diff --git a/.gitignore b/.gitignore
index 41cfcf5f04ebb0dbc6f619e74d575e99763686e5..cdbb25f589828eb8434050ebceb1fe7bd5c573ed 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,4 @@ mlms.Rproj
/docs
renv.lock
/data-raw/output.log
+/vignettes/download_files
diff --git a/DESCRIPTION b/DESCRIPTION
index 6c611eb11e473b34e50ab785cce491a22bc0c668..2c9f4dc03ca6283db87190ce608c57c6150977d6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: mlms
Title: Multilevel Monitoring System Data for Wells in the USGS INL Aquifer Monitoring Network
-Version: 1.0.2
+Version: 1.0.3
Authors@R: c(
person(given = c("Jason", "C."),
family = "Fisher",
@@ -39,6 +39,8 @@ Imports:
tools,
utils
Suggests:
+ archive,
+ arrow,
connectapi,
covr,
dm,
@@ -59,7 +61,8 @@ Suggests:
roxygen2,
tinytest,
V8,
- webmap
+ webmap,
+ writexl
License: CC0
Copyright: This software is in the public domain because it contains materials
that originally came from the United States Geological Survey (USGS), an
@@ -69,7 +72,7 @@ Copyright: This software is in the public domain because it contains materials
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
-URL: https://code.usgs.gov/inl/mlms
+URL: https://rconnect.usgs.gov/INLPO/mlms-main/, https://code.usgs.gov/inl/mlms
BugReports: https://code.usgs.gov/inl/mlms/-/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
diff --git a/NEWS.md b/NEWS.md
index 599c93958818bd914317729874b8f53f9f0b9e1c..ad3ea077321c7596450934178bdca2cdf303c903 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,11 @@
+# mlms 1.0.3
+
+- Update the package logo.
+- Add a new vignette titled "Download",
+ providing users with the ability to download datasets in multiple formats.
+- Implement a maximum width restriction for SVG images on the package website to
+ ensure consistent display and prevent oversized visuals.
+
# mlms 1.0.2
- Response to CRAN review comments by B. Altmann.
diff --git a/README.Rmd b/README.Rmd
index 76b8fcad58116d614bc4317ed7a1727e62e1005e..0737d0da685ae77bcbe67ff054e6f3ec216237e1 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -39,11 +39,11 @@ npcodes <- samples$pcode |>
```
-The [R](https://www.r-project.org/) package **mlms** is used to store and process Multilevel Monitoring System (MLMS) data for wells in the U.S. Geological Survey (USGS) aquifer-monitoring network, Idaho National Laboratory (INL), Idaho. Supported by the U.S. Department of Energy (DOE), the USGS collected `r npress` discrete hydraulic head measurements at various depths from `r nwells` wells in the eastern Snake River Plain (ESRP) aquifer between `r dt_range_press[1]` and `r dt_range_press[2]`. These measurements were derived from data on fluid pressure, fluid temperature, and atmospheric pressure. Each well was equipped with an MLMS, which included valved measurement ports, packer bladders, casing segments, and couplers. The MLMS allowed monitoring at `r nzones` hydraulically-isolated depth intervals, reaching depths as great as `r depth_max` feet below the land surface. Additionally, `r nsamples` groundwater samples were collected from these wells between `r dt_range_sample[1]` to `r dt_range_press[2]`, and analyzed for a wide range of chemical and physical parameters.
+The [R](https://www.r-project.org/) package **mlms** is used to store and process Multilevel Monitoring System (MLMS) data for wells in the U.S. Geological Survey (USGS) aquifer-monitoring network, Idaho National Laboratory (INL), Idaho. Supported by the U.S. Department of Energy (DOE), the USGS collected `r npress` discrete hydraulic head measurements at various depths from `r nwells` wells in the eastern Snake River Plain (ESRP) aquifer from `r dt_range_press[1]`--`r dt_range_press[2]`. These measurements were derived from data on fluid pressure, fluid temperature, and atmospheric pressure. Each well was equipped with an MLMS, which included valved measurement ports, packer bladders, casing segments, and couplers. The MLMS allowed monitoring at `r nzones` hydraulically-isolated depth intervals, reaching depths as great as `r depth_max` feet below the land surface. Additionally, `r nsamples` groundwater samples were collected from these wells from `r dt_range_sample[1]`--`r dt_range_press[2]`, and analyzed for a wide range of chemical and physical parameters.
-Many investigations have assessed the geology and hydrology of the ESRP aquifer at and near the INL, with a comprehensive listing of USGS Idaho National Laboratory Project Office (INLPO) publications available [online]. Fisher and Twining (2011) documented the use of Multilevel Monitoring Systems (MLMSs) to examine hydraulic head and temperature in six wells from 2007 to 2008. Subsequent expansions included nine wells (Twining and Fisher, 2012), 11 wells (Twining and Fisher, 2015), and 12 wells (Twining and others, 2021).
+Many investigations have assessed the geology and hydrology of the ESRP aquifer at and near the INL, with a comprehensive listing of USGS Idaho National Laboratory Project Office ([INLPO]) publications available [online]. Fisher and Twining (2011) documented the use of Multilevel Monitoring Systems to examine hydraulic head and temperature in six wells from 2007--2008. Subsequent expansions included nine wells (Twining and Fisher, 2012), 11 wells (Twining and Fisher, 2015), and 12 wells (Twining and others, 2021).
-Various studies have documented water chemistry at different depths in the ESRP aquifer, with summaries of water-quality data collected from 2005-2008 provided by Bartholomay and Twining (2010), 2009-2011 provided by Davis and others (2013), 2009-2013 provided by Bartholomay and others (2015), 2012-2015 provided by Bartholomay and others (2017), and 2014-2018 provided by Twining and others (2021). A tracer study by Bartholomay and others (2013) examined whether drilling fluids could remain in the MLMSs and found that the tracer moved out of the formation for most of the zones analyzed.
+Various studies have documented water chemistry at different depths in the ESRP aquifer, with summaries of water-quality data collected from 2005--2008 provided by Bartholomay and Twining (2010), 2009--2011 provided by Davis and others (2013), 2009--2013 provided by Bartholomay and others (2015), 2012--2015 provided by Bartholomay and others (2017), and 2014--2018 provided by Twining and others (2021). A tracer study by Bartholomay and others (2013) examined whether drilling fluids could remain in the MLMS wells and found that the tracer moved out of the formation for most of the monitoring zones analyzed.
<p>
<figure class="figure">
@@ -68,12 +68,11 @@ To install the package along with its dependencies, which are required to run ex
install.packages("mlms", dependencies = TRUE)
```
-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, and set an environment variable named `GITLAB_PAT` with your USGS GitLab personal access token.
+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
remotes::install_gitlab(
repo = "inl/mlms@develop",
- auth_token = Sys.getenv("GITLAB_PAT"),
host = "code.usgs.gov",
dependencies = TRUE
)
@@ -154,7 +153,7 @@ cat(s)
Bartholomay, R.C., Hopkins, C.B., and Maimer, N.V., 2015, Chemical constituents in groundwater from multiple zones in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2009--13: U.S. Geological Survey Scientific Investigations Report 2015--5002 (DOE/ID--22232), 110 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20155002.
-Bartholomay, R.C., Maimer, N.V., Rattray, G.W., and Fisher, J.C., 2017, An update of hydrologic conditions and distribution of selected constituents in water, eastern Snake River Plain aquifer and perched groundwater zones, Idaho National Laboratory, Idaho, emphasis 2012-15: U.S. Geological Survey Scientific Investigations Report 2017--5021 (DOE/ID--22242), 87 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20175021.
+Bartholomay, R.C., Maimer, N.V., Rattray, G.W., and Fisher, J.C., 2017, An update of hydrologic conditions and distribution of selected constituents in water, eastern Snake River Plain aquifer and perched groundwater zones, Idaho National Laboratory, Idaho, emphasis 2012--15: U.S. Geological Survey Scientific Investigations Report 2017--5021 (DOE/ID--22242), 87 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20175021.
Bartholomay, R. C., and Twining, B.V., 2010, Chemical constituents in groundwater from multiple zones in the eastern Snake River Plain aquifer at the Idaho National Laboratory, Idaho, 2005--08: U.S. Geological Survey Scientific Investigations Report 2010--5116 (DOE/ID--22211), 81 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20105116.
@@ -162,13 +161,13 @@ Bartholomay, R.C., Twining, B.V., Rose, P.E, 2013, Ambient Changes in Tracer Con
Davis, L.C., Bartholomay, R.C., and Rattray, G.W., 2013, An update of hydrologic conditions and distribution of selected constituents in water, eastern Snake River Plain aquifer and perched groundwater zones, Idaho National Laboratory, Idaho, emphasis 2009--11: U.S. Geological Survey Scientific Investigations Report 2013--5214, (DOE/ID--22226), 90 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20135214.
-Fisher, J.C., and Twining, B.V., 2011, Multilevel groundwater monitoring of hydraulic head and temperature in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2007-08: U.S. Geological Survey Scientific Investigations Report 2010--5253, 62 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20105253.
+Fisher, J.C., and Twining, B.V., 2011, Multilevel groundwater monitoring of hydraulic head and temperature in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2007--08: U.S. Geological Survey Scientific Investigations Report 2010--5253, 62 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20105253.
Twining, B.V., Bartholomay, R.C., Fisher, J.C., and Anderson, C., 2021, Multilevel groundwater monitoring of hydraulic head, water temperature, and chemical constituents in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2014--18: U.S. Geological Survey Scientific Investigations Report 2021--5002, 82 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20215002.
-Twining, B.V., and Fisher, J.C., 2012, Multilevel groundwater monitoring of hydraulic head and temperature in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2009-10: U.S. Geological Survey Scientific Investigations Report 2012--5259, 44 p., plus appendixes, accessed November 16, 2024, at https://doi.org/10.3133/sir20125259.
+Twining, B.V., and Fisher, J.C., 2012, Multilevel groundwater monitoring of hydraulic head and temperature in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2009--10: U.S. Geological Survey Scientific Investigations Report 2012--5259, 44 p., plus appendixes, accessed November 16, 2024, at https://doi.org/10.3133/sir20125259.
-Twining, B.V., and Fisher, J.C., 2015, Multilevel groundwater monitoring of hydraulic head and temperature in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2011-13: U.S. Geological Survey Scientific Investigations Report 2015--5042 (DOE/ID--22235), 49 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20155042.
+Twining, B.V., and Fisher, J.C., 2015, Multilevel groundwater monitoring of hydraulic head and temperature in the eastern Snake River Plain aquifer, Idaho National Laboratory, Idaho, 2011--13: U.S. Geological Survey Scientific Investigations Report 2015--5042 (DOE/ID--22235), 49 p., accessed November 16, 2024, at https://doi.org/10.3133/sir20155042.
<!-- Embedded References -->
@@ -185,6 +184,7 @@ Twining, B.V., and Fisher, J.C., 2015, Multilevel groundwater monitoring of hydr
[tinytest]: https://CRAN.R-project.org/package=tinytest
[0000-0001-9032-8912]: https://orcid.org/0000-0001-9032-8912
[0000-0003-1321-4721]: https://orcid.org/0000-0003-1321-4721
-[CRAN]: https://cran.r-project.org/
+[cran]: https://cran.r-project.org/
[online]: https://rconnect.usgs.gov/INLPO/inlpubs-main/articles/inlpo-pubs.html
[remotes]: https://CRAN.R-project.org/package=remotes
+[inlpo]: https://www.usgs.gov/centers/idaho-water-science-center/science/idaho-national-laboratory-project-office
diff --git a/README.md b/README.md
index a9a53333cd3feea9010efa050980c5480b446e2c..47ae2e77b88a5fc1057a5720187a197dc51e4a53 100644
--- a/README.md
+++ b/README.md
@@ -12,34 +12,36 @@ U.S. Geological Survey (USGS) aquifer-monitoring network, Idaho National
Laboratory (INL), Idaho. Supported by the U.S. Department of Energy
(DOE), the USGS collected 6,058 discrete hydraulic head measurements at
various depths from 12 wells in the eastern Snake River Plain (ESRP)
-aquifer between 2007 and 2023. These measurements were derived from data
-on fluid pressure, fluid temperature, and atmospheric pressure. Each
-well was equipped with an MLMS, which included valved measurement ports,
+aquifer from 2007–2023. These measurements were derived from data on
+fluid pressure, fluid temperature, and atmospheric pressure. Each well
+was equipped with an MLMS, which included valved measurement ports,
packer bladders, casing segments, and couplers. The MLMS allowed
monitoring at 145 hydraulically-isolated depth intervals, reaching
depths as great as 1,427 feet below the land surface. Additionally, 715
-groundwater samples were collected from these wells between 2005 to
-2023, and analyzed for a wide range of chemical and physical parameters.
+groundwater samples were collected from these wells from 2005–2023, and
+analyzed for a wide range of chemical and physical parameters.
Many investigations have assessed the geology and hydrology of the ESRP
aquifer at and near the INL, with a comprehensive listing of USGS Idaho
-National Laboratory Project Office (INLPO) publications available
+National Laboratory Project Office
+([INLPO](https://www.usgs.gov/centers/idaho-water-science-center/science/idaho-national-laboratory-project-office))
+publications available
[online](https://rconnect.usgs.gov/INLPO/inlpubs-main/articles/inlpo-pubs.html).
Fisher and Twining (2011) documented the use of Multilevel Monitoring
-Systems (MLMSs) to examine hydraulic head and temperature in six wells
-from 2007 to 2008. Subsequent expansions included nine wells (Twining
-and Fisher, 2012), 11 wells (Twining and Fisher, 2015), and 12 wells
+Systems to examine hydraulic head and temperature in six wells from
+2007–2008. Subsequent expansions included nine wells (Twining and
+Fisher, 2012), 11 wells (Twining and Fisher, 2015), and 12 wells
(Twining and others, 2021).
Various studies have documented water chemistry at different depths in
the ESRP aquifer, with summaries of water-quality data collected from
-2005-2008 provided by Bartholomay and Twining (2010), 2009-2011 provided
-by Davis and others (2013), 2009-2013 provided by Bartholomay and others
-(2015), 2012-2015 provided by Bartholomay and others (2017), and
-2014-2018 provided by Twining and others (2021). A tracer study by
+2005–2008 provided by Bartholomay and Twining (2010), 2009–2011 provided
+by Davis and others (2013), 2009–2013 provided by Bartholomay and others
+(2015), 2012–2015 provided by Bartholomay and others (2017), and
+2014–2018 provided by Twining and others (2021). A tracer study by
Bartholomay and others (2013) examined whether drilling fluids could
-remain in the MLMSs and found that the tracer moved out of the formation
-for most of the zones analyzed.
+remain in the MLMS wells and found that the tracer moved out of the
+formation for most of the monitoring zones analyzed.
<p>
<figure class="figure">
@@ -74,14 +76,11 @@ install.packages("mlms", dependencies = TRUE)
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, and set an
-environment variable named `GITLAB_PAT` with your USGS GitLab personal
-access token.
+Make sure the **remotes** package for R is installed.
``` r
remotes::install_gitlab(
repo = "inl/mlms@develop",
- auth_token = Sys.getenv("GITLAB_PAT"),
host = "code.usgs.gov",
dependencies = TRUE
)
@@ -261,7 +260,7 @@ Geological Survey Scientific Investigations Report 2015–5002
Bartholomay, R.C., Maimer, N.V., Rattray, G.W., and Fisher, J.C., 2017,
An update of hydrologic conditions and distribution of selected
constituents in water, eastern Snake River Plain aquifer and perched
-groundwater zones, Idaho National Laboratory, Idaho, emphasis 2012-15:
+groundwater zones, Idaho National Laboratory, Idaho, emphasis 2012–15:
U.S. Geological Survey Scientific Investigations Report 2017–5021
(DOE/ID–22242), 87 p., accessed November 16, 2024, at
<https://doi.org/10.3133/sir20175021>.
@@ -287,7 +286,7 @@ p., accessed November 16, 2024, at
Fisher, J.C., and Twining, B.V., 2011, Multilevel groundwater monitoring
of hydraulic head and temperature in the eastern Snake River Plain
-aquifer, Idaho National Laboratory, Idaho, 2007-08: U.S. Geological
+aquifer, Idaho National Laboratory, Idaho, 2007–08: U.S. Geological
Survey Scientific Investigations Report 2010–5253, 62 p., accessed
November 16, 2024, at <https://doi.org/10.3133/sir20105253>.
@@ -300,14 +299,14 @@ Scientific Investigations Report 2021–5002, 82 p., accessed November 16,
Twining, B.V., and Fisher, J.C., 2012, Multilevel groundwater monitoring
of hydraulic head and temperature in the eastern Snake River Plain
-aquifer, Idaho National Laboratory, Idaho, 2009-10: U.S. Geological
+aquifer, Idaho National Laboratory, Idaho, 2009–10: U.S. Geological
Survey Scientific Investigations Report 2012–5259, 44 p., plus
appendixes, accessed November 16, 2024, at
<https://doi.org/10.3133/sir20125259>.
Twining, B.V., and Fisher, J.C., 2015, Multilevel groundwater monitoring
of hydraulic head and temperature in the eastern Snake River Plain
-aquifer, Idaho National Laboratory, Idaho, 2011-13: U.S. Geological
+aquifer, Idaho National Laboratory, Idaho, 2011–13: U.S. Geological
Survey Scientific Investigations Report 2015–5042 (DOE/ID–22235), 49 p.,
accessed November 16, 2024, at <https://doi.org/10.3133/sir20155042>.
diff --git a/man/figures/logo.ai b/man/figures/logo.ai
index 43992583f46ee2b7910916fe746cc88c29529436..68f0386bfdb05e24b936fbaaf0463eaf6421217f 100644
Binary files a/man/figures/logo.ai and b/man/figures/logo.ai differ
diff --git a/man/figures/logo.svg b/man/figures/logo.svg
index 28f0757013cf448325d9cb26b7c4caa1fae8c958..ae29007e9333e03530ece3ca1ad661f9173574a5 100644
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+ <path class="st8" d="M208.2,206.9v-80.9c0-3.7.8-6.6,2.5-8.5,1.7-1.9,3.9-2.9,6.7-2.9s5.1.9,6.8,2.8c1.7,1.9,2.6,4.7,2.6,8.5v80.9c0,3.8-.9,6.6-2.6,8.5-1.8,1.9-4,2.8-6.8,2.8s-5-1-6.7-2.9-2.6-4.8-2.6-8.4Z"/>
+ <path class="st8" d="M308.2,181.7v24.8c0,3.9-.9,6.9-2.7,8.8s-4.1,2.9-7,2.9-5.1-1-6.9-2.9c-1.8-2-2.6-4.9-2.6-8.8v-29.7c0-4.7-.2-8.3-.5-10.9-.3-2.6-1.2-4.7-2.6-6.4-1.4-1.7-3.6-2.5-6.7-2.5-6.1,0-10.1,2.1-12.1,6.3-1.9,4.2-2.9,10.2-2.9,18v25.2c0,3.9-.9,6.8-2.6,8.8-1.8,2-4.1,3-6.9,3s-5.1-1-6.9-3c-1.8-2-2.7-4.9-2.7-8.8v-53.4c0-3.5.8-6.2,2.4-8,1.6-1.8,3.7-2.7,6.4-2.7s4.7.9,6.4,2.6,2.6,4.1,2.6,7.1v1.8c3.2-3.9,6.7-6.7,10.4-8.5,3.7-1.8,7.8-2.7,12.3-2.7s8.7.9,12.1,2.8c3.4,1.9,6.2,4.7,8.3,8.5,3.1-3.8,6.5-6.7,10.1-8.5,3.6-1.8,7.6-2.8,12-2.8s9.5,1,13.2,3c3.7,2,6.4,4.9,8.3,8.6,1.6,3.4,2.4,8.7,2.4,15.9v36.4c0,3.9-.9,6.9-2.7,8.8s-4.1,2.9-7,2.9-5.1-1-6.9-3c-1.8-2-2.7-4.9-2.7-8.8v-31.4c0-4-.2-7.2-.5-9.6-.3-2.4-1.3-4.4-2.8-6.1s-3.8-2.5-6.8-2.5-4.8.7-7,2.2c-2.2,1.5-3.9,3.4-5.2,5.9-1.4,3.1-2.1,8.7-2.1,16.7Z"/>
+ <path class="st8" d="M430.1,193.8c0,5.2-1.3,9.6-3.8,13.2-2.5,3.7-6.2,6.4-11.1,8.3-4.9,1.9-10.9,2.8-17.9,2.8s-12.4-1-17.2-3.1-8.3-4.6-10.6-7.7c-2.3-3.1-3.4-6.2-3.4-9.3s.7-3.8,2.2-5.3,3.3-2.2,5.5-2.2,3.5.5,4.5,1.4c1,1,2.1,2.3,3,4,1.9,3.3,4.2,5.8,6.9,7.5s6.3,2.5,10.9,2.5,6.8-.8,9.2-2.5c2.4-1.7,3.6-3.6,3.6-5.7,0-3.3-1.2-5.7-3.7-7.2-2.5-1.5-6.6-2.9-12.3-4.3-6.4-1.6-11.7-3.3-15.7-5-4-1.8-7.3-4.1-9.7-6.9-2.4-2.9-3.6-6.4-3.6-10.6s1.1-7.3,3.3-10.6c2.2-3.3,5.5-6,9.9-8,4.4-2,9.6-3,15.8-3s9.2.5,13,1.5c3.9,1,7.1,2.3,9.6,4,2.6,1.7,4.5,3.6,5.9,5.6,1.3,2.1,2,4.1,2,6s-.7,3.9-2.2,5.3-3.5,2.1-6.1,2.1-3.5-.5-4.9-1.6c-1.3-1.1-2.9-2.7-4.6-4.9-1.4-1.8-3.1-3.3-5-4.4s-4.5-1.6-7.8-1.6-6.2.7-8.4,2.2c-2.2,1.4-3.3,3.2-3.3,5.4s.8,3.6,2.5,4.8c1.6,1.3,3.9,2.3,6.6,3.1,2.8.8,6.6,1.8,11.5,3,5.8,1.4,10.5,3.1,14.2,5.1,3.7,2,6.4,4.3,8.3,6.9,1.9,2.7,2.8,5.7,2.8,9.1Z"/>
+ </g>
+ </g>
+</svg>
\ No newline at end of file
diff --git a/man/mlms-package.Rd b/man/mlms-package.Rd
index 6095eaa1ddc4e675a9b3fea6887d23b56a4ea1af..3c7bedd55fdea4775390ab095ba84077d1780ecf 100644
--- a/man/mlms-package.Rd
+++ b/man/mlms-package.Rd
@@ -11,6 +11,7 @@ Analysis-ready datasets detailing the Multilevel Monitoring System (MLMS) wells
\seealso{
Useful links:
\itemize{
+ \item \url{https://rconnect.usgs.gov/INLPO/mlms-main/}
\item \url{https://code.usgs.gov/inl/mlms}
\item Report bugs at \url{https://code.usgs.gov/inl/mlms/-/issues}
}
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index b2488fbe8e62f4b907ed738216a080eef4dc2092..dc0979890f56789930828f55b97c0be184bfed80 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -23,7 +23,9 @@ navbar:
href: articles/statistics.html
- text: Entity Relationship Diagram
href: articles/erd.html
- - text: Completions
+ - text: Methods
+ href: articles/methods.html
+ - text: Completion
menu:
- text: MIDDLE 2050A
href: articles/MIDDLE-2050A.html
@@ -49,8 +51,8 @@ navbar:
href: articles/USGS-137A.html
- text: USGS 149
href: articles/USGS-149.html
- - text: Methods
- href: articles/methods.html
+ - text: Download
+ href: articles/download.html
- text: Changelog
href: news/index.html
right:
diff --git a/vignettes/MIDDLE-2050A.Rmd b/vignettes/MIDDLE-2050A.Rmd
index 3736ac30ad64578048cf88b8210d307ccb185e71..93a45c26a09f7d03196df898c7ac124550374523 100644
--- a/vignettes/MIDDLE-2050A.Rmd
+++ b/vignettes/MIDDLE-2050A.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for MIDDLE-2050A well, Idaho National La
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/MIDDLE-2050A.svg" alt="MIDDLE 2050A" width="55%" />
+ <img src="../man/figures/MIDDLE-2050A.svg" class="figure-img img-fluid" alt="MIDDLE 2050A" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/MIDDLE-2051.Rmd b/vignettes/MIDDLE-2051.Rmd
index 9f06d18518e0d12b89ab2e231fd42c8137962c50..a3ede6cdb572ac635b1899f294030e3b83deaada 100644
--- a/vignettes/MIDDLE-2051.Rmd
+++ b/vignettes/MIDDLE-2051.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for MIDDLE-2051 well, Idaho National Lab
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/MIDDLE-2051.svg" alt="MIDDLE 2051" width="55%" />
+ <img src="../man/figures/MIDDLE-2051.svg" class="figure-img img-fluid" alt="MIDDLE 2051" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-103.Rmd b/vignettes/USGS-103.Rmd
index 461d9dc4427dc8e1dfe2539435b721bc9adc8a15..92b5e051e7a83a46a57079af3a6f2c6b66c26eb4 100644
--- a/vignettes/USGS-103.Rmd
+++ b/vignettes/USGS-103.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-103 well, Idaho National Labora
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-103.svg" alt="USGS 103" width="55%" />
+ <img src="../man/figures/USGS-103.svg" class="figure-img img-fluid" alt="USGS 103" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-105.Rmd b/vignettes/USGS-105.Rmd
index c891d10eb4938052bd1a9d2e1c6d5bd552706c7b..620cc967e7eda2cf428d23a91c4f951eaa596258 100644
--- a/vignettes/USGS-105.Rmd
+++ b/vignettes/USGS-105.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-105 well, Idaho National Labora
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-105.svg" alt="USGS 105" width="55%" />
+ <img src="../man/figures/USGS-105.svg" class="figure-img img-fluid" alt="USGS 105" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-108.Rmd b/vignettes/USGS-108.Rmd
index af310b65ddbe46dcf16d79f0af0aacc3e89717ee..ae3ba6163bf552e81c6dc30a9cfcab7e0f4a093d 100644
--- a/vignettes/USGS-108.Rmd
+++ b/vignettes/USGS-108.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-108 well, Idaho National Labora
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-108.svg" alt="USGS 108" width="55%" />
+ <img src="../man/figures/USGS-108.svg" class="figure-img img-fluid" alt="USGS 108" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-131A.Rmd b/vignettes/USGS-131A.Rmd
index bf5cb7284e3c6b3bfefb472f2fda7328f66c6d32..137bc04ae94a7dff771e8f333d7693d4650510d2 100644
--- a/vignettes/USGS-131A.Rmd
+++ b/vignettes/USGS-131A.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-131A well, Idaho National Labor
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-131A.svg" alt="USGS 131A" width="55%" />
+ <img src="../man/figures/USGS-131A.svg" class="figure-img img-fluid" alt="USGS 131A" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-132.Rmd b/vignettes/USGS-132.Rmd
index 65cb4d0dbcb375c311ea198099494f06f65a56b6..c77fc9e21fc13e30f06d0e10cf2bda2eeb79d9eb 100644
--- a/vignettes/USGS-132.Rmd
+++ b/vignettes/USGS-132.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-132 well, Idaho National Labora
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-132.svg" alt="USGS 132" width="55%" />
+ <img src="../man/figures/USGS-132.svg" class="figure-img img-fluid" alt="USGS 132" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-133.Rmd b/vignettes/USGS-133.Rmd
index 55b6c45c43fcbd0676391010fefae1e227d745ce..f14dd57573e1ee36d3b63636085564863be1faf6 100644
--- a/vignettes/USGS-133.Rmd
+++ b/vignettes/USGS-133.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-133 well, Idaho National Labora
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-133.svg" alt="USGS 133" width="55%" />
+ <img src="../man/figures/USGS-133.svg" class="figure-img img-fluid" alt="USGS 133" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-134.Rmd b/vignettes/USGS-134.Rmd
index 560c786a4329598e5a8b6a735ca8b4eb56518791..1d4d264d8ec5f0e7b62dd077d5e2848b5a632729 100644
--- a/vignettes/USGS-134.Rmd
+++ b/vignettes/USGS-134.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-134 well, Idaho National Labora
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-134.svg" alt="USGS 134" width="55%" />
+ <img src="../man/figures/USGS-134.svg" class="figure-img img-fluid"alt="USGS 134" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-135.Rmd b/vignettes/USGS-135.Rmd
index 372a3d05ec01c80a133c6d57412962ce8d0218cf..4c12e7dec7971525b6c242d84de57f496585a69b 100644
--- a/vignettes/USGS-135.Rmd
+++ b/vignettes/USGS-135.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-135 well, Idaho National Labora
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-135.svg" alt="USGS 135" width="55%" />
+ <img src="../man/figures/USGS-135.svg" class="figure-img img-fluid" alt="USGS 135" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-137A.Rmd b/vignettes/USGS-137A.Rmd
index 818bc74facde54c1e5b66419fd81e80677734a86..e641bd1af175aec220741093ebffc5703466a3ad 100644
--- a/vignettes/USGS-137A.Rmd
+++ b/vignettes/USGS-137A.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-137A well, Idaho National Labor
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-137A.svg" alt="USGS 137A" width="55%" />
+ <img src="../man/figures/USGS-137A.svg" class="figure-img img-fluid" alt="USGS 137A" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/USGS-149.Rmd b/vignettes/USGS-149.Rmd
index d865cd7b5c261d79d8f1a23ac9b4bb512f203f57..c82942147cc17773fde85d98a269241d190bb0b5 100644
--- a/vignettes/USGS-149.Rmd
+++ b/vignettes/USGS-149.Rmd
@@ -6,7 +6,7 @@ Lithology log and multilevel completion for USGS-149 well, Idaho National Labora
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/USGS-149.svg" alt="USGS 149" width="55%" />
+ <img src="../man/figures/USGS-149.svg" class="figure-img img-fluid" alt="USGS 149" style="max-width: 430px;" />
</figure>
</p>
diff --git a/vignettes/download.Rmd b/vignettes/download.Rmd
new file mode 100644
index 0000000000000000000000000000000000000000..a9e263f15dcf4ad68863372c2dd114f1f88ca2cf
--- /dev/null
+++ b/vignettes/download.Rmd
@@ -0,0 +1,181 @@
+---
+title: "Download"
+resource_files:
+ - download_files
+---
+
+The **mlms** package offers a comprehensive collection of datasets in various formats. Users may download individual files for specific data needs, or all datasets in a compressed ZIP file for efficiency. These datasets can be easily imported into data analysis software or programming languages for further analysis.
+
+```{r include=FALSE}
+
+pkg <- "mlms"
+destdir <- "download_files"
+paste0(destdir, "/*") |> unlink()
+
+files <- inldata::write_datasets(
+ package = pkg,
+ destdir = destdir,
+ gzip = c("json", "geojson"),
+ pretty = FALSE
+) |> basename()
+exts <- inldata::get_file_ext(files)
+fmts <- exts |> unique() |> sort()
+paths <- lapply(fmts,
+ FUN = function(x) {
+ paste(destdir, files[exts %in% x], sep = "/")
+ }
+)
+names(paths) <- fmts
+
+cols <- rbind(
+ c(
+ "txt",
+ "Text",
+ "Text-based format."
+ ),
+ c(
+ "csv",
+ "CSV",
+ "Text-based format storing tabular data, commonly used for data exchange due to its simplicity."
+ ),
+ c(
+ "xlsx",
+ "Spreadsheet",
+ "A Microsoft Excel file, part of the Office Open XML standard, used for storing and processing tabular data."
+ ),
+ c(
+ "parquet",
+ "Parquet",
+ "An Arrow Parquet file, used for efficient storage and high-speed processing of big data."
+ ),
+ c(
+ "json.gz",
+ "JSON",
+ paste(
+ "A text-based format compressed using Gzip.",
+ "Widely used for system interoperability due to its readability."
+ )
+ ),
+ c(
+ "geojson.gz",
+ "GeoJSON",
+ paste(
+ "A text-based format compressed using Gzip.",
+ "Used for encoding geographic features and their nonspatial attributes."
+ )
+ ),
+ c(
+ "zip",
+ "Shapefile",
+ paste(
+ "A compressed (ZIP format) file serving as a container for storing geographical features",
+ "and their associated attributes, optimizing transfer efficiency."
+ )
+ ),
+ c(
+ "tiff",
+ "GeoTIFF",
+ paste(
+ "A standard TIFF (Tagged Image File Format) with embedded geospatial metadata",
+ "allowing geographic information to be associated with the image data."
+ )
+ )
+) |>
+ as.data.frame()
+colnames(cols) <- c("ext", "header", "title")
+cols <- cols[cols$ext %in% exts, ]
+
+paths <- paths[cols$ext]
+rows <- unlist(paths) |>
+ basename() |>
+ tools::file_path_sans_ext(compression = TRUE) |>
+ unique()
+
+m <- matrix(
+ nrow = length(rows),
+ ncol = nrow(cols),
+ dimnames = list(rows, cols$ext)
+)
+
+hrefs <- unlist(paths) |>
+ as.character()
+sizes <- inldata::get_file_size(hrefs)
+titles <- sprintf("%s (%s)", basename(hrefs), sizes)
+icon <- fontawesome::fa(
+ name = "file",
+ fill = "steelblue",
+ prefer_type = "solid"
+)
+data <- sprintf(
+ fmt = "<a href='%s' title='%s' target='_blank'>%s</a>",
+ hrefs, titles, icon
+)
+
+i <- basename(hrefs) |>
+ tools::file_path_sans_ext(compression = TRUE) |>
+ match(rownames(m))
+j <- inldata::get_file_ext(hrefs) |>
+ match(colnames(m))
+m[cbind(i, j)] <- data
+tbl <- m
+
+m <- utils::data(package = pkg)$results
+titles <- m[, "Title"]
+names(titles) <- m[, "Item"]
+titles <- titles[rownames(tbl)]
+
+ds_nm <- sprintf(
+ fmt = "<a href='../reference/%s.html' title='%s'>%s</a>",
+ rownames(tbl), titles, rownames(tbl)
+)
+tbl <- cbind(ds_nm, tbl)
+rownames(tbl) <- NULL
+
+headers <- c("Dataset", cols$header)
+titles <- c("Name of the package dataset.", cols$title)
+col_names <- sprintf(
+ fmt = "<span title='%s'>%s</span>",
+ titles, headers
+)
+
+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)
+
+```
+
+<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,
+ align = align,
+ table.attr = 'style="width:100%; text-align:center;"'
+)
+
+```
+
+```{r echo=FALSE, results="asis"}
+
+fontawesome::fa("download") |>
+ htmltools::tagList(
+ sprintf("Download all (%s)", archive_size)
+ ) |>
+ htmltools::a(
+ href = archive,
+ target = "_blank",
+ title = "Download a unified ZIP file that contains all compressed files.",
+ ) |>
+ htmltools::tagList() |>
+ htmltools::p()
+
+```
diff --git a/vignettes/erd.Rmd b/vignettes/erd.Rmd
index 80deaf46f46e62384350233f03733c3595384e3a..31adf13ed21e2b8f46e387c9a9191caf93b1243f 100644
--- a/vignettes/erd.Rmd
+++ b/vignettes/erd.Rmd
@@ -6,7 +6,7 @@ The Entity Relationship Diagram (ERD) for the mlms package datasets illustrates
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/erd.svg" alt="erd" width="80%" />
+ <img src="../man/figures/erd.svg" class="figure-img img-fluid" alt="erd" style="max-width: 860px;" />
</figure>
</p>
diff --git a/vignettes/methods.Rmd b/vignettes/methods.Rmd
index bcc5788c8c512b3dd6d187c9b4d57dd5991747ba..031d7fe19404d7909057228d56b14f587bb19c6f 100644
--- a/vignettes/methods.Rmd
+++ b/vignettes/methods.Rmd
@@ -11,7 +11,7 @@ Two versions of the Westbay™ System were employed in this study: the MP55
<p>
<figure class="figure">
- <img class="figure-img img-fluid" src="../man/figures/methods.svg" alt="methods" width="100%" />
+ <img src="../man/figures/methods.svg" class="figure-img img-fluid" alt="methods" style="max-width: 860px;" />
<figcaption class="figure-caption">
<b>Figure 1.</b> Terms used in the calculation of hydraulic head based on the portable probe position when coupled with a measurement port in the multilevel monitoring system (Modified from Westbay™, written commun., 2009).
</figcaption>
@@ -26,7 +26,8 @@ Fluid pressure and temperature were measured using a pressure transducer, which
Data on fluid pressure and temperature are transmitted to the land surface via a wireline communication cable, processed using a data acquisition system, and recorded on a datalogger. Simultaneously, atmospheric pressure is measured and recorded at the land surface using a handheld barometric sensor. The hydraulic head at each measurement port is then calculated using the fluid pressure, fluid temperature, and atmospheric pressure measurements. Assuming 100 percent barometric efficiency, hydraulic head is expressed as
$$
-h_i = Z - D_i + \Psi( P_{out,i,t}, T_{i,t}, P_{atm,t} ) \quad \text{for} \, i \in \{1, 2, \ldots, n\} \, \text{and} \, t = t_i \text{.} {\tag{1}}
+h_i = Z - D_i + \Psi( P_{out,i,t}, T_{i,t}, P_{atm,t} ) \\
+\text{for} \, i \in \{1, 2, \ldots, n\} \, \text{and} \, t = t_i \text{.} {\tag{1}}
$$
Where
@@ -104,7 +105,7 @@ Where
The specific weight of water ($\gamma_w$ in eq. 2) was calculated solely as a function of temperature (McCutcheon and others, 1993), assuming negligible salinity and gravitational differences between measurements, and expressed as
$$
-\gamma_w(T) = 62.43 \times \left[ 1 - \left( \left[ \frac{T + 288.94}{508929 \times (T + 68.13)} \right] \times (T - 3.99)^2 \right) \right] \text{.} {\tag{3}}
+\gamma_w(T) = 62.43 \times \left[ 1 - \left( \frac{T + 288.94}{508929 \times (T + 68.13)} \times (T - 3.99)^2 \right) \right] \text{.} {\tag{3}}
$$
@@ -121,7 +122,8 @@ After recording fluid pressure and temperature measurements, the transducer was
The multilevel completion of a borehole is characterized by: the measured depth to the pressure transducer at a port coupling ($D_i$ in eq. 1), and the dimensions of MLMS components documented in the MLMS installation log. The depth to the transducer plane is calculated by adding the water level depth to the pressure head measured inside the multiport casing, and is expressed as follows:
$$
-D_i = L( \ell_{e,t} ) + \Psi( P_{in,i,t}, T_{i,t}, P_{atm,t} ) \quad \text{for} \, i \in \{1, 2, \ldots, n\} \, \text{and} \, t = t_i \text{.} {\tag{4}}
+D_i = L( \ell_{e,t} ) + \Psi( P_{in,i,t}, T_{i,t}, P_{atm,t} ) \\
+\text{for} \, i \in \{1, 2, \ldots, n\} \, \text{and} \, t = t_i \text{.} {\tag{4}}
$$
Where
@@ -205,7 +207,8 @@ Simultaneous measurements of $P_{in}$, $T$, $P_{atm}$ (eq. 4), and $\ell_e$ (eqs
The location of MLMS components in a borehole are determined by the measured depth to the pressure transducer plane at a port coupling ($D_i$ in eq. 4) and its position within the MLMS installation log. For example, the depth to the top of each monitoring zone is determined by subtracting the distance between the transducer plane and the bottom of the adjacent upper packer from the depth to the transducer plane, or
$$
-D_{top,z} = D_i - a_i \quad \text{for} \, z \in \{1, 2, \ldots, m\} \, \text{ and } \, i \in \{1, 2, \ldots, n\} \setminus E \text{.} {\tag{6}}
+D_{top,z} = D_i - a_i \\
+\text{for} \, z \in \{1, 2, \ldots, m\} \, \text{ and } \, i \in \{1, 2, \ldots, n\} \setminus E \text{.} {\tag{6}}
$$
Where