Commit 62918289 authored by Fisher, Jason C.'s avatar Fisher, Jason C.
Browse files

Leverage markdown in help documentation

parent a6e5a08e
Pipeline #58605 passed with stage
in 10 minutes and 33 seconds
......@@ -35,4 +35,5 @@ Copyright: This software is in the public domain because it contains materials
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
......@@ -8,20 +8,20 @@
#' and are not influenced by waste and wastewater disposal at the INL
#' (Bartholomay and Hall, 2016, p. 3).
#'
#' @format A data frame with 73 records and 4 variables:
#' @format A data frame with 4 variables:
#' \describe{
#' \item{\code{parm_cd}}{U.S. Geological Survey 5-digit parameter code,
#' see \code{\link{parameters}} dataset for details.}
#' \item{\code{bkgrd_min}, \code{bkgrd_max}}{minimum and maximum limits of background concentration}
#' \item{\code{reference}}{source of background concentration limits.
#' \item{`parm_cd`}{U.S. Geological Survey 5-digit parameter code,
#' see [`parameters`] dataset for details.}
#' \item{`bkgrd_min`, `bkgrd_max`}{minimum and maximum limits of background concentration}
#' \item{`reference`}{source of background concentration limits.
#' Reference citations are:
#' \code{"Bartholomay and Hall (2016)"},
#' \code{"Knobel and others (1992)"},
#' \code{"Michel (1989)"}, and
#' \code{"Orr and others (1991)"}.}
#' `"Bartholomay and Hall (2016)"`,
#' `"Knobel and others (1992)"`,
#' `"Michel (1989)"`, and
#' `"Orr and others (1991)"`.}
#' }
#' Row names for the data frame indicate the Substance Registry Services
#' (\href{https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do}{SRS})
#' ([SRS](https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do))
#' name and parameter units.
#'
#' @references Bartholomay, R.C., and Hall, L.F., 2016, Evaluation of background concentrations
......@@ -50,5 +50,4 @@
#' @examples
#' str(background)
#' rownames(background)
#'
"background"
\ No newline at end of file
......@@ -3,32 +3,32 @@
#' Water-quality benchmark concentrations of
#' selected radionuclides, organic compounds, and chemical constituents.
#' Benchmarks include:
#' the U.S. Environmental Protection Agency (USEPA) Maximum Contaminant Levels
#' (\href{https://www.epa.gov/ground-water-and-drinking-water/national-primary-drinking-water-regulations}{MCLs}) and
#' U.S. Environmental Protection Agency (USEPA) Maximum Contaminant Levels
#' ([MCLs](https://www.epa.gov/ground-water-and-drinking-water/national-primary-drinking-water-regulations)),
#' Human Health Benchmarks for Pesticides
#' (\href{https://iaspub.epa.gov/apex/pesticides/f?p=HHBP:home}{HHBPs}), and
#' the U.S. Geological Survey (USGS) Health-Based Screening Levels
#' (\href{https://water.usgs.gov/water-resources/hbsl/}{HBSLs}).
#' ([HHBPs](https://iaspub.epa.gov/apex/pesticides/f?p=HHBP:home)), and
#' U.S. Geological Survey (USGS) Health-Based Screening Levels
#' ([HBSLs](https://water.usgs.gov/water-resources/hbsl/)).
#'
#' @format A data frame with 74 records and 9 variables:
#' @format A data frame with 9 variables:
#' \describe{
#' \item{\code{parm_cd}}{USGS 5-digit parameter code, see \code{\link{parameters}} dataset for details.}
#' \item{\code{mcl}}{USEPA MCLs.}
#' \item{\code{hhbp_noncancer}}{USEPA Chronic Noncancer HHBPs}
#' \item{\code{hhbp_cancer_min}}{USEPA Carcinogenic HHBPs for a one-in-one million cancer risk.}
#' \item{\code{hhbp_cancer_max}}{USEPA Carcinogenic HHBPs for a one-in-ten thousand cancer risk.}
#' \item{\code{hbsl_noncancer}}{USGS Noncancer HBSLs}
#' \item{\code{hbsl_cancer_min}}{USGS Cancer HBSLs for a one-in-one million cancer risk.}
#' \item{\code{hbsl_cancer_max}}{USGS Cancer HBSLs for a one-in-ten thousand cancer risk.}
#' \item{\code{remark}}{comments}
#' \item{`parm_cd`}{USGS 5-digit parameter code, see [`parameters`] dataset for details.}
#' \item{`mcl`}{USEPA MCLs.}
#' \item{`hhbp_noncancer`}{USEPA Chronic Noncancer HHBPs}
#' \item{`hhbp_cancer_min`}{USEPA Carcinogenic HHBPs for a one-in-one million cancer risk.}
#' \item{`hhbp_cancer_max`}{USEPA Carcinogenic HHBPs for a one-in-ten thousand cancer risk.}
#' \item{`hbsl_noncancer`}{USGS Noncancer HBSLs}
#' \item{`hbsl_cancer_min`}{USGS Cancer HBSLs for a one-in-one million cancer risk.}
#' \item{`hbsl_cancer_max`}{USGS Cancer HBSLs for a one-in-ten thousand cancer risk.}
#' \item{`remark`}{comments}
#' }
#' Row names for the data frame indicate the Substance Registry Services
#' (\href{https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do}{SRS})
#' ([SRS](https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do))
#' name and parameter units.
#'
#' @source Many of the water-quality benchmarks were accessed from the
#' U.S. Geological Survey Health-Based Screening Levels database,
#' accessed on August 8, 2017, from \url{https://water.usgs.gov/water-resources/hbsl/}.
#' accessed on August 8, 2017, from <https://water.usgs.gov/water-resources/hbsl/>.
#' Benchmarks for total Trihalomethanes, Tritium, and Strontium-90 were
#' provided by the U.S. Environmental Protection Agency (2015).
#' Note that MCL benchmark values reported in millirem per year were
......@@ -46,5 +46,4 @@
#' @examples
#' str(benchmarks)
#' rownames(benchmarks)
#'
"benchmarks"
\ No newline at end of file
......@@ -2,13 +2,13 @@
#'
#' Cities and towns (populated places) in the vicinity of Idaho National Laboratory, eastern Idaho.
#'
#' @format A SpatialPointsDataFrame of the \pkg{sp} package with 24 records and 16 variables.
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' @format A SpatialPointsDataFrame of the \pkg{sp} package with 16 variables.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Department of Commerce, U.S. Census Bureau, Geography Division/Cartographic Products Branch.
#' Spatial extract from the Master Address File / Topologically Integrated Geographic Encoding and Referencing
#' (\href{https://catalog.data.gov/dataset/tiger-line-shapefile-2019-series-information-for-the-current-place-state-based-shapefile}{MAF/TIGER}) Database (MTDB),
#' 2019 data collection, released April 2, 2020.
#' ([MAF/TIGER](https://catalog.data.gov/dataset/tiger-line-shapefile-2019-series-information-for-the-current-place-state-based-shapefile))
#' Database (MTDB), 2019 data collection, released April 2, 2020.
#'
#' @keywords datasets
#'
......@@ -16,7 +16,7 @@
#' inlmisc::PlotMap(cities, dms.tick = TRUE)
#' sp::plot(cities, pch = 19, add = TRUE)
#' raster::text(cities, cities@data$NAME,
#' pos = 1, cex = 0.6)
#' pos = 1, cex = 0.6
#' )
#' str(cities@data)
#'
"cities"
\ No newline at end of file
#' County Boundaries
#'
#' Boundaries of counties
#' in the vicinity of Idaho National Laboratory, eastern Idaho, as of January 1, 2015.
#' Boundaries of counties in the vicinity of Idaho National Laboratory, eastern Idaho, as of January 1, 2015.
#'
#' @format A SpatialLines of the \pkg{sp} package with 45 features.
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Department of Commerce, U.S. Census Bureau, Geography Division/Cartographic Products Branch.
#' Spatial extract from the Master Address File / Topologically Integrated Geographic Encoding and Referencing
#' (\href{https://catalog.data.gov/dataset/tiger-line-shapefile-2019-series-information-for-the-current-place-state-based-shapefile}{MAF/TIGER}) Database (MTDB),
#' 2019 data collection, released April 2, 2020.
#' ([MAF/TIGER](https://catalog.data.gov/dataset/tiger-line-shapefile-2019-series-information-for-the-current-place-state-based-shapefile))
#' Database (MTDB), 2019 data collection, released April 2, 2020.
#'
#' @keywords datasets
#'
#' @examples
#' inlmisc::PlotMap(counties, dms.tick = TRUE)
#' sp::plot(counties, lty = 5, add = TRUE)
#'
"counties"
\ No newline at end of file
......@@ -3,15 +3,15 @@
#' Analytical method detection limits of selected radionuclides,
#' which are based on laboratory procedures.
#'
#' @format A data frame with 8 records and 6 variables:
#' @format A data frame with 6 variables:
#' \describe{
#' \item{\code{srsname}}{Substance Registry Services
#' (\href{https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do}{SRS}) name.}
#' \item{\code{parm_cd}}{U.S. Geological Survey 5-digit parameter code.}
#' \item{\code{parameter_units}}{parameter units}
#' \item{\code{lab_det_lim_va}}{laboratory detection limit concentration}
#' \item{\code{sdate}}{date that the detection limit went into effect.}
#' \item{\code{reference}}{source of detection limit.}
#' \item{`srsname`}{Substance Registry Services
#' ([SRS](https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do)) name.}
#' \item{`parm_cd`}{U.S. Geological Survey 5-digit parameter code.}
#' \item{`parameter_units`}{parameter units}
#' \item{`lab_det_lim_va`}{laboratory detection limit concentration}
#' \item{`sdate`}{date that the detection limit went into effect.}
#' \item{`reference`}{source of detection limit.}
#' }
#'
#' @source Detection limits reported by:
......@@ -29,15 +29,14 @@
#' Field methods and quality-assurance plan for water-quality activities and
#' water-level measurements, U.S. Geological Survey, Idaho National Laboratory, Idaho:
#' U.S. Geological Survey Open-File Report 2014--1146 (DOE/ID--22230), 64 p.
#' \url{https://pubs.usgs.gov/of/2014/1146/}.
#' <https://pubs.usgs.gov/of/2014/1146/>.
#'
#' Bodnar, L.Z., and Percival, D.R., eds., 1982,
#' Analytical Chemistry Branch procedures manual---Radiological and Environmental Sciences Laboratory:
#' U.S. Department of Energy Report IDO--12096 [variously paged].
#' U.S. Department of Energy Report IDO--12096 \[variously paged\].
#'
#' @keywords datasets
#'
#' @examples
#' str(dl)
#'
"dl"
\ No newline at end of file
......@@ -3,10 +3,10 @@
#' Boundary of the eastern Snake River Plain, Idaho.
#'
#' @format A SpatialPolygonsDataFrame of the \pkg{sp} package object with 1 feature and 1 variable.
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Geological Survey
#' \href{https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office}{Idaho National Laboratory Project Office}
#' [Idaho National Laboratory Project Office](https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office)
#'
#' @keywords datasets
#'
......@@ -14,5 +14,4 @@
#' inlmisc::PlotMap(esrp, dms.tick = TRUE)
#' sp::plot(esrp, col = "red", add = TRUE)
#' str(esrp@data)
#'
"esrp"
\ No newline at end of file
#' Idaho National Laboratory Facilities
#'
#' Federal research facilities at the
#' Idaho National Laboratory (\href{https://inl.gov/}{INL}).
#' Federal research facilities at the Idaho National Laboratory ([INL](https://inl.gov/)).
#'
#' @format A SpatialPolygonsDataFrame object with 7 features and 1 variable.
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Geological Survey
#' \href{https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office}{Idaho National Laboratory Project Office}
#' [Idaho National Laboratory Project Office](https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office)
#'
#' @keywords datasets
#'
......@@ -15,7 +14,7 @@
#' inlmisc::PlotMap(facilities, dms.tick = TRUE)
#' sp::plot(facilities, col = "red", add = TRUE)
#' raster::text(facilities, facilities@data$NAME,
#' cex = 0.6, pos = 1)
#' cex = 0.6, pos = 1
#' )
#' str(facilities@data)
#'
"facilities"
\ No newline at end of file
......@@ -3,17 +3,16 @@
#' Groundwater level measurements in wells in the
#' U.S. Geological Survey (USGS) water-level aquifer monitoring network,
#' Idaho National Laboratory and vicinity, Idaho.
#' Data was obtained from the National Water Information System
#' (\doi{10.5066/F7P55KJN}{NWIS}) (U.S. Geological Survey, 2020).
#' Data was obtained from the National Water Information System (NWIS) (U.S. Geological Survey, 2020).
#'
#' @format A data frame with 54,417 records and 5 variables:
#' @format A data frame with 5 variables:
#' \describe{
#' \item{\code{site_no}}{USGS site number}
#' \item{\code{lev_dt}}{date the water level was measured.}
#' \item{\code{lev_va}}{water level value, in feet below land surface.
#' \item{`site_no`}{USGS site number}
#' \item{`lev_dt`}{date the water level was measured.}
#' \item{`lev_va`}{water level value, in feet below land surface.
#' A water-level elevation may be calculated by subtracting the depth-to-water
#' (\code{lev_va}) from the land-surface elevation (\code{alt_va} in the \code{\link{sites}} dataset).}
#' \item{\code{lev_status_cd}}{a code indicating the status of the site
#' (`lev_va`) from the land-surface elevation (`alt_va` in the [`sites`] dataset).}
#' \item{`lev_status_cd`}{a code indicating the status of the site
#' at the time the water level was measured.
#' The codes and their meanings are:
#' "A" water level was affected by atmospheric pressure,
......@@ -24,8 +23,8 @@
#' "R" the site had been pumped recently,
#' "S" a nearby site that taps the same aquifer was being pumped, and
#' "X" the water level was affected by stage in nearby surface-water site.}
#' \item{\code{date_time}}{date and time the water level was measured.
#' Missing values of time were substituted with \dQuote{00:00} (12:00 midnight and start of day).}
#' \item{`date_time`}{date and time the water level was measured.
#' Missing values of time were substituted with "00:00" (12:00 midnight and start of day).}
#' }
#'
#' @source Data obtained from the NWIS database (U.S. Geological Survey, 2020).
......@@ -40,22 +39,29 @@
#' xlim <- as.Date(c("1989-01-01", "2019-01-01"))
#' d <- gwl[gwl$site_no == site_no, c("lev_dt", "lev_va")]
#' main <- sites@data[sites@data$site_no == site_no, "site_nm"]
#' ylab <- sprintf("Water level, in %s below land surface",
#' c("feet", "meters"))
#' inlmisc::PlotGraph(d, ylab = ylab, main = main, xlim = xlim,
#' ylab <- sprintf(
#' "Water level, in %s below land surface",
#' c("feet", "meters")
#' )
#' inlmisc::PlotGraph(d,
#' ylab = ylab, main = main, xlim = xlim,
#' type = "p", pch = 19, seq.date.by = "year",
#' conversion.factor = 0.3048,
#' center.date.labels = TRUE)
#' center.date.labels = TRUE
#' )
#' str(gwl)
#'
#' alt_va <- sites@data[sites@data$site_no == site_no, "alt_va"]
#' y <- alt_va - d$lev_va
#' ylab <- sprintf("Water level, in %s above sea level",
#' c("feet", "meters"))
#' inlmisc::PlotGraph(d$lev_dt, y, ylab = ylab, main = main,
#' ylab <- sprintf(
#' "Water level, in %s above sea level",
#' c("feet", "meters")
#' )
#' inlmisc::PlotGraph(d$lev_dt, y,
#' ylab = ylab, main = main,
#' xlim = xlim, type = "p", pch = 19,
#' seq.date.by = "year",
#' conversion.factor = 0.3048,
#' center.date.labels = TRUE)
#'
#' center.date.labels = TRUE
#' )
"gwl"
\ No newline at end of file
......@@ -4,17 +4,16 @@
#' a state in the northwestern region of the United States.
#'
#' @format A SpatialPolygons of the \pkg{sp} package with 1 feature.
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Department of Commerce, U.S. Census Bureau, Geography Division/Cartographic Products Branch.
#' Spatial extract from the Master Address File / Topologically Integrated Geographic Encoding and Referencing
#' (\href{https://catalog.data.gov/dataset/tiger-line-shapefile-2019-series-information-for-the-current-place-state-based-shapefile}{MAF/TIGER}) Database (MTDB),
#' 2019 data collection, released April 2, 2020.
#' ([MAF/TIGER](https://catalog.data.gov/dataset/tiger-line-shapefile-2019-series-information-for-the-current-place-state-based-shapefile))
#' Database (MTDB), 2019 data collection, released April 2, 2020.
#'
#' @keywords datasets
#'
#' @examples
#' inlmisc::PlotMap(idaho, dms.tick = TRUE)
#' sp::plot(idaho, col = "red", add = TRUE)
#'
"idaho"
\ No newline at end of file
#' Idaho National Laboratory Boundary
#'
#' Boundary of the Idaho National Laboratory (\href{https://inl.gov/}{INL}).
#' Boundary of the Idaho National Laboratory ([INL](https://inl.gov/)).
#'
#' @format A SpatialPolygonsDataFrame of the \pkg{sp} package object with 1 feature and 4 variables.
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Geological Survey
#' \href{https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office}{Idaho National Laboratory Project Office}
#' [Idaho National Laboratory Project Office](https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office)
#'
#' @keywords datasets
#'
......@@ -14,5 +14,4 @@
#' inlmisc::PlotMap(inl, dms.tick = TRUE)
#' sp::plot(inl, col = "red", add = TRUE)
#' str(inl@data)
#'
"inl"
\ No newline at end of file
......@@ -2,27 +2,27 @@
#'
#' Map labels in the vicinity of Idaho National Laboratory, eastern Idaho.
#'
#' @format A SpatialPointsDataFrame of the \pkg{sp} package with 50 features and 7 variables:
#' @format A SpatialPointsDataFrame of the \pkg{sp} package with multiple features and 7 variables:
#' \describe{
#' \item{\code{labels}}{text to be written}
#' \item{\code{cex}}{character expansion factor}
#' \item{\code{col}, \code{font}}{color and font to be used, respectively.}
#' \item{\code{srt}}{string rotation in degrees.}
#' \item{\code{halo}}{if true, a "halo" is printed around text.}
#' \item{\code{map}}{map index}
#' \item{`labels`}{text to be written}
#' \item{`cex`}{character expansion factor}
#' \item{`col`, `font`}{color and font to be used, respectively.}
#' \item{`srt`}{string rotation in degrees.}
#' \item{`halo`}{if true, a "halo" is printed around text.}
#' \item{`map`}{map index}
#' }
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Geological Survey
#' \href{https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office}{Idaho National Laboratory Project Office}
#' [Idaho National Laboratory Project Office](https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office)
#'
#' @keywords datasets
#'
#' @examples
#' inlmisc::PlotMap(labels, dms.tick = TRUE)
#' lab <- labels[labels$map == 1L, names(labels) != "map"]
#' for (i in seq_along(lab))
#' for (i in seq_along(lab)) {
#' do.call(raster::text, c(lab[i, ], as.list(lab@data[i, ])))
#' }
#' str(labels@data)
#'
"labels"
\ No newline at end of file
......@@ -2,8 +2,8 @@
#'
#' Perennial lakes and ponds in the vicinity of Idaho National Laboratory, eastern Idaho.
#'
#' @format A SpatialPolygonsDataFrame of the \pkg{sp} package with 155 features of 12 variables.
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' @format A SpatialPolygonsDataFrame of the \pkg{sp} package with multiple features and 12 variables.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Geological Survey (USGS), National Geospatial Technical Operations Center,
#' USGS National Hydrography Dataset (NHD) Medium Resolution for Idaho,
......@@ -12,8 +12,9 @@
#' @keywords datasets
#'
#' @examples
#' inlmisc::PlotMap(lakes, dms.tick = TRUE,
#' lakes = list(lakes, "lwd" = 1))
#' inlmisc::PlotMap(lakes,
#' dms.tick = TRUE,
#' lakes = list(lakes, "lwd" = 1)
#' )
#' str(lakes@data)
#'
"lakes"
\ No newline at end of file
......@@ -3,11 +3,11 @@
#' Simplified representation of the mountain ranges and buttes in the
#' vicinity of Idaho National Laboratory, eastern Idaho.
#'
#' @format A SpatialPolygonsDataFrame of the \pkg{sp} package with 17 features and 1 variable.
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' @format A SpatialPolygonsDataFrame of the \pkg{sp} package with multiple features and 1 variable.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Geological Survey
#' \href{https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office}{Idaho National Laboratory Project Office}
#' [Idaho National Laboratory Project Office](https://www.usgs.gov/centers/id-water/science/idaho-national-laboratory-project-office)
#'
#' @keywords datasets
#'
......@@ -15,5 +15,4 @@
#' inlmisc::PlotMap(mountains, dms.tick = TRUE)
#' sp::plot(mountains, col = "gray", add = TRUE)
#' str(mountains@data)
#'
"mountains"
\ No newline at end of file
......@@ -5,28 +5,29 @@
#' wells in the U.S. Geological Survey (USGS) water-quality aquifer monitoring network,
#' Idaho National Laboratory and vicinity, Idaho.
#'
#' @format A data frame with 74 records and 7 variables:
#' @format A data frame with 7 variables:
#' \describe{
#' \item{\code{parm_cd}}{USGS 5-digit parameter code}
#' \item{\code{parameter_group_nm}}{parameter group name, such as \code{"Radiochemical"}}
#' \item{\code{parameter_nm}}{long parameter name, such as \code{"Strontium-90, water, unfiltered, picocuries per liter"}}
#' \item{\code{casrn}}{Chemical Abstracts Service
#' (\href{https://www.cas.org/support/documentation/chemical-substances/faqs}{CAS}) registry number,
#' such as \code{"10098-97-2"} for Strontium-90}
#' \item{\code{srsname}}{Substance Registry Services
#' (\href{https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do}{SRS}) name,
#' such as \code{"Strontium-90"}}
#' \item{\code{parameter_units}}{parameter units.
#' \item{`parm_cd`}{USGS 5-digit parameter code}
#' \item{`parameter_group_nm`}{parameter group name, such as `"Radiochemical"`}
#' \item{`parameter_nm`}{long parameter name,
#' such as `"Strontium-90, water, unfiltered, picocuries per liter"`}
#' \item{`casrn`}{Chemical Abstracts Service
#' ([CAS](https://www.cas.org/support/documentation/chemical-substances/faqs)) registry number,
#' such as `"10098-97-2"` for Strontium-90}
#' \item{`srsname`}{Substance Registry Services
#' ([SRS](https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do)) name,
#' such as `"Strontium-90"`}
#' \item{`parameter_units`}{parameter units.
#' Unit abbreviations and descriptions are:
#' \code{"mg/L"} milligrams per liter,
#' \code{"mg/L as N"} milligrams per liter as Nitrogen,
#' \code{"ug/L"} microgram per liter, and
#' \code{"pCi/L"} picocuries per liter.}
#' \item{\code{siunitx}}{parameter units formatted for LaTeX using the \code{siunitx} package notation.}
#' `"mg/L"` milligrams per liter,
#' `"mg/L as N"` milligrams per liter as Nitrogen,
#' `"ug/L"` microgram per liter, and
#' `"pCi/L"` picocuries per liter.}
#' \item{`siunitx`}{parameter units formatted for LaTeX using the `siunitx` package notation.}
#' }
#'
#' @source USGS water data acquired from the National Water Information System (U.S. Geological Survey, 2019).
#' The \href{https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do}{SRS} name (\code{srsname})
#' The [SRS](https://iaspub.epa.gov/sor_internet/registry/substreg/home/overview/home.do) name (`srsname`)
#' for "Trihalomethanes (four), total, from SDWA NPDWR" was shorten to its preferred acronym "TTHM4".
#'
#' @references U.S. Geological Survey, 2019, National Water Information System---web services,
......@@ -36,5 +37,4 @@
#'
#' @examples
#' str(parameters)
#'
"parameters"
\ No newline at end of file
#' Coordinate Reference System
#'
#' \href{https://proj4.org/}{PROJ.4} string defining a
#' [PROJ.4](https://proj4.org/) string defining a
#' custom coordinate reference system (CRS) used by the
#' U.S. Geological Survey Idaho National Laboratory Project Office.
#' The CRS is based on the following attributes:
......@@ -18,5 +18,4 @@
#' @examples
#' crs <- sp::CRS(projection) # convert to class "CRS"
#' print(crs)
#'
"projection"
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......@@ -3,19 +3,20 @@
#' Primary and secondary roads in the vicinity of Idaho National Laboratory, eastern Idaho.
#'
#' @format A SpatialLinesDataFrame of the \pkg{sp} package with 1,616 features and 5 variables.
#' See \code{\link{projection}} dataset for coordinate reference system information.
#' See [`projection`] dataset for coordinate reference system information.
#'
#' @source U.S. Department of Commerce, U.S. Census Bureau, Geography Division/Cartographic Products Branch.
#' Spatial extract from the Master Address File / Topologically Integrated Geographic Encoding and Referencing
#' (\href{https://catalog.data.gov/dataset/tiger-line-shapefile-2019-series-information-for-the-current-place-state-based-shapefile}{MAF/TIGER}) Database (MTDB),
#' 2019 data collection, released April 2, 2020.
#' ([MAF/TIGER](https://catalog.data.gov/dataset/tiger-line-shapefile-2019-series-information-for-the-current-place-state-based-shapefile))
#' Database (MTDB), 2019 data collection, released April 2, 2020.
#'
#' @keywords datasets
#'
#' @examples
#' inlmisc::PlotMap(roads, dms.tick = TRUE,
#' roads = list(roads, "lwd" = 1))
#' inlmisc::PlotMap(roads,
#' dms.tick = TRUE,
#' roads = list(roads, "lwd" = 1)
#' )
#' sp::plot(roads[roads@data$PRISEC, ], col = "red", add = TRUE)
#' str(roads@data)
#'
"roads"
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#' Idaho National Laboratory and vicinity, Idaho.
#' Data was obtained from the National Water Information System (U.S. Geological Survey, 2019).
#'
#' @format A data frame with 159,554 records and 19 variables:
#' @format A data frame with 19 variables:
#' \describe{
#' \item{\code{site_no}}{USGS site identification number}
#' \item{\code{sample_dt}}{date sample was collected}
#' \item{\code{medium_cd}}{3-digit medium code that identifies the material type and quality assurance type of the sample.
#' \item{`site_no`}{USGS site identification number}
#' \item{`sample_dt`}{date sample was collected}
#' \item{`medium_cd`}{3-digit medium code that identifies the material type
#' and quality assurance type of the sample.
#' The codes and their meanings are:
#' \code{"WG"} water below land surface contained in the saturated zone (groundwater); and
#' \code{"WGQ"} groundwater quality-control (QC) sample.}
#' \item{\code{db_no}}{2-digit NWIS database number.
#' `"WG"` water below land surface contained in the saturated zone (groundwater); and
#' `"WGQ"` groundwater quality-control (QC) sample.}
#' \item{`db_no`}{2-digit NWIS database number.
#' The codes and their meanings are:
#' \code{"01"} is the environmental database, and
#' \code{"10"} is the quality-assurance (QA) database.}
#' \item{\code{anl_ent_cd}}{analyzing entity code of the organizational unit that
#' `"01"` is the environmental database, and
#' `"10"` is the quality-assurance (QA) database.}
#' \item{`anl_ent_cd`}{analyzing entity code of the organizational unit that
#' performed the sample analysis used to obtain the result.}
#' \item{\code{parm_cd}}{USGS 5-digit parameter code.
#' For example, the parameter code for Tritium is \code{"07000"}.}
#' \item{\code{remark_cd}}{1-digit remark code (result level) used to qualify the parameter value.
#' \item{`parm_cd`}{USGS 5-digit parameter code.
#' For example, the parameter code for Tritium is `"07000"`.}
#' \item{`remark_cd`}{1-digit remark code (result level) used to qualify the parameter value.
#' The codes and their meanings are:
#' \code{""} quantified value.
#' \code{"<"} actual value is known to be less than the value reported,
#' that is, the measured concentration is below the reporting limit (RL) and represented as a censored (or nondetection) value.
#' `""` quantified value.
#' `"<"` actual value is known to be less than the value reported,
#' that is, the measured concentration is below the reporting limit (RL)
#' and represented as a censored (or nondetection) value.
#' For censored values, the value reported is the RL.
#' \code{"E"} value is estimated, that is, the actual value is greater than the minimum detection limit (MDL)
#' `"E"` value is estimated, that is, the actual value is greater than the minimum detection limit (MDL)
#' and less than the laboratory reporting level (LRL).
#' \code{"R"} nondetect, result less than sample-specific critical level.
#' \code{"U"} material specifically analyzed for but not detected.
#' \code{"V"} value affected by contamination.}
#' \item{\code{result_va}}{parameter value;
#' see \code{parameter_units} variable in the \code{\link{parameters}} dataset for the units of measurement.}
#' \item{\code{lab_std_dev_va}}{laboratory standard deviation (SD).
#' `"R"` nondetect, result less than sample-specific critical level.
#' `"U"` material specifically analyzed for but not detected.
#' `"V"` value affected by contamination.}
#' \item{`result_va`}{parameter value;
#' see `parameter_units` variable in the [`projection`] dataset for the units of measurement.}
#' \item{`lab_std_dev_va`}{laboratory standard deviation (SD).
#' For radiochemical data, SD is determined from the counting error.
#' Prior to January 1, 2018, counting error was reported as two SD, therefore, these values were divied by 2.}
#' \item{\code{dqi_cd}}{1-digit data quality indicator code that indicates the review status of a result.
#' \item{`dqi_cd`}{1-digit data quality indicator code that indicates the review status of a result.
#' The codes and their meanings are:
#' \code{"A"} historical data,
#' \code{"S"} presumed satisfactory, and
#' \code{"R"} reviewed and accepted.}
#' \item{\code{rpt_lev_va}}{laboratory reporting limit in effect for the parameter and
#' `"A"` historical data,
#' `"S"` presumed satisfactory, and
#' `"R"` reviewed and accepted.}
#' \item{`rpt_lev_va`}{laboratory reporting limit in effect for the parameter and
#' method at the time the measurement was made.}
#' \item{\code{rpt_lev_cd}}{reporting level code that identifies the analytical reporting level appropriate for the analytical method.
#' \item{`rpt_lev_cd`}{reporting level code that identifies the analytical reporting level
#' appropriate for the analytical method.
#' The codes and their meanings are:
#' \code{"DLBLK"} detection limit by blank data;
#' \code{"DLDQC"} detection limit by DQCALC, lowest concentration that with 90 percent confidence will be exceeded no more than
#' 1 percent of the time when a blank sample is measured;
#' \code{"IRL"} interim reporting level, a temporary reporting level;
#' \code{"LRL"} laboratory reporting level, equal to twice the yearly-determined LT-MDL;
#' \code{"LT-MDL"} long-term method detection limit, a detection level derived by determining the standard deviation of
#' `"DLBLK"` detection limit by blank data;
#' `"DLDQC"` detection limit by DQCALC, lowest concentration that with 90 percent confidence will be
#' exceeded no more than 1 percent of the time when a blank sample is measured;
#' `"IRL"` interim reporting level, a temporary reporting level;
#' `"LRL"` laboratory reporting level, equal to twice the yearly-determined LT-MDL;
#' `"LT-MDL"` long-term method detection limit, a detection level derived by determining the standard deviation of
#' a minimum of 24 MDL spike sample measurements over an extended period of time;
#' \code{"MDL"} method detection limit, minimum concentration of a substance that can be measured and reported with
#' `"MDL"` method detection limit, minimum concentration of a substance that can be measured and reported with
#' a 99 percent confidence that the analyte concentration in greater than zero;
#' \code{"PQL"} practical quantitation limits;
#' \code{"MRL"} minimum reporting level, smallest measured concentration that can be reliably measured using
#' `"PQL"` practical quantitation limits;
#' `"MRL"` minimum reporting level, smallest measured concentration that can be reliably measured using
#' a given analytical method;
#' \code{"RLDQC"} reporting limit by DQCALC, is greater than or equal to two times the DLDQC;
#' \code{"SSLC"} sample-specific critical level, the calculated and reported value is below which the radiochemistry result