Bingo,
I knew it was something simple and that I wasn't seeing the wood for the
trees.
David, Ista
Apologies for the vague description, which I thought was clear enough, but
yes I now think that I understand that I need to count the 1's and be able
to sum the total of 1' and 0's by ignoring the NA's, which as David you have
correctly identified is in res. Of course as you have quite correctly said
by the time it's melt-cast there is now way to distinguish between NA's and
0's.
Here is the original code so that you can see where res comes from; Ista I
hope that this is now clearer for you.
library(reshape)
# Enter file name to Read & Save data
FileName=readline("Enter File name:\n")
SampleName=readline("Enter Sample (A,B or C):\n")
#for (sname in 1 : 3) {
#if (sname == 1)
# SampleName = "A"
# if (sname == 2)
# SampleName = "B"
# if (sname == 3)
# SampleName = "C"
#for ( fname in 1 : 4) {
#if (fname == 1)
# FileName = "SPC"
# if (fname == 2)
# FileName = "Coli"
# if (fname == 3)
# FileName = "Colif"
# if (fname == 4)
# FileName = "Ecoli"
# Find first occurance of file
for ( rloop1 in 1 : 6) {
ReadFile=paste(rloop1,SampleName,"_",FileName,"_Stats.csv", sep="")
if (file.exists(ReadFile))
break
}
x = data.frame(read.csv(ReadFile, header=T),rnd=rloop1)
for ( rloop2 in (rloop1+1) : 6) {
ReadFile=paste(rloop2,SampleName,"_",FileName,"_Stats.csv", sep="")
if (file.exists(ReadFile)) {
y = data.frame(read.csv(ReadFile, header=T),rnd = rloop2)
if (rloop2 == (rloop1+1))
z=merge(x,y,all=T)
z=merge(y,z,all=T)
## The next piece of code is where there are not two successive rounds of
data.
## It must be modified for each year's summary
##
##if ( (FileName == "Coli") & (SampleName == "B")) {
## if (rloop2 == (rloop1+3))
## z=merge(x,y,all=T)
## z=merge(y,z,all=T)
## }
##
##
}
}
results <- z
res = data.frame(
lab=results[,"lab_id"],bw=results[,"ZBW"],wi=results[,"ZWI"],pf_zbw=0,pf_zwi=0,r
= results[,"rnd"])
#
# Establish no of samples recorded
nsmpls = length(res[,c("lab")])
#Evaluate Z_scores for Between Lab Results
for ( i in 1 : nsmpls) {
if (res[i,"bw"] > 3 | res[i,"bw"] < -3)
res[i,"pf_zbw"]=1
}
#Evaluate Z_scores for Within Lab Results
for ( i in 1 : nsmpls) {
if (res[i,"wi"] > 3 | res[i,"wi"] < -3)
res[i,"pf_zwi"]=1
}
# Melt and Cast the 'res' frame and then order it
bw = melt(res, id=c("lab","r"), "pf_zbw")
# b = cast(bw, lab ~ r)
# bw_eval = b[order(as.character(b$lab)),]
##### Code for summing the no of Fails for Between Results
#bsum = cast(bw, lab ~ r, margins=TRUE, sum)
## Save Summary of Between Results
## FileSaveBw=paste(SampleName,"_",FileName,"_2009Between.csv",sep="")
## write.csv(bw_eval,file=FileSaveBw)
##
##
##
####
# Melt and Cast the 'res' frame and then order it
wi = melt(res, id=c("lab","r"), "pf_zwi")
w = cast(wi, lab ~ r)
wi_eval = w[order(as.character(w$lab)),]
##### Code for summing the no of Fails for Within Results
#wsum = cast(wi, lab ~ r, margins=TRUE, sum)
##
## Save Summary of Within Results
## FileSaveWi=paste(SampleName,"_",FileName,"_2009Within.csv",sep="")
## write.csv(wi_eval,file=FileSaveWi)
###### cat ("File Name: ",FileName,"Sample Name: ",SampleName, "\n")
# }
#}
end
Once again thanks for your interest
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 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