core_commons.R 8.22 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
    colnames(df) <- newnames;
Holger Brandl's avatar
Holger Brandl committed
131
132
    return(df)
}
Holger Brandl's avatar
Holger Brandl committed
133
134
#iris %>% set_names(c("setosa", "hallo")) %>% head
#iris %>% set_names("setosa", "hallo") %>% head
Holger Brandl's avatar
Holger Brandl committed
135
136


Holger Brandl's avatar
Holger Brandl committed
137
138
head_html <- function(df, n=5) head(df, n) %>% knitr::kable(format="html") %>% print()

Holger Brandl's avatar
Holger Brandl committed
139
140
print_head <- function(df, desc=NULL){
    print(head(df))
Holger Brandl's avatar
Holger Brandl committed
141
    print(nrow(df))
Holger Brandl's avatar
Holger Brandl committed
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
    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
162
## replace R within pipe change just use ... %>% do(replaceNA(0)) %>% ...
Holger Brandl's avatar
Holger Brandl committed
163
replaceNA <- function(x, withValue) { x[is.na(x)] <- withValue; x }
Holger Brandl's avatar
Holger Brandl committed
164

Holger Brandl's avatar
Holger Brandl committed
165
166
167
168
169

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

Holger Brandl's avatar
Holger Brandl committed
170

Holger Brandl's avatar
Holger Brandl committed
171
########################################################################################################################
Holger Brandl's avatar
Holger Brandl committed
172
#### Result Caching for long running tasks
Holger Brandl's avatar
Holger Brandl committed
173

Holger Brandl's avatar
Holger Brandl committed
174
175
## related: http://cran.r-project.org/web/packages/R.cache/R.cache.pdf

176
cache_it <- function(expr, filePrefix="cache"){
177
    cacheFile <- paste0(filePrefix, "_", substr(digest::digest(deparse(expr)), 1,6)) %>% paste0(".", ., ".RData")
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
    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
190
191
#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
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219

########################################################################################################################
#### 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
220
221
## Deprecated: use trim_ext instead
trimEnd <- function(fileNames, ...) trim_ext(fileNames, ...)
Holger Brandl's avatar
Holger Brandl committed
222

Holger Brandl's avatar
Holger Brandl committed
223
trim_ext <-function(fileNames, exts=c()){
Holger Brandl's avatar
Holger Brandl committed
224
225
226
227
228
229
230
    for(fileExt in exts){
        fileNames <- str_replace(fileNames, paste(fileExt, "$",sep=""), "")
    }

    fileNames
}

Holger Brandl's avatar
Holger Brandl committed
231
232
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
233
234
235
236
237
238
239
240
241
242
}

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

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


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

Holger Brandl's avatar
Holger Brandl committed
243

Holger Brandl's avatar
Holger Brandl committed
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
# 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
270
# shorthand that just shows top 1 results
Holger Brandl's avatar
Holger Brandl committed
271
272
273
274
lsosh <- function(..., n=10) {
    lsos(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}

Holger Brandl's avatar
Holger Brandl committed
275
276
277
278
279
280
281
282
283
284
285
########################################################################################################################
### 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)))