Leverage markdown in help documentation

DESCRIPTION

@@ -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

R/background.R

@@ -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

R/benchmarks.R

@@ -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

R/cities.R

@@ -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

R/counties.R

 #' 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

R/dl.R

@@ -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

R/esrp.R

@@ -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

R/facilities.R

 #' 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

R/gwl.R

@@ -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

R/idaho.R

@@ -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

R/inl.R

 #' 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

R/labels.R

@@ -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

R/lakes.R

@@ -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

R/mountains.R

@@ -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

R/parameters.R

@@ -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

R/projection.R

 #' 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"
\ No newline at end of file

R/roads.R

@@ -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"
\ No newline at end of file

R/samples.R

@@ -5,86 +5,90 @@
 #' 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