Import system - main functions • tinycodet

library(tinycodet)
#> Run `?tinycodet::tinycodet` to open the introduction help page of 'tinycodet'.

Introduction

One can use a package without attaching (for example using ::), or one can attach a package (for example using library() or require()).

The advantages and disadvantages of using without attaching a package versus attaching a package - at least those relevant for this article - can be compactly presented in the following table:

	aspect	::	attach
1	prevent masking functions from other packages	Yes (+)	No (-)
2	prevent masking core R functions	Yes (+)	No (-)
3	clarify which function came from which package	Yes (+)	No (-)
4	place/expose functions only in current environment instead of globally	Yes (+)	No (-)
5	prevent namespace pollution	Yes (+)	No (-)
6	minimize typing - especially for infix operators (i.e. typing package::`%op%`(x, y) instead of `x %op% y` is cumbersome)	No (-)	Yes (+)
7	use multiple related packages, without constantly switching between package prefixes	No (-)	Yes (+)
	NOTE: + = advantage, - = disadvantage

What tinycodet attempts to do with its import system, is to somewhat find the best of both worlds. It does this by introducing the following functions:

import_as(): Import a main package, and optionally its re-exports + its dependencies + its extensions, under a single alias. This essentially combines the attaching advantage of using multiple related packages (row 7 on the table above), whilst keeping most advantages of using without attaching a package.
import_inops(): Expose infix operators from a package or an alias object to the current environment. This gains the attaching advantage of less typing (row 6 in table above), whilst simultaneously avoiding the disadvantage of attaching functions from a package globally (row 4).
import_data(): Directly return a data set from a package, to allow straight-forward assignment.

The import package system presented here is just another option provided, just like the import and box packages provide their own alternative import systems. Please feel free to completely ignore this article if you’re really adamant on attaching packages using library()/require() :-).

This article is rather lengthy, so I will start with a quick example code using tinycodet’ import system:

# importing "tidytable" + its re-exports + "data.table" under alias "tdt.":
import_as( 
  ~ tdt., "tidytable", dependencies = "data.table"
)
#> Importing packages and registering methods...
#> Done
#> You can now access the functions using `tdt.$`
#> For conflicts report, packages order, and other attributes, run `attr.import(tdt.)`

# exposing operators from `magrrittr` to current environment:
import_inops("magrittr")
#> Checking for conflicting infix operators in the current environment...
#> Placing infix operators in current environment...
#> Done

# directly assigning the "starwars" dataset to object "d":
d <- import_data("dplyr", "starwars") 

# see it in action:
d %>% tdt.$filter(species == "Droid") %>%
  tdt.$select(name, tdt.$ends_with("color"))
#> # A tidytable: 6 × 4
#>   name   hair_color skin_color  eye_color
#>   <chr>  <chr>      <chr>       <chr>    
#> 1 C-3PO  NA         gold        yellow   
#> 2 R2-D2  NA         white, blue red      
#> 3 R5-D4  NA         white, red  red      
#> 4 IG-88  none       metal       red      
#> 5 R4-P17 none       silver, red red, blue
#> 6 BB8    none       none        black

rm(list=ls()) # clearing everything

The above code is run without attaching any of the packages or its dependencies. So none of the problems with attaching a package is present.

Despite the length of this article, which is mostly due to me being overly detailed, the import system is made to be very simple for the user.

What follows are descriptions of the main functions that together form this new, infix-operator friendly & multi-package assignment friendly, import management system.

import_as

The import_as() function imports an R package + its re-exports under an alias, and also imports any specified direct dependencies and/or direct extensions of the package under the very same alias. It also informs the user which objects from a package will overwrite which objects from other packages, so you will never be surprised.

The main arguments of the import_as() function are:

alias: the name of the alias object under which to import the package(s). Can be given as a single string or as a formula with a single term. To keep aliases easily distinguishable from other objects that can also be subset with the $ operator, I recommend ending (not starting!) all alias names with a dot (.).
main_package: the name (string) of the main package to import.
re_exports: Some R packages export functions that are not defined in their own package, but in their direct dependencies - “re-exports”. If TRUE (default), the re-exports of the main_package are added to the alias, analogous to the behaviour of base R’s :: operator. If FALSE, re-exports are not added.
dependencies: an optional character vector giving the dependencies of the main_package to import under the alias also.
extensions: an optional character vector giving the extensions of the main_package to import under the same alias also.
lib.loc: the library paths to look for the packages; defaults to .libPaths(). This argument is present in all import_ - functions.

Here is one example. Lets import data.table and its extensions tidytable, under the same alias, which I will call “tdt.” (for “tidy data.table”):

import_as(~ tdt., "data.table", extensions = "tidytable") # this creates the tdt. object
#> Importing packages and registering methods...
#> Done
#> You can now access the functions using `tdt.$`
#> For conflicts report, packages order, and other attributes, run `attr.import(tdt.)`

Now one can use the imported functions using: tdt.$some_function().

import_inops

When aliasing an R package, infix operators are also imported in the alias. However, it may be cumbersome to use them from the alias. For example this:

import_as(~ to., "tinycodet")
to.$`%row~%`(x, mat)

or this:

tinycodet::`%row~%`(x, mat)

is very cumbersome.

Therefore, tinycodet also adds the import_inops() function, which exposes the infix operators. The infix operators are exposed to the current environment, but does not attach the functions to the namespace.

For example, to expose the infix operators in the alias object from before to the current environment, one can do the following:

import_inops(expose = tdt.)
#> Checking for conflicting infix operators in the current environment...
#> Placing infix operators in current environment...
#> Done

One can give the unexpose argument instead of the expose argument, which will delete the infix operators from those packages/package alias exposed in the current environment by import_inops(). Infix operators defined by the user will not be touched. For example:

import_inops(unexpose = tdt.)
#> Removing the following infix operators:
#> %inrange%, %chin%, :=, %between%, %ilike%, %notin%, %flike%, %like%, %in%, %plike%
#> Done

One can also expose and unexpose the infix operators directly from a package, instead of via an alias object. In that case the package name must be given as a string.

For example, the following code exposes the infix operators from the data.table R package:

import_inops(expose ="data.table")
#> Checking for conflicting infix operators in the current environment...
#> Placing infix operators in current environment...
#> Done

And similarly one can remove the exposed infix operators again from the current environment as follows:

import_inops(unexpose = "data.table")
#> Removing the following infix operators:
#> %between%, %like%, %ilike%, %chin%, %flike%, %inrange%, %plike%, :=, %notin%
#> Done

The import_inops() function has the exclude and include.only arguments to specify exactly which infix operators to expose to the current environment, as well as the overwrite and inherits arguments to specify what to do when the infix operators you are about to expose already exist in the current environment (and loaded namespaces). This can be handy to prevent overwriting any (user defined) infix operators already present in the current environment or loaded namespaces.

Examples:

import_inops(expose = tdt., include.only = ":=")
#> Checking for conflicting infix operators in the current environment...
#> Placing infix operators in current environment...
#> Done
import_inops(unexpose = tdt.)
#> Removing the following infix operators:
#> :=
#> Done
import_inops(expose = "data.table", , include.only = ":=")
#> Checking for conflicting infix operators in the current environment...
#> Placing infix operators in current environment...
#> Done
import_inops(unexpose = "data.table")
#> Removing the following infix operators:
#> :=
#> Done

If the user would rather attach the infix operators to the (global) namespace, tinycodet provides the pkg_lsf() function, which returns a character vector listing all functions or infix operators from a package. This vector can then be used in the include.only argument of the library() function. Like so:

library(magrittr, include.only = pkg_lsf("magrittr", type = "inops"))

import_data

The import_as() and import_inops() functions get all functions from the package namespace. But packages often also have data sets, which are often not part of the namespace.

The data() function in core R can already load data from packages, but this function loads the data into the global environment, instead of returning the data directly, making assigning the data to a specific variable a bit annoying. Therefore, the tinycodet package introduces the import_data() function, which directly returns a data set from a package.

For example, to import the chicago data set from the gamair R package, and assign it directly to a variable (without having to do re-assignment and so on), one simply runs the following:

d <- import_data("gamair", "chicago")
head(d)
#>   death pm10median pm25median  o3median  so2median    time tmpd
#> 1   130 -7.4335443         NA -19.59234  1.9280426 -2556.5 31.5
#> 2   150         NA         NA -19.03861 -0.9855631 -2555.5 33.0
#> 3   101 -0.8265306         NA -20.21734 -1.8914161 -2554.5 33.0
#> 4   135  5.5664557         NA -19.67567  6.1393413 -2553.5 29.0
#> 5   126         NA         NA -19.21734  2.2784649 -2552.5 32.0
#> 6   130  6.5664557         NA -17.63400  9.8585839 -2551.5 40.0

When to use or not to use the new import system

The ‘tinycodet’ import system is helpful particularly for packages that have at least one of the following properties:

The namespace of the package(s) conflicts with other packages.
The namespace of the package(s) conflicts with core R, or with those of recommended R packages.
The package(s) have function names that are generic enough, such that it is not obvious which function came from which package.

There is no necessity for using the ‘tinycodet’ import system with every single package. One can safely attach the ‘stringi’ package, for example, as ‘stringi’ uses a unique and immediately recognisable naming scheme (virtually all ‘stringi’ functions start with “stri_”), and this naming scheme does not conflict with core R, nor with most other packages.

Of course, if one wishes to use ‘stringi’ only within a specific environment, it becomes advantageous to import ‘stringi’ using the ‘tinycodet’ import system. In that case the import_LL() function would be most applicable.

Function attributes

All the functions imported by import_as(), import_inops(), and import_LL() functions will have a “package” attribute, so you will always know which function came from which package.

For example:

import_inops("magrittr")
#> Checking for conflicting infix operators in the current environment...
#> Placing infix operators in current environment...
#> Done
attributes(`%>%`)
#> $package
#> [1] "magrittr"
#> 
#> $function_name
#> [1] "%>%"
#> 
#> $tinyimport
#> [1] "tinyimport"
#> 
#> $class
#> [1] "function"   "tinyimport"

Example

One R package that could benefit from the import system introduced by tinycodet, is the dplyr R package. The dplyr R package overwrites core R functions (including base R) and it overwrites functions from pre-installed recommended R packages (such as MASS). I.e.:

rm(list=ls()) # clearing environment again
library(MASS)
library(dplyr) # <- notice dplyr overwrites base R and recommended R packages
#> 
#> Attaching package: 'dplyr'
#> The following object is masked from 'package:MASS':
#> 
#>     select
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

# detaching dplyr again:
detach("package:dplyr")

Moreover, dplyr’s function names are sometimes generic enough that there is no obvious way to tell if a function came from dplyr or some other package (for comparison: one can generally recognize stringi functions as they all start with stri_). If you look at the CRAN page for dplyr, you’ll notice it has some interesting extensions you might want to use, such as powerjoin.

To prevent masking base R functions, and to prevent obscurity regarding which functions come from dplyr and powerjoin, and which functions come from core R, one could constantly use dplyr:: and powerjoin::. But constantly switching between package prefixes or aliases is perhaps undesirable.

So here tinycodet’ import_as() function might help. Below is an example where dplyr is imported (including its re-exports), along with powerjoin (which is an extension), all under one alias which I’ll call “dpr.”. Moreover, all infix operators from magrittr are exposed to the current environment.

import_as(
  ~ dpr., "dplyr", extensions = "powerjoin", lib.loc = .libPaths()
)
#> Importing packages and registering methods...
#> Done
#> You can now access the functions using `dpr.$`
#> For conflicts report, packages order, and other attributes, run `attr.import(dpr.)`

import_inops("magrittr") # getting the infix operators from `magrittr`
#> Checking for conflicting infix operators in the current environment...
#> Placing infix operators in current environment...
#> Done

The functions from dplyr can now be used with the dpr.$ prefix. This way, base R functions are no longer overwritten, and it will be clear for someone who reads your code whether functions like the filter() function is the base R filter function, or the dplyr filter function, as the latter would be called as dpr.$filter().

Let’s first run a simple example code with the imported functions:

d <- import_data("dplyr", "starwars")
d %>%
  dpr.$filter(.data$species == "Droid") %>% # notice the ".data" pronoun can be used without problems
  dpr.$select(name, dpr.$ends_with("color"))
#> # A tibble: 6 × 4
#>   name   hair_color skin_color  eye_color
#>   <chr>  <chr>      <chr>       <chr>    
#> 1 C-3PO  NA         gold        yellow   
#> 2 R2-D2  NA         white, blue red      
#> 3 R5-D4  NA         white, red  red      
#> 4 IG-88  none       metal       red      
#> 5 R4-P17 none       silver, red red, blue
#> 6 BB8    none       none        black

Just add dpr.$ in front of the functions you’d normally use, and everything works just as expected.

Now lets run an example from the powerjoin GitHub page (https://github.com/moodymudskipper/powerjoin), using the above alias:

male_penguins <- dpr.$tribble(
     ~name,    ~species,     ~island, ~flipper_length_mm, ~body_mass_g,
 "Giordan",    "Gentoo",    "Biscoe",               222L,        5250L,
  "Lynden",    "Adelie", "Torgersen",               190L,        3900L,
  "Reiner",    "Adelie",     "Dream",               185L,        3650L
)

female_penguins <- dpr.$tribble(
     ~name,    ~species,  ~island, ~flipper_length_mm, ~body_mass_g,
  "Alonda",    "Gentoo", "Biscoe",               211,        4500L,
     "Ola",    "Adelie",  "Dream",               190,        3600L,
"Mishayla",    "Gentoo", "Biscoe",               215,        4750L,
)
dpr.$check_specs()
#> # powerjoin check specifications
#> ℹ implicit_keys
#> → column_conflict
#> → duplicate_keys_left
#> → duplicate_keys_right
#> → unmatched_keys_left
#> → unmatched_keys_right
#> → missing_key_combination_left
#> → missing_key_combination_right
#> → inconsistent_factor_levels
#> → inconsistent_type
#> → grouped_input
#> → na_keys

dpr.$power_inner_join(
  male_penguins[c("species", "island")],
  female_penguins[c("species", "island")]
)
#> Joining, by = c("species", "island")
#> # A tibble: 3 × 2
#>   species island
#>   <chr>   <chr> 
#> 1 Gentoo  Biscoe
#> 2 Gentoo  Biscoe
#> 3 Adelie  Dream

Notice that the only change made, is that all functions start with dpr.$, the rest is the same. No need for constantly switching between dplyr::..., powerjoin::... and so on - yet it is still clear from the code that the functions came from the dplyr + powerjoin family, and there is no fear of overwriting functions from other R packages - let alone core R functions.