├── 00-DISSERTATION.parent.Rmd ├── 00-DISSERTATION.parent.log ├── 00-DISSERTATION.parent.pdf ├── 01-titlepage.Rmd ├── 01-titlepage.pdf ├── 02-copyright.Rmd ├── 02-copyright.pdf ├── 03-abstract.Rmd ├── 03-abstract.pdf ├── 04-acknowledgements.Rmd ├── 04-acknowledgements.pdf ├── 05-chapter1.Rmd ├── 05-chapter1.pdf ├── 06-chapter2.Rmd ├── 06-chapter2.pdf ├── 07-chapter3.Rmd ├── 07-chapter3.pdf ├── 08-chapter4.Rmd ├── 08-chapter4.pdf ├── 09-chapter5.Rmd ├── 09-chapter5.pdf ├── 10-vita.Rmd ├── 10-vita.pdf ├── Data ├── PSCAA_Data.xls ├── bc.28feb2017.csv ├── dylos.28feb2017.csv ├── nanoscan.28feb2017.csv └── qtrak.28feb2017.csv ├── Figs ├── above-sampling-1.pdf ├── bc-boxplot-1.pdf ├── below-sampling-1.pdf ├── dy-boxplot-1.pdf ├── nn-boxplot-1.pdf └── size-distribution-nn-plots-1.pdf ├── Images ├── AboveSampling.png ├── BC_PM_PSCA.png ├── BelowSampling1.png ├── CO_PSCA.png ├── Rosanna.png └── TEMP_PSCA.png ├── LICENSE ├── LightningTalk.Rmd ├── LightningTalk.html ├── LightningTalk.md ├── README.md ├── council-of-science-editors.csl ├── environmental-health-perspectives.csl ├── example-dissertation.Rproj ├── science-modified1.csl └── thesis-references.bib /00-DISSERTATION.parent.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | date: '`r format(Sys.Date(), "%d %B %Y")`' 3 | output: 4 | bookdown::pdf_document2: 5 | toc: no 6 | geometry: margin = 1in 7 | fontsize: 11pt 8 | bibliography: thesis-references.bib 9 | csl: science-modified1.csl 10 | link-citations: yes 11 | linkcolor: blue 12 | urlcolor: blue 13 | header-includes: 14 | - \usepackage{placeins} 15 | - \usepackage{fancyhdr} 16 | - \usepackage{setspace} 17 | - \usepackage{chngcntr} 18 | - \usepackage{microtype} 19 | - \counterwithin{figure}{section} 20 | - \counterwithin{table}{section} 21 | - \setlength{\parindent}{1em} 22 | - \doublespacing 23 | - \usepackage{float} 24 | - \usepackage{amsmath} 25 | - \DeclareMathOperator{\logit}{logit} 26 | --- 27 | 28 | 29 | 30 | ```{r knitr.global_options, include=F} 31 | knitr::opts_chunk$set(fig.width=12, fig.height=8, fig.path='Figs/', echo=FALSE, warning=FALSE, message=FALSE, tidy.opts=list(width.cutoff=60), tidy=TRUE) 32 | ``` 33 | 34 | \pagenumbering{gobble} 35 | 36 | ```{r child = '01-titlepage.Rmd'} 37 | ``` 38 | 39 | \newpage 40 | 41 | ```{r child = '02-copyright.Rmd'} 42 | ``` 43 | 44 | \newpage 45 | 46 | ```{r child = '03-abstract.Rmd'} 47 | ``` 48 | 49 | \FloatBarrier 50 | 51 | \newpage 52 | \fancyhead[LE,RO]{} 53 | \fancyhead[LO,RE]{} 54 | \renewcommand{\headrulewidth}{0.4pt} 55 | \renewcommand{\footrulewidth}{0pt} 56 | \pagestyle{fancy} 57 | \pagenumbering{roman} 58 | \fancyhead[CO,CE]{Table of Contents} 59 | \setcounter{tocdepth}{3} 60 | \linespread{1}\selectfont 61 | \tableofcontents 62 | 63 | \FloatBarrier 64 | 65 | \newpage 66 | \fancyhead[CO,CE]{List of Figures} 67 | \addcontentsline{toc}{section}{List of Figures} 68 | \listoffigures 69 | 70 | \FloatBarrier 71 | 72 | \newpage 73 | \fancyhead[CO,CE]{List of Tables} 74 | \addcontentsline{toc}{section}{List of Tables} 75 | \listoftables 76 | 77 | \FloatBarrier 78 | 79 | \newpage 80 | \fancyhead[CO,CE]{Acknowledgements} 81 | \section*{Acknowledgements} 82 | 83 | ```{r child = '04-acknowledgements.Rmd'} 84 | ``` 85 | 86 | \FloatBarrier 87 | 88 | \clearpage 89 | 90 | \pagenumbering{arabic} 91 | \fancyhead[CO,CE]{Chapter 1. Introduction} 92 | 93 | ```{r child = '05-chapter1.Rmd'} 94 | ``` 95 | 96 | \FloatBarrier 97 | 98 | \clearpage 99 | 100 | \fancyhead[CO,CE]{Chapter 2. Photo Journalism} 101 | 102 | ```{r child = '06-chapter2.Rmd'} 103 | ``` 104 | 105 | \FloatBarrier 106 | 107 | \clearpage 108 | 109 | \fancyhead[CO,CE]{Chapter 3. Webbing Fluid} 110 | 111 | ```{r child = '07-chapter3.Rmd'} 112 | ``` 113 | 114 | \FloatBarrier 115 | 116 | \clearpage 117 | 118 | \fancyhead[CO,CE]{Chapter 4. Fighting Crime} 119 | 120 | ```{r child = '08-chapter4.Rmd'} 121 | ``` 122 | 123 | \FloatBarrier 124 | 125 | \clearpage 126 | 127 | \fancyhead[CO,CE]{Chapter 5. Conclusions} 128 | 129 | ```{r child = '09-chapter5.Rmd'} 130 | ``` 131 | 132 | \FloatBarrier 133 | 134 | \newpage 135 | \fancyhead[CO,CE]{References} 136 | \linespread{1.0}\selectfont 137 | 138 | # References 139 | 140 | \setlength{\parindent}{0cm} 141 | 142 |
143 | 144 | \FloatBarrier 145 | 146 | \newpage 147 | \fancyhead[CO,CE]{Acronyms and Abbreviations} 148 | \linespread{1.0}\selectfont 149 | 150 | # Acronyms and abbreviations 151 | 152 | ```{r acronyms, message=F, warnings=F, results='asis', echo=F} 153 | tabl <- " 154 | ---------------------------------------------------------------------------------------- 155 | Code Full name 156 | ------------------ --------------------------------------------------------------------- 157 | AM Arithmetic Mean 158 | 159 | API Application Programmable Interface 160 | 161 | ASD Arithmetic Standard Deviation 162 | 163 | CDC Centers for Disease Control and Prevention 164 | 165 | WAC Washington Administrative Code 166 | 167 | WSU Washington State University 168 | 169 | Zn Zinc 170 | ---------------------------------------------------------------------------------------- 171 | 172 | " 173 | cat(tabl) 174 | ``` 175 | 176 | \FloatBarrier 177 | 178 | \newpage 179 | \fancyhead[CO,CE]{Vita} 180 | \linespread{1.0}\selectfont 181 | 182 | ```{r child = '10-vita.Rmd'} 183 | ``` 184 | 185 | -------------------------------------------------------------------------------- /00-DISSERTATION.parent.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/00-DISSERTATION.parent.pdf -------------------------------------------------------------------------------- /01-titlepage.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: pdf_document 3 | --- 4 | 5 | \linespread{1}\selectfont 6 | 7 | \vspace*{1.75 cm} 8 | 9 | \begin{centering} 10 | 11 | \Large 12 | On Preventing Crime in New York City: \break 13 | Photo Journalism and Web-based Super Powers 14 | 15 | \vspace{1.75 cm} 16 | 17 | \normalsize 18 | Peter Parker 19 | 20 | \vspace{1.75 cm} 21 | 22 | \normalsize 23 | A dissertation submitted in partial fulfillment \break 24 | of the requirements for the degree of 25 | 26 | \vspace{1 cm} 27 | 28 | Doctor of Philosophy 29 | 30 | \vspace{1 cm} 31 | 32 | University of Washington 33 | 34 | 2017 35 | 36 | \vspace{1 cm} 37 | 38 | Reading Committee: 39 | 40 | Jane J. Doe, Chair \break 41 | John L. Doe \break 42 | Stan Lee \break 43 | 44 | \vspace{1 cm} 45 | 46 | Program Authorized to Offer Degree: \break 47 | Department of Environmental and Occupational Health Sciences 48 | 49 | \end{centering} 50 | 51 | \linespread{1.6}\selectfont 52 | 53 | -------------------------------------------------------------------------------- /01-titlepage.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/01-titlepage.pdf -------------------------------------------------------------------------------- /02-copyright.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: pdf_document 3 | --- 4 | 5 | \linespread{1}\selectfont 6 | 7 | \begin{centering} 8 | 9 | © Copyright 2017 \break 10 | Peter Parker 11 | 12 | \end{centering} 13 | 14 | \linespread{1.6}\selectfont 15 | -------------------------------------------------------------------------------- /02-copyright.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/02-copyright.pdf -------------------------------------------------------------------------------- /03-abstract.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: 3 | bookdown::pdf_document2: 4 | geometry: margin = 1in 5 | fontsize: 11pt 6 | header-includes: 7 | - \usepackage{placeins} 8 | - \usepackage{setspace} 9 | - \usepackage{chngcntr} 10 | - \usepackage{microtype} 11 | - \counterwithin{figure}{section} 12 | - \counterwithin{table}{section} 13 | - \usepackage{float} 14 | - \usepackage{amsmath} 15 | - \renewcommand{\contentsname}{} 16 | --- 17 | 18 | \linespread{1}\selectfont 19 | 20 | \begin{centering} 21 | 22 | \normalsize 23 | 24 | University of Washington 25 | 26 | \vspace{0.25 cm} 27 | 28 | {\bf Abstract} 29 | 30 | \vspace{0.25 cm} 31 | 32 | On Preventing Crime in New York City: \break 33 | Photo Journalism and Web-based Super Powers 34 | 35 | \vspace{0.25 cm} 36 | 37 | Peter Parker 38 | 39 | \vspace{0.25 cm} 40 | 41 | Chair of the Supervisory Committee:\break 42 | Professor Jane K. Doe\break 43 | Department of Environmental and Occupational Health Sciences 44 | 45 | \end{centering} 46 | 47 | \vspace{1 cm} 48 | 49 | \linespread{1}\selectfont 50 | 51 | \setlength{\parindent}{0em} 52 | 53 | Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Augue eget arcu dictum varius duis. Duis tristique sollicitudin nibh sit amet commodo. Morbi tristique senectus et netus et malesuada fames ac. Venenatis lectus magna fringilla urna. Odio eu feugiat pretium nibh ipsum consequat nisl vel. Aliquet nibh praesent tristique magna sit amet purus gravida. Massa placerat duis ultricies lacus. Sodales neque sodales ut etiam. Diam donec adipiscing tristique risus. Duis ut diam quam nulla porttitor. Neque sodales ut etiam sit amet nisl. 54 | 55 | Et tortor at risus viverra adipiscing. Leo integer malesuada nunc vel risus commodo viverra maecenas accumsan. Tellus molestie nunc non blandit massa enim nec. Risus ultricies tristique nulla aliquet enim tortor at auctor. Vitae sapien pellentesque habitant morbi tristique senectus et netus et. Mattis aliquam faucibus purus in massa tempor nec feugiat nisl. Ac placerat vestibulum lectus mauris ultrices eros in cursus turpis. Vel risus commodo viverra maecenas accumsan lacus vel facilisis. Luctus venenatis lectus magna fringilla. Ullamcorper eget nulla facilisi etiam dignissim diam quis enim. Arcu odio ut sem nulla pharetra diam. 56 | 57 | Lacus laoreet non curabitur gravida arcu ac tortor. Semper auctor neque vitae tempus quam pellentesque nec nam. Volutpat diam ut venenatis tellus in metus. Massa tempor nec feugiat nisl pretium. Id leo in vitae turpis massa sed elementum tempus. Est ante in nibh mauris cursus. In ornare quam viverra orci sagittis eu volutpat. Arcu cursus vitae congue mauris rhoncus aenean vel. Fusce id velit ut tortor. Ut tellus elementum sagittis vitae. Iaculis nunc sed augue lacus. Est ultricies integer quis auctor elit sed vulputate. 58 | -------------------------------------------------------------------------------- /03-abstract.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/03-abstract.pdf -------------------------------------------------------------------------------- /04-acknowledgements.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: 3 | bookdown::pdf_document2: 4 | geometry: margin = 1in 5 | fontsize: 11pt 6 | header-includes: 7 | - \usepackage{placeins} 8 | - \usepackage{setspace} 9 | - \usepackage{chngcntr} 10 | - \usepackage{microtype} 11 | - \counterwithin{figure}{section} 12 | - \counterwithin{table}{section} 13 | - \usepackage{float} 14 | - \usepackage{amsmath} 15 | - \renewcommand{\contentsname}{} 16 | --- 17 | 18 | \linespread{1}\selectfont 19 | 20 | It takes a village to raise a graduate student. I gratefully acknowledge the contributions of many groups and individuals who assisted with this research. 21 | 22 | **Doctoral Supervisory Committee.** Drs. Doe and Lee were instrumental in this work. Sed risus pretium quam vulputate dignissim. Posuere morbi leo urna molestie. Consequat interdum varius sit amet mattis vulputate enim nulla. Leo vel orci porta non pulvinar. Est lorem ipsum dolor sit amet consectetur adipiscing elit. Gravida arcu ac tortor dignissim convallis aenean et tortor. Imperdiet nulla malesuada pellentesque elit eget gravida cum sociis. Aliquam purus sit amet luctus venenatis lectus magna fringilla urna. Sit amet tellus cras adipiscing. Vivamus arcu felis bibendum ut tristique et. Convallis convallis tellus id interdum. Sapien pellentesque habitant morbi tristique senectus et netus et malesuada. Lectus sit amet est placerat. Posuere urna nec tincidunt praesent. Est pellentesque elit ullamcorper dignissim cras tincidunt lobortis. 23 | 24 | **Funding Agencies.** This disseration was supported by Award Number E123456. Additional support was provided by the Department of Environmental and Occupational Health Sciences (DEOHS) at the University of Washington. Ultrices eros in cursus turpis massa tincidunt dui ut. Odio facilisis mauris sit amet. Vitae tortor condimentum lacinia quis vel eros donec. Nulla pellentesque dignissim enim sit. Vulputate eu scelerisque felis imperdiet proin fermentum. Pretium lectus quam id leo in vitae turpis massa sed. Quis lectus nulla at volutpat diam ut. Blandit volutpat maecenas volutpat blandit. Nunc pulvinar sapien et ligula ullamcorper malesuada. Dolor sed viverra ipsum nunc aliquet bibendum. Non diam phasellus vestibulum lorem sed risus ultricies tristique nulla. 25 | 26 | **Family and Friends.** Finally, I would like to thank my family and friends for their support. Etiam erat velit scelerisque in dictum non. Risus quis varius quam quisque. Duis at consectetur lorem donec massa sapien faucibus. Eu feugiat pretium nibh ipsum consequat nisl. Nisi vitae suscipit tellus mauris a diam. Id nibh tortor id aliquet lectus. Nec tincidunt praesent semper feugiat nibh sed. Gravida quis blandit turpis cursus. Facilisi morbi tempus iaculis urna id volutpat. Sed augue lacus viverra vitae congue eu consequat. -------------------------------------------------------------------------------- /04-acknowledgements.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/04-acknowledgements.pdf -------------------------------------------------------------------------------- /05-chapter1.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Chapter 1: Introduction' 3 | date: '`r format(Sys.Date(), "%d %B %Y")`' 4 | output: 5 | bookdown::pdf_document2: 6 | number_sections: yes 7 | toc: yes 8 | geometry: margin = 1in 9 | fontsize: 11pt 10 | bibliography: thesis-references.bib 11 | csl: science-modified1.csl 12 | link-citations: true 13 | linkcolor: blue 14 | urlcolor: blue 15 | header-includes: 16 | - \usepackage{placeins} 17 | - \usepackage{setspace} 18 | - \usepackage{chngcntr} 19 | - \usepackage{microtype} 20 | - \counterwithin{figure}{section} 21 | - \counterwithin{table}{section} 22 | - \usepackage{float} 23 | - \usepackage{amsmath} 24 | - \DeclareMathOperator{\logit}{logit} 25 | --- 26 | 27 | \linespread{1.6}\selectfont 28 | \setlength{\parindent}{1em} 29 | 30 | # Introduction 31 | 32 | ## Lorem ipsum dolor sit amet 33 | 34 | ### Consectetur adipiscing elit, sed do eiusmod tempor 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Lectus urna duis convallis convallis tellus. Vitae auctor eu augue ut lectus arcu bibendum at varius. Lectus nulla at volutpat diam ut venenatis tellus. Adipiscing vitae 64\% ($\frac{43}{67}$) proin sagittis nisl rhoncus mattis rhoncus urna. Nunc lobortis mattis aliquam faucibus purus in massa tempor nec. Amet porttitor eget dolor morbi non arcu risus. Arcu risus quis varius quam quisque. Ultrices eros in cursus turpis massa tincidunt dui ut. Faucibus et molestie ac feugiat sed lectus vestibulum. Porttitor rhoncus dolor purus non enim praesent elementum facilisis leo. Eget mauris pharetra et ultrices neque ornare aenean euismod elementum. Interdum varius sit amet mattis vulputate. Pretium vulputate sapien nec sagittis. Scelerisque mauris pellentesque pulvinar pellentesque. 37 | 38 | ### Labore et dolore magna aliqua 39 | 40 | Egestas sed sed risus pretium quam vulputate dignissim suspendisse in. Amet tellus cras adipiscing enim eu turpis egestas pretium aenean. Rhoncus urna neque viverra justo nec. Mauris commodo quis imperdiet massa tincidunt nunc pulvinar. Malesuada nunc vel risus commodo viverra maecenas accumsan lacus vel. Ut aliquam purus sit amet. Porttitor leo a diam sollicitudin tempor id. Urna cursus eget nunc scelerisque. Placerat duis ultricies lacus sed. Feugiat scelerisque varius morbi enim nunc faucibus a pellentesque. 41 | 42 | ### Tempus urna et pharetra pharetra 43 | 44 | Viverra vitae congue eu consequat ac felis donec et odio. Feugiat in fermentum posuere urna nec tincidunt. Mauris ultrices eros in cursus turpis. Nec feugiat nisl pretium fusce id velit ut tortor. Ullamcorper malesuada proin libero nunc. Tortor id aliquet lectus proin nibh nisl condimentum. Lectus mauris ultrices eros in cursus. Sit amet mauris commodo quis imperdiet massa tincidunt nunc pulvinar. Vulputate mi sit amet mauris commodo quis imperdiet massa. Et malesuada fames ac turpis egestas sed tempus urna. Ornare quam viverra orci sagittis. Ornare quam viverra orci sagittis eu volutpat. Turpis massa tincidunt dui ut. Mauris nunc congue nisi vitae. Hac habitasse platea dictumst quisque sagittis purus sit amet. Dui id ornare arcu odio ut sem nulla. Arcu cursus euismod quis viverra nibh cras pulvinar. Accumsan tortor posuere ac ut consequat semper viverra. Morbi quis commodo odio aenean sed. 45 | 46 | ### Malesuada nunc vel risus 47 | 48 | Nunc eget lorem dolor sed. Eu tincidunt tortor aliquam nulla facilisi. Pulvinar pellentesque habitant morbi tristique senectus et netus et malesuada. Nulla malesuada pellentesque elit eget gravida cum. Pellentesque elit ullamcorper dignissim cras tincidunt lobortis feugiat vivamus at. Mi in nulla posuere sollicitudin aliquam ultrices sagittis. Eu augue ut lectus arcu bibendum at varius vel pharetra. Aenean pharetra magna ac placerat vestibulum lectus. Tincidunt praesent semper feugiat nibh sed pulvinar. Purus ut faucibus pulvinar elementum integer enim neque volutpat ac. Ut eu sem integer vitae justo eget magna fermentum. Feugiat sed lectus vestibulum mattis ullamcorper velit sed. 49 | 50 | ## Ut aliquam purus sit amet 51 | 52 | ### Hac habitasse platea dictumst 53 | 54 | Sapien eget mi proin sed libero enim sed faucibus. Tortor at auctor urna nunc id. Turpis egestas integer eget aliquet nibh praesent. Id ornare arcu odio ut sem nulla pharetra diam sit. Viverra aliquet eget sit amet tellus cras. Nascetur ridiculus mus mauris vitae ultricies leo integer. Cras fermentum odio eu feugiat pretium nibh ipsum. Sapien pellentesque habitant morbi tristique senectus. Aliquam vestibulum morbi blandit cursus risus at. Blandit cursus risus at ultrices mi tempus imperdiet nulla. Id aliquet lectus proin nibh. Urna condimentum mattis pellentesque id. Ornare massa eget egestas purus. Montes nascetur ridiculus mus mauris. Ipsum consequat nisl vel pretium lectus quam. Quam adipiscing vitae proin sagittis nisl rhoncus. Quis lectus nulla at volutpat diam ut venenatis tellus. 55 | 56 | ### Vel fringilla est ullamcorper eget nulla facilisi etiam 57 | 58 | Ullamcorper sit amet risus nullam eget felis eget nunc lobortis. Id aliquet lectus proin nibh nisl condimentum. Lorem dolor sed viverra ipsum nunc aliquet bibendum enim. Dolor morbi non arcu risus. Orci eu lobortis elementum nibh tellus. Egestas dui id ornare arcu odio ut. Nibh venenatis cras sed felis eget velit aliquet sagittis. Rhoncus est pellentesque elit ullamcorper dignissim cras tincidunt. Suspendisse in est ante in. Vitae proin sagittis nisl rhoncus. Massa enim nec dui nunc. Tellus mauris a diam maecenas sed enim. Massa id neque aliquam vestibulum morbi blandit cursus risus at. Mauris sit amet massa vitae tortor condimentum lacinia. Ultricies integer quis auctor elit sed vulputate mi sit amet. 59 | 60 | Nisi quis eleifend quam adipiscing vitae proin. Imperdiet sed euismod nisi porta lorem mollis aliquam ut porttitor. Vestibulum lorem sed risus ultricies tristique. Interdum varius sit amet mattis vulputate enim. Egestas egestas fringilla phasellus faucibus scelerisque eleifend donec. Nibh ipsum consequat nisl vel pretium. Interdum velit euismod in pellentesque massa. Gravida quis blandit turpis cursus in hac habitasse platea. Elementum curabitur vitae nunc sed velit dignissim sodales. Laoreet sit amet cursus sit amet dictum sit amet. Dignissim diam quis enim lobortis scelerisque fermentum dui. Non curabitur gravida arcu ac tortor. Dui accumsan sit amet nulla. Ut diam quam nulla porttitor massa id neque aliquam. Morbi tincidunt augue interdum velit euismod in. 61 | 62 | \linespread{1}\selectfont 63 | 64 | * One star: 25-49 \% 65 | * Two stars: 50-74 \% 66 | * Three stars: 75-89 \% 67 | * Four stars: 90+ \% 68 | 69 | \linespread{1.6}\selectfont 70 | 71 | Facilisis leo vel fringilla est. Eu volutpat odio facilisis mauris sit amet. Nisi quis eleifend quam adipiscing vitae. Consequat ac felis donec et odio pellentesque diam volutpat commodo. Cras pulvinar mattis nunc sed blandit libero volutpat sed. Sed augue lacus viverra vitae congue eu consequat. At erat pellentesque adipiscing commodo. 72 | 73 | ### Ipsum faucibus vitae aliquet nec ullamcorper 74 | 75 | Facilisis leo vel fringilla est. Eu volutpat odio facilisis mauris sit amet. Nisi quis eleifend quam adipiscing vitae. Consequat ac felis donec et odio pellentesque diam volutpat commodo. Cras pulvinar mattis nunc sed blandit libero volutpat sed. Sed augue lacus viverra vitae congue eu consequat. 76 | 77 | At erat pellentesque adipiscing commodo. Purus gravida quis blandit turpis cursus in hac. Semper auctor neque vitae tempus quam pellentesque nec. Ipsum faucibus vitae aliquet nec ullamcorper sit amet risus. Feugiat nisl pretium fusce id. Tortor condimentum lacinia quis vel eros donec ac odio tempor. Velit ut tortor pretium viverra suspendisse potenti nullam ac. Enim ut sem viverra aliquet eget. 78 | 79 | \linespread{1}\selectfont 80 | 81 | > "Odio facilisis mauris sit amet massa vitae. Ac ut consequat semper viverra. Faucibus vitae aliquet nec ullamcorper. Adipiscing at in tellus integer feugiat. Lacinia quis vel eros donec ac odio. Eget nunc lobortis mattis aliquam faucibus. Amet nisl purus in mollis. Quam id leo in vitae turpis. Egestas tellus rutrum tellus pellentesque. Nibh mauris cursus mattis molestie a iaculis at erat pellentesque. Varius sit amet mattis vulputate enim nulla aliquet porttitor lacus. Nunc vel risus commodo viverra. Enim diam vulputate ut pharetra. Tristique nulla aliquet enim tortor." --*Book Title p. 123* [@ramachandran-2005] 82 | 83 | \linespread{1.6}\selectfont 84 | 85 | Odio facilisis mauris sit amet massa vitae. Ac ut consequat semper viverra. Faucibus vitae aliquet nec ullamcorper. Adipiscing at in tellus integer feugiat. Lacinia quis vel eros donec ac odio. Eget nunc lobortis mattis aliquam faucibus. Amet nisl purus in mollis. Quam id leo in vitae turpis. Egestas tellus rutrum tellus pellentesque. Nibh mauris cursus mattis molestie a iaculis at erat pellentesque. Varius sit amet mattis vulputate enim nulla aliquet porttitor lacus. Nunc vel risus commodo viverra. Enim diam vulputate ut pharetra. Tristique nulla aliquet enim tortor. 86 | 87 | Sed risus pretium quam vulputate dignissim. Posuere morbi leo urna molestie. Consequat interdum varius sit amet mattis vulputate enim nulla. Leo vel orci porta non pulvinar. Est lorem ipsum dolor sit amet consectetur adipiscing elit. Gravida arcu ac tortor dignissim convallis aenean et tortor. Imperdiet nulla malesuada pellentesque elit eget gravida cum sociis. Aliquam purus sit amet luctus venenatis lectus magna fringilla urna. Sit amet tellus cras adipiscing. Vivamus arcu felis bibendum ut tristique et. Convallis convallis tellus id interdum. Sapien pellentesque habitant morbi tristique senectus et netus et malesuada. Lectus sit amet est placerat. Posuere urna nec tincidunt praesent. Est pellentesque elit ullamcorper dignissim cras tincidunt lobortis. 88 | 89 | \newpage 90 | 91 | ## Study aims 92 | 93 | This study seeks to identify ways to become a superhero. The dissertation is organized according to the following specific aims: 94 | 95 | \linespread{1}\selectfont 96 | 97 | * __Chapter 2: Establish photo journalism career__ 98 | 99 | + Sub-aim 1 100 | 101 | + Sub-aim 2 102 | 103 | + Sub-aim 3 104 | 105 | * __Chapter 3: Evaluate webbing fluid materials__ 106 | 107 | + Sub-aim 1 108 | 109 | + Sub-aim 2 110 | 111 | * __Chapter 4: Assess crime-fighting abilities__ 112 | 113 | + Sub-aim 1 114 | 115 | + Sub-aim 2 116 | 117 | * __Chapter 5: Summary of findings and conclusions__ 118 | 119 | -------------------------------------------------------------------------------- /05-chapter1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/05-chapter1.pdf -------------------------------------------------------------------------------- /06-chapter2.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Chapter 2: Photo Journalism' 3 | date: '`r format(Sys.Date(), "%d %B %Y")`' 4 | output: 5 | bookdown::pdf_document2: 6 | number_sections: yes 7 | toc: yes 8 | geometry: margin = 1in 9 | fontsize: 11pt 10 | bibliography: thesis-references.bib 11 | csl: science-modified1.csl 12 | link-citations: true 13 | linkcolor: blue 14 | urlcolor: blue 15 | header-includes: 16 | - \usepackage{placeins} 17 | - \usepackage{setspace} 18 | - \usepackage{chngcntr} 19 | - \usepackage{microtype} 20 | - \counterwithin{figure}{section} 21 | - \counterwithin{table}{section} 22 | - \usepackage{float} 23 | - \usepackage{amsmath} 24 | - \DeclareMathOperator{\logit}{logit} 25 | --- 26 | 27 | ```{r knitr.global.options.ch2, include=F} 28 | knitr::opts_chunk$set(echo=F, 29 | warning=F, 30 | fig.align='center', 31 | fig.pos='H', 32 | fig.width=12, 33 | fig.height=8, 34 | fig.path='Figs/', 35 | tidy.opts=list(width.cutoff=60), 36 | tidy=TRUE) 37 | 38 | ``` 39 | 40 | ```{r load.packages.ch2, include=F} 41 | 42 | ## Load pacman, installing as necessary. 43 | my_repo <- 'http://cran.r-project.org' 44 | if (!require("pacman")) {install.packages("pacman", repos = my_repo)} 45 | 46 | ## Load the other packages, installing as needed. 47 | pacman::p_load(knitr, bookdown, reshape2, tidyverse, lubridate, ggthemes, png, 48 | grid, gridExtra, beeswarm) 49 | 50 | ``` 51 | 52 | ```{r load.themes.function.ch2, include=F} 53 | 54 | ## Koundy's theme #### 55 | # Source: https://github.com/koundy/ggplot_theme_Publication/blob/master/R/ggplot_theme_Publication.R 56 | 57 | theme_HEI <- function(base_size=18) { 58 | library(grid) 59 | library(ggthemes) 60 | (theme_foundation(base_size=base_size) 61 | + theme(plot.title = element_text(face = "bold", 62 | size = rel(1.2), hjust = 0.5), 63 | text = element_text(), 64 | panel.background = element_rect(colour = NA), 65 | plot.background = element_rect(colour = NA), 66 | panel.border = element_rect(colour = NA), 67 | axis.title = element_text(face = "bold",size = rel(1)), 68 | axis.title.y = element_text(angle=90,vjust =2), 69 | axis.title.x = element_text(vjust = -0.2), 70 | axis.text = element_text(), 71 | axis.line = element_line(colour="black"), 72 | axis.ticks = element_line(), 73 | panel.grid.major = element_line(colour="#f0f0f0"), 74 | panel.grid.minor = element_blank(), 75 | legend.key = element_rect(colour = NA), 76 | legend.position = "bottom", 77 | legend.direction = "horizontal", 78 | legend.key.size= unit(0.6, "cm"), 79 | legend.spacing = unit(0, "cm"), 80 | legend.title = element_blank(), 81 | plot.margin=unit(c(4,4,4,4),"mm"), 82 | strip.background=element_rect(colour="#f0f0f0",fill="#f0f0f0"), 83 | strip.text = element_text(face="bold") 84 | )) 85 | 86 | } 87 | 88 | ``` 89 | 90 | ```{r upload.and.clean.data.ch2, include=F} 91 | 92 | ## Read in integrated sampling data from .csv file 93 | bc <- read.csv('Data/bc.28feb2017.csv', header=T) 94 | dylos <- read.csv('Data/dylos.28feb2017.csv', header=T) 95 | qtrak <- read.csv('Data/qtrak.28feb2017.csv', header=T) 96 | nano <- read.csv('Data/nanoscan.28feb2017.csv', header=T) 97 | 98 | ## Deal with time data 99 | bc$time <- as.POSIXct(bc$time, format="%H:%M:%S") 100 | dylos$time <- as.POSIXct(dylos$time, format="%H:%M") 101 | qtrak$time <- as.POSIXct(qtrak$time, format="%H:%M") 102 | nano$date.time <- as.POSIXct(nano$date.time, format="%m/%d/%y %H:%M") 103 | nano$time <- format(nano$date.time, "%H:%M") 104 | nano$time <- as.POSIXct(nano$time, format="%H:%M") 105 | 106 | ## Convert Dylos data from #/0.01 ft3 to #/cm^3 107 | dylos$n_gte_0.5um_cm3 <- dylos$bin1 / 283.1685 108 | dylos$n_gte_1.0um_cm3 <- dylos$bin2 / 283.1685 109 | dylos$n_gte_2.5um_cm3 <- dylos$bin3 / 283.1685 110 | dylos$n_gte_10.0um_cm3 <- dylos$bin4 / 283.1685 111 | 112 | ## Determine counts for each bin range 113 | dylos$n_0.5_1.0um_cm3 <- dylos$n_gte_0.5um_cm3 - dylos$n_gte_1.0um_cm3 114 | dylos$n_1.0_2.5um_cm3 <- dylos$n_gte_1.0um_cm3 - dylos$n_gte_2.5um_cm3 115 | dylos$n_2.5_10.0um_cm3 <- dylos$n_gte_2.5um_cm3 - dylos$n_gte_10.0um_cm3 116 | 117 | ## set_ref_time(): Set times as difference from reference times 118 | set_ref_time <- function(df, ref.df) { 119 | df %>% left_join(ref.df, by = c('location', 'period', 'day')) %>% 120 | mutate(`seconds` = as.numeric(seconds(interval(`time`, ref.datetime)))) 121 | } 122 | 123 | ## Create reference time dataframe 124 | ref.date <- as.character(Sys.Date()) 125 | ref.time <- c('12:50:00', '12:56:00', '13:33:00', '13:36:00', 126 | '15:31:00', '16:14:00', '16:10:00', '16:55:00') 127 | ref.datetime <- paste(ref.date, ref.time) 128 | ref.df <- data.frame(location = factor(rep(c(rep('above', 2), rep('below', 2)), 2), 129 | levels = c('', 'above', 'below')), 130 | period = factor(c(rep('off peak', 4), rep('peak', 4)), 131 | levels = c('', 'off peak', 'peak')), 132 | day = rep(c(1L, 2L), 4), ref.datetime = ref.datetime, 133 | stringsAsFactors = FALSE) 134 | 135 | ## Set seconds variable from reference dataframe 136 | bc.final <- set_ref_time(bc, ref.df) 137 | dy.final <- set_ref_time(dylos, ref.df) 138 | qt.final <- set_ref_time(qtrak, ref.df) 139 | nn.final <- set_ref_time(nano, ref.df) 140 | 141 | ## Melt from wide to long 142 | bc.long <- melt(bc.final, id = c("time","seconds","location","period","day"), measure.vars = c("bc")) 143 | 144 | dy.long <- melt(dy.final, id = c("time","seconds","location","period","day"), measure.vars = c("n_0.5_1.0um_cm3","n_1.0_2.5um_cm3","n_2.5_10.0um_cm3","n_gte_10.0um_cm3")) 145 | 146 | qt.long <- melt(qt.final, id = c("time","seconds","location","period","day"), measure.vars = c("co2.ppm","co.ppm")) 147 | 148 | nn.long <- melt(nn.final, id = c("time","seconds","location","period","day"), measure.vars = c("bin_11.5","bin_15.4","bin_20.5","bin_27.4","bin_36.5","bin_48.7","bin_64.9","bin_86.6","bin_115.5","bin_154","bin_205.4","bin_273.8","bin_365.2","total.conc.num.cm3")) 149 | 150 | ## Concatenate location and period 151 | bc.long$location.period <- paste(bc.long$location,bc.long$period) 152 | dy.long$location.period <- paste(dy.long$location,dy.long$period) 153 | qt.long$location.period <- paste(qt.long$location,qt.long$period) 154 | nn.long$location.period <- paste(nn.long$location,nn.long$period) 155 | 156 | bc.long$location.period.day <- paste(bc.long$location,bc.long$period,bc.long$day) 157 | dy.long$location.period.day <- paste(dy.long$location,dy.long$period,dy.long$day) 158 | qt.long$location.period.day <- paste(qt.long$location,qt.long$period,qt.long$day) 159 | nn.long$location.period.day <- paste(nn.long$location,nn.long$period,nn.long$day) 160 | 161 | ``` 162 | 163 | \linespread{1.6}\selectfont 164 | 165 | # Photo Journalism 166 | 167 | ## Abstract 168 | 169 | Ornare lectus sit amet est placerat in. Volutpat sed cras ornare arcu dui vivamus arcu. Lacinia quis vel eros donec. Magna ac placerat vestibulum lectus mauris ultrices. Et tortor at risus viverra adipiscing at in tellus. Dictum sit amet justo donec enim diam. Ut consequat semper viverra nam libero justo laoreet sit amet. Lorem dolor sed viverra ipsum nunc aliquet bibendum enim facilisis. Sit amet consectetur adipiscing elit duis tristique sollicitudin nibh sit. Nunc faucibus a pellentesque sit. Scelerisque in dictum non consectetur. Iaculis nunc sed augue lacus viverra vitae congue eu. Nulla facilisi nullam vehicula ipsum a arcu. Tortor pretium viverra suspendisse potenti nullam ac. Augue ut lectus arcu bibendum at varius vel. Vitae purus faucibus ornare suspendisse sed. Tristique senectus et netus et malesuada fames. Morbi non arcu risus quis varius quam. Quis vel eros donec ac. 170 | 171 | Non nisi est sit amet facilisis magna. In dictum non consectetur a erat nam at lectus. Ac ut consequat semper viverra nam. Bibendum est ultricies integer quis auctor. Adipiscing enim eu turpis egestas pretium aenean. Vulputate eu scelerisque felis imperdiet proin. Nulla at volutpat diam ut venenatis tellus. Aliquam faucibus purus in massa. Et netus et malesuada fames ac turpis egestas. Nec nam aliquam sem et tortor consequat id porta nibh. Et netus et malesuada fames. Gravida quis blandit turpis cursus in hac. Neque viverra justo nec ultrices dui sapien. Tristique magna sit amet purus gravida quis blandit. 172 | 173 | This chapter addresses the following sub-aims: 174 | 175 | \linespread{1}\selectfont 176 | 177 | * Take pictures to hone image capturing skills 178 | * Develop film and practice writing about subject matter 179 | 180 | \linespread{1.6}\selectfont 181 | 182 | ## Introduction 183 | 184 | Varius quam quisque id diam vel quam elementum pulvinar. Congue quisque egestas diam in arcu cursus euismod quis. Amet cursus sit amet dictum sit. Nisl rhoncus mattis rhoncus urna neque viverra justo. Integer feugiat scelerisque varius morbi enim nunc faucibus a. Eros in cursus turpis massa. Tincidunt eget nullam non nisi est sit amet. Elit duis tristique sollicitudin nibh. Aliquam ut porttitor leo a diam sollicitudin tempor id eu. Aenean et tortor at risus 51\% ($\frac{67}{131}$) viverra. Et netus et malesuada fames ac turpis. Tincidunt praesent semper feugiat nibh sed pulvinar proin gravida. Phasellus vestibulum 64\% ($\frac{43}{67}$) lorem sed risus ultricies tristique nulla aliquet. Magna sit amet purus gravida quis blandit. 185 | 186 | ## Methods 187 | 188 | ### Vel orci porta non pulvinar neque laoreet 189 | 190 | Consequat mauris nunc congue nisi vitae. Eleifend quam adipiscing vitae proin sagittis nisl rhoncus mattis rhoncus. Eget velit aliquet sagittis id consectetur purus. Tincidunt nunc pulvinar sapien et. Amet consectetur adipiscing elit duis tristique sollicitudin nibh sit amet. Egestas pretium aenean pharetra magna. Vestibulum rhoncus est pellentesque elit ullamcorper. Cras sed felis eget velit aliquet sagittis id consectetur purus. Turpis cursus in hac habitasse platea dictumst quisque sagittis. Sit amet risus nullam eget. Ipsum faucibus vitae aliquet nec ullamcorper sit. Scelerisque felis imperdiet proin fermentum leo vel. In hac habitasse platea dictumst quisque sagittis. Quam adipiscing vitae proin sagittis nisl. Mauris commodo quis imperdiet massa (Figure \@ref(fig:above-sampling)). Nulla pellentesque dignissim enim sit amet venenatis. Ante metus dictum at tempor commodo ullamcorper a lacus vestibulum (Figure \@ref(fig:below-sampling)). Sem viverra aliquet eget sit amet tellus cras. 191 | 192 | ### Diam ut venenatis tellus in metus 193 | 194 | Aenean et tortor at risus viverra adipiscing at in tellus (Figure \@ref(fig:bc-boxplot). Amet mauris commodo quis imperdiet massa (Figure \@ref(fig:dy-boxplot)). Luctus venenatis lectus magna fringilla urna porttitor rhoncus (Figure \@ref(fig:nn-boxplot)). Suspendisse interdum consectetur libero id. Diam ut venenatis tellus in metus. Faucibus purus in massa tempor nec feugiat nisl. Ullamcorper malesuada proin libero nunc consequat interdum varius sit amet ([Appendix A][Appendix A: Some Text Here]). Venenatis urna cursus eget nunc scelerisque viverra mauris. Sed pulvinar proin gravida hendrerit lectus a. Vulputate eu scelerisque felis imperdiet. Odio euismod lacinia at quis risus sed vulputate odio. Ac turpis egestas integer eget aliquet nibh praesent. Mattis aliquam faucibus purus in massa tempor nec feugiat ([Appendix B][Appendix B: Other Text Here]). 195 | 196 | #### Tincidunt eget nullam non nisi est sit amet 197 | 198 | Pellentesque elit eget gravida cum sociis. Dui id ornare arcu odio ut sem. Id donec ultrices tincidunt arcu non sodales neque sodales. Suspendisse sed nisi lacus sed (Figure \@ref(fig:size-distribution-nn-plots). Faucibus interdum posuere lorem ipsum. Nisi vitae suscipit tellus mauris a diam. Mattis ullamcorper velit sed ullamcorper morbi tincidunt ornare massa. Congue mauris rhoncus aenean vel elit scelerisque mauris. Tellus id interdum velit laoreet id donec ultrices tincidunt arcu. Ultricies mi quis hendrerit dolor magna eget. Nunc id cursus metus aliquam eleifend mi in nulla posuere. Amet nisl suscipit adipiscing bibendum est ultricies integer quis. Morbi blandit cursus risus at ultrices mi tempus imperdiet. Egestas maecenas pharetra convallis posuere morbi leo urna. Neque ornare aenean euismod elementum nisi quis eleifend. Nisi lacus sed viverra tellus. Senectus et netus et malesuada. Egestas erat imperdiet sed euismod nisi porta lorem mollis aliquam: 199 | 200 | \linespread{1}\selectfont 201 | 202 | 1. Elimination 203 | 2. Substitution 204 | 3. Engineering controls 205 | 4. Administrative controls 206 | 5. Personal protective equipment 207 | 208 | \linespread{1.6}\selectfont 209 | 210 | Non nisi est sit amet facilisis magna. In dictum non consectetur a erat nam at lectus. Ac ut consequat semper viverra nam. Bibendum est ultricies integer quis auctor. Adipiscing enim eu turpis egestas pretium aenean. Vulputate eu scelerisque felis imperdiet proin. Nulla at volutpat diam ut venenatis tellus. Aliquam faucibus purus in massa. Et netus et malesuada fames ac turpis egestas. Nec nam aliquam sem et tortor consequat id porta nibh. Et netus et malesuada fames. Gravida quis blandit turpis cursus in hac. Neque viverra justo nec ultrices dui sapien. Tristique magna sit amet purus gravida quis blandit. 211 | 212 | Data were managed and analyzed with R version 3.4.0 (2017-04-21) using the following packages: beeswarm, bookdown, ggplot2, ggthemes, gridExtra, knitr, lattice, lubridate, pander, reshape, and survival [@r-beeswarm; @r-bookdown; @r-ggplot; @r-ggthemes; @r-gridExtra; @r-knitr; @r-lattice; @r-lubridate; @r-pander; @r-reshape; @r-survival]. 213 | 214 | ### Habitant morbi tristique senectus et netus et 215 | 216 | Consequat mauris nunc congue nisi vitae. Eleifend quam adipiscing vitae proin sagittis nisl rhoncus mattis rhoncus. Eget velit aliquet sagittis id consectetur purus. Tincidunt nunc pulvinar sapien et. Amet consectetur adipiscing elit duis tristique sollicitudin nibh sit amet. Egestas pretium aenean pharetra magna. Vestibulum rhoncus est pellentesque elit ullamcorper. Cras sed felis eget velit aliquet sagittis id consectetur purus. Turpis cursus in hac habitasse platea dictumst quisque sagittis. Sit amet risus nullam eget. Ipsum faucibus vitae aliquet nec ullamcorper sit. Scelerisque felis imperdiet proin fermentum leo vel. In hac habitasse platea dictumst quisque sagittis. Quam *adipiscing vitae proin* sagittis nisl. Mauris commodo quis imperdiet massa. Nulla pellentesque dignissim enim sit amet venenatis. Ante metus **dictum at tempor commodo** ullamcorper a lacus vestibulum. Sem viverra aliquet eget sit amet tellus cras at the $\alpha$ = 0.05 level. 217 | 218 | We created the following model (Equation \@ref(eq:superhero-model)). 219 | 220 | \begin{equation} 221 | \logit(Outcome) = \beta_{0} + \beta_{1} Superhero + \beta_{2} Age + \beta_{3} Superhero \times Age + \epsilon 222 | (\#eq:superhero-model) 223 | \end{equation} 224 | 225 | Varius quam quisque id diam vel quam elementum pulvinar. Congue quisque egestas diam in arcu cursus euismod quis. Amet cursus sit amet dictum sit. Nisl rhoncus mattis rhoncus urna neque viverra justo. Integer feugiat scelerisque varius morbi enim nunc faucibus a. Eros in cursus turpis massa. Tincidunt eget nullam non nisi est sit amet. Elit duis tristique sollicitudin nibh. Aliquam ut porttitor leo a diam sollicitudin tempor id eu. Aenean et tortor at risus viverra. Et netus et malesuada fames ac turpis. Tincidunt praesent semper feugiat nibh sed pulvinar proin gravida. Phasellus vestibulum lorem sed risus ultricies tristique nulla aliquet. Magna sit amet purus gravida quis blandit. 226 | 227 | ## Results 228 | 229 | Nisi vitae suscipit tellus mauris a diam. Mattis ullamcorper velit sed ullamcorper morbi tincidunt ornare massa. Congue mauris rhoncus aenean vel elit scelerisque mauris. Tellus id interdum velit laoreet id donec ultrices tincidunt arcu. Ultricies mi quis hendrerit dolor magna eget. 230 | 231 | ### Congue mauris rhoncus 232 | 233 | #### Et netus et malesuada fames 234 | 235 | Bibendum arcu vitae elementum curabitur. Augue lacus viverra vitae congue eu consequat ac felis donec (Table \@ref(tab:summary-table)). 236 | 237 | Fames ac turpis egestas sed tempus urna et pharetra pharetra. Nulla pellentesque dignissim enim sit (Table \@ref(tab:sampling-times-day1)). 238 | 239 | #### Aenean et tortor at risus viverra 240 | 241 | Aliquet nibh praesent tristique magna sit amet purus gravida quis. Faucibus vitae aliquet nec ullamcorper. Augue mauris augue neque gravida in fermentum et sollicitudin ac. Interdum posuere lorem ipsum dolor sit. Sollicitudin ac orci phasellus egestas. Sit amet mattis vulputate enim nulla aliquet porttitor. Sollicitudin nibh sit amet commodo nulla. Auctor eu augue ut lectus arcu bibendum at varius. At lectus urna duis convallis convallis tellus id interdum velit. Purus sit amet luctus venenatis lectus magna fringilla urna porttitor. Fermentum iaculis eu non diam phasellus. Eget gravida cum sociis natoque penatibus et. Pellentesque nec nam aliquam sem et. Fusce ut placerat orci nulla. Eu tincidunt tortor aliquam nulla facilisi cras fermentum odio eu. Varius morbi enim nunc faucibus a pellentesque sit amet. Ipsum dolor sit amet consectetur adipiscing. Proin sed libero enim sed faucibus turpis. 242 | 243 | ## Discussion 244 | 245 | Morbi tincidunt augue interdum velit euismod. Pulvinar mattis nunc sed blandit libero volutpat sed. Gravida cum sociis natoque penatibus et magnis. Mattis enim ut tellus elementum. Orci phasellus egestas tellus rutrum tellus pellentesque eu. Risus nullam eget felis eget nunc lobortis. Nisl purus in mollis nunc sed id semper risus. Montes nascetur ridiculus mus mauris vitae ultricies. Arcu vitae elementum curabitur vitae nunc sed. Ut faucibus pulvinar elementum integer enim. Convallis posuere morbi leo urna molestie. Vestibulum morbi blandit cursus risus at ultrices mi tempus. Id aliquet risus feugiat in ante. Dolor sit amet consectetur adipiscing elit duis tristique sollicitudin nibh. Dictumst quisque sagittis purus sit amet volutpat consequat mauris nunc. In nulla posuere sollicitudin aliquam ultrices. Massa tempor nec feugiat nisl pretium. Euismod quis viverra nibh cras pulvinar mattis. 246 | 247 | 254 | 255 | \clearpage 256 | 257 | \linespread{1}\selectfont 258 | 259 | ## Tables 260 | 261 | Table: (\#tab:summary-table)Examples of different instruments available for sampling various contaminants. 262 | 263 | ```{r summary-table, fig.cap = '(tab:summary-table)', message=F, warnings=F, results='asis', echo=F} 264 | tabl <- " 265 | ----------------------------------------------------------------------------------- 266 | Contaminant - Instrument Units Above Above Below Below 267 | Off Peak Peak Off Peak Peak 268 | -------------------------- ---------- ---------- -------- ------------ ------------ 269 | CO - Q-Trak * ppm 0.031 0.094 0.037 **0.121** 270 | 271 | CO~2~ - Q-Trak ppm 484 559 531 **622** 272 | 273 | BC - MicroAeth fg/cm^3^ 2,940 6,280 **16,300** 5,760 274 | 275 | PM - Nanos (12-365 nm) #/cm^3^ 23,990 27,080 **37,860** 22,190 276 | 277 | PM - Dylos (0.5-10 µm) #/cm^3^ 11.04 13.00 12.78 **14.70** 278 | ----------------------------------------------------------------------------------- 279 | " 280 | cat(tabl) 281 | ``` 282 | 283 | Table: (\#tab:sampling-times-day1)Traffic at time of crime. (*) Some footnote. (\*\*) Another footnote. 284 | 285 | ```{r sampling-times-day1, fig.cap = '(tab:sampling-times-day1)', message=F, warnings=F, results='asis', echo=F} 286 | tabl <- " 287 | --------------------------------------------------- 288 | Traffic level Date Start Stop 289 | ---------------- -------------- --------- -------- 290 | Above Off Peak 28 Feb 2017 12:50 13:20 291 | 292 | Below Off Peak 28 Feb 2017 13:33 14:03 293 | 294 | Above Peak* 28 Feb 2017 15:31 16:01 295 | 296 | Below Peak** 28 Feb 2017 16:10 16:40 297 | --------------------------------------------------- 298 | " 299 | cat(tabl) 300 | ``` 301 | 302 | \clearpage 303 | 304 | ## Figures 305 | 306 | (ref:above-sampling) Above ground sampling image. 307 | 308 | ```{r above-sampling, fig.cap='(ref:above-sampling)', fig.width=6, fig.height=6, echo=F} 309 | library(png) 310 | library(grid) 311 | img <- readPNG("Images/AboveSampling.png") 312 | grid.raster(img) 313 | ``` 314 | 315 | (ref:below-sampling) Below ground sampling image. 316 | 317 | ```{r below-sampling, fig.cap='(ref:below-sampling)', fig.width=6, fig.height=6, echo=F} 318 | library(png) 319 | library(grid) 320 | img <- readPNG("Images/BelowSampling1.png") 321 | grid.raster(img) 322 | ``` 323 | 324 | (ref:bc-boxplot) Box plot of black carbon. 325 | 326 | ```{r bc-boxplot, fig.cap='(ref:bc-boxplot)', fig.width=10, fig.height=10, fig.align="center"} 327 | 328 | par(cex.axis=1, cex.lab=1, cex.main=1.2) 329 | 330 | boxplot(value ~ location.period, data = bc.long, outline = FALSE, main = 'BC Monitoring', xlab="Location and Period", ylab="Concentration (fg/cm3)") 331 | beeswarm(value ~ location.period, data = bc.long, method='center', pwcol = day, pch = 16, add = TRUE) 332 | 333 | legend('topleft',legend=c('Day 1','Day 2'), pch=16, col=1:2, cex=1.1, pt.cex = 1) 334 | 335 | ``` 336 | 337 | (ref:dy-boxplot) Box plot of Dylos particle sizer. 338 | 339 | ```{r dy-boxplot, fig.cap='(ref:dy-boxplot)', cache=F, fig.height=10} 340 | 341 | par(cex.axis=1.25, cex.lab=1.25, cex.main=1.5) 342 | 343 | ggplot(dy.long, aes(factor(variable), value)) + geom_boxplot(aes(fill = factor(location.period))) + labs(title = "Dylos Particle Monitoring", x="Bin Size (µm)", y="Concentration (Particles/cm3)") + theme(plot.title = element_text(hjust = 0.5), legend.title=element_blank()) + scale_x_discrete(labels=c('0.5-1.0','1.0-2.5','2.5-10.0','>10.0')) + theme_HEI(16) 344 | 345 | ``` 346 | 347 | (ref:nn-boxplot) Box plot of nanoscan particle sizer. 348 | 349 | ```{r nn-boxplot, fig.cap='(ref:nn-boxplot)', cache=F, fig.height=10} 350 | 351 | par(cex.axis=1.25, cex.lab=1.25, cex.main=1.5) 352 | 353 | ggplot(nn.long[nn.long$variable!='total.conc.num.cm3',], aes(factor(variable), value)) + geom_boxplot(aes(fill = factor(location.period))) + labs(title = "Nanoscan Particle Monitoring", x="Bin Size (nm)", y="Concentration (Particles/cm3)") + theme(plot.title = element_text(hjust = 0.5), legend.title=element_blank()) + scale_x_discrete(labels=c('11.5','15.4','20.5','27.4','36.5','48.7','64.9','86.6','115.5','154','205.4','273.8','365.2')) + scale_y_continuous(breaks=seq(0, 15000, 2000)) + theme_HEI(16) 354 | 355 | ``` 356 | 357 | (ref:size-distribution-nn-plots) Ultrafine size distribution plots. 358 | 359 | ```{r size-distribution-nn-plots, fig.cap='(ref:size-distribution-nn-plots)', fig.width=10, fig.height=10, fig.align="center"} 360 | 361 | lab <- c('12','15','21','27','37','49','65','87','116','154','205','274','365') 362 | 363 | nn.abv.ofpk.dist<-aggregate(value~variable,nn.long[nn.long$location.period=='above off peak',],FUN= function(x)exp(mean(log(x)))) 364 | 365 | nn.blw.ofpk.dist<-aggregate(value~variable,nn.long[nn.long$location.period=='below off peak',],FUN= function(x)exp(mean(log(x)))) 366 | 367 | nn.abv.peak.dist<-aggregate(value~variable,nn.long[nn.long$location.period=='above peak',],FUN= function(x)exp(mean(log(x)))) 368 | 369 | nn.blw.peak.dist<-aggregate(value~variable,nn.long[nn.long$location.period=='below peak',],FUN= function(x)exp(mean(log(x)))) 370 | 371 | a <- ggplot(nn.abv.ofpk.dist[nn.abv.ofpk.dist$variable!='total.conc.num.cm3',], aes(x=variable, y=value)) + geom_bar(stat="identity") + scale_y_continuous(limits = c(0, 6000)) + scale_x_discrete(labels=lab) + labs(title = "Above Off Peak", x="", y="Particles / cm3") + theme(plot.title = element_text(hjust = 0.5)) + theme_HEI(14) 372 | 373 | b <- ggplot(nn.blw.ofpk.dist[nn.blw.ofpk.dist$variable!='total.conc.num.cm3',], aes(x=variable, y=value)) + geom_bar(stat="identity") + scale_y_continuous(limits = c(0, 6000)) + scale_x_discrete(labels=lab) + labs(title = "Below Off Peak", x="", y="") + theme(plot.title = element_text(hjust = 0.5)) + theme_HEI(14) 374 | 375 | c <- ggplot(nn.abv.peak.dist[nn.abv.peak.dist$variable!='total.conc.num.cm3',], aes(x=variable, y=value)) + geom_bar(stat="identity") + scale_y_continuous(limits = c(0, 6000)) + scale_x_discrete(labels=lab) + labs(title = "Above Peak", x="Particle Size (nm)", y="Particles / cm3") + theme(plot.title = element_text(hjust = 0.5)) + theme_HEI(14) 376 | 377 | d <- ggplot(nn.blw.peak.dist[nn.blw.peak.dist$variable!='total.conc.num.cm3',], aes(x=variable, y=value)) + geom_bar(stat="identity") + scale_y_continuous(limits = c(0, 6000)) + scale_x_discrete(labels=lab) + labs(title = "Below Peak", x="Particle Size (nm)", y="") + theme(plot.title = element_text(hjust = 0.5)) + theme_HEI(14) 378 | 379 | 380 | grid.arrange(a, b, c, d, nrow=2) 381 | 382 | 383 | ``` 384 | 385 | \clearpage 386 | 387 | ## Appendices 388 | 389 | ### Appendix A: Some Text Here 390 | 391 | Scelerisque eu ultrices vitae auctor eu augue ut lectus arcu. Consequat id porta nibh venenatis cras sed felis eget. Neque sodales ut etiam sit amet nisl purus. Mi in nulla posuere sollicitudin aliquam ultrices sagittis orci a. Suspendisse interdum consectetur libero id faucibus. Nisl nunc mi ipsum faucibus. Aenean sed adipiscing diam donec adipiscing. Sed adipiscing diam donec adipiscing tristique risus. Elit scelerisque mauris pellentesque pulvinar pellentesque habitant morbi. Tellus integer feugiat scelerisque varius morbi enim nunc. Lectus urna duis convallis convallis tellus id interdum velit. Turpis tincidunt id aliquet risus feugiat in ante metus dictum. Libero nunc consequat interdum varius sit amet. Sit amet dictum sit amet justo. Vitae ultricies leo integer malesuada nunc vel risus commodo. Arcu cursus vitae congue mauris. Arcu vitae elementum curabitur vitae nunc. Tellus at urna condimentum mattis. 392 | 393 | Sed id semper risus in hendrerit. Auctor eu augue ut lectus arcu bibendum at. Lacus vestibulum sed arcu non odio euismod lacinia. Fermentum leo vel orci porta non pulvinar. Enim facilisis gravida neque convallis. Lectus nulla at volutpat diam ut venenatis tellus in. Volutpat odio facilisis mauris sit amet massa vitae tortor. Sit amet massa vitae tortor condimentum lacinia quis. Ornare arcu dui vivamus arcu felis bibendum ut. Est ullamcorper eget nulla facilisi. Porta lorem mollis aliquam ut porttitor. Malesuada fames ac turpis egestas sed. Iaculis urna id volutpat lacus laoreet non curabitur gravida. Blandit aliquam etiam erat velit scelerisque in dictum. Tristique senectus et netus et. At imperdiet dui accumsan sit amet nulla facilisi morbi tempus. Mi in nulla posuere sollicitudin aliquam ultrices sagittis orci. Luctus venenatis lectus magna fringilla urna porttitor. 394 | 395 | ### Appendix B: Other Text Here 396 | 397 | Insert other text, figure, or table here. 398 | -------------------------------------------------------------------------------- /06-chapter2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/06-chapter2.pdf -------------------------------------------------------------------------------- /07-chapter3.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Chapter 3: Webbing Fluid' 3 | date: '`r format(Sys.Date(), "%d %B %Y")`' 4 | output: 5 | bookdown::pdf_document2: 6 | number_sections: yes 7 | toc: yes 8 | geometry: margin = 1in 9 | fontsize: 11pt 10 | bibliography: thesis-references.bib 11 | csl: science-modified1.csl 12 | link-citations: true 13 | linkcolor: blue 14 | urlcolor: blue 15 | header-includes: 16 | - \usepackage{placeins} 17 | - \usepackage{setspace} 18 | - \usepackage{chngcntr} 19 | - \usepackage{microtype} 20 | - \counterwithin{figure}{section} 21 | - \counterwithin{table}{section} 22 | - \usepackage{float} 23 | - \usepackage{amsmath} 24 | - \DeclareMathOperator{\logit}{logit} 25 | --- 26 | 27 | ```{r knitr.global.options.ch3, include=F} 28 | knitr::opts_chunk$set(echo=F, 29 | warning=F, 30 | fig.align='center', 31 | fig.pos='H', 32 | fig.width=12, 33 | fig.height=8, 34 | fig.path='Figs/', 35 | tidy.opts=list(width.cutoff=60), 36 | tidy=TRUE) 37 | 38 | ``` 39 | 40 | ```{r load.packages.ch3, include=F} 41 | 42 | # Load pacman, installing as necessary. 43 | my_repo <- 'http://cran.r-project.org' 44 | if (!require("pacman")) {install.packages("pacman", repos = my_repo)} 45 | 46 | # Load the other packages, installing as needed. 47 | pacman::p_load(knitr, bookdown, reshape2, tidyverse, lubridate, ggthemes, png, 48 | grid, gridExtra, beeswarm, datasets, GGally) 49 | 50 | ``` 51 | 52 | ```{r load.themes.function.ch3, include=F} 53 | 54 | ## Koundy's theme #### 55 | # Source: https://github.com/koundy/ggplot_theme_Publication/blob/master/R/ggplot_theme_Publication.R 56 | theme_HEI <- function(base_size=18) { 57 | library(grid) 58 | library(ggthemes) 59 | (theme_foundation(base_size=base_size) 60 | + theme(plot.title = element_text(face = "bold", 61 | size = rel(1.2), hjust = 0.5), 62 | text = element_text(), 63 | panel.background = element_rect(colour = NA), 64 | plot.background = element_rect(colour = NA), 65 | panel.border = element_rect(colour = NA), 66 | axis.title = element_text(face = "bold",size = rel(1)), 67 | axis.title.y = element_text(angle=90,vjust =2), 68 | axis.title.x = element_text(vjust = -0.2), 69 | axis.text = element_text(), 70 | axis.line = element_line(colour="black"), 71 | axis.ticks = element_line(), 72 | panel.grid.major = element_line(colour="#f0f0f0"), 73 | panel.grid.minor = element_blank(), 74 | legend.key = element_rect(colour = NA), 75 | legend.position = "bottom", 76 | legend.direction = "horizontal", 77 | legend.key.size= unit(0.6, "cm"), 78 | legend.spacing = unit(0, "cm"), 79 | legend.title = element_blank(), 80 | plot.margin=unit(c(4,4,4,4),"mm"), 81 | strip.background=element_rect(colour="#f0f0f0",fill="#f0f0f0"), 82 | strip.text = element_text(face="bold") 83 | )) 84 | 85 | } 86 | 87 | ``` 88 | 89 | ```{r upload.and.clean.data.ch3, include=F} 90 | 91 | ## Read in datasets from R datasets package 92 | 93 | cars <- cars 94 | mtcars <- mtcars 95 | 96 | ``` 97 | 98 | \linespread{1.6}\selectfont 99 | 100 | # Making Webbing Fluid 101 | 102 | ## Abstract 103 | 104 | Quis risus sed vulputate odio ut enim blandit volutpat maecenas. Lacinia quis vel eros donec ac. Varius morbi enim nunc faucibus a pellentesque sit. Mauris pharetra et ultrices neque ornare. Non nisi est sit amet facilisis. Viverra mauris in aliquam sem fringilla ut morbi tincidunt augue. Arcu odio ut sem nulla pharetra diam sit. Varius quam quisque id diam vel quam. In arcu cursus euismod quis viverra nibh cras pulvinar. Id faucibus nisl tincidunt eget nullam non nisi est. Mauris ultrices eros in cursus turpis massa tincidunt dui ut. Nisi porta lorem mollis aliquam ut porttitor leo a diam. Ut enim blandit volutpat maecenas volutpat blandit. Netus et malesuada fames ac turpis egestas integer. Diam maecenas sed enim ut sem viverra aliquet. 105 | 106 | This chapter addresses the following sub-aims: 107 | 108 | \linespread{1}\selectfont 109 | 110 | * Test elemental composition of webbing 111 | 112 | * Produce models to determine which webbing type that is most appropriate for different conditions 113 | 114 | \linespread{1.6}\selectfont 115 | 116 | ## Introduction 117 | 118 | Euismod elementum nisi quis eleifend quam adipiscing vitae. Leo vel orci porta non pulvinar neque laoreet. Fermentum iaculis eu non diam phasellus. Nec ullamcorper sit amet risus nullam eget felis eget nunc [@r-lattice]. Pretium vulputate sapien nec sagittis aliquam. Posuere ac ut consequat semper viverra nam libero justo. Nibh tortor id aliquet lectus proin nibh nisl condimentum. Tortor at risus viverra adipiscing. Mauris nunc congue nisi vitae suscipit. Volutpat sed cras ornare arcu dui vivamus. Magna fermentum iaculis eu non diam [@ramachandran-2005]. Sed sed risus pretium quam [@lorem-ipsum-2017]. At varius vel pharetra vel turpis nunc. Viverra mauris in aliquam sem fringilla ut morbi. 119 | 120 | ## Methods 121 | 122 | ### Duis at tellus at urna 123 | 124 | #### In hac habitasse platea 125 | 126 | Nec dui nunc mattis enim ut tellus elementum sagittis vitae. Tincidunt nunc pulvinar sapien et ligula. A iaculis at erat pellentesque adipiscing. Magna etiam tempor orci eu lobortis elementum nibh tellus. Fusce ut placerat orci nulla pellentesque dignissim enim. Turpis egestas pretium aenean pharetra magna ac placerat vestibulum lectus. Porttitor massa id neque aliquam vestibulum morbi blandit cursus risus. In nibh mauris cursus mattis. Faucibus turpis in eu mi. Sed tempus urna et pharetra pharetra. Massa tincidunt nunc pulvinar sapien et ligula. Pellentesque elit ullamcorper dignissim cras tincidunt lobortis feugiat vivamus. Libero id faucibus nisl tincidunt eget nullam non nisi. Ut faucibus pulvinar elementum integer enim neque. Tortor condimentum lacinia quis vel eros donec. Varius duis at consectetur lorem. Ultricies leo integer malesuada nunc. Ac placerat vestibulum lectus mauris ultrices eros in cursus. 127 | 128 | #### Mi in nulla posuere sollicitudin aliquam 129 | 130 | **Odio morbi quis commodo odio** 131 | 132 | Nullam ac tortor vitae purus. Et egestas quis ipsum suspendisse. Massa tincidunt dui ut ornare lectus. Cursus vitae congue mauris rhoncus aenean vel. Velit egestas dui id ornare arcu odio. Justo eget magna fermentum iaculis eu non. Nibh praesent tristique magna sit amet purus gravida. Nunc sed id semper risus in. Arcu cursus euismod quis viverra nibh cras pulvinar mattis nunc. Etiam non quam lacus suspendisse faucibus interdum posuere lorem. Viverra accumsan in nisl nisi scelerisque eu ultrices vitae. Vivamus at augue eget arcu dictum varius duis at consectetur. Gravida quis blandit turpis cursus. 133 | 134 | Posuere urna nec tincidunt praesent semper feugiat. Morbi tristique senectus et netus et malesuada fames ac. Tempus iaculis urna id volutpat lacus laoreet non curabitur. Id porta nibh venenatis cras sed felis eget velit. *Eu volutpat* odio facilisis mauris sit. Scelerisque fermentum dui faucibus in ornare quam. Egestas dui id ornare arcu odio. Donec ultrices tincidunt arcu non sodales neque sodales ut etiam. Adipiscing diam donec adipiscing tristique. Egestas dui id ornare arcu odio ut sem nulla. 135 | 136 | **Nullam non nisi** 137 | 138 | Sed faucibus turpis in eu mi bibendum neque egestas. Ut lectus arcu bibendum at varius vel pharetra. Morbi tristique senectus et netus et malesuada fames ac turpis. Ipsum dolor sit amet consectetur adipiscing elit pellentesque. Iaculis nunc sed augue lacus viverra vitae congue. Tincidunt dui ut ornare lectus sit amet est. Dignissim diam quis enim lobortis. Leo urna molestie at elementum eu facilisis sed odio morbi. Arcu felis bibendum ut tristique. 139 | 140 | ### Etiam non quam 141 | 142 | Nullam ac tortor vitae purus. Dolor purus non enim praesent elementum facilisis leo vel fringilla. Id diam maecenas ultricies mi eget mauris pharetra. Dignissim suspendisse in est ante in. Eget duis at tellus at urna condimentum mattis pellentesque. Ullamcorper a lacus vestibulum sed arcu. At in tellus integer feugiat scelerisque varius morbi enim nunc. 143 | 144 | #### Id semper risus 145 | 146 | Velit scelerisque in dictum non consectetur. Pellentesque habitant morbi tristique senectus et. Et ligula ullamcorper malesuada proin. At volutpat diam ut venenatis tellus in. Nisl rhoncus mattis rhoncus urna neque viverra justo nec. Euismod elementum nisi quis eleifend quam adipiscing vitae [@r-lattice]. Nunc congue nisi vitae suscipit tellus ([Appendix A][Appendix A: Purus faucibus ornare]). Consectetur libero id faucibus nisl. In cursus turpis massa tincidunt dui. Id semper risus in hendrerit gravida rutrum. Diam vel quam elementum pulvinar etiam non [@lorem-ipsum-2017]. Sit amet cursus sit amet dictum sit amet. Integer malesuada nunc vel risus commodo viverra maecenas accumsan lacus. *Leo duis ut diam quam nulla.* Quam quisque id diam vel quam elementum pulvinar etiam. Magnis dis parturient montes nascetur. Auctor urna nunc id cursus metus aliquam eleifend mi in. Id leo in vitae turpis massa sed. Fringilla est ullamcorper eget nulla facilisi etiam. Ipsum dolor sit amet consectetur adipiscing elit pellentesque habitant. 147 | 148 | #### Application 149 | 150 | Duis ut diam quam nulla. Urna condimentum mattis pellentesque id nibh tortor id. Habitant morbi tristique senectus et netus et malesuada fames [@lorem-ipsum-2017]. Mauris in aliquam sem fringilla ut morbi tincidunt augue interdum. Nascetur ridiculus mus mauris vitae. Sapien pellentesque habitant morbi tristique. Sed libero enim sed faucibus turpis in eu 70\% Zn. Dui sapien eget mi proin sed libero enim sed. Maecenas ultricies mi eget mauris pharetra et. Pellentesque diam volutpat commodo sed egestas. Risus nec feugiat in fermentum posuere urna nec tincidunt praesent. Etiam erat velit scelerisque in dictum non (43\% Cu). Facilisi etiam dignissim diam quis enim lobortis scelerisque fermentum dui. Facilisi cras fermentum odio eu feugiat pretium nibh. 151 | 152 | Pellentesque habitant morbi tristique senectus et. Quis ipsum suspendisse ultrices gravida. Tellus in hac habitasse platea. Pretium nibh ipsum consequat nisl vel pretium. Urna molestie at elementum eu facilisis sed odio [@lorem-ipsum-2017]. Dis parturient montes nascetur ridiculus mus. Interdum velit euismod in pellentesque massa placerat. Viverra maecenas accumsan lacus vel. Erat velit scelerisque in dictum. Mi in nulla posuere sollicitudin aliquam ultrices sagittis orci. Nec sagittis aliquam malesuada bibendum arcu. Felis imperdiet proin fermentum leo vel orci porta. Ut consequat semper viverra nam libero. Facilisis mauris sit amet massa vitae tortor. 153 | 154 | #### Vulputate enim nulla 155 | 156 | Lectus proin nibh nisl condimentum id venenatis. Pharetra vel turpis nunc eget lorem. Vulputate enim nulla aliquet porttitor. Consectetur libero id faucibus nisl tincidunt eget nullam non nisi. Orci porta non pulvinar neque laoreet suspendisse interdum consectetur. Volutpat maecenas volutpat blandit aliquam etiam erat. Libero justo laoreet sit amet cursus. Adipiscing vitae proin sagittis nisl rhoncus mattis rhoncus. Risus at ultrices mi tempus imperdiet nulla malesuada pellentesque. Aliquam etiam erat velit scelerisque in dictum. 157 | 158 | Hendrerit gravida rutrum quisque non tellus orci. Tempor id eu nisl nunc mi ipsum. Consequat nisl vel pretium lectus quam id leo. Mattis aliquam faucibus purus in massa tempor nec feugiat. Non diam phasellus vestibulum lorem sed. Facilisis leo vel fringilla est ullamcorper eget ($\frac{1}{4}$). At quis risus sed vulputate odio ut enim blandit volutpat. Quis auctor elit sed vulputate. Netus et malesuada fames ac turpis egestas sed tempus urna. Eu augue ut lectus arcu bibendum at varius vel. Elementum tempus egestas sed sed risus pretium quam vulputate dignissim. Arcu felis bibendum ut tristique ($E_{\Sigma}$), as described in Equation \@ref(eq:singlefiber): 159 | 160 | \begin{equation} 161 | E_{\Sigma} = \frac{number \ collected \ on \ unit \ length}{number \ geometrically \ incident \ on \ unit \ length} 162 | (\#eq:singlefiber) 163 | \end{equation} 164 | 165 | Parturient montes nascetur ($E_{R}$), ridiculus mus ($E_{I}$), and ligula ullamcorper ($E_{G}$) hendrerit gravida rutrum quisque non tellus orci. Tempor id eu nisl nunc mi ipsum. Consequat nisl vel pretium lectus quam id leo. Mattis aliquam faucibus purus in massa tempor nec feugiat. Non diam phasellus vestibulum lorem sed. Facilisis leo vel fringilla est ullamcorper eget. At quis risus sed vulputate odio ut enim blandit volutpat. Quis auctor elit sed vulputate. Netus et malesuada fames ac turpis egestas sed tempus urna. Eu augue ut lectus arcu bibendum at varius vel. Elementum tempus egestas sed sed risus pretium quam vulputate dignissim. Arcu felis bibendum ut tristique. 166 | 167 | Data were managed and analyzed with R version 3.3.3 (2017-03-06) using the following packages: beeswarm, bookdown, ggplot2, ggthemes, gridExtra, knitr, lattice, lme4, lubridate, pander, and reshape [@r-beeswarm; @r-bookdown; @r-ggplot; @r-ggthemes; @r-gridExtra; @r-knitr; @r-lattice; @r-lme4; @r-lubridate; @r-pander; @r-reshape]. We produced plots of distributions, arithmetic and geometric means and standard deviations, scatter plots, box plots, and a heat map. 168 | 169 | The following criteria were used: 170 | 171 | * Tortor aliquam nulla facilisi cras 172 | * Dignissim suspendisse in est ante in 173 | * Auctor urna nunc id cursus metus [@icy-2017] 174 | 175 | ## Results 176 | 177 | ### Adipiscing at in tellus integer feugiat 178 | 179 | Pellentesque habitant morbi tristique senectus et. Quis ipsum suspendisse ultrices gravida. Tellus in hac habitasse platea. Pretium nibh ipsum consequat nisl vel pretium. Urna molestie at elementum eu facilisis sed odio. Dis 30\% parturient montes nascetur ridiculus mus. Interdum velit euismod in pellentesque massa placerat. Viverra maecenas accumsan lacus vel. Erat velit scelerisque in dictum 52\%. Mi in nulla posuere sollicitudin aliquam ultrices sagittis orci (Figure \@ref(fig:car-wt-mpg)). Nec sagittis aliquam malesuada bibendum arcu. Felis imperdiet proin fermentum leo vel orci porta (Figure \@ref(fig:car-scatter). Ut consequat semper viverra nam libero. Facilisis mauris sit amet massa vitae tortor. 180 | 181 | Vestibulum rhoncus est pellentesque elit ullamcorper dignissim. Lacus sed turpis tincidunt id aliquet risus feugiat. Nullam non nisi est sit. Diam maecenas sed enim ut sem viverra aliquet. A erat nam at lectus. Nunc non blandit massa enim nec dui nunc mattis enim. Consectetur adipiscing elit ut aliquam purus sit amet luctus venenatis. Quis ipsum suspendisse ultrices gravida. Sodales ut eu sem integer vitae justo eget magna (Table \@ref(tab:indiv-workrel)). Blandit volutpat maecenas volutpat blandit aliquam etiam erat. Leo urna molestie at elementum eu facilisis sed odio morbi. Sed libero enim sed faucibus turpis in eu mi bibendum. Urna neque viverra justo nec. Sed sed risus pretium quam vulputate dignissim suspendisse in est. Erat nam at lectus urna (Table \@ref(tab:indiv-activity). Morbi tincidunt augue interdum velit euismod in pellentesque massa. Nunc eget lorem dolor sed viverra ipsum nunc aliquet bibendum. Parturient montes nascetur ridiculus mus. 182 | 183 | ### Tellus integer feugiat 184 | 185 | Hendrerit gravida rutrum quisque non tellus orci. Tempor id eu nisl nunc mi ipsum. Consequat nisl vel pretium lectus quam id leo. Mattis aliquam faucibus purus in massa tempor nec feugiat. Non diam phasellus vestibulum lorem sed. Facilisis leo vel fringilla est ullamcorper eget. At quis risus sed vulputate odio ut enim blandit volutpat ($\frac{10}{15}$), vestibulum lorem sed at 20\% ($\frac{3}{15}$), and posuere sollicitudin ($\frac{2}{15}$). Quis auctor elit sed vulputate. Netus et malesuada fames ac turpis egestas sed tempus urna. Eu augue ut lectus arcu bibendum at varius vel. Elementum tempus egestas sed sed risus pretium quam vulputate dignissim. Arcu felis bibendum ut tristique. 186 | 187 | ## Discussion 188 | 189 | Velit scelerisque in dictum non consectetur. Pellentesque habitant morbi tristique senectus et. Et ligula ullamcorper malesuada proin. At volutpat diam ut venenatis tellus in. Nisl rhoncus mattis rhoncus urna neque viverra justo nec. Euismod elementum nisi quis eleifend quam adipiscing vitae. Nunc congue nisi vitae suscipit tellus. Consectetur libero id faucibus nisl. In cursus turpis massa tincidunt dui. Id semper risus in hendrerit gravida rutrum. Diam vel quam elementum pulvinar etiam non. Sit amet cursus sit amet dictum sit amet. Integer malesuada nunc vel risus commodo viverra maecenas accumsan lacus. Leo duis ut diam quam nulla. Quam quisque id diam vel quam elementum pulvinar etiam. Magnis dis parturient montes nascetur. Auctor urna nunc id cursus metus aliquam eleifend mi in. Id leo in vitae turpis massa sed. Fringilla est ullamcorper eget nulla facilisi etiam. Ipsum dolor sit amet consectetur adipiscing elit pellentesque habitant. 190 | 191 | Odio facilisis mauris sit amet. Lacus sed viverra tellus in. Mattis vulputate enim nulla aliquet porttitor lacus luctus. Purus faucibus ornare suspendisse sed nisi lacus sed viverra tellus. Feugiat scelerisque varius morbi enim nunc faucibus a pellentesque. Hendrerit gravida rutrum quisque non tellus orci ac auctor augue. Donec et odio pellentesque diam volutpat. Metus vulputate eu scelerisque felis imperdiet proin fermentum leo. Placerat orci nulla pellentesque dignissim enim sit amet venenatis urna. Velit ut tortor pretium viverra suspendisse potenti. Ipsum consequat nisl vel pretium lectus. Facilisis volutpat est velit egestas dui id ornare. Aliquam etiam erat velit scelerisque in dictum non. Morbi tristique senectus et netus et. Sagittis eu volutpat odio facilisis mauris sit amet massa. Eget est lorem ipsum dolor sit amet consectetur. Volutpat consequat mauris nunc congue nisi vitae suscipit tellus. Pulvinar sapien et ligula ullamcorper malesuada proin libero. Pulvinar mattis nunc sed blandit libero volutpat sed. 192 | 193 | 198 | 199 | \clearpage 200 | 201 | \linespread{1}\selectfont 202 | 203 | ## Tables 204 | 205 | Table: (\#tab:indiv-workrel)Superheros who exercise more than once per week. 206 | 207 | ```{r indiv-workrel, fig.cap = '(tab:indiv-workrel)', message=F, warnings=F, results='asis', echo=F} 208 | tabl <- " 209 | ----------------------------------------------------- 210 | Weekly workout Cardio Strength-training 211 | n(%) n(%) 212 | --------------- ---------------- -------------------- 213 | Yes 476 (69.0) 216 (67.5) 214 | 215 | No 214 (31.0) 104 (32.5) 216 | 217 | Total 690 (100) 320 (100) 218 | ----------------------------------------------------- 219 | 220 | " 221 | cat(tabl) 222 | ``` 223 | 224 | Table: (\#tab:indiv-activity)Activity at time of crime. (*) Some footnote. (\*\*) Another footnote. 225 | 226 | ```{r indiv-activity, fig.cap = '(tab:indiv-activity)', message=F, warnings=F, results='asis', echo=F} 227 | tabl <- " 228 | --------------------------------------------------------------------------------- 229 | Activity at time of crime All crops Tree fruit 230 | n(%) n(%) 231 | --------------------------------------------------- -------------- -------------- 232 | Bibendum enim facilisis* 467 (67.7) 210 (65.6) 233 | 234 | Malesuada fames ac turpis 129 (18.7) 75 (23.4) 235 | 236 | Pretium vulputate sapien nec sagittis 83 (12.0) 27 (8.4) 237 | 238 | Enim sit amet venenatis urna** 8 (1.2) 5 (1.6) 239 | 240 | Fringilla est ullamcorper 3 (0.4) 3 (0.9) 241 | 242 | Total 690 (100) 320 (100) 243 | --------------------------------------------------------------------------------- 244 | 245 | " 246 | cat(tabl) 247 | 248 | ``` 249 | 250 | \clearpage 251 | 252 | ## Figures 253 | 254 | (ref:car-wt-mpg) Scatter plot of car and miles per gallon. 255 | 256 | ```{r car-wt-mpg, fig.cap='(ref:car-wt-mpg)', fig.width=6, fig.height=6} 257 | 258 | ggplot(mtcars, aes(x=wt, y=mpg)) + geom_point() + theme_HEI(14) 259 | 260 | ``` 261 | 262 | (ref:car-scatter) Scatter plot matrix of cars. 263 | 264 | ```{r car-scatter, fig.cap='(ref:car-scatter)', fig.width=6, fig.height=6} 265 | 266 | ggpairs(mtcars, columns=c(1,3,4,5,6,7)) 267 | 268 | ``` 269 | 270 | \clearpage 271 | 272 | ## Appendices 273 | 274 | ### Appendix A: Purus faucibus ornare 275 | 276 | Velit scelerisque in dictum non consectetur. Pellentesque habitant morbi tristique senectus et. Et ligula ullamcorper malesuada proin. At volutpat diam ut venenatis tellus in. Nisl rhoncus mattis rhoncus urna neque viverra justo nec. Euismod elementum nisi quis eleifend quam adipiscing vitae. Nunc congue nisi vitae suscipit tellus. Consectetur libero id faucibus nisl. In cursus turpis massa tincidunt dui. Id semper risus in hendrerit gravida rutrum. Diam vel quam elementum pulvinar etiam non. Sit amet cursus sit amet dictum sit amet. Integer malesuada nunc vel risus commodo viverra maecenas accumsan lacus. Leo duis ut diam quam nulla. Quam quisque id diam vel quam elementum pulvinar etiam. Magnis dis parturient montes nascetur. Auctor urna nunc id cursus metus aliquam eleifend mi in. Id leo in vitae turpis massa sed. Fringilla est ullamcorper eget nulla facilisi etiam. Ipsum dolor sit amet consectetur adipiscing elit pellentesque habitant. 277 | -------------------------------------------------------------------------------- /07-chapter3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/07-chapter3.pdf -------------------------------------------------------------------------------- /08-chapter4.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Chapter 4: Fighting Crime' 3 | date: '`r format(Sys.Date(), "%d %B %Y")`' 4 | output: 5 | bookdown::pdf_document2: 6 | number_sections: yes 7 | toc: yes 8 | geometry: margin = 1in 9 | fontsize: 11pt 10 | bibliography: thesis-references.bib 11 | csl: science-modified1.csl 12 | link-citations: true 13 | linkcolor: blue 14 | urlcolor: blue 15 | header-includes: 16 | - \usepackage{placeins} 17 | - \usepackage{setspace} 18 | - \usepackage{chngcntr} 19 | - \usepackage{microtype} 20 | - \counterwithin{figure}{section} 21 | - \counterwithin{table}{section} 22 | - \usepackage{float} 23 | - \usepackage{amsmath} 24 | - \DeclareMathOperator{\logit}{logit} 25 | --- 26 | 27 | \linespread{1.6}\selectfont 28 | 29 | # Fighting Crime 30 | 31 | ## Abstract 32 | 33 | Fighting crime is a difficult job. More text for abstract goes here. Libero nunc consequat interdum varius sit amet mattis. Sed vulputate mi sit amet mauris commodo. Curabitur vitae nunc sed velit dignissim. Pulvinar etiam non quam lacus suspendisse faucibus. Vestibulum lectus mauris ultrices eros in cursus turpis. Cursus eget nunc scelerisque viverra mauris in aliquam sem fringilla. Gravida quis blandit turpis cursus in hac. Enim blandit volutpat maecenas volutpat blandit aliquam. Dictum at tempor commodo ullamcorper a lacus vestibulum sed. Feugiat nibh sed pulvinar proin gravida hendrerit lectus a. 34 | 35 | This chapter addresses the following sub-aims: 36 | 37 | \linespread{1}\selectfont 38 | 39 | * Use spider webs to catch criminals 40 | 41 | * Work normal day job to stay disguised 42 | 43 | \linespread{1.6}\selectfont 44 | 45 | ## Introduction 46 | 47 | ### Porttitor rhoncus 48 | 49 | Nulla facilisi cras fermentum odio eu feugiat pretium. At consectetur lorem donec massa sapien faucibus et molestie ac. Interdum velit euismod in pellentesque massa placerat. Etiam dignissim diam quis enim lobortis scelerisque fermentum dui faucibus. Faucibus a pellentesque sit amet porttitor eget. Sed cras ornare arcu dui vivamus. Porttitor rhoncus dolor purus non enim. Aliquam sem fringilla ut morbi tincidunt augue interdum velit euismod. Velit sed ullamcorper morbi tincidunt ornare. Aliquet nec ullamcorper sit amet risus nullam eget felis [@lorem-ipsum-2017]. Turpis tincidunt id aliquet risus. Nulla aliquet porttitor lacus luctus accumsan tortor. Id venenatis a condimentum vitae sapien. Pellentesque diam volutpat commodo sed egestas egestas fringilla phasellus faucibus. Maecenas sed enim ut sem viverra aliquet. Lacus sed viverra tellus in hac habitasse. Volutpat maecenas volutpat blandit aliquam etiam erat velit. Quis commodo odio aenean sed. Vitae justo eget magna fermentum. Fames ac turpis egestas maecenas. 50 | 51 | ### Eget est lorem ipsum 52 | 53 | Tincidunt tortor aliquam nulla facilisi cras. Id leo in vitae turpis massa. Aenean et tortor at risus viverra adipiscing. Massa tempor nec feugiat nisl pretium fusce id velit. Donec ac odio tempor orci dapibus ultrices in. Tincidunt id aliquet risus feugiat in ante metus dictum at. Nibh sit amet commodo nulla facilisi nullam vehicula ipsum a. Amet consectetur adipiscing elit duis. Morbi leo urna molestie at elementum [@lorem-ipsum-2017]. Sed id semper risus in hendrerit gravida rutrum quisque. Eget est lorem ipsum dolor sit amet consectetur adipiscing elit. Vel pretium lectus quam id leo in vitae. Sed elementum tempus egestas sed sed risus. Donec pretium vulputate sapien nec sagittis aliquam malesuada. Tellus mauris a diam maecenas sed enim ut sem. Libero volutpat sed cras ornare arcu dui vivamus arcu felis. Facilisis sed odio morbi quis commodo [@lorem-ipsum-2017]. Condimentum lacinia quis vel eros donec ac odio tempor. Nisi porta lorem mollis aliquam ut porttitor leo a. 54 | 55 | ## Methods 56 | 57 | ### Tellus mauris a diam maecenas sed enim 58 | 59 | Sit amet nisl suscipit adipiscing bibendum est ultricies integer. Blandit libero volutpat sed cras. Ultrices mi tempus imperdiet nulla malesuada pellentesque elit eget. Ac auctor augue mauris augue neque gravida. Semper auctor neque vitae tempus quam. Scelerisque felis imperdiet proin fermentum. Amet luctus venenatis lectus magna fringilla urna porttitor rhoncus. Justo eget magna fermentum iaculis eu non diam. Aliquam faucibus purus in massa tempor nec feugiat. At risus viverra adipiscing at in. Dui ut ornare lectus sit amet est placerat in. Lectus proin nibh nisl condimentum id venenatis a condimentum. Ornare arcu odio ut sem nulla pharetra. 60 | 61 | 1. Yes 62 | 2. No 63 | 3. Maybe 64 | 65 | ## Results 66 | 67 | Velit scelerisque in dictum non consectetur. Pellentesque habitant morbi tristique senectus et. Et ligula ullamcorper malesuada proin. At volutpat diam ut venenatis tellus in. Nisl rhoncus mattis rhoncus urna neque viverra justo nec. Euismod elementum nisi quis eleifend quam adipiscing vitae (Table \@ref(tab:table-1-summary)). Nunc congue nisi vitae suscipit tellus. Consectetur libero id faucibus nisl. In cursus turpis massa tincidunt dui. Id semper risus in hendrerit gravida rutrum. Diam vel quam elementum pulvinar etiam non. Sit amet cursus sit amet dictum sit amet. Integer malesuada nunc vel risus commodo viverra maecenas accumsan lacus. Leo duis ut diam quam nulla (Table \@ref(tab:table-2-summary)). Quam quisque id diam vel quam elementum pulvinar etiam. Magnis dis parturient montes nascetur. Auctor urna nunc id cursus metus aliquam eleifend mi in. Id leo in vitae turpis massa sed. Fringilla est ullamcorper eget nulla facilisi etiam. Ipsum dolor sit amet consectetur adipiscing elit pellentesque habitant. 68 | 69 | ## Discussion 70 | 71 | Duis ut diam quam nulla. Urna condimentum mattis pellentesque id nibh tortor id. Habitant morbi tristique senectus et netus et malesuada fames. Mauris in aliquam sem fringilla ut morbi tincidunt augue interdum. Nascetur ridiculus mus mauris vitae. Sapien pellentesque habitant morbi tristique. Sed libero enim sed faucibus turpis in eu. Dui sapien eget mi proin sed libero enim sed. Maecenas ultricies mi eget mauris pharetra et. Pellentesque diam volutpat commodo sed egestas. Risus nec feugiat in fermentum posuere urna nec tincidunt praesent. Etiam erat velit scelerisque in dictum non. Facilisi etiam dignissim diam quis enim lobortis scelerisque fermentum dui. Facilisi cras fermentum odio eu feugiat pretium nibh. 72 | 73 | 78 | 79 | \clearpage 80 | 81 | \linespread{1}\selectfont 82 | 83 | ## Tables 84 | 85 | Table: (\#tab:table-1-summary)Another table. 86 | 87 | ```{r table-1-summary, fig.cap = '(tab:table-1-summary)', message=F, warnings=F, results='asis', echo=F} 88 | tabl <- " 89 | ----------------------------------------------------------------------------------- 90 | Contaminant - Instrument Units Above Above Below Below 91 | Off Peak Peak Off Peak Peak 92 | -------------------------- ---------- ---------- -------- ------------ ------------ 93 | CO - Q-Trak * ppm 0.031 0.094 0.037 **0.121** 94 | 95 | CO~2~ - Q-Trak ppm 484 559 531 **622** 96 | 97 | ----------------------------------------------------------------------------------- 98 | " 99 | cat(tabl) 100 | ``` 101 | 102 | Table: (\#tab:table-2-summary)Last table. Enter additional text here. 103 | 104 | ```{r table-2-summary, fig.cap = '(tab:table-2-summary)', message=F, warnings=F, results='asis', echo=F} 105 | tabl <- " 106 | ----------------------------------------------------------- 107 | Compound Wavelength (µm) Wavenumber (cm^-1^) 108 | ----------------- ----------------- ---------------------- 109 | C~2~H~4~F~2~ 3.3 3030 110 | 111 | 7.3 1370 112 | 113 | 8.8 1140 114 | 115 | 10.8 930 116 | 117 | TCE 4.2 2380 118 | 119 | 10.8 930 120 | 121 | 11.8 847 122 | 123 | 12.8 780 124 | 125 | MEK (MIBK proxy) 5.7 1750 126 | 127 | 7.3 1370 128 | 129 | 8.5 1180 130 | 131 | Toluene 3.3 3030 132 | 133 | 4.2 2380 134 | 135 | 6.6 1520 136 | 137 | 13.7 730 138 | ----------------------------------------------------------- 139 | " 140 | cat(tabl) 141 | ``` 142 | -------------------------------------------------------------------------------- /08-chapter4.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/08-chapter4.pdf -------------------------------------------------------------------------------- /09-chapter5.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: 'Chapter 5: Conclusions' 3 | date: '`r format(Sys.Date(), "%d %B %Y")`' 4 | output: 5 | bookdown::pdf_document2: 6 | number_sections: yes 7 | toc: no 8 | geometry: margin = 1in 9 | fontsize: 11pt 10 | bibliography: thesis-references.bib 11 | csl: science-modified1.csl 12 | link-citations: true 13 | linkcolor: blue 14 | urlcolor: blue 15 | header-includes: 16 | - \usepackage{placeins} 17 | - \usepackage{setspace} 18 | - \usepackage{chngcntr} 19 | - \usepackage{microtype} 20 | - \counterwithin{figure}{section} 21 | - \counterwithin{table}{section} 22 | - \usepackage{float} 23 | - \usepackage{amsmath} 24 | - \DeclareMathOperator{\logit}{logit} 25 | --- 26 | 27 | \linespread{1.6}\selectfont 28 | 29 | # Conclusions 30 | 31 | Here are some conclusions. Some references were particularly helpful [@r-ggplot; @ramachandran-2005]. Maecenas volutpat blandit aliquam etiam erat. Pharetra vel turpis nunc eget lorem dolor sed viverra ipsum. Turpis egestas maecenas pharetra convallis posuere morbi leo. In eu mi bibendum neque egestas congue quisque egestas. Pellentesque nec nam aliquam sem et. Sit amet purus gravida quis blandit turpis cursus in hac. Bibendum est ultricies integer quis auctor elit sed vulputate mi. Pretium fusce id velit ut tortor pretium viverra suspendisse. Ultrices eros in cursus turpis. Consectetur adipiscing elit duis tristique sollicitudin nibh sit. Aliquam vestibulum morbi blandit cursus risus at ultrices. Arcu dui vivamus arcu felis bibendum ut tristique et. Cursus vitae congue mauris rhoncus aenean. Risus sed vulputate odio ut enim. -------------------------------------------------------------------------------- /09-chapter5.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/09-chapter5.pdf -------------------------------------------------------------------------------- /10-vita.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: bookdown::pdf_document2 3 | --- 4 | 5 | \linespread{1}\selectfont 6 | \setlength{\parindent}{0em} 7 | 8 | Peter Parker was born and raised in Queens, New York. He is a science nerd and a photographer who lived with his Uncle Ben and Aunt May and later became a superhero. Maecenas volutpat blandit aliquam etiam erat. Pharetra vel turpis nunc eget lorem dolor sed viverra ipsum. Turpis egestas maecenas pharetra convallis posuere morbi leo. In eu mi bibendum neque egestas congue quisque egestas. Pellentesque nec nam aliquam sem et. Sit amet purus gravida quis blandit turpis cursus in hac. Bibendum est ultricies integer quis auctor elit sed vulputate mi. Pretium fusce id velit ut tortor pretium viverra suspendisse. Ultrices eros in cursus turpis. Consectetur adipiscing elit duis tristique sollicitudin nibh sit. Aliquam vestibulum morbi blandit cursus risus at ultrices. Arcu dui vivamus arcu felis bibendum ut tristique et. Cursus vitae congue mauris rhoncus aenean. Risus sed vulputate odio ut enim. -------------------------------------------------------------------------------- /10-vita.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/10-vita.pdf -------------------------------------------------------------------------------- /Data/PSCAA_Data.xls: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eddiekasner/example-dissertation/f7b85b114f14c5b80ae4305e7c4745e665fef00c/Data/PSCAA_Data.xls -------------------------------------------------------------------------------- /Data/dylos.28feb2017.csv: -------------------------------------------------------------------------------- 1 | date,time,bin1,bin2,bin3,bin4,dylos,location,period,day 2/28/17,12:48,2740,694,230,5,7,,,1 2/28/17,12:49,4210,2154,1613,806,7,,,1 2/28/17,12:50,2919,760,329,24,7,above,off peak,1 2/28/17,12:51,2069,488,171,9,7,above,off peak,1 2/28/17,12:52,1975,480,185,6,7,above,off peak,1 2/28/17,12:53,3060,638,244,11,7,above,off peak,1 2/28/17,12:54,5997,1263,456,19,7,above,off peak,1 2/28/17,12:55,5618,883,280,14,7,above,off peak,1 2/28/17,12:56,5596,878,297,17,7,above,off peak,1 2/28/17,12:57,4564,796,303,17,7,above,off peak,1 2/28/17,12:58,5372,993,369,22,7,above,off peak,1 2/28/17,12:59,3092,754,298,17,7,above,off peak,1 2/28/17,13:00,3614,779,302,16,7,above,off peak,1 2/28/17,13:01,4878,897,282,16,7,above,off peak,1 2/28/17,13:02,3396,688,268,20,7,above,off peak,1 2/28/17,13:03,2196,550,233,9,7,above,off peak,1 2/28/17,13:04,1856,460,184,7,7,above,off peak,1 2/28/17,13:05,4940,773,236,9,7,above,off peak,1 2/28/17,13:06,4935,769,218,10,7,above,off peak,1 2/28/17,13:07,2939,570,204,7,7,above,off peak,1 2/28/17,13:08,1740,426,173,10,7,above,off peak,1 2/28/17,13:09,2069,480,177,12,7,above,off peak,1 2/28/17,13:10,3448,617,206,10,7,above,off peak,1 2/28/17,13:11,4244,764,235,12,7,above,off peak,1 2/28/17,13:12,3951,683,207,8,7,above,off peak,1 2/28/17,13:13,2668,619,221,10,7,above,off peak,1 2/28/17,13:14,2673,694,286,15,7,above,off peak,1 2/28/17,13:15,2363,584,234,12,7,above,off peak,1 2/28/17,13:16,2417,515,190,8,7,above,off peak,1 2/28/17,13:17,2142,649,303,21,7,above,off peak,1 2/28/17,13:18,2570,629,228,5,7,above,off peak,1 2/28/17,13:19,3047,857,388,22,7,above,off peak,1 2/28/17,13:20,3917,1296,593,32,7,above,off peak,1 2/28/17,13:21,3766,1158,526,33,7,,,1 2/28/17,13:22,3502,974,406,22,7,,,1 2/28/17,13:23,3926,1156,417,9,7,,,1 2/28/17,13:24,3707,1122,346,7,7,,,1 2/28/17,13:25,3987,1107,331,6,7,,,1 2/28/17,13:26,4355,1231,374,8,7,,,1 2/28/17,13:27,4218,1223,363,7,7,,,1 2/28/17,13:28,3656,1064,334,3,7,,,1 2/28/17,13:29,3590,1000,298,3,7,,,1 2/28/17,13:30,3438,980,301,3,7,,,1 2/28/17,13:31,2830,831,282,10,7,,,1 2/28/17,13:32,3524,1042,325,8,7,,,1 2/28/17,13:33,3555,1006,303,6,7,below,off peak,1 2/28/17,13:34,3221,872,252,2,7,below,off peak,1 2/28/17,13:35,3047,868,257,3,7,below,off peak,1 2/28/17,13:36,3001,831,245,3,7,below,off peak,1 2/28/17,13:37,3143,884,276,5,7,below,off peak,1 2/28/17,13:38,3062,841,255,7,7,below,off peak,1 2/28/17,13:39,2908,811,223,4,7,below,off peak,1 2/28/17,13:40,2803,793,229,5,7,below,off peak,1 2/28/17,13:41,2845,777,218,5,7,below,off peak,1 2/28/17,13:42,2938,813,242,4,7,below,off peak,1 2/28/17,13:43,3084,849,267,4,7,below,off peak,1 2/28/17,13:44,3637,1036,296,7,7,below,off peak,1 2/28/17,13:45,3694,1032,314,5,7,below,off peak,1 2/28/17,13:46,4296,1211,344,6,7,below,off peak,1 2/28/17,13:47,4192,1128,319,6,7,below,off peak,1 2/28/17,13:48,4186,1156,321,5,7,below,off peak,1 2/28/17,13:49,4655,1298,363,9,7,below,off peak,1 2/28/17,13:50,4513,1292,390,7,7,below,off peak,1 2/28/17,13:51,4459,1261,368,8,7,below,off peak,1 2/28/17,13:52,4242,1195,348,6,7,below,off peak,1 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16:28,951.0403,1772.3671,1822.3488,2782.137,3037.8718,2715.6934,2256.304,1962.1176,1518.7378,789.1518,24.4871,0,0,19632.2565,40.6791,51.6207,40.902,36.5174,1.9917,1.2,below,peak,1 5,20,2/28/17 16:29,890.0286,1726.066,1767.3232,2698.4856,2982.5559,2716.7998,2274.811,1929.0648,1373.871,575.1682,0,0,0,18934.1742,40.4728,50.1874,40.2814,36.5174,1.956,1.2,below,peak,1 5,21,2/28/17 16:30,908.0276,1479.8641,1474.8983,2524.1116,2888.9954,2625.2449,2157.0183,1826.442,1355.2472,642.4427,0,0,0,17882.2922,41.3723,51.4303,41.2069,36.5174,1.9654,1.2,below,peak,1 5,22,2/28/17 16:31,709.6223,1354.2531,1538.3815,2597.675,2936.0303,2661.9673,2188.8245,1842.2284,1340.4457,604.5287,0,0,0,17773.9567,41.7034,51.6584,41.8215,36.5174,1.931,1.2,below,peak,1 5,23,2/28/17 16:32,788.5132,1578.14,1660.9816,2529.2029,2933.8955,2807.0068,2376.3674,1887.0122,1217.864,446.9435,0,0,0,18225.9272,41.235,49.8079,40.5208,36.5174,1.9196,1.2,below,peak,1 5,24,2/28/17 16:33,782.461,1579.4596,1627.5112,2460.3167,2855.4404,2718.2756,2269.3364,1768.7081,1140.2682,432.2131,0,0,0,17633.9904,40.7852,49.3117,40.079,36.5174,1.9203,1.2,below,peak,1 5,25,2/28/17 16:34,726.9329,1382.9354,1523.855,2510.4612,2872.0039,2652.6719,2194.8955,1794.5975,1220.4226,478.7873,0,0,0,17357.5632,41.3552,50.4901,41.0713,36.5174,1.918,1.2,below,peak,1 5,26,2/28/17 16:35,771.4971,1449.5983,1599.2264,2635.6057,3014.5781,2741.3499,2194.6643,1732.528,1192.8378,522.3818,0,0,0,17854.2673,40.6863,49.8796,40.5141,36.5174,1.9176,1.2,below,peak,1 5,27,2/28/17 16:36,756.8553,1380.9999,1539.9751,2644.5989,2945.5,2592.9661,2067.5115,1736.9619,1270.8876,565.9129,0,0,0,17502.1691,40.7372,50.6487,40.9437,36.5174,1.9315,1.2,below,peak,1 5,28,2/28/17 16:37,708.402,1321.1465,1549.3578,2528.4712,2926.6709,2729.5977,2251.6462,1784.9884,1196.5946,488.5788,0,0,0,17485.4541,41.5464,50.5328,41.243,36.5174,1.9072,1.2,below,peak,1 5,29,2/28/17 16:38,706.9641,1270.1881,1397.766,2500.2776,3038.7217,2892.6541,2345.4636,1762.7418,1067.3517,330.8151,0,0,0,17312.9438,41.7043,49.4359,40.9296,36.5174,1.868,1.2,below,peak,1 5,30,2/28/17 16:39,732.1128,1207.0778,1250.6379,2378.2795,3012.0293,2915.3848,2332.6414,1671.6115,960.5582,282.4494,0,0,0,16742.7824,41.8686,49.0041,40.779,36.5174,1.8554,1.2,below,peak,1 5,31,2/28/17 16:40,635.6411,1215.2748,1409.1987,2435.7795,3003.0215,2915.4094,2380.2705,1734.2598,1020.5864,325.5636,0,0,0,17075.0053,42.0343,49.5502,41.1923,36.5174,1.8551,1.2,below,peak,1 6,1,3/2/17 12:55,890.881,1410.7968,1505.8441,2923.1516,3835.6211,4074.6531,3819.8203,3301.3057,2283.1255,922.0965,0,0,0,24967.2957,49.2939,56.9166,46.8591,48.6968,1.9081,1.2,,,2 6,2,3/2/17 12:56,556.237,1153.1761,1512.7295,2920.5,3626.8401,3731.6423,3519.3289,3193.3965,2329.2068,993.301,0,0,0,23536.3582,50.2183,58.4794,48.3804,48.6968,1.8863,1.2,above,off peak,2 6,3,3/2/17 12:57,471.5741,1098.6141,1578.6021,2834.5383,3524.5618,3619.8962,3315.7097,2815.5417,1924.1366,770.4803,0,0,0,21953.655,48.3736,56.3625,46.8919,48.6968,1.8613,1.2,above,off peak,2 6,4,3/2/17 12:58,485.4313,1113.3341,1476.4171,2661.7024,3351.7734,3462.4397,3153.7874,2640.6023,1778.5879,699.5569,0,0,0,20823.6325,48.0375,55.8763,46.451,48.6968,1.8647,1.2,above,off peak,2 6,5,3/2/17 12:59,510.9733,1092.9015,1391.3374,2618.2151,3266.6428,3312.3694,2984.136,2534.5032,1736.2456,689.61,0,0,0,20136.9343,47.7054,55.7954,46.2655,48.6968,1.8726,1.2,above,off peak,2 6,6,3/2/17 13:00,979.5488,1931.8146,2272.7952,4322.6172,5750.6074,5806.4492,4641.2666,2985.2871,1284.2372,0,0,0,0,29974.6233,42.1066,46.942,40.43,48.6968,1.7552,1.2,above,off peak,2 6,7,3/2/17 13:01,1098.6947,1652.9155,1991.2906,4565.8594,5910.5977,5568.1138,4165.8599,2729.1819,1378.4432,231.2326,0,0,0,29292.1892,41.5735,47.5452,40.6278,36.5174,1.7714,1.2,above,off peak,2 6,8,3/2/17 13:02,1231.5319,1546.856,1617.1683,3016.2891,4005.7402,4145.3442,3606.9932,2726.7131,1596.8214,454.1275,0,0,0,23947.5849,44.5138,51.2235,42.3761,48.6968,1.8879,1.2,above,off peak,2 6,9,3/2/17 13:03,1050.4926,1704.4503,1894.1185,3730.7371,5373.6533,5843.4907,5000.1411,3354.2834,1489.2609,20.7432,0,0,0,29461.3711,44.9835,49.2363,42.3358,48.6968,1.7705,1.2,above,off peak,2 6,10,3/2/17 13:04,669.5375,1316.4606,1609.4083,2915.4111,3715.1482,3823.4375,3407.1396,2742.2483,1748.8281,596.3843,0,0,0,22544.0036,46.4948,53.9061,44.8393,48.6968,1.8637,1.2,above,off peak,2 6,11,3/2/17 13:05,522.028,1039.2615,1363.2267,2639.4373,3380.4563,3476.6648,3123.1516,2586.7817,1731.5033,669.3624,0,0,0,20531.8735,48.0086,55.762,46.4644,48.6968,1.8579,1.2,above,off peak,2 6,12,3/2/17 13:06,660.1775,909.2991,1426.6104,3523.218,4944.2944,5122.0625,4247.7598,2936.4924,1430.3286,114.1092,0,0,0,25314.352,45.9185,50.9694,44.291,48.6968,1.7252,1.2,above,off peak,2 6,13,3/2/17 13:07,1146.7975,1874.455,2013.087,4043.1055,5400.0747,5356.9282,4178.5767,2664.1191,1220.1896,144.4668,0,0,0,28041.8,41.706,46.981,40.0637,36.5174,1.7848,1.2,above,off peak,2 6,14,3/2/17 13:08,563.6227,1077.0253,1366.0942,2744.4436,3741.1697,3992.876,3554.2908,2734.031,1613.2886,466.1679,0,0,0,21853.0097,47.7111,54.135,45.757,48.6968,1.8153,1.2,above,off peak,2 6,15,3/2/17 13:09,541.2167,1053.4154,1361.6462,2642.4966,3880.9685,4381.5249,3928.3889,2775.823,1343.4352,146.4535,0,0,0,22055.3689,47.6274,52.1893,44.9855,48.6968,1.7588,1.2,above,off peak,2 6,16,3/2/17 13:10,448.9973,1048.1381,1392.4316,2607.2107,3473.8875,3719.4421,3368.2507,2644.0762,1568.6027,430.4802,0,0,0,20701.5171,47.8798,54.316,45.9224,48.6968,1.8133,1.2,above,off peak,2 6,17,3/2/17 13:11,491.6781,1008.2769,1359.9711,2676.4089,3666.114,3976.998,3607.1121,2795.8845,1619.8361,400.2246,0,0,0,21602.5043,48.3198,54.3922,46.2119,48.6968,1.8,1.2,above,off peak,2 6,18,3/2/17 13:12,510.7527,1042.952,1383.374,2725.2866,3762.957,4085.8196,3672.9333,2789.8445,1569.4448,361.4746,0,0,0,21904.8392,47.9183,53.7955,45.791,48.6968,1.7939,1.2,above,off peak,2 6,19,3/2/17 13:13,576.0749,1052.3187,1322.4564,2810.0374,3788.1086,3959.2805,3467.5286,2682.0107,1598.9635,454.5804,0,0,0,21711.3598,47.2969,53.8969,45.5624,48.6968,1.8135,1.2,above,off peak,2 6,20,3/2/17 13:14,530.3701,1452.2671,1913.2289,3179.1418,3948.0579,4007.5391,3472.3293,2632.0881,1501.312,354.8922,0,0,0,22991.2266,44.2827,51.1325,43.0491,48.6968,1.8191,1.2,above,off peak,2 6,21,3/2/17 13:15,591.8498,963.2897,1396.4882,3411.9797,4621.7183,4503.0122,3398.3201,2104.6184,943.3295,83.7171,0,0,0,22018.323,42.6823,47.987,41.8041,36.5174,1.71,1.2,above,off peak,2 6,22,3/2/17 13:16,947.5374,1545.5939,1596.9095,2896.3958,3793.2,3859.0774,3232.6765,2314.5212,1248.9004,276.9963,0,0,0,21711.8084,42.8879,49.306,41.2166,48.6968,1.8492,1.2,above,off peak,2 6,23,3/2/17 13:17,594.3805,1045.1119,1221.6538,2625.325,3781.1143,4077.5027,3475.6328,2382.3799,1133.665,98.616,0,0,0,20435.3819,45.9183,50.6319,43.6222,48.6968,1.7589,1.2,above,off peak,2 6,24,3/2/17 13:18,1297.9265,1936.2838,2025.5924,4184.9336,5271.3652,4664.873,2989.1426,1372.8912,231.2601,0,0,0,0,23974.2686,37.0904,40.0582,34.9938,36.5174,1.7063,1.2,above,off peak,2 6,25,3/2/17 13:19,1202.8978,2691.0088,2764.8601,3889.6182,4382.7314,3966.5452,2965.0771,1902.1006,916.4914,136.4461,0,0,0,24817.7767,36.4745,42.5475,35.5345,36.5174,1.829,1.2,above,off peak,2 6,26,3/2/17 13:20,632.243,1243.8131,1481.6416,2672.0583,3473.6006,3586.7268,3103.0437,2316.9932,1291.9667,278.8159,0,0,0,20080.903,44.735,51.0854,43.0056,48.6968,1.8262,1.2,above,off peak,2 6,27,3/2/17 13:21,489.5516,1075.4081,1479.0045,2831.3137,3711.5811,3857.1504,3385.2959,2610.8184,1565.6655,481.2066,0,0,0,21486.9958,46.8683,53.7214,45.3401,48.6968,1.8146,1.2,above,off peak,2 6,28,3/2/17 13:22,467.9955,1086.4377,1525.6964,2896.8635,3720.2031,3955.9626,3753.2,3280.4763,2269.3743,904.4153,0,0,0,23860.6248,50.6287,58.2729,48.6751,48.6968,1.8546,1.2,above,off peak,2 6,29,3/2/17 13:23,402.3598,1063.6584,1515.9542,2736.2881,3917.3938,4868.0508,5294.3491,4933.5195,3510.8127,1423.1279,0,0,0,29665.5144,57.9952,64.1419,54.2772,64.9382,1.83,1.2,above,off peak,2 6,30,3/2/17 13:24,433.9439,964.5297,1490.0587,2957.3809,4151.1841,5209.0386,5960.3745,6000.0503,4561.9243,1995.8237,0,0,0,33724.3087,62.0824,67.5325,57.3016,86.5964,1.8269,1.2,above,off peak,2 6,31,3/2/17 13:25,464.238,960.2009,1409.8021,2886.7136,4050.325,5085.9868,5864.4214,5987.2266,4621.3716,2056.6262,0,0,0,33386.9122,62.7508,68.0925,57.7178,86.5964,1.8328,1.2,above,off peak,2 6,32,3/2/17 13:26,456.3772,1026.6508,1498.8158,2988.4377,4228.2456,4980.2192,5098.3452,4541.5435,3095.127,1150.6029,0,0,0,29064.3648,54.9726,61.5731,52.1814,64.9382,1.818,1.2,above,off peak,2 7,1,3/2/17 13:36,643.7109,1268.0204,1605.8776,2908.5725,3663.7581,4167.7568,4588.4668,4764.7212,3927.8411,2061.2495,44.2568,0,0,29644.2316,59.1484,66.3533,54.5967,86.5964,1.9293,1.2,below,off peak,2 7,2,3/2/17 13:37,843.7,1236.3152,1347.8615,2824.0227,4040.4961,4301.146,3673.8574,2660.7161,1733.296,947.5368,272.5074,0,0,23881.4551,48.0529,57.0236,46.6583,48.6968,1.9048,1.2,below,off peak,2 7,3,3/2/17 13:38,790.9476,1309.0386,1568.9711,3122.8086,3980.3682,3883.4902,3164.3867,2336.4968,1418.7979,495.1638,0,0,0,22070.4694,43.5698,51.1727,42.7153,36.5174,1.845,1.2,below,off peak,2 7,4,3/2/17 13:39,574.9168,1152.6046,1578.0811,3015.4509,3855.2188,4109.312,3983.6726,3630.2112,2705.2166,1280.8508,0,0,0,25885.5353,52.1739,60.3794,50.0014,48.6968,1.8873,1.2,below,off peak,2 7,5,3/2/17 13:40,543.7082,1243.0105,1626.3329,2737.1775,3386.613,3782.3596,4056.3293,4096.687,3347.1553,1783.4591,88.8212,0,0,26691.6537,56.9418,65.1591,53.3358,86.5964,1.9382,1.2,below,off peak,2 7,6,3/2/17 13:41,81.093,2549.6309,4889.5864,6930.2437,6663.9575,5639.2437,5043.7915,5078.8843,4321.0083,2291.9485,0,0,0,43489.3877,44.1951,56.7408,46.0437,27.3842,1.9119,1.2,below,off peak,2 7,7,3/2/17 13:42,1056.0857,3747.1233,5217.1284,7376.4458,7676.5151,7177.9995,6764.5728,6547.2124,5175.0786,2481.8728,0,0,0,53220.0344,45.6493,56.2748,45.3813,36.5174,1.95,1.2,below,off peak,2 7,8,3/2/17 13:43,1461.0314,6818.3457,7875.2114,8815.3408,7923.1479,6786.0254,6311.1113,6369.144,5288.2866,2705.2446,0,0,0,60352.8893,38.9533,51.9184,40.6209,27.3842,2.0165,1.2,below,off peak,2 7,9,3/2/17 13:44,1038.3223,2834.7092,3634.9238,5266.3774,5572.8086,5406.7017,5420.8018,5572.4204,4622.5537,2373.0911,0,0,0,41742.71,49.2414,59.2944,47.4979,36.5174,1.9872,1.2,below,off peak,2 7,10,3/2/17 13:45,841.7916,2880.3494,3586.2188,4626.1152,4761.0811,4533.5493,4319.6055,4081.3752,3066.1658,1333.8049,0,0,0,34030.0567,43.6085,54.1417,43.4472,36.5174,1.9631,1.2,below,off peak,2 7,11,3/2/17 13:46,930.8719,1778.0713,2535.4333,4846.6167,5356.2524,5048.5654,4986.3975,5462.5913,5056.7432,3107.051,518.0623,0,0,39626.6564,54.8965,66.3695,53.0075,86.5964,2.0031,1.2,below,off peak,2 7,12,3/2/17 13:47,603.1114,2078.4036,3201.8857,5111.105,5364.9097,5773.8008,7157.729,8866.9502,8425.707,5111.7329,740.301,0,0,52435.6362,67.6313,73.7399,59.9238,86.5964,1.978,1.2,below,off peak,2 7,13,3/2/17 13:48,669.7604,2268.3494,3134.0701,4568.0415,4857.3472,5488.6641,6937.9878,8416.8135,7773.4995,4561.7373,529.8335,0,0,49206.1041,66.6961,72.4529,58.7792,86.5964,1.9873,1.2,below,off peak,2 7,14,3/2/17 13:49,781.694,2000.4767,2565.2563,3820.8164,4379.5176,5070.2397,6129.6445,6993.4917,6248.5728,3669.2351,551.6472,0,0,42210.592,64.507,71.2505,57.6178,86.5964,1.9941,1.2,below,off peak,2 7,15,3/2/17 13:50,747.7561,1959.4064,2459.7673,3921.7061,4552.7705,5113.6636,5905.1211,6543.957,5680.9985,3131.1931,177.7187,0,0,40194.0585,61.1239,68.0908,55.4347,86.5964,1.9669,1.2,below,off peak,2 7,16,3/2/17 13:51,593.5653,1947.2902,2615.2888,3788.0613,4304.0571,5077.8521,6250.7075,7133.7456,6208.7856,3399.6475,194.3492,0,0,41513.3502,64.186,69.9246,57.2075,86.5964,1.957,1.2,below,off peak,2 7,17,3/2/17 13:52,393.0601,2147.6138,2934.7969,3539.8386,4215.2378,5905.7891,8118.7778,9415.2842,8016.3906,4373.9668,540.3254,0,0,49601.081,70.0381,74.3758,61.6123,86.5964,1.9261,1.2,below,off peak,2 7,18,3/2/17 13:53,593.3746,1878.2744,2616.6929,4190.2148,5680.1733,8146.3306,11127.5977,12985.5088,11446.4365,6512.3843,732.8161,0,0,65909.804,73.5913,77.8434,65.7517,86.5964,1.8625,1.2,below,off peak,2 7,19,3/2/17 13:54,544.2252,1690.8159,2316.7178,3712.0227,4754.0947,6083.6875,7561.0918,8367.6104,7103.2554,3826.8235,181.5905,0,0,46141.9353,66.7657,71.8193,59.905,86.5964,1.8959,1.2,below,off peak,2 7,20,3/2/17 13:55,579.8825,1683.6797,2198.7317,3477.9609,4490.6538,5777.8198,7163.2056,7877.9448,6625.1484,3576.2009,289.157,0,0,43740.3853,66.5036,71.8073,59.6643,86.5964,1.9086,1.2,below,off peak,2 7,21,3/2/17 13:56,389.2867,1532.3422,2246.321,3454.1191,4689.9487,6687.7988,8986.6426,10281.6787,8917.792,5023.8462,582.8129,0,0,52792.589,72.4142,76.9579,64.9762,86.5964,1.8597,1.2,below,off peak,2 7,22,3/2/17 13:57,546.5594,1493.516,2118.7979,3566.3162,4190.811,5318.0337,7170.0669,8783.4219,7962.2554,4483.1323,315.567,0,0,45948.4776,71.9883,75.81,63.2515,86.5964,1.906,1.2,below,off peak,2 7,23,3/2/17 13:58,518.109,1479.3737,2035.3164,3331.0596,4424.3311,5761.6055,7137.3511,7801.854,6608.8066,3625.8145,292.6895,0,0,43016.3108,67.327,72.6385,60.6612,86.5964,1.891,1.2,below,off peak,2 7,24,3/2/17 13:59,474.5774,1402.9955,1995.0416,3471.9795,4384.2661,5609.375,7138.4702,8145.1216,6918.8086,3545.9104,0,0,0,43086.5459,67.9802,72.1874,60.7355,86.5964,1.8703,1.2,below,off peak,2 7,25,3/2/17 14:00,371.1534,1351.0002,2015.6664,3181.6277,4126.1201,5401.9526,6773.6265,7416.2378,6087.769,3038.0547,0,0,0,39763.2085,66.4246,70.9266,59.7351,86.5964,1.8626,1.2,below,off peak,2 7,26,3/2/17 14:01,498.3686,1227.4718,1615.1459,2657.7097,3059.4177,3445.1572,4057.657,4590.7974,3975.9043,2124.467,29.5977,0,0,27281.6944,62.1301,68.3058,55.9678,86.5964,1.95,1.2,below,off peak,2 7,27,3/2/17 14:02,447.508,1317.0204,1666.5522,2551.6711,3072.5417,3671.9392,4379.438,4794.209,4041.0374,2112.5911,0,0,0,28054.5081,62.4427,68.1562,56.1378,86.5964,1.9344,1.2,below,off peak,2 7,28,3/2/17 14:03,477.8874,1237.9806,1584.0743,2616.5972,3365.2288,4201.1646,5070.2373,5509.8066,4618.0171,2453.7009,93.7404,0,0,31228.4352,64.7831,70.2245,58.3036,86.5964,1.9102,1.2,below,off peak,2 7,29,3/2/17 14:04,505.6689,1241.9854,1582.0459,2611.1584,3331.4539,4725.7852,6664.5366,8057.5347,7034.0176,3663.1396,0,0,0,39417.3262,73.0548,75.7954,64.1467,86.5964,1.8662,1.2,below,off peak,2 7,30,3/2/17 14:05,718.356,1392.452,1640.1388,3071.3577,3816.4465,4354.4067,4936.0137,5349.9478,4539.5815,2408.8447,27.9056,0,0,32255.451,61.1732,67.6989,55.6653,86.5964,1.9384,1.2,below,off peak,2 7,31,3/2/17 14:06,722.5289,1569.3199,1856.4965,3045.5107,3785.2607,4331.2104,4776.3359,4903.3384,3980.4768,2038.7104,0,0,0,31009.1888,57.5882,64.8698,53.1086,86.5964,1.9458,1.2,below,off peak,2 8,1,3/2/17 16:15,313.0052,856.9328,1386.5165,2576.7756,3216.9763,4093.3162,5310.0908,6247.9341,5518.9648,3005.8772,67.8787,0,0,32594.2683,70.5696,74.6349,63.0223,86.5964,1.8585,1.2,above,peak,2 8,2,3/2/17 16:16,149.3794,1208.6366,2028.174,2954.5027,3347.718,3474.4463,3446.6533,3190.7625,2305.3474,943.1895,0,0,0,23048.8095,50.1162,58.3946,48.4507,48.6968,1.8674,1.2,above,peak,2 8,3,3/2/17 16:17,1498.6797,2382.3918,2329.8137,3486.1565,3703.8054,3141.3831,2449.4792,2047.2338,1534.4889,731.4529,0,0,0,23304.8851,37.5767,47.7032,37.7508,36.5174,1.9844,1.2,above,peak,2 8,4,3/2/17 16:18,1279.3446,2258.1589,2247.5286,3107.4744,3354.0256,3494.7793,3866.959,4235.5454,3621.115,1912.9218,0,0,0,29377.8525,52.5383,61.41,48.275,86.5964,2.0716,1.2,above,peak,2 8,5,3/2/17 16:19,1150.8757,2153.5049,2286.9524,3374.9854,3757.6565,3505.9932,3026.4197,2584.3699,1876.1766,853.3754,0,0,0,24570.3096,41.3626,51.3704,41.0898,36.5174,1.9703,1.2,above,peak,2 8,6,3/2/17 16:20,1172.1936,2381.074,2642.8699,3812.5398,3940.72,3211.2229,2299.9446,1723.4127,1217.9154,580.8758,0,0,0,22982.7686,35.9603,45.1577,36.4384,36.5174,1.9117,1.2,above,peak,2 8,7,3/2/17 16:21,1172.7921,2037.618,2089.7729,3169.7273,3481.6895,3406.8135,3410.5642,3542.2646,3052.2979,1729.8226,182.0398,0,0,27275.4025,49.6401,60.5724,47.3671,86.5964,2.0684,1.2,above,peak,2 8,8,3/2/17 16:22,613.4509,414.8998,1808.2225,6011.1616,8489.543,8457.4434,6656.9966,4508.9673,2436.532,632.9344,0,0,0,40030.1515,47.1064,53.4265,46.9275,36.5174,1.6693,1.2,above,peak,2 8,9,3/2/17 16:23,1298.7806,2250.697,2212.2256,4336.2095,5971.856,6314.3262,5440.4058,3979.7151,2236.9673,596.5077,0,0,0,34637.6907,45.4181,51.6054,43.2477,48.6968,1.845,1.2,above,peak,2 8,10,3/2/17 16:24,482.3989,1485.7524,2373.4373,5102.5146,7578.0278,8320.2549,6971.061,4348.8198,1599.1713,0,0,0,0,38261.4381,46.2084,49.992,44.2291,48.6968,1.6636,1.2,above,peak,2 8,11,3/2/17 16:25,623.5184,1432.1143,1689.8447,2792.3044,3491.3679,4083.957,4627.3057,4850.4253,3970.9111,2031.9962,0,0,0,29593.7451,59.6176,66.1888,54.3947,86.5964,1.9375,1.2,above,peak,2 8,12,3/2/17 16:26,325.2908,835.9495,1229.901,2219.8293,2713.8804,3314.051,4150.7886,4811.5444,4218.8608,2305.2664,107.984,0,0,26233.3462,68.1294,72.95,60.8975,86.5964,1.8945,1.2,above,peak,2 8,13,3/2/17 16:27,363.807,827.9503,1198.9075,2292.3193,2807.7917,3342.301,4090.3694,4716.6812,4145.2632,2273.7878,110.2388,0,0,26169.4172,67.2488,72.4196,60.3359,86.5964,1.8993,1.2,above,peak,2 8,14,3/2/17 16:28,395.6757,888.095,1345.1652,2664.3547,3310.6375,3719.6252,4136.5215,4426.5073,3723.2832,1970.8483,47.1055,0,0,26627.8191,61.3544,68.1965,56.6973,86.5964,1.8925,1.2,above,peak,2 8,15,3/2/17 16:29,695.6475,1235.0186,1384.603,2509.4417,3031.4739,3367.3955,3790.8606,4163.832,3617.3308,2007.2911,137.2327,0,0,25940.1273,60.549,67.8733,55.0569,86.5964,1.9819,1.2,above,peak,2 8,16,3/2/17 16:30,297.8475,1014.8679,1493.7992,2315.0471,2982.6328,3694.7295,4292.1196,4368.4658,3335.8291,1453.5269,0,0,0,25248.8655,60.4621,66.064,55.3333,86.5964,1.8701,1.2,above,peak,2 8,17,3/2/17 16:31,642.0457,1389.047,1934.1196,3372.4512,3784.6897,3746.3523,3795.9094,3998.5264,3451.3206,1914.0553,122.9339,0,0,28151.4511,53.8096,63.6849,51.4185,86.5964,1.9712,1.2,above,peak,2 8,18,3/2/17 16:32,335.7523,926.7642,1375.1893,2323.0288,2838.054,3282.4209,3756.1843,4014.2754,3345.8298,1755.6857,29.873,0,0,23983.0577,61.41,67.8768,56.2391,86.5964,1.9062,1.2,above,peak,2 8,19,3/2/17 16:33,1269.5349,1989.7833,2075.2395,4667.1182,6696.8853,7054.1196,5818.2017,3874.9551,1839.3175,197.6609,0,0,0,35482.8159,44.7079,49.6017,42.5319,48.6968,1.7742,1.2,above,peak,2 8,20,3/2/17 16:34,1272.4952,2224.5686,2517.927,5298.8325,7499.8159,7787.3901,6199.4453,3776.6213,1426.3263,0,0,0,0,38003.4224,42.9503,47.1849,40.9489,48.6968,1.7345,1.2,above,peak,2 8,21,3/2/17 16:35,538.7483,1080.1437,1363.9377,2640.0496,3441.7996,3873.9756,4062.5898,3991.5479,3149.8701,1585.0636,0,0,0,25727.7258,56.5431,64.3195,53.2605,64.9382,1.9016,1.2,above,peak,2 8,22,3/2/17 16:36,677.2219,1257.5834,1356.8995,2967.0369,5010.5161,6381.7695,6372.3687,4983.3989,2690.6367,448.1883,0,0,0,32145.6198,53.3032,57.71,49.9206,48.6968,1.7583,1.2,above,peak,2 8,23,3/2/17 16:37,459.782,974.0266,1344.7251,2596.8708,3209.9824,3514.8123,3748.6638,3856.8035,3116.1462,1518.9287,0,0,0,24340.7414,57.1722,64.8536,53.689,86.5964,1.9023,1.2,above,peak,2 8,24,3/2/17 16:38,655.2717,1939.9907,2200.8293,3129.333,3456.3955,3473.0332,3429.0225,3344.6067,2674.054,1353.512,0,0,0,25656.0485,48.5244,58.2009,46.6647,48.6968,1.9831,1.2,above,peak,2 8,25,3/2/17 16:39,827.7833,1939.3125,2715.7141,4738.104,5279.6597,4592.7036,3506.6926,2737.3135,1900.6089,820.9334,0,0,0,29058.8256,40.6469,49.9692,41.2187,36.5174,1.8611,1.2,above,peak,2 8,26,3/2/17 16:40,529.1522,1469.0845,1927.1377,3079.7949,3802.6506,3988.835,3727.2412,3160.2712,2182.3723,936.3726,0,0,0,24802.9122,48.2845,56.3511,46.5283,48.6968,1.8863,1.2,above,peak,2 8,27,3/2/17 16:41,368.4126,907.9209,1837.4633,3821.9875,5024.8726,5134.0825,4386.3198,3276.2415,1920.5269,583.341,0,0,0,27261.1685,47.2292,54.0805,46.3778,48.6968,1.7541,1.2,above,peak,2 8,28,3/2/17 16:42,432.3761,1032.3951,1301.6492,2252.6301,2715.5823,2825.0056,2784.8792,2675.2532,2140.9067,1117.8668,20.5035,0,0,19299.0478,52.2394,61.2536,49.9582,48.6968,1.9366,1.2,above,peak,2 8,29,3/2/17 16:43,454.4653,1008.4938,1290.7108,2263.3396,2644.5022,2663.1077,2597.1824,2538.9878,2024.6952,1008.7949,0,0,0,18494.2796,51.068,60.1914,49.0274,48.6968,1.9392,1.2,above,peak,2 8,30,3/2/17 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2/28/17,16:31:35,614,52.4,49.9,0.1,below,peak,1 2/28/17,16:32:35,632,52.4,50.1,0.1,below,peak,1 2/28/17,16:33:35,628,52.3,49.4,0.2,below,peak,1 2/28/17,16:34:35,627,52.5,49.7,0.2,below,peak,1 2/28/17,16:35:35,622,52.6,49.3,0.1,below,peak,1 2/28/17,16:36:35,618,52.6,48.6,0.1,below,peak,1 2/28/17,16:37:35,617,52.8,48.5,0.2,below,peak,1 2/28/17,16:38:35,598,52.6,47.5,0.1,below,peak,1 2/28/17,16:39:35,587,52.5,46.7,0.1,below,peak,1 2/28/17,16:40:35,597,52.6,47.5,0.2,below,peak,1 3/2/17,12:55:08,482,55.1,51.1,0.1,,,2 3/2/17,12:56:08,451,54.3,53.4,0,above,off peak,2 3/2/17,12:57:08,512,55.1,56.5,0,above,off peak,2 3/2/17,12:58:08,550,55.4,57.5,0,above,off peak,2 3/2/17,12:59:08,543,55.5,57,0,above,off peak,2 3/2/17,13:00:08,528,55.3,57.3,0,above,off peak,2 3/2/17,13:01:08,520,55.2,57.7,0,above,off peak,2 3/2/17,13:02:08,505,55.1,57.3,0,above,off peak,2 3/2/17,13:03:08,468,54.7,55.8,0,above,off peak,2 3/2/17,13:04:08,503,54.9,57.4,0,above,off peak,2 3/2/17,13:05:08,492,54.4,56.5,0,above,off 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3/2/17,16:41:38,585,55,57.2,0,above,peak,2 3/2/17,16:42:38,642,55.6,58.5,0.1,above,peak,2 3/2/17,16:43:38,657,55.9,58.5,0.1,above,peak,2 3/2/17,16:44:38,656,55.9,58.1,0.2,above,peak,2 3/2/17,16:45:38,654,56,57.8,0.1,,,2 3/2/17,16:46:38,651,55.9,57.8,0.3,,,2 3/2/17,16:47:38,646,56,57.9,0.1,,,2 3/2/17,16:48:38,606,54.9,57.5,0.1,,,2 3/2/17,16:53:35,625,54.7,61.1,0,,,2 3/2/17,16:54:35,640,55.1,61.5,0,,,2 3/2/17,16:55:35,667,55.6,61.3,0,below,peak,2 3/2/17,16:56:35,677,55.9,60.8,0,below,peak,2 3/2/17,16:57:35,628,55.4,59,0,below,peak,2 3/2/17,16:58:35,645,55.9,60,0,below,peak,2 3/2/17,16:59:35,633,55.9,58.9,0,below,peak,2 3/2/17,17:00:35,660,56,59.7,0.1,below,peak,2 3/2/17,17:01:35,698,56.1,59.7,0.1,below,peak,2 3/2/17,17:02:35,699,56.1,59.5,0.1,below,peak,2 3/2/17,17:03:35,673,56.1,60,0.1,below,peak,2 3/2/17,17:04:35,670,55.9,60.1,0,below,peak,2 3/2/17,17:05:35,639,55.2,58.7,0.1,below,peak,2 3/2/17,17:06:35,649,55.7,59.7,0.1,below,peak,2 3/2/17,17:07:35,653,55.7,59.6,0,below,peak,2 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-------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2017 eddiekasner 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /LightningTalk.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: 3 | slidy_presentation: 4 | keep_md: true 5 | 6 | incremental: true 7 | --- 8 | 9 | Dissertation, Thesis, or Project
with Knitr and Markdown 10 | ======================================================== 11 | 1. Motivation 12 | + Reproducibility 13 | + Integrate data analysis and report writing 14 | + Plain text! Focus on content not formatting (back end) 15 | 2. Toolkit 16 | + Reference manager (.bib file) 17 | + Citation style (.csl file) 18 | + R Studio (Knitr and Bookdown packages) 19 | 3. Making it work for you (example) 20 | + https://github.com/eddiekasner/example-dissertation 21 | 22 | Motivation 23 | ======================================================== 24 |
25 | 26 | ![](Images/Rosanna.png) 27 |
28 | 29 | Image source: [rosannavanhespenresearch.wordpress.com](https://rosannavanhespenresearch.wordpress.com/2016/02/03/writing-your-thesis-with-r-markdown-1-getting-started/) 30 | 31 | 32 | Toolkit 33 | ======================================================== 34 | * Reference manager that can export to BibTeX (.bib file) 35 | + BibTeX: Plain text tool and file format for processing lists of references (LaTeX documents) 36 | + Examples: [Zotero](https://libguides.mit.edu/ld.php?content_id=34248570), [Mendeley](http://guides.library.ubc.ca/bibtex/mendeley), [EndNote](https://www.rhizobia.co.nz/latex/convert), [Paperpile](http://forum.paperpile.com/t/how-to-export-a-document-and-citations-to-latex-and-bibtex/784) 37 | 38 | * Preferred citation style (.csl file) 39 | + Citation Style Language (.csl): XML-based language for formatting citations and bibliographies 40 | + Reference managers need descriptions of each citation style in language computer can understand 41 | + GitHub has a [repository of ~8500+ .csl files](https://github.com/citation-style-language/styles) 42 | + Example: [Council of Science Editors](https://writing.wisc.edu/Handbook/DocCSE.html) 43 | 44 | * R Studio 45 | + [Knitr package (Yihui Xie)](https://yihui.name/knitr/) 46 | + [Bookdown package (Yihui Xie)](https://bookdown.org/yihui/bookdown/) 47 | + YAML: An R Markdown file always has a formatting header ('front matter') written in [YAML syntax](https://en.wikipedia.org/wiki/YAML) 48 | 49 | References 50 | ======================================================== 51 | 52 | 64 | 65 |
66 | 67 | 1. Stack Overflow 68 | 2. Dr. Google 69 | 3. R Markdown & R Studio Resources 70 | + [R Studio Intro](http://rmarkdown.rstudio.com/lesson-1.html) 71 | + [Authoring Bibliographies and Citations](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) 72 | + [Knitr Package (Yihui Xie)](https://yihui.name/knitr/) 73 | + [Bookdown Package (Yihui Xie)](https://bookdown.org/yihui/bookdown/) 74 | 4. $\LaTeX$ ("Lay-tech" or "La-tech") 75 | + [LaTeX Wiki](https://en.wikipedia.org/wiki/LaTeX) 76 | + [LaTeX Website](https://www.latex-project.org/) 77 | 5. Managing References for LaTeX use (.bib files) 78 | + [Bibdesk (Apple-Mac)](http://bibdesk.sourceforge.net/) 79 | + [JabRef](http://www.jabref.org/) 80 | + [Others](https://tex.stackexchange.com/questions/9454/bibdesk-like-software-for-windows) 81 | 6. Citation Style Langauge Resources (.csl files) 82 | + [CSL Primer](http://docs.citationstyles.org/en/stable/primer.html) 83 | + [GitHub Repository](https://github.com/citation-style-language/styles) 84 | + [CSL Editor](http://editor.citationstyles.org/about/) 85 | 7. Example Thesis and Templates for Academic Manuscripts 86 | + [Rosanna's Research](https://rosannavanhespenresearch.wordpress.com/2016/02/03/writing-your-thesis-with-r-markdown-1-getting-started/) 87 | + [An R Markdown Template for Academic Manuscripts](http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/) 88 |
89 | -------------------------------------------------------------------------------- /LightningTalk.md: -------------------------------------------------------------------------------- 1 | 2 | Dissertation, Thesis, or Project
with Knitr and Markdown 3 | ======================================================== 4 | 1. Motivation 5 | + Reproducibility 6 | + Integrate data analysis and report writing 7 | + Plain text! Focus on content not formatting (back end) 8 | 2. Toolkit 9 | + Reference manager (.bib file) 10 | + Citation style (.csl file) 11 | + R Studio (Knitr and Bookdown packages) 12 | 3. Making it work for you (example) 13 | + https://github.com/eddiekasner/example-dissertation 14 | 15 | Motivation 16 | ======================================================== 17 |
18 | 19 | ![](Images/Rosanna.png) 20 |
21 | 22 | Image source: [rosannavanhespenresearch.wordpress.com](https://rosannavanhespenresearch.wordpress.com/2016/02/03/writing-your-thesis-with-r-markdown-1-getting-started/) 23 | 24 | 25 | Toolkit 26 | ======================================================== 27 | * Reference manager that can export to BibTeX (.bib file) 28 | + BibTeX: Plain text tool and file format for processing lists of references (LaTeX documents) 29 | + Examples: [Zotero](https://libguides.mit.edu/ld.php?content_id=34248570), [Mendeley](http://guides.library.ubc.ca/bibtex/mendeley), [EndNote](https://www.rhizobia.co.nz/latex/convert), [Paperpile](http://forum.paperpile.com/t/how-to-export-a-document-and-citations-to-latex-and-bibtex/784) 30 | 31 | * Preferred citation style (.csl file) 32 | + Citation Style Language (.csl): XML-based language for formatting citations and bibliographies 33 | + Reference managers need descriptions of each citation style in language computer can understand 34 | + GitHub has a [repository of ~8500+ .csl files](https://github.com/citation-style-language/styles) 35 | + Example: [Council of Science Editors](https://writing.wisc.edu/Handbook/DocCSE.html) 36 | 37 | * R Studio 38 | + [Knitr package (Yihui Xie)](https://yihui.name/knitr/) 39 | + [Bookdown package (Yihui Xie)](https://bookdown.org/yihui/bookdown/) 40 | + YAML: An R Markdown file always has a formatting header ('front matter') written in [YAML syntax](https://en.wikipedia.org/wiki/YAML) 41 | 42 | References 43 | ======================================================== 44 | 45 | 57 | 58 |
59 | 60 | 1. Stack Overflow 61 | 2. Dr. Google 62 | 3. R Markdown & R Studio Resources 63 | + [R Studio Intro](http://rmarkdown.rstudio.com/lesson-1.html) 64 | + [Authoring Bibliographies and Citations](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) 65 | + [Knitr Package (Yihui Xie)](https://yihui.name/knitr/) 66 | + [Bookdown Package (Yihui Xie)](https://bookdown.org/yihui/bookdown/) 67 | 4. $\LaTeX$ ("Lay-tech" or "La-tech") 68 | + [LaTeX Wiki](https://en.wikipedia.org/wiki/LaTeX) 69 | + [LaTeX Website](https://www.latex-project.org/) 70 | 5. Managing References for LaTeX use (.bib files) 71 | + [Bibdesk (Apple-Mac)](http://bibdesk.sourceforge.net/) 72 | + [JabRef](http://www.jabref.org/) 73 | + [Others](https://tex.stackexchange.com/questions/9454/bibdesk-like-software-for-windows) 74 | 6. Citation Style Langauge Resources (.csl files) 75 | + [CSL Primer](http://docs.citationstyles.org/en/stable/primer.html) 76 | + [GitHub Repository](https://github.com/citation-style-language/styles) 77 | + [CSL Editor](http://editor.citationstyles.org/about/) 78 | 7. Example Thesis and Templates for Academic Manuscripts 79 | + [Rosanna's Research](https://rosannavanhespenresearch.wordpress.com/2016/02/03/writing-your-thesis-with-r-markdown-1-getting-started/) 80 | + [An R Markdown Template for Academic Manuscripts](http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/) 81 |
82 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # example-dissertation 2 | 3 | This repo provides a template for anyone wanting to write a dissertation or thesis using R Markdown. It is a minimal example with dummy code and text to show how all of the elements come together to produce the final document, as specified by the University of Washington requirements. Here are the [slides from a "lightning talk"](LightningTalk.md) and a [video recording](https://youtu.be/AP_nU9jd0mk) that walks through the example. 4 | 5 | For more resources, please visit: 6 | 1. [Bookdown Package](https://bookdown.org/yihui/bookdown/) and [yihui's GitHub page](https://github.com/yihui) 7 | 2. [Rosanna's Research](https://rosannavanhespenresearch.wordpress.com/2016/02/03/writing-your-thesis-with-r-markdown-1-getting-started/) and [rosannav's GitHub page](https://github.com/rosannav) 8 | 9 | Dependencies: knitr, bookdown, pdf creator (TeX) 10 | 11 | Collaborators: [Brian High](https://github.com/brianhigh) 12 | 13 | [License](https://github.com/eddiekasner/example-dissertation/blob/master/LICENSE) 14 | -------------------------------------------------------------------------------- /council-of-science-editors.csl: -------------------------------------------------------------------------------- 1 | 2 | 268 | -------------------------------------------------------------------------------- /environmental-health-perspectives.csl: -------------------------------------------------------------------------------- 1 | 2 | 227 | -------------------------------------------------------------------------------- /example-dissertation.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | -------------------------------------------------------------------------------- /science-modified1.csl: -------------------------------------------------------------------------------- 1 | 2 | 246 | -------------------------------------------------------------------------------- /thesis-references.bib: -------------------------------------------------------------------------------- 1 | %% This BibTeX bibliography file was created using BibDesk. 2 | %% http://bibdesk.sourceforge.net/ 3 | 4 | 5 | %% Created for Eddie Kasner at 2017-11-16 15:28:21 -0800 6 | 7 | 8 | %% Saved with string encoding Unicode (UTF-8) 9 | 10 | 11 | 12 | @webpage{r-beeswarm, 13 | Author = {Eklund, Aron}, 14 | Date-Added = {2017-11-16 23:27:24 +0000}, 15 | Date-Modified = {2017-11-16 23:28:06 +0000}, 16 | Keywords = {Thesis}, 17 | Lastchecked = {September 23, 2017}, 18 | Note = {September 23, 2017}, 19 | Title = {{beeswarm}: The Bee Swarm Plot, an Alternative to Stripchart. R package version 0.2.3}, 20 | Url = {https://CRAN.R-project.org/package=beeswarm}, 21 | Year = {2016}, 22 | Bdsk-Url-1 = {https://CRAN.R-project.org/package=beeswarm}} 23 | 24 | @webpage{r-bookdown, 25 | Accessed = {September 23, 2017}, 26 | Author = {Xie, Yihui}, 27 | Date-Added = {2017-11-16 23:27:24 +0000}, 28 | Date-Modified = {2017-11-16 23:28:06 +0000}, 29 | Keywords = {Thesis}, 30 | Lastchecked = {September 23, 2017}, 31 | Note = {September 23, 2017}, 32 | Title = {{bookdown}: Authoring Books and Technical Documents with R Markdown. R package version 0.4}, 33 | Url = {https://bookdown.org/yihui/bookdown/}, 34 | Year = {2017}, 35 | Bdsk-Url-1 = {https://bookdown.org/yihui/bookdown/}} 36 | 37 | @webpage{r-core, 38 | Accessed = {September 23, 2017}, 39 | Author = {{R Core Team}}, 40 | Date-Added = {2017-11-16 23:27:24 +0000}, 41 | Date-Modified = {2017-11-16 23:28:06 +0000}, 42 | Keywords = {Thesis}, 43 | Lastchecked = {September 23, 2017}, 44 | Note = {September 23, 2017}, 45 | Title = {R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria}, 46 | Url = {https://www.R-project.org/}, 47 | Year = {2017}, 48 | Bdsk-Url-1 = {https://www.R-project.org/}} 49 | 50 | @webpage{r-ggplot, 51 | Accessed = {September 23, 2017}, 52 | Author = {Wickham, Hadley}, 53 | Date-Added = {2017-11-16 23:27:24 +0000}, 54 | Date-Modified = {2017-11-16 23:28:06 +0000}, 55 | Keywords = {Thesis}, 56 | Lastchecked = {September 23, 2017}, 57 | Note = {September 23}, 58 | Title = {{ggplot2}: Elegant Graphics for Data Analysis. Springer-Verlag New York}, 59 | Url = {http://ggplot2.org}, 60 | Year = {2009}, 61 | Bdsk-Url-1 = {http://ggplot2.org}} 62 | 63 | @webpage{r-ggthemes, 64 | Accessed = {September 23, 2017}, 65 | Author = {Arnold, Jeffrey B.}, 66 | Date-Added = {2017-11-16 23:27:24 +0000}, 67 | Date-Modified = {2017-11-16 23:28:06 +0000}, 68 | Keywords = {Thesis}, 69 | Lastchecked = {ggthemes: Extra Themes, Scales and Geoms for 'ggplot2'. R package version 3.4.0}, 70 | Note = {September 23, 2017}, 71 | Title = {{ggthemes}: Extra Themes, Scales and Geoms for 'ggplot2'. R package version 3.4.0}, 72 | Url = {https://CRAN.R-project.org/package=ggthemes}, 73 | Year = {2017}, 74 | Bdsk-Url-1 = {https://CRAN.R-project.org/package=ggthemes}} 75 | 76 | @webpage{r-gridExtra, 77 | Author = {Auguie, Baptiste}, 78 | Date-Added = {2017-11-16 23:27:24 +0000}, 79 | Date-Modified = {2017-11-16 23:28:06 +0000}, 80 | Keywords = {Thesis}, 81 | Lastchecked = {September 23, 2017}, 82 | Note = {September 23, 2017}, 83 | Title = {{gridExtra}: Miscellaneous Functions for "Grid" Graphics. R package version 2.2.1}, 84 | Url = {https://CRAN.R-project.org/package=gridExtra}, 85 | Year = {2016}, 86 | Bdsk-Url-1 = {https://CRAN.R-project.org/package=gridExtra}} 87 | 88 | @webpage{r-knitr, 89 | Accessed = {September 23, 2017}, 90 | Author = {Xie, Yihui}, 91 | Date-Added = {2017-11-16 23:27:24 +0000}, 92 | Date-Modified = {2017-11-16 23:28:06 +0000}, 93 | Keywords = {Thesis}, 94 | Lastchecked = {September 23, 2017}, 95 | Note = {September 23, 2017}, 96 | Title = {{knitr}: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.16}, 97 | Url = {https://yihui.name/knitr/}, 98 | Year = {2017}, 99 | Bdsk-Url-1 = {https://yihui.name/knitr/}} 100 | 101 | @webpage{r-lattice, 102 | Accessed = {September 23, 2017}, 103 | Author = {Sarkar, Deepayan}, 104 | Date-Added = {2017-11-16 23:27:24 +0000}, 105 | Date-Modified = {2017-11-16 23:28:06 +0000}, 106 | Keywords = {Thesis}, 107 | Lastchecked = {September 23, 2017}, 108 | Note = {September 23, 2017}, 109 | Title = {{lattice}: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5}, 110 | Url = {http://lmdvr.r-forge.r-project.org}, 111 | Year = {2008}, 112 | Bdsk-Url-1 = {http://lmdvr.r-forge.r-project.org}} 113 | 114 | @webpage{r-lme4, 115 | Accessed = {September 23, 2017}, 116 | Author = {Bates, Douglas and Maechler, Martin and Bolker, Ben and Walker, Steve}, 117 | Date-Added = {2017-11-16 23:27:24 +0000}, 118 | Date-Modified = {2017-11-16 23:28:06 +0000}, 119 | Keywords = {Thesis}, 120 | Lastchecked = {September 23, 2017}, 121 | Note = {September 23, 2017}, 122 | Title = {Fitting Linear Mixed-Effects Models Using {lme4}}, 123 | Url = {https://www.jstatsoft.org/article/view/v067i01/0}, 124 | Year = {2015}, 125 | Bdsk-Url-1 = {https://www.jstatsoft.org/article/view/v067i01/0}} 126 | 127 | @webpage{r-lubridate, 128 | Accessed = {September 23, 2017}, 129 | Author = {Grolemund, Garrett and Wickham, Hadley}, 130 | Date-Added = {2017-11-16 23:27:24 +0000}, 131 | Date-Modified = {2017-11-16 23:28:06 +0000}, 132 | Keywords = {Thesis}, 133 | Lastchecked = {September 23, 2017}, 134 | Note = {September 23, 2017}, 135 | Title = {Dates and Times Made Easy with {lubridate}. Journal of Statistical Software, 40(3), 1-25}, 136 | Url = {http://www.jstatsoft.org/v40/i03/}, 137 | Year = {2011}, 138 | Bdsk-Url-1 = {http://www.jstatsoft.org/v40/i03/}} 139 | 140 | @webpage{r-pander, 141 | Accessed = {September 23, 2017}, 142 | Author = {Dar{\'o}czi, Gergely and Tsegelskyi, Roman}, 143 | Date-Added = {2017-11-16 23:27:24 +0000}, 144 | Date-Modified = {2017-11-16 23:28:06 +0000}, 145 | Keywords = {Thesis}, 146 | Lastchecked = {September 23, 2017}, 147 | Note = {September 23, 2017}, 148 | Title = {{pander}: An R Pandoc Writer. R package version 0.6.0}, 149 | Url = {https://CRAN.R-project.org/package=pander}, 150 | Year = {2015}, 151 | Bdsk-Url-1 = {https://CRAN.R-project.org/package=pander}} 152 | 153 | @webpage{r-reshape, 154 | Accessed = {September 23, 2017}, 155 | Author = {Wickham, Hadley}, 156 | Date-Added = {2017-11-16 23:27:24 +0000}, 157 | Date-Modified = {2017-11-16 23:28:06 +0000}, 158 | Keywords = {Thesis}, 159 | Lastchecked = {September 23, 2017}, 160 | Note = {September 23, 2017}, 161 | Title = {Reshaping data with the {reshape} package. Journal of Statistical Software, 21(12)}, 162 | Url = {http://www.jstatsoft.org/v21/i12/paper}, 163 | Year = {2007}, 164 | Bdsk-Url-1 = {http://www.jstatsoft.org/v21/i12/paper}} 165 | 166 | @webpage{r-survival, 167 | Accessed = {September 23, 2017}, 168 | Author = {Therneau, T}, 169 | Date-Added = {2017-11-16 23:27:24 +0000}, 170 | Date-Modified = {2017-11-16 23:28:06 +0000}, 171 | Keywords = {Thesis}, 172 | Lastchecked = {September 23, 2017}, 173 | Note = {September 23, 2017}, 174 | Title = {{survival}: A Package for Survival Analysis in S. version 2.38}, 175 | Url = {https://CRAN.R-project.org/package=survival}, 176 | Year = {2015}, 177 | Bdsk-Url-1 = {https://CRAN.R-project.org/package=survival}} 178 | 179 | @webpage{lorem-ipsum-2017, 180 | Accessed = {November 16, 2017}, 181 | Author = {Cicero}, 182 | Date-Added = {2017-11-16 23:10:04 +0000}, 183 | Date-Modified = {2017-11-16 23:13:55 +0000}, 184 | Keywords = {Thesis}, 185 | Lastchecked = {November 16, 2017}, 186 | Note = {November 16}, 187 | Title = {Lorem Ipsum is placeholder text commonly used in the graphic, print, and publishing industries for previewing layouts and visual mockups.}, 188 | Url = {https://loremipsumgenerator.com/}, 189 | Year = {2017}, 190 | Bdsk-Url-1 = {https://loremipsumgenerator.com/}} 191 | 192 | @webpage{skc-iom, 193 | Author = {{SKC, Inc}}, 194 | Date-Added = {2017-04-22 06:59:32 +0000}, 195 | Date-Modified = {2017-11-14 08:32:35 +0000}, 196 | Keywords = {Thesis}, 197 | Lastchecked = {April 22, 2017}, 198 | Note = {April 22, 2017}, 199 | Title = {IOM Personal Samplers and IOM Samplers with MultiDust}, 200 | Url = {http://www.skcinc.com/catalog/pdf/instructions/37372.pdf}, 201 | Year = {Undated}, 202 | Bdsk-Url-1 = {http://www.skcinc.com/catalog/pdf/instructions/37372.pdf}} 203 | 204 | @webpage{icy-2017, 205 | Author = {Icy}, 206 | Date-Added = {2017-04-08 06:02:32 +0000}, 207 | Date-Modified = {2017-11-14 08:32:35 +0000}, 208 | Keywords = {Thesis}, 209 | Lastchecked = {April 7, 2017}, 210 | Note = {April 7, 2017}, 211 | Title = {Icy: an open community platform for bioimage informatics}, 212 | Url = {http://icy.bioimageanalysis.org/}, 213 | Year = {2017}, 214 | Bdsk-Url-1 = {http://icy.bioimageanalysis.org/}} 215 | 216 | @article{ramachandran-2005, 217 | Author = {Ramachandran, G}, 218 | Date-Modified = {2017-11-14 08:32:35 +0000}, 219 | Keywords = {Thesis}, 220 | Publisher = {Taylor \& Francis}, 221 | Title = {Occupational Exposure Assessment for Air Contaminants}, 222 | Year = 2005} 223 | --------------------------------------------------------------------------------