{ "_id": "6a1f008eb401979e7341add6", "Package": "slimr", "Title": "Create, Run and Post-Process 'SLiM' Population Genetics Forward\nSimulations", "Version": "0.4.1", "Authors@R": "c(person(given = \"Russell\",\nfamily = \"Dinnage\",\nrole = c(\"aut\", \"cre\", \"cph\"),\nemail = \"russell.dinnage@gmail.com\",\ncomment = c(ORCID = \"0000-0003-0846-2819\")),\nperson(given = \"Stephen\",\nfamily = \"Sarre\",\nrole = \"aut\"),\nperson(given = \"Bernd\",\nfamily = \"Gruber\",\nrole = \"aut\"),\nperson(given = \"Richard\",\nfamily = \"Duncan\",\nrole = \"aut\"),\nperson(given = \"Benjamin\",\nfamily = \"Haller\",\nrole = \"ctb\"),\nperson(given = \"Philip\",\nfamily = \"Messer\",\nrole = \"ctb\"))", "Description": "Lets you write 'SLiM' scripts (population genomics\nsimulation) using your favourite R IDE, using a syntax as close\nas possible to the original 'SLiM' language. It offer many\ntools to manipulate those scripts, as well as run them in the\n'SLiM' software from R, as well as capture and post-process\ntheir output, after or even during a simulation.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "URL": "https://rdinnager.github.io/slimr,\nhttps://rdinnager.github.io/slimr/index.html,\nhttps://github.com/rdinnager/slimr", "BugReports": "https://github.com/rdinnager/slimr/issues", "RoxygenNote": "7.3.3", "Language": "en-GB", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev libx11-dev", "Repository": "https://rdinnager.r-universe.dev", "Date/Publication": "2025-10-20 18:19:31 UTC", "RemoteUrl": "https://github.com/rdinnager/slimr", "RemoteRef": "HEAD", "RemoteSha": "4f6c549d39a2deb81fa1ce64a7a4d151253fe112", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-18 08:52:39 UTC", "User": "root" }, "Author": "Russell Dinnage [aut, cre, cph] (ORCID:\n),\nStephen Sarre 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"Eidos$asin", "eidos_asin" ] }, { "page": "eidos_asInteger", "title": "Eidos method asInteger", "concept": [ "Eidos" ], "topics": [ ".E$asInteger", "Eidos$asInteger", "eidos_asInteger" ] }, { "page": "eidos_asLogical", "title": "Eidos method asLogical", "concept": [ "Eidos" ], "topics": [ ".E$asLogical", "Eidos$asLogical", "eidos_asLogical" ] }, { "page": "eidos_assert", "title": "Eidos method assert", "concept": [ "Eidos" ], "topics": [ ".E$assert", "Eidos$assert", "eidos_assert" ] }, { "page": "eidos_asString", "title": "Eidos method asString", "concept": [ "Eidos" ], "topics": [ ".E$asString", "Eidos$asString", "eidos_asString" ] }, { "page": "eidos_atan", "title": "Eidos method atan", "concept": [ "Eidos" ], "topics": [ ".E$atan", "Eidos$atan", "eidos_atan" ] }, { "page": "eidos_atan2", "title": "Eidos method atan2", "concept": [ "Eidos" ], "topics": [ ".E$atan2", "Eidos$atan2", "eidos_atan2" ] }, { "page": "eidos_beep", "title": "Eidos method beep", "concept": [ "Eidos" ], "topics": [ ".E$beep", "Eidos$beep", "eidos_beep" ] }, { "page": "eidos_c", "title": "Eidos method c", "concept": [ "Eidos" ], "topics": [ ".E$c", "Eidos$c", "eidos_c" ] }, { "page": "eidos_cat", "title": "Eidos method cat", "concept": [ "Eidos" ], "topics": [ ".E$cat", "Eidos$cat", "eidos_cat" ] }, { "page": "eidos_catn", "title": "Eidos method catn", "concept": [ "Eidos" ], "topics": [ ".E$catn", "Eidos$catn", "eidos_catn" ] }, { "page": "eidos_cbind", "title": "Eidos method cbind", "concept": [ "Eidos" ], "topics": [ ".E$cbind", "Eidos$cbind", "eidos_cbind" ] }, { "page": "eidos_ceil", "title": "Eidos method ceil", "concept": [ "Eidos" ], "topics": [ ".E$ceil", "Eidos$ceil", "eidos_ceil" ] }, { "page": "eidos_citation", "title": "Eidos method citation", "concept": [ "Eidos" ], "topics": [ ".E$citation", "Eidos$citation", "eidos_citation" ] }, { "page": "eidos_clock", "title": "Eidos method clock", "concept": [ "Eidos" ], "topics": [ ".E$clock", "Eidos$clock", "eidos_clock" ] }, { "page": "eidos_cmColors", "title": "Eidos method cmColors", "concept": [ "Eidos" ], "topics": [ ".E$cmColors", "Eidos$cmColors", "eidos_cmColors" ] }, { "page": "eidos_color2rgb", "title": "Eidos method color2rgb", "concept": [ "Eidos" ], "topics": [ ".E$color2rgb", "Eidos$color2rgb", "eidos_color2rgb" ] }, { "page": "eidos_colors", "title": "Eidos method colors", "concept": [ "Eidos" ], "topics": [ ".E$colors", "Eidos$colors", "eidos_colors" ] }, { "page": "eidos_cor", "title": "Eidos method cor", "concept": [ "Eidos" ], "topics": [ ".E$cor", "Eidos$cor", "eidos_cor" ] }, { "page": "eidos_cos", "title": "Eidos method cos", "concept": [ "Eidos" ], "topics": [ ".E$cos", "Eidos$cos", "eidos_cos" ] }, { "page": "eidos_cov", "title": "Eidos method cov", "concept": [ "Eidos" ], "topics": [ ".E$cov", "Eidos$cov", "eidos_cov" ] }, { "page": "eidos_createDirectory", "title": "Eidos method createDirectory", "concept": [ "Eidos" ], "topics": [ ".E$createDirectory", "Eidos$createDirectory", "eidos_createDirectory" ] }, { "page": "eidos_cumProduct", "title": "Eidos method cumProduct", "concept": [ "Eidos" ], "topics": [ ".E$cumProduct", "Eidos$cumProduct", "eidos_cumProduct" ] }, { "page": "eidos_cumSum", "title": "Eidos method cumSum", "concept": [ "Eidos" ], "topics": [ ".E$cumSum", "Eidos$cumSum", "eidos_cumSum" ] }, { "page": "eidos_date", "title": "Eidos method date", "concept": [ "Eidos" ], "topics": [ ".E$date", "Eidos$date", "eidos_date" ] }, { "page": "eidos_dbeta", "title": "Eidos method dbeta", "concept": [ "Eidos" ], "topics": [ ".E$dbeta", "Eidos$dbeta", "eidos_dbeta" ] }, { "page": "eidos_debugIndent", "title": "Eidos method debugIndent", "concept": [ "Eidos" ], "topics": [ ".E$debugIndent", "Eidos$debugIndent", "eidos_debugIndent" ] }, { "page": "eidos_defineConstant", "title": "Eidos method defineConstant", "concept": [ "Eidos" ], "topics": [ ".E$defineConstant", "Eidos$defineConstant", "eidos_defineConstant" ] }, { "page": "eidos_defineGlobal", "title": "Eidos method defineGlobal", "concept": [ "Eidos" ], "topics": [ ".E$defineGlobal", "Eidos$defineGlobal", "eidos_defineGlobal" ] }, { "page": "eidos_deleteFile", "title": "Eidos method deleteFile", "concept": [ "Eidos" ], "topics": [ ".E$deleteFile", "Eidos$deleteFile", "eidos_deleteFile" ] }, { "page": "eidos_dexp", "title": "Eidos method dexp", "concept": [ "Eidos" ], "topics": [ ".E$dexp", "Eidos$dexp", "eidos_dexp" ] }, { "page": "eidos_dgamma", "title": "Eidos method dgamma", "concept": [ "Eidos" ], "topics": [ ".E$dgamma", "Eidos$dgamma", "eidos_dgamma" ] }, { "page": "eidos_diag", "title": "Eidos method diag", "concept": [ "Eidos" ], "topics": [ ".E$diag", "Eidos$diag", "eidos_diag" ] }, { "page": "eidos_dim", "title": "Eidos method dim", "concept": [ "Eidos" ], "topics": [ ".E$dim", "Eidos$dim", "eidos_dim" ] }, { "page": "eidos_dmvnorm", "title": "Eidos method dmvnorm", "concept": [ "Eidos" ], "topics": [ ".E$dmvnorm", "Eidos$dmvnorm", "eidos_dmvnorm" ] }, { "page": "eidos_dnorm", "title": "Eidos method dnorm", "concept": [ "Eidos" ], "topics": [ ".E$dnorm", "Eidos$dnorm", "eidos_dnorm" ] }, { "page": "eidos_drop", "title": "Eidos method drop", "concept": [ "Eidos" ], "topics": [ ".E$drop", "Eidos$drop", "eidos_drop" ] }, { "page": "eidos_elementType", "title": "Eidos method elementType", "concept": [ "Eidos" ], "topics": [ ".E$elementType", "Eidos$elementType", "eidos_elementType" ] }, { "page": "eidos_exists", "title": "Eidos method exists", "concept": [ "Eidos" ], "topics": [ ".E$exists", "Eidos$exists", "eidos_exists" ] }, { "page": "eidos_exp", "title": "Eidos method exp", "concept": [ "Eidos" ], "topics": [ ".E$exp", "Eidos$exp", "eidos_exp" ] }, { "page": "eidos_fileExists", "title": "Eidos method fileExists", "concept": [ "Eidos" ], "topics": [ ".E$fileExists", "Eidos$fileExists", "eidos_fileExists" ] }, { "page": "eidos_filesAtPath", "title": "Eidos method filesAtPath", "concept": [ "Eidos" ], "topics": [ ".E$filesAtPath", "Eidos$filesAtPath", "eidos_filesAtPath" ] }, { "page": "eidos_findInterval", "title": "Eidos method findInterval", "concept": [ "Eidos" ], "topics": [ ".E$findInterval", "Eidos$findInterval", "eidos_findInterval" ] }, { "page": "eidos_float", "title": "Eidos method float", "concept": [ "Eidos" ], "topics": [ ".E$float", "Eidos$float", "eidos_float" ] }, { "page": "eidos_floor", "title": "Eidos method floor", "concept": [ "Eidos" ], "topics": [ ".E$floor", "Eidos$floor", "eidos_floor" ] }, { "page": "eidos_flushFile", "title": "Eidos method flushFile", "concept": [ "Eidos" ], "topics": [ ".E$flushFile", "Eidos$flushFile", "eidos_flushFile" ] }, { "page": "eidos_format", "title": "Eidos method format", "concept": [ "Eidos" ], "topics": [ ".E$format", "Eidos$format", "eidos_format" ] }, { "page": "eidos_functionSignature", "title": "Eidos method functionSignature", "concept": [ "Eidos" ], "topics": [ ".E$functionSignature", "Eidos$functionSignature", "eidos_functionSignature" ] }, { "page": "eidos_functionSource", "title": "Eidos method functionSource", "concept": [ "Eidos" ], "topics": [ ".E$functionSource", "Eidos$functionSource", "eidos_functionSource" ] }, { "page": "eidos_getSeed", "title": "Eidos method getSeed", "concept": [ "Eidos" ], "topics": [ ".E$getSeed", "Eidos$getSeed", "eidos_getSeed" ] }, { "page": "eidos_getwd", "title": "Eidos method getwd", "concept": [ "Eidos" ], "topics": [ ".E$getwd", "Eidos$getwd", "eidos_getwd" ] }, { "page": "eidos_heatColors", "title": "Eidos method heatColors", "concept": [ "Eidos" ], "topics": [ ".E$heatColors", "Eidos$heatColors", "eidos_heatColors" ] }, { "page": "eidos_hsv2rgb", "title": "Eidos method hsv2rgb", "concept": [ "Eidos" ], "topics": [ ".E$hsv2rgb", "Eidos$hsv2rgb", "eidos_hsv2rgb" ] }, { "page": "eidos_identical", "title": "Eidos method identical", "concept": [ "Eidos" ], "topics": [ ".E$identical", "Eidos$identical", "eidos_identical" ] }, { "page": "eidos_ifelse", "title": "Eidos method ifelse", "concept": [ "Eidos" ], "topics": [ ".E$ifelse", "Eidos$ifelse", "eidos_ifelse" ] }, { "page": "eidos_integer", "title": "Eidos method integer", "concept": [ "Eidos" ], "topics": [ ".E$integer", "Eidos$integer", "eidos_integer" ] }, { "page": "eidos_integerDiv", "title": "Eidos method integerDiv", "concept": [ "Eidos" ], "topics": [ ".E$integerDiv", "Eidos$integerDiv", "eidos_integerDiv" ] }, { "page": "eidos_integerMod", "title": "Eidos method integerMod", "concept": [ "Eidos" ], "topics": [ ".E$integerMod", "Eidos$integerMod", "eidos_integerMod" ] }, { "page": "eidos_isFinite", "title": "Eidos method isFinite", "concept": [ "Eidos" ], "topics": [ ".E$isFinite", "Eidos$isFinite", "eidos_isFinite" ] }, { "page": "eidos_isFloat", "title": "Eidos method isFloat", "concept": [ "Eidos" ], "topics": [ ".E$isFloat", "Eidos$isFloat", "eidos_isFloat" ] }, { "page": "eidos_isInfinite", "title": "Eidos method isInfinite", "concept": [ "Eidos" ], "topics": [ ".E$isInfinite", "Eidos$isInfinite", "eidos_isInfinite" ] }, { "page": "eidos_isInteger", "title": "Eidos method isInteger", "concept": [ "Eidos" ], "topics": [ ".E$isInteger", "Eidos$isInteger", "eidos_isInteger" ] }, { "page": "eidos_isLogical", "title": "Eidos method isLogical", "concept": [ "Eidos" ], "topics": [ ".E$isLogical", "Eidos$isLogical", "eidos_isLogical" ] }, { "page": "eidos_isNAN", "title": "Eidos method isNAN", "concept": [ "Eidos" ], "topics": [ ".E$isNAN", "Eidos$isNAN", "eidos_isNAN" ] }, { "page": "eidos_isNULL", "title": "Eidos method isNULL", "concept": [ "Eidos" ], "topics": [ ".E$isNULL", "Eidos$isNULL", "eidos_isNULL" ] }, { "page": "eidos_isObject", "title": "Eidos method isObject", "concept": [ "Eidos" ], "topics": [ ".E$isObject", "Eidos$isObject", "eidos_isObject" ] }, { "page": "eidos_isString", "title": "Eidos method isString", "concept": [ "Eidos" ], "topics": [ ".E$isString", "Eidos$isString", "eidos_isString" ] }, { "page": "eidos_length", "title": "Eidos method length", "concept": [ "Eidos" ], "topics": [ ".E$length", "Eidos$length", "eidos_length" ] }, { "page": "eidos_license", "title": "Eidos method license", "concept": [ "Eidos" ], "topics": [ ".E$license", "Eidos$license", "eidos_license" ] }, { "page": "eidos_log", "title": "Eidos method log", "concept": [ "Eidos" ], "topics": [ ".E$log", "Eidos$log", "eidos_log" ] }, { "page": "eidos_log10", "title": "Eidos method log10", "concept": [ "Eidos" ], "topics": [ ".E$log10", "Eidos$log10", "eidos_log10" ] }, { "page": "eidos_log2", "title": "Eidos method log2", "concept": [ "Eidos" ], "topics": [ ".E$log2", "Eidos$log2", "eidos_log2" ] }, { "page": "eidos_logical", "title": "Eidos method logical", "concept": [ "Eidos" ], "topics": [ ".E$logical", "Eidos$logical", "eidos_logical" ] }, { "page": "eidos_lowerTri", "title": "Eidos method lowerTri", "concept": [ "Eidos" ], "topics": [ ".E$lowerTri", "Eidos$lowerTri", "eidos_lowerTri" ] }, { "page": "eidos_ls", "title": "Eidos method ls", "concept": [ "Eidos" ], "topics": [ ".E$ls", "Eidos$ls", "eidos_ls" ] }, { "page": "eidos_match", "title": "Eidos method match", "concept": [ "Eidos" ], "topics": [ ".E$match", "Eidos$match", "eidos_match" ] }, { "page": "eidos_matrix", "title": "Eidos method matrix", "concept": [ "Eidos" ], "topics": [ ".E$matrix", "Eidos$matrix", "eidos_matrix" ] }, { "page": "eidos_matrixMult", "title": "Eidos method matrixMult", "concept": [ "Eidos" ], "topics": [ ".E$matrixMult", "Eidos$matrixMult", "eidos_matrixMult" ] }, { "page": "eidos_max", "title": "Eidos method max", "concept": [ "Eidos" ], "topics": [ ".E$max", "Eidos$max", "eidos_max" ] }, { "page": "eidos_mean", "title": "Eidos method mean", "concept": [ "Eidos" ], "topics": [ ".E$mean", "Eidos$mean", "eidos_mean" ] }, { "page": "eidos_min", "title": "Eidos method min", "concept": [ "Eidos" ], "topics": [ ".E$min", "Eidos$min", "eidos_min" ] }, { "page": "eidos_nchar", "title": "Eidos method nchar", "concept": [ "Eidos" ], "topics": [ ".E$nchar", "Eidos$nchar", "eidos_nchar" ] }, { "page": "eidos_ncol", "title": "Eidos method ncol", "concept": [ "Eidos" ], "topics": [ ".E$ncol", "Eidos$ncol", "eidos_ncol" ] }, { "page": "eidos_nrow", "title": "Eidos method nrow", "concept": [ "Eidos" ], "topics": [ ".E$nrow", "Eidos$nrow", "eidos_nrow" ] }, { "page": "eidos_object", "title": "Eidos method object", "concept": [ "Eidos" ], "topics": [ ".E$object", "Eidos$object", "eidos_object" ] }, { "page": "eidos_order", "title": "Eidos method order", "concept": [ "Eidos" ], "topics": [ ".E$order", "Eidos$order", "eidos_order" ] }, { "page": "eidos_paste", "title": "Eidos method paste", "concept": [ "Eidos" ], "topics": [ ".E$paste", "Eidos$paste", "eidos_paste" ] }, { "page": "eidos_paste0", "title": "Eidos method paste0", "concept": [ "Eidos" ], "topics": [ ".E$paste0", "Eidos$paste0", "eidos_paste0" ] }, { "page": "eidos_pmax", "title": "Eidos method pmax", "concept": [ "Eidos" ], "topics": [ ".E$pmax", "Eidos$pmax", "eidos_pmax" ] }, { "page": "eidos_pmin", "title": "Eidos method pmin", "concept": [ "Eidos" ], "topics": [ ".E$pmin", "Eidos$pmin", "eidos_pmin" ] }, { "page": "eidos_pnorm", "title": "Eidos method pnorm", "concept": [ "Eidos" ], "topics": [ ".E$pnorm", "Eidos$pnorm", "eidos_pnorm" ] }, { "page": "eidos_print", "title": "Eidos method print", "concept": [ "Eidos" ], "topics": [ ".E$print", "Eidos$print", "eidos_print" ] }, { "page": "eidos_product", "title": "Eidos method product", "concept": [ "Eidos" ], "topics": [ ".E$product", "Eidos$product", "eidos_product" ] }, { "page": "eidos_qnorm", "title": "Eidos method qnorm", "concept": [ "Eidos" ], "topics": [ ".E$qnorm", "Eidos$qnorm", "eidos_qnorm" ] }, { "page": "eidos_quantile", "title": "Eidos method quantile", "concept": [ "Eidos" ], "topics": [ ".E$quantile", "Eidos$quantile", "eidos_quantile" ] }, { "page": "eidos_rainbow", "title": "Eidos method rainbow", "concept": [ "Eidos" ], "topics": [ ".E$rainbow", "Eidos$rainbow", "eidos_rainbow" ] }, { "page": "eidos_range", "title": "Eidos method range", "concept": [ "Eidos" ], "topics": [ ".E$range", "Eidos$range", "eidos_range" ] }, { "page": "eidos_rank", "title": "Eidos method rank", "concept": [ "Eidos" ], "topics": [ ".E$rank", "Eidos$rank", "eidos_rank" ] }, { "page": "eidos_rbeta", "title": "Eidos method rbeta", "concept": [ "Eidos" ], "topics": [ ".E$rbeta", "Eidos$rbeta", "eidos_rbeta" ] }, { "page": "eidos_rbind", "title": "Eidos method rbind", "concept": [ "Eidos" ], "topics": [ ".E$rbind", "Eidos$rbind", "eidos_rbind" ] }, { "page": "eidos_rbinom", "title": "Eidos method rbinom", "concept": [ "Eidos" ], "topics": [ ".E$rbinom", "Eidos$rbinom", "eidos_rbinom" ] }, { "page": "eidos_rcauchy", "title": "Eidos method rcauchy", "concept": [ "Eidos" ], "topics": [ ".E$rcauchy", "Eidos$rcauchy", "eidos_rcauchy" ] }, { "page": "eidos_rdunif", "title": "Eidos method rdunif", "concept": [ "Eidos" ], "topics": [ ".E$rdunif", "Eidos$rdunif", "eidos_rdunif" ] }, { "page": "eidos_readCSV", "title": "Eidos method readCSV", "concept": [ "Eidos" ], "topics": [ ".E$readCSV", "Eidos$readCSV", "eidos_readCSV" ] }, { "page": "eidos_readFile", "title": "Eidos method readFile", "concept": [ "Eidos" ], "topics": [ ".E$readFile", "Eidos$readFile", "eidos_readFile" ] }, { "page": "eidos_rep", "title": "Eidos method rep", "concept": [ "Eidos" ], "topics": [ ".E$rep", "Eidos$rep", "eidos_rep" ] }, { "page": "eidos_repEach", "title": "Eidos method repEach", "concept": [ "Eidos" ], "topics": [ ".E$repEach", "Eidos$repEach", "eidos_repEach" ] }, { "page": "eidos_rev", "title": "Eidos method rev", "concept": [ "Eidos" ], "topics": [ ".E$rev", "Eidos$rev", "eidos_rev" ] }, { "page": "eidos_rexp", "title": "Eidos method rexp", "concept": [ "Eidos" ], "topics": [ ".E$rexp", "Eidos$rexp", "eidos_rexp" ] }, { "page": "eidos_rf", "title": "Eidos method rf", "concept": [ "Eidos" ], "topics": [ ".E$rf", "Eidos$rf", "eidos_rf" ] }, { "page": "eidos_rgamma", "title": "Eidos method rgamma", "concept": [ "Eidos" ], "topics": [ ".E$rgamma", "Eidos$rgamma", "eidos_rgamma" ] }, { "page": "eidos_rgb2color", "title": "Eidos method rgb2color", "concept": [ "Eidos" ], "topics": [ ".E$rgb2color", "Eidos$rgb2color", "eidos_rgb2color" ] }, { "page": "eidos_rgb2hsv", "title": "Eidos method rgb2hsv", "concept": [ "Eidos" ], "topics": [ ".E$rgb2hsv", "Eidos$rgb2hsv", "eidos_rgb2hsv" ] }, { "page": "eidos_rgeom", "title": "Eidos method rgeom", "concept": [ "Eidos" ], "topics": [ ".E$rgeom", "Eidos$rgeom", "eidos_rgeom" ] }, { "page": "eidos_rlnorm", "title": "Eidos method rlnorm", "concept": [ "Eidos" ], "topics": [ ".E$rlnorm", "Eidos$rlnorm", "eidos_rlnorm" ] }, { "page": "eidos_rm", "title": "Eidos method rm", "concept": [ "Eidos" ], "topics": [ ".E$rm", "Eidos$rm", "eidos_rm" ] }, { "page": "eidos_rmvnorm", "title": "Eidos method rmvnorm", "concept": [ "Eidos" ], "topics": [ ".E$rmvnorm", "Eidos$rmvnorm", "eidos_rmvnorm" ] }, { "page": "eidos_rnbinom", "title": "Eidos method rnbinom", "concept": [ "Eidos" ], "topics": [ ".E$rnbinom", "Eidos$rnbinom", "eidos_rnbinom" ] }, { "page": "eidos_rnorm", "title": "Eidos method rnorm", "concept": [ "Eidos" ], "topics": [ ".E$rnorm", "Eidos$rnorm", "eidos_rnorm" ] }, { "page": "eidos_round", "title": "Eidos method round", "concept": [ "Eidos" ], "topics": [ ".E$round", "Eidos$round", "eidos_round" ] }, { "page": "eidos_rpois", "title": "Eidos method rpois", "concept": [ "Eidos" ], "topics": [ ".E$rpois", "Eidos$rpois", "eidos_rpois" ] }, { "page": "eidos_runif", "title": "Eidos method runif", "concept": [ "Eidos" ], "topics": [ ".E$runif", "Eidos$runif", "eidos_runif" ] }, { "page": "eidos_rweibull", "title": "Eidos method rweibull", "concept": [ "Eidos" ], "topics": [ ".E$rweibull", "Eidos$rweibull", "eidos_rweibull" ] }, { "page": "eidos_sample", "title": "Eidos method sample", "concept": [ "Eidos" ], "topics": [ ".E$sample", "Eidos$sample", "eidos_sample" ] }, { "page": "eidos_sapply", "title": "Eidos method sapply", "concept": [ "Eidos" ], "topics": [ ".E$sapply", "Eidos$sapply", "eidos_sapply" ] }, { "page": "eidos_sd", "title": "Eidos method sd", "concept": [ "Eidos" ], "topics": [ ".E$sd", "Eidos$sd", "eidos_sd" ] }, { "page": "eidos_seq", "title": "Eidos method seq", "concept": [ "Eidos" ], "topics": [ ".E$seq", "Eidos$seq", "eidos_seq" ] }, { "page": "eidos_seqAlong", "title": "Eidos method seqAlong", "concept": [ "Eidos" ], "topics": [ ".E$seqAlong", "Eidos$seqAlong", "eidos_seqAlong" ] }, { "page": "eidos_seqLen", "title": "Eidos method seqLen", "concept": [ "Eidos" ], "topics": [ ".E$seqLen", "Eidos$seqLen", "eidos_seqLen" ] }, { "page": "eidos_setDifference", "title": "Eidos method setDifference", "concept": [ "Eidos" ], "topics": [ ".E$setDifference", "Eidos$setDifference", "eidos_setDifference" ] }, { "page": "eidos_setIntersection", "title": "Eidos method setIntersection", "concept": [ "Eidos" ], "topics": [ ".E$setIntersection", "Eidos$setIntersection", "eidos_setIntersection" ] }, { "page": "eidos_setSeed", "title": "Eidos method setSeed", "concept": [ "Eidos" ], "topics": [ ".E$setSeed", "Eidos$setSeed", "eidos_setSeed" ] }, { "page": "eidos_setSymmetricDifference", "title": "Eidos method setSymmetricDifference", "concept": [ "Eidos" ], "topics": [ ".E$setSymmetricDifference", "Eidos$setSymmetricDifference", "eidos_setSymmetricDifference" ] }, { "page": "eidos_setUnion", "title": "Eidos method setUnion", "concept": [ "Eidos" ], "topics": [ ".E$setUnion", "Eidos$setUnion", "eidos_setUnion" ] }, { "page": "eidos_setwd", "title": "Eidos method setwd", "concept": [ "Eidos" ], "topics": [ ".E$setwd", "Eidos$setwd", "eidos_setwd" ] }, { "page": "eidos_sin", "title": "Eidos method sin", "concept": [ "Eidos" ], "topics": [ ".E$sin", "Eidos$sin", "eidos_sin" ] }, { "page": "eidos_size", "title": "Eidos method size", "concept": [ "Eidos" ], "topics": [ ".E$size", "Eidos$size", "eidos_size" ] }, { "page": "eidos_sort", "title": "Eidos method sort", "concept": [ "Eidos" ], "topics": [ ".E$sort", "Eidos$sort", "eidos_sort" ] }, { "page": "eidos_sortBy", "title": "Eidos method sortBy", "concept": [ "Eidos" ], "topics": [ ".E$sortBy", "Eidos$sortBy", "eidos_sortBy" ] }, { "page": "eidos_source", "title": "Eidos method source", "concept": [ "Eidos" ], "topics": [ ".E$source", "Eidos$source", "eidos_source" ] }, { "page": "eidos_sqrt", "title": "Eidos method sqrt", "concept": [ "Eidos" ], "topics": [ ".E$sqrt", "Eidos$sqrt", "eidos_sqrt" ] }, { "page": "eidos_stop", "title": "Eidos method stop", "concept": [ "Eidos" ], "topics": [ ".E$stop", "Eidos$stop", "eidos_stop" ] }, { "page": "eidos_str", "title": "Eidos method str", "concept": [ "Eidos" ], "topics": [ ".E$str", "Eidos$str", "eidos_str" ] }, { "page": "eidos_strcontains", "title": "Eidos method strcontains", "concept": [ "Eidos" ], "topics": [ ".E$strcontains", "Eidos$strcontains", "eidos_strcontains" ] }, { "page": "eidos_strfind", "title": "Eidos method strfind", "concept": [ "Eidos" ], "topics": [ ".E$strfind", "Eidos$strfind", "eidos_strfind" ] }, { "page": "eidos_string", "title": "Eidos method string", "concept": [ "Eidos" ], "topics": [ ".E$string", "Eidos$string", "eidos_string" ] }, { "page": "eidos_strprefix", "title": "Eidos method strprefix", "concept": [ "Eidos" ], "topics": [ ".E$strprefix", "Eidos$strprefix", "eidos_strprefix" ] }, { "page": "eidos_strsplit", "title": "Eidos method strsplit", "concept": [ "Eidos" ], "topics": [ ".E$strsplit", "Eidos$strsplit", "eidos_strsplit" ] }, { "page": "eidos_strsuffix", "title": "Eidos method strsuffix", "concept": [ "Eidos" ], "topics": [ ".E$strsuffix", "Eidos$strsuffix", "eidos_strsuffix" ] }, { "page": "eidos_substr", "title": "Eidos method substr", "concept": [ "Eidos" ], "topics": [ ".E$substr", "Eidos$substr", "eidos_substr" ] }, { "page": "eidos_sum", "title": "Eidos method sum", "concept": [ "Eidos" ], "topics": [ ".E$sum", "Eidos$sum", "eidos_sum" ] }, { "page": "eidos_sumExact", "title": "Eidos method sumExact", "concept": [ "Eidos" ], "topics": [ ".E$sumExact", "Eidos$sumExact", "eidos_sumExact" ] }, { "page": "eidos_suppressWarnings", "title": "Eidos method suppressWarnings", "concept": [ "Eidos" ], "topics": [ ".E$suppressWarnings", "Eidos$suppressWarnings", "eidos_suppressWarnings" ] }, { "page": "eidos_sysinfo", "title": "Eidos method sysinfo", "concept": [ "Eidos" ], "topics": [ ".E$sysinfo", "Eidos$sysinfo", "eidos_sysinfo" ] }, { "page": "eidos_system", "title": "Eidos method system", "concept": [ "Eidos" ], "topics": [ ".E$system", "Eidos$system", "eidos_system" ] }, { "page": "eidos_t", "title": "Eidos method t", "concept": [ "Eidos" ], "topics": [ ".E$t", "Eidos$t", "eidos_t" ] }, { "page": "eidos_tabulate", "title": "Eidos method tabulate", "concept": [ "Eidos" ], "topics": [ ".E$tabulate", "Eidos$tabulate", "eidos_tabulate" ] }, { "page": "eidos_tan", "title": "Eidos method tan", "concept": [ "Eidos" ], "topics": [ ".E$tan", "Eidos$tan", "eidos_tan" ] }, { "page": "eidos_tempdir", "title": "Eidos method tempdir", "concept": [ "Eidos" ], "topics": [ ".E$tempdir", "Eidos$tempdir", "eidos_tempdir" ] }, { "page": "eidos_terrainColors", "title": "Eidos method terrainColors", "concept": [ "Eidos" ], "topics": [ ".E$terrainColors", "Eidos$terrainColors", "eidos_terrainColors" ] }, { "page": "eidos_time", "title": "Eidos method time", "concept": [ "Eidos" ], "topics": [ ".E$time", "Eidos$time", "eidos_time" ] }, { "page": "eidos_trunc", "title": "Eidos method trunc", "concept": [ "Eidos" ], "topics": [ ".E$trunc", "Eidos$trunc", "eidos_trunc" ] }, { "page": "eidos_ttest", "title": "Eidos method ttest", "concept": [ "Eidos" ], "topics": [ ".E$ttest", "Eidos$ttest", "eidos_ttest" ] }, { "page": "eidos_type", "title": "Eidos method type", "concept": [ "Eidos" ], "topics": [ ".E$type", "Eidos$type", "eidos_type" ] }, { "page": "eidos_unique", "title": "Eidos method unique", "concept": [ "Eidos" ], "topics": [ ".E$unique", "Eidos$unique", "eidos_unique" ] }, { "page": "eidos_upperTri", "title": "Eidos method upperTri", "concept": [ "Eidos" ], "topics": [ ".E$upperTri", "Eidos$upperTri", "eidos_upperTri" ] }, { "page": "eidos_usage", "title": "Eidos method usage", "concept": [ "Eidos" ], "topics": [ ".E$usage", "Eidos$usage", "eidos_usage" ] }, { "page": "eidos_var", "title": "Eidos method var", "concept": [ "Eidos" ], "topics": [ ".E$var", "Eidos$var", "eidos_var" ] }, { "page": "eidos_version", "title": "Eidos method version", "concept": [ "Eidos" ], "topics": [ ".E$version", "Eidos$version", "eidos_version" ] }, { "page": "eidos_which", "title": "Eidos method which", "concept": [ "Eidos" ], "topics": [ ".E$which", "Eidos$which", "eidos_which" ] }, { "page": "eidos_whichMax", "title": "Eidos method whichMax", "concept": [ "Eidos" ], "topics": [ ".E$whichMax", "Eidos$whichMax", "eidos_whichMax" ] }, { "page": "eidos_whichMin", "title": "Eidos method whichMin", "concept": [ "Eidos" ], "topics": [ ".E$whichMin", "Eidos$whichMin", "eidos_whichMin" ] }, { "page": "eidos_writeFile", "title": "Eidos method writeFile", "concept": [ "Eidos" ], "topics": [ ".E$writeFile", "Eidos$writeFile", "eidos_writeFile" ] }, { "page": "eidos_writeTempFile", "title": "Eidos method writeTempFile", "concept": [ "Eidos" ], "topics": [ ".E$writeTempFile", "Eidos$writeTempFile", "eidos_writeTempFile" ] }, { "page": "end_gen", "title": "Extract or set end generation", "topics": [ "end_gen", "end_gen<-" ] }, { "page": "evaluate", "title": "SLiM method evaluate", "concept": [ "InteractionType" ], "topics": [ ".IT$evaluate", "evaluate", "InteractionType$evaluate" ] }, { "page": "exp", "title": "SLiM method exp", "concept": [ "SpatialMap" ], "topics": [ ".SM$exp", "exp", "SpatialMap$exp" ] }, { "page": "first", "title": "SLiM first() callback", "concept": [ "callbacks" ], "topics": [ "first" ] }, { "page": "fitness", "title": "SLiM fitness() callback", "concept": [ "callbacks" ], "topics": [ "fitness" ] }, { "page": "fitnessEffect", "title": "SLiM fitnessEffect() callback", "concept": [ "callbacks" ], "topics": [ "fitnessEffect" ] }, { "page": "flush", "title": "SLiM method flush", "concept": [ "LogFile" ], "topics": [ ".LF$flush", "flush", "LogFile$flush" ] }, { "page": "Genome_Class", "title": "Genome", "concept": [ "Genome" ], "topics": [ "G", "Genome" ] }, { "page": "GenomicElement_Class", "title": "GenomicElement", "concept": [ "GenomicElement" ], "topics": [ "GE", "GenomicElement" ] }, { "page": "genomicElementTypesWithIDs", "title": "SLiM method genomicElementTypesWithIDs", "concept": [ "Community" ], "topics": [ ".Co$genomicElementTypesWithIDs", "Community$genomicElementTypesWithIDs", "genomicElementTypesWithIDs" ] }, { "page": "GenomicElementType_Class", "title": "GenomicElementType", "concept": [ "GenomicElementType" ], "topics": [ "GenomicElementType", "GET" ] }, { "page": "get_block", "title": "Extract a single code block from a 'slimr_script'", "topics": [ "get_block" ] }, { "page": "get_slim_call", "title": "Get the call information for running SLiM. Doubles as a check for SLiM availability.", "topics": [ "get_slim_call" ] }, { "page": "gridValues", "title": "SLiM method gridValues", "concept": [ "SpatialMap" ], "topics": [ ".SM$gridValues", "gridValues", "SpatialMap$gridValues" ] }, { "page": "Individual_Class", "title": "Individual", "concept": [ "Individual" ], "topics": [ "In", "Individual" ] }, { "page": "individualsWithPedigreeIDs", "title": "SLiM method individualsWithPedigreeIDs", "concept": [ "Species" ], "topics": [ ".Sp$individualsWithPedigreeIDs", "individualsWithPedigreeIDs", "Species$individualsWithPedigreeIDs" ] }, { "page": "Initialize_Class", "title": "Initialize", "concept": [ "Initialize" ], "topics": [ "Init", "Initialize" ] }, { "page": "callback_initialize", "title": "SLiM initialize() callback", "concept": [ "callbacks" ], "topics": [ "initialize" ] }, { "page": "initializeAncestralNucleotides", "title": "SLiM method initializeAncestralNucleotides", "concept": [ "Initialize" ], "topics": [ ".Init$initializeAncestralNucleotides", "Initialize$initializeAncestralNucleotides", "initializeAncestralNucleotides" ] }, { "page": "initializeGeneConversion", "title": "SLiM method initializeGeneConversion", "concept": [ "Initialize" ], "topics": [ ".Init$initializeGeneConversion", "Initialize$initializeGeneConversion", "initializeGeneConversion" ] }, { "page": "initializeGenomicElement", "title": "SLiM method initializeGenomicElement", "concept": [ "Initialize" ], "topics": [ ".Init$initializeGenomicElement", "Initialize$initializeGenomicElement", "initializeGenomicElement" ] }, { "page": "initializeGenomicElementType", "title": "SLiM method initializeGenomicElementType", "concept": [ "Initialize" ], "topics": [ ".Init$initializeGenomicElementType", "Initialize$initializeGenomicElementType", "initializeGenomicElementType" ] }, { "page": "initializeHotspotMap", "title": "SLiM method initializeHotspotMap", "concept": [ "Initialize" ], "topics": [ ".Init$initializeHotspotMap", "Initialize$initializeHotspotMap", "initializeHotspotMap" ] }, { "page": "initializeInteractionType", "title": "SLiM method initializeInteractionType", "concept": [ "Initialize" ], "topics": [ ".Init$initializeInteractionType", "Initialize$initializeInteractionType", "initializeInteractionType" ] }, { "page": "initializeMutationRate", "title": "SLiM method initializeMutationRate", "concept": [ "Initialize" ], "topics": [ ".Init$initializeMutationRate", "Initialize$initializeMutationRate", "initializeMutationRate" ] }, { "page": "initializeMutationType", "title": "SLiM method initializeMutationType", "concept": [ "Initialize" ], "topics": [ ".Init$initializeMutationType", "Initialize$initializeMutationType", "initializeMutationType" ] }, { "page": "initializeMutationTypeNuc", "title": "SLiM method initializeMutationTypeNuc", "concept": [ "Initialize" ], "topics": [ ".Init$initializeMutationTypeNuc", "Initialize$initializeMutationTypeNuc", "initializeMutationTypeNuc" ] }, { "page": "initializeRecombinationRate", "title": "SLiM method initializeRecombinationRate", "concept": [ "Initialize" ], "topics": [ ".Init$initializeRecombinationRate", "Initialize$initializeRecombinationRate", "initializeRecombinationRate" ] }, { "page": "initializeSex", "title": "SLiM method initializeSex", "concept": [ "Initialize" ], "topics": [ ".Init$initializeSex", "Initialize$initializeSex", "initializeSex" ] }, { "page": "initializeSLiMModelType", "title": "SLiM method initializeSLiMModelType", "concept": [ "Initialize" ], "topics": [ ".Init$initializeSLiMModelType", "Initialize$initializeSLiMModelType", "initializeSLiMModelType" ] }, { "page": "initializeSLiMOptions", "title": "SLiM method initializeSLiMOptions", "concept": [ "Initialize" ], "topics": [ ".Init$initializeSLiMOptions", "Initialize$initializeSLiMOptions", "initializeSLiMOptions" ] }, { "page": "initializeSpecies", "title": "SLiM method initializeSpecies", "concept": [ "Initialize" ], "topics": [ ".Init$initializeSpecies", "Initialize$initializeSpecies", "initializeSpecies" ] }, { "page": "initializeTreeSeq", "title": "SLiM method initializeTreeSeq", "concept": [ "Initialize" ], "topics": [ ".Init$initializeTreeSeq", "Initialize$initializeTreeSeq", "initializeTreeSeq" ] }, { "page": "interactingNeighborCount", "title": "SLiM method interactingNeighborCount", "concept": [ "InteractionType" ], "topics": [ ".IT$interactingNeighborCount", "interactingNeighborCount", "InteractionType$interactingNeighborCount" ] }, { "page": "interaction", "title": "SLiM interaction() callback", "concept": [ "callbacks" ], "topics": [ "interaction" ] }, { "page": "interactionDistance", "title": "SLiM method interactionDistance", "concept": [ "InteractionType" ], "topics": [ ".IT$interactionDistance", "interactionDistance", "InteractionType$interactionDistance" ] }, { "page": "interactionTypesWithIDs", "title": "SLiM method interactionTypesWithIDs", "concept": [ "Community" ], "topics": [ ".Co$interactionTypesWithIDs", "Community$interactionTypesWithIDs", "interactionTypesWithIDs" ] }, { "page": "interpolate", "title": "SLiM method interpolate", "concept": [ "SpatialMap" ], "topics": [ ".SM$interpolate", "interpolate", "SpatialMap$interpolate" ] }, { "page": "InteractionType_Class", "title": "InteractionType", "concept": [ "InteractionType" ], "topics": [ "InteractionType", "IT" ] }, { "page": "killIndividuals", "title": "SLiM method killIndividuals", "concept": [ "Species" ], "topics": [ ".Sp$killIndividuals", "killIndividuals", "Species$killIndividuals" ] }, { "page": "late", "title": "SLiM late() callback", "concept": [ "callbacks" ], "topics": [ "late" ] }, { "page": "LogFile_Class", "title": "LogFile", "concept": [ "LogFile" ], "topics": [ "LF", "LogFile" ] }, { "page": "load_herm", "title": "Download and load herm.rdata file containing SNP data from Sandy Inland Mouse Details can be found in the article at https://rdinnager.github.io/slimr/articles/Main_manuscript_example_v2.html", "topics": [ "load_herm" ] }, { "page": "localPopulationDensity", "title": "SLiM method localPopulationDensity", "concept": [ "InteractionType" ], "topics": [ ".IT$localPopulationDensity", "InteractionType$localPopulationDensity", "localPopulationDensity" ] }, { "page": "logRow", "title": "SLiM method logRow", "concept": [ "LogFile" ], "topics": [ ".LF$logRow", "LogFile$logRow", "logRow" ] }, { "page": "Mutation_Class", "title": "Mutation", "concept": [ "Mutation" ], "topics": [ "M", "Mutation" ] }, { "page": "mapColor", "title": "SLiM method mapColor", "concept": [ "SpatialMap" ], "topics": [ ".SM$mapColor", "mapColor", "SpatialMap$mapColor" ] }, { "page": "mapImage", "title": "SLiM method mapImage", "concept": [ "SpatialMap" ], "topics": [ ".SM$mapImage", "mapImage", "SpatialMap$mapImage" ] }, { "page": "mapValue", "title": "SLiM method mapValue", "concept": [ "SpatialMap" ], "topics": [ ".SM$mapValue", "mapValue", "SpatialMap$mapValue" ] }, { "page": "mateChoice", "title": "SLiM mateChoice() callback", "concept": [ "callbacks" ], "topics": [ "mateChoice" ] }, { "page": "minimal_slim_sim", "title": "Generate a minimal SLiM simulation script", "topics": [ "minimal_slim_sim" ] }, { "page": "minimal_slimr_script", "title": "Generate a minimal slimr_script object", "topics": [ "minimal_slimr_script" ] }, { "page": "mm16To256", "title": "SLiM method mm16To256", "concept": [ "SLiMBuiltin" ], "topics": [ ".SB$mm16To256", "mm16To256", "SLiMBuiltin$mm16To256" ] }, { "page": "mmJukesCantor", "title": "SLiM method mmJukesCantor", "concept": [ "SLiMBuiltin" ], "topics": [ ".SB$mmJukesCantor", "mmJukesCantor", "SLiMBuiltin$mmJukesCantor" ] }, { "page": "mmKimura", "title": "SLiM method mmKimura", "concept": [ "SLiMBuiltin" ], "topics": [ ".SB$mmKimura", "mmKimura", "SLiMBuiltin$mmKimura" ] }, { "page": "modifyChild", "title": "SLiM modifyChild() callback", "concept": [ "callbacks" ], "topics": [ "modifyChild" ] }, { "page": "MutationType_Class", "title": "MutationType", "concept": [ "MutationType" ], "topics": [ "MT", "MutationType" ] }, { "page": "multiply", "title": "SLiM method multiply", "concept": [ "SpatialMap" ], "topics": [ ".SM$multiply", "multiply", "SpatialMap$multiply" ] }, { "page": "Mutation", "title": "SLiM mutation() callback", "concept": [ "callbacks" ], "topics": [ "mutation" ] }, { "page": "mutationCounts", "title": "SLiM method mutationCounts", "concept": [ "Species" ], "topics": [ ".Sp$mutationCounts", "mutationCounts", "Species$mutationCounts" ] }, { "page": "mutationCountsInGenomes", "title": "SLiM method mutationCountsInGenomes", "concept": [ "Genome" ], "topics": [ ".G$mutationCountsInGenomes", "Genome$mutationCountsInGenomes", "mutationCountsInGenomes" ] }, { "page": "mutationEffect", "title": "SLiM mutationEffect() callback", "concept": [ "callbacks" ], "topics": [ "mutationEffect" ] }, { "page": "mutationFrequencies", "title": "SLiM method mutationFrequencies", "concept": [ "Species" ], "topics": [ ".Sp$mutationFrequencies", "mutationFrequencies", "Species$mutationFrequencies" ] }, { "page": "mutationFrequenciesInGenomes", "title": "SLiM method mutationFrequenciesInGenomes", "concept": [ "Genome" ], "topics": [ ".G$mutationFrequenciesInGenomes", "Genome$mutationFrequenciesInGenomes", "mutationFrequenciesInGenomes" ] }, { "page": "mutationsOfType", "title": "SLiM method mutationsOfType", "concept": [ "Genome", "Species" ], "topics": [ ".G$mutationsOfType", ".Sp$mutationsOfType", "Genome$mutationsOfType", "mutationsOfType", "Species$mutationsOfType" ] }, { "page": "mutationTypesWithIDs", "title": "SLiM method mutationTypesWithIDs", "concept": [ "Community" ], "topics": [ ".Co$mutationTypesWithIDs", "Community$mutationTypesWithIDs", "mutationTypesWithIDs" ] }, { "page": "nearestInteractingNeighbors", "title": "SLiM method nearestInteractingNeighbors", "concept": [ "InteractionType" ], "topics": [ ".IT$nearestInteractingNeighbors", "InteractionType$nearestInteractingNeighbors", "nearestInteractingNeighbors" ] }, { "page": "nearestNeighbors", "title": "SLiM method nearestNeighbors", "concept": [ "InteractionType" ], "topics": [ ".IT$nearestNeighbors", "InteractionType$nearestNeighbors", "nearestNeighbors" ] }, { "page": "nearestNeighborsOfPoint", "title": "SLiM method nearestNeighborsOfPoint", "concept": [ "InteractionType" ], "topics": [ ".IT$nearestNeighborsOfPoint", "InteractionType$nearestNeighborsOfPoint", "nearestNeighborsOfPoint" ] }, { "page": "neighborCount", "title": "SLiM method neighborCount", "concept": [ "InteractionType" ], "topics": [ ".IT$neighborCount", "InteractionType$neighborCount", "neighborCount" ] }, { "page": "neighborCountOfPoint", "title": "SLiM method neighborCountOfPoint", "concept": [ "InteractionType" ], "topics": [ ".IT$neighborCountOfPoint", "InteractionType$neighborCountOfPoint", "neighborCountOfPoint" ] }, { "page": "new_slimr_script_coll", "title": "Make a new 'slimr_script_coll' object", "topics": [ "new_slimr_script_coll" ] }, { "page": "nucleotideCounts", "title": "SLiM method nucleotideCounts", "concept": [ "SLiMBuiltin" ], "topics": [ ".SB$nucleotideCounts", "nucleotideCounts", "SLiMBuiltin$nucleotideCounts" ] }, { "page": "nucleotideFrequencies", "title": "SLiM method nucleotideFrequencies", "concept": [ "SLiMBuiltin" ], "topics": [ ".SB$nucleotideFrequencies", "nucleotideFrequencies", "SLiMBuiltin$nucleotideFrequencies" ] }, { "page": "nucleotides", "title": "SLiM method nucleotides", "concept": [ "Genome" ], "topics": [ ".G$nucleotides", "Genome$nucleotides", "nucleotides" ] }, { "page": "nucleotidesToCodons", "title": "SLiM method nucleotidesToCodons", "concept": [ "SLiMBuiltin" ], "topics": [ ".SB$nucleotidesToCodons", "nucleotidesToCodons", "SLiMBuiltin$nucleotidesToCodons" ] }, { "page": "openDocument", "title": "SLiM method openDocument", "concept": [ "SLiMgui" ], "topics": [ ".SG$openDocument", "openDocument", "SLiMgui$openDocument" ] }, { "page": "output", "title": "SLiM method output", "concept": [ "Genome" ], "topics": [ ".G$output", "Genome$output", "output" ] }, { "page": "outputFixedMutations", "title": "SLiM method outputFixedMutations", "concept": [ "Species" ], "topics": [ ".Sp$outputFixedMutations", "outputFixedMutations", "Species$outputFixedMutations" ] }, { "page": "outputFull", "title": "SLiM method outputFull", "concept": [ "Species" ], "topics": [ ".Sp$outputFull", "outputFull", "Species$outputFull" ] }, { "page": "outputMS", "title": "SLiM method outputMS", "concept": [ "Genome" ], "topics": [ ".G$outputMS", "Genome$outputMS", "outputMS" ] }, { "page": "outputMSSample", "title": "SLiM method outputMSSample", "concept": [ "Subpopulation" ], "topics": [ ".P$outputMSSample", "outputMSSample", "Subpopulation$outputMSSample" ] }, { "page": "outputMutations", "title": "SLiM method outputMutations", "concept": [ "Species" ], "topics": [ ".Sp$outputMutations", "outputMutations", "Species$outputMutations" ] }, { "page": "outputSample", "title": "SLiM method outputSample", "concept": [ "Subpopulation" ], "topics": [ ".P$outputSample", "outputSample", "Subpopulation$outputSample" ] }, { "page": "outputUsage", "title": "SLiM method outputUsage", "concept": [ "Community" ], "topics": [ ".Co$outputUsage", "Community$outputUsage", "outputUsage" ] }, { "page": "outputVCF", "title": "SLiM method outputVCF", "concept": [ "Genome" ], "topics": [ ".G$outputVCF", "Genome$outputVCF", "outputVCF" ] }, { "page": "outputVCFSample", "title": "SLiM method outputVCFSample", "concept": [ "Subpopulation" ], "topics": [ ".P$outputVCFSample", "outputVCFSample", "Subpopulation$outputVCFSample" ] }, { "page": "Subpopulation_Class", "title": "Subpopulation", "concept": [ "Subpopulation" ], "topics": [ "P", "Subpopulation" ] }, { "page": "pauseExecution", "title": "SLiM method pauseExecution", "concept": [ "SLiMgui" ], "topics": [ ".SG$pauseExecution", "pauseExecution", "SLiMgui$pauseExecution" ] }, { "page": "pointDeviated", "title": "SLiM method pointDeviated", "concept": [ "Subpopulation" ], "topics": [ ".P$pointDeviated", "pointDeviated", "Subpopulation$pointDeviated" ] }, { "page": "pointInBounds", "title": "SLiM method pointInBounds", "concept": [ "Subpopulation" ], "topics": [ ".P$pointInBounds", "pointInBounds", "Subpopulation$pointInBounds" ] }, { "page": "pointPeriodic", "title": "SLiM method pointPeriodic", "concept": [ "Subpopulation" ], "topics": [ ".P$pointPeriodic", "pointPeriodic", "Subpopulation$pointPeriodic" ] }, { "page": "pointReflected", "title": "SLiM method pointReflected", "concept": [ "Subpopulation" ], "topics": [ ".P$pointReflected", "pointReflected", "Subpopulation$pointReflected" ] }, { "page": "pointStopped", "title": "SLiM method pointStopped", "concept": [ "Subpopulation" ], "topics": [ ".P$pointStopped", "pointStopped", "Subpopulation$pointStopped" ] }, { "page": "pointUniform", "title": "SLiM method pointUniform", "concept": [ "Subpopulation" ], "topics": [ ".P$pointUniform", "pointUniform", "Subpopulation$pointUniform" ] }, { "page": "positionsOfMutationsOfType", "title": "SLiM method positionsOfMutationsOfType", "concept": [ "Genome" ], "topics": [ ".G$positionsOfMutationsOfType", "Genome$positionsOfMutationsOfType", "positionsOfMutationsOfType" ] }, { "page": "power", "title": "SLiM method power", "concept": [ "SpatialMap" ], "topics": [ ".SM$power", "power", "SpatialMap$power" ] }, { "page": "r_inline", "title": "Insert R objects into SLiM scripts", "topics": [ "r_inline", "slimr_inline" ] }, { "page": "r_message", "title": "Send SLiM output to the R console as a message while a simulation is running", "topics": [ "r_message", "slimr_message" ] }, { "page": "r_output", "title": "Tell SLiM to produce easily parseable output", "topics": [ "r_output", "slimr_output" ] }, { "page": "r_output_coords", "title": "Utility function to tell SLiM to output coordinates from spatial simulations", "topics": [ "r_output_coords", "slimr_output_coords" ] }, { "page": "r_output_full", "title": "Utility function to tell SLiM to output its outputFull() output", "topics": [ "r_output_full", "slimr_output_full" ] }, { "page": "r_output_nucleotides", "title": "Utility function to tell SLiM to output Nucleotides", "topics": [ "r_output_nucleotides", "slimr_output_nucleotides" ] }, { "page": "r_output_sex", "title": "Utility function to tell SLim to output sexes of individuals", "topics": [ "r_output_sex", "slimr_output_sex" ] }, { "page": "r_output_snp", "title": "Utility function to tell SLiM to output SNP format data", "topics": [ "r_output_snp", "slimr_output_snp" ] }, { "page": "r_template", "title": "Create a templated variable", "topics": [ "r_template", "slimr_template" ] }, { "page": "r_template_constant", "title": "Like slimr_template but automatically inserts code to setup variable as a defineConstant() call in the SLiM initialization block.", "topics": [ "r_template_constant", "slimr_template_constant" ] }, { "page": "range", "title": "SLiM method range", "concept": [ "SpatialMap" ], "topics": [ ".SM$range", "range", "SpatialMap$range" ] }, { "page": "readFromMS", "title": "SLiM method readFromMS", "concept": [ "Genome" ], "topics": [ ".G$readFromMS", "Genome$readFromMS", "readFromMS" ] }, { "page": "readFromPopulationFile", "title": "SLiM method readFromPopulationFile", "concept": [ "Species" ], "topics": [ ".Sp$readFromPopulationFile", "readFromPopulationFile", "Species$readFromPopulationFile" ] }, { "page": "readFromVCF", "title": "SLiM method readFromVCF", "concept": [ "Genome" ], "topics": [ ".G$readFromVCF", "Genome$readFromVCF", "readFromVCF" ] }, { "page": "recalculateFitness", "title": "SLiM method recalculateFitness", "concept": [ "Species" ], "topics": [ ".Sp$recalculateFitness", "recalculateFitness", "Species$recalculateFitness" ] }, { "page": "recombination", "title": "SLiM recombination() callback", "concept": [ "callbacks" ], "topics": [ "recombination" ] }, { "page": "reconstruct", "title": "Reconstruct slimrlang code to make this slimr_script", "topics": [ "reconstruct" ] }, { "page": "reconstruct.slimr_script", "title": "Reconstruct slimrlang code to make this slimr_script", "topics": [ "reconstruct.slimr_script" ] }, { "page": "registerEarlyEvent", "title": "SLiM method registerEarlyEvent", "concept": [ "Community" ], "topics": [ ".Co$registerEarlyEvent", "Community$registerEarlyEvent", "registerEarlyEvent" ] }, { "page": "registerFirstEvent", "title": "SLiM method registerFirstEvent", "concept": [ "Community" ], "topics": [ ".Co$registerFirstEvent", "Community$registerFirstEvent", "registerFirstEvent" ] }, { "page": "registerFitnessEffectCallback", "title": "SLiM method registerFitnessEffectCallback", "concept": [ "Species" ], "topics": [ ".Sp$registerFitnessEffectCallback", "registerFitnessEffectCallback", "Species$registerFitnessEffectCallback" ] }, { "page": "registerInteractionCallback", "title": "SLiM method registerInteractionCallback", "concept": [ "Community" ], "topics": [ ".Co$registerInteractionCallback", "Community$registerInteractionCallback", "registerInteractionCallback" ] }, { "page": "registerLateEvent", "title": "SLiM method registerLateEvent", "concept": [ "Community" ], "topics": [ ".Co$registerLateEvent", "Community$registerLateEvent", "registerLateEvent" ] }, { "page": "registerMateChoiceCallback", "title": "SLiM method registerMateChoiceCallback", "concept": [ "Species" ], "topics": [ ".Sp$registerMateChoiceCallback", "registerMateChoiceCallback", "Species$registerMateChoiceCallback" ] }, { "page": "registerModifyChildCallback", "title": "SLiM method registerModifyChildCallback", "concept": [ "Species" ], "topics": [ ".Sp$registerModifyChildCallback", "registerModifyChildCallback", "Species$registerModifyChildCallback" ] }, { "page": "registerMutationCallback", "title": "SLiM method registerMutationCallback", "concept": [ "Species" ], "topics": [ ".Sp$registerMutationCallback", "registerMutationCallback", "Species$registerMutationCallback" ] }, { "page": "registerMutationEffectCallback", "title": "SLiM method registerMutationEffectCallback", "concept": [ "Species" ], "topics": [ ".Sp$registerMutationEffectCallback", "registerMutationEffectCallback", "Species$registerMutationEffectCallback" ] }, { "page": "registerRecombinationCallback", "title": "SLiM method registerRecombinationCallback", "concept": [ "Species" ], "topics": [ ".Sp$registerRecombinationCallback", "registerRecombinationCallback", "Species$registerRecombinationCallback" ] }, { "page": "registerReproductionCallback", "title": "SLiM method registerReproductionCallback", "concept": [ "Species" ], "topics": [ ".Sp$registerReproductionCallback", "registerReproductionCallback", "Species$registerReproductionCallback" ] }, { "page": "registerSurvivalCallback", "title": "SLiM method registerSurvivalCallback", "concept": [ "Species" ], "topics": [ ".Sp$registerSurvivalCallback", "registerSurvivalCallback", "Species$registerSurvivalCallback" ] }, { "page": "relatedness", "title": "SLiM method relatedness", "concept": [ "Individual" ], "topics": [ ".I$relatedness", "Individual$relatedness", "relatedness" ] }, { "page": "removeMutations", "title": "SLiM method removeMutations", "concept": [ "Genome" ], "topics": [ ".G$removeMutations", "Genome$removeMutations", "removeMutations" ] }, { "page": "removeSpatialMap", "title": "SLiM method removeSpatialMap", "concept": [ "Subpopulation" ], "topics": [ ".P$removeSpatialMap", "removeSpatialMap", "Subpopulation$removeSpatialMap" ] }, { "page": "removeSubpopulation", "title": "SLiM method removeSubpopulation", "concept": [ "Subpopulation" ], "topics": [ ".P$removeSubpopulation", "removeSubpopulation", "Subpopulation$removeSubpopulation" ] }, { "page": "reproduction", "title": "SLiM reproduction() callback", "concept": [ "callbacks" ], "topics": [ "reproduction" ] }, { "page": "rescale", "title": "SLiM method rescale", "concept": [ "SpatialMap" ], "topics": [ ".SM$rescale", "rescale", "SpatialMap$rescale" ] }, { "page": "rescheduleScriptBlock", "title": "SLiM method rescheduleScriptBlock", "concept": [ "Community" ], "topics": [ ".Co$rescheduleScriptBlock", "Community$rescheduleScriptBlock", "rescheduleScriptBlock" ] }, { "page": "Substitution_Class", "title": "Substitution", "concept": [ "Substitution" ], "topics": [ "S", "Substitution" ] }, { "page": "sampleImprovedNearbyPoint", "title": "SLiM method sampleImprovedNearbyPoint", "concept": [ "SpatialMap" ], "topics": [ ".SM$sampleImprovedNearbyPoint", "sampleImprovedNearbyPoint", "SpatialMap$sampleImprovedNearbyPoint" ] }, { "page": "sampleIndividuals", "title": "SLiM method sampleIndividuals", "concept": [ "Subpopulation" ], "topics": [ ".P$sampleIndividuals", "sampleIndividuals", "Subpopulation$sampleIndividuals" ] }, { "page": "sampleNearbyPoint", "title": "SLiM method sampleNearbyPoint", "concept": [ "SpatialMap" ], "topics": [ ".SM$sampleNearbyPoint", "sampleNearbyPoint", "SpatialMap$sampleNearbyPoint" ] }, { "page": "SLiMBuiltin_Class", "title": "SLiMBuiltin", "concept": [ "SLiMBuiltin" ], "topics": [ "SB", "SLiMBuiltin" ] }, { "page": "scriptBlocksWithIDs", "title": "SLiM method scriptBlocksWithIDs", "concept": [ "Community" ], "topics": [ ".Co$scriptBlocksWithIDs", "Community$scriptBlocksWithIDs", "scriptBlocksWithIDs" ] }, { "page": "SLiMEidosBlock_Class", "title": "SLiMEidosBlock", "concept": [ "SLiMEidosBlock" ], "topics": [ "SEB", "SLiMEidosBlock" ] }, { "page": "setAncestralNucleotides", "title": "SLiM method setAncestralNucleotides", "concept": [ "Chromosome" ], "topics": [ ".Ch$setAncestralNucleotides", "Chromosome$setAncestralNucleotides", "setAncestralNucleotides" ] }, { "page": "setCloningRate", "title": "SLiM method setCloningRate", "concept": [ "Subpopulation" ], "topics": [ ".P$setCloningRate", "setCloningRate", "Subpopulation$setCloningRate" ] }, { "page": "setConstraints", "title": "SLiM method setConstraints", "concept": [ "InteractionType" ], "topics": [ ".IT$setConstraints", "InteractionType$setConstraints", "setConstraints" ] }, { "page": "setDistribution", "title": "SLiM method setDistribution", "concept": [ "MutationType" ], "topics": [ ".MT$setDistribution", "MutationType$setDistribution", "setDistribution" ] }, { "page": "setFilePath", "title": "SLiM method setFilePath", "concept": [ "LogFile" ], "topics": [ ".LF$setFilePath", "LogFile$setFilePath", "setFilePath" ] }, { "page": "setGeneConversion", "title": "SLiM method setGeneConversion", "concept": [ "Chromosome" ], "topics": [ ".Ch$setGeneConversion", "Chromosome$setGeneConversion", "setGeneConversion" ] }, { "page": "setGenomicElementType", "title": "SLiM method setGenomicElementType", "concept": [ "GenomicElement" ], "topics": [ ".GE$setGenomicElementType", "GenomicElement$setGenomicElementType", "setGenomicElementType" ] }, { "page": "setHotspotMap", "title": "SLiM method setHotspotMap", "concept": [ "Chromosome" ], "topics": [ ".Ch$setHotspotMap", "Chromosome$setHotspotMap", "setHotspotMap" ] }, { "page": "setInteractionFunction", "title": "SLiM method setInteractionFunction", "concept": [ "InteractionType" ], "topics": [ ".IT$setInteractionFunction", "InteractionType$setInteractionFunction", "setInteractionFunction" ] }, { "page": "setLogInterval", "title": "SLiM method setLogInterval", "concept": [ "LogFile" ], "topics": [ ".LF$setLogInterval", "LogFile$setLogInterval", "setLogInterval" ] }, { "page": "setMigrationRates", "title": "SLiM method setMigrationRates", "concept": [ "Subpopulation" ], "topics": [ ".P$setMigrationRates", "setMigrationRates", "Subpopulation$setMigrationRates" ] }, { "page": "setMutationFractions", "title": "SLiM method setMutationFractions", "concept": [ "GenomicElementType" ], "topics": [ ".GET$setMutationFractions", "GenomicElementType$setMutationFractions", "setMutationFractions" ] }, { "page": "setMutationMatrix", "title": "SLiM method setMutationMatrix", "concept": [ "GenomicElementType" ], "topics": [ ".GET$setMutationMatrix", "GenomicElementType$setMutationMatrix", "setMutationMatrix" ] }, { "page": "setMutationRate", "title": "SLiM method setMutationRate", "concept": [ "Chromosome" ], "topics": [ ".Ch$setMutationRate", "Chromosome$setMutationRate", "setMutationRate" ] }, { "page": "setMutationType", "title": "SLiM method setMutationType", "concept": [ "Mutation" ], "topics": [ ".M$setMutationType", "Mutation$setMutationType", "setMutationType" ] }, { "page": "setRecombinationRate", "title": "SLiM method setRecombinationRate", "concept": [ "Chromosome" ], "topics": [ ".Ch$setRecombinationRate", "Chromosome$setRecombinationRate", "setRecombinationRate" ] }, { "page": "setSelectionCoeff", "title": "SLiM method setSelectionCoeff", "concept": [ "Mutation" ], "topics": [ ".M$setSelectionCoeff", "Mutation$setSelectionCoeff", "setSelectionCoeff" ] }, { "page": "setSelfingRate", "title": "SLiM method setSelfingRate", "concept": [ "Subpopulation" ], "topics": [ ".P$setSelfingRate", "setSelfingRate", "Subpopulation$setSelfingRate" ] }, { "page": "setSexRatio", "title": "SLiM method setSexRatio", "concept": [ "Subpopulation" ], "topics": [ ".P$setSexRatio", "setSexRatio", "Subpopulation$setSexRatio" ] }, { "page": "setSpatialBounds", "title": "SLiM method setSpatialBounds", "concept": [ "Subpopulation" ], "topics": [ ".P$setSpatialBounds", "setSpatialBounds", "Subpopulation$setSpatialBounds" ] }, { "page": "setSpatialPosition", "title": "SLiM method setSpatialPosition", "concept": [ "Individual" ], "topics": [ ".I$setSpatialPosition", "Individual$setSpatialPosition", "setSpatialPosition" ] }, { "page": "setSubpopulationSize", "title": "SLiM method setSubpopulationSize", "concept": [ "Subpopulation" ], "topics": [ ".P$setSubpopulationSize", "setSubpopulationSize", "Subpopulation$setSubpopulationSize" ] }, { "page": "setSuppliedValue", "title": "SLiM method setSuppliedValue", "concept": [ "LogFile" ], "topics": [ ".LF$setSuppliedValue", "LogFile$setSuppliedValue", "setSuppliedValue" ] }, { "page": "setValue", "title": "SLiM method setValue", "concept": [ "LogFile" ], "topics": [ ".LF$setValue", "LogFile$setValue", "setValue" ] }, { "page": "SLiMgui_Class", "title": "SLiMgui", "concept": [ "SLiMgui" ], "topics": [ "SG", "SLiMgui" ] }, { "page": "sharedParentCount", "title": "SLiM method sharedParentCount", "concept": [ "Individual" ], "topics": [ ".I$sharedParentCount", "Individual$sharedParentCount", "sharedParentCount" ] }, { "page": "simulationFinished", "title": "SLiM method simulationFinished", "concept": [ "Community", "Species" ], "topics": [ ".Co$simulationFinished", ".Sp$simulationFinished", "Community$simulationFinished", "simulationFinished", "Species$simulationFinished" ] }, { "page": "skipTick", "title": "SLiM method skipTick", "concept": [ "Species" ], "topics": [ ".Sp$skipTick", "skipTick", "Species$skipTick" ] }, { "page": "slim_block", "title": "Setup a SLiM code block", "topics": [ "slim_block" ] }, { "page": "slim_block_add_subpops", "title": "Generate a code block that just adds subpopulations to a SLiM simulation", "topics": [ "slim_block_add_subpops" ] }, { "page": "slim_block_finish", "title": "Generate simulationFinished Block", "topics": [ "slim_block_finish" ] }, { "page": "slim_block_init_minimal", "title": "Generate minimal initialize() block", "topics": [ "slim_block_init_minimal" ] }, { "page": "slim_block_progress", "title": "Insert slim_block to track progress when using slim_run", "topics": [ "slim_block_progress" ] }, { "page": "slim_callbacks", "title": "SLiM Callbacks", "concept": [ "callbacks" ], "topics": [ "slim_callbacks" ] }, { "page": "slim_classes", "title": "SLiM Classes", "topics": [ "slim_classes" ] }, { "page": "slim_code_Rify", "title": "Rify some SLiM code", "topics": [ "slim_code_Rify" ] }, { "page": "slim_code_SLiMify", "title": "Rify some SLiM code", "topics": [ "slim_code_SLiMify" ] }, { "page": "slim_extract_full", "title": "Extract Elements from SLiM's outputFull()", "topics": [ "slim_extract_full" ] }, { "page": "slim_extract_genlight", "title": "Extract data into a genlight object", "topics": [ "slim_extract_genlight" ] }, { "page": "slim_extract_genome", "title": "Extract Elements from SLiM's output() for genomes", "topics": [ "slim_extract_genome" ] }, { "page": "slim_extract_output_data", "title": "Extract data produced by SLiM", "topics": [ "slim_extract_output_data" ] }, { "page": "slim_file", "title": "Make sure a file name is compatible with using in a SLiM script.", "topics": [ "slim_file" ] }, { "page": "slim_function", "title": "Specify an Eidos function to be included in the SLiM script", "topics": [ "slim_function" ] }, { "page": "slim_get_recipe", "title": "Get a SLiM recipe", "topics": [ "slim_get_recipe" ] }, { "page": "slim_get_recipes", "title": "Get a list of SLiM recipes (as text)", "topics": [ "slim_get_recipes" ] }, { "page": "slim_install_path", "title": "Find the SLiM executable path `slimr` is using", "topics": [ "slim_install_path" ] }, { "page": "slim_is_avail", "title": "Check if SLiM is installed and 'slimr' can find it", "topics": [ "slim_is_avail" ] }, { "page": "slim_load_globals", "title": "Load SLiM Globals into R Global environment", "topics": [ "slim_load_globals" ] }, { "page": "slim_make_pop_input", "title": "Create a file to initialise a population in SLiM", "topics": [ "slim_make_pop_input" ] }, { "page": "slim_open", "title": "Title", "topics": [ "slim_open" ] }, { "page": "slim_recipes", "title": "Dataset of all recipes available in SLiM", "topics": [ "slim_recipes" ] }, { "page": "slim_results_to_data", "title": "Convert output data from a slimr_results object to a tibble", "topics": [ "slim_results_to_data" ] }, { "page": "slim_run", "title": "Run a SLiM script from R", "topics": [ "slim_run", "slim_run.character", "slim_run.slimr_script", "slim_run.slimr_script_coll" ] }, { "page": "slim_script", "title": "Create a SLiMR script", "topics": [ "slim_script" ] }, { "page": "slim_script_duration", "title": "Set the duration of a slimr_script", "topics": [ "slim_script_duration" ] }, { "page": "slim_script_render", "title": "Render a SLiM script with special slimrlang formatting", "topics": [ "slim_script_render" ] }, { "page": "slim_script_render_dots", "title": "Version of `slim_script_render()` that takes dots (named arguments) instead of a template list", "topics": [ "slim_script_render_dots" ] }, { "page": "slim_setup", "title": "Attempt to install and / or setup SLiM for use with slimr", "topics": [ "slim_setup" ] }, { "page": "slim_template_info", "title": "Get information on templating in a slimr_script", "topics": [ "slim_template_info" ] }, { "page": "slim_unload_globals", "title": "Unload SLiM Globals from R Global environment", "topics": [ "slim_unload_globals" ] }, { "page": "slim_version", "title": "Find out what version of SLiM is being used by 'slimr'", "topics": [ "slim_version" ] }, { "page": "slimr_clip_original", "title": "Copy original slimrlang code used to create a slimr_script object to the clipboard", "topics": [ "slimr_clip_original" ] }, { "page": "slimr_code", "title": "Create a 'slimr_code' object", "topics": [ "slimr_code" ] }, { "page": "slimr_name", "title": "Convert a string to a SLiM object name", "topics": [ "slimr_name" ] }, { "page": "slimr_open_original", "title": "Open original slimrlang code used to create a slimr_script object in a new document", "topics": [ "slimr_open_original" ] }, { "page": "slimr_script_coll", "title": "Make a new 'slimr_script_coll' object", "topics": [ "slimr_script_coll" ] }, { "page": "slimr_write", "title": "Write a slimr_script object to a text file", "topics": [ "slimr_write" ] }, { "page": "SpatialMap_Class", "title": "SpatialMap", "concept": [ "SpatialMap" ], "topics": [ "SM", "SpatialMap" ] }, { "page": "smooth", "title": "SLiM method smooth", "concept": [ "SpatialMap" ], "topics": [ ".SM$smooth", "smooth", "SpatialMap$smooth" ] }, { "page": "Species_Class", "title": "Species", "concept": [ "Species" ], "topics": [ "Sp", "Species" ] }, { "page": "spatialMapColor", "title": "SLiM method spatialMapColor", "concept": [ "Subpopulation" ], "topics": [ ".P$spatialMapColor", "spatialMapColor", "Subpopulation$spatialMapColor" ] }, { "page": "spatialMapImage", "title": "SLiM method spatialMapImage", "concept": [ "Subpopulation" ], "topics": [ ".P$spatialMapImage", "spatialMapImage", "Subpopulation$spatialMapImage" ] }, { "page": "spatialMapValue", "title": "SLiM method spatialMapValue", "concept": [ "Subpopulation" ], "topics": [ ".P$spatialMapValue", "spatialMapValue", "Subpopulation$spatialMapValue" ] }, { "page": "speciesWithIDs", "title": "SLiM method speciesWithIDs", "concept": [ "Community" ], "topics": [ ".Co$speciesWithIDs", "Community$speciesWithIDs", "speciesWithIDs" ] }, { "page": "SLiMSim_Class", "title": "SLiMSim was a class used prior to v4.0 in SLiM. It remains in `slimr` for backwards compatibility but its use is now deprecated.", "topics": [ "SS" ] }, { "page": "strength", "title": "SLiM method strength", "concept": [ "InteractionType" ], "topics": [ ".IT$strength", "InteractionType$strength", "strength" ] }, { "page": "subpopulationsWithIDs", "title": "SLiM method subpopulationsWithIDs", "concept": [ "Community" ], "topics": [ ".Co$subpopulationsWithIDs", "Community$subpopulationsWithIDs", "subpopulationsWithIDs" ] }, { "page": "subsetIndividuals", "title": "SLiM method subsetIndividuals", "concept": [ "Subpopulation" ], "topics": [ ".P$subsetIndividuals", "Subpopulation$subsetIndividuals", "subsetIndividuals" ] }, { "page": "subsetMutations", "title": "SLiM method subsetMutations", "concept": [ "Species" ], "topics": [ ".Sp$subsetMutations", "Species$subsetMutations", "subsetMutations" ] }, { "page": "subtract", "title": "SLiM method subtract", "concept": [ "SpatialMap" ], "topics": [ ".SM$subtract", "SpatialMap$subtract", 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