Fetch commonly used site/pedon/horizon data or component from NASIS, returned as a SoilProfileCollection object.

fetchNASIS(
  from = "pedons",
  url = NULL,
  SS = TRUE,
  rmHzErrors = TRUE,
  nullFragsAreZero = TRUE,
  soilColorState = "moist",
  lab = FALSE,
  fill = FALSE,
  stringsAsFactors = default.stringsAsFactors(),
  dsn = NULL
)

Arguments

from

determines what objects should fetched? ('pedons' | 'components' | 'pedon_report')

url

string specifying the url for the NASIS pedon_report (default: NULL)

SS

fetch data from the currently loaded selected set in NASIS or from the entire local database (default: TRUE)

rmHzErrors

should pedons with horizon depth errors be removed from the results? (default: TRUE)

nullFragsAreZero

should fragment volumes of NULL be interpreted as 0? (default: TRUE), see details

soilColorState

which colors should be used to generate the convenience field soil_color? ('moist' or 'dry')

lab

should the phlabresults child table be fetched with site/pedon/horizon data (default: FALSE)

fill

include pedon or component records without horizon data in result? (default: FALSE)

stringsAsFactors

logical: should character vectors be converted to factors? This argument is passed to the uncode() function. It does not convert those vectors that have been set outside of uncode() (i.e. hard coded).

dsn

Optional: path to local SQLite database containing NASIS table structure; default: NULL

Value

A SoilProfileCollection object

Details

This function imports data from NASIS into R as a SoilProfileCollection object. It "flattens" NASIS pedon and component tables, including their child tables, into several more easily manageable data frames. Primarily these functions access the local NASIS database using an ODBC connection. However using the fetchNASIS() argument from = "pedon_report", data can be read from the NASIS Report 'fetchNASIS', as either a txt file or url. The primary purpose of fetchNASIS(from = "pedon_report") is to facilitate importing datasets larger than 8000+ pedons/components.

The value of nullFragsAreZero will have a significant impact on the rock fragment fractions returned by fetchNASIS. Set nullFragsAreZero = FALSE in those cases where there are many data-gaps and NULL rock fragment values should be interpreted as NULL. Set nullFragsAreZero = TRUE in those cases where NULL rock fragment values should be interpreted as 0.

This function attempts to do most of the boilerplate work when extracting site/pedon/horizon or component data from a local NASIS database. Pedons that are missing horizon data, or have errors in their horizonation are excluded from the returned object, however, their IDs are printed on the console. Pedons with combination horizons (e.g. B/C) are erroneously marked as errors due to the way in which they are stored in NASIS as two overlapping horizon records.

Tutorials:

Author

D. E. Beaudette, J. M. Skovlin, S.M. Roecker, A.G. Brown