You can access the contents of a SoilProfileCollection by profile and horizon "index", i and j, respectively: spc[i, j, ...]. Subset operations are propagated to other slots (such as diagnostics or spatial) when they result in removal of sites from a collection.
i refers to the profile position within the collection. By default the order is based on the C SORT order of the variable that you specified as your unique profile ID at time of object construction. Note that if your ID variable was numeric, then it has been sorted as a character.
j refers to the horizon or "slice" index. This index is most useful when either a) working with slice'd SoilProfileCollection or b) working with single-profile collections. j returns the layer in the specified index positions for all profiles in a collection.
... is an area to specify an expression that is evaluated in the subset. Currently supported
.LAST (last horizon in each profile): return the last horizon from each profile. This uses i but ignores the regular j index.
.FIRST (first horizon in each profile): return the last horizon from each profile. This uses i but ignores the regular j index.
.HZID (horizon index): return the horizon indices corresponding to i+j+... ("k") constraints
.NHZ (number of horizons): return the number of horizons in the profiles resulting from i+j+... ("k") constraints
# S4 method for SoilProfileCollection
[(x, i, j, ..., drop = TRUE)a SoilProfileCollection
a numeric or logical value denoting profile indices to select in a subset
a numeric or logical value denoting horizon indices to select in a subset
non-standard expressions to evaluate in a subset
Default: TRUE. When drop=FALSE placeholder horizons (profile ID with all other values NA) are created where the specified j index results in removal of all horizons.