Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories, a method for
variable selection based on the SVD, Bézier lines with arrows complementing the
ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.3 dated 2016-01-15 and 1.3.1 dated 2016-02-07
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS | 4 ++++ 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Metric Unfolding
Description: Multidimensional unfolding using Schoeneman's algorithm for metric
and Procrustes rotation of unfolding results.
Author: Martin Elff
Maintainer: Martin Elff <martin@elff.eu>
Diff between munfold versions 0.3-3 dated 2015-01-27 and 0.3.4 dated 2016-02-07
munfold-0.3-3/munfold/inst/NEWS |only munfold-0.3.4/munfold/DESCRIPTION | 16 ++++++++-------- munfold-0.3.4/munfold/MD5 | 6 +++--- munfold-0.3.4/munfold/NAMESPACE | 4 ++++ munfold-0.3.4/munfold/inst/ChangeLog |only 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Tools for Management of Survey Data and the Presentation of
Analysis Results
Description: One of the aims of this package is to make life easier for
useRs who deal with survey data sets. It provides an
infrastructure for the management of survey data including
value labels, definable missing values, recoding of variables,
production of code books, and import of (subsets of) SPSS and
Stata files. Further, it provides functionality to produce
tables and data frames of arbitrary descriptive statistics and
(almost) publication-ready tables of regression model
estimates, which can be exported to LaTeX and HTML.
Author: Martin Elff (with contributions from Christopher N. Lawrence, Dave Atkins, Jason W. Morgan, Achim Zeileis)
Maintainer: Martin Elff <memisc@elff.eu>
Diff between memisc versions 0.99.3.2 dated 2016-01-25 and 0.99.5 dated 2016-02-07
DESCRIPTION | 8 MD5 | 47 +- NAMESPACE | 9 R/AllClasses.R | 17 R/AllInternalGenerics.R | 2 R/item-more-methods-Date.R |only R/item-more-methods-datetime.R | 28 + R/mtable-format-delim.R | 2 R/mtable-manip.R | 4 build/vignette.rds |binary inst/ChangeLog | 13 inst/NEWS.Rd | 6 inst/doc/anes48.Rmd | 16 inst/doc/anes48.html | 149 ++++---- inst/doc/ftable-matrix.Rmd | 2 inst/doc/ftable-matrix.html | 18 inst/doc/items.Rmd | 29 - inst/doc/items.html | 83 ++-- inst/doc/mtable-html.Rmd | 4 inst/doc/mtable-html.html | 755 +++++++++++++++++++++++++++++------------ man/items.Rd | 9 vignettes/anes48.Rmd | 16 vignettes/ftable-matrix.Rmd | 2 vignettes/items.Rmd | 29 - vignettes/mtable-html.Rmd | 4 25 files changed, 814 insertions(+), 438 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre],
Maxime Herv\'e [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.22 dated 2016-01-26 and 2.22-1 dated 2016-02-07
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/NEWS | 3 +++ inst/doc/using-lsmeans.pdf |binary 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Nested Block Designs for Unstructured Treatments
Description: Constructs nested and crossed block designs
for unstructured treatment sets with arbitrary replication not necessarily all equal.
Blocks can be nested to any required depth of nesting and blocks are optimized
hierarchically from the top down with successive nested blocks strata optimized within
the levels of all preceding blocks strata. Block sizes are all equal in any one stratum if the number
of blocks in that stratum exactly divides the number of plots, otherwise they differ by at most one plot.
The design output is a data table showing a randomised allocation of treatments to blocks together with
plans showing the allocation of treatments to blocks for each block in the bottom stratum of the design.
D and A-efficiency factors are shown for each stratum together with A-efficiency upper bounds,
where available.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 1.9 dated 2015-11-23 and 2.0 dated 2016-02-07
blocksdesign-1.9/blocksdesign/build |only blocksdesign-1.9/blocksdesign/inst/doc/blocksdesign.Rmd |only blocksdesign-1.9/blocksdesign/vignettes |only blocksdesign-2.0/blocksdesign/DESCRIPTION | 29 blocksdesign-2.0/blocksdesign/MD5 | 14 blocksdesign-2.0/blocksdesign/R/blocks.r | 928 +++++++------- blocksdesign-2.0/blocksdesign/R/blocksdesign-package.r | 18 blocksdesign-2.0/blocksdesign/inst/doc/blocksdesign.R |only blocksdesign-2.0/blocksdesign/man/blocks.Rd | 131 + blocksdesign-2.0/blocksdesign/man/blocksdesign-package.Rd | 18 10 files changed, 613 insertions(+), 525 deletions(-)
Title: Multinomial Probit Bayesian Additive Regression Trees
Description: Fits Multinomial Probit Bayesian Additive Regression Trees.
Author: Bereket Kindo [aut, cre]
Maintainer: Bereket Kindo <bpkindo@gmail.com>
Diff between mpbart versions 0.1 dated 2016-02-06 and 0.2 dated 2016-02-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/funs.cpp | 4 ++-- src/rmnpMDA.cpp | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Bayesian Treed Gaussian Process Models
Description: Bayesian nonstationary, semiparametric nonlinear regression
and design by treed Gaussian processes (GPs) with jumps to the limiting
linear model (LLM). Special cases also implemented include Bayesian
linear models, CART, treed linear models, stationary separable and
isotropic GPs, and GP single-index models. Provides 1-d and 2-d plotting functions
(with projection and slice capabilities) and tree drawing, designed for
visualization of tgp-class output. Sensitivity analysis and
multi-resolution models are supported. Sequential experimental
design and adaptive sampling functions are also provided, including ALM,
ALC, and expected improvement. The latter supports derivative-free
optimization of noisy black-box functions.
Author: Robert B. Gramacy <rbgramacy@chicagobooth.edu> and Matt A. Taddy <taddy@chicagobooth.edu>
Maintainer: Robert B. Gramacy <rbgramacy@chicagobooth.edu>
Diff between tgp versions 2.4-11 dated 2014-12-08 and 2.4-14 dated 2016-02-07
ChangeLog | 23 ++++++++ DESCRIPTION | 12 ++-- MD5 | 106 +++++++++++++++++++-------------------- NAMESPACE | 9 +++ build/vignette.rds |binary data/exp2d.rda |binary inst/doc/tgp.Rnw | 16 ++--- inst/doc/tgp.pdf |binary inst/doc/tgp2.pdf |binary man/btgp.Rd | 2 man/default.itemps.Rd | 2 man/exp2d.Rd | 2 man/exp2d.Z.Rd | 2 man/exp2d.rand.Rd | 2 man/friedman.1.data.Rd | 2 man/interp.loess.Rd | 2 man/itemps.Rd | 2 man/mapT.Rd | 2 man/optim.tgp.Rd | 2 man/partition.Rd | 2 man/plot.tgp.Rd | 2 man/predict.tgp.Rd | 2 man/tgp-internal.Rd | 2 man/tgp-package.Rd | 2 man/tgp.default.params.Rd | 2 man/tgp.design.Rd | 2 man/tgp.trees.Rd | 2 src/all_draws.c | 18 +++--- src/corr.cc | 22 ++++---- src/dopt.c | 6 +- src/exp.cc | 18 +++--- src/exp_sep.cc | 24 ++++---- src/gen_covar.c | 1 src/gp.cc | 124 +++++++++++++++++++++++----------------------- src/lh.c | 6 +- src/lik_post.c | 7 +- src/matern.cc | 26 ++++----- src/matrix.c | 76 ++++++++++++++-------------- src/matrix.h | 4 - src/model.cc | 112 ++++++++++++++++++++--------------------- src/mr_exp_sep.cc | 32 +++++------ src/mstructs.cc | 6 +- src/params.cc | 18 +++--- src/predict.c | 15 ++--- src/rand_draws.c | 9 +-- src/rand_pdf.c | 2 src/rhelp.c | 32 +++++------ src/rhelp.h | 22 ++++---- src/sim.cc | 30 +++++------ src/temper.cc | 28 +++++----- src/tgp.cc | 48 ++++++++--------- src/tree.cc | 41 +++++++-------- vignettes/tgp.Rnw | 16 ++--- vignettes/tgp.bib | 11 ++++ 54 files changed, 505 insertions(+), 451 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Mixed model equation solver allowing the specification of variance covariance structures of random effects and residual structures. ML/REML estimates are obtained using the Average Information and/or Expectation-Maximization algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominant and epistatic relationship structures.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between sommer versions 1.1 dated 2016-01-24 and 1.2 dated 2016-02-07
CHANGELOG |only DESCRIPTION | 8 - MD5 | 74 ++++++----- NAMESPACE | 16 +- R/A.mat.R | 311 ++++++++++++++++++++++++----------------------- R/AI.R | 324 ++++++++++++++++++++++++++++++++++---------------- R/AI2.R |only R/AI3.R |only R/D.mat.R | 53 ++++++-- R/E.mat.R | 10 - R/EM.R | 41 ++++-- R/EMMA.R | 13 +- R/atcg1234.R |only R/design.score.R |only R/fdr.R | 85 +++---------- R/hdm.R | 41 ++---- R/map.plot2.R | 277 +++++++++++++++++++++++------------------- R/mmer.R | 118 ++++++++++-------- R/mmer2.R | 42 +++++- R/poe.R | 152 +++++++++++------------ R/score.calc.R | 117 ++++++------------ data/PolyData.RData |only data/datalist |only inst |only man/A.mat.Rd | 8 + man/AI.Rd | 11 + man/AI2.Rd |only man/AI3.Rd |only man/CPdata.Rd | 1 man/D.mat.Rd | 4 man/E.mat.Rd | 4 man/EM.Rd | 2 man/EMMA.Rd | 3 man/HDdata.Rd | 11 + man/PolyData.Rd |only man/atcg1234.Rd |only man/design.score.Rd |only man/fdr.Rd | 29 +++- man/hdm.Rd | 15 +- man/mmer.Rd | 29 +++- man/mmer2.Rd | 13 +- man/randef.Rd |only man/score.calc.Rd | 22 +-- man/sommer-package.Rd | 10 - man/wheatLines.Rd | 3 45 files changed, 1052 insertions(+), 795 deletions(-)
Title: Miscellaneous Tools for Reproducible Research
Description: Tools to load 'R' packages
and automatically generate BibTeX files citing them as well as load and
cache plain-text and 'Excel' formatted data stored on 'GitHub', and
from other sources.
Author: Christopher Gandrud [aut, cre]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between repmis versions 0.4.4 dated 2015-06-03 and 0.5 dated 2016-02-07
DESCRIPTION | 13 ++-- MD5 | 34 ++++++------ NAMESPACE | 10 +++ NEWS | 5 + R/InstallOldPackages.R | 2 R/LoadandCite.R | 1 R/source_DropboxData.R | 122 +++++++++++++--------------------------------- R/source_GitHubData.R | 17 +++--- R/utils.R | 8 ++- README.md | 16 ++---- man/InstallOldPackages.Rd | 2 man/LoadandCite.Rd | 2 man/git_stamp.Rd | 2 man/scan_https.Rd | 2 man/set_valid_wd.Rd | 10 +++ man/source_DropboxData.Rd | 70 +------------------------- man/source_XlsxData.Rd | 2 man/source_data.Rd | 2 18 files changed, 118 insertions(+), 202 deletions(-)
Title: Read and Write BAM (Binary Alignment) Files
Description: Provides an interface to functions of the 'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
Diff between rbamtools versions 2.13.0 dated 2016-02-02 and 2.14.3 dated 2016-02-07
DESCRIPTION | 9 MD5 | 31 +-- R/rbamtools.r | 3 inst/doc/rbamtools.pdf |binary man/bamAlign-class.Rd | 1 man/bamHeader-class.Rd | 1 man/bamReader-class.Rd | 1 man/bamWriter-class.Rd | 1 man/getHeaderText-methods.Rd | 1 man/headerProgram-class.Rd | 1 man/headerReadGroup-class.Rd | 1 man/rbamtools-package.Rd | 2 man/refSeqDict-class.Rd | 1 src/data_frame.h | 13 - tests/test-all.R | 1 tests/test_genome_partition.r |only vignettes/rbamtools.Rnw | 402 +++++++++++++++++++++--------------------- 17 files changed, 231 insertions(+), 238 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
Diff between nodiv versions 1.1.2 dated 2015-10-26 and 1.1.3 dated 2016-02-07
DESCRIPTION | 10 +- MD5 | 28 ++++--- NAMESPACE | 8 +- R/Add_to_data_object.R | 160 +++++++++++++++++++++---------------------- R/General_figure_functions.R | 85 +++++++++++++++++++--- R/Methods_for_data_objects.R | 70 ++++++++++++++---- R/Prepare_data.R | 2 R/colors.R | 9 +- R/two_color_map.R |only inst/CITATION | 2 man/Nspecies.Rd | 3 man/add_sitestat.Rd | 7 + man/nodiv-package.Rd | 6 - man/phyplot.Rd |only man/plot_points.Rd | 27 ++++++- man/read.tree.Rd |only man/two_color_map.Rd |only 17 files changed, 280 insertions(+), 137 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.5-0 dated 2015-10-27 and 3.5-1 dated 2016-02-07
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ R/auc.R | 29 ++++++----------------------- R/cv.ncvreg.R | 6 +++++- R/cv.ncvsurv.R | 9 +++++---- README.md | 3 +++ man/auc.Rd | 24 ++++++++++++------------ man/cv.ncvreg.Rd | 4 ++++ man/ncvreg-package.Rd | 4 ++-- 10 files changed, 59 insertions(+), 56 deletions(-)
More information about MixedDataImpute at CRAN
Permanent link
Title: Multiple Imputation by Distance Aided Donor Selection
Description: Contains the function mice.impute.midastouch(). Technically this function is to be run from within the 'mice' package (van Buuren et al. 2011), type ??mice. It substitutes the method 'pmm' within mice by 'midastouch'. The authors have shown that 'midastouch' is superior to default 'pmm'. Many ideas are based on Siddique / Belin 2008's MIDAS.
Author: Philipp Gaffert [aut, cre],
Florian Meinfelder [aut],
Volker Bosch [aut]
Maintainer: Philipp Gaffert <philipp.gaffert@web.de>
Diff between midastouch versions 1.1 dated 2016-01-12 and 1.3 dated 2016-02-07
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/mice.impute.midastouch.R | 2 +- man/mice.impute.midastouch.Rd | 4 +++- 4 files changed, 12 insertions(+), 10 deletions(-)
Title: Ensembles of Caret Models
Description: Functions for creating ensembles of caret models: caretList
and caretStack. caretList is a convenience function for fitting multiple
caret::train models to the same dataset. caretStack will make linear or
non-linear combinations of these models, using a caret::train model as a
meta-model, and caretEnsemble will make a robust linear combination of
models using a glm.
Author: Zachary A. Deane-Mayer [aut, cre],
Jared E. Knowles [aut]
Maintainer: Zachary A. Deane-Mayer <zach.mayer@gmail.com>
Diff between caretEnsemble versions 1.0.0 dated 2015-01-16 and 2.0.0 dated 2016-02-07
caretEnsemble-1.0.0/caretEnsemble/R/OptRMSE.R |only caretEnsemble-1.0.0/caretEnsemble/R/optAUC.R |only caretEnsemble-1.0.0/caretEnsemble/inst/testdata |only caretEnsemble-1.0.0/caretEnsemble/man/autoplot.caretEnsemble.Rd |only caretEnsemble-1.0.0/caretEnsemble/man/fortify.caretEnsemble.Rd |only caretEnsemble-1.0.0/caretEnsemble/man/greedOptAUC.Rd |only caretEnsemble-1.0.0/caretEnsemble/man/greedOptRMSE.Rd |only caretEnsemble-1.0.0/caretEnsemble/man/metricsSD.Rd |only caretEnsemble-1.0.0/caretEnsemble/man/predict.caretEnsemble.Rd |only caretEnsemble-1.0.0/caretEnsemble/man/safeOptAUC.Rd |only caretEnsemble-1.0.0/caretEnsemble/tests/testthat/test-optimizers.R |only caretEnsemble-2.0.0/caretEnsemble/DESCRIPTION | 40 caretEnsemble-2.0.0/caretEnsemble/MD5 | 144 +- caretEnsemble-2.0.0/caretEnsemble/NAMESPACE | 65 - caretEnsemble-2.0.0/caretEnsemble/R/S3GenericExtenstions.R |only caretEnsemble-2.0.0/caretEnsemble/R/caretEnsemble-package.R |only caretEnsemble-2.0.0/caretEnsemble/R/caretEnsemble.R | 516 ++------ caretEnsemble-2.0.0/caretEnsemble/R/caretList.R | 123 +- caretEnsemble-2.0.0/caretEnsemble/R/caretStack.R | 135 +- caretEnsemble-2.0.0/caretEnsemble/R/helper_functions.R | 198 +-- caretEnsemble-2.0.0/caretEnsemble/README.md | 25 caretEnsemble-2.0.0/caretEnsemble/build/vignette.rds |binary caretEnsemble-2.0.0/caretEnsemble/data |only caretEnsemble-2.0.0/caretEnsemble/inst/data-raw/build_test_data.R | 135 -- caretEnsemble-2.0.0/caretEnsemble/inst/doc/caretEnsemble-intro.R | 132 +- caretEnsemble-2.0.0/caretEnsemble/inst/doc/caretEnsemble-intro.Rmd | 135 +- caretEnsemble-2.0.0/caretEnsemble/inst/doc/caretEnsemble-intro.html | 531 ++++---- caretEnsemble-2.0.0/caretEnsemble/man/autoplot.Rd |only caretEnsemble-2.0.0/caretEnsemble/man/bestPreds.Rd |only caretEnsemble-2.0.0/caretEnsemble/man/c.caretList.Rd |only caretEnsemble-2.0.0/caretEnsemble/man/c.train.Rd |only caretEnsemble-2.0.0/caretEnsemble/man/caretEnsemble.Rd | 21 caretEnsemble-2.0.0/caretEnsemble/man/caretList.Rd | 24 caretEnsemble-2.0.0/caretEnsemble/man/caretModelSpec.Rd | 4 caretEnsemble-2.0.0/caretEnsemble/man/caretStack.Rd | 10 caretEnsemble-2.0.0/caretEnsemble/man/check_bestpreds_indexes.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/check_bestpreds_obs.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/check_bestpreds_preds.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/check_bestpreds_resamples.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/check_caretList_classes.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/check_caretList_model_types.Rd | 4 caretEnsemble-2.0.0/caretEnsemble/man/data.Rd |only caretEnsemble-2.0.0/caretEnsemble/man/dotplot.caretStack.Rd | 12 caretEnsemble-2.0.0/caretEnsemble/man/extractBestPreds.Rd | 4 caretEnsemble-2.0.0/caretEnsemble/man/extractCaretTarget.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/extractCaretTarget.default.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/extractCaretTarget.formula.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/extractModFrame.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/extractModRes.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/extractModelTypes.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/fortify.Rd |only caretEnsemble-2.0.0/caretEnsemble/man/is.caretEnsemble.Rd |only caretEnsemble-2.0.0/caretEnsemble/man/is.caretList.Rd |only caretEnsemble-2.0.0/caretEnsemble/man/is.caretStack.Rd |only caretEnsemble-2.0.0/caretEnsemble/man/makePredObsMatrix.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/methodCheck.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/metrics.Rd | 41 caretEnsemble-2.0.0/caretEnsemble/man/multiResiduals.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/plot.caretEnsemble.Rd | 4 caretEnsemble-2.0.0/caretEnsemble/man/plot.caretStack.Rd | 10 caretEnsemble-2.0.0/caretEnsemble/man/predict.caretList.Rd | 6 caretEnsemble-2.0.0/caretEnsemble/man/predict.caretStack.Rd | 25 caretEnsemble-2.0.0/caretEnsemble/man/print.caretStack.Rd | 10 caretEnsemble-2.0.0/caretEnsemble/man/residuals.caretEnsemble.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/summary.caretEnsemble.Rd | 6 caretEnsemble-2.0.0/caretEnsemble/man/summary.caretStack.Rd | 10 caretEnsemble-2.0.0/caretEnsemble/man/trControlCheck.Rd | 4 caretEnsemble-2.0.0/caretEnsemble/man/tuneCheck.Rd | 2 caretEnsemble-2.0.0/caretEnsemble/man/varImp.caretEnsemble.Rd | 8 caretEnsemble-2.0.0/caretEnsemble/man/wtd.sd.Rd | 8 caretEnsemble-2.0.0/caretEnsemble/tests/testthat/test-S3-generic-extensions.R |only caretEnsemble-2.0.0/caretEnsemble/tests/testthat/test-a-skip.R |only caretEnsemble-2.0.0/caretEnsemble/tests/testthat/test-caretList.R | 283 +++- caretEnsemble-2.0.0/caretEnsemble/tests/testthat/test-caretStack.R | 114 + caretEnsemble-2.0.0/caretEnsemble/tests/testthat/test-ensemble.R | 417 ++---- caretEnsemble-2.0.0/caretEnsemble/tests/testthat/test-ensembleMethods.R | 609 +++------- caretEnsemble-2.0.0/caretEnsemble/tests/testthat/test-helper_functions.R | 196 +-- caretEnsemble-2.0.0/caretEnsemble/tests/testthat/test-lintr.R |only caretEnsemble-2.0.0/caretEnsemble/tests/testthat/test-parallel.R |only caretEnsemble-2.0.0/caretEnsemble/vignettes/caretEnsemble-intro.Rmd | 135 +- 80 files changed, 2025 insertions(+), 2151 deletions(-)
Title: Bayesian Sampling for Stick-Breaking Mixtures
Description: This is a bare-bones implementation of sampling algorithms
for a variety of Bayesian stick-breaking (marginally DP)
mixture models, including particle learning and Gibbs sampling
for static DP mixtures, particle learning for dynamic BAR
stick-breaking, and DP mixture regression. The software is
designed to be easy to customize to suit different situations
and for experimentation with stick-breaking models. Since
particles are repeatedly copied, it is not an especially
efficient implementation.
Author: Matt Taddy <taddy@chicagobooth.edu>
Maintainer: Matt Taddy <taddy@chicagobooth.edu>
Diff between Bmix versions 0.5 dated 2015-04-01 and 0.6 dated 2016-02-07
DESCRIPTION | 8 +++----- MD5 | 12 ++++++------ NAMESPACE | 2 ++ src/matrix.cc | 5 ++--- src/mix.cc | 2 ++ src/particle.cc | 3 ++- src/rhelp.c | 1 - 7 files changed, 17 insertions(+), 16 deletions(-)
Title: The Bayesian Dynamic Conditional Correlation GARCH Model
Description: Bayesian estimation of dynamic conditional correlation GARCH model for multivariate time series volatility (Fioruci, J.A., Ehlers, R.S. and Andrade-Filho, M.G., (2014), DOI:10.1080/02664763.2013.839635).
Author: Jose A Fiorucci <jafioruci@gmail.com>, Ricardo S Ehlers <ehlers@icmc.usp.br>, Francisco Louzada <louzada@icmc.usp.br>
Maintainer: Jose A Fiorucci <jafioruci@gmail.com>
Diff between bayesDccGarch versions 1.2 dated 2015-07-30 and 2.0 dated 2016-02-07
ChangeLog | 4 DESCRIPTION | 12 +- MD5 | 17 ++-- NAMESPACE | 11 +- R/mainFunctions.R | 177 +++++++++++++++++++++++++++++++++++++------ man/bayesDccGarch-package.Rd | 45 ++++++---- man/bayesDccGarch.Rd | 78 +++++++++++------- man/plot.bayesDccGarch.Rd |only man/plotVol.Rd | 9 +- src/bayesDccGarch.c | 83 +++++++++++++++++++- 10 files changed, 342 insertions(+), 94 deletions(-)
Title: Structural Equation Modelling in R with OpenMx
Description: Create, run, and report structural equation and twin models quickly.
If you're just starting out, try typing ?umx.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.1.0 dated 2015-12-10 and 1.1.1 dated 2016-02-07
DESCRIPTION | 21 - MD5 | 196 ++++++------ NAMESPACE | 16 + NEWS | 29 + R/build_run_modify.r | 446 ++++++++++++++++++++++++---- R/fit_and_reporting.r | 496 +++++++++++++++++++++++++++---- R/misc_and_utility.r | 507 +++++++++++++++++++++++--------- R/xmu.r | 40 +- README.md | 25 - man/RMSEA.MxModel.Rd | 4 man/RMSEA.Rd | 4 man/RMSEA.summary.mxmodel.Rd | 4 man/confint.MxModel.Rd | 4 man/dl_from_dropbox.Rd | 6 man/extractAIC.MxModel.Rd | 4 man/logLik.Rd | 4 man/plot.MxModel.Rd | 4 man/reliability.Rd | 2 man/residuals.MxModel.Rd | 6 man/summaryAPA.Rd | 23 + man/umx.Rd | 17 - man/umxACE.Rd | 32 +- man/umxACESexLim.Rd | 20 - man/umxACEcov.Rd |only man/umxCF_SexLim.Rd | 14 man/umxCI.Rd | 5 man/umxCI_boot.Rd | 4 man/umxCP.Rd | 19 - man/umxCompare.Rd | 5 man/umxCov2cor.Rd | 2 man/umxCovData.Rd | 5 man/umxEval.Rd | 2 man/umxExpCov.Rd | 7 man/umxExpMeans.Rd | 7 man/umxFactor.Rd | 3 man/umxFitIndices.Rd | 5 man/umxGxE.Rd | 30 + man/umxGxE_window.Rd | 14 man/umxHetCor.Rd | 11 man/umxIP.Rd | 19 - man/umxPadAndPruneForDefVars.Rd | 3 man/umxPlotACE.Rd | 3 man/umxPlotACEcov.Rd |only man/umxPlotCP.Rd | 14 man/umxPlotGxE.Rd | 14 man/umxRAM.Rd | 27 + man/umxStandardizeModel.Rd | 4 man/umxSummary.MxModel.Rd | 4 man/umxSummaryACE.Rd | 52 ++- man/umxSummaryACEcov.Rd |only man/umxSummaryCP.Rd | 14 man/umxSummaryGxE.Rd | 14 man/umxSummaryIP.Rd | 14 man/umx_APA_pval.Rd | 11 man/umx_RAM_ordinal_objective.Rd | 3 man/umx_SQL_from_Excel.Rd |only man/umx_as_numeric.Rd | 3 man/umx_check_model.Rd | 2 man/umx_check_parallel.Rd | 1 man/umx_cont_2_ordinal.Rd | 1 man/umx_cor.Rd | 7 man/umx_cov2raw.Rd | 1 man/umx_drop_ok.Rd | 5 man/umx_fake_data.Rd | 14 man/umx_find_object.Rd | 2 man/umx_get_checkpoint.Rd | 1 man/umx_get_cores.Rd | 21 - man/umx_get_optimizer.Rd | 6 man/umx_has_CIs.Rd | 2 man/umx_has_been_run.Rd | 2 man/umx_has_square_brackets.Rd | 2 man/umx_is_MxModel.Rd | 2 man/umx_is_cov.Rd | 2 man/umx_lower2full.Rd | 2 man/umx_make_TwinData.Rd |only man/umx_make_bin_cont_pair_data.Rd | 5 man/umx_merge_CIs.Rd | 3 man/umx_move_file.Rd | 6 man/umx_open.Rd | 7 man/umx_pb_note.Rd | 3 man/umx_print.Rd | 2 man/umx_read_lower.Rd | 3 man/umx_rename_file.Rd | 3 man/umx_reorder.Rd | 5 man/umx_residualize.Rd | 4 man/umx_round.Rd | 3 man/umx_scale.Rd | 5 man/umx_scale_wide_twin_data.Rd | 5 man/umx_set_auto_run.Rd |only man/umx_set_checkpoint.Rd | 1 man/umx_set_cores.Rd | 20 - man/umx_set_optimizer.Rd | 12 man/umx_standardize_ACE.Rd | 1 man/umx_standardize_ACEcov.Rd |only man/umx_standardize_CP.Rd | 1 man/umx_standardize_IP.Rd | 1 man/umx_string_to_algebra.Rd | 2 man/umx_swap_a_block.Rd | 3 man/umx_time.Rd | 5 man/umx_trim.Rd | 5 man/xmuLabel_Matrix.Rd | 2 tests/testthat/test_umxACE.r |only tests/testthat/test_umx_set_cores.r |only tests/testthat/test_umx_set_optimizer.r |only 104 files changed, 1759 insertions(+), 663 deletions(-)
Title: Tufte's Styles for R Markdown Documents
Description: Provides R Markdown output formats to use Tufte styles for PDF and HTML output.
Author: Yihui Xie [aut, cre],
JJ Allaire [aut],
Dave Liepmann [ctb] (Tufte CSS in
inst/rmarkdown/templates/tufte_html/resources),
RStudio, Inc. [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tufte versions 0.1 dated 2016-01-20 and 0.2 dated 2016-02-07
DESCRIPTION | 8 ++-- MD5 | 12 ++++-- NEWS.md |only README.md | 2 - inst/NEWS.Rd |only inst/rmarkdown/templates/tufte_ctex |only inst/rmarkdown/templates/tufte_handout/resources/tufte-handout.tex | 19 ++++++++++ inst/rmarkdown/templates/tufte_html/skeleton/skeleton.Rmd | 1 8 files changed, 33 insertions(+), 9 deletions(-)