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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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$LifeForm
tmp<-matrix(nrow=nrow(test.veg),ncol=length(unique(names(test.veg))))
for (i in unique(names(test.veg)))
{test.out<-apply(test.veg[,names(test.veg)==i],1,sum)
tmp.match<-unique(names(test.veg))[unique(names(test.veg))==i]
tmp.col<-match(tmp.match,unique(names(test.veg)))
tmp[1:nrow(test.veg),tmp.col]<-test.out
tmp.out<-data.frame(row.names(test.veg),tmp,row.names=1);names(tmp.out)<-unique(names(test.veg))
tmp.out
tmp.out.sort<-tmp.out[,order(names(tmp.out))]
}
if(table(names(tmp.out))[i]==1)
tmp.match2<-names(tmp.out.sort)[names(tmp.out.sort)==i]
tmp.col2<-match(tmp.match2,names(tmp.out.sort))
tmp.out.sort[1:nrow(test.veg),tmp.col2]<-test.veg[,names(test.veg)==i]
return(tmp.out.sort)
else return(tmp.out.sort)
}
----Incorrect output when run as function-----
> test<-concov.test(ansveg_all,spplist.class)
> test
Bare_Ground Deciduous_Shrubs Deciduous_Tree Evergreen_Shrubs Evergreen_Tree
Forbs Grasses Lichens Mosses Sedges
ANSG_T01_01_2008 NA NA NA NA NA NA NA NA 95.0 NA
ANSG_T01_02_2008 NA NA NA NA NA NA NA NA 16.0 NA
ANSG_T01_03_2008 NA NA NA NA NA NA NA NA 71.0 NA
ANSG_T01_04_2008 NA NA NA NA NA NA NA NA 10.0 NA
ANSG_T02_01_2008 NA NA NA NA NA NA NA NA 92.2 NA
ANSG_T02_02_2008 NA NA NA NA NA NA NA NA 14.0 NA
.
.
.
----Correct output when code is run outside of a function----
> test.veg<-ansveg_all
> names(test.veg)<-spplist.class$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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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 > . > > . > > . > > > _________________________________________________________________ > Rediscover Hotmail: Get quick friend updates right in your inbox. > > Updates2_042009 > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. 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