Updates to slab()

 - closes #229

 - NA_real_ for proper expectation of missing weights passed to base
   weighted.mean() (minimal custom slab function)

R/genSlabLabels.R

@@ -1,54 +1,52 @@
 ## TODO: documentation / generalization
-# note source data must be normalixed via slice() first, e.g. all share the same number of horizons
+# note source data must be "normalized" via dice() first; assumes each profile has the same number of horizons
 
 # generate labels for slabs
-genSlabLabels <- function(slab.structure=1, max.d, n.profiles) {
+genSlabLabels <- function(slab.structure = 1, max.d, n.profiles) {
 
   # fixed-size slabs
-  if(length(slab.structure) == 1) {
+  if (length(slab.structure) == 1) {
     # generate sequence of segment labels
-    seg.label <- rep(1:ceiling(max.d / slab.structure), each=slab.structure, length=max.d)
+    seg.label <- rep(1:ceiling(max.d / slab.structure), each = slab.structure, length = max.d)
+
     # general segment labels
-    seg.label.levels <- tapply(1:max.d, seg.label, function(i) {r <- range(i); paste(c(r[1]-1, r[2]), collapse='-') } )
+    seg.label.levels <- tapply(1:max.d, seg.label, 
+                               function(i) {
+                                 r <- range(i, na.rm = TRUE)
+                                 paste(c(r[1] - 1, r[2]), collapse = '-')
+                               })
   }
 
   # user-defined slabs
-  if(length(slab.structure) > 1) {
-    # trival case where segments start from 0
-    if(slab.structure[1] == 0 & length(slab.structure) > 2)
-      seg.label <- rep(slab.structure[-1], times=diff(slab.structure))[1:max.d]
+  if (length(slab.structure) > 1) {
+    if (slab.structure[1] == 0 & length(slab.structure) > 2) {
+      # trivial case where segments start from 0
+
+      seg.label <- rep(slab.structure[-1], times = diff(slab.structure))[1:max.d]
 
-    # other case: user defines an arbitrary lower and upper limit
-    else {
-      if(length(slab.structure) != 2)
+    } else {
+      # other case: user defines an arbitrary lower and upper limit
+      if (length(slab.structure) != 2)
         stop('user-defined slab boundaries must either start from 0, or contain two values between 0 and the max soil depth')
 
-      # proceed
+      # calculate thickness of slab
       slab.thickness <- diff(slab.structure)
-      # how many slices of NA before the slab?
-      padding.before <- rep(NA, times=slab.structure[1])
-      # how many slices of NA afer the slab
-      padding.after <- rep(NA, times=abs(max.d - slab.structure[2]))
+
       # make a new label for the slab
-      new.label <- paste(slab.structure, collapse='-')
-      # generate an index for the slab
-      slab.idx <- rep(new.label, times=slab.thickness)
-      # generate the entire index: padding+slab+padding = total number of slices (max_d)
-      # seg.label <- c(padding.before, slab.idx, padding.after)
-      seg.label <- slab.idx 
+      new.label <- paste(slab.structure, collapse = '-')
+
+      slab.idx <- rep(new.label, times = slab.thickness)
+      seg.label <- slab.idx
     }
 
     # generate segment labels	
-    seg.label.levels <- sapply(1:(length(slab.structure)-1), function(i) paste(c(slab.structure[i], slab.structure[i+1]), collapse='-'))
+    seg.label.levels <- sapply(1:(length(slab.structure) - 1), function(i) {
+      paste(c(slab.structure[i], slab.structure[i + 1]), collapse = '-')
+    })
   }
 
   # covert into a factor that can be used to split profiles into slabs
-  res <- factor(rep(seg.label, times=n.profiles), labels=seg.label.levels)
+  res <- factor(rep(seg.label, times = n.profiles), labels = seg.label.levels)
 
   return(res)
 }
-
-
-
-
-