This function combines information from the table of individuals and table of nodes into a single data frame which can be used in downstream analyses.

ts_data(ts, remembered = NULL, retained = NULL, alive = NULL)

Arguments

ts

pyslim.SlimTreeSequence object

remembered, retained, alive

Only extract information about nodes and times of individuals with the specific flag

Value

Data frame with processed information from the tree sequence object. If the model which generated this data was spatial, result will be returned as a spatial object of the class sf. See description for more information.

Details

The source of data (tables of individuals and nodes recorded in the tree sequence generated by SLiM) are combined into a single data frame. If the model which generated the data was spatial, coordinates of nodes (which are pixel-based by default because SLiM spatial simulations occur on a raster), the coordinates are automatically converted to an explicit spatial object of the sf class unless spatial = FALSE. See https://r-spatial.github.io/sf/ for an extensive introduction to the sf package and the ways in which spatial data can be processed, analysed, and visualised.

See also

ts_individuals ts_nodes ts_edges for accessing raw tree sequence tables without added metadata annotation. See also ts_ancestors to learn how to extract information about relationship beteween nodes in the tree sequence, and how to analysed data about distances between nodes in the spatial context.