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> ### > attach(NULL, name = "CheckExEnv") > assign(".CheckExEnv", as.environment(2), pos = length(search())) # base > ## add some hooks to label plot pages for base and grid graphics > setHook("plot.new", ".newplot.hook") > setHook("persp", ".newplot.hook") > setHook("grid.newpage", ".gridplot.hook") > > assign("cleanEx", + function(env = .GlobalEnv) { + rm(list = ls(envir = env, all.names = TRUE), envir = env) + RNGkind("default", "default") + set.seed(1) + options(warn = 1) + delayedAssign("T", stop("T used instead of TRUE"), + assign.env = .CheckExEnv) + delayedAssign("F", stop("F used instead of FALSE"), + assign.env = .CheckExEnv) + sch <- search() + newitems <- sch[! sch %in% .oldSearch] + for(item in rev(newitems)) + eval(substitute(detach(item), list(item=item))) + missitems <- .oldSearch[! .oldSearch %in% sch] + if(length(missitems)) + warning("items ", paste(missitems, collapse=", "), + " have been removed from the search path") + }, + env = .CheckExEnv) > assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now > assign("ptime", proc.time(), env = .CheckExEnv) > grDevices::postscript("qtlDesign-Examples.ps") > assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv) > options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly")) > options(warn = 1) > library('qtlDesign') > > assign(".oldSearch", search(), env = .CheckExEnv) > assign(".oldNS", loadedNamespaces(), env = .CheckExEnv) > cleanEx(); ..nameEx <- "fracmiss" > > ### * fracmiss > > flush(stderr()); flush(stdout()) > > ### Name: fracmiss > ### Title: Calculate fraction of missing information for single observation > ### Aliases: fracmiss > ### Keywords: design > > ### ** Examples > > fracmiss(1,0) [1] 0.2419707 > fracmiss(1,0,1,0.1) [1] 0.04355473 > fracmiss(1,0,c(1,1),c(0.1,0.1)) [1] 0.004780397 > > > > cleanEx(); ..nameEx <- "info.null" > > ### * info.null > > flush(stderr()); flush(stdout()) > > ### Name: Information under null > ### Title: Information under null hypothesis of equal means > ### Aliases: info.null info.bc.null info.f2.null deflate.bc deflate.f2 > ### Keywords: design > > ### ** Examples > > info.null(0.5) [1] 0.928674 > info.bc.null(0.5) [1] 0.928674 > info.f2.null(0.5) $add [1] 0.928674 $dom [1] 0.928674 > info.bc.null(0.5,0.1) [1] 0.825488 > info.f2.null(0.5,0.1) $add [1] 0.825488 $dom [1] 0.729293 > deflate.bc(0.1) [1] 0.8888889 > deflate.f2(0.1) $add [1] 0.8888889 $dom [1] 0.7853056 > > > > cleanEx(); ..nameEx <- "info2cost.bc.null" > > ### * info2cost.bc.null > > flush(stderr()); flush(stdout()) > > ### Name: Information-cost ratios > ### Title: Functions to calculate information-cost ratios, and to find > ### optimal selection fractions > ### Aliases: info2cost.bc.null optalpha.bc > ### Keywords: design > > ### ** Examples > > info2cost.bc.null(0.5,1) [1] 0.619116 > info2cost.bc.null(0.5,1,0.1,14.50) [1] 0.01137571 > optalpha.bc(1) [1] 0.4298516 > optalpha.bc(0.001,0.1,14.50) [1] 0.7187163 > > > > cleanEx(); ..nameEx <- "missinfo" > > ### * missinfo > > flush(stderr()); flush(stdout()) > > ### Name: missinfo > ### Title: Calculate fraction of missing information by numerical > ### integration > ### Aliases: missinfo > ### Keywords: design > > ### ** Examples > > missinfo(0,0.5) [1] 0.0713259 > missinfo(0,0.5,0.1) [1] 0.4056486 > missinfo(0,0.5,c(0.1,0.1)) [1] 0.2751812 > > > > cleanEx(); ..nameEx <- "missinfo.sim" > > ### * missinfo.sim > > flush(stderr()); flush(stdout()) > > ### Name: missinfo.sim > ### Title: Calculate fraction of missing information by simulation > ### Aliases: missinfo.sim > ### Keywords: design > > ### ** Examples > > missinfo.sim(0,10000,0.5) [1] 0.07093653 > missinfo.sim(0,10000,0.5,0.1) [1] 0.4022543 > missinfo.sim(0,10000,0.5,c(0.1,0.1)) [1] 0.5121268 > > > > cleanEx(); ..nameEx <- "power.bc" > > ### * power.bc > > flush(stderr()); flush(stdout()) > > ### Name: power.bc > ### Title: Power calculations for Backcross > ### Aliases: power.bc detectable.bc > ### Keywords: design > > ### ** Examples > > power.bc(100,0.2,alpha=0.5,theta=0.1) [1] 0.7955686 > detectable.bc(100,0.8,alpha=0.5,theta=0.1) [1] 0.2011046 > > > > cleanEx(); ..nameEx <- "power.f2" > > ### * power.f2 > > flush(stderr()); flush(stdout()) > > ### Name: power.f2 > ### Title: Power calculations for F2 intercross > ### Aliases: power.f2 detectable.f2 > ### Keywords: design > > ### ** Examples > > power.f2(100,c(3/4,0),alpha=0.5,theta=0.1) [1] 0.8888524 > detectable.f2(100,alpha=0.5,theta=0.1) [1] 0.1923609 > > > > cleanEx(); ..nameEx <- "qtlDesign-internal" > > ### * qtlDesign-internal > > flush(stderr()); flush(stdout()) > > ### Name: qtlDesign-internal > ### Title: qtlDesign-internal > ### Aliases: fracmiss0 fracmiss1 fracmiss2 missinfo0 missinfo1 missinfo2 > ### missinfo0.sim missinfo1.sim missinfo2.sim > ### Keywords: internal > > ### ** Examples > > > > > cleanEx(); ..nameEx <- "utility" > > ### * utility > > flush(stderr()); flush(stdout()) > > ### Name: Utility > ### Title: Utility functions > ### Aliases: recomb genetic.dist pmixnorm prop2delta.bc delta2prop.bc > ### prop2delta.f2 delta2prop.f2 prop2gv gv2prop > ### Keywords: utilities > > ### ** Examples > > recomb(0.1) [1] 0.09063462 > genetic.dist(0.1) [1] 0.1115718 > prop2delta.bc(0.1) [1] 0.3333333 > delta2prop.bc(0.1) [1] 0.00990099 > > > > ### *