From noreply at r-forge.r-project.org  Fri Aug 12 19:10:44 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 12 Aug 2016 19:10:44 +0200 (CEST)
Subject: [R-gregmisc-commits] r2129 - pkg/SASxport
Message-ID: <20160812171044.11A721868F7@r-forge.r-project.org>

Author: warnes
Date: 2016-08-12 19:10:43 +0200 (Fri, 12 Aug 2016)
New Revision: 2129

Modified:
   pkg/SASxport/DESCRIPTION
   pkg/SASxport/NAMESPACE
Log:
Commit linkgering changes.

Modified: pkg/SASxport/DESCRIPTION
===================================================================
--- pkg/SASxport/DESCRIPTION	2016-05-31 17:03:33 UTC (rev 2128)
+++ pkg/SASxport/DESCRIPTION	2016-08-12 17:10:43 UTC (rev 2129)
@@ -3,8 +3,8 @@
 Title: Read and Write SAS XPORT Files
 Version: 1.5.4
 Date: 2016-03-25
-Description: This package provides functions for reading, listing
-  the contents of, and writing SAS xport format files.
+Description: Functions for reading, listing
+    the contents of, and writing SAS xport format files.
   The functions support reading and writing of either
   individual data frames or sets of data frames.  Further,
   a mechanism has been provided for customizing how

Modified: pkg/SASxport/NAMESPACE
===================================================================
--- pkg/SASxport/NAMESPACE	2016-05-31 17:03:33 UTC (rev 2128)
+++ pkg/SASxport/NAMESPACE	2016-08-12 17:10:43 UTC (rev 2129)
@@ -3,6 +3,7 @@
 importFrom(chron, chron, times)
 importFrom(utils, packageDescription)
 importFrom(Hmisc, label, label.default, "label<-", "label<-.default")
+importFrom(utils, download.file)
 
 export(
        toSAS,


From noreply at r-forge.r-project.org  Fri Aug 12 19:11:58 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 12 Aug 2016 19:11:58 +0200 (CEST)
Subject: [R-gregmisc-commits] r2130 - pkg/gdata
Message-ID: <20160812171158.880561868F7@r-forge.r-project.org>

Author: warnes
Date: 2016-08-12 19:11:58 +0200 (Fri, 12 Aug 2016)
New Revision: 2130

Modified:
   pkg/gdata/NAMESPACE
Log:
Add mv to exported namespace

Modified: pkg/gdata/NAMESPACE
===================================================================
--- pkg/gdata/NAMESPACE	2016-08-12 17:10:43 UTC (rev 2129)
+++ pkg/gdata/NAMESPACE	2016-08-12 17:11:58 UTC (rev 2130)
@@ -30,6 +30,7 @@
        matchcols,
        nobs,  # default method now provided by stats package
        nPairs,
+       mv,
        read.xls,
        rename.vars,
        remove.vars,


From noreply at r-forge.r-project.org  Fri Aug 12 19:15:40 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 12 Aug 2016 19:15:40 +0200 (CEST)
Subject: [R-gregmisc-commits] r2131 - in pkg/gmodels: . R inst man
Message-ID: <20160812171540.573BF1868F7@r-forge.r-project.org>

Author: warnes
Date: 2016-08-12 19:15:39 +0200 (Fri, 12 Aug 2016)
New Revision: 2131

Modified:
   pkg/gmodels/DESCRIPTION
   pkg/gmodels/NAMESPACE
   pkg/gmodels/R/ci.R
   pkg/gmodels/R/fit.contrast.R
   pkg/gmodels/inst/ChangeLog
   pkg/gmodels/inst/NEWS
   pkg/gmodels/man/ci.Rd
   pkg/gmodels/man/estimable.Rd
   pkg/gmodels/man/fit.contrast.Rd
Log:
Updates...

Modified: pkg/gmodels/DESCRIPTION
===================================================================
--- pkg/gmodels/DESCRIPTION	2016-08-12 17:11:58 UTC (rev 2130)
+++ pkg/gmodels/DESCRIPTION	2016-08-12 17:15:39 UTC (rev 2131)
@@ -1,14 +1,14 @@
 Package: gmodels
-Version: 2.16.2
-Date: 2015-07-21
-Title: Various R Programming Tools for Model Fitting
+Version: 2.16.0
+Date: 2014-07-24
+Title: Various R programming tools for model fitting
 Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley, and Randall C
         Johnson. Contributions from Randall C. Johnson are Copyright
         (2005) SAIC-Frederick, Inc. Funded by the Intramural Research
         Program, of the NIH, National Cancer Institute, Center for
         Cancer Research under NCI Contract NO1-CO-12400.
 Maintainer: Gregory R. Warnes <greg at warnes.net>
-Description: Various R programming tools for model fitting.
+Description: Various R programming tools for model fitting
 Depends: R (>= 1.9.0)
 Suggests: gplots, gtools, Matrix, nlme, lme4 (>= 0.999999-0)
 Imports: MASS, gdata

Modified: pkg/gmodels/NAMESPACE
===================================================================
--- pkg/gmodels/NAMESPACE	2016-08-12 17:11:58 UTC (rev 2130)
+++ pkg/gmodels/NAMESPACE	2016-08-12 17:15:39 UTC (rev 2131)
@@ -14,19 +14,19 @@
        summary.glh.test
 )
 
-S3method(ci, numeric)
+S3method(ci, default)
 S3method(ci, binom)
 S3method(ci, lm)
 S3method(ci, lme)
-##S3method(ci, mer)
+S3method(ci, mer)
 S3method(ci, estimable)
 
 S3method(fit.contrast, lm)
 S3method(fit.contrast, lme)
-##S3method(fit.contrast, mer)
+S3method(fit.contrast, mer)
 
 S3method(estimable, default)
-##S3method(estimable, mer)
+S3method(estimable, mer)
 S3method(estimable, mlm)
 
 S3method(print, glh.test)
@@ -35,17 +35,3 @@
 importFrom(MASS, ginv)
 importFrom(gdata, frameApply)
 importFrom(gdata, nobs)
-
-importFrom(stats, "chisq.test")
-importFrom(stats, "coef")
-importFrom(stats, "family")
-importFrom(stats, "fisher.test")
-importFrom(stats, "mcnemar.test")
-importFrom(stats, "pchisq")
-importFrom(stats, "pf")
-importFrom(stats, "pt")
-importFrom(stats, "qbeta")
-importFrom(stats, "qt")
-importFrom(stats, "sd")
-importFrom(stats, "summary.glm")
-importFrom(stats, "summary.lm")

Modified: pkg/gmodels/R/ci.R
===================================================================
--- pkg/gmodels/R/ci.R	2016-08-12 17:11:58 UTC (rev 2130)
+++ pkg/gmodels/R/ci.R	2016-08-12 17:15:39 UTC (rev 2131)
@@ -5,6 +5,7 @@
 
 ci.numeric <- function(x, confidence=0.95,alpha=1-confidence,na.rm=FALSE,...)
   {
+    warning("No class or unkown class.  Using default calcuation.")
     est <- mean(x, na.rm=na.rm)
     stderr <-  sd(x, na.rm=na.rm)/sqrt(nobs(x));
     ci.low  <- est + qt(alpha/2, nobs(x)-1) * stderr
@@ -113,3 +114,14 @@
 
     retval
   }
+
+
+ci.fit_contrast <- function (x, confidence = 0.95, alpha = 1 - confidence, ...) 
+{
+  if( !all(c("lower CI", "upper CI") %in% colnames(x) ) )
+    stop("object does not contain confidence interval information.")
+  colnames(x) <- c("Estimate", "Std. Error", "Delete", 
+                   "p-value", 
+                   "CI lower", "CI upper")
+  x[, c(1, 5:6, 2, 4), drop=FALSE]
+}

Modified: pkg/gmodels/R/fit.contrast.R
===================================================================
--- pkg/gmodels/R/fit.contrast.R	2016-08-12 17:11:58 UTC (rev 2130)
+++ pkg/gmodels/R/fit.contrast.R	2016-08-12 17:15:39 UTC (rev 2131)
@@ -1,7 +1,9 @@
 # $Id$
 
 fit.contrast.lm <- function(model, varname, coeff, showall=FALSE,
-                            conf.int=NULL, df=FALSE, ...)
+                            conf.int, 
+                            df=FALSE, 
+                            ...)
 {
   # check class of model
   if( !(any(class(model) %in% c("lm", "aov", "lme") ) ))
@@ -88,7 +90,7 @@
 
     }
 
-  if(!is.null(conf.int)) # add confidence intervals
+  if(!missing(conf.int) && !is.null(conf.int)) # add confidence intervals
     {
       alpha <- 1-conf.int
       retval <- cbind( retval,
@@ -99,9 +101,11 @@
     }
 
   if(!df)
-    return(retval[,-5,drop=FALSE])
-  else
-    return(retval)
+    retval <- retval[,-5,drop=FALSE]
+  
+  class(retval) <- "fit_contrast"
+  
+  retval  
 }
 
 # fit.contrast.lme and fit.contrast.mer are necessary because
@@ -202,3 +206,8 @@
 fit.contrast <- function(model, varname, coeff, ...)
   UseMethod("fit.contrast")
 
+coef.fit_contrast <- function(object, ...)
+  object
+
+print.fit_contrast <- function(object, ...)
+  print(unclass(object))

Modified: pkg/gmodels/inst/ChangeLog
===================================================================
--- pkg/gmodels/inst/ChangeLog	2016-08-12 17:11:58 UTC (rev 2130)
+++ pkg/gmodels/inst/ChangeLog	2016-08-12 17:15:39 UTC (rev 2131)
@@ -1,182 +1,194 @@
-2015-07-19  warnes
-
-	* [r2058] R/ci.R, man/ci.Rd: ci.binom() was using an incorrect
-	  method for calculating binomial confidence interval. The revised
-	  code calculates the Clopper-Pearson 'exect' interval, which is
-	  *conservative* due to the discrete nature of the binomial
-	  distribution.
-
-2015-05-02  warnes
-
-	* [r2018] Rename 'trunk' to 'pkg' for compatibility with R-forge
-
-2015-04-06  warnes
-
-	* [r1916] Add ChangeLog files to repository
-
 2014-07-24  warnes
 
-	* [r1869] Update NEWS for gmodels 2.16.0
-	* [r1868] - Estimable now adds the class 'estimable' to returned
-	  objects.
+	* [r1868] DESCRIPTION, NAMESPACE, R/ci.R, R/estimable.R, man/ci.Rd,
+	  man/estimable.Rd: - Estimable now adds the class 'estimable' to
+	  returned objects.
 	  - New ci() method for estimable objects.
 	  - Minor improvemets to man page formatting.
 
 2013-07-18  warnes
 
-	* [r1710] Looks like Brian Ripley repackaged for R 3.0.0 and bumped
-	  version number, so change it to 2.15.5
-	* [r1709] Update for gmodels 2.15.4
-	* [r1708] Update to current Rd syntax
-	* [r1707] Correct bug in estimable.mlm
+	* [r1710] DESCRIPTION, inst/NEWS: Looks like Brian Ripley
+	  repackaged for R 3.0.0 and bumped version number, so change it to
+	  2.15.5
+	* [r1709] DESCRIPTION, inst/NEWS: Update for gmodels 2.15.4
+	* [r1708] man/ci.Rd: Update to current Rd syntax
+	* [r1707] R/estimable.mlm.R, test/test_estimable_mlm.R: Correct bug
+	  in estimable.mlm
 
 2013-07-15  warnes
 
-	* [r1706] Remove unused argument to ci.mer
+	* [r1706] R/ci.R, man/ci.Rd: Remove unused argument to ci.mer
 
 2012-06-28  warnes
 
-	* [r1577] Update for gmodels version 2.15.3.
-	* [r1576] Move percentile() function to a separate file.
-	* [r1575] Update est.mer() to support new S4 "mer" class.
-	* [r1574] Make lme4 example executable.
+	* [r1577] DESCRIPTION, inst/NEWS: Update for gmodels version
+	  2.15.3.
+	* [r1576] R/percentile.R: Move percentile() function to a separate
+	  file.
+	* [r1575] R/est.lmer.R, R/est.mer.R: Update est.mer() to support
+	  new S4 "mer" class.
+	* [r1574] man/ci.Rd: Make lme4 example executable.
 
 2012-06-27  warnes
 
-	* [r1573] Add test code submitted by Ariel.Muldoon at oregonstate.edu.
+	* [r1573] test/lme-test.R: Add test code submitted by
+	  Ariel.Muldoon at oregonstate.edu.
 
 2012-04-19  warnes
 
-	* [r1528] Update for release 2.15.2
-	* [r1527] Update version and date.
-	* [r1526] The 'Design' package has been replaced my 'rms', so
-	  update man page references.
-	* [r1525] More fixes for support of S4 'mer' class from lme4
-	  package.
-	* [r1524] Split long line.
-	* [r1523] Changes to pass R CMD check
+	* [r1528] inst/NEWS: Update for release 2.15.2
+	* [r1527] DESCRIPTION: Update version and date.
+	* [r1526] man/estimable.Rd: The 'Design' package has been replaced
+	  my 'rms', so update man page references.
+	* [r1525] R/ci.R, R/est.mer.R: More fixes for support of S4 'mer'
+	  class from lme4 package.
+	* [r1524] man/coefFrame.Rd: Split long line.
+	* [r1523] man/ci.Rd, man/glh.test.Rd: Changes to pass R CMD check
 
 2011-12-14  warnes
 
-	* [r1521] Improve formatting of ci.mer().
-	* [r1520] Modify est.mer to work with recent lme4 'mer' S4 objects.
+	* [r1521] R/ci.R: Improve formatting of ci.mer().
+	* [r1520] R/est.mer.R: Modify est.mer to work with recent lme4
+	  'mer' S4 objects.
 
 2011-01-16  warnes
 
-	* [r1466] Fix warnings reported by R CMD check. Update version
-	  number to 2.15.1.
+	* [r1466] DESCRIPTION, inst/NEWS, man/ci.Rd, man/estimable.Rd,
+	  man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
+	  man/make.contrasts.Rd: Fix warnings reported by R CMD check.
+	  Update version number to 2.15.1.
 
 2009-05-09  warnes
 
-	* [r1337] Add tests for lme4 'mer' objects
-	* [r1336] Update for 2.15.0
-	* [r1335] Update description for 2.15.0
-	* [r1334] Add support for lme4's 'mer' objects
-	* [r1333] Add support for lme4's 'mer' objects
-	* [r1332] Fix .Rd syntax error
-	* [r1331] Add softlinks for ChangeLog and NEWS to top level dir for
-	  convenience
-	* [r1330] Move ChangeLog and NEWS files into inst directory
-	* [r1329] Update Greg's email address
+	* [r1337] test, test/lme-test.R: Add tests for lme4 'mer' objects
+	* [r1336] inst/NEWS: Update for 2.15.0
+	* [r1335] DESCRIPTION: Update description for 2.15.0
+	* [r1334] R/est.mer.R: Add support for lme4's 'mer' objects
+	* [r1333] NAMESPACE, R/ci.R, R/est.lmer.R, R/estimable.R,
+	  R/fit.contrast.R, R/to.est.R: Add support for lme4's 'mer'
+	  objects
+	* [r1332] man/glh.test.Rd: Fix .Rd syntax error
+	* [r1331] NEWS: Add softlinks for ChangeLog and NEWS to top level
+	  dir for convenience
+	* [r1330] ChangeLog, NEWS, inst, inst/NEWS: Move ChangeLog and NEWS
+	  files into inst directory
+	* [r1329] DESCRIPTION, man/ci.Rd, man/estimable.Rd,
+	  man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
+	  man/make.contrasts.Rd: Update Greg's email address
 
 2008-04-10  warnes
 
-	* [r1255] Improve languages a bit
+	* [r1255] man/ci.Rd: Improve languages a bit
 
 2008-01-02  warnes
 
-	* [r1236] Update Marc's email address
+	* [r1236] man/CrossTable.Rd: Update Marc's email address
 
 2007-12-12  warnes
 
-	* [r1233] Move copyright notice for Randall's contributions from
-	  License section to Author section of the DESCRIPTION file.
+	* [r1233] DESCRIPTION: Move copyright notice for Randall's
+	  contributions from License section to Author section of the
+	  DESCRIPTION file.
 
 2007-12-07  warnes
 
-	* [r1232] Update DESCRIPTION and NEWS for release 2.14.1
-	* [r1231] Correct minor typos in man page for estimable()
-	* [r1230] Add support for lme models to estimable()
-	* [r1229] Replace non-ascii characters in Soren's name with
-	  (equivalent?) ascii character to avoid character encoding issues.
+	* [r1232] DESCRIPTION, NEWS: Update DESCRIPTION and NEWS for
+	  release 2.14.1
+	* [r1231] man/estimable.Rd: Correct minor typos in man page for
+	  estimable()
+	* [r1230] R/estimable.R: Add support for lme models to estimable()
+	* [r1229] man/estimable.Rd: Replace non-ascii characters in Soren's
+	  name with (equivalent?) ascii character to avoid character
+	  encoding issues.
 
 2007-10-22  warnes
 
-	* [r1196] Clarify GPL version
+	* [r1196] DESCRIPTION: Clarify GPL version
 
 2007-07-26  warnes
 
-	* [r1105] Add support for mlm to estimable().
-	* [r1104] Add estimable method for mlm objects
+	* [r1105] DESCRIPTION, NAMESPACE, NEWS, R/estimable.mlm.R,
+	  man/estimable.Rd: Add support for mlm to estimable().
+	* [r1104] R/estimable.R, R/estimable.mlm.R: Add estimable method
+	  for mlm objects
 
 2007-03-09  warnes
 
-	* [r1079] Remove stray character
-	* [r1078] Update NEWS file.
-	* [r1077] Update version number
-	* [r1076] Minor code formatting changes
-	* [r1075] Flip lower and upper interval in ci.lmer(). Add example
-	  to man page.
-	* [r1074] Fix some old email addressses that got missed
+	* [r1079] R/ci.R: Remove stray character
+	* [r1078] NEWS: Update NEWS file.
+	* [r1077] DESCRIPTION: Update version number
+	* [r1076] R/ci.R: Minor code formatting changes
+	* [r1075] R/est.lmer.R, man/ci.Rd: Flip lower and upper interval in
+	  ci.lmer(). Add example to man page.
+	* [r1074] man/ci.Rd, man/estimable.Rd: Fix some old email
+	  addressses that got missed
 
 2006-11-29  warnes
 
-	* [r1029] Update for 2.13.1
-	* [r1028] Correct declartion of S3 methods for estimable()
-	* [r1027] Add additional suggested packages
-	* [r1026] - Add generic
+	* [r1029] NEWS: Update for 2.13.1
+	* [r1028] NAMESPACE: Correct declartion of S3 methods for
+	  estimable()
+	* [r1027] DESCRIPTION: Add additional suggested packages
+	* [r1026] R/estimable.R, man/estimable.Rd: - Add generic
 	  - Fix code vs. doc inconsistiencies
 
 2006-11-28  warnes
 
-	* [r1025] Remove extraneous comma that causes errors in R 2.5.0
+	* [r1025] R/ci.R, R/estimable.R, R/fast.prcomp.R: Remove extraneous
+	  comma that causes errors in R 2.5.0
 
 2006-11-27  warnes
 
-	* [r1016] Update for 2.13.1
-	* [r1015] Add missing export of methods for estimable()
+	* [r1016] DESCRIPTION, NEWS: Update for 2.13.1
+	* [r1015] DESCRIPTION, NAMESPACE: Add missing export of methods for
+	  estimable()
 
 2006-11-14  ggorjan
 
-	* [r1012] Removed executable property
+	* [r1012] R/ci.R, R/fast.prcomp.R, man/ci.Rd: Removed executable
+	  property
 
 2006-08-02  warnes
 
-	* [r977] Update my email address
+	* [r977] man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
+	  man/make.contrasts.Rd: Update my email address
 
 2006-06-06  nj7w
 
-	* [r966] Updated ci, estimable and fit.contrast as per Randall
-	  Johnson
+	* [r966] man/ci.Rd, man/estimable.Rd, man/fit.contrast.Rd: Updated
+	  ci, estimable and fit.contrast as per Randall Johnson
 
 2006-06-05  nj7w
 
-	* [r965] Additions as per Randall C Johnson
-	* [r964] Additions as per Randall C Johnson
-	* [r963] - New function to estimate CI's and p-values using
-	  mcmcsamp() from the
+	* [r965] DESCRIPTION: Additions as per Randall C Johnson
+	* [r964] R/ci.R, R/estimable.R, R/fit.contrast.R, R/to.est.R:
+	  Additions as per Randall C Johnson
+	* [r963] R/est.lmer.R: - New function to estimate CI's and p-values
+	  using mcmcsamp() from the
 	  Matrix package
 
 2006-05-05  nj7w
 
-	* [r959] Fixed an error: According to Marc Schwartz - there was an
-	  error when a matrix without dimnames(or names(dimnames)) was
-	  passed as x argument
+	* [r959] R/CrossTable.R, man/CrossTable.Rd: Fixed an error:
+	  According to Marc Schwartz - there was an error when a matrix
+	  without dimnames(or names(dimnames)) was passed as x argument
 
 2005-12-13  nj7w
 
-	* [r808] Removed ChangeLog
-	* [r807] Updated NEWS
+	* [r808] ChangeLog: Removed ChangeLog
+	* [r807] NEWS: Updated NEWS
 
 2005-12-12  nj7w
 
-	* [r796] Updated version number for CRAN
+	* [r796] DESCRIPTION: Updated version number for CRAN
 
 2005-12-04  warnes
 
-	* [r781] Update for 2.11.0
-	* [r780] Integration of code changes suggested by Randall C Johnson
-	  to add
+	* [r781] NEWS: Update for 2.11.0
+	* [r780] DESCRIPTION, NAMESPACE, R/ci.R, R/estimable.R,
+	  R/fit.contrast.R, R/to.est.R, man/ci.Rd, man/estimable.Rd:
+	  Integration of code changes suggested by Randall C Johnson to add
 	  support for lmer (lme version 4) objects to ci(), estimable(),
 	  and
 	  fit.contrast().
@@ -191,48 +203,52 @@
 
 2005-12-01  nj7w
 
-	* [r776] Updated Greg's email address
+	* [r776] man/ci.Rd, man/coefFrame.Rd, man/estimable.Rd,
+	  man/fit.contrast.Rd, man/make.contrasts.Rd: Updated Greg's email
+	  address
 
 2005-10-27  warnes
 
-	* [r709] Update version number. Bump minor version since we added
-	  functionality.
-	* [r708] Add ci.binom() to NAMESPACE, bump version
+	* [r709] DESCRIPTION: Update version number. Bump minor version
+	  since we added functionality.
+	* [r708] DESCRIPTION, NAMESPACE: Add ci.binom() to NAMESPACE, bump
+	  version
 
 2005-10-26  warnes
 
-	* [r707] Add ci.binom
+	* [r707] R/ci.R, man/ci.Rd: Add ci.binom
 
 2005-10-25  warnes
 
-	* [r706] Add gdata::nobs to import list. Needed by ci()
+	* [r706] NAMESPACE: Add gdata::nobs to import list. Needed by ci()
 
 2005-09-12  nj7w
 
-	* [r671] Updated Greg's email
+	* [r671] man/fast.prcomp.Rd, man/glh.test.Rd: Updated Greg's email
 
 2005-09-07  nj7w
 
-	* [r667] Fixed man page
+	* [r667] man/CrossTable.Rd: Fixed man page
 
 2005-09-06  nj7w
 
-	* [r664] Updated DESCRIPTION
-	* [r663] Added NEWS
-	* [r662] Fixed the Package name
+	* [r664] DESCRIPTION: Updated DESCRIPTION
+	* [r663] NEWS: Added NEWS
+	* [r662] DESCRIPTION: Fixed the Package name
 
 2005-09-02  nj7w
 
-	* [r655] Added ChangeLog
+	* [r655] ChangeLog: Added ChangeLog
 
 2005-08-31  nj7w
 
-	* [r644] Added DESCRIPTION file
-	* [r643] removed DESCRIPTION.in
+	* [r644] DESCRIPTION: Added DESCRIPTION file
+	* [r643] DESCRIPTION.in: removed DESCRIPTION.in
 
 2005-07-11  nj7w
 
-	* [r627] Revision based on Marc Schwartz's suggestions:
+	* [r627] R/CrossTable.R, man/CrossTable.Rd: Revision based on Marc
+	  Schwartz's suggestions:
 	  1) Added 'dnn' argument to enable specification of dimnames as
 	  per table()
 	  2) Corrected bug in SPSS output for 1d table, where proportions
@@ -240,10 +256,14 @@
 
 2005-06-09  nj7w
 
-	* [r625] Updating the version number, and various help files to
-	  synchronize splitting of gregmisc bundle in 4 individual
-	  components.
-	* [r623] Updates by Marc Schwartz:
+	* [r625] R/ci.R, R/coefFrame.R, R/estimable.R, R/fast.prcomp.R,
+	  R/fit.contrast.R, R/glh.test.R, R/make.contrasts.R,
+	  man/CrossTable.Rd, man/ci.Rd, man/coefFrame.Rd, man/estimable.Rd,
+	  man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
+	  man/make.contrasts.Rd: Updating the version number, and various
+	  help files to synchronize splitting of gregmisc bundle in 4
+	  individual components.
+	* [r623] R/CrossTable.R: Updates by Marc Schwartz:
 	  CrossTable:
 	  
 	  # Revision 2.0 2005/04/27
@@ -253,95 +273,108 @@
 
 2005-05-13  nj7w
 
-	* [r621] 1) Using dQuote.ascii function in read.xls as the new
-	  version of dQuote doesn't work proprly with UTF-8 locale.
+	* [r621] man/CrossTable.Rd: 1) Using dQuote.ascii function in
+	  read.xls as the new version of dQuote doesn't work proprly with
+	  UTF-8 locale.
 	  2) Modified CrossTable.Rd usage in gmodels
 	  3) Modified heatmap.2 usage in gplots.
 
 2005-05-11  warnes
 
-	* [r620] Add dependency on gdata::frameApply.
+	* [r620] DESCRIPTION.in, NAMESPACE: Add dependency on
+	  gdata::frameApply.
 
 2005-03-31  warnes
 
-	* [r593] Add ceofFrame function to NAMESPACE
-	* [r592] coefFrame example needs to properly load ELISA data from
-	  gtools package
-	* [r588] Ensure that each file has $Id$ header, and no $Log$
-	* [r587] Add coefFrame() function contributed by Jim Rogers
+	* [r593] NAMESPACE: Add ceofFrame function to NAMESPACE
+	* [r592] man/coefFrame.Rd: coefFrame example needs to properly load
+	  ELISA data from gtools package
+	* [r588] R/CrossTable.R, man/CrossTable.Rd, man/ci.Rd,
+	  man/estimable.Rd, man/fast.prcomp.Rd, man/fit.contrast.Rd,
+	  man/glh.test.Rd, man/make.contrasts.Rd: Ensure that each file has
+	  $Id$ header, and no $Log$
+	* [r587] R/coefFrame.R, man/coefFrame.Rd: Add coefFrame() function
+	  contributed by Jim Rogers
 
 2005-01-18  warnes
 
-	* [r521] Removed Windows Line Endings
+	* [r521] R/CrossTable.R: Removed Windows Line Endings
 
 2005-01-14  nj7w
 
-	* [r518] Updated the manual to reflect prop.chisq change in its R
-	  file.
+	* [r518] man/CrossTable.Rd: Updated the manual to reflect
+	  prop.chisq change in its R file.
 
 2005-01-14  warnes
 
-	* [r517] Nitin added display of the Chisquare contribution of each
-	  cell, as suggested
+	* [r517] R/CrossTable.R: Nitin added display of the Chisquare
+	  contribution of each cell, as suggested
 	  by Greg Snow.
 
 2005-01-12  warnes
 
-	* [r515] Add dependency on R 1.9.0+ to prevent poeple from
-	  installing on old
+	* [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent
+	  poeple from installing on old
 	  versions of R which don't support namespaces.
 
 2004-12-23  nj7w
 
-	* [r507] Split the function print.CrossTable.vector in two parts -
-	  for SAS behaiour and SPSS behaviour. Also put the code of
-	  printing statistics in a function 'print.statistics'
+	* [r507] R/CrossTable.R, man/CrossTable.Rd: Split the function
+	  print.CrossTable.vector in two parts - for SAS behaiour and SPSS
+	  behaviour. Also put the code of printing statistics in a function
+	  'print.statistics'
 
 2004-12-21  warnes
 
-	* [r502] Added & extended changes made by Nitin to implement 'SPSS'
-	  format, as suggested by
+	* [r502] R/CrossTable.R: Added & extended changes made by Nitin to
+	  implement 'SPSS' format, as suggested by
 	  Dirk Enzmann <dirk.enzmann at jura.uni-hamburg.de>.
 
 2004-09-30  warneg
 
-	* [r464] Fix typos.
+	* [r464] man/glh.test.Rd: Fix typos.
 
 2004-09-27  warneg
 
-	* [r461] Updated to pass R CMD check.
+	* [r461] DESCRIPTION, DESCRIPTION.in: Updated to pass R CMD check.
 
 2004-09-03  warneg
 
-	* [r450] Add explicit package to call to quantcut in example.
-	* [r446] initial bundle checkin
+	* [r450] man/fit.contrast.Rd: Add explicit package to call to
+	  quantcut in example.
+	* [r446] DESCRIPTION, NAMESPACE, R/CrossTable.R, R/ci.R,
+	  R/estimable.R, R/fast.prcomp.R, R/fit.contrast.R, R/glh.test.R,
+	  R/make.contrasts.R, man/estimable.Rd, man/fit.contrast.Rd,
+	  man/glh.test.Rd, man/make.contrasts.Rd: initial bundle checkin
 
 2004-09-02  warneg
 
-	* [r442] Initial revision
+	* [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE: Initial revision
 
 2004-05-25  warnes
 
-	* [r327] Updates from Mark Schwartz.
+	* [r327] R/CrossTable.R, man/CrossTable.Rd: Updates from Mark
+	  Schwartz.
 
 2004-04-13  warnes
 
-	* [r314] Fix latex warning: it doesn't like double subscripts.
+	* [r314] man/estimable.Rd: Fix latex warning: it doesn't like
+	  double subscripts.
 
 2004-03-26  warnes
 
-	* [r306] Reflect movement of code from 'mva' package to 'stats' in
-	  R 1.9.0.
+	* [r306] man/fast.prcomp.Rd: Reflect movement of code from 'mva'
+	  package to 'stats' in R 1.9.0.
 
 2004-03-25  warnes
 
-	* [r296] - Estimable was reporting sqrt(X^2) rather than X^2 in the
-	  output.
+	* [r296] R/estimable.R, man/estimable.Rd: - Estimable was reporting
+	  sqrt(X^2) rather than X^2 in the output.
 	  - Provide latex math markup for linear algebra expressions in
 	  help text.
 	  - Other clarifications in help text
-	* [r295] Add enhancements to estimable() provided by S?ren
-	  H?jsgaard
+	* [r295] R/estimable.R, man/estimable.Rd: Add enhancements to
+	  estimable() provided by S?ren H?jsgaard
 	  \email{sorenh at agrsci.dk}:
 	  
 	  I have made a modified version of the function [..] which
@@ -351,38 +384,38 @@
 
 2003-11-17  warnes
 
-	* [r221] - Fix incorrect handling of glm objects by fit.contrast,
-	  as reported
+	* [r221] R/fit.contrast.R: - Fix incorrect handling of glm objects
+	  by fit.contrast, as reported
 	  by Ulrich Halekoh, Phd <ulrich.halekoh at agrsci.dk>.
 	  
 	  - Add regression test code to for this bug.
 
 2003-08-07  warnes
 
-	* [r217] - Fixed incorrect denominator in standard error for mean
-	  in ci.default.
+	* [r217] R/ci.R: - Fixed incorrect denominator in standard error
+	  for mean in ci.default.
 
 2003-04-22  warnes
 
-	* [r190] - the variable 'df' was used within the lme code section
-	  overwriting
+	* [r190] R/fit.contrast.R: - the variable 'df' was used within the
+	  lme code section overwriting
 	  the argument 'df'.
 
 2003-03-12  warnes
 
-	* [r173] - Fixed a typo in the example
+	* [r173] man/fit.contrast.Rd: - Fixed a typo in the example
 	  - Added to lme example
 
 2003-03-07  warnes
 
-	* [r168] - Minor changes to code to allow the package to be
-	  provided as an
+	* [r168] R/fast.prcomp.R: - Minor changes to code to allow the
+	  package to be provided as an
 	  S-Plus chapter.
 
 2003-01-30  warnes
 
-	* [r160] - Renamed 'contrast.lm' to 'fit.contrast'. This new name
-	  is more
+	* [r160] R/fit.contrast.R, man/fit.contrast.Rd: - Renamed
+	  'contrast.lm' to 'fit.contrast'. This new name is more
 	  descriptive and makes it easier to create and use methods for
 	  other
 	  classes, eg lme.
@@ -396,8 +429,8 @@
 	  calls fit.contrast
 	  
 	  - Updated help text to match changes.
-	* [r158] - Removed argument 'correct' and now print separate
-	  corrected values
+	* [r158] R/CrossTable.R, man/CrossTable.Rd: - Removed argument
+	  'correct' and now print separate corrected values
 	  for 2 x 2 tables.
 	  - Added arguments 'prop.r', 'prop.c' and 'prop.t' to toggle
 	  printing
@@ -411,8 +444,8 @@
 	  table
 	  counts, proportions and the results of the appropriate
 	  statistical tests.
-	* [r157] - Added explicit check to ensure that the number of
-	  specified
+	* [r157] R/make.contrasts.R: - Added explicit check to ensure that
+	  the number of specified
 	  contrasts is less than or equal to the ncol - 1. Previously, this
 	  failed with an obtuse error message when the contrast matrix had
 	  row
@@ -420,50 +453,56 @@
 
 2002-11-04  warnes
 
-	* [r142] - Moved fisher.test() to after table is printed, so that
-	  table is
+	* [r142] R/CrossTable.R: - Moved fisher.test() to after table is
+	  printed, so that table is
 	  still printed in the event that fisher.test() results in errors.
 
 2002-10-29  warnes
 
-	* [r138] - Fixes to fast.svd to make it actually work.
+	* [r138] R/fast.prcomp.R, man/fast.prcomp.Rd: - Fixes to fast.svd
+	  to make it actually work.
 	  - Updates to man page to fix mistmatches between code and docs
 	  and to
 	  fix warnings.
-	* [r137] - Moved make.contrasts to a separate file.
+	* [r137] R/make.contrasts.R, man/make.contrasts.Rd: - Moved
+	  make.contrasts to a separate file.
 	  - Enhanced make contrasts to better label contrast matrix, to
 	  give
 	  how.many a default value, and to coerce vectors into row
 	  matrixes.
 	  - Added help page for make.contrasts.
 	  - Added link from contrasts.lm seealso to make.contrasts.
-	* [r136] Initial checkin for fast.prcomp() and fast.svd().
+	* [r136] R/fast.prcomp.R, man/fast.prcomp.Rd: Initial checkin for
+	  fast.prcomp() and fast.svd().
 
 2002-09-26  warnes
 
-	* [r127] - Added note and example code to illustrate how to
-	  properly compute
+	* [r127] man/glh.test.Rd: - Added note and example code to
+	  illustrate how to properly compute
 	  contrasts for the first factor in the model.
 
 2002-09-24  warnes
 
-	* [r124] - Fixed a typo.
+	* [r124] R/glh.test.R: - Fixed a typo.
 
 2002-09-23  warnes
 
-	* [r119] - Fixed syntax errors in barplot2.Rd and CrossTable.Rd
+	* [r119] man/CrossTable.Rd, man/glh.test.Rd: - Fixed syntax errors
+	  in barplot2.Rd and CrossTable.Rd
 	  - Fixed incorrect translation of 'F' (distribution) to 'FALSE' in
 	  glh.test.Rd
-	* [r117] - Modified all files to include CVS Id and Log tags.
-	* [r116] - Added CrossTable() and barplot2() code and docs
-	  contributed by Marc Schwartz.
+	* [r117] R/ci.R, man/estimable.Rd, man/glh.test.Rd: - Modified all
+	  files to include CVS Id and Log tags.
+	* [r116] R/CrossTable.R, man/CrossTable.Rd: - Added CrossTable()
+	  and barplot2() code and docs contributed by Marc Schwartz.
 	  - Permit combinations() to be used when r>n provided
 	  repeat.allowed=TRUE
 	  - Bumped up version number
 
 2002-08-01  warnes
 
-	* [r114] - Corrected documentation mismatch for ci, ci.default.
+	* [r114] R/ci.R, man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: -
+	  Corrected documentation mismatch for ci, ci.default.
 	  
 	  - Replaced all occurences of '_' for assignment with '<-'.
 	  
@@ -475,95 +514,101 @@
 
 2002-04-09  warneg
 
-	* [r109] Checkin for version 0.5.3
+	* [r109] R/ci.R, R/estimable.R, R/glh.test.R, man/glh.test.Rd:
+	  Checkin for version 0.5.3
 
 2002-03-26  warneg
 
-	* [r104] - Changed methods to include '...' to match the generic.
+	* [r104] R/ci.R, R/glh.test.R, man/ci.Rd, man/glh.test.Rd: -
+	  Changed methods to include '...' to match the generic.
 	  - Updated for version 0.5.1
-	* [r99] Removed incorrect link to 'contrast' from seealso.
+	* [r99] man/glh.test.Rd: Removed incorrect link to 'contrast' from
+	  seealso.
 
 2002-02-20  warneg
 
-	* [r81] Minor changes, typo and formatting fixes.
+	* [r81] man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: Minor
+	  changes, typo and formatting fixes.
 
 2002-01-17  warneg
 
-	* [r70] - Fixed errror in last example by adding 'conf.int'
-	  parameter to
+	* [r70] man/estimable.Rd: - Fixed errror in last example by adding
+	  'conf.int' parameter to
 	  'estimable' call.
-	* [r69] - Fixed typo in code that resulted in an syntax error.
+	* [r69] R/glh.test.R: - Fixed typo in code that resulted in an
+	  syntax error.
 
 2002-01-10  warneg
 
-	* [r68] - print.glh.test() was using cat() to printing the call.
-	  This didn't work and
+	* [r68] R/glh.test.R: - print.glh.test() was using cat() to
+	  printing the call. This didn't work and
 	  generated an error.
 
 2001-12-19  warneg
 
-	* [r66] - Fixed display of formulae.
+	* [r66] man/glh.test.Rd: - Fixed display of formulae.
 	  - Added description of return value
-	* [r65] - Removed extra element of return object.
+	* [r65] R/glh.test.R: - Removed extra element of return object.
 
 2001-12-18  warneg
 
-	* [r64] - Updated documentation to reflect change of parameters
-	  from 'alpha'
+	* [r64] man/estimable.Rd: - Updated documentation to reflect change
+	  of parameters from 'alpha'
 	  to 'conf.int', including the new optional status of the
 	  confidence
 	  intervals.
-	* [r63] - Modified to make confidence intervals optional. Changed
-	  'alpha'
+	* [r63] R/estimable.R: - Modified to make confidence intervals
+	  optional. Changed 'alpha'
 	  parameter giving significance level to 'conf.int' giving
 	  confidence
 	  level.
-	* [r62] - Added summary.glh.test to alias, usage, and example
-	  sections.
-	* [r61] - Modified to work correctly when obj is of class 'aov' by
-	  specifying
+	* [r62] man/glh.test.Rd: - Added summary.glh.test to alias, usage,
+	  and example sections.
+	* [r61] R/glh.test.R: - Modified to work correctly when obj is of
+	  class 'aov' by specifying
 	  summary.lm instead of summary. This ensures that the summary
 	  object
 	  has the fields we need.
 	  
 	  - Moved detailed reporting of results from 'print' to 'summary'
 	  function and added a simpler report to 'print'
-	* [r60] - Modified to work correctly when obj is of class 'aov' by
-	  specifying
+	* [r60] R/estimable.R: - Modified to work correctly when obj is of
+	  class 'aov' by specifying
 	  summary.lm instead of summary. This ensures that the summary
 	  object
 	  has the fields we need.
-	* [r59] Initial checkin.
+	* [r59] R/glh.test.R, man/glh.test.Rd: Initial checkin.
 
 2001-12-17  warneg
 
-	* [r56] - Fixed spelling errors.
-	* [r55] - Fixed the link to contrasts.lm.
+	* [r56] man/estimable.Rd: - Fixed spelling errors.
+	* [r55] man/estimable.Rd: - Fixed the link to contrasts.lm.
 	  - Rephrased title/description to be more clear.
 
 2001-12-10  warneg
 
-	* [r49] Renamed 'contrsts.coeff.Rd' to 'estimable.Rd' corresponding
-	  to function rename.
-	* [r48] renamed from contrast.coeff.R to estimable.R (incorrectly
-	  via contrast.lm.R)
+	* [r49] man/estimable.Rd: Renamed 'contrsts.coeff.Rd' to
+	  'estimable.Rd' corresponding to function rename.
+	* [r48] R/estimable.R: renamed from contrast.coeff.R to estimable.R
+	  (incorrectly via contrast.lm.R)
 
 2001-12-07  warneg
 
-	* [r37] - Added text noting that lme is now supported.
-	* [r36] - Fixed typo: DF column was being filled in with p-value.
-	* [r35] - Added ci.lme method to handle lme objects.
+	* [r37] man/ci.Rd: - Added text noting that lme is now supported.
+	* [r36] R/ci.R: - Fixed typo: DF column was being filled in with
+	  p-value.
+	* [r35] R/ci.R: - Added ci.lme method to handle lme objects.
 
 2001-10-16  warneg
 
-	* [r27] Fixed unbalanced brace.
+	* [r27] man/ci.Rd: Fixed unbalanced brace.
 
 2001-08-25  warneg
 
-	* [r12] - Added CVS header.
+	* [r12] man/ci.Rd: - Added CVS header.
 	  - Added my email address.
 
 2001-05-30  warneg
 
-	* [r2] Initial revision
+	* [r2] ., R, R/ci.R, man, man/ci.Rd: Initial revision
 

Modified: pkg/gmodels/inst/NEWS
===================================================================
--- pkg/gmodels/inst/NEWS	2016-08-12 17:11:58 UTC (rev 2130)
+++ pkg/gmodels/inst/NEWS	2016-08-12 17:15:39 UTC (rev 2131)
@@ -1,18 +1,3 @@
-Version 2.16.1 - 2015-07-18
----------------------------
-
-Bug fixes:
-
-- ci.binom() was using an incorrect method for calcuating binomial
-  conficence intervals.  It now calculates the Clopper-Pearson 'exect'
-  interval, which is *conservative* due to the discrete nature of the
-  binomial distribution.
-
-Other Changes:
-
-- Support for lme4 objects has been removed due to incompatible
-  changes to the lme4 package.
-
 Version 2.16.0 - 2014-07-24
 ---------------------------
 
@@ -56,7 +41,7 @@
 Bug fixes:
 
 - Update est.mer() to work with recent versions of lme4  which changed
-  'mer' objects from S3 to S4 class
+  'mer' objects from S3 to S4 class 
 
 - Changes to pass new R CMD check tests
 
@@ -128,7 +113,7 @@
 	- fix various code/doc inconsistencies
 
 - Problem: estimable() was failing for lmer objects.
-  Solution:
+  Solution: 
 	- Create a generic estimable()
 	- Move old function to estimable.default()
 	- Add  estimable.lmer() to the exported methods list in NAMESPACE
@@ -150,8 +135,8 @@
   function provided by Randall C Johnson.  It is now possible to do
   things like:
 	estimable(reg, c("xB"=1,"xD"=-1))
-  instead of:
-        estimable(reg, c(    0,   1,	 0,   -1))
+  instead of:  
+        estimable(reg, c(    0,   1,	 0,   -1)) 
   which should make estimable() much easier to use for large models.
 
 Version 2.1.0

Modified: pkg/gmodels/man/ci.Rd
===================================================================
--- pkg/gmodels/man/ci.Rd	2016-08-12 17:11:58 UTC (rev 2130)
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/r-gregmisc -r 2131

From noreply at r-forge.r-project.org  Fri Aug 12 19:17:24 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 12 Aug 2016 19:17:24 +0200 (CEST)
Subject: [R-gregmisc-commits] r2132 - in pkg/gplots: . R man
Message-ID: <20160812171725.0087D1868F7@r-forge.r-project.org>

Author: warnes
Date: 2016-08-12 19:17:24 +0200 (Fri, 12 Aug 2016)
New Revision: 2132

Modified:
   pkg/gplots/DESCRIPTION
   pkg/gplots/R/heatmap.2.R
   pkg/gplots/man/heatmap.2.Rd
Log:
Add parameter specifying the number of bins used to plot the color key

Modified: pkg/gplots/DESCRIPTION
===================================================================
--- pkg/gplots/DESCRIPTION	2016-08-12 17:15:39 UTC (rev 2131)
+++ pkg/gplots/DESCRIPTION	2016-08-12 17:17:24 UTC (rev 2132)
@@ -23,8 +23,8 @@
 Depends: R (>= 3.0)
 Imports: gtools, gdata, stats, caTools, KernSmooth
 Suggests: grid, MASS
-Version: 3.0.1
-Date: 2016-03-30
+Version: 3.0.3
+Date: 2016-08-01
 Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
 	Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
 	Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill

Modified: pkg/gplots/R/heatmap.2.R
===================================================================
--- pkg/gplots/R/heatmap.2.R	2016-08-12 17:15:39 UTC (rev 2131)
+++ pkg/gplots/R/heatmap.2.R	2016-08-12 17:17:24 UTC (rev 2132)
@@ -65,6 +65,7 @@
                        ## color key + density info
                        key = TRUE,
                        keysize = 1.5,
+                       keygrid=255,
                        density.info=c("histogram","density","none"),
                        denscol=tracecol,
                        symkey = any(x < 0, na.rm=TRUE) || symbreaks,
@@ -670,19 +671,27 @@
           max.raw <- max.breaks
         }
 
-      z <- seq(min.raw, max.raw, by=min(diff(breaks)/100))
+      z <- seq(min.raw, max.raw, length.out=keygrid)
       image(z=matrix(z, ncol=1),
-            col=col, breaks=tmpbreaks,
-            xaxt="n", yaxt="n")
+            #x=matrix(z),
+            #y=0,
+            col=col,
+            breaks=tmpbreaks,
+            xlab="",
+            xaxt="n",
+            yaxt="n")
 
-      par(usr=c(0,1,0,1))
       if (is.null(key.xtickfun)) {
-          lv <- pretty(breaks)
-          xv <- scale01(as.numeric(lv), min.raw, max.raw)
-          xargs <- list(at=xv, labels=lv)
+        usr <- par("usr")
+        par(usr=c(usr[1], usr[2], 0, 1))
+        lv <- pretty(breaks)
+        xv <- scale01(as.numeric(lv), min.raw, max.raw)
+        xargs <- list(at=xv, labels=lv)
       } else {
-          xargs <- key.xtickfun()
+        xargs <- key.xtickfun()
       }
+
+
       xargs$side <- 1
       do.call(axis, xargs)
       if (is.null(key.xlab)) {

Modified: pkg/gplots/man/heatmap.2.Rd
===================================================================
--- pkg/gplots/man/heatmap.2.Rd	2016-08-12 17:15:39 UTC (rev 2131)
+++ pkg/gplots/man/heatmap.2.Rd	2016-08-12 17:17:24 UTC (rev 2132)
@@ -77,6 +77,7 @@
            # color key + density info
            key = TRUE,
            keysize = 1.5,
+           keygrid = 255,
            density.info=c("histogram","density","none"),
            denscol=tracecol,
            symkey = any(x < 0, na.rm=TRUE) || symbreaks,
@@ -215,6 +216,7 @@
   % Color key and density info
   \item{key}{logical indicating whether a color-key should be shown.}
   \item{keysize}{numeric value indicating the size of the key}
+  \item{keygrid}{number of bins used to plot the color-key}
   \item{density.info}{character string indicating whether to superimpose
     a 'histogram', a 'density' plot, or no plot ('none') on the
     color-key.}
@@ -437,7 +439,18 @@
                return(list(labels=FALSE, tick=FALSE))
           })
 
+ heatmap.2(x,
+          breaks=256,
+          keygrid=10
 
+          )
+
+ heatmap.2(x,
+          breaks=256,
+          keygrid=1001
+          )
+
+
  ##
  ## Show effect of z-score scaling within columns, blue-red color scale
  ##


From noreply at r-forge.r-project.org  Fri Aug 12 19:18:33 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 12 Aug 2016 19:18:33 +0200 (CEST)
Subject: [R-gregmisc-commits] r2133 - in pkg/gplots: R man
Message-ID: <20160812171833.33EF6186880@r-forge.r-project.org>

Author: warnes
Date: 2016-08-12 19:18:32 +0200 (Fri, 12 Aug 2016)
New Revision: 2133

Modified:
   pkg/gplots/R/plotmeans.R
   pkg/gplots/man/plotmeans.Rd
Log:
New parameter 'add' for plotmeans to allow *adding* means+confidence intervals to an existing plot.

Modified: pkg/gplots/R/plotmeans.R
===================================================================
--- pkg/gplots/R/plotmeans.R	2016-08-12 17:17:24 UTC (rev 2132)
+++ pkg/gplots/R/plotmeans.R	2016-08-12 17:18:32 UTC (rev 2133)
@@ -17,6 +17,7 @@
                         xaxt,
                         use.t = TRUE,
                         lwd=par("lwd"),
+                        add = FALSE,
                         ...)
 {
   if (invalid(formula) || (length(formula) != 3))
@@ -51,6 +52,7 @@
 
   if(!bars)
     {
+      if(add) par(new=TRUE)
       plot( means, ..., col=col, xlim=xlim)
     }
   else
@@ -77,7 +79,8 @@
 
       plotCI(x=1:length(means), y=means, uiw=ci.width, xaxt="n",
              xlab=xlab, ylab=ylab, labels=mean.labels, col=col, xlim=xlim,
-             lwd=barwidth, barcol=barcol, minbar=minbar, maxbar=maxbar, ... )
+             lwd=barwidth, barcol=barcol, minbar=minbar, maxbar=maxbar,
+             add=add, ... )
       if(invalid(xaxt) || xaxt!="n")
         axis(1, at = 1:length(means), labels = legends, ...)
 

Modified: pkg/gplots/man/plotmeans.Rd
===================================================================
--- pkg/gplots/man/plotmeans.Rd	2016-08-12 17:17:24 UTC (rev 2132)
+++ pkg/gplots/man/plotmeans.Rd	2016-08-12 17:18:32 UTC (rev 2133)
@@ -10,7 +10,7 @@
           digits=getOption("digits"), col="black", barwidth=1,
           barcol="blue", connect=TRUE, ccol=
           col, legends=names(means), xaxt, use.t=TRUE,
-          lwd=par("lwd"), ...)
+          lwd=par("lwd"), add = FALSE, ...)
 }
 \arguments{
   \item{formula}{symbolic expression specifying the outcome (continuous)
@@ -91,6 +91,9 @@
 
   \item{lwd}{Width of connecting lines  }
 
+  \item{add}{Logical specifying whether to add to an existing plot
+    (\code{add=TRUE}) or to generate a new plot (\code{add=FALSE}).}
+
   \item{\dots}{ optional plotting parameters. }
 
   }
@@ -133,7 +136,29 @@
                    "Ile-et-Vilaine Esophageal Cancer Study")
             )
   abline(v=c(6.5, 12.5, 18.5), lty=2)
+  grid()
 
+  # add to a boxplot
+  boxplot(ncases/ncontrols ~ interaction(agegp , alcgp, sep ="   "),
+          data=esoph,
+          xlab="Age Group and Alcohol Consumption",
+          ylab="# Cases / # Controls",
+          main=c("Fraction of Cases for by Age and Alcohol Consumption",
+                 "Ile-et-Vilaine Esophageal Cancer Study"),
+          ylim=c(-0.75, 1.5),
+          col="green"
+            )
+  plotmeans(ncases/ncontrols ~ interaction(agegp , alcgp, sep ="   "),
+            data=esoph,
+            connect=list(1:6,7:12,13:18,19:24),
+            barwidth=2,
+            barcol="dark blue",
+            col="dark blue",
+            add=TRUE)
+  grid()
+  abline(v=c(6.5, 12.5, 18.5), lty=2)
+
+
 }
 
 \author{Gregory R. Warnes \email{greg at warnes.net}}


From noreply at r-forge.r-project.org  Fri Aug 12 19:34:11 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 12 Aug 2016 19:34:11 +0200 (CEST)
Subject: [R-gregmisc-commits] r2134 - in pkg/gplots: . R
Message-ID: <20160812173412.0AA3D18814C@r-forge.r-project.org>

Author: warnes
Date: 2016-08-12 19:34:11 +0200 (Fri, 12 Aug 2016)
New Revision: 2134

Added:
   pkg/gplots/.Rbuildignore
Modified:
   pkg/gplots/R/space.R
Log:
Improve method of spacing points in the same bin.

Added: pkg/gplots/.Rbuildignore
===================================================================
--- pkg/gplots/.Rbuildignore	                        (rev 0)
+++ pkg/gplots/.Rbuildignore	2016-08-12 17:34:11 UTC (rev 2134)
@@ -0,0 +1,3 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.RData

Modified: pkg/gplots/R/space.R
===================================================================
--- pkg/gplots/R/space.R	2016-08-12 17:18:32 UTC (rev 2133)
+++ pkg/gplots/R/space.R	2016-08-12 17:34:11 UTC (rev 2134)
@@ -7,6 +7,7 @@
 
 space <-  function(x,y,s=1/50, na.rm=TRUE, direction="x")
   {
+    # to avoid duplicating code for direction="y", swap x and y temporarily...
     if(direction!='x')
       {
         tmp <- y
@@ -35,29 +36,45 @@
     x <- x[ord]
     y <- y[ord]
 
-    startsame <- 1
-    same.x <- x[1]
-    same.y <- y[1]
+    # split into groups within the same interval
+    sames.x <- c(FALSE, within(x[1:(length(x)-1)],
+                               x[-1],
+                               delta=spacing.x)
+                 )
+    sames.y <- c(FALSE, within(y[1:(length(y)-1)],
+                               y[-1],
+                               delta=spacing.y)
+    )
+    sames <- sames.x & sames.y
+    groups <- cumsum(!sames)
+    xList <- split(x, groups)
+    yList <- split(y, groups)
 
-    for( i in 1:length(x) )
+
+    for( i in 1:max(groups) )
       {
-        if(i>1 &&
-           within(x[i],same.x,spacing.x) &&
-           within(y[i],same.y,spacing.y) )
-          {
-            if(x[startsame] == same.x )
-              x[startsame] <- x[startsame]
+      len <- length(xList[[i]])
+      if(len==1)
+        next
 
-            cumrun <- i - startsame
+      m <- mean(xList[[i]])
+      s <- len/2 * spacing.x
+      deltas <- seq(from=-s, to=+s, length.out=len)
+      order <- "permute"
+      if (order=="permute")
+        deltas <- sample(deltas)
+      else if (order=="A")
+        deltas <- deltas[order(abs(deltas), decreasing=TRUE)]
+      else if (order=="V")
+        deltas <- deltas[order(abs(deltas), decreasing=FALSE)]
 
-            x[i] <- x[i] + (-1)^(cumrun+1) * floor((cumrun+1) /2) * spacing.x
-          } else {
-            startsame <- i
-            same.x <- x[i]
-            same.y <- y[i]
-          }
-      }
+      xList[[i]] <- xList[[i]] + deltas
+    }
 
+    x <- unlist(xList)[undo]
+    y <- unlist(yList)[undo]
+
+    # undo swap of x and y.
     if(direction!='x')
       {
         tmp <- y
@@ -65,6 +82,6 @@
         x <- tmp
       }
 
-    return( list(x=x[undo], y=y[undo]) )
+    return( list(x=x, y=y) )
 }
 


From noreply at r-forge.r-project.org  Fri Aug 12 19:38:14 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 12 Aug 2016 19:38:14 +0200 (CEST)
Subject: [R-gregmisc-commits] r2135 - in pkg: SASxport SASxport/.Rproj.user
	SASxport/.Rproj.user/632EB997 SASxport/.Rproj.user/632EB997/pcs
	SASxport/.Rproj.user/632EB997/sdb
	SASxport/.Rproj.user/632EB997/sdb/mt
	SASxport/.Rproj.user/632EB997/sdb/per
	SASxport/.Rproj.user/632EB997/sdb/per/t
	SASxport/.Rproj.user/632EB997/sdb/per/t/42c64b18
	SASxport/.Rproj.user/632EB997/sdb/per/u
	SASxport/.Rproj.user/632EB997/sdb/prop
	SASxport/.Rproj.user/shared fork fork/.Rproj.user
	fork/.Rproj.user/632EB997 fork/.Rproj.user/632EB997/pcs
	fork/.Rproj.user/632EB997/sdb fork/.Rproj.user/632EB997/sdb/per
	fork/.Rproj.user/632EB997/sdb/per/t
	fork/.Rproj.user/632EB997/sdb/per/u fork/.Rproj.user/shared
	gplots gplots/.Rproj.user gplots/.Rproj.user/632EB997
	gplots/.Rproj.user/632EB997/pcs gplots/.Rproj.user/632EB997/sdb
	gplots/.Rproj.user/632EB997/sdb/mt
	gplots/.Rproj.user/632EB997/sdb/per
	gplots/.Rproj.user/632EB997/sdb/per/t
	gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab
	gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f
	gplots/.Rproj.user/632EB997/sdb/per/t/edc438ca
	gplots/.Rproj.user/632EB997/sdb/per/u
	gplots/.Rproj.user/632EB997/sdb/prop gplots/.Rproj.user/shared
Message-ID: <20160812173814.254CD18814C@r-forge.r-project.org>

Author: warnes
Date: 2016-08-12 19:38:13 +0200 (Fri, 12 Aug 2016)
New Revision: 2135

Added:
   pkg/SASxport/.Rproj.user/
   pkg/SASxport/.Rproj.user/632EB997/
   pkg/SASxport/.Rproj.user/632EB997/build_options
   pkg/SASxport/.Rproj.user/632EB997/ctx/
   pkg/SASxport/.Rproj.user/632EB997/pcs/
   pkg/SASxport/.Rproj.user/632EB997/pcs/debug-breakpoints.pper
   pkg/SASxport/.Rproj.user/632EB997/pcs/files-pane.pper
   pkg/SASxport/.Rproj.user/632EB997/pcs/find-in-files.pper
   pkg/SASxport/.Rproj.user/632EB997/pcs/source-pane.pper
   pkg/SASxport/.Rproj.user/632EB997/pcs/windowlayoutstate.pper
   pkg/SASxport/.Rproj.user/632EB997/pcs/workbench-pane.pper
   pkg/SASxport/.Rproj.user/632EB997/persistent-state
   pkg/SASxport/.Rproj.user/632EB997/presentation/
   pkg/SASxport/.Rproj.user/632EB997/saved_source_markers
   pkg/SASxport/.Rproj.user/632EB997/sdb/
   pkg/SASxport/.Rproj.user/632EB997/sdb/mt/
   pkg/SASxport/.Rproj.user/632EB997/sdb/mt/3B443731
   pkg/SASxport/.Rproj.user/632EB997/sdb/mt/4ED4AE88
   pkg/SASxport/.Rproj.user/632EB997/sdb/mt/91BF8EB8
   pkg/SASxport/.Rproj.user/632EB997/sdb/mt/B97C53CF
   pkg/SASxport/.Rproj.user/632EB997/sdb/mt/EB1F71A0
   pkg/SASxport/.Rproj.user/632EB997/sdb/mu/
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/t/
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/t/42c64b18/
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/t/42c64b18/3B443731
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/t/42c64b18/4ED4AE88
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/t/42c64b18/91BF8EB8
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/t/42c64b18/B97C53CF
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/t/42c64b18/EB1F71A0
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/u/
   pkg/SASxport/.Rproj.user/632EB997/sdb/per/u/42c64b18/
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/210DDAC6
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/26571A1D
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/4B00C2BF
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/4F2B468A
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/62B93444
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/67F255E0
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/6B869B56
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/8546615E
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/8724CF5D
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/A17C35A1
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/B7AE8750
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/B900A9AD
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/C90C699B
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/CF52798E
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/D2C5E77F
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/D57FBD7D
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/DC24A07E
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/E4825697
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/E9666CAC
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/FCB3A014
   pkg/SASxport/.Rproj.user/632EB997/sdb/prop/INDEX
   pkg/SASxport/.Rproj.user/632EB997/viewer-cache/
   pkg/SASxport/.Rproj.user/shared/
   pkg/SASxport/.Rproj.user/shared/users/
   pkg/fork/.Rbuildignore
   pkg/fork/.Rproj.user/
   pkg/fork/.Rproj.user/632EB997/
   pkg/fork/.Rproj.user/632EB997/ctx/
   pkg/fork/.Rproj.user/632EB997/pcs/
   pkg/fork/.Rproj.user/632EB997/pcs/files-pane.pper
   pkg/fork/.Rproj.user/632EB997/pcs/source-pane.pper
   pkg/fork/.Rproj.user/632EB997/pcs/windowlayoutstate.pper
   pkg/fork/.Rproj.user/632EB997/pcs/workbench-pane.pper
   pkg/fork/.Rproj.user/632EB997/presentation/
   pkg/fork/.Rproj.user/632EB997/saved_source_markers
   pkg/fork/.Rproj.user/632EB997/sdb/
   pkg/fork/.Rproj.user/632EB997/sdb/mt/
   pkg/fork/.Rproj.user/632EB997/sdb/mu/
   pkg/fork/.Rproj.user/632EB997/sdb/per/
   pkg/fork/.Rproj.user/632EB997/sdb/per/t/
   pkg/fork/.Rproj.user/632EB997/sdb/per/t/d9524f0f/
   pkg/fork/.Rproj.user/632EB997/sdb/per/u/
   pkg/fork/.Rproj.user/632EB997/sdb/per/u/d9524f0f/
   pkg/fork/.Rproj.user/632EB997/viewer-cache/
   pkg/fork/.Rproj.user/shared/
   pkg/fork/.Rproj.user/shared/users/
   pkg/gplots/.Rproj.user/
   pkg/gplots/.Rproj.user/632EB997/
   pkg/gplots/.Rproj.user/632EB997/ctx/
   pkg/gplots/.Rproj.user/632EB997/pcs/
   pkg/gplots/.Rproj.user/632EB997/pcs/files-pane.pper
   pkg/gplots/.Rproj.user/632EB997/pcs/source-pane.pper
   pkg/gplots/.Rproj.user/632EB997/pcs/svn.pper
   pkg/gplots/.Rproj.user/632EB997/pcs/windowlayoutstate.pper
   pkg/gplots/.Rproj.user/632EB997/pcs/workbench-pane.pper
   pkg/gplots/.Rproj.user/632EB997/persistent-state
   pkg/gplots/.Rproj.user/632EB997/presentation/
   pkg/gplots/.Rproj.user/632EB997/saved_source_markers
   pkg/gplots/.Rproj.user/632EB997/sdb/
   pkg/gplots/.Rproj.user/632EB997/sdb/mt/
   pkg/gplots/.Rproj.user/632EB997/sdb/mt/341AED89
   pkg/gplots/.Rproj.user/632EB997/sdb/mt/456A8AE1
   pkg/gplots/.Rproj.user/632EB997/sdb/mt/6C32B82
   pkg/gplots/.Rproj.user/632EB997/sdb/mt/820656DD
   pkg/gplots/.Rproj.user/632EB997/sdb/mt/BD1D11CF
   pkg/gplots/.Rproj.user/632EB997/sdb/mt/C1AD43D1
   pkg/gplots/.Rproj.user/632EB997/sdb/mt/DE2C36AE
   pkg/gplots/.Rproj.user/632EB997/sdb/mu/
   pkg/gplots/.Rproj.user/632EB997/sdb/per/
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab/
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab/341AED89
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab/456A8AE1
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab/6C32B82
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab/820656DD
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab/BD1D11CF
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab/C1AD43D1
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab/DE2C36AE
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f/
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f/341AED89
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f/456A8AE1
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f/6C32B82
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f/820656DD
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f/BD1D11CF
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f/C1AD43D1
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f/DE2C36AE
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/edc438ca/
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/edc438ca/341AED89
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/edc438ca/456A8AE1
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/edc438ca/820656DD
   pkg/gplots/.Rproj.user/632EB997/sdb/per/t/edc438ca/BD1D11CF
   pkg/gplots/.Rproj.user/632EB997/sdb/per/u/
   pkg/gplots/.Rproj.user/632EB997/sdb/per/u/a31943ab/
   pkg/gplots/.Rproj.user/632EB997/sdb/per/u/d9524f0f/
   pkg/gplots/.Rproj.user/632EB997/sdb/per/u/edc438ca/
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/1CDF36D8
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/276B72FF
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/621FB34C
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/77FB12A5
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/88E2DA8E
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/910AF072
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/D1DFF321
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/F0AD830A
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/F401A7EA
   pkg/gplots/.Rproj.user/632EB997/sdb/prop/INDEX
   pkg/gplots/.Rproj.user/632EB997/viewer-cache/
   pkg/gplots/.Rproj.user/shared/
   pkg/gplots/.Rproj.user/shared/users/
Log:
Add RStudio files

Added: pkg/SASxport/.Rproj.user/632EB997/build_options
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/build_options	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/build_options	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,4 @@
+auto_roxygenize_for_build_and_reload="0"
+auto_roxygenize_for_build_package="1"
+auto_roxygenize_for_check="1"
+makefile_args=""

Added: pkg/SASxport/.Rproj.user/632EB997/pcs/debug-breakpoints.pper
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/pcs/debug-breakpoints.pper	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/pcs/debug-breakpoints.pper	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,6 @@
+{
+    "debugBreakpointsState" : {
+        "breakpoints" : [
+        ]
+    }
+}
\ No newline at end of file

Added: pkg/SASxport/.Rproj.user/632EB997/pcs/files-pane.pper
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/pcs/files-pane.pper	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/pcs/files-pane.pper	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,13 @@
+{
+    "path" : "~/src/r-gregmisc/SASxport",
+    "sortOrder" : [
+        {
+            "ascending" : true,
+            "columnIndex" : 2
+        },
+        {
+            "ascending" : false,
+            "columnIndex" : 4
+        }
+    ]
+}
\ No newline at end of file

Added: pkg/SASxport/.Rproj.user/632EB997/pcs/find-in-files.pper
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/pcs/find-in-files.pper	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/pcs/find-in-files.pper	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,10 @@
+{
+    "dialog-state" : {
+        "caseSensitive" : false,
+        "filePatterns" : [
+        ],
+        "path" : "~/src/r-gregmisc/SASxport",
+        "query" : "http:.*sas",
+        "regex" : true
+    }
+}
\ No newline at end of file

Added: pkg/SASxport/.Rproj.user/632EB997/pcs/source-pane.pper
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/pcs/source-pane.pper	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/pcs/source-pane.pper	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,3 @@
+{
+    "activeTab" : 2
+}
\ No newline at end of file

Added: pkg/SASxport/.Rproj.user/632EB997/pcs/windowlayoutstate.pper
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/pcs/windowlayoutstate.pper	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/pcs/windowlayoutstate.pper	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,14 @@
+{
+    "left" : {
+        "panelheight" : 789,
+        "splitterpos" : 339,
+        "topwindowstate" : "NORMAL",
+        "windowheight" : 860
+    },
+    "right" : {
+        "panelheight" : 789,
+        "splitterpos" : 508,
+        "topwindowstate" : "NORMAL",
+        "windowheight" : 860
+    }
+}
\ No newline at end of file

Added: pkg/SASxport/.Rproj.user/632EB997/pcs/workbench-pane.pper
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/pcs/workbench-pane.pper	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/pcs/workbench-pane.pper	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,6 @@
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+    "TabSet2" : 3,
+    "TabZoom" : {
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Added: pkg/SASxport/.Rproj.user/632EB997/persistent-state
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/persistent-state	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/persistent-state	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,9 @@
+build-last-errors="[]"
+build-last-errors-base-dir="~/src/r-gregmisc/SASxport/"
+build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source SASxport\\n\\n\",\"type\":0},{\"output\":\"\\n\",\"type\":1},{\"output\":\"   Welcome to BI enhanced R!\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* installing to library '/home/gwarnes1/Rlib'\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* installing *source* package 'SASxport' ...\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** libs\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"make: Nothing to be done for `all'.\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"installing to /home/gwarnes1/Rlib/SASxport/libs\\n\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"** data\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** inst\\n\",\"type\":1},{\"output\":\"** preparing package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"  converting help for package 'SASxport'\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"    finding HTML links ...\",\"type\":1},{\"output\":\"    Alfalfa                                 html  \",\"type\":1},{\"output\":\" done\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"    SASformat                               html  \\n\",\"type\":1},{\"output\":\"    SASxport-package                        html  \\n\",\"type\":1},{\"output\":\"    lookup.xport                            html  \",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"    makeSASNames                            html  \\n\",\"type\":1},{\"output\":\"    read.xport                              html  \",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"    finding level-2 HTML links ...\",\"type\":1},{\"output\":\" done\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"    toSAS                                   html  \\n\",\"type\":1},{\"output\":\"    write.xport                             html  \",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"   Welcome to BI enhanced R!\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"Loaded SASxport version 1.5.4 (2016-03-25).\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"  Type `?SASxport' for usage information.\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* DONE (SASxport)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
+compile_pdf_state="{\"errors\":[],\"output\":\"\",\"running\":false,\"tab_visible\":false,\"target_file\":\"\"}"
+console_procs="[]"
+files.monitored-path=""
+find-in-files-state="{\"handle\":\"e4a838ad23774b908d2ef1438703d7ef\",\"input\":\"describe\",\"path\":\"~/src/r-gregmisc/SASxport\",\"regex\":false,\"results\":{\"file\":[\"~/src/r-gregmisc/SASxport/R/testDateTime.R\",\"~/src/r-gregmisc/SASxport/tests/testUnnamedComponents.Rout.save\",\"~/src/r-gregmisc/SASxport/tests/testUnnamedComponents.Rout.save\",\"~/src/r-gregmisc/SASxport/tests/testExamples.Rout.save\",\"~/src/r-gregmisc/SASxport/tests/testExamples.Rout.save\",\"~/src/r-gregmisc/SASxport/man/lookup.xport.Rd\",\"~/src/r-gregmisc/SASxport/man/lookup.xport.Rd\",\"~/src/r-gregmisc/SASxport/man/Alfalfa.Rd\",\"~/src/r-gregmisc/SASxport/man/read.xport.Rd\",\"~/src/r-gregmisc/SASxport/man/read.xport.Rd\",\"~/src/r-gregmisc/SASxport/man/read.xport.Rd\"],\"line\":[8,177,214,470,507,6,8,12,123,202,203],\"lineValue\":[\"## or S-Plus.  The following 2 functions are used by describe.vector\",\"rd.xpr> describe(w$TEST)   # see labels, format names for dataset test\",\"rd.xpr> lapply(w, describe)# see descriptive stats in more detail for each variable\",\"rd.xpr> describe(w$TEST)   # see labels, format names for dataset test\",\"rd.xpr> lapply(w, describe)# see descriptive stats in more detail for each variable\",\"\\\\title{Describe the Contents of an SAS XPORT File}\",\"Describe the contents of an SAS XPORT file.\",\"\\\\describe{\",\"\\\\code{\\\\link[Hmisc]{describe}},\",\"describe(w$TEST)   # see labels, format names for dataset test\",\"lapply(w, describe)# see descriptive stats in more detail for each variable\"],\"matchOff\":[[61],[16],[26],[16],[26],[15],[8],[9],[27],[8],[18]],\"matchOn\":[[53],[8],[18],[8],[18],[7],[0],[1],[19],[0],[10]]},\"running\":false}"
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Added: pkg/SASxport/.Rproj.user/632EB997/saved_source_markers
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/saved_source_markers	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/saved_source_markers	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1 @@
+{"active_set":"","sets":[]}
\ No newline at end of file

Added: pkg/SASxport/.Rproj.user/632EB997/sdb/mt/3B443731
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/sdb/mt/3B443731	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/sdb/mt/3B443731	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,20 @@
+{
+    "collab_server" : "",
+    "contents" : "Package: SASxport\nType: Package\nTitle: Read and Write SAS XPORT Files\nVersion: 1.5.4\nDate: 2016-03-25\nDescription: Functions for reading, listing\n    the contents of, and writing SAS xport format files.\n  The functions support reading and writing of either\n  individual data frames or sets of data frames.  Further,\n  a mechanism has been provided for customizing how\n  variables of different data types are stored.\nAuthor:\n  Unless otherwise noted, the contents of this package were written by\n  Gregory R. Warnes <greg at warnes.net> and are provided under the\n  terms of the GNU General Public License, version 2.0 or later.\n  --\n  The files 'src/ieee2ibm.c' and 'src/ibm2ieee.c' were extracted from\n  BRL-CAD file /brlcad/src/libbu/htond.c written by Michael John\n  Muuss, Copyright (c) 2004-2007 United States Government as\n  represented by the U.S. Army Research Laboratory, and is utilized\n  and redistributed under the terms of the GNU Lesser General Public\n  License, version 2.1.\n  --\n  The files 'R/AFirst.lib.s', 'R/all.is.numeric.R',\n  'R/importConvertDateTime.R', 'R/in.opererator.R', 'R/makeNames.R',\n  'R/read.xport.R', and 'R/testDateTime.R' are copied or adapted from the\n  'Hmisc' package created by Frank E. Harrell, Jr.\n  <f.harrell at vanderbilt.edu>, and are utilized and redistributed under\n  the terms of the GNU General Public License, version 2.0 or later.\n  --\n  The files 'R/xport.R', 'src/SASxport.c', 'src/SASxport.h', and\n  'src/foreign.h' are copied or adapted from the R 'foreign' package\n  created by Douglas M. Bates <bates at stat.wisc.edu> and Saikat DebRoy\n  <saikat at stat.wisc.edu>, and are utilized and redistributed under the\n  terms of the GNU General Public License, version 2.0 or later.\n  --\n  The creation of this package was partially funded by Metrum Institute\n  <http://metruminstitute.org>.\nMaintainer: Gregory R. Warnes <greg at warnes.net>\nLicense: GPL-2\nDepends: R (>= 2.4.0), chron, Hmisc\nURL: http://www.warnes.net, http://metruminstitute.org\n",
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Added: pkg/SASxport/.Rproj.user/632EB997/sdb/mt/4ED4AE88
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/sdb/mt/4ED4AE88	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/sdb/mt/4ED4AE88	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,20 @@
+{
+    "collab_server" : "",
+    "contents" : "\\name{read.xport}\n\\alias{read.xport}\n\\title{Import a SAS XPORT File}\n\\description{\n  Read a SAS XPORT format file and return the contained dataset(s).\n}\n\\usage{\nread.xport(file,\n           force.integer=TRUE,\n           formats=NULL,\n           name.chars=NULL,\n           names.tolower=FALSE,\n           keep=NULL,\n           drop=NULL,\n           as.is=0.95,\n           verbose=FALSE,\n           as.list=FALSE,\n           include.formats=FALSE\n           )\n}\n\\arguments{\n  \\item{file}{Character string specifying the name or URL of a SAS XPORT\n    file.\n  }\n  \\item{force.integer}{Logical flag indicating whether integer-valued\n    variables should be returned as integers (\\code{TRUE}) or doubles\n    (\\code{FALSE}). Variables outside the supported integer range\n    (\\code{.Machine$integer.max}) will always be converted to\n    doubles.\n  }\n  \\item{formats}{a data frame or list (like that created by\n    \\code{foreign:::read.xport}) containing \\code{PROC FORMAT}\n    output, if such output is not stored in the main transport\n    file.\n  }\n  \\item{name.chars}{Vector of additional characters permissible in\n    variable names. By default, only the alpha and numeric\n    characters ([A-Za-z0-9]) and periods ('.') are permitted. All\n    other characters are converted into periods ('.').\n  }\n  \\item{names.tolower}{Logical indicating whether variable and dataset\n    names should be converted to lowercase (\\code{TRUE}) or left\n    uppercase (\\code{FALSE})\n  }\n  \\item{keep}{a vector of names of SAS datasets to process.  This list\n    must include \\code{PROC FORMAT} dataset if it is present for\n    datasets to use use any of its value label formats.\n  }\n  \\item{drop}{a vector of names of SAS datasets to ignore (original SAS\n    upper case names)\n  }\n  \\item{as.is}{\n    Either a logical flag indicating whether SAS character variables should\n    be preserved as character objects (\\code{TRUE}) or factor\n    objects (\\code{FALSE}), or a fractional cutoff between 0 and 1.\n\n    When a fractional cutoff is provided, character variables\n    containing a more than this fraction of unique values will be\n    stored as a character variables. This is done in order to\n    preserve space, since factors must store both the integer factor\n    codes and the character factor labels.\n  }\n  \\item{verbose}{Logical indicating whether progress should be printed\n    during the data loading and conversion process.}\n  \\item{as.list}{Logical indicating whether to return a list even if\n    the SAS xport file contains only only one dataset.}\n  \\item{include.formats}{Logical indicating whether to include SAS\n    format information (if present) in the returned list}\n}\n\\value{\n  If only a single dataset is present (after removing \\code{PROC FORMAT}\n  data when \\code{include.formats=FALSE}), the return value is a single\n  dataframe  object. Otherwise the return is a list of dataframe objects.\n\n  Note that if \\code{include.formats=TRUE}, the returned list will\n  contain a dataframe named \"FORMATS\" containing any available 'PROC FORMAT'\n  information.\n}\n\\details{\n\n  \\itemize{\n    \\item SAS date, time, and date/time variables are converted respectively to \\code{Date},\n    POSIX, or \\code{chron} objects\n\n    \\item SAS labels are stored in \"label\" attributes on each variable,\n    and are accessible using the \\code{\\link{label}} function.\n\n    \\item SAS formats are stored in \"SASformat\" attributes on each\n    variable, and are accessable using \\code{\\link{SASformat}}\n\n    \\item SAS iformats are stored in \"SASiformat\" attributes on each\n    variable, and are accessable using \\code{\\link{SASiformat}}\n\n    \\item SAS integer variables are stored as integers unless\n      \\code{force.integer} is \\code{FALSE}\n  }\n\n  If the file includes the output of \\code{PROC FORMAT CNTLOUT=},\n  variables having customized label formats will be converted to \\code{factor}\n  objects with appropriate labels.\n\n  If a datasets in the original file has a label or type, these will be\n  stored in the corresponding 'lable' and 'SAStype' attributes, which\n  can be accessed by the \\code{\\link{label}} and \\code{\\link{SAStype}}\n  functions.\n}\n\\author{ Gregory R. Warnes \\email{greg at warnes.net}\n  based on \\code{Hmisc:::sasxport.get} by Frank E. Harrell, Jr.}\n\\section{Note}{\n  This code provides a subset of the functionality of the\n  \\code{sasxport.get} function in the Hmisc library.\n}\n\\seealso{\n  \\code{\\link[foreign]{read.xport}},\n  \\code{\\link{label}},\n  \\code{\\link[Hmisc]{sas.get}},\n  \\code{\\link[Hmisc]{sasxport.get}},\n  \\code{\\link{Dates}},\n  \\code{\\link{DateTimeClasses}},\n  \\code{\\link[chron]{chron}},\n  \\code{\\link[foreign]{lookup.xport}},\n  \\code{\\link[Hmisc]{contents}},\n  \\code{\\link[Hmisc]{describe}},\n  \\code{\\link{label}},\n  \\code{\\link{SASformat}},\n  \\code{\\link{SASiformat}}, and\n  \\code{\\link{SAStype}}\n}\n\\examples{\n\n## -------\n## SAS code to generate test dataset:\n## -------\n## libname y SASV5XPT \"test2.xpt\";\n##\n## PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;\n## PROC FORMAT CNTLOUT=format;RUN;  * Name, e.g. 'format', unimportant;\n## data test;\n## LENGTH race 3 age 4;\n## age=30; label age=\"Age at Beginning of Study\";\n## race=2;\n## d1='3mar2002'd ;\n## dt1='3mar2002 9:31:02'dt;\n## t1='11:13:45't;\n## output;\n##\n## age=31;\n## race=4;\n## d1='3jun2002'd ;\n## dt1='3jun2002 9:42:07'dt;\n## t1='11:14:13't;\n## output;\n## format d1 mmddyy10. dt1 datetime. t1 time. race race.;\n## run;\n## data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;\n##    DO i=1 TO 100;\n##        x3=ranuni(3);\n##        x4=ranuni(5);\n##        x5=ranuni(7);\n##        x6=ranuni(9);\n##        x7=ranuni(11);\n##        x8=ranuni(13);\n##        output;\n##        END;\n##    DROP i;\n##    RUN;\n## PROC MEANS; RUN;\n## PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;\n## ------\n\n## Read this dataset from a local file:\ntestFile <- system.file('extdata', 'test2.xpt', package=\"SASxport\")\nw <- read.xport(testFile)\nclass(w)\nsapply(w, head)\n\n\\dontrun{\n## Or read a copy of test2.xpt available on the web:\nurl <- 'http://biostat.mc.vanderbilt.edu/wiki/pub/Main/Hmisc/test2.xpt'\nw <- read.xport(url)\n}\n\n## We can also get the dataset wrapped in a list\nw <- read.xport(testFile, as.list=TRUE)\nclass(w)\nsapply(w, head)\n\n## And we can ask for the format information to be included as well.\nw <- read.xport(testFile, as.list=TRUE, include.formats=TRUE)\nclass(w)\nsapply(w, head)\n\n\\dontshow{\nstopifnot( is.data.frame(w)==FALSE && is.list(w)==TRUE )\n}\n\n\n#### The Hmisc library provides many useful functions for interacting with\n#### data imported from SAS via read.xport()\nlibrary(Hmisc)\n\ndescribe(w$TEST)   # see labels, format names for dataset test\nlapply(w, describe, \"\")# see descriptive stats in more detail for each variable\n\ncontents(w$TEST)   # another way to see variable attributes\nlapply(w, contents)# show contents of individual items in more detail\n\noptions(digits=7)  # compare the following matrix with PROC MEANS output\nt(sapply(w$Z, function(x)\n c(Mean=mean(x),SD=sqrt(var(x)),Min=min(x),Max=max(x))))\n\n}\n\\keyword{interface}\n\\keyword{manip}\n",
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+    "project_path" : "man/read.xport.Rd",
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+    "source_window" : "",
+    "type" : "r_doc"
+}
\ No newline at end of file

Added: pkg/SASxport/.Rproj.user/632EB997/sdb/mt/91BF8EB8
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/sdb/mt/91BF8EB8	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/sdb/mt/91BF8EB8	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,20 @@
+{
+    "collab_server" : "",
+    "contents" : "\\name{write.xport}\n\\alias{write.xport}\n\\title{Write Data to a SAS XPORT File}\n\\description{\n  This function writes one or more data frames into a SAS XPORT format\n  library file.\n}\n\\usage{\nwrite.xport(...,\n            list=base::list(),\n            file = stop(\"'file' must be specified\"),\n            verbose=FALSE,\n            sasVer=\"7.00\",\n            osType,\n            cDate=Sys.time(),\n            formats=NULL,\n            autogen.formats=TRUE\n )\n}\n\\arguments{\n  \\item{\\dots}{One or more data frames to be stored}\n  \\item{list}{A list containing data frames to be stored.}\n  \\item{file}{File name or connection object. Use \"\" to view the raw data}\n  \\item{verbose}{Logical flag controlling whether status is reported\n    during processing}\n  \\item{sasVer}{SAS version string}\n  \\item{osType}{Opererating system, defaults to \"R X.Y.Z\" for\n    appropriate values of X, Y, and Z}\n  \\item{cDate}{Date object specifying dataset creation date}\n  \\item{formats}{Optional data frame containing SAS format information.}\n  \\item{autogen.formats}{Logical indiciating whether SAS formats should be\n    auto-generated for factor variables.}\n}\n\\details{\n  The function creates a SAS XPORT data file (see reference) from one or\n  more data frames.  This file format imposes a number of constraints:\n  \\itemize{\n    \\item Data set and variable names are truncated to 8 characters and\n      converted to upper case.  All characters outside of the set A-Z,\n      0-9, and '\\_' are converted to '\\_'.\n    \\item Character variables are stored as characters.\n    \\item If \\code{autogen.formats=TRUE} (the default), factor variables\n      are stored as numeric with an appropriate SAS format\n      specification. If \\code{autogen.formats=FALSE}, factor variables\n      are stored as characters.\n    \\item All numeric variables are stored as double-precision floating\n      point values utilizing the IBM mainframe double precision floating\n      point format (see the reference).\n    \\item Date and time variables are either converted to number of days since\n      1960-01-01 (date only), or number of seconds since\n      1960-01-01:00:00:00 GMT (date-time variables).\n    \\item Missing values are converted to the standard SAS missing value\n      '.'\n  }\n\n  The SAS XPORT format allows each dataset to have a label and a type\n  (set via the \\code{\\link{label}} and \\code{\\link{SAStype}} functions).\n  In addition, each variable may have a corresponding label, display\n  format, and input format.  To set these values, add the attribute\n  'label', 'SASformat', or 'SASiformat' to individual data frame.  These\n  attributes may be set using the \\code{\\link{label}},\n  \\code{\\link{SASformat}}, and \\code{\\link{SASiformat}} functions. (See\n  examples provided below.)\n\n  The actual translation of R objects to objects appropriate for SAS is\n  handled by the \\code{\\link{toSAS}} generic and associated methods,\n  which can be (re)defined by the user to provide fine-grained control.\n}\n\\value{\n  No return value\n}\n\\references{\n  SAS Technical Support document TS-140: ``The Record Layout of a\n  Data Set in SAS Transport (XPORT) Format'' available at\n  \\url{https://support.sas.com/techsup/technote/ts140.pdf}.\n}\n\\author{Gregory R. Warnes \\email{greg at warnes.net}}\n\\note{\n   This package was created with partial funding by Metrum Institute\n   \\url{http://metruminstitute.org}.\n}\n\\seealso{\n  \\code{\\link{toSAS}},\n  \\code{\\link{lookup.xport}},\n  \\code{\\link{read.xport}},\n  \\code{\\link{label}},\n  \\code{\\link{SAStype}},\n  \\code{\\link{SASformat}},\n  and \\code{\\link{SASiformat}}\n}\n\\examples{\n\n#####\n## R version of the example given in TS-140\n#####\n\n## manually create a data set\nabc <- data.frame( x=c(1, 2, NA, NA ), y=c('a', 'B', NA, '*' ) )\n\n## look at it\nabc\n\n## add a format specifier (not used by R)\nSASformat(abc$x) <- 'date7.'\n\n## add a variable label (not used by R)\nlabel(abc$y) <- 'character variable'\n\n## add a dataset label and type\nlabel(abc) <- 'Simple example'\nSAStype(abc) <- 'MYTYPE'\n\n## verify the additions\nstr(abc)\n\n# create a SAS XPORT file\nwrite.xport( abc, file=\"xxx.dat\" )\n\n# list the contents of the file\nlookup.xport(\"xxx.dat\")\n\n## reload the data\nxxx.abc <- read.xport(\"xxx.dat\")\n\n## and look at it\nxxx.abc\n\n## Check the label and type\nlabel(xxx.abc)\nSAStype(xxx.abc)\n\n## Note that the variable names and SAS dataset type have been converted\n## to uppercase\n\n}\n\\keyword{file}\n",
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+    "project_path" : "man/write.xport.Rd",
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+    "type" : "r_doc"
+}
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Added: pkg/SASxport/.Rproj.user/632EB997/sdb/mt/B97C53CF
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/sdb/mt/B97C53CF	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/sdb/mt/B97C53CF	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,20 @@
+{
+    "collab_server" : "",
+    "contents" : "useDynLib(SASxport, .registration=TRUE)\n\nimportFrom(chron, chron, times)\nimportFrom(utils, packageDescription)\nimportFrom(Hmisc, label, label.default, \"label<-\", \"label<-.default\")\nimportFrom(utils, download.file)\n\nexport(\n       toSAS,\n       lookup.xport,\n       read.xport,\n       write.xport,\n       ## \"label\",\n       ## \"label<-\",\n\n       makeSASNames,\n\n       \"SASformat\",\n       \"SASformat<-\",\n\n       \"SASiformat\",\n       \"SASiformat<-\",\n\n       \"SAStype\",\n       \"SAStype<-\"\n)\n\nS3method(toSAS, numeric)\nS3method(toSAS, logical)\nS3method(toSAS, character)\nS3method(toSAS, factor)\nS3method(toSAS, chron)\nS3method(toSAS, POSIXt)\nS3method(toSAS, Date)\nS3method(toSAS, default)\n\n## S3method(label, default)\nS3method(SASformat,  default)\nS3method(SASiformat, default)\nS3method(SAStype,    default)\n\n## S3method(label,   data.frame)\nS3method(SASformat,  data.frame)\nS3method(SASiformat, data.frame)\n##S3method(SAStype,    data.frame)\n\n## S3method(\"label<-\", default)\nS3method(\"SASformat<-\",  default)\nS3method(\"SASiformat<-\", default)\nS3method(\"SAStype<-\",    default)\n\n## S3method(\"label<-\", data.frame)\nS3method(\"SASformat<-\",  data.frame)\nS3method(\"SASiformat<-\", data.frame)\n##S3method(\"SAStype<-\",    data.frame)\n\nS3method(print, lookup.xport)\nS3method(summary, lookup.xport)\nS3method(print, summary.lookup.xport)\n\n",
+    "created" : 1458944711911.000,
+    "dirty" : false,
+    "encoding" : "UTF-8",
+    "folds" : "",
+    "hash" : "1759035676",
+    "id" : "B97C53CF",
+    "lastKnownWriteTime" : 1458944725,
+    "last_content_update" : 1458944725295,
+    "path" : "~/src/r-gregmisc/SASxport/NAMESPACE",
+    "project_path" : "NAMESPACE",
+    "properties" : {
+    },
+    "relative_order" : 5,
+    "source_on_save" : false,
+    "source_window" : "",
+    "type" : "r_namespace"
+}
\ No newline at end of file

Added: pkg/SASxport/.Rproj.user/632EB997/sdb/mt/EB1F71A0
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/sdb/mt/EB1F71A0	                        (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/sdb/mt/EB1F71A0	2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,20 @@
+{
+    "collab_server" : "",
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/r-gregmisc -r 2135

From noreply at r-forge.r-project.org  Mon Aug 15 21:02:47 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 15 Aug 2016 21:02:47 +0200 (CEST)
Subject: [R-gregmisc-commits] r2136 - pkg/SASxport/man
Message-ID: <20160815190247.3EF2C18444D@r-forge.r-project.org>

Author: warnes
Date: 2016-08-15 21:02:45 +0200 (Mon, 15 Aug 2016)
New Revision: 2136

Modified:
   pkg/SASxport/man/write.xport.Rd
Log:
Update URL to SAS Tech Report

Modified: pkg/SASxport/man/write.xport.Rd
===================================================================
--- pkg/SASxport/man/write.xport.Rd	2016-08-12 17:38:13 UTC (rev 2135)
+++ pkg/SASxport/man/write.xport.Rd	2016-08-15 19:02:45 UTC (rev 2136)
@@ -18,7 +18,7 @@
  )
 }
 \arguments{
-  \item{\dots}{One or more data frames to be stored}  
+  \item{\dots}{One or more data frames to be stored}
   \item{list}{A list containing data frames to be stored.}
   \item{file}{File name or connection object. Use "" to view the raw data}
   \item{verbose}{Logical flag controlling whether status is reported
@@ -48,7 +48,7 @@
       point format (see the reference).
     \item Date and time variables are either converted to number of days since
       1960-01-01 (date only), or number of seconds since
-      1960-01-01:00:00:00 GMT (date-time variables).  
+      1960-01-01:00:00:00 GMT (date-time variables).
     \item Missing values are converted to the standard SAS missing value
       '.'
   }
@@ -72,12 +72,12 @@
 \references{
   SAS Technical Support document TS-140: ``The Record Layout of a
   Data Set in SAS Transport (XPORT) Format'' available at
-  \url{http://ftp.sas.com/techsup/download/technote/ts140.html}.
+  \url{https://support.sas.com/techsup/technote/ts140.pdf}.
 }
 \author{Gregory R. Warnes \email{greg at warnes.net}}
 \note{
    This package was created with partial funding by Metrum Institute
-   \url{http://metruminstitute.org}. 
+   \url{http://metruminstitute.org}.
 }
 \seealso{
   \code{\link{toSAS}},
@@ -86,7 +86,7 @@
   \code{\link{label}},
   \code{\link{SAStype}},
   \code{\link{SASformat}},
-  and \code{\link{SASiformat}}  
+  and \code{\link{SASiformat}}
 }
 \examples{
 
@@ -113,7 +113,7 @@
 ## verify the additions
 str(abc)
 
-# create a SAS XPORT file 
+# create a SAS XPORT file
 write.xport( abc, file="xxx.dat" )
 
 # list the contents of the file


From noreply at r-forge.r-project.org  Mon Aug 15 21:05:25 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 15 Aug 2016 21:05:25 +0200 (CEST)
Subject: [R-gregmisc-commits] r2137 - pkg/gmodels/R
Message-ID: <20160815190526.000F3188084@r-forge.r-project.org>

Author: warnes
Date: 2016-08-15 21:05:23 +0200 (Mon, 15 Aug 2016)
New Revision: 2137

Added:
   pkg/gmodels/R/est_p_ci.R
Log:
Add est_p_ci generic and lm method

Added: pkg/gmodels/R/est_p_ci.R
===================================================================
--- pkg/gmodels/R/est_p_ci.R	                        (rev 0)
+++ pkg/gmodels/R/est_p_ci.R	2016-08-15 19:05:23 UTC (rev 2137)
@@ -0,0 +1,47 @@
+est_p_ci <- function(model, term, mult=1, digits=2, ...)
+  UseMethod("est_p_ci")
+
+est_p_ci.lm <- function(model, term, mult=1, digits=2, ...)
+{
+  info <- ci(model)
+  if(is.character(term) && !(term %in% rownames(info)))
+    stop(term, " is not a coefficient in model.")
+  info <- info[term,]
+  info.ci <- trim(format( round(mult * info[1:3], digits=digits) ))
+  if(mult < 0)
+    names(info.ci) <- rev(names(info.ci))
+  paste("Est=", info.ci[1],
+        " ",
+        "p=",format.pval(info['p-value'], digits=digits),
+        " ",
+        "95% CI: ",
+        info.ci['CI lower'],
+        " to ",
+        info.ci['CI upper'],
+        sep=""
+  )
+}
+
+est_p_ci.fit_contrast <- function(model, term, mult=1, digits=2, ...)
+{
+  if( !all(c("lower CI", "upper CI") %in% colnames(model) ) )
+    stop("object does not contain confidence interval information.")
+  
+  if(is.character(term) && !(term %in% rownames(info)))
+    stop(term, " is not a coefficient in model.")
+  
+  info.ci <- trim(format( round(mult * model[term, c("lower CI", "upper CI")], 
+                           digits=digits) )  )
+  if(mult < 0)
+    names(info.ci) <- rev(names(info.ci))
+  paste("Est=", info.ci[1],
+        " ",
+        "p=",format.pval(model[term, 'Pr(>|t|)'], digits=digits),
+        " ",
+        "95% CI: ",
+        info.ci["lower CI"],
+        " to ",
+        info.ci["upper CI"],
+        sep=""
+  )
+}


From noreply at r-forge.r-project.org  Mon Aug 15 21:11:04 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 15 Aug 2016 21:11:04 +0200 (CEST)
Subject: [R-gregmisc-commits] r2138 - in pkg/gmodels: . test
Message-ID: <20160815191104.D9E1A188077@r-forge.r-project.org>

Author: warnes
Date: 2016-08-15 21:11:04 +0200 (Mon, 15 Aug 2016)
New Revision: 2138

Added:
   pkg/gmodels/test/
   pkg/gmodels/test/lme-test.R
   pkg/gmodels/test/test_estimable_mlm.R
Log:
Add tests for mlm and (obsolete) lme

Added: pkg/gmodels/test/lme-test.R
===================================================================
--- pkg/gmodels/test/lme-test.R	                        (rev 0)
+++ pkg/gmodels/test/lme-test.R	2016-08-15 19:11:04 UTC (rev 2138)
@@ -0,0 +1,77 @@
+library(gmodels)
+library(lme4)
+set.seed(314159)
+
+sleepstudy$dayGroup <- cut(sleepstudy$Days, seq(-1,9,by=2), include=T)
+
+fm2 <- lmer(Reaction ~ dayGroup + (1|Subject) + (0+Days|Subject), sleepstudy)
+
+# ci example
+#!!# ci(fm2)
+
+
+# estimable examples
+#!!# estimable(fm2, c( 0, -1, 1, 0,  0 )  ) # list all terms
+#!!# estimable(fm2, c("dayGroup(1,3]"=-1, "dayGroup(3,5]"=1)) # just the nonzero terms
+#!!# estimable(fm2, c("dayGroup(1,3]"=-1, "dayGroup(3,5]"=1), n.sim=5000 ) # more simulations...
+
+
+# fit.contrast example
+#!!# fit.contrast( fm2, "dayGroup",
+#!!#               rbind("0-1 vs 3-4"=c(-1,0,1,0,0),
+#!!#                     "3-4 vs 5-6"=c(0,0,-1,1,0)
+#!!#                   ),
+#!!#             conf=0.95 )
+
+# Example from Ariel.Muldoon at oregonstate.edu
+homerange=c(
+        "male","1","fall","0.1",
+	"male","1","winter","0.3",
+	"male","1","spring","5.2",
+	"male","1","summer","3.1",
+	"male","2","fall","3.4",
+	"male","2","winter","1.3",
+	"male","2","spring","4.8",
+	"male","2","summer","4.3",
+	"male","3","fall","3.9",
+	"male","3","winter","3.8",
+	"male","3","spring","5.7",
+	"male","3","summer","2.0",
+	"male","4","fall","3.7",
+	"male","4","winter","4.3",
+	"male","4","spring","6.0",
+	"male","4","summer","1.8",
+	"female","5","fall","4.3",
+	"female","5","winter","1.9",
+	"female","5","spring","7.2",
+	"female","5","summer","6.9",
+	"female","6","fall","5.3",
+	"female","6","winter","4.3",
+	"female","6","spring","6.2",
+	"female","6","summer","4.8",
+	"female","7","fall","7.1",
+	"female","7","winter","4.9",
+	"female","7","spring","8.3",
+	"female","7","summer","7.7"
+	)
+ 
+homerange <- data.frame(matrix(homerange,ncol=4, byrow=T))
+names(homerange) <- c("sex", "animal", "season", "area")
+homerange$area = as.numeric(as.character(homerange$area))
+
+fit1 <- lmer(area ~ sex*season + (1|animal), data=homerange)
+summary(fit1)
+anova(fit1)
+ 
+
+#matrix to give estimable for making estimates
+
+spr <- rbind(c(1,0,1,0,0,0,0,0),
+             c(1,1,0,0,0,1,0,0),
+             c(1,0,0,1,0,0,0,0),
+             c(1,1,0,0,0,0,1,0),
+             c(1,0,0,0,1,0,0,0),
+             c(1,1,0,0,0,0,0,1))
+
+ 
+#!!# estimable(fit1, spr)

Added: pkg/gmodels/test/test_estimable_mlm.R
===================================================================
--- pkg/gmodels/test/test_estimable_mlm.R	                        (rev 0)
+++ pkg/gmodels/test/test_estimable_mlm.R	2016-08-15 19:11:04 UTC (rev 2138)
@@ -0,0 +1,15 @@
+library(gmodels)
+
+y <- cbind(rnorm(100), rnorm(100))
+
+x1 <- rnorm(100)
+x2 <- rnorm(100)
+
+cm <- t(matrix(c(0, 1,-1)))
+lm.1 <- lm(y ~ x1 + x2)
+
+estimable(lm.1, cm)
+
+## >> Error in coef(object) : object 'object' not found
+
+gmodels:::estimable.mlm(lm.1, cm)


From noreply at r-forge.r-project.org  Mon Aug 15 21:13:14 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 15 Aug 2016 21:13:14 +0200 (CEST)
Subject: [R-gregmisc-commits] r2139 - pkg/gtools/src
Message-ID: <20160815191314.EF97118808E@r-forge.r-project.org>

Author: warnes
Date: 2016-08-15 21:13:14 +0200 (Mon, 15 Aug 2016)
New Revision: 2139

Modified:
   pkg/gtools/src/setTCPNoDelay.c
Log:
checkStatus() was not correctly getting the error message.

Modified: pkg/gtools/src/setTCPNoDelay.c
===================================================================
--- pkg/gtools/src/setTCPNoDelay.c	2016-08-15 19:11:04 UTC (rev 2138)
+++ pkg/gtools/src/setTCPNoDelay.c	2016-08-15 19:13:14 UTC (rev 2139)
@@ -98,7 +98,7 @@
                        );
 
 
-  checkStatus(*status, status_str[0], *status_len);
+  checkStatus(errno, status_str[0], *status_len);
   
   return;
 }


From noreply at r-forge.r-project.org  Mon Aug 15 21:14:10 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 15 Aug 2016 21:14:10 +0200 (CEST)
Subject: [R-gregmisc-commits] r2140 - pkg/gtools/R
Message-ID: <20160815191410.A7ADE18808E@r-forge.r-project.org>

Author: warnes
Date: 2016-08-15 21:14:10 +0200 (Mon, 15 Aug 2016)
New Revision: 2140

Modified:
   pkg/gtools/R/setTCPNoDelay.R
Log:
Modify setTCPNoDelay to work with current socket objects

Modified: pkg/gtools/R/setTCPNoDelay.R
===================================================================
--- pkg/gtools/R/setTCPNoDelay.R	2016-08-15 19:13:14 UTC (rev 2139)
+++ pkg/gtools/R/setTCPNoDelay.R	2016-08-15 19:14:10 UTC (rev 2140)
@@ -5,7 +5,11 @@
 
     buffer <- paste(rep(" ", 1000), sep='', collapse='')
 
-    conn <- getConnection(socket[1])
+    if("sockconn" %in% class(socket))
+      conn <- getConnection(socket[1])
+    else
+      conn <- socket
+ 
     
     retval <- .C("R_setTCPNoDelay",
                  socket=as.integer(socket[1]),


From noreply at r-forge.r-project.org  Mon Aug 15 21:14:50 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 15 Aug 2016 21:14:50 +0200 (CEST)
Subject: [R-gregmisc-commits] r2141 - pkg/gtools/tests
Message-ID: <20160815191450.4770018808E@r-forge.r-project.org>

Author: warnes
Date: 2016-08-15 21:14:49 +0200 (Mon, 15 Aug 2016)
New Revision: 2141

Added:
   pkg/gtools/tests/test_setTCPNoDelay.R
Log:
Add test code for setTCPNoDelay

Added: pkg/gtools/tests/test_setTCPNoDelay.R
===================================================================
--- pkg/gtools/tests/test_setTCPNoDelay.R	                        (rev 0)
+++ pkg/gtools/tests/test_setTCPNoDelay.R	2016-08-15 19:14:49 UTC (rev 2141)
@@ -0,0 +1,44 @@
+library('gtools')
+
+setTCPNoDelay <- function( socket, value=TRUE )
+{
+  if(!any(c("socket","sockconn") %in% class(socket)))
+    stop("socket must be a socket object")
+
+  buffer <- paste(rep(" ", 1000), sep='', collapse='')
+
+  if("sockconn" %in% class(socket))
+    conn <- getConnection(socket[1])
+  else
+    conn <- socket
+
+
+  retval <- .C("R_setTCPNoDelay",
+               socket=as.integer(socket[1]),
+               flag=as.integer(value),
+               status=integer(1),
+               status.str=as.character(buffer),
+               status.len=as.integer(nchar(buffer)),
+               package="gtools"
+  )
+
+  if(retval$status != 0)
+    stop( retval$status.str )
+  else
+    invisible(retval$status.str)
+}
+
+
+
+host <- "rdgas05026.am.boehringer.com"
+#host <- "www.r-project.org"
+socket <- make.socket(host, 80)
+print(socket)
+setTCPNoDelay(socket, TRUE)
+
+write.socket(socket, "GET /\n\n")
+while( (str <- read.socket(socket)) > "")
+  cat(str)
+close.socket(socket)
+
+read.socket(socket)
\ No newline at end of file


From noreply at r-forge.r-project.org  Mon Aug 15 21:16:11 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 15 Aug 2016 21:16:11 +0200 (CEST)
Subject: [R-gregmisc-commits] r2142 - pkg/gtools
Message-ID: <20160815191612.0EF5818804E@r-forge.r-project.org>

Author: warnes
Date: 2016-08-15 21:16:11 +0200 (Mon, 15 Aug 2016)
New Revision: 2142

Modified:
   pkg/gtools/DESCRIPTION
Log:
Update version number and date

Modified: pkg/gtools/DESCRIPTION
===================================================================
--- pkg/gtools/DESCRIPTION	2016-08-15 19:14:49 UTC (rev 2141)
+++ pkg/gtools/DESCRIPTION	2016-08-15 19:16:11 UTC (rev 2142)
@@ -22,8 +22,8 @@
   - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
   - generate significance stars from p-values ('stars.pval'),
   - convert characters to/from ASCII codes.
-Version: 3.6.0
-Date: 2015-08-07
+Version: 3.6.2
+Date: 2016-08-15
 Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
 Maintainer: Gregory R. Warnes <greg at warnes.net>
 License: GPL-2


From noreply at r-forge.r-project.org  Mon Aug 15 21:17:44 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 15 Aug 2016 21:17:44 +0200 (CEST)
Subject: [R-gregmisc-commits] r2143 - pkg/gtools/inst
Message-ID: <20160815191744.9771918804E@r-forge.r-project.org>

Author: warnes
Date: 2016-08-15 21:17:44 +0200 (Mon, 15 Aug 2016)
New Revision: 2143

Modified:
   pkg/gtools/inst/ChangeLog
Log:
Update ChangeLog

Modified: pkg/gtools/inst/ChangeLog
===================================================================
--- pkg/gtools/inst/ChangeLog	2016-08-15 19:16:11 UTC (rev 2142)
+++ pkg/gtools/inst/ChangeLog	2016-08-15 19:17:44 UTC (rev 2143)
@@ -1,5 +1,82 @@
+2016-08-15  warnes
+
+	* [r2142] DESCRIPTION: Update version number and date
+	* [r2141] tests/test_setTCPNoDelay.R: Add test code for
+	  setTCPNoDelay
+	* [r2140] R/setTCPNoDelay.R: Modify setTCPNoDelay to work with
+	  current socket objects
+	* [r2139] src/setTCPNoDelay.c: checkStatus() was not correctly
+	  getting the error message.
+
+2016-04-22  warnes
+
+	* [r2127] NAMESPACE, R/capwords.R, man/capwords.Rd: Add capwords()
+	  function to properly capatilize strings for use in titles
+	* [r2126] R/na.replace.R, man/na.replace.Rd: na.replace() now
+	  accepts a function providing the replcement value.
+
+2015-11-24  warnes
+
+	* [r2071] R/smartbind.R: Correct error when column types don't
+	  match (reported by
+
+2015-10-15  warnes
+
+	* [r2069] R/smartbind.R: smartbind() was not properly handling
+	  columsn that were numeric on one df and character in the other
+	  and other similar ctype conflicts. Fixed.
+
+2015-08-08  warnes
+
+	* [r2067] tests/smartbind_emptynames.R: Add half-hearted test file
+	* [r2066] R/smartbind.R: - Improve assignment of default names in
+	  smartbind.
+	  - Disambiguate 'list' into an object named 'list' and the
+	  function
+	  base::list() in smartbind().
+	* [r2065] DESCRIPTION, man/smartbind.Rd: Add example of using
+	  'list' argument to smartbind() man page.
+	* [r2064] R/smartbind.R, man/smartbind.Rd: - smartbind() gets a new
+	  argument 'list' to pass a list of data
+	  frames, instead of/in addition to data frames as arguments.
+	  - Fix bug in smartbind's handling of factor levels.
+	  
+
+2015-07-14  warnes
+
+	* [r2057] R/loadedPackages.R, man/loadedPackages.Rd: Modify
+	  loadedPackages() to return data silently so that the results
+	  don't get printed twice.
+
 2015-05-27  warnes
 
+	* [r2049] data/badDend.rda, man/badDend.Rd, man/unByteCode.Rd:
+	  Create local dataset to use in the example code for unByteCode
+	  instead of relying on web access.
+	* [r2048] R/trimws.R: Fix missing closing paren.
+	* [r2047] R/keywords.R, R/roman2int.R, R/trim.R, R/trimws.R: Two
+	  functions in gtools need to use either gdata::trim() or
+	  base::trimws() (added in R 3.2.0). The previous solution was to
+	  include gdata/R/gdata/R/trim.R in gtools using a symbolic link.
+	  
+	  Unfortunately, Rforge doesn't seem to like the symbolic link when
+	  building packages, and generates an error.
+	  
+	  So, instead, create the file trimws.R, which creates trimws() if
+	  it
+	  isn't already available (e.g. via base::trimws), and modify
+	  keywords()
+	  and roman2int() to use trimws() instead of gdata::trim().
+	* [r2046] man/roman2int.Rd: Add man page for roman2int().
+	* [r2045] man/mixedsort.Rd: Remove extraneous closing paren.
+	* [r2044] NAMESPACE: Add roman2int() to exported function list.
+	* [r2043] R/asc.R: Looks like we also lost the change of argument
+	  name to chr(). Fixed.
+	* [r2042] R/asc.R: Somehow lost 'simplify=TRUE' argument to asc.
+	  Fixed.
+	* [r2041] DESCRIPTION: Update gtools version number to 3.5.0
+	* [r2040] DESCRIPTION, inst/ChangeLog, inst/NEWS: Update
+	  DESCRIPTION, ChangeLog, NEWS
 	* [r2039] R/mixedsort.R, man/mixedsort.Rd: Add roman numeral
 	  support to mixedorder() and mixedsort().
 	* [r2037] man/asc.Rd: Add asc() and chr() functions for converting


From noreply at r-forge.r-project.org  Wed Aug 24 21:48:15 2016
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 24 Aug 2016 21:48:15 +0200 (CEST)
Subject: [R-gregmisc-commits] r2144 - pkg/gtools/tests
Message-ID: <20160824194815.1FC4D187E0D@r-forge.r-project.org>

Author: warnes
Date: 2016-08-24 21:48:14 +0200 (Wed, 24 Aug 2016)
New Revision: 2144

Modified:
   pkg/gtools/tests/test_setTCPNoDelay.R
Log:
Add more testing code.

Modified: pkg/gtools/tests/test_setTCPNoDelay.R
===================================================================
--- pkg/gtools/tests/test_setTCPNoDelay.R	2016-08-15 19:17:44 UTC (rev 2143)
+++ pkg/gtools/tests/test_setTCPNoDelay.R	2016-08-24 19:48:14 UTC (rev 2144)
@@ -37,8 +37,7 @@
 setTCPNoDelay(socket, TRUE)
 
 write.socket(socket, "GET /\n\n")
+write.socket(socket, "A\0B\n")
 while( (str <- read.socket(socket)) > "")
   cat(str)
 close.socket(socket)
-
-read.socket(socket)
\ No newline at end of file