gregmisc/0000755000176200001440000000000012163405435012055 5ustar liggesusersgregmisc/MD50000644000176200001440000000102312163405435012361 0ustar liggesusers9aad35da5f4a0c97e74f4150542a672b *ChangeLog 461df9b24ea6ca4ab67ca45879ec7df7 *DESCRIPTION 4a821d3c6b4e0bea9d90609c1aa5112f *NAMESPACE 7dff524a2dc667b87acf2f87a8d9af21 *NEWS 23eff6d0a25ff85afbb5a335ad7280e0 *R/onAttach.R 9aad35da5f4a0c97e74f4150542a672b *inst/ChangeLog 7dff524a2dc667b87acf2f87a8d9af21 *inst/NEWS 99af68b9933865da35d30b3f0d4606be *inst/doc/Rnews.dtx d8a604720424e018b8b6002d2b8a35a1 *inst/doc/Rnews.sty 93161c1ec28d5aef3bb004a482ca94e8 *inst/doc/gregmisc.pdf 42910957695a1267a83d7b28a87d836c *inst/doc/gregmisc.tex gregmisc/inst/0000755000176200001440000000000012163402266013031 5ustar liggesusersgregmisc/inst/doc/0000755000176200001440000000000012143472660013601 5ustar liggesusersgregmisc/inst/doc/gregmisc.tex0000644000176200001440000000647412143472613016134 0ustar liggesusers\documentclass{report} \usepackage{Rnews} \begin{document} \author{by Gregory R. Warnes} \title{The gregmisc package: something for everyone} \subtitle{} \maketitle The gregmisc package is a repository for functions that I find myself needing but that don't seem to be available somewhere else. In contrast to many packages, it is not organized thematically, rather it contains a hodge-podge of different routines that make my life a little easer. I've taken the time to bundle these functions up as a package for three reasons, first to share my efforts with others, second to get feedback (particularly bug reports and feature enhancements), and third to force myself to properly document and test the code. The function in the gregmisc library fall into six general areas: permutations and combinations, tools for linear models, plots, data manipulation, fixed or extended versions of existing functions, and other. \begin{enumerate} \item{permutation and combinations} \begin{description} \item[combinations]{ Enumerate the combinations of the elements of a vector} \item[permutations]{ Enumerate the permutations of the elements of a vector} \item[factorial]{ Compute the factorial function} \end{description} \item{tools for linear models} \begin{description} \item[ci]{ Compute confidence intervals} \item[contrast.lm]{ Compute (and test) arbitrary single-term contrasts for regression objects} \item[estimable]{ Compute and test estimable linear functions of the fitted coefficients (including contrasts) of regression objects} \item[glh.test]{ Test a general linear hypothesis for regression objects} \end{description} \item{plots} \begin{description} \item[boxplot.n]{Produce a boxplot annotated with the number of observations} \item[plotCI]{ Plot error bars} \item[plotmeans]{ Plot group means and confidence intervals} \item[wapply]{ Compute the value of a function over a local region of an x-y plot} \item[space]{ Deterministically space points in an x-y plot so they don't overlap.} \item[hist2d]{ Create and Plot a 2-dimensional histogram.} \item[bandplot] {Plot x-y points with locally smoothed mean and standard deviation} \end{description} \item{data manipulation} \begin{description} \item[combine]{ Combine R objects (such as dataframes) and add an additional column labeling the source} \item[rename.vars]{ Rename variables in a dataframe} \end{description} \item{fixed or extended versions of current functions} \begin{description} \item[lowess]{ Extend built-in \verb+lowess+ function to handle model formulae } \item[plot.lm]{ Extend the built-in \verb+plot.lm+ function: } \begin{itemize} \item residual plots: add rug, zero line, mean and 1-sigma smooths \item residual quantile plots: add \verb+qqline+ \item add plots of each predictor against the residuals. \end{itemize} \end{description} \item{other} \begin{description} \item[running]{ Apply a function over adjacent subsets of a vector} \end{description} \end{enumerate} I welcome comments and contributions. The current package includes code by Ben Bolker, Bendix Carstensen, Don MacQueen, and William Venables. \address{Gregory R. Warnes \\ Center for Biodefense Immune Modeling \\ University of Rochester \\ \emph{warnes@bst.rochester.edu} } %%!!!%% \end{multicols} %%!!!%% \end{document} gregmisc/inst/doc/gregmisc.pdf0000644000176200001440000023652012143472613016102 0ustar liggesusers%PDF-1.5 % 9 0 obj << /Length 2724 /Filter /FlateDecode >> stream xڽY[s۶~[ xSM3iRǧNH$4(K]HJ3sl ]|{.śW7g1eq/n6 |%&_|n~<_ｹ|k;{~|x槫_sxϛ.oξq_E, Șqx˳~^Ld,aYX|8.%iQg %c,;FmKmvr@}ԥjwM p2X:[<ԕ58:: )X틫朧֍#\3<=Tʸ⣽8H%,#)BvK+I(^}J/k[GhqU%ɹ꺂݄yN8J+KA[R`TJ ~wh*{%K֠4V>ԅ\n7uSV0KRQ0Hʒu6ҴvoYaHAsa*<}=cUh5[pػkYsYsG#R# ZhV-}zoUkߧYݵD/g+gg Cd7"{Bc0Ey-]ᮧU^5ㆈp0OR;@~E46R۝Uۉ4p\BpkX8E, hn ՝nwvTp+ 7 x> O~e f+dS'TA0XeV$+%ۮWTZGq`0{lpcD8&c 0$}86;u48X/) 8x\ZYg81 }uYn#3M8%P&' kc^^Sr@O`EC:)"F`hV4ٍ9tl$~NH,^uZat[Fpqq6;.f:+JVl|SbI̊ -xJ"[4{'1/8%#Lw{H"[~bֿMLq#c # {U': ަ_y *h$Z*S J5cP+Ay>xCN?kޓq+f%VCE>KxkC_D ;-B_2Ju:enҕo('Oz%0R sc[SmwK|JDNI$zg\B gs S 2/9.H,s+txaHzGY6Smdl Vc4Rn!Bz`*脷]O(SY\iV:VL CٗtoV˙Գ!mΆWGWc4xT NhBȾ%8лg0CKt띛JT0MRlΕ1"?uA^X5tۣ 뺘`@!W!x[v; 2g!W\ $@1EOIF8bzUC+qT?TE}I\wV.ڥ\/<=i`uw+Qpa;Y ^)d)w@ltQ% T;#PS:j¦srNM󅘪ńM>w}ş| G1.yG61~q̰Kcz|mxv c/̗FoKghgY^AL.Stju^X }|<~.+&NAE(z y糾׫rM-Z[=㋊+ɰi'F0cϺ=l|jpC%%Ku8j8ÌWyaf:ׇ'vj 2Ҕ* #B,ʾ:TU"n3⺍ǿ1 F bLPΰUoG|?Ѡ.>۞0*J~ Q+'oN ?"O%FApNR\7DSդ J6ȿ_eW[ #wSi zLk1>d;iu؊Wy79KG)> HE endstream endobj 33 0 obj << /Length1 1403 /Length2 6029 /Length3 0 /Length 6987 /Filter /FlateDecode >> stream xڍx4ֶ Zhчu{NDc0D{ !: G'JM=5k={_{p (!mHZ$(i PD&0пD&Pw ;ؔh P<@"H\ Re'-xD@QDJHWw#S[7Pp `@v`*Bp!}#*%$%vA "dy^0#{B(t.?8F0_C= ` p@aB<vPw:PC E Ht%!~!+C8ap(@WUKv`8 {ap-{`>a sEQ0/B`ڬSB@hѯ)ܡL}3{eCa*dy@5`0&h(PRLLG_|\~HW=4f|P@  B`gǘ1X1>(TL PSQ H H .. guoz`؟GF =  L&GƆ :HP\@!,{Gpo?_v} 0z@cfCCM 6^ 43# @P0o qKK!Q_L_>A1~g]ikE`wwF(U;oH4&G:X(@#1vxc0^u( !ABÜ^(0x l୬vF'E9g9jgM)ؽ37W11|Qwnrz>Ko]P`qI0&NqDfckb:s.#rPr(9%gMg@)ub?1ge_E?"naakhimn_Qfo؋J:*ytIPXJilt.86? ےD<to>~QY>b1.Dr99ڑ&]t(ZߋK \֞Bka/4?snLK ||(gv7]auZ/yҌ%qmPO! dpYG& &*bZYd5OB^TA~^[Cyɹq#Y#mLBsp)rRJ/L/= iI>^?@^~KMD[C!a+·6:\a'gZS=~o#IAB]CxtjdwL3_vpm{7\RI +D[-Z'=O,ΤmZ}j9pQᦨ M5.)B;S8$PmxC BѾh.@Sk9BqQ/ 8DU⇧ȇBfbo}]_n[1(hE[)=h(4O~Whru%n-rEK9R=͏D=IG5A߆$9?0aa2VI=*jI> gQyEmzɬgX_$DPRMi? 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(The sources need not necessarily be %% in the same archive or directory.) \def\fileversion{v0.3.1} \def\filename{Rnews} \def\filedate{2001/09/04} \def\docdate {2001/09/04} %% %% Package `Rnews' to use with LaTeX2e %% Copyright (C) 2001 by the R Core Development Team %% Please report errors to KH or FL %% %% -*- LaTeX -*- \NeedsTeXFormat{LaTeX2e}[1995/12/01] \ProvidesPackage{\filename}[\filedate\space\fileversion\space Rnews package] \typeout{Package: `\filename\space\fileversion \@spaces <\filedate>'} \typeout{English documentation as of <\docdate>} \RequirePackage{ifthen} \newboolean{Rnews@driver} \DeclareOption{driver}{\setboolean{Rnews@driver}{true}} \DeclareOption*{\PackageWarning{\filename}{Unknown option `\CurrentOption'}} \ProcessOptions\relax \ifthenelse{\boolean{Rnews@driver}}{}{ \RequirePackage{multicol,graphicx,color,fancyhdr,hyperref} \newcommand{\volume}[1]{\def\Rnews@volume{#1}} \newcommand{\volnumber}[1]{\def\Rnews@number{#1}} \renewcommand{\date}[1]{\def\Rnews@date{#1}} \setcounter{secnumdepth}{-1} \renewcommand{\author}[1]{\def\Rnews@author{#1}} \renewcommand{\title}[1]{\def\Rnews@title{#1}} \newcommand{\subtitle}[1]{\def\Rnews@subtitle{#1}} \newenvironment{article}{% \author{}\title{}\subtitle{}}{\end{multicols}} \renewcommand{\maketitle}{ \chapter{\Rnews@title} \refstepcounter{chapter} \begin{multicols}{2} \ifx\empty\Rnews@subtitle\else\par\addvspace{\baselineskip} \noindent\textbf{\Rnews@subtitle}\fi \ifx\empty\Rnews@author\else\par\addvspace{\baselineskip} \noindent\textit{\Rnews@author}\fi} \renewcommand\chapter{\secdef\@chapter\@schapter} \renewcommand*\l@chapter{\@dottedtocline{0}{0pt}{1em}} \def\@makechapterhead#1{% \addvspace{2\baselineskip}% {\parindent \z@ \raggedright \normalfont \ifnum \c@secnumdepth >\m@ne \huge\bfseries \@chapapp\space \thechapter \par\nobreak \vskip 20\p@ \fi \interlinepenalty\@M \Huge \bfseries #1\par\nobreak}} \def\@schapter#1{\section*#1} \renewenvironment{figure}[1][]{% \def\@captype{figure} \begin{minipage}{0.9\columnwidth}}{ \end{minipage}\par\addvspace{\baselineskip}} \renewcommand{\theequation}{\@arabic\c@equation} \renewcommand{\thefigure}{\@arabic\c@figure} \renewcommand{\thetable}{\@arabic\c@table} \renewcommand{\contentsname}{Contents of this issue:} \renewcommand\tableofcontents{% \section*{\contentsname \@mkboth{% \MakeUppercase\contentsname}{\MakeUppercase\contentsname}}% \@starttoc{toc}} \renewcommand{\titlepage}{% \noindent \rule{\textwidth}{1pt}\\[-.8\baselineskip] \rule{\textwidth}{.5pt} \begin{center} \includegraphics[height=2cm]{Rlogo}\hspace{7mm} \fontsize{2cm}{2cm}\selectfont News \end{center} The Newsletter of the R Project\hfill Volume \Rnews@volume/\Rnews@number, \Rnews@date\\[-.5\baselineskip] \rule{\textwidth}{.5pt}\\[-.8\baselineskip] \rule{\textwidth}{1pt} \vspace{1cm} \fancyhf{} \fancyhead[L]{Vol.~\Rnews@volume/\Rnews@number, \Rnews@date} \fancyhead[R]{\thepage} \fancyfoot[L]{R News} \fancyfoot[R]{ISSN 1609-3631} \thispagestyle{empty} \begin{bottombox} \begin{multicols}{2} \setcounter{tocdepth}{0} \tableofcontents \setcounter{tocdepth}{2} \end{multicols} \end{bottombox}} \setlength{\textheight}{250mm} \setlength{\topmargin}{-10mm} \setlength{\textwidth}{17cm} \setlength{\oddsidemargin}{-6mm} \setlength{\columnseprule}{.1pt} \setlength{\columnsep}{20pt} \RequirePackage{ae,mathpple} \RequirePackage[T1]{fontenc} \renewcommand{\rmdefault}{ppl} \renewcommand{\sfdefault}{aess} \renewcommand{\ttdefault}{aett} \definecolor{Red}{rgb}{0.7,0,0} \definecolor{Blue}{rgb}{0,0,0.8} \definecolor{hellgrau}{rgb}{0.55,0.55,0.55} \newcommand{\R}{R} \newcommand{\address}[1]{\addvspace{\baselineskip}\noindent\emph{#1}} \newcommand{\email}[1]{\href{mailto:#1}{\normalfont\texttt{#1}}} \newsavebox{\Rnews@box} \newlength{\Rnews@len} \newenvironment{bottombox}{% \begin{figure*}[b] \begin{center} \noindent \begin{lrbox}{\Rnews@box} \begin{minipage}{0.99\textwidth}}{% \end{minipage} \end{lrbox} \addtolength{\Rnews@len}{\fboxsep} \addtolength{\Rnews@len}{\fboxrule} \hspace*{-\Rnews@len}\fbox{\usebox{\Rnews@box}} \end{center} \end{figure*}} \newenvironment{boxedverbatim}{% \begin{lrbox}{\Rnews@box} \begin{smallverbatim}}{% \end{smallverbatim} \end{lrbox} \hspace*{-\fboxsep}\fbox{\usebox{\Rnews@box}}} \pagestyle{fancy} } % \ifthenelse{\boolean{Rnews@driver}} \newcommand\code{\bgroup\@codex} \def\@codex#1{{\normalfont\ttfamily\hyphenchar\font=-1 #1}\egroup} \newcommand{\kbd}[1]{{\normalfont\texttt{#1}}} \newcommand{\key}[1]{{\normalfont\texttt{\uppercase{#1}}}} \newcommand\samp{`\bgroup\@noligs\@sampx} \def\@sampx#1{{\normalfont\texttt{#1}}\egroup'} \newcommand{\var}[1]{{\normalfont\textsl{#1}}} \let\env=\code \newcommand{\file}[1]{{`\normalfont\textsf{#1}'}} \let\command=\code \let\option=\samp \newcommand{\dfn}[1]{{\normalfont\textsl{#1}}} \newcommand{\acronym}[1]{{\normalfont\textsc{\lowercase{#1}}}} \newcommand{\strong}[1]{{\normalfont\fontseries{b}\selectfont #1}} \let\pkg=\strong \RequirePackage{alltt} \newenvironment{example}{\begin{alltt}}{\end{alltt}} \newenvironment{smallexample}{\begin{alltt}\small}{\end{alltt}} \newenvironment{display}{\list{}{}\item\relax}{\endlist} \providecommand{\operatorname}[1]{% \mathop{\operator@font#1}\nolimits} \renewcommand{\P}{% \mathop{\operator@font I\hspace{-1.5pt}P\hspace{.13pt}}} \newcommand{\E}{% \mathop{\operator@font I\hspace{-1.5pt}E\hspace{.13pt}}} \newcommand{\VAR}{\operatorname{var}} \newcommand{\COV}{\operatorname{cov}} \newcommand{\COR}{\operatorname{cor}} \RequirePackage{amsfonts} \endinput %% %% End of file `Rnews.sty'. gregmisc/inst/doc/Rnews.dtx0000644000176200001440000004601512143472613015424 0ustar liggesusers\def\fileversion{v0.3.1} \def\filename{Rnews} \def\filedate{2001/09/04} \def\docdate {2001/09/04} % % \iffalse % %% %% Package `Rnews' to use with LaTeX2e %% Copyright (C) 2001 by the R Core Development Team %% Please report errors to KH or FL %% %% -*- LaTeX -*- % % \fi % % \iffalse % \changes{v0.1}{2001/01/05}{First draft.} % \changes{v0.2}{2001/07/01} % {Added macros \cmd\P, \cmd\E, \cmd\VAR, \cmd\COV, \cmd\COR, and % \cmd\operatorname. Require \pkg{amsfonts} to produce symbols for % sets of positive integers etc.} % \changes{v0.3}{2001/08/02} % {Add package option `driver' for typesetting the driver. % Change article environment to use chapters. % Ensure unique figure labels.} % \changes{v0.3.1}{2001/09/04} % {Remove redefinition of |\caption|, which had figures hard-wired. % Instead, have our |figure| environment set |\@captype|.} % \fi % % \MakeShortVerb{\|} % % \newcommand{\AmS}{$${\protect\the\textfont2 A}\kern-.1667em\lower % .5ex\hbox{\protect\the\textfont2 M}\kern % -.125em{\protect\the\textfont2 S}} % \newcommand{\AmSLaTeX}{\mbox{\AmS-\LaTeX}} % % \title{The package \pkg{\filename}} % \author{Kurt Hornik \and Friedrich Leisch} % % \maketitle % % \section{Introduction} % % The \LaTeXe{} package \pkg{\filename} provides commands for formatting % the R Newsletter. % % \section{Documentation} % % \subsection{Marking Words and Phrases} % % The \pkg{Rnews} package provides roughly the same commands for marking % words and phrases as does Texinfo (but note that the \LaTeX special % characters still need special treatment). These commands are % \begin{description} % \item[\code{\cmd{\code}\{\var{sample-code}\}}] % Indicate text that is a literal example of a piece of a program. % \item[\code{\cmd{\kbd}\{\var{keyboard-characters}\}}] % Indicate keyboard input. % \item[\code{\cmd{\key}\{\var{key-name}\}}] % Indicate the conventional name for a key on a keyboard. % \item[\code{\cmd{\samp}\{\var{text}\}}] % Indicate text that is a literal example of a sequence of % characters. % \item[\code{\cmd{\var}\{\var{metasyntactic-variable}\}}] % Indicate a metasyntactic variable. % \item[\code{\cmd{\env}\{\var{environment-variable}\}}] % Indicate an environment variable. % \item[\code{\cmd{\file}\{\var{file-name}\}}] % Indicate the name of a file. % \item[\code{\cmd{\command}\{\var{command-name}\}}] % Indicate a command name (such as \samp{ls}). % \item[\code{\cmd{\option}\{\var{option-name}\}}] % Indicate a command line option. % \item[\code{\cmd{\dfn}\{\var{term}\}}] % Indicate the introductory or defining use of a term. % \item[\code{\cmd{\acronym}\{\var{acronym}\}}] % Use for abbreviattions written in all capital letters, such as % \samp{NASA}. % \end{description} % If this sounds rather confusing, please see the Texinfo documentation % for more details. % % \DescribeMacro{\strong} % There is also a |\strong| command for emphasizing text more strongly % than with |\emph|. For example, |\strong{Note:}| gives \strong{Note:}. % % \DescribeMacro{\pkg} % Finally, use |\pkg| for indicating R packages. % % \subsection{Quotations and Examples} % % In addition to the standard \LaTeX{} for quotations and examples (such % as |quote|, |quotation|, |flushleft|, |center| and |flushright|), the % \pkg{\filename} package provides the following environments. % \begin{description} % \item[\code{example}] % Illustrate code, commands, and the like. The text is printed in a % fixed-width font, and indented but not filled. % \item[\code{smallexample}] % Similar to \code{example}, except that text is typeset in a smaller % font. % \end{description} % % \subsection{Mathematics} % % \DescribeMacro{\P} % \DescribeMacro{\E} % \DescribeMacro{\VAR} % \DescribeMacro{\COV} % \DescribeMacro{\COR} % The commands |\P|, |\E|, |\VAR|, |\COV|, and |\COR| produce symbols % for probability, expectation, variance, covariance and correlation. % For example, Chebyshev's inequality % \DeleteShortVerb{\|} % \begin{displaymath} % \P(|\xi-\E\xi|>\lambda) \le \frac{\VAR(\xi)}{\lambda^2}. % \end{displaymath} % can be coded as % \MakeShortVerb{\|} % \begin{quote} % \verb+\P(|\xi-\E\xi|>\lambda) \le \frac{\VAR(\xi)}{\lambda^2}+. % \end{quote} % % \DescribeMacro{\mathbb} % The symbols % \begin{displaymath} % \mathbb{N}\quad\mathbb{Z}\quad\mathbb{Q}\quad\mathbb{R}\quad\mathbb{C} % \end{displaymath} % for the positive integers, the integers, and the rational, real and % complex numbers, respectively, can be obtained using |\mathbb| from % package \pkg{amsfonts} as % \begin{quote} % |\mathbb{N}| |\mathbb{Z}| |\mathbb{Q}| |\mathbb{R}| |\mathbb{C}| % \end{quote} % % \section{The Code} % % \subsection{The Batch File} % % First comes the code for creating the batch file \file{\filename.ins} % which in turn can be used for producing the package and driver files. % % \begin{macrocode} %<*install> \begin{filecontents}{\filename.ins} % Simply TeX or LaTeX this file to extract various files from the source % file `Rnews.dtx'. \def\filedate{2001/01/05} \def\batchfile{Rnews.ins} \input docstrip.tex \preamble \endpreamble \generateFile{Rnews.drv}{t}{\from{Rnews.dtx}{driver}} \generateFile{Rnews.sty}{t}{\from{Rnews.dtx}{package}} \Msg{***********************************************************} \Msg{* For documentation, run LaTeX on Rnews.dtx or Rnews.drv. *} \Msg{***********************************************************} \end{filecontents} % % \end{macrocode} % % \subsection{The Driver} % % Next comes the documentation driver file for \TeX{}, i.e., the file % that will produce the documentation you are currently reading. It % will be extracted from this file by the \texttt{docstrip} program. % Since it is the first code in the file one can alternatively process % this file directly with \LaTeXe{} to obtain the documentation. % % \begin{macrocode} %<*driver> \documentclass[fleqn]{ltxdoc} \usepackage[driver]{\filename} \renewcommand{\pkg}[1]{\textsf{#1}} \begin{document} \DocInput{\filename.dtx} \end{document} % % \end{macrocode} % % \subsection{The Code} % % Now comes the code for the package. % % It the current format is not \LaTeXe{}, we abort immediately. % Otherwise, we provide ourselves and show the current version of the % package on the screen and in the transscript file. % \begin{macrocode} %<*package> \NeedsTeXFormat{LaTeX2e}[1995/12/01] \ProvidesPackage{\filename}[\filedate\space\fileversion\space Rnews package] \typeout{Package: `\filename\space\fileversion \@spaces <\filedate>'} \typeout{English documentation as of <\docdate>} % \end{macrocode} % % Next, we set up a more or less trivial option handler. We use option % `driver' for conditionalizing package code we do not want executed % when typesetting the driver file. % \begin{macrocode} \RequirePackage{ifthen} \newboolean{Rnews@driver} \DeclareOption{driver}{\setboolean{Rnews@driver}{true}} \DeclareOption*{\PackageWarning{\filename}{Unknown option `\CurrentOption'}} \ProcessOptions\relax % \end{macrocode} % % Now comes the real code. % % \begin{macrocode} \ifthenelse{\boolean{Rnews@driver}}{}{ % \end{macrocode} % % First we load some utility packages. % \begin{macrocode} \RequirePackage{multicol,graphicx,color,fancyhdr,hyperref} % \end{macrocode} % % \subsubsection{Basic Structure} % % Issues of of \emph{R News} are created from the standard \LaTeX{} % document class \pkg{report}. Individual articles correspond to % chapters, and are contained in |article| environments. This makes it % easy to have figures counted within articles and hence hyperlinked % correctly. % % Basic front matter information about the issue: volume, number, and % date. % \begin{macrocode} \newcommand{\volume}[1]{\def\Rnews@volume{#1}} \newcommand{\volnumber}[1]{\def\Rnews@number{#1}} \renewcommand{\date}[1]{\def\Rnews@date{#1}} % \end{macrocode} % % We do not want numbered sections. % \begin{macrocode} \setcounter{secnumdepth}{-1} % \end{macrocode} % % \begin{macro}{\author} % \begin{macro}{\title} % \begin{macro}{\subtitle} % An article has an author, a title, and optionally a subtitle. We use % the obvious commands for specifying these. % \begin{macrocode} \renewcommand{\author}[1]{\def\Rnews@author{#1}} \renewcommand{\title}[1]{\def\Rnews@title{#1}} \newcommand{\subtitle}[1]{\def\Rnews@subtitle{#1}} % \end{macrocode} % \end{macro} % \end{macro} % \end{macro} % % \begin{environment}{article} % Environment |article| clears the article header information its begin % and restores single column mode at its end. % \begin{macrocode} \newenvironment{article}{% \author{}\title{}\subtitle{}}{\end{multicols}} % \end{macrocode} % \end{environment} % % \begin{macro}{\maketitle} % The real work is done by a redefined version of |\maketitle|, which % also switches to double column mode. Note that even though we do not % want chapters (articles) numbered, we need to increment the chapter % counter, so that figures get correct labelling. % \begin{macrocode} \renewcommand{\maketitle}{ \chapter{\Rnews@title} \refstepcounter{chapter} \begin{multicols}{2} \ifx\empty\Rnews@subtitle\else\par\addvspace{\baselineskip} \noindent\textbf{\Rnews@subtitle}\fi \ifx\empty\Rnews@author\else\par\addvspace{\baselineskip} \noindent\textit{\Rnews@author}\fi} % \end{macrocode} % \end{macro} % % Now for some ugly redefinitions. We do not want articles to start a % new page. % \begin{macrocode} \renewcommand\chapter{\secdef\@chapter\@schapter} % \end{macrocode} % TOC entries for articles (chapters) should really look like sections. % \begin{macrocode} \renewcommand*\l@chapter{\@dottedtocline{0}{0pt}{1em}} % \end{macrocode} % We need to adjust vertical spacing in |\@makechapterhead|: extra space % before the title only if not at the beginning, no extra space after % it. % \begin{macrocode} \def\@makechapterhead#1{% \addvspace{2\baselineskip}% {\parindent \z@ \raggedright \normalfont \ifnum \c@secnumdepth >\m@ne \huge\bfseries \@chapapp\space \thechapter \par\nobreak \vskip 20\p@ \fi \interlinepenalty\@M \Huge \bfseries #1\par\nobreak}} % \end{macrocode} % We want bibliographies as starred sections within articles. As the % standard |thebibliography| environment uses |chapter*|, we simply % redefine the latter according to our needs. % \begin{macrocode} \def\@schapter#1{\section*#1} % \end{macrocode} % % Package \pkg{multicol}, which is used for producing two-column output, % only allows for starred (single-column) floats (figures and tables). % Therefore, we provide a simple non-floating |figure| environment % ourselves. % \begin{macrocode} \renewenvironment{figure}[1][]{% \def\@captype{figure} \begin{minipage}{0.9\columnwidth}}{ \end{minipage}\par\addvspace{\baselineskip}} % \end{macrocode} % Equations, figures and tables are counted within articles, but we do % not show the article number. % \begin{macrocode} \renewcommand{\theequation}{\@arabic\c@equation} \renewcommand{\thefigure}{\@arabic\c@figure} \renewcommand{\thetable}{\@arabic\c@table} % \end{macrocode} % % \begin{macro}{\tableofcontents} % Need to provide our own version of |\tableofcontents| (no fiddling % with the number of columns). Note that |\section*| is really the same % as |\chapter*|). % \begin{macrocode} \renewcommand{\contentsname}{Contents of this issue:} \renewcommand\tableofcontents{% \section*{\contentsname \@mkboth{% \MakeUppercase\contentsname}{\MakeUppercase\contentsname}}% \@starttoc{toc}} % \end{macrocode} % \end{macro} % \begin{macro}{\titlepage} % The title page of each issue features logo et al at the top and the % TOC. We start with the top. % \begin{macrocode} \renewcommand{\titlepage}{% \noindent \rule{\textwidth}{1pt}\\[-.8\baselineskip] \rule{\textwidth}{.5pt} \begin{center} \includegraphics[height=2cm]{Rlogo}\hspace{7mm} \fontsize{2cm}{2cm}\selectfont News \end{center} The Newsletter of the R Project\hfill Volume \Rnews@volume/\Rnews@number, \Rnews@date\\[-.5\baselineskip] \rule{\textwidth}{.5pt}\\[-.8\baselineskip] \rule{\textwidth}{1pt} \vspace{1cm} % \end{macrocode} % Now set up the header and footer information for the rest of the % document. % \begin{macrocode} \fancyhf{} \fancyhead[L]{Vol.~\Rnews@volume/\Rnews@number, \Rnews@date} \fancyhead[R]{\thepage} \fancyfoot[L]{R News} \fancyfoot[R]{ISSN 1609-3631} \thispagestyle{empty} % \end{macrocode} % And finally, put the TOC at the bottom in a framed box. Note the way % |tocdepth| is adjusted before and after producing the TOC: thus, we % can ensure that only articles show up in the printed TOC, but that in % the PDF version, bookmarks are created for sections and subsections as % well (provided that the non-starred forms are used). % \begin{macrocode} \begin{bottombox} \begin{multicols}{2} \setcounter{tocdepth}{0} \tableofcontents \setcounter{tocdepth}{2} \end{multicols} \end{bottombox}} % \end{macrocode} % \end{macro} % % \subsubsection{Layout, Fonts and Color} % % \paragraph{Layout.} % We set the basic layout parameters in a way that printouts should be % fine for both A4 and Letter paper. % \begin{macrocode} \setlength{\textheight}{250mm} \setlength{\topmargin}{-10mm} \setlength{\textwidth}{17cm} \setlength{\oddsidemargin}{-6mm} \setlength{\columnseprule}{.1pt} \setlength{\columnsep}{20pt} % \end{macrocode} % % \paragraph{Fonts.} % We use the following fonts (all with T1 encoding): % \begin{center} % \begin{tabular}{lp{0.8\textwidth}} % rm & palatino \\ % tt & almost european (computer modern working with T1) \\ % & Reason for aett: uses less horizontal space than courier, % which is better for example code \\ % sf & almost european \\ % math & palatino % \end{tabular} % \end{center} % % \begin{macrocode} \RequirePackage{ae,mathpple} \RequirePackage[T1]{fontenc} \renewcommand{\rmdefault}{ppl} \renewcommand{\sfdefault}{aess} \renewcommand{\ttdefault}{aett} % \end{macrocode} % % \paragraph{Colors.} These are actually used for |\hypersetup| but we % do not call this here, although we should. % \marginpar{FIXME} % \begin{macrocode} \definecolor{Red}{rgb}{0.7,0,0} \definecolor{Blue}{rgb}{0,0,0.8} \definecolor{hellgrau}{rgb}{0.55,0.55,0.55} % \end{macrocode} % % \subsubsection{Miscellania} % % \begin{macrocode} \newcommand{\R}{R} \newcommand{\address}[1]{\addvspace{\baselineskip}\noindent\emph{#1}} \newcommand{\email}[1]{\href{mailto:#1}{\normalfont\texttt{#1}}} % \end{macrocode} % % \begin{environment}{bottombox} % Used for creating the TOC and the back matter editorial information. % \begin{macrocode} \newsavebox{\Rnews@box} \newlength{\Rnews@len} \newenvironment{bottombox}{% \begin{figure*}[b] \begin{center} \noindent \begin{lrbox}{\Rnews@box} \begin{minipage}{0.99\textwidth}}{% \end{minipage} \end{lrbox} \addtolength{\Rnews@len}{\fboxsep} \addtolength{\Rnews@len}{\fboxrule} \hspace*{-\Rnews@len}\fbox{\usebox{\Rnews@box}} \end{center} \end{figure*}} % \end{macrocode} % \end{environment} % % \begin{environment}{boxedverbatim} % This does not seem to be used any more. % \marginpar{FIXME} % \begin{macrocode} \newenvironment{boxedverbatim}{% \begin{lrbox}{\Rnews@box} \begin{smallverbatim}}{% \end{smallverbatim} \end{lrbox} \hspace*{-\fboxsep}\fbox{\usebox{\Rnews@box}}} % \end{macrocode} % \end{environment} % % Finally, we turn on fancy page style. % \begin{macrocode} \pagestyle{fancy} } % \ifthenelse{\boolean{Rnews@driver}} % \end{macrocode} % % \subsubsection{Marking Words and Phrases} % % Simple font selection is not good enough. For example, |\texttt{--}| % gives `\texttt{--}', i.e., an endash in typewriter font. Hence, we % need to turn off ligatures, which currently only happens for commands % |\code| and |\samp| and the ones derived from them. Hyphenation is % another issue; it should really be turned off inside |\samp|. And % most importantly, \LaTeX{} special characters are a nightmare. E.g., % one needs |\~{}| to produce a tilde in a file name marked by |\file|. % Perhaps a few years ago, most users would have agreed that this may be % unfortunate but should not be changed to ensure consistency. But with % the advent of the WWW and the need for getting `|~|' and `|#|' into % URLs, commands which only treat the escape and grouping characters % specially have gained acceptance (in fact, this is also what % \pkg{alltt} does, and hence environments based on it such as our % |smallexample|). Hence, in the long run we should implement the same % for |\code|, |\kbd|, |\samp|, |\var|, and |\file|. (The other % Texinfo-style commands do not need this.) % % \begin{macrocode} %\newcommand\code{\bgroup\@noligs\@codex} \newcommand\code{\bgroup\@codex} \def\@codex#1{{\normalfont\ttfamily\hyphenchar\font=-1 #1}\egroup} \newcommand{\kbd}[1]{{\normalfont\texttt{#1}}} \newcommand{\key}[1]{{\normalfont\texttt{\uppercase{#1}}}} \newcommand\samp{`\bgroup\@noligs\@sampx} \def\@sampx#1{{\normalfont\texttt{#1}}\egroup'} \newcommand{\var}[1]{{\normalfont\textsl{#1}}} \let\env=\code \newcommand{\file}[1]{{`\normalfont\textsf{#1}'}} \let\command=\code \let\option=\samp \newcommand{\dfn}[1]{{\normalfont\textsl{#1}}} \newcommand{\acronym}[1]{{\normalfont\textsc{\lowercase{#1}}}} \newcommand{\strong}[1]{{\normalfont\fontseries{b}\selectfont #1}} \let\pkg=\strong % \end{macrocode} % % \subsubsection{Quotations and Examples} % % \begin{macrocode} \RequirePackage{alltt} \newenvironment{example}{\begin{alltt}}{\end{alltt}} \newenvironment{smallexample}{\begin{alltt}\small}{\end{alltt}} \newenvironment{display}{\list{}{}\item\relax}{\endlist} % \end{macrocode} % % \subsubsection{Mathematics} % % \begin{macro}{\operatorname} % The implementation of |\operatorname| is similar to the mechanism % \LaTeXe{} uses for functions like sin and cos, and simpler than the % one of \AmSLaTeX{}. We use |\providecommand| for the definition in % order to keep the one of the \pkg{amstex} if this package has % already been loaded. % \begin{macrocode} \providecommand{\operatorname}[1]{% \mathop{\operator@font#1}\nolimits} % \end{macrocode} % \end{macro} % % \begin{macro}{\P} % \begin{macro}{\E} % \begin{macro}{\VAR} % \begin{macro}{\COV} % \begin{macro}{\COR} % Next, we provide commands for probability, expectation, variance, % covariance and correlation which are obviously useful in probability % theory and statistics. % (Of course, originally |\P| gives \mathhexbox27B.) % \begin{macrocode} \renewcommand{\P}{% \mathop{\operator@font I\hspace{-1.5pt}P\hspace{.13pt}}} \newcommand{\E}{% \mathop{\operator@font I\hspace{-1.5pt}E\hspace{.13pt}}} \newcommand{\VAR}{\operatorname{var}} \newcommand{\COV}{\operatorname{cov}} \newcommand{\COR}{\operatorname{cor}} % \end{macrocode} % \end{macro} % \end{macro} % \end{macro} % \end{macro} % \end{macro} % % Finally, we load package \pkg{amsfonts} so that |\mathbb| is available % for producing the symbols for positive integers etc. % \begin{macrocode} \RequirePackage{amsfonts} % \end{macrocode} % % This ends the implementation of the \pkg{\filename} package. % \begin{macrocode} % % \end{macrocode} gregmisc/inst/NEWS0000644000176200001440000001572512163401624013537 0ustar liggesusersThis file provides a brief list of major feature enhancements associated with each package release. For a more detailed list of changes see the ChangeLog file. Version 2.1.5 ------------- Use .onAttach() instead of .First.lib() to show startup message. Version 2.0.6 ------------- Bug fixes: * gplots::overplot() - Troels Ring noted that overplot() was reporting Error in eval(expr, envir, enclos) : couldn't find function "lowess.formula" Fixed by changing reference to gplots:::lowess.formula in panel.overplot. Version 2.0.5 ------------- New functions: * gmodels::coefFrame() - Fits a model to each subgroup defined by \code{by}, then returns a data frame with one row for each fit and one column for each parameter. Function changes: * frameApply() and drop.levels() have been moved to the gdata package from the gtools package. * gtools::quantcut() now properly handles cases where where more than one quantile obtains the same value. Bug fixes: * Minor change to avoid 'R CMD check' warnings generated by example code for the depreciated gdata::elem() function. * Fixed a bug in gtools::mixedsort when only a single value is provided. Version 2.0.4 ------------- New functions: * ConvertMedUnits.R - Convert Medical measurements between International Standard (SI) and US 'Conventional' Units. New data: * MedUnits data set provides conversions between American US 'Conventional' and Standard Intertional (SI) medical units. Bug fixes: * Fix behavior of ll() with some data types. * Minor update to remove 'R CMD check' warnings. New sub-package: * Add a 'gregmisc' subpackage. This package simply loads all of the other packages. This should help individuals who are used to the old gregmisc package.. Version 2.0.3 ------------- New functions: * gdata::unmatrix - function for converting a matrix into a well-labeled vector * gtools::frameApply - Apply a functon the the rows of a data frame. * gtools::drop.levels remove unused factor levels from the factors contained in a data frame Feature enhancements: * gdata::ll - Now handles list-like objects, including data frames * gmodels::CrossTable - Added 'SPSS' format, as suggested by Dirk Enzmann * gplots::heatmap.2 - - Add new parameters for controlling color key - - New parameter to allow control of height and width of separator box * gmodels::CrossTable - Show Chisquare contribution of each cell, suggested by Greg Snow. * gdata::read.xls - Add ability to specify the perl executable and path. Bug fixes: * gplots::heatmap2 - - cell note layout was incorrect - Fix handling of rowsep::colsep. - Ignore missing values when computing symmetric range. * gplots::bandplot - Fix problem in passing graphical parameters * add import of 'reorder' and 'na.omit' from 'stats' package to satisfy packages depending on us. Other changes: * gplots::textplot - Code can be simplified because R now supports selecting a fixed width font. * gplots::plotmeans - Add more extensive example. * gdata::elem - depreciated in favor of gdata::ll Version 2.0.0 ------------- First release as a package bundle. Functions are now segregated into four topic-specific packages: gplots gmodels gtool gmisc Thanks to Nitin Jain for doing most of the work of the conversion to a package bundle. Version 1.11.2 -------------- - Simpify and fix the build process on both *nix and Windows by simply providing pre-built perl modules. Version 1.11.1 -------------- - Fix building of of gregmisc on Windows: Runtime Requirements: ActiveState perl in the PATH Build Requirements: ActiveState perl and Microsoft's NMAKE utility in the PATH (A self extracting archive file containing NMAKE is available from .) This was tested on Windows2000 Pro with ActivePerl-5.8.3.809-MSWin32-x86.msi - (Hopefully) Fix building on Linux with Perl 5.8.0. Perl 5.8.3 is reported to work without error on Linux, as does perl 5.6.1 on Solaris. Version 1.11.0 -------------- - Bump version number to 1.11.0 to better reflect the production status of the package. - Add read.xls(), a function to read Microsoft Excel files by translating them to csv files via the xls2csv.pl script, which has also been added to the package. I've provided scripts to run xls2csv: Unix systems: $PACKAGE$/gregmisc/bin/xls2csv MS-Windows: $PACKAGE$/gregmisc/bin/xls2csv.bat or you can execute the perl code directly: $PACKAGE$/gregmisc/perl/xls2csv.pl The perl script explicitly loads its libraries from the installed gregmisc so you don't have to worry about paths. To get usage and parameter information, simply execute the script via any of the above methods without providing any command-line arguments. - Improvements to CrossTable() by Marc Schwartz - Improvements to ooplot() by Lodewijk Bonebakker - plotCI() and plotmeans() now have improved argument handling. - The running() function now has an additional parameter `simplify' which controls whether the returned values are simplified into a vector/matrix or left as a list. - A makefile that will download and attempt to install all available packages from CRAN and Bioconductor is now provided in $PACKAGE$/gregmisc/tools/ - space() can now space points along the 'y' dimension. - Fix an error in the permutations code for repeats.allow=T and r>2. Both the bug report and fix are from Elizabeth Purdom . - Various fixes for compatibility with R 1.9.X. Version 0.10.2 -------------- - Fixed latex warning. - Fixed smartlegend() positioning when x and/or y axis are log-scale. - Add function remove.vars(). Version 0.10.1 -------------- - Fixed bug in textplot() reported by Kevin Wright . Version 0.10.0 -------------- - Now works with and requires R 1.9.0 - Added ooplot() function that mimics Open-Office style plots. Contributed by Lodewijk Bonebakker - Fixed bug in running() that arose when the called function really neaded a minimum number of elements to work on. - Added several new features to running(), it can now allow sequences shorter than the requested width to be present at the front, the back, or on both sides of the full lenth sequences. This allows one to align the data so that the window is before, after, or around the indexed point. - Add enhancements to estimable() provided by Sren Hjsgaard : The estimable function now 1) also works on geese and gee objects and 2) can test hypotheses af the forb L * beta = beta0 both as a single Wald test and row-wise for each row in L. - Add colorpanel function, which generates a smoothly varying band of colors over a three color range (lo, mid, high). gregmisc/inst/ChangeLog0000644000176200001440000001534412163401276014612 0ustar liggesusers2013-06-28 warnes * [r1686] R/First.R, R/onAttach.R: Rename .First.lib to .onAttach 2012-12-14 warnes * [r1638] .Rinstignore, .Rinstingore: Fix typo in filename * [r1637] .Rinstingore: Move file to correct directory * [r1635] NAMESPACE: Add requisite NAMESPACE file. * [r1634] DESCRIPTION: Bump version number. * [r1633] inst/doc/gregmisc.pdf: Add gregmisc.pdf to subversion. * [r1632] man/First.lib.Rd: Update author email address. 2011-09-01 warnes * [r1492] R/First.R: Minor rewording of startup message. 2011-08-26 warnes * [r1483] R/First.R: Use packageStartupMessage() instead of warning() to display a startup message on package load. * [r1479] DESCRIPTION: Update Greg's email address 2007-10-22 warnes * [r1196] DESCRIPTION: Clarify GPL version 2006-11-29 warnes * [r1032] man, man/First.lib.Rd: Add dummy manual page to make 'R CMD check' happy * [r1031] DESCRIPTION: Update for new release * [r1030] DESCRIPTION, R, TODO, gregmisc: Remove extraneous subdirectory 2006-08-02 warnes * [r977] DESCRIPTION, gregmisc/DESCRIPTION.standalone, inst/doc/gregmisc.tex: Update my email address 2006-04-20 nj7w * [r956] gregmisc/DESCRIPTION.in: Changed the typ of Backword to Backward 2005-05-11 warnes * [r620] DESCRIPTION: Add dependency on gdata::frameApply. 2005-04-04 warnes * [r604] NEWS: Update for release 2.0.6. 2005-04-02 warnes * [r601] TODO: Update TODO file. 2005-03-31 warnes * [r589] DESCRIPTION, NEWS: Update for 2.0.5 release 2005-03-22 warnes * [r578] DESCRIPTION, NEWS: Fixes to pass `R CMD check'. * [r575] gregmisc, gregmisc/DESCRIPTION.in, gregmisc/DESCRIPTION.standalone, gregmisc/R, gregmisc/R/First.R: Create backwords compatibility sub-package 'gregmisc' which loads the other packages and warns the user. 2005-02-25 warnes * [r560] DESCRIPTION, NEWS: Update for release 2.0.3 * [r558] .tnatr:fnmap, DESCRIPTION: Add drop.levels, frameApply to namespace export. 2005-02-04 nj7w * [r537] .tnatr:fnmap: Initial revision 2005-01-28 warnes * [r525] DESCRIPTION: Update version number and date. 2004-09-27 warneg * [r463] inst, inst/doc, inst/doc/Rnews.dtx, inst/doc/Rnews.sty, inst/doc/gregmisc.tex: Move gdata/inst/doc/* to inst/doc/* * [r461] .Rhistory, DESCRIPTION: Updated to pass R CMD check. 2004-09-03 warneg * [r445] DESCRIPTION, NEWS, TODO: *** empty log message *** 2004-09-02 warneg * [r442] .Rhistory: Initial revision 2004-07-16 warnes * [r421] TODO: *** empty log message *** 2004-06-09 warnes * [r373] NEWS: Belated update for 1.11.2. 2004-06-08 warnes * [r368] DESCRIPTION: Add better acknowledgement of authors. 2004-06-05 warnes * [r366] NEWS: Update NEWS file for release 1.11.1. * [r361] DESCRIPTION, NEWS: - Merge Makefile.win into Makefile. Makefile.win now just redirects to Makefile. - Update xls2csv.bat and xls2csv shell script to correctly obtain thier installion path and infer the location of the perl code and libraries. - The xls2csv.pl script now assumes that the libraries it needs are installed into the same directory where it is. 2004-05-27 warnes * [r356] NEWS: Clarify text describing xls2csv scripts. * [r355] DESCRIPTION, NEWS: Updated for release. 2004-05-26 warnes * [r348] NEWS: Update for 1.11.0 release. 2004-05-25 warnes * [r331] DESCRIPTION: Bump version number to 1.11.0 to reflect the actual 'production' status of the package. 2004-04-13 warnes * [r316] DESCRIPTION: Update for 0.10.2 * [r315] NEWS: Updated for 0.10.2 2004-03-30 warnes * [r311] DESCRIPTION: - Fix bug in textplot() reported by Wright, Kevin . 2004-03-26 warnes * [r310] NEWS: Updated for release 0.10.0. * [r309] TODO: Change proposed names of new packages. * [r308] DESCRIPTION: - Add Lodewijk Bonebakker to list of authors - Improve description text - Note dependency on R 1.9.0. 2004-02-18 warnes * [r291] TODO: Add need for split into sub-package. 2004-02-02 warnes * [r286] DESCRIPTION: Update version number for new release. 2004-01-21 warnes * [r284] TODO: Add TODO to contain 'to do' list. * [r280] DESCRIPTION: Updated for 0.8.8 release. 2003-12-03 warnes * [r255] DESCRIPTION: - Updated for version 0.8.7 2003-11-24 warnes * [r241] DESCRIPTION: Updated for release. 2003-11-10 warnes * [r220] DESCRIPTION: - Add files contributed by Arni Magnusson . As well as some of my own. 2003-05-20 warnes * [r194] DESCRIPTION: - Added function trim() and assocated docs. 2003-04-22 warnes * [r192] DESCRIPTION: - Update version number. 2003-04-04 warnes * [r184] DESCRIPTION: - Version 0.8.3 2003-03-08 warnes * [r170] DESCRIPTION: - Bumped up version number. 2003-03-07 warnes * [r168] DESCRIPTION: - Minor changes to code to allow the package to be provided as an S-Plus chapter. 2003-01-30 warnes * [r162] DESCRIPTION: - New release. 2003-01-02 warnes * [r151] DESCRIPTION: Updated version number and added Kjetil to list of contributors. 2002-11-04 warnes * [r144] DESCRIPTION: - Added dependency on R >= 1.6.0 due to code in barplot2() - Since MASS is now a dependency in DESCRIPTION, I removed the now redundant check for MASS in .First.lib(). 2002-10-30 warnes * [r140] DESCRIPTION: Updated version number for 2002-10-29 release. 2002-10-11 warnes * [r134] DESCRIPTION: - Updated version number in DESCRIPTION. 2002-09-30 warnes * [r129] DESCRIPTION: - Updated version number after adding rdirichlet() and ddirichlet() 2002-09-24 warnes * [r125] DESCRIPTION: Update version number after fixing bugs and adding regression tests. * [r123] DESCRIPTION: Updated to version 0.6.1, corresponding to some bug fixes. 2002-09-23 warnes * [r116] DESCRIPTION: - 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] DESCRIPTION: - Corrected documentation mismatch for ci, ci.default. - Replaced all occurences of '_' for assignment with '<-'. - Replaced all occurences of 'T' or 'F' for 'TRUE' and 'FALSE' with the spelled out version. - Updaded version number and date. 2002-04-09 warneg * [r109] DESCRIPTION: Checkin for version 0.5.3 2002-03-26 warneg * [r103] DESCRIPTION: Updated for version 0.5.1 2001-12-17 warneg * [r57] DESCRIPTION: Updated to include new functions and thier contributors. 2001-09-18 warneg * [r18] DESCRIPTION: Release 0.3.2 2001-09-01 warneg * [r16] DESCRIPTION: Release 0.3.0 2001-06-05 warneg * [r5] DESCRIPTION: Updated with addition of concat.R and concat.Rd. 2001-05-30 warneg * [r2] ., DESCRIPTION: Initial revision gregmisc/R/0000755000176200001440000000000012163401144012247 5ustar liggesusersgregmisc/R/onAttach.R0000644000176200001440000000070012163401026014127 0ustar liggesusers# $Id: onAttach.R 1686 2013-06-28 21:37:23Z warnes $ .onAttach <- function(libname, pkgname) { packageStartupMessage( "All functionality of the `gregmisc' package has been moved", "into the four 'g' packages: gdata, gtools, gmodels, and gplots. ", "This package is retained to make it easy to install and load", "the full set. Please consider loading these packages directly." ) } gregmisc/NEWS0000644000176200001440000001572512163401624012562 0ustar liggesusersThis file provides a brief list of major feature enhancements associated with each package release. For a more detailed list of changes see the ChangeLog file. Version 2.1.5 ------------- Use .onAttach() instead of .First.lib() to show startup message. Version 2.0.6 ------------- Bug fixes: * gplots::overplot() - Troels Ring noted that overplot() was reporting Error in eval(expr, envir, enclos) : couldn't find function "lowess.formula" Fixed by changing reference to gplots:::lowess.formula in panel.overplot. Version 2.0.5 ------------- New functions: * gmodels::coefFrame() - Fits a model to each subgroup defined by \code{by}, then returns a data frame with one row for each fit and one column for each parameter. Function changes: * frameApply() and drop.levels() have been moved to the gdata package from the gtools package. * gtools::quantcut() now properly handles cases where where more than one quantile obtains the same value. Bug fixes: * Minor change to avoid 'R CMD check' warnings generated by example code for the depreciated gdata::elem() function. * Fixed a bug in gtools::mixedsort when only a single value is provided. Version 2.0.4 ------------- New functions: * ConvertMedUnits.R - Convert Medical measurements between International Standard (SI) and US 'Conventional' Units. New data: * MedUnits data set provides conversions between American US 'Conventional' and Standard Intertional (SI) medical units. Bug fixes: * Fix behavior of ll() with some data types. * Minor update to remove 'R CMD check' warnings. New sub-package: * Add a 'gregmisc' subpackage. This package simply loads all of the other packages. This should help individuals who are used to the old gregmisc package.. Version 2.0.3 ------------- New functions: * gdata::unmatrix - function for converting a matrix into a well-labeled vector * gtools::frameApply - Apply a functon the the rows of a data frame. * gtools::drop.levels remove unused factor levels from the factors contained in a data frame Feature enhancements: * gdata::ll - Now handles list-like objects, including data frames * gmodels::CrossTable - Added 'SPSS' format, as suggested by Dirk Enzmann * gplots::heatmap.2 - - Add new parameters for controlling color key - - New parameter to allow control of height and width of separator box * gmodels::CrossTable - Show Chisquare contribution of each cell, suggested by Greg Snow. * gdata::read.xls - Add ability to specify the perl executable and path. Bug fixes: * gplots::heatmap2 - - cell note layout was incorrect - Fix handling of rowsep::colsep. - Ignore missing values when computing symmetric range. * gplots::bandplot - Fix problem in passing graphical parameters * add import of 'reorder' and 'na.omit' from 'stats' package to satisfy packages depending on us. Other changes: * gplots::textplot - Code can be simplified because R now supports selecting a fixed width font. * gplots::plotmeans - Add more extensive example. * gdata::elem - depreciated in favor of gdata::ll Version 2.0.0 ------------- First release as a package bundle. Functions are now segregated into four topic-specific packages: gplots gmodels gtool gmisc Thanks to Nitin Jain for doing most of the work of the conversion to a package bundle. Version 1.11.2 -------------- - Simpify and fix the build process on both *nix and Windows by simply providing pre-built perl modules. Version 1.11.1 -------------- - Fix building of of gregmisc on Windows: Runtime Requirements: ActiveState perl in the PATH Build Requirements: ActiveState perl and Microsoft's NMAKE utility in the PATH (A self extracting archive file containing NMAKE is available from .) This was tested on Windows2000 Pro with ActivePerl-5.8.3.809-MSWin32-x86.msi - (Hopefully) Fix building on Linux with Perl 5.8.0. Perl 5.8.3 is reported to work without error on Linux, as does perl 5.6.1 on Solaris. Version 1.11.0 -------------- - Bump version number to 1.11.0 to better reflect the production status of the package. - Add read.xls(), a function to read Microsoft Excel files by translating them to csv files via the xls2csv.pl script, which has also been added to the package. I've provided scripts to run xls2csv: Unix systems: $PACKAGE$/gregmisc/bin/xls2csv MS-Windows: $PACKAGE$/gregmisc/bin/xls2csv.bat or you can execute the perl code directly: $PACKAGE$/gregmisc/perl/xls2csv.pl The perl script explicitly loads its libraries from the installed gregmisc so you don't have to worry about paths. To get usage and parameter information, simply execute the script via any of the above methods without providing any command-line arguments. - Improvements to CrossTable() by Marc Schwartz - Improvements to ooplot() by Lodewijk Bonebakker - plotCI() and plotmeans() now have improved argument handling. - The running() function now has an additional parameter `simplify' which controls whether the returned values are simplified into a vector/matrix or left as a list. - A makefile that will download and attempt to install all available packages from CRAN and Bioconductor is now provided in $PACKAGE$/gregmisc/tools/ - space() can now space points along the 'y' dimension. - Fix an error in the permutations code for repeats.allow=T and r>2. Both the bug report and fix are from Elizabeth Purdom . - Various fixes for compatibility with R 1.9.X. Version 0.10.2 -------------- - Fixed latex warning. - Fixed smartlegend() positioning when x and/or y axis are log-scale. - Add function remove.vars(). Version 0.10.1 -------------- - Fixed bug in textplot() reported by Kevin Wright . Version 0.10.0 -------------- - Now works with and requires R 1.9.0 - Added ooplot() function that mimics Open-Office style plots. Contributed by Lodewijk Bonebakker - Fixed bug in running() that arose when the called function really neaded a minimum number of elements to work on. - Added several new features to running(), it can now allow sequences shorter than the requested width to be present at the front, the back, or on both sides of the full lenth sequences. This allows one to align the data so that the window is before, after, or around the indexed point. - Add enhancements to estimable() provided by Sren Hjsgaard : The estimable function now 1) also works on geese and gee objects and 2) can test hypotheses af the forb L * beta = beta0 both as a single Wald test and row-wise for each row in L. - Add colorpanel function, which generates a smoothly varying band of colors over a three color range (lo, mid, high). gregmisc/NAMESPACE0000644000176200001440000000033612143472613013276 0ustar liggesusers# Default NAMESPACE created by R # Remove the previous line if you edit this file # Export all names exportPattern(".") # Import all packages listed as Imports or Depends import( gdata, gmodels, gplots, gtools ) gregmisc/DESCRIPTION0000755000176200001440000000147412163405435013574 0ustar liggesusersPackage: gregmisc Title: Greg's Miscellaneous Functions Description: Description: The former gregmisc bundle is a repository for a variety of useful functions. The gregmisc package has been split into a set of more focused packages: gdata, gmodels, gplots, gtools. The purpose of this 'new' gregmisc is to provide an easy way to access the original combined functionality. To this end, it simply depends on all of the new packages so that these will installed/loaded when this package is installed/loaded. Depends: gdata, gmodels, gplots, gtools Version: 2.1.5 Author: Gregory R. Warnes. Maintainer: Gregory R. Warnes License: GPL-2 Packaged: 2013-06-28 21:48:38 UTC; warnes NeedsCompilation: no Repository: CRAN Date/Publication: 2013-06-29 00:15:57 gregmisc/ChangeLog0000644000176200001440000001534412163401276013635 0ustar liggesusers2013-06-28 warnes * [r1686] R/First.R, R/onAttach.R: Rename .First.lib to .onAttach 2012-12-14 warnes * [r1638] .Rinstignore, .Rinstingore: Fix typo in filename * [r1637] .Rinstingore: Move file to correct directory * [r1635] NAMESPACE: Add requisite NAMESPACE file. * [r1634] DESCRIPTION: Bump version number. * [r1633] inst/doc/gregmisc.pdf: Add gregmisc.pdf to subversion. * [r1632] man/First.lib.Rd: Update author email address. 2011-09-01 warnes * [r1492] R/First.R: Minor rewording of startup message. 2011-08-26 warnes * [r1483] R/First.R: Use packageStartupMessage() instead of warning() to display a startup message on package load. * [r1479] DESCRIPTION: Update Greg's email address 2007-10-22 warnes * [r1196] DESCRIPTION: Clarify GPL version 2006-11-29 warnes * [r1032] man, man/First.lib.Rd: Add dummy manual page to make 'R CMD check' happy * [r1031] DESCRIPTION: Update for new release * [r1030] DESCRIPTION, R, TODO, gregmisc: Remove extraneous subdirectory 2006-08-02 warnes * [r977] DESCRIPTION, gregmisc/DESCRIPTION.standalone, inst/doc/gregmisc.tex: Update my email address 2006-04-20 nj7w * [r956] gregmisc/DESCRIPTION.in: Changed the typ of Backword to Backward 2005-05-11 warnes * [r620] DESCRIPTION: Add dependency on gdata::frameApply. 2005-04-04 warnes * [r604] NEWS: Update for release 2.0.6. 2005-04-02 warnes * [r601] TODO: Update TODO file. 2005-03-31 warnes * [r589] DESCRIPTION, NEWS: Update for 2.0.5 release 2005-03-22 warnes * [r578] DESCRIPTION, NEWS: Fixes to pass `R CMD check'. * [r575] gregmisc, gregmisc/DESCRIPTION.in, gregmisc/DESCRIPTION.standalone, gregmisc/R, gregmisc/R/First.R: Create backwords compatibility sub-package 'gregmisc' which loads the other packages and warns the user. 2005-02-25 warnes * [r560] DESCRIPTION, NEWS: Update for release 2.0.3 * [r558] .tnatr:fnmap, DESCRIPTION: Add drop.levels, frameApply to namespace export. 2005-02-04 nj7w * [r537] .tnatr:fnmap: Initial revision 2005-01-28 warnes * [r525] DESCRIPTION: Update version number and date. 2004-09-27 warneg * [r463] inst, inst/doc, inst/doc/Rnews.dtx, inst/doc/Rnews.sty, inst/doc/gregmisc.tex: Move gdata/inst/doc/* to inst/doc/* * [r461] .Rhistory, DESCRIPTION: Updated to pass R CMD check. 2004-09-03 warneg * [r445] DESCRIPTION, NEWS, TODO: *** empty log message *** 2004-09-02 warneg * [r442] .Rhistory: Initial revision 2004-07-16 warnes * [r421] TODO: *** empty log message *** 2004-06-09 warnes * [r373] NEWS: Belated update for 1.11.2. 2004-06-08 warnes * [r368] DESCRIPTION: Add better acknowledgement of authors. 2004-06-05 warnes * [r366] NEWS: Update NEWS file for release 1.11.1. * [r361] DESCRIPTION, NEWS: - Merge Makefile.win into Makefile. Makefile.win now just redirects to Makefile. - Update xls2csv.bat and xls2csv shell script to correctly obtain thier installion path and infer the location of the perl code and libraries. - The xls2csv.pl script now assumes that the libraries it needs are installed into the same directory where it is. 2004-05-27 warnes * [r356] NEWS: Clarify text describing xls2csv scripts. * [r355] DESCRIPTION, NEWS: Updated for release. 2004-05-26 warnes * [r348] NEWS: Update for 1.11.0 release. 2004-05-25 warnes * [r331] DESCRIPTION: Bump version number to 1.11.0 to reflect the actual 'production' status of the package. 2004-04-13 warnes * [r316] DESCRIPTION: Update for 0.10.2 * [r315] NEWS: Updated for 0.10.2 2004-03-30 warnes * [r311] DESCRIPTION: - Fix bug in textplot() reported by Wright, Kevin . 2004-03-26 warnes * [r310] NEWS: Updated for release 0.10.0. * [r309] TODO: Change proposed names of new packages. * [r308] DESCRIPTION: - Add Lodewijk Bonebakker to list of authors - Improve description text - Note dependency on R 1.9.0. 2004-02-18 warnes * [r291] TODO: Add need for split into sub-package. 2004-02-02 warnes * [r286] DESCRIPTION: Update version number for new release. 2004-01-21 warnes * [r284] TODO: Add TODO to contain 'to do' list. * [r280] DESCRIPTION: Updated for 0.8.8 release. 2003-12-03 warnes * [r255] DESCRIPTION: - Updated for version 0.8.7 2003-11-24 warnes * [r241] DESCRIPTION: Updated for release. 2003-11-10 warnes * [r220] DESCRIPTION: - Add files contributed by Arni Magnusson . As well as some of my own. 2003-05-20 warnes * [r194] DESCRIPTION: - Added function trim() and assocated docs. 2003-04-22 warnes * [r192] DESCRIPTION: - Update version number. 2003-04-04 warnes * [r184] DESCRIPTION: - Version 0.8.3 2003-03-08 warnes * [r170] DESCRIPTION: - Bumped up version number. 2003-03-07 warnes * [r168] DESCRIPTION: - Minor changes to code to allow the package to be provided as an S-Plus chapter. 2003-01-30 warnes * [r162] DESCRIPTION: - New release. 2003-01-02 warnes * [r151] DESCRIPTION: Updated version number and added Kjetil to list of contributors. 2002-11-04 warnes * [r144] DESCRIPTION: - Added dependency on R >= 1.6.0 due to code in barplot2() - Since MASS is now a dependency in DESCRIPTION, I removed the now redundant check for MASS in .First.lib(). 2002-10-30 warnes * [r140] DESCRIPTION: Updated version number for 2002-10-29 release. 2002-10-11 warnes * [r134] DESCRIPTION: - Updated version number in DESCRIPTION. 2002-09-30 warnes * [r129] DESCRIPTION: - Updated version number after adding rdirichlet() and ddirichlet() 2002-09-24 warnes * [r125] DESCRIPTION: Update version number after fixing bugs and adding regression tests. * [r123] DESCRIPTION: Updated to version 0.6.1, corresponding to some bug fixes. 2002-09-23 warnes * [r116] DESCRIPTION: - 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] DESCRIPTION: - Corrected documentation mismatch for ci, ci.default. - Replaced all occurences of '_' for assignment with '<-'. - Replaced all occurences of 'T' or 'F' for 'TRUE' and 'FALSE' with the spelled out version. - Updaded version number and date. 2002-04-09 warneg * [r109] DESCRIPTION: Checkin for version 0.5.3 2002-03-26 warneg * [r103] DESCRIPTION: Updated for version 0.5.1 2001-12-17 warneg * [r57] DESCRIPTION: Updated to include new functions and thier contributors. 2001-09-18 warneg * [r18] DESCRIPTION: Release 0.3.2 2001-09-01 warneg * [r16] DESCRIPTION: Release 0.3.0 2001-06-05 warneg * [r5] DESCRIPTION: Updated with addition of concat.R and concat.Rd. 2001-05-30 warneg * [r2] ., DESCRIPTION: Initial revision gregmisc/.Rinstignore0000644000176200001440000000007712143472613014365 0ustar liggesusersinst/doc/.*sty$ inst/doc/.*tex$ inst/doc/.*log$ inst/doc/.*aux$