SoilProfileCollection-class: An S4 object representation of a group of soil profiles.

In aqp: Algorithms for Quantitative Pedology

An S4 object representation of a group of soil profiles.

Description

In general, one should use depths() to initiate a SoilProfileCollection object from data. However, sometimes there are instances where either an empty, or very specific, object is needed. If that is the case, the general constructor SoilProfileCollection is available.

Usage

SoilProfileCollection(
  idcol = "id",
  hzidcol = "hzID",
  depthcols = c("top", "bottom"),
  metadata = list(aqp_df_class = "data.frame", aqp_group_by = "", aqp_hzdesgn = "",
    aqp_hztexcl = "", stringsAsFactors = FALSE),
  horizons = data.frame(id = character(0), hzID = character(0), top = numeric(0), bottom
    = numeric(0), stringsAsFactors = FALSE),
  site = data.frame(id = character(0), stringsAsFactors = FALSE),
  diagnostic = data.frame(stringsAsFactors = FALSE),
  restrictions = data.frame(stringsAsFactors = FALSE)
)

Arguments

idcol	character. Profile ID Column Name
hzidcol	character. Horizon ID Column Name
depthcols	character. length 2 Top and Bottom Depth Column Names
metadata	list. metadata including data.frame class in use and depth units
horizons	data.frame. An object inheriting from data.frame containing Horizon data.
site	data.frame. An object inheriting from data.frame containing Site data.
diagnostic	data.frame. An object inheriting from data.frame containing diagnostic feature data. Must contain profile ID. See diagnostic_hz()
restrictions	data.frame. An object inheriting from data.frame containing restrictive feature data. Must contain profile ID. See restrictions()

Details

After aqp 2.0.2, the ⁠@sp⁠ slot was removed from the SoilProfileCollection object. If you run into errors related to old object definitions, use rebuildSPC() on the problematic object.

Slots

idcol

character.

hzidcol

character.

depthcols

character.

metadata

list.

horizons

data.frame.

site

data.frame.

diagnostic

data.frame.

restrictions

data.frame.

Author(s)

Pierre Roudier, Dylan E. Beaudette, Andrew G. Brown

Examples

## structure of default, empty SoilProfileCollection
str(SoilProfileCollection())


## use the depths() formula interface to specify
## profile ID, top and bottom depth and set up
## a SPC that is topologically correct and complete

d <- do.call('rbind', lapply(1:10, random_profile))

# promote to SoilProfileCollection and plot
depths(d) <- id ~ top + bottom
plot(d)

# split into new SoilProfileCollection objects by index
d.1 <- d[1, ]
d.2 <- d[2, ]
d.345 <- d[3:5, ]

# combine profile collections
# note that profiles are sorted according to ID
d.new <- c(d.345, d.1, d.2)
plot(d.new)

data(sp1)

## init SoilProfileCollection objects from data.frame
depths(sp1) <- id ~ top + bottom

## depth units
du <- depth_units(sp1)
depth_units(sp1) <- 'in'
depth_units(sp1) <- du

## horizon designation column
hzdesgnname(sp1) <- "name"
hzdesgnname(sp1)

## all designations in an SPC (useful for single profile SPC)
hzDesgn(sp1)

## horizon texture class column
hztexclname(sp1) <- "texture"
hztexclname(sp1)

## get/set metadata on SoilProfileCollection objects
# this is a 1-row data.frame
m <- metadata(sp1)
m$sampler <- 'Dylan'
metadata(sp1) <- m

## extract horizon data from SoilProfileCollection objects as data.frame
h <- horizons(sp1)

# also merge (left-join) of new columns and
# replacement of existing columns via horizons<-
horizons(sp1) <- h

# get number of horizons
nrow(sp1)


## getting site-level data
site(sp1)

## setting site-level data
# site-level data from horizon-level data (stored in @horizons)
site(sp1) <- ~ group


# make some fake site data, and append from data.frame
# a matching ID column must be present in both @site and new data
# note that IDs should all be character class
d <- data.frame(id=profile_id(sp1), p=runif(n=length(sp1)), stringsAsFactors=FALSE)
site(sp1) <- d

# edit horizon depths
horizonDepths(sp1) <- c('t', 'b')
horizonDepths(sp1)

# edit profile IDs
p <- sprintf("%s-new", profile_id(sp1))
profile_id(sp1) <- p
profile_id(sp1)

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