update to glottolog 5.1

ropensci · Oct 29, 2024 · 27485c6 · 27485c6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: lingtypology
 Type: Package
 Title: Linguistic Typology and Mapping
-Version: 1.1.19
+Version: 1.1.20
 Depends: R (>= 3.5.0)
 Imports:
     leaflet,
@@ -31,7 +31,7 @@ License: GPL (>= 2)
 URL: https://CRAN.R-project.org/package=lingtypology, https://github.com/ropensci/lingtypology/, https://ropensci.github.io/lingtypology/
 BugReports: https://github.com/ropensci/lingtypology/issues
 LazyData: TRUE
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.2.9000
 Encoding: UTF-8
 Suggests:
     knitr,

diff --git a/NEWS b/NEWS
@@ -1,3 +1,6 @@
+lingtypology 1.1.20
+- update Glottolog to v. 5.1
+
 lingtypology 1.1.19
 - update `lang.gltc()` function
 

diff --git a/R/glottolog.R b/R/glottolog.R
@@ -5,14 +5,14 @@
 #' and coordinates.
 #'
 #' Hammarstrom, Harald and Forkel, Robert and Haspelmath, Martin and Bank, Sebastian. 2023.
-#' Glottolog 5.0.
+#' Glottolog 5.1.
 #' Leipzig: Max Planck Institute for Evolutionary Anthropology.
 #' https://doi.org/10.5281/zenodo.10804357
 #' (Available online at http://glottolog.org, Accessed on 2024-03-12.)
 #'
-#' @format A data frame with 26879 rows and 10 variables:
+#' @format A data frame with 26953 rows and 10 variables:
 #' \describe{
-#'   \item{glottocode}{languoid code from Glottolog 5.0}
+#'   \item{glottocode}{languoid code from Glottolog 5.1}
 #'   \item{language}{name of the language}
 #'   \item{iso}{code based on ISO 639--3 \url{https://iso639-3.sil.org/}}
 #'   \item{level}{languoid type: dialect or language (possible values are dialect, language, family, bookkeeping, pseudo family, sign language, unclassifiable, pidgin, unattested, artificial language, speech register, mixed language)}

diff --git a/R/zzz.r b/R/zzz.r
@@ -5,5 +5,5 @@
 
 .onAttach <- function(libname = find.package("lingtypology"),
                     pkgname = "lingtypology") {
-  packageStartupMessage("Based on the Glottolog v. 5.0")
+  packageStartupMessage("Based on the Glottolog v. 5.1")
 }
diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.815028.svg)](https://doi.org/10.5281/zenodo.815028)
 
 
-`lingtypology` package connects R with the [Glottolog database (v. 5.0)](https://glottolog.org/) and provides additional functionality for linguistic mapping. The Glottolog database contains the catalogue of the world's languages. This package helps researchers to make linguistic maps, using philosophy of [the Cross-Linguistic Linked Data project](https://clld.org/), which uniform access to the data across publications. This package is based on [`leaflet` package](https://rstudio.github.io/leaflet/), so `lingtypology` package is a package for linguistic interactive mapping. You also might be interested in looking into some alternatives to lingtypology:
+`lingtypology` package connects R with the [Glottolog database (v. 5.1)](https://glottolog.org/) and provides additional functionality for linguistic mapping. The Glottolog database contains the catalogue of the world's languages. This package helps researchers to make linguistic maps, using philosophy of [the Cross-Linguistic Linked Data project](https://clld.org/), which uniform access to the data across publications. This package is based on [`leaflet` package](https://rstudio.github.io/leaflet/), so `lingtypology` package is a package for linguistic interactive mapping. You also might be interested in looking into some alternatives to lingtypology:
 
 * [lingtypology](https://pypi.org/project/lingtypology/) in Python by Michael Voronov;
 * [glottospace](https://github.com/glottospace/glottospace) -- R package for the geospatial analysis based on Glottolog by Sietze Norder et al;

diff --git a/codemeta.json b/codemeta.json
@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/ropensci/lingtypology/",
   "issueTracker": "https://github.com/ropensci/lingtypology/issues",
   "license": "https://spdx.org/licenses/GPL-2.0",
-  "version": "1.1.15",
+  "version": "1.1.20",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.3.1 (2023-06-16)",
+  "runtimePlatform": "R version 4.3.3 (2024-02-29)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -101,29 +101,10 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=testthat"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "covr",
-      "name": "covr",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=covr"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "MASS",
-      "name": "MASS",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=MASS"
+      "name": "MASS"
     },
     {
       "@type": "SoftwareApplication",
@@ -234,7 +215,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "2227.264KB",
+  "fileSize": "2238.975KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",

diff --git a/data/glottolog.RData b/data/glottolog.RData
diff --git a/database_creation/glottolog.csv b/database_creation/glottolog.csv
diff --git a/docs/index.Rmd b/docs/index.Rmd
@@ -5,7 +5,7 @@ author: "[George Moroz](mailto:agricolamz@gmail.com), [NRU HSE Linguistic Conver
 
 ### What is `lingtypology`?
 
-The `lingtypology` package connects R with the [Glottolog database (v. 5.0)](https://glottolog.org/) and provides an additional functionality for linguistic typology. The Glottolog database contains a catalogue of the world's languages. This package helps researchers to make linguistic maps, using the philosophy of [the Cross-Linguistic Linked Data project](https://clld.org/), which is creating a uniform access to linguistic data across publications. This package is based on the [leaflet package](https://rstudio.github.io/leaflet/), so `lingtypology` is a package for interactive linguistic mapping. In addition, the package provides an ability to download data from typological databases such as WALS, AUTOTYP and others (see section 4). The functionality of this package intersects with 
+The `lingtypology` package connects R with the [Glottolog database (v. 5.1)](https://glottolog.org/) and provides an additional functionality for linguistic typology. The Glottolog database contains a catalogue of the world's languages. This package helps researchers to make linguistic maps, using the philosophy of [the Cross-Linguistic Linked Data project](https://clld.org/), which is creating a uniform access to linguistic data across publications. This package is based on the [leaflet package](https://rstudio.github.io/leaflet/), so `lingtypology` is a package for interactive linguistic mapping. In addition, the package provides an ability to download data from typological databases such as WALS, AUTOTYP and others (see section 4). The functionality of this package intersects with 
 
 - [lingtypology](https://pypi.org/project/lingtypology/) in Python by Michael Voronov;
 - [glottospace](https://github.com/glottospace/glottospace) -- R package for the geospatial analysis based on Glottolog by Sietze Norder et al;

diff --git a/docs/index.html b/docs/index.html
@@ -14,7 +14,7 @@
 
 <title>lingtypology: introduction and installation</title>
 
-<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.28/header-attrs.js"></script>
 <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/lumen.min.css" rel="stylesheet" />
@@ -69,7 +69,7 @@
 }
 @media print {
 pre > code.sourceCode { white-space: pre-wrap; }
-pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; }
 }
 pre.numberSource code
   { counter-reset: source-line 0; }
@@ -449,7 +449,7 @@ <h4 class="author"><a href="mailto:agricolamz@gmail.com">George
 <div id="what-is-lingtypology" class="section level3">
 <h3>What is <code>lingtypology</code>?</h3>
 <p>The <code>lingtypology</code> package connects R with the <a
-href="https://glottolog.org/">Glottolog database (v. 5.0)</a> and
+href="https://glottolog.org/">Glottolog database (v. 5.1)</a> and
 provides an additional functionality for linguistic typology. The
 Glottolog database contains a catalogue of the world’s languages. This
 package helps researchers to make linguistic maps, using the philosophy
@@ -492,7 +492,7 @@ <h3>1. Installation</h3>
 <span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">&quot;ropensci/lingtypology&quot;</span>)</span></code></pre></div>
 <p>Load the package:</p>
 <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">library</span>(lingtypology)</span></code></pre></div>
-<pre><code>## Based on the Glottolog v. 5.0</code></pre>
+<pre><code>## Based on the Glottolog v. 5.1</code></pre>
 </div>
 <div id="citing-lingtyplogy" class="section level3">
 <h3>2. Citing <code>lingtyplogy</code></h3>

diff --git a/docs/site_libs/header-attrs-2.28/header-attrs.js b/docs/site_libs/header-attrs-2.28/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/man/glottolog.Rd b/man/glottolog.Rd
diff --git a/tests/testthat/test-glottolog-database.R b/tests/testthat/test-glottolog-database.R
@@ -10,6 +10,6 @@ test_that("is.glottolog spell checker", {
   skip_on_cran()
   expect_that(warning(is.glottolog("Kabardia")), gives_warning())
   expect_that(warning(is.glottolog("Kabardia", response = TRUE)), gives_warning("Language Kabardia is absent in our version of the Glottolog database. Did you mean Kabardian, Greater Kabardian?"))
-  expect_that(warning(is.glottolog("Romagnolo", response = TRUE)), gives_warning("Language Romagnolo is absent in our version of the Glottolog database. Did you mean Romagnol, Northern Romagnolo, Southern Romagnolo, Emiliano-Romagnolo?"))
+  expect_that(warning(is.glottolog("Romagnolo", response = TRUE)), gives_warning("Language Romagnolo is absent in our version of the Glottolog database. Did you mean Romagnol, Southern Romagnolo, Northern Romagnolo, Emiliano-Romagnolo?"))
   expect_that(warning(is.glottolog(c("Kabardia", "Laz"), response = TRUE)), gives_warning("Language Kabardia is absent in our version of the Glottolog database. Did you mean Kabardian, Greater Kabardian?"))
 })
diff --git a/tests/testthat/test-lang-aff.R b/tests/testthat/test-lang-aff.R
@@ -7,19 +7,19 @@ test_that("lang.aff", {
     expect_equal(lang.aff("Baltic"), c("Lithuanian", "Latvian"))
     expect_equal(lang.aff(df), c(my_langs1 = "Lithuanian",
                                  my_langs2 = "Latvian"))
-    expect_equal(lang.aff(c("Brythonic", "Goidelic")), c("Welsh",
+    expect_equal(lang.aff(c("Brythonic", "Goidelic")), c("Old Cornish",
+                                                         "Welsh",
                                                          "Old-Middle Welsh",
-                                                         "Old Cornish",
                                                          "Breton",
                                                          "Cornish",
                                                          "Early Irish",
                                                          "Irish",
                                                          "Scottish Gaelic",
                                                          "Manx"))
     expect_equal(lang.aff(c("Brythonic", "Goidelic"), list = TRUE),
-                 list(c("Welsh",
+                 list(c("Old Cornish",
+                        "Welsh",
                         "Old-Middle Welsh",
-                        "Old Cornish",
                         "Breton",
                         "Cornish"),
                       c("Early Irish",

diff --git a/vignettes/lingtypology_intro.R b/vignettes/lingtypology_intro.R
@@ -1,13 +1,13 @@
-## ----eval=FALSE---------------------------------------------------------------
+## ----eval=FALSE----------------------------------------------
 #  install.packages("lingtypology", dependencies = TRUE)
 
-## ----eval= FALSE--------------------------------------------------------------
+## ----eval= FALSE---------------------------------------------
 #  install.packages("remotes")
 #  remotes::install_github("ropensci/lingtypology")
 
-## -----------------------------------------------------------------------------
+## ------------------------------------------------------------
 library(lingtypology)
 
-## -----------------------------------------------------------------------------
+## ------------------------------------------------------------
 citation("lingtypology")
 
diff --git a/vignettes/lingtypology_intro.Rmd b/vignettes/lingtypology_intro.Rmd
@@ -11,7 +11,7 @@ vignette: >
 
 ### What is `lingtypology`?
 
-The `lingtypology` package connects R with the [Glottolog database (v. 5.0)](https://glottolog.org/) and provides an additional functionality for linguistic typology. The Glottolog database contains a catalogue of the world's languages. This package helps researchers to make linguistic maps, using the philosophy of [the Cross-Linguistic Linked Data project](https://clld.org/), which is creating a uniform access to linguistic data across publications. This package is based on the [leaflet package](https://rstudio.github.io/leaflet/), so `lingtypology` is a package for interactive linguistic mapping. In addition, the package provides an ability to download data from typological databases such as WALS, AUTOTYP and others (see section 4). The functionality of this package intersects with 
+The `lingtypology` package connects R with the [Glottolog database (v. 5.1)](https://glottolog.org/) and provides an additional functionality for linguistic typology. The Glottolog database contains a catalogue of the world's languages. This package helps researchers to make linguistic maps, using the philosophy of [the Cross-Linguistic Linked Data project](https://clld.org/), which is creating a uniform access to linguistic data across publications. This package is based on the [leaflet package](https://rstudio.github.io/leaflet/), so `lingtypology` is a package for interactive linguistic mapping. In addition, the package provides an ability to download data from typological databases such as WALS, AUTOTYP and others (see section 4). The functionality of this package intersects with 
 
 - [lingtypology](https://pypi.org/project/lingtypology/) in Python by Michael Voronov;
 - [glottospace](https://github.com/glottospace/glottospace) -- R package for the geospatial analysis based on Glottolog by Sietze Norder et al;

diff --git a/vignettes/lingtypology_intro.html b/vignettes/lingtypology_intro.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="George Moroz" />
 
-<meta name="date" content="2024-09-20" />
+<meta name="date" content="2024-10-30" />
 
 <title>lingtypology: introduction and installation</title>
 
@@ -62,7 +62,7 @@
 }
 @media print {
 pre > code.sourceCode { white-space: pre-wrap; }
-pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; }
 }
 pre.numberSource code
 { counter-reset: source-line 0; }
@@ -341,13 +341,13 @@
 <h1 class="title toc-ignore"><code>lingtypology</code>: introduction and
 installation</h1>
 <h4 class="author">George Moroz</h4>
-<h4 class="date">2024-09-20</h4>
+<h4 class="date">2024-10-30</h4>
 
 
 
 <div id="what-is-lingtypology" class="section level3">
 <h3>What is <code>lingtypology</code>?</h3>
-<p>The <code>lingtypology</code> package connects R with the <a href="https://glottolog.org/">Glottolog database (v. 5.0)</a> and
+<p>The <code>lingtypology</code> package connects R with the <a href="https://glottolog.org/">Glottolog database (v. 5.1)</a> and
 provides an additional functionality for linguistic typology. The
 Glottolog database contains a catalogue of the world’s languages. This
 package helps researchers to make linguistic maps, using the philosophy
@@ -395,7 +395,8 @@ <h3>2. Citing <code>lingtyplogy</code></h3>
 <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="fu">citation</span>(<span class="st">&quot;lingtypology&quot;</span>)</span></code></pre></div>
 <pre><code>## To cite package &#39;lingtypology&#39; in publications use:
 ## 
-##   Moroz G (2017). _lingtypology: easy mapping for Linguistic Typology_.
+##   Moroz G (2017). _lingtypology: easy mapping for
+##   Linguistic Typology_.
 ##   &lt;https://CRAN.R-project.org/package=lingtypology&gt;.
 ## 
 ## A BibTeX entry for LaTeX users is