Title: A Calculator for Single-Case Effect Sizes
Description: Provides R functions for calculating basic effect size indices for
single-case designs, including several non-overlap measures and parametric
effect size measures, and for estimating the gradual effects model developed
by Swan and Pustejovsky (2018) <DOI:10.1080/00273171.2018.1466681>.
Standard errors and confidence intervals (based on the assumption that the outcome
measurements are mutually independent) are provided for the subset of effect sizes
indices with known sampling distributions.
Author: James E. Pustejovsky [aut, cre],
Daniel M. Swan [aut]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between SingleCaseES versions 0.4.0 dated 2018-07-31 and 0.4.1 dated 2019-01-06
DESCRIPTION | 10 +- MD5 | 24 ++-- NEWS.md | 6 + R/calculate-effect-sizes.R | 10 +- inst/shiny-examples/SCD-effect-sizes/server.R | 127 ++++++++++++++------------ man/IRD.Rd | 4 man/NAP.Rd | 5 - man/PEM.Rd | 4 man/PND.Rd | 4 man/SMD.Rd | 4 man/Tau.Rd | 5 - man/batch_calc_ES.Rd | 10 -- tests/testthat/test-Pustejovsky-2015.R | 3 13 files changed, 119 insertions(+), 97 deletions(-)
Title: Functions for Hierarchical Bayesian Estimation: A Flexible
Approach
Description: Functions for estimating models using a Hierarchical Bayesian (HB) framework. The flexibility comes in allowing the user to specify the likelihood function directly instead of assuming predetermined model structures. Types of models that can be estimated with this code include the family of discrete choice models (Multinomial Logit, Mixed Logit, Nested Logit, Error Components Logit and Latent Class) as well ordered response models like ordered probit and ordered logit. In addition, the package allows for flexibility in specifying parameters as either fixed (non-varying across individuals) or random with continuous distributions. Parameter distributions supported include normal, positive/negative log-normal, positive/negative censored normal, and the Johnson SB distribution. Kenneth Train's Matlab and Gauss code for doing Hierarchical Bayesian estimation has served as the basis for a few of the functions included in this package. These Matlab/Gauss functions have been rewritten to be optimized within R. Considerable code has been added to increase the flexibility and usability of the code base. Train's original Gauss and Matlab code can be found here: <http://elsa.berkeley.edu/Software/abstracts/train1006mxlhb.html> See Train's chapter on HB in Discrete Choice with Simulation here: <http://elsa.berkeley.edu/books/choice2.html>; and his paper on using HB with non-normal distributions here: <http://eml.berkeley.edu//~train/trainsonnier.pdf>. The authors would also like to thank the invaluable contributions of Stephane Hess and the Choice Modelling Centre: <https://cmc.leeds.ac.uk/>.
Author: Jeff Dumont [aut, cre],
Jeff Keller [aut],
Chase Carpenter [ctb]
Maintainer: Jeff Dumont <Jeff.Dumont@rsginc.com>
Diff between RSGHB versions 1.2.0 dated 2018-10-17 and 1.2.1 dated 2019-01-06
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS | 4 ++++ R/doHB.R | 2 +- R/hb.R | 12 +++++++----- R/writeModel.R | 6 ++++-- inst/doc/RSGHB_HowTo.pdf |binary man/doHB.Rd | 6 +++--- 8 files changed, 31 insertions(+), 23 deletions(-)
Title: Compute Directly Standardized Rates, Ratios and Differences
Description: A set of functions to compute and compare directly standardized rates, rate differences and ratios. A variety of user defined options for analysis (e.g confidence intervals) and formatting are included.
Author: Matthew Kumar <mattkumar@gmail.com>
Maintainer: Matthew Kumar <mattkumar@gmail.com>
Diff between dsr versions 0.1.0 dated 2018-07-22 and 0.2.0 dated 2019-01-06
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++++--------- NAMESPACE | 3 +++ R/dsr.R | 27 +++++++++++++++++---------- R/dsrr.R | 26 ++++++++++++++++++++------ R/dsrrec.R |only R/globals.R | 1 + build/vignette.rds |binary inst/doc/dsr.Rmd | 5 ++++- inst/doc/dsr.html | 6 +++--- inst/doc/dsrre.R |only inst/doc/dsrre.Rmd |only inst/doc/dsrre.html |only man/dsrrec.Rd |only vignettes/dsr.Rmd | 5 ++++- vignettes/dsrre.Rmd |only 16 files changed, 71 insertions(+), 34 deletions(-)
Title: Functions for Thermal Comfort Research
Description: Functions to calculate various common and less common thermal comfort indices, convert physical variables, and evaluate the performance of thermal comfort indices.
Author: Marcel Schweiker [aut, cre] and Sophia Mueller [aut] and Michael Kleber [ctr] and Boris Kingma [ctr] and Masanori Shukuya [ctr]
Maintainer: Marcel Schweiker <marcel.schweiker@kit.edu>
Diff between comf versions 0.1.7 dated 2017-05-09 and 0.1.8 dated 2019-01-06
DESCRIPTION | 10 MD5 | 27 +- NAMESPACE | 1 NEWS | 9 R/fctOther.r | 6 R/fctPMVPPD.r | 4 R/fctTNZPDF.r |only README.md |only build/vignette.rds |binary inst/doc/R_packages-comf.ltx | 473 ++++++++++++++++++++---------------------- inst/doc/R_packages-comf.pdf |binary man/calcHumidity.Rd | 6 man/calcTNZPDF.Rd |only man/calcdTNZ.Rd | 3 man/comf-package.Rd | 8 vignettes/R_packages-comf.ltx | 473 ++++++++++++++++++++---------------------- 16 files changed, 521 insertions(+), 499 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R
Description: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Author: Xiaowei Zhan [aut, cre],
Dajiang Liu [aut],
Attractive Chaos [cph] (We have used the following software and made
minimal necessary changes: Tabix, Heng Li <lh3@live.co.uk> (MIT
license). We removed standard IO related functions, e.g. printf,
fprintf ; also changed its un-safe pointer arithmetics.),
Broad Institute / Massachusetts Institute of Technology [cph],
Genome Research Ltd (GRL) [cph],
Facebook, Inc [cph]
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 6.7 dated 2018-12-06 and 7.0 dated 2019-01-06
ChangeLog | 8 ++ DESCRIPTION | 8 +- MD5 | 45 +++++++------ NAMESPACE | 1 R/seqminer.R | 34 ++++++++++ inst/plink |only man/readPlinkToMatrixByIndex.Rd |only src/BGenFile.cpp | 19 ++++- src/BitReader.h | 9 ++ src/FreqTable.h | 1 src/Gene.h | 4 - src/Makevars.in | 18 +++-- src/R_CPP_interface.cpp | 136 ++++++++++++++++++++++++---------------- src/R_CPP_interface.h | 32 ++++----- src/Rannotation.cpp | 10 ++ src/Rannotation.h | 6 + src/TimeUtil.h |only src/bcfutils.c | 4 - src/bgen2genoLoader.cpp | 51 ++++++++++----- src/plink2genoLoader.cpp |only src/plink2genoLoader.h |only src/rvMetaLoader.cpp | 5 + src/seqminer.c | 14 ++++ src/seqminer_init.c | 2 src/vcf2genoLoader.cpp | 6 + 25 files changed, 283 insertions(+), 130 deletions(-)
Title: 'Rcpp' Integration of the 'Streamulus' 'DSEL' for Stream
Processing
Description: The 'Streamulus' (template, header-only) library by
Irit Katriel (at <https://github.com/iritkatriel/streamulus>)
provides a very powerful yet convenient framework for stream
processing. This package connects 'Streamulus' to R by providing
both the header files and all examples.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppStreams versions 0.1.1 dated 2016-08-05 and 0.1.2 dated 2019-01-06
ChangeLog | 29 + DESCRIPTION | 8 MD5 | 32 - NAMESPACE | 2 R/RcppExports.R | 10 README.md | 2 inst/NEWS.Rd | 9 inst/include/engine.h | 166 +++---- inst/include/grammar.h | 468 ++++++++++----------- inst/include/operators.h | 758 +++++++++++++++++------------------ inst/include/stream.h | 140 +++--- inst/include/stream_base.h | 18 inst/include/strop.h | 140 +++--- inst/include/strop_func.h | 584 +++++++++++++------------- inst/include/strop_sliding_window.h | 32 - inst/include/strop_stream_producer.h | 38 - src/RcppExports.cpp | 55 +- 17 files changed, 1271 insertions(+), 1220 deletions(-)
Title: Regression Helper Functions
Description: Methods for manipulating regression models and for describing these in a style adapted for medical journals.
Contains functions for generating an HTML table with crude and adjusted estimates, plotting hazard ratio, plotting model
estimates and confidence intervals using forest plots, extending this to comparing multiple models in a single forest plots.
In addition to the descriptive methods, there are add-ons for the robust covariance matrix provided by the 'sandwich'
package, a function for adding non-linearities to a model, and a wrapper around the 'Epi' package's Lexis() functions for
time-splitting a dataset when modeling non-proportional hazards in Cox regressions.
Author: Max Gordon [aut, cre],
Reinhard Seifert [aut] (Author of original plotHR)
Maintainer: Max Gordon <max@gforge.se>
Diff between Greg versions 1.2.2 dated 2018-04-21 and 1.3 dated 2019-01-06
Greg-1.2.2/Greg/inst/doc/Print_crude_and_adjusted_models.R |only Greg-1.2.2/Greg/inst/doc/Print_crude_and_adjusted_models.Rmd |only Greg-1.2.2/Greg/inst/doc/Print_crude_and_adjusted_models.html |only Greg-1.2.2/Greg/tests/testthat/Rplots.pdf |only Greg-1.2.2/Greg/vignettes/Print_crude_and_adjusted_models.Rmd |only Greg-1.3/Greg/DESCRIPTION | 14 + Greg-1.3/Greg/MD5 | 71 ++++------ Greg-1.3/Greg/NEWS | 4 Greg-1.3/Greg/R/Greg.R | 3 Greg-1.3/Greg/R/printCrudeAndAdjustedModel.R | 2 Greg-1.3/Greg/README.md | 5 Greg-1.3/Greg/build/vignette.rds |binary Greg-1.3/Greg/inst/doc/printCrudeAndAdjustedModel.R |only Greg-1.3/Greg/inst/doc/printCrudeAndAdjustedModel.Rmd |only Greg-1.3/Greg/inst/doc/printCrudeAndAdjustedModel.html |only Greg-1.3/Greg/inst/doc/timeSplitter.Rmd | 2 Greg-1.3/Greg/inst/doc/timeSplitter.html | 43 ++++-- Greg-1.3/Greg/man/Greg-package.Rd | 3 Greg-1.3/Greg/man/SimpleRmsAnova.Rd | 4 Greg-1.3/Greg/man/addNonlinearity.Rd | 4 Greg-1.3/Greg/man/caDescribeOpts.Rd | 3 Greg-1.3/Greg/man/forestplotCombineRegrObj.Rd | 9 - Greg-1.3/Greg/man/forestplotRegrObj.Rd | 1 Greg-1.3/Greg/man/isFitFn.Rd | 4 Greg-1.3/Greg/man/plotHR.Rd | 14 - Greg-1.3/Greg/man/prCaAddRefAndStat.Rd | 1 Greg-1.3/Greg/man/prCaAddReference.Rd | 1 Greg-1.3/Greg/man/prCaAddUserReferences.Rd | 1 Greg-1.3/Greg/man/prCaGetImputationCols.Rd | 1 Greg-1.3/Greg/man/prCaGetRowname.Rd | 1 Greg-1.3/Greg/man/prCaGetVnStats.Rd | 1 Greg-1.3/Greg/man/prCaPrepareCrudeAndAdjusted.Rd | 1 Greg-1.3/Greg/man/prCaReorder.Rd | 1 Greg-1.3/Greg/man/prCaReorderReferenceDescribe.Rd | 1 Greg-1.3/Greg/man/prCaSelectAndOrderVars.Rd | 1 Greg-1.3/Greg/man/prCaSetRownames.Rd | 1 Greg-1.3/Greg/man/prNlChooseDf.Rd | 4 Greg-1.3/Greg/man/printCrudeAndAdjustedModel.Rd | 11 - Greg-1.3/Greg/tests/test-nonlin_4_coxph.R | 3 Greg-1.3/Greg/vignettes/printCrudeAndAdjustedModel.Rmd |only Greg-1.3/Greg/vignettes/timeSplitter.Rmd | 2 41 files changed, 128 insertions(+), 89 deletions(-)
Title: Bayesian Group Sparse Multi-Task Regression
Description: Fits a Bayesian group-sparse multi-task regression model using Gibbs
sampling. The hierarchical prior encourages shrinkage of the estimated regression
coefficients at both the gene and SNP level. The model has been extended to a
spatial model that allows for two type correlation in neuroimaging genetics data and
been applied successfully to imaging phenotypes of dimension up to 100; it can be used
more generally for multivariate (non-imaging) phenotypes.
Author: Yin Song, Shufei Ge, Liangliang Wang, Farouk S. Nathoo, Keelin Greenlaw, Mary Lesperance
Maintainer: Yin Song <yinsong@uvic.ca>
Diff between bgsmtr versions 0.4 dated 2019-01-03 and 0.5 dated 2019-01-06
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 2 +- R/all_functions.R | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other
applications of genomics and metagenomics. Companion package for the
Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
<DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between enveomics.R versions 1.4.2 dated 2018-11-13 and 1.4.3 dated 2019-01-06
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NAMESPACE | 4 ++-- R/recplot2.R | 14 ++++++++++++++ README.md | 1 + man/enve.recplot2.aucp.Rd |only 6 files changed, 25 insertions(+), 9 deletions(-)
Title: A Small Message Queue for Parallel Processes
Description: This queue is a data structure that lets
parallel processes send and receive messages,
and it can help coordinate the work
of complicated parallel tasks.
Processes can push new messages to the queue,
pop old messages, and obtain a
log of all the messages ever pushed. File locking
preserves the integrity of the data even when
multiple processes access the queue simultaneously.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Ian E. Fellows [ctb],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between txtq versions 0.1.1 dated 2018-10-24 and 0.1.2 dated 2019-01-06
DESCRIPTION | 16 ++++++++++++---- MD5 | 9 +++++---- NEWS.md | 4 ++++ R/txtq.R | 36 +++++++++++++++++++++--------------- inst |only tests/testthat/test-txtq.R | 10 ++++++++++ 6 files changed, 52 insertions(+), 23 deletions(-)
Title: Dynamic Linear Regression
Description: Dynamic linear models and time series regression.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between dynlm versions 0.3-5 dated 2016-08-05 and 0.3-6 dated 2019-01-06
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- NEWS | 6 ++++++ R/dynlm.R | 11 +++++++---- data/M1Germany.rda |binary inst/CITATION | 23 +++++++---------------- 6 files changed, 32 insertions(+), 31 deletions(-)
Title: Wavelet Analysis of Multiple Time Series
Description: Computes the continuous wavelet transform of
irregularly sampled time series.
Author: Timothy H. Keitt
Maintainer: ORPHANED
Diff between mvcwt versions 1.3 dated 2014-07-17 and 1.3.1 dated 2019-01-06
DESCRIPTION | 19 +++++++++++-------- MD5 | 8 ++++---- NAMESPACE | 8 ++++++++ data/lrlake.RData |binary man/mvcwt-package.Rd | 2 +- 5 files changed, 24 insertions(+), 13 deletions(-)
Title: Estimation of Life Expectancies Using Multi-State Models
Description: Functions to compute state-specific and marginal life expectancies. The computation is based on a fitted continuous-time multi-state model that includes an absorbing death state; see Van den Hout (2017, ISBN:9781466568402). The fitted multi-state model model should be estimated using the 'msm' package using age as the time-scale.
Author: Ardo van den Hout and Mei Sum Chan
Maintainer: Ardo van den Hout <Ardo.vandenHout@ucl.ac.uk>
Diff between elect versions 1.1.2 dated 2018-05-10 and 1.1.3 dated 2019-01-06
elect-1.1.2/elect/R/elect_functions_1.12.r |only elect-1.1.3/elect/DESCRIPTION | 6 +++--- elect-1.1.3/elect/MD5 | 8 ++++---- elect-1.1.3/elect/NEWS | 7 +++++++ elect-1.1.3/elect/R/elect_functions_1.1.3.r |only elect-1.1.3/elect/R/hazards.r | 9 ++++++--- 6 files changed, 20 insertions(+), 10 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014 <doi:10.1007/s00362-012-0488-4>). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut],
Stanislav Nagy [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.3.7 dated 2018-12-10 and 1.3.8 dated 2019-01-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ddalpha-internal.r | 6 +++++- R/depth.graph.r | 15 +++++++++++++-- R/routines.r | 2 ++ man/ddalpha-package.Rd | 4 ++-- 6 files changed, 31 insertions(+), 14 deletions(-)
Title: Basic Functions for Supporting an Implementation of Case 2
Best-Worst Scaling
Description: Provides three basic functions that support an implementation of Case 2 (profile case) best-worst scaling. The first is to convert an orthogonal main-effect design into questions, the second is to create a dataset suitable for analysis, and the third is to calculate count-based scores.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS2 versions 0.1-2 dated 2018-06-29 and 0.2-1 dated 2019-01-06
DESCRIPTION | 8 +- MD5 | 20 ++--- NEWS | 19 +++- R/bws2.count.R | 56 ++++++-------- R/bws2.dataset.R | 68 ++++++++++++++--- R/bws2.dataset.marginal.R | 78 ++++++++++++++++---- R/bws2.dataset.paired.R | 35 ++++++--- R/sum.bws2.count.R | 9 +- man/agritourism.Rd | 62 +++++++++------- man/bws2.dataset.Rd | 170 ++++++++++++++++++++++---------------------- man/support.BWS2-package.Rd | 3 11 files changed, 328 insertions(+), 200 deletions(-)
Title: Copula-Based Estimation and Statistical Process Control for
Serially Correlated Time Series
Description: Estimation and statistical process control are performed under
copula-based time-series models.
Available are statistical methods in Long and Emura (2014 JCSA),
Emura et al. (2017 Commun Stat-Simul) <DOI:10.1080/03610918.2015.1073303>,
and Chen and Emura (2018-, submitted).
Author: Takeshi Emura, Weiru Chen, Ting-Hsuan Long, Xinwei Huang
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between Copula.Markov versions 2.1 dated 2018-07-23 and 2.2 dated 2019-01-06
DESCRIPTION | 10 +++++----- MD5 | 12 +++++++++--- NAMESPACE | 4 ++-- R/Clayton.Markov.GOF.R |only R/Clayton.Markov2.DATA.R |only R/Clayton.Markov2.MLE.R |only man/Clayton.Markov.GOF.Rd |only man/Clayton.Markov2.DATA.Rd |only man/Clayton.Markov2.MLE.Rd |only man/Copula.Markov-package.Rd | 13 ++++++++----- 10 files changed, 24 insertions(+), 15 deletions(-)