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
45	14CARHU
61	14SEA Project: A 14C database for Southeast Europe and Anatolia (10,000–3000 calBC)
43	AGEAS
36	Amalthea: a Database of Isotopic measurements on Archaeological and Forensic Tooth Dentine Increments
57	ARCHIPELAGO human stable isotope database
58	AustArch: A Database of 14C and Luminescence Ages from Archaeological Sites in Australia
54	BASE DE DATOS Iber-Crono
56	CARD 2.0
22	CIMA: Compendium Isotoporum Medii Aevi
40	Database for European 14C dates for the Bronze and Early Iron Age
60	Database our way to Europe
44	dIANA
59	Edaphobase Open access Data Warehouse for Soil Biodiversity
55	EPRG Jomon
50	INTIMATE: WG1 Database
48	Intramolecular 2H profiles
47	LiVES isotopic database
39	New Zealand Radicarbon Database
46	Northern Hemisphere Modern leaf wax δDn-alkane dataset
42	ORAU database
41	Radiocarbon Palaeolithic Europe Database v28
37	RADON - Radiocarbon dates online
49	Royal Institute for Cultural Heritage Radiocarbon and stable isotope measurements
38	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
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")]  %>% 
  knitr::kable()

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
Animal isotopic data CSV	csv
Human isotopic data CSV	csv
Plant isotopic data 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
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