Using browser() in R

Interactive Debugging with Environment Browser
Leon Kim | www.betweentwotests.com

Overview of base::browser()
This is a brief overview of base::browser() and how to use
it for debugging in R.
browser() is default function found in R.
Useful tool to “hack into” R functions (that you or other
people wrote)

Typical day in lab
head(iris)
## Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1 5.1 3.5 1.4 0.2 setosa
## 2 4.9 3.0 1.4 0.2 setosa
## 3 4.7 3.2 1.3 0.2 setosa
## 4 4.6 3.1 1.5 0.2 setosa
## 5 5.0 3.6 1.4 0.2 setosa
## 6 5.4 3.9 1.7 0.4 setosa
Task: Researcher’s ruler was oﬀ by 5 inches. Let’s adjust it!

Oops
# Loop through each column and add 5
df <- iris
for(j in 1:ncol(df)){
df[,j] <- df[,j] + 5
}
## Warning in Ops.factor(df[, j], 5): '+' not meaningful for factors
unlist(lapply(iris, class))
## "numeric" "numeric" "numeric" "numeric" "factor"
Forgot that Species column is not numeric!

Quick and dirty solution
# Loop through each column EXCEPT the last one
df <- iris
for(j in 1:(ncol(df)-1)){
df[,j] <- df[,j] + 5
}
head(df)
## 1 10.1 8.5 6.4 5.2 setosa
## 2 9.9 8.0 6.4 5.2 setosa
## 3 9.7 8.2 6.3 5.2 setosa
## 4 9.6 8.1 6.5 5.2 setosa
## 5 10.0 8.6 6.4 5.2 setosa
## 6 10.4 8.9 6.7 5.4 setosa

We got lucky
Not all error messages are obvious
Not all bugs come from such easy code
Not all bugs are this easy to ﬁx

More likely scenario
foo_1 <- function(x) { ... }
foo_2 <- function(x) { ... }
# Code that produces some error
foo_1(df[,j]); foo_2(df[,j])
}
foos <- function(x) {
foo_1(foo_2(x))
}
super_foo <- function(df) {
# Code that produces some error
foos(df[,j])
}
}
super_foo(iris)

browser() to the rescue
browser() <--------
foo_1(df[,j])
foo_2(df[,j])
}

Example
add_five <- function(x) {x + 5}
df <- iris
outside_var <- "I'm outside the loop"
print(paste("start of the iteration:", j))
inside_var <- "I'm inside the loop"
browser()
df[,j] <- add_five(df[,j])
print(paste("end of the interation:", j))
}

Trigger browser() mode
Run your code
Run expressions within browser() mode

What can I do in browser() mode?
Type help for list of avaiable commands

‘c’: execute all of the function
Executes everything left (until the next browser() call that is)
Sanity check: has the ﬁrst column of df been changed?

‘n’: Go to the next line
Moves to beginning of the next line
Also executes your current line (before moving to next ine)

‘s’: R-ception
Go into the function call

In RStudio
GUI supports (for function calls)

Access everything inside the function environment
Access variables as the function sees it

Eﬀectively use browser() : #1
add_five <- function(x) {x + 5}
df <- iris
if(j == 5) {
browser()
}
df[,j] <- add_five(df[,j])
}

Eﬀectively use browser() : #2
library(dplyr)
df <- iris
df %>%
group_by(Species) %>%
mutate(avg_sepal_length =
list(Species = Species,
Sepal.Length = Sepal.Length) %>%
browser()
)

Look at individual group
Pass data to browser()

tl;dr
browser() allows you to interactively code in any environment
scope during R execution

Using browser() in R

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