Aligning equations within a box in rmarkdown - latex

Question

I am trying to get aligned equations within a box in rmarkdown. I am knitting to pdf.
The reason the box is necessary is because the YAML metadata I use automatically left-aligns all the text, but I want the equations centered.
Here is my rmarkdown code. As you can see when you run it, the equations are centered but the second set of = signs are not aligned across the two lines.
Any help much appreciated.
---
title: "Aligning equations in a box"
output:
pdf_document: default
html_document: null
word_document: null
toc: yes
linestretch: 1.3
classoption: fleqn
header-includes:
- \setlength{\mathindent}{0pt}
- \setlength\parindent{0pt}
---
\setlength{\abovedisplayskip}{-15pt}
\setlength{\belowdisplayskip}{1pt}
\setlength{\abovedisplayshortskip}{1pt}
\setlength{\belowdisplayshortskip}{1pt}
```{r global_options, include=FALSE, echo = FALSE}
knitr::opts_chunk$set(fig.width=12, fig.height=8, fig.path='Figs/',
echo=FALSE, warning=FALSE, message=FALSE, dev = 'pdf')
```
These words are automatically left-aligned by the YAML meta-data above so a box is necessary to centre equations.
### Equation 11.6
\[\large
\makebox[\linewidth]{$\displaystyle
\begin{aligned}
\text{when}\ PT &= 0:logit\ h(t_{j})\ &= [\alpha_{7}D_{7} + \alpha_{8}D_{8} + \cdots + \alpha_{12}D_{12}]\\
\text{when}\ PT &= 1:logit\ h(t_{j})\ &= [\alpha_{7}D_{7} + \alpha_{8}D_{8} + \cdots + \alpha_{12}D_{12}] + \beta_{1}
\end{aligned}
$}
\]

Answer 1

Not sure I understand, but is it necessary to have a big space between? If not, you can just remove the &,
\[\large
\makebox[\linewidth]{$\displaystyle
\begin{aligned}
\text{when}\ PT =& 0:logit\ h(t_{j})\ = [\alpha_{7}D_{7} + \alpha_{8}D_{8} + \cdots + \alpha_{12}D_{12}]\\
\text{when}\ PT =& 1:logit\ h(t_{j})\ = [\alpha_{7}D_{7} + \alpha_{8}D_{8} + \cdots + \alpha_{12}D_{12}] + \beta_{1}
\end{aligned}
$}
\]
this gives
If you want a space you could use something like \qquad or \quad
\[\large
\makebox[\linewidth]{$\displaystyle
\begin{aligned}
\text{when}\ PT =& 0:logit\ h(t_{j})\ \qquad= [\alpha_{7}D_{7} + \alpha_{8}D_{8} + \cdots + \alpha_{12}D_{12}]\\
\text{when}\ PT =& 1:logit\ h(t_{j})\ \qquad= [\alpha_{7}D_{7} + \alpha_{8}D_{8} + \cdots + \alpha_{12}D_{12}] + \beta_{1}
\end{aligned}
$}
\]
which gives me
EDIT:
Answering the question in your comment. Wrap the blocks in between two &.
\[\large
\makebox[\linewidth]{$\displaystyle
\begin{aligned}
\text{whenmoretext}\ PT &= 0:logit\ h(t_{j})\ & &= [\alpha_{7}D_{7} + \alpha_{8}D_{8} + \cdots + \alpha_{12}D_{12}]\\
\text{when}\ PT &= 1:logit\ h(t_{j})\ & &= [\alpha_{7}D_{7} + \alpha_{8}D_{8} + \cdots + \alpha_{12}D_{12}] + \beta_{1}
\end{aligned}
$}
\]