[Rcpp-commits] r2419 - in pkg/RcppDE: . inst/DEoptim-docs

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Nov 8 13:40:32 CET 2010


Author: edd
Date: 2010-11-08 13:40:32 +0100 (Mon, 08 Nov 2010)
New Revision: 2419

Added:
   pkg/RcppDE/inst/DEoptim-docs/CHANGES
   pkg/RcppDE/inst/DEoptim-docs/NEWS
   pkg/RcppDE/inst/DEoptim-docs/README
   pkg/RcppDE/inst/DEoptim-docs/THANKS
Removed:
   pkg/RcppDE/CHANGES
   pkg/RcppDE/NEWS
   pkg/RcppDE/README
   pkg/RcppDE/THANKS
Log:
moved files from DEoptim a level down


Deleted: pkg/RcppDE/CHANGES
===================================================================
--- pkg/RcppDE/CHANGES	2010-11-08 12:38:57 UTC (rev 2418)
+++ pkg/RcppDE/CHANGES	2010-11-08 12:40:32 UTC (rev 2419)
@@ -1,31 +0,0 @@
-version 1.3-0, 2008-12-03
-- The function DEoptim has two arguments: 'storepopfrom' and 'storepopfreq', for tracking intermediate
-  populations; the output contains also the list 'storepop' which belongs to the 'member' list's element.
-- Small bug fixed for the number of iterations.
-
-version 1.2-1, 2007-09-12
-- Fix a bug in the optimization procedure. Thanks to Tarmo Leinonen for pointing out this bug
-- Add a demo to show how to increase the number of printed digits while performing the optimization
-
-version 1.2-0, 2007-09-10
-- The function DEoptim has the new argument 'initial', which is an initial or starting population.
-  You can therefore introduce a starting population in the optimization procedure. This can be useful
-  when the optimization has to be run many times on data sets which differ sligthly. Thanks to
-  Tarmo Leinonen for this nice suggestion.
-
-- The function DEoptim outputs now 'pop' in the 'member' list's element. This is the population obtained
-  at the last iteration which can be used as a starting population in DEoptim via the argument 'initial'.
-  
-- The function stops if any 'NA' or 'NaN' value is returned by the function 'FUN' to be optimized.
-
-- The function DEoptim does not handle exponential crossover anymore. This is so to simplify and
-  accelerate the optimization procedure. Thanks to Vladimir Eremeev for pointing out a 
-  bug with the exponential crossover.
-
-- The function DEoptim outputs a list of lists. This is more natural and in the same spirit 
-  of usual optimization functions. Thanks to Vladimir Eremeev for proposing this change.
-  
-- documentation for the 'digits'. Thanks to Eugene Demidenko for pointing out this.
-
-version 1.8-0, 2007/02/02
-- The documentation of DEoptim has been modified. Corrections of some references.
\ No newline at end of file

Deleted: pkg/RcppDE/NEWS
===================================================================
--- pkg/RcppDE/NEWS	2010-11-08 12:38:57 UTC (rev 2418)
+++ pkg/RcppDE/NEWS	2010-11-08 12:40:32 UTC (rev 2419)
@@ -1,129 +0,0 @@
-Changes in version 2.0-7
-  o Many improvements in the C code, including removal of all global variables 
-    thanks to Joshua Ulrich.
-  o Thanks to Ralf Tautenhahn and Joshua Ulrich, a bug with bs=TRUE is removed.
-  o Thanks to Dirk Eddelbuettel several bugs (some possibly causing segfaults)
-    removed. 
-  o Added DE/current-to-p-best/1 strategy.
-  o Added ability to only print every "trace" iterations.
-Changes in version 2.0-6
-  o Added dataset documentation now required by R CMD check.
-Changes in version 2.0-5
-  o CITATION file modified, updated references. 
-  o Removed check on length of parameter vector (it was left over from versions
-    prior to 2.0-3, thanks to Jean-Luc Jannink.
-Changes in version 2.0-4
-  o added check to prevent the C code being called with NP<4, thanks to Joshua 
-    Ulrich.  
-  o fixed bug introduced in version 2.0-3 that made the objective function 
-    values associated with the winning population members incorrect
-  o added new options checkWinner and avWinner to the 'control' arguement. 
-
-Changes in version 2.0-3
-  o Re-write of much of the underlying C code.  Now dynamically allocate 
-    storage, so can optimize on parameter vectors of arbitrary size, in a 
-    population of arbitrary size.  Changed the documentation to reflect the
-    new lack of limitations.    
-  o Stop with an error right away if a NaN objective function value occurs.
-  o Default value of CR changed to .9 from .5.     
-  o Added reference and minor changes to documentation.   
-
-Changes in version 2.0-2
-  o The maximum number of parameters that can be optimized (set
-    statically in de.h with #define MAXDIM) was changed from 20 to
-    200.
-  o zzz.R file removed and replaced with call to `useDynLib(DEoptim)' in 
-    NAMESPACE
-  o Brian Peterson pointed out problems occurring when the objective
-    function returns a NaN value.  Error messages are now added to
-    report when this happens. 
-  o permute patched, see below.  Thanks to Hans Werner Borchers for pointing
-    out that the problem was not fixed in the CRAN version. 
-
-Changes in version 2.0-1
-  o Soren Macbeth and Joshua Ulrich pointed out and patched bugs in the 
-    function 'permute'.  Note that the version 2.0-1 on CRAN does not patch
-    these bugs correctly.  The correction is made in the next version.
-
-Changes in version 2.0-0
-  o The R-based implementation of Differential Evolution has been
-    replaced with a C-based implementation similar to the MS Visual C++
-    v5.0 implementation accompanying the book `Differential Evolution -
-    A Practical Approach to Global Optimization',downloaded from
-    http://www.icsi.berkeley.edu/~storn/DeWin.zip.
-
-    The new C implementation is significantly faster. 
-
-  o The S3 method for plotting has been enhanced. It allows now to plot
-    the intermediate populations if provided.
-
-  o The package maintainer has been changed to Katharine Mullen,
-    <katharine.mullen at nist.gov>.
-
-  o A NAMESPACE has been added.
-
-  o Argument FUN for DEoptim is now called fn for compatibility with optim.
-
-  o demo file has been removed
-
-  o CITATION file modified
-
-
-Changes in version 1.3-3
-
-  o CITATION file modified.
-
-
-Changes in Version 1.3-2
-
-  o CITATION file modified.
-
-
-Changes in Version 1.3-1
-
-  o new plotting argument 'storepop' which displays intermediate
-    population locations.
-
-
-Changes in Version 1.3-0
-
-  o the function 'DEoptim' has two arguments: 'storepopfrom' and
-    'storepopfreq', for tracking intermediate populations; the output
-    contains also the list 'storepop' which belongs to the 'member'
-    list's element.
-
-  o small bug fixed for the number of iterations.
-
-
-Changes in Version 1.2-1
-
-  o fix a bug in the optimization procedure.
-
-  o add a demo to show how to increase the number of printed digits
-    while performing the optimization.
-
-
-Changes in Version 1.2-0
-
-  o the function 'DEoptim' has the new argument 'initial', which is an
-    initial or starting population.  You can therefore introduce a
-    starting population in the optimization procedure. This can be
-    useful when the optimization has to be run many times on data sets
-    which differ sligthly.
-
-  o the function 'DEoptim' outputs now 'pop' in the 'member' list's
-    element. This is the population obtained at the last iteration
-    which can be used as a starting population in 'DEoptim' via the
-    argument 'initial'.
-
-  o the function stops if any 'NA' or 'NaN' value is returned by the
-    function 'FUN' to be optimized.
-
-  o the function DEoptim does not handle exponential crossover
-    anymore. This is so to simplify and accelerate the optimization
-    procedure.
-
-  o the function 'DEoptim' outputs a list of lists. This is more
-    natural and in the same spirit of usual optimization functions.
-
-  o documentation for the 'digits'.
\ No newline at end of file

Deleted: pkg/RcppDE/README
===================================================================
--- pkg/RcppDE/README	2010-11-08 12:38:57 UTC (rev 2418)
+++ pkg/RcppDE/README	2010-11-08 12:40:32 UTC (rev 2419)
@@ -1,9 +0,0 @@
-DEoptim is an R implementation of the Differential Evolution
-optimization algorithm.  It is still under development and is
-distributed without warranty.
-
-Further details can be found at
-http://www.icsi.berkeley.edu/~storn/code.html.
-
-Report bugs or make suggestions to <david.ardia at unifr.ch> or
-<katharine.mullen at nist.gov>.
\ No newline at end of file

Deleted: pkg/RcppDE/THANKS
===================================================================
--- pkg/RcppDE/THANKS	2010-11-08 12:38:57 UTC (rev 2418)
+++ pkg/RcppDE/THANKS	2010-11-08 12:40:32 UTC (rev 2419)
@@ -1,11 +0,0 @@
-The authors would like to thank the following people for their help:
-
-  Tarmo Leinonen
-  Eugene Demidenko
-  Rainer Storn
-  Soren Macbeth		
-  Hans Werner Borchers
-  Enrico Schumann
-  Jean-Luc Jannink
-  Dirk Eddelbuettel
-  Ralf Tautenhahn
\ No newline at end of file

Copied: pkg/RcppDE/inst/DEoptim-docs/CHANGES (from rev 2417, pkg/RcppDE/CHANGES)
===================================================================
--- pkg/RcppDE/inst/DEoptim-docs/CHANGES	                        (rev 0)
+++ pkg/RcppDE/inst/DEoptim-docs/CHANGES	2010-11-08 12:40:32 UTC (rev 2419)
@@ -0,0 +1,31 @@
+version 1.3-0, 2008-12-03
+- The function DEoptim has two arguments: 'storepopfrom' and 'storepopfreq', for tracking intermediate
+  populations; the output contains also the list 'storepop' which belongs to the 'member' list's element.
+- Small bug fixed for the number of iterations.
+
+version 1.2-1, 2007-09-12
+- Fix a bug in the optimization procedure. Thanks to Tarmo Leinonen for pointing out this bug
+- Add a demo to show how to increase the number of printed digits while performing the optimization
+
+version 1.2-0, 2007-09-10
+- The function DEoptim has the new argument 'initial', which is an initial or starting population.
+  You can therefore introduce a starting population in the optimization procedure. This can be useful
+  when the optimization has to be run many times on data sets which differ sligthly. Thanks to
+  Tarmo Leinonen for this nice suggestion.
+
+- The function DEoptim outputs now 'pop' in the 'member' list's element. This is the population obtained
+  at the last iteration which can be used as a starting population in DEoptim via the argument 'initial'.
+  
+- The function stops if any 'NA' or 'NaN' value is returned by the function 'FUN' to be optimized.
+
+- The function DEoptim does not handle exponential crossover anymore. This is so to simplify and
+  accelerate the optimization procedure. Thanks to Vladimir Eremeev for pointing out a 
+  bug with the exponential crossover.
+
+- The function DEoptim outputs a list of lists. This is more natural and in the same spirit 
+  of usual optimization functions. Thanks to Vladimir Eremeev for proposing this change.
+  
+- documentation for the 'digits'. Thanks to Eugene Demidenko for pointing out this.
+
+version 1.8-0, 2007/02/02
+- The documentation of DEoptim has been modified. Corrections of some references.
\ No newline at end of file

Copied: pkg/RcppDE/inst/DEoptim-docs/NEWS (from rev 2417, pkg/RcppDE/NEWS)
===================================================================
--- pkg/RcppDE/inst/DEoptim-docs/NEWS	                        (rev 0)
+++ pkg/RcppDE/inst/DEoptim-docs/NEWS	2010-11-08 12:40:32 UTC (rev 2419)
@@ -0,0 +1,129 @@
+Changes in version 2.0-7
+  o Many improvements in the C code, including removal of all global variables 
+    thanks to Joshua Ulrich.
+  o Thanks to Ralf Tautenhahn and Joshua Ulrich, a bug with bs=TRUE is removed.
+  o Thanks to Dirk Eddelbuettel several bugs (some possibly causing segfaults)
+    removed. 
+  o Added DE/current-to-p-best/1 strategy.
+  o Added ability to only print every "trace" iterations.
+Changes in version 2.0-6
+  o Added dataset documentation now required by R CMD check.
+Changes in version 2.0-5
+  o CITATION file modified, updated references. 
+  o Removed check on length of parameter vector (it was left over from versions
+    prior to 2.0-3, thanks to Jean-Luc Jannink.
+Changes in version 2.0-4
+  o added check to prevent the C code being called with NP<4, thanks to Joshua 
+    Ulrich.  
+  o fixed bug introduced in version 2.0-3 that made the objective function 
+    values associated with the winning population members incorrect
+  o added new options checkWinner and avWinner to the 'control' arguement. 
+
+Changes in version 2.0-3
+  o Re-write of much of the underlying C code.  Now dynamically allocate 
+    storage, so can optimize on parameter vectors of arbitrary size, in a 
+    population of arbitrary size.  Changed the documentation to reflect the
+    new lack of limitations.    
+  o Stop with an error right away if a NaN objective function value occurs.
+  o Default value of CR changed to .9 from .5.     
+  o Added reference and minor changes to documentation.   
+
+Changes in version 2.0-2
+  o The maximum number of parameters that can be optimized (set
+    statically in de.h with #define MAXDIM) was changed from 20 to
+    200.
+  o zzz.R file removed and replaced with call to `useDynLib(DEoptim)' in 
+    NAMESPACE
+  o Brian Peterson pointed out problems occurring when the objective
+    function returns a NaN value.  Error messages are now added to
+    report when this happens. 
+  o permute patched, see below.  Thanks to Hans Werner Borchers for pointing
+    out that the problem was not fixed in the CRAN version. 
+
+Changes in version 2.0-1
+  o Soren Macbeth and Joshua Ulrich pointed out and patched bugs in the 
+    function 'permute'.  Note that the version 2.0-1 on CRAN does not patch
+    these bugs correctly.  The correction is made in the next version.
+
+Changes in version 2.0-0
+  o The R-based implementation of Differential Evolution has been
+    replaced with a C-based implementation similar to the MS Visual C++
+    v5.0 implementation accompanying the book `Differential Evolution -
+    A Practical Approach to Global Optimization',downloaded from
+    http://www.icsi.berkeley.edu/~storn/DeWin.zip.
+
+    The new C implementation is significantly faster. 
+
+  o The S3 method for plotting has been enhanced. It allows now to plot
+    the intermediate populations if provided.
+
+  o The package maintainer has been changed to Katharine Mullen,
+    <katharine.mullen at nist.gov>.
+
+  o A NAMESPACE has been added.
+
+  o Argument FUN for DEoptim is now called fn for compatibility with optim.
+
+  o demo file has been removed
+
+  o CITATION file modified
+
+
+Changes in version 1.3-3
+
+  o CITATION file modified.
+
+
+Changes in Version 1.3-2
+
+  o CITATION file modified.
+
+
+Changes in Version 1.3-1
+
+  o new plotting argument 'storepop' which displays intermediate
+    population locations.
+
+
+Changes in Version 1.3-0
+
+  o the function 'DEoptim' has two arguments: 'storepopfrom' and
+    'storepopfreq', for tracking intermediate populations; the output
+    contains also the list 'storepop' which belongs to the 'member'
+    list's element.
+
+  o small bug fixed for the number of iterations.
+
+
+Changes in Version 1.2-1
+
+  o fix a bug in the optimization procedure.
+
+  o add a demo to show how to increase the number of printed digits
+    while performing the optimization.
+
+
+Changes in Version 1.2-0
+
+  o the function 'DEoptim' has the new argument 'initial', which is an
+    initial or starting population.  You can therefore introduce a
+    starting population in the optimization procedure. This can be
+    useful when the optimization has to be run many times on data sets
+    which differ sligthly.
+
+  o the function 'DEoptim' outputs now 'pop' in the 'member' list's
+    element. This is the population obtained at the last iteration
+    which can be used as a starting population in 'DEoptim' via the
+    argument 'initial'.
+
+  o the function stops if any 'NA' or 'NaN' value is returned by the
+    function 'FUN' to be optimized.
+
+  o the function DEoptim does not handle exponential crossover
+    anymore. This is so to simplify and accelerate the optimization
+    procedure.
+
+  o the function 'DEoptim' outputs a list of lists. This is more
+    natural and in the same spirit of usual optimization functions.
+
+  o documentation for the 'digits'.
\ No newline at end of file

Copied: pkg/RcppDE/inst/DEoptim-docs/README (from rev 2417, pkg/RcppDE/README)
===================================================================
--- pkg/RcppDE/inst/DEoptim-docs/README	                        (rev 0)
+++ pkg/RcppDE/inst/DEoptim-docs/README	2010-11-08 12:40:32 UTC (rev 2419)
@@ -0,0 +1,9 @@
+DEoptim is an R implementation of the Differential Evolution
+optimization algorithm.  It is still under development and is
+distributed without warranty.
+
+Further details can be found at
+http://www.icsi.berkeley.edu/~storn/code.html.
+
+Report bugs or make suggestions to <david.ardia at unifr.ch> or
+<katharine.mullen at nist.gov>.
\ No newline at end of file

Copied: pkg/RcppDE/inst/DEoptim-docs/THANKS (from rev 2417, pkg/RcppDE/THANKS)
===================================================================
--- pkg/RcppDE/inst/DEoptim-docs/THANKS	                        (rev 0)
+++ pkg/RcppDE/inst/DEoptim-docs/THANKS	2010-11-08 12:40:32 UTC (rev 2419)
@@ -0,0 +1,11 @@
+The authors would like to thank the following people for their help:
+
+  Tarmo Leinonen
+  Eugene Demidenko
+  Rainer Storn
+  Soren Macbeth		
+  Hans Werner Borchers
+  Enrico Schumann
+  Jean-Luc Jannink
+  Dirk Eddelbuettel
+  Ralf Tautenhahn
\ No newline at end of file



More information about the Rcpp-commits mailing list