Mark Needham

Thoughts on Software Development

R: Filter a data frame based on values in two columns

with one comment

In the most recent assignment of the Computing for Data Analysis course we had to filter a data frame which contained N/A values in two columns to only return rows which had no N/A’s.

I started with a data frame that looked like this:

> data <- read.csv("specdata/002.csv") 
> # we'll just use a few rows to make it easier to see what's going on
> data[2494:2500,]
           Date sulfate nitrate ID
2494 2007-10-30    3.25   0.902  2
2495 2007-10-31      NA      NA  2
2496 2007-11-01      NA      NA  2
2497 2007-11-02    6.56   1.270  2
2498 2007-11-03      NA      NA  2
2499 2007-11-04      NA      NA  2
2500 2007-11-05    6.10   0.772  2

We want to only return the rows which have a value in both the ‘sulfate’ and the ‘nitrate’ columns.

I initially tried to use the Filter function but wasn’t very successful:

> smallData <- data[2494:2500,]
> Filter(function(x) !is.na(x$sulfate), smallData)
Error in x$sulfate : $ operator is invalid for atomic vectors

I’m not sure that Filter is designed to filter data frames – it seems more appropriate for lists or vectors – so I ended up filtering the data frame using what I think is called an extract operation:

> smallData[!is.na(smallData$sulfate) & !is.na(smallData$nitrate),]
           Date sulfate nitrate ID
2494 2007-10-30    3.25   0.902  2
2497 2007-11-02    6.56   1.270  2
2500 2007-11-05    6.10   0.772  2

The code inside the square brackets returns a collection indicating whether or not we should return each row:

> !is.na(smallData$sulfate) & !is.na(smallData$nitrate)
[1]  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE

which is equivalent to doing this:

> smallData[c(TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE),]
           Date sulfate nitrate ID
2494 2007-10-30    3.25   0.902  2
2497 2007-11-02    6.56   1.270  2
2500 2007-11-05    6.10   0.772  2

We put a comma after the list of true/false values to indicate that we want to return all the columns otherwise we’d get this error:

> smallData[c(TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE)]
Error in `[.data.frame`(smallData, c(TRUE, FALSE, FALSE, TRUE, FALSE,  : 
  undefined columns selected

We could filter the columns as well if we wanted to:

> smallData[c(TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE), c(1,2)]
           Date sulfate
2494 2007-10-30    3.25
2497 2007-11-02    6.56
2500 2007-11-05    6.10

As is no doubt obvious, I don’t know much R so if there’s a better way to do anything please let me know.

The full code is on github if you’re interested in seeing it in context.

Written by Mark Needham

January 23rd, 2013 at 10:34 pm

Posted in R

Tagged with

  • http://julioes.com/ Julio Espinoza-Sokal

    I think you were looking for the complete.cases function. smallData[complete.cases(smallData)] will filter the same rows.