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) --------------------------