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I have two vectors of variables, $X$, and $\beta_0$ that I am writing about.

Each are indexed by $i=1,\ldots,n$

If I want to talk about $X_i$ and $\beta_{0_i}$, using \beta_{0_i}, the $i$ on the beta is too small to see. Even if I use \beta{_0}_i: $\beta{_0}_i$, the $0$ seems to get in the way of making a visual comparison. Is there any reason not to use $\beta_{0,i}$, since the $0$ is not really an index?

At this point, I am sure that I am over-thinking this, but before I go with $\beta_{0,i}$, I'd appreciate feedback - and other suggestions as well.

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    Then I would suggest using the index $a$s a superindex instead of a subindex (with suitable explanation ahead of time).2012-06-28

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That (or any other easy to read notation) is perfectly fine, so long as you explain it clearly. I also happen to be growing more and more fond of a raised index as well, so perhaps something like $\beta_0 = (\beta_0^1, \beta_0^2, \dots)$, or the other standard $(\beta_0)_i$.

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If you’re not going to have $\beta_1$, $\beta_2$, etc., then use a single different letter. If there will be all those other betas, you might even consider using prefixes, such as $_2\beta_i$ or $^3\beta_i$.

I might also point out that any notation has no intrinsic meaning: you have to explain any notation you use. And clearly, please!