Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb],
Boris Grinshpun [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.1.6 dated 2025-02-05 and 0.2.0 dated 2025-03-12
NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail_input.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMcreateDoses_16.rds |only NMsim-0.2.0/NMsim/DESCRIPTION | 6 NMsim-0.2.0/NMsim/MD5 | 127 - NMsim-0.2.0/NMsim/NAMESPACE | 1 NMsim-0.2.0/NMsim/NEWS.md | 72 NMsim-0.2.0/NMsim/R/NMcreateDoses.R | 11 NMsim-0.2.0/NMsim/R/NMexec.R | 6 NMsim-0.2.0/NMsim/R/NMreadFilters.R |only NMsim-0.2.0/NMsim/R/NMreadInits.R |only NMsim-0.2.0/NMsim/R/NMreadSim.R | 12 NMsim-0.2.0/NMsim/R/NMreadSimModTab.R | 107 - NMsim-0.2.0/NMsim/R/NMreadTabFast.R |only NMsim-0.2.0/NMsim/R/NMreplaceInits.R | 3 NMsim-0.2.0/NMsim/R/NMsim.R | 810 ++++++---- NMsim-0.2.0/NMsim/R/NMsimDataPrepare.R |only NMsim-0.2.0/NMsim/R/NMsim_NWPRI.R | 6 NMsim-0.2.0/NMsim/R/NMsim_VarCov.R | 5 NMsim-0.2.0/NMsim/R/NMsim_default.R | 2 NMsim-0.2.0/NMsim/R/NMsim_helpers.R | 55 NMsim-0.2.0/NMsim/R/NMupdateInits.R | 6 NMsim-0.2.0/NMsim/R/NMwriteFilters.R |only NMsim-0.2.0/NMsim/R/NMwriteInits.R | 35 NMsim-0.2.0/NMsim/R/addClass.R | 5 NMsim-0.2.0/NMsim/R/addEVID2.R | 42 NMsim-0.2.0/NMsim/R/expandCovs.R | 2 NMsim-0.2.0/NMsim/README.md | 13 NMsim-0.2.0/NMsim/man/NMcreateDoses.Rd | 4 NMsim-0.2.0/NMsim/man/NMexec.Rd | 2 NMsim-0.2.0/NMsim/man/NMreadFilters.Rd |only NMsim-0.2.0/NMsim/man/NMreadInits.Rd |only NMsim-0.2.0/NMsim/man/NMreadSimModTab.Rd | 3 NMsim-0.2.0/NMsim/man/NMreadSimModTabOne.Rd | 3 NMsim-0.2.0/NMsim/man/NMsim.Rd | 354 ++-- NMsim-0.2.0/NMsim/man/NMsim_NWPRI.Rd | 7 NMsim-0.2.0/NMsim/man/NMsim_VarCov.Rd | 4 NMsim-0.2.0/NMsim/man/NMupdateInits.Rd | 2 NMsim-0.2.0/NMsim/man/NMwriteInits.Rd | 11 NMsim-0.2.0/NMsim/man/addClass.Rd |only NMsim-0.2.0/NMsim/man/addEVID2.Rd | 6 NMsim-0.2.0/NMsim/man/count_ij.Rd |only NMsim-0.2.0/NMsim/man/expandCovs.Rd | 2 NMsim-0.2.0/NMsim/man/initsToExt.Rd |only NMsim-0.2.0/NMsim/man/itriag.Rd |only NMsim-0.2.0/NMsim/man/jtriag.Rd |only NMsim-0.2.0/NMsim/man/triagSize.Rd |only NMsim-0.2.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/NMsimData_xgxr021_nmtranfail.csv | 10 NMsim-0.2.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/NMsimData_xgxr021_nmtranfail.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail.lst | 42 NMsim-0.2.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail.mod | 36 NMsim-0.2.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testData/nonmem/xgxr041.mod |only NMsim-0.2.0/NMsim/tests/testthat/testData/simres/xgxr021_sd1_NMreadSim_MetaData.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testData/simres/xgxr021_sd1_NMreadSim_ResultsData.fst |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMreadSim_01.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMreadSim_02.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMreadSim_03.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_01.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_01_noMeta.rds |only NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_02.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_02b.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_09.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_10.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_EBE_03.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_NWPRI_01.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_NWPRI_02.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_inits_06.rds |binary NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_sizes_05.rds |binary NMsim-0.2.0/NMsim/tests/testthat/test_NMcreateDoses.R | 19 NMsim-0.2.0/NMsim/tests/testthat/test_NMreadSim.R | 10 NMsim-0.2.0/NMsim/tests/testthat/test_NMsim.R | 187 ++ NMsim-0.2.0/NMsim/tests/testthat/test_NMsim_NWPRI.R | 17 NMsim-0.2.0/NMsim/tests/testthat/test_addEVID2.R | 12 73 files changed, 1356 insertions(+), 701 deletions(-)
Title: Template Engine Inspired by 'Jinja'
Description: Template engine powered by the 'inja' C++ library. Users
write a template document, using syntax inspired by the 'Jinja' Python
package, and then render the final document by passing data from R.
The template syntax supports features such as variables, loops,
conditions and inheritance.
Author: David Hall [aut, cre, cph] ,
Lars Berscheid [cph] ,
Niels Lohmann [cph]
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between jinjar versions 0.3.1 dated 2023-11-01 and 0.3.2 dated 2025-03-12
DESCRIPTION | 8 +- MD5 | 18 ++--- NEWS.md | 5 + README.md | 5 - build/vignette.rds |binary inst/doc/auxiliary-templates.R | 4 - inst/doc/auxiliary-templates.html | 102 ++++++++++++++-------------- inst/doc/template-syntax.html | 134 +++++++++++++++++++------------------- src/inja/inja.hpp | 16 ++-- src/inja/nlohmann/json.hpp | 4 - 10 files changed, 150 insertions(+), 146 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matt Higham [aut] ,
Ryan A. Hill [ctb] ,
Michael Mahon [ctb] ,
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.9.0 dated 2024-11-06 and 0.10.0 dated 2025-03-12
DESCRIPTION | 6 MD5 | 36 - NEWS.md | 9 R/esv.R | 421 +++++++++-------- R/get_esv.R | 113 +++- R/get_esv_dotlist.R | 117 ++-- R/plot.R | 670 ++++++++++++++-------------- R/spautor.R | 19 R/spautorRF.R | 270 +++++------ R/spgautor.R | 774 ++++++++++++++++----------------- man/esv.Rd | 12 man/plot.spmodel.Rd | 2 man/spautor.Rd | 6 man/spgautor.Rd | 7 tests/testthat/test-extras-spautor.R | 24 + tests/testthat/test-extras-spautorRF.R | 14 tests/testthat/test-extras-spgautor.R | 25 + tests/testthat/test-extras-splm.R | 9 tests/testthat/test-extras.R | 14 19 files changed, 1372 insertions(+), 1176 deletions(-)
Title: Predicting Ethnic Group from Names
Description: Implementation of the race/ethnicity prediction method, described
in "rethnicity: An R package for predicting ethnicity from names"
by Fangzhou Xie (2022) <doi:10.1016/j.softx.2021.100965> and
"Rethnicity: Predicting Ethnicity from Names"
by Fangzhou Xie (2021) <doi:10.48550/arXiv.2109.09228>.
Author: Fangzhou Xie [aut, cre, cph]
Maintainer: Fangzhou Xie <fangzhou.xie@rutgers.edu>
Diff between rethnicity versions 0.2.6 dated 2024-10-18 and 0.2.7 dated 2025-03-12
DESCRIPTION | 11 MD5 | 16 build/vignette.rds |binary inst/doc/advanced_usage.html | 4 inst/doc/introduction.Rmd | 9 inst/doc/introduction.html | 45 inst/include/nlohmann/json.hpp |14842 ++++++++++++++++++--------------------- tests/testthat/test_prediction.R | 62 vignettes/introduction.Rmd | 9 9 files changed, 6944 insertions(+), 8054 deletions(-)
Title: 32-Bit Floats
Description: R comes with a suite of utilities for linear algebra with "numeric"
(double precision) vectors/matrices. However, sometimes single precision (or
less!) is more than enough for a particular task. This package extends R's
linear algebra facilities to include 32-bit float (single precision) data.
Float vectors/matrices have half the precision of their "numeric"-type
counterparts but are generally faster to numerically operate on, for a
performance vs accuracy trade-off. The internal representation is an S4
class, which allows us to keep the syntax identical to that of base R's.
Interaction between floats and base types for binary operators is generally
possible; in these cases, type promotion always defaults to the higher
precision. The package ships with copies of the single precision 'BLAS' and
'LAPACK', which are automatically built in the event they are not available
on the system.
Author: Drew Schmidt [aut, cre, cph],
Wei-Chen Chen [aut],
Dmitriy Selivanov [ctb] ,
ORNL [cph]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between float versions 0.3-2 dated 2023-12-10 and 0.3-3 dated 2025-03-12
ChangeLog | 4 +++ DESCRIPTION | 6 ++--- MD5 | 58 +++++++++++++++++++++++++++--------------------------- R/02-libflags.r | 4 +-- README.md | 4 +-- configure | 6 ++--- configure.ac | 6 ++--- src/NA.c | 8 +++---- src/backsolve.c | 6 ++--- src/binary.c | 34 +++++++++++++++---------------- src/chol.c | 2 - src/chol2inv.c | 2 - src/colSums.c | 4 +-- src/cond.c | 2 - src/converters.c | 16 +++++++------- src/crossprod.c | 8 +++---- src/eigen.c | 4 +-- src/extremes.c | 16 +++++++------- src/isSymmetric.c | 4 +-- src/math.c | 16 +++++++------- src/matmult.c | 4 +-- src/norm.c | 4 +-- src/qr.c | 18 ++++++++-------- src/scale.c | 4 +-- src/sign.c | 4 +-- src/solve.c | 8 +++---- src/sum.c | 4 +-- src/svd.c | 4 +-- src/sweep.c | 4 +-- src/xpose.c | 4 +-- 30 files changed, 136 insertions(+), 132 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-08 0.5.2
2019-01-25 0.5.1
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data
mining tasks such as clustering and classification. The development of
this package was supported in part by NSF IIS-0948893, NSF CMMI
1728612, and NIH R21HG005912. Hahsler et al (2017)
<doi:10.18637/jss.v076.i14>.
Author: Michael Hahsler [aut, cre, cph]
,
Matthew Bolanos [ctb],
John Forrest [ctb],
Matthias Carnein [ctb],
Dennis Assenmacher [ctb],
Dalibor Krleza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 2.0-2 dated 2024-04-21 and 2.0-3 dated 2025-03-12
DESCRIPTION | 52 ++-- MD5 | 124 ++++++----- NAMESPACE | 2 NEWS.md | 9 R/AAA.R | 9 R/AAA_stream-package.R | 1 R/DSAggregate.R | 2 R/DSAggregate_Sample.R | 12 - R/DSC.R | 2 R/DSC_BICO.R | 23 +- R/DSC_DBSCAN.R | 2 R/DSC_DBSTREAM.R | 6 R/DSC_DStream.R | 4 R/DSC_Hierarchical.R | 2 R/DSC_Kmeans.R | 4 R/DSC_R.R | 2 R/DSClassifier_SlidingWindow.R | 4 R/DSD.R | 10 R/DSD_Gaussians.R | 8 R/DSD_MG.R | 6 R/DSD_ReadDB.R | 6 R/DSD_UniformNoise.R | 2 R/DSD_mlbenchData.R | 2 R/DSD_mlbenchGenerator.R | 2 R/DSF.R | 2 R/DSF_Convolve.R | 8 R/DSF_Downsample.R | 2 R/DSF_ExponentialMA.R | 4 R/DSF_FeaturesSelection.R | 4 R/DSF_Func.R | 2 R/DSF_Scale.R | 2 R/DSF_dplyr.R | 6 R/DST.R | 4 R/MGC.R | 2 R/MGC_Linear.R | 2 R/animate_cluster.R | 8 R/backports.R |only R/evaluate.DSC.R | 8 R/kmeansW.R | 4 R/map.R | 2 R/predict.R | 2 R/recluster.R | 2 R/update.R | 2 R/utils-pipe.R |only README.md | 15 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/extending_stream.pdf |binary inst/doc/stream.pdf |binary man/DSC_BICO.Rd | 11 - man/DSClassifier_SlidingWindow.Rd | 4 man/DSD_ReadDB.Rd | 6 man/DSF_dplyr.Rd | 5 man/pipe.Rd |only tests/testthat.R | 4 tests/testthat/helpers.R |only tests/testthat/test-DSC.R | 153 ++++++-------- tests/testthat/test-DSC_BICO.R | 51 ++-- tests/testthat/test-DSC_BIRCH.R | 44 ++-- tests/testthat/test-DSC_formula.R | 68 ++---- tests/testthat/test-DSC_read_write.R | 133 +++++------- tests/testthat/test-DSD.R | 369 +++++++++++++++++------------------ tests/testthat/test-DSF.R | 173 ++++++++-------- tests/testthat/test-DSF_Scale.R | 33 +-- tests/testthat/test-write_stream.R | 123 +++++------ 65 files changed, 767 insertions(+), 787 deletions(-)
Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre] ,
Peter Rousseeuw [aut] ,
Anja Struyf [aut] ,
Mia Hubert [aut] ,
Kurt Hornik [trl, ctb] ,
<https://orcid.org/0000-0003-4198-9911>),
Matthias Studer [ctb],
Pierre Roudier [ctb],
Juan Gonzalez [ctb],
Kamil Kozlowski [ctb],
Er [...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.1.8 dated 2024-12-11 and 2.1.8.1 dated 2025-03-12
DESCRIPTION | 12 ++++++------ MD5 | 32 ++++++++++++++++---------------- R/silhouette.R | 2 +- build/partial.rdb |binary inst/NEWS.Rd | 11 +++++++++++ man/agnes.Rd | 12 ++++++------ man/clara.Rd | 2 +- man/clusGap.Rd | 14 +++++++------- man/daisy.Rd | 2 +- man/diana.Rd | 2 +- man/ellipsoidhull.Rd | 2 +- man/medoids.Rd | 2 +- man/plot.agnes.Rd | 2 +- man/plot.diana.Rd | 4 ++-- man/summary.clara.Rd | 2 +- tests/agnes-ex.R | 2 +- tests/agnes-ex.Rout.save | 2 +- 17 files changed, 58 insertions(+), 47 deletions(-)
Title: Quantile G-Computation Extensions for Effect Measure
Modification
Description: G-computation for a set of time-fixed exposures
with quantile-based basis functions, possibly under linearity and
homogeneity assumptions. Effect measure modification in this method is a way
to assess how the effect of the mixture varies by a binary, categorical or continuous variable.
Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and
Alexandra J. White (2019) A quantile-based g-computation approach to
addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <alex.keil@nih.gov>
Diff between qgcompint versions 0.7.0 dated 2022-03-22 and 1.0.0 dated 2025-03-12
qgcompint-0.7.0/qgcompint/man/qgcomp.emm.boot.Rd |only qgcompint-0.7.0/qgcompint/man/qgcomp.emm.noboot.Rd |only qgcompint-1.0.0/qgcompint/DESCRIPTION | 20 qgcompint-1.0.0/qgcompint/MD5 | 67 qgcompint-1.0.0/qgcompint/NAMESPACE | 33 qgcompint-1.0.0/qgcompint/NEWS.md | 51 qgcompint-1.0.0/qgcompint/R/base.R | 158 - qgcompint-1.0.0/qgcompint/R/base_boot.R | 186 - qgcompint-1.0.0/qgcompint/R/base_bounds.R | 378 +- qgcompint-1.0.0/qgcompint/R/base_calcweights.R | 137 - qgcompint-1.0.0/qgcompint/R/base_esteq.R |only qgcompint-1.0.0/qgcompint/R/base_experimental.R | 191 - qgcompint-1.0.0/qgcompint/R/base_generics.R | 247 + qgcompint-1.0.0/qgcompint/R/base_plot.R | 333 +- qgcompint-1.0.0/qgcompint/R/base_simhelpers.R | 128 qgcompint-1.0.0/qgcompint/R/base_survival.R | 73 qgcompint-1.0.0/qgcompint/R/base_utility.R | 375 ++ qgcompint-1.0.0/qgcompint/README.md | 47 qgcompint-1.0.0/qgcompint/build/vignette.rds |binary qgcompint-1.0.0/qgcompint/inst/doc/qgcompint-vignette.R | 409 ++- qgcompint-1.0.0/qgcompint/inst/doc/qgcompint-vignette.Rmd | 573 +++- qgcompint-1.0.0/qgcompint/inst/doc/qgcompint-vignette.html | 1716 ++++++------- qgcompint-1.0.0/qgcompint/man/getjointeffects.Rd | 10 qgcompint-1.0.0/qgcompint/man/getstrateffects.Rd | 10 qgcompint-1.0.0/qgcompint/man/getstratweights.Rd | 8 qgcompint-1.0.0/qgcompint/man/modelbound.Rd | 34 qgcompint-1.0.0/qgcompint/man/plot.qgcompemmfit.Rd | 77 qgcompint-1.0.0/qgcompint/man/pointwisebound.Rd | 32 qgcompint-1.0.0/qgcompint/man/print.qgcompemmfit.Rd | 10 qgcompint-1.0.0/qgcompint/man/qgcomp.emm.cox.noboot.Rd | 8 qgcompint-1.0.0/qgcompint/man/qgcomp.emm.glm.boot.Rd |only qgcompint-1.0.0/qgcompint/man/qgcomp.emm.glm.ee.Rd |only qgcompint-1.0.0/qgcompint/man/qgcomp.emm.glm.noboot.Rd |only qgcompint-1.0.0/qgcompint/man/simdata_quantized_emm.Rd | 6 qgcompint-1.0.0/qgcompint/tests/test.R | 402 +-- qgcompint-1.0.0/qgcompint/tests/test_catmod.R | 16 qgcompint-1.0.0/qgcompint/tests/test_tibble.R |only qgcompint-1.0.0/qgcompint/vignettes/qgcompint-vignette.Rmd | 573 +++- 38 files changed, 3768 insertions(+), 2540 deletions(-)
Title: PaleoPhyloGeographic Modeling of Climate Niches and Species
Distributions
Description: Reconstruction of paleoclimate niches using phylogenetic comparative
methods and projection reconstructed niches onto paleoclimate maps.
The user can specify various models of trait evolution or estimate the best fit
model, include fossils, use one or multiple phylogenies for inference, and make
animations of shifting suitable habitat through time. This model was first used
in Lawing and Polly (2011), and further implemented in Lawing et al (2016) and
Rivera et al (2020).
Lawing and Polly (2011) <doi:10.1371/journal.pone.0028554> "Pleistocene climate,
phylogeny and climate envelope models: An integrative approach to better
understand species' response to climate change"
Lawing et al (2016) <doi:10.1086/687202> "Including fossils in phylogenetic
climate reconstructions: A deep time perspective on the climatic niche evolution
and diversification of spiny lizards (Sceloporus)"
Rivera et al (2020) <doi:10.1111/jbi.13915> "Reconstructing historical shifts
in suitable habit [...truncated...]
Author: A. Michelle Lawing [aut, cph],
Alexandra Howard [aut, cre],
Maria-Aleja Hurtado-Materon [aut]
Maintainer: Alexandra Howard <alexandra.howard@ag.tamu.edu>
Diff between ppgm versions 1.0.3 dated 2024-06-11 and 1.1 dated 2025-03-12
ppgm-1.0.3/ppgm/tests/testthat/_snaps/plotAnimatedPPGM.md |only ppgm-1.0.3/ppgm/tests/testthat/_snaps/plotAnimatedPPGMMultiPhylo.md |only ppgm-1.1/ppgm/DESCRIPTION | 18 - ppgm-1.1/ppgm/MD5 | 88 +++-- ppgm-1.1/ppgm/NAMESPACE | 6 ppgm-1.1/ppgm/NEWS.md | 13 ppgm-1.1/ppgm/R/getBioclimVars.R | 15 ppgm-1.1/ppgm/R/getLineageClimate.R | 2 ppgm-1.1/ppgm/R/nodeEstimate.R | 35 +- ppgm-1.1/ppgm/R/nodeEstimateEnvelopes.R | 4 ppgm-1.1/ppgm/R/paleoclimate.R | 32 - ppgm-1.1/ppgm/R/plotAnimatedPPGM.R | 17 - ppgm-1.1/ppgm/R/plotAnimatedPPGMMultiPhylo.R | 25 - ppgm-1.1/ppgm/R/ppgm.R | 114 +++++- ppgm-1.1/ppgm/R/ppgmConsensus.R | 34 +- ppgm-1.1/ppgm/R/ppgmMESS.R | 12 ppgm-1.1/ppgm/R/sampletrees.R | 8 ppgm-1.1/ppgm/README.md | 8 ppgm-1.1/ppgm/build |only ppgm-1.1/ppgm/data/paleoclimate.rda |binary ppgm-1.1/ppgm/inst |only ppgm-1.1/ppgm/man/getLineageClimate.Rd | 2 ppgm-1.1/ppgm/man/nodeEstimate.Rd | 8 ppgm-1.1/ppgm/man/nodeEstimateEnvelopes.Rd | 170 +++++----- ppgm-1.1/ppgm/man/occurrences.Rd | 52 +-- ppgm-1.1/ppgm/man/paleoclimate.Rd | 82 ++-- ppgm-1.1/ppgm/man/plotAnimatedPPGM.Rd | 4 ppgm-1.1/ppgm/man/plotAnimatedPPGMMultiPhylo.Rd | 5 ppgm-1.1/ppgm/man/ppgm.Rd | 20 - ppgm-1.1/ppgm/man/ppgmConsensus.Rd | 4 ppgm-1.1/ppgm/man/sampletrees.Rd | 50 +- ppgm-1.1/ppgm/tests/testthat.R | 24 - ppgm-1.1/ppgm/tests/testthat/Rplots.pdf |only ppgm-1.1/ppgm/tests/testthat/_snaps/plotAnimatedPPGM |only ppgm-1.1/ppgm/tests/testthat/_snaps/plotAnimatedPPGMMultiPhylo |only ppgm-1.1/ppgm/tests/testthat/_snaps/plotTraitGram.md | 24 - ppgm-1.1/ppgm/tests/testthat/_snaps/plotTraitGramMultiPhylo.md | 14 ppgm-1.1/ppgm/tests/testthat/geo_rates.jpg |only ppgm-1.1/ppgm/tests/testthat/ppgm.gif |only ppgm-1.1/ppgm/tests/testthat/test-plotAnimatedPPGM.R | 2 ppgm-1.1/ppgm/tests/testthat/test-plotAnimatedPPGMMultiPhylo.R | 3 ppgm-1.1/ppgm/tests/testthat/test-ppgm.R | 6 ppgm-1.1/ppgm/tests/testthat/test-ppgmConsensus.R | 4 ppgm-1.1/ppgm/tests/testthat/test-ppgmMESS.R | 2 ppgm-1.1/ppgm/vignettes |only 45 files changed, 542 insertions(+), 365 deletions(-)
Title: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages
Description: Individual based simulations of hybridizing populations,
where the accumulation of junctions is tracked. Furthermore,
mathematical equations are provided to verify simulation outcomes.
Both simulations and mathematical equations are based on Janzen
(2018, <doi:10.1101/058107>) and Janzen (2022,
<doi:10.1111/1755-0998.13519>).
Author: Thijs Janzen [aut, cre]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between junctions versions 2.1.0 dated 2024-02-13 and 2.1.1 dated 2025-03-12
junctions-2.1.0/junctions/man/calculate_MAT.Rd |only junctions-2.1.1/junctions/DESCRIPTION | 15 junctions-2.1.1/junctions/MD5 | 88 +-- junctions-2.1.1/junctions/NEWS.md | 5 junctions-2.1.1/junctions/R/estimate_time.R | 1 junctions-2.1.1/junctions/R/estimate_time_diploid.R | 2 junctions-2.1.1/junctions/R/estimate_time_one_chrom.R | 1 junctions-2.1.1/junctions/R/number_of_junctions_backcross.R | 1 junctions-2.1.1/junctions/R/number_of_junctions_di.R | 2 junctions-2.1.1/junctions/R/sim_backcrossing.R | 4 junctions-2.1.1/junctions/R/sim_fin_chrom.R | 1 junctions-2.1.1/junctions/R/sim_inf_chrom.R | 1 junctions-2.1.1/junctions/R/util.R | 7 junctions-2.1.1/junctions/README.md | 4 junctions-2.1.1/junctions/build/vignette.rds |binary junctions-2.1.1/junctions/inst/doc/Overview_of_the_junctions_package.Rmd | 2 junctions-2.1.1/junctions/inst/doc/Overview_of_the_junctions_package.html | 20 junctions-2.1.1/junctions/inst/doc/junctions_vignette.Rmd | 4 junctions-2.1.1/junctions/inst/doc/junctions_vignette.html | 290 ---------- junctions-2.1.1/junctions/inst/doc/phased_and_unphased_data.html | 84 +- junctions-2.1.1/junctions/man/calculate_mat.Rd |only junctions-2.1.1/junctions/man/estimate_time.Rd | 1 junctions-2.1.1/junctions/man/estimate_time_one_chrom.Rd | 1 junctions-2.1.1/junctions/man/number_of_junctions_backcross.Rd | 1 junctions-2.1.1/junctions/man/number_of_junctions_di.Rd | 2 junctions-2.1.1/junctions/man/sim_backcrossing.Rd | 4 junctions-2.1.1/junctions/man/sim_fin_chrom.Rd | 1 junctions-2.1.1/junctions/man/sim_inf_chrom.Rd | 1 junctions-2.1.1/junctions/src/Fish.cpp | 46 - junctions-2.1.1/junctions/src/Fish.h | 59 -- junctions-2.1.1/junctions/src/Makevars | 1 junctions-2.1.1/junctions/src/Makevars.win | 1 junctions-2.1.1/junctions/src/Output.cpp | 29 - junctions-2.1.1/junctions/src/Output.h | 7 junctions-2.1.1/junctions/src/RcppExports.cpp | 8 junctions-2.1.1/junctions/src/backcrossing.cpp | 16 junctions-2.1.1/junctions/src/estimate_time_unphased.cpp | 32 - junctions-2.1.1/junctions/src/main_functions.cpp | 34 - junctions-2.1.1/junctions/src/random_functions.h | 6 junctions-2.1.1/junctions/src/unphased.cpp | 43 - junctions-2.1.1/junctions/tests/testthat/test-estim_time_haploid.R | 14 junctions-2.1.1/junctions/tests/testthat/test-marker_dist.R | 3 junctions-2.1.1/junctions/tests/testthat/test-one-chrom.R | 6 junctions-2.1.1/junctions/tests/testthat/test-unphased.R | 72 ++ junctions-2.1.1/junctions/vignettes/Overview_of_the_junctions_package.Rmd | 2 junctions-2.1.1/junctions/vignettes/junctions_vignette.Rmd | 4 46 files changed, 332 insertions(+), 594 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm
(Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6>. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Hege Boevelstad [ctb] ,
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 0.9.5 dated 2025-02-07 and 0.9.6 dated 2025-03-12
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NEWS.md | 14 ++++++++++++++ R/SuppressionFromDecimals.R | 14 ++++++++++++-- man/figures |only tests/testthat/test-GaussSuppressionFromData.R | 17 ++++++++++++++--- 6 files changed, 49 insertions(+), 13 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: Tools for Choice Model Estimation and Application
Description: Choice models are a widely used technique across numerous scientific disciplines. The Apollo package is a very flexible tool for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<http://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and [...truncated...]
Author: Stephane Hess [aut, cre],
David Palma [aut],
Thomas Hancock [ctb]
Maintainer: Stephane Hess <S.Hess@leeds.ac.uk>
Diff between apollo versions 0.3.4 dated 2024-10-01 and 0.3.5 dated 2025-03-12
DESCRIPTION | 12 MD5 | 116 ++-- NAMESPACE | 3 R/apollo_attach.R | 6 R/apollo_bootstrap.R | 4 R/apollo_classAlloc.R | 4 R/apollo_cnl2.R |only R/apollo_combineModels.R | 18 R/apollo_combineResults.R | 6 R/apollo_deltaMethod.R | 6 R/apollo_dft.R | 13 R/apollo_el.R | 2 R/apollo_emdc.R | 16 R/apollo_emdc1.R | 980 +++++++++++++++++------------------ R/apollo_emdc2.R | 826 +++++++++++++++--------------- R/apollo_estimate.R | 14 R/apollo_initialise.R | 2 R/apollo_lc.R | 6 R/apollo_longToWide.R | 68 +- R/apollo_makeCluster.R | 526 ++++++++++--------- R/apollo_mdcev.R | 4 R/apollo_mdcnev.R | 1064 +++++++++++++++++++-------------------- R/apollo_mnl.R | 4 R/apollo_modelOutput.R | 4 R/apollo_modifyUserDefFunc.R | 92 +++ R/apollo_normalDensity.R | 2 R/apollo_ol.R | 2 R/apollo_op.R | 2 R/apollo_outOfSample.R | 31 - R/apollo_ownModel.R | 20 R/apollo_preprocess.R | 10 R/apollo_rrm.R | 6 R/apollo_setWorkDir.R |only R/apollo_validate.R | 4 R/apollo_validateControl.R | 16 R/apollo_validateHBControl.R | 2 R/onAttach.R | 7 inst/doc/apollofirstexample.R | 318 +++++------ inst/doc/apollofirstexample.html | 905 ++++++++++++++++----------------- man/apollo_classAlloc.Rd | 4 man/apollo_cnl2.Rd |only man/apollo_combineResults.Rd | 6 man/apollo_deltaMethod.Rd | 6 man/apollo_dft.Rd | 8 man/apollo_el.Rd | 2 man/apollo_emdc.Rd | 16 man/apollo_emdc1.Rd | 16 man/apollo_emdc2.Rd | 14 man/apollo_lc.Rd | 2 man/apollo_longToWide.Rd | 10 man/apollo_mdcev.Rd | 2 man/apollo_mdcnev.Rd | 4 man/apollo_mnl.Rd | 4 man/apollo_normalDensity.Rd | 16 man/apollo_ol.Rd | 2 man/apollo_op.Rd | 2 man/apollo_outOfSample.Rd | 30 - man/apollo_ownModel.Rd | 20 man/apollo_rrm.Rd | 6 man/apollo_setWorkDir.Rd |only man/apollo_validateHBControl.Rd | 2 61 files changed, 2749 insertions(+), 2544 deletions(-)
Title: An Implementation of the RESTK Algorithm
Description: Implementation of the RESTK algorithm based on Markov's Inequality from Vilardell, Sergi, Serra, Isabel, Mezzetti, Enrico, Abella, Jaume, Cazorla, Francisco J. and Del Castillo, J. (2022). "Using Markov's Inequality with Power-Of-k Function for Probabilistic WCET Estimation". In 34th Euromicro Conference on Real-Time Systems (ECRTS 2022). Leibniz International Proceedings in Informatics (LIPIcs) 231 20:1-20:24. <doi:10.4230/LIPIcs.ECRTS.2022.20>. This work has been supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 772773).
Author: Sergi Vilardell [aut, cre]
Maintainer: Sergi Vilardell <sergi.vilardell@bsc.es>
Diff between RESTK versions 1.0.0 dated 2023-08-22 and 1.0.1 dated 2025-03-12
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/estimate_quantiles_maxk.R | 1 - R/linear_adjust.R | 2 +- 4 files changed, 7 insertions(+), 8 deletions(-)
Title: An Implementation of the Hedged Random Forest Algorithm
Description: This algorithm is described in detail in the paper "Hedging Forecast Combinations With an Application to the Random Forest" by Beck et al. (2024) <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5032102>. The package provides a function hedgedrf() that can be used to train a Hedged Random Forest model on a dataset, and a function predict.hedgedrf() that can be used to make predictions with the model.
Author: Elliot Beck [aut, cre]
Maintainer: Elliot Beck <elliotleeroy.beck@uzh.ch>
Diff between hedgedrf versions 0.0.1 dated 2024-07-14 and 1.0.1 dated 2025-03-12
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 0.22.1 dated 2024-11-27 and 0.23.0 dated 2025-03-12
DESCRIPTION | 27 ++- MD5 | 215 ++++++++++++++++--------------- NAMESPACE | 14 ++ NEWS.md | 13 + R/BenchmarkResult.R | 14 +- R/CallbackResample.R |only R/ContextResample.R |only R/DataBackendRename.R | 4 R/HotstartStack.R | 4 R/Learner.R | 122 +++++++++++++++-- R/LearnerClassifDebug.R | 10 - R/LearnerClassifFeatureless.R | 2 R/LearnerClassifRpart.R | 8 - R/LearnerRegr.R | 6 R/LearnerRegrFeatureless.R | 2 R/LearnerRegrRpart.R | 4 R/Measure.R | 10 - R/MeasureClassifCosts.R | 2 R/MeasureDebug.R | 2 R/MeasureInternalValidScore.R | 2 R/MeasureSelectedFeatures.R | 2 R/Prediction.R | 4 R/PredictionClassif.R | 2 R/PredictionDataClassif.R | 4 R/PredictionDataRegr.R | 8 - R/PredictionRegr.R | 8 - R/ResampleResult.R | 16 +- R/Resampling.R | 2 R/ResamplingBootstrap.R | 2 R/ResamplingCV.R | 2 R/ResamplingHoldout.R | 2 R/ResamplingRepeatedCV.R | 2 R/ResamplingSubsampling.R | 2 R/ResultData.R | 60 ++++++-- R/Task.R | 98 ++++++++++---- R/TaskGeneratorMoons.R | 2 R/as_learner.R | 1 R/as_measure.R | 20 +- R/as_resampling.R | 3 R/as_result_data.R | 21 ++- R/as_task.R | 8 + R/as_task_classif.R | 2 R/as_task_regr.R | 2 R/assertions.R | 57 +++++++- R/auto_convert.R | 29 ++++ R/benchmark.R | 21 +-- R/helper.R | 5 R/mlr_callbacks.R |only R/mlr_reflections.R | 10 - R/reexports.R | 9 + R/resample.R | 31 +++- R/set_validate.R | 2 R/worker.R | 99 +++++++++++--- R/zzz.R | 9 - inst/testthat/helper_autotest.R | 28 +++- inst/testthat/helper_expectations.R | 18 +- man/CallbackResample.Rd |only man/ContextResample.Rd |only man/Learner.Rd | 65 ++++++++- man/LearnerClassif.Rd | 6 man/LearnerRegr.Rd | 14 ++ man/ResampleResult.Rd | 3 man/Resampling.Rd | 2 man/ResultData.Rd | 31 ++++ man/Task.Rd | 20 ++ man/as_measure.Rd | 20 +- man/as_resampling.Rd | 1 man/as_result_data.Rd | 4 man/as_task.Rd | 2 man/as_task_classif.Rd | 2 man/as_task_regr.Rd | 2 man/assert_empty_ellipsis.Rd |only man/assert_resample_callback.Rd |only man/benchmark.Rd | 7 - man/callback_resample.Rd |only man/mlr3-package.Rd | 5 man/mlr3.holdout_task.Rd |only man/mlr3.model_extractor.Rd |only man/mlr_assertions.Rd | 15 ++ man/mlr_learners_classif.debug.Rd | 3 man/mlr_learners_classif.featureless.Rd | 3 man/mlr_learners_classif.rpart.Rd | 1 man/mlr_learners_regr.debug.Rd | 1 man/mlr_learners_regr.featureless.Rd | 3 man/mlr_learners_regr.rpart.Rd | 1 man/mlr_measures_internal_valid_score.Rd | 2 man/reexports.Rd | 5 man/resample.Rd | 7 - tests/testthat/Rplots.pdf |only tests/testthat/teardown.R | 1 tests/testthat/test_CallbackResample.R |only tests/testthat/test_ContextEvaluation.R |only tests/testthat/test_DataBackendRbind.R | 6 tests/testthat/test_HotstartStack.R | 12 - tests/testthat/test_Learner.R | 154 +++++++++++++++++++--- tests/testthat/test_Measure.R | 4 tests/testthat/test_PredictionRegr.R | 4 tests/testthat/test_Task.R | 54 +++++-- tests/testthat/test_TaskClassif.R | 50 +++++++ tests/testthat/test_TaskRegr.R | 18 ++ tests/testthat/test_as_learner.R | 8 - tests/testthat/test_as_measure.R | 4 tests/testthat/test_as_resampling.R | 4 tests/testthat/test_as_task.R | 4 tests/testthat/test_assertions.R |only tests/testthat/test_auto_convert.R | 6 tests/testthat/test_benchmark.R | 33 +++- tests/testthat/test_convert_task.R | 4 tests/testthat/test_encapsulate.R | 4 tests/testthat/test_hashes.R | 4 tests/testthat/test_lgr.R | 4 tests/testthat/test_marshal.R | 2 tests/testthat/test_mlr_callbacks.R |only tests/testthat/test_resample.R | 6 tests/testthat/test_resultdata.R | 177 +++++++++++++++++++++++++ tests/testthat/test_warn_deprecated.R | 8 - 116 files changed, 1429 insertions(+), 419 deletions(-)
Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API,
enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R.
This package facilitates seamless integration with Google Gemini, allowing for advanced language processing,
text generation, and other AI-driven capabilities within the R environment.
For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] ,
Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>
Diff between gemini.R versions 0.8.0 dated 2025-02-05 and 0.9.2 dated 2025-03-12
gemini.R-0.8.0/gemini.R/R/Urrecipe.R |only gemini.R-0.8.0/gemini.R/README.md |only gemini.R-0.8.0/gemini.R/inst/quarto |only gemini.R-0.9.2/gemini.R/DESCRIPTION | 6 - gemini.R-0.9.2/gemini.R/MD5 | 38 +++--- gemini.R-0.9.2/gemini.R/NEWS.md | 23 +++- gemini.R-0.9.2/gemini.R/R/gemini.R | 105 +++++++++++++++---- gemini.R-0.9.2/gemini.R/R/gemini_audio.R | 115 ++++++++++++++++++--- gemini.R-0.9.2/gemini.R/R/gemini_chat.R | 44 +++++--- gemini.R-0.9.2/gemini.R/R/gemini_image.R | 102 ++++++++++++++++-- gemini.R-0.9.2/gemini.R/R/gen_docs.R | 14 +- gemini.R-0.9.2/gemini.R/R/gen_tests.R | 11 +- gemini.R-0.9.2/gemini.R/R/vertex.R | 21 ++- gemini.R-0.9.2/gemini.R/man/gemini.Rd | 25 +++- gemini.R-0.9.2/gemini.R/man/gemini.vertex.Rd | 27 ++++ gemini.R-0.9.2/gemini.R/man/gemini_audio.Rd | 31 ++++- gemini.R-0.9.2/gemini.R/man/gemini_audio.vertex.Rd | 22 +++- gemini.R-0.9.2/gemini.R/man/gemini_chat.Rd | 24 +++- gemini.R-0.9.2/gemini.R/man/gemini_image.Rd | 24 +++- gemini.R-0.9.2/gemini.R/man/gemini_image.vertex.Rd | 24 ++++ gemini.R-0.9.2/gemini.R/man/token.vertex.Rd | 13 ++ 21 files changed, 533 insertions(+), 136 deletions(-)
Title: Word and Document Vector Models
Description: Create dense vector representation of words and documents using 'quanteda'. Currently implements Word2vec (Mikolov et al., 2013) <doi:10.48550/arXiv.1310.4546> and Latent Semantic Analysis (Deerwester et al., 1990) <doi:10.1002/(SICI)1097-4571(199009)41:6%3C391::AID-ASI1%3E3.0.CO;2-9>.
Author: Kohei Watanabe [aut, cre, cph]
,
Jan Wijffels [aut] ,
BNOSAC [cph] ,
Max Fomichev [ctb, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordvector versions 0.2.0 dated 2025-01-07 and 0.3.0 dated 2025-03-12
DESCRIPTION | 6 +- MD5 | 33 +++++++------- NAMESPACE | 3 + NEWS.md | 6 ++ R/doc2vec.R | 56 +++++++++++++++++------- R/lsa.R | 17 ++++++- R/utils.R | 63 ++++++++++++++++++++++++++- inst/WORDLIST | 1 man/probability.Rd |only man/similarity.Rd | 4 - man/textmodel_doc2vec.Rd | 11 +++- src/word2vec/trainThread.cpp | 18 ++++--- src/word2vec/trainThread.hpp | 2 src/word2vec/word2vec.cpp | 6 +- src/word2vec/word2vec.hpp | 10 ++-- tests/testthat/test-lsa.R | 50 ++++++++-------------- tests/testthat/test-utils.R | 93 +++++++++++++++++++++++++++++++++++++++++ tests/testthat/test-word2vec.R | 54 +++++++++-------------- 18 files changed, 308 insertions(+), 125 deletions(-)
Title: Power Under Multiplicity Project
Description: Estimates power, minimum detectable effect size (MDES) and sample size requirements. The context is multilevel randomized experiments with multiple outcomes. The estimation takes into account the use of multiple testing procedures. Development of this package was supported by a grant from the Institute of Education Sciences (R305D170030). For a full package description, including a detailed technical appendix, see <doi:10.18637/jss.v108.i06>.
Author: Luke Miratrix [aut, cre] ,
Kristen Hunter [aut] ,
Zarni Htet [aut],
Kristin Porter [aut],
MDRC [cph],
Institute of Education Sciences [fnd]
Maintainer: Luke Miratrix <luke_miratrix@gse.harvard.edu>
Diff between PUMP versions 1.0.3 dated 2024-02-29 and 1.0.4 dated 2025-03-12
DESCRIPTION | 26 MD5 | 86 R/designs_and_models.R | 44 R/grid_functions.R | 4 R/optimize_power.R | 952 +++---- R/plots.R | 1194 +++++----- R/pump_power.R | 90 R/pumpgridresult.R | 30 R/pumpresult.R | 127 - R/simulation.R | 127 - R/util.R | 3 README.md | 39 build/partial.rdb |binary build/vignette.rds |binary inst/doc/pump_demo.R | 109 inst/doc/pump_demo.Rmd | 1 inst/doc/pump_demo.html | 88 inst/doc/pump_sample_demo.html | 12 inst/doc/pump_simulate.R | 110 inst/doc/pump_simulate.Rmd | 23 inst/doc/pump_simulate.html | 4 man/PUMP-package.Rd | 5 man/gen_sim_data.Rd | 12 man/parse_d_m.Rd | 16 man/plot.pumpgridresult.power.Rd | 8 man/print_context.Rd | 10 man/pump_mdes_grid.Rd | 8 man/pumpgridresult.Rd | 6 man/pumpresult.Rd | 13 tests/testthat/Rplots.pdf |binary tests/testthat/test-pumpgridresult.R | 15 tests/testthat/test-pumpresult.R | 23 tests/testthat/test-sim-gen.R | 5 tests/testthat/test-simulation.R | 1 tests/testthat/test-update_functions.R | 65 tests/testthat/test-validation_check.R | 19 vignettes/pump_demo.Rmd | 1 vignettes/pump_demo_files/figure-html/ICCgrid-compile-1.png |binary vignettes/pump_demo_files/figure-html/numzerogrid-compile-1.png |binary vignettes/pump_demo_files/figure-html/othercorrections-compile-1.png |binary vignettes/pump_demo_files/figure-html/plotsamplepowercurve-1.png |binary vignettes/pump_demo_files/figure-html/unnamed-chunk-5-1.png |binary vignettes/pump_simulate.Rmd | 23 vignettes/refs.bib | 2 44 files changed, 1815 insertions(+), 1486 deletions(-)
Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] ,
Riccardo Corradin [aut],
Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Diff between BayesChange versions 1.1.2 dated 2025-02-21 and 2.0.0 dated 2025-03-12
BayesChange-1.1.2/BayesChange/man/get_clust_VI.Rd |only BayesChange-1.1.2/BayesChange/man/psm.Rd |only BayesChange-1.1.2/BayesChange/tests/testthat/test-test-clust_cp_epi.R |only BayesChange-1.1.2/BayesChange/tests/testthat/test-test-clust_cp_multi.R |only BayesChange-1.1.2/BayesChange/tests/testthat/test-test-clust_cp_uni.R |only BayesChange-1.1.2/BayesChange/tests/testthat/test-test-detect_cp_multi.R |only BayesChange-1.1.2/BayesChange/tests/testthat/test-test-detect_cp_uni.R |only BayesChange-1.1.2/BayesChange/tests/testthat/test-test-get_clust_VI.R |only BayesChange-1.1.2/BayesChange/tests/testthat/test-test-psm.R |only BayesChange-2.0.0/BayesChange/DESCRIPTION | 8 BayesChange-2.0.0/BayesChange/MD5 | 60 - BayesChange-2.0.0/BayesChange/NAMESPACE | 14 BayesChange-2.0.0/BayesChange/NEWS.md | 4 BayesChange-2.0.0/BayesChange/R/ClustCpObj.R |only BayesChange-2.0.0/BayesChange/R/DetectCpObj.R |only BayesChange-2.0.0/BayesChange/R/RcppExports.R | 63 - BayesChange-2.0.0/BayesChange/R/clust_cp.R |only BayesChange-2.0.0/BayesChange/R/detect_cp.R |only BayesChange-2.0.0/BayesChange/README.md | 114 +- BayesChange-2.0.0/BayesChange/inst/doc/tutorial.R | 233 +++-- BayesChange-2.0.0/BayesChange/inst/doc/tutorial.Rmd | 127 +-- BayesChange-2.0.0/BayesChange/inst/doc/tutorial.html | 402 ++++++---- BayesChange-2.0.0/BayesChange/man/ClustCpObj.Rd |only BayesChange-2.0.0/BayesChange/man/DetectCpObj.Rd |only BayesChange-2.0.0/BayesChange/man/clust_cp.Rd |only BayesChange-2.0.0/BayesChange/man/clust_cp_epi.Rd | 4 BayesChange-2.0.0/BayesChange/man/clust_cp_multi.Rd | 9 BayesChange-2.0.0/BayesChange/man/clust_cp_uni.Rd | 11 BayesChange-2.0.0/BayesChange/man/detect_cp.Rd |only BayesChange-2.0.0/BayesChange/man/detect_cp_multi.Rd | 135 +-- BayesChange-2.0.0/BayesChange/man/detect_cp_uni.Rd | 121 +-- BayesChange-2.0.0/BayesChange/man/plot.ClustCpObj.Rd |only BayesChange-2.0.0/BayesChange/man/plot.DetectCpObj.Rd |only BayesChange-2.0.0/BayesChange/man/posterior_estimate.ClustCpObj.Rd |only BayesChange-2.0.0/BayesChange/man/posterior_estimate.DetectCpObj.Rd |only BayesChange-2.0.0/BayesChange/man/posterior_estimate.Rd |only BayesChange-2.0.0/BayesChange/man/print.ClustCpObj.Rd |only BayesChange-2.0.0/BayesChange/man/print.DetectCpObj.Rd |only BayesChange-2.0.0/BayesChange/man/summary.ClustCpObj.Rd |only BayesChange-2.0.0/BayesChange/man/summary.DetectCpObj.Rd |only BayesChange-2.0.0/BayesChange/src/RcppExports.cpp | 51 - BayesChange-2.0.0/BayesChange/src/code.cpp | 304 ++----- BayesChange-2.0.0/BayesChange/tests/testthat/test-test-clust_cp.R |only BayesChange-2.0.0/BayesChange/tests/testthat/test-test-detect_cp.R |only BayesChange-2.0.0/BayesChange/vignettes/tutorial.Rmd | 127 +-- 45 files changed, 952 insertions(+), 835 deletions(-)
Title: High Dimensional Categorical Data Visualization
Description: Easy visualization for datasets with more than two categorical variables and additional continuous variables. 'diceplot' is particularly useful for exploring complex categorical data in the context of pathway analysis across multiple conditions. For a detailed documentation please visit <https://dice-and-domino-plot.readthedocs.io/en/latest/>.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between diceplot versions 0.1.4 dated 2024-11-20 and 0.1.5 dated 2025-03-12
DESCRIPTION | 6 MD5 | 14 - NAMESPACE | 1 R/diceplot.R | 179 +++++++++++++++--------- R/dominoplot.R | 283 ++++++++++++++++++++++++++++----------- man/dice_plot.Rd | 52 ++++--- man/domino_plot.Rd | 40 +++-- tests/test_reordering_diceplot.R | 2 8 files changed, 400 insertions(+), 177 deletions(-)
Title: B-Spline Interpolation and Regression
Description: Build and use B-splines for interpolation and regression.
In case of regression, equality constraints as well as monotonicity
and/or positivity of B-spline weights can be imposed. Moreover,
knot positions can be on regular grid or be part of
optimized parameters too (in addition to the spline weights).
For this end, 'bspline' is able to calculate
Jacobian of basis vectors as function of knot positions. User is provided with
functions calculating spline values at arbitrary points. These
functions can be differentiated and integrated to obtain B-splines calculating
derivatives/integrals at any point. B-splines of this package can
simultaneously operate on a series of curves sharing the same set of
knots. 'bspline' is written with concern about computing
performance that's why the basis and Jacobian calculation is implemented in C++.
The rest is implemented in R but without notable impact on computing speed.
Author: Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between bspline versions 2.3.0 dated 2025-02-05 and 2.4.0 dated 2025-03-12
DESCRIPTION | 11 +- MD5 | 16 +-- NEWS.md | 12 ++ R/bspline.R | 188 ++++++++++++++++++++++++++++------------- inst/unitTests/runit.bspline.R | 8 - man/bspline.Rd | 4 man/iknots.Rd | 17 ++- man/par2bsp.Rd | 9 - man/smbsp.Rd | 8 + 9 files changed, 186 insertions(+), 87 deletions(-)
Title: R Interface to NLopt
Description: Solve optimization problems using an R interface to NLopt. NLopt is a
free/open-source library for nonlinear optimization, providing a common
interface for a number of different free optimization routines available
online as well as original implementations of various other algorithms.
See <https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/> for more
information on the available algorithms. Building from included sources
requires 'CMake'. On Linux and 'macOS', if a suitable system build of
NLopt (2.7.0 or later) is found, it is used; otherwise, it is built
from included sources via 'CMake'. On Windows, NLopt is obtained through
'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for
'R >= 4.2.0'.
Author: Jelmer Ypma [aut],
Steven G. Johnson [aut] ,
Aymeric Stamm [ctb, cre] ,
Hans W. Borchers [ctb],
Dirk Eddelbuettel [ctb],
Brian Ripley [ctb] ,
Kurt Hornik [ctb] ,
Julien Chiquet [ctb],
Avraham Adler [ctb] ,
Xiongtao Dai [ctb],
Jeroen Ooms [ctb],
Tomas [...truncated...]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between nloptr versions 2.1.1 dated 2024-06-25 and 2.2.0 dated 2025-03-12
nloptr-2.1.1/nloptr/inst/include/nlopt.f |only nloptr-2.1.1/nloptr/inst/include/nlopt.h |only nloptr-2.1.1/nloptr/inst/include/nlopt.hpp |only nloptr-2.1.1/nloptr/inst/tinytest/test-banana-global.R |only nloptr-2.1.1/nloptr/inst/tinytest/test-banana.R |only nloptr-2.1.1/nloptr/src/scripts/cmake_config.sh |only nloptr-2.2.0/nloptr/DESCRIPTION | 18 nloptr-2.2.0/nloptr/MD5 | 46 nloptr-2.2.0/nloptr/NEWS.md | 18 nloptr-2.2.0/nloptr/R/is.nloptr.R | 2 nloptr-2.2.0/nloptr/R/nloptr.get.default.options.R | 8 nloptr-2.2.0/nloptr/R/zzz.R | 2 nloptr-2.2.0/nloptr/README.md | 36 nloptr-2.2.0/nloptr/build/vignette.rds |binary nloptr-2.2.0/nloptr/configure | 630 ++-- nloptr-2.2.0/nloptr/configure.ac | 25 nloptr-2.2.0/nloptr/inst/doc/nloptr.R | 12 nloptr-2.2.0/nloptr/inst/doc/nloptr.html | 11 nloptr-2.2.0/nloptr/inst/tinytest/test-Rosenbrock-banana.R |only nloptr-2.2.0/nloptr/inst/tinytest/test-nloptr.R | 58 nloptr-2.2.0/nloptr/inst/tinytest/test-wrapper-global.R | 106 nloptr-2.2.0/nloptr/src/Makevars.in | 2 nloptr-2.2.0/nloptr/src/init_nloptr.c | 11 nloptr-2.2.0/nloptr/src/nloptr.c | 1803 ++++++------- nloptr-2.2.0/nloptr/src/nloptr.h | 2 nloptr-2.2.0/nloptr/src/scripts/nlopt_cleanup.sh | 1 nloptr-2.2.0/nloptr/tools/cmake_call.sh | 9 nloptr-2.2.0/nloptr/tools/cmake_config.sh |only 28 files changed, 1488 insertions(+), 1312 deletions(-)
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene
sets typically used with the 'Gene Set Enrichment Analysis' (GSEA)
software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>,
Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al.
2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package
includes the human genes as listed in MSigDB as well as the
corresponding symbols and IDs for frequently studied model organisms
such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 7.5.1 dated 2022-03-30 and 10.0.0 dated 2025-03-12
msigdbr-10.0.0/msigdbr/DESCRIPTION | 28 ++--- msigdbr-10.0.0/msigdbr/LICENSE | 2 msigdbr-10.0.0/msigdbr/MD5 | 44 +++++--- msigdbr-10.0.0/msigdbr/NAMESPACE | 13 +- msigdbr-10.0.0/msigdbr/NEWS.md | 18 +++ msigdbr-10.0.0/msigdbr/R/msigdbr-check-data.R |only msigdbr-10.0.0/msigdbr/R/msigdbr-collections.R |only msigdbr-10.0.0/msigdbr/R/msigdbr-package.R |only msigdbr-10.0.0/msigdbr/R/msigdbr-species.R |only msigdbr-10.0.0/msigdbr/R/msigdbr.R |only msigdbr-10.0.0/msigdbr/R/sysdata.rda |binary msigdbr-10.0.0/msigdbr/R/zzz.R |only msigdbr-10.0.0/msigdbr/README.md | 28 +++-- msigdbr-10.0.0/msigdbr/build/partial.rdb |only msigdbr-10.0.0/msigdbr/man/figures |only msigdbr-10.0.0/msigdbr/man/msigdbr-package.Rd |only msigdbr-10.0.0/msigdbr/man/msigdbr.Rd | 49 ++++++---- msigdbr-10.0.0/msigdbr/man/msigdbr_check_data.Rd |only msigdbr-10.0.0/msigdbr/man/msigdbr_collections.Rd | 10 +- msigdbr-10.0.0/msigdbr/man/msigdbr_species.Rd | 5 - msigdbr-10.0.0/msigdbr/tests/testthat/test-msigdbr-collections.R |only msigdbr-10.0.0/msigdbr/tests/testthat/test-msigdbr-species.R |only msigdbr-10.0.0/msigdbr/tests/testthat/test-msigdbr.R |only msigdbr-7.5.1/msigdbr/R/functions.R |only msigdbr-7.5.1/msigdbr/R/utils-pipe.R |only msigdbr-7.5.1/msigdbr/build/vignette.rds |only msigdbr-7.5.1/msigdbr/inst |only msigdbr-7.5.1/msigdbr/man/msigdbr_show_species.Rd |only msigdbr-7.5.1/msigdbr/man/pipe.Rd |only msigdbr-7.5.1/msigdbr/tests/testthat/test-functions.R |only msigdbr-7.5.1/msigdbr/vignettes |only 31 files changed, 122 insertions(+), 75 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-17 0.1.6.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-18 2.3.0
2023-10-30 2.2.0
2023-05-30 2.1.3
2023-03-08 2.1.2
2023-01-27 2.1.1
2022-04-05 2.1.0
2022-03-05 2.0.0
2022-01-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-22 1.1.0
2023-10-26 1.0.0
Title: Spatial Empirical Dynamic Modeling
Description: Inferring causal associations in cross-sectional earth system data through empirical dynamic modeling (EDM), with extensions to convergent cross mapping from Sugihara et al. (2012) <doi:10.1126/science.1227079>, partial cross mapping as outlined in Leng et al. (2020) <doi:10.1038/s41467-020-16238-0>, and cross mapping cardinality as described in Tao et al. (2023)<doi:10.1016/j.fmre.2023.01.007>.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between spEDM versions 1.4 dated 2025-02-10 and 1.5 dated 2025-03-12
spEDM-1.4/spEDM/src/IntersectionCardinality.cpp |only spEDM-1.4/spEDM/src/IntersectionCardinality.h |only spEDM-1.5/spEDM/DESCRIPTION | 6 spEDM-1.5/spEDM/MD5 | 118 +-- spEDM-1.5/spEDM/NAMESPACE | 3 spEDM-1.5/spEDM/NEWS.md | 168 ++-- spEDM-1.5/spEDM/R/RcppExports.R | 108 ++ spEDM-1.5/spEDM/R/embedded.R | 11 spEDM-1.5/spEDM/R/formatoutput.R | 73 + spEDM-1.5/spEDM/R/gccm.R | 51 - spEDM-1.5/spEDM/R/multiview.R |only spEDM-1.5/spEDM/R/simplex.R | 94 +- spEDM-1.5/spEDM/R/smap.R | 36 spEDM-1.5/spEDM/R/variable_check_prepare.R | 105 ++ spEDM-1.5/spEDM/R/xmapdf.R | 38 spEDM-1.5/spEDM/build/vignette.rds |binary spEDM-1.5/spEDM/inst/doc/GCCM.Rmd | 678 +++++++---------- spEDM-1.5/spEDM/inst/doc/GCCM.html | 565 +++++--------- spEDM-1.5/spEDM/man/embedded.Rd | 10 spEDM-1.5/spEDM/man/figures/gccm/fig1-1.png |binary spEDM-1.5/spEDM/man/figures/gccm/fig2-1.png |binary spEDM-1.5/spEDM/man/figures/gccm/fig3-1.png |binary spEDM-1.5/spEDM/man/figures/logo.png |binary spEDM-1.5/spEDM/man/gccm.Rd | 24 spEDM-1.5/spEDM/man/multiview.Rd |only spEDM-1.5/spEDM/man/simplex.Rd | 38 spEDM-1.5/spEDM/man/smap.Rd | 40 - spEDM-1.5/spEDM/src/CppGridUtils.cpp | 389 ++++++++- spEDM-1.5/spEDM/src/CppGridUtils.h | 46 - spEDM-1.5/spEDM/src/CppLatticeUtils.cpp | 720 ++++++++++++------ spEDM-1.5/spEDM/src/CppLatticeUtils.h | 46 - spEDM-1.5/spEDM/src/CppStats.cpp | 489 ++++++++++-- spEDM-1.5/spEDM/src/CppStats.h | 50 + spEDM-1.5/spEDM/src/CrossMappingCardinality.cpp |only spEDM-1.5/spEDM/src/CrossMappingCardinality.h |only spEDM-1.5/spEDM/src/DeLongPlacements.cpp |only spEDM-1.5/spEDM/src/DeLongPlacements.h |only spEDM-1.5/spEDM/src/Forecast4Grid.cpp | 60 + spEDM-1.5/spEDM/src/Forecast4Grid.h | 12 spEDM-1.5/spEDM/src/Forecast4Lattice.cpp | 60 + spEDM-1.5/spEDM/src/Forecast4Lattice.h | 12 spEDM-1.5/spEDM/src/ForecastExp.cpp | 100 ++ spEDM-1.5/spEDM/src/GCCM4Grid.cpp | 719 ++++++++++++++++-- spEDM-1.5/spEDM/src/GCCM4Grid.h | 144 +++ spEDM-1.5/spEDM/src/GCCM4Lattice.cpp | 249 ++++-- spEDM-1.5/spEDM/src/GCCM4Lattice.h | 12 spEDM-1.5/spEDM/src/GridExp.cpp | 647 +++++++++++++--- spEDM-1.5/spEDM/src/HelperFuns.cpp | 111 ++ spEDM-1.5/spEDM/src/HelperFuns.h | 36 spEDM-1.5/spEDM/src/LatticeExp.cpp | 287 ++++++- spEDM-1.5/spEDM/src/MultiViewEmbedding.cpp |only spEDM-1.5/spEDM/src/MultiViewEmbedding.h |only spEDM-1.5/spEDM/src/RcppExports.cpp | 383 +++++++-- spEDM-1.5/spEDM/src/SCPCM4Grid.cpp | 937 ++++++++++++++++++++---- spEDM-1.5/spEDM/src/SCPCM4Grid.h | 228 +++++ spEDM-1.5/spEDM/src/SCPCM4Lattice.cpp | 401 +++++----- spEDM-1.5/spEDM/src/SCPCM4Lattice.h | 89 ++ spEDM-1.5/spEDM/src/SMap.cpp | 64 + spEDM-1.5/spEDM/src/SMap.h | 6 spEDM-1.5/spEDM/src/SimplexProjection.cpp | 64 + spEDM-1.5/spEDM/src/SimplexProjection.h | 6 spEDM-1.5/spEDM/src/StatsExp.cpp | 178 ++++ spEDM-1.5/spEDM/src/spEDMDataStruct.h | 18 spEDM-1.5/spEDM/vignettes/GCCM.Rmd | 678 +++++++---------- spEDM-1.5/spEDM/vignettes/GCCM.Rmd.orig | 132 +-- 65 files changed, 6711 insertions(+), 2828 deletions(-)