http://permalink.gmane.org/gmane.comp.lang.r.packages hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://permalink.gmane.org/gmane.comp.lang.r.packages/602 <pre>A new 'dataframe' package is on CRAN. This is a modified version of the data frame code in R, modified to make fewer copies of the inputs and run faster, e.g. as.data.frame(a vector) makes 1 copy of the vector rather than 3, data.frame(a vector) makes 3 copies rather than 6, and x[, "a"] &lt;- newValue makes (2,2,1) copies of (old data frame, new column, integer vector of row names) rather than (6,4,2). Functionality should be identical to existing R code, with two exceptions: * bug fix, if x has two columns, then x[[4]] &lt;- value will fail rather than producing an illegal data frame * round(a data frame with numeric and factor columns) rounds the numeric columns and leaves the factor columns unchanged, rather than failing. Tim Hesterberg NEW! Mathematical Statistics with Resampling and R, Chihara &amp; Hesterberg http://www.amazon.com/Mathematical-Statistics-Resampling-Laura-Chihara/dp/1118029852/ref=sr_1_1?ie=UTF8 http://home.comcast.net/~timhesterberg (resampling, water bottle rockets, computer</pre> Tim Hesterberg 2012-05-22T13:47:42 http://permalink.gmane.org/gmane.comp.lang.r.packages/601 <pre>Hello, All: fda_2.2.8 (functional data analysis) is now available on CRAN. This revision includes the following improvements: 1. A bug in pca.fd has been fixed. 2. Many functions have a new argument "returnMatrix", which if TRUE allows the function to use the sparse matrix representations in library(Matrix). This should allow users to solve some larger problems and provides a speed advantage in a few cases. 3. A few other minor bugs have been fixed including problems with some of the script files in system.files('scripts', package='fda'). A package using the returnMatrix argument will also need Matrix in the dependencies in DESCRIPTION and something like import(Matrix) in NAMESPACE. Each use will require adding returnMatrix = TRUE to an appropriate fda function call. Best Wishes, Jim Ramsay, Giles Hooker, Spencer Graves </pre> Spencer Graves 2012-05-17T03:12:57 http://permalink.gmane.org/gmane.comp.lang.r.packages/600 <pre>The "bigml" package is an R wrapper for the BigML API: https://bigml.com/developers It contains straightforward methods for most of the relevant API end points, as well as some fancier methods that allow for direct translations from R dataframes directly into datasets appropriate for BigML. Excerpt from an upcoming blog post, which describes the package in more detail: Today BigML releases the bigml package for R. R is already well known for Apologies for sending this e-mail a bit late. Best, -Justin </pre> Justin Donaldson 2012-05-08T22:46:24 http://permalink.gmane.org/gmane.comp.lang.r.packages/599 <pre>Dear all, the commented source code for the ROCR package (http://cran.r-project.org/web/packages/ROCR) is now available on github -- feel free to fork, add improvements, and contribute back! https://github.com/ipa-tys/ROCR Kind regards, Tobias </pre> Tobias Sing 2012-05-05T18:25:10 http://permalink.gmane.org/gmane.comp.lang.r.packages/598 <pre>The knitr package version 0.5 is on CRAN now. It has gone through extensive development in the past few months, and about 200 issues were solved (https://github.com/yihui/knitr/issues) thanks to the feedback of users, which greatly improved the quality and usefulness of this package. For a complete list of changes, see https://github.com/yihui/knitr/blob/master/NEWS Most notable new features are: - chunk options can be arbitrary valid R code, e.g. &lt;&lt;echo=!TRUE, results=ifelse(x, 'asis', 'markup')&gt;&gt;=; this makes a document really programmable, and the syntax is also consistent with normal R code; http://yihui.name/knitr/demo/sweave/ - the listings package is supported via render_listings(), and the styles are based on Sweavel.sty (courtesy of Frank Harrell); http://yihui.name/knitr/demo/listings/ - for HTML/markdown documents, R plots can be automatically uploaded to Imgur to make sure the output is self-contained (no need to copy images when publishing the output); http://yihui.name/knitr/demo/upload/ - ar</pre> Yihui Xie 2012-05-02T21:31:51 http://permalink.gmane.org/gmane.comp.lang.r.packages/597 <pre>Dear all, Version 0.3 of the bcrm package is now available on CRAN. The package allows users to fit Bayesian Continuous Reassessment Method Phase I trial designs. This version has the following new developments from version 0.1: * Stopping rules have been added, allowing stopping to be based on a maximum sample size, the maximum number to be treated at the final MTD estimate, the precision of the MTD estimate, and a minumum sample size. * Implementation of escalation based on posterior toxicity intervals using loss functions. * Posterior summaries after each recruited cohort can now be plotted using the "each" argument of plot.bcrm. * When simulating, operating characteristics are also now presented by true regions of toxicity risk. * Simulations now run faster, as they use information from identical previous simulations to choose next dose. This is only implemented if nsims&lt;=1000, otherwise the computation time to search previous simulations becomes unmanageable. * Plot and print commands now r</pre> Michael Sweeting 2012-05-02T07:24:46 http://permalink.gmane.org/gmane.comp.lang.r.packages/596 <pre>Dear all, I'm pleased to announce the release on CRAN of the "mmand" package (for Mathematical Morphology in Any Number of Dimensions). It provides functions for performing mathematical morphology (erode, dilate, etc.), smoothing, and other kernel-based operations on array-like objects of any dimensionality. The package is centred around a flexible function called morph(), which can apply any kernel to array elements, optionally conditioned on their value or number of nonzero neighbours. Operations such as erode and dilate are provided for 2D data by the EBImage Bioconductor package, but mmand can be used for higher (and lower!) dimensional data, can produce and apply anisotropic kernels, and does not have external dependencies--except for the small, pure R package "reportr" (also on CRAN), which is used for message reporting. Owing to its more general, dimensionality-independent implementation, mmand is a little slower than EBImage; but due to various performance optimisations, run time is still very rea</pre> Jon Clayden 2012-04-30T16:17:50 http://permalink.gmane.org/gmane.comp.lang.r.packages/595 <pre>New version RExcel 3.2.7-1 Download wrapper for new version of RExcel. </pre> Neuwirth Erich 2012-04-30T07:07:05 http://permalink.gmane.org/gmane.comp.lang.r.packages/594 <pre>rreval 1.1 is now available on CRAN. This release fixes a Window specific bug. It is required for cloudRmpi 1.1 (which is also now available on CRAN). rreval is a means for using R on a remote system from within a local R session. Any R expression can be evaluated on the remote server. All non-graphical results are returned to the local R session: this includes the results of remote evaluations and (nearly) all textual output, including errors and warnings. rreval uses socket level communication via ssh port forwarding. It supports uploading and downloading R objects and scp file tranfers. Cheers, Barnet Wagman </pre> Barnet Wagman 2012-04-24T15:31:33 http://permalink.gmane.org/gmane.comp.lang.r.packages/593 <pre> Dear all, Recurrent events are common in many areas: psychology, engineering, medicine, physics, astronomy, biology, economics and so on . Such events are very common in the real world: viral diseases, carcinogenic tumors, machinery and equipment failures, births, murders, rain, industrial accidents, car accidents and so on . The availability of computerized tools for the analysis is indispensable. The development of tools for the statistical analysis of recurrent events is relatively recent and is not fully known. The purpose of this package is to present statistical tests for the analysis of recurrent event data. Now, a new package called “ TestSurvRec_1.01 ” is available. “ TestSurvRec_1.01 ” computes the p-values of tests to compare two survival curves of groups with recurrent events. Function for plotting of survival curves [estimates by PHS, Peña et al. ( 2001 )] of the groups is also available. The recurrent events of the units are plotted. Counting process a</pre> Carlos M. Martinez Manrique 2012-04-27T04:32:19 http://permalink.gmane.org/gmane.comp.lang.r.packages/592 <pre>Dear All, I have just submitted a new version of the QCAGUI package on CRAN, it should be propagated in a couple of days. This version is nothing but a quick update to the latest Rcmdr base package, and works (as usual) with the QCA package up to version 0.6-5 For the later versions of the QCA package, I will start adapting the GUI in the shortest time possible. Best wishes, Adrian </pre> Adrian Duşa 2012-04-23T09:38:30 http://permalink.gmane.org/gmane.comp.lang.r.packages/591 <pre>Dear R and hydrological/environmental community, I would like to draw your attention to hydroPSO, a newly developed R package for the calibration/optimisation of (complex) environmental models. hydroPSO implements a state-of-the-art Particle Swarm Optimisation (PSO) algorithm, which is a global optimisation technique with a surge of attention given its flexibility, ease of implementation and efficiency. Key features of hydroPSO are: 1) Model-independent calibration engine 2) Minimal user intervention to define I/O functions for interfacing hydroPSO with the model code 3) Several fine-tuning options to customise the calibration engine (for advanced PSO users) 4) Sensitivity analysis included, using the Latin Hypercube One-factor-At-a-Time (LH-OAT) 5) Several functions for post-processing of the calibration results hydroPSO is already available on CRAN: http://cran.r-project.org/web/packages/hydroPSO/ you can install it with: &gt; install.packages("hydroPSO") This package includes a vignette (tu</pre> Mauricio Zambrano-Bigiarini 2012-04-18T08:12:52 http://permalink.gmane.org/gmane.comp.lang.r.packages/590 <pre>Dear R users, Version 3.0-0 of the sem package is now on CRAN. From the package NEWS file: o Compiled code for optimization. o Added multi-group models. o Modification indices for equality-constrained parameters. o weights argument added to tsls(). o raw argument added to cfa(). Of these changes, the first two are the most significant, and the first -- the use of compiled code to improve performance substantially -- was implemented by Zhengua Nie, who has joined me and Jarrett Byrnes as a co-developer of the package. Best, John -------------------------------- John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox </pre> John Fox 2012-04-15T14:50:49 http://permalink.gmane.org/gmane.comp.lang.r.packages/589 <pre>Dear all, There have been some recent major updates to the TractoR and RNiftyReg packages, which are available for medical image analysis applications. If you use R for these purposes, I hope you will find the updates useful. RNiftyReg is an image registration package, which provides a clean R-like interface to the NiftyReg library developed at University College London [1]. It is aimed at medical image registration, but could be applied to 2D or 3D coalignment of images of any type. RNiftyReg version 0.6 adds an interface to the NiftyReg nonlinear registration tool "f3d", which performs fast freeform deformation-based registration based on a grid of control points. This is a fast implementation, which can perform 3D registration in under a minute for some medical images. The package is on CRAN, and development is coordinated through GitHub [2]. TractoR is a larger project for medical image analysis, particularly with magnetic resonance images [3]. It provides tools for reading, writing, visualising, mani</pre> Jon Clayden 2012-04-11T22:22:54 http://permalink.gmane.org/gmane.comp.lang.r.packages/588 <pre>One of the products of Project MOSAIC (funded by an NSF CCLI grant) has been the development of an R package with the goal of making it easier to use R, especially in teaching situations. We're not quite ready to declare that we've reached version 1.0, but version 0.4 does represent a fairly large step in that direction. You can find out more about the package on CRAN or by installing it, but here are some of the highlights (some example code appears at the end of this message): * extensions of syntax to promote consistency across functions and make wider use of the formula interface * simplified ways of creating and plotting functions, including extracting model fits as functions * a tally() function that combines features of table() and xtabs() and more in a common syntax * expanded syntax for summary functions like mean(), median(), max(), sd(), var(), etc. that accepts formulas and data frames * a do() function that simplifies resampling-based statistical analysis * numerical in</pre> Randall Pruim 2012-04-11T12:31:41 http://permalink.gmane.org/gmane.comp.lang.r.packages/587 <pre>Greetings: rockchalk is a collection of functions to facilitate presentation of regression models. It includes some functions that I have been circulating for quite some time (such as "outreg") as well as several others. The main aim is to allow people who do not understand very much R to survive a course in intermediate regression analysis. The examples included with the functions include more than the usual amount of detail. This version features 1) a full vignette called "rockchalk" that illustrates many of the functions in the package. The vignette includes an explanation of why mean-centering and residual-centering do not help with the "inessential multicollinearity" problem that concerns users of regression models in which there are interactions or squared terms. 2) a function "summarize" that is intended to remedy some of the shortcomings I perceive in R's summary function. The package is not coordinated with any particular textbook and should help in any class in which students are expected to </pre> Paul Johnson 2012-04-09T21:31:42 http://permalink.gmane.org/gmane.comp.lang.r.packages/586 <pre>Dear All, I have just uploaded a new version of the QCA (Qualitative Comparative Analysis) on CRAN, and it will be propagated in a couple of days. This is version 1.0-0 ("Easter edition") of the package, straight from the previous version 0.6-5, and it represent a major re-write of the package in order to accomodate fuzzy-sets. I am pleased to welcome Alrik Thiem as a co-author of this package, his skills and knowledge have been paramount to developing the current code. This version has numerous changes in the code (probably too many to present in this email) and new additional functions. Most notably, the previous qmcc() function is now obsolete, given that all our tests have shown that eqmcc() yield the same exact results but it's by far superior in speed. A very happy Easter, and happy QCA-ing, Adrian and Alrik </pre> Adrian Dusa 2012-04-08T09:57:16 http://permalink.gmane.org/gmane.comp.lang.r.packages/585 <pre>Dear all, A new package 'IC2' is now available. IC2 computes some indices of inequality and concentration (SGini, Atkinson, GEI). For each index, it provides decomposition between subgroups. Plotting of Lorenz and concentration curves are also available. Sampling weights can be used. Regards, -- Didier Plat Laboratoire d'Economie des Transports (CNRS -ENTPE -Université Lumiere) ENTPE-rue Maurice AUDIN-69518 VAULX-EN-VELIN CEDEX-FRANCE didier.plat-BhoPxl9ykkA&lt; at &gt;public.gmane.org http://www.entpe.fr/ http://www.let.fr/ [[alternative HTML version deleted]] _______________________________________________ R-packages mailing list R-packages-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-packages </pre> PLAT didier 2012-04-02T13:05:34 http://permalink.gmane.org/gmane.comp.lang.r.packages/584 <pre>Dear All, The 'joineR' package for the joint analysis of repeated measurements and time-to-event outcomes is now available on CRAN. The package contains utilities for creating and manipulating 'jointdata' objects, graphical summaries, a variogram function for estimating correlation structure, and maximum likelihood estimation for a class of random effects joint models. Best wishes, Pete. Pete Philipson Lecturer in Statistics School of Computing, Engineering and Information Sciences Northumbria University email: pete.philipson-jxvoDc5D0OBqP4mUvfwYy1pr/1R2p/CL&lt; at &gt;public.gmane.org [[alternative HTML version deleted]] </pre> Pete Philipson 2012-03-31T18:00:46 http://permalink.gmane.org/gmane.comp.lang.r.packages/583 <pre>Version 2.0-0 of meta (an R package for meta-analysis) is now available on CRAN. Changes are described below. Yours, Guido Major revision R package meta linked to R package metafor by Wolfgang Viechtbauer to provide additional statistical methods, e.g. meta-regression and other estimates for tau-squared (REML, ...) New functions: - metareg (meta-regression) - metabias (generic method for function metabias) - metabias.default (generic method for function metabias) - metabias.meta (generic method for function metabias) - metabias.rm5 (generic method for function metabias) - print.rm5 (generic method for rm5-object) - print.summary.rm5 (generic method for rm5-object) - summary.rm5 (generic method for rm5-object) - catmeth (function used internally) - crtitle (function used internally) - hypergeometric (function used internally) - is.installed.metafor (function used internally) - k</pre> Guido Schwarzer 2012-03-28T07:30:34 http://permalink.gmane.org/gmane.comp.lang.r.packages/582 <pre>Dear R users, Over the past month there have been a number of package updates in the deducer ecosystem. Deducer is a general purpose, extensible, data analysis GUI. It is designed to be a free easy to use alternative to proprietary data analysis software such as SPSS, JMP, and Minitab. It has a menu system to do common data manipulation and analysis tasks, and an excel-like spreadsheet in which to view and edit data frames. More information is available in the online manual: http://www.deducer.org/pmwiki/pmwiki.php?n=Main.DeducerManual And there is an intro video in youtube: http://www.youtube.com/watch?v=AjLToyuluSM&amp;lr=1 ------------------------------------------------------------------------------------------------------- Deducer 0.6-3 ------------------------------------------------------------------------------------------------------- The main change in Deducer 0.6-3 is an update to the (award winning) Plot Builder GUI to make use of the new features in ggplot2 0.9-0. New plot builder fea</pre> Ian Fellows 2012-03-28T04:42:53 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.packages