How to use the Pandora Data Package

library(Pandora)
library(magrittr)

Introduction

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 %>% 
  knitr::kable()

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")]  %>% 
  knitr::kable()

	Repository
69	14CARHU
84	14SEA Project: A 14C database for Southeast Europe and Anatolia (10,000–3000 calBC)
67	AGEAS
60	Amalthea: a Database of Isotopic measurements on Archaeological and Forensic Tooth Dentine Increments
80	ARCHIPELAGO human stable isotope database
81	AustArch: A Database of 14C and Luminescence Ages from Archaeological Sites in Australia
77	BASE DE DATOS Iber-Crono
79	CARD 2.0
20	CIMA: Compendium Isotoporum Medii Aevi
64	Database for European 14C dates for the Bronze and Early Iron Age
83	Database our way to Europe
68	dIANA
82	Edaphobase Open access Data Warehouse for Soil Biodiversity
78	EPRG Jomon
73	INTIMATE: WG1 Database
71	Intramolecular 2H profiles
12	LiVES isotopic database
15	NEENA Stable Isotopes v.1
63	New Zealand Radicarbon Database
70	Northern Hemisphere Modern leaf wax δDn-alkane dataset
66	ORAU database
65	Radiocarbon Palaeolithic Europe Database v28
61	RADON - Radiocarbon dates online
72	Royal Institute for Cultural Heritage Radiocarbon and stable isotope measurements
62	SWVID: Stable Water Vapor Isotope datasets

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  %>% 
  knitr::kable()

	name	format
15	14carhu	xlsx
22	14sea-project-a-14c-database-for-southeast-europe-and-anatolia-10-000-3000-calbc	xlsx
14	ageas	html
8	amalthea-a-database-of-isotopic-measurements-on-archaeological-and-forensic-tooth-dentine-increments	xlsx
9	amalthea-a-database-of-isotopic-measurements-on-archaeological-and-forensic-tooth-dentine-increments	docx
10	amalthea-a-database-of-isotopic-measurements-on-archaeological-and-forensic-tooth-dentine-increments	csv
18	archipelago-human-stable-isotope-database	csv
19	archipelago-human-stable-isotope-database	xlsx
20	archipelago-human-stable-isotope-database	rdata
21	austarch-a-database-of-14c-and-luminescence-ages-from-archaeological-sites-in-australia	csv
4	cima-compendium-isotoporum-medii-aevi	xlsx
5	cima-compendium-isotoporum-medii-aevi	docx
6	cima-compendium-isotoporum-medii-aevi	rdata
7	cima-compendium-isotoporum-medii-aevi	csv
17	eprg-jomon	xlsx
1	lives-isotopic-database	xlsx
2	neena-stable-isotopes	xlsx
3	neena-stable-isotopes	csv
12	new-zealand-radicarbon-database	perl
16	northern-hemisphere-modern-leaf-wax-ddn-alkane-dataset	xlsx
13	radiocarbon-palaeolithic-europe-database-v28	xlsx
11	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")]  %>% 
  knitr::kable()

name	format
Isotopic measurements in CSV format	csv
Metadata description CSV	csv
ADS_database_metadata_template_LV.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
IsoChina human dataset in CSV format	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 (2024) csv	csv
Isotòpia Humans (2024) csv	csv
Isotòpia Plants (2024) csv	csv
MAIA Animals CSV	csv
MAIA Humans CSV	csv
MAIA Plants CSV	csv
Animal isotopic data CSV	csv
Human isotopic data CSV	csv
Plant isotopic data CSV	csv
NEENA_Animals-v1.csv	csv
NEENA_Humans-v1.csv	csv
NEENA_Plants-v1.csv	csv
PleIStO_ArchAID_Fauna_V.1.csv	csv
PleIStO_ArchAID_Hominin_V.1.csv	csv
saaid_V.2.0_2023_Animals.csv	csv
saaid_V.2.0_2023_Humans.csv	csv
saaid_V.2.0_2023_Plants.csv	csv
OAPID 25.5.25	csv
Wanyika chronological database in CSV format	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")) %>%
  knitr::kable()

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