Merge branch 'develop'

.github/ISSUE_TEMPLATE.md

@@ -1,2 +1,2 @@
-Instructions: please remove these sentences, replacing them with (1) a sentence or two describing the issue, (2) a pared-down code example, and (3) the output from `sessionInfo()`. An ideal way to prepare your code is to use the `reprex` function from the `reprex` package. If your code needs data, please attach relevant files to your comment, or, if the data are private, email the files to the developers ([email protected] and [email protected]), who will respect your privacy.
+Instructions: please remove these sentences, replacing them with (1) a sentence or two describing the issue, (2) a pared-down code example, and (3) the output from `sessionInfo()`. An ideal way to prepare your code is to use the `reprex` function from the `reprex` package (see https://dankelley.github.io/dek_blog/2024/03/06/reprex.html for how to use `reprex`). If your code needs data, please attach relevant files to your comment, or, if the data are private, email the files to the developers ([email protected] and [email protected]), who will respect your privacy.
 

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.lintr

@@ -1,6 +1,6 @@
 linters:linters_with_defaults(
     indentation_linter=NULL,
-    line_length_linter(150),
+    line_length_linter(200),
     object_name_linter=NULL,
     infix_spaces_linter=NULL,
     brace_linter=NULL,

CODE_OF_CONDUCT.md

@@ -2,7 +2,12 @@
 
 ## Our Pledge
 
-In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
 
 ## Our Standards
 
@@ -16,31 +21,54 @@ Examples of behavior that contributes to creating a positive environment include
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
 * Trolling, insulting/derogatory comments, and personal or political attacks
 * Public or private harassment
-* Publishing others' private information, such as a physical or electronic address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a professional setting
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
 ## Our Responsibilities
 
-Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
 
-Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
 
 ## Scope
 
-This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [email protected]. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at <[email protected]>. The project
+team will review and investigate all complaints, and will respond in a way that
+it deems appropriate to the circumstances. The project team is obligated to
+maintain confidentiality with regard to the reporter of an incident. Further
+details of specific enforcement policies may be posted separately.
 
-Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.4, available at
+[http://contributor-covenant.org/version/1/4][version]
 
 [homepage]: http://contributor-covenant.org
 [version]: http://contributor-covenant.org/version/1/4/

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: oce
 Title: Analysis of Oceanographic Data
-Version: 1.8-2
+Version: 1.8-3
 Authors@R: c(
     person(given="Dan", family="Kelley", email="[email protected]", role=c("aut", "cre"), comment=c(ORCID="https://orcid.org/0000-0001-7808-5911")),
     person(given="Clark", family="Richards", email="[email protected]", role=c("aut"), comment=c(ORCID="https://orcid.org/0000-0002-7833-206X")),
     person(given="Chantelle", family="Layton", email="[email protected]", role=c("ctb"), comment=c(ORCID="https://orcid.org/0000-0002-3199-5763", "curl() coauthor")),
     person(given="British Geological Survey", role=c("ctb","cph"), comment="magnetic-field subroutine"))
 Maintainer: Dan Kelley <[email protected]>
-Depends: R (>= 2.15), gsw, methods, utils
+Depends: R (>= 4.1.0), gsw, methods, utils
 Suggests:
     automap,
     DBI,
@@ -39,7 +39,7 @@ Encoding: UTF-8
 URL: https://dankelley.github.io/oce/
 LazyData: false
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 BuildVignettes: true
 VignetteBuilder: knitr
 NeedsCompilation: yes

NAMESPACE

@@ -140,6 +140,7 @@ export(
     equatorialToLocalHorizontal,
     errorbars,
     fillGap,
+    fillGapMatrix,
     findBottom,
     firstFinite,
     formatCI,
@@ -368,6 +369,9 @@ export(
     swSoundSpeed,
     swSpecificHeat,
     swSpice,
+    swSpiciness0,
+    swSpiciness1,
+    swSpiciness2,
     swSR,
     swSstar,
     swSTrho,

NEWS.md

@@ -1,57 +1,92 @@
-# oce 1.8.2
+# oce 1.8.3
+
+* Add `swSpiciness0()`, `swSpiciness1()`, and `swSpiciness2()` (issue #2188). 
+* Change `binMean2D()` to use previous (6-month-old) method (issue #2199).
+* Change `[[` for many seawater properties to handle `argo` data (issues #2207 and #2208).
+* Change `concatenate()` to handle `data` slots that are data frames (issue #2213).
+* Change `ctdDecimate()` to add the `na.rm` argument (issue #2192).
+* Change `mapDirectionField()` to allow wind barbs (issue #2191).
+* Change `mapContour()` to discuss longitude conventions (issue #2218).
+* Change `mapImage()` to handle a user-provided gridding function (issue #2199).
+* Change `mapImage()` to add the `gridCoarseness` parameter (issue #2199).
+* Change `oceMagic()` to close netcdf files after checking them (issue #2209).
+* Change `plot.amsr()` to add the `zlab` parameter (issue #2220).
+* Change `plot.argo()` to handle `which="sigma0 profile"` (issue #2184).
+* Change `plot.sealevel()` to add the `grid` parameter (issue #2204).
+* Change `plot.sealevel()` to improve labelling (issue #2203).
+* Change `plot.section()` to handle bottom traces better (issue #2194).
+* Change `plot.section()` to show data as points properly (issue #2195).
+* Change `plotProfile()` to handle `xaxs` and `yaxs` when `xtype="spiciness0"` (issue #2215).
+* Change `plotTaylor()` to handle a few more parameters.
+* Change `read.adp.rdi()` to handle large (> 2.147 GB) files (issue #2196).
+* Change `read.amsr()` to read start/end times plus other metadata (issue #2219).
+* Change `read.argo()` to handle non-UTF characters in metadata (issue #2206).
+* Change `read.ctd.sbe()` to name `specc` as `specificConductance` (issue #2211).
+* Change `read.met()` to return `data` slots that are lists (issue #2213).
+* Change `resizableLabel()` to document partial-match behaviour (issue #2197).
+* Change `resizableLabel()` to handle `item=`"N"` (issue #2197).
+* Change `summary()` to skip time in the threenum table (issue #2198).
+* Change `sunAngle()` to handle vector arguments better (issue #2178).
+* Change `sunAngle()` to detect non-logical values of `useRefraction` (issue #2225).
+* Change some byte-level work from C to C++ to improve maintainability (issue #2201).
+
+# oce 1.8.2 (on CRAN)
 
 * Add `package?oce` documentation (had been missing with a Roxygen2 change).
-* Add `read.ctd.saiv()` to read data from SAIV instruments (issue 2141).
-* Remove many dontrun examples from the docs (issue 2152).
-* Remove `trimString()`, after it had been deprecated for a long time (issue 2123).
-* Remove use of the deprecated `sp` package (issue 2154).
-* Change `amsr` dataset and functions to handle new format (issues 2124 to 2133, 2147).
-* Change `as.ctd()` to handle multi-profile Argo better (issue 2173).
-* Change `as.tidem()` to handle NOAA constituent names and frequencies (issues 2143, 2144 and 2146).
-* Change C/C++ `sprintf()` calls so all formats match arguments (issue 2172).
+* Add `read.ctd.saiv()` to read data from SAIV instruments (issue #2141).
+* Remove many dontrun examples from the docs (issue #2152).
+* Remove `trimString()`, after it had been deprecated for a long time (issue #2123).
+* Remove use of the deprecated `sp` package (issue #2154).
+* Change `amsr` dataset and functions to handle new format (issues #2124 to #2133 plus
+  issue #2147).
+* Change `as.ctd()` to handle multi-profile Argo better (issue #2173).
+* Change `as.tidem()` to handle NOAA constituent names and frequencies (issues #2143,
+  #2144 and #2146).
+* Change C/C++ `sprintf()` calls so all formats match arguments (issue #2172).
 * Change `computableWaterProperties` to handle a vector of variable names.
-* Change `plot.adp()` to obey `xlab` if x axis represents time (issue 2162).
-* Change `plot.cm()` to obey `xlim`, `ylim`, `xaxs` and `yaxs` (issue 2121).
+* Change `plot.adp()` to obey `xlab` if x axis represents time (issue #2162).
+* Change `plot.cm()` to obey `xlim`, `ylim`, `xaxs` and `yaxs` (issue #2121).
 * Change `plotTS()` and `plotProfile()` to accept `type="b"`.
-* Change `plot.windrose()` for `type="fivenum"` (issue 2164).
+* Change `plot.windrose()` for `type="fivenum"` (issue #2164).
 
 # oce 1.8.1 (on CRAN)
 
 * Change `as.ctd()` to handle `startTime`, `PRES`, `PSAL` and `TEMP` better.
-* Change `binCount1D()` + 6 related functions by adding `include.lowest` parameter (issue 2113).
-* Change C++ files to avoid an error relating to include statements (issue 2119).
-* Change `imagep()` to ensure `z` (if provided) is a matrix (issue 2091).
-* Change `plot.section()` to skip the kriging example (issue 2080).
-* Change `plot.section()` to show palette triangles if necessary (issue 2083).
-* Change `plot.section()` to show data and bottom correctly (issue 2092).
-* Change `plotTS()` to obey the `rho1000` parameter again (issue 2085).
+* Change `binCount1D()` + 6 related functions by adding `include.lowest` parameter (issue
+#2113).
+* Change C++ files to avoid an error relating to include statements (issue #2119).
+* Change `imagep()` to ensure `z` (if provided) is a matrix (issue #2091).
+* Change `plot.section()` to skip the kriging example (issue #2080).
+* Change `plot.section()` to show palette triangles if necessary (issue #2083).
+* Change `plot.section()` to show data and bottom correctly (issue #2092).
+* Change `plotTS()` to obey the `rho1000` parameter again (issue #2085).
 * Change `read.argo()` to translate more variable names.
 * Change `read.netcdf()` to read more items.
-* Change `read.rsk()` to obey the `tz` parameter (issue 2108).
-* Change `summary.adp()` to handle the new format for AD2CP data (issue 2087).
+* Change `read.rsk()` to obey the `tz` parameter (issue #2108).
+* Change `summary.adp()` to handle the new format for AD2CP data (issue #2087).
 
 # oce 1.8.0 (on CRAN)
 
-* Add `advSontekAdrFileTrim()` (issue 1994).
-* Add `ctdFindProfilesRBR()` (issue 2027).
-* Change `applyMagneticDeclination()` to also handle `adp` and `adv` (issue 2038).
-* Change `download.topo()` to handle new NOAA database (issue 2015).
+* Add `advSontekAdrFileTrim()` (issue #1994).
+* Add `ctdFindProfilesRBR()` (issue #2027).
+* Change `applyMagneticDeclination()` to also handle `adp` and `adv` (issue #2038).
+* Change `download.topo()` to handle new NOAA database (issue #2015).
 * Change `inst/extdata` by compressing some files.
-* Change `mapPlot()` to remove an infrequent low-level error (issue 2036).
-* Change `mapPlot()` to require `projection` to be a string (issue 2076).
-* Change `numberAsPOSIXct(t, type="gps")` to handle week rollover (issue 2077).
-* Change `plot.echosounder()` to use `oceColorsViridis()` by default (issue 2060).
-* Change `plotProfile()` to create xlab on vector input (issue 2047).
-* Change `plotTS()` to compute isopycnals more accurately (issue 2046).
+* Change `mapPlot()` to remove an infrequent low-level error (issue #2036).
+* Change `mapPlot()` to require `projection` to be a string (issue #2076).
+* Change `numberAsPOSIXct(t, type="gps")` to handle week rollover (issue #2077).
+* Change `plot.echosounder()` to use `oceColorsViridis()` by default (issue #2060).
+* Change `plotProfile()` to create xlab on vector input (issue #2047).
+* Change `plotTS()` to compute isopycnals more accurately (issue #2046).
 * Change `plotTS()` to handle lobo objects directly.
-* Change `plot.tidem()` to obey `...` parameter (issue 2035).
-* Change `read.adp.ad2cp()`, and structure of AD2CP objects (issue 2005).
-* Change `read.rsk()` to read geographic information (issue 2024).
+* Change `plot.tidem()` to obey `...` parameter (issue #2035).
+* Change `read.adp.ad2cp()`, and structure of AD2CP objects (issue #2005).
+* Change `read.rsk()` to read geographic information (issue #2024).
 * Change `sectionSmooth()` to handle `method="kriging"` again
-* Change `tidem()` (and summary method) to handle 6-hourly data (issue 2034).
-* Remove package dependence on `rgeos` and `raster` packages (issue 2028).
-* Remove `plotAD2CP()`, now superseded by generic `plot()` method (issue 2005).
-* Remove plotting tests but retain in developer suite (issue 2073).
+* Change `tidem()` (and summary method) to handle 6-hourly data (issue #2034).
+* Remove package dependence on `rgeos` and `raster` packages (issue #2028).
+* Remove `plotAD2CP()`, now superseded by generic `plot()` method (issue #2005).
+* Remove plotting tests but retain in developer suite (issue #2073).
 
 # oce 1.7.10 (on CRAN)
 

R/.lintr

@@ -1,6 +1,6 @@
 linters:linters_with_defaults(
     indentation_linter=NULL,
-    line_length_linter(150),
+    line_length_linter(200),
     object_name_linter=NULL,
     infix_spaces_linter=NULL,
     brace_linter=NULL,