On Jan 18, 2010, at 8:53 AM, David Winsemius wrote:
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) ) )
Ooops, forgot the negation operator to turn not(NA) into TRUE:
apply(b[,-1], 2, function(x) sum(!is.na(x) ) )
b) The total number of 1's, ie Fails per round
apply(b[,-1], 2, sum, na.rm=TRUE )
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