Merge pull request #136 from ropensci/remove_emedyd

deprecated get_emedyd
ropensci · Apr 26, 2021 · e8f6c2c · e8f6c2c
2 parents 55a88d3 + e64dd23
commit e8f6c2c
Show file tree

Hide file tree

Showing 15 changed files with 35 additions and 90 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: c14bazAAR
 Title: Download and Prepare C14 Dates from Different Source Databases
-Description: Query different C14 date databases and apply basic data cleaning, merging and calibration steps. Currently available databases: 14cpalaeolithic, 14sea, adrac, austarch, bda, calpal, context, emedyd, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, nerd, pacea, palmisano, radon, radonb, rxpand.
-Version: 2.2.0
+Description: Query different C14 date databases and apply basic data cleaning, merging and calibration steps. Currently available databases: 14cpalaeolithic, 14sea, adrac, austarch, bda, calpal, context, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, nerd, pacea, palmisano, radon, radonb, rxpand.
+Version: 2.3.0
 Authors@R: 
     c(person(given = "Clemens",
              family = "Schmid",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# 2.3.0
+
+- deprecated `get_emedyd`, because the emedyd database was superseded by the nerd database
+
 # 2.2.0
 
 - added getter function for rxpand database: `get_rxpand`

diff --git a/R/deprecated_functions.R b/R/deprecated_functions.R
@@ -45,3 +45,12 @@ standardize_country_name <- function(...) {
   )
 }
 
+#' @rdname deprecated_functions
+#' @export
+get_emedyd <- function(...) {
+  stop(
+    "The emedyd database was removed from c14bazAAR, because it was ",
+    "superseded by the nerd database."
+  )
+}
+
diff --git a/R/get_emedyd.R b/R/get_emedyd.R
diff --git a/README.md b/README.md
@@ -169,7 +169,6 @@ To suggest other archives to be queried you can join the discussion [here](https
 * [`get_c14data("bda")`](R/get_bda.R) [**BDA**](https://nakala.fr/10.34847/nkl.dde9fnm8): Base de Données Archéologiques by **Thomas Perrin** (1994).
 * [`get_c14data("calpal")`](R/get_calpal.R) [**calpal**](https://uni-koeln.academia.edu/BernhardWeninger/CalPal): Radiocarbon Database of the CalPal software package by Bernhard Weninger. See [nevrome/CalPal-Database](https://github.com/nevrome/CalPal-Database) for an interface.
 * [`get_c14data("context")`](R/get_context.R) [**context**](http://context-database.uni-koeln.de/): Collection of radiocarbon dates from sites in the Near East and neighboring regions (20.000 - 5.000 calBC) by Utz Böhner and Daniel Schyle.
-* [`get_c14data("emedyd")`](R/get_emedyd.R) [**emedyd**](https://discovery.ucl.ac.uk/id/eprint/1570274/): Radiocarbon dates from the Eastern Mediterranean and Southwest Asia, 16,000 – 9000 cal BP, compiled by Alessio Palmisano, Andrew Bevan, and Stephen Shennan (in [Roberts et al. 2017](https://doi.org/10.1016/j.quascirev.2017.09.011)).
 * [`get_c14data("eubar")`](R/get_eubar.R) [**eubar**](https://telearchaeology.org/eubar-c14-database/): A database of 14C measurements for the European Bronze Age by [Gacomo Capuzzo](https://telearchaeology.org/EUBAR/).
 * [`get_c14data("euroevol")`](R/get_euroevol.R) [**euroevol**](https://discovery.ucl.ac.uk/1469811/): Cultural Evolution of Neolithic Europe Dataset by [Katie Manning, Sue Colledge, Enrico Crema, Stephen Shennan and Adrian Timpson](https://openarchaeologydata.metajnl.com/articles/10.5334/joad.40/).
 * [`get_c14data("irdd")`](R/get_irdd.R) [**irdd**](https://sites.google.com/site/chapplearchaeology/irish-radiocarbon-dendrochronological-dates): [Robert M Chapple](https://doi.org/10.5281/zenodo.3367518)'s Catalogue of Radiocarbon Determinations & Dendrochronology Dates is a free-to-download resource for Irish archaeology.

diff --git a/codemeta.json b/codemeta.json
@@ -5,18 +5,18 @@
   ],
   "@type": "SoftwareSourceCode",
   "identifier": "c14bazAAR",
-  "description": "Query different C14 date databases and apply basic data cleaning, merging and calibration steps. Currently available databases: 14cpalaeolithic, 14sea, adrac, austarch, calpal, context, emedyd, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, pacea, palmisano, radon, radonb.",
+  "description": "Query different C14 date databases and apply basic data cleaning, merging and calibration steps. Currently available databases: 14cpalaeolithic, 14sea, adrac, austarch, bda, calpal, context, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, nerd, pacea, palmisano, radon, radonb, rxpand.",
   "name": "c14bazAAR: Download and Prepare C14 Dates from Different Source Databases",
   "codeRepository": "https://github.com/ropensci/c14bazAAR",
   "issueTracker": "https://github.com/ropensci/c14bazAAR/issues",
   "license": "https://spdx.org/licenses/GPL-2.0",
-  "version": "1.2.0.9000",
+  "version": "2.3.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.0.2 (2020-06-22)",
+  "runtimePlatform": "R version 4.0.5 (2021-03-31)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -74,6 +74,13 @@
     }
   ],
   "contributor": [
+    {
+      "@type": "Person",
+      "givenName": "Thomas",
+      "familyName": "Huet",
+      "email": "[email protected]",
+      "@id": "https://orcid.org/0000-0002-1112-6122"
+    },
     {
       "@type": "Person",
       "givenName": "Nils",
@@ -129,14 +136,7 @@
     {
       "@type": "SoftwareApplication",
       "identifier": "dataverse",
-      "name": "dataverse",
-      "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=dataverse"
+      "name": "dataverse"
     },
     {
       "@type": "SoftwareApplication",
@@ -481,7 +481,7 @@
   ],
   "releaseNotes": "https://github.com/ropensci/c14bazAAR/blob/master/NEWS.md",
   "readme": "https://github.com/ropensci/c14bazAAR/blob/master/README.md",
-  "fileSize": "10731.197KB",
+  "fileSize": "1433.241KB",
   "contIntegration": ["https://travis-ci.org/ropensci/c14bazAAR", "https://codecov.io/github/ropensci/c14bazAAR?branch=master"],
   "keywords": [
     "radiocarbon-dates",

diff --git a/data-raw/db_info_table.csv b/data-raw/db_info_table.csv
@@ -17,7 +17,6 @@ pacea,2020-01-22,1,http://www.paleoanthro.org/media/journal/content/PA20110001_S
 14cpalaeolithic,2020-01-23,1,https://ees.kuleuven.be/geography/projects/14c-palaeolithic/radiocarbon-palaeolithic-europe-database-v26-extract.xlsx
 medafricarbon,2020-03-20,1,https://zenodo.org/record/3689716/files/data_v1.0.3.zip
 jomon,2020-03-23,1,https://raw.githubusercontent.com/ercrema/jomonPhasesAndPopulation/master/data/c14dates.csv
-emedyd,2017,1,https://discovery.ucl.ac.uk/id/eprint/1570274/1/robertsetal17.zip
 katsianis,2020-08-20,1,https://rdr.ucl.ac.uk/ndownloader/files/23166314
 rapanui,2020-08-21,1,https://github.com/clipo/rapanui-radiocarbon/archive/master.zip
 mesorad,2020-09-01,1,https://github.com/eehh-stanford/price2020/raw/master/MesoRAD-v.1.1_FINAL_no_locations.xlsx

diff --git a/data-raw/url_reference.csv b/data-raw/url_reference.csv
@@ -17,7 +17,6 @@ pacea,2020-01-22,1,http://www.paleoanthro.org/media/journal/content/PA20110001_S
 14cpalaeolithic,2020-01-23,1,https://ees.kuleuven.be/geography/projects/14c-palaeolithic/radiocarbon-palaeolithic-europe-database-v26-extract.xlsx
 medafricarbon,2020-03-20,1,https://zenodo.org/record/3689716/files/data_v1.0.3.zip
 jomon,2020-03-23,1,https://raw.githubusercontent.com/ercrema/jomonPhasesAndPopulation/master/data/c14dates.csv
-emedyd,2017,1,https://discovery.ucl.ac.uk/id/eprint/1570274/1/robertsetal17.zip
 katsianis,2020-08-20,1,https://rdr.ucl.ac.uk/ndownloader/files/23166314
 rapanui,2020-08-21,1,https://github.com/clipo/rapanui-radiocarbon/archive/master.zip
 mesorad,2020-09-01,1,https://github.com/eehh-stanford/price2020/raw/master/MesoRAD-v.1.1_FINAL_no_locations.xlsx

diff --git a/data/country_thesaurus.rda b/data/country_thesaurus.rda
diff --git a/data/db_info_table.rda b/data/db_info_table.rda
diff --git a/data/example_c14_date_list.rda b/data/example_c14_date_list.rda
diff --git a/data/material_thesaurus.rda b/data/material_thesaurus.rda
diff --git a/man/c14bazAAR-package.Rd b/man/c14bazAAR-package.Rd
diff --git a/man/db_getter_backend.Rd b/man/db_getter_backend.Rd
diff --git a/man/deprecated_functions.Rd b/man/deprecated_functions.Rd