[R-gregmisc-commits] r2059 - in pkg/gmodels: . inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jul 19 04:34:48 CEST 2015
Author: warnes
Date: 2015-07-19 04:34:45 +0200 (Sun, 19 Jul 2015)
New Revision: 2059
Modified:
pkg/gmodels/DESCRIPTION
pkg/gmodels/inst/ChangeLog
pkg/gmodels/inst/NEWS
Log:
Update DESCRIPTION, ChangeLog, and NEWS for gmodels 2.16.1
Modified: pkg/gmodels/DESCRIPTION
===================================================================
--- pkg/gmodels/DESCRIPTION 2015-07-19 02:30:05 UTC (rev 2058)
+++ pkg/gmodels/DESCRIPTION 2015-07-19 02:34:45 UTC (rev 2059)
@@ -1,6 +1,6 @@
Package: gmodels
-Version: 2.16.0
-Date: 2014-07-24
+Version: 2.16.1
+Date: 2015-07-18
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
Modified: pkg/gmodels/inst/ChangeLog
===================================================================
--- pkg/gmodels/inst/ChangeLog 2015-07-19 02:30:05 UTC (rev 2058)
+++ pkg/gmodels/inst/ChangeLog 2015-07-19 02:34:45 UTC (rev 2059)
@@ -1,194 +1,182 @@
+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
- * [r1868] DESCRIPTION, NAMESPACE, R/ci.R, R/estimable.R, man/ci.Rd,
- man/estimable.Rd: - Estimable now adds the class 'estimable' to
- returned objects.
+ * [r1869] Update NEWS for gmodels 2.16.0
+ * [r1868] - 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] 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
+ * [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
2013-07-15 warnes
- * [r1706] R/ci.R, man/ci.Rd: Remove unused argument to ci.mer
+ * [r1706] Remove unused argument to ci.mer
2012-06-28 warnes
- * [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.
+ * [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.
2012-06-27 warnes
- * [r1573] test/lme-test.R: Add test code submitted by
- Ariel.Muldoon at oregonstate.edu.
+ * [r1573] Add test code submitted by Ariel.Muldoon at oregonstate.edu.
2012-04-19 warnes
- * [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
+ * [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
2011-12-14 warnes
- * [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.
+ * [r1521] Improve formatting of ci.mer().
+ * [r1520] Modify est.mer to work with recent lme4 'mer' S4 objects.
2011-01-16 warnes
- * [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.
+ * [r1466] Fix warnings reported by R CMD check. Update version
+ number to 2.15.1.
2009-05-09 warnes
- * [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
+ * [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
2008-04-10 warnes
- * [r1255] man/ci.Rd: Improve languages a bit
+ * [r1255] Improve languages a bit
2008-01-02 warnes
- * [r1236] man/CrossTable.Rd: Update Marc's email address
+ * [r1236] Update Marc's email address
2007-12-12 warnes
- * [r1233] DESCRIPTION: Move copyright notice for Randall's
- contributions from License section to Author section of the
- DESCRIPTION file.
+ * [r1233] Move copyright notice for Randall's contributions from
+ License section to Author section of the DESCRIPTION file.
2007-12-07 warnes
- * [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.
+ * [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.
2007-10-22 warnes
- * [r1196] DESCRIPTION: Clarify GPL version
+ * [r1196] Clarify GPL version
2007-07-26 warnes
- * [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
+ * [r1105] Add support for mlm to estimable().
+ * [r1104] Add estimable method for mlm objects
2007-03-09 warnes
- * [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
+ * [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
2006-11-29 warnes
- * [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
+ * [r1029] Update for 2.13.1
+ * [r1028] Correct declartion of S3 methods for estimable()
+ * [r1027] Add additional suggested packages
+ * [r1026] - Add generic
- Fix code vs. doc inconsistiencies
2006-11-28 warnes
- * [r1025] R/ci.R, R/estimable.R, R/fast.prcomp.R: Remove extraneous
- comma that causes errors in R 2.5.0
+ * [r1025] Remove extraneous comma that causes errors in R 2.5.0
2006-11-27 warnes
- * [r1016] DESCRIPTION, NEWS: Update for 2.13.1
- * [r1015] DESCRIPTION, NAMESPACE: Add missing export of methods for
- estimable()
+ * [r1016] Update for 2.13.1
+ * [r1015] Add missing export of methods for estimable()
2006-11-14 ggorjan
- * [r1012] R/ci.R, R/fast.prcomp.R, man/ci.Rd: Removed executable
- property
+ * [r1012] Removed executable property
2006-08-02 warnes
- * [r977] man/fast.prcomp.Rd, man/fit.contrast.Rd, man/glh.test.Rd,
- man/make.contrasts.Rd: Update my email address
+ * [r977] Update my email address
2006-06-06 nj7w
- * [r966] man/ci.Rd, man/estimable.Rd, man/fit.contrast.Rd: Updated
- ci, estimable and fit.contrast as per Randall Johnson
+ * [r966] Updated ci, estimable and fit.contrast as per Randall
+ Johnson
2006-06-05 nj7w
- * [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
+ * [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
Matrix package
2006-05-05 nj7w
- * [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
+ * [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
2005-12-13 nj7w
- * [r808] ChangeLog: Removed ChangeLog
- * [r807] NEWS: Updated NEWS
+ * [r808] Removed ChangeLog
+ * [r807] Updated NEWS
2005-12-12 nj7w
- * [r796] DESCRIPTION: Updated version number for CRAN
+ * [r796] Updated version number for CRAN
2005-12-04 warnes
- * [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
+ * [r781] Update for 2.11.0
+ * [r780] Integration of code changes suggested by Randall C Johnson
+ to add
support for lmer (lme version 4) objects to ci(), estimable(),
and
fit.contrast().
@@ -203,52 +191,48 @@
2005-12-01 nj7w
- * [r776] man/ci.Rd, man/coefFrame.Rd, man/estimable.Rd,
- man/fit.contrast.Rd, man/make.contrasts.Rd: Updated Greg's email
- address
+ * [r776] Updated Greg's email address
2005-10-27 warnes
- * [r709] DESCRIPTION: Update version number. Bump minor version
- since we added functionality.
- * [r708] DESCRIPTION, NAMESPACE: Add ci.binom() to NAMESPACE, bump
- version
+ * [r709] Update version number. Bump minor version since we added
+ functionality.
+ * [r708] Add ci.binom() to NAMESPACE, bump version
2005-10-26 warnes
- * [r707] R/ci.R, man/ci.Rd: Add ci.binom
+ * [r707] Add ci.binom
2005-10-25 warnes
- * [r706] NAMESPACE: Add gdata::nobs to import list. Needed by ci()
+ * [r706] Add gdata::nobs to import list. Needed by ci()
2005-09-12 nj7w
- * [r671] man/fast.prcomp.Rd, man/glh.test.Rd: Updated Greg's email
+ * [r671] Updated Greg's email
2005-09-07 nj7w
- * [r667] man/CrossTable.Rd: Fixed man page
+ * [r667] Fixed man page
2005-09-06 nj7w
- * [r664] DESCRIPTION: Updated DESCRIPTION
- * [r663] NEWS: Added NEWS
- * [r662] DESCRIPTION: Fixed the Package name
+ * [r664] Updated DESCRIPTION
+ * [r663] Added NEWS
+ * [r662] Fixed the Package name
2005-09-02 nj7w
- * [r655] ChangeLog: Added ChangeLog
+ * [r655] Added ChangeLog
2005-08-31 nj7w
- * [r644] DESCRIPTION: Added DESCRIPTION file
- * [r643] DESCRIPTION.in: removed DESCRIPTION.in
+ * [r644] Added DESCRIPTION file
+ * [r643] removed DESCRIPTION.in
2005-07-11 nj7w
- * [r627] R/CrossTable.R, man/CrossTable.Rd: Revision based on Marc
- Schwartz's suggestions:
+ * [r627] 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
@@ -256,14 +240,10 @@
2005-06-09 nj7w
- * [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:
+ * [r625] Updating the version number, and various help files to
+ synchronize splitting of gregmisc bundle in 4 individual
+ components.
+ * [r623] Updates by Marc Schwartz:
CrossTable:
# Revision 2.0 2005/04/27
@@ -273,108 +253,95 @@
2005-05-13 nj7w
- * [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.
+ * [r621] 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] DESCRIPTION.in, NAMESPACE: Add dependency on
- gdata::frameApply.
+ * [r620] Add dependency on gdata::frameApply.
2005-03-31 warnes
- * [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
+ * [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
2005-01-18 warnes
- * [r521] R/CrossTable.R: Removed Windows Line Endings
+ * [r521] Removed Windows Line Endings
2005-01-14 nj7w
- * [r518] man/CrossTable.Rd: Updated the manual to reflect
- prop.chisq change in its R file.
+ * [r518] Updated the manual to reflect prop.chisq change in its R
+ file.
2005-01-14 warnes
- * [r517] R/CrossTable.R: Nitin added display of the Chisquare
- contribution of each cell, as suggested
+ * [r517] Nitin added display of the Chisquare contribution of each
+ cell, as suggested
by Greg Snow.
2005-01-12 warnes
- * [r515] DESCRIPTION.in: Add dependency on R 1.9.0+ to prevent
- poeple from installing on old
+ * [r515] 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] 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'
+ * [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'
2004-12-21 warnes
- * [r502] R/CrossTable.R: Added & extended changes made by Nitin to
- implement 'SPSS' format, as suggested by
+ * [r502] 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] man/glh.test.Rd: Fix typos.
+ * [r464] Fix typos.
2004-09-27 warneg
- * [r461] DESCRIPTION, DESCRIPTION.in: Updated to pass R CMD check.
+ * [r461] Updated to pass R CMD check.
2004-09-03 warneg
- * [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
+ * [r450] Add explicit package to call to quantcut in example.
+ * [r446] initial bundle checkin
2004-09-02 warneg
- * [r442] DESCRIPTION, DESCRIPTION.in, NAMESPACE: Initial revision
+ * [r442] Initial revision
2004-05-25 warnes
- * [r327] R/CrossTable.R, man/CrossTable.Rd: Updates from Mark
- Schwartz.
+ * [r327] Updates from Mark Schwartz.
2004-04-13 warnes
- * [r314] man/estimable.Rd: Fix latex warning: it doesn't like
- double subscripts.
+ * [r314] Fix latex warning: it doesn't like double subscripts.
2004-03-26 warnes
- * [r306] man/fast.prcomp.Rd: Reflect movement of code from 'mva'
- package to 'stats' in R 1.9.0.
+ * [r306] Reflect movement of code from 'mva' package to 'stats' in
+ R 1.9.0.
2004-03-25 warnes
- * [r296] R/estimable.R, man/estimable.Rd: - Estimable was reporting
- sqrt(X^2) rather than X^2 in the output.
+ * [r296] - 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] R/estimable.R, man/estimable.Rd: Add enhancements to
- estimable() provided by S�ren H�jsgaard
+ * [r295] 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
@@ -384,38 +351,38 @@
2003-11-17 warnes
- * [r221] R/fit.contrast.R: - Fix incorrect handling of glm objects
- by fit.contrast, as reported
+ * [r221] - 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] R/ci.R: - Fixed incorrect denominator in standard error
- for mean in ci.default.
+ * [r217] - Fixed incorrect denominator in standard error for mean
+ in ci.default.
2003-04-22 warnes
- * [r190] R/fit.contrast.R: - the variable 'df' was used within the
- lme code section overwriting
+ * [r190] - the variable 'df' was used within the lme code section
+ overwriting
the argument 'df'.
2003-03-12 warnes
- * [r173] man/fit.contrast.Rd: - Fixed a typo in the example
+ * [r173] - Fixed a typo in the example
- Added to lme example
2003-03-07 warnes
- * [r168] R/fast.prcomp.R: - Minor changes to code to allow the
- package to be provided as an
+ * [r168] - Minor changes to code to allow the package to be
+ provided as an
S-Plus chapter.
2003-01-30 warnes
- * [r160] R/fit.contrast.R, man/fit.contrast.Rd: - Renamed
- 'contrast.lm' to 'fit.contrast'. This new name is more
+ * [r160] - 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.
@@ -429,8 +396,8 @@
calls fit.contrast
- Updated help text to match changes.
- * [r158] R/CrossTable.R, man/CrossTable.Rd: - Removed argument
- 'correct' and now print separate corrected values
+ * [r158] - 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
@@ -444,8 +411,8 @@
table
counts, proportions and the results of the appropriate
statistical tests.
- * [r157] R/make.contrasts.R: - Added explicit check to ensure that
- the number of specified
+ * [r157] - 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
@@ -453,56 +420,50 @@
2002-11-04 warnes
- * [r142] R/CrossTable.R: - Moved fisher.test() to after table is
- printed, so that table is
+ * [r142] - 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] R/fast.prcomp.R, man/fast.prcomp.Rd: - Fixes to fast.svd
- to make it actually work.
+ * [r138] - 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] R/make.contrasts.R, man/make.contrasts.Rd: - Moved
- make.contrasts to a separate file.
+ * [r137] - 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] R/fast.prcomp.R, man/fast.prcomp.Rd: Initial checkin for
- fast.prcomp() and fast.svd().
+ * [r136] Initial checkin for fast.prcomp() and fast.svd().
2002-09-26 warnes
- * [r127] man/glh.test.Rd: - Added note and example code to
- illustrate how to properly compute
+ * [r127] - Added note and example code to illustrate how to
+ properly compute
contrasts for the first factor in the model.
2002-09-24 warnes
- * [r124] R/glh.test.R: - Fixed a typo.
+ * [r124] - Fixed a typo.
2002-09-23 warnes
- * [r119] man/CrossTable.Rd, man/glh.test.Rd: - Fixed syntax errors
- in barplot2.Rd and CrossTable.Rd
+ * [r119] - Fixed syntax errors in barplot2.Rd and CrossTable.Rd
- Fixed incorrect translation of 'F' (distribution) to 'FALSE' in
glh.test.Rd
- * [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.
+ * [r117] - Modified all files to include CVS Id and Log tags.
+ * [r116] - 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] R/ci.R, man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: -
- Corrected documentation mismatch for ci, ci.default.
+ * [r114] - Corrected documentation mismatch for ci, ci.default.
- Replaced all occurences of '_' for assignment with '<-'.
@@ -514,101 +475,95 @@
2002-04-09 warneg
- * [r109] R/ci.R, R/estimable.R, R/glh.test.R, man/glh.test.Rd:
- Checkin for version 0.5.3
+ * [r109] Checkin for version 0.5.3
2002-03-26 warneg
- * [r104] R/ci.R, R/glh.test.R, man/ci.Rd, man/glh.test.Rd: -
- Changed methods to include '...' to match the generic.
+ * [r104] - Changed methods to include '...' to match the generic.
- Updated for version 0.5.1
- * [r99] man/glh.test.Rd: Removed incorrect link to 'contrast' from
- seealso.
+ * [r99] Removed incorrect link to 'contrast' from seealso.
2002-02-20 warneg
- * [r81] man/ci.Rd, man/estimable.Rd, man/glh.test.Rd: Minor
- changes, typo and formatting fixes.
+ * [r81] Minor changes, typo and formatting fixes.
2002-01-17 warneg
- * [r70] man/estimable.Rd: - Fixed errror in last example by adding
- 'conf.int' parameter to
+ * [r70] - Fixed errror in last example by adding 'conf.int'
+ parameter to
'estimable' call.
- * [r69] R/glh.test.R: - Fixed typo in code that resulted in an
- syntax error.
+ * [r69] - Fixed typo in code that resulted in an syntax error.
2002-01-10 warneg
- * [r68] R/glh.test.R: - print.glh.test() was using cat() to
- printing the call. This didn't work and
+ * [r68] - print.glh.test() was using cat() to printing the call.
+ This didn't work and
generated an error.
2001-12-19 warneg
- * [r66] man/glh.test.Rd: - Fixed display of formulae.
+ * [r66] - Fixed display of formulae.
- Added description of return value
- * [r65] R/glh.test.R: - Removed extra element of return object.
+ * [r65] - Removed extra element of return object.
2001-12-18 warneg
- * [r64] man/estimable.Rd: - Updated documentation to reflect change
- of parameters from 'alpha'
+ * [r64] - Updated documentation to reflect change of parameters
+ from 'alpha'
to 'conf.int', including the new optional status of the
confidence
intervals.
- * [r63] R/estimable.R: - Modified to make confidence intervals
- optional. Changed 'alpha'
+ * [r63] - Modified to make confidence intervals optional. Changed
+ 'alpha'
parameter giving significance level to 'conf.int' giving
confidence
level.
- * [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
+ * [r62] - Added summary.glh.test to alias, usage, and example
+ sections.
+ * [r61] - 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] R/estimable.R: - Modified to work correctly when obj is of
- class 'aov' by specifying
+ * [r60] - 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] R/glh.test.R, man/glh.test.Rd: Initial checkin.
+ * [r59] Initial checkin.
2001-12-17 warneg
- * [r56] man/estimable.Rd: - Fixed spelling errors.
- * [r55] man/estimable.Rd: - Fixed the link to contrasts.lm.
+ * [r56] - Fixed spelling errors.
+ * [r55] - Fixed the link to contrasts.lm.
- Rephrased title/description to be more clear.
2001-12-10 warneg
- * [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)
+ * [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)
2001-12-07 warneg
- * [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.
+ * [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.
2001-10-16 warneg
- * [r27] man/ci.Rd: Fixed unbalanced brace.
+ * [r27] Fixed unbalanced brace.
2001-08-25 warneg
- * [r12] man/ci.Rd: - Added CVS header.
+ * [r12] - Added CVS header.
- Added my email address.
2001-05-30 warneg
- * [r2] ., R, R/ci.R, man, man/ci.Rd: Initial revision
+ * [r2] Initial revision
Modified: pkg/gmodels/inst/NEWS
===================================================================
--- pkg/gmodels/inst/NEWS 2015-07-19 02:30:05 UTC (rev 2058)
+++ pkg/gmodels/inst/NEWS 2015-07-19 02:34:45 UTC (rev 2059)
@@ -1,3 +1,14 @@
+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.
+
+
Version 2.16.0 - 2014-07-24
---------------------------
@@ -41,7 +52,7 @@
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
@@ -113,7 +124,7 @@
- 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
@@ -135,8 +146,8 @@
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
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