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aaron wells

2009-Apr-22 19:51 UTC

[R] function output with for loop and if statement

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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aaron wells

2009-Apr-22 20:51 UTC

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[R] function output with for loop and if statement

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.

     Thanks again,

                 Aaron

Date: Wed, 22 Apr 2009 15:24:24 -0500
From: markleeds@verizon.net
To: awells10@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@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)
> testBare_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.sortBare_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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Mobile2_042009
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Gavin Simpson

2009-Apr-23 08:18 UTC

head link

[R] function output with for loop and if statement

On Wed, 2009-04-22 at 15:51 -0400, aaron wells 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!  
It would help a lot if you spaced your code out a bit around key
operators and structural elements.

Anyway, you didn't enclose the if/else blocks in {} in such cases, only
the line following the if(...) is run if the clause is TRUE - the lines
after that, but the code you provided doesn't even load into R - the
lone else is a syntax error. So it is a bit difficult to see what is
going on and you don;t provide an example any of us can reproduce as we
don't have your data objects.

I edited your functions below to do what I think you intended and to
clean it up a bit. Perhaps we can use this as starting point if the
function here:

`concov.test` <- function(vegetation, specieslist)
{
    test.veg <- vegetation
    names(test.veg) <- specieslist$LifeForm
    nams <- unique(names(test.veg))
    tmp <- matrix(nrow = nrow(test.veg), ncol = length(nams))
    for (i in nams) {
        test.out <- apply(test.veg[, names(test.veg)==i], 1, sum)
        tmp.match <- nams[nams==i]
        tmp.col <- match(tmp.match, nams)
        tmp[1:nrow(test.veg), tmp.col] <- test.out
        tmp.out <- data.frame(row.names(test.veg), tmp, row.names = 1)
        names(tmp.out) <- nams
        ## do you need this or is this for debugging?
        print(tmp.out)
        tmp.out.sort <- tmp.out[, order(names(tmp.out))]
    }
    if(table(names(tmp.out))[i] == 1) {
        nams.srt <- names(tmp.out.sort)
        tmp.match2 <- nams.srt[nams.srt == i]
        tmp.col2 <- match(tmp.match2, names.srt)
        tmp.out.sort[1:nrow(test.veg), tmp.col2] <-
            test.veg[, names(test.veg)==i]
        return(tmp.out.sort)
    } else {
        return(tmp.out.sort)
    }
}

doesn't do what you want. Please provide a small, reproducible example
(that means with data, dummy or otherwise) so we can run the code and
test changes against your data.

HTH

G
>  
> 
>          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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> 
> Updates2_042009
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> 
> ______________________________________________
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> PLEASE do read the posting guide
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