[R] Trying to understand a function passed to lapply

2015-03-30 Thread John Sorkin 
Colleagues,
I am trying to understand the syntax of a function passed to apply. The code 
below generates a matrix, and passes the matrix to a function that is called by 
apply. I don't understand the syntax of the function. In some way the function 
computes data[,delta]/data[,SE]. I can't understand how the body of the 
function, x[c1]/x[c2] refers to the columns data and SE of the matrix data. 
Can someone help me understand the syntax? 
Thank you,
John

myfun - function(x, c1, c2) x[c1]/x[c2]
apply(data,1,myfun,c1=delta,c2=SE)

CODE:

data-matrix(data=c(-0.70 ,-0.90, -0.50, 20, 20,
-0.30 ,-0.43, -0.17, 43, 43,
-0.50 ,-1.05,  0.05, 16, 18,
 0.00 ,-0.21,  0.21, 22, 23,
-1.30 ,-1.48, -1.12, 28, 32,
-0.90 ,-1.01, -0.79, 18, 15,
-0.20 ,-0.47,  0.07, 39, 39,
-0.30 ,-0.83,  0.23, 27, 27),
 nrow=8,ncol=5,byrow=TRUE)
dimnames(data) - list(NULL,c(delta,low,high,n1,n2))
data
CI - data[,high]-data[,low]
data - cbind(data,CI)
data
data - cbind(data,SE=data[,CI]/(4*1.96))
data
data - cbind(data,SD=data[,SE]*sqrt(data[,n1]+data[,n2]))
data
myfun - function(x, c1, c2) x[c1]/x[c2]
apply(data,1,myfun,c1=delta,c2=SE)

John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric 
Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) 

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Re: [R] Trying to understand a function passed to lapply

2015-03-30 Thread William Dunlap 
 I can't understand how the body of the function, x[c1]/x[c2] refers to
the columns data and SE of the matrix data.

If you put the line 'str(x)' at the start of myfun(), as in
   myfun - function(x, c1, c2) {
  str(x)
  x[c1]/x[c2]
   }
you would start to see why it works - extracting a row from a matrix gives
you a vector with names copied from the column names of the matrix.
Thus subscripting with a single name (or number) works.
   apply(data,1,myfun,c1=delta,c2=SE)
   Named num [1:8] -0.7 -0.9 -0.5 20 20 ...
   - attr(*, names)= chr [1:8] delta low high n1 ...
   Named num [1:8] -0.3 -0.43 -0.17 43 43 ...
   - attr(*, names)= chr [1:8] delta low high n1 ...
   Named num [1:8] -0.5 -1.05 0.05 16 18 ...
   ...
   Named num [1:8] -0.3 -0.83 0.23 27 27 ...
   - attr(*, names)= chr [1:8] delta low high n1 ...
  [1] -13.72  -9.046154  -3.563636   0.00 -28.31 -32.072727
 -2.903704  -2.218868

By the way, that call to apply is just a slow way of dividing two columns
of the matrix
   data[, delta]/data[, SE]
  [1] -13.72  -9.046154  -3.563636   0.00 -28.31 -32.072727
 -2.903704  -2.218868


Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Mon, Mar 30, 2015 at 6:48 PM, John Sorkin jsor...@grecc.umaryland.edu
wrote:

 Colleagues,
 I am trying to understand the syntax of a function passed to apply. The
 code below generates a matrix, and passes the matrix to a function that is
 called by apply. I don't understand the syntax of the function. In some way
 the function computes data[,delta]/data[,SE]. I can't understand how
 the body of the function, x[c1]/x[c2] refers to the columns data and SE
 of the matrix data. Can someone help me understand the syntax?
 Thank you,
 John

 myfun - function(x, c1, c2) x[c1]/x[c2]
 apply(data,1,myfun,c1=delta,c2=SE)

 CODE:

 data-matrix(data=c(-0.70 ,-0.90, -0.50, 20, 20,
 -0.30 ,-0.43, -0.17, 43, 43,
 -0.50 ,-1.05,  0.05, 16, 18,
  0.00 ,-0.21,  0.21, 22, 23,
 -1.30 ,-1.48, -1.12, 28, 32,
 -0.90 ,-1.01, -0.79, 18, 15,
 -0.20 ,-0.47,  0.07, 39, 39,
 -0.30 ,-0.83,  0.23, 27, 27),
  nrow=8,ncol=5,byrow=TRUE)
 dimnames(data) - list(NULL,c(delta,low,high,n1,n2))
 data
 CI - data[,high]-data[,low]
 data - cbind(data,CI)
 data
 data - cbind(data,SE=data[,CI]/(4*1.96))
 data
 data - cbind(data,SD=data[,SE]*sqrt(data[,n1]+data[,n2]))
 data
 myfun - function(x, c1, c2) x[c1]/x[c2]
 apply(data,1,myfun,c1=delta,c2=SE)

 John David Sorkin M.D., Ph.D.
 Professor of Medicine
 Chief, Biostatistics and Informatics
 University of Maryland School of Medicine Division of Gerontology and
 Geriatric Medicine
 Baltimore VA Medical Center
 10 North Greene Street
 GRECC (BT/18/GR)
 Baltimore, MD 21201-1524
 (Phone) 410-605-7119
 (Fax) 410-605-7913 (Please call phone number above prior to faxing)

 Confidentiality Statement:
 This email message, including any attachments, is for ...{{dropped:16}}

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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Trying to understand a function passed to lapply

2015-03-30 Thread Jim Lemon 
Hi John,
What happens is that you have passed two named arguments to your function
myfun along with the matrix data. Because these arguments have
associated values (delta, SE), these values are substituted into the
expression like this:

x[delta]/x[SE]

which is the return value of myfun. If you just type in:

data[delta]
data[SE]

you will see the values that are successively selected for the calculation
in myfun

Jim


On Tue, Mar 31, 2015 at 12:48 PM, John Sorkin jsor...@grecc.umaryland.edu
wrote:

 Colleagues,
 I am trying to understand the syntax of a function passed to apply. The
 code below generates a matrix, and passes the matrix to a function that is
 called by apply. I don't understand the syntax of the function. In some way
 the function computes data[,delta]/data[,SE]. I can't understand how
 the body of the function, x[c1]/x[c2] refers to the columns data and SE
 of the matrix data. Can someone help me understand the syntax?
 Thank you,
 John

 myfun - function(x, c1, c2) x[c1]/x[c2]
 apply(data,1,myfun,c1=delta,c2=SE)

 CODE:

 data-matrix(data=c(-0.70 ,-0.90, -0.50, 20, 20,
 -0.30 ,-0.43, -0.17, 43, 43,
 -0.50 ,-1.05,  0.05, 16, 18,
  0.00 ,-0.21,  0.21, 22, 23,
 -1.30 ,-1.48, -1.12, 28, 32,
 -0.90 ,-1.01, -0.79, 18, 15,
 -0.20 ,-0.47,  0.07, 39, 39,
 -0.30 ,-0.83,  0.23, 27, 27),
  nrow=8,ncol=5,byrow=TRUE)
 dimnames(data) - list(NULL,c(delta,low,high,n1,n2))
 data
 CI - data[,high]-data[,low]
 data - cbind(data,CI)
 data
 data - cbind(data,SE=data[,CI]/(4*1.96))
 data
 data - cbind(data,SD=data[,SE]*sqrt(data[,n1]+data[,n2]))
 data
 myfun - function(x, c1, c2) x[c1]/x[c2]
 apply(data,1,myfun,c1=delta,c2=SE)

 John David Sorkin M.D., Ph.D.
 Professor of Medicine
 Chief, Biostatistics and Informatics
 University of Maryland School of Medicine Division of Gerontology and
 Geriatric Medicine
 Baltimore VA Medical Center
 10 North Greene Street
 GRECC (BT/18/GR)
 Baltimore, MD 21201-1524
 (Phone) 410-605-7119
 (Fax) 410-605-7913 (Please call phone number above prior to faxing)

 Confidentiality Statement:
 This email message, including any attachments, is for ...{{dropped:16}}

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.