Title: Beta Regression
Description: Beta regression for modeling beta-distributed dependent variables, e.g., rates and proportions.
In addition to maximum likelihood regression (for both mean and precision of a beta-distributed
response), bias-corrected and bias-reduced estimation as well as finite mixture models and
recursive partitioning for beta regressions are provided.
Author: Achim Zeileis [aut, cre],
Francisco Cribari-Neto [aut],
Bettina Gruen [aut],
Ioannis Kosmidis [aut],
Alexandre B. Simas [ctb] (earlier version by),
Andrea V. Rocha [ctb] (earlier version by)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between betareg versions 3.0-5 dated 2014-09-24 and 3.1-0 dated 2016-08-05
DESCRIPTION | 18 MD5 | 76 +-- NAMESPACE | 102 ++--- NEWS | 17 R/betamix.R | 48 ++ R/betareg.R | 6 R/betatree.R | 275 ++++++------- build/vignette.rds |binary data/CarTask.rda |binary data/FoodExpenditure.rda |binary data/GasolineYield.rda |binary data/ImpreciseTask.rda |binary data/MockJurors.rda |binary data/ReadingSkills.rda |binary data/StressAnxiety.rda |binary data/WeatherTask.rda |binary inst/doc/betareg-ext.R | 7 inst/doc/betareg-ext.Rnw | 44 +- inst/doc/betareg-ext.pdf |binary inst/doc/betareg.pdf |binary man/betamix.Rd | 7 man/betareg.Rd | 2 man/betareg.control.Rd | 2 man/betatree.Rd | 57 -- man/gleverage.Rd | 1 man/predict.betareg.Rd | 2 man/residuals.betareg.Rd | 2 man/summary.betareg.Rd | 2 tests/Examples/betareg-Ex.Rout.save | 714 ++++++++++++++++-------------------- tests/betamix.R | 4 tests/betamix.Rout.save | 120 +++--- tests/betatree.R | 5 tests/betatree.Rout.save | 130 +++--- tests/bias.R | 2 tests/bias.Rout.save | 170 ++++---- vignettes/betareg-ext.Rnw | 44 +- vignettes/betareg-ext.Rout.save | 75 +-- vignettes/betareg.Rout.save | 2 vignettes/betareg.bib | 9 39 files changed, 972 insertions(+), 971 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for Bayesian estimation of
antigen-driven selection in immunoglobulin (Ig) sequences, providing an
intuitive means of analyzing selection by quantifying the degree of
selective pressure. Also provides tools to profile mutations in Ig
sequences, build models of somatic hypermutation (SHM) in Ig sequences,
and make model-dependent distance comparisons of Ig repertoires.
Author: Mohamed Uduman [aut],
Gur Yaari [aut],
Namita Gupta [aut],
Jason Vander Heiden [aut, cre],
Ang Cui [ctb],
Susanna Marquez [ctb],
Julian Zhou [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between shazam versions 0.1.3 dated 2016-07-31 and 0.1.4 dated 2016-08-05
DESCRIPTION | 8 ++--- MD5 | 24 ++++++++--------- NEWS.md | 15 ++++++++++ R/Baseline.R | 12 +++++--- R/MutationProfiling.R | 50 ++++++++++++++++++------------------ R/TargetingModels.R | 13 +++++++-- inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Targeting-Vignette.pdf |binary man/calcBaseline.Rd | 5 ++- man/collapseClones.Rd | 28 ++++++++++---------- man/createMutabilityMatrix.Rd | 10 +++++-- man/plotMutability.Rd | 2 - 13 files changed, 101 insertions(+), 66 deletions(-)
Title: Functions for Calculating Ontological Similarities
Description: Functions for calculating semantic similarities between ontological terms or sets of ontological terms based on term information content and assessing statistical significance of similarity in the context of a collection of sets of ontological terms.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologySimilarity versions 1.0 dated 2016-01-13 and 2.0 dated 2016-08-05
ontologySimilarity-1.0/ontologySimilarity/inst/doc/ontologySimilarity-guide.R |only ontologySimilarity-1.0/ontologySimilarity/inst/doc/ontologySimilarity-guide.Rmd |only ontologySimilarity-1.0/ontologySimilarity/inst/doc/ontologySimilarity-guide.html |only ontologySimilarity-1.0/ontologySimilarity/man/get_sim_mat.Rd |only ontologySimilarity-1.0/ontologySimilarity/man/get_sim_sample.Rd |only ontologySimilarity-1.0/ontologySimilarity/man/get_sim_to_profile_p.Rd |only ontologySimilarity-1.0/ontologySimilarity/man/get_stratified_sim_p.Rd |only ontologySimilarity-1.0/ontologySimilarity/man/get_stratified_sim_p_sorted.Rd |only ontologySimilarity-1.0/ontologySimilarity/src/PhenoSim.cpp |only ontologySimilarity-1.0/ontologySimilarity/src/PhenoSim.h |only ontologySimilarity-1.0/ontologySimilarity/vignettes/ontologySimilarity-guide.Rmd |only ontologySimilarity-2.0/ontologySimilarity/DESCRIPTION | 10 ontologySimilarity-2.0/ontologySimilarity/MD5 | 77 - ontologySimilarity-2.0/ontologySimilarity/NAMESPACE | 28 ontologySimilarity-2.0/ontologySimilarity/R/functions.R | 539 ++-------- ontologySimilarity-2.0/ontologySimilarity/R/group-sim.R |only ontologySimilarity-2.0/ontologySimilarity/R/term-set-sim.R |only ontologySimilarity-2.0/ontologySimilarity/build/vignette.rds |binary ontologySimilarity-2.0/ontologySimilarity/inst/doc/ontologySimilarity-examples.R |only ontologySimilarity-2.0/ontologySimilarity/inst/doc/ontologySimilarity-examples.Rmd |only ontologySimilarity-2.0/ontologySimilarity/inst/doc/ontologySimilarity-examples.html |only ontologySimilarity-2.0/ontologySimilarity/inst/doc/ontologySimilarity-introduction.R |only ontologySimilarity-2.0/ontologySimilarity/inst/doc/ontologySimilarity-introduction.Rmd |only ontologySimilarity-2.0/ontologySimilarity/inst/doc/ontologySimilarity-introduction.html |only ontologySimilarity-2.0/ontologySimilarity/man/create_sim_index.Rd |only ontologySimilarity-2.0/ontologySimilarity/man/descendants_IC.Rd |only ontologySimilarity-2.0/ontologySimilarity/man/get_asym_sim_grid.Rd |only ontologySimilarity-2.0/ontologySimilarity/man/get_profile_sims.Rd |only ontologySimilarity-2.0/ontologySimilarity/man/get_sim.Rd | 34 ontologySimilarity-2.0/ontologySimilarity/man/get_sim_grid.Rd | 36 ontologySimilarity-2.0/ontologySimilarity/man/get_sim_p.Rd | 38 ontologySimilarity-2.0/ontologySimilarity/man/get_sim_p_from_ontology.Rd |only ontologySimilarity-2.0/ontologySimilarity/man/get_similarity_rank_matrix.Rd | 12 ontologySimilarity-2.0/ontologySimilarity/man/get_term_set_to_term_sims.Rd | 15 ontologySimilarity-2.0/ontologySimilarity/man/get_term_sim_mat.Rd | 20 ontologySimilarity-2.0/ontologySimilarity/man/lin.Rd | 11 ontologySimilarity-2.0/ontologySimilarity/man/ontologySimilarity-package.Rd | 19 ontologySimilarity-2.0/ontologySimilarity/man/resnik.Rd | 11 ontologySimilarity-2.0/ontologySimilarity/man/sample_group_sim.Rd |only ontologySimilarity-2.0/ontologySimilarity/man/sample_group_sim_from_ontology.Rd |only ontologySimilarity-2.0/ontologySimilarity/src/Makevars |only ontologySimilarity-2.0/ontologySimilarity/src/PVal.cpp | 61 - ontologySimilarity-2.0/ontologySimilarity/src/PVal.h | 83 - ontologySimilarity-2.0/ontologySimilarity/src/RcppExports.cpp | 345 +++--- ontologySimilarity-2.0/ontologySimilarity/src/RcppExports.h | 101 - ontologySimilarity-2.0/ontologySimilarity/src/Sampling.cpp | 49 ontologySimilarity-2.0/ontologySimilarity/src/Sampling.h | 35 ontologySimilarity-2.0/ontologySimilarity/src/SimMatrix.cpp | 90 - ontologySimilarity-2.0/ontologySimilarity/src/SimMatrix.h | 31 ontologySimilarity-2.0/ontologySimilarity/src/TermList.cpp | 20 ontologySimilarity-2.0/ontologySimilarity/src/TermList.h | 3 ontologySimilarity-2.0/ontologySimilarity/src/TermSetSimData.cpp |only ontologySimilarity-2.0/ontologySimilarity/src/TermSetSimData.h |only ontologySimilarity-2.0/ontologySimilarity/vignettes/ontologySimilarity-examples.Rmd |only ontologySimilarity-2.0/ontologySimilarity/vignettes/ontologySimilarity-introduction.Rmd |only 55 files changed, 698 insertions(+), 970 deletions(-)
More information about ontologySimilarity at CRAN
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Title: Dynamic Linear Regression
Description: Dynamic linear models and time series regression.
Author: Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between dynlm versions 0.3-3 dated 2014-02-20 and 0.3-5 dated 2016-08-05
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 12 ++++++++++++ R/dynlm.R | 17 ++++++++++++----- data/M1Germany.rda |binary 5 files changed, 33 insertions(+), 14 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of
the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial
clustering of applications with noise) and OPTICS (ordering points to identify
the clustering structure) clustering algorithms and the LOF (local outlier
factor) algorithm. The implementations uses the kd-tree data structure (from
library ANN) for faster k-nearest neighbor search. An R interface to fast kNN
and fixed-radius NN search is also provided.
Author: Michael Hahsler [aut, cre, cph],
Matthew Piekenbrock [ctb, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 0.9-7 dated 2016-04-14 and 0.9-8 dated 2016-08-05
DESCRIPTION | 8 ++-- MD5 | 28 +++++++++------- NAMESPACE | 6 ++- R/hullplot.R |only R/kNNdist.R | 2 - R/optics.R | 28 ++++++++++++---- R/opticsXi.R | 63 ++++++++++++++++++++++++++++++-------- README.md | 21 +++++++++++- inst/test_data/elki_optics_xi.rda |binary man/dbscan.Rd | 47 ++++++++++++---------------- man/frNN.Rd | 4 +- man/hullplot.Rd |only man/optics.Rd | 18 ++++++---- src/R_frNN.cpp | 7 +++- src/R_optics.cpp | 32 ++++++++++--------- tests/testthat/test-opticsXi.R | 7 ++-- 16 files changed, 173 insertions(+), 98 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides immunoglobulin (Ig) sequence lineage reconstruction,
diversity profiling, and amino acid property analysis. Also provides
core functionality for other tools in the Change-O suite.
Author: Jason Vander Heiden [aut, cre],
Namita Gupta [aut],
Susanna Marquez [ctb],
Daniel Gadala-Maria [ctb],
Roy Jiang [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between alakazam versions 0.2.4 dated 2016-07-28 and 0.2.5 dated 2016-08-05
DESCRIPTION | 8 ++--- MD5 | 34 +++++++++++----------- NEWS.md | 10 ++++++ R/RcppExports.R | 7 +--- R/Sequence.R | 13 ++++++-- R/Topology.R | 8 +++++ inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.pdf |binary inst/doc/Lineage-Vignette.pdf |binary inst/doc/Topology-Vignette.pdf |binary man/getAAMatrix.Rd | 5 ++- man/plotEdgeTest.Rd | 2 + man/plotMRCATest.Rd | 2 + man/seqEqual.Rd | 5 +-- man/testEdges.Rd | 2 + man/testMRCA.Rd | 2 + src/RcppDistance.cpp | 60 +++++++-------------------------------- src/RcppExports.cpp | 12 ------- 18 files changed, 77 insertions(+), 93 deletions(-)
Title: Utilities for Learning Sparse Bayesian Networks
Description: A set of tools for representing and estimating sparse Bayesian networks from continuous and discrete data.
Author: Bryon Aragam [aut, cre],
Jiaying Gu [aut]
Maintainer: Bryon Aragam <sparsebn@gmail.com>
Diff between sparsebnUtils versions 0.0.1 dated 2016-04-29 and 0.0.2 dated 2016-08-05
sparsebnUtils-0.0.1/sparsebnUtils/man/estimate.covariance.Rd |only sparsebnUtils-0.0.1/sparsebnUtils/man/fit_dag.Rd |only sparsebnUtils-0.0.1/sparsebnUtils/man/lambda.grid.Rd |only sparsebnUtils-0.0.1/sparsebnUtils/man/plot.sparsebnFit.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/DESCRIPTION | 20 sparsebnUtils-0.0.2/sparsebnUtils/MD5 | 94 ++- sparsebnUtils-0.0.2/sparsebnUtils/NAMESPACE | 62 +- sparsebnUtils-0.0.2/sparsebnUtils/R/bnlearn-compatibility.R |only sparsebnUtils-0.0.2/sparsebnUtils/R/graph-compatibility.R | 10 sparsebnUtils-0.0.2/sparsebnUtils/R/igraph-compatibility.R | 28 - sparsebnUtils-0.0.2/sparsebnUtils/R/network-compatibility.R | 15 sparsebnUtils-0.0.2/sparsebnUtils/R/s3-edgeList.R | 98 ++- sparsebnUtils-0.0.2/sparsebnUtils/R/s3-generics.R | 87 ++- sparsebnUtils-0.0.2/sparsebnUtils/R/s3-sparsebnData.R | 131 ++++ sparsebnUtils-0.0.2/sparsebnUtils/R/s3-sparsebnFit.R | 135 ++-- sparsebnUtils-0.0.2/sparsebnUtils/R/s3-sparsebnPath.R | 82 ++- sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-covariance.R |only sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-defaults.R |only sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-functions.R | 122 ++++ sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-generate.R |only sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-inference.R | 271 ++++++---- sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-messages.R | 41 + sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-options.R | 46 + sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-selection.R |only sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-show.R |only sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils-utils.R | 4 sparsebnUtils-0.0.2/sparsebnUtils/R/sparsebnUtils.R | 6 sparsebnUtils-0.0.2/sparsebnUtils/README.md | 2 sparsebnUtils-0.0.2/sparsebnUtils/man/coerce_discrete.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/estimate.parameters.Rd | 3 sparsebnUtils-0.0.2/sparsebnUtils/man/fit_glm_dag.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/fit_multinom_dag.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/get.covariance.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/get.lambdas.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/get.solution.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/plot.edgeList.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/random.dag.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/random.psd.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/select.parameter.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/setGraphPackage.Rd | 13 sparsebnUtils-0.0.2/sparsebnUtils/man/show.parents.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/man/sparsebn-functions.Rd | 33 + sparsebnUtils-0.0.2/sparsebnUtils/man/sparsebn-messages.Rd | 22 sparsebnUtils-0.0.2/sparsebnUtils/man/sparsebnData.Rd | 56 +- sparsebnUtils-0.0.2/sparsebnUtils/man/sparsebnFit.Rd | 19 sparsebnUtils-0.0.2/sparsebnUtils/man/sparsebnPath.Rd | 6 sparsebnUtils-0.0.2/sparsebnUtils/man/sparsebnUtils.Rd | 6 sparsebnUtils-0.0.2/sparsebnUtils/man/to_bn.Rd |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/helper-sparsebnUtils-generate_objects.R | 96 +++ sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-coerce_discrete.R |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-compatibility.R | 102 +++ sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-edgeList.R | 17 sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-fit_multinom_dag.R |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-get_adjacency_matrix.R | 6 sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-get_coef_matrix.R |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-get_solution.R |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-graphNEL.R |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-inference.R |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-num_edges.R | 6 sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-select_parameter.R |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-show_parents.R |only sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-sparsebnData.R | 26 sparsebnUtils-0.0.2/sparsebnUtils/tests/testthat/test-sparsebnFit.R | 2 63 files changed, 1289 insertions(+), 378 deletions(-)
Title: Multivariate Linear Model with Analytic p-Values
Description: Allows a user to conduct multivariate multiple regression using analytic p-values rather than classic approximate F-tests.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>
Diff between MVLM versions 0.0.0 dated 2016-06-16 and 0.0.1 dated 2016-08-05
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/MVLM-package.R | 11 +++++++---- R/mvlm.R | 18 +++++++++++------- inst/doc/mvlm-vignette.Rmd | 6 +++--- inst/doc/mvlm-vignette.html | 10 +++++----- man/MVLM-package.Rd | 11 +++++++---- man/mvlm.Rd | 12 +++++++----- man/summary.mvlm.Rd | 6 ++++-- vignettes/mvlm-vignette.Rmd | 6 +++--- 11 files changed, 66 insertions(+), 48 deletions(-)
Title: Multivariate Distance Matrix Regression
Description: Allows a user to conduct multivariate distance matrix regression using analytic p-values and compute measures of effect size.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>
Diff between MDMR versions 0.4.0 dated 2016-03-31 and 0.4.1 dated 2016-08-05
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++------------ R/MDMR-package.R | 12 +++++------ R/mdmr.R | 45 ++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/mdmr-vignette.Rmd | 16 +++++++-------- inst/doc/mdmr-vignette.html | 33 +++++++++++++++----------------- man/MDMR-package.Rd | 12 +++++------ man/delta.Rd | 16 +++++++-------- man/mdmr.Rd | 15 +++++++------- man/print.mdmr.Rd | 2 - man/summary.mdmr.Rd | 8 +++---- vignettes/mdmr-vignette.Rmd | 16 +++++++-------- 13 files changed, 104 insertions(+), 103 deletions(-)
Title: Average Positive Predictive Values (AP) for Binary Outcomes and
Censored Event Times
Description: We provide tools to estimate two prediction performance metrics,
the average positive predictive values (AP) as well as the well-known AUC
(the area under the receiver operator characteristic curve) for risk scores
or marker. The outcome of interest is either binary or censored event time.
Note that for censored event time, our functions estimate the AP and the
AUC are time-dependent for pre-specified time interval(s). A function that
compares the APs of two risk scores/markers is also included. Optional
outputs include positive predictive values and true positive fractions at
the specified marker cut-off values, and a plot of the time-dependent AP
versus time (available for event time data).
Author: Hengrui Cai <hengruicai@gmail.com>, Yan Yuan <yyuan@ualberta.ca>, Qian
Michelle Zhou <qz70@msstate.edu>, Bingying Li<dorisli1120@gmail.com>
Maintainer: Hengrui Cai <hengruicai@gmail.com>
Diff between APtools versions 2.0 dated 2016-06-22 and 3.0 dated 2016-08-05
DESCRIPTION | 8 - MD5 | 18 ++-- NAMESPACE | 2 R/APBinary.R | 45 +++++++--- R/APSurv.R | 182 ++++++++++++++++++++++++++++++------------- R/CompareAP.R | 228 +++++++++++++++++++++++++++++++++++++++---------------- man/APBinary.Rd | 13 +-- man/APSurv.Rd | 8 - man/APtools.Rd | 14 ++- man/CompareAP.Rd | 7 - 10 files changed, 359 insertions(+), 166 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre],
David Meyer [aut],
Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between slam versions 0.1-35 dated 2016-06-14 and 0.1-37 dated 2016-08-05
DESCRIPTION | 6 - MD5 | 36 +++++----- NAMESPACE | 2 R/array.R | 28 +++++--- R/matrix.R | 44 ++++++++---- R/reduce.R | 9 +- R/rollup.R | 39 +++-------- R/subassign.R | 20 +++-- man/rollup.Rd | 4 - src/grouped.c | 157 ++++++++++++++++++++++++++++++++++----------- src/sparse.c | 76 +++++++++++++++------ tests/apply.R | 6 + tests/apply.Rout.save | 19 ++++- tests/extract.R | 22 ++++++ tests/extract.Rout.save | 43 +++++++++++- tests/stm.R | 36 ++++++++++ tests/stm.Rout.save | 52 +++++++++++++- tests/stm_rollup.R | 32 +++++++++ tests/stm_rollup.Rout.save | 48 ++++++++++++- 19 files changed, 516 insertions(+), 163 deletions(-)
Title: Fragment Analysis in R
Description: Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Author: Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Brandon Schlautman, Walter Salazar, Juan Zalapa.
Maintainer: Giovanny Covarrubias-Pazaran <covarrubiasp@wisc.edu>
Diff between Fragman versions 1.0.5 dated 2016-06-24 and 1.0.6 dated 2016-08-05
DESCRIPTION | 8 ++-- MD5 | 22 ++++++------ NAMESPACE | 2 - R/find.ladder.R | 47 +++++++++++++++++++------- R/ladder.corrector.R | 82 +++++++++++++++++++++++++++++++++------------- R/ladder.info.attach.R | 12 ++++-- R/overview2.R | 6 +-- R/score.easy.R | 4 +- man/ladder.info.attach.Rd | 20 ++--------- man/overview.Rd | 5 +- man/overview2.Rd | 23 ++++-------- man/score.easy.Rd | 40 ++++++++-------------- 12 files changed, 154 insertions(+), 117 deletions(-)
Title: Feature Set Enrichment Analysis for Metabolomics and
Transcriptomics
Description: Methods and feature set definitions for feature or gene set
enrichment analysis in transcriptional and metabolic profiling data.
Package includes tests for enrichment based on ranked lists of features,
functions for visualisation and multivariate functional analysis.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between tmod versions 0.27 dated 2016-06-04 and 0.30 dated 2016-08-05
tmod-0.27/tmod/vignettes/tmod_cache |only tmod-0.27/tmod/vignettes/tmod_files |only tmod-0.30/tmod/DESCRIPTION | 8 tmod-0.30/tmod/MD5 | 281 ++---------------- tmod-0.30/tmod/NAMESPACE | 4 tmod-0.30/tmod/NEWS | 17 + tmod-0.30/tmod/R/panelplots.R | 197 +++++------- tmod-0.30/tmod/R/plotwidgets.R |only tmod-0.30/tmod/R/visualizations.R | 62 +++- tmod-0.30/tmod/build/vignette.rds |binary tmod-0.30/tmod/data/Egambia.rda |binary tmod-0.30/tmod/data/modmetabo.rda |binary tmod-0.30/tmod/data/tbmprof.rda |binary tmod-0.30/tmod/data/tmod.rda |binary tmod-0.30/tmod/inst/doc/tmod.R | 446 ++++++++++++++++++++++++++++- tmod-0.30/tmod/inst/doc/tmod.pdf |binary tmod-0.30/tmod/inst/doc/tmod.rmd | 10 tmod-0.30/tmod/man/Egambia.Rd | 4 tmod-0.30/tmod/man/evidencePlot.Rd | 2 tmod-0.30/tmod/man/extract-methods.Rd | 2 tmod-0.30/tmod/man/getGenes.Rd | 2 tmod-0.30/tmod/man/getModuleMembers.Rd | 2 tmod-0.30/tmod/man/hgEnrichmentPlot.Rd | 2 tmod-0.30/tmod/man/modmetabo.Rd | 4 tmod-0.30/tmod/man/pvalEffectPlot.Rd | 11 tmod-0.30/tmod/man/showGene.Rd | 4 tmod-0.30/tmod/man/showModule.Rd | 2 tmod-0.30/tmod/man/simplePie.Rd | 48 ++- tmod-0.30/tmod/man/tmod-class.Rd | 6 tmod-0.30/tmod/man/tmod-data.Rd | 4 tmod-0.30/tmod/man/tmod-package.Rd | 2 tmod-0.30/tmod/man/tmodAUC.Rd | 2 tmod-0.30/tmod/man/tmodDecideTests.Rd | 6 tmod-0.30/tmod/man/tmodImportMSigDB.Rd | 2 tmod-0.30/tmod/man/tmodLimmaDecideTests.Rd | 4 tmod-0.30/tmod/man/tmodLimmaTest.Rd | 2 tmod-0.30/tmod/man/tmodLimmaTopTable.Rd | 2 tmod-0.30/tmod/man/tmodPCA.Rd | 6 tmod-0.30/tmod/man/tmodPal.Rd |only tmod-0.30/tmod/man/tmodPanelPlot.Rd | 12 tmod-0.30/tmod/man/tmodSummary.Rd | 6 tmod-0.30/tmod/man/tmodTagcloud.Rd | 2 tmod-0.30/tmod/man/tmodUtest.Rd | 6 tmod-0.30/tmod/vignettes/tmod.rmd | 10 44 files changed, 757 insertions(+), 423 deletions(-)
Title: 'Rcpp' Integration of the 'Streamulus' 'DSEL' for Stream
Processing
Description: The 'Streamulus' (template, header-only) library by
Irit Katriel (at <https://github.com/iritkatriel/streamulus>)
provides a very powerful yet convenient framework for stream
processing. This package connects 'Streamulus' to R by providing
both the header files and all examples.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppStreams versions 0.1.0 dated 2015-01-31 and 0.1.1 dated 2016-08-05
ChangeLog | 27 +++++++++++++ DESCRIPTION | 26 +++++++------ MD5 | 39 ++++++++++--------- README.md | 23 ++++++++--- inst/NEWS.Rd | 12 ++++++ inst/include/RcppStreams.h |only inst/include/composed_func.h | 2 - inst/include/engine.h | 12 +++--- inst/include/streamulus.h | 6 ++- inst/include/strop_data_source.h | 8 ++-- inst/include/transforms.h | 14 +++---- man/commonSubexpressions.Rd | 2 - man/crossAlert.Rd | 2 - man/helloStream.Rd | 2 - man/slidingWindow.Rd | 2 - src/Makevars | 6 ++- src/RcppExports.cpp | 53 +++++++++----------------- src/common.cpp | 5 +- src/hello.cpp | 31 +-------------- src/movavg.cpp | 78 +++++++++++++++++++++++++++------------ src/sliding.cpp | 2 - 21 files changed, 201 insertions(+), 151 deletions(-)
Title: Compositional Data Analysis
Description: A collection of functions for compositional data analysis.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Compositional versions 1.6 dated 2016-08-01 and 1.8 dated 2016-08-05
Compositional-1.6/Compositional/R/d.dirichlet.R |only Compositional-1.6/Compositional/man/d.dirichlet.Rd |only Compositional-1.8/Compositional/DESCRIPTION | 8 Compositional-1.8/Compositional/MD5 | 138 +++++------ Compositional-1.8/Compositional/NAMESPACE | 8 Compositional-1.8/Compositional/R/alfa.R | 6 Compositional-1.8/Compositional/R/alfa.knn.R | 8 Compositional-1.8/Compositional/R/alfa.profile.R | 2 Compositional-1.8/Compositional/R/alfa.rda.R | 1 Compositional-1.8/Compositional/R/alfa.reg.R | 8 Compositional-1.8/Compositional/R/alfa.ridge.R | 1 Compositional-1.8/Compositional/R/alfa.tune.R | 2 Compositional-1.8/Compositional/R/alfadist.R | 4 Compositional-1.8/Compositional/R/alfainv.R | 4 Compositional-1.8/Compositional/R/alfaknn.tune.R | 6 Compositional-1.8/Compositional/R/alfapcr.tune.R | 4 Compositional-1.8/Compositional/R/alfareg.tune.R | 7 Compositional-1.8/Compositional/R/alfaridge.tune.R | 7 Compositional-1.8/Compositional/R/bic.mixcompnorm.R | 5 Compositional-1.8/Compositional/R/bivt.contour.R | 4 Compositional-1.8/Compositional/R/comp.den.R | 8 Compositional-1.8/Compositional/R/comp.kerncontour.R | 4 Compositional-1.8/Compositional/R/comp.knn.R | 24 - Compositional-1.8/Compositional/R/comp.reg.R | 4 Compositional-1.8/Compositional/R/comp.test.R | 2 Compositional-1.8/Compositional/R/compknn.tune.R | 22 - Compositional-1.8/Compositional/R/ddiri.R |only Compositional-1.8/Compositional/R/diri.contour.R | 5 Compositional-1.8/Compositional/R/diri.est.R | 2 Compositional-1.8/Compositional/R/diri.nr.R | 4 Compositional-1.8/Compositional/R/diri.reg.R | 8 Compositional-1.8/Compositional/R/diri.reg2.R | 6 Compositional-1.8/Compositional/R/dirimean.test.R | 2 Compositional-1.8/Compositional/R/eel.test1.R | 4 Compositional-1.8/Compositional/R/el.test1.R | 2 Compositional-1.8/Compositional/R/frechet.R | 6 Compositional-1.8/Compositional/R/glm.pcr.R | 6 Compositional-1.8/Compositional/R/glmpcr.tune.R | 11 Compositional-1.8/Compositional/R/helm.R | 3 Compositional-1.8/Compositional/R/js.compreg.R | 6 Compositional-1.8/Compositional/R/kl.compreg.R | 6 Compositional-1.8/Compositional/R/kl.diri.R | 2 Compositional-1.8/Compositional/R/maov.R | 4 Compositional-1.8/Compositional/R/mix.compnorm.R | 8 Compositional-1.8/Compositional/R/mixnorm.contour.R | 6 Compositional-1.8/Compositional/R/mkde.R | 6 Compositional-1.8/Compositional/R/multivreg.R | 4 Compositional-1.8/Compositional/R/multivt.R | 4 Compositional-1.8/Compositional/R/norm.contour.R | 6 Compositional-1.8/Compositional/R/ols.compreg.R | 6 Compositional-1.8/Compositional/R/pcr.R | 2 Compositional-1.8/Compositional/R/pcr.tune.R | 11 Compositional-1.8/Compositional/R/rcompnorm.R | 4 Compositional-1.8/Compositional/R/rcompsn.R | 2 Compositional-1.8/Compositional/R/rcompt.R | 2 Compositional-1.8/Compositional/R/rda.R | 4 Compositional-1.8/Compositional/R/rda.tune.R | 6 Compositional-1.8/Compositional/R/rdiri.R | 2 Compositional-1.8/Compositional/R/ridge.reg.R | 4 Compositional-1.8/Compositional/R/ridge.tune.R | 6 Compositional-1.8/Compositional/R/rmixcomp.R | 4 Compositional-1.8/Compositional/R/skewnorm.contour.R | 4 Compositional-1.8/Compositional/R/spatmed.reg.R | 4 Compositional-1.8/Compositional/R/sscov.R | 2 Compositional-1.8/Compositional/R/ternary.R | 6 Compositional-1.8/Compositional/man/Compositional-package.Rd | 9 Compositional-1.8/Compositional/man/alfa.reg.Rd | 3 Compositional-1.8/Compositional/man/ddiri.Rd |only Compositional-1.8/Compositional/man/diri.est.Rd | 2 Compositional-1.8/Compositional/man/diri.nr.Rd | 2 Compositional-1.8/Compositional/man/dirimean.test.Rd | 2 Compositional-1.8/Compositional/man/el.test1.Rd | 4 72 files changed, 246 insertions(+), 243 deletions(-)
Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>
Diff between survey versions 3.30-3 dated 2014-08-15 and 3.31 dated 2016-08-05
DESCRIPTION | 21 ++++++----- MD5 | 88 ++++++++++++++++++++++++----------------------- NAMESPACE | 6 ++- R/DBI.R | 44 +++++++++++------------ R/chisqsum.R | 7 +-- R/dbiupdate.R | 10 ++--- R/grake.R | 5 +- R/logrank.R | 2 - R/mrb.R | 4 +- R/odbc.R | 8 ++-- R/olr.R | 11 ++--- R/pFsum.R | 6 +-- R/pps.R | 2 - R/regtest.R | 3 + R/survey.R | 5 +- R/surveyby.R | 6 +-- R/surveygraph.R | 18 ++++----- R/surveyrep.R | 9 ++-- R/svykm.R | 2 - R/svymi.R | 31 ++++++++-------- R/svypredmeans.R |only R/svysmooth.R | 14 ++----- R/sysdata.rda |binary R/twophase2.R | 1 THANKS | 1 build/vignette.rds |binary data/api.rda |binary data/crowd.rda |binary data/election.rda |binary data/fpc.rda |binary data/hospital.rda |binary data/mu284.rda |binary data/nhanes.rda |binary data/scd.rda |binary inst/CITATION | 6 +-- inst/NEWS | 32 +++++++++++++++++ man/calibrate.Rd | 2 - man/hadamard.Rd | 2 - man/marginpred.Rd | 4 +- man/pchisqsum.Rd | 2 - man/postStratify.Rd | 1 man/regTermTest.Rd | 4 ++ man/svypredmeans.Rd |only tests/nwts-cch.Rout.save | 44 ++++++++++++----------- tests/scoping.Rout.save | 29 ++++++++------- tests/twophase.Rout.save | 19 +++------- 46 files changed, 238 insertions(+), 211 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 1.4.24 dated 2016-02-02 and 1.4.25 dated 2016-08-05
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- R/invgauss.R | 18 ++++++++++++++++-- R/permp.R | 8 ++++---- R/qres.R | 34 +++++++++++++++++----------------- inst/CITATION |only inst/NEWS | 21 ++++++++++++++++++++- man/invgauss.Rd | 34 +++++++--------------------------- man/permp.Rd | 2 +- man/remlscorgamma.Rd | 4 ++-- 10 files changed, 80 insertions(+), 66 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Athineou, Michail Tsagris, Giorgos Borboudakis, Anna Roumpelaki
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>
Diff between MXM versions 0.9.3 dated 2016-07-10 and 0.9.4 dated 2016-08-05
DESCRIPTION | 10 - MD5 | 49 ++++---- NAMESPACE | 6 - R/MMPC.R | 106 +++++++----------- R/SES.R | 128 +++++++++++---------- R/auc.R |only R/cat.ci.R | 29 ++-- R/cvmmpc.par.R | 2 R/cvses.par.R | 2 R/gSquare.R | 7 - R/glm.fsreg.R | 50 ++++++-- R/lm.fsreg.R | 29 +++- R/mmmb.R | 288 +++++++++++++++++++++++++------------------------ R/pc.skel.R | 49 ++++---- R/ridge.plot.R | 6 - R/ridge.reg.R | 4 R/ridgereg.cv.R | 10 - R/tc.plot.R | 8 - R/testIndFisher.R | 2 R/testIndSpearman.R | 11 - inst |only man/MXM-package.Rd | 4 man/SES.Rd | 5 man/auc.Rd |only man/gSquare.Rd | 6 - man/ridgereg.cv.Rd | 2 man/testIndLogistic.Rd | 2 27 files changed, 429 insertions(+), 386 deletions(-)
Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local and Zellner priors. Bayes factors, marginal densities and variable selection in regression setups. Routines to sample, evaluate prior densities, distribution functions and quantiles are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 1.7.1 dated 2016-05-17 and 1.8.0 dated 2016-08-05
mombf-1.7.1/mombf/R/dimom.R |only mombf-1.7.1/mombf/R/emom.R |only mombf-1.7.1/mombf/R/g2mode.R |only mombf-1.7.1/mombf/R/imombf.R |only mombf-1.7.1/mombf/R/imombf.lm.R |only mombf-1.7.1/mombf/R/imomknown.R |only mombf-1.7.1/mombf/R/imomunknown.R |only mombf-1.7.1/mombf/R/margpemom.R |only mombf-1.7.1/mombf/R/margpimom.R |only mombf-1.7.1/mombf/R/margpmom.R |only mombf-1.7.1/mombf/R/margskewnorm.R |only mombf-1.7.1/mombf/R/mode2g.R |only mombf-1.7.1/mombf/R/mombf.lm.R |only mombf-1.7.1/mombf/R/momknown.R |only mombf-1.7.1/mombf/R/momunknown.R |only mombf-1.7.1/mombf/R/pimom.R |only mombf-1.7.1/mombf/R/pmom.R |only mombf-1.7.1/mombf/R/priorp2g.R |only mombf-1.7.1/mombf/R/qimom.R |only mombf-1.7.1/mombf/R/qmom.R |only mombf-1.8.0/mombf/ChangeLog | 8 mombf-1.8.0/mombf/DESCRIPTION | 19 mombf-1.8.0/mombf/MD5 | 64 - mombf-1.8.0/mombf/NAMESPACE | 12 mombf-1.8.0/mombf/R/alapl.R |only mombf-1.8.0/mombf/R/bms_ortho.R | 114 + mombf-1.8.0/mombf/R/dmom.R | 264 ++++ mombf-1.8.0/mombf/R/modelSelection.R | 126 +- mombf-1.8.0/mombf/R/mombf.R | 170 ++ mombf-1.8.0/mombf/R/nlpMarginal.R |only mombf-1.8.0/mombf/R/pmomLM.R | 16 mombf-1.8.0/mombf/R/pmomPM.R | 10 mombf-1.8.0/mombf/inst/doc/mombf.R | 372 ++++-- mombf-1.8.0/mombf/inst/doc/mombf.Rnw | 1057 +++++++++++------- mombf-1.8.0/mombf/inst/doc/mombf.pdf |binary mombf-1.8.0/mombf/man/dalapl.Rd |only mombf-1.8.0/mombf/man/modelSelection.Rd | 57 mombf-1.8.0/mombf/man/nlpMarginals.Rd | 70 - mombf-1.8.0/mombf/src/do_mombf.h | 15 mombf-1.8.0/mombf/src/modelSel.cpp | 1666 +++++++++++++++++++++++------ mombf-1.8.0/mombf/src/modelSel.h | 57 mombf-1.8.0/mombf/src/modselIntegrals.cpp | 4 mombf-1.8.0/mombf/vignettes/auto |only mombf-1.8.0/mombf/vignettes/mombf.Rnw | 1057 +++++++++++------- mombf-1.8.0/mombf/vignettes/references.bib | 98 + 45 files changed, 3754 insertions(+), 1502 deletions(-)
More information about MetaIntegrator at CRAN
Permanent link
Title: Dockerize R Markdown Documents
Description: Dockerize R Markdown documents with support for Rabix.
Author: Miaozhu Li [ctb],
Tengfei Yin [ctb],
Nan Xiao [aut, cre]
Maintainer: Nan Xiao <me@nanx.me>
Diff between liftr versions 0.3 dated 2015-10-11 and 0.4 dated 2016-08-05
DESCRIPTION | 16 ++++---- MD5 | 36 +++++++++--------- NAMESPACE | 2 - NEWS.md | 7 +++ R/drender.R | 5 +- R/lift.R | 2 - R/liftr-package.R | 4 +- R/utils.R | 2 - README.md | 8 ++-- build/vignette.rds |binary inst/doc/liftr-intro.Rmd | 9 +++- inst/doc/liftr-intro.html | 91 ++++++++++++++++++++++------------------------ inst/docker.Rmd | 2 - inst/rabix.Rmd | 2 - man/drender.Rd | 2 - man/lift.Rd | 2 - man/liftr-package.Rd | 6 +-- vignettes/header.html |only vignettes/liftr-intro.Rmd | 9 +++- vignettes/liftr.css |only 20 files changed, 111 insertions(+), 94 deletions(-)
Title: Sparse Generalized Linear Model with L0 Approximation for
Feature Selection
Description: An efficient procedure for feature selection for generalized linear models with L0 penalty, including linear, logistic, Poisson, gamma, inverse Gaussian regression. Adaptive ridge algorithms are used to fit the models.
Author: Wenchuan Guo, Zhenqiu Liu, Fengzhu Sun, Dermot P McGovern, Sandra
Orsulic
Maintainer: Wenchuan Guo <wguo007@ucr.edu>
Diff between l0ara versions 0.1.2 dated 2016-07-26 and 0.1.3 dated 2016-08-05
DESCRIPTION | 8 +++--- MD5 | 30 +++++++++++++------------ NAMESPACE | 1 NEWS |only R/cv.l0ara.R | 41 +++++++++++++++++++++++++++------- R/l0ara.R | 46 +++++--------------------------------- R/summary.R | 60 +++++++++++++++++++++++++++++++++++--------------- README.md | 21 +++++++++++++++-- man/coef.cv.l0ara.Rd | 2 - man/coef.l0ara.Rd | 2 - man/cv.l0ara.Rd | 6 +++-- man/l0ara.Rd | 12 +++++----- man/plot.cv.l0ara.Rd |only man/plot.l0ara.Rd | 4 ++- man/predict.l0ara.Rd | 2 - man/print.cv.l0ara.Rd | 2 - man/print.l0ara.Rd | 2 - 17 files changed, 141 insertions(+), 98 deletions(-)
Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for
reproducible model validation, calibration, and comparison.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <me@nanx.me>
Maintainer: Nan Xiao <me@nanx.me>
Diff between hdnom versions 4.0 dated 2016-07-05 and 4.1 dated 2016-08-05
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/hdnom-package.R | 2 +- inst/doc/hdnom.html | 4 ++-- man/hdnom-package.Rd | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Description: Convert the 'Ensembl' gene identifiers from Genotype-Tissue Expression (GTEx) data to identifiers in other annotation systems, including 'Entrez', 'HGNC', and 'UniProt'.
Author: Nan Xiao <me@nanx.me>, Gao Wang <gaow@uchicago.edu>, Lei Sun <sunl@uchicago.edu>
Maintainer: Nan Xiao <me@nanx.me>
Diff between grex versions 1.1 dated 2016-06-13 and 1.2 dated 2016-08-05
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/grex-package.R | 5 +++-- README.md | 3 ++- build/vignette.rds |binary inst/doc/grex.Rmd | 6 +++--- inst/doc/grex.html | 12 ++++++------ man/grex-package.Rd | 5 +++-- vignettes/grex.Rmd | 6 +++--- vignettes/header.html | 2 +- 10 files changed, 35 insertions(+), 32 deletions(-)
Title: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by scientific journals and science fiction TV shows.
Author: Nan Xiao <me@nanx.me>, Miaozhu Li <miaozhu.li@duke.edu>
Maintainer: Nan Xiao <me@nanx.me>
Diff between ggsci versions 1.1 dated 2016-04-04 and 1.5 dated 2016-08-05
DESCRIPTION | 11 +++---- MD5 | 69 +++++++++++++++++++++++----------------------- R/01.npg.R | 4 +- R/02.aaas.R | 4 +- R/03.lancet.R | 4 +- R/04.jco.R | 4 +- R/05.ucscgb.R | 4 +- R/06.uchicago.R | 4 +- R/07.simpsons.R | 4 +- R/08.rickandmorty.R | 4 +- R/ggsci-package.R | 2 - README.md | 6 ++-- TODO | 2 + build/vignette.rds |binary inst/doc/ggsci.Rmd | 10 ++++-- inst/doc/ggsci.html | 37 ++++++++++++------------ man/ggsci-package.Rd | 2 - man/pal_aaas.Rd | 2 - man/pal_jco.Rd | 2 - man/pal_lancet.Rd | 2 - man/pal_npg.Rd | 2 - man/pal_rickandmorty.Rd | 2 - man/pal_simpsons.Rd | 2 - man/pal_uchicago.Rd | 2 - man/pal_ucscgb.Rd | 2 - man/scale_aaas.Rd | 2 - man/scale_jco.Rd | 2 - man/scale_lancet.Rd | 2 - man/scale_npg.Rd | 2 - man/scale_rickandmorty.Rd | 2 - man/scale_simpsons.Rd | 2 - man/scale_uchicago.Rd | 2 - man/scale_ucscgb.Rd | 2 - vignettes/ggsci.Rmd | 10 ++++-- vignettes/ggsci.css | 19 +++++++++--- vignettes/header.html |only 36 files changed, 126 insertions(+), 106 deletions(-)
Title: Create 'Formattable' Data Structures
Description: Provides functions to create formattable vectors and data frames.
'Formattable' vectors are printed with text formatting, and formattable
data frames are printed with multiple types of formatting in HTML
to improve the readability of data presented in tabular form rendered in
web pages.
Author: Kun Ren [aut, cre],
Kenton Russell [aut]
Maintainer: Kun Ren <ken@renkun.me>
Diff between formattable versions 0.2 dated 2016-07-28 and 0.2.0.1 dated 2016-08-05
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/formattable.R | 2 +- inst/doc/formattable-data-frame.html | 14 +++++++------- inst/doc/introduction.html | 30 +++++++++++++++--------------- tests/testthat/test-formattable.R | 14 ++++++++++++++ 6 files changed, 47 insertions(+), 33 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer,
Brenton Kenkel, the R Core Team, Michael Benesty, Reynald Lescarbeau,
Andrew Ziem, Luca Scrucca, Yuan Tang, and Can Candan.
Maintainer: Max Kuhn <Max.Kuhn@pfizer.com>
Diff between caret versions 6.0-70 dated 2016-06-13 and 6.0-71 dated 2016-08-05
DESCRIPTION | 15 MD5 | 44 +- NAMESPACE | 17 R/aaa.R | 6 R/calibration.R | 38 +- R/confusionMatrix.R | 90 ++--- R/createModel.R | 3 R/misc.R | 23 + R/prec_rec.R |only R/print.confusionMatrix.R | 171 ++++----- R/print.train.R | 14 R/train.default.R | 27 + R/workflows.R | 750 +++++++++++++++++++++---------------------- build/vignette.rds |binary data/datalist | 3 data/scat.RData |only inst/NEWS.Rd | 13 inst/models/models.RData |binary man/calibration.Rd | 7 man/confusionMatrix.Rd | 21 - man/models.Rd | 49 ++ man/postResample.Rd | 10 man/prec_recall.Rd |only man/print.confusionMatrix.Rd | 4 man/scat.Rd |only 25 files changed, 730 insertions(+), 575 deletions(-)