diff --git a/DESCRIPTION b/DESCRIPTION
index 7aca8b5a54bc6491cbb6767419029c3adcec22da..8645de8b42c9df00b7f977c167bd39903920e403 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: inldata
Title: Collection of Datasets for the USGS-INL Monitoring Networks
-Version: 1.2.7
+Version: 1.2.8
Authors@R: c(
person(given = c("Jason", "C."),
family = "Fisher", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 11581bfed5c1bd650cc9064f69c8e4d5a9823b21..10280c5953c0f4ae31acc2cda7f938a7f378a93d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# inldata 1.2.8
+
+- Refine the package installation notes in the top-level README file.
+- Adjust the order of items in the Exploration pull-down menu on the package website to enhance navigation.
+
# inldata 1.2.7
- Calculate the water level in feet above vertical datum (`gwl$sl_lev_va`) rather than download from NWIS.
diff --git a/README.Rmd b/README.Rmd
index f76c444dcdd0f1b9399dc81b17b5aae718dc9cb0..e53be8e852189e47c647b837f69f1155bb7c71f8 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -22,7 +22,7 @@ ran_samples <- samples$sample_dt |> range() |> format(format = "%Y")
The **inldata** package is a practical resource that consolidates datasets for the groundwater and surface-water monitoring networks of the U.S. Geological Survey - Idaho National Laboratory (USGS-INL). Managed by the [USGS-INL Project Office] in collaboration with the U.S. Department of Energy, it provides data from the Idaho National Laboratory and surrounding areas. This data is crucial in understanding the effects of waste disposal on the eastern Snake River Plain aquifer in southeastern Idaho and assessing the long-term availability of water.
-The package compiles historical water-quality samples from `r ran_samples[1]` to `r ran_samples[2]`, groundwater-level measurements from `r ran_gwl[1]` to `r ran_gwl[2]`, and surface-water measurements from `r ran_swm[1]` to `r ran_swm[2]`. Geospatial data, which outlines the areas of sample collection or observation, is also part of the package.
+The package compiles historical water-quality samples from `r ran_samples[1]`--`r ran_samples[2]`, groundwater-level measurements from `r ran_gwl[1]`--`r ran_gwl[2]`, and surface-water measurements from `r ran_swm[1]`--`r ran_swm[2]`. Geospatial data, which outlines the areas of sample collection or observation, is also part of the package.
By integrating this data into a single [R] package, the process of data handling is simplified for researchers. It also offers a standard format for data distribution along with its documentation. The geospatial datasets are provided in a common projection and datum, and the geohydrologic data is structured to facilitate analysis. Overall, the **inldata** package serves as a convenient tool for those studying the impact of waste disposal on water quality and availability.
@@ -40,12 +40,10 @@ To install the package along with its dependencies, which are required to run ex
install.packages("inldata", dependencies = TRUE)
```
-To install the development version of the package, you need to clone the repository and build from source, or run the following commands:
+To install the development version of the package, you can either clone the repository and build it from source, or run the following commands. Make sure the **remotes** package for R is installed.
```r
-if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_gitlab("inl/inldata@develop",
- auth_token = Sys.getenv("GITLAB_PAT"),
host = "code.usgs.gov",
dependencies = TRUE,
build_vignettes = TRUE
diff --git a/README.md b/README.md
index dca37725a2a3bc7f4a9563ab0d60fc99c2165ba6..826d2bbe7b83277b4c593d84e708d1e5fa18bc0c 100644
--- a/README.md
+++ b/README.md
@@ -17,10 +17,10 @@ crucial in understanding the effects of waste disposal on the eastern
Snake River Plain aquifer in southeastern Idaho and assessing the
long-term availability of water.
-The package compiles historical water-quality samples from 1949 to 2024,
-groundwater-level measurements from 1922 to 2024, and surface-water
-measurements from 1959 to 2024. Geospatial data, which outlines the
-areas of sample collection or observation, is also part of the package.
+The package compiles historical water-quality samples from 1949–2024,
+groundwater-level measurements from 1922–2024, and surface-water
+measurements from 1959–2024. Geospatial data, which outlines the areas
+of sample collection or observation, is also part of the package.
By integrating this data into a single [R](https://www.r-project.org/)
package, the process of data handling is simplified for researchers. It
@@ -49,13 +49,12 @@ datasets, and create a USGS data release, run:
install.packages("inldata", dependencies = TRUE)
```
-To install the development version of the package, you need to clone the
-repository and build from source, or run the following commands:
+To install the development version of the package, you can either clone
+the repository and build it from source, or run the following commands.
+Make sure the **remotes** package for R is installed.
``` r
-if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_gitlab("inl/inldata@develop",
- auth_token = Sys.getenv("GITLAB_PAT"),
host = "code.usgs.gov",
dependencies = TRUE,
build_vignettes = TRUE
diff --git a/data-raw/output.log b/data-raw/output.log
index 4fd51de2e3c9f77d96aaeee936c35bfda1a6a554..1a1895e455fd573c2b2af191968a28a008f8f219 100644
--- a/data-raw/output.log
+++ b/data-raw/output.log
@@ -1,7 +1,7 @@
running
'/usr/lib/R/bin/R --no-echo --no-restore --no-save --no-restore --file=data-raw/make-datasets.R'
-TIMESTAMP: 2024-07-30 21:39:41 PDT
+TIMESTAMP: 2024-09-09 13:00:42 PDT
STATUS: making 'crs' dataset ...
STATUS: making 'parameters' dataset ...
@@ -301,12 +301,10 @@ STATUS: making 'cities' dataset ...
STATUS: making 'counties' dataset ...
STATUS: making 'roads' dataset ...
STATUS: making 'lakes' dataset ...
-â ™ 21 extracted | 211 MB (104 MB/s) | 2s
-â ¹ 21 extracted | 331 MB ( 66 MB/s) | 5s
+â ™ 21 extracted | 338 MB ( 71 MB/s) | 4.8s
STATUS: making 'streams' dataset ...
-â ™ 21 extracted | 270 MB ( 86 MB/s) | 3.1s
-â ¹ 26 extracted | 398 MB ( 65 MB/s) | 6.1s
+â ™ 21 extracted | 298 MB ( 80 MB/s) | 3.7s
STATUS: compress dataset files ...
STATUS: copy dataset files to destination directory ...
-DURATION: 6.900758 mins
+DURATION: 6.878001 mins
diff --git a/data/gwl.rda b/data/gwl.rda
index 7eecafa6d42a8fd0b682fc56cb1bfe857fc58730..4c25ba6e73c34a4120c859db3844dd7dde46b7a9 100644
Binary files a/data/gwl.rda and b/data/gwl.rda differ
diff --git a/data/sites.rda b/data/sites.rda
index 530d0ec2f7943e772e3bc216b3eb1dab1ded3a3a..5a5fdec617162028b6c0bd80032f2abb9e7b278f 100644
Binary files a/data/sites.rda and b/data/sites.rda differ
diff --git a/data/swm.rda b/data/swm.rda
index 0b183dc0e692cb1d58cbf4bde819c8d147378683..5af2fa595ddf66491e02fb8560d6259670654168 100644
Binary files a/data/swm.rda and b/data/swm.rda differ
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 74345078834d6d2517124a4c61efbfbd7875547c..03a6d7149bc40bd6a066c2c24aeaeb52126daab5 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -7,30 +7,22 @@ navbar:
href: reference/index.html
- text: Explore
menu:
- - text: Background Concentrations
- href: articles/background.html
- - text: Benchmark Concentrations
- href: articles/benchmarks.html
+ - text: Site Information
+ href: articles/sites.html
- text: Cities and Towns
href: articles/cities.html
- text: County Boundaries
href: articles/counties.html
- - text: Digital Elevation Model
- href: articles/dem.html
- - text: Eastern Snake River Plain Boundary
+ - text: ESRP Boundary
href: articles/esrp.html
- - text: Idaho National Laboratory Boundary
+ - text: INL Boundary
href: articles/inl.html
- - text: Idaho National Laboratory Facilities
+ - text: INL Facilities
href: articles/facilities.html
- text: Industrial Waste Ditch
href: articles/iwd.html
- - text: Laboratory Detection Limits
- href: articles/dl.html
- text: Lakes and Ponds
href: articles/lakes.html
- - text: Parameter Information
- href: articles/parameters.html
- text: Percolation Ponds
href: articles/percponds.html
- text: Rivers and Streams
@@ -39,14 +31,22 @@ navbar:
href: articles/mountains.html
- text: Road Network
href: articles/roads.html
- - text: Site Information
- href: articles/sites.html
- text: State of Idaho Boundary
href: articles/idaho.html
+ - text: Digital Elevation Model
+ href: articles/dem.html
+ - text: Background Concentrations
+ href: articles/background.html
+ - text: Benchmark Concentrations
+ href: articles/benchmarks.html
+ - text: Laboratory Detection Limits
+ href: articles/dl.html
+ - text: Parameter Information
+ href: articles/parameters.html
- text: Units of Measurement
href: articles/units.html
- - text: ERD
- href: articles/erd.html
+ - text: Entity Relationship Diagram
+ href: articles/erd.html
- text: Download
href: articles/download.html
- text: Changelog
diff --git a/vignettes/download.Rmd b/vignettes/download.Rmd
index dcf04242edd103f35b203bde8a247122962bfe21..bca1403d769056bd3cfc4c57f65d86f876625af8 100644
--- a/vignettes/download.Rmd
+++ b/vignettes/download.Rmd
@@ -8,11 +8,12 @@ The **inldata** package offers a comprehensive collection of datasets in various
```{r include=FALSE}
+pkg <- "inldata"
destdir <- "download_files"
paste0(destdir, "/*") |> unlink()
files <- inldata::write_datasets(
- package = "inldata",
+ package = pkg,
destdir = destdir,
gzip = c("json", "geojson"),
pretty = FALSE
@@ -118,7 +119,7 @@ j <- inldata::get_file_ext(hrefs) |>
m[cbind(i, j)] <- data
tbl <- m
-m <- utils::data(package = "inldata")$results
+m <- utils::data(package = pkg)$results
titles <- m[, "Title"]
names(titles) <- m[, "Item"]
titles <- titles[rownames(tbl)]
@@ -137,18 +138,29 @@ col_names <- sprintf(
titles, headers
)
-ver <- utils::packageVersion(pkg = "inldata") |> format()
-archive <- sprintf("%s/inldata-datasets-%s.zip", destdir, ver)
+ver <- utils::packageVersion(pkg = pkg) |> format()
+archive <- sprintf("%s/%s-datasets-v%s.zip", destdir, pkg, ver)
checkmate::assert_path_for_output(archive, overwrite = TRUE)
archive::archive_write_dir(archive, dir = destdir, format = "zip")
archive_size <- inldata::get_file_size(archive)
```
-```{r echo=FALSE, results="asis"}
+<style>
+ table th {
+ text-align: center;
+ }
+</style>
+```{r echo=FALSE, results="asis"}
+align <- c("l", rep("c", ncol(tbl) - 1L))
options(knitr.kable.NA = '-')
-knitr::kable(tbl, row.names = FALSE, col.names = col_names)
+knitr::kable(tbl,
+ row.names = FALSE,
+ col.names = col_names,
+ align = align,
+ table.attr = 'style="width:100%; text-align:center;"'
+)
```
diff --git a/vignettes/facilities.Rmd b/vignettes/facilities.Rmd
index 9fed9536c4491fefce9b9d27cb582a388860300e..d30d7856ca9da9d621b45fd84371a6dabeec6002 100644
--- a/vignettes/facilities.Rmd
+++ b/vignettes/facilities.Rmd
@@ -18,7 +18,7 @@ map <- webmap::make_map(
popup = ~name,
label = ~id,
labelOptions = leaflet::labelOptions(noHide = TRUE, textOnly = TRUE),
- color = "#0033FF",
+ color = "#A40802",
opacity = 0.5,
weight = 2
) |>
diff --git a/vignettes/iwd.Rmd b/vignettes/iwd.Rmd
index 50f65890a5843c54d9d4256b79a9d139d57426b0..9e00938d0c0e2065e8ebaba9754696f7469431ac 100644
--- a/vignettes/iwd.Rmd
+++ b/vignettes/iwd.Rmd
@@ -14,7 +14,7 @@ map <- webmap::make_map(
) |>
leaflet::addPolylines(
data = spdf,
- color = "#025D8C",
+ color = "#A40802",
weight = 3,
opacity = 0.5
) |>
diff --git a/vignettes/lakes.Rmd b/vignettes/lakes.Rmd
index 74df55608c368299ccc53c9d875eb5e7a55dc072..16a234d20a862e53b7eb990b21f06c388c378313 100644
--- a/vignettes/lakes.Rmd
+++ b/vignettes/lakes.Rmd
@@ -26,7 +26,7 @@ map <- webmap::make_map(
data = spdf,
popup = ~popup,
label = ~gnis_nm,
- color = "#3399CC",
+ color = "#A40802",
opacity = 0.5,
weight = 2
) |>
diff --git a/vignettes/mountains.Rmd b/vignettes/mountains.Rmd
index 4b2c18b33d63ca66be1a512663c5c9db181918be..55b7f645b86e69b4fe133da110cb8ef46659883e 100644
--- a/vignettes/mountains.Rmd
+++ b/vignettes/mountains.Rmd
@@ -16,7 +16,7 @@ map <- webmap::make_map(
data = spdf,
popup = ~name,
labelOptions = leaflet::labelOptions(noHide = TRUE, textOnly = TRUE),
- color = "#0033FF",
+ color = "#A40802",
opacity = 0.5,
weight = 2
) |>
diff --git a/vignettes/percponds.Rmd b/vignettes/percponds.Rmd
index 78b8c94ef2cc346480dbcbda0a45b839cec41241..9135002e6963f3c04d09954bc8d3a161f19cc128 100644
--- a/vignettes/percponds.Rmd
+++ b/vignettes/percponds.Rmd
@@ -25,7 +25,7 @@ map <- webmap::make_map(
data = spdf,
popup = ~popup,
label = ~name,
- color = "#025D8C",
+ color = "#A40802",
opacity = 0.5,
weight = 3
) |>
diff --git a/vignettes/streams.Rmd b/vignettes/streams.Rmd
index 8a80438a4603424eaa00a26463e6b0691ff89e7a..4cba4a24b6298c442783c1c00fdb22a726ea44fb 100644
--- a/vignettes/streams.Rmd
+++ b/vignettes/streams.Rmd
@@ -26,7 +26,7 @@ map <- webmap::make_map(
data = spdf,
popup = ~popup,
label = ~gnis_nm,
- color = "#3399CC",
+ color = "#A40802",
weight = 2,
opacity = 0.5
) |>