[R] counting run lengths

[Martin Morgan]

Hi Mario --

This function

f <- function(m) {
    ## next 2 lines due to Bill Dunlap
    ## http://tolstoy.newcastle.edu.au/R/e4/devel/08/04/1206.html
    csum <- cumsum(!m)
    crun <- csum - cummax(m * csum)
    matrix(ifelse(crun > 0, (crun-1) %% nrow(m) + 1, 0),
           nrow=nrow(m))
}

returns a matrix with elements indicating the number of successive
0's so far in the column

> f(Atr)
     [,1] [,2] [,3] [,4]
[1,]    0    0    0    0
[2,]    0    0    1    0
[3,]    0    0    2    0
[4,]    0    0    3    0
[5,]    1    0    4    0
[6,]    2    0    5    0
[7,]    3    0    6    0
[8,]    4    0    7    0

from which the last row is easily extracted

> f(Atr)[nrow(Atr),]
[1] 4 0 7 0

Martin

Mario Lavezzi <lavezzi at unipa.it> writes:

> Hello,
> I have the following problem.
>
> I am running simulations on possible states of a set of agents
> (1=employed, 0=unemployed).
>
> I store these simulated time series in a matrix like the following,
> where rows indicates time periods, columns the number of agents (4
> agents and 8 periods in this case):
>
> Atr=[
> 1    1    1    1
> 1    1    0    1
> 1    1    0    1
> 1    1    0    1
> 0    1    0    1
> 0    1    0    1
> 0    1    0    1
> 0    1    0    1]
>
> At this point, I need to update a vector ("unSpells") which contains
> the lenghts of unemployment spells, and is initialized with
> ones. Practically, in the case represented I need to store the value
> "4" at position 1 of unSpells and "7" at position 3 of unSpells (that
> is, I care only of those who, in the last row, are zeros).
>
> I am doing this in the following way (tt+1 indicates the time period
> reached by the simulation, n the number of agents):
>
>     unSpells = matrix(1,nrow=1,ncol=n)
>     ppp=apply(Atr[1:(tt+1),],2,rle)
>     for(i in (1:n)[Atr[tt+1,]==0]){
>         unSpells[i]=tail(ppp[[i]]$lengths,1)
>     }
>
> It works, but the for (i in ...) loop slows down the simulation a lot.
>
> Any suggestion on how to avoid this loop? (or in general, to speed up
> this part of the simulation)
>
> Thanks!!
> Mario
>
> -- 
> Andrea Mario Lavezzi
> Dipartimento di Studi su Politica, Diritto e Società
> Università di Palermo
> Piazza Bologni 8
> 90134 Palermo, Italy
> tel. ++39 091 6625600
> fax ++39 091 6112023
> skype: lavezzimario
> email: lavezzi (at) unipa.it
> web: http://www.unipa.it/~lavezzi
>
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> and provide commented, minimal, self-contained, reproducible code.

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793