initial commit

_bookdown.yml

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+book_filename: "AFTS"
+chapter_name: "Chapter "
+rmd_files: 
+  - "index.Rmd"
+  - "Lab-basic-matrix/basic-matrix-math-content.Rmd"
+  - "Lab-linear-regression/linear-regression-models-matrix-content.Rmd"
+  - "Lab-intro-to-ts/intro-ts-funcs-content.Rmd"
+  - "Lab-fitting-uni-ss-models/fitting-univariate-state-space-content.Rmd"
+  - "Lab-fitting-multi-ss-models/multivariate-ss-content.Rmd"
+  - "Lab-fitting-DLMs/DLM-content.Rmd"
+  - "Lab-dynamic-factor-analysis/intro-to-dfa.Rmd"
+  - "Lab-intro-to-jags/intro-to-jags-content.Rmd"
+  - "Lab-intro-to-stan/fitting-models-with-stan.Rmd"
+output_dir: "docs"

_output.yml

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+bookdown::gitbook:
+  css: style.css
+  split_by: section
+  config:
+    toc: 
+      collapse: section
+      before: |
+        <li><a href="./">AFTS</a></li>
+      after: |
+        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
+bookdown::pdf_book:
+  includes:
+    in_header: tex/preamble.tex
+  latex_engine: xelatex
+  citation_package: natbib
+  toc_depth: 2
+  toc_unnumbered: no
+bookdown::epub_book:
+  stylesheet: style.css

convertRnws.R

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+#run translations
+source("rnw_to_rmd.R")
+basefile="Lab-basic-matrix/basic-matrix-math-content"
+rnw.to.rmd(basefile,"basicmat")
+#replace.defs("tex/defs.tex", paste(basefile,".Rmd",sep=""))
+
+source("rnw_to_rmd.R")
+basefile="Lab-linear-regression/linear-regression-models-matrix-content"
+rnw.to.rmd(basefile,"mlr")
+#replace.defs("tex/defs.tex", paste(basefile,".Rmd",sep=""))
+
+source("rnw_to_rmd.R")
+basefile="Lab-intro-to-ts/intro-ts-funcs-content"
+rnw.to.rmd(basefile,"ts")
+#replace.defs("tex/defs.tex", paste(basefile,".Rmd",sep=""))
+
+source("rnw_to_rmd.R")
+basefile="Lab-intro-to-jags/intro-to-jags-content"
+rnw.to.rmd(basefile,"jags")
+#replace.defs("tex/defs.tex", paste(basefile,".Rmd",sep=""))
+
+source("rnw_to_rmd.R")
+basefile="Lab-fitting-uni-ss-models/fitting-univariate-state-space-content"
+rnw.to.rmd(basefile,"uss")
+#replace.defs("tex/defs.tex", paste(basefile,".Rmd",sep=""))
+
+source("rnw_to_rmd.R")
+basefile="Lab-fitting-multi-ss-models/multivariate-ss-content"
+rnw.to.rmd(basefile,"mss")
+#replace.defs("tex/defs.tex", paste(basefile,".Rmd",sep=""))
+
+source("rnw_to_rmd.R")
+basefile="Lab-fitting-DLMs/DLM-content"
+rnw.to.rmd(basefile,"dlm")
+#replace.defs("tex/defs.tex", paste(basefile,".Rmd",sep=""))
+
+
+# source("rnw_to_rmd.R")
+# basefile="test"
+# rnw.to.rmd(basefile)

read-this-before-writing-rmarkdown.txt

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+Label all your chunks uniquely and don't use "." or ":" in your chunk names. "-" is ok.
+So foo-foo and foo:foo are ok and foo.foo is not
+
+all chapter, section and subsection labels need to be on same line as \chapter or \section or next line
+This ->
+\chapter{Number 1} \label{chap:number1}
+Or ->
+\chapter{Number 1}
+\label{chap:number1}
+
+If you put the label after \chapter or \section, then label should be by itself on a line. So don't do this ->
+\label{chap:number1} And now I start my chapter. Yada, yada.
+
+Chapter labels should be of the form with the "chap:" prefix
+chap:foo
+Section and subsection labels should be of the form with the "sec:" prefix
+sec:foo
+
+Why? Because rmarkdown uses different ref formats for sections and I need to know what kind of \label this is.
+
+all equations that will be numbered need a label
+
+\verb@foo@ will put foo in r code so will be shaded
+\texttt{foo} will make foo as courier font
+
+If you make a plot, but don't want it plotted, use fig=FALSE even if you have eval=FALSE
+
+cross-refs for figures are automatically generated from the chunk label.  If chunk is foo, then ref is fig:foo.
+example:
+\begin{figure}[htp]
+\begin{center}
+<<foo, fig=TRUE>>=
+plot(1,1)
+@
+\end{center}
+\caption{Correlogram of the observed atmospheric CO$_2$ concentration at Mauna Loa, Hawai'i obtained with the function \texttt{plot.acf}.}
+\end{figure}
+
+This is Figure \ref{fig:foo}.
+
+chunk labels should have either of the two formats
+<<foo, #no space between <<, label, and ","
+or
+<<label=foo, #no space between <<label=, label, and ","
+
+
+If you want to cross-reference figures or tables generated from a code chunk, please make sure the chunk label only contains alphanumeric characters (a-z, A-Z, 0-9), slashes (/), or dashes (-). 

references.Rmd

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+
+`r if (knitr:::is_html_output()) '# References {-}'`