[R] indexing in a function doesn't work?

Petr PIKAL petr.pikal at precheza.cz
Tue Apr 3 07:33:37 CEST 2012 

Hi

There is some mismatch in curly braces in your plotter function but when I 
try to use it I get

> 
plotter(10,3,fram=rwb,framvec=rwb$prcnt.char.depth,obj=prcnt.char.depth,form1=
+ post.f.crwn.length~shigo.av,form2=post.f.crwn.length~shigo.av-1,
+ form3=leaf.area~(1/exp(shigo.av*x))*n,type=2,xlm=70,ylm=35)
Error in sub.plotter(i, fram, framvec, obj, form1, form2, form3, type,  : 
  object 'rwb' not found

You did not mention where we can get rwb so it is quite difficult to 
present any help.

Your function nesting seems to me also a little bit weird as the result 
from nested function is not known to enclosing function.


> test<- function (a,b) {
+ g <- a/b
+ sub.test <- function (a, b, d=10000) (e <- a*b*d)
+ c(g, e)
+ }
> 
> test(2,4)
Error in test(2, 4) : object 'e' not found

But when you define sub.test outside of test

> sub.test <- function (a, b, d=10000) {
+ e <- a*b*d
+ e
+ }
> 
> test<- function (a,b) {
+ g <- a/b
+ e <- sub.test(a,b)
+ c(g, e)
+ }
> test(2,4)
[1] 5e-01 8e+04

everything works. And it seems to me easier to maintain smaller chunks of 
working code and put them together like a puzzle. Its a behaviour I was 
taught in ancient times when "gosub" was a standard way of Basic 
programming paradigm and much more preferred from "goto".

Best regards
Petr

 



 

> 
> Josh,
> 
> Many thanks - here's a subset of the data and a couple examples:
> 
> 
plotter(10,3,fram=rwb,framvec=rwb$prcnt.char.depth,obj=prcnt.char.depth,form1=
> post.f.crwn.length~shigo.av,form2=post.f.crwn.length~shigo.av-1,
> form3=leaf.area~(1/exp(shigo.av*x))*n,type=2,xlm=70,ylm=35)
> 
> plotter(10,3,fram=rwb, framvec=rwb$prcnt.char.depth, 
obj=prcnt.char.depth,
> form1= post.f.crwn.length~leaf.area, 
form2=post.f.crwn.length~leaf.area-1,
> form3=leaf.area~(1/exp(shigo.av*x))*n,type=1, xlm=1500, ylm=35,
> sx=.01,sn=25)
> 
> 
> 
> 
> plotter<-function(a,b,fram,framvec,obj,form1,form2,form3, type=1, xlm, 
ylm,
> sx=.01,sn=25){
> g<-ceiling(a/b)
> par(mfrow=c(b,g))
> num<-rep(0,a)
> sub.plotter<-function(i,fram,framvec,obj,form1,form2,form3,type,
> xlm,ylm,var1,var2){
> temp.i<-fram[framvec <=(i*.10),] #trees in the list that have an 
attribute
> less than or equal to a progressively larger percentage
>  plot(form1, data=temp.i, xlim=c(0,xlm), ylim=c(0,ylm), 
main=((i-1)*.10))
> if(type==1){
>  mod<-lm(form2,data=temp.i)
> r2<-summary(mod)$adj.r.squared
> num[i]<-r2
>  legend("bottomright", legend=signif(r2), col="black")
> abline(mod)
>  num}
> else{
> if(type==2){
>  try(mod<-nls(form3, data=temp.i, start=list(x=sx,n=sn),
> na.action="na.omit"), silent=TRUE)
> try(x1<-summary(mod)$coefficients[1,1], silent=TRUE)
>  try(n1<-summary(mod)$coefficients[2,1], silent=TRUE)
> try(lines((1/exp(c(0:70)*x1)*n1)), silent=TRUE)
>  try(num[i]<-AIC(mod), silent=TRUE)
> try(legend("bottomright", legend=round(num[i],3) , col="black"),
> silent=TRUE)
>  try((num), silent=TRUE)
>   }
> }}
> for(i in 0:a+1){
>  num<-sub.plotter(i,fram,framvec,obj,form1,form2,form3,type,xlm,ylm)
> }
> plot.cor<-function(x){
> temp<-a+1
> lengthx<-c(1:temp)
> plot(x~c(1:temp))
> m2<-lm(x~c(1:temp))
> abline(m2)
> n<-summary(m2)$adj.r.squared
> legend("bottomright", legend=signif(n), col="black")
> slope<-(coef(m2)[2])# slope
> values<-(num)#values for aic or adj r2
> r2ofr2<-(n) #r2 of r2 or AIC
> output<-data.frame(lengthx,slope,values,r2ofr2)
> }
> plot.cor(num)
> write.csv(plot.cor(num)$output,"output.csv") # can't seem to use
> paste(substitute(form3),".csv",sep="") to name it at the moment
> par(mfrow=c(1,1))
> }
> 
> 
> 
> 
> On Sun, Apr 1, 2012 at 3:25 PM, Joshua Wiley <jwiley.psych at gmail.com> 
wrote:
> 
> > Hi,
> >
> > Glancing through your code it was not immediately obvious to me why it
> > does not work, but I can see a lot of things that could be simplified.
> >  It would really help if you could give us a reproducible example.
> > Find/upload/create (in R) some data, and examples of how you would use
> > the function.  Right now, I can only guess what your data etc. are
> > like and based on your description plus what the code you wrote seems
> > to expect to be given.  I could try to give code suggestions, but I
> > have no easy way of testing them so it would be very easy to make
> > typos, etc.  Then you just get back my edits to your code that still
> > do not work and maybe it is because of something fundamentally wrong
> > with what I have done, a simple typo, or something else still wrong in
> > your code that I did not fix.
> >
> > Anyway, if you send some data and an example using your function
> > (i.e., using the data you send, write our form1, form2, type, etc.), I
> > will take a look at your function and see if I can make it run.
> >
> > Cheers,
> >
> > Josh
> >
> > On Sun, Apr 1, 2012 at 3:13 PM, Benjamin Caldwell
> > <btcaldwell at berkeley.edu> wrote:
> > > Hello,
> > >
> > > I've written a small function that's supposed to save me some time, 
and
> > > it's ending up killing it- the intention is to iteratively subset a
> > dataset
> > > fram on framevec, fit a model (either lm or nls depending on type) 
and
> > > return the r2 or AIC from the model, respectively. Although as far 
as I
> > can
> > > tell in my code the plots are dependent on the fit of the model to 
the
> > data
> > > and the r2 and AIC reported are also dependent on the re-fitted 
model,
> > the
> > > plots show the same linear or non-linear model used for every subset 
of
> > the
> > > data.
> > >
> > > However, the r2 and AIC values come back different for each subset.
> > >
> > > When I do the subsetting and model fitting outside the function, the
> > model
> > > fit is different, with different slopes, for each subset of the 
data.
> > >
> > > I'm going to end up doing this without the function if I don't solve 
this
> > > soon. Any help much appreciated.
> > >
> > >
> > > #a is the number of times to loop the tenth of percent, b is first
> > > dimension of mfrow, frame is the dataframe, framevec is the vector 
within
> > > the dataframe you're using to subset (should be a percentage), form 
1 is
> > > the simple y~x for the plot, form 2 is y~x for regression, type is 
lm 1
> > or
> > > 2 nls ,form 3 is the formula for the nls, sx and sn are the start 
values
> > > for nls
> > >
> > > plotter<-function(a,b,fram,framvec,form1,form2,form3, type=1, xlm, 
ylm,
> > > sx=.01,sn=25){
> > > g<-ceiling(a/b)
> > > par(mfrow=c(b,g))
> > >  num<-rep(0,a)
> > > sub.plotter<-function(i,fram,framvec,form1,form2,form3,type,
> > > xlm,ylm,var1,var2){
> > > temp.i<-fram[framvec <=(i*.10),]
> > >  plot(form1, data=temp.i, xlim=c(0,xlm), ylim=c(0,ylm), 
main=((i-1)*.10))
> > > if(type==1){
> > >  mod<-lm(form2,data=temp.i)
> > > r2<-summary(mod)$adj.r.squared
> > > num<-r2
> > >  legend("bottomright", legend=signif(r2), col="black")
> > > abline(mod)
> > >  num}
> > > else{
> > > if(type==2){
> > >  try(mod<-nls(form3, data=temp.i, start=list(x=sx,n=sn),
> > > na.action="na.omit"), silent=TRUE)
> > > try(x1<-summary(mod)$coefficients[1,1], silent=TRUE)
> > >  try(n1<-summary(mod)$coefficients[2,1], silent=TRUE)
> > > try(lines((1/exp(c(0:70)*x1)*n1)), silent=TRUE)
> > >  try(num[i]<-AIC(mod), silent=TRUE)
> > > try(legend("bottomright", legend=round(num[i],3) , col="black"),
> > > silent=TRUE)
> > >  try((num), silent=TRUE)
> > >  }
> > > }}
> > > for(i in 0:a+1){
> > >  num<-sub.plotter(i,fram,framvec,form1,form2,form3,type,xlm,ylm)
> > > }
> > > plot.cor<-function(x){
> > > temp<-a+1
> > > lengthx<-c(1:temp)
> > >  plot(x~c(1:temp))
> > > m2<-lm(x~c(1:temp))
> > > abline(m2)
> > >  n<-summary(m2)$adj.r.squared
> > > legend("bottomright", legend=signif(n), col="black")
> > >  slope<-(coef(m2)[2])# slope
> > > values<-(num)#values for aic or adj r2
> > > r2ofr2<-(n) #r2 of r2 or AIC
> > >  output<-data.frame(lengthx,slope,values,r2ofr2)
> > > }
> > > plot.cor(num)
> > > write.csv(plot.cor(num)$output,"output.csv") # can't seem to use
> > > paste(substitute(form3),".csv",sep="") to name it at the moment
> > > par(mfrow=c(1,1))
> > > }
> > >
> > > Ben
> > >
> > >        [[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.
> >
> >
> >
> > --
> > Joshua Wiley
> > Ph.D. Student, Health Psychology
> > Programmer Analyst II, Statistical Consulting Group
> > University of California, Los Angeles
> > https://joshuawiley.com/
> >
> ______________________________________________
> 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.

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