Title: Creating and Annotating a Composite Plot in 'ggplot2'
Description: Provides functions for creating and annotating a composite plot in 'ggplot2'. Offers background themes and shortcut plotting functions that produce figures that are appropriate for the format of scientific journals. Some methods are described in Min and Zhou (2021) <doi:10.3389/fgene.2021.802894>.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun (Sam) Min <seung.min@mail.mcgill.ca>
Diff between smplot2 versions 0.2.0 dated 2024-04-14 and 0.2.1 dated 2024-04-27
smplot2-0.2.0/smplot2/R/sm_add_arrow.R |only smplot2-0.2.0/smplot2/R/sm_add_line.R |only smplot2-0.2.0/smplot2/R/sm_add_polygon.R |only smplot2-0.2.0/smplot2/R/sm_add_rect.R |only smplot2-0.2.0/smplot2/man/sm_add_arrow.Rd |only smplot2-0.2.0/smplot2/man/sm_add_line.Rd |only smplot2-0.2.0/smplot2/man/sm_add_polygon.Rd |only smplot2-0.2.0/smplot2/man/sm_add_rect.Rd |only smplot2-0.2.1/smplot2/DESCRIPTION | 12 ++--- smplot2-0.2.1/smplot2/MD5 | 38 ++++++---------- smplot2-0.2.1/smplot2/NAMESPACE | 4 - smplot2-0.2.1/smplot2/NEWS.md | 6 ++ smplot2-0.2.1/smplot2/R/sm_add_legend.R | 2 smplot2-0.2.1/smplot2/R/sm_add_point.R | 10 +--- smplot2-0.2.1/smplot2/R/sm_add_text.R | 8 +-- smplot2-0.2.1/smplot2/R/sm_auc_all.R | 2 smplot2-0.2.1/smplot2/R/sm_common_axis.R | 63 ++++++++++++++++++++------- smplot2-0.2.1/smplot2/R/sm_plot_clean.R | 42 +++++++++++++----- smplot2-0.2.1/smplot2/R/sm_put_together.R | 45 ++++++++++++++++--- smplot2-0.2.1/smplot2/R/sm_slope_all.R | 2 smplot2-0.2.1/smplot2/man/sm_add_point.Rd | 6 -- smplot2-0.2.1/smplot2/man/sm_add_text.Rd | 9 +-- smplot2-0.2.1/smplot2/man/sm_common_axis.Rd | 10 ++-- smplot2-0.2.1/smplot2/man/sm_put_together.Rd | 22 +++++++++ 24 files changed, 188 insertions(+), 93 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>), univariate and multivariate (<doi:10.1186/s12711-022-00730-w>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.7 dated 2024-04-04 and 2.2.8 dated 2024-04-27
bWGR-2.2.7/bWGR/src/RegisteringDynamic.c |only bWGR-2.2.7/bWGR/src/added20230407.cpp |only bWGR-2.2.7/bWGR/src/eigen20220714.cpp |only bWGR-2.2.7/bWGR/src/emm20220213.cpp |only bWGR-2.2.7/bWGR/src/mega20231111.cpp |only bWGR-2.2.7/bWGR/src/mega20240303.cpp |only bWGR-2.2.7/bWGR/src/mrr20220709.cpp |only bWGR-2.2.7/bWGR/src/wgr20210213.cpp |only bWGR-2.2.8/bWGR/DESCRIPTION | 8 bWGR-2.2.8/bWGR/MD5 | 24 bWGR-2.2.8/bWGR/R/RcppExports.R | 276 +++---- bWGR-2.2.8/bWGR/R/mix.R | 77 +- bWGR-2.2.8/bWGR/man/bWGR.Rd | 4 bWGR-2.2.8/bWGR/man/mvr.Rd | 12 bWGR-2.2.8/bWGR/man/xtra.Rd | 9 bWGR-2.2.8/bWGR/src/Rcpp20230423.cpp |only bWGR-2.2.8/bWGR/src/RcppEigen20230423.cpp |only bWGR-2.2.8/bWGR/src/RcppExports.cpp | 1153 +++++++++++++++--------------- 18 files changed, 823 insertions(+), 740 deletions(-)
Title: Easily Create Pretty Popup Messages (Modals) in 'Shiny'
Description: Easily create pretty popup messages (modals) in 'Shiny'. A modal can
contain text, images, OK/Cancel buttons, an input to get a response from the
user, and many more customizable options.
Author: Dean Attali [aut, cre] ,
Tristan Edwards [aut] ,
Zhengjia Wang [ctb]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between shinyalert versions 3.0.0 dated 2021-12-20 and 3.1.0 dated 2024-04-27
shinyalert-3.0.0/shinyalert/inst/www |only shinyalert-3.1.0/shinyalert/DESCRIPTION | 12 +- shinyalert-3.1.0/shinyalert/LICENSE | 2 shinyalert-3.1.0/shinyalert/MD5 | 32 +++-- shinyalert-3.1.0/shinyalert/NEWS.md | 7 + shinyalert-3.1.0/shinyalert/R/shinyalert-package.R |only shinyalert-3.1.0/shinyalert/R/shinyalert.R | 19 --- shinyalert-3.1.0/shinyalert/R/useShinyalert.R | 4 shinyalert-3.1.0/shinyalert/R/utils.R | 57 ++++------ shinyalert-3.1.0/shinyalert/README.md | 64 ++++++----- shinyalert-3.1.0/shinyalert/inst/assets |only shinyalert-3.1.0/shinyalert/man/shinyalert-package.Rd |only shinyalert-3.1.0/shinyalert/man/shinyalert.Rd | 4 shinyalert-3.1.0/shinyalert/man/useShinyalert.Rd | 102 +++++++++--------- 14 files changed, 149 insertions(+), 154 deletions(-)
Title: Convert Addresses to Standard Inputs
Description: Efficient tools for parsing and standardizing Australian
addresses from textual data. It utilizes optimized algorithms to accurately identify and
extract components of addresses, such as street names, types, and postcodes, especially
for large batched data in contexts where sending addresses to internet services may be
slow or inappropriate. The core functionality is built on fast string processing techniques
to handle variations in address formats and abbreviations commonly found in Australian
address data. Designed for data scientists, urban planners, and logistics analysts, the
package facilitates the cleaning and normalization of address information, supporting
better data integration and analysis in urban studies, geography, and related fields.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between healthyAddress versions 0.2.0 dated 2024-02-07 and 0.4.1 dated 2024-04-27
DESCRIPTION | 8 - MD5 | 43 ++++--- NAMESPACE | 10 + NEWS.md | 27 +++- R/download_latlon_data.R |only R/healthyAddress-package.R | 5 R/latlon.R |only R/mutate_latlon.R |only R/postcode2ste.R | 105 +++++++++--------- R/unique_Postcodes.R | 43 +++++-- inst/extdata/POSTCODE-STREET_TYPE_CODE-STREET_NAME.qs |binary inst/tinytest/test_compress_latlon.R |only inst/tinytest/test_healthyAddress.R | 6 + inst/tinytest/test_is_postcode.R | 2 inst/tinytest/test_unique_Postcodes.R | 3 man/compress_latlon.Rd |only man/download_latlon_data.Rd |only man/healthyAddress-package.Rd | 8 + man/mutate_latlon.Rd |only man/unique_Postcodes.Rd | 44 ++++--- src/StandardAddress.c | 95 +++++++++------- src/constants.c |only src/healthyAddress.h | 19 ++- src/init.c | 16 ++ src/latlon.c |only src/postcode2intrnl.c | 7 - src/verifyEquiStr.c | 13 ++ 27 files changed, 303 insertions(+), 151 deletions(-)
More information about healthyAddress at CRAN
Permanent link
Title: 'teal' Modules for Standard Clinical Outputs
Description: Provides user-friendly tools for creating and customizing
clinical trial reports. By leveraging the 'teal' framework, this
package provides 'teal' modules to easily create an interactive panel
that allows for seamless adjustments to data presentation, thereby
streamlining the creation of detailed and accurate reports.
Author: Joe Zhu [aut, cre],
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Mahmoud Hallal [aut],
Dawid Kaledkowski [aut],
Rosemary Li [aut],
Heng Wang [aut],
Pawel Rucki [aut],
Nikolas Burkoff [aut],
Konrad Paga [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between teal.modules.clinical versions 0.9.0 dated 2024-02-23 and 0.9.1 dated 2024-04-27
teal.modules.clinical-0.9.0/teal.modules.clinical/man/teal.modules.clinical.Rd |only teal.modules.clinical-0.9.1/teal.modules.clinical/DESCRIPTION | 45 - teal.modules.clinical-0.9.1/teal.modules.clinical/MD5 | 355 +++++----- teal.modules.clinical-0.9.1/teal.modules.clinical/NAMESPACE | 1 teal.modules.clinical-0.9.1/teal.modules.clinical/NEWS.md | 16 teal.modules.clinical-0.9.1/teal.modules.clinical/R/argument_convention.R | 16 teal.modules.clinical-0.9.1/teal.modules.clinical/R/arm_ref_comp.R | 8 teal.modules.clinical-0.9.1/teal.modules.clinical/R/labels.R | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/R/string_ops.R | 13 teal.modules.clinical-0.9.1/teal.modules.clinical/R/teal.modules.clinical.R | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_a_gee.R | 50 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_a_mmrm.R | 138 +-- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_barchart_simple.R | 71 -- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_ci.R | 34 teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_forest_rsp.R | 155 ++-- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_forest_tte.R | 143 ++-- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_ipp.R | 42 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_km.R | 176 +++- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_lineplot.R | 48 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_pp_adverse_events.R | 46 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_pp_patient_timeline.R | 67 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_pp_therapy.R | 48 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_g_pp_vitals.R | 54 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_abnormality.R | 43 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_abnormality_by_worst_grade.R | 63 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_ancova.R | 72 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_binary_outcome.R | 130 ++- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_coxreg.R | 82 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_events.R | 50 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_events_by_grade.R | 72 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_events_patyear.R | 46 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_events_summary.R | 53 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_exposure.R | 39 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_logistic.R | 76 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_mult_events.R | 44 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_pp_basic_info.R | 40 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_pp_laboratory.R | 46 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_pp_medical_history.R | 42 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_pp_prior_medication.R | 36 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_shift_by_arm.R | 56 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_shift_by_arm_by_worst.R | 60 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_shift_by_grade.R | 46 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_smq.R | 36 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_summary.R | 64 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_summary_by.R | 66 - teal.modules.clinical-0.9.1/teal.modules.clinical/R/tm_t_tte.R | 86 +- teal.modules.clinical-0.9.1/teal.modules.clinical/R/utils.R | 13 teal.modules.clinical-0.9.1/teal.modules.clinical/R/validate_standard_inputs.R | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/R/zzz.R | 3 teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adae.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adaette.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adcm.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adeg.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adex.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adlb.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_admh.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adqs.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adrs.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adsl.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_adtte.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/data/tmc_ex_advs.rda |binary teal.modules.clinical-0.9.1/teal.modules.clinical/inst/WORDLIST | 1 teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/generate_tmc_test_data.R | 100 +- teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/generate_tmc_test_data.Rmd | 103 +- teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/generate_tmc_test_data.html | 251 +++---- teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/quickstart_substitute.R | 38 - teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/quickstart_substitute.Rmd | 15 teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/quickstart_substitute.html | 25 teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/teal-modules-clinical.Rmd | 14 teal.modules.clinical-0.9.1/teal.modules.clinical/inst/doc/teal-modules-clinical.html | 18 teal.modules.clinical-0.9.1/teal.modules.clinical/man/add_expr.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/arm_ref_comp_observer.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/column_annotation_label.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/extract_input.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/h_concat_expr.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/make_barchart_simple_call.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/module_arguments.Rd | 10 teal.modules.clinical-0.9.1/teal.modules.clinical/man/teal.modules.clinical-package.Rd |only teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_a_gee.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_abnormality.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_abnormality_by_worst_grade.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_adverse_events.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_ancova.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_arguments.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_binary_outcome.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_coxreg_m.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_coxreg_u.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_events.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_events_by_grade.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_events_col_by_grade.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_events_patyear.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_exposure.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_fit_mmrm.Rd | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_forest_rsp.Rd | 14 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_forest_tte.Rd | 9 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_g_ci.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_g_ipp.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_g_km.Rd | 49 - teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_g_lineplot.Rd | 24 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_logistic.Rd | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_mult_events.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_patient_timeline.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_shift_by_arm.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_shift_by_arm_by_worst.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_shift_by_grade.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_smq.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_summary.Rd | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_summary_by.Rd | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_therapy.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_tte.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/template_vitals.Rd | 2 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_a_gee.Rd | 8 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_a_mmrm.Rd | 14 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_barchart_simple.Rd | 11 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_ci.Rd | 10 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_forest_rsp.Rd | 29 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_forest_tte.Rd | 27 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_ipp.Rd | 10 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_km.Rd | 37 - teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_lineplot.Rd | 26 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_pp_adverse_events.Rd | 10 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_pp_patient_timeline.Rd | 11 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_pp_therapy.Rd | 10 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_g_pp_vitals.Rd | 10 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_abnormality.Rd | 7 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_abnormality_by_worst_grade.Rd | 7 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_ancova.Rd | 8 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_binary_outcome.Rd | 27 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_coxreg.Rd | 8 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_events.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_events_by_grade.Rd | 11 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_events_patyear.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_events_summary.Rd | 11 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_exposure.Rd | 11 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_logistic.Rd | 8 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_mult_events.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_pp_basic_info.Rd | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_pp_laboratory.Rd | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_pp_medical_history.Rd | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_pp_prior_medication.Rd | 4 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_shift_by_arm.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_shift_by_arm_by_worst.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_shift_by_grade.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_smq.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_summary.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_summary_by.Rd | 6 teal.modules.clinical-0.9.1/teal.modules.clinical/man/tm_t_tte.Rd | 8 teal.modules.clinical-0.9.1/teal.modules.clinical/tests/testthat/_snaps/tm_g_forest_rsp.md | 18 teal.modules.clinical-0.9.1/teal.modules.clinical/tests/testthat/_snaps/tm_g_forest_tte.md | 18 teal.modules.clinical-0.9.1/teal.modules.clinical/tests/testthat/_snaps/tm_g_km.md | 51 - 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More information about teal.modules.clinical at CRAN
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Title: Data Package for 'pathfindR'
Description: This is a data-only package, containing data needed to run the CRAN
package 'pathfindR', a package for enrichment analysis utilizing active
subnetworks. This package contains protein-protein interaction network data,
data related to gene sets and example input/output data.
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR.data versions 2.0.0 dated 2023-04-27 and 2.1.0 dated 2024-04-27
DESCRIPTION | 8 +- MD5 | 86 ++++++++++++++-------------- NEWS.md | 16 +++++ R/data.R | 72 ++++++++++++----------- R/sysdata.rda |binary data/biocarta_descriptions.rda |binary data/biocarta_genes.rda |binary data/cell_markers_descriptions.rda |binary data/cell_markers_gsets.rda |binary data/example_active_snws.rda |binary data/example_comparison_output.rda |binary data/example_custom_genesets_result.rda |binary data/example_mmu_output.rda |binary data/example_pathfindR_output.rda |binary data/example_pathfindR_output_clustered.rda |binary data/go_all_genes.rda |binary data/kegg_descriptions.rda |binary data/kegg_genes.rda |binary data/mmu_kegg_descriptions.rda |binary data/mmu_kegg_genes.rda |binary data/pathfindR.data_updates.rda |binary data/reactome_descriptions.rda |binary data/reactome_genes.rda |binary man/biocarta_descriptions.Rd | 2 man/biocarta_genes.Rd | 2 man/cell_markers_descriptions.Rd | 2 man/cell_markers_gsets.Rd | 2 man/example_active_snws.Rd | 4 - man/example_comparison_output.Rd | 4 - man/example_custom_genesets_result.Rd | 4 - man/example_experiment_matrix.Rd | 2 man/example_mmu_input.Rd | 2 man/example_mmu_output.Rd | 4 - man/example_pathfindR_input.Rd | 2 man/example_pathfindR_output.Rd | 4 - man/example_pathfindR_output_clustered.Rd | 4 - man/go_all_genes.Rd | 4 - man/kegg_descriptions.Rd | 4 - man/kegg_genes.Rd | 4 - man/mmu_kegg_descriptions.Rd | 4 - man/mmu_kegg_genes.Rd | 4 - man/pathfindR.data_updates.Rd | 6 + man/reactome_descriptions.Rd | 4 - man/reactome_genes.Rd | 4 - 44 files changed, 137 insertions(+), 117 deletions(-)
More information about pathfindR.data at CRAN
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Title: Collapsed Gibbs Sampling Methods for Topic Models
Description: Implements latent Dirichlet allocation (LDA)
and related models. This includes (but is not limited
to) sLDA, corrLDA, and the mixed-membership stochastic
blockmodel. Inference for all of these models is
implemented via a fast collapsed Gibbs sampler written
in C. Utility functions for reading/writing data
typically used in topic models, as well as tools for
examining posterior distributions are also included.
Author: Jonathan Chang
Maintainer: Santiago Olivella <olivella@unc.edu>
Diff between lda versions 1.4.2 dated 2015-11-22 and 1.5.2 dated 2024-04-27
DESCRIPTION | 17 ++-- MD5 | 63 +++++++++-------- NAMESPACE | 12 ++- R/lda.collapsed.gibbs.sampler.R | 2 R/slda.em.R | 4 - README.md |only build |only data/cora.cites.rda |binary data/cora.documents.rda |binary data/cora.titles.rda |binary data/cora.vocab.rda |binary data/newsgroup.label.map.rda |binary data/newsgroup.test.documents.rda |binary data/newsgroup.test.labels.rda |binary data/newsgroup.train.documents.rda |binary data/newsgroup.train.labels.rda |binary data/newsgroup.vocab.rda |binary data/poliblog.documents.rda |binary data/poliblog.ratings.rda |binary data/poliblog.vocab.rda |binary data/sampson.rda |binary demo/lda.R | 5 - demo/mmsb.R | 9 +- demo/rtm.R | 20 +++-- demo/slda.R | 22 ++---- man/lda-package.Rd | 30 +++----- man/lda.collapsed.gibbs.sampler.Rd | 5 - man/links.as.edgelist.Rd | 14 +-- man/nubbi.collapsed.gibbs.sampler.Rd | 3 man/read.documents.Rd | 4 - man/top.topic.words.Rd | 2 src/cvb0.c | 1 src/gibbs.c | 124 +++++++++++++++++++++++------------ src/lda-init.c |only 34 files changed, 197 insertions(+), 140 deletions(-)
Title: Bayesian Post-Estimation on the Mean Scale
Description: Computes Bayesian posterior distributions of predictions, marginal effects, and differences of marginal effects for various generalized linear models. Importantly, the posteriors are on the mean (response) scale, allowing for more natural interpretation than summaries on the link scale. Also, predictions and marginal effects of the count probabilities for Poisson and negative binomial models can be computed.
Author: David M. Dalenberg [aut, cre]
Maintainer: David M. Dalenberg <dalenbe2@gmail.com>
Diff between bayesMeanScale versions 0.1.0 dated 2024-04-23 and 0.1.1 dated 2024-04-27
DESCRIPTION | 13 +-- MD5 | 17 ++-- NEWS.md |only R/bayes-count-marg-effects.R | 8 +- R/bayes-count-preds.R | 6 + R/bayes-marg-effects.R | 8 +- R/bayes-preds.R | 8 +- R/mean-count-pred.R | 13 +-- R/mean-pred.R | 11 +- inst/doc/introduction.html | 172 +++++++++++++++++++++---------------------- 10 files changed, 134 insertions(+), 122 deletions(-)
More information about bayesMeanScale at CRAN
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Title: Estimation, Variable Selection and Prediction for Functional
Semiparametric Models
Description: Routines for the estimation or simultaneous estimation and variable selection in several functional semiparametric models with scalar responses are provided. These models include the functional single-index model, the semi-functional partial linear model, and the semi-functional partial linear single-index model. Additionally, the package offers algorithms for handling scalar covariates with linear effects that originate from the discretization of a curve. This functionality is applicable in the context of the linear model, the multi-functional partial linear model, and the multi-functional partial linear single-index model.
Author: German Aneiros [aut],
Silvia Novo [aut, cre]
Maintainer: Silvia Novo <snovo@est-econ.uc3m.es>
Diff between fsemipar versions 1.0.1 dated 2024-02-21 and 1.1.0 dated 2024-04-27
fsemipar-1.0.1/fsemipar/R/normaliza.R |only fsemipar-1.1.0/fsemipar/DESCRIPTION | 15 - fsemipar-1.1.0/fsemipar/MD5 | 177 ++++++------- fsemipar-1.1.0/fsemipar/NAMESPACE | 16 - fsemipar-1.1.0/fsemipar/R/FASSMR.kNN.R | 70 ++++- fsemipar-1.1.0/fsemipar/R/FASSMR.kNN.fit.R | 47 +-- fsemipar-1.1.0/fsemipar/R/FASSMR.kernel.R | 68 +++- fsemipar-1.1.0/fsemipar/R/FASSMR.kernel.fit.R | 63 ++-- fsemipar-1.1.0/fsemipar/R/H.fsim.kernel.R | 2 fsemipar-1.1.0/fsemipar/R/IASSMR.kNN.R | 76 ++++- fsemipar-1.1.0/fsemipar/R/IASSMR.kNN.fit.R | 40 +- fsemipar-1.1.0/fsemipar/R/IASSMR.kernel.R | 68 +++- fsemipar-1.1.0/fsemipar/R/IASSMR.kernel.fit.R | 47 +-- fsemipar-1.1.0/fsemipar/R/LASSOmia.R |only fsemipar-1.1.0/fsemipar/R/PVS.R | 52 +++ fsemipar-1.1.0/fsemipar/R/PVS.fit.R | 8 fsemipar-1.1.0/fsemipar/R/PVS.kNN.R | 51 +++ fsemipar-1.1.0/fsemipar/R/PVS.kNN.fit.R | 7 fsemipar-1.1.0/fsemipar/R/PVS.kernel.R | 51 +++ fsemipar-1.1.0/fsemipar/R/PVS.kernel.fit.R | 7 fsemipar-1.1.0/fsemipar/R/fnp.kNN.GCV.R | 8 fsemipar-1.1.0/fsemipar/R/fnp.kNN.fit.R | 4 fsemipar-1.1.0/fsemipar/R/fnp.kNN.fit.test.loc.R | 2 fsemipar-1.1.0/fsemipar/R/fnp.kernel.fit.R | 37 +- fsemipar-1.1.0/fsemipar/R/fnp.kernel.test.R | 2 fsemipar-1.1.0/fsemipar/R/fsim.kNN.R | 34 +- fsemipar-1.1.0/fsemipar/R/fsim.kNN.fit.R | 149 +++++++--- fsemipar-1.1.0/fsemipar/R/fsim.kNN.fit.fixedtheta.R | 56 ++-- fsemipar-1.1.0/fsemipar/R/fsim.kNN.fit.fixedtheta.com.R |only fsemipar-1.1.0/fsemipar/R/fsim.kNN.fit.optim.R |only fsemipar-1.1.0/fsemipar/R/fsim.kNN.test.R | 2 fsemipar-1.1.0/fsemipar/R/fsim.kernel.R | 32 +- fsemipar-1.1.0/fsemipar/R/fsim.kernel.fit.R | 128 ++++++--- fsemipar-1.1.0/fsemipar/R/fsim.kernel.fit.fixedtheta.R | 25 - fsemipar-1.1.0/fsemipar/R/fsim.kernel.fit.fixedtheta.com.R |only fsemipar-1.1.0/fsemipar/R/fsim.kernel.fit.optim.R |only fsemipar-1.1.0/fsemipar/R/fsim.kernel.test.R | 6 fsemipar-1.1.0/fsemipar/R/fun.kNN.R | 2 fsemipar-1.1.0/fsemipar/R/fun.kNN.fixedtheta.R | 31 -- fsemipar-1.1.0/fsemipar/R/fun.kernel.R | 8 fsemipar-1.1.0/fsemipar/R/fun.kernel.fixedtheta.R | 43 +-- fsemipar-1.1.0/fsemipar/R/funopare.kNN.R | 8 fsemipar-1.1.0/fsemipar/R/globals.R |only fsemipar-1.1.0/fsemipar/R/lm.pels.R | 30 +- fsemipar-1.1.0/fsemipar/R/lm.pels.fit.R | 16 - fsemipar-1.1.0/fsemipar/R/projec.R | 4 fsemipar-1.1.0/fsemipar/R/sfpl.kNN.R | 30 +- fsemipar-1.1.0/fsemipar/R/sfpl.kNN.fit.R | 24 - fsemipar-1.1.0/fsemipar/R/sfpl.kernel.R | 30 +- fsemipar-1.1.0/fsemipar/R/sfpl.kernel.fit.R | 22 - fsemipar-1.1.0/fsemipar/R/sfplsim.kNN.R | 43 ++- fsemipar-1.1.0/fsemipar/R/sfplsim.kNN.fit.R | 146 ++++++++-- fsemipar-1.1.0/fsemipar/R/sfplsim.kNN.fit.fixedtheta.R | 33 +- fsemipar-1.1.0/fsemipar/R/sfplsim.kernel.R | 45 ++- fsemipar-1.1.0/fsemipar/R/sfplsim.kernel.fit.R | 160 ++++++++--- fsemipar-1.1.0/fsemipar/R/sfplsim.kernel.fit.fixedtheta.R | 69 ++--- fsemipar-1.1.0/fsemipar/build/partial.rdb |binary fsemipar-1.1.0/fsemipar/man/FASSMR.kNN.fit.Rd | 120 ++++---- fsemipar-1.1.0/fsemipar/man/FASSMR.kernel.fit.Rd | 113 +++----- fsemipar-1.1.0/fsemipar/man/IASSMR.kNN.fit.Rd | 159 +++++------ fsemipar-1.1.0/fsemipar/man/IASSMR.kernel.fit.Rd | 158 +++++------ fsemipar-1.1.0/fsemipar/man/PVS.fit.Rd | 105 +++---- fsemipar-1.1.0/fsemipar/man/PVS.kNN.fit.Rd | 151 +++++------ fsemipar-1.1.0/fsemipar/man/PVS.kernel.fit.Rd | 146 +++++----- fsemipar-1.1.0/fsemipar/man/Sugar.Rd | 8 fsemipar-1.1.0/fsemipar/man/Tecator.Rd | 12 fsemipar-1.1.0/fsemipar/man/fsemipar-package.Rd | 46 +-- fsemipar-1.1.0/fsemipar/man/fsemipar.internal.Rd | 5 fsemipar-1.1.0/fsemipar/man/fsim.kNN.fit.Rd | 96 +++---- fsemipar-1.1.0/fsemipar/man/fsim.kNN.fit.optim.Rd |only fsemipar-1.1.0/fsemipar/man/fsim.kNN.test.Rd | 62 ++-- fsemipar-1.1.0/fsemipar/man/fsim.kernel.fit.Rd | 70 ++--- fsemipar-1.1.0/fsemipar/man/fsim.kernel.fit.optim.Rd |only fsemipar-1.1.0/fsemipar/man/fsim.kernel.test.Rd | 61 ++-- fsemipar-1.1.0/fsemipar/man/lm.pels.fit.Rd | 95 +++--- fsemipar-1.1.0/fsemipar/man/plot.classes.Rd | 92 ++++-- fsemipar-1.1.0/fsemipar/man/predict.IASSMR.Rd | 39 +- fsemipar-1.1.0/fsemipar/man/predict.fsim.Rd | 11 fsemipar-1.1.0/fsemipar/man/predict.lm.Rd | 14 - fsemipar-1.1.0/fsemipar/man/predict.mfplm.Rd | 47 +-- fsemipar-1.1.0/fsemipar/man/predict.sfpl.Rd | 25 - fsemipar-1.1.0/fsemipar/man/predict.sfplsim.FASSMR.Rd | 35 +- fsemipar-1.1.0/fsemipar/man/print.summary.fsim.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.lm.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.mfpl.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.mfplsim.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.sfpl.Rd | 8 fsemipar-1.1.0/fsemipar/man/print.summary.sfplsim.Rd | 8 fsemipar-1.1.0/fsemipar/man/projec.Rd | 10 fsemipar-1.1.0/fsemipar/man/semimetric.projec.Rd | 16 - fsemipar-1.1.0/fsemipar/man/sfpl.kNN.fit.Rd | 126 ++++----- fsemipar-1.1.0/fsemipar/man/sfpl.kernel.fit.Rd | 126 ++++----- fsemipar-1.1.0/fsemipar/man/sfplsim.kNN.fit.Rd | 134 ++++----- fsemipar-1.1.0/fsemipar/man/sfplsim.kernel.fit.Rd | 123 +++------ 94 files changed, 2435 insertions(+), 1912 deletions(-)
Title: Interpretable Machine Learning
Description: Interpretability methods to analyze the behavior and
predictions of any machine learning model. Implemented methods are:
Feature importance described by Fisher et al. (2018)
<doi:10.48550/arxiv.1801.01489>, accumulated local effects plots described by Apley
(2018) <doi:10.48550/arxiv.1612.08468>, partial dependence plots described by
Friedman (2001) <www.jstor.org/stable/2699986>, individual conditional
expectation ('ice') plots described by Goldstein et al. (2013)
<doi:10.1080/10618600.2014.907095>, local models (variant of 'lime')
described by Ribeiro et. al (2016) <doi:10.48550/arXiv.1602.04938>, the Shapley
Value described by Strumbelj et. al (2014)
<doi:10.1007/s10115-013-0679-x>, feature interactions described by
Friedman et. al <doi:10.1214/07-AOAS148> and tree surrogate models.
Author: Giuseppe Casalicchio [aut, cre],
Christoph Molnar [aut],
Patrick Schratz [aut]
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@lmu.de>
Diff between iml versions 0.11.2 dated 2024-03-29 and 0.11.3 dated 2024-04-27
DESCRIPTION | 18 MD5 | 20 NEWS.md | 288 ++++----- R/FeatureEffect.R | 1536 ++++++++++++++++++++++++------------------------- R/LocalModel.R | 658 ++++++++++---------- R/Predictor.R | 377 ++++++------ R/create_predict_fun.R | 314 +++++----- R/utils.R | 658 ++++++++++---------- inst/doc/parallel.html | 20 man/FeatureEffect.Rd | 2 man/Predictor.Rd | 8 11 files changed, 1956 insertions(+), 1943 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.0.10 dated 2024-01-24 and 0.0.11 dated 2024-04-27
ChangeLog | 22 ++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- build/partial.rdb |binary inst/NEWS.Rd | 13 +++++++++++-- src/ql/time/calendar.cpp | 12 +++++++++--- src/ql/time/calendars/brazil.cpp | 2 +- src/ql/time/calendars/brazil.hpp | 2 +- src/ql/time/calendars/india.cpp | 30 ++++++++++++++++++------------ src/ql/time/calendars/singapore.cpp | 18 ++++++++++++++++++ src/ql/time/calendars/singapore.hpp | 3 ++- src/ql/time/calendars/southafrica.cpp | 4 +++- src/ql/time/calendars/thailand.cpp | 3 ++- src/ql/time/calendars/unitedstates.cpp | 11 +++++++++-- 14 files changed, 113 insertions(+), 41 deletions(-)
Title: Factor and Autoregressive Models for Tensor Time Series
Description: Factor and autoregressive models for matrix and tensor valued time series. We provide functions for estimation, simulation and prediction. The models are discussed in
Li et al (2021) <doi:10.48550/arXiv.2110.00928>, Chen et al (2020) <DOI:10.1080/01621459.2021.1912757>,
Chen et al (2020) <DOI:10.1016/j.jeconom.2020.07.015>, and Xiao et al (2020) <doi:10.48550/arXiv.2006.02611>.
Author: Zebang Li [aut, cre],
Ruofan Yu [aut],
Rong Chen [aut],
Yuefeng Han [aut],
Han Xiao [aut],
Dan Yang [aut]
Maintainer: Zebang Li <zl326@stat.rutgers.edu>
Diff between tensorTS versions 1.0.1 dated 2023-05-07 and 1.0.2 dated 2024-04-27
DESCRIPTION | 10 +-- MD5 | 10 +-- R/tenFM.R | 164 +++++++++++++---------------------------------------- man/taxi.sim.FM.Rd | 15 ---- man/tenFM.est.Rd | 2 man/tenFM.rank.Rd | 32 +++++----- 6 files changed, 74 insertions(+), 159 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.73 dated 2024-04-09 and 2.0.74 dated 2024-04-27
DESCRIPTION | 8 +-- MD5 | 34 +++++++------- NEWS | 10 +++- R/epi.betabuster.R | 24 +++++++-- inst/doc/epiR_descriptive.R | 2 inst/doc/epiR_descriptive.html | 47 +++++++------------ inst/doc/epiR_measures_of_association.R | 34 +++++++------- inst/doc/epiR_measures_of_association.html | 12 ++-- inst/doc/epiR_sample_size.R | 2 inst/doc/epiR_sample_size.html | 4 - inst/doc/epiR_surveillance.R | 2 inst/doc/epiR_surveillance.html | 14 ++--- man/epi.2by2.Rd | 20 ++++---- man/epi.betabuster.Rd | 22 ++++----- man/epi.ccc.Rd | 30 +++++++----- man/epi.edr.Rd | 70 ++++++++++++++--------------- man/epi.empbayes.Rd | 15 +++--- man/epi.psi.Rd | 1 18 files changed, 185 insertions(+), 166 deletions(-)
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for
k-centroids cluster analysis supporting arbitrary distance measures
and centroid computation. Further cluster methods include hard
competitive learning, neural gas, and QT clustering. There are
numerous visualization methods for cluster results (neighborhood
graphs, convex cluster hulls, barcharts of centroids, ...), and
bootstrap methods for the analysis of cluster stability.
Author: Friedrich Leisch [aut] ,
Evgenia Dimitriadou [ctb],
Bettina Gruen [ctb, cre]
Maintainer: Bettina Gruen <Bettina.Gruen@R-project.org>
Diff between flexclust versions 1.4-1 dated 2022-04-08 and 1.4-2 dated 2024-04-27
DESCRIPTION | 28 ++++++------- MD5 | 16 +++---- NEWS | 4 + R/histogram.R | 2 inst/CITATION | 101 ++++++++++++++--------------------------------- man/cclust.Rd | 4 - man/histogram-methods.Rd | 5 +- man/randIndex.Rd | 4 - man/vacmot.Rd | 4 - 9 files changed, 68 insertions(+), 100 deletions(-)