Title: Modeling Workflows
Description: Managing both a 'parsnip' model and its data preparation steps,
such as a model formula or recipe from 'recipes', can often be challenging.
The goal of 'workflows' is to streamline this process by bundling the
model with its data preparation, all within the same object.
Author: Davis Vaughan [aut],
Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between workflows versions 1.1.4 dated 2024-02-19 and 1.2.0 dated 2025-02-18
DESCRIPTION | 30 +- MD5 | 134 ++++++------ NAMESPACE | 23 ++ NEWS.md | 20 + R/action.R | 11 - R/broom.R | 9 R/butcher.R | 16 + R/control.R | 5 R/extract.R | 50 +++- R/fit-action-model.R | 37 ++- R/fit.R | 44 +++- R/generics.R | 8 R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/pre-action-case-weights.R | 22 +- R/pre-action-formula.R | 35 ++- R/pre-action-recipe.R | 45 ++-- R/pre-action-variables.R | 33 ++- R/predict.R | 13 - R/pull.R | 2 R/reexports.R | 12 + R/sparsevctrs.R |only R/stage.R | 18 + R/survival-censoring-weights.R | 2 R/utils.R | 19 + R/workflow.R | 16 - R/workflows-package.R | 2 R/zzz.R | 4 README.md | 4 build/vignette.rds |binary inst/doc/stages.Rmd | 4 inst/doc/stages.html | 247 ----------------------- man/add_formula.Rd | 6 man/add_recipe.Rd | 2 man/extract-workflow.Rd | 12 + man/fit-workflow.Rd | 2 man/glance.workflow.Rd | 2 man/is_trained_workflow.Rd | 2 man/predict-workflow.Rd | 2 man/reexports.Rd | 7 man/workflow-extractors.Rd | 2 man/workflow.Rd | 2 man/workflows-internals.Rd | 2 man/workflows-package.Rd | 2 tests/testthat/_snaps/control.md | 2 tests/testthat/_snaps/fit-action-model.md | 2 tests/testthat/_snaps/pre-action-case-weights.md | 25 -- tests/testthat/_snaps/pre-action-formula.md | 2 tests/testthat/_snaps/pre-action-recipe.md | 2 tests/testthat/_snaps/pre-action-variables.md | 2 tests/testthat/_snaps/pull.md | 10 tests/testthat/_snaps/sparsevctrs.md |only tests/testthat/_snaps/workflow.md | 10 tests/testthat/helper-sparsevctrs.R |only tests/testthat/test-broom.R | 5 tests/testthat/test-butcher.R | 2 tests/testthat/test-extract.R | 42 +++ tests/testthat/test-fit-action-model.R | 2 tests/testthat/test-fit.R | 2 tests/testthat/test-generics.R | 4 tests/testthat/test-pre-action-case-weights.R | 19 + tests/testthat/test-pre-action-formula.R | 2 tests/testthat/test-pre-action-recipe.R | 2 tests/testthat/test-pre-action-variables.R | 5 tests/testthat/test-predict.R | 5 tests/testthat/test-printing.R | 2 tests/testthat/test-pull.R | 2 tests/testthat/test-sparsevctrs.R |only tests/testthat/test-workflow.R | 2 vignettes/extras/getting-started.Rmd | 14 - vignettes/stages.Rmd | 4 71 files changed, 567 insertions(+), 510 deletions(-)
Title: Global Optimization by Differential Evolution in C++
Description: An efficient C++ based implementation of the 'DEoptim'
function which performs global optimization by differential evolution.
Its creation was motivated by trying to see if the old approximation "easier,
shorter, faster: pick any two" could in fact be extended to achieving all
three goals while moving the code from plain old C to modern C++. The
initial version did in fact do so, but a good part of the gain was due to
an implicit code review which eliminated a few inefficiencies which have
since been eliminated in 'DEoptim'.
Author: Dirk Eddelbuettel [aut, cre] ,
David Ardia [aut] ,
Katharine Mullen [aut] ,
Brian Peterson [aut] ,
Joshua Ulrich [aut] ,
Kris Boudt [ctb] ,
Rainer Storn [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDE versions 0.1.7 dated 2022-12-20 and 0.1.8 dated 2025-02-18
ChangeLog | 27 +++++++++++++++++++++++++++ DESCRIPTION | 27 ++++++++++++++++++++------- MD5 | 14 +++++++------- README.md | 9 +++++---- build/vignette.rds |binary inst/doc/RcppDE.pdf |binary src/Makevars | 4 +--- src/devol.cpp | 10 +++++----- 8 files changed, 65 insertions(+), 26 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 3.0.3 dated 2025-01-18 and 3.0.4 dated 2025-02-18
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 7 +++++++ R/focei.R | 4 +++- R/hook.R | 9 +++++++++ R/nlmixr2_md5.R | 2 +- R/preProcessCovariatesPresent.R | 1 + tests/testthat/test-addCwres.R | 36 ++++++++++++++++++++++++++++++++++++ tests/testthat/test-cwres-3.0.3.qs |only 9 files changed, 68 insertions(+), 12 deletions(-)
Title: Interpreting Latent Variables with AI
Description: A small package designed for interpreting continuous and categorical latent variables. You provide a data set with a latent variable you want to understand and some other explanatory variables. It provides a description of the latent variable based on the explanatory variables. It also provides a name to the latent variable.
Author: Nel Herve [aut],
Sebastien Le [aut, cre]
Maintainer: Sebastien Le <sebastien.le@institut-agro.fr>
Diff between NaileR versions 1.2.1 dated 2024-11-11 and 1.2.2 dated 2025-02-18
DESCRIPTION | 12 +- MD5 | 44 ++++---- NAMESPACE | 8 + R/datasets.R | 40 +++---- R/globals.R | 4 R/nail_catdes.R | 100 +++++++++++++++++- R/nail_qda.R | 232 +++++++++++++++++++------------------------- README.md | 10 + data/atomic_habit.rda |binary data/atomic_habit_clust.rda |binary man/agri_studies.Rd | 2 man/beard_cont.Rd | 2 man/beard_wide.Rd | 4 man/boss.Rd | 2 man/fabric.Rd | 4 man/glossophobia.Rd | 2 man/local_food.Rd | 2 man/nail_catdes.Rd | 6 + man/nail_qda.Rd | 3 man/nutriscore.Rd | 3 man/quality.Rd | 5 man/rorschach.Rd | 12 -- man/waste.Rd | 2 23 files changed, 285 insertions(+), 214 deletions(-)
Title: Multivariate (Dynamic) Generalized Additive Models
Description: Fit Bayesian Dynamic Generalized Additive Models to multivariate observations. Users can build nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2022) <doi:10.1111/2041-210X.13974>.
Author: Nicholas J Clark [aut, cre] ,
Sarah Heaps [ctb] ,
Scott Pease [ctb] ,
Matthijs Hollanders [ctb]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Diff between mvgam versions 1.1.3 dated 2024-09-03 and 1.1.4 dated 2025-02-18
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mvgam-1.1.4/mvgam/man/print.mvgam.Rd | 4 mvgam-1.1.4/mvgam/man/reexports.Rd | 25 mvgam-1.1.4/mvgam/man/residual_cor.jsdgam.Rd |only mvgam-1.1.4/mvgam/man/residuals.mvgam.Rd | 19 mvgam-1.1.4/mvgam/man/score.mvgam_forecast.Rd | 37 mvgam-1.1.4/mvgam/man/series_to_mvgam.Rd | 3 mvgam-1.1.4/mvgam/man/sim_mvgam.Rd | 49 mvgam-1.1.4/mvgam/man/stability.mvgam.Rd |only mvgam-1.1.4/mvgam/man/summary.mvgam.Rd | 5 mvgam-1.1.4/mvgam/man/update.mvgam.Rd | 156 mvgam-1.1.4/mvgam/src/Makevars.txt | 2 mvgam-1.1.4/mvgam/tests/testthat/setup.R | 85 mvgam-1.1.4/mvgam/tests/testthat/test-RW.R | 498 - mvgam-1.1.4/mvgam/tests/testthat/test-backends.R | 56 mvgam-1.1.4/mvgam/tests/testthat/test-binomial.R | 684 - mvgam-1.1.4/mvgam/tests/testthat/test-dynamic.R | 14 mvgam-1.1.4/mvgam/tests/testthat/test-example_processing.R | 940 +- mvgam-1.1.4/mvgam/tests/testthat/test-families.R | 1126 +-- mvgam-1.1.4/mvgam/tests/testthat/test-gp.R | 227 mvgam-1.1.4/mvgam/tests/testthat/test-jsdgam.R |only mvgam-1.1.4/mvgam/tests/testthat/test-marginaleffects.R | 198 mvgam-1.1.4/mvgam/tests/testthat/test-monotonic.R | 198 mvgam-1.1.4/mvgam/tests/testthat/test-mvgam-methods.R | 192 mvgam-1.1.4/mvgam/tests/testthat/test-mvgam.R | 1683 ++-- mvgam-1.1.4/mvgam/tests/testthat/test-mvgam_priors.R | 92 mvgam-1.1.4/mvgam/tests/testthat/test-nmixture.R | 2 mvgam-1.1.4/mvgam/tests/testthat/test-offset.R | 214 mvgam-1.1.4/mvgam/tests/testthat/test-piecewise.R | 371 - mvgam-1.1.4/mvgam/tests/testthat/test-sim_mvgam.R | 92 mvgam-1.1.4/mvgam/tests/testthat/test-tidier_methods.R |only mvgam-1.1.4/mvgam/tests/testthat/test-update.R | 106 mvgam-1.1.4/mvgam/vignettes/SS_model.svg | 510 - mvgam-1.1.4/mvgam/vignettes/data_in_mvgam.Rmd | 710 - mvgam-1.1.4/mvgam/vignettes/forecast_evaluation.Rmd | 110 mvgam-1.1.4/mvgam/vignettes/mvgam_overview.Rmd | 25 mvgam-1.1.4/mvgam/vignettes/nmixtures.Rmd | 4 mvgam-1.1.4/mvgam/vignettes/shared_states.Rmd | 650 - mvgam-1.1.4/mvgam/vignettes/time_varying_effects.Rmd | 28 mvgam-1.1.4/mvgam/vignettes/trend_formulas.Rmd | 942 +- 228 files changed, 29061 insertions(+), 25454 deletions(-)
Title: An R Package to Extend 'ACER ConQuest'
Description: Extends 'ACER ConQuest' through a family of functions
designed to improve graphical outputs and help with advanced analysis
(e.g., differential item functioning). Allows R users to call
'ACER ConQuest' from within R and read 'ACER ConQuest' System Files
(generated by the command `put` <https://conquestmanual.acer.org/s4-00.html#put>).
Requires 'ACER ConQuest' version 5.40 or later.
A demonstration version can be downloaded from <https://shop.acer.org/acer-conquest-5.html>.
Author: Dan Cloney [aut, cre] ,
Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>
Diff between conquestr versions 1.3.4 dated 2024-07-24 and 1.4.5 dated 2025-02-18
DESCRIPTION | 17 MD5 | 204 - NEWS.md | 33 R/ReadConQuestLibrary.R | 200 - R/ReadConQuestState.R | 13 R/conquestr.R | 26 R/conquestrFunc.R | 55 R/generateHelpers.R | 300 + R/generateItems.R |only R/itanalHelpers.R | 581 ++- README.md | 11 build/vignette.rds |binary inst/doc/data-cleaning-functions-in-conquestr.R | 6 inst/doc/data-cleaning-functions-in-conquestr.Rmd | 48 inst/doc/data-cleaning-functions-in-conquestr.html | 515 --- inst/doc/generateResponses.html | 58 inst/doc/intro-to-conquestr.html | 16 inst/doc/itanal-in-conquestr.R | 6 inst/doc/itanal-in-conquestr.Rmd | 68 inst/doc/itanal-in-conquestr.html | 31 inst/doc/plotting.html | 12 inst/doc/responseProbs.html | 12 inst/doc/test_item_review_sheet_markdown.html | 3261 ++++++++++++++++++++- inst/extdata/ex1.cqc | 4 inst/extdata/mysysfile.cqs |binary inst/extdata/mysysfile_v26.cqs |only man/ConQuestRout.Rd | 11 man/ReadADesignMatrices.Rd | 2 man/ReadAllCaseEstimates.Rd | 2 man/ReadAllGroupsData.Rd | 2 man/ReadAllResponseData.Rd | 2 man/ReadAllY.Rd | 2 man/ReadAnchor.Rd | 2 man/ReadAnchorList.Rd | 2 man/ReadBDesignMatrices.Rd | 2 man/ReadBandDefine.Rd | 2 man/ReadBandDefinesList.Rd | 2 man/ReadBitSet.Rd | 2 man/ReadBoolean.Rd | 2 man/ReadCDesignMatrices.Rd | 2 man/ReadCategorise.Rd | 2 man/ReadCategoriseList.Rd | 2 man/ReadCodeList.Rd | 2 man/ReadDataRecord.Rd | 2 man/ReadDouble.Rd | 2 man/ReadDoubleList.Rd | 2 man/ReadEstimatesRecord.Rd | 2 man/ReadFit.Rd | 2 man/ReadFitList.Rd | 2 man/ReadGExportOptions.Rd | 2 man/ReadGExportOptionsList.Rd | 2 man/ReadGraph.Rd | 2 man/ReadGroupsOneCase.Rd | 2 man/ReadHistory.Rd | 2 man/ReadIRecode.Rd | 2 man/ReadIRecodeList.Rd | 2 man/ReadImplicitVar.Rd | 2 man/ReadInteger.Rd | 2 man/ReadIntegerList.Rd | 2 man/ReadIntegerListList.Rd | 2 man/ReadItemSet.Rd | 2 man/ReadItemSetList.Rd | 2 man/ReadKeyList.Rd | 2 man/ReadLabel.Rd | 2 man/ReadLabelList.Rd | 2 man/ReadLookUp.Rd | 2 man/ReadLookUpList.Rd | 2 man/ReadMatrix.Rd | 2 man/ReadMatrixList.Rd | 2 man/ReadMatrixVars.Rd | 2 man/ReadNamedStringList.Rd |only man/ReadParameters.Rd | 2 man/ReadParametersList.Rd | 2 man/ReadPoint.Rd | 2 man/ReadRandomStructure.Rd | 2 man/ReadRegression.Rd | 2 man/ReadRegressionList.Rd | 2 man/ReadRegressionListLeg.Rd | 2 man/ReadResponse.Rd | 2 man/ReadResponseList.Rd | 2 man/ReadSeries.Rd | 2 man/ReadString.Rd | 2 man/ReadStringList.Rd | 2 man/ReadTerms.Rd | 2 man/ReadTermsList.Rd | 2 man/ReadVarInfo.Rd | 2 man/ReadVarList.Rd | 2 man/ReadVariable.Rd | 2 man/ReadVariableList.Rd | 2 man/ReadYOneCase.Rd | 2 man/fmtCqItanal.Rd | 3 man/genItems.Rd | 67 man/genItems_deltaDots.Rd |only man/genItems_taus.Rd |only man/getCqHist.Rd | 20 man/getCqItanal.Rd | 12 man/makeItemDfs.Rd |only man/makeItemList.Rd | 4 man/simplep.Rd | 2 tests/testthat/test-ConQuestRout.R | 2 tests/testthat/test-ConQuestSys.R |only tests/testthat/test-genHelpers.R | 12 tests/testthat/test-genItems.R |only tests/testthat/test-getCqItanal.R | 8 tests/testthat/test-plotItemMap.R | 4 vignettes/data-cleaning-functions-in-conquestr.Rmd | 48 vignettes/itanal-in-conquestr.Rmd | 68 107 files changed, 4541 insertions(+), 1321 deletions(-)
Title: Sample Size Estimation for Bio-Equivalence Trials Through
Simulation
Description: Sample size estimation for bio-equivalence trials is supported through a simulation-based approach
that extends the Two One-Sided Tests (TOST) procedure. The methodology provides flexibility in
hypothesis testing, accommodates multiple treatment comparisons, and accounts for correlated endpoints.
Users can model complex trial scenarios, including parallel and crossover designs, intra-subject variability,
and different equivalence margins. Monte Carlo simulations enable accurate estimation of power and type I error
rates, ensuring well-calibrated study designs. The statistical framework builds on established methods for
equivalence testing and multiple hypothesis testing in bio-equivalence studies, as described in Schuirmann (1987)
<doi:10.1007/BF01068419>, Mielke et al. (2018) <doi:10.1080/19466315.2017.1371071>, Shieh (2022)
<doi:10.1371/journal.pone.0269128>, and Sozu et al. (2015) <doi:10.1007/978-3-319-22005-5>.
Comprehensive documentation and vignettes guid [...truncated...]
Author: Thomas Debray [aut, cre] ,
Johanna Munoz [aut],
Dewi Amaliah [ctb],
Wei Wei [ctb],
Marian Mitroiu [ctb],
Scott McDonald [ctb],
Biogen Inc [cph, fnd]
Maintainer: Thomas Debray <tdebray@fromdatatowisdom.com>
Diff between SimTOST versions 1.0.1 dated 2025-02-18 and 1.0.2 dated 2025-02-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ src/RcppExports.cpp | 36 ++++++++++++++++++------------------ src/module.cpp | 18 +++++++++--------- 5 files changed, 41 insertions(+), 34 deletions(-)
Title: Linear Model Evaluation with Randomized Residuals in a
Permutation Procedure
Description: Linear model calculations are made for many random versions of data.
Using residual randomization in a permutation procedure, sums of squares are
calculated over many permutations to generate empirical probability distributions
for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many
permutations can be used for various procedures including pairwise tests, prediction, classification, and
model comparison. This package should provide most tools one could need for the analysis of
high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre] ,
Dean Adams [aut]
Maintainer: Michael Collyer <mlcollyer@gmail.com>
Diff between RRPP versions 2.1.1 dated 2025-02-09 and 2.1.2 dated 2025-02-18
DESCRIPTION | 9 ++++----- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/RRPP.utils.r | 2 +- inst/CITATION | 2 +- inst/doc/ANOVA.vs.MANOVA.html | 4 ++-- inst/doc/Using.RRPP.html | 4 ++-- 7 files changed, 22 insertions(+), 17 deletions(-)
Title: Visualize the Climate Scenario Alignment of a Financial
Portfolio
Description: Create plots to visualize the alignment of a corporate
lending financial portfolio to climate change scenarios based on
climate indicators (production and emission intensities) across key
climate relevant sectors of the 'PACTA' methodology (Paris Agreement Capital
Transition Assessment; <https://www.transitionmonitor.com/>).
Financial institutions use 'PACTA' to study how their capital
allocation decisions align with climate change mitigation goals.
Author: Monika Furdyna [aut, ctr, cre]
,
Mauro Lepore [aut, ctr] ,
Alex Axthelm [aut, ctr] ,
RMI [cph, fnd]
Maintainer: Monika Furdyna <monika.furdyna@gmail.com>
Diff between r2dii.plot versions 0.5.0 dated 2025-02-12 and 0.5.1 dated 2025-02-18
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NEWS.md | 4 ++++ R/prep_trajectory.R | 2 ++ data/data_dictionary.rda |binary man/prep_trajectory.Rd | 3 ++- tests/testthat/test-data_dictionary.R |only 7 files changed, 19 insertions(+), 11 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on
'Windows', 'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between ps versions 1.8.1 dated 2024-10-28 and 1.9.0 dated 2025-02-18
DESCRIPTION | 6 MD5 | 28 ++-- NEWS.md | 8 + R/low-level.R | 18 +- R/ps.R | 319 ++++++++++++++++++++++++++++++++++++++++------- configure | 2 man/ps.Rd | 50 ++++++- man/ps_memory_info.Rd | 2 src/api-posix.c | 10 + src/api-windows.c | 6 src/dummy.c | 1 src/init.c | 1 src/ps.h | 1 tests/testthat/helpers.R | 2 tests/testthat/test-ps.R | 6 15 files changed, 387 insertions(+), 73 deletions(-)
Title: Penalized Linear Mixed Models for Correlated Data
Description: Fits penalized linear mixed models that correct for
unobserved confounding factors. 'plmmr' infers and corrects for the
presence of unobserved confounding effects such as population
stratification and environmental heterogeneity. It then fits a linear
model via penalized maximum likelihood. Originally designed for the
multivariate analysis of single nucleotide polymorphisms (SNPs)
measured in a genome-wide association study (GWAS), 'plmmr' eliminates
the need for subpopulation-specific analyses and post-analysis p-value
adjustments. Functions for the appropriate processing of 'PLINK'
files are also supplied. For examples, see the package homepage.
<https://pbreheny.github.io/plmmr/>.
Author: Tabitha K. Peter [aut] ,
Anna C. Reisetter [aut] ,
Patrick J. Breheny [aut, cre] ,
Yujing Lu [aut]
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>
Diff between plmmr versions 4.1.0 dated 2024-10-23 and 4.2.0 dated 2025-02-18
plmmr-4.1.0/plmmr/R/file_sans_ext.R |only plmmr-4.1.0/plmmr/R/index_std_X.R |only plmmr-4.1.0/plmmr/R/untransform_filebacked.R |only plmmr-4.1.0/plmmr/man/file_sans_ext.Rd |only plmmr-4.1.0/plmmr/man/index_std_X.Rd |only plmmr-4.1.0/plmmr/man/untransform_filebacked.Rd |only plmmr-4.2.0/plmmr/DESCRIPTION | 8 plmmr-4.2.0/plmmr/MD5 | 89 ++++----- plmmr-4.2.0/plmmr/NAMESPACE | 1 plmmr-4.2.0/plmmr/NEWS.md | 40 ++-- plmmr-4.2.0/plmmr/R/construct_variance.R | 5 plmmr-4.2.0/plmmr/R/create_design_filebacked.R | 4 plmmr-4.2.0/plmmr/R/cv-plmm.R | 235 +++++++++--------------- plmmr-4.2.0/plmmr/R/cvf.R | 121 +++++++----- plmmr-4.2.0/plmmr/R/plmm.R | 172 +++++++---------- plmmr-4.2.0/plmmr/R/plmm_checks.R | 36 ++- plmmr-4.2.0/plmmr/R/plmm_fit.R | 62 +----- plmmr-4.2.0/plmmr/R/plmm_format.R | 63 +++--- plmmr-4.2.0/plmmr/R/plmm_prep.R | 39 --- plmmr-4.2.0/plmmr/R/plmmr-package.R | 1 plmmr-4.2.0/plmmr/R/plot-cv-plmm.R | 12 - plmmr-4.2.0/plmmr/R/predict-plmm.R | 115 ++++++----- plmmr-4.2.0/plmmr/R/predict_within_cv.R | 63 +----- plmmr-4.2.0/plmmr/R/print-summary-cv-plmm.R | 2 plmmr-4.2.0/plmmr/R/rotate_filebacked.R | 2 plmmr-4.2.0/plmmr/R/standardize_filebacked.R | 3 plmmr-4.2.0/plmmr/R/summary-cv-plmm.R | 2 plmmr-4.2.0/plmmr/R/untransform.R | 27 ++ plmmr-4.2.0/plmmr/R/untransform_delim.R |only plmmr-4.2.0/plmmr/R/untransform_in_memory.R | 1 plmmr-4.2.0/plmmr/R/untransform_plink.R |only plmmr-4.2.0/plmmr/R/zzz.R |only plmmr-4.2.0/plmmr/README.md | 3 plmmr-4.2.0/plmmr/build/partial.rdb |binary plmmr-4.2.0/plmmr/build/vignette.rds |binary plmmr-4.2.0/plmmr/inst/CITATION | 16 + plmmr-4.2.0/plmmr/inst/doc/getting-started.html | 6 plmmr-4.2.0/plmmr/man/cv_plmm.Rd | 35 --- plmmr-4.2.0/plmmr/man/cvf.Rd | 4 plmmr-4.2.0/plmmr/man/plmm.Rd | 73 +++---- plmmr-4.2.0/plmmr/man/plmm_checks.Rd | 3 plmmr-4.2.0/plmmr/man/plmm_fit.Rd | 44 ---- plmmr-4.2.0/plmmr/man/plmm_format.Rd | 18 + plmmr-4.2.0/plmmr/man/plmm_prep.Rd | 7 plmmr-4.2.0/plmmr/man/predict.plmm.Rd | 20 +- plmmr-4.2.0/plmmr/man/predict_within_cv.Rd | 30 --- plmmr-4.2.0/plmmr/man/summary.cv_plmm.Rd | 2 plmmr-4.2.0/plmmr/man/untransform.Rd | 17 + plmmr-4.2.0/plmmr/man/untransform_delim.Rd |only plmmr-4.2.0/plmmr/man/untransform_plink.Rd |only plmmr-4.2.0/plmmr/src/big_standardize.cpp | 18 + 51 files changed, 654 insertions(+), 745 deletions(-)
Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Maximilian Muecke [aut, cre] ,
Damir Pulatov [aut],
Michel Lang [aut] ,
Marc Becker [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3cluster versions 0.1.10 dated 2024-10-03 and 0.1.11 dated 2025-02-18
mlr3cluster-0.1.10/mlr3cluster/tests/testthat/Rplots.pdf |only mlr3cluster-0.1.11/mlr3cluster/DESCRIPTION | 28 +- mlr3cluster-0.1.11/mlr3cluster/MD5 | 95 ++++------ mlr3cluster-0.1.11/mlr3cluster/NEWS.md | 11 - mlr3cluster-0.1.11/mlr3cluster/R/LearnerClust.R | 19 +- mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustAffinityPropagation.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustAgnes.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustDiana.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustFeatureless.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustHclust.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustMclust.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustMeanShift.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustMiniBatchKMeans.R | 2 mlr3cluster-0.1.11/mlr3cluster/R/LearnerClustPAM.R | 5 mlr3cluster-0.1.11/mlr3cluster/R/MeasureClust.R | 20 +- mlr3cluster-0.1.11/mlr3cluster/R/PredictionClust.R | 3 mlr3cluster-0.1.11/mlr3cluster/R/PredictionDataClust.R | 4 mlr3cluster-0.1.11/mlr3cluster/R/as_prediction_clust.R | 7 mlr3cluster-0.1.11/mlr3cluster/R/as_task_clust.R | 4 mlr3cluster-0.1.11/mlr3cluster/R/zzz.R | 4 mlr3cluster-0.1.11/mlr3cluster/README.md | 78 ++++---- mlr3cluster-0.1.11/mlr3cluster/build/partial.rdb |binary mlr3cluster-0.1.11/mlr3cluster/man/mlr3cluster-package.Rd | 5 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/helper_expectations.R | 16 - mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_LearnerClust.R | 2 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_agnes.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_ap.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_bico.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_birch.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_cmeans.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_cobweb.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_dbscan_fpc.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_diana.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_em.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_fanny.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_featureless.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_ff.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_hclust.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_hdbscan.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_kkmeans.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_kmeans.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_mbatchkmeans.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_mclust.R | 8 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_meanshift.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_optics.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_pam.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_simplekmeans.R | 6 mlr3cluster-0.1.11/mlr3cluster/tests/testthat/test_mlr_learners_clust_xmeans.R | 6 49 files changed, 251 insertions(+), 220 deletions(-)
Title: Statistical Tools for the Analysis of Psychophysical Data
Description: Tools for the analysis of psychophysical data in R. This package allows to estimate the Point of Subjective Equivalence (PSE)
and the Just Noticeable Difference (JND), either from a psychometric function or from a Generalized Linear Mixed Model (GLMM).
Additionally, the package allows plotting the fitted models and the response data, simulating psychometric functions of different shapes, and simulating data sets.
For a description of the use of GLMMs applied to psychophysical data, refer to Moscatelli et al. (2012).
Author: Alessandro Moscatelli [aut, cre]
,
Priscilla Balestrucci [aut]
Maintainer: Alessandro Moscatelli <moskante@gmail.com>
Diff between MixedPsy versions 1.1.0 dated 2021-11-08 and 1.2.0 dated 2025-02-18
DESCRIPTION | 11 +-- MD5 | 24 ++++--- NAMESPACE | 13 +++ R/PsySimulate.R | 163 +++++++++++++++++++++++++++--------------------- R/mix_utils.R | 4 - R/psych_utils.R | 2 R/psych_utils_multi.R |only R/xplode.R | 6 - man/PsySimulate.Rd | 59 ++++++++++------- man/PsychInterpolate.Rd |only man/PsychModels.Rd |only man/PsychParameters.Rd |only man/PsychShape.Rd | 2 man/pseMer.Rd | 4 - man/xplode.Rd | 6 - 15 files changed, 173 insertions(+), 121 deletions(-)
Title: Meta-Analysis for Detecting Genotype x Environment Associations
Description: Provides functions to perform all steps of genome-wide
association meta-analysis for studying Genotype x Environment
interactions, from collecting the data to the manhattan plot. The
procedure accounts for the potential correlation between studies. In
addition to the Fixed and Random models, one can investigate the
relationship between QTL effects and some qualitative or quantitative
covariate via the test of contrast and the meta-regression,
respectively. The methodology is available from: (De Walsche, A., et
al. (2023) \doi{10.1101/2023.03.01.530237}).
Author: Annaig De Walsche [aut, cre] ,
Tristan Mary-Huard [aut]
Maintainer: Annaig De Walsche <annaig.de-walsche@inrae.fr>
Diff between metaGE versions 1.1.0 dated 2024-07-31 and 1.2.0 dated 2025-02-18
DESCRIPTION | 10 ++--- MD5 | 26 ++++++------- R/metaGEfit.R | 3 + R/metaGEmatcor.R | 60 ++++++++++++++++++------------ R/metaGEplot.R | 22 +++++++---- R/metaGEtest.R | 4 +- inst/doc/metaGE-vignette.html | 84 +++++++++++++++++++++--------------------- man/FastKerFdr.Rd | 11 +++++ man/metaGE.cor.Rd | 5 +- man/metaGE.fit.Rd | 3 + man/metaGE.heatmap.Rd | 2 + man/metaGE.manhattan.Rd | 11 +++-- man/metaGE.pvalplot.Rd | 2 + man/metaGE.test.Rd | 4 +- 14 files changed, 144 insertions(+), 103 deletions(-)
Title: A Logging Utility Focus on Clinical Trial Programming Workflows
Description: A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
Author: Nathan Kosiba [aut, cre],
Thomas Bermudez [aut],
Ben Straub [aut],
Michael Rimler [aut],
Nicholas Masel [aut],
Sam Parmar [aut],
GSK/Atorus JPT [cph, fnd]
Maintainer: Nathan Kosiba <nhkosiba@gmail.com>
Diff between logrx versions 0.3.1 dated 2024-04-11 and 0.3.2 dated 2025-02-18
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 3 +++ build/vignette.rds |binary inst/doc/approved.html | 30 ++++++++++++++++-------------- inst/doc/execution.R | 16 ++++++++-------- inst/doc/execution.html | 5 +++-- inst/doc/logrx.R | 2 +- inst/doc/logrx.html | 5 +++-- inst/doc/options.html | 2 ++ tests/testthat/test-get.R | 19 ++++++++++--------- tests/testthat/test-writer.R | 27 ++++++++++++++------------- 12 files changed, 75 insertions(+), 64 deletions(-)
Title: Calculate Genetic Interactions for Paired CRISPR Targets
Description: Helps find meaningful patterns in complex genetic experiments. First gimap takes data from paired CRISPR (Clustered regularly interspaced short palindromic repeats) screens that has been pre-processed to counts table of paired gRNA (guide Ribonucleic Acid) reads. The input data will have cell counts for how well cells grow (or don't grow) when different genes or pairs of genes are disabled. The output of the 'gimap' package is genetic interaction scores which are the distance between the observed CRISPR score and the expected CRISPR score. The expected CRISPR scores are what we expect for the CRISPR values to be for two unrelated genes. The further away an observed CRISPR score is from its expected score the more we suspect genetic interaction. The work in this package is based off of original research from the Alice Berger lab at Fred Hutchinson Cancer Center (2021) <doi:10.1016/j.celrep.2021.109597>.
Author: Candace Savonen [aut, cre],
Phoebe Parrish [aut],
Kate Isaac [aut],
Howard Baek [aut],
Daniel Grosso [aut],
Siobhan O'Brien [aut],
Alice Berger [aut]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between gimap versions 1.0.1 dated 2025-02-03 and 1.0.2 dated 2025-02-18
DESCRIPTION | 6 +- MD5 | 34 ++++++------ NEWS.md | 7 ++ R/02-gimap_filter.R | 108 ++++++++++++++-------------------------- R/03-annotate.R | 7 +- R/utils.R | 2 inst/doc/quick-start.Rmd | 18 ++++++ inst/doc/quick-start.html | 90 +++++++++++++++++++-------------- inst/doc/timepoint-example.Rmd | 18 ++++++ inst/doc/timepoint-example.html | 96 ++++++++++++++++++++--------------- inst/doc/treatment_example.Rmd | 18 ++++++ inst/doc/treatment_example.html | 108 ++++++++++++++++++++++------------------ man/gimap_annotate.Rd | 2 man/gimap_filter.Rd | 16 ++--- man/qc_filter_zerocounts.Rd | 2 vignettes/quick-start.Rmd | 18 ++++++ vignettes/timepoint-example.Rmd | 18 ++++++ vignettes/treatment_example.Rmd | 18 ++++++ 18 files changed, 359 insertions(+), 227 deletions(-)
Title: Benchmark and Frontier Analysis Using DEA and SFA
Description: Methods for frontier
analysis, Data Envelopment Analysis (DEA), under different
technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+),
and using different efficiency measures (input based, output based,
hyperbolic graph, additive, super, and directional efficiency). Peers
and slacks are available, partial price information can be included,
and optimal cost, revenue and profit can be calculated. Evaluation of
mergers is also supported. Methods for graphing the technology sets
are also included. There is also support for comparative methods based
on Stochastic Frontier Analyses (SFA) and for convex nonparametric
least squares of convex functions (STONED). In general, the methods
can be used to solve not only standard models, but also many other
model variants. It complements the book, Bogetoft and Otto,
Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of
course also be used as a stand-alone package.
Author: Peter Bogetoft [aut],
Lars Otto [aut, cre]
Maintainer: Lars Otto <larsot23@gmail.com>
Diff between Benchmarking versions 0.32 dated 2024-03-13 and 0.33 dated 2025-02-18
Benchmarking-0.32/Benchmarking/R/Benchmarking.R |only Benchmarking-0.33/Benchmarking/DESCRIPTION | 18 ++++++++++++----- Benchmarking-0.33/Benchmarking/MD5 | 17 +++++++--------- Benchmarking-0.33/Benchmarking/NEWS | 9 +++++++- Benchmarking-0.33/Benchmarking/R/bootStat.R | 6 ++--- Benchmarking-0.33/Benchmarking/R/profit.R | 3 +- Benchmarking-0.33/Benchmarking/R/sfa.R | 2 - Benchmarking-0.33/Benchmarking/man/eladder.Rd | 12 +++++++---- Benchmarking-0.33/Benchmarking/man/sfa.Rd | 25 ++++++++++++------------ Benchmarking-0.33/Benchmarking/man/stoned.Rd | 10 +++++++-- 10 files changed, 64 insertions(+), 38 deletions(-)
Title: Measure Climate Scenario Alignment of Corporate Loans
Description: These tools help you to assess if a corporate lending
portfolio aligns with climate goals. They summarize key climate
indicators attributed to the portfolio (e.g. production, emission
factors), and calculate alignment targets based on climate scenarios.
They implement in R the last step of the free software 'PACTA' (Paris
Agreement Capital Transition Assessment;
<https://www.transitionmonitor.com/>). Financial institutions use 'PACTA'
to study how their capital allocation decisions align with climate
change mitigation goals.
Author: Jacob Kastl [aut, cre, ctr] ,
Alex Axthelm [aut, ctr] ,
Jackson Hoffart [aut, ctr] ,
Mauro Lepore [aut, ctr] ,
Klaus Hogedorn [aut],
Nicky Halterman [aut],
RMI [cph, fnd]
Maintainer: Jacob Kastl <jacob.kastl@gmail.com>
Diff between r2dii.analysis versions 0.5.0 dated 2025-02-13 and 0.5.1 dated 2025-02-18
DESCRIPTION | 10 +-- MD5 | 19 +++--- NEWS.md | 4 + R/join_abcd_scenario.R | 37 ++++++++----- R/target_market_share.R | 2 R/utils.R | 9 +-- data/data_dictionary.rda |binary man/join_abcd_scenario.Rd | 8 +- tests/testthat/test-data_dictionary.R |only tests/testthat/test-join_abcd_scenario.R | 36 ++++++++++++ tests/testthat/test-summarize_weighted_production.R | 56 +++++++++++++++++++- 11 files changed, 145 insertions(+), 36 deletions(-)
More information about r2dii.analysis at CRAN
Permanent link
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Lucas Mation [aut]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between enderecobr versions 0.4.0 dated 2025-01-14 and 0.4.1 dated 2025-02-18
DESCRIPTION | 6 ++--- MD5 | 14 +++++------ NEWS.md | 12 ++++++++++ R/padronizar_ceps.R | 8 +++++- R/padronizar_numeros.R | 4 ++- tests/testthat/_snaps/padronizar_enderecos.md | 31 ++++++++++++++++++++++++++ tests/testthat/test-padronizar_enderecos.R | 27 ++++++++++++++++++++++ tests/testthat/test-padronizar_numeros.R | 1 8 files changed, 90 insertions(+), 13 deletions(-)
Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre],
Muhammed Ali Yilmaz [aut],
Ozgur Asar [ctb],
Ozlem Ilk [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between AID versions 3.0 dated 2024-11-22 and 3.1 dated 2025-02-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/boxcoxmeta.R | 10 +++++----- R/boxcoxnc.R | 8 ++++---- 4 files changed, 16 insertions(+), 16 deletions(-)
Title: Assesses the Quality of Estimates Made by Complex Sample Designs
Description: Assesses the quality of estimates made by complex sample designs,
following the methodology developed by the National Institute of Statistics Chile (2020, <https://www.ine.cl/docs/default-source/institucionalidad/buenas-pr%C3%A1cticas/clasificaciones-y-estandares/est%C3%A1ndar-evaluaci%C3%B3n-de-calidad-de-estimaciones-publicaci%C3%B3n-27022020.pdf>)
and by Economic Commission for Latin America and
Caribbean (2020, <https://repositorio.cepal.org/bitstream/handle/11362/45681/1/S2000293_es.pdf>), (2024, <https://repositorio.cepal.org/server/api/core/bitstreams/f04569e6-4f38-42e7-a32b-e0b298e0ab9c/content>).
Author: Klaus Lehmann [aut, cre],
Ricardo Pizarro [aut],
Ignacio Agloni [ctb],
Andrea Lopez [ctb],
Javiera Preuss [ctb]
Maintainer: Klaus Lehmann <klehmann@fen.uchile.cl>
Diff between calidad versions 0.6.0 dated 2024-10-16 and 0.7.0 dated 2025-02-18
DESCRIPTION | 13 +- MD5 | 28 ++-- NEWS.md | 5 R/create_external.R | 14 +- R/create_internal.R | 68 +++++++--- R/data.R | 35 +++++ data/enusc_2023.rda |only inst/doc/tutorial.R | 8 + inst/doc/tutorial.Rmd | 12 + inst/doc/tutorial.html | 240 ++++++++++++++++++++------------------ man/create_prop.Rd | 5 man/create_prop_internal.Rd | 5 man/enusc.Rd | 2 man/enusc_2023.Rd |only tests/testthat/test-create_prop.R | 91 ++++++++++++++ vignettes/tutorial.Rmd | 12 + 16 files changed, 376 insertions(+), 162 deletions(-)
More information about UAHDataScienceSF at CRAN
Permanent link
Title: Manage Data from Cardiopulmonary Exercise Testing
Description: Import, process, summarize and visualize raw data from
metabolic carts. See Robergs, Dwyer, and Astorino (2010) <doi:10.2165/11319670-000000000-00000> for more details on data processing.
Author: Simon Nolte [aut, cre] ,
Manuel Ramon [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/541>),
James Hunter [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/541>)
Maintainer: Simon Nolte <s.nolte@dshs-koeln.de>
Diff between spiro versions 0.2.1 dated 2023-08-14 and 0.2.3 dated 2025-02-18
DESCRIPTION | 8 LICENSE | 2 MD5 | 67 NEWS.md | 24 R/spiro-package.R | 14 R/spiro.R | 4 R/spiro_get.R | 30 R/spiro_plot.R | 41 R/spiro_raw.R | 6 README.md | 45 build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/import_processing.R | 90 inst/doc/import_processing.Rmd | 66 inst/doc/import_processing.html | 18 inst/doc/summarizing_plotting.R | 9 inst/doc/summarizing_plotting.Rmd | 9 inst/doc/summarizing_plotting.html | 20 man/spiro-package.Rd | 24 man/spiro.Rd | 4 tests/testthat/_snaps/spiro_plot/basic.svg | 4188 ++++++++++---------- tests/testthat/_snaps/spiro_plot/bsmooth.svg | 4188 ++++++++++---------- tests/testthat/_snaps/spiro_plot/color.svg | 5414 +++++++++++++------------- tests/testthat/_snaps/spiro_plot/grid.svg | 1468 +++---- tests/testthat/_snaps/spiro_plot/hr.svg | 5414 +++++++++++++------------- tests/testthat/_snaps/spiro_plot/style.svg | 4188 ++++++++++---------- tests/testthat/_snaps/spiro_plot/theme.svg | 4188 ++++++++++---------- tests/testthat/_snaps/spiro_plot/tsmooth.svg | 4194 ++++++++++---------- tests/testthat/_snaps/spiro_plot/vertline.svg | 4212 ++++++++++---------- tests/testthat/_snaps/spiro_summary.md | 2 tests/testthat/test-spiro_raw.R | 1 tests/testthat/test_spiro_plot.R | 3 vignettes/import_processing.Rmd | 66 vignettes/summarizing_plotting.Rmd | 9 35 files changed, 19045 insertions(+), 18972 deletions(-)
Title: Non-Interactive Spatial Tools for Raster Processing and
Visualization
Description: S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.
Author: Nikita Platonov [aut, cre]
Maintainer: Nikita Platonov <platonov@sev-in.ru>
Diff between ursa versions 3.11.2 dated 2025-01-14 and 3.11.3 dated 2025-02-18
DESCRIPTION | 14 -- MD5 | 181 ++++++++++++++------------- NAMESPACE | 5 NEWS.md | 31 ++++ R/classCRS.R | 77 ++++++++++- R/classRaster.Extract.R | 21 ++- R/classRaster_as.matrix.R | 6 R/classRaster_hist.R | 2 R/colorize.R | 3 R/compose_close.R | 10 + R/compose_legend.R | 2 R/conn.open_gdal.R | 3 R/conn.read_gdal.R | 3 R/cubehelix.R | 4 R/glance.R | 2 R/legend_colorbar.R | 2 R/legend_mtext.R | 2 R/panel_annotation.R | 4 R/panel_coastline.R | 2 R/panel_contour.R | 2 R/panel_graticule.R | 4 R/panel_new.R | 9 - R/panel_plot.R | 4 R/panel_raster.R | 18 +- R/panel_scalebar.R | 2 R/polygonize.R | 3 R/spatial_write.R | 18 ++ R/unix |only R/ursa_blank.R | 2 R/windows |only R/xxx.geomap.R | 18 +- R/xxx.panel_basemap.R | 4 R/xxx.panel_cluster.R | 10 + R/xxx.panel_legend.R | 2 R/xxx.spatialize.R | 3 R/yyy.cache.R | 2 R/yyy.getPrm.R | 254 +++++++++++++++++++-------------------- R/yyy.tile.R | 2 R/yyy.util.R | 96 ++++++++++++++ R/zzz.R | 2 inst/requisite/browseURL.html |only inst/requisite/coast-l.rds |binary man/Ops.band_stat.Rd | 2 man/Ops.focal_mean.Rd | 2 man/Ops.focal_special.Rd | 2 man/Ops.global_group.Rd | 2 man/Ops.local_group.Rd | 2 man/allocate.Rd | 2 man/chunk.Rd | 2 man/classCRS.Rd | 2 man/classColorTable.Rd | 2 man/classConnection.Rd | 2 man/classGrid.Rd | 2 man/classRaster.Extract.Rd | 2 man/classRaster_GroupGeneric.Rd | 2 man/classRaster_as.data.frame.Rd | 2 man/classRaster_as.table.Rd | 2 man/classRaster_c.Rd | 2 man/classRaster_is.na.Rd | 2 man/classRaster_length.Rd | 2 man/classRaster_names.Rd | 2 man/classRaster_sort.Rd | 2 man/classRaster_summary.Rd | 2 man/codec.Rd | 2 man/compose_close.Rd | 2 man/compose_design.Rd | 2 man/compose_open.Rd | 2 man/compose_panel.Rd | 2 man/conn.create_any.Rd | 2 man/conn.open_gdal.Rd | 2 man/conn.write_envi.Rd | 2 man/cubehelix.Rd | 2 man/display_rgb.Rd | 2 man/display_stack.Rd | 2 man/get_earthdata.Rd | 2 man/identify.Rd | 2 man/legend_align.Rd | 2 man/package_raster.Rd | 2 man/package_sf.Rd | 2 man/panel_coastline.Rd | 2 man/panel_contour.Rd | 2 man/panel_new.Rd | 2 man/panel_raster.Rd | 2 man/panel_scalebar.Rd | 2 man/progressBar.Rd | 2 man/regrid.Rd | 2 man/session.Rd | 2 man/temporal_mean.Rd | 2 man/trackline.Rd | 2 man/ursa_as.Rd | 2 man/ursa_blank.Rd | 2 man/ursa_crs.Rd | 2 man/ursa_new.Rd | 2 93 files changed, 591 insertions(+), 340 deletions(-)
Title: Processing Proteomics Data, Statistical Analysis and
Visualization
Description: The 'Proteomics Eye' ('ProtE') offers a comprehensive and intuitive framework for the univariate analysis of label-free proteomics data. By integrating essential data wrangling and processing steps into a single function, 'ProtE' streamlines pairwise statistical comparisons for categorical variables. It provides quality checks and generates publication-ready visualizations, enabling efficient and robust data analysis. 'ProtE' is compatible with proteomics data outputs from 'MaxQuant' (Cox & Mann, (2008) <doi:10.1038/nbt.1511>), 'DIA-NN' (Demichev et al., (2020) <doi:10.1038/s41592-019-0638-x>), and 'Proteome Discoverer' (Thermo Fisher Scientific, version 2.5). The package leverages 'ggplot2' for visualization (Wickham, (2016) <doi:10.1007/978-3-319-24277-4>) and 'limma' for statistical analysis (Ritchie et al., (2015) <doi:10.1093/nar/gkv007>).
Author: Theodoros Margelos [aut, cre, cph],
Rafael Stroggilos [ctb, cph]
Maintainer: Theodoros Margelos <ted.margelos02@gmail.com>
Diff between ProtE versions 1.0.2 dated 2025-02-17 and 1.0.3 dated 2025-02-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 2 ++ R/DIAnn.R | 2 +- R/new_vers_PD.R | 2 +- R/path_res.R | 2 +- 6 files changed, 13 insertions(+), 11 deletions(-)
Title: Interior Point Conic Optimization Solver
Description: A versatile interior point solver that solves linear programs (LPs), quadratic programs (QPs), second-order cone programs (SOCPs), semidefinite programs (SDPs), and problems with exponential and power cone constraints (<https://clarabel.org/stable/>). For quadratic objectives, unlike interior point solvers based on the standard homogeneous self-dual embedding (HSDE) model, Clarabel handles quadratic objective without requiring any epigraphical reformulation of its objective function. It can therefore be significantly faster than other HSDE-based solvers for problems with quadratic objective functions. Infeasible problems are detected using using a homogeneous embedding technique.
Author: Balasubramanian Narasimhan [aut, cre],
Paul Goulart [aut, cph],
Yuwen Chen [aut],
Hiroaki Yutani [ctb] ,
David Zimmermann-Kollenda [ctb] ,
Hiroaki Yutani [ctb] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between clarabel versions 0.9.0.1 dated 2024-09-03 and 0.10.0 dated 2025-02-18
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 27 +++++++++++++++------------ NEWS.md | 9 +++++++++ R/clarabel.R | 6 +++++- build/vignette.rds |binary configure | 6 +++++- configure.win |only inst/doc/clarabel.html | 5 +++-- man/clarabel_control.Rd | 3 +++ src/Makevars.in | 6 +++++- src/Makevars.win | 4 +--- src/rust/Cargo.lock |only src/rust/Cargo.toml | 10 +++++++--- src/rust/cargo_vendor_config.toml | 11 ++++++++++- src/rust/vendor.tar.xz |binary tools |only 16 files changed, 78 insertions(+), 32 deletions(-)
Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut],
Martin Studer [cre],
The Apache Software Foundation [ctb, cph] ,
Graph Builder [ctb, cph] ,
Brett Woolridge [ctb, cph]
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>
Diff between XLConnect versions 1.1.0 dated 2024-08-22 and 1.2.0 dated 2025-02-18
XLConnect-1.1.0/XLConnect/inst/java/XLConnect-3.0.0-SNAPSHOT.jar |only XLConnect-1.2.0/XLConnect/DESCRIPTION | 6 +- XLConnect-1.2.0/XLConnect/MD5 | 18 +++--- XLConnect-1.2.0/XLConnect/NEWS | 11 ++-- XLConnect-1.2.0/XLConnect/R/onLoad.R | 26 +++++----- XLConnect-1.2.0/XLConnect/build/vignette.rds |binary XLConnect-1.2.0/XLConnect/inst/COPYRIGHTS | 2 XLConnect-1.2.0/XLConnect/inst/doc/XLConnect.pdf |binary XLConnect-1.2.0/XLConnect/inst/doc/XLConnectImpatient.pdf |binary XLConnect-1.2.0/XLConnect/inst/java/XLConnect-3.1.0.jar |only XLConnect-1.2.0/XLConnect/inst/java/log4j2.system.properties | 3 - 11 files changed, 35 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-04 1.0.0
Title: Analysis and Visualization of Multi-Omics Data
Description: A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10. [...truncated...]
Author: Dongyue Yu [aut, cre, cph]
Maintainer: Dongyue Yu <yudongyue@mail.nankai.edu.cn>
Diff between TransProR versions 1.0.2 dated 2025-02-14 and 1.0.3 dated 2025-02-18
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 1 - R/CircosFruits.R | 3 --- inst/doc/TransProR.html | 4 ++-- 5 files changed, 12 insertions(+), 16 deletions(-)
Title: Small Area Estimation Using Model-Assisted Projection Method
Description: Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Author: Ridson Al Farizal P [aut, cre, cph]
,
Azka Ubaidillah [aut] ,
Silvi Ajeng Larasati [aut]
Maintainer: Ridson Al Farizal P <ridsonalfarizal15@gmail.com>
Diff between sae.projection versions 0.1.1 dated 2025-02-15 and 0.1.2 dated 2025-02-18
sae.projection-0.1.1/sae.projection/R/Projection_rf.R |only sae.projection-0.1.1/sae.projection/R/Projection_rf_CorrectedBias.R |only sae.projection-0.1.1/sae.projection/man/Projection_rf.Rd |only sae.projection-0.1.1/sae.projection/man/Projection_rf_CorrectedBias.Rd |only sae.projection-0.1.2/sae.projection/DESCRIPTION | 6 sae.projection-0.1.2/sae.projection/MD5 | 22 sae.projection-0.1.2/sae.projection/NAMESPACE | 25 sae.projection-0.1.2/sae.projection/R/data.R | 256 +-- sae.projection-0.1.2/sae.projection/R/proj_random_forest.R |only sae.projection-0.1.2/sae.projection/R/projection.R | 688 +++++----- sae.projection-0.1.2/sae.projection/README.md | 502 +++---- sae.projection-0.1.2/sae.projection/data/df_susenas_sep2020.rda |binary sae.projection-0.1.2/sae.projection/man/df_susenas_sep2020.Rd | 2 sae.projection-0.1.2/sae.projection/man/proj_random_forest.Rd |only sae.projection-0.1.2/sae.projection/man/projection_rf.Rd |only sae.projection-0.1.2/sae.projection/man/projection_rf_CorrectedBias.Rd |only 16 files changed, 751 insertions(+), 750 deletions(-)
More information about sae.projection at CRAN
Permanent link
Title: Install and Load the 'dartRverse' Suits of Packages
Description: Provides a single function that supports the installation of all packages
belonging to the 'dartRverse'. The 'dartRverse' is a set of packages that work
together to analyse SNP (single nuclear polymorphism) data. All packages aim to have a similar 'look and feel'
and are based on the same type of data structure ('genlight'), with additional
metadata for loci and individuals (samples). For more information visit the
'GitHub' pages <https://github.com/green-striped-gecko/dartRverse>.
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Peter J. Unmack [aut],
Oliver Berry [aut]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartRverse versions 1.0.2 dated 2024-05-24 and 1.0.6 dated 2025-02-18
DESCRIPTION | 12 +++---- MD5 | 8 +++- NAMESPACE | 28 ++++++++++------ R/gl.download.binary.r |only man/dartRverse_install.Rd | 76 +++++++++++++++++++++++----------------------- man/gl.download.binary.Rd |only 6 files changed, 66 insertions(+), 58 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] ,
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.2.2 dated 2024-11-27 and 0.2.3 dated 2025-02-18
cardx-0.2.2/cardx/tests/spelling.R |only cardx-0.2.3/cardx/DESCRIPTION | 21 cardx-0.2.3/cardx/MD5 | 57 - cardx-0.2.3/cardx/NAMESPACE | 1 cardx-0.2.3/cardx/NEWS.md | 22 cardx-0.2.3/cardx/R/ard_categorical.survey.design.R | 9 cardx-0.2.3/cardx/R/ard_categorical_ci.R | 391 ++++++++-- cardx-0.2.3/cardx/R/ard_categorical_max.R |only cardx-0.2.3/cardx/R/ard_missing.survey.design.R | 7 cardx-0.2.3/cardx/R/ard_survival_survfit.R | 20 cardx-0.2.3/cardx/R/proportion_ci.R | 21 cardx-0.2.3/cardx/README.md | 36 cardx-0.2.3/cardx/inst/WORDLIST | 2 cardx-0.2.3/cardx/man/ard_categorical_ci.Rd | 15 cardx-0.2.3/cardx/man/ard_categorical_ci.survey.design.Rd | 4 cardx-0.2.3/cardx/man/ard_categorical_max.Rd |only cardx-0.2.3/cardx/man/ard_survival_survfit.Rd | 3 cardx-0.2.3/cardx/man/cardx-package.Rd | 2 cardx-0.2.3/cardx/man/dot-strata_normal_quantile.Rd | 6 cardx-0.2.3/cardx/man/dot-update_weights_strat_wilson.Rd | 4 cardx-0.2.3/cardx/man/proportion_ci.Rd | 13 cardx-0.2.3/cardx/tests/testthat.R | 2 cardx-0.2.3/cardx/tests/testthat/_snaps/ard_categorical.survey.design.md | 16 cardx-0.2.3/cardx/tests/testthat/_snaps/ard_categorical_max.md |only cardx-0.2.3/cardx/tests/testthat/_snaps/ard_proportion_ci.md | 26 cardx-0.2.3/cardx/tests/testthat/_snaps/ard_survival_survfit.md | 24 cardx-0.2.3/cardx/tests/testthat/_snaps/proportion_ci.md | 57 + cardx-0.2.3/cardx/tests/testthat/test-ard_categorical.survey.design.R | 52 + cardx-0.2.3/cardx/tests/testthat/test-ard_categorical_ci.data.frame.R | 319 +++++++- cardx-0.2.3/cardx/tests/testthat/test-ard_categorical_max.R |only cardx-0.2.3/cardx/tests/testthat/test-ard_missing.survey.design.R | 33 cardx-0.2.3/cardx/tests/testthat/test-ard_survival_survfit.R | 9 32 files changed, 994 insertions(+), 178 deletions(-)
Title: Interpolation and Extrapolation for Three Dimensions of
Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from
genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D)
of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional
diversity (FD). This package provides functions to compute standardized 3D diversity estimates
with a common sample size or sample coverage. A unified framework based on Hill numbers
and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates
are in the same units of species/lineage equivalents and can be meaningfully compared.
The package features size- and coverage-based rarefaction and extrapolation sampling
curves to facilitate rigorous comparison of 3D diversity across individual assemblages.
Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021)
<doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.3D versions 1.0.7 dated 2025-01-22 and 1.0.8 dated 2025-02-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 5 +++++ R/ChaoUtility_Fun.R | 24 ++++++++++++++++-------- R/CommonFun.R | 2 +- inst/doc/Introduction.pdf |binary 6 files changed, 30 insertions(+), 17 deletions(-)