{"id":18313022,"url":"https://github.com/zkamvar/dissertation","last_synced_at":"2026-02-07T07:01:40.903Z","repository":{"id":67409938,"uuid":"65860703","full_name":"zkamvar/dissertation","owner":"zkamvar","description":"Zhian Kamvar's Ph. 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Kamvar\n\n## Abstract\n\nResearch on the population genetics of microbial organisms requires the use of\nspecialized analyses designed for clonal organisms to avoid violating the\nassumptions of traditional population genetic models. The tools necessary for\nperforming these analyses existed as a set of unrelated software with \nnon-overlapping capabilities and did not cover all aspects of analysis. This\nmeant that researchers not only had to reshape their data into different formats\nfor each analysis, but they also had to switch computing platforms, thus\ncreating a drain in time, and increasing the risk of propagating human\nerror into the analysis. To address this problem, we created the software\npackage *poppr*, written in the R statistical language, available on all\ncomputing platforms. This package is designed for analysis of clonal, partially\nclonal, and sexual populations, empowering researchers to perform their work in\na reproducible manner. We additionally demonstrate the utility of *poppr* for\nboth plant pathological and theoretical questions by using real-world and\nsimulated data. In chapter 4, we apply these new tools to demonstrate evidence\nfor at least two origins for the outbreak of the Sudden Oak Death pathogen,\n*Phytophthora ramorum* in Curry County, Oregon. In chapter 5, we use *poppr* to\nassess the power of the index of association with clone-correction, showing that\nclone-correction has the potential to reduce the power of detecting clonal\nreproduction. All of the software and analyses in this work were performed in an\nopen and reproducible framework, serving as an example of the power of\nreproducible research in plant pathology.\n\n\n## Links\n\n - Web: https://zkamvar.github.io/dissertation \n - Scholars Archive at Oregon State University: http://hdl.handle.net/1957/60042\n\n----\n\n# Building the document\n\nThis was built with the unofficial Oregon State University RMarkdown thesis\ntemplate. You can find a copy of this template at\nhttps://github.com/zkamvar/beaverdown.\n\nThis should comply with the [thesis guide for Oregon State University][4]. It's\nbased off of the [overleaf template][5]\n\n## Installation\n\nTo install the template, be sure you have the following:\n\n - [pandoc][0]\n - [LaTeX][1]\n - [R \u003e= 3.3.0][2]\n - [RStudio][3] (optional, but it helps)\n\nOpen RStudio and run the following code:\n\n```r\nif (!require(\"beaverdown\")){\n  if (!require(\"devtools\") || packageVersion(\"devtools\") \u003c package_version(\"1.6\")){\n    install.packages(\"devtools\", repos = \"http://cran.rstudio.com\")\n  }\n  devtools::install_github(\"zkamvar/beaverdown\")\n}\ninstall.packages(\"poppr\")\n```\n\n## Rendering\n\n### HTML\n\nOpen `index.Rmd` in RStudio and then hit the \"knit\" button. Alternatively, you\ncan use:\n\n```r\n# In R\nbookdown::render_book(\"index.Rmd\")\n```\n\n```sh\n# In the Terminal\n$ ./render.sh\n# ----------------------------------------------------------------------\n# Rendering HTML\n# \n# If you want to render the PDF, set the pdf flag\n# \n#     ./render.sh pdf\n# ----------------------------------------------------------------------\n# \n# \n# \n# processing file: thesis.Rmd\n#   |.................................................................| 100%\n#    inline R code fragments\n# \n# \n# output file: thesis.knit.md\n# \n# /usr/local/bin/pandoc +RTS -K512m -RTS thesis.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output thesis.html --smart --email-obfuscation none --standalone --section-divs --table-of-contents --toc-depth 3 --template /Users/zhian/R/bookdown/templates/gitbook.html --number-sections --include-in-header /var/folders/qd/dpdhfsz12wb3c7wz0xdm6dbm0000gn/T//Rtmpyw5Xnp/rmarkdown-strd456e0723e9.html --mathjax --highlight-style pygments --bibliography bib/fronteirs_citations.bib --bibliography bib/main_bibliography.bib --filter /usr/local/bin/pandoc-citeproc\n# \n# Output created: _book/1-introduction.html\n```\n\nYou can view the rendered html document by typing (in osx):\n\n```sh\nopen _book/1-introduction.html\n```\n\n### PDF\n\n```sh\n# On the command line\n./render.sh pdf\n```\n\n```r\n# In R, make sure to edit index.Rmd to beaverdown::thesis_pdf\nbookdown::render_book(\"index.Rmd\")\n```\n\nYou can find the dissertation in [**_book/dissertation.pdf**](_book/dissertation.pdf)\n\n## Components\n\n### [_bookdown.yml](_bookdown.yml)\n\nThis is the main configuration file for the dissertation. \n\n### [index.Rmd](index.Rmd)\n\nThis file contains all the meta information that goes at the beginning of the pdf\ndocument.\n\n### [pre/](pre/)\n\nThis folder contains all of the Rmd files to be included in the pretext of the\ndissertation (e.g. abstract, acknowledgments, author contributions, etc.).\n\nThere is a slight caveat to all of these files: the very first line must be \nplain text or the rendering will be screwed up.\n\n### [chapters/](chapters/)\n\nThis folder contains the Rmd files for each chapter in the dissertation. \n\n### [bib/](bib/)\n\nThis is where any bibliographies may live\n\n### [csl/](csl/)\n\nSpecific style files for bibliographies should be stored here. A good source for\ncitation styles is https://github.com/citation-style-language/styles#readme\n\n### [figure/](figure/) and [data/](data/)\n\nThese should be self explanatory. Figures and data are stored here.\n\n\n [0]: http://pandoc.org/\n [1]: https://www.latex-project.org/get/\n [2]: https://r-project.org\n [3]: https://rstudio.org\n [4]: http://gradschool.oregonstate.edu/progress/thesis-guide\n [5]: https://www.overleaf.com/latex/templates/oregon-state-university-thesis-and-dissertation/wnvzcdhqshxf\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzkamvar%2Fdissertation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzkamvar%2Fdissertation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzkamvar%2Fdissertation/lists"}