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Recent Releases of soilDB

soilDB - soilDB 2.8.13

soilDB 2.8.13 (2025-09-26)

  • Added get_SDA_NASIS_key() for obtaining NASIS record IDs for component and component horizon data from Soil Data Access (#409)
  • SDA_spatialQuery() fixed a bug with new addFields argument and geomIntersection=TRUE (#414)
  • get_OSD() replace old base URL for result='html'
  • SDA_query() include soilDB package version in User-Agent string
  • Vignette updates
  • Validate SDA_spatialQuery what and as_Spatial inputs (@jslatane #411)
  • get_SDA_property() fixed a bug in SQL dialect syntax with local SQLite dsn

What's Changed

New Contributors

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.12...2.8.13

Natural Resources - Soil and Land - R
Published by brownag 5 months ago

soilDB - soilDB 2.8.12

soilDB 2.8.12 (2025-08-29)

  • New Vignettes:
    • Added vignette for thematic maps of dominant ecological site using Soil Data Access via SDA_spatialQuery() and get_SDA_coecoclass()
    • Added vignette for creating and using local SSURGO databases via downloadSSURGO() and createSSURGO()
  • SDA_spatialQuery() now supports addFields argument to add columns to the result from other non-spatial tables.
    • You can now specify columns from:
      • "legend", "mapunit", and "muaggatt" tables for what equal to "mupolygon", "mupoint", "muline" or "mukey"
      • "legend" table for what equal to "areasymbol" or "sapolygon"
      • "featdesc" for what equal to "featpoint" or "featline"
  • createSSURGO():
    • Added append argument to fix overwrite behavior
    • Fixed bug in creating non-GeoPackage, non-spatial SQLite output
    • Improved handling of empty export files and overwrite logic for non-file-based RDBMS
  • fetchNASIS(): fixed bug when fill=TRUE and there are no horizons in the source data for any profile
  • get_component_from_SDA() fixed bug in join of "chorizon" and "chfrags" tables, now uses merge(incomparables=NA)
  • get_vegplot_tree_si_summary_from_NASIS_db() updated for new siteindexcurve table in NASIS data model version 7.4.3

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.11...2.8.12

Natural Resources - Soil and Land - R
Published by brownag 6 months ago

soilDB - soilDB 2.8.11

soilDB 2.8.11 (2025-07-10)

  • Update to NASIS metadata for data model version 7.4.3
  • fetchSDA_spatial() geom.src="mlrapolygon" uses a new URL on the DSHub S3 bucket
  • Added "projectsubtype" and "milestonetype" to the "project" set for get_NASIS_table_name_by_purpose()
  • Initial phase of syntax cleanup affecting many functions

soilDB 2.8.10 (2025-04-28)

  • fetchVegdata() add nullFragsAreZero argument (passed to get_site_data_from_NASIS_db())
  • Added soilDB_user_dir() for caching local copies of data for use in soilDB functions (#377)
  • Added fetchHWSD() and get_HWSD_path() for the FAO Harmonized World Soil Database (#391)
  • Added get_phroots_from_NASIS_db() for getting pedon horizon root information from NASIS (#393)

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.9...2.8.11

Natural Resources - Soil and Land - R
Published by brownag 7 months ago

soilDB - soilDB 2.8.9

soilDB 2.8.9 (2025-04-04)

  • soilDB now requires aqp >= 2.1.0
  • Added get_vegplot_groundsurface_from_NASIS_db() thanks to Greg Schmidt (@phytoclast; #373)
  • Added "transectgroundsurfcover" table to "vegetation" set for get_NASIS_table_name_by_purpose()
  • Added missing fetchNASIS("components") deprecation messages for maat_l, maat_r, maat_h, mast_r, ecosite_id, ecosite_name, othervegid, and othervegclass columns
  • fetchSDA_spatial(geom.src="mlrapolygon"): uses an AWS (S3) source and Seek-optimized ZIP file (thanks to @jneme910)
  • get_SDA_property() (method "weighted average" and "min/max"), get_SDA_hydric(), and get_SDA_interpretation() (method "weighted average") now use Common Table Expressions (CTEs) and therefore are compatible with local (SQLite or other) data sources

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.8...2.8.9

Natural Resources - Soil and Land - R
Published by brownag 10 months ago

soilDB - soilDB 2.8.8

soilDB 2.8.8 (2025-02-10)

This is a patch release with several bug fixes.

  • fetchSCAN(): Bug fix in when sensor column contains all NA
  • ROSETTA() now uses HTTPS URL
  • fetchNASIS() bug fix for (now deprecated) pedon_id in horizon slot rather than site
  • Rebuilt SPC datasets: loafercreek, gopheridge, mineralKing
  • fetchNASISLabData(): use ncsspedonlabdataiid as unique pedon ID

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.7...2.8.8

Natural Resources - Soil and Land - R
Published by brownag about 1 year ago

soilDB - soilDB 2.8.7

soilDB 2.8.7 (2025-01-16)

  • Several aliases of NASIS physical column names have been deprecated and will be removed in the next minor release (2.9.x). See https://ncss-tech.github.io/AQP/soilDB/bulletins/2025.01-1-soilDB-NASIS-column-aliases.html for details (#369)
  • fetchVegdata()
    • Added "ecostateid", "ecostatename", "commphaseid", "commphasename" to columns from site and siteobs joined into "vegplot" result.
    • Fixed "site" join used for "vegplot" table result. Now using LEFT join to add siteecositehistory information
    • Sites without vegetation plots are now excluded from the result
  • get_vegplot_trhi_from_NASIS_db() & get_vegplot_transect_from_NASIS_db() no longer join to the pedon table. Use the "siteobsiid" or vegetation plot "assocuserpedonid" to join to pedon records when necessary.
    • This change avoids issues with unintended duplication of records e.g. lab pedons that have multiple pedons per site observation. Thanks to Nathan Roe for suggestion.
  • get_vegplot_*() functions use INNER join to vegtransect table where applicable, so records are only returned for vegplots with an associated transect. Thanks to Zach Van Abbema for suggestion.
  • createSSURGO(): more informative error message when no export files found for import
  • Improved soilDBdata data sets used for unit tests of fetchNASIS() and fetchVegdata() when a local NASIS instance is not available
  • Updated NASIS SoilProfileCollection data sets (loafercreek, gopheridge, mineralKing)

soilDB 2.8.6 (2024-12-23)

  • fetchNASIS() and get_site_data_from_NASIS_db() now return Ecological Site State and Community Phase information (ecostatename, ecostateid, commphasename, commphaseid columns) from Site Observation table
  • createStaticNASIS() bug fixes
    • Removed workaround for {odbc}/nanoodbc VARCHAR(MAX) columns; now can directly use DBI::dbReadTable() for all tables via NASIS ODBC connection
    • Fixed error when output_path=NULL
  • fetchNASIS() changed default behavior to mixColors=FALSE which returns dominant condition for each moisture state rather than mixing LAB color coordinates
    • get_colors_from_NASIS_db() deprecate mixColors argument, add method argument with options "dominant", "mixed", and "none". New aggregation method "none" returns long format representation of color data from phcolor table with no aggregation applied.
  • createSSURGO() updates:
    • Added incremental write of tabular data by table and soil survey area, which is much more memory efficient
    • Added maxruledepth argument to allow filtering of cointerp table, and set default to 0.
      • This reduces number of cointerp rows by about 75% for published SSURGO. Generally, Web Soil Survey exports have maximum rule depth of 1, but custom NASIS exports can be "deeper"
    • Updated behavior of filename argument when conn DBIConnection is specified and improved overwrite logic
    • Added dissolve_field to facilitate creating aggregate geometries by "mukey" or other spatial attribute
    • Added include_tabular argument to support omitting tabular data when building a database
    • Now include_spatial and include_tabular are allowed to be a character vectors of table names
      • TRUE is all tables, FALSE is no tables. This allows for subsets of the SSURGO data model to be specified with finer user control over database contents.
    • Now a composite "soil_metadata" table is made with "areasymbol" column and one row per soil survey area, rather than one table per soil survey area. This is more compact and scales better to larger databases.

What's Changed

New Contributors

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.5...2.8.7

Natural Resources - Soil and Land - R
Published by brownag about 1 year ago

soilDB - soilDB 2.8.5

soilDB 2.8.5 (2024-11-04)

  • fetchLDM() add support for area_type argument with local database connections (dsn argument)
  • fetchSCAN() updates:
    • Improved SCAN, CSCAN, SNOTEL, SNOWLITE station metadata (#61) via @jskovlin
    • Timezone support for hourly data requested by fetchSCAN() (#184)
    • All above-ground sensors are now returned, instead of just the first of each type (#359)
  • Added new help file on NASIS database sources; see ?NASISLocalDatabase (#360)
  • get_SDA_*() function updates related to consistent parameters for miscellaneous areas and minor components (#361)
  • fetchSOLUS(): New function for downloading data from Soil Landscapes of the United States 100-meter (SOLUS100) soil property maps project repository (#362)
  • fetchNASIS() more consistent QC messages and output for multiple site observations and lab samples
  • Updated SoilProfileCollection data sets (loafercreek, gopheridge, mineralKing) for aqp 2.1.x object definition and recent changes to fetchNASIS() (#363)

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.4...2.8.5

Natural Resources - Soil and Land - R
Published by brownag over 1 year ago

soilDB - soilDB 2.8.4

soilDB 2.8.4 (2024-08-19)

  • createSSURGO() bug fixes following changes in 2.8.3
    • generating gpkg_contents for GeoPackage files failed to add entries for "features" data_type
    • filename argument not properly handled in some cases
  • SDA_query() handle another possible failure point in error handling code
  • createStaticNASIS() use odbc::dbListFields() instead of odbc::odbcConnectionColumns()
  • fetchNASIS Vignette

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.3...2.8.4

Natural Resources - Soil and Land - R
Published by brownag over 1 year ago

soilDB - soilDB 2.8.3

soilDB 2.8.3 (2024-06-11)

  • Updates to SoilWeb web coverage services
    • ISSR800 authoritative grid system altered slightly
    • ISSR800.wcs() and soilColor.wcs() now set color table internally when possible
    • updated source data: ISSR800 (FY24) and soil color (FY23)
  • SDA_query() updates
    • Better messaging on error
    • Handle try-error result more gracefully in high-level functions (#352)
  • createSSURGO(): added support for creating DuckDB, PostgreSQL, and other DBI-compatible databases (#352) via conn argument
  • fetchSDA() and get_chorizon_from_SDA() concatenate multiple texcl using a comma when a texture group contains multiple texture classes (e.g. stratified textures) (fixes #353)
  • fetchNASIS()/.formatLandformString(): append geomfmod column to landscape, landform, and microfeature strings where present; thanks to Gabriel Benitez for suggestion
  • fetchNASIS()/get_extended_data_from_NASIS_db(): fix conversion of codes to labels for microrelief
  • fetchSCAN(): fix header format; thanks to @dschlaep for reporting and providing a fix

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.2...2.8.3

Natural Resources - Soil and Land - R
Published by brownag over 1 year ago

soilDB - soilDB 2.8.2

soilDB 2.8.2 (2024-04-22)

  • SoilWeb Web Coverage Service MUKEY grid data source (used for mukey.wcs()) and metadata have been updated for FY2024
    • Note that ISSR800 WCS (ISSR800.wcs() source) is still using FY2023/FY2022 data
  • get_SDA_coecoclass() default data returned for methods "Dominant Component", "Dominant Condition" and "None" now include localphase column
  • get_soilseries_from_NASIS() and get_competing_soilseries_from_NASIS(): add SS argument for parity with all other NASIS "get" methods
    • default to FALSE for backward compatibility/common use cases
  • get_site_data_from_NASIS_db() gains Frost Free Days, MAP, REAP, MAAT, MAST, MSAT, MSST, MWAT, MWST, and Parent Material Group Name; thanks to Zach Van Abbema for suggestion
  • Changes in column names related to Area table / "areasymbol" (#272); thanks to Zach Van Abbema for suggestion
    • get_site_data_from_NASIS_db(): Add state, county, and MLRA areasymbol references ("site_state", "site_county", "site_mlra")
    • get_mapunit_from_NASIS_db(): Add dominant MLRA areasymbol reference column "lmapunit_mlra"
    • get_soilseries_from_NASIS(): replace areasymbol column to use relationship-style name "soilseries_typelocst" (minor breaking change)
  • fetchSDA_spatial(): Add support for querying mapunit point ("mupoint"), mapunit line ("muline"), special feature point ("featpoint"), special feature line ("featline") by mukey or featkey, geometry type selectable via geom.src argument
  • SDA_spatialQuery(): Add support for querying mapunit point ("mupoint"), mapunit line ("muline"), special feature point ("featpoint"), special feature line ("featline") for a spatial extent, geometry type selectable via what argument
  • simplifyFragmentData() / simplifyArtifactData() efficiency improvement when all records are missing data

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.1...2.8.2

Natural Resources - Soil and Land - R
Published by brownag almost 2 years ago

soilDB - soilDB 2.8.1

soilDB 2.8.1 (2024-01-09)

  • get_mapunit_from_NASIS(), get_lmuaoverlap_from_NASIS() and get_legend_from_NASIS() gain areatypename argument used for filtering legends by areatypename.
    • Default results include "Non-MLRA Soil Survey Area" and "MLRA Soil Survey Area". Set to NULL for no filter.
  • Fixed bugs in waterDayYear() and summarizeSoilTemperature() for leap years (#333)
  • fetchSoilGrids() upgrades
    • Fixed a bug with data.frame output
    • Requests for more than 5 sites now include a call to Sys.sleep() to conform with ISRIC "Fair Use" policy
    • Upgraded SoilProfileCollection spatial promotion for aqp 2.0+
    • Added 10 kPa, 33 kPa and 1500 kPa water content estimates to default variable sets for point and grid queries
  • fetchSDA_spatial() gains ability to query mapunit delineations by Ecological Site ID (by.col="ecoclassid")
  • get_SDA_coecoclass() default ecoclasstypename is now c("NRCS Rangeland Site", "NRCS Forestland Site"), as this is the most common type of aggregation and is least prone to producing unusual composition-related errors due to duplications
    • Fixed bug related to merging tables/integer data type
    • Fixed bug in calculation of "Not assigned" fraction of mapunits which could result in negative aggregate component percentages below the default threshold

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.8.0...2.8.1

Natural Resources - Soil and Land - R
Published by brownag about 2 years ago

soilDB - soilDB 2.8.0

soilDB 2.8.0 (2023-12-22)

  • Minimum {aqp} version set to v2.0.2. This is due to changes in the namespace related to aqp::col2Munsell(), to "encourage" users to update to the more efficient routines provided in {aqp} 2+ (if they haven't already), and prepare for future updates in the 2.x series.
  • Fix bugs in get_SDA_interpretation() when dsn refers to a local SQLite source and in concatenation of reason string when wide_reason=TRUE. Thanks to Kevin Wolz (@kevinwolz)
  • createSSURGO() updates:
    • Breaking change: Now uses the standard SSURGO layer names for spatial data (e.g. "mupolygon" rather than "soilmu_a").
    • Creates indices for foreign keys and other columns important for data analysis, dramatically improving the performance of standard queries on SQLite sources.
    • Now works properly on STATSGO data sets for individual states or CONUS. Previously tabular data would be transferred but spatial data were not.
  • downloadSSURGO() gains db argument which gives ability to download STATSGO by state or all of US from Web Soil Survey. Thanks to Meghan Krueger for suggestion.
  • get_SDA_property(): weighted average/dominant component numeric methods now return mukey in first column position; for parity with other get_SDA* methods recently updated/already doing this, making it easier to use these columns for raster attribute tables via terra::set.levels()
  • fetchNASIS(lab=TRUE) fixed a bug when multiple phlabresults records are present for a single horizon, but one or both is missing bottom depth. Thanks to Meyer Bohn (@MollicMeyer) for reporting.
  • SoilProfileCollection objects now include a time stamp in their metadata, accessed as: metadata(x)$created (#235)
  • Added area_type argument to fetchLDM() for non-SSA area queries (#328)
  • Added grid argument to fetchSoilGrids() for downloading Cloud-Optimized GeoTIFF subsets for spatial extent (#329)
  • fetchOSD() now automatically batches requests into sets of 100 series, allowing arbitrarily large requests to be made (#239)

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.7.10...2.8.0

Natural Resources - Soil and Land - R
Published by brownag about 2 years ago

soilDB - soilDB 2.7.10

soilDB 2.7.10 (2023-11-16)

  • fetchSDA_spatial() gains geom.src="mlrapolygon" for obtaining Major Land Resource Area (MLRA) polygon boundaries. When using this geometry source x is a vector of MLRARSYM (MLRA Symbols).

    • The geometry source is the MLRA Geographic Database v5.2 (2022) which is not (yet) part of Soil Data Access. Instead of SDA, GDAL utilities are used to read a zipped ESRI Shapefile from a remote URL: https://www.nrcs.usda.gov/sites/default/files/2022-10/MLRA_52_2022.zip. Therefore, most additional fetchSDA_spatial() arguments are not currently supported for the MLRA geometry source. In the future a mlrapolygon table may be added to SDA (analogous to mupolygon and sapolygon), and the function will be updated accordingly at that time.

  • Web coverage services and related raster attribute tables provided by SoilWeb (mukey.wcs() etc.) are now using the SoilWeb load-balancer URL

  • get_SDA_coecoclass() gains method="all" for aggregating information about ecological sites and related components. The method performs a condition-based aggregation for each ecological site condition in the map unit, producing a "wide" data.frame result with as many columns as needed to portray all site conditions.

  • fetchLDM() gains new argument WHERE for supplying a custom SQL where clause for selecting sites of interest. For example: fetchLDM(WHERE = "CASE WHEN corr_name IS NOT NULL THEN LOWER(corr_name) ELSE LOWER(samp_name) END = 'musick'")

soilDB 2.7.9 (2023-09-01)

  • Added new method options for fetchSDA_spatial(). Aggregation grouping is controlled by the by.col argument. This works for mapunit and survey area polygon geometries, aggregating all polygons in the group for each mukey, nationalmusym, lkey, or areasymbol extent.
  • method="extent" method calculates a bounding rectangle
  • method="convexhull" calculates the convex hull
  • method="union" returns a MULTIPOLYGON
  • method="collection" returns a GEOMETRYCOLLECTION

Bug Fixes

  • Bug fix for get_vegplot_transpoints_from_NASIS_db(); using wrong record ID for transect points

  • get_NASIS_table_name_by_purpose() now includes "pointplantcoverdetails", "plantprodquadratdetails" in the "vegetation" table purpose group

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.7.8...2.7.10

Natural Resources - Soil and Land - R
Published by brownag about 2 years ago

soilDB - soilDB 2.7.8

soilDB 2.7.8 (2023-08-29)

  • Added new SoilWeb "Web Coverage Service" vignette (https://ncss-tech.github.io/soilDB/articles/wcs-ssurgo.html) related to creating thematic maps using grids of mapunit keys from SoilWeb with aggregated tabular data from Soil Data Access.

  • get_SDA_*() functions now all return mukey values in first column

  • mukey.wcs() gains a 30m gridded version of Hawaii and Puerto Rico SSURGO data via db="HI_SSURGO" and db="PR_SSURGO", respectively.

  • get_vegplot_data_from_NASIS_db(): now uses LEFT join to plant table so that empty records can be diagnosed; thanks to @natearoe for suggestion

  • Added new NASIS query functions for vegetation transect point and quadrat details: get_vegplot_prodquadrats_from_NASIS_db() and get_vegplot_transpoints_from_NASIS_db(); thanks to Zach Van Abbema for suggestion

Bug Fixes

  • get_SDA_property(method="Dominant Component (Numeric)") now includes minors by default, fixing issues with STATSGO mapunits that have no major components flagged. (@dylanbeaudette)

  • get_component_data_from_NASIS_db(): removed duplicated hydricrating column, also now includes climate columns with standard names. This is a continuation of the idea that custom aliases for standard NASIS columns are deprecated (https://github.com/ncss-tech/soilDB/issues/242)

  • .pickBestEcosite() now considers record_when_last_updated in lieu of correlation date; this stabilizes sort order from SQLite snapshot v.s. NASIS local database sources (https://github.com/ncss-tech/soilDB/issues/295)

  • get_component_from_GDB(): fixes for batching over component geomorphic description and parent material group @smroecker

  • get_mapunit_from_SDA(): handle possibility of mapunit-level SDA query failure

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.7.7...2.7.8

Natural Resources - Soil and Land - R
Published by brownag over 2 years ago

soilDB - soilDB 2.7.7

soilDB 2.7.7 (2023-03-10)

Enhancements

  • fetchNASIS(from="pedons") and get_site_data_from_NASIS_db() now return siteobsiid column (@natearoe)

  • mukey.wcs() gains experimental gridded STATSGO layer (300m)

  • Add get_NASIS_table_metadata() for returning information about columns in NASIS tables.

  • simplifyFragment/ArtifactData(): downgrade warnings

  • get_cosoilmoist_from_SDA(): mukey and cokey now included when duplicates=TRUE; thanks to @andypaolucci for catching this

  • fetchSoilGrids()

    • Add SpatVector coercion for input locations (already supported sf/sp classes)

    • Add handling for messages from API about erroneous input

  • Add fetchNASIS("pedons") columns vignette

  • Add get_NASIS_table_metadata() and optional argument include_description for get_NASIS_metadata() and get_NASIS_column_metadata()

  • get_SDA_cosurfmorph() + get_SDA_pmgroupname(): support for including or excluding misc. areas via miscellaneous_areas argument

  • get_site_data_from_NASIS_db():

    • Omit "multiple horizontal datums" warning

    • Remove calculated X/Y long/lat + add proper NASIS alias for long/lat

    • Add siteothvegclass id/name - add tables to default lookup/site sets

Bug fixes

  • dbQueryNASIS(..., close=TRUE) now calls dbDisconnect() on.exit() (ensuring connections get closed on error)

  • fetchSCAN():

    • 2x requests when timeseries argument not specified

    • Account for no results (e.g. year = 1800)

    • Bug fix in vectorization when daily + hourly data requested

  • downloadSSURGO():

    • Handle SDA_query() with invalid syntax in WHERE clause

    • Fix for include_template=FALSE

  • createSSURGO()

    • Attribute tables are now added to gpkg_contents when output filename is a GeoPackage

  • Fix for .get_comonth_from_SDA()

  • Fix selected set (SS argument) for get_ecosite_history_from_NASIS_db() in get_site_data_from_NASIS_db()

  • get_SDA_pmgroupname: return NA (not "NULL") for empty/missing pmgroupname when simplify=TRUE

  • SDA_spatialQuery():

    • geomIntersection=TRUE with db="SAPOLYGON" now correctly labels the areasymbol column (previously was mukey) to match geomIntersection=FALSE and SDA schema

    • Bounding box extent polygons are now only calculated for SpatRaster (not SpatVector) input

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.7.6...2.7.7

Natural Resources - Soil and Land - R
Published by brownag almost 3 years ago

soilDB - soilDB 2.7.6

soilDB 2.7.6

  • All references to soilDB.env have been replaced with a function that returns that environment object (get_soilDB_env()); thanks to @MollicMeyer for identifying this as a problem in #277. This object used to be exported but was unintentionally omitted from NAMESPACE; this has been fixed.

  • fetchNASIS(lab=TRUE) bug fix related to many:1 relationships between lab samples and morphologic horizons with all-missing columns having logical datatype (#277)

  • Added get_SRI() and fetchSRI() functions for accessing USFS Region 6 Soil Resource Inventory information from https://ecoshare.info/; thanks to @joshualerickson for the contribution (https://github.com/ncss-tech/soilDB/pull/274)

  • fetchLDM() now sets the horizon designation metadata like other fetch* functions that return SoilProfileCollection objects (@dylanbeaudette)

  • mukey.wcs() fix spurious warnings occasionally given due to minor differences (rounding) of grid dimensions

  • {curl} has been moved from Suggests to Imports

  • simplfyFragmentData() alias for simplifyFragmentData() removed (@infotroph)

What's Changed

New Contributors

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.7.5...2.7.6

Natural Resources - Soil and Land - R
Published by brownag about 3 years ago

soilDB - soilDB 2.7.5

soilDB 2.7.5 (2022-10-17)

  • Updates to SSURGO File Geodatabase functions (fetchGDB() and related) by @smroecker
  • Added soilColor.wcs() to access a web coverage service for soil color at various depths by @dylanbeaudette
  • waterDayYear(): fix for CRAN and different timezones; now defaults to tz="UTC" #268
    • summarizeSoilTemperature(): set default timezone to tz="UTC"
  • Fix for uncode() on pre-decoded values when ChoiceName and ChoiceLabel overlap #273
    • Fix for NASISChoiceList() related to #273
  • get_soilseries_from_NASIS(): Remove areaacres and obterm for #272 by @smroecker
  • Fix for get_OSD(..., fix_ocr_errors = TRUE) with empty typical profile for #271 by @dylanbeaudette
  • fetchNASIS() drops non-representative and additional when dropNotRepresentative/dropAdditional are set (@natearoe)
  • Fix for as.POSIXct() in R 4.3+; for #265
  • Fix for "status was 'SSL connect error" for fetchKSSL() and other functions that download JSON (@kramdog)
    • Now uses standard soilDB {curl} handle, which includes a longer timeout and ssl_verifyhost=0
  • Fixes for compatibility with {jsonlite} >1.8.1 that now uses {base} rather than {curl}
  • Update row count expectations for end of FY22 SSURGO refresh

Natural Resources - Soil and Land - R
Published by brownag over 3 years ago

soilDB - soilDB 2.7.4

soilDB 2.7.4 (2022-09-30)

Natural Resources - Soil and Land - R
Published by brownag over 3 years ago

soilDB - soilDB 2.7.3

soilDB 2.7.3 (2022-08-19)

  • get_SDA_property() all methods now support miscellaneous_areas argument. This defaults to FALSE for the methods it was previously implemented for--so be aware that queries using "Dominant Component" or "Dominant Condition" (which previously did not respond to miscellaneous_areas) may have the number of rows in result reduced due to omission of miscellaneous land types. If this is unexpected or undesired, please use miscellaneous_areas=TRUE. (https://github.com/ncss-tech/soilDB/issues/257)

  • Adds get_NASIS_metadata() and helper method get_NASIS_column_metadata() and other new tools for working with uncode(), factors and NASIS metadata cached in the package.

  • Bug fix for get_cosoilmoist_from_SDA(); thanks to Monika Shea @monikashea for reporting the problem (https://github.com/ncss-tech/soilDB/issues/253)

  • fetchNASIS_report() now works with the output from "get_site_from_NASIS" report (useful for site records without associated pedons)

  • createSSURGO() gains arguments quiet and include_spatial to toggle messages and inclusion of spatial data in created SQLite database, respectively

  • downloadSSURGO() now handles queries against sacatalog that return no results more gracefully

  • get_OSD(): Add fix_ocr_errors argument for result='json' to fix common optical character recognition errors associated with horizon designations and colors (NOTE: does NOT fix depths)

  • fetchSCAN() gains timeseries argument to support batch downloads of hourly data. Additional arguments (...) are passed as a raw request, allowing other parameters sent in request to be modified if needed, and bypassing batch functionality. This is similar to the req argument syntax used in earlier versions of this function, which had been deprecated for some time now. Thanks to Matthew Morriss for raising the discussion item @morrismc99 (https://github.com/ncss-tech/soilDB/discussions/260).

  • {curl} moved from Suggests to Imports; curl::curl_download() is now used instead of utils::download.file() because it seems to handle SSL certificates better on some networks.

Natural Resources - Soil and Land - R
Published by brownag over 3 years ago

soilDB - soilDB 2.7.2

soilDB 2.7.2 (2022-06-27)

  • fetchNASIS("components'): Fix and refactor ( breaking change from 2.7.1, which introduced a bug/inconsistency) of recent change; duplicates argument is now required to merge in data from mapunit/legend tables (where many:1 relationships between legend/mapunit and datamapunit are possible). In 2.7.1 possibly incomplete mapunit/legend tables could be joined to SoilProfileCollection result (if and only if the tables were populated in selected set/local DB). Does not change historic (<=2.7.0) default behavior. Thanks to @dylanbeaudette for suggesting use of get_component_correlation_data_from_NASIS_db() here.

  • Several fixes for Roxygen documentation (notably for ROSETTA() and various NASIS web report related functions) that were missing @export tags. Several previously-exported functions missed being explicitly exported in the new Roxygen-generate NAMESPACE. These unintentional omissions from 2.7.1 NAMESPACE have been resolved.

  • Fixes an old bug in fetchSDA()/get_chorizon_from_SDA() related to LEFT OUTER versus RIGHT JOIN to chtexture table

Natural Resources - Soil and Land - R
Published by brownag over 3 years ago

soilDB - soilDB 2.7.1

soilDB 2.7.1 (2022-06-10)

  • get_SDA_coecoclass() better handling of NULL ecoclassref; support for filtering on ecoclasstypename; not_assigned_value now applies to ecoclassname, ecoclasstypename and ecoclassref columns in addition to ecoclassid; Thanks to Andy Paolucci and Jason Nemecek. Also, added additional columns from legend/mapunit tables (areasymbol, lkey, muname).
  • fetchNASIS(from="components") now returns mapunit and legend information (if loaded in local NASIS database); results now contain mustatus and repdmu which can be used to remove components from additional mapunits and non-representative data mapunits; thanks to Nathan Roe
  • Convert UTF-8 strings in us_ss_timeline result to ASCII
  • SDA_query(): Fixed POST request that could produce unhandled errors on network failure (now returns try-error like other error-causing code)
  • SDA_query(): In the event of a syntax error, error contents are now returned as a message, not a warning.
  • uncode() and code() now work with data.table and tibble objects.
  • Various fixes to tests and error handling code to reduce likelihood of thrown errors from network problems or missing suggested packages.

Natural Resources - Soil and Land - R
Published by brownag over 3 years ago

soilDB - soilDB 2.7.0

soilDB 2.7.0 (2022-05-18)

  • Spatial
    • Dropped imports from sp and raster which means soilDB no longer requires the soon-to-retire rgdal package.
    • All spatial data processing has been moved to sf and terra, which have been added to Suggests.
      • (breaking change) Classes from these packages (e.g. sf, SpatRaster) will be returned by default rather than Spatial*DataFrame or RasterLayer from sp and raster.
      • (breaking change) Spatial functions that take spatial input will return the same class type as the input unless otherwise specified.
        • fetchSDA_spatial() and SDA_spatialQuery() gain as_Spatial argument; when TRUE equivalent (backward compatible) sp and raster data types are returned.
        • Alternately, you may set options(soilDB.return_Spatial=TRUE)
    • mukey.wcs() and ISSR800.wcs() bug fix for some instances where the target extent was miscalculated, resulting in slight differences from requested resolution (res argument) of result.
    • mukey.wcs() gains a new possible data source db="RSS" which accesses a Web Coverage Service containing grids from Raster Soil Surveys in the United States.
    • See: https://github.com/ncss-tech/soilDB/pull/229 for more details on what has changed.
  • NASIS
    • (breaking change) rmHzErrors argument now defaults to FALSE. Please let us know if allowing horizon errors results in unexpected behavior so we can repair various interfaces that rely on no errors being present. See aqp::checkHzDepthLogic() for more information on the types of things that used to result in profiles being removed from results and for guidelines on how to fix.
    • Added several new columns from the plotplantinventory table to get_vegplot_species_from_NASIS_db() result; thanks to Zachary Van Abbema for suggestion and feedback
    • Local NASIS metadata used for uncode() are now cached within an R session which results in faster query processing times for users with a local NASIS database connection set up.
      • The db argument to uncode() has been deprecated. Now, code() and uncode() can use ChoiceName and/or ChoiceLabel in coding and decoding ChoiceValue for all data sources.
    • Rock fragment and artifact sieving now uses <76mm as the upper boundary for gravel fraction, and a related QC message has been removed
  • SSURGO / Soil Data Access
    • Added get_SDA_cosurfmorph(): a new function in "SSURGO On Demand" style. Users can customize the WHERE clause, target tables and the grouping variable used to calculate proportions (default by="compname")
      • "cosurfmorphgc" summarizes "geomposmntn", "geomposhill", "geomposflats", "geompostrce"
      • "cosurfmorphhpp" summarizes "hillslopeprof"
      • "cosurfmorphss" summarizes "shapeacross", "shapedown", and concatenated "surfaceshape"
    • Several fixes for logic of get_SDA_property() with method="weighted average" and include_minors=TRUE/miscellaneous_areas=TRUE, thanks to Andy Paolucci and Dylan Beaudette for testing and providing feedback on the queries.
    • All get_SDA_*() methods (except get_SDA_metrics()) now support input of custom WHERE clause in lieu of mukeys/areasymbols arguments and gain a dsn argument for specifying a local SQLite database or DBIConnection.
    • Added downloadSSURGO() for downloading/extraction of the SSURGO data by survey area from Web Soil Survey.
    • Added createSSURGO() for building of local databases as SQLite/Geopackage from one or more SSURGO exports.

What's Changed

Full Changelog: https://github.com/ncss-tech/soilDB/compare/2.6.15...2.7.0

Natural Resources - Soil and Land - R
Published by brownag over 3 years ago

soilDB - soilDB 2.6.15

soilDB 2.6.15 (2022-04-13)

  • fetchNASIS()
    • New mixColors argument used to toggle color mixing for pedon horizons with multiple colors per moisture state.
      • Default TRUE mixes colors based on reported color percentage via estimateColorMixture(). FALSE returns the dominant color in each moisture state, or first record for cases without colorpct populated.
    • Added taxreaction and taxfamhahatmatcl to extended taxonomic information
    • Added new option (soilDB.NASIS.skip_uncode) to bypass uncode() in NASIS functions (mostly used for debugging or special database instances that come pre-decoded)
    • An instance in fetchNASIS(from="components") where local database connection was left open was fixed
  • Added fetchLDM() function to access Kellogg Soil Survey Lab Data Mart via Soil Data Access or local SQLite snapshot (https://github.com/ncss-tech/soilDB/pull/243)
  • Added get_SDA_metrics() for accessing usage metrics for Soil Data Access, Web Soil Survey and the Lab Data Mart. Thanks to Jason Nemecek for submitting the base SQL query
  • get_SDA_interpretation(method = "dominant condition") now includes total_comppct_* columns reflecting the summed component percentage of the dominant condition
  • Updated metadata for SCAN sites that were missing pedlabsampnum (KSSL Pedon Sample ID)

Natural Resources - Soil and Land - R
Published by brownag almost 4 years ago

soilDB - CRAN Release 2.6.14

soilDB 2.6.14 (2022-03-15)

  • waterYearDay() bug fix for more specific (sub-daily) date-time formats
  • fetchSCAN() better handling of empty results in multi-site queries
  • Updates to queries, metadata and sample datasets for NASIS 7.4.1 Database Model
    • fetchNASIS("pedons") no longer includes pmweathering
    • fetchNASIS("components") no longer includes ecositeorigin
    • New Component Ecological Site attributes added
  • stringsAsFactors argument to soilDB functions has been deprecated in favor of a package option
    • Default behavior for NASIS domains is to return character labels rather than coded factors
    • Use NASISDomainsAsFactor(TRUE) to toggle package option soilDB.NASIS.DomainsAsFactor

Natural Resources - Soil and Land - R
Published by brownag almost 4 years ago

soilDB - CRAN Release 2.6.13

soilDB 2.6.13 (2022-01-29)

  • fetchSDA_spatial now supports by.col "areaname", "mlraoffice", and "mouagencyresp"; thanks to suggestion by Jay Skovlin
  • fetchNASIS fix for multiple site observation records with surface fragments; thanks to bug report from Brianna Wegner
  • waterYearDay() use format and timezone for start date conversion
  • fetchNASIS fix for from="components", SS=FALSE and queries where no NASIS local database is present (e.g. from SQLite source)
  • Update to NASIS_table_column_keys dataset of NASIS primary and foreign keys by table name to include many more tables
  • fetchVegdata() no longer errors for child table queries unless site/site observation/vegetation plot records are missing
  • fetchOSD(extended=TRUE) now returns an element "NCCPI" containing the National Commodity Crop Production Index summaries. The values returned are quantiles at the 1, 5, 25, 50, 75, 95, and 99% levels over all SSURGO components with compname matching series for irrigated and non-irrigated condition.

Natural Resources - Soil and Land - R
Published by brownag about 4 years ago

soilDB - CRAN Release 2.6.12

soilDB 2.6.12 (2022-01-07)

  • get_SDA_property() now works with mixed component and horizon-level properties; thanks to Matthieu Stigler for the bug report
  • Added get_SDV_legend_elements() for fetching and parsing XML for Soil Data Viewer / Web Soil Survey-style symbol themes for soil interpretations from Soil Data Access
  • fetchNASIS() pedon and component geomorphic summaries now include columns for landscape, microfeature, microrelief, 2D/3D morphometry, and slope shape
  • fetchNASIS('pedons') now uses simplifyFragmentData() for surface fragments

soilDB 2.6.11 (2021-12-21)

  • fetchSDA() handle NULL component-level results with an informative error
  • fetchSDA() now (again) returns mapunit/legend-level information via get_mapunit_from_NASIS()
  • createStaticNASIS() and queries to SQLite NASIS snapshots now preserve date/time using RSQLite 2.2.4+ via extended_types=TRUE argument to dbConnect()
  • get_soilseries_from_NASIS() now returns soiltaxclasslastupdated as a date/time and stores the year in calculated column soiltaxclassyearlastupdated
  • Added several tables to thematic groups in get_NASIS_table_name_by_purpose()
  • fetchOSD() gains surface shape proportions in extended shape_across and shape_down tables
  • SDA_spatialQuery() what='mukey' now works with db='STATSGO'
  • Added metadata to loafercreek, gopheridge and mineralKing
  • waterYearDay() pass through format argument for POSIX time conversion

Natural Resources - Soil and Land - R
Published by brownag about 4 years ago

soilDB - CRAN Release 2.6.10

soilDB 2.6.10 (2021-12-14)

  • waterDayYear() and .formatDates() allow optional format and tz argument; used for consistent POSIX time conversion in tests where date/time has granularity finer than one day
  • fetchSDA() extensions for better handling of components with no horizon data
  • SDA_spatialQuery() and processSDA_WKT() fully use {sf}, replacing {sp} in these contexts
  • SDA_spatialQuery() gains argument byFeature to use multiple single-feature queries and combine the results with a unique feature ID specified by idcol argument. This allows for specific feature intersection results without secondary spatial overlay of the polygons (https://github.com/ncss-tech/soilDB/issues/222)
  • dbConnectNASIS() no longer requires that the NASIS credentials option be set if the dsn argument is specified.
  • Rebuilt loafercreek, gopheridge and mineralKing from latest fetchNASIS() results.

Natural Resources - Soil and Land - R
Published by brownag about 4 years ago

soilDB - CRAN Release 2.6.9

soilDB 2.6.9 (2021-12-03)

  • Replaced functionality using {plyr}/{reshape2} with {base}/{data.table}
  • processSDA_WKT(): replaced {rgeos} with {wk} and {sf}
  • SDA_spatialQuery(): added query_string argument
  • get_SDA_property(): fixes for MIN/MAX aggregation (https://github.com/ncss-tech/soilDB/issues/219)
  • get_component_from_SDA(): fragment size thresholds now conform with new (clarified) NSSH definitions

soilDB 2.6.8 (2021-11-05)

  • fetchNASIS() upgrades: use data.table and base internally for data aggregation
  • fetchNASIS("components") now "sieves" rock fragments and human artifacts using same routines as for pedons; respects nullFragsAreZero argument
  • fetchKSSL(..., returnGeochemicalData = TRUE) safely returns 0-length data.frame when no data available

soilDB 2.6.7 (2021-10-27)

  • Removed several packages from Suggests: {gridExtra}, {ggplot2}, {viridisLite}, {mapview}, {rasterVis}
  • get_OSD(): Handle "NA" and type conversion for JSON results an convert spaces to underscores for file names as needed
  • fetchSCAN(): graceful handling of timeout and converted from {plyr} to {data.table}; (https://github.com/ncss-tech/soilDB/issues/161, https://github.com/ncss-tech/soilDB/issues/184)
  • get_EDIT_ecoclass_by_geoUnit(): graceful handling of timeout
  • get_SDA_muaggatt(): add query_string argument for parity with other "SSURGO on demand" / get_SDA_*() functions

soilDB 2.6.6 (2021-09-24)

  • get_SDA_pmgroupname() and get_SDA_hydric() now support alternate aggregation methods.
    • Default for get_SDA_pmgroupname() is "dominant component", now also supports "dominant condition" and "none".
    • Default for get_SDA_hydric() is a map unit level aggregation of components and assigns new classes ; now supports "dominant component", "dominant condition" and "none"

Natural Resources - Soil and Land - R
Published by brownag about 4 years ago

soilDB - CRAN Release 2.6.5

soilDB 2.6.5 (CRAN: 2021-08-21)

  • API calls that return geometry in projected coordinates (AEA/NAD83) now use ESPG:5070 instead of EPSG:6350

soilDB 2.6.4 (unreleased; 2021-08-06)

  • fetchNASIS(from="pedons") now supports fill=TRUE argument just like from="components" to include pedons that have no horizon records
  • createStaticNASIS(): column order should match NASIS, even if data types require reorder for ODBC driver
  • fetchSoilGrids() bug fixes, updates to metadata and references in documentation (https://github.com/ncss-tech/soilDB/issues/201)
    • Corrected the conversion factor used for predicted nitrogen values (conversion from cg/kg to g/kg)
    • Corrected the conversion factor used for uncertainty in bdod and nitrogen (SoilGrids uncertainty layer always uses factor of 10 to create integers)
    • Improved error handling
    • Added progress and verbose arguments for text progress bar and additional message output
    • Added support for {sf} and {sp} POINT geometry inputs
  • Add get_SDA_coecoclass() SOD-style method for mapunit/component level summaries of ecological site and other vegetation class information

Natural Resources - Soil and Land - R
Published by brownag over 4 years ago

soilDB - CRAN Release 2.6.3

soilDB 2.6.3 (2021-07-23)

  • SDA_query() and all functions that call SDA_query() get proper column class handling (related to #190), however:
    • be careful with the use of CAST(): unknown datatypes may not be correctly interpreted
    • previous column classes that were incorrectly guessed by type.convert() may have changed (e.g. component.wei)
  • SDA_spatialQuery() can now be used to return soil survey area symbols or geometry using what="areasymbol" or what="sapolygon", respectively
  • Added new columns to soil classification ("SC") table result of get_soilseries_from_NASIS(); now including taxonomic mineralogy class which may contain multiple parts for series with strongly contrasting control sections
  • Updates to get_SDA_*() methods
    • Extends get_SDA_property(property = ...) and get_SDA_interpretation(rulename = ...) vectorization over property/rulename to work with any aggregation method.
      • Now supports: Dominant Condition, Min, Max, Dominant Component, Weighted Average
    • Add query_string argument (default: FALSE). Set as TRUE to skip submitting query to SDA, instead returning a string of the query that would have been sent instead of data.frame result
    • get_SDA_property: better handling of NULL, miscellaneous areas, and property-specific weighting
      • Remove ISNULL(x, 0) logic that affected weighted averages in presence of missing data
      • Conditional calculation of horizon weights considering NULL values for requested properties (unique weights for each property)
      • New default argument include_minors=FALSE includes only components where majcompflag = 'Yes' in result
      • New default argument miscellaneous_areas=FALSE removes miscellaneous land types compkind values from result
      • Organic and bedrock layers are no longer removed from "Weighted Average", "MIN" or "MAX" aggregations
    • get_SDA_interpretation: added argument not_rated_value with default value of NA to set "not rated"" values across methods/queries. For backwards compatibility with original SQL use not_rated_value = 99.0
    • Standardizing MUKEY column name (and other keys) as lowercase in results
    • More informative error messages for bad input / arguments inconsistent with specified method
  • Thanks to @hammerly who pointed out weighted averaging of NASIS phlabresults wasn't working as expected and for highlighting some more improvements (https://github.com/ncss-tech/soilDB/issues/192)
  • get_OSD() TXT and HTML formats now supported (in addition to JSON) through a common function interface
  • Added get_NASIS_table_key_by_name() get_NASIS_fkey_by_name(), get_NASIS_pkeyref_by_name(), get_NASIS_pkey_by_name(), get_NASIS_table_name_by_purpose() methods for helping get information on primary/foreign keys and thematic groups of NASIS tables (useful for creating SQLite/external snapshots of NASIS tables)
  • get_mapunit_from_NASIS(), get_legend_from_NASIS() and get_lmuaoverlap_from_NASIS() now works for "MLRA Survey Area" areatypename and no longer is limited by constraints on legendsuituse or mustatus

Natural Resources - Soil and Land - R
Published by brownag over 4 years ago

soilDB - CRAN Release 2.6.2

soilDB 2.6.2 (2021-05-16)

  • Added formativeElement argument to taxaExtent() (SoilWeb taxon extent function)
    • "Formative elements" are derived from the dictionary provided by the {SoilTaxonomy} package (https://cran.r-project.org/package=SoilTaxonomy)
    • For example: taxaExtent("abruptic", level = 'subgroup', formativeElement = TRUE) will get an 800m grid (for SSURGO data in CONUS) showing extent of taxa that have "abruptic" in subgroup-level taxon name
  • fetchNASIS(from="pedons") result now contains the "taxclname" (full family-level taxon name) field from the NASIS pedon table; this value is calculated based on contents of petaxhistory child table
  • get_SDA_interpretation and get_SDA_property now support aggregation method="NONE" allowing for returning properties, classes and ratings for individual components or horizons (https://github.com/ncss-tech/soilDB/pull/181)
  • ISSR800.wcs and mukey.wcs now return a result that inherits from try-error (and a message) if the Web Coverage Service query fails

Natural Resources - Soil and Land - R
Published by brownag over 4 years ago

soilDB - CRAN Release 2.6.1

This marks the acceptance of CRAN Release 2.6.1 (submitted https://github.com/ncss-tech/soilDB/commit/0c2085c700d73a5f72cf9aa9864f404beffa33a5, which is too old to be tagged in this release).

Updates by patch version since last CRAN release.

soilDB 2.6.1 (2021-04-07)

  • Connections to local NASIS and various MS Access databases now use DBI and odbc, replacing RODBC
  • New methods dbConnectNASIS and dbQueryNASIS for NASIS access with read-only credentials, fetching query results, and closing the DBIConnection upon completion
  • NASIS methods use dsn argument to specify a local "static" SQLite file containing NASIS tables, or custom DBIConnection to a database with NASIS schema
    • Default dsn = NULL uses "nasis_local" ODBC connection to local NASIS SQL Server
  • Horizon depth logic checking is now done with aqp::checkHzDepthLogic(), powered by {data.table}
  • Added several new SDA query methods based on https://github.com/ncss-tech/ssurgoOnDemand by @jneme910 and @cferguso:
    • get_SDA_property, get_SDA_interpretation, get_SDA_muaggatt, get_SDA_hydric, get_SDA_pmgroupname

soilDB 2.6.0 (2021-02-18)

  • OSDquery gets a new argument (everything) for searching the entire document
  • fetchNASIS(..., rmHzErrors=TRUE) -- spurious removals of data due to missing "extended" records. fetchNASIS now uses aqp::horizons<- after building a minimal SoilProfileCollection from NASIS site and horizon tables. This allows aqp integrity methods to trigger where needed--preventing unintentional re-ordering or removals of "valid" horizon data.

Natural Resources - Soil and Land - R
Published by brownag almost 5 years ago

soilDB - CRAN Release 2.5.9

soilDB 2.5.9 (2021-01-26)

  • HenryTimeLine moved to {sharpshootR} package
  • new functions mukey.wcs() and ISSR800.wcs() for hitting web coverage service (WCS) for gSSURGO, gNATSGO, and ISSR-800 grids
  • new function ROSETTA() for accessing the new ROSETTA model API (c/o Todd Skaggs, USDA-ARS)
  • fetchOSD(..., extended=TRUE) gains geographically associated soils, parsed from OSD (thanks AGB)
  • fetchSDA_spatial now can return soil survey area polygons using geom.src = "sapolygon" with x as a vector of area symbols (areasymbol) or legend keys (lkey). For sapolygon results, the method and add.field arguments work the same as for mupolygon, only now both geometries can be returned with fields from the legend table.
  • fetchSDA_spatial now can return STATSGO gsmmupolygon geometry with db = "STATSGO"; these data are linked to mapunit and (national) legend just like mupolygon.

Natural Resources - Soil and Land - R
Published by brownag about 5 years ago

soilDB - soilDB 2.5.8

Updates since last CRAN release on 2020-01-29.

soilDB manual

soilDB 2.5.8 (2020-10-20)

  • fetchNASIS / soilDB:::.rockFragmentSieve now uses fragment RV, soilDB:::.sieve uses < operator (https://github.com/ncss-tech/soilDB/issues/1)
  • fetchKSSL(..., returnMorphologicData=TRUE) now returns redoximorphic features by horizon
  • new function taxaExtent returns 800m gridded taxonomic grids for CONUS
  • seriesExtent can now return 800m gridded series extents for CONUS
  • SDA_spatialQuery can now retrieve SSURGO and STATSGO geometry c/o dschlaep (https://github.com/ncss-tech/soilDB/issues/141)
  • new import: data.table; beginning to implement data.table-aware methods

soilDB 2.5.7 (2020-09-03)

  • add fetchGDB for querying tabular data from SSURGO/gNATSGO/STATSGO File Geodatabases
  • add get_NOAA_GHCND() and get_NOAA_stations_nearXY() for batch queries of NOAA Daily Climate Data (requires free API token)
  • bug fix for fetchSDA_spatial with chunk.size > 1 resulting in duplicate data in result
  • major improvements to fetchSDA_spatial to handle queries that exceed JSON Serialization Limit
  • add fetchSoilGrids for point data queries to SoilGrids v2 API with SoilProfileCollection output

soilDB 2.5.6 (2020-06-16)

  • bug fixes in fetchKSSL related to vectorization, all arguments vectorized except for bbox
  • KSSL_VG_model output cleaned-up, now returns phi -> theta function

soilDB 2.5.3 (2020-03-22)

  • fetchKSSL is now fully vectorized and builds on new SoilWeb JSON API

soilDB 2.5.2 (2020-02-05)

  • add get_concentrations_from_NASIS_db() and get_phfmp_from_NASIS_db() for fetching Pedon Horizon Concentrations and Field Measured Properties from NASIS local database

Natural Resources - Soil and Land - R
Published by brownag over 5 years ago

soilDB - soilDB 2.5

soilDB 2.5

This is a release of soilDB with new functionality and documentation, updates to conform with aqp 1.19, as well as bug-fixes and other quality-of-life enhancements.

Notably: we are back on CRAN. Tests and examples have been altered to minimize likelihood of failure on CRAN check farm machines, which has been an on-going issue. By making tests that contact remote APIs skip if missing the nasis_local ODBC connection, we can effectively filter tests to run only on the local (work) machine.

Recent Changes

soilDB 2.5 (2020-01-23)

  • CRAN release
  • simplifyColorData and mix_and_clean_colors always use CIELAB colorspace for weighted averages, and best-available metric for transformation to Munsell notation
  • fetchSDA_spatial - new fetch function that simplifies getting spatial data associated with a vector of mukey or nationalmusym. The function has options for customizing result attribute table and is designed to automatically use makeChunks() to prevent timeout on large queries.
  • aqp::test_hz_logic is now deprecated -- refactored affected fetch functions

soilDB 2.4.3 (2020-01-07)

  • surface water depth added to fetchNASIS_pedons()
  • fetchNASIS() has @restrictions set automaticlly if data are populated
  • new function for accessing pedon RMF in local NASIS DB: get_RMF_from_NASIS_db()

Natural Resources - Soil and Land - R
Published by brownag about 6 years ago

soilDB - soilDB 2.4.1

This is a maintenance release of soilDB addressing bug-fixes, small enhancements, and documentation gaps. Dependencies have been reduced by moving some packages from IMPORTS to SUGGESTS.

Recent Changes

soilDB 2.3.9 (2019-07-25)

  • SDA_query() no longer writes temporary files, c/o suggestion from Kyle Bocinsky (#106 / #108)
  • fetchOSD() gets a sanity check to protect against going over GET request limits
  • makeChunks() added to util functions, useful for splitting data before sending API calls

soilDB 2.3.8 (2019-03-22)

soilDB 2.3.7 (2019-03-12)

  • sharpshootR added to SUGGESTS
  • fetchHenry() and fetchSCAN() now include water year/day (Oct 1 -- Sep 30)
  • HenryTimeLine() convenience function added
  • bug fix in fetchOSD(..., extended=TRUE) when no climate data available
  • bug fix in SDA_query()

soilDB 2.3.6 (2019-02-12)

  • simplifyFragmentData() and related functions now 4-5x faster
  • fetchOSD() now returns metadata when extended=TRUE

Natural Resources - Soil and Land - R
Published by dylanbeaudette over 6 years ago

soilDB - soilDB 2.3

The source code for soilDB 2.3 has posted to CRAN, expecting binary packages later this week.

The soilDB package contains a convenient interface to many USDA-NCSS soil databases, including:

  • SDA: SSURGO/STATSGO
  • NASIS
  • KSSL via SoilWeb
  • An approximate "soil series" database via SoilWeb
  • Henry Soil Temperature and Water Database
  • SCAN/SNOTEL
  • CDEC

New / Updated Documentation

Enhancements

  • new function for exploring soil series co-occurrence data: siblings()
  • fetchOSD gets an overhaul, new API and features
  • fetchOSD(..., extended=TRUE) gets competing soil series
  • new function for spatial queries: SDA_spatialQuery(), still needs testing and documentation
  • experimental interface to SoillWeb OSD fulltext search: OSDquery()
  • get_mutext_from_NASIS_db() added for extraction of map unit text notes
  • exposing some of the internal functionality used by fetchHenry

Bug Fixes

Misc. Changes

  • removed old sample gSSURGO chunk and related documentation
  • updated loafercreek and gopheridge sample datasets and manual page to reflect latest fetchNASIS

Natural Resources - Soil and Land - R
Published by dylanbeaudette about 7 years ago