The answer was (thanks to Mark Leeds) to do with the use of a factor
instead of a vector.

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on [2017-08-05] at 08:57 Myles English writes:
> I am having trouble understanding how the 'by' function works. Using
> this bit of code:
>
> i <- data.frame(x=c(1,2,3), y=c(0,0,0), B=c("red","blue","blue"))
> j <- data.frame(x=c(1,2,3), y=c(1,1,1), B=c('red','blue','green'))
The use of I() prevents conversion to a factor:
i <- data.frame(x=c(1,2,3), y=c(0,0,0), B=I(c("red","blue","blue")))
j <- data.frame(x=c(1,2,3), y=c(1,1,1), B=I(c('red','blue','green')))
> plot(0, 0, type="n", xlim=c(0,4), ylim=c(0,1))
> by(i, i$B, function(s){ points(s$x, s$y, col=s$B) })
> by(j, j$B, function(s){ points(s$x, s$y, col=s$B) })
>
> I would have expected the point at (1,1) to be coloured red. When
> plotted, this row is indeed red:
>
>> i[1,]
> x y B
> 1 1 0 red
>
> however, this next point is green on the plot even though I would like
> it to be red:
>
>> j[1,]
> x y B
> 1 1 1 red
>
> How can I achieve that?
>
> Myles
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