animate_model           Animate the simulated population dynamics
area                    Calculate the area covered by the given slendr
                        object
check_dependencies      Check that the required dependencies are
                        available for slendr to work
check_env               Check that the active Python environment is
                        setup for slendr
clear_env               Remove the automatically created slendr Python
                        environment
compile_model           Compile a slendr demographic model
distance                Calculate the distance between a pair of
                        spatial boundaries
expand_range            Expand the population range
explore_model           Open an interactive browser of the spatial
                        model
extract_parameters      Extract information from a compiled model or a
                        simulated tree sequence
gene_flow               Define a gene-flow event between two
                        populations
get_python              Get a path to internal Python interpreter of
                        slendr
init_env                Activate the Python environment of slendr
join                    Merge two spatial 'slendr' objects into one
move                    Move the population to a new location in a
                        given amount of time
msprime                 Run a slendr model in msprime
overlap                 Generate the overlap of two 'slendr' objects
plot_map                Plot 'slendr' geographic features on a map
plot_model              Plot demographic history encoded in a slendr
                        model
population              Define a population
print.slendr_pop        Print a short summary of a 'slendr' object
print.slendr_ts         Print tskit's summary table of the Python
                        tree-sequence object
read_model              Read a previously serialized model
                        configuration
region                  Define a geographic region
reproject               Reproject coordinates between coordinate
                        systems
resize                  Change the population size
schedule_sampling       Define sampling events for a given set of
                        populations
set_dispersal           Change dispersal parameters
set_range               Update the population range
setup_env               Setup a dedicated Python virtual environment
                        for slendr
shrink_range            Shrink the population range
slim                    Run a slendr model in SLiM
substitute_values       Substitute values of parameters in a SLiM
                        extension template
subtract                Generate the difference between two 'slendr'
                        objects
summary.slendr_nodes    Summarise the contents of a 'ts_nodes' result
ts_afs                  Compute the allele frequency spectrum (AFS)
ts_ancestors            Extract (spatio-)temporal ancestral history for
                        given nodes/individuals
ts_coalesced            Check that all trees in the tree sequence are
                        fully coalesced
ts_descendants          Extract all descendants of a given
                        tree-sequence node
ts_divergence           Calculate pairwise divergence between sets of
                        individuals
ts_diversity            Calculate diversity in given sets of
                        individuals
ts_draw                 Plot a graphical representation of a single
                        tree
ts_edges                Extract spatio-temporal edge annotation table
                        from a given tree or tree sequence
ts_eigenstrat           Convert genotypes to the EIGENSTRAT file format
ts_extend               Extend the span of sequences covered by
                        ancestral nodes (EXPERIMENTAL)
ts_f2                   Calculate the f2, f3, f4, and f4-ratio
                        statistics
ts_fst                  Calculate pairwise statistics between sets of
                        individuals
ts_genotypes            Extract genotype table from the tree sequence
ts_ibd                  Extract Identity-by-Descent (IBD) segments
                        (EXPERIMENTAL)
ts_load                 Read a tree sequence from a file
ts_metadata             Extract list with tree sequence metadata saved
                        by SLiM
ts_mutate               Add mutations to the given tree sequence
ts_names                Extract names of individuals in a tree sequence
ts_nodes                Extract combined annotated table of individuals
                        and nodes
ts_phylo                Convert a tree in the tree sequence to an
                        object of the class 'phylo'
ts_read                 Read a tree sequence from a file
ts_recapitate           Recapitate the tree sequence
ts_samples              Extract names and times of individuals of
                        interest in the current tree sequence (either
                        all sampled individuals or those that the user
                        simplified to)
ts_save                 Write a tree sequence to a file
ts_segregating          Calculate the density of segregating sites for
                        the given sets of individuals
ts_simplify             Simplify the tree sequence down to a given set
                        of individuals
ts_table                Get the table of
                        individuals/nodes/edges/mutations/sites from
                        the tree sequence
ts_tajima               Calculate Tajima's D for given sets of
                        individuals
ts_tracts               Extract ancestry tracts from a tree sequence
                        (EXPERIMENTAL)
ts_tree                 Get a tree from a given tree sequence
ts_vcf                  Save genotypes from the tree sequence as a VCF
                        file
ts_write                Save a tree sequence to a file
world                   Define a world map for all spatial operations
