Title: Create Consort Diagram
Description: To make it easy to create CONSORT diagrams for the transparent reporting of participant allocation in randomized, controlled clinical trials. This is done by creating a standardized disposition data, and using this data as the source for the creation a standard CONSORT diagram. Human effort by supplying text labels on the node can also be achieved.
Author: Alim Dayim [aut, cre]
Maintainer: Alim Dayim <ad938@cam.ac.uk>
Diff between consort versions 1.2.2 dated 2024-06-04 and 1.2.3 dated 2026-04-25
consort-1.2.2/consort/man/consort-package.Rd |only consort-1.2.3/consort/DESCRIPTION | 10 consort-1.2.3/consort/MD5 | 113 + consort-1.2.3/consort/NAMESPACE | 4 consort-1.2.3/consort/NEWS.md | 9 consort-1.2.3/consort/R/add_box.R | 14 consort-1.2.3/consort/R/add_label_box.R | 27 consort-1.2.3/consort/R/add_side_box.R | 10 consort-1.2.3/consort/R/add_split.R | 15 consort-1.2.3/consort/R/build_grid.R | 36 consort-1.2.3/consort/R/build_grviz.R | 49 consort-1.2.3/consort/R/connect_box.R | 102 + consort-1.2.3/consort/R/consort.R | 11 consort-1.2.3/consort/R/consort_plot.R | 16 consort-1.2.3/consort/R/defaults.R |only consort-1.2.3/consort/R/gen_text.R | 108 + consort-1.2.3/consort/R/grid_util.R | 424 +++---- consort-1.2.3/consort/R/grviz_util.R | 166 ++ consort-1.2.3/consort/R/markup.R |only consort-1.2.3/consort/R/textbox.R | 182 ++- consort-1.2.3/consort/R/utils.R | 3 consort-1.2.3/consort/README.md | 13 consort-1.2.3/consort/build/vignette.rds |binary consort-1.2.3/consort/inst/doc/consort_diagram.R | 97 + consort-1.2.3/consort/inst/doc/consort_diagram.Rmd | 100 + consort-1.2.3/consort/inst/doc/consort_diagram.html | 578 ++++++---- consort-1.2.3/consort/man/add_label_box.Rd | 5 consort-1.2.3/consort/man/build_grid.Rd | 2 consort-1.2.3/consort/man/connect_box.Rd | 26 consort-1.2.3/consort/man/consort.Rd |only consort-1.2.3/consort/man/consort_plot.Rd | 6 consort-1.2.3/consort/man/figures/README-diagram-1.png |binary consort-1.2.3/consort/man/gen_text.Rd | 18 consort-1.2.3/consort/man/set_consort_defaults.Rd |only consort-1.2.3/consort/man/textbox.Rd | 16 consort-1.2.3/consort/tests/testthat/Rplots.pdf |binary consort-1.2.3/consort/tests/testthat/_snaps/auto/auto-grviz.gv | 37 consort-1.2.3/consort/tests/testthat/_snaps/auto/auto-last-grviz.gv | 23 consort-1.2.3/consort/tests/testthat/_snaps/auto/auto-nolab-grviz.gv | 19 consort-1.2.3/consort/tests/testthat/_snaps/auto/autogen-last.png |binary consort-1.2.3/consort/tests/testthat/_snaps/auto/autogen-nolab.png |binary consort-1.2.3/consort/tests/testthat/_snaps/auto/autogen.png |binary consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/build-grviz-withopts.png |only consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/build-grviz.png |binary consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/empty-middle-grviz.gv | 23 consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/end-miss-grviz.gv | 25 consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/end-miss-grviz.png |binary consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/grviz-withopts.gv |only consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/grviz.gv | 37 consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/multi-miss-grviz.gv | 29 consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/multi-miss-grviz.png |binary consort-1.2.3/consort/tests/testthat/_snaps/build_grviz/split-comb-grviz.gv | 37 consort-1.2.3/consort/tests/testthat/_snaps/manually/manually-gen.png |binary consort-1.2.3/consort/tests/testthat/_snaps/multiple-split/multiple-split-nokick.gv | 63 - consort-1.2.3/consort/tests/testthat/_snaps/multiple-split/multiple-split-nokick.png |binary consort-1.2.3/consort/tests/testthat/_snaps/multiple-split/multiple-split.gv | 75 - consort-1.2.3/consort/tests/testthat/_snaps/multiple-split/multiple-split.png |binary consort-1.2.3/consort/tests/testthat/test-build_grviz.R | 33 consort-1.2.3/consort/tests/testthat/test-markup.R |only consort-1.2.3/consort/tests/testthat/test-textbox.R | 12 consort-1.2.3/consort/tests/testthat/test-utils.R |only consort-1.2.3/consort/vignettes/consort_diagram.Rmd | 100 + 62 files changed, 1778 insertions(+), 895 deletions(-)
Title: Two-/Three-Stage Designs for Phase 1&2 Clinical Trials
Description: Calculates Zhong's optimal two-/three-stage Phase II designs
for single-arm trials, generates target-toxicity decision tables for
two-/three-stage Phase I dose-finding, and supports dose-finding
simulations using custom decision tables. The Phase II design is based on
Zhong (2012) <doi:10.1016/j.cct.2012.07.006>.
Author: Wenchuan Guo [aut, cre],
Jianan Hui [aut],
Bob Zhong [aut]
Maintainer: Wenchuan Guo <wguo1017@gmail.com>
Diff between tsdf versions 1.1-8 dated 2020-05-09 and 1.1-9 dated 2026-04-25
DESCRIPTION | 30 - MD5 | 56 +- NAMESPACE | 30 - NEWS | 53 +- R/adj.two.R | 165 +++---- R/dec.sim.R | 310 ++++++++------ R/dec.table.R | 178 ++++---- R/internal.R | 1006 +++++++++++++++++++++++++--------------------- R/opt.design.R | 91 ++-- R/sl.sim.R | 96 ++-- R/utility.R | 576 +++++++++++++------------- README.md | 16 build/vignette.rds |binary inst/doc/my-vignette.R | 80 ++- inst/doc/my-vignette.Rmd | 350 +++++++++------- inst/doc/my-vignette.html | 593 +++++++++++++++------------ inst/extdata/decTable.csv | 24 - inst/extdata/testS.csv | 6 man/adj.two.Rd | 53 +- man/dec.sim.Rd | 79 ++- man/dec.table.Rd | 64 +- man/opt.design.Rd | 89 ++-- man/plot.dec.sim.Rd | 32 - man/plot.dec.table.Rd | 13 man/print.dec.table.Rd | 14 man/print.opt.design.Rd | 11 man/sl.sim.Rd | 46 +- man/summary.dec.sim.Rd | 22 - vignettes/my-vignette.Rmd | 350 +++++++++------- 29 files changed, 2475 insertions(+), 1958 deletions(-)
Title: Testing Pleiotropy in Multiparental Populations
Description: We implement an
adaptation of Jiang & Zeng's (1995) <doi:10.1093/genetics/140.3.1111> likelihood ratio test for testing
the null hypothesis of pleiotropy against the alternative hypothesis,
two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995)
and that in Tian et al. (2016) <doi:10.1534/genetics.115.183624> in
that our test accommodates multiparental populations.
Author: Frederick J Boehm [aut, cre]
Maintainer: Frederick J Boehm <frederick.boehm@gmail.com>
Diff between qtl2pleio versions 1.4.3 dated 2020-12-02 and 1.4.4 dated 2026-04-25
qtl2pleio-1.4.3/qtl2pleio/build |only qtl2pleio-1.4.3/qtl2pleio/inst/doc |only qtl2pleio-1.4.3/qtl2pleio/man/qtl2pleio.Rd |only qtl2pleio-1.4.3/qtl2pleio/vignettes |only qtl2pleio-1.4.4/qtl2pleio/DESCRIPTION | 17 +-- qtl2pleio-1.4.4/qtl2pleio/MD5 | 24 +--- qtl2pleio-1.4.4/qtl2pleio/NEWS.md | 25 ++++ qtl2pleio-1.4.4/qtl2pleio/R/qtl2pleio-package.r | 4 qtl2pleio-1.4.4/qtl2pleio/README.md | 54 ++++------ qtl2pleio-1.4.4/qtl2pleio/inst/CITATION | 21 ++- qtl2pleio-1.4.4/qtl2pleio/man/figures/README-1d-lod-plots-1.png |binary qtl2pleio-1.4.4/qtl2pleio/man/figures/README-profile-plot-1.png |binary qtl2pleio-1.4.4/qtl2pleio/man/qtl2pleio-package.Rd |only qtl2pleio-1.4.4/qtl2pleio/src/matrix.cpp | 2 14 files changed, 80 insertions(+), 67 deletions(-)
Title: Multi-Visit Closed Population Mark-Recapture Estimates
Description: Compute bootstrap confidence intervals for the adjusted Schnabel and Schumacher-Eschmeyer multi-visit mark-recapture estimators based on Dettloff (2023) <doi:10.1016/j.fishres.2023.106756>.
Author: Kyle Dettloff [aut, cre, cph]
Maintainer: Kyle Dettloff <kyle.dettloff@noaa.gov>
Diff between mRc versions 0.1.1 dated 2026-03-23 and 0.1.2 dated 2026-04-25
mRc-0.1.1/mRc/R/mrc_boot_CI.R |only mRc-0.1.2/mRc/DESCRIPTION | 8 +-- mRc-0.1.2/mRc/LICENSE | 4 - mRc-0.1.2/mRc/MD5 | 12 ++-- mRc-0.1.2/mRc/NEWS.md | 7 ++ mRc-0.1.2/mRc/R/closedCI.R |only mRc-0.1.2/mRc/build/partial.rdb |binary mRc-0.1.2/mRc/man/closedCI.Rd | 102 ++++++++++++++++++++-------------------- 8 files changed, 69 insertions(+), 64 deletions(-)
Title: Discriminant Adaptive Nearest Neighbor Classification
Description: Discriminant Adaptive Nearest Neighbor Classification is a
variation of k nearest neighbors where the shape of the neighborhood is
data driven. This package implements dann and sub_dann from
Hastie (1996) <https://web.stanford.edu/~hastie/Papers/dann_IEEE.pdf>.
Author: Greg McMahan [aut, cre]
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between dann versions 1.0.2 dated 2025-04-12 and 1.1.0 dated 2026-04-25
dann-1.0.2/dann/man/DANN_distance.Rd |only dann-1.0.2/dann/man/MODE.Rd |only dann-1.0.2/dann/man/class_proportions.Rd |only dann-1.0.2/dann/man/figures/README-Circle-2.png |only dann-1.0.2/dann/man/figures/README-Cluster-1.png |only dann-1.0.2/dann/man/figures/README-Cluster-2.png |only dann-1.0.2/dann/src/internal_helpers_C.cpp |only dann-1.1.0/dann/DESCRIPTION | 14 dann-1.1.0/dann/MD5 | 37 -- dann-1.1.0/dann/NEWS.md | 3 dann-1.1.0/dann/R/RcppExports.R | 13 dann-1.1.0/dann/R/dann.R | 105 +----- dann-1.1.0/dann/R/internal_helpers.R | 40 -- dann-1.1.0/dann/R/sub_dann.R | 11 dann-1.1.0/dann/README.md | 32 +- dann-1.1.0/dann/src/RcppExports.cpp | 35 -- dann-1.1.0/dann/src/internal_armadillo_helpers.cpp | 216 +++++++++++++- dann-1.1.0/dann/tests/testthat/test_A_dann.R | 12 dann-1.1.0/dann/tests/testthat/test_B_sub_dann.R | 12 dann-1.1.0/dann/tests/testthat/test_C_predict_dann.R | 84 ++--- dann-1.1.0/dann/tests/testthat/test_D_predict_sub_dann.R | 84 ++--- dann-1.1.0/dann/tests/testthat/test_E_graph_eigenvalues.R | 14 dann-1.1.0/dann/tests/testthat/test_F_print.R | 2 23 files changed, 398 insertions(+), 316 deletions(-)
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 1.1.4 dated 2026-03-02 and 1.1.5 dated 2026-04-25
DESCRIPTION | 6 MD5 | 161 +- NAMESPACE | 1 NEWS.md | 49 R/Studio_Classifier_Create.R | 2 R/Studio_DocumentationPage.R | 53 R/Studio_Error_Checks.R | 136 +- R/Studio_ExtendedTasks.R | 50 R/Studio_FeatureExtractor_Create.R | 2 R/Studio_ProgressModal.R | 80 - R/Studio_Tabs_Embed.R | 2 R/Studio_Tabs_Training.R | 2 R/Studio_TextEmbeddingModel_Create.R | 4 R/def_DocumentationDesc.R | 8 R/def_ParameterDefinitions.R | 64 - R/install_and_config.R | 115 + R/obj_AIFEBaseModel.R | 28 R/obj_BaseModelCore.R | 66 - R/obj_BaseModelMPNet.R | 24 R/obj_ClassifiersBasedOnTextEmbeddings.R | 24 R/obj_DataManager.R | 18 R/obj_FeatureExtractor.R | 30 R/obj_ModelsBasedOnTextEmbeddings.R | 41 R/obj_TEClassifierParallel.R | 2 R/obj_TEClassifierParallelPrototype.R | 2 R/obj_TEClassifierProtoNet.R | 9 R/obj_TEClassifierRegular.R | 7 R/obj_TEClassifierSequential.R | 2 R/obj_TEClassifierSequentialPrototype.R | 2 R/obj_TEClassifiersBasedOnProtoNet.R | 9 R/obj_TEClassifiersBasedOnRegular.R | 4 R/obj_TextEmbeddingModel.R | 52 R/obj_Tokenizer.R | 12 R/onLoad.R | 2 R/saving_and_loading.R | 2 R/utils_DataManager.R | 257 ++-- R/utils_Studio.R | 5 R/utils_general.R | 83 + R/utils_log.R | 7 R/utils_test_that.R | 13 inst/doc/aifeducation.html | 20 inst/python/DataCollatorForMPLM_PT.py | 33 inst/python/data_collator.py | 2 inst/python/py_log.py | 51 inst/python/pytorch_autoencoder.py | 325 +++-- inst/python/pytorch_cls_training_loops.py | 1176 +++++++++----------- inst/python/pytorch_layers.py | 40 inst/python/pytorch_layers_normalization.py | 10 inst/python/pytorch_loss_fct.py | 42 inst/python/pytorch_predict_batch.py | 91 - inst/python/pytorch_stack_layers.py | 4 inst/python/pytorch_text_embedding_model.py | 1 man/BaseModelCore.Rd | 4 man/BaseModelMPNet.Rd | 2 man/TEClassifierParallel.Rd | 4 man/TEClassifierParallelPrototype.Rd | 4 man/TEClassifierSequential.Rd | 4 man/TEClassifierSequentialPrototype.Rd | 4 man/TEClassifiersBasedOnProtoNet.Rd | 12 man/TEClassifiersBasedOnRegular.Rd | 10 man/TEFeatureExtractor.Rd | 10 man/TextEmbeddingModel.Rd | 2 man/WordPieceTokenizer.Rd | 2 man/build_layer_stack_documentation_for_vignette.Rd | 2 man/check_adjust_n_samples_on_CI.Rd | 5 man/create_synthetic_units_from_matrix.Rd | 8 man/get_recommended_py_versions.Rd | 11 man/get_synthetic_cases_from_matrix.Rd | 5 man/install_py_modules.Rd | 20 src/KNNOR.cpp | 64 - tests/testthat/test-00_03_doc_fcts.R |only tests/testthat/test-01_01_install_and_config.R | 23 tests/testthat/test-01_06_logging.R | 2 tests/testthat/test-01_07_DataCollator.R | 2 tests/testthat/test-02_06_BaseModels.R | 89 + tests/testthat/test-02_07_BaseModels_from_hf.R | 19 tests/testthat/test-03_03_EmbeddedText.R | 77 + tests/testthat/test-03_04_DataManager.R | 78 - tests/testthat/test-03_05_FeatureExtractor.R | 16 tests/testthat/test-03_06_TextEmbeddingModels.R | 3 tests/testthat/test-03_08_TEClassifiers_core.R | 89 + tests/testthat/test-03_09_TEClassifiersPrototype.R | 21 82 files changed, 2215 insertions(+), 1608 deletions(-)
Title: Complex Partial Least Squares Structural Equation Modeling
Description: Estimate complex Structural Equation Models (SEMs) by fitting Partial
Least Squares Structural Equation Modeling (PLS-SEM) and Partial Least
Squares consistent Structural Equation Modeling (PLSc-SEM) specifications
that handle categorical data, non-linear relations, and multilevel
structures. The implementation follows Lohmöller (1989) for the classic PLS-SEM
algorithm, Dijkstra and Henseler (2015) for consistent PLSc-SEM, Dijkstra et al.,
(2014) for nonlinear PLSc-SEM, and Schuberth, Henseler, Dijkstra (2018)
for ordinal PLS-SEM and PLSc-SEM. Additional extensions are under development.
The MC-OrdPLSc algorithm, used to handle ordinal interaction models is detailed
in Slupphaug et al., (2026).
References:
Lohmöller, J.-B. (1989, ISBN:9783790803002).
"Latent Variable Path Modeling with Partial Least Squares."
Dijkstra, T. K., & Henseler, J. (2015).
<doi:10.1016/j.jmva.2015.06.002>.
"Consistent partial least squares path modeling."
Dijkstra, T. K., & Schermelleh-Engel, K. [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between plssem versions 0.1.0 dated 2026-03-23 and 0.1.1 dated 2026-04-25
DESCRIPTION | 22 MD5 | 127 ++-- NAMESPACE | 13 R/bootstrap.R | 272 ++++++++- R/datasets.R | 36 + R/djikstra_correction.R | 36 + R/fit_measures.R |only R/formatted_objects.R | 3 R/generics.R | 141 ++++ R/knn_impute.R |only R/lmer.R | 153 ++++- R/mcpls.R | 117 ++-- R/mean_impute.R |only R/model.R | 358 ++++++++++-- R/parse_model.R | 27 R/pls.R | 190 +++++- R/pls_data.R |only R/predict.R |only R/robbins-monro.R |only R/simulate_data.R | 220 ++++++- R/step0_5.R | 3 R/step1.R | 5 R/step8.R | 5 R/utils.R | 165 ++--- R/utils_higher_order.R |only R/zzz.R | 3 README.md | 34 - build/vignette.rds |binary data/titanic.rda |only inst/CITATION |only inst/doc/categorical-models.R | 2 inst/doc/categorical-models.Rmd | 2 inst/doc/categorical-models.html | 178 +++--- inst/doc/higher-order.R |only inst/doc/higher-order.Rmd |only inst/doc/higher-order.html |only inst/doc/interaction-models.R | 4 inst/doc/interaction-models.Rmd | 4 inst/doc/interaction-models.html | 260 ++++----- inst/doc/linear-models.R | 2 inst/doc/linear-models.Rmd | 2 inst/doc/linear-models.html | 180 +++--- inst/doc/missing-imputation.R |only inst/doc/missing-imputation.Rmd |only inst/doc/missing-imputation.html |only inst/doc/multilevel-models.R | 8 inst/doc/multilevel-models.Rmd | 8 inst/doc/multilevel-models.html | 632 +++++++++++----------- inst/doc/ordinal-regression.R |only inst/doc/ordinal-regression.Rmd |only inst/doc/ordinal-regression.html |only inst/doc/parallel-bootstrapping.R |only inst/doc/parallel-bootstrapping.Rmd |only inst/doc/parallel-bootstrapping.html |only man/boot.Rd |only man/figures |only man/isMC_PLS.Rd |only man/parameter_estimates.plssem.Rd | 6 man/pls.Rd | 98 ++- man/pls_construct_scores.Rd |only man/pls_predict.Rd |only man/print.PlsSemPredict.Rd |only man/print.SummaryPlsSem.Rd | 6 man/print.plssem.Rd | 6 man/summary.plssem.Rd | 12 man/titanic.Rd |only tests/testthat/test_formative.R | 12 tests/testthat/test_higher_order.R |only tests/testthat/test_multilevel_random_intercept.R | 12 tests/testthat/test_multilevel_random_slope.R | 34 - tests/testthat/test_oneint.R | 17 tests/testthat/test_predict.R |only tests/testthat/test_titanic.R |only tests/testthat/test_tpb.R | 22 vignettes/categorical-models.Rmd | 2 vignettes/higher-order.Rmd |only vignettes/interaction-models.Rmd | 4 vignettes/linear-models.Rmd | 2 vignettes/missing-imputation.Rmd |only vignettes/multilevel-models.Rmd | 8 vignettes/ordinal-regression.Rmd |only vignettes/parallel-bootstrapping.Rmd |only 82 files changed, 2354 insertions(+), 1099 deletions(-)
Title: Indian Alien Flora Information Database Retrieval
Description: The Indian Alien Flora Information (ILORA) database contains 14 invasion-relevant variables for 1388 alien plant species in India. The package enables exploration of the database using user-defined criteria. Using this package, users can retrieve variable-specific and species-level data from the database. The package also supports exploratory data analysis and visualization to give users an idea of the variables of interest. Further details about the database are available at <https://iloradb.wixsite.com/alienflora>.
Author: Ruqaiya Shaikh [aut, cre],
Achyut Kumar Banerjee [aut],
Abhishek Mukherjee [aut],
Amiya Ranjan Bhowmick [aut]
Maintainer: Ruqaiya Shaikh <ruqaiyashaikh41@gmail.com>
Diff between ILORA versions 0.1.0 dated 2026-04-13 and 0.1.1 dated 2026-04-25
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Descriptive, Reliability, and Inferential Tables for
Psychometric Scales and Demographic Data
Description: Provides functions to format and summarise already computed outputs from commonly used statistical and psychometric functions into compact, single-row tables and simple graphs, with utilities to export results to CSV, Word, and Excel formats. The package does not implement new statistical methods or estimation procedures; instead, it organises and presents results obtained from existing functions such as psych::describe(), psych::alpha(), stats::t.test(), and gtsummary::tbl_summary() to streamline reporting workflows in clinical and psychological research.
Author: Darshankumar Dharaiya [aut, cre]
Maintainer: Darshankumar Dharaiya <dharaiya.darshan@gmail.com>
Diff between scaledescr versions 0.2.5 dated 2026-04-18 and 0.2.6 dated 2026-04-25
DESCRIPTION | 8 +-- MD5 | 10 ++- NAMESPACE | 6 ++ NEWS.md | 96 +++++++++++++++++++++++++------------ R/make_lavaan_analysis_tables.R |only inst/CITATION | 2 man/make_lavaan_analysis_tables.Rd |only 7 files changed, 84 insertions(+), 38 deletions(-)
Title: Spatial Projection of Network Signals along Geodesic Paths
Description: For a given graph containing vertices, edges, and a signal
associated with the vertices, the 'PathwaySpace' package performs a convolution
operation, which involves a weighted combination of neighboring vertices and
their associated signals. The package uses a decay function to project these
signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' has various
applications, such as visualizing network data in a graphical format that
highlights the relationships and signal strengths between vertices. By
combining graph theory, signal processing, and visualization, 'PathwaySpace'
provides a way of representing graph data on a continuous projection space.
Based on methods introduced in Tercan et al. (2025)
<doi:10.1016/j.xpro.2025.103681> and Ellrott et al. (2025)
<doi:10.1016/j.ccell.2024.12.002>.
Author: Sysbiolab Team [aut],
Victor Apolonio [ctb],
Jonathan Back [ctb],
Lana Querne [ctb],
Vinicius Chagas [ctb],
Bahar Tercan [ctb],
Mauro Castro [cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between PathwaySpace versions 1.1.1 dated 2026-02-28 and 1.2.0 dated 2026-04-25
DESCRIPTION | 44 +++++++--- MD5 | 43 +++++---- NAMESPACE | 4 R/pspaceMethods.R | 23 ++--- R/pspaceMisc.R | 31 +++++++ R/pspacePlots.R | 169 ++++++++++----------------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/PathwaySpace.R | 30 ++++-- inst/doc/PathwaySpace.Rmd | 44 +++++----- inst/doc/PathwaySpace.html | 120 ++++++++++++++------------- man/buildPathwaySpace.Rd | 4 man/getNearestNode.Rd |only man/plotPathwaySpace-methods.Rd | 5 - man/silhouetteMapping-methods.Rd | 4 vignettes/PathwaySpace.Rmd | 44 +++++----- vignettes/figures/fig2.png |binary vignettes/figures/fig3.png |binary vignettes/figures/fig4.png |binary vignettes/figures/fig5.png |binary vignettes/figures/fig6.png |binary vignettes/figures/fig7.png |binary vignettes/figures/fig8.png |binary 23 files changed, 283 insertions(+), 282 deletions(-)
Title: Performing Comprehensive Overlap Assessments
Description: The implementation of a statistical framework for performing overlap assessments on
lists comprising sets of strings (such as lists of gene sets) described in Stoica (2023)
<https://ora.ox.ac.uk/objects/uuid:b0847284-a02f-47ee-88e3-a3c4e0cdb8b1>.
It can assess overlaps of pairs of sets of strings selected either from the same universe or
from different universes, and overlaps of triplets of sets of strings selected from the same
universe. Designed for single-cell RNA-sequencing data analysis applications, but suitable
for other purposes as well.
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Diff between LISTO versions 0.6.5 dated 2026-03-06 and 0.7.3 dated 2026-04-25
DESCRIPTION | 10 ++-- MD5 | 16 ++++--- R/multiple_testing.R | 92 ++++++++++++++++++++++++++++++-------------- R/run_listo.R | 8 +-- README.md | 31 ++++++++++---- man/bfCorrectV.Rd |only man/mtCorrectDF.Rd | 28 +++++-------- man/mtCorrectHelper.Rd |only man/runLISTO.Rd | 6 +- tests/testthat/test-LISTO.R | 19 +++++---- 10 files changed, 129 insertions(+), 81 deletions(-)
Title: Numerical Solution of Integral Equations
Description: An R implementation of Matthew Thomas's 'Python' library 'inteq'. First, this solves Fredholm integral equations of the first kind ($f(s) = \int_a^b K(s, y) g(y) dy$) using methods described by Twomey (1963) <doi:10.1145/321150.321157>. Second, this solves Volterra integral equations of the first kind ($f(s) = \int_0^s K(s,y) g(t) dt$) using methods from Betto and Thomas (2021) <doi:10.48550/arXiv.2106.08496>. Third, this solves Voltera integral equations of the second kind ($g(s) = f(s) + \int_a^s K(s,y) g(y) dy$) using methods from Linz (1969) <doi:10.1137/0706034>.
Author: Mark Clements [aut, cre],
Aaron Jehle [aut],
Matthew Thomas [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between inteq versions 1.0 dated 2025-07-29 and 1.1 dated 2026-04-25
DESCRIPTION | 6 +- MD5 | 10 ++-- inst/doc/documentation.R | 6 +- inst/doc/documentation.Rmd | 6 +- inst/doc/documentation.html | 109 ++++++++++++++++++++++++++++++++++++++++++-- vignettes/documentation.Rmd | 6 +- 6 files changed, 123 insertions(+), 20 deletions(-)
Title: Functions to Streamline Statistical Analysis and Reporting
Description: Built upon popular R packages such as 'ggstatsplot' and 'ARTool', this collection offers a wide array of tools for simplifying reproducible analyses, generating high-quality visualizations, and producing 'APA'-compliant outputs. The primary goal of this package is to significantly reduce repetitive coding efforts, allowing you to focus on interpreting results. Whether you're dealing with ANOVA assumptions, reporting effect sizes, or creating publication-ready visualizations, this package makes these tasks easier.
Author: Mark Colley [aut, cre, cph]
Maintainer: Mark Colley <mark.colley@yahoo.de>
This is a re-admission after prior archival of version 0.0.2 dated 2026-01-08
Diff between colleyRstats versions 0.0.2 dated 2026-01-08 and 0.0.3 dated 2026-04-25
DESCRIPTION | 24 MD5 | 13 NEWS.md |only R/plotting.R | 1557 +++++++++++++++++----------------- R/reporting.R | 2066 +++++++++++++++++++++++----------------------- R/setup.R | 4 man/colleyRstats_setup.Rd | 2 man/generateMoboPlot2.Rd | 5 8 files changed, 1841 insertions(+), 1830 deletions(-)
Title: Statistical Tools Designed for End Users
Description: The statistical tools in this package do one of four things:
1) Enhance basic statistical functions with more
flexible inputs, smarter defaults, and richer, clearer, and ready-to-use
output (e.g., t.test2())
2) Produce publication-ready commonly needed figures with one line of code (e.g., plot_cdf())
3) Implement novel analytical tools developed by the authors (e.g., twolines())
4) Deliver niche functions of high value to the authors that are not easily
available elsewhere (e.g., clear(), convert_to_sql(), resize_images()).
Author: Uri Simonsohn [aut, cre]
Maintainer: Uri Simonsohn <urisohn@gmail.com>
Diff between statuser versions 0.1.9 dated 2026-02-26 and 0.2.1 dated 2026-04-25
DESCRIPTION | 16 MD5 | 91 - NAMESPACE | 155 +- NEWS.md |only R/desc_var.R | 90 + R/interprobe.R |only R/interprobe_helpers.R |only R/plot_cdf.R | 75 - R/plot_density.R | 63 R/plot_freq.R | 551 ++++++-- R/plot_gam.R | 24 R/plot_means.R |only R/scatter.gam.R | 31 R/statuser-package.R | 16 R/t.test2.R | 17 R/text2.R | 31 R/utils.R | 39 R/validate.R | 252 ++- R/var_labels.R |only R/zzz.R | 6 README.md | 8 man/desc_var.Rd | 9 man/interprobe.Rd |only man/plot_cdf.Rd | 14 man/plot_density.Rd | 13 man/plot_freq.Rd | 54 man/plot_means.Rd |only man/statuser-package.Rd | 15 man/t.test2.Rd | 122 - man/var_labels.Rd |only tests/UNIT_TESTS.md |only tests/testthat/Rplots.pdf |binary tests/testthat/_annotate_test_ids.R |only tests/testthat/helper-backend_equivalence.R |only tests/testthat/test-backend_equivalence.R |only tests/testthat/test-convert_to_sql.R | 7 tests/testthat/test-desc_var.R | 541 ++++---- tests/testthat/test-format_pvalue.R | 239 +-- tests/testthat/test-gam_functions.R | 656 +++++----- tests/testthat/test-interprobe.R |only tests/testthat/test-list2.R | 7 tests/testthat/test-lm2.R | 1802 ++++++++++++++-------------- tests/testthat/test-message2.R | 104 - tests/testthat/test-plot_cdf.R | 587 ++++----- tests/testthat/test-plot_density.R | 498 ++++--- tests/testthat/test-plot_freq.R | 227 ++- tests/testthat/test-plot_means.R |only tests/testthat/test-print_functions.R | 108 - tests/testthat/test-resize_images.R | 101 - tests/testthat/test-t.test2.R | 35 tests/testthat/test-table2.R | 1540 ++++++++++++----------- tests/testthat/test-text2.R | 24 tests/testthat/test-validate_plot.R | 292 ++-- tests/testthat/test-var_labels.R |only 54 files changed, 4647 insertions(+), 3813 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Schaid Daniel [aut],
Jason P. Sinnwell [aut, cre]
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
This is a re-admission after prior archival of version 1.9.8.3 dated 2026-03-13
Diff between haplo.stats versions 1.9.8.3 dated 2026-03-13 and 1.9.8.7 dated 2026-04-25
DESCRIPTION | 11 MD5 | 16 - NAMESPACE | 2 R/anova.haplo.glm.q | 7 R/haplo.score.q | 108 --------- inst/doc/haplostats.R | 58 +---- inst/doc/haplostats.Rmd | 109 +-------- inst/doc/haplostats.html | 537 +++++++++++++++++++---------------------------- vignettes/haplostats.Rmd | 109 +-------- 9 files changed, 297 insertions(+), 660 deletions(-)
Title: Identification of Dichotomous Differential Item Functioning
(DIF) using Angoff's Delta Plot Method
Description: The deltaPlotR package implements Angoff's Delta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality assumption or by prior determination. Item purification is supported (Magis and Facon (2014) <doi:10.18637/jss.v059.c01>).
Author: David Magis [aut] ,
Bruno Facon [aut] ,
Adela Hladka [cre]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between deltaPlotR versions 1.6 dated 2018-03-16 and 1.9 dated 2026-04-25
DESCRIPTION | 27 ++++- MD5 | 16 +-- NEWS | 24 +++-- R/deltaPlot.R | 236 +++++++++++++++++++++++++-------------------------- inst/CITATION | 34 +++---- man/adjustExtreme.Rd | 24 ++--- man/deltaPlot.Rd | 66 +++++++------- man/diagPlot.Rd | 45 ++++----- man/verbal.rd | 10 +- 9 files changed, 254 insertions(+), 228 deletions(-)
Title: Interface to 'Sensor Tower' Mobile App Intelligence API
Description: Interface to the 'Sensor Tower' API <https://app.sensortower.com/api/docs/app_analysis>
for mobile app analytics and market intelligence. Provides a small, consistent
set of functions to retrieve app metadata, publisher information, download and
revenue estimates, active user metrics, category rankings, and market trends.
Four core verbs ('st_metrics', 'st_rankings', 'st_app'/'st_apps', 'st_filter')
cover the common workflows with standardized parameters and tidyverse-friendly
output. Supports both iOS and Android app ecosystems with unified data structures
for cross-platform analysis.
Author: Phillip Black [aut, cre]
Maintainer: Phillip Black <pblack@gameeconomistconsulting.com>
Diff between sensortowerR versions 0.9.7 dated 2026-03-18 and 1.0.0 dated 2026-04-25
sensortowerR-0.9.7/sensortowerR/man/clean_numeric_column.Rd |only sensortowerR-0.9.7/sensortowerR/man/find_column.Rd |only sensortowerR-0.9.7/sensortowerR/man/format_vector.Rd |only sensortowerR-0.9.7/sensortowerR/man/get_column_spec.Rd |only sensortowerR-0.9.7/sensortowerR/man/map_region_columns.Rd |only sensortowerR-0.9.7/sensortowerR/man/require_column.Rd |only sensortowerR-0.9.7/sensortowerR/man/select_columns_safe.Rd |only sensortowerR-0.9.7/sensortowerR/man/select_robust.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_app_details.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_app_info.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_app_lookup.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_batch_metrics.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_category_rankings.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_combine_filters.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_compare_filter_results.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_create_simple_filter.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_custom_fields_filter.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_custom_fields_filter_by_id.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_filter_by_date.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_filter_by_genre.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_filter_by_monetization.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_filter_by_publisher.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_filter_by_sdk.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_generate_example_filter_ids.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_sales_report.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_smart_metrics.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_top_charts.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_top_publishers.Rd |only sensortowerR-0.9.7/sensortowerR/man/st_unified_sales_report.Rd |only sensortowerR-0.9.7/sensortowerR/man/try_column_operation.Rd |only sensortowerR-0.9.7/sensortowerR/man/validate_columns.Rd |only sensortowerR-0.9.7/sensortowerR/man/validate_top_charts_data.Rd |only sensortowerR-0.9.7/sensortowerR/tests/testthat/test-api-endpoints.R |only sensortowerR-0.9.7/sensortowerR/tests/testthat/test-app-id-validation.R |only sensortowerR-0.9.7/sensortowerR/tests/testthat/test-custom-fields.R |only sensortowerR-0.9.7/sensortowerR/tests/testthat/test-deduplication.R |only sensortowerR-0.9.7/sensortowerR/tests/testthat/test-publishers.R |only sensortowerR-0.9.7/sensortowerR/tests/testthat/test-refactored-batch-metrics.R |only sensortowerR-1.0.0/sensortowerR/DESCRIPTION | 24 sensortowerR-1.0.0/sensortowerR/MD5 | 149 +- sensortowerR-1.0.0/sensortowerR/NAMESPACE | 20 sensortowerR-1.0.0/sensortowerR/R/app_id_validation.R | 6 sensortowerR-1.0.0/sensortowerR/R/column_helpers.R | 52 sensortowerR-1.0.0/sensortowerR/R/data_validation.R | 26 sensortowerR-1.0.0/sensortowerR/R/defunct.R |only sensortowerR-1.0.0/sensortowerR/R/formatting_helpers.R | 10 sensortowerR-1.0.0/sensortowerR/R/st_active_users.R | 2 sensortowerR-1.0.0/sensortowerR/R/st_api_diagnostics.R | 14 sensortowerR-1.0.0/sensortowerR/R/st_app.R |only sensortowerR-1.0.0/sensortowerR/R/st_app_details.R | 5 sensortowerR-1.0.0/sensortowerR/R/st_app_enriched.R | 4 sensortowerR-1.0.0/sensortowerR/R/st_app_info.R | 5 sensortowerR-1.0.0/sensortowerR/R/st_app_lookup.R | 11 sensortowerR-1.0.0/sensortowerR/R/st_batch_app_lookup.R | 2 sensortowerR-1.0.0/sensortowerR/R/st_batch_metrics.R | 34 sensortowerR-1.0.0/sensortowerR/R/st_category_rankings.R | 5 sensortowerR-1.0.0/sensortowerR/R/st_custom_fields.R | 10 sensortowerR-1.0.0/sensortowerR/R/st_custom_fields_utils.R | 82 - sensortowerR-1.0.0/sensortowerR/R/st_custom_fields_workflow.R | 17 sensortowerR-1.0.0/sensortowerR/R/st_demographics.R | 4 sensortowerR-1.0.0/sensortowerR/R/st_filter.R |only sensortowerR-1.0.0/sensortowerR/R/st_filter_helpers.R | 16 sensortowerR-1.0.0/sensortowerR/R/st_get_unified_mapping.R | 6 sensortowerR-1.0.0/sensortowerR/R/st_id_cache.R | 2 sensortowerR-1.0.0/sensortowerR/R/st_metrics.R | 529 ++++++---- sensortowerR-1.0.0/sensortowerR/R/st_publisher_apps.R | 2 sensortowerR-1.0.0/sensortowerR/R/st_publisher_portfolio.R | 8 sensortowerR-1.0.0/sensortowerR/R/st_rankings.R |only sensortowerR-1.0.0/sensortowerR/R/st_retention.R | 4 sensortowerR-1.0.0/sensortowerR/R/st_sales_report.R | 7 sensortowerR-1.0.0/sensortowerR/R/st_session_metrics.R | 2 sensortowerR-1.0.0/sensortowerR/R/st_smart_metrics.R | 13 sensortowerR-1.0.0/sensortowerR/R/st_top_charts.R | 5 sensortowerR-1.0.0/sensortowerR/R/st_top_publishers.R | 5 sensortowerR-1.0.0/sensortowerR/R/st_unified_sales_report.R | 7 sensortowerR-1.0.0/sensortowerR/R/st_yoy_metrics.R | 4 sensortowerR-1.0.0/sensortowerR/R/utils.R | 93 + sensortowerR-1.0.0/sensortowerR/README.md | 248 ++-- sensortowerR-1.0.0/sensortowerR/build/vignette.rds |binary sensortowerR-1.0.0/sensortowerR/inst/doc/custom-fields.Rmd | 451 +------- sensortowerR-1.0.0/sensortowerR/inst/doc/custom-fields.html | 513 ++------- sensortowerR-1.0.0/sensortowerR/inst/doc/migrating-to-1.0.Rmd |only sensortowerR-1.0.0/sensortowerR/inst/doc/migrating-to-1.0.html |only sensortowerR-1.0.0/sensortowerR/inst/doc/tidy-active-users.Rmd | 19 sensortowerR-1.0.0/sensortowerR/inst/doc/tidy-active-users.html | 39 sensortowerR-1.0.0/sensortowerR/man/sensortowerR-defunct.Rd |only sensortowerR-1.0.0/sensortowerR/man/st_app.Rd |only sensortowerR-1.0.0/sensortowerR/man/st_apps.Rd |only sensortowerR-1.0.0/sensortowerR/man/st_batch_app_lookup.Rd |only sensortowerR-1.0.0/sensortowerR/man/st_filter.Rd |only sensortowerR-1.0.0/sensortowerR/man/st_metrics.Rd | 128 +- sensortowerR-1.0.0/sensortowerR/man/st_rankings.Rd |only sensortowerR-1.0.0/sensortowerR/tests/testthat/test-active-users-wrapper.R | 2 sensortowerR-1.0.0/sensortowerR/tests/testthat/test-defunct.R |only sensortowerR-1.0.0/sensortowerR/tests/testthat/test-enrichment.R | 2 sensortowerR-1.0.0/sensortowerR/tests/testthat/test-os-parameter.R | 126 -- sensortowerR-1.0.0/sensortowerR/tests/testthat/test-sensortowerR.R | 87 - sensortowerR-1.0.0/sensortowerR/tests/testthat/test-st_filter.R |only sensortowerR-1.0.0/sensortowerR/tests/testthat/test-st_metrics.R |only sensortowerR-1.0.0/sensortowerR/tests/testthat/test-st_rankings.R |only sensortowerR-1.0.0/sensortowerR/vignettes/custom-fields.Rmd | 451 +------- sensortowerR-1.0.0/sensortowerR/vignettes/migrating-to-1.0.Rmd |only sensortowerR-1.0.0/sensortowerR/vignettes/tidy-active-users.Rmd | 19 103 files changed, 1322 insertions(+), 1948 deletions(-)
Title: Scrutinizing Collections of Structured Datasets
Description: Provides a coherent interface for exploring and transforming
multiple related data frames that share a common structure.
Complements single-dataset inspection tools by operating across an
entire collection at once. Also includes lightweight utilities for
related file and folder management tasks.
Author: Daniel Rakotomalala [aut, cre]
Maintainer: Daniel Rakotomalala <rakdanielh@gmail.com>
Diff between scrutr versions 0.3.0 dated 2026-04-22 and 0.3.1 dated 2026-04-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/detect_chars_structure_datasets.R | 12 +++++++----- README.md | 2 ++ man/detect_chars_structure_datasets.Rd | 12 +++++++----- tests/testthat/test-detect_chars_structure_datasets.R | 6 ++++-- 7 files changed, 37 insertions(+), 21 deletions(-)
Title: Management Strategy Evaluation for Salmon Species
Description: Simulation tools to evaluate the long-term effects of salmon management strategies, including a combination of habitat, harvest, and
habitat actions. The stochastic age-structured operating model accommodates complex life histories, including freshwater survival across
early life stages, juvenile survival and fishery exploitation in the marine life stage, partial maturity by age class, and fitness impacts of
hatchery programs on natural spawning populations. 'salmonMSE' also provides an age-structured conditioning model to develop operating models
fitted to data.
Author: Quang Huynh [aut, cre]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between salmonMSE versions 2.0.0 dated 2026-04-16 and 2.1.0 dated 2026-04-25
DESCRIPTION | 8 MD5 | 24 NEWS.md | 91 +- R/MMSE2SMSE.R | 10 R/Rel.R | 2 R/SOM2MOM.R | 1632 +++++++++++++++++++++++------------------------ R/hatchery.R | 14 R/plot-SOM.R | 390 +++++------ R/plot-statevar.R | 1740 +++++++++++++++++++++++++-------------------------- R/ref.R | 686 ++++++++++---------- R/salmonMSE.R | 53 + build/partial.rdb |binary man/plot_tradeoff.Rd | 4 13 files changed, 2348 insertions(+), 2306 deletions(-)
Title: A Lightweight Interface Between 'igraph' and 'ggplot2' Graphics
Description: An interface to integrate 'igraph' and 'ggplot2' graphics
within a normalized coordinate system. 'RGraphSpace' implements
geometric objects based on 'ggplot2' prototypes, optimized for
the representation of large networks. The package provides three
specialized 'geoms' to translate graph data into geometric layers,
supporting customization of aesthetics and visual styles. These
'geoms' use a dual-anchor normalization approach to align layers,
required for analyses where network elements must be referenced
to a spatial map. 'RGraphSpace' aims to facilitate side-by-side
visualization of multiple graphs spatially aligned with reference
maps and images.
Author: Sysbiolab Team [aut],
Flavio Kessler [ctb],
Jonathan Back [ctb],
Lana Querne [ctb],
Victor Apolonio [ctb],
Vinicius Chagas [ctb],
Mauro Castro [cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between RGraphSpace versions 1.1.1 dated 2026-02-28 and 1.2.0 dated 2026-04-25
RGraphSpace-1.1.1/RGraphSpace/R/gspaceChecks.R |only RGraphSpace-1.1.1/RGraphSpace/R/gspaceClasses.R |only RGraphSpace-1.1.1/RGraphSpace/R/gspaceConstructor.R |only RGraphSpace-1.1.1/RGraphSpace/R/gspaceGenerics.R |only RGraphSpace-1.1.1/RGraphSpace/R/gspaceGeom.R |only RGraphSpace-1.1.1/RGraphSpace/R/gspaceMethods.R |only RGraphSpace-1.1.1/RGraphSpace/R/gspaceMisc.R |only RGraphSpace-1.1.1/RGraphSpace/R/gspaceSupplements.R |only RGraphSpace-1.1.1/RGraphSpace/R/gspaceValidation.R |only RGraphSpace-1.1.1/RGraphSpace/man/GraphSpace.Rd |only RGraphSpace-1.1.1/RGraphSpace/man/legend-accessors.Rd |only RGraphSpace-1.2.0/RGraphSpace/DESCRIPTION | 50 - RGraphSpace-1.2.0/RGraphSpace/MD5 | 81 + RGraphSpace-1.2.0/RGraphSpace/NAMESPACE | 49 - RGraphSpace-1.2.0/RGraphSpace/R/geom-edgespace.R |only RGraphSpace-1.2.0/RGraphSpace/R/geom-graphspace.R |only RGraphSpace-1.2.0/RGraphSpace/R/geom-nodespace.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-checks.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-classes.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-constructor.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-generics.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-methods.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-misc.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-normalize.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-supplements.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-themes.R |only RGraphSpace-1.2.0/RGraphSpace/R/gspace-validation.R |only RGraphSpace-1.2.0/RGraphSpace/R/inject-nodespace.R |only RGraphSpace-1.2.0/RGraphSpace/build/vignette.rds |binary RGraphSpace-1.2.0/RGraphSpace/data/gtoy1.RData |binary RGraphSpace-1.2.0/RGraphSpace/inst/CITATION | 32 RGraphSpace-1.2.0/RGraphSpace/inst/doc/RGraphSpace.R | 182 +++ RGraphSpace-1.2.0/RGraphSpace/inst/doc/RGraphSpace.Rmd | 327 ++++++ RGraphSpace-1.2.0/RGraphSpace/inst/doc/RGraphSpace.html | 481 +++++++--- RGraphSpace-1.2.0/RGraphSpace/man/GeomEdgeSpace.Rd | 39 RGraphSpace-1.2.0/RGraphSpace/man/GeomGraphSpace.Rd |only RGraphSpace-1.2.0/RGraphSpace/man/GeomNodeSpace.Rd | 44 RGraphSpace-1.2.0/RGraphSpace/man/GraphSpace-accessors.Rd | 6 RGraphSpace-1.2.0/RGraphSpace/man/GraphSpace-class.Rd | 2 RGraphSpace-1.2.0/RGraphSpace/man/GraphSpace-methods.Rd |only RGraphSpace-1.2.0/RGraphSpace/man/RGraphSpace-package.Rd | 39 RGraphSpace-1.2.0/RGraphSpace/man/as_colorraster.Rd |only RGraphSpace-1.2.0/RGraphSpace/man/figures |only RGraphSpace-1.2.0/RGraphSpace/man/geom_edgespace.Rd | 144 +- RGraphSpace-1.2.0/RGraphSpace/man/geom_graphspace.Rd |only RGraphSpace-1.2.0/RGraphSpace/man/geom_nodespace.Rd | 126 +- RGraphSpace-1.2.0/RGraphSpace/man/getGraphSpace-methods.Rd | 4 RGraphSpace-1.2.0/RGraphSpace/man/gtoys.Rd | 2 RGraphSpace-1.2.0/RGraphSpace/man/inject_nodespace.Rd |only RGraphSpace-1.2.0/RGraphSpace/man/normalizeGraphSpace-methods.Rd |only RGraphSpace-1.2.0/RGraphSpace/man/plot.GraphSpace.Rd | 4 RGraphSpace-1.2.0/RGraphSpace/man/plotGraphSpace-methods.Rd | 48 RGraphSpace-1.2.0/RGraphSpace/man/theme_gspace.Rd |only RGraphSpace-1.2.0/RGraphSpace/vignettes/RGraphSpace.Rmd | 327 ++++++ RGraphSpace-1.2.0/RGraphSpace/vignettes/bibliography.bib | 19 RGraphSpace-1.2.0/RGraphSpace/vignettes/figs |only 56 files changed, 1543 insertions(+), 463 deletions(-)
Title: Data Quality Check Framework for Clinical and Analytical Data
Description: A configuration-driven framework for running domain-level data quality checks and consolidating findings into structured Excel reports with role-based feedback routing.
It supports trial-level and study-level checks across multiple data domains.
Reports are routed to separate feedback channels for Data Management (DM), Medical Writing (MW), Study Data Tabulation Model (SDTM) programmers, and Analysis Data Model (ADaM) programmers, as well as other relevant data roles.
Reviewer responses are incorporated automatically on re-run.
Author: Ganesh Babu G [aut, cre]
Maintainer: Ganesh Babu G <ganeshbabu346@gmail.com>
Diff between rCoreGage versions 1.0.0 dated 2026-04-22 and 1.1.0 dated 2026-04-25
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md |only R/runner.R | 2 +- README.md | 6 +++++- 5 files changed, 13 insertions(+), 8 deletions(-)
Title: Transcriptomic Atlas of Neuroimaging Derived Phenotypes
Description: Contains functions to query and visualize the Neuroimaging features
associated with genetically regulated gene expression (GReX). The primary utility,
neuroimaGene(), relies on a list of user-defined genes and returns a table of
neuroimaging features (NIDPs) associated with each gene. This resource
is designed to assist in the interpretation of genome-wide and transcriptome-wide
association studies that evaluate brain related traits. Bledsoe (2024)
<doi:10.1016/j.ajhg.2024.06.002>. In addition there are several visualization
functions that generate summary plots and 2-dimensional visualizations of regional
brain measures. Mowinckel (2020).
Author: Xavier Bledsoe [aut, cre] ,
Eric Gamazon [aut]
Maintainer: Xavier Bledsoe <xavier.bledsoe@vanderbilt.edu>
This is a re-admission after prior archival of version 0.1.2 dated 2024-12-09
Diff between neuroimaGene versions 0.1.2 dated 2024-12-09 and 0.1.3 dated 2026-04-25
neuroimaGene-0.1.2/neuroimaGene/README.md |only neuroimaGene-0.1.2/neuroimaGene/inst/extdata/dest_atlas.rda |only neuroimaGene-0.1.2/neuroimaGene/inst/extdata/dkt_atlas.rda |only neuroimaGene-0.1.3/neuroimaGene/DESCRIPTION | 15 neuroimaGene-0.1.3/neuroimaGene/MD5 | 25 - neuroimaGene-0.1.3/neuroimaGene/NAMESPACE | 1 neuroimaGene-0.1.3/neuroimaGene/R/check_db.R | 2 neuroimaGene-0.1.3/neuroimaGene/R/neuro_vis.R | 187 ++++++---- neuroimaGene-0.1.3/neuroimaGene/R/neuroimagene_pkg.R | 3 neuroimaGene-0.1.3/neuroimaGene/R/plot_gn_nidp.R | 2 neuroimaGene-0.1.3/neuroimaGene/R/plot_nidps.R | 1 neuroimaGene-0.1.3/neuroimaGene/build/vignette.rds |binary neuroimaGene-0.1.3/neuroimaGene/inst/doc/neuroimaGene.html | 30 + neuroimaGene-0.1.3/neuroimaGene/inst/extdata/dest_atlas_new.rda |only neuroimaGene-0.1.3/neuroimaGene/inst/extdata/dkt_atlas_new.rda |only neuroimaGene-0.1.3/neuroimaGene/man/neuro_vis.Rd | 4 16 files changed, 170 insertions(+), 100 deletions(-)
Title: Consensus Seriation for Binary Data
Description: Determining consensus seriations for binary incidence matrices, using a two-step process of Procrustes-fit correspondence analysis for heuristic selection of partial seriations and iterative regression to establish a single consensus. Contains the Lakhesis Calculator, a graphical platform for identifying seriated sequences. Collins-Elliott (2024) <https://volweb.utk.edu/~scolli46/sceLakhesis.pdf>.
Author: Stephen A. Collins-Elliott [aut, cre]
Maintainer: Stephen A. Collins-Elliott <sce@utk.edu>
Diff between lakhesis versions 0.0.1 dated 2024-06-10 and 1.1 dated 2026-04-25
lakhesis-0.0.1/lakhesis/data/qfStrands.rda |only lakhesis-0.0.1/lakhesis/man/ca.procrustes.Rd |only lakhesis-0.0.1/lakhesis/man/ca.procrustes.curve.Rd |only lakhesis-0.0.1/lakhesis/man/ca.procrustes.poly.Rd |only lakhesis-0.0.1/lakhesis/man/concentration.col.Rd |only lakhesis-0.0.1/lakhesis/man/element.eval.Rd |only lakhesis-0.0.1/lakhesis/man/im.csv.read.Rd |only lakhesis-0.0.1/lakhesis/man/im.long.Rd |only lakhesis-0.0.1/lakhesis/man/im.merge.Rd |only lakhesis-0.0.1/lakhesis/man/im.ref.Rd |only lakhesis-0.0.1/lakhesis/man/kappa.coef.Rd |only lakhesis-0.0.1/lakhesis/man/qfStrands.Rd |only lakhesis-0.0.1/lakhesis/man/spearman.sq.Rd |only lakhesis-0.0.1/lakhesis/man/strand.extract.Rd |only lakhesis-0.0.1/lakhesis/man/strand.suppress.Rd |only lakhesis-1.1/lakhesis/DESCRIPTION | 23 lakhesis-1.1/lakhesis/MD5 | 79 + lakhesis-1.1/lakhesis/NAMESPACE | 80 + lakhesis-1.1/lakhesis/R/RcppExports.R |only lakhesis-1.1/lakhesis/R/app.R | 47 - lakhesis-1.1/lakhesis/R/criterion.R |only lakhesis-1.1/lakhesis/R/data.R | 78 - lakhesis-1.1/lakhesis/R/incidence.R | 339 ++++---- lakhesis-1.1/lakhesis/R/lakhesize.R | 415 ++++++---- lakhesis-1.1/lakhesis/R/print.R |only lakhesis-1.1/lakhesis/R/procrustes.R | 494 ++++++------ lakhesis-1.1/lakhesis/R/strand.R | 434 ++++------ lakhesis-1.1/lakhesis/README.md | 433 ++++++---- lakhesis-1.1/lakhesis/build/partial.rdb |binary lakhesis-1.1/lakhesis/build/vignette.rds |only lakhesis-1.1/lakhesis/data/qf_strands.rda |only lakhesis-1.1/lakhesis/data/quattrofontanili.rda |binary lakhesis-1.1/lakhesis/inst/CITATION | 19 lakhesis-1.1/lakhesis/inst/REFERENCES.bib | 274 ++++-- lakhesis-1.1/lakhesis/inst/app/server.R | 853 +++++++++++---------- lakhesis-1.1/lakhesis/inst/app/ui.R | 179 ++-- lakhesis-1.1/lakhesis/inst/doc |only lakhesis-1.1/lakhesis/man/LC.Rd | 5 lakhesis-1.1/lakhesis/man/ca_procrustes.Rd |only lakhesis-1.1/lakhesis/man/ca_procrustes_ser.Rd |only lakhesis-1.1/lakhesis/man/conc_c.Rd |only lakhesis-1.1/lakhesis/man/conc_wrc.Rd |only lakhesis-1.1/lakhesis/man/cor_sq.Rd |only lakhesis-1.1/lakhesis/man/element_eval.Rd |only lakhesis-1.1/lakhesis/man/im_long.Rd |only lakhesis-1.1/lakhesis/man/im_merge.Rd |only lakhesis-1.1/lakhesis/man/im_read_csv.Rd |only lakhesis-1.1/lakhesis/man/im_ref.Rd |only lakhesis-1.1/lakhesis/man/lakhesize.Rd | 44 - lakhesis-1.1/lakhesis/man/qf_strands.Rd |only lakhesis-1.1/lakhesis/man/spearman_sq.Rd |only lakhesis-1.1/lakhesis/man/strand_add.Rd |only lakhesis-1.1/lakhesis/man/strand_create.Rd |only lakhesis-1.1/lakhesis/man/strand_extract.Rd |only lakhesis-1.1/lakhesis/man/strand_suppress.Rd |only lakhesis-1.1/lakhesis/man/strands_create.Rd |only lakhesis-1.1/lakhesis/src |only lakhesis-1.1/lakhesis/vignettes |only 58 files changed, 2139 insertions(+), 1657 deletions(-)
Title: Native R Implementation of an Efficient BLAST-Like Algorithm
Description: Implementation of an efficient BLAST-like sequence
comparison algorithm, written in 'C++11' and using
native R datatypes. Blaster is based on 'nsearch' -
Schmid et al (2018) <doi:10.1101/399782>.
Author: Manu Tamminen [aut, cre] ,
Timothy Julian [aut] ,
Aditya Jeevennavar [aut] ,
Steven Schmid [aut]
Maintainer: Manu Tamminen <mavatam@utu.fi>
This is a re-admission after prior archival of version 1.0.7 dated 2023-08-22
Diff between blaster versions 1.0.7 dated 2023-08-22 and 1.0.9 dated 2026-04-25
blaster-1.0.7/blaster/R/blaster-package.R |only blaster-1.0.7/blaster/build |only blaster-1.0.7/blaster/man/blaster-package.Rd |only blaster-1.0.9/blaster/DESCRIPTION | 19 ++++++++++--------- blaster-1.0.9/blaster/MD5 | 10 ++++------ blaster-1.0.9/blaster/R/blaster.R | 4 ++-- blaster-1.0.9/blaster/README.md | 2 +- blaster-1.0.9/blaster/man/blaster.Rd |only 8 files changed, 17 insertions(+), 18 deletions(-)
Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut],
Nikolas Barkas [aut],
Peter Kharchenko [aut],
Weiliang Qiu [ctb],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between conos versions 1.5.3 dated 2026-04-01 and 1.5.4 dated 2026-04-25
DESCRIPTION | 16 ++++++++-------- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 11 insertions(+), 11 deletions(-)
Title: Tesselation Visualization Plots for 2D Data
Description: Creates visualization plots for 2D data including ellipse plots, Voronoi tesselation plots, and combined ellipse-Voronoi plots. Designed to visualize class separation in 2D data, raw of from projection techniques like principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) or others. For more details see Lotsch and Kringel (2026) and Lotsch, J., and Kringel, D. (2026) <doi:10.1371/journal.pone.0333653>.
Author: Jorn Lotsch [aut, cre]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Diff between VoronoiBiomedPlot versions 0.3 dated 2026-03-07 and 0.3.2 dated 2026-04-25
DESCRIPTION | 10 +- MD5 | 14 +-- R/create_tesselation_plots.R | 154 ++++++++++++++++++++-------------------- R/create_voronoi_plot.R | 96 ++++++++++++------------ build/partial.rdb |binary inst/CITATION | 18 ++-- man/create_tesselation_plots.Rd | 17 ++++ man/create_voronoi_plot.Rd | 6 + 8 files changed, 173 insertions(+), 142 deletions(-)
More information about VoronoiBiomedPlot at CRAN
Permanent link
Title: Chart Generation for 'Microsoft Word', 'Microsoft Excel' and
'Microsoft PowerPoint' Documents
Description: Create native charts for 'Microsoft PowerPoint', 'Microsoft
Excel' and 'Microsoft Word' documents. The resulting charts can then
be edited and annotated in the host application. It provides functions
to create charts and to modify their content and formatting. The
chart's underlying data is automatically saved within the 'Word',
'Excel' or 'PowerPoint' file. It extends the 'officer' package, which
does not provide native 'Microsoft' chart production.
Author: David Gohel [aut, cre],
ArData [cph],
YouGov [fnd],
Jan Marvin Garbuszus [ctb] ,
Stefan Moog [ctb] ,
Eli Daniels [ctb],
Marlon Molina [ctb] ,
Rokas Klydzia [ctb] ,
David Camposeco [ctb] ,
Dan Joplin [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between mschart versions 0.4.1 dated 2025-08-18 and 0.4.3 dated 2026-04-25
mschart-0.4.1/mschart/inst/tinytest |only mschart-0.4.1/mschart/tests/tinytest.R |only mschart-0.4.3/mschart/DESCRIPTION | 74 - mschart-0.4.3/mschart/MD5 | 129 +- mschart-0.4.3/mschart/NAMESPACE | 19 mschart-0.4.3/mschart/NEWS.md | 73 + mschart-0.4.3/mschart/R/as_series.R | 124 +- mschart-0.4.3/mschart/R/axis_codes.R | 127 +- mschart-0.4.3/mschart/R/axis_setting.R | 341 ++++-- mschart-0.4.3/mschart/R/body_add_chart.R | 132 +- mschart-0.4.3/mschart/R/chart_data_labels.R | 109 +- mschart-0.4.3/mschart/R/chart_data_styles.R | 251 +++- mschart-0.4.3/mschart/R/chart_labels.R | 23 mschart-0.4.3/mschart/R/chart_settings.R | 310 +++++ mschart-0.4.3/mschart/R/datasets.R | 19 mschart-0.4.3/mschart/R/excel_series.R | 22 mschart-0.4.3/mschart/R/helpers.R | 33 mschart-0.4.3/mschart/R/ms_chart.R | 855 ++++++++++++++- mschart-0.4.3/mschart/R/package.R | 38 mschart-0.4.3/mschart/R/ph_with_chart.R | 68 - mschart-0.4.3/mschart/R/series.R | 87 - mschart-0.4.3/mschart/R/simple_types.R | 49 mschart-0.4.3/mschart/R/sppr_codes.R | 18 mschart-0.4.3/mschart/R/table_setting.R | 22 mschart-0.4.3/mschart/R/theme.R | 253 +++- mschart-0.4.3/mschart/R/themes.R | 40 mschart-0.4.3/mschart/R/to_pml.R | 862 ++++++++++++---- mschart-0.4.3/mschart/R/utils.R | 91 + mschart-0.4.3/mschart/R/xlsx_add_chart.R |only mschart-0.4.3/mschart/README.md | 67 - mschart-0.4.3/mschart/man/as_bar_stack.Rd | 14 mschart-0.4.3/mschart/man/body_add_chart.Rd | 10 mschart-0.4.3/mschart/man/browser_data.Rd | 7 mschart-0.4.3/mschart/man/browser_ts.Rd | 9 mschart-0.4.3/mschart/man/chart_ax_x.Rd | 43 mschart-0.4.3/mschart/man/chart_ax_y.Rd | 36 mschart-0.4.3/mschart/man/chart_data_fill.Rd | 16 mschart-0.4.3/mschart/man/chart_data_labels.Rd | 19 mschart-0.4.3/mschart/man/chart_data_line_style.Rd | 3 mschart-0.4.3/mschart/man/chart_data_line_width.Rd | 7 mschart-0.4.3/mschart/man/chart_data_size.Rd | 3 mschart-0.4.3/mschart/man/chart_data_smooth.Rd | 7 mschart-0.4.3/mschart/man/chart_data_stroke.Rd | 5 mschart-0.4.3/mschart/man/chart_data_symbol.Rd | 3 mschart-0.4.3/mschart/man/chart_labels.Rd | 12 mschart-0.4.3/mschart/man/chart_labels_text.Rd | 3 mschart-0.4.3/mschart/man/chart_settings.Rd | 71 + mschart-0.4.3/mschart/man/chart_table.Rd | 13 mschart-0.4.3/mschart/man/ms_areachart.Rd | 29 mschart-0.4.3/mschart/man/ms_barchart.Rd | 73 + mschart-0.4.3/mschart/man/ms_bubblechart.Rd |only mschart-0.4.3/mschart/man/ms_chart_combine.Rd |only mschart-0.4.3/mschart/man/ms_linechart.Rd | 29 mschart-0.4.3/mschart/man/ms_piechart.Rd |only mschart-0.4.3/mschart/man/ms_radarchart.Rd |only mschart-0.4.3/mschart/man/ms_scatterchart.Rd | 29 mschart-0.4.3/mschart/man/ms_stockchart.Rd |only mschart-0.4.3/mschart/man/mschart.Rd | 41 mschart-0.4.3/mschart/man/ph_with.ms_chart.Rd | 12 mschart-0.4.3/mschart/man/print.ms_chart.Rd | 9 mschart-0.4.3/mschart/man/set_theme.Rd | 46 mschart-0.4.3/mschart/man/sheet_add_drawing.ms_chart.Rd |only mschart-0.4.3/mschart/man/us_indus_prod.Rd | 9 mschart-0.4.3/mschart/tests/testthat |only mschart-0.4.3/mschart/tests/testthat.R |only 65 files changed, 3809 insertions(+), 985 deletions(-)
Title: Fast, Sensitive, and Accurate Integration of Single Cell Data
Description: Implementation of the Harmony algorithm for single cell integration, described in Patikas, Yao, et al. <doi:10.64898/2026.03.16.711825>. Package includes a standalone Harmony function and interfaces to external frameworks.
Author: Nikolaos Patikas [aut, ctb] ,
Hongcheng Yao [aut, ctb] ,
Ilya Korsunsky [cre, aut] ,
Martin Hemberg [aut] ,
Nghia Millard [aut] ,
Jean Fan [aut, ctb] ,
Kamil Slowikowski [aut, ctb] ,
Miles Smith [ctb],
Soumya Raychaudhuri [aut]
Maintainer: Ilya Korsunsky <ilya.korsunsky@gmail.com>
Diff between harmony versions 1.2.4 dated 2025-10-10 and 2.0.2 dated 2026-04-25
harmony-1.2.4/harmony/R/harmony-package.r |only harmony-1.2.4/harmony/man/HarmonyMatrix.Rd |only harmony-1.2.4/harmony/man/moe_ridge_get_betas.Rd |only harmony-1.2.4/harmony/src/Makevars |only harmony-1.2.4/harmony/src/Makevars.win |only harmony-2.0.2/harmony/DESCRIPTION | 33 harmony-2.0.2/harmony/MD5 | 80 harmony-2.0.2/harmony/NAMESPACE | 4 harmony-2.0.2/harmony/R/RcppExports.R | 4 harmony-2.0.2/harmony/R/RunHarmony.R | 5 harmony-2.0.2/harmony/R/harmony-package.R |only harmony-2.0.2/harmony/R/harmony_option.R | 50 harmony-2.0.2/harmony/R/ui.R | 40 harmony-2.0.2/harmony/R/utils.R | 13 harmony-2.0.2/harmony/R/zzz.R |only harmony-2.0.2/harmony/build/partial.rdb |binary harmony-2.0.2/harmony/build/vignette.rds |binary harmony-2.0.2/harmony/cleanup |only harmony-2.0.2/harmony/cleanup.win |only harmony-2.0.2/harmony/configure |only harmony-2.0.2/harmony/configure.win |only harmony-2.0.2/harmony/inst/doc/Seurat.R | 72 harmony-2.0.2/harmony/inst/doc/Seurat.Rmd | 22 harmony-2.0.2/harmony/inst/doc/Seurat.html | 255 +-- harmony-2.0.2/harmony/inst/doc/detailedWalkthrough.R | 236 +- harmony-2.0.2/harmony/inst/doc/detailedWalkthrough.Rmd | 215 +- harmony-2.0.2/harmony/inst/doc/detailedWalkthrough.html | 910 +++++------ harmony-2.0.2/harmony/inst/doc/quickstart.R | 4 harmony-2.0.2/harmony/inst/doc/quickstart.Rmd | 2 harmony-2.0.2/harmony/inst/doc/quickstart.html | 104 - harmony-2.0.2/harmony/man/RunHarmony.Seurat.Rd | 4 harmony-2.0.2/harmony/man/RunHarmony.SingleCellExperiment.Rd | 4 harmony-2.0.2/harmony/man/RunHarmony.default.Rd | 8 harmony-2.0.2/harmony/man/harmony.Rd | 34 harmony-2.0.2/harmony/man/harmony_options.Rd | 12 harmony-2.0.2/harmony/src/Makevars.in |only harmony-2.0.2/harmony/src/RcppExports.cpp | 17 harmony-2.0.2/harmony/src/harmony.cpp | 589 +++++-- harmony-2.0.2/harmony/src/harmony.h | 30 harmony-2.0.2/harmony/src/timer.cpp |only harmony-2.0.2/harmony/src/timer.h |only harmony-2.0.2/harmony/src/types.h | 16 harmony-2.0.2/harmony/src/utils.cpp | 115 + harmony-2.0.2/harmony/src/utils.h | 8 harmony-2.0.2/harmony/tests/testthat/test_integration.R | 23 harmony-2.0.2/harmony/vignettes/Seurat.Rmd | 22 harmony-2.0.2/harmony/vignettes/detailedWalkthrough.Rmd | 215 +- harmony-2.0.2/harmony/vignettes/quickstart.Rmd | 2 48 files changed, 1821 insertions(+), 1327 deletions(-)
Title: Deal with Dependencies
Description: Manage dependencies during package development. This can
retrieve all dependencies that are used in ".R" files in the "R/"
directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2'
documentation of functions. There is a function to update the
"DESCRIPTION" file of your package with 'CRAN' packages or any other
remote package. All functions to retrieve dependencies of ".R"
scripts and ".Rmd" or ".qmd" files can be used independently of a
package development.
Author: Vincent Guyader [cre, aut] ,
Sebastien Rochette [aut] ,
Murielle Delmotte [aut] ,
Swann Floc'hlay [aut] ,
ThinkR [cph, fnd]
Maintainer: Vincent Guyader <vincent@thinkr.fr>
Diff between attachment versions 0.4.5 dated 2025-03-14 and 1.0.0 dated 2026-04-25
DESCRIPTION | 20 +- MD5 | 60 ++++--- NEWS.md | 65 ++++++++ R/amend_with_config.R | 1 R/att_from_rmds.R | 29 ++- R/att_from_rscripts.R | 190 ++++++++++++++++++++++--- R/att_to_description.R | 2 R/attachment-deprecated.R | 2 R/create_dependencies_file.R | 1 R/create_renv.R | 5 R/dependencies_file_text.R | 1 build/vignette.rds |binary inst/doc/a-fill-pkg-description.html | 13 - inst/doc/b-bookdown-and-scripts.html | 9 - inst/doc/create-dependencies-file.Rmd | 1 inst/doc/create-dependencies-file.html | 6 inst/doc/use_renv.html | 5 man/att_amend_desc.Rd | 10 - man/att_from_rmd.Rd | 10 - man/att_from_rmds.Rd | 17 +- man/att_from_rscript.Rd | 21 ++ man/att_from_rscripts.Rd | 7 man/attachment-deprecated.Rd | 8 - man/create_renv_for_dev.Rd | 3 tests/testthat/f_edge_cases.R |only tests/testthat/test-amend_with_config.R | 7 tests/testthat/test-create_dependencies_file.R | 1 tests/testthat/test-dependencies_file_text.R | 1 tests/testthat/test-edge-cases.R |only tests/testthat/test-inside-rmd-autodetect.R |only tests/testthat/test-quarto-vignettes.R |only tests/testthat/test-rscript.R | 12 + vignettes/create-dependencies-file.Rmd | 1 33 files changed, 388 insertions(+), 120 deletions(-)