Sorely needed update

.Rbuildignore

@@ -28,3 +28,4 @@ vignettes/figure
 ^cran-comments\.md$
 ^codecov\.yml$
 ^CRAN-RELEASE$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: kitagawa
 Type: Package
 Title: Spectral Response of Water Wells to Harmonic Strain and Pressure Signals
-Version: 3.1.0
-Date: 2020-06-21
+Version: 3.1.1
+Date: 2023-08-13
 Authors@R:
     c(person(given = c("Andrew","J."),
              family = "Barbour",
@@ -55,4 +55,4 @@ Suggests:
     covr
 VignetteBuilder: knitr
 Encoding: UTF-8
-RoxygenNote: 7.1.0
+RoxygenNote: 7.2.3

R/utilities.R

@@ -189,6 +189,7 @@ sensing_volume <- function(rad_grout, len_grout, rad_screen, len_screen){
 #' @param t.ratio numeric; the ratio of minor to major tick lengths.
 #' @param major.ticks numeric; the axis limits.
 #' @param base numeric; the base of the logarithm (somewhat experimental)
+#' @param ticks.only logical; on the axis
 #' @param ... additional parameters passed to the \code{axis} call for the major ticks.
 #' 
 #' @author A. J. Barbour <andy.barbour@@gmail.com>
@@ -199,9 +200,16 @@ sensing_volume <- function(rad_grout, len_grout, rad_screen, len_screen){
 #' @examples
 #' x <- 10^(0:8)
 #' y <- 1:9
+#' 
+#' plot(log10(x),y,xaxt="n",xlab="x",xlim=c(0,9))
+#' logticks()
+#' logticks(ax=3, ticks.only=TRUE)
+#' 
+#' par(tcl=0.5) # have tick marks show up on inside instead
 #' plot(log10(x),y,xaxt="n",xlab="x",xlim=c(0,9))
 #' logticks()
-logticks <- function(ax=1, n.minor=9, t.lims, t.ratio=0.5, major.ticks=NULL, base=c("ten","ln","two"), ...){
+#' logticks(ax=3, ticks.only=TRUE)
+logticks <- function(ax=1, n.minor=9, t.lims, t.ratio=0.5, major.ticks=NULL, base=c("ten","ln","two"), ticks.only=FALSE, ...){
   # axis limits
   lims <- par("usr")
   # x or y axis
@@ -222,7 +230,11 @@ logticks <- function(ax=1, n.minor=9, t.lims, t.ratio=0.5, major.ticks=NULL, bas
   base <- switch(base, two=2, ln="e", ten=10)
 
   # create tick label expressions
-  tick.labels <- sapply(major.ticks, function(i) as.expression(bquote(.(base) ^ .(i))) )
+  tick.labels <- if (ticks.only){
+    FALSE
+  } else {
+    sapply(major.ticks, function(i) as.expression(bquote(.(base) ^ .(i))) )
+  }
   # add major ticks
   axis(ax, at=major.ticks, labels=tick.labels, ...)
 

README.md

@@ -4,9 +4,14 @@ Tools to calculate the theoretical spectral response
 of fluid-pressure in a water well
 to harmonic strains (e.g., tides, long-period seismic waves).
 
-
-[![Travis Build Status](https://travis-ci.org/abarbour/kitagawa.svg)](https://travis-ci.org/abarbour/kitagawa) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/abarbour/kitagawa?branch=master&svg=true)](https://ci.appveyor.com/project/abarbour/kitagawa) [![Code Coverage](https://codecov.io/gh/abarbour/kitagawa/branch/master/graph/badge.svg)](https://codecov.io/gh/abarbour/kitagawa?branch=master) [![License](https://img.shields.io/badge/license-GPL-orange.svg)](https://www.gnu.org/licenses/gpl-2.0.html) [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/kitagawa)](https://cran.r-project.org/package=kitagawa) [![Downloads](https://cranlogs.r-pkg.org/badges/kitagawa)](https://www.r-pkg.org/pkg/kitagawa)
-
+  <!-- badges: start -->
+  [![R-CMD-check](https://github.com/abarbour/kitagawa/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abarbour/kitagawa/actions/workflows/R-CMD-check.yaml)\
+[![Code Coverage](https://codecov.io/gh/abarbour/kitagawa/branch/master/graph/badge.svg)](https://codecov.io/gh/abarbour/kitagawa?branch=master)\
+[![License](https://img.shields.io/badge/license-GPL-orange.svg)](https://www.gnu.org/licenses/gpl-2.0.html)\
+[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/kitagawa)](https://cran.r-project.org/package=kitagawa)\
+[![Downloads](https://cranlogs.r-pkg.org/badges/kitagawa)](https://www.r-pkg.org/pkg/kitagawa)
+  <!-- badges: end -->
+
 ## Models of spectral response
 
 This code calculates the response at two types of wells: a sealed well and

TODO

@@ -18,12 +18,7 @@
 *** open_well_response [X]
 *** well_response [ ]
 
-[ ] Method to estimate transfer function between two series
-*** MT CSD <-- perhaps include in  psd
-
 [ ] Datasets:
-*** Honshu timeseries [X] <-- in  psd
 *** PBO-PP well information (and calculated sensing volumes)
-*** Slug test series???
 
 

cran-comments.md

@@ -1,10 +1,5 @@
-## Test environments
-* local R installation, R 4.0.1
-* Debian Linux (on rhub)
-* remote R installation (on travis-ci), R devel (2020-06-22 r78735)
-* ubuntu 16.04 (on travis-ci), R 4.0.1 (and devel)
-* win-builder (devel)
+## R CMD check results
 
-* This fixes build errors caused by removal of linked package 'sapa'
+0 errors | 0 warnings | 1 note
 
-Thanks for all you do for the community!
+* This is a new release.

inst/NEWS.Rd

@@ -19,9 +19,11 @@ News for package \kitagawa{}: \CRANpkg{kitagawa} -- \GITpkg{kitagawa} --
 
 \encoding{UTF-8}
 
-\section{CHANGES IN VERSION 3.1 (2020-06-21)}{
+\section{CHANGES IN VERSION 3.1+ (last updated 2023-08-13)}{
   \itemize{
-    \item Added the model of Wang et al (2018; \href{https://doi.org/10.1029/2018WR022793}{10.1029/2018WR022793}),
+    \item 3.1.1: added a \code{ticks.only} option to \code{logticks}
+
+    \item 3.1: Added the model of Wang et al (2018; \href{https://doi.org/10.1029/2018WR022793}{10.1029/2018WR022793}),
     to the model toolbox and to the ResponseModels toolbox. Thanks to \JK for contributing this.
     \item New test validating Wang model against Hsieh model (they are equivalent when specific leakage is zero).
     Thanks to \JK for contributing this.

revdep/README.md

@@ -1,16 +1,17 @@
 # Platform
 
-|field    |value                        |
-|:--------|:----------------------------|
-|version  |R version 4.0.1 (2020-06-06) |
-|os       |macOS Mojave 10.14.6         |
-|system   |x86_64, darwin17.0           |
-|ui       |X11                          |
-|language |(EN)                         |
-|collate  |en_US.UTF-8                  |
-|ctype    |en_US.UTF-8                  |
-|tz       |America/Los_Angeles          |
-|date     |2020-06-22                   |
+|field    |value                         |
+|:--------|:-----------------------------|
+|version  |R version 4.2.3 (2023-03-15)  |
+|os       |macOS Catalina 10.15.7        |
+|system   |x86_64, darwin17.0            |
+|ui       |X11                           |
+|language |(EN)                          |
+|collate  |en_US.UTF-8                   |
+|ctype    |en_US.UTF-8                   |
+|tz       |UTC                           |
+|date     |2023-08-13                    |
+|pandoc   |3.1.1 @ /opt/local/bin/pandoc |
 
 # Dependencies