Merge pull request #36 from xiaoyuanf/master

get medol.R back
STAT547-UBC-2019-20 · Mar 17, 2020 · 4914e7e · 4914e7e
2 parents 8462707 + 9e91d26
commit 4914e7e
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diff --git a/docs/finalreport.html b/docs/finalreport.html
diff --git a/docs/finalreport.pdf b/docs/finalreport.pdf
diff --git a/docs/finalreport.tex b/docs/finalreport.tex
@@ -1,35 +1,96 @@
-\documentclass[]{article}
+% Options for packages loaded elsewhere
+\PassOptionsToPackage{unicode}{hyperref}
+\PassOptionsToPackage{hyphens}{url}
+%
+\documentclass[
+]{article}
 \usepackage{lmodern}
 \usepackage{amssymb,amsmath}
 \usepackage{ifxetex,ifluatex}
-\usepackage{fixltx2e} % provides \textsubscript
 \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
   \usepackage[T1]{fontenc}
   \usepackage[utf8]{inputenc}
-\else % if luatex or xelatex
-  \ifxetex
-    \usepackage{mathspec}
-  \else
-    \usepackage{fontspec}
-  \fi
-  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
+  \usepackage{textcomp} % provide euro and other symbols
+\else % if luatex or xetex
+  \usepackage{unicode-math}
+  \defaultfontfeatures{Scale=MatchLowercase}
+  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
 \fi
-% use upquote if available, for straight quotes in verbatim environments
+% Use upquote if available, for straight quotes in verbatim environments
 \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
-% use microtype if available
-\IfFileExists{microtype.sty}{%
-\usepackage{microtype}
-\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+\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}
+\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
+\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
+\hypersetup{
+  pdftitle={Final report},
+  pdfauthor={Margot Chen, Qi Yang},
+  hidelinks,
+  pdfcreator={LaTeX via pandoc}}
+\urlstyle{same} % disable monospaced font for URLs
 \usepackage[margin=1in]{geometry}
-\usepackage{hyperref}
-\hypersetup{unicode=true,
-            pdftitle={Final report},
-            pdfauthor={Margot Chen, Qi Yang},
-            pdfborder={0 0 0},
-            breaklinks=true}
-\urlstyle{same}  % don't use monospace font for urls
+\usepackage{color}
+\usepackage{fancyvrb}
+\newcommand{\VerbBar}{|}
+\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
+\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
+% Add ',fontsize=\small' for more characters per line
+\usepackage{framed}
+\definecolor{shadecolor}{RGB}{248,248,248}
+\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
+\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
+\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
+\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\BuiltInTok}[1]{#1}
+\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
+\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
+\newcommand{\ExtensionTok}[1]{#1}
+\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\ImportTok}[1]{#1}
+\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\NormalTok}[1]{#1}
+\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
+\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
+\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\RegionMarkerTok}[1]{#1}
+\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
 \usepackage{longtable,booktabs}
+% 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,grffile}
 \makeatletter
 \def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
@@ -39,52 +100,18 @@
 % margins by default, and it is still possible to overwrite the defaults
 % using explicit options in \includegraphics[width, height, ...]{}
 \setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
-\IfFileExists{parskip.sty}{%
-\usepackage{parskip}
-}{% else
-\setlength{\parindent}{0pt}
-\setlength{\parskip}{6pt plus 2pt minus 1pt}
-}
-\setlength{\emergencystretch}{3em}  % prevent overfull lines
+% 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}{0}
-% Redefines (sub)paragraphs to behave more like sections
-\ifx\paragraph\undefined\else
-\let\oldparagraph\paragraph
-\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
-\fi
-\ifx\subparagraph\undefined\else
-\let\oldsubparagraph\subparagraph
-\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
-\fi
-
-%%% Use protect on footnotes to avoid problems with footnotes in titles
-\let\rmarkdownfootnote\footnote%
-\def\footnote{\protect\rmarkdownfootnote}
-
-%%% Change title format to be more compact
-\usepackage{titling}
-
-% Create subtitle command for use in maketitle
-\providecommand{\subtitle}[1]{
-  \posttitle{
-    \begin{center}\large#1\end{center}
-    }
-}
-
-\setlength{\droptitle}{-2em}
-
-  \title{Final report}
-    \pretitle{\vspace{\droptitle}\centering\huge}
-  \posttitle{\par}
-    \author{Margot Chen, Qi Yang}
-    \preauthor{\centering\large\emph}
-  \postauthor{\par}
-      \predate{\centering\large\emph}
-  \postdate{\par}
-    \date{2020/3/14}
+\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
 
+\title{Final report}
+\author{Margot Chen, Qi Yang}
+\date{2020/3/14}
 
 \begin{document}
 \maketitle
@@ -255,6 +282,26 @@ \subsubsection{5.Line chart}\label{line-chart}}
 \hypertarget{analysis-methods}{%
 \subsection{Analysis methods}\label{analysis-methods}}
 
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{lm <-}\StringTok{ }\KeywordTok{readRDS}\NormalTok{(}\DataTypeTok{file=}\NormalTok{here}\OperatorTok{::}\KeywordTok{here}\NormalTok{(}\StringTok{"docs"}\NormalTok{, }\StringTok{"model.rds"}\NormalTok{))}
+\KeywordTok{tidy}\NormalTok{(lm)}
+\end{Highlighting}
+\end{Shaded}
+
+\begin{verbatim}
+## # A tibble: 7 x 5
+##   term        estimate std.error statistic   p.value
+##   <chr>          <dbl>     <dbl>     <dbl>     <dbl>
+## 1 (Intercept) 1836.      72.9       25.2   5.25e-139
+## 2 DEWP           4.10     0.0518    79.2   0.       
+## 3 TEMP          -6.29     0.0675   -93.1   0.       
+## 4 PRES          -1.62     0.0712   -22.8   2.52e-114
+## 5 cbwdNE       -28.9      1.45     -20.0   2.78e- 88
+## 6 cbwdNW       -39.9      1.13     -35.1   9.70e-267
+## 7 cbwdSE         0.435    1.10       0.397 6.92e-  1
+\end{verbatim}
+
 \hypertarget{results}{%
 \subsection{Results}\label{results}}
 
@@ -345,5 +392,4 @@ \subsubsection{References}\label{references}}
 weather impact, APEC and winter heating. Proceedings of the Royal
 Society A, 471, 20150257.
 
-
 \end{document}
diff --git a/docs/model.rds b/docs/model.rds
diff --git a/images/corr.png b/images/corr.png
diff --git a/images/facted_hist.png b/images/facted_hist.png
diff --git a/images/heatmap.png b/images/heatmap.png
diff --git a/images/season_PM2.5.png b/images/season_PM2.5.png
diff --git a/images/year_PM2.5.png b/images/year_PM2.5.png
diff --git a/scripts/model.R b/scripts/model.R
@@ -0,0 +1,39 @@
+# author: Margot Chen
+# date: 2020-03-16
+
+"This script carries out a linear regression for the Beijing pm2.5 dataset and
+exports the model to a user defined location. 
+Usage: model.R --clean_path=<clean_data_path> --model_path=<model_path>
+"->doc
+
+# Load packages
+suppressMessages(library(tidyverse))
+suppressMessages(library(here))
+suppressMessages(library(docopt))
+
+opt <- docopt(doc)
+
+# Main function
+main <- function(clean_path, model_path) {
+  # Load data
+  df_clean <- read.csv(here(clean_path))
+
+  # Linear regression
+  model <- lm(pm2.5 ~ DEWP + TEMP + PRES + cbwd, data=df_clean)
+
+  # Save model
+  saveRDS(model, file = here(model_path))
+
+  # message for users
+  print("Linear regression has run successfully!")
+}
+
+
+
+#' @param clean_path is the path to the cleaned data file.
+#' 
+#' @param model_path is the location where the users would like to save the model.
+#' 
+
+
+main(opt$clean_path, opt$model_path)