Help using Cast (Text) Version

On Jan 18, 2010, at 7:58 AM, Steve Sidney wrote:

Hi David

Thanks for your patience, as well as thanks to Dennis Murphy and  
James Rome for trying to help.

I have tried all your suggestions but still no joy.

In order to try and resolve the problem I am attaching the  
following files, hope the system allows this.

1) Test_data_res.txt (used dput and this is all the data to be  
evaluated )
2) Test_data_b.txt ( after performing the melt-cast. See the code)
3) Annual Results NLA WMS Ver1.r ( the code for one of the  
parameters to be evaluated. In this case SPC)

Background; the data is from a laboratory Proficiency Testing  
Scheme and the z-scores outside the |3| range, are identified as  
"fails". My code assigns a 1 or 0 depending on this evaluation and  
because not every lab participates in every round NA are assigned  
where there are no results.

What I am looking for is the following for each round (1-6)
a) The total number of participants which in this case are  
represented by 1's and 0' per round

apply(b[,-1], 2, function(x) sum(is.na(x) ) )

[1] 32 21 21 18 14 15

b) The total number of 1's, ie Fails per round

apply(b[,-1], 2, sum, na.rm=TRUE )

[1] 5 2 4 3 5 7

Regards
Steve



----- Original Message ----- From: "David Winsemius" <dwinsemius at comcast.net 

To: "Steve Sidney" <sbsidney at mweb.co.za>
Cc: <r-help at r-project.org>
Sent: Monday, January 18, 2010 12:38 AM
Subject: Re: [R] Help using Cast (Text) Version

On Jan 17, 2010, at 4:37 PM, Steve Sidney wrote:

Well now I am totally baffled !!!!!!!!!!

Using

sum( !is.na(b[,3])) I get the total of all col 3 except those  
that  are NA -
Great solves the first problem

What I can't seem to do is use the same logic to count all the  
1's  in that
col, which are there before I use the cast with margins.

So it seems to me that somehow   is wrong and is the part of my  
understanding that's missing.

My guess is that that before using margins and sum in the cast   
statement the col is a character type and in order for == 1 to  
work  I need to convert this to an integer.

Yiu can test your theory with:

sum(as.integer(b[,3]) == 1)

Or you could post some reproducible data using dput ....

-- 
David.

Hope this helps you to understand the problem.

Regards
Steve

Your help is much appreciated
----- Original Message ----- From: "David Winsemius" <dwinsemius at comcast.net

To: "Steve Sidney" <sbsidney at mweb.co.za>
Cc: <r-help at r-project.org>
Sent: Sunday, January 17, 2010 7:36 PM
Subject: Re: [R] Help using Cast (Text) Version

On Jan 17, 2010, at 11:56 AM, Steve Sidney wrote:

David

Thanks, I'll try that......but no what I need is the total  
(1's) for
each of the rows, labelled 1-6 at the top of each col in the  
table
provided.

Part of my confusion with your request (which remains  
unaddressed) is
what you mean by "valid". The melt-cast operation has turned a   
bunch of
NA's into 0's which are now indistinguishable from the  
original   0's. So I
don't see any way that operating on "b" could tell you the   
numbers  you
are asking for. If you were working on the original data,   
"res", you
might have gotten the column-wise "valid" counts of column  2 with
something like:

sum( !is.na(res[,2]) )

What I guess I am not sure of is how to identify the col after   
the melt
and cast.

The cast object represents columns as a list of vectors. The i- 
th column
is b[[i]] which could be further referenced as a vector. So the   
j- th row
entry for the i-th column would be b[[i]][j].

Steve

----- Original Message ----- From: "David Winsemius"
<dwinsemius at comcast.net

To: "Steve Sidney" <sbsidney at mweb.co.za>
Cc: <r-help at r-project.org>
Sent: Sunday, January 17, 2010 4:39 PM
Subject: Re: [R] Help using Cast (Text) Version

On Jan 17, 2010, at 5:31 AM, Steve Sidney wrote:

Sorry to repeat the meassage, not sure if the HTML version  
has   been
received - Apologies for duplication

Dear list

I am trying to count the no of occurances in a column of a   
data frame
and there is missing data identifed by NA.

I am able to melt and cast the data correctly as well as sum  
the
occurances using margins and sum.

Here are the melt and cast commands

bw = melt(res, id=c("lab","r"), "pf_zbw")
b = cast(bw, lab ~ r, sum, margins = T)

Sample Data (before using sum and margins)

lab  1  2  3  4  5  6
1  4er66  1 NA  1  0 NA  0
2  4gcyi  0  0  1  0  0  0
3  5d3hh  0  0  0 NA  0  0
4  5d3wt  0  0  0  0  0  0
.
. lines deleted to save space
.
69 v3st5 NA NA  1 NA NA NA
70 a22g5 NA  0 NA NA NA NA
71 b5dd3 NA  0 NA NA NA NA
72 g44d2 NA  0 NA NA NA NA

Data after using sum and margins

lab 1 2 3 4 5 6 (all)
1  4er66 1 0 1 0 0 0     2
2  4gcyi 0 0 1 0 0 0     1
3  5d3hh 0 0 0 0 0 0     0
4  5d3wt 0 0 0 0 0 0     0
5  6n44r 0 0 0 0 0 0     0
.
.lines deleted to save space
.
70 a22g5 0 0 0 0 0 0     0
71 b5dd3 0 0 0 0 0 0     0
72 g44d2 0 0 0 0 0 0     0
73 (all) 5 2 4 3 5 7    26

Uisng length just tells me how many total rows there are.

What I need to do is count how many rows there is valid  
data,  in this
case either a one (1) or a zero (0) in b

I'm guessing that you mean to apply that test to the column in b
labeled "(all)" . If that's the case, then something like    
(obviously
untested):

sum( b$'(all)' == 1 | b$'(all)' == 0)

I have a report to construct for tomorrow Mon so any help  
would be
appreciated

Regards
Steve

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

<Test_data_b.txt><Test_data_res.txt><Annual Results NLA WMS Ver1.r>

David Winsemius, MD
Heritage Laboratories
West Hartford, CT