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*!
>
> [[alternative HTML version deleted]]
Please read the Posting Guide and learn to post in plain text.
--
David Winsemius
Alameda, CA, USA
______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
