diff --git a/R/geodesic-path.r b/R/geodesic-path.r index 8a72b4b6..7e7a2e64 100644 --- a/R/geodesic-path.r +++ b/R/geodesic-path.r @@ -14,7 +14,7 @@ #' indicating that the tour should stop. #' #' @param name name to give tour path -#' @param generate basis generator function +#' @param generator basis generator function #' @param frozen matrix giving frozen variables, as described in #' \code{\link{freeze}} #' @export diff --git a/R/geodesic.r b/R/geodesic.r index d4c87e13..fcb226b9 100644 --- a/R/geodesic.r +++ b/R/geodesic.r @@ -7,8 +7,10 @@ #' Frozen variables allow us to keep certain values of the projection #' fixed and generate a geodesic across the subspace generated by those #' -#' @param new_target_f function that generates new frame, with previous -#' frame as argument +#' @param current starting projection +#' @param target ending projection +#' @param frozen matrix giving frozen variables, as described in +#' \code{\link{freeze}} #' @keywords internal #' @export #' @return diff --git a/R/section-pursuit.r b/R/section-pursuit.r index 2b462aac..8c4dce69 100644 --- a/R/section-pursuit.r +++ b/R/section-pursuit.r @@ -185,7 +185,7 @@ radial_bin_weight_inv <- function(r1, r2, R, p) { #' Computes weights for the rescaling of radial bin counts. #' -#' @param hsisto input histogram (for bin definitions) +#' @param histo input histogram (for bin definitions) #' @param p number of variables #' #' @keywords internal diff --git a/R/tour-little.r b/R/tour-little.r index 3ab3d476..b1e19cf8 100644 --- a/R/tour-little.r +++ b/R/tour-little.r @@ -38,7 +38,7 @@ little_tour <- function(d = 2) { #' Generate bases for the little tour #' #' @keywords internal -#' @param n dimensionality of data +#' @param p dimensionality of data #' @param d dimensionality of target projection bases_little <- function(p, d = 2) { b <- diag(rep(1, p)) diff --git a/docs/articles/edges_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/edges_files/figure-html/unnamed-chunk-2-1.png index 63fef84c..828e04ea 100644 Binary files a/docs/articles/edges_files/figure-html/unnamed-chunk-2-1.png and b/docs/articles/edges_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/docs/articles/edges_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/edges_files/figure-html/unnamed-chunk-3-1.png index 90cd6a2a..29c9edad 100644 Binary files a/docs/articles/edges_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/edges_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/docs/articles/tourr.html b/docs/articles/tourr.html index 9b08da2d..c680e8d0 100644 --- a/docs/articles/tourr.html +++ b/docs/articles/tourr.html @@ -182,7 +182,7 @@

Tour typesanimate(f, tour_path = guided_tour(holes()), display = display_xy()) -#> Value 1.000 27.3 % better - NEW BASIS +#> Value 1.103 35.5 % better - NEW BASIS #> Using half_range 4.4

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

Tour typesanimate(f, tour_path = guided_tour(holes()), display = display_xy(col = flea$species)) -#> Value 1.084 13.9 % better - NEW BASIS +#> Value 1.059 8.6 % better - NEW BASIS #> Using half_range 4.4

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

Tour typesanimate(f, tour_path = guided_tour(holes()), display = display_xy(col = flea_col)) -#> Value 1.182 28.5 % better - NEW BASIS +#> Value 0.848 7.2 % better - NEW BASIS #> Using half_range 4.4

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a/docs/reference/bases_little.html +++ b/docs/reference/bases_little.html @@ -71,12 +71,12 @@

Generate bases for the little tour

Arguments

-
d
-

dimensionality of target projection

+
p
+

dimensionality of data

-
n
-

dimensionality of data

+
d
+

dimensionality of target projection

diff --git a/docs/reference/dependence_tour-1.png b/docs/reference/dependence_tour-1.png index d63220a8..624fdc0f 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 903e4de4..8028c638 100644 Binary files a/docs/reference/dependence_tour-2.png and b/docs/reference/dependence_tour-2.png differ diff --git a/docs/reference/dependence_tour-3.png b/docs/reference/dependence_tour-3.png index 73429099..29de2e42 100644 Binary files a/docs/reference/dependence_tour-3.png and b/docs/reference/dependence_tour-3.png differ diff --git a/docs/reference/display_andrews-11.png b/docs/reference/display_andrews-11.png index f707f745..52d0d94f 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 f707f745..52d0d94f 100644 Binary files a/docs/reference/display_andrews-12.png and b/docs/reference/display_andrews-12.png differ diff --git a/docs/reference/display_andrews-3.png b/docs/reference/display_andrews-3.png index 48be0e8f..1d0ba371 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 5e3aeb05..2a54813b 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 05fc9a9e..adb4a045 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 637f1f66..4eb24468 100644 --- a/docs/reference/display_andrews.html +++ b/docs/reference/display_andrews.html @@ -147,12 +147,12 @@

Examples

#> Value -0.582 -0.0 % better #> No better bases found after 25 tries. Giving up. #> Final projection: -#> 0.147 0.730 -#> -0.201 -0.306 -#> 0.136 0.463 -#> -0.087 0.314 -#> 0.549 -0.026 -#> -0.781 0.244 +#> -0.284 -0.009 +#> 0.251 -0.348 +#> -0.393 0.093 +#> 0.303 0.912 +#> 0.651 -0.161 +#> -0.433 0.115 diff --git a/docs/reference/display_density2d-11.png b/docs/reference/display_density2d-11.png index 0cfdf325..1b31ea32 100644 Binary files a/docs/reference/display_density2d-11.png and b/docs/reference/display_density2d-11.png differ diff --git a/docs/reference/display_density2d-12.png b/docs/reference/display_density2d-12.png index d723d37c..4a03a6b5 100644 Binary files a/docs/reference/display_density2d-12.png and b/docs/reference/display_density2d-12.png differ diff --git a/docs/reference/display_density2d-13.png b/docs/reference/display_density2d-13.png index 5bb0804e..c2b486dd 100644 Binary files a/docs/reference/display_density2d-13.png and b/docs/reference/display_density2d-13.png differ diff --git a/docs/reference/display_density2d-14.png b/docs/reference/display_density2d-14.png index 740a730f..d499e55b 100644 Binary files a/docs/reference/display_density2d-14.png and b/docs/reference/display_density2d-14.png differ diff --git a/docs/reference/display_density2d-15.png b/docs/reference/display_density2d-15.png index b051f064..25e20cb3 100644 Binary files a/docs/reference/display_density2d-15.png and b/docs/reference/display_density2d-15.png differ diff --git a/docs/reference/display_density2d-16.png b/docs/reference/display_density2d-16.png index 7ceb63a3..ffa085a4 100644 Binary files a/docs/reference/display_density2d-16.png and b/docs/reference/display_density2d-16.png differ diff --git a/docs/reference/display_density2d-17.png b/docs/reference/display_density2d-17.png index 2797513b..321e521c 100644 Binary files a/docs/reference/display_density2d-17.png and b/docs/reference/display_density2d-17.png differ diff --git a/docs/reference/display_density2d-18.png b/docs/reference/display_density2d-18.png index 161b81c1..e2585f0b 100644 Binary files a/docs/reference/display_density2d-18.png and b/docs/reference/display_density2d-18.png differ diff --git a/docs/reference/display_density2d-2.png b/docs/reference/display_density2d-2.png index bda1cf4d..0d6f7d53 100644 Binary files a/docs/reference/display_density2d-2.png and b/docs/reference/display_density2d-2.png differ diff --git a/docs/reference/display_density2d-21.png b/docs/reference/display_density2d-21.png index 86b5330f..eaeae4e0 100644 Binary files a/docs/reference/display_density2d-21.png and b/docs/reference/display_density2d-21.png differ diff --git a/docs/reference/display_density2d-24.png b/docs/reference/display_density2d-24.png index bb4e5760..5ff9760c 100644 Binary files a/docs/reference/display_density2d-24.png and b/docs/reference/display_density2d-24.png differ diff --git a/docs/reference/display_density2d-27.png b/docs/reference/display_density2d-27.png index 61332fb5..4e219e0a 100644 Binary files a/docs/reference/display_density2d-27.png and b/docs/reference/display_density2d-27.png differ diff --git a/docs/reference/display_density2d-3.png b/docs/reference/display_density2d-3.png index 5b09815f..abe06e84 100644 Binary files a/docs/reference/display_density2d-3.png and b/docs/reference/display_density2d-3.png differ diff --git a/docs/reference/display_density2d-30.png b/docs/reference/display_density2d-30.png index 64ba9c3a..c39b2e75 100644 Binary files a/docs/reference/display_density2d-30.png and b/docs/reference/display_density2d-30.png differ diff --git a/docs/reference/display_density2d-31.png b/docs/reference/display_density2d-31.png index d3fab9b1..ebc4816c 100644 Binary files a/docs/reference/display_density2d-31.png and b/docs/reference/display_density2d-31.png differ diff --git a/docs/reference/display_density2d-34.png b/docs/reference/display_density2d-34.png index ab1219bc..67702108 100644 Binary files a/docs/reference/display_density2d-34.png and b/docs/reference/display_density2d-34.png differ diff --git a/docs/reference/display_density2d-5.png b/docs/reference/display_density2d-5.png index 53899492..b9ba4207 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 a4adfbe8..17252ffd 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 85f843fd..bed42350 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 f5a7188d..3c363c06 100644 --- a/docs/reference/display_density2d.html +++ b/docs/reference/display_density2d.html @@ -203,9 +203,9 @@

Examples

#> Value 1.582 0.0 % better #> No better bases found after 25 tries. Giving up. #> Final projection: -#> 0.016 -0.899 -#> 0.778 0.286 -#> -0.628 0.331 +#> -0.483 -0.388 +#> -0.860 0.379 +#> -0.165 -0.840 #> Using half_range 65 diff --git a/docs/reference/display_depth-1.png b/docs/reference/display_depth-1.png index 84dca95a..e46081f4 100644 Binary files a/docs/reference/display_depth-1.png and b/docs/reference/display_depth-1.png differ diff --git a/docs/reference/display_dist-10.png b/docs/reference/display_dist-10.png index 523113f1..eac73293 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 926835f6..59ae3de4 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 8156fb2a..4457d40c 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 a329c261..df2e3832 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 d8538b74..8258fab4 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 72133909..716aab0c 100644 Binary files a/docs/reference/display_dist-8.png and b/docs/reference/display_dist-8.png differ diff --git a/docs/reference/display_faces-2.png b/docs/reference/display_faces-2.png index 014cfec5..2565b475 100644 Binary files a/docs/reference/display_faces-2.png and b/docs/reference/display_faces-2.png differ diff --git a/docs/reference/display_faces-4.png b/docs/reference/display_faces-4.png index 116e1e82..cfac7b58 100644 Binary files a/docs/reference/display_faces-4.png and b/docs/reference/display_faces-4.png differ diff --git a/docs/reference/display_faces-6.png b/docs/reference/display_faces-6.png index 550b7576..5613065c 100644 Binary files a/docs/reference/display_faces-6.png and b/docs/reference/display_faces-6.png differ diff --git a/docs/reference/display_groupxy-2.png b/docs/reference/display_groupxy-2.png index 957f2406..d9ae6279 100644 Binary files a/docs/reference/display_groupxy-2.png and b/docs/reference/display_groupxy-2.png differ diff --git a/docs/reference/display_groupxy-4.png b/docs/reference/display_groupxy-4.png index ff897651..b4ee5166 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 f98a4f3c..53b9d9d7 100644 --- a/docs/reference/display_groupxy.html +++ b/docs/reference/display_groupxy.html @@ -186,7 +186,7 @@

Examples

x.edges.col <- factor(c(rep("A", 2), rep("B", 2), rep("C", 3))) animate_groupxy(x[,1:3], col=x$cl, group_by=x$cl, edges=x.edges, edges.col=x.edges.col) #> Converting input data to the required matrix format. -#> Using half_range 1.4 +#> Using half_range 1.5 #> Warning: "shapes" is not a graphical parameter #> Warning: "shapes" is not a graphical parameter #> Warning: "shapes" is not a graphical parameter diff --git a/docs/reference/display_pca-1.png b/docs/reference/display_pca-1.png index 7567ebdd..157a5954 100644 Binary files a/docs/reference/display_pca-1.png and b/docs/reference/display_pca-1.png differ diff --git a/docs/reference/display_pcp-1.png b/docs/reference/display_pcp-1.png index 96fabddd..4c217bc0 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 2d6c840f..84d9cf5c 100644 Binary files a/docs/reference/display_pcp-2.png and 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a/docs/reference/display_xy.html b/docs/reference/display_xy.html index 3031a02a..2de3221f 100644 --- a/docs/reference/display_xy.html +++ b/docs/reference/display_xy.html @@ -177,7 +177,7 @@

Examples

animate_xy(flea[, 1:3], tour_path = guided_tour(holes()), sphere = TRUE) #> Converting input data to the required matrix format. -#> Value 0.827 2.5 % better - NEW BASIS +#> Value 0.837 0.6 % better - NEW BASIS #> Using half_range 3.2 animate_xy(flea[, 1:6], center = FALSE) diff --git a/docs/reference/draw_tour_axes-1.png b/docs/reference/draw_tour_axes-1.png index b7768846..28b196fe 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 fcaed233..ed2f01ad 100644 Binary files a/docs/reference/draw_tour_axes-2.png and b/docs/reference/draw_tour_axes-2.png differ diff --git a/docs/reference/freeze.html b/docs/reference/freeze.html index d2df8e34..6ebf7499 100644 --- a/docs/reference/freeze.html +++ b/docs/reference/freeze.html @@ -90,22 +90,22 @@

Examples

input <- basis_random(4, 2) freeze(input, frozen) #> [,1] [,2] -#> [1,] -0.1515432 -0.6462411 -#> [2,] 0.7354669 0.3831480 +#> [1,] -0.6038761 0.7002916 +#> [2,] -0.1800735 -0.4007407 #> [3,] 0.0000000 0.0000000 -#> [4,] -0.6140834 0.6538525 +#> [4,] 0.7000045 0.5719757 thaw(input, frozen) #> [,1] [,2] -#> [1,] -0.1312403 -0.5596612 -#> [2,] 0.6369330 0.3318159 +#> [1,] -0.5229720 0.6064703 +#> [2,] -0.1559482 -0.3470516 #> [3,] 0.5000000 0.5000000 -#> [4,] -0.5318118 0.5662529 +#> [4,] 0.6062217 0.4953455 freeze(basis_random(4, 2), frozen) -#> [,1] [,2] -#> [1,] -0.1074163 -0.1271482 -#> [2,] -0.4536378 0.7338281 -#> [3,] 0.0000000 0.0000000 -#> [4,] 0.5209596 -0.2412205 +#> [,1] [,2] +#> [1,] 0.2581632 -0.09488073 +#> [2,] -0.7594302 -0.58362240 +#> [3,] 0.0000000 0.00000000 +#> [4,] -0.5952164 0.66664063 diff --git a/docs/reference/frozen_tour-1.png b/docs/reference/frozen_tour-1.png index 35c3e61d..5eb777cd 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 e491d69e..b87218d9 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 4b96fd49..267c55f1 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 bff3ef77..a57c5047 100644 Binary files a/docs/reference/frozen_tour-4.png and b/docs/reference/frozen_tour-4.png differ diff --git a/docs/reference/geodesic_path.html b/docs/reference/geodesic_path.html index e6d58dad..576600c9 100644 --- a/docs/reference/geodesic_path.html +++ b/docs/reference/geodesic_path.html @@ -75,9 +75,17 @@

Generate geodesic path.

Arguments

-
new_target_f
-

function that generates new frame, with previous -frame as argument

+
current
+

starting projection

+ + +
target
+

ending projection

+ + +
frozen
+

matrix giving frozen variables, as described in +freeze

@@ -121,12 +129,12 @@

Examples

path <- geodesic_path(a, b) path$dist -#> [1] 1.161552 +#> [1] 1.414265 all.equal(a, path$interpolate(0)) #> [1] TRUE # Not true generally - a rotated into plane of b all.equal(b, path$interpolate(1)) -#> [1] "Mean relative difference: 1.600941" +#> [1] "Mean relative difference: 1.783492"
diff --git a/docs/reference/grand_tour-2.png b/docs/reference/grand_tour-2.png index 0741707f..27448f75 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 ca122c91..71b5887f 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 44a85658..f89496bd 100644 Binary files a/docs/reference/grand_tour-4.png and b/docs/reference/grand_tour-4.png differ diff --git a/docs/reference/new_geodesic_path.html b/docs/reference/new_geodesic_path.html index d3964477..7b60b666 100644 --- a/docs/reference/new_geodesic_path.html +++ b/docs/reference/new_geodesic_path.html @@ -83,14 +83,14 @@

Arguments

name to give tour path

+
generator
+

basis generator function

+ +
frozen

matrix giving frozen variables, as described in freeze

- -
generate
-

basis generator function

-

Details

diff --git a/docs/reference/weights_bincount_radial.html b/docs/reference/weights_bincount_radial.html index 445b0a79..e5561f9e 100644 --- a/docs/reference/weights_bincount_radial.html +++ b/docs/reference/weights_bincount_radial.html @@ -71,12 +71,12 @@

Computes weights for the rescaling of radial bin counts.

Arguments

-
p
-

number of variables

+
histo
+

input histogram (for bin definitions)

-
hsisto
-

input histogram (for bin definitions)

+
p
+

number of variables

diff --git a/man/bases_little.Rd b/man/bases_little.Rd index 30d9a785..1749d1ee 100644 --- a/man/bases_little.Rd +++ b/man/bases_little.Rd @@ -7,9 +7,9 @@ bases_little(p, d = 2) } \arguments{ -\item{d}{dimensionality of target projection} +\item{p}{dimensionality of data} -\item{n}{dimensionality of data} +\item{d}{dimensionality of target projection} } \description{ Generate bases for the little tour diff --git a/man/geodesic_path.Rd b/man/geodesic_path.Rd index 858f23be..63cc247b 100644 --- a/man/geodesic_path.Rd +++ b/man/geodesic_path.Rd @@ -7,8 +7,12 @@ geodesic_path(current, target, frozen = NULL, ...) } \arguments{ -\item{new_target_f}{function that generates new frame, with previous -frame as argument} +\item{current}{starting projection} + +\item{target}{ending projection} + +\item{frozen}{matrix giving frozen variables, as described in +\code{\link{freeze}}} } \value{ \item{interpolate}{A function with single parameter in [0, 1] that diff --git a/man/new_geodesic_path.Rd b/man/new_geodesic_path.Rd index 2a313f20..723cb177 100644 --- a/man/new_geodesic_path.Rd +++ b/man/new_geodesic_path.Rd @@ -9,10 +9,10 @@ new_geodesic_path(name, generator, frozen = NULL, ...) \arguments{ \item{name}{name to give tour path} +\item{generator}{basis generator function} + \item{frozen}{matrix giving frozen variables, as described in \code{\link{freeze}}} - -\item{generate}{basis generator function} } \description{ A tour path is a function that when called with the current projection diff --git a/man/weights_bincount_radial.Rd b/man/weights_bincount_radial.Rd index 617f6893..d14b686b 100644 --- a/man/weights_bincount_radial.Rd +++ b/man/weights_bincount_radial.Rd @@ -7,9 +7,9 @@ weights_bincount_radial(histo, p) } \arguments{ -\item{p}{number of variables} +\item{histo}{input histogram (for bin definitions)} -\item{hsisto}{input histogram (for bin definitions)} +\item{p}{number of variables} } \description{ Computes weights for the rescaling of radial bin counts.