Title: String Functions for Compact R Code
Description: A collection of string functions designed for writing
compact and expressive R code. 'yasp' (Yet Another String Package) is simple,
fast, dependency-free, and written in pure R. The package provides: a
coherent set of abbreviations for paste() from package 'base' with a
variety of defaults, such as p() for "paste" and pcc() for "paste and
collapse with commas"; wrap(), bracket(), and others for wrapping a
string in flanking characters; unwrap() for removing pairs of characters
(at any position in a string); and sentence() for cleaning whitespace
around punctuation and capitalization appropriate for prose sentences.
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <tkalinow@asu.edu>
Diff between yasp versions 0.1.0 dated 2017-11-13 and 0.2.0 dated 2018-05-29
yasp-0.1.0/yasp/tests |only yasp-0.2.0/yasp/DESCRIPTION | 28 +-- yasp-0.2.0/yasp/MD5 | 17 - yasp-0.2.0/yasp/NAMESPACE | 44 ++-- yasp-0.2.0/yasp/R/paste.R | 108 +++++++---- yasp-0.2.0/yasp/README.md | 313 +++++++++++++++++----------------- yasp-0.2.0/yasp/man/paste-variants.Rd | 164 ++++++++++------- yasp-0.2.0/yasp/man/sentence.Rd | 92 ++++----- yasp-0.2.0/yasp/man/unwrap.Rd | 122 ++++++------- yasp-0.2.0/yasp/man/wrap.Rd | 110 +++++------ 10 files changed, 537 insertions(+), 461 deletions(-)
Title: Koul's Minimum Distance Estimation in Linear Regression and
Autoregression Model by Coordinate Descent Algorithm
Description: Consider linear regression model and autoregressive model of
order q where errors in the linear regression model and innovations in the
autoregression model are independent and symmetrically distributed. Hira L. Koul
(1986) <DOI:10.1214/aos/1176350059> proposed a nonparametric minimum distance
estimation method by minimizing L2-type distance between certain weighted
residual empirical processes. He also proposed a simpler version of the loss
function by using symmetry of the integrating measure in the distance. Kim
(2018) <DOI:10.1080/00949655.2017.1392527> proposed a fast computational method
which enables practitioners to compute the minimum distance estimator of the vector
of general multiple regression parameters for several integrating measures. This
package contains three functions: KoulLrMde(), KoulArMde(), and Koul2StageMde().
The former two provide minimum distance estimators for linear regression model
and autoregression model, respectively, where both are based on Koul's method.
These two functions take much less time for the computation than those based
on parametric minimum distance estimation methods. Koul2StageMde() provides
estimators for regression and autoregressive coefficients of linear regression
model with autoregressive errors through minimum distant method of two stages.
The new version is written in Rcpp and dramatically reduces computational time.
Author: Jiwoong Kim <kimjiwo2@stt.msu.edu>
Maintainer: Jiwoong Kim <kimjiwo2@stt.msu.edu>
Diff between KoulMde versions 3.0.0 dated 2017-02-01 and 3.1.0 dated 2018-05-29
KoulMde-3.0.0/KoulMde/R/RevisedMdeFunc.R |only KoulMde-3.0.0/KoulMde/src/CLosscpp.cpp |only KoulMde-3.0.0/KoulMde/src/GetDY.cpp |only KoulMde-3.0.0/KoulMde/src/GetGvec.cpp |only KoulMde-3.0.0/KoulMde/src/GetHvec.cpp |only KoulMde-3.0.0/KoulMde/src/GetLowerInterval.cpp |only KoulMde-3.0.0/KoulMde/src/GetPV.cpp |only KoulMde-3.0.0/KoulMde/src/GetUpperInterval.cpp |only KoulMde-3.0.0/KoulMde/src/GetXpm.cpp |only KoulMde-3.0.0/KoulMde/src/RevisedPMM.cpp |only KoulMde-3.1.0/KoulMde/DESCRIPTION | 17 +-- KoulMde-3.1.0/KoulMde/MD5 | 27 +---- KoulMde-3.1.0/KoulMde/NAMESPACE | 4 KoulMde-3.1.0/KoulMde/R/MdeFunc31.R |only KoulMde-3.1.0/KoulMde/R/RcppExports.R | 37 ------- KoulMde-3.1.0/KoulMde/man/Koul2StageMde.Rd | 28 +++-- KoulMde-3.1.0/KoulMde/man/KoulArMde.Rd | 44 +++++--- KoulMde-3.1.0/KoulMde/man/KoulLrMde.Rd | 48 ++++++--- KoulMde-3.1.0/KoulMde/src/FuncLib.cpp |only KoulMde-3.1.0/KoulMde/src/Makevars.win |only KoulMde-3.1.0/KoulMde/src/RcppExports.cpp | 130 ++++--------------------- 21 files changed, 128 insertions(+), 207 deletions(-)
Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) <doi:10.1126/science.28.706.49> for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi: 10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman [aut, cre],
Christopher Chang [ctb],
Xavi Puig [ctb],
Jan Wigginton [ctb]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between HardyWeinberg versions 1.5.9 dated 2017-12-16 and 1.6.1 dated 2018-05-29
DESCRIPTION | 16 ++-- MD5 | 22 +++--- R/HWChisq.R | 4 - R/HWMissing.R | 149 +++++++++++++++++++++++-------------------- R/recode.R | 4 - build/vignette.rds |binary inst/doc/HardyWeinberg.Rnw | 4 - inst/doc/HardyWeinberg.pdf |binary man/HWPerm.Rd | 4 - man/HardyWeinberg-package.Rd | 18 +---- man/recode.Rd | 6 + vignettes/HardyWeinberg.Rnw | 4 - 12 files changed, 120 insertions(+), 111 deletions(-)
Title: Generalized Order-Restricted Information Criterion
Description: Generalized Order-Restricted Information Criterion (GORIC) value for a set of hypotheses in multivariate linear models and generalised linear models.
Author: Daniel Gerhard [aut, cre],
Rebecca M. Kuiper [aut]
Maintainer: Daniel Gerhard <00gerhard@gmail.com>
Diff between goric versions 0.0-95 dated 2017-01-10 and 1.1-0 dated 2018-05-29
goric-0.0-95/goric/R/set_functions.r |only goric-0.0-95/goric/inst/doc/goric-vignette.R |only goric-0.0-95/goric/inst/doc/goric-vignette.Rmd |only goric-0.0-95/goric/inst/doc/goric-vignette.html |only goric-0.0-95/goric/man/goric-package.Rd |only goric-0.0-95/goric/man/ormodel_methods.Rd |only goric-0.0-95/goric/vignettes/goric-vignette.Rmd |only goric-1.1-0/goric/DESCRIPTION | 14 - goric-1.1-0/goric/MD5 | 57 ++--- goric-1.1-0/goric/R/constrMat.R |only goric-1.1-0/goric/R/constrSet.R |only goric-1.1-0/goric/R/data.R |only goric-1.1-0/goric/R/goric.R | 61 +++++ goric-1.1-0/goric/R/goric_penalty.R | 15 + goric-1.1-0/goric/R/orglm.R | 69 ++++++ goric-1.1-0/goric/R/orgls.R | 72 ++++++ goric-1.1-0/goric/R/orglsSet.R |only goric-1.1-0/goric/R/orlm.R | 107 +++++++++ goric-1.1-0/goric/R/orlmSet.R |only goric-1.1-0/goric/R/orlmcontrol.R | 13 + goric-1.1-0/goric/R/sim.R | 31 ++ goric-1.1-0/goric/build/vignette.rds |binary goric-1.1-0/goric/inst/doc/goric.R |only goric-1.1-0/goric/inst/doc/goric.Rmd |only goric-1.1-0/goric/inst/doc/goric.html |only goric-1.1-0/goric/man/constrMat.Rd | 72 +++--- goric-1.1-0/goric/man/constrSet.Rd | 76 +++--- goric-1.1-0/goric/man/goric.Rd | 181 +++++++--------- goric-1.1-0/goric/man/goric_penalty.Rd |only goric-1.1-0/goric/man/orglm.Rd | 253 +++++++---------------- goric-1.1-0/goric/man/orgls.Rd | 199 ++++++++---------- goric-1.1-0/goric/man/orglsSet.Rd | 95 +++----- goric-1.1-0/goric/man/orlm.Rd | 264 +++++++++++------------- goric-1.1-0/goric/man/orlmSet.Rd | 120 ++++------ goric-1.1-0/goric/man/orlmcontrol.Rd | 39 ++- goric-1.1-0/goric/man/sim.Rd | 92 ++++---- goric-1.1-0/goric/man/vinylidene.Rd | 41 +-- goric-1.1-0/goric/vignettes/goric.Rmd |only 38 files changed, 1032 insertions(+), 839 deletions(-)
Title: Affinity Propagation Clustering
Description: Implements Affinity Propagation clustering introduced by Frey and
Dueck (2007) <DOI:10.1126/science.1136800>. The algorithms are largely
analogous to the 'Matlab' code published by Frey and Dueck.
The package further provides leveraged affinity propagation and an
algorithm for exemplar-based agglomerative clustering that can also be
used to join clusters obtained from affinity propagation. Various
plotting functions are available for analyzing clustering results.
Author: Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier,
Nikola Kostic
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
Diff between apcluster versions 1.4.6 dated 2018-05-28 and 1.4.7 dated 2018-05-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/NEWS | 3 +++ inst/doc/apcluster.Rnw | 4 ++++ inst/doc/apcluster.pdf |binary src/aggExClusterC.cpp | 4 ++-- vignettes/apcluster.Rnw | 4 ++++ 7 files changed, 23 insertions(+), 12 deletions(-)
Title: Significant Zero Crossings
Description: Calculates and plots the SiZer map for scatterplot data. A
SiZer map is a way of examining when the p-th derivative of a
scatterplot-smoother is significantly negative, possibly zero or
significantly positive across a range of smoothing bandwidths.
Author: Derek Sonderegger [aut, cre]
Maintainer: Derek Sonderegger <derek.sonderegger@gmail.com>
Diff between SiZer versions 0.1-4 dated 2011-03-21 and 0.1-5 dated 2018-05-29
SiZer-0.1-4/SiZer/INDEX |only SiZer-0.1-5/SiZer/DESCRIPTION | 33 - SiZer-0.1-5/SiZer/MD5 |only SiZer-0.1-5/SiZer/NAMESPACE |only SiZer-0.1-5/SiZer/R/Arkansas.R |only SiZer-0.1-5/SiZer/R/SiZer.R | 124 ++++++ SiZer-0.1-5/SiZer/R/bent.cable.R | 77 +++- SiZer-0.1-5/SiZer/R/locally.weighted.polynomial.R | 145 +++++-- SiZer-0.1-5/SiZer/R/piecewise.linear.R | 301 +++++++++------- SiZer-0.1-5/SiZer/man/Arkansas.Rd | 47 +- SiZer-0.1-5/SiZer/man/SiZer.Rd | 108 ++--- SiZer-0.1-5/SiZer/man/bent.cable.Rd | 96 ++--- SiZer-0.1-5/SiZer/man/locally.weighted.polynomial.Rd | 119 +++--- SiZer-0.1-5/SiZer/man/logLik.PiecewiseLinear.Rd |only SiZer-0.1-5/SiZer/man/logLik.bent_cable.Rd |only SiZer-0.1-5/SiZer/man/piecewise.linear.Rd | 100 ++--- SiZer-0.1-5/SiZer/man/plot.LocallyWeightedPolynomial.Rd | 58 +-- SiZer-0.1-5/SiZer/man/plot.PiecewiseLinear.Rd |only SiZer-0.1-5/SiZer/man/plot.SiZer.Rd | 96 ++--- SiZer-0.1-5/SiZer/man/predict.PiecewiseLinear.Rd |only SiZer-0.1-5/SiZer/man/predict.bent_cable.Rd |only SiZer-0.1-5/SiZer/man/print.PiecewiseLinear.Rd |only 22 files changed, 791 insertions(+), 513 deletions(-)
Title: Interactive Q-Learning
Description: Estimate an optimal dynamic treatment regime using Interactive Q-learning.
Author: Kristin A. Linn, Eric B. Laber, Leonard A. Stefanski
Maintainer: Kristin A. Linn <klinn@pennmedicine.upenn.edu>
Diff between iqLearn versions 1.4 dated 2015-08-19 and 1.5 dated 2018-05-29
iqLearn-1.4/iqLearn/man/iqLearn-package.Rd |only iqLearn-1.5/iqLearn/DESCRIPTION | 10 +++++----- iqLearn-1.5/iqLearn/MD5 | 7 +++---- iqLearn-1.5/iqLearn/build/vignette.rds |binary iqLearn-1.5/iqLearn/inst/doc/iqLearn.pdf |binary 5 files changed, 8 insertions(+), 9 deletions(-)
Title: Normalizing Transformation Functions
Description: Estimate a suite of normalizing transformations, including
a new adaptation of a technique based on ranks which can guarantee
normally distributed transformed data if there are no ties: ordered
quantile normalization (ORQ). ORQ normalization combines a rank-mapping
approach with a shifted logit approximation that allows
the transformation to work on data outside the original domain. It is
also able to handle new data within the original domain via linear
interpolation. The package is built to estimate the best normalizing
transformation for a vector consistently and accurately. It implements
the Box-Cox transformation, the Yeo-Johnson transformation, three types
of Lambert WxF transformations, and the ordered quantile normalization
transformation.
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan-peterson@uiowa.edu>
Diff between bestNormalize versions 1.0.1 dated 2018-02-05 and 1.1.0 dated 2018-05-29
DESCRIPTION | 12 - MD5 | 50 ++--- NAMESPACE | 2 NEWS.md | 5 R/bestNormalize.R | 23 +- R/boxcox.R | 17 + R/lambert.R | 19 + R/orderNorm.R | 2 R/yeojohnson.R | 18 + README.md | 11 - inst/doc/bestNormalize.R | 38 +-- inst/doc/bestNormalize.Rmd | 47 ++-- inst/doc/bestNormalize.html | 348 +++++++++++++++++------------------- man/bestNormalize.Rd | 8 man/boxcox.Rd | 6 man/lambert.Rd | 6 man/orderNorm.Rd | 6 man/yeojohnson.Rd | 7 tests/testthat.R | 2 tests/testthat/test_bestNormalize.R | 96 +++++---- tests/testthat/test_binarize.R | 4 tests/testthat/test_boxcox.R | 36 +++ tests/testthat/test_lambert.R | 29 ++- tests/testthat/test_orderNorm.R | 4 tests/testthat/test_yeojohnson.R | 35 +++ vignettes/bestNormalize.Rmd | 47 ++-- 26 files changed, 492 insertions(+), 386 deletions(-)
Title: Ensemble Penalized Cox Regression for Survival Prediction
Description: The top-performing ensemble-based Penalized Cox Regression (ePCR) framework developed during the DREAM 9.5 mCRPC Prostate Cancer Challenge <https://www.synapse.org/ProstateCancerChallenge> presented in Guinney J, Wang T, Laajala TD, et al. (2017) <doi:10.1016/S1470-2045(16)30560-5> is provided here-in, together with the corresponding follow-up work. While initially aimed at modeling the most advanced stage of prostate cancer, metastatic Castration-Resistant Prostate Cancer (mCRPC), the modeling framework has subsequently been extended to cover also the non-metastatic form of advanced prostate cancer (CRPC). Readily fitted ensemble-based model S4-objects are provided, and a simulated example dataset based on a real-life cohort is provided from the Turku University Hospital, to illustrate the use of the package. Functionality of the ePCR methodology relies on constructing ensembles of strata in patient cohorts and averaging over them, with each ensemble member consisting of a highly optimized penalized/regularized Cox regression model. Various cross-validation and other modeling schema are provided for constructing novel model objects.
Author: Teemu Daniel Laajala <teelaa@utu.fi> [aut, cre], Mika Murtoj<e4>rvi <mianmu2@hotmail.com> [ctb]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between ePCR versions 0.9.9-4 dated 2017-12-21 and 0.9.9-6 dated 2018-05-29
ePCR-0.9.9-4/ePCR/inst/CITATION |only ePCR-0.9.9-6/ePCR/DESCRIPTION | 12 ++++++---- ePCR-0.9.9-6/ePCR/MD5 | 26 +++++++++++++--------- ePCR-0.9.9-6/ePCR/NEWS |only ePCR-0.9.9-6/ePCR/R/ext.R | 2 - ePCR-0.9.9-6/ePCR/R/int.R | 37 ++++++++++++++++++++++++++++++++ ePCR-0.9.9-6/ePCR/R/pep.R | 27 +++++++++++++++++------ ePCR-0.9.9-6/ePCR/R/psp.R | 5 +++- ePCR-0.9.9-6/ePCR/build |only ePCR-0.9.9-6/ePCR/data/TYKSSIMU.RData |binary ePCR-0.9.9-6/ePCR/data/ePCRmodels.RData |binary ePCR-0.9.9-6/ePCR/inst/doc |only ePCR-0.9.9-6/ePCR/man/PEP-methods.Rd | 6 +++-- ePCR-0.9.9-6/ePCR/man/meanrank.Rd | 2 - ePCR-0.9.9-6/ePCR/vignettes |only 15 files changed, 90 insertions(+), 27 deletions(-)
Title: Temporal Sensory Data Analysis
Description: Analysis and visualization of data from temporal sensory methods, including for temporal check-all-that-apply (TCATA) and temporal dominance of sensations (TDS).
Author: J. C. Castura [aut, cre]
Maintainer: J. C. Castura <jcastura@compusense.com>
Diff between tempR versions 0.9.9.14 dated 2018-05-20 and 0.9.9.15 dated 2018-05-29
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/tds.R | 5 ++++- 3 files changed, 9 insertions(+), 6 deletions(-)
Title: Statistical Methods and Models for Claims Reserving in General
Insurance
Description: Various statistical methods and models which are
typically used for the estimation of outstanding claims reserves
in general insurance, including those to estimate the claims
development result as required under Solvency II.
Author: Markus Gesmann [aut, cre],
Daniel Murphy [aut],
Yanwei (Wayne) Zhang [aut],
Alessandro Carrato [aut],
Giuseppe Crupi [aut],
Christophe Dutang [ctb],
Arnaud Lacoume [ctb],
Arthur Charpentier [ctb],
Mario Wuthrich [aut],
Fabio Concina [aut],
Vincent Goulet [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between ChainLadder versions 0.2.5 dated 2017-10-19 and 0.2.6 dated 2018-05-29
DESCRIPTION | 18 - MD5 | 30 - NAMESPACE | 16 - R/Triangles.R | 104 ++++-- README.md | 2 build/vignette.rds |binary demo/ChainLadder.R | 12 inst/doc/ChainLadder.R | 229 +++++++------- inst/doc/ChainLadder.Rnw | 722 +++++++++++++++++++++++----------------------- inst/doc/ChainLadder.pdf |binary inst/doc/NEWS.Rmd | 5 inst/doc/NEWS.html | 14 man/Triangles.Rd | 104 ++++-- vignettes/ChainLadder.Rnw | 722 +++++++++++++++++++++++----------------------- vignettes/ChainLadder.bib | 15 vignettes/NEWS.Rmd | 5 16 files changed, 1096 insertions(+), 902 deletions(-)
Title: False Discovery Control Procedure Integrating the Prior
Structure Information
Description: Perform more powerful false discovery control (FDR) for microbiome data, taking into account the prior phylogenetic relationship among bacteria species. As a general methodology, it is applicable to any type of (genomic) data with prior structure information.
Author: Jun Chen
Maintainer: Jun Chen <chen.jun2@mayo.edu>
Diff between StructFDR versions 1.2 dated 2017-04-13 and 1.3 dated 2018-05-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/StructFDR.R | 8 ++++++-- man/MicrobiomeSeqTreeFDR.Rd | 8 +++++--- man/StructFDR.Rd | 5 +++-- man/TreeFDR.Rd | 6 +++--- 6 files changed, 26 insertions(+), 19 deletions(-)
Title: Sensitivity Analysis of Ordinary Differential Equations
Description: Performs sensitivity analysis in ordinary differential equation (ode) models.
The package utilize the ode interface from 'deSolve' and connects it with the
sensitivity analysis from 'sensitivity'. Additionally we add a method to
run the sensitivity analysis on variables with class 'ODEnetwork'. A detailed
plotting function provides outputs on the calculations.
The method is described by Weber, Theers, Surmann, Ligges, and Weihs (2018) <doi:10.17877/DE290R-18874>.
Author: Frank Weber [aut],
Stefan Theers [aut],
Dirk Surmann [ctb, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <surmann@statistik.tu-dortmund.de>
Diff between ODEsensitivity versions 1.1.0 dated 2018-05-23 and 1.1.1 dated 2018-05-29
DESCRIPTION | 13 +++++---- MD5 | 22 ++++++++-------- NEWS.md | 3 ++ R/ODEmorris.default.R | 4 +-- R/ODEsensitivity-package.R | 6 +++- R/ODEsobol.default.R | 5 ++- R/tdcc.R | 56 +++++++++++++++++++++++-------------------- inst/doc/ODEsensitivity.html | 4 +-- man/ODEmorris.default.Rd | 4 +-- man/ODEsobol.default.Rd | 5 ++- man/tdcc.Rd | 30 +++++++++++++---------- tests/testthat/Rplots.pdf |binary 12 files changed, 85 insertions(+), 67 deletions(-)
More information about ODEsensitivity at CRAN
Permanent link
Title: Generation of IRT Response Patterns under Computerized Adaptive
Testing
Description: Provides routines for the generation of response patterns under unidimensional dichotomous and polytomous computerized adaptive testing (CAT) framework. It holds many standard functions to estimate ability, select the first item(s) to administer and optimally select the next item, as well as several stopping rules. Options to control for item exposure and content balancing are also available (Magis and Barrada (2017) <doi:10.18637/jss.v076.c01>).
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@uliege.be>
Diff between catR versions 3.13 dated 2017-08-31 and 3.14 dated 2018-05-29
DESCRIPTION | 12 +-- MD5 | 70 +++++++++--------- NAMESPACE | 3 NEWS | 62 ++++++++++++++++ R/fullDist.R |only R/randomCAT.R | 166 +++++++++++++++++++++++++++++++-------------- R/semTheta.R | 162 ++++++++++++++++++++++++++++++------------- R/simulateRespondents.R | 6 + R/testList.R | 36 ++++++--- R/thetaEst.R | 70 +++++++++++++++--- build/partial.rdb |binary man/EPV.Rd | 4 - man/GDI.Rd | 4 - man/Ii.Rd | 4 - man/Ji.Rd | 4 - man/KL.Rd | 4 - man/MEI.Rd | 4 - man/MWI.Rd | 4 - man/OIi.Rd | 4 - man/Pi.Rd | 4 - man/breakBank.Rd | 4 - man/checkStopRule.Rd | 4 - man/eapEst.Rd | 4 - man/eapSem.Rd | 6 - man/fullDist.Rd |only man/genDichoMatrix.Rd | 4 - man/genPattern.Rd | 4 - man/genPolyMatrix.Rd | 4 - man/integrate.catR.Rd | 10 -- man/nextItem.Rd | 10 +- man/randomCAT.Rd | 71 ++++++++++++------- man/semTheta.Rd | 110 +++++++++++++++++++++++++---- man/simulateRespondents.Rd | 29 ++----- man/startItems.Rd | 14 +-- man/test.cbList.Rd | 4 - man/testList.Rd | 5 - man/thetaEst.Rd | 42 ++++++++--- 37 files changed, 649 insertions(+), 299 deletions(-)
Title: Analysis of Growth Data
Description: Tools for the analysis of growth data: to extract an
LMS table from a gamlss object, to calculate the standard
deviation scores and its inverse, and to superpose two wormplots
from different models. The package contains a some varieties of
reference tables, especially for The Netherlands.
Author: Stef van Buuren <stef.vanbuuren@tno.nl>
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between AGD versions 0.35 dated 2015-05-28 and 0.39 dated 2018-05-29
AGD-0.35/AGD/R/zzz.R |only AGD-0.39/AGD/DESCRIPTION | 20 AGD-0.39/AGD/MD5 | 38 - AGD-0.39/AGD/NAMESPACE | 56 + AGD-0.39/AGD/R/AGD-package.R | 439 ++++++------ AGD-0.39/AGD/R/agd.r | 1055 +++++++++++++++--------------- AGD-0.39/AGD/R/extractLMS.r | 369 +++++----- AGD-0.39/AGD/R/wp.twin.r | 1266 ++++++++++++++++++------------------- AGD-0.39/AGD/data/who.hdc.rda |only AGD-0.39/AGD/inst/CITATION | 32 AGD-0.39/AGD/inst/NEWS | 125 +-- AGD-0.39/AGD/man/References-CDC.Rd | 9 AGD-0.39/AGD/man/References-NL3.Rd | 5 AGD-0.39/AGD/man/References-NL4.Rd | 19 AGD-0.39/AGD/man/References-WHO.Rd | 21 AGD-0.39/AGD/man/ageGrid.Rd | 6 AGD-0.39/AGD/man/boys7482.Rd | 19 AGD-0.39/AGD/man/extractLMS.Rd | 8 AGD-0.39/AGD/man/wp.twin.Rd | 12 AGD-0.39/AGD/man/y2z.Rd | 41 - AGD-0.39/AGD/man/z2y.Rd | 33 21 files changed, 1813 insertions(+), 1760 deletions(-)
Title: Resistome Predicter
Description: Predicts Escherichia coli's resistome for candidate drug. It utilizes two algorithms viz. deterministic model and stochastic model (manuscript under preparation) for the prediction of drug class. Once the drug class is predicted, the resistome is fetched from the database for the predicted class.
Author: Saurav Bhaskar Saha, Vipul Gupta, Pramod Wasudeo Ramteke
Maintainer: Saurav Bhaskar Saha <saurav.saha@shiats.edu.in>
Diff between uCAREChemSuiteCLI versions 0.1.0 dated 2018-05-18 and 0.1.1 dated 2018-05-29
DESCRIPTION | 10 - LICENSE | 2 MD5 | 7 - R/uCAREChemSuiteCLI.R | 278 ++++++++++++++++++++++++++++---------------------- README.md |only 5 files changed, 169 insertions(+), 128 deletions(-)
More information about uCAREChemSuiteCLI at CRAN
Permanent link
Title: Time Series from S-PLUS
Description: A collection of classes and methods for working with time series.
The code was originally available in S-PLUS.
Author: TIBCO Software Inc.
Maintainer: Stephen Kaluzny <skaluzny@tibco.com>
Diff between splusTimeSeries versions 1.5.0-74 dated 2016-05-03 and 1.5.0-75 dated 2018-05-29
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 6 +++--- NAMESPACE | 1 - 4 files changed, 8 insertions(+), 9 deletions(-)
More information about splusTimeSeries at CRAN
Permanent link
Title: Multi-States Semi-Markov Models
Description: Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model. Reference: A. Krol and P. Saint-Pierre (2015) <doi:10.18637/jss.v066.i06>.
Author: Agnieszka Listwon-Krol, Philippe Saint-Pierre
Maintainer: Agnieszka Listwon-Krol <krol@lunenfeld.ca>
Diff between SemiMarkov versions 1.4.3 dated 2016-01-19 and 1.4.4 dated 2018-05-29
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/SemiMarkov.r | 20 ++++++++++---------- man/hazard.Rd | 2 +- man/plot.hazard.Rd | 2 +- man/semiMarkov.Rd | 2 +- 6 files changed, 24 insertions(+), 24 deletions(-)
Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high
dimensional data. Ensembles of classification, regression, survival and
probability prediction trees are supported. Data from genome-wide association
studies can be analyzed efficiently. In addition to data frames, datasets of
class 'gwaa.data' (R package 'GenABEL') and 'dgCMatrix' (R package 'Matrix')
can be directly analyzed.
Author: Marvin N. Wright [aut, cre], Stefan Wager [ctb], Philipp Probst [ctb]
Maintainer: Marvin N. Wright <cran@wrig.de>
Diff between ranger versions 0.9.0 dated 2018-01-09 and 0.10.0 dated 2018-05-29
ranger-0.10.0/ranger/DESCRIPTION | 10 ranger-0.10.0/ranger/MD5 | 117 ++-- ranger-0.10.0/ranger/NEWS | 11 ranger-0.10.0/ranger/R/RcppExports.R | 4 ranger-0.10.0/ranger/R/importance.R | 3 ranger-0.10.0/ranger/R/infinitesimalJackknife.R | 2 ranger-0.10.0/ranger/R/predict.R | 15 ranger-0.10.0/ranger/R/print.R | 6 ranger-0.10.0/ranger/R/ranger.R | 153 ++++- ranger-0.10.0/ranger/R/treeInfo.R | 6 ranger-0.10.0/ranger/R/utility.R |only ranger-0.10.0/ranger/inst/include/ranger.h | 3 ranger-0.10.0/ranger/man/ranger.Rd | 41 - ranger-0.10.0/ranger/man/treeInfo.Rd | 2 ranger-0.10.0/ranger/src/Data.cpp | 117 ++-- ranger-0.10.0/ranger/src/Data.h | 104 ++- ranger-0.10.0/ranger/src/DataChar.cpp | 47 - ranger-0.10.0/ranger/src/DataChar.h | 61 -- ranger-0.10.0/ranger/src/DataDouble.h | 70 +- ranger-0.10.0/ranger/src/DataFloat.cpp | 46 - ranger-0.10.0/ranger/src/DataFloat.h | 67 +- ranger-0.10.0/ranger/src/DataRcpp.h |only ranger-0.10.0/ranger/src/DataSparse.cpp | 18 ranger-0.10.0/ranger/src/DataSparse.h | 38 - ranger-0.10.0/ranger/src/Forest.cpp | 263 +++++----- ranger-0.10.0/ranger/src/Forest.h | 89 +-- ranger-0.10.0/ranger/src/ForestClassification.cpp | 97 ++- ranger-0.10.0/ranger/src/ForestClassification.h | 72 +- ranger-0.10.0/ranger/src/ForestProbability.cpp | 107 ++-- ranger-0.10.0/ranger/src/ForestProbability.h | 114 +--- ranger-0.10.0/ranger/src/ForestRegression.cpp | 76 +- ranger-0.10.0/ranger/src/ForestRegression.h | 65 +- ranger-0.10.0/ranger/src/ForestSurvival.cpp | 102 ++- ranger-0.10.0/ranger/src/ForestSurvival.h | 76 +- ranger-0.10.0/ranger/src/RcppExports.cpp | 16 ranger-0.10.0/ranger/src/Tree.cpp | 88 +-- ranger-0.10.0/ranger/src/Tree.h | 67 +- ranger-0.10.0/ranger/src/TreeClassification.cpp | 249 +++++---- ranger-0.10.0/ranger/src/TreeClassification.h | 109 ++-- ranger-0.10.0/ranger/src/TreeProbability.cpp | 234 +++++--- ranger-0.10.0/ranger/src/TreeProbability.h | 112 ++-- ranger-0.10.0/ranger/src/TreeRegression.cpp | 130 ++-- ranger-0.10.0/ranger/src/TreeRegression.h | 78 +- ranger-0.10.0/ranger/src/TreeSurvival.cpp | 117 +--- ranger-0.10.0/ranger/src/TreeSurvival.h | 77 +- ranger-0.10.0/ranger/src/globals.h | 38 - ranger-0.10.0/ranger/src/rangerCpp.cpp | 143 +++-- ranger-0.10.0/ranger/src/utility.cpp | 108 ++-- ranger-0.10.0/ranger/src/utility.h | 134 +++-- ranger-0.10.0/ranger/src/utilityRcpp.cpp | 2 ranger-0.10.0/ranger/tests/testthat/test_classweights.R |only ranger-0.10.0/ranger/tests/testthat/test_genabel.R |only ranger-0.10.0/ranger/tests/testthat/test_importance_pvalues.R | 11 ranger-0.10.0/ranger/tests/testthat/test_jackknife.R | 7 ranger-0.10.0/ranger/tests/testthat/test_maxstat.R | 22 ranger-0.10.0/ranger/tests/testthat/test_probability.R | 13 ranger-0.10.0/ranger/tests/testthat/test_quantreg.R | 6 ranger-0.10.0/ranger/tests/testthat/test_ranger.R | 92 ++- ranger-0.10.0/ranger/tests/testthat/test_sparse.R | 20 ranger-0.10.0/ranger/tests/testthat/test_treeInfo.R | 8 ranger-0.10.0/ranger/tests/testthat/test_unordered.R | 46 + ranger-0.9.0/ranger/src/DataDouble.cpp |only 62 files changed, 2148 insertions(+), 1781 deletions(-)
Title: Interface to 'D3' Visualizations
Description: Suite of tools for using 'D3', a library for producing dynamic, interactive data
visualizations. Supports translating objects into 'D3' friendly data structures, rendering
'D3' scripts, publishing 'D3' visualizations, incorporating 'D3' in R Markdown, creating
interactive 'D3' applications with Shiny, and distributing 'D3' based 'htmlwidgets' in R
packages.
Author: Javier Luraschi [aut, cre],
JJ Allaire [aut],
Mike Bostock [ctb, cph] (d3.js library, http://d3js.org),
RStudio [cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between r2d3 versions 0.2.0 dated 2018-05-29 and 0.2.1 dated 2018-05-29
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/publish.R | 5 +++++ inst/doc/visualization_options.html | 4 ++-- inst/htmlwidgets/lib/r2d3/r2d3-render.js | 2 ++ man/save_d3_html.Rd | 4 ++++ tests/testthat/test-knit.R | 3 +++ tests/testthat/test-save.R | 3 +++ 9 files changed, 35 insertions(+), 13 deletions(-)
Title: Tools at the Intersection of 'purrr' and 'dplyr'
Description: Some functions at the intersection of 'dplyr' and 'purrr' that
formerly lived in 'purrr'.
Author: Lionel Henry [aut, cre],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between purrrlyr versions 0.0.2 dated 2017-05-13 and 0.0.3 dated 2018-05-29
DESCRIPTION | 19 +++++++++---------- MD5 | 16 ++++++++-------- NEWS.md | 20 ++++++++++++++++++-- R/rows.R | 2 +- R/utils.R | 2 +- README.md | 10 +++++++++- man/by_row.Rd | 4 +++- man/dmap.Rd | 2 +- src/utils.cpp | 26 ++++++++++++++++++++------ 9 files changed, 70 insertions(+), 31 deletions(-)
Title: Functional Programming Tools
Description: A complete and consistent functional programming toolkit for R.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between purrr versions 0.2.4 dated 2017-10-18 and 0.2.5 dated 2018-05-29
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NEWS.md | 7 ++++++- build/vignette.rds |binary inst/doc/other-langs.html | 2 +- src/extract.c | 19 +++++-------------- tests/testthat/test-flatten.R | 2 +- 7 files changed, 24 insertions(+), 27 deletions(-)
Title: Finding Rhythms Using Extended Circadian Harmonic Oscillators
(ECHO)
Description: Provides a function (echo_find()) designed to find rhythms
from data using extended harmonic oscillators. For more information,
see H. De los Santos et al. (2017) <doi:10.1145/3107411.3107420> .
Author: Hannah De los Santos [aut, cre],
Emily Collins [aut],
Jonathan Shewchuk [ctb],
E.F. Harding [ctb],
Kristin Bennett [aut],
Jennifer Hurley [aut]
Maintainer: Hannah De los Santos <delosh@rpi.edu>
Diff between echo.find versions 1.0.0 dated 2018-05-27 and 1.0.1 dated 2018-05-29
echo.find-1.0.0/echo.find/man/alt_form.Rd |only echo.find-1.0.0/echo.find/man/avg_all_rep.Rd |only echo.find-1.0.0/echo.find/man/calc_tau_and_p_jtk.Rd |only echo.find-1.0.0/echo.find/man/calc_var.Rd |only echo.find-1.0.0/echo.find/man/calc_weights.Rd |only echo.find-1.0.0/echo.find/man/calculate_param.Rd |only echo.find-1.0.0/echo.find/man/de_linear_trend_all.Rd |only echo.find-1.0.0/echo.find/man/expansion.sum.Rd |only echo.find-1.0.0/echo.find/man/fast.two.sum.Rd |only echo.find-1.0.0/echo.find/man/genes_unexpressed_all.Rd |only echo.find-1.0.0/echo.find/man/is_deviating.Rd |only echo.find-1.0.0/echo.find/man/jtkdist.Rd |only echo.find-1.0.0/echo.find/man/normalize_all.Rd |only echo.find-1.0.0/echo.find/man/smoothing_all_tied.Rd |only echo.find-1.0.0/echo.find/man/smoothing_all_untied.Rd |only echo.find-1.0.0/echo.find/man/two.sum.Rd |only echo.find-1.0.1/echo.find/DESCRIPTION | 6 echo.find-1.0.1/echo.find/MD5 | 25 echo.find-1.0.1/echo.find/R/echo_package_functions.R | 979 ----------------- echo.find-1.0.1/echo.find/R/echo_utils.R |only echo.find-1.0.1/echo.find/inst/CITATION | 4 echo.find-1.0.1/echo.find/inst/doc/echo-vignette.html | 4 22 files changed, 13 insertions(+), 1005 deletions(-)
Title: Linear and Nonlinear Methods for Analyzing Dendroclimatological
Data
Description: Provides novel dendroclimatological methods, primarily used by the
Tree-ring research community. There are two core functions. The first one is
daily_response(), which finds the optimal sequence of days that are related
to one or more tree-ring proxy records. The second one is compare_methods(),
which effectively compares several linear and nonlinear regression algorithms.
Author: Jernej Jevsenak [aut, cre], Tom Levanic [ctb]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between dendroTools versions 0.0.8 dated 2018-05-20 and 0.0.9 dated 2018-05-29
DESCRIPTION | 6 - MD5 | 18 +-- NEWS.md | 7 - R/calculate_metrics.R | 54 +++++++--- R/compare_methods.R | 143 ++++++++++++++++++---------- R/daily_response.R | 7 + inst/doc/Examples_daily_response.html | 42 ++++---- inst/doc/compare_methods_vignette.html | 163 ++++++++++++++------------------- man/calculate_metrics.Rd | 15 ++- man/compare_methods.Rd | 2 10 files changed, 258 insertions(+), 199 deletions(-)
Title: A Class for Vectors of 1-Bit Booleans
Description: True boolean datatype (no NAs),
coercion from and to logicals, integers and integer subscripts;
fast boolean operators and fast summary statistics.
With 'bit' vectors you can store true binary booleans {FALSE,TRUE} at the
expense of 1 bit only, on a 32 bit architecture this means factor 32 less
RAM and ~ factor 32 more speed on boolean operations. Due to overhead of
R calls, actual speed gain depends on the size of the vector: expect gains
for vectors of size > 10000 elements. Even for one-time boolean operations
it can pay-off to convert to bit, the pay-off is obvious, when such
components are used more than once.
Reading from and writing to bit is approximately as fast as accessing
standard logicals - mostly due to R's time for memory allocation. The package
allows to work with pre-allocated memory for return values by calling .Call()
directly: when evaluating the speed of C-access with pre-allocated vector
memory, coping from bit to logical requires only 70% of the time for copying
from logical to logical; and copying from logical to bit comes at a
performance penalty of 150%. the package now contains further classes for
representing logical selections: 'bitwhich' for very skewed selections and
'ri' for selecting ranges of values for chunked processing. All three index
classes can be used for subsetting 'ff' objects (ff-2.1-0 and higher).
Author: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Diff between bit versions 1.1-13 dated 2018-05-15 and 1.1-14 dated 2018-05-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 9 +++++++++ src/bit.c | 4 ++-- 4 files changed, 17 insertions(+), 8 deletions(-)
Title: Semiparametric Bayesian Gaussian Copula Estimation and
Imputation
Description: Estimation and inference for parameters in a Gaussian copula model,
treating the univariate marginal distributions as nuisance
parameters as described in Hoff (2007) <doi:10.1214/07-AOAS107>.
This package also provides a
semiparametric imputation procedure for missing multivariate
data.
Author: Peter Hoff
Maintainer: Peter Hoff <peter.hoff@duke.edu>
Diff between sbgcop versions 0.975 dated 2010-03-09 and 0.980 dated 2018-05-29
sbgcop-0.975/sbgcop/man/sbgcop.package.Rd |only sbgcop-0.980/sbgcop/DESCRIPTION | 23 +++--- sbgcop-0.980/sbgcop/MD5 |only sbgcop-0.980/sbgcop/NAMESPACE |only sbgcop-0.980/sbgcop/R/ldmvnorm.R | 20 ++++++ sbgcop-0.980/sbgcop/R/plotci.sA.R | 16 ++++ sbgcop-0.980/sbgcop/R/qM.sM.R | 16 ++++ sbgcop-0.980/sbgcop/R/rwish.R | 13 +++ sbgcop-0.980/sbgcop/R/sR.sC.R | 20 ++++++ sbgcop-0.980/sbgcop/R/sbgcop-package.R |only sbgcop-0.980/sbgcop/R/sbgcop.mcmc.R | 42 ++++++++++++ sbgcop-0.980/sbgcop/man/ldmvnorm.Rd | 39 ++++++----- sbgcop-0.980/sbgcop/man/plotci.sA.Rd | 31 ++++++--- sbgcop-0.980/sbgcop/man/qM.sM.Rd | 29 +++++--- sbgcop-0.980/sbgcop/man/rwish.Rd | 37 ++++++----- sbgcop-0.980/sbgcop/man/sR.sC.Rd | 35 ++++++---- sbgcop-0.980/sbgcop/man/sbgcop-package.Rd |only sbgcop-0.980/sbgcop/man/sbgcop.mcmc.Rd | 99 ++++++++++++++++-------------- 18 files changed, 299 insertions(+), 121 deletions(-)
Title: Algorithms using Alternating Direction Method of Multipliers
Description: Provides algorithms to solve popular optimization problems in statistics such as regression or denoising based on Alternating Direction Method of Multipliers (ADMM).
See Boyd et al (2010) <doi:10.1561/2200000016> for complete introduction to the method.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>),
Xiaozhi Zhu [aut]
Maintainer: Kisung You <kyou@nd.edu>
Diff between ADMM versions 0.2.2 dated 2018-02-25 and 0.3.0 dated 2018-05-29
DESCRIPTION | 8 ++-- MD5 | 25 +++++++------- NAMESPACE | 7 ++++ R/RcppExports.R | 6 +++ R/admm-package.R | 3 + R/admm.lad.R | 2 + R/admm.lasso.R | 21 ++++++++++++ R/auxiliary.R | 84 ++++++++++++++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary man/LAD.Rd | 2 + man/LASSO.Rd | 2 + src/RcppExports.cpp | 16 +++++++++ src/admm_auxiliary.cpp |only src/admm_lasso.cpp | 2 - 14 files changed, 160 insertions(+), 18 deletions(-)
Title: Generalized Survival Models
Description: R implementation of generalized survival models, where g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects. This also includes a smooth implementation of accelerated failure time models.
Author: Mark Clements [aut, cre],
Xing-Rong Liu [aut],
Paul Lambert [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.4.1 dated 2017-09-20 and 1.4.2 dated 2018-05-29
rstpm2-1.4.1/rstpm2/man/predictnl.default.Rd |only rstpm2-1.4.2/rstpm2/DESCRIPTION | 14 rstpm2-1.4.2/rstpm2/MD5 | 72 +- rstpm2-1.4.2/rstpm2/NAMESPACE | 21 rstpm2-1.4.2/rstpm2/NEWS.md |only rstpm2-1.4.2/rstpm2/R/aft.R | 55 - rstpm2-1.4.2/rstpm2/R/gaussquad.R |only rstpm2-1.4.2/rstpm2/R/pm2-3.R | 735 ++++++++++----------- rstpm2-1.4.2/rstpm2/build/vignette.rds |binary rstpm2-1.4.2/rstpm2/inst/aft.log | 75 +- rstpm2-1.4.2/rstpm2/inst/aft.pdf |binary rstpm2-1.4.2/rstpm2/inst/doc/Introduction.R | 101 ++ rstpm2-1.4.2/rstpm2/inst/doc/Introduction.Rnw | 275 +++++++ rstpm2-1.4.2/rstpm2/inst/doc/Introduction.pdf |binary rstpm2-1.4.2/rstpm2/inst/doc/predictnl.R |only rstpm2-1.4.2/rstpm2/inst/doc/predictnl.Rnw |only rstpm2-1.4.2/rstpm2/inst/doc/predictnl.pdf |only rstpm2-1.4.2/rstpm2/inst/test.do | 17 rstpm2-1.4.2/rstpm2/inst/working_code.R | 153 ++++ rstpm2-1.4.2/rstpm2/man/aft.Rd | 5 rstpm2-1.4.2/rstpm2/man/eform.Rd |only rstpm2-1.4.2/rstpm2/man/lines.Rd |only rstpm2-1.4.2/rstpm2/man/plot-methods.Rd | 48 - rstpm2-1.4.2/rstpm2/man/predict-methods.Rd | 30 rstpm2-1.4.2/rstpm2/man/predictnl-methods.Rd | 8 rstpm2-1.4.2/rstpm2/man/predictnl.Rd | 134 +++ rstpm2-1.4.2/rstpm2/man/pstpm2-class.Rd | 4 rstpm2-1.4.2/rstpm2/man/pstpm2.Rd | 10 rstpm2-1.4.2/rstpm2/man/stpm2-class.Rd | 4 rstpm2-1.4.2/rstpm2/man/stpm2.Rd | 9 rstpm2-1.4.2/rstpm2/src/c_optim.cpp | 2 rstpm2-1.4.2/rstpm2/src/gaussq2.f |only rstpm2-1.4.2/rstpm2/src/package_init.c | 10 rstpm2-1.4.2/rstpm2/src/test-nmmin.cpp | 51 + rstpm2-1.4.2/rstpm2/vignettes/Introduction-007.pdf |only rstpm2-1.4.2/rstpm2/vignettes/Introduction-008.pdf |only rstpm2-1.4.2/rstpm2/vignettes/Introduction.Rnw | 275 +++++++ rstpm2-1.4.2/rstpm2/vignettes/auto/Introduction.el | 27 rstpm2-1.4.2/rstpm2/vignettes/auto/Sweave.el |only rstpm2-1.4.2/rstpm2/vignettes/auto/predictnl.el |only rstpm2-1.4.2/rstpm2/vignettes/auto/test.el |only rstpm2-1.4.2/rstpm2/vignettes/enumitem.sty |only rstpm2-1.4.2/rstpm2/vignettes/predictnl-003.pdf |only rstpm2-1.4.2/rstpm2/vignettes/predictnl-004.pdf |only rstpm2-1.4.2/rstpm2/vignettes/predictnl-005.pdf |only rstpm2-1.4.2/rstpm2/vignettes/predictnl-006.pdf |only rstpm2-1.4.2/rstpm2/vignettes/predictnl.Rnw |only 47 files changed, 1551 insertions(+), 584 deletions(-)
Title: Project Future Case Incidence
Description: Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R0 in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>.
Author: Thibaut Jombart [aut, cre],
Pierre Nouvellet [aut]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between projections versions 0.0.1 dated 2017-12-06 and 0.1.1 dated 2018-05-29
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- NEWS.md | 17 ++++++++++++ R/internals.R | 10 +++++++ R/project.R | 58 ++++++++++++++++++++++++++++++------------ man/project.Rd | 9 +++++- tests/testthat/test-project.R | 3 -- 7 files changed, 87 insertions(+), 28 deletions(-)
Title: Factor Adjusted Robust Multiple Testing
Description: Performs robust multiple testing for means in the presence of known and unknown latent factors. It implements a robust procedure to estimate distribution parameters using the Huber's loss function and accounts for strong dependence among coordinates via an approximate factor model. This method is particularly suitable for high dimensional data when there are many variables but only a small number of observations available. Moreover, the method is tailored to cases when the underlying distribution deviates from Gaussian, which is commonly assumed in the literature. Besides the results of hypotheses testing, the estimated underlying factors and diagnostic plots are also output. Multiple comparison correction is done after estimating the proportion of true null hypotheses using the method in Storey (2015) <https://github.com/jdstorey/qvalue>. For detailed description of methods and further references, see the papers on the 'FarmTest' method: Fan et al. (2017) <arXiv:1711.05386> and Zhou et al. (2017) <arXiv:1711.05381>.
Author: Koushiki Bose [aut, cre],
Yuan Ke [aut],
Wen-xin Zhou [aut]
Maintainer: Koushiki Bose <koush.bose@gmail.com>
Diff between FarmTest versions 1.0.2 dated 2018-03-14 and 1.0.3 dated 2018-05-29
DESCRIPTION | 12 MD5 | 36 +- R/FarmTest-package.r | 5 R/RcppExports.R | 16 + R/load.R | 531 +++++++++++++++++++++++++++++----------- inst/doc/farmtest-vignette.R | 31 +- inst/doc/farmtest-vignette.Rmd | 107 +++++--- inst/doc/farmtest-vignette.html | 111 ++++---- man/FarmTest.Rd | 6 man/farm.cov.Rd | 15 + man/farm.mean.Rd | 15 + man/farm.scree.Rd | 23 + man/farm.test.Rd | 50 ++- man/plot.farm.scree.Rd | 5 man/print.farm.scree.Rd | 2 man/print.farm.test.Rd | 4 src/Cfunctions.cpp | 151 ++++++++++- src/RcppExports.cpp | 54 ++++ vignettes/farmtest-vignette.Rmd | 107 +++++--- 19 files changed, 963 insertions(+), 318 deletions(-)
Title: Create Interactive Chart with the JavaScript 'Billboard' Library
Description: Provides an 'htmlwidgets' interface to 'billboard.js',
a re-usable easy interface JavaScript chart library, based on D3 v4+.
Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts.
All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
NAVER Corp [cph] (billboard library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between billboarder versions 0.2.1 dated 2018-01-28 and 0.2.2 dated 2018-05-29
billboarder-0.2.1/billboarder/inst/htmlwidgets/lib/D3-4.10.0 |only billboarder-0.2.1/billboarder/inst/htmlwidgets/lib/D3-4.12.2 |only billboarder-0.2.1/billboarder/inst/htmlwidgets/lib/billboard-1.0.1 |only billboarder-0.2.1/billboarder/inst/htmlwidgets/lib/billboard-1.1.0 |only billboarder-0.2.1/billboarder/inst/htmlwidgets/lib/billboard-1.1.1 |only billboarder-0.2.1/billboarder/inst/htmlwidgets/lib/billboard-1.2.0 |only billboarder-0.2.2/billboarder/DESCRIPTION | 6 billboarder-0.2.2/billboarder/MD5 | 53 ++--- billboarder-0.2.2/billboarder/NAMESPACE | 1 billboarder-0.2.2/billboarder/NEWS.md | 8 billboarder-0.2.2/billboarder/R/bb_helpers.R | 67 +++++- billboarder-0.2.2/billboarder/R/bb_utils.R | 16 + billboarder-0.2.2/billboarder/R/billboard-mapping.R | 47 +++- billboarder-0.2.2/billboarder/README.md | 66 ++++-- billboarder-0.2.2/billboarder/build/vignette.rds |binary billboarder-0.2.2/billboarder/inst/doc/billboarder-intro.html | 100 +++++----- billboarder-0.2.2/billboarder/inst/doc/billboarder-mapping.html | 48 ++-- billboarder-0.2.2/billboarder/inst/doc/billboarder-options.html | 88 ++++---- billboarder-0.2.2/billboarder/inst/htmlwidgets/billboarder.js | 40 ++-- billboarder-0.2.2/billboarder/inst/htmlwidgets/billboarder.yaml | 10 - billboarder-0.2.2/billboarder/inst/htmlwidgets/lib/D3-5.1.0 |only billboarder-0.2.2/billboarder/inst/htmlwidgets/lib/billboard-1.3.0 |only billboarder-0.2.2/billboarder/inst/htmlwidgets/lib/billboard-1.4.1 |only billboarder-0.2.2/billboarder/inst/img/linechart_range.png |only billboarder-0.2.2/billboarder/inst/img/scatter_bubble.png |only billboarder-0.2.2/billboarder/man/bb_barchart.Rd | 4 billboarder-0.2.2/billboarder/man/bb_linechart.Rd | 34 +++ billboarder-0.2.2/billboarder/man/bb_scatterplot.Rd | 10 + billboarder-0.2.2/billboarder/man/bb_svg.Rd |only 29 files changed, 382 insertions(+), 216 deletions(-)
Title: Robust Estimation for Compositional Data
Description: Methods for analysis of compositional data including robust
methods, imputation, methods to replace rounded zeros, (robust) outlier
detection for compositional data, (robust) principal component analysis for
compositional data, (robust) factor analysis for compositional data, (robust)
discriminant analysis for compositional data (Fisher rule), robust regression
with compositional predictors and (robust) Anderson-Darling normality tests for
compositional data as well as popular log-ratio transformations (addLR, cenLR,
isomLR, and their inverse transformations). In addition, visualisation and
diagnostic tools are implemented as well as high and low-level plot functions
for the ternary diagram.
Author: Matthias Templ [aut, cre],
Karel Hron [aut],
Peter Filzmoser [aut],
Petra Kynclova [ctb],
Jan Walach [ctb],
Veronika Pintar [ctb],
Jiajia Chen [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between robCompositions versions 2.0.7 dated 2018-04-08 and 2.0.8 dated 2018-05-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 3 +++ inst/doc/imputation.R | 3 --- inst/doc/imputation.Rnw | 12 ++++++------ inst/doc/imputation.pdf |binary inst/doc/robCompositions-overview.pdf |binary vignettes/imputation.Rnw | 12 ++++++------ 8 files changed, 26 insertions(+), 26 deletions(-)
More information about robCompositions at CRAN
Permanent link
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.35 dated 2018-02-02 and 5.36 dated 2018-05-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/anova.R | 12 ++++++------ inst/ChangeLog | 7 ++++++- man/anova.rq.Rd | 6 +++--- 5 files changed, 22 insertions(+), 17 deletions(-)
Title: Simulation of Synthetic Populations for Survey Data Considering
Auxiliary Information
Description: Tools and methods to simulate populations for surveys based
on auxiliary data. The tools include model-based methods, calibration and
combinatorial optimization algorithms. The package was developed with support of
the International Household Survey Network, DFID Trust Fund TF011722 and funds
from the World bank.
Author: Bernhard Meindl, Matthias Templ, Andreas Alfons, Alexander Kowarik and
with contributions from Mathieu Ribatet, Johannes Gussenbauer and Gregor De Cillia
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between simPop versions 1.1.0 dated 2018-04-17 and 1.1.1 dated 2018-05-29
simPop-1.1.0/simPop/tests/testthat/Rplots.pdf |only simPop-1.1.1/simPop/DESCRIPTION | 8 simPop-1.1.1/simPop/MD5 | 25 - simPop-1.1.1/simPop/build/partial.rdb |binary simPop-1.1.1/simPop/data/eusilc13puf.rda |binary simPop-1.1.1/simPop/data/eusilcP.RData |binary simPop-1.1.1/simPop/data/eusilcS.RData |binary simPop-1.1.1/simPop/data/ghanaS.RData |binary simPop-1.1.1/simPop/data/totalsRG.rda |binary simPop-1.1.1/simPop/data/totalsRGtab.rda |binary simPop-1.1.1/simPop/tests/testthat/debug_ipu.r | 2 simPop-1.1.1/simPop/tests/testthat/simInitSpatialTest.R | 218 ++++++++++------ simPop-1.1.1/simPop/tests/testthat/test_calibPop.R | 13 simPop-1.1.1/simPop/tests/testthat/test_sprague.R | 1 14 files changed, 171 insertions(+), 96 deletions(-)
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between rJava versions 0.9-9 dated 2017-10-12 and 0.9-10 dated 2018-05-29
DESCRIPTION | 7 MD5 | 260 +++++----- NEWS | 33 - R/call.R | 6 R/exceptions.R | 4 R/windows/FirstLib.R | 8 R/zzz.R.in | 4 configure | 36 + configure.ac | 28 - inst/java/ArrayDimensionException.class |binary inst/java/ArrayWrapper.class |binary inst/java/ArrayWrapper_Test.class |binary inst/java/DummyPoint.class |binary inst/java/FlatException.class |binary inst/java/NotAnArrayException.class |binary inst/java/NotComparableException.class |binary inst/java/ObjectArrayException.class |binary inst/java/PrimitiveArrayException.class |binary inst/java/RJavaArrayIterator.class |binary inst/java/RJavaArrayTools$ArrayDimensionMismatchException.class |binary inst/java/RJavaArrayTools.class |binary inst/java/RJavaArrayTools_Test.class |binary inst/java/RJavaComparator.class |binary inst/java/RJavaImport.class |binary inst/java/RJavaTools.class |binary inst/java/RJavaTools_Test$DummyNonStaticClass.class |binary inst/java/RJavaTools_Test$ExampleClass.class |binary 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inst/javadoc/RJavaArrayIterator.html | 4 inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 4 inst/javadoc/RJavaArrayTools.html | 4 inst/javadoc/RJavaArrayTools_Test.html | 4 inst/javadoc/RJavaClassLoader.html | 4 inst/javadoc/RJavaComparator.html | 4 inst/javadoc/RJavaImport.html | 4 inst/javadoc/RJavaTools.html | 4 inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 4 inst/javadoc/RJavaTools_Test.TestException.html | 4 inst/javadoc/RJavaTools_Test.html | 4 inst/javadoc/RectangularArrayBuilder.html | 4 inst/javadoc/RectangularArrayBuilder_Test.html | 4 inst/javadoc/RectangularArrayExamples.html | 4 inst/javadoc/RectangularArraySummary.html | 4 inst/javadoc/TestException.html | 4 inst/javadoc/allclasses-frame.html | 4 inst/javadoc/allclasses-noframe.html | 4 inst/javadoc/constant-values.html | 4 inst/javadoc/deprecated-list.html | 4 inst/javadoc/help-doc.html | 4 inst/javadoc/index-all.html | 4 inst/javadoc/index.html | 2 inst/javadoc/overview-tree.html | 4 inst/javadoc/package-frame.html | 4 inst/javadoc/package-summary.html | 4 inst/javadoc/package-tree.html | 4 inst/javadoc/serialized-form.html | 4 inst/jri/JRIEngine.jar |binary inst/jri/REngine.jar |binary jri/Makefile.all | 2 jri/Makefile.in | 1 jri/REngine/JRI/Makefile | 2 jri/REngine/Rserve/Makefile | 2 jri/REngine/Rserve/test/Makefile | 2 jri/bootstrap/Makefile | 2 jri/configure | 70 ++ jri/configure.ac | 43 + jri/src/Makefile.all | 6 jri/src/Makefile.in | 1 jri/src/Rengine.c | 4 jri/src/jri.h | 2 man/javaImport.Rd | 4 man/jinit.Rd | 2 man/jnew.Rd | 7 man/jpackage.Rd | 2 man/loader.Rd | 2 src/Rglue.c | 25 src/callJNI.c | 15 src/fields.c | 4 src/init.c | 4 src/java/ArrayDimensionException.class |binary src/java/ArrayWrapper.class |binary src/java/ArrayWrapper_Test.class |binary src/java/DummyPoint.class |binary src/java/FlatException.class |binary src/java/NotAnArrayException.class |binary src/java/NotComparableException.class |binary src/java/ObjectArrayException.class |binary src/java/PrimitiveArrayException.class |binary src/java/RJavaArrayIterator.class |binary src/java/RJavaArrayTools$ArrayDimensionMismatchException.class |binary src/java/RJavaArrayTools.class |binary src/java/RJavaArrayTools_Test.class |binary src/java/RJavaClassLoader$RJavaObjectInputStream.class |binary src/java/RJavaClassLoader$UnixDirectory.class |binary src/java/RJavaClassLoader$UnixFile.class |binary src/java/RJavaClassLoader$UnixJarFile.class |binary src/java/RJavaClassLoader.class |binary src/java/RJavaComparator.class |binary src/java/RJavaImport.class |binary src/java/RJavaTools.class |binary src/java/RJavaTools_Test$DummyNonStaticClass.class |binary src/java/RJavaTools_Test$ExampleClass.class |binary src/java/RJavaTools_Test$TestException.class |binary src/java/RJavaTools_Test.class |binary src/java/RectangularArrayBuilder.class |binary src/java/RectangularArrayBuilder_Test.class |binary src/java/RectangularArrayExamples.class |binary src/java/RectangularArraySummary.class |binary src/java/TestException.class |binary src/jri_glue.c | 2 src/rJava.h | 6 131 files changed, 461 insertions(+), 281 deletions(-)
Title: Rating Scale Reduction Procedure
Description: Describes a new procedure of reducing items in a rating scale called Rating Scale Reduction (RSR). The new stop criterion in RSR procedure is added (stop global max). Data sets are added.
Author: Waldemar W. Koczkodaj,Feng Li ,Alicja Wolny-Dominiak
Maintainer: Alicja Wolny-Dominiak <alicja.wolny-dominiak@ue.katowice.pl>
Diff between RatingScaleReduction versions 1.2.1 dated 2018-04-12 and 1.2.2 dated 2018-05-29
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++++-------- R/CheckAttr4Inclusion.R | 23 ++--------------------- R/diffExamples.R | 20 ++------------------ R/grayExamples.R | 19 ++----------------- R/rsr.R | 46 +++++----------------------------------------- R/startAuc.R | 19 ++----------------- R/totalAuc.R | 23 ++--------------------- data |only man/SHSData.Rd |only man/totalAuc.Rd | 20 ++++---------------- man/wineData.Rd |only 12 files changed, 36 insertions(+), 164 deletions(-)
More information about RatingScaleReduction at CRAN
Permanent link
Title: Robust Adaptive Metropolis Algorithm
Description: Function for adapting the shape of the random walk Metropolis proposal
as specified by robust adaptive Metropolis algorithm by Vihola (2012) <DOI:10.1007/s11222-011-9269-5>.
Package also includes fast functions for rank-one Cholesky update and downdate.
These functions can be used directly from R or the corresponding C++ header files
can be easily linked to other R packages.
Author: Jouni Helske
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between ramcmc versions 0.1.0 dated 2016-11-30 and 0.1.0-1 dated 2018-05-29
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/RcppExports.R | 6 +++--- build/vignette.rds |binary inst/doc/ramcmc.html | 41 +++++++++++++++++++++++------------------ src/RcppExports.cpp | 18 +++++++++++++++--- 6 files changed, 51 insertions(+), 34 deletions(-)
Title: Likelihood Inference in Meta-Analysis and Meta-Regression Models
Description: First- and higher-order likelihood inference in
meta-analysis and meta-regression models.
Author: Annamaria Guolo and Cristiano Varin
Maintainer: Cristiano Varin <sammy@unive.it>
Diff between metaLik versions 0.42.0 dated 2015-06-21 and 0.43.0 dated 2018-05-29
metaLik-0.42.0/metaLik/NEWS |only metaLik-0.43.0/metaLik/DESCRIPTION | 8 ++++---- metaLik-0.43.0/metaLik/MD5 | 9 ++++----- metaLik-0.43.0/metaLik/NAMESPACE | 21 ++++++++++++--------- metaLik-0.43.0/metaLik/R/metaLik.R | 16 +++------------- metaLik-0.43.0/metaLik/man/simulate.metaLik.Rd | 3 +-- 6 files changed, 24 insertions(+), 33 deletions(-)
Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') to store and manage
temporal-context data in a data-centric format, which is built on top of
the 'tibble'. The 'tsibble' aims at easily manipulating and analysing temporal
data, including counting and filling time gaps, aggregate over calendar periods,
performing rolling window calculations, and etc.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>),
Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>),
Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>),
Mitchell O'Hara-Wild [ctb]
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between tsibble versions 0.2.0 dated 2018-05-11 and 0.3.0 dated 2018-05-29
tsibble-0.2.0/tsibble/R/tsummarise.R |only tsibble-0.2.0/tsibble/man/defunct.Rd |only tsibble-0.2.0/tsibble/man/tsibble-deprecated.Rd |only tsibble-0.2.0/tsibble/tests/testthat/test-tsummarise.R |only tsibble-0.3.0/tsibble/DESCRIPTION | 28 - tsibble-0.3.0/tsibble/MD5 | 84 ++-- tsibble-0.3.0/tsibble/NAMESPACE | 45 +- tsibble-0.3.0/tsibble/NEWS.md | 19 + tsibble-0.3.0/tsibble/R/RcppExports.R | 4 tsibble-0.3.0/tsibble/R/as-tsibble.R | 69 +-- tsibble-0.3.0/tsibble/R/dplyr-verbs.R | 25 - tsibble-0.3.0/tsibble/R/fill-na.R | 8 tsibble-0.3.0/tsibble/R/format.R | 2 tsibble-0.3.0/tsibble/R/index-by.R | 29 + tsibble-0.3.0/tsibble/R/parse-key.R | 16 tsibble-0.3.0/tsibble/R/period.R | 15 tsibble-0.3.0/tsibble/R/reexports.R | 16 tsibble-0.3.0/tsibble/R/subset.R | 6 tsibble-0.3.0/tsibble/R/tidyr-verbs.R | 302 +++++++++++++++-- tsibble-0.3.0/tsibble/R/time-wise.R |only tsibble-0.3.0/tsibble/R/ts2tsibble.R | 4 tsibble-0.3.0/tsibble/R/tsibble-pkg.R | 34 + tsibble-0.3.0/tsibble/R/tsibble2ts.R | 36 +- tsibble-0.3.0/tsibble/R/type-sum.R | 40 +- tsibble-0.3.0/tsibble/R/utils.R | 8 tsibble-0.3.0/tsibble/README.md | 22 - tsibble-0.3.0/tsibble/inst/doc/intro-tsibble.Rmd | 12 tsibble-0.3.0/tsibble/inst/doc/intro-tsibble.html | 16 tsibble-0.3.0/tsibble/man/difference.Rd |only tsibble-0.3.0/tsibble/man/figures |only tsibble-0.3.0/tsibble/man/gather.Rd |only tsibble-0.3.0/tsibble/man/nest.Rd |only tsibble-0.3.0/tsibble/man/reexports.Rd | 10 tsibble-0.3.0/tsibble/man/spread.Rd |only tsibble-0.3.0/tsibble/man/tsibble-package.Rd | 31 + tsibble-0.3.0/tsibble/man/tsibble.Rd | 14 tsibble-0.3.0/tsibble/man/unnest.Rd |only tsibble-0.3.0/tsibble/src/RcppExports.cpp | 15 tsibble-0.3.0/tsibble/src/time-wise.cpp |only tsibble-0.3.0/tsibble/tests/testthat.R | 1 tsibble-0.3.0/tsibble/tests/testthat/test-dplyr.R | 12 tsibble-0.3.0/tsibble/tests/testthat/test-index-fun.R | 4 tsibble-0.3.0/tsibble/tests/testthat/test-indexby.R | 30 - tsibble-0.3.0/tsibble/tests/testthat/test-misc.R | 6 tsibble-0.3.0/tsibble/tests/testthat/test-subset.R | 3 tsibble-0.3.0/tsibble/tests/testthat/test-tidyr.R |only tsibble-0.3.0/tsibble/tests/testthat/test-timewise.R |only tsibble-0.3.0/tsibble/tests/testthat/test-tsibble.R | 3 tsibble-0.3.0/tsibble/tests/testthat/test-tsibble2ts.R | 3 tsibble-0.3.0/tsibble/vignettes/intro-tsibble.Rmd | 12 50 files changed, 735 insertions(+), 249 deletions(-)
Title: Read Ethoscope Data
Description: Handling of behavioural data from the Ethoscope platform
(Geissmann, Garcia Rodriguez, Beckwith, French, Jamasb and Gilestro (2017) <DOI:10.1371/journal.pbio.2003026>).
Ethoscopes (<http://gilestrolab.github.io/ethoscope/>) are an open source/open hardware framework made of
interconnected raspberry pis (<https://www.raspberrypi.org>) designed to quantify the behaviour of multiple
small animals in a distributed and real-time fashion. The default tracking algorithm records primary variables
such as xy coordinates, dimensions and speed.
This package is part of the rethomics framework <http://rethomics.github.io/>.
Author: Quentin Geissmann [aut, cre]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Diff between scopr versions 0.3.1 dated 2018-05-18 and 0.3.2 dated 2018-05-29
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ R/make-index-file.R | 10 ++++++---- tests/testthat/test-build_query.R | 3 ++- tests/testthat/test-make_index_file.R | 6 ++++-- tests/testthat/test-parse_single_roi.R | 5 ++++- tests/testthat/test-read_single_roi.R | 5 +---- 7 files changed, 28 insertions(+), 22 deletions(-)
Title: Information Decomposition of Two-Phase Experiments
Description: The main purpose of this package is to generate the structure of the analysis of variance
(ANOVA) table of the two-phase experiments. The user only need to input the design and the
relationships of the random and fixed factors using the Wilkinson-Rogers' syntax,
this package can then quickly generate the structure of the ANOVA table with the
coefficients of the variance components for the expected mean squares.
Thus, the balanced incomplete block design and provides the efficiency
factors of the fixed effects can also be studied and compared much easily.
Author: Kevin Chang [aut, cre],
Katya Ruggiero [aut]
Maintainer: Kevin Chang <k.chang@auckland.ac.nz>
Diff between infoDecompuTE versions 0.6.0 dated 2017-03-06 and 0.6.1 dated 2018-05-29
infoDecompuTE-0.6.0/infoDecompuTE/man/getCoefVC.Rd |only infoDecompuTE-0.6.0/infoDecompuTE/man/getFixedEF.Rd |only infoDecompuTE-0.6.0/infoDecompuTE/man/getVMat.Rd |only infoDecompuTE-0.6.0/infoDecompuTE/man/toLatexTable.rd |only infoDecompuTE-0.6.1/infoDecompuTE/DESCRIPTION | 14 infoDecompuTE-0.6.1/infoDecompuTE/MD5 | 120 +- infoDecompuTE-0.6.1/infoDecompuTE/NAMESPACE | 59 - infoDecompuTE-0.6.1/infoDecompuTE/NEWS.md | 6 infoDecompuTE-0.6.1/infoDecompuTE/R/J.R | 39 infoDecompuTE-0.6.1/infoDecompuTE/R/K.R | 48 - infoDecompuTE-0.6.1/infoDecompuTE/R/adjustEffectNames.r | 118 +- infoDecompuTE-0.6.1/infoDecompuTE/R/adjustMissingLevels.r | 60 - infoDecompuTE-0.6.1/infoDecompuTE/R/compareAovOnePhase.R |only infoDecompuTE-0.6.1/infoDecompuTE/R/data.R |only infoDecompuTE-0.6.1/infoDecompuTE/R/getCoefVC.onePhase.R | 256 +++-- infoDecompuTE-0.6.1/infoDecompuTE/R/getCoefVC.twoPhase.R | 304 +++--- infoDecompuTE-0.6.1/infoDecompuTE/R/getEffFactor.R | 265 +++-- infoDecompuTE-0.6.1/infoDecompuTE/R/getFixedEF.onePhase.R | 249 +++-- infoDecompuTE-0.6.1/infoDecompuTE/R/getFixedEF.twoPhase.R | 286 +++--- infoDecompuTE-0.6.1/infoDecompuTE/R/getTrtCoef.R | 74 + infoDecompuTE-0.6.1/infoDecompuTE/R/getTrtRep.R | 252 +++-- infoDecompuTE-0.6.1/infoDecompuTE/R/getVMat.onePhase.R | 40 infoDecompuTE-0.6.1/infoDecompuTE/R/getVMat.twoPhase.R | 106 +- infoDecompuTE-0.6.1/infoDecompuTE/R/identityMat.R | 38 infoDecompuTE-0.6.1/infoDecompuTE/R/infoDecompMat.R | 130 +- infoDecompuTE-0.6.1/infoDecompuTE/R/infoDecompuTE-package.R |only infoDecompuTE-0.6.1/infoDecompuTE/R/invInfMat.R | 52 - infoDecompuTE-0.6.1/infoDecompuTE/R/makeBlkDesMat.R | 148 +-- infoDecompuTE-0.6.1/infoDecompuTE/R/makeContrMat.R | 461 +++++---- infoDecompuTE-0.6.1/infoDecompuTE/R/makeOrthProjectors.R | 113 +- infoDecompuTE-0.6.1/infoDecompuTE/R/makeOverDesMat.R | 99 +- infoDecompuTE-0.6.1/infoDecompuTE/R/projMat.R | 44 infoDecompuTE-0.6.1/infoDecompuTE/R/summaryAovOnePhase.R | 90 + infoDecompuTE-0.6.1/infoDecompuTE/R/summaryAovTwoPhase.R | 156 +++ infoDecompuTE-0.6.1/infoDecompuTE/R/toLatexTable.r | 471 +++++----- infoDecompuTE-0.6.1/infoDecompuTE/R/tr.R | 44 infoDecompuTE-0.6.1/infoDecompuTE/R/unity.R | 40 infoDecompuTE-0.6.1/infoDecompuTE/README.md | 58 + infoDecompuTE-0.6.1/infoDecompuTE/data |only infoDecompuTE-0.6.1/infoDecompuTE/man/J.Rd | 8 infoDecompuTE-0.6.1/infoDecompuTE/man/K.Rd | 2 infoDecompuTE-0.6.1/infoDecompuTE/man/adjustEffectNames.Rd | 68 - infoDecompuTE-0.6.1/infoDecompuTE/man/adjustMissingLevels.Rd | 80 - infoDecompuTE-0.6.1/infoDecompuTE/man/chrisEx1.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/chrisEx2.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/chrisEx3.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/getCoefVC.onePhase.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/getCoefVC.twoPhase.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/getEffFactor.Rd | 159 +-- infoDecompuTE-0.6.1/infoDecompuTE/man/getFixedEF.onePhase.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/getFixedEF.twoPhase.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/getTrtCoef.Rd | 91 - infoDecompuTE-0.6.1/infoDecompuTE/man/getTrtRep.Rd | 104 +- infoDecompuTE-0.6.1/infoDecompuTE/man/getVMat.onePhase.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/getVMat.twoPhase.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/identityMat.Rd | 2 infoDecompuTE-0.6.1/infoDecompuTE/man/infoDecompMat.Rd | 136 +- infoDecompuTE-0.6.1/infoDecompuTE/man/infoDecompuTE-package.Rd | 54 - infoDecompuTE-0.6.1/infoDecompuTE/man/invInfMat.Rd | 82 - infoDecompuTE-0.6.1/infoDecompuTE/man/makeBlkDesMat.Rd | 6 infoDecompuTE-0.6.1/infoDecompuTE/man/makeContrMat.Rd | 150 +-- infoDecompuTE-0.6.1/infoDecompuTE/man/makeOrthProjectors.Rd | 91 + infoDecompuTE-0.6.1/infoDecompuTE/man/makeOverDesMat.Rd | 120 +- infoDecompuTE-0.6.1/infoDecompuTE/man/projMat.Rd | 2 infoDecompuTE-0.6.1/infoDecompuTE/man/summaryAovOnePhase.Rd | 205 ++-- infoDecompuTE-0.6.1/infoDecompuTE/man/summaryAovTwoPhase.Rd | 179 ++- infoDecompuTE-0.6.1/infoDecompuTE/man/toLatexTable.Rd |only infoDecompuTE-0.6.1/infoDecompuTE/man/tr.Rd | 2 infoDecompuTE-0.6.1/infoDecompuTE/man/unity.Rd | 2 69 files changed, 3549 insertions(+), 2234 deletions(-)
Title: Wavelet Deconvolution
Description: Makes available code necessary to reproduce figures and
tables in papers on the WaveD method for wavelet deconvolution
of noisy signals as presented in The WaveD Transform in R,
Journal of Statistical Software Volume 21, No. 3, 2007.
Author: Marc Raimondo <marcr@maths.usyd.edu.au> and Michael Stewart
<michael.stewart@sydney.edu.au>
Maintainer: Michael Stewart <michael.stewart@sydney.edu.au>
Diff between waved versions 1.1-2 dated 2012-11-07 and 1.2 dated 2018-05-29
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- NAMESPACE | 7 ++++++- man/FWaveD.Rd | 2 +- man/WaveD.Rd | 4 +++- man/multires.Rd | 2 +- 6 files changed, 25 insertions(+), 18 deletions(-)
Title: Fuzzy Clustering of Vegetation Data
Description: A set of functions to perform fuzzy clustering of vegetation data [De Caceres et al. (2010) <doi:10.1111/j.1654-1103.2010.01211.x>] and to assess ecological community ressemblance on the basis of structure and composition [De Caceres et al. (2013): <doi:10.1111/2041-210X.12116>].
Author: Miquel De Cáceres [aut, cre]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between vegclust versions 1.7.1 dated 2017-09-17 and 1.7.4 dated 2018-05-29
vegclust-1.7.1/vegclust/inst/doc/MedRegExample.Rnw |only vegclust-1.7.1/vegclust/inst/doc/MedRegExample.pdf |only vegclust-1.7.1/vegclust/inst/doc/TrajectoryAnalysis.R |only vegclust-1.7.1/vegclust/inst/doc/TrajectoryAnalysis.Rnw |only vegclust-1.7.1/vegclust/inst/doc/TrajectoryAnalysis.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-008.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-009.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-011.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-012.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-013.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-014.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-015.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-016.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-018.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-019.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-021.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-022.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-023.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-025.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-026.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-027.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-028.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-030.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample-031.pdf |only vegclust-1.7.1/vegclust/vignettes/MedRegExample.Rnw |only vegclust-1.7.1/vegclust/vignettes/TrajectoryAnalysis.Rnw |only vegclust-1.7.4/vegclust/DESCRIPTION | 16 vegclust-1.7.4/vegclust/MD5 | 75 vegclust-1.7.4/vegclust/NAMESPACE | 32 vegclust-1.7.4/vegclust/NEWS | 44 vegclust-1.7.4/vegclust/R/RcppExports.R | 54 vegclust-1.7.4/vegclust/R/documentationAvoca.R |only vegclust-1.7.4/vegclust/R/stratifyvegdata.R | 12 vegclust-1.7.4/vegclust/R/trajectoryClustering.R | 646 ++--- vegclust-1.7.4/vegclust/R/trajectoryDistances.R | 1098 ++++++---- vegclust-1.7.4/vegclust/R/vegclustdist.R | 514 ++-- vegclust-1.7.4/vegclust/build/partial.rdb |only vegclust-1.7.4/vegclust/build/vignette.rds |binary vegclust-1.7.4/vegclust/data/avoca.rda |only vegclust-1.7.4/vegclust/inst/doc/CTA.R |only vegclust-1.7.4/vegclust/inst/doc/CTA.Rmd |only vegclust-1.7.4/vegclust/inst/doc/CTA.html |only vegclust-1.7.4/vegclust/inst/doc/MedRegExample.R | 401 +-- vegclust-1.7.4/vegclust/inst/doc/MedRegExample.Rmd |only vegclust-1.7.4/vegclust/inst/doc/MedRegExample.html |only vegclust-1.7.4/vegclust/inst/doc/VegetationClassification.R | 807 +++---- vegclust-1.7.4/vegclust/inst/doc/VegetationClassification.Rnw | 1046 ++++----- vegclust-1.7.4/vegclust/inst/doc/VegetationClassification.pdf |binary vegclust-1.7.4/vegclust/man/avoca.Rd |only vegclust-1.7.4/vegclust/man/trajectories.Rd | 322 +- vegclust-1.7.4/vegclust/man/vegclust-package.Rd | 38 vegclust-1.7.4/vegclust/man/vegclust.Rd | 310 +- vegclust-1.7.4/vegclust/src/RcppExports.cpp | 91 vegclust-1.7.4/vegclust/src/trajectories.cpp | 106 vegclust-1.7.4/vegclust/vignettes/CTA.Rmd |only vegclust-1.7.4/vegclust/vignettes/MedRegExample.Rmd |only vegclust-1.7.4/vegclust/vignettes/VegetationClassification.Rnw | 1046 ++++----- 57 files changed, 3518 insertions(+), 3140 deletions(-)
Title: Scale-Dependent Hyperpriors in Structured Additive
Distributional Regression
Description: Utility functions for scale-dependent and alternative hyperpriors. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend
on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. Hyperpriors for all effects can be elicitated within the package. Including complex tensor product interaction terms and variable selection priors. The basic model is explained in in Klein and Kneib (2016) <doi:10.1214/15-BA983>.
Author: Nadja Klein [aut, cre],
Thomas Kneib [aut]
Maintainer: Nadja Klein <n.klein@mbs.edu>
Diff between sdPrior versions 0.3 dated 2015-07-15 and 0.5 dated 2018-05-29
DESCRIPTION | 20 +++++++++----- MD5 | 68 +++++++++++++++++++++++++++--------------------- NAMESPACE | 21 +++++++++++--- R/get_theta.r | 7 +++- R/get_theta_aunif.r | 3 ++ R/get_theta_ga.r | 5 ++- R/get_theta_gbp.r | 5 ++- R/get_theta_ig.r | 3 ++ R/get_theta_linear.r |only R/hyperpar.r |only R/hyperpar_mod.r |only R/hyperparlin.r |only R/mdbeta.r |only R/mdf_aunif.r | 3 +- R/mdf_ga.r | 2 + R/mdf_gbp.r | 7 ++-- R/mdf_ig.r | 2 + R/mdf_sd.r | 7 ++-- R/utils_sdPrior.r | 24 +++++++++++----- man/DesignM.Rd | 18 ++++++------ man/dapprox_unif.Rd | 14 ++++----- man/get_theta.Rd | 19 +++++++------ man/get_theta_aunif.Rd | 23 ++++++++-------- man/get_theta_ga.Rd | 27 +++++++++---------- man/get_theta_gbp.Rd | 27 +++++++++---------- man/get_theta_ig.Rd | 23 ++++++++-------- man/get_theta_linear.Rd |only man/hyperpar.Rd |only man/hyperpar_mod.Rd |only man/hyperparlin.Rd |only man/mdbeta.Rd |only man/mdf_aunif.Rd | 17 ++++++------ man/mdf_ga.Rd | 15 +++++----- man/mdf_gbp.Rd | 17 ++++++------ man/mdf_ig.Rd | 15 +++++----- man/mdf_sd.Rd | 15 +++++----- man/papprox_unif.Rd | 12 ++++---- man/rapprox_unif.Rd | 12 ++++---- man/zambia_graph.Rd | 4 +- man/zambia_height92.Rd | 4 +- 40 files changed, 252 insertions(+), 187 deletions(-)
Title: Select and Download Climate Data from 'DWD' (German Weather
Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see
<https://www.dwd.de/EN/climate_environment/cdc/cdc.html> for more information).
Choose files with 'selectDWD()', download and process data sets with 'dataDWD()' and 'readDWD()'.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rdwd versions 0.10.1 dated 2018-03-29 and 0.10.2 dated 2018-05-29
rdwd-0.10.1/rdwd/tests/testthat/test-index.R |only rdwd-0.10.2/rdwd/DESCRIPTION | 9 rdwd-0.10.2/rdwd/MD5 | 43 +- rdwd-0.10.2/rdwd/NAMESPACE | 66 +-- rdwd-0.10.2/rdwd/inst/doc/mapDWD.html | 8 rdwd-0.10.2/rdwd/inst/doc/rdwd.Rmd | 2 rdwd-0.10.2/rdwd/inst/doc/rdwd.html | 46 +- rdwd-0.10.2/rdwd/man/createIndex.Rd | 176 ++++----- rdwd-0.10.2/rdwd/man/dataDWD.Rd | 262 +++++++------- rdwd-0.10.2/rdwd/man/dirDWD.Rd | 82 ++-- rdwd-0.10.2/rdwd/man/findID.Rd | 124 +++--- rdwd-0.10.2/rdwd/man/index.Rd | 108 +++--- rdwd-0.10.2/rdwd/man/indexFTP.Rd | 160 ++++---- rdwd-0.10.2/rdwd/man/lldist.Rd | 92 ++--- rdwd-0.10.2/rdwd/man/metaInfo.Rd | 60 +-- rdwd-0.10.2/rdwd/man/nearbyStations.Rd | 212 +++++------ rdwd-0.10.2/rdwd/man/rdwd.Rd | 70 +-- rdwd-0.10.2/rdwd/man/readDWD.Rd | 130 +++---- rdwd-0.10.2/rdwd/man/release_questions.Rd | 24 - rdwd-0.10.2/rdwd/man/rowDisplay.Rd | 52 +- rdwd-0.10.2/rdwd/man/selectDWD.Rd | 374 ++++++++++----------- rdwd-0.10.2/rdwd/tests/testthat/test-development.R | 150 +------- rdwd-0.10.2/rdwd/vignettes/rdwd.Rmd | 2 23 files changed, 1071 insertions(+), 1181 deletions(-)
Title: Missing not at Random Imputation Models for Multiple Imputation
by Chained Equation
Description: Provides imputation models and functions for binary or continuous Missing Not At Random (MNAR) outcomes through the use of the 'mice' package. The mice.impute.hecknorm() function provides imputation model for continuous outcome based on Heckman's model also named sample selection model as described in Galimard et al (2016) <doi:10.1002/sim.6902>. The mice.impute.heckprob() function provides imputation model for binary outcome based on bivariate probit model.
Author: Jacques-Emmanuel Galimard [aut, cre] (INSERM, U1153, ECSTRA team),
Matthieu Resche-Rigon [aut] (INSERM, U1153, ECSTRA team)
Maintainer: Jacques-Emmanuel Galimard <jacques-emmanuel.galimard@inserm.fr>
Diff between miceMNAR versions 1.0 dated 2018-04-12 and 1.0.1 dated 2018-05-29
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/MNARargument.R | 9 +++++---- R/mice.impute.hecknorm.R | 3 ++- R/mice.impute.hecknorm2step.R | 3 ++- R/mice.impute.heckprob.R | 5 +++-- build/partial.rdb |binary man/MNARargument.Rd | 14 ++++++++------ man/generate_JointModelEq.Rd | 8 ++++---- man/mice.impute.hecknorm.Rd | 2 +- man/mice.impute.hecknorm2step.Rd | 2 +- man/mice.impute.heckprob.Rd | 4 ++-- 12 files changed, 44 insertions(+), 38 deletions(-)
Title: Cryptocurrency Market Data
Description: Retrieves crypto currency current and historical information as well as information on the exchanges they are listed on. For current and historical it will retrieve the daily open, high, low and close values for all crypto currencies. This retrieves the historical market data by web scraping tables provided by 'Cryptocurrency Market Capitalizations' <https://coinmarketcap.com>.
Author: Jesse Vent [aut, cre]
Maintainer: Jesse Vent <cryptopackage@icloud.com>
Diff between crypto versions 0.1.7 dated 2018-05-01 and 1.0.1 dated 2018-05-29
DESCRIPTION | 12 ++++----- MD5 | 38 +++++++++++++++++----------- NAMESPACE | 10 +++++++ NEWS.md | 19 ++++++++++++++ R/crypto2xts.R | 47 ++++++++++++++++++++++------------- R/crypto_markets.R |only R/encoding.R |only R/getCoins.R | 38 +++++++++++++++++++--------- R/getExchanges.R | 37 ++++++++++++++++++---------- R/getPrices.R | 59 +++++++++++++++++++++++++-------------------- R/global_markets.R |only R/listCoins.R | 29 +++++++++++++++------- R/scraper.R | 8 ++++-- README.md | 28 ++++++++++++++++----- man/crypto2xts.Rd | 3 ++ man/daily_market.Rd |only man/getCoins.Rd | 4 +++ man/getExchanges.Rd | 4 +++ man/getPrices.Rd | 3 ++ man/global_market.Rd |only man/listCoins.Rd | 3 ++ man/repair_dependencies.Rd |only man/replace_encoding.Rd |only man/reset_encoding.Rd |only 24 files changed, 234 insertions(+), 108 deletions(-)
Title: Deriving Expressions of Joint Interventional Distributions and
Transport Formulas in Causal Models
Description: Functions for identification and transportation of causal effects. Provides a conditional causal effect identification algorithm (IDC) by Shpitser, I. and Pearl, J. (2006) <http://ftp.cs.ucla.edu/pub/stat_ser/r329-uai.pdf>, an algorithm for transportability from multiple domains with limited experiments by Bareinboim, E. and Pearl, J. (2014) <http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf> and a selection bias recovery algorithm by Bareinboim, E. and Tian, J. (2015) <http://ftp.cs.ucla.edu/pub/stat_ser/r445.pdf>. All of the previously mentioned algorithms are based on a causal effect identification algorithm by Tian , J. (2002) <http://ftp.cs.ucla.edu/pub/stat_ser/r309.pdf>.
Author: Santtu Tikka
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between causaleffect versions 1.3.7 dated 2018-03-07 and 1.3.8 dated 2018-05-29
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++++-------- NAMESPACE | 2 +- NEWS | 3 +++ R/descendants.R | 2 +- R/so.factorize.R |only R/soid.R |only R/surrogate.outcome.R |only R/trmz.R | 41 +++++++++++++++++++++++------------------ R/trso.R |only build/vignette.rds |binary inst/doc/causaleffect.pdf |binary inst/doc/simplification.pdf |binary man/surrogate.outcome.Rd |only 14 files changed, 45 insertions(+), 32 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons. This test
enables to compare two groups of observations in randomized trials(e.g treated
vs. control patients) on several prioritized outcomes. Pairwise comparisons
require consideration of all possible pairs of individuals, one taken from the
treatment group and the other taken from the control group. The outcomes of the
two individuals forming a pair are compared. Thresholds of minimal clinically
significant differences can be defined. It is possible to analyze simultaneously
several outcomes by prioritizing the variables that capture them. The highest
priority is assigned to the variable considered the most clinically relevant.
A natural way of handling uninformative or neutral pairs is to consider the
outcomes in descending order of priority: whenever a pair is uninformative or
neutral for an outcome of higher priority, the outcomes of lower priority are
examined In the case of time-to-event endpoint, four methods to handle censored
observations are available in this package (Gehan, Peto, Efron, and Peron).
Author: Brice Ozenne[aut, cre], Julien Peron[aut]
Maintainer: brice ozenne <brice.ozenne@orange.fr>
Diff between BuyseTest versions 1.0 dated 2016-08-17 and 1.3.2 dated 2018-05-29
BuyseTest-1.0/BuyseTest/R/FCT_BuyseTest.R |only BuyseTest-1.0/BuyseTest/R/FCT_Valid.R |only BuyseTest-1.0/BuyseTest/R/FCT_simul.R |only BuyseTest-1.0/BuyseTest/R/FCT_support.R |only BuyseTest-1.0/BuyseTest/R/FCTi-computation.R |only BuyseTest-1.0/BuyseTest/R/FCTi-initilization.R |only BuyseTest-1.0/BuyseTest/R/FCTi-print.R |only BuyseTest-1.0/BuyseTest/R/METHOD_get.R |only BuyseTest-1.0/BuyseTest/R/METHOD_print.R |only BuyseTest-1.0/BuyseTest/R/METHOD_summary.R |only BuyseTest-1.0/BuyseTest/R/OBJECT_BuyseTest.R |only BuyseTest-1.0/BuyseTest/inst/BuysePower |only BuyseTest-1.0/BuyseTest/inst/Internal_tests |only BuyseTest-1.0/BuyseTest/inst/TODO.txt |only BuyseTest-1.0/BuyseTest/inst/man_save |only BuyseTest-1.0/BuyseTest/inst/save |only BuyseTest-1.0/BuyseTest/man/internal-computation.Rd |only BuyseTest-1.0/BuyseTest/man/internal-intilisation.Rd |only BuyseTest-1.0/BuyseTest/tests/FCT |only BuyseTest-1.0/BuyseTest/tests/Results-version1.0 |only BuyseTest-1.0/BuyseTest/tests/testBT_noStrata.R |only BuyseTest-1.0/BuyseTest/tests/testBT_strata.R |only BuyseTest-1.0/BuyseTest/tests/test_Julien.R |only BuyseTest-1.0/BuyseTest/tests/test_initSurvival.R |only BuyseTest-1.0/BuyseTest/tests/test_parallel.R |only BuyseTest-1.0/BuyseTest/tests/test_valid.R |only BuyseTest-1.3.2/BuyseTest/DESCRIPTION | 32 BuyseTest-1.3.2/BuyseTest/MD5 | 144 - BuyseTest-1.3.2/BuyseTest/NAMESPACE | 73 BuyseTest-1.3.2/BuyseTest/NEWS |only BuyseTest-1.3.2/BuyseTest/R/0-onLoad.R |only BuyseTest-1.3.2/BuyseTest/R/1-setGeneric.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseRes-confint.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseRes-object.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseRes-summary.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseRes_get.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseRes_show.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseTest-check.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseTest-inference.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseTest-initialization.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseTest-package.R | 46 BuyseTest-1.3.2/BuyseTest/R/BuyseTest-print.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseTest.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseTest.options-object.R |only BuyseTest-1.3.2/BuyseTest/R/BuyseTest.options.R |only BuyseTest-1.3.2/BuyseTest/R/RcppExports.R | 82 BuyseTest-1.3.2/BuyseTest/R/constStrata.R |only BuyseTest-1.3.2/BuyseTest/R/examples/EX_BuyseTest.R | 183 -- BuyseTest-1.3.2/BuyseTest/R/seBuyseTest.R |only BuyseTest-1.3.2/BuyseTest/R/simBuyseTest.R |only BuyseTest-1.3.2/BuyseTest/R/tableComparison.R |only BuyseTest-1.3.2/BuyseTest/R/valid.R |only BuyseTest-1.3.2/BuyseTest/inst/CITATION |only BuyseTest-1.3.2/BuyseTest/inst/TestCpp11 |only BuyseTest-1.3.2/BuyseTest/inst/todo.org |only BuyseTest-1.3.2/BuyseTest/man/BuyseRes-class.Rd | 92 - BuyseTest-1.3.2/BuyseTest/man/BuyseRes-confint.Rd |only BuyseTest-1.3.2/BuyseTest/man/BuyseRes-getCount.Rd | 63 BuyseTest-1.3.2/BuyseTest/man/BuyseRes-show.Rd | 75 BuyseTest-1.3.2/BuyseTest/man/BuyseRes-summary.Rd | 151 - BuyseTest-1.3.2/BuyseTest/man/BuyseTest-package.Rd |only BuyseTest-1.3.2/BuyseTest/man/BuyseTest.Rd | 398 ++-- BuyseTest-1.3.2/BuyseTest/man/BuyseTest.options-class.Rd |only BuyseTest-1.3.2/BuyseTest/man/BuyseTest.options-methods.Rd |only BuyseTest-1.3.2/BuyseTest/man/BuyseTest.options.Rd |only BuyseTest-1.3.2/BuyseTest/man/BuyseTest_cpp.Rd | 124 - BuyseTest-1.3.2/BuyseTest/man/constStrata.Rd | 100 - BuyseTest-1.3.2/BuyseTest/man/internal-initialization.Rd |only BuyseTest-1.3.2/BuyseTest/man/internal-print.Rd | 37 BuyseTest-1.3.2/BuyseTest/man/simulation.Rd | 164 + BuyseTest-1.3.2/BuyseTest/man/testArgs.Rd |only BuyseTest-1.3.2/BuyseTest/man/validFCTs.Rd | 200 +- BuyseTest-1.3.2/BuyseTest/src/FCT_buyseTest.cpp | 704 +++---- BuyseTest-1.3.2/BuyseTest/src/FCT_calcAllPairs.h | 1168 ++++++------- BuyseTest-1.3.2/BuyseTest/src/FCT_calcOnePair.h | 802 ++++---- BuyseTest-1.3.2/BuyseTest/src/FCT_calcStatistic.h |only BuyseTest-1.3.2/BuyseTest/src/RcppExports.cpp | 55 BuyseTest-1.3.2/BuyseTest/tests/testthat |only BuyseTest-1.3.2/BuyseTest/tests/testthat.R |only 79 files changed, 2181 insertions(+), 2512 deletions(-)
Title: Penalized Likelihood Estimation and Dynamic Prediction under the
Joint Frailty-Copula Models Between Tumour Progression and
Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction methods under
the joint frailty-copula model between tumour progression and death for meta-analysis.
A penalized likelihood is employed for estimating model parameters, where the baseline hazard functions are approximated by smoothing splines.
The methods are applicable for meta-analytic data combining several studies.
The methods can analyze data having information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
See Emura et al. (2015) <doi:10.1177/0962280215604510> and
Emura et al. (2017) <doi:10.1177/0962280216688032> for details.
Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.14 dated 2017-11-23 and 2.15 dated 2018-05-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- R/F.window.Weibull.R |only R/F.windows.Weibull.R |only man/F.window.Rd | 2 +- man/F.window.Weibull.Rd |only man/F.windows.Rd | 2 +- man/F.windows.Weibull.Rd |only man/joint.Cox-package.Rd | 4 ++-- 9 files changed, 16 insertions(+), 12 deletions(-)
Title: An Algorithm for Morphometric Characters Selection and
Statistical Validation in Morphological Taxonomy
Description: An algorithm which identifies the morphometric features that significantly discriminate two taxa and validates the morphological distinctness between them via a Monte-Carlo test, polar coordinates and overlap of the area under the density curve.
Author: Cstor Guisande Gonzlez
Maintainer: Cstor Guisande Gonzlez <castor@uvigo.es>
Diff between VARSEDIG versions 1.6 dated 2018-04-12 and 1.7 dated 2018-05-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/VARSEDIG.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Text mining for word processing and sentiment analysis using
'dplyr', 'ggplot2', and other tidy tools.
Author: Gabriela De Queiroz [ctb],
Emil Hvitfeldt [ctb],
Os Keyes [ctb] (<https://orcid.org/0000-0001-5196-609X>),
Kanishka Misra [ctb],
David Robinson [aut],
Julia Silge [aut, cre] (<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between tidytext versions 0.1.8 dated 2018-03-21 and 0.1.9 dated 2018-05-29
DESCRIPTION | 11 - MD5 | 88 +++++------ NEWS.md | 7 R/bind_tf_idf.R | 8 - R/corpus_tidiers.R | 12 - R/dictionary_tidiers.R | 3 R/globals.R | 10 - R/lda_tidiers.R | 6 R/mallet_tidiers.R | 5 R/sparse_casters.R | 33 ++-- R/sparse_tidiers.R | 3 R/stm_tidiers.R | 22 +- R/stop_words.R | 7 R/unnest_tokens.R | 119 ++++++++++----- README.md | 1 build/vignette.rds |binary inst/doc/tf_idf.R | 3 inst/doc/tf_idf.Rmd | 3 inst/doc/tf_idf.html | 17 +- inst/doc/tidying_casting.R | 3 inst/doc/tidying_casting.Rmd | 3 inst/doc/tidying_casting.html | 47 ++--- inst/doc/tidytext.R | 3 inst/doc/tidytext.Rmd | 3 inst/doc/tidytext.html | 19 +- inst/doc/topic_modeling.R | 5 inst/doc/topic_modeling.Rmd | 5 inst/doc/topic_modeling.html | 169 ++++++++++++--------- man/bind_tf_idf.Rd | 3 man/deprecated-se.Rd | 8 - man/unnest_tokens.Rd | 20 +- tests/testthat/test-corpus-tidiers.R | 15 - tests/testthat/test-dictionary-tidiers.R | 12 + tests/testthat/test-lda-tidiers.R | 3 tests/testthat/test-sentiments.R | 28 ++- tests/testthat/test-sparse-casters.R | 12 - tests/testthat/test-sparse-tidiers.R | 6 tests/testthat/test-stm-tidiers.R | 11 - tests/testthat/test-stop-words.R | 2 tests/testthat/test-tf-idf.R | 40 +++-- tests/testthat/test-unnest-tokens.R | 243 ++++++++++++++++++++----------- vignettes/tf_idf.Rmd | 3 vignettes/tidying_casting.Rmd | 3 vignettes/tidytext.Rmd | 3 vignettes/topic_modeling.Rmd | 5 45 files changed, 597 insertions(+), 435 deletions(-)
Title: Statistical Methods for Modeling Operational Risk
Description: Functions for computing the Value-at-Risk in compound Poisson models.
The implementation comprises functions for modeling loss frequencies and loss severities with plain, mixed (Frigessi et al. (2012) <doi:10.1023/A:1024072610684>) or spliced distributions using Maximum Likelihood estimation and Bayesian approaches (Ergashev et al. (2013) <doi:10.21314/JOP.2013.131>).
In particular, the parametrization of tail distributions includes the fitting of Tukey-type distributions (Kuo and Headrick (2014) <doi:10.1155/2014/645823>). Furthermore, the package contains the modeling of bivariate dependencies between loss severities and frequencies, Monte Carlo simulation for total loss estimation as well as a closed-form approximation based on Degen (2010) <doi:10.21314/JOP.2010.084> to determine the value-at-risk.
Author: Christina Zou [aut,cre],
Marius Pfeuffer [aut],
Matthias Fischer [aut],
Kristina Dehler [ctb], Nicole Derfuss [ctb], Benedikt Graswald [ctb], Linda Moestel [ctb], Jixuan Wang [ctb], Leonie Wicht [ctb]
Maintainer: Christina Zou <christina.zou@maths.ox.ac.uk>
Diff between OpVaR versions 1.0 dated 2018-01-09 and 1.0.5 dated 2018-05-29
DESCRIPTION | 19 + MD5 | 20 - NAMESPACE | 1 R/SLA.R | 494 +++++++++++++++++++++---------------------- R/buildSevdist.R | 2 R/print.sevdist.R | 148 ++++++------ build/partial.rdb |binary data/lossdat.rda |binary inst/doc/OpVaR_vignette.html | 17 + man/FitSpliced.Rd | 128 +++++------ man/OpVaR-package.Rd | 6 11 files changed, 423 insertions(+), 412 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It works with data from a Freesurfer analysis (cortical thickness,
volumes, local gyrification index, surface area), diffusion tensor
tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from
DPABI). It contains a graphical user interface for graph visualization and
data exploration, along with several functions for generating useful
figures.
Author: Christopher G. Watson <cgwatson@bu.edu>
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 2.0.2 dated 2018-02-23 and 2.2.0 dated 2018-05-29
brainGraph-2.0.2/brainGraph/man/glm_fit_helper.Rd |only brainGraph-2.0.2/brainGraph/man/rich_club_coeff.Rd |only brainGraph-2.0.2/brainGraph/man/rich_club_norm.Rd |only brainGraph-2.0.2/brainGraph/man/rich_core.Rd |only brainGraph-2.0.2/brainGraph/man/setup_glm.Rd |only brainGraph-2.0.2/brainGraph/man/setup_randomise.Rd |only brainGraph-2.0.2/brainGraph/man/summary.NBS.Rd |only brainGraph-2.0.2/brainGraph/man/summary.brainGraph_boot.Rd |only brainGraph-2.0.2/brainGraph/man/summary.brainGraph_resids.Rd |only brainGraph-2.0.2/brainGraph/man/summary.mtpc.Rd |only brainGraph-2.2.0/brainGraph/DESCRIPTION | 11 brainGraph-2.2.0/brainGraph/MD5 | 135 ++--- brainGraph-2.2.0/brainGraph/NAMESPACE | 246 +++++----- brainGraph-2.2.0/brainGraph/NEWS.md | 68 ++ brainGraph-2.2.0/brainGraph/R/NBS.R | 11 brainGraph-2.2.0/brainGraph/R/boot_global.R | 53 -- brainGraph-2.2.0/brainGraph/R/brainGraph_GLM.R | 52 +- brainGraph-2.2.0/brainGraph/R/brainGraph_init.R | 14 brainGraph-2.2.0/brainGraph/R/brainGraph_mediate.R | 6 brainGraph-2.2.0/brainGraph/R/corr_matrix.R | 94 ++- brainGraph-2.2.0/brainGraph/R/create_graphs.R | 41 + brainGraph-2.2.0/brainGraph/R/create_mats.R | 4 brainGraph-2.2.0/brainGraph/R/get_resid.R | 237 ++++++---- brainGraph-2.2.0/brainGraph/R/individ_contrib.R | 62 +- brainGraph-2.2.0/brainGraph/R/mtpc.R | 21 brainGraph-2.2.0/brainGraph/R/permute_group.R | 55 -- brainGraph-2.2.0/brainGraph/R/plot_brainGraph.R | 12 brainGraph-2.2.0/brainGraph/R/plot_brainGraph_gui.R | 260 +++++------ brainGraph-2.2.0/brainGraph/R/plot_group_means.R | 10 brainGraph-2.2.0/brainGraph/R/random_graphs.R | 10 brainGraph-2.2.0/brainGraph/R/rich_club.R | 65 +- brainGraph-2.2.0/brainGraph/R/set_brainGraph_attributes.R | 24 - brainGraph-2.2.0/brainGraph/R/vertex_roles.R | 5 brainGraph-2.2.0/brainGraph/man/NBS.Rd | 13 brainGraph-2.2.0/brainGraph/man/aal116.Rd | 6 brainGraph-2.2.0/brainGraph/man/aal2.120.Rd | 9 brainGraph-2.2.0/brainGraph/man/aal2.94.Rd | 9 brainGraph-2.2.0/brainGraph/man/aal90.Rd | 6 brainGraph-2.2.0/brainGraph/man/analysis_random_graphs.Rd | 2 brainGraph-2.2.0/brainGraph/man/brainGraph_GLM_design.Rd | 28 - brainGraph-2.2.0/brainGraph/man/brainGraph_boot.Rd | 16 brainGraph-2.2.0/brainGraph/man/brainGraph_init.Rd | 14 brainGraph-2.2.0/brainGraph/man/brainGraph_permute.Rd | 21 brainGraph-2.2.0/brainGraph/man/corr.matrix.Rd | 35 + brainGraph-2.2.0/brainGraph/man/craddock200.Rd | 6 brainGraph-2.2.0/brainGraph/man/destrieux.Rd | 5 brainGraph-2.2.0/brainGraph/man/destrieux.scgm.Rd | 5 brainGraph-2.2.0/brainGraph/man/dk.Rd | 5 brainGraph-2.2.0/brainGraph/man/dk.scgm.Rd | 5 brainGraph-2.2.0/brainGraph/man/dkt.Rd | 5 brainGraph-2.2.0/brainGraph/man/dkt.scgm.Rd | 5 brainGraph-2.2.0/brainGraph/man/dosenbach160.Rd | 6 brainGraph-2.2.0/brainGraph/man/get.resid.Rd | 47 + brainGraph-2.2.0/brainGraph/man/get_lm_vars.Rd |only brainGraph-2.2.0/brainGraph/man/glm_helpers.Rd |only brainGraph-2.2.0/brainGraph/man/hoa112.Rd | 5 brainGraph-2.2.0/brainGraph/man/individ_contrib.Rd | 3 brainGraph-2.2.0/brainGraph/man/lpba40.Rd | 6 brainGraph-2.2.0/brainGraph/man/mtpc.Rd | 18 brainGraph-2.2.0/brainGraph/man/plot.bg_GLM.Rd | 7 brainGraph-2.2.0/brainGraph/man/plot.brainGraph_GLM.Rd | 2 brainGraph-2.2.0/brainGraph/man/plot.brainGraph_NBS.Rd | 5 brainGraph-2.2.0/brainGraph/man/plot.brainGraph_mediate.Rd | 3 brainGraph-2.2.0/brainGraph/man/plot.brainGraph_mtpc.Rd | 2 brainGraph-2.2.0/brainGraph/man/plot.brainGraph_resids.Rd | 12 brainGraph-2.2.0/brainGraph/man/plot.mtpc.Rd | 2 brainGraph-2.2.0/brainGraph/man/plot_rich_norm.Rd | 5 brainGraph-2.2.0/brainGraph/man/plot_volumetric.Rd | 4 brainGraph-2.2.0/brainGraph/man/random_graphs.Rd | 16 brainGraph-2.2.0/brainGraph/man/randomise.Rd | 30 - brainGraph-2.2.0/brainGraph/man/rich_club.Rd |only brainGraph-2.2.0/brainGraph/man/rich_club_attrs.Rd | 5 brainGraph-2.2.0/brainGraph/man/rstudent_mat.Rd | 11 brainGraph-2.2.0/brainGraph/man/set_brainGraph_attr.Rd | 24 - brainGraph-2.2.0/brainGraph/man/symmetrize_mats.Rd | 7 75 files changed, 1049 insertions(+), 862 deletions(-)