fix checks

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

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)

R/interesting-indices.r

@@ -84,6 +84,7 @@ splines2d <- function() {
 }
 
 #' @rdname spline-loess
+#' @importFrom stats loess
 #' @export
 loess2d <- function() {
  function(mat) {

R/search-jellyfish.R

@@ -1,15 +1,20 @@
-#' 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
 #' @param tries the counter of the outer loop of the opotimiser
 #' @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"))

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

R/util.r

@@ -162,3 +162,5 @@ mapShapes <- function(x, shapeset) {
  shapes <- shapeset
  shapes[as.numeric(x)]
 }
+
+