diff --git a/configure.ac b/configure.ac
index 6cb694aa45bffa5c09dda7596846154f090fa178..9a5d3e56c77e63ba9399693c0e2d75cc0e67dcb7 100644
--- a/configure.ac
+++ b/configure.ac
@@ -174,6 +174,7 @@ AC_CONFIG_FILES([Makefile
doc/userguide/Makefile
doc/parallel/Makefile
doc/internals/Makefile
+ doc/gsa/Makefile
tests/Makefile
matlab/dynare_version.m
windows/dynare-version.nsi
diff --git a/doc/Makefile.am b/doc/Makefile.am
index cd1b4dfae18692120aabf8dc1edb6eb99e9b6747..70bec7dc8054610e62760e7bd18bdc1ccd1ab12f 100644
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -1,4 +1,4 @@
-SUBDIRS = preprocessor macroprocessor userguide parallel internals
+SUBDIRS = preprocessor macroprocessor userguide parallel internals gsa
PDF_TARGETS =
diff --git a/doc/gsa/Makefile.am b/doc/gsa/Makefile.am
new file mode 100644
index 0000000000000000000000000000000000000000..5e99bf96f37b08878f801588446e7cedd8f55f24
--- /dev/null
+++ b/doc/gsa/Makefile.am
@@ -0,0 +1,18 @@
+if HAVE_PDFLATEX
+if HAVE_BIBTEX
+pdf-local: gsa.pdf
+endif
+endif
+
+SRC = gsa.tex marco.bib
+
+EXTRA_DIST = $(SRC)
+
+gsa.pdf: $(SRC)
+ $(PDFLATEX) gsa
+ $(BIBTEX) gsa
+ $(PDFLATEX) gsa
+ $(PDFLATEX) gsa
+
+clean-local:
+ rm -f *.pdf *.log *.aux *.toc *.lof *.blg *.bbl *.out *~
diff --git a/doc/gsa/dyn_tbx.aux b/doc/gsa/dyn_tbx.aux
deleted file mode 100644
index 50cec3f0ae933f015179f3850b77d1bded803c1e..0000000000000000000000000000000000000000
--- a/doc/gsa/dyn_tbx.aux
+++ /dev/null
@@ -1,24 +0,0 @@
-\relax
-\citation{Ratto_CompEcon_2008}
-\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{2}}
-\newlabel{s:intro}{{1}{2}}
-\@writefile{toc}{\contentsline {section}{\numberline {2}Use of the Toolbox}{2}}
-\@writefile{toc}{\contentsline {section}{\numberline {3}List of options}{3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Sampling options}{3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Stability mapping}{3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.3}Reduced form mapping}{4}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.4}Mapping the fit}{5}}
-\citation{Iskrev2009}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.5}Screening analysis}{6}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.6}Identification analysis (under development)}{6}}
-\citation{Iskrev2009}
-\@writefile{toc}{\contentsline {section}{\numberline {4}Directory structure}{8}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Binary data files}{8}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Stability analysis}{8}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.3}RMSE analysis}{9}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.4}Reduced form mapping}{10}}
-\bibstyle{plainnat}
-\bibdata{marco}
-\bibcite{Iskrev2009}{{1}{2009}{{Iskrev}}{{}}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.5}Screening analysis}{11}}
-\bibcite{Ratto_CompEcon_2008}{{2}{2008}{{Ratto}}{{}}}
diff --git a/doc/gsa/dyn_tbx.bbl b/doc/gsa/dyn_tbx.bbl
deleted file mode 100644
index 74d2e6a2c118d17a05dea5313c56a190b5365499..0000000000000000000000000000000000000000
--- a/doc/gsa/dyn_tbx.bbl
+++ /dev/null
@@ -1,18 +0,0 @@
-\begin{thebibliography}{2}
-\providecommand{\natexlab}[1]{#1}
-\providecommand{\url}[1]{\texttt{#1}}
-\expandafter\ifx\csname urlstyle\endcsname\relax
- \providecommand{\doi}[1]{doi: #1}\else
- \providecommand{\doi}{doi: \begingroup \urlstyle{rm}\Url}\fi
-
-\bibitem[Iskrev(2009)]{Iskrev2009}
-Nikolay Iskrev.
-\newblock Local identification in \textsc{DSGE} models.
-\newblock mimeo, 2009.
-
-\bibitem[Ratto(2008)]{Ratto_CompEcon_2008}
-M.~Ratto.
-\newblock Analysing dsge models with global sensitivity analysis.
-\newblock \emph{Computational Economics}, 31:\penalty0 115--139, 2008.
-
-\end{thebibliography}
diff --git a/doc/gsa/dyn_tbx.blg b/doc/gsa/dyn_tbx.blg
deleted file mode 100644
index 49545423c27b613573a5331f1ada0783ea2d81e8..0000000000000000000000000000000000000000
--- a/doc/gsa/dyn_tbx.blg
+++ /dev/null
@@ -1,30 +0,0 @@
-This is BibTeX, Version 0.99cThe top-level auxiliary file: dyn_tbx.aux
-The style file: plainnat.bst
-Database file #1: marco.bib
-I was expecting a `,' or a `}'---line 921 of file marco.bib
- :
- : pages = {},
-(Error may have been on previous line)
-I'm skipping whatever remains of this entry
-I was expecting a `,' or a `}'---line 1177 of file marco.bib
- :
- : organisation = {Los Alamos National Laboratories}
-(Error may have been on previous line)
-I'm skipping whatever remains of this entry
-I was expecting a `,' or a `}'---line 1364 of file marco.bib
- :
- : organisation = {}
-(Error may have been on previous line)
-I'm skipping whatever remains of this entry
-You're missing a field name---line 2210 of file marco.bib
- :
- : %@ARTICLE{kn:NIH,
-(Error may have been on previous line)
-I'm skipping whatever remains of this entry
-You're missing a field name---line 2211 of file marco.bib
- :
- : % author = {NIH},
-(Error may have been on previous line)
-I'm skipping whatever remains of this entry
-Warning--empty institution in Iskrev2009
-(There were 5 error messages)
diff --git a/doc/gsa/dyn_tbx.dvi b/doc/gsa/dyn_tbx.dvi
deleted file mode 100644
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Binary files a/doc/gsa/dyn_tbx.dvi and /dev/null differ
diff --git a/doc/gsa/dyn_tbx.log b/doc/gsa/dyn_tbx.log
deleted file mode 100644
index 9476b8f98b9829beabad0ee0a6bead2bb04bd724..0000000000000000000000000000000000000000
--- a/doc/gsa/dyn_tbx.log
+++ /dev/null
@@ -1,284 +0,0 @@
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-%% The original source files were:
-%%
-%% psfrag.dtx (with options: `filepro')
-%%
-%% Copyright (c) 1996 Craig Barratt, Michael C. Grant, and David Carlisle.
-%% All rights reserved.
-%%
-%% This file is part of the PSfrag package.
-%%
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-cleartomark
-%%EndFont
-%%BeginFont: CMBX12
-%!PS-AdobeFont-1.1: CMBX12 1.0
-%%CreationDate: 1991 Aug 20 16:34:54
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMBX12) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Bold) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMBX12 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
-0 1 255 {1 index exch /.notdef put} for
-dup 12 /fi put
-dup 40 /parenleft put
-dup 41 /parenright put
-dup 46 /period put
-dup 49 /one put
-dup 50 /two put
-dup 51 /three put
-dup 52 /four put
-dup 53 /five put
-dup 54 /six put
-dup 66 /B put
-dup 68 /D put
-dup 69 /E put
-dup 73 /I put
-dup 76 /L put
-dup 77 /M put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 85 /U put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
-dup 108 /l put
-dup 109 /m put
-dup 110 /n put
-dup 111 /o put
-dup 112 /p put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 118 /v put
-dup 120 /x put
-dup 121 /y put
-readonly def
-/FontBBox{-53 -251 1139 750}readonly def
-currentdict end
-currentfile eexec
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-%%EndFont
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-%%CreationDate: 1991 Aug 20 16:45:46
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMTT12) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle 0 def
-/isFixedPitch true def
-end readonly def
-/FontName /CMTT12 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
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-dup 41 /parenright put
-dup 42 /asterisk put
-dup 44 /comma put
-dup 46 /period put
-dup 48 /zero put
-dup 49 /one put
-dup 50 /two put
-dup 59 /semicolon put
-dup 60 /less put
-dup 61 /equal put
-dup 62 /greater put
-dup 64 /at put
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-dup 78 /N put
-dup 82 /R put
-dup 83 /S put
-dup 89 /Y put
-dup 92 /backslash put
-dup 95 /underscore put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
-dup 106 /j put
-dup 107 /k put
-dup 108 /l put
-dup 109 /m put
-dup 110 /n put
-dup 111 /o put
-dup 112 /p put
-dup 113 /q put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 118 /v put
-dup 119 /w put
-dup 120 /x put
-dup 121 /y put
-readonly def
-/FontBBox{-1 -234 524 695}readonly def
-currentdict end
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-%%EndFont
-%%BeginFont: CMR12
-%!PS-AdobeFont-1.1: CMR12 1.0
-%%CreationDate: 1991 Aug 20 16:38:05
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.0) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMR12) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMR12 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
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-dup 6 /Sigma put
-dup 11 /ff put
-dup 12 /fi put
-dup 13 /fl put
-dup 14 /ffi put
-dup 33 /exclam put
-dup 37 /percent put
-dup 39 /quoteright put
-dup 40 /parenleft put
-dup 41 /parenright put
-dup 43 /plus put
-dup 44 /comma put
-dup 45 /hyphen put
-dup 46 /period put
-dup 48 /zero put
-dup 49 /one put
-dup 50 /two put
-dup 51 /three put
-dup 52 /four put
-dup 53 /five put
-dup 54 /six put
-dup 55 /seven put
-dup 56 /eight put
-dup 57 /nine put
-dup 58 /colon put
-dup 59 /semicolon put
-dup 61 /equal put
-dup 63 /question put
-dup 65 /A put
-dup 66 /B put
-dup 67 /C put
-dup 68 /D put
-dup 69 /E put
-dup 70 /F put
-dup 71 /G put
-dup 72 /H put
-dup 73 /I put
-dup 74 /J put
-dup 75 /K put
-dup 76 /L put
-dup 77 /M put
-dup 78 /N put
-dup 79 /O put
-dup 80 /P put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 85 /U put
-dup 86 /V put
-dup 87 /W put
-dup 89 /Y put
-dup 91 /bracketleft put
-dup 93 /bracketright put
-dup 94 /circumflex put
-dup 96 /quoteleft put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
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-dup 107 /k put
-dup 108 /l put
-dup 109 /m put
-dup 110 /n put
-dup 111 /o put
-dup 112 /p put
-dup 113 /q put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 118 /v put
-dup 119 /w put
-dup 120 /x put
-dup 121 /y put
-dup 122 /z put
-dup 123 /endash put
-readonly def
-/FontBBox{-34 -251 988 750}readonly def
-currentdict end
-currentfile eexec
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-%%EndFont
-%%BeginFont: CMR10
-%!PS-AdobeFont-1.1: CMR10 1.00B
-%%CreationDate: 1992 Feb 19 19:54:52
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
-/version (1.00B) readonly def
-/Notice (Copyright (C) 1997 American Mathematical Society. All Rights Reserved) readonly def
-/FullName (CMR10) readonly def
-/FamilyName (Computer Modern) readonly def
-/Weight (Medium) readonly def
-/ItalicAngle 0 def
-/isFixedPitch false def
-end readonly def
-/FontName /CMR10 def
-/PaintType 0 def
-/FontType 1 def
-/FontMatrix [0.001 0 0 0.001 0 0] readonly def
-/Encoding 256 array
-0 1 255 {1 index exch /.notdef put} for
-dup 12 /fi put
-dup 40 /parenleft put
-dup 41 /parenright put
-dup 44 /comma put
-dup 45 /hyphen put
-dup 46 /period put
-dup 48 /zero put
-dup 50 /two put
-dup 52 /four put
-dup 54 /six put
-dup 55 /seven put
-dup 56 /eight put
-dup 58 /colon put
-dup 65 /A put
-dup 66 /B put
-dup 67 /C put
-dup 68 /D put
-dup 69 /E put
-dup 70 /F put
-dup 71 /G put
-dup 73 /I put
-dup 74 /J put
-dup 75 /K put
-dup 76 /L put
-dup 77 /M put
-dup 78 /N put
-dup 79 /O put
-dup 80 /P put
-dup 82 /R put
-dup 83 /S put
-dup 84 /T put
-dup 89 /Y put
-dup 97 /a put
-dup 98 /b put
-dup 99 /c put
-dup 100 /d put
-dup 101 /e put
-dup 102 /f put
-dup 103 /g put
-dup 104 /h put
-dup 105 /i put
-dup 107 /k put
-dup 108 /l put
-dup 109 /m put
-dup 110 /n put
-dup 111 /o put
-dup 112 /p put
-dup 114 /r put
-dup 115 /s put
-dup 116 /t put
-dup 117 /u put
-dup 118 /v put
-dup 119 /w put
-dup 120 /x put
-dup 121 /y put
-readonly def
-/FontBBox{-251 -250 1009 969}readonly def
-currentdict end
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-%%CreationDate: 1991 Aug 20 16:38:24
-% Copyright (C) 1997 American Mathematical Society. All Rights Reserved.
-11 dict begin
-/FontInfo 7 dict dup begin
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-\begin{document}
-
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-\title{Sensitivity Analysis Toolbox for DYNARE}%
-
-\author{Marco Ratto\\
-European Commission, Joint Research Centre \\
-TP361, IPSC, via E. Fermi 1\\21020 Ispra
-(VA) Italy\\
-\texttt{marco.ratto@jrc.it}
-\thanks{The author gratefully thanks Christophe Planas, Kenneth Judd, Michel Juillard,
-Alessandro Rossi, Frank Schorfheide and the participants to the
-Courses on Global Sensitivity Analysis for Macroeconomic
-Models (Ispra, 2006-2007-2008) for interesting discussions and
-helpful suggestions.}}
-
-%%% To have the current date inserted, use \date{\today}:
-%%% To insert a footnote, add thanks in the date/title/author fields:
-\date{\today}
-%\date{\today \thanks{Authors gratefully acknowledge the
-%contribution by ... for ...}}
-\maketitle %\tableofcontents
-
-%\doublespacing
-
-%-----------------------------------------------------------------------
-\begin{abstract}
-\noindent The Sensitivity Analysis Toolbox for DYNARE is a set of
-MATLAB routines for the analysis of DSGE models with global
-sensitivity analysis. The routines are thought to be used within
-the DYNARE v4 environment.
-
-
-\begin{description}
- \item \textbf{Keywords}: Stability Mapping , Reduced form solution, DSGE models,
- Monte Carlo filtering, Global Sensitivity Analysis.
-\end{description}
-\end{abstract}
-\newpage
-% ----------------------------------------------------------------
-\section{Introduction} \label{s:intro}
-The Sensitivity Analysis Toolbox for DYNARE is a collection of
-MATLAB routines implemented to answer the following questions: (i)
-Which is the domain of structural coefficients assuring the
-stability and determinacy of a DSGE model? (ii) Which parameters
-mostly drive the fit of, e.g., GDP and which the fit of inflation?
-Is there any conflict between the optimal fit of one observed
-series versus another one? (iii) How to represent in a direct,
-albeit approximated, form the relationship between structural
-parameters and the reduced form of a rational expectations model?
-
-The discussion of the methodologies and their application is
-described in \cite{Ratto_CompEcon_2008}.
-
-
-\section{Use of the Toolbox}
-The DYNARE parser now recognizes sensitivity analysis commands.
-The syntax is based on a single command:
-\vspace{0.5cm}
-
-\verb"dynare_sensitivity(option1=<opt1_val>,option2=<opt2_val>,...)"
-
-\vspace{0.5cm} \noindent with a list of options described in the
-next section.
-
-With respect to the previous version of the toolbox, in order to
-work properly, the sensitivity analysis Toolbox \emph{no longer}
-needs that the DYNARE estimation environment is set-up.
-
-Therefore, \verb"dynare_sensitivity" is the only command to run to
-make a sensitivity analysis on a DSGE model\footnote{Of course,
-when the user needs to perform the mapping of the fit with a
-posterior sample, a Bayesian estimation has to be performed
-beforehand}.
-
-
-\section{List of options}
-
-\subsection{Sampling options}
-\begin{tabular}{r|l|l}
- % after \\ : \hline or \cline{col1-col2} \cline{col3-col4} ...
- option name & default & description \\ \hline
- \verb"Nsam"& 2048& Size of MC sample \\
- \verb"ilptau"& 1& 1 = use $LP_\tau$ quasi-Monte Carlo \\
- & & 0 = use LHS Monte Carlo \\
- \verb"pprior"& 1& 1 = sample from prior distributions\\
- & & 0 = sample from multivariate
- normal \\
- & & \hspace{0.5 cm} $N(\hat{\theta},\Sigma)$, $\hat{\theta}$ is posterior mode \\
- & & \hspace{0.5 cm} $\Sigma = H^{-1}$, $H$ is Hessian at the mode\\
- \verb"prior_range"& 1& 1 = sample \textit{uniformly} from prior ranges\\
- & & 0 = sample from prior distributions: \\
- & & this requires MATLAB Statistics Toolbox\\
- \verb"morris"& 0& 0 = no Morris sampling for screening \\
- & & 1 = Morris sampling for screening \\
- \verb"morris_nliv"& 6& number of levels in Morris design\\
- \verb"morris_ntra"& 20& number of trajectories in Morris design\\
- \verb"ppost"& 0& 0 = don't use Metropolis posterior sample\\
- & & 1 = use Metropolis posterior sample: this \\
- & & \hspace{0.5 cm} overrides any other sampling option! \\ \hline
-\end{tabular}
-\subsection{Stability mapping}
-\begin{tabular}{r|l|l}
- option name & default & description \\ \hline
- \verb"stab"& 1& 1 = perform stability mapping \\
- & & 0 = no stability mapping is performed\\
- \verb"load_stab"& 0& 0 = generate a new sample\\
- & & 1 = load a previously created sample \\
- \verb"alpha2_stab"& 0.4& critical value for correlations $\rho$ in filtered samples:\\
- & & plot couples of parameters with \\
- & & $|\rho|>$\verb"alpha2_stab"\\
- \verb"ksstat"& 0.1& critical value for Smirnov statistics $d$: \\
- & & plot parameters with $d>$\verb"ksstat"\\ \hline
-\end{tabular}
-
-\newpage
-\subsection{Reduced form mapping}% and identification}
-The mapping of the reduced form solution forces the use of samples
-from prior ranges or prior distributions, i.e.:
-\\
-\verb"options_.opt_gsa.pprior=1;"\\
-\verb"options_.opt_gsa.ppost=0;"\\
-
-It uses 250 samples to optimize smoothing parameters and 1000
-samples to compute the fit. The rest of the sample is used for
-out-of-sample validation. \vspace{0.5cm}
-
-
-\begin{tabular}{r|l|l}
- option name & default & description \\ \hline
- \verb"redform"& 0& 0 = don't prepare MC sample of \\
- & & reduced form matrices \\
- & & 1 = prepare MC sample of \\
- & & reduced form matrices \\
- \verb"load_redform"& 0& 0 = estimate the mapping of \\
- & & reduced form model\\
- & & 1 = load previously estimated mapping\\
- \verb"logtrans_redform"& 0& 0 = use raw entries\\
- & & 1 = use log-transformed entries \\
- \verb"threshold_redform"& []& [] = don't filter MC entries \\
- & & of reduced form coefficients\\
- & & [\verb"max" \verb"max"] = analyse filtered \\
- & & entries within the range [\verb"max" \verb"max"] \\
- \verb"ksstat_redform"& 0.1& critical value for Smirnov statistics $d$ \\
- & & when reduced form entries are filtered\\
- \verb"alpha2_redform"& 0.3& critical value for correlation $\rho$ \\
- & & when reduced form entries are filtered\\
- \verb"namendo"& () & list of endogenous variables \\
- & : & jolly character to indicate ALL endogenous \\
- \verb"namlagendo"& () & list of lagged endogenous variables:\\
- & & analyse entries [\verb"namendo"$\times$\verb"namlagendo"]\\
- & : & jolly character to indicate ALL endogenous \\
- \verb"namexo"& ()& list of exogenous variables:\\
- & & analyse entries
- [\verb"namendo"$\times$\verb"namexo"]\\
- & : & jolly character to indicate ALL exogenous \\\hline
-\end{tabular}
-\vspace{0.5cm} \\
-
-One can also load a previously estimated mapping
-with a new MC sample, to look at the forecast for the new MC sample.\\
-
-\subsection{Mapping the fit}
-The RMSE analysis can be performed with different types of
-sampling options:
-\begin{enumerate}
-\item when \verb"pprior=1" and \verb"ppost=0", the Toolbox analyses the RMSE's for
-the MC sample obtained by sampling parameters from their prior
-distributions (or prior ranges): this analysis provides some hints
-about what parameter drives the fit of which observed series,
-prior to the full estimation;
-\item when \verb"pprior=0" and \verb"ppost=0", the Toolbox analyses the RMSE's for
-a multivariate normal MC sample, with covariance matrix based on
-the inverse Hessian at the optimum: this analysis is useful when
-ML estimation is done (i.e. no Bayesian estimation);
-\item when \verb"ppost=1" the Toolbox analyses
-the RMSE's for the posterior sample obtained by DYNARE's
-Metropolis procedure.
-\end{enumerate}
-
-The use of cases 2. and 3. requires an estimation step beforehand!
-To facilitate the sensitivity analysis after estimation, the
-\verb"dynare_sensitivity" command also allows to indicate some
-options of \verb"dynare_estimation". These are:
-\begin{itemize}
- \item \verb"datafile"
- \item \verb"mode_file"
- \item \verb"first_obs"
- \item \verb"nobs"
- \item \verb"prefilter"
- \item \verb"presample"
- \item \verb"loglinear"
-\end{itemize}
-
-
- \vspace{1cm}
-
-\begin{tabular}{r|l|l}
- option name & default & description \\ \hline
- \verb"rmse"& 0& 0 = no RMSE analysis\\
- & & 1 = do RMSE analysis \\
- \verb"load_rmse"& 0& 0 = make a new RMSE analysis\\
- & & 1 = load previous RMSE analysis \\
- \verb"lik_only"& 0& 0 = compute RMSE's for all observed series\\
- & & 1 = compute only likelihood and posterior \\
- \verb"var_rmse"& varobs& list of observed series to be considered\\
- \verb"pfilt_rmse"& 0.1& filtering threshold for RMSE's: default it to\\
- & & filter the best 10\% for each observed series\\
- \verb"istart_rmse"& 1& start computing RMSE's from \verb"istart_rmse":\\
- & & use 2 to avoid big initial error \\
- \verb"alpha_rmse"& 0.002& critical value for Smirnov statistics $d$:\\
- & & plot parameters with $d>$\verb"alpha_rmse"\\
- \verb"alpha2_rmse"& 1& critical value for correlation $\rho$\\
- & & plot couples of parameters with
- $|\rho|>$\verb"alpha2_rmse"\\
- \verb"glue"& 0& prepare for GLUE graphical interface\\\hline
-\end{tabular}
-
-\subsection{Screening analysis}
-The screening analysis does not require any additional options
-with respect to those listed in the `Sampling options':
-\verb"morris", \verb"morris_nliv", \verb"morris_ntra". The Toolbox
-performs all the analyses required and displays results.
-
-
-\subsection{Identification analysis (under development)}
-Setting the option \verb"identification=1", an identification
-analysis based on theoretical moments is performed. Sensitivity plots are provided that
-allow to infer which parameters are most likely to be less
-identifiable.
-
-Prerequisite for properly running all the identification routines, is the keyword
-\verb"identification;" in the DYNARE model file. This keyword triggers the computation of analytic derivatives of the model with respect to estimated parameters and shocks. This is required for options \verb"morris=2" below, which implement \cite{Iskrev2009} identification analysis.
-\vspace{1cm}
-
-
-\begin{tabular}{r|l|l}
- option name & default & description \\ \hline
- \verb"identification"& 0 & 0 = no identification analysis \\
- & & 1 = performs identification analysis:\\
- & & this forces \verb"redform"=0 and default\verb"morris"=1\\
- \verb"morris"& 1 & 1 = Screening analysis (Type II error)\\
- & & 0 = ANOVA Mapping (Type I error)\\
- & & 2 = Analytic derivatives (similar to Type II error)\\
- \verb"morris_nliv"& 6 & number of levels in Morris design\\
- \verb"morris_ntra"& 20& number of trajectories in Morris design\\
- \verb"trans_ident"& 0 & data transformation for ANOVA Mapping\\
- & & 0 = no transformation\\
- & & 1 = log-transformation\\
- & & 2 = rank-transformation\\\hline
-\end{tabular}
-
-\vspace{1cm}
-\noindent For example, the following commands in the DYNARE model file
-
-\vspace{1cm}
-\noindent\verb"identification;"\\
-\verb"dynare_sensitivity(identification=1, morris=2);"
-
-\vspace{1cm}
-\noindent trigger the identification analysis using analytic derivatives \citep{Iskrev2009}, jointly with the mapping of the acceptable region.
-
-The identification analysis with derivatives can also be triggered by the commands
-
-\vspace{1cm}
-\noindent\verb"identification;"\\
-\verb"dynare_identification;"
-
-\vspace{1cm}
-This does not do the mapping of acceptable regions for the model and uses the standard random sampler of DYNARE. It completely offsets any use of the sensitivity analysis toolbox.
-\newpage
-\section{Directory structure}
-Sensitivity analysis results are saved on the hard-disk of the
-computer. The Toolbox uses a dedicated folder called \verb"GSA",
-located in \\
-\\
-\verb"<DYNARE_file>\GSA", \\
-\\
-where \verb"<DYNARE_file>.mod" is the name of the DYNARE model
-file.
-
-\subsection{Binary data files}
-A set of binary data files is saved in the \verb"GSA" folder:
-\begin{description}
-\item[]\verb"<DYNARE_file>_prior.mat": this file stores
-information about the analyses performed sampling from the prior
-ranges, i.e. \verb"pprior=1" and \verb"ppost=0";
-\item[]\verb"<DYNARE_file>_mc.mat": this file stores
-information about the analyses performed sampling from
-multivariate normal, i.e. \verb"pprior=0" and \verb"ppost=0";
-\item[]\verb"<DYNARE_file>_post.mat": this file stores information
-about analyses performed using the Metropolis posterior sample,
-i.e. \verb"ppost=1".
-\end{description}
-
-\begin{description}
-\item[]\verb"<DYNARE_file>_prior_*.mat": these files store
-the filtered and smoothed variables for the prior MC sample,
-generated when doing RMSE analysis (\verb"pprior=1" and
-\verb"ppost=0");
-\item[]\verb"<DYNARE_file>_mc_*.mat": these files store
-the filtered and smoothed variables for the multivariate normal MC
-sample, generated when doing RMSE analysis (\verb"pprior=0" and
-\verb"ppost=0").
-\end{description}
-
-\subsection{Stability analysis}
-Figure files \verb"<DYNARE_file>_prior_*.fig" store results for
-the stability mapping from prior MC samples:
-\begin{description}
-\item[]\verb"<DYNARE_file>_prior_stab_SA_*.fig": plots of the Smirnov
-test analyses confronting the cdf of the sample fulfilling
-Blanchard-Kahn conditions with the cdf of the rest of the sample;
-\item[]\verb"<DYNARE_file>_prior_stab_indet_SA_*.fig": plots of the Smirnov
-test analyses confronting the cdf of the sample producing
-indeterminacy with the cdf of the original prior sample;
-\item[]\verb"<DYNARE_file>_prior_stab_unst_SA_*.fig": plots of the Smirnov
-test analyses confronting the cdf of the sample producing unstable
-(explosive roots) behaviour with the cdf of the original prior
-sample;
-\item[]\verb"<DYNARE_file>_prior_stable_corr_*.fig": plots of
-bivariate projections of the sample fulfilling Blanchard-Kahn
-conditions;
-\item[]\verb"<DYNARE_file>_prior_indeterm_corr_*.fig": plots of
-bivariate projections of the sample producing indeterminacy;
-\item[]\verb"<DYNARE_file>_prior_unstable_corr_*.fig": plots of
-bivariate projections of the sample producing instability;
-\item[]\verb"<DYNARE_file>_prior_unacceptable_corr_*.fig": plots of
-bivariate projections of the sample producing unacceptable
-solutions, i.e. either instability or indeterminacy or the
-solution could not be found (e.g. the steady state solution could
-not be found by the solver).
-\end{description}
-Similar conventions apply for \verb"<DYNARE_file>_mc_*.fig" files,
-obtained when samples from multivariate normal are used.
-
-\subsection{RMSE analysis}
-Figure files \verb"<DYNARE_file>_rmse_*.fig" store results for the
-RMSE analysis.
-\begin{description}
-\item[]\verb"<DYNARE_file>_rmse_prior*.fig": save results for
-the analysis using prior MC samples;
-\item[]\verb"<DYNARE_file>_rmse_mc*.fig": save results for
-the analysis using multivariate normal MC samples;
-\item[]\verb"<DYNARE_file>_rmse_post*.fig": save results for
-the analysis using Metropolis posterior samples.
-\end{description}
-
-The following types of figures are saved (we show prior sample to
-fix ideas, but the same conventions are used for multivariate
-normal and posterior):
-\begin{description}
-\item[]\verb"<DYNARE_file>_rmse_prior_*.fig": for each parameter, plots the cdf's
-corresponding to the best 10\% RMES's of each observed series;
-\item[]\verb"<DYNARE_file>_rmse_prior_dens_*.fig": for each parameter, plots the pdf's
-corresponding to the best 10\% RMES's of each observed series;
-\item[]\verb"<DYNARE_file>_rmse_prior_<name of observedseries>_corr_*.fig": for each observed series plots the
-bi-dimensional projections of samples with the best 10\% RMSE's,
-when the correlation is significant;
-\item[]\verb"<DYNARE_file>_rmse_prior_lnlik*.fig": for each observed
-series, plots \emph{in red} the cdf of the log-likelihood
-corresponding to the best 10\% RMSE's, \emph{in green} the cdf of
-the rest of the sample and \emph{in blue }the cdf of the full
-sample; this allows to see the presence of some idiosyncratic
-behaviour;
-\item[]\verb"<DYNARE_file>_rmse_prior_lnpost*.fig": for each observed
-series, plots \emph{in red} the cdf of the log-posterior
-corresponding to the best 10\% RMSE's, \emph{in green} the cdf of
-the rest of the sample and \emph{in blue }the cdf of the full
-sample; this allows to see idiosyncratic behaviour;
-\item[]\verb"<DYNARE_file>_rmse_prior_lnprior*.fig": for each observed
-series, plots \emph{in red} the cdf of the log-prior corresponding
-to the best 10\% RMSE's, \emph{in green} the cdf of the rest of
-the sample and \emph{in blue }the cdf of the full sample; this
-allows to see idiosyncratic behaviour;
-\item[]\verb"<DYNARE_file>_rmse_prior_lik_SA_*.fig": when
-\verb"lik_only=1", this shows the Smirnov tests for the filtering
-of the best 10\% log-likelihood values;
-\item[]\verb"<DYNARE_file>_rmse_prior_post_SA_*.fig": when
-\verb"lik_only=1", this shows the Smirnov test for the filtering
-of the best 10\% log-posterior values.
-\end{description}
-
-\subsection{Reduced form mapping}
-In the case of the mapping of the reduced form solution, synthetic
-figures are saved in the \verb"\GSA" folder:
-
-\begin{description}
-\item[]\verb"<DYNARE_file>_redform_<endo name>_vs_lags_*.fig":
-shows bar charts of the sensitivity indices for the \emph{ten most
-important} parameters driving the reduced form coefficients of the
-selected endogenous variables (\verb"namendo") versus lagged
-endogenous variables (\verb"namlagendo"); suffix \verb"log"
-indicates the results for log-transformed entries;
-\item[]\verb"<DYNARE_file>_redform_<endo name>_vs_shocks_*.fig":
-shows bar charts of the sensitivity indices for the \emph{ten most
-important} parameters driving the reduced form coefficients of the
-selected endogenous variables (\verb"namendo") versus exogenous
-variables (\verb"namexo"); suffix \verb"log" indicates the results
-for log-transformed entries;
-\item[]\verb"<DYNARE_file>_redform_GSA(_log).fig": shows bar chart of
-all sensitivity indices for each parameter: this allows to notice
-parameters that have a minor effect for \emph{any} of the reduced
-form coefficients,
-\end{description}
-
-Detailed results of the analyses are shown in the subfolder
-\verb"\GSA\redform_stab", where the detailed results of the
-estimation of the single functional relationships between
-parameters $\theta$ and reduced form coefficient are stored in
-separate directories named as:
-\begin{description}
-\item[]\verb"<namendo>_vs_<namlagendo>": for the entries of the
-transition matrix;
-\item[]\verb"<namendo>_vs_<namexo>": for entries of the matrix of
-the shocks.
-\end{description}
-Moreover, analyses for log-transformed entries are denoted with
-the following suffixes ($y$ denotes the generic reduced form
-coefficient):
-\begin{description}
-\item[]\verb"log": $y^*=\log(y)$;
-\item[]\verb"minuslog": $y^*=\log(-y)$;
-\item[]\verb"logsquared": $y^*=\log(y^2)$ for symmetric fat tails;
-\item[]\verb"logskew": $y^*=\log(|y+\lambda|)$ for asymmetric fat tails.
-\end{description}
-The optimal type of transformation is automatically selected
-without the need of any user's intervention.
-
-\subsection{Screening analysis}
-The results of the screening analysis with Morris sampling design
-are stored in the subfolder \verb"\GSA\SCREEN". The data file
-\verb"<DYNARE_file>_prior" stores all the information of the
-analysis (Morris sample, reduced form coefficients, etc.).
-
-Screening analysis merely concerns reduced form coefficients.
-Similar synthetic bar charts as for the reduced form analysis with
-MC samples are saved:
-\begin{description}
-\item[]\verb"<DYNARE_file>_redform_<endo name>_vs_lags_*.fig":
-shows bar charts of the elementary effect tests for the \emph{ten
-most important} parameters driving the reduced form coefficients
-of the selected endogenous variables (\verb"namendo") versus
-lagged endogenous variables (\verb"namlagendo");
-\item[]\verb"<DYNARE_file>_redform_<endo name>_vs_shocks_*.fig":
-shows bar charts of the elementary effect tests for the \emph{ten
-most important} parameters driving the reduced form coefficients
-of the selected endogenous variables (\verb"namendo") versus
-exogenous variables (\verb"namexo");
-\item[]\verb"<DYNARE_file>_redform_screen.fig": shows bar chart of
-all elementary effect tests for each parameter: this allows to
-identify parameters that have a minor effect for \emph{any} of the
-reduced form coefficients.
-\end{description}
-
-
-% ----------------------------------------------------------------
-\bibliographystyle{plainnat}
-%\bibliographystyle{amsplain}
-%\bibliographystyle{alpha}
-\bibliography{marco}
-
-\newpage
-
-
-\end{document}
-% ----------------------------------------------------------------
diff --git a/doc/gsa/dyn_tbx.tex b/doc/gsa/gsa.tex
similarity index 100%
rename from doc/gsa/dyn_tbx.tex
rename to doc/gsa/gsa.tex
diff --git a/doc/gsa/marco.bib b/doc/gsa/marco.bib
index 362f631ebb4b6b0539d779ac3274bf2ac999a3a6..a6fbcdd20956e139d28e76631259a763da23d7fb 100644
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diff --git a/doc/gsa/marco.bib.bak b/doc/gsa/marco.bib.bak
deleted file mode 100644
index a9cd299bc8a79d0a09afdb98123d0341623f75d5..0000000000000000000000000000000000000000
--- a/doc/gsa/marco.bib.bak
+++ /dev/null
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-TITLE={ State-of-the-Art Report on Current Methodologies and
-Practices for Composite Indicator Development }, YEAR={2002},
-INSTITUTION={ European Commission }, TYPE={ EUR 20408 EN }, NOTE={
-Joint Research Centre, Ispra, Italy,
-http://farmweb.jrc.cec.eu.int/CI/Document/state-of-the-art_EUR20408.pdf},
-NUMBER={} }
-
-@INCOLLECTION{TomlTura97,
- author = { Tomlin, A. and Tur�nyi, T.},
- title = {},
- pages = {293},
- publisher = { Elsevier },
- address = {},
- year = { 1997},
- booktitle = { Low temperature Combustion and Autoignition },
- editor = { Pilling, M.J., and Hancock, G.}
-}
-
-@INCOLLECTION{TuraRabi00,
- author = { Tur�nyi, T. and Rabitz, H.},
- title = {},
- pages = {81},
- publisher = { John Wiley & Sons },
- address = { Chichester },
- year = {2000},
- booktitle = { Sensitivity Analysis },
- editor = { Chan, K. and Scott, M.},
-}
-
-@TECHREPORT{SchuBaur06,
- AUTHOR={ Schulze, N. and Baur, D. },
- TITLE={ Economic Impact Study on Clearing and Settlement -
- Annex II},
- YEAR={2006},
- MONTH= {May},
- INSTITUTION={European Commission, DG-JRC},
- TYPE={},
- note={available at $http://ec.europa.eu/internal_market/financial-markets/clearing/index_en.htm$},
-}
-
-
-@ARTICLE{kn:EcuyerAndres97,
- author = {l'Ecuyer, P. and Andres, T.H. },
- title = {A random number generator based on the combination
- of four \textsc{LCG}s},
- journal = {Mathematics and Computers in Simulation},
- year = {1997},
- volume = {44},
- number = {},
- pages = {99-107},
-}
-
-@ARTICLE{kn:WichmanHill82,
- author = {Wichman, B.A. and Hill, I.D.},
- title = {Algorithm \textsc{AS} 183: An Efficient and
-Portable Pseudo-Random Number Generator},
- journal = {Applied Statistics},
- year = {1982},
- volume = {31},
- number = {},
- pages = {188-190},
-
-%@ARTICLE{kn:NIH,
-% author = {NIH},
-% title = {Framingham \textsc{H}eart \textsc{S}tudy: 50 Years of Research Success},
-% publisher = {National Institutes of Health, National Heart, Lung and Blood Institute},
-% year = {2002},
-%}
-
-@BOOK{kn:NIH1,
- author = {NIH},
- title = {Framingham \textsc{H}eart \textsc{S}tudy: 50 Years of Research Success},
- publisher = {National Institutes of Health, National Heart, Lung and Blood Institute},
- year = {2002},
- note = {www.nhlbi.nih.gov/about/framingham},
-}
-
-
-% note = {www.nhlbi.nih.gov$\backslash$about$\backslash$framingham},
-
-@BOOK{kn:NHS,
- editor = {Hankinson, S. E. Sc.D., et al.},
- title = {Healthy Women, Healthy Lives: A Guide to Preventing Disease, form the Landmark Nurses' Health Study},
- publisher = {Free Press},
- year = {2001},
-}
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-@BOOK{kn:Biometry,
- author = {Sokal, R. R. and James, R. F.},
- title = {Biometry},
- publisher = {W.H. Freeman and Company},
- year = {1994},
- address = {New York},
-}
-
-@BOOK{kn:CRC,
- editor = {Colbourn, C.J. and Dinitz, J.H.},
- title = {\textsc{CRC} Handbook of Combinatorial Designs},
- publisher = {CRC Press},
- year = {1996},
-}
-
-@BOOK{kn:Press,
- author = {Press, W. H. and Teukolsky, S.A. and Vetterling, W. T. and Flannery, B. P. },
- title = {Numerical Recipes in Fortran 77: The Art of Scientific Computing},
- edition = {Second},
- volume = {1},
- publisher = {Cambridge University Press},
- year = {1997},
- address = {New York},
-}
-
-@BOOK{kn:Fixx,
- author = {Fixx, J. F. },
- title = {Games for the Super Intelligent},
- publisher = {Doubleday \& Co. Inc.},
- year = {1972},
- address = {Garden City, NY},
-}
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-@ARTICLE{kn:Andres,
- author = { Andres, T.H.},
- title = {Sampling methods and sensitivity analysis for large. parameter sets},
- journal = {J Stat Comput Simul},
- year = {1997},
- volume = {57},
- pages = {77--110},
-}
diff --git a/windows/dynare.nsi b/windows/dynare.nsi
index f56fbd80ffb0f3a8e4b4198917a68d58d02a24a3..d314893773ff7d8f4e9d823207fcfd4686b16532 100644
--- a/windows/dynare.nsi
+++ b/windows/dynare.nsi
@@ -120,7 +120,7 @@ SectionEnd
Section "Documentation and examples (Dynare and Dynare++)"
SetOutPath $INSTDIR\doc
- File ..\doc\manual.pdf ..\doc\guide.pdf ..\doc\userguide\UserGuide.pdf ..\doc\bvar-a-la-sims.pdf ..\doc\dr.pdf ..\doc\macroprocessor\macroprocessor.pdf ..\doc\preprocessor\preprocessor.pdf ..\doc\parallel\parallel.pdf
+ File ..\doc\manual.pdf ..\doc\guide.pdf ..\doc\userguide\UserGuide.pdf ..\doc\bvar-a-la-sims.pdf ..\doc\dr.pdf ..\doc\macroprocessor\macroprocessor.pdf ..\doc\preprocessor\preprocessor.pdf ..\doc\parallel\parallel.pdf ..\doc\gsa\gsa.pdf
SetOutPath $INSTDIR\doc\manual-html
File ..\doc\manual-html\*.html