Stratigraphy from an Edge List

Usage

as_stratigraphy(x, y, ...)

# S4 method for character,character
as_stratigraphy(x, y, reduce = TRUE)

# S4 method for numeric,numeric
as_stratigraphy(x, y, reduce = TRUE)

# S4 method for list,missing
as_stratigraphy(x, reduce = TRUE)

# S4 method for matrix,missing
as_stratigraphy(x, reduce = TRUE)

Arguments

x, y: A character vector giving the names/IDs of the bottom and top layers (edge list), respectively (will be coerced to character with as.character()). If y is missing, x should be a two-columns observation table that records the stratigraphic relationships between younger contexts and older contexts.
...: Currently not used.
reduce: A logical scalar: should transitive reduction be performed?

Value

A StratigraphicMatrix object.

Details

A stratigraphic matrix represents directed relationships between stratigraphic units. A stratigraphic matrix is an adjacency matrix (a non symmetric square matrix with zeros on its main diagonal), suitable to build a directed acyclic graph (DAG).

References

Dye, T. S. & Buck, C. E. (2015). Archaeological Sequence Diagrams and Bayesian Chronological Models. Journal of Archaeological Science, 63: 84-93. doi:10.1016/j.jas.2015.08.008 .

Author

N. Frerebeau

Examples

## Principles of Archaeological Stratigraphy, fig. 12
## Build an adjacency list
harris <- data.frame(
  younger = c(1, 1, 1, 2, 3, 4, 5, 6, 6, 6, 7, 8, 1, 1),
  older = c(2, 3, 4, 5, 5, 5, 6, 7, 8, 9, 9, 9, 7, 8)
)

## Coerce to adjacency matrix
strati <- as_stratigraphy(harris, reduce = TRUE)

## Define interface layers
set_interface(strati) <- c("1" = FALSE, "2" = TRUE,  "3" = FALSE,
                           "4" = FALSE, "5" = FALSE, "6" = TRUE,
                           "7" = FALSE, "8" = FALSE, "9" = FALSE)

## Stratigraphic graph
graph <- as_graph(strati)
plot(graph)