├── 2023diary ├── main.mw ├── Content │ ├── July │ │ ├── 1July2023.tex │ │ ├── 2July2023.tex │ │ ├── 3July2023.tex │ │ ├── 4July2023.tex │ │ ├── 5July2023.tex │ │ ├── 6July2023.tex │ │ ├── 7July2023.tex │ │ ├── 8July2023.tex │ │ ├── 9July2023.tex │ │ ├── 10July2023.tex │ │ ├── 11July2023.tex │ │ ├── 12July2023.tex │ │ ├── 13July2023.tex │ │ ├── 14July2023.tex │ │ ├── 15July2023.tex │ │ ├── 16July2023.tex │ │ ├── 17July2023.tex │ │ ├── 18July2023.tex │ │ ├── 19July2023.tex │ │ ├── 20July2023.tex │ │ ├── 21July2023.tex │ │ ├── 22July2023.tex │ │ ├── 23July2023.tex │ │ ├── 24July2023.tex │ │ ├── 25July2023.tex │ │ ├── 26July2023.tex │ │ ├── 27July2023.tex │ │ ├── 28July2023.tex │ │ ├── 29July2023.tex │ │ ├── 30July2023.tex │ │ ├── 31July2023.tex │ │ └── July2023.tex │ ├── June │ │ ├── 1June2023.tex │ │ ├── 2June2023.tex │ │ ├── 3June2023.tex │ │ ├── 4June2023.tex │ │ ├── 5June2023.tex │ │ ├── 6June2023.tex │ │ ├── 7June2023.tex │ │ ├── 8June2023.tex │ │ ├── 9June2023.tex │ │ ├── 10June2023.tex │ │ ├── 11June2023.tex │ │ ├── 12June2023.tex │ │ ├── 13June2023.tex │ │ ├── 14June2023.tex │ │ ├── 15June2023.tex │ │ ├── 16June2023.tex │ │ ├── 17June2023.tex │ │ ├── 18June2023.tex │ │ ├── 19June2023.tex │ │ ├── 20June2023.tex │ │ ├── 21June2023.tex │ │ ├── 22June2023.tex │ │ ├── 23June2023.tex │ │ ├── 24June2023.tex │ │ ├── 25June2023.tex │ │ ├── 26June2023.tex │ │ ├── 27June2023.tex │ │ ├── 28June2023.tex │ │ ├── 29June2023.tex │ │ ├── 30June2023.tex │ │ └── June2023.tex │ ├── May │ │ ├── 10May2023.tex │ │ ├── 11May2023.tex │ │ ├── 12May2023.tex │ │ ├── 13May2023.tex │ │ ├── 14May2023.tex │ │ ├── 15May2023.tex │ │ ├── 16May2023.tex │ │ ├── 17May2023.tex │ │ ├── 18May2023.tex │ │ ├── 19May2023.tex │ │ ├── 1May2023.tex │ │ ├── 20May2023.tex │ │ ├── 21May2023.tex │ │ ├── 22May2023.tex │ │ ├── 23May2023.tex │ │ ├── 24May2023.tex │ │ ├── 25May2023.tex │ │ ├── 26May2023.tex │ │ ├── 27May2023.tex │ │ ├── 28May2023.tex │ │ ├── 29May2023.tex │ │ ├── 2May2023.tex │ │ ├── 30May2023.tex │ │ ├── 31May2023.tex │ │ ├── 3May2023.tex │ │ ├── 4May2023.tex │ │ ├── 5May2023.tex │ │ ├── 6May2023.tex │ │ ├── 7May2023.tex │ │ ├── 8May2023.tex │ │ ├── 9May2023.tex │ │ └── May2023.tex │ ├── April │ │ ├── 10April2023.tex │ │ ├── 11April2023.tex │ │ ├── 12April2023.tex │ │ ├── 13April2023.tex │ │ ├── 14April2023.tex │ │ ├── 15April2023.tex │ │ ├── 16April2023.tex │ │ ├── 17April2023.tex │ │ ├── 18April2023.tex │ │ ├── 19April2023.tex │ │ ├── 1April2023.tex │ │ ├── 20April2023.tex │ │ ├── 21April2023.tex │ │ ├── 22April2023.tex │ │ ├── 23April2023.tex │ │ ├── 24April2023.tex │ │ ├── 25April2023.tex │ │ ├── 26April2023.tex │ │ ├── 27April2023.tex │ │ ├── 28April2023.tex │ │ ├── 29April2023.tex │ │ ├── 2April2023.tex │ │ ├── 30April2023.tex │ │ ├── 3April2023.tex │ │ ├── 4April2023.tex │ │ ├── 5April2023.tex │ │ ├── 6April2023.tex │ │ ├── 7April2023.tex │ │ ├── 8April2023.tex │ │ ├── 9April2023.tex │ │ ├── .DS_Store │ │ └── April2023.tex │ ├── August │ │ ├── 10August2023.tex │ │ ├── 11August2023.tex │ │ ├── 12August2023.tex │ │ ├── 13August2023.tex │ │ ├── 14August2023.tex │ │ ├── 15August2023.tex │ │ ├── 16August2023.tex │ │ ├── 17August2023.tex │ │ ├── 18August2023.tex │ │ ├── 19August2023.tex │ │ ├── 1August2023.tex │ │ ├── 20August2023.tex │ │ ├── 21August2023.tex │ │ ├── 22August2023.tex │ │ ├── 23August2023.tex │ │ ├── 24August2023.tex │ │ ├── 25August2023.tex │ │ ├── 26August2023.tex │ │ ├── 27August2023.tex │ │ ├── 28August2023.tex │ │ ├── 29August2023.tex │ │ ├── 2August2023.tex │ │ ├── 30August2023.tex │ │ ├── 31August2023.tex │ │ ├── 3August2023.tex │ │ ├── 4August2023.tex │ │ ├── 5August2023.tex │ │ ├── 6August2023.tex │ │ ├── 7August2023.tex │ │ ├── 8August2023.tex │ │ ├── 9August2023.tex │ │ └── August2023.tex │ ├── March │ │ ├── 10March2023.tex │ │ ├── 11March2023.tex │ │ ├── 12March2023.tex │ │ ├── 13March2023.tex │ │ ├── 14March2023.tex │ │ ├── 15March2023.tex │ │ ├── 16March2023.tex │ │ ├── 17March2023.tex │ │ ├── 18March2023.tex │ │ ├── 19March2023.tex │ │ ├── 1March2023.tex │ │ ├── 20March2023.tex │ │ ├── 21March2023.tex │ │ ├── 22March2023.tex │ │ ├── 23March2023.tex │ │ ├── 24March2023.tex │ │ ├── 25March2023.tex │ │ ├── 26March2023.tex │ │ ├── 27March2023.tex │ │ ├── 28March2023.tex │ │ ├── 29March2023.tex │ │ ├── 2March2023.tex │ │ ├── 30March2023.tex │ │ ├── 31March2023.tex │ │ ├── 3March2023.tex │ │ ├── 4March2023.tex │ │ ├── 5March2023.tex │ │ ├── 6March2023.tex │ │ ├── 7March2023.tex │ │ ├── 8March2023.tex │ │ ├── 9March2023.tex │ │ └── March2023.tex │ ├── December │ │ ├── 10December2023.tex │ │ ├── 11December2023.tex │ │ ├── 12December2023.tex │ │ ├── 13December2023.tex │ │ ├── 14December2023.tex │ │ ├── 15December2023.tex │ │ ├── 16December2023.tex │ │ ├── 17December2023.tex │ │ ├── 18December2023.tex │ │ ├── 19December2023.tex │ │ ├── 1December2023.tex │ │ ├── 20December2023.tex │ │ ├── 21December2023.tex │ │ ├── 22December2023.tex │ │ ├── 23December2023.tex │ │ ├── 24December2023.tex │ │ ├── 25December2023.tex │ │ ├── 26December2023.tex │ │ ├── 27December2023.tex │ │ ├── 28December2023.tex │ │ ├── 29December2023.tex │ │ ├── 2December2023.tex │ │ ├── 30December2023.tex │ │ ├── 31December2023.tex │ │ ├── 3December2023.tex │ │ ├── 4December2023.tex │ │ ├── 5December2023.tex │ │ ├── 6December2023.tex │ │ ├── 7December2023.tex │ │ ├── 8December2023.tex │ │ ├── 9December2023.tex │ │ ├── December2023.tex │ │ └── makeDaily750PagesVerB.py │ ├── February │ │ ├── 10February2023.tex │ │ ├── 11February2023.tex │ │ ├── 12February2023.tex │ │ ├── 13February2023.tex │ │ ├── 14February2023.tex │ │ ├── 15February2023.tex │ │ ├── 16February2023.tex │ │ ├── 17February2023.tex │ │ ├── 18February2023.tex │ │ ├── 19February2023.tex │ │ ├── 1February2023.tex │ │ ├── 20February2023.tex │ │ ├── 21February2023.tex │ │ ├── 22February2023.tex │ │ ├── 23February2023.tex │ │ ├── 24February2023.tex │ │ ├── 25February2023.tex │ │ ├── 26February2023.tex │ │ ├── 27February2023.tex │ │ ├── 28February2023.tex │ │ ├── 2February2023.tex │ │ ├── 3February2023.tex │ │ ├── 4February2023.tex │ │ ├── 5February2023.tex │ │ ├── 6February2023.tex │ │ ├── 7February2023.tex │ │ ├── 8February2023.tex │ │ ├── 9February2023.tex │ │ └── February2023.tex │ ├── January │ │ ├── 10January2023.tex │ │ ├── 11January2023.tex │ │ ├── 12January2023.tex │ │ ├── 13January2023.tex │ │ ├── 14January2023.tex │ │ ├── 15January2023.tex │ │ ├── 16January2023.tex │ │ ├── 17January2023.tex │ │ ├── 18January2023.tex │ │ ├── 19January2023.tex │ │ ├── 1January2023.tex │ │ ├── 20January2023.tex │ │ ├── 21January2023.tex │ │ ├── 22January2023.tex │ │ ├── 23January2023.tex │ │ ├── 24January2023.tex │ │ ├── 25January2023.tex │ │ ├── 26January2023.tex │ │ ├── 27January2023.tex │ │ ├── 28January2023.tex │ │ ├── 29January2023.tex │ │ ├── 2January2023.tex │ │ ├── 30January2023.tex │ │ ├── 31January2023.tex │ │ ├── 3January2023.tex │ │ ├── 4January2023.tex │ │ ├── 5January2023.tex │ │ ├── 6January2023.tex │ │ ├── 7January2023.tex │ │ ├── 8January2023.tex │ │ ├── 9January2023.tex │ │ └── January2023.tex │ ├── November │ │ ├── 10November2023.tex │ │ ├── 11November2023.tex │ │ ├── 12November2023.tex │ │ ├── 13November2023.tex │ │ ├── 14November2023.tex │ │ ├── 15November2023.tex │ │ ├── 16November2023.tex │ │ ├── 17November2023.tex │ │ ├── 18November2023.tex │ │ ├── 19November2023.tex │ │ ├── 1November2023.tex │ │ ├── 20November2023.tex │ │ ├── 21November2023.tex │ │ ├── 22November2023.tex │ │ ├── 23November2023.tex │ │ ├── 24November2023.tex │ │ ├── 25November2023.tex │ │ ├── 26November2023.tex │ │ ├── 27November2023.tex │ │ ├── 28November2023.tex │ │ ├── 29November2023.tex │ │ ├── 2November2023.tex │ │ ├── 30November2023.tex │ │ ├── 3November2023.tex │ │ ├── 4November2023.tex │ │ ├── 5November2023.tex │ │ ├── 6November2023.tex │ │ ├── 7November2023.tex │ │ ├── 8November2023.tex │ │ ├── 9November2023.tex │ │ └── November2023.tex │ ├── October │ │ ├── 10October2023.tex │ │ ├── 11October2023.tex │ │ ├── 12October2023.tex │ │ ├── 13October2023.tex │ │ ├── 14October2023.tex │ │ ├── 15October2023.tex │ │ ├── 16October2023.tex │ │ ├── 17October2023.tex │ │ ├── 18October2023.tex │ │ ├── 19October2023.tex │ │ ├── 1October2023.tex │ │ ├── 20October2023.tex │ │ ├── 21October2023.tex │ │ ├── 22October2023.tex │ │ ├── 23October2023.tex │ │ ├── 24October2023.tex │ │ ├── 25October2023.tex │ │ ├── 26October2023.tex │ │ ├── 27October2023.tex │ │ ├── 28October2023.tex │ │ ├── 29October2023.tex │ │ ├── 2October2023.tex │ │ ├── 30October2023.tex │ │ ├── 31October2023.tex │ │ ├── 3October2023.tex │ │ ├── 4October2023.tex │ │ ├── 5October2023.tex │ │ ├── 6October2023.tex │ │ ├── 7October2023.tex │ │ ├── 8October2023.tex │ │ ├── 9October2023.tex │ │ └── October2023.tex │ ├── September │ │ ├── 1September2023.tex │ │ ├── 2September2023.tex │ │ ├── 3September2023.tex │ │ ├── 4September2023.tex │ │ ├── 5September2023.tex │ │ ├── 6September2023.tex │ │ ├── 7September2023.tex │ │ ├── 8September2023.tex │ │ ├── 9September2023.tex │ │ ├── 10September2023.tex │ │ ├── 11September2023.tex │ │ ├── 12September2023.tex │ │ ├── 13September2023.tex │ │ ├── 14September2023.tex │ │ ├── 15September2023.tex │ │ ├── 16September2023.tex │ │ ├── 17September2023.tex │ │ ├── 18September2023.tex │ │ ├── 19September2023.tex │ │ ├── 20September2023.tex │ │ ├── 21September2023.tex │ │ ├── 22September2023.tex │ │ ├── 23September2023.tex │ │ ├── 24September2023.tex │ │ ├── 25September2023.tex │ │ ├── 26September2023.tex │ │ ├── 27September2023.tex │ │ ├── 28September2023.tex │ │ ├── 29September2023.tex │ │ ├── 30September2023.tex │ │ ├── .DS_Store │ │ └── September2023.tex │ ├── .DS_Store │ ├── Figures │ │ └── scatter2.png │ ├── annotatedBibliography │ │ ├── Makefile.txt │ │ ├── compile.sh │ │ ├── AnnoBibMyBDA.tex │ │ ├── AAAreadme.txt │ │ └── AnnoBibMyBDA.bib │ ├── ChGrantDeadlines.tex │ ├── latexmarkdn.sty │ ├── 0AAAcontents.tex │ └── Preface.tex ├── Deadlines.tex ├── epipart.sty ├── test.sh ├── indexStyle.ist ├── natbib.cfg ├── main.tex ├── times.sty ├── output-globalConstants.tex ├── latexmkrc ├── output-globalSymbols.tex ├── latexmarkdn.sty ├── output-globalAcronyms.tex ├── output-globalGlossary.tex ├── crop.sty └── preambleOnOverleaf.tex └── README.md /2023diary/main.mw: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /2023diary/Content/July/1July2023.tex: -------------------------------------------------------------------------------- 1 | %!TEX root = ../../main.tex 2 | 3 | -------------------------------------------------------------------------------- /2023diary/Content/July/2July2023.tex: -------------------------------------------------------------------------------- 1 | %!TEX root = ../../main.tex 2 | 3 | -------------------------------------------------------------------------------- /2023diary/Content/July/3July2023.tex: 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*.ain *.aux *.bbl *.blg *.glo *.idx *.ilg *.ind *.ist *.lof *.log *.lol *.lot *.syg *.out *.toc 4 | pdflatex -shell-escape main.tex 5 | open -a "Preview" main.pdf 6 | -------------------------------------------------------------------------------- /2023diary/indexStyle.ist: -------------------------------------------------------------------------------- 1 | headings_flag 1 2 | 3 | heading_prefix "\n\\centering\\large\\sffamily\\bfseries% 4 | \\noindent\\textbf{"heading_suffix "}\\par\\nopagebreak\n" 5 | 6 | item_0 "\n \\item \\small " 7 | 8 | delim_0 " \\hfill " 9 | delim_1 " \\hfill " 10 | delim_2 " \\hfill " -------------------------------------------------------------------------------- /2023diary/natbib.cfg: -------------------------------------------------------------------------------- 1 | \AtBeginDocument{% 2 | \@ifpackageloaded{authorindex}{% 3 | \ifNAT@numbers 4 | \let\org@@citex\NAT@citexnum 5 | \else 6 | \let\org@@citex\NAT@citex 7 | \fi 8 | \def\@citex[#1][#2]#3{% 9 | \typeout{indexing: [#1][#2]{#3}}% 10 | \org@@citex[#1][#2]{#3}% 11 | \@aicitey{#3}}% 12 | \renewcommand\NAT@wrout[5]{% 13 | \if@filesw{% 14 | \let\protect\noexpand\let~\relax 15 | \immediate\write\@auxout{\string\aibibcite{#5}{#1}}% 16 | \immediate\write\@auxout{\string\bibcite{#5}{{#1}{#2}{{#3}}{{#4}}}}}% 17 | \fi}}{}} 18 | \endinput 19 | -------------------------------------------------------------------------------- /2023diary/Content/annotatedBibliography/Makefile.txt: -------------------------------------------------------------------------------- 1 | # Makefile for IEEE formatted annotated bibliography. 2 | # 3 | # Author: Titus Barik (titus@barik.net) 4 | 5 | annot.pdf: annotNAR.tex annotNAR.bib 6 | pdflatex annotNAR 7 | bibtex annotNAR 8 | pdflatex annotNAR 9 | pdflatex annotNAR 10 | @echo "================================================" 11 | @echo "All done! annot.pdf has been created. - Titus" 12 | @echo "================================================" 13 | 14 | clean: 15 | rm -rf annotNAR.log annotNAR.blg annotNAR.bbl annotNAR.aux 16 | -------------------------------------------------------------------------------- /2023diary/main.tex: -------------------------------------------------------------------------------- 1 | % 2 | % This is the top document that is selected for compiling this document. The 3 | % context that is relevant resides outside of this folder in 4 | % /Users/blaine-mooers/Documents/Databases/750words2015/Appendices/MyWritingSecrets.tex 5 | % 6 | % The content is in one file for now. Much later on, I while dice it into chapters. 7 | % 8 | % The bibliography is global.bib which is stored in ~/Manuscripts/BibtexLibraries 9 | % 10 | \documentclass[openany,envcountsame,envcountchap]{svmono} 11 | \input{preambleOnOverleaf} 12 | \input{./Content/0AAAcontents} 13 | -------------------------------------------------------------------------------- /2023diary/Content/ChGrantDeadlines.tex: -------------------------------------------------------------------------------- 1 | %!TEX root = ../main.tex 2 | 3 | \chapter{Grant Deadlines} 4 | \index{grant deadlines} 5 | 6 | \section{Introduction} 7 | 8 | 9 | \section{Winter 2019 Internal Deadlines} 10 | \begin{table}[htp] 11 | \caption{Metadata.} 12 | \label{tab:grantGeadlne} 13 | \begin{center} 14 | \begin{tabular}{ll} 15 | % \begin{tabular}{l p{12cm}} % use p when you have to control the column width 16 | \toprule 17 | Grant & Deadline \\ 18 | \midrule 19 | R01 & Feb 2th \\ 20 | R21 & Feb 12th \\ 21 | OCAST & Feb 29th \\ 22 | Teaching Academy & Feb. 24th \\ 23 | PHF equipment: & Feb. 28th \\ 24 | PHF equipment: & Feb. 28th \\ 25 | PHF equipment: & Feb. 28th \\ 26 | COMMA & March 28th \\ 27 | \bottomrule 28 | \end{tabular} 29 | \end{center} 30 | \end{table} -------------------------------------------------------------------------------- /2023diary/times.sty: -------------------------------------------------------------------------------- 1 | %% 2 | %% This is file `times.sty', 3 | %% generated with the docstrip utility. 4 | %% 5 | %% The original source files were: 6 | %% 7 | %% psfonts.dtx (with options: `times') 8 | %% 9 | %% IMPORTANT NOTICE: 10 | %% 11 | %% For the copyright see the source file. 12 | %% 13 | %% You are *not* allowed to modify this file. 14 | %% 15 | %% You are *not* allowed to distribute this file. 16 | %% For distribution of the original source see the terms 17 | %% for copying and modification in the file psfonts.dtx. 18 | %% 19 | \ProvidesPackage{times} 20 | [2000/01/12 PSNFSS-v8.1 21 | Times font as default roman (SPQR) 22 | ] 23 | \renewcommand{\sfdefault}{cmss} 24 | \renewcommand{\rmdefault}{ptm} 25 | \renewcommand{\ttdefault}{pcr} 26 | \endinput 27 | %% 28 | %% End of file `times.sty'. 29 | -------------------------------------------------------------------------------- /2023diary/Content/annotatedBibliography/compile.sh: -------------------------------------------------------------------------------- 1 | # Makefile for NAR formatted annotated bibliography. 2 | # 3 | # Author: Titus Barik (titus@barik.net) 4 | # 5 | # Modified by Blaine Mooers 6 | # 7 | # Has to be run in the main directory with the main.aux generated after the full running of the compile.sh script. 8 | # bibtool -x main.aux -o ./AnnotatedBibliography/AnnoBibMyBDA.bib 9 | cd ../ 10 | bibtool -x main.aux -o ./annotatedBibliography/AnnoBibMain.bib 11 | cd ./annotatedBibliography 12 | pdflatex AnnoBibMain 13 | bibtex AnnoBibMain 14 | pdflatex AnnoBibMain 15 | pdflatex AnnoBibMain 16 | open -a "Preview.app" AnnoBibMain.pdf 17 | echo "================================================" 18 | echo "All done! AnnoBibMyBDA.pdf has been created. - Blaine" 19 | echo "================================================" 20 | 21 | # clean: 22 | rm -rf AnnoBibMain.log AnnoBibMain.blg AnnoBibMain.bbl AnnoBibMain.aux 23 | -------------------------------------------------------------------------------- /2023diary/Content/annotatedBibliography/AnnoBibMyBDA.tex: -------------------------------------------------------------------------------- 1 | %% This is annot.tex. 2 | %% 3 | %% You'll need to change the title and author fields to reflect your 4 | %% information. 5 | %% 6 | %% Author: Titus Barik (titus@barik.net) 7 | %% Homepage: http://www.barik.net/sw/ieee/ 8 | %% Reference: http://www.ctan.org/tex-archive/info/simplified-latex/ 9 | %% bibtool -x ../main.aux -o AnnoBibMyBDA.bib 10 | \documentclass[11pt]{article} 11 | \usepackage[letterpaper, total={7in, 9in}]{geometry} 12 | \usepackage{apacite} 13 | \title{Annotated Bibliography} 14 | \author{Blaine Mooers (blaine-mooers@ouhsc.edu)\\University of Oklahoma Health Sciences Center} 15 | 16 | 17 | \begin{document} 18 | 19 | \begin{center} 20 | { 21 | \Large\textbf{Annotated Bibliography} 22 | \medskip 23 | 24 | { \large Blaine H. M. Mooers, Ph.D. \\ 25 | \medskip 26 | Department of Biochemistry and Molecular Biology \\ 27 | \medskip 28 | University of Oklahoma Health Sciences Center \\ 29 | \medskip 30 | \today} 31 | } 32 | \end{center} 33 | 34 | \nocite{*} 35 | \bibliographystyle{apacannx} 36 | \bibliography{AnnoBibMyBDA} 37 | \end{document} 38 | 39 | -------------------------------------------------------------------------------- /2023diary/output-globalConstants.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%% Constant list % I need to research this matter when I have more time. 2 | \newglossary[slg]{symbolslist}{syi}{syg}{Constantslist} % create add. symbolslist 3 | 4 | 5 | \glsaddkey{unit}{\glsentrytext{\glslabel}}{\glsentryunit}{\GLsentryunit}{\glsunit}{\Glsunit}{\GLSunit} 6 | 7 | \makeglossaries % activate glossaries-package 8 | 9 | \loadglsentries{\jobname-globalSymbols} 10 | %==== EXEMPLARY ENTRY FOR SYMBOLS LIST ========================================= 11 | 12 | \newglossaryentry{lightspeed}{name=\ensuremath{c}, 13 | description={speed of light in vacuum}, 14 | values={2.99792}, 15 | 16 | unit={\si{ 10^8}m s^1}}, 17 | cgsunits={\si{m}}, 18 | 19 | 20 | type=symbolslist} 21 | 22 | 23 | \newglossaryentry{height}{name=\ensuremath{h}, 24 | description={Height of tower}, 25 | unit={\si{m}}, 26 | type=symbolslist} 27 | 28 | \newglossaryentry{energyconsump}{name=\ensuremath{P}, 29 | description={Energy consumption}, 30 | unit={\si{kW}}, 31 | type=symbolslist} 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /2023diary/latexmkrc: -------------------------------------------------------------------------------- 1 | add_cus_dep('aux', 'ain', 0, 'authorindex'); 2 | sub authorindex { 3 | system("authorindex \"$_[0]\""); 4 | system("makeindex \"$_[0]\""); 5 | } 6 | 7 | 8 | ### Following are other rules in Overleaf's default latexmkrc file 9 | # support for the glossaries package: 10 | add_cus_dep('glo', 'gls', 0, 'makeglossaries'); 11 | add_cus_dep('acn', 'acr', 0, 'makeglossaries'); 12 | sub makeglossaries { 13 | system("makeglossaries \"$_[0]\""); 14 | } 15 | 16 | # support for the nomencl package: 17 | add_cus_dep('nlo', 'nls', 0, 'makenlo2nls'); 18 | sub makenlo2nls { 19 | system("makeindex -s nomencl.ist -o \"$_[0].nls\" \"$_[0].nlo\""); 20 | } 21 | 22 | # from the documentation for V. 2.03 of asymptote: 23 | sub asy {return system("asy \"$_[0]\"");} 24 | add_cus_dep("asy","eps",0,"asy"); 25 | add_cus_dep("asy","pdf",0,"asy"); 26 | add_cus_dep("asy","tex",0,"asy"); 27 | 28 | # metapost rule from http://tex.stackexchange.com/questions/37134 29 | add_cus_dep('mp', '1', 0, 'mpost'); 30 | sub mpost { 31 | my $file = $_[0]; 32 | my ($name, $path) = fileparse($file); 33 | pushd($path); 34 | my $return = system "mpost $name"; 35 | popd(); 36 | return $return; 37 | } 38 | -------------------------------------------------------------------------------- /2023diary/Content/annotatedBibliography/AAAreadme.txt: -------------------------------------------------------------------------------- 1 | Remember to add reference to the global bib file in alphabetical order. 2 | 3 | ~/Manuscripts/BibtexLibraries/global.bib 4 | 5 | I wonder if there is a tool to merge bib files with references in cite keys in alphabetical order. 6 | 7 | "bibtool -s bibliography1.bib bibliography2.bib # will merge two bib files, keeping duplicate entries. 8 | 9 | bibtool -s -d bibliography1.bib bibliography2.bib # will merge two bib files, commenting out one of the duplicated entries." 10 | 11 | printf "Script to make an annotated bibliography from global.bib.\n" && 12 | printf "It uses the annote field in the bibtex entry and the plain-annote.bst file." && 13 | printf "Use two pairs of backslashes to separate paragraphs with a blank line. \n"&& 14 | printf "Use the \cite{} command to specify entries. Use the \cite{*} to print everything.\n" && 15 | printf 16 | printf "To write out the cited bib entries from global.bib, use bibtool with the tex file's corresponding *.aux file.\n" && 17 | printf "bibtool -x annotatedbibglobal.aux -o annotatedbibglobal.bib\n" && 18 | 19 | 20 | JabRef and BibDesk can merge and identify duplicates. See {http://tex.stackexchange.com/questions/20027/merge-two-bibtex-files} -------------------------------------------------------------------------------- /2023diary/output-globalSymbols.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%% Symbol list 2 | \newglossary[slg]{symbolslist}{syi}{syg}{Symbolslist} % create add. symbolslist 3 | 4 | 5 | \glsaddkey{unit}{\glsentrytext{\glslabel}}{\glsentryunit}{\GLsentryunit}{\glsunit}{\Glsunit}{\GLSunit} 6 | 7 | \makeglossaries % activate glossaries-package 8 | 9 | \loadglsentries{\jobname-globalSymbols} 10 | %==== EXEMPLARY ENTRY FOR SYMBOLS LIST ========================================= 11 | \newglossaryentry{symb:Pi}{name=\ensuremath{\pi}, 12 | description={Geometrical value}, 13 | unit={}, 14 | type=symbolslist} 15 | 16 | \newglossaryentry{height}{name=\ensuremath{h}, 17 | description={Height of tower}, 18 | unit={\si{m}}, 19 | type=symbolslist} 20 | 21 | \newglossaryentry{energyconsump}{name=\ensuremath{P}, 22 | description={Energy consumption}, 23 | unit={\si{kW}}, 24 | type=symbolslist} 25 | 26 | \newglossaryentry{symb:Phi}{ 27 | name = $\varphi$, 28 | description = {Any angle.} , 29 | Sort = symbolphi, type = symbolslist 30 | } 31 | 32 | \newglossaryentry{symb:lambda}{ 33 | name = $\lambda$, 34 | description = { An arbitrary number, with the following expression 35 | Is multiplied. } , 36 | Sort = symbollambda, type = symbolslist 37 | } 38 | 39 | \newglossaryentry{symb:alpha}{ 40 | name = $\alpha$, 41 | description = { angle } , 42 | Sort = symbollambda, type = symbolslist 43 | } 44 | 45 | \newglossaryentry{symb:beta}{ 46 | name = $\beta$, 47 | description = { angle } , 48 | Sort = symbollambda, type = symbolslist 49 | } -------------------------------------------------------------------------------- /2023diary/latexmarkdn.sty: -------------------------------------------------------------------------------- 1 | \ProvidesPackage{latexmarkdn} 2 | 3 | \RequirePackage{luatexbase} 4 | 5 | \RequirePackage{kvoptions} 6 | \DeclareStringOption{extensions} 7 | \DeclareStringOption{template} 8 | \DeclareBoolOption{document} 9 | \ProcessKeyvalOptions* 10 | 11 | \directlua{% 12 | unpack = unpack or table.unpack 13 | loadstring = loadstring or load 14 | local extensionstring = "\latexmarkdn@extensions" 15 | local extensions 16 | if string.len(extensionstring) > 0 then 17 | %local extensions = {} 18 | extensions= string.explode(extensionstring,",") 19 | end 20 | %for _,ex in ipairs() do 21 | % local ex = ex:gsub(" ","") 22 | % extensions[ex] = true 23 | %end 24 | latexmark = require "latexmarkdn" 25 | latexmark.init(extensions) 26 | latexmark.save_template("\latexmarkdn@template") 27 | } 28 | 29 | \newcommand\latexmark@start{\directlua{luatexbase.add_to_callback("process_input_buffer",latexmark.callback,"latexmark")}} 30 | \newcommand\latexmark@end{\directlua{% 31 | luatexbase.remove_from_callback("process_input_buffer", "latexmark") 32 | latexmark.process() 33 | }} 34 | 35 | \iflatexmarkdn@document 36 | \AtBeginDocument{% 37 | \latexmark@start 38 | \directlua{latexmark.end_env = '\noexpand\\end{document}'} 39 | } 40 | \AtEndDocument{\latexmark@end} 41 | \fi 42 | 43 | \newenvironment{latexmark} 44 | {\latexmark@start} 45 | {\latexmark@end} 46 | 47 | \newcommand\markdownfile[1]{% 48 | \directlua{% 49 | local f = io.open("\luatexluaescapestring{#1}","r") 50 | if not f then 51 | print('latexmark warning: file "#1" cannot be found') 52 | else 53 | local lines = f:read("*all") 54 | latexmark.callback(lines, true) 55 | f:close() 56 | latexmark.process() 57 | end 58 | } 59 | } 60 | 61 | \endinput 62 | 63 | -------------------------------------------------------------------------------- /2023diary/Content/latexmarkdn.sty: -------------------------------------------------------------------------------- 1 | \ProvidesPackage{latexmarkdn} 2 | 3 | \RequirePackage{luatexbase} 4 | 5 | \RequirePackage{kvoptions} 6 | \DeclareStringOption{extensions} 7 | \DeclareStringOption{template} 8 | \DeclareBoolOption{document} 9 | \ProcessKeyvalOptions* 10 | 11 | \directlua{% 12 | unpack = unpack or table.unpack 13 | loadstring = loadstring or load 14 | local extensionstring = "\latexmarkdn@extensions" 15 | local extensions 16 | if string.len(extensionstring) > 0 then 17 | %local extensions = {} 18 | extensions= string.explode(extensionstring,",") 19 | end 20 | %for _,ex in ipairs() do 21 | % local ex = ex:gsub(" ","") 22 | % extensions[ex] = true 23 | %end 24 | latexmark = require "latexmarkdn" 25 | latexmark.init(extensions) 26 | latexmark.save_template("\latexmarkdn@template") 27 | } 28 | 29 | \newcommand\latexmark@start{\directlua{luatexbase.add_to_callback("process_input_buffer",latexmark.callback,"latexmark")}} 30 | \newcommand\latexmark@end{\directlua{% 31 | luatexbase.remove_from_callback("process_input_buffer", "latexmark") 32 | latexmark.process() 33 | }} 34 | 35 | \iflatexmarkdn@document 36 | \AtBeginDocument{% 37 | \latexmark@start 38 | \directlua{latexmark.end_env = '\noexpand\\end{document}'} 39 | } 40 | \AtEndDocument{\latexmark@end} 41 | \fi 42 | 43 | \newenvironment{latexmark} 44 | {\latexmark@start} 45 | {\latexmark@end} 46 | 47 | \newcommand\markdownfile[1]{% 48 | \directlua{% 49 | local f = io.open("\luatexluaescapestring{#1}","r") 50 | if not f then 51 | print('latexmark warning: file "#1" cannot be found') 52 | else 53 | local lines = f:read("*all") 54 | latexmark.callback(lines, true) 55 | f:close() 56 | latexmark.process() 57 | end 58 | } 59 | } 60 | 61 | \endinput 62 | 63 | -------------------------------------------------------------------------------- /2023diary/Content/May/May2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{May 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{May 1} 13 | \input{./Content/May/1May2023} 14 | \section{May 2} 15 | \input{./Content/May/2May2023} 16 | \section{May 3} 17 | \input{./Content/May/3May2023} 18 | \section{May 4} 19 | \input{./Content/May/4May2023}: 20 | \section{May 5} 21 | \input{./Content/May/5May2023} 22 | \section{May 6} 23 | \input{./Content/May/6May2023} 24 | \section{May 7} 25 | \input{./Content/May/7May2023} 26 | \section{May 8} 27 | \input{./Content/May/8May2023} 28 | \section{May 9} 29 | \input{./Content/May/9May2023} 30 | \section{May 10} 31 | \input{./Content/May/11May2023} 32 | \section{May 11} 33 | \input{./Content/May/11May2023} 34 | \section{May 12} 35 | \input{./Content/May/13May2023} 36 | \section{May 13} 37 | \input{./Content/May/14May2023} 38 | \section{May 14} 39 | \input{./Content/May/15May2023} 40 | \section{May 15} 41 | \input{./Content/May/15May2023} 42 | \section{May 16} 43 | \input{./Content/May/16May2023} 44 | \section{May 17} 45 | \input{./Content/May/17May2023} 46 | \section{May 18} 47 | \input{./Content/May/18May2023} 48 | \section{May 19} 49 | \input{./Content/May/19May2023} 50 | \section{May 20} 51 | \input{./Content/May/20May2023} 52 | \section{May 21} 53 | \input{./Content/May/21May2023} 54 | \section{May 22} 55 | \input{./Content/May/22May2023} 56 | \section{May 23} 57 | \input{./Content/May/23May2023} 58 | \section{May 24} 59 | \input{./Content/May/24May2023} 60 | \section{May 25} 61 | \input{./Content/May/25May2023} 62 | \section{May 26} 63 | \input{./Content/May/26May2023} 64 | \section{May 27} 65 | \input{./Content/May/27May2023} 66 | \section{May 28} 67 | \input{./Content/May/28May2023} 68 | \section{May 29} 69 | \input{./Content/May/29May2023} 70 | \section{May 30} 71 | \input{./Content/May/30May2023} 72 | \section{May 31} 73 | \input{./Content/May/31May2023} 74 | -------------------------------------------------------------------------------- /2023diary/Content/June/June2023.tex: -------------------------------------------------------------------------------- 1 | June%%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{June 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{June 1} 13 | \input{./Content/June/1June2023} 14 | \section{June 2} 15 | \input{./Content/June/2June2023} 16 | \section{June 3} 17 | \input{./Content/June/3June2023} 18 | \section{June 4} 19 | \input{./Content/June/4June2023} 20 | \section{June 5} 21 | \input{./Content/June/5June2023} 22 | \section{June 6} 23 | \input{./Content/June/6June2023} 24 | \section{June 7} 25 | \input{./Content/June/7June2023} 26 | \section{June 8} 27 | \input{./Content/June/8June2023} 28 | \section{June 9} 29 | \input{./Content/June/9June2023} 30 | \section{June 10} 31 | \input{./Content/June/11June2023} 32 | \section{June 11} 33 | \input{./Content/June/11June2023} 34 | \section{June 12} 35 | \input{./Content/June/13June2023} 36 | \section{June 13} 37 | \input{./Content/June/14June2023} 38 | \section{June 14} 39 | \input{./Content/June/15June2023} 40 | \section{June 15} 41 | \input{./Content/June/15June2023} 42 | \section{June 16} 43 | \input{./Content/June/16June2023} 44 | \section{June 17} 45 | \input{./Content/June/17June2023} 46 | \section{June 18} 47 | \input{./Content/June/18June2023} 48 | \section{June 19} 49 | \input{./Content/June/19June2023} 50 | \section{June 20} 51 | \input{./Content/June/20June2023} 52 | \section{June 21} 53 | \input{./Content/June/21June2023} 54 | \section{June 22} 55 | \input{./Content/June/22June2023} 56 | \section{June 23} 57 | \input{./Content/June/23June2023} 58 | \section{June 24} 59 | \input{./Content/June/24June2023} 60 | \section{June 25} 61 | \input{./Content/June/25June2023} 62 | \section{June 26} 63 | \input{./Content/June/26June2023} 64 | \section{June 27} 65 | \input{./Content/June/27June2023} 66 | \section{June 28} 67 | \input{./Content/June/28June2023} 68 | \section{June 29} 69 | \input{./Content/June/29June2023} 70 | \section{June 30} 71 | \input{./Content/June/30June2023} 72 | -------------------------------------------------------------------------------- /2023diary/Content/July/July2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{July 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{July 1} 13 | \input{./Content/July/1July2023} 14 | \section{July 2} 15 | \input{./Content/July/2July2023} 16 | \section{July 3} 17 | \input{./Content/July/3July2023} 18 | \section{July 4} 19 | \input{./Content/July/4July2023} 20 | \section{July 5} 21 | \input{./Content/July/5July2023} 22 | \section{July 6} 23 | \input{./Content/July/6July2023} 24 | \section{July 7} 25 | \input{./Content/July/7July2023} 26 | \section{July 8} 27 | \input{./Content/July/8July2023} 28 | \section{July 9} 29 | \input{./Content/July/9July2023} 30 | \section{July 10} 31 | \input{./Content/July/11July2023} 32 | \section{July 11} 33 | \input{./Content/July/11July2023} 34 | \section{July 12} 35 | \input{./Content/July/13July2023} 36 | \section{July 13} 37 | \input{./Content/July/14July2023} 38 | \section{July 14} 39 | \input{./Content/July/15July2023} 40 | \section{July 15} 41 | \input{./Content/July/15July2023} 42 | \section{July 16} 43 | \input{./Content/July/16July2023} 44 | \section{July 17} 45 | \input{./Content/July/17July2023} 46 | \section{July 18} 47 | \input{./Content/July/18July2023} 48 | \section{July 19} 49 | \input{./Content/July/19July2023} 50 | \section{July 20} 51 | \input{./Content/July/20July2023} 52 | \section{July 21} 53 | \input{./Content/July/21July2023} 54 | \section{July 22} 55 | \input{./Content/July/22July2023} 56 | \section{July 23} 57 | \input{./Content/July/23July2023} 58 | \section{July 24} 59 | \input{./Content/July/24July2023} 60 | \section{July 25} 61 | \input{./Content/July/25July2023} 62 | \section{July 26} 63 | \input{./Content/July/26July2023} 64 | \section{July 27} 65 | \input{./Content/July/27July2023} 66 | \section{July 28} 67 | \input{./Content/July/28July2023} 68 | \section{July 29} 69 | \input{./Content/July/29July2023} 70 | \section{July 30} 71 | \input{./Content/July/30July2023} 72 | \section{July 31} 73 | \input{./Content/July/31July2023} 74 | -------------------------------------------------------------------------------- /2023diary/Content/April/April2023.tex: -------------------------------------------------------------------------------- 1 | April%%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{April 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{April 1} 13 | \input{./Content/April/1April2023} 14 | \section{April 2} 15 | \input{./Content/April/2April2023} 16 | \section{April 3} 17 | \input{./Content/April/3April2023} 18 | \section{April 4} 19 | \input{./Content/April/4April2023} 20 | \section{April 5} 21 | \input{./Content/April/5April2023} 22 | \section{April 6} 23 | \input{./Content/April/6April2023} 24 | \section{April 7} 25 | \input{./Content/April/7April2023} 26 | \section{April 8} 27 | \input{./Content/April/8April2023} 28 | \section{April 9} 29 | \input{./Content/April/9April2023} 30 | \section{April 10} 31 | \input{./Content/April/11April2023} 32 | \section{April 11} 33 | \input{./Content/April/11April2023} 34 | \section{April 12} 35 | \input{./Content/April/13April2023} 36 | \section{April 13} 37 | \input{./Content/April/14April2023} 38 | \section{April 14} 39 | \input{./Content/April/15April2023} 40 | \section{April 15} 41 | \input{./Content/April/15April2023} 42 | \section{April 16} 43 | \input{./Content/April/16April2023} 44 | \section{April 17} 45 | \input{./Content/April/17April2023} 46 | \section{April 18} 47 | \input{./Content/April/18April2023} 48 | \section{April 19} 49 | \input{./Content/April/19April2023} 50 | \section{April 20} 51 | \input{./Content/April/20April2023} 52 | \section{April 21} 53 | \input{./Content/April/21April2023} 54 | \section{April 22} 55 | \input{./Content/April/22April2023} 56 | \section{April 23} 57 | \input{./Content/April/23April2023} 58 | \section{April 24} 59 | \input{./Content/April/24April2023} 60 | \section{April 25} 61 | \input{./Content/April/25April2023} 62 | \section{April 26} 63 | \input{./Content/April/26April2023} 64 | \section{April 27} 65 | \input{./Content/April/27April2023} 66 | \section{April 28} 67 | \input{./Content/April/28April2023} 68 | \section{April 29} 69 | \input{./Content/April/29April2023} 70 | \section{April 30} 71 | \input{./Content/April/30April2023} 72 | -------------------------------------------------------------------------------- /2023diary/Content/March/March2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{March 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{March 1} 13 | \input{./Content/March/1March2023} 14 | \section{March 2} 15 | \input{./Content/March/2March2023} 16 | \section{March 3} 17 | \input{./Content/March/3March2023} 18 | \section{March 4} 19 | \input{./Content/March/4March2023} 20 | \section{March 5} 21 | \input{./Content/March/5March2023} 22 | \section{March 6} 23 | \input{./Content/March/6March2023} 24 | \section{March 7} 25 | \input{./Content/March/7March2023} 26 | \section{March 8} 27 | \input{./Content/March/8March2023} 28 | \section{March 9} 29 | \input{./Content/March/9March2023} 30 | \section{March 10} 31 | \input{./Content/March/11March2023} 32 | \section{March 11} 33 | \input{./Content/March/11March2023} 34 | \section{March 12} 35 | \input{./Content/March/13March2023} 36 | \section{March 13} 37 | \input{./Content/March/14March2023} 38 | \section{March 14} 39 | \input{./Content/March/15March2023} 40 | \section{March 15} 41 | \input{./Content/March/15March2023} 42 | \section{March 16} 43 | \input{./Content/March/16March2023} 44 | \section{March 17} 45 | \input{./Content/March/17March2023} 46 | \section{March 18} 47 | \input{./Content/March/18March2023} 48 | \section{March 19} 49 | \input{./Content/March/19March2023} 50 | \section{March 20} 51 | \input{./Content/March/20March2023} 52 | \section{March 21} 53 | \input{./Content/March/21March2023} 54 | \section{March 22} 55 | \input{./Content/March/22March2023} 56 | \section{March 23} 57 | \input{./Content/March/23March2023} 58 | \section{March 24} 59 | \input{./Content/March/24March2023} 60 | \section{March 25} 61 | \input{./Content/March/25March2023} 62 | \section{March 26} 63 | \input{./Content/March/26March2023} 64 | \section{March 27} 65 | \input{./Content/March/27March2023} 66 | \section{March 28} 67 | \input{./Content/March/28March2023} 68 | \section{March 29} 69 | \input{./Content/March/29March2023} 70 | \section{March 30} 71 | \input{./Content/March/30March2023} 72 | \section{March 31} 73 | \input{./Content/March/31March2023} 74 | -------------------------------------------------------------------------------- /2023diary/Content/February/February2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{February 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{February 1} 13 | \input{./Content/February/1February2023} 14 | \section{February 2} 15 | \input{./Content/February/2February2023} 16 | \section{February 3} 17 | \input{./Content/February/3February2023} 18 | \section{February 4} 19 | \input{./Content/February/4February2023} 20 | \section{February 5} 21 | \input{./Content/February/5February2023} 22 | \section{February 6} 23 | \input{./Content/February/6February2023} 24 | \section{February 7} 25 | \input{./Content/February/7February2023} 26 | \section{February 8} 27 | \input{./Content/February/8February2023} 28 | \section{February 9} 29 | \input{./Content/February/9February2023} 30 | \section{February 10} 31 | \input{./Content/February/11February2023} 32 | \section{February 11} 33 | \input{./Content/February/11February2023} 34 | \section{February 12} 35 | \input{./Content/February/13February2023} 36 | \section{February 13} 37 | \input{./Content/February/14February2023} 38 | \section{February 14} 39 | \input{./Content/February/15February2023} 40 | \section{February 15} 41 | \input{./Content/February/15February2023} 42 | \section{February 16} 43 | \input{./Content/February/16February2023} 44 | \section{February 17} 45 | \input{./Content/February/17February2023} 46 | \section{February 18} 47 | \input{./Content/February/18February2023} 48 | \section{February 19} 49 | \input{./Content/February/19February2023} 50 | \section{February 20} 51 | \input{./Content/February/20February2023} 52 | \section{February 21} 53 | \input{./Content/February/21February2023} 54 | \section{February 22} 55 | \input{./Content/February/22February2023} 56 | \section{February 23} 57 | \input{./Content/February/23February2023} 58 | \section{February 24} 59 | \input{./Content/February/24February2023} 60 | \section{February 25} 61 | \input{./Content/February/25February2023} 62 | \section{February 26} 63 | \input{./Content/February/26February2023} 64 | \section{February 27} 65 | \input{./Content/February/27February2023} 66 | \section{February 28} 67 | \input{./Content/February/28February2023} 68 | -------------------------------------------------------------------------------- /2023diary/Content/August/August2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{August 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{August 1} 13 | \input{./Content/August/1August2023} 14 | \section{August 2} 15 | \input{./Content/August/2August2023} 16 | \section{August 3} 17 | \input{./Content/August/3August2023} 18 | \section{August 4} 19 | \input{./Content/August/4August2023} 20 | \section{August 5} 21 | \input{./Content/August/5August2023} 22 | \section{August 6} 23 | \input{./Content/August/6August2023} 24 | \section{August 7} 25 | \input{./Content/August/7August2023} 26 | \section{August 8} 27 | \input{./Content/August/8August2023} 28 | \section{August 9} 29 | \input{./Content/August/9August2023} 30 | \section{August 10} 31 | \input{./Content/August/11August2023} 32 | \section{August 11} 33 | \input{./Content/August/11August2023} 34 | \section{August 12} 35 | \input{./Content/August/13August2023} 36 | \section{August 13} 37 | \input{./Content/August/14August2023} 38 | \section{August 14} 39 | \input{./Content/August/15August2023} 40 | \section{August 15} 41 | \input{./Content/August/15August2023} 42 | \section{August 16} 43 | \input{./Content/August/16August2023} 44 | \section{August 17} 45 | \input{./Content/August/17August2023} 46 | \section{August 18} 47 | \input{./Content/August/18August2023} 48 | \section{August 19} 49 | \input{./Content/August/19August2023} 50 | \section{August 20} 51 | \input{./Content/August/20August2023} 52 | \section{August 21} 53 | \input{./Content/August/21August2023} 54 | \section{August 22} 55 | \input{./Content/August/22August2023} 56 | \section{August 23} 57 | \input{./Content/August/23August2023} 58 | \section{August 24} 59 | \input{./Content/August/24August2023} 60 | \section{August 25} 61 | \input{./Content/August/25August2023} 62 | \section{August 26} 63 | \input{./Content/August/26August2023} 64 | \section{August 27} 65 | \input{./Content/August/27August2023} 66 | \section{August 28} 67 | \input{./Content/August/28August2023} 68 | \section{August 29} 69 | \input{./Content/August/29August2023} 70 | \section{August 30} 71 | \input{./Content/August/30August2023} 72 | \section{August 31} 73 | \input{./Content/August/31August2023} 74 | -------------------------------------------------------------------------------- /2023diary/Content/January/January2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{January 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{January 1} 13 | \input{./Content/January/1January2023} 14 | \section{January 2} 15 | \input{./Content/January/2January2023} 16 | \section{January 3} 17 | \input{./Content/January/3January2023} 18 | \section{January 4} 19 | \input{./Content/January/4January2023} 20 | \section{January 5} 21 | \input{./Content/January/5January2023} 22 | \section{January 6} 23 | \input{./Content/January/6January2023} 24 | \section{January 7} 25 | \input{./Content/January/7January2023} 26 | \section{January 8} 27 | \input{./Content/January/8January2023} 28 | \section{January 9} 29 | \input{./Content/January/9January2023} 30 | \section{January 10} 31 | \input{./Content/January/11January2023} 32 | \section{January 11} 33 | \input{./Content/January/11January2023} 34 | \section{January 12} 35 | \input{./Content/January/13January2023} 36 | \section{January 13} 37 | \input{./Content/January/14January2023} 38 | \section{January 14} 39 | \input{./Content/January/15January2023} 40 | \section{January 15} 41 | \input{./Content/January/15January2023} 42 | \section{January 16} 43 | \input{./Content/January/16January2023} 44 | \section{January 17} 45 | \input{./Content/January/17January2023} 46 | \section{January 18} 47 | \input{./Content/January/18January2023} 48 | \section{January 19} 49 | \input{./Content/January/19January2023} 50 | \section{January 20} 51 | \input{./Content/January/20January2023} 52 | \section{January 21} 53 | \input{./Content/January/21January2023} 54 | \section{January 22} 55 | \input{./Content/January/22January2023} 56 | \section{January 23} 57 | \input{./Content/January/23January2023} 58 | \section{January 24} 59 | \input{./Content/January/24January2023} 60 | \section{January 25} 61 | \input{./Content/January/25January2023} 62 | \section{January 26} 63 | \input{./Content/January/26January2023} 64 | \section{January 27} 65 | \input{./Content/January/27January2023} 66 | \section{January 28} 67 | \input{./Content/January/28January2023} 68 | \section{January 29} 69 | \input{./Content/January/29January2023} 70 | \section{January 30} 71 | \input{./Content/January/30January2023} 72 | \section{January 31} 73 | \input{./Content/January/31January2023} 74 | -------------------------------------------------------------------------------- /2023diary/Content/October/October2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{October 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{October 1} 13 | \input{./Content/October/1October2023} 14 | \section{October 2} 15 | \input{./Content/October/2October2023} 16 | \section{October 3} 17 | \input{./Content/October/3October2023} 18 | \section{October 4} 19 | \input{./Content/October/4October2023} 20 | \section{October 5} 21 | \input{./Content/October/5October2023} 22 | \section{October 6} 23 | \input{./Content/October/6October2023} 24 | \section{October 7} 25 | \input{./Content/October/7October2023} 26 | \section{October 8} 27 | \input{./Content/October/8October2023} 28 | \section{October 9} 29 | \input{./Content/October/9October2023} 30 | \section{October 10} 31 | \input{./Content/October/11October2023} 32 | \section{October 11} 33 | \input{./Content/October/11October2023} 34 | \section{October 12} 35 | \input{./Content/October/13October2023} 36 | \section{October 13} 37 | \input{./Content/October/14October2023} 38 | \section{October 14} 39 | \input{./Content/October/15October2023} 40 | \section{October 15} 41 | \input{./Content/October/15October2023} 42 | \section{October 16} 43 | \input{./Content/October/16October2023} 44 | \section{October 17} 45 | \input{./Content/October/17October2023} 46 | \section{October 18} 47 | \input{./Content/October/18October2023} 48 | \section{October 19} 49 | \input{./Content/October/19October2023} 50 | \section{October 20} 51 | \input{./Content/October/20October2023} 52 | \section{October 21} 53 | \input{./Content/October/21October2023} 54 | \section{October 22} 55 | \input{./Content/October/22October2023} 56 | \section{October 23} 57 | \input{./Content/October/23October2023} 58 | \section{October 24} 59 | \input{./Content/October/24October2023} 60 | \section{October 25} 61 | \input{./Content/October/25October2023} 62 | \section{October 26} 63 | \input{./Content/October/26October2023} 64 | \section{October 27} 65 | \input{./Content/October/27October2023} 66 | \section{October 28} 67 | \input{./Content/October/28October2023} 68 | \section{October 29} 69 | \input{./Content/October/29October2023} 70 | \section{October 30} 71 | \input{./Content/October/30October2023} 72 | \section{October 31} 73 | \input{./Content/October/31October2023} 74 | -------------------------------------------------------------------------------- /2023diary/Content/November/November2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{November 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{November 1} 13 | \input{./Content/November/1November2023} 14 | \section{November 2} 15 | \input{./Content/November/2November2023} 16 | \section{November 3} 17 | \input{./Content/November/3November2023} 18 | \section{November 4} 19 | \input{./Content/November/4November2023} 20 | \section{November 5} 21 | \input{./Content/November/5November2023} 22 | \section{November 6} 23 | \input{./Content/November/6November2023} 24 | \section{November 7} 25 | \input{./Content/November/7November2023} 26 | \section{November 8} 27 | \input{./Content/November/8November2023} 28 | \section{November 9} 29 | \input{./Content/November/9November2023} 30 | \section{November 10} 31 | \input{./Content/November/11November2023} 32 | \section{November 11} 33 | \input{./Content/November/11November2023} 34 | \section{November 12} 35 | \input{./Content/November/13November2023} 36 | \section{November 13} 37 | \input{./Content/November/14November2023} 38 | \section{November 14} 39 | \input{./Content/November/15November2023} 40 | \section{November 15} 41 | \input{./Content/November/15November2023} 42 | \section{November 16} 43 | \input{./Content/November/16November2023} 44 | \section{November 17} 45 | \input{./Content/November/17November2023} 46 | \section{November 18} 47 | \input{./Content/November/18November2023} 48 | \section{November 19} 49 | \input{./Content/November/19November2023} 50 | \section{November 20} 51 | \input{./Content/November/20November2023} 52 | \section{November 21} 53 | \input{./Content/November/21November2023} 54 | \section{November 22} 55 | \input{./Content/November/22November2023} 56 | \section{November 23} 57 | \input{./Content/November/23November2023} 58 | \section{November 24} 59 | \input{./Content/November/24November2023} 60 | \section{November 25} 61 | \input{./Content/November/25November2023} 62 | \section{November 26} 63 | \input{./Content/November/26November2023} 64 | \section{November 27} 65 | \input{./Content/November/27November2023} 66 | \section{November 28} 67 | \input{./Content/November/28November2023} 68 | \section{November 29} 69 | \input{./Content/November/29November2023} 70 | \section{November 30} 71 | \input{./Content/November/30November2023} 72 | -------------------------------------------------------------------------------- /2023diary/Content/December/December2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{December 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{December 1} 13 | \input{./Content/December/1December2023} 14 | \section{December 2} 15 | \input{./Content/December/2December2023} 16 | \section{December 3} 17 | \input{./Content/December/3December2023} 18 | \section{December 4} 19 | \input{./Content/December/4December2023} 20 | \section{December 5} 21 | \input{./Content/December/5December2023} 22 | \section{December 6} 23 | \input{./Content/December/6December2023} 24 | \section{December 7} 25 | \input{./Content/December/7December2023} 26 | \section{December 8} 27 | \input{./Content/December/8December2023} 28 | \section{December 9} 29 | \input{./Content/December/9December2023} 30 | \section{December 10} 31 | \input{./Content/December/11December2023} 32 | \section{December 11} 33 | \input{./Content/December/11December2023} 34 | \section{December 12} 35 | \input{./Content/December/13December2023} 36 | \section{December 13} 37 | \input{./Content/December/14December2023} 38 | \section{December 14} 39 | \input{./Content/December/15December2023} 40 | \section{December 15} 41 | \input{./Content/December/15December2023} 42 | \section{December 16} 43 | \input{./Content/December/16December2023} 44 | \section{December 17} 45 | \input{./Content/December/17December2023} 46 | \section{December 18} 47 | \input{./Content/December/18December2023} 48 | \section{December 19} 49 | \input{./Content/December/19December2023} 50 | \section{December 20} 51 | \input{./Content/December/20December2023} 52 | \section{December 21} 53 | \input{./Content/December/21December2023} 54 | \section{December 22} 55 | \input{./Content/December/22December2023} 56 | \section{December 23} 57 | \input{./Content/December/23December2023} 58 | \section{December 24} 59 | \input{./Content/December/24December2023} 60 | \section{December 25} 61 | \input{./Content/December/25December2023} 62 | \section{December 26} 63 | \input{./Content/December/26December2023} 64 | \section{December 27} 65 | \input{./Content/December/27December2023} 66 | \section{December 28} 67 | \input{./Content/December/28December2023} 68 | \section{December 29} 69 | \input{./Content/December/29December2023} 70 | \section{December 30} 71 | \input{./Content/December/30December2023} 72 | \section{December 31} 73 | \input{./Content/December/31December2023} 74 | -------------------------------------------------------------------------------- /2023diary/Content/September/September2023.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%% chapter.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample chapter 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | 9 | \chapter{September 2023} 10 | \label{intro} % Always give a unique label 11 | 12 | \section{September 1} 13 | \input{./Content/September/1September2023} 14 | \section{September 2} 15 | \input{./Content/September/2September2023} 16 | \section{September 3} 17 | \input{./Content/September/3September2023} 18 | \section{September 4} 19 | \input{./Content/September/4September2023} 20 | \section{September 5} 21 | \input{./Content/September/5September2023} 22 | \section{September 6} 23 | \input{./Content/September/6September2023} 24 | \section{September 7} 25 | \input{./Content/September/7September2023} 26 | \section{September 8} 27 | \input{./Content/September/8September2023} 28 | \section{September 9} 29 | \input{./Content/September/9September2023} 30 | \section{September 10} 31 | \input{./Content/September/11September2023} 32 | \section{September 11} 33 | \input{./Content/September/11September2023} 34 | \section{September 12} 35 | \input{./Content/September/13September2023} 36 | \section{September 13} 37 | \input{./Content/September/14September2023} 38 | \section{September 14} 39 | \input{./Content/September/15September2023} 40 | \section{September 15} 41 | \input{./Content/September/15September2023} 42 | \section{September 16} 43 | \input{./Content/September/16September2023} 44 | \section{September 17} 45 | \input{./Content/September/17September2023} 46 | \section{September 18} 47 | \input{./Content/September/18September2023} 48 | \section{September 19} 49 | \input{./Content/September/19September2023} 50 | \section{September 20} 51 | \input{./Content/September/20September2023} 52 | \section{September 21} 53 | \input{./Content/September/21September2023} 54 | \section{September 22} 55 | \input{./Content/September/22September2023} 56 | \section{September 23} 57 | \input{./Content/September/23September2023} 58 | \section{September 24} 59 | \input{./Content/September/24September2023} 60 | \section{September 25} 61 | \input{./Content/September/25September2023} 62 | \section{September 26} 63 | \input{./Content/September/26September2023} 64 | \section{September 27} 65 | \input{./Content/September/27September2023} 66 | \section{September 28} 67 | \input{./Content/September/28September2023} 68 | \section{September 29} 69 | \input{./Content/September/29September2023} 70 | \section{September 30} 71 | \input{./Content/September/30September2023} 72 | -------------------------------------------------------------------------------- /2023diary/Content/December/makeDaily750PagesVerB.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # -*- coding: utf-8 -*- 3 | from __future__ import division, print_function 4 | import sys, os 5 | Usage=""" 6 | ./makeDaily750Pages.py year month startCalDay endCalDay 7 | example: 8 | ./makeDaily750Pages.py 2017 'November' 6 30 9 | """ 10 | 11 | """ 12 | Purpose: write out the plain text files for the month. 13 | There is one file per day. 14 | 15 | Read in from command line the following parameters: 16 | 17 | year # as four digit integer 18 | month # as string 19 | startCalDay # as integer 20 | endCalDay 21 | 22 | Thus script initially will write the files for one month or part of a month. 23 | 24 | Write out plain tex files for each day with the following first line: 25 | %!TEX root = ../../main.tex 26 | 27 | %awk '/^\%TODO/' 22October2017.tex > 22October2017TODOawk.tex 28 | %sed -n '/^\%TODO/p' 22October2017.tex > 22October2017TODOsed.tex 29 | %grep '^\%TODO' 22October2017.tex > 22October2017TODOgrep.tex 30 | 31 | Blaine Mooers 32 | 33 | 5 November 2017 34 | 35 | Updated to write boilerplate to a comment environment at the bottom of the page. 36 | This spares the need to use percent signs to comment out the boilerplate. 37 | 38 | 6 July 2019 39 | """ 40 | 41 | def makeDailyPages(): 42 | year=sys.argv[1] 43 | syear=str(year) 44 | print(syear) 45 | 46 | month=sys.argv[2] 47 | smonth=str(month) 48 | print(month) 49 | 50 | startCalDay=sys.argv[3] 51 | sstartCalDay=str(startCalDay) 52 | istartCalDay=int(startCalDay) 53 | print(sstartCalDay) 54 | 55 | endCalDay=sys.argv[4] 56 | sendCalDay=str(endCalDay) 57 | iendCalDay=int(endCalDay) 58 | print(sendCalDay) 59 | 60 | print("Usage: ./makeDaily750Pages.py year month startday endday") 61 | print("Example: ./makeDaily750Pages.py 2017 'November' 6 30") 62 | inumAtJobs = ((iendCalDay - istartCalDay) + 1) 63 | print(str(inumAtJobs)) 64 | writeJobs = [x for x in range(inumAtJobs)] 65 | day = istartCalDay 66 | sday =str(day) 67 | for job in writeJobs: 68 | sday = str(day) 69 | newfile = sday + month + syear + ".tex" 70 | h = open(newfile, 'w') 71 | h.write(r'%!TEX root = ../../main.tex' + '\n') 72 | h.write('\n') 73 | day = day + 1 74 | h.close() 75 | 76 | if __name__ == '__main__': 77 | makeDailyPages() 78 | 79 | """ 80 | Enhancements could include making folders for each month 81 | and writing the files to each folder. 82 | 83 | Alternately, a bash script can be used to run this 84 | script to generate the files for a year. 85 | 86 | #!/usr/bin/bash 87 | ./makeDaily750Pages.py 2017 'November' 6 30 88 | ./makeDaily750Pages.py 2017 'December' 1 31 89 | 90 | """ 91 | -------------------------------------------------------------------------------- /2023diary/Content/0AAAcontents.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%%%%%%%%% Need to edit below %%%%%%%%%%%%%%%%%%%%%%% 2 | %%%%%%%%%%%%%%%%%%%%%%% Title, Subtitle, and Author(s) %%%%%%%%%%%%%% 3 | %\titlehead{\centering\inputgraphics[width=6cm]{images/xtal}}, does not work in this svmono.cls 4 | 5 | % %%%%%%%%%%%%%%%%%%%%%%%%%%% Candidate Titles %%%%%%%%%%%%%%%% 6 | % Solution Scattering Studies in Integrative Structural Molecular Biology Research 7 | % A Practical Biological Solution Scattering 8 | % Practical X-ray Solution Scattering for Biologists 9 | %%%%%%%%%%%%%%%%%%%%%%%%%%%% Need to edit image %%%%%%%%%%%%%%%%%%%%%%% 10 | % Definition of \maketitle 11 | \title{Daily Writing} 12 | \subtitle{Everything included} 13 | \author{Blaine Mooers} 14 | % \subtitle{-- Monograph --} 15 | \makeatletter 16 | \def\@maketitle{ 17 | \begin{center} 18 | {\Huge \bfseries \sffamily \@title }\\[4ex] 19 | {\Large \bfseries \sffamily \@subtitle }\\[4ex] 20 | {\Large \@author}\\[4ex] 21 | \@date\\[8ex] 22 | \vspace{1cm} 23 | \includegraphics[width = 150mm]{./Content/Figures/scatter2.png} 24 | \end{center}} 25 | \makeatother 26 | 27 | %%%%% Begin document here %%%%%%%%%%%%%%%%%%%%%%%%%%% 28 | 29 | \begin{document} 30 | \maketitle 31 | \newpage 32 | \frontmatter%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 33 | 34 | %\include{dedic} 35 | \include{./Content/Preface} 36 | \tableofcontents 37 | \listoffigures 38 | \listoftables 39 | \renewcommand\listoflistingscaption{List of source codes} 40 | \listoflistings 41 | \mainmatter%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 42 | %Set the chapter counter so that the first chapter is counted as Chapter 1. 43 | 44 | \part{2022} 45 | \setcounter{chapter}{0} 46 | \input{./Content/January/January2023} 47 | \input{./Content/February/February2023} 48 | \input{./Content/March/March2023} 49 | \input{./Content/April/April2023} 50 | \input{./Content/May/May2023} 51 | \input{./Content/June/June2023} 52 | \input{./Content/July/July2023} 53 | \input{./Content/August/August2023} 54 | \input{./Content/September/September2023} 55 | \input{./Content/October/October2023} 56 | \input{./Content/November/November2023} 57 | \input{./Content/December/December2023} 58 | 59 | \part{Appendices} 60 | This is a test \cite{Mooers2016DirectMethodsStructureDeterminationOfATrypanosomeRNAEditingSubstrateFragmentWithTranslationalPseudosymmetry}. 61 | \appendix 62 | %\input{./Content/ChDeadlines2022} 63 | %\input{./Content/ChAccomplishments2022} 64 | % \input{./Content/ChAccomplishments2021} 65 | % \input{./Content/ChAccomplishments2020} 66 | %\input{./Content/ChAnnualPlan2022} 67 | % \input{./Content/ChAnnualPlan2021} 68 | % \input{./Content/ChAnnualPlan2020} 69 | % \input{./Content/ChBookReviews} 70 | % \input{./Content/ChBSCOKCLBSFoutreach} 71 | % \input{./Content/ChGiftIdeas} 72 | % \input{./Content/ChGrantDeadlines} 73 | % \input{./Content/ChImprovingGraduateEducation} 74 | % \input{./Content/ChMeetingDeadlines} 75 | % \input{./Content/ChMyBiographies} 76 | % \input{./Content/ChPublicationHeirarchy} 77 | % \input{./Content/ChPythonSelfStudy} 78 | % \input{./Content/ChPythonWorkshop} 79 | % \input{./Content/ChReadingLists} 80 | % \input{./Content/ChSCUGtalks} 81 | % \input{./Content/ChToBeDone} 82 | \part{Backmatter} 83 | \backmatter %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 84 | \bibliography{global} 85 | % listofauthors must come before index 86 | %\listofauthors 87 | \printindex 88 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 89 | \end{document} 90 | -------------------------------------------------------------------------------- /2023diary/Content/Preface.tex: -------------------------------------------------------------------------------- 1 | %!TEX root = ../main.tex 2 | %%%%%%%%%%%%%%%%%%%%%% pref.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 3 | % 4 | % sample preface 5 | % 6 | % Use this file as a template for your own input. 7 | % 8 | %%%%%%%%%%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 9 | 10 | \preface 11 | \index{preface} 12 | %% Please write your preface here 13 | Here come the golden words 14 | 15 | 16 | %% Please "sign" your preface 17 | \vspace{1cm} 18 | \begin{flushright}\noindent 19 | place(s),\hfill {\it First name Surname}\\ 20 | month year\hfill {\it First name Surname}\\ 21 | \end{flushright} 22 | 23 | 24 | \section*{Known issues with typesetting this document} 25 | \index{750words} 26 | 27 | \subsection{Author index generation} 28 | The documentclass does not support author indices directly. 29 | The author index is formatted with a command called listofauthors. 30 | This command is defined in the Preamble. 31 | I found this command online. 32 | I tried to add the multicols environment. 33 | The rightmost column overlapped with the header line on the first page of the index. 34 | Hide this line might solve the problem. 35 | 36 | \subsection{Underscores and the xurl package} 37 | This package cannot handle underscores in URLs. 38 | I obtained a memory error. 39 | The solution was to comment out the xrul package. 40 | The solution was provided by Dr. LainTze Lim of Overleaf. 41 | 42 | \subsection{Stop overusing labels} 43 | Add labels only when you need them, else they will be unreferenced and trigger a lot of warnings. 44 | In addition, do not use labels in templates that write tex files unless you write only unique labels. 45 | Otherwise, you will get a warning about multiple identical labels. 46 | It is the situation with the month.tex files. 47 | All twelve had an intro label. 48 | 49 | 50 | \section*{Generation of daily record tex files for a year.} 51 | \index{750words!daily page generation} 52 | \index{setting up words for year!making pages} 53 | The month.tex files for 2021 are found in the \url{~/db/750words2015Current} subdirectory of the db subdirectory. 54 | They are in twelve separate folders labeled by month. 55 | 56 | The daily files were generated by running a Python script \emph{makeDailyPagesVarB.py} in each folder. 57 | This was done with a batch script. 58 | 59 | \begin{code}{} 60 | \index{setting up words for year!making pages} 61 | \label{lst750wordsMakingWords} 62 | \caption{Contents of genPages.sh.} 63 | \begin{minted}[frame=lines,framerule=2pt,linenos=false,xleftmargin=\parindent,breaklines]{bash} 64 | #!/bin/bash 65 | cd January 66 | ../makeDaily750PagesVerB.py 2021 'January' 1 31 67 | cd ../February 68 | ../makeDaily750PagesVerB.py 2021 'February' 1 28 69 | cd ../March 70 | ../makeDaily750PagesVerB.py 2021 'March' 1 31 71 | cd ../April 72 | ../makeDaily750PagesVerB.py 2021 'April' 1 30 73 | cd ../May 74 | ../makeDaily750PagesVerB.py 2021 'May' 1 31 75 | cd ../June 76 | ../makeDaily750PagesVerB.py 2021 'June' 1 30 77 | cd ../July 78 | ../makeDaily750PagesVerB.py 2021 'July' 1 31 79 | cd ../July 80 | ../makeDaily750PagesVerB.py 2021 'July' 1 31 81 | cd ../August 82 | ../makeDaily750PagesVerB.py 2021 'August' 1 31 83 | cd ../September 84 | ../makeDaily750PagesVerB.py 2021 'September' 1 30 85 | cd ../October 86 | ../makeDaily750PagesVerB.py 2021 'October' 1 31 87 | cd ../November 88 | ../makeDaily750PagesVerB.py 2021 'November' 1 30 89 | cd ../December 90 | ../makeDaily750PagesVerB.py 2021 'December' 1 31 91 | \end{minted} 92 | \end{code} 93 | 94 | 95 | RAM may limit 750words to one document per year. 96 | 97 | 98 | \section*{Correcting monthly.tex and making daily.tex files} 99 | \index{latex!updating tex files!sed} 100 | 101 | I used colons as delimiters in the following sed commands. 102 | 103 | \begin{code}{} 104 | \index{setting up words for year!correcting existing files} 105 | \label{lst:750words} 106 | \caption{Correcting existing files.} 107 | \begin{minted}[frame=lines,framerule=2pt,linenos=false,xleftmargin=\parindent,breaklines]{bash} 108 | find . -name "February2021.tex" -type f | xargs sed -i -e 's:2020:2021:g' 109 | find . -name "February2021.tex" -type f | xargs sed -i -e 's:./February:./Content/February:g' 110 | find . -name "./Content/October/October2021.tex" -type f | xargs sed -i -e 's:./October:./Content/October:g' 111 | find . -name "./Content/November/November2021.tex" -type f | xargs sed -i -e 's:./November:./Content/November:g' 112 | find . -name "./Content/December/December2021.tex" -type f | xargs sed -i -e 's:./December:./Content/December:g' 113 | \end{minted} 114 | \end{code} -------------------------------------------------------------------------------- /2023diary/output-globalAcronyms.tex: -------------------------------------------------------------------------------- 1 | \newacronym{ADVI}{ADVI}{Automatic Differentiation Variational Inference} 2 | \newacronym{AED}{AED}{Associative Experimental Design} 3 | \newacronym{AIC}{AIC}{Akaile Information Criterion} 4 | \newacronym{ANCOVA}{ANCOVA}{analysis of covariance} 5 | \newacronym{ANOVA}{ANOVA}{analysis of variance} 6 | \newacronym{AWS}{AWS}{Amazon.com Web Services} 7 | 8 | \newacronym{BDA}{BDA}{Bayesian data analysis} 9 | \newacronym{BEST}{BEST}{Bayesian Estimation Supercedes the T-test} 10 | \newacronym{BIC}{BIC}{Bayesian Information Criterion} 11 | \newacronym{BN}{BN}{Bayesian Network} 12 | \newacronym{BP}{BP}{Belief Propagation} 13 | \newacronym{BUGS}{BUGS}{Bayesian inference Using Gibbs Sampling} 14 | 15 | \newacronym{CLI}{CLI}{Command Line Interface} 16 | \newacronym{CMD}{CMD}{Conventional Model Discrimination} 17 | \newacronym{CRI}{CRI}{Credible Interval} 18 | 19 | \newacronym{DBN}{DBN}{Dynamic Bayesian Network} 20 | \newacronym{DIC}{DIC}{Deviance Information Criterion} 21 | \newacronym{DOE}{DOE}{Design of Experiments} 22 | 23 | \newacronym{EAP}{EAP}{Expected a posterior} 24 | \newacronym{eLLG}{eLLGI}{estimated Log-likelihood Gain on the Intensities} 25 | \newacronym{EM}{EM}{Expectation Maximization} 26 | \newacronym{ESDA}{ESDA}{exploratory sequential data analysis} 27 | 28 | \newacronym{FTP}{FTP}{File Transfer Protocol} 29 | \newacronym{FORTRAN}{FORTRAN}{FORMULA TRANSLATION} 30 | 31 | \newacronym{GA}{GA}{Genetic Algorithm} 32 | \newacronym{GAM}{GAM}{Generalized Additive Models} 33 | \newacronym{GEE}{GEE}{Generalized Esimating Equations} 34 | \newacronym{GLM}{GLM}{General Linear Models} 35 | \newacronym{GLMM}{GLMM}{General Linear Mixed Models} 36 | 37 | \newacronym{GMRF}{GMRF}{Gaussian Markov Random Field} 38 | \newacronym{GMM}{GMM}{Generalized Methods of Moments} 39 | \newacronym{GP}{GP}{Gaussian Processes} 40 | 41 | \newacronym{HM}{HM}{Hierarchical Model} 42 | \newacronym{HMC}{HMC}{Hamiltonian Monte Carlo or Hybrid MC} 43 | \newacronym{HMM}{HMM}{Hidden Markov Model} 44 | \newacronym{HPDI}{HPDI}{Highest Posterior Density Interval} 45 | 46 | \newacronym{IFE}{IFE}{Incomplete Factorial Experiments} 47 | \newacronym{IMSE}{IMSE}{Integrated Mean Squared Error} 48 | \newacronym{INLA}{INLA}{Integrated Nested Laplace Approximation} 49 | \newacronym{IW}{IW}{Inverse Wishart distribution} 50 | \newacronym{IRLS}{IRLS}{Iterative Re-Weighted Least-Squares} 51 | \newacronym{IWLS}{IWLS}{Iterative Weighted Least-Squares} 52 | 53 | \newacronym{JAGS}{JAGS}{Just Another Gibbs Sampler} 54 | 55 | \newacronym{LASSO}{LASSO}{least absobute shrinkage and selection operator} 56 | \newacronym{L-BFGS}{L-BFGS}{limited-memory Broyden-Fletcher-Goldfarb-Shanno optimizer} 57 | \newacronym{LM-BFGS}{LM-BFGS}{limited-memory Broyden-Fletcher-Goldfarb-Shanno optimizer} 58 | \newacronym{LM}{LM}{Linear Models} 59 | \newacronym{LMM}{LMM}{Linear Mixed Models} 60 | \newacronym{LKJ}{LKJ}{LKJ Distribution} 61 | \newacronym{LLGI}{LLGI}{log-likelihood Gain on the Intensities} 62 | \newacronym{LOO}{LOO}{Leave-One-Out} 63 | \newacronym{LSF}{LSF}{Load Sharing Facility} 64 | 65 | \newacronym{MALA}{MALA}{Metropolis adjusted Langevin algorithms} 66 | \newacronym{MAP}{MAP}{Maximum a posterior} 67 | \newacronym{MAXS}{MAXS}{Medium Angle X-ray Scattering} 68 | \newacronym{MCEM}{MCEM}{Monte Carlo Expectation Maximization} 69 | \newacronym{MCMC}{MCMC}{Markov chain Monte Carlo} 70 | \newacronym{ML}{ML}{Maximum Likelihood} 71 | \newacronym{MLE}{MLE}{Maximum Likelihood Estimate} 72 | \newacronym{MRF}{MRF}{Markov Random Field} 73 | \newacronym{MLIRT}{MLIRT}{multilevel item response theory} 74 | 75 | \newacronym{NB}{NB}{negative binomial} 76 | \newacronym{NB1}{NB1}{negative binomial model 1} 77 | \newacronym{NB2}{NB2}{negative binomial model 2} 78 | \newacronym{NIMBLE}{NIMBLE}{Numerical Inference Models Bayesian Likelihood Estimation} 79 | \newacronym{NUTS}{NUTS}{No U-Turn Sampler} 80 | 81 | \newacronym{OBsMD}{OBsMD}{Objective Bayesian Model Discrimination} 82 | \newacronym{ODBC}{ODBC}{Open Database Connectivity} 83 | \newacronym{OLS}{OLS}{Ordinary Least Squares} 84 | \newacronym{OMD}{OMD}{Objective Model Descrimination} 85 | 86 | \newacronym{PB}{PB}{Plackett and Burman design} 87 | \newacronym{PDF}{PDF}{Probability Density Function} 88 | \newacronym{PDDF}{PDDF}{Pairwise Distance Distribution Function (also P(r))} 89 | \newacronym{PDB}{PDB}{Protein Data Bank} 90 | \newacronym{pMCMC}{pMCMC}{particle MCMC} 91 | \newacronym{PPC}{PPC}{Posterior Predictive Checking} 92 | 93 | \newacronym{RDBMS}{RDBMS}{relational database management system} 94 | \newacronym{REST}{REST}{Representational State Transfer} 95 | \newacronym{RMHMC}{RMHMC}{Riemannian manifold Hamiltonian Monte Carlo} 96 | \newacronym{RJ-MCMC}{RJ-MCMC}{Reverse Jump-MCMC} 97 | \newacronym{RPS}{RPS}{Rotational Pseudosymmetry} 98 | \newacronym{RSM}{RSM}{Response Surface Methods} 99 | 100 | \newacronym{SAXS}{SAXS}{Small Angle X-ray Scattering} 101 | \newacronym{SFX}{SFX}{Serial Femtosecond Crystallography} 102 | \newacronym{SWAXS}{SWAXS}{Small and Wide Angle X-ray Scattering} 103 | \newacronym{SOAP}{SOAP}{Simple Object Access Processing} 104 | \newacronym{SEM}{SEM}{Structural Equation Modeling} 105 | \newacronym{SLURM}{SLURM}{Simple Linux Utility for Resource Management} 106 | \newacronym{SMS}{SMS}{Sparse Matrix Sampling} 107 | \newacronym{SMILES}{SMILES}{Simplified Molecular Input Line Entry System} 108 | \newacronym{SQL}{SQL}{Structured query language} 109 | 110 | \newacronym{TPS}{TPS}{Translational Pseudo Symmetry} 111 | 112 | \newacronym{UML}{UML}{Unified Modeling Language} 113 | 114 | \newacronym{VGAM}{VGAM}{Vector Generalizer Additive Model} 115 | \newacronym{VGLM}{VGLM}{Vector Generalizer Linear Model} 116 | 117 | \newacronym{WAIC}{WAIC}{Watanabe-Akaile Information Criterion} 118 | \newacronym{WAXS}{WAXS}{Wide Angle X-ray Scattering} 119 | \newacronym{WSDL}{WSDL}{Web services description language} 120 | 121 | \newacronym{XML}{XML}{Extensible Markup Language} 122 | 123 | \newacronym{ZINB}{ZIP}{Zero-Inflated Negative Binomial distribution} 124 | \newacronym{ZIP}{ZIP}{Zero-Inflated Poisson distribution} 125 | \newacronym{ZTNB}{ZTNB}{Zero-Truncated Negative Binomial distribution} 126 | \newacronym{ZTP}{ZTP}{Zero-Truncated Poisson distribution} 127 | 128 | 129 | -------------------------------------------------------------------------------- /2023diary/output-globalGlossary.tex: -------------------------------------------------------------------------------- 1 | \newglossaryentry{adaptive design}{name=\textbf{adaptive design},description={See Hybrid Monte Carlo.}} 2 | \newglossaryentry{Approximate Bayesian Computation}{name=\textbf{Approximate Bayesian Computation},description={A class of computational methods rooted in Bayesian statistics. ABC methods bypass the evaluation of the likelihood function and widen the realm of models for which statistical inference can be considered. ABC methods make assumptions and approximations whose impact needs to be carefully assessed. Furthermore, the wider application domain of ABC exacerbates the challenges of parameter estimation and model selection.}} 3 | \newglossaryentry{autocorrelation time}{name=\textbf{autocorrelation time},description={The number of observations from an MCMC simulation that is equivalent to a single independent observation. It is also called the correlation length, and is often represented by $\tau$. Estimates based on a MCMC simulation with a correlation time of $\tau$ will have standard errors that are about the same as those from an independent sample that is smaller in size by a factor of $\tau$.}} 4 | \newglossaryentry{candidate kernel}{name=\textbf{candidate kernel},description={The Metropolis-Hastings algorithm associated with a target density $\pi$ requires the choice a proposal kernel or candidate kernel or a conditional density from the transition of the Markov chain, $X^(t)$, from time, $t$, and its value, $X^(t+1)$, at time $(t+1)$.}} 5 | \newglossaryentry{censored data}{name=\textbf{censored data},description={Censoring hides values from points that are too large, too small, or both. The number of data points that were censored is known, unlike the case for truncated data. Data are right-censored if the value is greater than a threshold. The data are left-censored if the value is below a threshold. The censored data can be treated as missing data. In Stan, the censored data have their own array and their mean and sigma are sampled.}} 6 | \newglossaryentry{correlation length}{name=\textbf{correlation length},description={See autocorrelation time.}} 7 | \newglossaryentry{curse of dimensionality}{name=\textbf{curse of dimensionality},description={The various phenomena that arise when analyzing and organizing data in high-dimensional spaces (often with hundreds or thousands of dimensions). These phenomena do not occur in the analysis of 3-D data. The problem is caused by the exponential increase in volume associated with adding extra dimensions to a (mathematical) space. The term was coined by the applied mathematician Richard Ernest Bellman (August 26, 1920 – March 19, 1984) who introduced dynamic programming in 1953.}} 8 | \newglossaryentry{diminishing adaptation condition}{name=\textbf{diminishing adaptation condition},description={The distance between two consecutive Markov kernels must uniformly decrease to zero.}} 9 | \newglossaryentry{effective sample size}{name=\textbf{effective sample size},description={With regards to MCMC, this is the correction factor, $\tau_T$, such that $\sigma^2_T / \tau_T$ is the variance of the empirical average.}} 10 | \newglossaryentry{equidispersion}{name=\textbf{equidispersion},description={Equal dispersion of parameter values.}} 11 | \newglossaryentry{extra-dispersion}{name=\textbf{extra-dispersion},description={Extra dispersion.}} 12 | \newglossaryentry{Hybrid Monte Carlo}{name=\textbf{Hybrid Monte Carlo},description={Also known as Hamiltonian Monte Carlo. A Markov chain Monte Carlo method for obtaining a sequence of random samples from a probability distribution for which direct sampling is difficult. This sequence can be used to approximate the distribution (i.e., to generate a histogram), or to compute an integral (such as an expected value). It differs from the Metropolis–Hastings algorithm by reducing the correlation between successive sampled states by using a Hamiltonian evolution between states and additionally by targeting states with a higher acceptance criteria than the observed probability distribution. This causes it to converge more quickly to the absolute probability distribution. It was devised by Simon Duane, A.D. Kennedy, Brian Pendleton and Duncan Roweth in 1987.}} 13 | \newglossaryentry{Hamiltonian Monte Carlo}{name=\textbf{Hamiltonian Monte Carlo},description={See Hybrid Monte Carlo.}} 14 | \newglossaryentry{irreducibility}{name=\textbf{irreducibility},description={When a Markov chain has a stationary distribution and can eventually reach any region of the state space, no matter the initial value.}} 15 | \newglossaryentry{leapfrog approximation}{name=\textbf{leapfrog approximation},description={The Metropolis-Hastings correction required by the Hamiltonian Monte Carlo.}} 16 | %\newglossaryentry{Limited-memory Broyden–Fletcher–Goldfarb–Shanno}{name=\textbf{Limited-memory Broyden–Fletcher–Goldfarb–Shanno},description={The L-BFGS is an optimization algorithm in the family of quasi-Newton methods. It approximates the Broyden–Fletcher–Goldfarb–Shanno (BFGS) algorithm using a limited amount of computer memory. It is a popular algorithm for parameter estimation in machine learning. The L-BFGS estimates the inverse Hessian matrix to steer its search through variable space. On the other hand, the BFGS stores a dense n×n approximation to the inverse Hessian, where n is the number of variables in the problem. L-BFGS stores only a few vectors that represent the approximation implicitly.}} 17 | \newglossaryentry{Markov Chain Monte Carlo}{name=\textbf{Markov Chain Monte Carlo},description={A class of algorithms that simulates a Markov chain whose stationary distribution is the target distribution of interest. The stationary chain generates a sample from the target distribution.}} 18 | \newglossaryentry{Metropolis-within-Gibbs algorithm}{name=\textbf{Metropolis-within-Gibbs algorithm},description={This alogorithm aims to simulate a multidimensional distribution by successively simulating from some of the associated conditional distributions (the Gibbs part) and by using one Metropolis-Hastings steps.}} 19 | \newglossaryentry{No U-turn sampler}{name=\textbf{No U-turn sampler},description={An adaptive algorithm that aims to find the best parameter settings by tracking the sample path and preventing HMC from retracing its steps in this path.}} 20 | \newglossaryentry{overdispersion}{name=\textbf{overdispersion},description={When the observed variance is greater than the mean in count data.}} 21 | \newglossaryentry{Poisson overdispersion}{name=\textbf{Poisson overdispersion},description={The Poisson distribution has a mean that is equal to its variance. When the observed variance is greater than the mean; this is known as overdispersion and indicates that the Poisson model is not appropriate. A common reason for overdispersikon ais the omission of relevant explanatory variables, or dependent observations. Under some circumstances, the problem of overdispersion can be solved by using quasi-likelihood estimation or a negative binomial distribution instead.}} 22 | \newglossaryentry{Riemannian manifold Hamiltonian Monte Carlo}{name=\textbf{Riemannian manifold Hamiltonian Monte Carlo},description={aims to find the best parameter settings by providing adaptations using Riemannian geometry.}} 23 | \newglossaryentry{simultaneous statistical inference}{name=\textbf{simultaneous statistical inference},description={See Hybrid Monte Carlo.}} 24 | \newglossaryentry{'shock' nucleation}{name=\textbf{'shock' nucleation},description={Crystal nucleation as a result of the contact of highly concentrated protein stock solution with precipitant stock solution before mixing is complete. Shock nucleation causes the formation of crystal nuclei in solutions that are really in the metastable region of the phase diagram. }} 25 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | ![Version](https://img.shields.io/static/v1?label=diary2023inLaTeX&message=0.2&color=brightcolor) 3 | [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) 4 | 5 | # Diary for 2023 in LaTeX 6 | 7 | Go to this [site](https://github.com/MooersLab/diary2024inLaTeX) for the 2024 version of this diary. 8 | 9 | ## What is this? 10 | 11 | This repo contains a template book with 365 blank tex files, one for each day of the year. 12 | These tex files are collated and rendered into a PDF with latex and bibtex compilers. 13 | It is set up for 2023. 14 | It is configured to generate the following automatically: 15 | 16 | - Chapter headings and section headings (add subsections and lower in your daily writing). 17 | - Chapters and sections are automatically numbered. 18 | - Table of Contents, hyperlinked 19 | - References Cited, hyperlinked 20 | - Index, hyperlinked 21 | - Lists of code listings, hyperlinked 22 | - List of Figures, hyperlinked 23 | - List of Tables, hyperlinked 24 | - An appendix that uses chapters that are arranged in alphabetical order by letters instead of numbers. 25 | - Page numbers 26 | - Epigraphs for Chapter header pages 27 | - URLs in footnotes to prevent them from running into the right margin. 28 | - Syntax highlighting of code via the minted package 29 | - Supports the use of equations with captions (i.e., makes it possible to generate lists of equations). 30 | 31 | 32 | The document is based on the Springer book format, but it has a 7 by 9-inch area for writing and conservative margins to save paper. 33 | 34 | 35 | ## What is this good for? 36 | 37 | This can be used for the following purposes: 38 | 39 | - diary 40 | - laboratory notebook 41 | - log book 42 | - managing todo lists and plans 43 | - provide material for an autobiography, biography, or to stimulate nonfiction and fiction books. 44 | - to document one's life to inspire one's descendants 45 | - storage site for daily writing on sites like 750words.com 46 | 47 | This document's design was stimulated by the last use. 48 | I wanted an independent place to store my daily writing on [750words.com](https://750words.com), where it is stored in plain text files that are hard to search. 49 | I wanted that writing to be indexable and searchable in a single PDF for a calendar year rather than 365 files. 50 | This document has been very useful for finding information, including data wrangling protocols and computer code, that I used in the past. 51 | It can gather information for annual reports if used as a "Captian's log" of one's personal Enterprise. 52 | For example, lists of accomplishments can be stored in the Appendices. 53 | 54 | ## Prior Experience 55 | 56 | I have been using something like this since 2012, and this document has been in its current format since 2015. 57 | Each year's document has run about 1000-1200 pages in length. 58 | It is part of my daily routine to paste the day's writing into this document before retiring for the day or first thing in the following morning. 59 | 60 | ## Limitations 61 | 62 | Writing in LaTeX has some limitations: 63 | 64 | - The document is limited by computer RAM to one year. 65 | - The document is limited by RAM regarding the number of lists and indices that can be generated simultaneously. 66 | - Debugging can sometimes involve commenting out chapters in the 0AAAContent document to isolate the error. 67 | 68 | Not to worry! The debugger on Overleaf will locate the bug by document name and line number. 69 | A click on an arrow will take you to the bug in the correct file. 70 | 71 | I generally fall behind on my debugging and will comment out earlier chapters to prevent their errors from stopping compiling. 72 | I debug the old writing occasionally during the year when I am too tired to do anything else and during winter break before the start of the new year. 73 | 74 | ## Compiling 75 | 76 | The *main.tex* document is fed to the compiler. 77 | 78 | Compile with lualatex and the `-escape-shell` key (for the minted package). 79 | The `compile.sh` script runs at the top level of the folder `2023diary`, which you can rename. 80 | The document is easy to compile with the click of a button using the Overleaf website. 81 | The empty shell document takes several seconds to compile. 82 | A 1000-page document will be compiled in about 60 seconds. 83 | 84 | This long compile time is another advantage of the modular approach as opposed to having everything in one tex file. 85 | I comment out the inactive months in the *0AAAContents.tex* file to shorten the compile time to a few seconds. 86 | 87 | ## Role of the 0AAAContents.tex file. 88 | 89 | The *0AAAContents.tex* file is the central nervous system of the document. 90 | It is trival to comment out entire chapters via a single percent sign. 91 | It is also trivial in Emacs to shuffle the order of the chapters by moving lines up or down. 92 | You can add prose to the *0AAAContents.tex* file, but I find it adds clutter to this file. 93 | 94 | ## Configuration 95 | 96 | - Edit the title and author at the top of the A000Contents.tex file in the Content subfolder. 97 | - Change the cover figure to suit by loading a new image into the ./Content/Figures subfolder and by editing the path to the image to specify this new figure. Some image file formats like tiff are not supported. Png and PDF are reliable. 98 | - Comment out the lists you do not intend to use in 0AAAContent. For example, if you do not save computer code, the list of listings will not be used. 99 | - Add new appendices like your annual plan as a text file. 100 | 101 | ## Daily use 102 | 103 | The documents to be edited are in chapter subfolders in the Content subfolders. 104 | Each day's entry is in a separate tex file. 105 | Navigate to the file corresponding to the current date and write on line two. 106 | The code on the first line must remain in place for the document to compile. 107 | 108 | Each file forms a section of a chapter. 109 | This book has one chapter per month. 110 | All sections for a month are in a chapter subfolder in the Content folder. 111 | 112 | ## On-line editor 113 | 114 | I recommend using the online editor Overleaf for the smoothest operation. 115 | I have been editing this document on Overleaf for six years. 116 | You do NOT have to run each of the steps of compiling separately. 117 | You just click a button, and the latex and bibtex compilers are run seamlessly. 118 | I store the URL for this project on my private home page for rapid access. 119 | 120 | You can compile the entire document with any document open in the text area because the main document is set in the menu panel on the left. 121 | This menu is also where you configure the compiler, key bindings, color theme, etc. 122 | 123 | ## Local editors 124 | 125 | In terms of local editing, there are many (>20) freely available text editors that are highly supported for editing documents in LaTeX. 126 | The following are perhaps the most popular general-purpose editors that have great support for LaTeX: 127 | 128 | - TextMate for the Mac (very easy to compile with `cmd-R`) 129 | - Sublime Text 130 | - VSC 131 | - Vim 132 | - Emacs 133 | 134 | TextMate for the Mac does not get enough love these days. 135 | It starts lightning fast. 136 | I open the editor most frequently, although I am trying to migrate to Emacs. 137 | 138 | Thanks to elisp and a dedicated developer community, Emacs is the most configurable editor. 139 | 140 | ### Emacs 141 | 142 | Must be configured to use laulatex and -escape-shell. 143 | It might be easiest to call the shell with `M-!` and enter `compile.sh, main.tex` to compile and open in your default PDF viewer. 144 | Or just run the compile.sh script externally to Emacs. 145 | 146 | See the `latex-emacs` repo for a sample configuration. 147 | If you have citations, you will have to run bibtex on main.tex. 148 | 149 | ## Best of both worlds: use local editor to edit today's entry on Overleaf 150 | 151 | The Google Chrome extension [GhostText](https://ghosttext.fregante.com/) supports using several kinds of local editors to edit text areas in web browsers. 152 | The opened *toadayDate.tex* file is a text area in Overleaf. 153 | You can bring your favorite LaTeX snippets to bear on Overleaf, which does not support snippets directly. 154 | 155 | For example, I start the day by opening Emacs, logging into 750words, and clicking on the GhostText icon to open the connection to Emacs. 156 | In Emacs in the **Write your words** buffer, I enter `start` and hit `TAB` or `C-o`. 157 | This action inserts the following boilerplate from the `start` snippet file, which is available above. 158 | I have [configured](https://github.com/MooersLab/latex-emacs) the Emacs package [atomic-chrome](https://github.com/alpha22jp/atomic-chrome) to open `Write your words` in the latex-mode so that I can have access to my latex-mode snippets, which are available [here](https://github.com/MooersLab/snippet-latex-mode). 159 | 160 | ```latex 161 | \subsection{Last night} 162 | change me 163 | 164 | 165 | \subsection{This morning} 166 | change me 167 | 168 | 169 | \subsection{To Be Done Today} 170 | \index{To Be Done!2022-09-04} 171 | \begin{itemize} 172 | \item change me 173 | \item change me 174 | \item change me 175 | \item change me 176 | \item change me 177 | \item change me 178 | \item change me 179 | \item change me 180 | \item change me 181 | \item change me 182 | \end{itemize} 183 | 184 | ``` 185 | 186 | The cursor advances to `change me` under *Last night*. 187 | I write some notes about what I did. 188 | Then I hit tab to advance to the next `change me` to write notes about the morning. 189 | I hit tab again to advance to the first item in my TODO list for the day. 190 | When I reach the bottom of the list, I enter `C-c C-j` to enter the next **\item** properly aligned and with the cursor in the right position. 191 | 192 | A call to a macro inside the yasnippet snippet called *start* inserts the correct date in the index key. 193 | I create an index key without lifting a finger. 194 | **See, Life can be Good in Emacs!** 195 | 196 | See the end of this [slideshow](https://github.com/MooersLab/BerlinEmacsAugust2022) for the application of GhostText to LaTeX editing with Emacs. 197 | For Jupyter users, you can likewise use GhostText to edit code and markdown cells with your favorite editor. 198 | See [slideshow](https://github.com/MooersLab/DSW22ghosttext) about this exciting topic. 199 | See the corresponding [video](https://mediasite.ouhsc.edu/Mediasite/Channel/python/watch/4da0872f028c4255ae12935655e911321d). 200 | 201 | ## Related projects of possible interest 202 | 203 | - [LaTeX manuscript template](https://github.com/MooersLab/manuscriptInLaTeX/edit/main/README.md) 204 | - [Writing log template in LaTeX](https://github.com/MooersLab/writingLogTemplate) 205 | - [Slideshow template in LaTeX](https://github.com/MooersLab/slideshowTemplateLaTeX) 206 | - [Annotated bibliography Template in LaTeX](https://github.com/MooersLab/annotatedBibliography) 207 | - [Diary for 2022 in LaTeX](https://github.com/MooersLab/diary2022inLaTeX) 208 | - [Diary for 2023 in LaTeX](https://github.com/MooersLab/diary2023inLaTeX) 209 | - [latex-emacs profile](https://github.com/MooersLab/latex-emacs) 210 | - [snippets for latex-mode in Emacs](https://github.com/MooersLab/snippet-latex-mode) 211 | - [Quizzes about Emacs to improve recall of keybindings](https://github.com/MooersLab/qemacs) 212 | - [Slides from talk about GhostText, Data Science Workshop, July 2022](https://github.com/MooersLab/DSW22ghosttext) 213 | - [Video link to talk about GhostText, Data Science Workshop, July 2022](https://mediasite.ouhsc.edu/Mediasite/Channel/python/watch/4da0872f028c4255ae12935655e911321d) 214 | - [The writer's law](https://github.com/MooersLab/thewriterslaw) 215 | 216 | ## Update history 217 | 218 | |Version | Changes | Date | 219 | |:-----------:|:------------------------------------------------------------------------------------------------------------------------------------------:|:--------------------:| 220 | | Version 0.2 | Added badges, funding, and update table. | 2024 May 23 | 221 | 222 | 223 | ## Sources of funding 224 | 225 | - NIH: R01 CA242845 226 | - NIH: R01 AI088011 227 | - NIH: P30 CA225520 (PI: R. Mannel) 228 | - NIH: P20 GM103640 and P30 GM145423 (PI: A. West) 229 | 230 | -------------------------------------------------------------------------------- /2023diary/crop.sty: -------------------------------------------------------------------------------- 1 | %% 2 | %% This is file `crop.sty', 3 | %% generated with the docstrip utility. 4 | %% 5 | %% The original source files were: 6 | %% 7 | %% crop.dtx (with options: `package') 8 | %% 9 | %% IMPORTANT NOTICE: 10 | %% 11 | %% For the copyright see the source file. 12 | %% 13 | %% Any modified versions of this file must be renamed 14 | %% with new filenames distinct from crop.sty. 15 | %% 16 | %% For distribution of the original source see the terms 17 | %% for copying and modification in the file crop.dtx. 18 | %% 19 | %% This generated file may be distributed as long as the 20 | %% original source files, as listed above, are part of the 21 | %% same distribution. (The sources need not necessarily be 22 | %% in the same archive or directory.) 23 | %% File: crop.dtx Copyright (C) 1998, 1999, 2000, 2001 Melchior FRANZ 24 | %% $Id: crop.dtx,v 1.21 2001/11/16 21:12:14 m Exp $ 25 | \NeedsTeXFormat{LaTeX2e} 26 | \ProvidesPackage{crop}[2001/11/16 v1.6 cropmarks (mf)] 27 | \newdimen\CROP@width \CROP@width\z@ 28 | \newdimen\CROP@height \CROP@height\z@ 29 | \newcount\CROP@index \CROP@index\z@ 30 | \newcommand*\CROP@includegraphics{% 31 | \PackageError{crop}% 32 | {Package file `graphics.sty' not found.}{The options 33 | `nographics' and `graphics' require the graphics package.}} 34 | \newcommand*\CROP@driver{} 35 | \IfFileExists{graphics.sty}{% 36 | \RequirePackage{graphics}% 37 | \let\CROP@includegraphics\includegraphics 38 | \ifx\Gin@driver\@empty\else 39 | \filename@parse{\Gin@driver}% 40 | \edef\CROP@driver{\filename@base}% 41 | \fi 42 | }{} 43 | \newcommand*\CROP@font{} 44 | \newcommand*\CROP@size[2]{\CROP@width#1 \CROP@height#2 } 45 | \DeclareOption{landscape}{% 46 | \def\CROP@size#1#2{\CROP@height#1 \CROP@width#2 }} 47 | \DeclareOption{a0}{\CROP@size{841truemm}{1189truemm}} 48 | \DeclareOption{a1}{\CROP@size{595truemm}{841truemm}} 49 | \DeclareOption{a2}{\CROP@size{420truemm}{595truemm}} 50 | \DeclareOption{a3}{\CROP@size{297truemm}{420truemm}} 51 | \DeclareOption{a4}{\CROP@size{210truemm}{297truemm}} 52 | \DeclareOption{a5}{\CROP@size{149truemm}{210truemm}} 53 | \DeclareOption{a6}{\CROP@size{105truemm}{149truemm}} 54 | \DeclareOption{b0}{\CROP@size{1000truemm}{1414truemm}} 55 | \DeclareOption{b1}{\CROP@size{707truemm}{1000truemm}} 56 | \DeclareOption{b2}{\CROP@size{500truemm}{707truemm}} 57 | \DeclareOption{b3}{\CROP@size{353truemm}{500truemm}} 58 | \DeclareOption{b4}{\CROP@size{250truemm}{353truemm}} 59 | \DeclareOption{b5}{\CROP@size{176truemm}{250truemm}} 60 | \DeclareOption{b6}{\CROP@size{125truemm}{176truemm}} 61 | \DeclareOption{letter}{\CROP@size{8.5truein}{11truein}} 62 | \DeclareOption{legal}{\CROP@size{8.5truein}{14truein}} 63 | \DeclareOption{executive}{\CROP@size{7.25truein}{10.5truein}} 64 | \DeclareOption{center}{\AtEndOfPackage{\CROP@center}} 65 | \newcommand*\CROP@center{% 66 | \ifdim\CROP@width=\z@ 67 | \PackageError{crop}{no printing paper size selected}{% 68 | you have to select a paper size before you can use % 69 | the `center' option 70 | }% 71 | \else 72 | \voffset\CROP@height 73 | \advance\voffset-\paperheight\voffset.5\voffset 74 | \hoffset\CROP@width 75 | \advance\hoffset-\paperwidth\hoffset.5\hoffset 76 | \fi 77 | } 78 | \DeclareOption*{\CROP@execopt\CurrentOption} 79 | \newcommand*\crop[1][cam,noaxes]{% 80 | \@for\CROP@@:=#1\do{\CROP@execopt\CROP@@}} 81 | \newcommand*\CROP@execopt[1]{% 82 | \def\CROP@##1=##2=##3\@nil{\def\CROP@{##1}\def\CROP@@{##2}}% 83 | \expandafter\CROP@#1==\@nil% 84 | \@ifundefined{CROP@opt@\CROP@}% 85 | {\PackageError{crop}{Requested option `#1' not provided}% 86 | {Note that the `*center' options are obsolete. You have to 87 | request\MessageBreak e.g. [a4,center] instead of [a4center].}}% 88 | {\@nameuse{CROP@opt@\CROP@}}} 89 | \newcommand*\cropdef[6][\CROP@@info]{% 90 | \@namedef{CROP@opt@#6}{% 91 | \CROP@on 92 | \def\CROP@info{#1}% 93 | \let\CROP@ulc#2 94 | \let\CROP@urc#3 95 | \let\CROP@llc#4 96 | \let\CROP@lrc#5}} 97 | \newcommand*\CROP@@vaxis{% 98 | \hfil 99 | \setbox\z@\hbox{\vtop{\hrule\@height12\p@\@depth-2\p@\@width.4\p@ 100 | \vskip\paperheight\vskip4\p@ 101 | \hrule\@height\z@\@depth10\p@\@width.4\p@}}% 102 | \ht\z@\z@ \dp\z@\z@ \box\z@ 103 | \hfil} 104 | \newcommand*\CROP@@haxis{% 105 | \vfil 106 | \hb@xt@\paperwidth{% 107 | \llap{\vrule\@height.2\p@\@depth.2\p@\@width10\p@\hskip2\p@}% 108 | \hfil 109 | \rlap{\hskip2\p@\vrule\@height.2\p@\@depth.2\p@\@width10\p@}}% 110 | \vfil} 111 | \newcommand*\CROP@time{} 112 | {\count@\time \divide\time60 \count\@ne\time 113 | \multiply\time60 \advance\count@-\time 114 | \xdef\CROP@time{\the\count\@ne:\two@digits{\count@}}} 115 | \newcommand*\CROP@@info{{\global\advance\CROP@index\@ne 116 | \def\x{\discretionary{}{}{\hbox{\kern.5em---\kern.5em}}}% 117 | \hskip10\p@\advance\paperwidth-20\p@ 118 | \raise8\p@\vbox to\z@{\centering\hsize\paperwidth\vss 119 | \normalfont\let\protect\relax\CROP@font{% 120 | ``\jobname''\x\the\year/\the\month/\the\day\x\CROP@time\x 121 | page\kern.5em\thepage\x\#\the\CROP@index\strut}}}} 122 | \newcommand*\CROP@opt@font{\let\CROP@font\CROP@@} 123 | \newcommand*\CROP@@ulc{% 124 | \begin{picture}(0,0)\unitlength\p@\thinlines 125 | \put(-30,0){\circle{10}} 126 | \put(-30,-5){\line(0,1){10}} 127 | \put(-35,0){\line(1,0){30}} 128 | \put(0,30){\circle{10}} 129 | \put(-5,30){\line(1,0){10}} 130 | \put(0,35){\line(0,-1){30}} 131 | \end{picture}} 132 | \newcommand*\CROP@@urc{% 133 | \begin{picture}(0,0)\unitlength\p@\thinlines 134 | \put(30,0){\circle{10}} 135 | \put(30,-5){\line(0,1){10}} 136 | \put(35,0){\line(-1,0){30}} 137 | \put(0,30){\circle{10}} 138 | \put(-5,30){\line(1,0){10}} 139 | \put(0,35){\line(0,-1){30}} 140 | \end{picture}} 141 | \newcommand*\CROP@@llc{% 142 | \begin{picture}(0,0)\unitlength\p@\thinlines 143 | \put(-30,0){\circle{10}} 144 | \put(-30,-5){\line(0,1){10}} 145 | \put(-35,0){\line(1,0){30}} 146 | \put(0,-30){\circle{10}} 147 | \put(-5,-30){\line(1,0){10}} 148 | \put(0,-35){\line(0,1){30}} 149 | \end{picture}} 150 | \newcommand*\CROP@@lrc{% 151 | \begin{picture}(0,0)\unitlength\p@\thinlines 152 | \put(30,0){\circle{10}} 153 | \put(30,-5){\line(0,1){10}} 154 | \put(35,0){\line(-1,0){30}} 155 | \put(0,-30){\circle{10}} 156 | \put(-5,-30){\line(1,0){10}} 157 | \put(0,-35){\line(0,1){30}} 158 | \end{picture}} 159 | \cropdef\CROP@@ulc\CROP@@urc\CROP@@llc\CROP@@lrc{cam} 160 | \newcommand*\CROP@@cross{% 161 | \begin{picture}(0,0)\unitlength1in\thinlines 162 | \put(-1,0){\line(1,0){2}} 163 | \put(0,-1){\line(0,1){2}} 164 | \end{picture}} 165 | \cropdef\CROP@@cross\CROP@@cross\CROP@@cross\CROP@@cross{cross} 166 | \newcommand*\CROP@@frame{% 167 | \begin{picture}(0,0)\unitlength\p@\thinlines 168 | \put(0,0){\line(1,0){\strip@pt\paperwidth}} 169 | \put(0,0){\line(0,-1){\strip@pt\paperheight}} 170 | \put(\strip@pt\paperwidth,0){\line(0,-1){\strip@pt\paperheight}} 171 | \put(0,-\strip@pt\paperheight){\line(1,0){\strip@pt\paperwidth}} 172 | \end{picture}} 173 | \cropdef\CROP@@frame\relax\relax\relax{frame} 174 | \let\CROP@shipout\shipout 175 | \renewcommand*\shipout{\afterassignment\CROP@ship\setbox\@cclv=} 176 | \newcommand*\CROP@ship{% 177 | \ifvoid\@cclv\expandafter\aftergroup\fi\CROP@@ship} 178 | \newcommand*\CROP@shiplist{\CROP@@@ship\box\@cclv} 179 | \newcommand*\CROP@@ship{\CROP@shipout\vbox{\CROP@shiplist}} 180 | \newcommand*\CROP@shipadd[1]{\begingroup 181 | \toks@\expandafter{\expandafter#1\expandafter{\CROP@shiplist}}% 182 | \xdef\CROP@shiplist{\the\toks@}% 183 | \endgroup} 184 | \newcommand*\CROP@kernel{\color@setgroup 185 | \vbox to\z@{\vskip\CROP@vorigin 186 | \hb@xt@\z@{\hskip\CROP@horigin 187 | \CROP@every 188 | \vbox to\paperheight{% 189 | \hb@xt@\paperwidth{% 190 | \setbox\z@\hbox{\normalfont\CROP@@@info}% 191 | \ht\z@\z@ \dp\z@\z@ \wd\z@\z@ \box\z@ 192 | \CROP@ulc\CROP@uedge\CROP@urc}% 193 | \CROP@ledge 194 | \hb@xt@\paperwidth{% 195 | \CROP@llc\hfil\CROP@lrc}}% 196 | \hss}% 197 | \vss}\color@endgroup} 198 | \newcommand*\CROP@opt@horigin{\let\CROP@horigin\CROP@@} 199 | \newcommand*\CROP@opt@vorigin{\let\CROP@vorigin\CROP@@} 200 | \newcommand*\CROP@@@ship{} 201 | \newcommand*\CROP@on{\let\CROP@@@ship\CROP@kernel} 202 | \newcommand*\CROP@opt@off{\let\CROP@@@ship\relax} 203 | \newcommand*\CROP@@@info{} 204 | \newcommand*\CROP@opt@info{\def\CROP@@@info{\CROP@info}} 205 | \newcommand*\CROP@opt@noinfo{\let\CROP@@@info\relax} 206 | \newcommand*\CROP@opt@axes{% 207 | \let\CROP@uedge\CROP@@vaxis 208 | \let\CROP@ledge\CROP@@haxis} 209 | \newcommand*\CROP@opt@noaxes{% 210 | \let\CROP@uedge\hfil 211 | \let\CROP@ledge\vfil} 212 | \expandafter\newcommand\expandafter*\csname CROP@opt@mount1\endcsname 213 | {\let\CROP@every\relax} 214 | \newcount\CROP@offset 215 | \expandafter\newcommand\expandafter*\csname CROP@opt@mount2\endcsname 216 | {\CROP@offset=\ifx\CROP@@\empty\z@\else\CROP@@\fi 217 | \def\CROP@every{\count@\c@page 218 | \advance\count@\CROP@offset 219 | \ifodd\count@ 220 | \let\CROP@ulc\relax\let\CROP@llc\relax 221 | \else 222 | \let\CROP@urc\relax\let\CROP@lrc\relax\let\CROP@info\relax 223 | \fi}} 224 | \DeclareOption{mirror}{% 225 | \AtBeginDocument{\CROP@shipadd\CROP@reflect\CROP@setps}} 226 | \newcommand*\CROP@reflect[1]{% 227 | \vbox to\z@{\vskip\CROP@vorigin\hb@xt@\z@{\hskip\CROP@horigin 228 | \CROP@ps{gsave currentpoint}\kern\paperwidth 229 | \CROP@ps{currentpoint}\hss}\vss}% 230 | \CROP@ps{translate -1 1 scale neg exch neg exch translate}% 231 | \vbox{#1}% 232 | \CROP@ps{grestore}} 233 | \DeclareOption{rotate}{% 234 | \AtBeginDocument{\CROP@shipadd\CROP@rotate\CROP@setps}} 235 | \newcommand*\CROP@rotate[1]{% 236 | \hb@xt@\z@{\hskip\CROP@horigin\vbox to\z@{\vskip\CROP@vorigin 237 | \CROP@ps{gsave currentpoint}\kern\paperheight 238 | \hb@xt@\z@{\kern\paperwidth\CROP@ps{currentpoint}\hss}\vss}\hss}% 239 | \CROP@ps{translate 180 rotate neg exch neg exch translate}% 240 | \vbox{#1}% 241 | \CROP@ps{grestore}} 242 | \newcommand*\CROP@setps{% 243 | \ifx\Gin@PS@raw\@undefined 244 | \PackageWarning{crop}{internal PostScript interface used}% 245 | \newcommand*\CROP@ps[1]{\special{ps: ##1}}% 246 | \else 247 | \PackageInfo{crop}{graphics/color PostScript interface used}{}% 248 | \let\CROP@ps\Gin@PS@raw 249 | \fi 250 | \let\CROP@setps\relax} 251 | \DeclareOption{invert}{% 252 | \AtEndOfPackage{\RequirePackage{color}}% 253 | \AtBeginDocument{\CROP@invert{black}}} 254 | \newcommand*\CROP@invert[1]{% 255 | \ifx\color\@undefined 256 | \PackageWarning{crop}% 257 | {The `color' package could not be loaded, so I'm\MessageBreak 258 | ignoring the `invert' and `notext' option}% 259 | \else 260 | \pagecolor{#1}\color{white}% 261 | \newcommand\CROP@color[2][]{}% 262 | \DeclareRobustCommand\color{\CROP@color}% 263 | \DeclareRobustCommand\pagecolor{\CROP@color}% 264 | \DeclareRobustCommand\textcolor{\CROP@color}% 265 | \let\normalcolor\relax 266 | \fi 267 | \let\CROP@invert\relax} 268 | \DeclareOption{notext}{% 269 | \AtEndOfPackage{\RequirePackage{color}}% 270 | \AtBeginDocument{\CROP@invert{white}}} 271 | \newcommand*\CROP@incgrph{} 272 | \newcommand*\CROP@opt@nographics{% 273 | \def\includegraphics##1##{\bgroup 274 | \let\special\@gobble 275 | \CROP@incgrph{##1} 276 | }% 277 | \def\CROP@incgrph##1##2{% 278 | \CROP@includegraphics##1{##2}\egroup 279 | }% 280 | } 281 | \newcommand*\CROP@opt@graphics{% 282 | \let\includegraphics\CROP@includegraphics} 283 | \newcommand*\CROP@compat{\PackageWarning{crop}{center options like 284 | `a4center' are obsolete and only\MessageBreak provided for 285 | compatibility reasons. They will be removed\MessageBreak in future 286 | releases. Use the new options `a4'\MessageBreak and 287 | `center' separately instead.}} 288 | \DeclareOption{landscapecenter}{% 289 | \CROP@compat\ExecuteOptions{landscape,center}} 290 | \DeclareOption{a4center}{% 291 | \CROP@compat\ExecuteOptions{a4,center}} 292 | \DeclareOption{a5center}{% 293 | \CROP@compat\ExecuteOptions{a5,center}} 294 | \DeclareOption{b5center}{% 295 | \CROP@compat\ExecuteOptions{b5,center}} 296 | \DeclareOption{b4center}{% 297 | \CROP@compat\ExecuteOptions{b4,center}} 298 | \DeclareOption{lettercenter}{% 299 | \CROP@compat\ExecuteOptions{letter,center}} 300 | \DeclareOption{legalcenter}{% 301 | \CROP@compat\ExecuteOptions{legal,center}} 302 | \DeclareOption{executivecenter}{% 303 | \CROP@compat\ExecuteOptions{executive,center}} 304 | \DeclareOption{vtex}{\renewcommand*\CROP@driver{vtex}} 305 | \DeclareOption{pdftex}{\renewcommand*\CROP@driver{pdftex}} 306 | \DeclareOption{pdflatex}{\renewcommand*\CROP@driver{pdftex}} 307 | \DeclareOption{dvips}{\renewcommand*\CROP@driver{dvips}} 308 | \newcommand*\CROP@init@dvips{% 309 | \PackageInfo{crop}{using dvips graphics driver}% 310 | \ifdim\CROP@width=\z@\else 311 | \special{papersize=\the\CROP@width,\the\CROP@height}% 312 | \fi 313 | } 314 | \newcommand*\CROP@init@pdftex{% 315 | \PackageInfo{crop}{using pdf(la)tex graphics driver}% 316 | \ifx\@undefined\pdfpagewidth 317 | \PackageWarning{crop}{implicit or explicit pdf(la)tex option 318 | ignored:^^JThis isn't pdftex!}% 319 | \else 320 | \ifdim\CROP@width=\z@\else 321 | \pdfpagewidth\CROP@width 322 | \pdfpageheight\CROP@height 323 | \fi 324 | \renewcommand*\CROP@opt@nographics{% 325 | \renewcommand\includegraphics[2][]{% 326 | \phantom{\CROP@includegraphics[####1]{####2}} 327 | }% 328 | }% 329 | \fi 330 | } 331 | \newcommand*\CROP@init@vtex{% 332 | \PackageInfo{crop}{using vtex graphics driver}% 333 | \ifdim\CROP@width=\z@\else 334 | \ifx\@undefined\mediawidth 335 | \PackageWarning{crop}{implicit or explicit vtex option 336 | ignored:^^JThis isn't vtex!}% 337 | \else 338 | \mediawidth\CROP@width \mediaheight\CROP@height 339 | \fi 340 | \fi 341 | } 342 | \newcommand*\CROP@horigin{-1truein} 343 | \newcommand*\CROP@vorigin{-1truein} 344 | \crop[off,noaxes,info,mount1] 345 | \InputIfFileExists{crop.cfg}% 346 | {\PackageInfo{crop}{Local config file crop.cfg used}}{} 347 | \ProcessOptions 348 | \AtEndOfPackage{\@nameuse{CROP@init@\CROP@driver}} 349 | \endinput 350 | %% 351 | %% End of file `crop.sty'. 352 | -------------------------------------------------------------------------------- /2023diary/Content/annotatedBibliography/AnnoBibMyBDA.bib: -------------------------------------------------------------------------------- 1 | @Book{ albert2009bayesiancomputationwithr, 2 | title = {Bayesian computation with R}, 3 | publisher = {Springer Science \& Business Media}, 4 | year = {2009}, 5 | author = {Albert, Jim}, 6 | annote = {This is a concise book for someone with a strong 7 | background in math and statistics. A biologist may view 8 | this an intermediate-level book. It would be worth reading 9 | after mastering Kery 2010 in order to deepen your 10 | understanding of Bayesian statistics and to realize that 11 | you do not have to use WinBUGS or Stan with every 12 | problem.}, 13 | endnotereftype= {Book}, 14 | owner = {blaine-mooers}, 15 | shorttitle = {Bayesian computation with R} 16 | } 17 | 18 | @Article{ chaloner1995bayesianexperimentaldesignareview, 19 | author = {Chaloner, Kathryn and Verdinelli, Isabella}, 20 | title = {Bayesian experimental design: A review}, 21 | journal = {Statistical Science}, 22 | year = {1995}, 23 | volume = {10}, 24 | pages = {273-304}, 25 | endnotereftype= {Journal Article}, 26 | owner = {blaine-mooers}, 27 | shorttitle = {Bayesian experimental design: A review} 28 | } 29 | 30 | @Article{ kass1995bayesfactors, 31 | author = {Kass, Robert E. and Raftery, Adrian E.}, 32 | title = {Bayes factors}, 33 | journal = {Journal of the american statistical association}, 34 | year = {1995}, 35 | volume = {90}, 36 | number = {430}, 37 | pages = {773-795}, 38 | endnotereftype= {Journal Article}, 39 | owner = {blaine-mooers}, 40 | publisher = {Taylor \& Francis Group}, 41 | shorttitle = {Bayes factors} 42 | } 43 | 44 | @Book{ kery2010introductiontowinbugsforecologists, 45 | title = {Introduction to WinBUGS for ecologists: Bayesian approach 46 | to regression, ANOVA, mixed models and related analyses}, 47 | publisher = {Academic Press}, 48 | year = {2010}, 49 | author = {K{\'e}ry, Marc}, 50 | annote = {I have this book. It is unique in that is presents data 51 | simulations along with linear models using Bayesian and 52 | frequentist approaches. This parts that I have read I like 53 | very much. The book is very well organized.} 54 | } 55 | 56 | @Book{ lesaffre2012bayesianbiostatisticsa, 57 | title = {Bayesian biostatistics}, 58 | publisher = {John Wiley \& Sons}, 59 | year = {2012}, 60 | author = {Lesaffre, Emmanuel and Lawson, Andrew B.}, 61 | annote = {I have a copy of this book. I have written a brief review 62 | of it for myself.}, 63 | endnotereftype= {Book}, 64 | owner = {blaine-mooers}, 65 | shorttitle = {Bayesian biostatistics} 66 | } 67 | 68 | @Book{ mcgrayne2011theorythatwouldnotdie, 69 | title = {The theory that would not die: how Bayes' rule cracked the 70 | enigma code, hunted down Russian submarines, \& emerged 71 | triumphant from two centuries of controversy}, 72 | publisher = {Yale University Press}, 73 | year = {2011}, 74 | author = {McGrayne, Sharon Bertsch} 75 | } 76 | 77 | @Book{ lunn2012thebugsbook, 78 | title = {The {BUGS} Book: A Practical Introduction to {B}ayesian 79 | Analysis}, 80 | publisher = {Chapman \& Hall/CRC Press}, 81 | year = {2012}, 82 | author = {Lunn, David}, 83 | series = {Chapman \& Hall/CRC Texts in Statistical Science series}, 84 | address = {Boca Raton, FL}, 85 | abstract = {Bayesian statistical methods have become widely used for 86 | data analysis and modelling in recent years, and the BUGS 87 | software has become the most popular software for Bayesian 88 | analysis worldwide. Authored by the team that originally 89 | developed this software, The BUGS Book provides a practical 90 | introduction to this program and its use. The text presents 91 | complete coverage of all the functionalities of BUGS, 92 | including prediction, missing data, model criticism, and 93 | prior sensitivity. It also features a large number of 94 | worked examples and a wide range of applications from 95 | various disciplines. The book introduces regression models, 96 | techniques for criticism and comparison, and a wide range 97 | of modelling issues before going into the vital area of 98 | hierarchical models, one of the most common applications of 99 | Bayesian methods. It deals with essentials of modelling 100 | without getting bogged down in complexity. The book 101 | emphasises model criticism, model comparison, sensitivity 102 | analysis to alternative priors, and thoughtful choice of 103 | prior distributions---all those aspects of the ``art'' of 104 | modelling that are easily overlooked in more theoretical 105 | expositions. More pragmatic than ideological, the authors 106 | systematically work through the large range of ``tricks'' 107 | that reveal the real power of the BUGS software, for 108 | example, dealing with missing data, censoring, grouped 109 | data, prediction, ranking, parameter constraints, and so 110 | on. Many of the examples are biostatistical, but they do 111 | not require domain knowledge and are generalisable to a 112 | wide range of other application areas. Full code and data 113 | for examples, exercises, and some solutions can be found on 114 | the book's website.}, 115 | isbn = {978-1-5848-8849-9}, 116 | orderinfo = {crcpress.txt}, 117 | owner = {blaine-mooers}, 118 | timestamp = {2016.08.03}, 119 | url = {http://www.crcpress.com/product/isbn/9781584888499} 120 | } 121 | 122 | @Article{ gelfand1990illustrationofbayesianinferenceinnormaldatamodelsusinggibbssampling, 123 | author = {Gelfand, Alan E and Hills, Susan E and Racine-Poon, Amy 124 | and Smith, Adrian FM}, 125 | title = {Illustration of Bayesian inference in normal data models 126 | using Gibbs sampling}, 127 | journal = {Journal of the American Statistical Association}, 128 | year = {1990}, 129 | volume = {85}, 130 | number = {412}, 131 | pages = {972--985}, 132 | annnote = {This is the first article about using Gibbs sampling. It 133 | has been cited 1068 times according to Google Scholar. It 134 | includes the Rat growth example. In this example, the 135 | gorwth of 30 rats were monitored for five weeks. Larger 136 | Rats are assumed to gain weight faster. In other words, the 137 | slope and intercept of their growth data are correlated. 138 | This statistical model was a multivariate model that 139 | allowed for the correlation betwen the slope and intercept. 140 | }, 141 | publisher = {Taylor \& Francis Group}, 142 | url = {http://people.umass.edu/bioep740/yr2009/topics/gelfand-1990-jasa.pdf} 143 | } 144 | 145 | @Article{ carpenter2016stanaprobabilisticprogramminglanguage, 146 | author = {Carpenter, Bob and Gelman, Andrew and Hoffman, Matt and 147 | Lee, Daniel and Goodrich, Ben and Betancourt, Michael and 148 | Brubaker, Michael A and Guo, Jiqiang and Li, Peter and 149 | Riddell, Allen}, 150 | title = {Stan: A probabilistic programming language}, 151 | journal = {J Stat Softw}, 152 | year = {2016}, 153 | volume = {0}, 154 | pages = {000-000} 155 | } 156 | 157 | @Book{ gelman2014bayesiandataanalysis, 158 | title = {Bayesian data analysis}, 159 | publisher = {Chapman \& Hall/CRC Boca Raton, FL, USA}, 160 | year = {2014}, 161 | author = {Gelman, Andrew and Carlin, John B and Stern, Hal S and 162 | Rubin, Donald B}, 163 | volume = {2}, 164 | annote = {This is the third edition. Its shorthand reference is 165 | BDA3. It has been cited over 17000 times in two years! 166 | Appendix C introduces using R and STAN together.} 167 | } 168 | 169 | @Book{ kruschke2014doingbayesiandatanalysisatutorrialwithrjagsstan, 170 | title = {Doing Bayesian data analysis: A tutorial with R, JAGS, and 171 | Stan}, 172 | publisher = {Academic Press}, 173 | year = {2015}, 174 | author = {Kruschke, John}, 175 | edition = {2nd}, 176 | annote = {This is the second edition of the Puppy Dog book. The 177 | author is a Mr. Rodgers kind of guy, judging from the 178 | videos that he posted that explain the annalysis behind 179 | Bayesian t-tests. Contrary to the title of the book, most 180 | of the examples are in JAGS. I bought this book for 181 | Victoria. It starts off slow and simple but looks are 182 | decieving. It rises to a high level of sophistication.} 183 | } 184 | 185 | @Book{ davidson2015bayesianmethodsforhackers, 186 | title = {Bayesian Methods for Hackers: Probabilistic Programming 187 | and Bayesian Inference}, 188 | publisher = {Addison-Wesley Professional}, 189 | year = {2015}, 190 | author = {Davidson-Pilon, Cameron}, 191 | annote = {This book was a 2015 Christmas gift from my father. It is 192 | meant to be introductory but it does reach into advanced 193 | topics. It relies on the PyMC package.} 194 | } 195 | 196 | @Book{ marin2014bayesianessentialwithr, 197 | title = {Bayesian essentials with R}, 198 | publisher = {Springer}, 199 | year = {2014}, 200 | author = {Marin, Jean-Michel and Robert, Christian P}, 201 | annote = {I have a pdf of this book. This book looks really good as 202 | a second book on bayesian computation because it has more 203 | math while still having examples from R. It was written for 204 | scientists who have to apply Bayesian statistics. However, 205 | it was written by two statisticians. They may have included 206 | too much math.} 207 | } 208 | 209 | @Book{ sivia2006dataanalaysis, 210 | title = {Data analysis: a Bayesian tutorial}, 211 | publisher = {OUP Oxford}, 212 | year = {2006}, 213 | author = {Sivia, Devinderjit and Skilling, John} 214 | } 215 | 216 | @Book{ hamelryck2012bayesianmethodsinstructuralbioinformatics, 217 | title = {Bayesian methods in structural bioinformatics}, 218 | publisher = {Springer Science \& Business Media}, 219 | year = {2012}, 220 | author = {Hamelryck, Thomas and Mardia, Kanti and Ferkinghoff-Borg, 221 | Jesper}, 222 | annote = {I have this book. This is the first book to take a 223 | probablistic approach statistical structural 224 | bioinformatics. You need to a an advanced beginner or 225 | higher in Bayesian data analysis to get much out of this 226 | book. The book is not self-contained and there is no 227 | associated softeware. It is out a tutorial.} 228 | } 229 | 230 | @Book{ rupp2009biomolecularcrystallography, 231 | title = {Biomolecular crystallography: principles, practice, and 232 | application to structural biology}, 233 | publisher = {Garland Science}, 234 | year = {2009}, 235 | author = {Rupp, Bernhard}, 236 | annote = {I have this book. It has a nice discussion of Bayesian 237 | statistics in crystallography.} 238 | } 239 | 240 | @Book{ korner2015bayesiandataanalysisinecology, 241 | title = {Bayesian data analysis in ecology using linear models with 242 | R, BUGS, and Stan}, 243 | publisher = {Academic Press}, 244 | year = {2015}, 245 | author = {Korner-Nievergelt, Franzi and Roth, Tobias and von Felten, 246 | Stefanie and Gu{\'e}lat, J{\'e}r{\^o}me and Almasi, Bettina 247 | and Korner-Nievergelt, Pius}, 248 | annote = {This is a very accessbile book on using cutting edge BDA 249 | without a lot of math.} 250 | } 251 | 252 | @Article{ monnahan2016fasterestimatesofmodelswithstan, 253 | author = {Monnahan, Cole C and Thorson, James T and Branch, Trevor 254 | A}, 255 | title = {Faster estimation of Bayesian models in ecology using 256 | Hamiltonian Monte Carlo}, 257 | journal = {Methods in Ecology and Evolution}, 258 | year = {2016}, 259 | volume = {0}, 260 | annote = {This looks like a good evaluatoin of Stan. This paper is a 261 | must read.}, 262 | publisher = {Wiley Online Library} 263 | } 264 | 265 | @Manual{ su2012r2jags, 266 | title = {R2jags: A Package for Running jags from R}, 267 | author = {Su, Yu-Sung and Yajima, Masanao}, 268 | year = {2012}, 269 | journal = {R package version 0.03-08, URL http://CRAN. R-project. 270 | org/package= R2jags} 271 | } 272 | 273 | @Book{ andreon2015bayesianmethodsforthephysicalscienceslearningfromexamplesinastronomyandphysics, 274 | title = {Bayesian Methods for the Physical Sciences: Learning from 275 | Examples in Astronomy and Physics}, 276 | publisher = {Springer}, 277 | year = {2015}, 278 | author = {Andreon, Stefano and Weaver, Brian}, 279 | annote = {This is a concise book for someone with a strong 280 | background in math and statistics. A biologist may view 281 | this an intermediate-level book. It would be worth reading 282 | after mastering Kery 2010 and Albert (2009) in order to 283 | deepen your understanding of Bayesian statistics and to 284 | realize that you do not have to use WinBUGS or Stan with 285 | every problem.} 286 | } 287 | 288 | @Article{ sturtz2005r2winbugs, 289 | author = {Sibylle Sturtz and Uwe Ligges and Andrew Gelman}, 290 | title = {R2WinBUGS: A Package for Running WinBUGS from R}, 291 | journal = {Journal of Statistical Software}, 292 | year = {2005}, 293 | volume = {12}, 294 | number = {3}, 295 | pages = {1--16}, 296 | url = {http://www.jstatsoft.org} 297 | } 298 | 299 | @Article{ gilks1994bugslanguage, 300 | author = {Gilks, Wally R and Thomas, Andrew and Spiegelhalter, David 301 | J}, 302 | title = {A language and program for complex Bayesian modelling}, 303 | journal = {The Statistician}, 304 | year = {1994}, 305 | volume = {0}, 306 | pages = {169--177}, 307 | publisher = {JSTOR} 308 | } 309 | 310 | @Article{ smith1987applyingmcmctobayesiancomputation, 311 | author = {Smith, AFM and Skene, AM and Shaw, JEH and Naylor, JC}, 312 | title = {Progress with numerical and graphical methods for 313 | practical Bayesian statistics}, 314 | journal = {The Statistician}, 315 | year = {1987}, 316 | volume = {0}, 317 | pages = {75--82}, 318 | annote = {I got this article from JSTOR. It is a key reference in 319 | computational Bayesian statistics.} 320 | } 321 | 322 | @InBook{ gilks1996introducingmcmc, 323 | chapter = {1}, 324 | pages = {1-19}, 325 | title = {Introducing markov chain monte carlo}, 326 | publisher = {Chapman and Hall}, 327 | year = {1996}, 328 | author = {Gilks, Walter R and Richardson, Sylvia and Spiegelhalter, 329 | David J}, 330 | address = {London}, 331 | annote = {I have a pdf of this chapter.}, 332 | book = {Markov chain Monte Carlo in practice} 333 | } 334 | 335 | @Book{ spiegelhalter2004bayesianapproachestoclinicaltrialsandhealth-careevaluation, 336 | title = {Bayesian Approaches to Clinical Trials and Health-Care 337 | Evaluation}, 338 | publisher = {Wiley}, 339 | year = {2004}, 340 | author = {Spiegelhalter, D. J. and Abrams, K. R. and Myles, J. P.}, 341 | volume = {13}, 342 | series = {Statistics in Practice}, 343 | note = {QA 279.5 .S65 2004}, 344 | annote = {OU Library}, 345 | endnotereftype= {Book}, 346 | isbn = {9780471499756}, 347 | owner = {blaine-mooers}, 348 | shorttitle = {Bayesian Approaches to Clinical Trials and Health-Care 349 | Evaluation}, 350 | url = {https://books.google.com/books?id=eZdRL53PuWsC} 351 | } 352 | 353 | @TechReport{ dreyfus1980fivestagemodel, 354 | author = {Dreyfus, Stuart E and Dreyfus, Hubert L}, 355 | title = {A five-stage model of the mental activities involved in 356 | directed skill acquisition}, 357 | institution = {DTIC Document}, 358 | year = {1980}, 359 | annote = {The famous Dreyfus and Dreyfus model of expertise. I have 360 | a pdf of this somewhere.}, 361 | owner = {blaine-mooers}, 362 | timestamp = {2012.09.01} 363 | } 364 | 365 | @Article{ skilling2006nestedsampling, 366 | author = {Skilling, John}, 367 | title = {Nested sampling for general Bayesian computation}, 368 | journal = {Bayesian analysis}, 369 | year = {2006}, 370 | volume = {1}, 371 | number = {4}, 372 | pages = {833--859}, 373 | abstract = {Nested sampling estimates directly how the likelihood 374 | function relates to prior mass. The evidence (alternatively 375 | the marginal likelihood, marginal density of the data, or 376 | the prior predictive) is immediately obtained by summation. 377 | It is the prime result of the computation, and is 378 | accompanied by an estimate of numerical uncertainty. 379 | Samples from the posterior distribution are an optional 380 | byproduct, obtainable for any temperature. The method 381 | relies on sampling within a hard constraint on likelihood 382 | value, as opposed to the softened likelihood of annealing 383 | methods. Progress depends only on the shape of the 384 | “nested” contours of likelihood, and not on the 385 | likelihood values. This invariance (over monotonic 386 | relabelling) allows the method to deal with a class of 387 | phase-change problems which effectively defeat thermal 388 | annealing.}, 389 | publisher = {International Society for Bayesian Analysis} 390 | } 391 | 392 | @Article{ feroz2009multinest, 393 | author = {Feroz, F and Hobson, MP and Bridges, M}, 394 | title = {MultiNest: an efficient and robust Bayesian inference tool 395 | for cosmology and particle physics}, 396 | journal = {Monthly Notices of the Royal Astronomical Society}, 397 | year = {2009}, 398 | volume = {398}, 399 | number = {4}, 400 | pages = {1601--1614}, 401 | annote = {Cited it the BMC paper as the feference for multitest.}, 402 | publisher = {Oxford University Press} 403 | } 404 | 405 | @Article{ johansen2009smctcsequentialmontecarloincpp, 406 | author = {Adam M. Johansen}, 407 | title = {SMCTC: Sequential Monte Carlo in C++}, 408 | journal = {Journal of Statistical Software}, 409 | year = {2009}, 410 | volume = {30}, 411 | number = {6}, 412 | pages = {1--41}, 413 | month = {4}, 414 | issn = {1548-7660}, 415 | annote = {I have the pdf. There is a R package RcppSMC that talks 416 | between R and SMCTC. I have the key book on the subject by 417 | Doucet in 2001: Sequential Monte Carlo Methods in 418 | Practice.}, 419 | coden = {JSSOBK}, 420 | url = {http://www.jstatsoft.org/v30/i06} 421 | } 422 | 423 | @Article{ johnson2013revisedstandardsforstatisticalevidencej, 424 | author = {Johnson, Valen E.}, 425 | title = {Revised standards for statistical evidence}, 426 | journal = {Proceedings of the National Academy of Sciences}, 427 | year = {2013}, 428 | volume = {110}, 429 | number = {48}, 430 | pages = {19313-19317}, 431 | endnotereftype= {Journal Article}, 432 | owner = {blaine-mooers}, 433 | publisher = {National Acad Sciences}, 434 | shorttitle = {Revised standards for statistical evidence} 435 | } 436 | 437 | @Article{ johnson2013revisedstandardsforstatisticalevidence, 438 | author = {Johnson, Valen E}, 439 | title = {Revised standards for statistical evidence}, 440 | journal = {Proceedings of the National Academy of Sciences}, 441 | year = {2013}, 442 | volume = {110}, 443 | number = {48}, 444 | pages = {19313--19317}, 445 | publisher = {National Acad Sciences} 446 | } 447 | -------------------------------------------------------------------------------- /2023diary/preambleOnOverleaf.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%% MyPython.tex %%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | % 3 | % sample root file for the chapters of your "monograph" 4 | % 5 | % Use this file as a template for your own input. 6 | % 7 | %%%%%%%%%%%%%%%% Springer-Verlag %%%%%%%%%%%%%%%%%%%%%%%%%% 8 | % usr/texbin/pdflatex -synctex=1 -shell-escape -interaction=nonstopmode "main".tex 9 | % I am using laulatex on Overleaf. 10 | % RECOMMENDED %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 11 | 12 | %\usepackage[utf8]{inputenc}% ignored with laulatex 13 | \usepackage{rotating} 14 | %\usepackage[toc,page]{appendix} 15 | \usepackage{appendix} 16 | % choose options for [] as required from the list 17 | % in the Reference Guide, Sect. 2.2 18 | \usepackage[letterpaper, total={7in, 9in}]{geometry} 19 | \usepackage[english]{babel} 20 | %package to introduce exercises and answers that are written elsewhere in the book 21 | %\usepackage{xsim} too new 22 | %\usepackage{exsheets} 23 | %\usepackage{exercise} 24 | %\usepackage[T1]{fontenc} 25 | % packages for typesetting code listings 26 | 27 | % \usepackage[activate={true,nocompatibility},final,tracking=true,kerning=true,spacing=true,factor=1100,stretch=10,shrink=10]{microtype} 28 | % Only works with pdftex 1.4. I am using laulatex for other reasons. 29 | % activate={true,nocompatibility} - activate protrusion and expansion 30 | % final - enable microtype; use "draft" to disable 31 | % tracking=true, kerning=true, spacing=true - activate these techniques 32 | % factor=1100 - add 10% to the protrusion amount (default is 1000) 33 | % stretch=10, shrink=10 - reduce stretchability/shrinkability (default is 20/20) 34 | % See http://www.khirevich.com/latex/microtype/ 35 | 36 | \usepackage{minted} 37 | \usepackage{caption} 38 | \usepackage{footnote} 39 | \makesavenoteenv{tabular} 40 | \makesavenoteenv{table} 41 | \usepackage[flushleft]{threeparttable} 42 | \usepackage[caption=false]{subfig} 43 | \usepackage{mdframed} 44 | \usepackage{textcomp} 45 | \usepackage{gensymb} 46 | \usepackage{verbatim} % provides the comment environment 47 | \newenvironment{code}{\captionsetup{type=listing}}{} 48 | \usepackage[parfill]{parskip} % add blank line between paragraphs 49 | \usepackage{latexmarkdn} 50 | 51 | 52 | % %%%%%%%%%%%%%%%%%%% index and authorindex %%%%%%%%%%%%%%%%%%%%% 53 | 54 | %\usepackage{imakeidx} 55 | %\makeindex[columns=2, title="Alphabetical Index", intoc, options= -s indexStyle.ist] 56 | 57 | 58 | \usepackage{makeidx} % allows index generation 59 | \usepackage[luatex,plainpages=false]{hyperref} 60 | \usepackage{multicol} % used for the two-column index 61 | 62 | \usepackage[bottom]{footmisc} % footnotes at the bottom of the page 63 | 64 | % Remake of the svgraybox command. Conflicts with something. 65 | % \makeatletter 66 | % \renewenvironment{svgraybox} 67 | % {\begin{shaded*}% 68 | % \list{}{\leftmargin=\p@\rightmargin=\p@\topsep=\p@}% 69 | % \expandafter\item\parindent=\svparindent 70 | % \hskip-\listparindent} 71 | % {\endlist\end{shaded*}} 72 | % \makeatother 73 | 74 | 75 | \newfloat{statsmodel}{H}{statsm}[chapter] 76 | \newfloat{email}{H}{email}[chapter] 77 | \newfloat{listeq}{H}{email}[chapter] 78 | 79 | %%%%%%%%%%%%%%%%%% author index %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 80 | % The Springer Monograph does not have a native author index. 81 | % The following command produces a single column author index. 82 | \RequirePackage{authorindex} 83 | % Use this, if you want hyperlinks back from list of author entry to page 84 | % where the citation was placed 85 | \def\theaipage{\string\hyperpage{\thepage}} 86 | \newcommand{\listofauthorsname}{List of Authors}% 87 | \newcommand{\listofauthors}{% 88 | \chapter*{\listofauthorsname}% 89 | %\begin{multicols*}{2} 90 | \phantomsection% 91 | \addcontentsline{toc}{chapter}{\listofauthorsname}% 92 | \noindent% 93 | \printauthorindex% 94 | %\end{multicols*} 95 | }% Please include this closing brace 96 | 97 | % Tip from staff of Overleaf on how to make authorindex 98 | 99 | % \usepackage{etoolbox} 100 | % \newcommand{\indexauthors}[1]{% 101 | % \forcsvlist{\index}{#1} 102 | % } 103 | 104 | 105 | 106 | % \newcommand{\listofstatsmodelsname}{List of Statistical Models}% 107 | 108 | % \newcommand{\listofstatsmodels}{% 109 | % \chapter*{\listofstatsmodelsname}% 110 | % %\begin{multicols*}{2} 111 | % \phantomsection% 112 | % \addcontentsline{toc}{chapter}{\listofstatsmodelsname}% 113 | % \noindent% 114 | % \printlistofstatmodels% 115 | % %\end{multicols*} 116 | % }% 117 | 118 | \newfloat{checklist}{H}{checklist}[chapter] 119 | \floatname{checklist}{Checklist} 120 | 121 | 122 | 123 | \newcounter{statmodel} 124 | \newcommand\liststatmodelname{List of Statistical Models} 125 | \newcommand\smcap[1]{% 126 | \stepcounter{statmodel}\addtocontents{sm}{\protect\makebox[2em][l]{\thestatmodel}#1}% 127 | \addtocontents{sm}{\vskip7pt\noindent}} 128 | \makeatletter 129 | \newcommand{\listofstatmodels}{% 130 | \chapter*{\liststatmodelname}\@starttoc{sm} 131 | \clearpage% to get on the right page 132 | \phantomsection% probably necessary only if using hyperref package 133 | \addcontentsline{toc}{chapter}{\liststatmodelname}% to add to table of contents 134 | \noindent% 135 | }% 136 | \makeatother 137 | 138 | 139 | \makeindex 140 | %%%%%%%%%%%% user-defined commands %%%%%%%%%%%%%% 141 | % % It is a good practice put all your user-defined commands in the preamble of your document. 142 | %% 143 | % % boxy: This give a boxed environment with a title. 144 | % %-------------------------------------------------- 145 | \newenvironment{boxy}[1] 146 | {\begin{center} 147 | #1\\[1ex] 148 | \begin{tabular}{|p{0.9\textwidth}|} 149 | \hline\\ 150 | } 151 | { 152 | \\\\\hline 153 | \end{tabular} 154 | \end{center} 155 | } 156 | 157 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 158 | % color highlighting with light colors 159 | % hlcyan, hllb, hllm, hllg, hllp, hlly, hlbr 160 | \usepackage{soul} 161 | \usepackage{color} 162 | \DeclareRobustCommand{\hlcyan}[1]{{\sethlcolor{cyan}\hl{#1}}} 163 | \definecolor{lightblue}{rgb}{.90,.95,1} 164 | \DeclareRobustCommand{\hllb}[1]{{\sethlcolor{lightblue}\hl{#1}}} 165 | \definecolor{lightmagenta}{rgb}{1,.8,1} 166 | \DeclareRobustCommand{\hllm}[1]{{\sethlcolor{lightmagenta}\hl{#1}}} 167 | \definecolor{lightgreen}{rgb}{.8,1,.8} 168 | \DeclareRobustCommand{\hllg}[1]{{\sethlcolor{lightgreen}\hl{#1}}} 169 | \definecolor{lightpurple}{rgb}{.8,.8,1} 170 | \DeclareRobustCommand{\hllp}[1]{{\sethlcolor{lightpurple}\hl{#1}}} 171 | \definecolor{lightyellow}{rgb}{1,1,.8} 172 | \DeclareRobustCommand{\hlly}[1]{{\sethlcolor{lightyellow}\hl{#1}}} 173 | \definecolor{lightbrown}{rgb}{1,.8,.6} 174 | \DeclareRobustCommand{\hllbr}[1]{{\sethlcolor{lightbrown}\hl{#1}}} 175 | 176 | 177 | 178 | 179 | 180 | %%%%%%%%%%%% enables the addition of images to title page %%%%%%%%%%%%%% 181 | \usepackage[cc]{titlepic} 182 | \usepackage{graphicx} % standard LaTeX graphics tool 183 | % when including figure files 184 | 185 | %%%%%%%%%%% epigraphs with expanding line width up to a max %%%%%%%%%%%%%%%%% 186 | \usepackage{epigraph,varwidth} 187 | \usepackage{epipart} 188 | \renewcommand{\epigraphsize}{\small} 189 | \setlength{\epigraphwidth}{0.6\textwidth} 190 | \renewcommand{\textflush}{flushright} 191 | \renewcommand{\sourceflush}{flushright} 192 | % A useful addition 193 | \newcommand{\epitextfont}{\itshape} 194 | \newcommand{\episourcefont}{\scshape} 195 | 196 | \makeatletter 197 | \newsavebox{\epi@textbox} 198 | \newsavebox{\epi@sourcebox} 199 | \newlength\epi@finalwidth 200 | \renewcommand{\epigraph}[2]{% 201 | \vspace{\beforeepigraphskip} 202 | {\epigraphsize\begin{\epigraphflush} 203 | \epi@finalwidth=\z@ 204 | \sbox\epi@textbox{% 205 | \varwidth{\epigraphwidth} 206 | \begin{\textflush}\epitextfont#1\end{\textflush} 207 | \endvarwidth 208 | }% 209 | \epi@finalwidth=\wd\epi@textbox 210 | \sbox\epi@sourcebox{% 211 | \varwidth{\epigraphwidth} 212 | \begin{\sourceflush}\episourcefont#2\end{\sourceflush}% 213 | \endvarwidth 214 | }% 215 | \ifdim\wd\epi@sourcebox>\epi@finalwidth 216 | \epi@finalwidth=\wd\epi@sourcebox 217 | \fi 218 | \leavevmode\vbox{ 219 | \hb@xt@\epi@finalwidth{\hfil\box\epi@textbox} 220 | \vskip1.75ex/ 221 | \hrule height \epigraphrule 222 | \vskip.75ex 223 | \hb@xt@\epi@finalwidth{\hfil\box\epi@sourcebox} 224 | }% 225 | \end{\epigraphflush} 226 | \vspace{\afterepigraphskip}}} 227 | \makeatother 228 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 229 | 230 | \usepackage{array} % Needed for controlling the wide of tables 231 | \usepackage{booktabs} % Needed for fancy tables 232 | 233 | \usepackage[authoryear,round]{natbib} 234 | \bibliographystyle{plainnat} 235 | \usepackage[bottom]{footmisc}% places footnotes at page bottom 236 | \usepackage{amssymb} 237 | \usepackage{amsmath} 238 | \usepackage[normalem]{ulem} % enables strikethrough with \sout 239 | \usepackage{scrextend} 240 | %\usepackage{minted} 241 | %\usepackage{color} 242 | 243 | \definecolor{codegreen}{rgb}{0,0.6,0} 244 | \definecolor{codegray}{rgb}{0.5,0.5,0.5} 245 | \definecolor{codepurple}{rgb}{0.58,0,0.82} 246 | \definecolor{backcolour}{rgb}{0.95,0.95,0.92} 247 | 248 | \usepackage{float} 249 | \floatstyle{plain} 250 | % How is this used?? 251 | \newfloat{myequation}{H}{eq}[section] 252 | \floatname{myequation}{Equation} 253 | 254 | % For making algorithm listings as pseudocode 255 | % http://tex.stackexchange.com/questions/204592/how-to-format-a-pseudocode-algorithm 256 | % source http://tex.stackexchange.com/questions/45538/list-of-algorithms-using-algorithm2e 257 | % \usepackage{tocbibind} 258 | % \usepackage[linesnumbered,ruled]{algorithm2e} 259 | % \newcommand{\listofalgorithmes}{\tocfile{\listalgorithmcfname}{loa}} 260 | 261 | % \usepackage{listings} 262 | % \lstdefinestyle{mystyle}{ 263 | % backgroundcolor=\color{backcolour}, 264 | % commentstyle=\color{codegreen}, 265 | % keywordstyle=\color{magenta}, 266 | % numberstyle=\tiny\color{codegray}, 267 | % stringstyle=\color{codepurple}, 268 | % basicstyle=\footnotesize, 269 | % breakatwhitespace=false, 270 | % breaklines=true, 271 | % captionpos=b, 272 | % keepspaces=true, 273 | % numbers=left, 274 | % numbersep=5pt, 275 | % showspaces=false, 276 | % showstringspaces=false, 277 | % showtabs=false, 278 | % tabsize=2 279 | % } 280 | % \lstset{style=mystyle} 281 | % \usepackage{fancyhdr} 282 | % \usepackage[us,12hr]{datetime} % `us' makes \today behave as usual in TeX/LaTeX 283 | % \fancypagestyle{plain}{ 284 | % \fancyhf{} 285 | % \rfoot{Compiled on {\ddmmyyyydate\today} at \currenttime} 286 | % \lfoot{Page \thepage} 287 | % \renewcommand{\headrulewidth}{0pt}} 288 | % %\pagestyle{plain} 289 | % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 290 | % \usepackage{tcolorbox} 291 | % \tcbuselibrary{minted,skins} 292 | % \newtcblisting{bashcode}[1][]{ 293 | % listing engine=minted, 294 | % colback=bg, 295 | % colframe=black!70, 296 | % listing only, 297 | % minted style=colorful, 298 | % minted language=bash, 299 | % minted options={linenos=true,numbersep=3mm,texcl=true,#1}, 300 | % left=5mm,enhanced, 301 | % overlay={\begin{tcbclipinterior}\fill[black!25] (frame.south west) 302 | % rectangle ([xshift=5mm]frame.north west);\end{tcbclipinterior}} 303 | % } 304 | % \newtcblisting{pythoncode}[1][]{ 305 | % listing engine=minted, 306 | % colback=bg, 307 | % colframe=black!70, 308 | % listing only, 309 | % minted style=colorful, 310 | % minted language=python, 311 | % minted options={linenos=true,numbersep=3mm,texcl=true,#1}, 312 | % left=5mm,enhanced, 313 | % overlay={\begin{tcbclipinterior}\fill[black!25] (frame.south west) 314 | % rectangle ([xshift=5mm]frame.north west);\end{tcbclipinterior}} 315 | % } 316 | 317 | % \definecolor{bg}{rgb}{0.97,0.97,0.97} 318 | % see the list of further useful packages 319 | % in the Reference Guide, Sects. 2.3, 3.1-3.3 320 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 321 | %\usepackage{filecontents} % not needed with laulatex 322 | % http://ctan.org/pkg/filecontents 323 | %\usepackage{listings}% http://ctan.org/pkg/listings 324 | \addtokomafont{labelinglabel}{\sffamily\bfseries} 325 | 326 | 327 | %%%%%% Acronyms, Glossaries, & Symbol lists, %%%%%%%%%%%%%%%%%%%%%%% 328 | % see https://www.sharelatex.com/learn/Glossaries#/Acronyms for example of making list of acronyms and glossary entries. 329 | %\usepackage{morewrites} % required when opening more than 16 files. Not needed with laulatex. 330 | \usepackage{siunitx} 331 | %\usepackage{hyperref} % Allows the use of \url{} 332 | \hypersetup{ 333 | colorlinks=true, 334 | linkcolor=blue, 335 | filecolor=magenta, 336 | urlcolor=cyan, 337 | } 338 | \usepackage{url} 339 | \urlstyle{sf} 340 | %\usepackage{xurl} %This package was causing Overleaf to choke on url's with underscores. Thanks to 341 | \usepackage{underscore} 342 | 343 | \usepackage[acronym,toc,smallcaps]{glossaries} % use glossaries-package 344 | 345 | % 346 | % footnote - The option footnote makes the full name appear as a footnote. 347 | % nohyperlinks - If hyperref is loaded, all acronyms will link to their glossary entry. With the option nohyperlinks these links can be suppressed. 348 | % printonlyused - Only list used acronyms 349 | % withpage - In printonlyused-mode show the page number where each acronym was first used. 350 | % smaller - Make the acronym appear smaller. 351 | % dua - The option dua stands for “don’t use acronyms”. It leads to a redefinition of \ac and \acp, making the full name appear all the time and suppressing all acronyms but the explicity requested by \acf or \acfp. 352 | % nolist - The option nolist stands for “don’t write the list of acronyms”. 353 | % 354 | \setlength{\glsdescwidth}{15cm} 355 | 356 | %\input{main-globalSymbols} 357 | %==== EXEMPLARY ENTRY FOR ACRONYMS LIST ======================================== 358 | % \newacronym{VRBD}{VRBD}{Violet-Red-Bile-Glucose-Agar} 359 | 360 | \loadglsentries[\acronymtype]{\jobname-globalAcronyms} 361 | 362 | 363 | %==== EXEMPLARY ENTRY FOR MAIN GLOSSARY ======================================== 364 | 365 | \loadglsentries{\jobname-globalGlossary} 366 | 367 | 368 | \newglossarystyle{symbunitlong}{% 369 | \setglossarystyle{long3col}% base this style on the list style 370 | \renewenvironment{theglossary}{% Change the table type --> 3 columns 371 | \begin{longtable}{lp{0.6\glsdescwidth}>{\centering\arraybackslash}p{2cm}}}% 372 | {\end{longtable}}% 373 | 374 | \renewcommand*{\glossaryheader}{% Change the table header 375 | \bfseries Sign & \bfseries Description & \bfseries Unit \\ 376 | \hline 377 | \endhead} 378 | \renewcommand*{\glossentry}[2]{% Change the displayed items 379 | \glstarget{##1}{\glossentryname{##1}} % 380 | & \glossentrydesc{##1}% Description 381 | & \glsunit{##1} \tabularnewline 382 | } 383 | } 384 | %\makeglossaries 385 | 386 | 387 | % To color the chapter titles Maroon 388 | \usepackage{sectsty} 389 | \chapterfont{\color{Maroon}} 390 | 391 | 392 | %%%%%%%%% Code for exercises in chapters and answers in appendix %%%%%%%% 393 | % \usepackage{amsfonts} 394 | % \usepackage{amssymb} 395 | % \usepackage{multicol} 396 | % \usepackage{ifthen} 397 | % \newboolean{firstanswerofthechapter} 398 | % \usepackage{xcolor} 399 | % \colorlet{lightcyan}{cyan!40!white} 400 | % \usepackage{chngcntr} 401 | % \usepackage{stackengine} 402 | % \usepackage{tasks} 403 | % \newlength{\longestlabel} 404 | % \settowidth{\longestlabel}{\bfseries viii.} 405 | % \settasks{counter-format={tsk[r].}, label-format={\bfseries}, label-width=\longestlabel, 406 | % item-indent=0pt, label-offset=2pt, column-sep={10pt}} 407 | 408 | % \usepackage[lastexercise,answerdelayed]{exercise} 409 | % %\counterwithin{Exercise}{chapter} 410 | % %\counterwithin{Answer}{chapter} 411 | % %\renewcounter{Exercise}[chapter] 412 | % \newcommand{\QuestionNB}{\bfseries\arabic{Question}.\ } 413 | % \renewcommand{\ExerciseName}{EXERCISES} 414 | % \renewcommand{\ExerciseHeader}{\noindent\def\stackalignment{l}% code from https://tex.stackexchange.com/a/195118/101651 415 | % \stackunder[0pt]{\colorbox{cyan}{\textcolor{white}{\textbf{\LARGE\ExerciseHeaderNB\;\large\ExerciseName}}}}{\textcolor{lightcyan}{\rule{\linewidth}{2pt}}}\medskip} 416 | % \renewcommand{\AnswerName}{Exercises} 417 | % \renewcommand{\AnswerHeader}{\ifthenelse{\boolean{firstanswerofthechapter}}% 418 | % {\bigskip\noindent\textcolor{cyan}{\textbf{CHAPTER \thechapter}}\newline\newline% 419 | % \noindent\bfseries\emph{\textcolor{cyan}{\AnswerName\ \ExerciseHeaderNB, page % 420 | % \pageref{\AnswerRef}}}\smallskip} 421 | % {\noindent\bfseries\emph{\textcolor{cyan}{\AnswerName\ \ExerciseHeaderNB, page \pageref{\AnswerRef}}}\smallskip}} 422 | % \setlength{\QuestionIndent}{16pt} 423 | 424 | % todolist env from https://tex.stackexchange.com/questions/247681/how-to-create-checkbox-todo-list 425 | % done and wontfix 426 | % https://mylatexnotes.wordpress.com/2017/07/31/text-x-mark-to-match-checkmark/ 427 | \usepackage{enumitem,amssymb} 428 | \newlist{todolist}{itemize}{2} 429 | \setlist[todolist]{label=$\square$} 430 | \usepackage{pifont} 431 | \newcommand{\cmark}{\ding{51}}% 432 | \newcommand{\xmark}{\ding{55}}% 433 | \newcommand{\wmark}{\ding{108}}% 434 | \newcommand{\done}{\rlap{$\square$}{\raisebox{2pt}{\large\hspace{1pt}\cmark}}% 435 | \hspace{-2.5pt}} 436 | \newcommand{\wontfix}{\rlap{$\square$}{\large\hspace{1pt}\xmark}} 437 | \newcommand{\waiting}{\rlap{\raisebox{0.18ex}{\hspace{0.17ex}\scriptsize \wmark}}$\square$} 438 | 439 | 440 | %%%%%%% hintBox, importantBox, noteBox 441 | 442 | \usepackage[most]{tcolorbox} 443 | %textmarker style from colorbox doc 444 | \tcbset{textmarker/.style={% 445 | enhanced, 446 | parbox=false,boxrule=0mm,boxsep=0mm,arc=0mm, 447 | outer arc=0mm,left=6mm,right=3mm,top=7pt,bottom=7pt, 448 | toptitle=1mm,bottomtitle=1mm,oversize}} 449 | 450 | 451 | % define new colorboxes 452 | \newtcolorbox{hintBox}{textmarker, 453 | borderline west={6pt}{0pt}{yellow}, 454 | colback=yellow!10!white} 455 | \newtcolorbox{importantBox}{textmarker, 456 | borderline west={6pt}{0pt}{red}, 457 | colback=red!10!white} 458 | \newtcolorbox{noteBox}{textmarker, 459 | borderline west={6pt}{0pt}{green}, 460 | colback=green!10!white} 461 | 462 | 463 | 464 | 465 | %%%%%%%%%%%% 466 | % 467 | \usepackage{listings} 468 | \usepackage{minted,xcolor,chngcntr} 469 | 470 | % Style Minted 471 | \usemintedstyle{default} 472 | \definecolor{codebg1}{rgb}{0.96,0.96,0.96} 473 | \definecolor{codebg2}{rgb}{0.98,0.98,0.98} 474 | \newminted{python}{bgcolor=codebg1, 475 | linenos=true, 476 | frame=lines, 477 | numbersep=5pt, 478 | fontsize=\footnotesize} 479 | \newminted{bash}{bgcolor=codebg2, 480 | linenos=true, 481 | frame=lines, 482 | numbersep=5pt, 483 | fontsize=\footnotesize} 484 | %\renewcommand\listoflistingscaption{LIST OF CODE SNIPPETS} 485 | %\renewcommand\listingscaption{Code Snippet} 486 | % Style Listings 487 | \counterwithin{listing}{section} 488 | 489 | % \begin{listing}[H] 490 | % \begin{pythoncode} 491 | % def get_path_leaf(path): 492 | % """ return the leaf of a path. """ 493 | % if not isinstance(path, str): 494 | % path = str(path) 495 | % head, tail = ntpath.split(path) 496 | % return tail or ntpath.basename(head) 497 | % \end{pythoncode} 498 | % \caption{SPARQL Endpoint} 499 | % %\label{lst:SPARQL Endpoint} 500 | % \end{listing} 501 | 502 | % Define a equ enivironment to make equations into floats. 503 | \DeclareCaptionType{equ}[][] 504 | 505 | --------------------------------------------------------------------------------