ts_table: Get the table of individuals/nodes/edges/mutations/sites from...

In bodkan/slendr: A Simulation Framework for Spatiotemporal Population Genetics

Get the table of individuals/nodes/edges/mutations/sites from the tree sequence

Description

This function extracts data from a given tree sequence table. All times are converted to model-specific time units from tskit's "generations backwards" time direction.

Usage

ts_table(ts, table = c("individuals", "edges", "nodes", "mutations", "sites"))

Arguments

ts	Tree sequence object of the class slendr_ts
table	Which tree sequence table to return

Details

For further processing and analyses, the output of the function ts_nodes might be more useful, as it merges the information in node and individual tables into one table and further annotates it with useful information from the model configuration data.

Value

Data frame with the information from the give tree-sequence table (can be either a table of individuals, edges, nodes, or mutations).

See Also

ts_nodes and ts_edges for accessing an annotated, more user-friendly and analysis-friendly tree-sequence table data

Examples

# 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 and add mutations to it
ts <- ts_read(slendr_ts, model) %>% ts_mutate(mutation_rate = 1e-8, random_seed = 42)

# get the 'raw' tskit table of individuals
ts_table(ts, "individuals")

# get the 'raw' tskit table of edges
ts_table(ts, "edges")

# get the 'raw' tskit table of nodes
ts_table(ts, "nodes")

# get the 'raw' tskit table of mutations
ts_table(ts, "mutations")

# get the 'raw' tskit table of sites
ts_table(ts, "sites")

bodkan/slendr documentation built on Dec. 19, 2024, 11:41 p.m.