From b053348bcc62e6225e38d0a07478e30fb29fdb5f Mon Sep 17 00:00:00 2001
From: MLopez-Ibanez <2620021+MLopez-Ibanez@users.noreply.github.com>
Date: Tue, 28 Nov 2023 18:41:48 +0000
Subject: [PATCH]  * Replace dots in function names with underscore () to
 silence CRAN Note.

---
 NEWS.md                   |   2 +
 R/eaf.R                   |  52 ++++++++---------
 R/eafplot.R               | 120 +++++++++++++++++++-------------------
 R/nondominated.R          |   2 +-
 R/vorob.R                 |  30 +++++-----
 man/attsurf2df.Rd         |   2 +-
 tests/testthat/test-eaf.R |   6 +-
 7 files changed, 108 insertions(+), 106 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 905eed3..551d5c1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,8 @@
  
  * Silence some warnings with GCC 12.
  
+ * Replace dots in function names with underscore (`_`) to silence CRAN Note.
+ 
 # eaf 2.4
 
  * If the installation cannot find the Gnu Scientific Library, it gives hints on
diff --git a/R/eaf.R b/R/eaf.R
index bccde98..c3439e3 100644
--- a/R/eaf.R
+++ b/R/eaf.R
@@ -48,7 +48,7 @@
 ################################################################################
 #dyn.load("../src/eaf.so")
 
-check.eaf.data <- function(x)
+check_eaf_data <- function(x)
 {
   name <- deparse(substitute(x))
   if (length(dim(x)) != 2L)
@@ -66,9 +66,9 @@ check.eaf.data <- function(x)
   return(x)
 }
 
-compute.eaf <- function(data, percentiles = NULL)
+compute_eaf <- function(data, percentiles = NULL)
 {
-  data <- check.eaf.data(data)
+  data <- check_eaf_data(data)
   setcol <- ncol(data)
   nobjs <- setcol - 1L
   # The C code expects points within a set to be contiguous.
@@ -90,9 +90,9 @@ compute.eaf <- function(data, percentiles = NULL)
                as.numeric(percentiles)))
 }
 
-compute.eaf.as.list <- function(data, percentiles = NULL)
+compute_eaf_as_list <- function(data, percentiles = NULL)
 {
-  eaf <- compute.eaf (data, percentiles = percentiles)
+  eaf <- compute_eaf (data, percentiles = percentiles)
   setcol <- ncol(eaf)
   nobjs <- setcol - 1L
   eaf_sets <- eaf[, setcol]
@@ -103,7 +103,7 @@ compute.eaf.as.list <- function(data, percentiles = NULL)
                                  labels = uniq_eaf_sets)))
 }
 
-compute.eafdiff.helper <- function(data, intervals)
+compute_eafdiff_helper <- function(data, intervals)
 {
   # Last column is the set number.
   setcol <- ncol(data)
@@ -201,12 +201,12 @@ eafdiff <- function(x, y, intervals = NULL, maximise = c(FALSE, FALSE),
   }
 
   data <- rbind_datasets(x, y)
-  data <- check.eaf.data(data)
+  data <- check_eaf_data(data)
   # FIXME: Is it faster to subset or to multiply the third column by 1?
-  data[,1:2] <- matrix.maximise(data[,1:2, drop=FALSE], maximise = maximise)
+  data[,1:2] <- matrix_maximise(data[,1:2, drop=FALSE], maximise = maximise)
   
-  DIFF <- if (rectangles) compute.eafdiff.rectangles(data, intervals = intervals)
-          else compute.eafdiff.helper(data, intervals = intervals)
+  DIFF <- if (rectangles) compute_eafdiff_rectangles(data, intervals = intervals)
+          else compute_eafdiff_helper(data, intervals = intervals)
   # FIXME: We should remove duplicated rows in C code.
 
   # FIXME: Check that we do not generate duplicated nor overlapping rectangles
@@ -215,9 +215,9 @@ eafdiff <- function(x, y, intervals = NULL, maximise = c(FALSE, FALSE),
   return(DIFF)
 }
 
-compute.eafdiff <- function(data, intervals)
+compute_eafdiff <- function(data, intervals)
 {
-  DIFF <- compute.eafdiff.helper(data, intervals)
+  DIFF <- compute_eafdiff_helper(data, intervals)
   #print(DIFF)
   # FIXME: Do this computation in C code. See compute_eafdiff_area_C
   setcol <- ncol(data)
@@ -230,7 +230,7 @@ compute.eafdiff <- function(data, intervals)
 
 
 # FIXME: The default intervals should be nsets / 2
-compute.eafdiff.rectangles <- function(data, intervals = 1L)
+compute_eafdiff_rectangles <- function(data, intervals = 1L)
 {
   # Last column is the set number.
   nobjs <- ncol(data) - 1L
@@ -248,7 +248,7 @@ compute.eafdiff.rectangles <- function(data, intervals = 1L)
 }
 
 # FIXME: The default intervals should be nsets / 2
-compute.eafdiff.polygon <- function(data, intervals = 1L)
+compute_eafdiff_polygon <- function(data, intervals = 1L)
 {
   # Last column is the set number.
   nobjs <- ncol(data) - 1L
@@ -272,7 +272,7 @@ compute.eafdiff.polygon <- function(data, intervals = 1L)
 }
 
 
-rm.inf <- function(x, xmax)
+rm_inf <- function(x, xmax)
 {
   x[is.infinite(x)] <- xmax
   return(x)
@@ -280,7 +280,7 @@ rm.inf <- function(x, xmax)
 
 
 # FIXME: Accept ...
-max.finite <- function (x)
+max_finite <- function (x)
 {
   x <- as.vector(x)
   x <- x[is.finite(x)]
@@ -289,7 +289,7 @@ max.finite <- function (x)
 }
 
 # FIXME: Accept ...
-min.finite <- function (x)
+min_finite <- function (x)
 {
   x <- as.vector(x)
   x <- x[is.finite(x)]
@@ -298,7 +298,7 @@ min.finite <- function (x)
 }
 
 # FIXME: Accept ...
-range.finite <- function(x)
+range_finite <- function(x)
 {
   x <- as.vector(x)
   x <- x[is.finite(x)]
@@ -306,7 +306,7 @@ range.finite <- function(x)
   return(NULL)
 }
 
-matrix.maximise <- function(z, maximise)
+matrix_maximise <- function(z, maximise)
 {
   stopifnot(ncol(z) == length(maximise))
   if (is.data.frame(z)) {
@@ -341,7 +341,7 @@ rbind_datasets <- function(x,y)
 ## polygon.
 ## Example: given ((1,2), (2,1)), it returns ((1,2), (2,2), (2,1)).
 ## Input should be already in the correct order.
-points.steps <- function(x)
+points_steps <- function(x)
 {
   n <- nrow(x)
   if (n == 1L) return(x)
@@ -419,12 +419,12 @@ eafs <- function (points, sets, groups = NULL, percentiles = NULL)
   
   points <- cbind(points, sets)
   if (is.null(groups)) {
-    attsurfs <- compute.eaf (points, percentiles)
+    attsurfs <- compute_eaf (points, percentiles)
   } else {
     attsurfs <- data.frame()
     groups <- factor(groups)
     for (g in levels(groups)) {
-      tmp <- compute.eaf(points[groups == g,], percentiles)
+      tmp <- compute_eaf(points[groups == g,], percentiles)
       attsurfs <- rbind(attsurfs, data.frame(tmp, groups = g))
     }
   }
@@ -433,7 +433,7 @@ eafs <- function (points, sets, groups = NULL, percentiles = NULL)
 
 
 # Get correct xlim or ylim when maximising / minimising.
-get.xylim <- function(lim, maximise, data)
+get_xylim <- function(lim, maximise, data)
 {
   # FIXME: This seems too complicated.
   if (!is.null(lim) && maximise) lim <- -lim 
@@ -442,7 +442,7 @@ get.xylim <- function(lim, maximise, data)
   lim
 }
   
-get.extremes <- function(xlim, ylim, maximise, log)
+get_extremes <- function(xlim, ylim, maximise, log)
 {
   if (length(log) && log != "")
     log <- strsplit(log, NULL)[[1L]]
@@ -461,7 +461,7 @@ get.extremes <- function(xlim, ylim, maximise, log)
   c(extreme1, extreme2)
 }
 
-add.extremes <- function(x, extremes, maximise)
+add_extremes <- function(x, extremes, maximise)
 {
   best1 <- if (maximise[1]) max else min
   best2 <- if (maximise[2]) max else min
@@ -474,7 +474,7 @@ add.extremes <- function(x, extremes, maximise)
 #'
 #' @param x (`list()`) List of data.frames or matrices. The names of the list
 #'   give the percentiles of the attainment surfaces.  This is the format
-#'   returned by [eafplot()] (and the internal function `compute.eaf.as.list`).
+#'   returned by [eafplot()] (and the internal function `compute_eaf_as_list`).
 #'
 #' @return A data.frame with as many columns as objectives and an additional column `percentiles`.
 #'
diff --git a/R/eafplot.R b/R/eafplot.R
index d469cf3..219ed3f 100644
--- a/R/eafplot.R
+++ b/R/eafplot.R
@@ -181,16 +181,16 @@ eafplot.default <-
     # efficient, one large matrix or separate points and sets, then be
     # consistent everywhere.
     if (!is.null(sets)) x <- cbind(x, sets)
-    x <- check.eaf.data(x)
+    x <- check_eaf_data(x)
     sets <- x[, 3L]
     x <- as.matrix(x[,1:2, drop=FALSE])
-    x <- matrix.maximise(x, maximise)
+    x <- matrix_maximise(x, maximise)
 
     # Transform EAF matrix into attsurfs list.
     if (is.null(groups)) {
-      attsurfs <- compute.eaf.as.list(cbind(x, sets), percentiles)
+      attsurfs <- compute_eaf_as_list(cbind(x, sets), percentiles)
     } else {
-      # FIXME: Is this equivalent to compute.eaf.as.list for each g?
+      # FIXME: Is this equivalent to compute_eaf_as_list for each g?
       EAF <- eafs(x, sets, groups, percentiles)
       attsurfs <- list()
       groups <- factor(EAF$groups)
@@ -202,13 +202,13 @@ eafplot.default <-
       }
     }
     # FIXME: rm(EAF) to save memory ?
-    attsurfs <- lapply(attsurfs, matrix.maximise, maximise = maximise)
+    attsurfs <- lapply(attsurfs, matrix_maximise, maximise = maximise)
   }
 
   # FIXME: We should take the range from the attsurfs to not make x mandatory.
-  xlim <- get.xylim(xlim, maximise[1], data = x[,1])
-  ylim <- get.xylim(ylim, maximise[2], data = x[,2])
-  extreme <- get.extremes(xlim, ylim, maximise, log)
+  xlim <- get_xylim(xlim, maximise[1], data = x[,1])
+  ylim <- get_xylim(ylim, maximise[2], data = x[,2])
+  extreme <- get_extremes(xlim, ylim, maximise, log)
 
   # FIXME: Find a better way to handle different x-y scale.
   yscale <- 1
@@ -241,8 +241,8 @@ eafplot.default <-
        xlim = xlim, ylim = ylim, log = log, axes = FALSE, las = las,
        panel.first = ({
          if (axes) {
-           plot.eaf.axis(xaxis.side, xlab, las = las, sci.notation = sci.notation)
-           plot.eaf.axis(yaxis.side, ylab, las = las, sci.notation = sci.notation,
+           plot_eaf_axis(xaxis.side, xlab, las = las, sci.notation = sci.notation)
+           plot_eaf_axis(yaxis.side, ylab, las = las, sci.notation = sci.notation,
                          # FIXME: eafplot uses 2.2, why the difference?
                          line = 2.75)
          }
@@ -260,14 +260,14 @@ eafplot.default <-
            } else if (length(col) != length(attsurfs)) {
              stop ("length(col) != 2, but with 'type=area', eafplot.default needs just two colors")
            }
-           plot.eaf.full.area(attsurfs, extreme, maximise, col = col)
+           plot_eaf_full_area(attsurfs, extreme, maximise, col = col)
          } else {
            ## Recycle values
            lwd <- rep(lwd, length=length(attsurfs))
            lty <- rep(lty, length=length(attsurfs))
            col <- rep(col, length=length(attsurfs))
            if (!is.null(pch)) pch <- rep(pch, length=length(attsurfs))
-           plot.eaf.full.lines(attsurfs, extreme, maximise,
+           plot_eaf_full_lines(attsurfs, extreme, maximise,
                                col = col, lty = lty, lwd = lwd, pch = pch, cex = cex.pch)
          }
        }), ...)
@@ -365,7 +365,7 @@ prettySciNotation <- function(x, digits = 1L)
                            list(base = base, exponent = exponent)))
 }
 
-axis.side <- function(side)
+axis_side <- function(side)
 {
   if (!is.character(side)) return(side)
   return(switch(side,
@@ -375,11 +375,11 @@ axis.side <- function(side)
                 right = 4))
 }
 
-plot.eaf.axis <- function(side, lab, las,
+plot_eaf_axis <- function(side, lab, las,
                           col = 'lightgray', lty = 'dotted', lwd = par("lwd"),
                           line = 2.1, sci.notation = FALSE)
 {
-  side <- axis.side(side)
+  side <- axis_side(side)
   ## FIXME: Do we still need lwd=0.5, lty="26" to work-around for R bug?
   at <- axTicks(if (side %% 2 == 0) 2 else 1)
   labels <- if (sci.notation) prettySciNotation(at) else formatC(at, format = "g")
@@ -409,7 +409,7 @@ plot.eaf.axis <- function(side, lab, las,
         las = 0)
 }
 
-plot.eaf.full.lines <- function(attsurfs, extreme, maximise,
+plot_eaf_full_lines <- function(attsurfs, extreme, maximise,
                                  col, lty, lwd, pch = NULL, cex = par("cex"))
 {
   ## Recycle values
@@ -419,7 +419,7 @@ plot.eaf.full.lines <- function(attsurfs, extreme, maximise,
   if (!is.null(pch))
     pch <- rep(pch, length = length(attsurfs))
 
-  attsurfs = lapply(attsurfs, add.extremes, extreme, maximise)
+  attsurfs = lapply(attsurfs, add_extremes, extreme, maximise)
   for (k in seq_along(attsurfs)) {
     # FIXME: Is there a way to plot points and steps in one call?
     if (!is.null(pch))
@@ -428,17 +428,17 @@ plot.eaf.full.lines <- function(attsurfs, extreme, maximise,
   }
 }
 
-plot.eaf.full.area <- function(attsurfs, extreme, maximise, col)
+plot_eaf_full_area <- function(attsurfs, extreme, maximise, col)
 {
   stopifnot(length(attsurfs) == length(col))
   for (i in seq_along(attsurfs)) {
-    poli <- add.extremes(points.steps(attsurfs[[i]]), extreme, maximise)
+    poli <- add_extremes(points_steps(attsurfs[[i]]), extreme, maximise)
     poli <- rbind(poli, extreme)
     polygon(poli[,1], poli[,2], border = NA, col = col[i])
   }
 }
 
-plot.eafdiff.side <- function (eafdiff, attsurfs = list(),
+plot_eafdiff_side <- function (eafdiff, attsurfs = list(),
                                col,
                                side = stop("Argument 'side' is required"),
                                type = "point",
@@ -480,7 +480,7 @@ plot.eafdiff.side <- function (eafdiff, attsurfs = list(),
   # will override the grid lines.
   col[col %in% c("white", "#FFFFFF")] <- "transparent"
 
-  extreme <- get.extremes(xlim, ylim, maximise, log)
+  extreme <- get_extremes(xlim, ylim, maximise, log)
   yscale <- 1
   ## FIXME log == "y" and yscaling
   #    yscale <- 60
@@ -497,18 +497,18 @@ plot.eafdiff.side <- function (eafdiff, attsurfs = list(),
   plot(xlim, ylim, type = "n", xlab = "", ylab = "",
        xlim = xlim, ylim = ylim, log = log, axes = FALSE, las = las,
        panel.first = ({
-         plot.eaf.axis (xaxis.side, xlab, las = las, sci.notation = sci.notation)
-         plot.eaf.axis (yaxis.side, ylab, las = las, sci.notation = sci.notation,
+         plot_eaf_axis (xaxis.side, xlab, las = las, sci.notation = sci.notation)
+         plot_eaf_axis (yaxis.side, ylab, las = las, sci.notation = sci.notation,
                         line = 2.2)
                          
          if (nrow(eafdiff)) {
            if (type == "area") {
              if (full.eaf) {
-               plot.eaf.full.area(split.data.frame(eafdiff[,1:2], eafdiff[,3]),
+               plot_eaf_full_area(split.data.frame(eafdiff[,1:2], eafdiff[,3]),
                                    extreme, maximise, col)
              } else {
-               eafdiff[,1] <- rm.inf(eafdiff[,1], extreme[1])
-               eafdiff[,2] <- rm.inf(eafdiff[,2], extreme[2])
+               eafdiff[,1] <- rm_inf(eafdiff[,1], extreme[1])
+               eafdiff[,2] <- rm_inf(eafdiff[,2], extreme[2])
                polycol <- attr(eafdiff, "col")
                #print(unique(polycol))
                #print(length(col))
@@ -544,7 +544,7 @@ plot.eafdiff.side <- function (eafdiff, attsurfs = list(),
     col <- c("black")
   }
 
-  plot.eaf.full.lines(attsurfs, extreme, maximise,
+  plot_eaf_full_lines(attsurfs, extreme, maximise,
                       col = col, lty = lty, lwd = lwd)
   mtext(title, 1, line = 3.5, cex = par("cex.lab"), las = 0, font = 2)
   box()
@@ -705,7 +705,7 @@ eafdiffplot <-
   type <- match.arg (type, c("point", "area"))
   # FIXME: check that it is either an integer or a character vector.
   if (length(intervals) == 1) {
-    intervals <- seq.intervals.labels(
+    intervals <- seq_intervals_labels(
       round(seq(0,1 , length.out = 1 + intervals), 4), digits = 1)
   }
   if (is.function(col)) { # It is a color-map, like viridis()
@@ -728,17 +728,17 @@ eafdiffplot <-
     stop("length of maximise must be either 1 or 2")
   }
 
-  data.left <- check.eaf.data(data.left)
-  data.left[,1:2] <- matrix.maximise(data.left[,1:2, drop=FALSE], maximise)
-  data.right <- check.eaf.data(data.right)
-  data.right[,1:2] <- matrix.maximise(data.right[,1:2, drop=FALSE], maximise)
+  data.left <- check_eaf_data(data.left)
+  data.left[,1:2] <- matrix_maximise(data.left[,1:2, drop=FALSE], maximise)
+  data.right <- check_eaf_data(data.right)
+  data.right[,1:2] <- matrix_maximise(data.right[,1:2, drop=FALSE], maximise)
 
   attsurfs.left <- attsurfs.right <- list()
   if (!any(is.na(percentiles))) {
-    attsurfs.left <- compute.eaf.as.list (data.left, percentiles)
-    attsurfs.left <- lapply(attsurfs.left, matrix.maximise, maximise = maximise)
-    attsurfs.right <- compute.eaf.as.list (data.right, percentiles)
-    attsurfs.right <- lapply(attsurfs.right, matrix.maximise, maximise = maximise)
+    attsurfs.left <- compute_eaf_as_list (data.left, percentiles)
+    attsurfs.left <- lapply(attsurfs.left, matrix_maximise, maximise = maximise)
+    attsurfs.right <- compute_eaf_as_list (data.right, percentiles)
+    attsurfs.right <- lapply(attsurfs.right, matrix_maximise, maximise = maximise)
   }
 
   # FIXME: We do not need this for the full EAF.
@@ -751,12 +751,12 @@ eafdiffplot <-
   if (full.eaf) {
     if (type == "area") {
       lower.boundaries <- 0:(length(intervals)-1) * 100 / length(intervals)
-      diff_left <- compute.eaf (data.left, percentiles = lower.boundaries)
-      diff_right <- compute.eaf (data.right, percentiles = lower.boundaries)
+      diff_left <- compute_eaf (data.left, percentiles = lower.boundaries)
+      diff_right <- compute_eaf (data.right, percentiles = lower.boundaries)
     } else if (type == "point") {
-      diff_left <- compute.eaf (data.left)
-      diff_right <- compute.eaf (data.right)
-      # Since plot.eafdiff.side uses floor to calculate the color, and
+      diff_left <- compute_eaf (data.left)
+      diff_right <- compute_eaf (data.right)
+      # Since plot_eafdiff_side uses floor to calculate the color, and
       # we want color[100] == color[99].
       diff_left[diff_left[,3] == 100, 3] <- 99
       diff_right[diff_right[,3] == 100, 3] <- 99
@@ -767,10 +767,10 @@ eafdiffplot <-
     #remove(data.left,data.right,data.combined) # Free memory?
   } else {
     if (type == "area") {
-      DIFF <- compute.eafdiff.polygon (data.combined, intervals = length(intervals))
+      DIFF <- compute_eafdiff_polygon (data.combined, intervals = length(intervals))
     } else if (type == "point") {
       #remove(data.left,data.right) # Free memory?
-      DIFF <- compute.eafdiff (data.combined, intervals = length(intervals))
+      DIFF <- compute_eafdiff (data.combined, intervals = length(intervals))
       #remove(data.combined) # Free memory?
     }
     diff_left <- DIFF$left
@@ -778,21 +778,21 @@ eafdiffplot <-
   }
     
   # FIXME: This can be avoided and just taken from the full EAF.
-  grand.attsurf <- compute.eaf.as.list (data.combined, c(0, 100))
+  grand.attsurf <- compute_eaf_as_list (data.combined, c(0, 100))
   grand.best <- grand.attsurf[["0"]]
   grand.worst <- grand.attsurf[["100"]]
 
-  xlim <- get.xylim(xlim, maximise[1],
+  xlim <- get_xylim(xlim, maximise[1],
                     data = c(grand.best[,1], grand.worst[,1],
-                             range.finite(diff_left[,1]), range.finite(diff_right[,1])))
-  ylim <- get.xylim(ylim, maximise[2],
+                             range_finite(diff_left[,1]), range_finite(diff_right[,1])))
+  ylim <- get_xylim(ylim, maximise[2],
                     data = c(grand.best[,2], grand.worst[,2],
-                             range.finite(diff_left[,2]), range.finite(diff_right[,2])))
+                             range_finite(diff_left[,2]), range_finite(diff_right[,2])))
 
-  grand.best <- matrix.maximise(grand.best, maximise)
-  grand.worst <- matrix.maximise(grand.worst, maximise)
-  diff_left[,1:2] <- matrix.maximise(diff_left[,1:2, drop=FALSE], maximise)
-  diff_right[,1:2] <- matrix.maximise(diff_right[,1:2, drop=FALSE], maximise)
+  grand.best <- matrix_maximise(grand.best, maximise)
+  grand.worst <- matrix_maximise(grand.worst, maximise)
+  diff_left[,1:2] <- matrix_maximise(diff_left[,1:2, drop=FALSE], maximise)
+  diff_right[,1:2] <- matrix_maximise(diff_right[,1:2, drop=FALSE], maximise)
   
   # FIXME: This does not generate empty space between the two plots, but the
   # plots are not squared.
@@ -824,7 +824,7 @@ eafdiffplot <-
     attsurfs <- attsurfs.left
   }
     
-  plot.eafdiff.side (diff_left,
+  plot_eafdiff_side (diff_left,
                      attsurfs = attsurfs,
                      col = col,
                      type = type, full.eaf = full.eaf,
@@ -848,7 +848,7 @@ eafdiffplot <-
   } else {
     attsurfs <- attsurfs.right
   }
-  plot.eafdiff.side (diff_right,
+  plot_eafdiff_side (diff_right,
                      attsurfs = attsurfs,
                      col = col,
                      type = type, full.eaf = full.eaf,
@@ -861,10 +861,10 @@ eafdiffplot <-
 }
 
 # Create labels:
-# eaf:::seq.intervals.labels(seq(0,1, length.out=5), digits = 1)
+# eaf:::seq_intervals_labels(seq(0,1, length.out=5), digits = 1)
 # "[0.0, 0.2)" "[0.2, 0.4)" "[0.4, 0.6)" "[0.6, 0.8)" "[0.8, 1.0]"
 # FIXME: Add examples and tests
-seq.intervals.labels <- function(s, first.open = FALSE, last.open = FALSE,
+seq_intervals_labels <- function(s, first.open = FALSE, last.open = FALSE,
                                  digits = NULL)
 {
   # FIXME:  This should use:
@@ -977,13 +977,13 @@ eafplot.list <- function(x, ...)
 
   groups <- if (!is.null(names(x))) names(x) else 1:length(x)
 
-  check.elem <- function(elem) {
-    elem <- check.eaf.data(elem)
+  check_elem <- function(elem) {
+    elem <- check_eaf_data(elem)
     if (ncol(elem) != 3L)
-      stop("Each element of the list have exactly three columns. If you have grouping and conditioning variables, please consider using this format: 'eafplot(formula, data, ...)'")
+      stop("Each element of the list have exactly three columns. If you have grouping and conditioning variables, please consider using this format: 'eafplot.formula, data, ...)'")
     return(elem)
   }
-  x <- lapply(x, check.elem)
+  x <- lapply(x, check_elem)
   groups <- rep(groups, sapply(x, nrow))
   x <- do.call(rbind, x)
   
diff --git a/R/nondominated.R b/R/nondominated.R
index c65d471..7c7b446 100644
--- a/R/nondominated.R
+++ b/R/nondominated.R
@@ -101,7 +101,7 @@ pareto_rank <- function(data, maximise = FALSE)
   nobjs <- ncol(data)
   npoints <- nrow(data)
   maximise <- as.logical(rep_len(maximise, nobjs))
-  data <- matrix.maximise(data, maximise)
+  data <- matrix_maximise(data, maximise)
   return(.Call(pareto_ranking_C,
                as.double(t(data)),
                as.integer(nobjs),
diff --git a/R/vorob.R b/R/vorob.R
index e48dc47..db6d1e5 100644
--- a/R/vorob.R
+++ b/R/vorob.R
@@ -35,7 +35,7 @@
 #' @export
 vorobT <- function(x, reference)
 {
-  x <- check.eaf.data(x)
+  x <- check_eaf_data(x)
   setcol <- ncol(x)
   nobjs <- setcol - 1L
 
@@ -81,10 +81,10 @@ vorobDev <- function(x, VE, reference)
   x.split <- split.data.frame(x[,1:nobjs, drop=FALSE], x[,setcol])
   H1 <- mean(sapply(x.split, hypervolume, reference = reference))
 
-  hv.union.VE <- function(y)
-    return(hypervolume(rbind(y[, 1:nobjs, drop=FALSE], VE), reference = reference))
+  hv_union_VE <- function(y)
+    hypervolume(rbind(y[, 1:nobjs, drop=FALSE], VE), reference = reference)
   
-  VD <- 2 * sum(sapply(x.split, hv.union.VE))
+  VD <- 2 * sum(sapply(x.split, hv_union_VE))
   nruns <- length(x.split)
   return((VD / nruns) - H1 - H2)
 }
@@ -131,8 +131,8 @@ symDifPlot <- function(x, VE, threshold, nlevels = 11,
 {
   # FIXME: These maybe should be parameters of the function in the future.
   maximise <- c(FALSE, FALSE)
-  xaxis.side <- "below"
-  yaxis.side <- "left"
+  xaxis_side <- "below"
+  yaxis_side <- "left"
   log <- ""
   xlab <- colnames(x)[1]
   ylab <- colnames(x)[2]
@@ -143,7 +143,7 @@ symDifPlot <- function(x, VE, threshold, nlevels = 11,
   threshold <- round(threshold, 4)
   seq.levs <- round(seq(0, 100, length.out = nlevels), 4)
   levs <- sort.int(unique.default(c(threshold, seq.levs)))
-  attsurfs <- compute.eaf.as.list(x, percentiles = levs)
+  attsurfs <- compute_eaf_as_list(x, percentiles = levs)
     
   # Denote p_n the attainment probability, the value of the symmetric
   # difference function is p_n if p_n < alpha (Vorob'ev threshold) and 1 - p_n
@@ -165,25 +165,25 @@ symDifPlot <- function(x, VE, threshold, nlevels = 11,
   names(levs) <- cols
     
   # FIXME: We should take the range from the attsurfs to not make x mandatory.
-  xlim <- get.xylim(xlim, maximise[1], data = x[,1])
-  ylim <- get.xylim(ylim, maximise[2], data = x[,2])
-  extreme <- get.extremes(xlim, ylim, maximise, log = log)
+  xlim <- get_xylim(xlim, maximise[1], data = x[,1])
+  ylim <- get_xylim(ylim, maximise[2], data = x[,2])
+  extreme <- get_extremes(xlim, ylim, maximise, log = log)
 
   plot(xlim, ylim, type = "n", xlab = "", ylab = "",
        xlim = xlim, ylim = ylim, log = log, axes = FALSE, las = las,
        main = main,
        panel.first = {
-         plot.eaf.full.area(attsurfs, extreme = extreme, maximise = maximise, col = cols)
+         plot_eaf_full_area(attsurfs, extreme = extreme, maximise = maximise, col = cols)
          # We place the axis after so that we get grid lines.
-         plot.eaf.axis (xaxis.side, xlab, las = las, sci.notation = sci.notation)
-         plot.eaf.axis (yaxis.side, ylab, las = las, sci.notation = sci.notation,
+         plot_eaf_axis (xaxis_side, xlab, las = las, sci.notation = sci.notation)
+         plot_eaf_axis (yaxis_side, ylab, las = las, sci.notation = sci.notation,
                         line = 2.2)
-         plot.eaf.full.lines(list(VE), extreme, maximise,
+         plot_eaf_full_lines(list(VE), extreme, maximise,
                              col = ve.col, lty = 1, lwd = 2)
        })
 
   # Use first.open to print "(0,X)", because the color for 0 is white.
-  intervals <- seq.intervals.labels(seq.levs, first.open = TRUE)
+  intervals <- seq_intervals_labels(seq.levs, first.open = TRUE)
   intervals <- intervals[1:max.interval]
   names(intervals) <- names(colscale)
   #names(intervals) <- names(colscale[1:max.interval])
diff --git a/man/attsurf2df.Rd b/man/attsurf2df.Rd
index 6d1f0b7..68f1854 100644
--- a/man/attsurf2df.Rd
+++ b/man/attsurf2df.Rd
@@ -9,7 +9,7 @@ attsurf2df(x)
 \arguments{
 \item{x}{(\code{list()}) List of data.frames or matrices. The names of the list
 give the percentiles of the attainment surfaces.  This is the format
-returned by \code{\link[=eafplot]{eafplot()}} (and the internal function \code{compute.eaf.as.list}).}
+returned by \code{\link[=eafplot]{eafplot()}} (and the internal function \code{compute_eaf_as_list}).}
 }
 \value{
 A data.frame with as many columns as objectives and an additional column \code{percentiles}.
diff --git a/tests/testthat/test-eaf.R b/tests/testthat/test-eaf.R
index 982c576..edbf346 100644
--- a/tests/testthat/test-eaf.R
+++ b/tests/testthat/test-eaf.R
@@ -4,7 +4,7 @@ test_that("eaf", {
 
   test.eaf.dataset <- function(name, percentiles = NULL) {
     dataset <- get(name)
-    x <- eaf:::compute.eaf(dataset, percentiles)
+    x <- eaf:::compute_eaf(dataset, percentiles)
     # FIXME: work-around for change in the computation
     x[,3] <- floor(x[,3])
     #saveRDS(x, paste0(name, "-eaf.rds"))
@@ -12,7 +12,7 @@ test_that("eaf", {
   }
   test.eaf.file <- function(file, percentiles = NULL) {
     dataset <- read_datasets(file)
-    x <- eaf:::compute.eaf(dataset, percentiles)
+    x <- eaf:::compute_eaf(dataset, percentiles)
     #saveRDS(x, paste0(basename(file), "-eaf.rds"))
     return(x)
   }
@@ -39,7 +39,7 @@ test_that("eaf3d", {
   data.combined[, nobjs + 1] <- data.combined[, nobjs + 1] + nruns.left
   data.combined <- rbind(lin, data.combined)
   # This may stop working once we filter uninteresting values in the C code directly.
-  DIFF <- eaf:::compute.eafdiff.helper(data.combined, intervals = nruns.left)
+  DIFF <- eaf:::compute_eafdiff_helper(data.combined, intervals = nruns.left)
   x <- as.matrix(read.table("lin.S-sph.S-diff.txt.xz", header = FALSE))
   dimnames(x) <- NULL
   x[, nobjs + 1] <- x[, nobjs + 1] - x[, nobjs + 2]