Importing in R; (read.csv) Ignore non-numeric columns automatically

Question

I want to import a tsv file including some non-numeric fields (i.e., date or string) in R:

num1    num2    date
1   2   2012-10-18 12:17:19
2   4   2014-11-16 09:30:23
4   11  2010-03-18 22:18:04
12  3   2015-02-18 12:55:50
13  1   2014-05-16 10:39:11
2   14  2011-05-26 20:48:54

I am using the following command:

a = read.csv("C:\test\testFile.tsv", sep="\t")

I want to ignore all non-numeric values automatically (or put something like "NA"). And don't want to mention all the string column names to be ignored.

I tried "stringsAsFactors" and "as.is" parameters, with no success.

Any ideas?

That's a good idea. Thank you. But, again, we have to check of the field types (for more than 10 fields in the real case). We want the correlation between numeric values. I tried rcorr(as.matrix(a[,1:2])) and it works for this case, but not for the more complicated case. — Alisa
– Alisa, Commented Jul 7, 2015 at 22:55
@Alisa - Maybe consider doing a <- a[sapply(a,is.numeric)] — thelatemail
– thelatemail, Commented Jul 7, 2015 at 22:59

daniel · Accepted Answer · 2015-07-08 03:14:19Z

1

You have quite a few options here. First, you can inform R while reading the table:

data <- read.csv("C:\test\testFile.tsv", 
sep="\t", 
colClasses=c(NA, NA, "NULL"))

If you have many nonnumeric columns, say 10, you can use rep as colClasses=c(NA, NA, rep("NULL", 10)).

Second, you can read everything and process deletion afterwards (note the stringsAsFactors):

data <- read.csv("C:\test\testFile.tsv", 
    sep="\t", stringsAsFactors = FALSE)

You can subset everything column that is identified as character.

df[, !sapply(df, is.character)]

Or then apply a destructive method to you data.frame:

  df[sapply(df, is.character)] <- list(NULL)

You can go further to make sure only numeric columns are left:

df[,-grep ("Date|factor|character", sapply(df, class))] <- list(NULL)

answered Jul 8, 2015 at 3:14

daniel

1,2662 gold badges13 silver badges26 bronze badges

Sign up to request clarification or add additional context in comments.

Comments

Alisa · Accepted Answer · 2015-07-07 22:49:39Z

0

Just found this solution:

a = read.csv("C:\test\testFile.tsv", sep="\t", colClasses=c(NA, NA, "NULL"))

It is not completely automatic though.

answered Jul 7, 2015 at 22:49

Alisa

3,1423 gold badges35 silver badges45 bronze badges

Collectives™ on Stack Overflow

Importing in R; (read.csv) Ignore non-numeric columns automatically

2 Answers 2

Comments

Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

Comments

Comments

Your Answer

Sign up or log in

Post as a guest

Related