accumulateDepths: Accumulate horizon depths, and reflect reversed depths,...
In aqp: Algorithms for Quantitative Pedology

accumulateDepths

R Documentation

Accumulate horizon depths, and reflect reversed depths, relative to new datum

Description

Fix old-style organic horizon depths or depths with a non-standard datum by the "depth accumulation" method.

Usage

accumulateDepths(
  x,
  id = NULL,
  hzdepths = NULL,
  hzname = NULL,
  hzdatum = 0,
  seqnum = NULL,
  pattern = "O",
  fix = TRUE
)

Arguments

`x`	A `data.frame` or `SoilProfileCollection`
`id`	unique profile ID. Default: `NULL`, if `x` is a SoilProfileCollection `idname(x)`
`hzdepths`	character vector containing horizon top and bottom depth column names. Default: `NULL`, if `x` is a SoilProfileCollection `horizonDepths(x)`
`hzname`	character vector containing horizon designation or other label column names. Default: `NULL`, if `x` is a SoilProfileCollection `hzdesgnname(x)`
`hzdatum`	a numeric vector to add to accumulated depths. Default: `0`. Can be equal in length to number of profiles if `x` is a `SoilProfileCollection` or number of (unique) IDs if `x` is a `data.frame`.
`seqnum`	Optional: character vector containing record "sequence number" column name; used in-lieu of `hzname` (when `NA`) to identify "first" record in a profile
`pattern`	pattern to search for in `hzname` to identify matching horizons to append the profile to
`fix`	apply adjustments to missing (`NA`) depths and expand 0-thickness horizons? Default: `TRUE`

Details

The "depth accumulation" method calculates thicknesses of individual horizons and then cumulative sums them after putting them in id + top depth order. The routine tries to determine context based on hzname and pattern. The main transformation is if a top depth is deeper than the bottom depth, the depths are reflected on the Z-axis (made negative). The data are then id + top depth sorted again, the thickness calculated and accumulated to replace the old depths.

This function uses several heuristics to adjust data before transformation and thickness calculation:

Regex matching of horizon designation patterns and similar

matches of pattern where both top and bottom depth NA -> ⁠[0,1]⁠ ⁠[top,bottom]⁠ depth
REMOVE horizons that do not match pattern where both top and bottom depths NA

Over-ride `hzname` handling with the sequence column argument `seqnum`

if seqnum column specified "first record with NA hzname" is considered a pattern match if seqnum == 1

Trigger "fixing" with the `fix` argument:

Add 1 cm to bottom-most horizons with NA bottom depth
Add 1 cm thickness to horizons with top and bottom depth equal
Add 1 cm thickness to horizons with NA top depth and bottom depth 0

Value

A horizon-level data.frame, suitable for promoting to SPC with ⁠depths<-⁠, or a SoilProfileCollection, depending on the class of x.

Examples


# example using hzdatum argument
data(sp4)
depths(sp4) <- id ~ top + bottom
hz <- accumulateDepths(sp4,
                       id = "id",
                       hzdepths = c("top", "bottom"),
                       hzname = "name",
                       hzdatum = 5 * 1:length(sp4))
plot(hz)
  
# example using old-style O horizons
hz <- read.table(text = "peiidref hzdept hzdepb hzname seqnum phiid
                    1        11      0      5      A      2   295
                    2        11      1      0     Oe      1   294
                    3        11      5     13     C1      3   296
                    4        11     13     58     C2      4   297
                    5        11     58    152     C3      5   298
                    6        13      0      5      A      2   303
                    7        13      1      0     Oe      1   302
                    8        13      5     25     Bw      3   304
                    9        13     25     61      C      4   305
                    10       13     61     NA      R      5   306
                    11      136      0     13     A1      3   695
                    12      136      1      0     Oe      2   694
                    13      136      2      1     Oi      1   693
                    14      136     13     61     C1      4   696
                    15      136     61     76     C2      5   697")
                    
depths(hz) <- peiidref ~ hzdept + hzdepb

hz_fixed <- accumulateDepths(hz,
                             id = "peiidref",
                             hzdepths = c("hzdept", "hzdepb"),
                             hzname = "hzname")
is_valid <- checkHzDepthLogic(hz_fixed)$valid

test0 <- subset(hz_fixed, !is_valid)
test1 <- subset(hz_fixed, is_valid)

origO <- subset(hz, grepl("O", hzname))
fixedO <- subset(hz_fixed, grepl("O", hzname))

par(mfrow=c(2,1), mar=c(0,0,3,2))
plotSPC(origO, max.depth = 25)
plotSPC(fixedO, max.depth = 25)

aqp documentation built on Oct. 19, 2024, 5:06 p.m.