Title: Transform Microplate Data into Tibbles
Description: The goal of 'tidyplate' is to help researchers convert
different types of microplates into tibbles which can be used in data
analysis. It accepts xlsx and csv files formatted in a specific way as
input. It supports all types of standard microplate formats such as
6-well, 12-well, 24-well, 48-well, 96-well, 384-well, and, 1536-well
plates.
Author: Shubham Dutta [aut, cre, cph]
Maintainer: Shubham Dutta <shubhamdutta26@gmail.com>
Diff between tidyplate versions 2.1.0 dated 2024-11-18 and 2.2.0 dated 2024-12-06
DESCRIPTION | 6 MD5 | 63 +++++++-- NEWS.md | 7 + R/utils.R | 5 README.md | 5 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/comparison.R |only inst/doc/comparison.Rmd |only inst/doc/comparison.html |only inst/extdata/example_12_well.csv | 22 +++ inst/extdata/example_1536_well.csv | 138 +++++++++++++++++++- inst/extdata/example_384_well.csv | 72 ++++++++++ inst/extdata/example_96_well.csv | 64 ++++----- inst/performance_tidy.R |only tests/spelling.R | 4 tests/testthat/template_6-well.csv |only tests/testthat/test-build_plate.R | 16 +- tests/testthat/test-tidy_plate.R | 12 + tests/testthat/test_data/12/allPlatesChar.csv |only tests/testthat/test_data/12/allPlatesChar.xlsx |only tests/testthat/test_data/12/allPlatesNumeric.csv |only tests/testthat/test_data/12/allPlatesNumeric.xlsx |only tests/testthat/test_data/1536/allPlatesChar.csv |only tests/testthat/test_data/1536/allPlatesChar.xlsx |only tests/testthat/test_data/1536/allPlatesNumeric.csv |only tests/testthat/test_data/1536/allPlatesNumeric.xlsx |only tests/testthat/test_data/24/allPlatesChar.csv |only tests/testthat/test_data/24/allPlatesChar.xlsx |only tests/testthat/test_data/24/allPlatesNumeric.csv |only tests/testthat/test_data/24/allPlatesNumeric.xlsx |only tests/testthat/test_data/384/allPlatesChar.csv |only tests/testthat/test_data/384/allPlatesChar.xlsx |only tests/testthat/test_data/384/allPlatesNumeric.csv |only tests/testthat/test_data/384/allPlatesNumeric.xlsx |only tests/testthat/test_data/48/allPlatesChar.csv |only tests/testthat/test_data/48/allPlatesChar.xlsx |only tests/testthat/test_data/48/allPlatesNumeric.csv |only tests/testthat/test_data/48/allPlatesNumeric.xlsx |only tests/testthat/test_data/6/allPlatesChar.csv |only tests/testthat/test_data/6/allPlatesChar.xlsx |only tests/testthat/test_data/6/allPlatesNumeric.csv |only tests/testthat/test_data/6/allPlatesNumeric.xlsx |only tests/testthat/test_data/6/badColRowName.csv | 2 tests/testthat/test_data/96/allPlatesChar.csv |only tests/testthat/test_data/96/allPlatesChar.xlsx |only tests/testthat/test_data/96/allPlatesNumeric.csv |only tests/testthat/test_data/96/allPlatesNumeric.xlsx |only vignettes/comparison.Rmd |only vignettes/images |only 50 files changed, 351 insertions(+), 66 deletions(-)
Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments.
Import 'oTree' data and clean them by using functions that handle
messy data, dropouts, and other problematic cases. Create IDs,
calculate the time, transfer variables between app data frames, and
delete sensitive information. Review your experimental data prior to
running the experiment and automatically generate a detailed summary
of the variables used in your 'oTree' code. Information on 'oTree' is
found in Chen, D. L., Schonger, M., & Wickens, C. (2016)
<doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>
Diff between gmoTree versions 1.3.0 dated 2024-12-06 and 1.3.1 dated 2024-12-06
gmoTree-1.3.0/gmoTree/vignettes/title.PNG |only gmoTree-1.3.1/gmoTree/DESCRIPTION | 6 +++--- gmoTree-1.3.1/gmoTree/MD5 | 10 +++++----- gmoTree-1.3.1/gmoTree/NEWS.md | 4 ++++ gmoTree-1.3.1/gmoTree/inst/CITATION | 4 ++-- gmoTree-1.3.1/gmoTree/inst/doc/intro_to_gmoTree.html | 18 +++++++++--------- gmoTree-1.3.1/gmoTree/vignettes/title.png |only 7 files changed, 23 insertions(+), 19 deletions(-)
Title: Statistical Quality Control Simulation
Description: This is a set of statistical quality control functions, that allows plotting control charts and its iterations, process capability for variable and attribute control, highlighting the xrs_gr() function, like a first iteration for variable chart, meanwhile the we_rules() function detects non random patterns in sample.
Author: Erick Marroquin [aut, cre]
Maintainer: Erick Marroquin <ericksuhel@gmail.com>
Diff between XRSCC versions 0.1 dated 2016-11-11 and 0.2 dated 2024-12-06
DESCRIPTION | 17 +++++++++++------ MD5 | 6 +++--- man/C_it.Rd | 3 +-- man/c_gr.Rd | 2 -- 4 files changed, 15 insertions(+), 13 deletions(-)
Title: Generalized Latent Markov Models
Description: Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.
Author: Francesco Bartolucci [aut, cre],
Silvia Pandolfi [aut],
Fulvia Pennoni [aut],
Alessio Farcomeni [ctb],
Alessio Serafini [ctb]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between LMest versions 3.2.3 dated 2024-11-05 and 3.2.4 dated 2024-12-06
DESCRIPTION | 8 ++--- MD5 | 46 +++++++++++++++--------------- R/bootstrap.R | 13 ++++++-- R/draw.R | 27 +++++++++++++++-- R/est_multilogit.R | 5 +-- R/expit.R | 7 ++-- R/functions.R | 1 R/lk_comp_latent_cont.R | 16 ++++++++-- R/lk_obs_latent.R | 14 ++++----- R/lk_obs_latent_cont.R | 25 ++++++++++------ R/lmbasic.cont.R | 2 - R/lmcovlatent.cont.R | 14 ++++----- R/lmestCont.R | 7 ++-- R/lmestDecoding.R | 15 ++++++--- R/lmestMc.R | 64 ++++++++++++++---------------------------- R/mccov.R | 6 +-- R/plot.LMbasic.R | 42 ++++++++++++++++++--------- R/plot.LMbasiccont.R | 31 +++++++++++++------- R/plot.LMlatent.R | 42 ++++++++++++++++++--------- R/plot.LMlatentcont.R | 30 +++++++++++++------ R/plot.LMsearch.R | 3 + R/prob_multilogit.R | 67 ++++++++++++++++++++++---------------------- R/prob_post_cov_cont.R | 66 +++++++++++++++++++++++++++++-------------- inst/doc/vignetteLMest.html | 14 ++++----- 24 files changed, 336 insertions(+), 229 deletions(-)
Title: Piecewise Geodesic Smoothing for Spherical Data
Description: Fitting a smooth path to a given set of noisy spherical data observed at known time points. It implements a piecewise geodesic curve fitting method on the unit sphere based on a velocity-based penalization scheme. The proposed approach is implemented using the Riemannian block coordinate descent algorithm. To understand the method and algorithm, one can refer to Bak, K. Y., Shin, J. K., & Koo, J. Y. (2023) <doi:10.1080/02664763.2022.2054962> for the case of order 1. Additionally, this package includes various functions necessary for handling spherical data.
Author: Jae-Hwan Jhong [aut] ,
Ja-Yong Koo [aut] ,
Seyoung Lee [aut] ,
Kwan-Young Bak [aut, cre, cph]
Maintainer: Kwan-Young Bak <kybak@sungshin.ac.kr>
Diff between spheresmooth versions 0.1.0 dated 2024-04-18 and 0.1.3 dated 2024-12-06
spheresmooth-0.1.0/spheresmooth/man/Exp.Rd |only spheresmooth-0.1.0/spheresmooth/man/Normalize.Rd |only spheresmooth-0.1.0/spheresmooth/man/cross_normalized.Rd |only spheresmooth-0.1.3/spheresmooth/DESCRIPTION | 35 + spheresmooth-0.1.3/spheresmooth/MD5 | 34 - spheresmooth-0.1.3/spheresmooth/NAMESPACE | 13 spheresmooth-0.1.3/spheresmooth/R/linear-spherical-spline.R | 210 ++++------ spheresmooth-0.1.3/spheresmooth/README.md | 71 ++- spheresmooth-0.1.3/spheresmooth/data/apw_spherical.rda |binary spheresmooth-0.1.3/spheresmooth/data/goni_spherical.rda |binary spheresmooth-0.1.3/spheresmooth/man/cartesian_to_spherical.Rd | 14 spheresmooth-0.1.3/spheresmooth/man/cross.Rd | 4 spheresmooth-0.1.3/spheresmooth/man/exp_map.Rd |only spheresmooth-0.1.3/spheresmooth/man/figures/README-unnamed-chunk-6-1.png |binary spheresmooth-0.1.3/spheresmooth/man/figures/README-unnamed-chunk-7-1.png |binary spheresmooth-0.1.3/spheresmooth/man/geodesic.Rd | 8 spheresmooth-0.1.3/spheresmooth/man/geodesic_lower.Rd |only spheresmooth-0.1.3/spheresmooth/man/normalize.Rd |only spheresmooth-0.1.3/spheresmooth/man/normalize_lower.Rd |only spheresmooth-0.1.3/spheresmooth/man/penalized_linear_spherical_spline.Rd | 16 spheresmooth-0.1.3/spheresmooth/man/spheresmooth.Rd |only spheresmooth-0.1.3/spheresmooth/man/spherical_to_cartesian.Rd | 10 22 files changed, 226 insertions(+), 189 deletions(-)
Title: Nested Data Summary, Adverse Events and REDCap
Description: Tools and code snippets for summarizing nested data, adverse events
and REDCap study information.
Author: Lisa Avery [aut] ,
Zeynep Baskurt [aut],
Osvaldo Espin-Garcia [aut],
Katrina Hueniken [aut],
Katherine Lajkosz [aut] ,
Xuan Li [aut],
Tyler Pittman [cre, aut] ,
Anna Santiago [aut] ,
Jessica Weiss [aut],
Wei Xu [aut]
Maintainer: Tyler Pittman <tyler.pittman@uhn.ca>
Diff between BiostatsUHNplus versions 0.0.10 dated 2024-05-24 and 1.0.1 dated 2024-12-06
DESCRIPTION | 6 MD5 | 70 +++++----- NEWS.md | 4 R/ae_timeline_plot.R | 5 R/covsum_nested.R | 9 - R/dsmb_ccru.R | 39 +++-- R/redcap_data_out.R | 16 +- README.md | 35 ++--- man/ae_timeline_plot.Rd | 5 man/covsum_nested.Rd | 4 man/figures/ae_category_attribStart_timeline_plot.png |binary man/figures/ae_category_timeline_plot.png |binary man/figures/ae_detail_timeline_plot.png |binary man/figures/ana10-1.png |binary man/figures/ana9-1.png |binary man/figures/caterpillar_plot_Cows_Model.png |binary man/figures/caterpillar_plot_Yards_Model.png |binary man/figures/caterpillar_plot_ae_category.png |binary man/figures/caterpillar_plot_subject.png |binary man/figures/variance_pie_plot.png |binary man/rm_covsum_nested.Rd | 5 man/tables/ae_detail_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/ae_detail_EXAMPLE_STUDY__30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/category_ByEvent_EXAMPLE_STUDY__30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_A_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_B_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_C_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY_Cohort_D_30OCT2020.xlsx |binary man/tables/category_BySubject_EXAMPLE_STUDY__30OCT2020.xlsx |binary 36 files changed, 107 insertions(+), 91 deletions(-)
More information about BiostatsUHNplus at CRAN
Permanent link
Title: Ultrasound Tongue Imaging
Description: A tool for processing Articulate
Assistant Advanced™ (AAA) export files and plot tongue contour data from any
system.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between rticulate versions 1.7.3 dated 2022-09-04 and 1.7.4 dated 2024-12-06
DESCRIPTION | 10 - MD5 | 20 +- NEWS.md | 5 build/vignette.rds |binary inst/doc/overview.html | 4 inst/doc/polar-gams.html | 380 +++++++++++++++++++++--------------------- inst/doc/tongue-imaging.R | 2 inst/doc/tongue-imaging.html | 204 +++++++++++----------- inst/doc/transform-coord.html | 100 +++++------ vignettes/filter-signals.R |only vignettes/filter-signals.html |only vignettes/kinematics.R |only vignettes/kinematics.html |only 13 files changed, 370 insertions(+), 355 deletions(-)
Title: Network Analysis of Dependencies of CRAN Packages
Description: The dependencies of CRAN packages can be analysed in a network fashion. For each package we can obtain the packages that it depends, imports, suggests, etc. By iterating this procedure over a number of packages, we can build, visualise, and analyse the dependency network, enabling us to have a bird's-eye view of the CRAN ecosystem. One aspect of interest is the number of reverse dependencies of the packages, or equivalently the in-degree distribution of the dependency network. This can be fitted by the power law and/or an extreme value mixture distribution <doi:10.1111/stan.12355>, of which functions are provided.
Author: Clement Lee [aut, cre]
Maintainer: Clement Lee <clement.lee.tm@outlook.com>
Diff between crandep versions 0.3.10 dated 2024-08-18 and 0.3.11 dated 2024-12-06
crandep-0.3.10/crandep/man/topo_sort_kahn.Rd |only crandep-0.3.11/crandep/DESCRIPTION | 6 +- crandep-0.3.11/crandep/MD5 | 27 ++++------ crandep-0.3.11/crandep/NAMESPACE | 5 - crandep-0.3.11/crandep/NEWS.md | 8 +++ crandep-0.3.11/crandep/R/data.R | 2 crandep-0.3.11/crandep/R/graph.R | 57 --------------------- crandep-0.3.11/crandep/build/vignette.rds |binary crandep-0.3.11/crandep/inst/doc/cran.html | 49 +++++++++--------- crandep-0.3.11/crandep/inst/doc/degree.html | 52 +++++++++---------- crandep-0.3.11/crandep/inst/doc/introduction.R | 11 ---- crandep-0.3.11/crandep/inst/doc/introduction.Rmd | 24 --------- crandep-0.3.11/crandep/inst/doc/introduction.html | 58 ++-------------------- crandep-0.3.11/crandep/man/chi_citations.Rd | 2 crandep-0.3.11/crandep/vignettes/introduction.Rmd | 24 --------- 15 files changed, 85 insertions(+), 240 deletions(-)
Title: Tidy Geospatial Networks
Description: Provides a tidy approach to spatial network
analysis, in the form of classes and functions that enable a seamless
interaction between the network analysis package 'tidygraph' and the
spatial analysis package 'sf'.
Author: Lucas van der Meer [aut, cre] ,
Lorena Abad [aut] ,
Andrea Gilardi [aut] ,
Robin Lovelace [aut]
Maintainer: Lucas van der Meer <luukvandermeer@live.nl>
Diff between sfnetworks versions 0.6.4 dated 2024-04-09 and 0.6.5 dated 2024-12-06
DESCRIPTION | 8 MD5 | 171 +- NAMESPACE | 505 +++---- NEWS.md | 515 +++---- R/agr.R | 228 +-- R/attrs.R | 602 ++++---- R/bbox.R | 136 +- R/blend.R | 1014 +++++++------- R/checks.R | 372 ++--- R/edge.R | 616 ++++----- R/geom.R | 436 +++--- R/igraph.R |only R/join.R | 142 +- R/messages.R | 136 +- R/morphers.R | 2377 +++++++++++++++++------------------ R/node.R | 458 +++--- R/paths.R | 874 ++++++------ R/plot.R | 178 +- R/require.R | 296 ++-- R/roxel.R | 32 R/s2.R | 18 R/sf.R | 1526 +++++++++++----------- R/sfnetwork.R | 950 ++++++------- R/sfnetworks-package.R | 16 R/spatstat.R | 158 +- R/tibble.R | 152 +- R/tidygraph.R | 314 ++-- R/utils.R | 912 ++++++------- R/zzz.R | 208 +-- README.md | 130 - build/vignette.rds |binary inst/doc/sfn01_structure.R | 418 +++--- inst/doc/sfn01_structure.Rmd | 714 +++++----- inst/doc/sfn01_structure.html | 2241 ++++++++++++++++---------------- inst/doc/sfn02_preprocess_clean.R | 672 ++++----- inst/doc/sfn02_preprocess_clean.Rmd | 938 ++++++------- inst/doc/sfn02_preprocess_clean.html | 2272 ++++++++++++++++----------------- inst/doc/sfn03_join_filter.R | 542 +++---- inst/doc/sfn03_join_filter.Rmd | 770 +++++------ inst/doc/sfn03_join_filter.html | 2021 ++++++++++++++--------------- inst/doc/sfn04_routing.R | 694 +++++----- inst/doc/sfn04_routing.Rmd | 930 ++++++------- inst/doc/sfn04_routing.html | 1990 ++++++++++++++--------------- inst/doc/sfn05_morphers.R | 538 +++---- inst/doc/sfn05_morphers.Rmd | 784 +++++------ inst/doc/sfn05_morphers.html | 2140 +++++++++++++++---------------- man/as.linnet.Rd | 58 man/as_sfnetwork.Rd | 194 +- man/as_tibble.Rd | 104 - man/autoplot.Rd | 50 man/figures/hexlogo.R | 122 - man/is.sfnetwork.Rd | 52 man/node_coordinates.Rd | 126 - man/plot.sfnetwork.Rd | 106 - man/reexports.Rd | 36 man/roxel.Rd | 56 man/s2.Rd | 34 man/sf.Rd | 450 +++--- man/sf_attr.Rd | 70 - man/sfnetwork.Rd | 246 +-- man/sfnetworks-package.Rd | 66 man/spatial_edge_measures.Rd | 178 +- man/spatial_edge_predicates.Rd | 228 +-- man/spatial_morphers.Rd | 530 +++---- man/spatial_node_predicates.Rd | 210 +-- man/st_network_bbox.Rd | 120 - man/st_network_blend.Rd | 212 +-- man/st_network_cost.Rd | 252 +-- man/st_network_join.Rd | 108 - man/st_network_paths.Rd | 344 ++--- tests/testthat.R | 8 tests/testthat/test_bbox.R | 66 tests/testthat/test_blend.R | 76 - tests/testthat/test_edges_nodes.R | 454 +++--- tests/testthat/test_join.R | 142 +- tests/testthat/test_morphers.R | 572 ++++---- tests/testthat/test_paths.R | 488 +++---- tests/testthat/test_plot.R | 44 tests/testthat/test_sf.R | 428 +++--- tests/testthat/test_sfnetworks.R | 118 - tests/testthat/test_spatstat.R | 38 tests/testthat/test_tidygraph.R | 42 vignettes/sfn01_structure.Rmd | 714 +++++----- vignettes/sfn02_preprocess_clean.Rmd | 938 ++++++------- vignettes/sfn03_join_filter.Rmd | 770 +++++------ vignettes/sfn04_routing.Rmd | 930 ++++++------- vignettes/sfn05_morphers.Rmd | 784 +++++------ 87 files changed, 20842 insertions(+), 20866 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] ,
Danielle Navarro [aut],
Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between rstanemax versions 0.1.6 dated 2024-12-05 and 0.1.7 dated 2024-12-06
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 7 +++++++ R/posterior_predict.R | 18 ++++++++++++++---- inst/doc/emaxmodel.html | 4 ++-- man/posterior_predict.Rd | 7 +++++-- tests/testthat/test-posterior_predict.R | 2 +- tests/testthat/test-stan_emax_binary.R | 1 + 8 files changed, 40 insertions(+), 19 deletions(-)
Title: Communicate with 'Ollama' to Run Large Language Models Locally
Description: Wraps the 'Ollama' <https://ollama.com> API, which can be used to
communicate with generative large language models locally.
Author: Johannes B. Gruber [aut, cre] ,
Maximilian Weber [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between rollama versions 0.1.0 dated 2024-05-01 and 0.2.0 dated 2024-12-06
rollama-0.1.0/rollama/vignettes/bench |only rollama-0.1.0/rollama/vignettes/benchmarking.Rmd.orig |only rollama-0.2.0/rollama/DESCRIPTION | 17 rollama-0.2.0/rollama/MD5 | 93 +-- rollama-0.2.0/rollama/NAMESPACE | 1 rollama-0.2.0/rollama/NEWS.md | 13 rollama-0.2.0/rollama/R/chat.r | 272 +++++++-- rollama-0.2.0/rollama/R/embedding.r | 83 +- rollama-0.2.0/rollama/R/lib.R | 195 ++++-- rollama-0.2.0/rollama/R/models.r | 47 + rollama-0.2.0/rollama/R/rollama-package.R | 9 rollama-0.2.0/rollama/R/utils.r | 109 +++ rollama-0.2.0/rollama/README.md | 370 ++++++------ rollama-0.2.0/rollama/build/vignette.rds |binary rollama-0.2.0/rollama/inst/WORDLIST | 16 rollama-0.2.0/rollama/inst/doc/annotation.Rmd | 326 ++++++---- rollama-0.2.0/rollama/inst/doc/annotation.html | 419 +++++++------- rollama-0.2.0/rollama/inst/doc/hf-gguf.Rmd |only rollama-0.2.0/rollama/inst/doc/hf-gguf.html |only rollama-0.2.0/rollama/inst/doc/image-annotation.Rmd | 46 - rollama-0.2.0/rollama/inst/doc/image-annotation.html | 42 - rollama-0.2.0/rollama/inst/doc/text-embedding.Rmd | 129 ++-- rollama-0.2.0/rollama/inst/doc/text-embedding.html | 149 ++-- rollama-0.2.0/rollama/inst/extdata/logo.png |only rollama-0.2.0/rollama/man/chat_history.Rd | 3 rollama-0.2.0/rollama/man/check_model_installed.Rd | 11 rollama-0.2.0/rollama/man/create_model.Rd | 4 rollama-0.2.0/rollama/man/embed_text.Rd | 14 rollama-0.2.0/rollama/man/list_models.Rd | 2 rollama-0.2.0/rollama/man/make_query.Rd |only rollama-0.2.0/rollama/man/ping_ollama.Rd | 2 rollama-0.2.0/rollama/man/pull_model.Rd | 24 rollama-0.2.0/rollama/man/query.Rd | 81 +- rollama-0.2.0/rollama/man/rollama-options.Rd | 8 rollama-0.2.0/rollama/man/rollama-package.Rd | 3 rollama-0.2.0/rollama/tests/testthat/_snaps |only rollama-0.2.0/rollama/tests/testthat/setup-models.R | 1 rollama-0.2.0/rollama/tests/testthat/test-aaa.R |only rollama-0.2.0/rollama/tests/testthat/test-chat.R | 55 + rollama-0.2.0/rollama/tests/testthat/test-embedding.R | 2 rollama-0.2.0/rollama/tests/testthat/test-make_query.R |only rollama-0.2.0/rollama/tests/testthat/test-models.R | 11 rollama-0.2.0/rollama/tests/testthat/test-utils.R | 2 rollama-0.2.0/rollama/vignettes/README.md | 6 rollama-0.2.0/rollama/vignettes/annotation.Rmd | 326 ++++++---- rollama-0.2.0/rollama/vignettes/annotation.Rmd.orig | 222 ++++--- rollama-0.2.0/rollama/vignettes/figures/smldemo-1.png |binary rollama-0.2.0/rollama/vignettes/hf-gguf.Rmd |only rollama-0.2.0/rollama/vignettes/hf-gguf.Rmd.orig |only rollama-0.2.0/rollama/vignettes/image-annotation.Rmd | 46 - rollama-0.2.0/rollama/vignettes/image-annotation.Rmd.orig | 4 rollama-0.2.0/rollama/vignettes/text-embedding.Rmd | 129 ++-- rollama-0.2.0/rollama/vignettes/text-embedding.Rmd.orig | 14 53 files changed, 1987 insertions(+), 1319 deletions(-)
Title: Project Future Case Incidence
Description: Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>. The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.
Author: Thibaut Jombart [aut, cre],
Pierre Nouvellet [aut],
Sangeeta Bhatia [ctb],
Zhian N. Kamvar [ctb],
Tim Taylor [ctb],
Stephane Ghozzi [ctb]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between projections versions 0.6.0 dated 2023-03-23 and 0.6.1 dated 2024-12-06
DESCRIPTION | 8 - MD5 | 41 ++++++---- NEWS.md | 9 ++ R/summary.R | 1 man/figures |only man/summary.projections.Rd | 37 ++++----- tests/testthat/_snaps/plots/basic-example-plot.svg | 14 +-- tests/testthat/_snaps/plots/evd-proj-box-no-outliers.svg | 14 +-- tests/testthat/_snaps/plots/evd-proj-no-box-custom-lines.svg | 16 +-- tests/testthat/_snaps/plots/evd-proj-no-ribbon.svg | 16 +-- tests/testthat/_snaps/plots/evd-proj-red-box.svg | 14 +-- tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-and-custom.svg | 30 +++---- tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence-no-box.svg | 14 +-- tests/testthat/_snaps/plots/evd-proj-with-incidence-incidence.svg | 16 +-- tests/testthat/_snaps/plots/evd-proj.svg | 16 +-- tests/testthat/test-project.R | 6 - 16 files changed, 138 insertions(+), 114 deletions(-)
Title: Space-Filling Design under Maximin Distance
Description: Constructs a space-filling design under the criterion of maximum-minimum distance. Both discrete and continuous searches are provided.
Author: Furong Sun [aut, cre],
Robert B. Gramacy [aut]
Maintainer: Furong Sun <furong.sun@gmail.com>
Diff between maximin versions 1.0-5 dated 2024-03-13 and 1.0-6 dated 2024-12-06
ChangeLog | 7 +++++++ DESCRIPTION | 19 ++++++++++++++----- MD5 | 8 ++++---- R/maximin.R | 9 +++++---- R/maximin_cand.R | 5 ++++- 5 files changed, 34 insertions(+), 14 deletions(-)
Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments.
Import 'oTree' data and clean them by using functions that handle
messy data, dropouts, and other problematic cases. Create IDs,
calculate the time, transfer variables between app data frames, and
delete sensitive information. Review your experimental data prior to
running the experiment and automatically generate a detailed summary
of the variables used in your 'oTree' code. Information on 'oTree' is
found in Chen, D. L., Schonger, M., & Wickens, C. (2016)
<doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>
Diff between gmoTree versions 1.2.0 dated 2024-09-30 and 1.3.0 dated 2024-12-06
gmoTree-1.2.0/gmoTree/tests/testthat/tests.R |only gmoTree-1.2.0/gmoTree/vignettes/title.png |only gmoTree-1.3.0/gmoTree/DESCRIPTION | 33 gmoTree-1.3.0/gmoTree/MD5 | 134 gmoTree-1.3.0/gmoTree/NEWS.md | 33 gmoTree-1.3.0/gmoTree/R/apptime.R | 19 gmoTree-1.3.0/gmoTree/R/assignv_to_aaw.R | 4 gmoTree-1.3.0/gmoTree/R/codebook.R | 1585 +++-- gmoTree-1.3.0/gmoTree/R/delete_cases.R | 28 gmoTree-1.3.0/gmoTree/R/delete_sessions.R | 28 gmoTree-1.3.0/gmoTree/R/extime.R | 7 gmoTree-1.3.0/gmoTree/R/make_ids.R | 120 gmoTree-1.3.0/gmoTree/R/messy_time.R | 4 gmoTree-1.3.0/gmoTree/R/oTree.R | 2 gmoTree-1.3.0/gmoTree/R/pagesec.R | 2 gmoTree-1.3.0/gmoTree/R/show_dropouts.R | 6 gmoTree-1.3.0/gmoTree/build/vignette.rds |binary gmoTree-1.3.0/gmoTree/inst/CITATION | 4 gmoTree-1.3.0/gmoTree/inst/doc/codebook.R | 8 gmoTree-1.3.0/gmoTree/inst/doc/codebook.Rmd | 75 gmoTree-1.3.0/gmoTree/inst/doc/codebook.html | 288 - gmoTree-1.3.0/gmoTree/inst/doc/intro_to_gmoTree.html | 18 gmoTree-1.3.0/gmoTree/inst/extdata/ocode_new/bargaining/__init__.py | 2 gmoTree-1.3.0/gmoTree/inst/extdata/ocode_new/dictator/__init__.py | 7 gmoTree-1.3.0/gmoTree/inst/extdata/ocode_z/rankaversion/models.py | 2 gmoTree-1.3.0/gmoTree/inst/extdata/ocode_z/rankaversion/pages.py | 1 gmoTree-1.3.0/gmoTree/inst/extdata/ocode_z/rankend/pages.py | 4 gmoTree-1.3.0/gmoTree/inst/extdata/ocode_z/settings.py | 4 gmoTree-1.3.0/gmoTree/inst/rmd/codebook.Rmd | 435 + gmoTree-1.3.0/gmoTree/man/codebook.Rd | 85 gmoTree-1.3.0/gmoTree/man/messy_time.Rd | 4 gmoTree-1.3.0/gmoTree/man/oTree.Rd | 4 gmoTree-1.3.0/gmoTree/tests/testthat/tessts.R |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_count |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_f1 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_f2 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_f3 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_f4 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_f5 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_g/effort_add/Task.html | 1 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_g/effort_add/__init__.py | 3 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_g/effort_add/tests.py | 3 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_new/bargaining/__init__.py | 5 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_new/dictator/__init__.py | 10 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z/rankaversion/models.py | 2 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z/rankaversion/pages.py | 1 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z/rankend/pages.py | 3 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z/settings.py | 4 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z10 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z11 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z13 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z2/rankaversion/models.py | 144 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z2/rankaversion/pages.py | 1 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z2/rankend/models.py | 16 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z2/rankend/pages.py | 3 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z2/settings.py | 8 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z3.1/rankaversion/pages.py | 2 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z3/rankaversion/models.py | 3 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z3/rankaversion/pages.py | 1 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z3/settings.py | 4 gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z4 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z5 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z6 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z7 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z8 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_z9 |only gmoTree-1.3.0/gmoTree/tests/testthat/testdata/ocode_zch |only gmoTree-1.3.0/gmoTree/tests/testthat/tests_codebook.R | 2768 ++++++---- gmoTree-1.3.0/gmoTree/vignettes/codebook.Rmd | 75 gmoTree-1.3.0/gmoTree/vignettes/title.PNG |only 70 files changed, 3885 insertions(+), 2118 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Tyson Barrett [aut, cre] ,
Matt Dowle [aut],
Arun Srinivasan [aut],
Jan Gorecki [aut],
Michael Chirico [aut] ,
Toby Hocking [aut] ,
Benjamin Schwendinger [aut] ,
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Ma [...truncated...]
Maintainer: Tyson Barrett <t.barrett88@gmail.com>
Diff between data.table versions 1.16.2 dated 2024-10-10 and 1.16.4 dated 2024-12-06
DESCRIPTION | 6 MD5 | 40 +-- NEWS.md | 6 R/bmerge.R | 144 +++++++----- build/vignette.rds |binary inst/doc/datatable-benchmarking.html | 2 inst/doc/datatable-faq.html | 2 inst/doc/datatable-importing.html | 2 inst/doc/datatable-intro.R | 48 ++-- inst/doc/datatable-intro.html | 2 inst/doc/datatable-keys-fast-subset.R | 22 - inst/doc/datatable-keys-fast-subset.html | 8 inst/doc/datatable-programming.html | 2 inst/doc/datatable-reference-semantics.R | 26 +- inst/doc/datatable-reference-semantics.html | 2 inst/doc/datatable-reshape.html | 2 inst/doc/datatable-sd-usage.html | 2 inst/doc/datatable-secondary-indices-and-auto-indexing.R | 12 - inst/doc/datatable-secondary-indices-and-auto-indexing.html | 8 inst/tests/tests.Rraw.bz2 |binary src/init.c | 2 21 files changed, 190 insertions(+), 148 deletions(-)
Title: Chronological Ordering for Fossils and Environmental Events
Description: While individual calibrated radiocarbon dates can span several centuries, combining multiple dates together with any chronological constraints can make a chronology much more robust and precise. This package uses Bayesian methods to enforce the chronological ordering of radiocarbon and other dates, for example for trees with multiple radiocarbon dates spaced at exactly known intervals (e.g., 10 annual rings). For methods see Christen 2003 <doi:10.11141/ia.13.2>. Another example is sites where the relative chronological position of the dates is taken into account - the ages of dates further down a site must be older than those of dates further up (Buck, Kenworthy, Litton and Smith 1991 <doi:10.1017/S0003598X00080534>; Nicholls and Jones 2001 <doi:10.1111/1467-9876.00250>). The paper accompanying this R package is Blaauw et al. 2024 <doi:10.1017/RDC.2024.56>.
Author: Maarten Blaauw [aut, cre] ,
Marco A. Aquino Lopez [aut, ctb]
,
J. Andres Christen [aut, ctb, cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between coffee versions 0.4.1 dated 2024-09-25 and 0.4.3 dated 2024-12-06
coffee-0.4.1/coffee/vignettes/strat_gaps.pdf |only coffee-0.4.3/coffee/DESCRIPTION | 9 coffee-0.4.3/coffee/MD5 | 49 coffee-0.4.3/coffee/NAMESPACE | 7 coffee-0.4.3/coffee/NEWS.md | 10 coffee-0.4.3/coffee/R/coffee-package.R | 2 coffee-0.4.3/coffee/R/coffee.R | 16 coffee-0.4.3/coffee/R/plots.R | 191 + coffee-0.4.3/coffee/R/readwrite.R | 9 coffee-0.4.3/coffee/R/strat.R | 113 - coffee-0.4.3/coffee/R/tree.R | 163 + coffee-0.4.3/coffee/R/twalk.R | 4 coffee-0.4.3/coffee/build/partial.rdb |binary coffee-0.4.3/coffee/build/vignette.rds |binary coffee-0.4.3/coffee/inst/doc/coffee.R | 45 coffee-0.4.3/coffee/inst/doc/coffee.Rmd | 49 coffee-0.4.3/coffee/inst/doc/coffee.html | 110 - coffee-0.4.3/coffee/man/MCMCrings.Rd |only coffee-0.4.3/coffee/man/draw.MCMCrings.Rd |only coffee-0.4.3/coffee/man/draw.strat.Rd | 30 coffee-0.4.3/coffee/man/strat.Rd | 11 coffee-0.4.3/coffee/vignettes/MCMCrings.png |only coffee-0.4.3/coffee/vignettes/coffee.Rmd | 49 coffee-0.4.3/coffee/vignettes/strats/mystrat/mystrat.csv | 10 coffee-0.4.3/coffee/vignettes/strats/mystrat/mystrat.out | 1100 +++++++++- coffee-0.4.3/coffee/vignettes/strats/mystrat/mystrat.pdf |only coffee-0.4.3/coffee/vignettes/strats/mystrat/mystrat.png |only coffee-0.4.3/coffee/vignettes/strats/mystrat/mystrat_ages.txt |only coffee-0.4.3/coffee/vignettes/strats/mystrat/mystrat_energy.out | 1100 +++++++++- 29 files changed, 2677 insertions(+), 400 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the
'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi'
library. 'textshaping' is a low-level utility package mainly for
graphic devices that expands upon the font tool-set provided by the
'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between textshaping versions 0.4.0 dated 2024-05-24 and 0.4.1 dated 2024-12-06
DESCRIPTION | 9 +- MD5 | 28 +++--- NEWS.md | 15 ++- R/cpp11.R | 4 R/shape_text.R | 56 +++++++----- build/vignette.rds |binary inst/doc/c_interface.html | 2 man/shape_text.Rd | 2 man/text_width.Rd | 38 ++++++-- src/cpp11.cpp | 8 - src/face_feature.cpp | 8 + src/string_metrics.cpp | 201 ++++++++++++++++++++++++++-------------------- src/string_metrics.h | 2 src/string_shape.cpp | 8 + src/utils.h | 2 15 files changed, 233 insertions(+), 150 deletions(-)
Title: Estimation of Spatial Autoregressive Models with and without
Heteroskedastic Innovations
Description: Functions for fitting Cliff-Ord-type spatial autoregressive models with and without heteroskedastic innovations using Generalized Method of Moments estimation are provided. Some support is available for fitting spatial HAC models, and for fitting with non-spatial endogeneous variables using instrumental variables.
Author: Gianfranco Piras [aut, cre] ,
Roger Bivand [ctb]
Maintainer: Gianfranco Piras <gpiras@mac.com>
Diff between sphet versions 2.0 dated 2022-01-05 and 2.1-1 dated 2024-12-06
sphet-2.0/sphet/R/check_imacts_trace_formula.R |only sphet-2.0/sphet/data/knn10columbus.txt |only sphet-2.0/sphet/man/impacts.Rd |only sphet-2.1-1/sphet/DESCRIPTION | 20 sphet-2.1-1/sphet/MD5 | 52 - sphet-2.1-1/sphet/NAMESPACE | 4 sphet-2.1-1/sphet/R/distance.R | 13 sphet-2.1-1/sphet/R/hidden_functions.R | 1067 +++++++++-------------- sphet-2.1-1/sphet/R/impacts.R | 29 sphet-2.1-1/sphet/R/s2slshac.R | 40 sphet-2.1-1/sphet/R/spreg.R | 138 ++- sphet-2.1-1/sphet/R/summary.sphet.R | 277 +++++- sphet-2.1-1/sphet/R/twostagels.R | 41 sphet-2.1-1/sphet/R/vc_impacts_formula.R | 18 sphet-2.1-1/sphet/build/partial.rdb |binary sphet-2.1-1/sphet/build/vignette.rds |binary sphet-2.1-1/sphet/data/knn10columbus.txt.gz |only sphet-2.1-1/sphet/inst/CITATION | 32 sphet-2.1-1/sphet/inst/doc/sphet.R | 52 - sphet-2.1-1/sphet/inst/doc/sphet.Rnw | 1130 ++++++++++++------------- sphet-2.1-1/sphet/inst/doc/sphet.pdf |binary sphet-2.1-1/sphet/man/gstslshet.Rd | 4 sphet-2.1-1/sphet/man/impacts.error_sphet.Rd | 2 sphet-2.1-1/sphet/man/impacts.gstsls.Rd | 17 sphet-2.1-1/sphet/man/impacts.ols_sphet.Rd | 2 sphet-2.1-1/sphet/man/impacts.stsls_sphet.Rd | 5 sphet-2.1-1/sphet/man/spreg.Rd | 123 ++ sphet-2.1-1/sphet/man/stslshac.Rd | 2 sphet-2.1-1/sphet/vignettes/sphet.Rnw | 1130 ++++++++++++------------- 29 files changed, 2265 insertions(+), 1933 deletions(-)
Title: Reconstructing the Regulatory Programs of Target Genes in
scRNA-Seq Data
Description: Implementation of the scregclust algorithm
described in Larsson, Held, et al. (2024) <doi:10.1038/s41467-024-53954-3>
which reconstructs regulatory programs of target genes in scRNA-seq data.
Target genes are clustered into modules and each module is associated with a linear
model describing the regulatory program.
Author: Felix Held [aut, cre] ,
Ida Larsson [aut] ,
Sven Nelander [aut] ,
Andre Armatowski [ctb]
Maintainer: Felix Held <felix.held@gmail.com>
Diff between scregclust versions 0.1.10 dated 2024-11-21 and 0.2.0 dated 2024-12-06
DESCRIPTION | 12 +- MD5 | 27 ++--- NEWS.md |only R/scregclust.R | 200 +++++++++++++++++++++++++++++++++-------- R/utils.R | 6 - README.md | 8 + inst/doc/pbmc.R | 2 inst/doc/pbmc.Rmd | 2 inst/doc/pbmc.html | 4 man/find_module_sizes.Rd | 2 man/get_target_gene_modules.Rd | 2 man/kmeanspp_init.Rd | 2 man/scregclust.Rd | 13 ++ man/split_sample.Rd | 2 vignettes/pbmc.Rmd | 2 15 files changed, 214 insertions(+), 70 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 14.2.0-1 dated 2024-11-18 and 14.2.2-1 dated 2024-12-06
ChangeLog | 18 +++++++++++ DESCRIPTION | 8 ++--- MD5 | 42 +++++++++++++-------------- configure | 18 +++++------ configure.ac | 2 - inst/NEWS.Rd | 20 ++++++++++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/Base_bones.hpp | 4 +- inst/include/armadillo_bits/Col_bones.hpp | 2 + inst/include/armadillo_bits/Col_meat.hpp | 10 +++--- inst/include/armadillo_bits/Cube_bones.hpp | 7 +++- inst/include/armadillo_bits/Cube_meat.hpp | 8 ++--- inst/include/armadillo_bits/Mat_bones.hpp | 6 ++- inst/include/armadillo_bits/Mat_meat.hpp | 10 +++--- inst/include/armadillo_bits/Row_bones.hpp | 2 + inst/include/armadillo_bits/Row_meat.hpp | 10 +++--- inst/include/armadillo_bits/SpBase_bones.hpp | 4 +- inst/include/armadillo_bits/arma_version.hpp | 2 - inst/include/armadillo_bits/op_max_meat.hpp | 35 +++++++++------------- inst/include/armadillo_bits/op_min_meat.hpp | 35 +++++++++------------- inst/include/armadillo_bits/sym_helper.hpp | 37 ++++++++++++++++++++--- 22 files changed, 172 insertions(+), 108 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 2.3.3 dated 2024-10-04 and 2.3.4 dated 2024-12-06
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 3 ++- R/curve_karcher_mean.R | 39 +++++++++++++++------------------------ R/elastic.distance.R | 2 +- R/multiple_align_functions.R | 9 +++++++-- R/time-warping.R | 7 ++++++- README.md | 4 ++-- man/elastic.distance.Rd | 2 +- man/multiple_align_functions.Rd | 3 +++ man/time_warping.Rd | 3 +++ 11 files changed, 54 insertions(+), 46 deletions(-)
Title: Read and Analyze 'MetIDQ™' Software Output Files
Description: The 'MetAlyzer' S4 object provides methods to read and reformat metabolomics data for convenient data handling, statistics and downstream analysis. The resulting format corresponds to input data of the Shiny app 'MetaboExtract' (<https://www.metaboextract.shiny.dkfz.de/MetaboExtract/>).
Author: Nils Mechtel [aut, cre] ,
Luis Herfurth [aut] ,
Carolin Andresen [aut] ,
Daniel Huebschmann [aut]
Maintainer: Nils Mechtel <nils.mech@gmail.com>
Diff between MetAlyzer versions 1.0.0 dated 2024-03-12 and 1.1.0 dated 2024-12-06
MetAlyzer-1.0.0/MetAlyzer/inst/extdata/pathway.xlsx |only MetAlyzer-1.0.0/MetAlyzer/man/apply_linear_model.Rd |only MetAlyzer-1.1.0/MetAlyzer/DESCRIPTION | 12 MetAlyzer-1.1.0/MetAlyzer/MD5 | 36 +- MetAlyzer-1.1.0/MetAlyzer/NAMESPACE | 13 MetAlyzer-1.1.0/MetAlyzer/NEWS.md | 5 MetAlyzer-1.1.0/MetAlyzer/R/MetAlyzer_dataset.R | 21 - MetAlyzer-1.1.0/MetAlyzer/R/MetAlyzer_fpaths.R | 2 MetAlyzer-1.1.0/MetAlyzer/R/calculate_log2FC.R | 141 +++------- MetAlyzer-1.1.0/MetAlyzer/R/plotly_log2FC.R |only MetAlyzer-1.1.0/MetAlyzer/R/plotly_network.R |only MetAlyzer-1.1.0/MetAlyzer/README.md | 3 MetAlyzer-1.1.0/MetAlyzer/build/vignette.rds |binary MetAlyzer-1.1.0/MetAlyzer/inst/doc/MetAlyzer_User_Guide.R | 6 MetAlyzer-1.1.0/MetAlyzer/inst/doc/MetAlyzer_User_Guide.html | 64 ++-- MetAlyzer-1.1.0/MetAlyzer/inst/extdata/Pathway_101024.xlsx |only MetAlyzer-1.1.0/MetAlyzer/man/calculate_log2FC.Rd | 4 MetAlyzer-1.1.0/MetAlyzer/man/plotly_network.Rd |only MetAlyzer-1.1.0/MetAlyzer/man/plotly_scatter.Rd |only MetAlyzer-1.1.0/MetAlyzer/man/plotly_vulcano.Rd |only MetAlyzer-1.1.0/MetAlyzer/vignettes/MetAlyzer_User_Guide_files/figure-html/plot_log2FC_scatter-1.png |binary MetAlyzer-1.1.0/MetAlyzer/vignettes/MetAlyzer_User_Guide_files/figure-html/plot_log2FC_vulcano-1.png |binary MetAlyzer-1.1.0/MetAlyzer/vignettes/MetAlyzer_User_Guide_files/figure-html/plot_network-1.png |binary 23 files changed, 143 insertions(+), 164 deletions(-)
Title: Collection of Functions for Working with Age Intervals
Description: Provides a collection of efficient functions for working with
individual ages and corresponding intervals. These include functions for
conversion from an age to an interval, aggregation of ages with associated
counts in to intervals and the splitting of interval counts based on
specified age distributions.
Author: Tim Taylor [aut, cre, cph] ,
Edwin van Leeuwen [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ageutils versions 0.0.6 dated 2024-11-27 and 0.0.7 dated 2024-12-06
DESCRIPTION | 6 ++-- MD5 | 10 +++---- NEWS.md | 5 +++ R/reaggregate_rates.R | 1 README.md | 2 - tests/testthat/test-reaggregate_rates.R | 45 ++++++++++++++++++++++++++++++++ 6 files changed, 60 insertions(+), 9 deletions(-)
Title: Secure in-Browser and Database Storage for 'shiny' Inputs,
Outputs, Views and User Likes
Description: Store persistent and synchronized data from 'shiny' inputs within the browser. Refresh 'shiny' applications and preserve user-inputs over multiple sessions. A database-like storage format is implemented using 'Dexie.js' <https://dexie.org>, a minimal wrapper for 'IndexedDB'. Transfer browser link parameters to 'shiny' input or output values. Store app visitor views, likes and followers.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between shinyStorePlus versions 1.2 dated 2024-08-17 and 1.3 dated 2024-12-06
DESCRIPTION | 12 +- MD5 | 32 +++--- NAMESPACE | 3 NEWS.md | 12 +- R/includes.R | 82 +++++++++++++++- R/setup_rpkg.R |only README.md | 43 ++++++++ build/vignette.rds |binary inst/doc/introduction_to_shinystoreplus.html | 4 inst/doc/shinystoreplus_v08.html | 4 inst/doc/shinystoreplus_v12.html | 4 inst/doc/store_shiny_visitor_views_likes_followers.R |only inst/doc/store_shiny_visitor_views_likes_followers.Rmd |only inst/doc/store_shiny_visitor_views_likes_followers.html |only inst/doc/using_shinystoreplus.html | 4 inst/example/visitViewsLikesFollowers |only inst/scripts/rpkg.js |only man/initStore.Rd | 56 ++++++++++ man/rpkgapi.Rd |only man/shinyStorePlus-package.Rd | 4 vignettes/store_shiny_visitor_views_likes_followers.Rmd |only 21 files changed, 224 insertions(+), 36 deletions(-)
More information about shinyStorePlus at CRAN
Permanent link
Title: R Interface to a 'PostGIS' Database
Description: Provides an interface between R and 'PostGIS'-enabled
'PostgreSQL' databases to transparently transfer spatial
data. Both vector (points, lines, polygons) and raster data are
supported in read and write modes. Also provides convenience
functions to execute common procedures in 'PostgreSQL/PostGIS'.
Author: Adrian Cidre Gonzalez [aut, cre]
,
Mathieu Basille [aut] ,
David Bucklin [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between rpostgis versions 1.5.1 dated 2023-11-20 and 1.6.0 dated 2024-12-06
rpostgis-1.5.1/rpostgis/R/rpostgis-package.R |only rpostgis-1.5.1/rpostgis/man/figures/Rlogo.svg |only rpostgis-1.5.1/rpostgis/man/figures/postgis-logo-body.png |only rpostgis-1.5.1/rpostgis/man/figures/postgis-logo-head.png |only rpostgis-1.5.1/rpostgis/man/figures/postgis-logo-head2.png |only rpostgis-1.5.1/rpostgis/man/figures/postgis-logo.png |only rpostgis-1.5.1/rpostgis/man/figures/rpostgis-1024-transp.png |only rpostgis-1.5.1/rpostgis/man/figures/rpostgis-1024-white.png |only rpostgis-1.5.1/rpostgis/man/figures/rpostgis-200-transp.png |only rpostgis-1.5.1/rpostgis/man/figures/rpostgis-200-white.png |only rpostgis-1.5.1/rpostgis/man/figures/rpostgis.svg |only rpostgis-1.5.1/rpostgis/man/rpostgis.Rd |only rpostgis-1.6.0/rpostgis/DESCRIPTION | 34 rpostgis-1.6.0/rpostgis/MD5 | 98 +- rpostgis-1.6.0/rpostgis/NAMESPACE | 20 rpostgis-1.6.0/rpostgis/NEWS.md | 36 rpostgis-1.6.0/rpostgis/R/all_db_wrapper_fns.R | 254 +++--- rpostgis-1.6.0/rpostgis/R/dbUtils_notExported.R | 84 +- rpostgis-1.6.0/rpostgis/R/dbWriteDataFrame.R | 161 ++- rpostgis-1.6.0/rpostgis/R/pgGetBoundary.R | 82 +- rpostgis-1.6.0/rpostgis/R/pgGetGeom.R | 104 +- rpostgis-1.6.0/rpostgis/R/pgGetRast.R | 192 ++-- rpostgis-1.6.0/rpostgis/R/pgInsertize.R | 226 ++--- rpostgis-1.6.0/rpostgis/R/pgListGeom.R | 4 rpostgis-1.6.0/rpostgis/R/pgMakePts.R | 51 - rpostgis-1.6.0/rpostgis/R/pgPostGIS.R | 192 ++-- rpostgis-1.6.0/rpostgis/R/pgSRID.R | 99 +- rpostgis-1.6.0/rpostgis/R/pgWriteGeom.R | 444 +++++------ rpostgis-1.6.0/rpostgis/R/pgWriteRast.R | 223 ++--- rpostgis-1.6.0/rpostgis/R/rposrgis-package.R |only rpostgis-1.6.0/rpostgis/R/startup.R | 18 rpostgis-1.6.0/rpostgis/README.md | 51 - rpostgis-1.6.0/rpostgis/man/dbAddKey.Rd | 4 rpostgis-1.6.0/rpostgis/man/dbAsDate.Rd | 6 rpostgis-1.6.0/rpostgis/man/dbColumn.Rd | 4 rpostgis-1.6.0/rpostgis/man/dbComment.Rd | 4 rpostgis-1.6.0/rpostgis/man/dbDrop.Rd | 8 rpostgis-1.6.0/rpostgis/man/dbIndex.Rd | 10 rpostgis-1.6.0/rpostgis/man/dbSchema.Rd | 7 rpostgis-1.6.0/rpostgis/man/dbTableInfo.Rd | 3 rpostgis-1.6.0/rpostgis/man/dbTableNameFix.Rd | 2 rpostgis-1.6.0/rpostgis/man/dbVacuum.Rd | 4 rpostgis-1.6.0/rpostgis/man/dbWriteDataFrame.Rd | 18 rpostgis-1.6.0/rpostgis/man/figures/logo.png |binary rpostgis-1.6.0/rpostgis/man/pgGetBoundary.Rd | 11 rpostgis-1.6.0/rpostgis/man/pgGetGeom.Rd | 8 rpostgis-1.6.0/rpostgis/man/pgGetRast.Rd | 28 rpostgis-1.6.0/rpostgis/man/pgInsert.Rd | 65 - rpostgis-1.6.0/rpostgis/man/pgInsertizeGeom.Rd | 32 rpostgis-1.6.0/rpostgis/man/pgListGeom.Rd | 4 rpostgis-1.6.0/rpostgis/man/pgMakePts.Rd | 13 rpostgis-1.6.0/rpostgis/man/pgPostGIS.Rd | 7 rpostgis-1.6.0/rpostgis/man/pgSRID.Rd | 9 rpostgis-1.6.0/rpostgis/man/pgWriteGeom.Rd | 57 - rpostgis-1.6.0/rpostgis/man/pgWriteRast.Rd | 24 rpostgis-1.6.0/rpostgis/man/rpostgis-package.Rd |only rpostgis-1.6.0/rpostgis/man/warn_deprecated_rc.Rd |only rpostgis-1.6.0/rpostgis/man/warn_deprecated_sp.Rd |only 58 files changed, 1394 insertions(+), 1307 deletions(-)
Title: Bayesian Network Learning with the PCHC and Related Algorithms
Description: Bayesian network learning using the PCHC, FEDHC, MMHC and variants of these algorithms. PCHC stands for PC Hill-Climbing, a new hybrid algorithm that uses PC to construct the skeleton of the BN and then
applies the Hill-Climbing greedy search. More algorithms and variants have been added, such as MMHC, FEDHC, and the Tabu search variants, PCTABU, MMTABU and FEDTABU.
The relevant papers are:
a) Tsagris M. (2021). "A new scalable Bayesian network learning algorithm with applications to economics". Computational Economics, 57(1): 341-367. <doi:10.1007/s10614-020-10065-7>.
b) Tsagris M. (2022). "The FEDHC Bayesian Network Learning Algorithm". Mathematics 2022, 10(15): 2604. <doi:10.3390/math10152604>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between pchc versions 1.2 dated 2023-09-06 and 1.3 dated 2024-12-06
DESCRIPTION | 15 +-- MD5 | 68 +++++++------- NAMESPACE | 1 R/dcor.fedhc.skel.R | 6 - R/dcor.mmhc.skel.R |only R/fedhc.skel.R | 226 +++++++++++++++++++++-------------------------- R/onAttach.R |only man/bn.skel.utils.Rd | 6 - man/bnmat.Rd | 2 man/bnplot.Rd | 2 man/cat.tests.Rd | 12 +- man/conf.edge.lower.Rd | 3 man/cor.fbed.Rd | 2 man/corpairs.Rd | 4 man/cortest.Rd | 2 man/dcor.fedhc.skel.Rd | 31 ++++-- man/fedhc.Rd | 10 +- man/fedhc.boot.Rd | 8 - man/fedhc.skel.Rd | 12 -- man/g2test.Rd | 7 - man/g2test_univariate.Rd | 7 - man/is.dag.Rd | 4 man/mmhc.Rd | 8 - man/mmhc.boot.Rd | 8 - man/mmhc.skel.Rd | 15 +-- man/mmpc.Rd | 16 +-- man/pc.sel.Rd | 3 man/pchc-package.Rd | 12 +- man/pchc.Rd | 11 +- man/pchc.boot.Rd | 11 +- man/pchc.skel.Rd | 10 +- man/pchc.skel.boot.Rd | 6 - man/pi0est.Rd | 5 - man/rbn2.Rd | 6 - man/rmcd.Rd | 13 +- man/topological_sort.Rd | 4 36 files changed, 274 insertions(+), 282 deletions(-)
Title: Testing Goodness-of-Fit with the Kernel Density Estimator
Description: Tests of goodness-of-fit based on a kernel smoothing of the data.
References:
Pavía (2015) <doi:10.18637/jss.v066.c01>.
Author: Jose M. Pavia [aut, cre]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between GoFKernel versions 2.1-1 dated 2018-05-26 and 2.1-3 dated 2024-12-06
DESCRIPTION | 20 ++++++++++++++------ MD5 | 6 +++--- inst/CITATION | 9 ++++----- man/inverse.Rd | 2 -- 4 files changed, 21 insertions(+), 16 deletions(-)
Title: Empirical Likelihood Ratio for Censored/Truncated Data
Description: Empirical likelihood ratio tests and confidence intervals for means/quantiles/hazards
from possibly censored and/or truncated data. In particular, the empirical likelihood
for the Kaplan-Meier/Nelson-Aalen estimator. Now does AFT regression too.
Author: Mai Zhou [aut, cre, cph],
Yifan Yang [aut],
Art Owen [aut]
Maintainer: Mai Zhou <maizhou@gmail.com>
Diff between emplik versions 1.3-1 dated 2023-09-07 and 1.3-2 dated 2024-12-06
DESCRIPTION | 27 +++++++++++++++++---------- MD5 | 42 +++++++++++++++++++++--------------------- README | 2 +- man/BJnoint.Rd | 9 ++++++--- man/RankRegTest.Rd | 2 +- man/RankRegTestH.Rd | 2 +- man/WRegEst.Rd | 6 +++--- man/WRegTest.Rd | 10 +++++----- man/bjtestII.Rd | 8 +++++--- man/el.cen.kmc1d.Rd | 26 ++------------------------ man/emplik-package.Rd | 12 ++++++------ man/emplikH1B.Rd | 2 +- man/emplikH1P.Rd | 3 +-- man/emplikH2B.Rd | 4 ++-- man/emplikH2P.Rd | 2 +- man/emplikHs.disc2.Rd | 2 +- man/emplikHs.test2.Rd | 4 +++- man/findLnew.Rd | 5 +++-- man/findUL.Rd | 2 +- man/findUL2.Rd | 2 +- man/findULold.Rd | 4 ++-- man/findUnew.Rd | 4 ++-- 22 files changed, 86 insertions(+), 94 deletions(-)
Title: Contrast Analyses for Factorial Designs
Description: Contrast analysis for factorial designs provides an
alternative to the traditional ANOVA approach, offering the distinct
advantage of testing targeted hypotheses. The foundation of this
package is primarily rooted in the works of Rosenthal, Rosnow, and
Rubin (2000, ISBN: 978-0521659802) as well as Sedlmeier and Renkewitz
(2018, ISBN: 978-3868943214).
Author: Johannes Titz [aut, cre],
Markus Burkhardt [aut],
Mirka Henninger [ctb],
Simone Malejka [ctb]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Diff between cofad versions 0.3.0 dated 2024-07-05 and 0.3.1 dated 2024-12-06
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++------- NEWS.md | 11 ++++++++++- R/data.R | 25 ++++++++++++++++++++++++- README.md | 48 ++++++++++-------------------------------------- build/partial.rdb |binary data/akan.rda |binary data/maraver.rda |only man/akan.Rd | 2 +- man/maraver.Rd |only 10 files changed, 58 insertions(+), 52 deletions(-)
Title: Bayesian Projection of Life Expectancy
Description: Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-012-0193-x>. Subnational projections are also supported.
Author: Hana Sevcikova [cre, aut],
Adrian Raftery [aut],
Jennifer Chunn [aut]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesLife versions 5.2-0 dated 2023-09-16 and 5.3-1 dated 2024-12-06
bayesLife-5.2-0/bayesLife/tests/last.dump.rda |only bayesLife-5.3-1/bayesLife/ChangeLog | 20 +++ bayesLife-5.3-1/bayesLife/DESCRIPTION | 26 +++- bayesLife-5.3-1/bayesLife/MD5 | 46 +++---- bayesLife-5.3-1/bayesLife/NAMESPACE | 1 bayesLife-5.3-1/bayesLife/R/diagnostics.R | 2 bayesLife-5.3-1/bayesLife/R/get_outputs.R | 20 ++- bayesLife-5.3-1/bayesLife/R/plot_functions.R | 84 ++++++++++---- bayesLife-5.3-1/bayesLife/R/project_subnat.R | 8 - bayesLife-5.3-1/bayesLife/R/projection_fcns.R | 62 +++++----- bayesLife-5.3-1/bayesLife/R/run_mcmc.R | 22 ++- bayesLife-5.3-1/bayesLife/R/wpp_data.R | 24 ++-- bayesLife-5.3-1/bayesLife/data/include_2024.rda |only bayesLife-5.3-1/bayesLife/man/convert.trajectories.Rd | 5 bayesLife-5.3-1/bayesLife/man/e0.median.set.Rd | 17 +- bayesLife-5.3-1/bayesLife/man/e0.predict.Rd | 7 - bayesLife-5.3-1/bayesLife/man/e0.predict.extra.Rd | 3 bayesLife-5.3-1/bayesLife/man/e0.predict.subnat.Rd | 5 bayesLife-5.3-1/bayesLife/man/e0.raftery.diag.Rd | 6 - bayesLife-5.3-1/bayesLife/man/e0.trajectories.plot.Rd | 3 bayesLife-5.3-1/bayesLife/man/get.e0.prediction.Rd | 19 ++- bayesLife-5.3-1/bayesLife/man/include.Rd | 2 bayesLife-5.3-1/bayesLife/man/run.e0.mcmc.Rd | 8 - bayesLife-5.3-1/bayesLife/man/write.projection.summary.Rd | 7 - bayesLife-5.3-1/bayesLife/tests/run_tests.R | 4 25 files changed, 266 insertions(+), 135 deletions(-)
Title: Covariance Measure Tests for Conditional Independence
Description: Covariance measure tests for conditional independence testing
against conditional covariance and nonlinear conditional mean alternatives.
Contains versions of the generalised covariance measure test
(Shah and Peters, 2020, <doi:10.1214/19-aos1857>) and projected covariance
measure test (Lundborg et al., 2023, <doi:10.48550/arXiv.2211.02039>).
Applications can be found in
Kook and Lundborg (2024, <doi:10.1093/bib/bbae475>).
Author: Lucas Kook [aut, cre],
Anton Rask Lundborg [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between comets versions 0.0-3 dated 2024-09-20 and 0.1-0 dated 2024-12-06
DESCRIPTION | 6 - MD5 | 27 +++---- NAMESPACE | 8 +- R/comet.R | 17 ++-- R/equiv.R | 2 R/gcm.R | 201 ++++++++++++++++++++++++++++++----------------------- R/pcm.R | 57 ++++++++------- R/regressions.R | 53 ++++++++++++- R/wgcm.R | 44 +++++++---- build/partial.rdb |binary man/comet.Rd | 7 + man/gcm.Rd | 2 man/pcm.Rd | 6 - man/regressions.Rd | 3 man/rgcm.Rd |only 15 files changed, 271 insertions(+), 162 deletions(-)