Title: Mean-Variance Regularization
Description: This is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data. It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm). Among those are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. Key features include:
(i) Normalization and/or variance stabilization of the data,
(ii) Computation of mean-variance-regularized t-statistics (F-statistics to follow),
(iii) Generation of diverse diagnostic plots,
(iv) Computationally efficient implementation using C/C++ interfacing and an option for parallel computing to enjoy a faster and easier experience in the R environment.
Author: Jean-Eudes Dazard [aut, cre],
Hua Xu [ctb],
Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>
Diff between MVR versions 1.32.0 dated 2017-05-29 and 1.32.1 dated 2018-04-16
MVR-1.32.0/MVR/inst/doc/MVR_1.32.0.pdf |only MVR-1.32.1/MVR/DESCRIPTION | 12 +++++++----- MVR-1.32.1/MVR/MD5 | 12 ++++++------ MVR-1.32.1/MVR/R/MVRr.internal.r | 25 ++++++++++++++----------- MVR-1.32.1/MVR/R/MVRr.r | 4 ++++ MVR-1.32.1/MVR/README.md | 12 +++++++----- MVR-1.32.1/MVR/inst/NEWS | 11 ++++++++++- MVR-1.32.1/MVR/inst/doc/MVR_1.32.1.pdf |only 8 files changed, 48 insertions(+), 28 deletions(-)
Title: Batching Routines in Parallel and Passing Command-Line Arguments
to R
Description: Functions to allow you to easily pass command-line arguments into R, and functions to aid in submitting your R code in parallel on a cluster and joining the results afterward (e.g. multiple parameter values for simulations running in parallel, splitting up a permutation test in parallel, etc.). See `parseCommandArgs(...)' for the main example of how to use this package.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between batch versions 1.1-4 dated 2013-06-05 and 1.1-5 dated 2018-04-16
DESCRIPTION | 16 +++++----------- MD5 | 6 +++--- NAMESPACE | 3 +++ R/batch.R | 6 +++--- 4 files changed, 14 insertions(+), 17 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.4-3 dated 2018-04-02 and 2.4-4 dated 2018-04-16
DESCRIPTION | 8 +++---- MD5 | 16 +++++++------- NEWS | 6 +++++ R/data-menu.R | 4 +-- inst/doc/Getting-Started-with-the-Rcmdr.R | 2 - inst/doc/Getting-Started-with-the-Rcmdr.Rnw | 30 --------------------------- inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary man/Rcmdr-package.Rd | 4 +-- vignettes/Getting-Started-with-the-Rcmdr.Rnw | 30 --------------------------- 9 files changed, 23 insertions(+), 77 deletions(-)
Title: Point Density for Geospatial Data
Description: The function pointdensity returns a density count and the temporal average for
every point in the original list. The dataframe returned includes four
columns: lat, lon, count, and date_avg. The "lat" column is the original
latitude data; the "lon" column is the original longitude data; the "count"
is the density count of the number of points within a radius of
radius*grid_size (the neighborhood); and the date_avg column includes the
average date of each point in the neighborhood.
Author: "Paul Evangelista <paul.evangelista@usma.edu> and Dave Beskow
<david.beskow@usma.edu>"
Maintainer: Paul Evangelista <paul.evangelista@usma.edu>
Diff between pointdensityP versions 0.3.2 dated 2018-01-13 and 0.3.3 dated 2018-04-16
pointdensityP-0.3.2/pointdensityP/R/pointdensity_0.3.2.R |only pointdensityP-0.3.3/pointdensityP/DESCRIPTION | 6 +++--- pointdensityP-0.3.3/pointdensityP/MD5 | 4 ++-- pointdensityP-0.3.3/pointdensityP/R/pointdensity_0.3.3.R |only 4 files changed, 5 insertions(+), 5 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: ORPHANED
Diff between XML versions 3.98-1.10 dated 2018-02-19 and 3.98-1.11 dated 2018-04-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 1 + R/assignChild.R | 6 +++++- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Helper Functions to Install and Maintain 'TeX Live', and Compile
'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, Inc. [cph],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.4 dated 2018-03-08 and 0.5 dated 2018-04-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/install.R | 3 ++- R/latex.R | 49 +++++++++++++++++++++++++++++++++---------------- 4 files changed, 41 insertions(+), 23 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Provides p-values in type I, II or III anova and summary
tables for lmer model fits (cf. lme4) via Satterthwaite's degrees of
freedom method. A Kenward-Roger method is also available via the pbkrtest
package. Model selection methods include step, drop1 and anova-like
tables for random effects (ranova). Methods for Least-Square means (LS-means)
and tests of linear contrasts of fixed effects are also available.
Author: Alexandra Kuznetsova [aut],
Per Bruun Brockhoff [aut, ths, cre],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>
Diff between lmerTest versions 2.0-36 dated 2017-11-30 and 3.0-0 dated 2018-04-16
lmerTest-2.0-36/lmerTest/NEWS |only lmerTest-2.0-36/lmerTest/R/anova_related.R |only lmerTest-2.0-36/lmerTest/R/classes.R |only lmerTest-2.0-36/lmerTest/R/deriv.R |only lmerTest-2.0-36/lmerTest/R/generalFunctions.R |only lmerTest-2.0-36/lmerTest/R/linearHypotheses.R |only lmerTest-2.0-36/lmerTest/R/lsmeans.R |only lmerTest-2.0-36/lmerTest/R/rand_related.R |only lmerTest-2.0-36/lmerTest/R/satterth.R |only lmerTest-2.0-36/lmerTest/R/step_related.R |only lmerTest-2.0-36/lmerTest/inst/testdata/MAMexampledata_red.RData |only lmerTest-2.0-36/lmerTest/inst/testdata/NSstdData.RData |only lmerTest-2.0-36/lmerTest/inst/testdata/ProblemSet.RData |only lmerTest-2.0-36/lmerTest/inst/testdata/bread.RData |only lmerTest-2.0-36/lmerTest/inst/testdata/bugSummaryData.RData |only lmerTest-2.0-36/lmerTest/inst/testdata/cltlike.RData |only lmerTest-2.0-36/lmerTest/inst/testdata/tree.RData |only lmerTest-2.0-36/lmerTest/inst/testdata/ttDamon.RData |only lmerTest-2.0-36/lmerTest/inst/tests |only lmerTest-2.0-36/lmerTest/man/anova-methods.Rd |only lmerTest-2.0-36/lmerTest/man/calcSatterth.Rd |only lmerTest-2.0-36/lmerTest/man/difflsmeans.Rd |only lmerTest-2.0-36/lmerTest/man/lsmeans.Rd |only lmerTest-2.0-36/lmerTest/man/lsmeansLT.Rd |only lmerTest-2.0-36/lmerTest/man/merModLmerTest-class.Rd |only lmerTest-2.0-36/lmerTest/man/rand.Rd |only lmerTest-2.0-36/lmerTest/man/summary-methods.Rd |only lmerTest-2.0-36/lmerTest/tests/DamonData.R |only lmerTest-2.0-36/lmerTest/tests/MAMSatterthKR.R |only lmerTest-2.0-36/lmerTest/tests/MAMex.R |only lmerTest-2.0-36/lmerTest/tests/NSstd.R |only lmerTest-2.0-36/lmerTest/tests/OneFixedEff.R |only lmerTest-2.0-36/lmerTest/tests/bugRand.R |only lmerTest-2.0-36/lmerTest/tests/bugRefit.R |only lmerTest-2.0-36/lmerTest/tests/bugUpdate.R |only lmerTest-2.0-36/lmerTest/tests/bugUpdateLmer.R |only lmerTest-2.0-36/lmerTest/tests/bugstep.R |only lmerTest-2.0-36/lmerTest/tests/convergeTest.R |only lmerTest-2.0-36/lmerTest/tests/envir.R |only lmerTest-2.0-36/lmerTest/tests/formulas.R |only lmerTest-2.0-36/lmerTest/tests/lmerMod.R |only lmerTest-2.0-36/lmerTest/tests/packageExamplesExtra.R |only lmerTest-2.0-36/lmerTest/tests/rankDeficiency.R |only lmerTest-2.0-36/lmerTest/tests/rankDeficiency2.R |only lmerTest-2.0-36/lmerTest/tests/summary.R |only lmerTest-2.0-36/lmerTest/tests/summaryDDF.R |only lmerTest-2.0-36/lmerTest/tests/testANCOVA.R |only lmerTest-2.0-36/lmerTest/tests/testContrasts.R |only lmerTest-2.0-36/lmerTest/tests/testExamplesFromPaper.R |only lmerTest-2.0-36/lmerTest/tests/testKeep.R |only lmerTest-2.0-36/lmerTest/tests/testNamesDDF.R |only lmerTest-2.0-36/lmerTest/tests/testRand.R |only lmerTest-2.0-36/lmerTest/tests/testSlopesFactors.R |only lmerTest-2.0-36/lmerTest/tests/testTVbo.R |only lmerTest-2.0-36/lmerTest/tests/testType2.R |only lmerTest-2.0-36/lmerTest/tests/updateData.R |only lmerTest-2.0-36/lmerTest/tests/zeroDenom.R |only lmerTest-3.0-0/lmerTest/DESCRIPTION | 34 - lmerTest-3.0-0/lmerTest/MD5 | 143 +++-- lmerTest-3.0-0/lmerTest/NAMESPACE | 140 +++-- lmerTest-3.0-0/lmerTest/NEWS.md |only lmerTest-3.0-0/lmerTest/R/anova_contrasts.R |only lmerTest-3.0-0/lmerTest/R/contest.R |only lmerTest-3.0-0/lmerTest/R/contrast_utils.R |only lmerTest-3.0-0/lmerTest/R/data_documentation.R |only lmerTest-3.0-0/lmerTest/R/drop1.R |only lmerTest-3.0-0/lmerTest/R/estimability.R |only lmerTest-3.0-0/lmerTest/R/lmer.R |only lmerTest-3.0-0/lmerTest/R/lmerTest.R |only lmerTest-3.0-0/lmerTest/R/lmer_anova.R |only lmerTest-3.0-0/lmerTest/R/lmer_summary.R |only lmerTest-3.0-0/lmerTest/R/ls_means.R |only lmerTest-3.0-0/lmerTest/R/ranova.R |only lmerTest-3.0-0/lmerTest/R/step.R |only lmerTest-3.0-0/lmerTest/R/terms_utils.R |only lmerTest-3.0-0/lmerTest/R/utils.R | 253 +++------- lmerTest-3.0-0/lmerTest/data/carrots.rda |binary lmerTest-3.0-0/lmerTest/inst/testdata/test_paper_objects.RData |only lmerTest-3.0-0/lmerTest/man/TVbo.Rd | 91 +-- lmerTest-3.0-0/lmerTest/man/anova.lmerModLmerTest.Rd |only lmerTest-3.0-0/lmerTest/man/as.data.frame.ls_means.Rd |only lmerTest-3.0-0/lmerTest/man/as_lmerModLmerTest.Rd |only lmerTest-3.0-0/lmerTest/man/carrots.Rd | 126 ++-- lmerTest-3.0-0/lmerTest/man/containment.Rd |only lmerTest-3.0-0/lmerTest/man/contest.Rd |only lmerTest-3.0-0/lmerTest/man/contest.lmerModLmerTest.Rd |only lmerTest-3.0-0/lmerTest/man/contest1D.lmerModLmerTest.Rd |only lmerTest-3.0-0/lmerTest/man/contestMD.lmerModLmerTest.Rd |only lmerTest-3.0-0/lmerTest/man/devfun_vp.Rd |only lmerTest-3.0-0/lmerTest/man/doolittle.Rd |only lmerTest-3.0-0/lmerTest/man/drop1.lmerModLmerTest.Rd |only lmerTest-3.0-0/lmerTest/man/ensure_full_rank.Rd |only lmerTest-3.0-0/lmerTest/man/get_Fstat_ddf.Rd |only lmerTest-3.0-0/lmerTest/man/get_contrasts_type1.Rd |only lmerTest-3.0-0/lmerTest/man/get_contrasts_type3.Rd |only lmerTest-3.0-0/lmerTest/man/get_covbeta.Rd |only lmerTest-3.0-0/lmerTest/man/get_model.Rd |only lmerTest-3.0-0/lmerTest/man/get_model_matrix.Rd |only lmerTest-3.0-0/lmerTest/man/get_rdX.Rd |only lmerTest-3.0-0/lmerTest/man/ham.Rd | 111 ++-- lmerTest-3.0-0/lmerTest/man/is_estimable.Rd |only lmerTest-3.0-0/lmerTest/man/lmer.Rd | 184 +++++-- lmerTest-3.0-0/lmerTest/man/lmerModLmerTest-class.Rd |only lmerTest-3.0-0/lmerTest/man/lmerTest-package.Rd | 246 +++++---- lmerTest-3.0-0/lmerTest/man/ls_means.Rd |only lmerTest-3.0-0/lmerTest/man/ls_means.lmerModLmerTest.Rd |only lmerTest-3.0-0/lmerTest/man/nullspace.Rd |only lmerTest-3.0-0/lmerTest/man/plot.ls_means.Rd |only lmerTest-3.0-0/lmerTest/man/plot.step_list.Rd |only lmerTest-3.0-0/lmerTest/man/qform.Rd |only lmerTest-3.0-0/lmerTest/man/ranova.Rd |only lmerTest-3.0-0/lmerTest/man/rbindall.Rd |only lmerTest-3.0-0/lmerTest/man/rm_complete_terms.Rd |only lmerTest-3.0-0/lmerTest/man/show_tests.Rd |only lmerTest-3.0-0/lmerTest/man/show_tests.anova.Rd |only lmerTest-3.0-0/lmerTest/man/show_tests.ls_means.Rd |only lmerTest-3.0-0/lmerTest/man/single_anova.Rd |only lmerTest-3.0-0/lmerTest/man/step.Rd | 171 +----- lmerTest-3.0-0/lmerTest/man/step.lmerModLmerTest.Rd |only lmerTest-3.0-0/lmerTest/man/summary.lmerModLmerTest.Rd |only lmerTest-3.0-0/lmerTest/man/term_contain.Rd |only lmerTest-3.0-0/lmerTest/tests/test_a_utils.R |only lmerTest-3.0-0/lmerTest/tests/test_anova.R |only lmerTest-3.0-0/lmerTest/tests/test_compare_sas.R |only lmerTest-3.0-0/lmerTest/tests/test_contest1D.R |only lmerTest-3.0-0/lmerTest/tests/test_contestMD.R |only lmerTest-3.0-0/lmerTest/tests/test_drop1.R |only lmerTest-3.0-0/lmerTest/tests/test_lmer.R |only lmerTest-3.0-0/lmerTest/tests/test_lmerTest_paper.R |only lmerTest-3.0-0/lmerTest/tests/test_ls_means.R |only lmerTest-3.0-0/lmerTest/tests/test_ranova_step.R |only lmerTest-3.0-0/lmerTest/tests/test_summary.R |only lmerTest-3.0-0/lmerTest/tests/test_zerovar.R |only lmerTest-3.0-0/lmerTest/tests/zlmerTest_zeroDenom.R |only 134 files changed, 760 insertions(+), 739 deletions(-)
Title: Multi-Purpose Core Subset Selection
Description: Core Hunter is a tool to sample diverse, representative subsets from large germplasm
collections, with minimum redundancy. Such so-called core collections have applications in plant
breeding and genetic resource management in general. Core Hunter can construct cores based on
genetic marker data, phenotypic traits or precomputed distance matrices, optimizing one of many
provided evaluation measures depending on the precise purpose of the core (e.g. high diversity,
representativeness, or allelic richness). In addition, multiple measures can be simultaneously
optimized as part of a weighted index to bring the different perspectives closer together.
The Core Hunter library is implemented in Java 8 as an open source project (see
<http://www.corehunter.org>).
Author: Herman De Beukelaer [aut, cre],
Guy Davenport [aut],
Veerle Fack [ths]
Maintainer: Herman De Beukelaer <herman.debeukelaer@gmail.com>
Diff between corehunter versions 3.2.0 dated 2017-09-08 and 3.2.1 dated 2018-04-16
DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- NEWS.md | 5 +++++ R/java.R | 16 ++++++++++++++-- tests/test.R | 1 + tests/testthat/testJava.R |only 6 files changed, 30 insertions(+), 11 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and R maintainer until
2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 2.41-3 dated 2017-04-04 and 2.42-3 dated 2018-04-16
survival-2.41-3/survival/R/Surv.S |only survival-2.41-3/survival/R/aareg.taper.S |only survival-2.41-3/survival/R/is.ratetable.S |only survival-2.41-3/survival/R/match.ratetable.S |only survival-2.41-3/survival/R/print.cox.zph.S |only survival-2.41-3/survival/R/print.ratetable.S |only survival-2.41-3/survival/R/ratetable.S |only survival-2.41-3/survival/R/ratetableDate.S |only survival-2.41-3/survival/R/summary.ratetable.S |only survival-2.41-3/survival/R/survexp.fit.S |only survival-2.41-3/survival/data/datalist |only survival-2.41-3/survival/tests/mrtest.R |only survival-2.41-3/survival/tests/mrtest.Rout.save |only survival-2.41-3/survival/tests/rounding.Rout.save |only survival-2.41-3/survival/vignettes/mstate.rda |only survival-2.42-3/survival/DESCRIPTION | 11 survival-2.42-3/survival/MD5 | 407 +++++++------- survival-2.42-3/survival/NAMESPACE | 23 survival-2.42-3/survival/R/Surv.R |only survival-2.42-3/survival/R/aareg.taper.R |only survival-2.42-3/survival/R/agexact.fit.S | 68 +- survival-2.42-3/survival/R/agreg.fit.R | 76 +- survival-2.42-3/survival/R/anova.coxph.R | 2 survival-2.42-3/survival/R/anova.coxph.penal.R | 2 survival-2.42-3/survival/R/anova.coxphlist.S | 2 survival-2.42-3/survival/R/cox.zph.S | 8 survival-2.42-3/survival/R/coxexact.fit.R | 78 +- survival-2.42-3/survival/R/coxpenal.fit.R | 9 survival-2.42-3/survival/R/coxph.R | 29 - survival-2.42-3/survival/R/coxph.fit.S | 83 +- survival-2.42-3/survival/R/finegray.R | 2 survival-2.42-3/survival/R/format.Surv.R |only survival-2.42-3/survival/R/frailty.gamma.S | 2 survival-2.42-3/survival/R/frailty.gaussian.S | 2 survival-2.42-3/survival/R/frailty.t.S | 2 survival-2.42-3/survival/R/is.ratetable.R |only survival-2.42-3/survival/R/logLik.coxph.R | 4 survival-2.42-3/survival/R/match.ratetable.R |only survival-2.42-3/survival/R/model.matrix.coxph.R | 8 survival-2.42-3/survival/R/plot.survfit.R | 65 +- survival-2.42-3/survival/R/predict.coxph.R | 17 survival-2.42-3/survival/R/print.aareg.S | 4 survival-2.42-3/survival/R/print.coxph.S | 16 survival-2.42-3/survival/R/print.coxph.penal.S | 11 survival-2.42-3/survival/R/print.ratetable.R |only survival-2.42-3/survival/R/print.summary.coxph.S | 13 survival-2.42-3/survival/R/print.summary.coxph.penal.S | 16 survival-2.42-3/survival/R/print.summary.survreg.S | 8 survival-2.42-3/survival/R/print.survdiff.S | 6 survival-2.42-3/survival/R/print.survreg.S | 6 survival-2.42-3/survival/R/print.survreg.penal.S | 10 survival-2.42-3/survival/R/pspline.R | 4 survival-2.42-3/survival/R/pyears.R | 110 +-- survival-2.42-3/survival/R/ratetable.R |only survival-2.42-3/survival/R/ratetableDate.R |only survival-2.42-3/survival/R/ratetableold.R |only survival-2.42-3/survival/R/residuals.survreg.R | 2 survival-2.42-3/survival/R/statefig.R | 88 ++- survival-2.42-3/survival/R/summary.aareg.S | 3 survival-2.42-3/survival/R/summary.coxph.S | 19 survival-2.42-3/survival/R/summary.coxph.penal.S | 4 survival-2.42-3/survival/R/summary.ratetable.R |only survival-2.42-3/survival/R/survSplit.R | 2 survival-2.42-3/survival/R/survexp.R | 7 survival-2.42-3/survival/R/survexp.fit.R |only survival-2.42-3/survival/R/survfit.R | 48 + survival-2.42-3/survival/R/survfit.coxph.R | 39 - survival-2.42-3/survival/R/survfitCI.R | 50 - survival-2.42-3/survival/R/survfitKM.S | 45 - survival-2.42-3/survival/R/survfitTurnbull.S | 3 survival-2.42-3/survival/R/survreg.S | 10 survival-2.42-3/survival/R/tmerge.R | 24 survival-2.42-3/survival/R/xtras.R | 39 - survival-2.42-3/survival/R/yates.R |only survival-2.42-3/survival/build/vignette.rds |binary survival-2.42-3/survival/cleanup | 2 survival-2.42-3/survival/data/kidney.rda |binary survival-2.42-3/survival/data/ovarian.rda |binary survival-2.42-3/survival/data/solder.rda |only survival-2.42-3/survival/data/survexp.rda |binary survival-2.42-3/survival/inst/NEWS.Rd | 118 ++++ survival-2.42-3/survival/inst/doc/adjcurve.R | 2 survival-2.42-3/survival/inst/doc/adjcurve.Rnw | 2 survival-2.42-3/survival/inst/doc/adjcurve.pdf |binary survival-2.42-3/survival/inst/doc/compete.pdf |binary survival-2.42-3/survival/inst/doc/multi.Rnw | 12 survival-2.42-3/survival/inst/doc/multi.pdf |binary survival-2.42-3/survival/inst/doc/population.R |only survival-2.42-3/survival/inst/doc/population.Rnw |only survival-2.42-3/survival/inst/doc/population.pdf |only survival-2.42-3/survival/inst/doc/splines.pdf |binary survival-2.42-3/survival/inst/doc/tests.R | 24 survival-2.42-3/survival/inst/doc/tests.Rnw | 4 survival-2.42-3/survival/inst/doc/tests.pdf |binary survival-2.42-3/survival/inst/doc/tiedtimes.R | 2 survival-2.42-3/survival/inst/doc/tiedtimes.Rnw | 1 survival-2.42-3/survival/inst/doc/tiedtimes.pdf |binary survival-2.42-3/survival/inst/doc/timedep.R | 59 +- survival-2.42-3/survival/inst/doc/timedep.Rnw | 152 ++++- survival-2.42-3/survival/inst/doc/timedep.pdf |binary survival-2.42-3/survival/inst/doc/validate.R | 2 survival-2.42-3/survival/inst/doc/validate.Rnw | 26 survival-2.42-3/survival/inst/doc/validate.pdf |binary survival-2.42-3/survival/man/agreg.fit.Rd | 12 survival-2.42-3/survival/man/coxph.Rd | 34 - survival-2.42-3/survival/man/coxph.control.Rd | 20 survival-2.42-3/survival/man/lines.survfit.Rd | 11 survival-2.42-3/survival/man/pbc.Rd | 1 survival-2.42-3/survival/man/pbcseq.Rd | 1 survival-2.42-3/survival/man/plot.survfit.Rd | 22 survival-2.42-3/survival/man/predict.coxph.Rd | 14 survival-2.42-3/survival/man/print.survfit.Rd | 3 survival-2.42-3/survival/man/ratetable.Rd | 92 ++- survival-2.42-3/survival/man/solder.Rd |only survival-2.42-3/survival/man/statefig.Rd | 26 survival-2.42-3/survival/man/summary.coxph.Rd | 3 survival-2.42-3/survival/man/summary.survfit.Rd | 2 survival-2.42-3/survival/man/survdiff.Rd | 8 survival-2.42-3/survival/man/survexp.us.Rd | 33 + survival-2.42-3/survival/man/survfit.coxph.Rd | 13 survival-2.42-3/survival/man/survfit.formula.Rd | 12 survival-2.42-3/survival/man/survival-internal.Rd | 14 survival-2.42-3/survival/man/survreg.Rd | 1 survival-2.42-3/survival/man/survreg.distributions.Rd | 5 survival-2.42-3/survival/man/tmerge.Rd | 8 survival-2.42-3/survival/man/vcov.coxph.Rd |only survival-2.42-3/survival/man/yates.Rd |only survival-2.42-3/survival/man/yates_setup.Rd |only survival-2.42-3/survival/noweb/Makefile | 4 survival-2.42-3/survival/noweb/Readme | 2 survival-2.42-3/survival/noweb/agreg.Rnw | 150 +++-- survival-2.42-3/survival/noweb/coxph.Rnw | 42 - survival-2.42-3/survival/noweb/coxsurv.Rnw | 39 - survival-2.42-3/survival/noweb/coxsurv2.Rnw | 2 survival-2.42-3/survival/noweb/finegray.Rnw | 2 survival-2.42-3/survival/noweb/main.Rnw | 14 survival-2.42-3/survival/noweb/msurv.nw | 2 survival-2.42-3/survival/noweb/plot.Rnw | 46 + survival-2.42-3/survival/noweb/plot.Rnw.orig |only survival-2.42-3/survival/noweb/pyears.Rnw | 107 +-- survival-2.42-3/survival/noweb/residuals.survreg.Rnw | 2 survival-2.42-3/survival/noweb/statefig.Rnw | 111 ++- survival-2.42-3/survival/noweb/survexp.Rnw | 7 survival-2.42-3/survival/noweb/survfit.Rnw | 85 ++ survival-2.42-3/survival/noweb/survfitCI.Rnw | 72 -- survival-2.42-3/survival/noweb/survfitKM.Rnw | 2 survival-2.42-3/survival/noweb/tmerge.Rnw | 24 survival-2.42-3/survival/noweb/yates.Rnw | 490 +++++++++-------- survival-2.42-3/survival/noweb/yates2.Rnw |only survival-2.42-3/survival/noweb/zph.Rnw |only survival-2.42-3/survival/src/agexact.c | 1 survival-2.42-3/survival/src/agfit4.c | 67 +- survival-2.42-3/survival/src/agscore.c | 1 survival-2.42-3/survival/src/chinv2.c | 6 survival-2.42-3/survival/src/chinv3.c | 1 survival-2.42-3/survival/src/cholesky2.c | 10 survival-2.42-3/survival/src/cholesky3.c | 11 survival-2.42-3/survival/src/cholesky5.c |only survival-2.42-3/survival/src/chsolve2.c | 6 survival-2.42-3/survival/src/chsolve3.c | 1 survival-2.42-3/survival/src/chsolve5.c |only survival-2.42-3/survival/src/coxdetail.c | 2 survival-2.42-3/survival/src/coxfit6.c | 101 +-- survival-2.42-3/survival/src/coxmart.c | 3 survival-2.42-3/survival/src/coxph_wtest.c | 2 survival-2.42-3/survival/src/coxscho.c | 2 survival-2.42-3/survival/src/coxscore.c | 2 survival-2.42-3/survival/src/doloop.c | 4 survival-2.42-3/survival/src/gchol.c |only survival-2.42-3/survival/src/init.c | 3 survival-2.42-3/survival/src/survConcordance.c | 2 survival-2.42-3/survival/src/survdiff2.c | 1 survival-2.42-3/survival/src/survfit4.c | 1 survival-2.42-3/survival/src/survproto.h | 7 survival-2.42-3/survival/src/survreg6.c | 8 survival-2.42-3/survival/tests/aareg.Rout.save | 15 survival-2.42-3/survival/tests/bladder.R | 3 survival-2.42-3/survival/tests/bladder.Rout.save | 37 - survival-2.42-3/survival/tests/book5.R | 11 survival-2.42-3/survival/tests/book5.Rout.save | 25 survival-2.42-3/survival/tests/book6.Rout.save | 14 survival-2.42-3/survival/tests/cancer.Rout.save | 16 survival-2.42-3/survival/tests/clogit.Rout.save | 17 survival-2.42-3/survival/tests/difftest.Rout.save | 15 survival-2.42-3/survival/tests/doaml.Rout.save | 14 survival-2.42-3/survival/tests/doweight.Rout.save | 24 survival-2.42-3/survival/tests/expected.R | 85 +- survival-2.42-3/survival/tests/expected.Rout.save | 96 +-- survival-2.42-3/survival/tests/expected2.R | 47 + survival-2.42-3/survival/tests/expected2.Rout.save | 61 +- survival-2.42-3/survival/tests/fr_cancer.Rout.save | 18 survival-2.42-3/survival/tests/fr_kidney.Rout.save | 30 - survival-2.42-3/survival/tests/fr_ovarian.Rout.save | 10 survival-2.42-3/survival/tests/fr_rat1.Rout.save | 12 survival-2.42-3/survival/tests/fr_rat2.Rout.save | 20 survival-2.42-3/survival/tests/fr_resid.Rout.save | 12 survival-2.42-3/survival/tests/jasa.Rout.save | 28 survival-2.42-3/survival/tests/ovarian.Rout.save | 30 - survival-2.42-3/survival/tests/r_capacitor.Rout.save | 40 - survival-2.42-3/survival/tests/r_donnell.Rout.save | 12 survival-2.42-3/survival/tests/r_lung.Rout.save | 39 - survival-2.42-3/survival/tests/r_peterson.Rout.save | 41 - survival-2.42-3/survival/tests/r_resid.Rout.save | 30 - survival-2.42-3/survival/tests/r_sas.R | 3 survival-2.42-3/survival/tests/r_sas.Rout.save | 29 - survival-2.42-3/survival/tests/r_stanford.Rout.save | 12 survival-2.42-3/survival/tests/r_strata.Rout.save | 18 survival-2.42-3/survival/tests/r_tdist.Rout.save | 24 survival-2.42-3/survival/tests/ratetable.R | 10 survival-2.42-3/survival/tests/ratetable.Rout.save | 153 ++--- survival-2.42-3/survival/tests/singtest.Rout.save | 13 survival-2.42-3/survival/tests/strata2.Rout.save | 16 survival-2.42-3/survival/tests/testci2.R | 12 survival-2.42-3/survival/tests/testci2.Rout.save | 19 survival-2.42-3/survival/tests/testreg.Rout.save | 89 +-- survival-2.42-3/survival/tests/yates0.R |only survival-2.42-3/survival/tests/yates1.R |only survival-2.42-3/survival/tests/yates1.Rout.save |only survival-2.42-3/survival/tests/yates2.R |only survival-2.42-3/survival/vignettes/adjcurve.Rnw | 2 survival-2.42-3/survival/vignettes/multi.Rnw | 12 survival-2.42-3/survival/vignettes/population.Rnw |only survival-2.42-3/survival/vignettes/refer.bib | 120 +++- survival-2.42-3/survival/vignettes/temp.r |only survival-2.42-3/survival/vignettes/tests.Rnw | 4 survival-2.42-3/survival/vignettes/tiedtimes.Rnw | 1 survival-2.42-3/survival/vignettes/timedep.Rnw | 152 ++++- survival-2.42-3/survival/vignettes/validate.Rnw | 26 228 files changed, 3151 insertions(+), 2039 deletions(-)
Title: Rosenbaum and Rubin Sensitivity
Description: Apply sensitivity analysis for offline policy evaluation, as
implemented in Jung et al. (2017) <arXiv:1702.04690> based
on Rosenbaum and Rubin (1983) <http://www.jstor.org/stable/2345524>.
Author: Jongbin Jung
Maintainer: Jongbin Jung <me@jongbin.com>
Diff between rnr versions 0.2.0 dated 2018-04-12 and 0.2.1 dated 2018-04-16
DESCRIPTION | 6 ++--- MD5 | 10 ++++----- NEWS.md | 4 +++ R/sensitize.R | 47 ++++++++++++++++++++++---------------------- man/sensitize.Rd | 10 ++++----- man/sensitize.data.frame.Rd | 10 +++++---- 6 files changed, 47 insertions(+), 40 deletions(-)
Title: Generation of ENVIREM Variables
Description: Generation of bioclimatic rasters that will be particularly
useful for species distribution modeling.
Author: Pascal O. Title, Jordan B. Bemmels
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between envirem versions 1.2 dated 2018-03-13 and 1.3 dated 2018-04-16
DESCRIPTION | 8 +++---- MD5 | 44 ++++++++++++++++++++-------------------- R/PETseasonality.R | 2 - R/aridityIndexThornthwaite.R | 2 - R/climaticMoistureIndex.R | 2 - R/continentality.R | 2 - R/envirem-package.R | 4 +-- R/layerCreation.R | 28 +++++++++++++++++++++++-- R/monthlyPET.R | 4 +-- R/otherTempExtremes.R | 2 - R/petExtremes.R | 4 +-- R/thermicityIndex.R | 2 - inst/CITATION | 8 +++---- man/PETseasonality.Rd | 2 - man/aridityIndexThornthwaite.Rd | 2 - man/climaticMoistureIndex.Rd | 2 - man/continentality.Rd | 2 - man/envirem.Rd | 4 +-- man/layerCreation.Rd | 4 +-- man/monthlyPET.Rd | 4 +-- man/otherTempExtremes.Rd | 2 - man/petExtremes.Rd | 4 +-- man/thermicityIndex.Rd | 2 - 23 files changed, 82 insertions(+), 58 deletions(-)
Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt [aut, cre],
Yue Hu [aut],
Oliver Keyes [ctb],
Ben Bolker [ctb],
Stefan Müller [ctb]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Diff between dotwhisker versions 0.4.0 dated 2018-04-14 and 0.4.1 dated 2018-04-16
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/add_brackets.R | 14 +++++++------- inst/doc/dotwhisker-vignette.html | 4 ++-- inst/doc/kl2007_examples.html | 6 +++--- 6 files changed, 30 insertions(+), 26 deletions(-)
Title: Analysis of Large Affymetrix Microarray Data Sets
Description: A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Author: Henrik Bengtsson [aut, cre, cph],
James Bullard [ctb],
Kasper Hansen [ctb],
Pierre Neuvial [ctb],
Elizabeth Purdom [ctb],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.affymetrix versions 3.1.0 dated 2017-03-24 and 3.1.1 dated 2018-04-16
DESCRIPTION | 14 MD5 | 582 - NAMESPACE | 26 NEWS | 28 R/006.fixVarArgs.R | 26 R/009.setup.R | 81 R/999.AromaAffymetrix.R | 99 R/999.DEPRECATED.R | 108 R/999.NonDocumentedObjects.R | 6 R/ASCRMAv2.R | 73 R/AbstractProbeSequenceNormalization.R | 1130 +-- R/AdditiveCovariatesNormalization.R | 1720 ++-- R/AffineCnPlm.R | 18 R/AffinePlm.R | 104 R/AffineSnpPlm.R | 17 R/AffyGenePDInfo.writeCdf.R | 894 +- R/AffymetrixAptSummaryFile.R | 266 R/AffymetrixCdfFile.COUNTS.R | 565 - R/AffymetrixCdfFile.MONOCELL.R | 1448 +--- R/AffymetrixCdfFile.PLOT.R | 154 R/AffymetrixCdfFile.R | 3447 ++++------ R/AffymetrixCdfFile.SNPs.R | 99 R/AffymetrixCdfFile.UNIQUE.R | 1398 ++-- R/AffymetrixCdfFile.computeAffinities.R | 1321 +-- R/AffymetrixCdfFile.getAlleleCellPairs.R | 370 - R/AffymetrixCdfFile.getAlleleProbePairs.R | 963 +- R/AffymetrixCdfFile.getAlleleProbePairs2.R | 261 R/AffymetrixCdfFile.getAlleleProbePairs3.R | 762 -- R/AffymetrixCdfFile.getCellQuartets.R | 605 - R/AffymetrixCdfFile.getProbeSequenceData.R | 316 R/AffymetrixCdfFile.getSubsetOfCellIndices.R | 403 - R/AffymetrixCdfFile.getSubsetOfUnits.R | 301 R/AffymetrixCdfFile.getUnitGroupCellMap.R | 555 - R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R | 195 R/AffymetrixCdfFile.groupUnitsByDimension.R | 393 - R/AffymetrixCdfFile.readDataFrame.R | 316 R/AffymetrixCdfFile.writeCdfByExcludingCells.R | 455 - R/AffymetrixCelFile.BG.R | 48 R/AffymetrixCelFile.PLOT.R | 1615 ++-- R/AffymetrixCelFile.R | 2018 ++--- R/AffymetrixCelFile.allocateFromCdf.R | 250 R/AffymetrixCelFile.createFrom.R | 530 - R/AffymetrixCelFile.extractMatrix.R | 141 R/AffymetrixCelFile.fitQuantileNormFcn.R | 211 R/AffymetrixCelFile.normalizeAffine.R | 174 R/AffymetrixCelFile.normalizeQuantile.R | 316 R/AffymetrixCelSet.BG.R | 344 R/AffymetrixCelSet.NORM.R | 699 -- R/AffymetrixCelSet.PLOT.R | 232 R/AffymetrixCelSet.R | 2646 +++---- R/AffymetrixCelSet.convertToUnique.R | 497 - R/AffymetrixCelSet.extractAffyBatch.R | 207 R/AffymetrixCelSet.extractFeatureSet.R | 51 R/AffymetrixCelSet.extractMatrix.R | 267 R/AffymetrixCelSet.getAverageFile.R | 718 -- R/AffymetrixCelSet.importFromDChip.R | 370 - R/AffymetrixCelSet.justSNPRMA.R | 429 - R/AffymetrixCelSet.writeSgr.R | 56 R/AffymetrixCelSetReporter.R | 209 R/AffymetrixCelSetTuple.R | 250 R/AffymetrixCnChpFile.R | 844 +- R/AffymetrixCnChpSet.R | 740 +- R/AffymetrixCnChpSet.extras.R | 228 R/AffymetrixCsvFile.R | 26 R/AffymetrixCsvGenomeInformation.R | 281 R/AffymetrixFile.R | 49 R/AffymetrixFileSet.R | 103 R/AffymetrixFileSet.getIdentifier.R | 36 R/AffymetrixFileSetReporter.R | 25 R/AffymetrixNetAffxCsvFile.R | 765 +- R/AffymetrixNetAffxCsvFile.XTRS.R | 677 - R/AffymetrixPgfFile.R | 767 +- R/AffymetrixPlatform.R | 19 R/AffymetrixProbeTabFile.R | 1398 +--- R/AffymetrixTabularFile.R | 40 R/AffymetrixTsvFile.R | 350 - R/AlleleSummation.R | 604 - R/AllelicCrosstalkCalibration.PLOT.R | 187 R/AllelicCrosstalkCalibration.R | 2632 +++---- R/AllelicCrosstalkCalibration.getSetsOfProbes.R | 644 - R/AromaCellCpgFile.AFFX.R | 84 R/AromaCellMatchScoreFile.AFFX.R | 80 R/AromaCellMatchScoreFile.R | 406 - R/AromaCellMatchScoreFile.importFromBpmap.R | 99 R/AromaCellPositionFile.AFFX.R | 84 R/AromaCellSequenceFile.AFFX.R | 827 +- R/AromaCellSequenceFile.importFromBpmap.R | 94 R/AromaChipTypeAnnotationFile.R | 132 R/AromaPipeline.R | 84 R/AromaUfcFile.R | 478 - R/AromaUflFile.AFFX.R | 209 R/AromaUgpFile.AFFX.R | 414 - R/AromaUnitGcContentFile.AFFX.R | 147 R/AromaUnitTabularBinaryFile.AFFX.PLOT.R | 141 R/AromaUnitTabularBinaryFile.AFFX.R | 334 R/ArrayExplorer.R | 667 - R/AvgCnPlm.R | 17 R/AvgPlm.R | 614 - R/AvgSnpPlm.R | 18 R/BackgroundCorrection.R | 20 R/BaseCountNormalization.R | 1265 +-- R/BasePositionNormalization.R | 412 - R/BasePositionNormalization.getFit.R | 52 R/ChipEffectFile.R | 1905 ++--- R/ChipEffectFile.TOFULL.R | 429 - R/ChipEffectFile.extractTheta.R | 149 R/ChipEffectFile.fromDataFile.R | 260 R/ChipEffectFile.getUnitGroupCellMatrixMap.R | 375 - R/ChipEffectFile.xam.R | 537 - R/ChipEffectGroupMerge.R | 638 - R/ChipEffectNnn.extractChromosomalDataFrame.R | 250 R/ChipEffectSet.PLOT.R | 27 R/ChipEffectSet.R | 795 +- R/ChipEffectSet.STATS.R | 633 - R/ChipEffectSet.TOFULL.R | 76 R/ChipEffectSet.calculateBaseline.R | 633 - R/ChipEffectSet.extractExpressionSet.R | 477 - R/ChipEffectSet.extractTheta.R | 241 R/ChipEffectSet.getBaseline.R | 276 R/ChipEffectSet.xam.R | 524 - R/ChipEffectSetTuple.R | 19 R/ChipEffectTransform.R | 103 R/ChromosomalModel.AFFX.R | 66 R/ChromosomalModel.getPositionChipTypeUnit.R | 251 R/ChromosomalModel.getXTheta.R | 100 R/CnChipEffectFile.R | 728 +- R/CnChipEffectFile.exportAromaSignalBinaryFileList.R | 15 R/CnChipEffectSet.R | 394 - R/CnChipEffectSet.importFromApt.R | 621 - R/CnChipEffectSet.importFromDChip.R | 871 +- R/CnChipEffectSet.writeWig.R | 381 - R/CnChipEffectSetTuple.R | 36 R/CnPlm.R | 272 R/CnProbeAffinityFile.R | 43 R/CnagCfhFile.R | 903 +- R/CnagCfhSet.R | 2065 ++--- R/CopyNumberChromosomalModel.applyCCF.R | 837 +- R/CopyNumberSegmentationModel.migrateTool.R | 171 R/CrlmmModel.EXT.R | 652 - R/CrlmmModel.R | 2093 ++---- R/CrlmmParametersFile.R | 256 R/CrlmmParametersSet.R | 33 R/DChipCdfBinFile.R | 352 - R/DChipCdfBinFile.mapToUnitNamesFile.R | 144 R/DChipDcpFile.R | 226 R/DChipDcpSet.R | 555 - R/DChipDcpSet.extras.R | 326 R/DChipGenomeInformation.R | 682 - R/DChipQuantileNormalization.R | 723 +- R/DChipSnpInformation.R | 508 - R/ExonChipEffectFile.R | 639 - R/ExonChipEffectSet.R | 68 R/ExonProbeAffinityFile.R | 24 R/ExonRmaPlm.R | 749 +- R/ExonRmaPlm.calculateWeights.R | 310 R/FirmaFile.R | 953 +- R/FirmaModel.R | 1506 ++-- R/FirmaSet.R | 415 - R/FragmentEquivalentClassNormalization.R | 1935 ++--- R/FragmentLengthNormalization.R | 2114 ++---- R/GcContentNormalization.R | 987 +- R/GcContentNormalization2.R | 183 R/GcContentNormalization2.plotCovariateEffects.R | 317 R/GcRmaBackgroundCorrection.R | 1088 +-- R/GenericReporter.R | 90 R/GenomeInformation.AFFX.R | 509 - R/GenomeInformation.R | 848 +- R/HetLogAddCnPlm.R | 17 R/HetLogAddPlm.R | 303 R/HetLogAddSnpPlm.R | 18 R/LimmaBackgroundCorrection.R | 737 +- R/LinearModelProbeSequenceNormalization.R | 962 +- R/MatNormalization.R | 1550 ++-- R/MatSmoothing.R | 1344 +-- R/MbeiCnPlm.R | 18 R/MbeiPlm.R | 138 R/MbeiSnpPlm.R | 17 R/Model.R | 184 R/MultiArrayUnitModel.R | 588 - R/NormExpBackgroundCorrection.R | 148 R/OpticalBackgroundCorrection.R | 463 - R/Package.XTRA.R | 44 R/ParameterCelFile.R | 401 - R/ParameterCelFile.extractNnn.R | 295 R/ParameterCelSet.R | 570 - R/ProbeAffinityFile.R | 92 R/ProbeLevelModel.R | 743 -- R/ProbeLevelModel.calculateResiduals.R | 732 -- R/ProbeLevelModel.calculateWeights.R | 290 R/ProbeLevelModel.fit.R | 1197 +-- R/ProbeLevelTransform.R | 14 R/ProbeLevelTransform3.R | 818 +- R/QualityAssessmentFile.R | 151 R/QualityAssessmentModel.R | 1183 +-- R/QualityAssessmentSet.R | 10 R/QuantileNormalization.R | 1178 +-- R/QuantileNormalization.xtra.R | 76 R/ReseqCrosstalkCalibration.R | 1432 ++-- R/ResidualFile.R | 990 +- R/ResidualSet.R | 528 - R/RmaBackgroundCorrection.R | 574 - R/RmaCnPlm.R | 17 R/RmaPlm.R | 1474 ++-- R/RmaSnpPlm.R | 29 R/ScaleNormalization.R | 1007 +- R/ScaleNormalization3.R | 645 - R/SingleArrayUnitModel.R | 382 - R/SingleArrayUnitModel.fit.R | 481 - R/SmoothMultiarrayModel.R | 243 R/SmoothMultiarrayModel.fit.R | 911 +- R/SmoothRmaModel.R | 23 R/SmoothSaModel.R | 21 R/SnpChipEffectFile.R | 637 - R/SnpChipEffectFile.exportTotalAndFracB.R | 296 R/SnpChipEffectFile.extractTotalAndFracB.R | 546 - R/SnpChipEffectGroupMerge.R | 64 R/SnpChipEffectNnn.extractCNT.R | 271 R/SnpChipEffectNnn.writeCNT.R | 371 - R/SnpChipEffectSet.R | 370 - R/SnpChipEffectSet.exportTotalAndFracB.R | 274 R/SnpChipEffectSet.extractAlleleSet.R | 401 - R/SnpChipEffectSet.extractSnpCnvQSet.R | 206 R/SnpChipEffectSet.extractSnpQSet.R | 280 R/SnpChipEffectSet.extractTotalAndFreqB.R | 418 - R/SnpCnvQSet.extractTheta.R | 97 R/SnpInformation.R | 814 +- R/SnpPlm.R | 228 R/SnpProbeAffinityFile.R | 27 R/SnpQSet.extractTheta.R | 118 R/SpatialReporter.R | 917 +- R/SpatialRowColumnNormalization.R | 406 - R/Transform.R | 251 R/TransformReport.R | 1056 +-- R/UflSnpInformation.R | 513 - R/UgpGenomeInformation.R | 592 - R/UnitModel.R | 385 - R/UnitModel.fitCnProbes.R | 334 R/UnitTypeScaleNormalization.R | 815 +- R/WeightsFile.R | 979 +- R/WeightsSet.R | 485 - R/bpmapCluster2Cdf.R | 1037 +-- R/createExonByTranscriptCdf.R | 927 +- R/doCRMAv1.R | 565 - R/doCRMAv2.R | 787 +- R/doFIRMA.R | 626 - R/doGCRMA.R | 633 - R/doRMA.R | 587 - R/dropCellsFromCdfList.R | 312 R/env2Cdf.R | 89 R/findByCdf2.R | 149 R/fitPlasqUnit.R | 799 +- R/getPlasqTypes.R | 16 R/isUnitGroupCellMap.R | 25 R/justRMA.R | 221 R/pdInfo2Cdf.R | 458 - R/plotBoxplotStats.list.R | 85 R/profileCGH.getRegions.R | 256 R/profileCGH.writeRegions.R | 84 R/readCdfGroupStrands.R | 100 R/readCfhHeader.R | 446 - R/readCfhUnits.R | 127 R/readCfnHeader.R | 280 R/readCfnUnits.R | 139 R/setCustomFindCdf.R | 21 R/setupExampleData.R | 11 R/zzz.R | 12 inst/testScripts/annotation/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R | 66 inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Nsp.R | 51 inst/testScripts/complete/dataSets/GSE12702/11.doASCRMAv2,Sty.R | 51 inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Nsp.R | 79 inst/testScripts/complete/dataSets/GSE12702/22.doASCRMAv2,CalMaTe,Sty.R | 79 inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Nsp.R | 3 inst/testScripts/complete/dataSets/GSE12702/31.doASCRMAv2,PairedPSCBS,Sty.R | 3 inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Nsp.R | 3 inst/testScripts/complete/dataSets/GSE12702/32.doASCRMAv2,CalMaTe,PairedPSCBS,Sty.R | 3 inst/testScripts/complete/dataSets/GSE13372/21.doASCRMAv2.R | 51 inst/testScripts/complete/dataSets/GSE13372/22.doASCRMAv2,CalMaTe.R | 79 inst/testScripts/complete/dataSets/GSE13372/31.doASCRMAv2,PairedPSCBS.R | 3 inst/testScripts/complete/dataSets/GSE13372/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 3 inst/testScripts/complete/dataSets/GSE19539/21.doASCRMAv2.R | 51 inst/testScripts/complete/dataSets/GSE19539/22.doASCRMAv2,CalMaTe.R | 79 inst/testScripts/complete/dataSets/GSE20584/21.doASCRMAv2.R | 51 inst/testScripts/complete/dataSets/GSE20584/31.doASCRMAv2,PairedPSCBS.R | 3 inst/testScripts/complete/dataSets/GSE27691/21.doASCRMAv2.R | 51 inst/testScripts/complete/dataSets/GSE34754/21.doASCRMAv2.R | 51 inst/testScripts/complete/dataSets/GSE34754/22.doASCRMAv2,CalMaTe.R | 79 inst/testScripts/complete/dataSets/GSE34754/31.doASCRMAv2,PairedPSCBS.R | 3 inst/testScripts/complete/dataSets/GSE34754/32.doASCRMAv2,CalMaTe,PairedPSCBS.R | 3 inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01a.downloadAnnotationData.R | 50 inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/01b.downloadRawData,GEO.R | 98 inst/testScripts/system/chipTypes/Mapping10K_Xba142/01b.downloadRawData.R | 86 man/createExonByTranscriptCdf.AffymetrixCdfFile.Rd | 12 292 files changed, 61297 insertions(+), 68051 deletions(-)
More information about aroma.affymetrix at CRAN
Permanent link
Title: Fast Imputations Using 'Rcpp' and 'Armadillo'
Description: Fast imputations under the object-oriented programming paradigm.
There was used quantitative models with a closed-form solution. Thus package is based on linear algebra operations.
The biggest improvement in time performance could be achieve for a calculation where a grouping variable have to be used.
A single evaluation of a quantitative model for the multiple imputations is another major enhancement.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between miceFast versions 0.0.2 dated 2018-03-25 and 0.1.0 dated 2018-04-16
DESCRIPTION | 11 + MD5 | 41 +++--- NEWS.md |only inst/doc/miceFast-intro.R | 65 +++++---- inst/doc/miceFast-intro.Rmd | 141 ++++++++++++++------ inst/doc/miceFast-intro.pdf |binary inst/extdata/images/g1.png |binary inst/extdata/images/g2.png |binary inst/extdata/images/g3.png |binary inst/extdata/images/g4.png |binary inst/extdata/images/g5.png |binary inst/extdata/images/g6.png |binary inst/extdata/images/g7.png |binary inst/extdata/images/g8.png |only inst/extdata/images/g9.png |only inst/extdata/performance_validity.R | 60 ++++++++ man/Rcpp_miceFast-class.Rd | 4 src/miceFast.h | 37 +++-- src/miceFast_additfunc.cpp | 33 ++++ src/miceFast_class.cpp | 244 +++++++++++++++++++++--------------- src/miceFast_quantmodels.cpp | 93 +++++++++---- tests/testthat/test-impute_N.R |only tests/testthat/test-vif.R |only vignettes/miceFast-intro.Rmd | 141 ++++++++++++++------ 24 files changed, 590 insertions(+), 280 deletions(-)
Title: Classification of Functional Data
Description: Efficient implementation of k-nearest neighbor estimation and kernel estimation for functional data classification.
Author: Thomas Maierhofer [aut, cre],
Karen Fuchs [ctb],
Florian Pfisterer [aut]
Maintainer: Thomas Maierhofer <thomasjmaierhofer@gmail.com>
Diff between classiFunc versions 0.1.0 dated 2017-05-29 and 0.1.1 dated 2018-04-16
DESCRIPTION | 20 MD5 | 65 +-- NAMESPACE | 6 R/classiFunc.R | 2 R/classiKernel.R | 42 +- R/classiKnn.R | 47 +- R/computeDistMat.R | 164 ++++++-- R/data.R | 174 ++++++++ R/fdataTransform.R | 22 - R/metricChoices.R | 3 README.md |only build/vignette.rds |binary data/BeetleFly.rda |only data/DTI.rda |only data/DTI_original.rda |only data/Growth.rda |only data/Growth_irregular.rda |only inst/doc/classiFunc.R | 102 +++-- inst/doc/classiFunc.Rmd | 116 ++++- inst/doc/classiFunc.html | 543 ++++++++++++++++++++------- man/ArrowHead.Rd | 2 man/BeetleFly.Rd |only man/DTI.Rd |only man/DTI_original.Rd |only man/Growth.Rd |only man/Growth_irregular.Rd |only man/Phoneme.Rd | 2 man/classiFunc.Rd | 1 man/classiKernel.Rd | 17 man/classiKnn.Rd | 20 man/computeDistMat.Rd | 32 + man/fdataTransform.Rd | 2 man/parallelComputeDistMat.Rd |only man/predict.classiKernel.Rd | 7 man/predict.classiKnn.Rd | 9 tests/testthat/test_classiKernel.R | 44 ++ tests/testthat/test_classiKnn.R | 116 +++++ tests/testthat/test_computeDistMat.R | 24 + tests/testthat/test_parallelComputeDistMat.R |only vignettes/classiFunc.Rmd | 116 ++++- 40 files changed, 1337 insertions(+), 361 deletions(-)
Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear models
(see, e.g., Piironen and Vehtari, 2017, <doi:10.1007/s11222-016-9649-y>).
The package is compatible with 'rstanarm' package, but other reference models
can also be used. See the package vignette for more information and examples.
Author: Markus Paasiniemi [cre,aut],
Juho Piironen [aut],
Aki Vehtari [aut],
Jonah Gabry [ctb]
Maintainer: Juho Piironen <juho.piironen@aalto.fi>
Diff between projpred versions 0.7.0 dated 2018-02-19 and 0.8.0 dated 2018-04-16
DESCRIPTION | 26 - MD5 | 70 +-- NAMESPACE | 3 R/cv_varsel.R | 38 +- R/methods.R | 181 +++++++--- R/misc.R | 52 -- R/project.R | 34 + R/projpred-package.R | 2 R/summary_funs.R | 30 - R/varsel.R | 15 build/vignette.rds |binary inst/doc/quickstart.R | 19 - inst/doc/quickstart.Rmd | 33 - inst/doc/quickstart.html | 51 +- man/cv_varsel.Rd | 4 man/project.Rd | 2 man/suggest_size.Rd |only man/varsel-statistics.Rd | 36 + man/varsel.Rd | 2 tests/testthat/test_init_refmodel.R | 2 tests/testthat/test_misc.R |only tests/testthat/test_proj_pred.R | 30 - tests/testthat/test_project.R | 2 tests/testthat/test_varsel.R | 10 vignettes/quickstart.Rmd | 33 - vignettes/quickstart_cache/html/unnamed-chunk-15_f72e24c6655c55da2ac2eb03feba0ecb.RData |binary vignettes/quickstart_cache/html/unnamed-chunk-15_f72e24c6655c55da2ac2eb03feba0ecb.rdb |binary vignettes/quickstart_cache/html/unnamed-chunk-15_f72e24c6655c55da2ac2eb03feba0ecb.rdx |binary vignettes/quickstart_cache/html/unnamed-chunk-18_cedc7110cb5bfa256619ba42ae45edef.RData |binary vignettes/quickstart_cache/html/unnamed-chunk-18_cedc7110cb5bfa256619ba42ae45edef.rdb |binary vignettes/quickstart_cache/html/unnamed-chunk-18_cedc7110cb5bfa256619ba42ae45edef.rdx |binary vignettes/quickstart_cache/html/unnamed-chunk-4_509b39674910f3aab30edb69d03fecb6.RData |binary vignettes/quickstart_cache/html/unnamed-chunk-4_509b39674910f3aab30edb69d03fecb6.rdb |binary vignettes/quickstart_cache/html/unnamed-chunk-4_509b39674910f3aab30edb69d03fecb6.rdx |binary vignettes/quickstart_cache/html/unnamed-chunk-7_53a3a6aefcc6069534dc0f47f73431a4.RData |binary vignettes/quickstart_cache/html/unnamed-chunk-7_53a3a6aefcc6069534dc0f47f73431a4.rdb |binary vignettes/quickstart_cache/html/unnamed-chunk-7_53a3a6aefcc6069534dc0f47f73431a4.rdx |binary 37 files changed, 380 insertions(+), 295 deletions(-)
Title: Multiscale Codependence Analysis
Description: Computation of Multiscale Codependence Analysis and spatial eigenvector maps, as an additional feature.
Author: Guillaume Guenard and Pierre Legendre, Bertrand Pages
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>
Diff between codep versions 0.7-1 dated 2018-01-04 and 0.8-1 dated 2018-04-16
DESCRIPTION | 14 +-- MD5 | 14 +-- NAMESPACE | 3 R/mca.R | 155 ++++++++++++++++++++++++++++++++++++++++++-- man/cdp-class.Rd | 6 - man/codep-package.Rd | 4 + man/mca.Rd | 42 ++++++++++- man/product-distribution.Rd | 6 - 8 files changed, 213 insertions(+), 31 deletions(-)
Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous or categorical data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between clustrd versions 1.2.0 dated 2017-05-29 and 1.2.1 dated 2018-04-16
clustrd-1.2.0/clustrd/data/underwear.rda |only clustrd-1.2.0/clustrd/man/underwear.Rd |only clustrd-1.2.1/clustrd/DESCRIPTION | 8 +- clustrd-1.2.1/clustrd/MD5 | 24 +++---- clustrd-1.2.1/clustrd/NAMESPACE | 1 clustrd-1.2.1/clustrd/R/EmptyKmeans.r | 5 - clustrd-1.2.1/clustrd/R/MCAk.r | 2 clustrd-1.2.1/clustrd/R/clusCA.R | 6 - clustrd-1.2.1/clustrd/R/clusmca.R | 3 clustrd-1.2.1/clustrd/R/cluspca.R | 85 ++++++++++++++-------------- clustrd-1.2.1/clustrd/R/outOfIndependence.r | 3 clustrd-1.2.1/clustrd/R/rosplit.r | 6 - clustrd-1.2.1/clustrd/man/plot.clusmca.Rd | 6 - clustrd-1.2.1/clustrd/man/tuneclus.Rd | 4 - 14 files changed, 74 insertions(+), 79 deletions(-)
Title: Semiparametic Regression
Description: Functions for semiparametric regression analysis, to
complement the book: Ruppert, D., Wand, M.P. and Carroll, R.J.
(2003). Semiparametric Regression. Cambridge University Press.
Author: Matt Wand <mwand@uts.edu.au>
Maintainer: Billy Aung Myint <r@use-r.com>
Diff between SemiPar versions 1.0-4.1 dated 2014-09-23 and 1.0-4.2 dated 2018-04-16
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 17 +++++++++++++++++ man/fitted.spm.Rd | 2 +- man/lines.spm.Rd | 4 ++-- man/plot.spm.Rd | 4 ++-- man/predict.spm.Rd | 2 +- man/print.spm.Rd | 2 +- man/residuals.spm.Rd | 2 +- man/spm.Rd | 4 ++-- man/summary.spm.Rd | 2 +- 11 files changed, 42 insertions(+), 25 deletions(-)
Title: Provides Access to Databases Through the JDBC Interface
Description: The RJDBC package is an implementation of R's DBI interface using JDBC as a back-end. This allows R to connect to any DBMS that has a JDBC driver.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between RJDBC versions 0.2-7 dated 2018-01-24 and 0.2-7.1 dated 2018-04-16
DESCRIPTION | 6 +++--- MD5 | 4 ++-- man/JDBCConnection-methods.Rd | 4 ++++ 3 files changed, 9 insertions(+), 5 deletions(-)
Title: Loading Google Adwords Data into R
Description: Aims at loading Google Adwords data into R. Adwords is an online
advertising service that enables advertisers to display advertising copy to web
users (see <https://developers.google.com/adwords/> for more information).
Therefore the package implements three main features. First, the package
provides an authentication process for R with the Google Adwords API (see
<https://developers.google.com/adwords/api/> for more information) via OAUTH2.
Second, the package offers an interface to apply the Adwords query language in
R and query the Adwords API with ad-hoc reports. Third, the received data are
transformed into suitable data formats for further data processing and data
analysis.
Author: Johannes Burkhardt <johannes.burkhardt@gmail.com>, Matthias Bannert
<matthias.bannert@gmail.com>
Maintainer: Johannes Burkhardt <johannes.burkhardt@gmail.com>
Diff between RAdwords versions 0.1.15 dated 2018-02-21 and 0.1.16 dated 2018-04-16
RAdwords-0.1.15/RAdwords/inst/extdata/api201702 |only RAdwords-0.1.15/RAdwords/inst/extdata/api201708 |only RAdwords-0.1.16/RAdwords/DESCRIPTION | 6 RAdwords-0.1.16/RAdwords/MD5 | 158 ++++++++---------------- RAdwords-0.1.16/RAdwords/NEWS | 7 + RAdwords-0.1.16/RAdwords/R/getData.R | 4 RAdwords-0.1.16/RAdwords/R/metrics.R | 7 - RAdwords-0.1.16/RAdwords/R/reports.R | 7 - RAdwords-0.1.16/RAdwords/R/transformData.R | 12 - RAdwords-0.1.16/RAdwords/inst/extdata/api201802 |only RAdwords-0.1.16/RAdwords/man/getData.Rd | 4 RAdwords-0.1.16/RAdwords/man/metrics.Rd | 4 RAdwords-0.1.16/RAdwords/man/reports.Rd | 4 RAdwords-0.1.16/RAdwords/man/transformData.Rd | 4 14 files changed, 87 insertions(+), 130 deletions(-)
Title: Implementation of POSIXct Work-Alike for 365 and 360 Day
Calendars
Description: Provides a work-alike to R's POSIXct class which implements
360- and 365-day calendars in addition to the gregorian calendar.
Author: David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate
Impacts Consortium (PCIC); portions based on code written by
the R-Core team and Ulrich Drepper.
Maintainer: David Bronaugh <bronaugh@uvic.ca>
Diff between PCICt versions 0.5-4 dated 2013-06-27 and 0.5-4.1 dated 2018-04-16
DESCRIPTION | 17 ++++++++--------- MD5 | 4 ++-- NAMESPACE | 14 ++++++++++++++ 3 files changed, 24 insertions(+), 11 deletions(-)
Title: Higher Order Inference for Nonlinear Heteroscedastic Models
Description: Likelihood inference based on higher order approximations
for nonlinear models with possibly non constant variance.
Author: S original by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>
and Ruggero Bellio <ruggero.bellio@uniud.it>. R port by Alessandra R.
Brazzale <alessandra.brazzale@unipd.it>, following earlier work by
Douglas Bates.
Maintainer: Alessandra R. Brazzale <alessandra.brazzale@unipd.it>
Diff between nlreg versions 1.2-2 dated 2014-04-03 and 1.2-2.1 dated 2018-04-16
nlreg-1.2-2.1/nlreg/DESCRIPTION | 10 +++---- nlreg-1.2-2.1/nlreg/MD5 | 29 +++++++++----------- nlreg-1.2-2.1/nlreg/NAMESPACE | 41 +++++++++++++++++++++++++++++ nlreg-1.2-2.1/nlreg/data/C1.rda |binary nlreg-1.2-2.1/nlreg/data/C2.rda |binary nlreg-1.2-2.1/nlreg/data/C3.rda |binary nlreg-1.2-2.1/nlreg/data/C4.rda |binary nlreg-1.2-2.1/nlreg/data/M2.rda |binary nlreg-1.2-2.1/nlreg/data/M4.rda |binary nlreg-1.2-2.1/nlreg/data/chlorsulfuron.rda |binary nlreg-1.2-2.1/nlreg/data/daphnia.rda |binary nlreg-1.2-2.1/nlreg/data/helicopter.rda |binary nlreg-1.2-2.1/nlreg/data/metsulfuron.rda |binary nlreg-1.2-2.1/nlreg/data/ria.rda |binary nlreg-1.2-2.1/nlreg/inst/CITATION | 6 ++-- nlreg-1.2-2/nlreg/INDEX |only 16 files changed, 63 insertions(+), 23 deletions(-)
Title: Night and Day Boundary Plot Function
Description: Computes and plots the boundary between night and day.
Author: Max Hughes-Brandl
Maintainer: Max Hughes-Brandl <gordonmax@hotmail.de>
Diff between NightDay versions 1.0.1 dated 2011-04-28 and 1.0.1.1 dated 2018-04-16
DESCRIPTION | 9 +++++---- MD5 |only NAMESPACE |only 3 files changed, 5 insertions(+), 4 deletions(-)
Title: Approximate Marginal Inference for Regression-Scale Models
Description: Likelihood inference based on higher order approximations
for linear nonnormal regression models.
Author: S original by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>.
R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following
earlier work by Douglas Bates.
Maintainer: Alessandra R. Brazzale <alessandra.brazzale@unipd.it>
Diff between marg versions 1.2-2 dated 2014-04-03 and 1.2-2.1 dated 2018-04-16
marg-1.2-2.1/marg/DESCRIPTION | 12 ++++++------ marg-1.2-2.1/marg/MD5 | 15 +++++++-------- marg-1.2-2.1/marg/NAMESPACE | 32 ++++++++++++++++++++++++++++++++ marg-1.2-2.1/marg/data/darwin.rda |binary marg-1.2-2.1/marg/data/houses.rda |binary marg-1.2-2.1/marg/data/nuclear.rda |binary marg-1.2-2.1/marg/data/venice.rda |binary marg-1.2-2.1/marg/inst/CITATION | 6 +++--- marg-1.2-2/marg/INDEX |only 9 files changed, 48 insertions(+), 17 deletions(-)
Title: Functions for Conditional Simulation in Regression-Scale Models
Description: Monte Carlo conditional inference for the parameters of a
linear nonnormal regression model.
Author: S original by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>.
R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>.
Maintainer: Alessandra R. Brazzale <alessandra.brazzale@unipd.it>
Diff between csampling versions 1.2-2 dated 2014-04-03 and 1.2-2.1 dated 2018-04-16
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 8 ++++++++ inst/CITATION | 6 +++--- 4 files changed, 19 insertions(+), 11 deletions(-)
Title: Approximate Conditional Inference for Logistic and Loglinear
Models
Description: Higher order likelihood-based inference for logistic and
loglinear models.
Author: S original by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>.
R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following
earlier work by Douglas Bates.
Maintainer: Alessandra R. Brazzale <alessandra.brazzale@unipd.it>
Diff between cond versions 1.2-3 dated 2014-06-27 and 1.2-3.1 dated 2018-04-16
cond-1.2-3.1/cond/DESCRIPTION | 14 +++++++------- cond-1.2-3.1/cond/MD5 | 23 +++++++++++------------ cond-1.2-3.1/cond/NAMESPACE | 18 ++++++++++++++++++ cond-1.2-3.1/cond/data/aids.rda |binary cond-1.2-3.1/cond/data/airway.rda |binary cond-1.2-3.1/cond/data/babies.rda |binary cond-1.2-3.1/cond/data/dormicum.rda |binary cond-1.2-3.1/cond/data/fraudulent.rda |binary cond-1.2-3.1/cond/data/fungal.rda |binary cond-1.2-3.1/cond/data/rabbits.rda |binary cond-1.2-3.1/cond/data/urine.rda |binary cond-1.2-3.1/cond/inst/CITATION | 6 +++--- cond-1.2-3/cond/INDEX |only 13 files changed, 39 insertions(+), 22 deletions(-)
Title: Comparative Analyses of Phylogenetics and Evolution in R
Description: Functions for performing phylogenetic comparative analyses.
Author: David Orme, Rob Freckleton, Gavin Thomas, Thomas Petzoldt, Susanne Fritz, Nick Isaac, Will Pearse
Maintainer: David Orme <d.orme@imperial.ac.uk>
Diff between caper versions 0.5.1 dated 2013-11-29 and 0.5.2.1 dated 2018-04-16
caper |only 1 file changed
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of a categorical
variable; modelsum(), which performs simple model fits on the same endpoint
for many variables (univariate or adjusted for standard covariates);
freqlist(), a powerful frequency table across many categorical variables;
compare.data.frame(), the S3 method for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 1.1.0 dated 2018-03-13 and 1.2.0 dated 2018-04-16
DESCRIPTION | 8 MD5 | 51 NAMESPACE | 3 NEWS.md | 6 R/summary.tableby.R | 2 R/tableby.control.R | 12 R/write2.R | 12 inst/doc/compare.html | 2 inst/doc/freqlist.html | 2 inst/doc/labels.html | 170 +- inst/doc/modelsum.html | 4 inst/doc/tableby.html | 2520 +++++++++++++++---------------- inst/doc/write2.R | 140 + inst/doc/write2.Rmd | 145 + inst/doc/write2.html | 145 + man/tableby.control.Rd | 12 man/write2.Rd | 9 tests/testthat/test_keep.labels.R | 20 tests/testthat/test_tableby.R | 692 ++++---- tests/testthat/test_write2.R | 13 tests/testthat/write2.multititles.pdf.md |only tests/testthat/write2.mylist.pdf.md | 12 tests/testthat/write2.mylist2.doc.md | 12 tests/testthat/write2.mylists.pdf.md | 24 tests/testthat/write2.tableby.html.md | 18 tests/testthat/write2.yaml.pdf.md | 12 vignettes/write2.Rmd | 145 + 27 files changed, 2174 insertions(+), 2017 deletions(-)
Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly minimizing the negative log likelihood function using the gradient descent algorithm. Multiple starting values should be used to avoid local minima.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun (Jack) Xu <zekunxu@gmail.com>
Diff between ziphsmm versions 2.0.3 dated 2018-04-06 and 2.0.4 dated 2018-04-16
DESCRIPTION | 10 MD5 | 39 +- NAMESPACE | 8 R/RcppExports.R | 58 +++- R/dist_learn.R | 24 - R/dist_learn2.R | 18 - R/dist_learn3.R |only R/fasthmmfit.cont.R | 3 R/fasthmmfit.cont3.R |only R/hmmsim2.cont.R | 1 R/hmmsim3.cont.R |only R/hmmsmooth.cont3.R |only R/package.R | 5 man/convolution.Rd |only man/dist_learn3.Rd |only man/fasthmmfit.cont.Rd | 5 man/fasthmmfit.cont3.Rd |only man/hmmsim2.cont.Rd | 1 man/hmmsim3.cont.Rd |only man/hmmsmooth.cont3.Rd |only man/package-ziphsmm.Rd | 4 man/retrieve_cov_cont3.Rd |only man/zipnegloglik_cov_cont3.Rd |only src/RcppExports.cpp | 142 ++++++++- src/init.c | 2 src/rcpparma_hello_world.cpp | 604 +++++++++++++++++++++++++++++++++++++++++- 26 files changed, 855 insertions(+), 69 deletions(-)
Title: Choose Univariate Class Intervals
Description: Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
Author: Roger Bivand [aut, cre] (<https://orcid.org/0000-0003-2392-6140>),
Hisaji Ono [ctb],
Richard Dunlap [ctb],
Matthieu Stigler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between classInt versions 0.1-24 dated 2017-04-16 and 0.2-3 dated 2018-04-16
classInt-0.1-24/classInt/data |only classInt-0.1-24/classInt/man/jenks71.Rd |only classInt-0.2-3/classInt/ChangeLog | 79 ++++++++++------- classInt-0.2-3/classInt/DESCRIPTION | 16 +-- classInt-0.2-3/classInt/MD5 | 24 ++--- classInt-0.2-3/classInt/NAMESPACE | 4 classInt-0.2-3/classInt/R/classInt.R | 10 +- classInt-0.2-3/classInt/inst/ChangeLog | 79 ++++++++++------- classInt-0.2-3/classInt/man/classIntervals.Rd | 6 - classInt-0.2-3/classInt/man/findColours.Rd | 2 classInt-0.2-3/classInt/man/findCols.Rd | 2 classInt-0.2-3/classInt/man/getBclustClassIntervals.Rd | 2 classInt-0.2-3/classInt/man/jenks.tests.Rd | 2 classInt-0.2-3/classInt/tests/test_Unique.Rout.save | 15 +-- 14 files changed, 144 insertions(+), 97 deletions(-)
Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation for finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the recent improvements in Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi (<http://orcid.org/0000-0001-9538-0648>)
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between bmixture versions 0.6 dated 2018-03-19 and 0.7 dated 2018-04-16
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/CITATION | 4 ++-- man/bmixture-package.Rd | 4 ++-- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>.
Some features are
1) Use of CDISC SDTM terms
2) Automatic slope selection with the same criterion of WinNonlin(R)
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between NonCompart versions 0.4.0 dated 2018-03-17 and 0.4.1 dated 2018-04-16
DESCRIPTION | 8 +++---- MD5 | 46 +++++++++++++++++++++++++---------------- NAMESPACE | 2 - R/DetSlope.R | 41 ++++++++++++++++++++++-------------- R/sNCA.R | 9 +++++--- R/tblNCA.R | 2 - inst/NEWS.Rd | 7 ++++++ inst/doc/NonCompart-manual.pdf |binary inst/doc/Validation.pdf |only man/BestSlope.Rd | 12 +++++----- man/DetSlope.Rd | 14 +++++++----- man/LinAUC.Rd | 8 +++---- man/LogAUC.Rd | 8 +++---- man/NonCompart-package.Rd | 2 - man/Slope.Rd | 12 +++++----- man/Unit.Rd | 4 +-- man/UnitUrine.Rd | 2 - man/sNCA.Rd | 6 ++--- man/tblNCA.Rd | 4 +-- tests |only 20 files changed, 110 insertions(+), 77 deletions(-)
Title: Calculate Key DHS Indicators
Description: Calculates key indicators such as fertility rates (Total Fertility Rate (TFR), General Fertility Rate (GFR),
and Age Specific Fertility Rate (ASFR)) using Demographic and Health Survey (DHS) women/individual data,
and childhood mortality rates such as Neonatal Mortality Rate (NNMR), Post-neonatal Mortality Rate (PNNMR),
Infant Mortality Rate (IMR), Child Mortality Rate (CMR), and Under-5 Mortality Rate (U5MR).
In addition to the indicators, the 'DHS.rates' package estimates precision indicators such as Standard Error (SE),
Design Effect (DEFT), Relative Standard Error (RSE) and Confidence Interval (CI).
The package is developed according to the DHS methodology of calculating the fertility indicators and
the childhood mortality rates outlined in the
"DHS Guide to Statistics" (Rutstein and Rojas 2006, <http://dhsprogram.com/pubs/pdf/DHSG1/Guide_to_DHS_Statistics_29Oct2012_DHSG1.pdf>)
and the DHS methodology of estimating the precision indicators outlined in
the "DHS Sampling and Household Listing Manual" (ICF International 2012, <https://dhsprogram.com/pubs/pdf/DHSM4/DHS6_Sampling_Manual_Sept2012_DHSM4.pdf>).
Author: Mahmoud Elkasabi
Maintainer: Mahmoud Elkasabi <mahmoud.elkasabi@icf.com>
Diff between DHS.rates versions 0.2.0 dated 2018-03-11 and 0.3.0 dated 2018-04-16
DESCRIPTION | 27 +++++++++++-------- MD5 | 34 ++++++++++++++---------- NAMESPACE | 1 R/ASFR.R | 8 ++--- R/CHMORT5.R |only R/DataPrepare.R | 8 +++-- R/GFR.R | 8 ++--- R/TFR.R | 8 ++--- R/chmort.R |only R/data.R | 17 ++++++++++++ R/fert.R | 26 +++++++++++------- build/vignette.rds |binary data/ADBR70.rda |only inst/doc/DHS.rates.R | 16 +++++++++++ inst/doc/DHS.rates.Rmd | 64 ++++++++++++++++++++++++++++++++++++++++----- inst/doc/DHS.rates.html | 68 +++++++++++++++++++++++++++++++++++++++++++----- man/ADBR70.Rd |only man/chmort.Rd |only man/fert.Rd | 6 ++-- vignettes/DHS.rates.Rmd | 64 ++++++++++++++++++++++++++++++++++++++++----- vignettes/rsconnect |only 21 files changed, 285 insertions(+), 70 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2016) <arXiv:1604.04768>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <http://www.jstor.org/stable/2345592>. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses, the adjusted score approaches return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre],
Kjell Konis [ctb],
Euloge Clovis Kenne Pagui [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 0.1.7 dated 2018-02-23 and 0.1.8 dated 2018-04-16
brglm2-0.1.7/brglm2/inst/dev_resids.R |only brglm2-0.1.7/brglm2/inst/doc/iteration.pdf |only brglm2-0.1.8/brglm2/DESCRIPTION | 15 - brglm2-0.1.8/brglm2/MD5 | 41 +-- brglm2-0.1.8/brglm2/NAMESPACE | 1 brglm2-0.1.8/brglm2/NEWS.md | 11 brglm2-0.1.8/brglm2/R/brglmFit.R | 4 brglm2-0.1.8/brglm2/R/brmultinom.R | 40 ++- brglm2-0.1.8/brglm2/README.md | 17 - brglm2-0.1.8/brglm2/build/vignette.rds |binary brglm2-0.1.8/brglm2/inst/doc/iteration.R | 7 brglm2-0.1.8/brglm2/inst/doc/iteration.Rmd | 7 brglm2-0.1.8/brglm2/inst/doc/iteration.html |only brglm2-0.1.8/brglm2/inst/doc/multinomial.R | 8 brglm2-0.1.8/brglm2/inst/doc/multinomial.Rmd | 11 brglm2-0.1.8/brglm2/inst/doc/multinomial.html | 328 ++++++++++++-------------- brglm2-0.1.8/brglm2/inst/doc/separation.R | 8 brglm2-0.1.8/brglm2/inst/doc/separation.Rmd | 10 brglm2-0.1.8/brglm2/inst/doc/separation.html | 166 ++++++------- brglm2-0.1.8/brglm2/man/brmultinom.Rd | 2 brglm2-0.1.8/brglm2/vignettes/iteration.Rmd | 7 brglm2-0.1.8/brglm2/vignettes/multinomial.Rmd | 11 brglm2-0.1.8/brglm2/vignettes/separation.Rmd | 10 23 files changed, 396 insertions(+), 308 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-10-15 2.0
2010-08-31 1.2.1
2008-04-02 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-06 0.4
2016-10-03 0.2
2016-10-01 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-23 1.0.3
2017-09-22 1.0.2
2016-01-02 1.0
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common univariate
statistics in concise tables available in a variety of
formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 0.8.2 dated 2018-02-11 and 0.8.3 dated 2018-04-16
summarytools-0.8.2/summarytools/R/misc.R |only summarytools-0.8.2/summarytools/inst/includes/stylesheets/custom.css |only summarytools-0.8.3/summarytools/DESCRIPTION | 7 summarytools-0.8.3/summarytools/MD5 | 62 summarytools-0.8.3/summarytools/NAMESPACE | 5 summarytools-0.8.3/summarytools/NEWS | 17 summarytools-0.8.3/summarytools/R/ctable.R | 110 summarytools-0.8.3/summarytools/R/descr.R | 417 + summarytools-0.8.3/summarytools/R/dfSummary.R | 222 - summarytools-0.8.3/summarytools/R/examens.R | 2 summarytools-0.8.3/summarytools/R/exams.R | 2 summarytools-0.8.3/summarytools/R/freq.R | 87 summarytools-0.8.3/summarytools/R/options.R |only summarytools-0.8.3/summarytools/R/parse_args.R | 22 summarytools-0.8.3/summarytools/R/print.summarytools.R | 667 ++- summarytools-0.8.3/summarytools/R/view.R | 217 summarytools-0.8.3/summarytools/build/vignette.rds |binary summarytools-0.8.3/summarytools/inst/doc/Introduction.R | 125 summarytools-0.8.3/summarytools/inst/doc/Introduction.Rmd | 442 +- summarytools-0.8.3/summarytools/inst/doc/Introduction.html | 1651 +++++-- summarytools-0.8.3/summarytools/inst/doc/Recommendations-rmarkdown.R | 50 summarytools-0.8.3/summarytools/inst/doc/Recommendations-rmarkdown.Rmd | 229 - summarytools-0.8.3/summarytools/inst/doc/Recommendations-rmarkdown.html | 2171 +++------- summarytools-0.8.3/summarytools/inst/includes/stylesheets/summarytools.css |only summarytools-0.8.3/summarytools/man/ctable.Rd | 28 summarytools-0.8.3/summarytools/man/descr.Rd | 59 summarytools-0.8.3/summarytools/man/dfSummary.Rd | 55 summarytools-0.8.3/summarytools/man/examens.Rd | 2 summarytools-0.8.3/summarytools/man/exams.Rd | 2 summarytools-0.8.3/summarytools/man/freq.Rd | 44 summarytools-0.8.3/summarytools/man/print.summarytools.Rd | 83 summarytools-0.8.3/summarytools/man/st_options.Rd |only summarytools-0.8.3/summarytools/vignettes/Introduction.Rmd | 442 +- summarytools-0.8.3/summarytools/vignettes/Recommendations-rmarkdown.Rmd | 229 - summarytools-0.8.3/summarytools/vignettes/dfSummary-iris.png |only 35 files changed, 4340 insertions(+), 3109 deletions(-)
Title: Database Query Interfaces
Description: Wrapper to 'RODBC'. Supports parameterised, multi-statement, 'SQL' scripts, with embedded 'R'. Implicit handling of connection channels and communication parameters.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>
Diff between SQRL versions 0.2.1 dated 2018-03-10 and 0.3.0 dated 2018-04-16
DESCRIPTION | 12 MD5 | 22 - R/SQRL.R | 1102 +++++++++++++++++++++++++++++++++++++++++++--------- build/partial.rdb |binary man/SQRL-package.Rd | 8 man/sqrlAll.Rd | 3 man/sqrlConfig.Rd | 6 man/sqrlParams.Rd | 16 man/sqrlScript.Rd | 24 - man/sqrlSource.Rd | 20 man/sqrlSources.Rd | 8 man/sqrlUsage.Rd | 67 ++- 12 files changed, 1039 insertions(+), 249 deletions(-)
Title: Omnibus Test for Genetic Association Analysis using the Rank
Normal Transformation
Description: Implementation of genetic association tests that utilize the rank based inverse normal transformation (INT). The primary contribution is an omnibus test, which synthesizes two complementary INT-based approaches. In simulations against phenotypes with skewed and heavy tailed residual distributions, the omnibus test provided valid inference in the absence of a genotypic effect, and provided power comparable to the more powerful of the component methods in the presence of a genotypic effect. Under these settings, standard linear regression often failed to control the type I error.
Author: Zachary McCaw [aut, cre]
Maintainer: Zachary McCaw <zmccaw@g.harvard.edu>
Diff between RNOmni versions 0.2.1 dated 2018-04-02 and 0.2.2 dated 2018-04-16
RNOmni-0.2.1/RNOmni/man/dotP.Rd |only RNOmni-0.2.1/RNOmni/man/eps.Rd |only RNOmni-0.2.1/RNOmni/man/errProj.Rd |only RNOmni-0.2.1/RNOmni/man/scaleParam.Rd |only RNOmni-0.2.1/RNOmni/man/scoreStat.Rd |only RNOmni-0.2.2/RNOmni/DESCRIPTION | 6 RNOmni-0.2.2/RNOmni/MD5 | 42 +++-- RNOmni-0.2.2/RNOmni/NAMESPACE | 15 + RNOmni-0.2.2/RNOmni/R/RankNormal.R | 236 +++++++++++++++++-------------- RNOmni-0.2.2/RNOmni/R/RcppExports.R | 141 ++++++++++++++---- RNOmni-0.2.2/RNOmni/inst/doc/RNOmni.html | 2 RNOmni-0.2.2/RNOmni/man/BAT.Rd | 4 RNOmni-0.2.2/RNOmni/man/DINT.Rd | 4 RNOmni-0.2.2/RNOmni/man/FIINT.Rd | 4 RNOmni-0.2.2/RNOmni/man/IINT.Rd | 4 RNOmni-0.2.2/RNOmni/man/RNOmni.Rd | 4 RNOmni-0.2.2/RNOmni/man/SchurC.Rd |only RNOmni-0.2.2/RNOmni/man/fastDet.Rd |only RNOmni-0.2.2/RNOmni/man/fastIP.Rd |only RNOmni-0.2.2/RNOmni/man/fastInv.Rd |only RNOmni-0.2.2/RNOmni/man/fastMMp.Rd |only RNOmni-0.2.2/RNOmni/man/fastMvp.Rd |only RNOmni-0.2.2/RNOmni/man/fastT.Rd |only RNOmni-0.2.2/RNOmni/man/fitNorm.Rd |only RNOmni-0.2.2/RNOmni/man/incP.Rd |only RNOmni-0.2.2/RNOmni/man/matQF.Rd |only RNOmni-0.2.2/RNOmni/man/vecCor.Rd |only RNOmni-0.2.2/RNOmni/man/vecQF.Rd |only RNOmni-0.2.2/RNOmni/src/MatrixOps.cpp |only RNOmni-0.2.2/RNOmni/src/RNOmni.cpp | 115 +++++---------- RNOmni-0.2.2/RNOmni/src/RcppExports.cpp | 152 +++++++++++++++---- 31 files changed, 456 insertions(+), 273 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.3.8.4 dated 2018-03-17 and 0.3.8.6 dated 2018-04-16
DESCRIPTION | 8 MD5 | 154 ++--- R/ANOVA.R | 85 +- R/ARMA.R | 318 +++++----- R/ARMA_optim.R | 91 +- R/Binary_ANOVA.R | 106 +-- R/Causal_matrix.R | 34 - R/Causation.R | 92 +- R/Co_PM_cor.R | 80 +- R/Correlation.R | 20 R/Dependence.R | 133 ++-- R/Dependence_matrix.R | 31 - R/FSD.R | 37 - R/LPM_UPM_VaR.R | 30 R/Multivariate_Regression.R | 342 ++++++----- R/NNS_term_matrix.R | 77 +- R/Normalization.R | 56 - R/Numerical_Differentiation.R | 173 ++--- R/Partial_Moments.R | 260 ++++---- R/Partition_Map.R | 306 +++++---- R/Regression.R | 584 ++++++++++--------- R/SD_Efficient_Set.R | 82 +- R/SSD.R | 33 - R/Seasonality_Test.R | 99 +-- R/Stack.R | 161 +++-- R/TSD.R | 28 R/Uni_Causation.R | 107 +-- R/Uni_SD_Routines.R | 89 +- R/dy_d_wrt.R | 169 +++-- R/dy_dx.R | 133 ++-- inst/doc/NNSvignette_Clustering_and_Regression.R | 26 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 36 - inst/doc/NNSvignette_Clustering_and_Regression.html | 42 - inst/doc/NNSvignette_Correlation_and_Dependence.R | 18 inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 18 inst/doc/NNSvignette_Correlation_and_Dependence.html | 18 inst/doc/NNSvignette_Forecasting.R | 30 inst/doc/NNSvignette_Forecasting.Rmd | 64 +- inst/doc/NNSvignette_Forecasting.html | 86 +- inst/doc/NNSvignette_Partial_Moments.R | 52 - inst/doc/NNSvignette_Partial_Moments.Rmd | 54 - inst/doc/NNSvignette_Partial_Moments.html | 54 - man/Co.LPM.Rd | 4 man/Co.UPM.Rd | 2 man/D.LPM.Rd | 4 man/D.UPM.Rd | 4 man/LPM.Rd | 4 man/LPM.VaR.Rd | 9 man/LPM.ratio.Rd | 12 man/NNS.ANOVA.Rd | 22 man/NNS.ARMA.Rd | 30 man/NNS.ARMA.optim.Rd | 17 man/NNS.FSD.Rd | 4 man/NNS.FSD.uni.Rd | 4 man/NNS.PDF.Rd | 4 man/NNS.SD.efficient.set.Rd | 8 man/NNS.SSD.Rd | 2 man/NNS.caus.Rd | 14 man/NNS.cor.Rd | 10 man/NNS.cor.hd.Rd | 6 man/NNS.dep.Rd | 10 man/NNS.diff.Rd | 12 man/NNS.norm.Rd | 8 man/NNS.part.Rd | 30 man/NNS.reg.Rd | 67 +- man/NNS.seas.Rd | 2 man/NNS.stack.Rd | 20 man/NNS.term.matrix.Rd | 10 man/PM.matrix.Rd | 8 man/UPM.Rd | 4 man/UPM.VaR.Rd | 9 man/UPM.ratio.Rd | 18 man/dy.d_.Rd | 35 - man/dy.dx.Rd | 23 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 36 - vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 18 vignettes/NNSvignette_Forecasting.Rmd | 64 +- vignettes/NNSvignette_Partial_Moments.Rmd | 54 - 78 files changed, 2666 insertions(+), 2338 deletions(-)
Title: Sparse Gaussian Markov Random Field Mixtures for Anomaly
Detection
Description: An implementation of sparse Gaussian Markov random field mixtures
presented by Ide et al. (2016) <doi:10.1109/ICDM.2016.0119>.
It provides a novel anomaly detection method for multivariate noisy sensor data.
It can automatically handle multiple operational modes.
And it can also compute variable-wise anomaly scores.
Author: Koji Makiyama [cre, aut]
Maintainer: Koji Makiyama <hoxo.smile@gmail.com>
Diff between sGMRFmix versions 0.2.0 dated 2018-03-18 and 0.3.0 dated 2018-04-16
DESCRIPTION | 6 ++-- MD5 | 18 +++++++------- NEWS.md | 6 ++++ R/GMRFmix.R | 8 ------ R/sGMRFmix.R | 18 +++++++++----- R/sparseGaussMix.R | 1 inst/doc/sGMRFmix.R | 12 ++++----- inst/doc/sGMRFmix.Rmd | 26 ++++++++++----------- inst/doc/sGMRFmix.html | 60 ++++++++++++++++++++++++------------------------- vignettes/sGMRFmix.Rmd | 26 ++++++++++----------- 10 files changed, 93 insertions(+), 88 deletions(-)
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of seven
National Meteorological and Hydrological Services.
The 'cmsaf' R-package provides a collection of R-operators for the analysis and
manipulation of CM SAF NetCDF formatted data. The 'cmsaf' R-package is tested
for CM SAF NetCDF data, which are structured in three-dimensional arrays
(longitude, latitude, time) on a rectangular grid. Layered CM SAF data have to
be converted with the provided levbox_mergetime() function. The 'cmsaf' R-package
operators have only minor checks for deviations from the recommended data structure,
and give only few specific error messages.
Scripts for an easy application of the 'cmsaf' package operators and the preparation
and visualization of CM SAF NetCDF data are provided at the CM SAF webpage
(<http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html>).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.9.0 dated 2018-02-08 and 1.9.1 dated 2018-04-16
DESCRIPTION | 8 +-- MD5 | 118 +++++++++++++++++++++++++-------------------------- R/box_mergetime.R | 2 R/checkfile.R | 10 ++++ R/cmsaf.add.R | 36 +++++++++++---- R/cmsaf.addc.R | 11 ++++ R/cmsaf.cat.R | 2 R/cmsaf.div.R | 22 ++++++++- R/cmsaf.divc.R | 13 ++++- R/cmsaf.mul.R | 22 ++++++++- R/cmsaf.mulc.R | 11 ++++ R/cmsaf.sub.R | 22 ++++++++- R/cmsaf.subc.R | 11 ++++ R/dayrange.R | 71 +++++++++++++++++------------- R/divdpm.R | 30 +++++++++--- R/extract.level.R | 15 ++++++ R/extract.period.R | 46 ++++++++++++------- R/fldmax.R | 11 ++++ R/fldmean.R | 11 ++++ R/fldmin.R | 11 ++++ R/levbox_mergetime.R | 2 R/mon.anomaly.R | 56 ++++++++++++++---------- R/monmax.R | 39 ++++++++++------ R/monmean.R | 47 ++++++++++++-------- R/monmin.R | 45 ++++++++++++------- R/monsd.R | 47 ++++++++++++-------- R/monsum.R | 17 +++++-- R/muldpm.R | 28 ++++++++---- R/multimonmean.R | 15 +++++- R/multimonsum.R | 11 ++++ R/remapbil.R | 34 +++++++++----- R/seas.anomaly.R | 39 ++++++++++------ R/seasmean.R | 23 +++++++-- R/sellonlatbox.R | 14 +++++- R/selmon.R | 28 ++++++++---- R/selperiod.R | 28 ++++++++---- R/selpoint.R | 94 +++++++++++++++++++++++----------------- R/selpoint.multi.R | 23 +++++++++ R/seltime.R | 14 +++++- R/selyear.R | 48 ++++++++++++-------- R/timmax.R | 23 +++++++-- R/timmean.R | 28 +++++++----- R/timmin.R | 23 +++++++-- R/timpctl.R | 11 ++++ R/timsd.R | 11 ++++ R/trend.R | 11 ++++ R/wfldmean.R | 42 +++++++++++------- R/year.anomaly.R | 31 +++++++++---- R/yearmean.R | 29 ++++++++---- R/yearsum.R | 27 +++++++---- R/ymonmax.R | 31 +++++++++---- R/ymonmean.R | 31 +++++++++---- R/ymonmin.R | 31 +++++++++---- R/ymonsd.R | 31 +++++++++---- R/ymonsum.R | 29 ++++++++---- R/yseasmax.R | 23 +++++++-- R/yseasmean.R | 23 +++++++-- R/yseasmin.R | 23 +++++++-- R/yseassd.R | 23 +++++++-- man/cmsaf-package.Rd | 4 - 60 files changed, 1118 insertions(+), 502 deletions(-)
More information about newTestSurvRec at CRAN
Permanent link
Title: Joint Modeling of Longitudinal and Survival Data
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JM versions 1.4-7 dated 2017-06-27 and 1.4-8 dated 2018-04-16
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- R/jointModel.R | 6 +++--- R/plot.survfitJM.R | 4 ++-- R/predict.jointModel.R | 5 +++-- R/print.survfitJM.R | 2 +- README.md |only man/JM.Rd | 4 ++-- man/predict.Rd | 3 +-- 9 files changed, 24 insertions(+), 23 deletions(-)
Title: Interface to Diverse Estimation Methods of Causal Networks
Description: Unified interface for the estimation of causal networks, including
the methods 'backShift' (from package 'backShift'), 'bivariateANM' (bivariate
additive noise model), 'bivariateCAM' (bivariate causal additive model),
'CAM' (causal additive model) (from package 'CAM'), 'hiddenICP' (invariant
causal prediction with hidden variables), 'ICP' (invariant causal prediction)
(from package 'InvariantCausalPrediction'), 'GES' (greedy equivalence
search), 'GIES' (greedy interventional equivalence search), 'LINGAM', 'PC' (PC
Algorithm), 'FCI' (fast causal inference),
'RFCI' (really fast causal inference) (all from package 'pcalg') and
regression.
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>,
Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Diff between CompareCausalNetworks versions 0.1.9 dated 2017-07-31 and 0.2.0 dated 2018-04-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/adjustOptions.R | 9 ++++++++- R/getParents.R | 9 +++++---- R/runCAM.R | 8 +++++++- R/runNonparaPC.R | 3 ++- R/runPC.R | 11 +++++++---- man/getParents.Rd | 2 +- 8 files changed, 41 insertions(+), 23 deletions(-)
More information about CompareCausalNetworks at CRAN
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