version 1.0.1

cran · Aug 22, 2023 · d65ed68 · d65ed68
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: aion
 Title: Archaeological Time Series
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: c(
     person("Nicolas", "Frerebeau", , "nicolas.frerebeau@u-bordeaux-montaigne.fr", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5759-4944", affiliation = "Université Bordeaux Montaigne")),
@@ -21,7 +21,7 @@ URL: https://packages.tesselle.org/aion/,
         https://github.com/tesselle/aion
 BugReports: https://github.com/tesselle/aion/issues
 Depends: R (>= 3.3)
-Imports: arkhe, graphics, grDevices, methods
+Imports: arkhe (>= 1.2.0), graphics, grDevices, methods
 Suggests: knitr, rmarkdown, rsvg, svglite, tinysnapshot, tinytest
 VignetteBuilder: knitr
 Encoding: UTF-8
@@ -33,11 +33,11 @@ Collate: 'AllClasses.R' 'AllGenerics.R' 'aion-internal.R'
         'operators.R' 'plot.R' 'series.R' 'show.R' 'subset.R' 'time.R'
         'validate.R' 'years.R' 'zzz.R'
 NeedsCompilation: no
-Packaged: 2023-06-12 15:49:02 UTC; nicolas
+Packaged: 2023-08-22 12:29:54 UTC; nicolas
 Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>,
     Université Bordeaux Montaigne),
   Joe Roe [aut] (<https://orcid.org/0000-0002-1011-1244>, Universität
     Bern),
   Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>)
 Repository: CRAN
-Date/Publication: 2023-06-13 08:10:07 UTC
+Date/Publication: 2023-08-22 13:20:06 UTC
diff --git a/MD5 b/MD5
@@ -1,10 +1,10 @@
-5d2b53c1b1d86c73136d92a804adc304 *DESCRIPTION
+fa4ea8bbfdd437726eb9b80f9f74c439 *DESCRIPTION
 c86f326ba18234f6525c1105935f3d19 *NAMESPACE
-e5a0f835e720e71940f3d1db2d3765b0 *NEWS.md
+a6f6bbe979140e2e9b6f7c3f78f87e8d *NEWS.md
 67960379b200bfe9aa8551629b7438aa *R/AllClasses.R
-d6ed79219a7b26be5c4ef90c775b952a *R/AllGenerics.R
+446910517e46c1374bf711f7d92914a5 *R/AllGenerics.R
 d38656be290fc75e1397c02d17dad773 *R/aion-internal.R
-c0ad5ccb3b679a12cc238855525334e1 *R/aion-package.R
+9d42a29455c74af54599f5f535417e0a *R/aion-package.R
 867ae0303a7ba79337c671554188f8eb *R/calendar-gregorian.R
 e57e25362b28aa0a30a778b47861295f *R/calendar-julian.R
 a1892ab0eeda755a2e7271606e127858 *R/calendar.R
@@ -13,28 +13,28 @@ a1892ab0eeda755a2e7271606e127858 *R/calendar.R
 04ffc4a2693131e7a2082e059b961f5d *R/data.R
 3885bdf16134fb80d9f885a2c93a6aa0 *R/mutators.R
 1b96b10ba44344b4742dd0122221b7d6 *R/operators.R
-fbe9b5120a01326e649d78d7052a5ada *R/plot.R
+966ef90cbe745df16eba048da6628f1b *R/plot.R
 20835ca69fc0e29f18693358d15d147c *R/series.R
 ccddcf756920a2721d9254965dfab749 *R/show.R
 120c05ad32491be24ee55207641add03 *R/subset.R
 6c67ffbfd786aac914cfdb29be035e57 *R/time.R
 5fddcd20cb47f4bfbb50afb8834befc2 *R/validate.R
 b27459412d6cfda6e7d74255c4366007 *R/years.R
 958b1e7880269969e082958ea8dffddf *R/zzz.R
-2702a67de81aa73965c6cac3b982ecd0 *README.md
-439bf689fa27cf9affd0335332142165 *build/partial.rdb
-61682881e88fca95f84ba15e696321d5 *build/vignette.rds
+94c8bbcca0696fe20302e68d9e47fdef *README.md
+7080893e02c49cd296d4424b9be55069 *build/partial.rdb
+76ae13cd86bd563b19ca20cb61c9e2d5 *build/vignette.rds
 7821d926987c8529109c3aa2f74a50c0 *data/dates.rda
-7a6c2fb7732b82f449b41a04f14ed49a *inst/CITATION
+ded1411252f430084e356392715bdf1d *inst/CITATION
 a84f50702f9ad242da4df77d2b4dd2f1 *inst/doc/aion.R
 63aee94a51d8aaab9139b45315816ce0 *inst/doc/aion.Rmd
-d430dba07ab2cea126d68a6a9cce8bd6 *inst/doc/aion.html
+be0a9944b5e25211c9a4f09ce5691a4f *inst/doc/aion.html
 46750e778a5cdb4d65c347f8e43df623 *inst/doc/bibliography.R
 1ce99d6139b36c341c6a9f8c293c7b24 *inst/doc/bibliography.Rmd
-d811ce583f3427e89330b77598e6bfe9 *inst/doc/bibliography.html
+2d59ea48aeba6e3c9cc2f4afeb93f552 *inst/doc/bibliography.html
 437b98c8ab52986e88ef007d96ed1186 *inst/doc/extending.R
 fb7cbe03ee29ac49bdeb5bf8a075dfd0 *inst/doc/extending.Rmd
-62a6dd420b5f1a8a41c361173a2cd367 *inst/doc/extending.html
+c0d1fe4e851b4b26032eb4957faaedef *inst/doc/extending.html
 b6df944a691946342c9c4cf20469b97f *inst/examples/ex-arith.R
 4b8b1a6a41d5b8208582b493cef2c30e *inst/examples/ex-axis.R
 ff525a5ae8022028c01805334c548649 *inst/examples/ex-calendar.R
@@ -80,7 +80,7 @@ d03ffb3c4be8c5957ace6bb965bd2aaf *man/BP-class.Rd
 526f4aca74cafd221b40801e8f31bc9c *man/RataDie-class.Rd
 32c76b530fee710bc27276f6a238dd58 *man/TimeScale-class.Rd
 0f5940509c0fe99ab1e531aca1a43d79 *man/TimeSeries-class.Rd
-1242c31c176e2fbe56e67d89960001ac *man/aion-package.Rd
+6a3bc23cebb6fb064fa6082fa743bd9d *man/aion-package.Rd
 28f8e7cee50e1a369a6df23d0554df6e *man/arithmetic.Rd
 aa97a7c0249003d54ff4c7f783c389e3 *man/as_date.Rd
 3f987dadfc8033b43d59c81282463c26 *man/as_decimal.Rd
@@ -105,7 +105,7 @@ dfc91cf91a638a4ea5cce1ae5bc98022 *man/gregorian.Rd
 60499796e6c4aca1bf1418a4646b9dd7 *man/julian.Rd
 33af9a3b552f75b45d0e96ada33fbba4 *man/plot.Rd
 cd920650b0333b7e33787d5aca4d7055 *man/pretty.Rd
-1b3563f69eb2d03549b85deb4503ee44 *man/series.Rd
+7186ca471db14dc172bdee5327f5ce49 *man/series.Rd
 790d3d636f529aa4faf42add2293324b *man/span.Rd
 780f3cf5452614a6797b9caf5e2711b6 *man/start.Rd
 02a43b46e3ab8b66893689c34322624d *man/subset.Rd

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# aion 1.0.1
+## Bugfixes & changes
+* `plot()` now supports missing values.
+
 # aion 1.0.0
 
 * First release.
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -452,8 +452,8 @@ NULL
 #' Create Time Series
 #'
 #' @param object A [`numeric`] `vector`, `matrix` or `array` of the observed
-#'  time-series values.
-#'  A [`data.frame`] will be coerced to a `numeric` `matrix` via [data.matrix()].
+#'  time-series values. A [`data.frame`] will be coerced to a `numeric` `matrix`
+#'  via [data.matrix()].
 #' @param time A [`numeric`] vector of (decimal) years or a [`RataDie-class`]
 #'  object (see [fixed()]).
 #' @param calendar A [`TimeScale-class`] object specifying the calendar of

diff --git a/R/aion-package.R b/R/aion-package.R
@@ -2,8 +2,9 @@
 #'  \tabular{ll}{
 #'   **Package:** \tab aion \cr
 #'   **Type:** \tab Package \cr
-#'   **Version:** \tab 1.0.0 \cr
+#'   **Version:** \tab 1.0.1 \cr
 #'   **License:** \tab GPL-3 \cr
+#'   **Zenodo:** \tab \doi{10.5281/zenodo.8032278} \cr
 #'  }
 #'
 #' @section Package options:

diff --git a/R/plot.R b/R/plot.R
@@ -100,7 +100,7 @@ setMethod("plot", c(x = "TimeSeries", y = "missing"), plot.TimeSeries)
   ## Set plotting coordinates
   years <- time(x, calendar = calendar)
   xlim <- xlim %||% xlim(x, calendar = calendar)
-  ylim <- ylim %||% range(x)
+  ylim <- ylim %||% range(x, na.rm = TRUE)
   graphics::plot.window(xlim = xlim, ylim = ylim)
 
   ## Evaluate pre-plot expressions
@@ -152,6 +152,8 @@ setMethod("plot", c(x = "TimeSeries", y = "missing"), plot.TimeSeries)
 #'  The default is [graphics::lines()].
 #' @param y_flip A [`logical`] scalar: should the y-axis (ticks and numbering)
 #'  be flipped from side 2 (left) to 4 (right) from series to series?
+#' @param y_fixed A [`logical`] scalar: should the y-scale be shared across
+#'  all series?
 #' @param ncol An [`integer`] specifying the number of columns to use.
 #'  Defaults to 1 for up to 4 series, otherwise to 2.
 #' @param main A [`character`] string giving a main title for the plot.
@@ -174,7 +176,7 @@ setMethod("plot", c(x = "TimeSeries", y = "missing"), plot.TimeSeries)
 #' @keywords internal
 #' @noRd
 .plot_multiple <- function(x, calendar, panel = graphics::lines,
-                           y_flip = TRUE, n_col = NULL,
+                           y_flip = TRUE, y_fixed = FALSE, n_col = NULL,
                            xlab = NULL, ylab = NULL,
                            main = NULL, sub = NULL,
                            ann = graphics::par("ann"), axes = TRUE,
@@ -211,12 +213,13 @@ setMethod("plot", c(x = "TimeSeries", y = "missing"), plot.TimeSeries)
 
   years <- time(x, calendar = calendar)
   xlim <- xlim(x, calendar = calendar)
+  ylim <- if (y_fixed) range(x, na.rm = TRUE) else NULL
   ylabs <- ylab %||% colnames(x) %||% paste("Series", n_seq, sep = " ")
   for (j in n_seq) {
     ## Plot
     xj <- x[, j, , drop = FALSE]
     .plot_single(xj, calendar = calendar, panel = panel,
-                 xlim = xlim, ylim = NULL,
+                 xlim = xlim, ylim = ylim,
                  main = NULL, sub = NULL, ann = FALSE, axes = FALSE,
                  frame.plot = frame.plot,
                  panel.first = panel.first, panel.last = panel.last, ...)
@@ -357,4 +360,3 @@ year_axis <- function(side, at = NULL, format = c("a", "ka", "Ma", "Ga"),
 
   graphics::axis(side, at = as.numeric(at), labels = labels, ...)
 }
-
diff --git a/README.md b/README.md
@@ -8,14 +8,27 @@
 [![R-CMD-check](https://github.com/tesselle/aion/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/aion/actions)
 [![codecov](https://codecov.io/gh/tesselle/aion/branch/main/graph/badge.svg?token=UgoOXsZW86)](https://app.codecov.io/gh/tesselle/aion)
 [![CodeFactor](https://www.codefactor.io/repository/github/tesselle/aion/badge/main)](https://www.codefactor.io/repository/github/tesselle/aion/overview/main)
+[![Dependencies](https://tinyverse.netlify.com/badge/aion)](https://cran.r-project.org/package=aion)
 
 <a href="https://tesselle.r-universe.dev" class="pkgdown-devel"><img
 src="https://tesselle.r-universe.dev/badges/aion"
 alt="r-universe" /></a>
+<a href="https://cran.r-project.org/package=aion"
+class="pkgdown-release"><img
+src="http://www.r-pkg.org/badges/version/aion" alt="CRAN Version" /></a>
+<a href="https://cran.r-project.org/web/checks/check_results_aion.html"
+class="pkgdown-release"><img
+src="https://badges.cranchecks.info/worst/aion.svg"
+alt="CRAN checks" /></a>
+<a href="https://cran.r-project.org/package=aion"
+class="pkgdown-release"><img src="http://cranlogs.r-pkg.org/badges/aion"
+alt="CRAN Downloads" /></a>
 
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8032278.svg)](https://doi.org/10.5281/zenodo.8032278)
 <!-- badges: end -->
 
 ## Overview
@@ -43,8 +56,9 @@ offers a simple API that can be used by other specialized packages.
     To cite aion in publications use:
 
       Frerebeau N, Roe J (2023). _aion: Archaeological Time Series_.
-      Université Bordeaux Montaigne, Pessac, France. R package version
-      1.0.0, <https://packages.tesselle.org/aion/>.
+      Université Bordeaux Montaigne, Pessac, France.
+      doi:10.5281/zenodo.8032278 <https://doi.org/10.5281/zenodo.8032278>,
+      R package version 1.0.1, <https://packages.tesselle.org/aion/>.
 
     Une entrée BibTeX pour les utilisateurs LaTeX est
 
@@ -54,8 +68,9 @@ offers a simple API that can be used by other specialized packages.
         year = {2023},
         organization = {Université Bordeaux Montaigne},
         address = {Pessac, France},
-        note = {R package version 1.0.0},
+        note = {R package version 1.0.1},
         url = {https://packages.tesselle.org/aion/},
+        doi = {10.5281/zenodo.8032278},
       }
 
     This package is a part of the tesselle project

diff --git a/build/partial.rdb b/build/partial.rdb
diff --git a/build/vignette.rds b/build/vignette.rds
diff --git a/inst/CITATION b/inst/CITATION
@@ -9,5 +9,6 @@ bibentry(
   organization = "Université Bordeaux Montaigne",
   address      = "Pessac, France",
   note         = sprintf("R package version %s", meta$Version),
-  url          = "https://packages.tesselle.org/aion/"
+  url          = "https://packages.tesselle.org/aion/",
+  doi          = "10.5281/zenodo.8032278"
 )
diff --git a/inst/doc/aion.html b/inst/doc/aion.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="N. Frerebeau" />
 
-<meta name="date" content="2023-06-12" />
+<meta name="date" content="2023-08-22" />
 
 <title>Introduction to aion</title>
 
@@ -362,7 +362,7 @@
 
 <h1 class="title toc-ignore">Introduction to aion</h1>
 <h4 class="author">N. Frerebeau</h4>
-<h4 class="date">2023-06-12</h4>
+<h4 class="date">2023-08-22</h4>
 
 
 <div id="TOC">

diff --git a/inst/doc/bibliography.html b/inst/doc/bibliography.html
@@ -11,7 +11,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 
 
-<meta name="date" content="2023-06-12" />
+<meta name="date" content="2023-08-22" />
 
 <title>Bibliography</title>
 
@@ -261,7 +261,7 @@
 <h1 class="title toc-ignore">Bibliography</h1>
 <h3 class="subtitle">Comprehensive list of references cited in the
 package</h3>
-<h4 class="date">2023-06-12</h4>
+<h4 class="date">2023-08-22</h4>
 
 
 

diff --git a/inst/doc/extending.html b/inst/doc/extending.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="N. Frerebeau" />
 
-<meta name="date" content="2023-06-12" />
+<meta name="date" content="2023-08-22" />
 
 <title>Extending aion</title>
 
@@ -362,7 +362,7 @@
 
 <h1 class="title toc-ignore">Extending aion</h1>
 <h4 class="author">N. Frerebeau</h4>
-<h4 class="date">2023-06-12</h4>
+<h4 class="date">2023-08-22</h4>
 
 
 <div id="TOC">

diff --git a/man/aion-package.Rd b/man/aion-package.Rd
diff --git a/man/series.Rd b/man/series.Rd