Soil Database Interface

A collection of functions for reading data from USDA-NCSS soil databases.


News

-------------------------- soilDB 2.0-1 (2018-01-23) ----------------------------

  • updated loafercreek and gopheridge sample datasets and manual page to reflect latest fetchNASIS

-------------------------- soilDB 2.0 (2017-12-23) ------------------------------

  • bug fixes, manual page updates, and stabilization of NASIS interaction
  • released to CRAN

-------------------------- soilDB 1.8.12 (2017-09-19) ----------------------------

  • bug fix in fetchHenry(), it is now possible to query only sensor metadata

-------------------------- soilDB 1.8.11 (2017-08-17) ----------------------------

  • temporary bug-fix related to SCAN data (https://github.com/ncss-tech/soilDB/issues/26)

-------------------------- soilDB 1.8.10 (2017-08-10) ----------------------------

  • re-write of mix_and_clean_colors() so that color mixing happens in CIE LAB space

-------------------------- soilDB 1.8.5 (2017-05-24) ----------------------------

  • re-write of SDA_query(), better error handling, support for multi-part result sets

-------------------------- soilDB 1.8.2 (2017-03-24) ----------------------------

  • fetchHenry() can now access water level data, see manual page

-------------------------- soilDB 1.8.1 (2017-01-23) ----------------------------

  • new function: get_comonth_from_NASIS_db() see manual page for details

-------------------------- soilDB 1.8-10 (2016-12-27) ----------------------------

  • converting all URLs to 'HTTPS', addressing bugs with fetchSCAN() and associated functions

-------------------------- soilDB 1.8-7 (2016-11-16) ----------------------------

  • sanity checks for fetchHenry()
  • SCAN_sensor_metadata() vectorized and documented
  • unique row names in SPDF returned by seriesExtent()

-------------------------- soilDB 1.8-6 (2016-11-04) ----------------------------

  • converted all links to SoilWeb servers to HTTPS
  • converted all NRCS web-service links to HTTPS

-------------------------- soilDB 1.8-4 (2016-10-07) ----------------------------

  • fetchOSD() now returns dry colors and the source "narrative" for each horizon; function gains an argument
  • fetchOSD() now returns texture class, coarse fragment modifier, pH, and pH class
  • fetchSCAN() re-written, see manual pages and http://ncss-tech.github.io/AQP/soilDB/fetchSCAN-demo.html

-------------------------- soilDB 1.8 (2016-04-29) ----------------------------

  • fetchKSSL() can now query basic morphologic data with the argument "returnMorphologicData"
  • two new functions for simplifying NASIS color and fragment data:
  • simplifyFragmentData()
  • simplifyColorData()
  • ^^^ these new functions are now used by fetchNASIS() to summarize color and fragment data (vs. SQL)
  • NOTE: soilDB now uses reshape2::dcast() instead of reshape::cast()

-------------------------- soilDB 1.7 (2016-04-18) ----------------------------

  • bug fix in colors returned by fetchNASIS(), reported by Andy Paolucci
  • bug fix in SDA_query(), due to changes in httr::content. Thanks Kyle Bocinsky for the fix!
  • SDA_query() now returns SQL errors generated by SDA
  • new columns from NASIS site table returned by fetchNASIS()
  • NASIS pedon ecosite data now returned by fetchNASIS() (c/o J. Skovlin)

-------------------------- soilDB 1.6.9 (2015-12-28) ----------------------------

  • clean-up in local NASIS queries, removed extra parens
  • NASIS component query function overhaul: previous code may be broken, details pending

-------------------------- soilDB 1.6.8 (2015-12-22) ----------------------------

  • added temperature class (temp_class) field from the pedon taxonomic history table (NASIS) [addition suggested by J. Baker]

-------------------------- soilDB 1.6.7 (2015-12-16) ----------------------------

  • experimental function for processing SDA queries that return geometry: processSDA_WKT()

-------------------------- soilDB 1.6.5 (2015-12-03) ----------------------------

  • bug fix for poorly specified gemomorphic descriptions, caused fetchNASIS() to barf
  • fetchKSSL() gains new query filters, see man page

-------------------------- soilDB 1.6.4 (2015-11-27) ----------------------------

  • package re-org, getting ready for soilDB 2.0:
  • dropping use of RCurl functions in favor of httr alternatives (done)
  • switch from reshape to reshape2 (pending)
  • possibly move some packages from SUGGESTS to IMPORTS

-------------------------- soilDB 1.6.3 (2015-11-20) ----------------------------

  • new spatial query helper functions for SDA
  • re-named SSURGO_spatial_query() to SoilWeb_spatial_query(), this function may be phased-out due to spatial support now available in SDA
  • removed MUKEYS_by_ll_bbox() function, no longer needed and web-service may be disabled at any time
  • mapunit_geom_by_ll_bbox() will probably be removed in the near future with an SDA-based alternative
  • KSSL data updated (server-side) to June 2015 snapshot, "site_id" column removed from fetchKSSL() results

-------------------------- soilDB 1.6 (2015-08-19) ----------------------------

  • soilDB now imports from the reshape package, will transition to reshape2 with soilDB 2.0
  • fetchHenry() officially added, complete with documentation
  • SDA_query() undergoing some upgrades, no longer requies SSOAP / XMLSchema packages
  • SSOAP / XMLSchema packages no longer in 'suggests' list

-------------------------- soilDB 1.5-8 (2015-08-13) ----------------------------

  • fetchKSSL() gets an argument for downloading data by MLRA

-------------------------- soilDB 1.5-7 (2015-03-10) ----------------------------

  • updated the loafercreek and gopheridge sample datasets

-------------------------- soilDB 1.5-3 (2015-03-10) ----------------------------

  • nullFragsAreZero argument to fetchNASIS() reset to TRUE, new documentation pending
  • consolidate of messages printed when running fetchNASIS()
  • introduction of new option "soilDB.verbose" (default is FALSE) for increasing the level of QC information printed
  • new tutorial on fetchNASIS()

-------------------------- soilDB 1.5-2 (2015-02-24) ----------------------------

  • RODBC temporarily moved from "suggested" package to "imported" package... not a good idea, reverted to "suggested"

-------------------------- soilDB 1.4-5 (2015-01-20) ----------------------------

  • mix_and_clean_colors() now returns back-transformed, mixed, munsell colors
  • added psctopdepth and pscbotdepth back to extended NASIS query (particle size control section depths)

-------------------------- soilDB 1.4-3 (2015-01-12) ----------------------------

  • get_hz_data_from_NASIS_db() no longer assumes fragment volume of NULL = 0
  • get_extended_data_from_NASIS_db() no longer assumes fragment volume of NULL = 0
  • fetchNASIS() has a new argument, nullFragsAreZero=FALSE; set to TRUE for past NULL -> 0 conversion

-------------------------- soilDB 1.4-2 (2014-12-23) ----------------------------

  • new internally-used function .formatLandformString() for flattening NASIS/PedonPC "landform" records
  • new internally-used function .formatParentMaterialString() for flattening NASIS/PedonPC "parent material" records
  • fetchNASIS() incorporates the results of these two new functions
  • new function SSURGO_spatial_query() queries SSURGO data from SoilWeb (see manual page for details)

-------------------------- soilDB 1.4 (2014-11-13) ----------------------------

  • moving most of the hard-to-install packages into suggests, and checking for package availability at function runtime. this will make soilDB more portable, as not every user will want or need all functionality.

-------------------------- soilDB 1.3-6 (2014-10-27) ----------------------------

  • fetchNASIS() gains argument rmHzErrors to optionally retain pedons with horizonation errors. use with caution.

-------------------------- soilDB 1.3-5 (2014-09-25) ----------------------------

  • loafercreek sample dataset re-created from new data
  • seriesExtent() now utilizes pre-cached GeoJSON files from [http://casoilresource.lawr.ucdavis.edu/see/]

-------------------------- soilDB 1.3 (2014-02-26) ----------------------------

  • Changes made to fetch functions to accommodate changes implemented in the NASIS 6.3 data structure
  • get_site_data_from_NASIS_db(): in cases where multiple records in site-bedrock exist, retain only the most shallow
  • fetchRaCA() has a new argument for querying data by rcasiteid

-------------------------- soilDB 1.2-9 (2014-01-06) ----------------------------

  • SOC concentration and stock values are temporarily disabled in fetchRaCA()
    • waiting for new estimates from the Soil Survey Center...

-------------------------- soilDB 1.2-6 (2013-12-05) ----------------------------

  • added new function contributed by J.M. Skovlin: get_veg_from_NPS_PLOTS_db()
  • bugfixes in get_extended_data_from_NASIS_db(): results from geomorph tables are now returned

-------------------------- soilDB 1.2-3 (2013-10-25) ----------------------------

  • added new function fetchSCAN() for downloading soil/climate data from USDA-NRCS SCAN stations (still experimental!)

-------------------------- soilDB 1.2-1 (2013-09-12) ----------------------------

  • bug fixing in fetchRaCA():
    • "#" characters no longer cause errors
    • duplicate IDs in source data have been fixed

-------------------------- soilDB 1.2 (2013-08-13) ----------------------------

  • fetchRaCA() function now stable, ready for general usage
  • fixed bug in fetchRaCA() function where the presence of single-quote character in horizon designation would throw and error

-------------------------- soilDB 1.1-3 (2013-07-30) ----------------------------

  • new function get_copedon_from_NASIS_db(): returns basic information associated with pedons linked to component data in NASIS
  • new function fetchRaCA(): gets data from the Rapid Carbon Assessment project [work in progress]

-------------------------- soilDB 1.1 (2013-06-27) ----------------------------

  • get_site_data_from_NASIS_db() no longer has problems when more than 1 site bedrock kind is defined; only the shallowest row is returned

-------------------------- soilDB 1.0 (2013-04-04) ----------------------------

  • fetchNASIS() is now much more efficient: faster / less memory used
  • new function! fetchKSSL(): experimental interface to (most of) the KSSL data
    • queries can be performed by series name or GCS bounding box
    • data are delivered via CA Soil Resource Lab server

-------------------------- soilDB 0.9-8 (2013-04-03) ----------------------------

  • fetchOSD() now immune to queries for non-soils
  • improved efficiency in fetch* functions
  • NASIS-DMU fetching functions now return more information, still not as complete as pedon-queries

-------------------------- soilDB 0.9-7 (2013-03-01) ----------------------------

  • NASIS query functions now return only records from the selected set, please test older code!

-------------------------- soilDB 0.9-6 (2013-02-26) ----------------------------

  • new function get_text_notes_from_NASIS_db() -- still needs proper documentation
  • bug fixes to PedonPC and NASIS queries, new data elements returned by extended query functions
  • SoilWeb queries via URL are now URL-encoded to allow for spaces in soil series names

-------------------------- soilDB 0.9-4 (2013-01-31) ----------------------------

  • new function: fetchOSD() returns basic OSD data as a SoilProfileCollection

-------------------------- soilDB 0.9-3 (2013-01-08) ----------------------------

  • speed-bump in color-fetching functions from NASIS/pedonPC
  • fetchNASIS() now attempts to correct for >1 pedon/site by appending peiid to pedon_id

-------------------------- soilDB 0.9-2 (2012-12-18) ----------------------------

  • new functions for getting / plotting the geographic extent of a soil series, using the SoilWeb query service: -seriesExtent() : fetches extent as a SpatialPolygonDataFrame -seriesExtentAsGmap() : fetches extent and plots on Google Maps (requires dismo package)

-------------------------- soilDB 0.9-1 (2012-11-27) ----------------------------

  • updated functionality in fetchNASIS_component_data() pulls mapunit-level data as well as component-level data
  • Munsell 'value' is now returned from PedonPC/NASIS fetching functions

-------------------------- soilDB 0.9 (2012-10-24) ----------------------------

  • added a surface fragment summary "surf_frag_summary" to the results of get_extended_data_from_NASIS()
    • note: this has not been ported to the related PedonPC queries
  • integrated surf_frag_summary data into data returned from fetchNASIS(), stored in @site
    • note: this has not been ported to the related PedonPC queries
  • minor bug-fix in horizon-level rock fragment summary SQL which previously mis-classified BD as ST in some, rare cases
    • note: this has not been ported to the related PedonPC queries

-------------------------- soilDB 0.8-3 (2012-09-28) ----------------------------

  • site-level data: {elev, slope, aspect} are now named {elev_field, slope_field, aspect_field}
    • this affects the data returned by fetchNASIS() and fetchPedonPC()

-------------------------- soilDB 0.8-2 (2012-08-23) ----------------------------

  • compatible with NASIS 6.2
  • bug fixes
  • taxhistory selection method is preserved in the results
  • 'taxonname' is used instead of 'sampled_as' / 'correlated_as' ! seems to work, but needs further testing

-------------------------- soilDB 0.8 (2012-08-20) ----------------------------

  • updating for PedonPC 5.0 and NASIS 6.2
    • site data contains the best-guessed corresponding row from the taxhistory table, based on: 1) most recent record, or 2) record with the least amount of missing data
    • taxhistory data are now included in the output from get_extended_data_from_pedon_db()
  • package is now partially compatible with NASIS 6.2

-------------------------- soilDB 0.6 (2012-06-19) ----------------------------

  • tidying up documentation, package dependencies, and NAMESPACE

-------------------------- soilDB 0.5-6 (2012-04-16) ----------------------------

  • adding preimlinary functions for querying component data from local NASIS
  • fixed minor bug in SDA_query() and added some links to related documentation

-------------------------- soilDB 0.5-1 (2012-02-22) ----------------------------

  • fetchNASIS() and fetchPedonPC() now integrate `extended' data
  • warning and error messages cleaned-up
  • multiple textures no longer cause duplicate HZ rows (NASIS only)
  • exteded queries now split frags/para-frags
  • silt fraction is estimated from 100-(sand+clay) when possible
  • added local NASIS ODBC connection vignette (thanks JMS)
  • removed dsn argument from NASIS functions as it should always be 'nasis_local'
  • new wide-formatted, boolean representation of diagnostic horizon data
  • queries standardized between NASIS/PedonPC
  • new fetchNASIS() function for 1-line access to local NASIS data
  • new sample data set 'loafercreek'
  • basic vignette added, switching to knitr-style vignettes

-------------------------- soilDB 0.3-3 (2012-01-10) --------------------------

  • SDA_query() now functional on MacOS/UNIX-like OSes with (SSOAP 0.8-1, XMLSchema 0.6-0, and XML 3.7-1)
    • thanks to D.T. Lang for the updates!
  • moving hard to find packages to 'suggested' status: SSOAP, RCurl, XML, rgdal
  • new wrapper function fetchPedonPC() for typical site/pedon/hz queries
  • new function getHzErrorsPedonPC() for ID-ing pedons with problem horizonation
  • NOTE: hz data queries will return 2 rows/hz (error) when multiple texture classes are assigned to a single horizon- this is a bug, not a feature!

-------------------------- soilDB 0.3-2 (2011-12-30) --------------------------

  • NASIS/pedonPC queries synced
  • minor bug fixes and documentation updates
  • updated query structure, switching over to native NASIS/PedonPC IDs
  • extended summaries added: NASIS only

-------------------------- soilDB 0.2 (2011-12-27) --------------------------

  • moved functions out of aqp package
  • basic query functionality from local NASIS DB (Jay)

-------------------------- soilDB 0.1 (2011-12-23) --------------------------

  • initial version on r-forge
  • functions still exist in aqp package... need to move over completely

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("soilDB")

2.3.5 by Dylan Beaudette, a month ago


http://ncss-tech.github.io/AQP/


Report a bug at https://github.com/ncss-tech/soilDB/issues


Browse source code at https://github.com/cran/soilDB


Authors: Dylan Beaudette [cre] , Jay Skovlin [aut] , Stephen Roecker [aut]


Documentation:   PDF Manual  


Task views:


GPL (>= 3) license


Imports grDevices, graphics, stats, utils, plyr, Hmisc, xml2, sp, reshape2, raster, curl

Depends on aqp

Suggests lattice, dismo, rgdal, jsonlite, RODBC, httr, rgeos, rvest, testthat, stringr


Imported by sharpshootR.

Suggested by aqp.


See at CRAN