WorkInR_forPrinter.Rnw

\documentclass[a4paper, 12pt]{article}
\title{This is my work in R}
\author{ MyFirstName MyLastName\\OrganizationName\\
         City, ZipCope, \underline{Country}\\
        \url{username@the.rest}}
\date{\today}  %% manually: \date{January 30, 2024} 
\usepackage[natbibapa]{apacite} %% for bibliography
\usepackage{rotating, graphicx} %% for rotating tables
\usepackage{adjustbox} % size of plots and tables
\usepackage{chngcntr}% section numbering
\counterwithin{table}{section}\counterwithin{figure}{section}
\begin{document} % every "begin: needs and "end"
\SweaveOpts{concordance=TRUE}
\maketitle 
\begin{abstract}
This is an example of an abstract in a paper. This is an example of an abstract in a paper. This is an example of an abstract in a paper. This is an example of an abstract in a paper.This is an example of an abstract in a paper.This is an example of an abstract in a paper.
\end{abstract}


\section*{Introduction} % * to unnumber

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\section{Exploring Tables}\label{explo-tables} % label for crossref

%footnote coming
Another section. I will use a footnot now \footnote{This is a footnote.}. I will soon use cross-ref.I will soon use cross-ref.I will soon use cross-ref.I will soon use cross-ref. I will soon use cross-ref. I will soon use cross-ref.I will soon use cross-ref.I will soon use cross-ref.I will soon use cross-ref.I will soon use cross-ref. I will soon use cross-ref. I will soon use cross-ref.
%cross-ref coming

%cross-ref coming
I will soon use cross-ref.I will soon use cross-ref: as we see in Section \ref{catexplor}.

% a chunk hidden (echo=FALSE) with some setup
% chunk has its own name 

<<collecting-DataTable, echo=FALSE>>=
# clean memory
rm(list = ls())
# paste the github link here (in two parts):
linkOrg=""
linkRepo=""
file_Name1="hdidemiso_plus.RDS"
link_file_Name1=paste0(linkOrg,linkRepo,file_Name1)
#link_file_Name1=url(link_file_Name1)
#opening data
mergedData=readRDS(link_file_Name1)
@

\subsection{Exploring Categorical Data}\label{catexplor}

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You can see the statistics of a categorical variable in Table \ref{catexploreTable}.

%the chunk name is NOT used in cross-ref for table.
%Table is created and displayed.

<<catexploreTable,results=tex,echo=FALSE>>=
## display frequency table of Freedom Index
library(summarytools)
library(tidyr)
library(knitr)
library(kableExtra)

namesHeaders=c("Democracy Level","count","pct","pct_cumm")
freq(mergedData$Regimetype, 
     plain.ascii = FALSE,
     report.nas=FALSE) %>%
    ## changes, we need data frame
    tb() %>%
     kable(format = "latex", 
           digits = 2,                #label cross-ref!!
           caption = "This is a table\\label{catexploreTable}",
           col.names = namesHeaders)%>%
    kable_styling(full_width = F,latex_options = "h")

@


%%%%%%

You can see this variable plotted in Figure \ref{catBarplot} on page \pageref{catBarplot}.

% NO need for figure caption in chunk header.
% Object will be created BUT NOT plotted
% the chunk name IS NOT used in cross-ref for figure

\begin{figure}[h]
\centering
\begin{adjustbox}{width=7cm,height=5cm} %resize
<<catBarplot, echo=FALSE, fig=TRUE>>=
library(ggplot2)

base=ggplot(data = mergedData)
bar=base + geom_bar(aes(x=Regimetype),
                    fill='orange',
                    color='red')
bar=bar + labs(title = "Democracy in the world (2021)",
           x= "Levels",
           y= "Count of countries",
           caption = 'Source: The Economist')
bar
@
\end{adjustbox}
\caption{Press Freedom Index in the World}  %title
\label{catBarplot} % for cross-ref
\end{figure}



\subsection{Exploring Numerical Data}\label{numexplo}

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<<summaryNumeric, results=tex, echo=FALSE>>=

## table of summary statistics for numerical columns
AllNumericNames=names(Filter(is.numeric, mergedData))
originalNumeric=AllNumericNames[!grepl('mM',AllNumericNames)]

## table of summary statistics
library(stargazer)
summaryHeaders=c("n","mean",'sd',"min",'p25','p75','max')
stargazer(mergedData[,originalNumeric],
          title = "Stat summary for numeric vars", 
          label = "summaryNumeric",# cross-ref
          font.size = 'scriptsize',
          digits = 2,
          summary.stat = summaryHeaders)
@

% Use of R object inline
In the Table \ref{summaryNumeric}, you realize that the mean of HDI is {\bf\Sexpr{round(mean(mergedData$HumanDevelopmentIndex),2)}}. It would be good to see a boxplot, check Figure \ref{numBoxplot} below.


\begin{figure}[h]
\centering
\begin{adjustbox}{width=12cm,height=8.5cm,clip,trim=0cm 0.5cm 0cm 0cm} 
<<numBoxplot, echo=FALSE, fig=TRUE>>=
scaledNumeric=AllNumericNames[grepl('mM',AllNumericNames)]

DataForBox=reshape2::melt(mergedData[,scaledNumeric])

base=ggplot(data=DataForBox)
box=base + geom_boxplot(aes(x=variable,y=value),
                        fill='lightblue',
                        color='red') + coord_flip()
## plotting
box
@
\end{adjustbox}
\caption{Money spent per country on Military stuff}  
\label{numBoxplot} 
\end{figure}

%%%%% A citation: author(year)
Boxplots were introduced by \citet{tukey_exploratory_1977}. You can also flip the Table \ref{summaryNumeric}, as shown in Table \ref{summaryNumeric-flip}.



<<summaryNumeric-flip, results=tex, echo=FALSE>>=
stargazer(mergedData[,originalNumeric],
          title = "Stat summary for numeric vars (flipped)", 
          label = "summaryNumeric-flip",# cross-ref
          font.size = 'scriptsize',
          digits = 2,
          summary.stat = summaryHeaders,
          float.env = "sidewaystable")
@

\pagebreak



%%%%
\section{My Regression}\label{regre}

Several times we need regression. This is a nice summary for two regressions, as shown in Table \ref{regsPrint}:

<<regresPrep, echo=FALSE>>=
## prepare regressions
h1=formula(HumanDevelopmentIndex~Functioningofgovernment)
regre1=glm(h1,data=mergedData,family = "gaussian")

h2=formula(HumanDevelopmentIndex~Functioningofgovernment + Politicalparticipation)
regre2=glm(h2,data=mergedData,family = "gaussian")
@





<<regsPrint, echo=FALSE,results=tex>>=
## show result of both 
stargazer(regre1,regre2,
          title = "Models for HDI",
          dep.var.labels   = "Human Development",
          covariate.labels = c("Bureaucracy", "Participation"),
          label = 'regsPrint')
@

I hope you like what you see in the Table \ref{regsPrint}. You can learn more on regression in 
other book \citep[150-160]{petrie_introduction_2016}

%%%%


\section{Other plots}\label{otherPlots}


\subsection{A map}\label{mapPlot}

Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.

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Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map.Let me show a nice map in Figure \ref{plot-cityMap}.

<<collecting-DataMap, message=FALSE, echo=FALSE>>=

# github link to data already saved!
 
file_Name2="MapSeattle.geojson"
file_Name3="calls911_geo.geojson"

link_file_Name2=paste0(linkOrg,linkRepo,file_Name2)
link_file_Name3=paste0(linkOrg,linkRepo,file_Name3)

#opening data
library(sf)
cityMap=read_sf(link_file_Name2)
eventsLocations=read_sf(link_file_Name3)
@

\begin{figure}[h]
\centering
\begin{adjustbox}{width=10cm,height=10cm} 
<<plot-cityMap, echo=FALSE, fig=TRUE>>=
library(ggplot2)
ggplot(cityMap) +geom_sf(aes(fill=ACRES_TOTAL))
@
\end{adjustbox}
\caption{Plot numeric colums.}  
\label{plot-cityMap} 
\end{figure}

Figure \ref{plot-cityMap} uses only one layer. Let's add another layer in the next map. Here, I continue doing this nice work, I hope you like it and read it. It has been a very hard work.Here, I continue doing this nice work, I hope you like it and read it. It has been a very hard work.Here, I continue doing this nice work, I hope you like it and read it. It has been a very hard work.Here, I continue doing this nice work, I hope you like it and read it.  Here, I continue doing this nice work, I hope you like it and read it. It has been a very hard work.Here, I continue doing this nice work, I hope you like it and read it. It has been a very hard work.Here, I continue doing this nice work, I hope you like it and read it. It has been a very hard work.Here, I continue doing this nice work, I hope you like it and read it.


\begin{figure}[h]
\centering
\begin{adjustbox}{width=10cm,height=10cm} 
<<plot-911Map, echo=FALSE, fig=TRUE>>=
base=ggplot(cityMap) + geom_sf() + theme_light()
eventsByTime=base + geom_sf(data = eventsLocations,
                         size=0.5,
                         aes(color=nightTime)) 

eventsByTime
@
\end{adjustbox}
\caption{Calls to 911 by time of day.}  
\label{plot-911Map} 
\end{figure}

You can see that Figure \ref{plot-911Map} actually uses one map on top of the other. 
Here, I continue doing this nice work, I hope you like it and read it. It has been a very hard work.Here, I continue doing this nice work, I hope you like it and read it. It has been a very hard work.Here, I continue doing this nice work, I hope you like it and read it. It has been a very hard work.Here, I continue doing this nice work, I hope you like it and read it. 

%% more than one author in a citation
Review other authors 
(\citealp[120-160]{brunsdon_introduction_2015};
\citealp[also, see][]{camara_spatial_nodate}) to know more.

\newpage

%%%%% adding bibliography
\bibliographystyle{apacite} %%style
%\renewcommand{\refname}{Bibliography}
\bibliography{Bib_winterschool} %% filename
\end{document} %% nothing after here