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library(Pandora)
library(magrittr)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.
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. |
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 | |
|---|---|
| 38 | 14CARHU |
| 54 | 14SEA Project: A 14C database for Southeast Europe and Anatolia (10,000–3000 calBC) |
| 36 | AGEAS |
| 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 |
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 |
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 |
| SAAID_V.2.0_2023_plants.csv | csv |
| Zanadamu CSV format | csv |
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 |
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