Title: Non-Parametric Causal Effects of Feasible Interventions Based on
Modified Treatment Policies
Description: Non-parametric estimators for casual effects based on longitudinal modified treatment
policies as described in Diaz, Williams, Hoffman, and Schenck <doi:10.1080/01621459.2021.1955691>, traditional point treatment,
and traditional longitudinal effects. Continuous, binary, categorical treatments, and multivariate treatments are allowed as well are
censored outcomes. The treatment mechanism is estimated via a density ratio classification procedure
irrespective of treatment variable type. For both continuous and binary outcomes, additive treatment effects
can be calculated and relative risks and odds ratios may be calculated for binary outcomes.
Author: Nicholas Williams [aut, cre, cph]
,
Ivan Diaz [aut, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between lmtp versions 1.3.3 dated 2024-03-26 and 1.4.0 dated 2024-06-26
DESCRIPTION | 16 - MD5 | 61 +++--- NAMESPACE | 3 NEWS.md | 18 + R/checks.R | 63 ++++++ R/contrasts.R | 14 + R/data.R | 16 + R/density_ratios.R | 51 +++-- R/estimators.R | 269 +++++++++++---------------- R/gcomp.R | 46 ++-- R/lmtp-package.R | 2 R/lmtp_Task.R | 25 +- R/lmtp_control.R |only R/nodelist.R | 12 - R/sdr.R | 54 +++-- R/shift.R | 62 ++++++ R/theta.R | 14 - R/tmle.R | 59 +++-- R/utils.R | 19 + README.md | 58 +++-- build/partial.rdb |binary data/multivariate_data.rda |only man/ipsi.Rd |only man/lmtp-package.Rd | 5 man/lmtp_control.Rd |only man/lmtp_ipw.Rd | 50 ++--- man/lmtp_sdr.Rd | 54 ++--- man/lmtp_sub.Rd | 41 ++-- man/lmtp_tmle.Rd | 54 ++--- man/multivariate_data.Rd |only tests/testthat/test-checks.R | 6 tests/testthat/test-shifted.R | 6 tests/testthat/test-survey.R | 2 tests/testthat/test-time_varying_treatment.R | 6 34 files changed, 649 insertions(+), 437 deletions(-)
Title: Double/Debiased Machine Learning
Description: Estimate common causal parameters using double/debiased machine
learning as proposed by Chernozhukov et al. (2018) <doi:10.1111/ectj.12097>.
'ddml' simplifies estimation based on (short-)stacking as discussed in
Ahrens et al. (2024) <doi:10.1177/1536867X241233641>, which leverages multiple base
learners to increase robustness to the underlying data generating process.
Author: Achim Ahrens [aut],
Christian B Hansen [aut],
Mark E Schaffer [aut],
Thomas Wiemann [aut, cre]
Maintainer: Thomas Wiemann <wiemann@uchicago.edu>
Diff between ddml versions 0.2.1 dated 2024-05-26 and 0.2.2 dated 2024-06-26
DESCRIPTION | 10 +-- MD5 | 60 ++++++++++---------- NAMESPACE | 6 ++ NEWS.md | 8 ++ R/ddml_ate.R | 68 +++++++++++++++++++--- R/ddml_att.R | 31 ++++++++-- R/ddml_fpliv.R | 18 ++++-- R/ddml_late.R | 47 +++++++++++---- R/ddml_pliv.R | 18 ++++-- R/ddml_plm.R | 43 +++++++++++++- R/ensemble.R | 2 R/help_functions.R | 40 +++++++++++-- R/ml_wrappers.R | 16 ++++- R/ols.R | 8 +- README.md | 16 ++--- inst/doc/ddml.Rmd | 18 +++--- inst/doc/ddml.html | 18 +++--- man/ddml_ate.Rd | 7 ++ man/ddml_late.Rd | 6 ++ man/mdl_ranger.Rd | 3 - man/ols.Rd | 2 man/print.summary.ddml_ate.Rd |only man/print.summary.ddml_plm.Rd |only tests/testthat/test-crossval.R | 10 ++- tests/testthat/test-ddml_ate.R | 98 +++++++++++++++++++------------- tests/testthat/test-ddml_att.R | 100 +++++++++++++++++++-------------- tests/testthat/test-ddml_fpliv.R | 3 - tests/testthat/test-ddml_late.R | 114 +++++++++++++++++++++----------------- tests/testthat/test-ddml_pliv.R | 6 +- tests/testthat/test-ddml_plm.R | 6 +- tests/testthat/test-ml_wrappers.R | 30 +++++++--- vignettes/ddml.Rmd | 18 +++--- 32 files changed, 553 insertions(+), 277 deletions(-)
Title: Parametric Bootstrap, Kenward-Roger and Satterthwaite Based
Methods for Test in Mixed Models
Description: Computes p-values based on (a) Satterthwaite or
Kenward-Rogers degree of freedom methods and (b) parametric bootstrap
for mixed effects models as implemented in the 'lme4'
package. Implements parametric bootstrap test for generalized linear
mixed models as implemented in 'lme4' and generalized linear
models. The package is documented in the paper by Halekoh and
Højsgaard, (2012, <doi:10.18637/jss.v059.i09>). Please see
'citation("pbkrtest")' for citation details.
Author: Ulrich Halekoh [aut, cph],
Soeren Hoejsgaard [aut, cre, cph]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between pbkrtest versions 0.5.2 dated 2023-01-19 and 0.5.3 dated 2024-06-26
pbkrtest-0.5.2/pbkrtest/R/KR-Sigma-G2.R |only pbkrtest-0.5.2/pbkrtest/R/KR-across-versions.R |only pbkrtest-0.5.2/pbkrtest/R/KR-modcomp.R |only pbkrtest-0.5.2/pbkrtest/R/KR-utils.R |only pbkrtest-0.5.2/pbkrtest/R/KR-vcovAdj.R |only pbkrtest-0.5.2/pbkrtest/R/NAMESPACE-pbkrtest.R |only pbkrtest-0.5.2/pbkrtest/R/PB-modcomp.R |only pbkrtest-0.5.2/pbkrtest/R/PB-refdist.R |only pbkrtest-0.5.2/pbkrtest/R/PB-utils.R |only pbkrtest-0.5.2/pbkrtest/R/SAT-modcomp.R |only pbkrtest-0.5.2/pbkrtest/R/data-beets.R |only pbkrtest-0.5.2/pbkrtest/R/data-budworm.R |only pbkrtest-0.5.2/pbkrtest/R/init-modcomp.R |only pbkrtest-0.5.2/pbkrtest/R/internal-pbkrtest.R |only pbkrtest-0.5.2/pbkrtest/R/model-coerce.R |only pbkrtest-0.5.2/pbkrtest/man/kr-modcomp.Rd |only pbkrtest-0.5.2/pbkrtest/man/pb-modcomp.Rd |only pbkrtest-0.5.2/pbkrtest/man/sat-modcomp.Rd |only pbkrtest-0.5.3/pbkrtest/DESCRIPTION | 15 pbkrtest-0.5.3/pbkrtest/MD5 | 84 +- pbkrtest-0.5.3/pbkrtest/NAMESPACE | 2 pbkrtest-0.5.3/pbkrtest/NEWS | 7 pbkrtest-0.5.3/pbkrtest/R/KR_Sigma_G2.R |only pbkrtest-0.5.3/pbkrtest/R/KR_modcomp.R |only pbkrtest-0.5.3/pbkrtest/R/KR_utils.R |only pbkrtest-0.5.3/pbkrtest/R/KR_vcovAdj.R |only pbkrtest-0.5.3/pbkrtest/R/NAMESPACE_pbkrtest.R |only pbkrtest-0.5.3/pbkrtest/R/PB_modcomp.R |only pbkrtest-0.5.3/pbkrtest/R/PB_refdist.R |only pbkrtest-0.5.3/pbkrtest/R/PB_utils.R |only pbkrtest-0.5.3/pbkrtest/R/SAT_modcomp.R |only pbkrtest-0.5.3/pbkrtest/R/data_beets.R |only pbkrtest-0.5.3/pbkrtest/R/data_budworm.R |only pbkrtest-0.5.3/pbkrtest/R/do_modcomp.R |only pbkrtest-0.5.3/pbkrtest/R/init_modcomp.R |only pbkrtest-0.5.3/pbkrtest/R/internal_pbkrtest.R |only pbkrtest-0.5.3/pbkrtest/R/model_coerce.R |only pbkrtest-0.5.3/pbkrtest/build/vignette.rds |binary pbkrtest-0.5.3/pbkrtest/inst/CITATION | 5 pbkrtest-0.5.3/pbkrtest/inst/doc/a01-pbkrtest.R | 2 pbkrtest-0.5.3/pbkrtest/inst/doc/a01-pbkrtest.html | 767 ++++++++------------- pbkrtest-0.5.3/pbkrtest/inst/doc/a01-pbkrtest.rmd | 2 pbkrtest-0.5.3/pbkrtest/inst/doc/a02-coercion.R | 2 pbkrtest-0.5.3/pbkrtest/inst/doc/a02-coercion.html | 574 +++++---------- pbkrtest-0.5.3/pbkrtest/inst/doc/a02-coercion.rmd | 2 pbkrtest-0.5.3/pbkrtest/man/compute_auxiliary.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/data-beets.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/data-budworm.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/devfun_vp.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/get_Fstat_ddf.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/get_covbeta.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/internal-pbkrtest.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/internal.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/kr-vcovAdj.Rd | 4 pbkrtest-0.5.3/pbkrtest/man/kr_modcomp.Rd |only pbkrtest-0.5.3/pbkrtest/man/model-coerce.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/pb-refdist.Rd | 2 pbkrtest-0.5.3/pbkrtest/man/pb_modcomp.Rd |only pbkrtest-0.5.3/pbkrtest/man/sat_modcomp.Rd |only pbkrtest-0.5.3/pbkrtest/vignettes/a01-pbkrtest.rmd | 2 pbkrtest-0.5.3/pbkrtest/vignettes/a02-coercion.rmd | 2 61 files changed, 595 insertions(+), 895 deletions(-)
Title: Sparse Group Lasso
Description: Efficient implementation of sparse group lasso with optional
bound constraints on the coefficients. It supports the use of a sparse
design matrix as well as returning coefficient estimates in a sparse
matrix. Furthermore, it correctly calculates the degrees of freedom to
allow for information criteria rather than cross-validation with very
large data. Finally, the interface to compiled code avoids unnecessary
copies and allows for the use of long integers.
Author: Daniel J. McDonald [aut, cre],
Xiaoxuan Liang [aut],
Anibal Solon Heinsfeld [aut],
Aaron Cohen [aut],
Yi Yang [ctb],
Hui Zou [ctb],
Jerome Friedman [ctb],
Trevor Hastie [ctb],
Rob Tibshirani [ctb],
Balasubramanian Narasimhan [ctb],
Kenneth Tay [ctb], [...truncated...]
Maintainer: Daniel J. McDonald <daniel@stat.ubc.ca>
Diff between sparsegl versions 1.0.2 dated 2023-09-25 and 1.1.0 dated 2024-06-26
sparsegl-1.0.2/sparsegl/R/imports.R |only sparsegl-1.0.2/sparsegl/man/figures/README-minimal-ex-1.png |only sparsegl-1.1.0/sparsegl/DESCRIPTION | 16 sparsegl-1.1.0/sparsegl/LICENSE |only sparsegl-1.1.0/sparsegl/MD5 | 95 +-- sparsegl-1.1.0/sparsegl/NAMESPACE | 8 sparsegl-1.1.0/sparsegl/NEWS.md | 13 sparsegl-1.1.0/sparsegl/R/calc_gamma.R | 12 sparsegl-1.1.0/sparsegl/R/cv.R | 83 +-- sparsegl-1.1.0/sparsegl/R/cv.sparsegl-methods.R | 44 - sparsegl-1.1.0/sparsegl/R/data.R | 5 sparsegl-1.1.0/sparsegl/R/enlist.R |only sparsegl-1.1.0/sparsegl/R/estimate_risk.R | 24 sparsegl-1.1.0/sparsegl/R/family.R | 23 sparsegl-1.1.0/sparsegl/R/glmnet-utilities.R | 38 - sparsegl-1.1.0/sparsegl/R/norms.R | 4 sparsegl-1.1.0/sparsegl/R/plot.cv.sparsegl.R | 24 sparsegl-1.1.0/sparsegl/R/plot.sparsegl.R | 14 sparsegl-1.1.0/sparsegl/R/sgl_irwls.R | 272 +++++----- sparsegl-1.1.0/sparsegl/R/sgl_logit.R | 73 +- sparsegl-1.1.0/sparsegl/R/sgl_ls.R | 47 - sparsegl-1.1.0/sparsegl/R/sparsegl-methods.R | 48 - sparsegl-1.1.0/sparsegl/R/sparsegl-package.R |only sparsegl-1.1.0/sparsegl/R/sparsegl.R | 100 +-- sparsegl-1.1.0/sparsegl/README.md | 12 sparsegl-1.1.0/sparsegl/build/partial.rdb |binary sparsegl-1.1.0/sparsegl/build/vignette.rds |binary sparsegl-1.1.0/sparsegl/inst/doc/sparsegl.R | 41 - sparsegl-1.1.0/sparsegl/inst/doc/sparsegl.Rmd | 33 - sparsegl-1.1.0/sparsegl/inst/doc/sparsegl.html | 68 +- sparsegl-1.1.0/sparsegl/man/estimate_risk.Rd | 2 sparsegl-1.1.0/sparsegl/man/figures/README-minimal-ex-1.svg |only sparsegl-1.1.0/sparsegl/man/grouped_sp_norm.Rd | 4 sparsegl-1.1.0/sparsegl/man/sparsegl-package.Rd |only sparsegl-1.1.0/sparsegl/man/sparsegl.Rd | 7 sparsegl-1.1.0/sparsegl/man/trust_experts.Rd | 5 sparsegl-1.1.0/sparsegl/src/Makevars | 23 sparsegl-1.1.0/sparsegl/tests/testthat/test-check_family.R | 2 sparsegl-1.1.0/sparsegl/tests/testthat/test-cv.R | 1 sparsegl-1.1.0/sparsegl/tests/testthat/test-groups_only.R | 6 sparsegl-1.1.0/sparsegl/tests/testthat/test-irwls.R | 49 + sparsegl-1.1.0/sparsegl/tests/testthat/test-irwls_comparisons.R | 43 - sparsegl-1.1.0/sparsegl/tests/testthat/test-l1penalty.R | 88 +-- sparsegl-1.1.0/sparsegl/tests/testthat/test-methods.R | 5 sparsegl-1.1.0/sparsegl/tests/testthat/test-model_base.R | 29 - sparsegl-1.1.0/sparsegl/tests/testthat/test-norms.R | 20 sparsegl-1.1.0/sparsegl/tests/testthat/test-predict.R | 64 +- sparsegl-1.1.0/sparsegl/tests/testthat/test-risk_estimation.R | 39 - sparsegl-1.1.0/sparsegl/tests/testthat/test-sgl_irwls.R | 46 - sparsegl-1.1.0/sparsegl/tests/testthat/test-sparsegl_comparisons.R | 8 sparsegl-1.1.0/sparsegl/tests/testthat/test-sparsegl_params.R | 51 - sparsegl-1.1.0/sparsegl/vignettes/sparsegl.Rmd | 33 - 52 files changed, 928 insertions(+), 694 deletions(-)
Title: Collection of Functions for Working with Age Intervals
Description: Provides a collection of efficient functions for working with
individual ages and corresponding intervals. These include functions for
conversion from an age to an interval, aggregation of ages with associated
counts in to intervals and the splitting of interval counts based on
specified age distributions.
Author: Tim Taylor [aut, cre, cph] ,
Edwin van Leeuwen [ctb]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ageutils versions 0.0.3 dated 2024-05-30 and 0.0.4 dated 2024-06-26
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ NEWS.md | 6 +++++ R/reaggregate_interval_rates.R | 8 ++----- README.md | 11 +++------- build/vignette.rds |binary inst/tinytest/test_reaggregate_interval_rates.R | 26 ++++++++++++++++++++++++ 7 files changed, 48 insertions(+), 21 deletions(-)
Title: Differential Gene Expression Analysis with R
Description: Analyses gene expression data derived from experiments to detect differentially expressed genes by employing the concept of majority voting with five different statistical models. It includes functions for differential expression analysis, significance testing, etc. It simplifies the process of uncovering meaningful patterns and trends within gene expression data, aiding researchers in downstream analysis. Boyer, R.S., Moore, J.S. (1991) <doi:10.1007/978-94-011-3488-0_5>.
Author: Koushik Bardhan [aut, cre, ctb]
,
Chiranjib Sarkar [aut, ths]
Maintainer: Koushik Bardhan <koushikbardhan2000@gmail.com>
Diff between DGEAR versions 0.1.3 dated 2023-08-30 and 0.1.4 dated 2024-06-26
DESCRIPTION | 13 +++++++------ LICENSE |only MD5 | 29 +++++++++++++++++------------ NAMESPACE | 34 ++++++++++++++++++---------------- NEWS.md |only R/D-Test.R | 15 ++++++++++++--- R/DGEAR.R | 28 +++++++++++++++++----------- R/H-Test.R | 14 ++++++++++++-- R/One-Way-ANOVA-Test.R | 15 ++++++++++++--- R/T-Test.R | 14 ++++++++++++-- R/U-Test.R | 15 ++++++++++++--- R/gene_exp_data.R | 4 ++-- README.md |only data/gene_exp_data.rda |binary inst |only man/DGEAR.Rd | 2 +- man/gene_exp_data.Rd | 4 ++-- tests/spelling.R |only 18 files changed, 124 insertions(+), 63 deletions(-)
Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to
plots using native data coordinates, while geom_table_npc(), geom_plot_npc()
and geom_grob_npc() do the same using "npc" coordinates through new
aesthetics "npcx" and "npcy". Statistics: select observations based on 2D
density. Positions: radial nudging away from a center point and nudging away
from a line or curve; combined stacking and nudging; combined dodging and
nudging.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Michal Krassowski [ctb] ,
Daniel Sabanes Bove [ctb],
Stella Banjo [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpp versions 0.5.7 dated 2024-05-06 and 0.5.8 dated 2024-06-26
DESCRIPTION | 8 MD5 | 48 NEWS.md | 7 R/position-nudge-to.R | 83 + R/stat-dens1d-filter.r | 2 R/stat-dens2d-filter.r | 2 README.md | 30 build/partial.rdb |binary build/vignette.rds |binary inst/doc/grammar-extensions.R | 34 inst/doc/grammar-extensions.Rmd | 43 inst/doc/grammar-extensions.html | 499 +++++----- inst/doc/nudge-examples.html | 6 man/position_nudge_to.Rd | 24 man/stat_dens1d_filter.Rd | 2 man/stat_dens2d_filter.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/position-nudge/nudge-to-contract-expand-x1.svg |only tests/testthat/_snaps/position-nudge/nudge-to-contract-expand-y1.svg |only tests/testthat/_snaps/position-nudge/nudge-to-contract-x1.svg |only tests/testthat/_snaps/position-nudge/nudge-to-contract-y1.svg |only tests/testthat/_snaps/position-nudge/nudge-to-expand-x1.svg |only tests/testthat/_snaps/position-nudge/nudge-to-expand-x1y1.svg |only tests/testthat/_snaps/position-nudge/nudge-to-expand-x2.svg |only tests/testthat/_snaps/position-nudge/nudge-to-expand-y1.svg |only tests/testthat/_snaps/position-nudge/nudge-to-expand-y2.svg |only tests/testthat/_snaps/position-nudge/nudge-to-spread-x1y1.svg |only tests/testthat/test-position-nudge.R | 141 ++ tests/testthat/test-try_data_frame.R | 71 + vignettes/grammar-extensions.Rmd | 43 30 files changed, 740 insertions(+), 305 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' and 'primer.tutorials' packages.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.2.7 dated 2024-05-06 and 0.3.0 dated 2024-06-26
DESCRIPTION | 13 +-- MD5 | 46 +++++++++--- NAMESPACE | 14 +++ NEWS.md | 8 ++ R/process_submissions.R |only R/show_file.R |only R/submission_functions.R | 61 +++++------------ R/write_answers.R | 82 +++-------------------- inst/child_documents/download_answers.Rmd | 2 inst/child_documents/info_section.Rmd | 6 - inst/doc/instructions.Rmd | 49 ++++++++++++- inst/doc/instructions.html | 35 ++++++++- inst/tutorials/getting-started/tutorial.Rmd | 7 + inst/tutorials/getting-started/tutorial.html | 40 +++++------ man/process_submissions.Rd |only man/show_file.Rd |only man/write_answers.Rd | 18 +---- tests/testthat/fixtures/process_submissions_dir |only tests/testthat/fixtures/process_submissions_dir2 |only tests/testthat/fixtures/show_file_test.txt |only tests/testthat/setup.R |only tests/testthat/teardown.R |only tests/testthat/test-process_submissions.R |only tests/testthat/test-show_file.R |only vignettes/instructions.Rmd | 49 ++++++++++++- 25 files changed, 250 insertions(+), 180 deletions(-)
More information about tutorial.helpers at CRAN
Permanent link
Title: One Sample Mendelian Randomization and Instrumental Variable
Analyses
Description: Useful functions for one-sample (individual level data)
Mendelian randomization and instrumental variable analyses. The
package includes implementations of; the Sanderson and Windmeijer
(2016) <doi:10.1016/j.jeconom.2015.06.004> conditional F-statistic,
the multiplicative structural mean model Hernán and Robins (2006)
<doi:10.1097/01.ede.0000222409.00878.37>, and two-stage predictor
substitution and two-stage residual inclusion estimators explained by
Terza et al. (2008) <doi:10.1016/j.jhealeco.2007.09.009>.
Author: Tom Palmer [aut, cre] ,
Wes Spiller [aut] ,
Eleanor Sanderson [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between OneSampleMR versions 0.1.4 dated 2024-06-13 and 0.1.5 dated 2024-06-26
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/msmm.R | 2 +- R/tsps.R | 2 +- R/tsri.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary 8 files changed, 18 insertions(+), 14 deletions(-)
Title: Items Response Theory Analysis with Steps and Interpretation
Description: Dichotomous and polytomous data analysis and their scoring using the unidimensional Item Response Theory model (Chalmers (2012) <doi:10.18637/jss.v048.i06>) with user-friendly graphic User Interface. Suitable for beginners who are learning item response theory.
Author: Hari Purnomo Susanto [aut, cre]
,
Heri Retnawati [ctb] ,
Agus Maman Abadi [ctb] ,
Haryanto Haryanto [ctb] ,
Hasan Djidu [ctb]
Maintainer: Hari Purnomo Susanto <haripurnomosusanto@gmail.com>
Diff between irtawsi versions 0.3.4 dated 2023-03-26 and 0.4.1 dated 2024-06-26
DESCRIPTION | 22 +- MD5 | 16 + NAMESPACE | 5 NEWS.md |only R/irtawsi.R | 4 README.md |only build/partial.rdb |binary inst/irtawsi/server.R | 322 ++++++++++++++++++++++++++++++++++++++ inst/irtawsi/ui.R | 416 ++++++++++++++++++++++++++++++++++++++++---------- man/irtawsi.Rd | 2 10 files changed, 683 insertions(+), 104 deletions(-)
Title: Summarises Package & Function Usage
Description: Consistent with 'knitr' syntax highlighting, 'usedthese' adds
a summary table of package & function usage to a Quarto document and
enables aggregation of usage across a website.
Author: Carl Goodwin [aut, cre, cph]
Maintainer: Carl Goodwin <carl.goodwin@quantumjitter.com>
Diff between usedthese versions 0.4.0 dated 2024-05-27 and 0.5.0 dated 2024-06-26
DESCRIPTION | 17 +- MD5 | 37 +++--- NAMESPACE | 47 +++++++ NEWS.md | 37 +++--- R/globals.R | 9 - R/used_here.R | 238 ++++++++++++++++++++++++--------------- R/used_there.R | 98 ++++++++++------ R/usedthese-package.R | 19 +++ README.md | 8 - build/vignette.rds |binary inst/CITATION | 4 inst/WORDLIST | 8 - inst/doc/multipage.html | 4 man/used_here.Rd | 33 +++-- man/used_there.Rd | 16 +- man/usedthese-package.Rd | 4 tests/testthat/_snaps |only tests/testthat/jitter.html |only tests/testthat/test-used_here.R | 6 tests/testthat/test-used_there.R | 29 ++-- 20 files changed, 395 insertions(+), 219 deletions(-)
Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics.
Output may be in LaTeX, HTML, plain text, or an R
matrix for further processing.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between tables versions 0.9.25 dated 2024-04-13 and 0.9.28 dated 2024-06-26
tables-0.9.25/tables/inst/doc/HTML.R |only tables-0.9.25/tables/inst/doc/HTML.Rmd |only tables-0.9.25/tables/inst/doc/HTML.html |only tables-0.9.25/tables/inst/doc/knitrTables.R |only tables-0.9.25/tables/inst/doc/knitrTables.Rmd |only tables-0.9.25/tables/inst/doc/knitrTables.pdf |only tables-0.9.28/tables/DESCRIPTION | 8 +++---- tables-0.9.28/tables/MD5 | 25 +++++++++--------------- tables-0.9.28/tables/NEWS.md | 8 +++++++ tables-0.9.28/tables/R/All.R | 2 - tables-0.9.28/tables/R/RowFactor.R | 2 - tables-0.9.28/tables/R/makeName.R |only tables-0.9.28/tables/R/tabular.R | 4 +-- tables-0.9.28/tables/build/vignette.rds |binary tables-0.9.28/tables/inst/doc/tables.pdf |binary tables-0.9.28/tables/man/knit_print.tabular.Rd | 4 +-- tables-0.9.28/tables/man/matrix_form.tabular.Rd | 10 +++++++-- 17 files changed, 36 insertions(+), 27 deletions(-)
Title: Auxiliary Routines for Influx Software
Description: Contains auxiliary routines for influx software. This packages is not intended to be used directly. Influx was published here: Sokol et al. (2012) <doi:10.1093/bioinformatics/btr716>.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between multbxxc versions 1.0.2 dated 2024-04-18 and 1.0.3 dated 2024-06-26
multbxxc-1.0.2/multbxxc/man/resize.Rd |only multbxxc-1.0.3/multbxxc/DESCRIPTION | 12 ++++----- multbxxc-1.0.3/multbxxc/MD5 | 11 +++----- multbxxc-1.0.3/multbxxc/NEWS | 6 ++++ multbxxc-1.0.3/multbxxc/R/RcppExports.R | 19 -------------- multbxxc-1.0.3/multbxxc/src/RcppExports.cpp | 12 --------- multbxxc-1.0.3/multbxxc/src/multbxxc.cpp | 37 ---------------------------- 7 files changed, 18 insertions(+), 79 deletions(-)
Title: Digitization of Phytosociological Relevés
Description: Simple and fast tool for transforming phytosociological
vegetation data into digital form for the following analysis.
Danihelka, Chrtek, and Kaplan (2012, ISSN:00327786).
Hennekens, and Schaminée (2001) <doi:10.2307/3237010>.
Tichý (2002) <doi:10.1111/j.1654-1103.2002.tb02069.x>.
Wickham, François, Henry, Müller (2022) <https://CRAN.R-project.org/package=dplyr>.
Author: Premysl Kral [aut, cre] ,
Jan Douda [aut]
Maintainer: Premysl Kral <kralp@fzp.czu.cz>
Diff between Rveg versions 0.1.4 dated 2024-03-31 and 0.1.5 dated 2024-06-26
DESCRIPTION | 10 MD5 | 32 R/RvegCheck.R | 172 R/RvegCombine.R | 198 R/RvegMERGE.r | 128 R/addReleve.R | 808 - R/createTABLE.R | 118 README.md | 276 build/vignette.rds |binary inst/doc/Rveg.R | 60 inst/doc/Rveg.pdf |binary inst/extdata/DANIHELKA2012rko.txt |22994 +++++++++++++++++++------------------- inst/extdata/SpeciesList.txt | 18 inst/extdata/example_dbHEAD.csv | 38 inst/extdata/example_dbREL.csv | 64 inst/extdata/tvexport.csv | 168 man/Rveg-package.Rd | 2 17 files changed, 12543 insertions(+), 12543 deletions(-)
Title: React Helpers
Description: Make it easy to use 'React' in R with 'htmlwidget' scaffolds,
helper dependency functions, an embedded 'Babel' 'transpiler',
and examples.
Author: Facebook Inc [aut, cph] ,
Michel Weststrate [aut, cph] ,
Kent Russell [aut, cre] ,
Alan Dipert [aut]
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between reactR versions 0.5.0 dated 2023-10-11 and 0.6.0 dated 2024-06-26
reactR-0.5.0/reactR/inst/www/react-tools/react-tools.js |only reactR-0.5.0/reactR/inst/www/react-tools/react-tools.js.map |only reactR-0.6.0/reactR/DESCRIPTION | 10 +- reactR-0.6.0/reactR/MD5 | 21 ++---- reactR-0.6.0/reactR/NEWS.md | 12 +++ reactR-0.6.0/reactR/R/dependencies.R | 4 - reactR-0.6.0/reactR/R/reacttools.R | 6 - reactR-0.6.0/reactR/inst/doc/intro_htmlwidgets.R | 2 reactR-0.6.0/reactR/inst/doc/intro_htmlwidgets.html | 4 - reactR-0.6.0/reactR/inst/doc/intro_inputs.R | 2 reactR-0.6.0/reactR/inst/doc/intro_inputs.html | 4 - reactR-0.6.0/reactR/inst/doc/intro_reactR.html | 38 +++++------ reactR-0.6.0/reactR/inst/www/react-tools/react-tools.umd.cjs |only 13 files changed, 57 insertions(+), 46 deletions(-)
Title: Deming, Theil-Sen, Passing-Bablock and Total Least Squares
Regression
Description: Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau.terry@mayo.edu>
Diff between deming versions 1.4 dated 2018-11-13 and 1.4-1 dated 2024-06-26
deming-1.4-1/deming/DESCRIPTION | 6 +++--- deming-1.4-1/deming/MD5 | 17 ++++++++--------- deming-1.4-1/deming/build/vignette.rds |binary deming-1.4-1/deming/inst/NEWS.Rd | 4 ++++ deming-1.4-1/deming/inst/doc/deming.Rnw | 2 +- deming-1.4-1/deming/inst/doc/deming.pdf |binary deming-1.4-1/deming/man/deming.Rd | 9 +++++---- deming-1.4-1/deming/man/theilsen.Rd | 2 +- deming-1.4-1/deming/vignettes/deming.Rnw | 2 +- deming-1.4/deming/vignettes/deming-001.pdf |only 10 files changed, 23 insertions(+), 19 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
DAVIES, D.L., BOULDIN, D.W. (1979) &l [...truncated...]
Author: Marek Walesiak [aut] ,
Andrzej Dudek [aut, cre]
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.51-3 dated 2023-06-10 and 0.51-4 dated 2024-06-26
DESCRIPTION | 24 ++++- MD5 | 94 +++++++++++------------ NAMESPACE | 1 R/cluster.Sim.r | 21 ----- man/HINoV.Mod.rd | 4 man/HINoV.Symbolic.rd | 6 - man/cluster.Description.rd | 4 man/cluster.Gen.rd | 10 +- man/cluster.Sim.rd | 25 +++--- man/comparing.Partitions.rd | 4 man/data.Normalization.rd | 8 - man/data_binary.rd | 6 - man/data_interval.rd | 2 man/data_mixed.rd | 2 man/data_nominal.rd | 2 man/data_ordinal.rd | 2 man/data_patternGDM1.rd | 2 man/data_patternGDM2.rd | 2 man/data_ratio.rd | 2 man/data_symbolic.rd | 2 man/data_symbolic_interval_polish_voivodships.rd | 2 man/dist.BC.rd | 6 - man/dist.GDM.rd | 8 - man/dist.SM.rd | 6 - man/dist.Symbolic.rd | 3 man/index.C.rd | 3 man/index.DB.rd | 6 - man/index.G1.rd | 6 - man/index.G2.rd | 6 - man/index.G3.rd | 3 man/index.GAP.rd | 6 - man/index.H.rd | 4 man/index.KL.rd | 4 man/index.S.rd | 6 - man/initial.Centers.rd | 4 man/interval_normalization.rd | 7 - man/ordinalToMetric.rd | 12 +- man/pattern.GDM1.rd | 13 +-- man/pattern.GDM2.rd | 14 +-- man/plotCategorial.rd | 4 man/plotInterval.rd | 4 man/replication.Mod.rd | 5 - man/shapes.blocks3d.rd | 4 man/shapes.circles2.rd | 4 man/shapes.circles3.rd | 4 man/shapes.two.moon.rd | 4 man/shapes.worms.rd | 4 man/speccl.rd | 12 +- 48 files changed, 192 insertions(+), 195 deletions(-)
Title: Describe Pedigree Relationships in Words
Description: Describe in words the genealogical relationship between two
members of a given pedigree, using the algorithm in Vigeland (2022)
<doi:10.1186/s12859-022-04759-y>. 'verbalisr' is part of the
'pedsuite' collection of packages for pedigree analysis. For a
demonstration of 'verbalisr', see the online app 'QuickPed' at
<https://magnusdv.shinyapps.io/quickped>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between verbalisr versions 0.5.2 dated 2024-03-13 and 0.6.0 dated 2024-06-26
verbalisr-0.5.2/verbalisr/man/format.pairrel.Rd |only verbalisr-0.6.0/verbalisr/DESCRIPTION | 6 - verbalisr-0.6.0/verbalisr/MD5 | 23 ++-- verbalisr-0.6.0/verbalisr/NEWS.md | 13 ++ verbalisr-0.6.0/verbalisr/R/pathData.R | 46 ++++++--- verbalisr-0.6.0/verbalisr/R/print.R | 37 ++++--- verbalisr-0.6.0/verbalisr/R/verbalise.R | 32 +++++- verbalisr-0.6.0/verbalisr/README.md | 58 +++++++----- verbalisr-0.6.0/verbalisr/build |only verbalisr-0.6.0/verbalisr/man/figures/README-dblcous-1.png |binary verbalisr-0.6.0/verbalisr/man/figures/README-habsburg-1.png |binary verbalisr-0.6.0/verbalisr/man/print.pairrel.Rd |only verbalisr-0.6.0/verbalisr/man/verbalise.Rd | 14 ++ verbalisr-0.6.0/verbalisr/man/verbalisr-package.Rd | 2 14 files changed, 153 insertions(+), 78 deletions(-)
Title: Revisiting Base Rapply
Description: The minimal 'rrapply'-package contains a single function rrapply(), providing an extended implementation of 'R'-base rapply() by allowing to recursively apply a function to elements of a nested list based on a general condition function and including the possibility to prune or aggregate nested list elements from the result. In addition, special arguments can be supplied to access the name, location, parents and siblings in the nested list of the element under evaluation. The rrapply() function builds upon rapply()'s native 'C' implementation and requires no other package dependencies.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between rrapply versions 1.2.6 dated 2022-10-16 and 1.2.7 dated 2024-06-26
DESCRIPTION | 12 +++++------ MD5 | 18 ++++++++--------- NEWS.md | 5 ++++ build/vignette.rds |binary inst/doc/rrapply_cheatsheet.pdf |binary inst/unit_tests/unit_test_rrapply.R | 2 - src/list.c | 12 ++++++++--- src/rrapply.c | 38 +++++++++++++++++------------------- src/rrapply.h | 1 src/utils.c | 11 ++-------- 10 files changed, 52 insertions(+), 47 deletions(-)
Title: Mixed Models for Repeated Measures
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see Cnaan, Laird and Slasor (1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>
for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso
(2008) <doi:10.1177/009286150804200402> for a review. This package
implements MMRM based on the marginal linear model without random
effects using Template Model Builder ('TMB') which enables fast and
robust model fitting. Users can specify a variety of covariance
matrices, weight observations, fit models with restricted or standard
maximum likelihood inference, perform hypothesis testing with
Satterthwaite or Kenward-Roger adjustment, and extract least square
means estimates by using 'emmeans'.
Author: Daniel Sabanes Bove [aut, cre],
Liming Li [aut],
Julia Dedic [aut],
Doug Kelkhoff [aut],
Kevin Kunzmann [aut],
Brian Matthew Lang [aut],
Christian Stock [aut],
Ya Wang [aut],
Craig Gower-Page [ctb],
Dan James [aut],
Jonathan Sidi [aut],
Daniel Leibov [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between mmrm versions 0.3.11 dated 2024-03-05 and 0.3.12 dated 2024-06-26
DESCRIPTION | 10 MD5 | 45 NEWS.md | 10 R/tmb-methods.R | 28 R/tmb.R | 23 R/utils.R | 28 build/partial.rdb |binary build/vignette.rds |binary inst/doc/empirical_wls.Rmd | 2 inst/doc/empirical_wls.html | 2 inst/doc/introduction.html | 2725 +++++++++++++++++++------------------- inst/doc/mmrm_review_methods.html | 86 - man/h_confirm_large_levels.Rd | 3 man/h_factor_ref.Rd | 3 man/h_factor_ref_data.Rd |only man/h_get_cov_default.Rd | 3 man/h_get_theta_from_cov.Rd | 3 man/h_mmrm_tmb_formula_parts.Rd | 1 man/mmrm-package.Rd | 2 man/mmrm_tmb_methods.Rd | 3 tests/testthat/test-tmb-methods.R | 42 tests/testthat/test-tmb.R | 12 tests/testthat/test-utils.R | 19 vignettes/empirical_wls.Rmd | 2 24 files changed, 1585 insertions(+), 1467 deletions(-)
Title: Object-Oriented Implementation of CRM Designs
Description: Implements a wide range of model-based dose
escalation designs, ranging from classical and modern continual
reassessment methods (CRMs) based on dose-limiting toxicity endpoints to
dual-endpoint designs taking into account a biomarker/efficacy outcome. The
focus is on Bayesian inference, making it very easy to setup a new design
with its own JAGS code. However, it is also possible to implement 3+3
designs for comparison or models with non-Bayesian estimation. The whole
package is written in a modular form in the S4 class system, making it very
flexible for adaptation to new models, escalation or stopping rules.
Author: Daniel Sabanes Bove [aut, cre],
Wai Yin Yeung [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 1.0.5 dated 2024-02-04 and 1.0.6 dated 2024-06-26
DESCRIPTION | 14 +- MD5 | 38 ++--- NEWS.md | 4 R/Simulations-methods.R | 18 +- R/crmPack-package.R | 2 build/vignette.rds |binary inst/doc/example.pdf |binary inst/doc/guidelines.Rmd | 2 inst/doc/guidelines.html | 106 +++++++++++----- man/crmPack-package.Rd | 2 man/plot-DualSimulations-missing-method.Rd | 2 man/plot-DualSimulationsSummary-missing-method.Rd | 2 man/plot-GeneralSimulations-missing-method.Rd | 2 man/plot-GeneralSimulationsSummary-missing-method.Rd | 2 man/plot-PseudoDualFlexiSimulations-missing-method.Rd | 2 man/plot-PseudoDualSimulations-missing-method.Rd | 2 man/plot-PseudoDualSimulationsSummary-missing-method.Rd | 2 man/plot-PseudoSimulationsSummary-missing-method.Rd | 2 man/plot-SimulationsSummary-missing-method.Rd | 2 vignettes/guidelines.Rmd | 2 20 files changed, 127 insertions(+), 79 deletions(-)
Title: Tools, Classes, and Methods for Interfacing with 'SaTScan'
Stand-Alone Software
Description: 'SaTScan'(TM) <https://www.satscan.org> is software for finding regions in
Time, Space, or Time-Space that have excess risk, based on scan statistics, and
uses Monte Carlo hypothesis testing to generate P-values for these regions. The
'rsatscan' package provides functions for writing R data frames in
'SaTScan'-readable formats, for setting 'SaTScan' parameters, for running 'SaTScan' in
the OS, and for reading the files that 'SaTScan' creates.
Author: Ken Kleinman [aut],
Scott Hostovich [cre],
Amer Moosa [ctb]
Maintainer: Scott Hostovich <HostovichS@imsweb.com>
Diff between rsatscan versions 1.0.7 dated 2023-10-24 and 1.0.8 dated 2024-06-26
DESCRIPTION | 10 ++--- MD5 | 36 ++++++++++---------- NAMESPACE | 1 NEWS | 8 ++++ R/methods.R | 4 ++ R/params.R | 81 +++++++++++++++++++++++++++++++++++++++++------ R/satscan.R | 2 - R/zzz.R | 19 +++++++++-- build/vignette.rds |binary inst/doc/rsatscan.R | 14 ++++---- inst/doc/rsatscan.Rmd | 8 ++-- inst/doc/rsatscan.html | 22 ++++++------ inst/doc/simulation.R | 4 +- inst/doc/simulation.Rmd | 2 - inst/doc/simulation.html | 10 ++--- man/rsatscan.Rd | 2 - man/ss.options.extra.Rd | 26 ++++++++++++--- vignettes/rsatscan.Rmd | 8 ++-- vignettes/simulation.Rmd | 2 - 19 files changed, 183 insertions(+), 76 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.fragstats.org/>) and new ones from the current
literature on landscape metrics. This package supports 'terra' SpatRaster objects
as input arguments. It further provides utility functions to visualize patches,
select metrics and building blocks to develop new metrics.
Author: Maximilian H.K. Hesselbarth [aut, cre]
,
Marco Sciaini [aut] ,
Jakub Nowosad [aut] ,
Sebastian Hanss [aut] ,
Laura J. Graham [ctb] ,
Jeffrey Hollister [ctb] ,
Kimberly A. With [ctb] ,
Florian Prive [ctb] function),
Project Nayuki [ctb] ,
Matt Strima [...truncated...]
Maintainer: Maximilian H.K. Hesselbarth <mhk.hesselbarth@gmail.com>
Diff between landscapemetrics versions 2.1.2 dated 2024-05-02 and 2.1.3 dated 2024-06-26
DESCRIPTION | 6 MD5 | 468 ++++++------- NEWS.md | 575 ++++++++--------- R/RcppExports.R | 218 +++--- R/calculate_lsm.R | 3 R/get_centroids.R | 119 +-- R/get_circumscribingcircle.R | 26 R/get_nearestneighbour.R | 3 R/lsm_c_area_cv.R | 3 R/lsm_c_area_mn.R | 171 ++--- R/lsm_c_area_sd.R | 171 ++--- R/lsm_c_ca.R | 6 R/lsm_c_cai_cv.R | 5 R/lsm_c_cai_mn.R | 189 ++--- R/lsm_c_cai_sd.R | 193 ++--- R/lsm_c_circle_cv.R | 195 ++--- R/lsm_c_circle_mn.R | 189 ++--- R/lsm_c_circle_sd.R | 191 ++--- R/lsm_c_cohesion.R | 3 R/lsm_c_core_cv.R | 3 R/lsm_c_core_mn.R | 185 ++--- R/lsm_c_core_sd.R | 189 ++--- R/lsm_c_cpland.R | 3 R/lsm_c_dcad.R | 3 R/lsm_c_dcore_mn.R | 182 ++--- R/lsm_c_dcore_sd.R | 187 ++--- R/lsm_c_division.R | 3 R/lsm_c_ed.R | 5 R/lsm_c_enn_cv.R | 3 R/lsm_c_enn_mn.R | 189 ++--- R/lsm_c_enn_sd.R | 189 ++--- R/lsm_c_frac_cv.R | 3 R/lsm_c_frac_mn.R | 175 ++--- R/lsm_c_frac_sd.R | 181 ++--- R/lsm_c_gyrate_cv.R | 3 R/lsm_c_gyrate_mn.R | 199 +++-- R/lsm_c_gyrate_sd.R | 3 R/lsm_c_lpi.R | 3 R/lsm_c_lsi.R | 3 R/lsm_c_mesh.R | 3 R/lsm_c_nlsi.R | 3 R/lsm_c_pafrac.R | 3 R/lsm_c_para_cv.R | 3 R/lsm_c_para_mn.R | 171 ++--- R/lsm_c_para_sd.R | 173 ++--- R/lsm_c_pd.R | 3 R/lsm_c_pland.R | 3 R/lsm_c_shape_cv.R | 3 R/lsm_c_shape_mn.R | 177 ++--- R/lsm_c_shape_sd.R | 179 ++--- R/lsm_c_split.R | 3 R/lsm_c_tca.R | 3 R/lsm_c_te.R | 3 R/lsm_l_ai.R | 6 R/lsm_l_area_cv.R | 3 R/lsm_l_area_mn.R | 175 ++--- R/lsm_l_area_sd.R | 173 ++--- R/lsm_l_cai_cv.R | 3 R/lsm_l_cai_mn.R | 191 ++--- R/lsm_l_cai_sd.R | 195 ++--- R/lsm_l_circle_cv.R | 183 ++--- R/lsm_l_circle_mn.R | 179 ++--- R/lsm_l_circle_sd.R | 185 ++--- R/lsm_l_cohesion.R | 3 R/lsm_l_condent.R | 5 R/lsm_l_core_cv.R | 3 R/lsm_l_core_mn.R | 187 ++--- R/lsm_l_core_sd.R | 189 ++--- R/lsm_l_dcad.R | 3 R/lsm_l_dcore_cv.R | 190 ++--- R/lsm_l_dcore_mn.R | 186 ++--- R/lsm_l_dcore_sd.R | 190 ++--- R/lsm_l_division.R | 5 R/lsm_l_ed.R | 5 R/lsm_l_enn_cv.R | 3 R/lsm_l_enn_mn.R | 181 ++--- R/lsm_l_enn_sd.R | 181 ++--- R/lsm_l_frac_cv.R | 3 R/lsm_l_frac_mn.R | 175 ++--- R/lsm_l_frac_sd.R | 175 ++--- R/lsm_l_gyrate_cv.R | 3 R/lsm_l_gyrate_mn.R | 193 ++--- R/lsm_l_gyrate_sd.R | 3 R/lsm_l_lpi.R | 3 R/lsm_l_lsi.R | 3 R/lsm_l_mesh.R | 5 R/lsm_l_msidi.R | 3 R/lsm_l_msiei.R | 10 R/lsm_l_mutinf.R | 4 R/lsm_l_pafrac.R | 3 R/lsm_l_para_cv.R | 3 R/lsm_l_para_mn.R | 171 ++--- R/lsm_l_para_sd.R | 171 ++--- R/lsm_l_pd.R | 3 R/lsm_l_prd.R | 3 R/lsm_l_relmutinf.R | 9 R/lsm_l_shape_cv.R | 3 R/lsm_l_shape_mn.R | 175 ++--- R/lsm_l_shape_sd.R | 175 ++--- R/lsm_l_split.R | 3 R/lsm_l_ta.R | 3 R/lsm_l_tca.R | 3 R/lsm_l_te.R | 3 R/lsm_p_area.R | 5 R/lsm_p_cai.R | 2 R/lsm_p_circle.R | 6 R/lsm_p_core.R | 3 R/lsm_p_enn.R | 3 R/lsm_p_frac.R | 7 R/lsm_p_gyrate.R | 3 R/lsm_p_para.R | 3 R/lsm_p_perim.R | 3 R/lsm_p_shape.R | 7 R/prepare_extras.R | 47 - R/sample_lsm.R | 7 R/show_correlation.R | 10 R/show_lsm.R | 6 R/show_patches.R | 14 R/spatialize_lsm.R | 3 R/window_lsm.R | 438 ++++++------- build/vignette.rds |binary inst/doc/get_started.R | 198 ++--- inst/doc/get_started.html | 1344 ++++++++++++++++++++-------------------- man/calculate_lsm.Rd | 3 man/get_circumscribingcircle.Rd | 3 man/get_nearestneighbour.Rd | 3 man/lsm_c_area_cv.Rd | 3 man/lsm_c_area_mn.Rd | 109 +-- man/lsm_c_area_sd.Rd | 109 +-- man/lsm_c_ca.Rd | 6 man/lsm_c_cai_cv.Rd | 5 man/lsm_c_cai_mn.Rd | 133 ++- man/lsm_c_cai_sd.Rd | 137 ++-- man/lsm_c_circle_cv.Rd | 127 +-- man/lsm_c_circle_mn.Rd | 123 +-- man/lsm_c_circle_sd.Rd | 123 +-- man/lsm_c_cohesion.Rd | 3 man/lsm_c_core_cv.Rd | 3 man/lsm_c_core_mn.Rd | 127 +-- man/lsm_c_core_sd.Rd | 129 +-- man/lsm_c_cpland.Rd | 3 man/lsm_c_dcad.Rd | 3 man/lsm_c_dcore_mn.Rd | 128 +-- man/lsm_c_dcore_sd.Rd | 133 +-- man/lsm_c_division.Rd | 3 man/lsm_c_ed.Rd | 4 man/lsm_c_enn_cv.Rd | 3 man/lsm_c_enn_mn.Rd | 125 +-- man/lsm_c_enn_sd.Rd | 125 +-- man/lsm_c_frac_cv.Rd | 3 man/lsm_c_frac_mn.Rd | 111 +-- man/lsm_c_frac_sd.Rd | 117 +-- man/lsm_c_gyrate_cv.Rd | 3 man/lsm_c_gyrate_mn.Rd | 131 +-- man/lsm_c_gyrate_sd.Rd | 3 man/lsm_c_lpi.Rd | 3 man/lsm_c_lsi.Rd | 3 man/lsm_c_mesh.Rd | 3 man/lsm_c_nlsi.Rd | 3 man/lsm_c_pafrac.Rd | 3 man/lsm_c_para_cv.Rd | 3 man/lsm_c_para_mn.Rd | 113 +-- man/lsm_c_para_sd.Rd | 113 +-- man/lsm_c_pd.Rd | 3 man/lsm_c_pland.Rd | 3 man/lsm_c_shape_cv.Rd | 3 man/lsm_c_shape_mn.Rd | 113 +-- man/lsm_c_shape_sd.Rd | 113 +-- man/lsm_c_split.Rd | 3 man/lsm_c_tca.Rd | 3 man/lsm_c_te.Rd | 3 man/lsm_l_ai.Rd | 6 man/lsm_l_area_cv.Rd | 3 man/lsm_l_area_mn.Rd | 109 +-- man/lsm_l_area_sd.Rd | 105 +-- man/lsm_l_cai_cv.Rd | 3 man/lsm_l_cai_mn.Rd | 133 ++- man/lsm_l_cai_sd.Rd | 137 ++-- man/lsm_l_circle_cv.Rd | 123 +-- man/lsm_l_circle_mn.Rd | 121 +-- man/lsm_l_circle_sd.Rd | 125 +-- man/lsm_l_cohesion.Rd | 3 man/lsm_l_condent.Rd | 5 man/lsm_l_core_cv.Rd | 3 man/lsm_l_core_mn.Rd | 129 +-- man/lsm_l_core_sd.Rd | 131 +-- man/lsm_l_dcad.Rd | 3 man/lsm_l_dcore_mn.Rd | 128 +-- man/lsm_l_dcore_sd.Rd | 132 +-- man/lsm_l_division.Rd | 5 man/lsm_l_ed.Rd | 4 man/lsm_l_enn_cv.Rd | 3 man/lsm_l_enn_mn.Rd | 125 +-- man/lsm_l_enn_sd.Rd | 125 +-- man/lsm_l_frac_cv.Rd | 3 man/lsm_l_frac_mn.Rd | 117 +-- man/lsm_l_frac_sd.Rd | 117 +-- man/lsm_l_gyrate_cv.Rd | 3 man/lsm_l_gyrate_mn.Rd | 131 +-- man/lsm_l_gyrate_sd.Rd | 3 man/lsm_l_lpi.Rd | 3 man/lsm_l_lsi.Rd | 3 man/lsm_l_mesh.Rd | 5 man/lsm_l_msidi.Rd | 3 man/lsm_l_msiei.Rd | 8 man/lsm_l_mutinf.Rd | 4 man/lsm_l_pafrac.Rd | 3 man/lsm_l_para_cv.Rd | 3 man/lsm_l_para_mn.Rd | 113 +-- man/lsm_l_para_sd.Rd | 113 +-- man/lsm_l_pd.Rd | 3 man/lsm_l_prd.Rd | 3 man/lsm_l_relmutinf.Rd | 9 man/lsm_l_shape_cv.Rd | 3 man/lsm_l_shape_mn.Rd | 113 +-- man/lsm_l_shape_sd.Rd | 113 +-- man/lsm_l_split.Rd | 3 man/lsm_l_ta.Rd | 3 man/lsm_l_tca.Rd | 3 man/lsm_l_te.Rd | 3 man/lsm_p_area.Rd | 3 man/lsm_p_cai.Rd | 3 man/lsm_p_circle.Rd | 3 man/lsm_p_core.Rd | 3 man/lsm_p_enn.Rd | 3 man/lsm_p_frac.Rd | 3 man/lsm_p_gyrate.Rd | 3 man/lsm_p_para.Rd | 3 man/lsm_p_perim.Rd | 3 man/lsm_p_shape.Rd | 3 man/sample_lsm.Rd | 7 man/show_correlation.Rd | 10 man/show_lsm.Rd | 6 man/spatialize_lsm.Rd | 3 man/window_lsm.Rd | 168 ++--- 235 files changed, 8572 insertions(+), 7946 deletions(-)
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Title: CFO-Type Designs in Phase I Clinical Trials
Description: In phase I clinical trials, the primary objective is to ascertain the maximum tolerated dose (MTD) corresponding to a specified target toxicity rate. The 'CFO' package facilitates the implementation of dose-finding trials by utilizing calibration-free odds type (CFO-type) designs. Specifically, it encompasses the calibration-free odds (CFO) (Jin and Yin (2022) <doi:10.1177/09622802221079353>), two-dimensional CFO (2dCFO) (Wang et al. (2023) <doi:10.3389/fonc.2023.1294258>), time-to-event CFO (TITE-CFO) (Jin and Yin (2023) <doi:10.1002/pst.2304>), fractional CFO (fCFO), accumulative CFO (aCFO), TITE-aCFO, and f-aCFO designs (Fang and Yin (2024) <doi: 10.1002/sim.10127>). The ‘CFO' package accommodates diverse CFO-type designs, allowing users to tailor the approach based on factors such as dose information inclusion, handling of late-onset toxicity, and the nature of the target drug (single-drug or drug-combination). The functionalities embedded in 'CFO' package i [...truncated...]
Author: Jialu Fang [aut, cre],
Wenliang Wang [aut],
Guosheng Yin [aut]
Maintainer: Jialu Fang <u3008682@connect.hku.hk>
Diff between CFO versions 1.3.0 dated 2024-06-22 and 1.3.1 dated 2024-06-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/lateonset.next.R | 14 +++++++++++--- man/lateonset.next.Rd | 3 +++ 4 files changed, 20 insertions(+), 9 deletions(-)
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Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for analyses of multiple social networks are delivered with this
package as described in Ostoic (2020) <DOI:10.18637/jss.v092.i11>. 'multiplex' makes
possible, among other things, to create and manipulate multiplex, multimode, and
multilevel network data with different formats. Effective ways are available to treat
multiple networks with routines that combine algebraic systems like the partially ordered
semigroup with decomposition procedures or semiring structures with the relational
bundles occurring in different types of multivariate networks. 'multiplex' provides also
an algebraic approach for affiliation networks through Galois derivations between families
of the pairs of subsets in the two domains of the network with visualization options.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 3.3 dated 2024-06-19 and 3.3-2 dated 2024-06-26
DESCRIPTION | 8 +- MD5 | 148 +++++++++++++++++++++---------------------- R/transf.R | 13 ++- inst/doc/TwoModeNetworks.pdf |binary man/as.semigroup.Rd | 12 +-- man/as.signed.Rd | 20 +---- man/as.strings.Rd | 7 -- man/bnd.Rd | 1 man/bundle.census.Rd | 2 man/bundles.Rd | 2 man/cngr.Rd | 9 +- man/comps.Rd | 13 +-- man/coor.Rd | 2 man/cpath.Rd | 3 man/cph.Rd | 8 +- man/cscl.Rd | 3 man/decomp.Rd | 14 +--- man/dhc.Rd | 1 man/diagram.levels.Rd | 14 +--- man/dichot.Rd | 8 +- man/edgS.Rd | 3 man/edgeT.Rd | 16 +--- man/edgel.Rd | 13 +-- man/expos.Rd | 10 -- man/fact.Rd | 8 +- man/flt.Rd | 1 man/fltr.Rd | 5 - man/galois.Rd | 4 - man/green.rel.Rd | 6 - man/hasse.Rd | 7 -- man/hierar.Rd | 13 +-- man/jnt.Rd | 1 man/men.Rd | 1 man/mlvl.Rd | 5 - man/mmp.Rd | 3 man/mnplx.Rd | 19 ++--- man/multiplex-package.Rd | 16 ++-- man/mxmn.Rd | 3 man/neighb.Rd | 12 +-- man/ngbs.Rd | 1 man/pacnet.Rd | 7 -- man/partial.order.Rd | 9 -- man/perm.Rd | 12 +-- man/pfvn.Rd | 13 +-- man/pi.rels.Rd | 17 +--- man/prev.Rd | 8 -- man/print.gml.Rd | 2 man/print.reduced.Rd | 1 man/rbox.Rd | 9 +- man/read.dl.Rd | 9 +- man/read.gml.Rd | 7 -- man/redl.Rd | 1 man/reduc.Rd | 11 +-- man/reducs.Rd | 1 man/rel.sys.Rd | 7 -- man/rm.isol.Rd | 6 - man/semigroup.Rd | 10 +- man/semiring.Rd | 6 - man/signed.Rd | 9 +- man/sprt.Rd | 1 man/strings.Rd | 6 - man/strng.Rd | 3 man/summaryBundles.Rd | 4 - man/swp.Rd | 1 man/ti.Rd | 3 man/transf.Rd | 5 - man/transl.Rd | 1 man/trnf.Rd | 2 man/wordT.Rd | 4 - man/write.dat.Rd | 7 -- man/write.dl.Rd | 8 -- man/write.edgel.Rd | 15 +--- man/write.gml.Rd | 7 -- man/zbind.Rd | 5 - man/zbnd.Rd | 1 75 files changed, 302 insertions(+), 351 deletions(-)
Title: Inferring Cell-Specific Gene Regulatory Network
Description: A method for inferring cell-specific gene regulatory network from single-cell sequencing data.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between inferCSN versions 1.0.3 dated 2024-04-17 and 1.0.5 dated 2024-06-26
inferCSN-1.0.3/inferCSN/R/crossweight.R |only inferCSN-1.0.3/inferCSN/R/weight_filter.R |only inferCSN-1.0.3/inferCSN/man/contrast.networks.Rd |only inferCSN-1.0.3/inferCSN/man/crossweight.Rd |only inferCSN-1.0.3/inferCSN/man/crossweight_params.Rd |only inferCSN-1.0.3/inferCSN/man/dynamic.networks.Rd |only inferCSN-1.0.3/inferCSN/man/net.format.Rd |only inferCSN-1.0.3/inferCSN/man/weight_filter.Rd |only inferCSN-1.0.5/inferCSN/DESCRIPTION | 17 inferCSN-1.0.5/inferCSN/MD5 | 72 - inferCSN-1.0.5/inferCSN/NAMESPACE | 21 inferCSN-1.0.5/inferCSN/R/RcppExports.R | 4 inferCSN-1.0.5/inferCSN/R/calculate.gene.rank.R | 21 inferCSN-1.0.5/inferCSN/R/import.R | 22 inferCSN-1.0.5/inferCSN/R/inferCSN.R | 220 +-- inferCSN-1.0.5/inferCSN/R/network.visualization.R | 323 +++- inferCSN-1.0.5/inferCSN/R/network_sift.R |only inferCSN-1.0.5/inferCSN/R/performance.calculate.R | 40 inferCSN-1.0.5/inferCSN/R/plotting_functions.R |only inferCSN-1.0.5/inferCSN/R/sparse.regression.R | 130 - inferCSN-1.0.5/inferCSN/R/utils.R | 333 +++- inferCSN-1.0.5/inferCSN/README.md | 2 inferCSN-1.0.5/inferCSN/man/acc.calculate.Rd | 9 inferCSN-1.0.5/inferCSN/man/as_matrix.Rd |only inferCSN-1.0.5/inferCSN/man/auc.calculate.Rd | 9 inferCSN-1.0.5/inferCSN/man/calculate.gene.rank.Rd | 11 inferCSN-1.0.5/inferCSN/man/check.parameters.Rd | 29 inferCSN-1.0.5/inferCSN/man/figures/logo.svg | 1126 ++++++---------- inferCSN-1.0.5/inferCSN/man/filter_sort_matrix.Rd | 6 inferCSN-1.0.5/inferCSN/man/inferCSN.Rd | 60 inferCSN-1.0.5/inferCSN/man/model.fit.Rd | 16 inferCSN-1.0.5/inferCSN/man/network.heatmap.Rd | 24 inferCSN-1.0.5/inferCSN/man/network_format.Rd |only inferCSN-1.0.5/inferCSN/man/network_sift.Rd |only inferCSN-1.0.5/inferCSN/man/parallelize_fun.Rd |only inferCSN-1.0.5/inferCSN/man/plot_contrast_networks.Rd |only inferCSN-1.0.5/inferCSN/man/plot_dynamic_networks.Rd |only inferCSN-1.0.5/inferCSN/man/plot_scatter.Rd |only inferCSN-1.0.5/inferCSN/man/plot_static_networks.Rd |only inferCSN-1.0.5/inferCSN/man/prepare.performance.data.Rd | 4 inferCSN-1.0.5/inferCSN/man/r_square.Rd |only inferCSN-1.0.5/inferCSN/man/rse.Rd |only inferCSN-1.0.5/inferCSN/man/single.network.Rd | 28 inferCSN-1.0.5/inferCSN/man/sparse.regression.Rd | 30 inferCSN-1.0.5/inferCSN/man/sse.Rd |only inferCSN-1.0.5/inferCSN/man/table.to.matrix.Rd | 13 inferCSN-1.0.5/inferCSN/src/RcppExports.cpp | 16 inferCSN-1.0.5/inferCSN/src/asMatrix.cpp |only 48 files changed, 1402 insertions(+), 1184 deletions(-)
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Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available
methods include generalized and classical Loewe formulations as well as Highest
Single Agent methodology. Response surfaces can be plotted in an interactive
3-D plot and formal statistical tests for presence of synergistic effects are
available. Implemented methods and tests are described in the article
"BIGL: Biochemically Intuitive Generalized Loewe null model for prediction
of the expected combined effect compatible with partial agonism and antagonism"
by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas,
Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017)
<doi:10.1038/s41598-017-18068-5>.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas, Stijn Hawinkel, Javier Franco Perez, Kathy Mutambanengwe
Maintainer: Kathy Mutambanengwe <kathy.mutambanengwe@openanalytics.eu>
Diff between BIGL versions 1.9.1 dated 2024-05-22 and 1.9.2 dated 2024-06-26
DESCRIPTION | 8 MD5 | 20 +- NEWS.md | 5 R/ResponseSurface-methods.R | 5 R/confInt-functions.R | 2 R/effectSize-functions.R | 5 inst/doc/analysis.R | 2 inst/doc/analysis.Rmd | 2 inst/doc/analysis.html | 397 +++++++++++++++++++++----------------------- inst/doc/methodology.html | 4 vignettes/analysis.Rmd | 2 11 files changed, 230 insertions(+), 222 deletions(-)
Title: Download Mexico City Pollution, Wind, and Temperature Data
Description: Tools for downloading hourly averages, daily maximums and
minimums from each of the pollution, wind, and temperature measuring
stations or geographic zones in the Mexico City metro area. The
package also includes the locations of each of the stations and zones.
See <http://aire.cdmx.gob.mx/> for more information.
Author: Diego Valle-Jones [aut, cre]
Maintainer: Diego Valle-Jones <diego@diegovalle.net>
Diff between aire.zmvm versions 0.9.0 dated 2024-02-12 and 1.0.0 dated 2024-06-26
DESCRIPTION | 6 +- MD5 | 64 +++++++++++++-------------- NEWS.md | 8 +++ R/convert_to_imeca.R | 2 R/convert_to_index.R | 2 R/download_archives.R | 22 ++++----- R/get_latest_imeca.R | 6 +- R/get_station_data.R | 14 ++--- R/get_station_imeca.R | 11 ++-- R/get_zone_imeca.R | 18 +++---- R/stations.R | 2 R/zones.R | 4 - man/convert_to_imeca.Rd | 2 man/convert_to_index.Rd | 2 man/download_24hr_average.Rd | 4 - man/download_deposition.Rd | 4 - man/download_lead.Rd | 4 - man/download_meteorological.Rd | 2 man/download_pollution.Rd | 2 man/download_pressure.Rd | 2 man/download_radiation.Rd | 4 - man/get_latest_imeca.Rd | 4 - man/get_station_data.Rd | 8 +-- man/get_station_imeca.Rd | 4 - man/get_station_month_data.Rd | 2 man/get_zone_imeca.Rd | 8 +-- man/stations.Rd | 2 man/zones.Rd | 4 - tests/testthat/test_get_latest.R | 1 tests/testthat/test_get_station_data.R | 3 - tests/testthat/test_get_station_imeca.R | 2 tests/testthat/test_get_station_month_data.R | 5 ++ tests/testthat/test_get_zone_imeca.R | 9 +++ 33 files changed, 131 insertions(+), 106 deletions(-)
Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for (1) data management (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and cluster scores, reading and writing Excel and SPSS files), (2) descriptive statistics (e.g., frequency table, cross tabulation, effect size measures), (3) missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), (4) multilevel data (e.g., multilevel descriptive statistics, within-group and between-group correlation matrix, multilevel confirmatory factor analysis, level-specific fit indices, cross-level measurement equivalence evaluation, multilevel composite reliability, and multilevel R-squared measures), (5) item analysis (e.g., confirmatory factor analysis, coefficient alpha and omega, between-group and longitudinal measurement equivalence evaluation), and (6) statistical analysis (e.g., confidence intervals, collinearity and residual [...truncated...]
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.6.3 dated 2024-05-14 and 0.6.4 dated 2024-06-26
misty-0.6.3/misty/R/run.mplus.R |only misty-0.6.3/misty/man/run.mplus.Rd |only misty-0.6.4/misty/DESCRIPTION | 8 misty-0.6.4/misty/MD5 | 150 +++---- misty-0.6.4/misty/NAMESPACE | 8 misty-0.6.4/misty/NEWS.md | 34 + misty-0.6.4/misty/R/aov.b.R | 8 misty-0.6.4/misty/R/aov.w.R | 8 misty-0.6.4/misty/R/check.collin.R | 2 misty-0.6.4/misty/R/chr.grep.R |only misty-0.6.4/misty/R/chr.gsub.R | 28 - misty-0.6.4/misty/R/chr.omit.R | 2 misty-0.6.4/misty/R/chr.trim.R | 2 misty-0.6.4/misty/R/ci.mean.R | 2 misty-0.6.4/misty/R/ci.mean.diff.R | 2 misty-0.6.4/misty/R/ci.mean.w.R | 2 misty-0.6.4/misty/R/ci.prop.R | 2 misty-0.6.4/misty/R/ci.prop.diff.R | 2 misty-0.6.4/misty/R/ci.var.R | 2 misty-0.6.4/misty/R/cohens.d.R | 2 misty-0.6.4/misty/R/cor.matrix.R | 2 misty-0.6.4/misty/R/crosstab.R | 2 misty-0.6.4/misty/R/descript.R | 2 misty-0.6.4/misty/R/dominance.R | 2 misty-0.6.4/misty/R/dominance.manual.R | 2 misty-0.6.4/misty/R/effsize.R | 2 misty-0.6.4/misty/R/freq.R | 2 misty-0.6.4/misty/R/indirect.R | 2 misty-0.6.4/misty/R/item.alpha.R | 2 misty-0.6.4/misty/R/item.cfa.R | 2 misty-0.6.4/misty/R/item.invar.R | 2 misty-0.6.4/misty/R/item.omega.R | 2 misty-0.6.4/misty/R/mplus.R |only misty-0.6.4/misty/R/mplus.lca.R | 26 - misty-0.6.4/misty/R/mplus.print.R |only misty-0.6.4/misty/R/mplus.run.R |only misty-0.6.4/misty/R/mplus.update.R |only misty-0.6.4/misty/R/multilevel.cfa.R | 2 misty-0.6.4/misty/R/multilevel.cor.R | 2 misty-0.6.4/misty/R/multilevel.descript.R | 2 misty-0.6.4/misty/R/multilevel.fit.R | 2 misty-0.6.4/misty/R/multilevel.indirect.R | 2 misty-0.6.4/misty/R/multilevel.invar.R | 2 misty-0.6.4/misty/R/multilevel.omega.R | 2 misty-0.6.4/misty/R/multilevel.r2.R | 2 misty-0.6.4/misty/R/multilevel.r2.manual.R | 2 misty-0.6.4/misty/R/na.auxiliary.R | 2 misty-0.6.4/misty/R/na.coverage.R | 2 misty-0.6.4/misty/R/na.descript.R | 2 misty-0.6.4/misty/R/na.pattern.R | 2 misty-0.6.4/misty/R/na.test.R | 2 misty-0.6.4/misty/R/print.misty.object.R | 20 misty-0.6.4/misty/R/read.sav.R | 2 misty-0.6.4/misty/R/read.xlsx.R | 2 misty-0.6.4/misty/R/result.lca.R | 4 misty-0.6.4/misty/R/robust.coef.R | 2 misty-0.6.4/misty/R/size.cor.R | 2 misty-0.6.4/misty/R/size.mean.R | 2 misty-0.6.4/misty/R/size.prop.R | 2 misty-0.6.4/misty/R/std.coef.R | 2 misty-0.6.4/misty/R/test.levene.R | 2 misty-0.6.4/misty/R/test.t.R | 2 misty-0.6.4/misty/R/test.welch.R | 10 misty-0.6.4/misty/R/test.z.R | 2 misty-0.6.4/misty/R/utils.R | 592 ++++++++++++++++------------- misty-0.6.4/misty/R/write.dta.R | 2 misty-0.6.4/misty/R/write.mplus.R | 134 +++--- misty-0.6.4/misty/man/aov.b.Rd | 4 misty-0.6.4/misty/man/aov.w.Rd | 4 misty-0.6.4/misty/man/chr.grep.Rd |only misty-0.6.4/misty/man/chr.gsub.Rd | 24 - misty-0.6.4/misty/man/chr.omit.Rd | 2 misty-0.6.4/misty/man/chr.trim.Rd | 2 misty-0.6.4/misty/man/mplus.Rd |only misty-0.6.4/misty/man/mplus.lca.Rd | 8 misty-0.6.4/misty/man/mplus.print.Rd |only misty-0.6.4/misty/man/mplus.run.Rd |only misty-0.6.4/misty/man/mplus.update.Rd |only misty-0.6.4/misty/man/result.lca.Rd | 2 misty-0.6.4/misty/man/test.welch.Rd | 2 misty-0.6.4/misty/man/write.dta.Rd | 2 misty-0.6.4/misty/man/write.mplus.Rd | 16 82 files changed, 650 insertions(+), 540 deletions(-)
Title: Visualise and Calculate Life History Parameters for Fisheries
Science using 'ggplot2'
Description: Contains functions to create life history parameter plots from raw data.
The plots are created using 'ggplot2', and calculations done using the 'tidyverse'
collection of packages. The package contains references to FishBase
(Froese R., Pauly D., 2023) <https://www.fishbase.se/>.
Author: Mikko Vihtakari [aut, cre]
Maintainer: Mikko Vihtakari <mikko.vihtakari@hi.no>
Diff between ggFishPlots versions 0.2.2 dated 2023-03-22 and 0.3.0 dated 2024-06-26
DESCRIPTION | 16 - MD5 | 45 ++- NAMESPACE | 3 R/plot_catchcurve.R |only R/plot_lw.R | 375 ++++++++++++++++++++++++------ R/plot_maturity.R | 25 +- R/zzz.R | 2 man/figures/README-catchcurvesep-1.png |only man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |only man/figures/README-unnamed-chunk-14-1.png |only man/figures/README-unnamed-chunk-15-1.png |only man/figures/README-unnamed-chunk-16-1.png |only man/figures/README-unnamed-chunk-17-1.png |only man/figures/README-unnamed-chunk-18-1.png |only man/figures/README-unnamed-chunk-19-1.png |only man/figures/README-unnamed-chunk-20-1.png |only man/figures/README-unnamed-chunk-21-1.png |only man/figures/README-unnamed-chunk-22-1.png |only man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/plot_catchcurve.Rd |only man/plot_growth.Rd | 4 man/plot_lw.Rd | 47 ++- man/plot_maturity.Rd | 4 30 files changed, 398 insertions(+), 123 deletions(-)
Title: Differential Expression Enrichment Tool
Description: Abstract of Manuscript. Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share sim [...truncated...]
Author: Dustin Sokolowski [aut, cre],
Jedid Ahn [aut],
Lauren Erdman [aut],
Kai Ellis [aut],
Huayun Hou [aut],
Anna Goldenberg [aut],
Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Diff between DEET versions 1.0.11 dated 2023-08-17 and 1.0.12 dated 2024-06-26
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/DEET_data_download.R | 6 +++--- inst/doc/DEET_vignette.Rmd | 10 +++++----- inst/doc/DEET_vignette.html | 16 ++++++++-------- vignettes/DEET_vignette.Rmd | 10 +++++----- 6 files changed, 29 insertions(+), 29 deletions(-)
Title: Interface to OGC Web-Services (OWS)
Description: Provides an Interface to Web-Services defined as standards by the Open Geospatial Consortium (OGC), including Web Feature Service
(WFS) for vector data, Web Coverage Service (WCS), Catalogue Service (CSW) for ISO/OGC metadata, Web Processing Service (WPS) for data processes,
and associated standards such as the common web-service specification (OWS) and OGC Filter Encoding. Partial support is provided for the Web Map
Service (WMS). The purpose is to add support for additional OGC service standards such as Web Coverage Processing Service (WCPS), the Sensor
Observation Service (SOS), or even new standard services emerging such OGC API or SensorThings.
Author: Emmanuel Blondel [aut, cre] ,
Alexandre Bennici [ctb] ,
Norbert Billet [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between ows4R versions 0.3-6 dated 2023-09-01 and 0.4 dated 2024-06-26
DESCRIPTION | 12 MD5 | 358 +++++++++++++------------- NAMESPACE | 2 NEWS.md | 26 + R/CASClient.R | 4 R/CSWCapabilities.R | 4 R/CSWClient.R | 41 ++ R/CSWConstraint.R | 4 R/CSWDescribeRecord.R | 4 R/CSWGetRecordById.R | 4 R/CSWGetRecords.R | 4 R/CSWHarvest.R | 4 R/CSWQuery.R | 4 R/CSWRecordProperty.R | 4 R/CSWTransaction.R | 4 R/OGCAbstractObject.R | 102 +++++++ R/OGCExpression.R | 70 ++--- R/OGCFilter.R | 4 R/OWSBoundingBox.R | 8 R/OWSCapabilities.R | 18 - R/OWSClient.R | 7 R/OWSCodeType.R | 6 R/OWSException.R |only R/OWSGetCapabilities.R | 4 R/OWSHttpRequest.R | 79 +++-- R/OWSNamespace.R | 4 R/OWSOperation.R | 6 R/OWSOperationsMetadata.R | 6 R/OWSRequest.R | 6 R/OWSServiceIdentification.R | 6 R/OWSServiceProvider.R | 8 R/OWSUtils.R | 2 R/OWSWGS84BoundingBox.R | 6 R/WCSCapabilities.R | 4 R/WCSClient.R | 4 R/WCSCoverage.R | 6 R/WCSCoverageDescription.R | 6 R/WCSCoverageDomain.R | 6 R/WCSCoverageSpatialDomain.R | 10 R/WCSCoverageSummary.R | 40 +- R/WCSCoverageTemporalDomain.R | 8 R/WCSDescribeCoverage.R | 4 R/WCSGSElevationDomain.R | 6 R/WCSGSTimeDomain.R | 6 R/WCSGetCoverage.R | 12 R/WCSGridCRS.R | 6 R/WFSCapabilities.R | 4 R/WFSClient.R | 4 R/WFSDescribeFeatureType.R | 4 R/WFSFeatureType.R | 42 ++- R/WFSFeatureTypeElement.R | 19 - R/WFSGetFeature.R | 6 R/WMSCapabilities.R | 4 R/WMSClient.R | 4 R/WMSGetFeatureInfo.R | 4 R/WMSLayer.R | 13 R/WPSBoundingBoxData.R | 6 R/WPSCapabilities.R | 4 R/WPSClient.R | 4 R/WPSComplexData.R | 8 R/WPSComplexInputDescription.R | 6 R/WPSComplexOutputDescription.R | 6 R/WPSDescribeProcess.R | 4 R/WPSDescriptionParameter.R | 6 R/WPSException.R | 8 R/WPSExecute.R | 4 R/WPSExecuteResponse.R | 8 R/WPSFormat.R | 6 R/WPSInput.R | 6 R/WPSInputDescription.R | 6 R/WPSLiteralData.R | 8 R/WPSLiteralInputDescription.R | 6 R/WPSLiteralOutputDescription.R | 6 R/WPSOutput.R | 8 R/WPSOutputDescription.R | 6 R/WPSParameter.R | 6 R/WPSProcess.R | 18 + R/WPSProcessDescription.R | 6 R/WPSResponseDocument.R | 6 R/WPSStatus.R | 8 R/ows4R.R | 3 README.md | 2 build/vignette.rds |binary inst/doc/csw.html | 184 ++++++++----- inst/doc/wcs.Rmd | 2 inst/doc/wcs.html | 180 +++++++------ man/And.Rd | 5 man/BBOX.Rd | 7 man/BinaryComparisonOpType.Rd | 5 man/BinaryLogicOpType.Rd | 5 man/CASClient.Rd | 4 man/CSWCapabilities.Rd | 5 man/CSWClient.Rd | 5 man/CSWConstraint.Rd | 5 man/CSWDescribeRecord.Rd | 6 man/CSWGetRecordById.Rd | 6 man/CSWGetRecords.Rd | 6 man/CSWHarvest.Rd | 6 man/CSWQuery.Rd | 5 man/CSWRecordProperty.Rd | 5 man/CSWTransaction.Rd | 6 man/Not.Rd | 5 man/OGCAbstractObject.Rd | 28 +- man/OGCExpression.Rd | 5 man/OGCFilter.Rd | 5 man/OWSBoundingBox.Rd | 9 man/OWSCapabilities.Rd | 5 man/OWSClient.Rd | 5 man/OWSCodeType.Rd | 7 man/OWSException.Rd |only man/OWSGetCapabilities.Rd | 6 man/OWSHttpRequest.Rd | 22 + man/OWSNamespace.Rd | 4 man/OWSOperation.Rd | 6 man/OWSOperationsMetadata.Rd | 6 man/OWSRequest.Rd | 7 man/OWSServiceIdentification.Rd | 6 man/OWSServiceProvider.Rd | 8 man/OWSUtils.Rd | 2 man/OWSWGS84BoundingBox.Rd | 7 man/Or.Rd | 5 man/PropertyIsBetween.Rd | 5 man/PropertyIsEqualTo.Rd | 5 man/PropertyIsGreaterThan.Rd | 5 man/PropertyIsGreaterThanOrEqualTo.Rd | 5 man/PropertyIsLessThan.Rd | 5 man/PropertyIsLessThanOrEqualTo.Rd | 5 man/PropertyIsLike.Rd | 5 man/PropertyIsNotEqualTo.Rd | 5 man/PropertyIsNull.Rd | 5 man/UnaryLogicOpType.Rd | 5 man/WCSCapabilities.Rd | 5 man/WCSClient.Rd | 5 man/WCSCoverage.Rd | 7 man/WCSCoverageDescription.Rd | 6 man/WCSCoverageDomain.Rd | 7 man/WCSCoverageSpatialDomain.Rd | 11 man/WCSCoverageSummary.Rd | 7 man/WCSCoverageTemporalDomain.Rd | 9 man/WCSDescribeCoverage.Rd | 6 man/WCSGSElevationDomain.Rd | 6 man/WCSGSTimeDomain.Rd | 6 man/WCSGetCoverage.Rd | 6 man/WCSGridCRS.Rd | 7 man/WFSCapabilities.Rd | 5 man/WFSClient.Rd | 5 man/WFSDescribeFeatureType.Rd | 6 man/WFSFeatureType.Rd | 10 man/WFSFeatureTypeElement.Rd | 10 man/WFSGetFeature.Rd | 6 man/WMSCapabilities.Rd | 5 man/WMSClient.Rd | 5 man/WMSGetFeatureInfo.Rd | 6 man/WMSLayer.Rd | 7 man/WPSBoundingBoxData.Rd | 7 man/WPSCapabilities.Rd | 5 man/WPSClient.Rd | 5 man/WPSComplexData.Rd | 9 man/WPSComplexInputDescription.Rd | 7 man/WPSComplexOutputDescription.Rd | 7 man/WPSDescribeProcess.Rd | 6 man/WPSDescriptionParameter.Rd | 7 man/WPSException.Rd | 9 man/WPSExecute.Rd | 6 man/WPSExecuteResponse.Rd | 9 man/WPSFormat.Rd | 7 man/WPSInput.Rd | 7 man/WPSInputDescription.Rd | 7 man/WPSLiteralData.Rd | 9 man/WPSLiteralInputDescription.Rd | 7 man/WPSLiteralOutputDescription.Rd | 7 man/WPSOutput.Rd | 9 man/WPSOutputDescription.Rd | 7 man/WPSParameter.Rd | 7 man/WPSProcess.Rd | 7 man/WPSProcessDescription.Rd | 7 man/WPSResponseDocument.Rd | 7 man/WPSStatus.Rd | 9 man/ows4R.Rd | 10 tests/testthat/test_WCSClient_v2_0_with_CAS.R | 2 vignettes/wcs.Rmd | 2 181 files changed, 1324 insertions(+), 870 deletions(-)
Title: Create Custom 'Bootstrap' Themes to Use in 'Shiny'
Description: Customize 'Bootstrap' and 'Bootswatch' themes, like colors, fonts, grid layout,
to use in 'Shiny' applications, 'rmarkdown' documents and 'flexdashboard'.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
Thomas Park [ctb, cph] ,
Mark Otto [ctb] ,
Jacob Thornton [ctb] ,
Bootstrap contributors [ctb] ,
Twitter, Inc [cph] ,
onkbear [ctb, cph] ,
Colorlib [ctb, cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between fresh versions 0.2.0 dated 2020-05-29 and 0.2.1 dated 2024-06-26
fresh-0.2.0/fresh/inst/assets/AdminLTE-3.0.4 |only fresh-0.2.0/fresh/inst/assets/bootstrap-4.3.1 |only fresh-0.2.0/fresh/man/bs_vars.Rd |only fresh-0.2.0/fresh/man/bs_vars_alert.Rd |only fresh-0.2.0/fresh/man/bs_vars_badge.Rd |only fresh-0.2.0/fresh/man/bs_vars_button.Rd |only fresh-0.2.0/fresh/man/bs_vars_color.Rd |only fresh-0.2.0/fresh/man/bs_vars_component.Rd |only fresh-0.2.0/fresh/man/bs_vars_dropdown.Rd |only fresh-0.2.0/fresh/man/bs_vars_font.Rd |only fresh-0.2.0/fresh/man/bs_vars_global.Rd |only fresh-0.2.0/fresh/man/bs_vars_input.Rd |only fresh-0.2.0/fresh/man/bs_vars_modal.Rd |only fresh-0.2.0/fresh/man/bs_vars_nav.Rd |only fresh-0.2.0/fresh/man/bs_vars_navbar.Rd |only fresh-0.2.0/fresh/man/bs_vars_panel.Rd |only fresh-0.2.0/fresh/man/bs_vars_pills.Rd |only fresh-0.2.0/fresh/man/bs_vars_progress.Rd |only fresh-0.2.0/fresh/man/bs_vars_state.Rd |only fresh-0.2.0/fresh/man/bs_vars_table.Rd |only fresh-0.2.0/fresh/man/bs_vars_tabs.Rd |only fresh-0.2.0/fresh/man/bs_vars_wells.Rd |only fresh-0.2.1/fresh/DESCRIPTION | 15 fresh-0.2.1/fresh/MD5 | 1026 ++--- fresh-0.2.1/fresh/NAMESPACE | 126 fresh-0.2.1/fresh/NEWS.md | 32 fresh-0.2.1/fresh/R/bs4Dash_theme.R |only fresh-0.2.1/fresh/R/bs_theme_nord.R |only fresh-0.2.1/fresh/R/create_pretty.R | 192 - fresh-0.2.1/fresh/R/create_theme.R | 430 +- fresh-0.2.1/fresh/R/fonts.R | 162 fresh-0.2.1/fresh/R/fresh-package.R | 15 fresh-0.2.1/fresh/R/search-vars.R | 360 +- fresh-0.2.1/fresh/R/use_theme.R | 145 fresh-0.2.1/fresh/R/use_vars_template.R | 206 - fresh-0.2.1/fresh/R/utils.R | 110 fresh-0.2.1/fresh/R/vars-adminlte.R | 592 +-- fresh-0.2.1/fresh/R/vars-bootstrap.R | 1558 ++++---- fresh-0.2.1/fresh/R/vars-bs4dash.R | 640 +-- fresh-0.2.1/fresh/README.md | 413 +- fresh-0.2.1/fresh/build/fresh.pdf |binary fresh-0.2.1/fresh/build/stage23.rdb |only fresh-0.2.1/fresh/build/vignette.rds |binary fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/LICENSE | 42 fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/README.md | 56 fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/bootstrap-sass/_bootstrap-compass.scss | 18 fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/bootstrap-sass/_bootstrap-mincer.scss | 38 fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/bootstrap-sass/_bootstrap-sprockets.scss | 18 fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/bootstrap-sass/_bootstrap.scss | 112 fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/bootstrap-sass/bootstrap/_alerts.scss | 146 fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/bootstrap-sass/bootstrap/_badges.scss | 136 fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/bootstrap-sass/bootstrap/_breadcrumbs.scss | 56 fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/bootstrap-sass/bootstrap/_button-groups.scss | 488 +- fresh-0.2.1/fresh/inst/assets/AdminLTE-2.4.10/bootstrap-sass/bootstrap/_buttons.scss | 336 - 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Title: Fast Implementation of the Diffusion Decision Model
Description: Provides the probability density function (PDF), cumulative
distribution function (CDF), the first-order and second-order partial
derivatives of the PDF, and a fitting function for the diffusion decision
model (DDM; e.g.,
Ratcliff & McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) with across-trial
variability in the drift rate. Because the PDF, its partial derivatives, and
the CDF of the DDM both contain an infinite sum, they need to be approximated.
'fddm' implements all published approximations
(Navarro & Fuss, 2009, <doi:10.1016/j.jmp.2009.02.003>;
Gondan, Blurton, & Kesselmeier, 2014, <doi:10.1016/j.jmp.2014.05.002>;
Blurton, Kesselmeier, & Gondan, 2017, <doi:10.1016/j.jmp.2016.11.003>;
Hartmann & Klauer, 2021, <doi:10.1016/j.jmp.2021.102550>) plus
new approximations. All approximations are implemented purely in 'C++'
providing faster speed than existing packages.
Author: Kendal B. Foster [aut],
Henrik Singmann [ctb, cre] ,
Achim Zeileis [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between fddm versions 0.5-2 dated 2022-09-09 and 1.0-1 dated 2024-06-26
fddm-0.5-2/fddm/NEWS |only fddm-0.5-2/fddm/src/dfddm_helper_functions |only fddm-0.5-2/fddm/src/parameter_checks.cpp |only fddm-0.5-2/fddm/src/parameter_checks.h |only fddm-0.5-2/fddm/src/pfddm_helper_functions |only fddm-1.0-1/fddm/DESCRIPTION | 28 fddm-1.0-1/fddm/MD5 | 138 fddm-1.0-1/fddm/NAMESPACE | 39 fddm-1.0-1/fddm/NEWS.md |only fddm-1.0-1/fddm/R/RcppExports.R | 1916 +++++++- fddm-1.0-1/fddm/R/ddm.R |only fddm-1.0-1/fddm/R/ddm_fit.R |only fddm-1.0-1/fddm/R/ddm_methods.R |only fddm-1.0-1/fddm/R/ezddm.R |only fddm-1.0-1/fddm/R/med_dec-data.R | 6 fddm-1.0-1/fddm/R/zzz.R | 7 fddm-1.0-1/fddm/README.md | 126 fddm-1.0-1/fddm/build/vignette.rds |binary fddm-1.0-1/fddm/data/med_dec.rda |binary fddm-1.0-1/fddm/inst/doc/benchmark.R | 338 - fddm-1.0-1/fddm/inst/doc/benchmark.Rmd | 391 - fddm-1.0-1/fddm/inst/doc/benchmark.html | 2393 +++++----- fddm-1.0-1/fddm/inst/doc/example.R | 66 fddm-1.0-1/fddm/inst/doc/example.Rmd | 181 fddm-1.0-1/fddm/inst/doc/example.html | 827 ++- fddm-1.0-1/fddm/inst/doc/math.Rmd | 64 fddm-1.0-1/fddm/inst/doc/math.html | 260 - fddm-1.0-1/fddm/inst/doc/pfddm.R | 4 fddm-1.0-1/fddm/inst/doc/pfddm.Rmd | 48 fddm-1.0-1/fddm/inst/doc/pfddm.html | 694 +- fddm-1.0-1/fddm/inst/doc/validity.R | 612 +- fddm-1.0-1/fddm/inst/doc/validity.Rmd | 654 +- fddm-1.0-1/fddm/inst/doc/validity.html | 1510 +++--- fddm-1.0-1/fddm/man/da2_dfddm.Rd |only fddm-1.0-1/fddm/man/da_dfddm.Rd |only fddm-1.0-1/fddm/man/ddm-methods.Rd |only fddm-1.0-1/fddm/man/ddm.Rd |only fddm-1.0-1/fddm/man/dfddm.Rd | 80 fddm-1.0-1/fddm/man/dsv2_dfddm.Rd |only fddm-1.0-1/fddm/man/dsv_dfddm.Rd |only fddm-1.0-1/fddm/man/dt02_dfddm.Rd |only fddm-1.0-1/fddm/man/dt0_dfddm.Rd |only fddm-1.0-1/fddm/man/dt2_dfddm.Rd |only fddm-1.0-1/fddm/man/dt_dfddm.Rd |only fddm-1.0-1/fddm/man/dv2_dfddm.Rd |only fddm-1.0-1/fddm/man/dv_dfddm.Rd |only fddm-1.0-1/fddm/man/dw2_dfddm.Rd |only fddm-1.0-1/fddm/man/dw_dfddm.Rd |only fddm-1.0-1/fddm/man/med_dec.Rd | 26 fddm-1.0-1/fddm/man/pfddm.Rd | 70 fddm-1.0-1/fddm/src/Makevars |only fddm-1.0-1/fddm/src/RcppExports.cpp | 272 + fddm-1.0-1/fddm/src/d-2_dfddm.cpp |only fddm-1.0-1/fddm/src/d-_dfddm.cpp |only fddm-1.0-1/fddm/src/dfddm.cpp | 39 fddm-1.0-1/fddm/src/fddm_fit.h |only fddm-1.0-1/fddm/src/fddm_fit_export.cpp |only fddm-1.0-1/fddm/src/helper_functions |only fddm-1.0-1/fddm/src/pfddm.cpp | 39 fddm-1.0-1/fddm/tests/testthat/test-ddm-fitting.R |only fddm-1.0-1/fddm/tests/testthat/test-density.R | 626 +- fddm-1.0-1/fddm/tests/testthat/test-distribution.R | 173 fddm-1.0-1/fddm/tests/testthat/test-parameter-checks.R | 18 fddm-1.0-1/fddm/tests/testthat/test-partial-derivatives.R |only fddm-1.0-1/fddm/tests/testthat/test-second-order-partial-derivatives.R |only fddm-1.0-1/fddm/tests/testthat/test-validity_vignette_fits.R | 4 fddm-1.0-1/fddm/vignettes/benchmark.Rmd | 391 - fddm-1.0-1/fddm/vignettes/example.Rmd | 181 fddm-1.0-1/fddm/vignettes/math.Rmd | 64 fddm-1.0-1/fddm/vignettes/pfddm.Rmd | 48 fddm-1.0-1/fddm/vignettes/stile.css | 8 fddm-1.0-1/fddm/vignettes/validity.Rmd | 654 +- 72 files changed, 7879 insertions(+), 5116 deletions(-)
Title: Antares Visualizations
Description: Visualize results generated by Antares, a powerful open source software
developed by RTE to simulate and study electric power systems
(more information about 'Antares' here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>).
This package provides functions that create interactive charts to help
'Antares' users visually explore the results of their simulations.
Author: Tatiana Vargas [aut, cre],
Jalal-Edine Zawam [aut],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Paul Plessiez [aut],
Baptiste Seguinot [ctb],
RTE [cph]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between antaresViz versions 0.18.0 dated 2023-09-25 and 0.18.1 dated 2024-06-26
antaresViz-0.18.0/antaresViz/tests/testthat/test-zzCleanTests.R |only antaresViz-0.18.1/antaresViz/DESCRIPTION | 12 antaresViz-0.18.1/antaresViz/MD5 | 83 antaresViz-0.18.1/antaresViz/NAMESPACE | 3 antaresViz-0.18.1/antaresViz/NEWS.md | 3 antaresViz-0.18.1/antaresViz/R/graph_utils.R | 65 antaresViz-0.18.1/antaresViz/R/h5_utils.R | 212 - antaresViz-0.18.1/antaresViz/R/h5_utils_plot.R | 32 antaresViz-0.18.1/antaresViz/R/map.R | 204 - antaresViz-0.18.1/antaresViz/R/map_layout.R | 20 antaresViz-0.18.1/antaresViz/R/map_options.R | 2 antaresViz-0.18.1/antaresViz/R/mod_XY.R | 10 antaresViz-0.18.1/antaresViz/R/mod_rpart.R | 2 antaresViz-0.18.1/antaresViz/R/plot.R | 51 antaresViz-0.18.1/antaresViz/R/plot_utils.R | 2 antaresViz-0.18.1/antaresViz/R/savePlotAsPng.R | 2 antaresViz-0.18.1/antaresViz/R/stack_exchanges.R | 44 antaresViz-0.18.1/antaresViz/R/stack_map.R | 2 antaresViz-0.18.1/antaresViz/R/stack_prod.R | 62 antaresViz-0.18.1/antaresViz/R/zzz.R | 115 antaresViz-0.18.1/antaresViz/build/vignette.rds |binary antaresViz-0.18.1/antaresViz/inst/doc/antaresViz.R | 6 antaresViz-0.18.1/antaresViz/inst/doc/antaresViz.html | 678 +++-- antaresViz-0.18.1/antaresViz/man/exchangesStack.Rd | 24 antaresViz-0.18.1/antaresViz/man/mapLayout.Rd | 10 antaresViz-0.18.1/antaresViz/man/modRpart.Rd | 2 antaresViz-0.18.1/antaresViz/man/plot.mapLayout.Rd | 6 antaresViz-0.18.1/antaresViz/man/plotMap.Rd | 22 antaresViz-0.18.1/antaresViz/man/plotMapLayout.Rd | 4 antaresViz-0.18.1/antaresViz/man/plotMapOptions.Rd | 2 antaresViz-0.18.1/antaresViz/man/prodStack.Rd | 26 antaresViz-0.18.1/antaresViz/man/savePlotAsPng.Rd | 2 antaresViz-0.18.1/antaresViz/man/stackMap.Rd | 2 antaresViz-0.18.1/antaresViz/man/tsLegend.Rd | 2 antaresViz-0.18.1/antaresViz/man/tsPlot.Rd | 48 antaresViz-0.18.1/antaresViz/tests/testthat.R | 4 antaresViz-0.18.1/antaresViz/tests/testthat/test-exchangesStack.R | 1258 +++++----- antaresViz-0.18.1/antaresViz/tests/testthat/test-graphUtils.R | 38 antaresViz-0.18.1/antaresViz/tests/testthat/test-plotMap.R | 270 +- antaresViz-0.18.1/antaresViz/tests/testthat/test-plotThermalGroupCapacities.R | 20 antaresViz-0.18.1/antaresViz/tests/testthat/test-plotXY.R | 20 antaresViz-0.18.1/antaresViz/tests/testthat/test-prodStack.R | 660 ++--- antaresViz-0.18.1/antaresViz/tests/testthat/test-ts_plot.R | 510 ++-- 43 files changed, 2395 insertions(+), 2145 deletions(-)
Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata',
'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of
'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka',
and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Swetlana Herbrandt [ctb],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Michael N [...truncated...]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-86 dated 2023-11-26 and 0.8-87 dated 2024-06-26
ChangeLog | 20 +++++++ DESCRIPTION | 8 +- MD5 | 42 +++++++-------- inst/po/de/LC_MESSAGES/foreign.mo |binary inst/po/en@quot/LC_MESSAGES/R-foreign.mo |binary inst/po/en@quot/LC_MESSAGES/foreign.mo |binary inst/po/fr/LC_MESSAGES/foreign.mo |binary inst/po/it/LC_MESSAGES/foreign.mo |binary inst/po/pl/LC_MESSAGES/foreign.mo |binary po/R-foreign.pot | 7 +- po/de.po | 84 +++++++++++++++---------------- po/foreign.pot | 74 +++++++++++++-------------- po/fr.po | 84 +++++++++++++++---------------- po/it.po | 84 +++++++++++++++---------------- po/pl.po | 84 +++++++++++++++---------------- src/Rdbfwrite.c | 8 ++ src/SASxport.c | 4 - src/dbfopen.c | 4 + src/foreign.h | 2 src/pfm-read.c | 6 +- src/sfm-read.c | 7 +- src/stataread.c | 4 - 22 files changed, 277 insertions(+), 245 deletions(-)
Title: Signal Processing
Description: A set of signal processing functions originally written for 'Matlab' and 'Octave'.
Includes filter generation utilities, filtering functions,
resampling routines, and visualization of filter models. It also
includes interpolation functions.
Author: Uwe Ligges [aut, cre] ,
Tom Short [aut] ,
Paul Kienzle [aut] ,
Sarah Schnackenberg [ctb] ,
David Billinghurst [ctb],
Hans-Werner Borchers [ctb],
Andre Carezia [ctb],
Pascal Dupuis [ctb],
John W. Eaton [ctb],
E. Farhi [ctb],
Kai Habel [ctb],
Kurt Horn [...truncated...]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between signal versions 1.8-0 dated 2023-11-27 and 1.8-1 dated 2024-06-26
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- build/partial.rdb |binary src/dpchim.f | 7 +++++-- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Variable Selection under Ranked Sparsity Principles for
Interactions and Polynomials
Description: An implementation of ranked sparsity methods, including
penalized regression methods such as the sparsity-ranked lasso, its
non-convex alternatives, and elastic net, as well as the sparsity-ranked
Bayesian Information Criterion. As described in Peterson and
Cavanaugh (2022) <doi:10.1007/s10182-021-00431-7>, ranked
sparsity is a philosophy with methods primarily useful for
variable selection in the presence of prior informational
asymmetry, which occurs in the context of trying to perform variable
selection in the presence of interactions and/or polynomials. Ultimately,
this package attempts to facilitate dealing with cumbersome interactions
and polynomials while not avoiding them entirely. Typically, models
selected under ranked sparsity principles will also be more transparent,
having fewer falsely selected interactions and polynomials than other
methods.
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>
Diff between sparseR versions 0.2.3 dated 2023-12-06 and 0.3.0 dated 2024-06-26
DESCRIPTION | 10 MD5 | 34 NEWS.md | 8 R/custom_step_helpers.R | 7 R/plot.sparseR.R | 35 R/sparseR.R | 6 README.md | 78 - build/vignette.rds |binary inst/doc/sparseR.R | 6 inst/doc/sparseR.Rmd | 22 inst/doc/sparseR.html | 2135 +++++++++++++++++----------------- man/effect_plot.Rd | 4 man/figures |only man/sparseR-package.Rd | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test_sparseR.R | 8 tests/testthat/test_sparseR_methods.R | 65 - vignettes/sparseR.Rmd | 22 18 files changed, 1298 insertions(+), 1143 deletions(-)