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tweak bib
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nhejazi committed Jul 6, 2023
1 parent c1beb14 commit 0f8b2c6
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6 changes: 3 additions & 3 deletions _output.yml
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
bookdown::bs4_book:
css: css/style.css
toc_depth: 5
config:
config:
toc:
collapse: section
edit:
link: https://github.com/tlverse/tlverse-handbook/edit/master/%s
text: "Edit"
text: "Edit"
sharing:
github: true
facebook: false
Expand All @@ -17,7 +17,7 @@ bookdown::bs4_book:
fg: "#2b2121"
bg: "#ffffff"
repo: https://github.com/tlverse/tlverse-handbook

bookdown::pdf_book:
latex_engine: pdflatex #xelatex
citation_package: natbib
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168 changes: 168 additions & 0 deletions biometrics.csl
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@@ -0,0 +1,168 @@
<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
<info>
<title>Biometrics</title>
<id>http://www.zotero.org/styles/biometrics</id>
<link href="http://www.zotero.org/styles/biometrics" rel="self"/>
<link href="http://www.biometrics.tibs.org/directions.html#references" rel="documentation"/>
<author>
<name>Sebastian Karcher</name>
</author>
<category citation-format="author-date"/>
<category field="social_science"/>
<issn>0006-341X</issn>
<eissn>1541-0420</eissn>
<updated>2013-09-27T22:18:36+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<macro name="editor-translator">
<names variable="editor translator" prefix="(" suffix=")" delimiter=", ">
<label form="short" suffix=" " strip-periods="true"/>
<name and="text" initialize-with="" delimiter=", "/>
</names>
</macro>
<macro name="author">
<names variable="author">
<name name-as-sort-order="all" and="text" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="never"/>
<label form="short" prefix=" (" suffix=")" strip-periods="true"/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
<text macro="title"/>
</substitute>
</names>
</macro>
<macro name="author-short">
<names variable="author">
<name form="short" and="text" delimiter=", " initialize-with=". " delimiter-precedes-last="never"/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<text variable="title" form="short" font-style="italic"/>
</if>
<else>
<text variable="title" form="short" quotes="true"/>
</else>
</choose>
</substitute>
</names>
</macro>
<macro name="title">
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
<text variable="title" font-style="italic" text-case="title"/>
</if>
<else>
<text variable="title"/>
</else>
</choose>
</macro>
<macro name="edition">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short" strip-periods="true"/>
</group>
</if>
<else>
<text variable="edition"/>
</else>
</choose>
</macro>
<macro name="publisher">
<group delimiter=", ">
<text variable="genre"/>
<text variable="publisher"/>
<text variable="publisher-place"/>
</group>
</macro>
<citation collapse="year-suffix" et-al-min="4" et-al-use-first="1" et-al-subsequent-min="3" et-al-subsequent-use-first="1" disambiguate-add-year-suffix="true">
<sort>
<key variable="issued"/>
<key variable="author"/>
</sort>
<layout prefix="(" suffix=")" delimiter="; ">
<group delimiter=", ">
<text macro="author-short"/>
<date variable="issued">
<date-part name="year"/>
</date>
<group>
<label variable="locator" form="short"/>
<text variable="locator" prefix=" "/>
</group>
</group>
</layout>
</citation>
<bibliography hanging-indent="true" et-al-min="7" et-al-use-first="6">
<sort>
<key macro="author-short"/>
<key variable="issued"/>
</sort>
<layout>
<text macro="author" suffix="."/>
<date variable="issued" prefix=" (" suffix=")">
<date-part name="year"/>
</date>
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
<group suffix=".">
<text macro="title" prefix=" "/>
<text macro="edition" prefix=", "/>
<text macro="editor-translator" prefix=" "/>
</group>
<text prefix=" " suffix="." macro="publisher"/>
</if>
<else-if type="chapter paper-conference" match="any">
<text macro="title" prefix=" "/>
<group prefix=".">
<group>
<text variable="container-title" font-style="italic" prefix=" "/>
<text variable="collection-title" prefix=" " suffix="."/>
<group suffix=".">
<text macro="edition" prefix=", "/>
<names variable="editor translator">
<label form="short" prefix=" (" suffix=" " strip-periods="true"/>
<name and="symbol" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="never" suffix="),"/>
</names>
<label variable="page" form="short" prefix=" " suffix=" "/>
<text variable="page" suffix="."/>
<text macro="publisher" prefix=" "/>
</group>
</group>
</group>
</else-if>
<else-if type="webpage">
<group prefix=" " delimiter=". ">
<text variable="title"/>
<text macro="publisher"/>
<group prefix="URL ">
<text variable="URL" suffix=" "/>
<date variable="accessed" prefix="[accessed " suffix="]" delimiter=" ">
<date-part name="day"/>
<date-part name="month"/>
<date-part name="year"/>
</date>
</group>
</group>
</else-if>
<else>
<group suffix=".">
<text macro="title" prefix=" "/>
<text macro="editor-translator" prefix=" "/>
</group>
<group prefix=" " suffix=".">
<text variable="container-title" font-style="italic"/>
<group prefix=", ">
<text variable="volume" font-weight="bold"/>
</group>
<text variable="page" prefix=", "/>
</group>
</else>
</choose>
</layout>
</bibliography>
</style>
40 changes: 19 additions & 21 deletions book.bib
Original file line number Diff line number Diff line change
Expand Up @@ -225,25 +225,23 @@ @incollection{cvtmle2010
}

@article{luedtke2016super,
Author = {Luedtke, Alex and {van der Laan}, Mark J},
Journal = {International Journal of Biostatistics},
Note = {PMID: 27227726},
Number = {1},
Pages = {305--332},
Title = {Super-learning of an optimal dynamic treatment rule},
Volume = {12},
title = {Super-learning of an optimal dynamic treatment rule},
author = {Luedtke, Alex and {van der Laan}, Mark J},
journal = {International Journal of Biostatistics},
volume = {12},
number = {1},
pages = {305--332},
year = {2016}
}

@article{vanderLaanLuedtke15,
Author = {{van der Laan}, Mark J and Luedtke, Alex},
Journal = {Journal of Causal Inference},
Note = {PMCID: PMC4517487},
Number = {1},
Pages = {61--95},
Title = {Targeted learning of the mean outcome under an optimal dynamic
title = {Targeted learning of the mean outcome under an optimal dynamic
treatment rule},
Volume = {3},
author = {{van der Laan}, Mark J and Luedtke, Alex},
journal = {Journal of Causal Inference},
volume = {3},
number = {1},
pages = {61--95},
year = {2015}
}

Expand Down Expand Up @@ -992,14 +990,14 @@ @article{leblanc1996combining
publisher={Taylor \& Francis}
}

@Article{bembom2007realistic,
Author={Bembom, Oliver and {van der Laan}, Mark J},
Title={A practical illustration of the importance of realistic
@article{bembom2007realistic,
author={Bembom, Oliver and {van der Laan}, Mark J},
title={A practical illustration of the importance of realistic
individualized treatment rules in causal inference},
Journal="Electronic Journal of Statistics",
year="2007",
Volume="1",
Pages="574--596"
journal="Electronic Journal of Statistics",
year="2007",
volume="1",
pages="574--596"
}

@article{montoya2021optimal,
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2 changes: 1 addition & 1 deletion index.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ lof: yes
fontsize: '12pt, krantz2'
monofontoptions: "Scale=0.7"
bibliography: [book.bib, packages.bib]
biblio-style: apalike
csl: biometrics.csl
link-citations: yes
colorlinks: yes
site: bookdown::bookdown_site
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1 change: 0 additions & 1 deletion latex_extras/preamble.tex
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@
\usepackage[inline]{enumitem}
\usepackage{float}
\usepackage{graphicx}
\usepackage[round]{natbib}
\usepackage{geometry}
\usepackage{tikz}
\usepackage[english]{babel}
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13 changes: 9 additions & 4 deletions packages.bib
Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,17 @@ @Manual{R-base
}

@Manual{R-bookdown,
title = {bookdown: Authoring Books and Technical Documents with R Markdown},
title = {bookdown: Authoring Books and Technical Documents with {R}
Markdown},
author = {Yihui Xie},
year = {2021},
note = {R package version 0.21.6},
url = {https://github.com/rstudio/bookdown},
}

@Manual{R-knitr,
title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
title = {knitr: A General-Purpose Package for Dynamic Report Generation in
R},
author = {Yihui Xie},
year = {2021},
note = {R package version 1.32},
Expand All @@ -25,14 +27,17 @@ @Manual{R-knitr

@Manual{R-rmarkdown,
title = {rmarkdown: Dynamic Documents for R},
author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi
and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and
Winston Chang and Richard Iannone},
year = {2021},
note = {R package version 2.7},
url = {https://CRAN.R-project.org/package=rmarkdown},
}

@Book{bookdown2016,
title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
title = {bookdown: Authoring Books and Technical Documents with {R}
Markdown},
author = {Yihui Xie},
publisher = {Chapman and Hall/CRC},
address = {Boca Raton, Florida},
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