Title: Rapidly Import Classifier Results into 'phyloseq'
Description: Import classification results from the 'RDP Classifier' (Ribosomal Database Project),' 'USEARCH sintax,' 'vsearch sintax' and the 'QIIME2' (Quantitative Insights into Microbial Ecology) classifiers into 'phyloseq' tax_table objects.
Author: John Quensen [aut, cre, cph]
Maintainer: John Quensen <quensenj@msu.edu>
Diff between speedytax versions 1.0.3 dated 2024-01-18 and 1.0.4 dated 2024-05-13
speedytax-1.0.3/speedytax/R/speedytax.R |only speedytax-1.0.3/speedytax/man/speedytax.Rd |only speedytax-1.0.4/speedytax/DESCRIPTION | 8 ++--- speedytax-1.0.4/speedytax/MD5 | 17 ++++++------ speedytax-1.0.4/speedytax/NEWS.md | 6 ++++ speedytax-1.0.4/speedytax/R/import_qiime2_tax_table.R | 19 +++++++++----- speedytax-1.0.4/speedytax/R/speedytax-package.R |only speedytax-1.0.4/speedytax/inst/extdata/qiime2_table_a.tsv |only speedytax-1.0.4/speedytax/man/import_qiime2_tax_table.Rd | 7 +++++ speedytax-1.0.4/speedytax/man/speedytax-package.Rd |only speedytax-1.0.4/speedytax/src/fix_qiime2_domain_C.cpp | 6 ---- speedytax-1.0.4/speedytax/src/fix_qiime2_rest_C.cpp | 16 ----------- 12 files changed, 40 insertions(+), 39 deletions(-)
Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework
for simulating data in state space models,
particularly when the number of subjects/units (n) exceeds one,
a scenario commonly encountered in social and behavioral sciences.
For an introduction to state space models in social and behavioral sciences,
refer to Chow, Ho, Hamaker, and Dolan (2010) <doi:10.1080/10705511003661553>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between simStateSpace versions 1.2.0 dated 2024-02-15 and 1.2.1 dated 2024-05-13
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 13 +++++++++++++ R/RcppExports.R | 4 ++-- build/partial.rdb |binary inst/CITATION | 2 +- man/LinSDE2SSM.Rd | 4 ++-- man/SimSSMLinSDEFixed.Rd | 2 +- man/SimSSMOUFixed.Rd | 2 +- src/source.cpp | 34 ++++++++++++++++++++++++---------- 10 files changed, 56 insertions(+), 29 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [ctb] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 0.5.3 dated 2024-04-02 and 0.6.0 dated 2024-05-13
DrugUtilisation-0.5.3/DrugUtilisation/man/figures/DrugUtilisation.png |only DrugUtilisation-0.5.3/DrugUtilisation/man/summariseCharacteristicsFromCodelist.Rd |only DrugUtilisation-0.5.3/DrugUtilisation/tests/testthat/test-largeScaleCharacteristics.R |only DrugUtilisation-0.6.0/DrugUtilisation/DESCRIPTION | 13 DrugUtilisation-0.6.0/DrugUtilisation/MD5 | 91 DrugUtilisation-0.6.0/DrugUtilisation/NAMESPACE | 7 DrugUtilisation-0.6.0/DrugUtilisation/R/addDrugUse.R | 1962 +++++----- DrugUtilisation-0.6.0/DrugUtilisation/R/addIndication.R | 693 +-- DrugUtilisation-0.6.0/DrugUtilisation/R/checkInputs.R | 4 DrugUtilisation-0.6.0/DrugUtilisation/R/dailyDose.R | 463 +- DrugUtilisation-0.6.0/DrugUtilisation/R/generateIngredientCohortSet.R | 268 - DrugUtilisation-0.6.0/DrugUtilisation/R/reexports-omopgenerics.R | 28 DrugUtilisation-0.6.0/DrugUtilisation/R/summariseCharacteristics.R | 38 DrugUtilisation-0.6.0/DrugUtilisation/R/summariseDrugUse.R | 239 - DrugUtilisation-0.6.0/DrugUtilisation/R/summariseIndication.R | 299 - DrugUtilisation-0.6.0/DrugUtilisation/R/summariseLargeScaleCharacteristics.R | 74 DrugUtilisation-0.6.0/DrugUtilisation/R/summariseTreatment.R | 464 +- DrugUtilisation-0.6.0/DrugUtilisation/R/utils-pipe.R | 28 DrugUtilisation-0.6.0/DrugUtilisation/README.md | 1219 +++++- DrugUtilisation-0.6.0/DrugUtilisation/build |only DrugUtilisation-0.6.0/DrugUtilisation/inst/doc |only DrugUtilisation-0.6.0/DrugUtilisation/man/DrugUtilisation-package.Rd | 2 DrugUtilisation-0.6.0/DrugUtilisation/man/addDrugUse.Rd | 2 DrugUtilisation-0.6.0/DrugUtilisation/man/addIndication.Rd | 5 DrugUtilisation-0.6.0/DrugUtilisation/man/figures/logo.png |only DrugUtilisation-0.6.0/DrugUtilisation/man/indicationToStrata.Rd | 2 DrugUtilisation-0.6.0/DrugUtilisation/man/reexports.Rd | 5 DrugUtilisation-0.6.0/DrugUtilisation/man/summariseDrugUse.Rd | 12 DrugUtilisation-0.6.0/DrugUtilisation/man/summariseIndication.Rd | 13 DrugUtilisation-0.6.0/DrugUtilisation/man/summariseTreatmentFromCohort.Rd | 10 DrugUtilisation-0.6.0/DrugUtilisation/tests/testthat/test-dailyDose.R | 434 +- DrugUtilisation-0.6.0/DrugUtilisation/tests/testthat/test-generateConceptCohortSet.R | 26 DrugUtilisation-0.6.0/DrugUtilisation/tests/testthat/test-indication.R | 3 DrugUtilisation-0.6.0/DrugUtilisation/tests/testthat/test-readConceptList.R | 28 DrugUtilisation-0.6.0/DrugUtilisation/vignettes |only 35 files changed, 3651 insertions(+), 2781 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Collection of Helper Functions
Description: Provides a collection of lightweight helper functions (imps) both
for interactive use and for inclusion within other packages. These include
functions for minimal input assertions, visualising colour palettes,
quoting user input, searching rows of a data frame and capturing string
tokens.
Author: Tim Taylor [aut, cre, cph] ,
R Core Team [cph] ,
Toby Hocking [cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ympes versions 1.0.0 dated 2024-02-02 and 1.1.0 dated 2024-05-13
DESCRIPTION | 13 +- MD5 | 19 +-- NAMESPACE | 41 +++++++ NEWS.md | 12 ++ R/assert.R | 86 +++++++++++++++ R/cc.R | 17 ++- R/fstrcapture.R | 19 +-- R/new_package.R | 33 +++-- inst/skeletons/pkg.Makefile | 13 +- inst/tinytest/test_assertions.R | 222 ++++++++++++++++++++-------------------- man/assertions.Rd |only 11 files changed, 312 insertions(+), 163 deletions(-)
Title: Clustering Analysis Using Survival Tree and Forest Algorithms
Description: An outcome-guided algorithm is developed to identify clusters of samples with similar characteristics and survival rate. The algorithm first builds a random forest and then defines distances between samples based on the fitted random forest. Given the distances, we can apply hierarchical clustering algorithms to define clusters. Details about this method is described in <https://github.com/luyouepiusf/SurvivalClusteringTree>.
Author: Lu You [aut, cre] ,
Lauric Ferrat [aut] ,
Hemang Parikh [aut] ,
Yanan Huo [aut] ,
Yuting Yang [aut] ,
Jeffrey Krischer [ctb] ,
Maria Redondo [ctb] ,
Richard Oram [ctb] ,
Andrea Steck [ctb]
Maintainer: Lu You <lu.you@epi.usf.edu>
Diff between SurvivalClusteringTree versions 1.0 dated 2023-09-11 and 1.1 dated 2024-05-13
DESCRIPTION | 10 MD5 | 31 +-- R/RcppExports.R | 8 R/grow_tree.R | 9 R/survival_forest_dataframe.R | 8 R/survival_forest_matrix.R | 8 R/survival_tree_dataframe.R | 10 R/survival_tree_matrix.R | 10 build/partial.rdb |binary inst/doc/user-guide.html | 4 man/survival_forest.Rd | 6 man/survival_forest_matrix.Rd | 6 man/survival_tree.Rd | 8 man/survival_tree_matrix.Rd | 8 src/RcppExports.cpp | 26 ++ src/find_best_split_cox_bone.cpp | 351 +++++++++++++++++------------------ src/find_best_split_cox_bone_old.cpp |only 17 files changed, 289 insertions(+), 214 deletions(-)
More information about SurvivalClusteringTree at CRAN
Permanent link
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' ('CTGOV', using the classic interface at
<https://classic.clinicaltrials.gov/>, and 'CTGOV2', using the
current interface at <https://www.clinicaltrials.gov/>), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Documents in registers associated with trials can also be downloaded.
Other functions identify deduplicated records,
easily find and extract variables (fields) of interest even
from complex nested data as used by the registers,
merge variables and update queries.
The pack [...truncated...]
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.17.2 dated 2024-02-25 and 1.18.0 dated 2024-05-13
ctrdata-1.17.2/ctrdata/inst/tinytest/more_test_ctrdata_duckdb_ctis.R |only ctrdata-1.17.2/ctrdata/inst/tinytest/more_test_ctrdata_postgres_ctgov2.R |only ctrdata-1.17.2/ctrdata/inst/tinytest/test_ctrdata_mongo_local_ctgov2.R |only ctrdata-1.17.2/ctrdata/inst/tinytest/test_ctrdata_mongo_local_ctis.R |only ctrdata-1.17.2/ctrdata/inst/tinytest/test_ctrdata_mongo_local_euctr.R |only ctrdata-1.17.2/ctrdata/inst/tinytest/test_ctrdata_mongo_local_isrctn.R |only ctrdata-1.18.0/ctrdata/DESCRIPTION | 6 ctrdata-1.18.0/ctrdata/LICENSE | 2 ctrdata-1.18.0/ctrdata/MD5 | 122 +- ctrdata-1.18.0/ctrdata/NAMESPACE | 2 ctrdata-1.18.0/ctrdata/NEWS.md | 96 -- ctrdata-1.18.0/ctrdata/R/ctrGetQueryUrl.R | 22 ctrdata-1.18.0/ctrdata/R/ctrLoadQueryIntoDb.R | 20 ctrdata-1.18.0/ctrdata/R/ctrLoadQueryIntoDbCtgov.R | 15 ctrdata-1.18.0/ctrdata/R/ctrLoadQueryIntoDbCtgov2.R | 227 ++++- ctrdata-1.18.0/ctrdata/R/ctrLoadQueryIntoDbCtis.R | 75 + ctrdata-1.18.0/ctrdata/R/ctrLoadQueryIntoDbEuctr.R | 13 ctrdata-1.18.0/ctrdata/R/ctrLoadQueryIntoDbIsrctn.R | 9 ctrdata-1.18.0/ctrdata/R/ctrdata-registers.R | 8 ctrdata-1.18.0/ctrdata/R/dbFindIdsUniqueTrials.R | 8 ctrdata-1.18.0/ctrdata/R/dbGetFieldsIntoDf.R | 1 ctrdata-1.18.0/ctrdata/R/dbQueryHistory.R | 3 ctrdata-1.18.0/ctrdata/R/dfName2Value.R | 15 ctrdata-1.18.0/ctrdata/R/utils.R | 86 + ctrdata-1.18.0/ctrdata/README.md | 345 ++++--- ctrdata-1.18.0/ctrdata/inst/WORDLIST | 5 ctrdata-1.18.0/ctrdata/inst/doc/ctrdata_install.pdf |binary ctrdata-1.18.0/ctrdata/inst/doc/ctrdata_retrieve.pdf |binary ctrdata-1.18.0/ctrdata/inst/doc/ctrdata_summarise.pdf |binary ctrdata-1.18.0/ctrdata/inst/tinytest/ctrdata_ctgov2.R | 60 + ctrdata-1.18.0/ctrdata/inst/tinytest/ctrdata_ctis.R | 10 ctrdata-1.18.0/ctrdata/inst/tinytest/ctrdata_euctr.R | 21 ctrdata-1.18.0/ctrdata/inst/tinytest/ctrdata_isrctn.R | 2 ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_duckdb_ctgov.R | 8 ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_duckdb_euctr.R | 8 ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_duckdb_isrctn.R | 8 ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_local_ctgov2.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_local_ctis.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_local_euctr.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_local_isrctn.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_ctgov.R | 8 ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_ctis.R | 8 ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_euctr.R | 8 ctrdata-1.18.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_isrctn.R | 8 ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_duckdb_ctgov2.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_duckdb_ctis.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_other_functions.R | 10 ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_postgres_ctgov2.R |only ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_ctgov.R | 9 ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_ctgov2.R | 9 ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_ctis.R | 9 ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_euctr.R | 15 ctrdata-1.18.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_isrctn.R | 9 ctrdata-1.18.0/ctrdata/man/ctrGetQueryUrl.Rd | 2 ctrdata-1.18.0/ctrdata/man/ctrLoadQueryIntoDb.Rd | 19 ctrdata-1.18.0/ctrdata/man/ctrdata-registers.Rd | 8 ctrdata-1.18.0/ctrdata/man/dfName2Value.Rd | 15 ctrdata-1.18.0/ctrdata/man/figures/README-ctrdata_across_registers.png |binary ctrdata-1.18.0/ctrdata/man/figures/README-ctrdata_results_neuroblastoma.png |binary ctrdata-1.18.0/ctrdata/vignettes/boxpep.png |binary ctrdata-1.18.0/ctrdata/vignettes/ctrdata_install.Rmd | 4 ctrdata-1.18.0/ctrdata/vignettes/ctrdata_retrieve.Rmd | 125 +- ctrdata-1.18.0/ctrdata/vignettes/ctrdata_summarise.Rmd | 447 ++++++---- ctrdata-1.18.0/ctrdata/vignettes/nb1.png |binary ctrdata-1.18.0/ctrdata/vignettes/nb2.png |binary ctrdata-1.18.0/ctrdata/vignettes/nbtrials.png |binary ctrdata-1.18.0/ctrdata/vignettes/phase23_paed_p_values.png |binary ctrdata-1.18.0/ctrdata/vignettes/phase23_paed_p_values_participants.png |binary ctrdata-1.18.0/ctrdata/vignettes/samplesizechanges.png |only 69 files changed, 1249 insertions(+), 661 deletions(-)
Title: Handle Data with Messy Header Rows and Broken Values
Description: Verb-like functions to work with messy data, often derived from
spreadsheets or parsed PDF tables. Includes functions for unwrapping
values broken up across rows, relocating embedded grouping values,
and to annotate meaningful formatting in spreadsheet files.
Author: Luis D. Verde Arregoitia [aut, cre]
Maintainer: Luis D. Verde Arregoitia <luis@liomys.mx>
Diff between unheadr versions 0.3.3 dated 2022-08-15 and 0.4.0 dated 2024-05-13
DESCRIPTION | 8 MD5 | 52 +- NAMESPACE | 1 NEWS.md | 8 R/annotate_mf.R | 84 ++-- R/annotate_mf_all.R | 70 ++- R/dataset_documentation.R | 6 R/mash_colnames.R | 4 R/re-export_pipe.R | 1 R/squish_newlines.R |only R/unbreak_fn.R | 22 - R/untangle_fn.R | 15 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 11 inst/doc/unheadr-vignette.R | 16 inst/doc/unheadr-vignette.Rmd | 28 + inst/doc/unheadr-vignette.html | 635 +++++++++++++++++----------------- man/AOEunits.Rd | 3 man/AOEunits_raw.Rd | 3 man/annotate_mf.Rd | 21 - man/annotate_mf_all.Rd | 13 man/mash_colnames.Rd | 4 man/pipe.Rd | 1 man/squish_newlines.Rd |only tests/testthat/dog_testblank.xlsx |only tests/testthat/test-annotate_mf_all.R | 5 tests/testthat/test-squish_n.R |only vignettes/unheadr-vignette.Rmd | 28 + 29 files changed, 595 insertions(+), 444 deletions(-)
Title: Distributional Synthetic Controls Estimation
Description: The method of synthetic controls is a widely-adopted tool for evaluating causal effects of policy changes in settings with observational data. In many settings where it is applicable, researchers want to identify causal effects of policy changes on a treated unit at an aggregate level while having access to data at a finer granularity. This package implements a simple extension of the synthetic controls estimator, developed in Gunsilius (2023) <doi:10.3982/ECTA18260>, that takes advantage of this additional structure and provides nonparametric estimates of the heterogeneity within the aggregate unit. The idea is to replicate the quantile function associated with the treated unit by a weighted average of quantile functions of the control units. The package contains tools for aggregating and plotting the resulting distributional estimates, as well as for carrying out inference on them.
Author: David Van Dijcke [aut, cre] ,
Florian Gunsilius [aut] ,
Siyun He [aut]
Maintainer: David Van Dijcke <dvdijcke@umich.edu>
Diff between DiSCos versions 0.0.1 dated 2024-03-14 and 0.1.0 dated 2024-05-13
DiSCos-0.0.1/DiSCos/inst/REFERENCES.bib.sb-6a7e8c2d-1rttMv |only DiSCos-0.0.1/DiSCos/inst/REFERENCES.rtf |only DiSCos-0.1.0/DiSCos/DESCRIPTION | 6 DiSCos-0.1.0/DiSCos/MD5 | 65 +-- DiSCos-0.1.0/DiSCos/NEWS.md | 13 DiSCos-0.1.0/DiSCos/R/DiSCo.R | 181 +++++++--- DiSCos-0.1.0/DiSCos/R/DiSCoTEA.R | 118 ++++-- DiSCos-0.1.0/DiSCos/R/DiSCo_CI.R | 223 ++++++++++--- DiSCos-0.1.0/DiSCos/R/DiSCo_iter.R | 38 +- DiSCos-0.1.0/DiSCos/R/DiSCo_mixture.R | 88 +++-- DiSCos-0.1.0/DiSCos/R/DiSCo_per.R | 54 +-- DiSCos-0.1.0/DiSCos/R/DiSCo_per_iter.R | 67 ++- DiSCos-0.1.0/DiSCos/R/DiSCo_weights_reg.R | 7 DiSCos-0.1.0/DiSCos/R/utils.R | 11 DiSCos-0.1.0/DiSCos/README.md | 12 DiSCos-0.1.0/DiSCos/build/partial.rdb |binary DiSCos-0.1.0/DiSCos/inst/REFERENCES.bib | 10 DiSCos-0.1.0/DiSCos/inst/doc/Dube2019.R | 5 DiSCos-0.1.0/DiSCos/inst/doc/Dube2019.Rmd | 7 DiSCos-0.1.0/DiSCos/inst/doc/Dube2019.html | 12 DiSCos-0.1.0/DiSCos/man/DiSCo.Rd | 64 +++ DiSCos-0.1.0/DiSCos/man/DiSCo_CI.Rd | 52 ++- DiSCos-0.1.0/DiSCos/man/DiSCo_CI_iter.Rd | 40 +- DiSCos-0.1.0/DiSCos/man/DiSCo_iter.Rd | 26 + DiSCos-0.1.0/DiSCos/man/DiSCo_mixture.Rd | 4 DiSCos-0.1.0/DiSCos/man/DiSCo_mixture_solve.Rd |only DiSCos-0.1.0/DiSCos/man/DiSCo_per.Rd | 21 - DiSCos-0.1.0/DiSCos/man/DiSCo_per_iter.Rd | 21 + DiSCos-0.1.0/DiSCos/man/DiSCo_weights_reg.Rd | 10 DiSCos-0.1.0/DiSCos/man/bootCounterfactuals.Rd |only DiSCos-0.1.0/DiSCos/man/checks.Rd | 13 DiSCos-0.1.0/DiSCos/man/myQuant.Rd | 2 DiSCos-0.1.0/DiSCos/man/parseBoots.Rd |only DiSCos-0.1.0/DiSCos/tests/testthat/test-DiSCo.R | 130 ++++++- DiSCos-0.1.0/DiSCos/tests/testthat/test-DiSCoTEA.R | 104 ++++++ DiSCos-0.1.0/DiSCos/vignettes/Dube2019.Rmd | 7 36 files changed, 1014 insertions(+), 397 deletions(-)
Title: Bayesian Screening and Variable Selection
Description: Performs Bayesian variable screening and selection for ultra-high dimensional linear regression models.
Author: Dongjin Li [aut, cre], Debarshi Chakraborty[aut], Somak Dutta [aut], Vivekananda Roy [ctb]
Maintainer: Dongjin Li <liyangxiaobei@gmail.com>
Diff between bravo versions 2.3.1 dated 2023-08-26 and 3.2.1 dated 2024-05-13
DESCRIPTION | 10 +- MD5 | 18 +++- NAMESPACE | 5 - R/mip.sven.R |only R/sven.R | 229 ++++++++++++++++++++++-------------------------------- R/sven.x.R |only R/xzaddpara.R |only R/xzaddvar.R |only R/xzdelvar.R |only R/xzsven.R |only R/xzsven_notemp.R |only R/xzsven_temp.R |only R/xzswapvar.R |only man/mip.sven.Rd |only man/sven.Rd | 84 +++++++++++-------- 15 files changed, 166 insertions(+), 180 deletions(-)
Title: Accelerated Derivative-Free Method for Large-Scale Nonlinear
Systems of Equations
Description: Secant acceleration applied to derivative-free Spectral
Residual Methods for solving large-scale nonlinear systems of
equations. The main reference follows: E. G. Birgin and
J. M. Martinez (2022) <doi:10.1137/20M1388024>.
Author: Ernesto G. Birgin [aut, ctb],
John L. Gardenghi [aut, cre, ctb, trl],
Diaulas S. Marcondes [aut, ctb, trl],
Jose M. Martinez [aut, ctb]
Maintainer: John L. Gardenghi <john.gardenghi@unb.br>
Diff between dfsaneacc versions 1.0.2 dated 2024-01-18 and 1.0.3 dated 2024-05-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 4 ++++ build/partial.rdb |binary src/qr.f95 | 34 +++++++++++++++++----------------- 5 files changed, 29 insertions(+), 25 deletions(-)
Title: Cross-Platform Perl Based R Function to Create Excel 2003 (XLS)
and Excel 2007 (XLSX) Files
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it contains
or can be specified by the user.
Author: Marc Schwartz <marc_schwartz@me.com> and various authors for Perl modules listed in each .pm file.
Maintainer: Marc Schwartz <marc_schwartz@me.com>
Diff between WriteXLS versions 6.5.0 dated 2024-01-09 and 6.6.0 dated 2024-05-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/WriteXLS.R | 2 ++ inst/Perl/WriteXLS.pl | 13 ++++++++++--- inst/Perl/WriteXLSX.pl | 13 ++++++++++--- man/WriteXLS.Rd | 22 ++++++++++++++++------ 6 files changed, 47 insertions(+), 21 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Luedecke [aut, cre] ,
Alexander Bartel [ctb] ,
Carsten Schwemmer [ctb],
Chuck Powell [ctb] ,
Amir Djalovski [ctb],
Johannes Titz [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.8.15 dated 2023-08-17 and 2.8.16 dated 2024-05-13
DESCRIPTION | 8 ++-- MD5 | 58 ++++++++++++++--------------- NAMESPACE | 1 R/plot_frq.R | 3 - R/plot_type_eff.R | 22 +++++------ R/plot_type_int.R | 18 ++++----- R/plot_type_ranef.R | 21 +++++----- R/tab_itemscale.R | 4 +- README.md | 2 - build/vignette.rds |binary inst/doc/blackwhitefigures.html | 6 +-- inst/doc/custplot.R | 2 - inst/doc/custplot.html | 16 ++++---- inst/doc/plot_interactions.html | 6 +-- inst/doc/plot_likert_scales.html | 20 +++++----- inst/doc/plot_marginal_effects.R | 2 - inst/doc/plot_marginal_effects.html | 6 +-- inst/doc/plot_model_estimates.html | 8 ++-- inst/doc/sjtitemanalysis.R | 2 - inst/doc/sjtitemanalysis.html | 6 +-- inst/doc/tab_bayes.R | 4 +- inst/doc/tab_bayes.html | 28 +++++++------- inst/doc/tab_mixed.R | 4 +- inst/doc/tab_mixed.html | 72 +++++++++++++++++------------------- inst/doc/tab_model_estimates.R | 2 - inst/doc/tab_model_estimates.html | 6 +-- inst/doc/tab_model_robust.R | 2 - inst/doc/tab_model_robust.html | 2 - inst/doc/table_css.html | 6 +-- man/tab_itemscale.Rd | 2 - 30 files changed, 166 insertions(+), 173 deletions(-)
Title: Read and Process 'Pamguard' Binary Data
Description: Functions for easily reading and processing binary data files created by
'Pamguard' (<https://www.pamguard.org/>). All functions for directly reading the
binary data files are based on 'MATLAB' code written by Michael Oswald.
Author: Taiki Sakai [aut, cre],
Michael Oswald [aut],
Douglas Gillespie [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PamBinaries versions 1.8.0 dated 2023-01-31 and 1.9.0 dated 2024-05-13
DESCRIPTION | 8 +-- MD5 | 22 +++++---- R/contourToFreq.R | 95 ++++++++++++++++++++++++++++++++++++---- R/loadPamguardBinaryFile.R | 10 +++- R/readDLModelData.R |only man/readBeamFormerAnnotation.Rd | 58 ++++++++++++------------ man/readBearingAnnotation.Rd | 58 ++++++++++++------------ man/readDLAnnotation.Rd | 58 ++++++++++++------------ man/readDLDetData.Rd | 58 ++++++++++++------------ man/readDLModelData.Rd |only man/readTDBLAnnotation.Rd | 58 ++++++++++++------------ man/readTMAnnotation.Rd | 58 ++++++++++++------------ man/readTritechTrack.Rd | 58 ++++++++++++------------ 13 files changed, 313 insertions(+), 228 deletions(-)
Title: Optimization Frameworks for Tie-Oriented and Actor-Oriented
Relational Event Models
Description: A comprehensive set of tools designed for optimizing likelihood within a tie-oriented (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) or an actor-oriented modelling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>) in relational event networks. The package accommodates both frequentist and Bayesian approaches. The frequentist approaches that the package incorporates are the Maximum Likelihood Optimization (MLE) and the Gradient-based Optimization (GDADAMAX). The Bayesian methodologies included in the package are the Bayesian Sampling Importance Resampling (BSIR) and the Hamiltonian Monte Carlo (HMC). The flexibility of choosing between frequentist and Bayesian optimization approaches allows researchers to select the estimation approach which aligns the most with their analytical preferences.
Author: Giuseppe Arena [aut, cre] ,
Rumana Lakdawala [aut],
Fabio Generoso Vieira [aut],
Marlyne Meijerink-Bosman [ctb],
Diana Karimova [ctb],
Mahdi Shafiee Kamalabad [ctb],
Roger Leenders [ctb],
Joris Mulder [ctb]
Maintainer: Giuseppe Arena <g.arena@tilburguniversity.edu>
Diff between remstimate versions 2.3.8 dated 2023-12-20 and 2.3.9 dated 2024-05-13
DESCRIPTION | 13 ++++---- LICENSE | 2 - MD5 | 28 ++++++++--------- R/data.R | 8 ++--- R/remstimate.R | 73 ++++++++++++++++++++++------------------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/remstimate.html | 42 +++++++++++++------------- man/diagnostics.Rd | 2 - man/plot.remstimate.Rd | 2 - man/print.remstimate.Rd | 2 - man/remstimate-package.Rd | 2 - man/remstimate.Rd | 2 - man/summary.remstimate.Rd | 4 +- src/remstimate.cpp | 3 - 15 files changed, 91 insertions(+), 92 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.1080/00031305.2023.2203177>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [aut] ,
Sandra Siegfried [aut] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.0-3 dated 2024-04-16 and 1.0-4 dated 2024-05-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/mmlt.R | 46 +++++++++++++++++++++++++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 9 ++++++++- inst/doc/mtram.pdf |binary inst/doc/tram.pdf |binary 8 files changed, 52 insertions(+), 25 deletions(-)
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] ,
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.34 dated 2023-11-28 and 0.36 dated 2024-05-13
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NEWS.md | 15 +++++++++++++++ R/index_snps.R | 1 + R/plot_snpasso_and_sdp.R | 2 +- R/plot_snpasso_sdp_and_genes.R | 2 +- R/scan1snps.R | 37 +++++++++++++++++++++++-------------- build/partial.rdb |binary data/CCaltcolors.RData |binary data/CCcolors.RData |binary data/CCorigcolors.RData |binary tests/testthat/test-scan1_pg.R | 2 +- tests/testthat/test-scan1snps.R | 14 +++++++++++++- 13 files changed, 72 insertions(+), 35 deletions(-)
Title: Pubmed Unified REtrieval for Multi-Output Exploration
Description: Access a variety of 'PubMed' data through a single, user-friendly interface, including abstracts <https://pubmed.ncbi.nlm.nih.gov/>, bibliometrics from 'iCite' <https://icite.od.nih.gov/>, pubtations from 'PubTator3' <https://www.ncbi.nlm.nih.gov/research/pubtator3/>, and full-text records from 'PMC' <https://www.ncbi.nlm.nih.gov/pmc/>.
Author: Jason Timm [aut, cre]
Maintainer: Jason Timm <JaTimm@salud.unm.edu>
Diff between puremoe versions 1.0.0 dated 2024-04-19 and 1.0.1 dated 2024-05-13
DESCRIPTION | 12 ++++------- LICENSE | 2 - MD5 | 17 ++++++++-------- NAMESPACE | 1 NEWS.md |only R/data_pharm_action.R | 2 - R/data_pmc_list.R | 53 +++++++++++++++++++++----------------------------- R/get_records.R | 12 +++++++---- README.md | 20 ++++++++++++------ man/get_records.Rd | 3 +- 10 files changed, 63 insertions(+), 59 deletions(-)
Title: Non-Negative Tensor Decomposition
Description: Some functions for performing non-negative matrix factorization, non-negative CANDECOMP/PARAFAC (CP) decomposition, non-negative Tucker decomposition, and generating toy model data. See Andrzej Cichock et al (2009) and the reference section of GitHub README.md <https://github.com/rikenbit/nnTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre],
Itoshi Nikaido [aut]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between nnTensor versions 1.2.0 dated 2023-06-22 and 1.3.0 dated 2024-05-13
DESCRIPTION | 6 MD5 | 22 +- R/kFoldMaskTensor.R | 58 +++++-- build/partial.rdb |binary inst/NEWS | 6 inst/doc/nnTensor-1.html | 66 ++++---- inst/doc/nnTensor-2.html | 134 ++++++++--------- inst/doc/nnTensor-3.html | 168 +++++++++++----------- inst/doc/nnTensor-4.html | 350 +++++++++++++++++++++++------------------------ man/GabrielNMF.Rd | 2 man/NMF.Rd | 8 - man/kFoldMaskTensor.Rd | 5 12 files changed, 428 insertions(+), 397 deletions(-)
Title: Estimation/Multiple Imputation for Mixed Categorical and
Continuous Data
Description: Estimation/multiple imputation programs for mixed categorical
and continuous data.
Author: Original by Joseph L. Schafer <jls@stat.psu.edu>.
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between mix versions 1.0-11 dated 2022-05-31 and 1.0-12 dated 2024-05-13
DESCRIPTION | 8 +-- MD5 | 6 +- data/stlouis.rda |binary src/mix.f | 114 +++++++++++++++++++++++++++---------------------------- 4 files changed, 64 insertions(+), 64 deletions(-)
Title: Statistical Matching or Data Fusion
Description: Integration of two data sources referred to the same target population which share a number of variables. Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.
Author: Marcello D'Orazio
Maintainer: Marcello D'Orazio <mdo.statmatch@gmail.com>
Diff between StatMatch versions 1.4.1 dated 2022-03-01 and 1.4.2 dated 2024-05-13
DESCRIPTION | 10 - MD5 | 22 +-- NAMESPACE | 1 NEWS | 314 +++++++++++++++++++++++++------------------------- R/comp.cont.R | 56 +++++--- R/create.imputed.R |only R/gower.dist.R | 13 +- R/plotCont.R | 47 ++++--- man/comp.cont.Rd | 2 man/create.fused.Rd | 2 man/create.imputed.Rd |only man/gower.dist.Rd | 7 - man/plotCont.Rd | 4 13 files changed, 257 insertions(+), 221 deletions(-)
Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data
transformation tasks like recoding, dichotomizing or grouping variables,
setting and replacing missing values. The data transformation functions
also support labelled data, and all integrate seamlessly into a
'tidyverse'-workflow.
Author: Daniel Luedecke [aut, cre] ,
Iago Gine-Vazquez [ctb],
Alexander Bartel [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.8.9 dated 2021-12-03 and 2.8.10 dated 2024-05-13
DESCRIPTION | 12 MD5 | 118 +-- NEWS.md | 8 R/add_columns.R | 3 R/frq.R | 4 R/helpfunctions.R | 2 R/spread_coef.R | 18 README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/design_philosophy.html | 772 ++++++++++++++------- inst/doc/exploringdatasets.html | 683 +++++++++++++------ inst/doc/recodingvariables.Rmd | 5 inst/doc/recodingvariables.html | 1249 +++++++++++++++++++++-------------- man/add_columns.Rd | 3 man/add_rows.Rd | 114 +-- man/add_variables.Rd | 116 +-- man/all_na.Rd | 54 - man/big_mark.Rd | 100 +- man/count_na.Rd | 114 +-- man/de_mean.Rd | 130 +-- man/dicho.Rd | 298 ++++---- man/find_var.Rd | 6 man/flat_table.Rd | 158 ++-- man/frq.Rd | 398 +++++------ man/group_str.Rd | 152 ++-- man/group_var.Rd | 346 ++++----- man/has_na.Rd | 158 ++-- man/is_crossed.Rd | 172 ++-- man/is_empty.Rd | 132 +-- man/move_columns.Rd | 148 ++-- man/numeric_to_factor.Rd | 68 - man/rec.Rd | 460 ++++++------ man/recode_to.Rd | 210 ++--- man/ref_lvl.Rd | 158 ++-- man/remove_var.Rd | 64 - man/replace_na.Rd | 212 ++--- man/reshape_longer.Rd | 224 +++--- man/rotate_df.Rd | 114 +-- man/row_count.Rd | 136 +-- man/row_sums.Rd | 214 ++--- man/set_na_if.Rd | 116 +-- man/split_var.Rd | 308 ++++---- man/spread_coef.Rd | 198 ++--- man/std.Rd | 298 ++++---- man/str_contains.Rd | 162 ++-- man/str_find.Rd | 172 ++-- man/str_start.Rd | 128 +-- man/tidy_values.Rd | 78 +- man/to_dummy.Rd | 118 +-- man/to_value.Rd | 114 +-- man/var_rename.Rd | 108 +-- man/var_type.Rd | 88 +- man/word_wrap.Rd | 64 - man/zap_inf.Rd | 96 +- tests/testthat/test-frq_whitespace.R | 32 tests/testthat/test-rec.R | 110 +-- tests/testthat/test-reflvl.R | 32 tests/testthat/test-setna.R | 46 - vignettes/recodingvariables.Rmd | 5 60 files changed, 5193 insertions(+), 4417 deletions(-)
Title: Client for Dataverse 4+ Repositories
Description: Provides access to Dataverse APIs <https://dataverse.org/> (versions 4-5),
enabling data search, retrieval, and deposit. For Dataverse versions <= 3.0,
use the archived 'dvn' package <https://cran.r-project.org/package=dvn>.
Author: Shiro Kuriwaki [aut, cre] ,
Will Beasley [aut] ,
Thomas J. Leeper [aut] ,
Philip Durbin [aut] ,
Sebastian Karcher [aut] ,
Jan Kanis [ctb],
Edward Jee [ctb],
Johannes Gruber [ctb]
Maintainer: Shiro Kuriwaki <shirokuriwaki@gmail.com>
Diff between dataverse versions 0.3.13 dated 2023-03-23 and 0.3.14 dated 2024-05-13
DESCRIPTION | 18 + MD5 | 59 +++--- NAMESPACE | 4 NEWS.md | 6 R/add_dataset_file.R | 60 +++--- R/get_dataframe.R | 16 - R/get_file.R | 4 R/get_file_by_id.R | 9 R/get_url.R |only README.md | 15 - build/vignette.rds |binary inst/constants.yml | 4 inst/doc/A-introduction.html | 32 +-- inst/doc/B-search.R | 79 +++++++- inst/doc/B-search.Rmd | 72 +++++++ inst/doc/B-search.html | 137 ++++++-------- inst/doc/C-download.R | 108 +++++++---- inst/doc/C-download.Rmd | 64 +++++- inst/doc/C-download.html | 132 ++++++------- man/URLs.Rd |only man/files.Rd | 7 man/get_dataframe.Rd | 16 - tests/testthat/tests-dataset_files.R | 2 tests/testthat/tests-dataset_metadata.R | 4 tests/testthat/tests-get_dataframe-dataframe-basketball.R | 17 - tests/testthat/tests-get_dataframe-original-basketball.R | 2 tests/testthat/tests-get_dataset.R | 24 +- tests/testthat/tests-get_file.R | 2 tests/testthat/tests-get_file_metadata.R | 2 tests/testthat/tests-get_url.R |only vignettes/B-search.Rmd | 72 +++++++ vignettes/C-download.Rmd | 64 +++++- 32 files changed, 682 insertions(+), 349 deletions(-)
Title: A Unified Time Series Event Detection Framework
Description: By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Antonio Castro [aut],
Antonio Mello [aut],
Ellen Paixao [aut],
Fernando Fraga [aut],
Heraldo Borges [aut],
Janio Lima [aut],
Jessica Souza [aut],
Lais Baroni [aut],
Lucas Tavares [aut],
Rebecca Salles [aut],
Diego [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between harbinger versions 1.0.777 dated 2024-05-04 and 1.0.787 dated 2024-05-13
DESCRIPTION | 6 +-- MD5 | 36 ++++++++++++-------- NAMESPACE | 7 +++ R/data.R | 19 ++++++++++ R/har_plot.R | 4 +- R/hdis_mp.R |only R/hdis_sax.R |only R/hmo_discord.R |only R/hmo_mp.R | 5 +- R/hmo_sax.R | 69 +++++++++++++++++++++++---------------- R/hmo_xsax.R | 4 +- README.md | 20 +++++------ data/examples_anomalies.RData |binary data/examples_changepoints.RData |binary data/examples_motifs.RData |only man/examples_motifs.Rd |only man/har_plot.Rd | 2 - man/hdis_mp.Rd |only man/hdis_sax.Rd |only man/hmo_discord.Rd |only man/hmo_mp.Rd | 4 +- man/hmo_sax.Rd | 6 +-- man/hmo_xsax.Rd | 4 +- 23 files changed, 118 insertions(+), 68 deletions(-)
Title: Calibration Plots for the Transition Probabilities from
Multistate Models
Description: Assess the calibration of an existing (i.e. previously developed) multistate
model through calibration plots.
Calibration is assessed using one of three methods. 1) Calibration methods for
binary logistic regression models applied at a fixed time point in conjunction
with inverse probability of censoring weights. 2) Calibration methods for
multinomial logistic regression models applied at a fixed time point in conjunction
with inverse probability of censoring weights. 3) Pseudo-values estimated using
the Aalen-Johansen estimator of observed risk. All methods are applied in conjunction
with landmarking when required. These calibration plots evaluate the calibration
(in a validation cohort of interest) of the transition probabilities estimated from an
existing multistate model. While package development has focused on multistate
models, calibration plots can be produced for any model which utilises information
post baseline to update predictions (e.g. dynamic models); competing risks mod [...truncated...]
Author: Alexander Pate [aut, cre, cph]
,
Glen P Martin [fnd, rev]
Maintainer: Alexander Pate <alexander.pate@manchester.ac.uk>
Diff between calibmsm versions 1.0.0 dated 2023-11-30 and 1.1.0 dated 2024-05-13
calibmsm-1.0.0/calibmsm/R/calib_blr.R |only calibmsm-1.0.0/calibmsm/R/calib_mlr.R |only calibmsm-1.0.0/calibmsm/R/calib_pv.R |only calibmsm-1.0.0/calibmsm/R/extract_ids_states.R |only calibmsm-1.0.0/calibmsm/man/calc_aj.Rd |only calibmsm-1.0.0/calibmsm/man/calc_pv_aj.Rd |only calibmsm-1.0.0/calibmsm/man/calib_blr.Rd |only calibmsm-1.0.0/calibmsm/man/calib_mlr.Rd |only calibmsm-1.0.0/calibmsm/man/calib_pv.Rd |only calibmsm-1.0.0/calibmsm/man/extract_ids_states.Rd |only calibmsm-1.0.0/calibmsm/man/plot.calib_blr.Rd |only calibmsm-1.0.0/calibmsm/man/plot.calib_pv.Rd |only calibmsm-1.1.0/calibmsm/DESCRIPTION | 20 calibmsm-1.1.0/calibmsm/MD5 | 78 - calibmsm-1.1.0/calibmsm/NAMESPACE | 14 calibmsm-1.1.0/calibmsm/NEWS.md | 14 calibmsm-1.1.0/calibmsm/R/calibmsm-misc.R | 5 calibmsm-1.1.0/calibmsm/R/calibmsm-package.R | 1 calibmsm-1.1.0/calibmsm/R/calibmsm.R |only calibmsm-1.1.0/calibmsm/R/data.R | 61 calibmsm-1.1.0/calibmsm/R/internal_calib_aj.R |only calibmsm-1.1.0/calibmsm/R/internal_calib_blr_ipcw.R |only calibmsm-1.1.0/calibmsm/R/internal_calib_mlr_ipcw.R |only calibmsm-1.1.0/calibmsm/R/internal_calib_pv.R |only calibmsm-1.1.0/calibmsm/R/internal_extract_ids_states.R |only calibmsm-1.1.0/calibmsm/R/plot_calib.R | 476 ++++-- calibmsm-1.1.0/calibmsm/R/weights.R | 4 calibmsm-1.1.0/calibmsm/README.md | 35 calibmsm-1.1.0/calibmsm/build/vignette.rds |binary calibmsm-1.1.0/calibmsm/data/ebmtcal.cmprsk.rda |only calibmsm-1.1.0/calibmsm/data/msebmtcal.cmprsk.rda |binary calibmsm-1.1.0/calibmsm/data/tp.cmprsk.j0.rda |binary calibmsm-1.1.0/calibmsm/inst/doc/Directory-of-vignettes.Rmd | 4 calibmsm-1.1.0/calibmsm/inst/doc/Directory-of-vignettes.html | 5 calibmsm-1.1.0/calibmsm/inst/doc/overview_guide.pdf |only calibmsm-1.1.0/calibmsm/inst/doc/overview_guide.pdf.asis |only calibmsm-1.1.0/calibmsm/man/calib_msm.Rd |only calibmsm-1.1.0/calibmsm/man/ebmtcal.Rd | 2 calibmsm-1.1.0/calibmsm/man/ebmtcal.cmprsk.Rd |only calibmsm-1.1.0/calibmsm/man/figures/README-example-1.png |binary calibmsm-1.1.0/calibmsm/man/msebmtcal.Rd | 2 calibmsm-1.1.0/calibmsm/man/msebmtcal.cmprsk.Rd | 2 calibmsm-1.1.0/calibmsm/man/plot.calib_mlr.Rd | 60 calibmsm-1.1.0/calibmsm/man/plot.calib_msm.Rd |only calibmsm-1.1.0/calibmsm/man/tp.cmprsk.j0.Rd | 4 calibmsm-1.1.0/calibmsm/tests/testthat/test-calib_aj.R |only calibmsm-1.1.0/calibmsm/tests/testthat/test-calib_blr.R | 751 ++++++----- calibmsm-1.1.0/calibmsm/tests/testthat/test-calib_mlr.R | 271 ++- calibmsm-1.1.0/calibmsm/tests/testthat/test-calib_pv.R | 573 ++++++-- calibmsm-1.1.0/calibmsm/tests/testthat/test-plot_calib.R | 256 ++- calibmsm-1.1.0/calibmsm/tests/testthat/test-weights.R | 15 calibmsm-1.1.0/calibmsm/vignettes/Directory-of-vignettes.Rmd | 4 calibmsm-1.1.0/calibmsm/vignettes/overview_guide.pdf.asis |only 53 files changed, 1719 insertions(+), 938 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-09 1.0.12
Title: Location Scale Standardized Distributions
Description: Location-Scale based distributions parameterized in terms of mean, standard deviation, skew and shape parameters and estimation using automatic differentiation. Distributions include the Normal, Student and GED as well as their skewed variants ('Fernandez and Steel'), the 'Johnson SU', and the Generalized Hyperbolic. Also included is the semi-parametric piece wise distribution ('spd') with Pareto tails and kernel interior.
Author: Alexios Galanos [aut, cre, cph]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsdistributions versions 1.0.0 dated 2024-03-17 and 1.0.1 dated 2024-05-13
DESCRIPTION | 15 ++--- MD5 | 86 +++++++++++++++++------------- NAMESPACE | 25 ++++++++ NEWS.md | 13 ++++ R/moments.R | 2 R/pdqr.R | 20 +++--- R/sandwich.R | 15 ++++- R/spd.R |only R/specification.R | 2 R/tsdistributions-package.R | 5 + R/utils.R |only build/partial.rdb |only build/vignette.rds |binary inst/REFERENCES.bib |only inst/doc/estimation_demo.html | 4 - inst/doc/location_scale_distributions.pdf |binary inst/doc/profile_demo.Rmd | 4 - inst/doc/profile_demo.html | 8 +- inst/doc/spd_demo.R |only inst/doc/spd_demo.Rmd |only inst/doc/spd_demo.html |only man/AIC.tsdistribution.estimate.Rd | 5 + man/BIC.tsdistribution.estimate.Rd | 5 + man/bread.tsdistribution.estimate.Rd | 7 +- man/coef.tsdistribution.estimate.Rd | 5 + man/ddist.Rd | 2 man/distribution_modelspec.Rd | 2 man/dskewness.Rd | 2 man/estfun.tsdistribution.estimate.Rd | 2 man/estimate.tsdistribution.spdspec.Rd |only man/ged.Rd | 2 man/gh.Rd | 2 man/ghst.Rd | 2 man/jsu.Rd | 2 man/logLik.tsdistribution.estimate.Rd | 5 + man/nig.Rd | 2 man/print.summary.tsdistribution.Rd | 11 +++ man/sged.Rd | 2 man/snorm.Rd | 2 man/spd.Rd |only man/spd_modelspec.Rd |only man/sstd.Rd | 2 man/std.Rd | 2 man/summary.tsdistribution.spdestimate.Rd |only man/tsdistributions-package.Rd | 2 man/vcov.tsdistribution.estimate.Rd | 5 + src/TMB/tsdistributions_TMBExports.cpp | 2 tests/testthat/test-quantile.R | 15 +++++ vignettes/profile_demo.Rmd | 4 - vignettes/spd_demo.Rmd |only 50 files changed, 199 insertions(+), 92 deletions(-)
More information about tsdistributions at CRAN
Permanent link
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb],
Shota Ochi [ctb],
Aaron Robotham [cre],
Rodrigo Tobar [ctb]
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between imager versions 1.0.1 dated 2024-04-26 and 1.0.2 dated 2024-05-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- inst/doc/gettingstarted.html | 6 +++--- inst/doc/pixsets.html | 4 ++-- inst/include/CImg.h | 17 +++++++++++++---- inst/include/NOTE_CImg | 37 +++++++++++++++++++++++++++++++++++-- src/Makevars.in | 1 - src/reductions.cpp | 2 +- 8 files changed, 64 insertions(+), 23 deletions(-)
Title: Plotting Decision Curve Analysis with Coloured Bars
Description: Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. The 'ggscidca' package adds coloured bars of discriminant relevance to the traditional decision curve. Improved practicality and aesthetics. This method was described by Balachandran VP (2015) <doi:10.1016/S1470-2045(14)71116-7>.
Author: Qiang Liu [aut, cre]
Maintainer: Qiang Liu <dege857@163.com>
Diff between ggscidca versions 0.2.0 dated 2024-03-20 and 0.2.1 dated 2024-05-13
DESCRIPTION | 8 ++++---- MD5 | 37 +++++++++++++++++++++---------------- NAMESPACE | 2 ++ R/cmprskstdca.R | 1 + R/demo.R |only R/getplot.R | 21 ++++++++++----------- R/modeldata.R | 6 ++++++ R/randomForest.R | 11 +++++++---- R/scidca.R | 19 ++++--------------- R/scidca.coxph.R | 12 +++++++----- R/scidca.glm.R | 11 +++++++---- R/scidcacrr.R | 7 +++++-- R/scidcaksvm.R |only data/demo.rda |only man/cmprskstdca.Rd | 2 ++ man/demo.Rd |only man/scidca.Rd | 19 ++++--------------- man/scidca.coxph.Rd | 5 ++++- man/scidca.crr.Rd | 5 ++++- man/scidca.glm.Rd | 5 ++++- man/scidca.ksvm.Rd |only man/scidca.randomForest.Rd | 5 ++++- 22 files changed, 96 insertions(+), 80 deletions(-)
Title: High Performance Colour Space Manipulation
Description: The encoding of colour can be handled in many different ways,
using different colour spaces. As different colour spaces have
different uses, efficient conversion between these representations are
important. The 'farver' package provides a set of functions that gives
access to very fast colour space conversion and comparisons
implemented in C++, and offers speed improvements over the
'convertColor' function in the 'grDevices' package.
Author: Thomas Lin Pedersen [cre, aut]
,
Berendea Nicolae [aut] ,
Romain Francois [aut] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between farver versions 2.1.1 dated 2022-07-06 and 2.1.2 dated 2024-05-13
farver-2.1.1/farver/src/Makevars |only farver-2.1.2/farver/DESCRIPTION | 21 farver-2.1.2/farver/MD5 | 45 - farver-2.1.2/farver/NEWS.md | 6 farver-2.1.2/farver/R/compare_colour.R | 60 +- farver-2.1.2/farver/R/convert_colour.R | 58 +- farver-2.1.2/farver/R/decode.R | 46 - farver-2.1.2/farver/R/native.R | 4 farver-2.1.2/farver/README.md | 84 +-- farver-2.1.2/farver/man/compare_colour.Rd | 8 farver-2.1.2/farver/man/farver-package.Rd | 7 farver-2.1.2/farver/man/figures/README-unnamed-chunk-7-1.png |binary farver-2.1.2/farver/man/figures/README-unnamed-chunk-8-1.png |binary farver-2.1.2/farver/man/native_encoding.Rd | 2 farver-2.1.2/farver/src/Comparison.cpp | 27 - farver-2.1.2/farver/src/Comparison.h | 4 farver-2.1.2/farver/src/Conversion.cpp | 53 +- farver-2.1.2/farver/src/encode.cpp | 256 ++++++----- farver-2.1.2/farver/src/farver.cpp | 59 +- farver-2.1.2/farver/src/farver.h | 14 farver-2.1.2/farver/src/init.cpp | 4 farver-2.1.2/farver/tests/testthat/test-comparison.R | 2 farver-2.1.2/farver/tests/testthat/test-conversion.R | 2 farver-2.1.2/farver/tests/testthat/test-non-finite.R | 9 24 files changed, 410 insertions(+), 361 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 9.3.5 dated 2024-05-01 and 9.3.5.1 dated 2024-05-13
DESCRIPTION | 8 +- MD5 | 62 ++++++++++---------- NEWS.md | 4 + R/rswipl.R | 4 + src/Makevars | 2 src/swipl-devel/boot/messages.pl | 1 src/swipl-devel/boot/toplevel.pl | 84 ++++++++++++++++++++++++---- src/swipl-devel/cmake/BuildType.cmake | 12 ++-- src/swipl-devel/cmake/Config.cmake | 9 +++ src/swipl-devel/library/qsave.pl | 55 ++++++++++++++---- src/swipl-devel/library/www_browser.pl | 2 src/swipl-devel/packages/clib/process.c | 6 +- src/swipl-devel/packages/clib/time.c | 14 ++-- src/swipl-devel/packages/http/http_files.pl | 8 ++ src/swipl-devel/scripts/configure | 4 + src/swipl-devel/scripts/gdbinit | 1 src/swipl-devel/scripts/mkchangelog | 2 src/swipl-devel/scripts/update-macports | 26 ++++++-- src/swipl-devel/src/config.h.cmake | 1 src/swipl-devel/src/libbf/libbf.c | 5 + src/swipl-devel/src/minizip/unzip.c | 5 + src/swipl-devel/src/minizip/zip.c | 3 + src/swipl-devel/src/mkvmi.c | 3 - src/swipl-devel/src/os/pl-buffer.c | 3 - src/swipl-devel/src/pl-comp.c | 48 ++++++++-------- src/swipl-devel/src/pl-gmp.c | 22 ++++--- src/swipl-devel/src/pl-index.c | 7 +- src/swipl-devel/src/pl-qlf.c | 2 src/swipl-devel/src/pl-read.c | 3 - src/swipl-devel/src/pl-thread.c | 6 +- src/swipl-devel/src/pl-trie.c | 27 +++++---- src/swipl-devel/src/pl-vmi.c | 2 32 files changed, 304 insertions(+), 137 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-15 1.0.1
2022-11-16 1.0.0