Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Diff between estimatr versions 1.0.2 dated 2024-01-17 and 1.0.4 dated 2024-03-31
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/estimatr_horvitz_thompson.R | 5 ++--- build/partial.rdb |binary man/estimatr.Rd | 2 +- man/horvitz_thompson.Rd | 5 ++--- tests/testthat/helper-lm-robust-se.R | 1 + tests/testthat/test-lm-cluster.R | 2 +- tests/testthat/test-modelsummary.R | 12 +++++++----- 10 files changed, 31 insertions(+), 26 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine and for various extensions in a recent version is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 2.3.5 dated 2024-01-21 and 2.3.6 dated 2024-03-31
DESCRIPTION | 11 MD5 | 10 NEWS.md | 11 inst/doc/RSQLite.html | 2 src/vendor/sqlite3/sqlite3.c | 499 +++++++++++++++++++++++++++++-------------- src/vendor/sqlite3/sqlite3.h | 8 6 files changed, 365 insertions(+), 176 deletions(-)
Title: A Unified Time Series Event Detection Framework
Description: By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Antonio Castro [aut],
Antonio Mello [aut],
Ellen Paixao [aut],
Fernando Fraga [aut],
Heraldo Borges [aut],
Janio Lima [aut],
Jessica Souza [aut],
Lais Baroni [aut],
Lucas Tavares [aut],
Rebecca Salles [aut],
Diego [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between harbinger versions 1.0.747 dated 2024-03-26 and 1.0.767 dated 2024-03-31
harbinger-1.0.747/harbinger/R/hmo_base36.R |only harbinger-1.0.747/harbinger/man/hmo_base36.Rd |only harbinger-1.0.767/harbinger/DESCRIPTION | 8 +-- harbinger-1.0.767/harbinger/MD5 | 28 +++++++++++-- harbinger-1.0.767/harbinger/NAMESPACE | 30 +++++++++++++- harbinger-1.0.767/harbinger/R/hanr_emd.R |only harbinger-1.0.767/harbinger/R/hanr_fft.R |only harbinger-1.0.767/harbinger/R/hanr_remd.R |only harbinger-1.0.767/harbinger/R/hanr_wavelet.R |only harbinger-1.0.767/harbinger/R/hcd_ddm.R |only harbinger-1.0.767/harbinger/R/hcd_eddm.R |only harbinger-1.0.767/harbinger/R/hcd_hddm.R |only harbinger-1.0.767/harbinger/R/hmo_sax.R | 50 +----------------------- harbinger-1.0.767/harbinger/R/hmo_xsax.R |only harbinger-1.0.767/harbinger/R/trans_sax.R |only harbinger-1.0.767/harbinger/R/trans_xsax.R |only harbinger-1.0.767/harbinger/man/hanr_emd.Rd |only harbinger-1.0.767/harbinger/man/hanr_fft.Rd |only harbinger-1.0.767/harbinger/man/hanr_remd.Rd |only harbinger-1.0.767/harbinger/man/hanr_wavelet.Rd |only harbinger-1.0.767/harbinger/man/hcd_ddm.Rd |only harbinger-1.0.767/harbinger/man/hcd_eddm.Rd |only harbinger-1.0.767/harbinger/man/hcd_hddm.Rd |only harbinger-1.0.767/harbinger/man/hmo_xsax.Rd |only harbinger-1.0.767/harbinger/man/trans_sax.Rd |only harbinger-1.0.767/harbinger/man/trans_xsax.Rd |only 26 files changed, 59 insertions(+), 57 deletions(-)
Title: Leveraging Experiment Lines to Data Analytics
Description: The natural increase in the complexity of current research experiments and data demands better tools to enhance productivity in Data Analytics. The package is a framework designed to address the modern challenges in data analytics workflows. The package is inspired by Experiment Line concepts. It aims to provide seamless support for users in developing their data mining workflows by offering a uniform data model and method API. It enables the integration of various data mining activities, including data preprocessing, classification, regression, clustering, and time series prediction. It also offers options for hyper-parameter tuning and supports integration with existing libraries and languages. Overall, the package provides researchers with a comprehensive set of functionalities for data science, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_2 [...truncated...]
Author: Eduardo Ogasawara [aut, ths, cre]
,
Antonio Castro [aut, ctb],
Heraldo Borges [aut, ths],
Diego Carvalho [aut, ths],
Joel Santos [aut, ths],
Eduardo Bezerra [aut, ths],
Rafaelli Coutinho [aut, ths],
Federal Center for Technological Education of Rio d [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolbox versions 1.0.747 dated 2024-03-25 and 1.0.767 dated 2024-03-31
DESCRIPTION | 62 ++++++++++------------------------------------------- LICENSE | 2 - MD5 | 11 +++++---- NAMESPACE | 1 R/reg_regression.R | 11 ++++++++- R/ts_reg.R | 17 +++++++++++++- man/R2.ts.Rd |only 7 files changed, 46 insertions(+), 58 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs. The methods are described in Leifeld, Cranmer and Desmarais (2018), JStatSoft <doi:10.18637/jss.v083.i06>.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@manchester.ac.uk>
Diff between btergm versions 1.10.11 dated 2023-10-05 and 1.10.12 dated 2024-03-31
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ R/btergm.R | 5 ++--- R/gofstatistics.R | 2 +- build/partial.rdb |binary man/btergm-package.Rd | 7 +++++++ man/gof-statistics.Rd | 2 +- 7 files changed, 24 insertions(+), 18 deletions(-)
Title: Fast General Purpose Date/Time Converter
Description: Fast general purpose date/time converter using 'Rust'. The package implements date time, date and epoch time parser for heterogeneous vectors of dates.
Author: David Schoch [aut, cre] ,
Rollie Ma [ctb, cph] ,
Brandon W. Maister [ctb, cph] ,
Dirkjan Ochtman [ctb, cph] ,
Seonghoon Kang [ctb, cph] ,
Eric Sheppard [ctb, cph] ,
Paul Dicker [ctb, cph]
Maintainer: David Schoch <david@schochastics.net>
Diff between timeless versions 0.2.0 dated 2024-03-29 and 0.2.1 dated 2024-03-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-timeless.R | 1 + 4 files changed, 11 insertions(+), 6 deletions(-)
Title: Pre-Commit Hooks
Description: Useful git hooks for R building on top of the multi-language
framework 'pre-commit' for hook management. This package provides git
hooks for common tasks like formatting files with 'styler' or spell
checking as well as wrapper functions to access the 'pre-commit'
executable.
Author: Lorenz Walthert
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between precommit versions 0.4.0 dated 2024-01-21 and 0.4.1 dated 2024-03-31
precommit-0.4.0/precommit/tests/testthat/test-hooks-regex-exclude.R |only precommit-0.4.0/precommit/tests/testthat/test-hooks.R |only precommit-0.4.1/precommit/DESCRIPTION | 18 precommit-0.4.1/precommit/MD5 | 68 +- precommit-0.4.1/precommit/NEWS.md | 10 precommit-0.4.1/precommit/R/config.R | 2 precommit-0.4.1/precommit/R/exec.R | 11 precommit-0.4.1/precommit/R/release.R | 8 precommit-0.4.1/precommit/R/roxygen2.R | 4 precommit-0.4.1/precommit/R/setup.R | 6 precommit-0.4.1/precommit/R/testing.R | 25 - precommit-0.4.1/precommit/R/utils.R | 4 precommit-0.4.1/precommit/inst/doc/available-hooks.Rmd | 12 precommit-0.4.1/precommit/inst/doc/available-hooks.html | 13 precommit-0.4.1/precommit/inst/doc/hook-order.Rmd | 2 precommit-0.4.1/precommit/inst/doc/hook-order.html | 3 precommit-0.4.1/precommit/inst/hooks/exported/spell-check.R | 51 +- precommit-0.4.1/precommit/inst/pre-commit-config-pkg.yaml | 4 precommit-0.4.1/precommit/inst/pre-commit-config-proj.yaml | 2 precommit-0.4.1/precommit/man/get_os.Rd |only precommit-0.4.1/precommit/man/run_test.Rd | 5 precommit-0.4.1/precommit/man/run_test_impl.Rd | 5 precommit-0.4.1/precommit/tests/testthat/in/spell-check-fail-2.md |only precommit-0.4.1/precommit/tests/testthat/reference-objects/pre-commit-config.yaml | 13 precommit-0.4.1/precommit/tests/testthat/test-conda.R | 39 + precommit-0.4.1/precommit/tests/testthat/test-exec.R | 104 ++-- precommit-0.4.1/precommit/tests/testthat/test-hook-codemeta-description-updated.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-deps-in-desc-R.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-lintr.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-no-browser-statement.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-no-debug-statement.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-no-print-statement.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-parsable-R.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-pkgdown.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-readme-rmd-rendered.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-roxygenize.R | 248 +++------- precommit-0.4.1/precommit/tests/testthat/test-hook-spell-check.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-style-files.R |only precommit-0.4.1/precommit/tests/testthat/test-hook-use-tidy-description.R |only precommit-0.4.1/precommit/tests/testthat/test-impl-hook-roxygenize.R |only precommit-0.4.1/precommit/tests/testthat/test-impl-hooks-regex-exclude.R |only precommit-0.4.1/precommit/tests/testthat/test-setup.R | 39 - precommit-0.4.1/precommit/vignettes/available-hooks.Rmd | 12 precommit-0.4.1/precommit/vignettes/hook-order.Rmd | 2 44 files changed, 373 insertions(+), 337 deletions(-)
Title: Digitization of Phytosociological Relevés
Description: Simple and fast tool for transforming phytosociological
vegetation data into digital form for the following analysis.
Danihelka, Chrtek, and Kaplan (2012, ISSN:00327786).
Hennekens, and Schaminée (2001) <doi:10.2307/3237010>.
Tichý (2002) <doi:10.1111/j.1654-1103.2002.tb02069.x>.
Wickham, François, Henry, Müller (2022) <https://CRAN.R-project.org/package=dplyr>.
Author: Premysl Kral [aut, cre] ,
Jan Douda [aut]
Maintainer: Premysl Kral <kralp@fzp.czu.cz>
Diff between Rveg versions 0.1.3 dated 2023-10-23 and 0.1.4 dated 2024-03-31
DESCRIPTION | 8 MD5 | 36 + NAMESPACE | 3 R/CreateChecklist.R |only R/Rveg-package.R | 1 R/RvegCheck.R | 181 ++++----- R/RvegCombine.R | 204 +++++----- R/RvegMERGE.r | 53 +- R/RvegToJuice.R | 439 +++++++++++++--------- R/addReleve.R | 821 +++++++++++++++++++++---------------------- R/createTABLE.R | 68 ++- inst/doc/Rveg.pdf |binary inst/extdata/SpeciesList.txt |only man/CreateChecklist.Rd |only man/RvegCheck.Rd | 10 man/RvegCombine.Rd | 14 man/RvegMerge.Rd | 15 man/RvegToJuice.Rd | 11 man/RvegToTv.Rd |only man/addReleve.Rd | 5 man/tvToRveg.Rd | 12 21 files changed, 987 insertions(+), 894 deletions(-)
Title: Robust Sparse PCA using the ROSPCA Algorithm
Description: Implementation of robust sparse PCA using the ROSPCA algorithm
of Hubert et al. (2016) <DOI:10.1080/00401706.2015.1093962>.
Author: Tom Reynkens [aut, cre] ,
Valentin Todorov [ctb] ,
Mia Hubert [ctb],
Eric Schmitt [ctb],
Tim Verdonck [ctb]
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>
Diff between rospca versions 1.0.4 dated 2018-02-26 and 1.1.0 dated 2024-03-31
DESCRIPTION | 11 +++++------ MD5 | 14 +++++++------- NAMESPACE | 3 +-- R/Rospca.R | 20 ++++++++++---------- R/SelectLambda.R | 2 +- R/Sim_aux.R | 26 +++++++++++++++++++------- inst/NEWS.Rd | 8 ++++++++ man/rospca.Rd | 6 +++--- 8 files changed, 54 insertions(+), 36 deletions(-)
Title: Penalized Regression Calibration (PRC) for the Dynamic
Prediction of Survival
Description: Computes penalized regression calibration (PRC), a
statistical method for the dynamic prediction of survival when many
longitudinal predictors are available. PRC is described in Signorelli
et al. (2021) <doi:10.1002/sim.9178> and Signorelli (2023)
<doi:10.48550/arXiv.2309.15600>.
Author: Mirko Signorelli [aut, cre, cph]
,
Pietro Spitali [ctb],
Roula Tsonaka [ctb],
Barbara Vreede [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between pencal versions 2.1.1 dated 2023-10-27 and 2.2.1 dated 2024-03-31
pencal-2.1.1/pencal/R/getlmm.R |only pencal-2.1.1/pencal/R/getmlpmm.R |only pencal-2.1.1/pencal/man/getlmm.Rd |only pencal-2.1.1/pencal/man/getmlpmm.Rd |only pencal-2.2.1/pencal/DESCRIPTION | 6 +- pencal-2.2.1/pencal/MD5 | 56 +++++++++++++------------ pencal-2.2.1/pencal/NAMESPACE | 9 +++- pencal-2.2.1/pencal/R/classes.R | 8 +++ pencal-2.2.1/pencal/R/fit_lmms.R | 6 ++ pencal-2.2.1/pencal/R/fit_mlpmms.R | 4 + pencal-2.2.1/pencal/R/fit_prclmm.R | 19 ++++++++ pencal-2.2.1/pencal/R/fit_prcmlpmm.R | 10 +++- pencal-2.2.1/pencal/R/print_prclmm.R | 1 pencal-2.2.1/pencal/R/summarize_lmms.R | 2 pencal-2.2.1/pencal/R/summarize_mlpmms.R | 2 pencal-2.2.1/pencal/R/summary_lmmfit.R |only pencal-2.2.1/pencal/R/summary_mlpmmfit.R |only pencal-2.2.1/pencal/R/summary_prclmm.R | 5 +- pencal-2.2.1/pencal/R/summary_ranefs.R |only pencal-2.2.1/pencal/R/survplot_prc.R |only pencal-2.2.1/pencal/R/survpred_prclmm.R | 6 +- pencal-2.2.1/pencal/data/fitted_prclmm.RData |binary pencal-2.2.1/pencal/data/fitted_prcmlpmm.RData |binary pencal-2.2.1/pencal/inst/NEWS.md | 14 ++++++ pencal-2.2.1/pencal/inst/doc/vignette.pdf |binary pencal-2.2.1/pencal/man/fit_lmms.Rd | 5 ++ pencal-2.2.1/pencal/man/fit_mlpmms.Rd | 3 + pencal-2.2.1/pencal/man/fit_prclmm.Rd | 9 +++- pencal-2.2.1/pencal/man/fit_prcmlpmm.Rd | 8 +++ pencal-2.2.1/pencal/man/summarize_lmms.Rd | 1 pencal-2.2.1/pencal/man/summarize_mlpmms.Rd | 1 pencal-2.2.1/pencal/man/summary.lmmfit.Rd |only pencal-2.2.1/pencal/man/summary.mlpmmfit.Rd |only pencal-2.2.1/pencal/man/summary.ranefs.Rd |only pencal-2.2.1/pencal/man/survplot_prc.Rd |only 35 files changed, 134 insertions(+), 41 deletions(-)
Title: Code Analysis Tools for R
Description: Code analysis tools for R.
Author: Luke Tierney <luke-tierney@uiowa.edu>
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between codetools versions 0.2-19 dated 2023-02-01 and 0.2-20 dated 2024-03-31
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/codetools.R | 9 ++++++++- man/checkUsage.Rd | 4 ++-- noweb/codetools.nw | 45 +++++++++++++++++++++++++++++++++++++++++++-- tests/tests.R | 13 ++++++++++--- 6 files changed, 71 insertions(+), 16 deletions(-)
Title: Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan'
Description: Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte
Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological
positions of survey respondents and political actors on a common scale using positional survey
data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform
other versions both in terms of yielding meaningful posterior distributions for respondent
positions and in terms of recovering true respondent positions in simulations. The package
contains functions for preparing data, fitting models, extracting estimates, plotting key
results, and comparing models using cross-validation. The original version of the default
model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Author: Joergen Boelstad [aut, cre]
Maintainer: Joergen Boelstad <jorgen.bolstad@stv.uio.no>
Diff between hbamr versions 2.2.1 dated 2024-02-23 and 2.3.0 dated 2024-03-31
hbamr-2.2.1/hbamr/inst/stan/FBAM_MINI.stan |only hbamr-2.2.1/hbamr/src/stanExports_FBAM_MINI.cc |only hbamr-2.2.1/hbamr/src/stanExports_FBAM_MINI.h |only hbamr-2.3.0/hbamr/DESCRIPTION | 16 hbamr-2.3.0/hbamr/MD5 | 80 hbamr-2.3.0/hbamr/NAMESPACE | 1 hbamr-2.3.0/hbamr/NEWS.md | 9 hbamr-2.3.0/hbamr/R/fbam.R | 20 hbamr-2.3.0/hbamr/R/hbam.R | 12 hbamr-2.3.0/hbamr/R/hbam_cv.R | 10 hbamr-2.3.0/hbamr/R/hbamr-package.R | 1 hbamr-2.3.0/hbamr/R/inits.R | 4 hbamr-2.3.0/hbamr/R/plot_stimuli.R | 6 hbamr-2.3.0/hbamr/R/prep_data.R | 32 hbamr-2.3.0/hbamr/R/stanmodels.R | 4 hbamr-2.3.0/hbamr/build/partial.rdb |binary hbamr-2.3.0/hbamr/build/vignette.rds |binary hbamr-2.3.0/hbamr/inst/doc/hbamr.R | 6 hbamr-2.3.0/hbamr/inst/doc/hbamr.Rmd | 30 hbamr-2.3.0/hbamr/inst/doc/hbamr.html | 90 hbamr-2.3.0/hbamr/inst/stan/FBAM.stan |only hbamr-2.3.0/hbamr/inst/stan/FBAM_MULTI.stan | 25 hbamr-2.3.0/hbamr/inst/stan/FBAM_MULTI_NF.stan | 16 hbamr-2.3.0/hbamr/inst/stan/HBAM.stan | 6 hbamr-2.3.0/hbamr/inst/stan/HBAM_MINI.stan | 6 hbamr-2.3.0/hbamr/inst/stan/HBAM_MULTI.stan | 6 hbamr-2.3.0/hbamr/inst/stan/HBAM_R_MINI.stan | 6 hbamr-2.3.0/hbamr/man/fbam.Rd | 16 hbamr-2.3.0/hbamr/man/hbam.Rd | 10 hbamr-2.3.0/hbamr/man/hbam_cv.Rd | 10 hbamr-2.3.0/hbamr/src/RcppExports.cpp | 4 hbamr-2.3.0/hbamr/src/stanExports_BAM.h | 1761 +++++------- hbamr-2.3.0/hbamr/src/stanExports_FBAM.cc |only hbamr-2.3.0/hbamr/src/stanExports_FBAM.h |only hbamr-2.3.0/hbamr/src/stanExports_FBAM_MULTI.h | 2894 ++++++++++---------- hbamr-2.3.0/hbamr/src/stanExports_FBAM_MULTI_NF.h | 2258 ++++++++-------- hbamr-2.3.0/hbamr/src/stanExports_HBAM.h | 2602 ++++++++---------- hbamr-2.3.0/hbamr/src/stanExports_HBAM_MINI.h | 2243 +++++++--------- hbamr-2.3.0/hbamr/src/stanExports_HBAM_MULTI.h | 3034 +++++++++------------- hbamr-2.3.0/hbamr/src/stanExports_HBAM_MULTI_NF.h | 2365 +++++++---------- hbamr-2.3.0/hbamr/src/stanExports_HBAM_NF.h | 1916 ++++++------- hbamr-2.3.0/hbamr/src/stanExports_HBAM_R_MINI.h | 2998 ++++++++++----------- hbamr-2.3.0/hbamr/vignettes/elpds.rda |binary hbamr-2.3.0/hbamr/vignettes/hbamr.Rmd | 30 44 files changed, 10458 insertions(+), 12069 deletions(-)
Title: Build SVG Custom User Interface
Description: Render SVG as interactive figures to display contextual
information, with selectable and clickable user interface elements.
These figures can be seamlessly integrated into 'rmarkdown' and 'Quarto'
documents, as well as 'shiny' applications, allowing manipulation of elements
and reporting actions performed on them.
Additional features include pan, zoom in/out functionality, and the ability
to export the figures in SVG or PNG formats.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between bscui versions 0.1.3 dated 2024-02-05 and 0.1.5 dated 2024-03-31
bscui-0.1.3/bscui/inst/htmlwidgets/lib/bscui-0.0.1 |only bscui-0.1.5/bscui/DESCRIPTION | 6 - bscui-0.1.5/bscui/MD5 | 24 ++-- bscui-0.1.5/bscui/build/vignette.rds |binary bscui-0.1.5/bscui/inst/doc/bscui.R | 2 bscui-0.1.5/bscui/inst/doc/bscui.Rmd | 5 bscui-0.1.5/bscui/inst/doc/bscui.html | 92 +++++++++++----- bscui-0.1.5/bscui/inst/examples/WP112.svg.gz |binary bscui-0.1.5/bscui/inst/examples/WP112.txt.gz |binary bscui-0.1.5/bscui/inst/examples/shiny-anatomogram/app.R | 27 ++-- bscui-0.1.5/bscui/inst/htmlwidgets/bscui.yaml | 4 bscui-0.1.5/bscui/inst/htmlwidgets/lib/bscui-0.0.3 |only bscui-0.1.5/bscui/inst/pkgdown.yml | 2 bscui-0.1.5/bscui/vignettes/bscui.Rmd | 5 14 files changed, 109 insertions(+), 58 deletions(-)
Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi:10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-alleli [...truncated...]
Author: Jan Graffelman [aut, cre],
Christopher Chang [ctb],
Xavi Puig [ctb],
Jan Wigginton [ctb],
Leonardo Ortoleva [ctb],
William R. Engels [ctb]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between HardyWeinberg versions 1.7.5 dated 2022-05-07 and 1.7.7 dated 2024-03-31
DESCRIPTION | 10 MD5 | 153 +++-- NAMESPACE | 18 R/CombineExact.R | 2 R/CritSam.R | 64 +- R/EAFExact.R | 54 + R/HWABO.R | 4 R/HWChisq.R | 46 - R/HWChisqStats.R | 7 R/HWData.R | 209 ++++--- R/HWEM.R |only R/HWExact.R | 51 - R/HWExactMat.R | 11 R/HWExactStats.R | 4 R/HWLindley.R | 4 R/HWLindley.cri.R |only R/HWLratio.R | 165 ++---- R/HWPerm.R | 22 R/HWPerm.mult.R | 9 R/HWPosterior.R | 47 - R/HWQqplot.R | 57 +- R/HWStr.R |only R/HWStrata.R |only R/HWTernaryPlot.R | 561 ++++++++++---------- R/HWTriExact.R | 20 R/HWf.R | 9 R/MakeColourVector.R |only R/MakeCounts.R | 107 ++- R/af.R | 23 R/afx.R |only R/getpvals.R | 2 R/he.R |only R/is.mono.R |only R/mac.R | 30 - R/maf.R | 109 +++- R/order.auto.R |only R/order.x.R |only R/qqunif.R |only R/shannon.R |only R/toTriangular.R | 28 - R/toTriangularfixed.R |only build/partial.rdb |binary build/vignette.rds |binary data/CEUchr22.rda |only inst/CITATION | 59 +- inst/doc/HardyWeinberg.R | 139 +++-- inst/doc/HardyWeinberg.Rnw | 788 +++++++++-------------------- inst/doc/HardyWeinberg.pdf |binary man/CEUchr22.Rd |only man/HWAlr.Rd | 2 man/HWAlrPlot.Rd | 2 man/HWChisq.Rd | 7 man/HWChisqMat.Rd | 18 man/HWClr.Rd | 2 man/HWClrPlot.Rd | 2 man/HWData.Rd | 64 +- man/HWEM.Rd |only man/HWExact.Rd | 11 man/HWExactMat.Rd | 9 man/HWIlr.Rd | 2 man/HWLindley.Rd | 6 man/HWLindley.cri.Rd |only man/HWLratio.Rd | 9 man/HWNetwork.Rd | 4 man/HWPerm.Rd | 28 - man/HWPosterior.Rd | 30 - man/HWQqplot.Rd | 6 man/HWStr.Rd |only man/HWStrata.Rd |only man/HWTernaryPlot.Rd | 73 ++ man/HWf.Rd | 6 man/HardyWeinberg-package.Rd | 4 man/JPTsnps.Rd | 7 man/af.Rd | 43 + man/afx.Rd |only man/agcounts.Rd | 2 man/alleles.Rd | 5 man/dlevene.bi.Rd | 2 man/fold.Rd | 2 man/he.Rd |only man/is.mono.Rd |only man/maf.Rd | 71 ++ man/order.auto.Rd |only man/order.x.Rd |only man/qqunif.Rd |only man/shannon.Rd |only man/vaf.Rd | 2 vignettes/HardyWeinberg.Rnw | 788 +++++++++-------------------- vignettes/HardyWeinberg.bib | 84 +-- vignettes/HardyWeinbergExampleSession.Rmd |only vignettes/HardyWeinbergExampleSession.html |only vignettes/Vignette01QQplots.pdf |only 92 files changed, 2014 insertions(+), 2089 deletions(-)
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use
in photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse ratios and
other derived quantities from spectral data. Local maxima and minima: peaks,
valleys and spikes. Conversion between energy-and photon-based units.
Wavelength interpolation. Astronomical calculations related solar angles and
day length. Colours and vision. This package is part of the 'r4photobiology'
suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb],
Agnese Fazio [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.11.1 dated 2024-02-26 and 0.11.2 dated 2024-03-31
DESCRIPTION | 8 - MD5 | 34 ++-- NAMESPACE | 2 NEWS.md | 26 +++ R/rbindspct.r | 7 R/spct.fscale.r | 204 ++++++++++++++++------------- R/spct.irrad.r | 3 R/spct.metadata.r | 2 R/spct.normalize.r | 185 +++++++++++++++++--------- R/spct.smooth.spct.r | 12 - R/sun.calc.r | 2 README.md | 8 - inst/doc/userguide-0-r4p-introduction.html | 2 inst/doc/userguide-1-radiation.html | 8 - inst/doc/userguide-2-astronomy.html | 46 +++--- man/fscale.Rd | 47 +++--- man/fscale_spct.Rd | 10 - man/normalize.Rd | 29 ++++ 18 files changed, 393 insertions(+), 242 deletions(-)
Title: Local Haplotype Clustering and Visualization
Description: A local haplotyping visualization toolbox to capture major patterns
of co-inheritance between clusters of linked variants, whilst connecting findings
to phenotypic and demographic traits across individuals. 'crosshap' enables users
to explore and understand genomic variation across a trait-associated region.
For an example of successful local haplotype analysis, see Marsh et al. (2022)
<doi:10.1007/s00122-022-04045-8>.
Author: Jacob Marsh [aut, cre] ,
Brady Johnston [aut] ,
Jakob Petereit [aut]
Maintainer: Jacob Marsh <jake.marsh@live.com.au>
Diff between crosshap versions 1.2.2 dated 2023-05-02 and 1.4.0 dated 2024-03-31
crosshap-1.2.2/crosshap/tests/testthat/_snaps/clustree/haptree.svg |only crosshap-1.2.2/crosshap/tests/testthat/_snaps/hapviz |only crosshap-1.4.0/crosshap/DESCRIPTION | 7 - crosshap-1.4.0/crosshap/MD5 | 34 +++-- crosshap-1.4.0/crosshap/R/pseudohaps.R | 8 + crosshap-1.4.0/crosshap/R/right_phenoplot.R | 6 - crosshap-1.4.0/crosshap/R/run_haplotyping_wrapper.R | 15 ++ crosshap-1.4.0/crosshap/R/summary_tables.R | 5 crosshap-1.4.0/crosshap/R/top_barplot.R | 6 - crosshap-1.4.0/crosshap/R/utils.R | 10 + crosshap-1.4.0/crosshap/README.md | 8 - crosshap-1.4.0/crosshap/inst/test |only crosshap-1.4.0/crosshap/man/crosshap-package.Rd | 1 crosshap-1.4.0/crosshap/tests/testthat/_snaps/clustree/haptreedata.svg |only crosshap-1.4.0/crosshap/tests/testthat/_snaps/crosshapviz |only crosshap-1.4.0/crosshap/tests/testthat/test-clustree.R | 8 - crosshap-1.4.0/crosshap/tests/testthat/test-crosshapviz.R |only crosshap-1.4.0/crosshap/tests/testthat/test-hapviz.R | 57 +++++----- 18 files changed, 107 insertions(+), 58 deletions(-)
Title: The Generalized Semi-Supervised Elastic-Net
Description: Implements the generalized semi-supervised elastic-net. This method extends the supervised elastic-net problem, and thus it is a practical solution to the problem of feature selection in semi-supervised contexts. Its mathematical formulation is presented from a general perspective, covering a wide range of models. We focus on linear and logistic responses, but the implementation could be easily extended to other losses in generalized linear models. We develop a flexible and fast implementation, written in 'C++' using 'RcppArmadillo' and integrated into R via 'Rcpp' modules. See Culp, M. 2013 <doi:10.1080/10618600.2012.657139> for references on the Joint Trained Elastic-Net.
Author: Juan C. Laria [aut, cre] ,
Line H. Clemmensen [aut]
Maintainer: Juan C. Laria <juank.laria@gmail.com>
Diff between s2net versions 1.0.4 dated 2022-06-30 and 1.0.7 dated 2024-03-31
DESCRIPTION | 8 MD5 | 24 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 29 +-- inst/doc/supervised.html | 430 ++++++++++++++++++++++++++++++++++------------- inst/rdevel |only inst/sid |only man/predict.s2netR.Rd | 2 man/print_misc.Rd | 2 man/s2Data.Rd | 4 man/s2net-class.Rd | 1 src/Makevars | 2 src/Makevars.win | 2 14 files changed, 351 insertions(+), 153 deletions(-)
Title: Testing DBI Backends
Description: A helper that tests DBI back ends for conformity to the
interface.
Author: Kirill Mueller [aut, cre] ,
RStudio [cph],
R Consortium [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between DBItest versions 1.8.0 dated 2023-12-21 and 1.8.1 dated 2024-03-31
DESCRIPTION | 18 +-- MD5 | 166 ++++++++++++++--------------- NAMESPACE | 33 ----- NEWS.md | 49 ++++++++ R/expectations.R | 12 +- R/import-testthat.R | 16 -- R/run.R | 44 +++---- R/spec-arrow-append-table-arrow.R | 78 +++++-------- R/spec-arrow-create-table-arrow.R | 82 ++++++++++++-- R/spec-arrow-fetch-arrow-chunk.R | 8 - R/spec-arrow-fetch-arrow.R | 8 - R/spec-arrow-get-query-arrow.R | 121 ++++++++++----------- R/spec-arrow-read-table-arrow.R | 14 +- R/spec-arrow-write-table-arrow.R | 118 +++++++++----------- R/spec-arrow.R | 19 +-- R/spec-connection-disconnect.R | 6 - R/spec-driver-constructor.R | 3 R/spec-driver-data-type.R | 8 - R/spec-meta-bind-.R | 19 +++ R/spec-meta-bind-arrow-stream.R | 77 +++++++++++++ R/spec-meta-bind-arrow.R | 87 ++++++++++++++- R/spec-meta-bind-expr.R | 19 +-- R/spec-meta-bind-runner.R | 42 +++---- R/spec-meta-bind-stream.R | 89 +++++++++++++++ R/spec-meta-bind.R | 92 +++++++++++++++- R/spec-meta-get-statement.R | 4 R/spec-result-fetch.R | 12 +- R/spec-result-get-query.R | 6 - R/spec-result-roundtrip.R | 65 ++++++----- R/spec-sql-append-table.R | 16 +- R/spec-sql-create-table.R | 49 +++++++- R/spec-sql-exists-table.R | 10 + R/spec-sql-list-objects.R | 40 ++---- R/spec-sql-list-tables.R | 13 +- R/spec-sql-quote-literal.R | 10 - R/spec-sql-read-table.R | 4 R/spec-sql-remove-table.R | 4 R/spec-sql-unquote-identifier.R | 6 - R/spec-sql-write-table.R | 32 +++-- R/spec-stress-connection.R | 4 R/spec-transaction-begin-commit-rollback.R | 12 +- R/test-all.R | 5 R/tweaks.R | 4 R/utils.R | 21 ++- inst/doc/DBItest.html | 4 man/spec_arrow_append_table_arrow.Rd | 11 - man/spec_arrow_create_table_arrow.Rd | 15 ++ man/spec_arrow_fetch_arrow.Rd | 4 man/spec_arrow_fetch_arrow_chunk.Rd | 4 man/spec_arrow_get_query_arrow.Rd | 64 ++++++++++- man/spec_arrow_read_table_arrow.Rd | 14 +- man/spec_arrow_send_query_arrow.Rd | 2 man/spec_arrow_write_table_arrow.Rd | 12 -- man/spec_connection_disconnect.Rd | 2 man/spec_driver_constructor.Rd | 3 man/spec_driver_data_type.Rd | 4 man/spec_meta_bind.Rd | 36 ++---- man/spec_meta_get_statement.Rd | 4 man/spec_result_clear_result.Rd | 2 man/spec_result_fetch.Rd | 12 +- man/spec_result_get_query.Rd | 4 man/spec_sql_append_table.Rd | 4 man/spec_sql_create_table.Rd | 10 + man/spec_sql_exists_table.Rd | 4 man/spec_sql_list_objects.Rd | 10 - man/spec_sql_list_tables.Rd | 4 man/spec_sql_read_table.Rd | 4 man/spec_sql_remove_table.Rd | 4 man/spec_sql_unquote_identifier.Rd | 4 man/spec_sql_write_table.Rd | 4 man/test_all.Rd | 5 man/test_arrow.Rd | 5 man/test_compliance.Rd | 5 man/test_connection.Rd | 5 man/test_data_type.Rd | 4 man/test_driver.Rd | 5 man/test_getting_started.Rd | 5 man/test_meta.Rd | 5 man/test_result.Rd | 5 man/test_sql.Rd | 5 man/test_stress.Rd | 5 man/test_transaction.Rd | 5 tests/testthat/test-DBItest.R | 8 + tests/testthat/test-consistency.R | 20 --- 84 files changed, 1191 insertions(+), 686 deletions(-)
Title: Optimal Test Design Approach to Fixed and Adaptive Test
Construction
Description: Uses the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and
van der Linden (2018) <doi:10.1201/9781315117430> to construct fixed, adaptive, and parallel tests.
Supports the following mixed-integer programming (MIP) solver packages: 'Rsymphony',
'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package is not available from CRAN; see <https://www.gurobi.com/downloads/>.
Author: Seung W. Choi [aut, cre] ,
Sangdon Lim [aut]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between TestDesign versions 1.5.1 dated 2023-01-30 and 1.6.1 dated 2024-03-31
TestDesign-1.5.1/TestDesign/src/Makevars.win |only TestDesign-1.5.1/TestDesign/tests/testthat/test-gfi.R |only TestDesign-1.5.1/TestDesign/tests/testthat/test-refresh-methods.R |only TestDesign-1.5.1/TestDesign/tests/testthat/test-selection-methods.R |only TestDesign-1.5.1/TestDesign/tests/testthat/test-theta-methods.R |only TestDesign-1.5.1/TestDesign/tests/testthat/test_deprecated.R |only TestDesign-1.6.1/TestDesign/DESCRIPTION | 9 TestDesign-1.6.1/TestDesign/MD5 | 180 ++-- TestDesign-1.6.1/TestDesign/NEWS.md | 19 TestDesign-1.6.1/TestDesign/R/bayes_functions.R | 93 +- TestDesign-1.6.1/TestDesign/R/calc_escore_functions.r | 20 TestDesign-1.6.1/TestDesign/R/calc_fisher_functions.r | 34 TestDesign-1.6.1/TestDesign/R/calc_hessian_functions.r | 35 TestDesign-1.6.1/TestDesign/R/calc_jacobian_functions.r | 32 TestDesign-1.6.1/TestDesign/R/calc_location_functions.r | 2 TestDesign-1.6.1/TestDesign/R/calc_loglikelihood_functions.r | 6 TestDesign-1.6.1/TestDesign/R/calc_prob_functions.r | 22 TestDesign-1.6.1/TestDesign/R/constraint_functions.R | 32 TestDesign-1.6.1/TestDesign/R/constraints_operators.R | 31 TestDesign-1.6.1/TestDesign/R/cpp_theta_documents.r | 6 TestDesign-1.6.1/TestDesign/R/eligibility_functions.R | 168 ++-- TestDesign-1.6.1/TestDesign/R/exposure_control_functions.R | 61 - TestDesign-1.6.1/TestDesign/R/helper_functions.R | 15 TestDesign-1.6.1/TestDesign/R/item_class.R | 4 TestDesign-1.6.1/TestDesign/R/loading_functions.R | 374 +++++----- TestDesign-1.6.1/TestDesign/R/other_functions.R | 35 TestDesign-1.6.1/TestDesign/R/partitioning_class.r | 2 TestDesign-1.6.1/TestDesign/R/partitioning_functions.r | 90 +- TestDesign-1.6.1/TestDesign/R/plot_functions.R | 34 TestDesign-1.6.1/TestDesign/R/print_functions.R | 4 TestDesign-1.6.1/TestDesign/R/runshiny.R | 4 TestDesign-1.6.1/TestDesign/R/shadow_class.R | 8 TestDesign-1.6.1/TestDesign/R/shadow_functions.R | 52 - TestDesign-1.6.1/TestDesign/R/shadowtest_functions.R | 101 +- TestDesign-1.6.1/TestDesign/R/sim_resp_functions.r | 2 TestDesign-1.6.1/TestDesign/R/simulation_data_cache_class.r | 6 TestDesign-1.6.1/TestDesign/R/solver_functions.R | 2 TestDesign-1.6.1/TestDesign/R/static_class.R | 4 TestDesign-1.6.1/TestDesign/R/static_functions.R | 24 TestDesign-1.6.1/TestDesign/R/summary_functions.R | 114 +-- TestDesign-1.6.1/TestDesign/R/theta_functions.R | 55 - TestDesign-1.6.1/TestDesign/R/xdata_functions.R | 22 TestDesign-1.6.1/TestDesign/build/vignette.rds |binary TestDesign-1.6.1/TestDesign/inst/doc/constraints.R | 26 TestDesign-1.6.1/TestDesign/inst/doc/constraints.Rmd | 84 -- TestDesign-1.6.1/TestDesign/inst/doc/constraints.html | 111 +- TestDesign-1.6.1/TestDesign/inst/doc/split.html | 42 - TestDesign-1.6.1/TestDesign/man/Shadow-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/Split-methods.Rd | 12 TestDesign-1.6.1/TestDesign/man/Static-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/TestDesign.Rd | 2 TestDesign-1.6.1/TestDesign/man/TestDesign_alias.Rd | 2 TestDesign-1.6.1/TestDesign/man/buildConstraints.Rd | 15 TestDesign-1.6.1/TestDesign/man/calcFisher-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/calcHessian-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/calcLocation-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/calcLogLikelihood-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/calcProb-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/constraint-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/constraints-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/createShadowTestConfig.Rd | 2 TestDesign-1.6.1/TestDesign/man/createStaticTestConfig.Rd | 2 TestDesign-1.6.1/TestDesign/man/eap-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/find_segment.Rd | 2 TestDesign-1.6.1/TestDesign/man/getSolution-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/getSolutionAttributes.Rd | 2 TestDesign-1.6.1/TestDesign/man/item_pool-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/item_pool_cluster-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/loadConstraints.Rd | 16 TestDesign-1.6.1/TestDesign/man/loadItemAttrib.Rd | 12 TestDesign-1.6.1/TestDesign/man/loadItemPool.Rd | 14 TestDesign-1.6.1/TestDesign/man/loadStAttrib.Rd | 12 TestDesign-1.6.1/TestDesign/man/mle-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/mlef-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/output_Shadow-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/output_Shadow_all-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/output_Split-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/output_Static-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/plot-methods.Rd | 3 TestDesign-1.6.1/TestDesign/man/runAssembly.Rd | 2 TestDesign-1.6.1/TestDesign/man/simResp-methods.Rd | 2 TestDesign-1.6.1/TestDesign/man/simulation_data_cache-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/test-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/test_cluster-class.Rd | 2 TestDesign-1.6.1/TestDesign/man/theta_EB.Rd | 2 TestDesign-1.6.1/TestDesign/man/theta_FB.Rd | 2 TestDesign-1.6.1/TestDesign/man/toggleConstraints.Rd | 2 TestDesign-1.6.1/TestDesign/src/Makevars |only TestDesign-1.6.1/TestDesign/src/other_functions.cpp | 6 TestDesign-1.6.1/TestDesign/src/theta_functions.cpp | 24 TestDesign-1.6.1/TestDesign/tests/testthat/test_combine_constraints.r |only TestDesign-1.6.1/TestDesign/tests/testthat/test_gfi.R |only TestDesign-1.6.1/TestDesign/tests/testthat/test_item_selection_methods.R |only TestDesign-1.6.1/TestDesign/tests/testthat/test_partitioning_methods.r | 130 +++ TestDesign-1.6.1/TestDesign/tests/testthat/test_refresh_methods.R |only TestDesign-1.6.1/TestDesign/tests/testthat/test_theta_estimation_methods.R |only TestDesign-1.6.1/TestDesign/vignettes/constraints.Rmd | 84 -- 97 files changed, 1275 insertions(+), 1084 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre] ,
Edward L. Ionides [aut] ,
Carles Breto [aut] ,
Stephen P. Ellner [ctb] ,
Matthew J. Ferrari [ctb],
Sebastian Funk [ctb] ,
Steven G. Johnson [ctb],
Bruce E. Kendall [ctb] ,
Michael Lavine [ctb],
Dao Nguyen [ctb] ,
Eamon B. O [...truncated...]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 5.6 dated 2024-02-14 and 5.7 dated 2024-03-31
DESCRIPTION | 8 MD5 | 40 ++-- R/melt.R | 2 R/objfun.R | 2 R/trajectory.R | 1 R/wquant.R | 1 build/partial.rdb |binary data/LondonYorke.rda |binary data/bsflu.rda |binary data/ebolaWA2014.rda |binary data/ewcitmeas.rda |binary data/ewmeas.rda |binary inst/NEWS | 9 + inst/NEWS.Rd | 9 - inst/doc/index.html | 410 --------------------------------------------------- man/melt.Rd | 3 man/trajectory.Rd | 4 src/dmeasure.c | 6 src/dprior.c | 6 src/dprocess.c | 15 + src/rinit.c | 13 + 21 files changed, 77 insertions(+), 452 deletions(-)
Title: Hierarchical Clustering-Based Portfolio Allocation Strategies
Description: Machine learning portfolio allocation strategies based on hierarchical clustering methods.
The implemented methods are:
Hierarchical risk parity (De Prado, 2016) <DOI: 10.3905/jpm.2016.42.4.059>.
Hierarchical clustering-based asset allocation (Raffinot, 2017)
<DOI: 10.3905/jpm.2018.44.2.089>.
Hierarchical equal risk contribution portfolio (Raffinot, 2018)
<DOI: 10.2139/ssrn.3237540>.
A Constrained Hierarchical Risk Parity Algorithm with Cluster-based Capital Allocation (Pfitzingera and Katzke, 2019)
<https://www.ekon.sun.ac.za/wpapers/2019/wp142019/wp142019.pdf>.
Author: Carlos Trucios and Moon Jun Kwon
Maintainer: Carlos Trucios <ctrucios@unicamp.br>
Diff between HierPortfolios versions 0.1.0 dated 2021-11-09 and 1.0.0 dated 2024-03-31
DESCRIPTION | 22 +++++++++++++--------- MD5 | 18 +++++++++++------- NAMESPACE | 2 ++ R/DHRP_Portfolio.R |only R/HCAA_Portfolio.R | 3 ++- R/HERC_Portfolio.R |only R/HRP_Portfolio.R | 3 ++- README.md | 13 +++++++------ man/DHRP_Portfolio.Rd |only man/HCAA_Portfolio.Rd | 5 ++++- man/HERC_Portfolio.Rd |only man/HRP_Portfolio.Rd | 5 ++++- 12 files changed, 45 insertions(+), 26 deletions(-)
More information about HierPortfolios at CRAN
Permanent link
Title: Fit Dynamic Structural Equation Models
Description: Applies dynamic structural equation models to time-series data
with generic and simplified specification for simultaneous and lagged
effects. Methods are described in Thorson et al. (2024)
"Dynamic structural equation models synthesize ecosystem dynamics
constrained by ecological mechanisms."
Author: James Thorson [aut, cre]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Diff between dsem versions 1.1.0 dated 2024-02-16 and 1.2.0 dated 2024-03-31
DESCRIPTION | 10 MD5 | 37 + NAMESPACE | 2 NEWS.md | 12 R/dsem.R | 110 ++++- R/make_dfa.R |only build/vignette.rds |binary data/bering_sea.rda |binary inst/doc/dynamic_factor_analysis.R |only inst/doc/dynamic_factor_analysis.Rmd |only inst/doc/dynamic_factor_analysis.html |only inst/doc/vignette.R | 26 - inst/doc/vignette.Rmd | 26 - inst/doc/vignette.html | 687 ++++++++++++++++------------------ inst/tmbstan/summary_mcmc.RDS |binary man/dsem.Rd | 11 man/dsem_control.Rd | 17 man/make_dfa.Rd |only src/dsem.cpp | 132 +++--- tests/testthat/test-gmrf-versions.R |only tests/testthat/test-platform.R | 38 + vignettes/dynamic_factor_analysis.Rmd |only vignettes/vignette.Rmd | 26 - 23 files changed, 657 insertions(+), 477 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data and some useful functions for
tabulation and plotting, as well as a number of epidemiological data
sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.47.1 dated 2023-04-25 and 2.48 dated 2024-03-31
Epi-2.47.1/Epi/inst/doc/index.html |only Epi-2.47.1/Epi/vignettes/2Bappended2addLexisrnw.txt |only Epi-2.47.1/Epi/vignettes/cpall |only Epi-2.47.1/Epi/vignettes/fixall |only Epi-2.48/Epi/CHANGES | 36 Epi-2.48/Epi/DESCRIPTION | 8 Epi-2.48/Epi/MD5 | 169 +- Epi-2.48/Epi/NAMESPACE | 17 Epi-2.48/Epi/R/AaJ.Lexis.R | 8 Epi-2.48/Epi/R/addCov.Lexis.R | 30 Epi-2.48/Epi/R/addDrug.Lexis.R | 132 +- Epi-2.48/Epi/R/bootLexis.R | 103 - Epi-2.48/Epi/R/boxes.MS.R | 35 Epi-2.48/Epi/R/ci.lin.R | 73 - Epi-2.48/Epi/R/cutLexis.R | 10 Epi-2.48/Epi/R/mh.R | 71 - Epi-2.48/Epi/R/print.Icens.r | 2 Epi-2.48/Epi/R/splitLexis.R | 8 Epi-2.48/Epi/R/stattable.R | 50 Epi-2.48/Epi/R/summary.Icens.r | 22 Epi-2.48/Epi/R/unLexis.R |only Epi-2.48/Epi/build/vignette.rds |binary Epi-2.48/Epi/data/B.dk.rda |binary Epi-2.48/Epi/data/BrCa.rda |binary Epi-2.48/Epi/data/DMconv.rda |binary Epi-2.48/Epi/data/DMepi.rda |binary Epi-2.48/Epi/data/DMlate.rda |binary Epi-2.48/Epi/data/DMrand.rda |binary Epi-2.48/Epi/data/M.dk.rda |binary Epi-2.48/Epi/data/N.dk.rda |binary Epi-2.48/Epi/data/S.typh.rda |binary Epi-2.48/Epi/data/Y.dk.rda |binary Epi-2.48/Epi/data/bdendo.rda |binary Epi-2.48/Epi/data/bdendo11.rda |binary Epi-2.48/Epi/data/births.rda |binary Epi-2.48/Epi/data/blcaIT.rda |binary Epi-2.48/Epi/data/brv.rda |binary Epi-2.48/Epi/data/diet.rda |binary Epi-2.48/Epi/data/ewrates.rda |binary Epi-2.48/Epi/data/gmortDK.rda |binary Epi-2.48/Epi/data/hivDK.rda |binary Epi-2.48/Epi/data/lep.rda |binary Epi-2.48/Epi/data/lungDK.rda |binary Epi-2.48/Epi/data/mortDK.rda |binary Epi-2.48/Epi/data/nickel.rda |binary Epi-2.48/Epi/data/occup.rda |binary Epi-2.48/Epi/data/pr.rda |binary Epi-2.48/Epi/data/st2alb.rda |binary Epi-2.48/Epi/data/st2clin.rda |binary Epi-2.48/Epi/data/steno2.rda |binary Epi-2.48/Epi/data/testisDK.rda |binary Epi-2.48/Epi/data/thoro.rda |binary Epi-2.48/Epi/inst/CITATION | 18 Epi-2.48/Epi/inst/doc/addLexis.R | 748 ++++++------- Epi-2.48/Epi/inst/doc/addLexis.pdf |binary Epi-2.48/Epi/inst/doc/addLexis.rnw | 284 ++-- Epi-2.48/Epi/inst/doc/crisk.R | 862 +++++++-------- Epi-2.48/Epi/inst/doc/crisk.pdf |binary Epi-2.48/Epi/inst/doc/flup.R | 1140 ++++++++++---------- Epi-2.48/Epi/inst/doc/flup.pdf |binary Epi-2.48/Epi/inst/doc/flup.rnw | 878 +++++++-------- Epi-2.48/Epi/inst/doc/simLexis.R | 816 +++++++------- Epi-2.48/Epi/inst/doc/simLexis.pdf |binary Epi-2.48/Epi/inst/doc/yll.R | 359 +++--- Epi-2.48/Epi/inst/doc/yll.pdf |binary Epi-2.48/Epi/inst/doc/yll.rnw | 184 +-- Epi-2.48/Epi/man/AaJ.Lexis.Rd | 5 Epi-2.48/Epi/man/Icens.Rd | 19 Epi-2.48/Epi/man/LCa.fit.Rd | 2 Epi-2.48/Epi/man/Lexis.Rd | 3 Epi-2.48/Epi/man/ROC.Rd | 4 Epi-2.48/Epi/man/addCov.Lexis.Rd | 3 Epi-2.48/Epi/man/addDrug.Lexis.Rd | 12 Epi-2.48/Epi/man/bootLexis.Rd | 44 Epi-2.48/Epi/man/cal.yr.Rd | 3 Epi-2.48/Epi/man/ci.lin.Rd | 20 Epi-2.48/Epi/man/cutLexis.Rd | 4 Epi-2.48/Epi/man/ewrates.Rd | 2 Epi-2.48/Epi/man/fit.add.Rd | 2 Epi-2.48/Epi/man/legendbox.Rd |only Epi-2.48/Epi/man/lls.Rd | 8 Epi-2.48/Epi/man/mh.Rd | 17 Epi-2.48/Epi/man/plotCIF.Rd | 2 Epi-2.48/Epi/man/unLexis.Rd |only Epi-2.48/Epi/vignettes/addLexis.rnw | 284 ++-- Epi-2.48/Epi/vignettes/fixall.bat |only Epi-2.48/Epi/vignettes/flup.rnw | 878 +++++++-------- Epi-2.48/Epi/vignettes/mvall.bat |only Epi-2.48/Epi/vignettes/topreport.tex | 7 Epi-2.48/Epi/vignettes/yll.rnw | 184 +-- 90 files changed, 3904 insertions(+), 3662 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-03 1.2.0
2023-12-07 1.1.0
Title: Hard and Soft Cluster Validity Indices
Description: Algorithms for checking the accuracy of a clustering result with known classes, computing cluster validity indices, and generating plots for comparing them.
The package is compatible with K-means, fuzzy C means, EM clustering, and hierarchical clustering (single, average, and complete linkage).
The details of the indices in this package can be found in:
C. Alok. (2010) <https://hdl.handle.net/10603/93443>,
J. C. Bezdek, M. Moshtaghi, T. Runkler, C. Leckie (2016) <doi:10.1109/TFUZZ.2016.2540063>,
T. Calinski, J. Harabasz (1974) <doi:10.1080/03610927408827101>,
C. H. Chou, M. C. Su, E. Lai (2004) <doi:10.1007/s10044-004-0218-1>,
D. L. Davies, D. W. Bouldin (1979) <doi:10.1109/TPAMI.1979.4766909>,
J. C. Dunn (1973) <doi:10.1080/01969727308546046>,
F. Haouas, Z. Ben Dhiaf, A. Hammouda, B. Solaiman (2017) <doi:10.1109/FUZZ-IEEE.2017.8015651>,
M. Kim, R. S. Ramakrishna (2005) <doi:10.1016/j.patrec.2005.04.007>,
S. H. Kwon (1998) <doi:10.1049 [...truncated...]
Author: Nathakhun Wiroonsri [cre, aut]
,
Onthada Preedasawakul [aut]
Maintainer: Nathakhun Wiroonsri <nathakhun.wir@kmutt.ac.th>
Diff between UniversalCVI versions 1.1.1 dated 2024-02-08 and 1.1.2 dated 2024-03-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 3 +++ R/AccClust.R | 9 +-------- 4 files changed, 10 insertions(+), 14 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
Description: A comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data.
Pedigrees can be read from text files or created on the fly with
built-in functions. A range of utilities enable modifications like
adding or removing individuals, breaking loops, and merging pedigrees.
An online tool for creating pedigrees interactively, based on
'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>.
'pedtools' is the hub of the 'pedsuite', a collection of packages for
pedigree analysis. A detailed presentation of the 'pedsuite' is given
in the book 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 2.5.0 dated 2023-11-05 and 2.6.0 dated 2024-03-31
DESCRIPTION | 8 MD5 | 80 ++++----- NAMESPACE | 3 NEWS.md | 38 ++++ R/marker.R | 4 R/marker_allelematrix.R | 10 - R/marker_distribute.R | 37 ++++ R/marker_genomatrix.R | 12 - R/marker_locusattributes.R | 17 + R/marker_select.R | 13 + R/marker_transfer.R | 33 ++- R/ped_convert.R | 14 + R/ped_labels.R | 21 +- R/ped_mask.R | 54 +++--- R/ped_methods.R | 2 R/ped_modify.R | 283 ++++++++++++++++---------------- R/ped_plot.R | 91 ++++++++-- R/ped_sex.R | 2 R/ped_subgroups.R | 89 +++++----- R/ped_utils.R | 28 ++- R/plot_internal.R | 114 +++++++++--- R/utils.R | 30 +++ build/vignette.rds |binary inst/doc/pedtools.R | 25 +- inst/doc/pedtools.Rmd | 40 ++-- inst/doc/pedtools.html | 256 +++++++++++++++------------- man/getGenotypes.Rd | 8 man/internalplot.Rd | 50 ++++- man/locusAttributes.Rd | 4 man/maskPed.Rd | 24 ++ man/ped_modify.Rd | 45 ++--- man/ped_subgroups.Rd | 38 ++-- man/pedtools-package.Rd | 2 man/plot.ped.Rd | 75 ++++++-- man/relabel.Rd | 9 - man/transferMarkers.Rd | 7 tests/testthat/test-marker-transfer.R | 30 +-- tests/testthat/test-ped-modifications.R | 186 +++++++++++---------- tests/testthat/test-ped-write.R | 2 tests/testthat/test-utils.R | 15 - vignettes/pedtools.Rmd | 40 ++-- 41 files changed, 1147 insertions(+), 692 deletions(-)