use message instead of cat for all the msg printing

R/geodesic-path.r

@@ -47,7 +47,6 @@ new_geodesic_path <- function(name, generator, frozen = NULL, ...) {
  return(NULL)
  }
 
- #cat("generation: dist = ", dist, "\n")
  }
  list(ingred = geodesic_path(current, target, frozen, ...), index = gen$index, tries = tries)
  }
@@ -62,7 +61,7 @@ new_geodesic_path <- function(name, generator, frozen = NULL, ...) {
 
 #' @export
 "print.tour_path" <- function(x, ...) {
- cat("Tour path:", attr(x, "name"), "\n")
+ message("Tour path: ", attr(x, "name"))
 
  # params <- as.list(environment(get("generator", environment(g))))
  # str(params)

R/geodesic.r

@@ -99,7 +99,7 @@ geodesic_info <- function(Fa, Fz, epsilon = 1e-6) {
  }
 
  # if (Fa.equivalent(Fz)) return();
- # cat("dim Fa",nrow(Fa),ncol(Fa),"dim Fz",nrow(Fz),ncol(Fz),"\n")
+ # message("dim Fa",nrow(Fa),ncol(Fa),"dim Fz",nrow(Fz),ncol(Fz))
 
  # Compute the SVD: Fa'Fz = Va lambda Vz' --------------------------------
  sv <- svd(t(Fa) %*% Fz)

R/search-better.r

@@ -48,7 +48,6 @@ search_better <- function(current, alpha = 0.5, index, tries, max.tries = Inf,..
  warning("cur_index is zero!")
  }
 
- cat("Old", cur_index, "\n")
  try <- 1
 
  while (try < max.tries) {
@@ -70,7 +69,7 @@ search_better <- function(current, alpha = 0.5, index, tries, max.tries = Inf,..
 
 
  if (new_index > cur_index) {
- cat("New", new_index, "try", try, "\n")
+ message("Target: ", sprintf("%.3f", new_index), ", try: ", try)
 
  nr <- nrow(rcd_env[["record"]])
  rcd_env[["record"]][nr, "info"] <- "new_basis"
@@ -83,24 +82,8 @@ search_better <- function(current, alpha = 0.5, index, tries, max.tries = Inf,..
  try <- try + 1
  }
 
- cat("No better bases found after ", max.tries, " tries. Giving up.\n",
- sep = ""
- )
- cat("Final projection: \n")
- if (ncol(current) == 1) {
- for (i in 1:length(current)) {
- cat(sprintf("%.3f", current[i]), " ")
- }
- cat("\n")
- }
- else {
- for (i in 1:nrow(current)) {
- for (j in 1:ncol(current)) {
- cat(sprintf("%.3f", current[i, j]), " ")
- }
- cat("\n")
- }
- }
+ message("No better bases found after ", max.tries, " tries. Giving up.")
+ print_final_proj(current)
 
  rcd_env[["record"]] <- dplyr::mutate(
  rcd_env[["record"]],
@@ -139,8 +122,6 @@ search_better_random <- function(current, alpha = 0.5, index, tries,
  if (cur_index == 0) {
  warning("cur_index is zero!")
  }
-
- cat("Old", cur_index, "\n")
  try <- 1
  while (try < max.tries) {
  new_basis <- basis_nearby(current, alpha, method)
@@ -160,8 +141,7 @@ search_better_random <- function(current, alpha = 0.5, index, tries,
  )
 
  if (new_index > cur_index) {
- cat("New", new_index, "try", try, "\n")
- cat("Accept \n")
+ message("Target: ", sprintf("%.3f", new_index), ", try: ", try, ", accept")
 
  nr <- nrow(rcd_env[["record"]])
  rcd_env[["record"]][nr, "info"] <- "new_basis"
@@ -176,8 +156,8 @@ search_better_random <- function(current, alpha = 0.5, index, tries,
  rand <- stats::runif(1)
 
  if (prob > rand) {
- cat("New", new_index, "try", try, "\n")
- cat("Accept with probability, prob =", prob, "\n")
+ message("Target: ", sprintf("%.3f", new_index), ", try: ", try,
+  ", probabilistic accept p = ", sprintf("%.3f", prob))
 
  nr <- nrow(rcd_env[["record"]])
  rcd_env[["record"]][nr, "info"] <- "new_basis"
@@ -193,24 +173,8 @@ search_better_random <- function(current, alpha = 0.5, index, tries,
  try <- try + 1
  }
 
- cat("No better bases found after ", max.tries, " tries. Giving up.\n",
- sep = ""
- )
- cat("Final projection: \n")
- if (ncol(current) == 1) {
- for (i in 1:length(current)) {
- cat(sprintf("%.3f", current[i]), " ")
- }
- cat("\n")
- }
- else {
- for (i in 1:nrow(current)) {
- for (j in 1:ncol(current)) {
- cat(sprintf("%.3f", current[i, j]), " ")
- }
- cat("\n")
- }
- }
+ message("No better bases found after ", max.tries, " tries. Giving up.")
+ print_final_proj(current)
 
  rcd_env[["record"]] <- dplyr::mutate(
  rcd_env[["record"]],

R/search-frozen-geodesic.r

@@ -44,13 +44,13 @@ search_frozen_geodesic <- function(current, index, tries, max.tries = 5, n = 5,
  dig3 <- function(x) sprintf("%.3f", x)
  pdiff <- (new_index - cur_index) / cur_index
  if (pdiff > 0.001) {
- cat("New index: ", dig3(new_index), " (", dig3(peak$alpha$maximum), " away)\n", sep = "")
+ message("New index: ", dig3(new_index), " (", dig3(peak$alpha$maximum), " away)", sep = "")
  current <<- new_basis
  cur_index <<- new_index
 
  return(list(target = new_basis[[1]]))
  }
- cat("Best was: ", dig3(new_index), " (", dig3(peak$alpha$maximum), " away). Trying again...\n", sep = "")
+ message("Best was: ", dig3(new_index), " (", dig3(peak$alpha$maximum), " away). Try again...", sep = "")
 
  try <- try + 1
  }

R/search-geodesic.r

@@ -58,44 +58,21 @@ search_geodesic <- function(current, alpha = 1, index, tries, max.tries = 5, ...
  warning("either the cur_index or the new_index is zero!")
  } else {
  pdiff <- (new_index - cur_index) / cur_index
-
- dig3 <- function(x) sprintf("%.3f", x)
-
- cat(
- "Value ", dig3(new_index), " ",
- sprintf("%.1f", pdiff * 100), "% better "
- )
  if (pdiff > 0.001 & proj_dist(current, new_basis[[1]]) > 1e-2) { # FIXME: pdiff should pbly be a changeable parameter
- cat(" - NEW BASIS\n")
-
+ message("Target: ", sprintf("%.3f", new_index), ", ",
+ sprintf("%.1f", pdiff * 100), "% better ")
  current <- new_basis
  cur_index <- new_index
 
  return(list(target = new_basis[[1]]))
  }
- cat("\n")
  }
 
  try <- try + 1
  }
- cat("No better bases found after ", max.tries, " tries. Giving up.\n",
- sep = ""
- )
- cat("Final projection: \n")
- if (ncol(current) == 1) {
- for (i in 1:length(current)) {
- cat(sprintf("%.3f", current[i]), " ")
- }
- cat("\n")
- }
- else {
- for (i in 1:nrow(current)) {
- for (j in 1:ncol(current)) {
- cat(sprintf("%.3f", current[i, j]), " ")
- }
- cat("\n")
- }
- }
+
+ message("No better bases found after ", max.tries, " tries. Giving up.")
+ print_final_proj(current)
 
  NULL
 }

R/search-jellyfish.R

@@ -48,7 +48,7 @@ search_jellyfish <- function(current, index, tries, max.tries = Inf, min.tries =
  target_idx <- sapply(target, index)
 
  best_id <- which.max(target_idx)
- cat("Best Index: ", max(target_idx), "\n")
+ message("Target: ", sprintf("%.3f", max(target_idx)))
  attr(target, "best_id") <- best_id
  class(target) <- c("multi-bases", class(target))
 
@@ -79,19 +79,3 @@ search_jellyfish <- function(current, index, tries, max.tries = Inf, min.tries =
 }
 
 
-print_final_proj <- function(current){
- cat("Final projection: \n")
- if (ncol(current) == 1) {
- for (i in 1:length(current)) {
- cat(sprintf("%.3f", current[i]), " ")
- }
- cat("\n")
- } else {
- for (i in 1:nrow(current)) {
- for (j in 1:ncol(current)) {
- cat(sprintf("%.3f", current[i, j]), " ")
- }
- cat("\n")
- }
- }
-}

R/search_polish.r

@@ -60,20 +60,20 @@ search_polish <- function(current, alpha = 0.5, index, tries, polish_max_tries =
  # check condition 1: the two bases can't be too close
 
  if (polish_dist < 1e-3) {
- cat("The new basis is too close to the current one! \n")
- cat("current basis: ", current, "cur_index: ", cur_index, "\n")
+ message("The new basis is too close to the current one!")
+ message("current basis: ", current, "cur_index: ", sprintf("%.3f", cur_index))
  return(list(target = current, alpha = alpha))
  }
 
  # check condition 2: there needs to be certain improvement
 
  if (polish_pdiff < 1e-5) {
- cat("The improvement is too small! \n")
- cat("current basis: ", current, "cur_index: ", cur_index, "\n")
+ message("The improvement is too small!")
+ message("current basis: ", current, "cur_index: ", sprintf("%.3f", cur_index))
  return(list(target = current, alpha = alpha))
  }
 
- cat("better basis found, index_val = ", best_row$index_val, "\n")
+ message("better basis found, index_val = ", sprintf("%.3f", best_row$index_val))
  cur_index <- best_row$index_val
  current <- best_row$basis[[1]]
  best_row <- dplyr::mutate(best_row,
@@ -86,40 +86,22 @@ search_polish <- function(current, alpha = 0.5, index, tries, polish_max_tries =
  } else {
  polish_cooling <- polish_cooling * 0.95
  alpha <- alpha * polish_cooling
- cat("alpha gets updated to", alpha, "\n")
+ message("alpha gets updated to", alpha, "\n")
 
  # check condition 3: alpha can't be too small
 
  if (alpha < 0.01) {
- cat("alpha is", alpha, "and it is too small! \n")
- cat("current basis: ", current, "cur_index: ", cur_index, "\n")
+ message("alpha is", alpha, "and it is too small!")
+ message("current basis: ", current, "cur_index: ", sprintf("%.3f", cur_index))
  return(list(target = current, alpha = alpha))
  }
  }
 
  try <- try + 1
  }
 
- cat("No better bases found after ", polish_max_tries, " tries. Giving up.\n",
- sep = ""
- )
- cat("Final projection: \n")
- if (ncol(current) == 1) {
- for (i in 1:length(current)) {
- cat(sprintf("%.3f", current[i]), " ")
- }
- cat("\n")
- }
- else {
- for (i in 1:nrow(current)) {
- for (j in 1:ncol(current)) {
- cat(sprintf("%.3f", current[i, j]), " ")
- }
- cat("\n")
- }
- }
-
- cat("current basis: ", current, "cur_index: ", cur_index, "\n")
+ message("No better bases found after ", polish_max_tries, " tries. Giving up.")
+ print_final_proj(current)
  return(list(target = current, alpha = alpha))
 }
 # globalVariables("index_val")

R/search_posse.R

@@ -31,7 +31,7 @@ search_posse <- function(current, alpha = 0.5, index, tries, max.tries = 300, cu
  )
 
  if (new_index > cur_index) {
- cat("New", new_index, "try", try, "\n")
+ message("Target: ", sprintf("%.3f", new_index), ", try: ", try)
 
  nr <- nrow(rcd_env[["record"]])
  rcd_env[["record"]][nr, "info"] <- "new_basis"
@@ -44,24 +44,8 @@ search_posse <- function(current, alpha = 0.5, index, tries, max.tries = 300, cu
  try <- try + 1
  }
 
- cat("No better bases found after ", max.tries, " tries. Giving up.\n",
- sep = ""
- )
- cat("Final projection: \n")
- if (ncol(current) == 1) {
- for (i in 1:length(current)) {
- cat(sprintf("%.3f", current[i]), " ")
- }
- cat("\n")
- }
- else {
- for (i in 1:nrow(current)) {
- for (j in 1:ncol(current)) {
- cat(sprintf("%.3f", current[i, j]), " ")
- }
- cat("\n")
- }
- }
+ message("No better bases found after ", max.tries, " tries. Giving up.")
+ print_final_proj(current)
 
  NULL
 }

R/section-pursuit.r

@@ -21,17 +21,17 @@ slice_index <- function(breaks_x, breaks_y, eps, bintype = "polar", power = 1, f
  reweight = FALSE, p = 4) {
  if (reweight) {
  if (bintype != "polar") {
- cat("Reweighting is only defined for polar binning and will be ignored.")
+ message("Reweighting is only defined for polar binning and will be ignored.")
  }
  else {
- cat(paste0("Reweighting assuming p=", p))
+ message(paste0("Reweighting assuming p=", p))
  }
  }
 
  resc <- 1
  if (bintype == "polar") {
  resc <- 1 / (1 - (1 / 10)^(1 / power))^power
- cat(paste0("Rescaling raw index by a factor ", resc))
+ message(paste0("Rescaling raw index by a factor ", resc))
  }
 
  function(mat, dists, h) {
@@ -133,7 +133,7 @@ slice_binning <- function(mat, dists, h, breaks_x, breaks_y, bintype = "square")
  ybin <- cut(ang, breaks_y)
  }
  else {
- cat(bintype, " is not a recognised bin type\n")
+ message(bintype, " is not a recognised bin type")
  return(0)
  }
 

R/tour-guided-section.r

@@ -68,24 +68,9 @@ guided_section_tour <- function(index_f, d = 2, alpha = 0.5, cooling = 0.99,
  cur_index <- index(current)
 
  if (cur_index > max.i) {
- cat("Found index ", cur_index, ", larger than selected maximum ", max.i, ". Stopping search.\n",
- sep = ""
- )
- cat("Final projection: \n")
- if (ncol(current) == 1) {
- for (i in 1:length(current)) {
- cat(sprintf("%.3f", current[i]), " ")
- }
- cat("\n")
- }
- else {
- for (i in 1:nrow(current)) {
- for (j in 1:ncol(current)) {
- cat(sprintf("%.3f", current[i, j]), " ")
- }
- cat("\n")
- }
- }
+ message("Found index ", sprintf("%.3f", cur_index), ",
+ larger than selected maximum ", max.i, ". Stopping search.")
+ print_final_proj(current)
  return(NULL)
  }
 

R/tour-guided.r

@@ -116,9 +116,8 @@ guided_tour <- function(index_f, d = 2, alpha = 0.5, cooling = 0.99, max.tries =
  }
 
  if (cur_index > max.i) {
- cat("Found index ", cur_index, ", larger than selected maximum ", max.i, ". Stopping search.\n",
- sep = ""
- )
+ message("Found index ", sprintf("%.3f", cur_index), ",
+ larger than selected maximum ", max.i, ". Stopping search.")
  print_final_proj(current)
  return(NULL)
  }