Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory models can be estimated with quadrature (EM)
or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modeling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete latent
variable models, including mixture and zero-inflated response models,
are supported.
Author: Phil Chalmers [aut, cre] ,
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.37.1 dated 2022-08-10 and 1.38.1 dated 2023-02-27
DESCRIPTION | 12 +- MD5 | 96 +++++++++--------- NEWS.md | 38 +++++++ R/02-item_methods.R | 2 R/03-estimation.R | 13 ++ R/DIF.R | 68 +++++++++---- R/DRF.R | 12 +- R/DTF.R | 2 R/PLCI.mirt.R | 2 R/SIBTEST.R | 8 - R/SingleGroup-methods.R | 147 +++++++++++++++++----------- R/boot.LR.R | 6 - R/boot.mirt.R | 12 +- R/empirical_plot.R | 2 R/extract.mirt.R | 6 + R/fscores.R | 35 ++++-- R/fscores.internal.R | 37 +++++-- R/itemfit.R | 53 +++++----- R/itemplot.R | 5 R/mdirt.R | 2 R/mirt.R | 46 ++++---- R/mirtCluster.R | 25 ++-- R/mixedmirt.R | 6 - R/multipleGroup.R | 2 R/personfit.R | 2 R/utils.R | 29 ++++- inst/CITATION | 6 - inst/doc/mirt-vignettes.html | 204 +++++++++++++-------------------------- man/DIF.Rd | 11 +- man/DRF.Rd | 2 man/DTF.Rd | 2 man/PLCI.mirt.Rd | 2 man/boot.LR.Rd | 2 man/coef-method.Rd | 5 man/extract.mirt.Rd | 2 man/fscores.Rd | 35 ++++-- man/itemfit.Rd | 4 man/itemplot.Rd | 5 man/mdirt.Rd | 2 man/mirt.Rd | 29 +---- man/mirtCluster.Rd | 25 ++-- man/mixedmirt.Rd | 4 man/multipleGroup.Rd | 2 man/plot-method.Rd | 8 + man/residuals-method.Rd | 2 man/traditional2mirt.Rd | 2 tests/tests/test-09-mirt.model.R | 4 tests/tests/test-16-DCIRT.R | 14 +- tests/tests/test-17-DIF_DRF.R | 59 +++++++++++ 49 files changed, 662 insertions(+), 437 deletions(-)
Title: Meta-Analysis of Medians
Description: Implements several methods to meta-analyze studies that report the
sample median of the outcome. When the primary studies are one-group
studies, the methods of McGrath et al. (2019) <doi:10.1002/sim.8013> and
Ozturk and Balakrishnan (2020) <doi:10.1002/sim.8738> can be applied to
estimate the pooled median. In the two-group context, the
methods of McGrath et al. (2020a) <doi:10.1002/bimj.201900036> can be
applied to estimate the pooled difference of medians across groups.
Additionally, a number of methods (e.g., McGrath et al. (2020b)
<doi:10.1177/0962280219889080>, Cai et al. (2021)
<doi:10.1177/09622802211047348>, and McGrath et al. (2023)
<doi:10.1177/09622802221139233>) are implemented to estimate
study-specific (difference of) means and their standard errors in order to
estimate the pooled (difference of) means.
Author: Sean McGrath [aut, cre] ,
XiaoFei Zhao [aut],
Stephan Katzenschlager [aut],
Omer Ozturk [aut],
Russell Steele [aut],
Andrea Benedetti [aut]
Maintainer: Sean McGrath <sean.mcgrath@mail.mcgill.ca>
Diff between metamedian versions 0.1.6 dated 2022-06-18 and 1.0.0 dated 2023-02-27
DESCRIPTION | 35 ++++++++++++++++++++++++++--------- MD5 | 38 ++++++++++++++++++++++++++++++++------ NAMESPACE | 5 +++++ NEWS.md | 18 ++++++++++++++++++ R/cd.R |only R/data.R |only R/describe_studies.R |only R/metamean.R |only R/metamedian.R |only R/qe.R | 15 ++++++++++++--- README.md | 35 ++++++++++++++++++++++++++++------- data |only man/cd.Rd |only man/dat.age.Rd |only man/dat.age_raw.Rd |only man/dat.asat.Rd |only man/dat.asat_raw.Rd |only man/dat.ck.Rd |only man/dat.ck_raw.Rd |only man/describe_studies.Rd |only man/metamean.Rd |only man/metamedian.Rd |only man/print.describe_studies.Rd |only man/qe.Rd | 3 +++ tests |only 25 files changed, 124 insertions(+), 25 deletions(-)
Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative
maps. The package is designed to be used with the 'mvp' class of
packages that use the STL map class: its purpose is to trap
plausible idiom that is ill-defined (implementation-specific) and
return an informative error, rather than returning a possibly
incorrect result. To cite the package in publications please use
Hankin (2022) <doi:10.48550/ARXIV.2210.03856>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between disordR versions 0.0-9-4 dated 2022-12-10 and 0.9 dated 2023-02-27
DESCRIPTION | 29 +--- MD5 | 24 +-- R/disordR.R | 2 README.md | 2 inst/CITATION | 11 - inst/doc/disordR.Rmd | 38 +++--- inst/doc/disordR.html | 277 ++++++++------------------------------------ man/disord.Rd | 47 ++++--- man/extract.Rd | 21 +++ man/misc.Rd | 22 +++ tests/testthat/test_aaa.R | 13 ++ vignettes/disordR.Rmd | 38 +++--- vignettes/disordR_arxiv.bib | 8 + 13 files changed, 210 insertions(+), 322 deletions(-)
Title: Trajectories and Phylogenies Simulator
Description: Generates stochastic time series and genealogies associated with a population dynamics model. Times series are simulated using the Gillespie exact and approximate algorithms and a new algorithm we introduce that uses both approaches to optimize the time execution of the simulations. Genealogies are simulated from a trajectory using a backwards-in-time based approach. Methods are described in Danesh G et al (2022) <doi:10.1111/2041-210X.14038>.
Author: Gonche Danesh [aut, cre, cph],
Emma Saulnier [aut, cph],
Olivier Gascuel [aut, cph],
Marc Choisy [aut, cph, ths],
Samuel Alizon [aut, cph, ths]
Maintainer: Gonche Danesh <gonche.danesh@gmail.com>
Diff between TiPS versions 1.2.1 dated 2022-08-26 and 1.2.2 dated 2023-02-27
DESCRIPTION | 13 +-- MD5 | 170 ++++++++++++++++++++++++++++++++++++++++-- README.md |only build/vignette.rds |binary inst/CITATION | 14 +-- inst/doc/TiPS.html | 206 +++++++++++++++++++++++---------------------------- inst/include/Node.h | 1 src/Makevars | 1 src/Node.cpp | 46 ----------- src/Phyloepid.cpp | 4 vignettes/TiPS_cache |only vignettes/TiPS_files |only 12 files changed, 273 insertions(+), 182 deletions(-)
Title: Iota Inter Coder Reliability for Content Analysis
Description: Routines and tools for assessing the quality of content
analysis on the basis of the Iota Reliability Concept. The concept is
inspired by item response theory and can be applied to any kind of
content analysis which uses a standardized coding scheme and discrete
categories. It is also applicable for content analysis conducted by
artificial intelligence. The package provides reliability measures
for a complete scale as well as for every single category. Analysis of
subgroup-invariance and error corrections are implemented. This
information can support the development process of a coding scheme and
allows a detailed inspection of the quality of the generated data.
Equations and formulas working in this package are part of Berding et
al. (2022)<doi:10.3389/feduc.2022.818365> and Berding and Pargmann
(2022) <doi:10.30819/5581>.
Author: Berding Florian [aut, cre] ,
Pargmann Julia [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between iotarelr versions 0.1.3 dated 2023-01-05 and 0.1.4 dated 2023-02-27
DESCRIPTION | 6 - MD5 | 24 +++--- NEWS.md | 7 + R/additional_functions.R | 36 ++++++---- inst/CITATION | 8 +- inst/doc/Old_01_How_to_use_Iota1.html | 4 - inst/doc/V_02_Estimating_Consequences_for_Subsequent_Analyses.html | 4 - inst/doc/V_03_Different_Guidance_Functioning.html | 32 ++++---- inst/doc/V_04_Error_Correction.html | 16 ++-- inst/doc/V_05_Test_New_Raters.html | 4 - inst/doc/iotarelr.html | 18 ++--- man/check_new_rater.Rd | 14 +++ tests/testthat/test_basic_funct.R | 9 +- 13 files changed, 106 insertions(+), 76 deletions(-)
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements the method
described in Aas, Jullum and Løland (2019) <arXiv:1903.10464>, which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
Author: Nikolai Sellereite [aut] ,
Martin Jullum [cre, aut] ,
Annabelle Redelmeier [aut],
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
Diff between shapr versions 0.2.0 dated 2021-01-28 and 0.2.1 dated 2023-02-27
DESCRIPTION | 9 MD5 | 134 - NAMESPACE | 160 - NEWS.md | 6 R/explanation.R | 916 +++++----- R/features.R | 656 +++---- R/models.R | 944 +++++----- R/observations.R | 968 +++++------ R/plot.R | 240 +- R/predictions.R | 164 - R/preprocess_data.R | 726 ++++---- R/sampling.R | 770 ++++---- R/shapley.R | 454 ++--- R/shapr-package.R | 50 R/transformation.R | 114 - R/utils.R | 16 R/zzz.R | 20 README.md | 21 build/vignette.rds |binary inst/REFERENCES.bib | 248 +- inst/doc/understanding_shapr.Rmd | 1404 ++++++++-------- inst/doc/understanding_shapr.html | 468 ++++- man/apply_dummies.Rd | 56 man/check_features.Rd | 84 man/create_ctree.Rd | 132 - man/explain.Rd | 468 ++--- man/feature_combinations.Rd | 108 - man/figures/README-basic_example-1.png |binary man/gaussian_transform.Rd | 42 man/gaussian_transform_separate.Rd | 48 man/get_data_specs.Rd | 86 man/get_list_approaches.Rd | 52 man/get_model_specs.Rd | 122 - man/get_supported_models.Rd | 24 man/inv_gaussian_transform.Rd | 48 man/make_dummies.Rd | 100 - man/model_checker.Rd | 110 - man/observation_impute.Rd | 82 man/plot.shapr.Rd | 154 - man/predict_model.Rd | 164 - man/prediction.Rd | 92 - man/prepare_data.Rd | 134 - man/preprocess_data.Rd | 88 - man/sample_combinations.Rd | 66 man/sample_copula.Rd | 78 man/sample_ctree.Rd | 128 - man/sample_gaussian.Rd | 54 man/shapley_weights.Rd | 60 man/shapr.Rd | 164 - man/update_data.Rd | 82 man/weight_matrix.Rd | 50 man/weight_matrix_cpp.Rd | 60 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 5 tests/testthat/manual_test_scripts/test_custom_models.R | 234 +- tests/testthat/test-a-shapley.R | 2 tests/testthat/test-explanation.R | 2 tests/testthat/test-features.R | 744 ++++---- tests/testthat/test-models.R | 984 +++++------ tests/testthat/test-observations.R | 108 - tests/testthat/test-plot.R | 96 - tests/testthat/test-predictions.R | 98 - tests/testthat/test-sampling.R | 580 +++--- tests/testthat/test-src_impute_data.R | 154 - tests/testthat/test-src_weighted_matrix.R | 158 - tests/testthat/test-transformation.R | 104 - vignettes/understanding_shapr.Rmd | 1404 ++++++++-------- 68 files changed, 8214 insertions(+), 7885 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] ,
George Athanasopoulos [aut] ,
Christoph Bergmeir [aut] ,
Gabriel Caceres [aut] ,
Leanne Chhay [aut],
Kirill Kuroptev [aut],
Mitchell O'Hara-Wild [aut] ,
Fotios Petropoulos [aut] ,
Slava Razbash [aut],
Earo Wang [aut] ,
F [...truncated...]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.20 dated 2023-01-06 and 8.21 dated 2023-02-27
DESCRIPTION | 6 MD5 | 33 ++--- NEWS.md | 266 +++++++++++++++++++++--------------------- R/checkresiduals.R | 85 ++++++------- R/ggplot.R | 139 +++++++++++---------- R/nnetar.R | 28 +++- README.md | 1 inst/CITATION | 2 inst/doc/JSS2008.pdf |binary man/checkresiduals.Rd | 11 - man/geom_forecast.Rd | 8 - man/nnetar.Rd | 4 src/Makevars | 8 - src/Makevars.win | 8 - tests/testthat/Rplots.pdf |only tests/testthat/test-ets.R | 8 - tests/testthat/test-modelAR.R | 4 tests/testthat/test-nnetar.R | 25 +++ 18 files changed, 332 insertions(+), 304 deletions(-)
Title: Forensic Bayesian Networks
Description: Open-source package for computing likelihood ratios in kinship testing and human identification cases (Chernomoretz et al. (2021) <doi:10.1016/j.fsir.2020.100132>). It has the core function of the software GENis, developed by Fundación Sadosky. It relies on a Bayesian Networks framework and is particularly well suited to efficiently perform large-size queries against databases of missing individuals (Darwiche (2009) <doi:10.1017/CBO9780511811357>).
Author: Franco Marsico [aut, cre],
Ariel Chernomoretz [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between fbnet versions 1.0.1 dated 2022-10-26 and 1.0.2 dated 2023-02-27
fbnet-1.0.1/fbnet/R/FamiliasLocus.R |only fbnet-1.0.1/fbnet/R/FamiliasPedigree.R |only fbnet-1.0.1/fbnet/R/allGenotypes.R |only fbnet-1.0.1/fbnet/R/as.matrix.linkdat.R |only fbnet-1.0.1/fbnet/R/convertPedformat.R |only fbnet-1.0.1/fbnet/R/familias2linkdat.R |only fbnet-1.0.1/fbnet/R/initBN.R |only fbnet-1.0.1/fbnet/R/initBN.fromPed.R |only fbnet-1.0.1/fbnet/R/initBN.fromVars.R |only fbnet-1.0.1/fbnet/R/is.linkdat.R |only fbnet-1.0.1/fbnet/R/likelihood.R |only fbnet-1.0.1/fbnet/R/linkdat.R |only fbnet-1.0.1/fbnet/R/loops.R |only fbnet-1.0.1/fbnet/R/markerSimfb.R |only fbnet-1.0.1/fbnet/R/markerfb.R |only fbnet-1.0.1/fbnet/R/mendelianCheckfb.R |only fbnet-1.0.1/fbnet/R/pedModify.R |only fbnet-1.0.1/fbnet/R/pedParts.R |only fbnet-1.0.1/fbnet/R/preparePed.R |only fbnet-1.0.1/fbnet/R/setModel.R |only fbnet-1.0.1/fbnet/R/utils.R |only fbnet-1.0.1/fbnet/man/Familias2linkdat.Rd |only fbnet-1.0.1/fbnet/man/FamiliasLocus.Rd |only fbnet-1.0.1/fbnet/man/FamiliasPedigree.Rd |only fbnet-1.0.1/fbnet/man/allGenotypes.Rd |only fbnet-1.0.1/fbnet/man/as.matrix.linkdat.Rd |only fbnet-1.0.1/fbnet/man/convertPedformat.Rd |only fbnet-1.0.1/fbnet/man/initBN.Rd |only fbnet-1.0.1/fbnet/man/initBN.fromPed.Rd |only fbnet-1.0.1/fbnet/man/initBN.fromVars.Rd |only fbnet-1.0.1/fbnet/man/is.linkdat.Rd |only fbnet-1.0.1/fbnet/man/likelihood.Rd |only fbnet-1.0.1/fbnet/man/linkdat.Rd |only fbnet-1.0.1/fbnet/man/markerSimfb.Rd |only fbnet-1.0.1/fbnet/man/markers.Rd |only fbnet-1.0.1/fbnet/man/mendelianCheckfb.Rd |only fbnet-1.0.1/fbnet/man/pedModify.Rd |only fbnet-1.0.1/fbnet/man/pedParts.Rd |only fbnet-1.0.1/fbnet/man/pedigreeLoops.Rd |only fbnet-1.0.1/fbnet/man/preparePed.Rd |only fbnet-1.0.1/fbnet/man/setAvailable.Rd |only fbnet-1.0.1/fbnet/man/setModel.Rd |only fbnet-1.0.1/fbnet/man/simpleSimfb.Rd |only fbnet-1.0.2/fbnet/DESCRIPTION | 23 ++++---- fbnet-1.0.2/fbnet/MD5 | 77 ++++++++--------------------- fbnet-1.0.2/fbnet/NAMESPACE | 64 ------------------------ fbnet-1.0.2/fbnet/R/bnet.R |only fbnet-1.0.2/fbnet/R/buildBN.R | 1 fbnet-1.0.2/fbnet/R/buildCPTs.R | 1 fbnet-1.0.2/fbnet/R/getLocusCPT.R | 1 fbnet-1.0.2/fbnet/R/pbn.R |only fbnet-1.0.2/fbnet/R/velim.bn.R | 1 fbnet-1.0.2/fbnet/README.md | 22 +++----- fbnet-1.0.2/fbnet/build/partial.rdb |binary fbnet-1.0.2/fbnet/data/bnet.rda |only fbnet-1.0.2/fbnet/data/pbn.rda |only fbnet-1.0.2/fbnet/man/bnet.Rd |only fbnet-1.0.2/fbnet/man/buildBN.Rd | 1 fbnet-1.0.2/fbnet/man/buildCPTs.Rd | 1 fbnet-1.0.2/fbnet/man/figures |only fbnet-1.0.2/fbnet/man/getLocusCPT.Rd | 1 fbnet-1.0.2/fbnet/man/pbn.Rd |only fbnet-1.0.2/fbnet/man/velim.bn.Rd | 1 63 files changed, 42 insertions(+), 152 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut],
Romain Francois [aut, cph],
Kevin Ushey [aut, cre],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Posit, PBC [cph],
Intel [aut, cph] ,
Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 5.1.6 dated 2023-01-09 and 5.1.7 dated 2023-02-27
RcppParallel-5.1.6/RcppParallel/inst/include/index.html |only RcppParallel-5.1.6/RcppParallel/inst/include/serial |only RcppParallel-5.1.6/RcppParallel/inst/include/tbb |only RcppParallel-5.1.6/RcppParallel/src/install.libs.R |only RcppParallel-5.1.6/RcppParallel/tools/tbb |only RcppParallel-5.1.7/RcppParallel/DESCRIPTION | 6 RcppParallel-5.1.7/RcppParallel/MD5 | 163 +--------- RcppParallel-5.1.7/RcppParallel/NEWS.md | 4 RcppParallel-5.1.7/RcppParallel/R/aaa.R |only RcppParallel-5.1.7/RcppParallel/R/skeleton.R | 2 RcppParallel-5.1.7/RcppParallel/R/tbb-autodetected.R.in |only RcppParallel-5.1.7/RcppParallel/R/tbb.R | 12 RcppParallel-5.1.7/RcppParallel/inst/include/RcppParallel/RMatrix.h | 37 +- RcppParallel-5.1.7/RcppParallel/inst/tests/runit.distance.R | 10 RcppParallel-5.1.7/RcppParallel/inst/tests/runit.innerproduct.R | 4 RcppParallel-5.1.7/RcppParallel/inst/tests/runit.sum.R | 3 RcppParallel-5.1.7/RcppParallel/inst/tests/runit.transform.R | 3 RcppParallel-5.1.7/RcppParallel/src/Makevars.in | 23 - RcppParallel-5.1.7/RcppParallel/src/install.libs.R.in |only RcppParallel-5.1.7/RcppParallel/src/tbb/include/tbb/compat/iterator.h |only RcppParallel-5.1.7/RcppParallel/src/tbb/include/tbb/concurrent_hash_map.h | 3 RcppParallel-5.1.7/RcppParallel/src/tbb/include/tbb/enumerable_thread_specific.h | 6 RcppParallel-5.1.7/RcppParallel/src/tbb/include/tbb/internal/_concurrent_queue_impl.h | 6 RcppParallel-5.1.7/RcppParallel/src/tbb/include/tbb/internal/_concurrent_unordered_impl.h | 4 RcppParallel-5.1.7/RcppParallel/src/tbb/src/tbbmalloc/proxy.cpp | 26 + RcppParallel-5.1.7/RcppParallel/src/tbb/src/test/test_container_move_support.h | 6 RcppParallel-5.1.7/RcppParallel/tools/config/cleanup.R | 5 RcppParallel-5.1.7/RcppParallel/tools/config/configure.R | 78 ++++ 28 files changed, 195 insertions(+), 206 deletions(-)
Title: Automates the Creation of New Statistical Analysis Projects
Description: Provides functions to
automatically build a directory structure for a new R
project. Using this structure, 'ProjectTemplate'
automates data loading, preprocessing, library
importing and unit testing.
Author: Aleksandar Blagotic [ctb],
Diego Valle-Jones [ctb],
Jeffrey Breen [ctb],
Joakim Lundborg [ctb],
John Myles White [aut, cph],
Josh Bode [ctb],
Kenton White [ctb, cre],
Kirill Mueller [ctb],
Matteo Redaelli [ctb],
Noah Lorang [ctb],
Patrick Schalk [ctb [...truncated...]
Maintainer: Kenton White <jkentonwhite@gmail.com>
Diff between ProjectTemplate versions 0.10.2 dated 2021-07-31 and 0.10.3 dated 2023-02-27
DESCRIPTION | 15 ++++++++------- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + NEWS.md | 8 ++++++++ R/config.R | 2 +- R/create.project.rstudio.R |only R/sql.reader.R | 2 +- R/stub.tests.R | 2 +- build/partial.rdb |binary inst/defaults/templates/full/config/global.dcf | 2 +- inst/defaults/templates/minimal/config/global.dcf | 2 +- inst/rstudio/templates |only tests/testthat/test-qs.R | 15 +++++---------- 13 files changed, 39 insertions(+), 32 deletions(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Precision Based Sample Size Calculation
Description: Bland (2009) <doi:10.1136/bmj.b3985> recommended to
base study sizes on the width of the confidence interval rather the power of
a statistical test. The goal of 'presize' is to provide functions for such
precision based sample size calculations. For a given sample size, the
functions will return the precision (width of the confidence interval), and
vice versa.
Author: Armando Lenz [aut],
Alan G. Haynes [cre, aut],
Andreas Limacher [aut],
Odile Stalder [ctb],
Marie Roumet [ctb]
Maintainer: Alan G. Haynes <alan.haynes@ctu.unibe.ch>
Diff between presize versions 0.3.3 dated 2022-08-29 and 0.3.7 dated 2023-02-27
DESCRIPTION | 17 MD5 | 40 NAMESPACE | 1 NEWS.md | 145 +- R/correlation_measures.R | 95 + R/descriptive_stats.R | 18 R/diagnostic.R | 6 R/differences.R | 5 R/helper_functions.R | 6 inst/doc/presize.html | 882 ++++++-------- inst/shinyApp/app.R | 22 inst/shinyApp/rsconnect/shinyapps.io/ctu-bern/presize.dcf | 6 inst/shinyApp/ui/04_meandiff.R | 2 inst/shinyApp/ui/19_cronbachsalpha.R |only inst/shinyApp/ui/99_helpers.R | 4 man/prec_cronb.Rd |only man/prec_icc.Rd | 3 man/prec_mean.Rd | 3 man/prec_meandiff.Rd | 3 man/presize-package.Rd | 1 tests/testthat/test-correlation_measures.R | 13 tests/testthat/test-differences.R | 4 22 files changed, 689 insertions(+), 587 deletions(-)
Title: 1d Water Level Interpolation along the Rivers Elbe and Rhine
Description: An S4 class and several functions which utilize internally stored
datasets and gauging data enable 1d water level interpolation. The S4 class
(WaterLevelDataFrame) structures the computation and visualisation
of 1d water level information along the German federal waterways Elbe and
Rhine. 'hyd1d' delivers 1d water level data - extracted from the 'FLYS'
database - and validated gauging data - extracted from the hydrological
database 'HyDaBa' - package-internally. For computations near real time
gauging data are queried externally from the 'PEGELONLINE REST API'
<https://pegelonline.wsv.de/webservice/dokuRestapi>.
Author: Arnd Weber [aut, cre] ,
Marcus Hatz [aut],
Wolfgang Stuermer [ctb],
Wilfried Wiechmann [ctb]
Maintainer: Arnd Weber <arnd.weber@bafg.de>
Diff between hyd1d versions 0.4.2 dated 2023-02-22 and 0.4.3 dated 2023-02-27
DESCRIPTION | 18 -- MD5 | 18 +- NEWS.md | 7 R/data.R | 380 +++++++++++++++++++++++----------------------- R/getPegelonlineW.R | 74 +++++--- R/waterLevelFlys3.R | 92 +++++------ build/partial.rdb |binary inst/doc/hyd1d.html | 34 ++-- inst/doc/vignette_DE.html | 32 +-- man/df.flys.Rd | 2 10 files changed, 339 insertions(+), 318 deletions(-)
Title: Parametric G-Formula
Description: Implements the parametric g-formula algorithm of Robins (1986)
<doi:10.1016/0270-0255(86)90088-6>. The g-formula can be used to estimate
the causal effects of hypothetical time-varying treatment interventions on
the mean or risk of an outcome from longitudinal data with time-varying
confounding. This package allows: 1) binary or continuous/multi-level
time-varying treatments; 2) different types of outcomes (survival or
continuous/binary end of follow-up); 3) data with competing events or
truncation by death and loss to follow-up and other types of censoring
events; 4) different options for handling competing events in the case of
survival outcomes; 5) a random measurement/visit process; 6) joint
interventions on multiple treatments; and 7) general incorporation of a
priori knowledge of the data structure.
Author: Victoria Lin [aut] ,
Sean McGrath [aut, cre] ,
Zilu Zhang [aut],
Roger W. Logan [aut],
Lucia C. Petito [aut],
Jing Li [aut],
Jessica G. Young [aut] ,
Miguel A. Hernan [aut] ,
2019 The President and Fellows of Harvard College [cph]
Maintainer: Sean McGrath <sean_mcgrath@g.harvard.edu>
Diff between gfoRmula versions 1.0.1 dated 2023-01-11 and 1.0.2 dated 2023-02-27
DESCRIPTION | 9 +++-- MD5 | 20 ++++++------ NEWS.md | 13 +++++++ R/bootstrap.R | 7 ---- R/comparisons.R | 79 ++++++++++-------------------------------------- R/gformula.R | 42 +++++++++---------------- R/helper.R | 2 - R/simulate.R | 24 +------------- man/bootstrap_helper.Rd | 8 ---- man/rmse_calculate.Rd | 41 ------------------------ man/simulate.Rd | 8 ---- 11 files changed, 67 insertions(+), 186 deletions(-)
Title: Flexible Co-Data Learning for High-Dimensional Prediction
Description: Fit linear, logistic and Cox survival regression models penalised with adaptive multi-group ridge penalties.
The multi-group penalties correspond to groups of covariates defined by (multiple) co-data sources.
Group hyperparameters are estimated with an empirical Bayes method of moments, penalised with an extra level of hyper shrinkage.
Various types of hyper shrinkage may be used for various co-data.
Co-data may be continuous or categorical.
The method accommodates inclusion of unpenalised covariates, posterior selection of covariates and multiple data types.
The model fit is used to predict for new samples.
The name 'ecpc' stands for Empirical Bayes, Co-data learnt, Prediction and Covariate selection.
See Van Nee et al. (2020) <arXiv:2005.04010>.
Author: Mirrelijn M. van Nee [aut, cre],
Lodewyk F.A. Wessels [aut],
Mark A. van de Wiel [aut]
Maintainer: Mirrelijn M. van Nee <m.vannee@amsterdamumc.nl>
Diff between ecpc versions 3.1 dated 2022-05-13 and 3.1.1 dated 2023-02-27
DESCRIPTION | 12 +-- MD5 | 6 - R/ecpc.R | 210 +++++++++++++++++++----------------------------------- build/partial.rdb |binary 4 files changed, 85 insertions(+), 143 deletions(-)
Title: Visualisation, Exploration, and Web Communication of
Archaeological Excavation Data
Description: An R 'Shiny' application for the visualisation, interactive exploration, and web communication of archaeological excavation data. It includes interactive 3D and 2D visualisations, generation of cross sections and maps of the remains, basic spatial analysis methods (convex hull, regression surfaces, 2D kernel density estimation), and excavation timeline visualisation. 'archeoViz' can be used locally or deployed on a server, either with interactive input of data or with a static data set.
Author: Sebastien Plutniak [aut, cre] ,
Renata Araujo [ctb] ,
Sara Giardino [ctb]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeoViz versions 0.2.2 dated 2023-01-10 and 1.0.0 dated 2023-02-27
DESCRIPTION | 23 MD5 | 65 +- NAMESPACE | 6 NEWS.md | 30 + R/app_server.R | 673 +++++++++++++++++++------ R/app_ui.R | 59 +- R/archeoViz.R | 73 ++ R/demo_objects_data.R | 8 R/do_by_layer_table.R | 7 R/do_by_variable_table.R | 9 R/do_coords_minmax.R | 19 R/do_objects_dataset.R | 31 - R/do_refits_preprocessing.R | 36 + R/do_section_plot.R | 47 + R/do_timelinedata.R | 9 R/get_cxhull_model.R | 8 R/load_interface_terms.R | 675 +++++++++++++++++++++----- TODO |only inst/CITATION | 14 inst/doc/archeoViz-vignette-fr.R | 37 + inst/doc/archeoViz-vignette-fr.Rmd | 164 +++++- inst/doc/archeoViz-vignette-fr.html | 192 +++++-- inst/doc/archeoViz-vignette.R | 35 + inst/doc/archeoViz-vignette.Rmd | 161 +++++- inst/doc/archeoViz-vignette.html | 198 ++++++- man/archeoViz.Rd | 46 + tests/testthat/test.do_by_layer_table.R | 11 tests/testthat/test.do_by_variable_table.R | 8 tests/testthat/test.do_coords_minmax.R | 2 tests/testthat/test.do_objects_dataset.R | 12 tests/testthat/test.do_refits_preprocessing.R | 28 - tests/testthat/test.do_section_plot.R | 2 vignettes/archeoViz-vignette-fr.Rmd | 164 +++++- vignettes/archeoViz-vignette.Rmd | 161 +++++- 34 files changed, 2438 insertions(+), 575 deletions(-)
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Kristian Hoden [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 3.3.0 dated 2023-01-24 and 3.3.1 dated 2023-02-27
OlinkAnalyze-3.3.0/OlinkAnalyze/tests/testthat/_snaps/pca_plot/pca-plot-minimal-no-index-removing-index-dependence.svg |only OlinkAnalyze-3.3.0/OlinkAnalyze/tests/testthat/_snaps/pca_plot/pca-plot-minimal-no-index.svg |only OlinkAnalyze-3.3.0/OlinkAnalyze/tests/testthat/_snaps/pca_plot/pca-plot-removing-index-dependence.svg |only OlinkAnalyze-3.3.1/OlinkAnalyze/DESCRIPTION | 8 OlinkAnalyze-3.3.1/OlinkAnalyze/MD5 | 28 +- OlinkAnalyze-3.3.1/OlinkAnalyze/NEWS.md | 8 OlinkAnalyze-3.3.1/OlinkAnalyze/R/Read_NPX_data.R | 115 +++++----- OlinkAnalyze-3.3.1/OlinkAnalyze/R/globals.R | 2 OlinkAnalyze-3.3.1/OlinkAnalyze/R/npxProcessing.R | 12 - OlinkAnalyze-3.3.1/OlinkAnalyze/R/olink_Pathway_Enrichment.R | 8 OlinkAnalyze-3.3.1/OlinkAnalyze/inst/doc/Vignett.html | 14 - OlinkAnalyze-3.3.1/OlinkAnalyze/inst/extdata/npx_data_ext_v1.zip |only OlinkAnalyze-3.3.1/OlinkAnalyze/inst/extdata/npx_data_ext_v2.zip |only OlinkAnalyze-3.3.1/OlinkAnalyze/inst/extdata/npx_data_v3.zip |only OlinkAnalyze-3.3.1/OlinkAnalyze/tests/testthat/_snaps/pca_plot/pca-plot-with-loadings.svg | 28 +- OlinkAnalyze-3.3.1/OlinkAnalyze/tests/testthat/test-Read_NPX_data.R | 43 +++ OlinkAnalyze-3.3.1/OlinkAnalyze/tests/testthat/test-npxProcessing.R | 15 + OlinkAnalyze-3.3.1/OlinkAnalyze/tests/testthat/test-olink_Pathway_Enrichment.R | 16 + 18 files changed, 196 insertions(+), 101 deletions(-)
Title: Penn World Table (Version 10.x)
Description: The Penn World Table 10.x (<https://www.rug.nl/ggdc/productivity/pwt/>) provides information
on relative levels of income, output, input, and productivity
for 183 countries between 1950 and 2019.
Author: Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between pwt10 versions 10.0-0 dated 2021-01-21 and 10.01-0 dated 2023-02-27
pwt10-10.0-0/pwt10/NEWS |only pwt10-10.01-0/pwt10/DESCRIPTION | 10 +++++----- pwt10-10.01-0/pwt10/MD5 | 12 +++++++----- pwt10-10.01-0/pwt10/NEWS.md |only pwt10-10.01-0/pwt10/build/partial.rdb |binary pwt10-10.01-0/pwt10/data/pwt10.01.rda |only pwt10-10.01-0/pwt10/inst/CITATION | 3 +-- pwt10-10.01-0/pwt10/man/pwt10.0.Rd | 10 +++++----- pwt10-10.01-0/pwt10/man/pwt10.01.Rd |only 9 files changed, 18 insertions(+), 17 deletions(-)
Title: Supplementary Tools for R Packages Developers
Description: Supplementary utils for CRAN maintainers and R packages developers.
Validating the library, packages and lock files.
Exploring a complexity of a specific package like evaluating its size in bytes with all dependencies.
The shiny app complexity could be explored too.
Assessing the life duration of a specific package version.
Checking a CRAN package check page status for any errors and warnings.
Retrieving a DESCRIPTION or NAMESPACE file for any package version.
Comparing DESCRIPTION or NAMESPACE files between different package versions.
Getting a list of all releases for a specific package.
The Bioconductor is partly supported.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between pacs versions 0.4.8 dated 2022-06-28 and 0.4.10 dated 2023-02-27
DESCRIPTION | 8 MD5 | 22 +- NEWS.md | 10 + R/valid.R | 8 README.md | 8 build/vignette.rds |binary inst/doc/GettingStarted.Rmd | 42 ++-- inst/doc/GettingStarted.html | 374 ++++++++++++++++++++----------------------- inst/doc/tinyverse.Rmd | 101 +++++------ inst/doc/tinyverse.html | 273 +++++++++++++++---------------- vignettes/GettingStarted.Rmd | 42 ++-- vignettes/tinyverse.Rmd | 101 +++++------ 12 files changed, 492 insertions(+), 497 deletions(-)
Title: A Metadata and Text Extraction and Manipulation Tool Set
Description: Provides a function collection to extract metadata, sectioned text and study characteristics from scientific articles in 'NISO-JATS' format. Articles in PDF format can be converted to 'NISO-JATS' with the 'Content ExtRactor and MINEr' ('CERMINE', <https://github.com/CeON/CERMINE>). For convenience, two functions bundle the extraction heuristics: JATSdecoder() converts 'NISO-JATS'-tagged XML files to a structured list with elements title, author, journal, history, 'DOI', abstract, sectioned text and reference list. study.character() extracts multiple study characteristics like number of included studies, statistical methods used, alpha error, power, statistical results, correction method for multiple testing, software used. An estimation of the involved sample size is performed based on reports within the abstract and the reported degrees of freedom within statistical results. In addition, the package contains some useful functions to process text (text2sentences(), text2num(), ng [...truncated...]
Author: Ingmar Boeschen [aut, cre]
Maintainer: Ingmar Boeschen <ingmar.boeschen@uni-hamburg.de>
Diff between JATSdecoder versions 1.1.1 dated 2022-10-21 and 1.1.2 dated 2023-02-27
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/JATSdecoder.R | 17 ++++++++++++----- R/character_get.stats.R | 16 ++++++++++++---- R/study.character.R | 12 ++++++++++-- man/JATSdecoder.Rd | 17 ++++++++++++----- man/get.stats.Rd | 16 ++++++++++++---- man/study.character.Rd | 13 +++++++++++-- 8 files changed, 81 insertions(+), 34 deletions(-)
Title: Force Measurement Analyses
Description: For cleaning and analysis of graphs, such as animal closing force
measurements.
'forceR' was initially written and optimized to deal with insect bite force
measurements, but can be used for any time series. Includes a full workflow
to load, plot and crop data, correct amplifier and baseline drifts,
identify individual peak shapes (bites), rescale (normalize) peak curves,
and find best polynomial fits to describe and analyze force curve shapes.
Author: Peter T. Ruehr [aut, cre] ,
Alexander Blanke [ctb]
Maintainer: Peter T. Ruehr <peter.ruehr@gmail.com>
Diff between forceR versions 1.0.15 dated 2022-06-07 and 1.0.18 dated 2023-02-27
DESCRIPTION | 26 +++- MD5 | 36 +++--- NEWS.md | 72 +++++++++---- R/cropping.R | 81 +++++++++------ R/drift_corrections_03.R | 76 ++++++++------ R/normalization.R | 18 ++- R/peak_finding.R | 8 - R/polynomial.R | 69 +++++++----- README.md | 39 ++++--- build/vignette.rds |binary inst/CITATION | 32 ++--- inst/doc/forceR.R | 4 inst/doc/forceR.Rmd | 6 - inst/doc/forceR.html | 241 +++++++++++++++++++++++---------------------- man/convert_measurement.Rd | 10 + man/correct_peak.Rd | 4 man/find_best_fits.Rd | 20 +++ man/red_peaks_100.Rd | 4 vignettes/forceR.Rmd | 6 - 19 files changed, 438 insertions(+), 314 deletions(-)
Title: Diffusion Distance for Complex Networks
Description: Enables the evaluation of diffusion distances for complex single-layer networks.
Given a network one can define different types of Laplacian (or transition)
matrices corresponding to different continuous-time random walks dynamics on the network.
This package enables the evaluation of Laplacians, stochastic matrices, and the
corresponding diffusion distance matrices. The metric structure induced by the network-driven
process is richer and more robust than the one given by shortest-paths and allows to study
the geometry induced by different types of diffusion-like communication mechanisms taking
place on complex networks.
For more details see: De Domenico, M. (2017) <doi:10.1103/physrevlett.118.168301> and
Bertagnolli, G. and De Domenico, M. (2021) <doi:10.1103/PhysRevE.103.042301>.
Author: Giulia Bertagnolli [aut, cre] ,
Manlio De Domenico [aut]
Maintainer: Giulia Bertagnolli <giulia.bertagnolli@gmail.com>
Diff between diffudist versions 1.0.0 dated 2021-11-30 and 1.0.1 dated 2023-02-27
diffudist-1.0.0/diffudist/inst/doc/diffusion-distances.R |only diffudist-1.0.0/diffudist/inst/doc/diffusion-distances.Rmd |only diffudist-1.0.0/diffudist/inst/doc/diffusion-distances.html |only diffudist-1.0.0/diffudist/vignettes/diffusion-distances.Rmd |only diffudist-1.0.1/diffudist/DESCRIPTION | 12 +- diffudist-1.0.1/diffudist/MD5 | 42 +++++----- diffudist-1.0.1/diffudist/R/get_diff_prob_matrix.R | 2 diffudist-1.0.1/diffudist/R/get_spectral.R | 10 +- diffudist-1.0.1/diffudist/R/plotting_diffudist.R | 13 ++- diffudist-1.0.1/diffudist/README.md | 10 +- diffudist-1.0.1/diffudist/build/partial.rdb |binary diffudist-1.0.1/diffudist/build/vignette.rds |binary diffudist-1.0.1/diffudist/inst/doc/diffudist-package.R |only diffudist-1.0.1/diffudist/inst/doc/diffudist-package.Rmd |only diffudist-1.0.1/diffudist/inst/doc/diffudist-package.html |only diffudist-1.0.1/diffudist/man/figures/plot-g-1.png |binary diffudist-1.0.1/diffudist/man/figures/plot_CRW-1.png |binary diffudist-1.0.1/diffudist/man/figures/plot_MERW-1.png |binary diffudist-1.0.1/diffudist/man/figures/plots-with-dendro-1.png |binary diffudist-1.0.1/diffudist/man/figures/plots-with-dendro-2.png |binary diffudist-1.0.1/diffudist/man/getSpectralDecomp.Rd | 6 + diffudist-1.0.1/diffudist/man/get_diffusion_probability_matrix.Rd | 4 diffudist-1.0.1/diffudist/man/get_distance_matrix.Rd | 4 diffudist-1.0.1/diffudist/man/get_mean_distance_matrix.Rd | 4 diffudist-1.0.1/diffudist/man/plotHeatmap.Rd | 2 diffudist-1.0.1/diffudist/vignettes/diffudist-package.Rmd |only 26 files changed, 64 insertions(+), 45 deletions(-)
Title: Retrieving, Managing and Analysing Air Quality and Weather Data
for Lombardy (Italy) using ARPA Lombardia Open Database
Description: Contains functions for retrieving, managing and analysing air quality and weather data from Regione Lombardia open database (<https://www.dati.lombardia.it/>).
Data are collected by ARPA Lombardia (Lombardia Environmental Protection Agency), Italy, through its ground monitoring network.
See the webpage <https://www.arpalombardia.it/Pages/ARPA_Home_Page.aspx> for further information on ARPA Lombardia's activities and history.
Data quality (e.g. missing values, exported values, graphical mapping) has been checked involving members of the ARPA Lombardia's office for air quality control.
The package makes available observations since 1989 (for weather) and 1996 (for air quality) and are updated with daily frequency by the regional agency.
Author: Paolo Maranzano [aut, cre, cph]
,
Andrea Algieri [aut, cph]
Maintainer: Paolo Maranzano <pmaranzano.ricercastatistica@gmail.com>
Diff between ARPALData versions 1.2.3 dated 2022-03-07 and 1.3.0 dated 2023-02-27
DESCRIPTION | 13 +++--- MD5 | 28 +++++++------- NAMESPACE | 54 ++++++++++++++-------------- R/ARPALdf_Summary.R | 15 +++++-- R/Excess_na_converter.R | 6 +-- R/Time_aggregate.R | 10 ++--- R/get_ARPA_Lombardia_AQ_data.R | 8 ++-- R/get_ARPA_Lombardia_AQ_municipal_data.R | 8 ++-- R/get_ARPA_Lombardia_AQ_municipal_data_1y.R | 2 - R/get_ARPA_Lombardia_W_data.R | 9 ++-- R/url_dataset_year.R | 9 +++- man/ARPALdf_Summary.Rd | 10 ++--- man/get_ARPA_Lombardia_AQ_data.Rd | 8 ++-- man/get_ARPA_Lombardia_AQ_municipal_data.Rd | 8 ++-- man/get_ARPA_Lombardia_W_data.Rd | 9 ++-- 15 files changed, 103 insertions(+), 94 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends on in an isolated,
portable, and reproducible way.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Kevin Ushey [aut],
Jonathan McPherson [aut],
Joe Cheng [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between packrat versions 0.9.0 dated 2023-01-09 and 0.9.1 dated 2023-02-27
DESCRIPTION | 44 +++++++++++++------- MD5 | 20 ++++++--- R/pkg.R | 3 - R/remote-info.R |only R/restore.R | 40 +----------------- README.md | 1 inst/resources/init-rprofile.R | 2 inst/resources/init.R | 2 tests/testthat/_snaps |only tests/testthat/resources/descriptions/github |only tests/testthat/resources/descriptions/github_subdir |only tests/testthat/resources/descriptions/gitlab |only tests/testthat/resources/descriptions/gitlab_subdir |only tests/testthat/test-pkg.R |only tests/testthat/test-remote-info.R |only 15 files changed, 50 insertions(+), 62 deletions(-)
Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running
program that seeks to monitor the status and trends of the breeding birds in
North America. Since its start in 1966, the BBS has accumulated over 50 years
of data for over 500 species of North American Birds. Given the temporal and
spatial structure of the data, hierarchical Bayesian models are used to assess
the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform
hierarchical Bayesian analysis of BBS data. You can run a full
model analysis for one or more species that you choose, or you can take
more control and specify how the data should be stratified, prepared
for 'JAGS', or modelled. The functions provided here allow you to replicate
analyses performed by the United State Geological Survey (USGS, see Link
and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service
(CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre],
Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <brandonedwards3@cmail.carleton.ca>
Diff between bbsBayes versions 2.5.2 dated 2022-10-11 and 2.5.3 dated 2023-02-27
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- README.md | 2 +- inst/CITATION | 27 +++++++++++++++------------ inst/models/first-difference.t.jags | 2 +- 5 files changed, 26 insertions(+), 23 deletions(-)
Title: Quaternions Splines
Description: Provides routines to create some quaternions splines:
Barry-Goldman algorithm, De Casteljau algorithm, and Kochanek-Bartels
algorithm. The implementations are based on the Python library
'splines'. Quaternions splines allow to construct spherical curves.
References: Barry and Goldman <doi:10.1145/54852.378511>,
Kochanek and Bartels <doi:10.1145/800031.808575>.
Author: Stephane Laurent [aut, cre],
Matthias Geier [aut]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between qsplines versions 1.0.0 dated 2022-07-18 and 1.0.1 dated 2023-02-27
DESCRIPTION | 8 MD5 | 40 +-- NAMESPACE | 26 +- NEWS.md | 21 + R/BarryGoldman.R | 204 +++++++++--------- R/KochanekBartels.R | 450 +++++++++++++++++++--------------------- R/RcppExports.R | 38 +-- R/aaa.R | 10 R/quaternionFromTo.R | 56 ++-- R/quaternions_splines_shared.R | 204 +++++++++--------- R/shinyKBS.R | 18 - README.md | 28 +- inst/shiny/threejs/global.R | 2 inst/shiny/threejs/server.R | 118 +++++----- inst/shiny/threejs/ui.R | 82 +++---- inst/shiny/threejs/www/scene.js | 370 ++++++++++++++++---------------- man/DeCasteljau.Rd | 100 ++++---- man/KochanekBartels.Rd | 221 +++++++++---------- src/Makevars | 2 src/Makevars.win | 1 src/casteljau.cpp | 2 21 files changed, 1000 insertions(+), 1001 deletions(-)
More information about saeHB.panel.beta at CRAN
Permanent link
Title: Support for Spatial Objects Within the 'mlr3' Ecosystem
Description: Extends the 'mlr3' ML framework with methods for spatial
objects. Data storage and prediction are supported for packages
'terra', 'raster' and 'stars'.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3spatial versions 0.3.1 dated 2022-12-16 and 0.4.0 dated 2023-02-27
DESCRIPTION | 10 ++--- MD5 | 24 ++++++------ NEWS.md | 6 +++ R/DataBackendRaster.R | 24 ++++-------- R/helper.R | 8 +++- R/predict_spatial.R | 15 +++---- README.md | 88 +++++++++++++++++++++++++++------------------ man/DataBackendRaster.Rd | 19 +++------ man/figures/land_cover.png |binary man/figures/sentinel.png |binary man/mlr3spatial-package.Rd | 4 +- man/predict_spatial.Rd | 11 ++--- man/write_raster.Rd | 5 +- 13 files changed, 116 insertions(+), 98 deletions(-)
Title: Bayesian Additive Regression Trees
Description: An advanced implementation of Bayesian Additive Regression Trees with expanded features for data analysis and visualization.
Author: Adam Kapelner and Justin Bleich
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between bartMachine versions 1.3.3 dated 2023-01-11 and 1.3.3.1 dated 2023-02-27
CHANGELOG | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/bartMachine.R | 43 ++++++++++++++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/bartMachine.pdf |binary 6 files changed, 52 insertions(+), 12 deletions(-)
Title: Missing Person Identification Tools
Description: Open-source software for computing Likelihood ratios thresholds and error rates in DNA kinship testing. Marsico FL. et al (2021) <doi:10.1016/j.fsigen.2021.102519>.
Author: Franco Marsico [aut, cre]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between mispitools versions 0.2.1 dated 2022-03-29 and 0.3.0 dated 2023-02-27
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- R/DeT.R | 2 +- R/LRdist.R | 2 +- R/Trates.R | 2 +- R/combLR.R | 2 +- R/deplot.R | 2 +- R/simLRgen.R | 9 ++++++--- R/simLRprelim.R | 2 +- README.md | 4 ++-- man/DeT.Rd | 2 +- man/LRdist.Rd | 2 +- man/Trates.Rd | 2 +- man/combLR.Rd | 2 +- man/deplot.Rd | 2 +- man/simLRgen.Rd | 6 +++--- 16 files changed, 40 insertions(+), 37 deletions(-)
Title: Species Distribution and Abundance Modelling at High
Spatio-Temporal Resolution
Description: A collection of novel tools for generating species distribution and abundance models (SDM) that are dynamic through both space and time. These highly flexible functions incorporate spatial and temporal aspects across key SDM stages; including when cleaning and filtering species occurrence data, generating pseudo-absence records, assessing and correcting sampling biases and autocorrelation, extracting explanatory variables and projecting distribution patterns. Throughout, functions utilise Google Earth Engine and Google Drive to minimise the computing power and storage demands associated with species distribution modelling at high spatio-temporal resolution.
Author: Rachel Dobson [aut, cre, ctb] ,
Andy J. Challinor [aut, ctb] ,
Robert A. Cheke [aut, ctb] ,
Stewart Jennings [aut, ctb] ,
Stephen G. Willis [aut, ctb] ,
Martin Dallimer [aut, ctb]
Maintainer: Rachel Dobson <eerdo@leeds.ac.uk>
Diff between dynamicSDM versions 1.0 dated 2023-02-17 and 1.1 dated 2023-02-27
DESCRIPTION | 8 MD5 | 76 +- NAMESPACE | 1 R/dynamicSDM-package.R | 1 R/dynamic_proj_GIF.R | 629 ++++++++++++-------- R/dynamic_proj_covariates.R | 34 - R/extract_buffered_raster.R | 31 + R/extract_coords_combine.R | 67 ++ R/extract_dynamic_coords.R | 722 ++++++++++++------------ R/extract_dynamic_raster.R | 799 +++++++++++++------------- R/spatiotemp_autocorr.R | 6 R/spatiotemp_bias.R | 15 R/spatiotemp_check.R | 18 R/spatiotemp_extent.R | 302 +++++----- R/spatiotemp_pseudoabs.R | 929 +++++++++++++++---------------- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignette1_response_data.html | 50 - inst/doc/vignette2_explanatory_data.html | 2 inst/doc/vignette3_modelling.Rmd | 262 ++++---- inst/doc/vignette3_modelling.html | 6 inst/doc/vignette4_projecting.Rmd | 504 ++++++++-------- inst/doc/vignette4_projecting.html | 4 man/dynamic_proj_GIF.Rd | 21 man/dynamic_proj_covariates.Rd | 8 man/extract_buffered_raster.Rd | 32 + man/extract_coords_combine.Rd | 39 + man/extract_dynamic_raster.Rd | 32 + man/figures/Figure1.png |binary man/figures/dynamicSDM_1.0.pdf |binary man/spatiotemp_autocorr.Rd | 2 man/spatiotemp_bias.Rd | 2 man/spatiotemp_check.Rd | 10 man/spatiotemp_pseudoabs.Rd | 7 tests/testthat/test-spatiotemp_check.R | 4 tests/testthat/test-spatiotemp_extent.R | 258 ++++---- vignettes/vignette3_modelling.Rmd | 262 ++++---- vignettes/vignette4_projecting.Rmd | 504 ++++++++-------- 39 files changed, 2997 insertions(+), 2654 deletions(-)
Title: Construction, Simulation and Analysis of Boolean Networks
Description: Functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks <doi:10.1093/bioinformatics/btq124>.
Author: Christoph Muessel [aut],
Martin Hopfensitz [aut],
Dao Zhou [aut],
Hans A. Kestler [aut, cre],
Armin Biere [ctb] ,
Troy D. Hanson [ctb]
Maintainer: Hans A. Kestler <hans.kestler@uni-ulm.de>
Diff between BoolNet versions 2.1.7 dated 2022-09-04 and 2.1.8 dated 2023-02-27
DESCRIPTION | 12 +++++------- MD5 | 22 +++++++++++----------- build/vignette.rds |binary inst/CITATION | 18 ++---------------- inst/doc/BoolNet_package_vignette.pdf |binary man/toPajek.Rd | 2 +- src/common.c | 2 +- src/init.c | 2 +- src/picosat.c | 14 +++++++------- src/random.h | 2 +- src/sat_search.c | 2 +- src/symbolic_simulator.c | 2 +- 12 files changed, 31 insertions(+), 47 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>, (Ef [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut]
,
Guido Schwarzer [aut, cre]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between netmeta versions 2.7-0 dated 2022-12-22 and 2.8-0 dated 2023-02-27
DESCRIPTION | 12 MD5 | 86 +++--- NAMESPACE | 28 ++ NEWS.md | 69 +++++ R/contribution.matrix.R | 5 R/forest.netmeta.R | 15 - R/funnel.netmeta.R | 7 R/hasse.R | 4 R/hatmatrix.R | 2 R/heatplot.R |only R/heatplot.netmeta.R |only R/meta-chk.R | 4 R/netconnection.R | 340 +++++++++++++++++++++----- R/netgraph.netmeta.R | 7 R/netleague.R | 4 R/netmeta-internal.R | 16 + R/netmeta-package.R | 7 R/netmeta.R | 20 + R/netmetabin.R | 34 ++ R/netpairwise.R | 588 +++++++++++++++++++++++++++++++++++++++++---- R/netposet.R | 34 +- R/netrank.R | 13 R/plot.netposet.R | 6 R/plot.netrank.R | 14 - R/print.decomp.design.R | 17 + R/print.netmeta.R | 97 ++++--- R/radial.netmeta.R |only R/rankogram.R | 8 R/ranksampling.R | 6 R/updateversion.R | 34 ++ man/forest.netmeta.Rd | 8 man/funnel.netmeta.Rd | 2 man/hasse.Rd | 4 man/hatmatrix.Rd | 2 man/heatplot.Rd |only man/heatplot.netmeta.Rd |only man/netconnection.Rd | 35 +- man/netleague.Rd | 4 man/netmeta.Rd | 6 man/netpairwise.Rd | 54 +++- man/netposet.Rd | 17 - man/netrank.Rd | 4 man/plot.netposet.Rd | 6 man/plot.netrank.Rd | 14 - man/print.decomp.design.Rd | 4 man/radial.netmeta.Rd |only man/rankogram.Rd | 6 47 files changed, 1325 insertions(+), 318 deletions(-)
Title: Get Data from the Swiss Statistical Office
Description: Search and download data from the Swiss Federal Statistical Office (BFS) <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between BFS versions 0.4.4 dated 2022-12-14 and 0.4.5 dated 2023-02-27
DESCRIPTION | 6 +- MD5 | 8 +-- NEWS.md | 4 + R/bfs_get_data_comments.R | 4 - README.md | 99 +++++++++++++++++++++------------------------- 5 files changed, 59 insertions(+), 62 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-09 2.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-28 1.3.2
2021-02-24 1.3.1
2019-09-09 1.3
2019-01-16 1.2
2016-09-26 1.1
2014-09-29 1.0
Title: Search and Retrieve Spatial Data from 'GUGiK'
Description: Automatic open data acquisition from resources of Polish Head Office
of Geodesy and Cartography ('Główny Urząd Geodezji i Kartografii')
(<https://www.gov.pl/web/gugik>).
Available datasets include various types of numeric, raster and vector data,
such as orthophotomaps, digital elevation models (digital terrain models,
digital surface model, point clouds), state register of borders, spatial
databases, geometries of cadastral parcels, 3D models of buildings, and more.
It is also possible to geocode addresses or objects using the geocodePL_get()
function.
Author: Krzysztof Dyba [aut, cre] ,
Jakub Nowosad [aut] ,
Maciej Beręsewicz [ctb] ,
GUGiK [ctb]
Maintainer: Krzysztof Dyba <adres7@gmail.com>
Diff between rgugik versions 0.3.3 dated 2022-08-29 and 0.4.0 dated 2023-02-27
DESCRIPTION | 10 MD5 | 51 - NEWS.md |only R/DEM_request.R | 51 - R/geocodePL_get.R | 8 R/geodb_download.R | 2 R/minmaxDTM_get.R | 2 R/ortho_request.R | 43 - R/parcel_get.R | 2 R/pointDTM100_download.R | 2 R/pointDTM_get.R | 8 R/tile_download.R | 28 R/utils.R | 3 README.md | 2 build/vignette.rds |binary inst/CITATION | 10 inst/doc/DEM.html | 1218 ++++++++++++++--------------- inst/doc/orthophotomap.html | 1126 +++++++++++++-------------- inst/doc/topodb.html | 1320 ++++++++++++++++---------------- man/DEM_request.Rd | 3 man/ortho_request.Rd | 3 man/tile_download.Rd | 13 tests/testthat/test-DEM_request.R | 2 tests/testthat/test-emuia_download.R | 2 tests/testthat/test-models3D_download.R | 2 tests/testthat/test-ortho_request.R | 2 tests/testthat/test-tile_download.R | 9 27 files changed, 1949 insertions(+), 1973 deletions(-)
Title: Base Functions and Resources for Rapporteket
Description: Provide common functions and resources for registry specific
R-packages at Rapporteket
<https://rapporteket.github.io/rapporteket/articles/short_introduction.html>.
This package is relevant for developers of packages/registries at
Rapporteket.
Author: Are Edvardsen [aut, cre] ,
Kevin Otto Thon [aut]
Maintainer: Are Edvardsen <biorakel@gmail.com>
Diff between rapbase versions 1.23.0 dated 2022-08-17 and 1.24.0 dated 2023-02-27
rapbase-1.23.0/rapbase/man/getUserEmail.Rd |only rapbase-1.23.0/rapbase/man/getUserFullName.Rd |only rapbase-1.23.0/rapbase/man/getUserGroups.Rd |only rapbase-1.23.0/rapbase/man/getUserName.Rd |only rapbase-1.23.0/rapbase/man/getUserPhone.Rd |only rapbase-1.23.0/rapbase/man/getUserReshId.Rd |only rapbase-1.23.0/rapbase/man/getUserRole.Rd |only rapbase-1.24.0/rapbase/DESCRIPTION | 17 rapbase-1.24.0/rapbase/MD5 | 80 - rapbase-1.24.0/rapbase/NAMESPACE | 5 rapbase-1.24.0/rapbase/NEWS.md | 20 rapbase-1.24.0/rapbase/R/autoReport.R | 48 - rapbase-1.24.0/rapbase/R/log.R | 35 rapbase-1.24.0/rapbase/R/misc.R | 3 rapbase-1.24.0/rapbase/R/moduleAutoReport.R | 449 ++++++++- rapbase-1.24.0/rapbase/R/moduleExport.R | 5 rapbase-1.24.0/rapbase/R/moduleNavbarWidget.R | 168 +++ rapbase-1.24.0/rapbase/R/sendEmail.R | 17 rapbase-1.24.0/rapbase/R/stagingData.R | 417 +++++++- rapbase-1.24.0/rapbase/R/userAttribute.R | 480 +++++----- rapbase-1.24.0/rapbase/README.md | 14 rapbase-1.24.0/rapbase/build |only rapbase-1.24.0/rapbase/inst/createStagingDb.sql |only rapbase-1.24.0/rapbase/inst/createStagingTab.sql |only rapbase-1.24.0/rapbase/inst/dbConfig.yml | 8 rapbase-1.24.0/rapbase/inst/doc |only rapbase-1.24.0/rapbase/inst/extdata |only rapbase-1.24.0/rapbase/inst/howWeDealWithPersonalData.Rmd | 2 rapbase-1.24.0/rapbase/inst/rapbaseConfig.yml | 20 rapbase-1.24.0/rapbase/man/appNavbarUserWidget.Rd | 3 rapbase-1.24.0/rapbase/man/autoReport.Rd | 53 - rapbase-1.24.0/rapbase/man/getSessionData.Rd | 6 rapbase-1.24.0/rapbase/man/logger.Rd | 7 rapbase-1.24.0/rapbase/man/makeAutoReportTab.Rd | 23 rapbase-1.24.0/rapbase/man/navbarWidget.Rd | 36 rapbase-1.24.0/rapbase/man/sanitizeLog.Rd | 1 rapbase-1.24.0/rapbase/man/sendEmail.Rd | 3 rapbase-1.24.0/rapbase/man/stagingData.Rd | 51 - rapbase-1.24.0/rapbase/man/stagingDataHelper.Rd |only rapbase-1.24.0/rapbase/man/unitAttribute.Rd |only rapbase-1.24.0/rapbase/man/userAttribute.Rd |only rapbase-1.24.0/rapbase/man/userInfo.Rd | 43 rapbase-1.24.0/rapbase/tests/testthat/setup.R | 1 rapbase-1.24.0/rapbase/tests/testthat/test-moduleAutoReport.R | 274 +++++ rapbase-1.24.0/rapbase/tests/testthat/test-moduleNavbarWidget.R | 36 rapbase-1.24.0/rapbase/tests/testthat/test-stagingData.R | 175 +++ rapbase-1.24.0/rapbase/tests/testthat/test-userInfo.R | 152 +++ rapbase-1.24.0/rapbase/vignettes |only 48 files changed, 2155 insertions(+), 497 deletions(-)
Title: Spatial and Spatio-Temporal Semiparametric Regression Models
with Spatial Lags
Description: Estimation and inference of spatial and spatio-temporal
semiparametric models including spatial or spatio-temporal non-parametric
trends, parametric and non-parametric covariates and, possibly, a spatial
lag for the dependent variable and temporal correlation in the noise.
The spatio-temporal trend can be decomposed in ANOVA way including main and
interaction functional terms. Use of SAP algorithm to estimate the spatial
or spatio-temporal trend and non-parametric covariates. The methodology of
these models can be found in next references
Basile, R. et al. (2014), <doi:10.1016/j.jedc.2014.06.011>;
Rodriguez-Alvarez, M.X. et al. (2015) <doi:10.1007/s11222-014-9464-2> and,
particularly referred to the focus of the package, Minguez, R.,
Basile, R. and Durban, M. (2020) <doi:10.1007/s10260-019-00492-8>.
Author: Roman Minguez [aut, cre] ,
Roberto Basile [aut] ,
Maria Durban [aut] ,
Gonzalo Espana-Heredia [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>
Diff between pspatreg versions 1.0.6 dated 2022-11-16 and 1.0.7 dated 2023-02-27
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/fit_terms.R | 2 +- R/pspatfit.R | 12 +++++++----- build/vignette.rds |binary inst/CITATION | 17 +++++++---------- inst/doc/A_pspatregPackage.html | 4 ++-- man/fit_terms.Rd | 2 +- 8 files changed, 30 insertions(+), 31 deletions(-)
Title: Detect and Remove Outliers in Phylogenomics Datasets
Description: Analyzis and filtering of phylogenomics datasets.
It takes an input either a collection of gene trees (then transformed to matrices) or directly a collection of gene matrices and performs an iterative process to identify
what species in what genes are outliers, and whose elimination significantly improves the concordance between the input matrices. The methods builds upon the Distatis approach (Abdi et al. (2005) <doi:10.1101/2021.09.08.459421>), a generalization of classical multidimensional scaling to multiple distance matrices.
Author: Damien M. de Vienne [aut],
Stephane Dray [aut],
Theo Tricou [aut],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between phylter versions 0.9.6 dated 2023-01-20 and 0.9.7 dated 2023-02-27
DESCRIPTION | 8 MD5 | 16 - R/impMean.R | 6 build/vignette.rds |binary inst/doc/phyltercontainer.R |only inst/doc/phyltercontainer.Rmd |only inst/doc/phyltercontainer.html |only inst/doc/runphylter.Rmd | 4 inst/doc/runphylter.html | 600 +++++++++++++---------------------------- vignettes/phyltercontainer.Rmd |only vignettes/runphylter.Rmd | 4 11 files changed, 224 insertions(+), 414 deletions(-)
Title: A Two-Sample Test for the Equality of Distributions for
High-Dimensional Data
Description: For high-dimensional data whose main feature is a large number, p, of variables but a small sample size, the null hypothesis that the marginal distributions of p variables are the same for two groups is tested. We propose a test statistic motivated by the simple idea of comparing, for each of the p variables, the empirical characteristic functions computed from the two samples. If one rejects this global null hypothesis of no differences in distributions between the two groups, a set of permutation p-values is reported to identify which variables are not equally distributed in both groups.
Author: Marta Cousido Rocha [aut, cre],
Jose Carlos Soage Gonzalez [ctr],
Jacobo de Una Álvarez [aut, ths],
Jeffrey D. Hart [aut]
Maintainer: Marta Cousido Rocha <martacousido@uvigo.es>
Diff between TwoSampleTest.HD versions 1.1 dated 2022-04-09 and 1.2 dated 2023-02-27
DESCRIPTION | 8 MD5 | 12 - NAMESPACE | 8 R/TwoSampleTest.HD-package.r | 6 R/TwoSampleTest.HD.r | 16 - man/TwoSampleTest.HD-package.Rd | 134 ++++++------- man/TwoSampleTest.HD.Rd | 400 ++++++++++++++++++++-------------------- 7 files changed, 292 insertions(+), 292 deletions(-)
More information about TwoSampleTest.HD at CRAN
Permanent link
Title: Structural Learning in Cox Models with Time-Dependent Covariates
Description: Efficient procedures for fitting and cross-validating the overlapping group Lasso (implemented in C++) for Cox models with time-dependent covariates. The penalty term is a weighted sum of infinity norms of (overlapping) groups of coefficients, which can select variables structurally with a specific grouping structure.
Author: Yi Lian [aut, cre],
Guanbo Wang [aut],
Archer Y. Yang [aut],
Julien Mairal [ctb]
Maintainer: Yi Lian <yi.lian@mail.mcgill.ca>
Diff between netcox versions 1.0 dated 2023-02-20 and 1.0.1 dated 2023-02-27
DESCRIPTION | 10 +- MD5 | 22 ++--- R/datadoc.R | 5 - R/netcox.R | 2 R/netcox_cv.R | 2 data/sim.rda |binary man/netcox.Rd | 2 man/netcox_cv.Rd | 2 man/sim.Rd | 5 - src/main.cpp | 163 +++++++++++++++++++++++++++++++------------ tests/testthat/Rplots.pdf |binary tests/testthat/test-netcox.R | 24 +++--- 12 files changed, 158 insertions(+), 79 deletions(-)
Title: Comprehensive Analysis of Nucleotide Conversion Sequencing Data
Description: Nucleotide conversion sequencing experiments have been
developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such
experiments require specialized tools for primary processing such as GRAND-SLAM,
(see 'Jürges et al' <doi:10.1093/bioinformatics/bty256>) and specialized tools for
downstream analyses. 'grandR' provides a comprehensive toolbox for quality control,
kinetic modeling, differential gene expression analysis and visualization of such data.
Author: Florian Erhard [aut, cre] ,
Teresa Rummel [ctb],
Lygeri Sakellaridi [ctb]
Maintainer: Florian Erhard <Florian.Erhard@uni-wuerzburg.de>
Diff between grandR versions 0.2.0 dated 2022-09-20 and 0.2.1 dated 2023-02-27
grandR-0.2.0/grandR/R/toxicity.R |only grandR-0.2.0/grandR/man/GetSparseMatrix.Rd |only grandR-0.2.0/grandR/man/toxicity.Rd |only grandR-0.2.1/grandR/DESCRIPTION | 23 grandR-0.2.1/grandR/MD5 | 126 grandR-0.2.1/grandR/NAMESPACE | 36 grandR-0.2.1/grandR/NEWS.md | 24 grandR-0.2.1/grandR/R/diagnostics.R | 230 + grandR-0.2.1/grandR/R/diffexp.R | 247 + grandR-0.2.1/grandR/R/dropout.R |only grandR-0.2.1/grandR/R/grandR.R | 352 ++ grandR-0.2.1/grandR/R/load.R | 466 ++- grandR-0.2.1/grandR/R/modeling.R | 215 + grandR-0.2.1/grandR/R/paramest.R | 136 - grandR-0.2.1/grandR/R/plot.R | 293 +- grandR-0.2.1/grandR/R/processing.R | 60 grandR-0.2.1/grandR/R/seurat.R | 48 grandR-0.2.1/grandR/R/shiny.R | 50 grandR-0.2.1/grandR/R/utils.R | 48 grandR-0.2.1/grandR/README.md | 27 grandR-0.2.1/grandR/build/vignette.rds |binary grandR-0.2.1/grandR/inst/CITATION | 30 grandR-0.2.1/grandR/inst/doc/getting-started.R | 30 grandR-0.2.1/grandR/inst/doc/getting-started.Rmd | 54 grandR-0.2.1/grandR/inst/doc/getting-started.html | 1307 +--------- grandR-0.2.1/grandR/man/Analyses.Rd | 11 grandR-0.2.1/grandR/man/CalibrateEffectiveLabelingTimeKineticFit.Rd | 4 grandR-0.2.1/grandR/man/ComputeExpressionPercentage.Rd | 12 grandR-0.2.1/grandR/man/ComputePseudoNtr.Rd |only grandR-0.2.1/grandR/man/ComputeSteadyStateHalfLives.Rd | 2 grandR-0.2.1/grandR/man/CreatePdfs.Rd |only grandR-0.2.1/grandR/man/DESeq2BIC.Rd |only grandR-0.2.1/grandR/man/Defer.Rd | 3 grandR-0.2.1/grandR/man/DesignSemantics.Rd | 4 grandR-0.2.1/grandR/man/EstimateRegulation.Rd | 14 grandR-0.2.1/grandR/man/Findno4sUPairs.Rd | 8 grandR-0.2.1/grandR/man/FitKinetics.Rd | 7 grandR-0.2.1/grandR/man/FitKineticsGeneLeastSquares.Rd | 6 grandR-0.2.1/grandR/man/FitKineticsGeneSnapshot.Rd | 10 grandR-0.2.1/grandR/man/FitKineticsSnapshot.Rd | 14 grandR-0.2.1/grandR/man/GetContrasts.Rd | 4 grandR-0.2.1/grandR/man/GetMatrix.Rd |only grandR-0.2.1/grandR/man/GetTable.Rd | 5 grandR-0.2.1/grandR/man/LFC.Rd | 3 grandR-0.2.1/grandR/man/LikelihoodRatioTest.Rd | 10 grandR-0.2.1/grandR/man/Pairwise.Rd |only grandR-0.2.1/grandR/man/PairwiseDESeq2.Rd | 8 grandR-0.2.1/grandR/man/PlotConversionFreq.Rd | 4 grandR-0.2.1/grandR/man/PlotGeneGroupsBars.Rd | 5 grandR-0.2.1/grandR/man/PlotGeneGroupsPoints.Rd | 7 grandR-0.2.1/grandR/man/PlotGeneOldVsNew.Rd | 2 grandR-0.2.1/grandR/man/PlotGeneSnapshotTimecourse.Rd | 2 grandR-0.2.1/grandR/man/PlotGeneTotalVsNtr.Rd | 2 grandR-0.2.1/grandR/man/PlotHeatmap.Rd | 5 grandR-0.2.1/grandR/man/PlotPCA.Rd | 5 grandR-0.2.1/grandR/man/PlotProfileLikelihood.Rd | 10 grandR-0.2.1/grandR/man/PlotScatter.Rd | 33 grandR-0.2.1/grandR/man/ReadCounts.Rd |only grandR-0.2.1/grandR/man/ReadGRAND.Rd | 3 grandR-0.2.1/grandR/man/ReadNewTotal.Rd |only grandR-0.2.1/grandR/man/SaveNtrSlot.Rd |only grandR-0.2.1/grandR/man/Semantics.concentration.Rd |only grandR-0.2.1/grandR/man/Slots.Rd | 4 grandR-0.2.1/grandR/man/Transform.no.Rd | 2 grandR-0.2.1/grandR/man/UpdateSymbols.Rd |only grandR-0.2.1/grandR/man/UseNtrSlot.Rd |only grandR-0.2.1/grandR/man/VulcanoPlot.Rd | 4 grandR-0.2.1/grandR/man/as.Seurat.grandR.Rd |only grandR-0.2.1/grandR/man/dropout.Rd |only grandR-0.2.1/grandR/man/figures |only grandR-0.2.1/grandR/man/grandR.Rd | 28 grandR-0.2.1/grandR/src |only grandR-0.2.1/grandR/vignettes/getting-started.Rmd | 54 73 files changed, 2287 insertions(+), 1810 deletions(-)
Title: Gaussian Process Fitting
Description: Fits a Gaussian process model to data. Gaussian processes
are commonly used in computer experiments to fit an interpolating model.
The model is stored as an 'R6' object and can be easily updated with new
data. There are options to run in parallel, and 'Rcpp'
has been used to speed up calculations.
For more info about Gaussian process software, see Erickson et al. (2018)
<doi:10.1016/j.ejor.2017.10.002>.
Author: Collin Erickson
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between GauPro versions 0.2.7 dated 2023-02-12 and 0.2.8 dated 2023-02-27
DESCRIPTION | 6 - MD5 | 20 +++--- NEWS.md | 5 + inst/doc/CrossValidationErrorCorrection.html | 22 +++---- inst/doc/GauPro.html | 4 - inst/doc/IntroductionToGPs.Rmd | 2 inst/doc/IntroductionToGPs.html | 6 - inst/doc/derivatives.html | 4 - inst/doc/surface_derivatives.html | 4 - tests/testthat/test_kernel_model_and_kernels.R | 78 +++++++++++++++++-------- vignettes/IntroductionToGPs.Rmd | 2 11 files changed, 95 insertions(+), 58 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic,
and programmer friendly through a flexible and robust API. Core functionality
includes a rich set of S3 generic grouped and weighted statistical functions
for vectors, matrices and data frames, which provide efficient low-level
vectorizations, OpenMP multithreading, and skip missing values by default.
These are integrated with fast grouping and ordering algorithms (also callable
from C), and efficient data manipulation functions. The package also provides
a flexible and rigorous approach to time series and panel data in R. It further
includes fast functions for common statistical procedures, detailed (grouped,
weighted) summary statistics, powerful tools to work with nested data, fast
data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data.
It is well integrated wit [...truncated...]
Author: Sebastian Krantz [aut, cre],
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [ [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 1.9.2 dated 2023-01-25 and 1.9.3 dated 2023-02-27
DESCRIPTION | 9 ++---- MD5 | 52 +++++++++++++++++------------------ NAMESPACE | 2 + NEWS.md | 8 +++++ R/BY.R | 6 ++-- R/GRP.R | 26 ++++++++++++++--- R/collap.R | 4 +- R/descr.R | 2 - R/fdiff_fgrowth.R | 16 +++++----- R/global_macros.R | 11 +++++-- R/psmat.R | 10 +++--- R/qtab.R | 2 - R/varying.R | 24 ++++++++-------- R/zzz.R | 3 +- inst/doc/collapse_documentation.html | 4 +- man/BY.Rd | 6 ++-- man/GRP.Rd | 6 ++-- man/collap.Rd | 4 +- man/collapse-documentation.Rd | 4 +- man/collapse-options.Rd | 6 ++-- man/fast-grouping-ordering.Rd | 4 +- man/funique.Rd | 21 ++++++++++++-- man/qF.Rd | 6 ++-- man/qtab.Rd | 2 - src/Makevars | 2 - src/Makevars.win | 2 - src/kit_dup.c | 7 ++-- 27 files changed, 148 insertions(+), 101 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-10 1.2.2
2019-12-17 1.2.1
2019-01-16 1.2
2014-03-04 1.1.1
2013-04-10 1.1
2012-07-07 1.0
Title: Spatial Modeling on Stream Networks
Description: Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance (Ver Hoef, J.M. and Peterson, E.E., 2010. <DOI:10.1198/jasa.2009.ap08248>.) Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.
Author: Jay Ver Hoef [aut, cre],
Erin Peterson [aut]
Maintainer: Jay Ver Hoef <ver.hoef@SpatialStreamNetworks.com>
Diff between SSN versions 1.1.16 dated 2023-02-09 and 1.1.17 dated 2023-02-27
SSN-1.1.16/SSN/R/split.predictions.R |only SSN-1.1.16/SSN/R/subsetSSN.r |only SSN-1.1.16/SSN/R/write.dbf.SSN.r |only SSN-1.1.16/SSN/R/writeSSN.r |only SSN-1.1.16/SSN/man/splitPredictions.Rd |only SSN-1.1.16/SSN/man/subsetSSN.Rd |only SSN-1.1.16/SSN/man/writeSSN.Rd |only SSN-1.1.16/SSN/src/RdbfwriteSSN.c |only SSN-1.1.17/SSN/DESCRIPTION | 8 ++++---- SSN-1.1.17/SSN/MD5 | 28 ++++++++++------------------ SSN-1.1.17/SSN/NAMESPACE | 2 +- SSN-1.1.17/SSN/R/createSSN.R | 2 ++ SSN-1.1.17/SSN/R/importPredpts.R | 3 +++ SSN-1.1.17/SSN/R/importSSN.R | 4 +++- SSN-1.1.17/SSN/data/mf04.rda |binary SSN-1.1.17/SSN/data/mf04p.rda |binary SSN-1.1.17/SSN/data/modelFits.rda |binary SSN-1.1.17/SSN/man/plot.glmssn.predict.Rd | 2 +- SSN-1.1.17/SSN/src/init.c | 4 ++-- 19 files changed, 26 insertions(+), 27 deletions(-)
Title: A Modular Framework for Statistical Simulations in R
Description: An open-source R package for structuring, maintaining, running, and debugging statistical simulations on both local and cluster-based computing environments.See full documentation at <https://avi-kenny.github.io/SimEngine/>.
Author: Avi Kenny [aut, cre],
Charles Wolock [aut]
Maintainer: Avi Kenny <avi.kenny@gmail.com>
Diff between SimEngine versions 1.1.0 dated 2022-04-28 and 1.2.0 dated 2023-02-27
SimEngine-1.1.0/SimEngine/R/SimEngine.R |only SimEngine-1.1.0/SimEngine/man/SimEngine.Rd |only SimEngine-1.2.0/SimEngine/DESCRIPTION | 13 SimEngine-1.2.0/SimEngine/MD5 | 105 - SimEngine-1.2.0/SimEngine/NAMESPACE | 4 SimEngine-1.2.0/SimEngine/NEWS.md | 20 SimEngine-1.2.0/SimEngine/R/SimEngine-package.R |only SimEngine-1.2.0/SimEngine/R/batch.R |only SimEngine-1.2.0/SimEngine/R/cluster_execute.R | 368 +--- SimEngine-1.2.0/SimEngine/R/create_function_reference.R | 12 SimEngine-1.2.0/SimEngine/R/get_complex.R | 15 SimEngine-1.2.0/SimEngine/R/js_support.R | 6 SimEngine-1.2.0/SimEngine/R/misc_functions.R | 305 +++ SimEngine-1.2.0/SimEngine/R/new_sim.R | 169 + SimEngine-1.2.0/SimEngine/R/run.R | 320 ++- SimEngine-1.2.0/SimEngine/R/run_on_cluster.R | 58 SimEngine-1.2.0/SimEngine/R/scratch.R | 253 ++ SimEngine-1.2.0/SimEngine/R/set_config.R | 68 SimEngine-1.2.0/SimEngine/R/set_levels.R | 141 + SimEngine-1.2.0/SimEngine/R/set_script.R | 7 SimEngine-1.2.0/SimEngine/R/summarize.R | 855 ++++------ SimEngine-1.2.0/SimEngine/R/update_sim.R | 200 -- SimEngine-1.2.0/SimEngine/R/update_sim_on_cluster.R | 35 SimEngine-1.2.0/SimEngine/R/use_method.R | 2 SimEngine-1.2.0/SimEngine/R/vars.R | 13 SimEngine-1.2.0/SimEngine/README.md | 6 SimEngine-1.2.0/SimEngine/build/vignette.rds |binary SimEngine-1.2.0/SimEngine/inst/doc/SimEngine.R | 18 SimEngine-1.2.0/SimEngine/inst/doc/SimEngine.Rmd | 34 SimEngine-1.2.0/SimEngine/inst/doc/SimEngine.html | 502 ++++- SimEngine-1.2.0/SimEngine/inst/doc/example_1.R | 2 SimEngine-1.2.0/SimEngine/inst/doc/example_1.Rmd | 6 SimEngine-1.2.0/SimEngine/inst/doc/example_1.html | 430 ++++- SimEngine-1.2.0/SimEngine/inst/doc/example_2.R | 28 SimEngine-1.2.0/SimEngine/inst/doc/example_2.Rmd | 30 SimEngine-1.2.0/SimEngine/inst/doc/example_2.html | 540 ++++-- SimEngine-1.2.0/SimEngine/man/SimEngine-package.Rd |only SimEngine-1.2.0/SimEngine/man/batch.Rd |only SimEngine-1.2.0/SimEngine/man/run.Rd | 7 SimEngine-1.2.0/SimEngine/man/run_on_cluster.Rd | 42 SimEngine-1.2.0/SimEngine/man/set_config.Rd | 35 SimEngine-1.2.0/SimEngine/man/set_levels.Rd | 19 SimEngine-1.2.0/SimEngine/man/summarize.Rd | 177 +- SimEngine-1.2.0/SimEngine/man/update_sim.Rd | 126 - SimEngine-1.2.0/SimEngine/man/update_sim_on_cluster.Rd | 21 SimEngine-1.2.0/SimEngine/man/use_method.Rd | 88 - SimEngine-1.2.0/SimEngine/man/vars.Rd | 122 - SimEngine-1.2.0/SimEngine/tests/testthat/test-batch.R |only SimEngine-1.2.0/SimEngine/tests/testthat/test-core-functions.R | 65 SimEngine-1.2.0/SimEngine/tests/testthat/test-error-handling.R | 38 SimEngine-1.2.0/SimEngine/tests/testthat/test-run_on_cluster.R | 27 SimEngine-1.2.0/SimEngine/tests/testthat/test-summary.R | 489 +++-- SimEngine-1.2.0/SimEngine/tests/testthat/test-update.R | 27 SimEngine-1.2.0/SimEngine/tests/testthat/test-update_on_cluster.R | 55 SimEngine-1.2.0/SimEngine/vignettes/SimEngine.Rmd | 34 SimEngine-1.2.0/SimEngine/vignettes/example_1.Rmd | 6 SimEngine-1.2.0/SimEngine/vignettes/example_2.Rmd | 30 57 files changed, 3558 insertions(+), 2415 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.7.2 dated 2023-02-23 and 1.7.2.1 dated 2023-02-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 3 +++ R/contr.R | 2 +- README.md | 9 +++++---- inst/doc/correlation.html | 6 +++--- inst/doc/nonlinear.html | 4 ++-- 7 files changed, 24 insertions(+), 20 deletions(-)
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
It offers additional options for protein quantification using
the N most intense fragment ions, using all fragment ions, and
a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
In general, the tool can be used to integrate multiple
proportional observations into a single quantitative value.
Author: Thang Pham [aut, cre, cph, ctb]
,
Alex Henneman [ctb]
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 1.9.7 dated 2023-01-06 and 1.9.9 dated 2023-02-27
DESCRIPTION | 6 - MD5 | 28 ++++---- R/iq-fast.R | 30 +++++---- R/iq.R | 2 inst/doc/iq-fast.html | 140 ++++++++++++++++++++++---------------------- inst/doc/iq.html | 18 ++--- man/create_protein_table.Rd | 2 man/fast_MaxLFQ.Rd | 4 - man/maxLFQ.Rd | 2 man/meanInt.Rd | 2 man/median_polish.Rd | 2 man/process_long_format.Rd | 2 man/topN.Rd | 2 src/Makevars | 1 src/iq.cpp | 32 +++++----- 15 files changed, 140 insertions(+), 133 deletions(-)
More information about HospitalNetwork at CRAN
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-02 0.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-14 1.0.1
2023-02-13 1.0.0
2020-08-01 0.9.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-20 1.1-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-09 0.5.4
2022-07-19 0.5.2
2020-12-07 0.4.1
2020-12-06 0.4.0
2020-07-27 0.2.21
2020-07-15 0.2.20
2020-07-05 0.2.18
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-14 0.1.1
2020-10-28 0.1.0