ropensci · MartinHinz · Sep 10, 2021 · Nov 29, 2024 · Nov 29, 2024 · Nov 29, 2024
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, agrichange, aida, austarch, bda, calpal, caribbean, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, neonet, neonetatl, nerd, p3k14c, pacea, palmisano, rado.nb, rxpand, sard.
-Version: 5.0.0
+Description: Query different C14 date databases and apply basic data cleaning, merging and calibration steps. Currently available databases: 14cpalaeolithic, 14sea, adrac, agrichange, aida, austarch, bda, calpal, caribbean, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, neonet, neonetatl, nerd, p3k14c, pacea, palmisano, rado.nb, rxpand, sard, xronos.
+Version: 5.1.0
 Authors@R: 
     c(person(given = "Clemens",
              family = "Schmid",
@@ -96,5 +96,5 @@ Suggests:
     testthat,
     tidyr (>= 0.6.3),
     writexl
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -63,6 +63,7 @@ export(get_radon)
 export(get_radonb)
 export(get_rxpand)
 export(get_sard)
+export(get_xronos)
 export(is.c14_date_list)
 export(mark_duplicates)
 export(order_variables)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# 5.1.0
+
+- added getter function for xronos database: `get_xronos`
+
 # 5.0.0
 
 - removed the databases radon and radon-b and replaced it with the new, merged database rado.nb
@@ -44,6 +48,7 @@
 # 3.2.0
 
 - added getter function for sard database: `get_sard`
+>>>>>>> master
 
 # 3.1.0
 

diff --git a/R/get_c14data.R b/R/get_c14data.R
@@ -153,7 +153,8 @@ get_all_parser_functions <- function() {
     "sard" = c14bazAAR::get_sard,
     "p3k14c" = c14bazAAR::get_p3k14c,
     "neonet" = c14bazAAR::get_neonet,
-    "neonet" = c14bazAAR::get_neonetatl
+    "neonet" = c14bazAAR::get_neonetatl,
+    "xronos" = c14bazAAR::get_xronos
   ))
 }
 

diff --git a/R/get_xronos.R b/R/get_xronos.R
@@ -0,0 +1,32 @@
+#' @rdname db_getter_backend
+#' @export
+get_xronos <- function(db_url = get_db_url("xronos")) {
+
+  check_connection_to_url("https://www.xronos.ch")
+
+  resp<-httr::GET(db_url)
+
+  xronos_data <- httr::content(resp,as="parsed") %>% unique() %>% tidyr::tibble()
+
+  xronos <- xronos_data %>%
+    dplyr::transmute(
+      labnr = .data[["labnr"]],
+      c14age = .data[["bp"]],
+      c14std = .data[["std"]],
+      c13val = .data[["delta_c13"]],
+      material = .data[["material"]],
+      species = .data[["species"]],
+      country = .data[["country"]],
+      site = .data[["site"]],
+      sitetype = .data[["site_type"]],
+      feature = .data[["feature"]],
+      lat = .data[["lat"]],
+      lon = .data[["lng"]]) %>%
+    dplyr::mutate(
+      sourcedb = "xronos",
+      sourcedb_version = get_db_version("xronos")
+    ) %>%
+    c14bazAAR::as.c14_date_list()
+
+  return(xronos)
+}
diff --git a/README.md b/README.md
@@ -178,6 +178,7 @@ To suggest other archives to be queried you can join the discussion [here](https
 | [**rado.nb**](https://radonb.ufg.uni-kiel.de) <br> latest <br> [`get_c14data("rado.nb")`](R/get_rado.nb.R) | Database for European 14C dates for the Neolithic, the Bronze Age and the Early Iron Age. [Christoph Rinne, Jutta Kneisel, Martin Hinz, Martin Furholt, Nina Krischke, Johannes Müller, Dirk Raetzel-Fabian, Marcel Rodens, Karl-Göran Sjögren, Helle Vandkilde and Hans-Peter Wotzka](https://radonb.ufg.uni-kiel.de). |
 | [**rxpand**](https://github.com/jgregoriods/rxpand) <br> 2020-10-20 <br> [`get_c14data("rxpand")`](R/get_rxpand.R) | Radiocarbon dates for the spread of farming and ceramics in tropical South America by Jonas Gregorio de Souza. |
 | [**sard**](https://github.com/emmaloftus/Southern-African-Radiocarbon-Database) <br> 2021-03-01 <br> [`get_c14data("sard")`](R/get_sard.R) | Southern-African-Radiocarbon-Database by [Emma Loftus, Peter J. Mitchell & Christopher Bronk Ramsey](https://www.cambridge.org/core/journals/antiquity/article/abs/an-archaeological-radiocarbon-database-for-southern-africa/26FE99E995C4507015704D552CB0C196). |
+| [**XRONOS**](https://xronos.ch) <br> latest <br> [`get_c14data("xronos")`](R/get_xronos.R)  | Open Access Database for absolute chronological archaeological information by Martin Hinz, Joe Roe and Clemens Schmid.
 
 #### Deprecated databases
 

diff --git a/codemeta.json b/codemeta.json
@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/ropensci/c14bazAAR",
   "issueTracker": "https://github.com/ropensci/c14bazAAR/issues",
   "license": "https://spdx.org/licenses/GPL-2.0",
-  "version": "5.0.0",
+  "version": "5.1.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.4.0 (2024-04-24)",
+  "runtimePlatform": "R version 4.4.2 (2024-10-31)",
   "author": [
     {
       "@type": "Person",
@@ -436,7 +436,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "3130.491KB",
+  "fileSize": "3277.558KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/data-raw/db_info_table.csv b/data-raw/db_info_table.csv
@@ -28,3 +28,4 @@ sard,2021-03-01,1,https://raw.githubusercontent.com/emmaloftus/Southern-African-
 p3k14c,2021-08-03,1,https://raw.githubusercontent.com/people3k/p3k14c/1.0.0/inst/p3k14c_scrubbed_fuzzed.csv
 neonet,2023-12-08,1,https://digitallib.unipi.it/fedora/objects/mag:2814/datastreams/MMb714bbfacf4af2ce1fd7025e3789a99b/content
 neonetatl,2023-12-08,1,https://digitallib.unipi.it/fedora/objects/mag:2627/datastreams/MM54ff3698c0ea78b77469ce6462c2ca36/content
+xronos,today,1,https://xronos.ch/data.csv
diff --git a/data-raw/variable_reference.csv b/data-raw/variable_reference.csv
@@ -601,3 +601,23 @@ shortref,neonetatl,bib
 site,neonetatl,Site Name
 sitetype,neonetatl,
 species,neonetatl,Material Species
+,xronos,id
+labnr,xronos,labnr
+,xronos,source_database
+c14age,xronos,bp
+c14std,xronos,std
+,xronos,cal_bp
+,xronos,cal_std
+site,xronos,site
+,xronos,site_phase
+feature,xronos,feature
+,xronos,period
+,xronos,typochronological_unit
+,xronos,ecochronological_unit
+material,xronos,material
+country,xronos,country
+c13val,xronos,delta_c13
+lat,xronos,lat
+lon,xronos,lng
+sitetype,xronos,site_type
+species,xronos,species
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/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/figures/README_map_figure.jpeg b/man/figures/README_map_figure.jpeg
diff --git a/tests/testthat/test_c14_date_list_convert.R b/tests/testthat/test_c14_date_list_convert.R
@@ -22,7 +22,7 @@ test_that("as.sf gives back a sf object with the correct columns", {
   expect_equal(
     colnames(result),
     c(
-      paste0("data.", colnames(example_c14_date_list)),
+      paste0(colnames(example_c14_date_list)),
       "geom"
     )
   )

diff --git a/vignettes/simple_plotting.Rmd b/vignettes/simple_plotting.Rmd
@@ -157,15 +157,15 @@ adrac_sf <- adrac %>% as.sf()
 This tabular data structure contains the spatial point information for each date in a column *geom*, but also the initial columns of the input dataset: *data.\**
 
 ```{r, echo=FALSE}
-adrac_sf %>% dplyr::select(data.labnr, data.c14age, data.c14std, geom)
+adrac_sf %>% dplyr::select(labnr, c14age, c14std, geom)
 ```
 
 It can be manipulated with the powerful dplyr functions. We `filter` out all dates from one particular publication (*Moga 2008*), `group` the dates `by` *site* and apply the `summarise` command to keep only one value per group. As we do not define an operation to fold the other variables in the input table, they are removed. Only the geometry column remains.
 
 ```{r}  
 Moga_spatial <- adrac_sf %>%
-  dplyr::filter(grepl("Moga 2008", data.shortref)) %>%
-  dplyr::group_by(data.site) %>%
+  dplyr::filter(grepl("Moga 2008", shortref)) %>%
+  dplyr::group_by(site) %>%
   dplyr::summarise(.groups = "drop")
 ```