Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, MPTinR can fit a wide variety of other cognitive models such as SDT models (see fit.model). MPTinR supports multicore fitting and FIA calculation using the snowfall package. MPTinR can generate data from a model for e.g., simulation or parametric bootstrap and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann
Diff between MPTinR versions 1.6.3 dated 2014-10-21 and 1.7.5 dated 2015-03-22
DESCRIPTION | 14 MD5 | 28 - NEWS | 65 ++- R/bmpt.fia.R | 2 R/fit.mpt.old.R | 4 R/fit.mptinr.R | 31 + R/select.mpt.R | 20 - data/d.broeder.rda |binary data/rb.fig1.data.rda |binary data/rb.fig2.data.rda |binary man/fit.mpt.Rd | 814 +++++++++++++++++++++++++------------------------- man/fit.mptinr.Rd | 2 man/gen.data.Rd | 3 man/select.mpt.Rd | 15 src/RcppExports.cpp | 58 +-- 15 files changed, 548 insertions(+), 508 deletions(-)
Title: Model Confidence Set Procedure
Description: Perform the model confidence set procedure of Hansen et al (2011).
Author: Leopoldo Catania & Mauro Bernardi
Maintainer: Leopoldo Catania
Diff between MCS versions 0.1.0 dated 2014-11-18 and 0.1.1 dated 2015-03-22
DESCRIPTION | 6 - MD5 | 8 +- R/MCS.R | 227 ++++++++++++++++++++++++++------------------------------- man/LossVaR.Rd | 2 man/LossVol.Rd | 4 - 5 files changed, 115 insertions(+), 132 deletions(-)
Title: Import Stata 13 Data Files
Description: Function to read and write the Stata 13 file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre],
R Core Team [cph]
Maintainer: Sebastian Jeworutzki
Diff between readstata13 versions 0.5-3 dated 2015-02-11 and 0.6 dated 2015-03-22
CHANGELOG | 4 + DESCRIPTION | 6 - MD5 | 33 +++++---- NAMESPACE | 2 R/dbcal.R |only R/save.R | 4 - R/tools.R | 167 ++++++++++++++++++++++++++++------------------ README.md |only inst/extdata/sp500.stbcal |only inst/extdata/statacar.dta |binary man/as.caldays.Rd |only man/get.label.Rd | 4 - man/get.origin.codes.Rd | 8 +- man/set.label.Rd | 9 +- man/set.lang.Rd | 10 ++ man/stbcal.Rd |only src/RcppExports.cpp | 32 +++----- src/rcpp_readstata.cpp | 3 src/rcpp_savestata.cpp | 5 - src/statadefines.h | 10 +- 20 files changed, 177 insertions(+), 120 deletions(-)
Title: Adaptive, Sine-Multitaper Power Spectral Density Estimation
Description: Produces power spectral density estimates through iterative
refinement of the optimal number of sine-tapers at each frequency. This
optimization procedure is based on the method of Riedel and Sidorenko
(1995), which minimizes the Mean Square Error (sum of variance and bias)
at each frequency, but modified for computational stability.
Author: Andrew J. Barbour and Robert L. Parker, with contributions from David
Myer
Maintainer: Andrew J. Barbour
Diff between psd versions 1.0-0 dated 2015-03-18 and 1.0-1 dated 2015-03-22
psd-1.0-0/psd/vignettes/fftw.synctex.gz |only psd-1.0-0/psd/vignettes/normalization.synctex.gz |only psd-1.0-0/psd/vignettes/psd_overview.synctex.gz |only psd-1.0-1/psd/DESCRIPTION | 13 +- psd-1.0-1/psd/MD5 | 81 ++++++++---------- psd-1.0-1/psd/R/func_pspectrum.R | 12 +- psd-1.0-1/psd/inst/Examples/rdex_confint.R | 12 ++ psd-1.0-1/psd/inst/Examples/rdex_constraintapers.R | 11 +- psd-1.0-1/psd/inst/Examples/rdex_normalization.R | 25 +++-- psd-1.0-1/psd/inst/Examples/rdex_parabolicweights.R | 13 +- psd-1.0-1/psd/inst/Examples/rdex_pilotspec.R | 11 +- psd-1.0-1/psd/inst/Examples/rdex_prewhiten.R | 34 ++++--- psd-1.0-1/psd/inst/Examples/rdex_psdcore.R | 12 +- psd-1.0-1/psd/inst/Examples/rdex_psdenv.R | 12 ++ psd-1.0-1/psd/inst/Examples/rdex_pspectrum.R | 64 ++------------ psd-1.0-1/psd/inst/Examples/rdex_riedsid.R | 14 ++- psd-1.0-1/psd/inst/Examples/rdex_spec.R | 20 ++-- psd-1.0-1/psd/inst/Examples/rdex_spectralproperties.R | 26 +---- psd-1.0-1/psd/inst/Examples/rdex_splinegrad.R | 9 +- psd-1.0-1/psd/inst/Examples/rdex_tapers.R | 4 psd-1.0-1/psd/inst/Examples/rdex_utilities.R | 3 psd-1.0-1/psd/inst/NEWS.Rd | 19 ++++ psd-1.0-1/psd/inst/doc/fftw.pdf |binary psd-1.0-1/psd/inst/doc/normalization.pdf |binary psd-1.0-1/psd/inst/doc/psd_overview.pdf |binary psd-1.0-1/psd/man/as.tapers.Rd | 4 psd-1.0-1/psd/man/parabolic_weights.Rd | 13 +- psd-1.0-1/psd/man/pilot_spec.Rd | 11 +- psd-1.0-1/psd/man/prewhiten.Rd | 34 ++++--- psd-1.0-1/psd/man/psd-environment.Rd | 12 ++ psd-1.0-1/psd/man/psd-normalization.Rd | 25 +++-- psd-1.0-1/psd/man/psd-utilities.Rd | 3 psd-1.0-1/psd/man/psdcore.Rd | 12 +- psd-1.0-1/psd/man/pspectrum.Rd | 76 +++------------- psd-1.0-1/psd/man/riedsid.Rd | 14 ++- psd-1.0-1/psd/man/spec-methods.Rd | 20 ++-- psd-1.0-1/psd/man/spec_confint.Rd | 12 ++ psd-1.0-1/psd/man/spectral_properties.Rd | 26 +---- psd-1.0-1/psd/man/splineGrad.Rd | 9 +- psd-1.0-1/psd/man/tapers-constraints.Rd | 11 +- psd-1.0-1/psd/src/RcppExports.cpp | 4 psd-1.0-1/psd/src/resample_fft.cpp | 23 +++-- psd-1.0-1/psd/tests/testthat/test-fft.R | 40 +++++--- 43 files changed, 383 insertions(+), 361 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel
Diff between mvMORPH versions 1.0.3 dated 2015-03-17 and 1.0.4 dated 2015-03-22
DESCRIPTION | 6 +++--- MD5 | 39 ++++++++++++++++++++------------------- R/fun.r | 2 +- R/mvBM.r | 4 ++-- R/mvEB.r | 4 ++-- R/mvSHIFT.r | 2 +- R/testLRT.r | 2 +- man/mv.Precalc.Rd | 4 ++-- man/mvBM.Rd | 2 +- man/mvEB.Rd | 18 +++++++++++------- man/mvSHIFT.Rd | 2 +- man/mvSIM.Rd | 4 ++-- src/covar-matrix-simmap.c | 2 +- src/covar.h |only src/kronecker.c | 4 +++- src/mvmorph-covar-mat.c | 2 +- src/mvmorph-covar-ou-sparse.c | 2 +- src/mvmorph.h | 14 -------------- src/pic_loglik_mvmorph.c | 8 ++++---- src/weight-matrix-mvmorph.c | 2 +- src/weight-matrix-simmap.c | 2 +- 21 files changed, 59 insertions(+), 66 deletions(-)
Title: Visualizing the Performance of Scoring Classifiers
Description: ROC graphs, sensitivity/specificity curves, lift charts,
and precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR
is a flexible tool for creating cutoff-parameterized 2D
performance curves by freely combining two from over 25
performance measures (new performance measures can be added
using a standard interface). Curves from different
cross-validation or bootstrapping runs can be averaged by
different methods, and standard deviations, standard errors or
box plots can be used to visualize the variability across the
runs. The parameterization can be visualized by printing cutoff
values at the corresponding curve positions, or by coloring the
curve according to cutoff. All components of a performance plot
can be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with
only three commands and reasonable default values for all
optional parameters.
Author: Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer
Maintainer: Billy Aung Myint
Diff between ROCR versions 1.0-5 dated 2013-05-16 and 1.0-6 dated 2015-03-22
ROCR-1.0-5/ROCR/README.unittests |only ROCR-1.0-5/ROCR/unittests |only ROCR-1.0-6/ROCR/DESCRIPTION | 16 +++++++++------- ROCR-1.0-6/ROCR/MD5 | 14 ++++---------- ROCR-1.0-6/ROCR/data/ROCR.hiv.rda |binary ROCR-1.0-6/ROCR/data/ROCR.simple.rda |binary ROCR-1.0-6/ROCR/data/ROCR.xval.rda |binary 7 files changed, 13 insertions(+), 17 deletions(-)
Title: Latent Position and Cluster Models for Statistical Networks
Description: Fit and simulate latent position and cluster models for statistical networks.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut],
Susan M. Shortreed [ctb],
Jeremy Tantrum [ctb],
Peter D. Hoff [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky
Diff between latentnet versions 2.6.0 dated 2014-12-24 and 2.7.0 dated 2015-03-22
latentnet-2.6.0/latentnet/R/ergmm.midarrow.R |only latentnet-2.6.0/latentnet/man/latentnet.Rd |only latentnet-2.7.0/latentnet/ChangeLog | 57 +++- latentnet-2.7.0/latentnet/DESCRIPTION | 18 - latentnet-2.7.0/latentnet/LICENSE | 4 latentnet-2.7.0/latentnet/MD5 | 193 ++++++++-------- latentnet-2.7.0/latentnet/NAMESPACE | 30 ++ latentnet-2.7.0/latentnet/R/InitErgmm.fixed.R | 12 latentnet-2.7.0/latentnet/R/InitErgmm.latent.R | 9 latentnet-2.7.0/latentnet/R/InitErgmm.random.R | 9 latentnet-2.7.0/latentnet/R/P.alloc.R | 9 latentnet-2.7.0/latentnet/R/bayesmbc.MCMC.C.R | 9 latentnet-2.7.0/latentnet/R/bayesmbc.R | 9 latentnet-2.7.0/latentnet/R/ergmm.MCMC.C.R | 10 latentnet-2.7.0/latentnet/R/ergmm.R | 13 - latentnet-2.7.0/latentnet/R/ergmm.defaults.R | 9 latentnet-2.7.0/latentnet/R/ergmm.draw.utils.R |only latentnet-2.7.0/latentnet/R/ergmm.families.R | 9 latentnet-2.7.0/latentnet/R/ergmm.geodesicmatrix.R | 9 latentnet-2.7.0/latentnet/R/ergmm.get.model.R | 9 latentnet-2.7.0/latentnet/R/ergmm.initvals.R | 11 latentnet-2.7.0/latentnet/R/ergmm.latent.effects.R | 9 latentnet-2.7.0/latentnet/R/ergmm.par.R | 11 latentnet-2.7.0/latentnet/R/ergmm.permutation.R | 9 latentnet-2.7.0/latentnet/R/ergmm.probs.R | 53 +--- latentnet-2.7.0/latentnet/R/ergmm.statseval.R | 40 +-- latentnet-2.7.0/latentnet/R/ergmm.tuner.R | 9 latentnet-2.7.0/latentnet/R/gof.ergmm.R | 9 latentnet-2.7.0/latentnet/R/label.switching.R | 9 latentnet-2.7.0/latentnet/R/latent.R | 9 latentnet-2.7.0/latentnet/R/mcmc.diagnostics.ergmm.R | 15 - latentnet-2.7.0/latentnet/R/merge.ergmm.R | 11 latentnet-2.7.0/latentnet/R/plot.ergmm.R | 23 - latentnet-2.7.0/latentnet/R/predict.ergmm.R | 9 latentnet-2.7.0/latentnet/R/print.ergmm.R | 9 latentnet-2.7.0/latentnet/R/print.ergmm.model.R | 9 latentnet-2.7.0/latentnet/R/procrustes.R | 19 - latentnet-2.7.0/latentnet/R/simulate.ergmm.R | 9 latentnet-2.7.0/latentnet/R/summary.ergmm.R | 37 +-- latentnet-2.7.0/latentnet/R/utilities.R | 9 latentnet-2.7.0/latentnet/R/zzz.R | 13 - latentnet-2.7.0/latentnet/data/davis.RData |binary latentnet-2.7.0/latentnet/inst/CITATION | 40 +++ latentnet-2.7.0/latentnet/man/as.mcmc.list.ergmm.Rd | 9 latentnet-2.7.0/latentnet/man/davis.Rd | 16 - latentnet-2.7.0/latentnet/man/ergmm.Rd | 15 - latentnet-2.7.0/latentnet/man/ergmm.control.Rd | 9 latentnet-2.7.0/latentnet/man/ergmm.drawpie.Rd |only latentnet-2.7.0/latentnet/man/ergmm.object.Rd | 9 latentnet-2.7.0/latentnet/man/ergmm.par.list.object.Rd | 10 latentnet-2.7.0/latentnet/man/ergmm.prior.Rd | 9 latentnet-2.7.0/latentnet/man/families.ergmm.Rd | 10 latentnet-2.7.0/latentnet/man/gof.ergmm.Rd | 12 latentnet-2.7.0/latentnet/man/latentnet-internal.Rd | 128 ---------- latentnet-2.7.0/latentnet/man/latentnet-package.Rd |only latentnet-2.7.0/latentnet/man/mcmc.diagnostics.ergmm.Rd | 9 latentnet-2.7.0/latentnet/man/merge.ergmm.Rd | 9 latentnet-2.7.0/latentnet/man/plot.ergmm.Rd | 9 latentnet-2.7.0/latentnet/man/predict.ergmm.Rd | 9 latentnet-2.7.0/latentnet/man/sampson.Rd | 9 latentnet-2.7.0/latentnet/man/simulate.ergmm.Rd | 9 latentnet-2.7.0/latentnet/man/summary.ergmm.Rd | 82 +++++- latentnet-2.7.0/latentnet/man/terms.ergmm.Rd | 11 latentnet-2.7.0/latentnet/man/tribes.Rd | 9 latentnet-2.7.0/latentnet/src/P_alloc.c | 9 latentnet-2.7.0/latentnet/src/P_alloc.h | 9 latentnet-2.7.0/latentnet/src/ergmm_families.c | 9 latentnet-2.7.0/latentnet/src/ergmm_families.h | 9 latentnet-2.7.0/latentnet/src/ergmm_latent_effects.c | 9 latentnet-2.7.0/latentnet/src/ergmm_latent_effects.h | 9 latentnet-2.7.0/latentnet/src/ergmm_probs.c | 11 latentnet-2.7.0/latentnet/src/ergmm_probs.h | 9 latentnet-2.7.0/latentnet/src/ergmm_sampler.c | 11 latentnet-2.7.0/latentnet/src/ergmm_sampler.h | 9 latentnet-2.7.0/latentnet/src/ergmm_structs.h | 9 latentnet-2.7.0/latentnet/src/ergmm_updaters.c | 9 latentnet-2.7.0/latentnet/src/ergmm_updaters.h | 9 latentnet-2.7.0/latentnet/src/ergmm_utils.c | 9 latentnet-2.7.0/latentnet/src/ergmm_utils.h | 9 latentnet-2.7.0/latentnet/src/kl_switch.c | 9 latentnet-2.7.0/latentnet/src/kl_switch.h | 9 latentnet-2.7.0/latentnet/src/matrix_utils.c | 9 latentnet-2.7.0/latentnet/src/matrix_utils.h | 9 latentnet-2.7.0/latentnet/src/mbc_sampler.c | 9 latentnet-2.7.0/latentnet/src/mbc_sampler.h | 9 latentnet-2.7.0/latentnet/src/mvnorm.c | 9 latentnet-2.7.0/latentnet/src/mvnorm.h | 9 latentnet-2.7.0/latentnet/src/post_predict.c | 11 latentnet-2.7.0/latentnet/src/post_predict.h | 9 latentnet-2.7.0/latentnet/src/procrustes.c | 9 latentnet-2.7.0/latentnet/src/procrustes.h | 9 latentnet-2.7.0/latentnet/src/wishart.c | 9 latentnet-2.7.0/latentnet/src/wishart.h | 9 latentnet-2.7.0/latentnet/tests/examples.R | 9 latentnet-2.7.0/latentnet/tests/missing.R | 9 latentnet-2.7.0/latentnet/tests/nolatent.R | 9 latentnet-2.7.0/latentnet/tests/nomcmc.R | 9 latentnet-2.7.0/latentnet/tests/nomixing.R | 9 latentnet-2.7.0/latentnet/tests/normal.R | 15 - latentnet-2.7.0/latentnet/tests/onlymcmc.R | 9 100 files changed, 378 insertions(+), 1131 deletions(-)
Title: A Tool for Downloading Functional Traits Data for Plant Species
Description: Plant ecologists often need to collect "traits" data
about plant species which are often scattered among various
databases: TR8 contains a set of tools which take care of
automatically retrieving some of those functional traits data
for plant species from publicly available databases (Biolflor,
The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg
values for Italian Flora, Mycorrhizal intensity databases, Catminat).
The TR8 name, inspired by "car plates" jokes, was chosen since
it both reminds of the main object of the package and is
extremely short to type.
Author: Gionata Bocci
Maintainer: Gionata Bocci
Diff between TR8 versions 0.9.12 dated 2015-03-04 and 0.9.13 dated 2015-03-22
DESCRIPTION | 11 +- MD5 | 55 +++++++------- NAMESPACE | 2 R/LEDA.R | 12 +-- R/biolflor.R | 5 + R/catminat.R |only R/catminat_download.R |only R/ecoflora.R | 46 +++++++++++- R/leda_download.R | 2 R/local_storage.R | 15 ++-- R/mycoflor.R | 15 ++-- R/results.R | 2 R/tr8.R | 96 ++++++++++++++++++++------ R/tr8_gui.R | 10 +- data/available_tr8.rda |binary data/column_list.rda |binary data/traits_eco.rda |binary inst/CITATION | 9 +- inst/doc/Expanding_TR8.pdf |binary inst/doc/TR8.R | 40 +++++++--- inst/doc/TR8.Rnw | 166 +++++++++++++++++++++++++++++++-------------- inst/doc/TR8.pdf |binary inst/doc/TR8_workflow.pdf |binary man/TR8-package.Rd | 19 ++++- man/Tr8-class.Rd | 7 + man/column_list.Rd | 126 +++++++++++++++++++++++----------- man/tr8.Rd | 11 ++ vignettes/TR8.Rnw | 166 +++++++++++++++++++++++++++++++-------------- vignettes/temp.ps |only vignettes/tr8.bib | 11 ++ 30 files changed, 592 insertions(+), 234 deletions(-)
Title: Regularized Cox Model
Description: Cox model regularized with net (L1 and Laplacian), elastic-net (L1 and L2) or lasso (L1) penalty. In addition, it can truncate the estimate by a hard threshold, which is selected simultaneously with other tuning parameters. Moreover, it can handle the adaptive version of these regularization forms, such as adaptive lasso and net adjusting for signs of linked coefficients. The package uses one-step coordinate descent algorithm and runs extremely fast by taking into account the sparsity structure of coefficients.
Author: Xiang Li, Donglin Zeng and Yuanjia Wang
Maintainer: Xiang Li
Diff between Coxnet versions 0.1 dated 2015-03-17 and 0.1-1 dated 2015-03-22
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ man/Coxnet-package.Rd | 6 +++--- man/Coxnet.Rd | 8 ++++---- man/coxsplit.Rd | 8 +++----- man/print.Coxnet.Rd | 1 - src/Coxnet.cpp | 2 +- 7 files changed, 22 insertions(+), 25 deletions(-)