Title: Geophysical Inverse Theory and Optimization
Description: Several functions introduced in Aster et al.'s book on inverse theory. The functions are often translations of MATLAB code developed by the authors to illustrate concepts of inverse theory as applied to geophysics. Generalized inversion, tomographic inversion algorithms (conjugate gradients, 'ART' and 'SIRT'), non-linear least squares, first and second order Tikhonov regularization, roughness constraints, and procedures for estimating smoothing parameters are included. Includes a wrapper for the FORTRAN based 'LSQR' (Paige and Saunders) routine.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between PEIP versions 2.0 dated 2015-06-09 and 2.0-1 dated 2015-06-10
DESCRIPTION | 6 +++--- MD5 | 5 +++-- src/Makevars | 3 +-- src/Makevars.win |only 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Perceptual Analysis, Visualization and Organization of Spectral
Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color from spectral data.
Author: Rafael Maia [aut, cre],
Chad Eliason [aut],
Pierre-Paul Bitton [aut]
Maintainer: Rafael Maia <rm72@zips.uakron.edu>
Diff between pavo versions 0.5-1 dated 2013-09-04 and 0.5-2 dated 2015-06-10
DESCRIPTION | 19 +- MD5 | 82 +++++----- NAMESPACE | 2 R/merge.rspec.R | 3 R/plot.rspec.r | 3 R/subset.rspec.R | 9 - R/summary.rspec.R | 3 R/summary.tcs.R | 3 R/summary.vismodel.R | 3 R/sysdata.rda |binary R/tcs.R | 2 R/vismodel.R | 8 - man/aggplot.Rd | 69 ++++----- man/aggspec.Rd | 48 ++---- man/as.rspec.Rd | 36 +--- man/bgandilum.Rd | 10 - man/coldist.Rd | 149 ++++++++----------- man/explorespec.Rd | 44 ++--- man/getspec.Rd | 54 +++---- man/irrad2flux.Rd | 25 +-- man/merge.rspec.Rd | 22 +- man/pavo-package.Rd | 20 +- man/peakshape.Rd | 55 +++---- man/plot.rspec.Rd | 54 +++---- man/plotsmooth.Rd | 38 ++--- man/procspec.Rd | 94 +++++------- man/projplot.Rd | 40 ++--- man/segclass.Rd | 31 +--- man/sensmodel.Rd | 102 +++++-------- man/sicalis.Rd | 10 - man/spec2rgb.Rd | 31 +--- man/subset.rspec.Rd | 25 +-- man/summary.rspec.Rd | 358 ++++++++++++++++++++---------------------------- man/summary.tcs.Rd | 69 +++------ man/summary.vismodel.Rd | 36 +--- man/tcs.Rd | 63 +++----- man/tcsplot.Rd | 122 ++++++---------- man/teal.Rd | 10 - man/ttvertex.Rd | 12 - man/vismodel.Rd | 174 ++++++++++------------- man/vissyst.Rd | 11 - man/voloverlap.Rd | 169 +++++++++------------- 42 files changed, 920 insertions(+), 1198 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-level 'MongoDB' client based on 'jsonlite' and 'mongoc' driver.
Includes support for aggregation, indexing, map-reduce, streaming, 'TLS'
encryption and 'SASL' authentication.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between mongolite versions 0.3 dated 2015-05-13 and 0.4 dated 2015-06-10
DESCRIPTION | 13 MD5 | 80 +- NAMESPACE | 4 NEWS | 5 R/jeroen.R | 5 R/mongo.R | 30 - R/object.R | 96 ++- R/stream.R | 66 ++ configure | 6 inst/doc/intro.Rmd | 32 + inst/doc/intro.html | 40 + man/mongo.Rd | 29 src/Makevars | 56 + src/Makevars.win | 5 src/bson.c | 11 src/bson/bson-config.h | 30 - src/bson/bson-stdint.h | 2 src/bson/bson-utf8.c | 17 src/bson/bson-version.h | 6 src/bson/bson.c | 11 src/cursor.c | 66 ++ src/mongoc/mongoc-bulk-operation.c | 73 ++ src/mongoc/mongoc-client.c | 2 src/mongoc/mongoc-cluster-private.h | 1 src/mongoc/mongoc-cluster.c | 87 ++ src/mongoc/mongoc-collection.c | 8 src/mongoc/mongoc-config.h | 11 src/mongoc/mongoc-error.h | 2 src/mongoc/mongoc-init.c | 74 ++ src/mongoc/mongoc-matcher-op.c | 104 +++ src/mongoc/mongoc-sasl.c | 18 src/mongoc/mongoc-stream.c | 9 src/mongoc/mongoc-uri.c | 18 src/mongoc/mongoc-util-private.h | 9 src/mongoc/mongoc-version.h | 6 src/mongoc/mongoc-write-command-private.h | 40 - src/mongoc/mongoc-write-command.c | 874 ++++++++++++++++++++---------- src/reader.c |only src/tests |only src/utils.c | 6 tests |only vignettes/intro.Rmd | 32 + 42 files changed, 1484 insertions(+), 500 deletions(-)
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov <valentin.todorov@chello.at>,
Andreas Ruckstuhl <andreas.ruckstuhl@zhaw.ch>,
Matias Salibian-Barrera <matias@stat.ubc.ca>,
Tobias Verbeke <tobias.verbeke@openanalytics.eu>,
Manuel Koller <mkoller@ispm.unibe.ch>,
Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.92-3 dated 2015-01-14 and 0.92-4 dated 2015-06-10
DESCRIPTION | 25 ++++---- MD5 | 82 +++++++++++++------------- NAMESPACE | 9 ++ R/AAA.R | 13 ++-- R/BYlogreg.R | 2 R/MTestimador2.R | 19 +++--- R/OGK.R | 3 R/glmrobMqle.R | 32 ++++------ R/huber.R | 4 - R/lmrob.MM.R | 59 +++++++++---------- R/lmrob.R | 2 R/ltsPlot.R | 130 +++++++++++++++--------------------------- R/plot.lmrob.R | 74 +++++++++++++++++++---- TODO | 4 - build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.pdf |binary inst/po |only man/adjbox.Rd | 17 ++--- man/colMedians.Rd | 4 - man/condroz.Rd | 8 -- man/lmrob..M..fit.Rd | 4 - man/lmrob.Rd | 6 - man/lmrob.control.Rd | 2 man/los.Rd | 7 -- man/mc.Rd | 5 - man/plot.lmrob.Rd | 28 +++++++-- man/predict.lmrob.Rd | 74 ++++++++++++++++++++++- man/pulpfiber.Rd | 2 man/salinity.Rd | 49 +++++++++++++-- man/sigma.Rd | 26 +++++--- po |only src/mc.c | 4 - tests/glmrob-1.R | 34 ++++++++++ vignettes/psi-GGW.pdf |binary vignettes/psi-Hampel.pdf |binary vignettes/psi-Huber.pdf |binary vignettes/psi-LQQ.pdf |binary vignettes/psi-Welsh.pdf |binary vignettes/psi-bisquare.pdf |binary vignettes/psi-optimal.pdf |binary 43 files changed, 451 insertions(+), 277 deletions(-)
Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between mpath versions 0.1-17 dated 2014-11-10 and 0.1-18 dated 2015-06-10
DESCRIPTION | 9 ++-- MD5 | 79 ++++++++++++++++++++------------------- NAMESPACE | 2 NEWS | 9 ++++ R/cv.glmregNegbin.R | 5 +- R/glmreg.R | 29 +++++++++++--- R/glmregNB.R | 4 - R/zipath.R | 8 --- build/vignette.rds |binary inst/doc/german.R | 65 ++++++++++++++++++++++++++------ inst/doc/german.Rnw | 45 +++++++++++++++++----- inst/doc/german.pdf |binary inst/doc/static_german.pdf |only inst/doc/static_german.pdf.asis |only man/be_zeroinfl.Rd | 4 - man/breadReg.Rd | 3 - man/cv.glmreg.Rd | 21 +++++----- man/cv.glmregNB.Rd | 20 ++++----- man/cv.glmreg_fit.Rd | 21 +++++----- man/cv.zipath.Rd | 13 ++---- man/estfunReg.Rd | 3 - man/glmreg.Rd | 3 - man/glmregNB.Rd | 2 man/glmreg_fit.Rd | 6 +- man/hessianReg.Rd | 2 man/meatReg.Rd | 2 man/methods.Rd | 6 +- man/mpath-internal.Rd | 2 man/p_zipath.Rd | 4 - man/predict.glmreg.Rd | 2 man/predict.zipath.Rd | 6 +- man/rzi.Rd | 4 - man/sandwichReg.Rd | 2 man/se.Rd | 2 man/summary.glmregNB.Rd | 2 man/tuning_zipath.Rd | 6 +- man/zipath.Rd | 6 +- src/lmnetGaussian.f | 27 ++++++------- src/midloop.f | 11 ++--- vignettes/german.Rnw | 45 +++++++++++++++++----- vignettes/mpath.bib | 5 +- vignettes/static_german.pdf.asis |only 42 files changed, 309 insertions(+), 176 deletions(-)
Title: Variable Selection for Model-Based Clustering using the
Integrated Complete-Data Likelihood of a Latent Class Model
Description: Uses a finite mixture model for performing the cluster analysis with variable selection of continuous data by assuming independence between classes. The package deals dataset with missing values by assuming that values are missing at random. The one-dimensional marginals of the components follow Gaussian distributions for facilitating both model interpretation and model selection. The variable selection is led by the Maximum Integrated Complete-Data Likelihood criterion. The maximum likelihood inference is done by an EM algorithm for the selected model. This package also performs the imputation of missing values.
Author: Matthieu Marbac and Mohammed Sedki
Maintainer: Mohammed Sedki <mohammed.sedki@u-psud.fr>
Diff between VarSelLCM versions 1.1 dated 2015-05-22 and 1.2 dated 2015-06-10
VarSelLCM-1.1/VarSelLCM/R/VSLCM_Classes.R |only VarSelLCM-1.1/VarSelLCM/R/VSLCM_initialization.R |only VarSelLCM-1.1/VarSelLCM/R/onAttach.R |only VarSelLCM-1.1/VarSelLCM/inst/CITATION |only VarSelLCM-1.1/VarSelLCM/inst/include/Algo.h |only VarSelLCM-1.1/VarSelLCM/man/VSLCMparameters-class.Rd |only VarSelLCM-1.1/VarSelLCM/man/VSLCMresults-class.Rd |only VarSelLCM-1.1/VarSelLCM/src/Algo.cpp |only VarSelLCM-1.1/VarSelLCM/src/Algo.h |only VarSelLCM-1.1/VarSelLCM/src/VarSelLCM.cpp |only VarSelLCM-1.2/VarSelLCM/DESCRIPTION | 22 VarSelLCM-1.2/VarSelLCM/MD5 | 68 +- VarSelLCM-1.2/VarSelLCM/NAMESPACE | 9 VarSelLCM-1.2/VarSelLCM/R/CheckInputs.R |only VarSelLCM-1.2/VarSelLCM/R/DataCstr.R |only VarSelLCM-1.2/VarSelLCM/R/DesignOutput.R |only VarSelLCM-1.2/VarSelLCM/R/ICLexact.R | 30 - VarSelLCM-1.2/VarSelLCM/R/Imputation.R |only VarSelLCM-1.2/VarSelLCM/R/Print.R | 35 - VarSelLCM-1.2/VarSelLCM/R/RcppExports.R | 4 VarSelLCM-1.2/VarSelLCM/R/Summary.R | 43 + VarSelLCM-1.2/VarSelLCM/R/VSLCMGrlClasses.R |only VarSelLCM-1.2/VarSelLCM/R/VarSelLCM.R | 238 ++++------ VarSelLCM-1.2/VarSelLCM/R/withoutmixture.R |only VarSelLCM-1.2/VarSelLCM/data |only VarSelLCM-1.2/VarSelLCM/inst/include/Algorithm.h |only VarSelLCM-1.2/VarSelLCM/inst/include/AlgorithmContinuous.h |only VarSelLCM-1.2/VarSelLCM/inst/include/Data.h |only VarSelLCM-1.2/VarSelLCM/inst/include/DataContinuous.h |only VarSelLCM-1.2/VarSelLCM/inst/include/Param.h |only VarSelLCM-1.2/VarSelLCM/inst/include/ParamContinuous.h |only VarSelLCM-1.2/VarSelLCM/inst/include/XEM.h |only VarSelLCM-1.2/VarSelLCM/inst/include/XEMContinuous.h |only VarSelLCM-1.2/VarSelLCM/man/VSLCMcriteria-class.Rd | 3 VarSelLCM-1.2/VarSelLCM/man/VSLCMdataContinuous-class.Rd |only VarSelLCM-1.2/VarSelLCM/man/VSLCMmodel-class.Rd | 2 VarSelLCM-1.2/VarSelLCM/man/VSLCMparametersContinuous-class.Rd |only VarSelLCM-1.2/VarSelLCM/man/VSLCMpartitions-class.Rd | 2 VarSelLCM-1.2/VarSelLCM/man/VSLCMresultsContinuous-class.Rd |only VarSelLCM-1.2/VarSelLCM/man/VSLCMstrategy-class.Rd |only VarSelLCM-1.2/VarSelLCM/man/VarSeLCluster.Rd | 102 ++-- VarSelLCM-1.2/VarSelLCM/man/VarSelImputation.Rd |only VarSelLCM-1.2/VarSelLCM/man/VarSelLCM-package.Rd | 45 - VarSelLCM-1.2/VarSelLCM/man/banknote.Rd |only VarSelLCM-1.2/VarSelLCM/man/print-methods.Rd | 11 VarSelLCM-1.2/VarSelLCM/man/summary-methods.Rd | 13 VarSelLCM-1.2/VarSelLCM/src/Algorithm.cpp |only VarSelLCM-1.2/VarSelLCM/src/AlgorithmContinuous.cpp |only VarSelLCM-1.2/VarSelLCM/src/DataContinuous.cpp |only VarSelLCM-1.2/VarSelLCM/src/ParamContinuous.cpp |only VarSelLCM-1.2/VarSelLCM/src/RcppExports.cpp | 20 VarSelLCM-1.2/VarSelLCM/src/VarSelLCMmixte.cpp |only VarSelLCM-1.2/VarSelLCM/src/XEM.cpp |only VarSelLCM-1.2/VarSelLCM/src/XEMContinuous.cpp |only 54 files changed, 342 insertions(+), 305 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.3-2 dated 2015-05-04 and 0.3-3 dated 2015-06-10
InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/R/computeDelta.R |only InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/R/edgeRetention.R |only InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/R/edgeSelection.R |only InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/R/hiddenICE.R |only InvariantCausalPrediction-0.3-2/InvariantCausalPrediction/man/hiddenICE.Rd |only InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/DESCRIPTION | 10 +++--- InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/MD5 | 15 +++------- InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/NAMESPACE | 4 +- InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/man/ICP.Rd | 5 +-- InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/man/InvariantCausalPrediction-package.Rd | 2 - InvariantCausalPrediction-0.3-3/InvariantCausalPrediction/man/hiddenICP.Rd | 5 ++- 11 files changed, 18 insertions(+), 23 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Automated C Code Generation for Use with the 'deSolve' and
'bvpSolve' Packages
Description: Generates all necessary C functions allowing the user to work with the compiled-code interface of ode() and bvptwp(). The implementation supports "forcings" and "events". Also provides functions to symbolically compute Jacobians, sensitivity equations and adjoint sensitivities being the basis for sensitivity analysis.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@physik.uni-freiburg.de>
Diff between cOde versions 0.1 dated 2015-03-09 and 0.2 dated 2015-06-10
DESCRIPTION | 14 - MD5 | 36 ++-- NAMESPACE | 3 R/cOde.R | 351 ++++++++++++++++++++++++++++++++++++--------- R/derivedEquations.R | 71 +++++---- R/symbolics.R | 63 +++++--- R/tools.R |only inst/code |only inst/examples/example1.R | 15 + inst/examples/example2_2.R |only inst/examples/example3.R | 2 inst/examples/example4.R | 2 inst/examples/example5.R | 2 man/adjointSymb.Rd | 2 man/bvptwpC.Rd | 2 man/cOde-package.Rd | 2 man/funC.Rd | 42 ++++- man/loadDLL.Rd | 2 man/odeC.Rd | 15 + man/reduceSensitivities.Rd |only man/sensitivitiesSymb.Rd | 8 - 21 files changed, 472 insertions(+), 160 deletions(-)
Title: Posterior Predictive Checks of Coalescent Models
Description: Conducts posterior predictive checks of coalescent models using gene and species trees generated by 'BEAST' or '*BEAST'. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites: 'genealogicalSorting' and 'phybase'. To use these optional packages, the installation of the Python libraries 'NumPy' (>= 1.9.0) and 'DendroPy' (= 3.12.0) is required.
Author: Michael Gruenstaeudl, Noah Reid
Maintainer: Michael Gruenstaeudl <mi.gruenstaeudl@gmail.com>
Diff between P2C2M versions 0.6 dated 2015-01-30 and 0.7.6 dated 2015-06-10
P2C2M-0.6/P2C2M/R/calc.coal_liu.R |only P2C2M-0.6/P2C2M/R/calc.coal_reid.R |only P2C2M-0.6/P2C2M/R/corehelpers.repl.R |only P2C2M-0.6/P2C2M/R/loghelpers.dbg.R |only P2C2M-0.6/P2C2M/R/loghelpers.prnt1.R |only P2C2M-0.6/P2C2M/R/loghelpers.prnt2.R |only P2C2M-0.6/P2C2M/R/loghelpers.wrt1.R |only P2C2M-0.6/P2C2M/R/loghelpers.wrt2.R |only P2C2M-0.6/P2C2M/R/p2c2M.statcalc.R |only P2C2M-0.6/P2C2M/R/p2c2m.init.R |only P2C2M-0.6/P2C2M/R/readhelpers.constit.R |only P2C2M-0.6/P2C2M/R/readhelpers.extract.R |only P2C2M-0.6/P2C2M/R/readhelpers.meta.R |only P2C2M-0.6/P2C2M/R/readhelpers.parse.R |only P2C2M-0.6/P2C2M/R/stats.acrossGenes.R |only P2C2M-0.7.6/P2C2M/DESCRIPTION | 17 - P2C2M-0.7.6/P2C2M/MD5 | 84 ++--- P2C2M-0.7.6/P2C2M/R/P2C2M-internal.R | 2 P2C2M-0.7.6/P2C2M/R/calc.coal.R |only P2C2M-0.7.6/P2C2M/R/calc.gsi.R | 16 - P2C2M-0.7.6/P2C2M/R/calc.lcwt.R |only P2C2M-0.7.6/P2C2M/R/calc.ndc.R | 8 P2C2M-0.7.6/P2C2M/R/calc.parse.R | 39 +- P2C2M-0.7.6/P2C2M/R/calchelpers.brprob.R | 10 P2C2M-0.7.6/P2C2M/R/calchelpers.descend.R | 14 P2C2M-0.7.6/P2C2M/R/calchelpers.dmvparse.R | 43 +- P2C2M-0.7.6/P2C2M/R/calchelpers.gtreeparse.R | 10 P2C2M-0.7.6/P2C2M/R/calchelpers.nodetips.R | 34 +- P2C2M-0.7.6/P2C2M/R/calchelpers.probcalc.R | 12 P2C2M-0.7.6/P2C2M/R/corehelpers.metrics.R | 34 +- P2C2M-0.7.6/P2C2M/R/loghelpers.prntmngr.R |only P2C2M-0.7.6/P2C2M/R/ms.exec.R | 86 ++--- P2C2M-0.7.6/P2C2M/R/p2c2m.analyze.R | 285 ++++++++++-------- P2C2M-0.7.6/P2C2M/R/p2c2m.complete.R | 115 +++---- P2C2M-0.7.6/P2C2M/R/p2c2m.readstarb.R | 187 +++++------ P2C2M-0.7.6/P2C2M/R/readhelpers.extract_br_and_meta.R |only P2C2M-0.7.6/P2C2M/R/readhelpers.formatmeta.R |only P2C2M-0.7.6/P2C2M/R/readhelpers.makeCFtable.R |only P2C2M-0.7.6/P2C2M/R/readhelpers.parsetrees.R |only P2C2M-0.7.6/P2C2M/R/readtree.gtree.R | 80 +++-- P2C2M-0.7.6/P2C2M/R/readtree.phybase.R | 18 - P2C2M-0.7.6/P2C2M/R/readtree.stree.R | 113 ++++--- P2C2M-0.7.6/P2C2M/R/sourceDir.R | 2 P2C2M-0.7.6/P2C2M/R/stats.acrGenes.R |only P2C2M-0.7.6/P2C2M/R/stats.coord.R |only P2C2M-0.7.6/P2C2M/R/stats.main.R | 97 ++---- P2C2M-0.7.6/P2C2M/R/stats.perGene.R | 15 P2C2M-0.7.6/P2C2M/R/statshelpers.cv.R | 6 P2C2M-0.7.6/P2C2M/R/statshelpers.diffrnce.R | 6 P2C2M-0.7.6/P2C2M/R/statshelpers.qntls.R | 6 P2C2M-0.7.6/P2C2M/R/statshelpers.sigsgn.R | 6 P2C2M-0.7.6/P2C2M/build/vignette.rds |binary P2C2M-0.7.6/P2C2M/exec/parseBEAUTiXML_1.8.py | 110 ++---- P2C2M-0.7.6/P2C2M/inst/doc/P2C2M_CmdList.pdf |binary P2C2M-0.7.6/P2C2M/man/p2c2m.complete.Rd | 30 + 55 files changed, 758 insertions(+), 727 deletions(-)
Title: Structural Equation Models
Description: Functions for fitting general linear structural
equation models (with observed and latent variables) using the RAM approach,
and for fitting structural equations in observed-variable models by two-stage least squares.
Author: John Fox [aut, cre],
Zhenghua Nie [aut],
Jarrett Byrnes [aut],
Michael Culbertson [ctb],
Saikat DebRoy [ctb],
Michael Friendly [ctb],
Goodrich Benjamin [ctb],
Richard H. Jones [ctb],
Adam Kramer [ctb],
Georges Monette [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between sem versions 3.1-5 dated 2014-08-03 and 3.1-6 dated 2015-06-10
sem-3.1-5/sem/data/Klein.txt.bz2 |only sem-3.1-6/sem/DESCRIPTION | 29 -- sem-3.1-6/sem/MD5 | 46 +-- sem-3.1-6/sem/NAMESPACE | 9 sem-3.1-6/sem/NEWS | 10 sem-3.1-6/sem/R/bootSem.R | 37 +- sem-3.1-6/sem/R/cfa.R |only sem-3.1-6/sem/R/miSem.R | 94 +++--- sem-3.1-6/sem/R/modIndices.R | 95 ------ sem-3.1-6/sem/R/pathDiagram.R | 457 ++++++++++++++++++++++++-------- sem-3.1-6/sem/R/readMoments.R | 6 sem-3.1-6/sem/R/robust.R | 2 sem-3.1-6/sem/R/specifyModel.R | 79 ----- sem-3.1-6/sem/R/update.R | 9 sem-3.1-6/sem/data/Bollen.rda |binary sem-3.1-6/sem/data/CNES.rda |binary sem-3.1-6/sem/data/Klein.txt.gz |only sem-3.1-6/sem/data/Kmenta.txt.gz |binary sem-3.1-6/sem/data/Tests.rda |binary sem-3.1-6/sem/inst/etc/GreekLetters.txt |only sem-3.1-6/sem/man/bootSem.Rd | 21 - sem-3.1-6/sem/man/miSem.Rd | 42 +- sem-3.1-6/sem/man/pathDiagram.Rd | 243 +++++++++++++---- sem-3.1-6/sem/man/readMoments.Rd | 28 + sem-3.1-6/sem/man/sem.Rd | 40 ++ sem-3.1-6/sem/man/specifyModel.Rd | 116 +++++++- 26 files changed, 912 insertions(+), 451 deletions(-)
Title: Adapt Numerical Records to Fit (in)Equality Restrictions
Description: Based on (optionally sparse) quadratic optimization with the main algorithms implemented in C. Includes features for easy processing of many (smaller) records. The algorithm has been tested on fairly large optimization problems with up to a few million variables and several hundred thousand restrictions.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between rspa versions 0.1-6 dated 2014-11-26 and 0.1-7 dated 2015-06-10
DESCRIPTION | 21 ++++++++++----------- MD5 | 24 ++++++++++++++---------- NAMESPACE | 2 +- NEWS | 7 +++++-- build |only inst/doc |only man/adjust.Rd | 5 +++-- man/adjustRecords.Rd | 3 ++- man/adjusted.Rd | 3 ++- man/adjustedRecords.Rd | 3 ++- man/rspa-package.Rd | 3 ++- man/sparseConstraints.Rd | 9 +++++---- vignettes/getting_started.Rnw | 20 +++++++------------- 13 files changed, 53 insertions(+), 47 deletions(-)
Title: UCA Rcmdr Plug-in
Description: Some extension to Rcmdr (R Commander) made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrPlugin.UCA versions 2.0-3 dated 2015-06-09 and 2.0-4 dated 2015-06-10
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 15 ++++++++------- R/RcmdrPlugin.UCA.R | 6 ++++-- man/RcmdrPlugin.UCA-internal.Rd | 2 ++ man/RcmdrPlugin.UCA-package.Rd | 2 +- man/RcmdrPlugin.UCA.es-package.Rd | 2 +- 7 files changed, 25 insertions(+), 20 deletions(-)
More information about RcmdrPlugin.UCA at CRAN
Permanent link
Title: Analise Multivariada (Brazilian Portuguese)
Description: Pacote para Analise Multivariada, que possui funcoes que executam Analise de Correspondencia Simples (CA) e Multipla (MCA), Analise de Componentes Principais (PCA), Analise de Multiplos Fatores (MFA) para dados Quantitativos, Qualitativos, Frequencia (MFACT) e dados Mistos. Tambem possuim outras funcoes uteis para a Analise Multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.0 dated 2014-12-30 and 1.1 dated 2015-06-10
DESCRIPTION | 8 +++---- MD5 | 38 +++++++++++++++++----------------- R/MFA.R | 20 +++++++++--------- R/Plot.MFA.R | 4 +-- man/CA.Rd | 5 +--- man/DataFreq.Rd | 4 +-- man/DataMix.Rd | 1 man/DataQuali.Rd | 1 man/DataQuan.Rd | 3 -- man/Data_Cafes.Rd | 7 ++++-- man/Data_Individuos.Rd | 6 +++-- man/GSVD.Rd | 3 -- man/IM.Rd | 1 man/MFA.Rd | 37 +++++++++++++++++++-------------- man/MVar.pt-package.Rd | 54 +++++++++++++++++++++++++++++-------------------- man/NormData.Rd | 1 man/PCA.Rd | 5 +--- man/Plot.CA.Rd | 1 man/Plot.MFA.Rd | 1 man/Plot.PCA.Rd | 1 20 files changed, 105 insertions(+), 96 deletions(-)
Title: Pretty Scientific Plotting with Minor-Tick and log Minor-Tick
Support
Description: Functions to make useful (and pretty) plots for scientific plotting. Additional plotting features are added for base plotting, with particular emphasis on making attractive log axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between magicaxis versions 1.9.3 dated 2014-09-29 and 1.9.4 dated 2015-06-10
DESCRIPTION | 14 +++++----- MD5 | 28 ++++++++++----------- NEWS | 30 +++++++++++++++++----- R/magaxis.R | 19 +++++++++----- R/magbar.R | 3 +- R/magcon.R | 3 +- R/magerr.R | 57 +++++++++++++++++++++++++++++++------------ R/magmap.R | 32 ++++++++++++++++++++---- R/magplot.R | 17 +++--------- R/magrun.R | 3 +- man/magaxis.Rd | 26 +++++++++++-------- man/magicaxis-package.Rd | 12 ++++----- man/maglab.Rd | 8 +++--- man/magmap.Rd | 33 ++++++++++++++++++++++--- man/magplot.Rd | 62 +++++++++++++++++++++++++++++------------------ 15 files changed, 228 insertions(+), 119 deletions(-)
Title: Generalized Mann-Whitney Type Tests
Description: Generalized Mann-Whitney type tests based on probabilistic
indices and new diagnostic plots.
Author: Daniel Fischer , Hannu Oja
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between gMWT versions 0.9 dated 2014-08-06 and 1.0 dated 2015-06-10
DESCRIPTION | 13 ++++++------- MD5 | 13 +++++++------ NAMESPACE | 2 +- inst/CITATION |only inst/ChangeLog | 8 ++++++++ man/gMWT-package.Rd | 10 +++++----- man/gmw.Rd | 2 +- src/helpFunctions.cpp | 28 ++++++++++++++++++++++------ 8 files changed, 50 insertions(+), 26 deletions(-)
Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main
function is ggMarginal(), which can be used to add marginal
histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ggExtra versions 0.1.0 dated 2015-03-26 and 0.1.5.2 dated 2015-06-10
ggExtra-0.1.0/ggExtra/vignettes/overview.md |only ggExtra-0.1.5.2/ggExtra/DESCRIPTION | 16 +- ggExtra-0.1.5.2/ggExtra/MD5 | 32 +++-- ggExtra-0.1.5.2/ggExtra/NAMESPACE | 3 ggExtra-0.1.5.2/ggExtra/NEWS.md |only ggExtra-0.1.5.2/ggExtra/R/ggExtra.R | 7 + ggExtra-0.1.5.2/ggExtra/R/ggMarginal.R | 138 ++++++++++++++++++----- ggExtra-0.1.5.2/ggExtra/R/runExample.R |only ggExtra-0.1.5.2/ggExtra/README.md | 98 +++++++++------- ggExtra-0.1.5.2/ggExtra/inst/examples |only ggExtra-0.1.5.2/ggExtra/man/ggExtra.Rd | 10 + ggExtra-0.1.5.2/ggExtra/man/ggMarginal.Rd | 36 ++++-- ggExtra-0.1.5.2/ggExtra/man/plotCount.Rd | 2 ggExtra-0.1.5.2/ggExtra/man/print.ggExtraPlot.Rd | 2 ggExtra-0.1.5.2/ggExtra/man/removeGrid.Rd | 2 ggExtra-0.1.5.2/ggExtra/man/rotateTextX.Rd | 2 ggExtra-0.1.5.2/ggExtra/man/runExample.Rd |only ggExtra-0.1.5.2/ggExtra/vignettes/overview.Rmd | 53 ++++---- 18 files changed, 275 insertions(+), 126 deletions(-)
Title: R Console Bindings for the 'Domino Command-Line Client'
Description: A wrapper on top of the 'Domino Command-Line Client'. It lets you run 'Domino' commands (e.g., "run", "upload", "download") directly from your R environment. Under the hood, it uses R's system function to run the 'Domino' executable, which must be installed as a prerequisite. 'Domino' is a service that makes it easy to run your code on scalable hardware, with integrated version control and collaboration features designed for analytical workflows (see <http://www.dominoup.com> for more information).
Author: Jacek Glodek <jacek@theiterators.com>
Maintainer: Nick Elprin <nick@dominoup.com>
Diff between domino versions 0.2-6 dated 2015-04-15 and 0.2-7 dated 2015-06-10
DESCRIPTION | 10 ++++---- MD5 | 8 +++---- R/domino.R | 56 ++++++++++++++++++++++++++++++++------------------ man/domino-package.Rd | 4 +-- man/domino.run.Rd | 6 ++++- 5 files changed, 52 insertions(+), 32 deletions(-)
Title: Get Energy Data from the UK Dept of Energy and Climate Change
Description: Provides functions for retrieving energy statistics from
the United Kingdom Department of Energy and Climate Change and
related data sources. The current version focuses on total final
energy consumption statistics at the local authority, MSOA, and
LSOA geographies. Methods for calculating the generation mix of
grid electricity and its associated carbon intensity are also
provided.
Author: James Keirstead <j.keirstead@imperial.ac.uk>
Maintainer: James Keirstead <j.keirstead@imperial.ac.uk>
Diff between decctools versions 0.2.0 dated 2014-08-04 and 0.2.1 dated 2015-06-10
DESCRIPTION | 28 +++++---- MD5 | 22 +++---- NEWS | 11 +++ R/carbon-intensity.r | 138 +++++++++++++++++++++++++++---------------------- R/lad.r | 5 + R/utils.r | 10 +-- README.md | 8 +- inst/CITATION | 20 +++---- man/get_geo_lookup.Rd | 4 - man/get_grid_carbon.Rd | 2 man/get_grid_mix.Rd | 2 man/get_last_date.Rd | 4 + 12 files changed, 145 insertions(+), 109 deletions(-)
Title: Collection of Common Astronomical Conversion Routines and
Functions
Description: Contains a number of common astronomy conversion routines, particularly the HMS and degrees schemes, which can be fiddly to convert between on mass due to the textural nature of the former. It allows users to coordinate match datasets quickly. It also contains functions for various cosmological calculations.
Author: Aaron Robotham
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between celestial versions 1.2 dated 2015-01-10 and 1.3 dated 2015-06-10
DESCRIPTION | 17 +- MD5 | 54 ++++-- NAMESPACE | 1 NEWS | 10 + R/IAUID.R | 2 R/coordmatch.R |only R/cosdist.R | 377 +++++++++++++++++++++++++++++++++++++++++++---- R/cosgrow.R |only R/coshalo.R |only R/cosmap.R |only R/cosorb.R |only R/cosvar.R |only R/cosvol.R | 16 + R/deg2dms.R | 9 - R/deg2hms.R | 9 - R/dms2deg.R | 12 - R/hms2deg.R | 13 + R/skyarea.R | 5 R/sph2car.R |only data |only man/IAUID.Rd | 6 man/celestial-package.Rd | 13 - man/coordmatch.Rd |only man/cosdist.Rd | 140 +++++++++++++---- man/cosgrow.Rd |only man/coshalo.Rd |only man/cosmap.Rd |only man/cosorb.Rd |only man/cosref.Rd |only man/cosvar.Rd |only man/cosvol.Rd | 30 ++- man/deg2dms.Rd | 5 man/deg2hms.Rd | 13 - man/hms2deg.Rd | 8 man/skyarea.Rd | 21 +- man/sph2car.Rd |only 36 files changed, 611 insertions(+), 150 deletions(-)
Title: Process the Apache Web Server Log Combined Files
Description: Provides a function to process Apache Log Combined files. The main functionality is to extract data from log files to data frames.
Author: Diogo Silveira Mendonca
Maintainer: Diogo Silveira Mendonca <diogosmendonca@gmail.com>
Diff between ApacheLogProcessor versions 0.1.3 dated 2015-05-28 and 0.1.5 dated 2015-06-10
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ApacheLogProcessor.R | 17 +++++++++++++++++ 3 files changed, 23 insertions(+), 6 deletions(-)
More information about ApacheLogProcessor at CRAN
Permanent link
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.3.0 dated 2015-05-05 and 0.3.2 dated 2015-06-10
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++++--------------- NAMESPACE | 3 +++ R/domain.R | 6 +++--- R/linpoormed.R | 5 +---- R/linqsr.R | 1 + R/linrmpg.R | 5 +---- R/vardchanges.R | 2 +- R/vardchangespoor.R |only R/vardcros.R | 15 +++++++-------- R/vardcrospoor.R |only R/varpoord.R | 9 +++++---- inst/CITATION | 4 ++-- inst/NEWS | 4 ++++ man/vardchanges.Rd | 3 ++- man/vardchangespoor.Rd |only man/vardcros.Rd | 2 +- man/vardcrospoor.Rd |only man/vardpoor-package.Rd | 11 +++++++++-- man/varpoord.Rd | 4 ++-- 20 files changed, 65 insertions(+), 51 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions from Heng Li
<lh3@live.co.uk> (Heng Li wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 3.9 dated 2015-05-21 and 4.2 dated 2015-06-10
ChangeLog | 12 + DESCRIPTION | 8 - MD5 | 8 - R/seqminer.R | 6 src/rvMetaLoader.cpp | 382 +++++++++++++++++++++++++++++++++++++++------------ 5 files changed, 323 insertions(+), 93 deletions(-)
Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Pade versions 0.1-1 dated 2015-06-09 and 0.1-2 dated 2015-06-10
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- README.md | 12 ++++++------ inst/NEWS.Rd | 10 ++++++++++ man/Pade-package.Rd | 4 ++-- man/Pade.Rd | 22 +++++++++++----------- 6 files changed, 40 insertions(+), 30 deletions(-)
Title: Estimate a Log-Concave Probability Density from iid Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), compute the maximum likelihood estimator (MLE) of a density as well as a smoothed version of it under the assumption that the density is log-concave, see Rufibach (2007) and Duembgen and Rufibach (2009). The main function of the package is 'logConDens' that allows computation of the log-concave MLE and its smoothed version. In addition, we provide functions to compute (1) the value of the density and distribution function estimates (MLE and smoothed) at a given point (2) the characterizing functions of the estimator, (3) to sample from the estimated distribution, (5) to compute a two-sample permutation test based on log-concave densities, (6) the ROC curve based on log-concave estimates within cases and controls, including confidence intervals for given values of false positive fractions (7) computation of a confidence interval for the value of the true density at a fixed point. Finally, three datasets that have been used to illustrate log-concave density estimation are made available.
Author: Kaspar Rufibach <kaspar.rufibach@gmail.com> and Lutz Duembgen <duembgen@stat.unibe.ch>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>
Diff between logcondens versions 2.1.2 dated 2014-09-06 and 2.1.3 dated 2015-06-10
DESCRIPTION | 10 ++--- MD5 | 74 +++++++++++++++++++-------------------- NAMESPACE | 5 ++ NEWS | 4 ++ inst/doc/logcondens.pdf |binary man/Jfunctions.Rd | 2 - man/Lhat_eta.Rd | 2 - man/Local_LL.Rd | 2 - man/Local_LL_all.Rd | 2 - man/MLE.Rd | 2 - man/Q00.Rd | 2 - man/activeSetLogCon.Rd | 2 - man/activeSetRoutines.Rd | 2 - man/brightstar.Rd | 5 +- man/confIntBootLogConROC_t0.Rd | 2 - man/evaluateLogConDens.Rd | 2 - man/icmaLogCon.Rd | 4 +- man/intECDF.Rd | 4 +- man/intF.Rd | 4 +- man/isoMean.Rd | 2 - man/logConDens.Rd | 2 - man/logconTwoSample.Rd | 2 - man/logcondens-package.Rd | 10 ++--- man/maxDiffCDF.Rd | 2 - man/plot.dlc.Rd | 2 - man/preProcess.Rd | 2 - man/qloglin.Rd | 2 - man/quadDeriv.Rd | 2 - man/quantilesLogConDens.Rd | 2 - man/reparametrizations.Rd | 2 - man/rlogcon.Rd | 2 - man/robust.Rd | 4 +- man/summary.dlc.Rd | 2 - vignettes/plots/-plot1.pdf |binary vignettes/plots/-plot2.pdf |binary vignettes/plots/-plot2sample.pdf |binary vignettes/plots/-plotSimul.pdf |binary vignettes/plots/-sim1.pdf |binary 38 files changed, 87 insertions(+), 81 deletions(-)
Title: Bayesian Accrual Prediction
Description: Subject recruitment for medical research is challenging. Slow patient accrual leads to delay in research. Accrual monitoring during the process of recruitment is critical. Researchers need reliable tools to manage the accrual rate. We developed a Bayesian method that integrates researcher's experience on previous trials and data from the current study, providing reliable prediction on accrual rate for clinical studies. In this R package, we present functions for Bayesian accrual prediction which can be easily used by statisticians and clinical researchers.
Author: Yu Jiang, Cen Wu, Steve Simon, Matthew S. Mayo , Rama Raghavan, Byron J. Gajewski
Maintainer: Yu Jiang <yu.jiang@yale.edu>
Diff between accrual versions 1.0 dated 2014-02-24 and 1.1 dated 2015-06-10
DESCRIPTION | 16 +- MD5 | 18 +-- NAMESPACE | 1 R/accrual.R | 268 ++++++++++++++++++------------------------------- man/accrual-package.Rd | 12 +- man/accrual.T.Rd | 10 - man/accrual.T.plot.Rd |only man/accrual.gui.Rd | 2 man/accrual.n.Rd | 10 - man/accrual.n.plot.Rd |only man/accrual.plots.Rd | 2 11 files changed, 139 insertions(+), 200 deletions(-)