# A Simulation Framework for Spatiotemporal Population Genetics

## Documentation for package ‘slendr’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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_env | Get the name of the current slendr Python environment
init_env | Activate slendr's own dedicated Python environment
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_map | Print a short summary of a 'slendr' object
print.slendr_model | Print a short summary of a 'slendr' object
print.slendr_pop | Print a short summary of a 'slendr' object
print.slendr_region | 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
setup_env | Setup a dedicated Python virtual environment for slendr
set_dispersal | Change dispersal parameters
set_range | Update the population range
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_f2 | Calculate the f2, f3, f4, and f4-ratio statistics
ts_f3 | Calculate the f2, f3, f4, and f4-ratio statistics
ts_f4 | Calculate the f2, f3, f4, and f4-ratio statistics
ts_f4ratio | 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 | Collect 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