Man pages for rdinnager/slimrlang
Write SLiM Population Genetics Simulation Scripts in R
| addCloned | SLiM method addCloned |
| addCrossed | SLiM method addCrossed |
| addEmpty | SLiM method addEmpty |
| addMutations | SLiM method addMutations |
| addNewDrawnMutation | SLiM method addNewDrawnMutation |
| addNewMutation | SLiM method addNewMutation |
| addRecombinant | SLiM method addRecombinant |
| addSelfed | SLiM method addSelfed |
| addSubpop | SLiM method addSubpop |
| addSubpopSplit | SLiM method addSubpopSplit |
| ancestralNucleotides | SLiM method ancestralNucleotides |
| as_slimr_script | Convert a character vector into a slim_script object |
| as_slim_text.slimr_script | Convert a slimr_script to a length 1 character vector |
| cachedFitness | SLiM method cachedFitness |
| Chromosome | Chromosome |
| codonsToAminoAcids | SLiM method codonsToAminoAcids |
| configureDisplay | SLiM method configureDisplay |
| containsMarkerMutation | SLiM method containsMarkerMutation |
| containsMutations | SLiM method containsMutations |
| countOfMutationsOfType | SLiM method countOfMutationsOfType |
| defineSpatialMap | SLiM method defineSpatialMap |
| deregisterScriptBlock | SLiM method deregisterScriptBlock |
| distance | SLiM method distance |
| distanceToPoint | SLiM method distanceToPoint |
| drawBreakpoints | SLiM method drawBreakpoints |
| drawByStrength | SLiM method drawByStrength |
| drawSelectionCoefficient | SLiM method drawSelectionCoefficient |
| evaluate | SLiM method evaluate |
| Genome | Genome |
| GenomicElement | GenomicElement |
| GenomicElementType | GenomicElementType |
| getValue | SLiM method getValue |
| grapes-.-grapes | slimrlang stub for the SLiM '.' operator |
| grapes-help-grapes | slimrlang stub for the first part of the SLiM ternary... |
| Individual | Individual |
| Initialize | Initialize |
| initializeAncestralNucleotides | SLiM method initializeAncestralNucleotides |
| initializeGeneConversion | SLiM method initializeGeneConversion |
| initializeGenomicElement | SLiM method initializeGenomicElement |
| initializeGenomicElementType | SLiM method initializeGenomicElementType |
| initializeHotspotMap | SLiM method initializeHotspotMap |
| initializeInteractionType | SLiM method initializeInteractionType |
| initializeMutationRate | SLiM method initializeMutationRate |
| initializeMutationType | SLiM method initializeMutationType |
| initializeMutationTypeNuc | SLiM method initializeMutationTypeNuc |
| initializeRecombinationRate | SLiM method initializeRecombinationRate |
| initializeSex | SLiM method initializeSex |
| initializeSLiMModelType | SLiM method initializeSLiMModelType |
| initializeSLiMOptions | SLiM method initializeSLiMOptions |
| initializeTreeSeq | SLiM method initializeTreeSeq |
| interactingNeighborCount | SLiM method interactingNeighborCount |
| interactionDistance | SLiM method interactionDistance |
| InteractionType | InteractionType |
| mm16To256 | SLiM method mm16To256 |
| mmJukesCantor | SLiM method mmJukesCantor |
| mmKimura | SLiM method mmKimura |
| Mutation | Mutation |
| mutationCounts | SLiM method mutationCounts |
| mutationFrequencies | SLiM method mutationFrequencies |
| mutationsOfType | SLiM method mutationsOfType |
| MutationType | MutationType |
| nearestInteractingNeighbors | SLiM method nearestInteractingNeighbors |
| nearestNeighbors | SLiM method nearestNeighbors |
| nearestNeighborsOfPoint | SLiM method nearestNeighborsOfPoint |
| nucleotideCounts | SLiM method nucleotideCounts |
| nucleotideFrequencies | SLiM method nucleotideFrequencies |
| nucleotides | SLiM method nucleotides |
| nucleotidesToCodons | SLiM method nucleotidesToCodons |
| output | SLiM method output |
| outputFixedMutations | SLiM method outputFixedMutations |
| outputFull | SLiM method outputFull |
| outputMS | SLiM method outputMS |
| outputMSSample | SLiM method outputMSSample |
| outputMutations | SLiM method outputMutations |
| outputSample | SLiM method outputSample |
| outputUsage | SLiM method outputUsage |
| outputVCF | SLiM method outputVCF |
| outputVCFSample | SLiM method outputVCFSample |
| pipe | Pipe operator |
| pointInBounds | SLiM method pointInBounds |
| pointPeriodic | SLiM method pointPeriodic |
| pointReflected | SLiM method pointReflected |
| pointStopped | SLiM method pointStopped |
| pointUniform | SLiM method pointUniform |
| positionsOfMutationsOfType | SLiM method positionsOfMutationsOfType |
| readFromMS | SLiM method readFromMS |
| readFromPopulationFile | SLiM method readFromPopulationFile |
| readFromVCF | SLiM method readFromVCF |
| recalculateFitness | SLiM method recalculateFitness |
| reconstruct.slimr_script | Reconstruct slimrlang code to make this slimr_script |
| registerEarlyEvent | SLiM method registerEarlyEvent |
| registerFitnessCallback | SLiM method registerFitnessCallback |
| registerInteractionCallback | SLiM method registerInteractionCallback |
| registerLateEvent | SLiM method registerLateEvent |
| registerMateChoiceCallback | SLiM method registerMateChoiceCallback |
| registerModifyChildCallback | SLiM method registerModifyChildCallback |
| registerMutationCallback | SLiM method registerMutationCallback |
| registerRecombinationCallback | SLiM method registerRecombinationCallback |
| registerReproductionCallback | SLiM method registerReproductionCallback |
| relatedness | SLiM method relatedness |
| removeMutations | SLiM method removeMutations |
| removeSubpopulation | SLiM method removeSubpopulation |
| rescheduleScriptBlock | SLiM method rescheduleScriptBlock |
| sampleIndividuals | SLiM method sampleIndividuals |
| setAncestralNucleotides | SLiM method setAncestralNucleotides |
| setCloningRate | SLiM method setCloningRate |
| setDistribution | SLiM method setDistribution |
| setGeneConversion | SLiM method setGeneConversion |
| setGenomicElementType | SLiM method setGenomicElementType |
| setHotspotMap | SLiM method setHotspotMap |
| setInteractionFunction | SLiM method setInteractionFunction |
| setMigrationRates | SLiM method setMigrationRates |
| setMutationFractions | SLiM method setMutationFractions |
| setMutationMatrix | SLiM method setMutationMatrix |
| setMutationRate | SLiM method setMutationRate |
| setMutationType | SLiM method setMutationType |
| setRecombinationRate | SLiM method setRecombinationRate |
| setSelectionCoeff | SLiM method setSelectionCoeff |
| setSelfingRate | SLiM method setSelfingRate |
| setSexRatio | SLiM method setSexRatio |
| setSpatialBounds | SLiM method setSpatialBounds |
| setSpatialPosition | SLiM method setSpatialPosition |
| setSubpopulationSize | SLiM method setSubpopulationSize |
| setValue | SLiM method setValue |
| simulationFinished | SLiM method simulationFinished |
| slim_block | Setup a SLiM code block |
| SLiMBuiltin | SLiMBuiltin |
| SLiMEidosBlock | SLiMEidosBlock |
| slimr_clip_original | Copy original slimrlang code used to create a slimr_script... |
| slimrlang-vctrs | Internal vctrs methods |
| slimr_open_original | Open original slimrlang code used to create a slimr_script... |
| slimr_output | Tell SLiM to produce easily parseable output |
| slimr_script_render | Render a SLiM script with special slimrlang formatting |
| slimr_template_info | Get information on templating in a slimr_script |
| slimr_write | Write a slimr_script object to a text file |
| slim_script | Create a SLiMR script |
| SLiMSim | SLiMSim |
| spatialMapColor | SLiM method spatialMapColor |
| spatialMapValue | SLiM method spatialMapValue |
| strength | SLiM method strength |
| Subpopulation | Subpopulation |
| subsetIndividuals | SLiM method subsetIndividuals |
| Substitution | Substitution |
| sumOfMutationsOfType | SLiM method sumOfMutationsOfType |
| takeMigrants | SLiM method takeMigrants |
| tidyeval | Tidy eval helpers |
| totalOfNeighborStrengths | SLiM method totalOfNeighborStrengths |
| treeSeqCoalesced | SLiM method treeSeqCoalesced |
| treeSeqOutput | SLiM method treeSeqOutput |
| treeSeqRememberIndividuals | SLiM method treeSeqRememberIndividuals |
| treeSeqSimplify | SLiM method treeSeqSimplify |
| unevaluate | SLiM method unevaluate |
| uniqueMutationsOfType | SLiM method uniqueMutationsOfType |
