How to use the Pandora Data Package



This vignette provides an overview of the basic functions within the Pandora Data package, allowing users to explore and retrieve information about networks, repositories, file types, and resources.

Show all Networks

To show all available networks use the getNetworks() function:

networks <- getNetworks()
networks %>% 
name display_name description
isomemo-group IsoMemo Network IsoMemo is a network of autonomous isotopic databases.

List Repositories

To list all available repositories use the getRepositories() function. You can filter the output using the network and pattern arguments. For instance, to list all repositories in the IsoMemo network:

reposIsomemo <- getRepositories(
  network = "IsoMemo"

reposIsomemo[c("Repository")]  %>% 
38 14CARHU
54 14SEA Project: A 14C database for Southeast Europe and Anatolia (10,000–3000 calBC)
50 ARCHIPELAGO human stable isotope database
29 Amalthea: a Database of Isotopic measurements on Archaeological and Forensic Tooth Dentine Increments
51 AustArch: A Database of 14C and Luminescence Ages from Archaeological Sites in Australia
47 BASE DE DATOS Iber-Crono
49 CARD 2.0
14 CIMA: Compendium Isotoporum Medii Aevi
33 Database for European 14C dates for the Bronze and Early Iron Age
53 Database our way to Europe
48 EPRG Jomon
52 Edaphobase Open access Data Warehouse for Soil Biodiversity
43 INTIMATE: WG1 Database
41 Intramolecular 2H profiles
40 LiVES isotopic database
32 New Zealand Radicarbon Database
39 Northern Hemisphere Modern leaf wax δDn-alkane dataset
35 ORAU database
30 RADON - Radiocarbon dates online
34 Radiocarbon Palaeolithic Europe Database v28
42 Royal Institute for Cultural Heritage Radiocarbon and stable isotope measurements
31 SWVID: Stable Water Vapor Isotope datasets
37 dIANA

List Available File Types

Use the getFileTypes() function to list all available file types. The following example showcases file types available in the ‘IsoMemo’ network:

fileTypesIsomemo <- getFileTypes(network = "isomemo")
fileTypesIsomemo  %>% 
name format
12 14carhu xlsx
19 14sea-project-a-14c-database-for-southeast-europe-and-anatolia-10-000-3000-calbc xlsx
11 ageas html
5 amalthea-a-database-of-isotopic-measurements-on-archaeological-and-forensic-tooth-dentine-increments xlsx
6 amalthea-a-database-of-isotopic-measurements-on-archaeological-and-forensic-tooth-dentine-increments docx
7 amalthea-a-database-of-isotopic-measurements-on-archaeological-and-forensic-tooth-dentine-increments csv
15 archipelago-human-stable-isotope-database csv
16 archipelago-human-stable-isotope-database xlsx
17 archipelago-human-stable-isotope-database rdata
18 austarch-a-database-of-14c-and-luminescence-ages-from-archaeological-sites-in-australia csv
1 cima-compendium-isotoporum-medii-aevi xlsx
2 cima-compendium-isotoporum-medii-aevi docx
3 cima-compendium-isotoporum-medii-aevi csv
4 cima-compendium-isotoporum-medii-aevi rdata
14 eprg-jomon xlsx
9 new-zealand-radicarbon-database perl
13 northern-hemisphere-modern-leaf-wax-ddn-alkane-dataset xlsx
10 radiocarbon-palaeolithic-europe-database-v28 xlsx
8 radon-radiocarbon-dates-online csv

Filter Resources by pattern or File Type

To list all available resources, employ the getResources() function. Filter the output using the network, repository, fileType, and pattern arguments. For instance, to list all CSV files whose meta information contains the string plants:

resourcesPlants <- getResources(
  fileType = c("csv"),
  pattern = "plant"

resourcesPlants[c("name", "format")]  %>% 
name format
Isotopic measurements in CSV format csv
Metadata description CSV csv
CIMA Animals 29.05.2021 CSV csv
CIMA Humans 29.05.2021 CSV csv
CIMA Plants 29.05.2021 CSV csv
Combined CIMA CSV 29.05.2021 csv
IsoMad Modern Biological Material v1 csv
IsoMedIta Animals 21-12-22 - CSV csv
IsoMedIta Humans 21-12-22 - CSV csv
IsoMedIta Plants 21-12-22 - CSV csv
Isotòpia Animals csv (19.09.2023) csv
Isotòpia Humans csv (19.09.2023) csv
Isotòpia Plants csv (19.09.2023) csv
MAIA Animals CSV csv
MAIA Humans CSV csv
MAIA Plants CSV csv
SAAID_V.2.0_2023_plants.csv csv
Zanadamu CSV format csv

Get the data of a Specific Resource

To retrieve data from a specific resource, use the getData() function. For text files one can specify e.g. the separator using the helper function dataOptions(). The example below demonstrates fetching data from the "CIMA Humans 29.05.2021 CSV" resource:

isotopicData <- getData(
  name = "CIMA Animals 29.05.2021 CSV",
  options = dataOptions(sep = ";")) 
#> Encoding: 'UTF-8'.
isotopicData  %>% 
  head(5)  %>% 
  dplyr::select(c("Entry_ID", "General_Category_Family", "Common_Name", "Sampled_Element", "Analysed_Component")) %>%
Entry_ID General_Category_Family Common_Name Sampled_Element Analysed_Component
1 Equid Horse Femur Collagen
2 Cricetid Vole Cranium Collagen
3 Cricetid Vole Mandible Collagen
4 Moronid European Bass Bone Collagen
5 Moronid European Bass Bone Collagen