Title: Latin Hypercube Designs (LHDs) Algorithms
Description: Contains functions for finding space-filling Latin Hypercube Designs (LHDs), e.g. maximin distance LHDs. Unlike other packages, our package is particularly useful in the area of Design and Analysis of Experiments (DAE). More specifically, it is very useful in design of computer experiments. One advantage of our package is its comprehensiveness. It contains a variety of heuristic algorithms (and their modifications) for searching maximin distance LHDs. In addition to that, it also contains other useful tools for developing and constructing maximin distance LHDs. In the future, algebraic construction methods will be added. Please refer to the function documentations for the detailed references of each function. Among all the references we used, one reference should be highlighted here, which is Ruichen Jin, Wei Chen, Agus Sudjianto (2005) <doi:10.1016/j.jspi.2004.02.014>. They provided a new form of phi_p criterion, which does not lose the space-filling property and simultaneously reduces the computational complexity when evaluating (or re-evaluating) an LHD. Their new phi_p criterion is a fundamental component of our many functions. Besides, the computation nature of the new phi_p criterion enables our functions to have less CPU time.
Author: Hongzhi Wang, Qian Xiao, Abhyuday Mandal
Maintainer: Hongzhi Wang <hw34508@uga.edu>
Diff between LHD versions 0.1.0 dated 2019-10-07 and 0.1.1 dated 2019-10-14
DESCRIPTION | 18 ++++-------------- MD5 | 5 +++-- NEWS.md |only build/vignette.rds |binary 4 files changed, 7 insertions(+), 16 deletions(-)
Title: A Class for Working with Time Series Based on 'data.table' and
'R6' with Largely Optional Reference Semantics
Description: Basic time series functionalities such as listing of missing
values, application of arbitrary aggregation as well as rolling window
functions and automatic detection of periodicity. As it is mainly based on
'data.table', it is fast and - in combination with the 'R6' package - offers
reference semantics. In addition to its native R6 interface, it provides an
S3 interface inclusive an S3 wrapper method generator for those who prefer
the latter.
Author: Gerold Hepp [aut, cre]
Maintainer: Gerold Hepp <ghepp@iwag.tuwien.ac.at>
Diff between DTSg versions 0.1.3 dated 2019-08-29 and 0.2.0 dated 2019-10-14
DESCRIPTION | 10 +- MD5 | 50 +++++----- NEWS.md | 13 ++ R/ClassDTSg.R | 174 +++++++++++++++++++++++++----------- R/S3WrapperGenerator.R | 25 ++--- R/Swrappers.R | 49 ++++++---- R/aaa.R | 9 + R/funby.R | 26 ++--- R/rollback.R | 2 README.md | 8 - inst/doc/a_basicUsage.R | 3 inst/doc/a_basicUsage.Rmd | 12 +- inst/doc/a_basicUsage.html | 198 +++++++++++++++++++----------------------- inst/doc/b_advancedUsage.R | 14 ++ inst/doc/b_advancedUsage.Rmd | 28 +++++ inst/doc/b_advancedUsage.html | 147 ++++++++++++++++--------------- man/DTSg.Rd | 27 ++++- man/S3WrapperGenerator.Rd | 16 +-- man/TALFs.Rd | 26 ++--- man/aggregate.DTSg.Rd | 8 - man/cols.DTSg.Rd | 5 - man/plot.DTSg.Rd | 13 +- man/values.DTSg.Rd | 22 +++- tests/testthat/test_DTSg.R | 132 +++++++++++++++++++++++----- vignettes/a_basicUsage.Rmd | 12 +- vignettes/b_advancedUsage.Rmd | 28 +++++ 26 files changed, 661 insertions(+), 396 deletions(-)
Title: Display Information About Nested Subsets of a Data Frame
Description: A tool for calculating and drawing "variable trees". Variable trees display information about hierarchical subsets of a data frame defined by values of categorical variables.
Author: Nick Barrowman
Maintainer: Nick Barrowman <nbarrowman@cheo.on.ca>
Diff between vtree versions 2.0.0 dated 2019-05-15 and 3.0.0 dated 2019-10-14
DESCRIPTION | 6 MD5 | 49 NAMESPACE | 18 NEWS.md | 261 +- R/VennTable.R |only R/around.R |only R/build.data.frame.R |only R/convertToHTML.R |only R/crosstabToCases.R |only R/flowcat.R |only R/grVizToPNG.R |only R/joinflow.R |only R/nodeMeanSD.R |only R/showflow.R |only R/splitlines.R |only R/summaryNodeFunction.R |only R/tableWithoutSort.R |only R/vtree.R | 4183 ++++++++++++++++++-------------------------- build/vignette.rds |binary inst/doc/vtree.R | 629 ++---- inst/doc/vtree.Rmd | 3064 ++++++++++++++++---------------- inst/doc/vtree.html | 2179 +++++++++++++--------- man/FakeData.Rd | 76 man/FakeRCT.Rd | 50 man/VennTable.Rd |only man/build.data.frame.Rd |only man/crosstabToCases.Rd | 54 man/grVizToPNG.Rd | 74 man/vtree.Rd | 854 ++++---- tests/testthat.R | 8 tests/testthat/test-vtree.R | 118 - vignettes/vtree.Rmd | 3064 ++++++++++++++++---------------- vignettes/vtreeVignette.css | 410 ++-- 33 files changed, 7698 insertions(+), 7399 deletions(-)
Title: Download and Manage Optional Package Data
Description: Manage optional data for your package. The data can be hosted anywhere, and you have to give a Uniform Resource Locator (URL) for each file. File integrity checks are supported. This is useful for package authors who need to ship more than the 5 Megabyte of data currently allowed by the the Comprehensive R Archive Network (CRAN).
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between pkgfilecache versions 0.1.0 dated 2019-10-07 and 0.1.1 dated 2019-10-14
DESCRIPTION | 9 +- MD5 | 21 ++-- R/filecache.R | 89 ++++++++++++++++++-- inst/doc/pkgfilecache.R | 2 inst/doc/pkgfilecache.Rmd | 19 +--- inst/doc/pkgfilecache.html | 13 +- man/get_abs_filenames.Rd | 5 - man/get_relative_file_subdir.Rd |only man/list_available.Rd | 2 man/make_pgk_cache_subdir_for_all_relative_files.Rd |only man/make_pgk_cache_subdir_for_relative_file.Rd |only tests/testthat/test-filecache.R | 51 +++++++++++ vignettes/pkgfilecache.Rmd | 19 +--- 13 files changed, 178 insertions(+), 52 deletions(-)
Title: Utilities for Graphical Rendering
Description: Useful tools for writing vector graphics devices.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
Yixuan Qiu [ctb],
R Core Team [cph] (Cairo code from X11 device),
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.2.0 dated 2019-09-03 and 0.2.1 dated 2019-10-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 12 ++++++++++++ R/font_family_exists.R | 7 +++---- src/CairoContext.cpp | 2 +- 5 files changed, 23 insertions(+), 12 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre],
Jeff Jones [ctb],
Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 1.91 dated 2019-10-07 and 1.92 dated 2019-10-14
DESCRIPTION | 8 - MD5 | 10 - R/SchmidLeiman.R | 285 ++++++++++++++++++++++++++++++---------------------- R/faX.R | 3 R/fareg.R | 12 +- man/SchmidLeiman.Rd | 19 ++- 6 files changed, 203 insertions(+), 134 deletions(-)
Title: Methods to Enrich R Objects with Extra Components
Description: Provides the "enrich" method to enrich list-like R objects with new, relevant components. The current version has methods for enriching objects of class 'family', 'link-glm', 'lm', 'glm' and 'betareg'. The resulting objects preserve their class, so all methods associated with them still apply. The package also provides the 'enriched_glm' function that has the same interface as 'glm' but results in objects of class 'enriched_glm'. In addition to the usual components in a `glm` object, 'enriched_glm' objects carry an object-specific simulate method and functions to compute the scores, the observed and expected information matrix, the first-order bias, as well as model densities, probabilities, and quantiles at arbitrary parameter values. The package can also be used to produce customizable source code templates for the structured implementation of methods to compute new components and enrich arbitrary objects.
Author: Ioannis Kosmidis [aut, cre]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between enrichwith versions 0.2 dated 2019-01-11 and 0.3 dated 2019-10-14
DESCRIPTION | 9 - MD5 | 18 +- NEWS.md | 9 + R/enrich.family.R | 122 +++++++++++------- build/vignette.rds |binary inst/doc/GLMs.html | 247 ++++++++++++++++++++----------------- inst/doc/bias.html | 173 +++++++++++++++---------- inst/doc/exponential_family.html | 125 +++++++++++------- man/enrich.family.Rd | 9 + man/get_information_function.lm.Rd | 4 10 files changed, 432 insertions(+), 284 deletions(-)
Title: Cox Mixed-Effects Model for Genome-Wide Association Studies
Description: Fast algorithms for fitting a Cox mixed-effects model for e.g., genome-wide association studies. See Liang He and Alexander Kulminski (2019) <doi:10.1101/729285>.
Author: Liang He
Maintainer: Liang He <liang.he@duke.edu>
Diff between coxmeg versions 1.0.7 dated 2019-09-16 and 1.0.8 dated 2019-10-14
DESCRIPTION | 12 - MD5 | 44 +-- R/RcppExports.R | 4 R/coxmeg.R | 186 ++++++++++------ R/coxmeg_m.R | 204 +++++++++++------ R/coxmeg_plink.R | 202 +++++++++++------ R/fit_ppl.R | 124 +++++++--- R/irls_ex.R | 12 - R/irls_fast_ap.R | 68 +++++ R/mll.R | 12 - build/partial.rdb |binary inst/doc/COXMEG_example.R | 20 - inst/doc/COXMEG_example.Rmd | 37 +-- inst/doc/COXMEG_example.html | 499 ++++++++++++++++++------------------------- man/COXMEG-package.Rd | 2 man/coxmeg.Rd | 30 +- man/coxmeg_m.Rd | 29 +- man/coxmeg_plink.Rd | 30 +- man/fit_ppl.Rd | 24 -- src/RcppExports.cpp | 16 + src/pcg_dense.cpp | 4 src/score.cpp | 68 +++++ vignettes/COXMEG_example.Rmd | 37 +-- 23 files changed, 985 insertions(+), 679 deletions(-)
Title: Fitting RT-MPT Models
Description: Fit response-time extended multinomial processing tree (RT-MPT) models by Klauer and
Kellen (2018) <doi:10.1016/j.jmp.2017.12.003>. The RT-MPT class not only incorporate
frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it
to estimate process completion times and encoding plus motor execution times next to the process probabilities
of traditional MPTs. 'rtmpt' is a Bayesian framework and posterior samples are sampled using a Metropolis-Gibbs
sampler like the one described in the Klauer and Kellen (2018), but with some modifications. Other than in
the original C++ program we use the free and open source GNU Scientific Library (GSL). There is also the
possibility to suppress single process completion times.
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Henrik Singmann [aut, ctb, cph],
Jean Marie Linhart [cph]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 0.1-16 dated 2019-10-08 and 0.1-17 dated 2019-10-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/SBC_fit_rtmpt.R | 5 ++++- R/simulate_rtmpt_SBC.R | 5 ++++- inst/doc/rtmpt_intro.Rmd | 2 +- inst/doc/rtmpt_intro.html | 6 +++--- man/fit_rtmpt_SBC.Rd | 6 +++++- man/sim_rtmpt_data_SBC.Rd | 6 +++++- vignettes/rtmpt_intro.Rmd | 2 +- 9 files changed, 34 insertions(+), 20 deletions(-)
Title: Network Fingerprint Framework in R
Description: An implementation of the network fingerprint framework that introduced
in paper "Network fingerprint: a knowledge-based characterization of biomedical
networks" (Cui, 2015) <doi:10.1038/srep13286>. This method worked by making
systematic comparisons to a set of well-studied "basic networks", measuring
both the functional and topological similarity. A biological could be
characterized as a spectrum-like vector consisting of similarities to basic
networks. It shows great potential in biological network study.
Author: Yang Cao [aut, cre],
Fei Li [aut]
Maintainer: Yang Cao <yiluheihei@gmail.com>
Diff between NFP versions 0.99.2 dated 2016-11-21 and 0.99.3 dated 2019-10-14
NFP-0.99.2/NFP/R/Untitled.R |only NFP-0.99.2/NFP/inst/doc/NFP.Rnw |only NFP-0.99.2/NFP/inst/doc/NFP.pdf |only NFP-0.99.2/NFP/vignettes/NFP.Rnw |only NFP-0.99.3/NFP/DESCRIPTION | 11 ++--- NFP-0.99.3/NFP/MD5 | 58 +++++++++++++-------------- NFP-0.99.3/NFP/NAMESPACE | 1 NFP-0.99.3/NFP/R/NFP.R | 2 NFP-0.99.3/NFP/R/calc_sim_score.R | 7 +++ NFP-0.99.3/NFP/README.md | 17 ++++--- NFP-0.99.3/NFP/build/vignette.rds |binary NFP-0.99.3/NFP/inst/doc/NFP.R | 54 ++++++++++++------------- NFP-0.99.3/NFP/inst/doc/NFP.Rmd |only NFP-0.99.3/NFP/inst/doc/NFP.html |only NFP-0.99.3/NFP/man/NFP-class.Rd | 2 NFP-0.99.3/NFP/man/NFP.Rd | 1 NFP-0.99.3/NFP/man/NFPRefnet-class.Rd | 2 NFP-0.99.3/NFP/man/calc_sim_score.Rd | 1 NFP-0.99.3/NFP/man/cluster_info-methods.Rd | 3 - NFP-0.99.3/NFP/man/group-methods.Rd | 3 - NFP-0.99.3/NFP/man/install_data_package.Rd | 1 NFP-0.99.3/NFP/man/kegg_refnet.Rd | 1 NFP-0.99.3/NFP/man/load_KEGG_refnet.Rd | 1 NFP-0.99.3/NFP/man/net-methods.Rd | 3 - NFP-0.99.3/NFP/man/perm_score-methods.Rd | 3 - NFP-0.99.3/NFP/man/plot_NFP-methods.Rd | 5 -- NFP-0.99.3/NFP/man/plot_NFPlist.Rd | 1 NFP-0.99.3/NFP/man/refnet_name-methods.Rd | 3 - NFP-0.99.3/NFP/man/show-methods.Rd | 3 - NFP-0.99.3/NFP/man/show_NFPRefnet-methods.Rd | 1 NFP-0.99.3/NFP/man/sub_NFP-methods.Rd | 3 - NFP-0.99.3/NFP/man/subnet-methods.Rd | 3 - NFP-0.99.3/NFP/vignettes/NFP.Rmd |only NFP-0.99.3/NFP/vignettes/bibliography.bib |only 34 files changed, 90 insertions(+), 100 deletions(-)
Title: Kernel Semi-Parametric Models
Description: To fit the kernel semi-parametric model and its extensions. It allows multiple kernels and unlimited interactions in the same model. Coefficients are estimated by maximizing a penalized log-likelihood; penalization terms and hyperparameters are estimated by minimizing leave-one-out error. It includes predictions with confidence/prediction intervals, statistical tests for the significance of each kernel, a procedure for variable selection and graphical tools for diagnostics and interpretation of covariate effects. Currently it is implemented for continuous dependent variables. The package is based on the paper of Liu et al. (2007), <doi:10.1111/j.1541-0420.2007.00799.x>.
Author: Catherine Schramm [aut, cre],
Aurelie Labbe [ctb],
Celia M. T. Greenwood [ctb]
Maintainer: Catherine Schramm <cath.schramm@gmail.com>
Diff between KSPM versions 0.1.2 dated 2019-04-07 and 0.2.0 dated 2019-10-14
KSPM-0.1.2/KSPM/tests |only KSPM-0.2.0/KSPM/DESCRIPTION | 11 ++++---- KSPM-0.2.0/KSPM/MD5 | 34 ++++++++++++++------------ KSPM-0.2.0/KSPM/NAMESPACE | 2 + KSPM-0.2.0/KSPM/R/caseNamesKspm.R | 15 ----------- KSPM-0.2.0/KSPM/R/devianceKspm.R | 4 ++- KSPM-0.2.0/KSPM/R/energy.R | 2 - KSPM-0.2.0/KSPM/R/flexibleSummary.R |only KSPM-0.2.0/KSPM/R/kernelTest.R | 41 +++++++++++++++++++++++--------- KSPM-0.2.0/KSPM/R/predictKspm.R | 2 - KSPM-0.2.0/KSPM/R/summaryKspm.R | 24 ++++++++++++++---- KSPM-0.2.0/KSPM/build |only KSPM-0.2.0/KSPM/inst |only KSPM-0.2.0/KSPM/man/energy.Rd | 2 - KSPM-0.2.0/KSPM/man/flexible.summary.Rd |only KSPM-0.2.0/KSPM/man/predict.kspm.Rd | 2 - KSPM-0.2.0/KSPM/man/summary.kspm.Rd | 4 --- KSPM-0.2.0/KSPM/man/test.function.Rd | 8 ++---- KSPM-0.2.0/KSPM/vignettes |only 19 files changed, 86 insertions(+), 65 deletions(-)
Title: Blind Source Separation and Supervised Dimension Reduction for
Time Series
Description: Different estimators are provided to solve the blind source separation problem for multivariate time series with stochastic volatility (Matilainen, Nordhausen and Oja (2015) <doi:10.1016/j.spl.2015.04.033>; Matilainen, Miettinen, Nordhausen, Oja and Taskinen (2017) <doi:10.17713/ajs.v46i3-4.671>) and supervised dimension reduction problem for multivariate time series (Matilainen, Croux, Nordhausen and Oja (2017) <doi:10.1016/j.ecosta.2017.04.002>). Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace.
Author: Markus Matilainen, Christophe Croux, Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen, Joni Virta
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>
Diff between tsBSS versions 0.5.4 dated 2019-10-09 and 0.5.5 dated 2019-10-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/gSOBI.R | 2 +- inst/ChangeLog | 3 +++ man/tsBSS-package.Rd | 4 ++-- 5 files changed, 14 insertions(+), 11 deletions(-)
Title: An Improved Wrapper of image()
Description: This is a wrapper function for image(), which makes reasonable
raster plots with nice axis and other useful features.
Author: Martin Seilmayer
Maintainer: Martin Seilmayer <m.seilmayer@hzdr.de>
Diff between rasterImage versions 0.3.0 dated 2016-09-09 and 0.4.0 dated 2019-10-14
DESCRIPTION | 10 +- MD5 | 13 +- NAMESPACE | 8 + NEWS.md |only R/colorPalette.R | 243 +++++++++++++++++++++++++--------------------------- R/rasterImage.r | 199 ++++++++++++++++++++++++++---------------- man/colorPalette.Rd | 9 - man/rasterImage2.Rd | 23 +++- 8 files changed, 282 insertions(+), 223 deletions(-)
Title: Interaction Analysis of Repeated Measure Data
Description: Extensive penalized variable selection methods have been developed in the past two decades for analyzing high dimensional omics data, such as gene expressions, single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and others. However, lipidomics data have been rarely investigated by using high dimensional variable selection methods. This package incorporates our recently developed penalization procedures to conduct interaction analysis for high dimensional lipidomics data with repeated measurements. The core module of this package is developed in C++. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Fei Zhou, Jie Ren, Xiaoxi Li, Cen Wu, Yu Jiang
Maintainer: Fei Zhou <feiz@ksu.edu>
Diff between interep versions 0.2.0 dated 2018-11-10 and 0.3.0 dated 2019-10-14
interep-0.2.0/interep/man/CorrR.Rd |only interep-0.2.0/interep/src/CorrR.cpp |only interep-0.2.0/interep/src/CorrR.h |only interep-0.2.0/interep/src/dmcp.cpp |only interep-0.2.0/interep/src/dmcp.h |only interep-0.2.0/interep/src/interep.cpp |only interep-0.2.0/interep/src/reformat.cpp |only interep-0.2.0/interep/src/reformat.h |only interep-0.3.0/interep/DESCRIPTION | 12 - interep-0.3.0/interep/MD5 | 40 ++--- interep-0.3.0/interep/NAMESPACE | 20 +- interep-0.3.0/interep/NEWS.md |only interep-0.3.0/interep/R/RcppExports.R | 136 ------------------- interep-0.3.0/interep/R/cv.interep.R | 212 ++++++++++++++++-------------- interep-0.3.0/interep/R/dmcp.R |only interep-0.3.0/interep/R/example.R | 2 interep-0.3.0/interep/R/interep.R |only interep-0.3.0/interep/R/penalty.R |only interep-0.3.0/interep/R/reformat.R |only interep-0.3.0/interep/data/dat.rda |binary interep-0.3.0/interep/man/cv.interep.Rd | 138 +++++++++++-------- interep-0.3.0/interep/man/dat.Rd | 34 ++-- interep-0.3.0/interep/man/dmcp.Rd | 81 ++++++----- interep-0.3.0/interep/man/interep.Rd | 159 ++++++++++++---------- interep-0.3.0/interep/man/penalty.Rd |only interep-0.3.0/interep/man/reformat.Rd | 42 ++--- interep-0.3.0/interep/src/RcppExports.cpp | 69 --------- interep-0.3.0/interep/src/ScoreU.cpp | 122 +++++++++++++---- 28 files changed, 508 insertions(+), 559 deletions(-)
Title: Dynamic Hazard Models using State Space Models
Description: Contains functions that lets you fit dynamic hazard models using
state space models. The first implemented model is described in Fahrmeir
(1992) <doi:10.1080/01621459.1992.10475232> and Fahrmeir (1994)
<doi:10.1093/biomet/81.2.317>. Extensions hereof are available where the
Extended Kalman filter is replaced by an unscented Kalman filter and other
options including particle filters. The implemented particle filters support
more general state space models.
Author: Benjamin Christoffersen [cre, aut],
Alan Miller [cph],
Anthony Williams [cph],
Boost developers [cph],
R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between dynamichazard versions 0.6.5 dated 2019-04-05 and 0.6.6 dated 2019-10-14
DESCRIPTION | 14 MD5 | 131 +- NAMESPACE | 1 NEWS.md | 15 R/PF.R | 205 ++-- R/ddhazard.R | 3 R/roxygen_tags.R | 1 build/vignette.rds |binary inst/doc/Bootstrap_illustration.pdf |binary inst/doc/Comparing_methods_for_logistic_models.pdf |binary inst/doc/Diagnostics.pdf |binary inst/doc/Particle_filtering.pdf |binary inst/doc/ddhazard.pdf |binary man/PF_control.Rd | 8 man/PF_get_score_n_hess.Rd | 29 src/BLAS_LAPACK/R_BLAS_LAPACK.cpp | 59 - src/BLAS_LAPACK/dchur.f | 29 src/Makevars | 3 src/Makevars.win | 1 src/PF.cpp | 46 src/PF/PF_data.h | 12 src/PF/PF_logger.cpp | 40 src/PF/PF_score_n_Hess.cpp | 502 +++++----- src/PF/PF_utils.cpp | 16 src/PF/PF_utils.h | 28 src/PF/PFs.cpp | 42 src/PF/cond_approx.cpp | 159 +-- src/PF/cond_approx.h | 23 src/PF/covarmat.cpp | 3 src/PF/dists.cpp | 16 src/PF/est_params.h | 4 src/PF/est_params_dens.cpp | 32 src/PF/importance_samplers.cpp | 27 src/PF/particles.h | 2 src/PF/r_to_cpp_clouds_n_reverse.cpp | 11 src/PF/resamplers.cpp | 4 src/PF/smoother_output.cpp | 2 src/PF_fixed_effects.cpp | 31 src/R_BLAS_LAPACK.h | 3 src/Rconfig-wrap.h |only src/arma_n_rcpp.h | 9 src/ddhazard_fit.cpp | 2 src/family.h | 6 src/parallel_glm.cpp | 4 tests/testthat.R | 4 tests/testthat/helper.R | 12 tests/testthat/previous_results/AUX_normal_approx_w_cloud_mean_cloud_means.RDS |binary tests/testthat/previous_results/AUX_normal_approx_w_particles_cloud_means.RDS |binary tests/testthat/previous_results/Brier_AUX_normal_w_particles_cloud_means.RDS |binary tests/testthat/previous_results/PF_VARS.RDS |binary tests/testthat/previous_results/PF_VARS_non_zero_mean_inter.RDS |binary tests/testthat/previous_results/PF_VARS_non_zero_mean_slope.RDS |binary tests/testthat/previous_results/PF_get_score_n_hess-help-res-O_N_sq-old.RDS |only tests/testthat/previous_results/PF_get_score_n_hess-help-res-O_N_sq.RDS |binary tests/testthat/previous_results/PF_get_score_n_hess-help-res-old.RDS |only tests/testthat/previous_results/PF_get_score_n_hess-help-res.RDS |binary tests/testthat/previous_results/PF_head_neck_cloud_means.RDS |binary tests/testthat/previous_results/PF_head_neck_w_Brier_method_cloud_means.RDS |binary tests/testthat/previous_results/PF_normal_approx_w_cloud_mean_cloud_means.RDS |binary tests/testthat/previous_results/PF_normal_approx_w_particles_cloud_means.RDS |binary tests/testthat/previous_results/n_smooth_final_RW.RDS |binary tests/testthat/previous_results/n_smooth_final_VAR.RDS |binary tests/testthat/previous_results/pf_t_dist_proposal.RDS |binary tests/testthat/previous_results/print-ddsurvcurve | 6 tests/testthat/previous_results/survival_lung_example_cloud_means.RDS |binary tests/testthat/test_PF.R | 240 +++- tests/testthat/test_cloglog.R | 3 tests/testthat/test_help_page_examples.R | 76 + 68 files changed, 999 insertions(+), 865 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-13 0.1-5
Title: Read, Validate, Analyze, and Map Files in the General Transit
Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Flavio Poletti [aut],
Tom Buckley [aut, cre],
Danton Noriega-Goodwin [aut],
Mark Padgham [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb],
Kearey Smith [ctb],
Dave Vautin [ctb],
Kyle Walker [ctb]
Maintainer: Tom Buckley <tom@tbuckl.com>
Diff between tidytransit versions 0.5.2 dated 2019-08-25 and 0.6 dated 2019-10-14
DESCRIPTION | 8 MD5 | 42 ++-- R/frequencies.R | 37 +--- R/globals.R | 1 R/import.R | 12 - R/plot.R | 22 -- R/service.R | 2 build/vignette.rds |binary inst/doc/frequency.R | 118 ++++++++++--- inst/doc/frequency.Rmd | 231 +++++++++++++++++++------- inst/doc/frequency.html | 359 +++++++++++++++++++++++------------------ inst/doc/introduction.R | 8 inst/doc/introduction.Rmd | 65 +++---- inst/doc/introduction.html | 174 ++++++++----------- inst/doc/servicepatterns.html | 308 ++++++++++++++++------------------- inst/doc/timetable.html | 230 +++++++++++--------------- man/get_route_frequency.Rd | 11 - man/get_stop_frequency.Rd | 8 man/read_gtfs.Rd | 7 tests/testthat/test-headways.R | 17 - vignettes/frequency.Rmd | 231 +++++++++++++++++++------- vignettes/introduction.Rmd | 65 +++---- 22 files changed, 1084 insertions(+), 872 deletions(-)
Title: Computation of Parameters Used in Preliminary Assessment of
Conservation Status
Description: Multi-species estimation of geographical range parameters
for preliminary assessment of conservation status following Criterion B of the
International Union for Conservation of Nature (IUCN,
see <http://www.iucnredlist.org>).
Author: Gilles Dauby
Maintainer: Gilles Dauby <gildauby@gmail.com>
Diff between ConR versions 1.2.3 dated 2019-05-07 and 1.2.4 dated 2019-10-14
ConR-1.2.3/ConR/R/Malagasy_amphibian.R |only ConR-1.2.3/ConR/R/plantspeciesdistribution.R |only ConR-1.2.4/ConR/DESCRIPTION | 7 ConR-1.2.4/ConR/MD5 | 33 ConR-1.2.4/ConR/R/IUCNeval.functionv11.R | 33 ConR-1.2.4/ConR/R/Madagascar.protec.R |only ConR-1.2.4/ConR/R/Malagasy.amphibian.R |only ConR-1.2.4/ConR/R/dataset.ex.R |only ConR-1.2.4/ConR/build/partial.rdb |binary ConR-1.2.4/ConR/build/vignette.rds |binary ConR-1.2.4/ConR/inst/doc/my-vignette.html | 448 +++++++--- ConR-1.2.4/ConR/man/AOO.computing.Rd | 2 ConR-1.2.4/ConR/man/IUCN.eval.Rd | 2 ConR-1.2.4/ConR/man/Madagascar.protec.Rd | 12 ConR-1.2.4/ConR/man/Malagasy.amphibian.Rd | 21 ConR-1.2.4/ConR/man/dataset.ex.Rd | 14 ConR-1.2.4/ConR/man/land.Rd | 3 ConR-1.2.4/ConR/tests/testthat/IUCN_results.xlsx |binary ConR-1.2.4/ConR/vignettes/IUCN__results_map/number_threatened_sp.png |binary ConR-1.2.4/ConR/vignettes/IUCN__results_map/proportion_threatened_sp.png |binary 20 files changed, 390 insertions(+), 185 deletions(-)
Title: Unconditional Exact Test
Description: Performs unconditional exact tests and power calculations for 2x2 contingency tables.
Author: Peter Calhoun [aut, cre]
Maintainer: Peter Calhoun <calhoun.peter@gmail.com>
Diff between Exact versions 1.7 dated 2016-10-22 and 2.0 dated 2019-10-14
Exact-1.7/Exact/R/boschloo_TX.R |only Exact-1.7/Exact/R/csmMod_Tbls.R |only Exact-1.7/Exact/R/csm_Tbls.R |only Exact-2.0/Exact/DESCRIPTION | 12 +- Exact-2.0/Exact/MD5 | 51 ++++++---- Exact-2.0/Exact/NAMESPACE | 4 Exact-2.0/Exact/R/binom.CI.R | 2 Exact-2.0/Exact/R/binomialCode.R | 88 ++++++++++-------- Exact-2.0/Exact/R/chisq_TX.R |only Exact-2.0/Exact/R/confInt.R |only Exact-2.0/Exact/R/confIntTemp.R |only Exact-2.0/Exact/R/csmApprox_TX.R | 45 ++++----- Exact-2.0/Exact/R/csmTemp.R |only Exact-2.0/Exact/R/csmTemp2sidedDelta.R |only Exact-2.0/Exact/R/dbinomCalc.R |only Exact-2.0/Exact/R/exact.reject.region.R |only Exact-2.0/Exact/R/exact.test.R | 100 +++++++++++--------- Exact-2.0/Exact/R/fisher.2x2.R | 47 ++++++--- Exact-2.0/Exact/R/maxPvalue.R | 44 +++------ Exact-2.0/Exact/R/maxPvalueLookup.R |only Exact-2.0/Exact/R/methodText.R |only Exact-2.0/Exact/R/moreExtreme.R |only Exact-2.0/Exact/R/moreExtremeCSM.R |only Exact-2.0/Exact/R/multinomialCode.R | 10 +- Exact-2.0/Exact/R/power.exact.test.R | 106 +++++++++++----------- Exact-2.0/Exact/R/santner_TX.R | 19 ++- Exact-2.0/Exact/R/searchExtreme.R |only Exact-2.0/Exact/R/zpooled_TX.R | 71 +++++++++++++- Exact-2.0/Exact/R/zunpooled_TX.R | 19 ++- Exact-2.0/Exact/build/partial.rdb |binary Exact-2.0/Exact/inst |only Exact-2.0/Exact/man/Exact-package.Rd | 66 +++---------- Exact-2.0/Exact/man/exact.reject.region.Rd |only Exact-2.0/Exact/man/exact.test.Rd | 139 ++++++++++++++++------------- Exact-2.0/Exact/man/power.exact.test.Rd | 55 +++++++---- 35 files changed, 496 insertions(+), 382 deletions(-)
Title: A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer
Maintainer: James Dalgleish <james.dalgleish@nih.gov>
Diff between CNVScope versions 2.7.2.5 dated 2019-09-22 and 2.7.7 dated 2019-10-14
CNVScope-2.7.2.5/CNVScope/vignettes/interchromosomal_view.png |only CNVScope-2.7.7/CNVScope/DESCRIPTION | 8 CNVScope-2.7.7/CNVScope/MD5 | 32 CNVScope-2.7.7/CNVScope/R/CNVScopeserver.R | 5 CNVScope-2.7.7/CNVScope/R/runCNVScopeShiny.R | 2 CNVScope-2.7.7/CNVScope/inst/doc/additonal_examples.Rmd | 580 +++++----- CNVScope-2.7.7/CNVScope/inst/doc/additonal_examples.html | 2 CNVScope-2.7.7/CNVScope/inst/doc/create_input_matrix.R | 7 CNVScope-2.7.7/CNVScope/inst/doc/create_input_matrix.Rmd | 288 ++-- CNVScope-2.7.7/CNVScope/inst/doc/create_input_matrix.html | 19 CNVScope-2.7.7/CNVScope/vignettes/NBL_custom_sample_matched_input_matrix_1e5binsize_parallel.rds |only CNVScope-2.7.7/CNVScope/vignettes/NBL_custom_sample_matched_input_matrix_1e7binsize.rds |only CNVScope-2.7.7/CNVScope/vignettes/NBL_custom_sample_matched_input_matrix_1e8binsize.rds |only CNVScope-2.7.7/CNVScope/vignettes/NBL_custom_sample_matched_input_matrix_2.5e5binsize_parallel.rds |only CNVScope-2.7.7/CNVScope/vignettes/NBL_data_files.png |binary CNVScope-2.7.7/CNVScope/vignettes/additonal_examples.Rmd | 580 +++++----- CNVScope-2.7.7/CNVScope/vignettes/chr11_1e5_nbl.jpg |only CNVScope-2.7.7/CNVScope/vignettes/chr11_1e6_nbl.jpg |only CNVScope-2.7.7/CNVScope/vignettes/chr11_1e7_nbl.jpg |only CNVScope-2.7.7/CNVScope/vignettes/chr11_1e8_nbl.jpg |only CNVScope-2.7.7/CNVScope/vignettes/chr11_2.5e5_nbl.jpg |only CNVScope-2.7.7/CNVScope/vignettes/create_input_matrix.Rmd | 288 ++-- 22 files changed, 930 insertions(+), 881 deletions(-)