Title: Spatial and Network Based Individual Level Models for Epidemics
Description: Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Author: Vineetha Warriyar. K. V. and Rob Deardon
Maintainer: Vineetha Warriyar. K. V. <vineethawarriyar.kod@ucalgary.ca>
Diff between EpiILM versions 1.4.1 dated 2018-02-18 and 1.4.2 dated 2018-03-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/epidata.Rd | 6 +++--- man/epimcmc.Rd | 14 +++++++------- 4 files changed, 17 insertions(+), 17 deletions(-)
Title: EBGM Scores for Mining Large Contingency Tables
Description: An implementation of DuMouchel's (1999)
<doi:10.1080/00031305.1999.10474456> Bayesian data mining method for the
market basket problem. Calculates Empirical Bayes Geometric Mean (EBGM) and
quantile scores from the posterior distribution using the Gamma-Poisson
Shrinker (GPS) model to find unusually large cell counts in large, sparse
contingency tables. Can be used to find unusually high reporting rates of
adverse events associated with products. In general, can be used to mine any
database where the co-occurrence of two variables or items is of interest.
Also calculates relative and proportional reporting ratios. Builds on the work
of the 'PhViD' package, from which much of the code is derived. Some of the
added features include stratification to adjust for confounding variables and
data squashing to improve computational efficiency. Now includes an
implementation of the EM algorithm for hyperparameter estimation loosely
derived from the 'mederrRank' package.
Author: John Ihrie [cre, aut],
Travis Canida [aut],
Ismaïl Ahmed [ctb] (author of 'PhViD' package (derived code)),
Antoine Poncet [ctb] (author of 'PhViD' package),
Sergio Venturini [ctb] (author of 'mederrRank' package (derived code))
Maintainer: John Ihrie <John.Ihrie@fda.hhs.gov>
Diff between openEBGM versions 0.3.0 dated 2017-11-15 and 0.4.0 dated 2018-03-09
DESCRIPTION | 19 - MD5 | 59 ++-- NAMESPACE | 2 NEWS | 10 R/f_EM_helpers.R |only R/f_EM_hyperEstimation.R |only R/f_EM_scoreFunctions.R |only R/f_EM_updateTheta.R |only R/f_checkInputs.R | 381 ++++++++++++++++---------- R/f_dataSquashing.R | 4 R/f_hyperConfIntervals.R |only R/f_hyperEstimation.R | 92 ------ R/openEBGM.R | 10 build/vignette.rds |binary inst/CITATION |only inst/doc/x1_introAndDataPrepVignette.Rmd | 114 ++++--- inst/doc/x1_introAndDataPrepVignette.html | 62 +++- inst/doc/x2_rawDataProcessingVignette.html | 4 inst/doc/x3_hyperParameterVignette.R | 26 + inst/doc/x3_hyperParameterVignette.Rmd | 99 +++++- inst/doc/x3_hyperParameterVignette.html | 109 ++++++- inst/doc/x4_posteriorCalculationVignette.Rmd | 4 inst/doc/x4_posteriorCalculationVignette.html | 8 inst/doc/x5_openEBGMObjectVignette.html | 18 - man/autoHyper.Rd | 7 man/exploreHypers.Rd | 9 man/hyperEM.Rd |only man/openEBGM.Rd | 10 man/squashData.Rd | 4 tests/testthat/testB_Squashing.R | 2 tests/testthat/testHypers.R | 162 +++++++++-- vignettes/x1_introAndDataPrepVignette.Rmd | 114 ++++--- vignettes/x3_hyperParameterVignette.Rmd | 99 +++++- vignettes/x4_posteriorCalculationVignette.Rmd | 4 34 files changed, 955 insertions(+), 477 deletions(-)
Title: Multivariate Independent Comparison of Observations
Description: A procedure for comparing multivariate samples associated with
different groups. It uses principal component analysis to convert
multivariate observations into a set of linearly uncorrelated statistical
measures, which are then compared using a number of statistical methods. The
procedure is independent of the distributional properties of samples and
automatically selects features that best explain their differences, avoiding
manual selection of specific points or summary statistics. It is appropriate
for comparing samples of time series, images, spectrometric measures or
similar multivariate observations.
Author: Nuno Fachada [aut, cre]
Maintainer: Nuno Fachada <faken@fakenmc.com>
Diff between micompr versions 1.0.2 dated 2017-06-24 and 1.1.0 dated 2018-03-09
DESCRIPTION | 16 ++++++------- LICENSE | 2 - MD5 | 46 +++++++++++++++++++------------------- R/assumptions.R | 26 ++++++++++++++------- R/cmpoutput.R | 14 +++++------ R/grpoutputs.R | 2 - R/latex_tables.R | 2 - R/micomp.R | 8 +++--- R/micompr.R | 8 ++++-- R/pphpc_diff.R | 2 - R/pphpc_noshuff.R | 2 - R/pphpc_ok.R | 2 - R/pphpc_testvlo.R | 4 +-- R/util.R | 2 - build/vignette.rds |binary inst/doc/paper.pdf |binary inst/doc/tolatex-examples.pdf |binary man/assumptions_manova.Rd | 2 - man/micompr.Rd | 6 +++- man/plot.assumptions_cmpoutput.Rd | 2 - man/plot.assumptions_manova.Rd | 2 - man/pphpc_testvlo.Rd | 2 - man/summary.assumptions_micomp.Rd | 2 - tests/testthat/test_assumptions.R | 2 - 24 files changed, 83 insertions(+), 71 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
Siem Heisterkamp [ctb] (Author fixed sigma),
Bert Van Willigen [ctb] (Programmer fixed sigma),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-135.5 dated 2018-02-16 and 3.1-136 dated 2018-03-09
ChangeLog | 68 +++++++++++++++++++++++++++++++++++++++++++++--- DESCRIPTION | 10 +++---- MD5 | 32 ++++++++++++---------- NAMESPACE | 2 + R/lmList.R | 6 ++-- R/lme.R | 10 ++++--- R/nlme.R | 36 +++++++++++++++++-------- inst/scripts/runme.R | 4 +- man/nlmeControl.Rd | 25 +++++++++++------ src/init.c | 3 -- src/nlme.c | 17 +++++++----- src/nlmefit.c | 17 +++++++----- src/nlmefit.h | 4 ++ src/pythag.c |only src/rs.f | 48 +++++++++++++++++++++------------ tests/deparse.R | 55 ++++---------------------------------- tests/nlme-stall.R |only tests/sigma-fixed-etc.R | 21 +++++++++----- 18 files changed, 217 insertions(+), 141 deletions(-)
Title: Interactive Tutorials for R
Description: Create interactive tutorials using R Markdown. Use a combination
of narrative, figures, videos, exercises, and quizzes to create self-paced
tutorials for learning about R and R packages.
Author: Barbara Borges [aut, cre],
JJ Allaire [aut],
RStudio, Inc. [cph],
Ajax.org B.V. [ctb, cph] (Ace library),
Zeno Rocha [ctb, cph] (clipboard.js library),
Nick Payne [ctb, cph] (Bootbox library),
Julie Cameron [ctb] (SlickQuiz library),
Quicken Loans [cph] (SlickQuiz library),
Mozilla [ctb, cph] (localforage library)
Maintainer: Barbara Borges <barbara@rstudio.com>
Diff between learnr versions 0.9.1 dated 2017-11-16 and 0.9.2 dated 2018-03-09
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NEWS.md | 15 ++++++++- R/tutorial-format.R | 46 +----------------------------- inst/htmlwidgets/quiz.js | 2 - inst/lib/tutorial/tutorial-diagnostics.js | 7 ++++ inst/tutorials/hello/hello.html | 4 +- inst/tutorials/slidy/slidy.html | 15 +++++---- 8 files changed, 45 insertions(+), 66 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival under the Cox Model
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2018-)<submitted>.
Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.7 dated 2018-01-03 and 3.8 dated 2018-03-09
DESCRIPTION | 19 ++++++----- MD5 | 24 +++++++------- R/dependCox.reg.CV.R | 21 +++++-------- R/dependCox.reg.R | 10 +++--- R/uni.Wald.R | 8 ++-- R/uni.score.R | 6 +-- R/uni.selection.R | 10 +++--- man/compound.Cox-package.Rd | 16 ++++++--- man/dependCox.reg.CV.Rd | 30 +++++++++--------- man/dependCox.reg.Rd | 71 +++++++++++++++++++------------------------- man/uni.Wald.Rd | 4 +- man/uni.score.Rd | 4 +- man/uni.selection.Rd | 7 +++- 13 files changed, 114 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-16 1.1.0
2017-08-09 1.0.0
Title: Functions to Facilitate Power and Sensitivity Analyses for
Genetic Studies of Natural Populations
Description: Functions for sensitivity and power analysis, for calculating statistics describing pedigrees from wild populations, and for viewing pedigrees.
Author: Michael Morrissey
Maintainer: Michael Morrissey <michael.morrissey@st-andrews.ac.uk>
Diff between pedantics versions 1.5 dated 2014-01-23 and 1.6 dated 2018-03-09
pedantics-1.5/pedantics/R/rpederrBird.R |only pedantics-1.5/pedantics/man/rpederrBird.Rd |only pedantics-1.6/pedantics/DESCRIPTION | 17 - pedantics-1.6/pedantics/MD5 | 17 - pedantics-1.6/pedantics/NAMESPACE | 13 + pedantics-1.6/pedantics/R/genomesim.R | 2 pedantics-1.6/pedantics/R/phensim.R | 2 pedantics-1.6/pedantics/man/drawPedigree.Rd | 15 - pedantics-1.6/pedantics/man/rpederr.Rd | 1 pedantics-1.6/pedantics/src/pedantics.cc | 275 --------------------------- pedantics-1.6/pedantics/src/pedantics_init.c |only 11 files changed, 45 insertions(+), 297 deletions(-)
Title: Weighted Generalized Estimating Equations and Model Selection
Description: Weighted generalized estimating equations (WGEE) is an extension of generalized linear models to longitudinal clustered data by incorporating the correlation within-cluster when data is missing at random (MAR). The parameters in mean, scale correlation structures are estimated based on quasi-likelihood. Multiple model selection criterion are provided for selection of mean model and working correlation structure based on WGEE/GEE.
Author: Cong Xu <congxu17@gmail.com>, Zheng Li <zheng.li@outlook.com>,
Ming Wang <mwang@phs.psu.edu>
Maintainer: Zheng Li <zheng.li@outlook.com>
Diff between wgeesel versions 1.4 dated 2017-07-23 and 1.5 dated 2018-03-09
DESCRIPTION | 10 MD5 | 22 +- NAMESPACE | 3 R/QICW.gee.R | 559 +++++++++++++++++++++++++--------------------------- R/cluster_est.R | 6 R/cs_con_str_est.R | 14 + R/drgee.R |only R/newton_raphson.R | 41 ++- R/phi_con_str_est.R | 4 R/us_matrix.R | 3 R/wgee.R | 26 +- man/drgee.Rd |only man/wgee.Rd | 12 - 13 files changed, 379 insertions(+), 321 deletions(-)