Title: Visualize Data on Spirals
Description: It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>.
It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high
resolution. 2. It is efficient for time series data to reveal periodic patterns.
Author: Zuguang Gu [aut, cre] (<https://orcid.org/0000-0002-7395-8709>)
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between spiralize versions 1.0.1 dated 2021-07-01 and 1.0.2 dated 2021-07-08
DESCRIPTION | 10 +- MD5 | 28 +++-- NAMESPACE | 3 NEWS | 8 + R/graphics.R | 187 ++++++++++++++++++++++++++++++++++++---- R/layout.R | 12 +- R/track.R | 27 +++++ R/transform.R | 152 +++++++++++++++++++++++++++++--- inst/doc/spiralize.Rmd | 2 inst/doc/spiralize.html | 6 - inst/extdata/github_commits.rds |only inst/extdata/life_tree.rds |only man/cartesian_to_xy.Rd |only man/is_in_track.Rd |only man/spiral_raster.Rd | 17 ++- man/spiral_track.Rd | 2 vignettes/spiralize.Rmd | 2 17 files changed, 393 insertions(+), 63 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Namita Gupta [aut],
Susanna Marquez [aut],
Julian Zhou [aut],
Nima Nouri [aut],
Ang Cui [ctb],
Jason Vander Heiden [aut, cre],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between shazam versions 1.0.2 dated 2020-08-11 and 1.1.0 dated 2021-07-08
DESCRIPTION | 14 MD5 | 86 ++- NAMESPACE | 8 NEWS.md | 35 + R/Baseline.R | 799 ++++++++++++++++++----------------- R/DistToNearest.R | 16 R/MutationDefinitions.R | 2 R/MutationProfiling.R | 388 ++++++++++++---- R/RegionDefinitions.R | 52 +- R/RegionsExtend.R |only R/Shazam.R | 9 R/TargetingModels.R | 20 README.md | 5 build/vignette.rds |binary data/IMGT_VDJ.rda |only data/IMGT_VDJ_BY_REGIONS.rda |only inst/doc/Baseline-Vignette.R | 22 inst/doc/Baseline-Vignette.Rmd | 81 ++- inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.R | 14 inst/doc/DistToNearest-Vignette.Rmd | 12 inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.Rmd | 8 inst/doc/Mutation-Vignette.pdf |binary inst/doc/Shmulate-Vignette.Rmd | 2 inst/doc/Shmulate-Vignette.pdf |binary inst/doc/Targeting-Vignette.R | 21 inst/doc/Targeting-Vignette.Rmd | 21 inst/doc/Targeting-Vignette.pdf |binary man/IMGT_SCHEMES.Rd | 46 +- man/MUTATION_SCHEMES.Rd | 2 man/calcBaseline.Rd | 16 man/collapseClones.Rd | 13 man/consensusSequence.Rd | 5 man/distToNearest.Rd | 4 man/expectedMutations.Rd | 14 man/makeGraphDf.Rd |only man/observedMutations.Rd | 46 +- man/setRegionBoundaries.Rd |only man/shazam.Rd | 1 man/slideWindowTune.Rd | 1 vignettes/Baseline-Vignette.Rmd | 81 ++- vignettes/DistToNearest-Vignette.Rmd | 12 vignettes/Mutation-Vignette.Rmd | 8 vignettes/Shmulate-Vignette.Rmd | 2 vignettes/Shmulate-Vignette.html |only vignettes/Targeting-Vignette.Rmd | 21 47 files changed, 1203 insertions(+), 684 deletions(-)
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic models
(assuming either presence or absence of the effect, heterogeneity, and
publication bias). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2021,
<doi:10.31234/osf.io/kvsp7>; Maier, Bartoš & Wagenmakers, in press,
<doi:10.31234/osf.io/u4cns>). Users can define a wide range of non-informative
or informative prior distributions for the effect size, heterogeneity,
and publication bias components (including selection models and PET-PEESE).
The package provides convenient functions for summary, visualizations, and
fit diagnostics.
Author: František Bartoš [aut, cre] (<https://orcid.org/0000-0002-0018-5573>),
Maximilian Maier [aut] (<https://orcid.org/0000-0002-9873-6096>),
Eric-Jan Wagenmakers [ths] (<https://orcid.org/0000-0003-1596-1034>),
Joris Goosen [ctb],
Matthew Denwood [cph] (Original copyright holder of some modified code
where indicated.),
Martyn Plummer [cph] (Original copyright holder of some modified code
where indicated.)
Maintainer: František Bartoš <f.bartos96@gmail.com>
Diff between RoBMA versions 1.2.1 dated 2021-02-16 and 2.0.0 dated 2021-07-08
RoBMA-1.2.1/RoBMA/R/methods.R |only RoBMA-1.2.1/RoBMA/inst/doc/WarningsAndErrors.R |only RoBMA-1.2.1/RoBMA/inst/doc/WarningsAndErrors.Rmd |only RoBMA-1.2.1/RoBMA/inst/doc/WarningsAndErrors.html |only RoBMA-1.2.1/RoBMA/man/plot.RoBMA.prior.Rd |only RoBMA-1.2.1/RoBMA/man/print.RoBMA.prior.Rd |only RoBMA-1.2.1/RoBMA/man/weightedt.Rd |only RoBMA-1.2.1/RoBMA/src/functions |only RoBMA-1.2.1/RoBMA/src/weightedt.cc |only RoBMA-1.2.1/RoBMA/tests/testthat/test-1-load.R |only RoBMA-1.2.1/RoBMA/tests/testthat/test-2-distributions.R |only RoBMA-1.2.1/RoBMA/tests/testthat/test-3-priors.R |only RoBMA-1.2.1/RoBMA/tests/testthat/test-4-fit.R |only RoBMA-1.2.1/RoBMA/tests/testthat/test-5-methods.R |only RoBMA-1.2.1/RoBMA/tests/testthat/test-6-plots.R |only RoBMA-1.2.1/RoBMA/tests/testthat/test-7-diagnostics.R |only RoBMA-1.2.1/RoBMA/vignettes/WarningsAndErrors.Rmd |only RoBMA-2.0.0/RoBMA/DESCRIPTION | 50 RoBMA-2.0.0/RoBMA/MD5 | 166 RoBMA-2.0.0/RoBMA/NAMESPACE | 77 RoBMA-2.0.0/RoBMA/NEWS.md | 19 RoBMA-2.0.0/RoBMA/R/RoBMA-package.R | 28 RoBMA-2.0.0/RoBMA/R/check-input-and-settings.R |only RoBMA-2.0.0/RoBMA/R/check-priors-and-models.R |only RoBMA-2.0.0/RoBMA/R/data.R | 26 RoBMA-2.0.0/RoBMA/R/diagnostics.R | 207 RoBMA-2.0.0/RoBMA/R/distributions.R | 1063 ++ RoBMA-2.0.0/RoBMA/R/fit-and-marglik.R |only RoBMA-2.0.0/RoBMA/R/inference-and-model-averaging.R |only RoBMA-2.0.0/RoBMA/R/main.R | 2925 ------- RoBMA-2.0.0/RoBMA/R/plots.R | 1921 +---- RoBMA-2.0.0/RoBMA/R/priors.R | 1421 --- RoBMA-2.0.0/RoBMA/R/summary.R |only RoBMA-2.0.0/RoBMA/R/tools.R |only RoBMA-2.0.0/RoBMA/R/transformations.R |only RoBMA-2.0.0/RoBMA/R/utilities.R |only RoBMA-2.0.0/RoBMA/R/zzz.R | 44 RoBMA-2.0.0/RoBMA/README.md | 425 - RoBMA-2.0.0/RoBMA/build/partial.rdb |binary RoBMA-2.0.0/RoBMA/build/vignette.rds |binary RoBMA-2.0.0/RoBMA/cleanup |only RoBMA-2.0.0/RoBMA/configure | 105 RoBMA-2.0.0/RoBMA/configure.ac | 89 RoBMA-2.0.0/RoBMA/data/Bem2011.RData |only RoBMA-2.0.0/RoBMA/inst/REFERENCES.bib | 69 RoBMA-2.0.0/RoBMA/inst/apa.csl | 3832 +++++----- RoBMA-2.0.0/RoBMA/inst/doc/CustomEnsembles.R | 59 RoBMA-2.0.0/RoBMA/inst/doc/CustomEnsembles.Rmd | 170 RoBMA-2.0.0/RoBMA/inst/doc/CustomEnsembles.html | 687 - RoBMA-2.0.0/RoBMA/inst/doc/ReproducingBMA.R | 43 RoBMA-2.0.0/RoBMA/inst/doc/ReproducingBMA.Rmd | 96 RoBMA-2.0.0/RoBMA/inst/doc/ReproducingBMA.html | 532 - RoBMA-2.0.0/RoBMA/man/Anderson2010.Rd | 9 RoBMA-2.0.0/RoBMA/man/Bem2011.Rd |only RoBMA-2.0.0/RoBMA/man/RoBMA-package.Rd | 38 RoBMA-2.0.0/RoBMA/man/RoBMA.Rd | 360 RoBMA-2.0.0/RoBMA/man/RoBMA_control.Rd |only RoBMA-2.0.0/RoBMA/man/RoBMA_options.Rd |only RoBMA-2.0.0/RoBMA/man/check_RoBMA.Rd |only RoBMA-2.0.0/RoBMA/man/check_setup.Rd | 113 RoBMA-2.0.0/RoBMA/man/combine_data.Rd |only RoBMA-2.0.0/RoBMA/man/diagnostics.Rd | 186 RoBMA-2.0.0/RoBMA/man/effect_sizes.Rd |only RoBMA-2.0.0/RoBMA/man/figures/README-fig_PETPEESE-1.png |only RoBMA-2.0.0/RoBMA/man/figures/README-fig_forest-1.png |only RoBMA-2.0.0/RoBMA/man/figures/README-fig_mu-1.png |binary RoBMA-2.0.0/RoBMA/man/figures/README-fig_mu_chain-1.png |binary RoBMA-2.0.0/RoBMA/man/figures/README-fig_mu_ind-1.png |binary RoBMA-2.0.0/RoBMA/man/figures/README-fig_tau-1.png |binary RoBMA-2.0.0/RoBMA/man/figures/README-fig_weightfunction-1.png |only RoBMA-2.0.0/RoBMA/man/forest.Rd |only RoBMA-2.0.0/RoBMA/man/is.RoBMA.Rd | 31 RoBMA-2.0.0/RoBMA/man/plot.RoBMA.Rd | 239 RoBMA-2.0.0/RoBMA/man/plot_models.Rd |only RoBMA-2.0.0/RoBMA/man/print.RoBMA.Rd | 41 RoBMA-2.0.0/RoBMA/man/print.summary.RoBMA.Rd | 41 RoBMA-2.0.0/RoBMA/man/prior.Rd | 177 RoBMA-2.0.0/RoBMA/man/prior_PEESE.Rd |only RoBMA-2.0.0/RoBMA/man/prior_PET.Rd |only RoBMA-2.0.0/RoBMA/man/prior_none.Rd |only RoBMA-2.0.0/RoBMA/man/prior_weightfunction.Rd |only RoBMA-2.0.0/RoBMA/man/sample_sizes.Rd |only RoBMA-2.0.0/RoBMA/man/standard_errors.Rd |only RoBMA-2.0.0/RoBMA/man/summary.RoBMA.Rd | 180 RoBMA-2.0.0/RoBMA/man/update.RoBMA.Rd | 193 RoBMA-2.0.0/RoBMA/man/weighted_normal.Rd |only RoBMA-2.0.0/RoBMA/src/Makevars.in | 39 RoBMA-2.0.0/RoBMA/src/Makevars.win | 90 RoBMA-2.0.0/RoBMA/src/RoBMA.cc |only RoBMA-2.0.0/RoBMA/src/distributions/DWN1.cc | 20 RoBMA-2.0.0/RoBMA/src/distributions/DWN1.h | 2 RoBMA-2.0.0/RoBMA/src/distributions/DWN2.cc | 20 RoBMA-2.0.0/RoBMA/src/distributions/DWN2.h | 2 RoBMA-2.0.0/RoBMA/src/distributions/DWT1.cc | 11 RoBMA-2.0.0/RoBMA/src/distributions/DWT1.h | 2 RoBMA-2.0.0/RoBMA/src/distributions/DWT2.cc | 9 RoBMA-2.0.0/RoBMA/src/distributions/DWT2.h | 2 RoBMA-2.0.0/RoBMA/src/init.c |only RoBMA-2.0.0/RoBMA/src/jagsversions.h |only RoBMA-2.0.0/RoBMA/src/testRoBMA.cc |only RoBMA-2.0.0/RoBMA/src/transformations |only RoBMA-2.0.0/RoBMA/tests/testthat/test-0-CRAN.R | 101 RoBMA-2.0.0/RoBMA/vignettes/CustomEnsembles.Rmd | 170 RoBMA-2.0.0/RoBMA/vignettes/ReproducingBMA.Rmd | 96 104 files changed, 6198 insertions(+), 10028 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.7.0 dated 2021-05-20 and 2.8.0 dated 2021-07-08
DESCRIPTION | 8 +++--- MD5 | 15 +++++++----- NAMESPACE | 3 ++ NEWS | 3 ++ R/labkey.defaults.R | 18 ++++++++++----- R/labkey.security.R | 37 +++++++++++++++++++++++++++++++ man/Rlabkey-package.Rd | 4 +-- man/labkey.security.impersonateUser.Rd |only man/labkey.security.stopImpersonating.Rd |only man/labkey.whoAmI.Rd |only 10 files changed, 70 insertions(+), 18 deletions(-)
Title: Hydrological Tools for Handling Hydro-Meteorological Data
Records
Description: Read, plot, manipulate and process hydro-meteorological data records (with special features for Argentina and Chile data-sets).
Author: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Maintainer: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Diff between hydrotoolbox versions 1.0.0 dated 2021-07-08 and 1.0.1 dated 2021-07-08
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ inst/doc/aic_arg.html | 4 ++-- inst/doc/cr2_cl.html | 4 ++-- inst/doc/dgi_arg.html | 4 ++-- inst/doc/ianigla_arg.html | 4 ++-- inst/doc/mnemos_arg.html | 4 ++-- inst/doc/package_overview.html | 4 ++-- inst/doc/snih_arg.html | 4 ++-- inst/doc/tidyhydat_can.html | 4 ++-- inst/doc/weathercan_can.html | 4 ++-- src/RcppExports.cpp | 5 +++++ src/col_stats.cpp | 12 ++++++------ 13 files changed, 44 insertions(+), 39 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using 'RcppParallel' and 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between dipsaus versions 0.1.5 dated 2021-02-20 and 0.1.6 dated 2021-07-08
DESCRIPTION | 11 MD5 | 49 NAMESPACE | 5 NEWS.md | 18 R/RcppExports.R | 16 R/cpp-fastcov2.R |only R/graphics.R | 50 R/strings.R | 20 R/utils-package.R | 2 R/utils-rstudio.R | 42 R/utils.R | 93 R/zzz.R | 20 build/vignette.rds |binary inst/doc/r_expr_addons.html | 478 - inst/doc/shiny_customized_widgets.html | 8343 ---------------------- inst/doc/utility_functions.html | 334 inst/shiny-addons/dipsaus/dipsaus-dipterix-lib.js | 196 man/attached_packages.Rd | 4 man/capture_expr.Rd | 17 man/fastcov2.Rd |only man/rs_exec.Rd | 7 man/rs_focus_console.Rd | 8 man/sexp_type2.Rd |only man/sumsquared.Rd |only src/RcppExports.cpp | 61 src/rcpp_fastCov.cpp |only src/utils.cpp | 68 src/utils.h | 4 28 files changed, 913 insertions(+), 8933 deletions(-)
Title: Assertion and Message Functions
Description: Enhanced message functions (cat() / message() / warning() / error())
using wrappers around sprintf(). Also, multiple assertion functions
(e.g. to check class, length, values, files, arguments, etc.).
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigassertr versions 0.1.4 dated 2021-04-16 and 0.1.5 dated 2021-07-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/assert.R | 11 ++++++++--- tests/testthat/test-assert.R | 12 ++++++++---- 4 files changed, 23 insertions(+), 14 deletions(-)
Title: Local Randomization Methods for RD Designs
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. Under the local randomization approach, RD designs can be interpreted as randomized experiments inside a window around the cutoff. This package provides tools to perform randomization inference for RD designs under local randomization: rdrandinf() to perform hypothesis testing using randomization inference, rdwinselect() to select a window around the cutoff in which randomization is likely to hold, rdsensitivity() to assess the sensitivity of the results to different window lengths and null hypotheses and rdrbounds() to construct Rosenbaum bounds for sensitivity to unobserved confounders. See Cattaneo, Titiunik and Vazquez-Bare (2016) <https://rdpackages.github.io/references/Cattaneo-Titiunik-VazquezBare_2016_Stata.pdf> for further methodological details.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@econ.ucsb.edu>
Diff between rdlocrand versions 0.8 dated 2021-06-15 and 0.9 dated 2021-07-08
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/rdlocrand_fun.R | 2 +- R/rdlocrand_package.R | 2 +- R/rdrandinf.R | 26 +++++++++++++------------- R/rdrbounds.R | 2 +- R/rdsensitivity.R | 2 +- R/rdwinselect.R | 15 +++++++++------ man/rdrandinf.Rd | 6 +++--- man/rdwinselect.Rd | 4 ++-- 10 files changed, 43 insertions(+), 40 deletions(-)
Title: Multivariate Statistical Methods with R Applications
Description: Data sets in the book entitled "Multivariate Statistical Methods with R Applications", H.Bulut (2018).
The book was published in Turkish and the original name of this book will be "R Uygulamalari ile Cok Degiskenli Istatistiksel Yontemler".
Author: Hasan BULUT
Maintainer: Hasan BULUT <hasan.bulut@omu.edu.tr>
Diff between MSMwRA versions 1.3 dated 2018-08-07 and 1.5 dated 2021-07-08
DESCRIPTION | 12 ++++----- MD5 | 21 ++++++++-------- NAMESPACE | 4 +-- inst |only man/Agriculture.Rd | 56 +++++++++++++++++++++++--------------------- man/PISA.Rd | 56 +++++++++++++++++++++++--------------------- man/SER.Rd | 52 +++++++++++++++++++++-------------------- man/Sim1.Rd | 40 ++++++++++++++++---------------- man/Sim2.Rd | 42 +++++++++++++++++---------------- man/ecodata.Rd | 56 +++++++++++++++++++++++--------------------- man/happiness.Rd | 52 +++++++++++++++++++++-------------------- man/ssl.Rd | 66 +++++++++++++++++++++++++++-------------------------- 12 files changed, 237 insertions(+), 220 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like
'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
https://github.com/mandreyel/ [cph] (mio library),
Jukka Jylänki [cph] (grisu3 implementation),
Mikkel Jørgensen [cph] (grisu3 implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between vroom versions 1.5.1 dated 2021-06-22 and 1.5.2 dated 2021-07-08
DESCRIPTION | 13 +- MD5 | 33 +++---- NEWS.md | 19 ++++ R/col_types.R | 42 ++++++--- R/generator.R | 2 R/path.R | 157 ++++++++++++++++++++++++++++++++++-- build/vroom.pdf |binary inst/WORDLIST | 5 + inst/doc/vroom.html | 2 src/Makevars | 1 src/collectors.h | 17 +-- src/fixed_width_index_connection.cc | 22 +++-- src/iconv_file.cc | 8 - src/parallel.h | 9 +- tests/testthat/mtcars.zip |only tests/testthat/test-path.R | 59 +++++++++++++ tests/testthat/test-vroom.R | 59 +++++++++++++ tests/testthat/test-vroom_fwf.R | 26 +++++ 18 files changed, 408 insertions(+), 66 deletions(-)
Title: Fitting Second-Order Tensor Data
Description: An implementation of fitting generalized linear models on
second-order tensor type data. The functions within this package mainly focus on
parameter estimation, including parameter coefficients and standard deviation.
Author: Mark Chen [aut, cre],
Sheng-Mao Chang [aut],
Wenbin Lu [aut],
Jung-Ying Tzeng [aut],
Ping-Yang Chen [aut]
Maintainer: Mark Chen <l501l501l@gmail.com>
Diff between TensorTest2D versions 1.0.2 dated 2021-04-24 and 1.0.3 dated 2021-07-08
TensorTest2D-1.0.2/TensorTest2D/R/TRtest.omics.R |only TensorTest2D-1.0.2/TensorTest2D/man/TRtest.omics.Rd |only TensorTest2D-1.0.2/TensorTest2D/man/drawpixelmarks.Rd |only TensorTest2D-1.0.3/TensorTest2D/DESCRIPTION | 12 - TensorTest2D-1.0.3/TensorTest2D/MD5 | 28 +-- TensorTest2D-1.0.3/TensorTest2D/NAMESPACE | 4 TensorTest2D-1.0.3/TensorTest2D/R/TRtest.R |only TensorTest2D-1.0.3/TensorTest2D/R/TensorTest2D.R | 2 TensorTest2D-1.0.3/TensorTest2D/R/omics-data.R | 2 TensorTest2D-1.0.3/TensorTest2D/R/summary.tsglm.R | 54 ++++- TensorTest2D-1.0.3/TensorTest2D/R/util.tsglm.R | 163 ++++++++++++------ TensorTest2D-1.0.3/TensorTest2D/man/TRtest.Rd |only TensorTest2D-1.0.3/TensorTest2D/man/TensorTest2D.Rd | 2 TensorTest2D-1.0.3/TensorTest2D/man/draw.coef.Rd |only TensorTest2D-1.0.3/TensorTest2D/man/omics.Rd | 2 TensorTest2D-1.0.3/TensorTest2D/man/plot.tsglm.Rd | 57 ++++-- TensorTest2D-1.0.3/TensorTest2D/man/predict.tsglm.Rd | 19 -- TensorTest2D-1.0.3/TensorTest2D/man/summary.tsglm.Rd | 24 +- 18 files changed, 255 insertions(+), 114 deletions(-)
Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets on solid state drives. This bypasses limitation of physical memory size as well as limited bandwidth of database interfaces. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface. The data is memory mapped into R and then accessed using usual R list and array subscription operators. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as standalone C library. libMVL has simple C API making it easy to interchange of datasets with outside programs.
Author: Vladimir Dergachev [aut, cre] (<https://orcid.org/0000-0003-4708-6625>)
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 0.0.1.3 dated 2021-06-26 and 0.0.1.4 dated 2021-07-08
DESCRIPTION | 7 ++++--- MD5 | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M. Draminski, J. Koronacki (2018) <doi:10.18637/jss.v085.i12>.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <michal.draminski@ipipan.waw.pl>
Diff between rmcfs versions 1.3.3 dated 2021-06-12 and 1.3.4 dated 2021-07-08
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- NEWS.md | 6 +++ R/rmcfs.R | 5 +- inst/doc/v85i12.pdf |binary inst/java/dmLab.jar |binary java/src/dmLab/DMLabInfo.java | 4 +- java/src/dmLab/mcfs/mcfsEngine/MCFSAutoParams.java | 5 ++ java/src/dmLab/mcfs/mcfsEngine/framework/MCFSPermutation.java | 2 - java/src/dmLab/mcfs/mcfsEngine/modules/Projection.java | 2 + 10 files changed, 31 insertions(+), 19 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb] (iSCAM functions)
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.1.0 dated 2021-07-03 and 3.1.1 dated 2021-07-08
MSEtool-3.1.0/MSEtool/R/MOM_functions.R |only MSEtool-3.1.1/MSEtool/DESCRIPTION | 8 MSEtool-3.1.1/MSEtool/MD5 | 36 - MSEtool-3.1.1/MSEtool/NAMESPACE | 5 MSEtool-3.1.1/MSEtool/NEWS.md | 9 MSEtool-3.1.1/MSEtool/R/Data_make_update.R | 16 MSEtool-3.1.1/MSEtool/R/Misc_Internal.R | 15 MSEtool-3.1.1/MSEtool/R/OM_plots.R | 8 MSEtool-3.1.1/MSEtool/R/SS2MOM.R | 39 + MSEtool-3.1.1/MSEtool/R/SS2MOM_plots.R |only MSEtool-3.1.1/MSEtool/R/SS2OM.R | 9 MSEtool-3.1.1/MSEtool/R/SSinternal.R | 23 - MSEtool-3.1.1/MSEtool/R/aaImportFrom.R | 10 MSEtool-3.1.1/MSEtool/R/multiMSE.R | 21 - MSEtool-3.1.1/MSEtool/R/popdyn.R | 25 - MSEtool-3.1.1/MSEtool/inst/Rmd/SS/SS2MOM.Rmd | 209 +--------- MSEtool-3.1.1/MSEtool/man/SS2MOM.Rd | 31 + MSEtool-3.1.1/MSEtool/man/simCAL.Rd | 3 MSEtool-3.1.1/MSEtool/src/popddynCPP.cpp | 16 MSEtool-3.1.1/MSEtool/tests/manual/test-code/test-MSE_Plotting.R | 1 20 files changed, 205 insertions(+), 279 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included.
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). A data-based power transformation for compositional data. Fourth International International Workshop on Compositional Data Analysis.
b) Tsagris M. (2014). The k-NN algorithm for compositional data: a revised approach with and without zero values present. Journal of Data Science, 12(3):519--534.
c) Tsagris M. (2015). A novel, divergence based, regression for compositional data. Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444.
d) Tsagris M. (2015). Regression analysis with compositional data containing zero values. Chilean Journal of Statistics, 6(2):47--57.
e) Tsagris M., Preston S. and Wood A.T.A. (2016). Improved supervised classification for compositional data using the alpha-transformation. Journal of Classification, 33(2):243--261. <doi:10.1007/s00357-016-9207-5>.
f) Tsagris M., Preston S. and Wood A.T.A. (2017). Nonparametric hypothesis testing for equality of means on the simplex. Journal of Statistical Computation and Simulation, 87(2): 406--422. <doi:10.1080/00949655.2016.1216554>.
g) Tsagris M. and Stewart C. (2018). A Dirichlet regression model for compositional data with zeros. Lobachevskii Journal of Mathematics,39(3): 398--412. <doi:10.1134/S1995080218030198>.
h) Alenazi A. (2019). Regression for compositional data with compositional data as predictor variables with or without zero values. Journal of Data Science, 17(1): 219--238. <doi:10.6339/JDS.201901_17(1).0010>.
i) Tsagris M. and Stewart C. (2020). A folded model for compositional data analysis. Australian and New Zealand Journal of Statistics, 62(2):249--277. <doi:10.1111/anzs.12289>.
j) Tsagris M., Alenazi A. and Stewart C. (2021). The alpha-k-NN regression for compositional data. <arXiv:2002.05137>.
We further include functions for percentages (or proportions).
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 4.7 dated 2021-05-13 and 4.8 dated 2021-07-08
DESCRIPTION | 8 +- MD5 | 131 +++++++++++++++++++++++-------------------- NAMESPACE | 2 R/akernreg.tune.R | 2 R/alfafda.tune.R | 5 - R/cv.lasso.compreg.R |only R/cv.lasso.klcompreg.R | 6 - R/fp.R | 2 R/frechet2.R | 9 +- R/glmpcr.tune.R | 3 R/js.compreg.R | 2 R/kl.compreg.R | 2 R/lasso.compreg.R |only R/lasso.klcompreg.R | 3 R/lc.reg.R | 68 +++++++++++++++------- R/lc.reg2.R |only R/lcreg.aov.R |only R/ols.compreg.R | 2 R/tv.compreg.R |only R/ulc.reg.R |only R/ulc.reg2.R |only man/Compositional-package.Rd | 19 +++--- man/akern.reg.Rd | 2 man/akernreg.tune.Rd | 2 man/aknn.reg.Rd | 2 man/aknnreg.tune.Rd | 2 man/alfa.pca.Rd | 2 man/alfa.reg.Rd | 2 man/alr.Rd | 2 man/alr.all.Rd | 2 man/bic.mixcompnorm.Rd | 2 man/bivt.contour.Rd | 2 man/comp.den.Rd | 2 man/comp.kerncontour.Rd | 2 man/comp.reg.Rd | 2 man/compbn.Rd | 2 man/cv.lasso.compreg.Rd |only man/cv.lasso.klcompreg.Rd | 10 +-- man/dda.Rd | 4 - man/ddiri.Rd | 2 man/diri.contour.Rd | 4 - man/diri.est.Rd | 4 - man/diri.reg.Rd | 6 - man/dirimean.test.Rd | 2 man/glm.pcr.Rd | 2 man/glmpcr.tune.Rd | 2 man/kl.compreg.Rd | 10 ++- man/kl.diri.Rd | 2 man/lasso.compreg.Rd |only man/lasso.klcompreg.Rd | 8 +- man/lassocoef.plot.Rd | 21 ++++-- man/lc.reg.Rd | 38 ++++++++---- man/lc.reg2.Rd |only man/lcreg.aov.Rd |only man/logpca.Rd | 2 man/maov.Rd | 2 man/mix.compnorm.Rd | 2 man/mixnorm.contour.Rd | 2 man/multivt.Rd | 6 - man/norm.contour.Rd | 2 man/ols.compreg.Rd | 2 man/rcompnorm.Rd | 2 man/rcompsn.Rd | 2 man/rcompt.Rd | 2 man/rdiri.Rd | 4 - man/skewnorm.contour.Rd | 2 man/sym.test.Rd | 2 man/ternary.Rd | 2 man/ternary.reg.Rd | 2 man/totvar.Rd | 2 man/ulc.reg.Rd |only man/ulc.reg2.Rd |only man/zadr.Rd | 2 73 files changed, 260 insertions(+), 187 deletions(-)
Title: Identify Mutually Exclusive Mutations
Description: An optimized method for identifying mutually
exclusive genomic events. Its main contribution is a
statistical analysis based on the Poisson-Binomial
distribution that takes into account that some samples
are more mutated than others. See [Canisius, Sander, John WM Martens,
and Lodewyk FA Wessels. (2016) "A novel independence test for
somatic alterations in cancer shows that
biology drives mutual exclusivity but chance explains
most co-occurrence." Genome biology 17.1 : 1-17. <doi:10.1186/s13059-016-1114-x>].
The mutations matrices are sparse matrices. The method developed takes
advantage of the advantages of this type of matrix to save
time and computing resources.
Author: Juan A. Ferrer-Bonsoms Developer [aut, cre],
Laura Jareno Developer [aut],
Angel Rubio User [aut, ctb]
Maintainer: Juan A. Ferrer-Bonsoms Developer <jafhernandez@tecnun.es>
Diff between Rediscover versions 0.1.0 dated 2021-04-07 and 0.2.0 dated 2021-07-08
DESCRIPTION | 10 - MD5 | 36 +++--- NAMESPACE | 1 NEWS | 1 R/discoversomaticInteractions.R | 26 +++- R/getMutex.R | 192 ++++++++++++++++++++++++----------- R/getMutexAB.R | 201 ++++++++++++++++++++++++++----------- R/getPM.R | 8 - data/PM_COAD.rda |binary data/TCGA_COAD.rda |binary inst/doc/Rediscover.R | 36 +++++- inst/doc/Rediscover.Rmd | 82 ++++++++++++--- inst/doc/Rediscover.html | 111 +++++++++++++------- inst/unitTests/test_getMutex.R | 13 ++ inst/unitTests/test_getMutexAB.R | 9 + man/discoversomaticInteractions.Rd | 16 ++ man/getMutex.Rd | 28 ++++- man/getMutexAB.Rd | 30 ++++- vignettes/Rediscover.Rmd | 82 ++++++++++++--- 19 files changed, 653 insertions(+), 229 deletions(-)
Title: Multivariate Hypothesis Tests
Description: Multivariate hypothesis tests and the confidence intervals. It can be used to test the hypothesizes about mean vector or vectors (one-sample, two independent samples, paired samples), covariance matrix (one or more matrices), and the correlation matrix. Moreover, it can be used for robust Hotelling T^2 test at one sample case in high dimensional data. For this package, we have benefited from the studies Rencher (2003), Nel and Merwe (1986) <DOI: 10.1080/03610928608829342>, Tatlidil (1996), Tsagris (2014), Villasenor Alva and Estrada (2009) <DOI: 10.1080/03610920802474465>.
Author: Hasan BULUT [aut,cre]
Maintainer: Hasan BULUT <hasan.bulut@omu.edu.tr>
Diff between MVTests versions 2.0.3 dated 2021-04-13 and 2.0.8 dated 2021-07-08
DESCRIPTION | 13 +++++++------ MD5 | 9 +++++++-- NAMESPACE | 5 +++++ R/RHT2.R |only R/simRHT2.R |only inst |only man/RHT2.Rd |only man/simRHT2.Rd |only 8 files changed, 19 insertions(+), 8 deletions(-)
Title: Structural Exploration of the Gene Ontology (GO) Knowledge Base
Description: It provides an effective, efficient, and fast way to explore the Gene Ontology (GO).
Given a set of genes, the package contains functions to assess the GO and obtain the
terms associated with the genes and the levels of the GO terms. The package provides
functions for the three different GO ontology. We discussed the methods explicitly in
the following article <doi:10.1038/s41598-020-73326-3>.
Author: Kalifa Manjang, Frank Emmert-Streib, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer
Maintainer: Kalifa Manjang <kalifamanjang1@gmail.com>
Diff between GOxploreR versions 1.2.1 dated 2021-06-07 and 1.2.2 dated 2021-07-08
DESCRIPTION | 10 +++--- MD5 | 20 ++++++------- NAMESPACE | 11 ++++--- R/drawGraph.R | 55 ++++++++++++++++--------------------- R/drawGraph4vis.R | 70 ++++++++++++++---------------------------------- R/gotermlevelcc.R | 4 +- R/supportedOrganism.R | 2 - inst/doc/GOxploreR.R | 12 ++++---- inst/doc/GOxploreR.Rmd | 15 ++++------ inst/doc/GOxploreR.pdf |binary vignettes/GOxploreR.Rmd | 15 ++++------ 11 files changed, 90 insertions(+), 124 deletions(-)
Title: Download Official Spatial Data Sets of Brazil
Description: Easy access to official spatial data sets of Brazil as 'sf' objects
in R. The package includes a wide range of geospatial data available
at various geographic scales and for various years with harmonized
attributes, projection and fixed topology.
Author: Rafael H. M. Pereira [aut, cre]
(<https://orcid.org/0000-0003-2125-7465>),
Caio Nogueira Goncalves [aut],
Paulo Henrique Fernandes de Araujo [ctb],
Guilherme Duarte Carvalho [ctb],
Rodrigo Almeida de Arruda [ctb],
Igor Nascimento [ctb],
Barbara Santiago Pedreira da Costa [ctb],
Welligtton Silva Cavedo [ctb],
Pedro R. Andrade [ctb],
Alan da Silva [ctb],
Carlos Kauê Vieira Braga [ctb],
Carl Schmertmann [ctb],
Alessandro Samuel-Rosa [ctb],
Daniel Ferreira [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geobr versions 1.6.1 dated 2021-04-16 and 1.6.2 dated 2021-07-08
DESCRIPTION | 15 ++++++++------- MD5 | 8 ++++---- R/lookup_muni.R | 2 +- build/partial.rdb |binary man/lookup_muni.Rd | 2 +- 5 files changed, 14 insertions(+), 13 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cre, cph],
Paul Buerkner [ctb],
Maxime Herve [ctb],
Jonathon Love [ctb],
Hannes Riebl [ctb],
Henrik Singmann [ctb]
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.6.1 dated 2021-06-01 and 1.6.2-1 dated 2021-07-08
DESCRIPTION | 8 - MD5 | 80 +++++++++---------- NAMESPACE | 2 NEWS.md | 12 ++ R/cld-emm.R | 43 ++++------ R/contrast.R | 2 R/emm-list.R | 11 -- R/emmGrid-methods.R | 2 R/multiv.R |only R/summary.R | 31 ++++++- R/zzz.R | 1 inst/doc/FAQs.Rmd | 2 inst/doc/FAQs.html | 12 +- inst/doc/basics.html | 12 +- inst/doc/comparisons.Rmd | 5 - inst/doc/comparisons.html | 47 +++++------ inst/doc/confidence-intervals.html | 72 ++++++++--------- inst/doc/interactions.R | 11 ++ inst/doc/interactions.Rmd | 54 ++++++++++++ inst/doc/interactions.html | 155 ++++++++++++++++++++++--------------- inst/doc/messy-data.html | 38 ++++----- inst/doc/models.html | 4 inst/doc/predictions.html | 4 inst/doc/sophisticated.html | 20 ++-- inst/doc/transformations.Rmd | 6 - inst/doc/transformations.html | 46 +++++----- inst/doc/utilities.html | 50 +++++------ inst/doc/vignette-topics.Rmd | 69 +++++++--------- inst/doc/vignette-topics.html | 122 ++++++++++++++--------------- inst/doc/xplanations.R | 2 inst/doc/xplanations.Rmd | 8 - inst/doc/xplanations.html | 10 +- inst/doc/xtending.html | 8 - man/CLD.emmGrid.Rd | 144 +++++++++++++++++----------------- man/mvcontrast.Rd |only man/update.emmGrid.Rd | 15 +++ vignettes/FAQs.Rmd | 2 vignettes/comparisons.Rmd | 5 - vignettes/interactions.Rmd | 54 ++++++++++++ vignettes/transformations.Rmd | 6 - vignettes/vignette-topics.Rmd | 69 +++++++--------- vignettes/xplanations.Rmd | 8 - 42 files changed, 717 insertions(+), 535 deletions(-)
Title: Optimizing Consistency and Coverage in Configurational Causal
Modeling
Description: This is an add-on to the 'cna' package <https://CRAN.R-project.org/package=cna> comprising various functions for optimizing consistency and coverage scores of models of configurational comparative methods as Coincidence Analysis (CNA) and Qualitative Comparative Analysis (QCA). The function conCovOpt() calculates con-cov optima, selectMax() selects con-cov maxima among the con-cov optima, DNFbuild() can be used to build models actually reaching those optima, and findOutcomes() identifies those factor values in analyzed data that can be modeled as outcomes. For a theoretical introduction to these functions see Baumgartner and Ambuehl (2021) <doi:10.1177/0049124121995554>.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cnaOpt versions 0.2.0 dated 2020-09-14 and 0.4.0 dated 2021-07-08
cnaOpt-0.2.0/cnaOpt/R/from_cna_namespace.R |only cnaOpt-0.2.0/cnaOpt/man/rreduce_ereduce.Rd |only cnaOpt-0.4.0/cnaOpt/DESCRIPTION | 13 - cnaOpt-0.4.0/cnaOpt/MD5 | 34 +-- cnaOpt-0.4.0/cnaOpt/NAMESPACE | 2 cnaOpt-0.4.0/cnaOpt/R/RcppExports.R | 8 cnaOpt-0.4.0/cnaOpt/R/cnaOpt.R | 56 ++++- cnaOpt-0.4.0/cnaOpt/R/conCovOpt.R | 39 +--- cnaOpt-0.4.0/cnaOpt/R/conCovOpt_utils.R | 3 cnaOpt-0.4.0/cnaOpt/inst/NEWS | 9 cnaOpt-0.4.0/cnaOpt/man/cnaOpt.Rd | 68 +++++-- cnaOpt-0.4.0/cnaOpt/man/conCovOpt.Rd | 221 +++++++++++------------ cnaOpt-0.4.0/cnaOpt/man/ereduce.Rd |only cnaOpt-0.4.0/cnaOpt/man/findOutcomes.Rd | 143 +++++++------- cnaOpt-0.4.0/cnaOpt/man/reprodAssign.Rd | 218 +++++++++++----------- cnaOpt-0.4.0/cnaOpt/man/selectMax.Rd | 14 - cnaOpt-0.4.0/cnaOpt/src/C_iterate.cpp | 6 cnaOpt-0.4.0/cnaOpt/src/RcppExports.cpp | 26 ++ cnaOpt-0.4.0/cnaOpt/src/min_hitting_sets_aux.cpp |only cnaOpt-0.4.0/cnaOpt/src/typedefs.h | 2 20 files changed, 492 insertions(+), 370 deletions(-)
Title: Non-Parametric Bayesian Multiple Imputation for Categorical Data
Description: These routines create multiple imputations of missing at random categorical data, and create multiply imputed synthesis of categorical data, with or without structural zeros. Imputations and syntheses are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling, described in Manrique-Vallier and Reiter (2014) <doi:10.1080/10618600.2013.844700>.
Author: Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter and Jingchen Hu
Maintainer: Jingchen Hu <jingchen.monika.hu@gmail.com>
Diff between NPBayesImputeCat versions 0.3 dated 2021-01-14 and 0.4 dated 2021-07-08
NPBayesImputeCat-0.3/NPBayesImputeCat/man/Rcpp_Lcm.Rd |only NPBayesImputeCat-0.4/NPBayesImputeCat/DESCRIPTION | 12 - NPBayesImputeCat-0.4/NPBayesImputeCat/MD5 | 29 +-- NPBayesImputeCat-0.4/NPBayesImputeCat/NAMESPACE | 3 NPBayesImputeCat-0.4/NPBayesImputeCat/R/NewUpdates_v2.R |only NPBayesImputeCat-0.4/NPBayesImputeCat/man/CreateModel.Rd | 10 - NPBayesImputeCat-0.4/NPBayesImputeCat/man/DPMPM_nozeros_imp.Rd | 2 NPBayesImputeCat-0.4/NPBayesImputeCat/man/DPMPM_nozeros_syn.Rd | 8 NPBayesImputeCat-0.4/NPBayesImputeCat/man/Lcm.Rd | 96 +++++++++- NPBayesImputeCat-0.4/NPBayesImputeCat/man/NPBayesImputCat-package.Rd | 4 NPBayesImputeCat-0.4/NPBayesImputeCat/man/Rcpp_Lcm-class.Rd | 88 --------- NPBayesImputeCat-0.4/NPBayesImputeCat/man/X.Rd | 30 ++- NPBayesImputeCat-0.4/NPBayesImputeCat/man/kstar_MCMCdiag.Rd |only NPBayesImputeCat-0.4/NPBayesImputeCat/man/ss16pusa_sample_nozeros.Rd | 7 NPBayesImputeCat-0.4/NPBayesImputeCat/man/ss16pusa_sample_nozeros_miss.Rd | 7 NPBayesImputeCat-0.4/NPBayesImputeCat/man/ss16pusa_sample_zeros.Rd | 15 + NPBayesImputeCat-0.4/NPBayesImputeCat/man/ss16pusa_sample_zeros_miss.Rd | 15 + 17 files changed, 176 insertions(+), 150 deletions(-)
More information about NPBayesImputeCat at CRAN
Permanent link
Title: Estimate Univariate Gaussian or Student's t Mixture
Autoregressive Model
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2021) <doi:10.1080/03610926.2021.1916531>,
Savi Virolainen (forthcoming), currently available as <arXiv:2003.05221>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.3.1 dated 2021-05-12 and 3.3.2 dated 2021-07-08
DESCRIPTION | 10 +- MD5 | 146 +++++++++++++++++----------------- NEWS.md | 8 + R/GSMARconstructor.R | 33 +++++-- R/MAINest.R | 51 +++++++---- R/WaldAndLR.R | 5 - R/argumentChecks.R | 50 +++++++---- R/data.R | 24 +++++ R/diagnosticPlot.R | 24 ++++- R/geneticAlgorithm.R | 69 ++++++++++------ R/loglikelihood.R | 68 +++++++++------ R/morePlots.R | 11 +- R/numericalDifferentiation.R | 37 +++++--- R/parameterReforms.R | 68 +++++++++------ R/pickAndChangeParams.R | 64 ++++++++------ R/plotMethods.R | 46 +++++++--- R/predictMethod.R | 19 ++-- R/printMethods.R | 56 ++++++++----- R/quantileResidualTests.R | 29 ++++-- R/quantileResiduals.R | 9 +- R/simulateGSMAR.R | 12 +- R/uncondMoments.R | 23 +++-- README.md | 14 +-- data/TBFF.rda |only inst/doc/uGMARpaper.Rnw | 106 ++++++++++++++++++++---- inst/doc/uGMARpaper.pdf |binary man/GAfit.Rd | 5 - man/GSMAR.Rd | 5 - man/LR_test.Rd | 5 - man/M10Y1Y.Rd | 2 man/T10Y1Y.Rd | 2 man/TBFF.Rd |only man/Wald_test.Rd | 5 - man/add_data.Rd | 5 - man/alt_gsmar.Rd | 5 - man/change_parametrization.Rd | 5 - man/condMoments.Rd | 5 - man/cond_moment_plot.Rd | 5 - man/cond_moments.Rd | 5 - man/condmomentPlot.Rd | 5 - man/diagnosticPlot.Rd | 5 - man/diagnostic_plot.Rd | 5 - man/fitGSMAR.Rd | 8 + man/get_alpha_mt.Rd | 5 - man/get_ar_roots.Rd | 5 - man/get_regime_autocovs.Rd | 5 - man/get_regime_means.Rd | 5 - man/get_regime_vars.Rd | 5 - man/get_test_Omega.Rd | 5 - man/isStationary.Rd | 5 - man/is_stationary.Rd | 5 - man/is_stationary_int.Rd | 5 - man/iterate_more.Rd | 5 - man/loglikelihood.Rd | 5 - man/loglikelihood_int.Rd | 5 - man/mixingWeights.Rd | 5 - man/mixing_weights.Rd | 5 - man/mixing_weights_int.Rd | 5 - man/predict.gsmar.Rd | 5 - man/profile_logliks.Rd | 5 - man/quantileResidualPlot.Rd | 5 - man/quantileResidualTests.Rd | 5 - man/quantileResiduals.Rd | 5 - man/quantile_residual_plot.Rd | 5 - man/quantile_residual_tests.Rd | 5 - man/quantile_residuals.Rd | 5 - man/quantile_residuals_int.Rd | 5 - man/simulateGSMAR.Rd | 5 - man/stmar_to_gstmar.Rd | 5 - man/swap_parametrization.Rd | 5 - man/uncond_moments.Rd | 5 - man/uncond_moments_int.Rd | 5 - vignettes/figures/diagplotfit42gs.png |binary vignettes/refs.bib | 49 ++++++----- vignettes/uGMARpaper.Rnw | 106 ++++++++++++++++++++---- 75 files changed, 895 insertions(+), 464 deletions(-)
Title: An Implementation of Sensitivity Analysis in Bayesian Networks
Description: An implementation of sensitivity and robustness methods in Bayesian networks in R. It includes methods to perform parameter variations via a variety of co-variation schemes, to compute sensitivity functions and to quantify the dissimilarity of two Bayesian networks via distances and divergences. It further includes diagnostic methods to assess the goodness of fit of a Bayesian networks to data, including global, node and parent-child monitors. References: H. Chan, A. Darwiche (2002) <doi:10.1613/jair.967>; R.G. Cowell, R.J. Verrall, Y.K. Yoon (2007) <doi:10.1111/j.1539-6975.2007.00235.x>; C. Goergen, M. Leonelli (2020) <ArXiv:1809.10794>.
Author: Manuele Leonelli [aut, cre],
Ramsiya Ramanathan [aut],
Rachel Wilkerson [aut]
Maintainer: Manuele Leonelli <manuele.leonelli@ie.edu>
Diff between bnmonitor versions 0.1.0 dated 2021-02-08 and 0.1.1 dated 2021-07-08
DESCRIPTION | 13 +-- MD5 | 42 +++++----- NAMESPACE | 7 - NEWS.md |only R/Jeffreys.R | 20 ++--- R/KL.R | 20 ++--- R/KL_bounds.R | 9 +- R/diabetes.R |only R/frobenius.R | 64 +++++++++++++--- R/global_monitor.R | 5 - R/influential_obs.R | 5 - R/model_pres_cov.R | 5 - R/parent_child_monitor.R | 5 - R/plot.R | 119 +++++++++++++++--------------- R/standard.R | 3 data/diabetes.RData |only man/diabetes.Rd |only man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/global_monitor.Rd | 4 - man/influential_obs.Rd | 4 - man/seq_pa_ch_monitor.Rd | 4 - 24 files changed, 184 insertions(+), 145 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.2.4 dated 2021-06-09 and 1.2.5 dated 2021-07-08
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ R/VolcanoPlotW.R | 35 +++++++++++++++++--------------- R/addBagPlot.R | 3 +- R/plotPCAw.R | 17 +++++++++++---- inst/doc/wrGraphVignette1.html | 44 ++++++++++++++++++++--------------------- man/plotPCAw.Rd | 2 - 7 files changed, 65 insertions(+), 54 deletions(-)
Title: R Interface to PXWEB APIs
Description: Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis
API is used by organizations such as Statistics Sweden and Statistics
Finland to disseminate data. The R package can interact with all
PX-Web/PC-Axis APIs to fetch information about the data hierarchy, extract
metadata and extract and parse statistics to R data.frame format. PX-Web is
a solution to disseminate PC-Axis data files in dynamic tables on the web.
Since 2013 PX-Web contains an API to disseminate PC-Axis files.
Author: Mans Magnusson [aut, cre],
Markus Kainu [aut],
Janne Huovari [aut],
Leo Lahti [aut] (<https://orcid.org/0000-0001-5537-637X>),
Jan Bruusgaard [ctb],
Øyvind Langsrud [ctb],
Love Hansson [ctb],
Eydun Nielsen [ctb],
Bo Werth [ctb],
Thomas Runarsson [ctb],
Torbjörn Lindquist [ctb],
Palmar Thorsteinsson [ctb],
Pyry Kantanen [ctb],
Sebastian Ankargren [ctb]
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between pxweb versions 0.10.4 dated 2021-02-24 and 0.11.0 dated 2021-07-08
DESCRIPTION | 16 ++-- MD5 | 26 +++---- R/onAttach.R | 2 R/pxweb_get.R | 119 +++++++++++++++++++++------------ inst/doc/pxweb.Rmd | 23 ++---- inst/doc/pxweb.html | 60 +++++++--------- inst/extdata/api.json | 36 +++------ man/pxweb_add_mandatory_variables.Rd |only man/pxweb_advanced_get.Rd | 6 - man/pxweb_get.Rd | 6 - man/pxweb_get_data.Rd | 2 tests/testthat/test-pxweb_get.R | 60 ++++++---------- tests/testthat/test-pxweb_query.R | 39 ++++++++++ tests/testthat/test_data/pxm1_test.rda |only vignettes/pxweb.Rmd | 23 ++---- 15 files changed, 225 insertions(+), 193 deletions(-)
Title: Management of Deterministic and Stochastic Projects
Description: Management problems of deterministic and stochastic projects. It obtains the duration of a project and the appropriate slack for each activity in a deterministic context. In addition it obtains a schedule of activities' time (Castro, Gómez & Tejada (2007) <doi:10.1016/j.orl.2007.01.003>). It also allows the management of resources. When the project is done, and the actual duration for each activity is known, then it can know how long the project is delayed and make a fair delivery of the delay between each activity (Bergantiños, Valencia-Toledo & Vidal-Puga (2018) <doi:10.1016/j.dam.2017.08.012>). In a stochastic context it can estimate the average duration of the project and plot the density of this duration, as well as, the density of the early and last times of the chosen activities. As in the deterministic case, it can make a distribution of the delay generated by observing the project already carried out.
Author: Juan Carlos Gonçalves Dosantos [aut, cre],
Ignacio García Jurado [aut],
Julián Costa Bouzas [aut]
Maintainer: Juan Carlos Gonçalves Dosantos <juan.carlos.goncalves@udc.es>
Diff between ProjectManagement versions 1.3.7 dated 2021-01-11 and 1.4.0 dated 2021-07-08
DESCRIPTION | 13 ++++++------- MD5 | 4 ++-- R/function_pert_calendario.R | 37 ++++++++++++++++++++++++++++++++----- 3 files changed, 40 insertions(+), 14 deletions(-)
More information about ProjectManagement at CRAN
Permanent link
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity
in all their dimensions (taxonomic, phylogenetic and functional).
It allows performing a number of analyses based on species
identities/abundances, phylogenetic/functional distances, trees,
convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Author: Pedro Cardoso [aut, cre],
Stefano Mammola [aut],
Francois Rigal [aut],
Jose Carvalho [aut]
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.6.0 dated 2021-05-12 and 2.6.1 dated 2021-07-08
DESCRIPTION | 8 ++--- MD5 | 22 +++++++-------- NAMESPACE | 1 R/BAT.R | 67 ++++++++++++++++++++++++++++++----------------- man/optim.alpha.Rd | 1 man/optim.alpha.stats.Rd | 1 man/optim.beta.Rd | 1 man/optim.beta.stats.Rd | 1 man/raster.alpha.Rd | 2 + man/raster.beta.Rd | 2 + man/raster.dispersion.Rd | 2 + man/raster.evenness.Rd | 2 + 12 files changed, 72 insertions(+), 38 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.11.0 dated 2021-03-31 and 2.12.0 dated 2021-07-08
DESCRIPTION | 8 MD5 | 68 NAMESPACE | 2 R/generic.predict.rfsrc.R | 167 R/get.tree.rfsrc.R | 132 R/partial.rfsrc.R | 179 R/plot.variable.rfsrc.R | 186 R/print.rfsrc.R | 113 R/rfsrc.R | 142 R/rfsrc.anonymous.R | 12 R/tune.nodesize.rfsrc.R | 10 R/tune.rfsrc.R | 10 R/utilities.R | 146 R/utilities.data.R | 252 - R/utilities.factor.R | 22 R/utilities.imbalanced.R |only R/utilities.performance.R | 12 R/utilities.predict.R |only configure | 1770 +++++--- configure.ac | 2 inst/NEWS | 16 man/get.tree.rfsrc.Rd | 60 man/imbalanced.rfsrc.Rd | 16 man/partial.rfsrc.Rd | 275 + man/plot.competing.risk.rfsrc.Rd | 10 man/plot.variable.rfsrc.Rd | 4 man/predict.rfsrc.Rd | 13 man/quantreg.rfsrc.Rd | 5 man/rfsrc.Rd | 55 man/rfsrc.anonymous.Rd | 24 man/sidClustering.rfsrc.Rd | 13 man/tune.rfsrc.Rd | 16 man/vimp.rfsrc.Rd | 15 src/R_init_randomForestSRC.c | 4 src/randomForestSRC.c | 8091 +++++++++++++++++++++++---------------- src/randomForestSRC.h | 955 +--- 36 files changed, 7787 insertions(+), 5018 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Quality Improvement Charts
Description: Functions for making run charts, Shewhart control charts and
Pareto charts for continuous quality improvement. Included control charts
are: I, MR, Xbar, S, T, C, U, U', P, P', and G charts. Non-random variation
in the form of minor to moderate persistent shifts in data over time is
identified by the Anhoej rules for unusually long runs and unusually few
crossing [Anhoej, Olesen (2014) <doi:10.1371/journal.pone.0113825>].
Non-random variation in the form of larger, possibly transient, shifts is
identified by Shewhart's 3-sigma rule [Mohammed, Worthington, Woodall (2008)
<doi:10.1136/qshc.2004.012047>].
Author: Jacob Anhoej [aut, cre]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts2 versions 0.7.1 dated 2020-10-28 and 0.7.2 dated 2021-07-08
DESCRIPTION | 8 MD5 | 27 - NEWS | 8 R/bchart.R | 2 R/data.R | 2 R/helper.functions.R | 27 - R/qic.R | 144 +++-- R/qic.plot.R | 21 build/partial.rdb |only build/vignette.rds |binary inst/doc/qicharts2.html | 1143 ++++++++++++++++++---------------------------- man/bchart.Rd | 2 man/nhs_accidents.Rd | 2 man/qic.Rd | 20 tests/testthat/test_hai.R | 7 15 files changed, 610 insertions(+), 803 deletions(-)
Title: Multivariate Independent Comparison of Observations
Description: A procedure for comparing multivariate samples associated with
different groups. It uses principal component analysis to convert
multivariate observations into a set of linearly uncorrelated statistical
measures, which are then compared using a number of statistical methods. The
procedure is independent of the distributional properties of samples and
automatically selects features that best explain their differences, avoiding
manual selection of specific points or summary statistics. It is appropriate
for comparing samples of time series, images, spectrometric measures or
similar multivariate observations.
Author: Nuno Fachada [aut, cre] (<https://orcid.org/0000-0002-8487-5837>)
Maintainer: Nuno Fachada <faken@fakenmc.com>
Diff between micompr versions 1.1.0 dated 2018-03-09 and 1.1.1 dated 2021-07-08
DESCRIPTION | 17 ++++++++-------- LICENSE | 2 - MD5 | 40 +++++++++++++++++++------------------- R/assumptions.R | 8 ++++--- README.md | 11 ++++------ build/vignette.rds |binary inst/CITATION | 5 ++-- inst/doc/paper.R | 20 +++++++++---------- inst/doc/paper.pdf |binary inst/doc/tolatex-examples.R | 32 +++++++++++++++--------------- inst/doc/tolatex-examples.pdf |binary man/cmpoutput.Rd | 3 -- man/grpoutputs.Rd | 11 ++++++++-- man/micomp.Rd | 12 +++++++++-- man/micompr.Rd | 1 man/pphpc_diff.Rd | 6 +++-- man/pphpc_noshuff.Rd | 6 +++-- man/pphpc_ok.Rd | 6 +++-- man/pphpc_testvlo.Rd | 6 +++-- man/toLatex.micomp.Rd | 35 +++++++++++++++++++++++---------- tests/testthat/test_assumptions.R | 2 - 21 files changed, 130 insertions(+), 93 deletions(-)
Title: Functions to Work with 'incidence2' Objects
Description: Provides functions to work with 'incidence2' objects, including a
simplified interface for trend fitting and peak estimation. This package is
part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for
outbreak analysis (<https://www.reconverse.org/).
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>),
Thibaut Jombart [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between i2extras versions 0.1.0 dated 2021-03-30 and 0.1.2 dated 2021-07-08
DESCRIPTION | 8 - MD5 | 20 +- NEWS.md | 4 R/utils.R | 13 - build/vignette.rds |binary inst/doc/fitting_epicurves.html | 220 +++++++++++++-------------- inst/doc/peak_estimation.R | 6 inst/doc/peak_estimation.Rmd | 6 inst/doc/peak_estimation.html | 272 ++++------------------------------ tests/testthat/test-rolling_average.R | 2 vignettes/peak_estimation.Rmd | 6 11 files changed, 177 insertions(+), 380 deletions(-)
Title: Heteroskedastic Gaussian Process Modeling and Design under
Replication
Description: Performs Gaussian process regression with heteroskedastic noise following the model by Binois, M., Gramacy, R., Ludkovski, M. (2016) <arXiv:1611.05902>, with implementation details in Binois, M. & Gramacy, R. B. (2021) <doi:10.18637/jss.v098.i13>. The input dependent noise is modeled as another Gaussian process. Replicated observations are encouraged as they yield computational savings. Sequential design procedures based on the integrated mean square prediction error and lookahead heuristics are provided, and notably fast update functions when adding new observations.
Author: Mickael Binois, Robert B. Gramacy
Maintainer: Mickael Binois <mickael.binois@inria.fr>
Diff between hetGP versions 1.1.3 dated 2021-03-17 and 1.1.4 dated 2021-07-08
DESCRIPTION | 10 ++-- MD5 | 21 ++++----- NAMESPACE | 2 NEWS | 4 + R/Covariance_functions.R | 2 R/RcppExports.R | 98 ++++++++++++++++++++++---------------------- R/hetGP-package.R | 15 ++++-- build/vignette.rds |binary inst/CITATION |only inst/doc/hetGP_vignette.pdf |binary man/hetGP-package.Rd | 14 ++++-- src/qEI.cpp | 47 +++++++++++---------- 12 files changed, 116 insertions(+), 97 deletions(-)
Title: An Interface to Google Drive
Description: Manage Google Drive files from R.
Author: Lucy D'Agostino McGowan [aut],
Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between googledrive versions 1.0.1 dated 2020-05-05 and 2.0.0 dated 2021-07-08
googledrive-1.0.1/googledrive/R/as_dribble.R |only googledrive-1.0.1/googledrive/R/as_id.R |only googledrive-1.0.1/googledrive/R/as_teamdrive.R |only googledrive-1.0.1/googledrive/R/dplyr-compat.R |only googledrive-1.0.1/googledrive/R/drive_example.R |only googledrive-1.0.1/googledrive/R/drive_reveal_path.R |only googledrive-1.0.1/googledrive/R/team_drive_create.R |only googledrive-1.0.1/googledrive/R/team_drive_find.R |only googledrive-1.0.1/googledrive/R/team_drive_get.R |only googledrive-1.0.1/googledrive/R/team_drive_params.R |only googledrive-1.0.1/googledrive/R/team_drive_rm.R |only googledrive-1.0.1/googledrive/R/team_drive_update.R |only googledrive-1.0.1/googledrive/R/tree-climbing.R |only googledrive-1.0.1/googledrive/inst/extdata/chicken.csv |only googledrive-1.0.1/googledrive/inst/extdata/chicken.jpg |only googledrive-1.0.1/googledrive/inst/extdata/chicken.pdf |only googledrive-1.0.1/googledrive/inst/extdata/chicken.txt |only googledrive-1.0.1/googledrive/inst/extdata/files_fields.csv |only googledrive-1.0.1/googledrive/inst/extdata/mime_tbl.csv |only googledrive-1.0.1/googledrive/inst/extdata/translate_mime_types.csv |only googledrive-1.0.1/googledrive/man/as_team_drive.Rd |only googledrive-1.0.1/googledrive/man/drive_example.Rd |only googledrive-1.0.1/googledrive/man/team_drive_create.Rd |only googledrive-1.0.1/googledrive/man/team_drive_find.Rd |only googledrive-1.0.1/googledrive/man/team_drive_get.Rd |only googledrive-1.0.1/googledrive/man/team_drive_rm.Rd |only googledrive-1.0.1/googledrive/man/team_drive_update.Rd |only googledrive-1.0.1/googledrive/man/team_drives.Rd |only googledrive-1.0.1/googledrive/tests/testthat/all-test-clean.R |only googledrive-1.0.1/googledrive/tests/testthat/all-test-setup.R |only googledrive-1.0.1/googledrive/tests/testthat/all-test-setup.html |only googledrive-1.0.1/googledrive/tests/testthat/test-as_id.R |only googledrive-1.0.1/googledrive/tests/testthat/test-dplyr-compatibility.R |only googledrive-1.0.1/googledrive/tests/testthat/test-dribble-class.R |only googledrive-1.0.1/googledrive/tests/testthat/test-generate_request.R |only googledrive-1.0.1/googledrive/tests/testthat/test-path-utils.R |only googledrive-1.0.1/googledrive/tests/testthat/test-pathification.R |only googledrive-1.0.1/googledrive/tests/testthat/test-team_drive_params.R |only googledrive-1.0.1/googledrive/tests/testthat/test-tree-climbing.R |only googledrive-1.0.1/googledrive/tests/testthat/testing-token.rds |only googledrive-2.0.0/googledrive/DESCRIPTION | 44 - googledrive-2.0.0/googledrive/MD5 | 328 +++++---- googledrive-2.0.0/googledrive/NAMESPACE | 77 ++ googledrive-2.0.0/googledrive/NEWS.md | 130 +++ googledrive-2.0.0/googledrive/R/aaa.R | 45 - googledrive-2.0.0/googledrive/R/camelCase.R | 47 - googledrive-2.0.0/googledrive/R/compat-dplyr.R |only googledrive-2.0.0/googledrive/R/compat-vctrs.R |only googledrive-2.0.0/googledrive/R/dribble.R | 330 ++++++---- googledrive-2.0.0/googledrive/R/drive_about.R | 14 googledrive-2.0.0/googledrive/R/drive_auth.R | 104 ++- googledrive-2.0.0/googledrive/R/drive_browse.R | 28 googledrive-2.0.0/googledrive/R/drive_cp.R | 127 ++- googledrive-2.0.0/googledrive/R/drive_create.R | 73 +- googledrive-2.0.0/googledrive/R/drive_download.R | 96 +- googledrive-2.0.0/googledrive/R/drive_examples.R |only googledrive-2.0.0/googledrive/R/drive_fields.R | 48 - googledrive-2.0.0/googledrive/R/drive_find.R | 97 +- googledrive-2.0.0/googledrive/R/drive_get.R | 154 +++- googledrive-2.0.0/googledrive/R/drive_get_path.R |only googledrive-2.0.0/googledrive/R/drive_id-class.R |only googledrive-2.0.0/googledrive/R/drive_ls.R | 44 - googledrive-2.0.0/googledrive/R/drive_mime_type.R | 22 googledrive-2.0.0/googledrive/R/drive_mkdir.R | 47 - googledrive-2.0.0/googledrive/R/drive_mv.R | 121 +-- googledrive-2.0.0/googledrive/R/drive_publish.R | 72 +- googledrive-2.0.0/googledrive/R/drive_put.R | 78 +- googledrive-2.0.0/googledrive/R/drive_read.R |only googledrive-2.0.0/googledrive/R/drive_rename.R | 26 googledrive-2.0.0/googledrive/R/drive_reveal.R | 240 +++++-- googledrive-2.0.0/googledrive/R/drive_rm.R | 68 +- googledrive-2.0.0/googledrive/R/drive_share.R | 114 +-- googledrive-2.0.0/googledrive/R/drive_trash.R | 80 +- googledrive-2.0.0/googledrive/R/drive_update.R | 95 +- googledrive-2.0.0/googledrive/R/drive_upload.R | 143 ++-- googledrive-2.0.0/googledrive/R/drive_user.R | 38 - googledrive-2.0.0/googledrive/R/googledrive-package.R | 64 + googledrive-2.0.0/googledrive/R/promote.R |only googledrive-2.0.0/googledrive/R/request_generate.R | 17 googledrive-2.0.0/googledrive/R/request_make.R | 46 - googledrive-2.0.0/googledrive/R/roxygen-templates.R |only googledrive-2.0.0/googledrive/R/shared_drive_create.R |only googledrive-2.0.0/googledrive/R/shared_drive_find.R |only googledrive-2.0.0/googledrive/R/shared_drive_get.R |only googledrive-2.0.0/googledrive/R/shared_drive_rm.R |only googledrive-2.0.0/googledrive/R/shared_drive_update.R |only googledrive-2.0.0/googledrive/R/shared_drives.R |only googledrive-2.0.0/googledrive/R/shortcut.R |only googledrive-2.0.0/googledrive/R/sysdata.rda |binary googledrive-2.0.0/googledrive/R/team_drive.R |only googledrive-2.0.0/googledrive/R/utils-io.R |only googledrive-2.0.0/googledrive/R/utils-paths.R | 94 +- googledrive-2.0.0/googledrive/R/utils-ui.R |only googledrive-2.0.0/googledrive/R/utils.R | 88 -- googledrive-2.0.0/googledrive/R/zzz.R |only googledrive-2.0.0/googledrive/README.md | 49 - googledrive-2.0.0/googledrive/build/vignette.rds |binary googledrive-2.0.0/googledrive/inst/WORDLIST | 47 - googledrive-2.0.0/googledrive/inst/doc/googledrive.html | 193 ----- googledrive-2.0.0/googledrive/inst/extdata/data |only googledrive-2.0.0/googledrive/inst/extdata/example_files |only googledrive-2.0.0/googledrive/man/as_dribble.Rd | 27 googledrive-2.0.0/googledrive/man/as_id.Rd | 16 googledrive-2.0.0/googledrive/man/as_shared_drive.Rd |only googledrive-2.0.0/googledrive/man/deprecated-team-drive-functions.Rd |only googledrive-2.0.0/googledrive/man/dribble-checks.Rd | 22 googledrive-2.0.0/googledrive/man/dribble.Rd | 23 googledrive-2.0.0/googledrive/man/drive_about.Rd | 14 googledrive-2.0.0/googledrive/man/drive_auth.Rd | 55 - googledrive-2.0.0/googledrive/man/drive_auth_configure.Rd | 4 googledrive-2.0.0/googledrive/man/drive_browse.Rd | 4 googledrive-2.0.0/googledrive/man/drive_cp.Rd | 125 ++- googledrive-2.0.0/googledrive/man/drive_create.Rd | 70 +- googledrive-2.0.0/googledrive/man/drive_download.Rd | 56 - googledrive-2.0.0/googledrive/man/drive_empty_trash.Rd | 10 googledrive-2.0.0/googledrive/man/drive_examples.Rd |only googledrive-2.0.0/googledrive/man/drive_fields.Rd | 28 googledrive-2.0.0/googledrive/man/drive_find.Rd | 70 +- googledrive-2.0.0/googledrive/man/drive_get.Rd | 150 ++-- googledrive-2.0.0/googledrive/man/drive_link.Rd | 14 googledrive-2.0.0/googledrive/man/drive_ls.Rd | 21 googledrive-2.0.0/googledrive/man/drive_mkdir.Rd | 72 +- googledrive-2.0.0/googledrive/man/drive_mv.Rd | 83 +- googledrive-2.0.0/googledrive/man/drive_publish.Rd | 36 - googledrive-2.0.0/googledrive/man/drive_put.Rd | 67 +- googledrive-2.0.0/googledrive/man/drive_read_string.Rd |only googledrive-2.0.0/googledrive/man/drive_rename.Rd | 28 googledrive-2.0.0/googledrive/man/drive_reveal.Rd | 170 +++-- googledrive-2.0.0/googledrive/man/drive_rm.Rd | 36 - googledrive-2.0.0/googledrive/man/drive_share.Rd | 51 - googledrive-2.0.0/googledrive/man/drive_token.Rd | 6 googledrive-2.0.0/googledrive/man/drive_trash.Rd | 29 googledrive-2.0.0/googledrive/man/drive_update.Rd | 66 +- googledrive-2.0.0/googledrive/man/drive_upload.Rd | 129 ++- googledrive-2.0.0/googledrive/man/drive_user.Rd | 20 googledrive-2.0.0/googledrive/man/expose.Rd | 2 googledrive-2.0.0/googledrive/man/figures/lifecycle-archived.svg |only googledrive-2.0.0/googledrive/man/figures/lifecycle-defunct.svg |only googledrive-2.0.0/googledrive/man/figures/lifecycle-deprecated.svg |only googledrive-2.0.0/googledrive/man/figures/lifecycle-experimental.svg |only googledrive-2.0.0/googledrive/man/figures/lifecycle-maturing.svg |only googledrive-2.0.0/googledrive/man/figures/lifecycle-questioning.svg |only googledrive-2.0.0/googledrive/man/figures/lifecycle-stable.svg |only googledrive-2.0.0/googledrive/man/figures/lifecycle-superseded.svg |only googledrive-2.0.0/googledrive/man/googledrive-configuration.Rd |only googledrive-2.0.0/googledrive/man/googledrive-deprecated.Rd | 5 googledrive-2.0.0/googledrive/man/googledrive-package.Rd | 2 googledrive-2.0.0/googledrive/man/request_generate.Rd | 10 googledrive-2.0.0/googledrive/man/request_make.Rd | 36 - 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Title: Estimation Methods for Causal Inference Based on Inverse
Probability Weighting
Description: Various estimators of causal effects based on inverse probability weighting, doubly robust estimation, and double machine learning. Specifically, the package includes methods for estimating average treatment effects, direct and indirect effects in causal mediation analysis, and dynamic treatment effects. The models refer to studies of Froelich (2007) <doi:10.1016/j.jeconom.2006.06.004>, Huber (2012) <doi:10.3102/1076998611411917>, Huber (2014) <doi:10.1080/07474938.2013.806197>, Huber (2014) <doi:10.1002/jae.2341>, Froelich and Huber (2017) <doi:10.1111/rssb.12232>, Hsu, Huber, Lee, and Lettry (2020) <doi:10.1002/jae.2765>, and others.
Author: Hugo Bodory [aut, cre] (<https://orcid.org/0000-0002-3645-1204>),
Martin Huber [aut] (<https://orcid.org/0000-0002-8590-9402>)
Maintainer: Hugo Bodory <hugo.bodory@unisg.ch>
Diff between causalweight versions 1.0.1 dated 2021-04-16 and 1.0.2 dated 2021-07-08
DESCRIPTION | 6 - MD5 | 18 ++-- R/RDDcovar.R | 2 R/dyntreatDML.R | 200 +++++++++++++++++++++++----------------------- R/treatDML.R | 142 ++++++++++++++++---------------- R/treatselDML.R | 174 ++++++++++++++++++++-------------------- R/ubduration.R | 62 +++++++------- inst/doc/bodory-huber.pdf |binary man/RDDcovar.Rd | 2 man/ubduration.Rd | 2 10 files changed, 304 insertions(+), 304 deletions(-)
More information about MedianaDesigner at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-24 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-07 0.1.8
Title: Linking R with the Open-Source 'SAGA-GIS' Software
Description: Provides an R scripting interface to the open-source 'SAGA-GIS' (System for Automated Geoscientific Analyses Geographical Information System) software. 'Rsagacmd' dynamically generates R functions for every 'SAGA-GIS' geoprocessing tool based on the user's currently installed 'SAGA-GIS' version. These functions are contained within an S3 object and are accessed as a named list of libraries and tools. This structure facilitates an easier scripting experience by organizing the large number of 'SAGA-GIS' geoprocessing tools (>700) by their respective library. Interactive scripting can fully take advantage of code autocompletion tools (e.g. in 'Rstudio'), allowing for each tools syntax to be quickly recognized. Furthermore, the most common types of spatial data (via the 'raster', 'terra', 'sp', and 'sf' packages) along with non-spatial data are automatically passed from R to the 'SAGA-GIS' command line tool for geoprocessing operations, and the results are loaded as the appropriate R object. Outputs from individual 'SAGA-GIS' tools can also be chained using pipes from the 'magrittr' and 'dplyr' packages to combine complex geoprocessing operations together in a single statement. 'SAGA-GIS' is available under a GPLv2 / LGPLv2 licence from <https://sourceforge.net/projects/saga-gis/> including Windows x86/x84 binaries. SAGA-GIS is also included in Debian/Ubuntu default software repositories and is available for macOS using homebrew (<https://brew.sh/>) from the osgeo/osgeo4mac (<https://github.com/OSGeo/homebrew-osgeo4mac>) formula tap. Rsagacmd has currently been tested on 'SAGA-GIS' versions from 2.3.1 to 7.9.0 on Windows, Linux and macOS.
Author: Steven Pawley [aut, cre]
Maintainer: Steven Pawley <dr.stevenpawley@gmail.com>
Diff between Rsagacmd versions 0.1.0 dated 2021-01-11 and 0.1.1 dated 2021-07-08
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