R: What are the best functions to deal with concatenating and averaging values in a data.frame?

Question

I have a data.frame from this code: ``` my_df = data.frame("read_time" = c("2010-02-15", "2010-02-15", "2010-02-16", "2010-02-16", "2010-02-16", "2010-02-17"), "OD" = c(0.1, 0.2, 0.1, 0.2, 0.4, 0.5) ) ``` which produces this: ``` > my_df read_time OD 1 2010-02-15 0.1 2 2010-02-15 0.2 3 2010-02-16 0.1 4 2010-02-16 0.2 5 2010-02-16 0.4 6 2010-02-17 0.5 ``` I want to average the OD column over each distinct read_time (notice some are replicated others are not) and I also would like to calculate the standard deviation, producing a table like this: ``` > my_df read_time OD stdev 1 2010-02-15 0.15 0.05 5 2010-02-16 0.3 0.1 6 2010-02-17 0.5 0 ``` Which are the best functions to deal with concatenating such values in a data.frame?

Accepted Answer

The plyr package is popular for this, but the base functions `by()` and `aggregate()` will also help.

```
> ddply(my_df, "read_time", function(X) data.frame(OD=mean(X$OD),stdev=sd(X$OD)))
   read_time      OD   stdev
1 2010-02-15 0.15000 0.07071
2 2010-02-16 0.23333 0.15275
3 2010-02-17 0.50000      NA
```

You can add the missing bit to return 0 instead of NA for the last std.dev.

Also, you don't need the quotes (on the variables) you had in the data.frame construction.

R: What are the best functions to deal with concatenating and averaging values in a data.frame?

Solution

Problem