diff --git a/LaTeX/CN/REVIEW_01/REVIEW_01.pdf b/LaTeX/CN/REVIEW_01/REVIEW_01.pdf index 1466822..dad3e9f 100644 Binary files a/LaTeX/CN/REVIEW_01/REVIEW_01.pdf and b/LaTeX/CN/REVIEW_01/REVIEW_01.pdf differ diff --git a/LaTeX/CN/REVIEW_01/REVIEW_01.tex b/LaTeX/CN/REVIEW_01/REVIEW_01.tex index ece6e0a..28a9878 100644 --- a/LaTeX/CN/REVIEW_01/REVIEW_01.tex +++ b/LaTeX/CN/REVIEW_01/REVIEW_01.tex @@ -122,7 +122,7 @@ \date{} \begin{document} - +\pagenumbering{Roman} \hypertarget{review-of-the-course-r-for-data-science-part-01talk-01-04}{% \section{Review of the course ``R for Data Science'' Part 01(Talk 01\textasciitilde{} @@ -137,6 +137,11 @@ \section{Review of the course ``R for Data Science'' Part 01(Talk This work is licensed under CC BY-NC-SA 4.0 +\tableofcontents + +\newpage +\setcounter{page}{1} +\pagenumbering{arabic} \hypertarget{multi-omics-data-analysis-and-visualisation-1}{% \section{Multi-omics data analysis and visualisation, \#1}\label{multi-omics-data-analysis-and-visualisation-1}} diff --git a/LaTeX/CN/REVIEW_02/REVIEW_02.pdf b/LaTeX/CN/REVIEW_02/REVIEW_02.pdf index cf8ade8..31328ff 100644 Binary files a/LaTeX/CN/REVIEW_02/REVIEW_02.pdf and b/LaTeX/CN/REVIEW_02/REVIEW_02.pdf differ diff --git a/LaTeX/CN/REVIEW_02/REVIEW_02.tex b/LaTeX/CN/REVIEW_02/REVIEW_02.tex index e687897..7212ce0 100644 --- a/LaTeX/CN/REVIEW_02/REVIEW_02.tex +++ b/LaTeX/CN/REVIEW_02/REVIEW_02.tex @@ -121,7 +121,7 @@ \date{} \begin{document} - +\pagenumbering{Roman} \hypertarget{review-of-the-course-r-for-data-science-part-02talk-05-08}{% \section{Review of the course ``R for Data Science'' Part 02(Talk 05\textasciitilde{} @@ -140,6 +140,11 @@ \section{Review of the course ``R for Data Science'' Part 02(Talk \begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} +\tableofcontents + +\newpage +\setcounter{page}{1} % 将页码计数器设置为 1 +\pagenumbering{arabic} % 使用阿拉伯数字重新编号页码 \hypertarget{r-for-bioinformatics-data-wrangler-part-1}{% \section{R for bioinformatics, data wrangler, part 1}\label{r-for-bioinformatics-data-wrangler-part-1}} diff --git a/LaTeX/CN/REVIEW_03/REVIEW_03.pdf b/LaTeX/CN/REVIEW_03/REVIEW_03.pdf index 16bfabd..5068d8d 100644 Binary files a/LaTeX/CN/REVIEW_03/REVIEW_03.pdf and b/LaTeX/CN/REVIEW_03/REVIEW_03.pdf differ diff --git a/LaTeX/CN/REVIEW_03/REVIEW_03.tex b/LaTeX/CN/REVIEW_03/REVIEW_03.tex index 6fabb8b..bddd5d5 100644 --- a/LaTeX/CN/REVIEW_03/REVIEW_03.tex +++ b/LaTeX/CN/REVIEW_03/REVIEW_03.tex @@ -121,7 +121,7 @@ \date{} \begin{document} - +\pagenumbering{Roman} \hypertarget{review-of-the-course-r-for-data-science-part-03talk-09-12}{% \section{Review of the course ``R for Data Science'' Part 03(Talk 09\textasciitilde{} @@ -137,7 +137,10 @@ \section{Review of the course ``R for Data Science'' Part 03(Talk This work is licensed under CC BY-NC-SA 4.0 \begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} +\tableofcontents +\newpage +\pagenumbering{arabic} \hypertarget{r-for-bioinformatics-data-visualisation}{% \section{R for bioinformatics, data visualisation}\label{r-for-bioinformatics-data-visualisation}} diff --git a/LaTeX/CN/REVIEW_CN.pdf b/LaTeX/CN/REVIEW_CN.pdf index eb27e8d..fd7e732 100644 Binary files a/LaTeX/CN/REVIEW_CN.pdf and b/LaTeX/CN/REVIEW_CN.pdf differ diff --git a/LaTeX/CN/REVIEW_CN_TOC.pdf b/LaTeX/CN/REVIEW_CN_TOC.pdf new file mode 100644 index 0000000..f31b603 Binary files /dev/null and b/LaTeX/CN/REVIEW_CN_TOC.pdf differ diff --git a/LaTeX/CN/REVIEW_CN_print.pdf b/LaTeX/CN/REVIEW_CN_print.pdf index 618a160..ff71dfd 100644 Binary files a/LaTeX/CN/REVIEW_CN_print.pdf and b/LaTeX/CN/REVIEW_CN_print.pdf differ diff --git a/LaTeX/EN/REVIEW.pdf b/LaTeX/EN/REVIEW.pdf index fe220c2..11929f5 100644 Binary files a/LaTeX/EN/REVIEW.pdf and b/LaTeX/EN/REVIEW.pdf differ diff --git a/LaTeX/EN/REVIEW_01/REVIEW_01.pdf b/LaTeX/EN/REVIEW_01/REVIEW_01.pdf index 44f195a..42166dc 100644 Binary files a/LaTeX/EN/REVIEW_01/REVIEW_01.pdf and b/LaTeX/EN/REVIEW_01/REVIEW_01.pdf differ diff --git a/LaTeX/EN/REVIEW_01/REVIEW_01.tex b/LaTeX/EN/REVIEW_01/REVIEW_01.tex index 8582a73..3611151 100644 --- a/LaTeX/EN/REVIEW_01/REVIEW_01.tex +++ b/LaTeX/EN/REVIEW_01/REVIEW_01.tex @@ -110,7 +110,7 @@ \date{} \begin{document} - +\pagenumbering{Roman} \hypertarget{review-of-the-course-r-for-data-science-part-01talk-01-04}{% \section{Review of the course ``R for Data Science'' Part 01(Talk 01\textasciitilde{} @@ -120,6 +120,10 @@ \section{Review of the course ``R for Data Science'' Part 01(Talk This work is licensed under CC BY-NC-SA 4.0 +\tableofcontents + +\newpage +\pagenumbering{arabic} \hypertarget{multi-omics-data-analysis-and-visualisation-1}{% \section{Multi-omics data analysis and visualisation, \#1}\label{multi-omics-data-analysis-and-visualisation-1}} @@ -298,13 +302,13 @@ \subsubsection{Vector maniulation}\label{vector-maniulation}} \begin{Highlighting}[] \CommentTok{\# (There\textquotesingle{}s already some data in workspace)} -\SpecialCharTok{$}\NormalTok{ m} +\SpecialCharTok{\$}\NormalTok{ m} \SpecialCharTok{\textgreater{}}\NormalTok{ (List the content of matrix }\StringTok{"m"}\NormalTok{)} -\SpecialCharTok{$}\NormalTok{ m[}\DecValTok{1}\NormalTok{, ]} +\SpecialCharTok{\$}\NormalTok{ m[}\DecValTok{1}\NormalTok{, ]} \SpecialCharTok{\textgreater{}}\NormalTok{ (List the first row of matrix }\StringTok{\textquotesingle{}m\textquotesingle{}}\NormalTok{)} -\SpecialCharTok{$}\NormalTok{ m[}\DecValTok{1}\SpecialCharTok{:}\DecValTok{2}\NormalTok{, ]} +\SpecialCharTok{\$}\NormalTok{ m[}\DecValTok{1}\SpecialCharTok{:}\DecValTok{2}\NormalTok{, ]} \SpecialCharTok{\textgreater{}}\NormalTok{ (List the first two rows of matrix }\StringTok{\textquotesingle{}m\textquotesingle{}}\NormalTok{)} \end{Highlighting} \end{Shaded} @@ -721,10 +725,10 @@ \subsubsection{\texorpdfstring{\texttt{data.frame} will do partial \begin{Shaded} \begin{Highlighting}[] \NormalTok{df }\OtherTok{=} \FunctionTok{data.frame}\NormalTok{(}\AttributeTok{abc =} \DecValTok{1}\NormalTok{) } -\NormalTok{df}\SpecialCharTok{$}\NormalTok{ab; }\CommentTok{\# Unwanted result ...} +\NormalTok{df}\SpecialCharTok{\$}\NormalTok{ab; }\CommentTok{\# Unwanted result ...} \NormalTok{df2 }\OtherTok{=} \FunctionTok{tibble}\NormalTok{(}\AttributeTok{abc =} \DecValTok{1}\NormalTok{)} -\NormalTok{df2}\SpecialCharTok{$}\NormalTok{a; }\CommentTok{\# Produce a warning and return NULL} +\NormalTok{df2}\SpecialCharTok{\$}\NormalTok{a; }\CommentTok{\# Produce a warning and return NULL} \end{Highlighting} \end{Shaded} @@ -1444,9 +1448,9 @@ \subsubsection{Usage of factors in drawing \NormalTok{res }\OtherTok{=} \FunctionTok{data.frame}\NormalTok{(responses)} \CommentTok{\# Sort by level of agreement from strong {-}\textgreater{} weak} -\NormalTok{res}\SpecialCharTok{$}\NormalTok{res }\OtherTok{=} +\NormalTok{res}\SpecialCharTok{\$}\NormalTok{res }\OtherTok{=} \FunctionTok{factor}\NormalTok{(} -\NormalTok{ res}\SpecialCharTok{$}\NormalTok{res,} +\NormalTok{ res}\SpecialCharTok{\$}\NormalTok{res,} \AttributeTok{levels =} \FunctionTok{c}\NormalTok{(}\StringTok{"Strongly Agree"}\NormalTok{, }\StringTok{"Agree"}\NormalTok{, }\StringTok{"Disagree"}\NormalTok{)} \NormalTok{ )} @@ -1563,8 +1567,8 @@ \subsubsection{\texorpdfstring{Delete useless \begin{Shaded} \begin{Highlighting}[] -\NormalTok{mouse.chr\_10\_12}\SpecialCharTok{$}\NormalTok{Chromosome.scaffold.name }\OtherTok{=} - \FunctionTok{droplevels}\NormalTok{(mouse.chr\_10\_12}\SpecialCharTok{$}\NormalTok{Chromosome.scaffold.name)} +\NormalTok{mouse.chr\_10\_12}\SpecialCharTok{\$}\NormalTok{Chromosome.scaffold.name }\OtherTok{=} + \FunctionTok{droplevels}\NormalTok{(mouse.chr\_10\_12}\SpecialCharTok{\$}\NormalTok{Chromosome.scaffold.name)} \end{Highlighting} \end{Shaded} diff --git a/LaTeX/EN/REVIEW_02/REVIEW_02 copy.pdf b/LaTeX/EN/REVIEW_02/REVIEW_02 copy.pdf new file mode 100644 index 0000000..bd48999 Binary files /dev/null and b/LaTeX/EN/REVIEW_02/REVIEW_02 copy.pdf differ diff --git a/LaTeX/EN/REVIEW_02/REVIEW_02.pdf b/LaTeX/EN/REVIEW_02/REVIEW_02.pdf index 1b3139d..d62f4a1 100644 Binary files a/LaTeX/EN/REVIEW_02/REVIEW_02.pdf and b/LaTeX/EN/REVIEW_02/REVIEW_02.pdf differ diff --git a/LaTeX/EN/REVIEW_02/REVIEW_02.tex b/LaTeX/EN/REVIEW_02/REVIEW_02.tex index 200939a..a6bd229 100644 --- a/LaTeX/EN/REVIEW_02/REVIEW_02.tex +++ b/LaTeX/EN/REVIEW_02/REVIEW_02.tex @@ -4,7 +4,6 @@ % \documentclass[ ]{article} -\usepackage{ctex} \usepackage{geometry} \geometry{a4paper,left=2.8cm,right=2.8cm,top=3cm,bottom=2.5cm} \usepackage{amsmath,amssymb} @@ -121,7 +120,7 @@ \date{} \begin{document} - +\pagenumbering{Roman} \hypertarget{review-of-the-course-r-for-data-science-part-02talk-05-08}{% \section{Review of the course ``R for Data Science'' Part 02(Talk 05\textasciitilde{} @@ -136,6 +135,10 @@ \section{Review of the course ``R for Data Science'' Part 02(Talk To reduce the size, all the codes listed will \emph{\textbf{NOT}} include the output as picture. +\tableofcontents + +\newpage +\pagenumbering{arabic} \hypertarget{r-for-bioinformatics-data-wrangler-part-1}{% \section{R for bioinformatics, data wrangler, part 1}\label{r-for-bioinformatics-data-wrangler-part-1}} diff --git a/LaTeX/EN/REVIEW_02/REVIEW_02.txt b/LaTeX/EN/REVIEW_02/REVIEW_02.txt new file mode 100644 index 0000000..a6bd229 --- /dev/null +++ b/LaTeX/EN/REVIEW_02/REVIEW_02.txt @@ -0,0 +1,1946 @@ +% Options for packages loaded elsewhere +\PassOptionsToPackage{unicode}{hyperref} +\PassOptionsToPackage{hyphens}{url} +% +\documentclass[ +]{article} +\usepackage{geometry} +\geometry{a4paper,left=2.8cm,right=2.8cm,top=3cm,bottom=2.5cm} +\usepackage{amsmath,amssymb} +\usepackage{graphicx} +\let\oldincludegraphics\includegraphics +\renewcommand{\includegraphics}[2][]{\begin{center}\oldincludegraphics[#1]{#2}\end{center}} +\usepackage{iftex} +\ifPDFTeX + \usepackage[T1]{fontenc} + \usepackage[utf8]{inputenc} + \usepackage{textcomp} % provide euro and other symbols +\else % if luatex or xetex + \usepackage{unicode-math} % this also loads fontspec + \defaultfontfeatures{Scale=MatchLowercase} + \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1} +\fi +\usepackage{lmodern} +\ifPDFTeX\else + % xetex/luatex font selection +\fi +% Use upquote if available, for straight quotes in verbatim environments +\IfFileExists{upquote.sty}{\usepackage{upquote}}{} +\IfFileExists{microtype.sty}{% use microtype if available + \usepackage[]{microtype} + \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts +}{} +\makeatletter +\@ifundefined{KOMAClassName}{% if non-KOMA class + \IfFileExists{parskip.sty}{% + \usepackage{parskip} + }{% else + \setlength{\parindent}{0pt} + \setlength{\parskip}{6pt plus 2pt minus 1pt}} +}{% if KOMA class + \KOMAoptions{parskip=half}} +\makeatother +\usepackage{xcolor} +\usepackage{color} +\usepackage{fancyvrb} +\newcommand{\VerbBar}{|} +\newcommand{\VERB}{\Verb[commandchars=\\\{\}]} +\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}} +% Add ',fontsize=\small' for more characters per line +\newenvironment{Shaded}{}{} +\newcommand{\AlertTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{#1}}} +\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}} +\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.49,0.56,0.16}{#1}} +\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{#1}} +\newcommand{\BuiltInTok}[1]{\textcolor[rgb]{0.00,0.50,0.00}{#1}} +\newcommand{\CharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}} +\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textit{#1}}} +\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}} +\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.53,0.00,0.00}{#1}} +\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{#1}}} +\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.56,0.13,0.00}{#1}} 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+\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.73,0.40,0.53}{#1}} +\newcommand{\StringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}} +\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.10,0.09,0.49}{#1}} +\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}} +\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}} +\usepackage{longtable,booktabs,array} +\usepackage{calc} % for calculating minipage widths +% Correct order of tables after \paragraph or \subparagraph +\usepackage{etoolbox} +\makeatletter +\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{} +\makeatother +% Allow footnotes in longtable head/foot +\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}} +\makesavenoteenv{longtable} +\usepackage{graphicx} +\makeatletter +\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi} +\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi} +\makeatother +% Scale images if necessary, so that they will not overflow the page +% margins by default, and it is still possible to overwrite the defaults +% using explicit options in \includegraphics[width, height, ...]{} +\setkeys{Gin}{width=0.5\textwidth,keepaspectratio} +% Set default figure placement to htbp +\makeatletter +\def\fps@figure{htbp} +\makeatother +\setlength{\emergencystretch}{3em} % prevent overfull lines +\providecommand{\tightlist}{% + \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}} +\setcounter{secnumdepth}{-\maxdimen} % remove section numbering +\ifLuaTeX + \usepackage{selnolig} % disable illegal ligatures +\fi +\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}} +\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available +\urlstyle{same} +\hypersetup{ + hidelinks, + pdfcreator={LaTeX via pandoc}} + +\author{} +\date{} + +\begin{document} +\pagenumbering{Roman} +\hypertarget{review-of-the-course-r-for-data-science-part-02talk-05-08}{% +\section{Review of the course ``R for Data Science'' Part 02(Talk +05\textasciitilde{} +08)}\label{review-of-the-course-r-for-data-science-part-02talk-05-08}} + +\textbf{By Haoran Nie @ HUST Life ST} + +This work is licensed under CC BY-NC-SA 4.0 + +\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} + +To reduce the size, all the codes listed will \emph{\textbf{NOT}} +include the output as picture. + +\tableofcontents + +\newpage +\pagenumbering{arabic} +\hypertarget{r-for-bioinformatics-data-wrangler-part-1}{% +\section{R for bioinformatics, data wrangler, part +1}\label{r-for-bioinformatics-data-wrangler-part-1}} + +\begin{quote} +Talk 05 +\end{quote} + +\hypertarget{toc}{% +\subsection{TOC}\label{toc}} + +\hypertarget{pipe}{% +\subsubsection{pipe}\label{pipe}} + +\hypertarget{dplyr}{% +\subsubsection{\texorpdfstring{\texttt{dplyr}}{dplyr}}\label{dplyr}} + +\hypertarget{tidyr-part-1}{% +\subsubsection{\texorpdfstring{\texttt{tidyr}, part +1}{tidyr, part 1}}\label{tidyr-part-1}} + +\hypertarget{pipe-in-r}{% +\subsection{Pipe in R}\label{pipe-in-r}} + +\hypertarget{what-is-pipe-in-r}{% +\subsubsection{What is pipe in R?}\label{what-is-pipe-in-r}} + +\begin{itemize} +\item + Pipe is \texttt{\%\textgreater{}\%}. +\item + It comes from the \texttt{magrittr} package by \textbf{Stefan Milton + Bache}. +\item + Packages in the \texttt{tidyverse} load + \texttt{\%\textbackslash{}\textgreater{}\%} for you automatically, so + you don\textquotesingle t usually load \texttt{magrittr} explicitly. +\item + The essence is the passing of intermediate values. +\end{itemize} + +\textbf{Example} + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{library}\NormalTok{(tidyverse)} +\FunctionTok{library}\NormalTok{(magrittr)} +\NormalTok{a }\OtherTok{=} + \FunctionTok{subset}\NormalTok{(swiss, Fertility }\SpecialCharTok{\textgreater{}} \DecValTok{20}\NormalTok{)} +\FunctionTok{cor.test}\NormalTok{(a}\SpecialCharTok{$}\NormalTok{Fertility, a}\SpecialCharTok{$}\NormalTok{Education)} +\end{Highlighting} +\end{Shaded} + +The code above can be replaced by: + +\begin{Shaded} +\begin{Highlighting}[] +\NormalTok{swiss }\SpecialCharTok{\%\textgreater{}\%} + \FunctionTok{subset}\NormalTok{(., Fertility }\SpecialCharTok{\textgreater{}} \DecValTok{20}\NormalTok{) }\SpecialCharTok{\%\$\%} + \FunctionTok{cor.test}\NormalTok{(Education, Fertility)} +\end{Highlighting} +\end{Shaded} + +You should remember that almost \textbf{all} the funtions support pipe. + +\hypertarget{other-kinds-of-pipe}{% +\subsubsection{Other kinds of pipe}\label{other-kinds-of-pipe}} + +\begin{itemize} +\item + \texttt{\%T\textgreater{}\%}: Return left-side values +\end{itemize} + +\begin{itemize} +\item + \texttt{\%\$\textgreater{}\%}: Attach \ldots{} +\end{itemize} + +\begin{itemize} +\item + \texttt{\%\textless{}\textgreater{}\%} +\end{itemize} + +\hypertarget{attention}{% +\paragraph{\texorpdfstring{\textbf{ATTENTION}}{ATTENTION}}\label{attention}} + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + The use of pipe makes the idea clearer; +\item + Therefore, try to use \texttt{\%\textgreater{}\%} (which has a clear + direction) instead of the other pipe, which has an unclear direction. +\end{enumerate} + +\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} + +\hypertarget{data-wrangler---dplyr}{% +\subsection{\texorpdfstring{Data Wrangler - +\texttt{dplyr}}{Data Wrangler - dplyr}}\label{data-wrangler---dplyr}} + +\hypertarget{what-is-dplyr}{% +\subsubsection{\texorpdfstring{What is +\texttt{dplyr}?}{What is dplyr?}}\label{what-is-dplyr}} + +\begin{itemize} +\item + The next iteration of \texttt{plyr}, +\item + Focusing on only data frames (also tibble), +\item + Row-based manipulation, +\item + \texttt{dplyr} is faster and has a more consistent API. +\end{itemize} + +\texttt{dplyr} provides a consistent set of verbs that help you +\textbf{solve the most common data manipulation challenges}: + +\begin{itemize} +\item + \href{https://dplyr.tidyverse.org/reference/select.html}{\texttt{select()}} + Select columns, based on column name rules. +\item + \href{https://dplyr.tidyverse.org/reference/filter.html}{\texttt{filter()}} + Filter rows by rule. +\item + \href{https://dplyr.tidyverse.org/reference/mutate.html}{\texttt{mutate()}} + Add new column, calculated from other columns (no change in number of + rows). +\item + \href{https://dplyr.tidyverse.org/reference/summarise.html}{\texttt{summarise()}} + Converts multiple values to a single value (via mean, median, sd, + etc.), generating new columns (total number of rows is reduced, + usually in conjunction with \texttt{group\_by}). +\item + \href{https://dplyr.tidyverse.org/reference/arrange.html}{\texttt{arrange()}} + Sorting the rows. +\end{itemize} + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Read the file} +\FunctionTok{library}\NormalTok{(tidyverse)} +\NormalTok{mouse.tibble }\OtherTok{=} + \FunctionTok{read\_delim}\NormalTok{(} + \AttributeTok{file =} \StringTok{"data/mouse\_genes\_biomart\_sep2018.txt"}\NormalTok{,} + \AttributeTok{delim =} \StringTok{"}\SpecialCharTok{\textbackslash{}t}\StringTok{"}\NormalTok{,} + \AttributeTok{quote =} \StringTok{""}\NormalTok{,} + \AttributeTok{show\_col\_types =} \ConstantTok{FALSE} +\NormalTok{ )} + +\CommentTok{\# View mouse.tibble content} +\NormalTok{ttype.stats }\OtherTok{=} +\NormalTok{ mouse.tibble }\SpecialCharTok{\%\textgreater{}\%} + \FunctionTok{count}\NormalTok{(}\StringTok{\textasciigrave{}}\AttributeTok{Transcript type}\StringTok{\textasciigrave{}}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%} + \FunctionTok{arrange}\NormalTok{(}\SpecialCharTok{{-}}\NormalTok{n)} + +\CommentTok{\# View mouse.tibble content, cont.} +\NormalTok{chr.stats }\OtherTok{=} +\NormalTok{ mouse.tibble }\SpecialCharTok{\%\textgreater{}\%} + \FunctionTok{count}\NormalTok{(}\StringTok{\textasciigrave{}}\AttributeTok{Chromosome/scaffold name}\StringTok{\textasciigrave{}}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%} + \FunctionTok{arrange}\NormalTok{(}\SpecialCharTok{{-}}\NormalTok{n)} +\end{Highlighting} +\end{Shaded} + +\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} + +\hypertarget{r-for-bioinformatics-data-wrangler-part-2}{% +\section{R for bioinformatics, data wrangler, part +2}\label{r-for-bioinformatics-data-wrangler-part-2}} + +\begin{quote} +Talk 06 +\end{quote} + +\hypertarget{toc-2}{% +\subsection{TOC}\label{toc-2}} + +\hypertarget{tidyr}{% +\subsubsection{\texorpdfstring{\texttt{tidyr}}{tidyr}}\label{tidyr}} + +\begin{itemize} +\item + \texttt{pivot\_longer()} to take the place of \texttt{gather} +\item + \texttt{pivot\_wider()} to take the place of \texttt{spread} +\end{itemize} + +\hypertarget{data-wrangler---tidyr}{% +\subsection{\texorpdfstring{Data Wrangler - +\texttt{tidyr}}{Data Wrangler - tidyr}}\label{data-wrangler---tidyr}} + +You can get \texttt{tidyr} in the package set \texttt{tidyverse}, or +simply install it the first time you want to use it via +\texttt{install.packages("tidyr")}. + +\hypertarget{the-usage-of-tidyr}{% +\subsubsection{\texorpdfstring{The usage of +\texttt{tidyr}}{The usage of tidyr}}\label{the-usage-of-tidyr}} + +\begin{itemize} +\item + Interconversion of wide and long data +\end{itemize} + +\begin{Shaded} +\begin{Highlighting}[] +\NormalTok{\# Eg 1} +\NormalTok{library(tidyverse)} +\NormalTok{grades2 =} +\NormalTok{ read\_tsv(file = "data/grades2.txt")} + +\NormalTok{grades3 =} +\NormalTok{ grades2 \%\textgreater{}\% } +\NormalTok{ pivot\_longer( } +\NormalTok{ {-} name,} +\NormalTok{ names\_to = "course",} +\NormalTok{ values\_to = "grade"} +\NormalTok{ )} + +\NormalTok{\# Eg 2} +\NormalTok{grades3\_wide = grades3\_long \%\textgreater{}\% } +\NormalTok{ pivot\_wider(} +\NormalTok{ names\_from = "course",} +\NormalTok{ values\_from = "grade"} +\NormalTok{ )} +\end{Highlighting} +\end{Shaded} + +\hypertarget{whats-the-difference-between-wide-and-long-data}{% +\subsubsection{What's the difference between wide and long +data?}\label{whats-the-difference-between-wide-and-long-data}} + +Here are pros and cons of wide data: + +\begin{itemize} +\item + Pros: +\item + Natural and easy to understand; +\item + Cons： +\item + Not easy to handle; + + \begin{itemize} + \item + More problematic when sparse. + \end{itemize} +\end{itemize} + +\hypertarget{if-you-meet-na-in-the-1st-example-you-can-do-like-this}{% +\subsubsection{\texorpdfstring{If you meet \texttt{NA} in the 1st +example, you can do like +this:}{If you meet NA in the 1st example, you can do like this:}}\label{if-you-meet-na-in-the-1st-example-you-can-do-like-this}} + +\begin{Shaded} +\begin{Highlighting}[] +\NormalTok{grades3\_1 }\OtherTok{=} +\NormalTok{ grades3[}\SpecialCharTok{!}\FunctionTok{is.na}\NormalTok{(grades3}\SpecialCharTok{\$}\NormalTok{grade), ]} +\NormalTok{grades3\_2 }\OtherTok{=} +\NormalTok{ grades3[}\FunctionTok{complete.cases}\NormalTok{(grades3), ]} + +\CommentTok{\# A better solution} +\NormalTok{grades3\_long }\OtherTok{=}\NormalTok{ grades2 }\SpecialCharTok{\%\textgreater{}\%} + \FunctionTok{pivot\_longer}\NormalTok{( }\SpecialCharTok{{-}}\NormalTok{ name, } + \AttributeTok{names\_to =} \StringTok{"course"}\NormalTok{, } + \AttributeTok{values\_to =} \StringTok{"grade"}\NormalTok{,} + \AttributeTok{values\_drop\_na =} \ConstantTok{TRUE}\NormalTok{)} + +\CommentTok{\# Pay attention to the variant named "values\_drop\_na"} +\end{Highlighting} +\end{Shaded} + +\hypertarget{more-functions-in-tidyr-see--httpsr4dshadleynzdata-tidyhtml}{% +\subsubsection{\texorpdfstring{More functions in \texttt{tidyr}: (See @ +\url{https://r4ds.hadley.nz/data-tidy.html})}{More functions in tidyr: (See @ https://r4ds.hadley.nz/data-tidy.html)}}\label{more-functions-in-tidyr-see--httpsr4dshadleynzdata-tidyhtml}} + +\begin{itemize} +\item + \texttt{tidyr::separate()} +\end{itemize} + +\begin{Shaded} +\begin{Highlighting}[] +\NormalTok{Usage:} + + +\NormalTok{separate(} +\NormalTok{ data,} +\NormalTok{ col,} +\NormalTok{ into,} +\NormalTok{ sep = "[\^{}[:alnum:]]+",} +\NormalTok{ remove = TRUE,} +\NormalTok{ convert = FALSE,} +\NormalTok{ extra = "warn",} +\NormalTok{ fill = "warn",} +\NormalTok{ ...} +\NormalTok{)} + +\NormalTok{\# Default parameters are listed.} + +\end{Highlighting} +\end{Shaded} + +\begin{itemize} +\item + \texttt{tidyr::unite()} +\end{itemize} + +\begin{Shaded} +\begin{Highlighting}[] +\NormalTok{Usage:} + + +\NormalTok{unite(} +\NormalTok{ data,} +\NormalTok{ col, } +\NormalTok{ ..., } +\NormalTok{ sep = "\_", } +\NormalTok{ remove = TRUE, } +\NormalTok{ na.rm = FALSE} +\NormalTok{)} + +\NormalTok{\# Default parameters are listed.} + + +\NormalTok{{-}{-}{-}} +\end{Highlighting} +\end{Shaded} + +\hypertarget{r-for-bioinformatics-strings-and-regular-expression}{% +\section{R for bioinformatics, Strings and regular +expression}\label{r-for-bioinformatics-strings-and-regular-expression}} + +\begin{quote} +Talk 07 +\end{quote} + +\hypertarget{toc-3}{% +\subsection{TOC}\label{toc-3}} + +\hypertarget{stringr}{% +\subsubsection{\texorpdfstring{\texttt{stringr}}{stringr}}\label{stringr}} + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + basics +\end{enumerate} + +\begin{itemize} +\item + length +\item + uppercase, lowercase +\item + unite, separate +\item + string comparisons, sub string +\end{itemize} + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + regular expression +\end{enumerate} + +\textbf{Note that} each link listed below provides many further links to +other interesting facilities and topics, you can \emph{\textbf{ONLY}} +open the links through VSCode built-in WebView. Sorry for the temporary +inconvenience, but due to time constraints I can only fix this bug +\emph{in the next release}, please contact me if you need help. + +\hypertarget{basics}{% +\subsection{Basics}\label{basics}} + +Before you start\ldots{} + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{library}\NormalTok{(stringr)} +\end{Highlighting} +\end{Shaded} + +\hypertarget{also-notice-other-famous-packages-used-to-manipulating-string}{% +\subsubsection{Also notice other famous packages used to manipulating +string:}\label{also-notice-other-famous-packages-used-to-manipulating-string}} + +\texttt{stringi}(Following are based on the official R Documentation) + +\hypertarget{description}{% +\paragraph{\texorpdfstring{\textbf{Description}}{Description}}\label{description}} + +\texttt{stringi} is THE R package for fast, correct, consistent, and +convenient string/text manipulation. It gives predictable results on +every platform, in each locale, and under any native character encoding. + +\hypertarget{facilities-available}{% +\paragraph{\texorpdfstring{\textbf{Facilities +available}}{Facilities available}}\label{facilities-available}} + +Refer to the following: + +\begin{itemize} +\item + \href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/stringi/help/about_search}{about\_search} + for string searching facilities; these include pattern searching, + matching, string splitting, and so on. The following independent + search engines are provided: +\item + \href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/stringi/help/about_search_regex}{about\_search\_regex} + -- with ICU (Java-like) regular expressions, + + \begin{itemize} + \item + \href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/stringi/help/about_search_fixed}{about\_search\_fixed} + -- fast, locale-independent, byte-wise pattern matching, + \item + \href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/stringi/help/about_search_coll}{about\_search\_coll} + -- locale-aware pattern matching for natural language processing + tasks, + \item + \href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/stringi/help/about_search_charclass}{about\_search\_charclass} + -- seeking elements of particular character classes, like ``all + whites-paces'' or ``all digits'', + \item + \href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/stringi/help/about_search_boundaries}{about\_search\_boundaries} + -- text boundary analysis. + \end{itemize} +\item + \texttt{stri\_datetime\_format} for date/time formatting and parsing. + Also refer to the links therein for other date/time/time zone- related + operations. +\item + \texttt{stri\_stats\_general} and \texttt{stri\_stats\_latex} for + gathering some fancy statistics on a character + vector\textquotesingle s contents. +\item + \texttt{stri\_join}, \texttt{stri\_dup}, \texttt{\%s+\%}, and + \texttt{stri\_flatten} for concatenation-based operations. +\item + \texttt{stri\_sub} for extracting and replacing substrings, and + \texttt{stri\_reverse} for a joyful function to reverse all code + points in a string. +\item + \texttt{stri\_length} (among others) for determining the number of + code points in a string. See also \texttt{stri\_count\_boundaries} for + counting the number of Unicode characters and \texttt{stri\_width} for + approximating the width of a string. +\item + \texttt{stri\_trim} (among others) for trimming characters from the + beginning or/and end of a string, see also + \href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/stringi/help/about_search_charclass}{about\_search\_charclass}, + and \texttt{stri\_pad} for padding strings so that they are of the + same width. Additionally, \texttt{stri\_wrap} wraps text into lines. +\item + \texttt{stri\_trans\_tolower} (among others) for case mapping, i.e., + conversion to lower, UPPER, or Title Case, \texttt{stri\_trans\_nfc} + (among others) for Unicode normalization, \texttt{stri\_trans\_char} + for translating individual code points, and + \texttt{stri\_trans\_general} for other universal text transforms, + including transliteration. +\item + \texttt{stri\_cmp}, \texttt{\%s\textless{}\%}, \texttt{stri\_order}, + \texttt{stri\_sort}, \texttt{stri\_rank}, \texttt{stri\_unique}, and + \texttt{stri\_duplicated} for collation-based, locale-aware + operations, see also + \href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/stringi/help/about_locale}{about\_locale}. +\item + \texttt{stri\_split\_lines} (among others) to split a string into text + lines. +\item + \texttt{stri\_escape\_unicode} (among others) for escaping some code + points. +\item + \texttt{stri\_rand\_strings}, \texttt{stri\_rand\_shuffle}, and + \texttt{stri\_rand\_lipsum} for generating (pseudo)random strings. +\item + \texttt{stri\_read\_raw}, \texttt{stri\_read\_lines}, and + \texttt{stri\_write\_lines} for reading and writing text files. +\end{itemize} + +\hypertarget{usage-of-writelines-from-official-r-documentation}{% +\subsubsection{\texorpdfstring{Usage of \texttt{writeLines()} (from +official R +Documentation)}{Usage of writeLines() (from official R Documentation)}}\label{usage-of-writelines-from-official-r-documentation}} + +\hypertarget{description-2}{% +\paragraph{Description}\label{description-2}} + +Write text lines to a connection. + +\hypertarget{usage}{% +\paragraph{Usage}\label{usage}} + +\begin{Shaded} +\begin{Highlighting}[] +\NormalTok{writeLines(text, con = stdout(), sep = "\textbackslash{}n", useBytes = FALSE)} +\end{Highlighting} +\end{Shaded} + +\hypertarget{arguments}{% +\paragraph{Arguments}\label{arguments}} + +\begin{longtable}[]{@{}ll@{}} +\toprule\noalign{} +\texttt{text} & A character vector \\ +\midrule\noalign{} +\endhead +\bottomrule\noalign{} +\endlastfoot +\texttt{con} & A +\href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/base/help/connection}{connection} +object or a character string. \\ +\texttt{sep} & character string. A string to be written to the +connection after each line of text. \\ +\texttt{useBytes} & logical. See `Details'. \\ +\end{longtable} + +\hypertarget{details}{% +\paragraph{Details}\label{details}} + +If the \texttt{con} is a character string, the function calls +\texttt{file} to obtain a file connection which is opened for the +duration of the function call. +(\href{vscode-webview://00i87qrgljff0t3jmc9gjufilst9usetvkh9gn773om0ic67o1j2/base/help/tilde\%20expansion}{tilde +expansion} of the file path is done by \texttt{file}.) + +If the connection is open it is written from its current position. If it +is not open, it is opened for the duration of the call in \texttt{"wt"} +mode and then closed again. + +Normally \texttt{writeLines} is used with a text-mode connection, and +the default separator is converted to the normal separator for that +platform (LF on Unix/Linux, CRLF on Windows). For more control, open a +binary connection and specify the precise value you want written to the +file in \texttt{sep}. For even more control, use \texttt{writeChar} on a +binary connection. + +\texttt{useBytes} is for expert use. Normally (when false) character +strings with marked encodings are converted to the current encoding +before being passed to the connection (which might do further +re-encoding). \texttt{useBytes\ =\ TRUE} suppresses the re-encoding of +marked strings so they are passed byte-by-byte to the connection: this +can be useful when strings have already been re-encoded by e.g. +\texttt{iconv}. (It is invoked automatically for strings with marked +encoding \texttt{"bytes"}.) + +\hypertarget{difference-between-double-quote-and-single-quote}{% +\subsubsection{\texorpdfstring{Difference between double +quote(\texttt{“”}) and single +quote(\texttt{‘’})}{Difference between double quote(``\,'') and single quote(`\,')}}\label{difference-between-double-quote-and-single-quote}} + +In R and its string manipulation package \texttt{stringr}, there is no +difference between strings defined with double quotes (\texttt{"}) and +single quotes (\texttt{\textquotesingle{}}). Both are used to define +strings and you can use either depending on your preference or the +situation. + +For instance, if your string contains a single quote, you might find it +easier to enclose the string in double quotes, and vice versa. +Here\textquotesingle s an example: + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Using double quotes when the string contains a single quote} +\NormalTok{string1 }\OtherTok{=} \StringTok{"It\textquotesingle{}s a beautiful day"} + +\CommentTok{\# Using single quotes when the string contains a double quote} +\NormalTok{string2 }\OtherTok{=} \StringTok{\textquotesingle{}He said, "Hello, world!"\textquotesingle{}} +\end{Highlighting} +\end{Shaded} + +In both cases, R will interpret the contents between the quotes as a +string. + +\hypertarget{some-of-the-functions-in-the-stringr-package-are-similar-in-function-to-those-that-come-with-the-system}{% +\subsubsection{\texorpdfstring{Some of the functions in the +\texttt{stringr} package are similar in function to those that come with +the +system.}{Some of the functions in the stringr package are similar in function to those that come with the system.}}\label{some-of-the-functions-in-the-stringr-package-are-similar-in-function-to-those-that-come-with-the-system}} + +Here are examples comparing some functions from the \texttt{stringr} +package with their counterparts from base R: + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{\texttt{str\_length()} vs. \texttt{nchar()}:} +\end{enumerate} + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{library}\NormalTok{(stringr)} + +\CommentTok{\# Using str\_length from stringr} +\NormalTok{string }\OtherTok{=} \FunctionTok{c}\NormalTok{(}\StringTok{"apple"}\NormalTok{, }\ConstantTok{NA}\NormalTok{, }\StringTok{"banana"}\NormalTok{, }\StringTok{""}\NormalTok{)} +\FunctionTok{str\_length}\NormalTok{(string)} +\CommentTok{\# Output: 5 NA 6 0} + +\CommentTok{\# Using nchar from base R} +\FunctionTok{nchar}\NormalTok{(string)} +\CommentTok{\# Output: 5 NA 6 0} +\end{Highlighting} +\end{Shaded} + +Both \texttt{str\_length()} and \texttt{nchar()} count the number of +characters in each string element. However, \texttt{str\_length()} +handles missing values (\texttt{NA}) more consistently by returning +\texttt{NA}, whereas \texttt{nchar()} might treat \texttt{NA} +differently in certain cases. + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{\texttt{str\_sub()} vs. \texttt{substr()}:} +\end{enumerate} + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Using str\_sub from stringr} +\NormalTok{string }\OtherTok{=} \FunctionTok{c}\NormalTok{(}\StringTok{"hello"}\NormalTok{, }\StringTok{"world"}\NormalTok{, }\StringTok{"example"}\NormalTok{)} +\FunctionTok{str\_sub}\NormalTok{(string, }\AttributeTok{start =} \DecValTok{2}\NormalTok{, }\AttributeTok{end =} \DecValTok{4}\NormalTok{)} +\CommentTok{\# Output: "ell" "orl" "xam"} + +\CommentTok{\# Using substr from base R} +\FunctionTok{substr}\NormalTok{(string, }\AttributeTok{start =} \DecValTok{2}\NormalTok{, }\AttributeTok{stop =} \DecValTok{4}\NormalTok{)} +\CommentTok{\# Output: "ell" "orl" "xam"} +\end{Highlighting} +\end{Shaded} + +Both \texttt{str\_sub()} and \texttt{substr()} extract substrings based +on specified start and end positions. However, \texttt{str\_sub()} +allows negative indices to count from the end of the string, and it +handles missing values more consistently. + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{\texttt{str\_replace()} vs. \texttt{sub()} or + \texttt{gsub()}:} +\end{enumerate} + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Using str\_replace from stringr} +\NormalTok{string }\OtherTok{=} \FunctionTok{c}\NormalTok{(}\StringTok{"apple pie"}\NormalTok{, }\StringTok{"banana bread"}\NormalTok{, }\StringTok{"cherry cake"}\NormalTok{)} +\FunctionTok{str\_replace}\NormalTok{(string, }\AttributeTok{pattern =} \StringTok{"a"}\NormalTok{, }\AttributeTok{replacement =} \StringTok{"X"}\NormalTok{)} +\CommentTok{\# Output: "Xpple pie" "bXnXnX breXd" "chXrry cXke"} + +\CommentTok{\# Using sub from base R} +\FunctionTok{sub}\NormalTok{(}\AttributeTok{pattern =} \StringTok{"a"}\NormalTok{, }\AttributeTok{replacement =} \StringTok{"X"}\NormalTok{, }\AttributeTok{x =}\NormalTok{ string)} +\CommentTok{\# Output: "Xpple pie" "bXnana bread" "cherry cake"} +\end{Highlighting} +\end{Shaded} + +Both \texttt{str\_replace()} and \texttt{sub()} are used for replacing +parts of a string. However, \texttt{str\_replace()} has a more intuitive +interface and handles missing values more gracefully compared to +\texttt{sub()}. + +These examples demonstrate how \texttt{stringr} functions can be more +consistent and user-friendly in handling various string operations +compared to their base R counterparts. + +\hypertarget{some-of-the-functions-in-the-stringi-package-are-similar-in-function-to-those-that-come-with-the-system}{% +\subsubsection{\texorpdfstring{Some of the functions in the +\texttt{stringi} package are similar in function to those that come with +the +system.}{Some of the functions in the stringi package are similar in function to those that come with the system.}}\label{some-of-the-functions-in-the-stringi-package-are-similar-in-function-to-those-that-come-with-the-system}} + +Here are some functions in the \texttt{stringi} package that share +similar functionalities with base R\textquotesingle s string functions, +along with examples showcasing their differences: + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{\texttt{stri\_length()} vs. \texttt{nchar()}}: + + \begin{itemize} + \item + \texttt{stri\_length()} in \texttt{stringi} calculates the number of + code points in a string, accounting for Unicode characters. + \item + \texttt{nchar()} in base R counts the number of characters in a + string, but it might not handle Unicode characters as accurately as + \texttt{stri\_length()}. + \end{itemize} + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{library}\NormalTok{(stringi)} + +\CommentTok{\# Using stri\_length from stringi} +\NormalTok{string }\OtherTok{=} \StringTok{"café"} +\FunctionTok{stri\_length}\NormalTok{(string)} +\CommentTok{\# Output: 4} + +\CommentTok{\# Using nchar from base R} +\FunctionTok{nchar}\NormalTok{(string)} +\CommentTok{\# Output: 4} +\end{Highlighting} +\end{Shaded} + + In this example, both \texttt{stri\_length()} and \texttt{nchar()} + return the same count for ASCII characters. However, when dealing with + Unicode characters, \texttt{stri\_length()} can accurately count them + as individual code points, whereas \texttt{nchar()} might not handle + them correctly. +\item + \textbf{\texttt{stri\_split\_*()} vs. \texttt{strsplit()}}: + + \begin{itemize} + \item + \texttt{stri\_split\_*()} functions in \texttt{stringi} split a + string based on various criteria like fixed patterns, regular + expressions, or character classes. + \item + \texttt{strsplit()} in base R performs a similar operation but might + differ in handling certain edge cases and Unicode characters. + \end{itemize} + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Using stri\_split\_* from stringi} +\NormalTok{string }\OtherTok{=} \StringTok{"apple, orange, café"} +\FunctionTok{stri\_split\_fixed}\NormalTok{(string, }\AttributeTok{pattern =} \StringTok{", "}\NormalTok{)} +\CommentTok{\# Output: list("apple", "orange", "café")} + +\CommentTok{\# Using strsplit from base R} +\FunctionTok{strsplit}\NormalTok{(string, }\AttributeTok{split =} \StringTok{", "}\NormalTok{)} +\CommentTok{\# Output: list("apple", "orange", "caf", "é")} +\end{Highlighting} +\end{Shaded} + + Here, \texttt{stri\_split\_fixed()} correctly splits the string, + including the accented character "é," while \texttt{strsplit()} treats + the accented "é" as two separate characters due to how it handles + Unicode. +\item + \textbf{\texttt{stri\_detect()} vs. \texttt{grepl()}}: + + \begin{itemize} + \item + \texttt{stri\_detect()} in \texttt{stringi} checks if a pattern + exists in a string and returns a logical value. + \item + \texttt{grepl()} in base R performs a similar task but might differ + in its handling of Unicode characters and certain pattern matching + options. + \end{itemize} + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Using stri\_detect from stringi} +\NormalTok{string }\OtherTok{=} \StringTok{"This is a café"} +\FunctionTok{stri\_detect}\NormalTok{(string, }\AttributeTok{regex =} \StringTok{"café"}\NormalTok{)} +\CommentTok{\# Output: TRUE} + +\CommentTok{\# Using grepl from base R} +\FunctionTok{grepl}\NormalTok{(}\StringTok{"café"}\NormalTok{, string)} +\CommentTok{\# Output: FALSE} +\end{Highlighting} +\end{Shaded} + + In this example, \texttt{stri\_detect()} correctly detects the + presence of the word "café," while \texttt{grepl()} returns a + different result due to potential differences in Unicode handling or + pattern matching options. +\end{enumerate} + +The examples highlight how \texttt{stringi} functions like +\texttt{stri\_length()}, \texttt{stri\_split\_*()}, and +\texttt{stri\_detect()} differ from their base R counterparts +(\texttt{nchar()}, \texttt{strsplit()}, and \texttt{grepl()}) by +providing more accurate handling of Unicode characters and often more +versatile string manipulation options. + +\hypertarget{in-the-slide-difference-between-toupper-tolower-and-strireverse}{% +\subsubsection{\texorpdfstring{\textbf{(In the slide)} Difference +between \texttt{toupper()}, \texttt{tolower()} and +\texttt{stri\_reverse()}}{(In the slide) Difference between toupper(), tolower() and stri\_reverse()}}\label{in-the-slide-difference-between-toupper-tolower-and-strireverse}} + +The functions \texttt{toupper()} and \texttt{tolower()} in base R and +\texttt{stri\_reverse()} in the \texttt{stringi} package perform similar +tasks, but there are some differences in their functionality and usage: + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{\texttt{toupper()} and \texttt{tolower()} in Base R:} + + \begin{itemize} + \item + \texttt{toupper()} converts characters in a string to uppercase. + \item + \texttt{tolower()} converts characters in a string to lowercase. + \end{itemize} + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Using toupper and tolower from base R} +\NormalTok{string }\OtherTok{=} \StringTok{"Hello World!"} + +\FunctionTok{toupper}\NormalTok{(string)} +\CommentTok{\# Output: "HELLO WORLD!"} + +\FunctionTok{tolower}\NormalTok{(string)} +\CommentTok{\# Output: "hello world!"} +\end{Highlighting} +\end{Shaded} + + These functions are straightforward and work well for ASCII + characters, converting them to uppercase or lowercase, respectively. + However, they might not handle Unicode characters or locale-specific + transformations. +\item + \textbf{\texttt{stri\_reverse()} in \texttt{stringi}:} + + \begin{itemize} + \item + \texttt{stri\_reverse()} reverses the order of characters in a + string, including handling multibyte characters and Unicode + sequences. + \end{itemize} + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{library}\NormalTok{(stringi)} + +\CommentTok{\# Using stri\_reverse from stringi} +\NormalTok{string }\OtherTok{=} \StringTok{"café"} + +\FunctionTok{stri\_reverse}\NormalTok{(string)} +\CommentTok{\# Output: "éfac"} +\end{Highlighting} +\end{Shaded} + + \texttt{stri\_reverse()} reverses the characters in the string + accurately, even when dealing with Unicode characters or multibyte + sequences. It ensures correct reversal of characters irrespective of + their encoding. +\end{enumerate} + +The key distinction lies in the handling of character cases and +character sequence reversal. While \texttt{toupper()} and +\texttt{tolower()} focus on case transformations for ASCII characters, +\texttt{stri\_reverse()} in \texttt{stringi} concentrates on accurately +reversing character sequences, making it more suitable for handling +multibyte characters and Unicode strings. + +\hypertarget{tricks}{% +\subsubsection{Tricks}\label{tricks}} + +\begin{itemize} +\item + \texttt{stringi} The functions in the package all start with + \texttt{stri\_}. +\item + \texttt{strinr} starts with \texttt{str\_}. +\end{itemize} + +\hypertarget{regex---regular-expression}{% +\subsection{Regex - Regular +Expression}\label{regex---regular-expression}} + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + Character classes:What characters are (not) matched? +\end{enumerate} + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Example 01} +\StringTok{"abc\_123\_??\$\$\^{}"} \SpecialCharTok{\%\textgreater{}\%} \FunctionTok{str\_extract}\NormalTok{(}\StringTok{"}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{s+"}\NormalTok{) }\CommentTok{\# Does this string include spaces? } +\StringTok{"abc\_123\_??\$\$\^{}"} \SpecialCharTok{\%\textgreater{}\%} \FunctionTok{str\_extract}\NormalTok{(}\StringTok{"}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{d+"}\NormalTok{) }\CommentTok{\# Numbers? } +\StringTok{"abc\_123\_??\$\$\^{}"} \SpecialCharTok{\%\textgreater{}\%} \FunctionTok{str\_extract}\NormalTok{(}\StringTok{"}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{w+"}\NormalTok{) }\CommentTok{\# [A{-}z0{-}9\_]} +\end{Highlighting} +\end{Shaded} + +\texttt{str\_extract} : Take out the first match. + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + Matching position +\end{enumerate} + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Example 02} +\CommentTok{\# STRING ending in \textquotesingle{}wei\textquotesingle{}} +\FunctionTok{c}\NormalTok{(}\StringTok{"chen wei hua"}\NormalTok{, }\StringTok{"chen wei"}\NormalTok{, }\StringTok{"chen"}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%} \FunctionTok{str\_subset}\NormalTok{(}\StringTok{"wei\$"}\NormalTok{)} + +\CommentTok{\# CHARACTER ending in \textquotesingle{}wei\textquotesingle{} } +\FunctionTok{c}\NormalTok{(}\StringTok{"chen wei hua"}\NormalTok{, }\StringTok{"chen wei"}\NormalTok{, }\StringTok{"chen"}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%} \FunctionTok{str\_subset}\NormalTok{(}\StringTok{"wei}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{b"}\NormalTok{)} +\end{Highlighting} +\end{Shaded} + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + Number of matches +\end{enumerate} + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Example 03} +\StringTok{"1234abc"} \SpecialCharTok{\%\textgreater{}\%} \FunctionTok{str\_extract}\NormalTok{(}\StringTok{"}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{d+"}\NormalTok{)} +\StringTok{"1234abc"} \SpecialCharTok{\%\textgreater{}\%} \FunctionTok{str\_extract}\NormalTok{(}\StringTok{"}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{d\{3\}"}\NormalTok{)} +\StringTok{"1234abc"} \SpecialCharTok{\%\textgreater{}\%} \FunctionTok{str\_extract}\NormalTok{(}\StringTok{"}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{d\{5,6\}"}\NormalTok{)} +\StringTok{"1234abc"} \SpecialCharTok{\%\textgreater{}\%} \FunctionTok{str\_extract}\NormalTok{(}\StringTok{"}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{d\{2,6\}"}\NormalTok{)} +\end{Highlighting} +\end{Shaded} + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + Classes and groups + + \includegraphics{/Users/lucas/Library/Mobile Documents/com~apple~CloudDocs/~~aa Study Materials/Grade 2 I/Learning/R for Data Science/Review of R/markdown/image/regexprs_classes_groups.png} +\item + Special characters + + \includegraphics{/Users/lucas/Library/Mobile Documents/com~apple~CloudDocs/~~aa Study Materials/Grade 2 I/Learning/R for Data Science/Review of R/markdown/image/regexprs_special_characters.png} +\end{enumerate} + +\begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} + +\hypertarget{r-for-bioinformatics-data-iteration--parallel-computing}{% +\section{R for bioinformatics, data iteration \& parallel +computing}\label{r-for-bioinformatics-data-iteration--parallel-computing}} + +\begin{quote} +Talk 08 +\end{quote} + +\hypertarget{toc-4}{% +\subsection{TOC}\label{toc-4}} + +\begin{itemize} +\item + for loop +\item + \texttt{apply} functions +\item + The essence of \texttt{dplyr} is traversal. +\item + \texttt{map} functions in \texttt{purrr} package +\item + Iteration and Parallel Computing +\end{itemize} + +\hypertarget{iteration-basics}{% +\subsection{\texorpdfstring{Iteration Basics +}{Iteration Basics }}\label{iteration-basics}} + +\hypertarget{for-loop--getting-data-ready}{% +\subsubsection{\texorpdfstring{\texttt{for\ loop} , getting data +ready}{for loop , getting data ready}}\label{for-loop--getting-data-ready}} + +Lookat this example: + +\begin{Shaded} +\begin{Highlighting}[] +\NormalTok{df }\OtherTok{=} + \FunctionTok{tibble}\NormalTok{( } + \AttributeTok{a =} \FunctionTok{rnorm}\NormalTok{(}\DecValTok{100}\NormalTok{), } + \AttributeTok{b =} \FunctionTok{rnorm}\NormalTok{(}\DecValTok{100}\NormalTok{), } + \AttributeTok{c =} \FunctionTok{rnorm}\NormalTok{(}\DecValTok{100}\NormalTok{), } + \AttributeTok{d =} \FunctionTok{rnorm}\NormalTok{(}\DecValTok{100}\NormalTok{)} +\NormalTok{ )} + +\CommentTok{\# Calculate row means } +\NormalTok{res1 }\OtherTok{=} + \FunctionTok{vector}\NormalTok{(}\StringTok{"double"}\NormalTok{, }\FunctionTok{nrow}\NormalTok{(df))} +\ControlFlowTok{for}\NormalTok{(row\_idx }\ControlFlowTok{in} \DecValTok{1}\SpecialCharTok{:}\FunctionTok{nrow}\NormalTok{(df))\{} +\NormalTok{ res1[row\_idx] }\OtherTok{=} + \FunctionTok{mean}\NormalTok{( }\FunctionTok{as.numeric}\NormalTok{(df[row\_idx, ]))} +\NormalTok{\}} + +\NormalTok{res2 }\OtherTok{=} \FunctionTok{c}\NormalTok{()} +\ControlFlowTok{for}\NormalTok{(row\_idx }\ControlFlowTok{in} \DecValTok{1}\SpecialCharTok{:}\FunctionTok{nrow}\NormalTok{(df))\{} +\NormalTok{ res2[}\FunctionTok{length}\NormalTok{(res2) }\SpecialCharTok{+} \DecValTok{1}\NormalTok{] }\OtherTok{=} + \FunctionTok{mean}\NormalTok{(}\FunctionTok{as.numeric}\NormalTok{(df[row\_idx, ]))} +\NormalTok{\}} + +\CommentTok{\# Similar to Python} + +\CommentTok{\# Calculate column means } +\NormalTok{res2 }\OtherTok{=} + \FunctionTok{vector}\NormalTok{(}\StringTok{"double"}\NormalTok{, }\FunctionTok{ncol}\NormalTok{(df))} +\ControlFlowTok{for}\NormalTok{(col\_idx }\ControlFlowTok{in} \DecValTok{1}\SpecialCharTok{:}\FunctionTok{ncol}\NormalTok{(df))\{} +\NormalTok{ res2[col\_idx] }\OtherTok{=} + \FunctionTok{mean}\NormalTok{(df[[col\_idx]])} +\NormalTok{\}} +\end{Highlighting} +\end{Shaded} + +You can replace it with \texttt{for\ loop}: + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{rowMeans}\NormalTok{(df)} +\FunctionTok{colMeans}\NormalTok{(df)} +\end{Highlighting} +\end{Shaded} + +Here are some other functions: + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{rowSums}\NormalTok{(df)} +\FunctionTok{colSums}\NormalTok{(df)} +\end{Highlighting} +\end{Shaded} + +\hypertarget{apply-functions}{% +\subsubsection{\texorpdfstring{\texttt{apply} +functions}{apply functions}}\label{apply-functions}} + +You can use \texttt{apply} with customizable function. + +\begin{Shaded} +\begin{Highlighting}[] +\NormalTok{df }\SpecialCharTok{\%\textgreater{}\%} \FunctionTok{apply}\NormalTok{(} +\NormalTok{ ., } + \DecValTok{2}\NormalTok{, } + \ControlFlowTok{function}\NormalTok{(x) \{ } + \FunctionTok{return}\NormalTok{(} + \FunctionTok{c}\NormalTok{(} + \AttributeTok{n =} \FunctionTok{length}\NormalTok{(x), } + \AttributeTok{mean =} \FunctionTok{mean}\NormalTok{(x), } + \AttributeTok{median =} \FunctionTok{median}\NormalTok{(x) } +\NormalTok{ )} +\NormalTok{ )} +\NormalTok{ \} } +\NormalTok{)} +\end{Highlighting} +\end{Shaded} + +\hypertarget{something-about-tapply}{% +\subsubsection{\texorpdfstring{Something about +\texttt{tapply()}:}{Something about tapply():}}\label{something-about-tapply}} + +The \texttt{tapply()} function in R is used to apply a function over +subsets of a vector, splitting it by a factor or list of factors. It +stands for "table apply" and is particularly useful for summarizing data +by groups or categories. + +Here\textquotesingle s a breakdown of its usage: + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{tapply}\NormalTok{(X, INDEX, FUN)} +\end{Highlighting} +\end{Shaded} + +\begin{itemize} +\item + \texttt{X}: The vector (or array) on which you want to apply the + function. +\item + \texttt{INDEX}: A factor or list of factors that define the groups. + These factors determine how the vector \texttt{X} is split. +\item + \texttt{FUN}: The function to be applied to each subset of \texttt{X}. +\end{itemize} + +For example: + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Creating a sample vector and a corresponding factor} +\NormalTok{values }\OtherTok{=} \FunctionTok{c}\NormalTok{(}\DecValTok{10}\NormalTok{, }\DecValTok{20}\NormalTok{, }\DecValTok{30}\NormalTok{, }\DecValTok{40}\NormalTok{, }\DecValTok{50}\NormalTok{)} +\NormalTok{categories }\OtherTok{=} \FunctionTok{factor}\NormalTok{(}\FunctionTok{c}\NormalTok{(}\StringTok{"A"}\NormalTok{, }\StringTok{"B"}\NormalTok{, }\StringTok{"A"}\NormalTok{, }\StringTok{"B"}\NormalTok{, }\StringTok{"A"}\NormalTok{))} + +\CommentTok{\# Applying the mean function over subsets defined by the categories} +\FunctionTok{tapply}\NormalTok{(values, categories, mean)} +\end{Highlighting} +\end{Shaded} + +In this example, \texttt{tapply()} calculates the mean of the +\texttt{values} vector for each category defined by the +\texttt{categories} factor. It splits the \texttt{values} vector into +subsets based on the categories and applies the \texttt{mean()} function +to each subset, returning the mean values for categories "A" and "B". + +The result would be something like: + +\begin{Shaded} +\begin{Highlighting}[] +\NormalTok{A B } +\NormalTok{30 30} +\end{Highlighting} +\end{Shaded} + +This indicates that the mean value for category "A" is 30, and the mean +value for category "B" is also 30 in this case. + +\texttt{lapply()}, \texttt{sapply()}, and similar functions work on +elements of lists or vectors. In contrast, \texttt{tapply()} focuses on +splitting a vector by factors and applying a function to these subsets, +providing aggregated results for each subset determined by the factors. + +\hypertarget{diffrences-between-apply-in-base-r-and-the-package-dplyr}{% +\subsubsection{\texorpdfstring{Diffrences between \texttt{apply} in base +R and the package +\texttt{dplyr}:}{Diffrences between apply in base R and the package dplyr:}}\label{diffrences-between-apply-in-base-r-and-the-package-dplyr}} + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{\texttt{apply} functions in base R:} + + \begin{itemize} + \item + The \texttt{apply} family of functions (\texttt{apply()}, + \texttt{lapply()}, \texttt{sapply()}, \texttt{vapply()}, etc.) in + base R are used for applying a function over margins of arrays or + data structures like matrices, arrays, and lists. + \item + \texttt{apply()} is used primarily for applying functions to the + rows or columns of matrices or arrays, while \texttt{lapply()} and + \texttt{sapply()} are more focused on lists. + \item + These functions are useful for repetitive operations across rows or + columns without explicitly using loops. + \end{itemize} + + Example: + +\begin{Shaded} +\begin{Highlighting}[] + \CommentTok{\# Creating a matrix} +\NormalTok{ mat }\OtherTok{=} \FunctionTok{matrix}\NormalTok{(}\DecValTok{1}\SpecialCharTok{:}\DecValTok{12}\NormalTok{, }\AttributeTok{nrow =} \DecValTok{3}\NormalTok{, }\AttributeTok{ncol =} \DecValTok{4}\NormalTok{)} + + \CommentTok{\# Applying sum function to rows (1) or columns (2) of the matrix} + \FunctionTok{apply}\NormalTok{(mat, }\DecValTok{1}\NormalTok{, sum) }\CommentTok{\# Sums of each row} + \FunctionTok{apply}\NormalTok{(mat, }\DecValTok{2}\NormalTok{, sum) }\CommentTok{\# Sums of each column} +\end{Highlighting} +\end{Shaded} +\item + \textbf{\texttt{dplyr} package:} + + \begin{itemize} + \item + \texttt{dplyr} is a powerful package in R for data manipulation and + transformation. It provides a set of functions (\texttt{filter()}, + \texttt{mutate()}, \texttt{select()}, \texttt{group\_by()}, + \texttt{summarize()}, etc.) that enable easy and intuitive data + manipulation. + \item + It\textquotesingle s designed to work well with data frames and + offers a more streamlined and readable syntax for performing common + data manipulation tasks. + \end{itemize} + + Example: + +\begin{Shaded} +\begin{Highlighting}[] + \FunctionTok{library}\NormalTok{(dplyr)} + + \CommentTok{\# Creating a sample data frame} +\NormalTok{ df }\OtherTok{=} \FunctionTok{data.frame}\NormalTok{(} + \AttributeTok{Name =} \FunctionTok{c}\NormalTok{(}\StringTok{"Alice"}\NormalTok{, }\StringTok{"Bob"}\NormalTok{, }\StringTok{"Charlie"}\NormalTok{),} + \AttributeTok{Age =} \FunctionTok{c}\NormalTok{(}\DecValTok{25}\NormalTok{, }\DecValTok{30}\NormalTok{, }\DecValTok{28}\NormalTok{),} + \AttributeTok{Salary =} \FunctionTok{c}\NormalTok{(}\DecValTok{40000}\NormalTok{, }\DecValTok{50000}\NormalTok{, }\DecValTok{45000}\NormalTok{)} +\NormalTok{ )} + + \CommentTok{\# Filtering and selecting specific rows and columns} +\NormalTok{ filtered\_df }\OtherTok{=}\NormalTok{ df }\SpecialCharTok{\%\textgreater{}\%} + \FunctionTok{filter}\NormalTok{(Age }\SpecialCharTok{\textgreater{}} \DecValTok{25}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%} + \FunctionTok{select}\NormalTok{(Name, Salary)} + +\NormalTok{ filtered\_df} +\end{Highlighting} +\end{Shaded} + + This \texttt{dplyr} example filters rows where \texttt{Age} is greater + than 25 and selects only the \texttt{Name} and \texttt{Salary} + columns. The \texttt{\%\textgreater{}\%} operator (pipe) chains + together multiple operations, making the code more readable and + concise. +\end{enumerate} + +In summary, the \texttt{apply} family in base R is ideal for applying +functions to matrices, arrays, or lists across rows or columns, while +\texttt{dplyr} focuses on intuitive data manipulation operations for +data frames, providing a cleaner syntax and ease of use for common data +transformation tasks. + +\hypertarget{more-on-iteration-purrr-package}{% +\subsection{\texorpdfstring{More on iteration: \texttt{purrr} +package}{More on iteration: purrr package}}\label{more-on-iteration-purrr-package}} + +\hypertarget{about-purrr-from-official-website-httpspurrrtidyverseorg}{% +\subsubsection{\texorpdfstring{About \texttt{purrr} (from official +website +\url{https://purrr.tidyverse.org})}{About purrr (from official website https://purrr.tidyverse.org)}}\label{about-purrr-from-official-website-httpspurrrtidyverseorg}} + +\texttt{purrr} enhances R's functional programming (FP) toolkit by +providing a complete and consistent set of tools for working with +functions and vectors. If you've never heard of FP before, the best +place to start is the family of \texttt{map()}functions which allow you +to replace many for loops with code that is both more succinct and +easier to read. The best place to learn about the \texttt{map()} +functions is the \href{https://r4ds.had.co.nz/iteration.html}{iteration +chapter} in R for data science. + +\textbf{Usage} + +The following example uses \texttt{purrr}to solve a fairly realistic +problem: split a data frame into pieces, fit a model to each piece, +compute the summary, then extract the R\textsuperscript{2}. + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{library}\NormalTok{(purrr)} + +\NormalTok{mtcars }\SpecialCharTok{|\textgreater{}} + \FunctionTok{split}\NormalTok{(mtcars}\SpecialCharTok{\$}\NormalTok{cyl) }\SpecialCharTok{|\textgreater{}} \CommentTok{\# from base R} + \FunctionTok{map}\NormalTok{(\textbackslash{}(df) }\FunctionTok{lm}\NormalTok{(mpg }\SpecialCharTok{\textasciitilde{}}\NormalTok{ wt, }\AttributeTok{data =}\NormalTok{ df)) }\SpecialCharTok{|\textgreater{}} + \FunctionTok{map}\NormalTok{(summary) }\SpecialCharTok{\%\textgreater{}\%} + \FunctionTok{map\_dbl}\NormalTok{(}\StringTok{"r.squared"}\NormalTok{)} + +\CommentTok{\#\textgreater{} 4 6 8 } +\CommentTok{\#\textgreater{} 0.5086326 0.4645102 0.4229655} +\end{Highlighting} +\end{Shaded} + +This example illustrates some of the advantages of \texttt{purrr} +functions over the equivalents in base R: + +\begin{itemize} +\item + The first argument is always the data, so purrr works naturally with + the pipe. +\item + All \texttt{purrr} functions are type-stable. They always return the + advertised output type (\texttt{map()} returns lists; + \texttt{map\_dbl()} returns double vectors), or they throw an error. +\item + All \texttt{map()} functions accept functions (named, anonymous, and + lambda), character vector (used to extract components by name), or + numeric vectors (used to extract by position). +\end{itemize} + +\hypertarget{detailed-usage}{% +\subsubsection{Detailed Usage}\label{detailed-usage}} + +\texttt{purrr} is a powerful package in R that focuses on enhancing and +simplifying the process of working with functions and vectors. Developed +as part of the tidyverse ecosystem, \texttt{purrr} provides a consistent +and coherent set of tools for functional programming, iteration, and +working with lists and vectors. + +Here are some key aspects and functionalities of \texttt{purrr}: + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{Functional Programming:} + + \begin{itemize} + \item + \texttt{purrr} promotes functional programming paradigms in R, + enabling users to work with functions as first-class objects. + \item + It provides functions like \texttt{map()}, \texttt{map2()}, + \texttt{pmap()}, \texttt{walk()}, and more, which allow applying + functions over elements of lists or vectors. + \end{itemize} +\item + \textbf{Consistency Across Data Structures:} + + \begin{itemize} + \item + \texttt{purrr} functions exhibit consistent behavior across various + data structures, such as lists, vectors, and data frames. + \item + These functions can work seamlessly with different data structures, + making code more readable and maintainable. + \end{itemize} +\item + \textbf{Iteration and Mapping:} + + \begin{itemize} + \item + \texttt{map()} is a key function in \texttt{purrr} that iterates + over elements of a list or vector, applying a function to each + element and returning the results. + \item + \texttt{map2()} is similar to \texttt{map()} but allows iterating + over two vectors simultaneously. + \item + \texttt{pmap()} extends this functionality to iterate over multiple + vectors or lists simultaneously. + \end{itemize} +\item + \textbf{Simplified and Cleaner Syntax:} + + \begin{itemize} + \item + \texttt{purrr} functions often provide a more consistent and cleaner + syntax compared to base R functions for similar operations. + \item + The use of the pipe \texttt{\%\textgreater{}\%} from the tidyverse + allows chaining \texttt{purrr} functions together, resulting in more + readable code. + \end{itemize} +\item + \textbf{Working with Lists and Data Frames:} + + \begin{itemize} + \item + \texttt{purrr} provides functions to efficiently manipulate and + iterate over elements in lists and data frames. + \item + Functions like \texttt{map()} and \texttt{map\_dbl()} can be used to + apply functions to each column of a data frame and collect results + in an output structure. + \end{itemize} +\end{enumerate} + +Example of \texttt{map()} in \texttt{purrr}: + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{library}\NormalTok{(purrr)} + +\CommentTok{\# Applying sqrt function to each element of a list} +\NormalTok{numbers }\OtherTok{=} \FunctionTok{list}\NormalTok{(}\AttributeTok{a =} \DecValTok{1}\SpecialCharTok{:}\DecValTok{5}\NormalTok{, }\AttributeTok{b =} \DecValTok{6}\SpecialCharTok{:}\DecValTok{10}\NormalTok{)} +\NormalTok{result }\OtherTok{=} \FunctionTok{map}\NormalTok{(numbers, sqrt)} + +\NormalTok{result} +\CommentTok{\# Output: List of 2} +\CommentTok{\# $ a: num [1:5] 1 1.41 1.73 2 2.24} +\CommentTok{\# $ b: num [1:5] 2.45 2.65 2.83 3 3.16} +\end{Highlighting} +\end{Shaded} + +This code applies the \texttt{sqrt()} function to each element of the +list \texttt{numbers}, returning a list with the square roots of each +element. + +\texttt{purrr} simplifies and enhances functional programming in R, +offering a consistent and expressive way to work with functions, lists, +vectors, and data frames, making data manipulation and iteration more +straightforward and concise. + +\hypertarget{examples}{% +\subsubsection{Examples}\label{examples}} + +Here are some specific functionalities and examples of \texttt{purrr}: + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{Mapping Functions:} + + \texttt{map()} applies a function to each element of a list or vector, + returning a list. + +\begin{Shaded} +\begin{Highlighting}[] + \FunctionTok{library}\NormalTok{(purrr)} + + \CommentTok{\# Squaring each element in a vector using map()} +\NormalTok{ numbers }\OtherTok{=} \DecValTok{1}\SpecialCharTok{:}\DecValTok{5} +\NormalTok{ squared }\OtherTok{=} \FunctionTok{map}\NormalTok{(numbers, }\SpecialCharTok{\textasciitilde{}}\NormalTok{ .x}\SpecialCharTok{\^{}}\DecValTok{2}\NormalTok{)} + +\NormalTok{ squared} + \CommentTok{\# Output: List of 5} + \CommentTok{\# \$ : int 1} + \CommentTok{\# \$ : int 4} + \CommentTok{\# \$ : int 9} + \CommentTok{\# \$ : int 16} + \CommentTok{\# \$ : int 25} +\end{Highlighting} +\end{Shaded} +\item + \textbf{Mapping Functions over Multiple Inputs:} + + \texttt{map2()} allows applying a function that takes two inputs to + corresponding elements of two vectors. + +\begin{Shaded} +\begin{Highlighting}[] + \CommentTok{\# Multiplying elements of two vectors element{-}wise} +\NormalTok{ vector1 }\OtherTok{=} \DecValTok{1}\SpecialCharTok{:}\DecValTok{5} +\NormalTok{ vector2 }\OtherTok{=} \DecValTok{6}\SpecialCharTok{:}\DecValTok{10} +\NormalTok{ product }\OtherTok{=} \FunctionTok{map2}\NormalTok{(vector1, vector2, }\SpecialCharTok{\textasciitilde{}}\NormalTok{ .x }\SpecialCharTok{*}\NormalTok{ .y)} + +\NormalTok{ product} + \CommentTok{\# Output: List of 5} + \CommentTok{\# \$ : int 6} + \CommentTok{\# \$ : int 14} + \CommentTok{\# \$ : int 24} + \CommentTok{\# \$ : int 36} + \CommentTok{\# \$ : int 50} +\end{Highlighting} +\end{Shaded} +\item + \textbf{Working with Data Frames:} + + \texttt{map\_df()} and similar functions allow applying a function to + each column of a data frame and combining results into a data frame. + +\begin{Shaded} +\begin{Highlighting}[] + \CommentTok{\# Creating a data frame} +\NormalTok{ df }\OtherTok{=} \FunctionTok{data.frame}\NormalTok{(}\AttributeTok{A =} \DecValTok{1}\SpecialCharTok{:}\DecValTok{5}\NormalTok{, }\AttributeTok{B =} \DecValTok{6}\SpecialCharTok{:}\DecValTok{10}\NormalTok{)} + + \CommentTok{\# Doubling each column in the data frame} +\NormalTok{ doubled }\OtherTok{=} \FunctionTok{map\_df}\NormalTok{(df, }\SpecialCharTok{\textasciitilde{}}\NormalTok{ .x }\SpecialCharTok{*} \DecValTok{2}\NormalTok{)} + +\NormalTok{ doubled} + \CommentTok{\# Output: A tibble: 5 × 2} + \CommentTok{\# A B} + \CommentTok{\# \textless{}dbl\textgreater{} \textless{}dbl\textgreater{}} + \CommentTok{\# 1 2 12} + \CommentTok{\# 2 4 14} + \CommentTok{\# 3 6 16} + \CommentTok{\# 4 8 18} + \CommentTok{\# 5 10 20} +\end{Highlighting} +\end{Shaded} +\item + \textbf{Iteration and Applying Functions:} + + \texttt{walk()} applies a function to each element without returning a + result, useful for side effects or performing operations without + output. + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Printing each element of a list using walk()} +\NormalTok{fruits }\OtherTok{=} \FunctionTok{list}\NormalTok{(}\StringTok{"apple"}\NormalTok{, }\StringTok{"banana"}\NormalTok{, }\StringTok{"orange"}\NormalTok{)} +\FunctionTok{walk}\NormalTok{(fruits, print)} +\CommentTok{\# Output:} +\CommentTok{\# [1] "apple"} +\CommentTok{\# [1] "banana"} +\CommentTok{\# [1] "orange"} +\end{Highlighting} +\end{Shaded} +\end{enumerate} + +\texttt{purrr} simplifies functional programming by providing intuitive +functions (\texttt{map()}, \texttt{map2()}, \texttt{walk()}, etc.) that +allow iteration over elements, applying functions, and collecting +results, making code more concise and readable in scenarios involving +lists, vectors, and data frames. + +\hypertarget{in-the-slide-function-reduce-and-accumulate}{% +\subsubsection{\texorpdfstring{(in the slide) Function \texttt{reduce()} +and +\texttt{accumulate()}}{(in the slide) Function reduce() and accumulate()}}\label{in-the-slide-function-reduce-and-accumulate}} + +Both \texttt{reduce()} and \texttt{accumulate()} are powerful functions +from the \texttt{purrr} package that facilitate iterative calculations +over a sequence, accumulating or reducing values based on a specified +function. + +Here\textquotesingle s an explanation of each: + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{\texttt{reduce()} Function:} + + \begin{itemize} + \item + \texttt{reduce()} is used to successively apply a function to pairs + of elements in a sequence, reducing it to a single value. + \item + The function provided to \texttt{reduce()} should take two arguments + and return a single value. + \item + It starts by applying the function to the first two elements, then + uses the result along with the next element, and so on, until the + sequence is exhausted. + \end{itemize} + + Example of \texttt{reduce()}: + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{library}\NormalTok{(purrr)} + +\CommentTok{\# Summing all elements in a vector using reduce()} +\NormalTok{numbers }\OtherTok{=} \DecValTok{1}\SpecialCharTok{:}\DecValTok{5} +\NormalTok{total\_sum }\OtherTok{=} \FunctionTok{reduce}\NormalTok{(numbers, }\StringTok{\textasciigrave{}}\AttributeTok{+}\StringTok{\textasciigrave{}}\NormalTok{)} + +\NormalTok{total\_sum} +\CommentTok{\# Output: 15 (1 + 2 + 3 + 4 + 5 = 15)} +\end{Highlighting} +\end{Shaded} + + Here, \texttt{reduce()} adds all the elements in the \texttt{numbers} + vector by applying the addition function (\texttt{+}) iteratively. +\item + \textbf{\texttt{accumulate()} Function:} + + \begin{itemize} + \item + \texttt{accumulate()} is similar to \texttt{reduce()} but returns a + sequence of intermediate results instead of a single value. + \item + It applies a function cumulatively to the sequence and returns a + vector of values, representing the intermediate results at each + step. + \end{itemize} + + Example of \texttt{accumulate()}: + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Calculating cumulative product of elements in a vector using accumulate()} +\NormalTok{factors }\OtherTok{=} \FunctionTok{c}\NormalTok{(}\DecValTok{2}\NormalTok{, }\DecValTok{3}\NormalTok{, }\DecValTok{4}\NormalTok{, }\DecValTok{5}\NormalTok{)} +\NormalTok{cumulative\_product }\OtherTok{=} \FunctionTok{accumulate}\NormalTok{(factors, }\StringTok{\textasciigrave{}}\AttributeTok{*}\StringTok{\textasciigrave{}}\NormalTok{)} + +\NormalTok{cumulative\_product} +\CommentTok{\# Output: 2 6 24 120 (2, 2*3, 2*3*4, 2*3*4*5)} +\end{Highlighting} +\end{Shaded} + + Here, \texttt{accumulate()} applies the multiplication function + (\texttt{*}) to each element in \texttt{factors}, returning a vector + of cumulative products at each step. +\end{enumerate} + +\texttt{reduce()} aggregates a sequence into a single value based on a +function, while \texttt{accumulate()} returns a sequence of intermediate +results. Both functions are helpful for iterative calculations and +provide different ways to process sequences of values in R. + +\hypertarget{parallel-computing}{% +\subsection{Parallel Computing}\label{parallel-computing}} + +\hypertarget{related-packages}{% +\subsubsection{Related Packages}\label{related-packages}} + +\begin{itemize} +\item + \texttt{parallel} package: displays the number of CPU cores to assign + all or part to a task. +\item + \texttt{foreach} package: provides \texttt{\%do\%} and + \texttt{\%dopar\%} operators to submit tasks for sequential or + parallel computation +\item + \texttt{\textasciigrave{}\ iterators} package: splits + \texttt{data.frame,\ tibble,\ matrix} into rows/columns for submitting + parallel tasks. +\end{itemize} + +\hypertarget{step-by-step-guidance}{% +\subsubsection{Step-by-step Guidance}\label{step-by-step-guidance}} + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{Prepare Data:} + + Assume you have a large data frame named \texttt{my\_data} that you + want to process in parallel. +\item + \textbf{Setup Parallel Processing:} + + Load necessary packages and initialize parallel processing + capabilities. + +\begin{Shaded} +\begin{Highlighting}[] + \FunctionTok{library}\NormalTok{(parallel)} + \FunctionTok{library}\NormalTok{(doParallel)} + \FunctionTok{library}\NormalTok{(foreach)} + \FunctionTok{library}\NormalTok{(iterators)} + + \CommentTok{\# Set the number of cores/processors to be used} +\NormalTok{ num\_cores }\OtherTok{=} \FunctionTok{detectCores}\NormalTok{()} + + \CommentTok{\# Initialize parallel backend} +\NormalTok{ cl }\OtherTok{=} \FunctionTok{makeCluster}\NormalTok{(num\_cores)} + \FunctionTok{registerDoParallel}\NormalTok{(cl)} +\end{Highlighting} +\end{Shaded} +\item + \textbf{Split Data Frame into Chunks:} + + Use the \texttt{iter()} function from the \texttt{iterators} package + to create an iterator for chunks of your data frame. + +\begin{Shaded} +\begin{Highlighting}[] + \CommentTok{\# Define chunk size} +\NormalTok{ chunk\_size }\OtherTok{=} \FunctionTok{nrow}\NormalTok{(my\_data) }\SpecialCharTok{/}\NormalTok{ num\_cores} + + \CommentTok{\# Create an iterator for the chunks} +\NormalTok{ my\_iterator }\OtherTok{=} \FunctionTok{iter}\NormalTok{(my\_data, }\AttributeTok{by =} \StringTok{"row"}\NormalTok{, }\AttributeTok{chunksize =}\NormalTok{ chunk\_size)} +\end{Highlighting} +\end{Shaded} +\item + \textbf{Perform Parallel Computation:} + + Use \texttt{foreach()} from the \texttt{foreach} package along with + \texttt{\%dopar\%} to apply a function to each chunk in parallel. + +\begin{Shaded} +\begin{Highlighting}[] + \CommentTok{\# Define a function to process each chunk} +\NormalTok{ process\_chunk }\OtherTok{=} \ControlFlowTok{function}\NormalTok{(chunk) \{} + \CommentTok{\# Your processing logic for each chunk goes here} + \CommentTok{\# For example: summary(chunk)} + \CommentTok{\# Replace summary() with your specific data processing task} +\NormalTok{ \}} + + \CommentTok{\# Apply the function to each chunk in parallel} +\NormalTok{ results }\OtherTok{=} \FunctionTok{foreach}\NormalTok{(}\AttributeTok{chunk =}\NormalTok{ my\_iterator, }\AttributeTok{.combine =}\NormalTok{ rbind) }\SpecialCharTok{\%dopar\%}\NormalTok{ \{} + \FunctionTok{process\_chunk}\NormalTok{(chunk)} +\NormalTok{ \}} +\end{Highlighting} +\end{Shaded} +\item + \textbf{Combine Results:} + + Collect and combine the results obtained from parallel processing. + +\begin{Shaded} +\begin{Highlighting}[] + \CommentTok{\# Combine or process the results obtained from parallel computation} +\NormalTok{ final\_result }\OtherTok{=} \FunctionTok{do.call}\NormalTok{(rbind, results)} + + \CommentTok{\# Close the parallel cluster} + \FunctionTok{stopCluster}\NormalTok{(cl)} +\end{Highlighting} +\end{Shaded} +\end{enumerate} + +Replace the \texttt{process\_chunk()} function with your specific data +processing task. This approach parallelizes the processing of chunks of +the data frame across multiple cores, allowing for faster computations, +especially with large datasets. + +\textbf{Note:} + +\begin{itemize} +\item + When the task is completed, the allocated CPU core is reclaimed. +\item + Ensure that your specific data processing task is compatible with + parallelization and that the benefits of parallel computing outweigh + the overhead of parallelization. +\item + Also, consider potential dependencies or shared resources among + iterations when parallelizing computations. +\end{itemize} + +\hypertarget{in-the-slide-function-foreach}{% +\subsubsection{\texorpdfstring{(in the slide) Function +\texttt{foreach()}}{(in the slide) Function foreach()}}\label{in-the-slide-function-foreach}} + +\hypertarget{simple-usage}{% +\paragraph{\texorpdfstring{\textbf{Simple usage}}{Simple usage}}\label{simple-usage}} + +\hypertarget{description-3}{% +\paragraph{Description}\label{description-3}} + +\texttt{⁠\%do\%⁠} and \texttt{⁠\%dopar\%⁠} are binary operators that operate +on a \texttt{foreach} object and an \texttt{R} expression. The +expression, \texttt{ex}, is evaluated multiple times in an environment +that is created by the \texttt{foreach} object, and that environment is +modified for each evaluation as specified by the \texttt{foreach} +object. \texttt{⁠\%do\%⁠} evaluates the expression sequentially, while +\texttt{⁠\%dopar\%⁠} evaluates it in parallel. The results of evaluating +\texttt{ex} are returned as a list by default, but this can be modified +by means of the \texttt{.combine} argument. + +\hypertarget{usage-2}{% +\paragraph{Usage}\label{usage-2}} + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{foreach}\NormalTok{(} +\NormalTok{ ...,} +\NormalTok{ .combine,} +\NormalTok{ .init,} + \AttributeTok{.final =} \ConstantTok{NULL}\NormalTok{,} + \AttributeTok{.inorder =} \ConstantTok{TRUE}\NormalTok{,} + \AttributeTok{.multicombine =} \ConstantTok{FALSE}\NormalTok{,} + \AttributeTok{.maxcombine =} \ControlFlowTok{if}\NormalTok{ (.multicombine) }\DecValTok{100} \ControlFlowTok{else} \DecValTok{2}\NormalTok{,} + \AttributeTok{.errorhandling =} \FunctionTok{c}\NormalTok{(}\StringTok{"stop"}\NormalTok{, }\StringTok{"remove"}\NormalTok{, }\StringTok{"pass"}\NormalTok{),} + \AttributeTok{.packages =} \ConstantTok{NULL}\NormalTok{,} + \AttributeTok{.export =} \ConstantTok{NULL}\NormalTok{,} + \AttributeTok{.noexport =} \ConstantTok{NULL}\NormalTok{,} + \AttributeTok{.verbose =} \ConstantTok{FALSE} +\NormalTok{)} +\NormalTok{e1 }\SpecialCharTok{\%:\%}\NormalTok{ e2} +\FunctionTok{when}\NormalTok{(cond)} +\NormalTok{obj }\SpecialCharTok{\%do\%}\NormalTok{ ex} +\NormalTok{obj }\SpecialCharTok{\%dopar\%}\NormalTok{ ex} +\FunctionTok{times}\NormalTok{(n)} +\end{Highlighting} +\end{Shaded} + +\hypertarget{nested-foreach}{% +\subsubsection{\texorpdfstring{Nested +\texttt{foreach}}{Nested foreach}}\label{nested-foreach}} + +\begin{quote} +Expanded knowledge, not featured on slide, for understanding only. +\end{quote} + +Nested \texttt{foreach} loops in R allow for the iteration over multiple +levels of nested structures or combinations of iterators. This approach +is particularly useful when dealing with hierarchical data or when you +need to perform computations on multiple levels of nested objects +simultaneously. + +Here\textquotesingle s an overview of nested \texttt{foreach} loops: + +\begin{enumerate} +\def\labelenumi{\arabic{enumi}.} +\item + \textbf{Nested Iteration:} + + \texttt{foreach} supports nesting, allowing you to iterate over + multiple levels of nested structures, such as lists within lists or + matrices within lists. + +\begin{Shaded} +\begin{Highlighting}[] +\FunctionTok{library}\NormalTok{(foreach)} + +\CommentTok{\# Example: Nested foreach loop iterating over a list of lists} +\NormalTok{outer\_list }\OtherTok{=} \FunctionTok{list}\NormalTok{(}\FunctionTok{list}\NormalTok{(}\AttributeTok{a =} \DecValTok{1}\NormalTok{, }\AttributeTok{b =} \DecValTok{2}\NormalTok{), }\FunctionTok{list}\NormalTok{(}\AttributeTok{c =} \DecValTok{3}\NormalTok{, }\AttributeTok{d =} \DecValTok{4}\NormalTok{))} + +\FunctionTok{foreach}\NormalTok{(}\AttributeTok{inner\_list =}\NormalTok{ outer\_list) }\SpecialCharTok{\%:\%}\NormalTok{ \{} + \FunctionTok{foreach}\NormalTok{(}\AttributeTok{element =}\NormalTok{ inner\_list) }\SpecialCharTok{\%do\%}\NormalTok{ \{} + \CommentTok{\# Process each element within the nested structure} + \FunctionTok{print}\NormalTok{(element)} +\NormalTok{ \}} +\NormalTok{\}} +\end{Highlighting} +\end{Shaded} + + This code iterates over each element of \texttt{outer\_list}, which + contains inner lists. Within each inner list, it iterates over the + elements. +\item + \textbf{Combining Iterators:} + + You can combine different iterators using \texttt{\%:\%} to create + nested iterations. + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Example: Nested foreach loop with combined iterators} +\NormalTok{values }\OtherTok{=} \DecValTok{1}\SpecialCharTok{:}\DecValTok{3} +\NormalTok{letters }\OtherTok{=}\NormalTok{ letters[}\DecValTok{1}\SpecialCharTok{:}\DecValTok{4}\NormalTok{]} + +\FunctionTok{foreach}\NormalTok{(}\AttributeTok{i =}\NormalTok{ values) }\SpecialCharTok{\%:\%} \FunctionTok{foreach}\NormalTok{(}\AttributeTok{letter =}\NormalTok{ letters) }\SpecialCharTok{\%do\%}\NormalTok{ \{} + \CommentTok{\# Perform operations using both iterators} + \FunctionTok{print}\NormalTok{(}\FunctionTok{paste}\NormalTok{(}\StringTok{"Value:"}\NormalTok{, i, }\StringTok{"| Letter:"}\NormalTok{, letter))} +\NormalTok{\}} +\end{Highlighting} +\end{Shaded} + + This code creates nested iterations, iterating over \texttt{values} + and \texttt{letters} simultaneously. +\item + \textbf{Applying Nested Functions:} + + Nested \texttt{foreach} loops are valuable when applying functions or + performing operations that require iterating over multiple levels of + nested data structures or combinations. + +\begin{Shaded} +\begin{Highlighting}[] +\CommentTok{\# Example: Applying a function with nested foreach loops} +\NormalTok{matrix\_list }\OtherTok{=} \FunctionTok{list}\NormalTok{(}\FunctionTok{matrix}\NormalTok{(}\DecValTok{1}\SpecialCharTok{:}\DecValTok{4}\NormalTok{, }\AttributeTok{nrow =} \DecValTok{2}\NormalTok{), }\FunctionTok{matrix}\NormalTok{(}\DecValTok{5}\SpecialCharTok{:}\DecValTok{8}\NormalTok{, }\AttributeTok{nrow =} \DecValTok{2}\NormalTok{))} + +\FunctionTok{foreach}\NormalTok{(}\AttributeTok{mat =}\NormalTok{ matrix\_list) }\SpecialCharTok{\%:\%} \FunctionTok{foreach}\NormalTok{(}\AttributeTok{element =} \FunctionTok{as.vector}\NormalTok{(mat)) }\SpecialCharTok{\%do\%}\NormalTok{ \{} + \CommentTok{\# Perform computations on each element of each matrix} + \FunctionTok{print}\NormalTok{(element }\SpecialCharTok{*} \DecValTok{2}\NormalTok{)} +\NormalTok{\}} +\end{Highlighting} +\end{Shaded} + + Here, it iterates over a list of matrices and then iterates over each + element within the matrices to perform computations. +\end{enumerate} + +Nested \texttt{foreach} loops in R allow for flexible and efficient +iterations over hierarchical or nested structures, enabling complex +computations, data manipulations, or simulations involving multiple +levels of nested objects or iterators. + +\end{document} diff --git a/LaTeX/EN/REVIEW_03/REVIEW_03 copy.pdf b/LaTeX/EN/REVIEW_03/REVIEW_03 copy.pdf new file mode 100644 index 0000000..20eda43 Binary files /dev/null and b/LaTeX/EN/REVIEW_03/REVIEW_03 copy.pdf differ diff --git a/LaTeX/EN/REVIEW_03/REVIEW_03.pdf b/LaTeX/EN/REVIEW_03/REVIEW_03.pdf index 7a006a0..6e64ac9 100644 Binary files a/LaTeX/EN/REVIEW_03/REVIEW_03.pdf and b/LaTeX/EN/REVIEW_03/REVIEW_03.pdf differ diff --git a/LaTeX/EN/REVIEW_03/REVIEW_03.tex b/LaTeX/EN/REVIEW_03/REVIEW_03.tex index 3c1e2e0..83e9178 100644 --- a/LaTeX/EN/REVIEW_03/REVIEW_03.tex +++ b/LaTeX/EN/REVIEW_03/REVIEW_03.tex @@ -4,7 +4,6 @@ % \documentclass[ ]{article} -\usepackage{ctex} \usepackage{geometry} \geometry{a4paper,left=2.8cm,right=2.8cm,top=3cm,bottom=2.5cm} \usepackage{amsmath,amssymb} @@ -111,7 +110,7 @@ \date{} \begin{document} - +\pagenumbering{Roman} \hypertarget{review-of-the-course-r-for-data-science-part-03talk-09-12}{% \section{Review of the course ``R for Data Science'' Part 03(Talk 09\textasciitilde{} @@ -123,6 +122,10 @@ \section{Review of the course ``R for Data Science'' Part 03(Talk \begin{center}\rule{0.5\linewidth}{0.5pt}\end{center} +\tableofcontents + +\newpage +\pagenumbering{arabic} \hypertarget{r-for-bioinformatics-data-visualisation}{% \section{R for bioinformatics, data visualisation}\label{r-for-bioinformatics-data-visualisation}} diff --git a/LaTeX/EN/REVIEW_TOC.pdf b/LaTeX/EN/REVIEW_TOC.pdf new file mode 100644 index 0000000..b77a361 Binary files /dev/null and b/LaTeX/EN/REVIEW_TOC.pdf differ diff --git a/LaTeX/EN/REVIEW_print.pdf b/LaTeX/EN/REVIEW_print.pdf index ae7af75..86c555e 100644 Binary files a/LaTeX/EN/REVIEW_print.pdf and b/LaTeX/EN/REVIEW_print.pdf differ