Title: Two-/Three-Stage Designs for Phase 1&2 Clinical Trials
Description: Calculate optimal Zhong's two-/three-stage Phase II designs (see Zhong (2012) <doi:10.1016/j.cct.2012.07.006>). Generate Target Toxicity decision table for Phase I dose-finding (two-/three-stage). This package also allows users to run dose-finding simulations based on customized decision table.
Author: Wenchuan Guo, Jianan Hui, Bob Zhong
Maintainer: Wenchuan Guo <wguo1017@gmail.com>
Diff between tsdf versions 1.1-4 dated 2018-01-11 and 1.1-7 dated 2019-05-31
DESCRIPTION | 19 MD5 | 52 +- NAMESPACE | 30 - NEWS | 105 ---- R/dec.sim.R | 270 +++++------ R/dec.table.R | 162 +++--- R/internal.R | 865 +++++++++++++++++++------------------ R/opt.design.R | 156 +++--- R/sl.sim.R | 86 +-- R/utility.R | 556 +++++++++++------------ README.md | 42 - build/vignette.rds |binary inst/doc/my-vignette.R | 188 ++++---- inst/doc/my-vignette.Rmd | 302 ++++++------ inst/doc/my-vignette.html | 1073 ++++++++++++++++++++++++---------------------- inst/extdata/decTable.csv | 24 - inst/extdata/testS.csv | 6 man/dec.sim.Rd | 98 ++-- man/dec.table.Rd | 119 ++--- man/opt.design.Rd | 156 +++--- man/plot.dec.sim.Rd | 86 +-- man/plot.dec.table.Rd | 48 +- man/print.dec.table.Rd | 44 - man/print.opt.design.Rd | 50 +- man/sl.sim.Rd | 90 +-- man/summary.dec.sim.Rd | 56 +- vignettes/my-vignette.Rmd | 302 ++++++------ 27 files changed, 2523 insertions(+), 2462 deletions(-)
Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear models
(see, Piironen, Paasiniemi and Vehtari, 2018, <arXiv:1810.02406>).
The package is compatible with the 'rstanarm' and 'brms' packages, but other
reference models can also be used. See the package vignette for more
information and examples.
Author: Juho Piironen [cre, aut],
Markus Paasiniemi [aut],
Aki Vehtari [aut],
Jonah Gabry [ctb],
Paul-Christian Bürkner [ctb]
Maintainer: Juho Piironen <juho@cai.fi>
Diff between projpred versions 1.1.1 dated 2019-03-12 and 1.1.2 dated 2019-05-31
DESCRIPTION | 10 +-- MD5 | 30 +++++----- NEWS.md | 4 + R/cv_varsel.R | 4 - R/methods.R | 12 ++-- R/misc.R | 8 +- R/projpred-package.R | 2 inst/doc/quickstart.html | 21 ++++--- tests/testthat/test_misc.R | 9 +-- vignettes/quickstart_files/figure-html/unnamed-chunk-10-1.png |binary vignettes/quickstart_files/figure-html/unnamed-chunk-11-1.png |binary vignettes/quickstart_files/figure-html/unnamed-chunk-26-1.png |binary vignettes/quickstart_files/figure-html/unnamed-chunk-27-1.png |binary vignettes/quickstart_files/figure-html/unnamed-chunk-28-1.png |binary vignettes/quickstart_files/figure-html/unnamed-chunk-6-1.png |binary vignettes/quickstart_files/figure-html/unnamed-chunk-9-1.png |binary 16 files changed, 54 insertions(+), 46 deletions(-)
Title: Multivariate State Space Models
Description: Provides methods to perform parameter estimation and
make analysis of multivariate observed outcomes through time which depends
on a latent state variable. All methods scale well in the dimension
of the observed outcomes at each time point. The package contains an
implementation of a Laplace approximation, particle filters like
suggested by Lin, Zhang, Cheng, & Chen (2005)
<doi:10.1198/016214505000000349>, and the gradient and observed information
matrix approximation suggested by Poyiadjis, Doucet, & Singh (2011)
<doi:10.1093/biomet/asq062>.
Author: Benjamin Christoffersen [cre, aut],
Anthony Williams [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between mssm versions 0.1.0 dated 2019-05-24 and 0.1.1 dated 2019-05-31
DESCRIPTION | 6 - MD5 | 26 +++--- README.md | 128 +++++++++++++++--------------- man/figures/README-plot_run_times_N-1.png |binary src/cloud.h | 6 - src/dists.h | 25 ++++- src/kd-tree.h | 1 src/laplace.cpp | 2 src/problem_data.h | 1 src/utils.h | 2 tests/testthat.R | 2 tests/testthat/KD-tree.RDS |binary tests/testthat/helper.R | 2 tests/testthat/test-gets-old-FSKA.R | 7 + 14 files changed, 119 insertions(+), 89 deletions(-)
Title: Generate PDFs and CDFs from Binned Data
Description: Provides several methods for generating density functions
based on binned data. Methods include step function, recursive
subdivision, and optimized spline. Data are assumed to be nonnegative,
but the bin widths need not be equal, and the top bin need not have an
upper bound. All PDF smoothing methods maintain the areas specified by
the binned data. (Equivalently, all CDF smoothing methods interpolate
the points specified by the binned data.) An estimate for the mean of
the distribution may be supplied as an optional argument, which greatly
improves the reliability of statistics computed from the smoothed density
functions. Includes methods for estimating the Gini coefficient, the
Theil index, percentiles, and random deviates from a smoothed
distribution. Among the three methods, the optimized spline (splinebins)
is recommended for most purposes. The percentile and random-draw
functions only support splinebins.
Author: David J. Hunter and McKalie Drown
Maintainer: Dave Hunter <dhunter@westmont.edu>
Diff between binsmooth versions 0.1.0 dated 2016-08-12 and 0.2.0 dated 2019-05-31
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 25 ++++++++++++++++++------- NEWS |only R/gini.R |only R/sb_percentiles.R |only R/sb_sample.R |only R/simcounty.R | 4 +++- R/splinebins.R | 10 ++++++++-- R/stats_from_distribution.R |only R/theil.R |only man/gini.Rd |only man/rsubbins.Rd | 6 ++++-- man/sb_percentiles.Rd |only man/sb_sample.Rd |only man/simcounty.Rd | 17 +++++++++++++---- man/splinebins.Rd | 14 +++++++++----- man/stats_from_distribution.Rd |only man/stepbins.Rd | 10 ++++++---- man/theil.Rd |only 19 files changed, 77 insertions(+), 36 deletions(-)
Title: Generator of Semi-Artificial Data
Description: Contains methods to generate and evaluate semi-artificial data sets.
Based on a given data set different methods learn data properties using machine learning algorithms and
generate new data with the same properties.
The package currently includes the following data generators:
i) a RBF network based generator using rbfDDA() from package 'RSNNS',
ii) a Random Forest based generator for both classification and regression problems
iii) a density forest based generator for unsupervised data
Data evaluation support tools include:
a) single attribute based statistical evaluation: mean, median, standard deviation, skewness, kurtosis, medcouple, L/RMC, KS test, Hellinger distance
b) evaluation based on clustering using Adjusted Rand Index (ARI) and FM
c) evaluation based on classification performance with various learning models, e.g., random forests.
Author: Marko Robnik-Sikonja
Maintainer: Marko Robnik-Sikonja <marko.robnik@fri.uni-lj.si>
Diff between semiArtificial versions 2.2.5 dated 2017-03-31 and 2.3.1 dated 2019-05-31
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/forestDataGen.R | 15 ++++++++++++--- R/misc.R | 40 ---------------------------------------- R/rbfDataGen.R | 5 +++++ man/cleanData.Rd | 11 ++++++----- man/newdata.Rd | 4 ++-- man/rbfDataGen.Rd | 2 +- 10 files changed, 44 insertions(+), 65 deletions(-)
More information about semiArtificial at CRAN
Permanent link
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 1.3 dated 2019-03-22 and 1.4 dated 2019-05-31
openssl-1.3/openssl/inst/mac-askpass |only openssl-1.4/openssl/DESCRIPTION | 24 openssl-1.4/openssl/MD5 | 61 openssl-1.4/openssl/NAMESPACE | 21 openssl-1.4/openssl/NEWS | 6 openssl-1.4/openssl/R/aes.R | 6 openssl-1.4/openssl/R/diffie.R | 4 openssl-1.4/openssl/R/hash.R | 2 openssl-1.4/openssl/R/info.R | 2 openssl-1.4/openssl/R/keygen.R | 16 openssl-1.4/openssl/R/list.R | 1 openssl-1.4/openssl/R/openssh.R | 18 openssl-1.4/openssl/R/signing.R | 7 openssl-1.4/openssl/R/ssh2.R | 21 openssl-1.4/openssl/R/x25519.R |only openssl-1.4/openssl/build/vignette.rds |binary openssl-1.4/openssl/inst/cacert.pem | 1979 +++++----------- openssl-1.4/openssl/inst/doc/bignum.html | 28 openssl-1.4/openssl/inst/doc/crypto_hashing.html | 8 openssl-1.4/openssl/inst/doc/keys.html | 42 openssl-1.4/openssl/inst/doc/secure_rng.html | 18 openssl-1.4/openssl/man/curve25519.Rd |only openssl-1.4/openssl/man/keygen.Rd | 6 openssl-1.4/openssl/man/signatures.Rd | 3 openssl-1.4/openssl/src/info.c | 12 openssl-1.4/openssl/src/keygen.c | 46 openssl-1.4/openssl/src/keys.c | 16 openssl-1.4/openssl/src/x25519.c |only openssl-1.4/openssl/tests/keys/id_ed25519 | 12 openssl-1.4/openssl/tests/keys/id_ed25519.openssh.pw |only openssl-1.4/openssl/tests/keys/id_ed25519.pem |only openssl-1.4/openssl/tests/keys/id_ed25519.pw |only openssl-1.4/openssl/tests/keys/message.sig.ed25519.raw |only openssl-1.4/openssl/tests/keys/message.sig.ed25519.sha1 |only openssl-1.4/openssl/tests/keys/signatures.txt | 3 openssl-1.4/openssl/tests/testthat/test_keys_ed25519.R |only openssl-1.4/openssl/tests/testthat/test_sodium.R |only 37 files changed, 990 insertions(+), 1372 deletions(-)
Title: Pedigree Functions
Description: Routines to handle family data with a pedigree object (2014, <doi: 10.1159/000363105>). The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.
Author: Jason Sinnwell [aut, cre],
Terry Therneau [aut],
Daniel Schaid [ctb],
Elizabeth Atkinson [ctb],
Carly Mester [ctb]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between kinship2 versions 1.6.4 dated 2015-08-03 and 1.8.4 dated 2019-05-31
kinship2-1.6.4/kinship2/inst/GPL2.txt |only kinship2-1.6.4/kinship2/inst/doc/pedigree.pdf |only kinship2-1.6.4/kinship2/inst/doc/pedigree.snw |only kinship2-1.6.4/kinship2/noweb/kinship.R |only kinship2-1.6.4/kinship2/noweb/pedigree.R |only kinship2-1.6.4/kinship2/tests/kin1.R |only kinship2-1.6.4/kinship2/tests/kin1.Rout.save |only kinship2-1.6.4/kinship2/tests/ped1.pdf |only kinship2-1.6.4/kinship2/tests/ped2.pdf |only kinship2-1.6.4/kinship2/tests/ped27_71.txt |only kinship2-1.6.4/kinship2/tests/ped3.txt |only kinship2-1.6.4/kinship2/tests/sampleped1.pdf |only kinship2-1.6.4/kinship2/tests/test.pedigree.legend.R |only kinship2-1.6.4/kinship2/tests/test.pedigree.legend.Rout.save |only kinship2-1.6.4/kinship2/tests/test.pedigree.trim.R |only kinship2-1.6.4/kinship2/tests/test.pedigree.trim.Rout.save |only kinship2-1.6.4/kinship2/vignettes/pedigree.snw |only kinship2-1.8.4/kinship2/DESCRIPTION | 42 kinship2-1.8.4/kinship2/MD5 | 118 kinship2-1.8.4/kinship2/NAMESPACE | 4 kinship2-1.8.4/kinship2/R/align.pedigree.R | 3 kinship2-1.8.4/kinship2/R/alignped1.R | 4 kinship2-1.8.4/kinship2/R/bitSize.R | 36 kinship2-1.8.4/kinship2/R/findAvailAffected.R | 111 kinship2-1.8.4/kinship2/R/findAvailNonInform.R | 45 kinship2-1.8.4/kinship2/R/findUnavailable.R | 353 kinship2-1.8.4/kinship2/R/fixParents.R |only kinship2-1.8.4/kinship2/R/legendPlot.R |only kinship2-1.8.4/kinship2/R/ped2df.R | 3 kinship2-1.8.4/kinship2/R/pedigree.R | 68 kinship2-1.8.4/kinship2/R/pedigree.legend.R | 13 kinship2-1.8.4/kinship2/R/pedigree.shrink.R | 134 kinship2-1.8.4/kinship2/R/pedigree.shrink.minor.R | 42 kinship2-1.8.4/kinship2/R/pedigree.trim.R | 24 kinship2-1.8.4/kinship2/R/pedigree.unrelated.R | 58 kinship2-1.8.4/kinship2/R/plot.pedigree.R | 12 kinship2-1.8.4/kinship2/R/plot.pedigree.shrink.R | 40 kinship2-1.8.4/kinship2/R/print.pedigree.shrink.R | 73 kinship2-1.8.4/kinship2/R/printBanner.R | 165 kinship2-1.8.4/kinship2/build/vignette.rds |binary kinship2-1.8.4/kinship2/data/sample.ped.tab.gz |binary kinship2-1.8.4/kinship2/data/testped1.tab.gz |binary kinship2-1.8.4/kinship2/inst/NEWS.Rd | 34 kinship2-1.8.4/kinship2/inst/doc/pedigree.R | 218 kinship2-1.8.4/kinship2/inst/doc/pedigree.Rmd |only kinship2-1.8.4/kinship2/inst/doc/pedigree.html |only kinship2-1.8.4/kinship2/man/fixParents.Rd |only kinship2-1.8.4/kinship2/man/minnbreast.Rd | 49 kinship2-1.8.4/kinship2/man/pedigree.Rd | 18 kinship2-1.8.4/kinship2/man/pedigree.legend.Rd | 2 kinship2-1.8.4/kinship2/man/plot.pedigree.Rd | 37 kinship2-1.8.4/kinship2/man/plot.pedigree.shrink.Rd | 33 kinship2-1.8.4/kinship2/noweb/Makefile | 7 kinship2-1.8.4/kinship2/noweb/align.Rnw | 3 kinship2-1.8.4/kinship2/noweb/align2.Rnw | 4 kinship2-1.8.4/kinship2/noweb/all.aux | 41 kinship2-1.8.4/kinship2/noweb/all.log | 712 - kinship2-1.8.4/kinship2/noweb/all.nw | 1391 +- kinship2-1.8.4/kinship2/noweb/all.out |only kinship2-1.8.4/kinship2/noweb/all.tex | 6104 +++++------ kinship2-1.8.4/kinship2/noweb/checks.Rnw | 184 kinship2-1.8.4/kinship2/noweb/kinship.Rnw | 1 kinship2-1.8.4/kinship2/noweb/noweb.sty | 985 - kinship2-1.8.4/kinship2/noweb/pedigree.Rmd |only kinship2-1.8.4/kinship2/noweb/pedigree.Rnw | 101 kinship2-1.8.4/kinship2/noweb/pedigree.shrink.Rnw | 1083 - kinship2-1.8.4/kinship2/noweb/plot.Rnw | 25 kinship2-1.8.4/kinship2/tests/failure.Rout.save | 10 kinship2-1.8.4/kinship2/tests/monozygote.R | 13 kinship2-1.8.4/kinship2/tests/monozygote.Rout.save | 57 kinship2-1.8.4/kinship2/tests/test.fixParents.R |only kinship2-1.8.4/kinship2/tests/test.pedigree.shrink.Rout.save | 25 kinship2-1.8.4/kinship2/vignettes/pedigree.Rmd |only 73 files changed, 5359 insertions(+), 7126 deletions(-)
Title: Interface to the Fish Tree of Life API
Description: An interface to the Fish Tree of Life API to download taxonomies,
phylogenies, fossil calibrations, and diversification rate information for
ray-finned fishes.
Author: Jonathan Chang [aut, cre] (<https://orcid.org/0000-0002-3811-1254>),
Michael E Alfaro [ctb],
Daniel L Rabosky [ctb],
Stephen A Smith [ctb]
Maintainer: Jonathan Chang <jonathan.chang@ucla.edu>
Diff between fishtree versions 0.3.0 dated 2019-04-03 and 0.3.1 dated 2019-05-31
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NAMESPACE | 2 -- NEWS.md | 6 ++++-- R/functions.R | 21 +++++++++++++-------- R/utils.R | 1 - build/vignette.rds |binary inst/CITATION | 8 +++----- inst/WORDLIST | 3 +++ inst/doc/community-analysis.html | 29 ++++++++++++++++------------- man/fishtree_phylogeny.Rd | 7 +++++++ 11 files changed, 59 insertions(+), 44 deletions(-)
Title: Analytic Insurance Rating Techniques
Description: Methods for insurance rating. It provides a data driven strategy for the construction of
insurance tariff classes. This strategy is based on the work by Antonio and Valdez (2012) <doi:10.1007/s10182-011-0152-7>.
The package also adds functionality showing additional lines for the reference
categories in the levels of the coefficients in the output of a generalized linear regression analysis.
In addition it implements a procedure determining the level of a factor with the largest exposure,
and thereafter changing the base level of the factor to this level.
Author: Martin Haringa
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between insurancerating versions 0.4.1 dated 2019-04-10 and 0.4.2 dated 2019-05-31
DESCRIPTION | 10 - MD5 | 19 +-- NAMESPACE | 3 NEWS.md | 5 R/construct_tariff_classes.R | 249 +++++++++++++++++++++++++++++++++------- R/plot_tariff_classes.R | 13 +- R/zzz.R | 2 man/autoplot.insurancerating.Rd | 9 + man/construct_tariff_classes.Rd | 43 +++++- man/figures/plaatje-1.png |binary man/get_splits.Rd |only 11 files changed, 283 insertions(+), 70 deletions(-)
More information about insurancerating at CRAN
Permanent link
Title: Fused Sparse Structural Equation Models to Jointly Infer Gene
Regulatory Network
Description: An optimizer of Fused-Sparse Structural Equation Models, which is
the state of the art jointly fused sparse maximum likelihood function
for structural equation models proposed by Xin Zhou and Xiaodong Cai (2018
<doi:10.1101/466623>).
Author: Xin Zhou, Xiaodong Cai
Maintainer: Xin Zhou <xxz220@miami.edu>
Diff between fssemR versions 0.1.3 dated 2019-03-15 and 0.1.4 dated 2019-05-31
DESCRIPTION | 9 - MD5 | 41 ++++--- NAMESPACE | 3 R/fssem.R | 59 +++++++---- R/fssemR-package.R | 10 - R/generator.R | 230 ++++++++++++++++++++++++++++++++++++++++++++ R/solver.R | 65 ++++++++---- R/utils.R | 45 ++++++++ README.md | 7 - build |only inst/02_FSSEMsolver.R | 22 ++-- inst/04_FSSEMsolver2.R | 24 ++-- inst/README.md |only inst/doc |only man/fssemR.Rd | 8 - man/multiFSSEMiPALM.Rd | 8 - man/multiFSSEMiPALM2.Rd | 8 - man/opt.multiFSSEMiPALM.Rd | 8 - man/opt.multiFSSEMiPALM2.Rd | 8 - man/randomFSSEMdata2.Rd |only src/fssemR.cpp | 17 ++- src/fssemR.h | 3 vignettes |only 23 files changed, 458 insertions(+), 117 deletions(-)
Title: Plot ForestGEO Data
Description: To help you access, transform, analyze, and
visualize ForestGEO data, we developed a collection of R packages
(<https://forestgeo.github.io/fgeo/>). This package, in particular,
helps you to plot ForestGEO data. To learn more about ForestGEO visit
<http://www.forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] (<https://orcid.org/0000-0002-1986-7988>),
CTFS-ForestGEO [cph, fnd]
Maintainer: Mauro Lepore <leporem@si.edu>
Diff between fgeo.plot versions 1.1.6 dated 2019-05-20 and 1.1.8 dated 2019-05-31
DESCRIPTION | 12 MD5 | 20 NEWS.md | 42 - R/autoplot-sp_elev.R | 410 +++++----- R/autoplot.fgeo_habitat.R | 54 - R/autoplot_by_species.R | 320 ++++---- R/plot_dbh_bubles_by_quadrat.R | 374 ++++----- R/plot_tag_status_by_subquadrat.R | 1068 ++++++++++++++-------------- README.md | 16 tests/testthat/test-autoplot-fgeo_habitat.R | 6 tests/testthat/test-plot-fgeo_habitat.R | 6 11 files changed, 1149 insertions(+), 1179 deletions(-)
Title: Simulate Models Based on the Generalized Linear Model
Description: Simulates regression models,
including both simple regression and generalized linear mixed
models with up to three level of nesting. Power simulations that are
flexible allowing the specification of missing data, unbalanced designs,
and different random error distributions are built into the package.
Author: Brandon LeBeau [aut, cre]
Maintainer: Brandon LeBeau <lebebr01+simglm@gmail.com>
Diff between simglm versions 0.7.2 dated 2019-01-23 and 0.7.4 dated 2019-05-31
DESCRIPTION | 11 MD5 | 41 NAMESPACE | 4 R/err_sim.r | 472 - R/fixef_sim.r | 1668 +++--- R/pow_sim.r | 2006 +++---- R/simglm_master_function.r | 110 build/vignette.rds |binary inst/doc/GeneralizedModels_legacy.html | 77 inst/doc/Intro_legacy.html | 322 - inst/doc/Power_legacy.html | 165 inst/doc/simulation_arguments.R | 27 inst/doc/simulation_arguments.Rmd | 1248 ++-- inst/doc/simulation_arguments.html | 8972 ++++++++++++++++----------------- inst/doc/tidy_simulation.R | 39 inst/doc/tidy_simulation.Rmd | 733 +- inst/doc/tidy_simulation.html | 416 - inst/doc/unbalanced_legacy.html | 7 man/replicate_simulation.Rd | 8 man/simulate_heterogeneity.Rd |only vignettes/simulation_arguments.Rmd | 1248 ++-- vignettes/tidy_simulation.Rmd | 733 +- 22 files changed, 9203 insertions(+), 9104 deletions(-)
Title: Access to Open Street Map Raster Images
Description: Accesses high resolution raster maps using the OpenStreetMap
protocol. Dozens of road, satellite, and topographic map servers are directly
supported, including Apple, Mapnik, Bing, and stamen. Additionally raster maps
may be constructed using custom tile servers. Maps can be
plotted using either base graphics, or ggplot2. This package is not affiliated
with the OpenStreetMap.org mapping project.
Author: Ian Fellows, using the JMapViewer library by Jan Peter Stotz
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between OpenStreetMap versions 0.3.3 dated 2016-09-09 and 0.3.4 dated 2019-05-31
DESCRIPTION | 10 - MD5 | 12 - R/osm.R | 114 +++++++-------- inst/java/JMapViewer.jar |binary inst/java/RTileController.jar |binary java/RTileController.java | 2 java/org/openstreetmap/gui/jmapviewer/OsmTileLoader.java | 2 7 files changed, 67 insertions(+), 73 deletions(-)
Title: Number and Brightness Image Analysis
Description: Calculation of molecular number and brightness from
fluorescence microscopy image series. The software was published in a 2016
paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for the
technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>. A review
of the technique was published in 2017 <doi:10.1016/j.ymeth.2017.12.001>.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>),
Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>),
Sergi Padilla-Parra [ctb, ths, cph]
(<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between nandb versions 2.0.0 dated 2018-11-11 and 2.0.1 dated 2019-05-31
DESCRIPTION | 24 ++++----- MD5 | 38 +++++++------- NEWS.md | 6 ++ R/brightness.R | 4 - R/cc_brightness.R | 4 - R/cc_number.R | 4 - R/number.R | 4 - R/utils.R | 79 ++++--------------------------- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 30 +++++++++-- inst/doc/batch-mode.html | 41 ++++++++++++---- inst/doc/brightness-timeseries.html | 7 +- inst/doc/single-images.R | 2 inst/doc/single-images.Rmd | 2 inst/doc/single-images.html | 51 ++++++++++++++------ tests/testthat/test-class_constructors.R | 28 +++++----- tests/testthat/test-number.R | 50 ++++++++++++------- tests/testthat/test-utils.R | 17 ------ vignettes/single-images.Rmd | 2 20 files changed, 205 insertions(+), 188 deletions(-)
Title: The Kernel Method of Test Equating
Description: Implements the kernel method of test equating as defined in von Davier, A. A., Holland, P. W. and Thayer, D. T. (2004) <doi: 10.1007/b97446> and Andersson, B. and Wiberg, M. (2017) <doi: 10.1007/s11336-016-9528-7> using the CB, EG, SG, NEAT CE/PSE and NEC designs, supporting Gaussian, logistic and uniform kernels and unsmoothed and pre-smoothed input data.
Author: Björn Andersson [aut, cre],
Kenny Bränberg [aut],
Marie Wiberg [aut]
Maintainer: Björn Andersson <bjoern.h.andersson@gmail.com>
Diff between kequate versions 1.6.1 dated 2017-03-12 and 1.6.2 dated 2019-05-31
DESCRIPTION | 20 +++-- MD5 | 18 ++-- NEWS | 6 + R/kernel.R | 190 +++++++++++++++++++++++++++++++------------------ build/vignette.rds |binary inst/doc/irtguide.pdf |binary inst/doc/kequate.pdf |binary man/irtose.Rd | 34 +++++--- man/kequate-package.Rd | 14 ++- man/kequate.Rd | 8 ++ 10 files changed, 190 insertions(+), 100 deletions(-)
Title: Dynamic Functional Connectivity Analysis
Description: An implementation of multivariate linear process bootstrap (MLPB) method and sliding window technique to assess the dynamic functional connectivity (dFC) estimate by providing its confidence bands, based on Maria Kudela (2017) <doi: 10.1016/j.neuroimage.2017.01.056>.
It also integrates features to visualize non-zero coverage for selected a-priori regions of interest estimated by the dynamic functional connectivity model (dFCM) and dynamic functional connectivity (dFC) curves for reward-related a-priori regions of interest where the activation-based analysis reported.
Author: Zikai Lin [aut, cre],
Maria Kudela [aut],
Jaroslaw Harezlak [aut],
Mario Dzemidzic [aut]
Maintainer: Zikai Lin <ziklin@iu.edu>
Diff between dfConn versions 0.1.1 dated 2019-03-25 and 0.2.0 dated 2019-05-31
DESCRIPTION | 6 MD5 | 29 - NAMESPACE | 3 R/lme_model0.r | 51 +- R/lme_model6.r | 955 ++++++++++++++++++++++++------------------------- R/mlpb.R | 128 ++---- R/nzc_mat_vis.r | 1 R/option_control.R |only R/summary_table.r | 150 ++++--- R/utils.r | 1 data/fMRI_dataList.rda |binary man/MLPB_boot.Rd | 39 -- man/lmmConn.Rd | 31 - man/lmmDyn.Rd | 41 -- man/nzc_vis.Rd | 3 man/options_boot.Rd |only man/options_lme.Rd |only 17 files changed, 700 insertions(+), 738 deletions(-)
Title: Linear and Nonlinear Methods for Analyzing Daily and Monthly
Dendroclimatological Data
Description: Provides novel dendroclimatological methods, primarily used by the
Tree-ring research community. There are four 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. Similar function is daily_response_seasorr(),
which implements partial correlations in the analysis of daily response functions.
For the enthusiast of monthly data, there is monthly_response() function.
The last core function is compare_methods(), which effectively compares several
linear and nonlinear regression algorithms on the task of climate reconstruction.
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between dendroTools versions 1.0.4 dated 2019-04-21 and 1.0.5 dated 2019-05-31
DESCRIPTION | 8 +- MD5 | 37 ++++++----- NAMESPACE | 40 ++++++------ NEWS.md | 8 ++ R/daily_response.R | 53 ++++++++++------- R/daily_response_seascorr.R | 102 +++++++++++++++++++++++---------- R/generics.R |only R/monthly_response.R | 43 ++++++++----- R/monthly_response_seascorr.R |only R/plot_extreme.R | 6 + R/plot_heatmap.R | 9 +- R/plot_specific.R | 8 ++ inst/doc/Examples_daily_response.R | 4 - inst/doc/Examples_daily_response.html | 80 ++++++++++++------------- inst/doc/compare_methods_vignette.R | 4 - inst/doc/compare_methods_vignette.html | 18 ++--- man/daily_response.Rd | 20 ++++-- man/daily_response_seascorr.Rd | 16 +++-- man/monthly_response.Rd | 17 +++-- man/monthly_response_seascorr.Rd |only tests/testthat/test_general.R | 6 - 21 files changed, 293 insertions(+), 186 deletions(-)
Title: Nonlinear Mixed Effects Models in Population Pharmacokinetics
and Pharmacodynamics
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'RxODE' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Yuan Xiong [aut],
Rik Schoemaker [aut] (<https://orcid.org/0000-0002-7538-3005>),
Justin Wilkins [aut] (<https://orcid.org/0000-0002-7099-9396>),
Mirjam Trame [aut],
Richard Hooijmaijers [aut],
Teun Post [aut],
Robert Leary [ctb],
Wenping Wang [aut, cre],
Hadley Wickham [ctb],
Dirk Eddelbuettel [cph],
Johannes Pfeifer [ctb],
Robert B. Schnabel [ctb],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Audrey Lavenu [ctb],
Marc Lavielle [ctb],
David Ardia [cph],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Katharine Mullen [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between nlmixr versions 1.1.0-8 dated 2019-05-31 and 1.1.0-9 dated 2019-05-31
nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.cmt-d-focei-799cc4a5d474b62a5cd8962ec60f5cd2.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.cmt-theo_sd-nlme-5a52a6e14c41d57f14800333b995589e.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-saem-fc93affe842124d57c37f8d5220fd1b9.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-fo-98c8da9f16794f97da80c121d03bf3b6.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-foce-9b02c0a9826f962259d3579e16918f7e.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-focei-8511f1da52ffb52a64046a9b12e4c314.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-focei-cdab62d4795084a5a33ff1bba675543c.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-focei-d62efb1b96bf7ef6ded9f8d993886f01.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-foi-7175e4305f95417e8f4ed3e440baaa7f.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-nlme-68bc30e34affcf0621de04c4741fbeb7.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-nlme-dd40fef2fc181a5a4bd7bc0af73f52dd.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-posthoc-72ed949e3f30b3fa912fea3b7e41654f.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-saem-a02da6689d701adddb9ee20db1120b28.rds |only nlmixr-1.1.0-8/nlmixr/inst/nlmixr-one.compartment-theo_sd-saem-fc93affe842124d57c37f8d5220fd1b9.rds |only nlmixr-1.1.0-9/nlmixr/DESCRIPTION | 6 nlmixr-1.1.0-9/nlmixr/MD5 | 23 nlmixr-1.1.0-9/nlmixr/inst/doc/running_nlmixr.html | 1597 +++++----- nlmixr-1.1.0-9/nlmixr/inst/nlmixr-one.cmt-theo_sd-nlme-fafbd54a79996a01ea5b7de6a8d7212c.rds |only nlmixr-1.1.0-9/nlmixr/inst/nlmixr-one.compartment-theo_sd-focei-a1f34f114ba648e90a70b82a36d8eb5b.rds |only nlmixr-1.1.0-9/nlmixr/inst/nlmixr-one.compartment-theo_sd-saem-1cb146fbba324a1fe760d0b6e8f83240.rds |only nlmixr-1.1.0-9/nlmixr/src/inner.cpp | 4 21 files changed, 824 insertions(+), 806 deletions(-)
More information about MultiwayRegression at CRAN
Permanent link
Title: Random Number Generation for Generalized Poisson Distribution
Description: Generation of univariate and multivariate data that follow the generalized Poisson distribution. The details of the univariate part are explained in Demirtas (2017), and the multivariate part is an extension of the correlated Poisson data generation routine that was introduced in Yahav and Shmueli (2012).
Author: Hesen Li, Ruizhe Chen, Hai Nguyen, Yu-che Chung, Ran Gao, Hakan Demirtas
Maintainer: Ruizhe Chen <rchen18@uic.edu>
Diff between RNGforGPD versions 1.0 dated 2018-04-10 and 1.0.1 dated 2019-05-31
RNGforGPD-1.0.1/RNGforGPD/DESCRIPTION | 16 +++--- RNGforGPD-1.0.1/RNGforGPD/MD5 | 30 ++++++------- RNGforGPD-1.0.1/RNGforGPD/R/GenMVGPois.R | 23 +++++---- RNGforGPD-1.0.1/RNGforGPD/R/GenUniGpois.R | 4 - RNGforGPD-1.0.1/RNGforGPD/R/QuantileGpois.R | 22 +++++++-- RNGforGPD-1.0.1/RNGforGPD/R/RNGforGPD-package.R | 25 ++++------ RNGforGPD-1.0.1/RNGforGPD/R/ValidCorrGpois.R | 8 +-- RNGforGPD-1.0.1/RNGforGPD/build/vignette.rds |binary RNGforGPD-1.0.1/RNGforGPD/inst/doc/RNGfroGPD_vignette.R |only RNGforGPD-1.0.1/RNGforGPD/inst/doc/RNGfroGPD_vignette.Rmd |only RNGforGPD-1.0.1/RNGforGPD/inst/doc/RNGfroGPD_vignette.html |only RNGforGPD-1.0.1/RNGforGPD/man/GenMVGpois.Rd | 18 +++---- RNGforGPD-1.0.1/RNGforGPD/man/GenUniGpois.Rd | 4 - RNGforGPD-1.0.1/RNGforGPD/man/RNGforGPD-package.Rd | 27 +++++------ RNGforGPD-1.0.1/RNGforGPD/man/ValidCorrGpois.Rd | 10 ++-- RNGforGPD-1.0.1/RNGforGPD/vignettes/RNGfroGPD_vignette.Rmd |only RNGforGPD-1.0/RNGforGPD/inst/doc/RNGforGPD_vignette.R |only RNGforGPD-1.0/RNGforGPD/inst/doc/RNGforGPD_vignette.Rmd |only RNGforGPD-1.0/RNGforGPD/inst/doc/RNGforGPD_vignette.html |only RNGforGPD-1.0/RNGforGPD/vignettes/RNGforGPD_vignette.Rmd |only 20 files changed, 100 insertions(+), 87 deletions(-)
Title: Multi-Parent Population QTL Analysis
Description: Analysis of experimental multi-parent populations to detect
regions of the genome (called quantitative trait loci, QTLs)
influencing phenotypic traits. The population must be composed of crosses
between a set of at least three parents (e.g. factorial design,
'diallel', or nested association mapping). The functions cover data
processing, QTL detection, and results visualization. The implemented
methodology is described by Garin, Wimmer, Mezmouk, Malosetti and
van Eeuwijk (2017) <doi:10.1007/s00122-017-2923-3>.
Author: Vincent Garin [aut, cre],
Valentin Wimmer [aut],
Dietrich Borchardt [ctb, dtc],
Fred van Eeuwijk [ctb, ths],
Marcos Malosetti [ctb, ths]
Maintainer: Vincent Garin <vincent.garin6@gmail.com>
Diff between mppR versions 1.1.10 dated 2018-07-01 and 1.2.0 dated 2019-05-31
DESCRIPTION | 18 ++-- MD5 | 55 +++++++------ NAMESPACE | 1 NEWS.md |only R/IBD.mppData.R | 6 - R/IBS.mppData.R | 4 R/IncMat_QTL_MAF.R | 2 R/QC.mppData.R | 12 ++ R/create.mppData.R | 16 +++ README.md | 7 + build/vignette.rds |binary inst/CITATION | 17 +--- inst/doc/mppR_vignette.R | 1 inst/doc/mppR_vignette.pdf |binary inst/doc/mppR_vignette.rnw | 102 ++++++++++++------------- man/QC.mppData.Rd | 4 man/QTL_R2.Rd | 3 man/QTL_pred_R2.Rd | 4 man/create.mppData.Rd | 4 man/mpp_CIM.Rd | 4 man/mpp_CV.Rd | 10 +- man/mpp_proc.Rd | 7 - man/plot.QTLprof.Rd | 3 tests |only vignettes/bibliography/Bibliography_Bibtex.bib | 2 vignettes/mppR_vignette.rnw | 102 ++++++++++++------------- 26 files changed, 203 insertions(+), 181 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Random Graph
Models to Egocentrically Sampled Network Data
Description: Utilities for managing egocentrically sampled network data and a wrapper around the 'ergm' package to facilitate ERGM inference and simulation from such data.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Steven M. Goodreau [ctb],
Martina Morris [ctb],
Kirk Li [ctb],
Emily N. Beylerian [ctb],
Michał Bojanowski [ctb] (<https://orcid.org/0000-0001-7503-852X>),
Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm.ego versions 0.4.0 dated 2018-08-17 and 0.5 dated 2019-05-31
ergm.ego-0.4.0/ergm.ego/tests/testthat/test-testthat.R |only ergm.ego-0.5/ergm.ego/DESCRIPTION | 28 - ergm.ego-0.5/ergm.ego/LICENSE | 2 ergm.ego-0.5/ergm.ego/MD5 | 66 +-- ergm.ego-0.5/ergm.ego/NAMESPACE | 15 ergm.ego-0.5/ergm.ego/R/EgoStat.R | 311 ++++++++++----- ergm.ego-0.5/ergm.ego/R/EgoStat.duration.R | 6 ergm.ego-0.5/ergm.ego/R/EgoStat.node.attr.R | 56 ++ ergm.ego-0.5/ergm.ego/R/InitErgmTerm.R | 6 ergm.ego-0.5/ergm.ego/R/control.ergm.ego.R | 11 ergm.ego-0.5/ergm.ego/R/control.simulate.ergm.ego.R | 6 ergm.ego-0.5/ergm.ego/R/degreedist.R | 41 + ergm.ego-0.5/ergm.ego/R/egodata.R | 96 ++++ ergm.ego-0.5/ergm.ego/R/ergm.ego.R | 36 + ergm.ego-0.5/ergm.ego/R/gof.ergm.ego.R | 32 - ergm.ego-0.5/ergm.ego/R/reweight.egodata.R | 6 ergm.ego-0.5/ergm.ego/R/simulate.ergm.ego.R | 36 - ergm.ego-0.5/ergm.ego/R/summary.ergm.ego.R | 6 ergm.ego-0.5/ergm.ego/R/summary.statistics.egodata.R | 8 ergm.ego-0.5/ergm.ego/R/zzz.R | 8 ergm.ego-0.5/ergm.ego/build/partial.rdb |binary ergm.ego-0.5/ergm.ego/inst/CITATION | 14 ergm.ego-0.5/ergm.ego/inst/NEWS.Rd | 110 +++++ ergm.ego-0.5/ergm.ego/man/control.ergm.ego.Rd | 5 ergm.ego-0.5/ergm.ego/man/degreedist.egodata.Rd | 9 ergm.ego-0.5/ergm.ego/man/egodata.Rd | 40 + ergm.ego-0.5/ergm.ego/man/mixingmatrix.egodata.Rd | 16 ergm.ego-0.5/ergm.ego/man/node-attr-api.Rd | 22 - ergm.ego-0.5/ergm.ego/man/simulate.ergm.ego.Rd | 28 - ergm.ego-0.5/ergm.ego/tests/EgoStat.tests.R | 50 +- ergm.ego-0.5/ergm.ego/tests/boot_jack.R | 6 ergm.ego-0.5/ergm.ego/tests/table_ppop.R | 6 ergm.ego-0.5/ergm.ego/tests/testthat.R | 6 ergm.ego-0.5/ergm.ego/tests/testthat/test-degreedist.R | 15 ergm.ego-0.5/ergm.ego/tests/testthat/test-statmismatch.R |only 35 files changed, 783 insertions(+), 320 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.15 dated 2019-04-03 and 3.16 dated 2019-05-31
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/dependCox.reg.R | 19 ++++++++++++++++--- man/compound.Cox-package.Rd | 4 ++-- man/dependCox.reg.Rd | 17 ++++++++++++++++- 5 files changed, 42 insertions(+), 14 deletions(-)
Title: Statistical Inference and Sure Independence Screening via Ball
Statistics
Description: Hypothesis tests and sure independence screening (SIS) procedure based on ball statistics, including ball divergence <doi:10.1214/17-AOS1579>, ball covariance <doi:10.1080/01621459.2018.1543600>, and ball correlation <doi:10.1080/01621459.2018.1462709>, are developed to analyze complex data in metric spaces, e.g, shape, directional, compositional and symmetric positive definite matrix data. The ball divergence and ball covariance based distribution-free tests are implemented to detecting distribution difference and association in metric spaces <arXiv:1811.03750>. Furthermore, several generic non-parametric feature selection procedures based on ball correlation, BCor-SIS and all of its variants, are implemented to tackle the challenge in the context of ultra high dimensional data.
Author: Xueqin Wang, Wenliang Pan, Heping Zhang, Hongtu Zhu, Yuan Tian, Weinan Xiao, Chengfeng Liu, Ruihuang Liu, Jin Zhu
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between Ball versions 1.3.7 dated 2018-12-14 and 1.3.8 dated 2019-05-31
Ball-1.3.7/Ball/src/utilize_R.c |only Ball-1.3.8/Ball/DESCRIPTION | 12 Ball-1.3.8/Ball/MD5 | 76 Ball-1.3.8/Ball/NAMESPACE | 1 Ball-1.3.8/Ball/NEWS.md | 6 Ball-1.3.8/Ball/R/Ball.R | 6 Ball-1.3.8/Ball/R/bcorsis.R | 126 - Ball-1.3.8/Ball/R/bcov.R | 300 +-- Ball-1.3.8/Ball/R/bd.R | 217 +- Ball-1.3.8/Ball/R/data.R | 5 Ball-1.3.8/Ball/R/nhdist.R | 4 Ball-1.3.8/Ball/R/utilize.R | 79 Ball-1.3.8/Ball/R/wrap_c.R | 10 Ball-1.3.8/Ball/README.md | 8 Ball-1.3.8/Ball/build/vignette.rds |binary Ball-1.3.8/Ball/inst/doc/Ball.R | 36 Ball-1.3.8/Ball/inst/doc/Ball.Rmd | 67 Ball-1.3.8/Ball/inst/doc/Ball.html | 542 ++++- Ball-1.3.8/Ball/man/bcorsis.Rd | 122 - Ball-1.3.8/Ball/man/bcov.Rd | 107 - Ball-1.3.8/Ball/man/bcov.test.Rd | 106 - Ball-1.3.8/Ball/man/bd.Rd | 77 Ball-1.3.8/Ball/man/bd.test.Rd | 79 Ball-1.3.8/Ball/man/nhdist.Rd | 4 Ball-1.3.8/Ball/src/BD.c | 1375 +++++---------- Ball-1.3.8/Ball/src/BD.h | 10 Ball-1.3.8/Ball/src/BI.c | 801 +++----- Ball-1.3.8/Ball/src/ball_init.c | 4 Ball-1.3.8/Ball/src/bcor.c | 1363 ++++++-------- Ball-1.3.8/Ball/src/bcor.h | 4 Ball-1.3.8/Ball/src/kbcov.c | 163 - Ball-1.3.8/Ball/src/kbd.c |only Ball-1.3.8/Ball/src/kbd.h |only Ball-1.3.8/Ball/src/utilities.c | 2364 +++++++++++++++----------- Ball-1.3.8/Ball/src/utilities.h | 37 Ball-1.3.8/Ball/src/utilize_R.h | 13 Ball-1.3.8/Ball/tests/testthat/test_bcorsis.R | 4 Ball-1.3.8/Ball/tests/testthat/test_bcov.R | 16 Ball-1.3.8/Ball/tests/testthat/test_bd.R | 45 Ball-1.3.8/Ball/tests/testthat/test_bd_gwas.R |only Ball-1.3.8/Ball/vignettes/Ball.Rmd | 67 41 files changed, 4200 insertions(+), 4056 deletions(-)
Title: Learn Text 'Embeddings' with 'Starspace'
Description: Wraps the 'StarSpace' library <https://github.com/facebookresearch/StarSpace>
allowing users to calculate word, sentence, article, document, webpage, link and entity 'embeddings'.
By using the 'embeddings', you can perform text based multi-label classification,
find similarities between texts and categories, do collaborative-filtering based recommendation
as well as content-based recommendation, find out relations between entities, calculate
graph 'embeddings' as well as perform semi-supervised learning and multi-task learning on plain text.
The techniques are explained in detail in the paper: 'StarSpace: Embed All The Things!' by Wu et al. (2017), available at <arXiv:1709.03856>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
BNOSAC [cph] (R wrapper),
Facebook, Inc. [cph] (Starspace (BSD licensed))
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between ruimtehol versions 0.2 dated 2019-05-08 and 0.2.1 dated 2019-05-31
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/ground-control-to-ruimtehol.pdf |binary src/Makevars | 10 +++++----- 5 files changed, 17 insertions(+), 13 deletions(-)
Title: Tools for Survival Analysis and Data Science
Description: Collection of functions to improve work-flow in survival analysis and data science.
The package features include: the generation of balanced datasets, live retrieval of
protein coding genes from two public databases, generation of random
matrix based on covariance matrix, cache function to store function results.
This work was supported by two grants from the Portuguese Foundation for Science
and technology, and the EU Commission under SOUND project.
Author: André Veríssimo [aut, cre],
Susana Vinga [aut]
Maintainer: André Veríssimo <andre.verissimo@tecnico.ulisboa.pt>
Diff between loose.rock versions 1.0.13 dated 2019-05-13 and 1.0.16 dated 2019-05-31
DESCRIPTION | 10 +- MD5 | 17 ++-- R/coding.genes.R | 52 +++++++++----- R/sysdata.rda |only build/vignette.rds |binary inst/doc/Overview.R | 16 +++- inst/doc/Overview.Rmd | 18 ++++ inst/doc/Overview.html | 136 +++++++++++++++++-------------------- tests/testthat/test-coding.genes.R | 2 vignettes/Overview.Rmd | 18 ++++ 10 files changed, 164 insertions(+), 105 deletions(-)
Title: Miscellaneous R Functions and Aliases
Description: Provides utility functions for, and drawing on, the 'data.table' package. The package also collates useful miscellaneous functions extending base R not available elsewhere. The name is a portmanteau of 'utils' and the author.
Author: Hugh Parsonage [aut, cre],
Michael Frasco [ctb],
Ben Hamner [ctb]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between hutils versions 1.4.0 dated 2019-03-09 and 1.5.0 dated 2019-05-31
DESCRIPTION | 8 MD5 | 125 ++-- NAMESPACE | 1 NEWS.md | 14 R/RQ.R | 6 R/Switch.R | 232 ++++---- R/aliases.R | 102 +-- R/all_same_sign.R | 86 +-- R/any_grepl.R | 108 ++-- R/auc.R | 304 +++++------ R/dev_copy2a4.R | 50 - R/drop_colr.R | 58 +- R/drop_constant_cols.R | 168 +++--- R/hull.R | 590 +++++++++++----------- R/isAttached.R | 20 R/isTrueFalse.R | 74 +- R/longest_affix.R | 340 ++++++------ R/mean_na.R | 28 - R/number2word.R | 224 ++++---- R/provide-dir.R | 6 R/provide-file.R |only R/replace_pattern_in.R | 102 +-- R/samp.R | 2 R/selector.R | 104 +-- R/set_seed.R | 2 R/unique-keys.R | 56 +- R/weight2rows.R | 334 ++++++------ R/weighted_ntile.R | 88 +-- R/weighted_quantile.R | 122 ++-- R/zzz.R | 12 README.md | 64 +- build/vignette.rds |binary inst/doc/hutils.R | 2 inst/doc/hutils.html | 509 +++++++++--------- inst/extdata/countfiles.ps1 | 6 man/RQ.Rd | 4 man/provide.dir.Rd | 3 man/provide.file.Rd |only tests/testthat/test-1-0-0-major-coalesce.R | 142 ++--- tests/testthat/test-1-1-0-notchin.R | 12 tests/testthat/test-1-2-0_any_grepl.R | 26 tests/testthat/test-1-2-0_drop_grep.R | 14 tests/testthat/test-ahull.R | 140 ++--- tests/testthat/test-any_grepl.R | 16 tests/testthat/test-auc.R | 168 +++--- tests/testthat/test-if_else-factor.R | 140 ++--- tests/testthat/test-replace_pattern_in.R | 42 - tests/testthat/test-switch.R | 192 +++---- tests/testthat/test_1-0-0_generate_LaTeX_manual.R | 26 tests/testthat/test_1-2-0_RQ.R | 44 - tests/testthat/test_1-2-0_aliases.R | 26 tests/testthat/test_1-2-0_all_same_sign.R | 26 tests/testthat/test_1-2-0_if_else.R | 34 - tests/testthat/test_1-2-0_mean_na.R | 16 tests/testthat/test_1-3-0_if_else.R | 72 +- tests/testthat/test_1-3-0_isTrueFalse.R | 28 - tests/testthat/test_1-3-0_longest_affix.R | 140 ++--- tests/testthat/test_1-3-0_mutate_ntile.R | 128 ++-- tests/testthat/test_1-3-0_weight2rows.R | 146 ++--- tests/testthat/test_1-3-0_weighted_ntile.R | 214 +++---- tests/testthat/test_1-4-0_numbers-v-words.R | 92 +-- tests/testthat/test_1-4-0_weight2rows.R | 60 +- tests/testthat/test_1-4-0_weighted-quantile.R | 78 +- tests/testthat/test_1-4-1_samp.R |only tests/testthat/test_benchmarks.R | 162 +++--- 65 files changed, 3086 insertions(+), 3052 deletions(-)
Title: Conditional Distance Correlation Based Feature Screening and
Conditional Independence Inference
Description: Conditional distance correlation <doi:10.1080/01621459.2014.993081> is a novel conditional dependence measurement of two multivariate random variables given a confounding variable. This package provides conditional distance correlation, performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data <doi:10.5705/ss.202014.0117>, and conducts conditional distance covariance test for conditional independence assumption of two multivariate variable.
Author: Wenhao Hu, Mian Huang, Wenliang Pan, Xueqin Wang, Canhong Wen, Yuan Tian, Heping Zhang, Jin Zhu
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between cdcsis versions 2.0.1 dated 2019-04-16 and 2.0.2 dated 2019-05-31
DESCRIPTION | 8 - MD5 | 42 ++++---- NEWS.md | 3 R/RcppExports.R | 4 R/cdcov.R | 87 ++++++++++++----- R/cdcsis-package.R | 3 R/cdcsis.R | 16 ++- man/cdcov.Rd | 16 +-- man/cdcov.test.Rd | 19 ++- man/cdcsis-package.Rd | 7 - man/cdcsis.Rd | 20 +-- src/RcppExports.cpp | 10 + src/cdc_stats.cpp | 151 ++++++++++++++++++++++++++---- src/cdc_stats.h | 13 ++ src/cdc_statstics_method.h | 2 src/cdcsisCpp.cpp | 37 ++++--- src/global.h | 4 src/kde.cpp | 220 +++++++++++++++++++++++++++++++++++++++---- src/kde.h | 50 +++++++++ src/utility.cpp | 221 ++++++++++++++++++++++++++++++++++++++++++-- src/utility.h | 38 +++++++ tests/testthat/test_stats.R | 12 -- 22 files changed, 817 insertions(+), 166 deletions(-)
Title: Touchard Model and Regression
Description: Tools for analyzing count data with the Touchard model (Matsushita et al., 2018, Comm Stat Th Meth <doi:10.1080/03610926.2018.1444177>). It includes univariate estimation (ML and MM) and regression tools developed by Andrade et al. (submitted).
Author: Bernardo Andrade and Sandro Oliveira
Maintainer: Bernardo Andrade <bbandrade@unb.br>
Diff between touchard versions 2.0 dated 2019-02-08 and 2.0.1 dated 2019-05-31
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 4 ++++ R/residuals.toureg.R | 8 ++++---- build/partial.rdb |binary 5 files changed, 16 insertions(+), 12 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 0.9.2 dated 2019-05-31 and 0.9.3 dated 2019-05-31
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/hr_plot.R | 4 ++++ R/or_plot.R | 4 ++++ inst/doc/all_tables_examples.html | 20 ++++++++++---------- inst/doc/bootstrap.html | 22 +++++++++++----------- 7 files changed, 42 insertions(+), 30 deletions(-)
Title: A Method to Search for Differentially Expressed Genes and to
Detect Recurrent Chromosomal Copy Number Aberrations
Description: A fold change rank based method is presented to search for genes with changing
expression and to detect recurrent chromosomal copy number aberrations. This
method may be useful for high-throughput biological data (micro-array, sequencing, ...).
Probabilities are associated with genes or probes in the data set and there is no
problem of multiple tests when using this method. For array-based comparative genomic
hybridization data, segmentation results are obtained by merging the significant
probes detected.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele <doulaye@igbmc.fr>
Diff between fcros versions 1.6 dated 2019-02-01 and 1.6.1 dated 2019-05-31
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NAMESPACE | 2 +- R/rankReads.R | 31 ++++++++++++++++++++----------- R/varBeta.R |only man/fcros-package.Rd | 4 ++-- man/rankReads.Rd | 2 +- man/varBeta.Rd |only 8 files changed, 35 insertions(+), 24 deletions(-)
Title: Help for Writing Unit Tests Based on Function Examples
Description: Take the examples written in your documentation of functions and
use them to create shells (skeletons which must be manually completed by
the user) of test files to be tested with the 'testthat' package.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>),
Thomas Quinn [rev] (<https://orcid.org/0000-0003-0286-6329>),
Laurent Gatto [rev] (<https://orcid.org/0000-0002-1520-2268>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between exampletestr versions 1.4.1 dated 2018-11-07 and 1.4.2 dated 2019-05-31
exampletestr-1.4.1/exampletestr/tests/testthat/test-exemplar.R |only exampletestr-1.4.2/exampletestr/DESCRIPTION | 8 exampletestr-1.4.2/exampletestr/MD5 | 19 - exampletestr-1.4.2/exampletestr/NEWS.md | 6 exampletestr-1.4.2/exampletestr/R/exemplar.R | 2 exampletestr-1.4.2/exampletestr/build/vignette.rds |binary exampletestr-1.4.2/exampletestr/inst/WORDLIST | 21 - exampletestr-1.4.2/exampletestr/inst/doc/one-file-at-a-time.html | 178 +++++----- exampletestr-1.4.2/exampletestr/inst/doc/one-function-at-a-time.html | 41 +- exampletestr-1.4.2/exampletestr/inst/doc/whole-package.html | 41 +- exampletestr-1.4.2/exampletestr/man/make-test-shells.Rd | 2 11 files changed, 205 insertions(+), 113 deletions(-)
Title: Conditional Random Fields for Labelling Sequential Data in
Natural Language Processing
Description: Wraps the 'CRFsuite' library <https://github.com/chokkan/crfsuite> allowing users
to fit a Conditional Random Field model and to apply it on existing data.
The focus of the implementation is in the area of Natural Language Processing where this R package allows you to easily build and apply models
for named entity recognition, text chunking, part of speech tagging, intent recognition or classification of any category you have in mind. Next to training, a small web application
is included in the package to allow you to easily construct training data.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
BNOSAC [cph] (R wrapper),
Naoaki Okazaki [aut, ctb, cph] (CRFsuite library (BSD licensed),
libLBFGS library (MIT licensed), Constant Quark Database software
(BSD licensed)),
Bob Jenkins [aut, ctb] (File src/cqdb/src/lookup3.c (Public Domain)),
Jorge Nocedal [aut, ctb, cph] (libLBFGS library (MIT licensed)),
Jesse Long [aut, ctb, cph] (RumAVL library (MIT licensed))
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between crfsuite versions 0.2 dated 2018-10-21 and 0.3 dated 2019-05-31
DESCRIPTION | 10 LICENSE | 4 MD5 | 46 - NAMESPACE | 4 NEWS.md | 9 R/data.R | 210 +++--- R/evaluation.R |only R/feature_engineering.R | 17 R/modelling.R | 195 ++++- R/pkg.R | 1 README.md | 10 build/vignette.rds |binary inst/app/annotation.Rmd | 19 inst/crftuning |only inst/doc/crfsuite-nlp.R | 30 inst/doc/crfsuite-nlp.Rmd | 32 inst/doc/crfsuite-nlp.html | 1409 ++++++++++++++++++++++++++++++++++++++++-- man/crf.Rd | 76 +- man/crf_caretmethod.Rd |only man/crf_evaluation.Rd |only man/ner_download_modeldata.Rd | 2 man/txt_feature.Rd | 12 src/Makevars | 10 src/include/crfsuite.hpp | 1204 +++++++++++++++++------------------ src/include/crfsuite_api.hpp | 826 ++++++++++++------------ vignettes/crfsuite-nlp.Rmd | 32 26 files changed, 2838 insertions(+), 1320 deletions(-)
Title: Time Series Forecasting Using Nearest Neighbors
Description: Allows to forecast time series using nearest neighbors regression
Francisco Martinez, Maria P. Frias, Maria D. Perez-Godoy and Antonio J.
Rivera (2017) <doi:10.1007/s10462-017-9593-z>. When the forecasting horizon
is higher than 1, two multi-step ahead forecasting strategies can be used.
The model built is autoregressive, that is, it is only based on the
observations of the time series. The nearest neighbors used in a prediction
can be consulted and plotted.
Author: Francisco Martinez [aut, cre]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between tsfknn versions 0.2.0 dated 2019-04-09 and 0.3.0 dated 2019-05-31
tsfknn-0.2.0/tsfknn/tests/testthat/test_changek.R |only tsfknn-0.3.0/tsfknn/DESCRIPTION | 8 - tsfknn-0.3.0/tsfknn/MD5 | 42 +++-- tsfknn-0.3.0/tsfknn/NAMESPACE | 4 tsfknn-0.3.0/tsfknn/NEWS.md | 6 tsfknn-0.3.0/tsfknn/R/forecasting.R | 79 ++-------- tsfknn-0.3.0/tsfknn/R/knn.R | 115 ++++++++++++--- tsfknn-0.3.0/tsfknn/R/plotting.R | 10 - tsfknn-0.3.0/tsfknn/R/print_knnForecast.R | 2 tsfknn-0.3.0/tsfknn/R/rolling_origin.R |only tsfknn-0.3.0/tsfknn/R/tsfknn.R | 3 tsfknn-0.3.0/tsfknn/R/utilities.R |only tsfknn-0.3.0/tsfknn/build/vignette.rds |binary tsfknn-0.3.0/tsfknn/inst/doc/tsfknn.R | 27 +++ tsfknn-0.3.0/tsfknn/inst/doc/tsfknn.Rmd | 77 +++++++++- tsfknn-0.3.0/tsfknn/inst/doc/tsfknn.html | 72 ++++++++- tsfknn-0.3.0/tsfknn/man/autoplot.knnForecast.Rd | 4 tsfknn-0.3.0/tsfknn/man/knn_forecasting.Rd | 19 +- tsfknn-0.3.0/tsfknn/man/plot.knnForecastRO.Rd |only tsfknn-0.3.0/tsfknn/man/predict.knnForecast.Rd |only tsfknn-0.3.0/tsfknn/man/rolling_origin.Rd |only tsfknn-0.3.0/tsfknn/man/tsfknn.Rd | 3 tsfknn-0.3.0/tsfknn/tests/testthat/test_predict.R |only tsfknn-0.3.0/tsfknn/tests/testthat/test_regression.R | 6 tsfknn-0.3.0/tsfknn/tests/testthat/test_rolling_origin.R |only tsfknn-0.3.0/tsfknn/vignettes/tsfknn.Rmd | 77 +++++++++- 26 files changed, 412 insertions(+), 142 deletions(-)
Title: Cache 'CRAN'-Like Metadata and R Packages
Description: Metadata and package cache for CRAN-like repositories.
This is a utility package to be used by package management tools
that want to take advantage of caching.
Author: Gábor Csárdi [aut, cre]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between pkgcache versions 1.0.4 dated 2019-05-13 and 1.0.5 dated 2019-05-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/async-http.R | 6 ++++-- README.md | 6 +++--- 5 files changed, 18 insertions(+), 12 deletions(-)
Title: Biterm Topic Models for Short Text
Description: Biterm Topic Models find topics in collections of short texts.
It is a word co-occurrence based topic model that learns topics by modeling word-word co-occurrences patterns which are called biterms.
This in contrast to traditional topic models like Latent Dirichlet Allocation and Probabilistic Latent Semantic Analysis
which are word-document co-occurrence topic models.
A biterm consists of two words co-occurring in the same short text window.
This context window can for example be a twitter message, a short answer on a survey, a sentence of a text or a document identifier.
The techniques are explained in detail in the paper 'A Biterm Topic Model For Short Text' by Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013) <https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/BTM-WWW13.pdf>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
BNOSAC [cph] (R wrapper),
Xiaohui Yan [ctb, cph] (BTM C++ library)
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between BTM versions 0.2 dated 2018-12-27 and 0.2.1 dated 2019-05-31
DESCRIPTION | 7 ++++--- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 10 insertions(+), 5 deletions(-)
Title: Time Series Representations
Description: Methods for representations (i.e. dimensionality reduction, preprocessing, feature extraction) of time series to help more accurate and effective time series data mining.
Non-data adaptive, data adaptive, model-based and data dictated (clipped) representation methods are implemented. Also min-max and z-score normalisations, and forecasting accuracy measures are implemented.
Author: Peter Laurinec [aut, cre] (<https://orcid.org/0000-0002-3501-8783>)
Maintainer: Peter Laurinec <tsreprpackage@gmail.com>
Diff between TSrepr versions 1.0.2 dated 2018-11-22 and 1.0.3 dated 2019-05-31
DESCRIPTION | 8 MD5 | 35 - NAMESPACE | 1 NEWS.md | 6 R/RcppExports.R | 95 ++- R/SAX.R | 2 inst/doc/TSrepr_extentions.html | 392 ++++++++++++---- inst/doc/TSrepr_representations_of_time_series.Rmd | 10 inst/doc/TSrepr_representations_of_time_series.html | 464 ++++++++++++++----- inst/doc/TSrepr_representations_use_case.html | 476 ++++++++++++++------ man/maape.Rd | 2 man/mse.Rd |only man/repr_feaclip.Rd | 3 src/FeatureClippingTrending.cpp | 3 src/RcppExports.cpp | 49 +- src/measures.cpp | 167 ++++--- tests/testthat/test_acc_measures.R | 17 tests/testthat/test_helpers.R | 2 vignettes/TSrepr_representations_of_time_series.Rmd | 10 19 files changed, 1249 insertions(+), 493 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 0.9.1 dated 2019-03-26 and 0.9.2 dated 2019-05-31
finalfit-0.9.1/finalfit/vignettes/export_cache |only finalfit-0.9.2/finalfit/DESCRIPTION | 11 finalfit-0.9.2/finalfit/MD5 | 129 - finalfit-0.9.2/finalfit/NAMESPACE | 15 finalfit-0.9.2/finalfit/NEWS.md | 11 finalfit-0.9.2/finalfit/R/catTest.R |only finalfit-0.9.2/finalfit/R/coxphmulti.R | 4 finalfit-0.9.2/finalfit/R/coxphuni.R | 2 finalfit-0.9.2/finalfit/R/crrmulti.R |only finalfit-0.9.2/finalfit/R/crruni.R |only finalfit-0.9.2/finalfit/R/ff_permute.R |only finalfit-0.9.2/finalfit/R/finalfit.R | 10 finalfit-0.9.2/finalfit/R/finalfit_internal_functions.R | 125 - finalfit-0.9.2/finalfit/R/finalfit_package.R | 21 finalfit-0.9.2/finalfit/R/fit2df.R | 403 ++- finalfit-0.9.2/finalfit/R/glmmixed.R | 2 finalfit-0.9.2/finalfit/R/glmmulti.R | 6 finalfit-0.9.2/finalfit/R/glmmultiboot.R | 2 finalfit-0.9.2/finalfit/R/glmuni.R | 6 finalfit-0.9.2/finalfit/R/lmmixed.R | 2 finalfit-0.9.2/finalfit/R/lmmulti.R | 4 finalfit-0.9.2/finalfit/R/lmuni.R | 4 finalfit-0.9.2/finalfit/R/summaryfactorlist.R | 64 finalfit-0.9.2/finalfit/R/svyglm.R |only finalfit-0.9.2/finalfit/README.md | 16 finalfit-0.9.2/finalfit/inst/doc/all_tables_examples.R | 199 + finalfit-0.9.2/finalfit/inst/doc/all_tables_examples.Rmd | 268 ++ finalfit-0.9.2/finalfit/inst/doc/all_tables_examples.html | 1346 ++++++++---- finalfit-0.9.2/finalfit/inst/doc/bootstrap.html | 65 finalfit-0.9.2/finalfit/inst/doc/data_prep.html | 39 finalfit-0.9.2/finalfit/inst/doc/export.R | 17 finalfit-0.9.2/finalfit/inst/doc/export.Rmd | 17 finalfit-0.9.2/finalfit/inst/doc/export.html | 73 finalfit-0.9.2/finalfit/inst/doc/finalfit.html | 39 finalfit-0.9.2/finalfit/inst/doc/missing.R | 2 finalfit-0.9.2/finalfit/inst/doc/missing.Rmd | 2 finalfit-0.9.2/finalfit/inst/doc/missing.html | 67 finalfit-0.9.2/finalfit/man/catTestfisher.Rd |only finalfit-0.9.2/finalfit/man/coxphmulti.Rd | 10 finalfit-0.9.2/finalfit/man/coxphuni.Rd | 8 finalfit-0.9.2/finalfit/man/crrmulti.Rd |only finalfit-0.9.2/finalfit/man/crruni.Rd |only finalfit-0.9.2/finalfit/man/extract_fit.Rd | 15 finalfit-0.9.2/finalfit/man/ff_permute.Rd |only finalfit-0.9.2/finalfit/man/figures/finalfit_hex.png |only finalfit-0.9.2/finalfit/man/finalfit-package.Rd | 18 finalfit-0.9.2/finalfit/man/finalfit.Rd | 10 finalfit-0.9.2/finalfit/man/fit2df.Rd | 102 finalfit-0.9.2/finalfit/man/glmmixed.Rd | 10 finalfit-0.9.2/finalfit/man/glmmulti.Rd | 12 finalfit-0.9.2/finalfit/man/glmmulti_boot.Rd | 10 finalfit-0.9.2/finalfit/man/glmuni.Rd | 12 finalfit-0.9.2/finalfit/man/lmmixed.Rd | 10 finalfit-0.9.2/finalfit/man/lmmulti.Rd | 10 finalfit-0.9.2/finalfit/man/lmuni.Rd | 10 finalfit-0.9.2/finalfit/man/summarise_continuous.Rd | 2 finalfit-0.9.2/finalfit/man/summary_factorlist.Rd | 19 finalfit-0.9.2/finalfit/man/summary_factorlist_groups.Rd | 3 finalfit-0.9.2/finalfit/man/svyglmmulti.Rd |only finalfit-0.9.2/finalfit/man/svyglmuni.Rd |only finalfit-0.9.2/finalfit/tests/testthat/Rplots.pdf |binary finalfit-0.9.2/finalfit/tests/testthat/test_all_in_one.R | 13 finalfit-0.9.2/finalfit/tests/testthat/test_internals.R | 17 finalfit-0.9.2/finalfit/tests/testthat/test_modelwrappers.R | 25 finalfit-0.9.2/finalfit/tests/testthat/test_tests.R |only finalfit-0.9.2/finalfit/vignettes/all_tables_examples.Rmd | 268 ++ finalfit-0.9.2/finalfit/vignettes/export.Rmd | 17 finalfit-0.9.2/finalfit/vignettes/missing.Rmd | 2 68 files changed, 2633 insertions(+), 941 deletions(-)
Title: Stepwise Regression Analysis
Description: Stepwise regression analysis for variable selection can be used to get the best candidate final regression model in univariate or multivariate regression analysis with the 'forward' and 'stepwise' steps. Procedure can use Akaike information criterion, corrected Akaike information criterion, Bayesian information criterion, Hannan and Quinn information criterion, corrected Hannan and Quinn information criterion, Schwarz criterion and significance levels as selection criteria. Multicollinearity detection in regression model are performed by checking tolerance value. Continuous variables nested within class effect and weighted stepwise regression are also considered in this package.
Author: Junhui Li,Kun Cheng,Wenxin Liu
Maintainer: Junhui Li <junhuili@cau.edu.cn>
Diff between StepReg versions 1.1.0 dated 2019-05-24 and 1.2.0 dated 2019-05-31
StepReg-1.1.0/StepReg/man/bestCandidate_RCpp.Rd |only StepReg-1.2.0/StepReg/DESCRIPTION | 10 StepReg-1.2.0/StepReg/MD5 | 18 - StepReg-1.2.0/StepReg/R/ModelFitStat.R |only StepReg-1.2.0/StepReg/R/RcppExports.R | 4 StepReg-1.2.0/StepReg/R/stepwise.R | 178 ++++++------- StepReg-1.2.0/StepReg/man/ModelFitStat.Rd |only StepReg-1.2.0/StepReg/man/StepReg-package.Rd | 10 StepReg-1.2.0/StepReg/man/optimization.Rd |only StepReg-1.2.0/StepReg/man/stepwise.Rd | 16 - StepReg-1.2.0/StepReg/src/RcppExports.cpp | 11 StepReg-1.2.0/StepReg/src/Rcppeigen_StepwiseRegression.cpp | 137 +++++----- 12 files changed, 210 insertions(+), 174 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 1.0.0 dated 2019-03-17 and 1.1.0 dated 2019-05-31
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Title: Nonlinear Mixed Effects Models in Population Pharmacokinetics
and Pharmacodynamics
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'RxODE' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Yuan Xiong [aut],
Rik Schoemaker [aut] (<https://orcid.org/0000-0002-7538-3005>),
Justin Wilkins [aut] (<https://orcid.org/0000-0002-7099-9396>),
Mirjam Trame [aut],
Richard Hooijmaijers [aut],
Teun Post [aut],
Robert Leary [ctb],
Wenping Wang [aut, cre],
Hadley Wickham [ctb],
Dirk Eddelbuettel [cph],
Johannes Pfeifer [ctb],
Robert B. Schnabel [ctb],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Audrey Lavenu [ctb],
Marc Lavielle [ctb],
David Ardia [cph],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Katharine Mullen [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between nlmixr versions 1.0.0-7 dated 2018-09-23 and 1.1.0-8 dated 2019-05-31
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Title: Exact Tests for Hardy-Weinberg Proportions
Description: Tests whether a set of genotype counts fits the HW expectations.
Exact tests performed by an efficient algorithm. Included test statistics
are likelihood ratio, probability, U-score and Pearson's X2.
Author: Bill Engels <wrengels@wisc.edu>
Maintainer: Bill Engels <wrengels@wisc.edu>
Diff between HWxtest versions 1.1.7 dated 2016-01-13 and 1.1.9 dated 2019-05-31
DESCRIPTION | 10 +-- MD5 | 14 ++-- build/vignette.rds |binary inst/doc/HWxtest.R | 9 +-- inst/doc/HWxtest.Rmd | 42 +------------- inst/doc/HWxtest.html | 147 ++++++++++++++++++++++++++++++++++---------------- src/HWxcount.c | 2 vignettes/HWxtest.Rmd | 42 +------------- 8 files changed, 130 insertions(+), 136 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
See Gile and Handcock (2010) <doi:10.1111/j.1467-9531.2010.01223.x> and
Gile and Handcock (2015) <doi:10.1111/rssa.12091>.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.8-1 dated 2017-12-01 and 0.9-0 dated 2019-05-31
RDS-0.8-1/RDS/man/impute.visibility.Rd |only RDS-0.9-0/RDS/DESCRIPTION | 13 ++-- RDS-0.9-0/RDS/MD5 | 66 ++++++++++----------- RDS-0.9-0/RDS/NAMESPACE | 6 - RDS-0.9-0/RDS/R/MA.estimates.R | 27 ++++---- RDS-0.9-0/RDS/R/MA.parallel.R | 4 - RDS-0.9-0/RDS/R/MA.sampling-c.R | 1 RDS-0.9-0/RDS/R/MA.util.R | 71 +++++++++++------------ RDS-0.9-0/RDS/R/bootstrap-intervals.R | 6 + RDS-0.9-0/RDS/R/differential-activity.R | 2 RDS-0.9-0/RDS/R/impute-degree.R | 2 RDS-0.9-0/RDS/R/me.impute.R | 4 - RDS-0.9-0/RDS/R/rds-doc.R | 2 RDS-0.9-0/RDS/R/rds.data.frame-utils.R | 2 RDS-0.9-0/RDS/R/rds.data.frame.R | 14 ++-- RDS-0.9-0/RDS/R/rds.interval.estimate.R | 2 RDS-0.9-0/RDS/man/MA.estimates.Rd | 30 ++++++++- RDS-0.9-0/RDS/man/RDS.bootstrap.intervals.Rd | 7 +- RDS-0.9-0/RDS/man/as.rds.data.frame.Rd | 22 +++---- RDS-0.9-0/RDS/man/assert.valid.rds.data.frame.Rd | 2 RDS-0.9-0/RDS/man/compute.weights.Rd | 6 - RDS-0.9-0/RDS/man/cumulative.estimate.Rd | 4 - RDS-0.9-0/RDS/man/get.id.Rd | 2 RDS-0.9-0/RDS/man/get.rid.Rd | 2 RDS-0.9-0/RDS/man/get.seed.rid.Rd | 4 - RDS-0.9-0/RDS/man/hcg.weights.Rd | 4 - RDS-0.9-0/RDS/man/impute.degree.Rd | 2 RDS-0.9-0/RDS/man/impute.visibility_mle.Rd |only RDS-0.9-0/RDS/man/print.summary.svyglm.RDS.Rd | 4 - RDS-0.9-0/RDS/man/rds.I.weights.Rd | 3 RDS-0.9-0/RDS/man/set.control.class.Rd | 4 - RDS-0.9-0/RDS/man/summary.svyglm.RDS.Rd | 4 - RDS-0.9-0/RDS/src/bsC.c | 2 RDS-0.9-0/RDS/src/llmeC.c | 8 +- RDS-0.9-0/RDS/tests/testthat/test-estimators.R | 6 - 35 files changed, 183 insertions(+), 155 deletions(-)
Title: Multi Calculator to Compute Scores of Adherence to Mediterranean
Diet
Description: Multi Calculator of different scores to measure adherence to Mediterranean Diet, to compute them in nutriepidemiological data. Additionally, a sample dataset of this kind of data is provided, and some other minor tools useful in epidemiological studies.
Author: Miguel Menendez [aut, cre],
David Lora [ctb],
Agustin Gomez-Camara [dtc]
Maintainer: Miguel Menendez <miguelmo@gmail.com>
Diff between MedDietCalc versions 0.1.0 dated 2017-04-07 and 0.1.1 dated 2019-05-31
DESCRIPTION | 10 - MD5 | 36 ++--- R/computeMDS03.R | 326 +++++++++++++++++++++++-------------------------- R/computeMDS05.R | 326 +++++++++++++++++++++++-------------------------- R/computeMDS12.R | 272 +++++++++++++++++++--------------------- R/computeMDS95.R | 303 +++++++++++++++++++++------------------------ R/computeMSDPS.R | 249 +++++++++++++++++-------------------- R/computeRMed.R | 280 +++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/vignette.R | 10 - inst/doc/vignette.Rmd | 14 +- inst/doc/vignette.html | 320 +++++++++++++++++++++++++----------------------- man/computeCardio.Rd | 4 man/computeMDS05.Rd | 9 - man/computeMDS12.Rd | 6 man/computeMDS95.Rd | 4 man/computeMSDPS.Rd | 2 man/nutriSample.Rd | 134 ++++++++++---------- vignettes/vignette.Rmd | 14 +- 19 files changed, 1128 insertions(+), 1191 deletions(-)
Title: Modelling Actual, Potential and Reference Crop
Evapotranspiration
Description: Uses data and constants to calculate potential evapotranspiration (PET) and actual evapotranspiration (AET) from 21 different formulations including Penman, Penman-Monteith FAO 56, Priestley-Taylor and Morton formulations.
Author: Danlu Guo [aut, cre] <danlu.guo@adelaide.edu.au>, Seth Westra [aut] <swestra@civeng.adelaide.edu.au>, Tim Peterson [ctb] <timjp@unimelb.edu.au>
Maintainer: Danlu Guo <danlu.guo@unimelb.edu.au>
Diff between Evapotranspiration versions 1.13 dated 2019-05-06 and 1.14 dated 2019-05-31
DESCRIPTION | 8 MD5 | 52 - NEWS | 17 R/Evapotranspiration.R | 1840 +++++++++++++++++++++++-------------------- R/Reading.R | 737 ++++++++++------- man/ET.Abtew.Rd | 7 man/ET.BlaneyCriddle.Rd | 7 man/ET.BrutsaertStrickler.Rd | 7 man/ET.ChapmanAustralian.Rd | 12 man/ET.GrangerGray.Rd | 10 man/ET.Hamon.Rd | 8 man/ET.HargreavesSamani.Rd | 9 man/ET.JensenHaise.Rd | 7 man/ET.Linacre.Rd | 8 man/ET.Makkink.Rd | 7 man/ET.MattShuttleworth.Rd | 7 man/ET.McGuinnessBordne.Rd | 8 man/ET.MortonCRAE.Rd | 8 man/ET.MortonCRWE.Rd | 8 man/ET.PenPan.Rd | 7 man/ET.Penman.Rd | 7 man/ET.PenmanMonteith.Rd | 7 man/ET.PriestleyTaylor.Rd | 7 man/ET.Romanenko.Rd | 8 man/ET.SzilagyiJozsa.Rd | 8 man/ET.Turc.Rd | 7 man/ReadInputs.Rd | 6 27 files changed, 1604 insertions(+), 1220 deletions(-)
More information about Evapotranspiration at CRAN
Permanent link
Title: Ocean Biogeographic Information System (OBIS) Client
Description: Client for the Ocean Biogeographic Information System (<https://obis.org>).
Author: Pieter Provoost [cre, aut],
Samuel Bosch [aut],
Ward Appeltans [ctb],
OBIS [cph]
Maintainer: Pieter Provoost <pieterprovoost@gmail.com>
Diff between robis versions 2.1.0 dated 2019-02-27 and 2.1.6 dated 2019-05-31
DESCRIPTION | 8 +++---- MD5 | 24 ++++++++++----------- NEWS.md | 8 +++++++ R/checklist.R | 5 +++- R/dataset.R | 9 +++++--- R/map.R | 43 +++++++++++++++++++++++++++++++++------ R/occurrence.R | 15 ++++++++++++- R/util.R | 11 +++++++++ man/checklist.Rd | 4 ++- man/dataset.Rd | 4 ++- man/map_leaflet.Rd | 5 +++- man/occurrence.Rd | 6 ++++- tests/testthat/test_occurrence.R | 10 +++++++++ 13 files changed, 121 insertions(+), 31 deletions(-)
Title: 32-Bit Floats
Description: R comes with a suite of utilities for linear algebra with "numeric"
(double precision) vectors/matrices. However, sometimes single precision (or
less!) is more than enough for a particular task. This package extends R's
linear algebra facilities to include 32-bit float (single precision) data.
Float vectors/matrices have half the precision of their "numeric"-type
counterparts but are generally faster to numerically operate on, for a
performance vs accuracy trade-off. The internal representation is an S4
class, which allows us to keep the syntax identical to that of base R's.
Interaction between floats and base types for binary operators is generally
possible; in these cases, type promotion always defaults to the higher
precision. The package ships with copies of the single precision 'BLAS' and
'LAPACK', which are automatically built in the event they are not available
on the system.
Author: Drew Schmidt [aut, cre, cph],
Wei-Chen Chen [aut],
Dmitriy Selivanov [ctb] (improvements in external package linking),
ORNL [cph]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between float versions 0.2-2 dated 2019-02-26 and 0.2-3 dated 2019-05-31
ChangeLog | 6 +++ DESCRIPTION | 8 ++-- MD5 | 82 +++++++++++++++++++++---------------------- README.md | 2 - configure | 10 ++--- configure.ac | 10 ++--- inst/doc/float.Rnw | 2 - inst/doc/float.pdf |binary inst/include/float/float32.h | 14 +++---- inst/include/float/slapack.h | 2 - src/Makevars.win | 14 +++---- src/NA.c | 52 +++++++++++++-------------- src/NA.h | 4 +- src/backsolve.c | 6 +-- src/binary.c | 48 ++++++++++++------------- src/chol.c | 6 +-- src/chol2inv.c | 2 - src/colSums.c | 58 +++++++++++++++--------------- src/cond.c | 2 - src/converters.c | 26 ++++++------- src/crossprod.c | 8 ++-- src/eigen.c | 18 ++++----- src/extremes.c | 32 ++++++++-------- src/float_native.c | 13 +++--- src/isSymmetric.c | 14 +++---- src/math.c | 28 +++++++------- src/matmult.c | 4 +- src/norm.c | 4 +- src/norm.h | 24 ++++++------ src/qr.c | 40 ++++++++++---------- src/rand.c | 8 ++-- src/scale.c | 36 +++++++++--------- src/sign.c | 8 ++-- src/solve.c | 12 +++--- src/sum.c | 12 +++--- src/svd.c | 18 ++++----- src/sweep.c | 14 +++---- src/utils/matmult.c | 17 ++++---- src/utils/symmetrize.c | 19 +++++---- src/utils/xpose.c | 12 +++--- src/xpose.c | 4 +- vignettes/float.Rnw | 2 - 42 files changed, 356 insertions(+), 345 deletions(-)
Title: Color Calculations with Emphasis on Spectral Data
Description: Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners.
Build complex systems from simpler parts using a spectral product algebra. For light sources,
compute CCT, CRI, and SSI. For object colors, compute optimal colors and Logvinenko coordinates.
Work with the standard CIE illuminants and color matching functions, and read spectra from
text files, including CGATS files. Estimate a spectrum from its response. A user guide and 8 vignettes are included.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between colorSpec versions 0.8-3 dated 2019-03-04 and 0.9-1 dated 2019-05-31
DESCRIPTION | 10 +++---- MD5 | 43 +++++++++++++++++++++----------- NEWS.md | 5 +++ R/colorSpec.CCT.R | 5 +++ R/datasets.R | 2 - build/vignette.rds |binary data/colorSpec.rda |binary inst/doc/MacbethCC.txt |only inst/doc/Thumbs.db |only inst/doc/blueflame.R |only inst/doc/blueflame.pdf |binary inst/doc/colorSpec-guide.R |only inst/doc/colorSpec-guide.html | 31 ++++++++++++----------- inst/doc/emulation.R |only inst/doc/emulation.pdf |binary inst/doc/gallery.R |only inst/doc/gallery.pdf |binary inst/doc/inversion.R |only inst/doc/inversion.pdf |binary inst/doc/lens-aging.R |only inst/doc/lens-aging.pdf |binary inst/doc/optimals.R |only inst/doc/optimals.pdf |binary inst/doc/phenolred.R |only inst/doc/phenolred.html | 56 ++++++++++++++++++++++++++++-------------- inst/doc/photoncounting.R |only inst/doc/photoncounting.html | 33 +++++++++++++----------- inst/doc/proofs.txt |only inst/doc/right-inverse.txt |only 29 files changed, 117 insertions(+), 68 deletions(-)