In ismayc/thesisdown: An updated R Markdown thesis template using the bookdown package
Mathematics and Science {#math-sci}
Math
\TeX\ is the best way to typeset mathematics. Donald Knuth designed \TeX\ when he got frustrated at how long it was taking the typesetters to finish his book, which contained a lot of mathematics. One nice feature of R Markdown is its ability to read LaTeX code directly.
If you are doing a thesis that will involve lots of math, you will want to read the following section which has been commented out. If you're not going to use math, skip over or delete this next commented section.
Chemistry 101: Symbols
Chemical formulas will look best if they are not italicized. Get around math mode's automatic italicizing in LaTeX by using the argument $\mathrm{formula here}$, with your formula inside the curly brackets. (Notice the use of the backticks here which enclose text that acts as code.)
So, $\mathrm{Fe_2^{2+}Cr_2O_4}$ is written $\mathrm{Fe_2^{2+}Cr_2O_4}$.
\noindent Exponent or Superscript: $\mathrm{O^-}$
\noindent Subscript: $\mathrm{CH_4}$
To stack numbers or letters as in $\mathrm{Fe_2^{2+}}$, the subscript is defined first, and then the superscript is defined.
\noindent Bullet: CuCl $\bullet$ $\mathrm{7H_{2}O}$
\noindent Delta: $\Delta$
\noindent Reaction Arrows: $\longrightarrow$ or $\xrightarrow{solution}$
\noindent Resonance Arrows: $\leftrightarrow$
\noindent Reversible Reaction Arrows: $\rightleftharpoons$
Typesetting reactions
You may wish to put your reaction in an equation environment, which means that LaTeX will place the reaction where it fits and will number the equations for you.
\begin{equation}
\mathrm{C_6H_{12}O_6 + 6O_2} \longrightarrow \mathrm{6CO_2 + 6H_2O}
(#eq:reaction)
\end{equation}
We can reference this combustion of glucose reaction via Equation \@ref(eq:reaction).
Other examples of reactions
$\mathrm{NH_4Cl_{(s)}}$ $\rightleftharpoons$ $\mathrm{NH_{3(g)}+HCl_{(g)}}$
\noindent $\mathrm{MeCH_2Br + Mg}$ $\xrightarrow[below]{above}$ $\mathrm{MeCH_2\bullet Mg \bullet Br}$
Physics
Many of the symbols you will need can be found on the math page https://web.reed.edu/cis/help/latex/math.html and the Comprehensive LaTeX Symbol Guide (https://mirror.utexas.edu/ctan/info/symbols/comprehensive/symbols-letter.pdf).
Biology
You will probably find the resources at https://www.lecb.ncifcrf.gov/~toms/latex.html helpful, particularly the links to bsts for various journals. You may also be interested in TeXShade for nucleotide typesetting (https://homepages.uni-tuebingen.de/beitz/txe.html). Be sure to read the proceeding chapter on graphics and tables.
ismayc/thesisdown documentation built on Nov. 1, 2024, 10 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Mathematics and Science {#math-sci}
Math
\TeX\ is the best way to typeset mathematics. Donald Knuth designed \TeX\ when he got frustrated at how long it was taking the typesetters to finish his book, which contained a lot of mathematics. One nice feature of R Markdown is its ability to read LaTeX code directly.
If you are doing a thesis that will involve lots of math, you will want to read the following section which has been commented out. If you're not going to use math, skip over or delete this next commented section.
Chemistry 101: Symbols
Chemical formulas will look best if they are not italicized. Get around math mode's automatic italicizing in LaTeX by using the argument $\mathrm{formula here}$, with your formula inside the curly brackets. (Notice the use of the backticks here which enclose text that acts as code.)
So, $\mathrm{Fe_2^{2+}Cr_2O_4}$ is written $\mathrm{Fe_2^{2+}Cr_2O_4}$.
\noindent Exponent or Superscript: $\mathrm{O^-}$
\noindent Subscript: $\mathrm{CH_4}$
To stack numbers or letters as in $\mathrm{Fe_2^{2+}}$, the subscript is defined first, and then the superscript is defined.
\noindent Bullet: CuCl $\bullet$ $\mathrm{7H_{2}O}$
\noindent Delta: $\Delta$
\noindent Reaction Arrows: $\longrightarrow$ or $\xrightarrow{solution}$
\noindent Resonance Arrows: $\leftrightarrow$
\noindent Reversible Reaction Arrows: $\rightleftharpoons$
Typesetting reactions
You may wish to put your reaction in an equation environment, which means that LaTeX will place the reaction where it fits and will number the equations for you.
\begin{equation} \mathrm{C_6H_{12}O_6 + 6O_2} \longrightarrow \mathrm{6CO_2 + 6H_2O} (#eq:reaction) \end{equation}
We can reference this combustion of glucose reaction via Equation \@ref(eq:reaction).
Other examples of reactions
$\mathrm{NH_4Cl_{(s)}}$ $\rightleftharpoons$ $\mathrm{NH_{3(g)}+HCl_{(g)}}$
\noindent $\mathrm{MeCH_2Br + Mg}$ $\xrightarrow[below]{above}$ $\mathrm{MeCH_2\bullet Mg \bullet Br}$
Physics
Many of the symbols you will need can be found on the math page https://web.reed.edu/cis/help/latex/math.html and the Comprehensive LaTeX Symbol Guide (https://mirror.utexas.edu/ctan/info/symbols/comprehensive/symbols-letter.pdf).
Biology
You will probably find the resources at https://www.lecb.ncifcrf.gov/~toms/latex.html helpful, particularly the links to bsts for various journals. You may also be interested in TeXShade for nucleotide typesetting (https://homepages.uni-tuebingen.de/beitz/txe.html). Be sure to read the proceeding chapter on graphics and tables.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.