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Query data from Kellogg Soil Survey Laboratory Data Mart via Soil Data Access or local SQLite snapshot

Source: R/fetchLDM.R
fetchLDM.Rd

LDM model diagram: https://jneme910.github.io/Lab_Data_Mart_Documentation/Documents/SDA_KSSL_Data_model.html

Usage

fetchLDM(
  x = NULL,
  what = "pedlabsampnum",
  bycol = "pedon_key",
  tables = c("lab_physical_properties", "lab_chemical_properties",
    "lab_calculations_including_estimates_and_default_values", "lab_rosetta_Key"),
  WHERE = NULL,
  chunk.size = 1000,
  ntries = 3,
  layer_type = c("horizon", "layer", "reporting layer"),
  area_type = c("ssa", "country", "state", "county", "mlra", "nforest", "npark"),
  prep_code = c("S", ""),
  analyzed_size_frac = c("<2 mm", ""),
  dsn = NULL
)

Arguments

x

A vector of values to find in column specified by what, default NULL uses no constraints on what

what

A single column name from tables: lab_combine_nasis_ncss, lab_webmap, lab_site, lab_pedon or lab_area

bycol

A single column name from lab_layer used for processing chunks; default: "pedon_key"

tables

A vector of table names; Default is "lab_physical_properties", "lab_chemical_properties", "lab_calculations_including_estimates_and_default_values", and "lab_rosetta_Key". May also include one or more of: "lab_mir", "lab_mineralogy_glass_count", "lab_major_and_trace_elements_and_oxides", "lab_xray_and_thermal" but it will be necessary to select appropriate prep_code and analyzed_size_frac for your analysis (see Details).

WHERE

character. A custom SQL WHERE clause, which overrides x, what, and bycol, such as CASE WHEN corr_name IS NOT NULL THEN LOWER(corr_name) ELSE LOWER(samp_name) END = 'musick'

chunk.size

Number of pedons per chunk (for queries that may exceed maxJsonLength)

ntries

Number of tries (times to halve chunk.size) before returning NULL; default 3

layer_type

Default: "horizon", "layer", and "reporting layer"

area_type

Default: "ssa" (Soil Survey Area). Other options include (choose one): "country", "state", "county", "mlra" (Major Land Resource Area), "nforest" (National Forest), "npark" (National Park)

prep_code

Default: "S" and "". May also include one or more of: "F", "HM", "HM_SK" "GP", "M", "N", or "S"

analyzed_size_frac

Default: "<2 mm" and "". May also include one or more of: "<0.002 mm", "0.02-0.05 mm", "0.05-0.1 mm", "0.1-0.25 mm", "0.25-0.5 mm", "0.5-1 mm", "1-2 mm", "0.02-2 mm", "0.05-2 mm"

dsn

Data source name; either a path to a SQLite database, an open DBIConnection or (default) NULL (to use soilDB::SDA_query)

Value

a SoilProfileCollection for a successful query, a try-error if no site/pedon locations can be found or NULL for an empty lab_layer (within sites/pedons) result

Details

If the chunk.size parameter is set too large and the Soil Data Access request fails, the algorithm will re-try the query with a smaller (halved) chunk.size argument. This will be attempted up to 3 times before returning NULL

Currently the lab_area tables are joined only for the "Soil Survey Area" related records.

When requesting data from "lab_major_and_trace_elements_and_oxides", "lab_mineralogy_glass_count", or "lab_xray_and_thermal" multiple preparation codes (prep_code) or size fractions (analyzed_size_frac) are possible. The default behavior of fetchLDM() is to attempt to return a topologically valid (minimal overlaps) SoilProfileCollection. This is achieved by setting prep_code="S" ("sieved") and analyzed_size_frac="<2 mm". You may specify alternate or additional preparation codes or fractions as needed, but note that this may cause "duplication" of some layers where measurements were made with different preparation or on fractionated samples

Examples

if (FALSE) {
  # fetch by ssa_key
  res <- fetchLDM(8297, what = "ssa_key")

  # physical properties correlated as taxonomic subgroup "Typic Argialbolls"
  res <- fetchLDM(x = "Typic Argialbolls", 
                  what = "corr_taxsubgrp", 
                  tables = "lab_physical_properties")

  # fetch by area_code (SSA only)  
  res <- fetchLDM("CA630", what = "area_code")
}