[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
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