Turns the files saved by fetch_sali into
PedonRecord objects for classify_asc3 and the
other keys: the site layer (layer/layer101_off*.json, or a data
frame saved as layer/layer101.rds), the site reports
(pdf/<PROJECT>_<SITE>.pdf) and the laboratory samples of the SALI
soil chemistry API (lab/<PROJECT>_<SITE>_samples.json). A site is
read when both its report and its laboratory file are on disk; sites
whose report was over the download cap, whose report has no morphology
table, or whose label names no ASC order (the layer's "Unclassified"
sites) are left out.
Usage
read_sali_pedons(
path,
sites = NULL,
cores = 1L,
max_n = NULL,
seed = NULL,
accessed = NULL,
verbose = TRUE
)Arguments
- path
The folder
fetch_saliwrote.- sites
Optional sites to read (a data frame with
project_codeandsite_id, or"<PROJECT>_<SITE>").- cores
Number of processes (
parallel::mclapply; always 1 on Windows).- max_n
Optional maximum number of sites read (a random sample).
- seed
Optional seed for that sample.
- accessed
Optional date the data were downloaded, for the citation.
- verbose
Print a summary.
Value
A named list of PedonRecord objects (names
SALI_<PROJECT>_<SITE>), with an attribute "sali_status": a
data frame of the sites considered and what became of each.
Details
The morphology exists only in the report (a PDF), read from the
coordinates of its words (pdftools). Each row of its Profile
morphology table is translated into the coded horizon of the NatSoil API
(Field Handbook codes) and read by the NatSoil reader's own conventions
(see load_natsoil_pedons), the laboratory samples too, so
both Australian panels are read alike. These readings (the SALI pilot of
2026-10-30, kept by Hugo) apply:
Observation 1 of the site is read (a report may hold several).
The surveyors' label of the layer is read by position (order, suborder, great group, subgroup) and each name matched, case-insensitive, to the 3rd edition (
inst/rules/asc3); a name the 3rd edition does not have staysNA. "No Available Class" isZZand "Class Undetermined"YY. A suborder with no great groups (Hypergypsic, Lutic, Stratic Rudosols) has its subgroup in the great-group column, as NatSoil has it. The edition the report cites is kept insite$sali_asc_edition, without changing the codes. The report's confidence phrases are the Field Handbook's 1-4; other phrases (a conversion from another classification, a rapid check of key attributes) are"C".An empty cell is not recorded; "No mottles", "No segregations" and "No coarse fragments" are recorded absent. A colour without its moisture status is moist. Mottles of biological mixing, mechanical mixing and substrate influence are not mottles; jarosite mottles are.
Textures: "Loam, fine sandy" is a loam; sandy and silty clays are clays of unspecified grade; heavy or light before a grade lighter than a clay is the + or - qualifier. The first structure listed is read; "Blocky" alone names no type. "Not recorded (historical)" is
NA. A strength without its moisture is not read.Field pH, by depth: Raupach and Tucker first, then an electrode in situ, then a 1:5 suspension by probe (the pH after peroxide and the field EC are not used); it is read only where the laboratory has no pH, as in NatSoil. The effervescence field test gives the horizon's effervescence.
Laboratory samples (not linked to horizons in SALI) are filed under the horizon holding their middle, then read by NatSoil's overlap rule; bulked samples count; results flagged invalid are dropped; "<x" is x / 2 with NatSoil's limit rule. A trailing letter of a method variant is dropped (6B2b is 6B2) and 2Z2_Clay is 2Z2_C.
Tidal landform spellings are NatSoil's (inter-tidal is intertidal); no tidal flooding is inferred, nor the soil water status; the depth to free water and the substrate are kept in the site (
sali_depth_to_free_water,sali_substrate) but not used.
And Hugo's decisions of 2026-10-30:
MIR predictions (method codes ending in _MC2, _MC91, _MQ01, _MQ02 and the like) are used only where nothing was measured for that attribute in that horizon (a field pH the horizon reads counts as measured), and the provenance marks them as predictions (source
"predicted_spectra", a note naming the MIR codes; two calibrations predicting the same method are averaged). MIR methods the NatSoil reader has no code for are read by the property their name gives: 15C2_CEC as the CEC, 6B4 as organic carbon and 15J2 as the effective CEC.The lab table printed in the report is used only when the API holds no samples for the site's observation.
The site keeps the surveyors' classification
(reference_asc_order, reference_asc_suborder,
reference_asc_great_group, reference_asc_subgroup,
reference_asc_confidence), as benchmark_sali and
benchmark_natsoil read it, the label and the report's ASC
name (sali_asc_label, sali_pdf_asc), names left unmatched
(sali_unmapped), the drainage, landform, surface condition,
microrelief and surface coarse fragments, coordinates (GDA94), the
licence and the citation (sali_citation), where the
laboratory values came from (sali_lab_source: "api",
"report table" or "none") and how many values are MIR
predictions (sali_n_predicted). The provenance has one row per
horizon for its morphology and one per laboratory value, which names the
source (the API or the report's table) and the method; the report's
notes are kept there too.
References
Queensland Government. Soil and Land Information (SALI). National Committee on Soil and Terrain (2009). Australian Soil and Land Survey Field Handbook, 3rd edition. CSIRO Publishing.