Re: [R] Hollander's test of bivariate symmetry

[joseph . g . boyer]

Couldn't find it anywhere, so for future users who stumble on this thread, 
here is some code.
Note: If your data has missing values, delete those observations from the 
data first before running this code.

Place these functions in the global environment (ie run the code below).

Then, to obtain the test statistic: H_bisym_stat(x,y)  (x and y are the 
two vectors you are comparing).

To obtain a p-value: H_bisym_stat(x,y). The p-value is calculated via a 
Monte Carlo algorithm.

You can use the permutations argument to H_bisym_stat to increase the 
number of Monte Carlo samples.


#Hollander's test of bivariate symmetry

#Calculating test statistic for Hollander's test of bivariate 
symmetry

H_bisym_stat - function(x,y){

minXY - pmin(x,y);
sortX - x[order(minXY)];
sortY - y[order(minXY)];
minXY - pmin(sortX, sortY);
R - as.numeric(sortX = sortY);
maxXY - pmax(sortX,sortY);
 
D1 - matrix(0, length(x), length(x));
D2 - matrix(0, length(x), length(x));

for (i in 1:length(x)){

for (j in 1:length(x)){

D1[i,j] = as.numeric(minXY[j]  
maxXY[i]  maxXY[i] = maxXY[j]);
D2[i,j] = as.numeric(minXY[i] = 
minXY[j]);

}

}

D = D1*D2;

S = 2*R - 1;

T = t( t(S) %*% D);

H_squared = (1/length(x)^2)*( t(T) %*% T );

H_squared};

#Create a permutation sample for paired data;

permsamp_paired - function(x,y){

new - rbinom(length(x),1,0.5);
x_new - x*new + y*(1 - new);
y_new - y*new + x*(1 - new);

list(x_new = x_new, y_new = y_new)};


#Calculate pvalue for Hollander statistic;

H_bisym_pv - function(x, y, permutations = 1000){

H_squared = H_bisym_stat(x=x, y=y);

numb_greater = 0;

for (i in 1:permutations) {

newvars - permsamp_paired(x=x, y=y);
x_new - newvars$x_new;
y_new - newvars$y_new;

newstat - H_bisym_stat(x=x_new, y=y_new);

numb_greater = numb_greater + 
as.numeric(newstat = H_squared);
 
}

pv - numb_greater/permutations;

pv };


Joe Boyer
Statistical Sciences 
GlaxoSmithKline
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[R] replying to old thread

[joseph . g . boyer]

If you come across an archived thread that you would like to reply to, how 
do you reply to it without starting a new thread?


Joe Boyer
Statistical Sciences 
Renaissance Bldg 510, 3233-D
Mail Stop RN0320
8-275-3661
cell: (610) 209-8531
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[R] Hollander's test of bivariate symmetry

[joseph . g . boyer]

Does anyone know if any R package has a function that will conduct 
Hollander's test of bivariate symmetry?

(Hollander, Biometrika, 1971)

Either the exact test or an asymptotic version would be sufficient for my 
purposes.

Thanks.





Joe Boyer
Statistical Sciences 
Renaissance Bldg 510, 3233-D
Mail Stop RN0320
8-275-3661
cell: (610) 209-8531
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and provide commented, minimal, self-contained, reproducible code.

[R] RExcel waiting for OLE action

[joseph . g . boyer]

When I run a macro that uses RExcel, I get a dialog box that says 
Microsoft Excel is waiting for another application to complete an OLE 
action.

There is no error in the RExcel commands in the macro, of that I am sure. 
The box appears to be related to the inclusion of RunRFile commands.

The macro will run through the second RunRFile command, but will not 
execute the Worksheet.Pictures.Insert statements or the GetArray 
statements until
the user clicks OK on the dialog box.

Any insight into how I can avoid the dialog box would be appreciated.

The macro is below. It's your basic, send-to-R, run R, retrieve-from-R 
macro.

Call Rinterface.StartRServer 

Call Rinterface.RRun(rm(list = ls()))
Call Rinterface.RRun(dev.off())
 
Call Rinterface.PutArray(mat1, Range(DATA_INPUT_OUTPUT!B7:I506))
Call Rinterface.PutArray(mat2, Range(DATA_INPUT_OUTPUT!J7:Q506))
Call Rinterface.PutArray(cpd, Range(DATA_INPUT_OUTPUT!A7:A506))
Call Rinterface.PutArray(name_of_assay_one, 
Range(DATA_INPUT_OUTPUT!B1))
Call Rinterface.PutArray(name_of_assay_two, 
Range(DATA_INPUT_OUTPUT!B2))
 
Call Rinterface.RunRFile(C:\Program Files\R\MDR 
Programs\AM_ACT_Macros.R)
Call Rinterface.RunRFile(C:\Program Files\R\MDR Programs\AM_ACT.R)
 
Worksheets(GRAPHS).Range(B58).Select
Worksheets(GRAPHS).Range(B58).Clear
 Worksheets(GRAPHS).Pictures.Insert(C:\TEMP\var_means_both.jpg).Select
 
Worksheets(GRAPHS).Range(B84).Select
Worksheets(GRAPHS).Range(B84).Clear
 Worksheets(GRAPHS).Pictures.Insert(C:\TEMP\var_means_one.jpg).Select
 
Worksheets(GRAPHS).Range(B110).Select
Worksheets(GRAPHS).Range(B110).Clear
 Worksheets(GRAPHS).Pictures.Insert(C:\TEMP\var_means_two.jpg).Select
 
Worksheets(GRAPHS).Range(B136).Select
Worksheets(GRAPHS).Range(B136).Clear
 Worksheets(GRAPHS).Pictures.Insert(C:\TEMP\normality_one.jpg).Select
 
Worksheets(GRAPHS).Range(B162).Select
Worksheets(GRAPHS).Range(B162).Clear
 Worksheets(GRAPHS).Pictures.Insert(C:\TEMP\normality_two.jpg).Select
 
Worksheets(GRAPHS).Range(B188).Select
Worksheets(GRAPHS).Range(B188).Clear
Worksheets(GRAPHS).Pictures.Insert(C:\TEMP\one_two.jpg).Select
 
Worksheets(GRAPHS).Range(B214).Select
Worksheets(GRAPHS).Range(B214).Clear
Worksheets(GRAPHS).Pictures.Insert(C:\TEMP\pvalue_mean.jpg).Select
 
Worksheets(GRAPHS).Range(B240).Select
Worksheets(GRAPHS).Range(B240).Clear
Worksheets(GRAPHS).Pictures.Insert(C:\TEMP\pvalue_hist.jpg).Select
 
Call Rinterface.GetArray(pred_output$quant_one, 
Range(ASYM_MAX_ANALYSIS!A33:A37))
Call Rinterface.GetArray(pred_output$quant_two, 
Range(ASYM_MAX_ANALYSIS!I33:I37))
Call Rinterface.GetArray(sd_output$sd_one, 
Range(ASYM_MAX_ANALYSIS!B33:B37))
Call Rinterface.GetArray(sd_output$sd_two, 
Range(ASYM_MAX_ANALYSIS!J33:J37))
Call Rinterface.GetArray(sd_output$iqr_one, 
Range(ASYM_MAX_ANALYSIS!D33:D37))
Call Rinterface.GetArray(sd_output$iqr_two, 
Range(ASYM_MAX_ANALYSIS!L33:L37))
 
Call Rinterface.GetArray(pred_output$quant_one, 
Range(ASYM_MAX_ANALYSIS!A42:A46))
Call Rinterface.GetArray(pred_output$pred, 
Range(ASYM_MAX_ANALYSIS!C42:C46))
Call Rinterface.GetArray(pred_output$up_cb, 
Range(ASYM_MAX_ANALYSIS!I42:I46))
Call Rinterface.GetArray(pred_output$low_cb, 
Range(ASYM_MAX_ANALYSIS!K42:K46))
 
Call Rinterface.GetArray(sd_output$sd_ee[1], 
Range(ASYM_MAX_ANALYSIS!E50))
Call Rinterface.GetArray(pv_data$pool_sd, 
Range(ASYM_MAX_ANALYSIS!C55))
Call Rinterface.GetArray(pv_data$lin_sd_comb, 
Range(ASYM_MAX_ANALYSIS!D55))
Call Rinterface.GetArray(pv_data$const_sd_comb, 
Range(ASYM_MAX_ANALYSIS!I55))
Call Rinterface.GetArray(pv_data$CV_sd_comb, 
Range(ASYM_MAX_ANALYSIS!J55))
 
Call Rinterface.GetArray(pv_data$lin_sd_one, 
Range(ASYM_MAX_ANALYSIS!D58))
Call Rinterface.GetArray(pv_data$const_sd_one, 
Range(ASYM_MAX_ANALYSIS!I58))
Call Rinterface.GetArray(pv_data$CV_sd_one, 
Range(ASYM_MAX_ANALYSIS!J58))
 
Call Rinterface.GetArray(pv_data$lin_sd_two, 
Range(ASYM_MAX_ANALYSIS!D61))
Call Rinterface.GetArray(pv_data$const_sd_two, 
Range(ASYM_MAX_ANALYSIS!I61))
Call Rinterface.GetArray(pv_data$CV_sd_two, 
Range(ASYM_MAX_ANALYSIS!J61))
 
Call Rinterface.GetArray(pv_data$N_one, 
Range(ASYM_MAX_ANALYSIS!C64))
Call Rinterface.GetArray(pv_data$N_two, 
Range(ASYM_MAX_ANALYSIS!D64))
Call Rinterface.GetArray(pv_data$lin, 
Range(ASYM_MAX_ANALYSIS!I64))
Call Rinterface.GetArray(pv_data$FO, Range(ASYM_MAX_ANALYSIS!J64))
 
Call Rinterface.RRun(dev.off())
Call Rinterface.StopRServer






Joe Boyer
Statistical Sciences 
Renaissance Bldg 510, 3233-D
Mail Stop RN0320
8-275-3661
cell: (610) 209-8531
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and provide commented, minimal, 

Re: [R] executing R batch files

[joseph . g . boyer]

Thank you, I appreciate your reply.

I have managed to get Shell(c:\TEMP\Rbatch.bat) to work.

What solved the problem was saving the Rbatch.bat file as type All files
as opposed to as a text file.

Why that worked, I have no idea.


Joe Boyer
Statistical Sciences 
Renaissance Bldg 510, 3233-D
Mail Stop RN0320
8-275-3661
cell: (610) 209-8531



Gabor Grothendieck ggrothendi...@gmail.com 
02-Feb-2009 18:53
 
To
joseph.g.bo...@gsk.com
cc
r-help@r-project.org
Subject
Re: [R] executing R batch files






Without the actual VBA commands you are using we
can't be sure but if you are using Shell then it requires an exe,
not a bat file.  Try
   cmd.exe /c RBatch.bat
so that it has an exe file to execute.

On Mon, Feb 2, 2009 at 6:42 PM,  joseph.g.bo...@gsk.com wrote:
 The following command, issued from the DOS command prompt (running 
Windows
 XP), produces the intended result of a .csv file created by program.R:

 ?c:\program files\R\R-2.8.0\bin\Rterm.exe? --save  c:\TEMP\program.R

 However, when I create a file called Rbatch.bat that contains exactly 
the
 line above, and try to execute it (by double clicking or via the Shell
 command
 in an Excel macro), nothing happens.

 Does anyone have an explanation, or any suggestions as to how to run an 
R
 program from within an Excel macro? (PS: I know about RExcel, can't 
quite
 get it to install
 correctly.)

 Much appreciated.



 Joe Boyer
 Statistical Sciences
 Renaissance Bldg 510, 3233-D
 Mail Stop RN0320
 8-275-3661
 cell: (610) 209-8531
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 __
 R-help@r-project.org 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.




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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] executing R batch files

[joseph . g . boyer]

The following command, issued from the DOS command prompt (running Windows 
XP), produces the intended result of a .csv file created by program.R:

?c:\program files\R\R-2.8.0\bin\Rterm.exe? --save  c:\TEMP\program.R

However, when I create a file called Rbatch.bat that contains exactly the 
line above, and try to execute it (by double clicking or via the Shell 
command
in an Excel macro), nothing happens.

Does anyone have an explanation, or any suggestions as to how to run an R 
program from within an Excel macro? (PS: I know about RExcel, can't quite 
get it to install
correctly.)

Much appreciated.



Joe Boyer
Statistical Sciences 
Renaissance Bldg 510, 3233-D
Mail Stop RN0320
8-275-3661
cell: (610) 209-8531
[[alternative HTML version deleted]]

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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] referring to calls in functions

[joseph . g . boyer]

The first program generates an error message and does not execute the 
regression of y on x.


x-1:10;
y-rnorm(10) + x;

prac - function( model, wghts ){ lm(model, weights = wghts) }

prac(model = y~x, wghts = rep(1, 10))



But the next program works:

x-1:10;
y-rnorm(10) + x;

prac - function( y, x, wghts ){ lm(y~x, weights = wghts) }

prac(y=y, x=x, wghts = rep(1, 10))


I would be grateful for an explanation of why the first program does not 
work. It seems to me like they should both give the same result.





Joe Boyer
Statistical Sciences 
Renaissance Bldg 510, 3233-D
Mail Stop RN0320
8-275-3661
cell: (610) 209-8531
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] understanding recursive functions

[joseph . g . boyer]

Jeffrey and Jeff,

Thank you for clearing this up.

The problem was that I didn't read page 47 of the guide carefully. The 
introduction of the - operator on page 44 leaves
me with the impression that - will create an assignment in the local 
environment THAT ALSO holds true for the next
higher environment.


Joe Boyer
Statistical Sciences 
Renaissance Bldg 510, 3233-D
Mail Stop RN0320
8-275-3661
cell: (610) 209-8531
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Re: [R] understanding lexical scope

[joseph . g . boyer]

Thomas, Jeff, Mark, Antonio,

Thank you for your answers. They have helped me clarify how R functions 
work. They work differently from SAS functions (which SAS calls macros.)

If you know SAS, consider the following code:

*
%macro q(y);

data one;
outvar = y. + x.; output;
call symputx(outvar, outvar, G);
run;

%mend;

%macro w(x);

%q(x.);
%put outvar.;

%mend;
**

Then %w(2); will result in the value 4 being placed in the SAS log.


To me, while the coding is quite awkward, the execution is logical. The 
variable x has been defined by the call to the macro w, so there is no 
problem when SAS encounters a reference to x in the macro q.

But in the equivalent code in R, 

q - function(y) y +x; w - function(x) q(x); w(2);

when R can't find the second argument of q in the local environment of the 
macro q, it doesn't look in the local environment of the macro w, it goes 
all the way back to 
the global environment, as you have all pointed out.

So in my little model of how R functions work, when a function is called

1. R rewrites the body of the function, replacing all of the parameter 
names with the values given to them in the function call.

2. R then tries to execute the expressions. But R only remembers the 
assignment of values to parameter names during step 1. Thus in our example
it has to go the global environment to find a value for x 
referenced in q.

Is this right?








Joe Boyer
Statistical Sciences 
Renaissance Bldg 510, 3233-D
Mail Stop RN0320
8-275-3661
cell: (610) 209-8531
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and provide commented, minimal, self-contained, reproducible code.

[R] understanding recursive functions

[joseph . g . boyer]

I'm trying to understand the use of recursive functions described on page 
45 of An Introduction to R by the R core development team.

A function is a list of expressions, which all get executed with only the 
last being assigned to a global variable, right? 
So if a function refers recursively to itself, it should simply start with 
the first
expression and go from there. At least that is my understanding of why the 
example given on page 45 works.

In light of the above, I would appreciate it if someone would understand 
why the following example does not work:

q - function(x,h) {if (x  2) {x - x+1; return(q(x))} else return(x)}

If x  1, this should add 1 to x and go back to the beginning of the if 
expression, and the final result should be 2. So q(0) should return 2. But 

it returns an error message.


Joe Boyer
Statistical Sciences 
Renaissance Bldg 510, 3233-D
Mail Stop RN0320
8-275-3661
cell: (610) 209-8531
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and provide commented, minimal, self-contained, reproducible code.