Title: Fitting and Testing Generalized Logistic Distributions
Diff between glogis versions 0.1-0 dated 2011-06-12 and 0.1-1 dated 2014-02-20
Description: Tools for the generalized logistic distribution (Type I,
also known as skew-logistic distribution), encompassing
basic distribution functions (p, q, d, r, score), maximum
likelihood estimation, and structural change methods.
Author: Achim Zeileis [aut, cre],
Thomas Windberger [aut]
Maintainer: Achim Zeileis
DESCRIPTION | 28 ++++++++++++++++------------
MD5 |only
NAMESPACE | 3 +--
NEWS | 8 ++++++++
data/HICP.rda |binary
data/hicps.rda |binary
inst/CITATION | 23 ++++++++++-------------
man/HICP.Rd | 8 ++------
man/breakpoints.glogisfit.Rd | 8 ++------
man/glogis.Rd | 8 ++------
man/glogisfit.Rd | 8 ++------
11 files changed, 43 insertions(+), 51 deletions(-)
Title: Dynamic Linear Regression
Diff between dynlm versions 0.3-2 dated 2013-04-25 and 0.3-3 dated 2014-02-20
Description: Dynamic linear models and time series regression.
Author: Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis
DESCRIPTION | 17 ++++++++---------
MD5 | 13 +++++++------
NAMESPACE | 12 +++++++++---
NEWS | 26 +++++++++++++++++++-------
R/dynlm.R | 8 +++++---
data/M1Germany.rda |binary
man/dynlm.Rd | 3 ++-
tests |only
8 files changed, 50 insertions(+), 29 deletions(-)
Title: Analytical Tools for Radiation Oncology
Diff between RadOnc versions 1.0.5 dated 2014-02-19 and 1.0.6 dated 2014-02-20
Description: This package is designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology. The tools herein enable import of DVH information from Varian's Aria/Eclipse platform and 3D structural representations and dosimetric information from DICOM-RT files. These tools also enable subsequent visualization and statistical analysis of these data.
Author: Reid F. Thompson
Maintainer: Reid F. Thompson
RadOnc-1.0.5/RadOnc/R/extract.DVH.R |only
RadOnc-1.0.6/RadOnc/DESCRIPTION | 6
RadOnc-1.0.6/RadOnc/MD5 | 28 ++-
RadOnc-1.0.6/RadOnc/NAMESPACE | 1
RadOnc-1.0.6/RadOnc/R/DVH.R | 7
RadOnc-1.0.6/RadOnc/R/calculate.DVH.R |only
RadOnc-1.0.6/RadOnc/R/read.DICOM.RT.R | 4
RadOnc-1.0.6/RadOnc/data/RadOnc.RData |binary
RadOnc-1.0.6/RadOnc/data/datalist |only
RadOnc-1.0.6/RadOnc/inst/NEWS.Rd | 36 ++++-
RadOnc-1.0.6/RadOnc/inst/doc/RadOnc.R | 109 ++++++++-------
RadOnc-1.0.6/RadOnc/inst/doc/RadOnc.Rnw | 74 ++++++----
RadOnc-1.0.6/RadOnc/inst/doc/RadOnc.pdf |binary
RadOnc-1.0.6/RadOnc/man/RadOnc.Rd | 220 ++++++++++++++++++++++++++++++-
RadOnc-1.0.6/RadOnc/man/calculate.DVH.Rd |only
RadOnc-1.0.6/RadOnc/vignettes/RadOnc.Rnw | 74 ++++++----
RadOnc-1.0.6/RadOnc/vignettes/RadOnc.bib | 10 +
17 files changed, 445 insertions(+), 124 deletions(-)
Title: Functions to fit mixtures of regressions.
Diff between mixreg versions 0.0-4 dated 2011-11-04 and 0.0-5 dated 2014-02-20
Description: Fits mixtures of (possibly multivariate) regressions
(which has been described as doing ANCOVA when you don't
know the levels).
Author: Rolf Turner
Maintainer: Rolf Turner
mixreg-0.0-4/mixreg/data/.Random.seed.save |only
mixreg-0.0-4/mixreg/data/.Rhistory |only
mixreg-0.0-4/mixreg/inst/READ_ME |only
mixreg-0.0-5/mixreg/ChangeLog | 13 +++++++++++++
mixreg-0.0-5/mixreg/DESCRIPTION | 12 +++++++-----
mixreg-0.0-5/mixreg/MD5 | 27 +++++++++++++--------------
mixreg-0.0-5/mixreg/R/First.R | 2 +-
mixreg-0.0-5/mixreg/man/aphids.Rd | 14 +++++++++-----
mixreg-0.0-5/mixreg/man/bootcomp.Rd | 4 ++++
mixreg-0.0-5/mixreg/man/cband.Rd | 4 ++++
mixreg-0.0-5/mixreg/man/covmix.Rd | 4 ++++
mixreg-0.0-5/mixreg/man/internal.Rd | 4 ++++
mixreg-0.0-5/mixreg/man/mixreg.Rd | 4 ++++
mixreg-0.0-5/mixreg/man/plot.cband.Rd | 4 ++++
mixreg-0.0-5/mixreg/man/plot.mresid.Rd | 4 ++++
mixreg-0.0-5/mixreg/man/qq.mix.Rd | 4 ++++
mixreg-0.0-5/mixreg/man/resid.mix.Rd | 4 ++++
17 files changed, 79 insertions(+), 25 deletions(-)
Title: Multidimensional Item Response Theory
Diff between mirt versions 1.1 dated 2013-12-20 and 1.2 dated 2014-02-20
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item functioning and modelling item and person
covariates.
Author: Phil Chalmers [aut, cre],
Joshua Pritikin [ctb]
Maintainer: Phil Chalmers
mirt-1.1/mirt/R/fitIndices.R |only
mirt-1.1/mirt/inst/tests/test-04-confmirtOne.R |only
mirt-1.1/mirt/inst/tests/test-05-confmirtTwo.R |only
mirt-1.1/mirt/inst/tests/test-06-multipleGroupOne.R |only
mirt-1.1/mirt/inst/tests/test-08-multipleGroupTwo.R |only
mirt-1.1/mirt/inst/tests/test-09-createItem.R |only
mirt-1.1/mirt/inst/tests/test-10-mirt.model.R |only
mirt-1.1/mirt/man/fitIndices.Rd |only
mirt-1.1/mirt/man/fitted-method.Rd |only
mirt-1.2/mirt/DESCRIPTION | 34
mirt-1.2/mirt/MD5 | 163 ++--
mirt-1.2/mirt/NAMESPACE | 4
mirt-1.2/mirt/NEWS | 124 ++-
mirt-1.2/mirt/R/00-classes.R | 39 -
mirt-1.2/mirt/R/01-itemtypes.R | 8
mirt-1.2/mirt/R/02-item_methods.R | 46 -
mirt-1.2/mirt/R/03-estimation.R | 151 ++--
mirt-1.2/mirt/R/04-derivatives.R | 221 ++---
mirt-1.2/mirt/R/Confirmatory-methods.R | 201 -----
mirt-1.2/mirt/R/DIF.R | 40 -
mirt-1.2/mirt/R/EMstep.group.R | 175 +---
mirt-1.2/mirt/R/Exploratory-methods.R | 397 ++++++----
mirt-1.2/mirt/R/LoadPars.R | 48 -
mirt-1.2/mirt/R/M2.R |only
mirt-1.2/mirt/R/MHRM.group.R | 242 +++---
mirt-1.2/mirt/R/Mixed-methods.R | 105 +-
mirt-1.2/mirt/R/MultipleGroup-methods.R | 133 ---
mirt-1.2/mirt/R/PLCI.mirt.R | 20
mirt-1.2/mirt/R/SE.methods.R |only
mirt-1.2/mirt/R/bfactor.R | 18
mirt-1.2/mirt/R/boot.mirt.R | 35
mirt-1.2/mirt/R/calcLogLik.R | 45 -
mirt-1.2/mirt/R/fscores.R | 6
mirt-1.2/mirt/R/fscores.internal.R | 126 +--
mirt-1.2/mirt/R/itemfit.R | 83 +-
mirt-1.2/mirt/R/itemplot.R | 17
mirt-1.2/mirt/R/itemplot.internal.R | 174 ++--
mirt-1.2/mirt/R/mirt-package.R | 9
mirt-1.2/mirt/R/mirt.R | 64 +
mirt-1.2/mirt/R/mirt.model.R | 6
mirt-1.2/mirt/R/mirtCluster.R | 8
mirt-1.2/mirt/R/mixedmirt.R | 33
mirt-1.2/mirt/R/mod2values.R | 2
mirt-1.2/mirt/R/multipleGroup.R | 47 -
mirt-1.2/mirt/R/personfit.R | 36
mirt-1.2/mirt/R/randef.R | 11
mirt-1.2/mirt/R/read.mirt.R | 21
mirt-1.2/mirt/R/simdata.R | 8
mirt-1.2/mirt/R/utils.R | 469 ++++--------
mirt-1.2/mirt/R/wald.R | 20
mirt-1.2/mirt/README.md | 23
mirt-1.2/mirt/inst/tests/test-01-mirtOne.R | 89 +-
mirt-1.2/mirt/inst/tests/test-02-mirtTwo.R | 94 +-
mirt-1.2/mirt/inst/tests/test-03-bfactor.R | 61 -
mirt-1.2/mirt/inst/tests/test-04-multipleGroup.R |only
mirt-1.2/mirt/inst/tests/test-05-confmirtOne.R |only
mirt-1.2/mirt/inst/tests/test-06-confmirtTwo.R |only
mirt-1.2/mirt/inst/tests/test-07-mixedmirt.R | 115 +--
mirt-1.2/mirt/inst/tests/test-08-createItem.R |only
mirt-1.2/mirt/inst/tests/test-09-mirt.model.R |only
mirt-1.2/mirt/man/Bock1997.Rd | 4
mirt-1.2/mirt/man/ConfirmatoryClass-class.Rd | 16
mirt-1.2/mirt/man/DIF.Rd | 4
mirt-1.2/mirt/man/ExploratoryClass-class.Rd | 17
mirt-1.2/mirt/man/M2.Rd |only
mirt-1.2/mirt/man/MixedClass-class.Rd | 13
mirt-1.2/mirt/man/MultipleGroupClass-class.Rd | 14
mirt-1.2/mirt/man/bfactor.Rd | 34
mirt-1.2/mirt/man/coef-method.Rd | 25
mirt-1.2/mirt/man/fscores.Rd | 9
mirt-1.2/mirt/man/itemfit.Rd | 19
mirt-1.2/mirt/man/itemplot.Rd | 18
mirt-1.2/mirt/man/mirt.Rd | 115 +--
mirt-1.2/mirt/man/mirtCluster.Rd | 5
mirt-1.2/mirt/man/mixedmirt.Rd | 12
mirt-1.2/mirt/man/multipleGroup.Rd | 68 -
mirt-1.2/mirt/man/personfit.Rd | 11
mirt-1.2/mirt/man/plot-method.Rd | 43 -
mirt-1.2/mirt/man/read.mirt.Rd | 15
mirt-1.2/mirt/man/residuals-method.Rd | 56 +
mirt-1.2/mirt/man/show-method.Rd | 2
mirt-1.2/mirt/man/summary-method.Rd | 4
mirt-1.2/mirt/man/wald.Rd | 15
mirt-1.2/mirt/src/Estep.cpp | 217 +++--
mirt-1.2/mirt/src/Estep.h |only
mirt-1.2/mirt/src/Makevars | 3
mirt-1.2/mirt/src/Makevars.win | 3
mirt-1.2/mirt/src/Misc.cpp | 63 +
mirt-1.2/mirt/src/Misc.h | 16
mirt-1.2/mirt/src/dpars.cpp | 752 ++++++++++++++------
mirt-1.2/mirt/src/traceLinePts.cpp | 593 ++++++++-------
mirt-1.2/mirt/src/traceLinePts.h |only
92 files changed, 3207 insertions(+), 2730 deletions(-)
Title: Wrapper for fftw3: includes 1-D, univariate and multivariate,
and 2-D transform
Diff between fftwtools versions 0.9-5 dated 2013-06-26 and 0.9-6 dated 2014-02-20
Description: This package is a wrapper for several fftw functions. Please see the fftw package for additional tools. This package provides access to the two-dimensional fft, the multivariate fft, and the one-dimensional real to complex fft using fftw3. The package includes the functions fftw and mvfftw which are designed to mimic the functionality of the R functions fftw and mvfft. The fft functions have a parameter that allows them to not return the redundant complex conjugate when the input is real data. Please see the package fftw for general one-dimensional use of fftw, the discrete cosine transform, and for more detailed use of performance enhancing plans when using fftw. The calls to fftw and mvfftw in this package mimic the standard routines in R.
Author: Karim Rahim
Maintainer: Karim Rahim
fftwtools-0.9-5/fftwtools/inst/doc/testTimeAndSimpleUse.bib |only
fftwtools-0.9-5/fftwtools/src/Makevars.in |only
fftwtools-0.9-6/fftwtools/DESCRIPTION | 20 +-----
fftwtools-0.9-6/fftwtools/MD5 | 15 +++--
fftwtools-0.9-6/fftwtools/build |only
fftwtools-0.9-6/fftwtools/inst/doc/testTimeAndSimpleUse.R | 19 +++---
fftwtools-0.9-6/fftwtools/inst/doc/testTimeAndSimpleUse.Rnw | 35 +++++-------
fftwtools-0.9-6/fftwtools/inst/doc/testTimeAndSimpleUse.pdf |binary
fftwtools-0.9-6/fftwtools/src/Makevars.win |only
fftwtools-0.9-6/fftwtools/vignettes |only
10 files changed, 39 insertions(+), 50 deletions(-)
Title: Diagnostic test summary measures for three ordinal groups
Diff between DiagTest3Grp versions 1.5 dated 2012-10-08 and 1.6 dated 2014-02-20
Description: The R package provides utilities to estimate and make inference on two summary measures for diagnostic tests when there are three ordinal groups ----volume under ROC surface (VUS) and the extended Youden index, assuming that diagnostic markers increase monotonically and stochastically with disease severity. Point estimates, variance, confidence interval and optimal cut-points both under the normal assumption and also the non-parametric method(s) will be provided for the summary measures. Statistical tests are implemented to compare multiple diagnostic tests and two diagnostic test. Sample size is calculated to estimate the summary measures within a user-specified margin of error for future study planning.
Author: Jingqin Luo, Chengjie Xiong
Maintainer: Jingqin Luo
DiagTest3Grp-1.5/DiagTest3Grp/inst/doc |only
DiagTest3Grp-1.6/DiagTest3Grp/DESCRIPTION | 22 ++--------
DiagTest3Grp-1.6/DiagTest3Grp/MD5 | 21 ++++-----
DiagTest3Grp-1.6/DiagTest3Grp/NAMESPACE | 2
DiagTest3Grp-1.6/DiagTest3Grp/R/Pairwise.DiagTest3Grp.Test.R | 1
DiagTest3Grp-1.6/DiagTest3Grp/R/Youden3Grp.BoxCox.lambda.R | 3 -
DiagTest3Grp-1.6/DiagTest3Grp/R/Youden3Grp.PointEst.R | 2
DiagTest3Grp-1.6/DiagTest3Grp/man/DiagTest3Grp.Test.Rd | 3 -
DiagTest3Grp-1.6/DiagTest3Grp/man/Pairwise.DiagTest3Grp.Test.Rd | 8 ++-
DiagTest3Grp-1.6/DiagTest3Grp/man/VUS.Rd | 5 +-
DiagTest3Grp-1.6/DiagTest3Grp/man/Youden3Grp.PointEst.Rd | 8 ++-
DiagTest3Grp-1.6/DiagTest3Grp/vignettes |only
12 files changed, 35 insertions(+), 40 deletions(-)
Title: Dependent Mixture Models
Diff between depmix versions 0.9.10 dated 2011-11-07 and 0.9.11 dated 2014-02-20
Description: Fit (multigroup) mixtures of latent Markov models on mixed categorical and continuous (timeseries) data
Author: Ingmar Visser
Maintainer: Ingmar Visser
DESCRIPTION | 13 +++----
MD5 | 34 +++++++++---------
NAMESPACE | 2 +
R/depmix-internal.R | 4 +-
R/depmix.R | 84 +++++++++++++++++++++++++---------------------
R/dmm.R | 82 ++++++++++++++++++++++----------------------
R/generate.R | 10 ++---
R/lca.R | 6 +--
R/mgdmm.R | 14 +++----
R/mixdmm.R | 8 ++--
data/discrimination.rda |binary
data/speed.rda |binary
inst/doc/depmix-intro.pdf |binary
man/fitdmm.Rd | 3 +
src/matrix.cc | 30 +++++++++-------
src/matrix.h | 2 -
src/mdmm.cc | 3 +
src/mgdmm.cc | 4 +-
18 files changed, 159 insertions(+), 140 deletions(-)
Title: Testthat code. Tools to make testing fun :)
Diff between testthat versions 0.7.1 dated 2013-03-27 and 0.8 dated 2014-02-20
Description: A testing package specifically tailored for R
that's fun, flexible and easy to set up.
Author: Hadley Wickham
Maintainer: Hadley Wickham
testthat-0.7.1/testthat/NEWS |only
testthat-0.7.1/testthat/inst/tests |only
testthat-0.7.1/testthat/man/MinimalReporter.Rd |only
testthat-0.7.1/testthat/man/Reporter.Rd |only
testthat-0.7.1/testthat/man/StopReporter.Rd |only
testthat-0.7.1/testthat/man/SummaryReporter.Rd |only
testthat-0.7.1/testthat/man/TapReporter.Rd |only
testthat-0.7.1/testthat/man/error_report.Rd |only
testthat-0.7.1/testthat/man/with_reporter.Rd |only
testthat-0.7.1/testthat/tests/dependencies.r |only
testthat-0.7.1/testthat/tests/test-all.R |only
testthat-0.8/testthat/DESCRIPTION | 31 -
testthat-0.8/testthat/LICENSE |only
testthat-0.8/testthat/MD5 | 168 +++++----
testthat-0.8/testthat/NAMESPACE | 39 +-
testthat-0.8/testthat/R/auto-test.r | 23 -
testthat-0.8/testthat/R/colour-text.r | 8
testthat-0.8/testthat/R/compare.r |only
testthat-0.8/testthat/R/context.r | 4
testthat-0.8/testthat/R/evaluate-promise.r |only
testthat-0.8/testthat/R/expect-that.r | 72 +++-
testthat-0.8/testthat/R/expectation.r | 43 ++
testthat-0.8/testthat/R/expectations.r | 352 +++++++++++++++++---
testthat-0.8/testthat/R/reporter-list.r |only
testthat-0.8/testthat/R/reporter-minimal.r | 5
testthat-0.8/testthat/R/reporter-multi.r |only
testthat-0.8/testthat/R/reporter-silent.r |only
testthat-0.8/testthat/R/reporter-stop.r | 13
testthat-0.8/testthat/R/reporter-summary.r | 63 ++-
testthat-0.8/testthat/R/reporter-tap.r | 19 -
testthat-0.8/testthat/R/reporter-teamcity.r |only
testthat-0.8/testthat/R/reporter-zzz.r | 53 +--
testthat-0.8/testthat/R/reporter.r | 7
testthat-0.8/testthat/R/test-files.r | 104 ++++-
testthat-0.8/testthat/R/test-package.r | 57 +++
testthat-0.8/testthat/R/test-that.r | 27 -
testthat-0.8/testthat/R/traceback.r |only
testthat-0.8/testthat/R/utils.r | 10
testthat-0.8/testthat/R/watcher.r | 29 +
testthat-0.8/testthat/README.md | 23 +
testthat-0.8/testthat/inst/CITATION |only
testthat-0.8/testthat/man/ListReporter-class.Rd |only
testthat-0.8/testthat/man/MinimalReporter-class.Rd |only
testthat-0.8/testthat/man/MultiReporter-class.Rd |only
testthat-0.8/testthat/man/Reporter-class.Rd |only
testthat-0.8/testthat/man/SilentReporter-class.Rd |only
testthat-0.8/testthat/man/StopReporter-class.Rd |only
testthat-0.8/testthat/man/SummaryReporter-class.Rd |only
testthat-0.8/testthat/man/TapReporter-class.Rd |only
testthat-0.8/testthat/man/TeamcityReporter-class.Rd |only
testthat-0.8/testthat/man/auto_test.Rd | 42 +-
testthat-0.8/testthat/man/auto_test_package.Rd | 8
testthat-0.8/testthat/man/colourise.Rd | 13
testthat-0.8/testthat/man/compare_state.Rd | 9
testthat-0.8/testthat/man/context.Rd | 10
testthat-0.8/testthat/man/dir_state.Rd | 5
testthat-0.8/testthat/man/equals.Rd | 40 +-
testthat-0.8/testthat/man/evaluate_promise.Rd |only
testthat-0.8/testthat/man/expect-compare.Rd |only
testthat-0.8/testthat/man/expect_that.Rd | 45 +-
testthat-0.8/testthat/man/expectation.Rd | 21 +
testthat-0.8/testthat/man/fail.Rd | 7
testthat-0.8/testthat/man/find_reporter.Rd | 5
testthat-0.8/testthat/man/gives_warning.Rd | 61 ++-
testthat-0.8/testthat/man/has_names.Rd |only
testthat-0.8/testthat/man/is_a.Rd | 40 +-
testthat-0.8/testthat/man/is_equivalent_to.Rd | 43 +-
testthat-0.8/testthat/man/is_false.Rd | 40 +-
testthat-0.8/testthat/man/is_identical_to.Rd | 37 +-
testthat-0.8/testthat/man/is_null.Rd |only
testthat-0.8/testthat/man/is_true.Rd | 46 +-
testthat-0.8/testthat/man/library_if_available.Rd | 14
testthat-0.8/testthat/man/make_expectation.Rd | 7
testthat-0.8/testthat/man/matches.Rd | 48 +-
testthat-0.8/testthat/man/not.Rd |only
testthat-0.8/testthat/man/prints_text.Rd | 45 +-
testthat-0.8/testthat/man/reporter-accessors.Rd |only
testthat-0.8/testthat/man/safe_digest.Rd |only
testthat-0.8/testthat/man/shows_message.Rd | 62 ++-
testthat-0.8/testthat/man/source_dir.Rd | 10
testthat-0.8/testthat/man/takes_less_than.Rd | 35 +
testthat-0.8/testthat/man/test_dir.Rd | 17
testthat-0.8/testthat/man/test_env.Rd |only
testthat-0.8/testthat/man/test_file.Rd | 10
testthat-0.8/testthat/man/test_package.Rd | 27 +
testthat-0.8/testthat/man/test_that.Rd | 19 -
testthat-0.8/testthat/man/throws_error.Rd | 43 +-
testthat-0.8/testthat/man/watch.Rd | 13
testthat-0.8/testthat/tests/testthat |only
testthat-0.8/testthat/tests/testthat.R |only
90 files changed, 1366 insertions(+), 606 deletions(-)
Title: Gene and Pathway p-values computed using the Adaptive Rank
Truncated Product
Diff between ARTP versions 2.0.3 dated 2013-07-30 and 2.0.4 dated 2014-02-20
Description: A package for calculating gene and pathway p-values using the Adaptive Rank Truncated Product test
Author: Kai Yu, Qizhai Li and William Wheeler
Maintainer: Bill Wheeler
DESCRIPTION | 6
MD5 | 25
build |only
data/gene_SNP_data.txt.gz |binary
data/obs_pvalues.txt.gz |binary
data/perm_pvalues.txt.gz |binary
data/pheno_data.txt.gz |binary
inst/doc/vignette.R |only
inst/doc/vignette.pdf |binary
inst/sampleData/gene_SNP_data.txt | 102 +--
inst/sampleData/geno_data.txt | 102 +--
inst/sampleData/obs_pvalues.txt | 10
inst/sampleData/perm_pvalues.txt | 202 +++----
inst/sampleData/pheno_data.txt | 1002 +++++++++++++++++++-------------------
vignettes |only
15 files changed, 726 insertions(+), 723 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-02-23 0.1
Title: Adobe Analytics Reporting API
Diff between RSiteCatalyst versions 1.3 dated 2014-02-03 and 1.3.1 dated 2014-02-20
Description: Functions for accessing the Adobe Analytics Reporting API
Author: Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch
RSiteCatalyst-1.3.1/RSiteCatalyst/DESCRIPTION | 8 ++++----
RSiteCatalyst-1.3.1/RSiteCatalyst/MD5 | 7 +++----
RSiteCatalyst-1.3.1/RSiteCatalyst/NAMESPACE | 6 +++---
RSiteCatalyst-1.3.1/RSiteCatalyst/NEWS | 5 +++++
RSiteCatalyst-1.3/RSiteCatalyst/README.md |only
5 files changed, 15 insertions(+), 11 deletions(-)
Title: OLS growth curve trajectories
Diff between OLScurve versions 0.1.3 dated 2012-03-16 and 0.2.0 dated 2014-02-20
Description: Provides tools for more easily organizing and
plotting individual ordinary least square (OLS) growth curve
trajectories.
Author: Phil Chalmers [cre, aut],
Carrie Smith [ctb],
Matthew Sigal [ctb]
Maintainer: Phil Chalmers
OLScurve-0.1.3/OLScurve/.gitignore |only
OLScurve-0.1.3/OLScurve/COPYING |only
OLScurve-0.1.3/OLScurve/OLScurve.Rproj |only
OLScurve-0.2.0/OLScurve/DESCRIPTION | 32 +
OLScurve-0.2.0/OLScurve/MD5 | 27 -
OLScurve-0.2.0/OLScurve/NAMESPACE | 16
OLScurve-0.2.0/OLScurve/NEWS | 5
OLScurve-0.2.0/OLScurve/R/OLScurve-package.R | 64 ++
OLScurve-0.2.0/OLScurve/R/OLScurve.R | 558 ++++++++++++++------------
OLScurve-0.2.0/OLScurve/R/parplot.R | 136 ++----
OLScurve-0.2.0/OLScurve/R/subjplot.R | 37 -
OLScurve-0.2.0/OLScurve/data |only
OLScurve-0.2.0/OLScurve/inst/tests |only
OLScurve-0.2.0/OLScurve/man/OLScurve.Rd | 301 +++++++-------
OLScurve-0.2.0/OLScurve/man/gender.Rd |only
OLScurve-0.2.0/OLScurve/man/nonlin.example.Rd |only
OLScurve-0.2.0/OLScurve/man/parplot.Rd | 95 ++--
OLScurve-0.2.0/OLScurve/man/subjplot.Rd | 87 ++--
OLScurve-0.2.0/OLScurve/tests |only
19 files changed, 737 insertions(+), 621 deletions(-)
Title: LOw Rand and sparsE Covariance matrix estimation
Diff between lorec versions 0.6 dated 2011-11-07 and 0.6.1 dated 2014-02-20
Description: Estimate covariance matrices that contain low rank and sparse components
Author: Xi (Rossi) LUO
Maintainer: Xi (Rossi) LUO
lorec-0.6.1/lorec/ChangeLog | 4 ++++
lorec-0.6.1/lorec/DESCRIPTION | 12 +++++++-----
lorec-0.6.1/lorec/MD5 | 5 ++---
lorec-0.6/lorec/src/Makevars.in |only
4 files changed, 13 insertions(+), 8 deletions(-)
Title: The Guardian API Wrapper
Diff between GuardianR versions 0.2 dated 2014-02-17 and 0.3 dated 2014-02-20
Description: Provides an interface to the Open Platform's Content API of the Guardian Media Group. It retrieves content from news outlets The Observer, The Guardian, and guardian.co.uk from 1999 to current day
Author: Marco Toledo Bastos & Cornelius Puschmann
Maintainer: Marco Toledo Bastos
ChangeLog | 4 +++-
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NAMESPACE | 1 -
R/guardianr.R | 7 +++----
man/GuardianR-package.Rd | 6 +++---
man/get_guardian_full.Rd | 18 +-----------------
7 files changed, 20 insertions(+), 36 deletions(-)
Title: Debugging with restore points
Diff between restorepoint versions 0.1 dated 2013-02-04 and 0.1.5 dated 2014-02-20
Description: Debugging with restore points instead of break points. A restore
point stores all local variables when called inside a function. The stored
values can later be retrieved and evaluated in a modified R console that
replicates the function's environment. To debug step by step, one can
simply copy & paste the function body from the R script. Particularly
convenient in combination with RStudio. See the github page for a tutorial.
Author: Sebastian Kranz
Maintainer: Sebastian Kranz
restorepoint-0.1.5/restorepoint/DESCRIPTION | 24
restorepoint-0.1.5/restorepoint/MD5 | 38
restorepoint-0.1.5/restorepoint/NAMESPACE | 4
restorepoint-0.1.5/restorepoint/NEWS | 21
restorepoint-0.1.5/restorepoint/R/restorepoint.R | 216 +++-
restorepoint-0.1.5/restorepoint/README.md | 487 +++++++++-
restorepoint-0.1.5/restorepoint/inst/examples |only
restorepoint-0.1.5/restorepoint/man/assert.Rd |only
restorepoint-0.1.5/restorepoint/man/calls.to.trace.Rd | 2
restorepoint-0.1.5/restorepoint/man/clone.environment.Rd |only
restorepoint-0.1.5/restorepoint/man/copy.into.env.Rd | 9
restorepoint-0.1.5/restorepoint/man/default.error.string.fun.Rd |only
restorepoint-0.1.5/restorepoint/man/env.console.Rd | 6
restorepoint-0.1.5/restorepoint/man/eval.with.error.trace.Rd | 6
restorepoint-0.1.5/restorepoint/man/restore.objects.Rd | 8
restorepoint-0.1.5/restorepoint/man/restore.point.Rd | 202 +---
restorepoint-0.1.5/restorepoint/man/restore.point.browser.Rd |only
restorepoint-0.1.5/restorepoint/man/set.restore.point.options.Rd | 8
restorepoint-0.1.5/restorepoint/man/store.objects.Rd | 4
restorepoint-0.1.5/restorepoint/vignettes |only
restorepoint-0.1/restorepoint/examples |only
restorepoint-0.1/restorepoint/inst/doc |only
restorepoint-0.1/restorepoint/restore.point.Rd |only
23 files changed, 777 insertions(+), 258 deletions(-)
Title: Bayesian semi and nonparametric growth curve models that
additionally include multiple membership random effects.
Diff between growcurves versions 0.2.3.7 dated 2014-01-11 and 0.2.3.8 dated 2014-02-20
Description: Employs a non-parametric formulation for by-subject random effect
parameters to borrow strength over a constrained number of repeated
measurement waves in a fashion that permits multiple effects per subject.
One class of models employs a Dirichlet process (DP) prior for the subject
random effects and includes an additional set of random effects that
utilize a different grouping factor and are mapped back to clients through
a multiple membership weight matrix; e.g. treatment(s) exposure or dosage.
A second class of models employs a dependent DP (DDP) prior for the subject
random effects that directly incorporates the multiple membership pattern.
Author: Terrance Savitsky
Maintainer: "terrance savitsky"
DESCRIPTION | 8 ++++----
MD5 | 9 +++++----
NEWS | 7 ++++++-
R/help.R | 16 ++++++++++------
inst/CITATION |only
man/growcurves-package.Rd | 18 +++++++++++-------
6 files changed, 36 insertions(+), 22 deletions(-)
Title: Density strips and other methods for compactly illustrating
distributions
Diff between denstrip versions 1.5.2 dated 2012-04-03 and 1.5.3 dated 2014-02-20
Description: Graphical methods for compactly illustrating probability distributions, including density strips, density regions, sectioned density plots and varying width strips.
Author: Christopher Jackson
Maintainer: Christopher Jackson
ChangeLog | 14 ++++++++++++++
DESCRIPTION | 15 +++++++--------
MD5 | 12 ++++++------
R/denstrip.R | 8 +++++---
inst/NEWS | 9 +++++++++
man/densregion.survfit.Rd | 17 ++++++++++-------
man/denstrip.Rd | 19 +++++++++++++------
7 files changed, 64 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-21 3.0.0-4
2012-07-03 3.0.0-3
2011-08-06 3.0.0-1
2010-11-18 0.9.5-2
2010-08-31 0.9.4
2010-07-06 0.9.3
2010-03-15 0.9.1
Title: R-MongoDB driver
Diff between rmongodb versions 1.4.2 dated 2014-01-29 and 1.5.3 dated 2014-02-20
Description: This R package provides an interface to the NoSQL MongoDB database
using the MongoDB C-driver.
Author: MongoDB, Inc. (mongo-c-driver) & Markus Schmidberger (mongosoup.de).
Formerly Gerald Lindsly.
Maintainer: Markus Schmidberger
rmongodb-1.4.2/rmongodb/src/bson.c |only
rmongodb-1.4.2/rmongodb/src/bson.h |only
rmongodb-1.4.2/rmongodb/src/encoding.c |only
rmongodb-1.4.2/rmongodb/src/encoding.h |only
rmongodb-1.4.2/rmongodb/src/env.c |only
rmongodb-1.4.2/rmongodb/src/env.h |only
rmongodb-1.4.2/rmongodb/src/gridfs.c |only
rmongodb-1.4.2/rmongodb/src/gridfs.h |only
rmongodb-1.4.2/rmongodb/src/md5.c |only
rmongodb-1.4.2/rmongodb/src/md5.h |only
rmongodb-1.4.2/rmongodb/src/mongo.c |only
rmongodb-1.4.2/rmongodb/src/mongo.h |only
rmongodb-1.4.2/rmongodb/src/numbers.c |only
rmongodb-1.5.3/rmongodb/DESCRIPTION | 19 ++++---
rmongodb-1.5.3/rmongodb/MD5 | 58 ++++++++++++----------
rmongodb-1.5.3/rmongodb/NEWS | 8 +++
rmongodb-1.5.3/rmongodb/R/bson_convert.R | 14 ++++-
rmongodb-1.5.3/rmongodb/README.md | 5 +
rmongodb-1.5.3/rmongodb/build |only
rmongodb-1.5.3/rmongodb/inst |only
rmongodb-1.5.3/rmongodb/man/mongo.bson.to.list.Rd | 6 +-
rmongodb-1.5.3/rmongodb/src/Makevars | 11 +++-
rmongodb-1.5.3/rmongodb/src/Makevars.win | 8 ++-
rmongodb-1.5.3/rmongodb/src/api.c | 2
rmongodb-1.5.3/rmongodb/src/api_bson.h | 2
rmongodb-1.5.3/rmongodb/src/api_gridfs.h | 2
rmongodb-1.5.3/rmongodb/src/api_mongo.c | 2
rmongodb-1.5.3/rmongodb/src/libmongo |only
rmongodb-1.5.3/rmongodb/src/utility.h | 4 -
rmongodb-1.5.3/rmongodb/tests/test_bson.R | 14 ++++-
rmongodb-1.5.3/rmongodb/vignettes |only
31 files changed, 108 insertions(+), 47 deletions(-)
Title: Conditional Correlation GARCH models
Diff between ccgarch versions 0.2.1 dated 2013-08-18 and 0.2.2 dated 2014-02-20
Description: Functions for estimating and simulating the family of the
CC-GARCH models.
Author: Tomoaki Nakatani
Maintainer: Tomoaki Nakatani
ChangeLog | 3 +
DESCRIPTION | 8 +--
MD5 | 31 ++++++++++++-
NAMESPACE | 98 ++++++++++++++++++++++----------------------
R/dcc_estimation.R | 3 -
man/analytical_Hessian.Rd |only
man/analytical_grad.Rd |only
man/d2lv.Rd |only
man/dcc_est.Rd |only
man/dcc_estimation1.Rd |only
man/dcc_estimation2.Rd |only
man/dcc_results.Rd |only
man/dlc.Rd |only
man/dlv.Rd |only
man/dlv_est.Rd |only
man/grad_dcc2.Rd |only
man/grad_full_likelihood.Rd |only
man/loglik_dcc.Rd |only
man/loglik_dcc1.Rd |only
man/loglik_dcc2.Rd |only
man/loglik_eccc.Rd |only
man/p_mat.Rd |only
man/tr_func.Rd |only
man/uni_vola.Rd |only
man/uni_vola_sim.Rd |only
man/vdR.Rd |only
man/vec_garch_derivative.Rd |only
man/vector_garch.Rd |only
28 files changed, 84 insertions(+), 59 deletions(-)
Title: Determining and evaluating high-risk zones
Diff between highriskzone versions 1.0 dated 2012-12-18 and 1.1 dated 2014-02-20
Description: Functions for determining and evaluating high-risk zones and
simulating and thinning point process data, as described in 'Determining
high risk zones using point process methodology - Realization by building
an R package' (Seibold, 2012) and 'Determining high-risk zones for
unexploded World War II bombs by using point process methodology' (Mahling
et al., 2013).
Author: Heidi Seibold
Maintainer: Heidi Seibold
DESCRIPTION | 34 ++++-----
LICENSE |only
MD5 | 95 ++++++++++++++-----------
NAMESPACE | 19 +++--
R/bootcorrect.R |only
R/bootcorrect_restr.R |only
R/data.R | 4 -
R/dethrz.R | 46 +++++++-----
R/dethrz_restr.R |only
R/dethrzbase.R | 32 ++++----
R/detnsintens_restr.R |only
R/estintens.R | 22 ++---
R/estintens_weight.R |only
R/evalhrz.R | 14 ++-
R/evalmethod.R | 30 ++++----
R/genericbootcorr.R |only
R/genericevalhrz.R | 8 +-
R/highriskzone-package.R | 20 +++--
R/readpppdata.R | 2
R/simulationbase.R | 34 ++++-----
data/craterA.RData |binary
data/craterB.RData |binary
man/bootcor.Rd |only
man/bootcor_restr.Rd |only
man/check_det_hrz_input.Rd | 22 ++---
man/craterA.Rd | 7 +
man/craterB.Rd | 7 +
man/det_alpha.Rd | 18 ++--
man/det_area.Rd | 16 ++--
man/det_hrz.Rd | 159 +++++++++++++++++++++++--------------------
man/det_hrz_restr.Rd |only
man/det_nnarea.Rd | 16 ++--
man/det_nsintens.Rd | 14 +--
man/det_nsintens_restr.Rd |only
man/det_radius.Rd | 19 ++---
man/det_threshold.Rd | 15 ++--
man/det_thresholdfromarea.Rd | 18 ++--
man/est_intens.Rd | 24 +++---
man/est_intens_weight.Rd |only
man/eval_hrz.Rd | 42 ++++++-----
man/eval_method.Rd | 156 ++++++++++++++++++++----------------------
man/highriskzone-package.Rd | 49 +++++++------
man/plot.bootcorr.Rd |only
man/plot.highriskzone.Rd | 16 +---
man/plot.hrzeval.Rd | 21 ++---
man/print.bootcorr.Rd |only
man/print.highriskzone.Rd | 14 +--
man/print.hrzeval.Rd | 16 ++--
man/read_pppdata.Rd | 21 ++---
man/sim_intens.Rd | 16 ++--
man/sim_nsppp.Rd | 79 ++++++++++-----------
man/sim_nsprocess.Rd | 22 ++---
man/summary.bootcorr.Rd |only
man/summary.highriskzone.Rd | 14 +--
man/summary.hrzeval.Rd | 14 +--
man/thin.Rd | 22 +++--
56 files changed, 631 insertions(+), 566 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.4.000.2 dated 2014-01-22 and 0.4.000.4 dated 2014-02-20
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to combine
several operations into one, and to reduce (or eliminate) the need for
temporaries. This is accomplished through recursive templates and template
meta-programming.
This library is useful if C++ has been decided as the language of choice
(due to speed and/or integration capabilities), rather than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo itself in
order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++ integration.
Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
bindings/bridge to Armadillo) is licensed under the GNU GPL version 2
or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
RcppArmadillo-0.4.000.2/RcppArmadillo/inst/skeleton/rcpparma_hello_world.R |only
RcppArmadillo-0.4.000.2/RcppArmadillo/inst/skeleton/rcpparma_hello_world.h |only
RcppArmadillo-0.4.000.4/RcppArmadillo/ChangeLog | 38 +
RcppArmadillo-0.4.000.4/RcppArmadillo/DESCRIPTION | 11
RcppArmadillo-0.4.000.4/RcppArmadillo/MD5 | 81 ++--
RcppArmadillo-0.4.000.4/RcppArmadillo/NAMESPACE | 2
RcppArmadillo-0.4.000.4/RcppArmadillo/R/RcppArmadillo.package.skeleton.R | 200 +++++-----
RcppArmadillo-0.4.000.4/RcppArmadillo/R/RcppExports.R | 43 ++
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/NEWS.Rd | 22 +
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |binary
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/Base_bones.hpp | 4
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/Base_meat.hpp | 2
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 2
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp | 8
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 2
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 12
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/field_meat.hpp | 42 --
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_det.hpp | 10
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_eig_sym.hpp | 2
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_find.hpp | 2
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_inplace_strans.hpp | 2
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_inplace_trans.hpp | 6
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_inv.hpp | 6
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_norm.hpp | 4
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_pinv.hpp | 2
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_solve.hpp | 4
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/fn_svd.hpp | 6
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/forward_bones.hpp | 5
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/memory.hpp | 10
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_meat.hpp | 46 +-
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/subview_field_bones.hpp | 4
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/include/armadillo_bits/subview_field_meat.hpp | 42 ++
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/skeleton/Makevars | 3
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/skeleton/Makevars.win | 6
RcppArmadillo-0.4.000.4/RcppArmadillo/inst/skeleton/rcpparma_hello_world.cpp | 55 ++
RcppArmadillo-0.4.000.4/RcppArmadillo/man/RcppArmadillo.package.skeleton.Rd | 3
RcppArmadillo-0.4.000.4/RcppArmadillo/man/armadillo_set_seed.Rd |only
RcppArmadillo-0.4.000.4/RcppArmadillo/man/armadillo_set_seed_random.Rd |only
RcppArmadillo-0.4.000.4/RcppArmadillo/man/armadillo_version.Rd |only
RcppArmadillo-0.4.000.4/RcppArmadillo/src/Makevars | 2
RcppArmadillo-0.4.000.4/RcppArmadillo/src/Makevars.win | 5
RcppArmadillo-0.4.000.4/RcppArmadillo/src/RcppArmadillo.cpp | 59 ++
RcppArmadillo-0.4.000.4/RcppArmadillo/src/RcppExports.cpp | 23 +
44 files changed, 513 insertions(+), 263 deletions(-)
Title: Analysis of Multivariate Event Times
Diff between mets versions 0.2.6 dated 2013-12-17 and 0.2.7 dated 2014-02-20
Description: Implementation of various statistical models for multivariate
event history data. Including multivariate cumulative incidence models, and
bivariate random effects probit models (Liability models). Also contains
two-stage binomial modelling that can do pairwise odds-ratio dependence
modelling based marginal logistic regression models. This is an alternative
to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst
DESCRIPTION | 21 +--
MD5 | 72 +++++------
NAMESPACE | 4
NEWS | 7 +
R/bicomprisk.R | 4
R/binomial.twostage.R | 155 -------------------------
R/casewise.R | 9 -
R/clusterindex-reshape.R | 7 -
R/cor.R | 71 ++++++-----
R/fastapprox.R | 2
R/fastpattern.R | 2
R/fastreshape.R | 39 +++---
R/mets-package.R | 6
R/normal0.R |only
R/onload.R | 3
R/plot.bptwin.R | 4
R/pmvn.R | 37 +++++
R/summary.biprobit.R | 2
R/summary.bptwin.R | 8 -
R/surv.boxarea.R | 4
R/twostage.R | 4
data/datalist | 2
inst/binomialtwostage.R |only
man/Grandom.cif.Rd | 9 -
man/binomial.twostage.Rd | 6
man/casewise.test.Rd | 9 -
man/cor.cif.Rd | 19 +--
man/internal.Rd | 3
man/random.cif.Rd | 15 +-
man/summary.cor.Rd | 4
src/Makevars.win | 7 -
src/binomial-plackett.cpp | 20 +--
src/clusterindex.cpp | 30 ++++
src/cor.cpp | 17 +-
src/mvn.cpp | 284 ++++++++++++++++++++++++++++++++--------------
src/mvn.h | 42 ++++--
src/mvt.f | 26 ++--
src/plackettMLE.cpp | 17 +-
38 files changed, 537 insertions(+), 434 deletions(-)
Title: diversitree: comparative phylogenetic analyses of
diversification
Diff between diversitree versions 0.9-6 dated 2013-06-13 and 0.9-7 dated 2014-02-20
Description: Contains a number of comparative phylogenetic methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of BiSSE (Binary State
Speciation and Extinction; Maddison et al. 2007: Syst. Biol. 56:
701) and its unresolved tree extensions (FitzJohn et al. 2009:
Syst. Biol. 58: 595), MuSSE (Multiple State Speciation and
Extinction), QuaSSE (Quantitative State Speciation and Extinction;
FitzJohn 2010: Syst. Biol. 59: 619), GeoSSE (Geographic State
Speciation and Extinction; Goldberg et al. 2011: Syst. Biol. 60:
451), and BiSSE-ness (Magnuson-Ford and Otto 2012: Am. Nat.)
Other included methods include Markov models of discrete and
continuous trait evolution and constant rate speciation and
extinction.
Author: Richard G. FitzJohn
Maintainer: Richard G. FitzJohn
diversitree-0.9-6/diversitree/R/model-ou-vcv.R |only
diversitree-0.9-6/diversitree/README |only
diversitree-0.9-6/diversitree/inst/tests/zzz.R |only
diversitree-0.9-7/diversitree/DESCRIPTION | 40 -
diversitree-0.9-7/diversitree/MD5 | 155 ++--
diversitree-0.9-7/diversitree/NAMESPACE | 23
diversitree-0.9-7/diversitree/R/check.R | 7
diversitree-0.9-7/diversitree/R/clade-tree.R | 2
diversitree-0.9-7/diversitree/R/continuous.R | 77 ++
diversitree-0.9-7/diversitree/R/expm.R | 4
diversitree-0.9-7/diversitree/R/mcmc.R | 54 +
diversitree-0.9-7/diversitree/R/mle.R | 28
diversitree-0.9-7/diversitree/R/model-bd-split.R | 2
diversitree-0.9-7/diversitree/R/model-bd-t.R | 2
diversitree-0.9-7/diversitree/R/model-bm-contrasts.R |only
diversitree-0.9-7/diversitree/R/model-bm-vcv.R | 1
diversitree-0.9-7/diversitree/R/model-bm.R | 29
diversitree-0.9-7/diversitree/R/model-eb.R |only
diversitree-0.9-7/diversitree/R/model-geosse-t.R |only
diversitree-0.9-7/diversitree/R/model-lambda.R |only
diversitree-0.9-7/diversitree/R/model-mkn-multitrait.R | 2
diversitree-0.9-7/diversitree/R/model-mkn-pij.R | 2
diversitree-0.9-7/diversitree/R/model-ou-pruning.R | 75 +-
diversitree-0.9-7/diversitree/R/model-ou.R | 48 +
diversitree-0.9-7/diversitree/R/model-pgls.R |only
diversitree-0.9-7/diversitree/R/plot-alt-extra.R | 73 +-
diversitree-0.9-7/diversitree/R/plot-alt.R | 37 -
diversitree-0.9-7/diversitree/R/profiles-plot.R | 31
diversitree-0.9-7/diversitree/R/rescale.R |only
diversitree-0.9-7/diversitree/R/sim-character.R | 32 -
diversitree-0.9-7/diversitree/R/util-tree.R | 3
diversitree-0.9-7/diversitree/R/util.R | 2
diversitree-0.9-7/diversitree/README.md |only
diversitree-0.9-7/diversitree/configure | 6
diversitree-0.9-7/diversitree/configure.ac | 4
diversitree-0.9-7/diversitree/inst/tests/helper-diversitree.R |only
diversitree-0.9-7/diversitree/inst/tests/run-tests.R | 8
diversitree-0.9-7/diversitree/inst/tests/test-asr-t.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-asr.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-bd-split.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-bd-t.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-bd.R | 6
diversitree-0.9-7/diversitree/inst/tests/test-bisse-split.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-bisse-t.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-bisse-td.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-bisse.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-bisseness.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-bm.R | 238 +++++--
diversitree-0.9-7/diversitree/inst/tests/test-branches.R | 4
diversitree-0.9-7/diversitree/inst/tests/test-classe.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-eb.R |only
diversitree-0.9-7/diversitree/inst/tests/test-expm.R | 4
diversitree-0.9-7/diversitree/inst/tests/test-geosse-t.R |only
diversitree-0.9-7/diversitree/inst/tests/test-geosse.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-lambda.R |only
diversitree-0.9-7/diversitree/inst/tests/test-mcmc.R | 155 ++++
diversitree-0.9-7/diversitree/inst/tests/test-mkn.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-mle.R | 39 +
diversitree-0.9-7/diversitree/inst/tests/test-musse-multitrait.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-musse-split.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-musse-t.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-musse.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-ode.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-ou.R | 320 +++++++++-
diversitree-0.9-7/diversitree/inst/tests/test-pgls.R |only
diversitree-0.9-7/diversitree/inst/tests/test-quasse-internal.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-quasse-split.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-quasse.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-rescale.R |only
diversitree-0.9-7/diversitree/inst/tests/test-time-machine.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-unresolved.R | 3
diversitree-0.9-7/diversitree/inst/tests/test-utils.R |only
diversitree-0.9-7/diversitree/man/make.bm.Rd | 45 +
diversitree-0.9-7/diversitree/man/make.geosse.t.Rd |only
diversitree-0.9-7/diversitree/man/make.musse.td.Rd | 2
diversitree-0.9-7/diversitree/man/make.pgls.Rd |only
diversitree-0.9-7/diversitree/man/mcmc.Rd | 10
diversitree-0.9-7/diversitree/man/profiles.plot.Rd | 9
diversitree-0.9-7/diversitree/man/sim.character.Rd | 2
diversitree-0.9-7/diversitree/man/trait.plot.Rd | 51 +
diversitree-0.9-7/diversitree/man/utils.Rd | 8
diversitree-0.9-7/diversitree/src/GslOdeBase.cpp | 16
diversitree-0.9-7/diversitree/src/Spline.cpp | 6
diversitree-0.9-7/diversitree/src/Spline.h | 2
diversitree-0.9-7/diversitree/src/TimeMachine.cpp | 16
diversitree-0.9-7/diversitree/src/continuous.c | 84 ++
diversitree-0.9-7/diversitree/src/continuous.h | 1
diversitree-0.9-7/diversitree/src/mkn-pij.c | 10
88 files changed, 1365 insertions(+), 476 deletions(-)
Title: Linear Model with Breakpoint
Diff between lm.br versions 2.4 dated 2013-10-29 and 2.5 dated 2014-02-20
Description: Exact significance tests for a changepoint in linear or multivariate linear regression.
Confidence regions with exact coverage probabilities for the changepoint.
Author: Marc Adams [aut, cre],
authors of R function 'lm' [ctb] (general interface),
authors of 'lm.gls' [ctb] (interface and R code for matrix weights),
U.S. NIST [ctb] (C++ code for TNT::Vector template)
Maintainer: Marc Adams
lm.br-2.4/lm.br/inst/CITATION |only
lm.br-2.4/lm.br/man/lm.br-internal.Rd |only
lm.br-2.5/lm.br/DESCRIPTION | 19 +++++-----
lm.br-2.5/lm.br/MD5 | 47 ++++++++++++-------------
lm.br-2.5/lm.br/R/lm.br.R | 62 +++++++++++++++++++++-------------
lm.br-2.5/lm.br/demo/testscript.R | 32 ++++++++---------
lm.br-2.5/lm.br/inst/doc/lm.br.R | 8 ++--
lm.br-2.5/lm.br/inst/doc/lm.br.Rnw | 26 +++++++-------
lm.br-2.5/lm.br/inst/doc/lm.br.pdf |binary
lm.br-2.5/lm.br/man/ci.Rd | 3 -
lm.br-2.5/lm.br/man/cr.Rd | 5 +-
lm.br-2.5/lm.br/man/lm.br.Rd | 53 ++++++++++-------------------
lm.br-2.5/lm.br/man/lm.br_internal.Rd |only
lm.br-2.5/lm.br/man/mle.Rd | 3 -
lm.br-2.5/lm.br/man/sety.Rd | 10 ++---
lm.br-2.5/lm.br/man/sl.Rd | 17 ++++-----
lm.br-2.5/lm.br/src/R_interface.cpp | 17 ++++-----
lm.br-2.5/lm.br/src/Rcpp_module.cpp | 49 ++++++++------------------
lm.br-2.5/lm.br/src/cr.cpp | 2 -
lm.br-2.5/lm.br/src/lmbr.cpp | 9 ++++
lm.br-2.5/lm.br/src/lmbr.h | 13 +++----
lm.br-2.5/lm.br/src/mle.cpp | 56 +++++++++++++++---------------
lm.br-2.5/lm.br/src/pre_calc.cpp | 2 +
lm.br-2.5/lm.br/src/set_theta0.cpp | 2 -
lm.br-2.5/lm.br/src/tnt_vector.h | 4 +-
lm.br-2.5/lm.br/vignettes/lm.br.Rnw | 26 +++++++-------
26 files changed, 231 insertions(+), 234 deletions(-)
Title: Interface for hyperspectral data, i.e. spectra + meta info
(spatial, time, concentration, ...)
Diff between hyperSpec versions 0.98-20120923 dated 2012-09-23 and 0.98-20140220 dated 2014-02-20
Description: This package is an interface to handle hyperspectral data sets in
R. I.e. spatially or time-resolved spectra, or spectra with any other kind
of information associated with each of the spectra. The spectra can be data
as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS,
etc. More generally, any data that is recorded over a discretized variable,
e.g. absorbance = f (wavelength), stored as a vector of absorbance values
for discrete wavelengths is suitable.
Author: Claudia Beleites
Maintainer: Claudia Beleites
hyperSpec-0.98-20120923/hyperSpec/R/read.spc.KaiserMap.R |only
hyperSpec-0.98-20120923/hyperSpec/man/read.jdx.Shimadzu.Rd |only
hyperSpec-0.98-20120923/hyperSpec/man/scan.txt.Witec.Rd |only
hyperSpec-0.98-20140220/hyperSpec/DESCRIPTION | 38 -
hyperSpec-0.98-20140220/hyperSpec/MD5 | 174 +++---
hyperSpec-0.98-20140220/hyperSpec/NAMESPACE | 13
hyperSpec-0.98-20140220/hyperSpec/R/Arith.R | 56 ++
hyperSpec-0.98-20140220/hyperSpec/R/all.equal.R | 25
hyperSpec-0.98-20140220/hyperSpec/R/apply.R | 1
hyperSpec-0.98-20140220/hyperSpec/R/as.data.frame.R | 4
hyperSpec-0.98-20140220/hyperSpec/R/chondro.R | 22
hyperSpec-0.98-20140220/hyperSpec/R/collapse.R | 10
hyperSpec-0.98-20140220/hyperSpec/R/decomposition.R | 100 +--
hyperSpec-0.98-20140220/hyperSpec/R/hyperspec-class.R | 6
hyperSpec-0.98-20140220/hyperSpec/R/initialize.R | 23
hyperSpec-0.98-20140220/hyperSpec/R/levelplot.R | 24
hyperSpec-0.98-20140220/hyperSpec/R/logentry.R | 8
hyperSpec-0.98-20140220/hyperSpec/R/map.identify.R | 1
hyperSpec-0.98-20140220/hyperSpec/R/mvtnorm.R | 1
hyperSpec-0.98-20140220/hyperSpec/R/plot.R | 7
hyperSpec-0.98-20140220/hyperSpec/R/plotmap.R | 12
hyperSpec-0.98-20140220/hyperSpec/R/plotmat.R | 2
hyperSpec-0.98-20140220/hyperSpec/R/qplot.R | 95 ++-
hyperSpec-0.98-20140220/hyperSpec/R/qplotmixmap.R | 25
hyperSpec-0.98-20140220/hyperSpec/R/read.ENVI.Nicolet.R | 2
hyperSpec-0.98-20140220/hyperSpec/R/read.ENVI.R | 27 -
hyperSpec-0.98-20140220/hyperSpec/R/read.cytomat.R |only
hyperSpec-0.98-20140220/hyperSpec/R/read.ini.R |only
hyperSpec-0.98-20140220/hyperSpec/R/read.jdx.R |only
hyperSpec-0.98-20140220/hyperSpec/R/read.jdx.Shimadzu.R | 21
hyperSpec-0.98-20140220/hyperSpec/R/read.spc.Kaiser.R |only
hyperSpec-0.98-20140220/hyperSpec/R/read.spc.R | 47 +
hyperSpec-0.98-20140220/hyperSpec/R/read.txt.Horiba.R |only
hyperSpec-0.98-20140220/hyperSpec/R/read.txt.Shimadzu.R | 262 +++++-----
hyperSpec-0.98-20140220/hyperSpec/R/read.txt.long.R | 10
hyperSpec-0.98-20140220/hyperSpec/R/read.txt.wide.R | 20
hyperSpec-0.98-20140220/hyperSpec/R/scale.R |only
hyperSpec-0.98-20140220/hyperSpec/R/scan.txt.Renishaw.R | 10
hyperSpec-0.98-20140220/hyperSpec/R/scan.txt.Witec.R | 48 +
hyperSpec-0.98-20140220/hyperSpec/R/spc.loess.R | 13
hyperSpec-0.98-20140220/hyperSpec/R/spc.rubberband.R |only
hyperSpec-0.98-20140220/hyperSpec/R/spc.spline.R |only
hyperSpec-0.98-20140220/hyperSpec/R/sysdata.rda |binary
hyperSpec-0.98-20140220/hyperSpec/R/wl.R | 10
hyperSpec-0.98-20140220/hyperSpec/R/wl2i.R | 8
hyperSpec-0.98-20140220/hyperSpec/build |only
hyperSpec-0.98-20140220/hyperSpec/data/barbiturates.rda |binary
hyperSpec-0.98-20140220/hyperSpec/data/flu.rda |binary
hyperSpec-0.98-20140220/hyperSpec/data/laser.rda |binary
hyperSpec-0.98-20140220/hyperSpec/data/paracetamol.rda |binary
hyperSpec-0.98-20140220/hyperSpec/inst/doc/baseline.R |only
hyperSpec-0.98-20140220/hyperSpec/inst/doc/baseline.Rnw | 89 ++-
hyperSpec-0.98-20140220/hyperSpec/inst/doc/baseline.pdf |binary
hyperSpec-0.98-20140220/hyperSpec/inst/doc/fileio.pdf |binary
hyperSpec-0.98-20140220/hyperSpec/inst/doc/flu.R |only
hyperSpec-0.98-20140220/hyperSpec/inst/doc/flu.pdf |binary
hyperSpec-0.98-20140220/hyperSpec/inst/doc/introduction.R |only
hyperSpec-0.98-20140220/hyperSpec/inst/doc/introduction.Rnw | 75 +-
hyperSpec-0.98-20140220/hyperSpec/inst/doc/introduction.pdf |binary
hyperSpec-0.98-20140220/hyperSpec/inst/doc/laser.R |only
hyperSpec-0.98-20140220/hyperSpec/inst/doc/laser.pdf |binary
hyperSpec-0.98-20140220/hyperSpec/inst/doc/plotting.R |only
hyperSpec-0.98-20140220/hyperSpec/inst/doc/plotting.pdf |binary
hyperSpec-0.98-20140220/hyperSpec/man/Comparison.Rd | 6
hyperSpec-0.98-20140220/hyperSpec/man/asdataframe.Rd | 5
hyperSpec-0.98-20140220/hyperSpec/man/chondro.Rd | 19
hyperSpec-0.98-20140220/hyperSpec/man/collapse.Rd | 5
hyperSpec-0.98-20140220/hyperSpec/man/decomposition.Rd | 95 +--
hyperSpec-0.98-20140220/hyperSpec/man/levelplot.Rd | 16
hyperSpec-0.98-20140220/hyperSpec/man/plot.Rd | 8
hyperSpec-0.98-20140220/hyperSpec/man/plotmat.Rd | 3
hyperSpec-0.98-20140220/hyperSpec/man/qplotc.Rd | 7
hyperSpec-0.98-20140220/hyperSpec/man/qplotmap.Rd | 14
hyperSpec-0.98-20140220/hyperSpec/man/qplotmix.Rd | 6
hyperSpec-0.98-20140220/hyperSpec/man/qplotmixmap.Rd | 3
hyperSpec-0.98-20140220/hyperSpec/man/qplotspc.Rd | 6
hyperSpec-0.98-20140220/hyperSpec/man/read-cytomat.Rd |only
hyperSpec-0.98-20140220/hyperSpec/man/read-ini.Rd |only
hyperSpec-0.98-20140220/hyperSpec/man/read-spc-Kaiser.Rd |only
hyperSpec-0.98-20140220/hyperSpec/man/read-spc.Rd | 55 --
hyperSpec-0.98-20140220/hyperSpec/man/read.jdx.Rd |only
hyperSpec-0.98-20140220/hyperSpec/man/read.txt.Horiba.Rd |only
hyperSpec-0.98-20140220/hyperSpec/man/read.txt.Shimadzu.Rd | 11
hyperSpec-0.98-20140220/hyperSpec/man/readENVI.Rd | 14
hyperSpec-0.98-20140220/hyperSpec/man/scale.Rd |only
hyperSpec-0.98-20140220/hyperSpec/man/scan-txt-Renishaw.Rd | 2
hyperSpec-0.98-20140220/hyperSpec/man/scan.dat.Witec.Rd |only
hyperSpec-0.98-20140220/hyperSpec/man/spc-loess.Rd | 2
hyperSpec-0.98-20140220/hyperSpec/man/spc-rubberband.Rd |only
hyperSpec-0.98-20140220/hyperSpec/man/spc-spline.Rd |only
hyperSpec-0.98-20140220/hyperSpec/man/textio.Rd | 2
hyperSpec-0.98-20140220/hyperSpec/man/wl.Rd | 2
hyperSpec-0.98-20140220/hyperSpec/vignettes/Rplots.pdf |binary
hyperSpec-0.98-20140220/hyperSpec/vignettes/baseline-pkg.bib | 4
hyperSpec-0.98-20140220/hyperSpec/vignettes/baseline.Rnw | 89 ++-
hyperSpec-0.98-20140220/hyperSpec/vignettes/fig-3D.png |binary
hyperSpec-0.98-20140220/hyperSpec/vignettes/introduction-pkg.bib | 24
hyperSpec-0.98-20140220/hyperSpec/vignettes/introduction.Rnw | 75 +-
hyperSpec-0.98-20140220/hyperSpec/vignettes/laser-pkg.bib | 69 +-
hyperSpec-0.98-20140220/hyperSpec/vignettes/plotting-pkg.bib | 18
hyperSpec-0.98-20140220/hyperSpec/vignettes/scan.txt.PerkinElmer.R | 6
101 files changed, 1092 insertions(+), 763 deletions(-)
Title: Dive analysis and calibration
Diff between diveMove versions 1.3.7 dated 2013-06-20 and 1.3.9 dated 2014-02-20
Description: Utilities to represent, visualize, filter, analyse, and summarize
time-depth recorder (TDR) data. Miscellaneous functions for
handling location data are also provided.
Author: Sebastian P. Luque
Maintainer: Sebastian P. Luque
diveMove-1.3.7/diveMove/inst/doc/Makefile |only
diveMove-1.3.7/diveMove/inst/doc/biblioSPL.bib |only
diveMove-1.3.7/diveMove/inst/doc/tcltk.png |only
diveMove-1.3.9/diveMove/ChangeLog | 24 +++++++++
diveMove-1.3.9/diveMove/DESCRIPTION | 12 ++--
diveMove-1.3.9/diveMove/MD5 | 42 ++++++++--------
diveMove-1.3.9/diveMove/NEWS | 12 ++++
diveMove-1.3.9/diveMove/R/AllClass.R | 4 -
diveMove-1.3.9/diveMove/R/AllMethod.R | 64 +++++++++++--------------
diveMove-1.3.9/diveMove/R/bouts.R | 6 +-
diveMove-1.3.9/diveMove/R/calibrate.R | 24 +++++----
diveMove-1.3.9/diveMove/R/detDive.R | 22 ++++----
diveMove-1.3.9/diveMove/R/detPhase.R | 8 +--
diveMove-1.3.9/diveMove/R/diveStats.R | 6 +-
diveMove-1.3.9/diveMove/R/oneDiveStats.R | 8 +--
diveMove-1.3.9/diveMove/R/plotTDR.R | 4 -
diveMove-1.3.9/diveMove/R/plotZOC.R | 12 ++--
diveMove-1.3.9/diveMove/R/readTDR.R | 8 +--
diveMove-1.3.9/diveMove/R/stampDive.R | 4 -
diveMove-1.3.9/diveMove/R/zoc.R | 6 +-
diveMove-1.3.9/diveMove/build |only
diveMove-1.3.9/diveMove/inst/doc/diveMove.pdf |binary
diveMove-1.3.9/diveMove/vignettes |only
23 files changed, 153 insertions(+), 113 deletions(-)
Title: Analysis of binary character evolution
Diff between corHMM versions 1.12 dated 2013-09-24 and 1.13 dated 2014-02-20
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/ancRECON.R | 30 +++++++++++++++++++++++-------
R/corDISC.R | 2 +-
R/corHMM.R | 6 +++---
R/corPAINT.R | 6 +++---
R/rayDISC.R | 2 +-
7 files changed, 41 insertions(+), 25 deletions(-)