Title: Unidimensional Item Response Theory Modeling
Description: Fit unidimensional item response theory (IRT) models to a mixture
of dichotomous and polytomous data, calibrate online item parameters
(i.e., pretest and operational items), estimate examinees' abilities,
and examine the IRT model-data fit on item-level in different ways
as well as provide useful functions related to IRT analyses such as
IRT model-data fit evaluation and differential item functioning analysis.
The bring.flexmirt() and write.flexmirt() functions were written by modifying
the read.flexmirt() function (Pritikin & Falk (2022) <doi:10.1177/0146621620929431>).
The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog()
and read.parscale() functions, respectively (Weeks (2010) <doi:10.18637/jss.v035.i12>).
The bisection() function was written by modifying the bisection() function
(Howard (2017, ISBN:9780367657918)). The code of the inverse test characteristic curve
scoring in the est_score() function was written by modifying the [...truncated...]
Author: Hwanggyu Lim [aut, cre],
Craig S. Wells [ctb],
James Howard [ctb],
Joshua Pritikin [ctb],
Jonathan P Weeks [ctb],
Jorge Gonzalez [ctb],
David Magis [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Diff between irtQ versions 0.2.0 dated 2023-07-06 and 0.2.1 dated 2024-08-24
DESCRIPTION | 15 MD5 | 189 +++--- NAMESPACE | 14 NEWS.md | 18 R/EM.R | 321 ++++++----- R/bisection.R | 22 R/breakdown.R | 13 R/bring_output.R | 490 ++++++++--------- R/cac_lee.R | 167 +++-- R/cac_rud.R | 150 +++-- R/catsib.R | 312 +++++------ R/chisq_stat.R | 22 R/collapse_ftable.R | 31 - R/confirm_df.R | 44 - R/covirt.R | 117 ++-- R/eap_sum.R | 49 - R/equation_scocat.R | 103 +-- R/est_irt.R | 1017 +++++++++++++++++++---------------- R/est_item.R | 382 +++++++------ R/est_mg.R | 1415 ++++++++++++++++++++++++++++---------------------- R/est_score.R | 436 +++++++-------- R/estimation.R | 528 ++++++++++-------- R/expFreq.R | 37 - R/gen_weight.R | 42 - R/getirt.R | 178 +++--- R/gradient.R | 509 ++++++++--------- R/grdif.R | 1180 ++++++++++++++++++++++++----------------- R/hessian.R | 646 ++++++++++++---------- R/info.R | 246 +++----- R/info_xpd.R | 168 +++-- R/inv_tcc.R | 221 ++++++- R/irtQ-package.R | 23 R/irtfit.R | 336 ++++++----- R/irtmodel.R | 50 - R/likelihood.R | 38 - R/ll_score.R | 63 -- R/llike_score.R | 87 +-- R/loglike_item.R | 197 +++--- R/logprior_deriv.R | 120 ++-- R/lubound.R | 45 - R/lwrc.R | 107 +-- R/parloc.R | 49 - R/pcd2.R |only R/plot_info.R | 136 ++-- R/plot_irtfit.R | 295 +++++----- R/plot_traceline.R | 174 +++--- R/posterior.R | 16 R/print.R | 483 +++++++++-------- R/rdif.R | 717 +++++++++++++------------ R/reval_mst.R |only R/run_flexmirt.R | 60 -- R/scale_prior.R | 15 R/set_startval.R | 38 - R/shape_df.R | 165 +++-- R/simMST.R |only R/simdat.R | 65 +- R/summary.R | 49 - R/sx2_fit.R | 481 +++++++++------- R/traceline.R | 228 ++++---- R/util.R | 13 R/write_flexmirt.R | 120 ++-- README.md | 445 +++++++-------- build/partial.rdb |binary data/simMST.rda |only man/bind.fill.Rd | 10 man/bisection.Rd | 8 man/bring.flexmirt.Rd | 4 man/cac_lee.Rd | 29 - man/cac_rud.Rd | 22 man/catsib.Rd | 31 - man/covirt.Rd | 4 man/drm.Rd | 6 man/est_irt.Rd | 200 ++++--- man/est_item.Rd | 31 - man/est_mg.Rd | 118 ++-- man/est_score.Rd | 29 - man/gen.weight.Rd | 6 man/getirt.Rd | 16 man/grdif.Rd | 51 - man/info.Rd | 38 - man/irtQ-package.Rd | 898 ++++++++++++++++--------------- man/irtfit.Rd | 37 - man/llike_score.Rd | 3 man/lwrc.Rd | 200 +++---- man/pcd2.Rd |only man/plot.info.Rd | 12 man/plot.irtfit.Rd | 25 man/plot.traceline.Rd | 22 man/prm.Rd | 5 man/rdif.Rd | 698 ++++++++++++------------ man/reval_mst.Rd |only man/run_flexmirt.Rd | 11 man/shape_df.Rd | 25 man/simMST.Rd |only man/simdat.Rd | 18 man/summary.Rd | 10 man/sx2_fit.Rd | 22 man/traceline.Rd | 12 man/write.flexmirt.Rd | 15 99 files changed, 8682 insertions(+), 7631 deletions(-)
Title: Sparse Group Lasso
Description: Efficient implementation of sparse group lasso with optional
bound constraints on the coefficients; see
<doi:10.18637/jss.v110.i06>. It supports the use of a sparse design
matrix as well as returning coefficient estimates in a sparse matrix.
Furthermore, it correctly calculates the degrees of freedom to allow
for information criteria rather than cross-validation with very large
data. Finally, the interface to compiled code avoids unnecessary
copies and allows for the use of long integers.
Author: Daniel J. McDonald [aut, cre],
Xiaoxuan Liang [aut],
Anibal Solon Heinsfeld [aut],
Aaron Cohen [aut],
Yi Yang [ctb],
Hui Zou [ctb],
Jerome Friedman [ctb],
Trevor Hastie [ctb],
Rob Tibshirani [ctb],
Balasubramanian Narasimhan [ctb],
Kenneth Tay [ctb], [...truncated...]
Maintainer: Daniel J. McDonald <daniel@stat.ubc.ca>
Diff between sparsegl versions 1.1.0 dated 2024-06-26 and 1.1.1 dated 2024-08-24
DESCRIPTION | 24 ++++++------- MD5 | 35 +++++++++++-------- NEWS.md | 4 ++ R/cv.R | 6 +++ R/estimate_risk.R | 11 +++++- R/sparsegl-package.R | 5 ++ R/sparsegl.R | 6 +++ README.md | 23 +++++++++++- inst/CITATION |only inst/doc/sparsegl.R | 3 + inst/doc/sparsegl.Rmd | 29 +++++++++++++--- inst/doc/sparsegl.html | 87 +++++++++++++++++++++++++++++++++--------------- inst/logo |only man/cv.sparsegl.Rd | 7 +++ man/estimate_risk.Rd | 6 +++ man/figures/logo.png |only man/sparsegl-package.Rd | 14 ++++++- man/sparsegl.Rd | 7 +++ vignettes/sparsegl.Rmd | 29 +++++++++++++--- 19 files changed, 226 insertions(+), 70 deletions(-)
Title: Package for Environmental Statistics, Including US EPA Guidance
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4,
<doi:10.1007/978-1-4614-8456-1>).
Author: Steven P. Millard [aut],
Alexander Kowarik [ctb, cre]
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between EnvStats versions 2.8.1 dated 2023-08-22 and 3.0.0 dated 2024-08-24
DESCRIPTION | 15 MD5 | 57 +- NAMESPACE | 3 NEWS | 49 + R/egammaAltCensored.mle.R | 19 R/elnormAltCensored.R | 14 R/enpar.R |only R/enpar.bootstrap.ci.R |only R/enpar.jackknife.R |only R/enparCensored.R | 200 ++++--- R/enparCensored.bootstrap.ci.R | 15 R/enparCensored.jackknife.R | 4 R/enparCensored.km.R | 76 +- R/pred.int.norm.k.of.m.on.r.K.R | 9 R/predIntNormSimultaneous.R | 29 - R/predIntNormSimultaneousK.R | 7 R/qnormMix.R | 51 + R/stripChart.default.R | 3 build/partial.rdb |binary data/BJC.2000.df.rda |only data/Beal.2010.Pb.df.rda |only data/ProUCL.5.2.TRS.df.rda |only inst/tinytest/test_enparCensored.R |only inst/tinytest/test_qnormMix.R | 6 man/BJC.2000.df.Rd |only man/Beal.2010.Pb.df.Rd |only man/Olympic.NH4.df.Rd | 2 man/ProUCL.5.2.TRS.df.Rd |only man/enpar.Rd |only man/enparCensored.Rd | 535 +++++++++++++------ man/eqpois.Rd | 494 ++++++++--------- man/plotPredIntLnormAltSimultaneousTestPowerCurve.Rd | 2 man/predIntLnormSimultaneous.Rd | 5 man/predIntNormSimultaneous.Rd | 220 +++++++ man/predIntNormSimultaneousK.Rd | 107 ++- 35 files changed, 1275 insertions(+), 647 deletions(-)
Title: Irish Grid Reference Utilities
Description: Convert between Irish grid references and Irish Grid coordinates. Irish grid
references can also be converted to or from an 'sf' object in any coordinate reference
system. Precisions from 1 m to 100 km including 2 km (tetrads) are supported, as are
datasets with mixed precision. Conversion to 'sf' polygons is precision-aware.
Author: John Kennedy [aut, cre, cph] ,
Digital Nature [fnd]
Maintainer: John Kennedy <john@digitalnature.ie>
Diff between igr versions 0.1.1 dated 2024-07-27 and 0.2.0 dated 2024-08-24
DESCRIPTION | 12 MD5 | 52 +- NEWS.md | 7 R/ig_to_igr.R | 43 +- R/igr_is_valid.R | 21 + R/igr_to_ig.R | 57 ++- R/st_igr_as_sf.R | 26 + R/st_irishgridrefs.R | 3 R/utils.R | 31 + README.md | 88 ++-- inst/doc/igr.R | 71 +++ inst/doc/igr.Rmd | 86 +++- inst/doc/igr.html | 462 ++++++++++++++------------ man/figures/README-example-igr-points-1.png |binary man/figures/README-example-igr-polygons-1.png |binary man/ig_to_igr.Rd | 120 +++--- man/igr-package.Rd | 2 man/igr_is_valid.Rd | 72 ++-- man/igr_to_ig.Rd | 97 +++-- man/st_igr_as_sf.Rd | 159 ++++---- man/st_irishgridrefs.Rd | 114 +++--- tests/testthat/test-ig_to_igr.R | 27 + tests/testthat/test-igr_is_valid.R | 19 + tests/testthat/test-igr_to_ig.R | 33 + tests/testthat/test-st_igr_as_sf.R | 36 +- tests/testthat/test-st_irishgridrefs.R | 17 vignettes/igr.Rmd | 86 +++- 27 files changed, 1096 insertions(+), 645 deletions(-)
Title: Constrained, Covariance-Matching Constrained and Universal Point
or Block Kriging
Description: Provides functions for efficient computation of non-linear spatial predictions with local change of support (Hofer, C. and Papritz, A. (2011) "constrainedKriging: An R-package for customary, constrained and covariance-matching constrained point or block kriging" <doi:10.1016/j.cageo.2011.02.009>). This package supplies functions for two-dimensional spatial interpolation by constrained (Cressie, N. (1993) "Aggregation in geostatistical problems" <doi:10.1007/978-94-011-1739-5_3>), covariance-matching constrained (Aldworth, J. and Cressie, N. (2003) "Prediction of nonlinear spatial functionals" <doi:10.1016/S0378-3758(02)00321-X>) and universal (external drift) Kriging for points or blocks of any shape from data with a non-stationary mean function and an isotropic weakly stationary covariance function. The linear spatial interpolation methods, constrained and covariance-matching constrained Kriging, provide approximately unbiased prediction for non-linear target value [...truncated...]
Author: Christoph Hofer [aut],
Andreas Papritz [ctb, cre]
Maintainer: Andreas Papritz <papritz@retired.ethz.ch>
Diff between constrainedKriging versions 0.2-7 dated 2023-12-19 and 0.2-8 dated 2024-08-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary inst/ChangeLog.txt | 9 ++++++++- man/internal.Rd | 8 ++++---- src/covariancefunctions.h | 3 ++- 6 files changed, 23 insertions(+), 15 deletions(-)
More information about constrainedKriging at CRAN
Permanent link
Title: High-Dimensional Mediation Analysis
Description: Allows to estimate and test high-dimensional mediation effects based on advanced mediator screening and penalized regression techniques. Methods used in the package refer to Zhang H, Zheng Y, Zhang Z, Gao T, Joyce B, Yoon G, Zhang W, Schwartz J, Just A, Colicino E, Vokonas P, Zhao L, Lv J, Baccarelli A, Hou L, Liu L. Estimating and Testing High-dimensional Mediation Effects in Epigenetic Studies. Bioinformatics. (2016) <doi:10.1093/bioinformatics/btw351>. PMID: 27357171.
Author: Yinan Zheng [aut, cre] ,
Haixiang Zhang [aut],
Lifang Hou [aut],
Lei Liu [aut, cph]
Maintainer: Yinan Zheng <y-zheng@northwestern.edu>
Diff between HIMA versions 2.2.1 dated 2023-09-10 and 2.2.2 dated 2024-08-24
DESCRIPTION | 16 - MD5 | 52 ++-- NAMESPACE | 1 R/HIMA-package.R | 36 +- R/dblassoHIMA.R | 106 +++++--- R/eHIMA.R |only R/hima.R | 264 ++++++++++---------- R/hima2.R | 419 ++++++++++++++++++++------------- R/himaDat.R | 89 +++---- R/microHIMA.R | 96 ++++--- R/onAttach.R | 37 +- R/qHIMA.R | 140 ++++++----- R/survHIMA.R | 103 ++++---- R/utils.R | 146 ++++++++--- README.md | 34 +- data/himaDat.rda |binary inst/CITATION | 64 ++++- inst/NEWS | 10 inst/scripts/Example_data_generation.R | 13 - man/HIMA-package.Rd | 32 +- man/dblassoHIMA.Rd | 191 +++++++-------- man/eHIMA.Rd |only man/hima.Rd | 28 +- man/hima2.Rd | 103 +++++--- man/himaDat.Rd | 135 +++++----- man/microHIMA.Rd | 41 +-- man/qHIMA.Rd | 170 ++++++------- man/survHIMA.Rd | 37 +- 28 files changed, 1383 insertions(+), 980 deletions(-)
Title: Hierarchical and Variation Partitioning for Canonical Analysis
Description: This function conducts variation partitioning and hierarchical partitioning to calculate the unique, shared (referred as to "common") and individual contributions of each predictor (or matrix) towards explained variation (R-square and adjusted R-square) on canonical analysis (RDA,CCA and db-RDA), applying the algorithm of Lai J.,Zou Y., Zhang J.,Peres-Neto P.(2022) Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package.Methods in Ecology and Evolution,13: 782-788 <DOI:10.1111/2041-210X.13800>.
Author: Jiangshan Lai [aut, cre] ,
Kim Nimon [aut],
Yao Liu [aut],
Pedro Peres-Neto [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between rdacca.hp versions 1.1-0 dated 2023-05-23 and 1.1-1 dated 2024-08-24
DESCRIPTION | 15 ++++++++++----- MD5 | 10 +++++----- R/plot.rdaccahp.r | 4 ++-- R/rdacca.hp.r | 5 ++--- man/plot.rdaccahp.Rd | 2 -- man/rdacca.hp.Rd | 6 +----- 6 files changed, 20 insertions(+), 22 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.5-1 dated 2024-04-16 and 1.5-2 dated 2024-08-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/R.R | 12 +++++++++++- R/mltoptim.R | 24 +++++++++++++++++++++--- build/partial.rdb |binary inst/NEWS.Rd | 14 ++++++++++++++ man/mltoptim.Rd | 2 +- 7 files changed, 57 insertions(+), 15 deletions(-)
Title: Toolbox for Integrative Pathomics Analysis
Description: Processing and analysis of pathomics, omics and other medical datasets.
'tRigon' serves as a toolbox for descriptive and statistical analysis, correlations,
plotting and many other methods for exploratory analysis of high-dimensional datasets.
Author: David Hoelscher [aut, cre] ,
Roman Buelow [ctb] ,
Michael Goedertier [ctb]
Maintainer: David Hoelscher <dhoelscher@ukaachen.de>
Diff between tRigon versions 0.3.2 dated 2023-10-30 and 0.3.3 dated 2024-08-24
tRigon-0.3.2/tRigon/README.md |only tRigon-0.3.3/tRigon/DESCRIPTION | 11 tRigon-0.3.3/tRigon/MD5 | 15 tRigon-0.3.3/tRigon/NEWS.md | 4 tRigon-0.3.3/tRigon/build/vignette.rds |binary tRigon-0.3.3/tRigon/inst/app/contact.Rmd | 2 tRigon-0.3.3/tRigon/inst/app/ui.R | 2 tRigon-0.3.3/tRigon/inst/doc/tRigon.R | 26 tRigon-0.3.3/tRigon/inst/doc/tRigon.html | 1068 +++++++++++++++---------------- 9 files changed, 566 insertions(+), 562 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, following Marcon, Traissac, Puech, and Lang (2015) <doi:10.18637/jss.v067.c03>.
Includes classical functions (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M).
Relies on 'spatstat' for some core calculation.
Author: Eric Marcon [aut, cre] ,
Gabriel Lang [aut] ,
Stephane Traissac [aut] ,
Florence Puech [aut]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between dbmss versions 2.9-0 dated 2023-12-11 and 2.9-2 dated 2024-08-24
DESCRIPTION | 11 ++-- MD5 | 94 ++++++++++++++++++++-------------------- NEWS.md | 8 +++ R/KinhomEnvelope.R | 23 +++++++-- README.md | 6 +- build/vignette.rds |binary inst/doc/dbmss.R | 3 + inst/doc/dbmss.Rmd | 3 + inst/doc/dbmss.html | 8 +-- man/DEnvelope.Rd | 2 man/Dhat.Rd | 6 +- man/FillEnvelope.Rd | 6 +- man/GlobalEnvelope.Rd | 2 man/GoFtest.Rd | 2 man/KEnvelope.Rd | 2 man/KdEnvelope.Rd | 2 man/Kdhat.Rd | 2 man/Khat.Rd | 4 - man/KinhomEnvelope.Rd | 4 - man/Kinhomhat.Rd | 10 ++-- man/KmmEnvelope.Rd | 2 man/Kmmhat.Rd | 6 +- man/Ktest.Rd | 2 man/LEnvelope.Rd | 2 man/Lhat.Rd | 2 man/LmmEnvelope.Rd | 2 man/Lmmhat.Rd | 2 man/MEnvelope.Rd | 2 man/Mhat.Rd | 2 man/Smooth.wmppp.Rd | 8 +-- man/as.Dtable.Rd | 2 man/as.wmppp.Rd | 6 +- man/autoplot.Rd | 2 man/dbmssEnvelope.Rd | 2 man/envelope.Dtable.Rd | 4 - man/gEnvelope.Rd | 2 man/generic.spatstat.Rd | 10 ++-- man/ghat.Rd | 4 - man/m_Envelope.Rd | 2 man/m_hat.Rd | 2 man/paracou16.Rd | 2 man/print.dbmssEnvelope.Rd | 2 man/rPopulationIndependenceK.Rd | 2 man/rRandomPositionK.Rd | 4 - man/summary.dbmssEnvelope.Rd | 2 man/wmppp.Rd | 2 man/wmppp.object.Rd | 6 +- vignettes/dbmss.Rmd | 3 + 48 files changed, 159 insertions(+), 128 deletions(-)
Title: Group Factor Analysis
Description: Several group factor analysis algorithms are implemented, including Canonical Correlation-based Estimation by Choi et al. (2021) <doi:10.1016/j.jeconom.2021.09.008> , Generalised Canonical Correlation Estimation by Lin and Shin (2023) <doi:10.2139/ssrn.4295429>, Circularly Projected Estimation by Chen (2022) <doi:10.1080/07350015.2022.2051520>, and Aggregated projection method.
Author: Jiaqi Hu [cre, aut],
Ting Li [aut],
Xueqin Wang [aut]
Maintainer: Jiaqi Hu <hujiaqi@mail.ustc.edu.cn>
Diff between GrFA versions 0.1.1 dated 2024-02-01 and 0.2 dated 2024-08-24
DESCRIPTION | 12 ++-- MD5 | 28 +++++------ R/APM.R | 131 ++++++++++++++++++++++++++++-------------------------- R/CCA.R | 88 +++++++++++++++++++----------------- R/CPE.R | 79 ++++++++++++++++---------------- R/GCC.R | 87 ++++++++++++++++++----------------- R/auxiliary.R | 16 ++---- R/gendata.R | 7 +- man/APM.Rd | 24 ++++----- man/CCA.Rd | 11 ++-- man/CP.Rd | 7 +- man/FA.Rd | 4 - man/GCC.Rd | 9 ++- man/TraceRatio.Rd | 8 --- man/gendata.Rd | 4 - 15 files changed, 264 insertions(+), 251 deletions(-)
Title: Tools to Study Bone Compactness
Description: Bone Profiler is a scientific method and a software used to model
bone section for paleontological and ecological studies. See Girondot and Laurin
(2003) <https://www.researchgate.net/publication/280021178_Bone_profiler_A_tool_to_quantify_model_and_statistically_compare_bone-section_compactness_profiles>
and Gônet, Laurin and Girondot (2022) <https://palaeo-electronica.org/content/2022/3590-bone-section-compactness-model>.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between BoneProfileR versions 2.5 dated 2024-04-10 and 3.1 dated 2024-08-24
DESCRIPTION | 24 +- MD5 | 38 ++-- NEWS | 11 + R/BP_ChooseForeground.R | 4 R/BP_DetectCenters.R | 18 + R/BP_EstimateCompactness.R | 68 +++++-- R/BP_FitMLRadialCompactness.R | 42 +++- R/BP_LnLCompactness.R | 2 R/BP_PlotBone.R | 18 + R/BP_contour.R | 358 ++++++++++++++++++++++----------------- R/BP_threshold.R | 20 +- R/BoneProfileR-package.R | 9 R/onAttach.R | 30 +-- data/Erinaceus_europaeus.rda |binary inst/shiny/ui.R | 2 man/BP_DetectCenters.Rd | 15 + man/BP_EstimateCompactness.Rd | 10 - man/BP_FitMLRadialCompactness.Rd | 8 man/BoneProfileR-package.Rd | 9 man/plot.BoneProfileR.Rd | 12 - 20 files changed, 440 insertions(+), 258 deletions(-)
Title: 'Open Scoring' API Client
Description: Creativity research involves the need to score open-ended problems.
Usually done by humans, automatic scoring using AI becomes more
and more accurate. This package provides a simple interface to
the 'Open Scoring' API <https://openscoring.du.edu/docs>, leading creativity scoring technology by
Organiscak et al. (2023) <doi:10.1016/j.tsc.2023.101356>. With it,
you can score your own data directly from an R script.
Author: Jakub Jedrusiak [aut, cre, cph]
,
Peter Organisciak [ctb] ,
Selcuk Acar [ctb] ,
Denis Dumas [ctb] ,
Pier-Luc de Chantal [ctb] ,
Kelly Berthiaume [ctb]
Maintainer: Jakub Jedrusiak <kuba23031999@gmail.com>
Diff between openscoring versions 1.0.3 dated 2024-08-21 and 1.0.4 dated 2024-08-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/oscai.R | 32 +++++++++++++++++--------------- man/oscai.Rd | 15 +++++++++------ 5 files changed, 39 insertions(+), 28 deletions(-)
Title: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data
Description: A protocol that facilitates the processing and analysis of Hydrogen-Deuterium Exchange Mass Spectrometry data using p-value statistics and Critical Interval analysis.
It provides a pipeline for analyzing data from 'HDXExaminer' (Sierra Analytics, Trajan Scientific),
automating matching and comparison of protein states through Welch's T-test and the Critical Interval statistical framework.
Additionally, it simplifies data export, generates 'PyMol' scripts, and ensures calculations meet publication standards.
'HDXBoxeR' assists in various aspects of hydrogen-deuterium exchange data analysis, including reprocessing data, calculating parameters, identifying significant peptides,
generating plots, and facilitating comparison between protein states.
For details check papers by Hageman and Weis (2019) <doi:10.1021/acs.analchem.9b01325>
and Masson et al. (2019) <doi:10.1038/s41592-019-0459-y>.
'HDXBoxeR' citation: Janowska et al. (2024) <doi:10.1093/bioinformatics/btae479>.
Author: Maria K. Janowska [aut, cre] ,
Katherine Reiter [ctb],
Pearl Magala [ctb],
Miklos Guttman [ctb],
Rachel E. Klevit [ctb]
Maintainer: Maria K. Janowska <mka.janowska@gmail.com>
Diff between HDXBoxeR versions 0.0.1 dated 2024-04-10 and 0.0.2 dated 2024-08-24
DESCRIPTION | 9 - MD5 | 40 +++-- NAMESPACE | 298 +++++++++++++++++++++---------------------- R/backexchange_calculation.R | 43 ++++-- R/deuteration_woods_plots.R | 2 R/nb_exchangeable_protons.R |only R/output_prep.R | 2 R/prep_info_functions.R | 24 +-- R/robot_2states_indexes.R | 2 R/robot_indexes_df.R | 8 - R/robot_plot_All.R | 2 R/select_indices.R | 6 README.md | 19 ++ inst/CITATION | 14 +- inst/doc/HDXBoxeR.R | 9 - inst/doc/HDXBoxeR.Rmd | 9 - inst/doc/HDXBoxeR.html | 53 +++---- man/nb_exch_deut.Rd |only man/robot_indexes.Rd | 2 man/robot_indexes_df.Rd | 2 man/woods_CI_plot.Rd | 106 +++++++-------- vignettes/HDXBoxeR.Rmd | 9 - 22 files changed, 343 insertions(+), 316 deletions(-)
Title: Hierarchical Partitioning of Marginal R2 for Generalized
Mixed-Effect Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor (fixed effects) towards marginal R2 for generalized linear mixed-effect model (including lm, glm and glmm) based on output of r.squaredGLMM() in 'MuMIn', applying the algorithm of Lai J.,Zou Y., Zhang S.,Zhang X.,Mao L.(2022)glmm.hp: an R package for computing individual effect of predictors in generalized linear mixed models.Journal of Plant Ecology,15(6)1302-1307<doi:10.1093/jpe/rtac096>.
Author: Jiangshan Lai [aut, cre] ,
Kim Nimon [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between glmm.hp versions 0.1-3 dated 2024-05-14 and 0.1-4 dated 2024-08-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/plot.glmmhp.r | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates balancing weights for causal effect estimation in observational studies with
binary, multi-category, or continuous point or longitudinal treatments by easing and
extending the functionality of several R packages and providing in-house estimation methods.
Available methods include those that rely on parametric modeling, optimization, and machine learning. Also
allows for assessment of weights and checking of covariate balance by interfacing directly
with the 'cobalt' package. Methods for estimating weighted regression models that take into account
uncertainty in the estimation of the weights via M-estimation or bootstrapping are available. See the vignette "Installing Supporting Packages" for instructions on how
to install any package 'WeightIt' uses, including those that may not be on CRAN.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 1.2.0 dated 2024-07-26 and 1.3.0 dated 2024-08-24
WeightIt-1.2.0/WeightIt/R/SHARED.R |only WeightIt-1.2.0/WeightIt/inst/doc/WeightIt.R |only WeightIt-1.2.0/WeightIt/inst/doc/estimating-effects.R |only WeightIt-1.2.0/WeightIt/inst/doc/installing-packages.R |only WeightIt-1.3.0/WeightIt/DESCRIPTION | 14 WeightIt-1.3.0/WeightIt/MD5 | 138 - WeightIt-1.3.0/WeightIt/NAMESPACE | 7 WeightIt-1.3.0/WeightIt/NEWS.md | 24 WeightIt-1.3.0/WeightIt/R/as.weightit.R | 26 WeightIt-1.3.0/WeightIt/R/calibrate.R | 4 WeightIt-1.3.0/WeightIt/R/chk-utilities.R | 26 WeightIt-1.3.0/WeightIt/R/dist_functions.R | 27 WeightIt-1.3.0/WeightIt/R/functions_for_processing.R | 909 +++++----- WeightIt-1.3.0/WeightIt/R/get_w_from_ps.R | 40 WeightIt-1.3.0/WeightIt/R/glm_weightit-methods.R | 625 ++++++ WeightIt-1.3.0/WeightIt/R/glm_weightit.R | 15 WeightIt-1.3.0/WeightIt/R/make_full_rank.R | 2 WeightIt-1.3.0/WeightIt/R/multinom_weightit.R | 12 WeightIt-1.3.0/WeightIt/R/ordinal_weightit.R | 6 WeightIt-1.3.0/WeightIt/R/plot.weightit.R | 15 WeightIt-1.3.0/WeightIt/R/predict.glm_weightit.R | 25 WeightIt-1.3.0/WeightIt/R/sbps.R | 23 WeightIt-1.3.0/WeightIt/R/summary.weightit.R | 73 WeightIt-1.3.0/WeightIt/R/trim.R | 20 WeightIt-1.3.0/WeightIt/R/utils.R |only WeightIt-1.3.0/WeightIt/R/weightit.R | 129 - WeightIt-1.3.0/WeightIt/R/weightit.fit.R | 272 +- WeightIt-1.3.0/WeightIt/R/weightit2bart.R | 39 WeightIt-1.3.0/WeightIt/R/weightit2cbps.R | 93 - WeightIt-1.3.0/WeightIt/R/weightit2ebal.R | 78 WeightIt-1.3.0/WeightIt/R/weightit2energy.R | 160 - WeightIt-1.3.0/WeightIt/R/weightit2gbm.R | 55 WeightIt-1.3.0/WeightIt/R/weightit2glm.R | 71 WeightIt-1.3.0/WeightIt/R/weightit2ipt.R | 147 - WeightIt-1.3.0/WeightIt/R/weightit2npcbps.R | 34 WeightIt-1.3.0/WeightIt/R/weightit2null.R |only WeightIt-1.3.0/WeightIt/R/weightit2optweight.R | 137 + WeightIt-1.3.0/WeightIt/R/weightit2super.R | 141 - WeightIt-1.3.0/WeightIt/R/weightit2user.R | 66 WeightIt-1.3.0/WeightIt/R/weightitMSM.R | 311 +-- WeightIt-1.3.0/WeightIt/R/weightit_methods.R |only WeightIt-1.3.0/WeightIt/README.md | 122 - WeightIt-1.3.0/WeightIt/build/stage23.rdb |binary WeightIt-1.3.0/WeightIt/build/vignette.rds |binary WeightIt-1.3.0/WeightIt/inst/doc/WeightIt.Rmd | 11 WeightIt-1.3.0/WeightIt/inst/doc/WeightIt.html | 85 WeightIt-1.3.0/WeightIt/inst/doc/estimating-effects.Rmd | 26 WeightIt-1.3.0/WeightIt/inst/doc/estimating-effects.html | 352 +-- WeightIt-1.3.0/WeightIt/inst/doc/installing-packages.Rmd | 54 WeightIt-1.3.0/WeightIt/inst/doc/installing-packages.html | 125 - WeightIt-1.3.0/WeightIt/man/WeightIt-package.Rd | 2 WeightIt-1.3.0/WeightIt/man/dot-weightit_methods.Rd |only WeightIt-1.3.0/WeightIt/man/get_w_from_ps.Rd | 30 WeightIt-1.3.0/WeightIt/man/glm_weightit-methods.Rd | 66 WeightIt-1.3.0/WeightIt/man/method_bart.Rd | 18 WeightIt-1.3.0/WeightIt/man/method_cbps.Rd | 7 WeightIt-1.3.0/WeightIt/man/method_ebal.Rd | 2 WeightIt-1.3.0/WeightIt/man/method_energy.Rd | 2 WeightIt-1.3.0/WeightIt/man/method_glm.Rd | 2 WeightIt-1.3.0/WeightIt/man/method_ipt.Rd | 9 WeightIt-1.3.0/WeightIt/man/method_npcbps.Rd | 2 WeightIt-1.3.0/WeightIt/man/method_optweight.Rd | 13 WeightIt-1.3.0/WeightIt/man/method_super.Rd | 42 WeightIt-1.3.0/WeightIt/man/plot.weightit.Rd | 7 WeightIt-1.3.0/WeightIt/man/predict.glm_weightit.Rd | 3 WeightIt-1.3.0/WeightIt/man/weightit.Rd | 5 WeightIt-1.3.0/WeightIt/man/weightit.fit.Rd | 7 WeightIt-1.3.0/WeightIt/tests/testthat/test-glm_weightit.R | 17 WeightIt-1.3.0/WeightIt/tests/testthat/test-method_glm.R | 22 WeightIt-1.3.0/WeightIt/tests/testthat/test-multinom_weightit.R | 25 WeightIt-1.3.0/WeightIt/tests/testthat/test-ordinal_weightit.R | 37 WeightIt-1.3.0/WeightIt/vignettes/WeightIt.Rmd | 11 WeightIt-1.3.0/WeightIt/vignettes/estimating-effects.Rmd | 26 WeightIt-1.3.0/WeightIt/vignettes/installing-packages.Rmd | 54 74 files changed, 2831 insertions(+), 2117 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices, vectors,
numerical solvers and related algorithms. It supports dense and sparse
matrices on integer, floating point and complex numbers, decompositions of
such matrices, and solutions of linear systems. Its performance on many
algorithms is comparable with some of the best implementations based on
'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header
files from the 'Eigen' C++ template library. Thus users do not need to
install 'Eigen' itself in order to use 'RcppEigen'. Since version 3.1.1,
'Eigen' is licensed under the Mozilla Public License (version 2); earlier
version were licensed under the GNU LGPL version 3 or later. 'RcppEigen'
(the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the GNU GPL
version 2 or later, as is the rest of 'Rcpp'.
Author: Doug Bates [aut] ,
Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Yixuan Qiu [aut] ,
Authors of Eigen [cph]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.4.0.1 dated 2024-08-16 and 0.3.4.0.2 dated 2024-08-24
ChangeLog | 7 +++++++ DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- inst/NEWS.Rd | 6 ++++++ inst/doc/RcppEigen-Introduction.pdf |binary 5 files changed, 25 insertions(+), 12 deletions(-)
Title: Conduct Simulation Study of Bayesian Optimal Interval Design
with BOIN-ET Family
Description: Bayesian optimal interval based on both efficacy and toxicity outcomes (BOIN-ET) design is a model-assisted oncology phase I/II trial design, aiming to establish an optimal biological dose accounting for efficacy and toxicity in the framework of dose-finding. Some extensions of BOIN-ET design are also available to allow for time-to-event efficacy and toxicity outcomes based on cumulative and pending data (time-to-event BOIN-ET: TITE-BOIN-ET), ordinal graded efficacy and toxicity outcomes (generalized BOIN-ET: gBOIN-ET), and their combination (TITE-gBOIN-ET). 'boinet' is a package to implement the BOIN-ET design family and supports the conduct of simulation studies to assess operating characteristics of BOIN-ET, TITE-BOIN-ET, gBOIN-ET, and TITE-gBOIN-ET, where users can choose design parameters in flexible and straightforward ways depending on their own application.
Author: Yusuke Yamaguchi [aut, cre],
Kentaro Takeda [aut]
Maintainer: Yusuke Yamaguchi <yamagubed@gmail.com>
Diff between boinet versions 1.0.0 dated 2023-06-08 and 1.1.0 dated 2024-08-24
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/boinet.R | 15 +++++++++++++-- R/gboinet.R | 15 +++++++++++++-- R/tite.boinet.R | 15 +++++++++++++-- R/tite.gboinet.R | 15 +++++++++++++-- man/boinet.Rd | 3 ++- man/gboinet.Rd | 3 ++- man/tite.boinet.Rd | 3 ++- man/tite.gboinet.Rd | 3 ++- 11 files changed, 80 insertions(+), 26 deletions(-)
Title: Inferring Cell-Specific Gene Regulatory Network
Description: An R package for inferring cell-type specific gene regulatory network from single-cell RNA data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 1.0.5 dated 2024-06-26 and 1.0.8 dated 2024-08-24
inferCSN-1.0.5/inferCSN/R/calculate.gene.rank.R |only inferCSN-1.0.5/inferCSN/R/network.visualization.R |only inferCSN-1.0.5/inferCSN/R/performance.calculate.R |only inferCSN-1.0.5/inferCSN/R/sparse.regression.R |only inferCSN-1.0.5/inferCSN/man/acc.calculate.Rd |only inferCSN-1.0.5/inferCSN/man/auc.calculate.Rd |only inferCSN-1.0.5/inferCSN/man/calculate.gene.rank.Rd |only inferCSN-1.0.5/inferCSN/man/check.parameters.Rd |only inferCSN-1.0.5/inferCSN/man/coef.SRM_fit.Rd |only inferCSN-1.0.5/inferCSN/man/model.fit.Rd |only inferCSN-1.0.5/inferCSN/man/network.heatmap.Rd |only inferCSN-1.0.5/inferCSN/man/predict.SRM_fit.Rd |only inferCSN-1.0.5/inferCSN/man/prepare.performance.data.Rd |only inferCSN-1.0.5/inferCSN/man/print.SRM_fit.Rd |only inferCSN-1.0.5/inferCSN/man/rse.Rd |only inferCSN-1.0.5/inferCSN/man/single.network.Rd |only inferCSN-1.0.5/inferCSN/man/sparse.regression.Rd |only inferCSN-1.0.5/inferCSN/man/sse.Rd |only inferCSN-1.0.5/inferCSN/man/table.to.matrix.Rd |only inferCSN-1.0.5/inferCSN/src/table_to_matrix.cpp |only inferCSN-1.0.8/inferCSN/DESCRIPTION | 29 inferCSN-1.0.8/inferCSN/MD5 | 158 - inferCSN-1.0.8/inferCSN/NAMESPACE | 36 inferCSN-1.0.8/inferCSN/R/RcppExports.R | 28 inferCSN-1.0.8/inferCSN/R/calculate_gene_rank.R |only inferCSN-1.0.8/inferCSN/R/import.R | 6 inferCSN-1.0.8/inferCSN/R/inferCSN-package.R | 5 inferCSN-1.0.8/inferCSN/R/inferCSN.R | 319 ++- inferCSN-1.0.8/inferCSN/R/network_sift.R | 135 - inferCSN-1.0.8/inferCSN/R/network_visualization.R |only inferCSN-1.0.8/inferCSN/R/performance_evaluation.R |only inferCSN-1.0.8/inferCSN/R/plotting_functions.R | 217 ++ inferCSN-1.0.8/inferCSN/R/sparse_regression.R |only inferCSN-1.0.8/inferCSN/R/utils.R | 791 +++++---- inferCSN-1.0.8/inferCSN/README.md | 7 inferCSN-1.0.8/inferCSN/man/as_matrix.Rd | 56 inferCSN-1.0.8/inferCSN/man/calculate_acc.Rd |only inferCSN-1.0.8/inferCSN/man/calculate_auc.Rd |only inferCSN-1.0.8/inferCSN/man/calculate_gene_rank.Rd |only inferCSN-1.0.8/inferCSN/man/check_sparsity.Rd |only inferCSN-1.0.8/inferCSN/man/coef.srm.Rd |only inferCSN-1.0.8/inferCSN/man/filter_sort_matrix.Rd | 11 inferCSN-1.0.8/inferCSN/man/fit_sparse_regression.Rd |only inferCSN-1.0.8/inferCSN/man/inferCSN-package.Rd | 4 inferCSN-1.0.8/inferCSN/man/inferCSN.Rd | 136 + inferCSN-1.0.8/inferCSN/man/log_message.Rd |only inferCSN-1.0.8/inferCSN/man/network_format.Rd | 12 inferCSN-1.0.8/inferCSN/man/network_sift.Rd | 68 inferCSN-1.0.8/inferCSN/man/normalization.Rd | 27 inferCSN-1.0.8/inferCSN/man/parallelize_fun.Rd | 13 inferCSN-1.0.8/inferCSN/man/plot_contrast_networks.Rd | 12 inferCSN-1.0.8/inferCSN/man/plot_dynamic_networks.Rd | 64 inferCSN-1.0.8/inferCSN/man/plot_embedding.Rd |only inferCSN-1.0.8/inferCSN/man/plot_network_heatmap.Rd |only inferCSN-1.0.8/inferCSN/man/plot_scatter.Rd | 26 inferCSN-1.0.8/inferCSN/man/plot_static_networks.Rd | 8 inferCSN-1.0.8/inferCSN/man/plot_weight_distribution.Rd |only inferCSN-1.0.8/inferCSN/man/predict.srm.Rd |only inferCSN-1.0.8/inferCSN/man/print.srm.Rd |only inferCSN-1.0.8/inferCSN/man/single_network.Rd |only inferCSN-1.0.8/inferCSN/man/sparse_regression.Rd |only inferCSN-1.0.8/inferCSN/man/table_to_matrix.Rd |only inferCSN-1.0.8/inferCSN/src/BetaVector.cpp | 53 inferCSN-1.0.8/inferCSN/src/CDL012LogisticSwaps.cpp | 327 ++- inferCSN-1.0.8/inferCSN/src/CDL012SquaredHingeSwaps.cpp | 210 +- inferCSN-1.0.8/inferCSN/src/CDL012Swaps.cpp | 203 +- inferCSN-1.0.8/inferCSN/src/Grid.cpp | 117 - inferCSN-1.0.8/inferCSN/src/Grid1D.cpp | 449 ++--- inferCSN-1.0.8/inferCSN/src/Grid2D.cpp | 227 +- inferCSN-1.0.8/inferCSN/src/Interface.cpp | 372 ++-- inferCSN-1.0.8/inferCSN/src/Makevars | 4 inferCSN-1.0.8/inferCSN/src/Makevars.win | 5 inferCSN-1.0.8/inferCSN/src/Normalize.cpp | 22 inferCSN-1.0.8/inferCSN/src/README.cpp | 104 - inferCSN-1.0.8/inferCSN/src/RcppExports.cpp | 87 - inferCSN-1.0.8/inferCSN/src/Test_Interface.cpp | 98 - inferCSN-1.0.8/inferCSN/src/asMatrix.cpp | 81 inferCSN-1.0.8/inferCSN/src/include/BetaVector.h | 22 inferCSN-1.0.8/inferCSN/src/include/CD.h | 845 +++++----- inferCSN-1.0.8/inferCSN/src/include/CDL0.h | 289 +-- inferCSN-1.0.8/inferCSN/src/include/CDL012.h | 289 +-- inferCSN-1.0.8/inferCSN/src/include/CDL012Logistic.h | 337 ++- inferCSN-1.0.8/inferCSN/src/include/CDL012LogisticSwaps.h | 67 inferCSN-1.0.8/inferCSN/src/include/CDL012SquaredHinge.h | 302 +-- inferCSN-1.0.8/inferCSN/src/include/CDL012SquaredHingeSwaps.h | 63 inferCSN-1.0.8/inferCSN/src/include/CDL012Swaps.h | 43 inferCSN-1.0.8/inferCSN/src/include/FitResult.h | 23 inferCSN-1.0.8/inferCSN/src/include/Grid.h | 55 inferCSN-1.0.8/inferCSN/src/include/Grid1D.h | 59 inferCSN-1.0.8/inferCSN/src/include/Grid2D.h | 55 inferCSN-1.0.8/inferCSN/src/include/GridParams.h | 57 inferCSN-1.0.8/inferCSN/src/include/Interface.h | 12 inferCSN-1.0.8/inferCSN/src/include/MakeCD.h | 60 inferCSN-1.0.8/inferCSN/src/include/Model.h | 27 inferCSN-1.0.8/inferCSN/src/include/Normalize.h | 78 inferCSN-1.0.8/inferCSN/src/include/Params.h | 120 - inferCSN-1.0.8/inferCSN/src/include/Test_Interface.h | 6 inferCSN-1.0.8/inferCSN/src/include/utils.h | 156 - inferCSN-1.0.8/inferCSN/src/tableToMatrix.cpp |only inferCSN-1.0.8/inferCSN/src/utils.cpp | 146 - 100 files changed, 4278 insertions(+), 3360 deletions(-)
Title: Rendering Font into 'data.frame'
Description: Extract glyph information from font data, and translate the
outline curves to flattened paths or tessellated polygons. The converted
data is returned as a 'data.frame' in easy-to-plot format.
Author: Hiroaki Yutani [aut, cre] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Hiroaki Yutani <yutani.ini@gmail.com>
Diff between string2path versions 0.1.7 dated 2024-05-31 and 0.1.8 dated 2024-08-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ configure | 4 ++++ configure.win | 4 ++++ 5 files changed, 19 insertions(+), 7 deletions(-)