core_commons.R 9.26 KB
Newer Older
Holger Brandl's avatar
Holger Brandl committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
########################################################################################################################
## set a default cran r mirror  and customize environment

#cat(".Rprofile: Setting Goettingen repository\n")
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)

# for sqldf to avoid the use of tckl
options(gsubfn.engine = "R")

Holger Brandl's avatar
Holger Brandl committed
20

Holger Brandl's avatar
Holger Brandl committed
21
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
22
## automatic package installation
Holger Brandl's avatar
Holger Brandl committed
23

24
require_auto <-  function(x){
Holger Brandl's avatar
Holger Brandl committed
25 26 27 28 29 30 31 32 33 34 35 36 37
    x <- as.character(substitute(x))

    if(isTRUE(x %in% .packages(all.available=TRUE))) {
        eval(parse(text=paste("require(", x, ",  quietly=T)", sep="")))
    } else {
    #        update.packages(ask=F) # update dependencies, if any.
        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")
38
#        biocLite(character(), ask=FALSE) # update dependencies, if any.
39
        eval(parse(text=paste("biocLite('", x, "', ask=FALSE)", sep="")))
Holger Brandl's avatar
Holger Brandl committed
40 41 42 43
        eval(parse(text=paste("require(", x, ",  quietly=T)", sep="")))
    }
}

44 45 46 47 48 49
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
50

Holger Brandl's avatar
Holger Brandl committed
51
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
52
## load core packages
Holger Brandl's avatar
Holger Brandl committed
53

54 55 56 57
require_auto(plyr)
require_auto(stringr)
require_auto(reshape2)
#require_auto(reshape2, quietly=T, warn.conflicts=F)
Holger Brandl's avatar
Holger Brandl committed
58

Holger Brandl's avatar
Holger Brandl committed
59
## load on purpose after plyr
60 61 62
require_auto(dplyr)
require_auto(magrittr)
require_auto(tidyr)
63

Holger Brandl's avatar
Holger Brandl committed
64
## needed for caching
65
require_auto(digest)
Holger Brandl's avatar
Holger Brandl committed
66 67

## moved into datatable_commons because replaced almost everywhere with dplyr
68
#require_auto(data.table)
Holger Brandl's avatar
Holger Brandl committed
69 70 71 72 73




########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
74
#### Convenience aliases
Holger Brandl's avatar
Holger Brandl committed
75 76


Holger Brandl's avatar
Holger Brandl committed
77
echo <- function(...) cat(paste(...), fill=T)
Holger Brandl's avatar
Holger Brandl committed
78 79 80 81

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

# string concatenation without space gaps (could/should use paste0 instead)
Holger Brandl's avatar
Holger Brandl committed
82 83
## Deprecated: use paste0 instead
#concat <- function(...) paste(..., sep="")
Holger Brandl's avatar
Holger Brandl committed
84 85 86 87 88

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

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

Holger Brandl's avatar
Holger Brandl committed
89 90
as.df <- function(dt) as.data.frame(dt)

Holger Brandl's avatar
Holger Brandl committed
91

Holger Brandl's avatar
Holger Brandl committed
92 93 94 95 96 97 98 99 100 101
########################################################################################################################
#### 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
102 103 104
#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
105 106 107 108 109

rownames2column <- function(df, colname){
    df <- as.df(df)
    df$tttt <- rownames(df);
    rownames(df) <- NULL;
Holger Brandl's avatar
Holger Brandl committed
110
    plyr::rename(df, c(tttt=colname))
Holger Brandl's avatar
Holger Brandl committed
111 112 113 114 115
}


column2rownames<- function(df, colname){
#browser()
Holger Brandl's avatar
Holger Brandl committed
116 117 118
    ## force into df to avoid dplyr problems
    df <- as.df(df)

Holger Brandl's avatar
Holger Brandl committed
119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134
    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
135 136 137 138
#http://astrostatistics.psu.edu/datasets/R/html/base/html/formals.html
set_names <- function(df, ...){
#browser()
    newnames <- as.character(unlist(list(...)))
139 140 141 142

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

143
    names(df) <- newnames;
Holger Brandl's avatar
Holger Brandl committed
144 145
    return(df)
}
Holger Brandl's avatar
Holger Brandl committed
146 147
#iris %>% set_names(c("setosa", "hallo")) %>% head
#iris %>% set_names("setosa", "hallo") %>% head
Holger Brandl's avatar
Holger Brandl committed
148 149


Holger Brandl's avatar
Holger Brandl committed
150 151
head_html <- function(df, n=5) head(df, n) %>% knitr::kable(format="html") %>% print()

Holger Brandl's avatar
Holger Brandl committed
152 153
print_head <- function(df, desc=NULL){
    print(head(df))
Holger Brandl's avatar
Holger Brandl committed
154
    print(nrow(df))
Holger Brandl's avatar
Holger Brandl committed
155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174
    return(df)
}


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

    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
175
## replace R within pipe change just use ... %>% do(replaceNA(0)) %>% ...
Holger Brandl's avatar
Holger Brandl committed
176
replaceNA <- function(x, withValue) { x[is.na(x)] <- withValue; x }
Holger Brandl's avatar
Holger Brandl committed
177

Holger Brandl's avatar
Holger Brandl committed
178

Holger Brandl's avatar
Holger Brandl committed
179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201

safe_ifelse <- function(cond, yes, no) {
  class.y <- class(yes)
  if ("factor" %in% class.y) {  # Note the small condition change here
    levels.y = levels(yes)
  }
  X <- ifelse(cond,yes,no)
  if ("factor" %in% class.y) {  # Note the small condition change here
    X = as.factor(X)
    levels(X) = levels.y
  } else {
    class(X) <- class.y
  }
  return(X)
}

## for na instead use mutate_each with:
empty_as_na <- function(x) safe_ifelse(x=="", NA, x)
## see http://stackoverflow.com/questions/24172111/change-the-blank-cells-to-na/33952598#33952598




Holger Brandl's avatar
Holger Brandl committed
202 203 204 205
## workaround for biomart
## Deprecated: load dplyr after biomart to avoid this problem
#dselect <- function(...) dplyr::select(...)

Holger Brandl's avatar
Holger Brandl committed
206

Holger Brandl's avatar
Holger Brandl committed
207
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
208
#### Result Caching for long running tasks
Holger Brandl's avatar
Holger Brandl committed
209

Holger Brandl's avatar
Holger Brandl committed
210 211
## related: http://cran.r-project.org/web/packages/R.cache/R.cache.pdf

212
cache_it <- function(expr, filePrefix="cache"){
213
    cacheFile <- paste0(filePrefix, "_", substr(digest::digest(deparse(expr)), 1,6)) %>% paste0(".", ., ".RData")
Holger Brandl's avatar
Holger Brandl committed
214

Holger Brandl's avatar
Holger Brandl committed
215 216 217 218 219 220 221 222 223 224 225
    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
226 227
#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
228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255

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


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
256 257
## Deprecated: use trim_ext instead
trimEnd <- function(fileNames, ...) trim_ext(fileNames, ...)
Holger Brandl's avatar
Holger Brandl committed
258

Holger Brandl's avatar
Holger Brandl committed
259
trim_ext <-function(fileNames, exts=c()){
Holger Brandl's avatar
Holger Brandl committed
260 261 262 263 264 265 266
    for(fileExt in exts){
        fileNames <- str_replace(fileNames, paste(fileExt, "$",sep=""), "")
    }

    fileNames
}

Holger Brandl's avatar
Holger Brandl committed
267 268
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
269 270 271 272 273 274 275 276 277 278
}

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

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


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

Holger Brandl's avatar
Holger Brandl committed
279

Holger Brandl's avatar
Holger Brandl committed
280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305
# improved list of objects
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)))
    names <- ls(pos = pos, pattern = pattern)
    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)
                        as.numeric(dim(x))[1:2]))
    vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
    obj.dim[vec, 1] <- napply(names, length)[vec]
    out <- data.frame(obj.type, obj.size, obj.dim)
    names(out) <- c("Type", "Size", "Rows", "Columns")
    if (!missing(order.by))
        out <- out[order(out[[order.by]], decreasing=decreasing), ]
    if (head)
        out <- head(out, n)
#        out
    out <- transform(out, var_name=rownames(out))
    rownames(out) <- NULL
    arrange(out, Size)
}

Holger Brandl's avatar
Holger Brandl committed
306
# shorthand that just shows top 1 results
Holger Brandl's avatar
Holger Brandl committed
307 308 309 310
lsosh <- function(..., n=10) {
    lsos(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}

Holger Brandl's avatar
Holger Brandl committed
311 312 313 314 315 316 317 318 319 320 321
########################################################################################################################
### 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))

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