Merge branch 'master' into devel

# Conflicts:
#	DESCRIPTION
#	NEWS.md

NEWS.md

@@ -16,6 +16,10 @@ Following the retirement of `rgdal` and `sp` we removed the dependence to `sp` a
 4. Change: the function `extent` was removed in consequence of (3) because it was inherited from `raster` and returned an object `Extent` from `raster`.
 5. Change: functions `crs`, `crs<-`, `projection`, `projection<-`, `wkt` and `area` inherited from `raster` are now generic. This may create clash with the `raster` package but anyway `raster` should no longer be used.
 
+### Fixes
+
+- Fix: [#726](https://github.com/r-lidar/lidR/issues/726) character palette causes error in plot.
+
 ## lidR v4.0.4 (Release date: 2023-09-07)
 
 - Fix: interpolation of NA pixels failed when a single pixel is missing [#684](https://github.com/r-lidar/lidR/issues/684)

R/metrics_stdmetrics.R

@@ -550,30 +550,29 @@ rumple_index.numeric <- function(x, y = NULL, z = NULL, ...)
 #' @rdname nstdmetrics
 gap_fraction_profile = function(z, dz = 1, z0 = 2)
 {
-  bk <- seq(floor((min(z) - z0)/dz)*dz + z0, ceiling((max(z) - z0)/dz)*dz + z0, dz)
-
-  if (length(bk) <= 1)
+  zrange = range(z)
+  if (z0 < zrange[1])
+    z0 = floor((zrange[1]- z0)/dz)*dz + z0
+
+  if (z0 >= zrange[2])
     return(data.frame(z = numeric(0), gf = numeric(0)))
-
-  histogram <- graphics::hist(z, breaks = bk, plot = F)
+
+  bk <- seq(z0, ceiling((zrange[2] - z0)/dz)*dz + z0, dz)
+
+  histogram <- graphics::hist(z, breaks = c(-Inf, bk), plot = F)
   h <- histogram$mids
-  p <- histogram$counts/sum(histogram$counts)
-
-  p <- c(p, 0)
-
+  p <- histogram$counts
+
   cs <- cumsum(p)
-  i <- data.table::shift(cs)/cs
+  i <- cs[1:(length(cs)-1)]/cs[2:length(cs)]
+
   i[is.na(i)] = 0
-
-  i[is.nan(i)] = NA
-
-  z = h #[-1]
-  i = i[-length(i)] #[-c(1, length(i))]
-
-  return(data.frame(z = z[z > z0], gf = i[z > z0]))
+
+  z = h[-1]
+
+  return(data.frame(z = z, gf = i))
 }
 
-
 #' @param k numeric. is the extinction coefficient
 #' @examples
 #' z <- c(rnorm(1e4, 25, 6), rgamma(1e3, 1, 8)*6, rgamma(5e2, 5,5)*10)
@@ -588,10 +587,7 @@ LAD = function(z, dz = 1, k = 0.5, z0 = 2) # (Bouvier et al. 2015)
 {
   ld <- gap_fraction_profile(z, dz, z0)
 
-  if (nrow(ld) <= 2)
-    return(data.frame(z = numeric(0), lad = numeric(0)))
-
-  if (anyNA(ld))
+  if (nrow(ld) == 0)
     return(data.frame(z = numeric(0), lad = numeric(0)))
 
   lad <- ld$gf

R/plot.R

@@ -287,7 +287,7 @@ plot.LAS = function(x, y, ...,
   has_col <- color %in% names(x)
   use_rgb <- color == "RGB"
   has_rgb <- all(c("R", "G", "B") %in% names(x))
-  autocol <- is.character(pal) && pal == "auto"
+  autocol <- is.character(pal) && length(pal) == 1 && pal == "auto"
 
   # Error handling
   assert_is_a_bool(clear_artifacts)