Man pages for slendr
A Simulation Framework for Spatiotemporal Population Genetics

animate_modelAnimate the simulated population dynamics
areaCalculate the area covered by the given slendr object
as.phylo.slendr_phyloConvert an annotated 'slendr_phylo' object to a 'phylo'...
check_dependenciesCheck that the required dependencies are available for slendr...
check_envCheck that the active Python environment is setup for slendr
clear_envRemove the automatically created slendr Python environment
compile_modelCompile a slendr demographic model
distanceCalculate the distance between a pair of spatial boundaries
expand_rangeExpand the population range
explore_modelOpen an interactive browser of the spatial model
gene_flowDefine a gene-flow event between two populations
get_envGet the name of the current slendr Python environment
init_envActivate slendr's own dedicated Python environment
joinMerge two spatial 'slendr' objects into one
moveMove the population to a new location in a given amount of...
msprimeRun a slendr model in msprime
overlapGenerate the overlap of two 'slendr' objects
pipePipe operator
plot_mapPlot 'slendr' geographic features on a map
plot_modelPlot demographic history encoded in a slendr model
populationDefine a population
print.slendr_popPrint a short summary of a 'slendr' object
print.slendr_tsPrint tskit's summary table of the Python tree-sequence...
read_modelRead a previously serialized model configuration
regionDefine a geographic region
reprojectReproject coordinates between coordinate systems
resizeChange the population size
schedule_samplingDefine sampling events for a given set of populations
set_dispersalChange dispersal parameters
set_rangeUpdate the population range
setup_envSetup a dedicated Python virtual environment for slendr
shrink_rangeShrink the population range
slendrA Simulation Framework for Spatiotemporal Population Genetics
slimRun a slendr model in SLiM
subtractGenerate the difference between two 'slendr' objects
summary.slendr_nodesSummarise the contents of a 'ts_nodes' result
ts_afsCompute the allele frequency spectrum (AFS)
ts_ancestorsExtract (spatio-)temporal ancestral history for given...
ts_coalescedCheck that all trees in the tree sequence are fully coalesced
ts_descendantsExtract all descendants of a given tree-sequence node
ts_divergenceCalculate pairwise divergence between sets of individuals
ts_diversityCalculate diversity in given sets of individuals
ts_drawPlot a graphical representation of a single tree
ts_edgesExtract spatio-temporal edge annotation table from a given...
ts_eigenstratConvert genotypes to the EIGENSTRAT file format
ts_f4ratioCalculate the f2, f3, f4, and f4-ratio statistics
ts_fstCalculate pairwise statistics between sets of individuals
ts_genotypesExtract genotype table from the tree sequence
ts_ibdCollect Identity-by-Descent (IBD) segments (EXPERIMENTAL)
ts_loadLoad a tree sequence file produced by a given model
ts_metadataExtract list with tree sequence metadata saved by SLiM
ts_mutateAdd mutations to the given tree sequence
ts_namesExtract names of individuals in a tree sequence
ts_nodesExtract combined annotated table of individuals and nodes
ts_phyloConvert a tree in the tree sequence to an object of the class...
ts_recapitateRecapitate the tree sequence
ts_samplesExtract names and times of individuals of interest in the...
ts_saveSave a tree sequence to a file
ts_segregatingCalculate the density of segregating sites for the given sets...
ts_simplifySimplify the tree sequence down to a given set of individuals
ts_tableGet the table of individuals/nodes/edges/mutations from the...
ts_tajimaCalculate Tajima's D for given sets of individuals
ts_tractsExtract ancestry tracts from a tree sequence (EXPERIMENTAL)
ts_treeGet a tree from a given tree sequence
ts_vcfSave genotypes from the tree sequence as a VCF file
worldDefine a world map for all spatial operations
slendr documentation built on June 22, 2024, 6:56 p.m.