Merge branch 'develop' into rename

R/oce.R

@@ -1276,6 +1276,13 @@ oce.plot.ts <- function(
     # Handle 'simplify' argument
     nx <- length(x)
     if (type == "l" && is.numeric(simplify) && nx > (5L * simplify)) {
+        # simplification works by replacing all the points in each sub-interval
+        # with just two points: one for the minimum y value there, and the other
+        # for the maximum y value there.  (NA is used if all the data in the
+        # interval are missing.)  This way, the graph displays the data quite
+        # faithfully in most cases.  By contrast, if we instead used, say, the
+        # mean y in each interval, the curve could get smoothed enough to
+        # be unrepresentative.
         warning("simplifying a large dataset; set simplify=NA to see raw data\n")
         xgrid <- seq(min(x, na.rm = TRUE), max(x, na.rm = TRUE), length.out = simplify)
         df <- data.frame(x, y)
@@ -1286,6 +1293,8 @@ oce.plot.ts <- function(
         tz <- attr(x, "tzone") # cause gridded x to inherit timezone from original x
         x <- rep(unname(sapply(dfSplit, function(DF) if (length(DF$x) > 2) mean(DF$x, na.rm = TRUE) else NA)), each = 2)
         x <- numberAsPOSIXct(x, tz = tz)
+        # FIXME: I think thhis might be faster if another 'apply' function were
+        # used, to return 2 values, but I (DEK) can't recall what that function is.
         ymin <- unname(sapply(
             dfSplit,
             function(DF) {
@@ -1299,10 +1308,6 @@ oce.plot.ts <- function(
             }
         ))
         y <- as.vector(rbind(ymin, ymax))
-        # Remove any segments for which min and max could not be computed
-        bad <- !is.finite(y)
-        x <- x[!bad]
-        y <- y[!bad]
     }
     xrange <- range(x, na.rm = TRUE)
     yrange <- range(y, finite = TRUE)

R/sealevel.R

@@ -611,8 +611,8 @@ setMethod(
                     xx@data[[i]] <- x@data[[i]][look]
                 }
                 if (any(is.finite(xx@data$elevation))) {
-                    xlim <- if (xlimGiven) xlim else (range(x@data$time, na.rm = TRUE))
-                    ylim <- if (ylimGiven) ylim else (range(x@data$elevation, na.rm = TRUE))
+                    xlim <- if (xlimGiven) xlim else (range(xx@data$time, na.rm = TRUE))
+                    ylim <- if (ylimGiven) ylim else (range(xx@data$elevation, na.rm = TRUE))
                     atWeek <- seq(from = from, to = to, by = "week")
                     atDay <- seq(from = from, to = to, by = "day")
                     plot(xx@data$time, xx@data$elevation,

R/tides.R

@@ -1579,17 +1579,12 @@ tidem <- function(
     icBad <- NULL
     sdCriterion <- 1e-2
     oceDebug(debug, vectorShow(sdCriterion))
-    # 20230122 danS <- danC <- NULL
     for (i in 1:nc) {
-        # 20230122 oceDebug(debug+1, "setting ", i, "-th coefficient (name=", name[i], " period=", 1/freq[i], " h)", "\n", sep="")
         ft <- freq[i] * hour2pi
         C <- cos(ft)
         S <- sin(ft)
         sdS <- sd(S)
         sdC <- sd(C)
-        # 20230122 danS <- c(danS, sdS) # FIXME: remove
-        # 20230122 danC <- c(danC, sdC) # FIXME: remove
-        # 20230122 oceDebug(debug+1, sprintf("    sdC %.4g; sdS %.4g\n", sdC, sdS))
         # Find whether anything is uncomputable. We ignore Z0 because that is handled later.
         if (name[i] != "Z0" && (sdS < sdCriterion || sdC < sdCriterion)) {
             oceDebug(debug, "    ** uncomputable at ", name[i], " (period ", 1 / freq[i], "h) **\n")
@@ -2086,7 +2081,7 @@ webtide <- function(
     plot = TRUE, tformat, debug = getOption("oceDebug"), ...) {
     debug <- max(0, min(floor(debug), 2))
     oceDebug(debug, "webtide(action=\"", action, "\", ...)\n",
-        sep = "", unindent = 1 
+        sep = "", unindent = 1
     )
     rpd <- atan2(1, 1) / 45 # radians per degree
     action <- match.arg(action)