1:6], holes1d), simplify = FALSE)
-# Interpolate between target bases
-itries <- lapply(tries, interpolate)
-
-paths <- paths_index(itries, holes())
-head(paths)
-
-if (require(ggplot2)) {
- qplot(step, value, data = paths, group = try, geom = "line")
- qplot(step, improvement, data = paths, group = try, geom = "line")
-}
-
-
-
diff --git a/test/planned_tour.r b/test/planned_tour.r
deleted file mode 100644
index 324b1bb9..00000000
--- a/test/planned_tour.r
+++ /dev/null
@@ -1,17 +0,0 @@
-### Name: planned_tour
-### Title: A planned tour path.
-### Aliases: planned_tour
-### Keywords: dynamic hplot
-
-### ** Examples
-
-twod <- save_history(flea[, 1:3], max = 5)
-str(twod)
-animate_xy(flea[, 1:3], planned_tour(twod))
-animate_xy(flea[, 1:3], planned_tour(twod, TRUE))
-
-oned <- save_history(flea[, 1:6], grand_tour(1), max = 3)
-animate_dist(flea[, 1:6], planned_tour(oned))
-
-
-
diff --git a/test/render.r b/test/render.r
deleted file mode 100644
index 16faab98..00000000
--- a/test/render.r
+++ /dev/null
@@ -1,19 +0,0 @@
-### Name: render
-### Title: Render frames of animation to disk
-### Aliases: render
-### Keywords: hplot
-
-### ** Examples
-
-tmp_path <- tempdir()
-render(flea[, 1:4], grand_tour(), display_xy(), "pdf",
- frames = 10,
- file.path(tmp_path, "test.pdf")
-)
-render(flea[, 1:4], grand_tour(), display_xy(), "png",
- frames = 10,
- file.path(tmp_path, "test-%03d.png")
-)
-
-
-
diff --git a/test/render_gif.r b/test/render_gif.r
deleted file mode 100644
index 5cef9f52..00000000
--- a/test/render_gif.r
+++ /dev/null
@@ -1,16 +0,0 @@
-### Name: render_gif
-### Title: Render frames of animation to a gif file
-### Aliases: render_gif
-
-### ** Examples
-
-# gifski needs to be installed to render a gif
-if (requireNamespace("gifski", quietly = TRUE)) {
- gif_file <- file.path(tempdir(), "test.gif")
- render_gif(flea[, 1:4], grand_tour(), display_xy(), gif_file)
- utils::browseURL(gif_file)
- unlink(gif_file)
-}
-
-
-
diff --git a/test/save_history.r b/test/save_history.r
deleted file mode 100644
index 2a1b53a3..00000000
--- a/test/save_history.r
+++ /dev/null
@@ -1,34 +0,0 @@
-### Name: save_history
-### Title: Save tour history.
-### Aliases: save_history
-
-### ** Examples
-
-# You can use a saved history to replay tours with different visualisations
-
-t1 <- save_history(flea[, 1:6], max = 3)
-animate_xy(flea[, 1:6], planned_tour(t1))
-## andrews_history(t1)
-## andrews_history(interpolate(t1))
-
-t1 <- save_history(flea[, 1:6], grand_tour(4), max = 3)
-animate_pcp(flea[, 1:6], planned_tour(t1))
-animate_scatmat(flea[, 1:6], planned_tour(t1))
-
-t1 <- save_history(flea[, 1:6], grand_tour(1), max = 3)
-animate_dist(flea[, 1:6], planned_tour(t1))
-
-testdata <- matrix(rnorm(100 * 3), ncol = 3)
-testdata[1:50, 1] <- testdata[1:50, 1] + 10
-testdata <- sphere_data(testdata)
-t2 <- save_history(testdata, guided_tour(holes(), max.tries = 100),
- max = 5, rescale = FALSE
-)
-animate_xy(testdata, planned_tour(t2))
-
-# Or you can use saved histories to visualise the path that the tour took.
-plot(path_index(interpolate(t2), holes()))
-plot(path_curves(interpolate(t2)))
-
-
-
diff --git a/test/search_better.r b/test/search_better.r
deleted file mode 100644
index be8d3340..00000000
--- a/test/search_better.r
+++ /dev/null
@@ -1,11 +0,0 @@
-### Name: search_better
-### Title: Search for a better projection near the current projection.
-### Aliases: search_better
-### Keywords: optimize
-
-### ** Examples
-
-animate_xy(flea[, 1:6], guided_tour(holes(), search_f = search_better))
-
-
-
diff --git a/test/search_better_random.r b/test/search_better_random.r
deleted file mode 100644
index 0e5c2a74..00000000
--- a/test/search_better_random.r
+++ /dev/null
@@ -1,11 +0,0 @@
-### Name: search_better_random
-### Title: Search for a better projection using simulated annealing
-### Aliases: search_better_random
-### Keywords: optimize
-
-### ** Examples
-
-animate_xy(flea[, 1:6], guided_tour(holes(), search_f = search_better_random))
-
-
-
diff --git a/test/search_geodesic.r b/test/search_geodesic.r
deleted file mode 100644
index d7c152a9..00000000
--- a/test/search_geodesic.r
+++ /dev/null
@@ -1,11 +0,0 @@
-### Name: search_geodesic
-### Title: A pseudo-derivative, line search algorithm.
-### Aliases: search_geodesic
-### Keywords: optimize
-
-### ** Examples
-
-animate_xy(flea[, 1:6], guided_tour(holes(), search_f = search_geodesic))
-
-
-
diff --git a/test/search_polish.r b/test/search_polish.r
deleted file mode 100644
index 0f133190..00000000
--- a/test/search_polish.r
+++ /dev/null
@@ -1,23 +0,0 @@
-### Name: search_polish
-### Title: Search very locally to find slightly better projections to
-### polish a broader search.
-### Aliases: search_polish
-### Keywords: optimize
-
-### ** Examples
-
-set.seed(2020)
-t1 <- save_history(flea[, 1:6], guided_tour(holes()), max = 100)
-attr(t1, "class") <- NULL
-best_proj <- t1[, , dim(t1)[3]]
-animate_xy(
- flea[, 1:6],
- guided_tour(holes(),
- search_f = search_polish,
- cur_index = 0
- ),
- start = best_proj
-)
-
-
-
diff --git a/vignettes/tourr.Rmd b/vignettes/tourr.Rmd
index 0746b7eb..68dce5fa 100644
--- a/vignettes/tourr.Rmd
+++ b/vignettes/tourr.Rmd
@@ -32,7 +32,7 @@ library(tourr)
To get started we can simply generate a tour animation for any numeric data matrix with default settings. Here we look at the flea data available in the package, drop the last column (the grouping variable), and call
```{r}
-f <- flea[, 1:6]
+f <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
animate(f)
```