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utils.R
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## Copyright 2013 Elliot Chow
## Licensed under the Apache License, Version 2.0 (the "License")
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
## http://www.apache.org/licenses/LICENSE-2.0
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
import('doMC',
'gdata',
'stringr',
'plyr',
'hash',
'R.oo',
'Hmisc',
'digest',
'sfsmisc',
'rjson',
'testthat',
'Matrix',
as.library='utils')
## options(width=110,scipen=6)
options(scipen=6, menu.graphics=FALSE)
####################
#### Logging
####################
if (!"SimpleLog" %in% ls()) {
setConstructorS3('SimpleLog',
## logging object
## id: id of the logger
## level: recognized logging levels
## colors: colors to use if colorizing logs
function(id='log',
level=c('info','warning','error','debug'),
colors = c('info'='light gray','warning'='yellow','error'='red','debug'='dark gray')
## outputs=stderr(),
## overwrite=TRUE
){
## if(overwrite){
## sapply(outputs[is.character(outputs) & outputs != ""],
## function(x){
## if(is.character(x)){
## file.remove(x)
## }
## })
## }
extend(Object(), 'SimpleLog',
id=id,
level=level,
colors=colors,
## outputs=outputs
outputs=stderr()
)
})
## logging levels
SimpleLog.INFO <- 'info'
SimpleLog.WARNING <- c(SimpleLog.INFO, 'warning')
SimpleLog.ERROR <- c(SimpleLog.WARNING, 'error')
SimpleLog.DEBUG <- c(SimpleLog.ERROR, 'debug')
if(!exists('SimpleLog.CONFIG', envir = globalenv())){
## global var to hold SimpleLog configuration
assign('SimpleLog.CONFIG', new.env(), envir=globalenv())
}
setMethodS3('write.msg','SimpleLog',
## write a message to standard error
## log: SimpleLog object
## ...: message (and string formatting parameters)
## level: level of the message
## sep: separating chars in log
## return.success: set to true if you should return whether or not the message was successfully written
function(log, ..., level=SimpleLog.INFO, sep=' - ', return.success=FALSE){
check <- TRUE
lvl <- intersect(tail(level,1), log$level)
if(length(lvl) > 0){
msg <- paste(list(format(Sys.time(), "%Y/%m/%d %H:%M:%S"), lvl, log$id, sprintf(...)), collapse = sep)
success <- all(sapply(log$outputs,
function(o) {
if((!is.null(globalenv()$SimpleLog.CONFIG$colorize) && globalenv()$SimpleLog.CONFIG$colorize) && (o %in% c(stderr(), stdout()))){
color <- log$colors[lvl]
if(!is.na(color))
msg <- colourise(msg, color)
}
tryCatch(is.null(cat(msg, '\n', file=o, append=TRUE)),
error = function(e) FALSE)
}))
if(return.success) success else invisible(success)
}
})
setConstructorS3('Timer',
## timer object
function(log=NULL){
if(is.null(log)){
log <- SimpleLog('timerLog')
}
extend(Object(), 'Timer',
log=log)
})
setMethodS3('start.timer', 'Timer',
## start timing
## msg: message to print on start
## ...: args for write.msg
function(self, msg=NULL, ...){
if(!is.null(msg)){
write.msg(self$log,msg, ...)
}
self$startTime <- proc.time()[3]
})
setMethodS3('stop.timer', 'Timer',
## stop timing
## ...: args for write.msg
function(self, ...){
self$stopTime <- proc.time()[3]
dt <- self$stopTime - self$startTime
m <- as.integer(dt / 60)
s <- round(dt - 60 * m,1)
write.msg(self$log,
sprintf('elapsed time: %s', paste(m, 'm', s, 's')),
...)
})
}
timer <- function(expr){
## simple timer for an expression
s.expr <- substitute(expr)
t <- Timer()
start.timer(t, 'timing %s', paste(deparse(s.expr), collapse=''))
res <- eval(s.expr, parent.frame())
stop.timer(t)
res
}
stop.if <- function(x, msg, ..., tags=list(), cleanup = function(){}, failed.cond = substitute(x)){
## throw an exception if condition is met
## x: boolean value (true to throw exception)
## msg: error message
## tags: list of tags and values to be attached to the exception
## cleanup: a function with no arguments to be executed (like finally)
## failed.cond: expression representing the failed condition
call <- sys.call(1)
if(x){
err <- csplat(tag, c(list(simpleError(paste(c(sprintf(msg, ...),
'\n Failed condition: ', failed.cond),
collapse=''),
call)),
tags))
cleanup()
stop(err)
}
}
stop.if.not <- function(x, ...){
## throw an exception if the condition isnot met
## ...: args for stop if
failed.cond <- substitute(!(x))
stop.if(!x, ..., failed.cond = failed.cond)
}
dump.frames.on.failure <- function(on = TRUE){
## dumps frames for debugging upon unexpected exit
## on: turn on/off
if(on)
options(error = quote({ dump.frames('dump-frames', to.file = TRUE)
system('echo "frames dumped to dump-frames.rda"')
q()
}
))
else
options(error = NULL)
}
####################
#### URL encoding
####################
## http://svn.python.org/view/*checkout*/python/tags/r265/Lib/urllib.py?revision=79064&content-type=text%2Fplain
url.always.safe.chars <- c("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z","a","b","c","d","e","f","g","h","i","j","k","l","m","n","o","p","q","r","s","t","u","v","w","x","y","z","0","1","2","3","4","5","6","7","8","9","_",".","-")
url.reserved.chars <- c(";", "/", "?", ":", "@", "&", "=", "+", "$", ",")
url.quote <- function(s, reserved = url.reserved.chars, plus.spaces = T){
## url encode a string
## s: string to encode
## reserved: vector of reserved characters
## plus.spaces: convert spaces to +
chars <- int.to.char(1:255)
safe <- named(ifelse(chars %in% c(url.always.safe.chars, reserved), chars, sprintf('%%%.2X', 1:255)),
chars)
if(plus.spaces)
safe[[' ']] <- '+'
unlist(lapply(strcodes(s), function(chars) paste(safe[chars], collapse = '')))
}
url.unquote <- function(s, reserved = NULL, plus.spaces = T){
## url decode a string
## s: string to decode
## reserved: vector of reserved characters
## plus.spaces: convert + to spaces
chars <- int.to.char(1:255)
safe <- named(chars,
ifelse(chars %in% c(url.always.safe.chars, reserved), chars, sprintf('%.2X', 1:255)))
z <- lapply(strsplit(s, '%'),
function(xs){
y <- paste(safe[str_sub(xs[-1], end = 2)],
str_sub(xs[-1], start = 3),
sep = '')
z <- paste(c(xs[1], y), collapse = '')
if(plus.spaces)
gsub('\\+',' ',z)
else
z
})
unlist(z)
}
url.encode.params <- function(params, ...){
## encode a named list as url parameters
## params: named list of params
## ...: args for url.quote
params <- unlist(params)
paste(paste(url.quote(names(params), ...),
url.quote(as.character(params), ...),
sep = '='),
collapse = '&')
}
url.parse.params <- function(params.str, ...){
## parse parameters to named list
## params.str: string of url parameters
lapply(strsplit(params.str, '&'),
function(kv) url.unquote(unlist(zip.to.named(strsplit(kv, '='))), ...))
}
url.qry.string <- function(url)
## exctract the query string from url
## url: url from which to extract qs
unlist(lapply(strsplit(url, '\\?'), function(x) x[[2]]))
####################
#### Functions
####################
## evaluate an expression within an environment
"%within%" <- function(expr, envir) eval(substitute(expr), envir=envir)
tag <- function(x,...) {
## tag a value with attributes
tagged <- x
dots <- list(...)
if(length(dots) > 0){
for(i in indices(dots))
attr(tagged, names(dots)[i]) <- dots[[i]]
}
tagged
}
## read var name as string
var.name <- function(x) deparse(substitute(x))
## test if an environment is the global environment
is.global.env <- function(env) environmentName(env) == 'R_GlobalEnv'
## curry a function with 1 argument
curry1 <- function(f, ...){
function(x)
f(x, ...)
}
####################
#### Files
####################
rrmdir <- function(path,rm.contents.only=FALSE){
## recursivedly remove directory
## path: path to remove
## rm.contents.only: leave path untouched
path <- gsub('/( )*$','',path)
isDir <- file.info(path)$isdir
if(!is.na(isDir) && isDir){
for(i in dir(path)){
rrmdir(file.path(path,i),FALSE)
}
}
if(!rm.contents.only){
file.remove(path)
}
}
curl.cmd <- function(url, output.path, params = NULL, method = 'get', show.progress = NULL, custom.opts = ''){
## construct a curl command
stop.if.not(method %in% c('get','post'), 'method must be get or post')
stop.if.not(is.null(show.progress) || show.progress %in% c('bar','text'), 'progress must be bar or text')
if(!is.null(params))
ps <- url.encode.params(params, reserved=NULL)
else
ps <- ''
if(is.null(show.progress))
progress.opt <- '-s'
else if (show.progress == 'bar')
progress.opt <- '-#'
else if(show.progress == 'text')
progress.opt <- ''
method.opt <- if(method == 'get') '-X GET' else '-X POST'
sprintf('curl %s %s --data "%s" -o %s %s "%s"',
method.opt,
custom.opts,
ps,
output.path,
progress.opt,
url)
}
cache.data <- function(path, ..., cache.path='.cache', force=FALSE, log.level = SimpleLog.INFO){
## cache data by downloading (if necessary) using curl; return connection
logger <- SimpleLog('cache.data', log.level)
if(str_detect(path,'http[s]?://')){
path.hash <- digest(csplat(paste, list(...), path), 'md5')
cached.file <- file.path(cache.path, path.hash)
cmd <- curl.cmd(path, cached.file, ...)
write.msg(logger, 'curl command: %s', cmd, level = SimpleLog.DEBUG)
write.msg(logger, 'caching to %s', cached.file)
dir.create(cache.path, showWarnings = FALSE)
exit.code <- 0
if(!file.exists(cached.file) || force)
exit.code <- system(cmd)
else
write.msg(logger, 'reading from cache', cmd)
stop.if.not(exit.code == 0, 'failed to download file', cleanup = function() file.remove(cached.file) )
conn <- cached.file
}else{
conn <- path
}
conn
}
load.data <- function(path, load.fun, ..., cache.path = '.cache', show.progress = NULL, force=FALSE, log.level = SimpleLog.INFO){
## cache/load data
logger <- SimpleLog('load.data', log.level)
if(missing(load.fun)){
write.msg(logger, 'missing "load.fun" function - calling load.table', level = SimpleLog.DEBUG)
return(load.table(path, ..., cache.path = cache.path, show.progress = show.progress, force = force, log.level = log.level))
}
if(is.list(path)){
path <- c(path, cache.path = cache.path, show.progress = show.progress, force = force, list(log.level = log.level))
conn <- cache.data %wargs% path
}else{
conn <- cache.data(path, cache.path = cache.path, force = force, log.level=log.level)
}
tryCatch({
options(warn=-1)
z <- get(load(conn))
options(warn=0)
z
},
error = function(e){
load.fun(conn, ...)
})
}
load.lines <- function(path, parser = NULL, cache.path='.cache', show.progress = NULL, force=FALSE, log.level = SimpleLog.INFO){
## cache/load data line by line
load <- function(conn)
readLines(conn, warn = F)
z <- load.data(path, load, cache.path = cache.path, show.progress = show.progress, force = force, log.level = log.level)
if(!is.null(parser))
lapply(z, parser)
else
z
}
load.string <- function(path, parser = NULL, cache.path='.cache', show.progress = NULL, force=FALSE, log.level = SimpleLog.INFO){
## cache/load data as string
load <- function(conn)
file.to.string(conn)
z <- load.data(path, load, cache.path = cache.path, show.progress = show.progress, force = force, log.level = log.level)
if(!is.null(parser))
parser(z)
else
z
}
load.table <- function(path, ..., sep='\t', header=T, comment.char='', quote='', cache.path='.cache', show.progress = NULL, force=FALSE, log.level = SimpleLog.INFO){
## cache/load data as table
load.fun <- function(conn)
read.table(conn, sep=sep, header=header, comment.char=comment.char, quote=quote, ...)
load.data(path, load.fun, cache.path = cache.path, show.progress = show.progress, force = force, log.level = log.level)
}
serialize.to.text <- function(object, encoder=I){
## text serialization
encoder(rawToChar(serialize(m, connection = NULL, ascii=T)))
}
unserialize.from.text <- function(s, decoder=I){
## text deserialization
unserialize(decoder(textConnection(s)))
}
streaming.group.by.key <- function(f, get.key=function(x) x[[1]]){
## group streaming data by key
## assumes sorted by key!
## s <- textConnection('1\t2\n1\ta\n3\tb\n5\t3\t10'); streaming.group.by.key(function(lines) print(read.table(textConnection(unlist(lines)),sep='\t',header=F)), function(x) strsplit(x,'\t')[[1]][1])(s, 1100)
function(con, chunk.size = 1000){
if(!isOpen(con))
con <- open(con, open='r')
done.reading <- FALSE
buf <- list()
buf.keys <- list()
current.key <- NULL
repeat {
incoming <- as.list(readLines(con, chunk.size))
if (length(incoming) == 0)
done.reading <- TRUE
if(done.reading && length(buf) == 0)
break
buf <- c(buf, incoming)
buf.keys <- c(buf.keys, lapply(incoming, get.key))
if(is.null(current.key))
current.key <- buf.keys[[1]]
last.buf.key <- tail(buf.keys, 1)
if((current.key != last.buf.key) || done.reading){
to.process <- buf.keys == current.key
f(buf[to.process])
buf <- buf[!to.process]
buf.keys <- buf.keys[!to.process]
current.key <- if(length(buf.keys) > 0) buf.keys[[1]] else NA
}
}
}
}
run.once <- function(expr, store = 'run.once.store__', algo='md5', lazy = TRUE, log.level=SimpleLog.INFO){
## execute and expression and cache it
logger <- SimpleLog('run.once', log.level)
g <- globalenv()
expr.q <- substitute(expr)
expr.s <- paste0(deparse(expr.q), collapse='\n ')
var.name <- digest(expr.s, algo=algo)
write.msg(logger, 'caching \n %s\n into %s (envir = %s)', expr.s, var.name, store, level=SimpleLog.DEBUG)
if(!exists(store, g)){
write.msg(logger, 'initializing store %s', store, level=SimpleLog.DEBUG)
assign(store, new.env(), envir=g)
}
if(!(var.name %in% ls(g[[store]]))){
write.msg(logger, 'computing %s', var.name, level=SimpleLog.DEBUG)
assign(var.name, eval(expr.q), g[[store]])
}
g[[store]][[var.name]]
}
file.to.string <- function(file){
## read file contents to string
readChar(file, file.info(file)$size)
}
brew.string <- function(s,...){
dots <- list(...)
e <- if(length(dots) == 0) new.env() else list2env(dots)
brewedSql <- tempfile()
brew(text=s,output=brewedSql,envir=e)
sql <- file.to.string(brewedSql)
sql
}
####################
#### Lists/Vectors
####################
get.or.else <- function(x, field, default){
z <- x[[field]]
if(is.null(z))
z <- default
z
}
with.defaults <- function(xs, defaults){
ys <- xs
c(ys, defaults[setdiff(names(defaults), names(xs))])
}
csplat <- function(f,a,...)
do.call(f, c(as.list(a),...))
"%wargs%" <- function(f, a)
do.call(f, as.list(a))
indices <- function(xs, type){
if(missing(type))
f <- length
else if(type == 'col')
f <- ncol
else if(type == 'row')
f <- nrow
len <- f(xs)
if(len > 0) 1:len else NULL
}
na.rm <- function(x, required, discard = is.na) {
if(is.data.frame(x)){
if(missing(required))
required <- names(x)
keep <- Reduce(function(a,b) a & b, lapply(subset(x,select=required), function(y) !discard(y)), init=TRUE)
x[keep,]
}else
x[!discard(x)]
}
inf.rm <- function(...) na.rm(..., discard = is.infinite)
nan.rm <- function(...) na.rm(..., discard = is.nan)
invalid.rm <- function(...) na.rm(..., discard = function(z) is.na(z) | is.nan(z) | is.infinite(z))
is.invalid <- function(z) is.na(z) | is.nan(z) | is.infinite(z)
replicate <- function(n, expr, .parallel=FALSE)
## same as base replicate with parallel option
llply(integer(n), eval.parent(substitute(function(...) expr)),
.parallel=.parallel)
grep <- function(pat, x, ..., value=FALSE){
## same as base grep with option to return boolean match/no match
stop.if.not(is.logical(value) || (value == 'logical'), 'unknown value type "%s"', value)
if(value == 'logical'){
i <- base::grep(pat, x, ..., value = FALSE)
(1:length(x)) %in% i
}else{
base::grep(pat, x, ..., value=value)
}
}
tapply <- function (X.expr, INDEX.expr, FUN = NULL, simplify = TRUE, ret.type='list', envir = NULL) {
## modified tapply: 1) lookup inputs in envir if supplied, 2) list of inputs for 1st argument, 3) various output formats
if(is.null(envir)){
X <- X.expr
INDEX <- INDEX.expr
}else{
X <- eval(substitute(X.expr), envir = envir)
INDEX <- eval(substitute(INDEX.expr), envir = envir)
}
FUN <- if(!is.null(FUN))
match.fun(FUN)
if(!is.list(INDEX))
INDEX <- list(INDEX)
if(!is.list(X))
X <- list(X)
names(X) <- NULL
nI <- length(INDEX)
namelist <- vector("list", nI)
names(namelist) <- names(INDEX)
extent <- integer(nI)
nx <- length(X[[1]])
one <- 1L
group <- rep.int(one, nx)
ngroup <- one
for(i in seq_along(INDEX)){
index <- as.factor(INDEX[[i]])
if(length(index) != nx)
stop("arguments must have same length")
namelist[[i]] <- levels(index)
extent[i] <- nlevels(index)
group <- group + ngroup * (as.integer(index) - one)
ngroup <- ngroup * nlevels(index)
}
if(is.null(FUN))
return(group)
## use mapply/split to allow for multiple inputs
ans <- do.call(mapply, c(FUN, lapply(X, function(x) split(x, group)), SIMPLIFY=FALSE))
index <- as.integer(names(ans))
if(simplify && all(unlist(lapply(ans, length)) == 1L)){
ansmat <- array(dim = extent, dimnames = namelist)
ans <- unlist(ans, recursive = FALSE)
}
else{
ansmat <- array(vector("list", prod(extent)), dim = extent,
dimnames = namelist)
}
if(length(index)){
names(ans) <- NULL
ansmat[index] <- ans
}
## return types
if(ret.type == 'df'){
## create data.frame by expanding grid
ansmat <- data.frame(expand.grid(dimnames(ansmat)),y=do.call(rbind,as.list(ansmat)))
}else if(ret.type == 'par'){
## put output values into original spots
z <- vector('list',length(X[[1]]))
split(z, group) <- ansmat
ansmat <- unlist(z)
}else{
stop.if(ret.type != 'list', 'unknown ret.type "%s"', ret.type, tag = 'unknown.type')
}
ansmat
}
lzip <- function(...){
## zip multiple lists together
delayedAssign('args', lapply(list(...), as.list))
n <- min(sapply(args,length))
if(n <= 0)
return(NULL)
lapply(1:n,
function(i){
zip.to.named(lapply(indices(args),
function(j){
y <- args[j]
list(names(y)[1], y[[1]][[i]])
}))
})
}
"%zip%" <- function(a,b) lzip(a, b)
zip.to.named <- function(x,nameCol=1,valCol=2){
## convert zipped list to named list
flatten(lapply(x,
function(y){
z <- list(y[[valCol]])
names(z) <- y[[nameCol]]
z
}))
}
named <- function(x, n, type=''){
if(type == 'row')
row.names(x) <- n
else if(type == 'col')
colnames(x) <- n
else
names(x) <- n
x
}
"%named%" <- function(x, n) named(x, n)
"%rnamed%" <- function(x, n) named(x, n, 'row')
"%cnamed%" <- function(x, n) named(x, n, 'col')
remove.names <- function(x, type='')
named(x, NULL, type)
keep.if <- function(x,f){
mask <- sapply(x,f)
x[mask]
}
flatten <- function(x)
do.call(c,x)
merge.lists <- function(all,FUN=function(n,x){x}){
allNames <- unique(do.call(c,lapply(all,names)))
z <- lapply(allNames,
function(n){
z <- FUN(n,lapply(all,
function(x){
tryCatch(x[[n]],
error=function(e){NULL})
}))
z
})
names(z) <- allNames
z
}
setdiff2 <- function(x,y){
list(setdiff(x,y), setdiff(y, x))
}
make.combinations <- function(...){
## generate combinations taking an element from each input vector
dots <- list(...)
apply(expand.grid %wargs% dots, 1,
function(z) as.list(z))
}
parameter.scan <- function(f, params.list, as.df=FALSE, .parallel=FALSE){
## apply f over a list of parameters
z <- llply(params.list,
function(params){
#cbind(as.data.frame(params), f = f %wargs% params)
c(list(params=params), list(f = f %wargs% params))
},
.parallel=.parallel)
if(as.df)
rbind.fill(lapply(z, as.data.frame))
else
z
}
sample.by <- function(x,...,as.filter=TRUE){
if(is.factor(x))
g <- levels(x)
else
g <- unique(x)
g.s <- sample(g, ...)
if(as.filter)
x %in% g.s
else
x[x %in% g.s]
}
####################
#### Matrices
####################
sparse.matrix.from.file <- function(path, ..., what=list(integer(),integer(),numeric())){
entries <- scan(path, what=what, ...)
sparseMatrix(i=entries[[1]], j=entries[[2]], x=entries[[3]])
}
####################
#### Data.frame
####################
sort.by <- function(x, ..., decreasing=FALSE){
dots <- list(...)
x[csplat(order, lapply(dots, function(i) x[[i]]), decreasing = decreasing), ]
}
rbind.fill.par <- function(lst, m = 1000) {
## chunk and parallelize rbind.fill
n <- length(lst)
ldply(1:ceiling(n / m),
function(offset){
select <- 1 + ((m * (offset - 1)) : (m * offset - 1))
select <- select[select <= n]
ds <- lst[select]
rbind.fill(ds)
},
.parallel = TRUE)
}
max.element.str.length <- function(data,.parallel=FALSE){
maxLengths <- llply(names(data),
function(i){
max(str_length(i),
max(str_length(data[[i]])))
},
.parallel=.parallel)
names(maxLengths) <- names(data)
maxLengths
}
str.align <- function(data, maxLengths, .parallel=FALSE){
result <- llply(names(maxLengths),
function(i){
sapply(data[[i]],
function(j){
x <- as.character(j)
if(is.na(x)){x <- 'NA'}
n <- maxLengths[[i]] - str_length(x)
if(is.na(n)){
n <- 2
x <- 'NA'
}
fmtd <- x
if(n > 0){
fmtd <- sprintf('%s%s', x, paste(rep(' ',n), collapse = ''))
}
fmtd
})},
.parallel=.parallel)
names(result) <- names(maxLengths)
result
}
dataframe.to.tsv <- function(x, file, ..., sep='\t', row.names=F, quote=FALSE)
write.table(x, file=file, ..., sep=sep, row.names=row.names, quote=quote)
pprint.dataframe <- function(data, sep=' | ', prepend.row.names = ' ', .parallel=FALSE){
## pretty print data frame in text format
if(is.matrix(data))
data <- as.data.frame(data)
stop.if.not(is.data.frame(data), 'input must be data.frame')
if(!is.null(prepend.row.names) && !is.null(row.names(data)))
data <- named(cbind(row.names(data), data), c(prepend.row.names, names(data)))
maxLengths <- max.element.str.length(data,.parallel=.parallel)
header <- as.list(names(maxLengths))
names(header) <- header
result <- str.align(data,maxLengths,.parallel=.parallel)
result <- as.data.frame(result)
header <- paste(str.align(header, maxLengths), collapse = sep)
paste(header,
paste(rep('-',str_length(header)), collapse = ''),
paste(apply(result, 1,
function(x) paste(x, collapse = sep)
),
collapse = '\n'),
'',
sep = '\n')
}
dataframe.to.textile <- function(x, attr.for = function(e, i, j) NA, header = T, prepend.row.names = ' ', .parallel=FALSE){
## print dataframe to textile
row.to.tt <- function(row) paste('|', paste(as.character(row), collapse = ' |'), ' |', sep='')
add.attr <- function(e, i, j) {
attr <- attr.for(e, i, j)
if(is.na(attr)) paste(' ', e, sep='') else paste(attr, e, sep='. ')
}
if(is.matrix(x))
x <- as.data.frame(x)
if(!is.null(prepend.row.names) && !is.null(row.names(x)))
x <- named(cbind(row.names(x), x), c(prepend.row.names, names(x)))
zz <- if(header) paste('_', names(x), sep='. ') else NULL
paste(
list(if(header) row.to.tt(paste('_', names(x), sep='. ')) else NULL),
llply(indices(x, 'row'),
function(i){
row.to.tt(sapply(indices(x, 'col'),
function(j) add.attr(x[i,j], i, j)))
},
.parallel=.parallel),
collapse = '\n')
}
dataframe.to.html.table <- function(x,
table.attrs='class="sortable" border="1"',
th.attrs='style=font-size:24px',
add.tr.attr=function(i){''},
add.td.attr=function(i,j){''},
prepend.row.names = ' ',
.parallel=FALSE){
## print dataframe to html
if(is.matrix(x))
x <- as.data.frame(x)
if(!is.null(prepend.row.names) && !is.null(row.names(x)))
x <- named(cbind(row.names(x), x), c(prepend.row.names, names(x)))
if(nrow(x) == 0){
rows <- ''
}else{
rows <- paste(llply(1:nrow(x),
function(i){
z <- sprintf('<tr %s>%s</tr>',
add.tr.attr(i),
paste(lapply(1:ncol(x),
function(j){
sprintf('<td %s>%s</td>',
add.td.attr(i,j),
x[i,j])
}),
collapse = ''))
z
},.parallel=.parallel),
collapse = '\n')
}
headers <- sprintf('<tr>%s</tr>',
paste(lapply(colnames(x), function(c){sprintf('<th %s>%s</th>', th.attrs, c)}),
collapse = ''))
sprintf('<table %s>\n%s\n%s\n</table>',
table.attrs,
headers,
rows)
}
sorttable.import <- function(loc='http://www.kryogenix.org/code/browser/sorttable/sorttable.js'){
## add import for simple sortable tables
sprintf('<script src="%s"></script>
<style media="screen" type="text/css">
table.sortable thead {
background-color:#eee;
color:#666666;
font-weight: bold;
cursor: default;
}
</style>',loc)
}
###################
#### Date
###################
STANDARD.TIMESTAMP.FORMAT <- "%Y-%m-%d %H:%M:%S"
EPOCH <- strptime("1970-01-01 00:00:00", STANDARD.TIMESTAMP.FORMAT, tz="UTC")
MIN.SEC <- 60
HOUR.SEC <- 60 * MIN.SEC
DAY.SEC <- 24 * HOUR.SEC
unix.timestamp.to.fmt <- function(ts, fmt=STANDARD.TIMESTAMP.FORMAT, tz='UTC')
strptime(as.POSIXct(ts,origin=EPOCH), fmt, tz=tz)
unix.timestamp.now <- function() unclass(Sys.time())
today <- function(sep='-') unix.timestamp.to.fmt(unix.timestamp.now(), paste('%Y','%m','%d', sep='-'))
####################
#### Misc
####################
str.fmt <- function(s,...){
## named string formatting
dots <- list(...)
named.pat <- '(^|[^%])(%)\\(([A-Za-z0-9_.]+?)\\)(([0-9.]+)?[sdf])' ## name params can contain alphanumeric chars, underscores, and periods
unnamed.pat <- '(^|[^%])(%[sdf])'
named <- str_detect(s,named.pat)
ss <- s
params <- dots
if(named){
n <- as.vector(sapply(str_extract_all(s,named.pat),
function(x) gsub(named.pat,'\\3', x)))
stop.if(is.null(names(dots)) || any(str_length(names(dots))==0),