[Lme4-commits] r1733 - in www: . misc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 15 22:01:21 CEST 2012
Author: bbolker
Date: 2012-05-15 22:01:21 +0200 (Tue, 15 May 2012)
New Revision: 1733
Added:
www/misc/lme4_compat_report.html
Modified:
www/index.php
www/misc/lme4_conversion.html
www/misc/lme4_conversion.md
Log:
tweaked index page
added current version of compatibility report, conversion guide
Modified: www/index.php
===================================================================
--- www/index.php 2012-05-15 19:35:07 UTC (rev 1732)
+++ www/index.php 2012-05-15 20:01:21 UTC (rev 1733)
@@ -43,22 +43,17 @@
<!-- end of project description -->
-<p> <strong>Doxygen</strong> documentation of the underlying C functions is <a href="./doxygen/"><strong>here</strong></a>. </p>
+<h2>Resources</h2>
+<ul>
+<li>A <a href="misc/lme4_conversion.html">guide</a> to changes in the upcoming release of <code>lme4</code> (<a href="misc/lme4_conversion.md">Markdown source</a>, <a href="misc/lme4_compat_report.html">downstream package compatibility report</a>)</li>
+<li>The <a href="http://<?php echo $domain; ?>/projects/<?php echo $group_name; ?>/">project summary page</a>, including links to the source code browser, bug and feature request trackers, etc.</li>
+<li><a href="./doxygen/"><em>Doxygen</em> documentation</a> of the underlying C functions</li>
+<li><a href="bib/lme4bib.html">References to articles and other research</a> using <code>nlme</code> or <code>lme4</code>, or the corresponding
+<a href="bib/lme4bib.bib">BibTeX file</a>. (If you would like to add your work to this database, please email <code>vasishth.shravan at gmail dot com</code>.)</li>
+<li><a href="./slides/">Slides</a> from short courses on <code>lme4</code></li>
+<li><a href="./lMMwR/">Chapter drafts</a> of the book <em>lme4:
+Mixed-effects Modeling with R</em></li>
-<p> The <strong>project summary page</strong> you can find <a href="http://<?php echo $domain; ?>/projects/<?php echo $group_name; ?>/"><strong>here</strong></a>. </p>
-
-<p> <strong>References to articles and other research using nlme or lme4</strong> can be found <a href="bib/lme4bib.html"><strong>here</strong></a>. The LaTeX bibliography file can be accessed from <a href="bib/lme4bib.bib">here</a>. If you would like to add your work to this database, please email vasishth.shravan at gmail dot com</p>
-
-<p>
-<strong>Slides</strong> from short courses on lme4 are
-<a href="./slides/"><strong>here</strong></a>.
-</p>
-
-<p> <strong>Chapter drafts</strong> of the book <em>lme4:
-Mixed-effects Modeling with R</em> are available <a
-href="./book/"><strong>here</strong></a>.
-</p>
-
<h2>Installation</h2>
<p>Binary and source packages of recent versions
of the development version (<code>lme4</code>, previously <code>lme4Eigen</code>) are available
Added: www/misc/lme4_compat_report.html
===================================================================
--- www/misc/lme4_compat_report.html (rev 0)
+++ www/misc/lme4_compat_report.html 2012-05-15 20:01:21 UTC (rev 1733)
@@ -0,0 +1,982 @@
+<html xmlns:mml="http://www.w3.org/1998/Math/MathML">
+<head>
+<title> lme4 downstream package report </title>
+<link rel=stylesheet href="R2HTML.css" type=text/css>
+<object id="mathplayer" classid="clsid:32F66A20-7614-11D4-BD11-00104BD3F987"></object>
+<?import namespace="mml" implementation="#mathplayer"?>
+<script type="text/javascript" src="ASCIIMathML.js"></script>
+<link href="./runtime/styles/xp/grid.css" rel="stylesheet" type="text/css" ></link>
+<link href="gridR2HTML.css" rel="stylesheet" type="text/css" ></link>
+
+<script src="./runtime/lib/grid.js"></script>
+
+<script src="./gridR2HTML.js"></script>
+<script>
+ nequations=0;
+</script>
+</head>
+<body onload="translate()" bgcolor= FFFFFF >
+<p class='character'><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></p>
+
+ <h1 > downstream lme4 package test report</h1>
+
+<p class='character'>lme4 version: 0.999902344.0</p>
+
+<p class='character'>Test date: Tue May 15 13:46:03 2012</p>
+
+ <h2 > Notes</h2>
+
+<p class='character'><ul></p>
+
+<br><li>contact: lme4-authors <at> r-forge.wu-wien.ac.at
+<br><li>'error_depfail' results are due to packages I haven't managed to get installed yet
+<br><li>'PIRLS step failed' errors are due to known, current GLMM issues (not your fault)
+<p class='character'></ul></p>
+
+
+<style>
+.tablesort {
+cursor: pointer ;
+ behavior:url(tablesort.htc);
+ -moz-binding: url(moz-behaviors.xml#tablesort.htc);
+}
+</style>
+
+<p align= center >
+<table cellspacing=0 border=1>
+<caption align=bottom class=captiondataframe></caption>
+<tr><td>
+ <table border=1 class=dataframe>
+ <tbody>
+ <tr class= firstline >
+ <th><b class="tablesort"> </b> </th>
+ <th><b class="tablesort">pkgname</b> </th>
+ <th><b class="tablesort">location</b> </th>
+ <th><b class="tablesort">version</b> </th>
+ <th><b class="tablesort">maintainer</b> </th>
+ <th><b class="tablesort">result</b> </th>
+ <th><b class="tablesort">diag</th>
+ </tr>
+<tr>
+<td class=firstcolumn>1
+</td>
+<td class=cellinside>agridat
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.4
+</td>
+<td class=cellinside>Kevin Wright
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>67: > summary(m1)@REmat<br>68: Error: trying to get slot "REmat" from an object (class "summary.mer") that is not an S4 object <br>69: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>2
+</td>
+<td class=cellinside>AICcmodavg
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.24
+</td>
+<td class=cellinside>Marc J. Mazerolle
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>179: Error in aictab(cand.set = Cands, modnames = Model.names, sort = TRUE) : <br>180: Function not yet defined for this object class<br>181: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>3
+</td>
+<td class=cellinside>amer
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.6.10
+</td>
+<td class=cellinside>Fabian Scheipl
+</td>
+<td class=cellinside><font style="color:red">error_install</font>
+</td>
+<td class=cellinside>** preparing package for lazy loading<br>Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : <br> No definition was found for superclass "mer" in the specification of class "amer"<br>Error : unable to load R code in package 'amer'<br>ERROR: lazy loading failed for package 'amer'<br>* removing '/mnt/hgfs/bolker/Documents/R/pkgs/lme4/pkgtests/amer.Rcheck/amer'
+</td></tr>
+
+<tr>
+<td class=firstcolumn>4
+</td>
+<td class=cellinside>aod
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.3
+</td>
+<td class=cellinside>Renaud Lancelot
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>63: could not find function "GHrule"<br>64: Calls: iccbin ... withCallingHandlers -> do.call -> <Anonymous> -> .Call -> cpp_exception<br>65: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>5
+</td>
+<td class=cellinside>arm
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.5-04
+</td>
+<td class=cellinside>Yu-Sung Su
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>122: unable to find an inherited method for function "display", for signature "lmerMod"<br>123: Calls: display -> <Anonymous><br>124: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>6
+</td>
+<td class=cellinside>benchmark
+</td>
+<td class=cellinside>Rforge
+</td>
+<td class=cellinside>0.3-4
+</td>
+<td class=cellinside>Manuel J. A. Eugster
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>7
+</td>
+<td class=cellinside>blme
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.01-4
+</td>
+<td class=cellinside>Vincent Dorie
+</td>
+<td class=cellinside><font style="color:red">error_install</font>
+</td>
+<td class=cellinside>** R<br>** inst<br>** preparing package for lazy loading<br>Error : class "mer" is not exported by 'namespace:lme4'<br>ERROR: lazy loading failed for package 'blme'<br>* removing '/mnt/hgfs/bolker/Documents/R/pkgs/lme4/pkgtests/blme.Rcheck/blme'
+</td></tr>
+
+<tr>
+<td class=firstcolumn>8
+</td>
+<td class=cellinside>boss
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.0
+</td>
+<td class=cellinside>Arend Voorman
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>70: Error in boss.set(y ~ x1 + x2 + factor(site) + (1 | id), id = data$id, : <br>71: no slot of name "X" for this object of class "lmerMod"<br>72: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>9
+</td>
+<td class=cellinside>BradleyTerry2
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.9-6
+</td>
+<td class=cellinside>Heather Turner
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>74: object 'expandSlash' not found<br>75: Calls: BTm -> do.call -> <Anonymous> -> Diff -> ::: -> get<br>76: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>10
+</td>
+<td class=cellinside>car
+</td>
+<td class=cellinside>Rforge
+</td>
+<td class=cellinside>2.0-13
+</td>
+<td class=cellinside>John Fox
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>11
+</td>
+<td class=cellinside>catdata
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.0
+</td>
+<td class=cellinside>Gunther Schauberger
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>12
+</td>
+<td class=cellinside>clusterPower
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.3
+</td>
+<td class=cellinside>Nicholas G. Reich
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>13
+</td>
+<td class=cellinside>cplm
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.5-1
+</td>
+<td class=cellinside>Wayne Zhang
+</td>
+<td class=cellinside><font style="color:purple">error_depfail</font>
+</td>
+<td class=cellinside>10: Package required but not available: 'amer'
+</td></tr>
+
+<tr>
+<td class=firstcolumn>14
+</td>
+<td class=cellinside>DAAG
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.12
+</td>
+<td class=cellinside>W. John Braun
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>15
+</td>
+<td class=cellinside>difR
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>4.2
+</td>
+<td class=cellinside>David Magis
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>16
+</td>
+<td class=cellinside>doBy
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>4.5.2
+</td>
+<td class=cellinside>Søren Højsgaard
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>17
+</td>
+<td class=cellinside>effects
+</td>
+<td class=cellinside>Rforge
+</td>
+<td class=cellinside>2.1-2
+</td>
+<td class=cellinside>John Fox
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>18
+</td>
+<td class=cellinside>EquiNorm
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>2.0
+</td>
+<td class=cellinside>Li-Xuan Qin
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>19
+</td>
+<td class=cellinside>ez
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>3.0-1
+</td>
+<td class=cellinside>Michael A. Lawrence
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>112: cannot coerce type 'closure' to vector of type 'character'<br>113: Calls: ezBoot ... formula -> formula.default -> eval -> eval -> eval -> parse<br>114: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>20
+</td>
+<td class=cellinside>flexmix
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>2.3-8
+</td>
+<td class=cellinside>Bettina Gruen
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>21
+</td>
+<td class=cellinside>gamm4
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.1-5
+</td>
+<td class=cellinside>Simon Wood
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>74: Error in b$FL : $ operator not defined for this S4 class<br>75: Calls: gamm4<br>76: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>22
+</td>
+<td class=cellinside>glmulti
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.0.4
+</td>
+<td class=cellinside>Vincent Calcagno
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>23
+</td>
+<td class=cellinside>gmodels
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>2.15.2
+</td>
+<td class=cellinside>Gregory R. Warnes
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>24
+</td>
+<td class=cellinside>GRRGI
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.1
+</td>
+<td class=cellinside>Walter Resch
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>81: unable to find an inherited method for function "sigma.hat", for signature "lmerMod"<br>82: Calls: MLGI -> sigma.hat -> <Anonymous><br>83: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>25
+</td>
+<td class=cellinside>HLMdiag
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.1.5
+</td>
+<td class=cellinside>Adam Loy
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>71: Error in case_delete(model = fm, group = TRUE, type = "both") : <br>72: no slot of name "fixef" for this object of class "lmerMod"<br>73: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>26
+</td>
+<td class=cellinside>HSAUR
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.3-0
+</td>
+<td class=cellinside>Torsten Hothorn
+</td>
+<td class=cellinside><font style="color:red">error_vignette</font>
+</td>
+<td class=cellinside>4857: Error: 'arg' should be one of "Laplace", "AGQ"<br>4858: Execution halted<br>4859:
+</td></tr>
+
+<tr>
+<td class=firstcolumn>27
+</td>
+<td class=cellinside>HSAUR2
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.1-1
+</td>
+<td class=cellinside>Torsten Hothorn
+</td>
+<td class=cellinside><font style="color:red">error_vignette</font>
+</td>
+<td class=cellinside>107: Error: PIRLS step failed<br>108: Execution halted<br>109:
+</td></tr>
+
+<tr>
+<td class=firstcolumn>28
+</td>
+<td class=cellinside>influence.ME
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.8.1
+</td>
+<td class=cellinside>Rense Nieuwenhuis
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>63: incorrect number of dimensions<br>64: Calls: estex -> grouping.levels<br>65: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>29
+</td>
+<td class=cellinside>kulife
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.1-9
+</td>
+<td class=cellinside>Claus Ekstrom
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>30
+</td>
+<td class=cellinside>languageR
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.4
+</td>
+<td class=cellinside><harald.baayen at uni-tuebingen.de>
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>31
+</td>
+<td class=cellinside>LMERConvenienceFunctions
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.6.8.2
+</td>
+<td class=cellinside>Antoine Tremblay
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>87: 'arg' should be one of "deviance", "pearson", "working", "response", "partial"<br>88: Calls: mcp.fnc ... residuals -> residuals.lmResp -> match.arg -> match.arg<br>89: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>32
+</td>
+<td class=cellinside>longpower
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.0-1
+</td>
+<td class=cellinside>Michael C. Donohue
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>33
+</td>
+<td class=cellinside>MEMSS
+</td>
+<td class=cellinside>Rforge
+</td>
+<td class=cellinside>0.9-0
+</td>
+<td class=cellinside><lme4-authors at R-forge.wu-wien.ac.at>
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>34
+</td>
+<td class=cellinside>MethComp
+</td>
+<td class=cellinside>Rforge
+</td>
+<td class=cellinside>1.15
+</td>
+<td class=cellinside>Bendix Carstensen
+</td>
+<td class=cellinside><font style="color:purple">error_depfail</font>
+</td>
+<td class=cellinside>9: Package suggested but not available: 'BRugs'
+</td></tr>
+
+<tr>
+<td class=firstcolumn>35
+</td>
+<td class=cellinside>mi
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.09-16
+</td>
+<td class=cellinside>Yu-Sung Su
+</td>
+<td class=cellinside><font style="color:red">error_install</font>
+</td>
+<td class=cellinside>** data<br>** inst<br>** preparing package for lazy loading<br>Error : objects 'coef', 'fitted', 'resid', 'residuals', 'plot' are not exported by 'namespace:lme4'<br>ERROR: lazy loading failed for package 'mi'<br>* removing '/mnt/hgfs/bolker/Documents/R/pkgs/lme4/pkgtests/mi.Rcheck/mi'
+</td></tr>
+
+<tr>
+<td class=firstcolumn>36
+</td>
+<td class=cellinside>mice
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>2.12
+</td>
+<td class=cellinside>Stef van Buuren
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>37
+</td>
+<td class=cellinside>mixAK
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>2.2
+</td>
+<td class=cellinside>Arnošt Komárek
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>38
+</td>
+<td class=cellinside>MixMod
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.0
+</td>
+<td class=cellinside>Alexandra Kuznetsova
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>64: no slot of name "ST" for this object of class "lmerMod"<br>65: Calls: totalAnalysis -> totalAnovaRandLsmeans -> checkCorr<br>66: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>39
+</td>
+<td class=cellinside>mlmRev
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.0-1
+</td>
+<td class=cellinside><lme4-authors at R-forge.wu-wien.ac.at>
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>82: Error in if (REML) p else 0L : argument is not interpretable as logical<br>83: Calls: lmer -> mkRespMod<br>84: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>40
+</td>
+<td class=cellinside>multcomp
+</td>
+<td class=cellinside>Rforge
+</td>
+<td class=cellinside>1.2-12
+</td>
+<td class=cellinside>Torsten Hothorn
+</td>
+<td class=cellinside><font style="color:red">error_vignette</font>
+</td>
+<td class=cellinside>115: Error: PIRLS step failed<br>116: Execution halted<br>117:
+</td></tr>
+
+<tr>
+<td class=firstcolumn>41
+</td>
+<td class=cellinside>MuMIn
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.7.7
+</td>
+<td class=cellinside>Kamil Bartoń
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>42
+</td>
+<td class=cellinside>NanoStringNorm
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.1.6
+</td>
+<td class=cellinside>Daryl Waggott
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>43
+</td>
+<td class=cellinside>NetworkAnalysis
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.3-1
+</td>
+<td class=cellinside>Cedric E Ginestet
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>44
+</td>
+<td class=cellinside>odprism
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.1
+</td>
+<td class=cellinside>Martijn van de Pol
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>167: caught warning: Cholmod warning 'not positive definite' at file:../Cholesky/t_cholmod_rowfac.c, line 432 <br>168: caught warning: Cholmod warning 'not positive definite' at file:../Cholesky/t_cholmod_rowfac.c, line 432 <br>169: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>45
+</td>
+<td class=cellinside>ordinal
+</td>
+<td class=cellinside>Rforge
+</td>
+<td class=cellinside>2012.05-09
+</td>
+<td class=cellinside>Rune Haubo B Christensen
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>46
+</td>
+<td class=cellinside>pamm
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.7
+</td>
+<td class=cellinside>Julien Martin
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>47
+</td>
+<td class=cellinside>pbkrtest
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.3-1
+</td>
+<td class=cellinside>Søren Højsgaard
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>100: no applicable method for 'KRmodcomp' applied to an object of class "c('lmerMod', 'merMod')"<br>101: Calls: KRmodcomp<br>102: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>48
+</td>
+<td class=cellinside>pedigreemm
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.2-4
+</td>
+<td class=cellinside>Ana Ines Vazquez
+</td>
+<td class=cellinside><font style="color:red">error_install</font>
+</td>
+<td class=cellinside>** preparing package for lazy loading<br>Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses, : <br> No definition was found for superclass "mer" in the specification of class "pedigreemm"<br>Error : unable to load R code in package 'pedigreemm'<br>ERROR: lazy loading failed for package 'pedigreemm'<br>* removing '/mnt/hgfs/bolker/Documents/R/pkgs/lme4/pkgtests/pedigreemm.Rcheck/pedigreemm'
+</td></tr>
+
+<tr>
+<td class=firstcolumn>49
+</td>
+<td class=cellinside>phmm
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.7-4
+</td>
+<td class=cellinside>Michael Donohue
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>132: "ddenseMatrix#dgeMatrix" would also be valid<br>133: Error: trying to get slot "AICtab" from an object (class "summary.mer") that is not an S4 object <br>134: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>50
+</td>
+<td class=cellinside>prLogistic
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.1
+</td>
+<td class=cellinside>Raydonal Ospina
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>92: PIRLS step failed<br>93: Calls: prLogisticDelta ... stopifnot -> fn -> pwrssUpdate -> .Call -> cpp_exception<br>94: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>51
+</td>
+<td class=cellinside>R2admb
+</td>
+<td class=cellinside>Rforge
+</td>
+<td class=cellinside>0.7.5.2
+</td>
+<td class=cellinside>Ben Bolker
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>52
+</td>
+<td class=cellinside>R2STATS
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>0.68-27
+</td>
+<td class=cellinside>Yvonnick Noel
+</td>
+<td class=cellinside><font style="color:red">error_install</font>
+</td>
+<td class=cellinside>** preparing package for lazy loading<br>Error in loadNamespace(i, c(lib.loc, .libPaths())) : <br> there is no package called 'RGtk2'<br>Error : package 'gWidgetsRGtk2' could not be loaded<br>ERROR: lazy loading failed for package 'R2STATS'<br>* removing '/mnt/hgfs/bolker/Documents/R/pkgs/lme4/pkgtests/R2STATS.Rcheck/R2STATS'
+</td></tr>
+
+<tr>
+<td class=firstcolumn>53
+</td>
+<td class=cellinside>RLRsim
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>2.0-11
+</td>
+<td class=cellinside>Fabian Scheipl
+</td>
+<td class=cellinside><font style="color:red">error_examples</font>
+</td>
+<td class=cellinside>79: > X <- m at X<br>80: Error: no slot of name "X" for this object of class "lmerMod"<br>81: Execution halted
+</td></tr>
+
+<tr>
+<td class=firstcolumn>54
+</td>
+<td class=cellinside>SASmixed
+</td>
+<td class=cellinside>Rforge
+</td>
+<td class=cellinside>1.0-1
+</td>
+<td class=cellinside><lme4-authors at R-forge.wu-wien.ac.at>
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>55
+</td>
+<td class=cellinside>sdtalt
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.03
+</td>
+<td class=cellinside>Dan Wright
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>56
+</td>
+<td class=cellinside>TripleR
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>1.1.6
+</td>
+<td class=cellinside>Felix Schönbrodt
+</td>
+<td class=cellinside><font style="color:blue">OK</font>
+</td>
+<td class=cellinside>
+</td></tr>
+
+<tr>
+<td class=firstcolumn>57
+</td>
+<td class=cellinside>Zelig
+</td>
+<td class=cellinside>CRAN
+</td>
+<td class=cellinside>3.5.5
+</td>
+<td class=cellinside>Kosuke Imai
+</td>
+<td class=cellinside><font style="color:red">error_vignette</font>
+</td>
+<td class=cellinside>118: Error: "nlmodel" is not a slot in class "glmerMod"<br>119: Execution halted<br>120:
+</td></tr>
+
+ </tbody>
+</table>
+ </td></table>
+ <br>
+
+<hr size=1>
+<font size=-1>
+ Generated on: <i>Tue May 15 13:46:03 2012</i> - <b>R2HTML</b>
+<hr size=1>
+ </body>
+</html>
\ No newline at end of file
Modified: www/misc/lme4_conversion.html
===================================================================
--- www/misc/lme4_conversion.html 2012-05-15 19:35:07 UTC (rev 1732)
+++ www/misc/lme4_conversion.html 2012-05-15 20:01:21 UTC (rev 1733)
@@ -1,9 +1,169 @@
-<div id="lme4-updating-guide"
+<div id="lme4-release-guide"
><h1
- >lme4 updating guide</h1
+ >lme4 release guide</h1
+ ><div id="version-numbering"
+ ><h2
+ >Version numbering</h2
+ ><p
+ >As previously announced on the mailing list, we will shortly be releasing a new version of <code
+ >lme4</code
+ >, a descendant of the previous development version <code
+ >lme4Eigen</code
+ >. For users who do not access any internal structures, there will be few backward-incompatible changes.</p
+ ><ul
+ ><li
+ >the version of <code
+ >lme4</code
+ > currently on R-forge (currently version 0.999902344-0, to be released as version 1.0 (!)) should be used for new projects</li
+ ><li
+ >The current CRAN version (0.999375-42) will be replaced by a nearly identical version called <code
+ >lme4.0</code
+ > (currently version 0.9999-2; the only backward-incompatible change in this version is a fix to the AGQ code contributed by Wayne Zhang). <code
+ >lme4.0</code
+ > is a maintenance version and will only be changed to fix documented bugs.</li
+ ><li
+ >all other versions (<code
+ >lme4a</code
+ >, <code
+ >lme4b</code
+ >, <code
+ >lme4Eigen</code
+ > from R-forge) are deprecated.</li
+ ></ul
+ ></div
+ ><div id="changes-in-behavior"
+ ><h2
+ >Changes in behavior</h2
+ ><ul
+ ><li
+ >Because the internal computational machinery has changed, results from the newest version of <code
+ >lme4</code
+ > will not be numerically identical to those from previous versions. For reasonably well-defined fits, they will be extremely close (within numerical tolerances of 1e-4 or so), but for unstable or poorly-defined fits the results may change, and very unstable fits may fail when they (apparently) succeeded with previous versions. Similarly, some fits may be slower with the new version, although on average the new version should be faster and more stable. There are more numerical tuning options available than before (see below); non-default settings may restore the speed and/or ability to fit a particular model without an error.</li
+ ><li
+ >In the past, <code
+ >lmer</code
+ > automatically called <code
+ >glmer</code
+ > when <code
+ >family</code
+ > was specified. It still does so, but now warns the user that they should preferably use <code
+ >glmer</code
+ > directly</li
+ ><li
+ ><code
+ >VarCorr</code
+ > returns its results in the same format as before (as a list of variance-covariance matrices with <code
+ >correlation</code
+ > and <code
+ >stddev</code
+ > attributes, plus a <code
+ >sc</code
+ > attribute giving the residual standard deviation/scale parameter when appropriate), but prints them in a different (nicer) way</li
+ ></ul
+ ></div
+ ><div id="other-user-visible-changes"
+ ><h2
+ >Other user-visible changes</h2
+ ><ul
+ ><li
+ >methods such as <code
+ >fixef</code
+ > no longer conflict with the <code
+ >nlme</code
+ > package</li
+ ><li
+ ><code
+ >[gn]lmer</code
+ > now produces objects of class <code
+ >merMod</code
+ > rather than class <code
+ >mer</code
+ > as before</li
+ ><li
+ ><code
+ >[gn]lmer</code
+ > now has an <code
+ >optimizer</code
+ > argument. <code
+ >"Nelder_Mead"</code
+ > is the default for <code
+ >[n]lmer</code
+ >, while a combination of <code
+ >"bobyqa"</code
+ > (an alternative derivative-free method) and <code
+ >"Nelder_Mead"</code
+ > is the default for <code
+ >glmer</code
+ >; to use the <code
+ >nlminb</code
+ > optimizer as in the old version of lme4, you can use <code
+ >optimizer="optimx"</code
+ > with <code
+ >control=list(method="nlminb")</code
+ > (you will need the <code
+ >optimx</code
+ > package to be installed and loaded). See the help pages for details.</li
+ ><li
+ >(FIXME: describe residuals)</li
+ ></ul
+ ></div
+ ><div id="new-features"
+ ><h2
+ >New features</h2
+ ><ul
+ ><li
+ >a general-purpose <code
+ >getME()</code
+ > accessor method has been used to allow extraction of a wide variety of components of a mixed-model fit; this has been backported to <code
+ >lme4.0</code
+ > for compatibility</li
+ ><li
+ ><code
+ >bootMer</code
+ >, a framework for obtaining parameter confidence intervals by parametric bootstrapping</li
+ ><li
+ ><code
+ >plot</code
+ > methods similar to those from the <code
+ >nlme</code
+ > package (although without <code
+ >augPred</code
+ >)</li
+ ><li
+ >a <code
+ >predict</code
+ > method, allowing a choice of which random effects are included in the prediction</li
+ ><li
+ >profiling (and profile confidence intervals) for <code
+ >lmer</code
+ > and <code
+ >glmer</code
+ > results</li
+ ><li
+ ><code
+ >nAGQ=0</code
+ >, an option to do fast (but inaccurate) fitting of GLMMs</li
+ ></ul
+ ></div
+ ><div id="still-non-existent-features"
+ ><h2
+ >Still non-existent features</h2
+ ><ul
+ ><li
+ >Automatic MCMC sampling based on the fit turns out to be very difficult to implement in a way that is really broadly reliable and robust; <code
+ >mcmcsamp</code
+ > will not be implemented in the near future</li
+ ><li
+ >"R-side" structures (within-block correlation and heteroscedasticity) are not on the current timetable</li
+ ></ul
+ ></div
><div id="for-package-writers:"
><h2
>For package writers:</h2
+ ><p
+ ><a href="./lme4_compat_report.html"
+ >Current package compatibilty test results</a
+ ></p
><ul
><li
><code
@@ -95,73 +255,5 @@
></ul
></div
></div
- ><div id="for-package-writers-and-regular-people:"
- ><h2
- >For package writers and regular people:</h2
- ><ul
- ><li
- >accessor functions and methods should all work the same (slight differences in printing format for <code
- >VarCorr</code
- >)</li
- ><li
- >there is now an <code
- >optimizer</code
- > argument. <code
- >"Nelder_Mead"</code
- > is the default, other options are <code
- >"bobyqa"</code
- > (an alternative derivative-free method); to use the <code
- >nlminb</code
- > optimizer as in the old version of lme4, you can use <code
- >optimizer="optimx"</code
- > with <code
- >control=list(method="nlminb")</code
- > (you will need the <code
- >optimx</code
- > package to be installed and loaded)</li
- ><li
- >(residuals)</li
- ></ul
- ></div
- ><div id="new-features"
- ><h2
- >New features</h2
- ><ul
- ><li
- ><code
- >bootMer</code
- ></li
- ><li
- >profiling</li
- ><li
- ><code
- >nAGQ=0</code
- ></li
- ><li
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/lme4 -r 1733
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