doc working

Author: mdsumner

.Rbuildignore

@@ -0,0 +1 @@
+^README\.Rmd$

README.Rmd

@@ -0,0 +1,41 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+# chapter2
+
+The goal of chapter2 is to resurrect and modernize the material of my thesis [chapter 2, The Tag Location Problem](https://eprints.utas.edu.au/12273/3/sumner.pdf). 
+
+This will accompany the [trip package](https://github.com/Trackage/trip). 
+
+See "chapter2.pdf". 
+
+
+
+## Build
+
+Working on Linux, couldn't get it on Windows. 
+
+
+```{r eval=FALSE}
+knitr::knit("chapter2.Rnw")
+tinytex::latexmk("chapter2.tex")
+```
+
+
+## Note
+
+* some hardcoded figures "figures/gunnArchival.png" and the KDE ones were copied from
+artefacts
+* no citations work, I can't find my bib file yet and `\citep` has been redefined in newcom.tex
+
+
+

README.md

@@ -0,0 +1,29 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# chapter2
+
+The goal of chapter2 is to resurrect and modernize the material of my
+thesis [chapter 2, The Tag Location
+Problem](https://eprints.utas.edu.au/12273/3/sumner.pdf).
+
+This will accompany the [trip
+package](https://github.com/Trackage/trip).
+
+See “chapter2.pdf”.
+
+## Build
+
+Working on Linux, couldn’t get it on Windows.
+
+``` r
+knitr::knit("chapter2.Rnw")
+tinytex::latexmk("chapter2.tex")
+```
+
+## Note
+
+  - some hardcoded figures “figures/gunnArchival.png” and the KDE ones
+    were copied from artefacts
+  - no citations work, I can’t find my bib file yet and `\citep` has
+    been redefined in newcom.tex

chapter2.Rnw

@@ -15,6 +15,7 @@
 \hypersetup{
  pdfstartview={XYZ null null 1}}
 \usepackage{breakurl}
+\include{newcom}
 \begin{document}
 
 <<setup, include=FALSE, cache=FALSE>>=
@@ -29,8 +30,6 @@ options(formatR.arrow=TRUE,width=90)
 \author{Michael D. Sumner}
 \maketitle
 
-\end document
-
 
 This chapter discusses problems faced with tracking data that concern
 the estimation of location and provides a flexible software
@@ -3141,7 +3140,7 @@ of track visualizations and other summaries.
 
 \begin{figure}[!ht]
   \begin{center}
- \includegraphics[width=120mm]{roughfigures/gunnArchival.png}
+ \includegraphics[width=120mm]{figures/gunnArchival.png}
   \end{center}
   \caption{ Light level geo-locations for black marlin in the Coral
     Sea. This image is taken from Figure~3a in \cite{Gunn:GEOL} and is

chapter2.log

@@ -65,6 +65,7 @@
 \hypersetup{
  pdfstartview={XYZ null null 1}}
 \usepackage{breakurl}
+\include{newcom}
 \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
 \begin{document}
 
@@ -75,7 +76,7 @@
 \author{Michael D. Sumner}
 \maketitle
 
-\end document
+
 This chapter discusses problems faced with tracking data that concern
 the estimation of location and provides a flexible software
 environment for exploring data and applying solutions. Examples are
@@ -2537,12 +2538,12 @@ \subsection{Filtering for unlikely movement}
 ## Number of points: 351
 ## Data attributes:
 ##    seal            date          local          gmt                      lq      class  
-##  c026:351   27-Jan-99: 10   14:42:21:  2   Min.   :1999-01-01 11:35:59   0: 38   Z:  0  
-##             17-Jan-99:  8   15:29:50:  2   1st Qu.:1999-01-30 01:28:14   1: 10   B:214  
-##             14-Mar-99:  7   0:04:01 :  1   Median :1999-02-26 12:22:56   2:  8   A: 80  
-##             15-Mar-99:  7   0:04:05 :  1   Mean   :1999-03-02 04:53:25   3:  1   0: 38  
-##             28-Jan-99:  7   0:10:34 :  1   3rd Qu.:1999-03-27 01:44:51   A: 80   1: 10  
-##             6-Feb-99 :  7   0:16:15 :  1   Max.   :1999-05-22 01:29:17   B:214   2:  8  
+##  c026:351   27-Jan-99: 10   14:42:21:  2   Min.   :1999-01-01 00:35:59   0: 38   Z:  0  
+##             17-Jan-99:  8   15:29:50:  2   1st Qu.:1999-01-29 14:28:14   1: 10   B:214  
+##             14-Mar-99:  7   0:04:01 :  1   Median :1999-02-26 01:22:56   2:  8   A: 80  
+##             15-Mar-99:  7   0:04:05 :  1   Mean   :1999-03-01 17:53:25   3:  1   0: 38  
+##             28-Jan-99:  7   0:10:34 :  1   3rd Qu.:1999-03-26 14:44:51   A: 80   1: 10  
+##             6-Feb-99 :  7   0:16:15 :  1   Max.   :1999-05-21 15:29:17   B:214   2:  8  
 ##             (Other)  :305   (Other) :343                                         3:  1  
 ##      ok         
 ##  Mode :logical  
@@ -3206,7 +3207,7 @@ \subsection{Location estimation from raw archival data}
 
 \begin{figure}[!ht]
   \begin{center}
- \includegraphics[width=120mm]{roughfigures/gunnArchival.png}
+ \includegraphics[width=120mm]{figures/gunnArchival.png}
   \end{center}
   \caption{ Light level geo-locations for black marlin in the Coral
     Sea. This image is taken from Figure~3a in \cite{Gunn:GEOL} and is

chapter2.pdf

@@ -0,0 +1,23 @@
+\relax 
+\providecommand\hyper@newdestlabel[2]{}
+\@setckpt{newcom}{
+\setcounter{page}{1}
+\setcounter{equation}{0}
+\setcounter{enumi}{0}
+\setcounter{enumii}{0}
+\setcounter{enumiii}{0}
+\setcounter{enumiv}{0}
+\setcounter{footnote}{0}
+\setcounter{mpfootnote}{0}
+\setcounter{part}{0}
+\setcounter{section}{0}
+\setcounter{subsection}{0}
+\setcounter{subsubsection}{0}
+\setcounter{paragraph}{0}
+\setcounter{subparagraph}{0}
+\setcounter{figure}{0}
+\setcounter{table}{0}
+\setcounter{Item}{0}
+\setcounter{Hfootnote}{0}
+\setcounter{bookmark@seq@number}{0}
+}

chapter2.tex

@@ -0,0 +1,13 @@
+% newcom.tex (new command definitions)
+
+% Some examples (yours may be different):
+%\newtheorem{theorem}{Theorem}[section]
+%\newtheorem{lemma}[theorem]{Lemma}
+%\newcommand{\bfx}{{\ensuremath{\mathbf{x}}}}
+
+
+\newcommand{\R}{R}
+\newcommand{\pkg}[1]{{\fontseries{b}\selectfont #1}}
+\newcommand{\proglang}[1]{\textsf{#1}}
+
+\newcommand{\citep}[1]{{\fontseries{b}\selectfont #1}}