In TxWRI/twriTemplates: Templates for TWRI reports

## load libraries
library(officer)
library(officedown)
library(flextable)
library(ragg)

## this sets our default code chunk options
knitr::opts_chunk$set(dev = "ragg_png",
                      echo = FALSE,
                      ## figure chunk options
                      fig.cap = TRUE,
                      fig.width = 6)

Texas Water Resources Institute

Texas A&M Agrilife

College Station, TX

TR-ABCD

This project was funded through a grant from a generous agency.

Insert other funding or partnership acknowledgments here.

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## after table of abbreviations
block_section(prop_section(type = "nextPage"))

::: {custom-style="Unnumbered Heading 1"}

Table of Contents

:::

::: {custom-style="Unnumbered Heading 1"}

Table of Figures

:::

::: {custom-style="Unnumbered Heading 1"}

Table of Tables

:::

::: {custom-style="Unnumbered Heading 1"}

Abbreviations

:::

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block_section(prop_section(type = "nextPage"))

Headings

Second Level Heading

Third Level Heading

First, second, and third level headings are defined by #, ##, and ### respectively.

Tables

This is an example of an unformatted table and how we cross-reference that table (Table \@ref(tab:mtcars)).

dat <- mtcars
head(dat, n = 10)

The flextable package provides additional formatting flexibility when exporting to Word (Table \@ref(tab:mtcarsflex)).

ft <- flextable(head(dat, n = 10))
ft

Figures

We can embed and cross-reference plots (Figure \@ref(fig:pressure)).

plot(pressure)

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## after table of abbreviations
block_section(prop_section(type = "nextPage"))

Landscape Section

x <- seq(1,30, by = .1)
plot(x, sin(x), type = "l", main = "", xlab = "", ylab = "", col = "#CC4300")

Math

Wrap variables or math in a single $ to show math inline. For example, $\varepsilon \sim \mathrm{N}(0,1)$. Standalone equations are wrapped with $$.

$$ \left(\prod_{i=1}^{n}y_i\right)^{\frac{1}{n}} = \exp\left[\frac{1}{n}\sum_{i=1}^n\log{y_i}\right], \quad \textrm{when} \quad y_1, y_2, ..., y_n > 0 $$

If the equations need to be numbered and cross-referenced the format as:

\begin{equation}
\left(\prod_{i=1}^{n}y_i\right)^{\frac{1}{n}} = \exp\left[\frac{1}{n}\sum_{i=1}^n\log{y_i}\right], \quad \textrm{when} \quad y_1, y_2, ..., y_n > 0
(\#eq:gmean)
\end{equation}

Which renders as (Equation \@ref(eq:gmean):

\begin{equation} \left(\prod_{i=1}^{n}y_i\right)^{\frac{1}{n}} = \exp\left[\frac{1}{n}\sum_{i=1}^n\log{y_i}\right], \quad \textrm{when} \quad y_1, y_2, ..., y_n > 0 (#eq:gmean) \end{equation}

References

In-text references and bibliography generation are handled automatically. It relies on creating a bibtex .bib file with your references. Software such as Zotero, Mendely, and even Google Scholar can generate the bibtex entries for you. The entries are stored in the bibliography.bib file inside the same directory as this .Rmd file. To make a in text citation, use the following syntax, [@helsel_statistical_2002] to generate the reference at the end of this sentence [@helsel_statistical_2002]. Use a semicolon to include multiple references [@helsel_statistical_2002; @hirsch2010weighted] [@helsel_statistical_2002; @hirsch2010weighted]. Or we might use @helsel_statistical_2002 without brackets to indicate @helsel_statistical_2002 provide a fundamental overview of water quality statistics. The bibliography will populate automatically.

Styling and fonts

This template uses Minion Pro for body fonts and Open Sans for headings following TWRI brand guidance and AgriLife brand guidance. I can't bundle Minion Pro in this package because of licensing, but you can download and install both fonts from AgriLife (https://agrilife.tamu.edu/wp-content/uploads/2021/03/AgriFonts.zip). I recommend downloading and installing the fonts before knitting your documents. Note that Minion Pro won't "embed" in Word documents because it is an OTF style font and currently Word only embeds TTF fonts. That means collaborators without the font installed on their system will see a different serif font on their system in Word. Once exported to pdf, both OTF and TTF fonts should be embedded correctly.

Bibliography {-}

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block_section(prop_section(type = "nextPage"))

Appendix A {-}

You can add more info, tables, and figures here.

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block_section(prop_section(type = "nextPage"))

TxWRI/twriTemplates documentation built on Oct. 20, 2023, 2:06 p.m.