[Bugs-r-devel] SF.net SVN: bugs-r: [67] trunk/R2WinBUGS

[<gg...@us...>]

Revision: 67
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=67&view=rev
Author:   ggorjan
Date:     2007-09-18 06:21:09 -0700 (Tue, 18 Sep 2007)

Log Message:
-----------
move so that NEWS file will be also in installed package

Added Paths:
-----------
    trunk/R2WinBUGS/inst/NEWS

Removed Paths:
-------------
    trunk/R2WinBUGS/Changes

Deleted: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes	2007-09-18 13:17:39 UTC (rev 66)
+++ trunk/R2WinBUGS/Changes	2007-09-18 13:21:09 UTC (rev 67)
@@ -1,237 +0,0 @@
-Changes to R2WinBUGS:
-=====================
-
-Update 2.1-6 (23 August 2007):
-- reverting back to use thin.updater since it is faster, however CODA files
-  have "wrong" indexes
-- WINE arguments are now set in such a way that defaults work on Windows
-  and Linux
-- minor formatting in the code and help files
-
-Update 2.1-5 (12 June 2007):
-- proper indexing of CODA files also in R version
-- fixed useWINE documentation in bugs help page
-- note on supported BUGS versions
-- as.bugs.array now returns info on used rule for pD i.e. var(deviance)/2
-    or Dbar-Dhat
-- some internal fixes related to handling of DIC
-- merging and reversing ChangeLog files
-
-Update 2.1-4 (20 May 2007):
-- Depending on coda now (Namespace issues)
-- some more fixes for codetools checks
-- Vignette has been updated
-
-Update 2.1-3 (13 May 2007):
-- Ported to S-PLUS by Insightful Corp.
-- some fixes for codetools checks
-
-Update 2.0-4 (01 November 2006):
-- print.bugs / plot.bugs documentation fixes
-- write.model() fix
-
-Update 2.0-3 (06 October 2006):
-- \\. -> [.] in regular expressions
-
-Update 2.0-2 (26 July 2006):
-- changes for DIC, making use of BUGS internal calculations
-- some doc fixes
-
-Update 2.0-1 (26 May 2006):
-- some wine patches for 2.2-0 by Gregor Gorjanc
-
-Update 2.0-0 (08 May 2006):
-- bugs() doc fix/updates on scrambling
-- bugs.run() has new arg useWINE (by Gregor Gorjanc)
-- bugs() and bugs.script() patched for WINEPATH issue
-- bugs.script() changed to save log file in ASCII
-- new function bugs.log() by Gregor Gorjanc
-- new functions as.bugs.array, openbugs and sort.name by
-  Jouni Kerman and Andrew Gelman
-- new function write.model() based on ideas from Jouni Kerman
-
-Update 1.1-1 (17 Feb 2006):
-- WINE tweaks (mainly by Gregor Gorjanc)
-
-Update 1.1-0 (14 Dec 2005):
-- Contribution by Ben Bolker and Yun Yan's rbugs package:
-  make R2WinBUGS work under WINE
-
-Update 1.0-1 (14 Nov 2005):
-- make inits=NULL work (again ?)
-
-Update 1.0-0 (05 Aug 2005):
-- attach.all(), detach.all(), attach.bugs() and detach.bugs() added/changed
-  more or less according to Andrew Gelman's current bugs.R
-
-Update 0.2-9 (26 July 2005):
-- bugs has new argument clearWD
-
-Update 0.2-8 (30 May 2005):
-- bugs passed DIC to bugs.script in order to be able to disable it
-
-Update 0.2-6 (18 May 2005):
-- bugs() changes in order to return a file names of coda output files
-- new read.bugs() returns a coda mcmc.list object, if codaPkg=TRUE.
-
-Update 0.2-5 (20 Oct 2004):
-- bugs() and bugs.script() have a new argument bin that allows to specify
-  a number of iterations. After each "bin" iterations the coda files are saved.
-
-Update 0.2-4 (05 Oct 2004):
-- bugs.script() did not work for large n.iter values in update step
-  (no scientific notation allowed)
-
-Update 0.2-3 (10 Sept 2004):
-- bugs.data.inits split to bugs.inits and bugs.data, the latter exported
-  from the Namespace.
-  Now we can use already written data files in bugs().
-
-Update 0.2-2 (28 Apr 2004):
-- schools data: original (see references) instead of the rounded data
-
-During the process of packaging R2WinBUGS_0.1 - R2WinBUGS_0.2-1,
-quite a lot of changes had been made. Those changes are not
-documented anywhere ...
-
-During the process of packaging R2WinBUGS_0.1, quite a lot of changes had
-been made. Those changes are not documented anywhere ...
-
-Changes prior to R2WinBUGS_0.1:
-===============================
-
-Update 30 Oct 2003:
-  1.  Minor change to a return() statement to be compatible with R 1.8
-  2.  Just a warning (from Ben Goodrich):  if you are running Bugs.R inside
-      a loop, you have to be careful with the data() and the inits()
-      functions since they will not necessarily recognize locally-defined
-      variables.  One workaround is to define the variables used in data()
-      and inits() using global assignments (<<-), but this can sometimes
-      make the program run slower.
-Update 29 Aug 2003:
-  1.  Fixed "bugs.data.inits" function so you can use data that have the
-      same names as R functions.
-  2.  Changed T and F to TRUE and FALSE everywhere in case the variables
-      T and F are used as data in the main program
-  3.  Caution:  if you are entering the data as a list of variable names
-      (see 10 Apr 2003 update, item 1), the data to be input into must
-      be global variables.  This can be relevant if you are running bugs()
-      inside an R function.
-  4.  Caution:  bugs() has difficulty processing ragged arrays.  It is
-      better to save a whole matrix (e.g., "theta") rather than parts
-      (e.g., "theta[1:10,1]", "theta[1:5,2]").  If you want to save
-      part of a vector, you should do it as "theta[1:2]", not "theta[1]",
-      "theta[2]".
-Update 30 Apr 2003:  added time monitoring
-Update 29 Apr 2003:
-  1.  The "attach.all" function (no longer called "attach2") overwrites
-      so that all components of a list or data frame get attached.
-  2.  Program now looks in the directory /winbug~1/ rather than /winbug~2/
-  3.  Graphics parameters for margins are returned to their original state
-      at the end of the program.
-  4.  Added "digits.summary" option to the numerical display.
-  5.  Added "last.values" output:  a list that can be input as "inits"
-      if you want to run the simulations longer.
-Update 13 Apr 2003:  fixed new bug in round.bugs().  Now all numbers are
-  saved in scientific notation.
-Update 10 Apr 2003:
-  1.  It is now possible to enter the data as a list of variable names.
-      For example, before you had to enter data as,
-        data <- list (n=8, y=c(28,8,-3,7,-1,1,18,12))
-      or
-        n <- 8
-        y <- c(28,8,-3,7,-1,1,18,12)
-        data <- list (n=n, y=y)
-      Now you can enter the data as,
-        n <- 8
-        y <- c(28,8,-3,7,-1,1,18,12)
-        data <- list ("n", "y")
-      The bugs() function will figure out which method you are using (based
-      on whether "data" is a list of numbers or a vector of character
-      strings).
-      This doesn't look like much, but it's convenient when you're entering
-      lots of data!
-  2.  It is now possible to enter the initial values as a function,
-      so as to automatically a random list of inits for each of the chains.
-      For example, in the 8-schools example below, we can do:
-        inits <- function()
-          list (theta=rnorm(J,0,1), mu.theta=rnorm(1,0,100), sigma.theta=runif(1,0,100))
-
-      to set up the inits as a function (rather than setting up n.chains
-      sets of specific initial values).  Then, the function call,
-        schools.sim <- bugs (data, inits, parameters, "schools.txt", n.chains=3, n.iter=1000)
-      automatically sets up 3 sets of initial values (each a list of
-      theta, mu.theta, sigma.theta).
-  3.  Bug in the initial rounding (the function round.bugs()) has been fixed.
-      Thanks for Mark Clements for finding the bug and fixing it!
-      Also, we have set the default rounding to 5 digits instead of 2.
-Update 01 Apr 2003:  use layout() rather than split.screen() for graphical
-  display
-Update 18 Mar 2003:
-  1.  Get the Bugs configuration information from the original file
-      (Registry_default.odc) rather than overwriting each time.  (Fixes a
-      bug that occurred when R was interrupted in the middle of a Bugs run.)
-  2.  Display different colored dots in the right panel of the graphical
-      display, to show the medians from each chain.
-Update 13 Mar 2003:  fix minor bug in monitor()
-Update 10 Mar 2003:  fix bug in pD and DIC calculations
-Update 7 Mar 2003:
-  1.  Fix display.parallel=T option by adding min.width so that very
-      intervals are still visible.
-  2.  Compute pD separately for each sequence (which gives much more
-      reasonable estimates before convergence).
-Update 8 Feb 2003:  minor fixes in graphical display
-Update 6 Feb 2003:
-  1.  Approximate "effective sample size" n.eff given for each parameter.
-  2.  More explanatory material displayed.
-  3.  Use bringToTop() to automatically bring up the graphics window.
-Update 4 Feb 2003:
-  1.  Automatically compute the deviance, DIC, and pD.  Bugs will not
-      always compute DIC and pD, so we do so using the definition,
-      DIC = E(deviance) + pD, using var(deviance)/2 as an estimate of pD.
-      (This is derived from the chi^2 distribution.  We can't use the
-      Spiegelhalter et al. definition of DIC because we don't have access
-      to the deviance function.)
-  2.  Set default for n.thin so that, after thinning, the total number
-      saved iterations, n.sims, is approximately 1000.
-Update 14 Jan 2003 to run with the new WinBugs1.4.  You may see an error
-  message and need to fix the dos.location assignment in bugs().
-Update 6 Jan 2003:
-  1.  Fix of bug that occurred with uppercase and lowercase variable names
-  2.  Set default for n.thin so that no more than about 500 iterations
-      will be saved from each sequence
-  3.  New option "display.parallel" added to show 80% inferences from
-      parallel sequences on the right panel of the graphical display.  This
-      can be useful to understand what is going on when there are
-      convergence problems.
-Update 26 Dec 2002:  fix of minwidth in bugs.plot.summary
-Update 11 Dec 2002:
-  1.  Automatic fixing of adaptive phases.  Now you no longer need to run
-      for thousands of iterations when slice or Metropolis sampling is used.
-  2.  Various minor fixes
-Update 10 Dec 2002:
-  1.  Cool graphical display of convergence and inferences!
-  2.  New "attach2" function that overwrites so that all components of
-      the list are attached
-Update 29 Nov 2002:
-  1.  Fix of bug in 24 Nov update.
-  2.  Fix of bug in 16 Nov update.
-  3.  Length of chains is now pecified in terms of "n.iter" rather than
-      "n.keep".
-Update 24 Nov 2002:  improved treatment of "parameters.to.save".  For
-  example, you can now use "alpha" to indicate an entire array of parameters,
-  whereas before you had to save "alpha[]" or "alpha[,]" or whatever.
-Update 16 Nov 2002:  mean, sd, median added to outputs
-Update 4 Nov 2002:  more error-flagging added
-Update 26 Oct 2002:
-  1.  Parameters saved in order of the "parameters.to.save" vector
-      (not alphabetical order).
-  2.  Output saved in both matrix and list form.
-  3.  With the attach.sims=T setting (which is the default), the simulations
-      for all the saved parameters are saved as R objects.  This is
-      convenient for later use of the simulations.
-Updates to 16 Oct 2002:  more error-flagging added, mean/sd added to summary,
-  fixing scientific notation so Bugs can always read data and inits
-Update 21 Sept 2002:  "quit=F" option changed to "debug=T"
-First version written 18 Sept 2002 by Andrew Gelman,
-  adapted from the EmBedBugs package by Kenneth Rice

Copied: trunk/R2WinBUGS/inst/NEWS (from rev 65, trunk/R2WinBUGS/Changes)
===================================================================
--- trunk/R2WinBUGS/inst/NEWS	                        (rev 0)
+++ trunk/R2WinBUGS/inst/NEWS	2007-09-18 13:21:09 UTC (rev 67)
@@ -0,0 +1,237 @@
+Changes to R2WinBUGS:
+=====================
+
+Update 2.1-6 (23 August 2007):
+- reverting back to use thin.updater since it is faster, however CODA files
+  have "wrong" indexes
+- WINE arguments are now set in such a way that defaults work on Windows
+  and Linux
+- minor formatting in the code and help files
+
+Update 2.1-5 (12 June 2007):
+- proper indexing of CODA files also in R version
+- fixed useWINE documentation in bugs help page
+- note on supported BUGS versions
+- as.bugs.array now returns info on used rule for pD i.e. var(deviance)/2
+    or Dbar-Dhat
+- some internal fixes related to handling of DIC
+- merging and reversing ChangeLog files
+
+Update 2.1-4 (20 May 2007):
+- Depending on coda now (Namespace issues)
+- some more fixes for codetools checks
+- Vignette has been updated
+
+Update 2.1-3 (13 May 2007):
+- Ported to S-PLUS by Insightful Corp.
+- some fixes for codetools checks
+
+Update 2.0-4 (01 November 2006):
+- print.bugs / plot.bugs documentation fixes
+- write.model() fix
+
+Update 2.0-3 (06 October 2006):
+- \\. -> [.] in regular expressions
+
+Update 2.0-2 (26 July 2006):
+- changes for DIC, making use of BUGS internal calculations
+- some doc fixes
+
+Update 2.0-1 (26 May 2006):
+- some wine patches for 2.2-0 by Gregor Gorjanc
+
+Update 2.0-0 (08 May 2006):
+- bugs() doc fix/updates on scrambling
+- bugs.run() has new arg useWINE (by Gregor Gorjanc)
+- bugs() and bugs.script() patched for WINEPATH issue
+- bugs.script() changed to save log file in ASCII
+- new function bugs.log() by Gregor Gorjanc
+- new functions as.bugs.array, openbugs and sort.name by
+  Jouni Kerman and Andrew Gelman
+- new function write.model() based on ideas from Jouni Kerman
+
+Update 1.1-1 (17 Feb 2006):
+- WINE tweaks (mainly by Gregor Gorjanc)
+
+Update 1.1-0 (14 Dec 2005):
+- Contribution by Ben Bolker and Yun Yan's rbugs package:
+  make R2WinBUGS work under WINE
+
+Update 1.0-1 (14 Nov 2005):
+- make inits=NULL work (again ?)
+
+Update 1.0-0 (05 Aug 2005):
+- attach.all(), detach.all(), attach.bugs() and detach.bugs() added/changed
+  more or less according to Andrew Gelman's current bugs.R
+
+Update 0.2-9 (26 July 2005):
+- bugs has new argument clearWD
+
+Update 0.2-8 (30 May 2005):
+- bugs passed DIC to bugs.script in order to be able to disable it
+
+Update 0.2-6 (18 May 2005):
+- bugs() changes in order to return a file names of coda output files
+- new read.bugs() returns a coda mcmc.list object, if codaPkg=TRUE.
+
+Update 0.2-5 (20 Oct 2004):
+- bugs() and bugs.script() have a new argument bin that allows to specify
+  a number of iterations. After each "bin" iterations the coda files are saved.
+
+Update 0.2-4 (05 Oct 2004):
+- bugs.script() did not work for large n.iter values in update step
+  (no scientific notation allowed)
+
+Update 0.2-3 (10 Sept 2004):
+- bugs.data.inits split to bugs.inits and bugs.data, the latter exported
+  from the Namespace.
+  Now we can use already written data files in bugs().
+
+Update 0.2-2 (28 Apr 2004):
+- schools data: original (see references) instead of the rounded data
+
+During the process of packaging R2WinBUGS_0.1 - R2WinBUGS_0.2-1,
+quite a lot of changes had been made. Those changes are not
+documented anywhere ...
+
+During the process of packaging R2WinBUGS_0.1, quite a lot of changes had
+been made. Those changes are not documented anywhere ...
+
+Changes prior to R2WinBUGS_0.1:
+===============================
+
+Update 30 Oct 2003:
+  1.  Minor change to a return() statement to be compatible with R 1.8
+  2.  Just a warning (from Ben Goodrich):  if you are running Bugs.R inside
+      a loop, you have to be careful with the data() and the inits()
+      functions since they will not necessarily recognize locally-defined
+      variables.  One workaround is to define the variables used in data()
+      and inits() using global assignments (<<-), but this can sometimes
+      make the program run slower.
+Update 29 Aug 2003:
+  1.  Fixed "bugs.data.inits" function so you can use data that have the
+      same names as R functions.
+  2.  Changed T and F to TRUE and FALSE everywhere in case the variables
+      T and F are used as data in the main program
+  3.  Caution:  if you are entering the data as a list of variable names
+      (see 10 Apr 2003 update, item 1), the data to be input into must
+      be global variables.  This can be relevant if you are running bugs()
+      inside an R function.
+  4.  Caution:  bugs() has difficulty processing ragged arrays.  It is
+      better to save a whole matrix (e.g., "theta") rather than parts
+      (e.g., "theta[1:10,1]", "theta[1:5,2]").  If you want to save
+      part of a vector, you should do it as "theta[1:2]", not "theta[1]",
+      "theta[2]".
+Update 30 Apr 2003:  added time monitoring
+Update 29 Apr 2003:
+  1.  The "attach.all" function (no longer called "attach2") overwrites
+      so that all components of a list or data frame get attached.
+  2.  Program now looks in the directory /winbug~1/ rather than /winbug~2/
+  3.  Graphics parameters for margins are returned to their original state
+      at the end of the program.
+  4.  Added "digits.summary" option to the numerical display.
+  5.  Added "last.values" output:  a list that can be input as "inits"
+      if you want to run the simulations longer.
+Update 13 Apr 2003:  fixed new bug in round.bugs().  Now all numbers are
+  saved in scientific notation.
+Update 10 Apr 2003:
+  1.  It is now possible to enter the data as a list of variable names.
+      For example, before you had to enter data as,
+        data <- list (n=8, y=c(28,8,-3,7,-1,1,18,12))
+      or
+        n <- 8
+        y <- c(28,8,-3,7,-1,1,18,12)
+        data <- list (n=n, y=y)
+      Now you can enter the data as,
+        n <- 8
+        y <- c(28,8,-3,7,-1,1,18,12)
+        data <- list ("n", "y")
+      The bugs() function will figure out which method you are using (based
+      on whether "data" is a list of numbers or a vector of character
+      strings).
+      This doesn't look like much, but it's convenient when you're entering
+      lots of data!
+  2.  It is now possible to enter the initial values as a function,
+      so as to automatically a random list of inits for each of the chains.
+      For example, in the 8-schools example below, we can do:
+        inits <- function()
+          list (theta=rnorm(J,0,1), mu.theta=rnorm(1,0,100), sigma.theta=runif(1,0,100))
+
+      to set up the inits as a function (rather than setting up n.chains
+      sets of specific initial values).  Then, the function call,
+        schools.sim <- bugs (data, inits, parameters, "schools.txt", n.chains=3, n.iter=1000)
+      automatically sets up 3 sets of initial values (each a list of
+      theta, mu.theta, sigma.theta).
+  3.  Bug in the initial rounding (the function round.bugs()) has been fixed.
+      Thanks for Mark Clements for finding the bug and fixing it!
+      Also, we have set the default rounding to 5 digits instead of 2.
+Update 01 Apr 2003:  use layout() rather than split.screen() for graphical
+  display
+Update 18 Mar 2003:
+  1.  Get the Bugs configuration information from the original file
+      (Registry_default.odc) rather than overwriting each time.  (Fixes a
+      bug that occurred when R was interrupted in the middle of a Bugs run.)
+  2.  Display different colored dots in the right panel of the graphical
+      display, to show the medians from each chain.
+Update 13 Mar 2003:  fix minor bug in monitor()
+Update 10 Mar 2003:  fix bug in pD and DIC calculations
+Update 7 Mar 2003:
+  1.  Fix display.parallel=T option by adding min.width so that very
+      intervals are still visible.
+  2.  Compute pD separately for each sequence (which gives much more
+      reasonable estimates before convergence).
+Update 8 Feb 2003:  minor fixes in graphical display
+Update 6 Feb 2003:
+  1.  Approximate "effective sample size" n.eff given for each parameter.
+  2.  More explanatory material displayed.
+  3.  Use bringToTop() to automatically bring up the graphics window.
+Update 4 Feb 2003:
+  1.  Automatically compute the deviance, DIC, and pD.  Bugs will not
+      always compute DIC and pD, so we do so using the definition,
+      DIC = E(deviance) + pD, using var(deviance)/2 as an estimate of pD.
+      (This is derived from the chi^2 distribution.  We can't use the
+      Spiegelhalter et al. definition of DIC because we don't have access
+      to the deviance function.)
+  2.  Set default for n.thin so that, after thinning, the total number
+      saved iterations, n.sims, is approximately 1000.
+Update 14 Jan 2003 to run with the new WinBugs1.4.  You may see an error
+  message and need to fix the dos.location assignment in bugs().
+Update 6 Jan 2003:
+  1.  Fix of bug that occurred with uppercase and lowercase variable names
+  2.  Set default for n.thin so that no more than about 500 iterations
+      will be saved from each sequence
+  3.  New option "display.parallel" added to show 80% inferences from
+      parallel sequences on the right panel of the graphical display.  This
+      can be useful to understand what is going on when there are
+      convergence problems.
+Update 26 Dec 2002:  fix of minwidth in bugs.plot.summary
+Update 11 Dec 2002:
+  1.  Automatic fixing of adaptive phases.  Now you no longer need to run
+      for thousands of iterations when slice or Metropolis sampling is used.
+  2.  Various minor fixes
+Update 10 Dec 2002:
+  1.  Cool graphical display of convergence and inferences!
+  2.  New "attach2" function that overwrites so that all components of
+      the list are attached
+Update 29 Nov 2002:
+  1.  Fix of bug in 24 Nov update.
+  2.  Fix of bug in 16 Nov update.
+  3.  Length of chains is now pecified in terms of "n.iter" rather than
+      "n.keep".
+Update 24 Nov 2002:  improved treatment of "parameters.to.save".  For
+  example, you can now use "alpha" to indicate an entire array of parameters,
+  whereas before you had to save "alpha[]" or "alpha[,]" or whatever.
+Update 16 Nov 2002:  mean, sd, median added to outputs
+Update 4 Nov 2002:  more error-flagging added
+Update 26 Oct 2002:
+  1.  Parameters saved in order of the "parameters.to.save" vector
+      (not alphabetical order).
+  2.  Output saved in both matrix and list form.
+  3.  With the attach.sims=T setting (which is the default), the simulations
+      for all the saved parameters are saved as R objects.  This is
+      convenient for later use of the simulations.
+Updates to 16 Oct 2002:  more error-flagging added, mean/sd added to summary,
+  fixing scientific notation so Bugs can always read data and inits
+Update 21 Sept 2002:  "quit=F" option changed to "debug=T"
+First version written 18 Sept 2002 by Andrew Gelman,
+  adapted from the EmBedBugs package by Kenneth Rice


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