[R] function output with for loop and if statement

Gavin Simpson gavin.simpson at ucl.ac.uk
Thu Apr 23 10:24:56 CEST 2009 

On Wed, 2009-04-22 at 16:51 -0400, aaron wells wrote:
> Mark, thanks for the suggestions.  Unfortunately that did not fix the
> problem.  I have experimented (with no success) with placing braces in
> different locations around the if/else statements and removing them
> all together.

Then your function is wrong. But as you haven't provided an example we
can run with data, dummy or otherwise, it is difficult to help. Also
note, that removing the braces around the if(...) block results in a
syntax error so removing them is a non starter.

Call

debug(concov.test)

Then run your function and step through the code checking that it is
doing what you expect at each stage of the analysis. If something is
wrong, fix it. Source the code back into R, set debug() back up and run
again until you have fixed the code so it works as you expect.

This:

if (table(names(tmp.out))[i]==1) {

looks a bit odd. Why are you tabling the names. What is wrong with:

if(names(tmp.out))[i] == 1) {

? If you change that, does it work?

G

> 
>  
> 
>      Thanks again,
> 
>                  Aaron
>  
> 
> 
> Date: Wed, 22 Apr 2009 15:24:24 -0500
> From: markleeds at verizon.net
> To: awells10 at hotmail.com
> Subject: Re: [R] function output with for loop and if statement
> 
> Hi Aaron: i just looked quickly because I have to go but try wrapping braces around the last if else like
> below and see if that helps. if you have multiple statements in an if else, i think you need them
> so I'm actually a little surpised that your function didn't give messages when you tried to run it ?
> 
> Also, braces in R can have some strange behavior ( because , if code is run at the prompt, and a statement can complete and there's no brace on that line then that statement is executed regardless f there's a brace later. that probably doesn't make much sense but it's kind of hard to explain  ) but I'm hoping that below fixes the problem. good luck.
> 
> 
> function ( ) { # brace for beginning of function
> 
> .....
> .....
> .....
> 
> 
> if (table(names(tmp.out))[i]==1) {
>    tmp.match2<-names(tmp.out.sort)[names(tmp.out.sort)==i]
>    tmp.col2<-match(tmp.match2,names(tmp.out.sort))
>    tmp.out.sort[1:nrow(test.veg),tmp.col2]<-test.veg[,names(test.veg)==i]
>    return(tmp.out.sort) 
>    } else {
>    return(tmp.out.sort)
>    }
> 
> } # brace for end of function 
> 
> 
> 
> 
> 
> On Apr 22, 2009, aaron wells <awells10 at hotmail.com> wrote: 
> 
> 
> 
> Hello all, turns out i'm having a bad R week. I am at my wits end with a function that I am trying to write. When I run the lines of code outside of a function, I get the desired output. When I wrap the lines of code into a function it doesn't work as expected. Not sure what is going on here. I suspected that the syntax of the if statement with the for loop was the culprit, but when I only ran the part of the code with the for loop with no if statement I still had the above problem (works outside function, fails when wrapped into a function). Below is the code and example output. Please help! 
> 
> 
> 
> Thanks, 
> 
> Aaron
> 
> 
> 
> concov.test<-function(vegetation,specieslist)
> {
> test.veg<-vegetation
> names(test.veg)<-specieslist$LifeForm
> tmp<-matrix(nrow=nrow(test.veg),ncol=length(unique(names(test.veg))))
> for (i in unique(names(test.veg))) {test.out<-apply(test.veg[,names(test.veg)==i],1,sum)
> tmp.match<-unique(names(test.veg))[unique(names(test.veg))==i]
> tmp.col<-match(tmp.match,unique(names(test.veg)))
> tmp[1:nrow(test.veg),tmp.col]<-test.out
> tmp.out<-data.frame(row.names(test.veg),tmp,row.names=1);names(tmp.out)<-unique(names(test.veg))
> tmp.out
> tmp.out.sort<-tmp.out[,order(names(tmp.out))]
> }
> if(table(names(tmp.out))[i]==1)
> tmp.match2<-names(tmp.out.sort)[names(tmp.out.sort)==i]
> tmp.col2<-match(tmp.match2,names(tmp.out.sort))
> tmp.out.sort[1:nrow(test.veg),tmp.col2]<-test.veg[,names(test.veg)==i]
> return(tmp.out.sort)
> else return(tmp.out.sort)
> }
> 
> 
> 
> ----Incorrect output when run as function-----
> 
> 
> 
> > test<-concov.test(ansveg_all,spplist.class)
> > test
> Bare_Ground Deciduous_Shrubs Deciduous_Tree Evergreen_Shrubs Evergreen_Tree Forbs Grasses Lichens Mosses Sedges
> ANSG_T01_01_2008 NA NA NA NA NA NA NA NA 95.0 NA
> ANSG_T01_02_2008 NA NA NA NA NA NA NA NA 16.0 NA
> ANSG_T01_03_2008 NA NA NA NA NA NA NA NA 71.0 NA
> ANSG_T01_04_2008 NA NA NA NA NA NA NA NA 10.0 NA
> ANSG_T02_01_2008 NA NA NA NA NA NA NA NA 92.2 NA
> ANSG_T02_02_2008 NA NA NA NA NA NA NA NA 14.0 NA
> 
> .
> 
> .
> 
> .
> 
> 
> 
> ----Correct output when code is run outside of a function----
> 
> 
> 
> > test.veg<-ansveg_all
> > names(test.veg)<-spplist.class$LifeForm
> > tmp<-matrix(nrow=nrow(test.veg),ncol=length(unique(names(test.veg))))
> > 
> > for (i in unique(names(test.veg))) {test.out<-apply(test.veg[,names(test.veg)==i],1,sum)
> + tmp.match<-unique(names(test.veg))[unique(names(test.veg))==i]
> + tmp.col<-match(tmp.match,unique(names(test.veg)))
> + tmp[1:nrow(test.veg),tmp.col]<-test.out
> + tmp.out<-data.frame(row.names(test.veg),tmp,row.names=1);names(tmp.out)<-unique(names(test.veg))
> + tmp.out
> + tmp.out.sort<-tmp.out[,order(names(tmp.out))]
> + }
> > if(table(names(tmp.out))[i]==1)
> + tmp.match2<-names(tmp.out.sort)[names(tmp.out.sort)==i]
> > tmp.col2<-match(tmp.match2,names(tmp.out.sort))
> > tmp.out.sort[1:nrow(test.veg),tmp.col2]<-test.veg[,names(test.veg)==i]
> > return(tmp.out.sort)
> > else return(tmp.out.sort)
> > 
> > 
> > tmp.out.sort
> Bare_Ground Deciduous_Shrubs Deciduous_Tree Evergreen_Shrubs Evergreen_Tree Forbs Grasses Lichens Mosses Sedges
> ANSG_T01_01_2008 0 57.0 1.0 40.0 35.0 22.0 5.0 35.0 95.0 1.1
> ANSG_T01_02_2008 0 0.0 0.0 0.0 0.0 34.0 0.0 0.0 16.0 24.0
> ANSG_T01_03_2008 0 31.0 0.0 47.0 1.0 9.1 3.0 3.0 71.0 14.0
> ANSG_T01_04_2008 0 0.0 0.0 12.0 0.0 13.2 0.0 0.0 10.0 16.0
> ANSG_T02_01_2008 0 15.0 1.0 22.0 36.0 9.2 2.0 38.0 92.2 0.1
> ANSG_T02_02_2008 0 33.0 66.0 23.0 2.0 5.0 0.0 3.0 14.0 0.0
> .
> 
> .
> 
> .
> 
> 
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