Retrieve site data from SoilProfileCollection — site,SoilProfileCollection-method • aqp

Get site data from SoilProfileCollection. Result is returned in the same data.frame class used to initially construct the SoilProfileCollection.

There are two options available via the site<- setter.

The first is a "normalization" by formula interface, whereby one specifies an attribute that is constant in horizons within profiles to be promoted to a site-level variable: site(spc) <- ~ horizonvariable

The second is creation of site data from an external data.frame via merge (LEFT JOIN). There must be one or more same-named columns (with at least some matching data) on the left and right hand side to facilitate the join: site(spc) <- newdata

# S4 method for SoilProfileCollection
site(object)

site(object) <- value

Arguments

object: A SoilProfileCollection
value: A formula or object inheriting data.frame

Examples


# load test data
data(sp2)

# promote to SPC
depths(sp2) <- id ~ top + bottom

# normalize a horizon-level attribute to site
site(sp2) <- ~ surface

# inspect site table
site(sp2)
#>        id         surface
#> 1   hon-1        holocene
#> 2  hon-10   lower modesto
#> 3  hon-11   lower modesto
#> 4  hon-13   upper modesto
#> 5  hon-14   upper modesto
#> 6  hon-17 lower riverbank
#> 7  hon-18 lower riverbank
#> 8  hon-19 lower riverbank
#> 9   hon-2        holocene
#> 10 hon-20 lower riverbank
#> 11 hon-21    lower laguna
#> 12 hon-22    lower laguna
#> 13  hon-3        holocene
#> 14  hon-4        holocene
#> 15  hon-5   upper modesto
#> 16  hon-6   upper modesto
#> 17  hon-7   upper modesto
#> 18  hon-8   upper modesto

# make some data: classify two geomorphic surfaces with numeric value
newdata <- data.frame(surface = c("holocene",
                                  "lower riverbank"),
                      newvalue = c(1,2))

# do left join based on newly-normalized "surface" attribute
site(sp2) <- newdata

# inspect site table: holocene & lower riverbank have values
site(sp2)
#>            surface     id newvalue
#> 1         holocene  hon-1        1
#> 2    lower modesto hon-10       NA
#> 3    lower modesto hon-11       NA
#> 4    upper modesto hon-13       NA
#> 5    upper modesto hon-14       NA
#> 6  lower riverbank hon-17        2
#> 7  lower riverbank hon-18        2
#> 8  lower riverbank hon-19        2
#> 9         holocene  hon-2        1
#> 10 lower riverbank hon-20        2
#> 11    lower laguna hon-21       NA
#> 12    lower laguna hon-22       NA
#> 13        holocene  hon-3        1
#> 14        holocene  hon-4        1
#> 15   upper modesto  hon-5       NA
#> 16   upper modesto  hon-6       NA
#> 17   upper modesto  hon-7       NA
#> 18   upper modesto  hon-8       NA