From 62c8f0bb040c91005556ce0599b52a2555dccffe Mon Sep 17 00:00:00 2001 From: "Andrew G. Brown" Date: Fri, 10 Mar 2023 12:59:40 -0800 Subject: [PATCH] spellcheck --- NEWS.md | 2 +- R/createSSURGO.R | 2 +- R/get_OSD.R | 2 +- R/get_RMF_from_NASIS_db.R | 2 +- R/get_cosoilmoist_from_SDA.R | 2 +- inst/WORDLIST | 133 +++++++++++++++++++++++++++++++---- man/downloadSSURGO.Rd | 2 +- man/fetchSDA.Rd | 2 +- man/get_OSD.Rd | 2 +- man/get_RMF_from_NASIS_db.Rd | 2 +- 10 files changed, 130 insertions(+), 21 deletions(-) diff --git a/NEWS.md b/NEWS.md index 62e3c604c..bd00bc6b1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -121,7 +121,7 @@ Bug fixes # 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 pr eviously 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) + * `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. diff --git a/R/createSSURGO.R b/R/createSSURGO.R index 8077381ad..5e34dd2e3 100644 --- a/R/createSSURGO.R +++ b/R/createSSURGO.R @@ -5,7 +5,7 @@ #' To specify the Soil Survey Areas you would like to obtain data you use a `WHERE` clause for query of `sacatalog` table such as `areasymbol = 'CA067'`, `"areasymbol IN ('CA628', 'CA067')"` or `areasymbol LIKE 'CT%'`. #' #' @param WHERE A SQL `WHERE` clause expression used to filter records in `sacatalog` table. Alternately `WHERE` can be any spatial object supported by `SDA_spatialQuery()` for defining the target extent. -#' @param areasymbols Character vector of soil survey area symbols e.g. `c("CA067", "CA077")`. Used in lieu of `WHERE` arugment. +#' @param areasymbols Character vector of soil survey area symbols e.g. `c("CA067", "CA077")`. Used in lieu of `WHERE` argument. #' @param destdir Directory to download ZIP files into. Default `tempdir()`. #' @param exdir Directory to extract ZIP archives into. May be a directory that does not yet exist. Each ZIP file will extract to a folder labeled with `areasymbol` in this directory. Default: `destdir` #' @param include_template Include the (possibly state-specific) MS Access template database? Default: `FALSE` diff --git a/R/get_OSD.R b/R/get_OSD.R index 9152a0d71..87339c940 100644 --- a/R/get_OSD.R +++ b/R/get_OSD.R @@ -8,7 +8,7 @@ #' #' @details The default `base_url` for `result="json"` is to JSON files stored in a GitHub repository that is regularly updated from the official source of Series Descriptions. Using format: `https://raw.githubusercontent.com/ncss-tech/SoilKnowledgeBase/main/inst/extdata/OSD/{LETTER}/{SERIES}.json` for JSON. And `"https://soilseriesdesc.sc.egov.usda.gov/OSD_Docs/{LETTER}/{SERIES}.html` is for `result="html"` (official source). #' -#' `fix_ocr_errors` by default is turned off (`FALSE`). When `TRUE`, assume that in color data hue/value/chroma lowercase "L" (`"l"`) is a 1, and a capital "O" is interpreted as zero. Also, in horizon desgignations assume lowercase "L" is a `1`, and a string that starts with `0` starts with the capital letter `"O"`. +#' `fix_ocr_errors` by default is turned off (`FALSE`). When `TRUE`, assume that in color data hue/value/chroma lowercase "L" (`"l"`) is a 1, and a capital "O" is interpreted as zero. Also, in horizon designations assume lowercase "L" is a `1`, and a string that starts with `0` starts with the capital letter `"O"`. #' @return For JSON result: A `data.frame` with 1 row per series, and 1 column per "section" in the OSD as defined in National Soil Survey Handbook. For TXT or HTML result a list of character vectors containing OSD text with 1 element per series and one value per line. #' @export #' @aliases get_OSD_JSON diff --git a/R/get_RMF_from_NASIS_db.R b/R/get_RMF_from_NASIS_db.R index 17861dfce..662408e11 100644 --- a/R/get_RMF_from_NASIS_db.R +++ b/R/get_RMF_from_NASIS_db.R @@ -10,7 +10,7 @@ #' #' @return a `list` with two `data.frame` objects: #' * `RMF`: contents of "phrdxfeatures" table, often >1 row per horizon -#' * `RMF_colors`: contents of "phredoxfcolor", pusually >1 row per record in "phrdxfeatures" +#' * `RMF_colors`: contents of "phredoxfcolor", usually >1 row per record in "phrdxfeatures" #' #' @export get_RMF_from_NASIS_db <- function(SS = TRUE, dsn = NULL) { diff --git a/R/get_cosoilmoist_from_SDA.R b/R/get_cosoilmoist_from_SDA.R index 68ef4ef25..9a4314830 100644 --- a/R/get_cosoilmoist_from_SDA.R +++ b/R/get_cosoilmoist_from_SDA.R @@ -1,6 +1,6 @@ #' @export #' @rdname fetchSDA -#' @param impute replace missing (i.e. `NULL`) values with `"Not_Populated"` forcategorical data, or the "RV" for numeric data or `201` cm if the "RV" is also`NULL` (default: `TRUE`) +#' @param impute replace missing (i.e. `NULL`) values with `"Not_Populated"` for categorical data, or the "RV" for numeric data or `201` cm if the "RV" is also`NULL` (default: `TRUE`) get_cosoilmoist_from_SDA <- function(WHERE = NULL, duplicates = FALSE, impute = TRUE, stringsAsFactors = NULL ) { diff --git a/inst/WORDLIST b/inst/WORDLIST index 0e68a888c..dff0ec37e 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -3,8 +3,10 @@ AGB AGR AKSite AOI +AQP ARS AWM +Abbema Albers Alfisols BBOX @@ -27,9 +29,18 @@ CRS CaCO CaCl Caliche +ChoiceDescription +ChoiceLabel +ChoiceName +ChoiceObsolete +ChoiceSequence +ChoiceValue Chufa Coccidioides +ColumnLogicalName +ColumnPhysicalName ColumnPhysicalNames +Colville Compactibility Crawfish DAYMET @@ -37,8 +48,15 @@ DBH DBIConnection DMU Deadweight +Deschutes Desertic +DirectDownLoad Disking +DisplayLabel +DomainID +DomainName +DomainRanked +ECOSHARE EPSG ESD ESG @@ -50,19 +68,32 @@ Erodibility Extractable FOTG FSG +Filterw GCS +GDB +GDB's +GDBs +GDGHome GHCND GRL Genuchten GeoJSON +GeoPackage Geochemical +Geodatabase Geodatabases +Geomorphic +Geopackage +Gifford +GiffordPinchot GlobalSoilMap Greatgroup Gridded HTTPS Hayland +Helens Heuvelink +Hillslope Hydrologic IRR ISDH @@ -81,8 +112,10 @@ Ki Klamath Kosugi LAWR +LDM LEP LIMS +LRADT Leij MAAT METACRAN @@ -93,8 +126,20 @@ MUKEY MUKEYS MWST MacOS +Malheur Mapunit +Matthieu Medusahead +MetadataDomainDetail +MetadataDomainMaster +MetadataTable +MetadataTableColumn +Microrelief +Monika +Morphometry +Morriss +MtBaker +MtHood Mtns Mualem Munsell @@ -116,22 +161,31 @@ Nemes Nonirrigated O'Geen ODBC +OGC OSD OSDquery +Ochoco +Okanogan Operability Oxalate PGI PIA POSIXlt +PRCP +PREC PROJ Palouse Paolucci +Pedology Pedon PedonPC Pedons Pedotransfer +Pinchot Poggio Proc +Propellor +Pyranometer RCurl RDC RFS @@ -142,29 +196,40 @@ RSQLite RaCA RangeDB Rangeland +RasterLayer Resour Ribeiro Roadfill +RogueRiver Rossiter +Roxygen SAR SDA SG SMR +SMS SNOTEL +SNWD SOH SPC SPDF SPSD +SRI +SRIs SSDS +SSL SSOAP SSSA SSURGO STATSGO +STO STR Schaap Schlaepfer Septage Shortleaf +Siskiyou +Siuslaw Skaggs Sodicity SoilGrids @@ -173,18 +238,24 @@ SoilTaxonomy SoilWeb SoillWeb Soilscapes +SpatRaster SpatialLines SpatialPoints SpatialPolygonDataFrame SpatialPolygons -SpatialPolygonsDataFrame +Stigler Storie Stormwater Sys +TAVG +TMAX +TMIN Trafficability UCD URB USFS +Umatilla +Umpqua Unrubbed VNIR Vadose @@ -193,12 +264,19 @@ Ver Vinifera WAQ WCS +WDIRV WGS WKT WLF WMS +WSPDV +WTEQ Walkinshaw +WallowaWhitman +Wegner +Wenatchee Windthrow +Winema XMLSchema XRD Yonggen @@ -228,12 +306,15 @@ argi argic argillic aridic +aspx +attr awc bbox bdod caco calci calcic +capacitive casoilresource cdo cec @@ -255,13 +336,19 @@ copedon corcon corsteel cosoilmoist +cosurfmorphgc +cosurfmorphhpp +cosurfmorphss +cran createStaticNASIS cryic cryo cryoturbation cumulic +datagateway datamapunit datatypes +datums dbfifteenbar dbovendry dbtenthbar @@ -293,7 +380,6 @@ endo entic epi epipedon -epsg esd eutr eutric @@ -321,6 +407,7 @@ fluv fluvaquentic formatLandformString formatParentMaterialString +fractionated fraggt fraghard fragi @@ -338,6 +425,8 @@ fulv fulvi gNATSGO gSSURGO +gage +gdb geoUnit geochem geochemical @@ -346,20 +435,23 @@ geodatabases geojson geomorph geomorphic +geomposflats +geomposhill +geomposmntn +geompostrce getHzErrorsPedonPC ggplot +github glac glacic glossaquic glossic glosso -gnatsgo gopheridge grano gridExtra gridded grossarenic -gssurgo gypsi gypsic gzip @@ -371,6 +463,7 @@ hemi hemic hg hillslope +hillslopeprof histo horizonation http @@ -390,13 +483,12 @@ hzdepb hzdept hzname illuvial -img ing -init interfingered io joaquin jornada +jsonlite kPa kandi kandic @@ -412,6 +504,7 @@ kwfact lamellae lamellic landform +langley lawr lep leptic @@ -423,18 +516,22 @@ loafercreek luvi makeChunks mapunit +mapunits mapview mcacl mdb melan melanic melano +microfeature +microrelief mineralking mis mmol molli mollic morphologic +morphometry mukey munsell mutext @@ -444,14 +541,15 @@ natr natri natric ncdc +ncss nm nmsu noaa +npar nrcs nullFragsAreZero ocd ocs -odbc ombroaquic osoluble oxyaquic @@ -470,7 +568,11 @@ petrogypsic petronodic ph phh +phiid phoxidized +phrdxfeatures +phrdxfiid +phredoxfcolor pkey pkeyref plac @@ -497,7 +599,6 @@ recalibration redoximorphic reflectance returnMorphologicData -rgb rgdal rgeos rhod @@ -522,10 +623,14 @@ sandvf sapr sapric sar +sc serializer seriesExtent seriesExtentAsGmap +shapeacross +shapedown sharpshootR +shp sieveno siltco siltfine @@ -533,7 +638,9 @@ silttotal simplifyColorData simplifyFragmentData sodic +soilColor soilVWC +soilseries soilsurvey soiltemp soilweb @@ -543,26 +650,29 @@ sp spatialQuery sphagnic sphagno -ssurgoOnDemand -stringsAsFactors +streamflow subtractive sulf sulfi sulfic sulfo sumbases +surfaceshape taxclname taxhistory taxonname taxorder taxsuborder taxtempregime +techsoilservice terric tfact th thaptic thapto +thermistor timeseries +timezones torri torric turbic @@ -576,6 +686,7 @@ umbr umbri umbric uncode +unhandled usda ust usti @@ -599,7 +710,6 @@ vitr vitri vitric waterlevel -wcc webservice weg wei @@ -617,6 +727,5 @@ xmax xmin xrd yeardatatypeid -yellowgreen ymax ymin diff --git a/man/downloadSSURGO.Rd b/man/downloadSSURGO.Rd index 0567f6a18..83a1858f6 100644 --- a/man/downloadSSURGO.Rd +++ b/man/downloadSSURGO.Rd @@ -19,7 +19,7 @@ downloadSSURGO( \arguments{ \item{WHERE}{A SQL \code{WHERE} clause expression used to filter records in \code{sacatalog} table. Alternately \code{WHERE} can be any spatial object supported by \code{SDA_spatialQuery()} for defining the target extent.} -\item{areasymbols}{Character vector of soil survey area symbols e.g. \code{c("CA067", "CA077")}. Used in lieu of \code{WHERE} arugment.} +\item{areasymbols}{Character vector of soil survey area symbols e.g. \code{c("CA067", "CA077")}. Used in lieu of \code{WHERE} argument.} \item{destdir}{Directory to download ZIP files into. Default \code{tempdir()}.} diff --git a/man/fetchSDA.Rd b/man/fetchSDA.Rd index 086891e1c..77d2fff1f 100644 --- a/man/fetchSDA.Rd +++ b/man/fetchSDA.Rd @@ -88,7 +88,7 @@ classes, which can waste space in tables and figures.} \item{rmHzErrors}{should pedons with horizonation errors be removed from the results? (default: FALSE)} -\item{impute}{replace missing (i.e. \code{NULL}) values with \code{"Not_Populated"} forcategorical data, or the "RV" for numeric data or \code{201} cm if the "RV" is also\code{NULL} (default: \code{TRUE})} +\item{impute}{replace missing (i.e. \code{NULL}) values with \code{"Not_Populated"} for categorical data, or the "RV" for numeric data or \code{201} cm if the "RV" is also\code{NULL} (default: \code{TRUE})} } \value{ A data.frame or SoilProfileCollection object. diff --git a/man/get_OSD.Rd b/man/get_OSD.Rd index 412276356..05b9752d3 100644 --- a/man/get_OSD.Rd +++ b/man/get_OSD.Rd @@ -35,7 +35,7 @@ Get Official Series Description Data from JSON, HTML or TXT sources \details{ The default \code{base_url} for \code{result="json"} is to JSON files stored in a GitHub repository that is regularly updated from the official source of Series Descriptions. Using format: \verb{https://raw.githubusercontent.com/ncss-tech/SoilKnowledgeBase/main/inst/extdata/OSD/\{LETTER\}/\{SERIES\}.json} for JSON. And \verb{"https://soilseriesdesc.sc.egov.usda.gov/OSD_Docs/\{LETTER\}/\{SERIES\}.html} is for \code{result="html"} (official source). -\code{fix_ocr_errors} by default is turned off (\code{FALSE}). When \code{TRUE}, assume that in color data hue/value/chroma lowercase "L" (\code{"l"}) is a 1, and a capital "O" is interpreted as zero. Also, in horizon desgignations assume lowercase "L" is a \code{1}, and a string that starts with \code{0} starts with the capital letter \code{"O"}. +\code{fix_ocr_errors} by default is turned off (\code{FALSE}). When \code{TRUE}, assume that in color data hue/value/chroma lowercase "L" (\code{"l"}) is a 1, and a capital "O" is interpreted as zero. Also, in horizon designations assume lowercase "L" is a \code{1}, and a string that starts with \code{0} starts with the capital letter \code{"O"}. } \examples{ \dontshow{if (curl::has_internet()) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} diff --git a/man/get_RMF_from_NASIS_db.Rd b/man/get_RMF_from_NASIS_db.Rd index d42b9f146..5e5e6433e 100644 --- a/man/get_RMF_from_NASIS_db.Rd +++ b/man/get_RMF_from_NASIS_db.Rd @@ -15,7 +15,7 @@ get_RMF_from_NASIS_db(SS = TRUE, dsn = NULL) a \code{list} with two \code{data.frame} objects: \itemize{ \item \code{RMF}: contents of "phrdxfeatures" table, often >1 row per horizon -\item \code{RMF_colors}: contents of "phredoxfcolor", pusually >1 row per record in "phrdxfeatures" +\item \code{RMF_colors}: contents of "phredoxfcolor", usually >1 row per record in "phrdxfeatures" } } \description{