fetchLDM()
add support for area_type
with local database connections (dsn
argument)fetchSCAN()
(#184) thanks to new WCIS APIcreateSSURGO()
bug fixes following changes in 2.8.3
gpkg_contents
for GeoPackage files failed to add entries for "features" data_typefilename
argument not properly handled in some casesSDA_query()
handle another possible failure point in error handling codecreateStaticNASIS()
use odbc::dbListFields()
instead of odbc::odbcConnectionColumns()
ISSR800.wcs()
and soilColor.wcs()
now set color table internally when possibleSDA_query()
updates
createSSURGO()
: added support for creating DuckDB, PostgreSQL, and other DBI-compatible databases (#352) via conn
argumentfetchSDA()
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 suggestionfetchNASIS()
/get_extended_data_from_NASIS_db()
: fix conversion of codes to labels for microrelieffetchSCAN()
: fix header format; thanks to @dschlaep for reporting and providing a fixmukey.wcs()
) and metadata have been updated for FY2024
ISSR800.wcs()
source) is still using FY2023/FY2022 dataget_SDA_coecoclass()
default data returned for methods "Dominant Component", "Dominant Condition" and "None" now include localphase
columnget_soilseries_from_NASIS()
and get_competing_soilseries_from_NASIS()
: add SS
argument for parity with all other NASIS "get" methods
FALSE
for backward compatibility/common use casesget_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"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
argumentSDA_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
argumentsimplifyFragmentData()
/ simplifyArtifactData()
efficiency improvement when all records are missing dataget_mapunit_from_NASIS()
, get_lmuaoverlap_from_NASIS()
and get_legend_from_NASIS()
gain areatypename
argument used for filtering legends by areatypename
.
"Non-MLRA Soil Survey Area"
and "MLRA Soil Survey Area"
. Set to NULL
for no filter.waterDayYear()
and summarizeSoilTemperature()
for leap years (#333)fetchSoilGrids()
upgrades
data.frame
outputSys.sleep()
to conform with ISRIC "Fair Use" policyfetchSDA_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
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.get_SDA_interpretation()
when dsn
refers to a local SQLite source
and in concatenation of reason string when wide_reason=TRUE
createSSURGO()
updates:
"mupolygon"
rather than "soilmu_a"
).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.metadata(x)$created
(#235)area_type
argument to fetchLDM()
for non-SSA area queries (#328)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)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).
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'")
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 rectanglemethod="convexhull"
calculates the convex hullmethod="union"
returns a MULTIPOLYGONmethod="collection"
returns a GEOMETRYCOLLECTIONBug 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
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()
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
get_mapunit_from_SDA()
: handle possibility of mapunit-level SDA query failure
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
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()
gpkg_contents
when output filename
is a GeoPackageFix 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
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)
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
NASISChoiceList()
related to #273get_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)
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
uncode()
replaced \(x)
syntax inadvertently included in a recent update to fix R < 4.1 compatibility; thanks to @cbrueffer for catching this (https://github.com/ncss-tech/soilDB/issues/262)!
get_SDA_property()
fixes for weighted average method (https://github.com/ncss-tech/soilDB/issues/229, https://github.com/ncss-tech/soilDB/issues/261)
fetchOSD()
now automatically encodes horizon distinctness codes to default depth offsets, stored in hz-level attr: hzd
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.
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
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 Roeus_ss_timeline
result to ASCIISDA_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.sp
and raster
which means soilDB
no longer requires the soon-to-retire rgdal
package.sf
and terra
, which have been added to Suggests.
sf
, SpatRaster
) will be returned by default rather than Spatial*DataFrame
or RasterLayer
from sp
and raster
.fetchSDA_spatial()
and SDA_spatialQuery()
gain as_Spatial
argument; when TRUE
equivalent (backward compatible) sp
and raster
data types are returned.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.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.plotplantinventory
table to get_vegplot_species_from_NASIS_db()
result; thanks to Zachary Van Abbema for suggestion and feedbackuncode()
are now cached within an R session which results in faster query processing times for users with a local NASIS database connection set up.
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.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"
)
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.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.downloadSSURGO()
for downloading/extraction of the SSURGO data by survey area from Web Soil Survey.createSSURGO()
for building of local databases as SQLite/Geopackage from one or more SSURGO exports.
downloadSSURGO()
, from NASIS or downloaded from other sources such as https://datagateway.nrcs.usda.gov/GDGHome_DirectDownLoad.aspx.fetchNASIS()
mixColors
argument used to toggle color mixing for pedon horizons with multiple colors per moisture state.
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.taxreaction
and taxfamhahatmatcl
to extended taxonomic informationsoilDB.NASIS.skip_uncode
) to bypass uncode()
in NASIS functions (mostly used for debugging or special database instances that come pre-decoded)fetchNASIS(from="components")
where local database connection was left open was fixedfetchLDM()
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)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 queryget_SDA_interpretation(method = "dominant condition")
now includes total_comppct_*
columns reflecting the summed component percentage of the dominant conditionpedlabsampnum
(KSSL Pedon Sample ID)waterYearDay()
bug fix for more specific (sub-daily) date-time formatsfetchSCAN()
better handling of empty results in multi-site queriesfetchNASIS("pedons")
no longer includes pmweathering
fetchNASIS("components")
no longer includes ecositeorigin
stringsAsFactors
argument to soilDB functions has been deprecated in favor of a package option
NASISDomainsAsFactor(TRUE)
to toggle package option soilDB.NASIS.DomainsAsFactor
fetchSDA_spatial
now supports by.col
"areaname"
, "mlraoffice"
, and "mouagencyresp"
; thanks to suggestion by Jay SkovlinfetchNASIS
fix for multiple site observation records with surface fragments; thanks to bug report from Brianna WegnerwaterYearDay()
use format and timezone for start date conversionfetchNASIS
fix for from="components", SS=FALSE
and queries where no NASIS local database is present (e.g. from SQLite source)NASIS_table_column_keys
dataset of NASIS primary and foreign keys by table name to include many more tablesfetchVegdata()
no longer errors for child table queries unless site/site observation/vegetation plot records are missingfetchOSD(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.get_SDA_property()
now works with mixed component and horizon-level properties; thanks to Matthieu Stigler for the bug reportget_SDV_legend_elements()
for fetching and parsing XML for Soil Data Viewer / Web Soil Survey-style symbol themes for soil interpretations from Soil Data AccessfetchNASIS()
pedon and component geomorphic summaries now include columns for landscape, microfeature, microrelief, 2D/3D morphometry, and slope shapefetchNASIS('pedons')
now uses simplifyFragmentData()
for surface fragmentsfetchSDA()
handle NULL component-level results with an informative errorfetchSDA()
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
get_NASIS_table_name_by_purpose()
fetchOSD()
gains surface shape proportions in extended shape_across
and shape_down
tablesSDA_spatialQuery()
what='mukey'
now works with db='STATSGO'
loafercreek
, gopheridge
and mineralKing
waterYearDay()
pass through format
argument for POSIX time conversionwaterDayYear()
and .formatDates()
allow optional format
and tz
argument; used for consistent POSIX time conversion in tests where date/time has granularity finer than one dayfetchSDA()
extensions for better handling of components with no horizon dataSDA_spatialQuery()
and processSDA_WKT()
fully use {sf}, replacing {sp} in these contextsSDA_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.loafercreek
, gopheridge
and mineralKing
from latest fetchNASIS()
results.processSDA_WKT()
: replaced {rgeos} with {wk} and {sf}SDA_spatialQuery()
: added query_string
argumentget_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 definitionsfetchNASIS()
upgrades: use data.table and base internally for data aggregationfetchNASIS("components")
now "sieves" rock fragments and human artifacts using same routines as for pedons; respects nullFragsAreZero
argumentfetchKSSL(..., returnGeochemicalData = TRUE)
safely returns 0-length data.frame
when no data availableget_OSD()
: Handle "NA" and type conversion for JSON results an convert spaces to underscores for file names as neededfetchSCAN()
: 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 timeoutget_SDA_muaggatt()
: add query_string
argument for parity with other "SSURGO on demand" / get_SDA_*()
functionsget_SDA_pmgroupname()
and get_SDA_hydric()
now support alternate aggregation methods.
get_SDA_pmgroupname()
is "dominant component"
, now also supports "dominant condition"
and "none"
.get_SDA_hydric()
is a map unit level aggregation of components and assigns new classes ; now supports "dominant component"
, "dominant condition"
and "none"
fetchNASIS(from="pedons")
now supports fill=TRUE
argument just like from="components"
to include pedons that have no horizon recordscreateStaticNASIS()
: column order should match NASIS, even if data types require reorder for ODBC driverfetchSoilGrids()
bug fixes, updates to metadata and references in documentation (https://github.com/ncss-tech/soilDB/issues/201)
nitrogen
values (conversion from cg/kg to g/kg)bdod
and nitrogen
(SoilGrids uncertainty layer always uses factor of 10 to create integers)progress
and verbose
arguments for text progress bar and additional message outputget_SDA_coecoclass()
SOD-style method for mapunit/component level summaries of ecological site and other vegetation class informationSDA_query()
and all functions that call SDA_query()
get proper column class handling (related to #190), however:
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"
, respectivelyget_soilseries_from_NASIS()
; now including taxonomic mineralogy class which may contain multiple parts for series with strongly contrasting control sectionsget_SDA_*()
methods
get_SDA_property(property = ...)
and get_SDA_interpretation(rulename = ...)
vectorization over property/rulename to work with any aggregation method.
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 resultget_SDA_property
: better handling of NULL, miscellaneous areas, and property-specific weighting
ISNULL(x, 0)
logic that affected weighted averages in presence of missing datainclude_minors=FALSE
includes only components where majcompflag = 'Yes'
in resultmiscellaneous_areas=FALSE
removes miscellaneous land types compkind
values from resultget_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
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 interfaceget_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
formativeElement
argument to taxaExtent()
(SoilWeb taxon extent function)
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 namefetchNASIS(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 tableget_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 failsDBI
and odbc
, replacing RODBC
dbConnectNASIS
and dbQueryNASIS
for NASIS access with read-only credentials, fetching query results, and closing the DBIConnection upon completiondsn
argument to specify a local "static" SQLite file containing NASIS tables, or custom DBIConnection to a database with NASIS schema
dsn = NULL
uses "nasis_local"
ODBC connection to local NASIS SQL Serveraqp::checkHzDepthLogic()
, powered by {data.table}get_SDA_property
, get_SDA_interpretation
, get_SDA_muaggatt
, get_SDA_hydric
, get_SDA_pmgroupname
OSDquery
gets a new argument (everything
) for searching the entire documentfetchNASIS(..., 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.HenryTimeLine
moved to {sharpshootR} packagemukey.wcs()
and ISSR800.wcs()
for hitting web coverage service (WCS) for gSSURGO, gNATSGO, and ISSR-800 gridsROSETTA()
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
.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 horizontaxaExtent
returns 800m gridded taxonomic grids for CONUSseriesExtent
can now return 800m gridded series extents for CONUSSDA_spatialQuery
can now retrieve SSURGO and STATSGO geometry c/o dschlaep (https://github.com/ncss-tech/soilDB/issues/141)data.table
; beginning to implement data.table-aware methods in aqp and soilDBfetchGDB
for querying tabular data from SSURGO/gNATSGO/STATSGO File Geodatabasesget_NOAA_GHCND()
and get_NOAA_stations_nearXY()
for batch queries of NOAA Daily Climate Data (requires free API token)fetchSDA_spatial
with chunk.size
> 1 resulting in duplicate data in resultfetchSDA_spatial
to handle queries that exceed JSON Serialization LimitfetchSoilGrids
for point data queries to SoilGrids v2 API with SoilProfileCollection outputfetchKSSL(..., returnGeochemicalData=TRUE)
now returns geochemical, optical and XRD/thermal datafetchKSSL
related to vectorization, all arguments vectorized except for bbox
KSSL_VG_model
output cleaned-up, now returns phi -> theta functionfetchKSSL
is now fully vectorized and builds on new SoilWeb JSON APIget_concentrations_from_NASIS_db()
and get_phfmp_from_NASIS_db()
for fetching Pedon Horizon Concentrations and Field Measured Properties from NASIS local databasefetchNASIS(from='components', fill=TRUE, rmHzErrors=TRUE)
in context of new ::hzDepthTests()
and non-unique chiid
due to NA
values introduced by fill
simplifyColorData
and mix_and_clean_colors
always use CIELAB colorspace for weighted averages, and best-available metric for transformation to Munsell notationfetchSDA_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 functionsfetchNASIS_pedons()
fetchNASIS()
has @restrictions set automatically if data are populatedget_RMF_from_NASIS_db()
SDA_query()
related to multi-line records (https://github.com/ncss-tech/soilDB/issues/28)sharpshootR
added to SUGGESTS
fetchHenry()
and fetchSCAN() now include water year/day (Oct 1 -- Sep 30)HenryTimeLine()
convenience function addedfetchOSD(..., extended=TRUE)
when no climate data availableSDA_query()
simplifyFragmentData()
and related functions now 4-5x faster
fetchOSD()
now returns metadata when extended=TRUEstringr
fetchNASIS()
related to conversion of NULL fragment volume to 0
fetchKSSL()
can now automatically simplify colors with simplifyColors = TRUE
siblings()
fetchOSD(..., extended=TRUE)
gets competing soil seriesfetchOSD()
gets an overhaul, new API and featuresOSDquery()
loafercreek
and gopheridge
sample datasets and manual page to reflect latest fetchNASISRCurl
functions in favor of httr
alternatives (done)
+ switch from reshape
to reshape2
(pending)
+ possibly move some packages from SUGGESTS to IMPORTSreshape
package, will transition to reshape2
with soilDB 2.0
loafercreek
and gopheridge
sample datasetssuggests
, and checking for package availability at function runtime. this will make soilDB more portable, as not every user will want or need all functionality.