Title: Rule- And Instance-Based Regression Modeling
Description: Regression modeling using rules with added instance-based
corrections.
Author: Max Kuhn [aut, cre],
Steve Weston [ctb],
Chris Keefer [ctb],
Nathan Coulter [ctb],
Ross Quinlan [aut] ,
Rulequest Research Pty Ltd. [cph]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between Cubist versions 0.4.2.1 dated 2023-03-09 and 0.4.4 dated 2024-07-01
DESCRIPTION | 13 MD5 | 18 NEWS.md | 10 build/vignette.rds |binary inst/doc/cubist.R | 54 +- inst/doc/cubist.Rmd | 67 +-- inst/doc/cubist.html | 1120 ++++++++++++++++++++++++++++----------------------- src/rules.c | 2 src/utility.c | 2 vignettes/cubist.Rmd | 67 +-- 10 files changed, 728 insertions(+), 625 deletions(-)
Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
Description: Facilitates spatial and general latent Gaussian modeling using
integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
Additionally, extends the GAM-like model class to more general nonlinear predictor
expressions, and implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data.
Model components are specified with general inputs and mapping methods to the
latent variables, and the predictors are specified via general R expressions,
with separate expressions for each observation likelihood model in
multi-likelihood models. A prediction method based on fast Monte Carlo sampling
allows posterior prediction of general expressions of the latent variables.
Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
<doi:10.1111/2041-210X.13168>.
Author: Finn Lindgren [aut, cre, cph] ,
Fabian E. Bachl [aut, cph] ,
David L. Borchers [ctb, dtc, cph] ,
Daniel Simpson [ctb, cph] ,
Lindesay Scott-Howard [ctb, dtc, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb, cph] ,
Roudier Pierre [ctb, cph] ,
Meehan Tim [ [...truncated...]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between inlabru versions 2.10.1 dated 2023-12-20 and 2.11.1 dated 2024-07-01
inlabru-2.10.1/inlabru/man/cprod.Rd |only inlabru-2.10.1/inlabru/man/gg.inla.mesh.1d.Rd |only inlabru-2.10.1/inlabru/man/gg.inla.mesh.Rd |only inlabru-2.10.1/inlabru/man/inla.stack.mjoin.Rd |only inlabru-2.10.1/inlabru/man/integration_weight_aggregation.Rd |only inlabru-2.10.1/inlabru/man/ipoints.Rd |only inlabru-2.10.1/inlabru/man/pixels.Rd |only inlabru-2.10.1/inlabru/tests/testthat/_snaps/latent_spde_2d.md |only inlabru-2.10.1/inlabru/tests/testthat/_snaps/lgcp_2d.md |only inlabru-2.10.1/inlabru/tests/testthat/test-lgcp_2d.R |only inlabru-2.10.1/inlabru/tests/testthat/test-old_integration.R |only inlabru-2.10.1/inlabru/tests/testthat/test-predict.R |only inlabru-2.11.1/inlabru/DESCRIPTION | 21 inlabru-2.11.1/inlabru/MD5 | 211 +- inlabru-2.11.1/inlabru/NAMESPACE | 75 - inlabru-2.11.1/inlabru/NEWS.md | 62 inlabru-2.11.1/inlabru/R/bru.inference.R | 208 ++ inlabru-2.11.1/inlabru/R/bru.integration.R | 495 ------ inlabru-2.11.1/inlabru/R/data.mrsea.R | 2 inlabru-2.11.1/inlabru/R/data.toypoints.R |only inlabru-2.11.1/inlabru/R/environment.R | 158 +- inlabru-2.11.1/inlabru/R/ggplot.R | 99 - inlabru-2.11.1/inlabru/R/inla.R | 151 +- inlabru-2.11.1/inlabru/R/integration.R | 10 inlabru-2.11.1/inlabru/R/mappers.R | 35 inlabru-2.11.1/inlabru/R/mesh.R | 47 inlabru-2.11.1/inlabru/R/model.R | 20 inlabru-2.11.1/inlabru/R/sampling.R | 2 inlabru-2.11.1/inlabru/R/stack.R | 58 inlabru-2.11.1/inlabru/R/track_plotting.R | 722 +++++++--- inlabru-2.11.1/inlabru/R/transformation.R | 30 inlabru-2.11.1/inlabru/R/utils.R | 9 inlabru-2.11.1/inlabru/README.md | 19 inlabru-2.11.1/inlabru/build/vignette.rds |binary inlabru-2.11.1/inlabru/data/toypoints.rda |only inlabru-2.11.1/inlabru/inst/doc/articles.html | 2 inlabru-2.11.1/inlabru/inst/doc/bru_mapper.html | 294 ++-- inlabru-2.11.1/inlabru/inst/doc/component.Rmd | 6 inlabru-2.11.1/inlabru/inst/doc/component.html | 10 inlabru-2.11.1/inlabru/inst/doc/linearapprox.html | 10 inlabru-2.11.1/inlabru/inst/doc/prediction_scores.html | 2 inlabru-2.11.1/inlabru/inst/examples/gg.inla.mesh.R | 2 inlabru-2.11.1/inlabru/man/bru_compute_linearisation.Rd | 2 inlabru-2.11.1/inlabru/man/bru_convergence_plot.Rd | 23 inlabru-2.11.1/inlabru/man/bru_get_mapper.Rd | 4 inlabru-2.11.1/inlabru/man/bru_inla.stack.mexpand.Rd |only inlabru-2.11.1/inlabru/man/bru_inla.stack.mjoin.Rd |only inlabru-2.11.1/inlabru/man/bru_log.Rd | 29 inlabru-2.11.1/inlabru/man/bru_log_bookmark.Rd | 4 inlabru-2.11.1/inlabru/man/bru_log_message.Rd | 6 inlabru-2.11.1/inlabru/man/bru_log_new.Rd | 10 inlabru-2.11.1/inlabru/man/bru_log_offset.Rd | 8 inlabru-2.11.1/inlabru/man/bru_log_reset.Rd | 4 inlabru-2.11.1/inlabru/man/bru_make_stack.Rd | 5 inlabru-2.11.1/inlabru/man/bru_mapper.Rd | 11 inlabru-2.11.1/inlabru/man/bru_mapper_aggregate.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_collect.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_const.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_factor.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_fm_mesh_1d.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_fm_mesh_2d.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_generics.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_harmonics.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_index.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_linear.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_logsumexp.Rd | 10 inlabru-2.11.1/inlabru/man/bru_mapper_marginal.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_matrix.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_mesh_B.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_multi.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_pipe.Rd | 21 inlabru-2.11.1/inlabru/man/bru_mapper_scale.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_shift.Rd | 4 inlabru-2.11.1/inlabru/man/bru_mapper_taylor.Rd | 4 inlabru-2.11.1/inlabru/man/bru_model.Rd | 10 inlabru-2.11.1/inlabru/man/bru_timings.Rd |only inlabru-2.11.1/inlabru/man/bru_used_update.Rd | 4 inlabru-2.11.1/inlabru/man/bru_used_vars.Rd | 4 inlabru-2.11.1/inlabru/man/figures/README-example-1.png |binary inlabru-2.11.1/inlabru/man/generate.Rd | 38 inlabru-2.11.1/inlabru/man/gg.Rd | 6 inlabru-2.11.1/inlabru/man/gg.SpatRaster.Rd | 4 inlabru-2.11.1/inlabru/man/gg.SpatialGridDataFrame.Rd | 4 inlabru-2.11.1/inlabru/man/gg.SpatialLines.Rd | 4 inlabru-2.11.1/inlabru/man/gg.SpatialPixels.Rd | 4 inlabru-2.11.1/inlabru/man/gg.SpatialPixelsDataFrame.Rd | 4 inlabru-2.11.1/inlabru/man/gg.SpatialPoints.Rd | 6 inlabru-2.11.1/inlabru/man/gg.SpatialPolygons.Rd | 4 inlabru-2.11.1/inlabru/man/gg.bru_prediction.Rd | 2 inlabru-2.11.1/inlabru/man/gg.data.frame.Rd | 2 inlabru-2.11.1/inlabru/man/gg.fm_mesh_1d.Rd |only inlabru-2.11.1/inlabru/man/gg.fm_mesh_2d.Rd |only inlabru-2.11.1/inlabru/man/gg.matrix.Rd | 2 inlabru-2.11.1/inlabru/man/gg.sf.Rd | 4 inlabru-2.11.1/inlabru/man/gm.Rd | 20 inlabru-2.11.1/inlabru/man/inlabru-deprecated.Rd | 137 + inlabru-2.11.1/inlabru/man/inlabru-package.Rd | 1 inlabru-2.11.1/inlabru/man/lgcp.Rd | 2 inlabru-2.11.1/inlabru/man/like.Rd | 10 inlabru-2.11.1/inlabru/man/local_testthat.Rd | 2 inlabru-2.11.1/inlabru/man/mrsea.Rd | 2 inlabru-2.11.1/inlabru/man/plot.bru.Rd | 51 inlabru-2.11.1/inlabru/man/toypoints.Rd |only inlabru-2.11.1/inlabru/tests/testthat/_snaps/01_lgcp_2d.md |only inlabru-2.11.1/inlabru/tests/testthat/test-01_lgcp_2d.R |only inlabru-2.11.1/inlabru/tests/testthat/test-02_predict.R |only inlabru-2.11.1/inlabru/tests/testthat/test-aggregate.R | 9 inlabru-2.11.1/inlabru/tests/testthat/test-component.R | 11 inlabru-2.11.1/inlabru/tests/testthat/test-copy.R | 92 + inlabru-2.11.1/inlabru/tests/testthat/test-data.R | 1 inlabru-2.11.1/inlabru/tests/testthat/test-latent_fixed_effects.R | 17 inlabru-2.11.1/inlabru/tests/testthat/test-latent_spde_2d.R | 119 - inlabru-2.11.1/inlabru/tests/testthat/test-lgcp_1d.R | 24 inlabru-2.11.1/inlabru/tests/testthat/test-lgcp_2d_plotsample.R | 12 inlabru-2.11.1/inlabru/tests/testthat/test-linearisation.R | 76 - inlabru-2.11.1/inlabru/tests/testthat/test-mapper.R | 36 inlabru-2.11.1/inlabru/tests/testthat/test-mdata.R | 368 +++-- inlabru-2.11.1/inlabru/vignettes/component.Rmd | 6 118 files changed, 2354 insertions(+), 1709 deletions(-)
Title: Interface to the 'OpenGWAS' Database API
Description: Interface to the 'OpenGWAS' database API <https://gwas-api.mrcieu.ac.uk/>. Includes a wrapper
to make generic calls to the API, plus convenience functions for
specific queries.
Author: Gibran Hemani [aut, cre, cph] ,
Ben Elsworth [aut] ,
Tom Palmer [aut] ,
Rita Rasteiro [aut]
Maintainer: Gibran Hemani <g.hemani@bristol.ac.uk>
Diff between ieugwasr versions 1.0.0 dated 2024-04-22 and 1.0.1 dated 2024-07-01
DESCRIPTION | 8 ++--- MD5 | 61 ++++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 7 +++- R/afl2.r | 8 ++--- R/api.R | 2 - R/globals.R | 2 - R/ieugwasr-package.R |only R/ld_clump.R | 6 +-- R/ld_matrix.R | 2 - R/query.R | 65 ++++++++++++++++++++++++++++++++++++++--- R/variants.R | 8 ++--- build/vignette.rds |binary inst/doc/local_ld.html | 9 +++-- man/afl2_chrpos.Rd | 2 - man/afl2_list.Rd | 2 - man/afl2_rsid.Rd | 2 - man/api_query.Rd | 5 ++- man/check_reset.Rd |only man/ieugwasr-package.Rd |only man/infer_ancestry.Rd | 2 - man/ld_clump.Rd | 2 - man/ld_clump_api.Rd | 2 - man/ld_matrix.Rd | 2 - man/ld_reflookup.Rd | 2 - man/set_reset.Rd |only man/variants_chrpos.Rd | 2 - man/variants_gene.Rd | 2 - man/variants_rsid.Rd | 2 - man/variants_to_rsid.Rd | 2 - tests/testthat/test_afl2.r | 8 ++--- tests/testthat/test_check429.r |only tests/testthat/test_ld.r | 1 tests/testthat/test_query.r | 6 ++- 34 files changed, 149 insertions(+), 74 deletions(-)
Title: Multiple Data Analysis Tools for Property Listing Tasks
Description: Application to estimate statistical values using properties provided by a group of individuals to describe
concepts using 'shiny'. It estimates the underlying distribution to generate new descriptive words
Canessa et al. (2023) <doi:10.3758/s13428-022-01811-w>, applies a new clustering model, and uses simulations to estimate
the probability that two persons describe the same words based on their descriptions
Canessa et al. (2022) <doi:10.3758/s13428-022-02030-z>.
Author: Sebastian Moreno [aut, cre],
Cristobal Heredia [aut],
Enrique Canessa [ths],
Sergio Chaigneau [ths]
Maintainer: Sebastian Moreno <sebastian.moreno.araya@gmail.com>
Diff between WordListsAnalytics versions 0.2.2 dated 2024-05-06 and 0.2.3 dated 2024-07-01
DESCRIPTION | 6 +-- MD5 | 6 +-- R/PLT_app.R | 80 +++++++++++++++++++++++++++++++++++++++++-- man/WordListsAnalytics.Rd | 84 +++++++++++++++++++++++++++++++++++++++++++--- 4 files changed, 160 insertions(+), 16 deletions(-)
More information about WordListsAnalytics at CRAN
Permanent link
Title: Data Access and Analytical Tools for 'VectorSurv' Users
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Diff between vectorsurvR versions 0.1.0 dated 2024-04-16 and 0.2.0 dated 2024-07-01
vectorsurvR-0.1.0/vectorsurvR/inst/doc/vectorsurv.R |only vectorsurvR-0.1.0/vectorsurvR/inst/doc/vectorsurv.Rmd |only vectorsurvR-0.1.0/vectorsurvR/inst/doc/vectorsurv.html |only vectorsurvR-0.1.0/vectorsurvR/vignettes/vectorsurv.Rmd |only vectorsurvR-0.2.0/vectorsurvR/DESCRIPTION | 6 vectorsurvR-0.2.0/vectorsurvR/MD5 | 52 vectorsurvR-0.2.0/vectorsurvR/R/ProcessAbunAnom.R | 2 vectorsurvR-0.2.0/vectorsurvR/R/getAbundance.R | 12 vectorsurvR-0.2.0/vectorsurvR/R/getAbundanceAnomaly.R | 8 vectorsurvR-0.2.0/vectorsurvR/R/getArthroCollections.R | 155 +- vectorsurvR-0.2.0/vectorsurvR/R/getPools.R | 26 vectorsurvR-0.2.0/vectorsurvR/R/getPoolsComparisonTable.R | 8 vectorsurvR-0.2.0/vectorsurvR/R/getToken.R | 18 vectorsurvR-0.2.0/vectorsurvR/R/getVectorIndex.R | 2 vectorsurvR-0.2.0/vectorsurvR/R/globals.R | 2 vectorsurvR-0.2.0/vectorsurvR/README.md | 609 +++++++++- vectorsurvR-0.2.0/vectorsurvR/build/vignette.rds |binary vectorsurvR-0.2.0/vectorsurvR/inst/doc/vectorsurvR.R |only vectorsurvR-0.2.0/vectorsurvR/inst/doc/vectorsurvR.Rmd |only vectorsurvR-0.2.0/vectorsurvR/inst/doc/vectorsurvR.html |only vectorsurvR-0.2.0/vectorsurvR/man/getAbundance.Rd | 8 vectorsurvR-0.2.0/vectorsurvR/man/getAbundanceAnomaly.Rd | 4 vectorsurvR-0.2.0/vectorsurvR/man/getArthroCollections.Rd | 10 vectorsurvR-0.2.0/vectorsurvR/man/getPools.Rd | 8 vectorsurvR-0.2.0/vectorsurvR/man/getPoolsComparisionTable.Rd | 6 vectorsurvR-0.2.0/vectorsurvR/man/getToken.Rd | 2 vectorsurvR-0.2.0/vectorsurvR/man/processAbunAnom.Rd | 2 vectorsurvR-0.2.0/vectorsurvR/tests/testthat/test-ProcessAbunAnom.R | 2 vectorsurvR-0.2.0/vectorsurvR/tests/testthat/test-getAbundance.R | 2 vectorsurvR-0.2.0/vectorsurvR/tests/testthat/test-getAbundanceAnomaly.R | 2 vectorsurvR-0.2.0/vectorsurvR/vignettes/vectorsurvR.Rmd |only 31 files changed, 811 insertions(+), 135 deletions(-)
Title: Simulation of Matrix Population Models with Defined Life History
Characteristics
Description: Allows users to simulate matrix population models with
particular characteristics based on aspects of life history such as
mortality trajectories and fertility trajectories. Also allows the
exploration of sampling error due to small sample size.
Author: Owen Jones [aut, cre]
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between mpmsim versions 2.0.0 dated 2024-01-15 and 3.0.0 dated 2024-07-01
mpmsim-2.0.0/mpmsim/inst/doc/age_from_stage.R |only mpmsim-2.0.0/mpmsim/inst/doc/age_from_stage.Rmd |only mpmsim-2.0.0/mpmsim/inst/doc/age_from_stage.html |only mpmsim-2.0.0/mpmsim/inst/doc/pca.R |only mpmsim-2.0.0/mpmsim/inst/doc/pca.Rmd |only mpmsim-2.0.0/mpmsim/inst/doc/pca.html |only mpmsim-2.0.0/mpmsim/vignettes/age_from_stage.Rmd |only mpmsim-2.0.0/mpmsim/vignettes/pca.Rmd |only mpmsim-3.0.0/mpmsim/DESCRIPTION | 15 mpmsim-3.0.0/mpmsim/MD5 | 110 - mpmsim-3.0.0/mpmsim/NAMESPACE | 13 mpmsim-3.0.0/mpmsim/NEWS.md | 12 mpmsim-3.0.0/mpmsim/R/add_mpm_error.R | 22 mpmsim-3.0.0/mpmsim/R/compute_ci.R | 3 mpmsim-3.0.0/mpmsim/R/compute_ci_U.R |only mpmsim-3.0.0/mpmsim/R/generate_mpm_set.R | 43 mpmsim-3.0.0/mpmsim/R/globals.R | 2 mpmsim-3.0.0/mpmsim/R/make_leslie_mpm.R | 106 + mpmsim-3.0.0/mpmsim/R/model_fertility.R | 68 mpmsim-3.0.0/mpmsim/R/model_mortality.R | 136 + mpmsim-3.0.0/mpmsim/R/rand_lefko_mpm.R |only mpmsim-3.0.0/mpmsim/R/rand_lefko_set.R |only mpmsim-3.0.0/mpmsim/R/rand_leslie_set.R |only mpmsim-3.0.0/mpmsim/R/random_mpm.R | 99 - mpmsim-3.0.0/mpmsim/R/reorganise_matrices.R |only mpmsim-3.0.0/mpmsim/R/summarise_mpms.R |only mpmsim-3.0.0/mpmsim/R/vital_rate_driver_simulation.R | 2 mpmsim-3.0.0/mpmsim/README.md | 623 ++++---- mpmsim-3.0.0/mpmsim/build/partial.rdb |binary mpmsim-3.0.0/mpmsim/build/vignette.rds |binary mpmsim-3.0.0/mpmsim/inst/WORDLIST | 19 mpmsim-3.0.0/mpmsim/inst/doc/error_propagation.R | 6 mpmsim-3.0.0/mpmsim/inst/doc/error_propagation.html | 2 mpmsim-3.0.0/mpmsim/inst/doc/generate_lefkovitch_models.R |only mpmsim-3.0.0/mpmsim/inst/doc/generate_lefkovitch_models.Rmd |only mpmsim-3.0.0/mpmsim/inst/doc/generate_lefkovitch_models.html |only mpmsim-3.0.0/mpmsim/inst/doc/generate_leslie_models.R |only mpmsim-3.0.0/mpmsim/inst/doc/generate_leslie_models.Rmd |only mpmsim-3.0.0/mpmsim/inst/doc/generate_leslie_models.html |only mpmsim-3.0.0/mpmsim/man/add_mpm_error.Rd | 15 mpmsim-3.0.0/mpmsim/man/calculate_errors.Rd | 3 mpmsim-3.0.0/mpmsim/man/compute_ci.Rd | 6 mpmsim-3.0.0/mpmsim/man/compute_ci_U.Rd |only mpmsim-3.0.0/mpmsim/man/figures/plot_a_matrix01.png |binary mpmsim-3.0.0/mpmsim/man/generate_mpm_set.Rd | 15 mpmsim-3.0.0/mpmsim/man/make_leslie_mpm.Rd | 29 mpmsim-3.0.0/mpmsim/man/model_fertility.Rd | 53 mpmsim-3.0.0/mpmsim/man/model_survival.Rd | 72 - mpmsim-3.0.0/mpmsim/man/plot_matrix.Rd | 4 mpmsim-3.0.0/mpmsim/man/rand_lefko_mpm.Rd |only mpmsim-3.0.0/mpmsim/man/rand_lefko_set.Rd |only mpmsim-3.0.0/mpmsim/man/rand_leslie_set.Rd |only mpmsim-3.0.0/mpmsim/man/random_mpm.Rd | 25 mpmsim-3.0.0/mpmsim/man/reorganise_matrices.Rd |only mpmsim-3.0.0/mpmsim/man/summarise_mpms.Rd |only mpmsim-3.0.0/mpmsim/tests/testthat/test-add_mpm_error.R | 700 ++++------ mpmsim-3.0.0/mpmsim/tests/testthat/test-calculate_errors.R | 313 ++-- mpmsim-3.0.0/mpmsim/tests/testthat/test-compute_ci.R | 242 +-- mpmsim-3.0.0/mpmsim/tests/testthat/test-compute_ci_U.R |only mpmsim-3.0.0/mpmsim/tests/testthat/test-generate_mpm_set.R | 40 mpmsim-3.0.0/mpmsim/tests/testthat/test-make_leslie_mpm.R | 123 + mpmsim-3.0.0/mpmsim/tests/testthat/test-model_fertility.R | 250 ++- mpmsim-3.0.0/mpmsim/tests/testthat/test-mortality_models.R | 248 ++- mpmsim-3.0.0/mpmsim/tests/testthat/test-plot_matrix.R | 96 - mpmsim-3.0.0/mpmsim/tests/testthat/test-rand_lefko_mpm.R |only mpmsim-3.0.0/mpmsim/tests/testthat/test-rand_lefko_set.R |only mpmsim-3.0.0/mpmsim/tests/testthat/test-rand_leslie_set.R |only mpmsim-3.0.0/mpmsim/tests/testthat/test-random_mpm.R | 138 + mpmsim-3.0.0/mpmsim/tests/testthat/test-reorganise_matrices.R |only mpmsim-3.0.0/mpmsim/tests/testthat/test-summarise_mpms.R |only mpmsim-3.0.0/mpmsim/tests/testthat/test-vital_rate_driver_simulation.R | 393 ++--- mpmsim-3.0.0/mpmsim/vignettes/generate_lefkovitch_models.Rmd |only mpmsim-3.0.0/mpmsim/vignettes/generate_leslie_models.Rmd |only 73 files changed, 2242 insertions(+), 1804 deletions(-)
Title: Logistic Knowledge Tracing
Description: Computes Logistic Knowledge Tracing ('LKT') which is a general method for tracking human learning in an educational software system. Please see Pavlik, Eglington, and Harrel-Williams (2021) <https://ieeexplore.ieee.org/document/9616435>. 'LKT' is a method to compute features of student data that are used as predictors of subsequent performance. 'LKT' allows great flexibility in the choice of predictive components and features computed for these predictive components. The system is built on top of 'LiblineaR', which enables extremely fast solutions compared to base glm() in R.
Author: Philip I. Pavlik Jr. [aut, ctb, cre]
,
Luke G. Eglington [aut, ctb]
Maintainer: Philip I. Pavlik Jr. <imrryr@gmail.com>
Diff between LKT versions 1.6.0 dated 2023-12-11 and 1.7.0 dated 2024-07-01
LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-15-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-15-2.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-15-3.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-23-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-24-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-24-2.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-25-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-25-2.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-26-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-26-2.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-27-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-27-2.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-28-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-28-2.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-29-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-29-2.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-30-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-30-2.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-32-1.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-32-2.png |only LKT-1.6.0/LKT/vignettes/vigfig-unnamed-chunk-32-3.png |only LKT-1.7.0/LKT/DESCRIPTION | 8 LKT-1.7.0/LKT/MD5 | 73 LKT-1.7.0/LKT/NAMESPACE | 4 LKT-1.7.0/LKT/NEWS.md | 7 LKT-1.7.0/LKT/R/LKTfunctions.R | 275 LKT-1.7.0/LKT/README.md | 3 LKT-1.7.0/LKT/build/vignette.rds |binary LKT-1.7.0/LKT/inst/doc/Basic_Operations.R | 2 LKT-1.7.0/LKT/inst/doc/Basic_Operations.Rmd | 76 LKT-1.7.0/LKT/inst/doc/Basic_Operations.html | 245 LKT-1.7.0/LKT/inst/doc/Examples.Rmd | 6093 ++------- LKT-1.7.0/LKT/inst/doc/Examples.html | 8562 ++++---------- LKT-1.7.0/LKT/man/LASSOLKTData.Rd | 3 LKT-1.7.0/LKT/man/LASSOLKTModel.Rd | 113 LKT-1.7.0/LKT/man/LKT.Rd | 176 LKT-1.7.0/LKT/man/LKT_HDI.Rd | 25 LKT-1.7.0/LKT/man/predict_lkt.Rd |only LKT-1.7.0/LKT/vignettes/AFMMATHia.RData |only LKT-1.7.0/LKT/vignettes/Basic_Operations.Rmd | 76 LKT-1.7.0/LKT/vignettes/Examples.Rmd | 6093 ++------- LKT-1.7.0/LKT/vignettes/Examples.Rmd.orig | 494 LKT-1.7.0/LKT/vignettes/emptyMATHia.RData |only LKT-1.7.0/LKT/vignettes/precompile.R | 3 LKT-1.7.0/LKT/vignettes/vigfig-AFMstartMATHiaCV-1.png |only LKT-1.7.0/LKT/vignettes/vigfig-AFMstartMATHiaCV-2.png |only LKT-1.7.0/LKT/vignettes/vigfig-EmptystartMATHiaCV-1.png |only LKT-1.7.0/LKT/vignettes/vigfig-EmptystartMATHiaCV-2.png |only LKT-1.7.0/LKT/vignettes/vigfig-KC_search_method-1.png |only LKT-1.7.0/LKT/vignettes/vigfig-KC_search_method-2.png |only LKT-1.7.0/LKT/vignettes/vigfig-KC_search_method-3.png |only LKT-1.7.0/LKT/vignettes/vigfig-LASSOLKT-1.png |only LKT-1.7.0/LKT/vignettes/vigfig-LASSOLKT-2.png |only LKT-1.7.0/LKT/vignettes/vigfig-LASSOLKT-3.png |only LKT-1.7.0/LKT/vignettes/vigfig-buildLKT_with_offset-1.png |only 55 files changed, 6339 insertions(+), 15992 deletions(-)
Title: Fast and Vectorized Base 64 Engine
Description: Provides a fast, lightweight, and vectorized base 64 engine
to encode and decode character and raw vectors as well as files stored
on disk. Common base 64 alphabets are supported out of the box
including the standard, URL-safe, bcrypt, crypt, 'BinHex', and
IMAP-modified UTF-7 alphabets. Custom engines can be created to
support unique base 64 encoding and decoding needs.
Author: Josiah Parry [aut, cre] ,
Etienne Bacher [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between b64 versions 0.1.0 dated 2024-01-15 and 0.1.1 dated 2024-07-01
DESCRIPTION | 22 +++++--- MD5 | 33 ++++++------- NAMESPACE | 1 NEWS.md | 4 + R/alphabet.R | 11 +--- R/b64-package.R | 1 R/config.R | 4 - R/encode.R | 4 - R/engine.R | 22 ++++---- R/extendr-wrappers.R | 22 +++----- README.md | 41 ++++++++-------- man/b64-package.Rd | 10 +++ man/figures |only man/utils.Rd | 2 src/rust/Cargo.lock | 16 +++--- src/rust/Cargo.toml | 8 ++- src/rust/src/lib.rs | 123 +++++++++++++++++++++---------------------------- src/rust/vendor.tar.xz |binary 18 files changed, 163 insertions(+), 161 deletions(-)
Title: Convenience Functions for Psychology
Description: Make your workflow faster and easier. Easily customizable
plots (via 'ggplot2'), nice APA tables (following the style of the
*American Psychological Association*) exportable to Word (via
'flextable'), easily run statistical tests or check assumptions, and
automatize various other tasks.
Author: Remi Theriault [aut, cre]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Diff between rempsyc versions 0.1.7 dated 2023-10-09 and 0.1.8 dated 2024-07-01
DESCRIPTION | 14 MD5 | 104 - NAMESPACE | 3 NEWS.md | 893 ++++++------ R/global_variables.R | 18 R/grouped_bar_chart.R |only R/nice_lm.R | 5 R/nice_randomize.R | 198 +- R/nice_reverse.R | 66 R/nice_t_test.R | 385 ++--- R/nice_table.R | 1842 +++++++++++++------------- R/plot_means_over_time.R |only R/rcompanion_groupwiseMean.R | 632 ++++---- R/scale_mad.R | 64 R/winsorize_mad.R | 70 R/zzz.R | 16 README.md | 74 - build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 28 inst/WORDLIST | 16 inst/doc/assumptions.html | 22 inst/doc/circles.html | 2 inst/doc/contrasts.html | 18 inst/doc/moderation.html | 24 inst/doc/randomize.html | 2 inst/doc/scatter.html | 4 inst/doc/t-test.Rmd | 2 inst/doc/t-test.html | 43 inst/doc/table.html | 60 inst/doc/violin.html | 34 man/figures/README-grouped_bar_chart-1.png |only man/figures/README-nice_contrasts-1.png |binary man/figures/README-nice_lm-1.png |binary man/figures/README-nice_lm_slopes-1.png |binary man/figures/README-nice_mod-1.png |binary man/figures/README-nice_normality-1.png |binary man/figures/README-nice_slopes-1.png |binary man/figures/README-nice_t_test-1.png |binary man/figures/README-nice_table-1.png |only man/figures/README-nice_varplot-1.png |binary man/figures/README-nice_violin-1.png |binary man/figures/README-plot_means_over_time-1.png |only man/figures/README-unnamed-chunk-1-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/grouped_bar_chart.Rd |only man/nice_t_test.Rd | 3 man/nice_table.Rd | 5 man/plot_means_over_time.Rd |only tests/testthat/_snaps/nice_t_test.md | 37 tests/testthat/test-best_duplicate.R | 18 tests/testthat/test-nice_t_test.R | 105 - vignettes/t-test.Rmd | 2 57 files changed, 2481 insertions(+), 2328 deletions(-)
Title: Estimate Incidence and Prevalence using the OMOP Common Data
Model
Description: Calculate incidence and prevalence using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Incidence and prevalence can be estimated for the total population in a database or for a stratification cohort.
Author: Edward Burn [aut, cre] ,
Berta Raventos [aut] ,
Marti Catala [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Ger Inberg [ctb] ,
Kim Lopez [ctb]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between IncidencePrevalence versions 0.7.3 dated 2024-06-15 and 0.7.4 dated 2024-07-01
IncidencePrevalence-0.7.3/IncidencePrevalence/R/bindEstimates.R |only IncidencePrevalence-0.7.3/IncidencePrevalence/R/exportIncidencePrevalenceResults.R |only IncidencePrevalence-0.7.3/IncidencePrevalence/man/bindIncidenceEstimates.Rd |only IncidencePrevalence-0.7.3/IncidencePrevalence/man/bindPrevalenceEstimates.Rd |only IncidencePrevalence-0.7.3/IncidencePrevalence/man/exportIncidencePrevalenceResults.Rd |only IncidencePrevalence-0.7.3/IncidencePrevalence/man/incidenceAttrition.Rd |only IncidencePrevalence-0.7.3/IncidencePrevalence/man/incidenceSet.Rd |only IncidencePrevalence-0.7.3/IncidencePrevalence/man/prevalenceAttrition.Rd |only IncidencePrevalence-0.7.3/IncidencePrevalence/man/prevalenceSet.Rd |only IncidencePrevalence-0.7.3/IncidencePrevalence/tests/testthat/test-bindEstimates.R |only IncidencePrevalence-0.7.3/IncidencePrevalence/tests/testthat/test-exportIncidencePrevalenceResults.R |only IncidencePrevalence-0.7.4/IncidencePrevalence/DESCRIPTION | 23 IncidencePrevalence-0.7.4/IncidencePrevalence/MD5 | 127 IncidencePrevalence-0.7.4/IncidencePrevalence/NAMESPACE | 21 IncidencePrevalence-0.7.4/IncidencePrevalence/R/benchmarkIncidencePrevalence.R | 494 - IncidencePrevalence-0.7.4/IncidencePrevalence/R/dateUtilities.R | 172 IncidencePrevalence-0.7.4/IncidencePrevalence/R/estimateIncidence.R | 956 +- IncidencePrevalence-0.7.4/IncidencePrevalence/R/estimatePrevalence.R | 1078 +-- IncidencePrevalence-0.7.4/IncidencePrevalence/R/generateDenominatorCohortSet.R | 23 IncidencePrevalence-0.7.4/IncidencePrevalence/R/getDenominatorCohorts.R | 862 +- IncidencePrevalence-0.7.4/IncidencePrevalence/R/getPrevalence.R | 76 IncidencePrevalence-0.7.4/IncidencePrevalence/R/inputValidation.R | 8 IncidencePrevalence-0.7.4/IncidencePrevalence/R/mockIncidencePrevalenceRef.R | 919 +- IncidencePrevalence-0.7.4/IncidencePrevalence/R/obscureCounts.R | 13 IncidencePrevalence-0.7.4/IncidencePrevalence/R/plotting.R | 554 - IncidencePrevalence-0.7.4/IncidencePrevalence/R/reexport-omopgenerics.R | 16 IncidencePrevalence-0.7.4/IncidencePrevalence/R/tables.R |only IncidencePrevalence-0.7.4/IncidencePrevalence/R/utils.R | 273 IncidencePrevalence-0.7.4/IncidencePrevalence/README.md | 12 IncidencePrevalence-0.7.4/IncidencePrevalence/build/vignette.rds |binary IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a01_Introduction_to_IncidencePrevalence.R | 19 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a01_Introduction_to_IncidencePrevalence.Rmd | 26 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a01_Introduction_to_IncidencePrevalence.html | 248 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a02_Creating_denominator_populations.R | 139 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a02_Creating_denominator_populations.Rmd | 162 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a02_Creating_denominator_populations.html | 749 +- IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a03_Creating_target_denominator_populations.R | 1 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a03_Creating_target_denominator_populations.Rmd | 337 - IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a03_Creating_target_denominator_populations.html | 9 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a04_Calculating_prevalence.R | 26 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a04_Calculating_prevalence.Rmd | 567 - IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a04_Calculating_prevalence.html | 305 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a05_Calculating_incidence.R | 25 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a05_Calculating_incidence.Rmd | 555 - IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a05_Calculating_incidence.html | 356 - IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a06_Plotting_options.R | 10 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a06_Plotting_options.Rmd | 198 IncidencePrevalence-0.7.4/IncidencePrevalence/inst/doc/a06_Plotting_options.html | 43 IncidencePrevalence-0.7.4/IncidencePrevalence/man/estimateIncidence.Rd | 4 IncidencePrevalence-0.7.4/IncidencePrevalence/man/figures/README-unnamed-chunk-11-1.png |binary IncidencePrevalence-0.7.4/IncidencePrevalence/man/generateDenominatorCohortSet.Rd | 4 IncidencePrevalence-0.7.4/IncidencePrevalence/man/mockIncidencePrevalenceRef.Rd | 2 IncidencePrevalence-0.7.4/IncidencePrevalence/man/optionsTableIncidence.Rd |only IncidencePrevalence-0.7.4/IncidencePrevalence/man/optionsTablePrevalence.Rd |only IncidencePrevalence-0.7.4/IncidencePrevalence/man/reexports.Rd | 6 IncidencePrevalence-0.7.4/IncidencePrevalence/tests/manual/test-eunomia.R | 458 - IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-benchmarkIncidencePrevalence.R | 2 IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-dateUtilities.R | 234 IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-estimateIncidence.R | 1340 ++- IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-estimatePrevalence.R | 503 - IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-generateDenominatorCohortSet.R | 3370 +++++----- IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-getStudyDays.R | 522 - IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-mockIncidencePrevalenceRef.R | 571 - IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-obscureCounts.R | 138 IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-plotting.R | 651 + IncidencePrevalence-0.7.4/IncidencePrevalence/tests/testthat/test-tables.R |only IncidencePrevalence-0.7.4/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence.Rmd | 26 IncidencePrevalence-0.7.4/IncidencePrevalence/vignettes/a02_Creating_denominator_populations.Rmd | 162 IncidencePrevalence-0.7.4/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations.Rmd | 337 - IncidencePrevalence-0.7.4/IncidencePrevalence/vignettes/a04_Calculating_prevalence.Rmd | 567 - IncidencePrevalence-0.7.4/IncidencePrevalence/vignettes/a05_Calculating_incidence.Rmd | 555 - IncidencePrevalence-0.7.4/IncidencePrevalence/vignettes/a06_Plotting_options.Rmd | 198 72 files changed, 9628 insertions(+), 9424 deletions(-)
More information about IncidencePrevalence at CRAN
Permanent link
Title: Convenience Functions for Package 'lavaan'
Description: Affords an alternative, vector-based syntax to 'lavaan', as well as other
convenience functions such as naming paths and defining indirect
links automatically, in addition to convenience formatting optimized
for a publication and script sharing workflow.
Author: Remi Theriault [aut, cre]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Diff between lavaanExtra versions 0.2.0 dated 2023-10-15 and 0.2.1 dated 2024-07-01
DESCRIPTION | 10 MD5 | 84 +-- NEWS.md | 18 R/cfa_fit_plot.R | 176 +++--- R/lavaan_cov.R | 102 +-- R/lavaan_defined.R | 142 ++--- R/lavaan_extract.R | 223 ++++---- R/lavaan_reg.R | 82 +-- R/lavaan_var.R | 152 ++--- R/nice_fit.R | 66 +- R/nice_lavaanPlot.R | 125 ++-- R/nice_modindices.R | 210 +++---- R/nice_tidySEM.R | 354 ++++++------- R/write_lavaan.R | 416 +++++++-------- README.md | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/example.html | 833 +++++++++++++++---------------- inst/doc/write_lavaan.Rmd | 102 +-- man/cfa_fit_plot.Rd | 2 man/figures/README-cfa2-1.png |binary man/figures/README-correlation-1.png |binary man/figures/README-covariance-1.png |binary man/figures/README-indirect2-1.png |binary man/figures/README-path2-1.png |binary man/figures/README-saturated-1.png |binary man/figures/README-saturated2-1.png |binary man/lavaan_defined.Rd | 164 +++--- man/lavaan_extract.Rd | 172 +++--- man/lavaan_var.Rd | 120 ++-- man/nice_fit.Rd | 5 man/nice_lavaanPlot.Rd | 2 tests/testthat/_snaps/lavaan_defined.md | 22 tests/testthat/_snaps/nice_modindices.md | 90 +-- tests/testthat/_snaps/write_lavaan.md | 498 +++++++++--------- tests/testthat/test-cfa_fit_plot.R | 4 tests/testthat/test-lavaan_cor.R | 74 +- tests/testthat/test-lavaan_cov.R | 74 +- tests/testthat/test-lavaan_reg.R | 72 +- tests/testthat/test-lavaan_var.R | 74 +- tests/testthat/test-nice_fit.R | 26 tests/testthat/test-nice_lavaanPlot.R | 5 vignettes/write_lavaan.Rmd | 102 +-- 43 files changed, 2348 insertions(+), 2265 deletions(-)
Title: Automates the Creation of New Statistical Analysis Projects
Description: Provides functions to
automatically build a directory structure for a new R
project. Using this structure, 'ProjectTemplate'
automates data loading, preprocessing, library
importing and unit testing.
Author: Aleksandar Blagotic [ctb],
Diego Valle-Jones [ctb],
Jeffrey Breen [ctb],
Joakim Lundborg [ctb],
John Myles White [aut, cph],
Josh Bode [ctb],
Kenton White [ctb, cre],
Kirill Mueller [ctb],
Matteo Redaelli [ctb],
Noah Lorang [ctb],
Patrick Schalk [ctb [...truncated...]
Maintainer: Kenton White <jkentonwhite@gmail.com>
Diff between ProjectTemplate versions 0.10.4 dated 2023-11-19 and 0.11.0 dated 2024-07-01
DESCRIPTION | 20 ++-- MD5 | 23 ++-- NAMESPACE | 3 NEWS.md | 6 + R/load.project.R | 14 ++ R/sql.reader.R | 2 build/partial.rdb |binary inst/defaults/templates/full/config/global.dcf | 2 inst/defaults/templates/minimal/config/global.dcf | 2 man/ProjectTemplate-package.Rd | 3 tests/testthat.R |only tests/testthat/test-load.R | 107 ++++++++++++++++++++-- tests/testthat/test-load.project.R |only tests/testthat/test-test-load.R |only 14 files changed, 147 insertions(+), 35 deletions(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Bayesian Model Averaging for Univariate Link Latent Gaussian
Models
Description: Bayesian model averaging (BMA) algorithms for univariate link latent Gaussian models (ULLGMs). For detailed information, refer to Steel M.F.J. & Zens G. (2024) "Model Uncertainty in Latent Gaussian Models with Univariate Link Function" <doi:10.48550/arXiv.2406.17318>. The package supports various g-priors and a beta-binomial prior on the model space. It also includes auxiliary functions for visualizing and tabulating BMA results. Currently, it offers an out-of-the-box solution for model averaging of Poisson log-normal (PLN) and binomial logistic-normal (BiL) models. The codebase is designed to be easily extendable to other likelihoods, priors, and link functions.
Author: Gregor Zens [aut, cre],
Mark F.J. Steel [aut]
Maintainer: Gregor Zens <zens@iiasa.ac.at>
Diff between LatentBMA versions 0.1.0 dated 2024-06-27 and 0.1.1 dated 2024-07-01
DESCRIPTION | 6 - MD5 | 6 - R/mcmc.R | 6 - inst/doc/LatentBMA_Vignette.html | 134 +++++++++++++++++++-------------------- 4 files changed, 75 insertions(+), 77 deletions(-)
Title: Extracting and Visualizing Output from 'jagsUI'
Description: Tools are provided to streamline Bayesian analyses in 'JAGS' using
the 'jagsUI' package. Included are functions for extracting output in
simpler format, functions for streamlining assessment of convergence, and
functions for producing summary plots of output. Also included is a
function that provides a simple template for running 'JAGS' from 'R'.
Referenced materials can be found at <DOI:10.1214/ss/1177011136>.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matttyersstat@gmail.com>
Diff between jagshelper versions 0.2.3 dated 2024-04-30 and 0.2.4 dated 2024-07-01
DESCRIPTION | 8 +- MD5 | 14 +-- NEWS.md | 6 + R/jagshelper1.R | 137 +++++++++++++++++++++++++++++--------- inst/doc/jagshelper-vignette.html | 4 - man/jagshelper-package.Rd | 4 - man/plotcor_jags.Rd | 4 - tests/testthat/test_jagshelper.R | 6 + 8 files changed, 133 insertions(+), 50 deletions(-)
Title: Interact with the 'Databrary.org' API
Description: 'Databrary.org' is a restricted access repository for
research data, especially video and audio. This package provides
commands to interact with the data stored on 'Databrary.org'.
Author: Rick O. Gilmore [aut, cre, cph],
Jeffrey Spies [aut],
National Science Foundation OAC-2032713 [fnd],
National Institutes of Health R01HD094830 [fnd]
Maintainer: Rick O. Gilmore <rog1@psu.edu>
Diff between databraryr versions 0.6.4 dated 2024-04-18 and 0.6.5 dated 2024-07-01
databraryr-0.6.4/databraryr/R/download_asset.R |only databraryr-0.6.4/databraryr/R/get_session_as_df.R |only databraryr-0.6.4/databraryr/R/get_video_stats.R |only databraryr-0.6.4/databraryr/R/list_assets_by_type.R |only databraryr-0.6.4/databraryr/R/list_assets_in_session.R |only databraryr-0.6.4/databraryr/R/list_assets_in_volume.R |only databraryr-0.6.4/databraryr/R/list_containers_records.R |only databraryr-0.6.4/databraryr/R/list_volume_metadata.R |only databraryr-0.6.4/databraryr/R/read_csv_data_as_df.R |only databraryr-0.6.4/databraryr/R/summarize_videos_in_volume.R |only databraryr-0.6.4/databraryr/man/DATABRARY_API.Rd |only databraryr-0.6.4/databraryr/man/download_asset.Rd |only databraryr-0.6.4/databraryr/man/get_session_as_df.Rd |only databraryr-0.6.4/databraryr/man/get_video_stats.Rd |only databraryr-0.6.4/databraryr/man/list_assets_by_type.Rd |only databraryr-0.6.4/databraryr/man/list_assets_in_session.Rd |only databraryr-0.6.4/databraryr/man/list_assets_in_volume.Rd |only databraryr-0.6.4/databraryr/man/list_containers_records.Rd |only databraryr-0.6.4/databraryr/man/list_specified_assets_in_session.Rd |only databraryr-0.6.4/databraryr/man/list_volume_metadata.Rd |only databraryr-0.6.4/databraryr/man/read_csv_data_as_df.Rd |only databraryr-0.6.4/databraryr/man/summarize_videos_in_volume.Rd |only databraryr-0.6.4/databraryr/tests/testthat/test-download_asset.R |only databraryr-0.6.4/databraryr/tests/testthat/test-get_session_as_df.R |only databraryr-0.6.4/databraryr/tests/testthat/test-get_video_stats.R |only databraryr-0.6.4/databraryr/tests/testthat/test-list_assets_by_type.R |only databraryr-0.6.4/databraryr/tests/testthat/test-list_assets_in_session.R |only databraryr-0.6.4/databraryr/tests/testthat/test-list_assets_in_volume.R |only databraryr-0.6.4/databraryr/tests/testthat/test-list_containers_records.R |only databraryr-0.6.4/databraryr/tests/testthat/test-list_volume_metadata.R |only databraryr-0.6.4/databraryr/tests/testthat/test-read_csv_data_as_df.R |only databraryr-0.6.4/databraryr/tests/testthat/test-summarize_videos_in_volume.R |only databraryr-0.6.5/databraryr/DESCRIPTION | 10 databraryr-0.6.5/databraryr/MD5 | 103 +++------ databraryr-0.6.5/databraryr/NAMESPACE | 10 databraryr-0.6.5/databraryr/NEWS.md | 9 databraryr-0.6.5/databraryr/R/CONSTANTS.R | 43 ++- databraryr-0.6.5/databraryr/R/assign_constants.R | 11 databraryr-0.6.5/databraryr/R/download_party_avatar.R | 12 - databraryr-0.6.5/databraryr/R/download_session_asset.R | 45 ++-- databraryr-0.6.5/databraryr/R/download_session_assets_fr_df.R | 11 databraryr-0.6.5/databraryr/R/download_session_csv.R | 66 ++--- databraryr-0.6.5/databraryr/R/download_session_zip.R | 26 +- databraryr-0.6.5/databraryr/R/download_single_session_asset_fr_df.R | 112 ++++------ databraryr-0.6.5/databraryr/R/download_video.R | 39 ++- databraryr-0.6.5/databraryr/R/download_volume_zip.R | 10 databraryr-0.6.5/databraryr/R/get_db_stats.R | 17 - databraryr-0.6.5/databraryr/R/get_party_by_id.R | 16 + databraryr-0.6.5/databraryr/R/list_individual_sponsors.R | 2 databraryr-0.6.5/databraryr/R/list_party_affiliates.R | 2 databraryr-0.6.5/databraryr/R/list_party_sponsors.R | 2 databraryr-0.6.5/databraryr/R/list_party_volumes.R | 3 databraryr-0.6.5/databraryr/R/list_people.R | 6 databraryr-0.6.5/databraryr/R/list_sponsors.R | 2 databraryr-0.6.5/databraryr/R/utils.R | 4 databraryr-0.6.5/databraryr/build/vignette.rds |binary databraryr-0.6.5/databraryr/inst/doc/accessing-data.html | 6 databraryr-0.6.5/databraryr/inst/doc/authorized-users.html | 2 databraryr-0.6.5/databraryr/inst/doc/databrary.html | 111 +++------ databraryr-0.6.5/databraryr/man/API_CONSTANTS.Rd |only databraryr-0.6.5/databraryr/man/download_session_asset.Rd | 8 databraryr-0.6.5/databraryr/man/download_session_assets_fr_df.Rd | 7 databraryr-0.6.5/databraryr/man/download_single_session_asset_fr_df.Rd | 7 databraryr-0.6.5/databraryr/man/download_video.Rd | 6 databraryr-0.6.5/databraryr/man/get_party_by_id.Rd | 13 - databraryr-0.6.5/databraryr/tests/testthat/test-download_session_assets_fr_df.R | 10 databraryr-0.6.5/databraryr/tests/testthat/test-download_session_csv.R | 9 databraryr-0.6.5/databraryr/tests/testthat/test-download_single_session_asset_fr_df.R | 5 databraryr-0.6.5/databraryr/tests/testthat/test-get_party_by_id.R | 4 69 files changed, 389 insertions(+), 360 deletions(-)
Title: Deal with Dependencies
Description: Manage dependencies during package development. This can
retrieve all dependencies that are used in ".R" files in the "R/"
directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2'
documentation of functions. There is a function to update the
"DESCRIPTION" file of your package with 'CRAN' packages or any other
remote package. All functions to retrieve dependencies of ".R"
scripts and ".Rmd" or ".qmd" files can be used independently of a
package development.
Author: Sebastien Rochette [cre, aut] ,
Vincent Guyader [aut] ,
Murielle Delmotte [aut] ,
Swann Floc'hlay [aut] ,
ThinkR [cph, fnd]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Diff between attachment versions 0.4.1 dated 2024-01-22 and 0.4.2 dated 2024-07-01
DESCRIPTION | 8 +-- MD5 | 70 ++++++++++++++++++++++++++------ NEWS.md | 6 ++ R/add_build_ignore.R |only R/amend_with_config.R | 56 +++++++++++++------------ R/create_renv.R | 23 ++++++++++ build/vignette.rds |binary inst/doc/a-fill-pkg-description.R | 24 +++++----- inst/doc/a-fill-pkg-description.html | 12 ++--- inst/doc/b-bookdown-and-scripts.R | 14 +++--- inst/doc/b-bookdown-and-scripts.html | 4 - inst/doc/create-dependencies-file.R | 2 inst/doc/use_renv.R | 8 +-- inst/dummyfolder |only man/attachment-package.Rd | 4 - tests/testdown |only tests/testthat/test-add_build_ignore.R |only tests/testthat/test-amend-description.R | 6 ++ tests/testthat/test-renv_create2.R |only 19 files changed, 158 insertions(+), 79 deletions(-)
Title: Handy Tools for TJU/TJUH Employees
Description: Functions for admin needs of employees of
Thomas Jefferson University and Thomas Jefferson
University Hospital, Philadelphia, PA.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between ThomasJeffersonUniv versions 0.1.2 dated 2024-04-30 and 0.1.3 dated 2024-07-01
DESCRIPTION | 26 +++++++++++++------------- MD5 | 41 +++++++++++++++++++++++++++-------------- NAMESPACE | 12 ++++++++++++ R/Excel2int.R |only R/Surv_3Date.R | 6 +++++- R/TJU_Cayuse.R | 2 +- R/addProbs.R |only R/as.difftime.POSIXt.R |only R/bibentry2rmd.R |only R/date_time.R | 4 +--- R/format_named.R | 32 +++++++++++++++++++------------- R/phone10_zip5.R | 3 ++- R/rbinds.R |only R/sign2.R |only R/splitDF.R | 15 +++++++++++---- R/style_.R | 13 +++++++++++-- R/subset_.R | 14 +++++++++----- R/trimws_.R |only man/addProbs.Rd |only man/bibentry2rmd.Rd |only man/format_named.Rd | 8 ++++---- man/hexavigesimalExcel.Rd |only man/matchDF.Rd | 2 +- man/phone10.Rd | 3 ++- man/rbinds.Rd |only man/sign2.Rd |only man/subset_.Rd | 2 ++ man/trimws_.Rd |only 28 files changed, 120 insertions(+), 63 deletions(-)
More information about ThomasJeffersonUniv at CRAN
Permanent link
Title: Read and Write 'Parquet' Files
Description: Self-sufficient reader and writer for flat 'Parquet' files.
Can read most 'Parquet' data types. Can write many 'R' data types,
including factors and temporal types. See docs for limitations.
Author: Gabor Csardi [aut, cre],
Hannes Muehleisen [aut, cph] ,
Google Inc. [cph],
Apache Software Foundation [cph],
Posit Software, PBC [cph],
RAD Game Tools [cph],
Valve Software [cph],
Tenacious Software LLC [cph],
Facebook, Inc. [cph]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between nanoparquet versions 0.3.0 dated 2024-06-17 and 0.3.1 dated 2024-07-01
DESCRIPTION | 8 +++----- MD5 | 19 ++++++++++--------- NEWS.md | 4 ++++ R/nanoparquet.R | 2 +- R/utils.R | 4 ++++ README.md | 1 + man/nanoparquet-package.Rd | 2 +- src/install.libs.R |only src/lib/RleBpEncoder.h | 2 +- src/rwrapper.cpp | 15 +++++++++++++++ tests/testthat/test-porcelain.R | 2 ++ 11 files changed, 42 insertions(+), 17 deletions(-)
Title: Langevin Analysis in One and Two Dimensions
Description: Estimate drift and diffusion functions from time series and
generate synthetic time series from given drift and diffusion coefficients.
Author: Philip Rinn [aut, cre],
Pedro G. Lind [aut],
David Bastine [ctb]
Maintainer: Philip Rinn <philip.rinn@uni-oldenburg.de>
Diff between Langevin versions 1.3.1 dated 2021-10-19 and 1.3.2 dated 2024-07-01
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/Langevin-package.r | 4 ++-- build/vignette.rds |binary inst/doc/Langevin.pdf |binary man/Langevin-package.Rd | 9 +++++++++ src/Langevin1D.cpp | 8 ++++---- src/Makevars | 2 -- src/Makevars.win | 2 -- 9 files changed, 28 insertions(+), 23 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],
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],
Henrik Singmann [ctb]
Maintainer: Russell V. Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.10.2 dated 2024-05-19 and 1.10.3 dated 2024-07-01
DESCRIPTION | 8 - MD5 | 56 +++++----- NEWS.md | 12 ++ R/contrast.R | 6 - R/helpers.R | 2 R/multiple-models.R | 18 +++ build/vignette.rds |binary inst/doc/AQuickStart.html | 4 inst/doc/FAQs.html | 8 - inst/doc/basics.html | 4 inst/doc/comparisons.html | 11 +- inst/doc/confidence-intervals.html | 21 ++-- inst/doc/interactions.html | 16 +-- inst/doc/messy-data.html | 4 inst/doc/models.Rmd | 55 ++++++---- inst/doc/models.html | 66 +++++++----- inst/doc/predictions.html | 4 inst/doc/re-engineering-clds.html | 4 inst/doc/sophisticated.html | 4 inst/doc/transformations.Rmd | 25 ++++ inst/doc/transformations.html | 33 +++++- inst/doc/utilities.html | 4 inst/doc/vignette-topics.Rmd | 100 +++++++++++++------ inst/doc/vignette-topics.html | 193 ++++++++++++++++++++++++++----------- inst/doc/xplanations.html | 4 inst/doc/xtending.html | 8 - vignettes/models.Rmd | 55 ++++++---- vignettes/transformations.Rmd | 25 ++++ vignettes/vignette-topics.Rmd | 100 +++++++++++++------ 29 files changed, 583 insertions(+), 267 deletions(-)
Title: Pre- And Post-Processing in Bayesian Evolutionary Analyses
Description: Functions are provided for prior specification in divergence time
estimation using fossils as well as other kinds of data. It
provides tools for interacting with the input and output of Bayesian
platforms in evolutionary biology such as 'BEAST2', 'MrBayes', 'RevBayes',
or 'MCMCTree'.
It Implements a simple measure similarity between probability
density functions for comparing prior and
posterior Bayesian densities, as well as code for calculating the
combination of distributions using conflation of Hill (2008). Functions for estimating the
origination time in collections of distributions using the x-intercept (e.g., Draper and Smith, 1998) and
stratigraphic intervals (Marshall 2010) are also available.
Hill, T. 2008. "Conflations of probability distributions". Transactions of the American Mathematical Society, 363:3351-3372. <doi:10.48550/arXiv.0808.1808>,
Draper, N. R. and Smith, H. 1998. "Applied Regression Analysis". 1--706. Wiley Interscience, New York. <DOI:10.1002/978111 [...truncated...]
Author: Gustavo A. Ballen [aut, cre],
Sandra Reinales [aut]
Maintainer: Gustavo A. Ballen <gustavo.a.ballen@gmail.com>
Diff between tbea versions 1.4.2 dated 2024-06-04 and 1.5.0 dated 2024-07-01
DESCRIPTION | 6 +-- MD5 | 13 ++++--- NAMESPACE | 1 R/c_truncauchy.R |only README.md | 62 ++++++++++++++++++++++++++----------- inst/doc/intro.html | 4 +- inst/doc/whyInitVals.html | 4 +- man/c_truncauchy.Rd |only tests/testthat/test-c_truncauchy.R |only 9 files changed, 61 insertions(+), 29 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre] ,
Edward L. Ionides [aut] ,
Carles Breto [aut] ,
Stephen P. Ellner [ctb] ,
Matthew J. Ferrari [ctb] ,
Sebastian Funk [ctb] ,
Steven G. Johnson [ctb],
Bruce E. Kendall [ctb] ,
Michael Lavine [ctb],
Dao Nguyen [ctb] ,
Eamon B. [...truncated...]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 5.9 dated 2024-06-02 and 5.10 dated 2024-07-01
DESCRIPTION | 14 ++-- MD5 | 32 +++++----- R/rprocess_spec.R | 2 R/userdata.R | 2 build/partial.rdb |binary data/LondonYorke.rda |binary data/bsflu.rda |binary data/ebolaWA2014.rda |binary data/ewcitmeas.rda |binary data/ewmeas.rda |binary inst/NEWS | 11 +++ inst/NEWS.Rd | 6 + man/rprocess_spec.Rd | 2 man/userdata.Rd | 2 src/decls.h | 160 +++++++++++++++++++++++++-------------------------- src/euler.c | 2 src/rprocess.c | 4 - 17 files changed, 127 insertions(+), 110 deletions(-)
Title: Parallel Partitioning-Around-Medoids (PAM) for Big Sets of Data
Description: Application of the Partitioning-Around-Medoids (PAM) clustering algorithm described in Schubert, E. and Rousseeuw, P.J.:
"Fast and eager k-medoids clustering: O(k) runtime improvement of the PAM, CLARA, and CLARANS algorithms." Information Systems,
vol. 101, p. 101804, (2021). <doi:10.1016/j.is.2021.101804>.
It uses a binary format for storing and retrieval of matrices developed for the 'jmatrix' package but the functionality of 'jmatrix'
is included here, so you do not need to install it. Also, it is used by package 'scellpam', so if you have installed it, you do not need
to install this package.
PAM can be applied to sets of data whose dissimilarity matrix can be very big. It has been tested with up to 100.000 points.
It does this with the help of the code developed for other package, 'jmatrix', which allows the matrix not to be loaded in 'R' memory (which
would force it to be of double type) but it gets from disk, which allows using float (or even smaller data types). Moreover [...truncated...]
Author: Juan Domingo [aut, cre] ,
Guillermo Ayala [ctb] ,
Spanish Ministry of Science and Innovation, MCIN/AEI
<doi:10.13039/501100011033> [fnd]
Maintainer: Juan Domingo <Juan.Domingo@uv.es>
Diff between parallelpam versions 1.4 dated 2023-10-09 and 1.4.2 dated 2024-07-01
DESCRIPTION | 7 MD5 | 38 +- NEWS | 9 build/vignette.rds |binary inst/doc/jmatrixpp.R | 2 inst/doc/jmatrixpp.html | 600 ++++++++++++++++++++--------------------- inst/doc/parallelpam.R | 14 inst/doc/parallelpam.html | 452 +++++++++++++++--------------- inst/include/fullmatrix.h | 10 inst/include/jmatrix.h | 15 - inst/include/symmetricmatrix.h | 4 src/dissimmat_full.cpp | 5 src/dissimmat_sparse.cpp | 5 src/fastpam.cpp | 1 src/fullmatrix.cpp | 62 ++-- src/jmatrix.cpp | 73 +++- src/silhouette.cpp | 8 src/sparsematrix.cpp | 43 +- src/symmetricmatrix.cpp | 52 ++- src/threadhelper.cpp | 3 20 files changed, 756 insertions(+), 647 deletions(-)
Title: Causal Inference with Super Learner and Deep Neural Networks
Description: Functions to estimate Conditional Average Treatment Effects (CATE)
and Population Average Treatment Effects on the Treated (PATT) from
experimental or observational data using the Super Learner (SL) ensemble
method and Deep neural networks. The package first provides functions to
implement meta-learners such as the Single-learner (S-learner) and
Two-learner (T-learner) described in Künzel et al. (2019)
<doi:10.1073/pnas.1804597116> for estimating the CATE. The S- and T-learner
are each estimated using the SL ensemble method and deep neural networks. It
then provides functions to implement the Ottoboni and Poulos (2020)
<doi:10.1515/jci-2018-0035> PATT-C estimator to obtain the PATT from
experimental data with noncompliance by using the SL ensemble method and
deep neural networks.
Author: Nguyen K. Huynh [aut, cre] ,
Bumba Mukherjee [aut] ,
Irvin Lee [aut]
Maintainer: Nguyen K. Huynh <khoinguyen.huynh@r.hit-u.ac.jp>
Diff between DeepLearningCausal versions 0.0.102 dated 2024-06-18 and 0.0.103 dated 2024-07-01
DESCRIPTION | 8 - MD5 | 31 +++---- NAMESPACE | 2 R/meta_learners.R | 45 +++++++++- R/neural_meta_learners.R | 44 +++++++++- R/patt_ensemble.R | 133 +++++++++++++++++++++++++----- R/patt_neural.R | 143 ++++++++++++++++++++++++++++----- R/utils.R | 2 README.md | 39 ++++++--- data/pop_data_full.rda |binary man/metalearner_deepneural.Rd | 9 +- man/metalearner_ensemble.Rd | 9 +- man/neuralnet_pattc_counterfactuals.Rd | 2 man/pattc_counterfactuals.Rd | 2 man/pattc_deepneural.Rd | 46 +++++++--- man/pattc_ensemble.Rd | 46 ++++++---- man/print.pattc_ensemble.Rd |only 17 files changed, 435 insertions(+), 126 deletions(-)
More information about DeepLearningCausal at CRAN
Permanent link
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre] ,
Peter Rousseeuw [ctb] ,
Christophe Croux [ctb] ,
Valentin Todorov [aut] ,
Andreas Ruckstuhl [aut] ,
Matias Salibian-Barrera [aut] ,
Tobias Verbeke [ctb, fnd] ,
Manuel Koller [aut] ,
Eduardo L. T. Conceicao [aut] ,
Maria A [...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.99-2 dated 2024-01-27 and 0.99-3 dated 2024-07-01
DESCRIPTION | 10 - MD5 | 28 +-- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 17 + inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.R | 60 +++--- inst/doc/lmrob_simulation.Rnw | 60 +++--- inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.Rnw | 8 inst/doc/psi_functions.pdf |binary inst/xtraR/subsample-fns.R | 357 ++++++++++++++++++++--------------------- tests/subsample.R | 17 + vignettes/lmrob_simulation.Rnw | 60 +++--- vignettes/psi_functions.Rnw | 8 15 files changed, 324 insertions(+), 301 deletions(-)
Title: 'LuaJIT' Scripting
Description: An interface to 'LuaJIT' <https://luajit.org>, a just-in-time
compiler for the 'Lua' scripting language <https://www.lua.org>. Allows
users to run 'Lua' code from 'R'.
Author: Mike Pall [aut, cph] ,
Lua.org, PUC-Rio [cph] ,
Nicholas Davies [cre, ctb, cph]
Maintainer: Nicholas Davies <nicholas.davies@lshtm.ac.uk>
Diff between luajr versions 0.1.7 dated 2024-04-24 and 0.1.8 dated 2024-07-01
DESCRIPTION | 6 +++--- MD5 | 34 ++++++++++++++++++---------------- NEWS.md | 19 +++++++++++++++++++ R/lua_shell.R | 11 +++++++++-- inst/doc/luajr.html | 8 ++++---- inst/include/luajr.h | 12 +++++++++--- inst/include/luajr_funcs.h | 12 +++++++++--- inst/module/luajr.lua | 2 +- man/lua_shell.Rd | 2 ++ src/lua_api.cpp | 8 ++++---- src/luajit/src/Makefile | 2 +- src/luajit/src/lib_io.c | 1 + src/luajit/src/lib_os.c | 1 + src/luajit/src/luajrio.h |only src/luajit/src/luajros.h |only src/push_to.cpp | 6 +++++- src/run_func.cpp | 22 +++++++++++++++------- src/setup.cpp | 20 ++++++++++++++++++++ src/shared.h | 2 ++ 19 files changed, 123 insertions(+), 45 deletions(-)
Title: Chemical Metrics for Microbial Communities
Description: Combines taxonomic classifications of high-throughput 16S rRNA
gene sequences with reference proteomes of archaeal and bacterial taxa to
generate amino acid compositions of community reference proteomes. Calculates
chemical metrics including carbon oxidation state ('Zc'), stoichiometric
oxidation and hydration state ('nO2' and 'nH2O'), H/C, N/C, O/C, and S/C
ratios, grand average of hydropathicity ('GRAVY'), isoelectric point ('pI'),
protein length, and average molecular weight of amino acid residues. Uses
precomputed reference proteomes for archaea and bacteria derived from the
Genome Taxonomy Database ('GTDB'). Also includes reference proteomes derived
from the NCBI Reference Sequence ('RefSeq') database and manual mapping from
the 'RDP Classifier' training set to 'RefSeq' taxonomy as described by Dick and
Tan (2023) <doi:10.1007/s00248-022-01988-9>. Processes taxonomic
classifications in 'RDP Classifier' format or OTU tables in 'phyloseq-class'
objects from the Bioconductor pa [...truncated...]
Author: Jeffrey Dick [aut, cre]
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between chem16S versions 1.0.0 dated 2023-07-17 and 1.1.0 dated 2024-07-01
chem16S-1.0.0/chem16S/R/calc_metrics.R |only chem16S-1.0.0/chem16S/data/mouse.GTDB.rda |only chem16S-1.0.0/chem16S/inst/extdata/DADA2 |only chem16S-1.0.0/chem16S/inst/extdata/GTDB |only chem16S-1.0.0/chem16S/inst/extdata/RDP-GTDB |only chem16S-1.0.0/chem16S/inst/extdata/RefSeq |only chem16S-1.0.0/chem16S/inst/tinytest/test-calc_metrics.R |only chem16S-1.0.0/chem16S/man/calc_metrics.Rd |only chem16S-1.1.0/chem16S/DESCRIPTION | 12 chem16S-1.1.0/chem16S/MD5 | 135 ++++----- chem16S-1.1.0/chem16S/NAMESPACE | 5 chem16S-1.1.0/chem16S/R/chemlab.R | 40 -- chem16S-1.1.0/chem16S/R/get_metadata.R | 2 chem16S-1.1.0/chem16S/R/get_metrics.R | 14 - chem16S-1.1.0/chem16S/R/map_taxa.R | 15 - chem16S-1.1.0/chem16S/R/phyloseq_integration.R | 39 +- chem16S-1.1.0/chem16S/R/plot_metrics.R | 55 +--- chem16S-1.1.0/chem16S/README.md | 55 ++-- chem16S-1.1.0/chem16S/build/partial.rdb |binary chem16S-1.1.0/chem16S/build/vignette.rds |binary chem16S-1.1.0/chem16S/data/mouse.GTDB_214.rda |only chem16S-1.1.0/chem16S/inst/CITATION |only chem16S-1.1.0/chem16S/inst/NEWS | 17 + chem16S-1.1.0/chem16S/inst/RefDB |only chem16S-1.1.0/chem16S/inst/doc/metrics.R | 16 - chem16S-1.1.0/chem16S/inst/doc/metrics.Rmd | 23 - chem16S-1.1.0/chem16S/inst/doc/metrics.html | 38 +- chem16S-1.1.0/chem16S/inst/doc/phyloseq.R | 32 +- chem16S-1.1.0/chem16S/inst/doc/phyloseq.Rmd | 42 +-- chem16S-1.1.0/chem16S/inst/doc/phyloseq.html | 73 ++--- chem16S-1.1.0/chem16S/inst/doc/plotting.R | 121 ++++++++ chem16S-1.1.0/chem16S/inst/doc/plotting.Rmd | 112 ++++++-- chem16S-1.1.0/chem16S/inst/doc/plotting.html | 137 +++++++--- chem16S-1.1.0/chem16S/inst/extdata/DADA2-GTDB_214 |only chem16S-1.1.0/chem16S/inst/extdata/RDP-GTDB_207 |only chem16S-1.1.0/chem16S/inst/images/plot_metrics.png |binary chem16S-1.1.0/chem16S/inst/tinytest/test-chemlab.R |only chem16S-1.1.0/chem16S/inst/tinytest/test-get_metadata.R | 4 chem16S-1.1.0/chem16S/inst/tinytest/test-get_metrics.R | 21 + chem16S-1.1.0/chem16S/inst/tinytest/test-map_taxa.R | 12 chem16S-1.1.0/chem16S/inst/tinytest/test_phyloseq_integration.R | 6 chem16S-1.1.0/chem16S/man/chem16S-data.Rd | 4 chem16S-1.1.0/chem16S/man/chem16S-package.Rd | 34 +- chem16S-1.1.0/chem16S/man/chemlab.Rd | 6 chem16S-1.1.0/chem16S/man/get_metadata.Rd | 4 chem16S-1.1.0/chem16S/man/get_metrics.Rd | 26 - chem16S-1.1.0/chem16S/man/map_taxa.Rd | 32 +- chem16S-1.1.0/chem16S/man/phyloseq_integration.Rd | 34 +- chem16S-1.1.0/chem16S/man/plot_metrics.Rd | 61 ++-- chem16S-1.1.0/chem16S/vignettes/chem16S.bib | 22 + chem16S-1.1.0/chem16S/vignettes/metrics.Rmd | 23 - chem16S-1.1.0/chem16S/vignettes/phyloseq.Rmd | 42 +-- chem16S-1.1.0/chem16S/vignettes/plotting.Rmd | 112 ++++++-- 53 files changed, 879 insertions(+), 547 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and
Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>.
'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 4.2.3 dated 2024-05-24 and 4.3.0 dated 2024-07-01
DESCRIPTION | 6 MD5 | 48 +++--- NAMESPACE | 1 NEWS | 13 + R/biblioNetwork.R | 2 R/cocMatrix.R | 2 R/collabByRegionPlot.R | 2 R/csvOA2df.R | 87 ++++++++++- R/mergeDbSources.R | 108 ++++++++------ R/networkPlot.R | 2 R/networkStat.R | 2 R/rpys.R | 16 +- R/zzz.R | 8 + build/partial.rdb |binary inst/biblioshiny/helpContent.R | 315 ++++++++++++++++++++++++++++++++++++++++- inst/biblioshiny/libraries.R | 8 - inst/biblioshiny/server.R | 125 +++++++++++++++- inst/biblioshiny/ui.R | 99 ++++++++++++ inst/biblioshiny/utils.R | 47 +++++- man/biblioNetwork.Rd | 2 man/cocMatrix.Rd | 2 man/collabByRegionPlot.Rd | 2 man/mergeDbSources.Rd | 10 - man/networkPlot.Rd | 2 man/networkStat.Rd | 2 25 files changed, 798 insertions(+), 113 deletions(-)
Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse
set of pipelining operators ('PipeOps') that can be composed into graphs.
Operations exist for data preprocessing, model fitting, and ensemble
learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can
therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre],
Florian Pfisterer [aut] ,
Lennart Schneider [aut] ,
Bernd Bischl [aut] ,
Michel Lang [aut] ,
Sebastian Fischer [aut] ,
Susanne Dandl [aut]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr3pipelines versions 0.5.2 dated 2024-04-23 and 0.6.0 dated 2024-07-01
DESCRIPTION | 14 - MD5 | 329 ++++++++++++++--------------- NAMESPACE | 11 NEWS.md | 6 R/Graph.R | 13 - R/GraphLearner.R | 217 ++++++++++++++++++- R/LearnerAvg.R | 8 R/NO_OP.R | 2 R/PipeOp.R | 34 ++ R/PipeOpBoxCox.R | 2 R/PipeOpBranch.R | 2 R/PipeOpChunk.R | 2 R/PipeOpClassBalancing.R | 4 R/PipeOpClassWeights.R | 2 R/PipeOpClassifAvg.R | 2 R/PipeOpColApply.R | 4 R/PipeOpColRoles.R | 2 R/PipeOpCollapseFactors.R | 2 R/PipeOpCopy.R | 2 R/PipeOpDateFeatures.R | 2 R/PipeOpEncode.R | 2 R/PipeOpEncodeImpact.R | 2 R/PipeOpEncodeLmer.R | 2 R/PipeOpEnsemble.R | 2 R/PipeOpFeatureUnion.R | 2 R/PipeOpFilter.R | 2 R/PipeOpFixFactors.R | 2 R/PipeOpHistBin.R | 2 R/PipeOpICA.R | 2 R/PipeOpImpute.R | 16 - R/PipeOpImputeConstant.R | 2 R/PipeOpImputeHist.R | 2 R/PipeOpImputeLearner.R | 27 ++ R/PipeOpImputeMean.R | 2 R/PipeOpImputeMedian.R | 2 R/PipeOpImputeMode.R | 2 R/PipeOpImputeOOR.R | 2 R/PipeOpImputeSample.R | 2 R/PipeOpKernelPCA.R | 2 R/PipeOpLearner.R | 86 +++++++ R/PipeOpLearnerCV.R | 34 ++ R/PipeOpMissingIndicators.R | 2 R/PipeOpModelMatrix.R | 2 R/PipeOpMultiplicity.R | 6 R/PipeOpMutate.R | 2 R/PipeOpNMF.R | 2 R/PipeOpNOP.R | 2 R/PipeOpOVR.R | 4 R/PipeOpPCA.R | 2 R/PipeOpProxy.R | 2 R/PipeOpQuantileBin.R | 2 R/PipeOpRandomProjection.R | 2 R/PipeOpRandomResponse.R | 2 R/PipeOpRegrAvg.R | 2 R/PipeOpRemoveConstants.R | 2 R/PipeOpRenameColumns.R | 2 R/PipeOpScale.R | 2 R/PipeOpScaleMaxAbs.R | 2 R/PipeOpScaleRange.R | 9 R/PipeOpSelect.R | 2 R/PipeOpSmote.R | 2 R/PipeOpSpatialSign.R | 2 R/PipeOpSubsample.R | 4 R/PipeOpTaskPreproc.R | 23 +- R/PipeOpTextVectorizer.R | 2 R/PipeOpThreshold.R | 2 R/PipeOpTrafo.R | 10 R/PipeOpTuneThreshold.R | 6 R/PipeOpUnbranch.R | 2 R/PipeOpVtreat.R | 2 R/PipeOpYeoJohnson.R | 2 R/mlr_graphs.R | 2 R/mlr_pipeops.R | 2 R/multiplicity.R | 18 + R/pipeline_robustify.R | 2 R/utils.R | 19 + R/zzz.R | 3 README.md | 51 ++-- inst/doc/extending.html | 30 -- inst/testthat/helper_functions.R | 41 +++ man/Graph.Rd | 14 - man/NO_OP.Rd | 2 man/PipeOp.Rd | 26 +- man/PipeOpEnsemble.Rd | 2 man/PipeOpImpute.Rd | 12 - man/PipeOpTargetTrafo.Rd | 2 man/PipeOpTaskPreproc.Rd | 10 man/PipeOpTaskPreprocSimple.Rd | 6 man/mlr3pipelines-package.Rd | 6 man/mlr_graphs.Rd | 2 man/mlr_graphs_robustify.Rd | 2 man/mlr_learners_avg.Rd | 6 man/mlr_learners_graph.Rd | 27 ++ man/mlr_pipeops.Rd | 2 man/mlr_pipeops_boxcox.Rd | 2 man/mlr_pipeops_branch.Rd | 2 man/mlr_pipeops_chunk.Rd | 2 man/mlr_pipeops_classbalancing.Rd | 4 man/mlr_pipeops_classifavg.Rd | 2 man/mlr_pipeops_classweights.Rd | 2 man/mlr_pipeops_colapply.Rd | 4 man/mlr_pipeops_collapsefactors.Rd | 2 man/mlr_pipeops_colroles.Rd | 2 man/mlr_pipeops_copy.Rd | 2 man/mlr_pipeops_datefeatures.Rd | 2 man/mlr_pipeops_encode.Rd | 2 man/mlr_pipeops_encodeimpact.Rd | 2 man/mlr_pipeops_encodelmer.Rd | 2 man/mlr_pipeops_featureunion.Rd | 2 man/mlr_pipeops_filter.Rd | 2 man/mlr_pipeops_fixfactors.Rd | 2 man/mlr_pipeops_histbin.Rd | 2 man/mlr_pipeops_ica.Rd | 2 man/mlr_pipeops_imputeconstant.Rd | 2 man/mlr_pipeops_imputehist.Rd | 2 man/mlr_pipeops_imputelearner.Rd | 4 man/mlr_pipeops_imputemean.Rd | 2 man/mlr_pipeops_imputemedian.Rd | 2 man/mlr_pipeops_imputemode.Rd | 2 man/mlr_pipeops_imputeoor.Rd | 2 man/mlr_pipeops_imputesample.Rd | 2 man/mlr_pipeops_kernelpca.Rd | 2 man/mlr_pipeops_learner.Rd | 17 + man/mlr_pipeops_learner_cv.Rd | 8 man/mlr_pipeops_missind.Rd | 2 man/mlr_pipeops_modelmatrix.Rd | 2 man/mlr_pipeops_multiplicityexply.Rd | 2 man/mlr_pipeops_multiplicityimply.Rd | 2 man/mlr_pipeops_mutate.Rd | 2 man/mlr_pipeops_nmf.Rd | 2 man/mlr_pipeops_nop.Rd | 2 man/mlr_pipeops_ovrsplit.Rd | 2 man/mlr_pipeops_ovrunite.Rd | 2 man/mlr_pipeops_pca.Rd | 2 man/mlr_pipeops_proxy.Rd | 2 man/mlr_pipeops_quantilebin.Rd | 2 man/mlr_pipeops_randomprojection.Rd | 2 man/mlr_pipeops_randomresponse.Rd | 2 man/mlr_pipeops_regravg.Rd | 2 man/mlr_pipeops_removeconstants.Rd | 2 man/mlr_pipeops_renamecolumns.Rd | 2 man/mlr_pipeops_replicate.Rd | 2 man/mlr_pipeops_scale.Rd | 2 man/mlr_pipeops_scalemaxabs.Rd | 2 man/mlr_pipeops_scalerange.Rd | 2 man/mlr_pipeops_select.Rd | 2 man/mlr_pipeops_smote.Rd | 2 man/mlr_pipeops_spatialsign.Rd | 2 man/mlr_pipeops_subsample.Rd | 4 man/mlr_pipeops_targetinvert.Rd | 2 man/mlr_pipeops_targetmutate.Rd | 2 man/mlr_pipeops_targettrafoscalerange.Rd | 2 man/mlr_pipeops_textvectorizer.Rd | 2 man/mlr_pipeops_threshold.Rd | 2 man/mlr_pipeops_tunethreshold.Rd | 6 man/mlr_pipeops_unbranch.Rd | 2 man/mlr_pipeops_updatetarget.Rd | 2 man/mlr_pipeops_vtreat.Rd | 2 man/mlr_pipeops_yeojohnson.Rd | 2 man/set_validate.GraphLearner.Rd |only tests/testthat/test_GraphLearner.R | 144 ++++++++++++ tests/testthat/test_PipeOp.R | 15 + tests/testthat/test_pipeop_impute.R | 12 + tests/testthat/test_pipeop_imputelearner.R | 14 + tests/testthat/test_pipeop_learner.R | 115 ++++++++++ tests/testthat/test_pipeop_learnercv.R | 85 +++++++ 166 files changed, 1345 insertions(+), 455 deletions(-)
Title: Hospital Data Analysis Workflow Tools
Description: Hospital data analysis workflow tools, modeling, and automations. This library
provides many useful tools to review common administrative hospital data. Some
of these include average length of stay, readmission rates, average net pay
amounts by service lines just to name a few. The aim is to provide a simple
and consistent verb framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR versions 0.2.1 dated 2023-04-06 and 0.2.2 dated 2024-07-01
healthyR-0.2.1/healthyR/R/data_files.R |only healthyR-0.2.1/healthyR/R/data_tbl_functions.R |only healthyR-0.2.1/healthyR/R/diverging-bar-plt.R |only healthyR-0.2.1/healthyR/R/diverging-lollipop-plt.R |only healthyR-0.2.1/healthyR/R/gartner_magic_chart.R |only healthyR-0.2.1/healthyR/R/los_ra_index_plt.R |only healthyR-0.2.1/healthyR/R/optimal_bin_size.R |only healthyR-0.2.1/healthyR/R/service-line-vec.R |only healthyR-0.2.1/healthyR/R/sql_string_split.R |only healthyR-0.2.1/healthyR/R/time_series_plots.R |only healthyR-0.2.1/healthyR/R/ts-census-los-tbl.R |only healthyR-0.2.1/healthyR/R/ts_median_excess_plt.R |only healthyR-0.2.1/healthyR/R/ts_signature_tbl.R |only healthyR-0.2.1/healthyR/R/utils.R |only healthyR-0.2.1/healthyR/man/figures/test7.png |only healthyR-0.2.2/healthyR/DESCRIPTION | 21 - healthyR-0.2.2/healthyR/MD5 | 103 ++++---- healthyR-0.2.2/healthyR/NEWS.md | 14 + healthyR-0.2.2/healthyR/R/data-files.R |only healthyR-0.2.2/healthyR/R/data-tbl-category-counts.R |only healthyR-0.2.2/healthyR/R/data-tbl-los-ra-index.R |only healthyR-0.2.2/healthyR/R/data-tbl-name-item-list.R |only healthyR-0.2.2/healthyR/R/data-tbl-top-n-counts.R |only healthyR-0.2.2/healthyR/R/data-ts-census-los-tbl.R |only healthyR-0.2.2/healthyR/R/data-ts-signature-tbl.R |only healthyR-0.2.2/healthyR/R/pallette-color-blind.R | 6 healthyR-0.2.2/healthyR/R/plt-alos.R |only healthyR-0.2.2/healthyR/R/plt-diverging-bar.R |only healthyR-0.2.2/healthyR/R/plt-diverging-lollipop.R |only healthyR-0.2.2/healthyR/R/plt-gartner-magic-chart.R |only healthyR-0.2.2/healthyR/R/plt-los-ra-index.R |only healthyR-0.2.2/healthyR/R/plt-readmit-rate.R |only healthyR-0.2.2/healthyR/R/plt-ts-median-excess.R |only healthyR-0.2.2/healthyR/R/plt-ts.R |only healthyR-0.2.2/healthyR/R/utils-optimal-bin-size.R |only healthyR-0.2.2/healthyR/R/utils-save-to-excel.R |only healthyR-0.2.2/healthyR/R/utils-sql-string-split.R |only healthyR-0.2.2/healthyR/R/vec-service-line.R |only healthyR-0.2.2/healthyR/README.md | 12 - healthyR-0.2.2/healthyR/build/vignette.rds |binary healthyR-0.2.2/healthyR/inst/doc/getting-started.R | 2 healthyR-0.2.2/healthyR/inst/doc/getting-started.html | 120 +++++----- healthyR-0.2.2/healthyR/man/category_counts_tbl.Rd | 11 healthyR-0.2.2/healthyR/man/color_blind.Rd | 6 healthyR-0.2.2/healthyR/man/diverging_bar_plt.Rd | 13 + healthyR-0.2.2/healthyR/man/diverging_lollipop_plt.Rd | 13 + healthyR-0.2.2/healthyR/man/dx_cc_mapping.Rd | 17 - healthyR-0.2.2/healthyR/man/figures/README-example-1.png |binary healthyR-0.2.2/healthyR/man/figures/README-gartner_chart-1.png |binary healthyR-0.2.2/healthyR/man/figures/logo.png |only healthyR-0.2.2/healthyR/man/gartner_magic_chart_plt.Rd | 95 ++++--- healthyR-0.2.2/healthyR/man/hr_scale_color_colorblind.Rd | 6 healthyR-0.2.2/healthyR/man/hr_scale_fill_colorblind.Rd | 6 healthyR-0.2.2/healthyR/man/los_ra_index_plt.Rd | 13 + healthyR-0.2.2/healthyR/man/los_ra_index_summary_tbl.Rd | 11 healthyR-0.2.2/healthyR/man/named_item_list.Rd | 11 healthyR-0.2.2/healthyR/man/opt_bin.Rd | 22 + healthyR-0.2.2/healthyR/man/px_cc_mapping.Rd | 17 - healthyR-0.2.2/healthyR/man/save_to_excel.Rd | 10 healthyR-0.2.2/healthyR/man/service_line_vec.Rd | 4 healthyR-0.2.2/healthyR/man/sql_left.Rd | 13 + healthyR-0.2.2/healthyR/man/sql_mid.Rd | 13 + healthyR-0.2.2/healthyR/man/sql_right.Rd | 13 + healthyR-0.2.2/healthyR/man/top_n_tbl.Rd | 11 healthyR-0.2.2/healthyR/man/ts_alos_plt.Rd | 13 + healthyR-0.2.2/healthyR/man/ts_census_los_daily_tbl.Rd | 11 healthyR-0.2.2/healthyR/man/ts_median_excess_plt.Rd | 13 + healthyR-0.2.2/healthyR/man/ts_plt.Rd | 12 - healthyR-0.2.2/healthyR/man/ts_readmit_rate_plt.Rd | 13 + healthyR-0.2.2/healthyR/man/ts_signature_tbl.Rd | 14 + 70 files changed, 453 insertions(+), 206 deletions(-)
Title: k-Prototypes Clustering for Mixed Variable-Type Data
Description: Functions to perform k-prototypes partitioning clustering for
mixed variable-type data according to Z.Huang (1998): Extensions to the k-Means
Algorithm for Clustering Large Data Sets with Categorical Variables, Data Mining
and Knowledge Discovery 2, 283-304.
Author: Gero Szepannek [aut, cre], Rabea Aschenbruck [aut]
Maintainer: Gero Szepannek <gero.szepannek@web.de>
Diff between clustMixType versions 0.3-14 dated 2023-12-10 and 0.4-2 dated 2024-07-01
clustMixType-0.3-14/clustMixType/man/kproto_gower.Rd |only clustMixType-0.4-2/clustMixType/DESCRIPTION | 8 clustMixType-0.4-2/clustMixType/MD5 | 25 clustMixType-0.4-2/clustMixType/NAMESPACE | 1 clustMixType-0.4-2/clustMixType/NEWS | 21 clustMixType-0.4-2/clustMixType/R/clustervalidation.R | 811 +++++---- clustMixType-0.4-2/clustMixType/R/kprototypes.R | 139 - clustMixType-0.4-2/clustMixType/R/kprototypes_gower.R | 145 - clustMixType-0.4-2/clustMixType/build/partial.rdb |binary clustMixType-0.4-2/clustMixType/man/kproto.Rd | 82 clustMixType-0.4-2/clustMixType/man/plot.kproto.Rd | 98 - clustMixType-0.4-2/clustMixType/man/validation_kproto.Rd | 14 clustMixType-0.4-2/clustMixType/tests/testthat/test_basics.R | 7 clustMixType-0.4-2/clustMixType/tests/testthat/test_clustervalidation.R | 858 +++++++--- 14 files changed, 1334 insertions(+), 875 deletions(-)
Title: Visualizations for 'mlr3'
Description: Visualization package of the 'mlr3' ecosystem. It features
plots for mlr3 objects such as tasks, learners, predictions, benchmark
results, tuning instances and filters via the 'autoplot()' generic of
'ggplot2'. The package draws plots with the 'viridis' color palette
and applies the minimal theme. Visualizations include barplots,
boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [aut] ,
Patrick Schratz [aut] ,
Raphael Sonabend [aut] ,
Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Damir Pulatov [ctb],
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3viz versions 0.8.0 dated 2024-03-05 and 0.9.0 dated 2024-07-01
mlr3viz-0.8.0/mlr3viz/R/OptimInstanceSingleCrit.R |only mlr3viz-0.8.0/mlr3viz/R/TuningInstanceSingleCrit.R |only mlr3viz-0.8.0/mlr3viz/man/autoplot.OptimInstanceSingleCrit.Rd |only mlr3viz-0.8.0/mlr3viz/man/autoplot.TuningInstanceSingleCrit.Rd |only mlr3viz-0.8.0/mlr3viz/tests/testthat/_snaps/PredictionClust/predictionclust-scatter.svg |only mlr3viz-0.8.0/mlr3viz/tests/testthat/_snaps/TaskClassif/taskclassif-pairs.svg |only mlr3viz-0.8.0/mlr3viz/tests/testthat/_snaps/TaskClust |only mlr3viz-0.8.0/mlr3viz/tests/testthat/_snaps/TaskRegr/taskregr-pairs.svg |only mlr3viz-0.9.0/mlr3viz/DESCRIPTION | 56 +++++----- mlr3viz-0.9.0/mlr3viz/MD5 | 34 +++--- mlr3viz-0.9.0/mlr3viz/NAMESPACE | 7 - mlr3viz-0.9.0/mlr3viz/NEWS.md | 6 + mlr3viz-0.9.0/mlr3viz/R/EnsembleFSResult.R |only mlr3viz-0.9.0/mlr3viz/R/OptimInstanceBatchSingleCrit.R |only mlr3viz-0.9.0/mlr3viz/R/TuningInstanceBatchSingleCrit.R |only mlr3viz-0.9.0/mlr3viz/inst/WORDLIST | 4 mlr3viz-0.9.0/mlr3viz/man/autoplot.EnsembleFSResult.Rd |only mlr3viz-0.9.0/mlr3viz/man/autoplot.OptimInstanceBatchSingleCrit.Rd |only mlr3viz-0.9.0/mlr3viz/man/autoplot.TuningInstanceBatchSingleCrit.Rd |only mlr3viz-0.9.0/mlr3viz/man/mlr3viz-package.Rd | 1 mlr3viz-0.9.0/mlr3viz/tests/testthat/_snaps/EnsembleFSResult |only mlr3viz-0.9.0/mlr3viz/tests/testthat/test_EnsembleFSResult.R |only mlr3viz-0.9.0/mlr3viz/tests/testthat/test_OptimInstanceSingleCrit.R | 8 - mlr3viz-0.9.0/mlr3viz/tests/testthat/test_TuningInstanceSingleCrit.R | 8 - 24 files changed, 70 insertions(+), 54 deletions(-)
Title: Triangle Meshes and Related Geometry Tools
Description: Generate planar and spherical triangle meshes,
compute finite element calculations for 1- and 2-dimensional flat and curved
manifolds with associated basis function spaces, methods for lines and
polygons, and transparent handling of coordinate reference systems and
coordinate transformation, including 'sf' and 'sp' geometries. The core
'fmesher' library code was originally part of the 'INLA' package, and
implements parts of "Triangulations and Applications" by
Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.
Author: Finn Lindgren [aut, cre, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb] ,
Fabian E. Bachl [ctb]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between fmesher versions 0.1.6 dated 2024-06-14 and 0.1.7 dated 2024-07-01
DESCRIPTION | 8 - MD5 | 30 ++-- NAMESPACE | 2 NEWS.md | 6 R/RcppExports.R | 19 +- R/bbox.R | 30 ++-- R/manifold.R | 8 + R/mesh.R | 163 +++++------------------ R/plot.R | 10 - R/print.R | 13 + build/partial.rdb |binary build/vignette.rds |binary man/fm_subdivide.Rd |only man/fmesher_subdivide.Rd | 18 +- src/Rcpp_interface.cc | 276 +++++++++++++++++++++++++++------------- tests/testthat/test-rcdt_2d.R | 3 tests/testthat/test-subdivide.R |only 17 files changed, 319 insertions(+), 267 deletions(-)
Title: Ecological Inference Applying Entropy
Description: Implements two estimations related to the foundations of info metrics applied to ecological inference. These methodologies assess the lack of disaggregated data and provide an approach to obtaining disaggregated territorial-level data. For more details, see the following references: Fernández-Vázquez, E., Díaz-Dapena, A., Rubiera-Morollón, F. et al. (2020) "Spatial Disaggregation of Social Indicators: An Info-Metrics Approach." <doi:10.1007/s11205-020-02455-z>. Díaz-Dapena, A., Fernández-Vázquez, E., Rubiera-Morollón, F., & Vinuela, A. (2021) "Mapping poverty at the local level in Europe: A consistent spatial disaggregation of the AROPE indicator for France, Spain, Portugal and the United Kingdom." <doi:10.1111/rsp3.12379>.
Author: Alberto Diaz-Dapena [aut, cph],
Silvia Maria Franco Anaya [aut, cre, cph],
Esteban Fernandez-Vazquez [aut, cph]
Maintainer: Silvia Maria Franco Anaya <sfrana@unileon.es>
Diff between EIEntropy versions 0.0.1 dated 2024-07-01 and 0.0.1.1 dated 2024-07-01
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Identifying Important Areas from Animal Tracking Data
Description: Functions for preparing and analyzing animal tracking data,
with the intention of identifying areas which are potentially important at
the population level and therefore of conservation interest. Areas identified
using this package may be checked against global or regionally-defined criteria,
such as those set by the Key Biodiversity Area program. The method
published herein is described in full in Beal et al. 2021 <doi:10.1111/2041-210X.13713>.
Author: Martin Beal [aut, cre] ,
Steffen Oppel [aut] ,
Maria Dias [aut] ,
Mark Miller [ctb],
Phillip Taylor [ctb],
Virginia Morera-Pujol [ctb] ,
Elizabeth Pearmain [ctb] ,
Jonathan Handley [ctb] ,
Ben Lascelles [ctb]
Maintainer: Martin Beal <martinbeal88@gmail.com>
Diff between track2KBA versions 1.1.1 dated 2023-09-27 and 1.1.2 dated 2024-07-01
DESCRIPTION | 10 MD5 | 8 R/estSpaceUse.r | 418 +++++++++++++++++++-------------------- inst/doc/track2kba_workflow.html | 2 man/estSpaceUse.Rd | 6 5 files changed, 222 insertions(+), 222 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: High-performance parallel code execution and distributed computing.
Designed for simplicity, a 'mirai' evaluates an R expression asynchronously,
on local or network resources, resolving automatically upon completion.
Modern networking and concurrency built on 'nanonext' and 'NNG' (Nanomsg
Next Gen) ensures reliable and efficient scheduling, over fast inter-process
communications or TCP/IP secured by TLS.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 1.1.0 dated 2024-06-06 and 1.1.1 dated 2024-07-01
DESCRIPTION | 12 +- MD5 | 78 ++++++++-------- NEWS.md | 8 + R/daemon.R | 12 +- R/daemons.R | 102 +++++++++++---------- R/dispatcher.R | 4 R/launchers.R | 43 ++++++--- R/map.R | 2 R/mirai-package.R | 7 - R/mirai.R | 14 +- README.md | 26 ++--- build/vignette.rds |binary inst/doc/databases.Rmd | 26 +---- inst/doc/databases.html | 26 ++--- inst/doc/mirai.Rmd | 196 ++++++++++++++++------------------------- inst/doc/mirai.html | 204 +++++++++++++++++++++---------------------- inst/doc/parallel.Rmd | 26 +---- inst/doc/parallel.html | 26 ++--- inst/doc/plumber.Rmd | 32 +++--- inst/doc/plumber.html | 32 +++--- inst/doc/promises.Rmd | 11 -- inst/doc/promises.html | 11 -- inst/doc/torch.Rmd | 57 +++++------- inst/doc/torch.html | 59 ++++++------ man/dispatcher.Rd | 4 man/dot-daemon.Rd | 2 man/figures/logo.png |binary man/mirai-package.Rd | 2 man/remote_config.Rd | 25 ++++- man/serialization.Rd | 46 +++++---- tests/tests.R | 19 ++-- vignettes/databases.Rmd | 26 +---- vignettes/databases.Rmd.orig | 8 + vignettes/mirai.Rmd | 196 ++++++++++++++++------------------------- vignettes/mirai.Rmd.orig | 45 +++++++-- vignettes/parallel.Rmd | 26 +---- vignettes/plumber.Rmd | 32 +++--- vignettes/promises.Rmd | 11 -- vignettes/torch.Rmd | 57 +++++------- vignettes/torch.Rmd.orig | 11 +- 40 files changed, 718 insertions(+), 806 deletions(-)
Title: Colour Schemes for Scientific Data Visualization
Description: Color schemes ready for each type of data (qualitative,
diverging or sequential), with colors that are distinct for all
people, including color-blind readers. This package provides an
implementation of Paul Tol (2018) and Fabio Crameri (2018)
<doi:10.5194/gmd-11-2541-2018> color schemes for use with 'graphics'
or 'ggplot2'. It provides tools to simulate color-blindness and to
test how well the colors of any palette are identifiable. Several
scientific thematic schemes (geologic timescale, land cover, FAO
soils, etc.) are also implemented.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Vincent Arel-Bundock [ctb] ,
Ulrik Stervbo [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between khroma versions 1.12.0 dated 2024-01-08 and 1.13.0 dated 2024-07-01
khroma-1.12.0/khroma/R/anomalize.R |only khroma-1.12.0/khroma/R/convert.R |only khroma-1.12.0/khroma/R/ggplot2.R |only khroma-1.12.0/khroma/R/ramp.R |only khroma-1.12.0/khroma/R/scale_colour_other.R |only khroma-1.12.0/khroma/inst/examples/ex-anomalize.R |only khroma-1.12.0/khroma/inst/examples/ex-ramp.R |only khroma-1.12.0/khroma/inst/tinytest/test_convert.R |only khroma-1.12.0/khroma/inst/tinytest/test_ramp.R |only khroma-1.12.0/khroma/man/convert.Rd |only khroma-1.12.0/khroma/man/ramp.Rd |only khroma-1.12.0/khroma/man/scale_crameri_cyclic.Rd |only khroma-1.12.0/khroma/man/scale_crameri_diverging.Rd |only khroma-1.12.0/khroma/man/scale_crameri_mutlisequential.Rd |only khroma-1.12.0/khroma/man/scale_crameri_sequential.Rd |only khroma-1.12.0/khroma/man/scale_logical_discrete.Rd |only khroma-1.12.0/khroma/man/scale_tol_discrete.Rd |only khroma-1.12.0/khroma/man/scale_tol_diverging.Rd |only khroma-1.12.0/khroma/man/scale_tol_sequential.Rd |only khroma-1.13.0/khroma/DESCRIPTION | 21 khroma-1.13.0/khroma/MD5 | 221 ++++---- khroma-1.13.0/khroma/NAMESPACE | 10 khroma-1.13.0/khroma/NEWS.md | 16 khroma-1.13.0/khroma/R/change.R |only khroma-1.13.0/khroma/R/color.R | 92 --- khroma-1.13.0/khroma/R/info.R | 206 ++++++++ khroma-1.13.0/khroma/R/khroma-defunct.R |only khroma-1.13.0/khroma/R/khroma-deprecated.R |only khroma-1.13.0/khroma/R/khroma-internal.R | 15 khroma-1.13.0/khroma/R/khroma-package.R | 2 khroma-1.13.0/khroma/R/palettes.R |only khroma-1.13.0/khroma/R/plot.R | 5 khroma-1.13.0/khroma/R/plot_map.R | 5 khroma-1.13.0/khroma/R/plot_scheme.R | 5 khroma-1.13.0/khroma/R/plot_scheme_colorblind.R | 7 khroma-1.13.0/khroma/R/plot_tiles.R | 5 khroma-1.13.0/khroma/R/scale_colour_crameri.R | 325 ++----------- khroma-1.13.0/khroma/R/scale_colour_picker.R |only khroma-1.13.0/khroma/R/scale_colour_tol.R | 185 +------ khroma-1.13.0/khroma/README.md | 48 - 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khroma-1.13.0/khroma/man/scale_crameri_vikO.Rd | 32 - khroma-1.13.0/khroma/man/scale_land.Rd | 1 khroma-1.13.0/khroma/man/scale_okabeito_discrete.Rd | 10 khroma-1.13.0/khroma/man/scale_picker.Rd | 10 khroma-1.13.0/khroma/man/scale_soil.Rd | 1 khroma-1.13.0/khroma/man/scale_stratigraphy.Rd | 1 khroma-1.13.0/khroma/man/scale_tol_BuRd.Rd | 11 khroma-1.13.0/khroma/man/scale_tol_PRGn.Rd | 11 khroma-1.13.0/khroma/man/scale_tol_YlOrBr.Rd | 15 khroma-1.13.0/khroma/man/scale_tol_bright.Rd | 18 khroma-1.13.0/khroma/man/scale_tol_dark.Rd | 18 khroma-1.13.0/khroma/man/scale_tol_discreterainbow.Rd | 16 khroma-1.13.0/khroma/man/scale_tol_highcontrast.Rd | 18 khroma-1.13.0/khroma/man/scale_tol_incandescent.Rd | 15 khroma-1.13.0/khroma/man/scale_tol_iridescent.Rd | 15 khroma-1.13.0/khroma/man/scale_tol_light.Rd | 18 khroma-1.13.0/khroma/man/scale_tol_mediumcontrast.Rd | 18 khroma-1.13.0/khroma/man/scale_tol_muted.Rd | 21 khroma-1.13.0/khroma/man/scale_tol_nightfall.Rd | 11 khroma-1.13.0/khroma/man/scale_tol_pale.Rd | 18 khroma-1.13.0/khroma/man/scale_tol_smoothrainbow.Rd | 15 khroma-1.13.0/khroma/man/scale_tol_sunset.Rd | 11 khroma-1.13.0/khroma/man/scale_tol_vibrant.Rd | 18 khroma-1.13.0/khroma/man/science.Rd |only khroma-1.13.0/khroma/man/tol.Rd |only 132 files changed, 1879 insertions(+), 1231 deletions(-)
Title: ADaM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Analysis Data Model (ADaM) datasets constructed using the
Study Data Tabulation Model (SDTM) datasets contained in the 'pharmaversesdtm' package and
the template scripts from the 'admiral' family of packages. ADaM dataset specifications are
described in: CDISC Analysis Data Model Team
(2021) <https://www.cdisc.org/system/files/members/standard/foundational/ADaMIG_v1.3.pdf>.
Author: Edoardo Mancini [aut, cre],
Kangjie Zhang [aut],
Stefan Bundfuss [aut],
Gayatri G [aut],
Daphne Grassely [aut],
Zelos Zhu [aut],
Sadchla Mascary [aut]
Maintainer: Edoardo Mancini <edoardo.mancini@roche.com>
Diff between pharmaverseadam versions 0.2.0 dated 2024-01-08 and 1.0.0 dated 2024-07-01
DESCRIPTION | 16 ++-- MD5 | 144 ++++++++++++++++++++--------------------- NEWS.md | 10 ++ R/adae.R | 5 - R/adbcva_ophtha.R | 4 - R/adce_vaccine.R | 4 - R/adcm.R | 4 - R/adeg.R | 4 - R/adex.R | 4 - R/adface_vaccine.R | 4 - R/adis_vaccine.R | 4 - R/adlb.R | 4 - R/adlbhy.R | 4 - R/admh.R | 4 - R/adoe_ophtha.R | 4 - R/adpc.R | 7 + R/adpp.R | 15 ++-- R/adppk.R | 12 +-- R/adrs_onco.R | 11 +-- R/adsl.R | 4 - R/adsl_vaccine.R | 4 - R/adtr_onco.R | 11 +-- R/adtte_onco.R | 6 - R/advfq_ophtha.R | 4 - R/advs.R | 8 -- README.md | 24 ++++-- data/adae.rda |binary data/adbcva_ophtha.rda |binary data/adce_vaccine.rda |binary data/adcm.rda |binary data/adeg.rda |binary data/adex.rda |binary data/adface_vaccine.rda |binary data/adis_vaccine.rda |binary data/adlb.rda |binary data/adlbhy.rda |binary data/admh.rda |binary data/adoe_ophtha.rda |binary data/adpc.rda |binary data/adpp.rda |binary data/adppk.rda |binary data/adrs_onco.rda |binary data/adsl.rda |binary data/adsl_vaccine.rda |binary data/adtr_onco.rda |binary data/adtte_onco.rda |binary data/advfq_ophtha.rda |binary data/advs.rda |binary inst/WORDLIST | 4 + inst/extdata/adams-specs.xlsx |binary man/adae.Rd | 4 - man/adbcva_ophtha.Rd | 4 - man/adce_vaccine.Rd | 4 - man/adcm.Rd | 4 - man/adeg.Rd | 4 - man/adex.Rd | 4 - man/adface_vaccine.Rd | 4 - man/adis_vaccine.Rd | 4 - man/adlb.Rd | 4 - man/adlbhy.Rd | 4 - man/admh.Rd | 4 - man/adoe_ophtha.Rd | 4 - man/adpc.Rd | 7 + man/adpp.Rd | 15 ++-- man/adppk.Rd | 12 +-- man/adrs_onco.Rd | 11 +-- man/adsl.Rd | 4 - man/adsl_vaccine.Rd | 4 - man/adtr_onco.Rd | 11 +-- man/adtte_onco.Rd | 6 - man/advfq_ophtha.Rd | 4 - man/advs.Rd | 8 -- man/pharmaverseadam-package.Rd | 3 73 files changed, 252 insertions(+), 210 deletions(-)
More information about pharmaverseadam at CRAN
Permanent link
Title: 'MATLAB' Emulation Package
Description: Emulate 'MATLAB' code using 'R'.
Author: P. Roebuck
Maintainer: P. Roebuck <proebuck1701@gmail.com>
Diff between matlab versions 1.0.4 dated 2022-06-01 and 1.0.4.1 dated 2024-07-01
matlab-1.0.4.1/matlab/DESCRIPTION | 6 +++--- matlab-1.0.4.1/matlab/MD5 | 6 +++--- matlab-1.0.4.1/matlab/build/stage23.rdb |only matlab-1.0.4.1/matlab/man/size_t-class.Rd | 2 +- matlab-1.0.4/matlab/build/matlab.pdf |only 5 files changed, 7 insertions(+), 7 deletions(-)
Title: Optimal Multilevel Matching using a Network Algorithm
Description: Performs multilevel matches for data with cluster-
level treatments and individual-level outcomes using a network
optimization algorithm. Functions for checking balance at the
cluster and individual levels are also provided, as are methods
for permutation-inference-based outcome analysis. Details in
Pimentel et al. (2018) <doi:10.1214/17-AOAS1118>. The optmatch
package, which is useful for running many of the provided
functions, may be downloaded from Github at
<https://github.com/markmfredrickson/optmatch> if not available on
CRAN.
Author: Luke Keele [aut],
Luke Miratrix [aut],
Sam Pimentel [aut, cre],
Paul Rosenbaum [ctb]
Maintainer: Sam Pimentel <spi@berkeley.edu>
Diff between matchMulti versions 1.1.12 dated 2023-05-11 and 1.1.12.1 dated 2024-07-01
matchMulti-1.1.12.1/matchMulti/DESCRIPTION | 10 - matchMulti-1.1.12.1/matchMulti/MD5 | 51 ++++------ matchMulti-1.1.12.1/matchMulti/R/matchMulti-package.R | 7 - matchMulti-1.1.12.1/matchMulti/build/vignette.rds |binary matchMulti-1.1.12.1/matchMulti/data/catholic_schools.RData |binary matchMulti-1.1.12.1/matchMulti/data/minischool.rda |binary matchMulti-1.1.12.1/matchMulti/inst/doc/multiMatch_vignette.pdf |binary matchMulti-1.1.12.1/matchMulti/man/agg.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/assembleMatch.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/buildCaliper.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/ci_func.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/handleNA.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/is.binary.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/match2distance.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/matchMulti-package.Rd | 17 ++- matchMulti-1.1.12.1/matchMulti/man/matchMulti.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/matchMultioutcome.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/matchMultisens.Rd | 4 matchMulti-1.1.12.1/matchMulti/man/matchSchools.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/matchStudents.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/pe_func.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/pval_func.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/rematchSchools.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/resolve.cols.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/sdiff.Rd | 2 matchMulti-1.1.12.1/matchMulti/man/students2schools.Rd | 2 matchMulti-1.1.12/matchMulti/build/matchMulti.pdf |only 27 files changed, 61 insertions(+), 62 deletions(-)
Title: Generic PK/PD Simulation Platform CAMPSIS
Description: A generic, easy-to-use and intuitive
pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on R
packages 'rxode2', 'RxODE' and 'mrgsolve'. CAMPSIS provides an
abstraction layer over the underlying processes of writing a PK/PD
model, assembling a custom dataset and running a simulation. CAMPSIS
has a strong dependency to the R package 'campsismod', which allows to
read/write a model from/to files and adapt it further on the fly in
the R environment. Package 'campsis' allows the user to assemble a
dataset in an intuitive manner. Once the user’s dataset is ready, the
package is in charge of preparing the simulation, calling 'rxode2',
'RxODE' or 'mrgsolve' (at the user's choice) and returning the
results, for the given model, dataset and desired simulation settings.
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsis versions 1.5.2 dated 2024-04-12 and 1.5.3 dated 2024-07-01
campsis-1.5.2/campsis/man/preprocessFunction.Rd |only campsis-1.5.3/campsis/DESCRIPTION | 18 ++-- campsis-1.5.3/campsis/MD5 | 39 +++++---- campsis-1.5.3/campsis/NAMESPACE | 5 - campsis-1.5.3/campsis/NEWS.md | 5 + campsis-1.5.3/campsis/R/default_plot.R | 2 campsis-1.5.3/campsis/R/global.R | 2 campsis-1.5.3/campsis/R/outfun.R |only campsis-1.5.3/campsis/R/scenario.R | 13 +-- campsis-1.5.3/campsis/R/simulate.R | 41 ++++++---- campsis-1.5.3/campsis/R/simulate_preprocess.R | 38 ++++++--- campsis-1.5.3/campsis/inst/doc/campsis.html | 2 campsis-1.5.3/campsis/man/Outfun.Rd |only campsis-1.5.3/campsis/man/output_function-class.Rd |only campsis-1.5.3/campsis/man/preprocessOutfun.Rd |only campsis-1.5.3/campsis/man/preprocessTablefun.Rd |only campsis-1.5.3/campsis/man/simulate.Rd | 22 ++--- campsis-1.5.3/campsis/man/simulateDelegate.Rd | 2 campsis-1.5.3/campsis/man/simulateDelegateCore.Rd | 2 campsis-1.5.3/campsis/man/simulateScenarios.Rd | 2 campsis-1.5.3/campsis/tests/testthat/_snaps/testSimulateReplicates |only campsis-1.5.3/campsis/tests/testthat/testScenario.R | 6 - campsis-1.5.3/campsis/tests/testthat/testSimulateReplicates.R | 31 +++++++ campsis-1.5.3/campsis/tests/testthat/testUtils.R | 2 24 files changed, 148 insertions(+), 84 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better than a random observation drawn from the other group (Mann-Whitney parameter). The net benefit and win ratio statistics, i.e. the difference and ratio between the probabilities relative to the intervention and control groups, can then also be estimated. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>), non-parametric bootstrap, or permutations. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O Brien test [...truncated...]
Author: Brice Ozenne [aut, cre] ,
Julien Peron [ctb],
Eva Cantagallo [aut],
William Anderson [ctb],
Johan Verbeeck [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 3.0.2 dated 2024-01-23 and 3.0.4 dated 2024-07-01
DESCRIPTION | 18 MD5 | 296 +-- NAMESPACE | 190 +- NEWS | 507 ++--- R/0-onLoad.R | 22 R/1-setGeneric.R | 136 - R/BuyseMultComp.R | 996 +++++----- R/BuyseTTEM.R | 1342 +++++++------- R/BuyseTest-Peron.R | 692 +++---- R/BuyseTest-check.R | 1127 ++++++------ R/BuyseTest-inference.R | 880 +++++---- R/BuyseTest-initialization.R | 1699 +++++++++--------- R/BuyseTest-package.R | 135 - R/BuyseTest-print.R | 354 +-- R/BuyseTest.R | 1520 ++++++++-------- R/BuyseTest.options.R | 222 +- R/CasinoTest.R | 666 +++---- R/PairScore.R | 108 - R/RcppExports.R | 461 ++-- R/S4-BuysePower-model.tables.R | 338 +-- R/S4-BuysePower-nobs.R | 96 - R/S4-BuysePower-print.R | 66 R/S4-BuysePower-show.R | 64 R/S4-BuysePower-summary.R | 350 +-- R/S4-BuysePower.R | 166 - R/S4-BuyseTest-coef.R | 663 +++---- R/S4-BuyseTest-confint.R | 2054 +++++++++++----------- R/S4-BuyseTest-get.R | 1639 ++++++++--------- R/S4-BuyseTest-model.tables.R | 563 +++--- R/S4-BuyseTest-nobs.R | 203 +- R/S4-BuyseTest-plot.R | 178 - R/S4-BuyseTest-print.R | 70 R/S4-BuyseTest-sensitivity.R | 730 +++---- R/S4-BuyseTest-show.R | 98 - R/S4-BuyseTest-summary.R | 898 +++++---- R/S4-BuyseTest.R | 610 +++--- R/S4-BuyseTest.options.R | 463 ++-- R/as.data.table.performance.R | 282 +-- R/auc.R | 792 ++++---- R/autoplot.S4BuyseTest.R | 341 +-- R/brier.R | 604 +++--- R/constStrata.R | 178 - R/discreteRoot.R | 580 +++--- R/iid.S3sensitivity.R | 50 R/iid.prodlim.R | 402 ++-- R/normexp.R | 424 ++-- R/performance.R | 2424 +++++++++++++------------- R/performanceResample.R | 572 +++--- R/plot.S3sensitivity.R | 358 +-- R/powerBuyseTest.R | 1589 ++++++++--------- R/predict.logit.R | 564 +++--- R/rbind.performanceResample.R | 226 +- R/simBuyseTest.R | 1404 +++++++-------- R/simCompetingRisks.R | 284 +-- R/summary.performance.R | 228 +- R/valid.R | 960 +++++----- build/vignette.rds |binary inst/CITATION | 102 - inst/doc/overview.pdf |binary inst/doc/overview.pdf.asis | 561 +++++- inst/doc/wilcoxonTest.pdf |binary inst/doc/wilcoxonTest.pdf.asis | 110 + man/BuyseMultComp.Rd | 230 +- man/BuyseTTEM.Rd | 156 - man/BuyseTest-package.Rd | 136 - man/BuyseTest.Rd | 628 +++--- man/BuyseTest.options-class.Rd | 32 man/BuyseTest.options-methods.Rd | 44 man/BuyseTest.options.Rd | 66 man/CasinoTest.Rd | 224 +- man/GPC_cpp.Rd | 376 ++-- man/S4BuysePower-class.Rd | 34 man/S4BuysePower-nobs.Rd | 50 man/S4BuysePower-summary.Rd | 118 - man/S4BuyseTest-class.Rd | 34 man/S4BuyseTest-coef.Rd | 132 - man/S4BuyseTest-confint.Rd | 254 +- man/S4BuyseTest-getCount.Rd | 58 man/S4BuyseTest-getIid.Rd | 160 - man/S4BuyseTest-getPairScore.Rd | 288 +-- man/S4BuyseTest-getPseudovalue.Rd | 140 - man/S4BuyseTest-getSurvival.Rd | 118 - man/S4BuyseTest-nobs.Rd | 62 man/S4BuyseTest-plot.Rd | 136 - man/S4BuyseTest-print.Rd | 52 man/S4BuyseTest-sensitivity.Rd | 188 +- man/S4BuyseTest-show.Rd | 72 man/S4BuyseTest-summary.Rd | 284 +-- man/as.data.table.performance.Rd | 66 man/auc.Rd | 166 - man/autoplot-S4BuyseTest.Rd | 82 man/calcIntegralSurv2_cpp.Rd | 94 - man/coef.BuyseTestAuc.Rd | 38 man/coef.BuyseTestBrier.Rd | 40 man/confint.BuyseTestAuc.Rd | 38 man/confint.BuyseTestBrier.Rd | 40 man/constStrata.Rd | 122 - man/dot-calcIntegralCif_cpp.Rd | 98 - man/dot-calcIntegralSurv_cpp.Rd | 84 man/dot-colCenter_cpp.Rd | 40 man/dot-colCumSum_cpp.Rd | 36 man/dot-colMultiply_cpp.Rd | 40 man/dot-colScale_cpp.Rd | 40 man/dot-rowCenter_cpp.Rd | 40 man/dot-rowCumProd_cpp.Rd | 36 man/dot-rowCumSum_cpp.Rd | 36 man/dot-rowMultiply_cpp.Rd | 40 man/dot-rowScale_cpp.Rd | 40 man/iid.BuyseTestAuc.Rd | 38 man/iid.BuyseTestBrier.Rd | 40 man/iid.prodlim.Rd | 110 - man/performance.Rd | 212 +- man/performanceResample.Rd | 114 - man/powerBuyseTest.Rd | 311 +-- man/predict.BuyseTTEM.Rd | 62 man/rbind.performance.Rd | 122 - man/simBuyseTest.Rd | 404 ++-- man/simCompetingRisks.Rd | 212 +- man/summary.performance.Rd | 46 man/validFCTs.Rd | 312 +-- src/FCT_buyseTest.cpp | 13 src/FCT_calcAllPairs.h | 8 src/FCT_calcOnePair.h | 22 src/RcppExports.cpp | 18 tests/testthat.R | 84 tests/testthat/test-BuysePower.R | 400 ++-- tests/testthat/test-BuyseTTEM.R | 502 ++--- tests/testthat/test-BuyseTest-CR.R | 468 ++--- tests/testthat/test-BuyseTest-PairScore.R | 240 +- tests/testthat/test-BuyseTest-Pairs.R | 1201 ++++++------ tests/testthat/test-BuyseTest-checkValues.R | 1148 ++++++------ tests/testthat/test-BuyseTest-correctionTTE.R | 450 ++-- tests/testthat/test-BuyseTest-engine.R | 214 +- tests/testthat/test-BuyseTest-iid.R | 1600 ++++++++--------- tests/testthat/test-BuyseTest-multcomp.R | 178 - tests/testthat/test-BuyseTest-neutralAsUnif.R | 206 +- tests/testthat/test-BuyseTest-operator.R | 202 +- tests/testthat/test-BuyseTest-previousBug.R | 1342 +++++++------- tests/testthat/test-BuyseTest-resampling.R | 1198 ++++++------ tests/testthat/test-BuyseTest-restricted.R | 188 +- tests/testthat/test-BuyseTest-strata.R | 864 ++++----- tests/testthat/test-BuyseTest-weightObs.R | 130 - tests/testthat/test-auc.R | 268 +- tests/testthat/test-initSurvival.R | 438 ++-- tests/testthat/test-initThreshold.R | 168 - tests/testthat/test-otherPackages.R | 394 ++-- vignettes/overview.pdf.asis | 561 +++++- vignettes/vignette_CR.Rmd | 146 - vignettes/wilcoxonTest.pdf.asis | 110 + 149 files changed, 27766 insertions(+), 25921 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-04 1.2.2
2022-05-02 1.2.1
2022-04-13 1.2.0
2022-04-08 1.1.0
2022-03-25 1.0.5
2022-03-08 1.0.4
2022-02-22 1.0.3
2022-02-08 1.0.2
2022-01-20 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-14 1.2-3
2020-04-22 1.2-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-22 1.1.1
Title: Penalized Semiparametric Bayesian Cox Models
Description: Algorithms to speed up the Bayesian Lasso Cox model (Lee et al., Int J Biostat, 2011 <doi:10.2202/1557-4679.1301>) and the Bayesian Lasso Cox with mandatory variables (Zucknick et al. Biometrical J, 2015 <doi:10.1002/bimj.201400160>).
Author: Zhi Zhao [aut, cre],
Manuela Zucknick [aut],
Maral Saadati [aut],
Axel Benner [aut]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between psbcSpeedUp versions 2.0.6 dated 2024-03-21 and 2.0.7 dated 2024-07-01
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- NAMESPACE | 1 + NEWS.md | 11 ++++------- R/psbcSpeedUp.R | 13 ++++++++----- README.md | 12 ++++++++---- build/vignette.rds |binary inst/CITATION |only man/psbcSpeedUp.Rd | 1 - src/psbc.cpp | 2 +- 10 files changed, 36 insertions(+), 31 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Lennart Schneider [cre, aut] ,
Jakob Richter [aut] ,
Marc Becker [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Lennart Schneider <lennart.sch@web.de>
Diff between mlr3mbo versions 0.2.2 dated 2024-03-01 and 0.2.3 dated 2024-07-01
DESCRIPTION | 12 MD5 | 136 +-- NEWS.md | 4 R/AcqFunction.R | 6 R/AcqFunctionAEI.R | 2 R/AcqFunctionCB.R | 2 R/AcqFunctionEHVI.R | 4 R/AcqFunctionEHVIGH.R | 10 R/AcqFunctionEI.R | 2 R/AcqFunctionEIPS.R | 6 R/AcqFunctionMean.R | 2 R/AcqFunctionPI.R | 2 R/AcqFunctionSD.R | 2 R/AcqFunctionSmsEgo.R | 2 R/AcqOptimizer.R | 4 R/OptimizerMbo.R | 6 R/ResultAssigner.R | 2 R/ResultAssignerArchive.R | 4 R/ResultAssignerSurrogate.R | 12 R/Surrogate.R | 2 R/SurrogateLearner.R | 2 R/SurrogateLearnerCollection.R | 2 R/TunerMbo.R | 8 R/bayesopt_ego.R | 12 R/bayesopt_emo.R | 10 R/bayesopt_mpcl.R | 12 R/bayesopt_parego.R | 14 R/bayesopt_smsego.R | 12 R/helper.R | 4 R/mbo_defaults.R | 16 R/zzz.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/mlr3mbo.R | 12 inst/doc/mlr3mbo.Rmd | 14 inst/doc/mlr3mbo.html | 1180 ++++++++++++++++------------------ man/AcqFunction.Rd | 1 man/AcqOptimizer.Rd | 2 man/ResultAssigner.Rd | 2 man/Surrogate.Rd | 4 man/SurrogateLearner.Rd | 6 man/SurrogateLearnerCollection.Rd | 6 man/default_acqoptimizer.Rd | 2 man/default_surrogate.Rd | 4 man/mlr_acqfunctions_aei.Rd | 5 man/mlr_acqfunctions_cb.Rd | 3 man/mlr_acqfunctions_ehvi.Rd | 5 man/mlr_acqfunctions_ehvigh.Rd | 5 man/mlr_acqfunctions_ei.Rd | 5 man/mlr_acqfunctions_eips.Rd | 9 man/mlr_acqfunctions_mean.Rd | 3 man/mlr_acqfunctions_pi.Rd | 5 man/mlr_acqfunctions_sd.Rd | 3 man/mlr_acqfunctions_smsego.Rd | 5 man/mlr_loop_functions_ego.Rd | 10 man/mlr_loop_functions_emo.Rd | 8 man/mlr_loop_functions_mpcl.Rd | 10 man/mlr_loop_functions_parego.Rd | 12 man/mlr_loop_functions_smsego.Rd | 10 man/mlr_optimizers_mbo.Rd | 12 man/mlr_result_assigners_archive.Rd | 2 man/mlr_result_assigners_surrogate.Rd | 4 man/mlr_tuners_mbo.Rd | 12 tests/testthat/helper.R | 8 tests/testthat/test_AcqOptimizer.R | 2 tests/testthat/test_TunerMbo.R | 16 tests/testthat/test_bayesopt_ego.R | 4 tests/testthat/test_mbo_defaults.R | 4 vignettes/mlr3mbo.Rmd | 14 69 files changed, 861 insertions(+), 865 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u',
'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, truncation,
rank transformation, and smoothing. An export function helps to generate
html and latex tables in a publication friendly style. More details can be
found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2023)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scan versions 0.60.0 dated 2023-08-08 and 0.61.0 dated 2024-07-01
scan-0.60.0/scan/R/export.sc_plm.R |only scan-0.60.0/scan/R/pkg-package.R |only scan-0.60.0/scan/R/print.sc_plm.R |only scan-0.60.0/scan/R/warnings-messages.R |only scan-0.61.0/scan/DESCRIPTION | 18 - scan-0.61.0/scan/MD5 | 217 +++++++------- scan-0.61.0/scan/NAMESPACE | 5 scan-0.61.0/scan/NEWS.md | 32 ++ scan-0.61.0/scan/R/add_l2.R | 26 - scan-0.61.0/scan/R/as.data.frame.scdf.R | 14 scan-0.61.0/scan/R/as_scdf.R | 37 +- scan-0.61.0/scan/R/autocorr.R | 38 -- scan-0.61.0/scan/R/batch_apply.R | 19 - scan-0.61.0/scan/R/cdc.R | 85 ++--- scan-0.61.0/scan/R/coefficents.sc_plm.R | 13 scan-0.61.0/scan/R/convert.R | 324 +++++++++++---------- scan-0.61.0/scan/R/corrected_tau.R | 15 scan-0.61.0/scan/R/deprecated.R | 36 ++ scan-0.61.0/scan/R/export.R | 139 ++++++++- scan-0.61.0/scan/R/export.sc_desc.R | 53 ++- scan-0.61.0/scan/R/export.sc_hplm.R | 89 ++++- scan-0.61.0/scan/R/export.sc_nap.R | 29 + scan-0.61.0/scan/R/export.sc_overlap.R | 5 scan-0.61.0/scan/R/export.sc_pem.R | 23 - scan-0.61.0/scan/R/export.sc_pet.R |only scan-0.61.0/scan/R/export.sc_pnd.R |only scan-0.61.0/scan/R/export.sc_power.R | 23 - scan-0.61.0/scan/R/export.sc_smd.R | 9 scan-0.61.0/scan/R/export.sc_tauu.R | 52 ++- scan-0.61.0/scan/R/export.sc_trend.R | 33 +- scan-0.61.0/scan/R/export.scdf.R | 52 ++- scan-0.61.0/scan/R/export.scdf_summary.R |only scan-0.61.0/scan/R/hplm.R | 31 +- scan-0.61.0/scan/R/message-system.R |only scan-0.61.0/scan/R/mplm.R | 7 scan-0.61.0/scan/R/nap.R | 48 ++- scan-0.61.0/scan/R/outlier.R | 11 scan-0.61.0/scan/R/overlap.R | 6 scan-0.61.0/scan/R/pand.R | 18 - scan-0.61.0/scan/R/pem.R | 10 scan-0.61.0/scan/R/pet.R | 37 +- scan-0.61.0/scan/R/print-export-plm.R |only scan-0.61.0/scan/R/print.sc_hplm.R | 8 scan-0.61.0/scan/R/print.sc_nap.R | 10 scan-0.61.0/scan/R/print.sc_pand.R | 2 scan-0.61.0/scan/R/print.sc_pem.R | 3 scan-0.61.0/scan/R/print.sc_pet.R | 12 scan-0.61.0/scan/R/print.sc_rand.R | 11 scan-0.61.0/scan/R/print.sc_rci.R | 19 - scan-0.61.0/scan/R/private_check.R | 9 scan-0.61.0/scan/R/private_options.R | 15 scan-0.61.0/scan/R/private_options_mc.R | 8 scan-0.61.0/scan/R/private_regression.R | 2 scan-0.61.0/scan/R/private_utilities.R | 6 scan-0.61.0/scan/R/rand_test.R | 381 +++++++++++++++++-------- scan-0.61.0/scan/R/rci.R | 117 ++++--- scan-0.61.0/scan/R/scan-Data.R | 2 scan-0.61.0/scan/R/scan-package.R |only scan-0.61.0/scan/R/scan.R | 9 scan-0.61.0/scan/R/scdf.R | 59 ++- scan-0.61.0/scan/R/smd.R | 1 scan-0.61.0/scan/R/summary.scdf.R | 7 scan-0.61.0/scan/data/Beretvas2008.rda |binary scan-0.61.0/scan/data/Borckardt2014.rda |binary scan-0.61.0/scan/data/Grosche2011.rda |binary scan-0.61.0/scan/data/Grosche2014.rda |binary scan-0.61.0/scan/data/GruenkeWilbert2014.rda |binary scan-0.61.0/scan/data/Huber2014.rda |binary scan-0.61.0/scan/data/Huitema2000.rda |binary scan-0.61.0/scan/data/Leidig2018.rda |binary scan-0.61.0/scan/data/Leidig2018_l2.rda |binary scan-0.61.0/scan/data/Lenz2013.rda |binary scan-0.61.0/scan/data/Parker2007.rda |binary scan-0.61.0/scan/data/Parker2009.rda |binary scan-0.61.0/scan/data/Parker2009b.rda |only scan-0.61.0/scan/data/Parker2011.rda |binary scan-0.61.0/scan/data/Parker2011b.rda |binary scan-0.61.0/scan/data/SSDforR2017.rda |binary scan-0.61.0/scan/data/Tarlow2017.rda |binary scan-0.61.0/scan/data/Waddell2011.rda |binary scan-0.61.0/scan/data/byHeart2011.rda |binary scan-0.61.0/scan/data/exampleA1B1A2B2.rda |binary scan-0.61.0/scan/data/exampleA1B1A2B2_zvt.rda |binary scan-0.61.0/scan/data/exampleAB.rda |binary scan-0.61.0/scan/data/exampleABAB.rda |binary scan-0.61.0/scan/data/exampleABC.rda |binary scan-0.61.0/scan/data/exampleABC_150.rda |binary scan-0.61.0/scan/data/exampleABC_outlier.rda |binary scan-0.61.0/scan/data/exampleAB_50.l2.rda |binary scan-0.61.0/scan/data/exampleAB_50.rda |binary scan-0.61.0/scan/data/exampleAB_add.rda |binary scan-0.61.0/scan/data/exampleAB_decreasing.rda |binary scan-0.61.0/scan/data/exampleAB_mpd.rda |binary scan-0.61.0/scan/data/exampleAB_score.rda |binary scan-0.61.0/scan/data/exampleAB_simple.rda |binary scan-0.61.0/scan/data/example_A24.rda |binary scan-0.61.0/scan/inst/shiny/resources.R | 20 - scan-0.61.0/scan/inst/shiny/server.R | 171 ++++++++--- scan-0.61.0/scan/inst/shiny/ui.R | 160 +++++++--- scan-0.61.0/scan/man/cdc.Rd | 9 scan-0.61.0/scan/man/corrected_tau.Rd | 4 scan-0.61.0/scan/man/deprecated-functions.Rd | 23 - scan-0.61.0/scan/man/example_data.Rd | 1 scan-0.61.0/scan/man/export.Rd | 67 +++- scan-0.61.0/scan/man/hplm.Rd | 16 - scan-0.61.0/scan/man/mplm.Rd | 4 scan-0.61.0/scan/man/nap.Rd | 11 scan-0.61.0/scan/man/print.sc.Rd | 34 +- scan-0.61.0/scan/man/rand_test.Rd | 25 - scan-0.61.0/scan/man/rci.Rd | 6 scan-0.61.0/scan/man/scan-package.Rd | 12 scan-0.61.0/scan/man/scdf.Rd | 6 scan-0.61.0/scan/man/smd.Rd | 5 scan-0.61.0/scan/man/tau_u.Rd | 9 scan-0.61.0/scan/tests/testthat/test-convert.R | 15 115 files changed, 1859 insertions(+), 974 deletions(-)
Title: Quality Control for RNA-Seq Data
Description: Functions for semi-automated quality control of bulk RNA-seq data.
Author: Frederik Ziebell [cre],
Frederik Ziebell [aut] ,
GlaxoSmithKline Research & Development Limited [cph]
Maintainer: Frederik Ziebell <f_ziebell@web.de>
Diff between RNAseqQC versions 0.1.4 dated 2022-06-15 and 0.2.0 dated 2024-07-01
DESCRIPTION | 30 + MD5 | 63 +-- NAMESPACE | 9 NEWS.md | 10 R/RNAseqQC-package.R | 13 R/counts_statistics.R | 92 +++-- R/diff_expression.R | 51 ++- R/global_vars.R |only R/other.R | 47 ++ R/pca.R | 377 +++++++++++++++++----- R/preprocessing.R | 37 +- build/partial.rdb |binary build/vignette.rds |binary data/T47D.rda |binary data/T47D_diff_testing.rda |binary inst/doc/data.R | 2 inst/doc/data.Rmd | 2 inst/doc/data.html | 226 ++++++------- inst/doc/introduction.R | 32 + inst/doc/introduction.Rmd | 10 inst/doc/introduction.html | 600 ++++++++++++++++++------------------ man/RNAseqQC-package.Rd | 15 man/all_numeric.Rd |only man/get_gene_id.Rd |only man/make_dds.Rd | 3 man/plot_library_complexity.Rd | 4 man/plot_loadings.Rd | 5 man/plot_pca.Rd | 11 man/plot_pca_scatters.Rd | 14 man/plot_sample_MAs.Rd | 6 man/plot_within_level_sample_MAs.Rd | 13 vignettes/data.Rmd | 2 vignettes/disp_ests.png |binary vignettes/introduction.Rmd | 10 34 files changed, 1027 insertions(+), 657 deletions(-)
Title: Build, Import, and Export GEXF Graph Files
Description: Create, read, and write 'GEXF' (Graph Exchange 'XML' Format) graph files (used in 'Gephi' and others). Using the 'XML' package, rgexf allows reading and writing GEXF files, including attributes, 'GEXF' visual attributes (such as color, size, and position), network dynamics (for both edges and nodes), and edges' weights. Users can build/handle graphs element-by-element or massively through data frames, visualize the graph on a web browser through 'gexf-js' (a 'javascript' library), and interact with the 'igraph' package.
Author: George Vega Yon [aut, cre] ,
Jorge Fabrega Lacoa [ctb],
Joshua Kunst [ctb],
Raphael Velt [cph] ,
Gephi Consortium [cph] ,
Cornelius Fritz [rev] ,
Jonathan Cardoso Silva [rev]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between rgexf versions 0.16.2 dated 2021-08-12 and 0.16.3 dated 2024-07-01
rgexf-0.16.2/rgexf/build/rgexf.pdf |only rgexf-0.16.3/rgexf/DESCRIPTION | 19 rgexf-0.16.3/rgexf/MD5 | 41 - rgexf-0.16.3/rgexf/NEWS.md | 5 rgexf-0.16.3/rgexf/R/gexf.R | 20 rgexf-0.16.3/rgexf/R/manipulation.R | 4 rgexf-0.16.3/rgexf/R/plot.R | 18 rgexf-0.16.3/rgexf/R/read.gexf.R | 2 rgexf-0.16.3/rgexf/R/rgexf-package.R | 9 rgexf-0.16.3/rgexf/README.md | 802 +++++++++++++--------------- rgexf-0.16.3/rgexf/build/vignette.rds |binary rgexf-0.16.3/rgexf/inst/CITATION | 8 rgexf-0.16.3/rgexf/inst/doc/rgexf.Rmd | 2 rgexf-0.16.3/rgexf/inst/doc/rgexf.html | 422 +++++++------- rgexf-0.16.3/rgexf/man/add.gexf.node.Rd | 8 rgexf-0.16.3/rgexf/man/figures/igraph-1.png |binary rgexf-0.16.3/rgexf/man/gexf-class.Rd | 11 rgexf-0.16.3/rgexf/man/new.gexf.graph.Rd | 2 rgexf-0.16.3/rgexf/man/plot.gexf.Rd | 22 rgexf-0.16.3/rgexf/man/read.gexf.Rd | 2 rgexf-0.16.3/rgexf/man/rgexf-package.Rd | 28 rgexf-0.16.3/rgexf/vignettes/rgexf.Rmd | 2 22 files changed, 727 insertions(+), 700 deletions(-)
Title: Multivariate (Dynamic) Generalized Additive Models
Description: Fit Bayesian Dynamic Generalized Additive Models to sets of time series. Users can build dynamic nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2022) <doi:10.1111/2041-210X.13974>.
Author: Nicholas J Clark [aut, cre]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Diff between mvgam versions 1.1.1 dated 2024-05-10 and 1.1.2 dated 2024-07-01
DESCRIPTION | 27 MD5 | 227 NAMESPACE | 534 +- NEWS.md | 12 R/add_MACor.R | 209 R/add_trend_lines.R | 60 R/backends.R |only R/conditional_effects.R | 25 R/dynamic.R | 2 R/evaluate_mvgams.R | 1726 +++--- R/families.R | 3184 ++++++------ R/forecast.mvgam.R | 11 R/get_linear_predictors.R | 330 - R/get_mvgam_priors.R | 48 R/gp.R | 23 R/hindcast.mvgam.R | 10 R/lfo_cv.mvgam.R | 41 R/logLik.mvgam.R | 388 - R/loo.mvgam.R | 115 R/marginaleffects.mvgam.R | 4 R/mcmc_plot.mvgam.R | 5 R/monotonic.R | 6 R/mvgam.R | 395 - R/mvgam_diagnostics.R | 9 R/mvgam_setup.R | 826 +++ R/noncent_trend.R |only R/pairs.mvgam.R | 3 R/piecewise_trends.R | 2 R/plot.mvgam.R | 7 R/plot_mvgam_factors.R | 2 R/plot_mvgam_series.R | 1001 +-- R/plot_mvgam_trend.R | 6 R/posterior_epred.mvgam.R | 10 R/ppc.mvgam.R | 4 R/predict.mvgam.R | 9 R/residuals.mvgam.R | 9 R/score.mvgam_forecast.R | 4 R/sim_mvgam.R | 1009 +-- R/stan_utils.R | 7779 +++++++++++++----------------- R/summary.mvgam.R | 1718 +++--- R/ti.R |only R/update.mvgam.R | 17 R/validations.R | 1553 +++-- README.md | 254 inst/doc/data_in_mvgam.R | 115 inst/doc/data_in_mvgam.html | 194 inst/doc/forecast_evaluation.R | 81 inst/doc/forecast_evaluation.Rmd | 33 inst/doc/forecast_evaluation.html | 308 - inst/doc/mvgam_overview.R | 228 inst/doc/mvgam_overview.html | 1378 ++--- inst/doc/nmixtures.R | 188 inst/doc/nmixtures.html | 286 - inst/doc/shared_states.R | 84 inst/doc/shared_states.Rmd | 40 inst/doc/shared_states.html | 401 - inst/doc/time_varying_effects.R | 115 inst/doc/time_varying_effects.Rmd | 47 inst/doc/time_varying_effects.html | 219 inst/doc/trend_formulas.R | 98 inst/doc/trend_formulas.Rmd | 22 inst/doc/trend_formulas.html | 185 man/conditional_effects.mvgam.Rd | 10 man/dynamic.Rd | 2 man/figures/README-beta_fc-1.png |binary man/figures/README-unnamed-chunk-12-1.png |only man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-15-1.png |binary man/figures/README-unnamed-chunk-16-1.png |binary man/figures/README-unnamed-chunk-17-1.png |binary man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-21-1.png |binary man/figures/README-unnamed-chunk-22-1.png |binary man/figures/README-unnamed-chunk-23-1.png |binary man/figures/README-unnamed-chunk-24-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/forecast.mvgam.Rd | 7 man/get_mvgam_priors.Rd | 5 man/hindcast.mvgam.Rd | 11 man/lfo_cv.mvgam.Rd | 20 man/logLik.mvgam.Rd | 4 man/loo.mvgam.Rd | 60 man/mcmc_plot.mvgam.Rd | 5 man/monotonic.Rd | 6 man/mvgam.Rd | 47 man/mvgam_diagnostics.Rd | 5 man/mvgam_families.Rd | 16 man/pairs.mvgam.Rd | 3 man/piecewise_trends.Rd | 2 man/plot.mvgam.Rd | 7 man/plot.mvgam_lfo.Rd | 4 man/plot_mvgam_factors.Rd | 2 man/plot_mvgam_series.Rd | 9 man/plot_mvgam_trend.Rd | 3 man/posterior_epred.mvgam.Rd | 3 man/posterior_linpred.mvgam.Rd | 7 man/ppc.mvgam.Rd | 4 man/predict.mvgam.Rd | 5 man/residuals.mvgam.Rd | 7 man/score.mvgam_forecast.Rd | 4 man/ti.Rd |only man/update.mvgam.Rd | 21 tests/testthat/test-RW.R | 423 - tests/testthat/test-binomial.R | 669 +- tests/testthat/test-example_processing.R | 106 tests/testthat/test-gp.R | 281 - tests/testthat/test-marginaleffects.R | 22 tests/testthat/test-mvgam.R | 1487 +++-- tests/testthat/test-nmixture.R | 455 - tests/testthat/test-piecewise.R | 274 - vignettes/forecast_evaluation.Rmd | 33 vignettes/shared_states.Rmd | 40 vignettes/time_varying_effects.Rmd | 47 vignettes/trend_formulas.Rmd | 22 117 files changed, 15219 insertions(+), 14545 deletions(-)
Title: Behavioural Studies of Large Language Models
Description: Efficient way to design and conduct psychological experiments for testing the performance of large language models. It simplifies the process of setting up experiments and data collection via language models’ API, facilitating a smooth workflow for researchers in the field of machine behaviour.
Author: Xufeng Duan, Shixuan Li, Zhenguang Cai
Maintainer: Xufeng Duan <dxfdxfdxf88@gmail.com>
Diff between MacBehaviour versions 1.2.2 dated 2024-06-17 and 1.2.4 dated 2024-07-01
DESCRIPTION | 22 MD5 | 18 NAMESPACE | 35 - NEWS.md |only R/experimentDesign.R | 227 +++---- R/gpt.R | 863 +++++++++++++------------- R/precheck.R | 319 ++++----- R/runExperiment.R | 1640 +++++++++++++++++++++++++-------------------------- R/tools.R | 845 +++++++++++++------------- README.md |only man/preCheck.Rd | 9 11 files changed, 1996 insertions(+), 1982 deletions(-)
Title: Bayesian Modal Regression Based on the GUD Family
Description: Provides probability density functions and sampling algorithms for three key distributions from the General Unimodal Distribution (GUD) family: the Flexible Gumbel (FG) distribution, the Double Two-Piece (DTP) Student-t distribution, and the Two-Piece Scale (TPSC) Student-t distribution. Additionally, this package includes a function for Bayesian linear modal regression, leveraging these three distributions for model fitting. The details of the Bayesian modal regression model based on the GUD family can be found at Liu, Huang, and Bai (2024) <doi:10.1016/j.csda.2024.108012>.
Author: Qingyang Liu [aut, cre] ,
Xianzheng Huang [aut] ,
Ray Bai [aut]
Maintainer: Qingyang Liu <qingyang@email.sc.edu>
Diff between GUD versions 1.0.0 dated 2024-06-29 and 1.0.2 dated 2024-07-01
DESCRIPTION | 18 - MD5 | 21 - NEWS.md | 8 R/Modalregression.R | 4 README.md |only build/partial.rdb |binary inst/doc/Bayesian-Modal-Regression-Analysis-of-2003-United-States-Crime-Data.R | 1 inst/doc/Bayesian-Modal-Regression-Analysis-of-2003-United-States-Crime-Data.Rmd | 7 inst/doc/Bayesian-Modal-Regression-Analysis-of-2003-United-States-Crime-Data.html | 157 ++++------ man/figures |only man/modal_regression.Rd | 2 vignettes/Bayesian-Modal-Regression-Analysis-of-2003-United-States-Crime-Data.Rmd | 7 12 files changed, 117 insertions(+), 108 deletions(-)
Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to
plots using native data coordinates, while geom_table_npc(), geom_plot_npc()
and geom_grob_npc() do the same using "npc" coordinates through new
aesthetics "npcx" and "npcy". Statistics: select observations based on 2D
density. Positions: radial nudging away from a center point and nudging away
from a line or curve; combined stacking and nudging; combined dodging and
nudging.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Michal Krassowski [ctb] ,
Daniel Sabanes Bove [ctb],
Stella Banjo [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpp versions 0.5.8 dated 2024-06-26 and 0.5.8-1 dated 2024-07-01
ggpp-0.5.8-1/ggpp/DESCRIPTION | 8 ggpp-0.5.8-1/ggpp/MD5 | 20 ggpp-0.5.8-1/ggpp/NEWS.md | 4 ggpp-0.5.8-1/ggpp/README.md | 7 ggpp-0.5.8-1/ggpp/inst/doc/grammar-extensions.html | 6 ggpp-0.5.8-1/ggpp/inst/doc/nudge-examples.R | 12 ggpp-0.5.8-1/ggpp/inst/doc/nudge-examples.Rmd | 15 ggpp-0.5.8-1/ggpp/inst/doc/nudge-examples.html | 752 ++++++++++----------- ggpp-0.5.8-1/ggpp/man/figures/logo.png |only ggpp-0.5.8-1/ggpp/man/ggpp-package.Rd | 2 ggpp-0.5.8-1/ggpp/vignettes/nudge-examples.Rmd | 15 ggpp-0.5.8/ggpp/man/figures/logo-ggpp.png |only 12 files changed, 419 insertions(+), 422 deletions(-)
Title: Clinical Significance Measures
Description: Provides measures of effect sizes for summarized continuous variables as well as diagnostic accuracy statistics for 2x2 table data. Includes functions for Cohen's d, robust effect size, Cohen's q, partial eta-squared, coefficient of variation, odds ratio, likelihood ratios, sensitivity, specificity, positive and negative predictive values, Youden index, number needed to treat, number needed to diagnose, and predictive summary index.
Author: Mike Malek-Ahmadi <michael.malekahmadi@bannerhealth.com>, Kjera Schack <kgschack@asu.edu>
Maintainer: Mike Malek-Ahmadi <michael.malekahmadi@bannerhealth.com>
Diff between ClinSigMeasures versions 1.1 dated 2024-06-03 and 1.2 dated 2024-07-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/sensitivity.R | 4 ++-- R/specificity.R | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
More information about ClinSigMeasures at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-17 0.2.1
Title: Soil Test Correlation and Calibration
Description: A compilation of functions designed to assist users on the correlation analysis of crop yield and soil test values. Functions to estimate crop response patterns to soil nutrient availability and critical soil test values using various approaches such as: 1) the modified arcsine-log calibration curve (Correndo et al. (2017) <doi:10.1071/CP16444>); 2) the graphical Cate-Nelson quadrants analysis (Cate & Nelson (1965)), 3) the statistical Cate-Nelson quadrants analysis (Cate & Nelson (1971) <doi:10.2136/sssaj1971.03615995003500040048x>), 4) the linear-plateau regression (Anderson & Nelson (1975) <doi:10.2307/2529422>), 5) the quadratic-plateau regression (Bullock & Bullock (1994) <doi:10.2134/agronj1994.00021962008600010033x>), and 6) the Mitscherlich-type exponential regression (Melsted & Peck (1977) <doi:10.2134/asaspecpub29.c1>). The package development stemmed from ongoing work with the Fertilizer Recommendation Support Tool (FRST) and [...truncated...]
Author: Adrian A. Correndo [aut, cre, cph]
,
Austin Pearce [aut] ,
Fernando Miguez [ctb] ,
Deanna Osmond [aut] ,
Ignacio A. Ciampitti [aut]
Maintainer: Adrian A. Correndo <acorrend@uoguelph.ca>
Diff between soiltestcorr versions 2.2.0 dated 2023-04-07 and 2.2.1 dated 2024-07-01
DESCRIPTION | 20 LICENSE | 4 MD5 | 144 +- NAMESPACE | 162 +-- NEWS.md | 289 +++-- R/cate_nelson_1965.R | 528 +++++----- R/cate_nelson_1971.R | 570 +++++------ R/data.R | 48 R/linear_plateau.R | 786 +++++++-------- R/mitscherlich.R | 880 ++++++++--------- R/mod_alcc.R | 750 +++++++-------- R/quadratic_plateau.R | 717 +++++++------- R/soiltestcorr-package.R | 24 README.md | 838 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 24 inst/doc/Introduction_to_soiltestcorr.R | 36 inst/doc/Introduction_to_soiltestcorr.Rmd | 150 +-- inst/doc/Introduction_to_soiltestcorr.html | 858 ++++++++--------- inst/doc/Shinyapp.R | 16 inst/doc/Shinyapp.Rmd | 58 - inst/doc/Shinyapp.html | 556 +++++------ inst/doc/SoftwareX_publication.R | 16 inst/doc/SoftwareX_publication.Rmd | 78 - inst/doc/SoftwareX_publication.html | 602 ++++++------ inst/doc/bootstrapping_tutorial.R | 460 ++++----- inst/doc/bootstrapping_tutorial.Rmd | 672 ++++++------- inst/doc/bootstrapping_tutorial.html | 1428 ++++++++++++++-------------- inst/doc/cate_nelson_1965_tutorial.R | 342 +++--- inst/doc/cate_nelson_1965_tutorial.Rmd | 562 +++++------ inst/doc/cate_nelson_1965_tutorial.html | 1431 ++++++++++++++--------------- inst/doc/cate_nelson_1971_tutorial.R | 320 +++--- inst/doc/cate_nelson_1971_tutorial.Rmd | 542 +++++----- inst/doc/cate_nelson_1971_tutorial.html | 1379 +++++++++++++-------------- inst/doc/linear_plateau_tutorial.R | 222 ++-- inst/doc/linear_plateau_tutorial.Rmd | 490 ++++----- inst/doc/linear_plateau_tutorial.html | 1348 +++++++++++++-------------- inst/doc/mitscherlich_tutorial.R | 232 ++-- inst/doc/mitscherlich_tutorial.Rmd | 492 ++++----- inst/doc/mitscherlich_tutorial.html | 1404 ++++++++++++++-------------- inst/doc/mod_alcc_tutorial.R | 290 ++--- inst/doc/mod_alcc_tutorial.Rmd | 538 +++++----- inst/doc/mod_alcc_tutorial.html | 1417 ++++++++++++++-------------- inst/doc/quadratic_plateau_tutorial.R | 220 ++-- inst/doc/quadratic_plateau_tutorial.Rmd | 490 ++++----- inst/doc/quadratic_plateau_tutorial.html | 1351 +++++++++++++-------------- man/cate_nelson_1965.Rd | 142 +- man/cate_nelson_1971.Rd | 138 +- man/data_test.Rd | 48 man/freitas1966.Rd | 48 man/linear_plateau.Rd | 212 ++-- man/mitscherlich.Rd | 240 ++-- man/mod_alcc.Rd | 182 +-- man/quadratic_plateau.Rd | 212 ++-- man/soiltestcorr-package.Rd | 75 - tests/testthat.R | 8 tests/testthat/test-cate_nelson_1965.R | 226 ++-- tests/testthat/test-cate_nelson_1971.R | 224 ++-- tests/testthat/test-linear_plateau.R | 366 +++---- tests/testthat/test-mitscherlich.R | 488 ++++----- tests/testthat/test-quadratic_plateau.R | 358 +++---- tests/testthat/test-soiltestcorr.R | 402 ++++---- vignettes/Introduction_to_soiltestcorr.Rmd | 150 +-- vignettes/Shinyapp.Rmd | 58 - vignettes/SoftwareX_publication.Rmd | 78 - vignettes/bootstrapping_tutorial.Rmd | 672 ++++++------- vignettes/cate_nelson_1965_tutorial.Rmd | 562 +++++------ vignettes/cate_nelson_1971_tutorial.Rmd | 542 +++++----- vignettes/linear_plateau_tutorial.Rmd | 490 ++++----- vignettes/mitscherlich_tutorial.Rmd | 492 ++++----- vignettes/mod_alcc_tutorial.Rmd | 538 +++++----- vignettes/quadratic_plateau_tutorial.Rmd | 490 ++++----- 73 files changed, 15599 insertions(+), 15626 deletions(-)
Title: Pam: Prediction Analysis for Microarrays
Description: Some functions for sample classification in microarrays.
Author: Trevor Hastie [aut],
Rob Tibshirani [aut],
Balasubramanian Narasimhan [aut, cre],
Gilbert Chu [aut]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between pamr versions 1.56.2.1 dated 2024-06-27 and 1.57 dated 2024-07-01
pamr-1.56.2.1/pamr/data/datalist |only pamr-1.56.2.1/pamr/man/pamr.internal.Rd |only pamr-1.56.2.1/pamr/src |only pamr-1.57/pamr/DESCRIPTION | 30 +- pamr-1.57/pamr/MD5 | 109 ++++----- pamr-1.57/pamr/NAMESPACE | 101 ++++---- pamr-1.57/pamr/R/khan.R |only pamr-1.57/pamr/R/pamr-package.R |only pamr-1.57/pamr/R/pamr.adaptthresh.R | 77 ++++++ pamr-1.57/pamr/R/pamr.confusion.R | 30 ++ pamr-1.57/pamr/R/pamr.cv.R | 46 ++++ pamr-1.57/pamr/R/pamr.decorrelate.R | 59 +++++ pamr-1.57/pamr/R/pamr.fdr.R | 35 +++ pamr-1.57/pamr/R/pamr.geneplot.R | 29 ++ pamr-1.57/pamr/R/pamr.indeterminate.R | 26 ++ pamr-1.57/pamr/R/pamr.listgenes.R | 41 +++ pamr-1.57/pamr/R/pamr.makeclasses.R | 60 +++++ pamr-1.57/pamr/R/pamr.menu.R | 22 + pamr-1.57/pamr/R/pamr.plotcen.R | 29 ++ pamr-1.57/pamr/R/pamr.plotcv.R | 25 ++ pamr-1.57/pamr/R/pamr.plotcvprob.R | 31 ++ pamr-1.57/pamr/R/pamr.plotfdr.R | 27 ++ pamr-1.57/pamr/R/pamr.plotstrata.R | 41 +++ pamr-1.57/pamr/R/pamr.predict.R | 35 +++ pamr-1.57/pamr/R/pamr.predictmany.R | 31 ++ pamr-1.57/pamr/R/pamr.survfuns.R | 195 ++++++++++++++++ pamr-1.57/pamr/R/pamr.train.R | 102 ++++++++ pamr-1.57/pamr/R/print.nsc.R | 1 pamr-1.57/pamr/R/print.nsccv.R | 3 pamr-1.57/pamr/R/print.pamrcved.R | 3 pamr-1.57/pamr/R/print.pamrtrained.R | 1 pamr-1.57/pamr/R/which.is.max.R | 8 pamr-1.57/pamr/README.md |only pamr-1.57/pamr/data/khan.rda |binary pamr-1.57/pamr/man/khan.Rd | 14 - pamr-1.57/pamr/man/pamr-package.Rd |only pamr-1.57/pamr/man/pamr.adaptthresh.Rd | 74 +++--- pamr-1.57/pamr/man/pamr.batchadjust.Rd | 54 ++-- pamr-1.57/pamr/man/pamr.confusion.Rd | 51 ++-- pamr-1.57/pamr/man/pamr.confusion.survival.Rd | 40 +-- pamr-1.57/pamr/man/pamr.cv.Rd | 89 +++---- pamr-1.57/pamr/man/pamr.decorrelate.Rd | 79 +++--- pamr-1.57/pamr/man/pamr.fdr.Rd | 68 +++-- pamr-1.57/pamr/man/pamr.geneplot.Rd | 50 ++-- pamr-1.57/pamr/man/pamr.indeterminate.Rd | 45 +-- pamr-1.57/pamr/man/pamr.listgenes.Rd | 58 ++--- pamr-1.57/pamr/man/pamr.makeclasses.Rd | 104 ++++----- pamr-1.57/pamr/man/pamr.menu.Rd | 36 +-- pamr-1.57/pamr/man/pamr.plotcen.Rd | 52 ++-- pamr-1.57/pamr/man/pamr.plotcv.Rd | 40 +-- pamr-1.57/pamr/man/pamr.plotcvprob.Rd | 47 ++-- pamr-1.57/pamr/man/pamr.plotfdr.Rd | 43 +-- pamr-1.57/pamr/man/pamr.plotstrata.Rd | 30 +- pamr-1.57/pamr/man/pamr.plotsurvival.Rd | 32 +- pamr-1.57/pamr/man/pamr.predict.Rd | 73 +++--- pamr-1.57/pamr/man/pamr.predictmany.Rd | 59 ++--- pamr-1.57/pamr/man/pamr.surv.to.class2.Rd | 79 +++--- pamr-1.57/pamr/man/pamr.test.errors.surv.compute.Rd | 42 +-- pamr-1.57/pamr/man/pamr.train.Rd | 230 ++++++++++---------- 59 files changed, 1826 insertions(+), 860 deletions(-)
Title: Evaluation of the Role of Control Variables in Structural
Equation Models
Description: Various opportunities to evaluate the effects of including one or more control variable(s) in structural equation models onto model-implied variances, covariances, and parameter estimates. The derivation of the methodology employed in this package can be obtained from Blötner (2023) <doi:10.31234/osf.io/dy79z>.
Author: Christian Bloetner [aut, cre]
Maintainer: Christian Bloetner <c.bloetner@gmail.com>
Diff between latcontrol versions 0.1.0 dated 2023-08-17 and 0.1.1 dated 2024-07-01
DESCRIPTION | 6 ++--- MD5 | 6 ++--- R/compare.res.R | 57 +++++++++++++++++++++++++++++++++++++++-------------- man/compare.res.Rd | 2 + 4 files changed, 50 insertions(+), 21 deletions(-)