slendr (version 1.0.0)

ts_nodes: Extract combined annotated table of individuals and nodes

Description

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.

Usage

ts_nodes(x, sf = TRUE)

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.

Arguments

x

Tree sequence object of the class slendr_ts or a phylo object extracted by ts_phylo

sf

Should spatial data be returned in an sf format? If FALSE, spatial geometries will be returned simply as x and y columns, instead of the standard POINT data type.

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_table 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.

Examples

check_dependencies(python = TRUE, quit = TRUE) # dependencies must be present

init_env()

# load an example model with an already simulated tree sequence
slendr_ts <- system.file("extdata/models/introgression_slim.trees", package = "slendr")
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

# load the tree-sequence object from disk
ts <- ts_read(slendr_ts, model)

# extract an annotated table with (spatio-)temporal node information
ts_nodes(ts)