Get top or bottom depths of horizons matching a regular expression pattern

Source: R/depthOf.R

The depthOf family of functions calculate depth of occurrence of a horizon designation pattern, or any other value that can be coerced to character and matched with a regular expression.

If you need all depths of occurrence for a particular pattern, depthOf is what you are looking for. minDepthOf and maxDepthOf are wrappers around depthOf that return the minimum and maximum depth. They are all set up to handle missing values and missing "contacts" with the target pattern.

depthOf(
  p,
  pattern,
  FUN = NULL,
  top = TRUE,
  hzdesgn = hzdesgnname(p, required = TRUE),
  no.contact.depth = NULL,
  no.contact.assigned = NA_real_,
  na.rm = TRUE,
  simplify = TRUE
)

maxDepthOf(
  p,
  pattern,
  top = TRUE,
  hzdesgn = hzdesgnname(p, required = TRUE),
  no.contact.depth = NULL,
  no.contact.assigned = NA,
  na.rm = TRUE,
  simplify = TRUE
)

minDepthOf(
  p,
  pattern,
  top = TRUE,
  hzdesgn = hzdesgnname(p, required = TRUE),
  no.contact.depth = NULL,
  no.contact.assigned = NA,
  na.rm = TRUE,
  simplify = TRUE
)

Arguments

p

a SoilProfileCollection

pattern

a regular expression to match in the horizon designation column. See:hzdesgn

FUN

a function that returns a single value, and takes argument na.rm

top

should the top (TRUE) or bottom (FALSE) depth be returned for matching horizons? Default: TRUE.

hzdesgn

column name containing horizon designations. Default: guessHzDesgnName(p)

no.contact.depth

depth to assume that contact did not occur.

no.contact.assigned

depth to assign when a contact did not occur.

na.rm

logical. Remove NA? (default: TRUE)

simplify

logical. Return single profile results as vector (default: TRUE) or data.frame (FALSE)

Value

a numeric vector containing specified depth(s) of horizons matching a pattern. If length(p) > 1 then a data.frame containing profile ID, horizon ID, top or bottom depths, horizon designation and pattern.

Author

Andrew G. Brown

Examples

# construct a fake profile
spc <- data.frame(id=1, taxsubgrp = "Lithic Haploxerepts",
                  hzname   = c("A","AB","Bw","BC","R"),
                  hzdept   = c(0,  20, 32, 42,  49),
                  hzdepb   = c(20, 32, 42, 49, 200),
                  clay     = c(19, 22, 22, 21,  NA),
                  texcl    = c("l","l","l", "l","br"),
                  d_value  = c(5,   5,  5,  6,  NA),
                  m_value  = c(2.5, 3,  3,  4,  NA),
                  m_chroma = c(2,   3,  4,  4,  NA))

# promote to SoilProfileCollection
depths(spc) <- id ~ hzdept + hzdepb
hzdesgnname(spc) <- 'hzname'
hztexclname(spc) <- 'texcl'

# multiple horizons contain B
depthOf(spc, "B")
#> [1] 20 32 42

# deepest top depth of horizon containing B
maxDepthOf(spc, "B")
#> [1] 42

# shallowest top depth
minDepthOf(spc, "B")
#> [1] 20

# deepest bottom depth
maxDepthOf(spc, "B", top = FALSE)
#> [1] 49

# deepest bottom depth above 35cm
maxDepthOf(spc, "B", top = FALSE, no.contact.depth = 35)
#> [1] 32

# assign infinity (Inf) if B horizon does not start within 10cm
minDepthOf(spc, "B", no.contact.depth = 10, no.contact.assigned = Inf)
#> [1] Inf