fixes for CRAN submission

DESCRIPTION

@@ -38,6 +38,6 @@ License: MIT + file LICENSE
 LazyData: true
 URL: https://github.com/ggobi/tourr
 BugReports: https://github.com/ggobi/tourr/issues
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 Encoding: UTF-8
 VignetteBuilder: knitr

NEWS.md

@@ -1,6 +1,8 @@
 # tourr 0.6.1
 
-A radial tour is added that will allow a variable to be zero'd from a projection.
+* A radial tour is added that will allow a variable to be zero'd from a projection.
+
+* Fixes made according to CRAN requests
 
 # tourr 0.6.0
 

R/animate.r

@@ -36,7 +36,7 @@ animate <- function(data, tour_path = grand_tour(), display = display_xy(),
                     start = NULL, aps = 1, fps = 10, max_frames = Inf,
                     rescale = TRUE, sphere = FALSE, ...) {
   record <-
-    dplyr::tibble(
+    tibble::tibble(
       basis = list(),
       index_val = numeric(),
       info = character(),

R/data.r

@@ -91,20 +91,17 @@ NULL
 #' Monthly ozone measurements over Central America
 #'
 #'
-#' This data set is a subset of the data from the 2006 ASA Data expo challenge,
-#' \url{https://community.amstat.org/jointscsg-section/dataexpo/new-item5}.
-#' The data are monthly ozone
-#' averages on a very coarse 24 by 24 grid covering Central America, from Jan
-#' 1995 to Dec 2000. The data is stored in a 3d area with the first two
-#' dimensions representing latitude and longitude, and the third representing
+#' This data set is a subset of the data from the 2006 ASA Data expo challenge.
+#' The data are monthly ozone averages on a very coarse 24 by 24 grid covering
+#' Central America, from Jan 1995 to Dec 2000. The data is stored in a 3d area
+#' with the first two dimensions representing latitude and longitude, and the
+#' third representing
 #' time.
 #'
-#'
 #' @name Ozone measurements
 #' @aliases ozone
 #' @docType data
 #' @format A 24 x 24 x 72 numeric array
-#' @references \url{https://community.amstat.org/jointscsg-section/dataexpo/new-item5}
 #' @keywords datasets
 #' @examples
 #'

R/display-xy.r

@@ -72,7 +72,7 @@ display_xy <- function(center = TRUE, axes = "center", half_range = NULL,
     rect(-1, -1, 1, 1, col = "#FFFFFFE6", border = NA)
   }
   render_data <- function(data, proj, geodesic) {
-    draw_tour_axes(proj, labels, limits = 1, axes)
+    draw_tour_axes(proj, labels, limits = 1, axes, ...)
 
     # Render projected points
     x <- data %*% proj
@@ -106,7 +106,7 @@ animate_xy <- function(data, tour_path = grand_tour(), ...) {
 
 #' Draw tour axes with base graphics
 #' @keywords internal
-draw_tour_axes <- function(proj, labels, limits, position) {
+draw_tour_axes <- function(proj, labels, limits, position, ...) {
   position <- match.arg(position, c("center", "bottomleft", "off"))
   if (position == "off") {
     return()
@@ -123,6 +123,11 @@ draw_tour_axes <- function(proj, labels, limits, position) {
   adj <- function(x) axis_pos + x * axis_scale
 
   segments(adj(0), adj(0), adj(proj[, 1]), adj(proj[, 2]), col = "grey50")
+#  if (!is.null(mvar)) { # colour manip var
+#    if ((mvar < (nrow(proj)+1)) & (mvar > 0)) {
+#      segments(adj(0), adj(0), adj(proj[, 1]), adj(proj[, 2]), col = "orange")
+#    }
+#  }
   theta <- seq(0, 2 * pi, length = 50)
   lines(adj(cos(theta)), adj(sin(theta)), col = "grey50")
   text(adj(proj[, 1]), adj(proj[, 2]), label = labels, col = "grey50")

R/geodesic-path.r

@@ -20,7 +20,7 @@
 #' @export
 #' @keywords internal
 new_geodesic_path <- function(name, generator, frozen = NULL, ...) {
-  tries <- 1
+  tries <- 1 # Needed for guided
 
   tour_path <- function(current, data, ...) {
     if (is.null(current)) {

R/history.r

@@ -49,7 +49,7 @@ save_history <- function(data, tour_path = grand_tour(), max_bases = 100, start
   if (sphere) data <- sphere_data(data)
 
   record <-
-    dplyr::tibble(
+    tibble::tibble(
       basis = list(),
       index_val = numeric(),
       info = character(),

R/interpolate.r

@@ -22,7 +22,7 @@ interpolate <- function(basis_set, angle = 0.05, cycle = FALSE) {
   }
 
   record <-
-    dplyr::tibble(
+    tibble::tibble(
       basis = list(),
       index_val = numeric(),
       info = character(),

R/render.r

@@ -39,7 +39,7 @@ render <- function(data, tour_path, display, dev, ..., apf = 1 / 10, frames = 50
   on.exit(dev.off())
 
   record <-
-    dplyr::tibble(
+    tibble::tibble(
       basis = list(),
       index_val = numeric(),
       info = character(),

R/search-frozen-geodesic.r

@@ -72,7 +72,7 @@ find_best_frozen_dir <- function(old, frozen, index, dist = 0.01, counter = 5) {
 
     larger <- max(index(forward), index(backward))
 
-    dplyr::tibble(
+    tibble::tibble(
       basis = c(list(forward), list(backward)),
       index_val = c(index(forward), index(backward)),
       info = "direction_search",

R/search-geodesic.r

@@ -126,7 +126,7 @@ find_best_dir <- function(old, index, dist = 0.01, counter = 5, ...) {
 
     larger <- max(index(forward), index(backward))
 
-    dplyr::tibble(
+    tibble::tibble(
       basis = c(list(forward), list(backward)),
       index_val = c(index(forward), index(backward)),
       info = "direction_search",
@@ -158,7 +158,7 @@ find_path_peak <- function(old, new, index, max_dist = pi / 4, ...) {
 
   alpha <- stats::optimize(index_pos, c(-max_dist, max_dist), maximum = TRUE, tol = 0.01)
 
-  best <- dplyr::tibble(
+  best <- tibble::tibble(
     basis = list(step_angle(interpolator, alpha$maximum)),
     index_val = alpha$objective,
     info = "best_line_search",

R/search_polish.r

@@ -32,7 +32,7 @@ search_polish <- function(current, alpha = 0.5, index, tries, polish_max_tries =
   while (try <= polish_max_tries) {
     # could use replicate here
     basis <- lapply(1:n_sample, function(x) {
-      dplyr::tibble(basis = list(basis_nearby(current,
+      tibble::tibble(basis = list(basis_nearby(current,
         alpha = alpha
       )))
     })

R/tour-guided.r

@@ -76,15 +76,15 @@ guided_tour <- function(index_f, d = 2, alpha = 0.5, cooling = 0.99, max.tries =
       },
       error = function(e){
         assign("record",
-               dplyr::tibble(basis = list(),
+               tibble::tibble(basis = list(),
                              index_val = numeric(),
                              info = character(),
                              method = character(),
                              alpha = numeric(),
                              tries = numeric(),
                              loop = numeric()),
                envir = parent.frame())
-        rcd_env[["record"]] <- dplyr::tibble(
+        rcd_env[["record"]] <- tibble::tibble(
           basis = list(current),
           index_val = cur_index,
           info = "new_basis",

R/tour-radial.r

@@ -8,25 +8,26 @@
 #' \code{\link{save_history}} or \code{\link{render}}.
 #'
 #' @param start initial projection matrix
-#' @param var variable chosen to rotate out
+#' @param mvar variable chosen to rotate out
+#' @param ... additional arguments for drawing
 #' @export
 #' @examples
-#' animate_xy(flea[, 1:6], radial_tour(basis_random(6, 2), var = 4))
-#' animate_dist(flea[, 1:6], radial_tour(basis_random(6, 1), var = 4))
-#' animate_scatmat(flea[, 1:6], radial_tour(basis_random(6, 3), var = 4))
-radial_tour <- function(start, var = 1) {
+#' animate_xy(flea[, 1:6], radial_tour(basis_random(6, 2), mvar = 4))
+#' animate_dist(flea[, 1:6], radial_tour(basis_random(6, 1), mvar = 4))
+#' animate_scatmat(flea[, 1:6], radial_tour(basis_random(6, 3), mvar = 4))
+radial_tour <- function(start, mvar = 1, ...) {
   first <- TRUE
   out <- TRUE
 
-  generator <- function(current, data, ...) {
+  generator <- function(current, data, mvar, ...) {
     if (first) {
       new_basis <- start
       first <<- FALSE
       return(new_basis)
     }
     if (out) {
       new <- start
-      new[var,] <- rep(0, ncol(start))
+      new[mvar,] <- rep(0, ncol(start))
       new <- orthonormalise(new)
       new_basis <- new
       out <<- !out

cran-comments.md

@@ -1,6 +1,6 @@
-## Additional authors
+## Fixes as requested by CRAN
 
-Several additional contributors have provided new methods.
+This removes the reported html errors.
 
 ## R CMD check results
 There were no ERRORs, NOTESs or WARNINGs.