Title: Structural Modeling for Multiple Latent Class Variables
Description: Provides comprehensive tools for the implementation of Structural Latent Class Models (SLCM), including
Latent Transition Analysis (LTA; Linda M. Collins and Stephanie T. Lanza, 2009) <doi:10.1002/9780470567333>,
Latent Class Profile Analysis (LCPA; Hwan Chung et al., 2010) <doi:10.1111/j.1467-985x.2010.00674.x>, and
Joint Latent Class Analysis (JLCA; Saebom Jeon et al., 2017) <doi:10.1080/10705511.2017.1340844>, and
any other extended models involving multiple latent class variables.
Author: Youngsun Kim [aut, cre] ,
Hwan Chung [aut]
Maintainer: Youngsun Kim <yskstat@gmail.com>
Diff between slca versions 1.2.0 dated 2024-11-01 and 1.3.0 dated 2024-12-12
slca-1.2.0/slca/R/addhealth.R |only slca-1.2.0/slca/R/gss7677.R |only slca-1.2.0/slca/R/nlys97.R |only slca-1.2.0/slca/R/regression.R |only slca-1.2.0/slca/R/simulate.slca.R |only slca-1.2.0/slca/man/confint.slca.Rd |only slca-1.2.0/slca/man/examples/diag.R |only slca-1.2.0/slca/man/examples/reg.R |only slca-1.2.0/slca/man/reorder.slca.Rd |only slca-1.3.0/slca/DESCRIPTION | 6 slca-1.3.0/slca/MD5 | 72 +++--- slca-1.3.0/slca/NAMESPACE | 22 + slca-1.3.0/slca/R/data.R |only slca-1.3.0/slca/R/data_encode.R | 25 ++ slca-1.3.0/slca/R/diagnostic.R | 80 +++---- slca-1.3.0/slca/R/estimate.R | 48 ++-- slca-1.3.0/slca/R/methods.R | 340 +++++++++++++++--------------- slca-1.3.0/slca/R/nlsy_fit.R | 9 slca-1.3.0/slca/R/plot.slca.R | 85 +++---- slca-1.3.0/slca/R/regress.R |only slca-1.3.0/slca/R/simulate.R |only slca-1.3.0/slca/R/slca.R | 97 +++++--- slca-1.3.0/slca/R/slcaControl.R | 24 +- slca-1.3.0/slca/data/nlsy_jlcpa.rda |binary slca-1.3.0/slca/data/nlsy_jlta.rda |only slca-1.3.0/slca/man/addhealth.Rd | 27 +- slca-1.3.0/slca/man/compare.Rd | 22 - slca-1.3.0/slca/man/confint.slcafit.Rd |only slca-1.3.0/slca/man/estimate.Rd | 65 ++++- slca-1.3.0/slca/man/examples/diagnostic.R |only slca-1.3.0/slca/man/examples/estimate.R |only slca-1.3.0/slca/man/examples/gss7677.R | 14 - slca-1.3.0/slca/man/examples/regress.R |only slca-1.3.0/slca/man/examples/sim.R | 82 ++++++- slca-1.3.0/slca/man/examples/simulate.R |only slca-1.3.0/slca/man/examples/slca.R | 24 +- slca-1.3.0/slca/man/gof.Rd | 31 +- slca-1.3.0/slca/man/gss7677.Rd | 56 ++-- slca-1.3.0/slca/man/nlsy97.Rd | 43 +-- slca-1.3.0/slca/man/nlsy_jlcpa.Rd | 11 slca-1.3.0/slca/man/param.Rd | 24 +- slca-1.3.0/slca/man/predict.slcafit.Rd |only slca-1.3.0/slca/man/regress.Rd | 52 ++-- slca-1.3.0/slca/man/reorder.slcafit.Rd |only slca-1.3.0/slca/man/simulate.slca.Rd | 62 +++-- slca-1.3.0/slca/man/slca.Rd | 105 +++++---- slca-1.3.0/slca/man/slcaControl.Rd | 27 +- 47 files changed, 833 insertions(+), 620 deletions(-)
Title: Computational Methods for Economic Complexity
Description: A wrapper of different methods from Linear Algebra for the equations
introduced in The Atlas of Economic Complexity and related literature. This
package provides standard matrix and graph output that can be used seamlessly
with other packages. See <doi:10.21105/joss.01866> for a summary
of these methods and its evolution in literature.
Author: Mauricio Vargas Sepulveda [aut, cre, cph]
,
Carlo Bottai [ctb] ,
Diego Kozlowski [ctb] ,
Nico Pintar [rev] ,
The World Bank [dtc] ,
Open Trade Statistics [dtc]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Diff between economiccomplexity versions 1.5.0 dated 2023-08-07 and 2.0.0 dated 2024-12-12
economiccomplexity-1.5.0/economiccomplexity/R/economiccomplexity-internals.R |only economiccomplexity-1.5.0/economiccomplexity/man/eigenvalues_method.Rd |only economiccomplexity-1.5.0/economiccomplexity/man/fitness_method.Rd |only economiccomplexity-1.5.0/economiccomplexity/man/reflections_method.Rd |only economiccomplexity-2.0.0/economiccomplexity/DESCRIPTION | 15 economiccomplexity-2.0.0/economiccomplexity/MD5 | 80 economiccomplexity-2.0.0/economiccomplexity/NAMESPACE | 10 economiccomplexity-2.0.0/economiccomplexity/R/balassa_index.R | 64 economiccomplexity-2.0.0/economiccomplexity/R/complexity_measures.R | 199 - economiccomplexity-2.0.0/economiccomplexity/R/complexity_outlook.R | 25 economiccomplexity-2.0.0/economiccomplexity/R/cpp11.R |only economiccomplexity-2.0.0/economiccomplexity/R/density.R | 7 economiccomplexity-2.0.0/economiccomplexity/R/distance.R | 21 economiccomplexity-2.0.0/economiccomplexity/R/economiccomplexity-package.R |only economiccomplexity-2.0.0/economiccomplexity/R/helpers.R |only economiccomplexity-2.0.0/economiccomplexity/R/productivity_levels.R | 41 economiccomplexity-2.0.0/economiccomplexity/R/projections.R | 40 economiccomplexity-2.0.0/economiccomplexity/R/proximity.R | 46 economiccomplexity-2.0.0/economiccomplexity/build/partial.rdb |binary economiccomplexity-2.0.0/economiccomplexity/build/vignette.rds |binary economiccomplexity-2.0.0/economiccomplexity/cleanup |only economiccomplexity-2.0.0/economiccomplexity/configure |only economiccomplexity-2.0.0/economiccomplexity/data/economiccomplexity_output.rda |binary economiccomplexity-2.0.0/economiccomplexity/inst/doc/economiccomplexity.R | 131 - economiccomplexity-2.0.0/economiccomplexity/inst/doc/economiccomplexity.Rmd | 161 - economiccomplexity-2.0.0/economiccomplexity/inst/doc/economiccomplexity.html | 1217 ++++------ economiccomplexity-2.0.0/economiccomplexity/man/balassa_index.Rd | 25 economiccomplexity-2.0.0/economiccomplexity/man/complexity_measures.Rd | 7 economiccomplexity-2.0.0/economiccomplexity/man/complexity_outlook.Rd | 9 economiccomplexity-2.0.0/economiccomplexity/man/country_aggregation.Rd | 2 economiccomplexity-2.0.0/economiccomplexity/man/country_product_aggregation.Rd | 2 economiccomplexity-2.0.0/economiccomplexity/man/dataframe_to_matrix.Rd | 2 economiccomplexity-2.0.0/economiccomplexity/man/density.Rd | 7 economiccomplexity-2.0.0/economiccomplexity/man/distance.Rd | 7 economiccomplexity-2.0.0/economiccomplexity/man/economiccomplexity-package.Rd |only economiccomplexity-2.0.0/economiccomplexity/man/economiccomplexity_output.Rd | 19 economiccomplexity-2.0.0/economiccomplexity/man/productivity_levels.Rd | 20 economiccomplexity-2.0.0/economiccomplexity/man/projections.Rd | 9 economiccomplexity-2.0.0/economiccomplexity/man/proximity.Rd | 7 economiccomplexity-2.0.0/economiccomplexity/man/world_gdp_avg_1998_to_2000.Rd | 22 economiccomplexity-2.0.0/economiccomplexity/man/world_trade_avg_1998_to_2000.Rd | 24 economiccomplexity-2.0.0/economiccomplexity/src |only economiccomplexity-2.0.0/economiccomplexity/tests/testthat/test-balassa_index.R | 21 economiccomplexity-2.0.0/economiccomplexity/tests/testthat/test-productivity_levels.R | 13 economiccomplexity-2.0.0/economiccomplexity/vignettes/economiccomplexity.Rmd | 161 - 45 files changed, 1189 insertions(+), 1225 deletions(-)
More information about economiccomplexity at CRAN
Permanent link
Title: Hexagonal Hierarchical Geospatial Indexing System
Description: Provides access to Uber's 'H3' geospatial indexing system via 'h3lib'
<https://CRAN.R-project.org/package=h3lib>. 'h3r' is designed to mimic the 'H3'
Application Programming Interface (API) <https://h3geo.org/docs/api/indexing/>,
so that any function in the API is also available in 'h3r'.
Author: David Cooley [aut, cre],
Ray Shao [aut]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between h3r versions 0.1.1 dated 2024-03-12 and 0.1.2 dated 2024-12-12
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/h3r-package.R | 2 +- man/stations.Rd | 2 +- src/h3rUtils.c | 3 ++- 5 files changed, 13 insertions(+), 12 deletions(-)
Title: Personalised Synthetic Controls
Description: Allows the comparison of data cohorts (DC) against a Counter Factual Model (CFM) and measures the difference in terms of an efficacy parameter. Allows the application of Personalised Synthetic Controls.
Author: Richard Jackson [cre, aut]
Maintainer: Richard Jackson <richJ23@liverpool.ac.uk>
Diff between psc versions 1.0.0 dated 2024-11-20 and 1.1.0 dated 2024-12-12
psc-1.0.0/psc/R/psc_ite.R |only psc-1.0.0/psc/man/psc_ite.Rd |only psc-1.1.0/psc/DESCRIPTION | 11 psc-1.1.0/psc/MD5 | 137 +- psc-1.1.0/psc/NAMESPACE | 9 psc-1.1.0/psc/NEWS.md | 2 psc-1.1.0/psc/R/acc.R | 2 psc-1.1.0/psc/R/bin.mod.R | 16 psc-1.1.0/psc/R/coef.psc.R | 3 psc-1.1.0/psc/R/cont.mod.R | 20 psc-1.1.0/psc/R/count.mod.R | 18 psc-1.1.0/psc/R/data.R | 3 psc-1.1.0/psc/R/dataComb.R | 8 psc-1.1.0/psc/R/dataComb.flexsurvreg.R | 28 psc-1.1.0/psc/R/dataComb.glm.R | 32 psc-1.1.0/psc/R/dataSumm.R |only psc-1.1.0/psc/R/data_match.R |only psc-1.1.0/psc/R/initParm.R | 6 psc-1.1.0/psc/R/lik.flexsurvreg.R | 18 psc-1.1.0/psc/R/lik.flexsurvreg.mtc.R | 17 psc-1.1.0/psc/R/lik.glm.R | 12 psc-1.1.0/psc/R/lik.glm.mtc.R | 11 psc-1.1.0/psc/R/linPred.R | 16 psc-1.1.0/psc/R/modelExtract.flexsurvreg.R | 16 psc-1.1.0/psc/R/modelExtract.glm.R | 10 psc-1.1.0/psc/R/modp.R | 3 psc-1.1.0/psc/R/plot.R | 82 - psc-1.1.0/psc/R/plot.psc.binary.R |only psc-1.1.0/psc/R/plot.psc.cont.R |only psc-1.1.0/psc/R/plot.psc.count.R |only psc-1.1.0/psc/R/plot.psc.flexsurvreg.R |only psc-1.1.0/psc/R/pscEst.flexsurvreg.R | 7 psc-1.1.0/psc/R/pscEst.glm.R | 7 psc-1.1.0/psc/R/pscSumm.R | 28 psc-1.1.0/psc/R/pscfit.R | 13 psc-1.1.0/psc/R/summary.R | 3 psc-1.1.0/psc/R/surv.mod.R | 9 psc-1.1.0/psc/R/surv_fpm.R | 13 psc-1.1.0/psc/README.md | 12 psc-1.1.0/psc/inst/doc/psc-vignette.R | 26 psc-1.1.0/psc/inst/doc/psc-vignette.Rmd | 204 ++-- psc-1.1.0/psc/inst/doc/psc-vignette.html | 1177 +++++++++++++++++++----- psc-1.1.0/psc/man/acc.Rd | 2 psc-1.1.0/psc/man/bin.mod.Rd | 16 psc-1.1.0/psc/man/coef.psc.Rd | 3 psc-1.1.0/psc/man/cont.mod.Rd | 20 psc-1.1.0/psc/man/count.mod.Rd | 18 psc-1.1.0/psc/man/data.Rd | 3 psc-1.1.0/psc/man/dataComb.Rd | 8 psc-1.1.0/psc/man/dataComb.flexsurvreg.Rd | 12 psc-1.1.0/psc/man/dataComb.glm.Rd | 14 psc-1.1.0/psc/man/dataSumm.Rd |only psc-1.1.0/psc/man/data_match.Rd |only psc-1.1.0/psc/man/figures/README-pressure-1.png |binary psc-1.1.0/psc/man/figures/example_plot.png |only psc-1.1.0/psc/man/initParm.Rd | 6 psc-1.1.0/psc/man/lik.flexsurvreg.Rd | 10 psc-1.1.0/psc/man/lik.flexsurvreg.mtc.Rd | 10 psc-1.1.0/psc/man/lik.glm.Rd | 10 psc-1.1.0/psc/man/lik.glm.mtc.Rd | 10 psc-1.1.0/psc/man/linPred.Rd | 9 psc-1.1.0/psc/man/modelExtract.flexsurvreg.Rd | 14 psc-1.1.0/psc/man/modelExtract.glm.Rd | 10 psc-1.1.0/psc/man/modp.Rd | 3 psc-1.1.0/psc/man/plot.psc.Rd | 19 psc-1.1.0/psc/man/plot.psc.binary.Rd |only psc-1.1.0/psc/man/plot.psc.cont.Rd |only psc-1.1.0/psc/man/plot.psc.count.Rd |only psc-1.1.0/psc/man/plot.psc.flexsurvreg.Rd |only psc-1.1.0/psc/man/pscEst.flexsurvreg.Rd | 6 psc-1.1.0/psc/man/pscEst.glm.Rd | 6 psc-1.1.0/psc/man/pscSumm.Rd | 5 psc-1.1.0/psc/man/pscfit.Rd | 13 psc-1.1.0/psc/man/summary.psc.Rd | 3 psc-1.1.0/psc/man/surv.mod.Rd | 10 psc-1.1.0/psc/man/surv_fpm.Rd | 11 psc-1.1.0/psc/vignettes/psc-vignette.Rmd | 204 ++-- 77 files changed, 1759 insertions(+), 675 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell V. Lenth [aut, cre, cph],
Balazs Banfai [ctb],
Ben Bolker [ctb],
Paul Buerkner [ctb],
Iago Gine-Vazquez [ctb],
Maxime Herve [ctb],
Maarten Jung [ctb],
Jonathon Love [ctb],
Fernando Miguez [ctb],
Julia Piaskowski [ctb],
Hannes Riebl [ctb],
Hen [...truncated...]
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.10.5 dated 2024-10-14 and 1.10.6 dated 2024-12-12
DESCRIPTION | 8 +- MD5 | 62 +++++++++++----------- NAMESPACE | 1 NEWS.md | 12 +++- R/eff-size.R | 19 ++++-- R/emmGrid-methods.R | 5 + R/factors.R | 28 +++++++++ R/rbind.R | 2 R/test.R | 3 - build/vignette.rds |binary inst/doc/AQuickStart.html | 4 - inst/doc/FAQs.html | 6 +- inst/doc/basics.html | 4 - inst/doc/comparisons.html | 10 +-- inst/doc/confidence-intervals.html | 14 ++-- inst/doc/interactions.html | 18 +++--- inst/doc/messy-data.html | 4 - inst/doc/models.Rmd | 5 + inst/doc/models.html | 104 +++++++++++++++++++------------------ inst/doc/predictions.html | 4 - inst/doc/re-engineering-clds.html | 4 - inst/doc/sophisticated.html | 4 - inst/doc/transformations.html | 4 - inst/doc/utilities.html | 4 - inst/doc/vignette-topics.html | 4 - inst/doc/xplanations.html | 4 - inst/doc/xtending.html | 8 +- man/eff_size.Rd | 11 +-- man/joint_tests.Rd | 3 - man/manip-factors.Rd | 20 +++++++ man/update.emmGrid.Rd | 5 + vignettes/models.Rmd | 5 + 32 files changed, 238 insertions(+), 151 deletions(-)
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Lucas Mation [aut]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between enderecobr versions 0.2.1 dated 2024-11-18 and 0.3.0 dated 2024-12-12
DESCRIPTION | 6 MD5 | 26 +- NEWS.md | 10 R/padronizar_ceps.R | 4 R/padronizar_enderecos.R | 42 ++- R/padronizar_estados.R | 49 ++-- build/vignette.rds |binary inst/doc/enderecobr.R | 2 inst/doc/enderecobr.html | 4 man/padronizar_enderecos.Rd | 6 man/padronizar_estados.Rd | 7 tests/testthat/_snaps/padronizar_enderecos.md | 318 +++++++++++++------------- tests/testthat/test-padronizar_enderecos.R | 28 ++ tests/testthat/test-padronizar_estados.R | 34 ++ 14 files changed, 323 insertions(+), 213 deletions(-)
Title: Simple, Consistent Package Options
Description: Simple mechanisms for defining and interpreting package options. Provides
helpers for interpreting environment variables, global options, defining
default values and more.
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Diff between options versions 0.2.0 dated 2024-05-12 and 0.3.0 dated 2024-12-12
DESCRIPTION | 12 ++-- MD5 | 25 ++++----- NAMESPACE | 3 + NEWS.md | 10 +++ R/envvars.R | 2 R/naming.R | 43 ++++++++++++++++ R/options_get.R | 71 ++++++++++++++++++++++++-- README.md | 2 inst/doc/envvars.R | 4 + inst/doc/envvars.html | 4 - inst/doc/options.R | 106 ++++++++++++++++++++-------------------- man/opt.Rd | 55 ++++++++++++++++++-- tests/testthat/test-envvars.R | 1 tests/testthat/test-opts_list.R |only 14 files changed, 249 insertions(+), 89 deletions(-)
Title: Superefficient Estimation of Future Conditional Hazards Based on
Marker Information
Description: Provides a nonparametric smoothed kernel density estimator for the future conditional hazard when time-dependent covariates are present. It also provides pointwise and uniform confidence bands and a bandwidth selection.
Author: Dimitrios Bagkavos [aut, cre],
Alex Isakson [ctb],
Enno Mammen [ctb],
Jens Nielsen [ctb],
Cecile Proust-Lima [ctb]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between HQM versions 0.1.2 dated 2024-12-04 and 0.1.4 dated 2024-12-12
DESCRIPTION | 6 ++-- MD5 | 4 +-- man/h_xt_vec.Rd | 68 +++++++++++++++++++++----------------------------------- 3 files changed, 31 insertions(+), 47 deletions(-)
Title: Packages and Functions for 'CourseKata' Courses
Description: Easily install and load all packages and functions used in
'CourseKata' courses. Aid teaching with helper functions and augment
generic functions to provide cohesion between the network of packages.
Learn more about 'CourseKata' at <https://coursekata.org>.
Author: Adam Blake [cre, aut] ,
Ji Son [aut] ,
Jim Stigler [aut]
Maintainer: Adam Blake <adam@coursekata.org>
Diff between coursekata versions 0.18.0 dated 2024-08-16 and 0.18.1 dated 2024-12-12
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/data.R | 6 ++++-- build/partial.rdb |binary data/Fingers.rda |binary data/FingersMessy.rda |binary man/Fingers.Rd | 3 ++- man/FingersMessy.Rd | 3 ++- 9 files changed, 24 insertions(+), 16 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.2.2 dated 2024-11-28 and 1.2.3 dated 2024-12-12
DESCRIPTION | 6 - MD5 | 16 +- NEWS.md | 4 R/addIntersect.R | 7 - inst/doc/cohort-intersect.html | 68 ++++++------ inst/doc/concept-intersect.html | 92 ++++++++-------- inst/doc/demographics.html | 218 ++++++++++++++++++++-------------------- inst/doc/summarise.html | 192 +++++++++++++++++------------------ inst/doc/table-intersect.html | 86 +++++++-------- 9 files changed, 346 insertions(+), 343 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: PD-Clustering and Related Methods
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution-free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership under the constraint that the product of the probability and the distance of each point to any cluster center is a constant. PD-clustering is a flexible method that can be used with elliptical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different sizes. GPDC and TPDC use a dissimilarity measure based on densities. Factor PD-clustering (FPDC) is a factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high-dimensional data sets.
Author: Cristina Tortora [aut, cre, cph],
Noe Vidales [aut],
Francesco Palumbo [aut],
Tina Kalra [aut],
Paul D. McNicholas [fnd]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between FPDclustering versions 2.3.1 dated 2024-01-29 and 2.3.2 dated 2024-12-12
DESCRIPTION | 36 ++++++++++++++++++++++++++++-------- MD5 | 3 ++- inst |only 3 files changed, 30 insertions(+), 9 deletions(-)
More information about ConjointChecks at CRAN
Permanent link
Title: Correct for Verification Bias in Diagnostic Accuracy & Agreement
Description: A standard test is observed on all specimens. We treat the second test (or sampled test) as being conducted on only a stratified sample of specimens. Verification Bias is this situation when the specimens for doing the second (sampled) test is not under investigator control. We treat the total sample as stratified two-phase sampling and use inverse probability weighting. We estimate diagnostic accuracy (category-specific classification probabilities; for binary tests reduces to specificity and sensitivity, and also predictive values) and agreement statistics (percent agreement, percent agreement by category, Kappa (unweighted), Kappa (quadratic weighted) and symmetry tests (reduces to McNemar's test for binary tests)). See: Katki HA, Li Y, Edelstein DW, Castle PE. Estimating the agreement and diagnostic accuracy of two diagnostic tests when one test is conducted on only a subsample of specimens. Stat Med. 2012 Feb 28; 31(5) <doi:10.1002/sim.4422>.
Author: Hormuzd A. Katki [aut],
David W. Edelstein [aut],
Hormuzd Katki [cre]
Maintainer: Hormuzd Katki <katkih@mail.nih.gov>
Diff between CompareTests versions 1.2 dated 2017-02-06 and 1.3 dated 2024-12-12
DESCRIPTION | 25 ++++++++++++++++++------- MD5 | 6 +++--- man/CompareTests.Rd | 4 ++-- man/fulltable.Rd | 4 ++-- 4 files changed, 25 insertions(+), 14 deletions(-)
Title: Cluster Analysis with Missing Values by Multiple Imputation
Description: Allows clustering of incomplete observations by addressing missing values using multiple imputation. For achieving this goal, the methodology consists in three steps, following Audigier and Niang 2022 <doi:10.1007/s11634-022-00519-1>. I) Missing data imputation using dedicated models. Four multiple imputation methods are proposed, two are based on joint modelling and two are fully sequential methods, as discussed in Audigier et al. (2021) <doi:10.48550/arXiv.2106.04424>. II) cluster analysis of imputed data sets. Six clustering methods are available (distances-based or model-based), but custom methods can also be easily used. III) Partition pooling. The set of partitions is aggregated using Non-negative Matrix Factorization based method. An associated instability measure is computed by bootstrap (see Fang, Y. and Wang, J., 2012 <doi:10.1016/j.csda.2011.09.003>). Among applications, this instability measure can be used to choose a number of clusters with missing value [...truncated...]
Author: Vincent Audigier [aut, cre] ,
Hang Joon Kim [ctb]
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between clusterMI versions 1.2.2 dated 2024-10-23 and 1.3 dated 2024-12-12
DESCRIPTION | 8 - MD5 | 50 +++++------ R/calculintra.intern.R | 7 + R/chooseB.R | 2 R/choosem.R | 2 R/choosemaxit.R | 2 R/choosenbclust.R | 109 ++++++------------------ R/chooser.R | 3 R/clusterMI-package.R | 2 R/clusterMI.R | 43 ++++++--- R/fastnmf.R | 20 +++- R/imputedata.R | 205 +++++++++++++++++++++++------------------------ R/myem.mix.R | 4 R/overimpute.R | 2 R/varselbest.R | 2 man/chooseB.Rd | 2 man/choosem.Rd | 2 man/choosemaxit.Rd | 2 man/choosenbclust.Rd | 2 man/chooser.Rd | 2 man/clusterMI-package.Rd | 2 man/clusterMI.Rd | 4 man/fastnmf.Rd | 4 man/imputedata.Rd | 2 man/overimpute.Rd | 2 man/varselbest.Rd | 2 26 files changed, 234 insertions(+), 253 deletions(-)
Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and
their confidence intervals using methods approved for use in the production
of Public Health England indicators such as those presented via Fingertips
(<https://fingertips.phe.org.uk/>). It provides functions for the generation
of proportions, crude rates, means, directly standardised rates, indirectly
standardised rates, standardised mortality ratios, slope and relative index
of inequality and life expectancy.
Statistical methods are referenced in the following publications.
Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>.
Dobson et al (1991) <doi:10.1002/sim.4780100317>.
Armitage P, Berry G (2002) <doi:10.1002/9780470773666>.
Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>.
Altman DG et al (2000, ISBN: 978-0-727-91375-3).
Chiang CL. (1968, ISBN: 978-0-882-75200-6).
Newell C. (1994, ISBN: 978-0-898-62451-9).
Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>.
S [...truncated...]
Author: Georgina Anderson [aut, cre],
Sebastian Fox [ctb],
Matthew Francis [ctb],
Paul Fryers [ctb],
Emma Clegg [ctb],
Annabel Westermann [ctb],
Joshua Woolner [ctb],
Charlotte Fellows [ctb],
Olivia Box Power [ctb]
Maintainer: Georgina Anderson <georgina.anderson@dhsc.gov.uk>
Diff between PHEindicatormethods versions 2.0.2 dated 2024-01-25 and 2.1.0 dated 2024-12-12
PHEindicatormethods-2.0.2/PHEindicatormethods/R/PHEindicatormethods.R |only PHEindicatormethods-2.0.2/PHEindicatormethods/man/PHEindicatormethods.Rd |only PHEindicatormethods-2.1.0/PHEindicatormethods/DESCRIPTION | 57 PHEindicatormethods-2.1.0/PHEindicatormethods/MD5 | 92 PHEindicatormethods-2.1.0/PHEindicatormethods/NAMESPACE | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/NEWS.md | 8 PHEindicatormethods-2.1.0/PHEindicatormethods/R/DSR.R | 625 +++-- PHEindicatormethods-2.1.0/PHEindicatormethods/R/ISRate.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/ISRatio.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/LifeExpectancy.R | 3 PHEindicatormethods-2.1.0/PHEindicatormethods/R/Means.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/PHEindicatormethods-package.R |only PHEindicatormethods-2.1.0/PHEindicatormethods/R/Proportions.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/Rates.R | 2 PHEindicatormethods-2.1.0/PHEindicatormethods/R/phe_DSR.R |only PHEindicatormethods-2.1.0/PHEindicatormethods/R/sysdata.rda |binary PHEindicatormethods-2.1.0/PHEindicatormethods/R/utils.R | 8 PHEindicatormethods-2.1.0/PHEindicatormethods/build/partial.rdb |only PHEindicatormethods-2.1.0/PHEindicatormethods/build/vignette.rds |binary PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/DSR-vignette.R | 151 + PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/DSR-vignette.Rmd | 345 +-- PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/DSR-vignette.html | 784 ++++--- PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/Introduction_to_PHEindicatormethods.R | 141 + PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/Introduction_to_PHEindicatormethods.Rmd | 102 PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/Introduction_to_PHEindicatormethods.html | 1104 +++++----- PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/WorkedExamples_phe_sii.R | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/WorkedExamples_phe_sii.Rmd | 10 PHEindicatormethods-2.1.0/PHEindicatormethods/inst/doc/WorkedExamples_phe_sii.html | 500 +++- PHEindicatormethods-2.1.0/PHEindicatormethods/man/PHEindicatormethods-package.Rd |only PHEindicatormethods-2.1.0/PHEindicatormethods/man/assign_funnel_significance.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_ISRate.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_ISRatio.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_dsr.Rd |only PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_funnel_limits.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/calculate_funnel_points.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/figures |only PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_dsr.Rd | 41 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_life_expectancy.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_mean.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_proportion.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_quantile.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_rate.Rd | 5 PHEindicatormethods-2.1.0/PHEindicatormethods/man/phe_sii.Rd | 1 PHEindicatormethods-2.1.0/PHEindicatormethods/tests/testthat/testDSRs.R | 478 +++- PHEindicatormethods-2.1.0/PHEindicatormethods/tests/testthat/testLifeExpectancy.R | 9 PHEindicatormethods-2.1.0/PHEindicatormethods/tests/testthat/testdata_DSR_ISR.xlsx |binary PHEindicatormethods-2.1.0/PHEindicatormethods/tests/testthat/testpheDSRs.R |only PHEindicatormethods-2.1.0/PHEindicatormethods/vignettes/DSR-vignette.Rmd | 345 +-- PHEindicatormethods-2.1.0/PHEindicatormethods/vignettes/Introduction_to_PHEindicatormethods.Rmd | 102 PHEindicatormethods-2.1.0/PHEindicatormethods/vignettes/WorkedExamples_phe_sii.Rmd | 10 50 files changed, 3122 insertions(+), 1841 deletions(-)
More information about PHEindicatormethods at CRAN
Permanent link
Title: Statistical Methods for Survival Data with Dependent Censoring
Description: Several statistical methods for analyzing survival data under various forms of dependent
censoring are implemented in the package. In addition to accounting for dependent censoring, it
offers tools to adjust for unmeasured confounding factors. The implemented approaches allow
users to estimate the dependency between survival time and dependent censoring time, based
solely on observed survival data. For more details on the methods, refer to Deresa and Van
Keilegom (2021) <doi:10.1093/biomet/asaa095>, Czado and Van Keilegom (2023)
<doi:10.1093/biomet/asac067>, Crommen et al. (2024) <doi:10.1007/s11749-023-00903-9>,
Deresa and Van Keilegom (2024) <doi:10.1080/01621459.2022.2161387> and Willems et al. (2024+)
<doi:10.48550/arXiv.2403.11860> and Ding and Van Keilegom (2024).
Author: Ilias Willems [aut] ,
Gilles Crommen [aut] ,
Negera Wakgari Deresa [aut, cre]
,
Jie Ding [aut] ,
Claudia Czado [aut] ,
Ingrid Van Keilegom [aut]
Maintainer: Negera Wakgari Deresa <negera.deresa@gmail.com>
Diff between depCensoring versions 0.1.4 dated 2024-12-04 and 0.1.5 dated 2024-12-12
DESCRIPTION | 17 ++++++++------ MD5 | 28 ++++++++++++++++++++--- NAMESPACE | 19 +++++++++++++++ NEWS.md | 36 +++++++++++++++--------------- R/SemiParametricCopulawithoutCovariates.R |only man/Kernel.Rd |only man/Likelihood.Parametric.Rd |only man/Likelihood.Profile.Kernel.Rd |only man/Likelihood.Profile.Solve.Rd |only man/Likelihood.Semiparametric.Rd |only man/Parameters.Constraints.Rd |only man/SurvDC.GoF.Rd |only man/SurvDC.Rd |only man/SurvFunc.CG.Rd |only man/SurvFunc.KM.Rd |only man/SurvMLE.Likelihood.Rd |only man/SurvMLE.Rd |only man/control.arguments.Rd |only man/copdist.Archimedean.Rd |only man/cophfunc.Rd |only man/coppar.to.ktau.Rd |only man/generator.Archimedean.Rd |only man/ktau.to.coppar.Rd |only man/parafam.d.Rd |only man/parafam.p.Rd |only man/parafam.trunc.Rd |only 26 files changed, 73 insertions(+), 27 deletions(-)
Title: Covariate-Based Covariance Functions for Nonstationary Spatial
Modeling
Description: Estimation, prediction, and simulation of nonstationary Gaussian process with modular covariate-based covariance functions.
Sources of nonstationarity, such as spatial mean, variance, geometric anisotropy, smoothness, and nugget, can be considered based on spatial characteristics.
An induced compact-supported nonstationary covariance function is provided, enabling fast and memory-efficient computations when handling densely sampled domains.
Author: Federico Blasi [aut, cre] ,
Reinhard Furrer [ctb]
Maintainer: Federico Blasi <federico.blasi@gmail.com>
Diff between cocons versions 0.1.3 dated 2024-10-15 and 0.1.4 dated 2024-12-12
cocons-0.1.3/cocons/man/getTrend.Rd |only cocons-0.1.3/cocons/man/show-methods.Rd |only cocons-0.1.4/cocons/DESCRIPTION | 12 cocons-0.1.4/cocons/MD5 | 51 +- cocons-0.1.4/cocons/NEWS.md | 30 + cocons-0.1.4/cocons/R/checkFunctions.R | 33 + cocons-0.1.4/cocons/R/cocons.R | 19 cocons-0.1.4/cocons/R/getFunctions.R | 56 +- cocons-0.1.4/cocons/R/methods.R | 85 --- cocons-0.1.4/cocons/R/neg2loglikelihood.R | 106 +++- cocons-0.1.4/cocons/R/optim.R | 63 +- cocons-0.1.4/cocons/R/plot.R | 18 cocons-0.1.4/cocons/R/predict.R | 57 +- cocons-0.1.4/cocons/R/sim.R | 7 cocons-0.1.4/cocons/inst/doc/cocons.pdf |binary cocons-0.1.4/cocons/man/GetNeg2loglikelihoodProfile.Rd | 2 cocons-0.1.4/cocons/man/GetNeg2loglikelihoodREML.Rd |only cocons-0.1.4/cocons/man/coco.Rd | 10 cocons-0.1.4/cocons/man/cocoOptim.Rd | 16 cocons-0.1.4/cocons/man/cocoPredict.Rd | 10 cocons-0.1.4/cocons/man/cocoSim.Rd | 2 cocons-0.1.4/cocons/man/cocons-package.Rd | 4 cocons-0.1.4/cocons/man/getCIs.Rd | 2 cocons-0.1.4/cocons/man/getDensityFromDelta.Rd |only cocons-0.1.4/cocons/man/getHessian.Rd | 2 cocons-0.1.4/cocons/man/getSpatMean.Rd |only cocons-0.1.4/cocons/src/cocons_full.cpp | 410 +++++++++++------ cocons-0.1.4/cocons/src/cocons_taper.cpp | 243 ++++++++-- cocons-0.1.4/cocons/src/cocons_types.h | 16 29 files changed, 842 insertions(+), 412 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut]
Maintainer: Brian Ripley <Brian.Ripley@R-project.org>
Diff between RODBC versions 1.3-25.1 dated 2024-12-11 and 1.3-26 dated 2024-12-12
ChangeLog | 10 +++++++++- DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- inst/doc/RODBC.pdf |binary src/RODBC.c | 24 ++++++++++++++++++++---- 5 files changed, 38 insertions(+), 14 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr [aut, cre]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between rms versions 6.8-2 dated 2024-08-23 and 6.9-0 dated 2024-12-12
rms-6.8-2/rms/R/lrm.fit.bare.r |only rms-6.8-2/rms/R/lrm.fit.s |only rms-6.8-2/rms/R/lrm.fit.strat.s |only rms-6.8-2/rms/man/lrm.fit.bare.Rd |only rms-6.8-2/rms/src/lrmfit.f |only rms-6.8-2/rms/src/ormuv.f |only rms-6.8-2/rms/src/robcovf.f |only rms-6.9-0/rms/DESCRIPTION | 10 - rms-6.9-0/rms/MD5 | 77 ++++---- rms-6.9-0/rms/NAMESPACE | 4 rms-6.9-0/rms/NEWS | 33 ++- rms-6.9-0/rms/R/LRchunktest.r | 6 rms-6.9-0/rms/R/anova.rms.s | 6 rms-6.9-0/rms/R/bootcov.s | 16 - rms-6.9-0/rms/R/lrm.fit.r |only rms-6.9-0/rms/R/lrm.s | 133 ++++---------- rms-6.9-0/rms/R/orm.fit.s | 72 +------ rms-6.9-0/rms/R/orm.s | 2 rms-6.9-0/rms/R/pentrace.s | 132 +++++++------- rms-6.9-0/rms/R/predab.resample.s | 9 rms-6.9-0/rms/R/recode2integer.r |only rms-6.9-0/rms/R/robcov.s | 2 rms-6.9-0/rms/R/val.prob.s | 2 rms-6.9-0/rms/R/validate.lrm.s | 80 ++++---- rms-6.9-0/rms/inst/tests/anova-lr.r | 5 rms-6.9-0/rms/inst/tests/lrm.ols.penalty.r | 4 rms-6.9-0/rms/inst/tests/lrm3.r |only rms-6.9-0/rms/inst/tests/lrmMean.s | 3 rms-6.9-0/rms/inst/tests/orm-bootcov.r | 3 rms-6.9-0/rms/inst/tests/robcov4.r |only rms-6.9-0/rms/inst/tests/robcov_Yuqi.r | 2 rms-6.9-0/rms/inst/tests/scale.r | 6 rms-6.9-0/rms/inst/tests/val.prob.r | 8 rms-6.9-0/rms/man/anova.rms.Rd | 6 rms-6.9-0/rms/man/bootcov.Rd | 3 rms-6.9-0/rms/man/gIndex.Rd | 9 rms-6.9-0/rms/man/lrm.Rd | 98 ++++------ rms-6.9-0/rms/man/lrm.fit.Rd | 273 ++++++++++++++--------------- rms-6.9-0/rms/man/orm.Rd | 2 rms-6.9-0/rms/man/orm.fit.Rd | 11 - rms-6.9-0/rms/man/pentrace.Rd | 8 rms-6.9-0/rms/man/recode2integer.Rd |only rms-6.9-0/rms/man/validate.lrm.Rd | 15 - rms-6.9-0/rms/src/init.c | 8 rms-6.9-0/rms/src/lrmll.f90 |only rms-6.9-0/rms/src/ormuv.f90 |only rms-6.9-0/rms/src/robcovf.f90 |only 47 files changed, 475 insertions(+), 573 deletions(-)
Title: Soil Defense Investments in Italy: Data Retrieval, Analysis,
Visualization
Description: Facilitates the retrieval and analysis of financial data related to public works in Italy,
focusing on soil defense investments. It extracts data from 'OpenCoesione', 'OpenBDAP',
and the 'ReNDiS' database, eliminating the need for direct access to these platforms.
The package boasts a user-friendly design, featuring real time updates and a set of functions
tailored for data retrieval and visualization.
See the webpages for further information
<http://www.rendis.isprambiente.it/rendisweb/>,
<https://opencoesione.gov.it/en/>, and
<https://bdap-opendata.rgs.mef.gov.it/>.
Author: Lorena Ricciotti [aut, cre] ,
Alessio Pollice [ths]
Maintainer: Lorena Ricciotti <lorena.ricciotti@uniba.it>
Diff between PublicWorksFinanceIT versions 0.3.0 dated 2024-10-29 and 0.3.1 dated 2024-12-12
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS.md | 38 ++++++++++++++++++++------------------ 3 files changed, 25 insertions(+), 23 deletions(-)
More information about PublicWorksFinanceIT at CRAN
Permanent link
Title: Generate Generative Data for a Data Source
Description: Generative Adversarial Networks are applied to generate generative data for a data source. A generative model consisting of a generator and a discriminator network is trained. During iterative training the distribution of generated data is converging to that of the data source. Direct applications of generative data are the created functions for data evaluation, missing data completion and data classification. A software service for accelerated training of generative models on graphics processing units is available. Reference: Goodfellow et al. (2014) <doi:10.48550/arXiv.1406.2661>.
Author: Werner Mueller [aut, cre]
Maintainer: Werner Mueller <werner.mueller5@chello.at>
Diff between ganGenerativeData versions 2.1.3 dated 2024-10-07 and 2.1.4 dated 2024-12-12
DESCRIPTION | 10 ++--- MD5 | 34 +++++++++-------- NAMESPACE | 2 + R/RcppExports.R | 29 ++++++++++++-- R/dsInt.R | 37 ++++++++++++++++++ R/gdTrain.R | 5 ++ R/gdTrainGenerate.R | 37 ++++++++++++++---- man/dsCalculateDensityValues.Rd |only man/dsDensityValueInverseQuantile.Rd |only man/figures/dvh.png |only man/figures/dviq.png |only man/ganGenerativeData-package.Rd | 62 ++++++++++++++++++++++++------- man/gdComplete.Rd | 2 - man/gdKNearestNeighbors.Rd | 4 +- man/gdTrainParameters.Rd | 2 - src/RcppExports.cpp | 30 +++++++++++++-- src/density.h | 3 + src/dsInt.cpp | 69 ++++++++++++++++++++++++++++++++--- src/gdInt.cpp | 7 +-- src/vpTree.h | 22 ++++++++++- 20 files changed, 290 insertions(+), 65 deletions(-)
More information about ganGenerativeData at CRAN
Permanent link
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 0.11.1 dated 2024-12-09 and 0.11.2 dated 2024-12-12
glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_bernoulli.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_beta.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_binomial.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_gamma.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_gaussian.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_poisson.stan |only glmmrBase-0.11.1/glmmrBase/inst/cmdstan/mcml_quantile.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_bernoulli.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_beta.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_binomial.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_gamma.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_gaussian.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_poisson.stan |only glmmrBase-0.11.1/glmmrBase/inst/stan/mcml_quantile.stan |only glmmrBase-0.11.1/glmmrBase/src/covariance_module.cpp |only glmmrBase-0.11.1/glmmrBase/src/linpred_module.cpp |only glmmrBase-0.11.1/glmmrBase/src/model_module_2.cpp |only glmmrBase-0.11.1/glmmrBase/src/model_module_extension.cpp |only glmmrBase-0.11.1/glmmrBase/src/openmp_utils.cpp |only glmmrBase-0.11.1/glmmrBase/src/other_functions.cpp |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_bernoulli.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_bernoulli.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_beta.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_beta.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_binomial.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_binomial.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_gamma.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_gamma.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_gaussian.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_gaussian.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_poisson.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_poisson.h |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_quantile.cc |only glmmrBase-0.11.1/glmmrBase/src/stanExports_mcml_quantile.h |only glmmrBase-0.11.2/glmmrBase/DESCRIPTION | 8 glmmrBase-0.11.2/glmmrBase/MD5 | 135 glmmrBase-0.11.2/glmmrBase/R/R6Model.R | 113 glmmrBase-0.11.2/glmmrBase/R/RcppExports.R | 88 glmmrBase-0.11.2/glmmrBase/R/extrafunctions.R | 68 glmmrBase-0.11.2/glmmrBase/R/stanmodels.R | 10 glmmrBase-0.11.2/glmmrBase/build/partial.rdb |binary glmmrBase-0.11.2/glmmrBase/inst/cmdstan/mcml.stan |only glmmrBase-0.11.2/glmmrBase/inst/include/glmmr.h | 1 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/calculator.hpp | 9 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/covariance.hpp | 23 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/family.hpp | 39 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/formulaparse.h | 16 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/general.h | 331 - glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/griddata.hpp | 1 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/interpreter.h | 99 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/maths.h | 32 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/model.hpp | 6 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/modelbits.hpp | 1 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 71 glmmrBase-0.11.2/glmmrBase/inst/include/glmmr/modeloptim.hpp | 10 glmmrBase-0.11.2/glmmrBase/inst/stan/mcml.stan |only glmmrBase-0.11.2/glmmrBase/man/Beta.Rd | 34 glmmrBase-0.11.2/glmmrBase/man/Salamanders.Rd | 28 glmmrBase-0.11.2/glmmrBase/man/SimGeospat.Rd | 48 glmmrBase-0.11.2/glmmrBase/man/SimTrial.Rd | 50 glmmrBase-0.11.2/glmmrBase/man/coef.Model.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/coef.mcml.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/confint.mcml.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/family.Model.Rd | 40 glmmrBase-0.11.2/glmmrBase/man/family.mcml.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/fitted.Model.Rd | 44 glmmrBase-0.11.2/glmmrBase/man/fitted.mcml.Rd | 40 glmmrBase-0.11.2/glmmrBase/man/fixed.effects.Rd | 34 glmmrBase-0.11.2/glmmrBase/man/formula.Model.Rd | 40 glmmrBase-0.11.2/glmmrBase/man/formula.mcml.Rd | 44 glmmrBase-0.11.2/glmmrBase/man/lme4_to_glmmr.Rd | 60 glmmrBase-0.11.2/glmmrBase/man/logLik.Model.Rd | 38 glmmrBase-0.11.2/glmmrBase/man/logLik.mcml.Rd | 50 glmmrBase-0.11.2/glmmrBase/man/mcml_lmer.Rd | 132 glmmrBase-0.11.2/glmmrBase/man/predict.Model.Rd | 62 glmmrBase-0.11.2/glmmrBase/man/predict.mcml.Rd | 40 glmmrBase-0.11.2/glmmrBase/man/random.effects.Rd | 34 glmmrBase-0.11.2/glmmrBase/man/residuals.Model.Rd | 56 glmmrBase-0.11.2/glmmrBase/man/residuals.mcml.Rd | 50 glmmrBase-0.11.2/glmmrBase/man/setParallel.Rd | 42 glmmrBase-0.11.2/glmmrBase/man/summary.Model.Rd | 42 glmmrBase-0.11.2/glmmrBase/man/vcov.Model.Rd | 44 glmmrBase-0.11.2/glmmrBase/man/vcov.mcml.Rd | 46 glmmrBase-0.11.2/glmmrBase/src/RcppExports.cpp | 164 glmmrBase-0.11.2/glmmrBase/src/heckman.cpp |only glmmrBase-0.11.2/glmmrBase/src/model_module.cpp | 2025 ++++++++++ glmmrBase-0.11.2/glmmrBase/src/stanExports_mcml.cc |only glmmrBase-0.11.2/glmmrBase/src/stanExports_mcml.h |only 88 files changed, 3239 insertions(+), 1261 deletions(-)
Title: Interface to 'JDemetra+' Seasonal Adjustment Software
Description: Interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially
recommended to the members of the European Statistical System (ESS) and the European System of Central Banks.
It offers full access to all options and outputs of 'JDemetra+', including the two leading seasonal adjustment methods
TRAMO/SEATS+ and X-12ARIMA/X-13ARIMA-SEATS.
Author: Alain Quartier-la-Tente [aut, cre]
,
Anna Michalek [aut],
Jean Palate [aut],
Raf Baeyens [aut]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between RJDemetra versions 0.2.7 dated 2024-10-01 and 0.2.8 dated 2024-12-12
DESCRIPTION | 6 - MD5 | 26 ++--- NEWS.md | 13 ++ R/export_workspace.R | 163 ++++++++++++++++++++----------- R/get_jmodel.R | 42 +++++--- R/get_jspec.R | 4 R/import_workspace.R | 73 ++++++++------ R/jsa2r.R | 2 R/regarima_rslts.R | 28 +++-- R/spec_rjd.R | 262 +++++++++++++++++++++++++++++++++------------------ R/tramoseats.R | 29 +++-- R/x13.R | 28 +++-- man/add_sa_item.Rd | 2 man/get_model.Rd | 18 +++ 14 files changed, 446 insertions(+), 250 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 2.0.4 dated 2024-10-28 and 2.0.5 dated 2024-12-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/dns.c | 25 +++++++++++++++++++++++++ tests/testthat/test-tcp.R | 4 ++-- 5 files changed, 38 insertions(+), 9 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>, is used to estimate the generalized, variable, and complete persistence models, Mariano et al. (2010) <doi:10.3102/1076998609346967>. These are multiple-membership linear mixed models with teachers modeled as "G-side" effects and students modeled with either "G-side" or "R-side" effects.
Author: Andrew Karl [cre, aut] ,
Yan Yang [aut],
Sharon Lohr [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.1-2 dated 2024-11-17 and 3.2-0 dated 2024-12-12
DESCRIPTION | 8 +++--- MD5 | 8 +++--- NEWS | 4 +++ R/bias.test.custom.R | 58 ++++++++++++------------------------------------ man/bias.test.custom.Rd | 12 +-------- 5 files changed, 29 insertions(+), 61 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.7-83 dated 2024-10-14 and 1.8-5 dated 2024-12-12
DESCRIPTION | 8 MD5 | 219 +++---- NAMESPACE | 62 - NEWS.md | 58 + R/Agenerics.R | 787 ++++++++++++------------- R/RGB.R | 31 R/Zdeprecated.R | 42 - R/aggregate.R | 2 R/app.R | 5 R/generics.R | 18 R/geom.R | 15 R/graticule.R | 26 R/lapp.R | 12 R/levels.R | 34 - R/plot.R | 11 R/plot_legend.R | 16 R/plot_let.R | 40 + R/plot_raster.R | 63 +- R/predict.R | 11 R/rast.R | 5 R/read.R | 128 ++-- R/replace_values.R | 18 R/rowSums.R | 168 ++--- R/sample.R | 18 R/show.R | 1280 ++++++++++++++++++++--------------------- R/tags.R | 62 + R/tapp.R | 18 R/tempfiles.R | 4 R/values.R | 5 R/vect.R | 9 R/wrap.R | 99 ++- R/zonal.R | 10 configure | 644 +++++++++++--------- configure.ac | 46 - inst/tinytest/test_rasterize.R | 2 man/RGB.Rd | 10 man/clamp.Rd | 2 man/classify.Rd | 2 man/compareGeom.Rd | 2 man/contour.Rd | 10 man/deprecated.Rd | 11 man/expanse.Rd | 4 man/global.Rd | 2 man/gridDist.Rd | 4 man/inplace.Rd | 2 man/lapp.Rd | 7 man/mappal.Rd | 14 man/metags.Rd | 4 man/patches.Rd | 13 man/plet.Rd | 10 man/plot.Rd | 6 man/rast.Rd | 12 man/rowSums.Rd |only man/selectHigh.Rd | 80 +- man/serialize.Rd | 2 man/sieve.Rd | 90 +- man/split.Rd | 2 man/subst.Rd | 2 man/surfArea.Rd |only man/tapp.Rd | 2 man/terra-package.Rd | 7 man/toMemory.Rd |only man/vect.Rd | 1 man/wrap.Rd | 2 man/writeVector.Rd | 5 src/RcppFunctions.cpp | 2 src/RcppModule.cpp | 14 src/arith.cpp | 38 - src/crs.cpp | 2 src/distRaster.cpp | 16 src/distance.cpp | 31 src/distance.h | 2 src/extract.cpp | 2 src/file_utils.cpp | 6 src/focal.cpp | 2 src/gdal_algs.cpp | 298 ++++++++- src/gdalio.cpp | 43 + src/geos_methods.cpp | 84 +- src/geos_spat.h | 2 src/geosphere.cpp | 2 src/math_utils.cpp | 2 src/mediancut.cpp | 2 src/memory.cpp | 2 src/movingWindow.cpp | 2 src/patches.cpp |only src/ram.cpp | 2 src/raster_methods.cpp | 216 +++++- src/raster_stats.cpp | 2 src/rasterize.cpp | 200 +++--- src/read.cpp | 2 src/read_gdal.cpp | 115 ++- src/read_ogr.cpp | 22 src/sample.cpp | 2 src/spatBase.cpp | 2 src/spatDataframe.cpp | 45 - src/spatDataframe.h | 1 src/spatRaster.cpp | 156 +++- src/spatRaster.h | 26 src/spatRasterMultiple.cpp | 46 + src/spatRasterMultiple.h | 9 src/spatSources.cpp | 2 src/spatTime.cpp | 22 src/spatVector.cpp | 4 src/spatVector2.cpp | 2 src/string_utils.cpp | 2 src/surfArea.cpp |only src/vecmath.cpp | 2 src/vecmath.h | 1 src/vecmathse.cpp | 2 src/vector_methods.cpp | 2 src/write.cpp | 2 src/write_gdal.cpp | 47 + src/write_ogr.cpp | 2 113 files changed, 3479 insertions(+), 2293 deletions(-)
Title: Pathways Longitudinal and Differential Analysis in Metabolomics
Description: Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition.
The method is based on a Principal Component Analysis step and on a linear mixed model.
Automatic query of metabolic pathways is also implemented.
Author: Camille Guilmineau [aut, cre],
Remi Servien [aut] ,
Nathalie Vialaneix [aut]
Maintainer: Camille Guilmineau <camille.guilmineau@inrae.fr>
Diff between phoenics versions 0.3 dated 2024-07-22 and 0.4 dated 2024-12-12
DESCRIPTION | 10 MD5 | 16 - NAMESPACE | 10 NEWS.md | 16 + R/pathwayRes-class.R | 139 +++++++++-- R/test_pathway.R | 95 +++++-- inst/adddata/ASICS_library_codes.txt | 434 +++++++++++++++++------------------ man/pathwayRes.Rd | 17 + man/test_pathway.Rd | 35 +- 9 files changed, 477 insertions(+), 295 deletions(-)
Title: Generate and Plot Voronoi or Sunburst Treemaps from Hierarchical
Data
Description: Treemaps are a visually appealing graphical representation of
numerical data using a space-filling approach. A plane or 'map' is
subdivided into smaller areas called cells. The cells in the map are
scaled according to an underlying metric which allows to grasp the
hierarchical organization and relative importance of many objects at
once. This package contains two different implementations of treemaps,
Voronoi treemaps and Sunburst treemaps. The Voronoi treemap function
subdivides the plot area in polygonal cells according to the highest
hierarchical level, then continues to subdivide those parental cells
on the next lower hierarchical level, and so on. The Sunburst treemap
is a computationally less demanding treemap that does not require
iterative refinement, but simply generates circle sectors that are
sized according to predefined weights. The Voronoi tesselation is
based on functions from Paul Murrell (2012)
<https://www.stat.auckland.ac.nz/~paul/Reports/VoronoiTreemap/voronoi [...truncated...]
Author: Michael Jahn [aut, cre] ,
David Leslie [aut],
Ahmadou Dicko [aut] ,
Dunipace Eric [aut] ,
Paul Murrell [aut, cph]
Maintainer: Michael Jahn <jahn@mpusp.mpg.de>
Diff between WeightedTreemaps versions 0.1.3 dated 2024-11-04 and 0.1.4 dated 2024-12-12
DESCRIPTION | 9 + MD5 | 18 +-- NEWS.md | 6 + R/drawTreemap.R | 14 ++- R/drawUtils.R | 98 +++++++++++---------- README.md | 5 - inst/doc/WeightedTreemaps.R | 186 ++++++++++++++++++++--------------------- inst/doc/WeightedTreemaps.html | 4 man/drawTreemap.Rd | 12 ++ src/Makevars | 2 10 files changed, 194 insertions(+), 160 deletions(-)
More information about WeightedTreemaps at CRAN
Permanent link
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic models
(assuming either presence or absence of the effect, heterogeneity, and
publication bias). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2022,
<doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022,
<doi:10.1037/met0000405>). Users can define a wide range of non-informative
or informative prior distributions for the effect size, heterogeneity,
and publication bias components (including selection models and PET-PEESE).
The package provides convenient functions for summary, visualizations, and
fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBMA versions 3.1.0 dated 2023-07-18 and 3.2.0 dated 2024-12-12
DESCRIPTION | 16 +- MD5 | 117 ++++++++++--------- NAMESPACE | 2 NEWS.md | 18 ++- R/BiBMA.R | 59 +++++++++ R/NoBMA.R | 14 +- R/RoBMA-reg.R | 55 +++++++-- R/RoBMA.R | 36 ++++-- R/datasets.R | 19 +++ R/fit-and-marglik.R | 4 R/summary-heterogeneity.R |only R/summary.R | 33 +---- R/tools.R | 73 +++++++++++- R/utilities.R | 8 + R/zzz.R | 4 README.md | 137 +++++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary data/Andrews2021.RData |only inst/REFERENCES.bib | 79 +++++++++++-- inst/doc/CustomEnsembles.R | 76 ++++++------ inst/doc/CustomEnsembles.Rmd | 29 ++-- inst/doc/CustomEnsembles.html | 141 ++++++++++++----------- inst/doc/HierarchicalBMA.R | 64 +++++----- inst/doc/HierarchicalBMA.Rmd | 24 ++-- inst/doc/HierarchicalBMA.html | 128 ++++++++++----------- inst/doc/MedicineBMA.R | 38 +++--- inst/doc/MedicineBMA.Rmd | 26 ++-- inst/doc/MedicineBMA.html | 158 +++++++++++++------------- inst/doc/MedicineBiBMA.R |only inst/doc/MedicineBiBMA.Rmd |only inst/doc/MedicineBiBMA.html |only inst/doc/MetaRegression.R |only inst/doc/MetaRegression.Rmd |only inst/doc/MetaRegression.html |only inst/doc/ReproducingBMA.R | 58 ++++----- inst/doc/ReproducingBMA.Rmd | 20 +-- inst/doc/ReproducingBMA.html | 166 ++++++++++++++-------------- inst/doc/Tutorial.R | 28 ++-- inst/doc/Tutorial.Rmd | 42 +++---- inst/doc/Tutorial.html | 143 ++++++++++++------------ man/Andrews2021.Rd |only man/BiBMA.Rd | 42 ++++++- man/NoBMA.Rd | 12 +- man/NoBMA.reg.Rd | 23 ++- man/RoBMA-package.Rd | 1 man/RoBMA.Rd | 18 +-- man/RoBMA.reg.Rd | 68 ++++++++--- man/check_RoBMA.Rd | 7 + man/check_setup.reg.Rd | 24 ++-- man/figures/README-fig_PETPEESE-1.png |binary man/figures/README-fig_forest-1.png |binary man/figures/README-fig_mu-1.png |binary man/figures/README-fig_mu_chain-1.png |binary man/figures/README-fig_mu_ind-1.png |binary man/figures/README-fig_tau-1.png |binary man/figures/README-fig_weightfunction-1.png |binary man/summary_heterogeneity.Rd |only tests/testthat/Rplots.pdf |only vignettes/CustomEnsembles.Rmd | 29 ++-- vignettes/HierarchicalBMA.Rmd | 24 ++-- vignettes/MedicineBMA.Rmd | 26 ++-- vignettes/MedicineBiBMA.Rmd |only vignettes/MetaRegression.Rmd |only vignettes/ReproducingBMA.Rmd | 20 +-- vignettes/Tutorial.Rmd | 42 +++---- 66 files changed, 1296 insertions(+), 855 deletions(-)
Title: 'GNU Unifont' Hex Fonts
Description: Contains most of the hex font files from the 'GNU Unifont Project' <https://unifoundry.com/unifont/> compressed by 'xz'. 'GNU Unifont' is a duospaced bitmap font that attempts to cover all the official Unicode glyphs plus several of the artificial scripts in the '(Under-)ConScript Unicode Registry' <https://www.kreativekorp.com/ucsur/>. Provides a convenience function for loading in several of them at the same time as a 'bittermelon' bitmap font object for easy rendering of the glyphs in an 'R' terminal or graphics device.
Author: Trevor L. Davis [aut, cre] ,
GNU Unifont authors [cph]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between hexfont versions 0.4.0 dated 2023-12-18 and 0.5.1 dated 2024-12-12
DESCRIPTION | 22 - MD5 | 66 ++--- NEWS.md | 17 + R/unifont.R | 45 +++ README.md | 83 ++---- build/vignette.rds |binary inst/doc/hexfont.R |only inst/doc/hexfont.Rmd | 34 +- inst/doc/hexfont.html | 85 +++--- inst/font/ChangeLog | 243 ++++++++++++++++++- inst/font/plane00/plane00-combining.txt | 1 inst/font/plane00/plane00-unassigned.hex.xz |binary inst/font/plane00csur/plane00csur-combining.txt | 32 ++ inst/font/plane00csur/plane00csur-unassigned.hex.xz |binary inst/font/plane00csur/plane00csur.hex.xz |binary inst/font/plane01/plane01-combining.txt | 60 ++++ inst/font/plane01/plane01-noscript.hex.xz |binary inst/font/plane01/plane01-unassigned.hex.xz |binary inst/font/plane01/plane01.hex.xz |binary inst/font/plane02/zh-plane02.hex.xz |binary inst/font/plane03/jp-plane03.hex.xz |only inst/font/plane03/zh-plane03.hex.xz |binary inst/font/plane0Fcsur/plane0Fcsur-combining.txt | 15 + inst/font/plane0Fcsur/plane0Fcsur-nonprinting.hex.xz |binary inst/font/plane0Fcsur/plane0Fcsur.hex.xz |binary inst/font/precompiled/unifont.hex.xz |binary inst/font/precompiled/unifont_jp.hex.xz |binary inst/font/precompiled/unifont_jp_sample.hex.xz |binary inst/font/precompiled/unifont_sample.hex.xz |binary inst/font/precompiled/unifont_upper.hex.xz |binary inst/font/precompiled/unifont_upper_sample.hex.xz |binary man/unifont.Rd | 24 + tests/testthat/test-combining.R | 8 tests/testthat/test-unifont.R | 4 vignettes/hexfont.Rmd | 34 +- 35 files changed, 581 insertions(+), 192 deletions(-)
Title: Extremal Dependence Models
Description: A set of procedures for parametric and non-parametric modelling of the dependence structure of multivariate extreme-values is provided. The statistical inference is performed with non-parametric estimators, likelihood-based estimators and Bayesian techniques. It adapts the methodologies of Beranger and Padoan (2015) <doi:10.48550/arXiv.1508.05561>, Marcon et al. (2016) <doi:10.1214/16-EJS1162>, Marcon et al. (2017) <doi:10.1002/sta4.145>, Marcon et al. (2017) <doi:10.1016/j.jspi.2016.10.004> and Beranger et al. (2021) <doi:10.1007/s10687-019-00364-0>. This package also allows for the modelling of spatial extremes using flexible max-stable processes. It provides simulation algorithms and fitting procedures relying on the Stephenson-Tawn likelihood as per Beranger at al. (2021) <doi:10.1007/s10687-020-00376-1>.
Author: Boris Beranger [aut],
Simone Padoan [cre, aut],
Giulia Marcon [aut],
Steven G. Johnson [ctb] ,
Rudolf Schuerer [ctb] ,
Brian Gough [ctb] ,
Alec G. Stephenson [ctb],
Anne Sabourin [ctb] ,
Philippe Naveau [ctb]
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between ExtremalDep versions 0.0.4-2 dated 2024-10-06 and 0.0.4-3 dated 2024-12-12
DESCRIPTION | 16 +++++++++------- MD5 | 6 ++++-- NAMESPACE | 11 ++++++----- R/PAMfmado.R |only man/PAMfmado.Rd |only 5 files changed, 19 insertions(+), 14 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep' and 'HCP' preprocessed
datasets and 'HippUnfold' hippocampal segmentation outputs for a given
sample by restructuring the data values into a single file. The single
file can then be used by the package for analyses independently from
its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.1.0 dated 2024-10-09 and 1.2.0 dated 2024-12-12
DESCRIPTION | 12 - MD5 | 65 +++++----- NAMESPACE | 3 NEWS.md |only R/CAT12vextract.R |only R/FSLRvextract.R | 12 + R/HIPvextract.R | 6 R/SURFvextract.R | 30 +++- R/VWRfirstrun.R | 169 ++++++++++++++++----------- R/miniconda_installer_url_py39.r |only R/otherfunc.R | 51 +++++--- R/plot_surf.R | 4 R/plot_surf3d.R | 4 R/python_custominstall.r | 4 R/vertTFCE.R | 8 - R/vertmixedTFCE.R | 5 R/vertwise.R | 15 +- README.md | 10 + inst/CITATION |only inst/doc/VertexWiseR_Example_1.html | 9 - inst/doc/VertexWiseR_Example_2.html | 100 +++++++++------ inst/doc/VertexWiseR_surface_extraction.html | 119 +++++++++++++++---- inst/python/brainstat.stats.SLM_VWR.py | 7 - man/CAT12vextract.Rd |only man/FSLRvextract.Rd | 2 man/RFT_vertex_analysis.Rd | 6 man/SURFvextract.Rd | 10 + man/TFCE_vertex_analysis.Rd | 2 man/TFCE_vertex_analysis_mixed.Rd | 2 man/plot_surf3d.Rd | 2 vignettes/FINK_tstatmaps.png |only vignettes/Python_troubleshooting.Rmd |only vignettes/SPRENG_tstatmaps.png |only vignettes/VertexWiseR_Example_1.Rmd | 2 vignettes/VertexWiseR_surface_extraction.Rmd | 62 ++++++++- vignettes/references.bib | 25 +++ vignettes/surfextract.jpg |binary vignettes/traj.png |only 38 files changed, 510 insertions(+), 236 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-16 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-24 1.0.3
2022-11-22 1.0.2
2022-07-01 1.0.1
2022-03-09 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-22 1.0.3
2022-06-26 1.0.2
2022-03-16 1.0.1
2022-03-07 1.0.0
Title: Enhance Reproducibility of R Code
Description: A collection of high-level, machine- and OS-independent tools
for making reproducible and reusable content in R.
The two workhorse functions are Cache() and prepInputs(). Cache()
allows for nested caching, is robust to environments and objects with
environments (like functions), and deals with some classes of
file-backed R objects e.g., from terra and raster packages.
Both functions have been developed to
be foundational components of data retrieval
and processing in continuous workflow situations. In both functions,
efforts are made to make the first and subsequent calls of functions have
the same result, but faster at subsequent times by way of checksums
and digesting. Several features are still under development, including
cloud storage of cached objects allowing for sharing between users. Several
advanced options are available, see ?reproducibleOptions().
Author: Eliot J B McIntire [aut, cre] ,
Alex M Chubaty [aut] ,
Tati Micheletti [ctb] ,
Ceres Barros [ctb] ,
Ian Eddy [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 2.1.0 dated 2024-05-29 and 2.1.2 dated 2024-12-12
DESCRIPTION | 25 MD5 | 92 - NEWS.md | 27 R/DBI.R | 7 R/cache-helpers.R | 4 R/cache.R | 35 R/download.R | 618 ++++++-- R/exportedMethods.R | 34 R/helpers.R | 46 R/messages.R | 177 +- R/options.R | 23 R/paths.R | 19 R/postProcessTo.R | 53 R/preProcess.R | 309 ++-- R/prepInputs.R | 386 ++--- R/robustDigest.R | 66 R/showCacheEtc.R | 12 R/zzz.R | 8 build/vignette.rds |binary inst/WORDLIST | 11 inst/doc/Intro-to-Cache.html | 2169 ++++++++++++++--------------- inst/examples/example_postProcess.R | 13 inst/examples/example_postProcessTo.R | 2 man/Cache.Rd | 21 man/downloadFile.Rd | 9 man/downloadRemote.Rd | 9 man/gdalwarpFns.Rd | 2 man/messageColoured.Rd | 2 man/postProcess.Rd | 13 man/postProcessTo.Rd | 5 man/preProcess.Rd | 2 man/prepInputs.Rd | 5 man/purge.Rd | 8 man/reproducibleOptions.Rd | 13 man/viewCache.Rd | 3 tests/testthat/helper-allEqual.R | 43 tests/testthat/test-cache.R | 345 ---- tests/testthat/test-cacheGeo.R | 4 tests/testthat/test-cloud.R | 6 tests/testthat/test-cluster.R | 12 tests/testthat/test-examples.R | 7 tests/testthat/test-gis.R | 4 tests/testthat/test-misc.R | 26 tests/testthat/test-postProcess.R | 22 tests/testthat/test-postProcessTerra.R | 18 tests/testthat/test-preProcessDoesntWork.R | 65 tests/testthat/test-prepInputs.R | 142 + 47 files changed, 2706 insertions(+), 2216 deletions(-)
Title: Gaussian Processes on Graphs and Lattices in 'Stan'
Description: Gaussian processes are flexible distributions to model functional data. Whilst
theoretically appealing, they are computationally cumbersome except for small datasets.
This package implements two methods for scaling Gaussian process inference in 'Stan'. First, a
sparse approximation of the likelihood that is generally applicable and, second, an exact method
for regularly spaced data modeled by stationary kernels using fast Fourier methods. Utility
functions are provided to compile and fit 'Stan' models using the 'cmdstanr' interface.
References: Hoffmann and Onnela (2022) <doi:10.48550/arXiv.2301.08836>.
Author: Till Hoffmann [aut, cre] ,
Jukka-Pekka Onnela [ctb]
Maintainer: Till Hoffmann <thoffmann@hsph.harvard.edu>
Diff between gptoolsStan versions 0.1.0 dated 2023-12-19 and 0.2.0 dated 2024-12-12
DESCRIPTION | 12 - MD5 | 24 +- NEWS.md | 5 R/model.R | 22 ++ README.md | 2 inst/doc/getting_started.R | 2 inst/doc/getting_started.Rmd | 2 inst/doc/getting_started.html | 28 +-- inst/extdata/gptools/fft1.stan | 7 inst/extdata/gptools/fft2.stan | 7 inst/extdata/gptools/graph.stan | 367 +++++++++++++++++++++++++++++++++++++++- man/gptools_include_path.Rd | 4 vignettes/getting_started.Rmd | 2 13 files changed, 433 insertions(+), 51 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-14 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-21 0.0.1.0
Title: Efficient Serialization of R Objects
Description: Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Francesc Alted [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs2 versions 0.1.3 dated 2024-12-02 and 0.1.4 dated 2024-12-12
ChangeLog | 7 +++++-- DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/qx_functions.R | 2 +- man/qx_dump.Rd | 2 +- src/io/zstd_module.h | 3 ++- src/qx_dump.h | 9 ++++++--- src/qx_functions.cpp | 8 +++++--- 8 files changed, 31 insertions(+), 22 deletions(-)