Reads the pre-packaged CSV files of the National Pedon Database (NPDB,
version 3, Agriculture and Agri-Food Canada, CanSIS) into
PedonRecord objects, with the survey's classification under
the Canadian System of Soil Classification as the reference.
Value
A named list of PedonRecord objects (names are the
NPDB PEDON_ID).
Details
The NPDB is not distributed with soilKey. It is published on the Open
Government Portal of Canada under the Open Government Licence - Canada
(dataset "National Pedon Database"); download the pre-packaged CSV files
and unzip them into a folder. Info.csv and Horizons.csv are
required; Morphology.csv, Physical.csv,
Chemical.csv and Profiles.csv are read when present.
What the reader does with the records:
records are split on CR-LF only, since some fields hold a lone carriage return ("subangular\r blocky");
the designation is rebuilt in the Canadian notation from its parts (lithologic numeral, master, suffixes, numeric modifier: "IICk1"), and the site declares
designation_system = "cssc";depths: organic and water horizons recorded upward from the mineral surface (top above bottom) become negative depths; a mineral horizon with its depths reversed or negative keeps |top| with no bottom when it is the deepest layer, and no depths otherwise; a missing top is taken from the layer above; every profile is shifted to begin at 0 cm, and
site$npdb_depth_order_mismatchflags profiles whose depth order differs from the order of their layers;colours: the codes ("100yr4030", "10yr2010", "025y 4020", "10.0yr4.0/3.0", "n 50") are read with hue numbers above 0 and up to 10; of the two matrix colours, the one that is never darker within a profile (and lighter at least once) is read as the dry colour and the other as the moist one; when they do not separate,
COLOUR_1is read as the moist colour and no dry colour is read;total N: the value 9 (a no-data code) and a value repeated over three or more horizons are not read; the units are told apart by the median C:N of each pedon (of its dataset when the pedon has too few values): 5 to 40 is read as percent, 0.5 to 4 as g/kg (divided by 10), anything else is not read; a horizon whose C:N then lies outside 3 to 60 is not read either;
base saturation: computed from the exchangeable bases and the CEC (at most 100 %) when they are recorded, the recorded value being kept when it agrees with it (one dataset records something else in that column);
pH: a dataset whose pH in CaCl2 is mostly above its pH in water has the two columns swapped back;
values outside their possible range are not read;
the survey's order, great group and subgroup words are turned into the names of the 3rd edition (1998) where they match one (
reference_cssc_order,reference_cssc_great_group,reference_cssc_subgroup), including the subgroups the 1998 edition merged (Solodic into Solonetzic); names of earlier editions with no 1998 equivalent are left out, and the raw words are kept inreference_cssc_raw.
The NPDB records no soil climate (mean annual soil temperature, moisture
subclass), the chemistry of the podzolic B (pyrophosphate-extractable Fe
and Al) or the contrast of mottles. The Chernozemic order and the Gray
Brown Luvisols, which ask for the climate, are undecided on these records
(see benchmark_npdb).
References
Agriculture and Agri-Food Canada (2021). National Pedon Database, version 3. Open Government Portal, Open Government Licence - Canada.
Examples
if (FALSE) { # \dontrun{
peds <- load_npdb_pedons("path/to/npdb_v3_csv")
b <- benchmark_npdb(peds, level = "order")
b$accuracy
} # }