http://blog.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://comments.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, computers to Costa Rica, shower = 2650 light bulbs, ...) </pre> Tim Hesterberg 2012-05-22T13:47:42 http://comments.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://comments.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://comments.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://comments.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/ - arbitrary recursive references of code chunks with &lt;&lt;label&gt;&gt; (e.g. chunk A can call chunk B which in turn calls C); http://yihui.name/knitr/demo/reference/ - for cached chunks, their dependencies can be automatically figured out by analyzing the R code for global and local variables (see the 'autodep' option) - new chunk options fig.cap and fig.scap to create figure environments with captions in LaTeX; - Sweave concordance was implemented and integrated with RStudio so that error navigation and PDF/Rnw sync become easy - more comprehensive support to markdown and reStructuredText; markdown is also well supported in RStudio (preview version); see http://yihui.name/en/2012/05/how-to-make-html5-slides-with-knitr/ - other languages like Python and Awk can also be supported, e.g. https://github.com/yihui/knitr/blob/master/inst/examples/knitr-lang.Rmd Suggestions and questions are welcome; please join the mailing list https://groups.google.com/group/knitr or file issues to Github. Thanks! Regards, Yihui -- Yihui Xie &lt;xieyihui-Re5JQEeQqe8AvxtiuMwx3w&lt; at &gt;public.gmane.org&gt; Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA </pre> Yihui Xie 2012-05-02T21:31:51 http://comments.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 refer to actual dose labels when they have been given by the user * Output from simulations can now be plotted as histograms using the function plot.bcrm.sim Best wishes Mike </pre> Michael Sweeting 2012-05-02T07:24:46 http://comments.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 reasonable. For example: [1] TRUE user system elapsed 1.791 0.047 1.837 user system elapsed 3.267 0.018 3.287 A single closing (dilate followed by erode) operation therefore takes around 1/30th of a second in this case. I hope that this contribution will be useful. All the best, Jon </pre> Jon Clayden 2012-04-30T16:17:50 http://comments.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://comments.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://comments.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://comments.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 (tutorial) showing how to calibrate SWAT-2005 (http://swatmodel.tamu.edu/software/swat-model/) and MODFLOW-2005 (http://water.usgs.gov/nrp/gwsoftware/modflow2005/modflow2005.html) for real-world case studies. You can download the vignette and all the files required to follow the two case studies from: http://www.rforge.net/hydroPSO/ For assistance/bugs report/comments contact/collaboration do not hesitate to contact the authors: Mauricio Zambrano-Bigiarini &lt;mzb.devel [at] gmail.com&gt; Rodrigo Rojas &lt;Rodrigo.RojasMujica [at] gmail.com&gt; Kind regards, Mauricio Zambrano-Bigiarini, PhD </pre> Mauricio Zambrano-Bigiarini 2012-04-18T08:12:52 http://comments.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://comments.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, manipulating and processing MR images in R. The tractor.base package is on CRAN, and forms the backbone of the project. Significant additions to this package in the 2.x series of releases include: - Extensive use of the reference classes introduced in R 2.12.0. - Coercion methods between TractoR's "MriImage" class and the "nifti" class in the oro.nifti package. - Specific support for sparse images (of any dimensionality). - The ability to read and write the MGH file format used by the Freesurfer software package. - A substantial number of other functionality and performance improvements, as well as bug fixes. The full TractoR distribution includes four other R packages, each somewhat more specialised than tractor.base, as well as a flexible command-line interface which can be used to perform common tasks quickly. Details can be found in a recent JSS paper on TractoR [4]. All the best, Jon [1] http://sourceforge.net/projects/niftyreg/ [2] https://github.com/jonclayden/RNiftyReg [3] http://www.tractor-mri.org.uk [4] http://www.jstatsoft.org/v44/i08/ -- Jonathan D Clayden, PhD Lecturer in Neuroimaging and Biophysics Imaging and Biophysics Unit UCL Institute of Child Health 30 Guilford Street LONDON WC1N 1EH United Kingdom t | +44 (0)20 7905 2708 f | +44 (0)20 7905 2358 w | www.homepages.ucl.ac.uk/~sejjjd2/ w | www.diffusion-mri.org.uk/people/1 </pre> Jon Clayden 2012-04-11T22:22:54 http://comments.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 integration and differentiation to support using calculus techniques in R * first drafts of vignettes on teaching resampling and calculus in R * some functions that add extra features to familiar functions (e.g., xchisq.test(), xhistogram(), xpnorm(), ...) * some data sets If you are using mosaic and discover bugs, or have suggestions for future development, consider submitting an issue on our github development site: http://github.com/rpruim/mosaic/issues/ You can also look there to see what's already on our to-do list. ---rjp (on behalf of the development team that includes Danny Kaplan and Nick Horton) ======================================================================== Randall Pruim phone: 616.526.7113 Dept. of Mathematics and Statistics email: rpruim-kP/DyHwX4NY3uPMLIKxrzw&lt; at &gt;public.gmane.org Calvin College office: NH 284 1740 Knollcrest Circle SE URL: http://www.calvin.edu/~rpruim/ Grand Rapids, MI 49546-4403 FAX: 616.526.6501 --------------------------------------------- Here are the promised code examples to give you a feel for what mosaic makes possible: [1] 35.65342 [1] 35.65342 female male 36.25234 35.46821 female.no male.no female.yes male.yes 37.56364 35.90173 34.86538 35.03468 probability of success lower upper 0.6433824 0.5832982 0.7003038 p.value 2.608528e-06 Pearson's Chi-squared test with Yates' continuity correction data: phs X-squared = 24.4291, df = 1, p-value = 7.71e-07 104.00 10933.00 ( 146.52) (10890.48) [12.34] [ 0.17] &lt;-3.51&gt; &lt; 0.41&gt; 189.00 10845.00 ( 146.48) (10887.52) [12.34] [ 0.17] &lt; 3.51&gt; &lt;-0.41&gt; key: observed (expected) [contribution to X-squared] &lt;residual&gt; 1 24.80017 fit lwr upr 1 24.80017 24.30979 25.29055 Flipping 10 coins [ Prob(Heads) = 0.5 ] ... T H T H H H T H H T Result: 6 heads. n heads tails 1 10 4 6 2 10 6 4 tasting tea 0 1 2 3 4 5 6 7 8 9 10 Total 5 52 221 573 1032 1227 1027 606 198 52 7 5000 0 1 2 3 4 5 6 7 8 9 10 Total 0.0010 0.0104 0.0442 0.1146 0.2064 0.2454 0.2054 0.1212 0.0396 0.0104 0.0014 1.0000 # do() extracts useful information from lm objects so that randomization tests are easy. Intercept width sexG sigma r-squared 1 9.646822 1.693137 -0.3057453 1.026824 0.4246224 2 11.416739 1.453416 0.4860068 1.013323 0.4396534 substance sex alcohol cocaine heroin Total female 36 41 30 107 male 141 111 94 346 Total 177 152 124 453 substance sex alcohol cocaine heroin female 0.2033898 0.2697368 0.2419355 male 0.7966102 0.7302632 0.7580645 Total 1.0000000 1.0000000 1.0000000 min Q1 median Q3 max mean sd n missing female.alcohol 23 33 37.0 45 58 39.16667 7.980333 36 0 male.alcohol 20 32 38.0 42 58 37.95035 7.575644 141 0 female.cocaine 24 31 34.0 38 49 34.85366 6.195002 41 0 male.cocaine 23 30 33.0 37 60 34.36036 6.889772 111 0 female.heroin 21 29 34.0 39 55 34.66667 8.035839 30 0 male.heroin 19 27 32.5 39 53 33.05319 7.973568 94 0 function (x, a) cos(a * x) * a [[alternative HTML version deleted]] </pre> Randall Pruim 2012-04-11T12:31:41 http://comments.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 estimate regression models, summarize them in professional-looking tables, and conduct various follow up diagnostics. Highlights: plotSlopes &amp; testSlopes: draw "simple slopes" graphs and conduct hypothesis tests for moderator variables. plotCurves: an attempt to provide a "termplot" replacement that allows plots that incorporate mediators. plotPlane: a wrapper for persp to plot regressions in 3d (similar to scatterplot3d) standardize, meanCenter, residualCenter: after fitting a non-centered model, use these to experiment with the benefits (or lack thereof) that flow from centering. </pre> Paul Johnson 2012-04-09T21:31:42 http://comments.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://comments.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://comments.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://comments.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) - kentau (function used internally) - linregcore (function used internally) - p2logit (function used internally) Functions metabin, metacont, metacor, metagen, metaprop: - new arguments: - hakn (Hartung-Knapp method) - method.tau (estimation method for tau-squared) - tau.preset (fixed value for tau) - TE.tau (prespecified treatment effect to estimate tau) - method.bias (test for funnel plot asymmetry used in metabias) - label.left (Label on left side of forest plot, new argument in functions metabin, metacont, and metagen) - label.right (Label on right side of forest plot, new argument in functions metabin, metacont, and metagen) - warn (print warning messages, new argument in functions metacont and metagen) - new list components of returned object: - se.tau2 (standard error of tau-squared) - hakn (Hartung-Knapp method) - method.tau (estimation method for tau-squared) - tau.preset (fixed value for tau) - TE.tau (prespecified treatment effect to estimate tau) - method.bias (test for funnel plot asymmetry used in metabias) - label.left (Label on left side of forst plot, new list component in functions metabin, metacont, and metagen) - label.right (Label on right side of forst plot, new list component in functions metabin, metacont, and metagen) - argument 'warn' suppresses more warning messages if FALSE - function metabin: studies are excluded from meta-analysis if (event.e &gt; n.e | event.c &gt; n.c) or (n.e &lt;= 0 | n.c &lt;= 0) or (event.e &lt; 0 | event.c &lt; 0) Function metacum and metainf: - modified so that NULL is returned if function is used with a single study - modified so that new arguments hakn, method.tau, tau.preset, method.bias, label.left, label.right are considered in execution of the function - argument level removed Function metaprop: - modified so that the correct variance function 1/(n+0.5) instead of 1/(n+1) is used for the Freeman-Tukey-Transformation (i.e. sm="PFT") - see also news on function asin2p Function asin2p: - completely rewritten as back transformation of Freeman-Tukey transformed proportions was inaccurate - back transformation of Freeman-Tukey proportions according to Miller (1978) - see help page of R command metaprop Function print.metabias: - print a warning if number of studies is too small to conduct a test for funnel plot asymmetry (see new argument k.min) Function print.summary.meta: - new argument bylab.nchar - print test for subgroup differences for both fixed effect and random effects model - value 'invisible(NULL)' returned for metacum and metainf objects Function metacr: - new arguments: - sm (summary measure) - method (pooling method) - comb.fixed (fixed effect model) - comb.random (random effects model) - swap.events (only for binary data) - method.tau (estimation method for between-study variance) - hakn (Hartung-Knapp adjustment) - title (Title of Cochrane review) - complab (Comparison label) - outclab (Outcome label) - warn (print warning messages) - removed argument: - smother (summary measure) - value 'NULL' returned if no data is available for selection of comp.no and outcome.no Function read.rm5: - changed substantially for reading of RevMan 5.1 files Function summary.meta: - modified so that new arguments hakn, method.tau, tau.preset, method.bias are considered in execution of the function - argument 'warn' suppresses more warning messages Function forest.meta: - modified so that the treatment effect and 95% confidence interval is printed in the correct order for objects of class metaprop if argument sort or order is used - symmetric forest plot by default (argument xlim="s") - new arguments: - smlab, smlab.pos, fs.smlab, fflab (Label for summary measure - at top of figure) - label.right, label.left, fs.lr, ff.lr (Label on right and left side) - overall.hetstat (heterogeneity information for overall effect) Function funnel.default and funnel.meta: - modified so that arguments col.fixed and col.random are recognised Function metabias.default and metabias.meta: - new argument k.min: test for funnel plot asymmetry only conducted if number of studies in meta-analysis is larger or equal to k.min - new argument '...' (ignored at the moment) Function trimfill.default and trimfill.meta: - value 'invisible(NULL)' returned if number of studies is smaller than 3 New datasets: amlodipine, cisapride File FLEISS93.MTV moved from directory data to directory extdata Update of several help pages. Some new help pages added. </pre> Guido Schwarzer 2012-03-28T07:30:34 http://comments.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 features: Part 1 http://www.youtube.com/watch?list=UUd1MSCNy5v9i8UGkSc6tCmg&amp;feature=player_detailpage&amp;v=K38IkTn5M_o New plot builder features: Part 2 http://www.youtube.com/watch?list=UUd1MSCNy5v9i8UGkSc6tCmg&amp;feature=player_detailpage&amp;v=bUTu597Mf3g ------------------------------------------------------------------------------------------------------- DeducerSpatial 0.4 ------------------------------------------------------------------------------------------------------- A Deducer plug-in for spatial data analysis. Includes The ability to plot and explore open street map and Bing satellite images. Currently there is not much here in terms of heavy data analysis, but there are some great tools for importing and exploring spatial data. http://www.youtube.com/watch?v=SXaBT22w8G4&amp;list=UUd1MSCNy5v9i8UGkSc6tCmg&amp;index=3&amp;feature=plcp ------------------------------------------------------------------------------------------------------- DeducerPlugInScaling 0.1-0 ------------------------------------------------------------------------------------------------------- A Deducer plug-in for factor analysis, reliability analysis and discriminant analysis. Version 0.1-0 includes some general improvements as well as a dialog for linear discriminant analysis (thanks to Helios De Rosario-Martinez). http://www.deducer.org/pmwiki/pmwiki.php?n=Main.LinearDiscriminantAnalysis ------------------------------------------------------------------------------------------------------- DeducerExtras 1.5 ------------------------------------------------------------------------------------------------------- Added functionality for Deducer. This package includes additional dialogs for calculating distribution function values, cluster analysis, and more. Version 1.5 includes some general improvements along with a new dialog implementing Friedman's test, and Kendall's W test (thanks to Helios De Rosario-Martinez). http://www.deducer.org/pmwiki/pmwiki.php?n=Main.RankingAnalysis </pre> Ian Fellows 2012-03-28T04:42:53 http://comments.gmane.org/gmane.comp.lang.r.packages/581 <pre>Package update: mediation Scholars across a range of disciplines are increasingly interested in identifying causal mechanisms, going beyond the estimation of causal effects. The mediation package (4.0) estimates mediation effects for a variety of experimental designs and statistical models. The update covers new models, designs, and includes many new functionalities. Dustin Tingley Government Department Harvard University http://scholar.harvard.edu/dtingley Director, Program on Experience Based Learning in the Social Sciences http://projects.iq.harvard.edu/peblss/ Contribute to the Research Reservoir: http://projects.iq.harvard.edu/undergradscholars/pages/research-resources [[alternative HTML version deleted]] </pre> dustin tingley 2012-03-28T18:19:30 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.packages