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output.tex
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output.tex
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\documentclass[11pt]{article}
\usepackage[breakable]{tcolorbox}
\usepackage{parskip} % Stop auto-indenting (to mimic markdown behaviour)
\usepackage{iftex}
\ifPDFTeX
\usepackage[T1]{fontenc}
\usepackage{mathpazo}
\else
\usepackage{fontspec}
\fi
% Basic figure setup, for now with no caption control since it's done
% automatically by Pandoc (which extracts  syntax from Markdown).
\usepackage{graphicx}
% Maintain compatibility with old templates. Remove in nbconvert 6.0
\let\Oldincludegraphics\includegraphics
% Ensure that by default, figures have no caption (until we provide a
% proper Figure object with a Caption API and a way to capture that
% in the conversion process - todo).
\usepackage{caption}
\DeclareCaptionFormat{nocaption}{}
\captionsetup{format=nocaption,aboveskip=0pt,belowskip=0pt}
\usepackage[Export]{adjustbox} % Used to constrain images to a maximum size
\adjustboxset{max size={0.9\linewidth}{0.9\paperheight}}
\usepackage{float}
\floatplacement{figure}{H} % forces figures to be placed at the correct location
\usepackage{xcolor} % Allow colors to be defined
\usepackage{enumerate} % Needed for markdown enumerations to work
\usepackage{geometry} % Used to adjust the document margins
\usepackage{amsmath} % Equations
\usepackage{amssymb} % Equations
\usepackage{textcomp} % defines textquotesingle
% Hack from http://tex.stackexchange.com/a/47451/13684:
\AtBeginDocument{%
\def\PYZsq{\textquotesingle}% Upright quotes in Pygmentized code
}
\usepackage{upquote} % Upright quotes for verbatim code
\usepackage{eurosym} % defines \euro
\usepackage[mathletters]{ucs} % Extended unicode (utf-8) support
\usepackage{fancyvrb} % verbatim replacement that allows latex
\usepackage{grffile} % extends the file name processing of package graphics
% to support a larger range
\makeatletter % fix for grffile with XeLaTeX
\def\Gread@@xetex#1{%
\IfFileExists{"\Gin@base".bb}%
{\Gread@eps{\[email protected]}}%
{\Gread@@xetex@aux#1}%
}
\makeatother
% The hyperref package gives us a pdf with properly built
% internal navigation ('pdf bookmarks' for the table of contents,
% internal cross-reference links, web links for URLs, etc.)
\usepackage{hyperref}
% The default LaTeX title has an obnoxious amount of whitespace. By default,
% titling removes some of it. It also provides customization options.
\usepackage{titling}
\usepackage{longtable} % longtable support required by pandoc >1.10
\usepackage{booktabs} % table support for pandoc > 1.12.2
\usepackage[inline]{enumitem} % IRkernel/repr support (it uses the enumerate* environment)
\usepackage[normalem]{ulem} % ulem is needed to support strikethroughs (\sout)
% normalem makes italics be italics, not underlines
\usepackage{mathrsfs}
% Colors for the hyperref package
\definecolor{urlcolor}{rgb}{0,.145,.698}
\definecolor{linkcolor}{rgb}{.71,0.21,0.01}
\definecolor{citecolor}{rgb}{.12,.54,.11}
% ANSI colors
\definecolor{ansi-black}{HTML}{3E424D}
\definecolor{ansi-black-intense}{HTML}{282C36}
\definecolor{ansi-red}{HTML}{E75C58}
\definecolor{ansi-red-intense}{HTML}{B22B31}
\definecolor{ansi-green}{HTML}{00A250}
\definecolor{ansi-green-intense}{HTML}{007427}
\definecolor{ansi-yellow}{HTML}{DDB62B}
\definecolor{ansi-yellow-intense}{HTML}{B27D12}
\definecolor{ansi-blue}{HTML}{208FFB}
\definecolor{ansi-blue-intense}{HTML}{0065CA}
\definecolor{ansi-magenta}{HTML}{D160C4}
\definecolor{ansi-magenta-intense}{HTML}{A03196}
\definecolor{ansi-cyan}{HTML}{60C6C8}
\definecolor{ansi-cyan-intense}{HTML}{258F8F}
\definecolor{ansi-white}{HTML}{C5C1B4}
\definecolor{ansi-white-intense}{HTML}{A1A6B2}
\definecolor{ansi-default-inverse-fg}{HTML}{FFFFFF}
\definecolor{ansi-default-inverse-bg}{HTML}{000000}
% commands and environments needed by pandoc snippets
% extracted from the output of `pandoc -s`
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\newenvironment{Shaded}{}{}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{{#1}}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.56,0.13,0.00}{{#1}}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textit{{#1}}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{{#1}}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.02,0.16,0.49}{{#1}}}
\newcommand{\RegionMarkerTok}[1]{{#1}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}}
\newcommand{\NormalTok}[1]{{#1}}
% Additional commands for more recent versions of Pandoc
\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.53,0.00,0.00}{{#1}}}
\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.73,0.40,0.53}{{#1}}}
\newcommand{\ImportTok}[1]{{#1}}
\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.73,0.13,0.13}{\textit{{#1}}}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{{#1}}}}}
\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{{#1}}}}}
\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.10,0.09,0.49}{{#1}}}
\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{{#1}}}}
\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.40,0.40,0.40}{{#1}}}
\newcommand{\BuiltInTok}[1]{{#1}}
\newcommand{\ExtensionTok}[1]{{#1}}
\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.74,0.48,0.00}{{#1}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.49,0.56,0.16}{{#1}}}
\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{{#1}}}}}
\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{{#1}}}}}
% Define a nice break command that doesn't care if a line doesn't already
% exist.
\def\br{\hspace*{\fill} \\* }
% Math Jax compatibility definitions
\def\gt{>}
\def\lt{<}
\let\Oldtex\TeX
\let\Oldlatex\LaTeX
\renewcommand{\TeX}{\textrm{\Oldtex}}
\renewcommand{\LaTeX}{\textrm{\Oldlatex}}
% Document parameters
% Document title
\title{output}
% Pygments definitions
\makeatletter
\def\PY@reset{\let\PY@it=\relax \let\PY@bf=\relax%
\let\PY@ul=\relax \let\PY@tc=\relax%
\let\PY@bc=\relax \let\PY@ff=\relax}
\def\PY@tok#1{\csname PY@tok@#1\endcsname}
\def\PY@toks#1+{\ifx\relax#1\empty\else%
\PY@tok{#1}\expandafter\PY@toks\fi}
\def\PY@do#1{\PY@bc{\PY@tc{\PY@ul{%
\PY@it{\PY@bf{\PY@ff{#1}}}}}}}
\def\PY#1#2{\PY@reset\PY@toks#1+\relax+\PY@do{#2}}
\expandafter\def\csname PY@tok@w\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}}
\expandafter\def\csname PY@tok@c\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PY@tok@cp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.74,0.48,0.00}{##1}}}
\expandafter\def\csname PY@tok@k\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@kp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@kt\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.69,0.00,0.25}{##1}}}
\expandafter\def\csname PY@tok@o\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\expandafter\def\csname PY@tok@ow\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}}
\expandafter\def\csname PY@tok@nb\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@nf\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
\expandafter\def\csname PY@tok@nc\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
\expandafter\def\csname PY@tok@nn\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
\expandafter\def\csname PY@tok@ne\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.82,0.25,0.23}{##1}}}
\expandafter\def\csname PY@tok@nv\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
\expandafter\def\csname PY@tok@no\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.53,0.00,0.00}{##1}}}
\expandafter\def\csname PY@tok@nl\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.63,0.63,0.00}{##1}}}
\expandafter\def\csname PY@tok@ni\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.60,0.60,0.60}{##1}}}
\expandafter\def\csname PY@tok@na\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.49,0.56,0.16}{##1}}}
\expandafter\def\csname PY@tok@nt\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@nd\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.67,0.13,1.00}{##1}}}
\expandafter\def\csname PY@tok@s\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@sd\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@si\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}}
\expandafter\def\csname PY@tok@se\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.73,0.40,0.13}{##1}}}
\expandafter\def\csname PY@tok@sr\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.40,0.53}{##1}}}
\expandafter\def\csname PY@tok@ss\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
\expandafter\def\csname PY@tok@sx\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@m\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\expandafter\def\csname PY@tok@gh\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
\expandafter\def\csname PY@tok@gu\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.50,0.00,0.50}{##1}}}
\expandafter\def\csname PY@tok@gd\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.63,0.00,0.00}{##1}}}
\expandafter\def\csname PY@tok@gi\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.63,0.00}{##1}}}
\expandafter\def\csname PY@tok@gr\endcsname{\def\PY@tc##1{\textcolor[rgb]{1.00,0.00,0.00}{##1}}}
\expandafter\def\csname PY@tok@ge\endcsname{\let\PY@it=\textit}
\expandafter\def\csname PY@tok@gs\endcsname{\let\PY@bf=\textbf}
\expandafter\def\csname PY@tok@gp\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
\expandafter\def\csname PY@tok@go\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.53,0.53,0.53}{##1}}}
\expandafter\def\csname PY@tok@gt\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.27,0.87}{##1}}}
\expandafter\def\csname PY@tok@err\endcsname{\def\PY@bc##1{\setlength{\fboxsep}{0pt}\fcolorbox[rgb]{1.00,0.00,0.00}{1,1,1}{\strut ##1}}}
\expandafter\def\csname PY@tok@kc\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@kd\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@kn\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@kr\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@bp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
\expandafter\def\csname PY@tok@fm\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
\expandafter\def\csname PY@tok@vc\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
\expandafter\def\csname PY@tok@vg\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
\expandafter\def\csname PY@tok@vi\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
\expandafter\def\csname PY@tok@vm\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.10,0.09,0.49}{##1}}}
\expandafter\def\csname PY@tok@sa\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@sb\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@sc\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@dl\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@s2\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@sh\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@s1\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@mb\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\expandafter\def\csname PY@tok@mf\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\expandafter\def\csname PY@tok@mh\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\expandafter\def\csname PY@tok@mi\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\expandafter\def\csname PY@tok@il\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\expandafter\def\csname PY@tok@mo\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\expandafter\def\csname PY@tok@ch\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PY@tok@cm\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PY@tok@cpf\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PY@tok@c1\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PY@tok@cs\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\def\PYZbs{\char`\\}
\def\PYZus{\char`\_}
\def\PYZob{\char`\{}
\def\PYZcb{\char`\}}
\def\PYZca{\char`\^}
\def\PYZam{\char`\&}
\def\PYZlt{\char`\<}
\def\PYZgt{\char`\>}
\def\PYZsh{\char`\#}
\def\PYZpc{\char`\%}
\def\PYZdl{\char`\$}
\def\PYZhy{\char`\-}
\def\PYZsq{\char`\'}
\def\PYZdq{\char`\"}
\def\PYZti{\char`\~}
% for compatibility with earlier versions
\def\PYZat{@}
\def\PYZlb{[}
\def\PYZrb{]}
\makeatother
% For linebreaks inside Verbatim environment from package fancyvrb.
\makeatletter
\newbox\Wrappedcontinuationbox
\newbox\Wrappedvisiblespacebox
\newcommand*\Wrappedvisiblespace {\textcolor{red}{\textvisiblespace}}
\newcommand*\Wrappedcontinuationsymbol {\textcolor{red}{\llap{\tiny$\m@th\hookrightarrow$}}}
\newcommand*\Wrappedcontinuationindent {3ex }
\newcommand*\Wrappedafterbreak {\kern\Wrappedcontinuationindent\copy\Wrappedcontinuationbox}
% Take advantage of the already applied Pygments mark-up to insert
% potential linebreaks for TeX processing.
% {, <, #, %, $, ' and ": go to next line.
% _, }, ^, &, >, - and ~: stay at end of broken line.
% Use of \textquotesingle for straight quote.
\newcommand*\Wrappedbreaksatspecials {%
\def\PYGZus{\discretionary{\char`\_}{\Wrappedafterbreak}{\char`\_}}%
\def\PYGZob{\discretionary{}{\Wrappedafterbreak\char`\{}{\char`\{}}%
\def\PYGZcb{\discretionary{\char`\}}{\Wrappedafterbreak}{\char`\}}}%
\def\PYGZca{\discretionary{\char`\^}{\Wrappedafterbreak}{\char`\^}}%
\def\PYGZam{\discretionary{\char`\&}{\Wrappedafterbreak}{\char`\&}}%
\def\PYGZlt{\discretionary{}{\Wrappedafterbreak\char`\<}{\char`\<}}%
\def\PYGZgt{\discretionary{\char`\>}{\Wrappedafterbreak}{\char`\>}}%
\def\PYGZsh{\discretionary{}{\Wrappedafterbreak\char`\#}{\char`\#}}%
\def\PYGZpc{\discretionary{}{\Wrappedafterbreak\char`\%}{\char`\%}}%
\def\PYGZdl{\discretionary{}{\Wrappedafterbreak\char`\$}{\char`\$}}%
\def\PYGZhy{\discretionary{\char`\-}{\Wrappedafterbreak}{\char`\-}}%
\def\PYGZsq{\discretionary{}{\Wrappedafterbreak\textquotesingle}{\textquotesingle}}%
\def\PYGZdq{\discretionary{}{\Wrappedafterbreak\char`\"}{\char`\"}}%
\def\PYGZti{\discretionary{\char`\~}{\Wrappedafterbreak}{\char`\~}}%
}
% Some characters . , ; ? ! / are not pygmentized.
% This macro makes them "active" and they will insert potential linebreaks
\newcommand*\Wrappedbreaksatpunct {%
\lccode`\~`\.\lowercase{\def~}{\discretionary{\hbox{\char`\.}}{\Wrappedafterbreak}{\hbox{\char`\.}}}%
\lccode`\~`\,\lowercase{\def~}{\discretionary{\hbox{\char`\,}}{\Wrappedafterbreak}{\hbox{\char`\,}}}%
\lccode`\~`\;\lowercase{\def~}{\discretionary{\hbox{\char`\;}}{\Wrappedafterbreak}{\hbox{\char`\;}}}%
\lccode`\~`\:\lowercase{\def~}{\discretionary{\hbox{\char`\:}}{\Wrappedafterbreak}{\hbox{\char`\:}}}%
\lccode`\~`\?\lowercase{\def~}{\discretionary{\hbox{\char`\?}}{\Wrappedafterbreak}{\hbox{\char`\?}}}%
\lccode`\~`\!\lowercase{\def~}{\discretionary{\hbox{\char`\!}}{\Wrappedafterbreak}{\hbox{\char`\!}}}%
\lccode`\~`\/\lowercase{\def~}{\discretionary{\hbox{\char`\/}}{\Wrappedafterbreak}{\hbox{\char`\/}}}%
\catcode`\.\active
\catcode`\,\active
\catcode`\;\active
\catcode`\:\active
\catcode`\?\active
\catcode`\!\active
\catcode`\/\active
\lccode`\~`\~
}
\makeatother
\let\OriginalVerbatim=\Verbatim
\makeatletter
\renewcommand{\Verbatim}[1][1]{%
%\parskip\z@skip
\sbox\Wrappedcontinuationbox {\Wrappedcontinuationsymbol}%
\sbox\Wrappedvisiblespacebox {\FV@SetupFont\Wrappedvisiblespace}%
\def\FancyVerbFormatLine ##1{\hsize\linewidth
\vtop{\raggedright\hyphenpenalty\z@\exhyphenpenalty\z@
\doublehyphendemerits\z@\finalhyphendemerits\z@
\strut ##1\strut}%
}%
% If the linebreak is at a space, the latter will be displayed as visible
% space at end of first line, and a continuation symbol starts next line.
% Stretch/shrink are however usually zero for typewriter font.
\def\FV@Space {%
\nobreak\hskip\z@ plus\fontdimen3\font minus\fontdimen4\font
\discretionary{\copy\Wrappedvisiblespacebox}{\Wrappedafterbreak}
{\kern\fontdimen2\font}%
}%
% Allow breaks at special characters using \PYG... macros.
\Wrappedbreaksatspecials
% Breaks at punctuation characters . , ; ? ! and / need catcode=\active
\OriginalVerbatim[#1,codes*=\Wrappedbreaksatpunct]%
}
\makeatother
% Exact colors from NB
\definecolor{incolor}{HTML}{303F9F}
\definecolor{outcolor}{HTML}{D84315}
\definecolor{cellborder}{HTML}{CFCFCF}
\definecolor{cellbackground}{HTML}{F7F7F7}
% prompt
\makeatletter
\newcommand{\boxspacing}{\kern\kvtcb@left@rule\kern\kvtcb@boxsep}
\makeatother
\newcommand{\prompt}[4]{
\ttfamily\llap{{\color{#2}[#3]:\hspace{3pt}#4}}\vspace{-\baselineskip}
}
% Prevent overflowing lines due to hard-to-break entities
\sloppy
% Setup hyperref package
\hypersetup{
breaklinks=true, % so long urls are correctly broken across lines
colorlinks=true,
urlcolor=urlcolor,
linkcolor=linkcolor,
citecolor=citecolor,
}
% Slightly bigger margins than the latex defaults
\geometry{verbose,tmargin=1in,bmargin=1in,lmargin=1in,rmargin=1in}
\begin{document}
\maketitle
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{1}{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{c+c1}{\PYZsh{}knitr::opts\PYZus{}chunk\PYZdl{}set(echo = TRUE)}
\PY{n+nf}{R.Version}\PY{p}{(}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
\begin{description}
\item[\$platform] 'x86\_64-w64-mingw32'
\item[\$arch] 'x86\_64'
\item[\$os] 'mingw32'
\item[\$system] 'x86\_64, mingw32'
\item[\$status] ''
\item[\$major] '4'
\item[\$minor] '0.2'
\item[\$year] '2020'
\item[\$month] '06'
\item[\$day] '22'
\item[\$`svn rev`] '78730'
\item[\$language] 'R'
\item[\$version.string] 'R version 4.0.2 (2020-06-22)'
\item[\$nickname] 'Taking Off Again'
\end{description}
Resulting graphs and cleaned and prepared data can be found at
https://drive.google.com/drive/folders/1Yo0IW4awCIvWMP6jYVKpn3kLgEolse0e?usp=sharing
for publication
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{3}{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{rm}\PY{p}{(}\PY{n}{list} \PY{o}{=} \PY{n+nf}{setdiff}\PY{p}{(}\PY{n+nf}{ls}\PY{p}{(}\PY{p}{)}\PY{p}{,} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{ECDC0\PYZsq{}}\PY{p}{,} \PY{l+s}{\PYZsq{}}\PY{l+s}{JHH0\PYZsq{}}\PY{p}{,} \PY{l+s}{\PYZsq{}}\PY{l+s}{JHH\PYZsq{}}\PY{p}{,} \PY{l+s}{\PYZsq{}}\PY{l+s}{ECDC\PYZsq{}}\PY{p}{,} \PY{l+s}{\PYZsq{}}\PY{l+s}{JHHRegios\PYZsq{}}\PY{p}{,} \PY{l+s}{\PYZsq{}}\PY{l+s}{ECDCRegios\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{testing\PYZsq{}}\PY{p}{)}\PY{p}{)}\PY{p}{)}
\PY{n+nf}{options}\PY{p}{(}\PY{n}{warn} \PY{o}{=} \PY{l+m}{0}\PY{p}{)}
\PY{n+nf}{if }\PY{p}{(}\PY{o}{!}\PY{n+nf}{exists}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{JHH\PYZsq{}}\PY{p}{)}\PY{p}{)} \PY{n+nf}{source}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{loadData.R\PYZsq{}}\PY{p}{)} \PY{n}{else}
\PY{n+nf}{if }\PY{p}{(}\PY{n+nf}{max}\PY{p}{(}\PY{n}{JHH}\PY{o}{\PYZdl{}}\PY{n}{Date}\PY{p}{)} \PY{o}{\PYZlt{}} \PY{n+nf}{Sys.Date}\PY{p}{(}\PY{p}{)} \PY{o}{\PYZhy{}} \PY{l+m}{1}\PY{p}{)} \PY{n+nf}{source}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{loadData.R\PYZsq{}}\PY{p}{)} \PY{n}{else} \PY{n+nf}{source}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{definitions.R\PYZsq{}}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
\begin{Verbatim}[commandchars=\\\{\}]
Error: package or namespace load failed for 'tidyverse' in loadNamespace(i,
c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace 'rlang' 0.4.5 is already loaded, but >= 0.4.6 is required
Installing package into 'D:/documents/R/win-library/4.0'
(as 'lib' is unspecified)
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
package 'tidyverse' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\textbackslash{}Users\textbackslash{}feltkamp\textbackslash{}AppData\textbackslash{}Local\textbackslash{}Temp\textbackslash{}RtmpIZ8FLS\textbackslash{}downloaded\_packages
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
Error: package or namespace load failed for 'tidyverse' in loadNamespace(i,
c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace 'rlang' 0.4.5 is already loaded, but >= 0.4.6 is required
Error: package or namespace load failed for 'JuliaCall' in loadNamespace(j <-
i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'xfun' 0.12 is being loaded, but >= 0.15 is required
Installing package into 'D:/documents/R/win-library/4.0'
(as 'lib' is unspecified)
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
package 'JuliaCall' successfully unpacked and MD5 sums checked
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
Warning message:
"cannot remove prior installation of package 'JuliaCall'"
Warning message in file.copy(savedcopy, lib, recursive = TRUE):
"problem copying D:\textbackslash{}documents\textbackslash{}R\textbackslash{}win-
library\textbackslash{}4.0\textbackslash{}00LOCK\textbackslash{}JuliaCall\textbackslash{}libs\textbackslash{}x64\textbackslash{}JuliaCall.dll to D:\textbackslash{}documents\textbackslash{}R\textbackslash{}win-
library\textbackslash{}4.0\textbackslash{}JuliaCall\textbackslash{}libs\textbackslash{}x64\textbackslash{}JuliaCall.dll: Permission denied"
Warning message:
"restored 'JuliaCall'"
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
The downloaded binary packages are in
C:\textbackslash{}Users\textbackslash{}feltkamp\textbackslash{}AppData\textbackslash{}Local\textbackslash{}Temp\textbackslash{}RtmpIZ8FLS\textbackslash{}downloaded\_packages
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
Error: package or namespace load failed for 'JuliaCall' in loadNamespace(j <-
i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'xfun' 0.12 is being loaded, but >= 0.15 is required
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
Error: package or namespace load failed for 'JuliaCall' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'xfun' 0.12 is being loaded, but >= 0.15 is required
Traceback:
1. source("definitions.R")
2. withVisible(eval(ei, envir))
3. eval(ei, envir)
4. eval(ei, envir)
5. source("requirements.R")
6. withVisible(eval(ei, envir))
7. eval(ei, envir)
8. eval(ei, envir)
9. library(JuliaCall)
10. tryCatch(\{
. attr(package, "LibPath") <- which.lib.loc
. ns <- loadNamespace(package, lib.loc)
. env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
. \}, error = function(e) \{
. P <- if (!is.null(cc <- conditionCall(e)))
. paste(" in", deparse(cc)[1L])
. else ""
. msg <- gettextf("package or namespace load failed for \%s\%s:\textbackslash{}n \%s",
. sQuote(package), P, conditionMessage(e))
. if (logical.return)
. message(paste("Error:", msg), domain = NA)
. else stop(msg, call. = FALSE, domain = NA)
. \})
11. tryCatchList(expr, classes, parentenv, handlers)
12. tryCatchOne(expr, names, parentenv, handlers[[1L]])
13. value[[3L]](cond)
14. stop(msg, call. = FALSE, domain = NA)
\end{Verbatim}
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{5}{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{update.packages}\PY{p}{(}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
\begin{Verbatim}[commandchars=\\\{\}]
Warning message:
"package 'nlme' in library 'C:/Program Files/R/R-4.0.2/library' will not be
updated"
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
Update? (Yes/no/cancel) no
Update? (Yes/no/cancel) no
Update? (Yes/no/cancel) cancel
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
backports :
Version 1.1.5 installed in D:/documents/R/win-library/4.0
Version 1.1.9 available at https://cran.r-project.org
dplyr :
Version 0.8.5 installed in D:/documents/R/win-library/4.0
Version 1.0.2 available at https://cran.r-project.org
fs :
Version 1.3.2 installed in D:/documents/R/win-library/4.0
Version 1.5.0 available at https://cran.r-project.org
cancelled by user
\end{Verbatim}
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{3}{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{save.image}\PY{p}{(}\PY{l+s}{\PYZdq{}}\PY{l+s}{.RData\PYZdq{}}\PY{p}{)} \PY{c+c1}{\PYZsh{}D:/gits/Covid19/}
\end{Verbatim}
\end{tcolorbox}
Graph active\_imputed, recovered, deaths, and confirmed for some
selected territories, based on JHH data:
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{graphit}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n}{regios}\PY{o}{\PYZdl{}}\PY{n}{Vincent}\PY{p}{,} \PY{n}{xvar} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{Date\PYZsq{}}\PY{p}{,}
\PY{n}{yvars} \PY{o}{=} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{net\PYZus{}active\PYZus{}imputed\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}recovered\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}deaths\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}confirmed\PYZsq{}}\PY{p}{)}\PY{p}{,}
\PY{n}{facet} \PY{o}{=} \PY{l+s}{\PYZdq{}}\PY{l+s}{PSCR\PYZdq{}}\PY{p}{,} \PY{n}{logy} \PY{o}{=} \PY{k+kc}{TRUE}\PY{p}{,}\PY{n}{from} \PY{o}{=} \PY{l+s}{\PYZdq{}}\PY{l+s}{2020\PYZhy{}06\PYZhy{}01\PYZdq{}}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{source}\PY{p}{(}\PY{l+s}{\PYZdq{}}\PY{l+s}{graphit.R\PYZdq{}}\PY{p}{)}
\PY{n+nf}{graphit}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n}{regios}\PY{o}{\PYZdl{}}\PY{n}{Vincent}\PY{p}{,} \PY{n}{xvar} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{day\PYZsq{}}\PY{p}{,} \PY{n}{logx} \PY{o}{=} \PY{k+kc}{TRUE} \PY{p}{,} \PY{n}{logy} \PY{o}{=} \PY{k+kc}{TRUE}\PY{p}{,} \PY{n}{from} \PY{o}{=} \PY{l+s}{\PYZdq{}}\PY{l+s}{2020\PYZhy{}07\PYZhy{}01\PYZdq{}}\PY{p}{,}
\PY{n}{yvars} \PY{o}{=} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}confirmed\PYZus{}p\PYZus{}M\PYZsq{}}\PY{p}{)}\PY{p}{,} \PY{n}{labmeth} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{repel\PYZus{}label\PYZsq{}}\PY{p}{,} \PY{n}{putlegend} \PY{o}{=} \PY{k+kc}{FALSE}\PY{p}{)}
\PY{n+nf}{graphit}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n}{regios}\PY{o}{\PYZdl{}}\PY{n}{Vincent}\PY{p}{,} \PY{n}{xvar} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{day\PYZsq{}}\PY{p}{,} \PY{n}{logx} \PY{o}{=} \PY{k+kc}{TRUE} \PY{p}{,} \PY{n}{logy} \PY{o}{=} \PY{k+kc}{TRUE}\PY{p}{,} \PY{n}{from} \PY{o}{=} \PY{l+s}{\PYZdq{}}\PY{l+s}{2020\PYZhy{}07\PYZhy{}01\PYZdq{}}\PY{p}{,}
\PY{n}{yvars} \PY{o}{=} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}confirmed\PYZus{}p\PYZus{}M\PYZsq{}}\PY{p}{)}\PY{p}{,} \PY{n}{labmeth} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{repel\PYZus{}text\PYZsq{}}\PY{p}{)}
\PY{n+nf}{graphit}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n}{regios}\PY{o}{\PYZdl{}}\PY{n}{Vincent}\PY{p}{,} \PY{n}{xvar} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{day\PYZsq{}}\PY{p}{,} \PY{n}{logx} \PY{o}{=} \PY{k+kc}{TRUE} \PY{p}{,} \PY{n}{logy} \PY{o}{=} \PY{k+kc}{TRUE}\PY{p}{,} \PY{n}{from} \PY{o}{=} \PY{l+s}{\PYZdq{}}\PY{l+s}{2020\PYZhy{}07\PYZhy{}01\PYZdq{}}\PY{p}{,}
\PY{n}{yvars} \PY{o}{=} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}confirmed\PYZus{}p\PYZus{}M\PYZsq{}}\PY{p}{)}\PY{p}{,} \PY{n}{labmeth} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{dl\PYZus{}polygon\PYZsq{}}\PY{p}{)}
\PY{n+nf}{graphit}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n}{regios}\PY{o}{\PYZdl{}}\PY{n}{Vincent}\PY{p}{,} \PY{n}{xvar} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{day\PYZsq{}}\PY{p}{,} \PY{n}{logx} \PY{o}{=} \PY{k+kc}{TRUE} \PY{p}{,} \PY{n}{logy} \PY{o}{=} \PY{k+kc}{TRUE}\PY{p}{,} \PY{n}{from} \PY{o}{=} \PY{l+s}{\PYZdq{}}\PY{l+s}{2020\PYZhy{}07\PYZhy{}01\PYZdq{}}\PY{p}{,}
\PY{n}{yvars} \PY{o}{=} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}confirmed\PYZus{}p\PYZus{}M\PYZsq{}}\PY{p}{)}\PY{p}{,} \PY{n}{labmeth} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{dl\PYZus{}bumpup\PYZsq{}}\PY{p}{,} \PY{n}{putlegend} \PY{o}{=} \PY{k+kc}{TRUE}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
Show table outputs:
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{c+c1}{\PYZsh{}show some data table output}
\PY{c+c1}{\PYZsh{}JHH[JHH\PYZdl{}Date == max(JHH\PYZdl{}Date),\PYZsq{}Date\PYZsq{}][1,1]}
\PY{n}{JHH} \PY{o}{\PYZpc{}\PYZgt{}\PYZpc{}} \PY{n+nf}{filter}\PY{p}{(}\PY{n}{Date} \PY{o}{==} \PY{n+nf}{max}\PY{p}{(}\PY{n}{Date}\PY{p}{)}\PY{p}{)} \PY{o}{\PYZpc{}\PYZgt{}\PYZpc{}} \PY{n+nf}{filter}\PY{p}{(}\PY{o}{!}\PY{n+nf}{is.nan}\PY{p}{(}\PY{n}{new\PYZus{}active\PYZus{}rate}\PY{p}{)}\PY{p}{)} \PY{o}{\PYZpc{}\PYZgt{}\PYZpc{}}
\PY{n+nf}{select}\PY{p}{(}\PY{n}{PSCR}\PY{p}{,}\PY{n}{confirmed}\PY{p}{,} \PY{n}{active\PYZus{}imputed}\PY{p}{,} \PY{n}{deaths}\PY{p}{,} \PY{n}{new\PYZus{}confirmed}\PY{p}{,} \PY{n}{new\PYZus{}active\PYZus{}rate}\PY{p}{,} \PY{n}{active\PYZus{}imputed\PYZus{}growthRate}\PY{p}{,}
\PY{n}{active\PYZus{}imputed\PYZus{}p\PYZus{}M}\PY{p}{)} \PY{o}{\PYZpc{}\PYZgt{}\PYZpc{}} \PY{n+nf}{arrange}\PY{p}{(}\PY{n}{new\PYZus{}active\PYZus{}rate}\PY{p}{)} \PY{o}{\PYZpc{}\PYZgt{}\PYZpc{}} \PY{n+nf}{tail}\PY{p}{(}\PY{l+m}{10}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
and Countries we're interested in latest numbers:
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n}{JHH}\PY{p}{[}\PY{n}{JHH}\PY{o}{\PYZdl{}}\PY{n}{Date} \PY{o}{==} \PY{n+nf}{max}\PY{p}{(}\PY{n}{JHH}\PY{o}{\PYZdl{}}\PY{n}{Date}\PY{p}{)} \PY{o}{\PYZam{}} \PY{n}{JHH}\PY{o}{\PYZdl{}}\PY{n}{PSCR} \PY{o}{\PYZpc{}in\PYZpc{}}
\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{EU\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{World\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZdq{}}\PY{l+s}{Kazakhstan\PYZdq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Belgium\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Spain\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Netherlands\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Europe\PYZsq{}}\PY{p}{,}
\PY{l+s}{\PYZsq{}}\PY{l+s}{Germany\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{France\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Africa\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Russia\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Brazil\PYZsq{}}\PY{p}{)}\PY{p}{,}
\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{PSCR\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{active\PYZus{}imputed\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{active\PYZus{}imputed\PYZus{}p\PYZus{}M\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}deaths\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}confirmed\PYZsq{}}\PY{p}{,}
\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}active\PYZus{}rate\PYZsq{}}\PY{p}{,} \PY{l+s}{\PYZsq{}}\PY{l+s}{active\PYZus{}imputed\PYZus{}growthRate\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{confirmed\PYZsq{}}\PY{p}{)} \PY{p}{]} \PY{o}{\PYZpc{}\PYZgt{}\PYZpc{}}
\PY{n+nf}{arrange}\PY{p}{(}\PY{n}{new\PYZus{}active\PYZus{}rate}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
Who overtakes us based the JHH data set on latest day data?
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{map\PYZus{}dfc}\PY{p}{(}\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Kazakhstan\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Belgium\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Netherlands\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Sweden\PYZsq{}}\PY{p}{)}\PY{p}{,}
\PY{n+nf}{function}\PY{p}{(}\PY{n}{x}\PY{p}{)} \PY{n+nf}{overtakeDays\PYZus{}df}\PY{p}{(}\PY{n}{JHH}\PY{p}{,}\PY{n}{x}\PY{p}{,}\PY{n}{who} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{theyme\PYZsq{}}\PY{p}{,}\PY{n}{lastDays} \PY{o}{=} \PY{l+m}{1}\PY{p}{)}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
And on 7 day averages in JHH?
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{map\PYZus{}dfc}\PY{p}{(}\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Kazakhstan\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Belgium\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Netherlands\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Sweden\PYZsq{}}\PY{p}{)}\PY{p}{,}
\PY{n+nf}{function}\PY{p}{(}\PY{n}{x}\PY{p}{)} \PY{n+nf}{overtakeDays\PYZus{}df}\PY{p}{(}\PY{n}{JHH}\PY{p}{,}\PY{n}{x}\PY{p}{,}\PY{n}{who} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{theyme\PYZsq{}}\PY{p}{,}\PY{n}{lastDays} \PY{o}{=} \PY{l+m}{7}\PY{p}{)}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
And according to ECDC?
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{map\PYZus{}dfc}\PY{p}{(}\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Kazakhstan\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Belgium\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Netherlands\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Sweden\PYZsq{}}\PY{p}{)}\PY{p}{,}
\PY{n+nf}{function}\PY{p}{(}\PY{n}{x}\PY{p}{)} \PY{n+nf}{overtakeDays\PYZus{}df}\PY{p}{(}\PY{n}{ECDC}\PY{p}{,}\PY{n}{x}\PY{p}{,}\PY{n}{who} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{theyme\PYZsq{}}\PY{p}{,}\PY{n}{lastDays} \PY{o}{=} \PY{l+m}{7}\PY{p}{)}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
Who is more affected?
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{graph3Dard\PYZus{}fia}\PY{p}{(}\PY{n}{ECDC}\PY{p}{,} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Kazakhstan\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Belgium\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Netherlands\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Sweden\PYZsq{}}\PY{p}{)}\PY{p}{)}
\PY{n+nf}{graph3Dard\PYZus{}fina}\PY{p}{(}\PY{n}{ECDC}\PY{p}{,} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Kazakhstan\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Belgium\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Netherlands\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Sweden\PYZsq{}}\PY{p}{)}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
Who do we overtake?
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{map\PYZus{}dfc}\PY{p}{(}\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Kazakhstan\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Belgium\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Netherlands\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Sweden\PYZsq{}}\PY{p}{)}\PY{p}{,}\PY{n+nf}{function}\PY{p}{(}\PY{n}{x}\PY{p}{)} \PY{n+nf}{overtakeDays\PYZus{}df}\PY{p}{(}\PY{n}{JHH}\PY{p}{,}\PY{n}{x}\PY{p}{,}\PY{n}{who} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{Ithem\PYZsq{}}\PY{p}{,}\PY{n}{lastDays} \PY{o}{=} \PY{l+m}{7}\PY{p}{)}\PY{p}{)}
\PY{n+nf}{map\PYZus{}dfc}\PY{p}{(}\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Kazakhstan\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Belgium\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Netherlands\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Sweden\PYZsq{}}\PY{p}{)}\PY{p}{,}\PY{n+nf}{function}\PY{p}{(}\PY{n}{x}\PY{p}{)} \PY{n+nf}{overtakeDays\PYZus{}df}\PY{p}{(}\PY{n}{ECDC}\PY{p}{,}\PY{n}{x}\PY{p}{,}\PY{n}{who} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{Ithem\PYZsq{}}\PY{p}{,}\PY{n}{lastDays} \PY{o}{=} \PY{l+m}{7}\PY{p}{)}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
Lets see who is going to overtake the UK, France, or GErmany soon:
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{graph3Dard\PYZus{}fia}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Germany\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{France\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{United Kingdom\PYZsq{}}\PY{p}{)}\PY{p}{)}
\PY{n+nf}{graph3Dard\PYZus{}fina}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Germany\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{France\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{United Kingdom\PYZsq{}}\PY{p}{)}\PY{p}{)}
\PY{n+nf}{map\PYZus{}dfc}\PY{p}{(}\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Germany\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{France\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{United Kingdom\PYZsq{}}\PY{p}{)}\PY{p}{,} \PY{n+nf}{function}\PY{p}{(}\PY{n}{x}\PY{p}{)} \PY{n+nf}{overtakeDays\PYZus{}df}\PY{p}{(}\PY{n}{JHH}\PY{p}{,}\PY{n}{x}\PY{p}{,}\PY{n}{who} \PY{o}{=} \PY{l+s}{\PYZdq{}}\PY{l+s}{theyme\PYZdq{}}\PY{p}{,} \PY{n}{lastDays} \PY{o}{=} \PY{l+m}{7}\PY{p}{)}\PY{p}{)}
\PY{n+nf}{map\PYZus{}dfc}\PY{p}{(}\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{Germany\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{France\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{United Kingdom\PYZsq{}}\PY{p}{)}\PY{p}{,} \PY{n+nf}{function}\PY{p}{(}\PY{n}{x}\PY{p}{)} \PY{n+nf}{overtakeDays\PYZus{}df}\PY{p}{(}\PY{n}{JHH}\PY{p}{,}\PY{n}{x}\PY{p}{,}\PY{n}{who} \PY{o}{=} \PY{l+s}{\PYZdq{}}\PY{l+s}{Ithem\PYZdq{}}\PY{p}{,} \PY{n}{lastDays} \PY{o}{=} \PY{l+m}{7}\PY{p}{)}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
Not overtaking anyone does not mean the epidemic is under control. It
just means your epidemic is alsready larger than all states that grow
slower. It also means you have better control than more severely touched
territories. For New York state, Indonesia, Peru, India:
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{graph3Dard\PYZus{}fina}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{New York,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{California,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Florida,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Texas,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Peru\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZdq{}}\PY{l+s}{Arizona,US\PYZdq{}}\PY{p}{)}\PY{p}{)}
\PY{n+nf}{map\PYZus{}dfc}\PY{p}{(}\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{New York,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{California,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Florida,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Texas,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Peru\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZdq{}}\PY{l+s}{Arizona,US\PYZdq{}}\PY{p}{)}\PY{p}{,}
\PY{n+nf}{function}\PY{p}{(}\PY{n}{x}\PY{p}{)} \PY{n+nf}{overtakeDays\PYZus{}df}\PY{p}{(}\PY{n}{JHH}\PY{p}{,}\PY{n}{x}\PY{p}{,}\PY{n}{who} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{Ithem\PYZsq{}}\PY{p}{)}\PY{p}{)}
\PY{n+nf}{map\PYZus{}dfc}\PY{p}{(}\PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{New York,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{California,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Florida,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Texas,US\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZsq{}}\PY{l+s}{Peru\PYZsq{}}\PY{p}{,}\PY{l+s}{\PYZdq{}}\PY{l+s}{Arizona,US\PYZdq{}}\PY{p}{)}\PY{p}{,}
\PY{n+nf}{function}\PY{p}{(}\PY{n}{x}\PY{p}{)} \PY{n+nf}{overtakeDays\PYZus{}df}\PY{p}{(}\PY{n}{JHH}\PY{p}{,}\PY{n}{x}\PY{p}{,}\PY{n}{who} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{theyme\PYZsq{}}\PY{p}{)}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
See how the most affected regions in the world are developing: (pop the
graph out to a new window and enlarge to see more detail)
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{graph6Dardcra\PYZus{}finyl}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n}{JHHRegios}\PY{o}{\PYZdl{}}\PY{n}{`JHH World1`}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{graph2crd\PYZus{}il}\PY{p}{(}\PY{n}{JHH}\PY{p}{,}\PY{n}{JHHRegios}\PY{o}{\PYZdl{}}\PY{n}{`JHH Europe3`}\PY{p}{)}
\PY{n+nf}{graph2crd\PYZus{}il}\PY{p}{(}\PY{n}{JHH}\PY{p}{,}\PY{n}{JHHRegios}\PY{o}{\PYZdl{}}\PY{n}{`JHH Europe2`}\PY{p}{)}
\PY{n+nf}{graph1dnar\PYZus{}iyl}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n}{JHHRegios}\PY{o}{\PYZdl{}}\PY{n}{`JHH Europe2`}\PY{p}{)}
\PY{n+nf}{graphit}\PY{p}{(}\PY{n}{JHH}\PY{p}{,} \PY{n}{JHHRegios}\PY{o}{\PYZdl{}}\PY{n}{`JHH Europe2`}\PY{p}{,} \PY{n}{minVal}\PY{o}{=}\PY{l+m}{1}\PY{p}{,} \PY{n}{xvar} \PY{o}{=} \PY{l+s}{\PYZsq{}}\PY{l+s}{day\PYZsq{}}\PY{p}{,}
\PY{n}{yvars} \PY{o}{=} \PY{n+nf}{c}\PY{p}{(}\PY{l+s}{\PYZsq{}}\PY{l+s}{new\PYZus{}active\PYZus{}rate\PYZsq{}}\PY{p}{)}\PY{p}{,} \PY{n}{logy} \PY{o}{=} \PY{k+kc}{TRUE}\PY{p}{,} \PY{n}{intercept} \PY{o}{=} \PY{n}{stableRate}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
If you want to write the data to disk, make sure to define the correct
datapath so that R can write to it. By default it is a subfolder of the
scripts folder. Note that the data will also be written to a subfolder
of the plots folder.
\texttt{\{r\ save\ the\ data\}\ dataPath\ \textless{}-\ \textquotesingle{}./data\textquotesingle{}\ if\ (!dir.exists(dataPath))\ dir.create(dataPath,\ recursive\ =\ TRUE)\ writeWithCounters(ECDC,name\ =\ "Covid19ECDC")\ writeWithCounters(JHH,name\ =\ "Covid19JHH")}
The motor in all this is the graphit function. It is quite powerful but
hass a lot of parameters. Several functions preset some parameters,
Below a lost of Graphs defined.
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{setdiff}\PY{p}{(}\PY{n}{myGraphList}\PY{p}{,} \PY{n+nf}{c}\PY{p}{(}\PY{n}{myGraphListbyDate}\PY{p}{,} \PY{n}{myGraphListbyDay}\PY{p}{,} \PY{n}{myGraphNrs}\PY{p}{)}\PY{p}{)}
\PY{n+nf}{c}\PY{p}{(} \PY{n}{myGraphListbyDate}\PY{p}{,} \PY{n}{myGraphListbyDay}\PY{p}{,} \PY{n}{myGraphNrs}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
There is a system in the naming:
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{graphCodes}\PY{p}{(}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{n+nf}{Sys.which}\PY{p}{(}\PY{l+s}{\PYZdq{}}\PY{l+s}{python\PYZdq{}}\PY{p}{)}
\PY{n+nf}{use\PYZus{}python}\PY{p}{(}\PY{l+s}{\PYZdq{}}\PY{l+s}{path/to/python\PYZdq{}}\PY{p}{)}
\end{Verbatim}
\end{tcolorbox}
\begin{tcolorbox}[breakable, size=fbox, boxrule=1pt, pad at break*=1mm,colback=cellbackground, colframe=cellborder]
\prompt{In}{incolor}{ }{\boxspacing}
\begin{Verbatim}[commandchars=\\\{\}]
\PY{o}{\PYZpc{}\PYZpc{}}\PY{n}{python}
\PY{l+m}{2}\PY{o}{\PYZca{}}\PY{l+m}{100}
\end{Verbatim}
\end{tcolorbox}
% Add a bibliography block to the postdoc
\end{document}