aqp (version 2.1.0)

SoilProfileCollection: 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()

Slots

idcol

character.

hzidcol

character.

depthcols

character.

metadata

list.

horizons

data.frame.

site

data.frame.

diagnostic

data.frame.

restrictions

data.frame.

Author

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

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.

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)