From 2e8f3f7df77a4598b93cb81cbe06ab949a83db62 Mon Sep 17 00:00:00 2001
From: Jason Fisher <jfisher@usgs.gov>
Date: Wed, 5 Feb 2025 13:55:23 -0800
Subject: [PATCH 1/2] add system requirements to description
---
DESCRIPTION | 1 +
README.md | 39 +++++++++++++++++++++++++++++++++++++++
data/calibrations.rda | Bin 632 -> 632 bytes
3 files changed, 40 insertions(+)
diff --git a/DESCRIPTION b/DESCRIPTION
index cd6b825..a6022c9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -70,6 +70,7 @@ Copyright: This software is in the public domain because it contains materials
see the official USGS copyright policy at
https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits
Encoding: UTF-8
+SystemRequirements: libarchive-dev (dev)
LazyData: true
LazyDataCompression: xz
URL: https://rconnect.usgs.gov/INLPO/mlms-main/, https://code.usgs.gov/inl/mlms
diff --git a/README.md b/README.md
index 47ae2e7..d75ba6b 100644
--- a/README.md
+++ b/README.md
@@ -44,16 +44,21 @@ 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">
+
<img src="man/figures/photo.jpg" class="figure-img img-fluid" alt="photo" width="860px" />
<figcaption class="figure-caption">
+
Hydrologic Technician, Jayson Blom (USGS), collecting pressure and
temperature data at well site USGS 137A. In the background is Big
Southern Butte, Idaho. Photograph taken on the INL in March 2014 by
Brian V. Twining, Supervisory Hydrologist, USGS INLPO, Idaho Falls,
Idaho.
</figcaption>
+
</figure>
+
</p>
## Installation
@@ -201,49 +206,83 @@ Additional metadata about this publication, not found in other parts of
the page is in this table.
<!--html_preserve-->
+
<table>
+
<tbody>
+
<tr>
+
<th scope="row">
+
Publication type
</th>
+
<td>
+
Formal R language package
</td>
+
</tr>
+
<tr>
+
<th scope="row">
+
DOI
</th>
+
<td>
+
10.5066/P9V6VCBO
</td>
+
</tr>
+
<tr>
+
<th scope="row">
+
Year published
</th>
+
<td>
+
2024
</td>
+
</tr>
+
<tr>
+
<th scope="row">
+
Version
</th>
+
<td>
+
<a href='https://code.usgs.gov/inl/mlms/-/tree/v1.0.0'>1.0.0</a>
</td>
+
</tr>
+
<tr>
+
<th scope="row">
+
IPDS
</th>
+
<td>
+
IP-151143
</td>
+
</tr>
+
</tbody>
+
</table>
<cr><!--/html_preserve-->
diff --git a/data/calibrations.rda b/data/calibrations.rda
index 267289f7a850f536320e09eef35a377fe076e8f5..66a36367e59cfefb7ab30f70d1fb1d94b1381e0a 100644
GIT binary patch
delta 357
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Dzzd;L
delta 357
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zc>E{^*PW4Cb*R8HFwmqb(cCCL00000s17{q00GeilnVd=g(SeyJ}?c70ssI200CKA
Dq<5i|
--
GitLab
From 8472b7578f31cd26a6b58f149517609ff64f2ac1 Mon Sep 17 00:00:00 2001
From: Jason Fisher <jfisher@usgs.gov>
Date: Mon, 10 Feb 2025 10:05:13 -0800
Subject: [PATCH 2/2] fix lintr issues
---
.lintr | 9 +++++----
Makefile | 6 +++++-
R/get_head_stats.R | 2 +-
R/plot_profile.R | 4 ++--
R/read_field_xlsx.R | 3 ++-
R/utils.R | 6 +++---
vignettes/download.Rmd | 3 +--
vignettes/heads.Rmd | 1 -
vignettes/ports.Rmd | 1 -
vignettes/samples.Rmd | 1 -
vignettes/statistics.Rmd | 1 -
vignettes/visits.Rmd | 2 +-
vignettes/wells.Rmd | 1 -
vignettes/zones.Rmd | 1 -
14 files changed, 20 insertions(+), 21 deletions(-)
diff --git a/.lintr b/.lintr
index f0c4585..bc81026 100644
--- a/.lintr
+++ b/.lintr
@@ -1,6 +1,7 @@
-linters: with_defaults(
- line_length_linter(120),
+linters: linters_with_defaults(
+ line_length_linter = line_length_linter(120),
object_usage_linter = NULL,
- undesirable_function_linter("sapply"),
- object_name_linter(styles = c("dotted.case", "snake_case", "symbols"))
+ assignment_linter = assignment_linter(),
+ function_left_parentheses_linter = function_left_parentheses_linter()
)
+encoding: "UTF-8"
diff --git a/Makefile b/Makefile
index 91be931..05d5fe4 100644
--- a/Makefile
+++ b/Makefile
@@ -40,6 +40,10 @@ cran-check: install
R CMD check --no-build-vignettes --as-cran $(PKGNAME)_$(PKGVERS).tar.gz
.PHONY: cran-check
+lintr:
+ R -q -e "lintr::lint_dir()"
+.PHONY: lintr
+
coverage:
R -q -e "covr::package_coverage(type = 'all')"
.PHONY: coverage
@@ -84,5 +88,5 @@ website: install
R -q -e "pkgdown::build_site()"
.PHONY: website
-everything: datasets erd install readme check coverage data-release website lockfile clean
+everything: datasets erd install readme check lintr coverage data-release website lockfile clean
.PHONY: everything
diff --git a/R/get_head_stats.R b/R/get_head_stats.R
index fa9cf99..a69682a 100644
--- a/R/get_head_stats.R
+++ b/R/get_head_stats.R
@@ -129,7 +129,7 @@ aggregate_data <- function(var_nm, digits = 2, by_port = TRUE) {
d <- do.call(rbind, args = l)
d <- data.frame("port_nu" = unique_ports, d)
- # aggregate by site only
+ # aggregate by site only
} else {
var_va <- heads[[var_nm]][is_site]
var_dt <- heads[["press_dt"]][is_site]
diff --git a/R/plot_profile.R b/R/plot_profile.R
index c0b780d..ae0d632 100644
--- a/R/plot_profile.R
+++ b/R/plot_profile.R
@@ -95,13 +95,13 @@ plot_profile <- function(site_nm,
xlab <- "Hydraulic head, in feet above the NAVD 88"
x <- d$total_head_va
- # set temperature data
+ # set temperature data
} else if (type == "temp") {
main <- "Temperature Profile"
xlab <- "Fluid temperature, in degree Celsius"
x <- d$temp_va
- # set water-quality data
+ # set water-quality data
} else {
d <- d[!is.na(d$sample_dt), ]
main <- "Water-Quality Profile"
diff --git a/R/read_field_xlsx.R b/R/read_field_xlsx.R
index 65b0e73..5f72716 100644
--- a/R/read_field_xlsx.R
+++ b/R/read_field_xlsx.R
@@ -187,7 +187,8 @@ read_excel_worksheet <- function(path, sheet, max_rows = 100L) {
# remove extraneous table rows
m <- apply(d, 1, function(x) all(is.na(x))) |>
- which() |> min() - 1L
+ which() |>
+ min() - 1L
d <- d[seq_len(m), , drop = FALSE]
# remove rows with missing values in required fields
diff --git a/R/utils.R b/R/utils.R
index 92cad62..334b7eb 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,7 +1,7 @@
# Function to calculate the specific weight of water in lb/ft^3, where temperature is in degC ----
calc_specific_weight <- function(temp) {
checkmate::assert_numeric(temp)
- rho <- 1000 * (1 - (temp + 288.9414) / (508929.2 * (temp + 68.12963)) * (temp - 3.9863)^2) # kg/m^3
+ rho <- 1000 * (1 - (temp + 288.9414) / (508929.2 * (temp + 68.12963)) * (temp - 3.9863)^2) # kg per cubic meter
sw <- rho * 9.80665 # N/m^3 or kg/(m^2*s^2)
sw * 0.22480894387 / 35.314666721
}
@@ -12,7 +12,7 @@ calc_press_head <- function(press_va, baro_va, temp_va) {
checkmate::assert_numeric(press_va)
checkmate::assert_numeric(baro_va)
checkmate::assert_numeric(temp_va)
- psf <- (press_va - baro_va) * 144 # lb/ft^2
+ psf <- (press_va - baro_va) * 144 # pounds per square foot
psf / calc_specific_weight(temp_va)
}
@@ -44,7 +44,7 @@ null_to_na <- function(x) {
# code adapted from a blog post by Stephen Turner,
# accessed on 2023-08-09 at
# https://gettinggeneticsdone.blogspot.com/2011/01/rstats-function-for-extracting-f-test-p.html
-get_p_value <- function (x) {
+get_p_value <- function(x) {
checkmate::assert_class(x, "lm")
f <- summary(x)$fstatistic
p <- stats::pf(f[1], f[2], f[3], lower.tail = FALSE)
diff --git a/vignettes/download.Rmd b/vignettes/download.Rmd
index a9e263f..2e00534 100644
--- a/vignettes/download.Rmd
+++ b/vignettes/download.Rmd
@@ -154,7 +154,7 @@ archive_size <- inldata::get_file_size(archive)
```{r echo=FALSE, results="asis"}
align <- c("l", rep("c", ncol(tbl) - 1L))
-options(knitr.kable.NA = '-')
+options(knitr.kable.NA = "-")
knitr::kable(tbl,
row.names = FALSE,
col.names = col_names,
@@ -177,5 +177,4 @@ fontawesome::fa("download") |>
) |>
htmltools::tagList() |>
htmltools::p()
-
```
diff --git a/vignettes/heads.Rmd b/vignettes/heads.Rmd
index 43de385..da5e7c3 100644
--- a/vignettes/heads.Rmd
+++ b/vignettes/heads.Rmd
@@ -191,5 +191,4 @@ mlms::heads[, names(columns)] |>
elementId = table_id
)
mlms::make_dl_button(table_id)
-
```
diff --git a/vignettes/ports.Rmd b/vignettes/ports.Rmd
index 8f762db..a8e294f 100644
--- a/vignettes/ports.Rmd
+++ b/vignettes/ports.Rmd
@@ -171,5 +171,4 @@ mlms::ports[, names(columns)] |>
elementId = table_id
)
mlms::make_dl_button(table_id)
-
```
diff --git a/vignettes/samples.Rmd b/vignettes/samples.Rmd
index c6f539f..be98e5a 100644
--- a/vignettes/samples.Rmd
+++ b/vignettes/samples.Rmd
@@ -166,5 +166,4 @@ mlms::samples[, names(columns)] |>
elementId = table_id
)
mlms::make_dl_button(table_id)
-
```
diff --git a/vignettes/statistics.Rmd b/vignettes/statistics.Rmd
index 6040d7a..f5a47cf 100644
--- a/vignettes/statistics.Rmd
+++ b/vignettes/statistics.Rmd
@@ -227,5 +227,4 @@ columns <- get_columns(
)
add_web_table(table_id, columns, var_nm = "total_head_va")
mlms::make_dl_button(table_id)
-
```
diff --git a/vignettes/visits.Rmd b/vignettes/visits.Rmd
index 0516666..d09ccdb 100644
--- a/vignettes/visits.Rmd
+++ b/vignettes/visits.Rmd
@@ -170,6 +170,6 @@ mlms::visits[, names(columns)] |>
compact = TRUE,
elementId = table_id
)
- mlms::make_dl_button(table_id)
+mlms::make_dl_button(table_id)
```
diff --git a/vignettes/wells.Rmd b/vignettes/wells.Rmd
index fc19433..7bcfda5 100644
--- a/vignettes/wells.Rmd
+++ b/vignettes/wells.Rmd
@@ -245,7 +245,6 @@ data[, names(columns)] |>
elementId = table_id
)
mlms::make_dl_button(table_id)
-
```
<!-- Embedded References -->
diff --git a/vignettes/zones.Rmd b/vignettes/zones.Rmd
index 04928c7..4db49c1 100644
--- a/vignettes/zones.Rmd
+++ b/vignettes/zones.Rmd
@@ -120,5 +120,4 @@ mlms::zones[, names(columns)] |>
elementId = table_id
)
mlms::make_dl_button(table_id)
-
```
--
GitLab