Utilise

detachAllPackages

Detach all the libraries except the official start-up libraries. Need it in development packages.

##' Detach all packages
##'
##'
##' @title utilities
##' @return nothing
##' @export
##' @author Yi Tang
detachAllPackages <- function() {

    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)

}

Object Size

Show all the objects and their size, watch out your R memory usage!

lsos()

# improved list of objects
.ls.objects <- 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)
    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
}
# shorthand
lsos <- function(..., n=10) {
    .ls.objects(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}

IO

#' save ggplot to a file which is right to be imported in World document.
my.png <- function(p, file = deparse(substitute(p))){
    png(paste(file, ".png", sep=""),  width = 12, height = 9, units = 'in', res = 300)
    print(p)
    dev.off()
}

estimate file size

##'  Estimate the space of output file
##'
##' more accurate than the object.size function.
##' @title
##' @param a.df a data.table or data.frame
##' @param n number of rows used in estimation, if n is less than 1, propoertion of rows used
##' @param ... args passed to write.csv
##' @return a estimated disk space to save a.df, in Mb unit.
##' @export
##' @author Yi Tang
SizeEst <- function(a.df, n,  ...) {
    file <- tempfile()
    if (n <= 1)
        n <- ceiling(n * nrow(a.df))
    df.subset <- a.df[seq_len(n), ]
    write.csv(df.subset, file = file, ...)
    disk.space <- file.info(file)$size
    file.remove(file)
    disk.space.est <- disk.space  / nrow(df.subset) * nrow(a.df)
    disk.space.est / (2 ^ 20) ## return as MB
}

Assorted

##'  Tests
##'
##' Test whether or not two data.table objects are identical.
##' @title
##' @param dt1
##' @param dt2
##' @param verbose
##' @return
##' @export
##' @author Yi Tang
identical.data.table <- function(dt1, dt2, verbose = TRUE) {
    if (nrow(dt1) != nrow(dt2))
        stop("different number of rows")
    if (ncol(dt1) != ncol(dt2))
        stop("different number of columns")
    if (names(dt1) != names(dt2))
        stop("different column names")
    n <- ncol(dt1)
    sapply(seq_len(n), function(i) {
        cat("\nTest columns", i)
        if(!identical(dt1[[i]], dt2[[i]]))
            stop("col ", i, " is different")
    })
    TRUE
}