Title: Incorporating Previous Findings When Evaluating New Data
Description: Functions for revealing what happens when effect size estimates
from previous studies are taken into account when evaluating each new dataset
in a study sequence. The analyses can be conducted for cumulative
meta-analyses and for Bayesian data analyses. The package contains sample
data for a wide selection of research topics. Jointly considering
previous findings along with new data is more likely to result in correct
conclusions than does the traditional practice of not incorporating previous
findings, which often results in a back and forth ping-pong of conclusions
when evaluating a sequence of studies.
O'Connor & Ermacora (2021, <doi:10.1037/cbs0000259>).
Author: Brian P. O'Connor
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between NO.PING.PONG versions 0.1.6 dated 2022-12-08 and 0.1.8.7 dated 2024-03-29
DESCRIPTION | 10 MD5 | 22 NAMESPACE | 9 R/CONVERT_ES.R | 406 +++++++++---- R/NO.PING.PONG.R | 1288 ++++++++++++++++++++++++++++++-------------- R/PLOT_NO.PING.PONG.R | 46 + R/boc.R | 323 ++++++++++- man/CONVERT_ES.Rd | 95 +-- man/NO.PING.PONG-package.Rd | 2 man/NO.PING.PONG.Rd | 166 +++-- man/PLOT_NO.PING.PONG.Rd | 38 - man/data_NPP.Rd | 6 12 files changed, 1713 insertions(+), 698 deletions(-)
Title: Tool for Diagnosis of Tables Joins and Complementary Join
Features
Description: Tool for diagnosing table joins. It combines the speed of `collapse`
and `data.table`, the flexibility of `dplyr`, and the diagnosis and features
of the `merge` command in `Stata`.
Author: R.Andres Castaneda [aut, cre],
Zander Prinsloo [aut],
Rossana Tatulli [aut]
Maintainer: R.Andres Castaneda <acastanedaa@worldbank.org>
Diff between joyn versions 0.1.4 dated 2021-12-14 and 0.2.0 dated 2024-03-29
joyn-0.1.4/joyn/R/merge.R |only joyn-0.1.4/joyn/R/update_NAs.R |only joyn-0.1.4/joyn/R/update_values.R |only joyn-0.1.4/joyn/inst/doc/advanced-use.R |only joyn-0.1.4/joyn/inst/doc/advanced-use.Rmd |only joyn-0.1.4/joyn/inst/doc/advanced-use.html |only joyn-0.1.4/joyn/inst/doc/general-use.R |only joyn-0.1.4/joyn/inst/doc/general-use.Rmd |only joyn-0.1.4/joyn/inst/doc/general-use.html |only joyn-0.1.4/joyn/tests/testthat/test-merge.R |only joyn-0.1.4/joyn/vignettes/advanced-use.Rmd |only joyn-0.1.4/joyn/vignettes/general-use.Rmd |only joyn-0.2.0/joyn/DESCRIPTION | 42 - joyn-0.2.0/joyn/MD5 | 134 +++- joyn-0.2.0/joyn/NAMESPACE | 15 joyn-0.2.0/joyn/NEWS.md | 23 joyn-0.2.0/joyn/R/aaa.R |only joyn-0.2.0/joyn/R/checks.R |only joyn-0.2.0/joyn/R/dplyr-joins.R |only joyn-0.2.0/joyn/R/freq_table.R | 2 joyn-0.2.0/joyn/R/info_display.R |only joyn-0.2.0/joyn/R/is_id.R | 23 joyn-0.2.0/joyn/R/joyn-merge.R |only joyn-0.2.0/joyn/R/joyn-package.R |only joyn-0.2.0/joyn/R/joyn_workhorse.R |only joyn-0.2.0/joyn/R/merge-data.table.R |only joyn-0.2.0/joyn/R/possible_ids.R | 12 joyn-0.2.0/joyn/R/prep_m_to_m_data.R |only joyn-0.2.0/joyn/R/update_na_vals.R |only joyn-0.2.0/joyn/R/utils.R |only joyn-0.2.0/joyn/R/zzz.R | 134 ++++ joyn-0.2.0/joyn/README.md | 523 ++++++++++------- joyn-0.2.0/joyn/build/vignette.rds |binary joyn-0.2.0/joyn/inst/doc/adv-functionalities.R |only joyn-0.2.0/joyn/inst/doc/adv-functionalities.Rmd |only joyn-0.2.0/joyn/inst/doc/adv-functionalities.html |only joyn-0.2.0/joyn/inst/doc/aux-functions.R |only joyn-0.2.0/joyn/inst/doc/aux-functions.Rmd |only joyn-0.2.0/joyn/inst/doc/aux-functions.html |only joyn-0.2.0/joyn/inst/doc/dplyr-joins.R |only joyn-0.2.0/joyn/inst/doc/dplyr-joins.Rmd |only joyn-0.2.0/joyn/inst/doc/dplyr-joins.html |only joyn-0.2.0/joyn/inst/doc/main-functionalities.R |only joyn-0.2.0/joyn/inst/doc/main-functionalities.Rmd |only joyn-0.2.0/joyn/inst/doc/main-functionalities.html |only joyn-0.2.0/joyn/inst/doc/merge-wrapper.R |only joyn-0.2.0/joyn/inst/doc/merge-wrapper.Rmd |only joyn-0.2.0/joyn/inst/doc/merge-wrapper.html |only joyn-0.2.0/joyn/inst/doc/messages.R |only joyn-0.2.0/joyn/inst/doc/messages.Rmd |only joyn-0.2.0/joyn/inst/doc/messages.html |only joyn-0.2.0/joyn/man/arguments_checks.Rd |only joyn-0.2.0/joyn/man/check_by_vars.Rd |only joyn-0.2.0/joyn/man/check_dt_by.Rd |only joyn-0.2.0/joyn/man/check_duplicate_names.Rd |only joyn-0.2.0/joyn/man/check_match_type.Rd |only joyn-0.2.0/joyn/man/check_new_y_vars.Rd |only joyn-0.2.0/joyn/man/check_reportvar.Rd |only joyn-0.2.0/joyn/man/check_unmatched_keys.Rd |only joyn-0.2.0/joyn/man/check_xy.Rd |only joyn-0.2.0/joyn/man/check_y_vars_to_keep.Rd |only joyn-0.2.0/joyn/man/clear_joynenv.Rd |only joyn-0.2.0/joyn/man/figures |only joyn-0.2.0/joyn/man/freq_table.Rd | 2 joyn-0.2.0/joyn/man/full_join.Rd |only joyn-0.2.0/joyn/man/get_joyn_options.Rd |only joyn-0.2.0/joyn/man/inner_join.Rd |only joyn-0.2.0/joyn/man/is_balanced.Rd |only joyn-0.2.0/joyn/man/is_id.Rd | 23 joyn-0.2.0/joyn/man/is_match_type_error.Rd |only joyn-0.2.0/joyn/man/is_valid_m_key.Rd |only joyn-0.2.0/joyn/man/joyn-package.Rd |only joyn-0.2.0/joyn/man/joyn.Rd |only joyn-0.2.0/joyn/man/joyn_msg.Rd |only joyn-0.2.0/joyn/man/joyn_msgs_exist.Rd |only joyn-0.2.0/joyn/man/joyn_report.Rd |only joyn-0.2.0/joyn/man/joyn_workhorse.Rd |only joyn-0.2.0/joyn/man/left_join.Rd |only joyn-0.2.0/joyn/man/merge.Rd | 237 +++---- joyn-0.2.0/joyn/man/msg_type_dt.Rd |only joyn-0.2.0/joyn/man/possible_ids.Rd | 2 joyn-0.2.0/joyn/man/process_by_vector.Rd |only joyn-0.2.0/joyn/man/rename_to_valid.Rd |only joyn-0.2.0/joyn/man/right_join.Rd |only joyn-0.2.0/joyn/man/roxygen |only joyn-0.2.0/joyn/man/set_col_names.Rd |only joyn-0.2.0/joyn/man/set_joyn_options.Rd |only joyn-0.2.0/joyn/man/split_match_type.Rd |only joyn-0.2.0/joyn/man/store_msg.Rd |only joyn-0.2.0/joyn/man/style.Rd |only joyn-0.2.0/joyn/man/type_choices.Rd |only joyn-0.2.0/joyn/man/unmatched_keys.Rd |only joyn-0.2.0/joyn/man/update_na_values.Rd |only joyn-0.2.0/joyn/tests/testthat/test-checks.R |only joyn-0.2.0/joyn/tests/testthat/test-dplyr-joins.R |only joyn-0.2.0/joyn/tests/testthat/test-fix_by_vars.R |only joyn-0.2.0/joyn/tests/testthat/test-freq_table.R | 10 joyn-0.2.0/joyn/tests/testthat/test-info_display.R |only joyn-0.2.0/joyn/tests/testthat/test-is_id.R | 7 joyn-0.2.0/joyn/tests/testthat/test-joyn.R |only joyn-0.2.0/joyn/tests/testthat/test-joyn_workhorse.R |only joyn-0.2.0/joyn/tests/testthat/test-merge-data.table.R |only joyn-0.2.0/joyn/tests/testthat/test-possible_ids.R | 5 joyn-0.2.0/joyn/tests/testthat/test-update_na_vals.R |only joyn-0.2.0/joyn/tests/testthat/test-utils.R |only joyn-0.2.0/joyn/vignettes/adv-functionalities.Rmd |only joyn-0.2.0/joyn/vignettes/aux-functions.Rmd |only joyn-0.2.0/joyn/vignettes/dplyr-joins.Rmd |only joyn-0.2.0/joyn/vignettes/main-functionalities.Rmd |only joyn-0.2.0/joyn/vignettes/merge-wrapper.Rmd |only joyn-0.2.0/joyn/vignettes/messages.Rmd |only 111 files changed, 779 insertions(+), 415 deletions(-)
Title: Query Composite Hypotheses
Description: Provides functions for the joint analysis of Q sets of
p-values obtained for the same list of items. This joint analysis is
performed by querying a composite hypothesis, i.e. an arbitrary
complex combination of simple hypotheses, as described in Mary-Huard
et al. (2021) <doi:10.1093/bioinformatics/btab592> and De Walsche et
al.(2023) <doi:10.1101/2024.03.17.585412>. In this approach, the
Q-uplet of p-values associated with each item is distributed as a
multivariate mixture, where each of the 2^Q components corresponds to
a specific combination of simple hypotheses. The dependence between
the p-value series is considered using a Gaussian copula function. A
p-value for the composite hypothesis test is derived from the
posterior probabilities.
Author: Tristan Mary-Huard [aut, cre] ,
Annaig De Walsche [aut] ,
Franck Gauthier [ctb]
Maintainer: Tristan Mary-Huard <tristan.mary-huard@agroparistech.fr>
Diff between qch versions 1.0.0 dated 2021-05-07 and 2.0.0 dated 2024-03-29
qch-1.0.0/qch/R/QCH_functions.R |only qch-1.0.0/qch/man/FastKerFdr.Rd |only qch-1.0.0/qch/man/GetHinfo.Rd |only qch-1.0.0/qch/man/GetHinfoEqual.Rd |only qch-2.0.0/qch/DESCRIPTION | 60 +++---- qch-2.0.0/qch/MD5 | 51 ++++-- qch-2.0.0/qch/NAMESPACE | 26 +-- qch-2.0.0/qch/R/Data.R | 41 +++- qch-2.0.0/qch/R/EM_functions.R |only qch-2.0.0/qch/R/FastKerFDR_functions.R |only qch-2.0.0/qch/R/GetHinfo.R |only qch-2.0.0/qch/R/RcppExports.R |only qch-2.0.0/qch/R/qch-package.R | 16 + qch-2.0.0/qch/R/qch_fit.R |only qch-2.0.0/qch/R/qch_test.R |only qch-2.0.0/qch/build |only qch-2.0.0/qch/data/PvalSets_cor.rda |only qch-2.0.0/qch/man/Copula.Hconfig_gaussian_density.Rd |only qch-2.0.0/qch/man/EM_calibration_gaussian.Rd |only qch-2.0.0/qch/man/EM_calibration_gaussian_memory.Rd |only qch-2.0.0/qch/man/EM_calibration_indep.Rd |only qch-2.0.0/qch/man/EM_calibration_indep_memory.Rd |only qch-2.0.0/qch/man/FastKerFdr_signed.Rd |only qch-2.0.0/qch/man/FastKerFdr_unsigned.Rd |only qch-2.0.0/qch/man/GetH1AtLeast.Rd |only qch-2.0.0/qch/man/GetH1Equal.Rd |only qch-2.0.0/qch/man/GetHconfig.Rd |only qch-2.0.0/qch/man/PvalSets_cor.Rd |only qch-2.0.0/qch/man/R.MLE.Rd |only qch-2.0.0/qch/man/R.MLE.check.Rd |only qch-2.0.0/qch/man/R.MLE.memory.Rd |only qch-2.0.0/qch/man/R_MLE_update_gaussian_copula_ptr_parallel.Rd |only qch-2.0.0/qch/man/f1_separation_signed.Rd |only qch-2.0.0/qch/man/fHconfig_sum_update_gaussian_copula_ptr_parallel.Rd |only qch-2.0.0/qch/man/fHconfig_sum_update_ptr_parallel.Rd |only qch-2.0.0/qch/man/gaussian_copula_density.Rd |only qch-2.0.0/qch/man/prior_update_arma_ptr_parallel.Rd |only qch-2.0.0/qch/man/prior_update_gaussian_copula_ptr_parallel.Rd |only qch-2.0.0/qch/man/qch-package.Rd | 63 ++++--- qch-2.0.0/qch/man/qch.fit.Rd | 85 ++++++++-- qch-2.0.0/qch/man/qch.test.Rd | 54 ++++-- qch-2.0.0/qch/src |only 42 files changed, 274 insertions(+), 122 deletions(-)
Title: Propensity Score Weighting for Causal Inference with
Observational Studies and Randomized Trials
Description: Supports propensity score weighting analysis of observational studies and randomized trials. Enables the estimation and inference of average causal effects with binary and multiple treatments using overlap weights (ATO), inverse probability of treatment weights (ATE), average treatment effect among the treated weights (ATT), matching weights (ATM) and entropy weights (ATEN), with and without propensity score trimming. These weights are members of the family of balancing weights introduced in Li, Morgan and Zaslavsky (2018) <doi:10.1080/01621459.2016.1260466> and Li and Li (2019) <doi:10.1214/19-AOAS1282>.
Author: Tianhui Zhou [aut],
Guangyu Tong [aut],
Fan Li [aut],
Laine Thomas [aut],
Fan Li [aut],
Yukang Zeng [cre]
Maintainer: Yukang Zeng <yukang.zeng@yale.edu>
Diff between PSweight versions 1.1.8 dated 2022-10-18 and 1.2.0 dated 2024-03-29
PSweight-1.1.8/PSweight/inst/doc/vignette.Rnw |only PSweight-1.1.8/PSweight/inst/doc/vignette.pdf |only PSweight-1.1.8/PSweight/vignettes/Software_vig.pdf |only PSweight-1.1.8/PSweight/vignettes/vignette.Rnw |only PSweight-1.2.0/PSweight/DESCRIPTION | 21 PSweight-1.2.0/PSweight/MD5 | 44 - PSweight-1.2.0/PSweight/NEWS.md |only PSweight-1.2.0/PSweight/R/OUTmethod.R | 362 ++++----- PSweight-1.2.0/PSweight/R/PSmethod.R | 437 +++++------ PSweight-1.2.0/PSweight/R/PStrim.R | 476 ++++++------ PSweight-1.2.0/PSweight/R/PSweight.R | 2 PSweight-1.2.0/PSweight/R/SumStat.R | 18 PSweight-1.2.0/PSweight/R/SumStat_cl.R | 28 PSweight-1.2.0/PSweight/R/bin_est.R | 20 PSweight-1.2.0/PSweight/R/mul_est.R | 8 PSweight-1.2.0/PSweight/R/plot_SumStat.R | 68 + PSweight-1.2.0/PSweight/R/sand_var.R | 4 PSweight-1.2.0/PSweight/R/summary_SumStat.R | 53 - PSweight-1.2.0/PSweight/README.md |only PSweight-1.2.0/PSweight/build/vignette.rds |binary PSweight-1.2.0/PSweight/inst/doc/Software_vig.Rmd |only PSweight-1.2.0/PSweight/inst/doc/Software_vig.pdf |only PSweight-1.2.0/PSweight/man/OUTmethod.Rd | 4 PSweight-1.2.0/PSweight/man/PSmethod.Rd | 6 PSweight-1.2.0/PSweight/man/SumStat.Rd | 8 PSweight-1.2.0/PSweight/man/SumStat_cl.Rd | 8 PSweight-1.2.0/PSweight/vignettes/Software_vig.Rmd |only PSweight-1.2.0/PSweight/vignettes/Software_vig_original.pdf |only 28 files changed, 833 insertions(+), 734 deletions(-)
Title: Explainers for Regression Models in HIV Research
Description: A dedicated viral-explainer model tool designed to empower researchers in the field of HIV research, particularly in viral load and CD4 (Cluster of Differentiation 4) lymphocytes regression modeling. Drawing inspiration from the 'tidymodels' framework for rigorous model building of Max Kuhn and Hadley Wickham (2020) <https://www.tidymodels.org>, and the 'DALEXtra' tool for explainability by Przemyslaw Biecek (2020) <arXiv:2009.13248>. It aims to facilitate interpretable and reproducible research in biostatistics and computational biology for the benefit of understanding HIV dynamics.
Author: Juan Pablo Acuna Gonzalez [aut, cre]
Maintainer: Juan Pablo Acuna Gonzalez <22253567@uagro.mx>
Diff between viralx versions 1.2.0 dated 2024-01-21 and 1.3.0 dated 2024-03-29
DESCRIPTION | 10 +++++----- MD5 | 10 +++++++--- NAMESPACE | 1 + R/glob_cub_vis.R |only man/glob_cr_vis.Rd |only tests/testthat/_snaps/glob_cub_vis |only tests/testthat/_snaps/viralx_knn_vis/viralx-knn-vis.svg | 2 +- tests/testthat/test-glob_cub_vis.R |only 8 files changed, 14 insertions(+), 9 deletions(-)
Title: Edit 'XMP' Metadata and 'PDF' Bookmarks and Documentation Info
Description: Edit 'XMP' metadata <https://en.wikipedia.org/wiki/Extensible_Metadata_Platform>
in a variety of media file formats as well as
edit bookmarks (aka outline aka table of contents) and documentation info entries in 'pdf' files.
Can detect and use a variety of command-line tools to perform these operations such as
'exiftool' <https://exiftool.org/>, 'ghostscript' <https://www.ghostscript.com/>,
and/or 'pdftk' <https://gitlab.com/pdftk-java/pdftk>.
Author: Trevor L Davis [aut, cre] ,
Linux Foundation [dtc]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between xmpdf versions 0.1.4 dated 2023-10-02 and 0.2.1 dated 2024-03-29
xmpdf-0.1.4/xmpdf/inst/gs |only xmpdf-0.2.1/xmpdf/DESCRIPTION | 16 xmpdf-0.2.1/xmpdf/LICENSE |only xmpdf-0.2.1/xmpdf/MD5 | 74 +-- xmpdf-0.2.1/xmpdf/NAMESPACE | 2 xmpdf-0.2.1/xmpdf/NEWS.md | 24 + xmpdf-0.2.1/xmpdf/R/as_docinfo.R | 2 xmpdf-0.2.1/xmpdf/R/bookmarks.R | 85 +++ xmpdf-0.2.1/xmpdf/R/docinfo.R | 36 - xmpdf-0.2.1/xmpdf/R/edit_docinfo.R | 4 xmpdf-0.2.1/xmpdf/R/edit_xmp.R | 4 xmpdf-0.2.1/xmpdf/R/n_pages.R | 4 xmpdf-0.2.1/xmpdf/R/supports.R | 6 xmpdf-0.2.1/xmpdf/R/utils-exiftool.R | 80 +-- xmpdf-0.2.1/xmpdf/R/utils-misc.R | 4 xmpdf-0.2.1/xmpdf/R/utils-pdftk.R | 7 xmpdf-0.2.1/xmpdf/R/xmp.R | 34 - xmpdf-0.2.1/xmpdf/R/zzz.R | 1 xmpdf-0.2.1/xmpdf/README.md | 41 - xmpdf-0.2.1/xmpdf/build/vignette.rds |binary xmpdf-0.2.1/xmpdf/data/spdx_licenses.rda |binary xmpdf-0.2.1/xmpdf/inst/doc/xmp.html | 322 ++++++++++++-- xmpdf-0.2.1/xmpdf/inst/doc/xmpdf.Rmd | 38 - xmpdf-0.2.1/xmpdf/inst/doc/xmpdf.html | 412 ++++++++++++++----- xmpdf-0.2.1/xmpdf/man/bookmarks.Rd | 6 xmpdf-0.2.1/xmpdf/man/cat_bookmarks.Rd | 5 xmpdf-0.2.1/xmpdf/man/docinfo.Rd | 2 xmpdf-0.2.1/xmpdf/man/supports.Rd | 4 xmpdf-0.2.1/xmpdf/man/xmp.Rd | 6 xmpdf-0.2.1/xmpdf/man/xmpdf.Rd | 3 xmpdf-0.2.1/xmpdf/tests/testthat/_snaps/bookmarks.md | 2 xmpdf-0.2.1/xmpdf/tests/testthat/_snaps/docinfo.md | 2 xmpdf-0.2.1/xmpdf/tests/testthat/_snaps/messages.md | 16 xmpdf-0.2.1/xmpdf/tests/testthat/_snaps/xmp.md | 8 xmpdf-0.2.1/xmpdf/tests/testthat/test-bookmarks.R | 62 ++ xmpdf-0.2.1/xmpdf/tests/testthat/test-docinfo.R | 1 xmpdf-0.2.1/xmpdf/tests/testthat/test-xmp.R | 2 xmpdf-0.2.1/xmpdf/vignettes/xmpdf.Rmd | 38 - 38 files changed, 948 insertions(+), 405 deletions(-)
Title: Fast General Purpose Date/Time Converter
Description: Fast general purpose date/time converter using 'Rust'. The package implements date time, date and epoch time parser for heterogeneous vectors of dates.
Author: David Schoch [aut, cre] ,
Rollie Ma [ctb, cph] ,
Brandon W. Maister [ctb, cph] ,
Dirkjan Ochtman [ctb, cph] ,
Seonghoon Kang [ctb, cph] ,
Eric Sheppard [ctb, cph] ,
Paul Dicker [ctb, cph]
Maintainer: David Schoch <david@schochastics.net>
Diff between timeless versions 0.1.0 dated 2024-03-04 and 0.2.0 dated 2024-03-29
DESCRIPTION | 6 +- MD5 | 20 ++++---- NEWS.md | 5 ++ R/chronos.R | 42 +++++++++------- R/sysdata.rda |binary R/utils.R | 8 ++- README.md | 102 +++++++++++++++++++++-------------------- man/chronos.Rd | 12 ++++ man/timeless-package.Rd | 2 src/rust/src/lib.rs | 25 ++++------ tests/testthat/test-timeless.R | 7 ++ 11 files changed, 129 insertions(+), 100 deletions(-)
Title: More Data Sets Useful for Modeling Examples
Description: More data sets used for demonstrating or testing model-related
packages are contained in this package. The data sets are downloaded and
cached, allowing for more and bigger data sets.
Author: Emil Hvitfeldt [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between modeldatatoo versions 0.2.1 dated 2023-08-25 and 0.3.0 dated 2024-03-29
DESCRIPTION | 9 +++++---- MD5 | 17 ++++++++++++----- NAMESPACE | 2 ++ NEWS.md | 6 ++++++ R/building_complaints.R |only R/building_complaints_old.R |only R/detectors.R |only README.md | 7 +++++-- build/partial.rdb |binary data |only man/building_complaints.Rd |only man/data_building_complaints.Rd |only man/data_detectors.Rd |only 13 files changed, 30 insertions(+), 11 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of 'MUMPS' (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'.
'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194>
and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre],
Emmanuel Agullo [ctb],
Patrick Amestoy [ctb, cph],
Maurice Bremond [ctb],
Alfredo Buttari [ctb],
Philippe Combes [ctb],
Marie Durand [ctb],
Aurelia Fevre [ctb],
Abdou Guermouche [ctb],
Guillaume Joslin [ctb],
Jacko Koster [c [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.2.1-28 dated 2024-02-26 and 5.2.1-29 dated 2024-03-29
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 8 +++++++- inst/include/rmumps.h | 1 + man/rmumps-package.Rd | 2 +- src/lib/scotch_6.0.9/src/esmumps/Makefile | 3 +-- src/lib/scotch_6.0.9/src/esmumps/symbol_fax_graph.c | 3 +++ src/rmumps_module.cpp | 10 +++++++++- tests/testthat/test_rmumps.R | 7 +++++++ 9 files changed, 41 insertions(+), 17 deletions(-)
Title: Text Analysis Through the 'Receptiviti' API
Description: Send text to the <https://www.receptiviti.com> API to be scored
by all available frameworks.
Author: Receptiviti Inc. [fnd, cph],
Kent English [cre],
Micah Iserman [aut, ctr]
Maintainer: Kent English <kenglish@receptiviti.com>
Diff between receptiviti versions 0.1.7 dated 2024-02-23 and 0.1.8 dated 2024-03-29
DESCRIPTION | 7 +++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/receptiviti.R | 2 +- README.md | 4 ++-- tests/testthat/test-receptiviti_status.R | 10 ++++++---- 6 files changed, 22 insertions(+), 16 deletions(-)
Title: Power Analysis and Data Simulation for Multilevel Models
Description: A declarative language for specifying multilevel models,
solving for population parameters based on specified variance-explained effect
size measures, generating data, and conducting power analyses to determine
sample size recommendations. The specification allows for any number of
within-cluster effects, between-cluster effects, covariate effects
at either level, and random coefficients. Moreover, the models do not
assume orthogonal effects, and predictors can correlate at either level
and accommodate models with multiple interaction effects.
Author: Brian T. Keller [aut, cre, cph]
Maintainer: Brian T. Keller <btkeller@missouri.edu>
Diff between mlmpower versions 1.0.6 dated 2024-03-15 and 1.0.7 dated 2024-03-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/simulation.R | 12 ++++++++---- 4 files changed, 18 insertions(+), 10 deletions(-)
Title: Project GENIE BioPharma Collaborative Data Processing Pipeline
Description: The American Association Research (AACR) Project
Genomics Evidence Neoplasia Information Exchange (GENIE) BioPharma
Collaborative represents a multi-year, multi-institution effort
to build a pan-cancer repository of linked clinico-genomic data.
The genomic and clinical data are provided in multiple releases (separate
releases for each cancer cohort with updates following data corrections),
which are stored on the data sharing platform
'Synapse' <https://www.synapse.org/>.
The 'genieBPC' package provides a seamless way to obtain the
data corresponding to each release from 'Synapse' and to prepare
datasets for analysis.
Author: Jessica A. Lavery [aut, cre] ,
Michael A. Curry [aut] ,
Samantha Brown [aut] ,
Karissa Whiting [aut] ,
Hannah Fuchs [aut] ,
Axel Martin [aut],
Daniel D. Sjoberg [ctb]
Maintainer: Jessica A. Lavery <laveryj@mskcc.org>
Diff between genieBPC versions 1.1.0 dated 2023-03-03 and 1.1.1 dated 2024-03-29
DESCRIPTION | 6 MD5 | 67 NEWS.md | 60 R/create_analytic_cohort.R | 23 R/data.R | 19 R/pull_data_synapse.R | 103 R/synapse_authentication.R | 2 R/synapse_version.R | 18 README.md | 110 build/vignette.rds |binary data/nsclc_test_data.rda |binary data/synapse_tables.rda |binary inst/WORDLIST | 32 inst/doc/create_analytic_cohort_vignette.R | 92 inst/doc/create_analytic_cohort_vignette.html | 2378 +++++ inst/doc/drug_regimen_sunburst_vignette.R | 66 inst/doc/drug_regimen_sunburst_vignette.html |12157 +++++++++++++++++++++++++- inst/doc/pull_data_synapse_vignette.R | 53 inst/doc/pull_data_synapse_vignette.Rmd | 49 inst/doc/pull_data_synapse_vignette.html | 660 + inst/doc/select_unique_ngs_vignette.R | 79 inst/doc/select_unique_ngs_vignette.html | 622 + man/dot-pull_data_by_cohort.Rd | 12 man/nsclc_test_data.Rd | 11 man/pull_data_synapse.Rd | 24 man/set_synapse_credentials.Rd | 2 man/synapse_tables.Rd | 8 man/synapse_version.Rd | 7 tests/testthat/test-create_analytic_cohort.R | 723 - tests/testthat/test-drug_regimen_sunburst.R | 14 tests/testthat/test-pull_data_synapse.R | 380 tests/testthat/test-select_unique_ngs.R | 38 tests/testthat/test-synapse_tables.R |only tests/testthat/test-synapse_version.R | 37 vignettes/pull_data_synapse_vignette.Rmd | 49 35 files changed, 17268 insertions(+), 633 deletions(-)
Title: Copula Based Cox Proportional Hazards Models for Dependent
Censoring
Description: Copula based Cox proportional hazards models for survival data subject to dependent
censoring. This approach does not assume that the parameter defining the copula is known. The
dependency parameter is estimated with other finite model parameters by maximizing a Pseudo
likelihood function. The cumulative hazard function is estimated via estimating equations
derived based on martingale ideas. Available copula functions include Frank, Gumbel and Normal
copulas. Only Weibull and lognormal models are allowed for the censoring model, even though any
parametric model that satisfies certain identifiability conditions could be used. Implemented
methods are described in the article "Copula based Cox proportional hazards models for dependent
censoring" by Deresa and Van Keilegom (2023) <doi:10.1080/01621459.2022.2161387>.
Author: Negera Wakgari Deresa [aut, cre]
,
Ingrid Van Keilegom [aut]
Maintainer: Negera Wakgari Deresa <negera.deresa@gmail.com>
Diff between SemiPar.depCens versions 0.1.1 dated 2024-02-29 and 0.1.2 dated 2024-03-29
DESCRIPTION | 6 MD5 | 38 +-- NAMESPACE | 48 ++-- NEWS.md | 13 - R/SolveL.R | 40 +-- R/bootstrapFunctions.R | 18 - R/data.R | 48 ++-- R/depCensoringFit-Results.R | 21 +- R/fitIndependentCensoringModels.R | 3 R/fitdependentCensorigModels.R | 13 - R/helper.R | 58 ++--- R/pseudoLikelihoodFunctions.R | 360 +++++++++++++++++------------------ man/SolveL.Rd | 142 ++++++------- man/SolveLI.Rd | 116 +++++------ man/fitDepCens.Rd | 7 man/fitIndepCens.Rd | 3 tests/testthat/helper_fitDepCens.R | 2 tests/testthat/helper_fitIndepCens.R | 38 +-- tests/testthat/test-fitDepCens.R | 40 +-- tests/testthat/test-fitIndepCens.R | 36 +-- 20 files changed, 534 insertions(+), 516 deletions(-)
More information about SemiPar.depCens at CRAN
Permanent link
Title: MultiLinear Algebra
Description: A set of tools for basic tensor operators. A tensor in the context of data analysis in a multidimensional array. The tools in this package rely on using any discrete transformation (e.g. Fast Fourier Transform (FFT)). Standard tools included are the Eigenvalue decomposition of a tensor, the QR decomposition and LU decomposition. Other functionality includes the inverse of a tensor and the transpose of a symmetric tensor. Functionality in the package is outlined in Kernfeld et al. (2015) <https://www.sciencedirect.com/science/article/pii/S0024379515004358>.
Author: Kyle Caudle [aut, cre],
Randy Hoover [ctb],
Jackson Cates [ctb]
Maintainer: Kyle Caudle <kyle.caudle@sdsmt.edu>
Diff between rTensor2 versions 0.2.0 dated 2024-02-22 and 2.0.0 dated 2024-03-29
rTensor2-0.2.0/rTensor2/R/randtensor.R |only rTensor2-0.2.0/rTensor2/R/tsym.R |only rTensor2-0.2.0/rTensor2/man/randtensor.Rd |only rTensor2-0.2.0/rTensor2/man/tsym.Rd |only rTensor2-2.0.0/rTensor2/DESCRIPTION | 10 rTensor2-2.0.0/rTensor2/MD5 | 33 +- rTensor2-2.0.0/rTensor2/NAMESPACE | 4 rTensor2-2.0.0/rTensor2/NEWS.md |only rTensor2-2.0.0/rTensor2/R/rand_tensor.R |only rTensor2-2.0.0/rTensor2/R/tDWT.R | 3 rTensor2-2.0.0/rTensor2/R/tLDA.R | 8 rTensor2-2.0.0/rTensor2/R/tSVDfft.R | 17 - rTensor2-2.0.0/rTensor2/R/t_tpose.R |only rTensor2-2.0.0/rTensor2/build/vignette.rds |binary rTensor2-2.0.0/rTensor2/data/raytrace.rda |only rTensor2-2.0.0/rTensor2/inst/doc/rTensor2.R | 84 ++++++ rTensor2-2.0.0/rTensor2/inst/doc/rTensor2.Rmd | 140 +++++++++++ rTensor2-2.0.0/rTensor2/inst/doc/rTensor2.html | 302 ++++++++++++++++++++++++- rTensor2-2.0.0/rTensor2/man/rand_tensor.Rd |only rTensor2-2.0.0/rTensor2/man/raytrace.Rd |only rTensor2-2.0.0/rTensor2/man/tQR.Rd | 6 rTensor2-2.0.0/rTensor2/man/t_tpose.Rd |only rTensor2-2.0.0/rTensor2/vignettes/rTensor2.Rmd | 140 +++++++++++ 23 files changed, 707 insertions(+), 40 deletions(-)
Title: Nonparametric Regression via Smoothing Splines
Description: Multiple and generalized nonparametric regression using smoothing spline ANOVA models and generalized additive models, as described in Helwig (2020) <doi:10.4135/9781526421036885885>. Includes support for Gaussian and non-Gaussian responses, smoothers for multiple types of predictors (including random intercepts), interactions between smoothers of mixed types, eight different methods for smoothing parameter selection, and flexible tools for diagnostics, inference, and prediction.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between npreg versions 1.0-9 dated 2022-07-20 and 1.1.0 dated 2024-03-29
ChangeLog | 31 +++++++++++++++++++++++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 36 ++++++++++++++++++++++-------------- NAMESPACE | 10 ++++++---- R/boot.gsm.R | 6 +++--- R/build_rkhs.R | 12 ++++++++++-- R/check_knot.R | 18 +++++++++++++++--- R/check_type.R | 18 ++++++++++++++---- R/check_type2.R | 16 ++++++++++++++-- R/color.legend.R |only R/knot1samp.R | 2 +- R/msqrt.R | 3 ++- R/plot.gsm.R |only R/plot.sm.R |only R/pred_rkhs.R | 17 ++++++++++++----- R/zzz.R |only build/partial.rdb |binary man/StartupMessage.Rd |only man/color.legend.Rd |only man/gsm.Rd | 25 +++++++++++++++++++++++++ man/plot.gsm.Rd |only man/plot.sm.Rd |only man/sm.Rd | 21 +++++++++++++++++++++ 23 files changed, 182 insertions(+), 45 deletions(-)
Title: Functional Help for Functions, Objects, and Packages
Description: Enhance R help system by fuzzy search and preview interface, pseudo-postfix operators, and more.
The `?.` pseudo-postfix operator and the `?` prefix operator displays documents and contents (source or structure) of objects simultaneously to help understanding the objects.
The `?p` pseudo-postfix operator displays package documents, and is shorter than help(package = foo).
Author: Atsushi Yasumoto [aut, cph, cre]
Maintainer: Atsushi Yasumoto <atusy.rpkg@gmail.com>
Diff between felp versions 0.3.0 dated 2022-10-09 and 0.4.0 dated 2024-03-29
DESCRIPTION | 14 - MD5 | 18 +- NEWS.md | 8 R/fuzzyhelp.R | 154 +++++++++++++++-- README.md | 23 +- build/vignette.rds |binary inst/doc/felp.R | 2 inst/doc/felp.html | 422 ++++++++++++++++++++---------------------------- inst/rstudio/addins.dcf | 2 man/fuzzyhelp.Rd | 19 ++ 10 files changed, 375 insertions(+), 287 deletions(-)
Title: Robust Bayesian Variable Selection via Expectation-Maximization
Description: Variable selection methods have been extensively developed for analyzing high-dimensional omics data within both the frequentist and Bayesian frameworks. This package implemented the spike-and-slab quantile LASSO which has been developed along the line of Bayesian hierarchical model but deeply rooted in the frequentist regularization methods by utilizing the Expectation–Maximization (EM) algorithm. Therefore, the proposed method borrows strength from both the frequentist and Bayesian frameworks while overcoming their respective limitations. The spike-and-slab quantile LASSO can handle data irregularity in terms of skewness and outliers in the disease trait, compared to its nonrobust alternative, the spike-and-slab LASSO, which has also been implemented in the package. The core module of this package is developed in 'C++'.
Author: Yuwen Liu [aut, cre],
Cen Wu [aut]
Maintainer: Yuwen Liu <yuwen@ksu.edu>
Diff between emBayes versions 0.1.4 dated 2023-11-07 and 0.1.5 dated 2024-03-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/cv.emBayes.R | 4 ++-- R/emBayes.R | 10 +++++++--- man/cv.emBayes.Rd | 4 ++-- man/emBayes.Rd | 2 +- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Process and Analyse Data from m-Path Sense
Description: Overcomes one of the major challenges in mobile (passive)
sensing, namely being able to pre-process the raw data that comes from
a mobile sensing app, specifically 'm-Path Sense' <https://m-path.io>.
The main task of 'mpathsenser' is therefore to read 'm-Path Sense'
JSON files into a database and provide several convenience functions
to aid in data processing.
Author: Koen Niemeijer [aut, cre] ,
Kristof Meers [ctb] ,
KU Leuven [cph, fnd]
Maintainer: Koen Niemeijer <koen.niemeijer@kuleuven.be>
Diff between mpathsenser versions 1.2.2 dated 2024-02-23 and 1.2.3 dated 2024-03-29
DESCRIPTION | 10 MD5 | 75 NEWS.md | 635 +++---- R/coverage.R | 711 ++++---- R/database.R | 1110 ++++++------ R/import.R | 1206 +++++++------- R/import_functions.R | 1236 +++++++------- R/input_checks.R | 369 ++-- R/linking.R | 2074 ++++++++++++------------ R/location_functions.R | 392 ++-- R/sensor_functions.R | 1940 +++++++++++----------- R/utils.R | 911 +++++----- build/vignette.rds |binary inst/WORDLIST |only inst/doc/mpathsenser.R | 16 inst/doc/mpathsenser.Rmd | 32 inst/doc/mpathsenser.html | 147 + man/copy_db.Rd | 3 man/decrypt_gps.Rd | 28 man/figures/lifecycle-archived.svg | 22 man/figures/lifecycle-defunct.svg | 22 man/figures/lifecycle-deprecated.svg | 22 man/figures/lifecycle-experimental.svg | 22 man/figures/lifecycle-maturing.svg | 22 man/figures/lifecycle-questioning.svg | 22 man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg | 30 man/figures/lifecycle-superseded.svg | 22 man/get_data.Rd | 16 man/link.Rd | 22 man/link_db.Rd | 6 man/link_gaps.Rd | 6 man/unzip_data.Rd | 8 tests/spelling.R |only tests/testthat/test-coverage.R | 168 - tests/testthat/test-import_functions.R | 1921 +++++++++++----------- tests/testthat/test-legacy-data.R | 1021 +++++------ tests/testthat/test-linking.R | 2583 +++++++++++++++--------------- tests/testthat/test-sensor_functions.R | 789 ++++----- vignettes/mpathsenser.Rmd | 32 40 files changed, 9023 insertions(+), 8628 deletions(-)
Title: Efficiently Retrieve and Process Satellite Imagery
Description: Downloads spatial data from spatiotemporal asset catalogs
('STAC'), computes standard spectral indices from the Awesome Spectral
Indices project (Montero et al. (2023) <doi:10.1038/s41597-023-02096-0>)
against raster data, and glues the outputs together into predictor bricks.
Methods focus on interoperability with the broader spatial ecosystem;
function arguments and outputs use classes from 'sf' and 'terra', and data
downloading functions support complex 'CQL2' queries using 'rstac'.
Author: Michael Mahoney [aut, cre] ,
Permian Global [cph, fnd]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between rsi versions 0.1.2 dated 2024-02-13 and 0.2.0 dated 2024-03-29
rsi-0.1.2/rsi/man/default_query_function.Rd |only rsi-0.2.0/rsi/DESCRIPTION | 10 rsi-0.2.0/rsi/MD5 | 69 + rsi-0.2.0/rsi/NAMESPACE | 6 rsi-0.2.0/rsi/NEWS.md | 56 + rsi-0.2.0/rsi/R/0-globals.R |only rsi-0.2.0/rsi/R/check_type_and_length.R | 2 rsi-0.2.0/rsi/R/data.R | 10 rsi-0.2.0/rsi/R/deprecated.R |only rsi-0.2.0/rsi/R/download.R |only rsi-0.2.0/rsi/R/get_stac_data.R | 523 ++++++-------- rsi-0.2.0/rsi/R/mask_functions.R | 51 + rsi-0.2.0/rsi/R/misc.R | 8 rsi-0.2.0/rsi/R/query_and_sign.R | 29 rsi-0.2.0/rsi/R/rsi-package.R | 1 rsi-0.2.0/rsi/R/stack_rasters.R | 38 - rsi-0.2.0/rsi/R/sysdata.rda |binary rsi-0.2.0/rsi/README.md | 6 rsi-0.2.0/rsi/build/partial.rdb |binary rsi-0.2.0/rsi/build/vignette.rds |binary rsi-0.2.0/rsi/data/alos_palsar_band_mapping.rda |only rsi-0.2.0/rsi/data/dem_band_mapping.rda |binary rsi-0.2.0/rsi/data/landsat_band_mapping.rda |binary rsi-0.2.0/rsi/data/sentinel1_band_mapping.rda |binary rsi-0.2.0/rsi/data/sentinel2_band_mapping.rda |binary rsi-0.2.0/rsi/inst/doc/rsi.Rmd | 14 rsi-0.2.0/rsi/inst/doc/rsi.html | 14 rsi-0.2.0/rsi/man/alos_palsar_band_mapping.Rd |only rsi-0.2.0/rsi/man/alos_palsar_mask_function.Rd |only rsi-0.2.0/rsi/man/deprecated.Rd |only rsi-0.2.0/rsi/man/get_stac_data.Rd | 84 ++ rsi-0.2.0/rsi/man/landsat_mask_function.Rd | 5 rsi-0.2.0/rsi/man/rsi_download_rasters.Rd |only rsi-0.2.0/rsi/man/rsi_query_api.Rd |only rsi-0.2.0/rsi/man/sign_planetary_computer.Rd | 2 rsi-0.2.0/rsi/tests/testthat/_snaps/misc.md | 8 rsi-0.2.0/rsi/tests/testthat/test-check_type_and_length.R | 10 rsi-0.2.0/rsi/tests/testthat/test-get_stac_data.R | 95 ++ rsi-0.2.0/rsi/tests/testthat/test-mask_functions.R |only rsi-0.2.0/rsi/tests/testthat/test-stack_rasters.R | 20 rsi-0.2.0/rsi/vignettes/rsi.Rmd | 14 41 files changed, 679 insertions(+), 396 deletions(-)
Title: Bunch-Gay-Welsch Statistical Estimation
Description: Performs statistical estimation and inference-related computations
by accessing and executing modified versions of 'Fortran' subroutines
originally published in the Association for Computing Machinery (ACM)
journal Transactions on Mathematical Software (TOMS) by Bunch, Gay and
Welsch (1993) <doi:10.1145/151271.151279>. The acronym 'BGW' (from the
authors' last names) will be used when making reference to technical
content (e.g., algorithm, methodology) that originally appeared in ACM TOMS.
A key feature of BGW is that it exploits the special structure of statistical
estimation problems within a trust-region-based optimization approach to
produce an estimation algorithm that is much more effective than the usual
practice of using optimization methods and codes originally developed for
general optimization. The 'bgw' package bundles 'R' wrapper (and related)
functions with modified 'Fortran' source code so that it can be compiled and
linked in the 'R' environment for fast execution [...truncated...]
Author: David S. Bunch [aut, cre] ,
David M. Gay [ctb],
Roy E. Welsch [ctb],
Stephane Hess [ctb],
David Palma [ctb]
Maintainer: David S. Bunch <dsbunch@ucdavis.edu>
Diff between bgw versions 0.1.2 dated 2023-07-13 and 0.1.3 dated 2024-03-29
bgw-0.1.2/bgw/src/drglg_mod.f95 |only bgw-0.1.3/bgw/DESCRIPTION | 28 ++++----- bgw-0.1.3/bgw/MD5 | 20 +++--- bgw-0.1.3/bgw/NEWS | 13 ++++ bgw-0.1.3/bgw/R/bgw_itsum.R | 1 bgw-0.1.3/bgw/R/bgw_mle.R | 38 +++++++----- bgw-0.1.3/bgw/build/vignette.rds |binary bgw-0.1.3/bgw/inst/doc/bgw-vignette.R | 2 bgw-0.1.3/bgw/inst/doc/bgw-vignette.html | 45 +++++++------- bgw-0.1.3/bgw/src/dglfg_bgw.f90 | 2 bgw-0.1.3/bgw/src/dmdc.f90 | 95 +++++++++++++++---------------- bgw-0.1.3/bgw/src/drglg_c_entry.f90 |only 12 files changed, 133 insertions(+), 111 deletions(-)
Title: Quick Look at your Data
Description: The goal is to print an "aperçu", a short view of a vector, a
matrix, a data.frame, a list or an array. By default, it prints the first 5
elements of each dimension. By default, the number of columns is equal to
the number of lines. If you want to control the selection of the elements,
you can pass a list, with each element being a vector giving the selection
for each dimension.
Author: Aurelien Chateigner <aurelien.chateigner@gmail.com>
Maintainer: Aurelien Chateigner <aurelien.chateigner@gmail.com>
Diff between apercu versions 0.2.4 dated 2019-12-06 and 0.2.5 dated 2024-03-29
DESCRIPTION | 11 MD5 | 28 +- NAMESPACE | 2 NEWS.md | 34 +- R/ap.R | 597 +++++++++++++++++++++++------------------------ README.md | 400 +++++++++++++++---------------- man/ap.Rd | 208 ++++++++-------- man/aperWrapper.Rd | 38 +- man/apercu.Rd | 40 +-- man/classDeterminer.Rd | 34 +- man/fittingLimits.Rd | 38 +- man/limitsLister.Rd | 34 +- man/print.ap.Rd | 38 +- tests/testthat.R | 8 tests/testthat/test-ap.R | 192 +++++++-------- 15 files changed, 849 insertions(+), 853 deletions(-)
Title: Versatile Curation of Table Metadata
Description: A YAML-based
mechanism for working with table metadata. Supports
compact syntax for creating, modifying, viewing, exporting,
importing, displaying, and plotting metadata coded as column
attributes. The 'yamlet' dialect is valid 'YAML' with
defaults and conventions chosen to improve readability.
See ?yamlet, ?decorate, ?modify, ?io_csv, and ?ggplot.decorated.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 1.0.0 dated 2024-02-16 and 1.0.3 dated 2024-03-29
yamlet-1.0.0/yamlet/inst/doc/scripted_html.R |only yamlet-1.0.0/yamlet/inst/doc/scripted_html.Rmd |only yamlet-1.0.0/yamlet/inst/doc/scripted_html.html |only yamlet-1.0.0/yamlet/inst/doc/scripted_pdf.R |only yamlet-1.0.0/yamlet/inst/doc/scripted_pdf.Rmd |only yamlet-1.0.0/yamlet/inst/doc/scripted_pdf.pdf |only yamlet-1.0.0/yamlet/vignettes/scripted_html.Rmd |only yamlet-1.0.0/yamlet/vignettes/scripted_pdf.Rmd |only yamlet-1.0.3/yamlet/DESCRIPTION | 10 yamlet-1.0.3/yamlet/MD5 | 56 ++- yamlet-1.0.3/yamlet/R/desolve.R | 9 yamlet-1.0.3/yamlet/R/ggplot.R | 212 +++++---------- yamlet-1.0.3/yamlet/R/ggplot_build.R |only yamlet-1.0.3/yamlet/R/resolve.R | 9 yamlet-1.0.3/yamlet/R/scripted.R | 121 +++++++- yamlet-1.0.3/yamlet/R/singularity.R | 5 yamlet-1.0.3/yamlet/R/yamlet.R | 16 - yamlet-1.0.3/yamlet/R/yamlet_options.R | 2 yamlet-1.0.3/yamlet/build/vignette.rds |binary yamlet-1.0.3/yamlet/inst/doc/scripted-html.R |only yamlet-1.0.3/yamlet/inst/doc/scripted-html.Rmd |only yamlet-1.0.3/yamlet/inst/doc/scripted-html.html |only yamlet-1.0.3/yamlet/inst/doc/scripted-pdf.R |only yamlet-1.0.3/yamlet/inst/doc/scripted-pdf.Rmd |only yamlet-1.0.3/yamlet/inst/doc/scripted-pdf.pdf |only yamlet-1.0.3/yamlet/inst/doc/yamlet-introduction.html | 4 yamlet-1.0.3/yamlet/man/ggplot_build.decorated_ggplot.Rd | 2 yamlet-1.0.3/yamlet/man/print.decorated_ggplot.Rd | 7 yamlet-1.0.3/yamlet/man/scripted.default.Rd | 23 + yamlet-1.0.3/yamlet/man/yamlet_options.Rd | 2 yamlet-1.0.3/yamlet/tests/testthat/121.rds |only yamlet-1.0.3/yamlet/tests/testthat/Rplots.pdf |binary yamlet-1.0.3/yamlet/tests/testthat/test-dvec.R | 3 yamlet-1.0.3/yamlet/tests/testthat/test-yamlet.R | 30 ++ yamlet-1.0.3/yamlet/vignettes/scripted-html.Rmd |only yamlet-1.0.3/yamlet/vignettes/scripted-html_files |only yamlet-1.0.3/yamlet/vignettes/scripted-pdf.Rmd |only yamlet-1.0.3/yamlet/vignettes/scripted-pdf_files |only 38 files changed, 316 insertions(+), 195 deletions(-)
Title: Octonions and Quaternions
Description: Quaternions and Octonions are four- and eight- dimensional
extensions of the complex numbers. They are normed division
algebras over the real numbers and find applications in spatial
rotations (quaternions), and string theory and relativity
(octonions). The quaternions are noncommutative and the octonions
nonassociative. See the package vignette for more details.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between onion versions 1.5-0 dated 2021-02-11 and 1.5-3 dated 2024-03-29
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Title: Monte Carlo Data Simulation Package
Description: Monte Carlo simulation allows testing different conditions given to the correct structural equation models. This package runs Monte Carlo simulations under different conditions (such as sample size or normality of data). Within the package data sets can be simulated and run based on the given model.
First, continuous and normal data sets are generated based on the given model. Later Fleishman's power method (1978) <DOI:10.1007/BF02293811> is used to add non-normality if exists.
When data generation is completed (or when generated data sets are given) model test can also be run.
Please cite as "Orçan, F. (2021). MonteCarloSEM: An R Package to Simulate Data for SEM. International Journal of Assessment Tools in Education, 8 (3), 704-713."
Author: Fatih Orcan [aut, cre]
Maintainer: Fatih Orcan <fatihorcan84@gmail.com>
Diff between MonteCarloSEM versions 0.0.6 dated 2023-05-02 and 0.0.7 dated 2024-03-29
DESCRIPTION | 10 +++++----- MD5 | 14 ++++++++------ NAMESPACE | 1 + R/Categorize.R |only R/run.sem.sim.R | 12 +++++++----- R/sim_Categoric.R | 12 ++++++++---- man/categorize.Rd |only man/fit.simulation.Rd | 7 +++++-- man/sim.categoric.Rd | 14 ++++++++++++-- 9 files changed, 46 insertions(+), 24 deletions(-)
Title: Data Quality in Epidemiological Research
Description: Data quality assessments guided by a
'data quality framework introduced by Schmidt and colleagues, 2021'
<doi:10.1186/s12874-021-01252-7> target the
data quality dimensions integrity, completeness, consistency, and
accuracy. The scope of applicable functions rests on the
availability of extensive metadata which can be provided in
spreadsheet tables. Either standardized (e.g. as 'html5' reports) or
individually tailored reports can be generated. For an introduction
into the specification of corresponding metadata, please refer to the
'package website'
<https://dataquality.qihs.uni-greifswald.de/Annotation_of_Metadata.html>.
Author: University Medicine Greifswald [cph],
Elisa Kasbohm [aut] ,
Joany Marino [aut] ,
Elena Salogni [aut] ,
Adrian Richter [aut] ,
Carsten Oliver Schmidt [aut] ,
Stephan Struckmann [aut, cre] ,
German Research Foundation [fnd],
National Research Data Inf [...truncated...]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
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dataquieR-2.1.0/dataquieR/man/prep_summary_to_classes.Rd |only dataquieR-2.1.0/dataquieR/man/print.dataquieR_result.Rd | 6 dataquieR-2.1.0/dataquieR/man/print.dataquieR_resultset.Rd | 28 dataquieR-2.1.0/dataquieR/man/print.dataquieR_summary.Rd |only dataquieR-2.1.0/dataquieR/man/sub-.dataquieR_result.Rd | 1 dataquieR-2.1.0/dataquieR/man/sub-sub-.dataquieR_result.Rd | 1 dataquieR-2.1.0/dataquieR/man/summary.dataquieR_resultset.Rd | 42 dataquieR-2.1.0/dataquieR/man/summary.dataquieR_resultset2.Rd | 6 dataquieR-2.1.0/dataquieR/man/util_3SD.Rd |only dataquieR-2.1.0/dataquieR/man/util_abbreviate.Rd | 18 dataquieR-2.1.0/dataquieR/man/util_adjust_data_type.Rd |only dataquieR-2.1.0/dataquieR/man/util_adjust_geom_text_for_plotly.Rd | 3 dataquieR-2.1.0/dataquieR/man/util_alias2caption.Rd | 22 dataquieR-2.1.0/dataquieR/man/util_all_ind_functions.Rd | 1 dataquieR-2.1.0/dataquieR/man/util_all_intro_vars_for_rv.Rd | 13 dataquieR-2.1.0/dataquieR/man/util_all_is_integer.Rd | 18 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dataquieR-2.1.0/dataquieR/man/util_ds1_eval_env.Rd | 3 dataquieR-2.1.0/dataquieR/man/util_empty.Rd | 22 dataquieR-2.1.0/dataquieR/man/util_ensure_character.Rd | 22 dataquieR-2.1.0/dataquieR/man/util_ensure_in.Rd | 22 dataquieR-2.1.0/dataquieR/man/util_ensure_label.Rd | 26 dataquieR-2.1.0/dataquieR/man/util_ensure_suggested.Rd | 23 dataquieR-2.1.0/dataquieR/man/util_error.Rd | 13 dataquieR-2.1.0/dataquieR/man/util_eval_rule.Rd | 7 dataquieR-2.1.0/dataquieR/man/util_eval_to_dataquieR_result.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_evaluate_calls.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_expect_data_frame.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_expect_scalar.Rd | 36 dataquieR-2.1.0/dataquieR/man/util_extract_all_ids.Rd |only dataquieR-2.1.0/dataquieR/man/util_extract_indicator_metrics.Rd |only dataquieR-2.1.0/dataquieR/man/util_extract_matches.Rd | 22 dataquieR-2.1.0/dataquieR/man/util_filter_missing_list_table_for_rv.Rd | 13 dataquieR-2.1.0/dataquieR/man/util_filter_names_by_regexps.Rd | 12 dataquieR-2.1.0/dataquieR/man/util_find_external_functions_in_stacktrace.Rd | 13 dataquieR-2.1.0/dataquieR/man/util_find_first_externally_called_functions_in_stacktrace.Rd | 12 dataquieR-2.1.0/dataquieR/man/util_find_free_missing_code.Rd |only dataquieR-2.1.0/dataquieR/man/util_find_indicator_function_in_callers.Rd |only dataquieR-2.1.0/dataquieR/man/util_find_var_by_meta.Rd | 17 dataquieR-2.1.0/dataquieR/man/util_first_row_to_colnames.Rd |only dataquieR-2.1.0/dataquieR/man/util_fix_rstudio_bugs.Rd | 22 dataquieR-2.1.0/dataquieR/man/util_float_index_menu.Rd | 22 dataquieR-2.1.0/dataquieR/man/util_formattable.Rd | 2 dataquieR-2.1.0/dataquieR/man/util_function_description.Rd | 1 dataquieR-2.1.0/dataquieR/man/util_generate_anchor_link.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_generate_anchor_tag.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_generate_calls.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_generate_calls_for_function.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_generate_pages_from_report.Rd | 13 dataquieR-2.1.0/dataquieR/man/util_generate_table_indicators_descriptors.Rd |only dataquieR-2.1.0/dataquieR/man/util_get_category_for_result.Rd |only dataquieR-2.1.0/dataquieR/man/util_get_code_list.Rd | 23 dataquieR-2.1.0/dataquieR/man/util_get_colors.Rd |only dataquieR-2.1.0/dataquieR/man/util_get_concept_info.Rd | 3 dataquieR-2.1.0/dataquieR/man/util_get_fg_color.Rd |only dataquieR-2.1.0/dataquieR/man/util_get_html_cell_for_result.Rd | 50 dataquieR-2.1.0/dataquieR/man/util_get_labels_grading_class.Rd |only dataquieR-2.1.0/dataquieR/man/util_get_message_for_result.Rd | 28 dataquieR-2.1.0/dataquieR/man/util_get_redcap_rule_env.Rd | 7 dataquieR-2.1.0/dataquieR/man/util_get_rule_sets.Rd |only dataquieR-2.1.0/dataquieR/man/util_get_ruleset_formats.Rd |only dataquieR-2.1.0/dataquieR/man/util_get_thresholds.Rd |only dataquieR-2.1.0/dataquieR/man/util_get_var_att_names_of_level.Rd | 14 dataquieR-2.1.0/dataquieR/man/util_get_vars_in_segment.Rd | 14 dataquieR-2.1.0/dataquieR/man/util_gg_var_label.Rd | 3 dataquieR-2.1.0/dataquieR/man/util_heatmap_1th.Rd | 7 dataquieR-2.1.0/dataquieR/man/util_hide_file_windows.Rd |only dataquieR-2.1.0/dataquieR/man/util_html_attr_quote_escape.Rd | 2 dataquieR-2.1.0/dataquieR/man/util_html_for_dims.Rd | 14 dataquieR-2.1.0/dataquieR/man/util_html_for_var.Rd | 16 dataquieR-2.1.0/dataquieR/man/util_html_table.Rd | 48 dataquieR-2.1.0/dataquieR/man/util_hubert.Rd | 11 dataquieR-2.1.0/dataquieR/man/util_iframe_it_if_needed.Rd |only dataquieR-2.1.0/dataquieR/man/util_int_duplicate_content_dataframe.Rd | 11 dataquieR-2.1.0/dataquieR/man/util_int_duplicate_content_segment.Rd | 12 dataquieR-2.1.0/dataquieR/man/util_int_duplicate_ids_dataframe.Rd | 11 dataquieR-2.1.0/dataquieR/man/util_int_duplicate_ids_segment.Rd | 11 dataquieR-2.1.0/dataquieR/man/util_int_unexp_records_set_dataframe.Rd | 11 dataquieR-2.1.0/dataquieR/man/util_int_unexp_records_set_segment.Rd | 12 dataquieR-2.1.0/dataquieR/man/util_interpret_limits.Rd | 12 dataquieR-2.1.0/dataquieR/man/util_interpret_range.Rd | 12 dataquieR-2.1.0/dataquieR/man/util_is_integer.Rd | 21 dataquieR-2.1.0/dataquieR/man/util_is_na_0_empty_or_false.Rd | 13 dataquieR-2.1.0/dataquieR/man/util_is_numeric_in.Rd | 37 dataquieR-2.1.0/dataquieR/man/util_is_valid_missing_codes.Rd |only dataquieR-2.1.0/dataquieR/man/util_load_manual.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_looks_like_missing.Rd | 14 dataquieR-2.1.0/dataquieR/man/util_make_data_slot_from_table_slot.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_make_function.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_map_all.Rd | 9 dataquieR-2.1.0/dataquieR/man/util_map_by_largest_prefix.Rd | 21 dataquieR-2.1.0/dataquieR/man/util_map_labels.Rd | 9 dataquieR-2.1.0/dataquieR/man/util_match_arg.Rd | 22 dataquieR-2.1.0/dataquieR/man/util_melt_summary.Rd |only dataquieR-2.1.0/dataquieR/man/util_merge_data_frame_list.Rd | 17 dataquieR-2.1.0/dataquieR/man/util_message.Rd | 13 dataquieR-2.1.0/dataquieR/man/util_no_value_labels.Rd | 14 dataquieR-2.1.0/dataquieR/man/util_normalize_cross_item.Rd | 1 dataquieR-2.1.0/dataquieR/man/util_observation_expected.Rd | 13 dataquieR-2.1.0/dataquieR/man/util_observations_in_subgroups.Rd | 26 dataquieR-2.1.0/dataquieR/man/util_online_ref.Rd | 1 dataquieR-2.1.0/dataquieR/man/util_only_NAs.Rd | 24 dataquieR-2.1.0/dataquieR/man/util_open_in_excel.Rd |only dataquieR-2.1.0/dataquieR/man/util_optimize_histogram_bins.Rd | 48 dataquieR-2.1.0/dataquieR/man/util_order_by_order.Rd | 20 dataquieR-2.1.0/dataquieR/man/util_par_pmap.Rd | 15 dataquieR-2.1.0/dataquieR/man/util_parse_assignments.Rd | 38 dataquieR-2.1.0/dataquieR/man/util_parse_interval.Rd | 10 dataquieR-2.1.0/dataquieR/man/util_parse_redcap_rule.Rd | 11 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Title: A Comprehensive Interface for Accessing the Protein Data Bank
Description: Streamlines the interaction with the RCSB Protein Data Bank (PDB) <https://www.rcsb.org/>. This interface offers an intuitive and
powerful tool for searching and retrieving a diverse range of data types from the PDB. It includes advanced functionalities like
BLAST and sequence motif queries. Built upon the existing XML-based API of the PDB, it simplifies the creation of custom requests,
thereby enhancing usability and flexibility for researchers.
Author: Selcuk Korkmaz [aut, cre] ,
Bilge Eren Yamasan [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between rPDBapi versions 1.0 dated 2024-01-17 and 1.1 dated 2024-03-29
DESCRIPTION | 11 - MD5 | 56 ++++----- NAMESPACE | 9 + R/SeqMotifOperator.R | 4 R/SequenceOperator.R | 2 R/add_property.R | 6 - R/data_fetcher.R | 8 + R/describe_chemical.R | 2 R/fetch_data.R | 9 - R/find_papers.R | 6 - R/find_results.R | 13 +- R/get_fasta_from_rcsb_entry.R | 55 +++++---- R/get_info.R | 63 +++++------ R/perform_search.R | 180 ++++++++++++++++--------------- R/query_search.R | 220 ++++++++++++++++++++++++--------------- R/return_data_as_dataframe.R | 126 +++++++++++++++++++++- R/search_client.R | 2 R/search_graphql.R | 5 R/walk_nested_dict.R | 1 man/SeqMotifOperator.Rd | 1 man/add_property.Rd | 6 - man/data_fetcher.Rd | 9 + man/describe_chemical.Rd | 2 man/find_papers.Rd | 5 man/find_results.Rd | 12 +- man/get_fasta_from_rcsb_entry.Rd | 3 man/get_info.Rd | 3 man/perform_search.Rd | 7 + man/query_search.Rd | 14 ++ 29 files changed, 547 insertions(+), 293 deletions(-)
Title: Read and Write Frictionless Data Packages
Description: Read and write Frictionless Data Packages. A 'Data Package'
(<https://specs.frictionlessdata.io/data-package/>) is a simple
container format and standard to describe and package a collection of
(tabular) data. It is typically used to publish FAIR
(<https://www.go-fair.org/fair-principles/>) and open datasets.
Author: Peter Desmet [aut, cre] ,
Damiano Oldoni [aut] ,
Pieter Huybrechts [aut] ,
Kyle Husmann [ctb] ,
Research Institute for Nature and Forest [cph]
,
LifeWatch Belgium [fnd] ,
Beatriz Milz [rev] ,
Joao Martins [rev]
Maintainer: Peter Desmet <peter.desmet.work@gmail.com>
Diff between frictionless versions 1.0.3 dated 2024-03-07 and 1.1.0 dated 2024-03-29
frictionless-1.0.3/frictionless/inst/doc/frictionless.R |only frictionless-1.0.3/frictionless/tests/testthat/data/resources_no_name.json |only frictionless-1.0.3/frictionless/tests/testthat/data/valid_minimal_extra.json |only frictionless-1.1.0/frictionless/DESCRIPTION | 29 frictionless-1.1.0/frictionless/MD5 | 111 +- frictionless-1.1.0/frictionless/NAMESPACE | 5 frictionless-1.1.0/frictionless/NEWS.md | 94 +- frictionless-1.1.0/frictionless/R/add_resource.R | 112 +- frictionless-1.1.0/frictionless/R/check_data.R |only frictionless-1.1.0/frictionless/R/check_package.R | 99 +- frictionless-1.1.0/frictionless/R/check_path.R |only frictionless-1.1.0/frictionless/R/check_schema.R | 88 - frictionless-1.1.0/frictionless/R/create_package.R | 58 - frictionless-1.1.0/frictionless/R/create_schema.R | 17 frictionless-1.1.0/frictionless/R/frictionless-package.R | 2 frictionless-1.1.0/frictionless/R/get_resource.R | 29 frictionless-1.1.0/frictionless/R/get_schema.R | 25 frictionless-1.1.0/frictionless/R/print.R |only frictionless-1.1.0/frictionless/R/read_package.R | 54 - frictionless-1.1.0/frictionless/R/read_resource.R | 140 +- frictionless-1.1.0/frictionless/R/remove_resource.R | 2 frictionless-1.1.0/frictionless/R/resources.R | 2 frictionless-1.1.0/frictionless/R/utils-problems.R |only frictionless-1.1.0/frictionless/R/utils.R | 91 - frictionless-1.1.0/frictionless/R/write_package.R | 22 frictionless-1.1.0/frictionless/R/write_resource.R | 33 frictionless-1.1.0/frictionless/README.md | 78 - frictionless-1.1.0/frictionless/build/vignette.rds |binary frictionless-1.1.0/frictionless/data/example_package.rda |binary frictionless-1.1.0/frictionless/inst/CITATION | 2 frictionless-1.1.0/frictionless/inst/doc/frictionless.Rmd | 239 +++-- frictionless-1.1.0/frictionless/inst/doc/frictionless.html | 470 +++++----- frictionless-1.1.0/frictionless/inst/extdata/datapackage.json | 1 frictionless-1.1.0/frictionless/man/add_resource.Rd | 23 frictionless-1.1.0/frictionless/man/check_package.Rd |only frictionless-1.1.0/frictionless/man/create_package.Rd | 35 frictionless-1.1.0/frictionless/man/example_package.Rd | 2 frictionless-1.1.0/frictionless/man/frictionless-package.Rd | 2 frictionless-1.1.0/frictionless/man/get_schema.Rd | 4 frictionless-1.1.0/frictionless/man/print.datapackage.Rd |only frictionless-1.1.0/frictionless/man/problems.Rd |only frictionless-1.1.0/frictionless/man/read_package.Rd | 7 frictionless-1.1.0/frictionless/man/read_resource.Rd | 23 frictionless-1.1.0/frictionless/man/remove_resource.Rd | 4 frictionless-1.1.0/frictionless/man/resources.Rd | 3 frictionless-1.1.0/frictionless/man/write_package.Rd | 9 frictionless-1.1.0/frictionless/tests/testthat/data/type_datetime.csv | 2 frictionless-1.1.0/frictionless/tests/testthat/test-add_resource.R | 197 ++-- frictionless-1.1.0/frictionless/tests/testthat/test-check_data.R |only frictionless-1.1.0/frictionless/tests/testthat/test-check_package.R | 118 +- frictionless-1.1.0/frictionless/tests/testthat/test-check_path.R |only frictionless-1.1.0/frictionless/tests/testthat/test-check_schema.R | 151 ++- frictionless-1.1.0/frictionless/tests/testthat/test-create_package.R | 50 - frictionless-1.1.0/frictionless/tests/testthat/test-create_schema.R | 8 frictionless-1.1.0/frictionless/tests/testthat/test-print.R |only frictionless-1.1.0/frictionless/tests/testthat/test-read_package.R | 111 -- frictionless-1.1.0/frictionless/tests/testthat/test-read_resource.R | 310 ++++-- frictionless-1.1.0/frictionless/tests/testthat/test-remove_resource.R | 30 frictionless-1.1.0/frictionless/tests/testthat/test-resources.R | 5 frictionless-1.1.0/frictionless/tests/testthat/test-utils.R | 19 frictionless-1.1.0/frictionless/tests/testthat/test-write_package.R | 120 +- frictionless-1.1.0/frictionless/vignettes/frictionless.Rmd | 239 +++-- frictionless-1.1.0/frictionless/vignettes/frictionless.Rmd.orig |only frictionless-1.1.0/frictionless/vignettes/precompile.R |only 64 files changed, 1964 insertions(+), 1311 deletions(-)
Title: Tabulate Descriptive Statistics in Multiple Formats
Description: Creates a table of descriptive statistics
for factor and numeric columns in a data frame. Displays
these by groups, if any. Highly customizable, with support
for 'html' and 'pdf' provided by 'kableExtra'. Respects
original column order, column labels, and factor level order.
See ?tablet.data.frame and vignettes.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between tablet versions 0.6.5 dated 2024-02-16 and 0.6.8 dated 2024-03-29
DESCRIPTION | 6 - MD5 | 16 ++--- R/tablet.R | 101 +++++++++++++++++++++++++++++---- R/tablette.R | 2 inst/doc/tablet-introduction-html.html | 4 - inst/doc/tablet-introduction-pdf.pdf |binary man/as_kable.tablet.Rd | 7 +- man/escape_latex.latex.Rd | 4 - man/tablet.data.frame.Rd | 4 + 9 files changed, 117 insertions(+), 27 deletions(-)
Title: Generalized Label Formatting
Description: The 'spork' syntax describes
label formatting concisely, supporting
mixed nesting of subscripts and superscripts
to arbitrary depth. It intends to be easy
to read and write in plain text, and easy
to convert to equivalent presentations
in 'plotmath', 'latex', and 'html'. Greek symbols
and a multiplication symbol are explicitly
supported. See ?as_spork and ?as_previews.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between spork versions 0.3.2 dated 2024-02-16 and 0.3.3 dated 2024-03-29
DESCRIPTION | 6 +++--- MD5 | 14 +++++++++----- NAMESPACE | 2 ++ R/explicit.R |only R/latex.R | 26 ++++++++++++++++++++------ man/as_latex.spork.Rd | 10 ++++++---- man/explicit.Rd |only man/explicit.spork.Rd |only tests/testthat/001.rds |only tests/testthat/test-spork.R | 5 ++++- 10 files changed, 44 insertions(+), 19 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)
<arXiv:1801.01489>, accumulated local effects plots described by Apley
(2018) <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) <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 0.11.1 dated 2022-09-08 and 0.11.2 dated 2024-03-29
iml-0.11.1/iml/tests |only iml-0.11.2/iml/DESCRIPTION | 18 iml-0.11.2/iml/LICENSE | 2 iml-0.11.2/iml/MD5 | 139 +- iml-0.11.2/iml/NAMESPACE | 76 - iml-0.11.2/iml/NEWS.md | 14 iml-0.11.2/iml/R/Data.R | 156 +- iml-0.11.2/iml/R/FeatureEffect-ale.R | 1068 +++++++++--------- iml-0.11.2/iml/R/FeatureEffect.R | 1536 +++++++++++++-------------- iml-0.11.2/iml/R/FeatureEffects.R | 2 iml-0.11.2/iml/R/FeatureImp.R | 778 ++++++------- iml-0.11.2/iml/R/Interaction.R | 608 +++++----- iml-0.11.2/iml/R/InterpretationMethod.R | 222 +-- iml-0.11.2/iml/R/LocalModel.R | 658 +++++------ iml-0.11.2/iml/R/MarginalGenerator.R | 214 +-- iml-0.11.2/iml/R/Predictor.R | 2 iml-0.11.2/iml/R/Shapley.R | 488 ++++---- iml-0.11.2/iml/R/TreeSurrogate.R | 576 +++++----- iml-0.11.2/iml/R/create_predict_fun.R | 306 ++--- iml-0.11.2/iml/R/find_data.R |only iml-0.11.2/iml/R/iml.R | 26 iml-0.11.2/iml/R/inferTask.R | 148 +- iml-0.11.2/iml/R/list_rules_party.R | 166 +- iml-0.11.2/iml/R/utils.R | 658 +++++------ iml-0.11.2/iml/build/vignette.rds |binary iml-0.11.2/iml/inst/CITATION | 28 iml-0.11.2/iml/inst/doc/intro.R | 162 +- iml-0.11.2/iml/inst/doc/intro.Rmd | 12 iml-0.11.2/iml/inst/doc/intro.html | 1188 ++++++++++---------- iml-0.11.2/iml/inst/doc/parallel.R | 130 +- iml-0.11.2/iml/inst/doc/parallel.Rmd | 8 iml-0.11.2/iml/inst/doc/parallel.html | 928 ++++++++-------- iml-0.11.2/iml/man/FeatureEffect.Rd | 624 +++++----- iml-0.11.2/iml/man/FeatureEffects.Rd | 382 +++--- iml-0.11.2/iml/man/FeatureImp.Rd | 498 ++++---- iml-0.11.2/iml/man/Interaction.Rd | 330 ++--- iml-0.11.2/iml/man/InterpretationMethod.Rd | 184 +-- iml-0.11.2/iml/man/LocalModel.Rd | 488 ++++---- iml-0.11.2/iml/man/Partial.Rd | 198 +-- iml-0.11.2/iml/man/Predictor.Rd | 372 +++--- iml-0.11.2/iml/man/Shapley.Rd | 336 ++--- iml-0.11.2/iml/man/TreeSurrogate.Rd | 352 +++--- iml-0.11.2/iml/man/calculate.ale.cat.Rd | 38 iml-0.11.2/iml/man/calculate.ale.num.Rd | 42 iml-0.11.2/iml/man/calculate.ale.num.cat.Rd | 42 iml-0.11.2/iml/man/calculate.ale.num.num.Rd | 46 iml-0.11.2/iml/man/extract.glmnet.effects.Rd | 42 iml-0.11.2/iml/man/has.predict.Rd | 28 iml-0.11.2/iml/man/iml-package.Rd | 45 iml-0.11.2/iml/man/impute_cells.Rd | 54 iml-0.11.2/iml/man/order_levels.Rd | 118 +- iml-0.11.2/iml/man/plot.FeatureEffect.Rd | 94 - iml-0.11.2/iml/man/plot.FeatureEffects.Rd | 114 +- iml-0.11.2/iml/man/plot.FeatureImp.Rd | 100 - iml-0.11.2/iml/man/plot.Interaction.Rd | 76 - iml-0.11.2/iml/man/plot.LocalModel.Rd | 66 - iml-0.11.2/iml/man/plot.Shapley.Rd | 80 - iml-0.11.2/iml/man/plot.TreeSurrogate.Rd | 72 - iml-0.11.2/iml/man/predict.LocalModel.Rd | 74 - iml-0.11.2/iml/man/predict.TreeSurrogate.Rd | 94 - iml-0.11.2/iml/man/probs.to.labels.Rd | 28 iml-0.11.2/iml/vignettes/intro.Rmd | 12 iml-0.11.2/iml/vignettes/parallel.Rmd | 8 63 files changed, 7689 insertions(+), 7665 deletions(-)
Title: Coordinated Networks Detection on Social Media
Description: Detects a variety of coordinated actions on social media and outputs the network of coordinated users along with related information.
Author: Nicola Righetti [aut, cre] ,
Paul Balluff [aut]
Maintainer: Nicola Righetti <nicola.righetti@univie.ac.at>
Diff between CooRTweet versions 2.0.1 dated 2024-03-18 and 2.0.2 dated 2024-03-29
DESCRIPTION | 8 +- MD5 | 18 ++--- NEWS.md | 4 + R/detect_groups.R | 51 +++++++-------- inst/doc/vignette.R | 21 ++++-- inst/doc/vignette.Rmd | 26 ++++++- inst/doc/vignette.html | 131 +++++++++++++++++++++------------------- man/detect_groups.Rd | 28 ++++---- man/filter_min_participation.Rd | 8 +- vignettes/vignette.Rmd | 26 ++++++- 10 files changed, 190 insertions(+), 131 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-27 1.1.1
2022-03-10 1.1.0
2021-02-17 1.0.3
2020-12-01 1.0.2
2020-11-30 1.0.1
2020-11-25 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-04 1.0.0
Title: Biological Geometries
Description: Is used to simulate and fit biological geometries. 'biogeom' incorporates several novel universal parametric equations that can generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings (Gielis (2003) <doi:10.3732/ajb.90.3.333>; Shi et al. (2020) <doi:10.3390/sym12040645>), three growth-rate curves representing the ontogenetic growth trajectories of animals and plants against time, and the axially symmetrical and integral forms of all these functions (Shi et al. (2017) <doi:10.1016/j.ecolmodel.2017.01.012>; Shi et al. (2021) <doi:10.3390/sym13081524>). The optimization method proposed by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> was used to estimate model parameters. 'biogeom' includes several real data sets of the boundary coordinates of natural shapes, including avian eggs, fruit, lanceolate and ovate leaves, tree rings, seeds, and sea stars,and can be potentially applied to other natural shapes. [...truncated...]
Author: Peijian Shi [aut, cre],
Johan Gielis [aut],
Brady K. Quinn [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
Diff between biogeom versions 1.4.2 dated 2024-03-13 and 1.4.3 dated 2024-03-29
DESCRIPTION | 8 - MD5 | 14 +- R/SCSE.R |only R/SHE.R |only R/SarabiaE.R |only R/fitLorenz.R | 309 ++++++++++++++++++++++++++++++++++++++++++++++++++++-- build/partial.rdb |binary man/SCSE.Rd |only man/SHE.Rd |only man/SarabiaE.Rd |only man/fitLorenz.Rd | 59 ++++++++-- 11 files changed, 363 insertions(+), 27 deletions(-)
Title: Genomic Prediction of Hybrid Performance
Description: Performs genomic prediction of hybrid performance using eight GS methods including GBLUP, BayesB, RKHS, PLS, LASSO, Elastic net, LightGBM and XGBoost. It also provides fast cross-validation and mating design scheme for training population (Xu S et al (2016) <doi:10.1111/tpj.13242>; Xu S (2017) <doi:10.1534/g3.116.038059>).
Author: Yang Xu, Guangning Yu, Yanru Cui, Shizhong Xu, Chenwu Xu
Maintainer: Yang Xu <xuyang_89@126.com>
Diff between predhy versions 2.0.1 dated 2024-02-24 and 2.1.0 dated 2024-03-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/cv.R | 6 +++--- R/predhy.predict.R | 9 +++++---- R/predhy.predict_NCII.R | 20 ++++++++++---------- 5 files changed, 26 insertions(+), 25 deletions(-)
Title: Calculating Ontological Similarities
Description: Calculate similarity between ontological terms and sets of ontological terms based on term information content and assess statistical significance of similarity in the context of a collection of terms sets - Greene et al. 2017 <doi:10.1093/bioinformatics/btw763>.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologySimilarity versions 2.4 dated 2021-02-10 and 2.7 dated 2024-03-29
DESCRIPTION | 15 MD5 | 79 +- NAMESPACE | 76 +- R/RcppExports.R | 54 - R/data.R | 9 R/functions.R | 17 R/group-sim.R | 82 ++ R/term-set-sim.R | 2 build/vignette.rds |binary data/GO_IC.RData |binary data/gene_GO_terms.RData |binary inst/doc/ontologySimilarity-GO-example.R | 79 +- inst/doc/ontologySimilarity-GO-example.Rmd | 3 inst/doc/ontologySimilarity-GO-example.html | 641 +++++++++++++------ inst/doc/ontologySimilarity-examples.R | 123 +-- inst/doc/ontologySimilarity-examples.Rmd | 4 inst/doc/ontologySimilarity-examples.html | 869 ++++++++++++++++---------- inst/doc/ontologySimilarity-introduction.R | 46 - inst/doc/ontologySimilarity-introduction.html | 647 +++++++++++++------ man/GO_IC.Rd | 24 man/create_sim_index.Rd | 68 +- man/descendants_IC.Rd | 34 - man/gene_GO_terms.Rd | 30 man/get_asym_sim_grid.Rd | 48 - man/get_profile_sims.Rd | 48 - man/get_sim.Rd | 86 +- man/get_sim_grid.Rd | 104 +-- man/get_sim_p.Rd | 122 +-- man/get_sim_p_from_ontology.Rd | 74 +- man/get_similarity_rank_matrix.Rd | 38 - man/get_term_set_to_term_sims.Rd | 48 - man/get_term_sim_mat.Rd | 68 +- man/group_term_enrichment.Rd |only man/lin.Rd | 58 - man/resnik.Rd | 58 - man/sample_group_sim.Rd | 104 +-- man/sample_group_sim_from_ontology.Rd | 74 +- src/RcppExports.cpp | 5 src/TermSetSimData.cpp | 1 vignettes/ontologySimilarity-GO-example.Rmd | 3 vignettes/ontologySimilarity-examples.Rmd | 4 41 files changed, 2331 insertions(+), 1514 deletions(-)
More information about ontologySimilarity at CRAN
Permanent link
Title: A Systematic Data Wrangling Idiom
Description: Supports systematic scrutiny, modification, and integration of
data. The function status() counts rows that have missing values in
grouping columns (returned by na() ), have non-unique combinations of
grouping columns (returned by dup() ), and that are not locally sorted
(returned by unsorted() ). Functions enumerate() and itemize() give
sorted unique combinations of columns, with or without occurrence counts,
respectively. Function ignore() drops columns in x that are present in y,
and informative() drops columns in x that are entirely NA; constant() returns
values that are constant, given a key. Data that have defined unique
combinations of grouping values behave more predictably during merge operations.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between wrangle versions 0.6.3 dated 2023-08-23 and 0.6.4 dated 2024-03-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/constant.R | 11 ++++++++++- man/constant.Rd | 2 +- man/constant.data.frame.Rd | 4 ++++ 5 files changed, 22 insertions(+), 9 deletions(-)