Title: Discrete Nonlinear Filtering for Stochastic Volatility Models
Description: Implements the discrete nonlinear filter (DNF) of Kitagawa (1987) <doi:10.1080/01621459.1987.10478534> to a wide class of stochastic volatility (SV) models with return and volatility jumps following the work of Bégin and Boudreault (2021) <doi:10.1080/10618600.2020.1840995> to obtain likelihood evaluations and maximum likelihood parameter estimates. Offers several built-in SV models and a flexible framework for users to create customized models by specifying drift and diffusion functions along with an arrival distribution for the return and volatility jumps. Allows for the estimation of factor models with stochastic volatility (e.g., heteroskedastic volatility CAPM) by incorporating expected return predictors. Also includes functions to compute filtering and prediction distribution estimates, to simulate data from built-in and custom SV models with jumps, and to forecast future returns and volatility values using Monte Carlo simulation from a given SV model.
Author: Louis Arsenault-Mahjoubi [aut, cre],
Jean-Francois Begin [aut],
Mathieu Boudreault [aut]
Maintainer: Louis Arsenault-Mahjoubi <larsenau@sfu.ca>
Diff between SVDNF versions 0.1.10 dated 2024-10-04 and 0.1.11 dated 2024-10-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/Methods.R | 8 ++++---- inst/doc/vignette.pdf |binary 4 files changed, 10 insertions(+), 10 deletions(-)
Title: A Software Development Kit for 'Nixtla''s 'TimeGPT'
Description: A Software Development Kit for working with 'Nixtla''s 'TimeGPT', a foundation
model for time series forecasting. 'API' is an acronym for 'application
programming interface'; this package allows users to interact with
'TimeGPT' via the 'API'. You can set and validate 'API' keys and generate forecasts
via 'API' calls. It is compatible with 'tsibble' and base R. For more details
visit <https://docs.nixtla.io/>.
Author: Mariana Menchero [aut, cre] ,
Nixtla [cph]
Maintainer: Mariana Menchero <mariana@nixtla.io>
Diff between nixtlar versions 0.6.1 dated 2024-10-09 and 0.6.2 dated 2024-10-28
nixtlar-0.6.1/nixtlar/R/get_api_key.R |only nixtlar-0.6.1/nixtlar/man/dot-get_api_key.Rd |only nixtlar-0.6.1/nixtlar/man/figures/diagram.png |only nixtlar-0.6.2/nixtlar/DESCRIPTION | 6 nixtlar-0.6.2/nixtlar/MD5 | 126 ++++++------ nixtlar-0.6.2/nixtlar/NAMESPACE | 3 nixtlar-0.6.2/nixtlar/NEWS.md | 18 + nixtlar-0.6.2/nixtlar/R/get_client_setup.R |only nixtlar-0.6.2/nixtlar/R/get_model_params.R | 7 nixtlar-0.6.2/nixtlar/R/infer_frequency.R | 14 + nixtlar-0.6.2/nixtlar/R/make_request.R | 9 nixtlar-0.6.2/nixtlar/R/nixtla_client_cross_validation.R | 8 nixtlar-0.6.2/nixtlar/R/nixtla_client_detect_anomalies.R | 6 nixtlar-0.6.2/nixtlar/R/nixtla_client_forecast.R | 34 +-- nixtlar-0.6.2/nixtlar/R/nixtla_client_historic.R | 6 nixtlar-0.6.2/nixtlar/R/nixtla_client_setup.R |only nixtlar-0.6.2/nixtlar/R/nixtla_set_api_key.R | 7 nixtlar-0.6.2/nixtlar/R/nixtla_validate_api_key.R | 9 nixtlar-0.6.2/nixtlar/README.md | 50 ++-- nixtlar-0.6.2/nixtlar/build/vignette.rds |binary nixtlar-0.6.2/nixtlar/inst/doc/anomaly-detection.Rmd | 9 nixtlar-0.6.2/nixtlar/inst/doc/anomaly-detection.html | 26 +- nixtlar-0.6.2/nixtlar/inst/doc/azure-quickstart.R |only nixtlar-0.6.2/nixtlar/inst/doc/azure-quickstart.Rmd |only nixtlar-0.6.2/nixtlar/inst/doc/azure-quickstart.html |only nixtlar-0.6.2/nixtlar/inst/doc/cross-validation.Rmd | 4 nixtlar-0.6.2/nixtlar/inst/doc/cross-validation.html | 18 - nixtlar-0.6.2/nixtlar/inst/doc/data-requirements.Rmd | 18 - nixtlar-0.6.2/nixtlar/inst/doc/data-requirements.html | 34 +-- nixtlar-0.6.2/nixtlar/inst/doc/exogenous-variables.R | 2 nixtlar-0.6.2/nixtlar/inst/doc/exogenous-variables.Rmd | 10 nixtlar-0.6.2/nixtlar/inst/doc/exogenous-variables.html | 15 - nixtlar-0.6.2/nixtlar/inst/doc/get-started.R | 17 + nixtlar-0.6.2/nixtlar/inst/doc/get-started.Rmd | 31 ++ nixtlar-0.6.2/nixtlar/inst/doc/get-started.html | 93 +++++--- nixtlar-0.6.2/nixtlar/inst/doc/historical-forecast.Rmd | 7 nixtlar-0.6.2/nixtlar/inst/doc/historical-forecast.html | 20 + nixtlar-0.6.2/nixtlar/inst/doc/long-horizon.Rmd | 14 - nixtlar-0.6.2/nixtlar/inst/doc/long-horizon.html | 50 ++-- nixtlar-0.6.2/nixtlar/inst/doc/prediction-intervals.Rmd | 6 nixtlar-0.6.2/nixtlar/inst/doc/prediction-intervals.html | 16 - nixtlar-0.6.2/nixtlar/inst/doc/quantiles.Rmd | 4 nixtlar-0.6.2/nixtlar/inst/doc/quantiles.html | 8 nixtlar-0.6.2/nixtlar/inst/doc/setting-up-your-api-key.R | 10 nixtlar-0.6.2/nixtlar/inst/doc/setting-up-your-api-key.Rmd | 31 ++ nixtlar-0.6.2/nixtlar/inst/doc/setting-up-your-api-key.html | 41 +++ nixtlar-0.6.2/nixtlar/inst/doc/special-topics.R | 4 nixtlar-0.6.2/nixtlar/inst/doc/special-topics.Rmd | 25 +- nixtlar-0.6.2/nixtlar/inst/doc/special-topics.html | 76 ++++--- nixtlar-0.6.2/nixtlar/man/dot-get_client_steup.Rd |only nixtlar-0.6.2/nixtlar/man/dot-get_model_params.Rd | 2 nixtlar-0.6.2/nixtlar/man/dot-make_request.Rd | 8 nixtlar-0.6.2/nixtlar/man/figures/azure_deploy.png |only nixtlar-0.6.2/nixtlar/man/figures/azure_endpoints.png |only nixtlar-0.6.2/nixtlar/man/figures/azure_landing.png |only nixtlar-0.6.2/nixtlar/man/figures/azure_models.png |only nixtlar-0.6.2/nixtlar/man/figures/diagram_setup.png |only nixtlar-0.6.2/nixtlar/man/nixtla_client_setup.Rd |only nixtlar-0.6.2/nixtlar/man/nixtla_set_api_key.Rd | 4 nixtlar-0.6.2/nixtlar/man/nixtla_validate_api_key.Rd | 2 nixtlar-0.6.2/nixtlar/vignettes/anomaly-detection.Rmd | 9 nixtlar-0.6.2/nixtlar/vignettes/azure-quickstart.Rmd |only nixtlar-0.6.2/nixtlar/vignettes/cross-validation.Rmd | 4 nixtlar-0.6.2/nixtlar/vignettes/data-requirements.Rmd | 18 - nixtlar-0.6.2/nixtlar/vignettes/exogenous-variables.Rmd | 10 nixtlar-0.6.2/nixtlar/vignettes/get-started.Rmd | 31 ++ nixtlar-0.6.2/nixtlar/vignettes/historical-forecast.Rmd | 7 nixtlar-0.6.2/nixtlar/vignettes/long-horizon.Rmd | 14 - nixtlar-0.6.2/nixtlar/vignettes/prediction-intervals.Rmd | 6 nixtlar-0.6.2/nixtlar/vignettes/quantiles.Rmd | 4 nixtlar-0.6.2/nixtlar/vignettes/setting-up-your-api-key.Rmd | 31 ++ nixtlar-0.6.2/nixtlar/vignettes/special-topics.Rmd | 25 +- 72 files changed, 631 insertions(+), 436 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 1.8.0 dated 2024-09-12 and 1.8.1 dated 2024-10-28
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 +++++- R/disk.R | 2 +- man/ps_disk_io_counters.Rd | 2 +- src/api-macos.c | 8 ++++++++ src/dummy.c | 1 + 7 files changed, 25 insertions(+), 12 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD
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 [ctb],
Rik Schoemaker [ctb] ,
Justin Wilkins [ctb] ,
Wenping Wang [ctb],
Mirjam Trame [ctb],
Huijuan Xu [ctb],
John Harrold [ctb],
Bill Denney [ctb] ,
Theodoros Papathanasiou [ctb],
Teun Post [ctb],
Richard Hooi [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2 versions 3.0.0 dated 2024-09-18 and 3.0.1 dated 2024-10-28
nlmixr2-3.0.0/nlmixr2/man/covarSearchAuto.Rd |only nlmixr2-3.0.1/nlmixr2/DESCRIPTION | 9 ++++----- nlmixr2-3.0.1/nlmixr2/MD5 | 11 +++++------ nlmixr2-3.0.1/nlmixr2/NAMESPACE | 1 - nlmixr2-3.0.1/nlmixr2/NEWS.md | 7 +++++++ nlmixr2-3.0.1/nlmixr2/R/hardReexports.R | 10 ---------- nlmixr2-3.0.1/nlmixr2/R/utils.R | 1 - 7 files changed, 16 insertions(+), 23 deletions(-)
Title: Moments of Folded and Doubly Truncated Multivariate
Distributions
Description: It computes arbitrary products moments (mean vector and variance-covariance matrix), for some double truncated (and folded) multivariate distributions. These distributions belong to the family of selection elliptical distributions, which includes well known skewed distributions as the unified skew-t distribution (SUT) and its particular cases as the extended skew-t (EST), skew-t (ST) and the symmetric student-t (T) distribution. Analogous normal cases unified skew-normal (SUN), extended skew-normal (ESN), skew-normal (SN), and symmetric normal (N) are also included. Density, probabilities and random deviates are also offered for these members.
Author: Christian E. Galarza [aut, cre, trl]
,
Raymond Kan [ctb] ,
Victor H. Lachos [aut, ths]
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between MomTrunc versions 6.0 dated 2022-06-15 and 6.1 dated 2024-10-28
DESCRIPTION | 8 ++++---- MD5 | 29 +++++++++++++++-------------- R/Citations.R |only R/TSLCT_mean.R | 2 +- R/USER_cdfFMD.R | 4 ++-- R/USER_dmvESN.R | 2 +- R/USER_dmvEST.R | 2 +- R/USER_meanvarFMD.R | 2 +- R/USER_momentsFMD.R | 2 +- R/USER_momentsTMD.R | 4 ++-- R/USER_onlymeanTMD.R | 4 ++-- R/USER_rmvESN.R | 2 +- R/USER_rmvEST.R | 2 +- R/USER_rmvSN.R | 2 +- build/partial.rdb |binary man/pmvtnormt.Rd | 4 ++-- 16 files changed, 35 insertions(+), 34 deletions(-)
Title: Check if a Remote Computer is Up
Description: Check if a remote computer is up. It can either just call the
system ping command, or check a specified TCP port.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pingr versions 2.0.3 dated 2023-12-10 and 2.0.4 dated 2024-10-28
pingr-2.0.3/pingr/src/Makevars |only pingr-2.0.4/pingr/DESCRIPTION | 9 ++--- pingr-2.0.4/pingr/MD5 | 17 +++++---- pingr-2.0.4/pingr/NEWS.md | 6 +++ pingr-2.0.4/pingr/R/ping-package.R | 21 +++++++++++- pingr-2.0.4/pingr/cleanup |only pingr-2.0.4/pingr/configure |only pingr-2.0.4/pingr/configure.win |only pingr-2.0.4/pingr/src/Makevars.in |only pingr-2.0.4/pingr/src/dns.c | 46 +++++++++++++++++++++------ pingr-2.0.4/pingr/src/rping.c | 1 pingr-2.0.4/pingr/tests/testthat/test-icmp.R | 2 + 12 files changed, 79 insertions(+), 23 deletions(-)
Title: Convert Words to Numbers in Multiple Languages
Description: Converts written out numbers into their equivalent numbers.
Supports numbers written out in English, French, or Spanish.
Author: Chris Hartgerink [rev] ,
Joshua W. Lambert [ctb] ,
Karim Mane [ctb] ,
Hugo Gruson [aut] ,
Bankole Ahadzie [aut, cre, cph]
Maintainer: Bankole Ahadzie <bankole.ahadzie@lshtm.ac.uk>
Diff between numberize versions 1.0.0 dated 2024-06-11 and 1.0.1 dated 2024-10-28
numberize-1.0.0/numberize/man/dot-numberize.Rd |only numberize-1.0.1/numberize/DESCRIPTION | 6 numberize-1.0.1/numberize/MD5 | 10 numberize-1.0.1/numberize/NEWS.md | 6 numberize-1.0.1/numberize/R/numberize.R | 268 ++++++-------- numberize-1.0.1/numberize/man/ambiguous.Rd |only numberize-1.0.1/numberize/tests/testthat/test-numberize.R | 15 7 files changed, 149 insertions(+), 156 deletions(-)
Title: Genotype Plus Genotype-by-Environment Biplots
Description: Create biplots for GGE (genotype plus
genotype-by-environment) and GGB (genotype plus
genotype-by-block-of-environments) models. See Laffont et al. (2013)
<doi:10.2135/cropsci2013.03.0178>.
Author: Kevin Wright [aut, cre, cph] ,
Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between gge versions 1.8 dated 2023-08-21 and 1.9 dated 2024-10-28
DESCRIPTION | 31 +-- LICENSE | 4 MD5 | 24 +- NEWS.md | 11 + R/gge.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/gge_examples.R | 51 +++-- inst/doc/gge_examples.Rmd | 103 ++++++---- inst/doc/gge_examples.html | 124 +++++++----- man/RedGrayBlue.Rd | 56 ++--- man/gge.Rd | 442 ++++++++++++++++++++++----------------------- vignettes/gge_examples.Rmd | 103 ++++++---- 13 files changed, 511 insertions(+), 440 deletions(-)
Title: Fine-Gray Regression via Forward-Backward Scan
Description: In competing risks regression, the proportional subdistribution hazards (PSH) model is popular for its direct assessment of covariate effects on the cumulative incidence function. This package allows for both penalized and unpenalized PSH regression in linear time using a novel forward-backward scan. Penalties include Ridge, Lease Absolute Shrinkage and Selection Operator (LASSO), Smoothly Clipped Absolute Deviation (SCAD), Minimax Concave Plus (MCP), and elastic net <doi: 10.32614/RJ-2021-010>.
Author: Eric S. Kawaguchi [aut, cre]
Maintainer: Eric S. Kawaguchi <ekawaguc@usc.edu>
Diff between fastcmprsk versions 1.24.5 dated 2024-05-15 and 1.24.10 dated 2024-10-28
DESCRIPTION | 18 ++++++----- MD5 | 24 +++++++-------- R/Crisk.R | 2 - R/fastCrrp.R | 64 ++++++++++++++++------------------------ README.md | 6 +-- man/fastCrrp.Rd | 3 + src/denseElastic.c | 32 ++++++++++---------- src/denseFit.c | 34 ++++++++++----------- src/denseGroupPen.c | 40 ++++++++++++------------- src/densePen.c | 34 ++++++++++----------- src/utils.c | 36 +++++++++++----------- tests/testthat/test-errors.R | 16 ++++++++++ tests/testthat/test-modelFits.R | 50 ++++++++++++++++++++++++++++++- 13 files changed, 210 insertions(+), 149 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous
posterior distributions with customisable trajectory length
termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for
the original Discontinuous Hamiltonian Monte Carlo,
Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016)
<doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian
Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@studenti.unipd.it>
Diff between XDNUTS versions 1.2 dated 2024-09-03 and 1.5 dated 2024-10-28
XDNUTS-1.2/XDNUTS/inst/doc/Intro_to_XDNUTS.R |only XDNUTS-1.2/XDNUTS/inst/doc/Intro_to_XDNUTS.Rmd |only XDNUTS-1.2/XDNUTS/inst/doc/Intro_to_XDNUTS.html |only XDNUTS-1.2/XDNUTS/vignettes/Intro_to_XDNUTS.Rmd |only XDNUTS-1.5/XDNUTS/DESCRIPTION | 12 XDNUTS-1.5/XDNUTS/MD5 | 56 XDNUTS-1.5/XDNUTS/NAMESPACE | 6 XDNUTS-1.5/XDNUTS/R/RcppExports.R | 4 XDNUTS-1.5/XDNUTS/R/interface.R | 3408 ++++++++---- XDNUTS-1.5/XDNUTS/build/partial.rdb |binary XDNUTS-1.5/XDNUTS/build/vignette.rds |binary XDNUTS-1.5/XDNUTS/inst/doc/Tutorial_for_main_functions.R |only XDNUTS-1.5/XDNUTS/inst/doc/Tutorial_for_main_functions.Rmd |only XDNUTS-1.5/XDNUTS/inst/doc/Tutorial_for_main_functions.html |only XDNUTS-1.5/XDNUTS/man/plot.XDNUTS.Rd | 25 XDNUTS-1.5/XDNUTS/man/print.XDNUTS.Rd |only XDNUTS-1.5/XDNUTS/man/print.summary.XDNUTS.Rd |only XDNUTS-1.5/XDNUTS/man/set_parameters.Rd | 4 XDNUTS-1.5/XDNUTS/man/summary.XDNUTS.Rd | 9 XDNUTS-1.5/XDNUTS/man/xdextract.Rd | 13 XDNUTS-1.5/XDNUTS/man/xdnuts.Rd | 8 XDNUTS-1.5/XDNUTS/man/xdtransform.Rd | 16 XDNUTS-1.5/XDNUTS/src/dnuts.cpp | 100 XDNUTS-1.5/XDNUTS/src/epsilon_adapt.cpp | 30 XDNUTS-1.5/XDNUTS/src/globals_functions.cpp | 105 XDNUTS-1.5/XDNUTS/src/globals_functions.h | 13 XDNUTS-1.5/XDNUTS/src/mcmc.cpp | 208 XDNUTS-1.5/XDNUTS/src/recursive_tree.cpp | 3182 +++++------ XDNUTS-1.5/XDNUTS/src/recursive_tree.h | 8 XDNUTS-1.5/XDNUTS/src/single_hmc.cpp | 248 XDNUTS-1.5/XDNUTS/src/single_nuts.cpp | 1578 +++-- XDNUTS-1.5/XDNUTS/src/single_nuts.h | 8 XDNUTS-1.5/XDNUTS/vignettes/REFERENCES.bib | 235 XDNUTS-1.5/XDNUTS/vignettes/Tutorial_for_main_functions.Rmd |only 34 files changed, 5510 insertions(+), 3766 deletions(-)
Title: SNPs-Based Whole Genome Association Studies
Description: Functions to perform most of the common analysis in genome
association studies are implemented. These analyses include descriptive
statistics and exploratory analysis of missing values, calculation of
Hardy-Weinberg equilibrium, analysis of association based on generalized
linear models (either for quantitative or binary traits), and analysis
of multiple SNPs (haplotype and epistasis analysis). Permutation test
and related tests (sum statistic and truncated product) are also
implemented. Max-statistic and genetic risk-allele score exact
distributions are also possible to be estimated. The methods are
described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.
Author: Victor Moreno [aut],
Juan R Gonzalez [aut] ,
Dolors Pelegri [aut, cre]
Maintainer: Dolors Pelegri <dolors.pelegri@isglobal.org>
Diff between SNPassoc versions 2.1-0 dated 2022-12-14 and 2.1-2 dated 2024-10-28
DESCRIPTION | 10 MD5 | 224 +- R/GenotypeRate.R | 16 R/Table.N.Per.R | 38 R/Table.mean.se.R | 24 R/WGassociation.R | 186 - R/WGstats.R | 32 R/additive.R | 6 R/additive.WGassociation.R | 12 R/additive.default.R | 14 R/additive.snp.R | 42 R/as.snp.R | 12 R/assoc.R | 98 R/association.R | 364 +-- R/association.fit.R | 630 +++--- R/c.WGassociation.r | 68 R/codominant.R | 6 R/codominant.WGassociation.R | 12 R/codominant.default.R | 16 R/codominant.snp.R | 16 R/crea.lab.R | 32 R/dominant.R | 6 R/dominant.WGassociation.R | 12 R/dominant.default.R | 24 R/dominant.snp.R | 12 R/extractPval.R | 44 R/extractPval.i.R | 74 R/getGeneSymbol.R | 166 - R/getNiceTable.R | 92 R/getSignificantSNPs.R | 80 R/int.R | 12 R/interactionPval.R | 330 +-- R/interleave.R | 74 R/intervals.R | 8 R/intervals.dif.R | 110 - R/intervals.haplo.glm.R | 136 - R/intervals.or.R | 84 R/is.Monomorphic.R | 28 R/is.quantitative.R | 24 R/is.snp.R | 12 R/labels.WGassociation.R | 6 R/labels.setupSNP.R | 6 R/maxstat.R | 4 R/maxstat.default.R | 32 R/maxstat.matrix.R | 438 ++-- R/maxstat.setupSNP.R | 28 R/maxstat.table.R | 12 R/modelTest.R | 80 R/odds.r | 102 R/orderChromosome.R | 30 R/overdominant.R | 6 R/overdominant.WGassociation.R | 12 R/overdominant.default.R | 26 R/overdominant.snp.R | 46 R/plot.permTest.R | 42 R/plot.setupSNP.R | 6 R/plot.snp.R | 60 R/plotMissing.R | 110 - R/plotWGassociation.R | 15 R/print.SNPinteraction.R | 12 R/print.WGassociation.R | 48 R/print.haploOut.R | 68 R/print.intervals.R | 94 R/print.maxstat.R | 6 R/print.permTest.R | 62 R/print.snp.r | 92 R/print.snpOut.R | 128 - R/print.summary.snp.R | 20 R/print.tableHWE.R | 26 R/pvalTest.R | 18 R/pvalues.R | 6 R/pvalues.WGassociation.R | 6 R/qqpval.r | 14 R/recessive.R | 6 R/recessive.WGassociation.R | 12 R/recessive.default.R | 44 R/recessive.snp.R | 16 R/scanWGassociation.R | 22 R/setupSNP.R | 88 R/snp.R | 282 +- R/summary.snp.R | 108 - R/table.corner.R | 344 +-- R/table.interaction.R | 370 +-- R/togeno.R | 22 R/trim.R | 10 R/z$.setupSNP.R | 8 R/z[.WGassociation.R | 72 R/z[.setupSNP.R | 40 R/z[.snp.r | 24 R/z[[_-.setupSNP.R | 64 R/z[_-.setupSNP.R | 10 README.md | 6 build/vignette.rds |binary inst/doc/SNPassoc.R | 421 ++-- inst/doc/SNPassoc.Rmd | 862 ++++---- inst/doc/SNPassoc.html | 4087 +++++++++++++-------------------------- inst/docs/changelog.txt | 4 man/BonferroniSig.Rd | 92 man/GenomicControl.Rd | 98 man/LD.Rd | 144 - man/association.Rd | 266 +- man/asthma.Rd | 40 man/interactionPval.Rd | 168 - man/makegeno.Rd | 78 man/maxstat.Rd | 128 - man/odds.Rd | 80 man/related.Rd | 44 man/setupSNP.Rd | 134 - man/snp.Rd | 288 +- man/sortSNPs.Rd | 88 man/tableHWE.Rd | 114 - vignettes/SNPassoc.Rmd | 862 ++++---- vignettes/multiomic.bib | 4232 ++++++++++++++++++++--------------------- 113 files changed, 8656 insertions(+), 9969 deletions(-)
Title: Manipulate SNOMED CT Diagnosis Lists
Description: Functions and methods for manipulating 'SNOMED CT' concepts.
The package contains functions for loading the 'SNOMED CT' release into
a convenient R environment, selecting 'SNOMED CT' concepts using regular
expressions, and navigating the 'SNOMED CT' ontology. It provides the
'SNOMEDconcept' S3 class for a vector of 'SNOMED CT' concepts (stored
as 64-bit integers) and the 'SNOMEDcodelist' S3 class for a table
of concepts IDs with descriptions. For more information about 'SNOMED CT'
visit <https://www.snomed.org/>.
Author: Anoop Shah [aut, cre]
Maintainer: Anoop Shah <anoop@doctors.org.uk>
Diff between Rdiagnosislist versions 1.2 dated 2023-04-18 and 1.3 dated 2024-10-28
Rdiagnosislist-1.2/Rdiagnosislist/man/Rdiagnosislist.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/DESCRIPTION | 10 Rdiagnosislist-1.3/Rdiagnosislist/MD5 | 120 Rdiagnosislist-1.3/Rdiagnosislist/NAMESPACE | 20 Rdiagnosislist-1.3/Rdiagnosislist/NEWS | 28 Rdiagnosislist-1.3/Rdiagnosislist/R/CONCEPT.R | 2 Rdiagnosislist-1.3/Rdiagnosislist/R/DESCRIPTION.R | 2 Rdiagnosislist-1.3/Rdiagnosislist/R/EXTENDEDMAP.R | 2 Rdiagnosislist-1.3/Rdiagnosislist/R/HISTORY.R | 2 Rdiagnosislist-1.3/Rdiagnosislist/R/MANUAL_SYNONYMS.R |only Rdiagnosislist-1.3/Rdiagnosislist/R/QUERY.R | 2 Rdiagnosislist-1.3/Rdiagnosislist/R/READMAPS.R | 2 Rdiagnosislist-1.3/Rdiagnosislist/R/REFSET.R | 2 Rdiagnosislist-1.3/Rdiagnosislist/R/RELATIONSHIP.R | 2 Rdiagnosislist-1.3/Rdiagnosislist/R/Rdiagnosislist.R | 5 Rdiagnosislist-1.3/Rdiagnosislist/R/SIMPLEMAP.R | 2 Rdiagnosislist-1.3/Rdiagnosislist/R/SNOMEDcodelist.R | 11 Rdiagnosislist-1.3/Rdiagnosislist/R/cdb.R |only Rdiagnosislist-1.3/Rdiagnosislist/R/compose.R |only Rdiagnosislist-1.3/Rdiagnosislist/R/concepts.R | 94 Rdiagnosislist-1.3/Rdiagnosislist/R/createComposeLookup.R |only Rdiagnosislist-1.3/Rdiagnosislist/R/decompose.R |only Rdiagnosislist-1.3/Rdiagnosislist/R/hierarchy.R | 159 - Rdiagnosislist-1.3/Rdiagnosislist/R/htmlCodelistHierarchy.R | 26 Rdiagnosislist-1.3/Rdiagnosislist/R/loadSNOMED.R | 86 Rdiagnosislist-1.3/Rdiagnosislist/R/mapping.R | 10 Rdiagnosislist-1.3/Rdiagnosislist/R/orphanet.R |only Rdiagnosislist-1.3/Rdiagnosislist/R/wordnet.R |only Rdiagnosislist-1.3/Rdiagnosislist/build/vignette.rds |binary Rdiagnosislist-1.3/Rdiagnosislist/data/CONCEPT.RData |binary Rdiagnosislist-1.3/Rdiagnosislist/data/DESCRIPTION.RData |binary Rdiagnosislist-1.3/Rdiagnosislist/data/MANUAL_SYNONYMS.csv.gz |only Rdiagnosislist-1.3/Rdiagnosislist/data/MANUAL_SYNONYMS.rda |only Rdiagnosislist-1.3/Rdiagnosislist/data/RELATIONSHIP.RData |binary Rdiagnosislist-1.3/Rdiagnosislist/inst/doc/SNOMEDcodelists.html | 1385 +++++----- Rdiagnosislist-1.3/Rdiagnosislist/inst/doc/convertingAndCreatingCodelists.html | 489 ++- Rdiagnosislist-1.3/Rdiagnosislist/inst/doc/creatingConceptDatabaseForNLP.R |only Rdiagnosislist-1.3/Rdiagnosislist/inst/doc/creatingConceptDatabaseForNLP.Rmd |only Rdiagnosislist-1.3/Rdiagnosislist/inst/doc/creatingConceptDatabaseForNLP.html |only Rdiagnosislist-1.3/Rdiagnosislist/inst/doc/customHierarchy.html | 426 ++- Rdiagnosislist-1.3/Rdiagnosislist/inst/tests |only Rdiagnosislist-1.3/Rdiagnosislist/man/HISTORY.Rd | 2 Rdiagnosislist-1.3/Rdiagnosislist/man/MANUAL_SYNONYMS.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/QUERY.Rd | 2 Rdiagnosislist-1.3/Rdiagnosislist/man/READMAPS.Rd | 2 Rdiagnosislist-1.3/Rdiagnosislist/man/Rdiagnosislist-package.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/SNOMED_CONCEPT.Rd | 2 Rdiagnosislist-1.3/Rdiagnosislist/man/SNOMED_DESCRIPTION.Rd | 2 Rdiagnosislist-1.3/Rdiagnosislist/man/SNOMED_EXTENDEDMAP.Rd | 2 Rdiagnosislist-1.3/Rdiagnosislist/man/SNOMED_REFSET.Rd | 2 Rdiagnosislist-1.3/Rdiagnosislist/man/SNOMED_RELATIONSHIP.Rd | 2 Rdiagnosislist-1.3/Rdiagnosislist/man/SNOMED_SIMPLEMAP.Rd | 2 Rdiagnosislist-1.3/Rdiagnosislist/man/acronyms.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/addWordnet.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/batchDecompose.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/compose.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/createCDB.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/createComposeLookup.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/createTransitive.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/decompose.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/description.Rd | 7 Rdiagnosislist-1.3/Rdiagnosislist/man/downloadOrphanet.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/downloadWordnet.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/exclude_irrelevant_findings.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/exportMiADECDB.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/htmlCodelistHierarchy.Rd | 5 Rdiagnosislist-1.3/Rdiagnosislist/man/loadREADMAPS.Rd | 4 Rdiagnosislist-1.3/Rdiagnosislist/man/loadSNOMED.Rd | 5 Rdiagnosislist-1.3/Rdiagnosislist/man/parents.Rd | 50 Rdiagnosislist-1.3/Rdiagnosislist/man/print.SNOMEDfindings.Rd |only Rdiagnosislist-1.3/Rdiagnosislist/man/semanticType.Rd | 4 Rdiagnosislist-1.3/Rdiagnosislist/tests/testthat/test_SNOMEDcodelist.R | 4 Rdiagnosislist-1.3/Rdiagnosislist/tests/testthat/test_cdb.R |only Rdiagnosislist-1.3/Rdiagnosislist/tests/testthat/test_concepts.R | 10 Rdiagnosislist-1.3/Rdiagnosislist/tests/testthat/test_hierarchy.R | 16 Rdiagnosislist-1.3/Rdiagnosislist/tests/testthat/test_std_term.R |only Rdiagnosislist-1.3/Rdiagnosislist/vignettes/creatingConceptDatabaseForNLP.Rmd |only 77 files changed, 1987 insertions(+), 1023 deletions(-)
More information about Rdiagnosislist at CRAN
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Title: Partial Dependence Plots
Description: A general framework for constructing partial dependence (i.e.,
marginal effect) plots from various types machine learning models
in R.
Author: Brandon M. Greenwell [aut, cre]
Maintainer: Brandon M. Greenwell <greenwell.brandon@gmail.com>
Diff between pdp versions 0.8.1 dated 2022-06-07 and 0.8.2 dated 2024-10-28
pdp-0.8.1/pdp/R/pdp.R |only pdp-0.8.1/pdp/man/get_training_data.Rd |only pdp-0.8.1/pdp/man/pdp.Rd |only pdp-0.8.2/pdp/DESCRIPTION | 8 +++--- pdp-0.8.2/pdp/MD5 | 33 +++++++++++++-------------- pdp-0.8.2/pdp/NEWS.md | 15 +++++++++++- pdp-0.8.2/pdp/R/get_task.R | 3 +- pdp-0.8.2/pdp/R/get_training_data.R | 32 ++++++++------------------ pdp-0.8.2/pdp/R/pdp-package.R |only pdp-0.8.2/pdp/build/vignette.rds |binary pdp-0.8.2/pdp/inst/CITATION | 9 ++++--- pdp-0.8.2/pdp/inst/doc/pdp-approximate.pdf |binary pdp-0.8.2/pdp/inst/doc/pdp-intro.pdf |binary pdp-0.8.2/pdp/inst/doc/pdp-link-function.pdf |binary pdp-0.8.2/pdp/man/pdp-package.Rd |only pdp-0.8.2/pdp/src/PartialGBM.cpp | 3 +- pdp-0.8.2/pdp/src/PartialGBM.h | 1 pdp-0.8.2/pdp/src/in_out.c | 3 +- pdp-0.8.2/pdp/src/pdp-init.c | 1 pdp-0.8.2/pdp/src/pdp.h | 1 20 files changed, 59 insertions(+), 50 deletions(-)
Title: High Dimensional Categorical Data Visualization
Description: Easy visualization for datasets with more than two categorical variables and additional continuous variables. 'diceplot' is particularly useful for exploring complex categorical data in the context of pathway analysis across multiple conditions. For a detailed documentation please visit <https://dice-and-domino-plot.readthedocs.io/en/latest/>.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between diceplot versions 0.1.1 dated 2024-10-21 and 0.1.2 dated 2024-10-28
diceplot-0.1.1/diceplot/R/dice_plot.R |only diceplot-0.1.1/diceplot/R/domino_plot.R |only diceplot-0.1.2/diceplot/DESCRIPTION | 11 diceplot-0.1.2/diceplot/LICENSE |only diceplot-0.1.2/diceplot/MD5 | 23 - diceplot-0.1.2/diceplot/NAMESPACE | 1 diceplot-0.1.2/diceplot/R/diceplot.R |only diceplot-0.1.2/diceplot/R/dominoplot.R |only diceplot-0.1.2/diceplot/R/utils.R | 28 + diceplot-0.1.2/diceplot/man/calculate_dot_size.Rd | 6 diceplot-0.1.2/diceplot/man/dice_plot.Rd | 36 +- diceplot-0.1.2/diceplot/man/domino_plot.Rd | 2 diceplot-0.1.2/diceplot/man/order_cat_b.Rd | 4 diceplot-0.1.2/diceplot/tests/test_diceplots.R | 320 +++++++--------------- diceplot-0.1.2/diceplot/tests/test_domino_base.R | 2 15 files changed, 188 insertions(+), 245 deletions(-)
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.3.1 dated 2024-06-04 and 1.3.2 dated 2024-10-28
DESCRIPTION | 6 +- MD5 | 30 +++++++------- NEWS.md | 14 ++++++ R/appMetadata.R | 21 ---------- R/bundlePackage.R | 2 R/bundlePackageRenv.R | 7 +++ R/client-connect.R | 32 ++++----------- R/tasks.R | 6 ++ inst/doc/custom-http.html | 4 - man/taskLog.Rd | 3 + man/tasks.Rd | 3 + tests/testthat/_snaps/appMetadata-quarto.md | 2 tests/testthat/_snaps/appMetadata.md | 12 ----- tests/testthat/_snaps/bundlePackage.md | 4 - tests/testthat/test-appMetadata.R | 58 +++++----------------------- tests/testthat/test-client-connect.R | 6 +- 16 files changed, 83 insertions(+), 127 deletions(-)
Title: Estimation of Natural Regeneration Potential
Description: Functions for estimating the potential dispersal of tree species
using regeneration densities and dispersal distances to nearest seed trees.
A quantile regression is implemented to determine the dispersal potential.
Spatial prediction can be used to identify natural regeneration potential for forest restoration as described in Axer et al (2021) <doi:10.1016/j.foreco.2020.118802>.
Author: Maximilian Axer [aut, cre] ,
Robert Schlicht [aut],
Robert Nuske [ctb] ,
Nordwestdeutsche Forstliche Versuchsanstalt [fnd],
Staatsbetrieb Sachsenforst [fnd],
Technische Universitaet Dresden [fnd, cph]
Maintainer: Maximilian Axer <maximilian.axer@nw-fva.de>
Diff between quaxnat versions 1.0.0 dated 2024-06-07 and 1.0.1 dated 2024-10-28
DESCRIPTION | 12 MD5 | 45 + NAMESPACE | 30 - NEWS.md | 9 R/dispersal_kernels.R | 754 ++++++++++++++++----------------- R/doc_data.R | 46 +- R/extract_dist.R | 86 +-- R/predict_quax.R | 98 ++-- R/quax.R | 558 ++++++++++++------------ R/seed_tree_distmap.R | 84 +-- README.md | 313 +++++++------ build/partial.rdb |binary man/extract_dist.Rd | 82 +-- man/figures/README-figure_raster-1.png |binary man/figures/logo.png |only man/k_exponential_power.Rd | 186 ++++---- man/k_lognormal.Rd | 144 +++--- man/k_power.Rd | 112 ++-- man/k_t.Rd | 144 +++--- man/k_weibull.Rd | 142 +++--- man/predict_quax.Rd | 104 ++-- man/quax.Rd | 420 +++++++++--------- man/regeneration.Rd | 56 +- man/summary.quax.Rd | 96 ++-- 24 files changed, 1764 insertions(+), 1757 deletions(-)
Title: Find Tools Needed to Build R Packages
Description: Provides functions used to build R packages. Locates
compilers needed to build R packages on various platforms and ensures
the PATH is configured appropriately so R can use them.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgbuild versions 1.4.4 dated 2024-03-17 and 1.4.5 dated 2024-10-28
DESCRIPTION | 10 ++++---- MD5 | 18 +++++++-------- NEWS.md | 8 ++++++ R/rtools-metadata.R | 5 ++++ R/rtools-path.R | 4 +++ R/rtools.R | 37 ++++++++++++++++++------------ tests/testthat/test-compiler-flags.R | 6 ----- tests/testthat/test-exclude.R | 16 +++++-------- tests/testthat/test-rtools.R | 2 - tests/testthat/test-utils.R | 42 +++++------------------------------ 10 files changed, 68 insertions(+), 80 deletions(-)
Title: Create Non-Confidential Multi-Resolution Grids
Description: Functionality for creating gridded data, respecting the confidentiality rules,
such as a minimum number of units and dominance by one or more units in the grid cell.
The functions also include the possibility for contextual suppression of data.
Author: Jon Olav Skoien [aut, cre],
Nicolas Lampach [aut]
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>
Diff between MRG versions 0.2.14 dated 2024-09-12 and 0.3.1 dated 2024-10-28
MRG-0.2.14/MRG/R/zzz.R |only MRG-0.3.1/MRG/DESCRIPTION | 6 MRG-0.3.1/MRG/MD5 | 36 +- MRG-0.3.1/MRG/NAMESPACE | 6 MRG-0.3.1/MRG/R/MRGmerge.R |only MRG-0.3.1/MRG/R/MRGpostProcess.R | 25 + MRG-0.3.1/MRG/R/createMRGobject.R | 11 MRG-0.3.1/MRG/R/gridData.R | 41 +-- MRG-0.3.1/MRG/R/ifsDoc.R | 4 MRG-0.3.1/MRG/R/multiResGrid.R | 369 +++++++++++++++++++---------- MRG-0.3.1/MRG/R/print.R |only MRG-0.3.1/MRG/R/remSmall.R | 25 + MRG-0.3.1/MRG/R/roxygen_eval.R | 34 ++ MRG-0.3.1/MRG/man/MRGmerge.Rd |only MRG-0.3.1/MRG/man/createMRGobject.Rd | 27 +- MRG-0.3.1/MRG/man/gridData.Rd | 26 +- MRG-0.3.1/MRG/man/ifs_dk.Rd | 4 MRG-0.3.1/MRG/man/multiResGrid.Rd | 193 +++++++++------ MRG-0.3.1/MRG/man/remSmall.Rd | 30 +- MRG-0.3.1/MRG/tests/multiResGrid.R | 27 +- MRG-0.3.1/MRG/tests/multiResGrid.Rout.save | 179 +++++++++----- 21 files changed, 680 insertions(+), 363 deletions(-)
Title: Data and Function to Work with Emojis
Description: Contains data about emojis with relevant metadata, and
functions to work with emojis when they are in strings.
Author: Emil Hvitfeldt [aut, cre] ,
Hadley Wickham [ctb] ,
Romain Francois [ctb]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between emoji versions 15.0 dated 2022-11-02 and 16.0.0 dated 2024-10-28
emoji-15.0/emoji/R/0_imports.R |only emoji-16.0.0/emoji/DESCRIPTION | 36 +++----- emoji-16.0.0/emoji/MD5 | 54 ++++++------ emoji-16.0.0/emoji/NAMESPACE | 1 emoji-16.0.0/emoji/NEWS.md | 6 + emoji-16.0.0/emoji/R/data.R | 29 +++--- emoji-16.0.0/emoji/R/emoji-package.R |only emoji-16.0.0/emoji/R/emoji.R | 3 emoji-16.0.0/emoji/R/emoji_p.R | 2 emoji-16.0.0/emoji/R/medal.R | 10 -- emoji-16.0.0/emoji/R/rx.R | 36 ++++++++ emoji-16.0.0/emoji/README.md | 104 ++++++++++--------------- emoji-16.0.0/emoji/data/emoji_keyword.rda |binary emoji-16.0.0/emoji/data/emoji_modifiers.rda |binary emoji-16.0.0/emoji/data/emoji_name.rda |binary emoji-16.0.0/emoji/data/emoji_rx.rda |binary emoji-16.0.0/emoji/data/emojis.rda |binary emoji-16.0.0/emoji/man/emoji-package.Rd |only emoji-16.0.0/emoji/man/emoji_detect.Rd | 2 emoji-16.0.0/emoji/man/emoji_glue.Rd | 4 emoji-16.0.0/emoji/man/emoji_keyword.Rd | 10 -- emoji-16.0.0/emoji/man/emoji_modifiers.Rd | 8 - emoji-16.0.0/emoji/man/emoji_name.Rd | 10 -- emoji-16.0.0/emoji/man/emoji_p.Rd | 2 emoji-16.0.0/emoji/man/emoji_replace_name.Rd |only emoji-16.0.0/emoji/man/emoji_subset.Rd | 2 emoji-16.0.0/emoji/man/emojis.Rd | 8 - emoji-16.0.0/emoji/man/medal.Rd | 12 +- emoji-16.0.0/emoji/tests/testthat/test-emoji.R | 12 ++ emoji-16.0.0/emoji/tests/testthat/test-glue.R | 5 - 30 files changed, 190 insertions(+), 166 deletions(-)
Title: Fit and Apply ComBat, LMM, or Prescaling Harmonization for
ENIGMA and Other Multisite MRI Data
Description: Fit and apply ComBat, linear mixed-effects models (LMM), or prescaling to harmonize magnetic resonance imaging (MRI) data from different sites. Briefly, these methods remove differences between sites due to using different scanning devices, and LMM additionally tests linear hypotheses. As detailed in the manual, the original ComBat function was first modified for the harmonization of MRI data (Fortin et al. (2017) <doi:10.1016/j.neuroimage.2017.11.024>) and then modified again to create separate functions for fitting and applying the harmonization and allow missing values and constant rows for its use within the Enhancing Neuro Imaging Genetics through Meta-Analysis (ENIGMA) Consortium (Radua et al. (2020) <doi:10.1016/j.neuroimage.2020.116956>); this package includes the latter version. LMM calls "lme" massively considering specific brain imaging details. Finally, prescaling is a good option for fMRI, where different devices can have varying units of measurement.
Author: Joaquim Radua [aut, cre]
Maintainer: Joaquim Radua <quimradua@gmail.com>
Diff between combat.enigma versions 1.1 dated 2024-10-17 and 1.1.1 dated 2024-10-28
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 9 +++++++++ man/combat_fit.Rd | 2 +- man/lmm_fit.Rd | 6 +++++- man/prescale_fit.Rd | 2 +- 6 files changed, 26 insertions(+), 13 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Hosszejni and Kastner (2021) <doi:10.18637/jss.v100.i12> and Kastner (2016) <doi:10.18637/jss.v069.i05> and the package examples.
Author: Darjus Hosszejni [aut, cre] ,
Gregor Kastner [aut]
Maintainer: Darjus Hosszejni <darjus.hosszejni@icloud.com>
Diff between stochvol versions 3.2.4 dated 2024-03-03 and 3.2.5 dated 2024-10-28
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- NEWS.md | 12 ++++++++++++ R/stochvol-package.R | 3 +-- R/utilities_svdraws.R | 6 +++--- R/wrappers.R | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary data/exrates.RData |binary inst/doc/article.pdf |binary inst/doc/article2.pdf |binary man/paradensplot.Rd | 2 +- man/plot.svdraws.Rd | 2 +- man/plot.svpredict.Rd | 4 ++-- man/stochvol-package.Rd | 8 ++++++++ man/svlm.Rd | 4 ++-- man/svsample.Rd | 4 ++-- man/updatesummary.Rd | 2 +- man/volplot.Rd | 2 +- src/utils_parameters.cc | 8 +++++--- 20 files changed, 66 insertions(+), 45 deletions(-)
Title: 'shiny' Application for Adverse Event Analysis of 'OnCore' Data
Description: An application for analysis of Adverse Events, as described in Chen, et al., (2023) <doi:10.3390/cancers15092521>.
The required data for the application includes demographics, follow up, adverse event, drug administration and optional tumor measurement data.
The app can produce swimmers plots of adverse events, Kaplan-Meier plots and Cox Proportional Hazards model results
for the association of adverse event biomarkers and overall survival and progression free survival.
The adverse event biomarkers include occurrence of grade 3, low grade (1-2), and treatment related adverse events.
Plots and tables of results are downloadable.
Author: Z Thompson [aut, cre],
A Obermayer [aut],
DT Chen [aut]
Maintainer: Z Thompson <zachary.thompson@moffitt.org>
Diff between AdverseEvents versions 0.0.1 dated 2024-10-11 and 0.0.2 dated 2024-10-28
AdverseEvents-0.0.1/AdverseEvents/vignettes/Oncore1.PNG |only AdverseEvents-0.0.1/AdverseEvents/vignettes/subsetofRECISTdata.PNG |only AdverseEvents-0.0.2/AdverseEvents/DESCRIPTION | 6 AdverseEvents-0.0.2/AdverseEvents/MD5 | 24 AdverseEvents-0.0.2/AdverseEvents/build/vignette.rds |binary AdverseEvents-0.0.2/AdverseEvents/inst/app/www/demo_ae_data.csv | 3692 ++--- AdverseEvents-0.0.2/AdverseEvents/inst/app/www/demo_da_data.csv | 3464 ++--- AdverseEvents-0.0.2/AdverseEvents/inst/app/www/demo_demo_data.csv | 258 AdverseEvents-0.0.2/AdverseEvents/inst/app/www/demo_fu_data.csv | 242 AdverseEvents-0.0.2/AdverseEvents/inst/app/www/demo_recist_data.csv | 6484 +++++----- AdverseEvents-0.0.2/AdverseEvents/inst/doc/AdverseEvents.Rmd | 7 AdverseEvents-0.0.2/AdverseEvents/inst/doc/AdverseEvents.html | 12 AdverseEvents-0.0.2/AdverseEvents/vignettes/AdverseEvents.Rmd | 7 AdverseEvents-0.0.2/AdverseEvents/vignettes/demographic_data.jpg |only AdverseEvents-0.0.2/AdverseEvents/vignettes/front_page_AE.jpg |only 15 files changed, 7091 insertions(+), 7105 deletions(-)
Title: Run Code 'With' Temporarily Modified Global State
Description: A set of functions to run code 'with' safely and temporarily
modified global state. Many of these functions were originally a part
of the 'devtools' package, this provides a simple package with limited
dependencies to provide access to these functions.
Author: Jim Hester [aut],
Lionel Henry [aut, cre],
Kirill Mueller [aut],
Kevin Ushey [aut],
Hadley Wickham [aut],
Winston Chang [aut],
Jennifer Bryan [ctb],
Richard Cotton [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between withr versions 3.0.1 dated 2024-07-31 and 3.0.2 dated 2024-10-28
DESCRIPTION | 6 MD5 | 8 - NEWS.md | 13 +- R/language.R | 33 ++--- inst/doc/withr.html | 338 ++++++++++++++++++++++++++-------------------------- 5 files changed, 204 insertions(+), 194 deletions(-)
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data
from disparate sources. Metadata is managed throughout the process to facilitate
reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] ,
Cory Merow [aut] ,
Brian Maitner [aut] ,
Jamie M. Kass [aut] ,
Vijay Barve [aut] ,
Robert P. Guralnick [aut] ,
Damiano Oldoni [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/407>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between occCite versions 0.5.8 dated 2024-09-05 and 0.5.9 dated 2024-10-28
DESCRIPTION | 15 +- MD5 | 32 ++--- NEWS.md | 4 R/occCiteData.R | 2 R/studyTaxonList.R | 6 - R/taxonRectification.R | 166 +++++++++++++++---------------- inst/CITATION | 2 inst/doc/a_Simple.R | 14 +- inst/doc/a_Simple.Rmd | 3 inst/doc/a_Simple.html | 28 ++--- inst/doc/b_Advanced.html | 160 ++++++++--------------------- man/occCiteData-class.Rd | 2 man/studyTaxonList.Rd | 6 - man/taxonRectification.Rd | 11 +- tests/testthat/test-occCitePrint.R | 33 ------ tests/testthat/test-taxonRectification.R | 83 ++++++++------- vignettes/a_Simple.Rmd | 3 17 files changed, 249 insertions(+), 321 deletions(-)
Title: Alerts, Notifications and Loading Screen in 'Shiny'
Description: Easily create alerts, notifications, modals, info tips and loading
screens in 'Shiny'. Includes several options to customize alerts and
notifications by including text, icons, images and buttons. When wrapped
around a 'Shiny' output, loading screen is automatically displayed while
the output is being recalculated.
Author: Aravind Hebbali [aut, cre],
Zong Bin [ctb, cph] ,
Tobias Ahlin [ctb, cph] ,
https://github.com/RIDICS [ctb, cph] ,
Raphael Fabini [ctb, cph] ,
Luke Hass [ctb, cph] ,
Mohammad Younes [ctb, cph] ,
Nick Payne [ctb, cph] ,
Indrashish Ghosh [ctb, cph] ,
h [...truncated...]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between standby versions 0.1.0 dated 2023-05-24 and 0.2.0 dated 2024-10-28
DESCRIPTION | 8 - MD5 | 40 +++---- NEWS.md | 10 + R/alertify-handler.R | 20 ++- R/pnotify-handler.R | 12 +- R/spinkit-handler.R | 4 R/standby.R | 12 +- README.md | 17 ++- build/vignette.rds |binary inst/doc/buzz.R | 2 inst/doc/buzz.html | 224 +++++++++++++++---------------------------- inst/doc/standby.R | 4 inst/doc/standby.Rmd | 2 inst/doc/standby.html | 178 +++++++++++++--------------------- inst/standby/css/standby.css | 4 inst/standby/js/standby.js | 22 ++-- man/alertify.Rd | 2 man/notify.Rd | 2 man/spinkit.Rd | 4 man/standby.Rd | 32 +++++- vignettes/standby.Rmd | 2 21 files changed, 278 insertions(+), 323 deletions(-)
More information about primarycensored at CRAN
Permanent link
Title: Linking Geographic Information Systems, Remote Sensing and Other
Command Line Tools
Description: Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.
Author: Chris Reudenbach [cre, aut],
Tim Appelhans [ctb]
Maintainer: Chris Reudenbach <reudenbach@uni-marburg.de>
Diff between link2GI versions 0.6-1 dated 2024-06-01 and 0.6-2 dated 2024-10-28
link2GI-0.6-1/link2GI/inst/doc/link2GI7.R |only link2GI-0.6-1/link2GI/inst/doc/link2GI7.Rmd |only link2GI-0.6-1/link2GI/inst/doc/link2GI7.html |only link2GI-0.6-1/link2GI/vignettes/link2GI7.Rmd |only link2GI-0.6-2/link2GI/DESCRIPTION | 10 link2GI-0.6-2/link2GI/MD5 | 79 +-- link2GI-0.6-2/link2GI/NEWS | 7 link2GI-0.6-2/link2GI/NEWS.md | 8 link2GI-0.6-2/link2GI/R/initProj.R | 7 link2GI-0.6-2/link2GI/R/link2giKarim.R | 12 link2GI-0.6-2/link2GI/R/parseOTB.R | 11 link2GI-0.6-2/link2GI/README.md | 2 link2GI-0.6-2/link2GI/build/vignette.rds |binary link2GI-0.6-2/link2GI/inst/doc/link2GI1.Rmd | 16 link2GI-0.6-2/link2GI/inst/doc/link2GI1.html | 16 link2GI-0.6-2/link2GI/inst/doc/link2GI2.Rmd | 24 - link2GI-0.6-2/link2GI/inst/doc/link2GI2.html | 23 - link2GI-0.6-2/link2GI/inst/doc/link2GI3.Rmd | 4 link2GI-0.6-2/link2GI/inst/doc/link2GI3.html | 6 link2GI-0.6-2/link2GI/inst/doc/link2GI4.Rmd | 2 link2GI-0.6-2/link2GI/inst/doc/link2GI4.html | 2 link2GI-0.6-2/link2GI/inst/doc/link2GI5.html | 2 link2GI-0.6-2/link2GI/inst/doc/link2GI6.R |only link2GI-0.6-2/link2GI/inst/doc/link2GI6.Rmd | 210 +++++++++ link2GI-0.6-2/link2GI/inst/doc/link2GI6.html | 213 +++++++++- link2GI-0.6-2/link2GI/inst/templates/advancedSpatial.brew | 22 - link2GI-0.6-2/link2GI/inst/templates/base.brew | 22 - link2GI-0.6-2/link2GI/inst/templates/baseSpatial.brew | 23 - link2GI-0.6-2/link2GI/inst/templates/config-default-projects.yml | 10 link2GI-0.6-2/link2GI/inst/templates/config-master-yml.brew | 20 link2GI-0.6-2/link2GI/inst/templates/post-processing.brew | 10 link2GI-0.6-2/link2GI/inst/templates/pre-processing.brew | 11 link2GI-0.6-2/link2GI/inst/templates/processing.brew | 14 link2GI-0.6-2/link2GI/inst/templates/script_control.brew | 7 link2GI-0.6-2/link2GI/inst/templates/script_setup.brew | 27 - link2GI-0.6-2/link2GI/inst/templates/yml.brew | 14 link2GI-0.6-2/link2GI/man/gvec2sf.Rd | 6 link2GI-0.6-2/link2GI/man/manuallyBuild.Rd | 7 link2GI-0.6-2/link2GI/vignettes/link2GI1.Rmd | 16 link2GI-0.6-2/link2GI/vignettes/link2GI2.Rmd | 24 - link2GI-0.6-2/link2GI/vignettes/link2GI3.Rmd | 4 link2GI-0.6-2/link2GI/vignettes/link2GI4.Rmd | 2 link2GI-0.6-2/link2GI/vignettes/link2GI6.Rmd | 210 +++++++++ 43 files changed, 833 insertions(+), 270 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 1.3.1 dated 2024-03-05 and 1.3.12 dated 2024-10-28
DESCRIPTION | 12 MD5 | 106 NEWS.md | 28 R/bgplot3d.R | 3 R/knitr.R | 3 R/ply.R | 90 R/r3d.rgl.R | 1 R/rglwidget.R | 18 R/stl.R | 49 R/zzz.R | 9 README.md | 32 build/vignette.rds |binary configure | 9 configure.ac | 9 inst/doc/WebGL.html | 141 inst/doc/demos.R | 4 inst/doc/demos.Rmd | 4 inst/doc/demos.html | 8973 ++++++++++++++++++++++++- inst/doc/deprecation.html | 2 inst/doc/pkgdown.R | 2 inst/doc/pkgdown.Rmd | 2 inst/doc/pkgdown.html | 8882 ++++++++++++++++++++++++ inst/doc/rgl.html | 143 inst/doc/transparency.R | 2 inst/doc/transparency.Rmd | 2 inst/doc/transparency.html | 8906 ++++++++++++++++++++++++ inst/htmlwidgets/lib/rglClass/axes.src.js | 4 inst/htmlwidgets/lib/rglClass/draw.src.js | 3 inst/htmlwidgets/lib/rglClass/pieces.src.js | 61 inst/htmlwidgets/lib/rglClass/rglClass.min.js | 10 inst/htmlwidgets/lib/rglClass/shadersrc.src.js | 8 man/playwidget.Rd | 2 man/plot3d.lm.Rd | 2 man/readSTL.Rd | 7 man/rglwidget.Rd | 17 man/snapshot.Rd | 7 man/writePLY.Rd | 4 src/build/autoconf/config.guess | 1327 ++- src/build/autoconf/config.sub | 306 src/build/autoconf/install-sh | 420 - src/subscene.cpp | 2 src/useNULL/Makevars | 4 tests/testthat/testdata/mergeVertices.rds |binary tests/testthat/testdata/obj.rds |binary tests/testthat/testdata/qmesh3d.rds |binary tests/testthat/testdata/r3d.rds |binary tests/testthat/testdata/shade3detc.rds |binary tests/testthat/testdata/subscenes.rds |binary tests/testthat/testdata/tmesh3d.rds |binary tests/testthat/testdata/transformations.rds |binary vignettes/demos.Rmd | 4 vignettes/pkgdown.Rmd | 2 vignettes/setup.R | 12 vignettes/transparency.Rmd | 2 54 files changed, 28419 insertions(+), 1217 deletions(-)
Title: "Eating the Liver of Data Science"
Description: Offers a suite of helper functions to simplify various data science techniques for non-experts. This package aims to enable individuals with only a minimal level of coding knowledge to become acquainted with these techniques in an accessible manner. Inspired by an ancient Persian idiom, we liken this process to "eating the liver of data science," suggesting a deep and intimate engagement with the field of data science. This package includes functions for tasks such as data partitioning for out-of-sample testing, calculating Mean Squared Error (MSE) to assess prediction accuracy, and data transformations (z-score and min-max). In addition to these helper functions, the 'liver' package also features several intriguing datasets valuable for multivariate analysis.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.16 dated 2024-09-05 and 1.17 dated 2024-10-28
DESCRIPTION | 6 +- MD5 | 94 ++++++++++++++++++++-------------------- NEWS.md | 4 + R/accuracy.R | 7 +-- R/conf.mat.R | 49 ++++++++++++--------- R/conf.mat.plot.R | 12 ++--- R/find.na.R | 14 +++--- R/kNN.R | 86 ++++++++++++++++++++----------------- R/kNN.plot.R | 101 +++++++++++++++++++++++--------------------- R/mae.R | 28 ++++++------ R/minmax.R | 71 +++++++++++++++++------------- R/mse.R | 28 ++++++------ R/partition.R | 49 +++++++++++++-------- R/skewness.R | 24 +++++----- R/skim.R | 8 +-- R/transform.R | 13 +++-- R/zscore.R | 58 ++++++++++++++----------- inst/doc/liver-example.html | 14 +++--- man/accuracy.Rd | 10 ++-- man/adult.Rd | 6 +- man/advertising.Rd | 6 +- man/bank.Rd | 6 +- man/cereal.Rd | 6 +- man/churn.Rd | 6 +- man/churnCredit.Rd | 7 +-- man/churnTel.Rd | 7 +-- man/conf.mat.Rd | 12 ++--- man/conf.mat.plot.Rd | 10 ++-- man/corona.Rd | 6 +- man/fertilizer.Rd | 6 +- man/find.na.Rd | 6 +- man/house.Rd | 6 +- man/housePrice.Rd | 6 +- man/insurance.Rd | 7 +-- man/kNN.Rd | 12 ++--- man/kNN.plot.Rd | 14 +++--- man/mae.Rd | 8 +-- man/marketing.Rd | 6 +- man/minmax.Rd | 6 +- man/mse.Rd | 8 +-- man/partition.Rd | 6 +- man/redWines.Rd | 6 +- man/risk.Rd | 6 +- man/skewness.Rd | 6 +- man/skim.Rd | 6 +- man/transform.Rd | 8 +-- man/whiteWines.Rd | 6 +- man/zscore.Rd | 6 +- 48 files changed, 478 insertions(+), 405 deletions(-)
Title: Two-Sample Empirical Likelihood
Description: Empirical likelihood (EL) inference for two-sample problems. The following statistics are included: the difference of two-sample means, smooth Huber estimators, quantile (qdiff) and cumulative distribution functions (ddiff), probability-probability (P-P) and quantile-quantile (Q-Q) plots as well as receiver operating characteristic (ROC) curves. EL calculations are based on J. Valeinis, E. Cers (2011) <http://home.lu.lv/~valeinis/lv/petnieciba/EL_TwoSample_2011.pdf>.
Author: Janis Valeinis [aut] ,
Edmunds Cers [aut],
Janis Gredzens [cre],
Reinis Alksnis [ctb]
Maintainer: Janis Gredzens <janis.gredzens@lu.lv>
Diff between EL versions 1.2 dated 2022-12-19 and 1.3 dated 2024-10-28
DESCRIPTION | 17 - MD5 | 13 NAMESPACE | 25 + NEWS.md |only R/BEL.R |only R/EL.R | 772 ++++++++++++++++++++++++++++++++----------------------- man/BEL.means.Rd |only man/EL.plot.Rd | 50 ++- man/EL.smooth.Rd | 7 9 files changed, 532 insertions(+), 352 deletions(-)
Title: High-Dimensional Mediation Analysis
Description: Allows to estimate and test high-dimensional mediation effects based on advanced mediator screening and penalized regression techniques. Methods used in the package refer to Zhang H, Zheng Y, Zhang Z, Gao T, Joyce B, Yoon G, Zhang W, Schwartz J, Just A, Colicino E, Vokonas P, Zhao L, Lv J, Baccarelli A, Hou L, Liu L. Estimating and Testing High-dimensional Mediation Effects in Epigenetic Studies. Bioinformatics. (2016) <doi:10.1093/bioinformatics/btw351>. PMID: 27357171.
Author: Yinan Zheng [aut, cre] ,
Haixiang Zhang [aut],
Lifang Hou [aut],
Lei Liu [aut, cph]
Maintainer: Yinan Zheng <y-zheng@northwestern.edu>
Diff between HIMA versions 2.2.2 dated 2024-08-24 and 2.3.0 dated 2024-10-28
HIMA-2.2.2/HIMA/R/hima.R |only HIMA-2.2.2/HIMA/R/hima2.R |only HIMA-2.2.2/HIMA/man/hima.Rd |only HIMA-2.2.2/HIMA/man/hima2.Rd |only HIMA-2.3.0/HIMA/DESCRIPTION | 12 HIMA-2.3.0/HIMA/MD5 | 48 +-- HIMA-2.3.0/HIMA/NAMESPACE | 4 HIMA-2.3.0/HIMA/R/HIMA-package.R | 66 ++-- HIMA-2.3.0/HIMA/R/classicHIMA.R |only HIMA-2.3.0/HIMA/R/dblassoHIMA.R | 314 +++++++++----------- HIMA-2.3.0/HIMA/R/eHIMA.R | 327 ++++++++++----------- HIMA-2.3.0/HIMA/R/himaDat.R | 6 HIMA-2.3.0/HIMA/R/himaFit.R |only HIMA-2.3.0/HIMA/R/microHIMA.R | 224 +++++++------- HIMA-2.3.0/HIMA/R/onAttach.R | 78 ++--- HIMA-2.3.0/HIMA/R/qHIMA.R | 247 +++++++--------- HIMA-2.3.0/HIMA/R/survHIMA.R | 263 +++++++++-------- HIMA-2.3.0/HIMA/R/utils.R | 549 ++++++++++++++++++------------------ HIMA-2.3.0/HIMA/README.md | 2 HIMA-2.3.0/HIMA/inst/NEWS | 5 HIMA-2.3.0/HIMA/man/HIMA-package.Rd | 23 - HIMA-2.3.0/HIMA/man/classicHIMA.Rd |only HIMA-2.3.0/HIMA/man/dblassoHIMA.Rd | 61 +--- HIMA-2.3.0/HIMA/man/eHIMA.Rd | 31 +- HIMA-2.3.0/HIMA/man/himaDat.Rd | 4 HIMA-2.3.0/HIMA/man/himaFit.Rd |only HIMA-2.3.0/HIMA/man/microHIMA.Rd | 30 + HIMA-2.3.0/HIMA/man/qHIMA.Rd | 39 +- HIMA-2.3.0/HIMA/man/survHIMA.Rd | 41 +- 29 files changed, 1206 insertions(+), 1168 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, simulation, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX and html code,
recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.
Author: Frank E Harrell Jr [aut, cre] ,
Charles Dupont [ctb]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between Hmisc versions 5.1-3 dated 2024-05-28 and 5.2-0 dated 2024-10-28
Hmisc-5.1-3/Hmisc/src/cidxcn.f |only Hmisc-5.1-3/Hmisc/src/cidxcp.f |only Hmisc-5.1-3/Hmisc/src/hoeffd.f |only Hmisc-5.1-3/Hmisc/src/jacklins.f |only Hmisc-5.1-3/Hmisc/src/maxempr.f |only Hmisc-5.1-3/Hmisc/src/rcorr.f |only Hmisc-5.1-3/Hmisc/src/wclosest.f |only Hmisc-5.2-0/Hmisc/DESCRIPTION | 12 ++++----- Hmisc-5.2-0/Hmisc/MD5 | 42 +++++++++++++++++--------------- Hmisc-5.2-0/Hmisc/NAMESPACE | 2 - Hmisc-5.2-0/Hmisc/NEWS | 9 ++++++ Hmisc-5.2-0/Hmisc/R/describe.s | 20 +++++++++------ Hmisc-5.2-0/Hmisc/R/pMedian.r |only Hmisc-5.2-0/Hmisc/R/qcrypt.r | 3 ++ Hmisc-5.2-0/Hmisc/inst/tests/pMedian.r |only Hmisc-5.2-0/Hmisc/man/Hmisc-internal.Rd | 1 Hmisc-5.2-0/Hmisc/man/describe.Rd | 6 ++-- Hmisc-5.2-0/Hmisc/man/latex.Rd | 4 +-- Hmisc-5.2-0/Hmisc/man/pMedian.Rd |only Hmisc-5.2-0/Hmisc/man/popower.Rd | 6 ++-- Hmisc-5.2-0/Hmisc/man/transcan.Rd | 2 - Hmisc-5.2-0/Hmisc/src/Hmisc.h | 8 ++++++ Hmisc-5.2-0/Hmisc/src/cidxcn.f90 |only Hmisc-5.2-0/Hmisc/src/cidxcp.f90 |only Hmisc-5.2-0/Hmisc/src/hlqest.f90 |only Hmisc-5.2-0/Hmisc/src/hoeffd.f90 |only Hmisc-5.2-0/Hmisc/src/init.c | 2 + Hmisc-5.2-0/Hmisc/src/jacklins.f90 |only Hmisc-5.2-0/Hmisc/src/maxempr.f90 |only Hmisc-5.2-0/Hmisc/src/rcorr.f90 |only Hmisc-5.2-0/Hmisc/src/wclosest.f90 |only 31 files changed, 73 insertions(+), 44 deletions(-)
Title: Stepwise Covariate Selection for the Fine & Gray Competing Risks
Regression Model
Description: Performs forward and backwards stepwise regression for the Proportional subdistribution hazards model in competing risks (Fine & Gray 1999). Procedure uses AIC, BIC and BICcr as selection criteria. BICcr has a penalty of k = log(n*), where n* is the number of primary events.
Author: Ravi Varadhan [aut, cre],
Deborah Kuk [aut],
Leon Wang [ctb]
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between crrstep versions 2023.1.1 dated 2023-08-22 and 2024.1.1 dated 2024-10-28
DESCRIPTION | 20 - MD5 | 6 R/crrstep.r | 956 ++++++++++++++++++++++++++++----------------------------- man/crrstep.Rd | 8 4 files changed, 504 insertions(+), 486 deletions(-)
Title: Analysis and Visualization of Circular Data
Description: Circumplex models, which organize constructs in a circle around two
underlying dimensions, are popular for studying interpersonal functioning,
mood/affect, and vocational preferences/environments. This package provides
tools for analyzing and visualizing circular data, including scoring
functions for relevant instruments and a generalization of the bootstrapped
structural summary method from Zimmermann & Wright (2017)
<doi:10.1177/1073191115621795> and functions for creating publication-ready
tables and figures from the results.
Author: Jeffrey Girard [aut, cre] ,
Johannes Zimmermann [aut] ,
Aidan Wright [aut]
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between circumplex versions 0.3.10 dated 2023-08-22 and 1.0.0 dated 2024-10-28
circumplex-0.3.10/circumplex/R/assertions.R |only circumplex-0.3.10/circumplex/R/ssm_visualization.R |only circumplex-0.3.10/circumplex/R/utils-pipe.R |only circumplex-0.3.10/circumplex/R/utils-tidy-eval.R |only circumplex-0.3.10/circumplex/R/zzz.R |only circumplex-0.3.10/circumplex/man/pipe.Rd |only circumplex-0.3.10/circumplex/man/ssm_append.Rd |only circumplex-0.3.10/circumplex/man/ssm_plot.Rd |only circumplex-0.3.10/circumplex/man/ssm_plot_scores.Rd |only circumplex-0.3.10/circumplex/man/standardize.Rd |only circumplex-0.3.10/circumplex/man/tidyeval.Rd |only circumplex-0.3.10/circumplex/tests/testthat/_snaps/ssm_visualization |only circumplex-0.3.10/circumplex/tests/testthat/test-assertions.R |only circumplex-0.3.10/circumplex/tests/testthat/test-ssm_visualization.R |only circumplex-1.0.0/circumplex/DESCRIPTION | 14 circumplex-1.0.0/circumplex/MD5 | 170 - circumplex-1.0.0/circumplex/NAMESPACE | 34 circumplex-1.0.0/circumplex/NEWS.md | 46 circumplex-1.0.0/circumplex/R/circumplex-package.R | 56 circumplex-1.0.0/circumplex/R/convenience_functions.R | 15 circumplex-1.0.0/circumplex/R/instrument_data.R | 32 circumplex-1.0.0/circumplex/R/instrument_oop.R | 70 circumplex-1.0.0/circumplex/R/ssm_analysis.R | 645 +++--- circumplex-1.0.0/circumplex/R/ssm_bootstrap.R | 104 - circumplex-1.0.0/circumplex/R/ssm_oop.R | 71 circumplex-1.0.0/circumplex/R/ssm_plot.R |only circumplex-1.0.0/circumplex/R/ssm_table.R |only circumplex-1.0.0/circumplex/R/tidying_functions.R | 222 +- circumplex-1.0.0/circumplex/R/utils.R | 104 - circumplex-1.0.0/circumplex/build/partial.rdb |binary circumplex-1.0.0/circumplex/build/vignette.rds |binary circumplex-1.0.0/circumplex/data/cais.rda |only circumplex-1.0.0/circumplex/data/csie.rda |binary circumplex-1.0.0/circumplex/data/csig.rda |binary circumplex-1.0.0/circumplex/data/csip.rda |binary circumplex-1.0.0/circumplex/data/csiv.rda |binary circumplex-1.0.0/circumplex/data/iei.rda |only circumplex-1.0.0/circumplex/data/igicr.rda |binary circumplex-1.0.0/circumplex/data/iip32.rda |binary circumplex-1.0.0/circumplex/data/iip64.rda |binary circumplex-1.0.0/circumplex/data/iipsc.rda |binary circumplex-1.0.0/circumplex/data/iis32.rda |binary circumplex-1.0.0/circumplex/data/iis64.rda |binary circumplex-1.0.0/circumplex/data/iitc.rda |binary circumplex-1.0.0/circumplex/data/ipipipc.rda |binary circumplex-1.0.0/circumplex/data/isc.rda |binary circumplex-1.0.0/circumplex/data/jz2017.rda |binary circumplex-1.0.0/circumplex/data/raw_iipsc.rda |binary circumplex-1.0.0/circumplex/inst/doc/intermediate-ssm-analysis.R | 134 - 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circumplex-1.0.0/circumplex/man/ssm_parameters.Rd | 18 circumplex-1.0.0/circumplex/man/ssm_plot_circle.Rd | 28 circumplex-1.0.0/circumplex/man/ssm_plot_contrast.Rd | 41 circumplex-1.0.0/circumplex/man/ssm_plot_curve.Rd |only circumplex-1.0.0/circumplex/man/ssm_score.Rd | 14 circumplex-1.0.0/circumplex/man/ssm_table.Rd | 33 circumplex-1.0.0/circumplex/tests/testthat/_snaps/instrument_oop.md | 127 + circumplex-1.0.0/circumplex/tests/testthat/_snaps/ssm_oop.md |only circumplex-1.0.0/circumplex/tests/testthat/_snaps/ssm_plot |only circumplex-1.0.0/circumplex/tests/testthat/_snaps/ssm_table.md |only circumplex-1.0.0/circumplex/tests/testthat/test-RcppExport.R.R | 2 circumplex-1.0.0/circumplex/tests/testthat/test-instrument_oop.R | 16 circumplex-1.0.0/circumplex/tests/testthat/test-ssm_analysis.R | 340 ++- circumplex-1.0.0/circumplex/tests/testthat/test-ssm_bootstrap.R | 40 circumplex-1.0.0/circumplex/tests/testthat/test-ssm_oop.R | 39 circumplex-1.0.0/circumplex/tests/testthat/test-ssm_plot.R |only circumplex-1.0.0/circumplex/tests/testthat/test-ssm_table.R |only circumplex-1.0.0/circumplex/tests/testthat/test-tidying_functions.R | 56 circumplex-1.0.0/circumplex/tests/testthat/test-utils.R | 20 circumplex-1.0.0/circumplex/vignettes/intermediate-ssm-analysis.Rmd | 187 - 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