make .hzTests() -- simpler accessor method to key 'logic' of checkHzD…

…epthLogic() #65

R/checkHzDepthLogic.R

@@ -19,27 +19,17 @@ checkHzDepthLogic <- function(x) {
     ID.i <- h[[idn]][1]
     .top <- h[[htb[1]]]
     .bottom <- h[[htb[2]]]
-    .n <- length(.top)
 
-    # bottom depth < top depth?
-    test.1 <- any(.bottom < .top, na.rm = TRUE)
-
-    # bottom depth == top depth
-    test.2 <- any(.top == .bottom, na.rm = TRUE)
-
-    # NA depths
-    test.3 <- any(is.na(.top) | is.na(.bottom), na.rm = TRUE)
-
-    # bottom != next top
-    test.4 <- any(.bottom[-.n] != .top[-1], na.rm = TRUE)
+    # hzTests takes two numeric vectors and returns named logical
+    test <- .hzTests(.top, .bottom)
 
     # pack into DF, 1 row per profile 
     res <- data.frame(
       .id=ID.i,
-      depthLogic=test.1, 
-      sameDepth=test.2, 
-      missingDepth=test.3,
-      overlapOrGap=test.4,
+      depthLogic=test[1], 
+      sameDepth=test[2], 
+      missingDepth=test[3],
+      overlapOrGap=test[4],
       stringsAsFactors = FALSE
     )
 
@@ -57,3 +47,23 @@ checkHzDepthLogic <- function(x) {
 
   return(res)
 }
+
+.hzTests <- function(top, bottom) {
+  n <- length(top)
+
+  # bottom depth < top depth?
+  test.1 <- any(bottom < top, na.rm = TRUE)
+
+  # bottom depth == top depth
+  test.2 <- any(top == bottom, na.rm = TRUE)
+
+  # NA depths
+  test.3 <- any(is.na(top) | is.na(bottom), na.rm = TRUE)
+
+  # bottom != next top
+  test.4 <- any(bottom[-n] != top[-1], na.rm = TRUE)
+
+  res <- as.logical(c(test.1, test.2, test.3, test.4))
+  names(res) <- c("depthLogic","sameDepth","missingDepth","overlapOrGap")
+  return(res)
+}

R/glom.R

@@ -1,20 +1,17 @@
 # glom returns a "clod" of horizons that have a common attribute (currently just depth interval supported)
 
-# returns unique index to all horizons occuring over the depth interval [z1, z2]. 
-# z2 is optional, in which case a single horizon with depth range containing z1 is returned
-# several wrapper functions around this for hzid
-
-# a 'clod' is a ragged group of soil pedon horizons (each with distinctness, horizons boundaries)
-# a clod references the original pedon data, it is not resampled like a slice or slab. 
-
 # the verb/function that creates a clod is "glom" 
 # "to glom" is "to steal" or to "become stuck or attached to". it is related to the 
 # compound "glomalin", which is a glycoprotein produced by mycorrhizal fungi in soil
 
 # gloms a set of horizons for a single-profile SPC `p`
-#  the horizons are aggregated by depth using clod.hz.ids() 
+#  the horizons are aggregated by depth using 
+#  clod.hz.ids() defined below
 glom <- function(p, z1, z2=NA, as.data.frame = FALSE) {
-  # aka glom.by.depth; just one type of glomming of many that we can support
+  # aka glom.by.depth; 
+  if(length(p) > 1)
+    stop("glom is intended for single-profile SPCs", call.=FALSE)
+
   idx <- clod.hz.ids(p, z1, z2)
   if(!all(is.na(idx))) {
     if(!as.data.frame) {
@@ -27,31 +24,32 @@ glom <- function(p, z1, z2=NA, as.data.frame = FALSE) {
   }
 }
 
-# create a vector of horizon IDs comprising a "clod" (by depth intersection of horizons)
+# returns unique index to all horizons occuring over the depth interval [z1, z2]. 
+# z2 is optional, in which case a single horizon with depth range containing z1 is returned
 clod.hz.ids <- function (p, z1, z2 = NA, as.list = FALSE) 
 {
+  # access SPC slots to get important info about p
+  hz <- horizons(p)
+  dz <- horizonDepths(p)
+  hzid <- hzidname(p)
+
+  # get top and bottom horizon depth vectors
+  tdep <- hz[[dz[1]]]
+  bdep <- hz[[dz[2]]]
+
   # short circuit test of hz logic
-  depthlogic <- checkHzDepthLogic(p)
+  depthlogic <- .hzTests(tdep, bdep)
   logic_tests <- c('depthLogic','missingDepth','overlapOrGap')
   logic_fail <- as.logical(depthlogic[logic_tests])
   if(any(logic_fail)) {
     # too much could possibly go wrong in presence of overlaps/gaps/missing depths etc
     warning(paste0('Horizon logic error(s) ',
                    paste0(logic_tests[logic_fail], collapse=","),
-                   ' found via `aqp::checkHzDepthLogic()`. Returning `NA` for ',idname(p),': ',
+                   ' found. Returning `NA` for ',idname(p),': ',
                    profile_id(p)), call.=FALSE)
     return(NA)
   }
 
-  # access SPC slots to get important info about p
-  hz <- horizons(p)
-  dz <- horizonDepths(p)
-  hzid <- hzidname(p)
-
-  # get top and bottom horizon depth vectors
-  tdep <- hz[[dz[1]]]
-  bdep <- hz[[dz[2]]]
-
   # determine top depths greater/equal to z1
   gt1 <- tdep >= z1
 
@@ -62,14 +60,14 @@ clod.hz.ids <- function (p, z1, z2 = NA, as.list = FALSE)
   idx.top <- which(gt1)
 
   if (!length(idx.top)) {
-    warning(paste0('Invalid upper bound. Check argument `z1`. Returning `NA` for ',idname(p),': ', profile_id(p)), call.=FALSE)
+    warning(paste0('Invalid upper bound. Check argument `z1`. Returning `NA` (',idname(p),': ', profile_id(p),')'), call.=FALSE)
     return(NA)
   }
 
   idx.top <- idx.top[1] # always returns the top horizon
 
   if(z1 < tdep[idx.top]) {
-    warning(paste0('Upper boundary `z1` (',z1,') shallower than top depth (',tdep[idx.top],') of shallowest horizon in subset. First horizon in profile @ ',min(tdep),'. (',idname(p),': ', profile_id(p), ')'), call.=FALSE)
+    warning(paste0('Upper boundary `z1` (',z1,') shallower than top depth (',tdep[idx.top],') of shallowest horizon in subset. (',idname(p),': ', profile_id(p), ')'), call.=FALSE)
   }
 
   # if a bottom depth of the clod interval is specified
@@ -94,7 +92,7 @@ clod.hz.ids <- function (p, z1, z2 = NA, as.list = FALSE)
     idx.bot <- idx.bot[1]
 
     if(z2 > bdep[idx.bot]) {
-      warning(paste0('Lower boundary `z2` (',z2,') is deeper than bottom depth of deepest horizon (', bdep[idx.bot],') in subset. ',idname(p),': ', profile_id(p)), call.=FALSE)
+      warning(paste0('Lower boundary `z2` (',z2,') is deeper than bottom depth of deepest horizon (', bdep[idx.bot],') in subset. (',idname(p),': ', profile_id(p),")"), call.=FALSE)
     }
 
     # not really sure how this could happen ... maybe with wrong depth units for z?