From savicky at cs.cas.cz  Wed Mar  9 17:00:40 2011
From: savicky at cs.cas.cz (Petr Savicky)
Date: Wed, 9 Mar 2011 17:00:40 +0100
Subject: [Rd] Anomaly with unique and match
In-Reply-To: <1299682090.12625.9.camel@punchbuggy>
References: <1299682090.12625.9.camel@punchbuggy>
Message-ID: <20110309160040.GA6512@cs.cas.cz>

On Wed, Mar 09, 2011 at 08:48:10AM -0600, Terry Therneau wrote:
> I stumbled onto this working on an update to coxph.  The last 6 lines
> below are the question, the rest create a test data set.
> 
> tmt585% R
> R version 2.12.2 (2011-02-25)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> # Lines of code from survival/tests/singtest.R
> > library(survival)
> Loading required package: splines
> > test1 <- data.frame(time=  c(4, 3,1,1,2,2,3),
> +     status=c(1,NA,1,0,1,1,0),
> +     x=     c(0, 2,1,1,1,0,0))
> > 
> > temp <- rep(0:3, rep(7,4))
> > 
> > stest <- data.frame(start  = 10*temp,
> +     stop   = 10*temp + test1$time,
> +     status = rep(test1$status,4),
> +     x      = c(test1$x+ 1:7, rep(test1$x,3)),
> +     epoch  = rep(1:4, rep(7,4)))
> > 
> > fit1 <- coxph(Surv(start, stop, status) ~ x * factor(epoch), stest)
> 
> ## New lines
> > temp1 <- fit1$linear.predictor
> > temp2 <- as.matrix(temp1)
> > match(temp1, unique(temp1))
>  [1] 1 2 3 4 4 5 6 7 7 7 6 6 6 8 8 8 6 6 6 9 9 9 6 6
> > match(temp2, unique(temp2))
>  [1]  1  2  3  4  4  5  6  7  7  7  6  6  6 NA NA NA  6  6  6  8  8  8
> 6  6
> 
> -----------------------
> 
>  I've solved it for my code by not calling match on a 1 column vector.  
>  In general, however, should I be using some other paradym for this "map
> to unique" operation?  For example match(as.character(x),
> unique(as.character(x)) ?

Let me suggest an alternative, which is consistent with unique() on
numeric vectors and uses a transformation of the column using rank().
For example,

  temp3 <- as.matrix(rank(temp1, ties.method="max"))
  match(temp3, unique(temp3))

  [1] 1 2 3 4 4 5 6 7 7 7 6 6 6 8 8 8 6 6 6 9 9 9 6 6

Can this be used in your code?

Petr Savicky.



[Rd] Anomaly with unique and match
Petr Savicky