Package: slimr 0.4.0.9000
Russell Dinnage
slimr: Create, Run and Post-Process 'SLiM' Population Genetics Forward Simulations
Lets you write 'SLiM' scripts (population genomics simulation) using your favourite R IDE, using a syntax as close as possible to the original 'SLiM' language. It offer many tools to manipulate those scripts, as well as run them in the 'SLiM' software from R, as well as capture and post-process their output, after or even during a simulation.
Authors:
slimr_0.4.0.9000.tar.gz
slimr_0.4.0.9000.zip(r-4.5)slimr_0.4.0.9000.zip(r-4.4)slimr_0.4.0.9000.zip(r-4.3)
slimr_0.4.0.9000.tgz(r-4.4-any)slimr_0.4.0.9000.tgz(r-4.3-any)
slimr_0.4.0.9000.tar.gz(r-4.5-noble)slimr_0.4.0.9000.tar.gz(r-4.4-noble)
slimr_0.4.0.9000.tgz(r-4.4-emscripten)slimr_0.4.0.9000.tgz(r-4.3-emscripten)
slimr.pdf |slimr.html✨
slimr/json (API)
NEWS
| # Install 'slimr' in R: |
| install.packages('slimr', repos = c('https://rdinnager.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rdinnager/slimr/issues
Datasets:
- slim_classes - SLiM Classes
- slim_recipes - Dataset of all recipes available in SLiM
Last updated 11 months agofrom:ddf6789db5 (on 0.4.0). Checks:ERROR: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Nov 15 2024 |
| R-4.5-win | ERROR | Nov 15 2024 |
| R-4.5-linux | ERROR | Nov 15 2024 |
| R-4.4-win | ERROR | Nov 15 2024 |
| R-4.4-mac | ERROR | Nov 15 2024 |
| R-4.3-win | ERROR | Nov 15 2024 |
| R-4.3-mac | ERROR | Nov 15 2024 |
Exports::=.data%?%%.%%>%%else%as_labelas_nameas_slim_textas_slimr_codeas_slimr_scriptcalcFSTcalcHeterozygositycalcInbreedingLoadcalcPairHeterozygositycalcVAcalcWattersonsThetaChChromosomeCocodecode<-codonsToAminoAcidsCommunityEearlyEidosend_genend_gen<-enquoenquosexprfirstfitnessfitnessEffectGGEGenomeGenomicElementGenomicElementTypeGETget_blockInIndividualInitinitializeInitializeinitializeAncestralNucleotidesinitializeGeneConversioninitializeGenomicElementinitializeGenomicElementTypeinitializeHotspotMapinitializeInteractionTypeinitializeMutationRateinitializeMutationTypeinitializeMutationTypeNucinitializeRecombinationRateinitializeSexinitializeSLiMModelTypeinitializeSLiMOptionsinitializeSpeciesinitializeTreeSeqinteractionInteractionTypeITlateLFLogFileMmateChoiceminimal_slim_simminimal_slimr_scriptmm16To256mmJukesCantormmKimuramodifyChildMTmutationMutationmutationEffectMutationTypenucleotideCountsnucleotideFrequenciesnucleotidesToCodonsPr_inliner_outputr_output_coordsr_output_fullr_output_nucleotidesr_output_sexr_output_snpr_templater_template_constantrecombinationreconstructreproductionSSBSEBSGslim_blockslim_block_add_subpopsslim_block_finishslim_block_init_minimalslim_block_progressslim_extract_fullslim_extract_genlightslim_extract_genomeslim_extract_output_dataslim_functionslim_get_recipeslim_get_recipesslim_install_pathslim_is_availslim_load_globalsslim_make_pop_inputslim_openslim_results_to_dataslim_runslim_scriptslim_script_durationslim_script_renderslim_setupslim_template_infoslim_unload_globalsSLiMBuiltinSLiMEidosBlockSLiMguislimr_clip_originalslimr_codeslimr_inlineslimr_nameslimr_open_originalslimr_outputslimr_output_coordsslimr_output_fullslimr_output_nucleotidesslimr_output_sexslimr_output_snpslimr_templateslimr_template_constantslimr_writeSMSpSpatialMapSpeciesSSSubpopulationSubstitutionsummarizeIndividualssurvivalsymsymstreeSeqMetadata
Dependencies:bitbit64clicliprcodetoolscpp11crayondplyrfansigenericsgluehmslifecyclemagrittrpillarpkgconfigprettycodeprettyunitsprocessxprogresspspurrrR6readrrlangstringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithrzeallot
Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| slimrlang stub for the first part of the SLiM ternary operator ('condition ? yes else no'). | %?% |
| slimrlang stub for the SLiM '.' operator | %.% |
| slimrlang stub for the second part of the SLiM ternary operator ('condition ? yes else no'). | %else% |
| SLiM method add | .SM$add add SpatialMap$add |
| SLiM method addCloned | .P$addCloned addCloned Subpopulation$addCloned |
| SLiM method addCrossed | .P$addCrossed addCrossed Subpopulation$addCrossed |
| SLiM method addCustomColumn | .LF$addCustomColumn addCustomColumn LogFile$addCustomColumn |
| SLiM method addCycle | .LF$addCycle addCycle LogFile$addCycle |
| SLiM method addCycleStage | .LF$addCycleStage addCycleStage LogFile$addCycleStage |
| SLiM method addEmpty | .P$addEmpty addEmpty Subpopulation$addEmpty |
| SLiM method addKeysAndValuesFrom | .LF$addKeysAndValuesFrom addKeysAndValuesFrom LogFile$addKeysAndValuesFrom |
| SLiM method addMeanSDColumns | .LF$addMeanSDColumns addMeanSDColumns LogFile$addMeanSDColumns |
| SLiM method addMutations | .G$addMutations addMutations Genome$addMutations |
| SLiM method addNewDrawnMutation | .G$addNewDrawnMutation addNewDrawnMutation Genome$addNewDrawnMutation |
| SLiM method addNewMutation | .G$addNewMutation addNewMutation Genome$addNewMutation |
| SLiM method addPopulationSexRatio | .LF$addPopulationSexRatio addPopulationSexRatio LogFile$addPopulationSexRatio |
| SLiM method addPopulationSize | .LF$addPopulationSize addPopulationSize LogFile$addPopulationSize |
| SLiM method addRecombinant | .P$addRecombinant addRecombinant Subpopulation$addRecombinant |
| SLiM method addSelfed | .P$addSelfed addSelfed Subpopulation$addSelfed |
| SLiM method addSpatialMap | .P$addSpatialMap addSpatialMap Subpopulation$addSpatialMap |
| SLiM method addSubpop | .Sp$addSubpop addSubpop Species$addSubpop |
| SLiM method addSubpopSplit | .Sp$addSubpopSplit addSubpopSplit Species$addSubpopSplit |
| SLiM method addSubpopulationSexRatio | .LF$addSubpopulationSexRatio addSubpopulationSexRatio LogFile$addSubpopulationSexRatio |
| SLiM method addSubpopulationSize | .LF$addSubpopulationSize addSubpopulationSize LogFile$addSubpopulationSize |
| SLiM method addSuppliedColumn | .LF$addSuppliedColumn addSuppliedColumn LogFile$addSuppliedColumn |
| SLiM method addTick | .LF$addTick addTick LogFile$addTick |
| SLiM method ancestralNucleotides | .Ch$ancestralNucleotides ancestralNucleotides Chromosome$ancestralNucleotides |
| Convert a slimr_script to a length 1 character vector | as_slim_text |
| Convert a slimr_script to a length 1 character vector | as_slim_text.slimr_script |
| Convert SLiM code text into equivalent `slimr` code to produce the same model | as_slimr_code |
| Convert a character vector into a slim_script object | as_slimr_script |
| SLiM method blend | .SM$blend blend SpatialMap$blend |
| SLiM method cachedFitness | .P$cachedFitness cachedFitness Subpopulation$cachedFitness |
| SLiM method calcFST | .SB$calcFST calcFST SLiMBuiltin$calcFST |
| SLiM method calcHeterozygosity | .SB$calcHeterozygosity calcHeterozygosity SLiMBuiltin$calcHeterozygosity |
| SLiM method calcInbreedingLoad | .SB$calcInbreedingLoad calcInbreedingLoad SLiMBuiltin$calcInbreedingLoad |
| SLiM method calcPairHeterozygosity | .SB$calcPairHeterozygosity calcPairHeterozygosity SLiMBuiltin$calcPairHeterozygosity |
| SLiM method calcVA | .SB$calcVA calcVA SLiMBuiltin$calcVA |
| SLiM method calcWattersonsTheta | .SB$calcWattersonsTheta calcWattersonsTheta SLiMBuiltin$calcWattersonsTheta |
| Chromosome | Ch Chromosome |
| SLiM method changeColors | .SM$changeColors changeColors SpatialMap$changeColors |
| SLiM method changeValues | .SM$changeValues changeValues SpatialMap$changeValues |
| SLiM method clearKeysAndValues | .LF$clearKeysAndValues clearKeysAndValues LogFile$clearKeysAndValues |
| SLiM method clippedIntegral | .IT$clippedIntegral clippedIntegral InteractionType$clippedIntegral |
| Community | Co Community |
| Extract or set code from a 'slimr_script' object | code code<- |
| SLiM method codonsToAminoAcids | .SB$codonsToAminoAcids codonsToAminoAcids SLiMBuiltin$codonsToAminoAcids |
| SLiM method configureDisplay | .P$configureDisplay configureDisplay Subpopulation$configureDisplay |
| SLiM method containsMarkerMutation | .G$containsMarkerMutation containsMarkerMutation Genome$containsMarkerMutation |
| SLiM method containsMutations | .G$containsMutations .I$containsMutations containsMutations Genome$containsMutations Individual$containsMutations |
| SLiM method countOfMutationsOfType | .G$countOfMutationsOfType .I$countOfMutationsOfType .Sp$countOfMutationsOfType countOfMutationsOfType Genome$countOfMutationsOfType Individual$countOfMutationsOfType Species$countOfMutationsOfType |
| SLiM method createLogFile | .Co$createLogFile Community$createLogFile createLogFile |
| SLiM method defineSpatialMap | .P$defineSpatialMap defineSpatialMap Subpopulation$defineSpatialMap |
| SLiM method deregisterScriptBlock | .Co$deregisterScriptBlock Community$deregisterScriptBlock deregisterScriptBlock |
| SLiM method distance | .IT$distance distance InteractionType$distance |
| SLiM method distanceFromPoint | .IT$distanceFromPoint distanceFromPoint InteractionType$distanceFromPoint |
| SLiM method divide | .SM$divide divide SpatialMap$divide |
| SLiM method drawBreakpoints | .Ch$drawBreakpoints Chromosome$drawBreakpoints drawBreakpoints |
| SLiM method drawByStrength | .IT$drawByStrength drawByStrength InteractionType$drawByStrength |
| SLiM method drawSelectionCoefficient | .MT$drawSelectionCoefficient drawSelectionCoefficient MutationType$drawSelectionCoefficient |
| Eidos | E Eidos |
| SLiM early() callback | early |
| Eidos method abs | .E$abs Eidos$abs eidos_abs |
| Eidos method acos | .E$acos Eidos$acos eidos_acos |
| Eidos method all | .E$all Eidos$all eidos_all |
| Eidos method any | .E$any Eidos$any eidos_any |
| Eidos method apply | .E$apply Eidos$apply eidos_apply |
| Eidos method array | .E$array Eidos$array eidos_array |
| Eidos method asFloat | .E$asFloat Eidos$asFloat eidos_asFloat |
| Eidos method asin | .E$asin Eidos$asin eidos_asin |
| Eidos method asInteger | .E$asInteger Eidos$asInteger eidos_asInteger |
| Eidos method asLogical | .E$asLogical Eidos$asLogical eidos_asLogical |
| Eidos method assert | .E$assert Eidos$assert eidos_assert |
| Eidos method asString | .E$asString Eidos$asString eidos_asString |
| Eidos method atan | .E$atan Eidos$atan eidos_atan |
| Eidos method atan2 | .E$atan2 Eidos$atan2 eidos_atan2 |
| Eidos method beep | .E$beep Eidos$beep eidos_beep |
| Eidos method c | .E$c Eidos$c eidos_c |
| Eidos method cat | .E$cat Eidos$cat eidos_cat |
| Eidos method catn | .E$catn Eidos$catn eidos_catn |
| Eidos method cbind | .E$cbind Eidos$cbind eidos_cbind |
| Eidos method ceil | .E$ceil Eidos$ceil eidos_ceil |
| Eidos method citation | .E$citation Eidos$citation eidos_citation |
| Eidos method clock | .E$clock Eidos$clock eidos_clock |
| Eidos method cmColors | .E$cmColors Eidos$cmColors eidos_cmColors |
| Eidos method color2rgb | .E$color2rgb Eidos$color2rgb eidos_color2rgb |
| Eidos method colors | .E$colors Eidos$colors eidos_colors |
| Eidos method cor | .E$cor Eidos$cor eidos_cor |
| Eidos method cos | .E$cos Eidos$cos eidos_cos |
| Eidos method cov | .E$cov Eidos$cov eidos_cov |
| Eidos method createDirectory | .E$createDirectory Eidos$createDirectory eidos_createDirectory |
| Eidos method cumProduct | .E$cumProduct Eidos$cumProduct eidos_cumProduct |
| Eidos method cumSum | .E$cumSum Eidos$cumSum eidos_cumSum |
| Eidos method date | .E$date Eidos$date eidos_date |
| Eidos method dbeta | .E$dbeta Eidos$dbeta eidos_dbeta |
| Eidos method debugIndent | .E$debugIndent Eidos$debugIndent eidos_debugIndent |
| Eidos method defineConstant | .E$defineConstant Eidos$defineConstant eidos_defineConstant |
| Eidos method defineGlobal | .E$defineGlobal Eidos$defineGlobal eidos_defineGlobal |
| Eidos method deleteFile | .E$deleteFile Eidos$deleteFile eidos_deleteFile |
| Eidos method dexp | .E$dexp Eidos$dexp eidos_dexp |
| Eidos method dgamma | .E$dgamma Eidos$dgamma eidos_dgamma |
| Eidos method diag | .E$diag Eidos$diag eidos_diag |
| Eidos method dim | .E$dim Eidos$dim eidos_dim |
| Eidos method dmvnorm | .E$dmvnorm Eidos$dmvnorm eidos_dmvnorm |
| Eidos method dnorm | .E$dnorm Eidos$dnorm eidos_dnorm |
| Eidos method drop | .E$drop Eidos$drop eidos_drop |
| Eidos method elementType | .E$elementType Eidos$elementType eidos_elementType |
| Eidos method exists | .E$exists Eidos$exists eidos_exists |
| Eidos method exp | .E$exp Eidos$exp eidos_exp |
| Eidos method fileExists | .E$fileExists Eidos$fileExists eidos_fileExists |
| Eidos method filesAtPath | .E$filesAtPath Eidos$filesAtPath eidos_filesAtPath |
| Eidos method findInterval | .E$findInterval Eidos$findInterval eidos_findInterval |
| Eidos method float | .E$float Eidos$float eidos_float |
| Eidos method floor | .E$floor Eidos$floor eidos_floor |
| Eidos method flushFile | .E$flushFile Eidos$flushFile eidos_flushFile |
| Eidos method format | .E$format Eidos$format eidos_format |
| Eidos method functionSignature | .E$functionSignature Eidos$functionSignature eidos_functionSignature |
| Eidos method functionSource | .E$functionSource Eidos$functionSource eidos_functionSource |
| Eidos method getSeed | .E$getSeed Eidos$getSeed eidos_getSeed |
| Eidos method getwd | .E$getwd Eidos$getwd eidos_getwd |
| Eidos method heatColors | .E$heatColors Eidos$heatColors eidos_heatColors |
| Eidos method hsv2rgb | .E$hsv2rgb Eidos$hsv2rgb eidos_hsv2rgb |
| Eidos method identical | .E$identical Eidos$identical eidos_identical |
| Eidos method ifelse | .E$ifelse Eidos$ifelse eidos_ifelse |
| Eidos method integer | .E$integer Eidos$integer eidos_integer |
| Eidos method integerDiv | .E$integerDiv Eidos$integerDiv eidos_integerDiv |
| Eidos method integerMod | .E$integerMod Eidos$integerMod eidos_integerMod |
| Eidos method isFinite | .E$isFinite Eidos$isFinite eidos_isFinite |
| Eidos method isFloat | .E$isFloat Eidos$isFloat eidos_isFloat |
| Eidos method isInfinite | .E$isInfinite Eidos$isInfinite eidos_isInfinite |
| Eidos method isInteger | .E$isInteger Eidos$isInteger eidos_isInteger |
| Eidos method isLogical | .E$isLogical Eidos$isLogical eidos_isLogical |
| Eidos method isNAN | .E$isNAN Eidos$isNAN eidos_isNAN |
| Eidos method isNULL | .E$isNULL Eidos$isNULL eidos_isNULL |
| Eidos method isObject | .E$isObject Eidos$isObject eidos_isObject |
| Eidos method isString | .E$isString Eidos$isString eidos_isString |
| Eidos method length | .E$length Eidos$length eidos_length |
| Eidos method license | .E$license Eidos$license eidos_license |
| Eidos method log | .E$log Eidos$log eidos_log |
| Eidos method log10 | .E$log10 Eidos$log10 eidos_log10 |
| Eidos method log2 | .E$log2 Eidos$log2 eidos_log2 |
| Eidos method logical | .E$logical Eidos$logical eidos_logical |
| Eidos method lowerTri | .E$lowerTri Eidos$lowerTri eidos_lowerTri |
| Eidos method ls | .E$ls Eidos$ls eidos_ls |
| Eidos method match | .E$match Eidos$match eidos_match |
| Eidos method matrix | .E$matrix Eidos$matrix eidos_matrix |
| Eidos method matrixMult | .E$matrixMult Eidos$matrixMult eidos_matrixMult |
| Eidos method max | .E$max Eidos$max eidos_max |
| Eidos method mean | .E$mean Eidos$mean eidos_mean |
| Eidos method min | .E$min Eidos$min eidos_min |
| Eidos method nchar | .E$nchar Eidos$nchar eidos_nchar |
| Eidos method ncol | .E$ncol Eidos$ncol eidos_ncol |
| Eidos method nrow | .E$nrow Eidos$nrow eidos_nrow |
| Eidos method object | .E$object Eidos$object eidos_object |
| Eidos method order | .E$order Eidos$order eidos_order |
| Eidos method paste | .E$paste Eidos$paste eidos_paste |
| Eidos method paste0 | .E$paste0 Eidos$paste0 eidos_paste0 |
| Eidos method pmax | .E$pmax Eidos$pmax eidos_pmax |
| Eidos method pmin | .E$pmin Eidos$pmin eidos_pmin |
| Eidos method pnorm | .E$pnorm Eidos$pnorm eidos_pnorm |
| Eidos method print | .E$print Eidos$print eidos_print |
| Eidos method product | .E$product Eidos$product eidos_product |
| Eidos method qnorm | .E$qnorm Eidos$qnorm eidos_qnorm |
| Eidos method quantile | .E$quantile Eidos$quantile eidos_quantile |
| Eidos method rainbow | .E$rainbow Eidos$rainbow eidos_rainbow |
| Eidos method range | .E$range Eidos$range eidos_range |
| Eidos method rank | .E$rank Eidos$rank eidos_rank |
| Eidos method rbeta | .E$rbeta Eidos$rbeta eidos_rbeta |
| Eidos method rbind | .E$rbind Eidos$rbind eidos_rbind |
| Eidos method rbinom | .E$rbinom Eidos$rbinom eidos_rbinom |
| Eidos method rcauchy | .E$rcauchy Eidos$rcauchy eidos_rcauchy |
| Eidos method rdunif | .E$rdunif Eidos$rdunif eidos_rdunif |
| Eidos method readCSV | .E$readCSV Eidos$readCSV eidos_readCSV |
| Eidos method readFile | .E$readFile Eidos$readFile eidos_readFile |
| Eidos method rep | .E$rep Eidos$rep eidos_rep |
| Eidos method repEach | .E$repEach Eidos$repEach eidos_repEach |
| Eidos method rev | .E$rev Eidos$rev eidos_rev |
| Eidos method rexp | .E$rexp Eidos$rexp eidos_rexp |
| Eidos method rf | .E$rf Eidos$rf eidos_rf |
| Eidos method rgamma | .E$rgamma Eidos$rgamma eidos_rgamma |
| Eidos method rgb2color | .E$rgb2color Eidos$rgb2color eidos_rgb2color |
| Eidos method rgb2hsv | .E$rgb2hsv Eidos$rgb2hsv eidos_rgb2hsv |
| Eidos method rgeom | .E$rgeom Eidos$rgeom eidos_rgeom |
| Eidos method rlnorm | .E$rlnorm Eidos$rlnorm eidos_rlnorm |
| Eidos method rm | .E$rm Eidos$rm eidos_rm |
| Eidos method rmvnorm | .E$rmvnorm Eidos$rmvnorm eidos_rmvnorm |
| Eidos method rnbinom | .E$rnbinom Eidos$rnbinom eidos_rnbinom |
| Eidos method rnorm | .E$rnorm Eidos$rnorm eidos_rnorm |
| Eidos method round | .E$round Eidos$round eidos_round |
| Eidos method rpois | .E$rpois Eidos$rpois eidos_rpois |
| Eidos method runif | .E$runif Eidos$runif eidos_runif |
| Eidos method rweibull | .E$rweibull Eidos$rweibull eidos_rweibull |
| Eidos method sample | .E$sample Eidos$sample eidos_sample |
| Eidos method sapply | .E$sapply Eidos$sapply eidos_sapply |
| Eidos method sd | .E$sd Eidos$sd eidos_sd |
| Eidos method seq | .E$seq Eidos$seq eidos_seq |
| Eidos method seqAlong | .E$seqAlong Eidos$seqAlong eidos_seqAlong |
| Eidos method seqLen | .E$seqLen Eidos$seqLen eidos_seqLen |
| Eidos method setDifference | .E$setDifference Eidos$setDifference eidos_setDifference |
| Eidos method setIntersection | .E$setIntersection Eidos$setIntersection eidos_setIntersection |
| Eidos method setSeed | .E$setSeed Eidos$setSeed eidos_setSeed |
| Eidos method setSymmetricDifference | .E$setSymmetricDifference Eidos$setSymmetricDifference eidos_setSymmetricDifference |
| Eidos method setUnion | .E$setUnion Eidos$setUnion eidos_setUnion |
| Eidos method setwd | .E$setwd Eidos$setwd eidos_setwd |
| Eidos method sin | .E$sin Eidos$sin eidos_sin |
| Eidos method size | .E$size Eidos$size eidos_size |
| Eidos method sort | .E$sort Eidos$sort eidos_sort |
| Eidos method sortBy | .E$sortBy Eidos$sortBy eidos_sortBy |
| Eidos method source | .E$source Eidos$source eidos_source |
| Eidos method sqrt | .E$sqrt Eidos$sqrt eidos_sqrt |
| Eidos method stop | .E$stop Eidos$stop eidos_stop |
| Eidos method str | .E$str Eidos$str eidos_str |
| Eidos method strcontains | .E$strcontains Eidos$strcontains eidos_strcontains |
| Eidos method strfind | .E$strfind Eidos$strfind eidos_strfind |
| Eidos method string | .E$string Eidos$string eidos_string |
| Eidos method strprefix | .E$strprefix Eidos$strprefix eidos_strprefix |
| Eidos method strsplit | .E$strsplit Eidos$strsplit eidos_strsplit |
| Eidos method strsuffix | .E$strsuffix Eidos$strsuffix eidos_strsuffix |
| Eidos method substr | .E$substr Eidos$substr eidos_substr |
| Eidos method sum | .E$sum Eidos$sum eidos_sum |
| Eidos method sumExact | .E$sumExact Eidos$sumExact eidos_sumExact |
| Eidos method suppressWarnings | .E$suppressWarnings Eidos$suppressWarnings eidos_suppressWarnings |
| Eidos method sysinfo | .E$sysinfo Eidos$sysinfo eidos_sysinfo |
| Eidos method system | .E$system Eidos$system eidos_system |
| Eidos method t | .E$t Eidos$t eidos_t |
| Eidos method tabulate | .E$tabulate Eidos$tabulate eidos_tabulate |
| Eidos method tan | .E$tan Eidos$tan eidos_tan |
| Eidos method tempdir | .E$tempdir Eidos$tempdir eidos_tempdir |
| Eidos method terrainColors | .E$terrainColors Eidos$terrainColors eidos_terrainColors |
| Eidos method time | .E$time Eidos$time eidos_time |
| Eidos method trunc | .E$trunc Eidos$trunc eidos_trunc |
| Eidos method ttest | .E$ttest Eidos$ttest eidos_ttest |
| Eidos method type | .E$type Eidos$type eidos_type |
| Eidos method unique | .E$unique Eidos$unique eidos_unique |
| Eidos method upperTri | .E$upperTri Eidos$upperTri eidos_upperTri |
| Eidos method usage | .E$usage Eidos$usage eidos_usage |
| Eidos method var | .E$var Eidos$var eidos_var |
| Eidos method version | .E$version Eidos$version eidos_version |
| Eidos method which | .E$which Eidos$which eidos_which |
| Eidos method whichMax | .E$whichMax Eidos$whichMax eidos_whichMax |
| Eidos method whichMin | .E$whichMin Eidos$whichMin eidos_whichMin |
| Eidos method writeFile | .E$writeFile Eidos$writeFile eidos_writeFile |
| Eidos method writeTempFile | .E$writeTempFile Eidos$writeTempFile eidos_writeTempFile |
| Extract or set end generation | end_gen end_gen<- |
| SLiM method evaluate | .IT$evaluate evaluate InteractionType$evaluate |
| SLiM method exp | .SM$exp exp SpatialMap$exp |
| SLiM first() callback | first |
| SLiM fitness() callback | fitness |
| SLiM fitnessEffect() callback | fitnessEffect |
| SLiM method flush | .LF$flush flush LogFile$flush |
| Genome | G Genome |
| GenomicElement | GE GenomicElement |
| SLiM method genomicElementTypesWithIDs | .Co$genomicElementTypesWithIDs Community$genomicElementTypesWithIDs genomicElementTypesWithIDs |
| GenomicElementType | GenomicElementType GET |
| Extract a single code block from a 'slimr_script' | get_block |
| Get the call information for running SLiM. Doubles as a check for SLiM availability. | get_slim_call |
| SLiM method gridValues | .SM$gridValues gridValues SpatialMap$gridValues |
| Individual | In Individual |
| SLiM method individualsWithPedigreeIDs | .Sp$individualsWithPedigreeIDs individualsWithPedigreeIDs Species$individualsWithPedigreeIDs |
| Initialize | Init Initialize |
| SLiM initialize() callback | initialize |
| SLiM method initializeAncestralNucleotides | .Init$initializeAncestralNucleotides Initialize$initializeAncestralNucleotides initializeAncestralNucleotides |
| SLiM method initializeGeneConversion | .Init$initializeGeneConversion Initialize$initializeGeneConversion initializeGeneConversion |
| SLiM method initializeGenomicElement | .Init$initializeGenomicElement Initialize$initializeGenomicElement initializeGenomicElement |
| SLiM method initializeGenomicElementType | .Init$initializeGenomicElementType Initialize$initializeGenomicElementType initializeGenomicElementType |
| SLiM method initializeHotspotMap | .Init$initializeHotspotMap Initialize$initializeHotspotMap initializeHotspotMap |
| SLiM method initializeInteractionType | .Init$initializeInteractionType Initialize$initializeInteractionType initializeInteractionType |
| SLiM method initializeMutationRate | .Init$initializeMutationRate Initialize$initializeMutationRate initializeMutationRate |
| SLiM method initializeMutationType | .Init$initializeMutationType Initialize$initializeMutationType initializeMutationType |
| SLiM method initializeMutationTypeNuc | .Init$initializeMutationTypeNuc Initialize$initializeMutationTypeNuc initializeMutationTypeNuc |
| SLiM method initializeRecombinationRate | .Init$initializeRecombinationRate Initialize$initializeRecombinationRate initializeRecombinationRate |
| SLiM method initializeSex | .Init$initializeSex Initialize$initializeSex initializeSex |
| SLiM method initializeSLiMModelType | .Init$initializeSLiMModelType Initialize$initializeSLiMModelType initializeSLiMModelType |
| SLiM method initializeSLiMOptions | .Init$initializeSLiMOptions Initialize$initializeSLiMOptions initializeSLiMOptions |
| SLiM method initializeSpecies | .Init$initializeSpecies Initialize$initializeSpecies initializeSpecies |
| SLiM method initializeTreeSeq | .Init$initializeTreeSeq Initialize$initializeTreeSeq initializeTreeSeq |
| SLiM method interactingNeighborCount | .IT$interactingNeighborCount interactingNeighborCount InteractionType$interactingNeighborCount |
| SLiM interaction() callback | interaction |
| SLiM method interactionDistance | .IT$interactionDistance interactionDistance InteractionType$interactionDistance |
| SLiM method interactionTypesWithIDs | .Co$interactionTypesWithIDs Community$interactionTypesWithIDs interactionTypesWithIDs |
| SLiM method interpolate | .SM$interpolate interpolate SpatialMap$interpolate |
| InteractionType | InteractionType IT |
| SLiM method killIndividuals | .Sp$killIndividuals killIndividuals Species$killIndividuals |
| SLiM late() callback | late |
| LogFile | LF LogFile |
| SLiM method localPopulationDensity | .IT$localPopulationDensity InteractionType$localPopulationDensity localPopulationDensity |
| SLiM method logRow | .LF$logRow LogFile$logRow logRow |
| Mutation | M Mutation |
| SLiM method mapColor | .SM$mapColor mapColor SpatialMap$mapColor |
| SLiM method mapImage | .SM$mapImage mapImage SpatialMap$mapImage |
| SLiM method mapValue | .SM$mapValue mapValue SpatialMap$mapValue |
| SLiM mateChoice() callback | mateChoice |
| Generate a minimal SLiM simulation script | minimal_slim_sim |
| Generate a minimal slimr_script object | minimal_slimr_script |
| SLiM method mm16To256 | .SB$mm16To256 mm16To256 SLiMBuiltin$mm16To256 |
| SLiM method mmJukesCantor | .SB$mmJukesCantor mmJukesCantor SLiMBuiltin$mmJukesCantor |
| SLiM method mmKimura | .SB$mmKimura mmKimura SLiMBuiltin$mmKimura |
| SLiM modifyChild() callback | modifyChild |
| MutationType | MT MutationType |
| SLiM method multiply | .SM$multiply multiply SpatialMap$multiply |
| SLiM mutation() callback | mutation |
| SLiM method mutationCounts | .Sp$mutationCounts mutationCounts Species$mutationCounts |
| SLiM method mutationCountsInGenomes | .G$mutationCountsInGenomes Genome$mutationCountsInGenomes mutationCountsInGenomes |
| SLiM mutationEffect() callback | mutationEffect |
| SLiM method mutationFrequencies | .Sp$mutationFrequencies mutationFrequencies Species$mutationFrequencies |
| SLiM method mutationFrequenciesInGenomes | .G$mutationFrequenciesInGenomes Genome$mutationFrequenciesInGenomes mutationFrequenciesInGenomes |
| SLiM method mutationsOfType | .G$mutationsOfType .Sp$mutationsOfType Genome$mutationsOfType mutationsOfType Species$mutationsOfType |
| SLiM method mutationTypesWithIDs | .Co$mutationTypesWithIDs Community$mutationTypesWithIDs mutationTypesWithIDs |
| SLiM method nearestInteractingNeighbors | .IT$nearestInteractingNeighbors InteractionType$nearestInteractingNeighbors nearestInteractingNeighbors |
| SLiM method nearestNeighbors | .IT$nearestNeighbors InteractionType$nearestNeighbors nearestNeighbors |
| SLiM method nearestNeighborsOfPoint | .IT$nearestNeighborsOfPoint InteractionType$nearestNeighborsOfPoint nearestNeighborsOfPoint |
| SLiM method neighborCount | .IT$neighborCount InteractionType$neighborCount neighborCount |
| SLiM method neighborCountOfPoint | .IT$neighborCountOfPoint InteractionType$neighborCountOfPoint neighborCountOfPoint |
| Make a new 'slimr_script_coll' object | new_slimr_script_coll |
| SLiM method nucleotideCounts | .SB$nucleotideCounts nucleotideCounts SLiMBuiltin$nucleotideCounts |
| SLiM method nucleotideFrequencies | .SB$nucleotideFrequencies nucleotideFrequencies SLiMBuiltin$nucleotideFrequencies |
| SLiM method nucleotides | .G$nucleotides Genome$nucleotides nucleotides |
| SLiM method nucleotidesToCodons | .SB$nucleotidesToCodons nucleotidesToCodons SLiMBuiltin$nucleotidesToCodons |
| SLiM method openDocument | .SG$openDocument openDocument SLiMgui$openDocument |
| SLiM method output | .G$output Genome$output output |
| SLiM method outputFixedMutations | .Sp$outputFixedMutations outputFixedMutations Species$outputFixedMutations |
| SLiM method outputFull | .Sp$outputFull outputFull Species$outputFull |
| SLiM method outputMS | .G$outputMS Genome$outputMS outputMS |
| SLiM method outputMSSample | .P$outputMSSample outputMSSample Subpopulation$outputMSSample |
| SLiM method outputMutations | .Sp$outputMutations outputMutations Species$outputMutations |
| SLiM method outputSample | .P$outputSample outputSample Subpopulation$outputSample |
| SLiM method outputUsage | .Co$outputUsage Community$outputUsage outputUsage |
| SLiM method outputVCF | .G$outputVCF Genome$outputVCF outputVCF |
| SLiM method outputVCFSample | .P$outputVCFSample outputVCFSample Subpopulation$outputVCFSample |
| Subpopulation | P Subpopulation |
| SLiM method pauseExecution | .SG$pauseExecution pauseExecution SLiMgui$pauseExecution |
| SLiM method pointDeviated | .P$pointDeviated pointDeviated Subpopulation$pointDeviated |
| SLiM method pointInBounds | .P$pointInBounds pointInBounds Subpopulation$pointInBounds |
| SLiM method pointPeriodic | .P$pointPeriodic pointPeriodic Subpopulation$pointPeriodic |
| SLiM method pointReflected | .P$pointReflected pointReflected Subpopulation$pointReflected |
| SLiM method pointStopped | .P$pointStopped pointStopped Subpopulation$pointStopped |
| SLiM method pointUniform | .P$pointUniform pointUniform Subpopulation$pointUniform |
| SLiM method positionsOfMutationsOfType | .G$positionsOfMutationsOfType Genome$positionsOfMutationsOfType positionsOfMutationsOfType |
| SLiM method power | .SM$power power SpatialMap$power |
| Insert R objects into SLiM scripts | r_inline slimr_inline |
| Tell SLiM to produce easily parseable output | r_output slimr_output |
| Utility function to tell SLiM to output coordinates from spatial simulations | r_output_coords slimr_output_coords |
| Utility function to tell SLiM to output its outputFull() output | r_output_full slimr_output_full |
| Utility function to tell SLiM to output Nucleotides | r_output_nucleotides slimr_output_nucleotides |
| Utility function to tell SLim to output sexes of individuals | r_output_sex slimr_output_sex |
| Utility function to tell SLiM to output SNP format data | r_output_snp slimr_output_snp |
| Create a templated variable | r_template slimr_template |
| Like slimr_template but automatically inserts code to setup variable as a defineConstant() call in the SLiM initialization block. | r_template_constant slimr_template_constant |
| SLiM method range | .SM$range range SpatialMap$range |
| SLiM method readFromMS | .G$readFromMS Genome$readFromMS readFromMS |
| SLiM method readFromPopulationFile | .Sp$readFromPopulationFile readFromPopulationFile Species$readFromPopulationFile |
| SLiM method readFromVCF | .G$readFromVCF Genome$readFromVCF readFromVCF |
| SLiM method recalculateFitness | .Sp$recalculateFitness recalculateFitness Species$recalculateFitness |
| SLiM recombination() callback | recombination |
| Reconstruct slimrlang code to make this slimr_script | reconstruct |
| Reconstruct slimrlang code to make this slimr_script | reconstruct.slimr_script |
| SLiM method registerEarlyEvent | .Co$registerEarlyEvent Community$registerEarlyEvent registerEarlyEvent |
| SLiM method registerFirstEvent | .Co$registerFirstEvent Community$registerFirstEvent registerFirstEvent |
| SLiM method registerFitnessEffectCallback | .Sp$registerFitnessEffectCallback registerFitnessEffectCallback Species$registerFitnessEffectCallback |
| SLiM method registerInteractionCallback | .Co$registerInteractionCallback Community$registerInteractionCallback registerInteractionCallback |
| SLiM method registerLateEvent | .Co$registerLateEvent Community$registerLateEvent registerLateEvent |
| SLiM method registerMateChoiceCallback | .Sp$registerMateChoiceCallback registerMateChoiceCallback Species$registerMateChoiceCallback |
| SLiM method registerModifyChildCallback | .Sp$registerModifyChildCallback registerModifyChildCallback Species$registerModifyChildCallback |
| SLiM method registerMutationCallback | .Sp$registerMutationCallback registerMutationCallback Species$registerMutationCallback |
| SLiM method registerMutationEffectCallback | .Sp$registerMutationEffectCallback registerMutationEffectCallback Species$registerMutationEffectCallback |
| SLiM method registerRecombinationCallback | .Sp$registerRecombinationCallback registerRecombinationCallback Species$registerRecombinationCallback |
| SLiM method registerReproductionCallback | .Sp$registerReproductionCallback registerReproductionCallback Species$registerReproductionCallback |
| SLiM method registerSurvivalCallback | .Sp$registerSurvivalCallback registerSurvivalCallback Species$registerSurvivalCallback |
| SLiM method relatedness | .I$relatedness Individual$relatedness relatedness |
| SLiM method removeMutations | .G$removeMutations Genome$removeMutations removeMutations |
| SLiM method removeSpatialMap | .P$removeSpatialMap removeSpatialMap Subpopulation$removeSpatialMap |
| SLiM method removeSubpopulation | .P$removeSubpopulation removeSubpopulation Subpopulation$removeSubpopulation |
| SLiM reproduction() callback | reproduction |
| SLiM method rescale | .SM$rescale rescale SpatialMap$rescale |
| SLiM method rescheduleScriptBlock | .Co$rescheduleScriptBlock Community$rescheduleScriptBlock rescheduleScriptBlock |
| Substitution | S Substitution |
| SLiM method sampleImprovedNearbyPoint | .SM$sampleImprovedNearbyPoint sampleImprovedNearbyPoint SpatialMap$sampleImprovedNearbyPoint |
| SLiM method sampleIndividuals | .P$sampleIndividuals sampleIndividuals Subpopulation$sampleIndividuals |
| SLiM method sampleNearbyPoint | .SM$sampleNearbyPoint sampleNearbyPoint SpatialMap$sampleNearbyPoint |
| SLiMBuiltin | SB SLiMBuiltin |
| SLiM method scriptBlocksWithIDs | .Co$scriptBlocksWithIDs Community$scriptBlocksWithIDs scriptBlocksWithIDs |
| SLiMEidosBlock | SEB SLiMEidosBlock |
| SLiM method setAncestralNucleotides | .Ch$setAncestralNucleotides Chromosome$setAncestralNucleotides setAncestralNucleotides |
| SLiM method setCloningRate | .P$setCloningRate setCloningRate Subpopulation$setCloningRate |
| SLiM method setConstraints | .IT$setConstraints InteractionType$setConstraints setConstraints |
| SLiM method setDistribution | .MT$setDistribution MutationType$setDistribution setDistribution |
| SLiM method setFilePath | .LF$setFilePath LogFile$setFilePath setFilePath |
| SLiM method setGeneConversion | .Ch$setGeneConversion Chromosome$setGeneConversion setGeneConversion |
| SLiM method setGenomicElementType | .GE$setGenomicElementType GenomicElement$setGenomicElementType setGenomicElementType |
| SLiM method setHotspotMap | .Ch$setHotspotMap Chromosome$setHotspotMap setHotspotMap |
| SLiM method setInteractionFunction | .IT$setInteractionFunction InteractionType$setInteractionFunction setInteractionFunction |
| SLiM method setLogInterval | .LF$setLogInterval LogFile$setLogInterval setLogInterval |
| SLiM method setMigrationRates | .P$setMigrationRates setMigrationRates Subpopulation$setMigrationRates |
| SLiM method setMutationFractions | .GET$setMutationFractions GenomicElementType$setMutationFractions setMutationFractions |
| SLiM method setMutationMatrix | .GET$setMutationMatrix GenomicElementType$setMutationMatrix setMutationMatrix |
| SLiM method setMutationRate | .Ch$setMutationRate Chromosome$setMutationRate setMutationRate |
| SLiM method setMutationType | .M$setMutationType Mutation$setMutationType setMutationType |
| SLiM method setRecombinationRate | .Ch$setRecombinationRate Chromosome$setRecombinationRate setRecombinationRate |
| SLiM method setSelectionCoeff | .M$setSelectionCoeff Mutation$setSelectionCoeff setSelectionCoeff |
| SLiM method setSelfingRate | .P$setSelfingRate setSelfingRate Subpopulation$setSelfingRate |
| SLiM method setSexRatio | .P$setSexRatio setSexRatio Subpopulation$setSexRatio |
| SLiM method setSpatialBounds | .P$setSpatialBounds setSpatialBounds Subpopulation$setSpatialBounds |
| SLiM method setSpatialPosition | .I$setSpatialPosition Individual$setSpatialPosition setSpatialPosition |
| SLiM method setSubpopulationSize | .P$setSubpopulationSize setSubpopulationSize Subpopulation$setSubpopulationSize |
| SLiM method setSuppliedValue | .LF$setSuppliedValue LogFile$setSuppliedValue setSuppliedValue |
| SLiM method setValue | .LF$setValue LogFile$setValue setValue |
| SLiMgui | SG SLiMgui |
| SLiM method sharedParentCount | .I$sharedParentCount Individual$sharedParentCount sharedParentCount |
| SLiM method simulationFinished | .Co$simulationFinished .Sp$simulationFinished Community$simulationFinished simulationFinished Species$simulationFinished |
| SLiM method skipTick | .Sp$skipTick skipTick Species$skipTick |
| Setup a SLiM code block | slim_block |
| Generate a code block that just adds subpopulations to a SLiM simulation | slim_block_add_subpops |
| Generate simulationFinished Block | slim_block_finish |
| Generate minimal initialize() block | slim_block_init_minimal |
| Insert slim_block to track progress when using slim_run | slim_block_progress |
| SLiM Callbacks | slim_callbacks |
| SLiM Classes | slim_classes |
| Rify some SLiM code | slim_code_Rify |
| Rify some SLiM code | slim_code_SLiMify |
| Extract Elements from SLiM's outputFull() | slim_extract_full |
| Extract data into a genlight object | slim_extract_genlight |
| Extract Elements from SLiM's output() for genomes | slim_extract_genome |
| Extract data produced by SLiM | slim_extract_output_data |
| Make sure a file name is compatible with using in a SLiM script. | slim_file |
| Specify an Eidos function to be included in the SLiM script | slim_function |
| Get a SLiM recipe | slim_get_recipe |
| Get a list of SLiM recipes (as text) | slim_get_recipes |
| Find the SLiM executable path `slimr` is using | slim_install_path |
| Check if SLiM is installed and 'slimr' can find it | slim_is_avail |
| Load SLiM Globals into R Global environment | slim_load_globals |
| Create a file to initialise a population in SLiM | slim_make_pop_input |
| Title | slim_open |
| Dataset of all recipes available in SLiM | slim_recipes |
| Convert output data from a slimr_results object to a tibble | slim_results_to_data |
| Run a SLiM script from R | slim_run slim_run.character slim_run.slimr_script slim_run.slimr_script_coll |
| Create a SLiMR script | slim_script |
| Set the duration of a slimr_script | slim_script_duration |
| Render a SLiM script with special slimrlang formatting | slim_script_render |
| Attempt to install and / or setup SLiM for use with slimr | slim_setup |
| Get information on templating in a slimr_script | slim_template_info |
| Unload SLiM Globals from R Global environment | slim_unload_globals |
| Copy original slimrlang code used to create a slimr_script object to the clipboard | slimr_clip_original |
| Create a 'slimr_code' object | slimr_code |
| Convert a string to a SLiM object name | slimr_name |
| Open original slimrlang code used to create a slimr_script object in a new document | slimr_open_original |
| Make a new 'slimr_script_coll' object | slimr_script_coll |
| Write a slimr_script object to a text file | slimr_write |
| SpatialMap | SM SpatialMap |
| SLiM method smooth | .SM$smooth smooth SpatialMap$smooth |
| Species | Sp Species |
| SLiM method spatialMapColor | .P$spatialMapColor spatialMapColor Subpopulation$spatialMapColor |
| SLiM method spatialMapImage | .P$spatialMapImage spatialMapImage Subpopulation$spatialMapImage |
| SLiM method spatialMapValue | .P$spatialMapValue spatialMapValue Subpopulation$spatialMapValue |
| SLiM method speciesWithIDs | .Co$speciesWithIDs Community$speciesWithIDs speciesWithIDs |
| SLiMSim was a class used prior to v4.0 in SLiM. It remains in `slimr` for backwards compatibility but its use is now deprecated. | SS |
| SLiM method strength | .IT$strength InteractionType$strength strength |
| SLiM method subpopulationsWithIDs | .Co$subpopulationsWithIDs Community$subpopulationsWithIDs subpopulationsWithIDs |
| SLiM method subsetIndividuals | .P$subsetIndividuals Subpopulation$subsetIndividuals subsetIndividuals |
| SLiM method subsetMutations | .Sp$subsetMutations Species$subsetMutations subsetMutations |
| SLiM method subtract | .SM$subtract SpatialMap$subtract subtract |
| SLiM method summarizeIndividuals | .SB$summarizeIndividuals SLiMBuiltin$summarizeIndividuals summarizeIndividuals |
| SLiM method sumOfMutationsOfType | .G$sumOfMutationsOfType .I$sumOfMutationsOfType Genome$sumOfMutationsOfType Individual$sumOfMutationsOfType sumOfMutationsOfType |
| SLiM survival() callback | survival |
| SLiM method takeMigrants | .P$takeMigrants Subpopulation$takeMigrants takeMigrants |
| SLiM method testConstraints | .IT$testConstraints InteractionType$testConstraints testConstraints |
| SLiM method totalOfNeighborStrengths | .IT$totalOfNeighborStrengths InteractionType$totalOfNeighborStrengths totalOfNeighborStrengths |
| SLiM method treeSeqCoalesced | .Sp$treeSeqCoalesced Species$treeSeqCoalesced treeSeqCoalesced |
| SLiM method treeSeqMetadata | .SB$treeSeqMetadata SLiMBuiltin$treeSeqMetadata treeSeqMetadata |
| SLiM method treeSeqOutput | .Sp$treeSeqOutput Species$treeSeqOutput treeSeqOutput |
| SLiM method treeSeqRememberIndividuals | .Sp$treeSeqRememberIndividuals Species$treeSeqRememberIndividuals treeSeqRememberIndividuals |
| SLiM method treeSeqSimplify | .Sp$treeSeqSimplify Species$treeSeqSimplify treeSeqSimplify |
| SLiM method unevaluate | .IT$unevaluate InteractionType$unevaluate unevaluate |
| SLiM method uniqueMutationsOfType | .I$uniqueMutationsOfType Individual$uniqueMutationsOfType uniqueMutationsOfType |
| SLiM method usage | .Co$usage Community$usage usage |
| SLiM method willAutolog | .LF$willAutolog LogFile$willAutolog willAutolog |