| animate_model | Animate the simulated population dynamics |
| area | Calculate the area covered by the given slendr object |
| as.phylo.slendr_phylo | Convert an annotated 'slendr_phylo' object to a 'phylo'... |
| check_dependencies | Check that the required dependencies are available for slendr... |
| 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... |
| 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... |
| msprime | Run a slendr model in msprime |
| overlap | Generate the overlap of two 'slendr' objects |
| pipe | Pipe operator |
| 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... |
| 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 |
| slendr | A Simulation Framework for Spatiotemporal Population Genetics |
| 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... |
| 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... |
| ts_eigenstrat | Convert genotypes to the EIGENSTRAT file format |
| 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... |
| 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... |
| ts_save | Write a tree sequence to a file |
| ts_segregating | Calculate the density of segregating sites for the given sets... |
| 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... |
| 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 |
