core_commons.R 8.35 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

Holger Brandl's avatar
Holger Brandl committed
24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43
require.auto <-  function(x){
    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")
        biocLite(character(), ask=FALSE) # update dependencies, if any.
        eval(parse(text=paste("biocLite('", x, "')", sep="")))
        eval(parse(text=paste("require(", x, ",  quietly=T)", sep="")))
    }
}

Holger Brandl's avatar
Holger Brandl committed
44

Holger Brandl's avatar
Holger Brandl committed
45
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
46
## load core packages
Holger Brandl's avatar
Holger Brandl committed
47

Holger Brandl's avatar
Holger Brandl committed
48 49 50 51 52
require.auto(plyr)
require.auto(stringr)
require.auto(reshape2)
#require.auto(reshape2, quietly=T, warn.conflicts=F)

Holger Brandl's avatar
Holger Brandl committed
53
## load on purpose after plyr
Holger Brandl's avatar
Holger Brandl committed
54
require.auto(dplyr)
55
require.auto(magrittr)
56
require.auto(tidyr)
57

Holger Brandl's avatar
Holger Brandl committed
58 59 60 61
## needed for caching
require.auto(digest)

## moved into datatable_commons because replaced almost everywhere with dplyr
Holger Brandl's avatar
Holger Brandl committed
62 63 64 65 66 67
#require.auto(data.table)




########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
68
#### Convenience aliases
Holger Brandl's avatar
Holger Brandl committed
69 70


Holger Brandl's avatar
Holger Brandl committed
71
echo <- function(...) cat(paste(...), fill=T)
Holger Brandl's avatar
Holger Brandl committed
72 73 74 75

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

# string concatenation without space gaps (could/should use paste0 instead)
Holger Brandl's avatar
Holger Brandl committed
76 77
## Deprecated: use paste0 instead
#concat <- function(...) paste(..., sep="")
Holger Brandl's avatar
Holger Brandl committed
78 79 80 81 82

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

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

Holger Brandl's avatar
Holger Brandl committed
83 84
as.df <- function(dt) as.data.frame(dt)

Holger Brandl's avatar
Holger Brandl committed
85

Holger Brandl's avatar
Holger Brandl committed
86 87 88 89 90 91 92 93 94 95
########################################################################################################################
#### 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
96 97 98
#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
99 100 101 102 103

rownames2column <- function(df, colname){
    df <- as.df(df)
    df$tttt <- rownames(df);
    rownames(df) <- NULL;
Holger Brandl's avatar
Holger Brandl committed
104
    plyr::rename(df, c(tttt=colname))
Holger Brandl's avatar
Holger Brandl committed
105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125
}


column2rownames<- function(df, colname){
#browser()
    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
126 127 128 129
#http://astrostatistics.psu.edu/datasets/R/html/base/html/formals.html
set_names <- function(df, ...){
#browser()
    newnames <- as.character(unlist(list(...)))
130 131 132 133

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

134
    names(df) <- newnames;
Holger Brandl's avatar
Holger Brandl committed
135 136
    return(df)
}
Holger Brandl's avatar
Holger Brandl committed
137 138
#iris %>% set_names(c("setosa", "hallo")) %>% head
#iris %>% set_names("setosa", "hallo") %>% head
Holger Brandl's avatar
Holger Brandl committed
139 140


Holger Brandl's avatar
Holger Brandl committed
141 142
head_html <- function(df, n=5) head(df, n) %>% knitr::kable(format="html") %>% print()

Holger Brandl's avatar
Holger Brandl committed
143 144
print_head <- function(df, desc=NULL){
    print(head(df))
Holger Brandl's avatar
Holger Brandl committed
145
    print(nrow(df))
Holger Brandl's avatar
Holger Brandl committed
146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165
    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
166
## replace R within pipe change just use ... %>% do(replaceNA(0)) %>% ...
Holger Brandl's avatar
Holger Brandl committed
167
replaceNA <- function(x, withValue) { x[is.na(x)] <- withValue; x }
Holger Brandl's avatar
Holger Brandl committed
168

Holger Brandl's avatar
Holger Brandl committed
169 170 171 172 173

## workaround for biomart
## Deprecated: load dplyr after biomart to avoid this problem
#dselect <- function(...) dplyr::select(...)

Holger Brandl's avatar
Holger Brandl committed
174

Holger Brandl's avatar
Holger Brandl committed
175
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
176
#### Result Caching for long running tasks
Holger Brandl's avatar
Holger Brandl committed
177

Holger Brandl's avatar
Holger Brandl committed
178 179
## related: http://cran.r-project.org/web/packages/R.cache/R.cache.pdf

180
cache_it <- function(expr, filePrefix="cache"){
181
    cacheFile <- paste0(filePrefix, "_", substr(digest::digest(deparse(expr)), 1,6)) %>% paste0(".", ., ".RData")
Holger Brandl's avatar
Holger Brandl committed
182

Holger Brandl's avatar
Holger Brandl committed
183 184 185 186 187 188 189 190 191 192 193
    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
194 195
#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
196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223

########################################################################################################################
#### 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
224 225
## Deprecated: use trim_ext instead
trimEnd <- function(fileNames, ...) trim_ext(fileNames, ...)
Holger Brandl's avatar
Holger Brandl committed
226

Holger Brandl's avatar
Holger Brandl committed
227
trim_ext <-function(fileNames, exts=c()){
Holger Brandl's avatar
Holger Brandl committed
228 229 230 231 232 233 234
    for(fileExt in exts){
        fileNames <- str_replace(fileNames, paste(fileExt, "$",sep=""), "")
    }

    fileNames
}

Holger Brandl's avatar
Holger Brandl committed
235 236
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
237 238 239 240 241 242 243 244 245 246
}

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

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


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

Holger Brandl's avatar
Holger Brandl committed
247

Holger Brandl's avatar
Holger Brandl committed
248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273
# 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
274
# shorthand that just shows top 1 results
Holger Brandl's avatar
Holger Brandl committed
275 276 277 278
lsosh <- function(..., n=10) {
    lsos(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}

Holger Brandl's avatar
Holger Brandl committed
279 280 281 282 283 284 285 286 287 288 289
########################################################################################################################
### 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)))