An S4 object representation of a group of soil profiles.

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.

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

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

Examples


## structure of default, empty SoilProfileCollection
str(SoilProfileCollection())
#> Formal class 'SoilProfileCollection' [package "aqp"] with 8 slots
#>   ..@ idcol       : chr "id"
#>   ..@ hzidcol     : chr "hzID"
#>   ..@ depthcols   : chr [1:2] "top" "bottom"
#>   ..@ metadata    :List of 6
#>   .. ..$ aqp_df_class    : chr "data.frame"
#>   .. ..$ aqp_group_by    : chr ""
#>   .. ..$ aqp_hzdesgn     : chr ""
#>   .. ..$ aqp_hztexcl     : chr ""
#>   .. ..$ depth_units     : chr "cm"
#>   .. ..$ stringsAsFactors: logi FALSE
#>   ..@ horizons    :'data.frame':	0 obs. of  4 variables:
#>   .. ..$ id    : chr(0) 
#>   .. ..$ hzID  : chr(0) 
#>   .. ..$ top   : num(0) 
#>   .. ..$ bottom: num(0) 
#>   ..@ site        :'data.frame':	0 obs. of  1 variable:
#>   .. ..$ id: chr(0) 
#>   ..@ diagnostic  :'data.frame':	0 obs. of  0 variables
#>   ..@ restrictions:'data.frame':	0 obs. of  0 variables


## 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)
#> [1] "name"

## all designations in an SPC (useful for single profile SPC)
hzDesgn(sp1)
#>  [1] "A1"   "A2"   "AB"   "BA"   "Bt"   "Rt"   "Oi"   "A"    "C1"   "C2"  
#> [11] "Oa/A" "AB"   "BA"   "Bt1"  "Bt2"  "A1"   "A2"   "A3"   "Bt1"  "Bt2" 
#> [21] "A"    "AB"   "Bt1"  "Bt2"  "Oi"   "A"    "AB1"  "AB2"  "AB3"  "C1"  
#> [31] "C2"   "2C1"  "2C2"  "3C"   "A1"   "A2"   "Bw1"  "Bw2"  "Bw3"  "C"   
#> [41] "2C"   "3Bwb" "3Cb"  "Oi"   "A"    "AB"   "Bw1"  "Bw2"  "2C1"  "2C2" 
#> [51] "3C"   "Oe"   "A1"   "A2"   "AB"   "Bw1"  "Bw2"  "2C"   "3Ab"  "3Bwb"

## horizon texture class column
hztexclname(sp1) <- "texture"
hztexclname(sp1)
#> [1] "texture"

## 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)
#> [1] 60


## getting site-level data
site(sp1)
#>     id
#> 1 P001
#> 2 P002
#> 3 P003
#> 4 P004
#> 5 P005
#> 6 P006
#> 7 P007
#> 8 P008
#> 9 P009

## 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)
#> [1] "t" "b"

# edit profile IDs
p <- sprintf("%s-new", profile_id(sp1))
profile_id(sp1) <- p
profile_id(sp1)
#> [1] "P001-new" "P002-new" "P003-new" "P004-new" "P005-new" "P006-new" "P007-new"
#> [8] "P008-new" "P009-new"