Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data.
Functions are provided to rapidly read from and write to VCF files. Once
VCF data is read into R a parser function extracts matrices of data. This
information can then be used for quality control or other purposes. Additional
functions provide visualization of genomic data. Once processing is complete
data may be written to a VCF file (*.vcf.gz). It also may be converted into
other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between
VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut] (<https://orcid.org/0000-0003-1665-4343>),
Niklaus J. Grunwald [aut] (<https://orcid.org/0000-0003-1656-7602>),
Eric C. Anderson [ctb],
David J. Winter [ctb],
Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>),
Javier F. Tabima [ctb] (<https://orcid.org/0000-0002-3603-2691>)
Maintainer: Brian J. Knaus <briank.lists@gmail.com>
Diff between vcfR versions 1.6.0 dated 2017-12-07 and 1.7.0 dated 2018-02-07
DESCRIPTION | 16 ++-- MD5 | 27 ++++---- R/genetic_diff.R | 6 + R/io_vcfR.R | 32 +++++++++ R/vcfR_to_tidy_functions.R | 82 ++++++++++++++---------- R/vep.R |only data/vep.RData |only inst/doc/converting_data.html | 8 +- inst/doc/intro_to_vcfR.html | 16 ++-- inst/doc/vcf_data.html | 4 - inst/doc/workflow.html | 4 - man/io_vcfR.Rd | 6 + man/vep.Rd |only tests/testthat/test_014_read_vcfR.R | 3 tests/testthat/test_genetic_diff.R | 119 +++++++++++++++++++++++++++++++++++- tests/testthat/test_vcfRtidy.R | 64 ++++++++++++++----- 16 files changed, 294 insertions(+), 93 deletions(-)
Title: Low Rank Quadratic Programming
Description: Solves quadratic programming problems where the Hessian is represented as the product of two matrices.
Author: John T. Ormerod [aut],
Matt P. Wand [aut, cre]
Maintainer: Matt P. Wand <matt.wand@uts.edu.au>
Diff between LowRankQP versions 1.0.2 dated 2012-12-06 and 1.0.3 dated 2018-02-07
LowRankQP-1.0.2/LowRankQP/CONTENTS |only LowRankQP-1.0.2/LowRankQP/INDEX |only LowRankQP-1.0.3/LowRankQP/DESCRIPTION | 26 ++++++++++++------------- LowRankQP-1.0.3/LowRankQP/MD5 | 9 +++----- LowRankQP-1.0.3/LowRankQP/NAMESPACE | 6 +---- LowRankQP-1.0.3/LowRankQP/R/zzz.r | 5 +--- LowRankQP-1.0.3/LowRankQP/src/LowRankQP_init.c |only 7 files changed, 21 insertions(+), 25 deletions(-)
Title: Plots Coefficients from Fitted Models
Description: Plots the coefficients from model objects. This very quickly shows the user the point estimates and confidence intervals for fitted models.
Author: Jared P. Lander
Maintainer: Jared P. Lander <packages@jaredlander.com>
Diff between coefplot versions 1.2.5 dated 2018-01-04 and 1.2.6 dated 2018-02-07
DESCRIPTION | 8 LICENSE | 6 MD5 | 116 ++-- NAMESPACE | 80 +-- NEWS.md | 118 ++-- R/buildPlot.r | 194 +++---- R/buildPlottingFrame.r | 394 +++++++-------- R/coefPredMatching.r | 650 ++++++++++++------------- R/coefpath.r | 253 +++++---- R/coefplot-package.r | 34 - R/coefplot.r | 854 ++++++++++++++++----------------- R/dodging.r | 284 +++++----- R/dyAnnotation.r | 38 - R/extractCoef.r | 716 ++++++++++++++------------- R/extractPath.r | 114 ++-- R/multiplot.r | 456 ++++++++--------- R/position.r | 340 ++++++------- R/transformations.r | 34 - README.md | 16 man/annotateSeries.Rd | 72 +- man/buildModelCI.Rd | 72 +- man/buildModelCI.default.Rd | 132 ++--- man/buildPlotting.default.Rd | 196 +++---- man/coefpath.Rd | 168 +++--- man/coefplot.Rd | 148 ++--- man/coefplot.data.frame.Rd | 198 +++---- man/coefplot.default.Rd | 250 ++++----- man/coefplot.glm.Rd | 66 +- man/coefplot.lm.Rd | 64 +- man/coefplot.rxGlm.Rd | 74 +- man/coefplot.rxLinMod.Rd | 70 +- man/coefplot.rxLogit.Rd | 70 +- man/doRegex.Rd | 54 +- man/extract.coef.Rd | 82 +-- man/extract.coef.cv.glmnet.Rd | 78 +-- man/extract.coef.default.Rd | 70 +- man/extract.coef.glm.Rd | 70 +- man/extract.coef.glmnet.Rd | 82 +-- man/extract.coef.lm.Rd | 70 +- man/extract.coef.maxLik.Rd | 82 +-- man/extract.coef.rxGlm.Rd | 72 +- man/extract.coef.rxLinMod.Rd | 68 +- man/extract.coef.rxLogit.Rd | 68 +- man/extract.coef.xgb.Booster.Rd | 85 +-- man/extractPath.Rd | 92 +-- man/get.assign.Rd | 50 - man/get.assign.glm.Rd | 50 - man/get.assign.lm.Rd | 50 - man/getCoefsFromPredictors.Rd | 54 +- man/getCoefsFromPredictors.default.Rd | 60 +- man/getCoefsFromPredictors.rxGlm.Rd | 60 +- man/getCoefsFromPredictors.rxLinMod.Rd | 60 +- man/getCoefsFromPredictors.rxLogit.Rd | 60 +- man/getCoefsFromPredictorsRevo.Rd | 58 +- man/invlogit.Rd | 58 +- man/matchCoefs.Rd | 84 +-- man/matchCoefs.default.Rd | 50 - man/multiplot.Rd | 320 ++++++------ man/position_dodgev.Rd | 92 +-- 59 files changed, 4199 insertions(+), 4165 deletions(-)
Title: Exact Test and Visualization of Multi-Set Intersections
Description: Identification of sets of objects with shared features is a common operation in all disciplines. Analysis of intersections among multiple sets is fundamental for in-depth understanding of their complex relationships. This package implements a theoretical framework for efficient computation of statistical distributions of multi-set intersections based upon combinatorial theory, and provides multiple scalable techniques for visualizing the intersection statistics. The statistical algorithm behind this package was published in Wang et al. (2015) <doi:10.1038/srep16923>.
Author: Minghui Wang, Yongzhong Zhao and Bin Zhang
Maintainer: Minghui Wang <minghui.wang@mssm.edu>
Diff between SuperExactTest versions 0.99.4 dated 2017-06-15 and 1.0.0 dated 2018-02-07
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/vis.R | 17 +++++++++-------- build/vignette.rds |binary inst/doc/set_html.R | 2 +- inst/doc/set_html.Rmd | 2 +- inst/doc/set_html.html | 10 +++++----- man/plot.Rd | 10 ++++++---- vignettes/set_html.Rmd | 2 +- 9 files changed, 35 insertions(+), 32 deletions(-)
More information about SuperExactTest at CRAN
Permanent link
Title: Tools for Time Series Analysis and Forecasting
Description: Provides a set of interactive visualization tools for time series analysis supporting ts, mts, zoo and xts objects. That includes visualization functions for forecasting model performance (forecasted vs. actual), time series interactive plots (single and multiple series) and seasonality plots.
Author: Rami Krispin
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between TSstudio versions 0.1.0 dated 2018-01-03 and 0.1.1 dated 2018-02-07
TSstudio-0.1.0/TSstudio/R/acf_ly.R |only TSstudio-0.1.0/TSstudio/R/fortest_ly.R |only TSstudio-0.1.0/TSstudio/R/pacf_ly.R |only TSstudio-0.1.0/TSstudio/R/seasonal_ly.R |only TSstudio-0.1.0/TSstudio/R/ts.plot_ly.R |only TSstudio-0.1.0/TSstudio/man/acf_ly.Rd |only TSstudio-0.1.0/TSstudio/man/fortest_ly.Rd |only TSstudio-0.1.0/TSstudio/man/pacf_ly.Rd |only TSstudio-0.1.0/TSstudio/man/seasonal_ly.Rd |only TSstudio-0.1.0/TSstudio/man/ts.plot_ly.Rd |only TSstudio-0.1.0/TSstudio/vignettes/rsconnect |only TSstudio-0.1.1/TSstudio/DESCRIPTION | 9 TSstudio-0.1.1/TSstudio/MD5 | 58 ++- TSstudio-0.1.1/TSstudio/NAMESPACE | 16 TSstudio-0.1.1/TSstudio/R/correlation_functions.R |only TSstudio-0.1.1/TSstudio/R/data.R |only TSstudio-0.1.1/TSstudio/R/forecast_tools.R |only TSstudio-0.1.1/TSstudio/R/ts_decompose.R |only TSstudio-0.1.1/TSstudio/R/ts_plot.R |only TSstudio-0.1.1/TSstudio/R/ts_seasonal.R |only TSstudio-0.1.1/TSstudio/R/util_functions.R |only TSstudio-0.1.1/TSstudio/README.md | 41 ++ TSstudio-0.1.1/TSstudio/data |only TSstudio-0.1.1/TSstudio/inst/doc/TSstudio_Intro.R | 206 ++++++++-- TSstudio-0.1.1/TSstudio/inst/doc/TSstudio_Intro.Rmd | 281 ++++++++++++-- TSstudio-0.1.1/TSstudio/inst/doc/TSstudio_Intro.html | 358 +++++++++++++++---- TSstudio-0.1.1/TSstudio/man/EURO_Brent.Rd |only TSstudio-0.1.1/TSstudio/man/Michigan_CS.Rd |only TSstudio-0.1.1/TSstudio/man/USUnRate.Rd |only TSstudio-0.1.1/TSstudio/man/USVSales.Rd |only TSstudio-0.1.1/TSstudio/man/USgas.Rd |only TSstudio-0.1.1/TSstudio/man/check_res.Rd |only TSstudio-0.1.1/TSstudio/man/res_hist.Rd |only TSstudio-0.1.1/TSstudio/man/test_forecast.Rd |only TSstudio-0.1.1/TSstudio/man/ts_acf.Rd |only TSstudio-0.1.1/TSstudio/man/ts_decompose.Rd |only TSstudio-0.1.1/TSstudio/man/ts_heatmap.Rd |only TSstudio-0.1.1/TSstudio/man/ts_lags.Rd |only TSstudio-0.1.1/TSstudio/man/ts_pacf.Rd |only TSstudio-0.1.1/TSstudio/man/ts_plot.Rd |only TSstudio-0.1.1/TSstudio/man/ts_polar.Rd |only TSstudio-0.1.1/TSstudio/man/ts_reshape.Rd |only TSstudio-0.1.1/TSstudio/man/ts_seasonal.Rd |only TSstudio-0.1.1/TSstudio/man/ts_split.Rd |only TSstudio-0.1.1/TSstudio/man/ts_surface.Rd |only TSstudio-0.1.1/TSstudio/man/xts_to_ts.Rd |only TSstudio-0.1.1/TSstudio/man/zoo_to_ts.Rd |only TSstudio-0.1.1/TSstudio/vignettes/TSstudio_Intro.Rmd | 281 ++++++++++++-- 48 files changed, 1042 insertions(+), 208 deletions(-)
Title: Time Series Analysis Toolkit Based on Symbolic Aggregate
Dicretization, i.e. SAX
Description: Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA
algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly),
and characteristic pattern discovery along with interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>
Diff between jmotif versions 1.0.2.900 dated 2016-06-13 and 1.0.3 dated 2018-02-07
DESCRIPTION | 8 - MD5 | 88 +++++------ R/RcppExports.R | 48 +++--- README.md | 7 inst/include/jmotif.h | 2 man/CBF.Rd | 1 man/Gun_Point.Rd | 1 man/alphabet_to_cuts.Rd | 1 man/bags_to_tfidf.Rd | 1 man/cosine_dist.Rd | 1 man/cosine_sim.Rd | 1 man/early_abandoned_dist.Rd | 1 man/ecg0606.Rd | 1 man/euclidean_dist.Rd | 1 man/find_discords_brute_force.Rd | 1 man/find_discords_hotsax.Rd | 1 man/find_discords_rra.Rd | 1 man/idx_to_letter.Rd | 1 man/is_equal_mindist.Rd | 1 man/is_equal_str.Rd | 1 man/letter_to_idx.Rd | 1 man/letters_to_idx.Rd | 1 man/manyseries_to_wordbag.Rd | 1 man/min_dist.Rd | 1 man/paa.Rd | 1 man/sax_by_chunking.Rd | 1 man/sax_distance_matrix.Rd | 1 man/sax_via_window.Rd | 1 man/series_to_chars.Rd | 1 man/series_to_string.Rd | 1 man/series_to_wordbag.Rd | 1 man/str_to_repair_grammar.Rd | 1 man/subseries.Rd | 1 man/znorm.Rd | 1 src/RcppExports.cpp | 264 +++++++++++++++++++--------------- src/discord.cpp | 8 - src/hot-sax.cpp | 13 + src/paa.cpp | 25 ++- src/repair.cpp | 135 +++++++++-------- src/repair_priority_queue.cpp | 25 ++- src/rra.cpp | 26 ++- src/sax-vsm.cpp | 18 -- src/sax.cpp | 45 +++++ tests/log.out |only tests/testthat/test_SAX_with_NAs.R |only tests/testthat/test_discord_hot_sax.R | 34 ++-- 46 files changed, 429 insertions(+), 346 deletions(-)
Title: Bayesian Variable Selection in High Dimensional Settings using
Non-Local Prior
Description: Variable/Feature selection in high or ultra-high dimensional
settings has gained a lot of attention recently specially in cancer genomic
studies. This package provides a Bayesian approach to tackle this problem,
where it exploits mixture of point masses at zero and nonlocal priors to
improve the performance of variable selection and coefficient estimation.
It performs variable selection for binary response and survival time
response datasets which are widely used in biostatistic and bioinformatics
community. Benefiting from parallel computing ability, it reports necessary
outcomes of Bayesian variable selection such as Highest Posterior
Probability Model (HPPM), Median Probability Model (MPM) and posterior
inclusion probability for each of the covariates in the model. The option
to use Bayesian Model Averaging (BMA) is also part of this package that can
be exploited for predictive power measurements in real datasets.
Author: Amir Nikooienejad [aut, cre], Valen E. Johnson [ths]
Maintainer: Amir Nikooienejad <amir@stat.tamu.edu>
Diff between BVSNLP versions 0.9.8 dated 2018-01-12 and 0.9.10 dated 2018-02-07
DESCRIPTION | 6 - MD5 | 16 +-- R/CoefEst.R | 155 +++++++++++++++-------------- R/bvs.R | 112 +++++++++++---------- R/predBMA.R | 284 +++++++++++++++++++++++++++--------------------------- R/zzz.R | 2 man/CoefEst.Rd | 5 man/bvs.Rd | 7 - src/Functions.cpp | 78 ++++++++------ 9 files changed, 344 insertions(+), 321 deletions(-)
Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text
'scholarly' data, including 'Biomed Central', Public Library of
Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ',
'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality
included for searching for articles, downloading full or partial
text, downloading supplementary materials, converting to various
data formats.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Will Pearse [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between fulltext versions 1.0.0 dated 2018-01-17 and 1.0.1 dated 2018-02-07
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 12 ++++++++++++ R/cache.R | 2 +- R/collect.R | 6 ++---- inst/doc/formats.Rmd | 18 ++++++------------ inst/doc/formats.html | 19 ++++++------------- man/ft_collect.Rd | 6 ++---- vignettes/formats.Rmd | 18 ++++++------------ 9 files changed, 47 insertions(+), 58 deletions(-)
Title: Power/Sample Size Calculation for Mediation Analysis
Description: Functions to
calculate power and sample size for testing
(1) mediation effects;
(2) the slope in a simple linear regression;
(3) odds ratio in a simple logistic regression;
(4) mean change for longitudinal study with 2 time points;
(5) interaction effect in 2-way ANOVA; and
(6) the slope in a simple Poisson regression.
Author: Weiliang Qiu <stwxq@channing.harvard.edu>
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>
Diff between powerMediation versions 0.2.8 dated 2017-09-12 and 0.2.9 dated 2018-02-07
powerMediation-0.2.8/powerMediation/INDEX |only powerMediation-0.2.9/powerMediation/DESCRIPTION | 8 ++++---- powerMediation-0.2.9/powerMediation/MD5 | 9 ++++----- powerMediation-0.2.9/powerMediation/NEWS | 3 +++ powerMediation-0.2.9/powerMediation/man/powerPoisson.Rd | 2 +- powerMediation-0.2.9/powerMediation/man/sizePoisson.Rd | 2 +- 6 files changed, 13 insertions(+), 11 deletions(-)
More information about powerMediation at CRAN
Permanent link
Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where
G is a weighted sum of genetic variants (genetic score) and E is a weighted
sum of environments (environmental score) using the alternating optimization algorithm
by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. This approach has greatly
enhanced predictive power over traditional GxE models which include only a single
genetic variant and a single environmental exposure. Although this approach was
originally made for GxE modelling, it is flexible and does not require the use of
genetic and environmental variables. It can also handle more than 2 latent variables
(rather than just G and E) and 3-way interactions or more. The LEGIT model produces
highly interpretable results and is very parameter-efficient thus it can even be
used with small sample sizes (n < 250). Tools to determine the type of interaction
(vantage sensitivity, diathesis-stress or differential susceptibility), with any
number of genetic variants or environments, are available <arXiv:1712.04058>.
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Diff between LEGIT versions 1.2.0 dated 2017-12-08 and 1.2.1 dated 2018-02-07
DESCRIPTION | 10 - MD5 | 27 +- NEWS |only R/LEGIT.R | 71 ++++--- inst/doc/GxE_testing.Rmd | 15 + inst/doc/GxE_testing.html | 382 ++++++++++++++++++++++++++++++--------- inst/doc/LEGIT.Rmd | 6 inst/doc/LEGIT.html | 409 +++++++++++++++++++++++++++++++----------- man/GxE_interaction_RoS.Rd | 2 man/GxE_interaction_test.Rd | 10 - man/LEGIT.Rd | 2 man/example_with_crossover.Rd | 4 man/plot.LEGIT.Rd | 10 - vignettes/GxE_testing.Rmd | 15 + vignettes/LEGIT.Rmd | 6 15 files changed, 718 insertions(+), 251 deletions(-)
Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to convert DICOM-format files to NIfTI-1 format.
Author: Jon Clayden [aut, cre],
Chris Rorden [aut],
Martin J Fiedler [cph],
Cong Xu [cph],
Pascal Gloor [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between divest versions 0.4.1 dated 2017-06-02 and 0.5.0 dated 2018-02-07
divest-0.4.1/divest/inst/extdata/testdata |only divest-0.4.1/divest/src/dcm2niix/nii_ostu_ml.cpp |only divest-0.4.1/divest/src/dcm2niix/nii_ostu_ml.h |only divest-0.5.0/divest/DESCRIPTION | 19 divest-0.5.0/divest/LICENCE | 2 divest-0.5.0/divest/MD5 | 54 divest-0.5.0/divest/NAMESPACE | 1 divest-0.5.0/divest/NEWS | 19 divest-0.5.0/divest/R/read.R | 128 + divest-0.5.0/divest/README.md | 220 +- divest-0.5.0/divest/inst/COPYRIGHTS | 2 divest-0.5.0/divest/inst/extdata/jpeg |only divest-0.5.0/divest/inst/extdata/jpl |only divest-0.5.0/divest/inst/extdata/raw |only divest-0.5.0/divest/man/readDicom.Rd | 60 divest-0.5.0/divest/src/dcm2niix/jpg_0XC3.cpp | 14 divest-0.5.0/divest/src/dcm2niix/nifti1_io_core.cpp | 6 divest-0.5.0/divest/src/dcm2niix/nii_dicom.cpp | 1373 +++++++++++++--- divest-0.5.0/divest/src/dcm2niix/nii_dicom.h | 43 divest-0.5.0/divest/src/dcm2niix/nii_dicom_batch.cpp | 1545 ++++++++++++++----- divest-0.5.0/divest/src/dcm2niix/nii_dicom_batch.h | 11 divest-0.5.0/divest/src/dcm2niix/nii_foreign.cpp | 41 divest-0.5.0/divest/src/dcm2niix/nii_ortho.cpp | 8 divest-0.5.0/divest/src/dcm2niix/print.h | 9 divest-0.5.0/divest/src/main.cpp | 34 divest-0.5.0/divest/src/ujpeg/ujpeg.cpp | 8 divest-0.5.0/divest/tests/testthat/test-05-read.R | 38 27 files changed, 2721 insertions(+), 914 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes, and the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015)
<DOI:10.1007/978-1-4939-2818-7>
gives details of the statistical framework and VGAM package.
Currently only fixed-effects models are implemented,
i.e., no random-effects models. Many (150+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE, using Fisher scoring. VGLMs can be
loosely thought of as multivariate GLMs. VGAMs are data-driven
VGLMs (i.e., with smoothing). The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecology, as well as constrained additive ordination
(CAO). Note that these functions are subject to change;
see the NEWS and ChangeLog files for latest changes.
Author: Thomas W. Yee <t.yee@auckland.ac.nz>
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 1.0-4 dated 2017-07-25 and 1.0-5 dated 2018-02-07
VGAM-1.0-4/VGAM/man/lrpvglm.Rd |only VGAM-1.0-5/VGAM/DESCRIPTION | 8 VGAM-1.0-5/VGAM/MD5 | 383 ++++++------ VGAM-1.0-5/VGAM/NAMESPACE | 12 VGAM-1.0-5/VGAM/NEWS | 51 + VGAM-1.0-5/VGAM/R/Links.R | 2 VGAM-1.0-5/VGAM/R/aamethods.q | 11 VGAM-1.0-5/VGAM/R/attrassign.R | 2 VGAM-1.0-5/VGAM/R/bAIC.q | 69 ++ VGAM-1.0-5/VGAM/R/build.terms.vlm.q | 2 VGAM-1.0-5/VGAM/R/calibrate.R | 714 ++++++++++++++++++++--- VGAM-1.0-5/VGAM/R/cao.R | 2 VGAM-1.0-5/VGAM/R/cao.fit.q | 41 - VGAM-1.0-5/VGAM/R/coef.vlm.q | 2 VGAM-1.0-5/VGAM/R/confint.vlm.R | 2 VGAM-1.0-5/VGAM/R/cqo.R | 13 VGAM-1.0-5/VGAM/R/cqo.fit.q | 35 - VGAM-1.0-5/VGAM/R/deviance.vlm.q | 2 VGAM-1.0-5/VGAM/R/effects.vglm.q | 2 VGAM-1.0-5/VGAM/R/family.actuary.R | 263 ++++---- VGAM-1.0-5/VGAM/R/family.aunivariate.R | 208 ++++-- VGAM-1.0-5/VGAM/R/family.basics.R | 99 ++- VGAM-1.0-5/VGAM/R/family.binomial.R | 2 VGAM-1.0-5/VGAM/R/family.bivariate.R | 90 +- VGAM-1.0-5/VGAM/R/family.categorical.R | 31 VGAM-1.0-5/VGAM/R/family.censored.R | 215 ++++-- VGAM-1.0-5/VGAM/R/family.circular.R | 4 VGAM-1.0-5/VGAM/R/family.exp.R | 2 VGAM-1.0-5/VGAM/R/family.extremes.R | 71 +- VGAM-1.0-5/VGAM/R/family.functions.R | 3 VGAM-1.0-5/VGAM/R/family.genetic.R | 2 VGAM-1.0-5/VGAM/R/family.glmgam.R | 162 +++-- VGAM-1.0-5/VGAM/R/family.loglin.R | 158 ++--- VGAM-1.0-5/VGAM/R/family.math.R | 33 + VGAM-1.0-5/VGAM/R/family.mixture.R | 2 VGAM-1.0-5/VGAM/R/family.nbd.R | 67 +- VGAM-1.0-5/VGAM/R/family.nonlinear.R | 23 VGAM-1.0-5/VGAM/R/family.normal.R | 84 +- VGAM-1.0-5/VGAM/R/family.oneinf.R | 24 VGAM-1.0-5/VGAM/R/family.others.R | 2 VGAM-1.0-5/VGAM/R/family.positive.R | 33 - VGAM-1.0-5/VGAM/R/family.qreg.R | 32 - VGAM-1.0-5/VGAM/R/family.rcim.R | 19 VGAM-1.0-5/VGAM/R/family.rcqo.R | 19 VGAM-1.0-5/VGAM/R/family.robust.R | 2 VGAM-1.0-5/VGAM/R/family.rrr.R | 183 +++-- VGAM-1.0-5/VGAM/R/family.sur.R | 4 VGAM-1.0-5/VGAM/R/family.survival.R | 2 VGAM-1.0-5/VGAM/R/family.ts.R | 14 VGAM-1.0-5/VGAM/R/family.univariate.R | 631 ++++++++++++-------- VGAM-1.0-5/VGAM/R/family.vglm.R | 4 VGAM-1.0-5/VGAM/R/family.zeroinf.R | 99 +-- VGAM-1.0-5/VGAM/R/fittedvlm.R | 2 VGAM-1.0-5/VGAM/R/formula.vlm.q | 2 VGAM-1.0-5/VGAM/R/generic.q | 2 VGAM-1.0-5/VGAM/R/getxvlmaug.R | 2 VGAM-1.0-5/VGAM/R/hdeff.R | 244 ++++++- VGAM-1.0-5/VGAM/R/links.q | 8 VGAM-1.0-5/VGAM/R/logLik.vlm.q | 2 VGAM-1.0-5/VGAM/R/lrp.R | 160 ----- VGAM-1.0-5/VGAM/R/lrwaldtest.R | 2 VGAM-1.0-5/VGAM/R/model.matrix.vglm.q | 44 - VGAM-1.0-5/VGAM/R/mux.q | 2 VGAM-1.0-5/VGAM/R/nobs.R | 2 VGAM-1.0-5/VGAM/R/plot.vgam.R | 19 VGAM-1.0-5/VGAM/R/plot.vglm.R | 2 VGAM-1.0-5/VGAM/R/predict.vgam.q | 2 VGAM-1.0-5/VGAM/R/predict.vglm.q | 2 VGAM-1.0-5/VGAM/R/predict.vlm.q | 2 VGAM-1.0-5/VGAM/R/print.vglm.q | 2 VGAM-1.0-5/VGAM/R/print.vlm.q | 2 VGAM-1.0-5/VGAM/R/psv2magic.R | 2 VGAM-1.0-5/VGAM/R/qrrvglm.control.q | 2 VGAM-1.0-5/VGAM/R/qtplot.q | 2 VGAM-1.0-5/VGAM/R/residuals.vlm.q | 2 VGAM-1.0-5/VGAM/R/rrvglm.R | 2 VGAM-1.0-5/VGAM/R/rrvglm.control.q | 11 VGAM-1.0-5/VGAM/R/rrvglm.fit.q | 2 VGAM-1.0-5/VGAM/R/s.q | 2 VGAM-1.0-5/VGAM/R/s.vam.q | 2 VGAM-1.0-5/VGAM/R/simulate.vglm.R | 2 VGAM-1.0-5/VGAM/R/sm.os.R | 2 VGAM-1.0-5/VGAM/R/sm.ps.R | 2 VGAM-1.0-5/VGAM/R/smart.R | 2 VGAM-1.0-5/VGAM/R/summary.vgam.q | 2 VGAM-1.0-5/VGAM/R/summary.vglm.q | 125 +++- VGAM-1.0-5/VGAM/R/summary.vlm.q | 134 ++++ VGAM-1.0-5/VGAM/R/vcov.pvgam.R | 2 VGAM-1.0-5/VGAM/R/vgam.R | 2 VGAM-1.0-5/VGAM/R/vgam.control.q | 2 VGAM-1.0-5/VGAM/R/vgam.fit.q | 2 VGAM-1.0-5/VGAM/R/vgam.match.q | 2 VGAM-1.0-5/VGAM/R/vglm.R | 2 VGAM-1.0-5/VGAM/R/vglm.control.q | 2 VGAM-1.0-5/VGAM/R/vglm.fit.q | 42 - VGAM-1.0-5/VGAM/R/vlm.R | 4 VGAM-1.0-5/VGAM/R/vlm.wfit.q | 2 VGAM-1.0-5/VGAM/R/vsmooth.spline.q | 2 VGAM-1.0-5/VGAM/R/wald0.R |only VGAM-1.0-5/VGAM/build |only VGAM-1.0-5/VGAM/data/Huggins89.t1.rda |binary VGAM-1.0-5/VGAM/data/Huggins89table1.rda |binary VGAM-1.0-5/VGAM/data/alclevels.rda |binary VGAM-1.0-5/VGAM/data/alcoff.rda |binary VGAM-1.0-5/VGAM/data/auuc.rda |binary VGAM-1.0-5/VGAM/data/backPain.rda |binary VGAM-1.0-5/VGAM/data/beggs.rda |binary VGAM-1.0-5/VGAM/data/car.all.rda |binary VGAM-1.0-5/VGAM/data/cfibrosis.rda |binary VGAM-1.0-5/VGAM/data/corbet.rda |binary VGAM-1.0-5/VGAM/data/crashbc.rda |binary VGAM-1.0-5/VGAM/data/crashf.rda |binary VGAM-1.0-5/VGAM/data/crashi.rda |binary VGAM-1.0-5/VGAM/data/crashmc.rda |binary VGAM-1.0-5/VGAM/data/crashp.rda |binary VGAM-1.0-5/VGAM/data/crashtr.rda |binary VGAM-1.0-5/VGAM/data/deermice.rda |binary VGAM-1.0-5/VGAM/data/ducklings.rda |binary VGAM-1.0-5/VGAM/data/finney44.rda |binary VGAM-1.0-5/VGAM/data/flourbeetle.rda |binary VGAM-1.0-5/VGAM/data/hspider.rda |binary VGAM-1.0-5/VGAM/data/lakeO.rda |binary VGAM-1.0-5/VGAM/data/leukemia.rda |binary VGAM-1.0-5/VGAM/data/marital.nz.rda |binary VGAM-1.0-5/VGAM/data/melbmaxtemp.rda |binary VGAM-1.0-5/VGAM/data/pneumo.rda |binary VGAM-1.0-5/VGAM/data/prinia.rda |binary VGAM-1.0-5/VGAM/data/ruge.rda |binary VGAM-1.0-5/VGAM/data/toxop.rda |binary VGAM-1.0-5/VGAM/data/venice.rda |binary VGAM-1.0-5/VGAM/data/venice90.rda |binary VGAM-1.0-5/VGAM/data/wine.rda |binary VGAM-1.0-5/VGAM/inst/doc |only VGAM-1.0-5/VGAM/man/AICvlm.Rd | 10 VGAM-1.0-5/VGAM/man/TICvlm.Rd |only VGAM-1.0-5/VGAM/man/Tol.Rd | 10 VGAM-1.0-5/VGAM/man/UtilitiesVGAM.Rd | 9 VGAM-1.0-5/VGAM/man/VGAM-package.Rd | 51 + VGAM-1.0-5/VGAM/man/bilogistic.Rd | 55 - VGAM-1.0-5/VGAM/man/binomialff.Rd | 22 VGAM-1.0-5/VGAM/man/bistudenttUC.Rd | 2 VGAM-1.0-5/VGAM/man/bmi.nz.Rd | 6 VGAM-1.0-5/VGAM/man/calibrate.qrrvglm.Rd | 48 + VGAM-1.0-5/VGAM/man/calibrate.qrrvglm.control.Rd | 2 VGAM-1.0-5/VGAM/man/calibrate.rrvglm.Rd | 6 VGAM-1.0-5/VGAM/man/calibrate.rrvglm.control.Rd | 2 VGAM-1.0-5/VGAM/man/cao.Rd | 2 VGAM-1.0-5/VGAM/man/cauchit.Rd | 3 VGAM-1.0-5/VGAM/man/cauchy.Rd | 34 - VGAM-1.0-5/VGAM/man/cens.poisson.Rd | 56 + VGAM-1.0-5/VGAM/man/confintvglm.Rd | 6 VGAM-1.0-5/VGAM/man/deermice.Rd | 2 VGAM-1.0-5/VGAM/man/expint3.Rd | 1 VGAM-1.0-5/VGAM/man/familyname.Rd |only VGAM-1.0-5/VGAM/man/fisk.Rd | 15 VGAM-1.0-5/VGAM/man/gengamma.Rd | 8 VGAM-1.0-5/VGAM/man/gev.Rd | 11 VGAM-1.0-5/VGAM/man/grc.Rd | 33 - VGAM-1.0-5/VGAM/man/hdeff.Rd | 249 ++++++-- VGAM-1.0-5/VGAM/man/is.buggy.Rd | 2 VGAM-1.0-5/VGAM/man/lambertW.Rd | 3 VGAM-1.0-5/VGAM/man/loglinb2.Rd | 5 VGAM-1.0-5/VGAM/man/loglinb3.Rd | 18 VGAM-1.0-5/VGAM/man/lognormal.Rd | 4 VGAM-1.0-5/VGAM/man/lrt.stat.Rd |only VGAM-1.0-5/VGAM/man/lrtest.Rd | 5 VGAM-1.0-5/VGAM/man/lvplot.rrvglm.Rd | 2 VGAM-1.0-5/VGAM/man/margeff.Rd | 2 VGAM-1.0-5/VGAM/man/micmen.Rd | 28 VGAM-1.0-5/VGAM/man/mills.ratio.Rd |only VGAM-1.0-5/VGAM/man/multinomial.Rd | 35 - VGAM-1.0-5/VGAM/man/nbcanlink.Rd | 18 VGAM-1.0-5/VGAM/man/nbolf.Rd | 4 VGAM-1.0-5/VGAM/man/normal.vcm.Rd | 3 VGAM-1.0-5/VGAM/man/notdocumentedyet.Rd | 14 VGAM-1.0-5/VGAM/man/poissonff.Rd | 1 VGAM-1.0-5/VGAM/man/profilevglm.Rd | 1 VGAM-1.0-5/VGAM/man/qrrvglm.control.Rd | 11 VGAM-1.0-5/VGAM/man/rrar.Rd | 4 VGAM-1.0-5/VGAM/man/score.stat.Rd |only VGAM-1.0-5/VGAM/man/summaryvglm.Rd | 138 +++- VGAM-1.0-5/VGAM/man/tobit.Rd | 1 VGAM-1.0-5/VGAM/man/undocumented-methods.Rd | 12 VGAM-1.0-5/VGAM/man/uninormal.Rd | 14 VGAM-1.0-5/VGAM/man/vcovvlm.Rd | 5 VGAM-1.0-5/VGAM/man/vglm.Rd | 6 VGAM-1.0-5/VGAM/man/vglmff-class.Rd | 20 VGAM-1.0-5/VGAM/man/vonmises.Rd | 3 VGAM-1.0-5/VGAM/man/vplot.profile.Rd | 1 VGAM-1.0-5/VGAM/man/vsmooth.spline.Rd | 2 VGAM-1.0-5/VGAM/man/wald.stat.Rd |only VGAM-1.0-5/VGAM/man/weightsvglm.Rd | 29 VGAM-1.0-5/VGAM/man/zipoisson.Rd | 8 VGAM-1.0-5/VGAM/vignettes |only 194 files changed, 3904 insertions(+), 1941 deletions(-)
Title: Functions for Plotting Graphical Shapes, Colors
Description: Functions for plotting graphical shapes
such as ellipses, circles, cylinders, arrows, ...
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between shape versions 1.4.3 dated 2017-08-16 and 1.4.4 dated 2018-02-07
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/Arrowhead.R | 4 ++-- R/Arrows.R | 4 ++-- build/vignette.rds |binary inst/doc/shape.pdf |binary man/Arrowhead.Rd | 5 +++-- man/Arrows.Rd | 17 ++++++++++++++++- 8 files changed, 35 insertions(+), 19 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M.Draminski, A.Rada-Iglesias, S.Enroth, C.Wadelius, J. Koronacki, J.Komorowski (2008) <doi:10.1093/bioinformatics/btm486>.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <michal.draminski@ipipan.waw.pl>
Diff between rmcfs versions 1.2.8 dated 2017-12-11 and 1.2.9 dated 2018-02-07
DESCRIPTION | 10 +++++----- MD5 | 40 ++++++++++++++++++++-------------------- NEWS.md | 6 ++++++ R/onLoad.R | 18 +++++++++--------- R/rmcfs.R | 7 +++++-- R/utils.R | 12 ++++++++++++ inst/doc/jss2621.pdf |binary man/build.idgraph.Rd | 4 ++-- man/export.result.Rd | 5 ++++- man/fix.data.Rd | 5 ++++- man/import.result.Rd | 3 +++ man/mcfs.Rd | 13 ++++++++----- man/plot.idgraph.Rd | 5 +++-- man/plot.mcfs.Rd | 5 ++++- man/print.mcfs.Rd | 5 ++++- man/prune.data.Rd | 5 ++++- man/read.adh.Rd | 5 ++++- man/read.adx.Rd | 5 ++++- man/write.adh.Rd | 5 ++++- man/write.adx.Rd | 5 ++++- man/write.arff.Rd | 5 ++++- 21 files changed, 113 insertions(+), 55 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices, vectors,
numerical solvers and related algorithms. It supports dense and sparse
matrices on integer, floating point and complex numbers, decompositions of
such matrices, and solutions of linear systems. Its performance on many
algorithms is comparable with some of the best implementations based on
'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header
files from the 'Eigen' C++ template library (currently version 3.3.4). Thus
users do not need to install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.3.3.1 dated 2017-11-19 and 0.3.3.4.0 dated 2018-02-07
ChangeLog | 24 + DESCRIPTION | 10 MD5 | 163 +++--- README.md | 2 build/vignette.rds |binary inst/NEWS.Rd | 11 inst/doc/RcppEigen-Introduction.pdf |binary inst/include/Eigen/Cholesky | 5 inst/include/Eigen/Core | 19 inst/include/Eigen/Eigenvalues | 4 inst/include/Eigen/LU | 4 inst/include/Eigen/QR | 4 inst/include/Eigen/QtAlignedMalloc | 2 inst/include/Eigen/SVD | 4 inst/include/Eigen/src/Cholesky/LDLT.h | 4 inst/include/Eigen/src/Cholesky/LLT.h | 26 - inst/include/Eigen/src/Core/Array.h | 8 inst/include/Eigen/src/Core/ArrayBase.h | 8 inst/include/Eigen/src/Core/ArrayWrapper.h | 6 inst/include/Eigen/src/Core/AssignEvaluator.h | 4 inst/include/Eigen/src/Core/CoreEvaluators.h | 6 inst/include/Eigen/src/Core/CwiseNullaryOp.h | 80 +-- inst/include/Eigen/src/Core/DenseBase.h | 8 inst/include/Eigen/src/Core/EigenBase.h | 4 inst/include/Eigen/src/Core/GeneralProduct.h | 21 inst/include/Eigen/src/Core/GenericPacketMath.h | 6 inst/include/Eigen/src/Core/Map.h | 17 inst/include/Eigen/src/Core/MathFunctions.h | 15 inst/include/Eigen/src/Core/MatrixBase.h | 13 inst/include/Eigen/src/Core/NumTraits.h | 2 inst/include/Eigen/src/Core/PlainObjectBase.h | 4 inst/include/Eigen/src/Core/ProductEvaluators.h | 6 inst/include/Eigen/src/Core/SelfCwiseBinaryOp.h | 8 inst/include/Eigen/src/Core/Solve.h | 4 inst/include/Eigen/src/Core/StableNorm.h | 5 inst/include/Eigen/src/Core/arch/AVX/Complex.h | 36 - inst/include/Eigen/src/Core/arch/AltiVec/Complex.h | 35 - inst/include/Eigen/src/Core/arch/CUDA/Half.h | 108 +++- inst/include/Eigen/src/Core/arch/CUDA/PacketMath.h | 2 inst/include/Eigen/src/Core/arch/CUDA/PacketMathHalf.h | 2 inst/include/Eigen/src/Core/arch/Default/ConjHelper.h |only inst/include/Eigen/src/Core/arch/NEON/Complex.h | 4 inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 15 inst/include/Eigen/src/Core/arch/SSE/Complex.h | 42 - inst/include/Eigen/src/Core/arch/ZVector/Complex.h | 3 inst/include/Eigen/src/Core/functors/NullaryFunctors.h | 11 inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h | 13 inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h | 10 inst/include/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h | 19 inst/include/Eigen/src/Core/products/GeneralMatrixVector.h | 8 inst/include/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h | 19 inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h | 48 +- inst/include/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h | 9 inst/include/Eigen/src/Core/products/TriangularMatrixMatrix.h | 11 inst/include/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h | 39 + inst/include/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h | 46 + inst/include/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h | 40 + inst/include/Eigen/src/Core/util/DisableStupidWarnings.h | 24 - inst/include/Eigen/src/Core/util/MKL_support.h | 10 inst/include/Eigen/src/Core/util/Macros.h | 11 inst/include/Eigen/src/Core/util/Memory.h | 12 inst/include/Eigen/src/Core/util/StaticAssert.h | 116 ++-- inst/include/Eigen/src/Geometry/AngleAxis.h | 2 inst/include/Eigen/src/Geometry/Quaternion.h | 39 - inst/include/Eigen/src/Geometry/arch/Geometry_SSE.h | 60 +- inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h | 27 - inst/include/Eigen/src/Jacobi/Jacobi.h | 238 +++++----- inst/include/Eigen/src/OrderingMethods/Eigen_Colamd.h | 2 inst/include/Eigen/src/PaStiXSupport/PaStiXSupport.h | 8 inst/include/Eigen/src/QR/ColPivHouseholderQR.h | 12 inst/include/Eigen/src/SVD/BDCSVD.h | 114 ++-- inst/include/Eigen/src/SVD/JacobiSVD_LAPACKE.h | 5 inst/include/Eigen/src/SVD/UpperBidiagonalization.h | 4 inst/include/Eigen/src/SparseCore/AmbiVector.h | 2 inst/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h | 67 +- inst/include/Eigen/src/SparseCore/SparseSelfAdjointView.h | 3 inst/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h | 22 inst/include/Eigen/src/UmfPackSupport/UmfPackSupport.h | 101 +++- inst/include/unsupported/Eigen/CXX11/src/Tensor/README.md | 6 inst/include/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h | 11 inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h | 41 + inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h | 11 inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h | 2 83 files changed, 1173 insertions(+), 804 deletions(-)
Title: Power and Sample Size Calculation for Survival Analysis of
Epidemiological Studies
Description: Functions to calculate power and
sample size for testing main effect or interaction effect in
the survival analysis of epidemiological studies
(non-randomized studies), taking into account the
correlation between the covariate of the
interest and other covariates. Some calculations also take
into account the competing risks and stratified analysis.
This package also includes
a set of functions to calculate power and sample size
for testing main effect in the survival analysis of
randomized clinical trials.
Author: Weiliang Qiu <stwxq@channing.harvard.edu>, Jorge Chavarro <JCHAVARR@hsph.harvard.edu>, Ross Lazarus <ross.lazarus@channing.harvard.edu>, Bernard Rosner <stbar@channing.harvard.edu>, Jing Ma <jing.ma@channing.harvard.edu>.
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>
Diff between powerSurvEpi versions 0.0.9 dated 2015-07-24 and 0.1.0 dated 2018-02-07
powerSurvEpi-0.0.9/powerSurvEpi/INDEX |only powerSurvEpi-0.1.0/powerSurvEpi/DESCRIPTION | 8 +++--- powerSurvEpi-0.1.0/powerSurvEpi/MD5 | 19 +++++++--------- powerSurvEpi-0.1.0/powerSurvEpi/NEWS | 5 ++++ powerSurvEpi-0.1.0/powerSurvEpi/data/Oph.rda |binary powerSurvEpi-0.1.0/powerSurvEpi/man/numDEpi.Rd | 4 +-- powerSurvEpi-0.1.0/powerSurvEpi/man/numDEpi.default.Rd | 4 +-- powerSurvEpi-0.1.0/powerSurvEpi/man/powerEpi.Rd | 4 +-- powerSurvEpi-0.1.0/powerSurvEpi/man/powerEpi.default.Rd | 4 +-- powerSurvEpi-0.1.0/powerSurvEpi/man/ssizeEpi.Rd | 4 +-- powerSurvEpi-0.1.0/powerSurvEpi/man/ssizeEpi.default.Rd | 4 +-- 11 files changed, 30 insertions(+), 26 deletions(-)
Title: Basic Biological Sequence Handling
Description: Basic functions for microbial sequence data analysis. The idea is to use the basic R data structures as much as possible, without building complex data types.
Author: Lars Snipen, Kristian Hovde Liland
Maintainer: Lars Snipen <lars.snipen@nmbu.no>
Diff between microseq versions 1.2 dated 2017-01-13 and 1.2.1 dated 2018-02-07
microseq-1.2.1/microseq/DESCRIPTION | 20 microseq-1.2.1/microseq/MD5 | 66 microseq-1.2.1/microseq/NAMESPACE | 3 microseq-1.2.1/microseq/R/RcppExports.R | 16 microseq-1.2.1/microseq/R/dnaManipulate.R | 90 microseq-1.2.1/microseq/R/fasta.R | 19 microseq-1.2.1/microseq/R/fastq.R | 20 microseq-1.2.1/microseq/R/multialign.R | 51 microseq-1.2.1/microseq/R/utilityfun.R | 6 microseq-1.2.1/microseq/inst/doc/vignette.pdf |binary microseq-1.2.1/microseq/inst/extdata/msa.fasta | 80 microseq-1.2.1/microseq/inst/extdata/small.fasta | 42 microseq-1.2.1/microseq/inst/extdata/small.fastq | 80 microseq-1.2.1/microseq/inst/extdata/ssu_bacteria.cm |21230 +++++++-------- microseq-1.2.1/microseq/man/cmalign.Rd | 7 microseq-1.2.1/microseq/man/gregexpr.Rd | 11 microseq-1.2.1/microseq/man/iupac2regex.Rd | 15 microseq-1.2.1/microseq/man/microseq-package.Rd | 3 microseq-1.2.1/microseq/man/msaTrim.Rd | 7 microseq-1.2.1/microseq/man/msalign.Rd | 7 microseq-1.2.1/microseq/man/muscle.Rd | 7 microseq-1.2.1/microseq/man/plot.Fasta.Rd | 8 microseq-1.2.1/microseq/man/plot.Fastq.Rd | 8 microseq-1.2.1/microseq/man/readFasta.Rd | 13 microseq-1.2.1/microseq/man/readFastq.Rd | 7 microseq-1.2.1/microseq/man/reverseComplement.Rd | 1 microseq-1.2.1/microseq/man/translate.Rd | 2 microseq-1.2.1/microseq/src/RcppExports.cpp | 72 microseq-1.2.1/microseq/src/init.c |only microseq-1.2.1/microseq/src/read_file.cpp | 70 microseq-1.2.1/microseq/src/translate.cpp | 10 microseq-1.2/microseq/R/primers.R |only microseq-1.2/microseq/build |only microseq-1.2/microseq/inst/doc/vignette.Rnw |only microseq-1.2/microseq/man/amplicon.Rd |only microseq-1.2/microseq/vignettes/framed.sty |only microseq-1.2/microseq/vignettes/vignette-concordance.tex |only microseq-1.2/microseq/vignettes/vignette.tex |only 38 files changed, 11034 insertions(+), 10937 deletions(-)
Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574> and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565>.
Also contains functions to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 3.5 dated 2017-10-01 and 3.6 dated 2018-02-07
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/dd_LR.R | 12 ++++++------ R/dd_ML.R | 40 ++++++++++++++++++++++++++++++++++++++-- R/dd_loglik.R | 1 - man/DDD-internal.Rd | 2 ++ man/DDD-package.Rd | 7 +++++-- man/dd_ML.Rd | 13 +++++-------- 8 files changed, 67 insertions(+), 30 deletions(-)
Title: Actuarial Functions and Heavy Tailed Distributions
Description: Functions and data sets for actuarial science:
modeling of loss distributions; risk theory and ruin theory;
simulation of compound models, discrete mixtures and compound
hierarchical models; credibility theory. Support for many additional
probability distributions to model insurance loss amounts and loss
frequency: 19 continuous heavy tailed distributions; the
Poisson-inverse Gaussian discrete distribution; zero-truncated and
zero-modified extensions of the standard discrete distributions.
Support for phase-type distributions commonly used to compute ruin
probabilities.
Author: Vincent Goulet [cre, aut],
Sébastien Auclair [ctb],
Christophe Dutang [aut],
Xavier Milhaud [ctb],
Tommy Ouellet [ctb],
Alexandre Parent [ctb],
Mathieu Pigeon [aut],
Louis-Philippe Pouliot [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 2.2-0 dated 2018-01-07 and 2.3-0 dated 2018-02-07
actuar-2.2-0/actuar/vignettes/auto |only actuar-2.3-0/actuar/DESCRIPTION | 18 actuar-2.3-0/actuar/MD5 | 317 +++++------- actuar-2.3-0/actuar/NAMESPACE | 1 actuar-2.3-0/actuar/R/BetaMoments.R | 2 actuar-2.3-0/actuar/R/Burr.R | 2 actuar-2.3-0/actuar/R/CTE.R | 2 actuar-2.3-0/actuar/R/ChisqSupp.R | 2 actuar-2.3-0/actuar/R/ExponentialSupp.R | 2 actuar-2.3-0/actuar/R/Extract.grouped.data.R | 2 actuar-2.3-0/actuar/R/GammaSupp.R | 2 actuar-2.3-0/actuar/R/GeneralizedBeta.R | 2 actuar-2.3-0/actuar/R/GeneralizedPareto.R | 2 actuar-2.3-0/actuar/R/Gumbel.R | 2 actuar-2.3-0/actuar/R/InverseBurr.R | 2 actuar-2.3-0/actuar/R/InverseExponential.R | 2 actuar-2.3-0/actuar/R/InverseGamma.R | 2 actuar-2.3-0/actuar/R/InverseGaussian.R | 2 actuar-2.3-0/actuar/R/InverseParalogistic.R | 2 actuar-2.3-0/actuar/R/InversePareto.R | 2 actuar-2.3-0/actuar/R/InverseTransformedGamma.R | 2 actuar-2.3-0/actuar/R/InverseWeibull.R | 2 actuar-2.3-0/actuar/R/Logarithmic.R | 2 actuar-2.3-0/actuar/R/Loggamma.R | 2 actuar-2.3-0/actuar/R/Loglogistic.R | 2 actuar-2.3-0/actuar/R/LognormalMoments.R | 2 actuar-2.3-0/actuar/R/NormalSupp.R | 2 actuar-2.3-0/actuar/R/Paralogistic.R | 2 actuar-2.3-0/actuar/R/Pareto.R | 2 actuar-2.3-0/actuar/R/PhaseType.R | 2 actuar-2.3-0/actuar/R/PoissonInverseGaussian.R | 2 actuar-2.3-0/actuar/R/SingleParameterPareto.R | 2 actuar-2.3-0/actuar/R/TransformedBeta.R | 2 actuar-2.3-0/actuar/R/TransformedGamma.R | 2 actuar-2.3-0/actuar/R/UniformSupp.R | 2 actuar-2.3-0/actuar/R/VaR.R | 2 actuar-2.3-0/actuar/R/WeibullMoments.R | 2 actuar-2.3-0/actuar/R/ZeroModifiedBinomial.R | 2 actuar-2.3-0/actuar/R/ZeroModifiedGeometric.R | 2 actuar-2.3-0/actuar/R/ZeroModifiedLogarithmic.R | 2 actuar-2.3-0/actuar/R/ZeroModifiedNegativeBinomial.R | 2 actuar-2.3-0/actuar/R/ZeroModifiedPoisson.R | 2 actuar-2.3-0/actuar/R/ZeroTruncatedBinomial.R | 2 actuar-2.3-0/actuar/R/ZeroTruncatedGeometric.R | 2 actuar-2.3-0/actuar/R/ZeroTruncatedNegativeBinomial.R | 2 actuar-2.3-0/actuar/R/ZeroTruncatedPoisson.R | 2 actuar-2.3-0/actuar/R/adjCoef.R | 2 actuar-2.3-0/actuar/R/aggregateDist.R | 2 actuar-2.3-0/actuar/R/bayes.R |only actuar-2.3-0/actuar/R/betaint.R | 2 actuar-2.3-0/actuar/R/bstraub.R | 36 - actuar-2.3-0/actuar/R/cm.R | 96 ++- actuar-2.3-0/actuar/R/coverage.R | 2 actuar-2.3-0/actuar/R/discretize.R | 2 actuar-2.3-0/actuar/R/elev.R | 2 actuar-2.3-0/actuar/R/emm.R | 2 actuar-2.3-0/actuar/R/exact.R | 2 actuar-2.3-0/actuar/R/grouped.data.R | 2 actuar-2.3-0/actuar/R/hache.R | 2 actuar-2.3-0/actuar/R/hache.barycenter.R | 2 actuar-2.3-0/actuar/R/hache.origin.R | 2 actuar-2.3-0/actuar/R/hierarc.R | 2 actuar-2.3-0/actuar/R/hist.grouped.data.R | 2 actuar-2.3-0/actuar/R/mde.R | 2 actuar-2.3-0/actuar/R/mean.grouped.data.R | 2 actuar-2.3-0/actuar/R/normal.R | 2 actuar-2.3-0/actuar/R/ogive.R | 2 actuar-2.3-0/actuar/R/panjer.R | 2 actuar-2.3-0/actuar/R/quantile.aggregateDist.R | 2 actuar-2.3-0/actuar/R/quantile.grouped.data.R | 2 actuar-2.3-0/actuar/R/rcompound.R | 2 actuar-2.3-0/actuar/R/rmixture.R | 2 actuar-2.3-0/actuar/R/ruin.R | 2 actuar-2.3-0/actuar/R/severity.R | 2 actuar-2.3-0/actuar/R/simS.R | 2 actuar-2.3-0/actuar/R/simul.R | 2 actuar-2.3-0/actuar/R/simul.summaries.R | 2 actuar-2.3-0/actuar/R/unroll.R | 2 actuar-2.3-0/actuar/demo/credibility.R | 2 actuar-2.3-0/actuar/demo/lossdist.R | 2 actuar-2.3-0/actuar/demo/risk.R | 2 actuar-2.3-0/actuar/demo/simulation.R | 2 actuar-2.3-0/actuar/inst/NEWS.Rd | 26 actuar-2.3-0/actuar/inst/doc/actuar.pdf |binary actuar-2.3-0/actuar/inst/doc/coverage.pdf |binary actuar-2.3-0/actuar/inst/doc/credibility.R | 34 - actuar-2.3-0/actuar/inst/doc/credibility.Rnw | 238 ++++++--- actuar-2.3-0/actuar/inst/doc/credibility.pdf |binary actuar-2.3-0/actuar/inst/doc/distributions.pdf |binary actuar-2.3-0/actuar/inst/doc/modeling.pdf |binary actuar-2.3-0/actuar/inst/doc/risk.pdf |binary actuar-2.3-0/actuar/inst/doc/simulation.R | 16 actuar-2.3-0/actuar/inst/doc/simulation.Rnw | 52 - actuar-2.3-0/actuar/inst/doc/simulation.pdf |binary actuar-2.3-0/actuar/inst/po/en@quot/LC_MESSAGES/R-actuar.mo |binary actuar-2.3-0/actuar/inst/po/en@quot/LC_MESSAGES/actuar.mo |binary actuar-2.3-0/actuar/inst/po/fr/LC_MESSAGES/R-actuar.mo |binary actuar-2.3-0/actuar/inst/po/fr/LC_MESSAGES/actuar.mo |binary actuar-2.3-0/actuar/man/aggregateDist.Rd | 8 actuar-2.3-0/actuar/man/cm.Rd | 122 +++- actuar-2.3-0/actuar/man/rcompound.Rd | 8 actuar-2.3-0/actuar/man/rmixture.Rd | 6 actuar-2.3-0/actuar/man/simul.summaries.Rd | 1 actuar-2.3-0/actuar/po/R-actuar.pot | 25 actuar-2.3-0/actuar/po/R-fr.po | 30 - actuar-2.3-0/actuar/po/actuar.pot | 36 - actuar-2.3-0/actuar/po/fr.po | 36 - actuar-2.3-0/actuar/src/beta.c | 2 actuar-2.3-0/actuar/src/betaint.c | 5 actuar-2.3-0/actuar/src/burr.c | 2 actuar-2.3-0/actuar/src/chisq.c | 2 actuar-2.3-0/actuar/src/dpq.c | 2 actuar-2.3-0/actuar/src/dpq.h | 2 actuar-2.3-0/actuar/src/dpqphtype.c | 2 actuar-2.3-0/actuar/src/exp.c | 2 actuar-2.3-0/actuar/src/gamma.c | 2 actuar-2.3-0/actuar/src/genbeta.c | 2 actuar-2.3-0/actuar/src/genpareto.c | 2 actuar-2.3-0/actuar/src/gumbel.c | 2 actuar-2.3-0/actuar/src/hierarc.c | 2 actuar-2.3-0/actuar/src/invburr.c | 2 actuar-2.3-0/actuar/src/invexp.c | 2 actuar-2.3-0/actuar/src/invgamma.c | 2 actuar-2.3-0/actuar/src/invgauss.c | 2 actuar-2.3-0/actuar/src/invparalogis.c | 2 actuar-2.3-0/actuar/src/invpareto.c | 2 actuar-2.3-0/actuar/src/invtrgamma.c | 2 actuar-2.3-0/actuar/src/invweibull.c | 2 actuar-2.3-0/actuar/src/lgamma.c | 2 actuar-2.3-0/actuar/src/llogis.c | 2 actuar-2.3-0/actuar/src/lnorm.c | 2 actuar-2.3-0/actuar/src/logarithmic.c | 2 actuar-2.3-0/actuar/src/names.c | 2 actuar-2.3-0/actuar/src/norm.c | 2 actuar-2.3-0/actuar/src/panjer.c | 2 actuar-2.3-0/actuar/src/paralogis.c | 2 actuar-2.3-0/actuar/src/pareto.c | 2 actuar-2.3-0/actuar/src/pareto1.c | 2 actuar-2.3-0/actuar/src/phtype.c | 2 actuar-2.3-0/actuar/src/poisinvgauss.c | 2 actuar-2.3-0/actuar/src/random.c | 2 actuar-2.3-0/actuar/src/randomphtype.c | 2 actuar-2.3-0/actuar/src/trbeta.c | 2 actuar-2.3-0/actuar/src/trgamma.c | 2 actuar-2.3-0/actuar/src/unif.c | 2 actuar-2.3-0/actuar/src/util.c | 2 actuar-2.3-0/actuar/src/weibull.c | 2 actuar-2.3-0/actuar/src/zmbinom.c | 2 actuar-2.3-0/actuar/src/zmgeom.c | 2 actuar-2.3-0/actuar/src/zmlogarithmic.c | 2 actuar-2.3-0/actuar/src/zmnbinom.c | 2 actuar-2.3-0/actuar/src/zmpois.c | 2 actuar-2.3-0/actuar/src/ztbinom.c | 2 actuar-2.3-0/actuar/src/ztgeom.c | 2 actuar-2.3-0/actuar/src/ztnbinom.c | 2 actuar-2.3-0/actuar/src/ztpois.c | 2 actuar-2.3-0/actuar/vignettes/credibility.Rnw | 238 ++++++--- actuar-2.3-0/actuar/vignettes/simulation.Rnw | 52 - 158 files changed, 1027 insertions(+), 620 deletions(-)
Title: Pricing of Variable Annuities
Description: Pricing of variable annuity life insurance
contracts by means of Monte Carlo methods. Monte Carlo is used to price
the contract in case the policyholder cannot surrender while
Least Squares Monte Carlo is used if the insured can surrender.
This package implements the pricing framework and algorithm described in
Bacinello et al. (2011) <doi:10.1016/j.insmatheco.2011.05.003>.
It also implements the state-dependent fee structure
discussed in Bernard et al. (2014) <doi:10.1017/asb.2014.13> as well as
a function which prices the contract by resolving the partial differential equation
described in MacKay et al. (2017) <doi:10.1111/jori.12094>.
Author: Ivan Zoccolan [aut, cre]
Maintainer: Ivan Zoccolan <ivan.zoccolan@gmail.com>
Diff between valuer versions 1.1.1 dated 2017-01-03 and 1.1.2 dated 2018-02-07
valuer-1.1.1/valuer/vignettes/News.Rmd |only valuer-1.1.2/valuer/DESCRIPTION | 16 +- valuer-1.1.2/valuer/MD5 | 109 ++++++++-------- valuer-1.1.2/valuer/NAMESPACE | 6 valuer-1.1.2/valuer/R/GMAB_GMDB_PDE_solver.R |only valuer-1.1.2/valuer/R/RcppExports.R | 6 valuer-1.1.2/valuer/R/parameters.R | 2 valuer-1.1.2/valuer/R/utils.R | 3 valuer-1.1.2/valuer/R/va_pricing_engine.R | 40 +++-- valuer-1.1.2/valuer/R/va_pricing_engine2.R | 10 - valuer-1.1.2/valuer/R/va_pricing_engine3.R | 25 +-- valuer-1.1.2/valuer/R/va_pricing_engine4.R | 23 +-- valuer-1.1.2/valuer/R/va_pricing_engine5.R | 23 +-- valuer-1.1.2/valuer/R/va_pricing_engine6.R |only valuer-1.1.2/valuer/R/va_product_3.R | 1 valuer-1.1.2/valuer/R/va_products.R | 5 valuer-1.1.2/valuer/R/va_products_2.R | 1 valuer-1.1.2/valuer/README.md | 5 valuer-1.1.2/valuer/build/vignette.rds |binary valuer-1.1.2/valuer/inst/doc/Introduction.Rmd | 2 valuer-1.1.2/valuer/inst/doc/Introduction.html | 10 - valuer-1.1.2/valuer/man/GMAB.Rd | 2 valuer-1.1.2/valuer/man/GMAB_GMDB.Rd | 4 valuer-1.1.2/valuer/man/GMDB.Rd | 2 valuer-1.1.2/valuer/man/GMIB.Rd | 2 valuer-1.1.2/valuer/man/GMWB.Rd | 2 valuer-1.1.2/valuer/man/calc_account.Rd | 1 valuer-1.1.2/valuer/man/constant_parameters.Rd | 2 valuer-1.1.2/valuer/man/data_gatherer.Rd | 2 valuer-1.1.2/valuer/man/financials_BBM2010.Rd | 1 valuer-1.1.2/valuer/man/financials_BMOP2011.Rd | 1 valuer-1.1.2/valuer/man/financials_BZ2016.Rd | 1 valuer-1.1.2/valuer/man/financials_BZ2016bis.Rd | 1 valuer-1.1.2/valuer/man/makeham.Rd | 1 valuer-1.1.2/valuer/man/mc_gatherer.Rd | 2 valuer-1.1.2/valuer/man/mortality_BBM2010.Rd | 1 valuer-1.1.2/valuer/man/mortality_BMOP2011.Rd | 1 valuer-1.1.2/valuer/man/mu.Rd | 1 valuer-1.1.2/valuer/man/payoff_GMWB.Rd | 2 valuer-1.1.2/valuer/man/payoff_guarantee.Rd | 2 valuer-1.1.2/valuer/man/payoff_ratchet.Rd | 2 valuer-1.1.2/valuer/man/payoff_rollup.Rd | 2 valuer-1.1.2/valuer/man/penalty_class.Rd | 2 valuer-1.1.2/valuer/man/sq.Rd | 1 valuer-1.1.2/valuer/man/va_bs_engine.Rd | 12 - valuer-1.1.2/valuer/man/va_bs_engine2.Rd |only valuer-1.1.2/valuer/man/va_engine.Rd | 12 - valuer-1.1.2/valuer/man/va_mkh_engine.Rd | 12 - valuer-1.1.2/valuer/man/va_pde_pricer.Rd |only valuer-1.1.2/valuer/man/va_product.Rd | 2 valuer-1.1.2/valuer/man/va_sde_engine.Rd | 12 - valuer-1.1.2/valuer/man/va_sde_engine2.Rd | 14 +- valuer-1.1.2/valuer/man/va_sde_engine3.Rd | 14 +- valuer-1.1.2/valuer/man/yr_fractions.Rd | 1 valuer-1.1.2/valuer/src/RcppExports.cpp | 22 ++- valuer-1.1.2/valuer/src/calc_account.cpp | 2 valuer-1.1.2/valuer/tests/testthat/test.penalty_class.R | 4 valuer-1.1.2/valuer/vignettes/Introduction.Rmd | 2 58 files changed, 225 insertions(+), 209 deletions(-)
Title: Quality Report Generation for MaxQuant Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (see <http://www.maxquant.org>).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow <chris.bielow@fu-berlin.de>
Maintainer: Chris Bielow <chris.bielow@fu-berlin.de>
Diff between PTXQC versions 0.92.0 dated 2017-10-13 and 0.92.3 dated 2018-02-07
PTXQC-0.92.0/PTXQC/inst/examples/report_v0.80.8__txt_5files_withMatch-100min.html |only PTXQC-0.92.0/PTXQC/inst/examples/report_v0.80.8__txt_5files_withMatch-100min.pdf |only PTXQC-0.92.3/PTXQC/DESCRIPTION | 10 PTXQC-0.92.3/PTXQC/MD5 | 268 ++--- PTXQC-0.92.3/PTXQC/NEWS | 11 PTXQC-0.92.3/PTXQC/R/MQDataReader.R | 19 PTXQC-0.92.3/PTXQC/R/fcn_MQ.R | 2 PTXQC-0.92.3/PTXQC/R/fcn_QCHeat.R | 9 PTXQC-0.92.3/PTXQC/R/fcn_YAML.R | 6 PTXQC-0.92.3/PTXQC/R/fcn_computeQC.R | 78 - PTXQC-0.92.3/PTXQC/R/fcn_misc.R | 25 PTXQC-0.92.3/PTXQC/R/fcn_qualities.R | 14 PTXQC-0.92.3/PTXQC/R/qcMetric_EVD.R | 125 ++ PTXQC-0.92.3/PTXQC/R/qcMetric_MSMSScans.R | 3 PTXQC-0.92.3/PTXQC/R/qcMetric_PG.R | 12 PTXQC-0.92.3/PTXQC/README.md | 17 PTXQC-0.92.3/PTXQC/build/vignette.rds |binary PTXQC-0.92.3/PTXQC/inst/doc/PTXQC-Basic_Guide_for_R_users.html | 531 ++++------ PTXQC-0.92.3/PTXQC/inst/doc/PTXQC-CustomizeReport.html | 20 PTXQC-0.92.3/PTXQC/inst/doc/PTXQC-DragNDrop.html | 20 PTXQC-0.92.3/PTXQC/inst/doc/PTXQC-FAQ.html | 20 PTXQC-0.92.3/PTXQC/inst/doc/PTXQC-Input_And_Output_Data.html | 20 PTXQC-0.92.3/PTXQC/inst/doc/PTXQC-ListOfMetrics.R |only PTXQC-0.92.3/PTXQC/inst/doc/PTXQC-ListOfMetrics.Rmd |only PTXQC-0.92.3/PTXQC/inst/doc/PTXQC-ListOfMetrics.html |only PTXQC-0.92.3/PTXQC/inst/examples/README.md | 4 PTXQC-0.92.3/PTXQC/inst/examples/report_v0.92.2__txt_5files_withMatch-100min.html |only PTXQC-0.92.3/PTXQC/inst/examples/report_v0.92.2__txt_5files_withMatch-100min.pdf |only PTXQC-0.92.3/PTXQC/inst/reportTemplate/PTXQC_report_template.Rmd | 2 PTXQC-0.92.3/PTXQC/man/CV.Rd | 1 PTXQC-0.92.3/PTXQC/man/LCS.Rd | 1 PTXQC-0.92.3/PTXQC/man/LCSn.Rd | 1 PTXQC-0.92.3/PTXQC/man/MQDataReader-cash-getInvalidLines.Rd | 1 PTXQC-0.92.3/PTXQC/man/MQDataReader-cash-getShortNames.Rd | 1 PTXQC-0.92.3/PTXQC/man/MQDataReader-cash-new.Rd | 1 PTXQC-0.92.3/PTXQC/man/MQDataReader-cash-plotNameMapping.Rd | 1 PTXQC-0.92.3/PTXQC/man/MQDataReader-cash-readMQ.Rd | 5 PTXQC-0.92.3/PTXQC/man/MQDataReader-cash-readMappingFile.Rd | 1 PTXQC-0.92.3/PTXQC/man/MQDataReader-cash-substitute.Rd | 1 PTXQC-0.92.3/PTXQC/man/MQDataReader-cash-writeMappingFile.Rd | 2 PTXQC-0.92.3/PTXQC/man/RSD.Rd | 1 PTXQC-0.92.3/PTXQC/man/RTalignmentTree.Rd | 1 PTXQC-0.92.3/PTXQC/man/ScoreInAlignWindow.Rd | 1 PTXQC-0.92.3/PTXQC/man/YAMLClass-class.Rd | 5 PTXQC-0.92.3/PTXQC/man/addGGtitle.Rd | 1 PTXQC-0.92.3/PTXQC/man/alignmentCheck.Rd | 1 PTXQC-0.92.3/PTXQC/man/appendEnv.Rd | 1 PTXQC-0.92.3/PTXQC/man/assignBlocks.Rd | 1 PTXQC-0.92.3/PTXQC/man/boxplotCompare.Rd | 3 PTXQC-0.92.3/PTXQC/man/brewer.pal.Safe.Rd | 1 PTXQC-0.92.3/PTXQC/man/byX.Rd | 1 PTXQC-0.92.3/PTXQC/man/byXflex.Rd | 1 PTXQC-0.92.3/PTXQC/man/computeMatchRTFractions.Rd | 1 PTXQC-0.92.3/PTXQC/man/correctSetSize.Rd | 1 PTXQC-0.92.3/PTXQC/man/createReport.Rd | 1 PTXQC-0.92.3/PTXQC/man/del0.Rd | 1 PTXQC-0.92.3/PTXQC/man/delLCP.Rd | 1 PTXQC-0.92.3/PTXQC/man/delLCS.Rd | 1 PTXQC-0.92.3/PTXQC/man/findAlignReference.Rd | 1 PTXQC-0.92.3/PTXQC/man/fixCalibration.Rd | 1 PTXQC-0.92.3/PTXQC/man/flattenList.Rd | 1 PTXQC-0.92.3/PTXQC/man/getAbundanceClass.Rd | 1 PTXQC-0.92.3/PTXQC/man/getECDF.Rd | 1 PTXQC-0.92.3/PTXQC/man/getFragmentErrors.Rd | 1 PTXQC-0.92.3/PTXQC/man/getHTMLTable.Rd | 1 PTXQC-0.92.3/PTXQC/man/getMQPARValue.Rd | 1 PTXQC-0.92.3/PTXQC/man/getMaxima.Rd | 1 PTXQC-0.92.3/PTXQC/man/getMetaData.Rd | 1 PTXQC-0.92.3/PTXQC/man/getMetricsObjects.Rd |only PTXQC-0.92.3/PTXQC/man/getPCA.Rd | 1 PTXQC-0.92.3/PTXQC/man/getPeptideCounts.Rd | 1 PTXQC-0.92.3/PTXQC/man/getProteinCounts.Rd | 1 PTXQC-0.92.3/PTXQC/man/getQCHeatMap.Rd | 1 PTXQC-0.92.3/PTXQC/man/getReportFilenames.Rd | 1 PTXQC-0.92.3/PTXQC/man/ggAxisLabels.Rd | 1 PTXQC-0.92.3/PTXQC/man/ggText.Rd | 1 PTXQC-0.92.3/PTXQC/man/grapes-plus-grapes.Rd | 1 PTXQC-0.92.3/PTXQC/man/grepv.Rd | 1 PTXQC-0.92.3/PTXQC/man/idTransferCheck.Rd | 1 PTXQC-0.92.3/PTXQC/man/inMatchWindow.Rd | 1 PTXQC-0.92.3/PTXQC/man/lcpCount.Rd | 1 PTXQC-0.92.3/PTXQC/man/lcsCount.Rd | 1 PTXQC-0.92.3/PTXQC/man/longestCommonPrefix.Rd | 1 PTXQC-0.92.3/PTXQC/man/longestCommonSuffix.Rd | 1 PTXQC-0.92.3/PTXQC/man/mosaicize.Rd | 1 PTXQC-0.92.3/PTXQC/man/pasten.Rd | 1 PTXQC-0.92.3/PTXQC/man/pastet.Rd | 1 PTXQC-0.92.3/PTXQC/man/peakSegmentation.Rd | 1 PTXQC-0.92.3/PTXQC/man/peakWidthOverTime.Rd | 1 PTXQC-0.92.3/PTXQC/man/plotTable.Rd | 1 PTXQC-0.92.3/PTXQC/man/plotTableRaw.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_CalibratedMSErr.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_Charge.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_ContEVD.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_ContUser.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_ContUserScore.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_ContsPG.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_CountData.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_IDRate.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_IDsOverRT.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_IonInjectionTimeOverRT.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_MBRAlign.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_MBRIDtransfer.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_MBRgain.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_MS2Decal.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_MS2Oversampling.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_MissedCleavages.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_RTPeakWidth.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_RatiosPG.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_ScanIDRate.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_TopN.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_TopNoverRT.Rd | 1 PTXQC-0.92.3/PTXQC/man/plot_UncalibratedMSErr.Rd | 1 PTXQC-0.92.3/PTXQC/man/pointsPutX.Rd | 1 PTXQC-0.92.3/PTXQC/man/print.PTXQC_table.Rd | 1 PTXQC-0.92.3/PTXQC/man/printWithFooter.Rd | 1 PTXQC-0.92.3/PTXQC/man/qcMetric-class.Rd | 5 PTXQC-0.92.3/PTXQC/man/qcMetric_MSMSScans_TopNoverRT-class.Rd | 2 PTXQC-0.92.3/PTXQC/man/qualBestKS.Rd | 1 PTXQC-0.92.3/PTXQC/man/qualCentered.Rd | 1 PTXQC-0.92.3/PTXQC/man/qualCenteredRef.Rd | 1 PTXQC-0.92.3/PTXQC/man/qualGaussDev.Rd | 1 PTXQC-0.92.3/PTXQC/man/qualHighest.Rd | 1 PTXQC-0.92.3/PTXQC/man/qualLinThresh.Rd | 1 PTXQC-0.92.3/PTXQC/man/qualMedianDist.Rd | 1 PTXQC-0.92.3/PTXQC/man/qualUniform.Rd | 1 PTXQC-0.92.3/PTXQC/man/read.MQ.Rd | 1 PTXQC-0.92.3/PTXQC/man/renameFile.Rd | 1 PTXQC-0.92.3/PTXQC/man/repEach.Rd | 1 PTXQC-0.92.3/PTXQC/man/scale01linear.Rd |only PTXQC-0.92.3/PTXQC/man/scale_x_discrete_reverse.Rd | 1 PTXQC-0.92.3/PTXQC/man/scale_y_discrete_reverse.Rd | 1 PTXQC-0.92.3/PTXQC/man/shortenStrings.Rd | 1 PTXQC-0.92.3/PTXQC/man/simplifyNames.Rd | 1 PTXQC-0.92.3/PTXQC/man/supCount.Rd | 1 PTXQC-0.92.3/PTXQC/man/theme_blank.Rd | 1 PTXQC-0.92.3/PTXQC/man/thinOut.Rd | 1 PTXQC-0.92.3/PTXQC/man/thinOutBatch.Rd | 1 PTXQC-0.92.3/PTXQC/man/wait_for_writable.Rd | 1 PTXQC-0.92.3/PTXQC/vignettes/PTXQC-ListOfMetrics.Rmd |only 140 files changed, 686 insertions(+), 654 deletions(-)
Title: Nonlinear Mixed Effects Models in Population Pharmacokinetics
and Pharmacodynamics
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'RxODE' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut],
Yuan Xiong [aut],
Rik Schoemaker [aut],
Justin Wilkins [aut],
Mirjam Trame [aut],
Teun Post [aut],
Robert Leary [ctb],
Wenping Wang [aut, cre],
Hadley Wickham [ctb],
Dirk Eddelbuettel [cph],
David Ardia [cph],
Katharine Mullen [cph],
Sylvan Elhay [cph],
Jaroslav Kautsky [cph],
John Burkardt [cph],
Shanjie Zhang [cph],
Jianming Jin [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between nlmixr versions 0.9.0-1 dated 2017-11-09 and 0.9.0-3 dated 2018-02-07
DESCRIPTION | 17 MD5 | 351 NAMESPACE | 384 - R/RcppExports.R | 274 R/bounds.R | 1576 ++-- R/focei.R | 922 +- R/focei_fit.R | 4779 ++++++------- R/nlme_fit.R | 122 R/nlme_fit_gen.R | 56 R/nlmixr.R | 81 R/saem_fit.R | 60 R/ui.R | 2934 ++++--- R/utils.R | 27 R/validate.R | 108 R/vpc.R | 2 build/vignette.rds |binary inst/COPYRIGHT | 34 inst/doc/installing_nlmixr.Rmd |only inst/doc/installing_nlmixr.html |only inst/doc/nlmixr-focei.R |only inst/doc/nlmixr-focei.Rmd |only inst/doc/nlmixr-focei.html |only inst/doc/nlmixr-intro.R |only inst/doc/nlmixr-intro.Rmd |only inst/doc/nlmixr-intro.html |only inst/doc/running_nlmixr.Rmd | 1364 +-- inst/doc/running_nlmixr.html | 78 inst/include/nlmixr_types.h | 13 inst/include/saem_class_rcpp.hpp | 6 man/Bolus_1CPT.Rd | 114 man/Bolus_1CPTMM.Rd | 112 man/Bolus_2CPT.Rd | 118 man/Bolus_2CPTMM.Rd | 116 man/Infusion_1CPT.Rd | 116 man/Oral_1CPT.Rd | 116 man/RxODE_focei_eta.Rd | 30 man/RxODE_focei_eta_lik.Rd | 34 man/RxODE_focei_eta_lp.Rd | 34 man/RxODE_focei_finalize_llik.Rd | 30 man/Wang2007.Rd | 50 man/as.data.frame.focei.fit.Rd | 56 man/as.focei.Rd | 62 man/as.nlme.Rd | 42 man/as.saem.Rd | 42 man/bootdata.Rd | 70 man/calcCov.Rd | 42 man/collectWarnings.Rd | 40 man/configsaem.Rd | 164 man/constructLinCmt.Rd | 42 man/dynmodel.Rd | 128 man/dynmodel.mcmc.Rd | 132 man/fitted.focei.fit.Rd | 82 man/focei.eta.Rd | 54 man/focei.fit.Rd | 134 man/focei.theta.Rd | 48 man/frwd_selection.Rd | 74 man/gauss.quad.Rd | 40 man/gen_saem_user_fn.Rd | 53 man/getOMEGA.Rd | 34 man/gnlmm.Rd | 204 man/instant.stan.extension.Rd | 32 man/invgaussian.Rd | 44 man/lin_cmt.Rd | 68 man/lincmt.Rd | 56 man/logLik.focei.fit.Rd | 44 man/metabolite.Rd | 46 man/nlmeModList.Rd | 54 man/nlme_gof.Rd | 32 man/nlme_lin_cmpt.Rd | 106 man/nlme_ode.Rd | 266 man/nlmixr.Rd | 1166 +-- man/nlmixrBounds.Rd | 42 man/nlmixrBounds.eta.names.Rd | 40 man/nlmixrBounds.focei.upper.lower.Rd | 44 man/nlmixrForget.Rd | 30 man/nlmixrLogo.Rd | 38 man/nlmixrPrint.Rd |only man/nlmixrUI.Rd | 41 man/nlmixrUI.focei.inits.Rd | 40 man/nlmixrUI.nlme.specs.Rd | 42 man/nlmixrUI.nlme.var.Rd | 42 man/nlmixrUI.nlmefun.Rd | 44 man/nlmixrUI.rxode.pred.Rd | 40 man/nlmixrUI.saem.ares.Rd | 40 man/nlmixrUI.saem.bres.Rd | 40 man/nlmixrUI.saem.eta.trans.Rd | 40 man/nlmixrUI.saem.fit.Rd | 40 man/nlmixrUI.saem.init.Rd | 40 man/nlmixrUI.saem.init.omega.Rd | 46 man/nlmixrUI.saem.init.theta.Rd | 40 man/nlmixrUI.saem.log.eta.Rd | 40 man/nlmixrUI.saem.model.Rd | 40 man/nlmixrUI.saem.model.omega.Rd | 40 man/nlmixrUI.saem.res.mod.Rd | 40 man/nlmixrUI.saem.res.name.Rd | 40 man/nlmixrUI.saem.theta.name.Rd | 40 man/nlmixrUI.theta.pars.Rd | 40 man/nlmixrUILinCmt.Rd | 46 man/nlmixrValidate.Rd | 38 man/nlmixrVersion.Rd | 28 man/nlmixr_fit.Rd | 76 man/nlmixrfindLhs.Rd | 42 man/nmDataConvert.Rd | 40 man/nmsimplex.Rd | 46 man/nmxInclude.Rd | 42 man/nobs.focei.fit.Rd | 44 man/par.hist.Rd | 62 man/plot.dyn.ID.Rd | 32 man/plot.dyn.mcmc.Rd | 32 man/plot.focei.fit.Rd | 38 man/plot.saemFit.Rd | 38 man/prediction.Rd | 120 man/print.dyn.ID.Rd | 32 man/print.dyn.mcmc.Rd | 32 man/print.focei.fit.Rd | 34 man/print.gnlmm.fit.Rd | 32 man/print.nlmixrUI.Rd | 38 man/print.saemFit.Rd | 38 man/pump.Rd | 62 man/rats.Rd | 96 man/residuals.focei.fit.Rd | 54 man/rxFoceiEta.Rd | 62 man/rxFoceiGrad.Rd | 50 man/rxFoceiInner.Rd | 86 man/rxFoceiLik.Rd | 54 man/rxFoceiLp.Rd | 54 man/rxFoceiTheta.Rd | 66 man/rxGrad.Rd | 30 man/rxHessian.Rd | 30 man/rxUpdateEtas.Rd | 46 man/saem.cleanup.Rd | 34 man/saem.fit.Rd | 158 man/saemControl.Rd | 160 man/simulate.focei.fit.Rd | 52 man/summary.dyn.ID.Rd | 32 man/summary.dyn.mcmc.Rd | 32 man/summary.saemFit.Rd | 38 man/theo_md.Rd | 60 man/theo_sd.Rd | 56 man/traceplot.Rd | 50 man/vcov.focei.fit.Rd | 54 man/vpc.Rd | 46 src/Makevars | 5 src/RcppExportMod.cpp | 2 src/RcppExports.cpp | 3 src/chkSolved.c | 38 src/evaluate.h | 2 src/focei.cpp | 13 src/focei_fit.cpp | 5 src/init.c | 2 src/merge3.c |only src/ode_cmt1.cpp | 1 tests/testthat/rx_2950d4229032b503bb2d9b927a22b2fe_x64.c |only tests/testthat/rx_3875b459ce859fab1fe06ac38182270c.inv |only tests/testthat/rx_403fe5334eaa0ae743cd219c85bdbae7.dll.prd |only tests/testthat/rx_9e913e285f74cc818d90cca53c8a734c_i386.c |only tests/testthat/test-focei-inner.R | 468 - tests/testthat/test-focei-wang2007.R | 334 tests/testthat/test-model01.R | 198 tests/testthat/test-model02.R | 198 tests/testthat/test-model04.R | 198 tests/testthat/test-model13.R | 250 tests/testthat/test-model14.R | 354 tests/testthat/test-model15.R | 248 tests/testthat/test-model20.R | 150 tests/testthat/test-model22.R | 144 tests/testthat/test-model23.R | 244 tests/testthat/test-model24.R | 238 tests/testthat/test-model25.R | 368 - tests/testthat/test-model26.R | 240 tests/testthat/test-model30.R | 148 tests/testthat/test-model31.R | 150 tests/testthat/test-model32.R | 286 tests/testthat/test-model34.R | 398 - tests/testthat/test-model35.R | 282 tests/testthat/test-model40.R | 152 tests/testthat/test-ui-bad-models.R | 430 - tests/testthat/test-ui-pred-err.R | 1 tests/testthat/test-ui-saem.R | 159 vignettes/cwres_vs_pred.png |only vignettes/dv_vs_ipred.png |only vignettes/dv_vs_pred.png |only vignettes/ind_plots.png |only vignettes/installing_nlmixr.Rmd |only vignettes/iwres_vs_pred.png |only vignettes/running_nlmixr.Rmd | 1364 +-- vignettes/saem3ef0785e1f30x64.cpp |only 187 files changed, 14301 insertions(+), 13688 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on undirected graphical models for accomplishing three important and interrelated goals in genetics: (1) linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-phenotype-environment interactions network. For this purpose, we use conditional (in)dependence relationships between variables. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent developments in Behrouzi and Wit (2017) <arXiv:1710.00894> and Behrouzi and Wit (2017) <arXiv:1710.01063> .
Author: Pariya Behrouzi and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 0.1.3.0 dated 2018-02-07 and 0.1.3.1 dated 2018-02-07
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on undirected graphical models for accomplishing three important and interrelated goals in genetics: (1) linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-phenotype-environment interactions network. For this purpose, we use conditional (in)dependence relationships between variables. The netgwas package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The package is implemented the recent developments in Behrouzi and Wit (2017) <arXiv:1710.00894> and Behrouzi and Wit (2017) <arXiv:1710.01063> .
Author: Pariya Behrouzi and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 0.1.2.0 dated 2018-01-12 and 0.1.3.0 dated 2018-02-07
DESCRIPTION | 6 +++--- MD5 | 14 +++++++++----- R/netmap.R | 8 ++++---- data/bp.RData |only data/hdl.RData |only man/CviCol.Rd | 6 +----- man/bp.Rd |only man/hdl.Rd |only man/tetraPotato.Rd | 10 ++-------- man/thaliana.Rd | 14 ++------------ 10 files changed, 21 insertions(+), 37 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <http://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [cph],
Jana Straková [cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.3 dated 2018-01-15 and 0.4 dated 2018-02-07
udpipe-0.3/udpipe/man/collocation.Rd |only udpipe-0.3/udpipe/man/phrases.Rd |only udpipe-0.4/udpipe/DESCRIPTION | 8 udpipe-0.4/udpipe/MD5 | 70 +++-- udpipe-0.4/udpipe/NAMESPACE | 14 + udpipe-0.4/udpipe/NEWS.md | 15 + udpipe-0.4/udpipe/R/nlp_collocation.R | 21 + udpipe-0.4/udpipe/R/nlp_cooccurrence.R | 111 +++++++- udpipe-0.4/udpipe/R/nlp_flow.R | 87 ++++++- udpipe-0.4/udpipe/R/nlp_phrase_sequences.R | 43 ++- udpipe-0.4/udpipe/R/nlp_rake.R |only udpipe-0.4/udpipe/R/pkg.R | 4 udpipe-0.4/udpipe/R/topicmodels.R | 1 udpipe-0.4/udpipe/R/udpipe_parse.R | 11 udpipe-0.4/udpipe/R/udpipe_train.R | 124 ++++++++++ udpipe-0.4/udpipe/README.md | 1 udpipe-0.4/udpipe/build/vignette.rds |binary udpipe-0.4/udpipe/inst/conll17 |only udpipe-0.4/udpipe/inst/doc/udpipe-annotation.html | 6 udpipe-0.4/udpipe/inst/doc/udpipe-train.html | 6 udpipe-0.4/udpipe/inst/doc/udpipe-tryitout.R | 6 udpipe-0.4/udpipe/inst/doc/udpipe-tryitout.Rmd | 18 + udpipe-0.4/udpipe/inst/doc/udpipe-tryitout.html | 22 + udpipe-0.4/udpipe/inst/doc/udpipe-usecase-postagging-lemmatisation.R |only udpipe-0.4/udpipe/inst/doc/udpipe-usecase-postagging-lemmatisation.Rmd |only udpipe-0.4/udpipe/inst/doc/udpipe-usecase-postagging-lemmatisation.html |only udpipe-0.4/udpipe/man/as_conllu.Rd |only udpipe-0.4/udpipe/man/as_cooccurrence.Rd |only udpipe-0.4/udpipe/man/as_word2vec.Rd |only udpipe-0.4/udpipe/man/cooccurrence.Rd | 46 ++- udpipe-0.4/udpipe/man/document_term_frequencies.Rd | 5 udpipe-0.4/udpipe/man/document_term_frequencies_statistics.Rd |only udpipe-0.4/udpipe/man/document_term_matrix.Rd | 2 udpipe-0.4/udpipe/man/dtm_bind.Rd | 10 udpipe-0.4/udpipe/man/dtm_colsums.Rd |only udpipe-0.4/udpipe/man/keywords_collocation.Rd |only udpipe-0.4/udpipe/man/keywords_phrases.Rd |only udpipe-0.4/udpipe/man/keywords_rake.Rd |only udpipe-0.4/udpipe/man/predict.LDA.Rd | 1 udpipe-0.4/udpipe/man/udpipe_annotate.Rd | 3 udpipe-0.4/udpipe/src/udpipe.cpp | 12 udpipe-0.4/udpipe/vignettes/coocurrence-example1.png |only udpipe-0.4/udpipe/vignettes/coocurrence-example2.png |only udpipe-0.4/udpipe/vignettes/udpipe-tryitout.Rmd | 18 + udpipe-0.4/udpipe/vignettes/udpipe-usecase-postagging-lemmatisation.Rmd |only 45 files changed, 537 insertions(+), 128 deletions(-)
Title: JavaScript Charts Tool
Description: Provides an R interface for using 'AmCharts' Library. Based on
'htmlwidgets', it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced but
can easily be added in the constructors. Complex properties (e.g. 'JavaScript'
object) can be passed as named list. See examples at <http://datastorm-
open.github.io/introduction_ramcharts/> and <http://www.amcharts.com/> for
more information about the library. The package includes the free version
of 'AmCharts' Library. Its only limitation is a small link to the web site
displayed on your charts. If you enjoy this library, do not hesitate to refer
to this page <http://www.amcharts.com/online-store/> to purchase a licence,
and thus support its creators and get a period of Priority Support. See also
<http://www.amcharts.com/about/> for more information about 'AmCharts' company.
Author: Benoit Thieurmel [aut, cre],
Antanas Marcelionis [aut, cph] ('AmCharts' library in th directory
htmlwidgets/lib/amcharts, refer to http://www.amcharts.com/),
Jeffery Petit [aut, ctb],
Elena Salette [aut, ctb],
Titouan Robert [aut, ctb]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between rAmCharts versions 2.1.5 dated 2017-06-30 and 2.1.6 dated 2018-02-07
DESCRIPTION | 43 MD5 | 615 +-- NAMESPACE | 436 +- R/base_data.R | 470 +- R/base_startupMessage.R | 10 R/chart_amBarplot.R | 530 +- R/chart_amBoxplot.R | 982 ++--- R/chart_amBullet.R | 252 - R/chart_amCandlestick.R | 284 - R/chart_amDataset.R | 356 - R/chart_amFloatingBar.R | 474 +- R/chart_amFunnel.R | 218 - R/chart_amGauge.R | 552 +- R/chart_amHist.R | 308 - R/chart_amMekko.R | 206 - R/chart_amOHLC.R | 240 - R/chart_amPie.R | 172 R/chart_amPlot.R | 1450 +++---- R/chart_amRadar.R | 264 - R/chart_amTimeSeries.R | 1030 ++--- R/chart_amWaterfall.R | 336 - R/chart_amWind.R | 260 - R/classUnions.R | 118 R/class_AmBalloon.R | 348 - R/class_AmChart.R | 498 +- R/class_AmChart_constructors.R | 368 - R/class_AmChart_setters.R | 1898 +++++----- R/class_AmChart_shinyUtils.R | 116 R/class_AmGraph.R | 426 +- R/class_AmLegend.R | 222 - R/class_AmObject.R | 438 +- R/class_AmStockChart.R | 384 +- R/class_AmStockChart_setters.R | 792 ++-- R/class_AxisBase.R | 40 R/class_AxisBase_setters.R | 64 R/class_CategoryAxis.R | 192 - R/class_ChartCursor.R | 180 R/class_ChartCursor_setters.R | 98 R/class_ChartScrollbar.R | 180 R/class_ChartScrollbar_setters.R | 108 R/class_DataSet.R | 204 - R/class_DataSetSelector.R | 174 R/class_DataSet_setters.R | 186 R/class_GaugeArrow.R | 138 R/class_GaugeArrow_setters.R | 74 R/class_GaugeAxis.R | 138 R/class_GaugeAxis_setters.R | 106 R/class_GaugeBand.R | 168 R/class_Guide.R | 190 - R/class_Guide_setters.R | 84 R/class_Label.R | 330 - R/class_PeriodSelector.R | 172 R/class_StockEvent.R | 132 R/class_StockEvent_setters.R | 66 R/class_StockPanel.R | 412 +- R/class_StockPanel_setters.R | 212 - R/class_Title.R | 218 - R/class_TrendLine.R | 222 - R/class_TrendLine_setters.R | 260 - R/class_ValueAxis.R | 184 R/shiny_examples.R | 54 R/shiny_modules_export.R | 646 +-- R/shiny_modules_timeSeries.R | 1582 ++++---- R/union_AmCharts.R | 1242 +++--- R/utils.R | 148 R/utils_amOptions.R | 590 +-- R/utils_amTests.R | 326 - R/utils_basicClassUnions.R | 8 R/utils_sharedGenerics.R | 154 inst/NOTICE.Rmd | 210 - inst/conf.yaml | 74 inst/htmlwidgets/amDrillChart.js | 278 - inst/htmlwidgets/amDrillChart.yaml | 70 inst/htmlwidgets/lib/amcharts.js | 790 ++-- inst/htmlwidgets/lib/amstock.js | 210 - inst/htmlwidgets/lib/funnel.js | 68 inst/htmlwidgets/lib/gantt.js | 10 inst/htmlwidgets/lib/gauge.js | 48 inst/htmlwidgets/lib/images/style.css | 70 inst/htmlwidgets/lib/pie.js | 58 inst/htmlwidgets/lib/plugins/animate/LICENSE | 402 +- inst/htmlwidgets/lib/plugins/animate/animate.min.js | 80 inst/htmlwidgets/lib/plugins/animate/bower.json | 54 inst/htmlwidgets/lib/plugins/animate/index.js | 4 inst/htmlwidgets/lib/plugins/animate/package.json | 20 inst/htmlwidgets/lib/plugins/dataloader/bower.json | 54 inst/htmlwidgets/lib/plugins/dataloader/index.js | 4 inst/htmlwidgets/lib/plugins/dataloader/package.json | 20 inst/htmlwidgets/lib/plugins/export/LICENSE | 404 +- inst/htmlwidgets/lib/plugins/export/bower.json | 54 inst/htmlwidgets/lib/plugins/export/export.css | 720 +-- inst/htmlwidgets/lib/plugins/export/export.min.js | 2 inst/htmlwidgets/lib/plugins/export/index.js | 4 inst/htmlwidgets/lib/plugins/export/lang/fr.js | 62 inst/htmlwidgets/lib/plugins/export/lang/pt.js | 74 inst/htmlwidgets/lib/plugins/export/libs/FileSaver.js/FileSaver.min.js | 2 inst/htmlwidgets/lib/plugins/export/libs/blob.js/blob.js | 420 +- inst/htmlwidgets/lib/plugins/export/libs/fabric.js/fabric.min.js | 14 inst/htmlwidgets/lib/plugins/export/libs/jszip/jszip.min.js | 26 inst/htmlwidgets/lib/plugins/export/libs/pdfmake/pdfmake.min.js | 34 inst/htmlwidgets/lib/plugins/export/libs/xlsx/LICENSE | 34 inst/htmlwidgets/lib/plugins/export/libs/xlsx/xlsx.min.js | 16 inst/htmlwidgets/lib/plugins/export/package.json | 20 inst/htmlwidgets/lib/plugins/responsive/bower.json | 54 inst/htmlwidgets/lib/plugins/responsive/index.js | 4 inst/htmlwidgets/lib/plugins/responsive/package.json | 20 inst/htmlwidgets/lib/plugins/responsive/responsive.min.js | 2 inst/htmlwidgets/lib/radar.js | 22 inst/htmlwidgets/lib/serial.js | 190 - inst/htmlwidgets/lib/xy.js | 82 inst/htmlwidgets/ramcharts_base.js | 486 +- inst/htmlwidgets/ramcharts_base.yaml | 14 inst/modules/global.R | 40 inst/modules/server.R | 75 inst/modules/ui.R | 31 inst/shiny/server.R | 92 inst/shiny/src/Information/information_ui.R | 46 inst/shiny/src/bar/ambar_server.R | 162 inst/shiny/src/bar/ambar_ui.R | 202 - inst/shiny/src/bar/bar_server.R | 654 +-- inst/shiny/src/bar/bar_ui.R | 342 - inst/shiny/src/bullet/ambullet_server.R | 88 inst/shiny/src/bullet/ambullet_ui.R | 154 inst/shiny/src/bullet/bullet_server.R | 118 inst/shiny/src/bullet/bullet_ui.R | 68 inst/shiny/src/candlestick/amcandlestick_server.R | 124 inst/shiny/src/candlestick/amcandlestick_ui.R | 160 inst/shiny/src/candlestick/candlestick_server.R | 74 inst/shiny/src/candlestick/candlestick_ui.R | 68 inst/shiny/src/drilldown/drilldown_server.R | 80 inst/shiny/src/drilldown/drilldown_ui.R | 18 inst/shiny/src/funnel/amfunnel_server.R | 104 inst/shiny/src/funnel/amfunnel_ui.R | 194 - inst/shiny/src/funnel/funnel_server.R | 132 inst/shiny/src/funnel/funnel_ui.R | 156 inst/shiny/src/gauge/amgauge_server.R | 158 inst/shiny/src/gauge/amgauge_ui.R | 220 - inst/shiny/src/gauge/gauge_server.R | 62 inst/shiny/src/gauge/gauge_ui.R | 66 inst/shiny/src/hist/amhist_server.R | 56 inst/shiny/src/hist/amhist_ui.R | 170 inst/shiny/src/hist/hist_ui.R | 20 inst/shiny/src/lines/amlines_server.R | 142 inst/shiny/src/lines/amlines_ui.R | 156 inst/shiny/src/lines/lines_server.R | 606 +-- inst/shiny/src/lines/lines_ui.R | 316 - inst/shiny/src/mekko/ammekko_server.R | 108 inst/shiny/src/mekko/ammekko_ui.R | 162 inst/shiny/src/mekko/mekko_server.R | 84 inst/shiny/src/mekko/mekko_ui.R | 68 inst/shiny/src/menu/menu.R | 148 inst/shiny/src/pie/ampie_server.R | 180 inst/shiny/src/pie/ampie_ui.R | 214 - inst/shiny/src/pie/pie_server.R | 288 - inst/shiny/src/pie/pie_ui.R | 380 +- inst/shiny/src/radar/amradar_server.R | 118 inst/shiny/src/radar/amradar_ui.R | 172 inst/shiny/src/radar/radar_server.R | 232 - inst/shiny/src/radar/radar_ui.R | 162 inst/shiny/src/serial/serial_server.R | 1470 +++---- inst/shiny/src/serial/serial_ui.R | 136 inst/shiny/src/stock/amstock_server.R | 206 - inst/shiny/src/stock/amstock_ui.R | 364 - inst/shiny/src/stock/stock_server.R | 388 +- inst/shiny/src/stock/stock_ui.R | 124 inst/shiny/src/xy/amxy_server.R | 194 - inst/shiny/src/xy/amxy_ui.R | 214 - inst/shiny/src/xy/xy_server.R | 276 - inst/shiny/src/xy/xy_ui.R | 158 inst/shiny/ui.R | 116 inst/shiny/www/style.css | 38 inst/tests |only man/AmBalloon-class.Rd | 92 man/AmBalloon.Rd | 158 man/AmChart-class.Rd | 276 - man/AmGraph-class.Rd | 78 man/AmGraph.Rd | 182 man/AmLegend-class.Rd | 62 man/AmObject-class.Rd | 48 man/AmStockChart-class.Rd | 112 man/AmStockChart.Rd | 580 +-- man/AxisBase-class.Rd | 54 man/CategoryAxis-class.Rd | 66 man/ChartCursor-class.Rd | 74 man/ChartScrollbar-class.Rd | 70 man/DataSet-class.Rd | 80 man/DataSet.Rd | 182 man/DataSetSelector-class.Rd | 66 man/DataSetSelector.Rd | 84 man/GaugeArrow-class.Rd | 62 man/GaugeArrow.Rd | 110 man/GaugeAxis-class.Rd | 60 man/GaugeAxis.Rd | 120 man/GaugeBand-class.Rd | 60 man/GaugeBand.Rd | 90 man/Guide-class.Rd | 74 man/Label-class.Rd | 70 man/Label.Rd | 148 man/PeriodSelector-class.Rd | 66 man/StockEvent-class.Rd | 68 man/StockPanel-class.Rd | 272 - man/Title-class.Rd | 64 man/Title.Rd | 98 man/TrendLine-class.Rd | 92 man/TrendLine.Rd | 218 - man/ValueAxis-class.Rd | 72 man/add_dataloader_dependency.Rd | 36 man/add_export_dependency.Rd | 36 man/add_responsive_dependency.Rd | 36 man/add_theme_dependency.Rd | 56 man/amAngularGauge.Rd | 108 man/amBarplot.Rd | 286 - man/amBoxplot.Rd | 236 - man/amBullet.Rd | 130 man/amCandlestick.Rd | 178 man/amChartsOutput.Rd | 40 man/amFloatingBar.Rd | 268 - man/amFunnel.Rd | 124 man/amHist.Rd | 172 man/amLines.Rd | 114 man/amMekko.Rd | 108 man/amOHLC.Rd | 158 man/amOptions.Rd | 222 - man/amPie.Rd | 100 man/amPlot.Rd | 304 - man/amRadar.Rd | 132 man/amSolidGauge.Rd | 130 man/amStockMultiSet.Rd | 126 man/amTimeSeries.Rd | 336 - man/amWaterfall.Rd | 84 man/amWind.Rd | 92 man/amcharts-setters.Rd | 84 man/api.Rd | 42 man/controlShinyPlot.Rd | 38 man/data_AirPassengers.Rd | 36 man/data_bar.Rd | 40 man/data_candleStick1.Rd | 44 man/data_candleStick2.Rd | 44 man/data_fbar.Rd | 42 man/data_funnel.Rd | 38 man/data_gantt.Rd | 42 man/data_gbar.Rd | 44 man/data_gdp.Rd | 42 man/data_mekko.Rd | 38 man/data_pie.Rd | 38 man/data_radar.Rd | 42 man/data_stock1.Rd | 38 man/data_stock_2.Rd | 38 man/data_stock_3.Rd | 42 man/data_waterfall.Rd | 40 man/data_wind.Rd | 40 man/getCurrentStockData.Rd | 104 man/getTransformTS.Rd | 112 man/initialize-AmChart.Rd | 1374 +++---- man/initialize-AmLegend.Rd | 80 man/initialize-AxisBase.Rd | 60 man/initialize-CategoryAxis.Rd | 94 man/initialize-ChartCursor.Rd | 128 man/initialize-ChartScrollbar.Rd | 138 man/initialize-Guide.Rd | 108 man/initialize-PeriodSelector.Rd | 90 man/initialize-StockEvent.Rd | 98 man/initialize-StockPanel.Rd | 376 - man/initialize-ValueAxis.Rd | 90 man/listProperties-AmObject.Rd | 50 man/methods-AmObject.Rd | 156 man/plot.AmChart.Rd | 58 man/print-AmObject-method.Rd | 54 man/rAmCharts-shinymodules-ts.Rd | 357 + man/rAmCharts-shinymodules.Rd | 154 man/renderAmCharts.Rd | 38 man/runExamples.Rd | 30 man/shared-generics.Rd | 158 man/show-AmChart-method.Rd | 38 man/show-AmObject-method.Rd | 42 man/show-AmStockChart-method.Rd | 38 man/stockGraph.Rd | 74 man/stockLegend.Rd | 60 tests/testthat.R | 6 tests/testthat/test_AmStockChart_setters.R | 64 tests/testthat/test_AxisBase_setters.R | 8 tests/testthat/test_ChartCursor_setters.R | 10 tests/testthat/test_ChartScrollbar_setters.R | 10 tests/testthat/test_DataSet_setters.R | 10 tests/testthat/test_GaugeArrow_setters.R | 10 tests/testthat/test_GaugeAxis_setters.R | 26 tests/testthat/test_Guide.R | 12 tests/testthat/test_StockEvent.R | 10 tests/testthat/test_StockPanel_setters.R | 36 tests/testthat/test_TrendLine_setters.R | 26 tests/testthat/test_amBarplot.R | 144 tests/testthat/test_amBoxplot.R | 110 tests/testthat/test_amBullet.R | 76 tests/testthat/test_amCandlestick.R | 126 tests/testthat/test_amFloatingBar.R | 106 tests/testthat/test_amFunnel.R | 60 tests/testthat/test_amHist.R | 68 tests/testthat/test_amMekko.R | 42 tests/testthat/test_amOHLC.R | 76 tests/testthat/test_amOptions.R | 278 - tests/testthat/test_amPie.R | 68 tests/testthat/test_amPlot.R | 186 tests/testthat/test_amRadar.R | 74 tests/testthat/test_amSolidGauge.R | 126 tests/testthat/test_amTests.R | 186 tests/testthat/test_amWaterfall.R | 34 tests/testthat/test_amWind.R | 46 tests/testthat/test_amchart_setters.R | 330 - tests/testthat/test_getAggregateTS.R | 332 - 309 files changed, 28119 insertions(+), 28024 deletions(-)
Title: Interface to the Knoema API
Description: Using this package, users can access to the largest collection of public data and statistics on the Internet featuring about 2.5 billion time series from thousands of sources collected in 'Knoema' repository and use rich R calculations in order to analyze the data. Because data in 'Knoema' is time series data, 'Knoema' function offers data in a number of formats usable in R such as 'ts', 'xts' or 'zoo'. For more information about 'Knoema' API go to <https://knoema.com/dev/docs>.
Author: Pavel Pimenov [aut, cre],
Ekaterina Chirkova [aut],
Knoema [cph]
Maintainer: Pavel Pimenov <pimenov@knoema.com>
Diff between Knoema versions 0.1.12 dated 2017-12-11 and 0.1.13 dated 2018-02-07
DESCRIPTION | 8 +-- MD5 | 16 +++--- NAMESPACE | 1 R/DataReader.R | 106 +++++++++++++++++++++++----------------- R/knoema.R | 4 - README.md | 46 ++++++----------- tests/testthat/test_dataframe.R | 11 ++++ tests/testthat/test_errors.R | 5 - tests/testthat/test_xts_zoo.R | 55 +++++++------------- 9 files changed, 122 insertions(+), 130 deletions(-)
Title: Variable Selection for Supervised Classification in High
Dimension
Description: The functions provided in the FADA (Factor Adjusted Discriminant Analysis) package aim at performing supervised classification of high-dimensional and correlated profiles. The procedure combines a decorrelation step based on a
factor modeling of the dependence among covariates and a classification method. The available methods are Lasso regularized logistic model
(see Friedman et al. (2010)), sparse linear discriminant analysis (see
Clemmensen et al. (2011)), shrinkage linear and diagonal discriminant
analysis (see M. Ahdesmaki et al. (2010)). More methods of classification can be used on the decorrelated data provided by the package FADA.
Author: Emeline Perthame (INRIA, Grenoble, France), Chloe Friguet
(Universite de Bretagne Sud, Vannes, France) and David Causeur (Agrocampus
Ouest, Rennes, France)
Maintainer: David Causeur <david.causeur@agrocampus-ouest.fr>
Diff between FADA versions 1.3.2 dated 2016-05-20 and 1.3.3 dated 2018-02-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/FADA.R | 2 +- man/FADA.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-05 1.37
2017-12-15 1.33