From 17fd891da93abb8d457d7daf4a0823774eac01dc Mon Sep 17 00:00:00 2001
From: huizezhang-sherry <huizezhangsh@gmail.com>
Date: Thu, 5 Sep 2024 00:12:39 +0200
Subject: [PATCH] fix checks

---
 DESCRIPTION                               |  2 +-
 NAMESPACE                                 |  2 +
 R/interesting-indices.r                   |  1 +
 R/search-jellyfish.R                      | 31 +++++++++--
 R/tour-guided.r                           |  1 +
 R/util.r                                  |  2 +
 man/anomaly_index.Rd                      | 12 ++++
 man/guided_anomaly_tour.Rd                | 67 +++++++++++++++++++++++
 man/guided_tour.Rd                        |  2 +
 man/{search_jellyfish.Rd => jellyfish.Rd} | 18 ++++--
 man/mahal_dist.Rd                         | 18 ++++++
 11 files changed, 147 insertions(+), 9 deletions(-)
 create mode 100644 man/anomaly_index.Rd
 create mode 100644 man/guided_anomaly_tour.Rd
 rename man/{search_jellyfish.Rd => jellyfish.Rd} (50%)
 create mode 100644 man/mahal_dist.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 30e3be8b..6f5af5c7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -41,6 +41,6 @@ License: MIT + file LICENSE
 LazyData: true
 URL: https://github.com/ggobi/tourr
 BugReports: https://github.com/ggobi/tourr/issues
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
index 133de2a4..75d9b2c1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -142,12 +142,14 @@ importFrom(graphics,rect)
 importFrom(graphics,segments)
 importFrom(graphics,stars)
 importFrom(graphics,text)
+importFrom(stats,loess)
 importFrom(stats,mahalanobis)
 importFrom(stats,na.omit)
 importFrom(stats,qchisq)
 importFrom(stats,quantile)
 importFrom(stats,residuals)
 importFrom(stats,rnorm)
+importFrom(stats,runif)
 importFrom(stats,var)
 importFrom(utils,globalVariables)
 importFrom(utils,tail)
diff --git a/R/interesting-indices.r b/R/interesting-indices.r
index e9b81479..65518d75 100644
--- a/R/interesting-indices.r
+++ b/R/interesting-indices.r
@@ -84,6 +84,7 @@ splines2d <- function() {
 }
 
 #' @rdname spline-loess
+#' @importFrom stats loess
 #' @export
 loess2d <- function() {
   function(mat) {
diff --git a/R/search-jellyfish.R b/R/search-jellyfish.R
index 36e14664..44a45403 100644
--- a/R/search-jellyfish.R
+++ b/R/search-jellyfish.R
@@ -1,4 +1,4 @@
-#' An jellyfish optimisers for the projection pursuit guided tour
+#' A jellyfish optimiser for projection pursuit guided tour
 #'
 #' @param current starting projection, a list of basis of class "multi-bases"
 #' @param index index function
@@ -6,10 +6,15 @@
 #' @param max.tries the maximum number of iteration before giving up
 #' @param ... other arguments being passed into the \code{search_jellyfish()}
 #' @keywords optimize
+#' @importFrom stats runif
+#' @rdname jellyfish
 #' @export
 #' @examples
-#' res <- animate_xy(flea[, 1:6], guided_tour(holes(), search_f = search_jellyfish))
-#' res
+#' library(dplyr)
+#' res <- animate_xy(flea[, 1:6], guided_tour(lda_pp(cl = flea$species),
+#' search_f = search_jellyfish))
+#' bases <- res |> filter(loop == 1) |> pull(basis) |> check_dup(0.1)
+#' animate_xy(data = flea[,1:6], tour_path = planned_tour(bases), col = flea$species)
 search_jellyfish <- function(current, index, tries, max.tries = 50, ...) {
   rcd_env <- parent.frame(n = 4)
   if (is.null(rcd_env[["record"]])) rcd_env <- parent.frame(n = 1)
@@ -44,7 +49,7 @@ search_jellyfish <- function(current, index, tries, max.tries = 50, ...) {
     target = lapply(current, function(i) {update_typeB(i, current)})
   }
 
-  target <- purrr::map2(current, target, correct_orientation)
+  target <- mapply(correct_orientation, current, target)
   target_idx <- sapply(target, index)
 
   # if the target is worse than current, use current
@@ -81,4 +86,22 @@ search_jellyfish <- function(current, index, tries, max.tries = 50, ...) {
   }
 }
 
+#' @param bases a list of bases extracted from the data collection object, see examples
+#' @param min_dist the minimum distance between two bases
+#' @rdname jellyfish
+check_dup <- function(bases, min_dist) {
+  res <- list()
+  res[[1]] <- bases[[1]]
+  i <- 1; j <- 2
+  while(j <= length(bases)){
+    if (proj_dist(bases[[i]], bases[[j]]) >= min_dist) {
+      res <- c(res, list(bases[[j]]))
+      i <- i + 1; j <- j + 1
+    } else{
+      j <- j + 1
+    }
+  }
+  return(res)
+}
 
+globalVariables(c("loop"))
diff --git a/R/tour-guided.r b/R/tour-guided.r
index 25fbe3cb..a3a4e1d7 100644
--- a/R/tour-guided.r
+++ b/R/tour-guided.r
@@ -21,6 +21,7 @@
 #'   a better projection before giving up
 #' @param max.i the maximum index value, stop search if a larger value is found
 #' @param n_sample number of samples to generate if \code{search_f} is \code{\link{search_polish}}
+#' @param n_jellies only used for \code{search_jellyfish}, the number of jellyfish to use
 #' @param ... arguments sent to the search_f
 #' @seealso \code{\link{cmass}}, \code{\link{holes}} and \code{\link{lda_pp}}
 #'   for examples of index functions.  The function should take a numeric
diff --git a/R/util.r b/R/util.r
index e2750d10..468de741 100644
--- a/R/util.r
+++ b/R/util.r
@@ -162,3 +162,5 @@ mapShapes <- function(x, shapeset) {
   shapes <- shapeset
   shapes[as.numeric(x)]
 }
+
+
diff --git a/man/anomaly_index.Rd b/man/anomaly_index.Rd
new file mode 100644
index 00000000..299c5b01
--- /dev/null
+++ b/man/anomaly_index.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/anomaly-pursuit.r
+\name{anomaly_index}
+\alias{anomaly_index}
+\title{Anomaly index.}
+\usage{
+anomaly_index()
+}
+\description{
+Calculates an index that looks for the best projection of
+observations that are outside a pre-determined p-D ellipse.
+}
diff --git a/man/guided_anomaly_tour.Rd b/man/guided_anomaly_tour.Rd
new file mode 100644
index 00000000..a9e81f27
--- /dev/null
+++ b/man/guided_anomaly_tour.Rd
@@ -0,0 +1,67 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tour-guided-anomaly.r
+\name{guided_anomaly_tour}
+\alias{guided_anomaly_tour}
+\title{A guided anomaly tour path.}
+\usage{
+guided_anomaly_tour(
+  index_f,
+  d = 2,
+  alpha = 0.5,
+  cooling = 0.99,
+  max.tries = 25,
+  max.i = Inf,
+  ellipse,
+  ellc = NULL,
+  ellmu = NULL,
+  search_f = search_geodesic,
+  ...
+)
+}
+\arguments{
+\item{index_f}{the section pursuit index function to optimise. The function
+needs to take two arguments, the projected data, indexes of anomalies.}
+
+\item{d}{target dimensionality}
+
+\item{alpha}{the initial size of the search window, in radians}
+
+\item{cooling}{the amount the size of the search window should be adjusted
+by after each step}
+
+\item{max.tries}{the maximum number of unsuccessful attempts to find
+a better projection before giving up}
+
+\item{max.i}{the maximum index value, stop search if a larger value is found}
+
+\item{ellipse}{pxp variance-covariance matrix defining ellipse, default NULL.
+Useful for comparing data with some hypothesized null.}
+
+\item{ellc}{This can be considered the equivalent of a critical value, used to
+scale the ellipse larger or smaller to capture more or fewer anomalies. Default 3.}
+
+\item{ellmu}{This is the centre of the ellipse corresponding to the mean of the
+normal population. Default vector of 0's}
+
+\item{search_f}{the search strategy to use}
+
+\item{...}{arguments sent to the search_f}
+}
+\description{
+The guided anomaly tour is a variation of the guided tour that is
+using an ellipse to determine anomalies on which to select target planes.
+}
+\details{
+Usually, you will not call this function directly, but will pass it to
+a method that works with tour paths like \code{\link{animate_slice}},
+\code{\link{save_history}} or \code{\link{render}}.
+}
+\examples{
+animate_xy(flea[, 1:6], guided_anomaly_tour(anomaly_index(),
+  ellipse=cov(flea[,1:6])), ellipse=cov(flea[,1:6]), axes="off")
+}
+\seealso{
+\code{\link{slice_index}} for an example of an index functions.
+\code{\link{search_geodesic}}, \code{\link{search_better}},
+  \code{\link{search_better_random}} for different search strategies
+}
diff --git a/man/guided_tour.Rd b/man/guided_tour.Rd
index 83375437..6ea88cb2 100644
--- a/man/guided_tour.Rd
+++ b/man/guided_tour.Rd
@@ -33,6 +33,8 @@ a better projection before giving up}
 \item{search_f}{the search strategy to use: \code{\link{search_geodesic}}, \code{\link{search_better}},
 \code{\link{search_better_random}}, \code{\link{search_polish}}. Default is \code{\link{search_geodesic}}.}
 
+\item{n_jellies}{only used for \code{search_jellyfish}, the number of jellyfish to use}
+
 \item{n_sample}{number of samples to generate if \code{search_f} is \code{\link{search_polish}}}
 
 \item{alpha}{the initial size of the search window, in radians}
diff --git a/man/search_jellyfish.Rd b/man/jellyfish.Rd
similarity index 50%
rename from man/search_jellyfish.Rd
rename to man/jellyfish.Rd
index c4fec8d1..0307cfa0 100644
--- a/man/search_jellyfish.Rd
+++ b/man/jellyfish.Rd
@@ -2,9 +2,12 @@
 % Please edit documentation in R/search-jellyfish.R
 \name{search_jellyfish}
 \alias{search_jellyfish}
-\title{An jellyfish optimisers for the projection pursuit guided tour}
+\alias{check_dup}
+\title{A jellyfish optimiser for projection pursuit guided tour}
 \usage{
 search_jellyfish(current, index, tries, max.tries = 50, ...)
+
+check_dup(bases, min_dist)
 }
 \arguments{
 \item{current}{starting projection, a list of basis of class "multi-bases"}
@@ -16,12 +19,19 @@ search_jellyfish(current, index, tries, max.tries = 50, ...)
 \item{max.tries}{the maximum number of iteration before giving up}
 
 \item{...}{other arguments being passed into the \code{search_jellyfish()}}
+
+\item{bases}{a list of bases extracted from the data collection object, see examples}
+
+\item{min_dist}{the minimum distance between two bases}
 }
 \description{
-An jellyfish optimisers for the projection pursuit guided tour
+A jellyfish optimiser for projection pursuit guided tour
 }
 \examples{
-res <- animate_xy(flea[, 1:6], guided_tour(holes(), search_f = search_jellyfish))
-res
+library(dplyr)
+res <- animate_xy(flea[, 1:6], guided_tour(lda_pp(cl = flea$species),
+search_f = search_jellyfish))
+bases <- res |> filter(loop == 1) |> pull(basis) |> check_dup(0.1)
+animate_xy(data = flea[,1:6], tour_path = planned_tour(bases), col = flea$species)
 }
 \keyword{optimize}
diff --git a/man/mahal_dist.Rd b/man/mahal_dist.Rd
new file mode 100644
index 00000000..7a67a42b
--- /dev/null
+++ b/man/mahal_dist.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/linear-algebra.r
+\name{mahal_dist}
+\alias{mahal_dist}
+\title{Calculate the Mahalanobis distance between points and center.}
+\usage{
+mahal_dist(x, vc)
+}
+\arguments{
+\item{x}{matrix of data}
+
+\item{vc}{pre-determined variance-covariance matrix}
+}
+\description{
+Computes the Mahalanobis distance using a provided variance-covariance
+matrix of observations from 0.
+}
+\keyword{algebra}