diff --git a/_variables.yml b/_variables.yml
index bdec965..8010c16 100644
--- a/_variables.yml
+++ b/_variables.yml
@@ -10,6 +10,7 @@
 dissertation:
   doi: ""
   github: https://github.com/bbartholdy/endgame
+  version: "![GitHub release (with filter)](https://img.shields.io/github/v/release/bbartholdy/endgame)"
 
 intro: 
   version: "![Current version](https://img.shields.io/badge/Version-v2-blue)"
diff --git a/endgame.tex b/endgame.tex
index 3c1a39e..30b12c0 100644
--- a/endgame.tex
+++ b/endgame.tex
@@ -101,6 +101,7 @@
 \newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{\strut#1\strut}}
 \newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
 \usepackage{booktabs}
+\usepackage{emptypage}
 \usepackage{amsthm}
 \makeatletter
 \def\thm@space@setup{%
@@ -109,10 +110,52 @@
 }
 \makeatother
 
+
+\makeatletter
+\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
+\begingroup
+\mbox{}
+\vspace*{\fill}
+\begin{center}
+\textit{This page is unintentionally left blank.}
+\end{center}
+\vspace{\fill}
+\thispagestyle{empty}
+\newpage
+\if@twocolumn\mbox{}\newpage\fi
+\endgroup\fi\fi}
+\makeatother
+
+
 %% Chapter formatting
 
-%Options: Sonny, Lenny, Glenn, Conny, Rejne, Bjarne, Bjornstrup
-%\usepackage[Lenny]{fncychap}
+
+%\def\fourtytwo{"All right," said Deep Thought. "The Answer to the Great Question..."\\
+%"Yes..!"\\
+%"Of Life, the Universe and Everything..." said Deep Thought.\\
+%"Yes...!"\\
+%"Is..." said Deep Thought, and paused.\\
+%"Yes...!"\\
+%"Is..."\\
+%"Yes...!!!...?"\\
+%"Forty-two," said Deep Thought, with infinite majesty and calm.}
+\def\fourtytwo{"How many roads must a man walk down?"}
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+\fancyhf{} % clear existing header/footer entries
+% Place Page X of Y on the right-hand
+% side of the footer
+%\fancyhead[LE]{\ifnum\value{page} = 42
+  %\huge\bfseries{\thepage}\else\thepage\fi}
+%\fancyhead[LE]{\ifnum\value{page} = 42
+%  \footnotesize\bfseries{\fourtytwo}\else\thepage\fi}
+%\fancyfoot[L]{\ifnum\value{page} = 42
+%\scriptsize\fourtytwo\fi}
+\fancyhead[LE]{\ifnum\value{page} = 42
+\textit\fourtytwo\else\thepage\enspace\MakeLowercase{\textsl{\leftmark}}\fi}
+\fancyhead[RO]{\MakeLowercase{\textsl{\rightmark}}\enspace\thepage}
+\renewcommand{\headrulewidth}{0pt}
+\renewcommand{\footrulewidth}{0pt}
 
 \usepackage{titlesec, blindtext, color} % titlesec needs `pandoc --variable subparagraph` to work
 \definecolor{gray75}{gray}{0.75}
@@ -120,11 +163,13 @@
 \titleformat{\chapter}[hang]{\Huge\bfseries}{\thechapter\hsp\textcolor{gray75}{|}\hsp}{0pt}{\Huge\bfseries}
 
 % chapter and section names in header
-\renewcommand{\chaptermark}[1]{\markboth{\MakeLowercase{\chaptername\ \thechapter\ -\ #1}}{}}
-\renewcommand*{\chaptermark}[1]{\markboth{\MakeLowercase{\chaptername\ \thechapter\ -\ #1}}{}}
+%\renewcommand{\chaptermark}[1]{\markboth{\MakeLowercase{\chaptername\_\thechapter\ <-\ #1}}{}}
+%\renewcommand{\chaptermark}[1]{\markboth{\MakeLowercase{\chaptername\_\thechapter\ <-\ #1}}{}}
+\renewcommand{\chaptermark}[1]{\markboth{\MakeLowercase{#1}}{}}
+\renewcommand{\chaptermark}[1]{\markboth{\MakeLowercase{#1}}{}}
 \renewcommand{\sectionmark}[1]{\markright{\MakeLowercase{#1}}{} }
 
-% fix header names for toc, lof, and lot
+% fix header names for toc, lof, and lot to match chapter and section names
 \usepackage{etoolbox}
 \patchcmd{\tableofcontents}{\MakeUppercase\contentsname}{\MakeLowercase\contentsname}{}{} 
 \patchcmd{\tableofcontents}{\MakeUppercase\contentsname}{\MakeLowercase\contentsname}{}{} % twice to remove on both sides of header
@@ -134,7 +179,6 @@
 \patchcmd{\listoftables}{\MakeUppercase\listtablename}{\MakeLowercase\listtablename}{}{} % twice to remove on both sides of header
 
 
-
 % modify captions for figures and tables
 \usepackage[labelfont=bf,
     labelsep=endash,
@@ -309,7 +353,8 @@
 Research Council under the European Union's Horizon 2020 research and
 innovation program, grant agreement number STG--677576
 (``HARVEST''). \\[0.4cm] 
-\textbf{Print version:} \href{https://doi.org/}{2024.04.0}
+\textbf{Print version:} \href{https://doi.org/10.5281/zenodo.11077009}{2024.04.1} \\[0.4cm] 
+ \textbf{Printed by:} Gildeprint \\[0.4cm] 
 \end{flushleft}
 \endgroup
 %% End: promotor and committee page %%
@@ -317,6 +362,15 @@
 \frontmatter
 %%%\maketitle
 %
+\clearpage
+\thispagestyle{empty}
+\vspace*{\fill}
+\vspace*{3cm}
+\hfill\textit{En bar røv at trutte i}
+\par
+\hfill\vspace*{4cm} Jan Bartholdy
+\vspace*{\fill}
+
 \renewcommand*\contentsname{Table of contents}
 {
 \setcounter{tocdepth}{2}
@@ -471,17 +525,9 @@ \chapter*{Open Science Statement}
 Science Framework (\href{https://doi.org/10.17605/OSF.IO/3YX8M}{DOI:
 10.17605/OSF.IO/3YX8M}).
 
+\begin{center}
 \includegraphics[width=1.04167in,height=\textheight]{figures/osf-qr.png}
-
-\clearpage
-\thispagestyle{empty}
-\vspace*{3cm}
-
-\hfill\textit{En bar røv at trutte i}
-
-\par
-
-\hfill\vspace*{4cm} Jan Bartholdy \vspace*{\fill}
+\end{center}
 
 \bookmarksetup{startatroot}
 
@@ -9192,10 +9238,10 @@ \section*{References cited}\label{references-cited-5}
 \phantomsection\label{supplementary-information}
 \bookmarksetup{startatroot}
 
-\chapter*{Supplementary information}
-\addcontentsline{toc}{chapter}{Supplementary information}
+\chapter*{Supplementary Information}
+\addcontentsline{toc}{chapter}{Supplementary Information}
 
-\markboth{Supplementary information}{Supplementary information}
+\markboth{Supplementary Information}{Supplementary Information}
 
 This dissertation contains a lot of supplementary materials. Therefore,
 none of it is included in the dissertation itself. I will instead
diff --git a/renv.lock b/renv.lock
index 5e0a5bc..77b2b62 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1,6 +1,6 @@
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-    "Version": "4.3.2",
+    "Version": "4.4.0",
     "Repositories": [
       {
         "Name": "BioCsoft",
@@ -29,7 +29,7 @@
     ]
   },
   "Bioconductor": {
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+    "Version": "3.19"
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     "ANCOMBC": {
@@ -73,31 +73,34 @@
     },
     "Biobase": {
       "Package": "Biobase",
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+      "Version": "2.64.0",
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+      "Hash": "9bc4cabd3bfda461409172213d932813"
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       "Package": "BiocBaseUtils",
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+      "Version": "1.6.0",
       "Source": "Bioconductor",
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       "Requirements": [
         "R",
         "methods",
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+      "Hash": "7fcaec00d8feb85919c022d9e4237133"
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       "Package": "BiocGenerics",
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+      "Version": "0.50.0",
       "Source": "Bioconductor",
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         "graphics",
@@ -105,7 +108,7 @@
         "stats",
         "utils"
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+      "Hash": "ef32d07aafdd12f24c5827374ae3590d"
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@@ -119,9 +122,9 @@
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       "Package": "BiocNeighbors",
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+      "Version": "1.22.0",
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+      "Repository": "Bioconductor 3.19",
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@@ -131,12 +134,13 @@
         "methods",
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+      "Hash": "da9f332c88453734623406dcca13ee03"
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       "Package": "BiocParallel",
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+      "Version": "1.38.0",
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         "R",
@@ -149,12 +153,13 @@
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+      "Hash": "7b6e79f86e3d1c23f62c5e2052e848d4"
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     "BiocSingular": {
       "Package": "BiocSingular",
-      "Version": "1.18.0",
+      "Version": "1.20.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "BiocParallel",
@@ -169,22 +174,23 @@
         "rsvd",
         "utils"
       ],
-      "Hash": "bed2b7ea3b0b0b31387d1d80286abb97"
+      "Hash": "9d2e9fbd803f4eddfeb307b1ee376aad"
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     "BiocVersion": {
       "Package": "BiocVersion",
-      "Version": "3.18.1",
+      "Version": "3.19.1",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "R"
       ],
-      "Hash": "2ecaed86684f5fae76ed5530f9d29c4a"
+      "Hash": "b892e27fc9659a4c8f8787d34c37b8b2"
     },
     "Biostrings": {
       "Package": "Biostrings",
-      "Version": "2.70.2",
+      "Version": "2.72.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "GenomeInfoDb",
@@ -194,12 +200,11 @@
         "XVector",
         "crayon",
         "grDevices",
-        "graphics",
         "methods",
         "stats",
         "utils"
       ],
-      "Hash": "b7cc779ab741dce3ad1b419ada1564c9"
+      "Hash": "48618c7c7b90b503837824ebcfee6363"
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     "CVXR": {
       "Package": "CVXR",
@@ -237,32 +242,31 @@
     },
     "DBI": {
       "Package": "DBI",
-      "Version": "1.2.1",
+      "Version": "1.2.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "9b4993e98e0e19da84c168460c032fef"
+      "Hash": "164809cd72e1d5160b4cb3aa57f510fe"
     },
     "DECIPHER": {
       "Package": "DECIPHER",
-      "Version": "2.30.0",
+      "Version": "3.0.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "Biostrings",
         "DBI",
         "IRanges",
         "R",
-        "RSQLite",
         "S4Vectors",
         "XVector",
         "methods",
-        "parallel",
         "stats"
       ],
-      "Hash": "ed6ffca930dbb0fc6510411bab734787"
+      "Hash": "d11d136f8ca6ede1ecfa471e35f3195f"
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       "Package": "DEoptimR",
@@ -276,8 +280,9 @@
     },
     "DelayedArray": {
       "Package": "DelayedArray",
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+      "Version": "0.30.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
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         "IRanges",
@@ -291,12 +296,13 @@
         "stats",
         "stats4"
       ],
-      "Hash": "0e5c84e543a3d04ce64c6f60ed46d7eb"
+      "Hash": "9141899d1bb4ce53e036810eb217721f"
     },
     "DelayedMatrixStats": {
       "Package": "DelayedMatrixStats",
-      "Version": "1.24.0",
+      "Version": "1.26.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
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         "IRanges",
@@ -306,7 +312,7 @@
         "methods",
         "sparseMatrixStats"
       ],
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+      "Hash": "5d9536664ccddb0eaa68a90afe4ee76e"
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       "Package": "DescTools",
@@ -339,8 +345,9 @@
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+      "Version": "1.46.0",
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@@ -348,7 +355,7 @@
         "methods",
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+      "Hash": "220a1c460ab5a750477fb5431e192abd"
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@@ -397,36 +404,37 @@
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+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "GenomeInfoDbData",
         "IRanges",
         "R",
-        "RCurl",
         "S4Vectors",
+        "UCSC.utils",
         "methods",
         "stats",
         "stats4",
         "utils"
       ],
-      "Hash": "7575d02551088d69cfcbf65a3a6f0b08"
+      "Hash": "614124bc9fb80d222cfa0d2e3e76c339"
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       "Source": "Bioconductor",
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+      "Version": "1.56.0",
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+      "Repository": "Bioconductor 3.19",
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@@ -439,15 +447,16 @@
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+      "Version": "5.1-2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "Formula",
+        "R",
         "base64enc",
         "cluster",
         "colorspace",
@@ -466,12 +475,13 @@
         "rpart",
         "viridis"
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+      "Version": "2.38.0",
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@@ -481,11 +491,11 @@
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@@ -496,7 +506,7 @@
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@@ -517,18 +527,20 @@
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+      "Version": "1.16.0",
       "Source": "Bioconductor",
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@@ -544,7 +556,7 @@
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@@ -566,37 +578,6 @@
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@@ -708,13 +689,13 @@
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@@ -756,13 +738,13 @@
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@@ -771,24 +753,26 @@
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@@ -799,13 +783,13 @@
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       "Requirements": [
         "systemfonts",
         "textshaping"
       ],
-      "Hash": "90a1b8b7e518d7f90480d56453b4d062"
+      "Hash": "082e1a198e3329d571f4448ef0ede4bc"
     },
     "rappdirs": {
       "Package": "rappdirs",
@@ -3123,11 +3107,11 @@
       "Version": "0.0.0.9000",
       "Source": "GitHub",
       "RemoteType": "github",
+      "RemoteHost": "api.github.com",
       "RemoteUsername": "paleolimbot",
       "RemoteRepo": "rbbt",
       "RemoteRef": "master",
       "RemoteSha": "ec1ebe1e9b7e60bc4523e6cb2ca47f73a9cbfba3",
-      "RemoteHost": "api.github.com",
       "Requirements": [
         "R",
         "clipr",
@@ -3232,7 +3216,7 @@
     },
     "remotes": {
       "Package": "remotes",
-      "Version": "2.4.2.1",
+      "Version": "2.5.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3242,17 +3226,17 @@
         "tools",
         "utils"
       ],
-      "Hash": "63d15047eb239f95160112bcadc4fcb9"
+      "Hash": "3ee025083e66f18db6cf27b56e23e141"
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.3",
+      "Version": "1.0.7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "utils"
       ],
-      "Hash": "41b847654f567341725473431dd0d5ab"
+      "Hash": "397b7b2a265bc5a7a06852524dabae20"
     },
     "reshape2": {
       "Package": "reshape2",
@@ -3269,26 +3253,26 @@
     },
     "rhdf5": {
       "Package": "rhdf5",
-      "Version": "2.46.1",
+      "Version": "2.48.0",
       "Source": "Bioconductor",
-      "Repository": "Bioconductor 3.18",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "R",
         "Rhdf5lib",
-        "S4Vectors",
         "methods",
         "rhdf5filters"
       ],
-      "Hash": "b0a244022c3427cd8213c33804c6b5de"
+      "Hash": "74d8c5aeb96d090ce8efc9ffd16afa2b"
     },
     "rhdf5filters": {
       "Package": "rhdf5filters",
-      "Version": "1.14.1",
+      "Version": "1.16.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "Rhdf5lib"
       ],
-      "Hash": "d27a2f6a89def6388fad5b0aae026220"
+      "Hash": "99e15369f8fb17dc188377234de13fc6"
     },
     "rlang": {
       "Package": "rlang",
@@ -3303,7 +3287,7 @@
     },
     "rmarkdown": {
       "Package": "rmarkdown",
-      "Version": "2.25",
+      "Version": "2.26",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3316,14 +3300,13 @@
         "jsonlite",
         "knitr",
         "methods",
-        "stringr",
         "tinytex",
         "tools",
         "utils",
         "xfun",
         "yaml"
       ],
-      "Hash": "d65e35823c817f09f4de424fcdfa812a"
+      "Hash": "9b148e7f95d33aac01f31282d49e4f44"
     },
     "rngtools": {
       "Package": "rngtools",
@@ -3419,10 +3402,10 @@
     },
     "rstudioapi": {
       "Package": "rstudioapi",
-      "Version": "0.15.0",
+      "Version": "0.16.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "5564500e25cffad9e22244ced1379887"
+      "Hash": "96710351d642b70e8f02ddeb237c46a7"
     },
     "rsvd": {
       "Package": "rsvd",
@@ -3462,7 +3445,7 @@
     },
     "sass": {
       "Package": "sass",
-      "Version": "0.4.8",
+      "Version": "0.4.9",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3472,7 +3455,7 @@
         "rappdirs",
         "rlang"
       ],
-      "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035"
+      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
     },
     "scales": {
       "Package": "scales",
@@ -3496,8 +3479,9 @@
     },
     "scater": {
       "Package": "scater",
-      "Version": "1.30.1",
+      "Version": "1.32.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "BiocNeighbors",
@@ -3526,7 +3510,7 @@
         "uwot",
         "viridis"
       ],
-      "Hash": "d92b4aa892e1f28148ce3ecad8e63cfb"
+      "Hash": "4a6eb8ab8a2b926fe67cf83aa731a3df"
     },
     "scs": {
       "Package": "scs",
@@ -3540,8 +3524,9 @@
     },
     "scuttle": {
       "Package": "scuttle",
-      "Version": "1.12.0",
+      "Version": "1.14.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "BiocGenerics",
         "BiocParallel",
@@ -3558,7 +3543,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "1412c4b6dfd8de528e1101e493e66a02"
+      "Hash": "6d94b72071aefd6e8b041c34ee83ebd0"
     },
     "sessioninfo": {
       "Package": "sessioninfo",
@@ -3575,7 +3560,7 @@
     },
     "shiny": {
       "Package": "shiny",
-      "Version": "1.8.0",
+      "Version": "1.8.1.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3585,7 +3570,6 @@
         "cachem",
         "commonmark",
         "crayon",
-        "ellipsis",
         "fastmap",
         "fontawesome",
         "glue",
@@ -3605,7 +3589,7 @@
         "withr",
         "xtable"
       ],
-      "Hash": "3a1f41807d648a908e3c7f0334bf85e6"
+      "Hash": "54b26646816af9960a4c64d8ceec75d6"
     },
     "sitmo": {
       "Package": "sitmo",
@@ -3641,7 +3625,7 @@
     },
     "sp": {
       "Package": "sp",
-      "Version": "2.1-3",
+      "Version": "2.1-4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3654,12 +3638,13 @@
         "stats",
         "utils"
       ],
-      "Hash": "1a0cc0cec2915700e63fd0921085cf6a"
+      "Hash": "75940133cca2e339afce15a586f85b11"
     },
     "sparseMatrixStats": {
       "Package": "sparseMatrixStats",
-      "Version": "1.14.0",
+      "Version": "1.16.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "Matrix",
         "MatrixGenerics",
@@ -3667,7 +3652,7 @@
         "matrixStats",
         "methods"
       ],
-      "Hash": "49383d0f6c6152ff7cb594f254c23cc8"
+      "Hash": "7e500a5a527460ca0406473bdcade286"
     },
     "stringi": {
       "Package": "stringi",
@@ -3701,7 +3686,7 @@
     },
     "survival": {
       "Package": "survival",
-      "Version": "3.5-7",
+      "Version": "3.5-8",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3713,7 +3698,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "b8e943d262c3da0b0febd3e04517c197"
+      "Hash": "184d7799bca4ba8c3be72ea396f4b9a3"
     },
     "svglite": {
       "Package": "svglite",
@@ -3736,14 +3721,14 @@
     },
     "systemfonts": {
       "Package": "systemfonts",
-      "Version": "1.0.5",
+      "Version": "1.0.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "cpp11"
       ],
-      "Hash": "15b594369e70b975ba9f064295983499"
+      "Hash": "6d538cff441f0f1f36db2209ac7495ac"
     },
     "tensorA": {
       "Package": "tensorA",
@@ -3758,7 +3743,7 @@
     },
     "testthat": {
       "Package": "testthat",
-      "Version": "3.2.1",
+      "Version": "3.2.1.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3783,7 +3768,7 @@
         "waldo",
         "withr"
       ],
-      "Hash": "4767a686ebe986e6cb01d075b3f09729"
+      "Hash": "3f6e7e5e2220856ff865e4834766bf2b"
     },
     "textshaping": {
       "Package": "textshaping",
@@ -3841,7 +3826,7 @@
     },
     "tidyselect": {
       "Package": "tidyselect",
-      "Version": "1.2.0",
+      "Version": "1.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3853,7 +3838,7 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "79540e5fcd9e0435af547d885f184fd5"
+      "Hash": "829f27b9c4919c16b593794a6344d6c0"
     },
     "tidytree": {
       "Package": "tidytree",
@@ -3879,18 +3864,19 @@
     },
     "tinytex": {
       "Package": "tinytex",
-      "Version": "0.49",
+      "Version": "0.50",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "xfun"
       ],
-      "Hash": "5ac22900ae0f386e54f1c307eca7d843"
+      "Hash": "be7a76845222ad20adb761f462eed3ea"
     },
     "treeio": {
       "Package": "treeio",
-      "Version": "1.26.0",
+      "Version": "1.28.0",
       "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
       "Requirements": [
         "R",
         "ape",
@@ -3902,9 +3888,10 @@
         "stats",
         "tibble",
         "tidytree",
-        "utils"
+        "utils",
+        "yulab.utils"
       ],
-      "Hash": "a09203806aa0bc49965563ca7016620e"
+      "Hash": "9e0a0b700763836cd36cb3a49be5a15d"
     },
     "tzdb": {
       "Package": "tzdb",
@@ -3933,7 +3920,7 @@
     },
     "usethis": {
       "Package": "usethis",
-      "Version": "2.2.2",
+      "Version": "2.2.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -3960,7 +3947,7 @@
         "withr",
         "yaml"
       ],
-      "Hash": "60e51f0b94d0324dc19e44110098fa9f"
+      "Hash": "d524fd42c517035027f866064417d7e6"
     },
     "utf8": {
       "Package": "utf8",
@@ -3974,12 +3961,13 @@
     },
     "uwot": {
       "Package": "uwot",
-      "Version": "0.1.16",
+      "Version": "0.2.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "FNN",
         "Matrix",
+        "RSpectra",
         "Rcpp",
         "RcppAnnoy",
         "RcppProgress",
@@ -3987,7 +3975,7 @@
         "irlba",
         "methods"
       ],
-      "Hash": "252deaa1c1d6d3da6946694243781ea3"
+      "Hash": "f693a0ca6d34b02eb432326388021805"
     },
     "vctrs": {
       "Package": "vctrs",
@@ -4118,14 +4106,15 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.41",
+      "Version": "0.43",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
+        "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "460a5e0fe46a80ef87424ad216028014"
+      "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e"
     },
     "xml2": {
       "Package": "xml2",
@@ -4142,14 +4131,14 @@
     },
     "xopen": {
       "Package": "xopen",
-      "Version": "1.0.0",
+      "Version": "1.0.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "processx"
       ],
-      "Hash": "6c85f015dee9cc7710ddd20f86881f58"
+      "Hash": "423df1e86d5533fcb73c6b02b4923b49"
     },
     "xtable": {
       "Package": "xtable",
@@ -4196,9 +4185,10 @@
     },
     "zlibbioc": {
       "Package": "zlibbioc",
-      "Version": "1.48.0",
+      "Version": "1.50.0",
       "Source": "Bioconductor",
-      "Hash": "50ad6f7b0baaaccf1a387d2f1ecce911"
+      "Repository": "Bioconductor 3.19",
+      "Hash": "3db02e3c460e1c852365df117a2b441b"
     },
     "zoo": {
       "Package": "zoo",
diff --git a/renv/activate.R b/renv/activate.R
index cb5401f..d13f993 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,11 +2,13 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.3"
+  version <- "1.0.7"
   attr(version, "sha") <- NULL
 
   # the project directory
-  project <- getwd()
+  project <- Sys.getenv("RENV_PROJECT")
+  if (!nzchar(project))
+    project <- getwd()
 
   # use start-up diagnostics if enabled
   diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
@@ -31,6 +33,14 @@ local({
     if (!is.null(override))
       return(override)
 
+    # if we're being run in a context where R_LIBS is already set,
+    # don't load -- presumably we're being run as a sub-process and
+    # the parent process has already set up library paths for us
+    rcmd <- Sys.getenv("R_CMD", unset = NA)
+    rlibs <- Sys.getenv("R_LIBS", unset = NA)
+    if (!is.na(rlibs) && !is.na(rcmd))
+      return(FALSE)
+
     # next, check environment variables
     # TODO: prefer using the configuration one in the future
     envvars <- c(
@@ -50,9 +60,22 @@ local({
 
   })
 
-  if (!enabled)
+  # bail if we're not enabled
+  if (!enabled) {
+
+    # if we're not enabled, we might still need to manually load
+    # the user profile here
+    profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
+    if (file.exists(profile)) {
+      cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
+      if (tolower(cfg) %in% c("true", "t", "1"))
+        sys.source(profile, envir = globalenv())
+    }
+
     return(FALSE)
 
+  }
+
   # avoid recursion
   if (identical(getOption("renv.autoloader.running"), TRUE)) {
     warning("ignoring recursive attempt to run renv autoloader")
@@ -108,6 +131,21 @@ local({
   
   }
   
+  heredoc <- function(text, leave = 0) {
+  
+    # remove leading, trailing whitespace
+    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+  
+    # split into lines
+    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+  
+    # compute common indent
+    indent <- regexpr("[^[:space:]]", lines)
+    common <- min(setdiff(indent, -1L)) - leave
+    paste(substring(lines, common), collapse = "\n")
+  
+  }
+  
   startswith <- function(string, prefix) {
     substring(string, 1, nchar(prefix)) == prefix
   }
@@ -610,6 +648,9 @@ local({
   
     # if the user has requested an automatic prefix, generate it
     auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (is.na(auto) && getRversion() >= "4.4.0")
+      auto <- "TRUE"
+  
     if (auto %in% c("TRUE", "True", "true", "1"))
       return(renv_bootstrap_platform_prefix_auto())
   
@@ -801,24 +842,23 @@ local({
   
     # the loaded version of renv doesn't match the requested version;
     # give the user instructions on how to proceed
-    remote <- if (!is.null(description[["RemoteSha"]])) {
+    dev <- identical(description[["RemoteType"]], "github")
+    remote <- if (dev)
       paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
-    } else {
+    else
       paste("renv", description[["Version"]], sep = "@")
-    }
   
     # display both loaded version + sha if available
     friendly <- renv_bootstrap_version_friendly(
       version = description[["Version"]],
-      sha     = description[["RemoteSha"]]
+      sha     = if (dev) description[["RemoteSha"]]
     )
   
-    fmt <- paste(
-      "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
-      "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
-      "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
-      sep = "\n"
-    )
+    fmt <- heredoc("
+      renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+      - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+      - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+    ")
     catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
   
     FALSE
@@ -1041,7 +1081,7 @@ local({
     # if jsonlite is loaded, use that instead
     if ("jsonlite" %in% loadedNamespaces()) {
   
-      json <- catch(renv_json_read_jsonlite(file, text))
+      json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
       if (!inherits(json, "error"))
         return(json)
   
@@ -1050,7 +1090,7 @@ local({
     }
   
     # otherwise, fall back to the default JSON reader
-    json <- catch(renv_json_read_default(file, text))
+    json <- tryCatch(renv_json_read_default(file, text), error = identity)
     if (!inherits(json, "error"))
       return(json)
   
@@ -1063,14 +1103,14 @@ local({
   }
   
   renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
-    text <- paste(text %||% read(file), collapse = "\n")
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
     jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
   }
   
   renv_json_read_default <- function(file = NULL, text = NULL) {
   
     # find strings in the JSON
-    text <- paste(text %||% read(file), collapse = "\n")
+    text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
     pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
     locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
   
@@ -1118,14 +1158,14 @@ local({
     map <- as.list(map)
   
     # remap strings in object
-    remapped <- renv_json_remap(json, map)
+    remapped <- renv_json_read_remap(json, map)
   
     # evaluate
     eval(remapped, envir = baseenv())
   
   }
   
-  renv_json_remap <- function(json, map) {
+  renv_json_read_remap <- function(json, map) {
   
     # fix names
     if (!is.null(names(json))) {
@@ -1152,7 +1192,7 @@ local({
     # recurse
     if (is.recursive(json)) {
       for (i in seq_along(json)) {
-        json[i] <- list(renv_json_remap(json[[i]], map))
+        json[i] <- list(renv_json_read_remap(json[[i]], map))
       }
     }
   
diff --git a/supp-mat.qmd b/supp-mat.qmd
index 25a104c..6f66375 100644
--- a/supp-mat.qmd
+++ b/supp-mat.qmd
@@ -1,4 +1,4 @@
-# Supplementary information {.unnumbered}
+# Supplementary Information {.unnumbered}
 
 This dissertation contains a lot of supplementary materials. Therefore,
 none of it is included in the dissertation itself. I will instead provide