[R-gregmisc-commits] r2131 - in pkg/gmodels: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 12 19:15:40 CEST 2016
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
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