Merge pull request #156 from ropensci/p3k14cv310

 p3k14c

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, context, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, nerd, pacea, palmisano, radon, radonb, rxpand, sard.
-Version: 3.3.0
+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, context, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, nerd, p3k14c, pacea, palmisano, radon, radonb, rxpand, sard.
+Version: 3.4.0
 Authors@R: 
     c(person(given = "Clemens",
              family = "Schmid",

NAMESPACE

@@ -53,6 +53,7 @@ export(get_kiteeastafrica)
 export(get_medafricarbon)
 export(get_mesorad)
 export(get_nerd)
+export(get_p3k14c)
 export(get_pacea)
 export(get_palmisano)
 export(get_radon)

NEWS.md

@@ -1,3 +1,7 @@
+# 3.4.0
+
+- added getter function for p3k14c database: `get_p3k14c`
+
 # 3.3.0
 
 - made the default plot function a bit more powerful (#154)

R/get_c14data.R

@@ -151,7 +151,8 @@ get_all_parser_functions <- function() {
     "nerd" = c14bazAAR::get_nerd,
     "bda" = c14bazAAR::get_bda,
     "rxpand" = c14bazAAR::get_rxpand,
-    "sard" = c14bazAAR::get_sard
+    "sard" = c14bazAAR::get_sard,
+    "p3k14c" = c14bazAAR::get_p3k14c
   ))
 }
 

R/get_p3k14c.R

@@ -0,0 +1,41 @@
+#' @rdname db_getter_backend
+#' @export
+get_p3k14c <- function(db_url = get_db_url("p3k14c")) {
+
+  check_connection_to_url(db_url)
+
+  # download and unzip data
+  p3k14c <- db_url %>%
+    data.table::fread(
+      colClasses = "character",
+      showProgress = FALSE,
+      na.strings = ""
+    ) %>%
+    dplyr::mutate(
+      d13C = suppressWarnings(as.numeric(.data[["d13C"]])),
+      d13C = ifelse(.data[["d13C"]] == 0, NA, .data[["d13C"]])
+    ) %>%
+    dplyr::transmute(
+      labnr = .data[["LabID"]],
+      c14age = .data[["Age"]],
+      c13val = .data[["d13C"]],
+      c14std = .data[["Error"]],
+      material = .data[["Material"]],
+      species = .data[["Taxa"]],
+      site = .data[["SiteName"]],
+      method = .data[["Method"]],
+      period = .data[["Period"]],
+      region = .data[["Continent"]],
+      country = .data[["Country"]],
+      lat = .data[["Lat"]],
+      lon = .data[["Long"]],
+      shortref = ifelse(is.na(.data[["Reference"]]), .data[["Source"]], .data[["Reference"]])
+    ) %>%
+    dplyr::mutate(
+      sourcedb = "p3k14c",
+      sourcedb_version = get_db_version("p3k14c")
+    ) %>%
+    as.c14_date_list()
+
+  return(p3k14c)
+}

README.md

@@ -170,6 +170,7 @@ To suggest other archives to be queried you can join the discussion [here](https
 * [`get_c14data("nerd")`](R/get_nerd.R) [**NERD**](https://github.com/apalmisano82/NERD): Near East Radiocarbon Dates Alessio Palmisano, Andrew Bevan, Dan Lawrence & Stephen Shennan (2021).
 * [`get_c14data("pacea")`](R/get_pacea.R) [**pacea**](http://www.paleoanthro.org/media/journal/content/PA20110001_S01.zip): PACEA Geo-Referenced Radiocarbon Database for the late Middle Paleolithic, Upper Paleolithic, and initial Holocene in Europe by [Francesco D'Errico, William E. Banks, Marian Vanhaeren, Véronique Laroulandie and Mathieu Langlais](http://www.paleoanthro.org/media/journal/content/PA20110001.pdf) (2011). 
 * [`get_c14data("palmisano")`](R/get_palmisano.R) [**palmisano**](https://dx.doi.org/10.14324/000.ds.1575442): Regional Demographic Trends and Settlement Patterns in Central Italy: Archaeological Sites and Radiocarbon Dates by [Alessio Palmisano, Andrew Bevan and Stephen Shennan](https://openarchaeologydata.metajnl.com/articles/10.5334/joad.43/) (2018).
+* [`get_c14data("p3k14c")`](R/get_p3k14c.R) [**p3k14c**](https://github.com/people3k): p3k14c: A synthetic global database of archaeological radiocarbon dates by [Darcy Bird, Lux Miranda, Marc Vander Linden, Robinson, Erick, R. Kyle Bocinsky, Chris Nicholson, José M. Capriles, Judson Byrd Finley, Eugenia M. Gayo, Adolfo Gil, Jade d’Alpoim Guedes, Julie A. Hoggarth, Andrea Kay, Emma Loftus, Umberto Lombardo, Madeline Mackie, Alessio Palmisano, Steinar Solheim, Robert L. Kelly, and Jacob Freeman](https://doi.org/10.1038/s41597-022-01118-7) (2022).
 * [`get_c14data("radon")`](R/get_radon.R) [**radon**](https://radon.ufg.uni-kiel.de/): Central European and Scandinavian database of 14C dates for the Neolithic and Early Bronze Age by [Dirk Raetzel-Fabian, Martin Furholt, Martin Hinz, Johannes Müller, Christoph Rinne, Karl-Göran Sjögren und Hans-Peter Wotzka](https://www.jna.uni-kiel.de/index.php/jna/article/view/65).
 * [`get_c14data("radonb")`](R/get_radonb.R) [**radonb**](https://radon-b.ufg.uni-kiel.de/): Database for European 14C dates for the Bronze and Early Iron Age by Jutta Kneisel, Martin Hinz, Christoph Rinne.
 * [`get_c14data("rxpand")`](R/get_rxpand.R) [**rxpand**](https://github.com/jgregoriods/rxpand): Radiocarbon dates for the spread of farming and ceramics in tropical South America by Jonas Gregorio de Souza.

codemeta.json

@@ -2,13 +2,13 @@
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@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, agrichange, aida, austarch, bda, calpal, caribbean, context, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, nerd, pacea, palmisano, radon, radonb, rxpand, sard.",
+  "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, context, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, nerd, p3k14c, pacea, palmisano, radon, radonb, rxpand, sard.",
   "name": "c14bazAAR: Download and Prepare C14 Dates from Different Source Databases",
   "relatedLink": "https://docs.ropensci.org/c14bazAAR",
   "codeRepository": "https://github.com/ropensci/c14bazAAR",
   "issueTracker": "https://github.com/ropensci/c14bazAAR/issues",
   "license": "https://spdx.org/licenses/GPL-2.0",
-  "version": "3.3.0",
+  "version": "3.4.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -453,7 +453,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1269.267KB",
+  "fileSize": "1136.508KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -492,10 +492,5 @@
         }
       }
     }
-  ],
-  "releaseNotes": "https://github.com/ropensci/c14bazAAR/blob/master/NEWS.md",
-  "readme": "https://github.com/ropensci/c14bazAAR/blob/master/README.md",
-  "contIntegration": ["https://github.com/ropensci/c14bazAAR/actions/workflows/check-release.yaml", "https://codecov.io/github/ropensci/c14bazAAR?branch=master"],
-  "developmentStatus": "https://www.repostatus.org/#active",
-  "keywords": ["radiocarbon-dates", "archaeology", "r"]
+  ]
 }

data-raw/db_info_table.csv

@@ -27,3 +27,4 @@ agrichange,2021-05-21,1,https://zenodo.org/record/4541470/files/AgriChange_14Cda
 caribbean,2021-05-21,1,https://raw.githubusercontent.com/philriris/caribbean-14C/main/data/caribbean_14C.csv
 aida,today,1,https://raw.githubusercontent.com/apalmisano82/AIDA/main/dates.csv
 sard,2021-03-01,1,https://raw.githubusercontent.com/emmaloftus/Southern-African-Radiocarbon-Database/main/SARD_Mar2021_14C.csv
+p3k14c,2021-08-03,1,https://raw.githubusercontent.com/people3k/p3k14c/1.0.0/inst/p3k14c_scrubbed_fuzzed.csv

data-raw/variable_reference.csv

@@ -594,3 +594,20 @@ shortref,sard,refcode
 ,sard,Biom
 ,sard,Sample context
 ,sard,Site Type
+labnr,p3k14c,LabID
+c14age,p3k14c,Age
+c14std,p3k14c,Error
+material,p3k14c,Material
+species,p3k14c,Taxa
+c13val,p3k14c,d13C
+method,p3k14c,Method
+lon,p3k14c,Long
+lat,p3k14c,Lat
+,p3k14c,LocAccuracy
+period,p3k14c,Period
+,p3k14c,SiteID
+site,p3k14c,SiteName
+country,p3k14c,Country
+,p3k14c,Province
+region,p3k14c,Continent
+shortref,p3k14c,Reference;Source

figures/README_map_figure.R

@@ -36,7 +36,7 @@ c14.map <- ggplot() +
     color = "black"
   ) +
   facet_wrap(~ sourcedb, ncol = 4) +
-  coord_sf(crs = st_crs('+proj=moll')) +
+  coord_sf(crs = sf::st_crs('+proj=moll')) +
   theme_bw() +
   theme(
     legend.position = "none",