diff --git a/.Rbuildignore b/.Rbuildignore index 2d0d5da6..448d8830 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -16,3 +16,5 @@ README.Rmd ^CRAN-SUBMISSION$ ^data-raw$ ^CITATION\.cff$ +^doc$ +^Meta$ diff --git a/.gitignore b/.gitignore index 3ff6fc9f..ff605604 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,5 @@ docs/reference/*.pdf README_files docs inst/doc +/doc/ +/Meta/ diff --git a/DESCRIPTION b/DESCRIPTION index 99cc0afe..2316f61a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,6 +19,7 @@ URL: https://ncss-tech.github.io/soilDB/, https://ncss-tech.github.io/AQP/ BugReports: https://github.com/ncss-tech/soilDB/issues RoxygenNote: 7.2.3 Encoding: UTF-8 +Language: en-US Roxygen: list(markdown = TRUE) LazyData: false VignetteBuilder: knitr diff --git a/R/fetchSoilGrids.R b/R/fetchSoilGrids.R index 29d313be..db7af362 100644 --- a/R/fetchSoilGrids.R +++ b/R/fetchSoilGrids.R @@ -41,7 +41,7 @@ #' - **Common soil chemical and physical properties:** #' Poggio, L., de Sousa, L. M., Batjes, N. H., Heuvelink, G. B. M., Kempen, B., Ribeiro, E., and Rossiter, D.: SoilGrids 2.0: producing soil information for the globe with quantified spatial uncertainty, SOIL, 7, 217–240, 2021. DOI: \doi{https://doi.org/10.5194/soil-7-217-2021} #' - **Soil water content at different pressure heads:** -#' Turek, M.E., Poggio, L., Batjes, N. H., Armindo, R. A., de Jong van Lier, Q., de Sousa, L.M., Heuvelink, G. B. M. : Global mapping of volumetric water retention at 100, 330 and 15 000 cm suction using the WoSIS database, International Soil and Water Conservation Research, 11-2, 225-239, 2023. DOI: \doi{https://doi.org/10.1016/j.iswcr.2022.08.001} +#' Turek, M.E., Poggio, L., Batjes, N. H., Armindo, R. A., de Jong van Lier, Q., de Sousa, L.M., Heuvelink, G. B. M. : Global mapping of volumetric water retention at 100, 330 and 15000 cm suction using the WoSIS database, International Soil and Water Conservation Research, 11-2, 225-239, 2023. DOI: \doi{https://doi.org/10.1016/j.iswcr.2022.08.001} #' #' @importFrom utils packageVersion #' diff --git a/R/get_SDA_coecoclass.R b/R/get_SDA_coecoclass.R index c049632d..21988049 100644 --- a/R/get_SDA_coecoclass.R +++ b/R/get_SDA_coecoclass.R @@ -15,7 +15,7 @@ #' @param not_rated_value Default: `"Not assigned"` #' @param miscellaneous_areas logical. Include miscellaneous areas (non-soil components)? #' @param include_minors logical. Include minor components? Default: `TRUE`. -#' @param threshold integer. Default: `0`. Minimum combined component percentage (RV) for inclusion of a mapunit's ecological site in wide-format tabular sumamry. Used only for `method="all"`. +#' @param threshold integer. Default: `0`. Minimum combined component percentage (RV) for inclusion of a mapunit's ecological site in wide-format tabular summary. Used only for `method="all"`. #' @param dsn Path to local SQLite database or a DBIConnection object. If `NULL` (default) use Soil Data Access API via `SDA_query()`. #' @export get_SDA_coecoclass <- function(method = "None", diff --git a/inst/WORDLIST b/inst/WORDLIST index dff0ec37..b438dac3 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -9,13 +9,17 @@ AWM Abbema Albers Alfisols +Armindo +Aronia BBOX BD BLM Batjes Bioaccumulation +Biochar Biosolids Bocinsky +Bohn Bouten CEC CIE @@ -26,6 +30,7 @@ CMECS CODELABEL CONUS CRS +CZSS CaCO CaCl Caliche @@ -47,10 +52,10 @@ DAYMET DBH DBIConnection DMU +DOI Deadweight Deschutes Desertic -DirectDownLoad Disking DisplayLabel DomainID @@ -66,19 +71,22 @@ Eelgrass Electrial Erodibility Extractable +FGDB FOTG FSG Filterw GCS +GDAL GDB GDB's GDBs -GDGHome +GEOMETRYCOLLECTION GHCND GRL Genuchten GeoJSON GeoPackage +GeoTIFF Geochemical Geodatabase Geodatabases @@ -93,17 +101,21 @@ HTTPS Hayland Helens Heuvelink +Highbush Hillslope Hydrologic IRR ISDH +ISRIC ISRIC's ISSR IUSS Infil +Interp Irr JMS JSON +Jong KSSL Karner Kempen @@ -111,19 +123,22 @@ Kf Ki Klamath Kosugi +Krueger LAWR LDM LEP LIMS LRADT +LZW Leij -MAAT +Lier METACRAN MLRA MLRAs MSST MUKEY MUKEYS +MULTIPOLYGON MWST MacOS Malheur @@ -151,6 +166,7 @@ NCCPI NCDC NCSS NIRR +NLI NOAA NPS NRCS @@ -168,7 +184,6 @@ Ochoco Okanogan Operability Oxalate -PGI PIA POSIXlt PRCP @@ -206,6 +221,8 @@ Roxygen SAR SDA SG +SHSI +SLAMM SMR SMS SNOTEL @@ -224,6 +241,7 @@ SSURGO STATSGO STO STR +Salinization Schaap Schlaepfer Septage @@ -239,6 +257,7 @@ SoilWeb SoillWeb Soilscapes SpatRaster +SpatVector SpatialLines SpatialPoints SpatialPolygonDataFrame @@ -250,8 +269,11 @@ Sys TAVG TMAX TMIN +TROP Trafficability +Turek UCD +UCDavis URB USFS Umatilla @@ -262,7 +284,6 @@ Vadose Veh Ver Vinifera -WAQ WCS WDIRV WGS @@ -277,6 +298,7 @@ Wegner Wenatchee Windthrow Winema +WoSIS XMLSchema XRD Yonggen @@ -306,9 +328,9 @@ argi argic argillic aridic -aspx attr awc +balancer bbox bdod caco @@ -339,13 +361,11 @@ cosoilmoist cosurfmorphgc cosurfmorphhpp cosurfmorphss -cran createStaticNASIS cryic cryo cryoturbation cumulic -datagateway datamapunit datatypes datums @@ -374,6 +394,7 @@ dystro ec ecec ecoclass +ecoclassid ecosite edu endo @@ -423,6 +444,7 @@ freeiron fulltext fulv fulvi +gNATGSO gNATSGO gSSURGO gage @@ -441,7 +463,6 @@ geomposmntn geompostrce getHzErrorsPedonPC ggplot -github glac glacic glossaquic @@ -485,7 +506,6 @@ hzname illuvial ing interfingered -io joaquin jornada jsonlite @@ -516,6 +536,7 @@ loafercreek luvi makeChunks mapunit +mapunit's mapunits mapview mcacl @@ -541,7 +562,6 @@ natr natri natric ncdc -ncss nm nmsu noaa @@ -591,8 +611,10 @@ psammo pscbotdepth psctopdepth ptotal +quadrat quartzi rasterVis +rasters rcasiteid rda recalibration @@ -623,6 +645,7 @@ sandvf sapr sapric sar +saturationt sc serializer seriesExtent @@ -656,6 +679,7 @@ sulf sulfi sulfic sulfo +sumamry sumbases surfaceshape taxclname @@ -665,6 +689,7 @@ taxorder taxsuborder taxtempregime techsoilservice +terra terric tfact th @@ -718,6 +743,7 @@ wps wsatiated wtenthbar wthirdbar +wv www xanthic xer diff --git a/man/fetchSoilGrids.Rd b/man/fetchSoilGrids.Rd index 92a1c051..8ba1fe70 100644 --- a/man/fetchSoilGrids.Rd +++ b/man/fetchSoilGrids.Rd @@ -131,7 +131,7 @@ Find out more information about the SoilGrids and GlobalSoilMap products here: \item \strong{Common soil chemical and physical properties:} Poggio, L., de Sousa, L. M., Batjes, N. H., Heuvelink, G. B. M., Kempen, B., Ribeiro, E., and Rossiter, D.: SoilGrids 2.0: producing soil information for the globe with quantified spatial uncertainty, SOIL, 7, 217–240, 2021. DOI: \doi{https://doi.org/10.5194/soil-7-217-2021} \item \strong{Soil water content at different pressure heads:} -Turek, M.E., Poggio, L., Batjes, N. H., Armindo, R. A., de Jong van Lier, Q., de Sousa, L.M., Heuvelink, G. B. M. : Global mapping of volumetric water retention at 100, 330 and 15 000 cm suction using the WoSIS database, International Soil and Water Conservation Research, 11-2, 225-239, 2023. DOI: \doi{https://doi.org/10.1016/j.iswcr.2022.08.001} +Turek, M.E., Poggio, L., Batjes, N. H., Armindo, R. A., de Jong van Lier, Q., de Sousa, L.M., Heuvelink, G. B. M. : Global mapping of volumetric water retention at 100, 330 and 15000 cm suction using the WoSIS database, International Soil and Water Conservation Research, 11-2, 225-239, 2023. DOI: \doi{https://doi.org/10.1016/j.iswcr.2022.08.001} } } \author{ diff --git a/man/get_SDA_coecoclass.Rd b/man/get_SDA_coecoclass.Rd index 8a7c758a..26c7e001 100644 --- a/man/get_SDA_coecoclass.Rd +++ b/man/get_SDA_coecoclass.Rd @@ -40,7 +40,7 @@ get_SDA_coecoclass( \item{include_minors}{logical. Include minor components? Default: \code{TRUE}.} -\item{threshold}{integer. Default: \code{0}. Minimum combined component percentage (RV) for inclusion of a mapunit's ecological site in wide-format tabular sumamry. Used only for \code{method="all"}.} +\item{threshold}{integer. Default: \code{0}. Minimum combined component percentage (RV) for inclusion of a mapunit's ecological site in wide-format tabular summary. Used only for \code{method="all"}.} \item{dsn}{Path to local SQLite database or a DBIConnection object. If \code{NULL} (default) use Soil Data Access API via \code{SDA_query()}.} } diff --git a/vignettes/fetchNASIS.Rmd b/vignettes/fetchNASIS.Rmd index 0e78f44c..c687999f 100644 --- a/vignettes/fetchNASIS.Rmd +++ b/vignettes/fetchNASIS.Rmd @@ -1,11 +1,6 @@ --- title: "fetchNASIS(from='pedons') Columns" -output: - rmarkdown::html_document: - toc: true - toc_float: - toc_collapsed: true - toc_depth: 3 +output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{fetchNASIS(from='pedons') Columns} %\VignetteEngine{knitr::rmarkdown} diff --git a/vignettes/wcs-ssurgo.Rmd b/vignettes/wcs-ssurgo.Rmd index 025ca09b..cb82cf73 100644 --- a/vignettes/wcs-ssurgo.Rmd +++ b/vignettes/wcs-ssurgo.Rmd @@ -2,7 +2,7 @@ title: "Map Unit Key Grids and Thematic Maps of Soil Survey Geographic (SSURGO) Data" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Map Unit Key Grids and Thematic Maps of SSURGO Data} + %\VignetteIndexEntry{Map Unit Key Grids and Thematic Maps of Soil Survey Geographic (SSURGO) Data} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} ---