diff --git a/DESCRIPTION b/DESCRIPTION index e8b25a0..37dc5aa 100644 --- 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 index 2b52ab5..41f79d8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# 2.3.0 + +- deprecated `get_emedyd`, because the emedyd database was superseded by the nerd database + # 2.2.0 - added getter function for rxpand database: `get_rxpand` diff --git a/R/deprecated_functions.R b/R/deprecated_functions.R index fafc0a9..dbc73c5 100644 --- 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 { + stop( + "The emedyd database was removed from c14bazAAR, because it was ", + "superseded by the nerd database."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 deleted file mode 100644 index 21f2fa8..0000000 --- a/R/get_emedyd.R +++ /dev/null @@ -1,64 +0,0 @@ -#' @rdname db_getter_backend -#' @export -get_emedyd <- function(db_url = get_db_url("emedyd")) { - - check_connection_to_url(db_url) - - # download and unzip data - temp <- tempfile() - utils::download.file(db_url, temp, quiet = TRUE) - radiocarbon_path <- utils::unzip( - temp, - file.path( - "robertsetal17", "csv", "emedyd.csv" - ), - exdir = tempdir() - ) - - # read data - radiocarbon_raw <- data.table::fread( - radiocarbon_path, - sep = ",", - encoding = "UTF-8", - drop = c("Region"), - colClasses = c( - "LabID" = "character", - "CRA" = "integer", - "Error" = "integer", - "Material" = "character", - "Species" = "character", - "SiteName" = "character", - "Country" = "character", - "Longitude" = "numeric", - "Latitude" = "numeric" - ), - showProgress = FALSE - ) - - # delete temporary files - unlink(temp) - file.remove(radiocarbon_path) - - # final data preparation - radiocarbon_raw %>% - base::replace(., . == "", NA) %>% - dplyr::transmute( - labnr = .data[["LabID"]], - c14age = .data[["CRA"]], - c14std = .data[["Error"]], - material = .data[["Material"]], - species = .data[["Species"]], - site = .data[["SiteName"]], - country = .data[["Country"]], - lat = .data[["Latitude"]], - lon = .data[["Longitude"]] - ) %>% - dplyr::mutate( - sourcedb = "emedyd", - sourcedb_version = get_db_version("emedyd") - ) %>% - as.c14_date_list() -> - emedyd - - return(emedyd) -} diff --git a/README.md b/README.md index 9c89658..0494e2f 100644 --- 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 index 1dfc4cd..6c08e48 100644 --- 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": "thomashuet7@gmail.com", + "@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 index 8a4fdad..f36bc2f 100644 --- 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 index c79a6ea..95e7cdc 100644 --- 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 index e41c18b..ec80ff7 100644 Binary files a/data/country_thesaurus.rda and b/data/country_thesaurus.rda differ diff --git a/data/db_info_table.rda b/data/db_info_table.rda index 9f76f90..d80ea17 100644 Binary files a/data/db_info_table.rda and b/data/db_info_table.rda differ diff --git a/data/example_c14_date_list.rda b/data/example_c14_date_list.rda index 008edfa..27603ff 100644 Binary files a/data/example_c14_date_list.rda and b/data/example_c14_date_list.rda differ diff --git a/data/material_thesaurus.rda b/data/material_thesaurus.rda index 5986aee..f16ecad 100644 Binary files a/data/material_thesaurus.rda and b/data/material_thesaurus.rda differ diff --git a/man/c14bazAAR-package.Rd b/man/c14bazAAR-package.Rd index 7911f20..127116e 100644 --- a/man/c14bazAAR-package.Rd +++ b/man/c14bazAAR-package.Rd @@ -8,7 +8,7 @@ \description{ \if{html}{\figure{logo.png}{options: align='right' alt='logo' width='120'}} -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. +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. } \seealso{ Useful links: diff --git a/man/db_getter_backend.Rd b/man/db_getter_backend.Rd index aa3eeae..495f066 100644 --- a/man/db_getter_backend.Rd +++ b/man/db_getter_backend.Rd @@ -1,11 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/get_14cpalaeolithic.R, R/get_14sea.R, % R/get_adrac.R, R/get_austarch.R, R/get_bda.R, R/get_c14data.R, -% R/get_calpal.R, R/get_context.R, R/get_emedyd.R, R/get_eubar.R, -% R/get_euroevol.R, R/get_irdd.R, R/get_jomon.R, R/get_katsianis.R, -% R/get_kiteeastafrica.R, R/get_medafricarbon.R, R/get_mesorad.R, -% R/get_nerd.R, R/get_pacea.R, R/get_palmisano.R, R/get_radon.R, -% R/get_radonb.R, R/get_rxpand.R +% R/get_calpal.R, R/get_context.R, R/get_eubar.R, R/get_euroevol.R, +% R/get_irdd.R, R/get_jomon.R, R/get_katsianis.R, R/get_kiteeastafrica.R, +% R/get_medafricarbon.R, R/get_mesorad.R, R/get_nerd.R, R/get_pacea.R, +% R/get_palmisano.R, R/get_radon.R, R/get_radonb.R, R/get_rxpand.R \name{get_14cpalaeolithic} \alias{get_14cpalaeolithic} \alias{get_14sea} @@ -15,7 +14,6 @@ \alias{get_all_dates} \alias{get_calpal} \alias{get_context} -\alias{get_emedyd} \alias{get_eubar} \alias{get_euroevol} \alias{get_irdd} @@ -48,8 +46,6 @@ get_calpal(db_url = get_db_url("calpal")) get_context(db_url = get_db_url("context")) -get_emedyd(db_url = get_db_url("emedyd")) - get_eubar(db_url = get_db_url("eubar")) get_euroevol(db_url = get_db_url("euroevol")) diff --git a/man/deprecated_functions.Rd b/man/deprecated_functions.Rd index b511c35..a4ef986 100644 --- a/man/deprecated_functions.Rd +++ b/man/deprecated_functions.Rd @@ -6,6 +6,7 @@ \alias{coordinate_precision} \alias{finalize_country_name} \alias{standardize_country_name} +\alias{get_emedyd} \title{Deprecated functions} \usage{ mark_duplicates(...) @@ -15,6 +16,8 @@ coordinate_precision(...) finalize_country_name(...) standardize_country_name(...) + +get_emedyd(...) } \arguments{ \item{...}{...}