`glomApply()`

is a function used for subsetting SoilProfileCollection objects by depth. It is a wrapper around `glom`

which is intended to subset single-profile SPCs based on depth intervals/intersection.

`glomApply`

works by accepting a function `.fun`

as argument. This function is used on each profile to process a multi-profile SPC for input to `glom`

(via `profileApply`

). For each profile, `.fun`

returns a 2-length numeric vector of top and bottom boundaries `glom`

arguments: `z1`

, `z2`

.

`glomApply`

provides the option to generate profile-specific glom depths for a large SPC and handles iteration and rebuilding of a subset SPC object. Optional arguments include: `truncate`

to cut the boundaries to specified `[z1, z2]`

; `invert`

to the portion outside `[z1, z2]`

, `modality`

to either `"all"`

horizons or `"thickest"`

horizon in the `glom`

interval. `...`

are various expressions you can run on the individual profiles using NSE, similar to `mutate`

.

```
glomApply(
object,
.fun = NULL,
truncate = FALSE,
invert = FALSE,
modality = "all",
...,
chunk.size = 100
)
```

- object
A SoilProfileCollection

- .fun
A function that returns vector with top and bottom depth (

`z1`

and`z2`

arguments to`glom`

) for a single profile`p`

(as passed by`profileApply`

)- truncate
Truncate horizon top and bottom depths to

`[z1, z2]`

- invert
Truncate horizon top and bottom depths to

`[z1, z2]`

and then invert result?- modality
Aggregation method for glom result. Default

`"all"`

: return all horizons;`"thickest"`

: return (shallowest) thickest horizon- ...
A set of comma-delimited R expressions that resolve to a transformation to be applied to a single profile e.g

`glomApply(hzdept = max(hzdept) - hzdept)`

like`aqp::mutate`

- chunk.size
Chunk size parameter for

`profileApply`

A SoilProfileCollection.

```
# keep examples from using more than 2 cores
data.table::setDTthreads(Sys.getenv("OMP_THREAD_LIMIT", unset = 2))
data(sp3)
depths(sp3) <- id ~ top + bottom
# init horizon designation column in metadata, used by estimateSoilDepth
hzdesgnname(sp3) <- 'name'
# constant depths, whole horizon returns by default
plot(glomApply(sp3, function(p) c(25,100)))
# constant depths, truncated
#(see aqp::trunc for helper function)
plot(glomApply(sp3, function(p) c(25,30), truncate = TRUE))
# constant depths, inverted
plot(glomApply(sp3, function(p) c(25,100), invert = TRUE))
# constant depths, inverted + truncated (same as above)
plot(glomApply(sp3, function(p) c(25,30), invert = TRUE, truncate=TRUE))
# random boundaries in each profile
plot(glomApply(sp3, function(p) round(sort(runif(2, 0, max(sp3))))))
# random boundaries in each profile (truncated)
plot(glomApply(sp3, function(p) round(sort(runif(2, 0, max(sp3)))), truncate = TRUE))
# calculate some boundaries as site level attribtes
sp3$glom_top <- profileApply(sp3, getMineralSoilSurfaceDepth)
#> Warning: found 1 profiles where pattern did not match and shallowest depth is greater than 0
#> Warning: found 1 profiles where pattern did not match and shallowest depth is greater than 0
#> Warning: found 1 profiles where pattern did not match and shallowest depth is greater than 0
sp3$glom_bottom <- profileApply(sp3, estimateSoilDepth)
# use site level attributes for glom intervals for each profile
plot(glomApply(sp3, function(p) return(c(p$glom_top, p$glom_bottom))))
```