Title: Multiple Imputation for Interval Censored Data
Description: Implements multiple imputation for proportional hazards regression
with interval censored data or proportional sub-distribution hazards
regression for interval censored competing risks data. The main functions
allow to estimate survival function, cumulative incidence function, Cox
and Fine & Gray regression coefficients and associated variance-covariance
matrix. 'MIICD' functions call 'Surv', 'survfit' and 'coxph' from the
'survival' package, 'crprep' from the 'mstate' package, and 'mvrnorm' from
the 'MASS' package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord <mdelord@gmail.com>
Diff between MIICD versions 2.1 dated 2015-03-31 and 2.2 dated 2015-12-17
MIICD-2.1/MIICD/R/DA.ci.R |only MIICD-2.1/MIICD/R/DA.surv.R |only MIICD-2.1/MIICD/man/DA.ci.Rd |only MIICD-2.1/MIICD/man/DA.surv.Rd |only MIICD-2.1/MIICD/man/MIICD-package.Rd |only MIICD-2.1/MIICD/man/plot.DA_ci.Rd |only MIICD-2.1/MIICD/man/plot.DA_surv.Rd |only MIICD-2.2/MIICD/DESCRIPTION | 23 ++-- MIICD-2.2/MIICD/MD5 | 51 ++++---- MIICD-2.2/MIICD/NAMESPACE | 11 - MIICD-2.2/MIICD/R/ANDA.coxph.R | 35 +++--- MIICD-2.2/MIICD/R/ANDA.crreg.R | 26 ++-- MIICD-2.2/MIICD/R/BBCI.R |only MIICD-2.2/MIICD/R/BBS.R |only MIICD-2.2/MIICD/R/MI.ci.R | 148 ++++++++++++++----------- MIICD-2.2/MIICD/R/MI.ci_1.R |only MIICD-2.2/MIICD/R/MI.surv.R | 183 +++++++++++++++++++------------- MIICD-2.2/MIICD/R/MI.surv_1.R |only MIICD-2.2/MIICD/R/MIICD.coxph.R | 24 +--- MIICD-2.2/MIICD/R/MIICD.crreg.R | 27 ++-- MIICD-2.2/MIICD/R/PMDA.coxph.R | 73 ++++++------ MIICD-2.2/MIICD/R/PMDA.crreg.R | 25 ++-- MIICD-2.2/MIICD/man/ICCRD.Rd | 3 MIICD-2.2/MIICD/man/MI.ci.Rd | 38 +++--- MIICD-2.2/MIICD/man/MI.surv.Rd | 36 +++--- MIICD-2.2/MIICD/man/MIICD.coxph.Rd | 27 ++-- MIICD-2.2/MIICD/man/MIICD.crreg.Rd | 33 +++-- MIICD-2.2/MIICD/man/bcos.Rd | 3 MIICD-2.2/MIICD/man/plot.MIICD_coxph.Rd | 3 MIICD-2.2/MIICD/man/plot.MIICD_crreg.Rd | 3 MIICD-2.2/MIICD/man/plot.MI_ci.Rd | 3 MIICD-2.2/MIICD/man/plot.MI_surv.Rd | 9 - 32 files changed, 426 insertions(+), 358 deletions(-)
Title: A More Scalable Alternative to Venn and Euler Diagrams for
Visualizing Intersecting Sets
Description: Creates visualizations of intersecting sets using a novel matrix design,
along with visualizations of several common set, element and attribute
related tasks.
Author: Jake Conway [cre],
Nils Gehlenborg [aut]
Maintainer: Jake Conway <jake_conway@student.uml.edu>
Diff between UpSetR versions 1.0.0 dated 2015-10-19 and 1.0.1 dated 2015-12-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 6 ++++++ R/Matrix.R | 6 ++++-- 4 files changed, 16 insertions(+), 8 deletions(-)
Title: Modeling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Author: Guillaume Guenard, with contribution from Pierre Legendre
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>
Diff between MPSEM versions 0.2-6 dated 2014-12-02 and 0.3-1 dated 2015-12-17
MPSEM-0.2-6/MPSEM/inst/doc/MPSEM.Rmd |only MPSEM-0.2-6/MPSEM/vignettes/MPSEM.Rmd |only MPSEM-0.2-6/MPSEM/vignettes/MPSEM.bib |only MPSEM-0.2-6/MPSEM/vignettes/MPSEM.html |only MPSEM-0.3-1/MPSEM/DESCRIPTION | 10 +++++----- MPSEM-0.3-1/MPSEM/MD5 | 20 ++++++++++---------- MPSEM-0.3-1/MPSEM/NAMESPACE | 16 ++++++++++++++-- MPSEM-0.3-1/MPSEM/R/PEM.R | 7 +++++++ MPSEM-0.3-1/MPSEM/build/vignette.rds |binary MPSEM-0.3-1/MPSEM/inst/doc/MPSEM.R |only MPSEM-0.3-1/MPSEM/inst/doc/MPSEM.Rnw |only MPSEM-0.3-1/MPSEM/inst/doc/MPSEM.pdf |binary MPSEM-0.3-1/MPSEM/man/PEM.Rd | 20 ++++++++++++++++++-- MPSEM-0.3-1/MPSEM/vignettes/MPSEM.Rnw |only MPSEM-0.3-1/MPSEM/vignettes/PEM_with_MPSEM.bib |only 15 files changed, 54 insertions(+), 19 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 2.21 dated 2015-12-04 and 2.21-1 dated 2015-12-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/NEWS | 3 +++ inst/doc/extending.pdf |binary inst/doc/using-lsmeans.pdf |binary 6 files changed, 12 insertions(+), 9 deletions(-)
Title: Tools for Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation
of repeatabilities in measurements and matrices, and general evolutionary
quantitative genetics tools.
Author: Ana Paula Assis, Diogo Melo, Edgar Zanella, Fabio Machado, Guilherme
Garcia
Maintainer: Diogo Melo <diogro@usp.br>
Diff between evolqg versions 0.2-1 dated 2015-11-04 and 0.2-2 dated 2015-12-17
DESCRIPTION | 12 ++++++------ MD5 | 12 +++++++----- NAMESPACE | 3 +++ R/DriftTest.R | 4 ++-- R/RSProjection.R |only inst/tests/test.DriftTest.r | 20 ++++++++++++++++++++ inst/tests/test.MonteCarloStat.r | 9 +++++++++ man/RSProjection.Rd |only 8 files changed, 47 insertions(+), 13 deletions(-)
Title: Bayesian Canonical Correlation Analysis and Group Factor
Analysis
Description: Variational Bayesian algorithms for learning canonical correlation analysis (CCA), inter-battery factor analysis (IBFA), and group factor analysis (GFA). Inference with several random initializations can be run with the functions CCAexperiment() and GFAexperiment().
Author: Seppo Virtanen [aut, cre],
Eemeli Leppaaho [aut],
Arto Klami [aut]
Maintainer: Seppo Virtanen <s.virtanen@warwick.ac.uk>
Diff between CCAGFA versions 1.0.7 dated 2015-10-20 and 1.0.8 dated 2015-12-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ R/CCAGFA.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)