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stratigraphr

stratigraphr is a tidy framework for working with archaeological stratigraphy and chronology in R. It includes tools for reading, analysing, and visualising stratigraphic sequences (Harris matrices) and as directed graphs and an R interface to OxCal’s Chronological Query Language (CQL).

Installation

You can install the latest release of era from CRAN with:

install.packages("stratigraphr")

Or install the development version from GitHub with pak:

# install.packages("pak")
devtools::install_github("joeroe/stratigraphr")

Usage

stratigraph() uses a data frame of stratigraphic relations to construct a stratigraphic graph:

library(stratigraphr)

# Example stratigraphy from Harris (1979), figure 12:
harris12
#>    context   above   below equal
#> 1        1      NA 2, 3, 4  <NA>
#> 2        2       1       5  <NA>
#> 3        3       1       5  <NA>
#> 4        4       1       5  <NA>
#> 5        5 2, 3, 4       6  <NA>
#> 6        6       5    7, 8  <NA>
#> 7        7       6       9     8
#> 8        8       6       9     7
#> 9        9    7, 8 natural  <NA>
#> 10 natural       9      NA  <NA>

stratigraph(harris12, "context", "above")
#> # A stratigraph: 10 units and 12 relations
#> # ✔ Valid stratigraphic graph
#>                 1
#> ┌───────────────┼───────────────┐
#> 2               3               4
#> └───────────────┼───────────────┘
#>                 5
#>                 │
#>                 6
#>         ┌───────┴───────┐
#>         7               8
#>         └───────┬───────┘
#>                 9
#>                 │
#>              natural

stratigraph objects are built on top of tidygraph, which gives access to a powerful tidy interface for manipulating and analysing the stratigraphy. It also works seamlessly with ggraph. For example, to approximate a conventional ‘Harris matrix’ visualisation with ggraph:

library("ggraph")
#> Loading required package: ggplot2

# Example data after Harris 1979, Fig. 12
harris12 |>
  stratigraph("context", "above") |>
  ggraph(layout = "sugiyama") +
    geom_edge_elbow() +
    geom_node_label(aes(label = context), label.r = unit(0, "mm")) +
    theme_graph()

For further information on:

This package previous contained functions for tidy radiocarbon data. These were deprecated in v0.3.0 and moved to the c14 package. See c14’s introductory vignette for further information.