profileApply: Iterate over profiles in a SoilProfileCollection

In aqp: Algorithms for Quantitative Pedology

Iterate over profiles in a SoilProfileCollection

Description

Iterate over all profiles in a SoilProfileCollection, calling FUN on a single-profile SoilProfileCollection for each step.

Usage

## S4 method for signature 'SoilProfileCollection'
profileApply(
  object,
  FUN,
  simplify = TRUE,
  frameify = FALSE,
  chunk.size = 100,
  column.names = NULL,
  APPLY.FUN = lapply,
  ...
)

Arguments

object	a SoilProfileCollection
FUN	a function to be applied to each profile within the collection
simplify	logical, should the result be simplified to a vector? default: TRUE; see examples
frameify	logical, should the result be collapsed into a data.frame? default: FALSE; overrides simplify argument; see examples
chunk.size	numeric, size of "chunks" for faster processing of large SoilProfileCollection objects; default: 100
column.names	character, optional character vector to replace frameify-derived column names; should match length of colnames() from FUN result; default: NULL
APPLY.FUN	function, optional alternate lapply()-like function for processing chunks. For example future.apply::future_lapply() for processing chunks in parallel. Default base::lapply().
...	additional arguments passed to FUN

Value

When simplify is TRUE, a vector of length nrow(object) (horizon data) or of length length(object) (site data). When simplify is FALSE, a list is returned. When frameify is TRUE, a data.frame is returned. An attempt is made to identify idname and/or hzidname in the data.frame result, safely ensuring that IDs are preserved to facilitate merging profileApply result downstream.

Examples

data(sp1)
depths(sp1) <- id ~ top + bottom

# estimate soil depth using horizon designations
profileApply(sp1, estimateSoilDepth, name='name')

# scale a single property 'prop' in horizon table
# scaled = (x - mean(x)) / sd(x)
sp1$d <- profileApply(sp1, FUN=function(x) round(scale(x$prop), 2))
plot(sp1, name='d')

# compute depth-wise differencing by profile
# note that our function expects that the column 'prop' exists
f <- function(x) { c(x$prop[1], diff(x$prop)) }
sp1$d <- profileApply(sp1, FUN=f)
plot(sp1, name='d')

# compute depth-wise cumulative sum by profile
# note the use of an anonymous function
sp1$d <- profileApply(sp1, FUN=function(x) cumsum(x$prop))
plot(sp1, name='d')

# compute profile-means, and save to @site
# there must be some data in @site for this to work
site(sp1) <- ~ group
sp1$mean_prop <- profileApply(sp1, FUN=function(x) mean(x$prop, na.rm=TRUE))

# re-plot using ranks defined by computed summaries (in @site)
plot(sp1, plot.order=rank(sp1$mean_prop))

## iterate over profiles, calculate on each horizon, merge into original SPC

# example data
data(sp1)

# promote to SoilProfileCollection
depths(sp1) <- id ~ top + bottom
site(sp1) <- ~ group

# calculate horizon thickness and proportional thickness
# returns a data.frame result with multiple attributes per horizon
thicknessFunction <- function(p) {
  hz <- horizons(p)
  depthnames <- horizonDepths(p)
  res <- data.frame(profile_id(p), hzID(p),
                    thk=(hz[[depthnames[[2]]]] - hz[[depthnames[1]]]))
  res$hz_prop <- res$thk / sum(res$thk)
  colnames(res) <- c(idname(p), hzidname(p), 'hz_thickness', 'hz_prop')
  return(res)
}

# list output option with simplify=F, list names are profile_id(sp1)
list.output <- profileApply(sp1, thicknessFunction, simplify = FALSE)
head(list.output)

# data.frame output option with frameify=TRUE
df.output <- profileApply(sp1, thicknessFunction, frameify = TRUE)
head(df.output)

# since df.output contains idname(sp1) and hzidname(sp1),
# it can safely be merged by a left-join via horizons<- setter
horizons(sp1) <- df.output

plot(density(sp1$hz_thickness, na.rm=TRUE), main="Density plot of Horizon Thickness")

## iterate over profiles, subsetting horizon data

# example data
data(sp1)

# promote to SoilProfileCollection
depths(sp1) <- id ~ top + bottom
site(sp1) <- ~ group

# make some fake site data related to a depth of some importance
sp1$dep <- profileApply(sp1, function(i) {round(rnorm(n=1, mean=mean(i$top)))})

# custom function for subsetting horizon data, by profile
# keep horizons with lower boundary < site-level attribute 'dep'
fun <- function(i) {
  # extract horizons
  h <- horizons(i)
  # make an expression to subset horizons
  exp <- paste('bottom < ', i$dep, sep='')
  # subset horizons, and write-back into current SPC
  slot(i, 'horizons') <- subset(h, subset=eval(parse(text=exp)))
  # return modified SPC
  return(i)
}

# list of modified SoilProfileCollection objects
l <- profileApply(sp1, fun, simplify=FALSE)

# re-combine list of SoilProfileCollection objects into a single SoilProfileCollection
sp1.sub <- pbindlist(l)

# graphically check
par(mfrow=c(2,1), mar=c(0,0,1,0))
plot(sp1)
points(1:length(sp1), sp1$dep, col='red', pch=7)
plot(sp1.sub)

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