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Get a pedon or component data SoilProfileCollection from NASIS

Source: R/fetchNASIS.R, R/get_concentrations_from_NASIS_db.R, R/get_phfmp_from_NASIS_db.R
fetchNASIS.Rd

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

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 manageable data frames. Primarily these functions access the local NASIS database using an ODBC connection. The dsn argument allows you to specify a path or DBIConnection to an SQLite database. The argument from = "pedon_report", data can be read from the NASIS Report 'fetchNASIS', from either text file or URL (specified as url). The primary purpose of fetchNASIS(from = "pedon_report") is 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. Pedon IDs that are missing horizon data, or have errors in their horizonation 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:

Usage

fetchNASIS(
  from = "pedons",
  url = NULL,
  SS = TRUE,
  rmHzErrors = FALSE,
  nullFragsAreZero = TRUE,
  soilColorState = "moist",
  mixColors = FALSE,
  lab = FALSE,
  fill = FALSE,
  dropAdditional = TRUE,
  dropNonRepresentative = TRUE,
  duplicates = FALSE,
  stringsAsFactors = NULL,
  dsn = NULL
)

get_concentrations_from_NASIS_db(
  SS = TRUE,
  stringsAsFactors = NULL,
  dsn = NULL
)

get_phfmp_from_NASIS_db(SS = TRUE, stringsAsFactors = NULL, dsn = NULL)

Arguments

from

Determines what objects should fetched? Default: 'pedons'. Alternately, 'components', or '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: FALSE)

nullFragsAreZero

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

soilColorState

Used only for from = 'pedons'; which colors should be used to generate the convenience field soil_color? ('moist' or 'dry')

mixColors

Should mixed colors be calculated where multiple colors are populated for the same moisture state in a horizon? Default FALSE takes the dominant color for each horizon moist/dry state.

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)

dropAdditional

Used only for from='components' with duplicates = TRUE. Prevent "duplication" of mustatus == "additional" mapunits? Default: TRUE

dropNonRepresentative

Used only for from='components' with duplicates = TRUE. Prevent "duplication" of non-representative data mapunits? Default: TRUE

duplicates

Used only for from='components'. Duplicate components for all instances of use (i.e. one for each legend data mapunit is used on; optionally for additional mapunits, and/or non-representative data mapunits?). This will include columns from get_component_correlation_data_from_NASIS_db() that identify which legend(s) a component is used on.

stringsAsFactors

deprecated

dsn

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

Value

A SoilProfileCollection object

See also

get_component_data_from_NASIS()

Author

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