README.md

In zoometh/zoowork: Miscellaneous of Functions for Archaeozoology

zoowork R package Methods for Archaeozoology

Thomas Huet, Ariadna Nieto-Espinet, Angela Trentacoste, Silvia Guimarães, Silvia Valenzuela-Lamas

The R package zoowork to provide functions to handle large archaeozoological datasets, like for this study. The main functions are:

| | | |-----|-----| |Symbols | zoo_legends() allows to record the most distinctive shape and color symbols in an XLSX file and use this symbology for the other mulifactorial analysis | |Mulifactorial analysis | zoo_ca() and zoo_hc() allow data visualisation reusing the same symbology and freezing the limits of the axes to facilitate comparisons through periods | | Isotops | zoo_isotops() plot a double Y-axis for Strontium (Sr) and Oxygen (O) isotops |

Install

Install the package from GitHub into R:

devtools::install_github("zoometh/zoowork")

Load the package

library(zoowork)

Principal functions

zoo_legends

Read a XLSX file of legend and plot the types of sites (by default)

zoo_legends()

Store the legend dataframes

sites_types <- zoo_legends(worksheets = c("sites_types"))
sites_zones <- zoo_legends(worksheets = c("sites_zones"))
taxon_types <- zoo_legends(worksheets = c("taxon_types"))

zoo_read

Read a sample of the NISP dataset used by Nieto-Espinet et al. 2021[^1] with this Supporting information (S1): https://doi.org/10.1371/journal.pone.0246201.s003

df <- zoo_read()

zoo_order_period

Intersects an ordered list of periods with the ones existing in the dataset

df <- zoo_read()
lorder_period <- zoo_order_period(df)

Will give: "LBA" "EIA" "MIA2" "RR" "ERE" "LA"

zoo_ca

Compute Correspondance Analysis on NISP and create a gglot

df <- zoo_read()
lorder_period <- zoo_order_period(df)
typsit_symb <- zoo_legends(worksheets = c("sites_types"))
zoo_ca(df = df, lorder_period = lorder_period, typsit_symb = typsit_symb,
       plot.width = 12, plot.height = 12)

zoo_hc

Compute Hierarchical clustering on NISP and create a gglot

df <- zoo_read()
lorder_period <- zoo_order_period(df)
typsit_symb <- zoo_legends(worksheets = c("sites_types"))
zoo_hc(df = df, lorder_period = lorder_period, typsit_symb = typsit_symb,
       plot.width = 6, plot.height = 10, per.label.sz = 2)

zoo_isotops

Plot the isotope dataset in a grid layout without confidence intervals

zoo_isotops(img.layout = "grid",
            iso.colors = c("red", "blue"),
            stat.ci = FALSE,
            img.format = ".png")

Align the different plot with confidence intervals and defaults colors

zoo_isotops(img.layout = "align",
            img.title = "O and Sr isotopic variations"
)

[^1]: Nieto-Espinet, A. N., Huet, T., Trentacoste, A., Guimarães, S., Orengo, H., & Valenzuela-Lamas, S. (2021). Resilience and livestock adaptations to demographic growth and technological change: A diachronic perspective from the Late Bronze Age to Late Antiquity in NE Iberia. PloS one, 16(2), e0246201. doi: https://doi.org/10.1371/journal.pone.0246201

zoometh/zoowork documentation built on Aug. 21, 2022, 5:11 a.m.