UsefulCode.tex

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\title{Useful R code}
\author{Matthew
Malishev\textsuperscript{1}*\\[2\baselineskip]\emph{\textsuperscript{1}
Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta,
GA, USA, 30322}}
\date{}

\begin{document}
\maketitle

{
\hypersetup{linkcolor=black}
\setcounter{tocdepth}{4}
\tableofcontents
}
~

Date: 2019-10-25\\
\texttt{R} version: 3.5.0\\
*Corresponding author:
\href{mailto:matthew.malishev@gmail.com}{\nolinkurl{matthew.malishev@gmail.com}}\\
This document can be found at
\url{https://github.com/darwinanddavis/UsefulCode}

\newpage  

\subsection{Overview}\label{overview}

This document outlines some useful \texttt{R} code for plotting, cool
functions, and other random tidbits.

\subsubsection{Install dependencies}\label{install-dependencies}

\subsubsection{Attributes}\label{attributes}

Access structural attributes of unique classes, such as raster and ggmap
(bbox).

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# Normal example}
\NormalTok{df <-}\StringTok{ }\KeywordTok{data.frame}\NormalTok{(}\DataTypeTok{X =} \KeywordTok{c}\NormalTok{(}\DecValTok{1}\OperatorTok{:}\DecValTok{5}\NormalTok{), }\DataTypeTok{Y =} \KeywordTok{c}\NormalTok{(}\DecValTok{6}\OperatorTok{:}\DecValTok{10}\NormalTok{))}
\KeywordTok{str}\NormalTok{(df)}
\NormalTok{df}\OperatorTok{$}\NormalTok{X}

\CommentTok{# `attr` method}
\KeywordTok{require}\NormalTok{(ggmap)}
\NormalTok{map <-}\StringTok{ }\KeywordTok{get_map}\NormalTok{(}\StringTok{"Atlanta"}\NormalTok{, }\DataTypeTok{zoom =} \DecValTok{12}\NormalTok{, }\DataTypeTok{source =} \StringTok{"stamen"}\NormalTok{, }
    \DataTypeTok{maptype =} \StringTok{"toner-lines"}\NormalTok{)}
\KeywordTok{str}\NormalTok{(map)}
\KeywordTok{attr}\NormalTok{(map, }\StringTok{"bb"}\NormalTok{)}\OperatorTok{$}\NormalTok{ll.lat}
\end{Highlighting}
\end{Shaded}

\subsubsection{Classes}\label{classes}

Convert character to factor to numeric without conversion error

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{read.table}\NormalTok{(f, }\DataTypeTok{header =}\NormalTok{ T, }\DataTypeTok{sep =} \StringTok{","}\NormalTok{, }\DataTypeTok{row.names =} \OtherTok{NULL}\NormalTok{, }
    \DataTypeTok{stringsAsFactors =} \OtherTok{FALSE}\NormalTok{, }\DataTypeTok{strip.white =} \OtherTok{TRUE}\NormalTok{)}
\NormalTok{f}\OperatorTok{$}\NormalTok{V2 <-}\StringTok{ }\KeywordTok{as.numeric}\NormalTok{(f}\OperatorTok{$}\NormalTok{V2)}
\end{Highlighting}
\end{Shaded}

See call options for class

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{methods}\NormalTok{(}\DataTypeTok{class =} \StringTok{"estUDm"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Set dynamic input for variable / assign variable to char vector

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{shadedens <-}\StringTok{ }\ControlFlowTok{function}\NormalTok{(shadedens) \{}
    \CommentTok{# set shade density to clumped (to match food) or}
    \CommentTok{# sparse}
    \ControlFlowTok{if}\NormalTok{ (shadedens }\OperatorTok{==}\StringTok{ "Random"}\NormalTok{) \{}
        \KeywordTok{NLCommand}\NormalTok{(}\StringTok{"set Shade-density }\CharTok{\textbackslash{}"}\StringTok{Random}\CharTok{\textbackslash{}"}\StringTok{ "}\NormalTok{)}
\NormalTok{    \} }\ControlFlowTok{else}\NormalTok{ \{}
        \KeywordTok{NLCommand}\NormalTok{(}\StringTok{"set Shade-density }\CharTok{\textbackslash{}"}\StringTok{Clumped}\CharTok{\textbackslash{}"}\StringTok{ "}\NormalTok{)}
\NormalTok{    \}}
\NormalTok{\}}
\KeywordTok{shadedens}\NormalTok{(}\StringTok{"Clumped"}\NormalTok{)  }\CommentTok{# set clumped resources}
\end{Highlighting}
\end{Shaded}

\subsubsection{D3 apps}\label{d3-apps}

Interactive network plots using d3

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# Load package}
\KeywordTok{install.packages}\NormalTok{(}\StringTok{"networkD3"}\NormalTok{)}
\KeywordTok{library}\NormalTok{(networkD3)}

\CommentTok{# Load energy projection data}
\NormalTok{URL <-}\StringTok{ "https://cdn.rawgit.com/christophergandrud/networkD3/master/JSONdata/energy.json"}
\NormalTok{Energy <-}\StringTok{ }\NormalTok{jsonlite}\OperatorTok{::}\KeywordTok{fromJSON}\NormalTok{(URL)}

\CommentTok{# Now we have 2 data frames: a 'links' data frame}
\CommentTok{# with 3 columns (from, to, value), and a 'nodes'}
\CommentTok{# data frame that gives the name of each node.}
\KeywordTok{head}\NormalTok{(Energy}\OperatorTok{$}\NormalTok{links)}
\KeywordTok{head}\NormalTok{(Energy}\OperatorTok{$}\NormalTok{nodes)}

\CommentTok{# Thus we can plot it}
\KeywordTok{sankeyNetwork}\NormalTok{(}\DataTypeTok{Links =}\NormalTok{ Energy}\OperatorTok{$}\NormalTok{links, }\DataTypeTok{Nodes =}\NormalTok{ Energy}\OperatorTok{$}\NormalTok{nodes, }
    \DataTypeTok{Source =} \StringTok{"source"}\NormalTok{, }\DataTypeTok{Target =} \StringTok{"target"}\NormalTok{, }\DataTypeTok{Value =} \StringTok{"value"}\NormalTok{, }
    \DataTypeTok{NodeID =} \StringTok{"name"}\NormalTok{, }\DataTypeTok{units =} \StringTok{"TWh"}\NormalTok{, }\DataTypeTok{fontSize =} \DecValTok{12}\NormalTok{, }
    \DataTypeTok{nodeWidth =} \DecValTok{30}\NormalTok{)}

\StringTok{`}\DataTypeTok{?}\StringTok{`}\NormalTok{(sankeyNetwork)}
\end{Highlighting}
\end{Shaded}

\subsubsection{Dataframes}\label{dataframes}

Optimal empty data frame

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{df <-}\StringTok{ }\KeywordTok{data.frame}\NormalTok{(}\DataTypeTok{Date =} \KeywordTok{as.Date}\NormalTok{(}\KeywordTok{character}\NormalTok{()), }\DataTypeTok{X =} \KeywordTok{numeric}\NormalTok{(), }
    \DataTypeTok{Y =} \KeywordTok{integer}\NormalTok{(), }\DataTypeTok{stringsAsFactors =} \OtherTok{FALSE}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Add df cols with \texttt{mutate}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(dplyr)}
\NormalTok{df <-}\StringTok{ }\KeywordTok{data.frame}\NormalTok{(}\DataTypeTok{a =} \KeywordTok{rnorm}\NormalTok{(}\DecValTok{10}\NormalTok{), }\DataTypeTok{b =}\NormalTok{ (}\DecValTok{1}\OperatorTok{:}\DecValTok{20}\NormalTok{))}
\NormalTok{df }\OperatorTok{%>%}\StringTok{ }\KeywordTok{mutate}\NormalTok{(}\DataTypeTok{c =} \KeywordTok{rnorm}\NormalTok{(}\DecValTok{20}\NormalTok{), }\DataTypeTok{b =}\NormalTok{ b }\OperatorTok{*}\StringTok{ }\DecValTok{67}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Change \texttt{df} column names

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{colnames}\NormalTok{(data)[}\KeywordTok{c}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DecValTok{2}\NormalTok{, }\DecValTok{3}\NormalTok{)] <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\StringTok{"TimeStamp"}\NormalTok{, }\StringTok{"Lat"}\NormalTok{, }
    \StringTok{"Long"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Remove multiple columns from df

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{### Remove multiple NA columns}
\NormalTok{rm_cols <-}\StringTok{ }\KeywordTok{grep}\NormalTok{(}\StringTok{"NA"}\NormalTok{, }\KeywordTok{names}\NormalTok{(tt), }\DataTypeTok{ignore.case =}\NormalTok{ F)}
\NormalTok{df[, }\KeywordTok{colnames}\NormalTok{(df[, rm_cols])] <-}\StringTok{ }\KeywordTok{list}\NormalTok{(}\OtherTok{NULL}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Check number of characters in each column

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{sapply}\NormalTok{(meso1, }\ControlFlowTok{function}\NormalTok{(x) }\KeywordTok{sum}\NormalTok{(}\KeywordTok{nchar}\NormalTok{(x)))}
\end{Highlighting}
\end{Shaded}

\subsubsection{Generic functions}\label{generic-functions}

Generic useful functions that I can't place under any other headings
here

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# dput() for converting outputs such as copied text}
\CommentTok{# or data tables into vectors}
\NormalTok{xx <-}\StringTok{ "Some copied text or table from the internet"}
\KeywordTok{dput}\NormalTok{(xx)}
\end{Highlighting}
\end{Shaded}

Round up integers to optimal rounded value

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{nn <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\DecValTok{46}\NormalTok{, }\DecValTok{11}\NormalTok{, }\DecValTok{23}\NormalTok{)}
\KeywordTok{round_any}\NormalTok{(nn, }\DecValTok{10}\NormalTok{)}
\KeywordTok{round_any}\NormalTok{(nn, }\DecValTok{10}\NormalTok{, ceiling)}
\KeywordTok{round_any}\NormalTok{(nn, }\DecValTok{10}\NormalTok{, floor)}
\end{Highlighting}
\end{Shaded}

Get summary stats for dataset (means)

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{means =}\StringTok{ }\KeywordTok{aggregate}\NormalTok{(Cumulative_cercs }\OperatorTok{~}\StringTok{ }\NormalTok{r }\OperatorTok{*}\StringTok{ }\NormalTok{hb, }\DataTypeTok{data =}\NormalTok{ df, }
    \DataTypeTok{FUN =}\NormalTok{ mean)}
\end{Highlighting}
\end{Shaded}

\subsubsection{Lists}\label{lists}

Find maximum value in entire list

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{master <-}\StringTok{ }\KeywordTok{list}\NormalTok{(}\DecValTok{1}\OperatorTok{:}\DecValTok{10}\NormalTok{, }\DecValTok{100}\NormalTok{, }\KeywordTok{rnorm}\NormalTok{(}\DecValTok{12}\NormalTok{))}
\KeywordTok{do.call}\NormalTok{(max, master)}
\end{Highlighting}
\end{Shaded}

Plot all elements in a list

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{xx <-}\StringTok{ }\KeywordTok{list}\NormalTok{(}\KeywordTok{sample}\NormalTok{(}\DecValTok{5}\NormalTok{, }\DecValTok{1000}\NormalTok{, }\DataTypeTok{replace =}\NormalTok{ T), }\KeywordTok{rnorm}\NormalTok{(}\DecValTok{1000}\NormalTok{), }
    \KeywordTok{sample}\NormalTok{(}\DecValTok{50}\NormalTok{, }\DecValTok{1000}\NormalTok{, }\DataTypeTok{replace =}\NormalTok{ T))}
\KeywordTok{plot}\NormalTok{(}\KeywordTok{unlist}\NormalTok{(xx), }\DataTypeTok{type =} \StringTok{"l"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Apply each row of df or vector to individual elements of a list

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{df =}\StringTok{ }\KeywordTok{data.frame}\NormalTok{(}\DataTypeTok{events =}\NormalTok{ LETTERS[}\DecValTok{1}\OperatorTok{:}\DecValTok{10}\NormalTok{], }\DataTypeTok{outs =} \DecValTok{1}\OperatorTok{:}\DecValTok{10}\NormalTok{)}
\KeywordTok{sapply}\NormalTok{(df}\OperatorTok{$}\NormalTok{outs, list)}
\end{Highlighting}
\end{Shaded}

Append extra element onto existing list

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{rv <-}\StringTok{ }\KeywordTok{sample}\NormalTok{(}\DecValTok{1000}\NormalTok{, }\DecValTok{15}\NormalTok{)  }\CommentTok{# random vector}
\NormalTok{listvec <-}\StringTok{ }\KeywordTok{sapply}\NormalTok{(}\KeywordTok{rep}\NormalTok{(}\OtherTok{NA}\NormalTok{, }\DecValTok{7}\NormalTok{), list)  }\CommentTok{# list with 7 empty elements}
\NormalTok{listvec_final <-}\StringTok{ }\KeywordTok{c}\NormalTok{(listvec, }\KeywordTok{list}\NormalTok{(rv))  }\CommentTok{# append rv}
\NormalTok{listvec_final <-}\StringTok{ }\KeywordTok{c}\NormalTok{(listvec, rv)  }\CommentTok{# to append rv contents as separate elements, remove internal list }
\end{Highlighting}
\end{Shaded}

\subsubsection{Loops}\label{loops}

Save loop output in master list

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{pars <-}\StringTok{ }\KeywordTok{seq}\NormalTok{(}\DecValTok{0}\NormalTok{, }\DecValTok{1}\NormalTok{, }\FloatTok{0.5}\NormalTok{)}
\NormalTok{master <-}\StringTok{ }\KeywordTok{list}\NormalTok{()}
\NormalTok{t_list <-}\StringTok{ }\KeywordTok{list}\NormalTok{()}
\ControlFlowTok{for}\NormalTok{ (p }\ControlFlowTok{in} \DecValTok{1}\OperatorTok{:}\KeywordTok{length}\NormalTok{(pars)) \{}
    \ControlFlowTok{for}\NormalTok{ (t }\ControlFlowTok{in} \DecValTok{5}\NormalTok{) \{}
\NormalTok{        tt <-}\StringTok{ }\KeywordTok{rnorm}\NormalTok{(}\DecValTok{1000} \OperatorTok{*}\StringTok{ }\NormalTok{t)}
\NormalTok{        t_list[t] <-}\StringTok{ }\NormalTok{tt}
\NormalTok{    \}}
\NormalTok{    master[[}\KeywordTok{length}\NormalTok{(master) }\OperatorTok{+}\StringTok{ }\DecValTok{1}\NormalTok{]] <-}\StringTok{ }\NormalTok{t_list  }\CommentTok{# store in master list}
\NormalTok{\}}
\end{Highlighting}
\end{Shaded}

Optimal way to save results to data frame in loop

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(dplyr)}

\NormalTok{fun <-}\StringTok{ }\NormalTok{sum  }\CommentTok{# sum # choose mean or sum  }
\NormalTok{out_first <-}\StringTok{ }\KeywordTok{list}\NormalTok{()  }\CommentTok{# create first empty list}
\NormalTok{out_second <-}\StringTok{ }\KeywordTok{list}\NormalTok{()  }\CommentTok{# create second empty list}

\ControlFlowTok{for}\NormalTok{ (me }\ControlFlowTok{in} \DecValTok{1}\OperatorTok{:}\DecValTok{10}\NormalTok{) \{}
\NormalTok{    global_output_fh =}\StringTok{ }\KeywordTok{paste0}\NormalTok{(}\KeywordTok{getwd}\NormalTok{(), }\StringTok{"/"}\NormalTok{, me, }\StringTok{".R"}\NormalTok{)  }\CommentTok{# get file handle}
\NormalTok{    output <-}\StringTok{ }\KeywordTok{readRDS}\NormalTok{(global_output_fh)  }\CommentTok{# read in file }
\NormalTok{    cercs <-}\StringTok{ }\NormalTok{output[[}\DecValTok{1}\NormalTok{]]  }\CommentTok{# get data }
    \CommentTok{# define function}
\NormalTok{    SEM =}\StringTok{ }\ControlFlowTok{function}\NormalTok{(x) \{}
        \KeywordTok{sd}\NormalTok{(x)}\OperatorTok{/}\KeywordTok{sqrt}\NormalTok{(}\KeywordTok{length}\NormalTok{(x))}
\NormalTok{    \}}
    \CommentTok{# create col name to pass to aggregate function}
\NormalTok{    cerc_outs =}\StringTok{ }\KeywordTok{list}\NormalTok{(}\DataTypeTok{Outs =}\NormalTok{ cercs)}
\NormalTok{    outs =}\StringTok{ }\KeywordTok{aggregate}\NormalTok{(Outs }\OperatorTok{~}\StringTok{ }\NormalTok{., }\DataTypeTok{data =}\NormalTok{ cerc_outs, }\DataTypeTok{FUN =}\NormalTok{ fun)}
\NormalTok{    cerc_se =}\StringTok{ }\KeywordTok{list}\NormalTok{(}\DataTypeTok{SEs =}\NormalTok{ cercs)}
\NormalTok{    se =}\StringTok{ }\KeywordTok{aggregate}\NormalTok{(SEs }\OperatorTok{~}\StringTok{ }\NormalTok{., }\DataTypeTok{data =}\NormalTok{ cerc_se, }\DataTypeTok{FUN =}\NormalTok{ SEM)}
    
    \CommentTok{# save to df by creating new df cols}
\NormalTok{    outs}\OperatorTok{$}\NormalTok{me <-}\StringTok{ }\NormalTok{me  }\CommentTok{# create new col with iteration}
\NormalTok{    out_first[[me]] <-}\StringTok{ }\NormalTok{outs  }\CommentTok{# add first output to list}
\NormalTok{    out_second[[me]] <-}\StringTok{ }\NormalTok{se  }\CommentTok{# add second output to list}
\NormalTok{\}  }\CommentTok{# end file read  }

\CommentTok{# option 1}
\NormalTok{out_final =}\StringTok{ }\KeywordTok{do.call}\NormalTok{(rbind, out_first)}
\CommentTok{# option 2}
\NormalTok{out_final <-}\StringTok{ }\KeywordTok{bind_rows}\NormalTok{(out_first)  }\CommentTok{# make fresh df }
\NormalTok{out_final}\OperatorTok{$}\NormalTok{Second <-}\StringTok{ }\KeywordTok{bind_rows}\NormalTok{(out_second)  }\CommentTok{# add second col}
\end{Highlighting}
\end{Shaded}

\subsubsection{Maps}\label{maps}

High res maps

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# https://hecate.hakai.org/rguide/mapping-in-r.html}
\KeywordTok{require}\NormalTok{(maptools)}
\NormalTok{d <-}\StringTok{ }\KeywordTok{map_data}\NormalTok{(}\StringTok{"worldHires"}\NormalTok{, }\KeywordTok{c}\NormalTok{(}\StringTok{"Colombia"}\NormalTok{, }\StringTok{"Ecuador"}\NormalTok{, }
    \StringTok{"Peru"}\NormalTok{, }\StringTok{"Panama"}\NormalTok{))}

\CommentTok{# plot}
\KeywordTok{ggplot}\NormalTok{() }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_polygon}\NormalTok{(}\DataTypeTok{data =}\NormalTok{ d, }\KeywordTok{aes}\NormalTok{(}\DataTypeTok{x =}\NormalTok{ long, }\DataTypeTok{y =}\NormalTok{ lat, }
    \DataTypeTok{group =}\NormalTok{ group), }\DataTypeTok{fill =} \StringTok{"black"}\NormalTok{, }\DataTypeTok{col =} \StringTok{"pink"}\NormalTok{) }\OperatorTok{+}\StringTok{ }
\StringTok{    }\CommentTok{# theme_tufte(ticks=F) +}
\KeywordTok{theme_nothing}\NormalTok{() }\OperatorTok{+}\StringTok{ }\KeywordTok{coord_map}\NormalTok{(}\StringTok{"mercator"}\NormalTok{, }\DataTypeTok{xlim =} \KeywordTok{c}\NormalTok{(}\OperatorTok{-}\DecValTok{75}\NormalTok{, }
    \OperatorTok{-}\DecValTok{81}\NormalTok{), }\DataTypeTok{ylim =} \KeywordTok{c}\NormalTok{(}\OperatorTok{-}\DecValTok{2}\NormalTok{, }\DecValTok{8}\NormalTok{))}
\end{Highlighting}
\end{Shaded}

Read in KMZ/KML data (Google Maps data)

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(sf)}
\NormalTok{zp <-}\StringTok{ }\NormalTok{sf}\OperatorTok{::}\KeywordTok{st_read}\NormalTok{(}\StringTok{"ziggy_test.kml"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\subsubsection{Messages}\label{messages}

Display status message of progress

\begin{Shaded}
\begin{Highlighting}[]
\ControlFlowTok{for}\NormalTok{ (i }\ControlFlowTok{in} \DecValTok{1}\OperatorTok{:}\DecValTok{10}\NormalTok{) \{}
    \KeywordTok{Sys.sleep}\NormalTok{(}\FloatTok{0.2}\NormalTok{)}
    \CommentTok{# Dirk says using cat() like this is naughty ;-)}
    \CommentTok{# cat(i,'\textbackslash{}r') So you can use message() like this,}
    \CommentTok{# thanks to Sharpie's comment to use}
    \CommentTok{# appendLF=FALSE.}
    \KeywordTok{message}\NormalTok{(i, }\StringTok{"}\CharTok{\textbackslash{}r}\StringTok{"}\NormalTok{, }\DataTypeTok{appendLF =} \OtherTok{FALSE}\NormalTok{)  }\CommentTok{# appendLF = new line }
    \KeywordTok{flush.console}\NormalTok{()}
\NormalTok{\}}
\end{Highlighting}
\end{Shaded}

Display popup progress bar

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(tcltk)}
\NormalTok{pb <-}\StringTok{ }\KeywordTok{tkProgressBar}\NormalTok{(}\StringTok{"test progress bar"}\NormalTok{, }\StringTok{"Some information in %"}\NormalTok{, }
    \DecValTok{0}\NormalTok{, }\DecValTok{100}\NormalTok{, }\DecValTok{50}\NormalTok{)}
\KeywordTok{Sys.sleep}\NormalTok{(}\FloatTok{0.5}\NormalTok{)}
\NormalTok{u <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\DecValTok{0}\NormalTok{, }\KeywordTok{sort}\NormalTok{(}\KeywordTok{runif}\NormalTok{(}\DecValTok{20}\NormalTok{, }\DecValTok{0}\NormalTok{, }\DecValTok{100}\NormalTok{)), }\DecValTok{100}\NormalTok{)}
\ControlFlowTok{for}\NormalTok{ (i }\ControlFlowTok{in}\NormalTok{ u) \{}
    \KeywordTok{Sys.sleep}\NormalTok{(}\FloatTok{0.1}\NormalTok{)}
\NormalTok{    info <-}\StringTok{ }\KeywordTok{sprintf}\NormalTok{(}\StringTok{"%d%% done"}\NormalTok{, }\KeywordTok{round}\NormalTok{(i))}
    \KeywordTok{setTkProgressBar}\NormalTok{(pb, i, }\KeywordTok{sprintf}\NormalTok{(}\StringTok{"test (%s)"}\NormalTok{, info), }
\NormalTok{        info)}
\NormalTok{\}}
\KeywordTok{Sys.sleep}\NormalTok{(}\DecValTok{5}\NormalTok{)}
\KeywordTok{close}\NormalTok{(pb)}
\end{Highlighting}
\end{Shaded}

\subsubsection{\texorpdfstring{\texttt{NAs} and
\texttt{NaNs}}{NAs and NaNs}}\label{nas-and-nans}

Replace NAs and NaNs with 0's

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{df[}\KeywordTok{is.na}\NormalTok{(df)] <-}\StringTok{ }\DecValTok{0}
\NormalTok{df[}\KeywordTok{is.nan}\NormalTok{(df)] <-}\StringTok{ }\DecValTok{0}  \CommentTok{# good for matrices }
\end{Highlighting}
\end{Shaded}

Replace X values less than given value (V) with 0

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{df}\OperatorTok{$}\NormalTok{X[df}\OperatorTok{$}\NormalTok{X }\OperatorTok{<}\StringTok{ }\NormalTok{V] <-}\StringTok{ }\DecValTok{0}
\end{Highlighting}
\end{Shaded}

Check for \texttt{NAs}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{sapply}\NormalTok{(df, }\ControlFlowTok{function}\NormalTok{(x) }\KeywordTok{sum}\NormalTok{(}\KeywordTok{is.na}\NormalTok{(x)))}
\end{Highlighting}
\end{Shaded}

snail.update{[}is.nan(snail.update){]} \textless{}- 0 Replace
\texttt{NaN} and \texttt{Inf} values with \texttt{NA}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{df}\OperatorTok{$}\NormalTok{col1[}\KeywordTok{which}\NormalTok{(}\OperatorTok{!}\KeywordTok{is.finite}\NormalTok{(df}\OperatorTok{$}\NormalTok{col1))] <-}\StringTok{ }\OtherTok{NA}
\end{Highlighting}
\end{Shaded}

Fill in missing data values in sequence with \texttt{NA}

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# /Users/malishev/Documents/Manuscripts/Chapter4/Sims/Chapter4_figs.R}
\KeywordTok{library}\NormalTok{(zoo)}
\NormalTok{data <-}\StringTok{ }\KeywordTok{data.frame}\NormalTok{(}\DataTypeTok{index =} \KeywordTok{c}\NormalTok{(}\DecValTok{1}\OperatorTok{:}\DecValTok{4}\NormalTok{, }\DecValTok{6}\OperatorTok{:}\DecValTok{10}\NormalTok{), }\DataTypeTok{data =} \KeywordTok{c}\NormalTok{(}\FloatTok{1.5}\NormalTok{, }
    \FloatTok{4.3}\NormalTok{, }\FloatTok{5.6}\NormalTok{, }\FloatTok{6.7}\NormalTok{, }\FloatTok{7.1}\NormalTok{, }\FloatTok{12.5}\NormalTok{, }\FloatTok{14.5}\NormalTok{, }\FloatTok{16.8}\NormalTok{, }\FloatTok{3.4}\NormalTok{))}
\CommentTok{# you can create a series}
\NormalTok{z <-}\StringTok{ }\KeywordTok{zoo}\NormalTok{(data}\OperatorTok{$}\NormalTok{data, data}\OperatorTok{$}\NormalTok{index)}
\CommentTok{# end extend it to the grid 1:10}
\NormalTok{z <-}\StringTok{ }\KeywordTok{merge}\NormalTok{(}\KeywordTok{zoo}\NormalTok{(, }\DecValTok{1}\OperatorTok{:}\DecValTok{10}\NormalTok{), z)}

\CommentTok{# worked example fill in missing Tb values}
\NormalTok{minTb.d <-}\StringTok{ }\KeywordTok{zoo}\NormalTok{(minTb}\OperatorTok{$}\NormalTok{Tick, minTb}\OperatorTok{$}\NormalTok{Days)}
\NormalTok{minTb.d <-}\StringTok{ }\KeywordTok{merge}\NormalTok{(}\KeywordTok{zoo}\NormalTok{(}\OtherTok{NULL}\NormalTok{, }\DecValTok{1}\OperatorTok{:}\NormalTok{days), minTb.d)  }\CommentTok{# make the minTb series match the temp series (117 days)}
\NormalTok{minTb.d <-}\StringTok{ }\KeywordTok{as.numeric}\NormalTok{(minTb.d)  }\CommentTok{# = time individuals reached VTMIN in ticks}
\NormalTok{minTb <-}\StringTok{ }\NormalTok{minTb.d }\OperatorTok{-}\StringTok{ }\NormalTok{temp}\OperatorTok{$}\NormalTok{Tick  }\CommentTok{# get diff between starting time and time to reach VTMIN}
\NormalTok{minTb <-}\StringTok{ }\NormalTok{minTb}\OperatorTok{/}\DecValTok{2}  \CommentTok{# convert ticks to minutes}
\NormalTok{minTb <-}\StringTok{ }\NormalTok{minTb}\OperatorTok{/}\DecValTok{60}  \CommentTok{#convert to hours}
\NormalTok{minTb <-}\StringTok{ }\KeywordTok{data.frame}\NormalTok{(}\DataTypeTok{Days =} \DecValTok{1}\OperatorTok{:}\NormalTok{days, }\DataTypeTok{Time =}\NormalTok{ minTb)}

\CommentTok{# then fill in missing values}
\KeywordTok{approx}\NormalTok{(minTb}\OperatorTok{$}\NormalTok{Time, }\DataTypeTok{method =} \StringTok{"linear"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Remove rows with NA

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{data <-}\StringTok{ }\NormalTok{data[}\OperatorTok{!}\KeywordTok{is.na}\NormalTok{(data}\OperatorTok{$}\NormalTok{X), ]}
\end{Highlighting}
\end{Shaded}

Turn NULLs in list into NAs to get numeric values (fix for `cannot
coerce double' error)

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{hl_list <-}\StringTok{ }\KeywordTok{lapply}\NormalTok{(hl_list, }\ControlFlowTok{function}\NormalTok{(x) }\KeywordTok{ifelse}\NormalTok{(x }\OperatorTok{==}\StringTok{ }
\StringTok{    "NULL"}\NormalTok{, }\OtherTok{NA}\NormalTok{, x))}
\end{Highlighting}
\end{Shaded}

Turn NaN or NAs in list into 0s

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# NaN}
\NormalTok{global_output <-}\StringTok{ }\KeywordTok{rapply}\NormalTok{(global_output, }\DataTypeTok{f =} \ControlFlowTok{function}\NormalTok{(x) }\KeywordTok{ifelse}\NormalTok{(}\KeywordTok{is.nan}\NormalTok{(x), }
    \DecValTok{0}\NormalTok{, x), }\DataTypeTok{how =} \StringTok{"replace"}\NormalTok{)}

\CommentTok{# NA}
\NormalTok{global_output <-}\StringTok{ }\KeywordTok{rapply}\NormalTok{(global_output, }\DataTypeTok{f =} \ControlFlowTok{function}\NormalTok{(x) }\KeywordTok{ifelse}\NormalTok{(}\KeywordTok{is.na}\NormalTok{(x), }
    \DecValTok{0}\NormalTok{, x), }\DataTypeTok{how =} \StringTok{"replace"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\subsubsection{Packages}\label{packages}

\href{https://blog.socialcops.com/technology/data-science/announcing-rlandsat-landsat-8-data/}{\texttt{rLandsat}}\\
Sourcing, requesting, and downloading NASA Landsat 8 satellite data.

\href{https://blog.rstudio.com/2018/09/19/radix-for-r-markdown/}{Radix}\\
Improved \texttt{RMarkdown} output and interaction.

\href{http://www.stats.gla.ac.uk/~adrian/rpanel/}{\texttt{rpanel}}\\
\href{https://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf}{Reference
guide}\\
Create interactive GUI control toggles from \texttt{R}. Like an early
Shiny.

\subsubsection{Plotting}\label{plotting}

Plot one plot window above and two below

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{layout}\NormalTok{(}\KeywordTok{matrix}\NormalTok{(}\KeywordTok{c}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DecValTok{1}\NormalTok{, }\DecValTok{2}\NormalTok{, }\DecValTok{3}\NormalTok{), }\DecValTok{2}\NormalTok{, }\DecValTok{2}\NormalTok{, }\DataTypeTok{byrow =} \OtherTok{TRUE}\NormalTok{))}
\end{Highlighting}
\end{Shaded}

Bookend axis ticks for plot E.g. at 0 and 100 when data is 1:99

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{axis}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DataTypeTok{at =} \KeywordTok{c}\NormalTok{(}\DecValTok{0}\NormalTok{, }\KeywordTok{length}\NormalTok{(loco}\OperatorTok{$}\NormalTok{X)), }\DataTypeTok{labels =} \KeywordTok{c}\NormalTok{(}\StringTok{""}\NormalTok{, }\StringTok{""}\NormalTok{))  }\CommentTok{# bookending axis tick marks}
\end{Highlighting}
\end{Shaded}

Optimal legend formatting for base

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{legend}\NormalTok{(}\StringTok{"right"}\NormalTok{, }\DataTypeTok{legend =} \KeywordTok{c}\NormalTok{(}\StringTok{"Small"}\NormalTok{, }\StringTok{"Intermediate"}\NormalTok{, }
    \StringTok{"Large"}\NormalTok{), }\DataTypeTok{col =} \KeywordTok{c}\NormalTok{(colfunc[colvec[}\DecValTok{1}\OperatorTok{:}\DecValTok{3}\NormalTok{]]), }\DataTypeTok{bty =} \StringTok{"n"}\NormalTok{, }
    \DataTypeTok{pch =} \DecValTok{20}\NormalTok{, }\DataTypeTok{pt.cex =} \FloatTok{1.5}\NormalTok{, }\DataTypeTok{cex =} \FloatTok{0.7}\NormalTok{, }\DataTypeTok{y.intersp =} \FloatTok{0.5}\NormalTok{, }
    \DataTypeTok{xjust =} \FloatTok{0.5}\NormalTok{, }\DataTypeTok{title =} \StringTok{"Size class"}\NormalTok{, }\DataTypeTok{title.adj =} \FloatTok{0.3}\NormalTok{, }
    \DataTypeTok{text.font =} \DecValTok{2}\NormalTok{, }\DataTypeTok{trace =}\NormalTok{ T, }\DataTypeTok{inset =} \FloatTok{0.1}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Plot inset plot in current plot
(\url{https://stackoverflow.com/questions/17041246/how-to-add-an-inset-subplot-to-topright-of-an-r-plot})

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# calculate position of inset}
\NormalTok{plotdim <-}\StringTok{ }\KeywordTok{par}\NormalTok{(}\StringTok{"plt"}\NormalTok{)  }\CommentTok{# get plot window dims as fraction of current plot dims }
\NormalTok{xleft =}\StringTok{ }\NormalTok{plotdim[}\DecValTok{2}\NormalTok{] }\OperatorTok{-}\StringTok{ }\NormalTok{(plotdim[}\DecValTok{2}\NormalTok{] }\OperatorTok{-}\StringTok{ }\NormalTok{plotdim[}\DecValTok{1}\NormalTok{]) }\OperatorTok{*}\StringTok{ }\FloatTok{0.5}
\NormalTok{xright =}\StringTok{ }\NormalTok{plotdim[}\DecValTok{2}\NormalTok{]  }\CommentTok{#}
\NormalTok{ybottom =}\StringTok{ }\NormalTok{plotdim[}\DecValTok{4}\NormalTok{] }\OperatorTok{-}\StringTok{ }\NormalTok{(plotdim[}\DecValTok{4}\NormalTok{] }\OperatorTok{-}\StringTok{ }\NormalTok{plotdim[}\DecValTok{3}\NormalTok{]) }\OperatorTok{*}\StringTok{ }
\StringTok{    }\FloatTok{0.5}  \CommentTok{#}
\NormalTok{ytop =}\StringTok{ }\NormalTok{plotdim[}\DecValTok{4}\NormalTok{]  }\CommentTok{#}

\CommentTok{# set position for plot inset}
\KeywordTok{par}\NormalTok{(}\DataTypeTok{fig =} \KeywordTok{c}\NormalTok{(xleft, xright, ybottom, ytop), }\DataTypeTok{mar =} \KeywordTok{c}\NormalTok{(}\DecValTok{0}\NormalTok{, }
    \DecValTok{0}\NormalTok{, }\DecValTok{0}\NormalTok{, }\DecValTok{0}\NormalTok{), }\DataTypeTok{new =} \OtherTok{TRUE}\NormalTok{)}

\KeywordTok{boxplot}\NormalTok{(Eggs }\OperatorTok{~}\StringTok{ }\NormalTok{Size, }\DataTypeTok{data =}\NormalTok{ meso2, }\DataTypeTok{col =} \KeywordTok{adjustcolor}\NormalTok{(colfunc[colvec[}\DecValTok{1}\OperatorTok{:}\DecValTok{3}\NormalTok{]], }
    \DataTypeTok{alpha =} \FloatTok{0.5}\NormalTok{), }\DataTypeTok{notch =}\NormalTok{ T, }\DataTypeTok{xlab =} \StringTok{"Week"}\NormalTok{, }\DataTypeTok{ylab =} \StringTok{"Diameter (mm)"}\NormalTok{, }
    \DataTypeTok{xaxs =} \StringTok{"i"}\NormalTok{, }\DataTypeTok{yaxs =} \StringTok{"i"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Interactive plots with rCharts (javascript and d3 viz)\\
\url{http://ramnathv.github.io/rCharts/}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(devtools)}
\KeywordTok{install_github}\NormalTok{(}\StringTok{"rCharts"}\NormalTok{, }\StringTok{"ramnathv"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Cluster plot\\
\url{https://rpubs.com/dgrtwo/technology-clusters}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{library}\NormalTok{(readr)}
\KeywordTok{library}\NormalTok{(dplyr)}
\KeywordTok{library}\NormalTok{(igraph)}
\KeywordTok{library}\NormalTok{(ggraph)}
\KeywordTok{library}\NormalTok{(ggforce)}

\CommentTok{# This shared file contains the number of question}
\CommentTok{# that have each pair of tags This counts only}
\CommentTok{# questions that are not deleted and have a}
\CommentTok{# positive score}
\NormalTok{tag_pair_data <-}\StringTok{ }\KeywordTok{read_csv}\NormalTok{(}\StringTok{"http://varianceexplained.org/files/tag_pairs.csv.gz"}\NormalTok{)}

\NormalTok{relationships <-}\StringTok{ }\NormalTok{tag_pair_data }\OperatorTok{%>%}\StringTok{ }\KeywordTok{mutate}\NormalTok{(}\DataTypeTok{Fraction =}\NormalTok{ Cooccur}\OperatorTok{/}\NormalTok{Tag1Total) }\OperatorTok{%>%}\StringTok{ }
\StringTok{    }\KeywordTok{filter}\NormalTok{(Fraction }\OperatorTok{>=}\StringTok{ }\FloatTok{0.35}\NormalTok{) }\OperatorTok{%>%}\StringTok{ }\KeywordTok{distinct}\NormalTok{(Tag1)}

\NormalTok{v <-}\StringTok{ }\NormalTok{tag_pair_data }\OperatorTok{%>%}\StringTok{ }\KeywordTok{select}\NormalTok{(Tag1, Tag1Total) }\OperatorTok{%>%}\StringTok{ }
\StringTok{    }\KeywordTok{distinct}\NormalTok{(Tag1) }\OperatorTok{%>%}\StringTok{ }\KeywordTok{filter}\NormalTok{(Tag1 }\OperatorTok{%in%}\StringTok{ }\NormalTok{relationships}\OperatorTok{$}\NormalTok{Tag1 }\OperatorTok{|}\StringTok{ }
\StringTok{    }\NormalTok{Tag1 }\OperatorTok{%in%}\StringTok{ }\NormalTok{relationships}\OperatorTok{$}\NormalTok{Tag2) }\OperatorTok{%>%}\StringTok{ }\KeywordTok{arrange}\NormalTok{(}\KeywordTok{desc}\NormalTok{(Tag1Total))}

\NormalTok{a <-}\StringTok{ }\NormalTok{grid}\OperatorTok{::}\KeywordTok{arrow}\NormalTok{(}\DataTypeTok{length =}\NormalTok{ grid}\OperatorTok{::}\KeywordTok{unit}\NormalTok{(}\FloatTok{0.08}\NormalTok{, }\StringTok{"inches"}\NormalTok{), }
    \DataTypeTok{ends =} \StringTok{"first"}\NormalTok{, }\DataTypeTok{type =} \StringTok{"closed"}\NormalTok{)}

\KeywordTok{set.seed}\NormalTok{(}\DecValTok{2016}\NormalTok{)}

\NormalTok{relationships }\OperatorTok{%>%}\StringTok{ }\KeywordTok{graph_from_data_frame}\NormalTok{(}\DataTypeTok{vertices =}\NormalTok{ v) }\OperatorTok{%>%}\StringTok{ }
\StringTok{    }\KeywordTok{ggraph}\NormalTok{(}\DataTypeTok{layout =} \StringTok{"fr"}\NormalTok{) }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_edge_link}\NormalTok{(}\KeywordTok{aes}\NormalTok{(}\DataTypeTok{alpha =}\NormalTok{ Fraction), }
    \DataTypeTok{arrow =}\NormalTok{ a) }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_node_point}\NormalTok{(}\KeywordTok{aes}\NormalTok{(}\DataTypeTok{size =}\NormalTok{ Tag1Total), }
    \DataTypeTok{color =} \StringTok{"lightblue"}\NormalTok{) }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_node_text}\NormalTok{(}\KeywordTok{aes}\NormalTok{(}\DataTypeTok{size =}\NormalTok{ Tag1Total, }
    \DataTypeTok{label =}\NormalTok{ name), }\DataTypeTok{check_overlap =} \OtherTok{TRUE}\NormalTok{) }\OperatorTok{+}\StringTok{ }\KeywordTok{scale_size_continuous}\NormalTok{(}\DataTypeTok{range =} \KeywordTok{c}\NormalTok{(}\DecValTok{2}\NormalTok{, }
    \DecValTok{9}\NormalTok{)) }\OperatorTok{+}\StringTok{ }\NormalTok{ggforce}\OperatorTok{::}\KeywordTok{theme_no_axes}\NormalTok{() }\OperatorTok{+}\StringTok{ }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.position =} \StringTok{"none"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Define global plotting graphics function.

The \texttt{plot\_it.R} function is updated on the
\href{https://raw.githubusercontent.com/darwinanddavis/plot_it/master/plot_it.R}{plot\_it
Github page}.

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(ggplot2)}
\KeywordTok{require}\NormalTok{(ggthemes)}
\NormalTok{### set plotting params plotting function (plot for}
\NormalTok{### MS or not, set bg color, set color palette from}
\NormalTok{### RColorBrewer, set alpha value for transperancy)}
\NormalTok{plot_it <-}\StringTok{ }\ControlFlowTok{function}\NormalTok{(manuscript, bg, cp1, cp2, alpha, }
\NormalTok{    family) \{}
    \KeywordTok{graphics.off}\NormalTok{()}
    \ControlFlowTok{if}\NormalTok{ (manuscript }\OperatorTok{==}\StringTok{ }\DecValTok{0}\NormalTok{) \{}
        \ControlFlowTok{if}\NormalTok{ (bg }\OperatorTok{==}\StringTok{ "black"}\NormalTok{) \{}
\NormalTok{            colvec <<-}\StringTok{ }\KeywordTok{magma}\NormalTok{(}\DecValTok{200}\NormalTok{, }\DecValTok{1}\NormalTok{)  }\CommentTok{# plot window bg # USES <<- OPERATOR}
            \KeywordTok{par}\NormalTok{(}\DataTypeTok{bg =}\NormalTok{ colvec[}\DecValTok{1}\NormalTok{], }\DataTypeTok{col.axis =} \StringTok{"white"}\NormalTok{, }
                \DataTypeTok{col.lab =} \StringTok{"white"}\NormalTok{, }\DataTypeTok{col.main =} \StringTok{"white"}\NormalTok{, }
                \DataTypeTok{fg =} \StringTok{"white"}\NormalTok{, }\DataTypeTok{bty =} \StringTok{"n"}\NormalTok{, }\DataTypeTok{las =} \DecValTok{1}\NormalTok{, }\DataTypeTok{mar =} \KeywordTok{c}\NormalTok{(}\DecValTok{5}\NormalTok{, }
                  \DecValTok{6}\NormalTok{, }\DecValTok{4}\NormalTok{, }\DecValTok{2}\NormalTok{), }\DataTypeTok{family =}\NormalTok{ family)  }\CommentTok{#mono}
\NormalTok{            border =}\StringTok{ }\KeywordTok{adjustcolor}\NormalTok{(}\StringTok{"purple"}\NormalTok{, }\DataTypeTok{alpha =} \FloatTok{0.5}\NormalTok{)}
\NormalTok{        \} }\ControlFlowTok{else}\NormalTok{ \{}
\NormalTok{            colvec <<-}\StringTok{ }\KeywordTok{bpy.colors}\NormalTok{(}\DecValTok{200}\NormalTok{)  }\CommentTok{# plot window bg # USES <<- OPERATOR}
            \KeywordTok{par}\NormalTok{(}\DataTypeTok{bg =}\NormalTok{ colvec[}\DecValTok{1}\NormalTok{], }\DataTypeTok{col.axis =} \StringTok{"white"}\NormalTok{, }
                \DataTypeTok{col.lab =} \StringTok{"white"}\NormalTok{, }\DataTypeTok{col.main =} \StringTok{"white"}\NormalTok{, }
                \DataTypeTok{fg =} \StringTok{"white"}\NormalTok{, }\DataTypeTok{bty =} \StringTok{"n"}\NormalTok{, }\DataTypeTok{las =} \DecValTok{1}\NormalTok{, }\DataTypeTok{mar =} \KeywordTok{c}\NormalTok{(}\DecValTok{5}\NormalTok{, }
                  \DecValTok{6}\NormalTok{, }\DecValTok{4}\NormalTok{, }\DecValTok{2}\NormalTok{), }\DataTypeTok{family =}\NormalTok{ family)}
\NormalTok{            border =}\StringTok{ }\KeywordTok{adjustcolor}\NormalTok{(}\StringTok{"blue"}\NormalTok{, }\DataTypeTok{alpha =} \FloatTok{0.5}\NormalTok{)}
\NormalTok{        \}}
\NormalTok{    \} }\ControlFlowTok{else}\NormalTok{ \{}
        \CommentTok{# graphics.off()}
        \KeywordTok{par}\NormalTok{(}\DataTypeTok{bty =} \StringTok{"n"}\NormalTok{, }\DataTypeTok{las =} \DecValTok{1}\NormalTok{, }\DataTypeTok{family =}\NormalTok{ family)}
\NormalTok{        colv <-}\StringTok{ "white"}
\NormalTok{    \}}
    \CommentTok{# color palettes}
    \CommentTok{# ifelse(manuscript==1,colvec<-adjustcolor(brewer.pal(9,cp1)[9],}
    \CommentTok{# alpha = alpha),colvec <-}
    \CommentTok{# adjustcolor(brewer.pal(9,cp1)[5], alpha = alpha))}
    \CommentTok{# # fine tune plotting colors for plotting bg}
    \CommentTok{# colfunc <<-}
    \CommentTok{# colorRampPalette(brewer.pal(9,cp1),alpha=alpha)}
\NormalTok{    cp1_info <-}\StringTok{ }\NormalTok{brewer.pal.info[cp1, ]}\OperatorTok{$}\NormalTok{maxcolors}
\NormalTok{    cp2_info <-}\StringTok{ }\NormalTok{brewer.pal.info[cp2, ]}\OperatorTok{$}\NormalTok{maxcolors}
\NormalTok{    colv <<-}\StringTok{ }\KeywordTok{brewer.pal}\NormalTok{(cp1_info, cp1)  }\CommentTok{# USES <<- OPERATOR}
\NormalTok{    colv2 <<-}\StringTok{ }\KeywordTok{brewer.pal}\NormalTok{(cp2_info, cp2)  }\CommentTok{# USES <<- OPERATOR}
\NormalTok{\}}

\CommentTok{# Setting ggplot theme graphics bg = colour to plot}
\CommentTok{# bg, family = font family}
\NormalTok{plot_it_gg <-}\StringTok{ }\ControlFlowTok{function}\NormalTok{(bg) \{}
    \ControlFlowTok{if}\NormalTok{ (bg }\OperatorTok{==}\StringTok{ "white"}\NormalTok{) \{}
\NormalTok{        bg <-}\StringTok{ "white"}
\NormalTok{        fg <-}\StringTok{ "black"}
        \KeywordTok{theme_tufte}\NormalTok{(}\DataTypeTok{base_family =} \StringTok{"HersheySans"}\NormalTok{) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{panel.border =} \KeywordTok{element_blank}\NormalTok{(), }\DataTypeTok{panel.grid.major =} \KeywordTok{element_blank}\NormalTok{(), }
                \DataTypeTok{panel.grid.minor =} \KeywordTok{element_blank}\NormalTok{(), }
                \DataTypeTok{panel.background =} \KeywordTok{element_rect}\NormalTok{(}\DataTypeTok{fill =}\NormalTok{ bg, }
                  \DataTypeTok{colour =}\NormalTok{ bg), }\DataTypeTok{plot.background =} \KeywordTok{element_rect}\NormalTok{(}\DataTypeTok{fill =}\NormalTok{ bg)) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{axis.line =} \KeywordTok{element_line}\NormalTok{(}\DataTypeTok{color =}\NormalTok{ fg)) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{axis.ticks =} \KeywordTok{element_line}\NormalTok{(}\DataTypeTok{color =}\NormalTok{ fg)) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{plot.title =} \KeywordTok{element_text}\NormalTok{(}\DataTypeTok{colour =}\NormalTok{ fg)) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{axis.title.x =} \KeywordTok{element_text}\NormalTok{(}\DataTypeTok{colour =}\NormalTok{ fg), }
                \DataTypeTok{axis.title.y =} \KeywordTok{element_text}\NormalTok{(}\DataTypeTok{colour =}\NormalTok{ fg)) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{axis.text.x =} \KeywordTok{element_text}\NormalTok{(}\DataTypeTok{color =}\NormalTok{ fg), }
                \DataTypeTok{axis.text.y =} \KeywordTok{element_text}\NormalTok{(}\DataTypeTok{color =}\NormalTok{ fg)) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.key =} \KeywordTok{element_rect}\NormalTok{(}\DataTypeTok{fill =}\NormalTok{ bg)) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.title =} \KeywordTok{element_text}\NormalTok{(}\DataTypeTok{colour =}\NormalTok{ fg)) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.text =} \KeywordTok{element_text}\NormalTok{(}\DataTypeTok{colour =}\NormalTok{ fg))}
\NormalTok{    \}}
\NormalTok{\}  }\CommentTok{# end gg}

\NormalTok{### Set plotting function}
\end{Highlighting}
\end{Shaded}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(}\StringTok{"RCurl"}\NormalTok{)}
\NormalTok{script <-}\StringTok{ }\KeywordTok{getURL}\NormalTok{(}\StringTok{"https://raw.githubusercontent.com/darwinanddavis/plot_it/master/plot_it.R"}\NormalTok{, }
    \DataTypeTok{ssl.verifypeer =} \OtherTok{FALSE}\NormalTok{)}
\KeywordTok{eval}\NormalTok{(}\KeywordTok{parse}\NormalTok{(}\DataTypeTok{text =}\NormalTok{ script))}

\KeywordTok{cat}\NormalTok{(}\StringTok{"plot_it( }\CharTok{\textbackslash{}n}\StringTok{0 for presentation, 1 for manuscript, }\CharTok{\textbackslash{}n}\StringTok{set colour for background, }\CharTok{\textbackslash{}n}\StringTok{set colour palette. use 'display.brewer.all()', }\CharTok{\textbackslash{}n}\StringTok{set alpha for colour transperancy, }\CharTok{\textbackslash{}n}\StringTok{set font style }\CharTok{\textbackslash{}n}\StringTok{)"}\NormalTok{)}
\KeywordTok{plot_it}\NormalTok{(}\DecValTok{0}\NormalTok{, }\StringTok{"blue"}\NormalTok{, }\StringTok{"Spectral"}\NormalTok{, }\StringTok{"Greens"}\NormalTok{, }\DecValTok{1}\NormalTok{, }\StringTok{"mono"}\NormalTok{)  }\CommentTok{# set col function params}
\KeywordTok{plot_it_gg}\NormalTok{(}\StringTok{"white"}\NormalTok{)  }\CommentTok{# same as above }
\end{Highlighting}
\end{Shaded}

Make plot cycle on one page

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{plot}\NormalTok{(m_abundance}\OperatorTok{$}\NormalTok{gam, }\DataTypeTok{pages =} \DecValTok{1}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Get plot summaries and values from plot

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{plot.gam}\NormalTok{(m_abundance}\OperatorTok{$}\NormalTok{gam, }\DataTypeTok{shade =}\NormalTok{ T, }\DataTypeTok{pages =} \DecValTok{1}\NormalTok{, }\DataTypeTok{seWithMean =}\NormalTok{ T)[}\DecValTok{1}\NormalTok{]  }\CommentTok{# everything}
\KeywordTok{plot.gam}\NormalTok{(m_abundance}\OperatorTok{$}\NormalTok{gam, }\DataTypeTok{shade =}\NormalTok{ T, }\DataTypeTok{pages =} \DecValTok{1}\NormalTok{, }\DataTypeTok{seWithMean =}\NormalTok{ T)[}\DecValTok{1}\NormalTok{][[}\DecValTok{1}\NormalTok{]]}\OperatorTok{$}\NormalTok{x  }\CommentTok{#subset x}
\KeywordTok{plot.gam}\NormalTok{(m_abundance}\OperatorTok{$}\NormalTok{gam, }\DataTypeTok{shade =}\NormalTok{ T, }\DataTypeTok{pages =} \DecValTok{1}\NormalTok{, }\DataTypeTok{seWithMean =}\NormalTok{ T)[}\DecValTok{1}\NormalTok{][[}\DecValTok{1}\NormalTok{]]}\OperatorTok{$}\NormalTok{fit  }\CommentTok{#get values to produce fit curve }
\end{Highlighting}
\end{Shaded}

Package for stock world maps

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# worldmap}
\KeywordTok{library}\NormalTok{(choroplethrMaps)}
\end{Highlighting}
\end{Shaded}

Circle packing, tree, dendogram, network plots

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# dendogram tree nested bubble circle packing}
\CommentTok{# network}
\CommentTok{# https://www.r-graph-gallery.com/313-basic-circle-packing-with-several-levels/}

\CommentTok{# circle packing plot Libraries}
\NormalTok{p <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\StringTok{"ggraph"}\NormalTok{, }\StringTok{"igraph"}\NormalTok{, }\StringTok{"tidyverse"}\NormalTok{, }\StringTok{"DeducerSpatial"}\NormalTok{, }
    \StringTok{"Rcpp"}\NormalTok{, }\StringTok{"car"}\NormalTok{)}
\KeywordTok{install.packages}\NormalTok{(p, }\DataTypeTok{dependencies =}\NormalTok{ T)}
\KeywordTok{lapply}\NormalTok{(p, library, }\DataTypeTok{character.only =}\NormalTok{ T)}

\CommentTok{# We need a data frame giving a hierarchical}
\CommentTok{# structure. Let's consider the flare dataset:}
\NormalTok{edges =}\StringTok{ }\NormalTok{flare}\OperatorTok{$}\NormalTok{edges}
\CommentTok{# edges cols = character}

\CommentTok{# Usually we associate another dataset that give}
\CommentTok{# information about each node of the dataset:}
\NormalTok{vertices =}\StringTok{ }\NormalTok{flare}\OperatorTok{$}\NormalTok{vertices}
\CommentTok{# vertices cols = character, numeric, character}

\CommentTok{# Create a subset of the dataset (I remove 1 level)}
\NormalTok{edges =}\StringTok{ }\NormalTok{flare}\OperatorTok{$}\NormalTok{edges }\OperatorTok{%>%}\StringTok{ }\KeywordTok{filter}\NormalTok{(to }\OperatorTok{%in%}\StringTok{ }\NormalTok{from) }\OperatorTok{%>%}\StringTok{ }\KeywordTok{droplevels}\NormalTok{()}
\NormalTok{vertices =}\StringTok{ }\NormalTok{flare}\OperatorTok{$}\NormalTok{vertices }\OperatorTok{%>%}\StringTok{ }\KeywordTok{filter}\NormalTok{(name }\OperatorTok{%in%}\StringTok{ }\KeywordTok{c}\NormalTok{(edges}\OperatorTok{$}\NormalTok{from, }
\NormalTok{    edges}\OperatorTok{$}\NormalTok{to)) }\OperatorTok{%>%}\StringTok{ }\KeywordTok{droplevels}\NormalTok{()}
\NormalTok{vertices}\OperatorTok{$}\NormalTok{size =}\StringTok{ }\KeywordTok{runif}\NormalTok{(}\KeywordTok{nrow}\NormalTok{(vertices))}

\CommentTok{# Then we have to make a 'graph' object using the}
\CommentTok{# igraph library:}
\NormalTok{mygraph <-}\StringTok{ }\KeywordTok{graph_from_data_frame}\NormalTok{(edges, }\DataTypeTok{vertices =}\NormalTok{ vertices)}

\CommentTok{# circle packing}
\KeywordTok{ggraph}\NormalTok{(mygraph, }\DataTypeTok{layout =} \StringTok{"circlepack"}\NormalTok{, }\DataTypeTok{weight =} \StringTok{"size"}\NormalTok{, }
    \DataTypeTok{sort.by =} \OtherTok{NULL}\NormalTok{, }\DataTypeTok{direction =} \StringTok{"out"}\NormalTok{) }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_node_circle}\NormalTok{(}\KeywordTok{aes}\NormalTok{(}\DataTypeTok{fill =}\NormalTok{ depth)) }\OperatorTok{+}\StringTok{ }
\StringTok{    }\KeywordTok{geom_node_text}\NormalTok{(}\KeywordTok{aes}\NormalTok{(}\DataTypeTok{label =}\NormalTok{ shortName, }\DataTypeTok{filter =}\NormalTok{ leaf, }
        \DataTypeTok{fill =}\NormalTok{ depth, }\DataTypeTok{size =}\NormalTok{ size)) }\OperatorTok{+}\StringTok{ }\KeywordTok{theme_void}\NormalTok{() }\OperatorTok{+}\StringTok{ }
\StringTok{    }\CommentTok{# theme(legend.position='F') + #show legend}
\KeywordTok{scale_fill_viridis}\NormalTok{(}\DataTypeTok{alpha =} \FloatTok{0.5}\NormalTok{, }\DataTypeTok{direction =} \OperatorTok{-}\DecValTok{1}\NormalTok{, }\DataTypeTok{option =} \StringTok{"magma"}\NormalTok{)}

\CommentTok{# scale_fill_distiller(palette = 'Blues')}

\CommentTok{# geom_node_label(aes(label=shortName, filter=leaf,}
\CommentTok{# size=size)) + # add text boxes}

\CommentTok{# circular dendo}
\KeywordTok{str}\NormalTok{(mygraph)}
\KeywordTok{ggraph}\NormalTok{(mygraph, }\DataTypeTok{layout =} \StringTok{"dendrogram"}\NormalTok{, }\DataTypeTok{circular =}\NormalTok{ T) }\OperatorTok{+}\StringTok{ }
\StringTok{    }\KeywordTok{geom_edge_diagonal}\NormalTok{(}\DataTypeTok{flipped =}\NormalTok{ F, }\DataTypeTok{label_colour =} \StringTok{"black"}\NormalTok{, }
        \DataTypeTok{label_alpha =} \DecValTok{1}\NormalTok{, }\DataTypeTok{angle_calc =} \StringTok{"rot"}\NormalTok{, }\DataTypeTok{force_flip =} \OtherTok{TRUE}\NormalTok{, }
        \DataTypeTok{label_dodge =} \OtherTok{NULL}\NormalTok{, }\DataTypeTok{label_push =} \OtherTok{NULL}\NormalTok{, }\DataTypeTok{show.legend =} \OtherTok{NA}\NormalTok{) }\OperatorTok{+}\StringTok{ }
\StringTok{    }\KeywordTok{theme_void}\NormalTok{() }\OperatorTok{+}\StringTok{ }\CommentTok{# theme(legend.position='none') +}
\KeywordTok{scale_fill_distiller}\NormalTok{(}\DataTypeTok{palette =} \StringTok{"Blues"}\NormalTok{)}

\CommentTok{# tree map}
\KeywordTok{ggraph}\NormalTok{(mygraph, }\StringTok{"treemap"}\NormalTok{, }\DataTypeTok{weight =} \StringTok{"size"}\NormalTok{) }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_node_tile}\NormalTok{(}\KeywordTok{aes}\NormalTok{(}\DataTypeTok{fill =}\NormalTok{ depth), }
    \DataTypeTok{size =} \FloatTok{0.25}\NormalTok{) }\OperatorTok{+}\StringTok{ }\KeywordTok{theme_void}\NormalTok{() }\OperatorTok{+}\StringTok{ }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.position =} \StringTok{"none"}\NormalTok{)}

\CommentTok{# circular partition}
\KeywordTok{ggraph}\NormalTok{(mygraph, }\StringTok{"partition"}\NormalTok{, }\DataTypeTok{circular =} \OtherTok{TRUE}\NormalTok{) }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_node_arc_bar}\NormalTok{(}\KeywordTok{aes}\NormalTok{(}\DataTypeTok{fill =}\NormalTok{ depth), }
    \DataTypeTok{size =} \FloatTok{0.25}\NormalTok{) }\OperatorTok{+}\StringTok{ }\KeywordTok{theme_void}\NormalTok{() }\OperatorTok{+}\StringTok{ }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.position =} \StringTok{"none"}\NormalTok{)}

\CommentTok{# node}
\KeywordTok{ggraph}\NormalTok{(mygraph) }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_edge_link}\NormalTok{() }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_node_point}\NormalTok{() }\OperatorTok{+}\StringTok{ }
\StringTok{    }\KeywordTok{theme_void}\NormalTok{() }\OperatorTok{+}\StringTok{ }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.position =} \StringTok{"none"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Insert an animal silhouette into a plot

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# 1. Get image from http://www.phylopic.org}
\KeywordTok{library}\NormalTok{(png)}
\NormalTok{ima <-}\StringTok{ }\KeywordTok{readPNG}\NormalTok{(}\StringTok{"thething.png"}\NormalTok{)}
\KeywordTok{plot}\NormalTok{(}\DecValTok{1}\OperatorTok{:}\DecValTok{3}\NormalTok{, }\DecValTok{1}\OperatorTok{:}\DecValTok{3}\NormalTok{)}
\KeywordTok{rasterImage}\NormalTok{(}\DataTypeTok{image =}\NormalTok{ ima, }\DataTypeTok{xleft =} \DecValTok{2}\NormalTok{, }\DataTypeTok{ybottom =} \FloatTok{1.8}\NormalTok{, }
    \DataTypeTok{xright =} \FloatTok{2.7}\NormalTok{, }\DataTypeTok{ytop =} \FloatTok{2.7}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Create an empty plot window

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# 1}
\KeywordTok{plot}\NormalTok{(}\DecValTok{0}\NormalTok{, }\DataTypeTok{type =} \StringTok{"n"}\NormalTok{, }\DataTypeTok{axes =} \OtherTok{FALSE}\NormalTok{, }\DataTypeTok{ann =} \OtherTok{FALSE}\NormalTok{)}
\CommentTok{# 2}
\KeywordTok{plot}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DataTypeTok{type =} \StringTok{"n"}\NormalTok{, }\DataTypeTok{xlab =} \StringTok{""}\NormalTok{, }\DataTypeTok{ylab =} \StringTok{""}\NormalTok{, }\DataTypeTok{xlim =} \KeywordTok{c}\NormalTok{(}\DecValTok{0}\NormalTok{, }
    \DecValTok{10}\NormalTok{), }\DataTypeTok{ylim =} \KeywordTok{c}\NormalTok{(}\DecValTok{0}\NormalTok{, }\DecValTok{10}\NormalTok{))}
\CommentTok{# 3}
\KeywordTok{plot.new}\NormalTok{()}
\end{Highlighting}
\end{Shaded}

Set color gradient, palette for smoothing data points

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(RColorBrewer)}

\NormalTok{alpha <-}\StringTok{ }\FloatTok{0.8}  \CommentTok{# transparency (0 to 1 value)}
\KeywordTok{set.seed}\NormalTok{(}\DecValTok{5000}\NormalTok{)}
\NormalTok{rr <-}\StringTok{ }\KeywordTok{rnorm}\NormalTok{(}\DecValTok{5000}\NormalTok{)}

\CommentTok{# user defined gradient}
\NormalTok{col <-}\StringTok{ }\KeywordTok{colorRampPalette}\NormalTok{(}\KeywordTok{c}\NormalTok{(}\StringTok{"steelblue"}\NormalTok{, }\StringTok{"lightblue"}\NormalTok{, }
    \StringTok{"orange"}\NormalTok{, }\StringTok{"red"}\NormalTok{))  }\CommentTok{# set your own col gradient with as many colours as you want}
\NormalTok{colfunc <-}\StringTok{ }\KeywordTok{col}\NormalTok{(}\KeywordTok{length}\NormalTok{(rr))[}\KeywordTok{as.numeric}\NormalTok{(}\KeywordTok{cut}\NormalTok{(rr, }\DataTypeTok{breaks =} \KeywordTok{length}\NormalTok{(rr)))]  }\CommentTok{# define breaks in col gradient}
\KeywordTok{plot}\NormalTok{(rr, }\DataTypeTok{col =}\NormalTok{ colfunc, }\DataTypeTok{pch =} \DecValTok{20}\NormalTok{)}

\CommentTok{# gradient from palette}
\KeywordTok{display.brewer.all}\NormalTok{()}
\NormalTok{col <-}\StringTok{ "Greens"}
\NormalTok{col <-}\StringTok{ }\KeywordTok{colorRampPalette}\NormalTok{(}\KeywordTok{brewer.pal}\NormalTok{(brewer.pal.info[col, }
\NormalTok{    ]}\OperatorTok{$}\NormalTok{maxcolors, col))  }\CommentTok{# col gradient}
\NormalTok{colfunc <-}\StringTok{ }\KeywordTok{col}\NormalTok{(}\KeywordTok{length}\NormalTok{(rr))[}\KeywordTok{as.numeric}\NormalTok{(}\KeywordTok{cut}\NormalTok{(rr, }\DataTypeTok{breaks =} \KeywordTok{length}\NormalTok{(rr)))]  }\CommentTok{# define breaks in col gradient}
\KeywordTok{plot}\NormalTok{(rr, }\DataTypeTok{col =}\NormalTok{ colfunc, }\DataTypeTok{pch =} \DecValTok{20}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Add plot point every nth element

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{n <-}\StringTok{ }\DecValTok{3}
\KeywordTok{plot}\NormalTok{(}\KeywordTok{runif}\NormalTok{(}\DecValTok{10}\NormalTok{, }\DecValTok{0}\NormalTok{, }\DecValTok{1}\NormalTok{), }\DataTypeTok{type =} \StringTok{"o"}\NormalTok{, }\DataTypeTok{pch =} \KeywordTok{c}\NormalTok{(}\DecValTok{20}\NormalTok{, }\KeywordTok{rep}\NormalTok{(}\OtherTok{NA}\NormalTok{, }
\NormalTok{    n)))}
\end{Highlighting}
\end{Shaded}

Create function to make line as default type in plot

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{lplot <-}\StringTok{ }\ControlFlowTok{function}\NormalTok{(...) }\KeywordTok{plot}\NormalTok{(..., }\DataTypeTok{type =} \StringTok{"l"}\NormalTok{)}
\KeywordTok{lplot}\NormalTok{(}\KeywordTok{runif}\NormalTok{(}\DecValTok{200}\NormalTok{))}
\end{Highlighting}
\end{Shaded}

Stack dataframe columns automatically in plot

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{head}\NormalTok{(outplot)}
\CommentTok{# time N P S I 1 0.00 200.000000 200.0000 20.00000}
\CommentTok{# 2.000000 2 0.01 78.245140 177.1952 20.58217}
\CommentTok{# 2.067159 3 0.02 34.785145 168.9650 21.12174}
\CommentTok{# 2.136073}
\NormalTok{dats <-}\StringTok{ }\KeywordTok{zoo}\NormalTok{(outplot)}
\KeywordTok{plot}\NormalTok{(dats)}
\end{Highlighting}
\end{Shaded}

Make 3D scatterplot

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(scatterplot3d)}
\NormalTok{xx <-}\StringTok{ }\KeywordTok{rnorm}\NormalTok{(}\DecValTok{1000}\NormalTok{)}
\NormalTok{yy <-}\StringTok{ }\KeywordTok{runif}\NormalTok{(}\DecValTok{1000}\NormalTok{)}
\NormalTok{dens <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\KeywordTok{rep}\NormalTok{(}\FloatTok{1e-04}\NormalTok{, }\DecValTok{500}\NormalTok{), }\KeywordTok{rep}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DecValTok{500}\NormalTok{))}
\NormalTok{controls <-}\StringTok{ }\KeywordTok{runif}\NormalTok{(}\DecValTok{3}\NormalTok{)}
\NormalTok{add.control <-}\StringTok{ }\DecValTok{1}
\NormalTok{dens_val <-}\StringTok{ }\DecValTok{1} \OperatorTok{*}\StringTok{ }\DecValTok{10}\OperatorTok{^-}\DecValTok{10}  \CommentTok{# 0 or 1*10^-10. value to knock out blanket of colour on plot surface }
\CommentTok{# linear model of r/ship between coords}
\NormalTok{dens_lm <-}\StringTok{ }\KeywordTok{lm}\NormalTok{(dens }\OperatorTok{~}\StringTok{ }\NormalTok{xx }\OperatorTok{+}\StringTok{ }\NormalTok{yy)}

\NormalTok{xlim <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\KeywordTok{min}\NormalTok{(xx), }\KeywordTok{max}\NormalTok{(xx))}
\NormalTok{ylim <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\KeywordTok{min}\NormalTok{(yy), }\KeywordTok{max}\NormalTok{(yy))}
\NormalTok{zlim =}\StringTok{ }\KeywordTok{c}\NormalTok{(}\KeywordTok{min}\NormalTok{(dens), }\KeywordTok{max}\NormalTok{(dens))  }\CommentTok{# set lims}
\NormalTok{colv <-}\StringTok{ "Blues"}
\NormalTok{colvv <-}\StringTok{ }\KeywordTok{colorRampPalette}\NormalTok{(}\KeywordTok{brewer.pal}\NormalTok{(brewer.pal.info[colv, }
\NormalTok{    ]}\OperatorTok{$}\NormalTok{maxcolors, colv))  }\CommentTok{# col gradient}
\NormalTok{colvv <-}\StringTok{ }\KeywordTok{colorRampPalette}\NormalTok{(}\KeywordTok{c}\NormalTok{(}\StringTok{"steelblue"}\NormalTok{, }\StringTok{"lightblue"}\NormalTok{, }
    \StringTok{"orange"}\NormalTok{, }\StringTok{"red"}\NormalTok{))  }\CommentTok{# set your own col gradient with as many colours as you want}
\CommentTok{# colvv<-colorRampPalette(magma(length(dens))) #}
\CommentTok{# set your own col gradient with as many colours as}
\CommentTok{# you want}

\CommentTok{# set col palette}
\NormalTok{colfunc <-}\StringTok{ }\KeywordTok{colvv}\NormalTok{(}\KeywordTok{length}\NormalTok{(dens))[}\KeywordTok{as.numeric}\NormalTok{(}\KeywordTok{cut}\NormalTok{(dens, }
    \DataTypeTok{breaks =} \KeywordTok{length}\NormalTok{(dens)))]  }\CommentTok{# define breaks in col gradient}
\NormalTok{bg <-}\StringTok{ }\KeywordTok{bpy.colors}\NormalTok{(}\DecValTok{1}\NormalTok{)}
\NormalTok{alpha <-}\StringTok{ }\FloatTok{0.8}

\CommentTok{# pdf(paste0(plot.dir,strat,'_',density,'_',stage,'_kudspdf.pdf'),width=8.27,height=11.69,paper='a4r')}

\CommentTok{# color=ifelse(col_heat==1, adjustcolor(colfunc,}
\CommentTok{# alpha=1),adjustcolor('lightgreen',alpha=0.2)),}
\KeywordTok{scatterplot3d}\NormalTok{(}\DataTypeTok{x =}\NormalTok{ xx, }\DataTypeTok{y =}\NormalTok{ yy, }\DataTypeTok{z =}\NormalTok{ dens, }\DataTypeTok{color =} \KeywordTok{ifelse}\NormalTok{(dens }\OperatorTok{<=}\StringTok{ }
\StringTok{    }\NormalTok{dens_val, }\KeywordTok{adjustcolor}\NormalTok{(}\KeywordTok{ifelse}\NormalTok{(bg }\OperatorTok{==}\StringTok{ }\KeywordTok{bpy.colors}\NormalTok{(}\DecValTok{1}\NormalTok{), }
    \KeywordTok{bpy.colors}\NormalTok{(}\DecValTok{1}\NormalTok{), }\StringTok{"white"}\NormalTok{), }\DataTypeTok{alpha =} \FloatTok{0.1}\NormalTok{), }\KeywordTok{adjustcolor}\NormalTok{(colfunc, }
    \DataTypeTok{alpha =}\NormalTok{ alpha)), }\DataTypeTok{las =} \DecValTok{1}\NormalTok{, }\DataTypeTok{pch =} \DecValTok{15}\NormalTok{, }\DataTypeTok{type =} \StringTok{"p"}\NormalTok{, }
    \DataTypeTok{lty.hplot =} \DecValTok{1}\NormalTok{, }\DataTypeTok{xlim =}\NormalTok{ xlim, }\DataTypeTok{ylim =}\NormalTok{ ylim, }\DataTypeTok{zlim =}\NormalTok{ zlim, }
    \DataTypeTok{xlab =} \StringTok{"X"}\NormalTok{, }\DataTypeTok{ylab =} \StringTok{"Y"}\NormalTok{, }\DataTypeTok{zlab =} \StringTok{"Density"}\NormalTok{, }\DataTypeTok{main =} \StringTok{"Main"}\NormalTok{, }
    \DataTypeTok{box =}\NormalTok{ F, }\DataTypeTok{lty.axis =} \KeywordTok{par}\NormalTok{(}\DecValTok{1}\NormalTok{), }\DataTypeTok{grid =}\NormalTok{ F, }\DataTypeTok{col.grid =} \KeywordTok{adjustcolor}\NormalTok{(}\StringTok{"gray"}\NormalTok{, }
        \DecValTok{1}\NormalTok{), }\DataTypeTok{lty.grid =} \KeywordTok{par}\NormalTok{(}\DecValTok{3}\NormalTok{), }\DataTypeTok{axis =}\NormalTok{ T)}

\CommentTok{# other plot options cex.symbols=dens*3,}
\CommentTok{# cex.symbols = ifelse(z<=0,0,0.5), highlight.3d=T,}
\CommentTok{# angle=70,}


\CommentTok{# append the below section starting at the '$' to}
\CommentTok{# the above closing bracket}

\CommentTok{# $plane3d(dens_lm, # add 3d linear model plane. #}
\CommentTok{# ??plane3d(Intercept, x.coef = NULL, y.coef =}
\CommentTok{# NULL, lty = 'dashed', lty.box = NULL, draw_lines}
\CommentTok{# = TRUE, draw_polygon = FALSE, polygon_args =}
\CommentTok{# list(border = NA, col = rgb(0,0,0,0.2))}
\CommentTok{# lty='dashed', lty.box = NULL, draw_lines = F,}
\CommentTok{# draw_polygon = T, polygon_args = list(border =}
\CommentTok{# NA, col = adjustcolor('light green',alpha=0.4)))}

\CommentTok{# add control dates}
\ControlFlowTok{if}\NormalTok{ (add.control }\OperatorTok{==}\StringTok{ }\DecValTok{1}\NormalTok{) \{}
    \KeywordTok{par}\NormalTok{(}\DataTypeTok{new =}\NormalTok{ T)}
    \KeywordTok{scatterplot3d}\NormalTok{(}\DataTypeTok{x =} \KeywordTok{rep}\NormalTok{(}\DecValTok{0}\NormalTok{, }\KeywordTok{length}\NormalTok{(controls)), }\DataTypeTok{y =}\NormalTok{ controls, }
        \DataTypeTok{z =} \KeywordTok{rep}\NormalTok{(}\KeywordTok{max}\NormalTok{(dens), }\KeywordTok{length}\NormalTok{(controls)), }\DataTypeTok{color =} \StringTok{"gray"}\NormalTok{, }
        \DataTypeTok{las =} \DecValTok{1}\NormalTok{, }\DataTypeTok{pch =} \StringTok{""}\NormalTok{, }\DataTypeTok{lty.hplot =} \DecValTok{1}\NormalTok{, }\DataTypeTok{xlim =}\NormalTok{ xlim, }
        \DataTypeTok{ylim =}\NormalTok{ ylim, }\DataTypeTok{zlim =}\NormalTok{ zlim, }\DataTypeTok{xlab =} \StringTok{""}\NormalTok{, }\DataTypeTok{ylab =} \StringTok{""}\NormalTok{, }
        \DataTypeTok{zlab =} \StringTok{""}\NormalTok{, }\DataTypeTok{box =}\NormalTok{ F, }\DataTypeTok{grid =}\NormalTok{ F, }\DataTypeTok{cex.symbols =} \DecValTok{2}\NormalTok{, }
        \DataTypeTok{axis =}\NormalTok{ F, }\DataTypeTok{type =} \StringTok{"h"}\NormalTok{)}
\NormalTok{\}}
\end{Highlighting}
\end{Shaded}

Adding title from separate list to plot in loop (\texttt{ggplot})

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# plot all sim results in one window}
\NormalTok{gspl <-}\StringTok{ }\KeywordTok{list}\NormalTok{()}
\NormalTok{ttl_list <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\StringTok{"cerc"}\NormalTok{, }\StringTok{"food"}\NormalTok{, }\StringTok{"juv"}\NormalTok{, }\StringTok{"adult"}\NormalTok{, }\StringTok{"infec"}\NormalTok{, }
    \StringTok{"infec (shed)"}\NormalTok{, }\StringTok{"host L"}\NormalTok{, }\StringTok{"parasite mass"}\NormalTok{)}

\CommentTok{# choose sim to plot}
\NormalTok{global_sim_plot <-}\StringTok{ }\NormalTok{global_detritus}

\ControlFlowTok{for}\NormalTok{ (g }\ControlFlowTok{in} \DecValTok{1}\OperatorTok{:}\DecValTok{10}\NormalTok{) \{}
\NormalTok{    gspl[[g]] <-}\StringTok{ }\KeywordTok{ggplot}\NormalTok{() }\OperatorTok{+}\StringTok{ }\KeywordTok{geom_line}\NormalTok{(}\DataTypeTok{data =}\NormalTok{ y_m, }\KeywordTok{aes}\NormalTok{(}\DataTypeTok{x =} \KeywordTok{rep.int}\NormalTok{(}\DecValTok{1}\OperatorTok{:}\NormalTok{n.ticks, }
        \KeywordTok{max}\NormalTok{(L1)), }\DataTypeTok{y =}\NormalTok{ value, }\DataTypeTok{group =}\NormalTok{ L1, }\DataTypeTok{colour =} \KeywordTok{factor}\NormalTok{(L1)), }
\NormalTok{        ) }\OperatorTok{+}\StringTok{ }\CommentTok{# scale_color_manual(values = viridis(length(mm)))}
\StringTok{    }\CommentTok{# + linetype=y_m$L1) +}
\StringTok{    }\KeywordTok{theme_tufte}\NormalTok{() }\OperatorTok{+}\StringTok{ }\KeywordTok{labs}\NormalTok{(}\DataTypeTok{title =}\NormalTok{ ttl_list[g], }\DataTypeTok{x =} \StringTok{""}\NormalTok{, }
        \DataTypeTok{y =} \StringTok{""}\NormalTok{) }\OperatorTok{+}\StringTok{ }\ControlFlowTok{if}\NormalTok{ (g }\OperatorTok{==}\StringTok{ }\KeywordTok{length}\NormalTok{(global_sim_plot)) \{}
        \KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.title =} \KeywordTok{element_text}\NormalTok{(}\DataTypeTok{size =} \FloatTok{0.2}\NormalTok{), }
            \DataTypeTok{legend.text =} \KeywordTok{element_text}\NormalTok{(}\DataTypeTok{size =} \FloatTok{0.2}\NormalTok{)) }\OperatorTok{+}\StringTok{ }
\StringTok{            }\KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.position =} \StringTok{"top"}\NormalTok{)}
        \KeywordTok{labs}\NormalTok{(}\DataTypeTok{x =} \StringTok{"Time"}\NormalTok{)}
\NormalTok{    \} }\ControlFlowTok{else}\NormalTok{ \{}
        \KeywordTok{theme}\NormalTok{(}\DataTypeTok{legend.position =} \StringTok{"none"}\NormalTok{)}
\NormalTok{    \}}
\NormalTok{\}}
\CommentTok{# + geom_text(x=,y=,label =}
\CommentTok{# max(value),check_overlap = TUE)}
\KeywordTok{do.call}\NormalTok{(grid.arrange, gspl)  }\CommentTok{# plot in one window }
\end{Highlighting}
\end{Shaded}

Using math expressions in plot labels

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{plot}\NormalTok{(}\KeywordTok{rnorm}\NormalTok{(}\DecValTok{1000}\NormalTok{), }\DataTypeTok{xlab =} \KeywordTok{expression}\NormalTok{(}\KeywordTok{paste}\NormalTok{(}\StringTok{"X values"}\OperatorTok{^}\DecValTok{2}\NormalTok{)), }
    \DataTypeTok{ylab =} \KeywordTok{expression}\NormalTok{(}\KeywordTok{paste}\NormalTok{(}\StringTok{"Y values"}\OperatorTok{^}\DecValTok{3}\NormalTok{, }\KeywordTok{hat}\NormalTok{(beta))))}
\end{Highlighting}
\end{Shaded}

Adding faint gridlines to plot

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# add gridlines}
\KeywordTok{grid}\NormalTok{(}\DataTypeTok{nx =} \OtherTok{NA}\NormalTok{, }\DataTypeTok{ny =} \OtherTok{NULL}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Storing current \texttt{par} variables for plotting

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{og_pars <-}\StringTok{ }\KeywordTok{par}\NormalTok{(}\DataTypeTok{no.readonly =}\NormalTok{ T)  }\CommentTok{# store current par values}
\end{Highlighting}
\end{Shaded}

Clear graphics memory

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{dput}\NormalTok{(}\KeywordTok{par}\NormalTok{(}\DataTypeTok{no.readonly =} \OtherTok{TRUE}\NormalTok{))  }\CommentTok{# reset graphical params }
\KeywordTok{par}\NormalTok{()}
\end{Highlighting}
\end{Shaded}

\subsubsection{Reading in files/data}\label{reading-in-filesdata}

Read in file manually

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{get.file.vol <-}\StringTok{ }\KeywordTok{read.table}\NormalTok{(}\KeywordTok{file.choose}\NormalTok{())  }\CommentTok{#read file manually}
\NormalTok{v.file <-}\StringTok{ }\NormalTok{get.file.vol[}\DecValTok{1}\OperatorTok{:}\DecValTok{100}\NormalTok{, }\DecValTok{1}\NormalTok{]  }\CommentTok{#get the volume}
\end{Highlighting}
\end{Shaded}

Loop through files from dir and append to list

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# option 1 reading in spdf (hrpath) files from}
\CommentTok{# drive}
\KeywordTok{setwd}\NormalTok{(}\StringTok{"/Users/camel/Desktop/Matt2016/Manuscripts/MalishevBullKearney/Resubmission/2016/barcoo sims/barcooresults/hrpath_75"}\NormalTok{)}
\NormalTok{file.list <-}\StringTok{ }\KeywordTok{list.files}\NormalTok{()}
\NormalTok{hrs75 <-}\StringTok{ }\KeywordTok{as.list}\NormalTok{(}\KeywordTok{rep}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DecValTok{100}\NormalTok{))  }\CommentTok{# empty list}
\ControlFlowTok{for}\NormalTok{ (f }\ControlFlowTok{in} \DecValTok{1}\OperatorTok{:}\DecValTok{100}\NormalTok{) \{}
    \KeywordTok{load}\NormalTok{(file.list[f])}
\NormalTok{    hrs75[f] <-}\StringTok{ }\NormalTok{hrpath}
\NormalTok{\}}

\CommentTok{# working version converting spdf into}
\CommentTok{# mcp(spdf,100,unout='m2)}
\NormalTok{ghr <-}\StringTok{ }\KeywordTok{list}\NormalTok{()}
\ControlFlowTok{for}\NormalTok{ (i }\ControlFlowTok{in}\NormalTok{ hrs75[}\DecValTok{1}\OperatorTok{:}\DecValTok{10}\NormalTok{]) \{}
\NormalTok{    m <-}\StringTok{ }\KeywordTok{mcp}\NormalTok{(i, }\DecValTok{100}\NormalTok{, }\DataTypeTok{unout =} \StringTok{"m2"}\NormalTok{)}
\NormalTok{    ghr <-}\StringTok{ }\KeywordTok{c}\NormalTok{(ghr, m)}
\NormalTok{\}}
\NormalTok{ghr}

\CommentTok{# option 2}
\NormalTok{wd <-}\StringTok{ }\KeywordTok{getwd}\NormalTok{()}
\NormalTok{me_list <-}\StringTok{ }\KeywordTok{list}\NormalTok{()  }\CommentTok{# create list }
\ControlFlowTok{for}\NormalTok{ (me_day }\ControlFlowTok{in} \KeywordTok{c}\NormalTok{(}\StringTok{"A"}\NormalTok{, }\StringTok{"B"}\NormalTok{, }\StringTok{"C"}\NormalTok{)) \{}
    \ControlFlowTok{for}\NormalTok{ (me_im }\ControlFlowTok{in} \DecValTok{1}\OperatorTok{:}\DecValTok{5}\NormalTok{) \{}
\NormalTok{        mes <-}\StringTok{ }\KeywordTok{readRDS}\NormalTok{(}\KeywordTok{paste0}\NormalTok{(wd, resource_type, }\StringTok{"_meday_"}\NormalTok{, }
\NormalTok{            me_day, }\StringTok{"_meim"}\NormalTok{, me_im, }\StringTok{".R"}\NormalTok{))  }\CommentTok{# read .R files from dir  }
        \KeywordTok{cat}\NormalTok{(}\StringTok{"}\CharTok{\textbackslash{}n}\StringTok{"}\NormalTok{, }\KeywordTok{paste0}\NormalTok{(wd, resource_type, }\StringTok{"_meday_"}\NormalTok{, }
\NormalTok{            me_day, }\StringTok{"_meim"}\NormalTok{, me_im, }\StringTok{".R"}\NormalTok{))}
        \KeywordTok{names}\NormalTok{(mes) <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\StringTok{"cerc"}\NormalTok{, }\StringTok{"food"}\NormalTok{, }\StringTok{"juv"}\NormalTok{, }\StringTok{"adult"}\NormalTok{, }
            \StringTok{"infected"}\NormalTok{, }\StringTok{"infected shedding"}\NormalTok{, }\StringTok{"mean host length"}\NormalTok{, }
            \StringTok{"mean parasite mass"}\NormalTok{, }\StringTok{"summed host biomass"}\NormalTok{, }
            \StringTok{"summed host eggs"}\NormalTok{, }\StringTok{"mean host eggs"}\NormalTok{, }\StringTok{"infected host length"}\NormalTok{)  }\CommentTok{# name all original R file list elements}
\NormalTok{        mes <-}\StringTok{ }\NormalTok{mes}\OperatorTok{$}\NormalTok{cerc  }\CommentTok{# get cercs (as list) use mes$'cerc'[[1]] for numeric }
        \KeywordTok{names}\NormalTok{(mes) <-}\StringTok{ }\KeywordTok{paste0}\NormalTok{(me_day, }\StringTok{"_"}\NormalTok{, me_im)  }\CommentTok{# name list elements according to loop iterations }
\NormalTok{        me_list <-}\StringTok{ }\KeywordTok{c}\NormalTok{(me_list, mes)  }\CommentTok{# bind to master list }
\NormalTok{    \}}
\NormalTok{\}}
\end{Highlighting}
\end{Shaded}

Read in PDF files from online source in R and save to drive.

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# from https://github.com/ropensci/pdftools}

\KeywordTok{require}\NormalTok{(pdftools)}
\NormalTok{url <-}\StringTok{ "https://raw.githubusercontent.com/darwinanddavis/499R/master/exp_pop_growth.pdf"}
\NormalTok{dir <-}\StringTok{ "FOLDER ON YOUR COMPUTER WHERE YOU WANT THE FILE SAVED"}
\NormalTok{f <-}\StringTok{ "NAME OF THE FILE"}
\NormalTok{f <-}\StringTok{ }\KeywordTok{paste0}\NormalTok{(f, }\StringTok{".pdf"}\NormalTok{)}

\CommentTok{# run all this}
\KeywordTok{download.file}\NormalTok{(url, }\KeywordTok{paste0}\NormalTok{(dir, }\StringTok{"/"}\NormalTok{, f), }\DataTypeTok{mode =} \StringTok{"wb"}\NormalTok{)}
\NormalTok{txt <-}\StringTok{ }\KeywordTok{pdf_text}\NormalTok{(}\KeywordTok{paste0}\NormalTok{(dir, }\StringTok{"/"}\NormalTok{, f))}

\CommentTok{# first page text}
\NormalTok{page <-}\StringTok{ }\DecValTok{1}  \CommentTok{# enter the page number}
\KeywordTok{cat}\NormalTok{(txt[page])}

\NormalTok{toc <-}\StringTok{ }\KeywordTok{pdf_toc}\NormalTok{(}\KeywordTok{paste0}\NormalTok{(dir, }\StringTok{"/"}\NormalTok{, f))}

\KeywordTok{require}\NormalTok{(jsonlite)}
\CommentTok{# Show as JSON}
\NormalTok{jsonlite}\OperatorTok{::}\KeywordTok{toJSON}\NormalTok{(toc, }\DataTypeTok{auto_unbox =} \OtherTok{TRUE}\NormalTok{, }\DataTypeTok{pretty =} \OtherTok{TRUE}\NormalTok{)}

\CommentTok{# show author, version, etc}
\NormalTok{info <-}\StringTok{ }\KeywordTok{pdf_info}\NormalTok{(f)}

\CommentTok{# renders pdf to bitmap array}
\NormalTok{bitmap <-}\StringTok{ }\KeywordTok{pdf_render_page}\NormalTok{(f, }\DataTypeTok{page =} \DecValTok{1}\NormalTok{)}

\CommentTok{# save bitmap image}
\NormalTok{png}\OperatorTok{::}\KeywordTok{writePNG}\NormalTok{(bitmap, }\StringTok{"page.png"}\NormalTok{)}
\NormalTok{jpeg}\OperatorTok{::}\KeywordTok{writeJPEG}\NormalTok{(bitmap, }\StringTok{"page.jpeg"}\NormalTok{)}
\NormalTok{webp}\OperatorTok{::}\KeywordTok{write_webp}\NormalTok{(bitmap, }\StringTok{"page.webp"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Read .txt files

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{readLines}\NormalTok{(}\StringTok{"search_terms.txt"}\NormalTok{)  }\CommentTok{# must have a blank line at end of file to avoid line read error  }
\end{Highlighting}
\end{Shaded}

Load in data to avoid `magic number error'

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# avoid load()}
\KeywordTok{readRDS}\NormalTok{(}\StringTok{"path to file .R"}\NormalTok{)  }\CommentTok{# can use .R and .Rdata}
\KeywordTok{source}\NormalTok{(}\StringTok{"path to file .R"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Access files anywhere without changing working dir

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# https://github.com/jennybc/here_here}
\KeywordTok{require}\NormalTok{(here)}
\KeywordTok{getwd}\NormalTok{()}
\CommentTok{# '/Users/malishev/Documents/Data/gggmap'}
\NormalTok{here_loc <-}\StringTok{ }\KeywordTok{here}\NormalTok{(}\StringTok{"here_test"}\NormalTok{, }\StringTok{"here_test.txt"}\NormalTok{)}
\NormalTok{here_loc}
\CommentTok{# '/Users/malishev/Documents/Data/gggmap/here_test/here_test.txt'}
\KeywordTok{readLines}\NormalTok{(here_loc)  }\CommentTok{# access the file even though your working dir is up N levels from the file in your dir }
\end{Highlighting}
\end{Shaded}

\subsubsection{\texorpdfstring{Regular expressions
(\texttt{regex})}{Regular expressions (regex)}}\label{regular-expressions-regex}

Get just numbers or characters

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{vec <-}\StringTok{ "16-Feb-2018 20:08:04 PM"}
\NormalTok{vecN <-}\StringTok{ }\KeywordTok{gsub}\NormalTok{(}\StringTok{"[^[:digit:]]"}\NormalTok{, }\StringTok{""}\NormalTok{, vec)}
\NormalTok{vec}
\KeywordTok{print}\NormalTok{(}\KeywordTok{paste0}\NormalTok{(}\StringTok{"Just numbers: "}\NormalTok{, vecN))}
\NormalTok{vecC <-}\StringTok{ }\KeywordTok{gsub}\NormalTok{(}\StringTok{"[[:digit:]]"}\NormalTok{, }\StringTok{""}\NormalTok{, vec)}
\NormalTok{vec}
\KeywordTok{print}\NormalTok{(}\KeywordTok{paste0}\NormalTok{(}\StringTok{"Just characters: "}\NormalTok{, vecC))}

\CommentTok{# with tidyr. requires data frame}
\KeywordTok{require}\NormalTok{(tidyr)}
\NormalTok{df <-}\StringTok{ }\KeywordTok{data.frame}\NormalTok{(}\DataTypeTok{N1 =} \KeywordTok{c}\NormalTok{(}\StringTok{"APPLE348744"}\NormalTok{, }\StringTok{"BANANA77845"}\NormalTok{, }
    \StringTok{"OATS2647892"}\NormalTok{, }\StringTok{"EGG98586456"}\NormalTok{))}
\KeywordTok{print}\NormalTok{(}\StringTok{"tidyr doesn't work with strings separated by spaces"}\NormalTok{)}
\NormalTok{df }\OperatorTok{%>%}\StringTok{ }\KeywordTok{separate}\NormalTok{(N1, }\DataTypeTok{into =} \KeywordTok{c}\NormalTok{(}\StringTok{"text"}\NormalTok{, }\StringTok{"num"}\NormalTok{), }\DataTypeTok{sep =} \StringTok{"(?<=[A-Za-z])(?=[0-9])"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Insert or replace a character in a string at a specific location

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{require}\NormalTok{(stringi)}
\NormalTok{vec <-}\StringTok{ "ABCEF"}
\KeywordTok{stri_sub}\NormalTok{(vec, }\DecValTok{4}\NormalTok{, }\DecValTok{2}\NormalTok{) <-}\StringTok{ "d"}
\KeywordTok{print}\NormalTok{(}\KeywordTok{paste0}\NormalTok{(}\StringTok{"Original: ABCEF"}\NormalTok{))}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## [1] "Original: ABCEF"
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{print}\NormalTok{(}\KeywordTok{paste0}\NormalTok{(}\StringTok{"New: "}\NormalTok{, vec))}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## [1] "New: ABCdEF"
\end{verbatim}

Testing regex expressions and their output

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# Testing regex expressions and their output}

\CommentTok{# https://regex101.com/r/ksY7HU/2}
\end{Highlighting}
\end{Shaded}

Removing multiple cols from df using grep

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{packages <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\StringTok{"dplyr"}\NormalTok{, }\StringTok{"purrr"}\NormalTok{)}

\NormalTok{fh <-}\StringTok{ "LEC100testrecords.txt"}
\NormalTok{tt <-}\StringTok{ }\KeywordTok{read.delim}\NormalTok{(}\KeywordTok{paste0}\NormalTok{(wd, }\StringTok{"/"}\NormalTok{, fh), }\DataTypeTok{header =}\NormalTok{ T, }\DataTypeTok{sep =} \StringTok{"}\CharTok{\textbackslash{}t}\StringTok{"}\NormalTok{)}

\CommentTok{# Enter data column you want to search}
\NormalTok{col2search <-}\StringTok{ "Title"}
\NormalTok{keyterms <-}\StringTok{ }\KeywordTok{c}\NormalTok{(}\StringTok{"evidence"}\NormalTok{, }\StringTok{"human"}\NormalTok{, }\StringTok{"africa"}\NormalTok{)}

\CommentTok{# 1. find key terms}
\NormalTok{final <-}\StringTok{ }\NormalTok{tt[}\KeywordTok{grep}\NormalTok{(keyterms, tt[, col2search], }\DataTypeTok{ignore.case =}\NormalTok{ T), }
\NormalTok{    ]  }\CommentTok{#}
\KeywordTok{length}\NormalTok{(final[, col2search])  }\CommentTok{# get number of results}
\NormalTok{tt[final[, col2search], col2search]  }\CommentTok{# show raw outputs }
\end{Highlighting}
\end{Shaded}

\subsubsection{R Markdown}\label{r-markdown}

Hide unwanted code output, such as inherent examples for functions

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# ```\{r, cache = TRUE, tidy = TRUE, lazy = TRUE,}
\CommentTok{# results='markup'\}}
\end{Highlighting}
\end{Shaded}

Math notation in R Markdown

x=y \(x = y\)\\
xy \(x > y\)\\
x≤y \(x \le y\)\\
x≥y \(x \ge y\)\\
xn \(x^{n}\)\\
xn \(x_{n}\)\\
x⎯⎯⎯ \(\overline{x}\)\\
x̂ \(\hat{x}\)\\
x̃ \(\tilde{x}\)\\
ab \(\frac{a}{b}\)\\
∂f∂x \(\frac{a}{b}\)\\
∂f∂x \(\displaystyle \frac{a}{b}\)\\
(nk) \(\binom{n}{k}\)\\
x1+x2+⋯+xn \(x_{1} + x_{2} + \cdots + x_{n}\)\\
x1,x2,\ldots{},xn \(x_{1}, x_{2}, \dots, x_{n}\)\\
x=⟨x1,x2,\ldots{},xn
\(\mathbf{x} = \langle x_{1}, x_{2}, \dots, x_{n}\rangle\)\\
x∈A \(x \in A\)\\
\textbar{}A\textbar{} \(|A|\)\\
x∈A \(x \in A\)\\
A⊂B \(x \subset B\)\\
A⊆B \(x \subseteq B\)\\
A∪B \(A \cup B\)\\
A∩B \(A \cap B\)\\
X∼𝖡𝗂𝗇𝗈𝗆(n,π) \(X \sim {\sf Binom}(n, \pi)\)

P(X≤x)=𝚙𝚋𝚒𝚗𝚘𝚖(x,n,π) \(\mathrm{P}(X \le x) = {\tt pbinom}(x, n, \pi)\)\\
P(A∣B) \(P(A \mid B)\)\\
P(A∣B) \(\mathrm{P}(A \mid B)\)\\
\{1,2,3\} \(\{1, 2, 3\}\)\\
sin(x) \(\sin(x)\)\\
log(x) \(\log(x)\)\\
∫ba \(\int_{a}^{b}\)\\
(∫baf(x)dx) \(\left(\int_{a}^{b} f(x) \; dx\right)\)\\
{[}∫∞−∞f(x)dx{]} \(\left[\int_{\-infty}^{\infty} f(x) \; dx\right]\)\\
F(x)\textbar{}ba \(\left. F(x) \right|_{a}^{b}\)\\
∑bx=af(x) \(\sum_{x = a}^{b} f(x)\)\\
∏bx=af(x) \(\prod_{x = a}^{b} f(x)\)\\
limx→∞f(x) \(\lim_{x \to \infty} f(x)\)\\
limx→∞f(x) \(\displaystyle \lim_{x \to \infty} f(x)\)

Greek Letters

αA \(\alpha A\)\\
νN \$\nu N \$\\
βB \(\beta B\)\\
ξΞ \(\xi\Xi\)\\
γΓ \(\gamma \Gamma\)\\
oO \(o O\) (omicron)\\
δΔ \(\delta \Delta\)\\
πΠ \(\pi \Pi\)\\
ϵεE \(\epsilon \varepsilon E\)\\
ρϱP \(\rho\varrho P\)\\
ζZ \(\zeta Z \sigma \,\!\)\\
Σ \(\sigma \Sigma\)\\
ηH \(\eta H\)\\
τT \(\tau T\)\\
θϑΘ \(\theta \vartheta \Theta\)\\
υΥ \(\upsilon \Upsilon\)\\
ιI \(\iota I\)\\
ϕφΦ \(\phi \varphi \Phi\)\\
κK \(\kappa K\)\\
χX \(\chi X\)\\
λΛ \(\lambda \Lambda\)\\
ψΨ \(\psi \Psi\)\\
μM \(\mu M\)\\
ω Ω\(\omega \Omega\)

\subsubsection{Subsetting}\label{subsetting}

Select specific rows E.g. select rows of sfeed\_move not in foodh

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{library}\NormalTok{(sqldf)}
\NormalTok{a1NotIna2_h <-}\StringTok{ }\KeywordTok{sqldf}\NormalTok{(}\StringTok{"SELECT * FROM sfeed_move EXCEPT SELECT * FROM foodh"}\NormalTok{)}
\NormalTok{a1NotIna2_l <-}\StringTok{ }\KeywordTok{sqldf}\NormalTok{(}\StringTok{"SELECT * FROM sfeed_move EXCEPT SELECT * FROM foodl"}\NormalTok{)}
\CommentTok{# select rows from sfeed_move that also appear in}
\CommentTok{# foodh}
\NormalTok{a1Ina2_h <-}\StringTok{ }\KeywordTok{sqldf}\NormalTok{(}\StringTok{"SELECT * FROM sfeed_move INTERSECT SELECT * FROM foodh"}\NormalTok{)}
\NormalTok{a1Ina2_l <-}\StringTok{ }\KeywordTok{sqldf}\NormalTok{(}\StringTok{"SELECT * FROM sfeed_move INTERSECT SELECT * FROM foodl"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Count occurrences of values in data frame

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{table}\NormalTok{(}\KeywordTok{unlist}\NormalTok{(df}\OperatorTok{$}\NormalTok{X))}
\end{Highlighting}
\end{Shaded}

Remove a specific column from a data frame

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{within}\NormalTok{(df, }\KeywordTok{rm}\NormalTok{(}\StringTok{"Col1"}\NormalTok{))}
\end{Highlighting}
\end{Shaded}

\subsubsection{Web scraping}\label{web-scraping}

Scraping web tables\\
\url{http://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/XML/html/readHTMLTable.html\%5Bhttp://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/XML/html/readHTMLTable.html\%5D}

\begin{Shaded}
\begin{Highlighting}[]
\KeywordTok{library}\NormalTok{(XML)}
\KeywordTok{readHTMLTable}\NormalTok{()}
\end{Highlighting}
\end{Shaded}

Scraping Twitter timelines\\
See complete example at
\url{http://varianceexplained.org/r/trump-tweets/}

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{# https://cran.r-project.org/web/packages/twitteR/}
\KeywordTok{library}\NormalTok{(dplyr)}
\KeywordTok{library}\NormalTok{(purrr)}
\KeywordTok{library}\NormalTok{(twitteR)}
\end{Highlighting}
\end{Shaded}

\printbibliography

\end{document}