R Markdown Math Equation Alignment

R Markdown Math Equation Alignment

I'm not quite sure what you're going for here, but line breaks, \\ go at the end of tthe line, not the beginning, and the aligmnent operator is &. So this:

$$
\begin{aligned}
 AR(p): Y_i &= c + \epsilon_i + \phi_i Y_{i-1} \dots \\
 Y_{i} &= c + \phi_i Y_{i-1} \dots
\end{aligned}
$$

produces this:

Markdown equations alignment

I ran your code on my system and it aligns just fine. Make sure you have the latest version of tools and packages installed. A minimal working example would be useful too.

How to align a math equation correctly in rmarkdown?

As suggested by one of the comments, & sign needs to be used at where I want it to align, and please see below solution. Edit: As suggested by another comment, log needs to be upright in the math equation and should use \log instead. And \left(, \right) is used to make sure the brackets are stretched

$$
\begin{aligned}
l(\theta_1,\theta_2,\sigma^2)
&=-\frac{1}{2}n\log(2\pi)-n\log\sigma-\frac{1}{2\sigma^2}\sum_{i=1}^{n}(y_i-\mu)^2\\
&=-\frac{1}{2}n\log(2\pi)-n\log\sigma-\frac{1}{2\sigma^2}\sum_{i=1}^{n}\left(y_i-\frac{\theta_1x_i}{\theta_2+x_i}\right)^2
\end{aligned}
$$   

How to left-align a series of equations in R Markdown?

You can align the equals signs as well if that's what you're looking to do like this:

\begin{align}
&\text{(1) Larvae (l): }&\ N_{l(t+1)} &=& P_l N_{l(t+1)} + F_a N_{a(t)}\\
&\text{(2) Pupae (p): }&\ N_{p(t+1)} &=& G_l N_{l(t)} + P_p N_{p(t)}\\
&\text{(3) Adults (a): }&\ N_{a(t+1)} &=& G_p N_{p(t)} + P_a N_{a(t)}\\
\end{align}

which will align your first part of the equation as well as the equals signs.

R markdown alignment with Latex equations

Markdown has a few rules to make sublists work. Most importantly in your case, sub-items only work if there is a parent item to it. As Stackoverflow uses the same syntax, we can show the examples inline. For example:

1. Item
2. Item
   * Mixed
   * Mixed 

1. Item
2. Item
   
   
   • Mixed
   • Mixed

In your case, you have put some none list items between the sub-items, as follows:

1. Item
2. Item
   * Mixed

Some Text    
   * Mixed 

1. Item
2. Item
   
   
   • Mixed

Some Text

* Mixed

As you can see, the list has been broken and is not recognised as an item.

Workaround

If you are only using PDF output, you are able to use LaTeX commands to achieve custom styling. In your case, you can use the hspace command to add a separation:

---
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

* Main Point

\hspace{1cm} + **Prediction** - Some text here

$$
\hat{Y}=\hat{f(X)}+\epsilon   ...............     (2.2)
$$
$$
E( Y - \hat{Y} )^2 
= E[f(X) + \epsilon - \hat{f(X)}]^2 
=[f(X) - \hat{f(X)}]^2+Var(\epsilon)     .........  (2.3) 
$$
\hspace{1cm} + **Inference** - Some text here

Align equations already created with {equation*}?

By adding a * to the normal align environment, you remove the numbering and possibility to use labels. Just don't do that if you want to label your expressions:

\documentclass{article}

\usepackage{amsmath}

\begin{document}

\begin{align}
%\begin{equation}
\frac{dF}{dt} &= - j_{FI}\label{eq1}
%\end{equation} 
\\
%\begin{equation}
\frac{dV}{dt} &= j_{VG}\label{eq2}
%\end{equation} 
\end{align}

\ref{eq1}

\ref{eq2}

\end{document}

Align environment in R Markdown which works for both docx and pdf output?

The following works for me:

---
output:
  bookdown::pdf_document2: default
  bookdown::word_document2: default
  bookdown::html_document2: default
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

\begin{equation*}
\begin{aligned}
 AR(p): Y_i &= c + \epsilon_i + \phi_i Y_{i-1} \dots \\
 Y_{i} &= c + \phi_i Y_{i-1} \dots
\end{aligned}
\end{equation*}

\begin{align*}
 AR(p): Y_i &= c + \epsilon_i + \phi_i Y_{i-1} \dots \\
 Y_{i} &= c + \phi_i Y_{i-1} \dots
\end{align*}

I am using the *-environments to get unnumbered equations in PDF. To get numbererd equations, you should use the environments without * and add labels.

Left aligning a LaTex equation

This latex solution on tex.SE gives an answer that we can adapt to knitr. To have all equation of the document aligned on the left, you can use classoption fleqn and write equation in regular pandoc latex-math style (surrounded with $$):

---
classoption: fleqn
header-includes:
- \setlength{\mathindent}{0pt}
---

$$\Delta PsuedoR^2_{\zeta_{0}} =  \frac {0.488 - 0.624}{0.488} = -0.219$$

Note that you don't have to add \usepackage{amsmath} because the default latex template already includes it.

---

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