Title: Fits Piecewise Constant Models with Data-Adaptive Knots
Description: Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2014). Fused Lasso Additive Model. arXiv preprint arXiv:1409.5391.
Author: Ashley Petersen
Maintainer: Ashley Petersen <ajpete@uw.edu>
Diff between flam versions 2.0 dated 2015-06-25 and 3.0 dated 2015-07-26
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 3 +++ R/RcppExports.R | 7 +------ R/flam_fcns.R | 4 ++-- man/flam-package.rd | 4 ++-- src/RcppExports.cpp | 8 ++++---- src/fit.cpp | 30 +++++++++++++++--------------- 8 files changed, 39 insertions(+), 41 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares or REML by adding the function r() to formulas of lm and glm. A collection of text-book statistics for higher education is also included, e.g. modifications of the functions lm, glm and associated summaries from the package stats.
Author: Kristian Hovde Liland [aut, cre],
Solve Sæbø [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.0.8.5 dated 2015-03-11 and 1.0.9.2 dated 2015-07-26
DESCRIPTION | 10 ++++------ MD5 | 10 +++++----- NAMESPACE | 11 ++++++++++- R/lm.R | 13 ++++++------- R/mixlm.R | 19 ------------------- R/statistics.R | 11 ++++++----- 6 files changed, 31 insertions(+), 43 deletions(-)
Title: Clinical Trial Simulations
Description: Provides a general framework for clinical trial simulations based on the Clinical Scenario Evaluation (CSE) approach. The package supports a broad class of data models (including clinical trials with continuous, binary, survival-type and count-type endpoints as well as multivariate outcomes that are based on combinations of different endpoints), analysis strategies and commonly used evaluation criteria.
Author: Gautier Paux, Alex Dmitrienko.
Maintainer: Gautier Paux <gautier@paux.fr>
Diff between Mediana versions 1.0 dated 2015-07-26 and 1.0.1 dated 2015-07-26
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- R/Mediana.R | 10 +++++----- man/Criterion.Rd | 2 +- man/Mediana-package.Rd | 4 ++-- man/SampleSize.Rd | 2 +- 6 files changed, 19 insertions(+), 18 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 V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.18 dated 2015-06-01 and 2.19 dated 2015-07-26
DESCRIPTION | 13 ++- MD5 | 54 ++++++++-------- NAMESPACE | 10 ++- R/MCMC-support.R | 18 +++-- R/aovlist-support.R | 28 +++++--- R/glht-support.R | 3 R/helpers.R | 145 +++++++++++++++++++++++++++++++------------- R/lsmeans.R | 20 +++--- R/lsmip.R | 8 +- R/nonlin-support.R | 4 - R/ordinal-support.R | 8 +- R/ref.grid.R | 12 +-- R/rms-support.R | 8 +- inst/NEWS | 21 ++++++ inst/doc/extending.R | 16 ++-- inst/doc/extending.pdf |binary inst/doc/extending.rnw | 12 ++- inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 2 man/extending.Rd | 22 ++++++ man/glht.Rd | 3 man/lsmeans-package.Rd | 2 man/lsmeans.Rd | 45 ++++++++++--- man/models.Rd | 8 +- man/ref.grid.Rd | 15 +++- tests/tests1.Rout.save | 4 - vignettes/extending.rnw | 12 ++- vignettes/using-lsmeans.rnw | 2 28 files changed, 338 insertions(+), 157 deletions(-)
Title: Synergy/Antagonism Analyses of Drug Combinations
Description: A comprehensive synergy/antagonism analyses of drug combinations with
quality graphics and data. The analyses can be performed by Bliss independence and Loewe
additivity models. COMBIA provides improved statistical analysis and makes only very weak assumption of data variability
while calculating bootstrap intervals (BIs). Finally, package saves analyzed data,
2D and 3D plots ready to use in research publications. COMBIA does not require manual
data entry. Data can be directly input from wetlab experimental platforms
for example fluostar, automated robots etc. One needs to call a single function only
to perform all analysis (examples are provided with sample data).
Author: Muhammad Kashif
Maintainer: Muhammad Kashif <Muhammad.Kashif@medsci.uu.se>
Diff between COMBIA versions 1.0-3 dated 2015-07-25 and 1.0-4 dated 2015-07-26
DESCRIPTION | 6 ++-- MD5 | 24 ++++++++-------- R/COMBIA.R | 42 +++++++++++++---------------- inst/raw/FluoOptima_384_2014-03-28test.xls |binary inst/raw/testData.xls |binary man/applyLoewe.Rd | 8 ++--- man/calculateSynergy.Rd | 2 - man/loeweModel.Rd | 4 +- man/readMacSynergyValues.Rd | 2 - man/readOtherValues.Rd | 4 +- man/removeOutliers.Rd | 4 +- man/synAntPlot.Rd | 2 - man/synergySignificant.Rd | 6 ++-- 13 files changed, 51 insertions(+), 53 deletions(-)
Title: 'Rcpp' Integration of Different "Ziggurat" Normal RNG
Implementations
Description: The Ziggurat generator for normally distributed random numbers,
originally proposed by Marsaglia and Tsang (JSS, 2000), has been improved
upon a few times starting with Leong et al (JSS, 2005). This package provides
an aggregation in order to compare different implementations. The goal is to
provide an 'faster but good enough' alternative for use with R and C++ code.
The package is still in an early state. Unless you know what you are doing,
sticking with the generators provided by R may be a good idea as these have
been extremely diligently tested.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppZiggurat versions 0.1.2 dated 2014-01-26 and 0.1.3 dated 2015-07-26
ChangeLog | 49 +++++ DESCRIPTION | 14 - MD5 | 56 +++--- NAMESPACE | 7 R/RcppExports.R | 4 README.md | 18 +- build/vignette.rds |binary demo/benchmark.R | 6 inst/NEWS.Rd | 19 ++ inst/doc/RcppZiggurat.R | 14 + inst/doc/RcppZiggurat.Rnw | 98 +++++++---- inst/doc/RcppZiggurat.bib | 14 - inst/doc/RcppZiggurat.pdf |binary inst/include/Ziggurat.h | 37 ++-- inst/include/ZigguratLZLLV.h | 12 - inst/include/ZigguratMT.h | 12 - inst/include/ZigguratR.h | 30 +-- inst/include/ZigguratV1.h | 33 +-- inst/include/ZigguratV1b.h | 35 ++-- man/ziggurat.Rd | 4 src/Makevars | 2 src/Makevars.win | 3 src/RcppExports.cpp | 334 +++++++++++++++------------------------- src/ziggurat.cpp | 8 tests/zigguratTest.Rout.save | 10 - tests/zigguratTestAll.R |only tests/zigguratTestAll.Rout.save |only vignettes/RcppZiggurat.RData |binary vignettes/RcppZiggurat.Rnw | 98 +++++++---- vignettes/RcppZiggurat.bib | 14 - 30 files changed, 510 insertions(+), 421 deletions(-)
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Diff between mvSLOUCH versions 1.1.5 dated 2015-01-21 and 1.2 dated 2015-07-26
DESCRIPTION | 11 +++-- MD5 | 44 ++++++++++++---------- NAMESPACE | 8 ++-- R/PhyloSDEestim.R | 20 +--------- R/estimMAXLIK.R | 45 ++-------------------- R/evolmodelest.R |only R/getESS.R |only R/modelparams.R | 2 - R/modelparamssummary.R | 3 + R/simulVasicekproc.R | 60 +++++++++++++++--------------- R/simulVasicekprocphyl.R | 14 +++---- man/BrownianMotionModel.Rd | 31 ++++++++++----- man/SummarizeBM.Rd | 29 ++++++++++---- man/SummarizeMVSLOUCH.Rd | 29 +++++++++----- man/SummarizeOUCH.Rd | 30 ++++++++++----- man/estimate.evolutionary.model.Rd |only man/fitch.mvsl.Rd | 31 ++++++++++----- man/generate.model.setups.Rd |only man/mvSLOUCH-internal.Rd | 2 + man/mvSLOUCH-package.Rd | 54 +++++++++++++++++++++------ man/mvslouchModel.Rd | 73 ++++++++++++++++++++++--------------- man/ouchModel.Rd | 43 ++++++++++++++------- man/simulBMProcPhylTree.Rd | 10 +++-- man/simulMVSLOUCHProcPhylTree.Rd | 9 +++- man/simulOUCHProcPhylTree.Rd | 23 ++++++++--- 25 files changed, 329 insertions(+), 242 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.6.1 dated 2015-07-17 and 1.6.2 dated 2015-07-26
DESCRIPTION | 10 +++--- MD5 | 20 ++++++------ NAMESPACE | 2 - NEWS | 8 ++++ R/helper.r | 6 ++- R/zzz.r | 2 - build/vignette.rds |binary inst/doc/checkmate.html | 78 ++++++++++++++++++------------------------------ src/any_nan.c | 4 -- src/checks.c | 2 - src/is_integerish.c | 4 +- 11 files changed, 60 insertions(+), 76 deletions(-)