R/Class-SoilProfileCollection.R, R/SoilProfileCollection-setters.R
site.RdGet 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 class 'SoilProfileCollection'
site(object)
site(object) <- value
# 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