R help - Dec 2007 - Why is the program too slow?

Hi,everyone.
I use the following program calculates Fisher's alpha from counts of
individuals and species. The program is wrote by Prof. Kyle Harm.
However, when I run the program, it can work very quickly sometimes, but it can
not work very well sometimes. It depends on the counts of individuals and
species.
For example,
> calc.alpha(1000,70)
[1] 17.14375
> calc.alpha(10000,70)
[1] 10.15460
> calc.alpha(100,7)
[1] 1.714375

But,
> calc.alpha(1580,30)
> calc.alpha(1000,7)
It is very slow.

So, what is the problem?
Thanks very much.
                                                      Jian Zhang


# The following function calculates Fisher's alpha from counts of
individuals and species.
# Note that this program assumes that the true value of alpha lies within the
range 0.001¨C10000
# (a likely assumption for local assemblages of organisms).
# The function returns "-1" if there is a problem.

calc.alpha=function(n.orig, s.orig)
 {
  a=numeric()

  len.n=length(n.orig)
  len.s=length(s.orig) 
   
  if(len.n != len.s)
    { return(-1)  }
   
  for(i in 1:len.n)
   {
     if(n.orig[i]<=0 | s.orig[i]<=0 | n.orig[i]<=s.orig[i])
 { a[i]=(-1) }
     
     else
      {
       low.a=0.001
       high.a=10000
       low.s = low.a*log(1+(n.orig[i]/low.a))
       high.s = high.a*log(1+(n.orig[i]/high.a)) 
       
       if((s.orig[i]<=low.s) | (s.orig[i]>=high.s))
        { a[i]=(-1) }
       
       else
        {
         use.s=s.orig[i]+1 
         while(s.orig[i] != use.s)
          {
           use.a=(low.a+high.a)/2
           use.s=use.a*log(1+(n.orig[i]/use.a))
           
           if(s.orig[i]<use.s)
  { high.a=use.a }

           if(s.orig[i]>use.s)
  { low.a=use.a }
          }
         a[i]=use.a 
        }
      }
   }

   return(a)
 }

	[[alternative HTML version deleted]]

zhang jian wrote:
> 
> Hi,everyone.
> I use the following program calculates Fisher's alpha from counts of
> individuals and species. The program is wrote by Prof. Kyle Harm.
> However, when I run the program, it can work very quickly sometimes, but
> it can not work very well sometimes. It depends on the counts of
> individuals and species.
> For example,
> 
>> calc.alpha(1000,70)
> [1] 17.14375
>> calc.alpha(10000,70)
> [1] 10.15460
>> calc.alpha(100,7)
> [1] 1.714375
> 
> But,
>> calc.alpha(1580,30)
>> calc.alpha(1000,7)
> 
> It is very slow.
> 
> So, what is the problem?
> Thanks very much.
>                                                       Jian Zhang
> 
Don't know, but I would try out the alternatives fisherfit [vegan package]
and fisher [untb package] and see if either behaves better (it was faster
for me to look these up than to dig through the code and see what's
going on for these examples).

   You could also try contacting Prof. Harms [sic] and asking him ...

  cheers
    Ben Bolker

-- 
View this message in context:
http://www.nabble.com/Why-is-the-program-too-slow--tf4936535.html#a14130312
Sent from the R help mailing list archive at Nabble.com.

try

RSiteSearch("Fisher's alpha")

which indicates that there is the fishers.alpha() function in package 
'untb' that does the same thing, e.g.,

fishers.alpha(1000, 70)

fishers.alpha(1580, 30)
fishers.alpha(1000, 7)


I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
     http://www.student.kuleuven.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "Jian Zhang" <jzhang1982 at gmail.com>
To: "R-help" <r-help at stat.math.ethz.ch>
Sent: Monday, December 03, 2007 2:12 PM
Subject: [R] Why is the program too slow?

> Hi,everyone.
> I use the following program calculates Fisher's alpha from counts of 
> individuals and species. The program is wrote by Prof. Kyle Harm.
> However, when I run the program, it can work very quickly sometimes, 
> but it can not work very well sometimes. It depends on the counts of 
> individuals and species.
> For example,
>
>> calc.alpha(1000,70)
> [1] 17.14375
>> calc.alpha(10000,70)
> [1] 10.15460
>> calc.alpha(100,7)
> [1] 1.714375
>
> But,
>> calc.alpha(1580,30)
>> calc.alpha(1000,7)
>
> It is very slow.
>
> So, what is the problem?
> Thanks very much.
>                                                      Jian Zhang
>
>
> # The following function calculates Fisher's alpha from counts of 
> individuals and species.
> # Note that this program assumes that the true value of alpha lies 
> within the range 0.001?C10000
> # (a likely assumption for local assemblages of organisms).
> # The function returns "-1" if there is a problem.
>
> calc.alpha=function(n.orig, s.orig)
> {
>  a=numeric()
>
>  len.n=length(n.orig)
>  len.s=length(s.orig)
>
>  if(len.n != len.s)
>    { return(-1)  }
>
>  for(i in 1:len.n)
>   {
>     if(n.orig[i]<=0 | s.orig[i]<=0 | n.orig[i]<=s.orig[i])
> { a[i]=(-1) }
>
>     else
>      {
>       low.a=0.001
>       high.a=10000
>       low.s = low.a*log(1+(n.orig[i]/low.a))
>       high.s = high.a*log(1+(n.orig[i]/high.a))
>
>       if((s.orig[i]<=low.s) | (s.orig[i]>=high.s))
>        { a[i]=(-1) }
>
>       else
>        {
>         use.s=s.orig[i]+1
>         while(s.orig[i] != use.s)
>          {
>           use.a=(low.a+high.a)/2
>           use.s=use.a*log(1+(n.orig[i]/use.a))
>
>           if(s.orig[i]<use.s)
>  { high.a=use.a }
>
>           if(s.orig[i]>use.s)
>  { low.a=use.a }
>          }
>         a[i]=use.a
>        }
>      }
>   }
>
>   return(a)
> }
>
> [[alternative HTML version deleted]]
>
>

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