Favorite R Tools

I find that the longer I use R, the more my preferred solutions converge around a decreasing number of commands. But every now and then I find something new that makes life so much easier and it finds its way into my repertoire. Here’s a quick post on some of these (code) life-changing commands. Some of these are fairly well-known, others less-so.

Base R functions

Here are a few that come from base R (and can be applied in any situation)

1. %in%

I don’t think I could live without %in%. As its name implies, it checks if an object or a value is present in some other object. So if you have a list fruit <- c('apples', 'oranges', 'bananas') and you want to know if pears is in your list: 'pears' %in% fruit will return a logical FALSE. This has numerous applications, but I probably use it most frequently for subsetting dataframes. So let’s take a toy example where you have some data that has observations for all US States, but you only want the ones for Texas and Wisconsin (obviously).

 dat <- read.csv('my_amazing_data.csv', 
                 header = T, 
                 sep = ",", 
                 stringsAsFactors = F)
 
 # The bad old way
 dat <- dat[which(dat$state == "Texas" | dat$state == "Wisconsin"),]
 
 # The better new way
 dat <- dat[which(dat$state %in% c("Texas", "Wisconsin"),]

Even when we only have a list of two things to test membership against, our code is shortened. The advantage obviously grows even more as that list grows.

2. match

This is closely related to %in% but serves a slightly different purpose. According to the help file,

match returns a vector of the positions of (first) matches of its first argument in its second.

Using the fruit example again, match('oranges', fruit) will return 2, indicating that 'oranges' is the second element in fruit. Note that if you tried match('pears', fruit), R would return NA. I find this to be a really intuitive way to assign values from one dataframe to another where some values may be repeated.

3. setdiff, union, and intersect

Logical operators for sets that can make life so much easier.¹ Fans of Venn diagrams will love these. They act logically according to their names, can be strung together, and are highly optimized.

4. get and mget

These two commands (a single and multiple version, respectively) will return an actual object from a quoted string. Let’s say you have a series of dataframes a1 through a4 and you need to create a new object that is a list of those four dataframes that you’ll pass on to some other function. If you just run df_list <- c('a1', 'a2', 'a3', 'a4'), you’ll end up with a list of four strings, not the dataframes themselves. You could solve this by changing your syntax to df_list <- mget('a1', 'a2', 'a3', 'a4'). And if you had a really long list of objects, say a1 through a999, then you could even do something like this: df_list <- mget(grep('a\\d+', ls(), value = T)).

This is often useful within custom functions. For example, if you have a function that takes a string argument but references an actual object. If you’re using the tidyverse you’ll have to solve this problem in other ways (read the dplyr documentation on quotation and quasiquotation.

5. assign

This is the full command version of the assignment arrow <-. The order of the arguments is the same, read left to right, but you need to quote the name you want to use. So my_var <- 5 is equivalent to assign('my_var', 5).

Like get, this can be very useful within custom functions for two reasons.² First, it allows you to create a function that takes a string to use as a name for an object created within the function. Second, the assign function has an additional argument envir that specifies the environment in which to create the object. Normally everything happening within a function happens within its own environment, so any variables that you create within the function will disappear when it completes. assign can overcome this and create in the global environment. Compare these two functions:

 func_1 <- function(x){
     draws <- rnorm(x)
 }
 func_1(10)
 print(draws)
 # Will return "Error in print(draws) : object 'draws' not found
 
 func_2 <- function(x){
     assign("draws", rnorm(x), envir = .GlobalEnv)
 }
 func_2(10)
 print(draws)
 # Will return the vector of values

6. do.call

From the documentation,

‘do.call’ constructs and executes a function call from a name or a function and a list of arguments to be passed to it.

The way I use this (and the only way I’ve seen others use it) is to repeat a function multiple times. In particular, it’s great for collapsing a list. The same thing can be accomplished with purrr::reduce. The advantage of do.call is that it’s base R (and you don’t have to try to remember how many Rs are in purrr).

Here’s a (mostly) real example from a project I’m working on. Note: don’t try to run this unless you want your computer to be busy for a very long time. The code defines a function then replicates it 100,000 times using parallel execution. The result is a list that needs to be flattened into a data.frame, which happens in the final line.

 rnd_experiment <- function(i){
   samp_data_a <- sample(nums, 150000, replace = TRUE)
   samp_data_b <- sample(nums, 150000, replace = TRUE)
   samp_data_c <- sample(nums, 150000, replace = TRUE)
   samp_dat <- as.data.frame(cbind(samp_data_a,
                                   samp_data_b,
                                   samp_data_c))
   samp_dat$score <- apply(samp_dat, 1, mean)
   rd_test <- rddensity::rddensity(samp_dat$score, c = 15.7)
   out_row <- c(t = rd_test$test$t_jk, p = rd_test$test$p_jk)
   return(out_row)
 }
 
 tests <- parallel::mclapply(1:1e5,
                             rnd_experiment,
                             mc.cores = (parallel::detectCores() - 1))
 tests <- as.data.frame(do.call("rbind", tests))

Tidyverse related

These either come from the tidyverse and/or are used exclusively with those packages

7. %>% and %<>%

I’m trying to move away from the tidyverse world, but that’s hard to do partly because of the amazing convenience of pipes. The simple forward pipe %>% is imported by dplyr these days, but it and its other pipe cousins actually come from the magrittr package. These pipes let you string together a series of transformations in a really easy and logical way.

 dat <- dat %>%
     filter(state %in% c("Texas", "Wisconsin") %>%
     select(state, year, other_column)

In short, this says “dat gets dat, THEN filter observations THEN select certain variables.” Easy! But dat <- dat is ugly. So let’s use the compound assignment pipe:

 dat %<>%
     filter(state %in% c("Texas", "Wisconsin") %>%
     select(state, year, other_column)

That’s better. magrittr has several other pipes (take a look here, but these are the only two that are in my current workflow.

8. do

For all those times when you want to combine a custom function you wrote (or even a base function that doesn’t have a tidy equivalent) with a dplyr-esque pipe. I find this really helpful when combined with group_by.

Other packages

And finally a few that come from other packages (but still work anywhere)

9. wrapr::qc()

Very basic function that takes unquoted names and returns a quoted list.

 # old way
 fruits <- c('apples', 'oranges', 'bananas')
 fruits
 
 # [1] "apples"  "oranges" "bananas"
 
 # new way
 fruits <- qc(apples, oranges, bananas)
 fruits
 # [1] "apples"  "oranges" "bananas"

Okay, so for this example that only saves 5 keystrokes, but for longer lists it can really come in handy. One downside is that I don’t really want to load the entire wrapr library and R doesn’t have a nice Python-esque from wrapr import qc option³, so I’m forced to add qc <- wrapr::qc to the start of my scripts.

10. countrycode::countrycode()

This is an enormously useful function for converting country codes from one standard to another for those times when you want to merge two datasets with country level observations and no shared identifier. This is a problem I face ALL THE TIME and will write a full post on it soon, but here’s a quick overview of what you can do with this one function.

 # Go from one standard to another, including a custom match
 cow$c1 <- countrycode::countrycode(cow$ccode1,
                                    origin = "cown",
                                    destination = "country.name",
                                    custom_match = c("710.1" = "Hong Kong"))
 # Go from a code to a readable name
 gn$country_name <- countrycode::countrycode(gn$country_code,
                                             origin = "iso2c",
                                             destination = "country.name")
 
 # Go from country to continent
 continents <- countrycode::countrycode(my_countries,
                                        origin = "country.name",
                                        destination = "continent")