Function reference • slimr

Install and setup SLiM software for use with slimr
`slim_setup()`	Attempt to install and / or setup SLiM for use with slimr
slimr verbs Functions that can be inserted in slimr code blocks for metaprogramming.
Main slimr verbs The three main functions that can be called inside `slim_block` calls for metaprogramming
`r_output()` `slimr_output()`	Tell SLiM to produce easily parseable output
`r_inline()` `slimr_inline()`	Insert R objects into SLiM scripts
`r_template()` `slimr_template()`	Create a templated variable
r_output_ special variants
`r_output_coords()` `slimr_output_coords()`	Utility function to tell SLiM to output coordinates from spatial simulations
`r_output_full()` `slimr_output_full()`	Utility function to tell SLiM to output its outputFull() output
`r_output_nucleotides()` `slimr_output_nucleotides()`	Utility function to tell SLiM to output Nucleotides
`r_output_sex()` `slimr_output_sex()`	Utility function to tell SLim to output sexes of individuals
`r_output_snp()` `slimr_output_snp()`	Utility function to tell SLiM to output SNP format data
r_template_ special variants
`r_template_constant()` `slimr_template_constant()`	Like slimr_template but automatically inserts code to setup variable as a defineConstant() call in the SLiM initialization block.
slimr_block_ verbs These function generate full code blocks and can be used inside `slim_script` calls.
`slim_block_add_subpops()`	Generate a code block that just adds subpopulations to a SLiM simulation
`slim_block_finish()`	Generate simulationFinished Block
`slim_block_init_minimal()`	Generate minimal initialize() block
`slim_block_progress()`	Insert slim_block to track progress when using slim_run
Creating slimr_script objects These functions help you create and manipulate `slimr_script` objects, which contain SLiM simulation instructions
`slim_script()`	Create a SLiMR script
`slim_block()`	Setup a SLiM code block
`slim_function()`	Specify an Eidos function to be included in the SLiM script
`slim_script_render()`	Render a SLiM script with special slimrlang formatting
`slim_load_globals()`	Load SLiM Globals into R Global environment
`slim_unload_globals()`	Unload SLiM Globals from R Global environment
Run a slimr_script object and return results to R
`slim_run()`	Run a SLiM script from R
Extract Output from slimr_results Objects
`slim_extract_full()`	Extract Elements from SLiM's outputFull()
`slim_extract_genlight()`	Extract data into a genlight object
`slim_extract_genome()`	Extract Elements from SLiM's output() for genomes
`slim_extract_output_data()`	Extract data produced by SLiM
Work with SLiM recipes from SLiM manual
`slim_get_recipe()`	Get a SLiM recipe
`slim_get_recipes()`	Get a list of SLiM recipes (as text)
Operators
`%.%`	slimrlang stub for the SLiM '.' operator
`%?%`	slimrlang stub for the first part of the SLiM ternary operator (`condition ? yes else no`).
`%else%`	slimrlang stub for the second part of the SLiM ternary operator (`condition ? yes else no`).
SLiM Callbacks Function stubs for SLiM callback Functions
`slim_callbacks()`	SLiM Callbacks
`initialize()`	SLiM initialize() callback
`late()`	SLiM late() callback
`early()`	SLiM early() callback
`fitness()`	SLiM fitness() callback
`fitnessEffect()`	SLiM fitnessEffect() callback
`mateChoice()`	SLiM mateChoice() callback
`modifyChild()`	SLiM modifyChild() callback
`mutation()`	SLiM mutation() callback
`mutationEffect()`	SLiM mutationEffect() callback
`recombination()`	SLiM recombination() callback
`interaction()`	SLiM interaction() callback
`reproduction()`	SLiM reproduction() callback
`survival()`	SLiM survival() callback
SLiM Class Objects Objects representing the different classes used in SLiM. These can be used to look up and autocomplete what methods or properties are available for a class
`Ch` `Chromosome`	Chromosome
`E` `Eidos`	Eidos
`G` `Genome`	Genome
`GE` `GenomicElement`	GenomicElement
`GET` `GenomicElementType`	GenomicElementType
`In` `Individual`	Individual
`Init` `Initialize`	Initialize
`IT` `InteractionType`	InteractionType
`LF` `LogFile`	LogFile
`M` `Mutation`	Mutation
`MT` `MutationType`	MutationType
`SB` `SLiMBuiltin`	SLiMBuiltin
`SEB` `SLiMEidosBlock`	SLiMEidosBlock
`SG` `SLiMgui`	SLiMgui
`SM` `SpatialMap`	SpatialMap
`SS`	SLiMSim was a class used prior to v4.0 in SLiM. It remains in `slimr` for backwards compatibility but its use is now deprecated.
`P` `Subpopulation`	Subpopulation
`S` `Substitution`	Substitution
`slim_classes`	SLiM Classes
SLiM Class Methods SLiM methods by SLiM class. Note that if a function appears multiple times within a class, that is because a method with the same name exists in other classes. Each links to the same documentation which combines documentation for all classes in one place. This is a bug created by limitation in the R documentation system, but shouldn’t cause the user any issues.
Chromosome
`ancestralNucleotides()`	SLiM method ancestralNucleotides
`Ch` `Chromosome`	Chromosome
`drawBreakpoints()`	SLiM method drawBreakpoints
`setAncestralNucleotides()`	SLiM method setAncestralNucleotides
`setGeneConversion()`	SLiM method setGeneConversion
`setHotspotMap()`	SLiM method setHotspotMap
`setMutationRate()`	SLiM method setMutationRate
`setRecombinationRate()`	SLiM method setRecombinationRate
Community
`Co` `Community`	Community
`createLogFile()`	SLiM method createLogFile
`deregisterScriptBlock()`	SLiM method deregisterScriptBlock
`genomicElementTypesWithIDs()`	SLiM method genomicElementTypesWithIDs
`interactionTypesWithIDs()`	SLiM method interactionTypesWithIDs
`mutationTypesWithIDs()`	SLiM method mutationTypesWithIDs
`outputUsage()`	SLiM method outputUsage
`registerEarlyEvent()`	SLiM method registerEarlyEvent
`registerFirstEvent()`	SLiM method registerFirstEvent
`registerInteractionCallback()`	SLiM method registerInteractionCallback
`registerLateEvent()`	SLiM method registerLateEvent
`rescheduleScriptBlock()`	SLiM method rescheduleScriptBlock
`scriptBlocksWithIDs()`	SLiM method scriptBlocksWithIDs
`simulationFinished()` `simulationFinished()`	SLiM method simulationFinished
`speciesWithIDs()`	SLiM method speciesWithIDs
`subpopulationsWithIDs()`	SLiM method subpopulationsWithIDs
`usage()`	SLiM method usage
Eidos
`eidos_abs()`	Eidos method abs
`eidos_acos()`	Eidos method acos
`eidos_all()`	Eidos method all
`eidos_any()`	Eidos method any
`eidos_apply()`	Eidos method apply
`eidos_array()`	Eidos method array
`eidos_asFloat()`	Eidos method asFloat
`eidos_asin()`	Eidos method asin
`eidos_asInteger()`	Eidos method asInteger
`eidos_asLogical()`	Eidos method asLogical
`eidos_assert()`	Eidos method assert
`eidos_asString()`	Eidos method asString
`eidos_atan()`	Eidos method atan
`eidos_atan2()`	Eidos method atan2
`eidos_beep()`	Eidos method beep
`eidos_c()`	Eidos method c
`eidos_cat()`	Eidos method cat
`eidos_catn()`	Eidos method catn
`eidos_cbind()`	Eidos method cbind
`eidos_ceil()`	Eidos method ceil
`eidos_citation()`	Eidos method citation
`E` `Eidos`	Eidos
`eidos_clock()`	Eidos method clock
`eidos_cmColors()`	Eidos method cmColors
`eidos_color2rgb()`	Eidos method color2rgb
`eidos_colors()`	Eidos method colors
`eidos_cor()`	Eidos method cor
`eidos_cos()`	Eidos method cos
`eidos_cov()`	Eidos method cov
`eidos_createDirectory()`	Eidos method createDirectory
`eidos_cumProduct()`	Eidos method cumProduct
`eidos_cumSum()`	Eidos method cumSum
`eidos_date()`	Eidos method date
`eidos_dbeta()`	Eidos method dbeta
`eidos_debugIndent()`	Eidos method debugIndent
`eidos_defineConstant()`	Eidos method defineConstant
`eidos_defineGlobal()`	Eidos method defineGlobal
`eidos_deleteFile()`	Eidos method deleteFile
`eidos_dexp()`	Eidos method dexp
`eidos_dgamma()`	Eidos method dgamma
`eidos_diag()`	Eidos method diag
`eidos_dim()`	Eidos method dim
`eidos_dmvnorm()`	Eidos method dmvnorm
`eidos_dnorm()`	Eidos method dnorm
`eidos_drop()`	Eidos method drop
`eidos_elementType()`	Eidos method elementType
`eidos_exists()`	Eidos method exists
`eidos_exp()`	Eidos method exp
`eidos_fileExists()`	Eidos method fileExists
`eidos_filesAtPath()`	Eidos method filesAtPath
`eidos_findInterval()`	Eidos method findInterval
`eidos_float()`	Eidos method float
`eidos_floor()`	Eidos method floor
`eidos_flushFile()`	Eidos method flushFile
`eidos_format()`	Eidos method format
`eidos_functionSignature()`	Eidos method functionSignature
`eidos_functionSource()`	Eidos method functionSource
`eidos_getSeed()`	Eidos method getSeed
`eidos_getwd()`	Eidos method getwd
`eidos_heatColors()`	Eidos method heatColors
`eidos_hsv2rgb()`	Eidos method hsv2rgb
`eidos_identical()`	Eidos method identical
`eidos_ifelse()`	Eidos method ifelse
`eidos_integer()`	Eidos method integer
`eidos_integerDiv()`	Eidos method integerDiv
`eidos_integerMod()`	Eidos method integerMod
`eidos_isFinite()`	Eidos method isFinite
`eidos_isFloat()`	Eidos method isFloat
`eidos_isInfinite()`	Eidos method isInfinite
`eidos_isInteger()`	Eidos method isInteger
`eidos_isLogical()`	Eidos method isLogical
`eidos_isNAN()`	Eidos method isNAN
`eidos_isNULL()`	Eidos method isNULL
`eidos_isObject()`	Eidos method isObject
`eidos_isString()`	Eidos method isString
`eidos_length()`	Eidos method length
`eidos_license()`	Eidos method license
`eidos_log()`	Eidos method log
`eidos_log10()`	Eidos method log10
`eidos_log2()`	Eidos method log2
`eidos_logical()`	Eidos method logical
`eidos_lowerTri()`	Eidos method lowerTri
`eidos_ls()`	Eidos method ls
`eidos_match()`	Eidos method match
`eidos_matrix()`	Eidos method matrix
`eidos_matrixMult()`	Eidos method matrixMult
`eidos_max()`	Eidos method max
`eidos_mean()`	Eidos method mean
`eidos_min()`	Eidos method min
`eidos_nchar()`	Eidos method nchar
`eidos_ncol()`	Eidos method ncol
`eidos_nrow()`	Eidos method nrow
`eidos_object()`	Eidos method object
`eidos_order()`	Eidos method order
`eidos_paste()`	Eidos method paste
`eidos_paste0()`	Eidos method paste0
`eidos_pmax()`	Eidos method pmax
`eidos_pmin()`	Eidos method pmin
`eidos_pnorm()`	Eidos method pnorm
`eidos_print()`	Eidos method print
`eidos_product()`	Eidos method product
`eidos_qnorm()`	Eidos method qnorm
`eidos_quantile()`	Eidos method quantile
`eidos_rainbow()`	Eidos method rainbow
`eidos_range()`	Eidos method range
`eidos_rank()`	Eidos method rank
`eidos_rbeta()`	Eidos method rbeta
`eidos_rbind()`	Eidos method rbind
`eidos_rbinom()`	Eidos method rbinom
`eidos_rcauchy()`	Eidos method rcauchy
`eidos_rdunif()`	Eidos method rdunif
`eidos_readCSV()`	Eidos method readCSV
`eidos_readFile()`	Eidos method readFile
`eidos_rep()`	Eidos method rep
`eidos_repEach()`	Eidos method repEach
`eidos_rev()`	Eidos method rev
`eidos_rexp()`	Eidos method rexp
`eidos_rf()`	Eidos method rf
`eidos_rgamma()`	Eidos method rgamma
`eidos_rgb2color()`	Eidos method rgb2color
`eidos_rgb2hsv()`	Eidos method rgb2hsv
`eidos_rgeom()`	Eidos method rgeom
`eidos_rlnorm()`	Eidos method rlnorm
`eidos_rm()`	Eidos method rm
`eidos_rmvnorm()`	Eidos method rmvnorm
`eidos_rnbinom()`	Eidos method rnbinom
`eidos_rnorm()`	Eidos method rnorm
`eidos_round()`	Eidos method round
`eidos_rpois()`	Eidos method rpois
`eidos_runif()`	Eidos method runif
`eidos_rweibull()`	Eidos method rweibull
`eidos_sample()`	Eidos method sample
`eidos_sapply()`	Eidos method sapply
`eidos_sd()`	Eidos method sd
`eidos_seq()`	Eidos method seq
`eidos_seqAlong()`	Eidos method seqAlong
`eidos_seqLen()`	Eidos method seqLen
`eidos_setDifference()`	Eidos method setDifference
`eidos_setIntersection()`	Eidos method setIntersection
`eidos_setSeed()`	Eidos method setSeed
`eidos_setSymmetricDifference()`	Eidos method setSymmetricDifference
`eidos_setUnion()`	Eidos method setUnion
`eidos_setwd()`	Eidos method setwd
`eidos_sin()`	Eidos method sin
`eidos_size()`	Eidos method size
`eidos_sort()`	Eidos method sort
`eidos_sortBy()`	Eidos method sortBy
`eidos_source()`	Eidos method source
`eidos_sqrt()`	Eidos method sqrt
`eidos_stop()`	Eidos method stop
`eidos_str()`	Eidos method str
`eidos_strcontains()`	Eidos method strcontains
`eidos_strfind()`	Eidos method strfind
`eidos_string()`	Eidos method string
`eidos_strprefix()`	Eidos method strprefix
`eidos_strsplit()`	Eidos method strsplit
`eidos_strsuffix()`	Eidos method strsuffix
`eidos_substr()`	Eidos method substr
`eidos_sum()`	Eidos method sum
`eidos_sumExact()`	Eidos method sumExact
`eidos_suppressWarnings()`	Eidos method suppressWarnings
`eidos_sysinfo()`	Eidos method sysinfo
`eidos_system()`	Eidos method system
`eidos_t()`	Eidos method t
`eidos_tabulate()`	Eidos method tabulate
`eidos_tan()`	Eidos method tan
`eidos_tempdir()`	Eidos method tempdir
`eidos_terrainColors()`	Eidos method terrainColors
`eidos_time()`	Eidos method time
`eidos_trunc()`	Eidos method trunc
`eidos_ttest()`	Eidos method ttest
`eidos_type()`	Eidos method type
`eidos_unique()`	Eidos method unique
`eidos_upperTri()`	Eidos method upperTri
`eidos_usage()`	Eidos method usage
`eidos_var()`	Eidos method var
`eidos_version()`	Eidos method version
`eidos_which()`	Eidos method which
`eidos_whichMax()`	Eidos method whichMax
`eidos_whichMin()`	Eidos method whichMin
`eidos_writeFile()`	Eidos method writeFile
`eidos_writeTempFile()`	Eidos method writeTempFile
Genome
`addMutations()`	SLiM method addMutations
`addNewDrawnMutation()`	SLiM method addNewDrawnMutation
`addNewMutation()`	SLiM method addNewMutation
`containsMarkerMutation()`	SLiM method containsMarkerMutation
`containsMutations()` `containsMutations()`	SLiM method containsMutations
`countOfMutationsOfType()` `countOfMutationsOfType()` `countOfMutationsOfType()`	SLiM method countOfMutationsOfType
`G` `Genome`	Genome
`mutationCountsInGenomes()`	SLiM method mutationCountsInGenomes
`mutationFrequenciesInGenomes()`	SLiM method mutationFrequenciesInGenomes
`mutationsOfType()` `mutationsOfType()`	SLiM method mutationsOfType
`nucleotides()`	SLiM method nucleotides
`output()`	SLiM method output
`outputMS()`	SLiM method outputMS
`outputVCF()`	SLiM method outputVCF
`positionsOfMutationsOfType()`	SLiM method positionsOfMutationsOfType
`readFromMS()`	SLiM method readFromMS
`readFromVCF()`	SLiM method readFromVCF
`removeMutations()`	SLiM method removeMutations
`sumOfMutationsOfType()` `sumOfMutationsOfType()`	SLiM method sumOfMutationsOfType
GenomicElement
`GE` `GenomicElement`	GenomicElement
`setGenomicElementType()`	SLiM method setGenomicElementType
GenomicElementType
`GET` `GenomicElementType`	GenomicElementType
`setMutationFractions()`	SLiM method setMutationFractions
`setMutationMatrix()`	SLiM method setMutationMatrix
Individual
`containsMutations()` `containsMutations()`	SLiM method containsMutations
`countOfMutationsOfType()` `countOfMutationsOfType()` `countOfMutationsOfType()`	SLiM method countOfMutationsOfType
`In` `Individual`	Individual
`relatedness()`	SLiM method relatedness
`setSpatialPosition()`	SLiM method setSpatialPosition
`sharedParentCount()`	SLiM method sharedParentCount
`sumOfMutationsOfType()` `sumOfMutationsOfType()`	SLiM method sumOfMutationsOfType
`uniqueMutationsOfType()`	SLiM method uniqueMutationsOfType
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
`initializeSpecies()`	SLiM method initializeSpecies
`initializeTreeSeq()`	SLiM method initializeTreeSeq
`Init` `Initialize`	Initialize
InteractionType
`clippedIntegral()`	SLiM method clippedIntegral
`distance()`	SLiM method distance
`distanceFromPoint()`	SLiM method distanceFromPoint
`drawByStrength()`	SLiM method drawByStrength
`evaluate()`	SLiM method evaluate
`interactingNeighborCount()`	SLiM method interactingNeighborCount
`interactionDistance()`	SLiM method interactionDistance
`IT` `InteractionType`	InteractionType
`localPopulationDensity()`	SLiM method localPopulationDensity
`nearestInteractingNeighbors()`	SLiM method nearestInteractingNeighbors
`nearestNeighbors()`	SLiM method nearestNeighbors
`nearestNeighborsOfPoint()`	SLiM method nearestNeighborsOfPoint
`neighborCount()`	SLiM method neighborCount
`neighborCountOfPoint()`	SLiM method neighborCountOfPoint
`setConstraints()`	SLiM method setConstraints
`setInteractionFunction()`	SLiM method setInteractionFunction
`strength()`	SLiM method strength
`testConstraints()`	SLiM method testConstraints
`totalOfNeighborStrengths()`	SLiM method totalOfNeighborStrengths
`unevaluate()`	SLiM method unevaluate
LogFile
`addCustomColumn()`	SLiM method addCustomColumn
`addCycle()`	SLiM method addCycle
`addCycleStage()`	SLiM method addCycleStage
`addKeysAndValuesFrom()`	SLiM method addKeysAndValuesFrom
`addMeanSDColumns()`	SLiM method addMeanSDColumns
`addPopulationSexRatio()`	SLiM method addPopulationSexRatio
`addPopulationSize()`	SLiM method addPopulationSize
`addSubpopulationSexRatio()`	SLiM method addSubpopulationSexRatio
`addSubpopulationSize()`	SLiM method addSubpopulationSize
`addSuppliedColumn()`	SLiM method addSuppliedColumn
`addTick()`	SLiM method addTick
`clearKeysAndValues()`	SLiM method clearKeysAndValues
`flush()`	SLiM method flush
`LF` `LogFile`	LogFile
`logRow()`	SLiM method logRow
`setFilePath()`	SLiM method setFilePath
`setLogInterval()`	SLiM method setLogInterval
`setSuppliedValue()`	SLiM method setSuppliedValue
`setValue()`	SLiM method setValue
`willAutolog()`	SLiM method willAutolog
Mutation
`M` `Mutation`	Mutation
`setMutationType()`	SLiM method setMutationType
`setSelectionCoeff()`	SLiM method setSelectionCoeff
MutationType
`drawSelectionCoefficient()`	SLiM method drawSelectionCoefficient
`MT` `MutationType`	MutationType
`setDistribution()`	SLiM method setDistribution
SLiMBuiltin
`calcFST()`	SLiM method calcFST
`calcHeterozygosity()`	SLiM method calcHeterozygosity
`calcInbreedingLoad()`	SLiM method calcInbreedingLoad
`calcPairHeterozygosity()`	SLiM method calcPairHeterozygosity
`calcVA()`	SLiM method calcVA
`calcWattersonsTheta()`	SLiM method calcWattersonsTheta
`codonsToAminoAcids()`	SLiM method codonsToAminoAcids
`mm16To256()`	SLiM method mm16To256
`mmJukesCantor()`	SLiM method mmJukesCantor
`mmKimura()`	SLiM method mmKimura
`nucleotideCounts()`	SLiM method nucleotideCounts
`nucleotideFrequencies()`	SLiM method nucleotideFrequencies
`nucleotidesToCodons()`	SLiM method nucleotidesToCodons
`SB` `SLiMBuiltin`	SLiMBuiltin
`summarizeIndividuals()`	SLiM method summarizeIndividuals
`treeSeqMetadata()`	SLiM method treeSeqMetadata
SLiMEidosBlock
`SEB` `SLiMEidosBlock`	SLiMEidosBlock
SLiMSim
SLiMgui
`openDocument()`	SLiM method openDocument
`pauseExecution()`	SLiM method pauseExecution
`SG` `SLiMgui`	SLiMgui
SpatialMap
`add()`	SLiM method add
`blend()`	SLiM method blend
`changeColors()`	SLiM method changeColors
`changeValues()`	SLiM method changeValues
`divide()`	SLiM method divide
`exp()`	SLiM method exp
`gridValues()`	SLiM method gridValues
`interpolate()`	SLiM method interpolate
`mapColor()`	SLiM method mapColor
`mapImage()`	SLiM method mapImage
`mapValue()`	SLiM method mapValue
`multiply()`	SLiM method multiply
`power()`	SLiM method power
`range()`	SLiM method range
`rescale()`	SLiM method rescale
`sampleImprovedNearbyPoint()`	SLiM method sampleImprovedNearbyPoint
`sampleNearbyPoint()`	SLiM method sampleNearbyPoint
`smooth()`	SLiM method smooth
`SM` `SpatialMap`	SpatialMap
`subtract()`	SLiM method subtract
Species
`addSubpop()`	SLiM method addSubpop
`addSubpopSplit()`	SLiM method addSubpopSplit
`countOfMutationsOfType()` `countOfMutationsOfType()` `countOfMutationsOfType()`	SLiM method countOfMutationsOfType
`individualsWithPedigreeIDs()`	SLiM method individualsWithPedigreeIDs
`killIndividuals()`	SLiM method killIndividuals
`mutationCounts()`	SLiM method mutationCounts
`mutationFrequencies()`	SLiM method mutationFrequencies
`mutationsOfType()` `mutationsOfType()`	SLiM method mutationsOfType
`outputFixedMutations()`	SLiM method outputFixedMutations
`outputFull()`	SLiM method outputFull
`outputMutations()`	SLiM method outputMutations
`readFromPopulationFile()`	SLiM method readFromPopulationFile
`recalculateFitness()`	SLiM method recalculateFitness
`registerFitnessEffectCallback()`	SLiM method registerFitnessEffectCallback
`registerMateChoiceCallback()`	SLiM method registerMateChoiceCallback
`registerModifyChildCallback()`	SLiM method registerModifyChildCallback
`registerMutationCallback()`	SLiM method registerMutationCallback
`registerMutationEffectCallback()`	SLiM method registerMutationEffectCallback
`registerRecombinationCallback()`	SLiM method registerRecombinationCallback
`registerReproductionCallback()`	SLiM method registerReproductionCallback
`registerSurvivalCallback()`	SLiM method registerSurvivalCallback
`simulationFinished()` `simulationFinished()`	SLiM method simulationFinished
`skipTick()`	SLiM method skipTick
`Sp` `Species`	Species
`subsetMutations()`	SLiM method subsetMutations
`treeSeqCoalesced()`	SLiM method treeSeqCoalesced
`treeSeqOutput()`	SLiM method treeSeqOutput
`treeSeqRememberIndividuals()`	SLiM method treeSeqRememberIndividuals
`treeSeqSimplify()`	SLiM method treeSeqSimplify
Subpopulation
`addCloned()`	SLiM method addCloned
`addCrossed()`	SLiM method addCrossed
`addEmpty()`	SLiM method addEmpty
`addRecombinant()`	SLiM method addRecombinant
`addSelfed()`	SLiM method addSelfed
`addSpatialMap()`	SLiM method addSpatialMap
`cachedFitness()`	SLiM method cachedFitness
`configureDisplay()`	SLiM method configureDisplay
`defineSpatialMap()`	SLiM method defineSpatialMap
`outputMSSample()`	SLiM method outputMSSample
`outputSample()`	SLiM method outputSample
`outputVCFSample()`	SLiM method outputVCFSample
`pointDeviated()`	SLiM method pointDeviated
`pointInBounds()`	SLiM method pointInBounds
`pointPeriodic()`	SLiM method pointPeriodic
`pointReflected()`	SLiM method pointReflected
`pointStopped()`	SLiM method pointStopped
`pointUniform()`	SLiM method pointUniform
`removeSpatialMap()`	SLiM method removeSpatialMap
`removeSubpopulation()`	SLiM method removeSubpopulation
`sampleIndividuals()`	SLiM method sampleIndividuals
`setCloningRate()`	SLiM method setCloningRate
`setMigrationRates()`	SLiM method setMigrationRates
`setSelfingRate()`	SLiM method setSelfingRate
`setSexRatio()`	SLiM method setSexRatio
`setSpatialBounds()`	SLiM method setSpatialBounds
`setSubpopulationSize()`	SLiM method setSubpopulationSize
`spatialMapColor()`	SLiM method spatialMapColor
`spatialMapImage()`	SLiM method spatialMapImage
`spatialMapValue()`	SLiM method spatialMapValue
`P` `Subpopulation`	Subpopulation
`subsetIndividuals()`	SLiM method subsetIndividuals
`takeMigrants()`	SLiM method takeMigrants
Substitution
`S` `Substitution`	Substitution
Convert between R-like and SLiM-like code
`slim_code_Rify()`	Rify some SLiM code
`slim_code_SLiMify()`	Rify some SLiM code
`as_slimr_script()`	Convert a character vector into a slim_script object
`as_slimr_code()`	Convert SLiM code text into equivalent `slimr` code to produce the same model
`as_slim_text()`	Convert a slimr_script to a length 1 character vector
`as_slim_text(<slimr_script>)`	Convert a slimr_script to a length 1 character vector
Datasets
`slim_recipes`	Dataset of all recipes available in SLiM
`load_herm()`	Download and load herm.rdata file containing SNP data from Sandy Inland Mouse Details can be found in the article at https://rdinnager.github.io/slimr/articles/Main_manuscript_example_v2.html
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`code()` `code<-`()	Extract or set code from a `slimr_script` object
`end_gen()` `end_gen<-`()	Extract or set end generation
`first()`	SLiM first() callback
`get_block()`	Extract a single code block from a `slimr_script`
`get_slim_call()`	Get the call information for running SLiM. Doubles as a check for SLiM availability.
`minimal_slim_sim()`	Generate a minimal SLiM simulation script
`minimal_slimr_script()`	Generate a minimal slimr_script object
`new_slimr_script_coll()`	Make a new `slimr_script_coll` object
`reconstruct()`	Reconstruct slimrlang code to make this slimr_script
`reconstruct(<slimr_script>)`	Reconstruct slimrlang code to make this slimr_script
`slimr_clip_original()`	Copy original slimrlang code used to create a slimr_script object to the clipboard
`slimr_code()`	Create a `slimr_code` object
`slimr_name()`	Convert a string to a SLiM object name
`slimr_open_original()`	Open original slimrlang code used to create a slimr_script object in a new document
`slimr_script_coll()`	Make a new `slimr_script_coll` object
`slim_template_info()`	Get information on templating in a slimr_script
`slimr_write()`	Write a slimr_script object to a text file
`slim_file()`	Make sure a file name is compatible with using in a SLiM script.
`slim_install_path()`	Find the SLiM executable path `slimr` is using
`slim_is_avail()`	Check if SLiM is installed and `slimr` can find it
`slim_make_pop_input()`	Create a file to initialise a population in SLiM
`slim_open()`	Title
`slim_results_to_data()`	Convert output data from a slimr_results object to a tibble
`slim_script_duration()`	Set the duration of a slimr_script

Reference

Install and setup SLiM software for use with slimr

slimr verbs

Main slimr verbs

r_output_ special variants

r_template_ special variants

slimr_block_ verbs

Creating slimr_script objects

Run a slimr_script object and return results to R

Extract Output from slimr_results Objects

Work with SLiM recipes from SLiM manual

Operators

SLiM Callbacks

SLiM Class Objects

SLiM Class Methods

Chromosome

Community

Eidos

Genome

GenomicElement

GenomicElementType

Individual

Initialize

InteractionType

LogFile

Mutation

MutationType

SLiMBuiltin

SLiMEidosBlock

SLiMSim

SLiMgui

SpatialMap

Species

Subpopulation

Substitution

Convert between R-like and SLiM-like code

Datasets

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