---
header-includes: 
  \usepackage{mathtools}
output: 
  pdf_document:
    toc: false
    toc_depth: 3
    includes:
      in_header: utils/header.tex

# fig_caption: yes

# the .bib files are to contain your references and your libraries use 
# these will be saved in report/utils/
bibliography: [utils/references.bib, utils/libraries.bib]

link-citations: yes
---

<!-- *********************************************************************** -->
<!-- *********************************************************************** -->

<!-- Save this .Rmd file in report/ 
When knit as pdf, the report will be in report/ 

Thing you need:

1. Your working scripts that perform all of the data cleaning of the raw data, 
that write out of cleaned/processed, that aggregate or create data summaries,
and the create all visualizations and associated .png files.

2. Your references in report/utils/references.bib (add your references); 
see citation of references examples in this document. 
Pull all reference documents like pdfs, in refs/ . For urls, these will likely
break or fail; print them as pdfs and save in refs/

3. A header file in report/utils/header.tex (don't modify)

4. Your written content

5. Other necessary elements

-->


<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Accessing all of your scripts in order to replicate and reproduce 
data files, visualizations, etc. -->
<!-- *********************************************************************** -->
<!-- *********************************************************************** -->

```{r include=FALSE}
# source functions or function directory 
R.utils::sourceDirectory(here::here("src", "functions"))

# load libraries needed for report (or lead in scripts)
pacman::p_load(knitr, rmarkdown)
```


```{r include=FALSE}
## All content must be dynamic and not hard coded. You should assume that all 
## objects are created with the code source()d here and do no exist otherwise. 
## If the code sourced()d in this R Markdown files does not create what you need
## for your report, then the report cannot be replicated with new data (e.g., rows).

## DO NOT include anything that cannot be reproduced with your code source()d 
## within the document. Any hard coding of paths, files, reference to objects, etc. 
## will likely not work when reproduced.

## Note: source relevant .R scripts in order of operation for proper execution
## and replication/reproducibility; ensure that you have fetched collaborator
## branch content so that those file are local. As the last step, these will
## need to be on the main branch of the remote repo. I will test this with the 
## main branch and with a data subset to ensure that the code reproduces appropriately


## raw data reading/cleaning/writing scripts(s) 
## Ex: source(here::here("src", "data", "data-cleaning-xyz.R"))

## (if any) data summary/aggregation/writing scripts(s) (which depend on cleaned data)
## Ex: source(here::here("src", "data", "data-summary-mpg.R"))

## visualization scripts that create plots and save .pngs (which depend on data previous)
## Ex: source(here::here("src", "figs", "point_plot_mpg_by_wt.png.R"))
```



<!-- code setup for plot files --> 

```{r echo=FALSE}
# some settings for figures in R Markdown
# settings in code chunks will override these global settings

knitr::opts_chunk$set(#fig.align = "center", 
                      fig.width = 12, 
                      fig.height = 8, 
                      fig.path = here::here("report", "figs"),
                      echo = TRUE, warning = FALSE, message = FALSE
                      )
```

<!-- insert logo file -->
```{r echo=FALSE,out.width="30%", fig.align='center'}
# including a logo
knitr::include_graphics(here::here("report", "images", "cmc-logo2.png"))
```

<!-- Page 1, Title Page -->
\centerline{}
\centerline{}
\centerline{}
\centerline{\textbf{CMC Data Visualization: PSYC167}}
\centerline{}
\centerline{\textbf{Final Report for}}
\centerline{\textit{Organization Name}}
\centerline{}
\centerline{}
\centerline{\large \textbf{Project Title}}
\centerline{}
\centerline{}
\centerline{Month, day, year}
\centerline{}
\centerline{}
\centerline{\textbf{Team Members}}
\centerline{Person A}
\centerline{Person B}
\centerline{Person C}
\centerline{Person D}
\centerline{}
\centerline{}
\centerline{\textbf{Project Advisor}}
\centerline{Gabriel I. Cook}
\centerline{}
\centerline{\textbf{Liaison}}
\centerline{Name}
\centerline{}
\centerline{}
\centerline{}
\centerline{\textbf{Code and Project Files}}
\centerline{GitHub: <https://github.com/slicesofdata/repository-name>}


<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Page 2, Abstract  -->
\newpage
\centerline{\textbf{Abstract}}

<!-- abstract keywords -->
*Keywords*: 



<!-- Page 3, Table of Contents -->
\newpage
\tableofcontents

<!-- Page 4, Acknowledgments -->
\newpage
\centerline{\textbf{Acknowledgments}}
<!-- Page 5, Main Content -->



\newpage
<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- introduction -->
## **Introduction**

Examples of citing references from the .bib file in utils/references.bib. 

Blah blah blah [@gill1980] for single citation 

Blah blah @gill1980 and @gill1980 [see also @gill1980, p.2]. In addition, [@anderson2015; @gill1980] say blah blah blah.

[@gill1980; @anderson2015] multiple citation can be separated by semi-colon

[-@gill1980] in order to suppress author name, and just display the year use a -

[see @gill1980 p. 12; also this ref @anderson2015] is also valid 


Libraries can cite in text also.

Blah blah @R-base, @R-knitr, @R-dplyr, and @R-ggplot2


^[Footnote goes here] <!-- number will appear in text but footnote will apper at end of section -->

<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Describing your problem statement-->
## **Problem Statement**

Blah blah ...






<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Data -->
## **Data** 
<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Describing your data Data -->
## *Sources*

Blah blah ...






<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Describing the characterstics of your data -->
## *Characteristics*

Blah blah ...






<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Describing your data cleaning and preprocessing -->
## *Data Quality and Preprocessing*

Blah blah ...





<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Describing limitations of data -->
## *Limitations*

Blah blah ...




<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Describing your findings -->
<!-- This is likely where you will referent your visualizations -->
## **Findings**

Blah blah ...

If you want to add sub-sections, use the ### flag.





<!-- when you need to include a plot, call the png file -->
```{r echo=FALSE, out.width="80%", fig.align="center", fig.cap="A good caption for the plot."}
## example
##| echo: false         # hide code
##| out.width: "80%"    # resize based on width (if pixels, example out.width: "300px")
##| out.height: "70%"   # resize based on height (if pixels, example out.height: "300px")
##| fig.align: "center" # align to center
##| fig.asp: 0.75       # aspect ratio
##| fig.width: 6        # figure width in inches
##| fig.height: 4       # figure height in inches
##| fig.cap: "A good caption" 

# when you need to include a plot, reference it by name at the location you want to insert it
knitr::include_graphics(here::here("report", "figs", "point_plot_mpg_by_wt.png"))
```


```{r echo=FALSE, out.width="60%", fig.align="center", fig.cap="A caption for a 60% width plot."}
# example
#| echo: false          # hide code
##| out.width: "40%"    # resize based on width (if pixels, example out.width: "300px")
##| out.height: "70%"   # resize based on height (if pixels, example out.height: "300px")
##| fig.align: "center" # align to center
##| fig.asp: 0.75       # aspect ratio
##| fig.width: 6        # figure width in inches
##| fig.height: 4       # figure height in inches
##| fig.cap: "A good caption"  

# when you need to include a plot, reference it by name at the place of insert
knitr::include_graphics(here::here("report", "figs", "point_plot_mpg_by_wt.png"))
```

<!-- alternatively, use LaTeX code (though I think this will be more difficult-->
<!--
\begin{center}
\includegraphics[width=0.8\textwidth]{images/cmc_logo2.png}
\end{center}
-->




<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Discussion  -->
## **Discussion**

Blah blah ...

If you want to add sub-sections, use the ### flag.




<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Conclusion  -->
## **Conclusion**

Blah blah ...





<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- Optional (remove if not used) -->
## **Challenges and Limitations**

Blah blah ...


<!-- *********************************************************************** -->
<!-- *********************************************************************** -->
<!-- REFERENCE BUILDING -->

<!-- put your references in a report/utils/references.bib file -->



<!-- to automate references used in the report -->
<!-- put your references in a report/utils/libraries.bib file -->

```{r include=FALSE}
# automatically create a bib database for R packages
if (file.exists(here::here("report", "utils",  "libraries.bib"))) {
  file.remove(here::here("report", "utils", "libraries.bib"))
} 
# will build a libraries.bib file based on loaded libraries
knitr::write_bib(
  x = c(.packages(), "knitr", "rmarkdown", "here"),
  file = here::here("report", "utils", "libraries.bib")
  )
```
<!-- https://inbo.github.io/tutorials/tutorials/r_citations_markdown/ -->
<!-- https://monashdatafluency.github.io/r-rep-res/citations.html -->

\newpage
## **References**
\centerline{}
\bibliographystyle{apacite}