fail (version 1.3)

fail: Create a file abstraction interface layer (FAIL) object.

Description

The general idea is to not bother about file path joining or file extensions. Instead, FAIL offers a key-value like interface to RData files in a specified directory. The filename (without extension) acts as the key while the stored R objects are the values. Fail provides an interface to the basic file system actions: listing, reading / loading, writing / saving, removing and applying functions on files. An implemented cache mechanism can be used to avoid repeated disk reads.

Usage

fail(path = getwd(), extension = "RData", all.files = FALSE, use.cache = FALSE, simplify = TRUE)

Arguments

path

[character(1)] Path to work in, will be created if it does not exists.

extension

[character(1)] File extension to work with. Default is “RData”.

all.files

[logical(1)] Also include hidden files, i.e. files whose name start with a dot (“.”). Default is FALSE.

use.cache

[logical(1)] Use a memory cache per global default. Global option which can locally be overwritten in most functions. Default is FALSE

simplify

[character(1)] If only one object is stored in a R data file, should the return value be simplified? If set to TRUE, instead of a list containing one element the object itself will be returned.

Value

Object of class fail. See details.

Details

For a quick introduction on the usage, see https://github.com/mllg/fail.

An object with the following functions is returned by fail:

ls(pattern=NULL)

Function to list keys in directory path matching a regular expression pattern pattern. Returns a character vector of keys.

get(key, use.cache)

Function to load a file identified by key from directory path. To load many objects at once, use as.list, assign or get together with lapply. Argument use.cache can be set to temporarily overwrite the global use.cache flag.

put(..., li, keys, use.cache)

Function to save objects to directory path. Names for objects provided via ... will be looked up or can be provided using a key = value syntax. More objects can be passed as a named list using the argument li: Each list item will be saved to a separate file. If you provide keys as a character vector, these names will be taken for the arguments passed via .... Argument use.cache temporarily overwrites the global use.cache flag. Returns a character vector of stored keys.

remove(keys)

Function to remove files identified by keys from directory path. Returns a character vector of deleted keys.

apply(FUN, ..., keys, use.cache, simplify=FALSE, use.names=TRUE)

Apply function FUN on files identified by keys. keys defaults to all keys available and will be used to name the returned list. The loaded R objects will be past unnamed as first argument. Use ... for additional function arguments. Argument use.cache can be set to temporarily overwrite the global use.cache flag. For arguments simplify and use.names, see lapply.

mapply(FUN, ..., keys, use.cache, moreArgs = NULL, simplify=FALSE, use.names=TRUE)

Apply function FUN on files identified by keys. keys defaults to all keys available and will be used to name the returned list. The function FUN must have the formal arguments “key” and “value”. Both key and value will be passed named. Use ... and/or moreArgs for additional function arguments. Argument use.cache can be set to temporarily overwrite the global use.cache flag. For arguments moreArgs, simplify and use.names, see mapply.

as.list(keys, use.cache)

Return a named list of objects identified by keys. keys defaults to all keys available. Argument use.cache can be set to temporarily overwrite the global use.cache flag.

assign(keys, envir=parent.frame(), use.cache)

Assigns all objects identified by the character vector keys in the environment envir. Argument use.cache can be set to temporarily overwrite the global use.cache flag. Returns a character vector of assigned keys.

clear(keys)

Clear the cache to free memory. keys defaults to all keys available. Returns a character vector of cleared keys.

cached()

Returns a character vector of keys of cached objects.

size(keys, unit="b")

Get the file size in Bytes of the files identified by keys. keys defaults to all keys available. Argument unit accepts “b”, “Kb”, “Mb” and “Gb” and can be used to convert Bytes to KiloBytes, MegaBytes or GigaBytes, respectively.

info()

Returns a named list with path, extension and use.cache. Internally used for the print method with a much nicer summary of the FAIL object.

Furthermore, the package provides S3 methods for print and as.list.

Be aware of the following restriction regarding file names and keys: The package performs some basic checks for illegal characters on the key names. In principle all characters matching the pattern “[a-zA-Z0-9._-]” are allowed and should work on most or all file systems. But be careful with key names which are not compatible with R's variable naming restrictions, e.g. using the minus character or key names starting with a number: these provoke unwanted side effects and will result in errors if used with assign.

If two files would collide on case-insensitive file systems like Windows' NTFS, the package will throw warnings. Best practice is to not rely on case sensitivity.

Examples

# initialize a FAIL in a temporary directory
path <- tempfile("")
files <- fail(path)

# save x and y, vectors of random numbers
x <- runif(100)
files$put(x, y = runif(100))

# save columns of the iris data set as separate files
files$put(li = as.list(iris))

# load all RData files in a named list as a one-liner
as.list(fail(path))

# load a single object from the file system
files$get("Species")
files$as.list(c("x", "y"))

# remove an object (and related file)
files$remove("Species")

# apply a function over files
files$apply(mean)
files$mapply(function(key, value) sprintf("%s -> %f", key, mean(value)), simplify = TRUE)

# show file size informations
files$size(unit = "Mb")

# get an object and cache it
files$get("x", use.cache = TRUE)
files$cached()
files$clear()
files$cached()

# assign variables in the current environment
files$assign("y")
mean(y)

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