core_commons.R 13.5 KB
Newer Older
Holger Brandl's avatar
Holger Brandl committed
1 2 3 4
########################################################################################################################
## set a default cran r mirror  and customize environment

#cat(".Rprofile: Setting Goettingen repository\n")
Holger Brandl's avatar
Holger Brandl committed
5 6
#todo consider to use chooseCRANmirror(graphics=FALSE, ind=10) instead

Holger Brandl's avatar
Holger Brandl committed
7 8 9 10 11 12 13 14 15 16 17 18
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)

19 20 21 22 23
## 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
Holger Brandl's avatar
Holger Brandl committed
24
#options(dplyr.width = 280); options(width=280) ## width
25

Holger Brandl's avatar
Holger Brandl committed
26 27 28
# for sqldf to avoid the use of tckl
options(gsubfn.engine = "R")

Holger Brandl's avatar
Holger Brandl committed
29

Holger Brandl's avatar
Holger Brandl committed
30
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
31
## automatic package installation
Holger Brandl's avatar
Holger Brandl committed
32

33
require_auto <-  function(x){
34 35
    warning("require_auto is deprecated, use loadpack() instead")

Holger Brandl's avatar
Holger Brandl committed
36 37 38 39 40
    x <- as.character(substitute(x))

    if(isTRUE(x %in% .packages(all.available=TRUE))) {
        eval(parse(text=paste("require(", x, ",  quietly=T)", sep="")))
    } else {
41
        #        update.packages(ask=F) # update dependencies, if any.
Holger Brandl's avatar
Holger Brandl committed
42 43 44 45 46 47 48
        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")
49
        #        biocLite(character(), ask=FALSE) # update dependencies, if any.
50
        eval(parse(text=paste("biocLite('", x, "', ask=FALSE)", sep="")))
Holger Brandl's avatar
Holger Brandl committed
51 52 53 54
        eval(parse(text=paste("require(", x, ",  quietly=T)", sep="")))
    }
}

55
## externalized installer to also allow for installation without loading
Holger Brandl's avatar
Holger Brandl committed
56
.inst_pack <- function(x){
57 58 59 60 61 62 63 64 65 66 67 68 69 70
    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="")))
        }
    }
71 72
}

Holger Brandl's avatar
Holger Brandl committed
73 74 75 76 77 78 79 80 81
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="")))
}

82
loadpack <-  function(x, warn_conflicts=T){
Holger Brandl's avatar
Holger Brandl committed
83 84
    warning("DEPRECATED Use load_pack() instead")

85 86
    x <- as.character(substitute(x));

Holger Brandl's avatar
Holger Brandl committed
87
   .inst_pack(x)
88 89

    ## load it using a library function so that loadpack errors if package is still not ins
Holger Brandl's avatar
Holger Brandl committed
90
    eval(parse(text=paste("library(", x, ",  quietly=T, warn.conflicts=", warn_conflicts, ")", sep="")))
91 92
}

93 94 95 96 97 98
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")
Holger Brandl's avatar
Holger Brandl committed
99

Holger Brandl's avatar
Holger Brandl committed
100
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
101
## load core packages
Holger Brandl's avatar
Holger Brandl committed
102

103 104 105
loadpack(plyr)
loadpack(stringr)
loadpack(reshape2)
106
#loadpack(reshape2, quietly=T, warn_conflicts=F)
Holger Brandl's avatar
Holger Brandl committed
107

Holger Brandl's avatar
Holger Brandl committed
108
## load on purpose after plyr
109 110 111
loadpack(dplyr, warn_conflicts=F)
loadpack(magrittr, warn_conflicts=F)
loadpack(tidyr, warn_conflicts=F)
112

Holger Brandl's avatar
Holger Brandl committed
113
## needed for caching
114 115 116 117
loadpack(digest)
loadpack(readr)
suppressWarnings(loadpack(readxl)) ## supress differring build number
#loadpack(readxl) ## supress differring build number
118 119 120


## common plotting requirements since they are omnipresent
121
loadpack(ggplot2)
122
loadpack(scales, warn_conflicts=F)
123
loadpack(grid)
124

Holger Brandl's avatar
Holger Brandl committed
125
## for table exploration without using Rstudio
126
loadpack(DT)
Holger Brandl's avatar
Holger Brandl committed
127

Holger Brandl's avatar
Holger Brandl committed
128 129

## moved into datatable_commons because replaced almost everywhere with dplyr
130
#loadpack(data.table)
Holger Brandl's avatar
Holger Brandl committed
131 132 133 134 135




########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
136
#### Convenience aliases
Holger Brandl's avatar
Holger Brandl committed
137 138


Holger Brandl's avatar
Holger Brandl committed
139
echo <- function(...) cat(paste(...), fill=T)
Holger Brandl's avatar
Holger Brandl committed
140 141 142 143

ac <- function(...) as.character(...)

# string concatenation without space gaps (could/should use paste0 instead)
Holger Brandl's avatar
Holger Brandl committed
144 145
## Deprecated: use paste0 instead
#concat <- function(...) paste(..., sep="")
Holger Brandl's avatar
Holger Brandl committed
146 147 148 149 150

unlen <- function(x) length(unique(x))

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

Holger Brandl's avatar
Holger Brandl committed
151 152
as.df <- function(dt) as.data.frame(dt)

Holger Brandl's avatar
Holger Brandl committed
153

Holger Brandl's avatar
Holger Brandl committed
154 155 156 157 158 159 160 161 162 163
########################################################################################################################
#### data.frame manipulation


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

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



Holger Brandl's avatar
Holger Brandl committed
164 165 166
#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)

Holger Brandl's avatar
Holger Brandl committed
167 168

rownames2column <- function(df, colname){
169 170
    warning("DEPRECATED Use dplyr::add_rownames directly")
    add_rownames(df, var=colname)
Holger Brandl's avatar
Holger Brandl committed
171 172 173 174
}


column2rownames<- function(df, colname){
175
    #browser()
Holger Brandl's avatar
Holger Brandl committed
176 177 178
    ## force into df to avoid dplyr problems
    df <- as.df(df)

Holger Brandl's avatar
Holger Brandl committed
179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194
    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))]
}


Holger Brandl's avatar
Holger Brandl committed
195 196
#http://astrostatistics.psu.edu/datasets/R/html/base/html/formals.html
set_names <- function(df, ...){
197
    #browser()
Holger Brandl's avatar
Holger Brandl committed
198
    newnames <- as.character(unlist(list(...)))
199 200 201 202

    ## automatically convert matrices to data.frames (otherwise the names set would fail
    if(is.matrix(df)) df %<>% as.data.frame()

203
    names(df) <- newnames;
Holger Brandl's avatar
Holger Brandl committed
204 205
    return(df)
}
Holger Brandl's avatar
Holger Brandl committed
206 207
#iris %>% set_names(c("setosa", "hallo")) %>% head
#iris %>% set_names("setosa", "hallo") %>% head
Holger Brandl's avatar
Holger Brandl committed
208 209


210 211 212 213 214 215
rify_names  <- function(df){
    warning("DEPRECATED: use pretty_columns instead");
    names(df) <- names(df) %>% str_replace_all(c(" "="_", "-"="_"));
    df
}

216 217 218 219 220 221 222 223
pretty_columns  <- function(df){
    names(df) <- names(df) %>%
        str_replace_all("[#=.()-]+", "_") %>%
        str_replace("[_]+$", "") %>%
        str_replace("^[_]+", "") %>%
        tolower;
    df
}
Holger Brandl's avatar
Holger Brandl committed
224 225


Holger Brandl's avatar
Holger Brandl committed
226 227
head_html <- function(df, n=5) head(df, n) %>% knitr::kable(format="html") %>% print()

Holger Brandl's avatar
Holger Brandl committed
228 229
print_head <- function(df, desc=NULL){
    print(head(df))
Holger Brandl's avatar
Holger Brandl committed
230
    print(nrow(df))
Holger Brandl's avatar
Holger Brandl committed
231 232 233 234 235
    return(df)
}


fac2char <- function(mydata, convert=names(mydata)[sapply(mydata, is.factor)]){
Holger Brandl's avatar
Holger Brandl committed
236 237 238
    if(length(convert)==0){
        return(mydata)
    }
Holger Brandl's avatar
Holger Brandl committed
239 240 241 242 243 244 245 246 247 248 249 250 251

    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)
}

Holger Brandl's avatar
Holger Brandl committed
252
## replace R within pipe change just use ... %>% do(replaceNA(0)) %>% ...
Holger Brandl's avatar
Holger Brandl committed
253
replaceNA <- function(x, withValue) { x[is.na(x)] <- withValue; x }
Holger Brandl's avatar
Holger Brandl committed
254

Holger Brandl's avatar
Holger Brandl committed
255

Holger Brandl's avatar
Holger Brandl committed
256

Holger Brandl's avatar
Holger Brandl committed
257
## todo still needed
Holger Brandl's avatar
Holger Brandl committed
258
safe_ifelse <- function(cond, yes, no) {
Holger Brandl's avatar
Holger Brandl committed
259 260 261 262 263 264
#browser()
    isfacOrChar <- function(x) class(x)  %in% c("factor", "character")

    if (isfacOrChar(yes) | isfacOrChar(no)) {
        yes <- ac(yes)
        no <- ac(no)
265
    }
Holger Brandl's avatar
Holger Brandl committed
266 267

    ifelse(cond,yes,no)
Holger Brandl's avatar
Holger Brandl committed
268 269
}

Holger Brandl's avatar
Holger Brandl committed
270

Holger Brandl's avatar
Holger Brandl committed
271
## for na instead use mutate_each with:
Holger Brandl's avatar
Holger Brandl committed
272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299
#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))
#}


Holger Brandl's avatar
Holger Brandl committed
300 301 302
## see http://stackoverflow.com/questions/24172111/change-the-blank-cells-to-na/33952598#33952598


303 304 305 306 307 308 309
reload_dplyr <- function(){
    unloadNamespace('tidyr')
    unloadNamespace('dplyr')
    require(tidyr);require(dplyr)
}


310
## from http://stackoverflow.com/questions/7505547/detach-all-packages-while-working-in-r
311
unload_packages <- function() {
312 313 314 315 316
    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)
}
Holger Brandl's avatar
Holger Brandl committed
317 318


Holger Brandl's avatar
Holger Brandl committed
319 320 321 322
## workaround for biomart
## Deprecated: load dplyr after biomart to avoid this problem
#dselect <- function(...) dplyr::select(...)

Holger Brandl's avatar
Holger Brandl committed
323

Holger Brandl's avatar
Holger Brandl committed
324
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
325
#### Result Caching for long running tasks
Holger Brandl's avatar
Holger Brandl committed
326

Holger Brandl's avatar
Holger Brandl committed
327 328
## related: http://cran.r-project.org/web/packages/R.cache/R.cache.pdf

329
cache_it <- function(expr, filePrefix="cache"){
330
    cacheFile <- paste0(filePrefix, "_", substr(digest::digest(deparse(expr)), 1,6)) %>% paste0(".", ., ".RData")
Holger Brandl's avatar
Holger Brandl committed
331

Holger Brandl's avatar
Holger Brandl committed
332 333 334 335 336 337 338 339 340 341 342
    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")
Holger Brandl's avatar
Holger Brandl committed
343 344
#mydata <- quote(iris %>% filter(Species=="setosa")) %>% cache_it()
#mydata <- quote( { print("evaluate expr"); iris %>% filter(Species=="setosa") } ) %>% cache_it()
Holger Brandl's avatar
Holger Brandl committed
345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362

########################################################################################################################
#### 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)))


Holger Brandl's avatar
Holger Brandl committed
363
## tbd: it would be more efficient to use Reduce here (see http://stackoverflow.com/questions/34344214/how-to-join-multiple-data-frames-using-dplyr)
Holger Brandl's avatar
Holger Brandl committed
364 365 366 367 368 369 370 371 372 373
rmerge <- function(LDF, by, ...){
    DF <- LDF[[1]]
    for (i in 2:length(LDF)) {
        DF <- merge(DF, LDF[[i]], by=by)
    }
    DF
}



Holger Brandl's avatar
Holger Brandl committed
374 375
## Deprecated: use trim_ext instead
trimEnd <- function(fileNames, ...) trim_ext(fileNames, ...)
Holger Brandl's avatar
Holger Brandl committed
376

Holger Brandl's avatar
Holger Brandl committed
377
trim_ext <-function(fileNames, exts=c()){
Holger Brandl's avatar
Holger Brandl committed
378 379 380 381 382 383 384
    for(fileExt in exts){
        fileNames <- str_replace(fileNames, paste(fileExt, "$",sep=""), "")
    }

    fileNames
}

Holger Brandl's avatar
Holger Brandl committed
385
## DEPRECATED Use write_tsv instead
Holger Brandl's avatar
Holger Brandl committed
386 387
write.delim <- function(df, file, header=TRUE,...){
    write.table(df, file, row.names=FALSE, col.names=header, sep="\t", ...)
Holger Brandl's avatar
Holger Brandl committed
388 389 390 391 392 393 394 395 396 397
}

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

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


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

Holger Brandl's avatar
Holger Brandl committed
398

Holger Brandl's avatar
Holger Brandl committed
399
# improved list of objects
Holger Brandl's avatar
Holger Brandl committed
400 401
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)))
Holger Brandl's avatar
Holger Brandl committed
402
    names <- ls(pos = pos, pattern = pattern)
Holger Brandl's avatar
Holger Brandl committed
403

Holger Brandl's avatar
Holger Brandl committed
404 405 406 407 408
    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)
Holger Brandl's avatar
Holger Brandl committed
409

410
    as.numeric(dim(x))[1:2]))
Holger Brandl's avatar
Holger Brandl committed
411 412
    vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
    obj.dim[vec, 1] <- napply(names, length)[vec]
Holger Brandl's avatar
Holger Brandl committed
413

Holger Brandl's avatar
Holger Brandl committed
414 415
    out <- data.frame(obj.type, obj.size, obj.dim)
    names(out) <- c("Type", "Size", "Rows", "Columns")
Holger Brandl's avatar
Holger Brandl committed
416

Holger Brandl's avatar
Holger Brandl committed
417
    if (!missing(order.by))
418
    out <- out[order(out[[order.by]], decreasing=decreasing), ]
Holger Brandl's avatar
Holger Brandl committed
419 420 421

    if (head) out <- head(out, n)

Holger Brandl's avatar
Holger Brandl committed
422 423 424 425 426
    out <- transform(out, var_name=rownames(out))
    rownames(out) <- NULL
    arrange(out, Size)
}

Holger Brandl's avatar
Holger Brandl committed
427
# shorthand that just shows top 1 results
Holger Brandl's avatar
Holger Brandl committed
428 429 430 431
lsosh <- function(..., n=10) {
    lsos(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}

Holger Brandl's avatar
Holger Brandl committed
432 433 434 435 436 437 438 439 440 441
########################################################################################################################
### 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))

Holger Brandl's avatar
Holger Brandl committed
442
se <- function(x) sd(x, na.rm=TRUE) / sqrt(sum(!is.na(x)))
443 444 445 446 447 448 449 450 451


########################################################################################################################
### Misc

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