iRamat

This R package provides a simple way to connect to the CHIPS API and retrieve data for further analysis and visualization. Documentation for the CHIPS database and API is available on the CHIPS website.

Install

Install from GitHub

# install.packages("devtools")
devtools::install_github("iramat/iRamat")

Load the iRamat package

library(iRamat)

Using the Database API

Connect to the database API using the db_api_connect() function.

Get a specific dataset

Connect to the database API using the default parameters. The default dataset is dataset_adisser17.

df <- db_api_connect()
names(df)
# [1] "dataset_adisser17"

The dataset can be accessed by its name. For example, and for the first row of dataset_adisser17:

df$dataset_adisser17[1, ]

context_name	id_chips	sample_name	typology	na	mg	al	si	p	s	cl	k	ca	mn	fe	loi	ag	arsenic	ba	be	bi	cd	ce	co	cr	cs	cu	dy	er	eu	deltafe56	deltafe57	ga	gd	ge	hf	ho	indium	la	li	lu	mo	nb	nd	ni	os	os187_os188	os187_os186	pb	pd	pr	rb	ru	sb	sc	se	sm	sn	sr	sr87_sr86	ta	tb	te	th	ti	tl	tm	u	v	w	y	yb	zn	zr	major_method	major_analytical_setup	trace_method	trace_analytical_setup	reference	url
Aux Minières	4967	MINHAO108-A	NA	0.04	0.03	3.23	4.45	0.04	0.00	0	0.07	0.09	0.03	53.17	7.90	NA	578.900	20.31	13.500	0.308	0.325	56.06	26.590	214.9	0.971	5.587	5.025	2.637	1.387	NA	NA	7.478	4.960	2.61	1.431	0.938	0.475	21.24	NA	0.372	5.362	2.808	24.37	63.140	NA	NA	NA	113.8444	NA	6.119	4.692	NA	127.50	1.342	NA	6.095	0.945	43.73	NA	0.227	0.843	NA	17.38	0.092	NA	0.397	9.352	857.3	0.563	22.17	2.776	112.60	58.04	ICP-OES	CRPG - Thermo Fisher Scientific Icap 6500	ICP-OES	CRPG - Thermo Fisher Scientific Icap 6500	Alexandre Disser, Philippe Dillmann, Marc Leroy, Maxime L'Héritier, Sylvain Bauvais, Philippe Fluzin (2017), Iron Supply for the Building of Metz Cathedral: New Methodological Development for Provenance Studies and Historical Considerations, Archaeometry, 59	https://onlinelibrary.wiley.com/doi/full/10.1111/arcm.12265

Column descriptions are available on CHIPS website.

Get all the datasets

Collect all data from API-available datasets by using the option all_datasets = TRUE. By default, all API-available datasets are listed in the CHIPS table hosted on GitHub: urls_data.tsv

df <- db_api_connect(all_datasets = TRUE)
# all_datasets = TRUE: collecting all datasets from urls_data.tsv
# Requesting: http://157.136.252.188:3000/dataset_tyoungxx
# Requesting: http://157.136.252.188:3000/dataset_adisser17
# Requesting: http://157.136.252.188:3000/dataset_gzabinski23
# Requesting: http://157.136.252.188:3000/dataset_gpages22
# Requesting: http://157.136.252.188:3000/dataset_vserneels93
# Requesting: http://157.136.252.188:3000/dataset_sleroy12
# Requesting: http://157.136.252.188:3000/dataset_pdillmann17
# Requesting: http://157.136.252.188:3000/dataset_amdesaulty8a
# Requesting: http://157.136.252.188:3000/dataset_amdesaulty8b
# Requesting: http://157.136.252.188:3000/dataset_jmilot16
# Requesting: http://157.136.252.188:3000/dataset_mpcoustures06
# Requesting: http://157.136.252.188:3000/dataset_gstdidier17
# Requesting: http://157.136.252.188:3000/dataset_mbrauns13
# Requesting: http://157.136.252.188:3000/dataset_lheritier20
# Requesting: http://157.136.252.188:3000/dataset_mleroy97
# Requesting: http://157.136.252.188:3000/dataset_mleroy24
# Requesting: http://157.136.252.188:3000/dataset_leschenlohr01
# Requesting: http://157.136.252.188:3000/dataset_tivancan21
# Requesting: http://157.136.252.188:3000/dataset_pmameli14
# Requesting: http://157.136.252.188:3000/dataset_kmittelstaedt22
# Requesting: http://157.136.252.188:3000/dataset_mbenvenuti13
# Requesting: http://157.136.252.188:3000/dataset_mberranger26
# Requesting: http://157.136.252.188:3000/dataset_rsaage26
# Collected and merged 23 datasets. Total rows: 3513

Chronology

Timelines of sites in CHIPS

The chrono() function models the chronological attribution of the site by creating a timeline:

df <- db_api_connect()
chrono(d = df$dataset_adisser17)

PeriodO timelines

PeriodO¹ periods can also be displayed. The default PeriodO authority (i.e. a set of different periods identified by the same author) is INRAP: Institut National de Recherches Archeologiques Préventive².

periodo(min_date = -700, max_date = 0, use_periodo = TRUE, time_match = 1)

PeriodO timelines by location

PeriodO records the spatial extent of periods. In the periodo() function, this spatial extent is represented by the variable location. Here, the PeriodO authority ArkeoGIS authors³ is used for periods in France only.

periodo(periodo_authority = "http://n2t.net/ark:/99152/p09hq4n", min_date = -500, max_date = 500, 
        use_periodo = TRUE, time_match = 1, location = "France")

Timelines of sites in CHIPS and PeriodO timelines

Site and PeriodO timelines can be merged into a single plot:

df <- db_api_connect()
plots <- chrono(df$dataset_adisser17, use_periodo = TRUE)
ggpubr::ggarrange(plots$sites, plots$periodo$periodo,
                  heights = c(1, 2), ncol = 1, align = "v")

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Talks

• WAIA: Présentation du package R iRamat - slides | video

Footnotes

1. https://client.perio.do/ ↩

2. https://n2t.net/ark:/99152/p02chr4 ↩

3. http://n2t.net/ark:/99152/p09hq4n ↩