[R] Making tapply code more efficient

ONKELINX, Thierry Thierry.ONKELINX at inbo.be
Fri Feb 27 16:23:38 CET 2009

Hi Harold,

What about this? You one have to make the crosstabulation once.

> qq <- data.frame(student = factor(c(1,1,2,2,2)), teacher =
> tab <- table(qq$student, qq$teacher)
> data.frame(Student = rownames(tab), Freq = rowSums(tab), tch =
rowSums(tab > 0) == 1)
  Student Freq   tch
1       1    2  TRUE
2       2    3 FALSE



ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be 

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than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

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ensure that a reasonable answer can be extracted from a given body of
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Doran, Harold
Verzonden: vrijdag 27 februari 2009 15:47
Aan: r-help at r-project.org
Onderwerp: [R] Making tapply code more efficient

Previously, I posed the question pasted down below to the list and
received some very helpful responses. While the code suggestions
provided in response indeed work, they seem to only work with *very*
small data sets and so I wanted to follow up and see if anyone had ideas
for better efficiency. I was quite embarrased on this as our SAS
programmers cranked out programs that did this in the blink of an eye
(with a few variables), but R was spinning for days on my Ubuntu machine
and ultimately I saw a message that R was "killed".

The data I am working with has 800967 total rows and 31 total columns.
The ID variable I use as the index variable in tapply() has 326397
unique cases.

> length(unique(qq$student_unique_id))
[1] 326397

To give a sense of what my data look like and the actual problem,
consider the following:

qq <- data.frame(student_unique_id = factor(c(1,1,2,2,2)),
teacher_unique_id = factor(c(10,10,20,20,25)))

This is a student achievement database where students occupy multiple
rows in the data and the variable teacher_unique_id denotes the class
the student was in. What I am doing is looking to see if the teacher is
the same for each instance of the unique student ID. So, if I implement
the following:

same <- function(x) length( unique(x) ) == 1
results <- data.frame(
        freq = tapply(qq$student_unique_id, qq$student_unique_id,
        tch = tapply(qq$teacher_unique_id, qq$student_unique_id, same)

I get the following results. I can see that student 1 appears in the
data twice and the teacher is always the same. However, student 2
appears three times and the teacher is not always the same.

> results
  freq   tch
1    2  TRUE
2    3 FALSE

Now, implementing this same procedure to a large data set with the
characteristics described above seems to be problematic in this

Does anyone have reactions on how this could be more efficient such that
it can run with large data as I described?


> sessionInfo()
R version 2.8.1 (2008-12-22)


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

##### Original question posted on 1/13/09
Suppose I have a dataframe as follows:

dat <- data.frame(id = c(1,1,2,2,2), var1 = c(10,10,20,20,25), var2 =
c('foo', 'foo', 'foo', 'foobar', 'foo'))

Now, if I were to subset by id, such as:

> subset(dat, id==1)
  id var1 var2
1  1   10  foo
2  1   10  foo

I can see that the elements in var1 are exactly the same and the
elements in var2 are exactly the same. However,

> subset(dat, id==2)
  id var1   var2
3  2   20    foo
4  2   20 foobar
5  2   25    foo

Shows the elements are not the same for either variable in this
instance. So, what I am looking to create is a data frame that would be
like this

id      freq    var1    var2
1       2       TRUE    TRUE   
2       3       FALSE   FALSE

Where freq is the number of times the ID is repeated in the dataframe. A
TRUE appears in the cell if all elements in the column are the same for
the ID and FALSE otherwise. It is insignificant which values differ for
my problem.

The way I am thinking about tackling this is to loop through the ID
variable and compare the values in the various columns of the dataframe.
The problem I am encountering is that I don't think all.equal or
identical are the right functions in this case.

So, say I was wanting to compare the elements of var1 for id ==1. I
would have

x <- c(10,10)

Of course, the following works

> all.equal(x[1], x[2])
[1] TRUE

As would a similar call to identical. However, what if I only have a
vector of values (or if the column consists of names) that I want to
assess for equality when I am trying to automate a process over
thousands of cases? As in the example above, the vector may contain only
two values or it may contain many more. The number of values in the
vector differ by id.

Any thoughts?


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