Title: Maximum Likelihood Estimation of a Log-Concave Density Function
Description: Contains functions for computing the nonparametric maximum likelihood estimate of a log-concave density function from univariate observations. This log-density estimate is always a piecewise linear function.
Author: Yu Liu, Yong Wang
Maintainer: Yong Wang <yongwang@auckland.ac.nz>
Diff between cnmlcd versions 1.0-0 dated 2015-10-16 and 1.2-0 dated 2018-02-15
cnmlcd-1.0-0/cnmlcd/man/Log-concave.Rd |only cnmlcd-1.0-0/cnmlcd/man/create.lcd.Rd |only cnmlcd-1.2-0/cnmlcd/DESCRIPTION | 13 cnmlcd-1.2-0/cnmlcd/MD5 | 30 cnmlcd-1.2-0/cnmlcd/NAMESPACE | 13 cnmlcd-1.2-0/cnmlcd/R/cnmlcd.R | 880 +++++++++++++---------------- cnmlcd-1.2-0/cnmlcd/data/logreturn.rda |binary cnmlcd-1.2-0/cnmlcd/data/logreturn2014.rda |only cnmlcd-1.2-0/cnmlcd/data/logvolatility.rda |binary cnmlcd-1.2-0/cnmlcd/man/cnmlcd.Rd | 207 +++--- cnmlcd-1.2-0/cnmlcd/man/lcd.Rd | 94 +-- cnmlcd-1.2-0/cnmlcd/man/log-concave.Rd |only cnmlcd-1.2-0/cnmlcd/man/logreturn.Rd | 65 +- cnmlcd-1.2-0/cnmlcd/man/logreturn2014.Rd |only cnmlcd-1.2-0/cnmlcd/man/logvolatility.Rd | 65 +- cnmlcd-1.2-0/cnmlcd/man/new.lcd.Rd |only cnmlcd-1.2-0/cnmlcd/man/plot.lcd.Rd | 124 ++-- cnmlcd-1.2-0/cnmlcd/man/plotgradient.Rd | 81 +- cnmlcd-1.2-0/cnmlcd/man/x.weight.Rd | 60 - 19 files changed, 800 insertions(+), 832 deletions(-)
Title: Open Source OCR Engine
Description: Bindings to 'Tesseract' <https://opensource.google.com/projects/tesseract>:
An OCR engine with unicode (UTF-8) support that can recognize over 100 languages
out of the box.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between tesseract versions 1.8 dated 2018-01-26 and 1.9 dated 2018-02-15
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 1 + NEWS | 4 ++++ R/tessdata.R | 13 ++++++++++--- R/tesseract.R | 20 ++++++++++++++++++++ configure | 18 +++++++++--------- man/tessdata.Rd | 5 ++++- man/tesseract.Rd | 10 ++++++++++ 9 files changed, 73 insertions(+), 27 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-25 0.1.1
2014-02-25 0.1.0
Title: Sparse Truncated Singular Value Decomposition (from 'SVDLIBC')
Description: Wrapper around the 'SVDLIBC' library for (truncated) singular value decomposition of a sparse matrix.
Currently, only sparse real matrices in Matrix package format are supported.
Author: Doug Rohde [aut],
Michael Berry [aut],
Theresa Do [aut],
Gavin O'Brien [aut],
Vijay Krishna [aut],
Sowmini Varadhan [aut],
University of Tennessee Research Foundation [cph] (files src/las2.c,
src/svdlib.[ch], src/svdutil.[ch]),
Stefan Evert [cre, aut, cph] (copyright holder for files src/main.c,
R/*, man/*, tests/*)
Maintainer: Stefan Evert <stefan.evert@fau.de>
Diff between sparsesvd versions 0.1-1 dated 2016-04-24 and 0.1-4 dated 2018-02-15
DESCRIPTION | 14 ++++++++------ MD5 | 15 ++++++++------- NAMESPACE | 2 +- NEWS | 11 +++++++++++ R/sparsesvd.R | 2 +- man/sparsesvd.Rd | 4 ++-- src/las2.c | 48 ++++++++++++++++++++++++------------------------ src/main.c | 11 +++++++++++ tests/stress_test.R |only 9 files changed, 66 insertions(+), 41 deletions(-)
Title: Bayesian Modelling of Raman Spectroscopy
Description: Sequential Monte Carlo (SMC) algorithms for fitting a generalised additive
mixed model (GAMM) to surface-enhanced resonance Raman spectroscopy (SERRS),
using the method of Moores et al. (2016) <arXiv:1604.07299>. Multivariate
observations of SERRS are highly collinear and lend themselves to a reduced-rank
representation. The GAMM separates the SERRS signal into three components: a
sequence of Lorentzian, Gaussian, or pseudo-Voigt peaks; a smoothly-varying baseline;
and additive white noise. The parameters of each component of the model are estimated
iteratively using SMC. The posterior distributions of the parameters given the observed
spectra are represented as a population of weighted particles.
Author: Matt Moores [aut, cre] (<https://orcid.org/0000-0003-4531-3572>),
Jake Carson [aut],
Mark Girolami [aut],
Engineering and Physical Sciences Research Council [fnd] (EPSRC
programme grant ref: EP/L014165/1),
University of Warwick [cph]
Maintainer: Matt Moores <M.T.Moores@warwick.ac.uk>
Diff between serrsBayes versions 0.3-10 dated 2018-02-14 and 0.3-11 dated 2018-02-15
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 8 +++++++- R/RcppExports.R | 30 ++++++++++++++++++++++++++++++ R/fitSpectraSMC.R | 2 +- R/fitVoigtPeaksSMC.R | 2 +- man/effectiveSampleSize.Rd | 4 ++++ man/fitSpectraSMC.Rd | 2 +- man/fitVoigtPeaksSMC.Rd | 2 +- man/mixedVoigt.Rd | 8 ++++++++ man/sumDlogNorm.Rd | 4 ++++ man/sumDnorm.Rd | 6 ++++++ man/weightedGaussian.Rd | 7 +++++++ man/weightedLorentzian.Rd | 7 +++++++ src/mixLorentz.cpp | 43 ++++++++++++++++++++++++++++++++++++++++--- src/mixVoigt.cpp | 19 +++++++++++++++++-- 16 files changed, 153 insertions(+), 29 deletions(-)
Title: Phylogenetic Reconstruction and Analysis
Description: Package contains methods for estimation of phylogenetic trees and
networks using Maximum Likelihood, Maximum Parsimony, distance methods and
Hadamard conjugation. Allows to compare trees, models selection and offers
visualizations for trees and split networks.
Author: Klaus Schliep [aut, cre],
Emmanuel Paradis [aut],
Leonardo de Oliveira Martins [aut],
Alastair Potts [aut],
Tim W. White [aut],
Cyrill Stachniss [ctb],
Michelle Kendall [ctb]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.3.1 dated 2017-11-01 and 2.4.0 dated 2018-02-15
phangorn-2.3.1/phangorn/R/pphmc.R |only phangorn-2.4.0/phangorn/DESCRIPTION | 9 phangorn-2.4.0/phangorn/MD5 | 123 phangorn-2.4.0/phangorn/NAMESPACE | 3 phangorn-2.4.0/phangorn/NEWS | 23 phangorn-2.4.0/phangorn/R/Densi.R | 12 phangorn-2.4.0/phangorn/R/SH.R | 45 phangorn-2.4.0/phangorn/R/SOWH.R | 40 phangorn-2.4.0/phangorn/R/ancestral_pml.R | 14 phangorn-2.4.0/phangorn/R/bootstrap.R | 12 phangorn-2.4.0/phangorn/R/dist.p.R | 2 phangorn-2.4.0/phangorn/R/distSeq.R | 34 phangorn-2.4.0/phangorn/R/fitch.R | 173 phangorn-2.4.0/phangorn/R/hadamard.R | 26 phangorn-2.4.0/phangorn/R/lento.R | 2 phangorn-2.4.0/phangorn/R/mast.R | 64 phangorn-2.4.0/phangorn/R/neighborNet.R | 198 phangorn-2.4.0/phangorn/R/networx.R | 21 phangorn-2.4.0/phangorn/R/parsimony.R | 78 phangorn-2.4.0/phangorn/R/phangorn-package.R | 2 phangorn-2.4.0/phangorn/R/phyDat.R | 104 phangorn-2.4.0/phangorn/R/phylo.R | 2043 +++++----- phangorn-2.4.0/phangorn/R/pmlMix.R | 4 phangorn-2.4.0/phangorn/R/pmlPart.R | 18 phangorn-2.4.0/phangorn/R/pmlPen.R | 2 phangorn-2.4.0/phangorn/R/sankoff.R | 58 phangorn-2.4.0/phangorn/R/simSeq.R | 126 phangorn-2.4.0/phangorn/R/superTree.R | 50 phangorn-2.4.0/phangorn/R/treeManipulation.R | 133 phangorn-2.4.0/phangorn/R/treeRearrangement.R | 10 phangorn-2.4.0/phangorn/R/treedist.R | 26 phangorn-2.4.0/phangorn/R/zzz.R | 4 phangorn-2.4.0/phangorn/build/vignette.rds |binary phangorn-2.4.0/phangorn/inst/doc/Ancestral.R | 25 phangorn-2.4.0/phangorn/inst/doc/Ancestral.Rnw | 27 phangorn-2.4.0/phangorn/inst/doc/Ancestral.pdf |binary phangorn-2.4.0/phangorn/inst/doc/IntertwiningTreesAndNetworks.html | 26 phangorn-2.4.0/phangorn/inst/doc/Networx.html | 16 phangorn-2.4.0/phangorn/inst/doc/Trees.R | 9 phangorn-2.4.0/phangorn/inst/doc/Trees.Rnw | 5 phangorn-2.4.0/phangorn/inst/doc/Trees.pdf |binary phangorn-2.4.0/phangorn/inst/doc/phangorn-specials.R | 4 phangorn-2.4.0/phangorn/inst/doc/phangorn-specials.Rnw | 2 phangorn-2.4.0/phangorn/inst/doc/phangorn-specials.pdf |binary phangorn-2.4.0/phangorn/man/CI.Rd | 9 phangorn-2.4.0/phangorn/man/SH.test.Rd | 17 phangorn-2.4.0/phangorn/man/add.tips.Rd |only phangorn-2.4.0/phangorn/man/phangorn-internal.Rd | 2 phangorn-2.4.0/phangorn/man/pmlCluster.Rd | 2 phangorn-2.4.0/phangorn/man/simSeq.Rd | 25 phangorn-2.4.0/phangorn/src/phangorn.c | 10 phangorn-2.4.0/phangorn/tests/testthat/test_Clanistics.R |only phangorn-2.4.0/phangorn/tests/testthat/test_SH.R | 7 phangorn-2.4.0/phangorn/tests/testthat/test_parsimony.R | 6 phangorn-2.4.0/phangorn/tests/testthat/test_phyDat.R | 13 phangorn-2.4.0/phangorn/tests/testthat/test_pml.R | 1 phangorn-2.4.0/phangorn/tests/testthat/test_pmlCluster.R |only phangorn-2.4.0/phangorn/tests/testthat/test_pmlPart.R | 45 phangorn-2.4.0/phangorn/tests/testthat/test_splits.R | 2 phangorn-2.4.0/phangorn/tests/testthat/test_treeManipulation.R | 13 phangorn-2.4.0/phangorn/vignettes/Ancestral.Rnw | 27 phangorn-2.4.0/phangorn/vignettes/Trees.Rnw | 5 phangorn-2.4.0/phangorn/vignettes/phangorn-specials.Rnw | 2 phangorn-2.4.0/phangorn/vignettes/phangorn.bib | 1 phangorn-2.4.0/phangorn/vignettes/seqLogo.pdf |only 65 files changed, 2037 insertions(+), 1723 deletions(-)
Title: Learning Interactions via Hierarchical Group-Lasso
Regularization
Description: Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015) <DOI:10.1080/10618600.2014.938812>.
Author: Michael Lim, Trevor Hastie
Maintainer: Michael Lim <michael626@gmail.com>
Diff between glinternet versions 1.0.6 dated 2017-11-29 and 1.0.7 dated 2018-02-15
DESCRIPTION | 8 +- MD5 | 6 - R/check_kkt.r | 33 ++++++---- R/get_candidates.r | 171 ++++++++++++++++++++++++++--------------------------- 4 files changed, 113 insertions(+), 105 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@glasgow.ac.uk>
Diff between btergm versions 1.9.0 dated 2017-03-31 and 1.9.1 dated 2018-02-15
DESCRIPTION | 8 ++-- MD5 | 30 ++++++++-------- NAMESPACE | 1 R/gofstatistics.R | 87 +++++++++++++++++++++++++++++++++++++++++++++++-- inst/CITATION | 38 +++++++++++---------- man/btergm-class.Rd | 2 - man/btergm-package.Rd | 4 +- man/btergm.Rd | 2 - man/checkdegeneracy.Rd | 2 - man/edgeprob.Rd | 4 +- man/gofmethods.Rd | 2 - man/gofplot.Rd | 2 - man/gofstatistics.Rd | 23 ++++++++++++ man/interpret.Rd | 4 +- man/simulate.btergm.Rd | 10 ++--- man/tergm-terms.Rd | 2 - 16 files changed, 165 insertions(+), 56 deletions(-)
Title: Normalisation Tools for Inter-Condition Variability of ChIP-Seq
Data
Description: Inter-sample condition variability is a key challenge of normalising ChIP-seq data. This implementation uses either spike-in or a second factor as a control for normalisation. Input can either be from 'DiffBind' or a matrix formatted for 'DESeq2'. The output is either a 'DiffBind' object or the default 'DESeq2' output. Either can then be processed as normal. Supporting manuscript Guertin, Markowetz and Holding (2017) <doi:10.1101/182261>.
Author: Andrew N Holding
Maintainer: Andrew N Holding <andrew.holding@cruk.cam.ac.uk>
Diff between Brundle versions 1.0.7 dated 2017-12-10 and 1.0.8 dated 2018-02-15
DESCRIPTION | 6 ++--- MD5 | 28 ++++++++++++------------ R/brundle.R | 4 +-- README.md | 42 ++++++++++++++++++++++++++++--------- data/dbaControl.rda |binary data/dbaExperiment.rda |binary data/jg.conditions.rda |binary data/jg.controlCountsTreated.rda |binary data/jg.controlCountsUntreated.rda |binary data/jg.controlPeakset.rda |binary data/jg.controlPeaksetDeSeq.rda |binary data/jg.controlResultsDeseq.rda |binary data/jg.experimentPeakset.rda |binary data/jg.experimentResultsDeseq.rda |binary man/jg.plotDeSeqCombined.Rd | 4 +-- 15 files changed, 53 insertions(+), 31 deletions(-)
Title: Finding Multiple-Objective Optimal Designs for the 4-Parameter
Logistic Model
Description: Provide tools for finding multiple-objective optimal designs for
estimating the shape of dose-response, the ED50 (the dose producing an effect
midway between the expected responses at the extreme doses) and the MED (the
minimum effective dose level) for the 2,3,4-parameter logistic models and for
evaluating its efficiencies for the three objectives. The acronym VNM stands
for V-algorithm using Newton Raphson method to search multiple-objective
optimal design.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Yarong Yang <yarongyang78@gmail.com>
Diff between VNM versions 5.1 dated 2017-06-28 and 6.1 dated 2018-02-15
VNM-5.1/VNM/src/registerDynamicSymbol.c |only VNM-6.1/VNM/DESCRIPTION | 8 +- VNM-6.1/VNM/MD5 | 25 ++++--- VNM-6.1/VNM/R/MOPT.R | 2 VNM-6.1/VNM/R/RcppExports.R | 59 +++++++++--------- VNM-6.1/VNM/inst |only VNM-6.1/VNM/man/Deff.Rd | 4 - VNM-6.1/VNM/man/MOPT.Rd | 4 - VNM-6.1/VNM/man/S.Weight.Rd | 8 +- VNM-6.1/VNM/man/VNM-package.Rd | 22 +++++- VNM-6.1/VNM/man/ceff1.Rd | 2 VNM-6.1/VNM/man/ceff2.Rd | 2 VNM-6.1/VNM/src/RcppExports.cpp | 103 +++++++++++++++++++++++--------- VNM-6.1/VNM/src/ff.cpp | 5 - VNM-6.1/VNM/src/rcpp_hello_world.cpp |only 15 files changed, 154 insertions(+), 90 deletions(-)
Title: Model-Based Clustering and Classification with the Multivariate
t Distribution
Description: Fits mixtures of multivariate t-distributions (with eigen-decomposed covariance structure) via the expectation conditional-maximization algorithm under a clustering or classification paradigm.
Author: Jeffrey L. Andrews, Jaymeson R. Wickins, Nicholas M. Boers, Paul D. McNicholas
Maintainer: Jeffrey L. Andrews <jeff.andrews@ubc.ca>
Diff between teigen versions 2.2.0 dated 2016-12-07 and 2.2.2 dated 2018-02-15
ChangeLog | 9 +++++++++ DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- R/teigen.R | 28 +++++++++++++++++++--------- inst/CITATION | 31 +++++++++++++++++++++++-------- man/teigen-package.Rd | 6 ++++-- src/init.c |only 7 files changed, 65 insertions(+), 28 deletions(-)
Title: An Individual-Based Population Genetic Simulation Environment
Description: An interface between R and the metasim simulation engine.
The simulation environment is documented in: "Strand, A.(2002) <DOI:10.1046/j.1471-8286.2002.00208.x> Metasim 1.0: an individual-based environment for simulating population genetics of
complex population dynamics. Mol. Ecol. Notes.
Please see the vignettes CreatingLandscapes and Simulating to get some ideas on how to use the packages.
See the rmetasim vignette to get an overview and to see important changes to the
code in the most recent version.
Author: Allan Strand <stranda@cofc.edu>,
James Niehaus
Maintainer: Allan Strand <stranda@cofc.edu>
Diff between rmetasim versions 3.1.6 dated 2018-01-04 and 3.1.7 dated 2018-02-15
DESCRIPTION | 8 ++-- MD5 | 20 ++++++------ R/runsimulation.R | 17 +++++----- build/vignette.rds |binary inst/doc/ApplyCarryToStage.html | 42 ++++++++++++------------- inst/doc/CreatingLandscapes.html | 52 ++++++++++++++++---------------- inst/doc/Sexuality-and-mating.html | 4 +- inst/doc/Simulating.html | 60 ++++++++++++++++++------------------- inst/doc/rmetasim.html | 4 +- man/landscape.simulate.Rd | 5 ++- src/Makevars | 2 - 11 files changed, 109 insertions(+), 105 deletions(-)
Title: Non-Negative and Sparse CCA
Description: Two implementations of canonical correlation analysis
(CCA) that are based on iterated regression. By choosing the
appropriate regression algorithm for each data domain, it is
possible to enforce sparsity, non-negativity or other kinds of
constraints on the projection vectors. Multiple canonical
variables are computed sequentially using a generalized
deflation scheme, where the additional correlation not
explained by previous variables is maximized. 'nscancor' is
used to analyze paired data from two domains, and has the same
interface as the 'cancor' function from the 'stats' package
(plus some extra parameters). 'mcancor' is appropriate for
analyzing data from three or more domains. See
<http://sigg-iten.ch/learningbits/2014/01/20/canonical-correlation-analysis-under-constraints/>
and Sigg et al. (2007) <doi:10.1109/MLSP.2007.4414315> for more
details.
Author: Christian Sigg [aut, cre] (<https://orcid.org/0000-0003-1067-9224>),
R Core team [ctb] (cancor interface and documentation)
Maintainer: Christian Sigg <christian@sigg-iten.ch>
Diff between nscancor versions 0.6 dated 2014-07-17 and 0.6.1-25 dated 2018-02-15
nscancor-0.6.1-25/nscancor/DESCRIPTION | 49 +- nscancor-0.6.1-25/nscancor/MD5 | 44 - nscancor-0.6.1-25/nscancor/NAMESPACE | 4 nscancor-0.6.1-25/nscancor/R/acor.R | 58 +- nscancor-0.6.1-25/nscancor/R/cardinality.R | 10 nscancor-0.6.1-25/nscancor/R/macor.R | 64 +- nscancor-0.6.1-25/nscancor/R/mcancor.R | 196 ++++---- nscancor-0.6.1-25/nscancor/R/nscancor-package.R | 16 nscancor-0.6.1-25/nscancor/R/nscancor.R | 200 ++++---- nscancor-0.6.1-25/nscancor/README.md | 5 nscancor-0.6.1-25/nscancor/inst/CITATION | 4 nscancor-0.6.1-25/nscancor/inst/atexample |only nscancor-0.6.1-25/nscancor/man/acor.Rd | 92 +--- nscancor-0.6.1-25/nscancor/man/cardinality.Rd | 10 nscancor-0.6.1-25/nscancor/man/macor.Rd | 66 +- nscancor-0.6.1-25/nscancor/man/mcancor.Rd | 237 ++++------ nscancor-0.6.1-25/nscancor/man/nscancor.Rd | 321 ++++++-------- nscancor-0.6.1-25/nscancor/tests/run-all.R | 11 nscancor-0.6.1-25/nscancor/tests/testthat/test_acor.R | 26 - nscancor-0.6.1-25/nscancor/tests/testthat/test_macor.R | 25 - nscancor-0.6.1-25/nscancor/tests/testthat/test_mcancor.R | 50 +- nscancor-0.6.1-25/nscancor/tests/testthat/test_nscancor.R | 31 - nscancor-0.6/nscancor/inst/mcancor_examples.R |only nscancor-0.6/nscancor/inst/nscancor_examples.R |only 24 files changed, 746 insertions(+), 773 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>, difference-in-means, and Horvitz-Thompson estimation.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb],
The R Core Team [ctb, cph] (For na.omit used in
na.omit_detailed.data.frame)
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between estimatr versions 0.2.0 dated 2018-01-29 and 0.4.0 dated 2018-02-15
estimatr-0.2.0/estimatr/build |only estimatr-0.2.0/estimatr/inst |only estimatr-0.2.0/estimatr/vignettes |only estimatr-0.4.0/estimatr/DESCRIPTION | 11 estimatr-0.4.0/estimatr/MD5 | 56 - estimatr-0.4.0/estimatr/NEWS.md | 11 estimatr-0.4.0/estimatr/R/S3_nobs.R | 16 estimatr-0.4.0/estimatr/R/S3_print.R | 22 estimatr-0.4.0/estimatr/R/estimatr_difference_in_means.R | 2 estimatr-0.4.0/estimatr/R/estimatr_horvitz_thompson.R | 2 estimatr-0.4.0/estimatr/R/estimatr_lm_lin.R | 6 estimatr-0.4.0/estimatr/R/estimatr_lm_robust.R | 4 estimatr-0.4.0/estimatr/R/helper_clean_model_data.R | 2 estimatr-0.4.0/estimatr/man/difference_in_means.Rd | 2 estimatr-0.4.0/estimatr/man/horvitz_thompson.Rd | 2 estimatr-0.4.0/estimatr/man/lm_lin.Rd | 4 estimatr-0.4.0/estimatr/man/lm_robust.Rd | 4 estimatr-0.4.0/estimatr/src/lm_robust_helper.cpp | 421 ++++------ estimatr-0.4.0/estimatr/tests/testthat/test-horvitz-thompson.R | 1 estimatr-0.4.0/estimatr/tests/testthat/test-lm-lin.R | 52 - estimatr-0.4.0/estimatr/tests/testthat/test-lm-robust.R | 29 estimatr-0.4.0/estimatr/tests/testthat/test-lm-robust_margins.R | 29 estimatr-0.4.0/estimatr/tests/testthat/test-na-omit-details.R | 1 estimatr-0.4.0/estimatr/tests/testthat/test-s3-methods.R | 1 estimatr-0.4.0/estimatr/tests/testthat/test-zzz.R |only 25 files changed, 333 insertions(+), 345 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.8.3 dated 2017-11-21 and 3.8.4 dated 2018-02-15
DESCRIPTION | 8 +++---- MD5 | 8 +++---- NEWS | 7 ++++++ R/Deriv.R | 58 +++++++++++++++++++++++++++++---------------------- man/Deriv-package.Rd | 4 +-- 5 files changed, 50 insertions(+), 35 deletions(-)
Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo
standard errors of commonly used summary statistics. This package is modelled
on the 'simsum' user-written command in 'Stata' (See White I.R., 2010
<http://www.stata-journal.com/article.html?article=st0200>).
Author: Alessandro Gasparini [aut, cre],
Ian R. White [aut]
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>
Diff between rsimsum versions 0.1.0 dated 2018-02-05 and 0.2.0 dated 2018-02-15
DESCRIPTION | 13 MD5 | 204 +- NAMESPACE | 61 R/data.R | 96 - R/dropbig.R | 22 R/dropbig.multisimsum.R | 54 R/dropbig.simsum.R | 58 R/format.multisimsum.R | 98 - R/format.simsum.R | 96 - R/get_data.R | 20 R/get_data.miss.R |only R/get_data.multisimsum.R | 97 - R/get_data.simsum.R | 103 - R/get_data.summary.multisimsum.R | 101 - R/get_data.summary.simsum.R | 105 - R/heat.R |only R/heat.multisimsum.R |only R/heat.simsum.R |only R/is.multisimsum.R | 14 R/is.simsum.R | 14 R/lolly.R |only R/lolly.multisimsum.R |only R/lolly.simsum.R |only R/miss.R |only R/multisimsum.R | 349 ++-- R/nsim.R | 84 - R/pattern.R |only R/pattern.multisimsum.R |only R/pattern.simsum.R |only R/pattern.simsum.R.R |only R/perfms.R | 272 +-- R/print.dropbig.multisimsum.R | 49 R/print.dropbig.simsum.R | 49 R/print.miss.R |only R/print.multisimsum.R | 93 - R/print.simsum.R | 81 - R/print.summary.multisimsum.R | 265 +-- R/print.summary.simsum.R | 249 +-- R/rsimsum.R |only R/simsum.R | 694 ++++----- R/summary.multisimsum.R | 82 - R/summary.simsum.R | 84 - R/zip.R |only R/zip.multisimsum.R |only R/zip.simsum.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.R | 166 +- inst/doc/introduction.Rmd | 624 ++++---- inst/doc/introduction.html | 2267 ++++++++++++++++-------------- inst/doc/plotting.R |only inst/doc/plotting.Rmd |only inst/doc/plotting.html |only inst/doc/relhaz.R | 444 ++--- inst/doc/relhaz.Rmd | 660 ++++---- inst/doc/relhaz.html | 1398 ++++++++++-------- inst/doc/rsimsumtidyverse.R | 68 inst/doc/rsimsumtidyverse.Rmd | 104 - inst/doc/rsimsumtidyverse.html | 1156 +++++++++------ man/MIsim.Rd | 61 man/dropbig.Rd | 35 man/dropbig.multisimsum.Rd | 61 man/dropbig.simsum.Rd | 63 man/format.multisimsum.Rd | 47 man/format.simsum.Rd | 47 man/format.summary.multisimsum.Rd | 50 man/format.summary.simsum.Rd | 47 man/frailty.Rd | 53 man/get_data.Rd | 35 man/get_data.miss.Rd |only man/get_data.multisimsum.Rd | 96 - man/get_data.simsum.Rd | 100 - man/get_data.summary.multisimsum.Rd | 98 - man/get_data.summary.simsum.Rd | 102 - man/heat.Rd |only man/heat.multisimsum.Rd |only man/heat.simsum.Rd |only man/is.multisimsum.Rd | 28 man/is.simsum.Rd | 28 man/lolly.Rd |only man/lolly.multisimsum.Rd |only man/lolly.simsum.Rd |only man/miss.Rd |only man/multisimsum.Rd | 127 - man/nsim.Rd | 79 - man/pattern.Rd |only man/pattern.multisimsum.Rd |only man/pattern.simsum.Rd |only man/print.dropbig.multisimsum.Rd | 38 man/print.dropbig.simsum.Rd | 38 man/print.miss.Rd |only man/print.multisimsum.Rd | 46 man/print.simsum.Rd | 44 man/print.summary.multisimsum.Rd | 96 - man/print.summary.simsum.Rd | 100 - man/relhaz.Rd | 65 man/rsimsum.Rd |only man/simsum.Rd | 131 - man/summary.multisimsum.Rd | 73 man/summary.simsum.Rd | 71 man/zip.Rd |only man/zip.multisimsum.Rd |only man/zip.simsum.Rd |only tests/testthat.R | 8 tests/testthat/test-data.R | 32 tests/testthat/test-dropbig.R | 100 - tests/testthat/test-format.R | 190 +- tests/testthat/test-get_data.R | 180 +- tests/testthat/test-heat.R |only tests/testthat/test-is.multisimsum.R | 18 tests/testthat/test-is.simsum.R | 18 tests/testthat/test-lolly.R |only tests/testthat/test-miss.R |only tests/testthat/test-multisimsum.R | 281 +-- tests/testthat/test-nsim.R | 108 - tests/testthat/test-pattern.R |only tests/testthat/test-simsum.R | 289 +-- tests/testthat/test-summary.multisimsum.R | 92 - tests/testthat/test-summary.simsum.R | 90 - tests/testthat/test-zip.R |only vignettes/introduction.Rmd | 624 ++++---- vignettes/plotting.Rmd |only vignettes/relhaz.Rmd | 660 ++++---- vignettes/rsimsumtidyverse.Rmd | 104 - 124 files changed, 7857 insertions(+), 7190 deletions(-)
Title: Generate Cofeature Matrices
Description: Generate cofeature (feature by sample) matrices. The package
utilizes ggplot2::geom_tile() to generate the matrix allowing for easy
additions from the base matrix.
Author: Fong Chun Chan [aut, cre]
Maintainer: Fong Chun Chan <fongchunchan@gmail.com>
Diff between cofeatureR versions 1.0.1 dated 2016-01-13 and 1.1.0 dated 2018-02-15
cofeatureR-1.0.1/cofeatureR/LICENSE |only cofeatureR-1.1.0/cofeatureR/DESCRIPTION | 10 - cofeatureR-1.1.0/cofeatureR/MD5 | 21 +-- cofeatureR-1.1.0/cofeatureR/NAMESPACE | 2 cofeatureR-1.1.0/cofeatureR/NEWS.md |only cofeatureR-1.1.0/cofeatureR/R/cofeatureR-package.R | 2 cofeatureR-1.1.0/cofeatureR/R/plot_cofeature_mat.R | 123 +++++++++++++----- cofeatureR-1.1.0/cofeatureR/README.md | 55 ++++++-- cofeatureR-1.1.0/cofeatureR/man/add_tiles.Rd |only cofeatureR-1.1.0/cofeatureR/man/cofeatureR.Rd | 7 - cofeatureR-1.1.0/cofeatureR/man/figures |only cofeatureR-1.1.0/cofeatureR/man/plot_cofeature_mat.Rd | 67 +++++++-- cofeatureR-1.1.0/cofeatureR/tests |only 13 files changed, 210 insertions(+), 77 deletions(-)
Title: Detecting Politeness Features in Text
Description: Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness (Brown & Levinson, 1987 <http://psycnet.apa.org/record/1987-97641-000>; Danescu-Niculescu-Mizil et al., 2013 <arXiv:1306.6078>; Voigt et al., 2017 <doi:10.1073/pnas.1702413114>). We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.
Author: Mike Yeomans, Alejandro Kantor, Dustin Tingley
Maintainer: Mike Yeomans <yeomans@fas.harvard.edu>
Diff between politeness versions 0.2.1 dated 2018-01-23 and 0.2.2 dated 2018-02-15
DESCRIPTION | 6 ++-- MD5 | 10 +++--- R/politenessProjection.R | 10 +++--- inst/doc/politeness.html | 16 +++++----- man/politenessProjection.Rd | 10 +++--- tests/testthat/test-findPoliteTexts.R | 50 +++++++++++++++++----------------- 6 files changed, 52 insertions(+), 50 deletions(-)
Title: Tree-Based Varying Coefficient Regression for Generalized Linear
and Ordinal Mixed Models
Description: Recursive partitioning for varying coefficient generalized linear models and ordinal linear mixed models. Special features are coefficient-wise partitioning, non-varying coefficients and partitioning of time-varying variables in longitudinal regression.
Author: Reto Buergin [aut, cre, cph],
Gilbert Ritschard [ctb, ths]
Maintainer: Reto Buergin <rbuergin@gmx.ch>
Diff between vcrpart versions 1.0-1 dated 2017-10-17 and 1.0-2 dated 2018-02-15
vcrpart-1.0-1/vcrpart/build |only vcrpart-1.0-1/vcrpart/inst/doc |only vcrpart-1.0-1/vcrpart/vignettes |only vcrpart-1.0-2/vcrpart/DESCRIPTION | 8 - vcrpart-1.0-2/vcrpart/MD5 | 31 +----- vcrpart-1.0-2/vcrpart/NEWS | 8 + vcrpart-1.0-2/vcrpart/R/olmm.R | 7 + vcrpart-1.0-2/vcrpart/R/tvcm-utils.R | 10 +- vcrpart-1.0-2/vcrpart/R/utils.R | 2 vcrpart-1.0-2/vcrpart/ToDo | 10 +- vcrpart-1.0-2/vcrpart/src/olmm.c | 175 +++++++++++++++++------------------ vcrpart-1.0-2/vcrpart/src/utils.c | 1 12 files changed, 130 insertions(+), 122 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Mary C. Meyer (2013)<doi:10.1080/10485252.2013.797577> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <liaoxiyue2011@gmail.com>
Diff between cgam versions 1.8 dated 2017-10-02 and 1.9 dated 2018-02-15
ChangeLog | 3 DESCRIPTION | 8 - MD5 | 6 - R/cgam.R | 263 +++++++++++++++++++++++++++++++----------------------------- 4 files changed, 147 insertions(+), 133 deletions(-)
Title: Statistical Methods for Analyzing Clustered Matched Pair Data
Description: Tests, utilities, and case studies for analyzing significance in
clustered binary matched-pair data. The central function clust.bin.pair uses
one of several tests to calculate a Chi-square statistic. Implemented are the
tests Eliasziw (1991) <doi:10.1002/sim.4780101211>, Obuchowski (1998)
<doi:10.1002/(SICI)1097-0258(19980715)17:13%3C1495::AID-SIM863%3E3.0.CO;2-I>,
Durkalski (2003) <doi:10.1002/sim.1438>, and Yang (2010)
<doi:10.1002/bimj.201000035> with McNemar (1947) <doi:10.1007/BF02295996>
included for comparison. The utility functions nested.to.contingency and
paired.to.contingency convert data between various useful formats. Thyroids
and psychiatry are the canonical datasets from Obuchowski and Petryshen (1989)
<doi:10.1016/0165-1781(89)90196-0> respectively.
Author: Dan Gopstein [aut, cre]
Maintainer: Dan Gopstein <dan@gopstein.com>
Diff between clust.bin.pair versions 0.0.6 dated 2016-10-26 and 0.1.2 dated 2018-02-15
DESCRIPTION | 23 ++++++++----- LICENSE | 2 - MD5 | 15 ++++---- NEWS |only R/clust.bin.pair.R | 59 ++++++++++++++++++----------------- R/util.R | 12 +++---- README.md | 34 +++++++++----------- man/clust.bin.pair.Rd | 9 +++-- tests/testthat/test_clust_bin_pair.R | 42 ++++++++++++------------ 9 files changed, 103 insertions(+), 93 deletions(-)
More information about clust.bin.pair at CRAN
Permanent link
Title: Interface to the 'g:Profiler' Toolkit
Description: Functional enrichment analysis, gene identifier conversion and
mapping homologous genes across related organisms via the 'g:Profiler' toolkit
(<https://biit.cs.ut.ee/gprofiler/>).
Author: Juri Reimand <juri.reimand@ut.ee>, Raivo Kolde
<rkolde@gmail.com>, Tambet Arak <tambet.arak@gmail.com>
Maintainer: Ivan Kuzmin <ivan.kuzmin@ut.ee>
Diff between gProfileR versions 0.6.3 dated 2018-01-30 and 0.6.4 dated 2018-02-15
ChangeLog | 4 ++++ DESCRIPTION | 7 ++++--- MD5 | 8 ++++---- R/gProfileR.R | 2 +- man/gprofiler.Rd | 2 +- 5 files changed, 14 insertions(+), 9 deletions(-)
Title: Interactive Circular Visualization of Genomic Data using
'htmlwidgets' and 'BioCircos.js'
Description: Implement in 'R' interactive Circos-like visualizations of genomic data, to map information
such as genetic variants, genomic fusions and aberrations to a circular genome, as proposed by the
'JavaScript' library 'BioCircos.js', based on the 'JQuery' and 'D3' technologies. The output is by
default displayed in stand-alone HTML documents or in the 'RStudio' viewer pane. Moreover it can be
integrated in 'R Markdown' documents and 'Shiny' applications.
Author: Loan Vulliard [trl, cre],
Xiaowei Chen [aut],
Ya Cui [aut]
Maintainer: Loan Vulliard <lvulliard@cemm.at>
Diff between BioCircos versions 0.2.2 dated 2017-12-21 and 0.3.3 dated 2018-02-15
DESCRIPTION | 10 MD5 | 30 - NAMESPACE | 4 R/BioCircos.R | 508 +++++++++++++++++++++++++- README.md | 24 + inst/doc/BioCircos.R | 142 ++++++- inst/doc/BioCircos.Rmd | 171 +++++++- inst/doc/BioCircos.html | 614 +++++++++++++++++++++++++------- inst/htmlwidgets/BioCircos.js | 220 +++++++++++ inst/htmlwidgets/lib/biocircos-1.1.2.js | 44 +- man/BioCircos.Rd | 142 +++++++ man/BioCircosArcTrack.Rd | 8 man/BioCircosBarTrack.Rd |only man/BioCircosCNVTrack.Rd |only man/BioCircosHeatmapTrack.Rd |only man/BioCircosLineTrack.Rd |only man/BioCircosSNPTrack.Rd | 6 vignettes/BioCircos.Rmd | 171 +++++++- 18 files changed, 1852 insertions(+), 242 deletions(-)
Title: Confidence Intervals for Comparisons of Binomial or Poisson
Rates
Description: Computes confidence intervals for the rate (or risk)
difference ('RD') or rate ratio (or relative risk, 'RR') for
binomial proportions or Poisson rates, or for odds ratio
('OR', binomial only). Also confidence intervals for a single
binomial or Poisson rate, and intervals for matched pairs.
Includes skewness-corrected asymptotic score ('SCAS') methods,
which have been developed in Laud (2017) <doi:10.1002/pst.1813>
from Miettinen & Nurminen (1985) <doi:10.1002/sim.4780040211> and
Gart & Nam (1988) <doi:10.2307/2531848>. Also includes MOVER methods
(Method Of Variance Estimates Recovery) for all contrasts, derived
from the Newcombe method but using equal-tailed Jeffreys intervals,
and generalised for Bayesian applications incorporating prior
information. So-called 'exact' methods for strictly conservative
coverage are approximated using continuity corrections.
Also includes methods for stratified calculations (e.g. meta-analysis),
either assuming fixed effects or incorporating stratum
heterogeneity.
Author: Pete Laud [aut, cre]
Maintainer: Pete Laud <p.j.laud@sheffield.ac.uk>
Diff between ratesci versions 0.2-0 dated 2017-04-21 and 0.3-0 dated 2018-02-15
DESCRIPTION | 28 MD5 | 43 - NAMESPACE | 6 NEWS.md | 33 R/moverci.R | 191 ++--- R/pairbinci.R | 257 +++++-- R/rateci.R |only R/ratesci-package.R | 63 + R/scoreci.R | 1606 ++++++++++++++++++++++---------------------- man/jeffreysci.Rd | 29 man/moverbci.Rd | 15 man/moverci.Rd | 74 +- man/pairbinci.Rd | 107 ++ man/rateci.Rd |only man/ratesci-package.Rd | 51 - man/scasci.Rd | 56 - man/scaspci.Rd |only man/scoreci.Rd | 179 ++-- man/tdasci.Rd | 48 - tests/testthat/Table3.Rdata |only tests/testthat/test1.R | 25 tests/testthat/test2.R | 75 +- tests/testthat/test3.R | 129 +++ tests/testthat/test4.R | 113 +-- tests/testthat/test5.R |only 25 files changed, 1823 insertions(+), 1305 deletions(-)
Title: Thresholds and Invariant Intervals for Network Meta-Analysis
Description: Calculation and presentation of decision-invariant bias adjustment
thresholds and intervals for Network Meta-Analysis, as described by
Phillippo et al. (2017) <doi:10.1111/rssa.12341>. These describe the
smallest changes to the data that would result in a change of decision.
Author: David Phillippo [aut, cre]
Maintainer: David Phillippo <david.phillippo@bristol.ac.uk>
Diff between nmathresh versions 0.1.1 dated 2018-01-26 and 0.1.2 dated 2018-02-15
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NAMESPACE | 5 +++++ NEWS.md | 6 ++++++ R/classes.R | 3 +++ R/thresh_forest.R | 47 ++++++++++++++++++++++++++++++++++------------- README.md |only inst/doc/Examples.html | 16 ++++++++-------- 8 files changed, 66 insertions(+), 30 deletions(-)
Title: Microbial Pan-Genome Analysis
Description: A collection of functions for computations and visualizations of microbial pan-genomes.
Author: Lars Snipen and Kristian Hovde Liland
Maintainer: Lars Snipen <lars.snipen@nmbu.no>
Diff between micropan versions 1.1.2 dated 2017-01-17 and 1.2 dated 2018-02-15
micropan-1.1.2/micropan/inst/extdata/Mpneumoniae_309_GID2.fsa.xz |only micropan-1.1.2/micropan/inst/extdata/Mpneumoniae_309_genome.fsa.xz |only micropan-1.1.2/micropan/inst/extdata/Mpneumoniae_309_protein.fsa.xz |only micropan-1.1.2/micropan/inst/extdata/Mpneumoniae_FH_GID3.fsa.xz |only micropan-1.1.2/micropan/inst/extdata/Mpneumoniae_M129_GID1.fsa.xz |only micropan-1.1.2/micropan/inst/extdata/microfam0.hmm.h3f.xz |only micropan-1.1.2/micropan/inst/extdata/microfam0.hmm.h3i.xz |only micropan-1.1.2/micropan/inst/extdata/microfam0.hmm.h3m.xz |only micropan-1.1.2/micropan/inst/extdata/microfam0.hmm.h3p.xz |only micropan-1.1.2/micropan/man/prodigalPredict.Rd |only micropan-1.1.2/micropan/vignettes/vignette-concordance.tex |only micropan-1.1.2/micropan/vignettes/vignette.tex |only micropan-1.2/micropan/DESCRIPTION | 19 - micropan-1.2/micropan/MD5 | 164 +++++----- micropan-1.2/micropan/NAMESPACE | 13 micropan-1.2/micropan/R/RcppExports.R |only micropan-1.2/micropan/R/bclust.R | 23 - micropan-1.2/micropan/R/bdist.R | 38 +- micropan-1.2/micropan/R/blasting.R | 108 +++--- micropan-1.2/micropan/R/domainclust.R | 29 + micropan-1.2/micropan/R/entrez.R | 30 + micropan-1.2/micropan/R/extern.R |only micropan-1.2/micropan/R/genomedistances.R | 12 micropan-1.2/micropan/R/gff.R |only micropan-1.2/micropan/R/hmmer3.R | 98 +++-- micropan-1.2/micropan/R/micropan.R |only micropan-1.2/micropan/R/mpneumoniae.R | 4 micropan-1.2/micropan/R/orfs.R |only micropan-1.2/micropan/R/panmat.R | 3 micropan-1.2/micropan/R/panpca.R | 3 micropan-1.2/micropan/R/panprep.R | 38 +- micropan-1.2/micropan/R/prodigal.R | 69 ++-- micropan-1.2/micropan/R/ssu.R |only micropan-1.2/micropan/R/xz.R | 21 - micropan-1.2/micropan/build/vignette.rds |binary micropan-1.2/micropan/demo/casestudy.R | 9 micropan-1.2/micropan/inst/doc/casestudy.pdf |binary micropan-1.2/micropan/inst/doc/vignette.R | 6 micropan-1.2/micropan/inst/doc/vignette.Rnw | 35 -- micropan-1.2/micropan/inst/doc/vignette.pdf |binary micropan-1.2/micropan/inst/extdata/Example.gff.xz |only micropan-1.2/micropan/inst/extdata/Example_genome.fasta.xz |only micropan-1.2/micropan/inst/extdata/Example_proteins.fasta.xz |only micropan-1.2/micropan/inst/extdata/Example_proteins_GID1.fasta.xz |only micropan-1.2/micropan/inst/extdata/Example_proteins_GID2.fasta.xz |only micropan-1.2/micropan/inst/extdata/Example_proteins_GID3.fasta.xz |only micropan-1.2/micropan/inst/extdata/GID1_vs_GID1.txt.xz |binary micropan-1.2/micropan/inst/extdata/GID1_vs_GID2.txt.xz |binary micropan-1.2/micropan/inst/extdata/GID1_vs_GID3.txt.xz |binary micropan-1.2/micropan/inst/extdata/GID2_vs_GID1.txt.xz |binary micropan-1.2/micropan/inst/extdata/GID2_vs_GID2.txt.xz |binary micropan-1.2/micropan/inst/extdata/GID2_vs_GID3.txt.xz |binary micropan-1.2/micropan/inst/extdata/GID3_vs_GID1.txt.xz |binary micropan-1.2/micropan/inst/extdata/GID3_vs_GID2.txt.xz |binary micropan-1.2/micropan/inst/extdata/GID3_vs_GID3.txt.xz |binary micropan-1.2/micropan/inst/extdata/microfam.hmm.h3f.xz |only micropan-1.2/micropan/inst/extdata/microfam.hmm.h3i.xz |only micropan-1.2/micropan/inst/extdata/microfam.hmm.h3m.xz |only micropan-1.2/micropan/inst/extdata/microfam.hmm.h3p.xz |only micropan-1.2/micropan/man/bClust.Rd | 7 micropan-1.2/micropan/man/bDist.Rd | 45 +- micropan-1.2/micropan/man/barrnap.Rd |only micropan-1.2/micropan/man/binomixEstimate.Rd | 7 micropan-1.2/micropan/man/blastAllAll.Rd | 54 +-- micropan-1.2/micropan/man/chao.Rd | 7 micropan-1.2/micropan/man/dClust.Rd | 33 +- micropan-1.2/micropan/man/distJaccard.Rd | 7 micropan-1.2/micropan/man/distManhattan.Rd | 7 micropan-1.2/micropan/man/entrezDownload.Rd | 18 - micropan-1.2/micropan/man/findOrfs.Rd |only micropan-1.2/micropan/man/fluidity.Rd | 7 micropan-1.2/micropan/man/geneWeights.Rd | 7 micropan-1.2/micropan/man/generic.Binomix.Rd | 11 micropan-1.2/micropan/man/generic.Panmat.Rd | 11 micropan-1.2/micropan/man/generic.Panpca.Rd | 11 micropan-1.2/micropan/man/generic.Pantree.Rd | 11 micropan-1.2/micropan/man/generic.Rarefac.Rd | 11 micropan-1.2/micropan/man/getAccessions.Rd | 19 - micropan-1.2/micropan/man/gff2fasta.Rd |only micropan-1.2/micropan/man/gffSignature.Rd |only micropan-1.2/micropan/man/heaps.Rd | 7 micropan-1.2/micropan/man/hmmerCleanOverlap.Rd | 7 micropan-1.2/micropan/man/hmmerScan.Rd | 56 +-- micropan-1.2/micropan/man/isOrtholog.Rd | 13 micropan-1.2/micropan/man/lorfs.Rd |only micropan-1.2/micropan/man/micropan.Rd |only micropan-1.2/micropan/man/mpneumoniae.Rd | 11 micropan-1.2/micropan/man/orfLength.Rd |only micropan-1.2/micropan/man/panMatrix.Rd | 7 micropan-1.2/micropan/man/panPrep.Rd | 38 +- micropan-1.2/micropan/man/panTree.Rd | 7 micropan-1.2/micropan/man/panpca.Rd | 7 micropan-1.2/micropan/man/prodigal.Rd |only micropan-1.2/micropan/man/rarefaction.Rd | 7 micropan-1.2/micropan/man/readBlastTable.Rd | 22 - micropan-1.2/micropan/man/readGFF.Rd |only micropan-1.2/micropan/man/readHmmer.Rd | 9 micropan-1.2/micropan/man/scores.loadings.Rd | 9 micropan-1.2/micropan/man/xz.Rd | 20 - micropan-1.2/micropan/src |only micropan-1.2/micropan/vignettes/vignette.Rnw | 35 -- 101 files changed, 703 insertions(+), 547 deletions(-)
Title: Aster Models
Description: Aster models are exponential family regression models for life
history analysis. They are like generalized linear models except that
elements of the response vector can have different families (e. g.,
some Bernoulli, some Poisson, some zero-truncated Poisson, some normal)
and can be dependent, the dependence indicated by a graphical structure.
Discrete time survival analysis, zero-inflated Poisson regression, and
generalized linear models that are exponential family (e. g., logistic
regression and Poisson regression with log link) are special cases.
Main use is for data in which there is survival over discrete time periods
and there is additional data about what happens conditional on survival
(e. g., number of offspring). Uses the exponential family canonical
parameterization (aster transform of usual parameterization).
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: ORPHANED
Diff between aster versions 0.9.1 dated 2017-03-15 and 0.9.1.1 dated 2018-02-15
DESCRIPTION | 14 ++++++++++---- MD5 | 14 +++++++------- man/chamae.Rd | 8 ++++---- man/chamae2.Rd | 8 ++++---- man/chamae3.Rd | 8 ++++---- src/mlogl.c | 10 +++++----- tests/pickle.R | 5 ++++- tests/pickle.Rout.save | 13 ++++++++----- 8 files changed, 46 insertions(+), 34 deletions(-)