fminsearch: Organized User Manual files

86 files changed, 10579 insertions, 13183 deletions

diff --git a/scilab_doc/neldermead/fminsearch-so.pdf b/scilab_doc/neldermead/fminsearch-so.pdf
index 9b0df46..f966125 100644
--- a/scilab_doc/neldermead/fminsearch-so.pdf
+++ b/scilab_doc/neldermead/fminsearch-so.pdf
diff --git a/scilab_doc/neldermead/fminsearch-so.tex b/scilab_doc/neldermead/fminsearch-so.tex
index e364aa9..708c090 100644
--- a/scilab_doc/neldermead/fminsearch-so.tex
+++ b/scilab_doc/neldermead/fminsearch-so.tex
@@ -69,7 +69,7 @@ September 2009
 
 \tableofcontents
 
-\include{fminsearch}
+\include{fminsearch/fminsearch}
 
 \clearpage
 
@@ -80,6 +80,7 @@ September 2009
 \bibliography{neldermead}
 
 % Index
+\addcontentsline{toc}{chapter}{Index}
 \printindex
 
 \end{document}
diff --git a/scilab_doc/neldermead/fminsearch.tex b/scilab_doc/neldermead/fminsearch/fminsearch.tex
index c5960f2..c0d954a 100644
--- a/scilab_doc/neldermead/fminsearch.tex
+++ b/scilab_doc/neldermead/fminsearch/fminsearch.tex
@@ -1,4 +1,5 @@
 \chapter{The \scifunction{fminsearch} function}
+\index{fminsearch}
 
 In this chapter, we analyze the implementation of the \scifunction{fminsearch}
 which is provided in Scilab. In the first part, we describe the specific 
@@ -23,6 +24,7 @@ accepted only if it improves over the reflection point.
 
 \subsection{The initial simplex}
 \index{Pfeffer, L.}
+\index{Fan, Ellen}
 
 The fminsearch algorithm uses a special initial simplex, which is an 
 heuristic depending on the initial guess. The strategy chosen by 
@@ -327,6 +329,8 @@ that is, produces the same intermediate steps.
 The following Matlab script allows to get deeper information by printing a message at each iteration
 with the "Display" option.
 
+\index{optimset}
+
 \lstset{language=matlabscript}
 \begin{lstlisting}
 % Matlab
@@ -434,6 +438,7 @@ Optimization terminated:
 
 The following Scilab script set the "Display" option to "iter" and 
 run the \scifunction{fminsearch} function.
+\index{optimset}
 
 \lstset{language=scilabscript}
 \begin{lstlisting}
@@ -577,6 +582,7 @@ drawnow
 
 The following Matlab script allows to perform the optimization
 so that the output function is called back at each iteration.
+\index{optimset}
 
 \lstset{language=matlabscript}
 \begin{lstlisting}
@@ -589,7 +595,7 @@ This produces the plot which is presented in figure \ref{fig-fminsearch-matlab-o
 
 \begin{figure}
 \begin{center}
-\includegraphics[width=10cm]{testFminsearchPlotMatlab.png}
+\includegraphics[width=10cm]{fminsearch/testFminsearchPlotMatlab.png}
 \end{center}
 \caption{Plot produced by Matlab's fminsearch, with customized output function.}
 \label{fig-fminsearch-matlab-outputfun}
@@ -620,6 +626,7 @@ Matlab also prints the following messages in the console.
 
 The following Scilab script sets the "OutputFcn" option and then calls 
 the \scifunction{fminsearch} in order to perform the optimization.
+\index{optimset}
 
 \lstset{language=scilabscript}
 \begin{lstlisting}
@@ -641,7 +648,7 @@ in figure \ref{fig-fminsearch-scilab-outputfun}.
 
 \begin{figure}
 \begin{center}
-\includegraphics[width=10cm]{testFminsearchPlotScilab.png}
+\includegraphics[width=10cm]{fminsearch/testFminsearchPlotScilab.png}
 \end{center}
 \caption{Plot produced by Scilab's fminsearch, with customized output function.}
 \label{fig-fminsearch-scilab-outputfun}
@@ -682,6 +689,10 @@ displays the type of the last performed step.
 
 \subsection{Predefined plot functions}
 
+\index{optimplotfval}
+\index{optimplotx}
+\index{optimplotfunccount}
+
 Several pre-defined plot functions are provided with 
 the \scifunction{fminsearch} function.
 These functions are 
@@ -693,6 +704,7 @@ These functions are
 
 In the following Matlab script, we use the \scifunction{optimplotfval}
 pre-defined function.
+\index{optimset}
 
 \lstset{language=matlabscript}
 \begin{lstlisting}
@@ -706,7 +718,7 @@ The previous script produces the plot which is presented in figure
 
 \begin{figure}
 \begin{center}
-\includegraphics[width=10cm]{testFminsearchOptimplotfvalMatlab.png}
+\includegraphics[width=10cm]{fminsearch/testFminsearchOptimplotfvalMatlab.png}
 \end{center}
 \caption{Plot produced by Matlab's fminsearch, with the \scifunction{optimplotfval} function.}
 \label{fig-fminsearch-matlab-optimplotfval}
@@ -714,6 +726,7 @@ The previous script produces the plot which is presented in figure
 
 The following Scilab script uses the \scifunction{optimplotfval}
 pre-defined function.
+\index{optimset}
 
 \lstset{language=scilabscript}
 \begin{lstlisting}
@@ -727,7 +740,7 @@ The previous script produces the plot which is presented in figure
 
 \begin{figure}
 \begin{center}
-\includegraphics[width=10cm]{testFminsearchOptimplotfvalScilab.png}
+\includegraphics[width=10cm]{fminsearch/testFminsearchOptimplotfvalScilab.png}
 \end{center}
 \caption{Plot produced by Scilab's fminsearch, with the \scifunction{optimplotfval} function.}
 \label{fig-fminsearch-scilab-optimplotfval}
@@ -744,7 +757,7 @@ functions.
 
 \begin{figure}
 \begin{center}
-\includegraphics[width=10cm]{testFminsearchOptimplotxScilab.png}
+\includegraphics[width=10cm]{fminsearch/testFminsearchOptimplotxScilab.png}
 \end{center}
 \caption{Plot produced by Scilab's fminsearch, with the \scifunction{optimplotx} function.}
 \label{fig-fminsearch-scilab-optimplotx}
@@ -752,7 +765,7 @@ functions.
 
 \begin{figure}
 \begin{center}
-\includegraphics[width=10cm]{testFminsearchOptimplotfunccountScilab.png}
+\includegraphics[width=10cm]{fminsearch/testFminsearchOptimplotfunccountScilab.png}
 \end{center}
 \caption{Plot produced by Scilab's fminsearch, with the \scifunction{optimplotfunccount} function.}
 \label{fig-fminsearch-scilab-optimplotfunccount}
diff --git a/scilab_doc/neldermead/testFminsearchOptimplotfunccountScilab.png b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotfunccountScilab.png
index 28ca428..28ca428 100644
--- a/scilab_doc/neldermead/testFminsearchOptimplotfunccountScilab.png
+++ b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotfunccountScilab.png
diff --git a/scilab_doc/neldermead/testFminsearchOptimplotfvalMatlab.png b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotfvalMatlab.png
index 8e50630..8e50630 100644
--- a/scilab_doc/neldermead/testFminsearchOptimplotfvalMatlab.png
+++ b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotfvalMatlab.png
diff --git a/scilab_doc/neldermead/testFminsearchOptimplotfvalScilab.png b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotfvalScilab.png
index 8651bdb..8651bdb 100644
--- a/scilab_doc/neldermead/testFminsearchOptimplotfvalScilab.png
+++ b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotfvalScilab.png
diff --git a/scilab_doc/neldermead/testFminsearchOptimplotxMatlab.png b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotxMatlab.png
index 9ef102a..9ef102a 100644
--- a/scilab_doc/neldermead/testFminsearchOptimplotxMatlab.png
+++ b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotxMatlab.png
diff --git a/scilab_doc/neldermead/testFminsearchOptimplotxScilab.png b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotxScilab.png
index 7697c0e..7697c0e 100644
--- a/scilab_doc/neldermead/testFminsearchOptimplotxScilab.png
+++ b/scilab_doc/neldermead/fminsearch/testFminsearchOptimplotxScilab.png
diff --git a/scilab_doc/neldermead/testFminsearchPlotMatlab.png b/scilab_doc/neldermead/fminsearch/testFminsearchPlotMatlab.png
index 09e3476..09e3476 100644
--- a/scilab_doc/neldermead/testFminsearchPlotMatlab.png
+++ b/scilab_doc/neldermead/fminsearch/testFminsearchPlotMatlab.png
diff --git a/scilab_doc/neldermead/testFminsearchPlotScilab.png b/scilab_doc/neldermead/fminsearch/testFminsearchPlotScilab.png
index 5408533..5408533 100644
--- a/scilab_doc/neldermead/testFminsearchPlotScilab.png
+++ b/scilab_doc/neldermead/fminsearch/testFminsearchPlotScilab.png
diff --git a/scilab_doc/neldermead/introduction-demos.png b/scilab_doc/neldermead/introduction/introduction-demos.png
index 2cd8327..2cd8327 100644
--- a/scilab_doc/neldermead/introduction-demos.png
+++ b/scilab_doc/neldermead/introduction/introduction-demos.png
diff --git a/scilab_doc/neldermead/introduction-help-fminsearch.png b/scilab_doc/neldermead/introduction/introduction-help-fminsearch.png
index 58fe455..58fe455 100644
--- a/scilab_doc/neldermead/introduction-help-fminsearch.png
+++ b/scilab_doc/neldermead/introduction/introduction-help-fminsearch.png
diff --git a/scilab_doc/neldermead/introduction-help.png b/scilab_doc/neldermead/introduction/introduction-help.png
index 2740b7b..2740b7b 100644
--- a/scilab_doc/neldermead/introduction-help.png
+++ b/scilab_doc/neldermead/introduction/introduction-help.png
diff --git a/scilab_doc/neldermead/introduction.tex b/scilab_doc/neldermead/introduction/introduction.tex
index 35677c0..d8d2647 100644
--- a/scilab_doc/neldermead/introduction.tex
+++ b/scilab_doc/neldermead/introduction/introduction.tex
@@ -7,6 +7,8 @@ show how to use the component with a simple example.
 \section{Overview}
 \index{Torczon, Virginia}
 \index{Wright, Margaret}
+\index{Nelder, John}
+\index{Mead, Roger}
 
 The Nelder-Mead simplex algorithm \cite{citeulike:3009487}, published in 1965, is an enormously 
 popular search method for multidimensional unconstrained optimization. 
@@ -31,6 +33,11 @@ function values. The algorithm attemps to replace the worst vertex with
 a new point, which depends on the worst point and the centre of the best 
 vertices. 
 
+\index{Spendley, W.}
+\index{Hext, G. R.}
+\index{Himsworth, F. R.}
+\index{Box, M. J.}
+
 The goal of this toolbox is to provide a Nelder-Mead (1965) direct search optimization method to solve the 
 following unconstrained optimization problem
 \begin{eqnarray}
@@ -39,7 +46,7 @@ following unconstrained optimization problem
 where $\bx\in \RR^n$, $n$ is the number of optimization parameters and $f$ is the objective 
 function $f:\RR^n\rightarrow \RR$.
 In order to solve the unconstrained optimization problem, the Nelder-Mead 
-algorithm uses a variable shape simplex. The toolbox also provide Spendley's et al. 
+algorithm uses a variable shape simplex. The toolbox also provide Spendley, Hext and Himsworth's  
 algorithm \cite{Spendley1962} (1962), which uses a fixed shape simplex. Historically, the algorithm created  
 by Nelder and Mead was designed as an improvement on Spendley's et al. algorithm.
 The Box complex algorithm \cite{Box1965} (1965), which is an extension of Spendley's  et al. algorithm, solves the 
@@ -281,7 +288,7 @@ corresponding functions, as well as many sample uses.
 
 \begin{figure}
 \begin{center}
-\includegraphics[width=15cm]{introduction-help.png}
+\includegraphics[width=15cm]{introduction/introduction-help.png}
 \end{center}
 \caption{Built-in help for the Nelder-Mead component}
 \label{fig-intro-help}
@@ -289,7 +296,7 @@ corresponding functions, as well as many sample uses.
 
 \begin{figure}
 \begin{center}
-\includegraphics[width=15cm]{introduction-help-fminsearch.png}
+\includegraphics[width=15cm]{introduction/introduction-help-fminsearch.png}
 \end{center}
 \caption{Built-in help for the \scifunction{fminsearch} function}
 \label{fig-intro-helpfminsearch}
@@ -301,7 +308,7 @@ and are presented in figure \ref{fig-intro-demos}.
 
 \begin{figure}
 \begin{center}
-\includegraphics[width=10cm]{introduction-demos.png}
+\includegraphics[width=10cm]{introduction/introduction-demos.png}
 \end{center}
 \caption{Built-in demonstration scripts for the Nelder-Mead component}
 \label{fig-intro-demos}
diff --git a/scilab_doc/neldermead/neldermead-introduction-so.pdf b/scilab_doc/neldermead/neldermead-introduction-so.pdf
index 16beed5..0e381d9 100644
--- a/scilab_doc/neldermead/neldermead-introduction-so.pdf
+++ b/scilab_doc/neldermead/neldermead-introduction-so.pdf
diff --git a/scilab_doc/neldermead/neldermead-introduction-so.tex b/scilab_doc/neldermead/neldermead-introduction-so.tex
index 6a05c35..e52c572 100644
--- a/scilab_doc/neldermead/neldermead-introduction-so.tex
+++ b/scilab_doc/neldermead/neldermead-introduction-so.tex
@@ -70,7 +70,7 @@ Micha\"el BAUDIN
 
 \renewcommand{\baselinestretch}{1.18}\small \normalsize
 
-\include{introduction}
+\include{introduction/introduction}
 
 \clearpage
 
@@ -81,5 +81,8 @@ Micha\"el BAUDIN
 \bibliographystyle{plain}
 \bibliography{neldermead}
 
+\addcontentsline{toc}{chapter}{Index}
+\printindex
+
 \end{document}
 
diff --git a/scilab_doc/neldermead/neldermead-neldermead-so.blg b/scilab_doc/neldermead/neldermead-neldermead-so.blg
deleted file mode 100644
index 57c6cd3..0000000
--- a/scilab_doc/neldermead/neldermead-neldermead-so.blg
+++ /dev/null
@@ -1,5 +0,0 @@
-This is BibTeX, Version 0.99cThe top-level auxiliary file: neldermead-neldermead-so.aux
-A level-1 auxiliary file: chapter-notations.aux
-A level-1 auxiliary file: method-neldermead.aux
-The style file: plain.bst
-Database file #1: neldermead.bib
diff --git a/scilab_doc/neldermead/neldermead-neldermead-so.pdf b/scilab_doc/neldermead/neldermead-neldermead-so.pdf
index b41a233..b22c0b6 100644
--- a/scilab_doc/neldermead/neldermead-neldermead-so.pdf
+++ b/scilab_doc/neldermead/neldermead-neldermead-so.pdf
diff --git a/scilab_doc/neldermead/neldermead-neldermead-so.tex b/scilab_doc/neldermead/neldermead-neldermead-so.tex
index a18a319..64b0fc0 100644
--- a/scilab_doc/neldermead/neldermead-neldermead-so.tex
+++ b/scilab_doc/neldermead/neldermead-neldermead-so.tex
@@ -80,7 +80,7 @@ September 2009
 \renewcommand{\baselinestretch}{1.18}\small \normalsize
 
 \include{chapter-notations}
-\include{method-neldermead}
+\include{neldermeadmethod/method-neldermead}
 
 \clearpage
 
@@ -92,6 +92,7 @@ September 2009
 \bibliography{neldermead}
 
 % Index
+\addcontentsline{toc}{chapter}{Index}
 \printindex
 
 \end{document}
diff --git a/scilab_doc/neldermead/neldermead-neldermead-so.toc b/scilab_doc/neldermead/neldermead-neldermead-so.toc
deleted file mode 100644
index 493f697..0000000
--- a/scilab_doc/neldermead/neldermead-neldermead-so.toc
+++ /dev/null
@@ -1,21 +0,0 @@
-\contentsline {chapter}{\numberline {1}Nelder-Mead method}{4}{chapter.1}
-\contentsline {section}{\numberline {1.1}Introduction}{4}{section.1.1}
-\contentsline {subsection}{\numberline {1.1.1}Overview}{4}{subsection.1.1.1}
-\contentsline {subsection}{\numberline {1.1.2}Algorithm}{5}{subsection.1.1.2}
-\contentsline {section}{\numberline {1.2}Geometric analysis}{9}{section.1.2}
-\contentsline {section}{\numberline {1.3}Convergence properties on a quadratic}{9}{section.1.3}
-\contentsline {subsection}{\numberline {1.3.1}With default parameters}{13}{subsection.1.3.1}
-\contentsline {subsection}{\numberline {1.3.2}With variable parameters}{17}{subsection.1.3.2}
-\contentsline {section}{\numberline {1.4}Numerical experiments}{20}{section.1.4}
-\contentsline {subsection}{\numberline {1.4.1}Quadratic function}{21}{subsection.1.4.1}
-\contentsline {subsubsection}{Badly scaled quadratic function}{22}{section*.3}
-\contentsline {subsection}{\numberline {1.4.2}Sensitivity to dimension}{24}{subsection.1.4.2}
-\contentsline {subsection}{\numberline {1.4.3}O'Neill test cases}{27}{subsection.1.4.3}
-\contentsline {subsection}{\numberline {1.4.4}Convergence to a non stationnary point}{32}{subsection.1.4.4}
-\contentsline {subsection}{\numberline {1.4.5}Han counter examples}{36}{subsection.1.4.5}
-\contentsline {subsubsection}{First counter example}{36}{section*.4}
-\contentsline {subsubsection}{Second counter example}{36}{section*.5}
-\contentsline {subsection}{\numberline {1.4.6}Torczon's numerical experiments}{37}{subsection.1.4.6}
-\contentsline {subsubsection}{Penalty \#1}{38}{section*.6}
-\contentsline {section}{\numberline {1.5}Conclusion}{40}{section.1.5}
-\contentsline {chapter}{Bibliography}{41}{section.1.5}
diff --git a/scilab_doc/neldermead/neldermead-simplex-so.pdf b/scilab_doc/neldermead/neldermead-simplex-so.pdf
index 607a426..fa13c27 100644
--- a/scilab_doc/neldermead/neldermead-simplex-so.pdf
+++ b/scilab_doc/neldermead/neldermead-simplex-so.pdf
diff --git a/scilab_doc/neldermead/neldermead-simplex-so.tex b/scilab_doc/neldermead/neldermead-simplex-so.tex
index 8251de3..78cb2f4 100644
--- a/scilab_doc/neldermead/neldermead-simplex-so.tex
+++ b/scilab_doc/neldermead/neldermead-simplex-so.tex
@@ -72,7 +72,7 @@ Micha\"el BAUDIN
 
 
 \include{chapter-notations}
-\include{section-simplex}
+\include{simplextheory/section-simplex}
 
 
 \clearpage
@@ -87,6 +87,7 @@ Micha\"el BAUDIN
 \bibliography{neldermead}
 
 % Index
+\addcontentsline{toc}{chapter}{Index}
 \printindex
 
 \end{document}
diff --git a/scilab_doc/neldermead/neldermead-spendley-so.pdf b/scilab_doc/neldermead/neldermead-spendley-so.pdf
index 01e42c8..7bb1f5b 100644
--- a/scilab_doc/neldermead/neldermead-spendley-so.pdf
+++ b/scilab_doc/neldermead/neldermead-spendley-so.pdf
diff --git a/scilab_doc/neldermead/neldermead-spendley-so.tex b/scilab_doc/neldermead/neldermead-spendley-so.tex
index a0c8fa7..3b9bcd0 100644
--- a/scilab_doc/neldermead/neldermead-spendley-so.tex
+++ b/scilab_doc/neldermead/neldermead-spendley-so.tex
@@ -71,7 +71,7 @@ Micha\"el BAUDIN
 \renewcommand{\baselinestretch}{1.18}\small \normalsize
 
 \include{chapter-notations}
-\include{method-spendley}
+\include{spendleymethod/method-spendley}
 
 \clearpage
 
@@ -83,6 +83,7 @@ Micha\"el BAUDIN
 \bibliography{neldermead}
 
 % Index
+\addcontentsline{toc}{chapter}{Index}
 \printindex
 
 \end{document}
diff --git a/scilab_doc/neldermead/neldermead.pdf b/scilab_doc/neldermead/neldermead.pdf
index f2b075a..1af1c93 100644
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