R devel - Mar 2011 - Anomaly with unique and match

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)) ?

Terry T

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.

match() is a red herring here -- it is really a very specific thing that has to
do with the fact that you're running unique() on a matrix. Also it's
much easier to reproduce:
> x=c(1,1+0.2e-15)
> x
[1] 1 1
> sprintf("%a",x)
[1] "0x1p+0"              
"0x1.0000000000001p+0"
> unique(x)
[1] 1 1
> sprintf("%a",unique(x))
[1] "0x1p+0"              
"0x1.0000000000001p+0"
> unique(matrix(x,2))
     [,1]
[1,]    1
 
and this comes from the fact that unique.matrix uses string representation since
it has to take into account all values of a row/column so it pastes all values
into one string, but for the two numbers that is the
same:
> as.character(x)
[1] "1" "1"

Cheers,
Simon


On Mar 9, 2011, at 9:48 AM, 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)) ?
> 
> Terry T
> 
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> 
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