[R] Why does matrix selection behave differently when using which?

[David Winsemius]

On Dec 17, 2012, at 11:22 AM, Asis Hallab wrote:

> Dear R community,
> 
> I have a medium sized matrix stored in variable "t" and a simple function "
> countRows" (see below) to count the number of rows in which a selected
> column "C" matches a given value. If I count all rows matching all pairwise
> distinct values in the column "C" and sum these counts up, I get the number
> or rows of "t". If I delete the "which" calls from function "countRows" the
> resulting sum of matching row numbers is much greater than the number of
> rows in "t".
> 
> The table "t" I use can be downloaded from here:
> https://github.com/groupschoof/PhyloFun/archive/test_selector.zip

What part of "minimal" example are you having difficulty understanding? That zip file expands to a 1.8 MB file!


> Unzip the file and read in the table "t" using t <- read.table("test.tbl")

Since it has a header line, you will be creating all factors and it's doubtful you are getting what you want.

Instead:

 t <- read.table("test.tbl", header=TRUE)
> 
> The above function "sumRows" is defined as follows:
> sumRows <- function( tbl, ps ) {
>  sum(
>    sapply(ps,

'ps'? What is ps????

>      function(x) {
>        t <- if ( is.na(x) ) {

I suspect that it is not `which` that is the problem, but rahter your understanding of how `if` processes vectors. (This also should be simplified greatly to avoid stepping through vectors one element at a time.)

>          tbl[ which( is.na(tbl[ , "Domain.Architecture.Distance" ]) ), ,
> drop=F]

You didn't do anything with that result!

>        } else {
>          tbl[ which( tbl[ , "Domain.Architecture.Distance" ] == x ), ,
> drop=F]
>        }
>        nrow(t)

That value will not depend in any manner on what preceded it.  ???? It will simply be the number of rows in the local copy of "t"

You goal is _only_ to get a count? 

Why not just this:

 sum( tbl[!is.na(tbl$Domain.Architecture.Distance), "Domain.Architecture.Distance" ] == x )

E.g.:

> sum( tbl[!is.na(tbl$Domain.Architecture.Distance), "Domain.Architecture.Distance" ] == 0.99)
[1] 3440

You should probably be creating a factor variable with `cut` to create reasonable intervals for grouping, and if you do not know this it suggests you need to do more stufy of the text or introductory materials.To get a quick look at the distribution this is useful"

plot( density(tbl[!is.na(tbl$Domain.Architecture.Distance), "Domain.Architecture.Distance" ] ))

(125 KB file so not attached)

> table( cut(tbl$Domain.Architecture.Distance, breaks=(0:10)/10) )

  (0,0.1] (0.1,0.2] (0.2,0.3] (0.3,0.4] (0.4,0.5] (0.5,0.6] (0.6,0.7] (0.7,0.8] (0.8,0.9]   (0.9,1] 
      616      1864       328       103       923      1763      1151      2490      3709     38563 

>      }
>    )
>  )
> }
> 
> What does cause the different behavior of sumRows, when the which calls are
> deleted?
> What does which do, I seem not to grasp?

The question ... as yet unanswered ....  is _how_ exactly are you calling that function. You posted a link to data "t" but there is no code that calls that function with the data. I do not see anything that would resemble a "ps"-object.


> Or is there an error in my test.tbl?

(See above.)

> * *
> Any help on this subject will be greatly appreciated.
> Kind regards and *merry christmas*!
> 
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-- 
David Winsemius
Alameda, CA, USA