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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