Title: Stable Specification Search in Structural Equation Models
Description: An exploratory and heuristic approach for specification search
in Structural Equation Modeling. The basic idea is to subsample the original
data and then search for optimal models on each subset. Optimality is defined
through two objectives: model fit and parsimony. As these objectives are
conflicting, we apply a multi-objective optimization methods, specifically
NSGA-II, to obtain optimal models for the whole range of model complexities.
From these optimal models, we consider only the relevant model specifications
(structures), i.e., those that are both stable (occur frequently) and
parsimonious and use those to infer a causal model.
Author: Ridho Rahmadi [aut, cre],
Perry Groot [aut, ths],
Tom Heskes [aut, ths]
Maintainer: Ridho Rahmadi <r.rahmadi@cs.ru.nl>
Diff between stablespec versions 0.1.3 dated 2016-04-08 and 0.2.3 dated 2016-11-17
stablespec-0.1.3/stablespec/R/adhd.R |only stablespec-0.1.3/stablespec/R/artificialLongiData.R |only stablespec-0.1.3/stablespec/data/adhd.rda |only stablespec-0.1.3/stablespec/data/artificialLongiData.rda |only stablespec-0.1.3/stablespec/man/adhd.Rd |only stablespec-0.1.3/stablespec/man/artificialLongiData.Rd |only stablespec-0.2.3/stablespec/DESCRIPTION | 28 stablespec-0.2.3/stablespec/MD5 | 56 - stablespec-0.2.3/stablespec/NAMESPACE | 39 - stablespec-0.2.3/stablespec/R/NSGAStuff.R | 14 stablespec-0.2.3/stablespec/R/consOperation.R | 24 stablespec-0.2.3/stablespec/R/crossdataV6.R |only stablespec-0.2.3/stablespec/R/dataReshape.R |only stablespec-0.2.3/stablespec/R/edgeOperation.R | 116 +-- stablespec-0.2.3/stablespec/R/getModelFitness.R | 37 - stablespec-0.2.3/stablespec/R/initialPopulation.R | 4 stablespec-0.2.3/stablespec/R/longiData4V3T.R |only stablespec-0.2.3/stablespec/R/modelFitness.R | 147 ++-- stablespec-0.2.3/stablespec/R/modelPop.R | 16 stablespec-0.2.3/stablespec/R/optimalModels.R | 23 stablespec-0.2.3/stablespec/R/plotStab.R | 80 +- stablespec-0.2.3/stablespec/R/relevantStructure.R | 300 ++++---- stablespec-0.2.3/stablespec/R/repairCyclicModel.R | 11 stablespec-0.2.3/stablespec/R/stableSpec.R | 93 +- stablespec-0.2.3/stablespec/data/crossdata6V.rda |only stablespec-0.2.3/stablespec/data/longiData4V3T.rda |only stablespec-0.2.3/stablespec/man/crossdata6V.Rd |only stablespec-0.2.3/stablespec/man/dataReshape.Rd |only stablespec-0.2.3/stablespec/man/getModelFitness.Rd | 114 +-- stablespec-0.2.3/stablespec/man/longiData4V3T.Rd |only stablespec-0.2.3/stablespec/man/modelPop.Rd | 115 +-- stablespec-0.2.3/stablespec/man/plotStability.Rd | 142 +--- stablespec-0.2.3/stablespec/man/repairCyclicModel.Rd | 117 +-- stablespec-0.2.3/stablespec/man/stableSpec.Rd | 352 +++++----- stablespec-0.2.3/stablespec/tests/testthat/test-modelFitness.R | 40 - stablespec-0.2.3/stablespec/tests/testthat/test-stablespec.R | 66 - 36 files changed, 1046 insertions(+), 888 deletions(-)
Title: Supplementary Item Response Theory Models
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, Rasch copula model, faceted and
hierarchical rater models, ordinal IRT model (ISOP),
DETECT statistic, local structural equation modeling (LSEM),
mean and covariance structure modelling for multivariate normally
distributed data.
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 1.12-2 dated 2016-07-19 and 1.13-1 dated 2016-11-17
sirt-1.12-2/sirt/R/linking.haberman.aux.R |only sirt-1.13-1/sirt/DESCRIPTION | 19 - sirt-1.13-1/sirt/MD5 | 179 +++++----- sirt-1.13-1/sirt/NAMESPACE | 43 ++ sirt-1.13-1/sirt/R/amh_compare_estimators.R | 13 sirt-1.13-1/sirt/R/categorize.R | 8 sirt-1.13-1/sirt/R/ccov.np.R |only sirt-1.13-1/sirt/R/conf.detect.R |only sirt-1.13-1/sirt/R/detect.R | 203 ------------ sirt-1.13-1/sirt/R/diag2.R |only sirt-1.13-1/sirt/R/expl.detect.R |only sirt-1.13-1/sirt/R/linking.haberman.R | 184 ++++++---- sirt-1.13-1/sirt/R/linking_haberman_als.R |only sirt-1.13-1/sirt/R/linking_haberman_als_residual_weights.R |only sirt-1.13-1/sirt/R/linking_haberman_als_vcov.R |only sirt-1.13-1/sirt/R/linking_haberman_vcov_transformation.R |only sirt-1.13-1/sirt/R/mlnormal.R | 6 sirt-1.13-1/sirt/R/mlnormal_proc.R | 11 sirt-1.13-1/sirt/R/mlnormal_proc_variance_shortcut.R | 8 sirt-1.13-1/sirt/R/mlnormal_proc_variance_shortcut_Z_R.R | 1 sirt-1.13-1/sirt/R/mlnormal_proc_variance_shortcut_Z_Rcpp.R | 1 sirt-1.13-1/sirt/R/smirt.R | 9 sirt-1.13-1/sirt/R/smirt_squeeze.R |only sirt-1.13-1/sirt/R/starts_cov.R |only sirt-1.13-1/sirt/R/starts_sim1dim.R |only sirt-1.13-1/sirt/R/summary.linking.haberman.R |only sirt-1.13-1/sirt/R/weighted_colMeans.R |only sirt-1.13-1/sirt/R/weighted_colSums.R |only sirt-1.13-1/sirt/R/weighted_rowMeans.R |only sirt-1.13-1/sirt/R/weighted_rowSums.R |only sirt-1.13-1/sirt/R/weighted_stats_extend_wgt.R |only sirt-1.13-1/sirt/data/data.activity.itempars.rda |binary sirt-1.13-1/sirt/data/data.big5.qgraph.rda |binary sirt-1.13-1/sirt/data/data.big5.rda |binary sirt-1.13-1/sirt/data/data.bs07a.rda |binary sirt-1.13-1/sirt/data/data.eid.rda |binary sirt-1.13-1/sirt/data/data.ess2005.rda |binary sirt-1.13-1/sirt/data/data.g308.rda |binary sirt-1.13-1/sirt/data/data.inv4gr.rda |binary sirt-1.13-1/sirt/data/data.liking.science.rda |binary sirt-1.13-1/sirt/data/data.long.rda |binary sirt-1.13-1/sirt/data/data.lsem01.rda |binary sirt-1.13-1/sirt/data/data.math.rda |binary sirt-1.13-1/sirt/data/data.mcdonald.LSAT6.rda |binary sirt-1.13-1/sirt/data/data.mcdonald.act15.rda |binary sirt-1.13-1/sirt/data/data.mcdonald.rape.rda |binary sirt-1.13-1/sirt/data/data.mixed1.rda |binary sirt-1.13-1/sirt/data/data.ml1.rda |binary sirt-1.13-1/sirt/data/data.ml2.rda |binary sirt-1.13-1/sirt/data/data.noharm18.rda |binary sirt-1.13-1/sirt/data/data.noharmExC.rda |binary sirt-1.13-1/sirt/data/data.pars1.2pl.rda |binary sirt-1.13-1/sirt/data/data.pars1.rasch.rda |binary sirt-1.13-1/sirt/data/data.pirlsmissing.rda |binary sirt-1.13-1/sirt/data/data.pisaMath.rda |binary sirt-1.13-1/sirt/data/data.pisaPars.rda |binary sirt-1.13-1/sirt/data/data.pisaRead.rda |binary sirt-1.13-1/sirt/data/data.pw01.rda |binary sirt-1.13-1/sirt/data/data.ratings1.rda |binary sirt-1.13-1/sirt/data/data.ratings2.rda |binary sirt-1.13-1/sirt/data/data.ratings3.rda |binary sirt-1.13-1/sirt/data/data.raw1.rda |binary sirt-1.13-1/sirt/data/data.read.rda |binary sirt-1.13-1/sirt/data/data.reck21.rda |binary sirt-1.13-1/sirt/data/data.reck61DAT1.rda |binary sirt-1.13-1/sirt/data/data.reck61DAT2.rda |binary sirt-1.13-1/sirt/data/data.reck73C1a.rda |binary sirt-1.13-1/sirt/data/data.reck73C1b.rda |binary sirt-1.13-1/sirt/data/data.reck75C2.rda |binary sirt-1.13-1/sirt/data/data.reck78ExA.rda |binary sirt-1.13-1/sirt/data/data.reck79ExB.rda |binary sirt-1.13-1/sirt/data/data.si01.rda |binary sirt-1.13-1/sirt/data/data.si02.rda |binary sirt-1.13-1/sirt/data/data.si03.rda |binary sirt-1.13-1/sirt/data/data.si04.rda |binary sirt-1.13-1/sirt/data/data.si05.rda |binary sirt-1.13-1/sirt/data/data.si06.rda |binary sirt-1.13-1/sirt/data/data.timss.rda |binary sirt-1.13-1/sirt/data/data.timss07.G8.RUS.rda |binary sirt-1.13-1/sirt/inst/NEWS | 22 + sirt-1.13-1/sirt/man/IRT.mle.Rd | 21 - sirt-1.13-1/sirt/man/categorize.Rd | 1 sirt-1.13-1/sirt/man/ccov.np.Rd | 5 sirt-1.13-1/sirt/man/conf.detect.Rd | 12 sirt-1.13-1/sirt/man/data.si.Rd | 2 sirt-1.13-1/sirt/man/expl.detect.Rd | 2 sirt-1.13-1/sirt/man/fuzcluster.Rd | 2 sirt-1.13-1/sirt/man/likelihood.adjustment.Rd | 1 sirt-1.13-1/sirt/man/linking.haberman.Rd | 58 +++ sirt-1.13-1/sirt/man/lsem.estimate.Rd | 2 sirt-1.13-1/sirt/man/mirt.wrapper.Rd | 2 sirt-1.13-1/sirt/man/mlnormal.Rd | 191 +++++++++++ sirt-1.13-1/sirt/man/prmse.subscores.scales.Rd | 11 sirt-1.13-1/sirt/man/rasch.jml.biascorr.Rd | 5 sirt-1.13-1/sirt/man/rasch.mml.Rd | 1 sirt-1.13-1/sirt/man/sirt-package.Rd | 177 +++++----- sirt-1.13-1/sirt/man/sirt-utilities.Rd | 6 sirt-1.13-1/sirt/man/smirt.Rd | 10 sirt-1.13-1/sirt/man/starts_cov.Rd |only sirt-1.13-1/sirt/man/xxirt.Rd | 14 100 files changed, 720 insertions(+), 510 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation("Rcpp")' for details on these last two.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,
Nathan Russell, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 0.12.7 dated 2016-09-04 and 0.12.8 dated 2016-11-17
Rcpp-0.12.7/Rcpp/inst/include/Rcpp/Date.h |only Rcpp-0.12.7/Rcpp/inst/include/Rcpp/DateVector.h |only Rcpp-0.12.7/Rcpp/inst/include/Rcpp/Datetime.h |only Rcpp-0.12.7/Rcpp/inst/include/Rcpp/DatetimeVector.h |only Rcpp-0.12.8/Rcpp/ChangeLog | 151 ++ Rcpp-0.12.8/Rcpp/DESCRIPTION | 12 Rcpp-0.12.8/Rcpp/MD5 | 104 + Rcpp-0.12.8/Rcpp/NAMESPACE | 5 Rcpp-0.12.8/Rcpp/R/Attributes.R | 4 Rcpp-0.12.8/Rcpp/R/exceptions.R | 12 Rcpp-0.12.8/Rcpp/README.md | 31 Rcpp-0.12.8/Rcpp/build/Rcpp.pdf |binary Rcpp-0.12.8/Rcpp/build/vignette.rds |binary Rcpp-0.12.8/Rcpp/cleanup | 3 Rcpp-0.12.8/Rcpp/inst/NEWS.Rd | 54 Rcpp-0.12.8/Rcpp/inst/doc/Rcpp-FAQ.pdf |binary Rcpp-0.12.8/Rcpp/inst/doc/Rcpp-attributes.pdf |binary Rcpp-0.12.8/Rcpp/inst/doc/Rcpp-extending.pdf |binary Rcpp-0.12.8/Rcpp/inst/doc/Rcpp-introduction.pdf |binary Rcpp-0.12.8/Rcpp/inst/doc/Rcpp-modules.pdf |binary Rcpp-0.12.8/Rcpp/inst/doc/Rcpp-package.pdf |binary Rcpp-0.12.8/Rcpp/inst/doc/Rcpp-quickref.pdf |binary Rcpp-0.12.8/Rcpp/inst/doc/Rcpp-sugar.pdf |binary Rcpp-0.12.8/Rcpp/inst/doc/Rcpp-unitTests.pdf |binary Rcpp-0.12.8/Rcpp/inst/doc/Rcpp.bib | 4 Rcpp-0.12.8/Rcpp/inst/include/Rcpp.h | 9 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/RNGScope.h |only Rcpp-0.12.8/Rcpp/inst/include/Rcpp/barrier.h | 12 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/config.h | 4 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/date_datetime |only Rcpp-0.12.8/Rcpp/inst/include/Rcpp/exceptions.h | 78 + Rcpp-0.12.8/Rcpp/inst/include/Rcpp/hash/IndexHash.h | 22 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/hash/SelfHash.h | 22 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/macros/dispatch.h | 84 - Rcpp-0.12.8/Rcpp/inst/include/Rcpp/routines.h | 40 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/stats/random/random.h | 6 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/sugar/Range.h | 20 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/sugar/functions/functions.h | 2 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/sugar/functions/rowSums.h |only Rcpp-0.12.8/Rcpp/inst/include/Rcpp/traits/one_type.h |only Rcpp-0.12.8/Rcpp/inst/include/Rcpp/traits/traits.h | 2 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/vector/Matrix.h | 2 Rcpp-0.12.8/Rcpp/inst/include/Rcpp/vector/MatrixBase.h | 37 Rcpp-0.12.8/Rcpp/inst/unitTests/cpp/Matrix.cpp | 66 + Rcpp-0.12.8/Rcpp/inst/unitTests/cpp/dates.cpp | 14 Rcpp-0.12.8/Rcpp/inst/unitTests/cpp/exceptions.cpp |only Rcpp-0.12.8/Rcpp/inst/unitTests/cpp/sugar.cpp | 113 ++ Rcpp-0.12.8/Rcpp/inst/unitTests/runit.Date.R | 36 Rcpp-0.12.8/Rcpp/inst/unitTests/runit.Matrix.R | 90 + Rcpp-0.12.8/Rcpp/inst/unitTests/runit.dispatch.R | 7 Rcpp-0.12.8/Rcpp/inst/unitTests/runit.exceptions.R |only Rcpp-0.12.8/Rcpp/inst/unitTests/runit.sugar.R | 544 +++++++++- Rcpp-0.12.8/Rcpp/src/api.cpp | 19 Rcpp-0.12.8/Rcpp/src/barrier.cpp | 12 Rcpp-0.12.8/Rcpp/vignettes/Rcpp.bib | 4 55 files changed, 1405 insertions(+), 220 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 0.1-0 dated 2016-11-10 and 0.1-1 dated 2016-11-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/mlt.R | 23 ++++++++++------------- inst/doc/mlt.Rnw | 27 ++++++++++++--------------- inst/doc/mlt.pdf |binary vignettes/mlt.Rnw | 27 ++++++++++++--------------- 8 files changed, 51 insertions(+), 54 deletions(-)
Title: IGM MEA Analysis
Description: Software tools developed by the Institute for Genomic Medicine, Columbia University, for the characterization of neuronal networks as recorded on Multi-Electrode Arrays (MEAs).
Author: Quanli Wang, Sahar Gelfman, Diana Hall, Ryan Dhindsa
Maintainer: Sahar Gelfman <sg3261@columbia.edu>
Diff between IGM.MEA versions 0.3.4 dated 2016-08-31 and 0.3.4.1 dated 2016-11-17
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/perm_plot.R | 4 ++-- R/plotDistributions.R | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Hierarchical Inference Testing
Description: Hierarchical inference testing (HIT) for (generalized) linear models with
correlated covariates applicable to high-dimensional settings.
Author: Jonas Klasen [aut, cre]
Maintainer: Jonas Klasen <qtcat@gmx.de>
Diff between hit versions 0.3.1 dated 2016-09-15 and 0.4.0 dated 2016-11-17
hit-0.3.1/hit/man/opt.penalty.Rd |only hit-0.3.1/hit/man/samp1.lasso.Rd |only hit-0.4.0/hit/DESCRIPTION | 6 +- hit-0.4.0/hit/MD5 | 17 +++-- hit-0.4.0/hit/NEWS.md | 7 ++ hit-0.4.0/hit/R/hit.R | 89 ++++++++++++++++++++++-------- hit-0.4.0/hit/README.md | 7 +- hit-0.4.0/hit/man/hit.Rd | 11 ++- hit-0.4.0/hit/man/samp1.lambda.overall.Rd |only hit-0.4.0/hit/man/samp1.lasso.overall.Rd |only hit-0.4.0/hit/man/samp1.lasso.split.Rd |only hit-0.4.0/hit/tests/testthat/test_hit.R | 4 - 12 files changed, 99 insertions(+), 42 deletions(-)
Title: Forecasting for Stationary and Non-Stationary Time Series
Description: Methods to compute linear h-step ahead prediction coefficients based
on localised and iterated Yule-Walker estimates and empirical mean squared
prediction errors for the resulting predictors. Also, functions to compute
autocovariances for AR(p) processes, to simulate tvARMA(p,q) time series,
and to verify an assumption from a paper by the authors.
Author: Tobias Kley [aut, cre],
Philip Preuss [aut],
Piotr Fryzlewicz [aut]
Maintainer: Tobias Kley <t.kley@lse.ac.uk>
Diff between forecastSNSTS versions 1.0-0 dated 2016-11-11 and 1.1-0 dated 2016-11-17
DESCRIPTION | 17 +++++++------ MD5 | 26 ++++++++++++------- NAMESPACE | 3 ++ NEWS | 10 ++++++- R/acfARp.R |only R/f.R |only R/forecastSNSTS-package.R | 28 +++++++++++++-------- R/models.R | 2 - R/mspe.R | 2 - man/MSPE.Rd | 2 - man/acfARp.Rd |only man/f.Rd |only man/forecastSNSTS-package.Rd | 26 ++++++++++++------- man/ts-models-tvARMA.Rd | 2 - tests/testthat/test-MSPE.R | 56 ++++++++++++++++++++++++++++++++++--------- tests/testthat/test-acfARp.R |only tests/testthat/test-f.R |only 17 files changed, 120 insertions(+), 54 deletions(-)
Title: Tool for Ensemble Feature Selection
Description: Provides a function to check the
importance of a feature based on a dependent classification
variable. An ensemble of feature selection methods
is used to determine the normalized importance value of
all features. Combining these methods in one function
(building the cumulative importance values) provides a
stable feature selection tool. This selection
can also be viewed in a barplot using the barplot_fs() function
and proved using the evaluation function efs_eval().
Author: Nikita Genze, Ursula Neumann
Maintainer: Ursula Neumann <u.neumann@wz-straubing.de>
Diff between EFS versions 1.0.0 dated 2016-08-02 and 1.0.1 dated 2016-11-17
EFS-1.0.0/EFS/R/logreg_test.R |only EFS-1.0.0/EFS/man/logreg_test.Rd |only EFS-1.0.1/EFS/DESCRIPTION | 19 +++++++++---------- EFS-1.0.1/EFS/MD5 | 16 ++++++++-------- EFS-1.0.1/EFS/NAMESPACE | 5 ++++- EFS-1.0.1/EFS/R/barplot_fs.R | 3 +-- EFS-1.0.1/EFS/R/efs_eval.R |only EFS-1.0.1/EFS/R/ensemble_fs.R | 32 ++++++++++++++------------------ EFS-1.0.1/EFS/man/barplot_fs.Rd | 3 +-- EFS-1.0.1/EFS/man/efs_eval.Rd |only EFS-1.0.1/EFS/man/ensemble_fs.Rd | 25 ++++++++++--------------- 11 files changed, 47 insertions(+), 56 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of Höhle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available monitoring procedures is
given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>.
For the retrospective analysis of epidemic spread, the package provides
three endemic-epidemic modeling frameworks with tools for visualization,
likelihood inference, and simulation. 'hhh4' estimates models for
(multivariate) count time series following Paul and Held (2011)
<doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>.
'twinSIR' models the susceptible-infectious-recovered (SIR) event
history of a fixed population, e.g, epidemics across farms or networks,
as a multivariate point process as proposed by Höhle (2009)
<doi:10.1002/bimj.200900050>. 'twinstim' estimates self-exciting point
process models for a spatio-temporal point pattern of infective events,
e.g., time-stamped geo-referenced surveillance data, as proposed by
Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>.
A recent overview of the implemented space-time modeling frameworks
for epidemic phenomena is given by Meyer et al. (2015)
<http://arxiv.org/abs/1411.0416>.
Author: Michael Höhle [aut, ths], Sebastian Meyer [aut, cre],
Michaela Paul [aut], Leonhard Held [ctb, ths],
Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb],
Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb],
Mikko Virtanen [ctb], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.12.1 dated 2016-05-18 and 1.12.2 dated 2016-11-17
DESCRIPTION | 14 MD5 | 186 +++++----- NAMESPACE | 11 R/AllGeneric.R | 16 R/RcppExports.R |only R/addSeason2formula.R | 2 R/bodaDelay.R | 13 R/calibration.R | 2 R/calibration_null.R | 2 R/checkDerivatives.R | 2 R/epidata.R | 2 R/epidataCS.R | 35 - R/epidataCS_aggregate.R | 2 R/epidataCS_animate.R | 2 R/epidataCS_methods.R | 2 R/epidataCS_plot.R | 2 R/epidata_animate.R | 2 R/epidata_plot.R | 2 R/gpc.poly-methods.R | 2 R/graphs.R | 2 R/hhh4.R | 9 R/hhh4_W.R | 2 R/hhh4_W_powerlaw.R | 2 R/hhh4_calibration.R | 2 R/hhh4_methods.R | 2 R/hhh4_oneStepAhead.R | 2 R/hhh4_plot.R | 2 R/hhh4_simulate.R | 2 R/hhh4_simulate_plot.R | 2 R/hhh4_simulate_scores.R | 2 R/intersectPolyCircle.R | 2 R/knox.R | 2 R/modifyListcall.R | 2 R/newtonRaphson.R | 2 R/nowcast.R | 10 R/options.R | 2 R/permutationTest.R | 2 R/pit.R | 2 R/plapply.R | 2 R/qlomax.R | 2 R/stK.R | 2 R/sts.R | 44 +- R/stsNC.R | 377 +++++++++++++++------ R/stsNClist_animate.R |only R/sts_animate.R | 31 + R/stsplot_space.R | 2 R/stsplot_spacetime.R | 2 R/stsplot_time.R | 2 R/twinSIR.R | 2 R/twinSIR_methods.R | 2 R/twinSIR_profile.R | 2 R/twinSIR_simulation.R | 2 R/twinstim.R | 17 R/twinstim_helper.R | 64 ++- R/twinstim_iafplot.R | 2 R/twinstim_intensity.R | 2 R/twinstim_methods.R | 2 R/twinstim_siaf.R | 2 R/twinstim_siaf_gaussian.R | 2 R/twinstim_siaf_powerlaw.R | 2 R/twinstim_siaf_powerlawL.R | 2 R/twinstim_siaf_step.R | 2 R/twinstim_siaf_student.R | 2 R/twinstim_simulation.R | 2 R/twinstim_step.R | 2 R/twinstim_tiaf.R | 2 R/twinstim_tiaf_exponential.R | 2 R/twinstim_tiaf_step.R | 2 R/untie.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 59 ++- inst/THANKS | 1 inst/doc/glrnb.pdf |binary inst/doc/hhh4.pdf |binary inst/doc/hhh4_spacetime.pdf |binary inst/doc/monitoringCounts.R | 44 +- inst/doc/monitoringCounts.Rnw | 16 inst/doc/monitoringCounts.pdf |binary inst/doc/surveillance.pdf |binary inst/doc/twinSIR.pdf |binary inst/doc/twinstim.pdf |binary man/algo.outbreakP.Rd | 2 man/measles.weser.Rd | 6 man/nowcast.Rd | 18 - man/stsNC-class.Rd | 17 man/stsNClist_animate.Rd |only man/sts_animate.Rd | 6 src/RcppExports.cpp |only src/determineSources.cc |only src/twins.cc | 156 ++++---- tests/testthat/test-determineSources.R |only vignettes/monitoringCounts-cache/boda.RData |binary vignettes/monitoringCounts-cache/boda.covars.RData |binary vignettes/monitoringCounts.Rnw | 16 vignettes/references.bib | 3 vignettes/surveillance-hmm.pdf |binary 97 files changed, 776 insertions(+), 503 deletions(-)
Title: Estimate Structured Additive Regression Models with 'BayesX'
Description: An R interface to estimate structured additive regression (STAR) models with 'BayesX'.
Author: Nikolaus Umlauf [aut, cre],
Thomas Kneib [aut],
Stefan Lang [aut],
Achim Zeileis [aut]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between R2BayesX versions 1.0-0 dated 2015-01-26 and 1.1-0 dated 2016-11-17
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 13 +++++++++++++ R/cpos.R | 3 +-- R/parse.bayesx.input.R | 10 ++++++++++ R/r.R | 3 +-- R/s4class.R | 4 ++++ R/write.gra.R | 1 + src/bayesx.c | 8 +++++++- 9 files changed, 52 insertions(+), 19 deletions(-)
Title: Hydrologic Indices for Daily Time Series Data
Description: Calculates a suite of hydrologic indices for daily time series data that are widely used in hydrology and stream ecology.
Author: Nick Bond
Maintainer: Nick Bond <n.bond@latrobe.edu.au>
Diff between hydrostats versions 0.2.4 dated 2015-10-18 and 0.2.5 dated 2016-11-17
hydrostats-0.2.4/hydrostats/data/Acheron.txt.gz |only hydrostats-0.2.4/hydrostats/data/Cooper.txt.gz |only hydrostats-0.2.5/hydrostats/DESCRIPTION | 10 +-- hydrostats-0.2.5/hydrostats/MD5 | 56 +++++++++--------- hydrostats-0.2.5/hydrostats/NAMESPACE | 1 hydrostats-0.2.5/hydrostats/NEWS | 13 ++++ hydrostats-0.2.5/hydrostats/R/Colwells.R | 20 +++--- hydrostats-0.2.5/hydrostats/R/high.spells.R | 17 +++-- hydrostats-0.2.5/hydrostats/R/low.spell.lengths.R |only hydrostats-0.2.5/hydrostats/README.md | 4 - hydrostats-0.2.5/hydrostats/data/Acheron.txt |only hydrostats-0.2.5/hydrostats/data/Cooper.txt |only hydrostats-0.2.5/hydrostats/man/CTF.Rd | 2 hydrostats-0.2.5/hydrostats/man/Colwells.Rd | 20 ++++-- hydrostats-0.2.5/hydrostats/man/ann.cv.Rd | 2 hydrostats-0.2.5/hydrostats/man/baseflows.Rd | 2 hydrostats-0.2.5/hydrostats/man/daily.cv.Rd | 2 hydrostats-0.2.5/hydrostats/man/day.dist.Rd | 2 hydrostats-0.2.5/hydrostats/man/flood.length.max.Rd | 2 hydrostats-0.2.5/hydrostats/man/four.digit.year.Rd | 2 hydrostats-0.2.5/hydrostats/man/get.days.Rd | 2 hydrostats-0.2.5/hydrostats/man/high.spell.lengths.Rd | 2 hydrostats-0.2.5/hydrostats/man/high.spells.Rd | 2 hydrostats-0.2.5/hydrostats/man/hydro.year.Rd | 2 hydrostats-0.2.5/hydrostats/man/hydrostats-package.Rd | 2 hydrostats-0.2.5/hydrostats/man/low.spell.lengths.Rd |only hydrostats-0.2.5/hydrostats/man/low.spells.Rd | 2 hydrostats-0.2.5/hydrostats/man/monthly.cv.Rd | 4 - hydrostats-0.2.5/hydrostats/man/partial.series.Rd | 2 hydrostats-0.2.5/hydrostats/man/recode.Rd | 2 hydrostats-0.2.5/hydrostats/man/seasonality.Rd | 2 hydrostats-0.2.5/hydrostats/man/ts.format.Rd | 2 32 files changed, 104 insertions(+), 75 deletions(-)
Title: Perform Factorial Analysis from 'FactoMineR' with a Shiny
Application
Description: Perform factorial analysis with a menu and draw graphs interactively thanks to 'FactoMineR' and a Shiny application.
Author: Pauline Vaissie, Astrid Monge, Francois Husson
Maintainer: Francois Husson <husson@agrocampus-ouest.fr>
Diff between Factoshiny versions 1.0.4 dated 2016-06-23 and 1.0.5 dated 2016-11-17
DESCRIPTION | 10 ++++---- MD5 | 28 +++++++++++----------- NAMESPACE | 2 - build/vignette.rds |binary inst/FactoCAapp2/server.R | 32 ++++++++++++------------- inst/FactoFAMDapp2/server.R | 38 +++++++++++++++--------------- inst/FactoHCPCapp2/server.R | 35 ++++++++++++++-------------- inst/FactoHCPCappdf2/server.R | 17 +++++++------ inst/FactoMCAapp2/server.R | 52 +++++++++++++++++++++--------------------- inst/FactoMCAapp2/ui.R | 6 ++-- inst/FactoMFAapp/server.R | 30 ++++++++++++------------ inst/FactoMFAapp2/server.R | 32 ++++++++++++------------- inst/FactoPCAapp2/server.R | 50 ++++++++++++++++++++-------------------- inst/FactoPCAapp2/ui.R | 4 +-- inst/doc/Factoshiny.pdf |binary 15 files changed, 169 insertions(+), 167 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.33 dated 2016-05-18 and 1.34 dated 2016-11-17
DESCRIPTION | 14 - MD5 | 64 ++-- NAMESPACE | 3 R/AovSum.r | 278 +++++++++++---------- R/CA.R | 4 R/DMFA.R | 4 R/HCPC.R | 2 R/MFA.R | 11 R/condes.r | 2 R/descfreq.R | 2 R/plot.FAMD.R | 6 R/plot.MCA.R | 10 R/plot.MFA.R | 89 ++++-- R/plot.PCA.R | 29 +- R/plotellipses.r | 623 ++++++++++++++++++++++++++---------------------- R/predict.FAMD.R | 2 R/predict.MCA.R | 8 R/predict.MFA.R | 4 R/simule.r | 7 R/svd.triplet.R | 2 R/tab.disjonctif.R | 2 R/textual.r | 1 build/vignette.rds |binary data/children.rda |binary data/poison.rda |binary data/poison.text.rda |binary inst/doc/FactoMineR.pdf |binary inst/doc/clustering.pdf |binary man/plot.FAMD.Rd | 4 man/plot.MCA.Rd | 5 man/plot.MFA.Rd | 4 man/plot.PCA.Rd | 6 man/textual.Rd | 2 33 files changed, 671 insertions(+), 517 deletions(-)
Title: Bayesian State-Space Models for Animal Movement
Description: Tools to fit Bayesian state-space models to animal tracking data. Models are provided for location
filtering, location filtering and behavioural state estimation, and their hierarchical versions.
The models are primarily intended for fitting to ARGOS satellite tracking data but options exist to fit
to other tracking data types. For Global Positioning System data, consider the 'moveHMM' package.
Simplified Markov Chain Monte Carlo convergence diagnostic plotting is provided but users are encouraged
to explore tools available in packages such as 'coda' and 'boa'.
Author: Ian Jonsen [aut, cre],
Sophie Bestley [ctb],
Simon Wotherspoon [ctb],
Michael Sumner [ctb]
Maintainer: Ian Jonsen <ian.jonsen@mq.edu.au>
Diff between bsam versions 1.1.0 dated 2016-11-01 and 1.1.1 dated 2016-11-17
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 8 ++++++++ R/bsam-package.R | 2 +- R/diag_ssm.R | 4 +++- R/fit_ssm.R | 9 ++++++--- R/hssm.R | 26 +++++++++++--------------- R/map_ssm.R | 4 ++-- R/plot_fit.R | 22 +++++++++++++--------- R/ssm.R | 5 +---- man/bsam-package.Rd | 2 +- man/map_ssm.Rd | 4 ++-- 12 files changed, 62 insertions(+), 52 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: Functions for working with biogas data. Both low- and high-level functions are included for carrying out common tasks for analysis of biogas and related data. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas and methane production can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>
Diff between biogas versions 1.4.0 dated 2016-05-24 and 1.5.0 dated 2016-11-17
ChangeLog | 92 ++++++++ DESCRIPTION | 8 MD5 | 70 +++--- NEWS | 37 +++ R/cumBg.R | 323 +++++++++++++++++++++---------- R/stdVol.R | 4 R/summBg.R | 65 +++++- R/watVap.R | 31 ++ build/vignette.rds |binary data/comp.rda |binary data/comp2.rda |binary data/mass.rda |binary data/massw.rda |binary data/s3compl.rda |only data/s3compw.rda |only data/s3lcombo.rda |only data/s3voll.rda |only data/s3volw.rda |only data/setup.rda |binary data/setup2.rda |binary data/strawComp.rda |binary data/strawMass.rda |binary data/strawPressure.rda |binary data/strawSetup.rda |binary data/vol.rda |binary data/vol2.rda |binary inst/doc/biogas_quick_start.R | 46 ++++ inst/doc/biogas_quick_start.Rnw | 75 +++++++ inst/doc/biogas_quick_start.pdf |binary inst/doc/predBg_function.pdf |binary man/cumBg.Rd | 84 +++++++- man/s3compl.Rd |only man/s3compw.Rd |only man/s3lcombo.Rd |only man/s3voll.Rd |only man/s3volw.Rd |only man/stdVol.Rd | 18 - man/summBg.Rd | 61 ++++- tests/testthat/test_HighLevelFunctions.R | 9 tests/testthat/test_LowLevelFunctions.R | 9 vignettes/biogas_quick_start.Rnw | 75 +++++++ 41 files changed, 808 insertions(+), 199 deletions(-)
Title: Implementation of Artificial Bee Colony (ABC) Optimization
Description: An implementation of Karaboga (2005) Artificial Bee Colony
Optimization algorithm <http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf>.
This (working) version is a Work-in-progress, which is
why it has been implemented using pure R code. This was developed upon the basic
version programmed in C and distributed at the algorithm's official website.
Author: George Vega Yon [aut, cre],
Enyelbert Muñoz [ctb]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between ABCoptim versions 0.13.11 dated 2013-11-06 and 0.14.0 dated 2016-11-17
ChangeLog |only DESCRIPTION | 28 ++- MD5 | 19 +- NAMESPACE | 9 + NEWS.md |only R/ABCoptim-package.R |only R/RcppExports.R |only R/abc_optim.R | 343 ++++++++++++++++++++++++++++++++---------------- inst |only man/ABCoptim-package.Rd | 65 ++++----- man/abc_optim.Rd | 131 +++++++++++++----- src |only tests |only 13 files changed, 399 insertions(+), 196 deletions(-)
Title: Udunits-2 Bindings for R
Description: Provides simple bindings to Unidata's udunits library.
Author: James Hiebert <hiebert@uvic.ca>
Maintainer: James Hiebert <hiebert@uvic.ca>
Diff between udunits2 versions 0.11 dated 2016-07-22 and 0.13 dated 2016-11-17
udunits2-0.11/udunits2/configure.win |only udunits2-0.13/udunits2/CHANGELOG | 9 +++++++++ udunits2-0.13/udunits2/DESCRIPTION | 8 ++++---- udunits2-0.13/udunits2/MD5 | 12 ++++++------ udunits2-0.13/udunits2/R/ud.functions.R | 19 ++++++++++++++----- udunits2-0.13/udunits2/src/Makevars.win | 17 ++++++++++++++++- udunits2-0.13/udunits2/src/udunits2_R.c | 18 +++++++++++------- udunits2-0.13/udunits2/tools |only 8 files changed, 60 insertions(+), 23 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.4.26 dated 2016-08-28 and 1.4.27 dated 2016-11-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/invgauss.R | 7 ++++++- inst/NEWS | 4 ++++ man/growthcurve.Rd | 3 +-- man/invgauss.Rd | 4 ++-- 7 files changed, 24 insertions(+), 16 deletions(-)
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Description: A set of functions used in teaching STATS 201/208 Data Analysis at the University of Auckland. The functions are designed to make parts of R more accessible to a large undergraduate population who are mostly not statistics majors.
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster, Brendan McArdle, Chris Wild
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between s20x versions 3.1-17 dated 2016-04-14 and 3.1-18 dated 2016-11-17
s20x-3.1-17/s20x/data/airpass.df.txt |only s20x-3.1-17/s20x/data/apples.df.txt |only s20x-3.1-17/s20x/data/arousal.df.txt |only s20x-3.1-17/s20x/data/beer.df.txt |only s20x-3.1-17/s20x/data/body.df.txt |only s20x-3.1-17/s20x/data/books.df.txt |only s20x-3.1-17/s20x/data/bursary.df.txt |only s20x-3.1-17/s20x/data/butterfat.df.txt |only s20x-3.1-17/s20x/data/camplake.df.txt |only s20x-3.1-17/s20x/data/chalk.df.txt |only s20x-3.1-17/s20x/data/computer.df.txt |only s20x-3.1-17/s20x/data/course.df.txt |only s20x-3.1-17/s20x/data/course2way.df.txt |only s20x-3.1-17/s20x/data/diamonds.df.txt |only s20x-3.1-17/s20x/data/fire.df.txt |only s20x-3.1-17/s20x/data/fruitfly.df.txt |only s20x-3.1-17/s20x/data/house.df.txt |only s20x-3.1-17/s20x/data/incomes.df.txt |only s20x-3.1-17/s20x/data/lakemary.df.txt |only s20x-3.1-17/s20x/data/larain.df.txt |only s20x-3.1-17/s20x/data/mazda.df.txt |only s20x-3.1-17/s20x/data/mening.df.txt |only s20x-3.1-17/s20x/data/mergers.df.txt |only s20x-3.1-17/s20x/data/mozart.df.txt |only s20x-3.1-17/s20x/data/nail.df.txt |only s20x-3.1-17/s20x/data/oysters.df.txt |only s20x-3.1-17/s20x/data/peru.df.txt |only s20x-3.1-17/s20x/data/rain.df.txt |only s20x-3.1-17/s20x/data/seeds.df.txt |only s20x-3.1-17/s20x/data/sheep.df.txt |only s20x-3.1-17/s20x/data/skulls.df.txt |only s20x-3.1-17/s20x/data/soyabean.df.txt |only s20x-3.1-17/s20x/data/teach.df.txt |only s20x-3.1-17/s20x/data/technitron.df.txt |only s20x-3.1-17/s20x/data/thyroid.df.txt |only s20x-3.1-17/s20x/data/toothpaste.df.txt |only s20x-3.1-17/s20x/data/zoo.df.txt |only s20x-3.1-18/s20x/DESCRIPTION | 8 +- s20x-3.1-18/s20x/MD5 | 78 ++++++++++++++--------------- s20x-3.1-18/s20x/NAMESPACE | 1 s20x-3.1-18/s20x/data/airpass.df.txt.gz |only s20x-3.1-18/s20x/data/apples.df.txt.gz |only s20x-3.1-18/s20x/data/arousal.df.txt.gz |only s20x-3.1-18/s20x/data/beer.df.txt.gz |only s20x-3.1-18/s20x/data/body.df.txt.gz |only s20x-3.1-18/s20x/data/books.df.txt.gz |only s20x-3.1-18/s20x/data/bursary.df.txt.gz |only s20x-3.1-18/s20x/data/butterfat.df.txt.gz |only s20x-3.1-18/s20x/data/camplake.df.txt.gz |only s20x-3.1-18/s20x/data/chalk.df.txt.gz |only s20x-3.1-18/s20x/data/computer.df.txt.gz |only s20x-3.1-18/s20x/data/course.df.txt.gz |only s20x-3.1-18/s20x/data/course2way.df.txt.gz |only s20x-3.1-18/s20x/data/diamonds.df.txt.gz |only s20x-3.1-18/s20x/data/fire.df.txt.gz |only s20x-3.1-18/s20x/data/fruitfly.df.txt.gz |only s20x-3.1-18/s20x/data/house.df.txt.gz |only s20x-3.1-18/s20x/data/incomes.df.txt.gz |only s20x-3.1-18/s20x/data/lakemary.df.txt.gz |only s20x-3.1-18/s20x/data/larain.df.txt.gz |only s20x-3.1-18/s20x/data/mazda.df.txt.gz |only s20x-3.1-18/s20x/data/mening.df.txt.gz |only s20x-3.1-18/s20x/data/mergers.df.txt.gz |only s20x-3.1-18/s20x/data/mozart.df.txt.gz |only s20x-3.1-18/s20x/data/nail.df.txt.gz |only s20x-3.1-18/s20x/data/oysters.df.txt.gz |only s20x-3.1-18/s20x/data/peru.df.txt.gz |only s20x-3.1-18/s20x/data/rain.df.txt.gz |only s20x-3.1-18/s20x/data/seeds.df.txt.gz |only s20x-3.1-18/s20x/data/sheep.df.txt.gz |only s20x-3.1-18/s20x/data/skulls.df.txt.gz |only s20x-3.1-18/s20x/data/soyabean.df.txt.gz |only s20x-3.1-18/s20x/data/teach.df.txt.gz |only s20x-3.1-18/s20x/data/technitron.df.txt.gz |only s20x-3.1-18/s20x/data/thyroid.df.txt.gz |only s20x-3.1-18/s20x/data/toothpaste.df.txt.gz |only s20x-3.1-18/s20x/data/zoo.df.txt.gz |only 77 files changed, 44 insertions(+), 43 deletions(-)
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate
'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for
each of the 'API' 'endpoints': data, data categories, data sets, data types,
locations, location categories, and stations. In addition, we have an interface
for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical
Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS',
tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut, cre],
Brooke Anderson [ctb],
Maëlle Salmon [ctb],
Adam Erickson [ctb],
Nicholas Potter [ctb],
Joseph Stachelek [ctb],
Alex Simmons [ctb],
Karthik Ram [ctb],
Hart Edmund [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 0.6.5 dated 2016-10-22 and 0.6.6 dated 2016-11-17
DESCRIPTION | 13 - MD5 | 65 +++---- NEWS.md | 27 +++ R/ghcnd.R | 10 - R/helpers_ghcnd.R | 8 R/homr.R | 114 +++++++------ R/homr_definitions.R | 9 - R/isd.R | 292 +++------------------------------- R/isd_read.R | 22 +- R/isd_stations.R | 9 - R/ncdc.r | 7 R/ncdc_datacats.r | 2 R/ncdc_datasets.r | 2 R/ncdc_datatypes.r | 4 R/ncdc_locs.r | 18 +- R/ncdc_locs_cats.r | 27 +-- R/ncdc_stations.r | 4 R/rnoaa-package.r | 46 ++--- build/vignette.rds |binary man/ghcnd_search.Rd | 2 man/ghcnd_splitvars.Rd | 2 man/homr.Rd | 90 +++++----- man/homr_definitions.Rd | 6 man/isd.Rd | 25 ++ man/isd_read.Rd | 12 + man/meteo_nearby_stations.Rd | 2 man/meteo_pull_monitors.Rd | 8 man/meteo_tidy_ghcnd.Rd | 10 - man/meteo_tidy_ghcnd_element.Rd | 6 man/rnoaa-package.Rd | 32 ++- man/storm_columns.Rd | 4 man/storm_names.Rd | 5 tests/testthat/test-ghcnd_splitvars.R |only tests/testthat/test-isd_read.R | 6 34 files changed, 386 insertions(+), 503 deletions(-)
More information about NestedCategBayesImpute at CRAN
Permanent link
More information about NegBinBetaBinreg at CRAN
Permanent link
Title: Longitudinal Targeted Maximum Likelihood Estimation
Description: Targeted Maximum Likelihood Estimation (TMLE) of
treatment/censoring specific mean outcome or marginal structural model for
point-treatment and longitudinal data.
Author: Joshua Schwab [aut, cre],
Samuel Lendle [aut],
Maya Petersen [aut],
Mark van der Laan [aut],
Susan Gruber [ctb]
Maintainer: Joshua Schwab <joshuaschwab@yahoo.com>
Diff between ltmle versions 0.9-8 dated 2016-04-20 and 0.9-9 dated 2016-11-17
DESCRIPTION | 14 MD5 | 45 NAMESPACE | 1 NEWS | 21 R/DeterministicFunctions.R | 45 R/GeneralUtilities.R | 30 R/ltmle-package.R | 2 R/ltmle.R | 1557 ++++++++++++++------------- R/ltmle_sg.R | 1 R/zzz.R | 2 man/deterministic.g.function_template.Rd | 3 man/ltmle-package.Rd | 7 man/ltmle.Rd | 91 - tests/testthat/test-AbarAndRegimes.R |only tests/testthat/test-BinaryToCensoring.R |only tests/testthat/test-CheckInputs.R | 27 tests/testthat/test-DeterministicFunctions.R |only tests/testthat/test-ErrorHandling.R |only tests/testthat/test-EstimateVariance.R | 59 - tests/testthat/test-GeneralUtilities.R |only tests/testthat/test-GetDefaultForm.R | 15 tests/testthat/test-Weights.R | 24 tests/testthat/test-print.R |only tests/testthat/test-print.summary.ltmleMSM.R | 49 tests/testthat/test-random.R | 26 tests/testthat/test-summary.ltmle.R | 14 tests/testthat/test_IDs.R |only 27 files changed, 1147 insertions(+), 886 deletions(-)
Title: Functional Summary and Meta-Analysis of Gene Expression Data
Description: Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between KOGMWU versions 1.0 dated 2015-03-05 and 1.1 dated 2016-11-17
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 6 +++++- R/corrPlot.R | 4 +--- data/adults.3dHeat.logFoldChange.rda |binary data/gene2kog.rda |binary data/larvae.longTerm.rda |binary data/larvae.shortTerm.rda |binary man/KOGMWU-package.Rd | 4 ++-- man/corrPlot.Rd | 4 ++-- 10 files changed, 23 insertions(+), 21 deletions(-)
Title: Leland Wilkinson's Algorithm for Detecting Multidimensional
Outliers
Description: An implementation of an algorithm for outlier detection that can handle a) data with a mixed categorical and continuous variables, b) many columns of data, c) many rows of data, d) outliers that mask other outliers, and e) both unidimensional and multidimensional datasets. Unlike ad hoc methods found in many machine learning papers, HDoutliers is based on a distributional model that uses probabilities to determine outliers. See <https://www.cs.uic.edu/~wilkinson/Publications/outliers.pdf>.
Author: Leland Wilkinson [aut], Chris Fraley [cre]
Maintainer: Chris Fraley <cfraley@tableau.com>
Diff between HDoutliers versions 0.9 dated 2016-11-01 and 0.12 dated 2016-11-17
CHANGELOG | 2 ++ DESCRIPTION | 12 +++++++----- MD5 | 6 +++--- R/getHDoutliers.R | 4 ++-- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Predicted Values and Discrete Changes for GLM
Description: Functions to calculate predicted values and the difference between
the two cases with confidence interval for glm(), glm.nb(), polr() and multinom().
Author: Benjamin Schlegel [aut,cre]
Maintainer: Benjamin Schlegel <kontakt@benjaminschlegel.ch>
Diff between glm.predict versions 2.3-0 dated 2016-10-06 and 2.4-0 dated 2016-11-17
DESCRIPTION | 12 +++++++----- MD5 | 34 +++++++++++++++++++++++----------- NAMESPACE | 2 +- R/discrete.changes.R | 12 +++++++----- R/nominal_discrete.changes.R | 12 ++++++------ R/ordinal_discrete.changes.R | 14 ++++++++------ R/predict_glm.R |only R/predict_multinom.R |only R/predict_polr.R |only R/predicts_glm.R |only R/predicts_multinom.R |only R/predicts_polr.R |only man/discrete.change.Rd | 2 +- man/discrete.changes.Rd | 2 +- man/nominal_discrete.change.Rd | 2 +- man/nominal_discrete.changes.Rd | 2 +- man/ordinal_discrete.change.Rd | 6 +++--- man/ordinal_discrete.changes.Rd | 2 +- man/predict_glm.Rd |only man/predict_multinom.Rd |only man/predict_polr.Rd |only man/predicts_glm.Rd |only man/predicts_multinom.Rd |only man/predicts_polr.Rd |only 24 files changed, 60 insertions(+), 42 deletions(-)
Title: A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations
Description: A fold change rank based method is presented to search for
differentially expressed genes and to detect recurrent chromosomal copy number aberrations.
This method may be useful for high-throughput biological data (microarray, sequencing, ...).
Probabilities are associated with genes/probes in the dataset and there is no problem of
multiple tests when using this method. For aCGH data, segmentation results are obtained by
merging the significant probes detected.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele <doulaye@igbmc.fr>
Diff between fcros versions 1.5.1 dated 2016-10-10 and 1.5.2 dated 2016-11-17
DESCRIPTION | 8 +- MD5 | 36 +++++------ R/chrSegment.R | 165 ++++++++++++++++++++++++++------------------------- R/fcros.R | 4 - R/pfco.R | 10 +-- R/pfcoMod.R | 4 - man/chrMerge.rd | 4 - man/chrPlot.rd | 4 - man/chrPlot2.rd | 4 - man/chrSegment.rd | 4 - man/dataSummary.rd | 4 - man/fc2Calc.rd | 3 man/fcros-package.Rd | 4 - man/fcrosMod.Rd | 3 man/moyStdCalc.rd | 3 man/pfco.rd | 3 man/pfcoMod.rd | 3 man/rmatTrim.rd | 3 man/tprobaCalc.rd | 3 19 files changed, 144 insertions(+), 128 deletions(-)