core_commons.R 13.7 KB
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########################################################################################################################
## set a default cran r mirror  and customize environment

#cat(".Rprofile: Setting Goettingen repository\n")
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#todo consider to use chooseCRANmirror(graphics=FALSE, ind=10) instead

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r = getOption("repos") # hard code the UK repo for CRAN

r["CRAN"] = "http://ftp5.gwdg.de/pub/misc/cran/"
options(repos = r)
rm(r)


## user browser for help
options(help_type="html")

## plot more characters per line
options(width=150)

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## adjust dplyr printing settings
## http://stackoverflow.com/questions/22471256/overriding-variables-not-shown-in-dplyr-to-display-all-columns-from-df
## http://stackoverflow.com/questions/29396111/dplyrtbl-df-fill-whole-screen
options(dplyr.print_max = 20) ## num rows
options(dplyr.width = 130) ## width
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#options(dplyr.width = 280); options(width=280) ## width
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# for sqldf to avoid the use of tckl
options(gsubfn.engine = "R")

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########################################################################################################################
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## automatic package installation
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require_auto <-  function(x){
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    warning("require_auto is deprecated, use loadpack() instead")

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    x <- as.character(substitute(x))

    if(isTRUE(x %in% .packages(all.available=TRUE))) {
        eval(parse(text=paste("require(", x, ",  quietly=T)", sep="")))
    } else {
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        #        update.packages(ask=F) # update dependencies, if any.
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        eval(parse(text=paste("install.packages('", x, "')", sep="")))
    }

    if(isTRUE(x %in% .packages(all.available=TRUE))) {
        eval(parse(text=paste("require(", x, ",  quietly=T)", sep="")))
    } else {
        source("http://bioconductor.org/biocLite.R")
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        #        biocLite(character(), ask=FALSE) # update dependencies, if any.
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        eval(parse(text=paste("biocLite('", x, "', ask=FALSE)", sep="")))
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        eval(parse(text=paste("require(", x, ",  quietly=T)", sep="")))
    }
}

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## externalized installer to also allow for installation without loading
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.inst_pack <- function(x){
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    if(!isTRUE(x %in% .packages(all.available=TRUE)) && any(available.packages()[,1]==x)) {
        # update.packages(ask=F) # update dependencies, if any.
        eval(parse(text=paste("install.packages('", x, "')", sep="")))
    }

    ## if it's still missing check if it's on bioconductor
    if(!isTRUE(x %in% .packages(all.available=TRUE))) {
        bcPackages <- as.vector(read.dcf(url("https://bioconductor.org/packages/3.3/bioc/src/contrib/PACKAGES"), "Package"))

        if(any(bcPackages==x)){
            source("http://bioconductor.org/biocLite.R")
            eval(parse(text=paste("biocLite('", x, "', ask=FALSE)", sep="")))
        }
    }
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}

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load_pack <-  function(x, warn_conflicts=T){
    x <- as.character(substitute(x));

   .inst_pack(x)

    ## load it using a library function so that loadpack errors if package is still not ins
    eval(parse(text=paste("library(", x, ",  quietly=T, warn.conflicts=", warn_conflicts, ")", sep="")))
}

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loadpack <-  function(x, warn_conflicts=T){
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    warning("DEPRECATED Use load_pack() instead")

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    x <- as.character(substitute(x));

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   .inst_pack(x)
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    ## load it using a library function so that loadpack errors if package is still not ins
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    eval(parse(text=paste("library(", x, ",  quietly=T, warn.conflicts=", warn_conflicts, ")", sep="")))
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}

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check_version = function(pkg_name, min_version) {
    cur_version = packageVersion(pkg_name)
    if(cur_version < min_version) stop(sprintf("Package %s needs a newer version,
               found %s, need at least %s", pkg_name, cur_version, min_version))
}
#check_version("dplyr", "0.4-1")
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########################################################################################################################
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## load core packages
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loadpack(plyr)
loadpack(stringr)
loadpack(reshape2)
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#loadpack(reshape2, quietly=T, warn_conflicts=F)
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## load on purpose after plyr
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loadpack(dplyr, warn_conflicts=F)
loadpack(magrittr, warn_conflicts=F)
loadpack(tidyr, warn_conflicts=F)
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## needed for caching
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loadpack(digest)
loadpack(readr)
suppressWarnings(loadpack(readxl)) ## supress differring build number
#loadpack(readxl) ## supress differring build number
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## common plotting requirements since they are omnipresent
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loadpack(ggplot2)
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loadpack(scales, warn_conflicts=F)
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loadpack(grid)
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## for table exploration without using Rstudio
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loadpack(DT)
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## moved into datatable_commons because replaced almost everywhere with dplyr
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#loadpack(data.table)
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########################################################################################################################
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#### Convenience aliases
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echo <- function(...) cat(paste(...), fill=T)
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ac <- function(...) as.character(...)

# string concatenation without space gaps (could/should use paste0 instead)
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## Deprecated: use paste0 instead
#concat <- function(...) paste(..., sep="")
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unlen <- function(x) length(unique(x))

pp <- function(dat) page(dat, method = "print")

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as.df <- function(dt) as.data.frame(dt)

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########################################################################################################################
#### data.frame manipulation


shuffle <- function(df) df[sample(nrow(df)),]

first <- function(x, n=1) head(x,n)



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#vec2df <- function(namedVec) namedVec %>% {data.frame(name=names(.), value=., row.names=NULL)}
vec2df <- function(namedVec) data.frame(name=names(namedVec), value=namedVec, row.names=NULL)

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rownames2column <- function(df, colname){
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    warning("DEPRECATED Use dplyr::add_rownames directly")
    add_rownames(df, var=colname)
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}


column2rownames<- function(df, colname){
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    #browser()
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    ## force into df to avoid dplyr problems
    df <- as.df(df)

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    rownames(df) <- ac(df[,colname])
    df[colname] <- NULL
    return(df)
}

## pushing some columns to the right end of a data.frame
push_right <- function(df, pushColNames){
    df[,c(setdiff(names(df),pushColNames), pushColNames)]
}


push_left <- function(df, pushColNames){
    df[,c(pushColNames, setdiff(names(df),pushColNames))]
}


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#http://astrostatistics.psu.edu/datasets/R/html/base/html/formals.html
set_names <- function(df, ...){
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    #browser()
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    newnames <- as.character(unlist(list(...)))
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    ## automatically convert matrices to data.frames (otherwise the names set would fail
    if(is.matrix(df)) df %<>% as.data.frame()

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    names(df) <- newnames;
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    return(df)
}
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#iris %>% set_names(c("setosa", "hallo")) %>% head
#iris %>% set_names("setosa", "hallo") %>% head
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rify_names  <- function(df){
    warning("DEPRECATED: use pretty_columns instead");
    names(df) <- names(df) %>% str_replace_all(c(" "="_", "-"="_"));
    df
}

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pretty_columns  <- function(df){
    names(df) <- names(df) %>%
        str_replace_all("[#=.()-]+", "_") %>%
        str_replace("[_]+$", "") %>%
        str_replace("^[_]+", "") %>%
        tolower;
    df
}
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head_html <- function(df, n=5) head(df, n) %>% knitr::kable(format="html") %>% print()

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print_head <- function(df, desc=NULL){
    print(head(df))
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    print(nrow(df))
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    return(df)
}


fac2char <- function(mydata, convert=names(mydata)[sapply(mydata, is.factor)]){
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    if(length(convert)==0){
        return(mydata)
    }
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    inputColOrder <- names(mydata)

    convertData <- subset(mydata, select= names(mydata)%in%convert)
    convertData <- as.data.frame(lapply(convertData, as.character), stringsAsFactors = FALSE)

    keepData <-  subset(mydata, select=!(names(mydata)%in%convert))
    newdata <- cbind(convertData, keepData)
    newdata <- newdata[,inputColOrder]

    return(newdata)
}

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## replace R within pipe change just use ... %>% do(replaceNA(0)) %>% ...
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replaceNA <- function(x, withValue) { x[is.na(x)] <- withValue; x }
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## todo still needed since there's if_else in dplyr now
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safe_ifelse <- function(cond, yes, no) {
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#browser()
    isfacOrChar <- function(x) class(x)  %in% c("factor", "character")

    if (isfacOrChar(yes) | isfacOrChar(no)) {
        yes <- ac(yes)
        no <- ac(no)
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    }
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    ifelse(cond,yes,no)
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}

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## for na instead use mutate_each with:
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#empty_as_na <- function(x) safe_ifelse(x=="", NA, x)
#empty_as_na <- function(x) ifelse(class(x)  %in% c("factor", "character") & x=="", NA, x)
empty_as_na <- function(x){
    if("factor" %in% class(x)) x <- as.character(x) ## since ifelse wont work with factors
    ifelse(as.character(x)!="", x, NA)
}

#if(F){ ## DEBUG of empty_as_na
#cond <- allJobs %>% head %$% submit_time %>% c("")
#empty_as_na( cond)
#cond <- allJobs %>% head %$% resubmission_of
#empty_as_na( cond)
#
#empty_as_na( c(1, 2, NA))
#empty_as_na( c("sdf", "sdf2", NA))
#empty_as_na( c("sdf", "sdf2", ""))
#
#myFac <- as.factor(c("sdf", "sdf2", NA))
#empty_as_na( myFac)
#ifelse(as.character(myFac)!="", myFac, NA)
#
#empty_as_na( c("sdf", "sdf2", ""))
#
#iris[1,1] <- ""
#apply(iris, 2, function(x) gsub("^$|^ $", NA, x))
#}


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## see http://stackoverflow.com/questions/24172111/change-the-blank-cells-to-na/33952598#33952598


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## apply dplyr::filter to df but use filter criterions for cross-tabulation beforehand
filter_count <- function(df, ...){
    print(count(df, ...))
    filter(df, ...)
}


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reload_dplyr <- function(){
    unloadNamespace('tidyr')
    unloadNamespace('dplyr')
    require(tidyr);require(dplyr)
}


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## from http://stackoverflow.com/questions/7505547/detach-all-packages-while-working-in-r
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unload_packages <- function() {
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    basic.packages <- c("package:stats","package:graphics","package:grDevices","package:utils","package:datasets","package:methods","package:base")
    package.list <- search()[ifelse(unlist(gregexpr("package:",search()))==1,TRUE,FALSE)]
    package.list <- setdiff(package.list,basic.packages)
    if (length(package.list)>0)  for (package in package.list) detach(package, character.only=TRUE)
}
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## workaround for biomart
## Deprecated: load dplyr after biomart to avoid this problem
#dselect <- function(...) dplyr::select(...)

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########################################################################################################################
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#### Result Caching for long running tasks
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## related: http://cran.r-project.org/web/packages/R.cache/R.cache.pdf

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cache_it <- function(expr, filePrefix="cache"){
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    cacheFile <- paste0(filePrefix, "_", substr(digest::digest(deparse(expr)), 1,6)) %>% paste0(".", ., ".RData")
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    if(file.exists(cacheFile)){
        local(get(load(cacheFile)))
    } else {
        result <- eval(expr)
        save(result, file=cacheFile)
        result
    }
}

## Examples
#mydata <- quote(iris %>% filter(Species=="setosa")) %>% cache_it("tt")
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#mydata <- quote(iris %>% filter(Species=="setosa")) %>% cache_it()
#mydata <- quote( { print("evaluate expr"); iris %>% filter(Species=="setosa") } ) %>% cache_it()
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########################################################################################################################
#### File System

is.directory <- function(dirname) !is.na(file.info(dirname)$isdir)


mcdir <- function(dirname){
    if(!file.exists(dirname)){
        dir.create(dirname)
    }

    setwd(dirname)
}

locload <- function(fileName) local(get(load(fileName)))


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## tbd: it would be more efficient to use Reduce here (see http://stackoverflow.com/questions/34344214/how-to-join-multiple-data-frames-using-dplyr)
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rmerge <- function(LDF, by, ...){
    DF <- LDF[[1]]
    for (i in 2:length(LDF)) {
        DF <- merge(DF, LDF[[i]], by=by)
    }
    DF
}



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## Deprecated: use trim_ext instead
trimEnd <- function(fileNames, ...) trim_ext(fileNames, ...)
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trim_ext <-function(fileNames, exts=c()){
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    for(fileExt in exts){
        fileNames <- str_replace(fileNames, paste(fileExt, "$",sep=""), "")
    }

    fileNames
}

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## DEPRECATED Use write_tsv instead
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write.delim <- function(df, file, header=TRUE,...){
    write.table(df, file, row.names=FALSE, col.names=header, sep="\t", ...)
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}

rmSomeElements <- function(vec, toDel) vec[!(vec %in% toDel)]

rmLastElement <- function(vec) vec[-length(vec)]


########################################################################################################################
## Memory management

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# improved list of objects
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lsos <- function (pos = 1, pattern, order.by, decreasing=FALSE, head=FALSE, n=5) {
    napply <- function(names, fn) sapply(names, function(x) fn(get(x, pos = pos)))
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    names <- ls(pos = pos, pattern = pattern)
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    obj.class <- napply(names, function(x) as.character(class(x))[1])
    obj.mode <- napply(names, mode)
    obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
    obj.size <- napply(names, object.size)/1000000
    obj.dim <- t(napply(names, function(x)
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    as.numeric(dim(x))[1:2]))
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    vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
    obj.dim[vec, 1] <- napply(names, length)[vec]
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    out <- data.frame(obj.type, obj.size, obj.dim)
    names(out) <- c("Type", "Size", "Rows", "Columns")
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    if (!missing(order.by))
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    out <- out[order(out[[order.by]], decreasing=decreasing), ]
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    if (head) out <- head(out, n)

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    out <- transform(out, var_name=rownames(out))
    rownames(out) <- NULL
    arrange(out, Size)
}

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# shorthand that just shows top 1 results
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lsosh <- function(..., n=10) {
    lsos(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}

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########################################################################################################################
### Statistics


## outlier handling
trim_outliers <- function(values, range=quantile(values, c(0.05, 0.95)))  pmax(range[1], pmin(range[2], values))

## use trim_outliers instead
#limit_range <- function(values, range)  pmax(range[1], pmin(range[2], values))

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se <- function(x) sd(x, na.rm=TRUE) / sqrt(sum(!is.na(x)))
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########################################################################################################################
### Misc

## inspired by http://stackoverflow.com/questions/8343509/better-error-message-for-stopifnot
assert <- function (expr, error) {
    if (! expr) stop(error, call. = FALSE)
}