Title: Space-Filling Designs
Description: Construct various types of space-filling designs, including Latin hypercube designs, clustering-based designs, maximin designs, maximum projection designs, and uniform designs (Joseph 2016 <doi:10.1080/08982112.2015.1100447>). It also offers the option to optimize designs based on user-defined criteria. This work is supported by U.S. National Science Foundation grant DMS-2310637.
Author: Shangkun Wang [aut, cre],
Roshan Joseph [aut]
Maintainer: Shangkun Wang <shangkunwang01@gmail.com>
Diff between SFDesign versions 0.1.2 dated 2025-06-21 and 0.1.3 dated 2025-09-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/RcppExports.R | 4 ++-- R/maxpro.R | 4 ++-- R/utils.R | 4 ++-- man/maxpro.crit.Rd | 2 +- src/RcppExports.cpp | 9 +++++---- src/pairwise_design.cpp | 36 +++++++++++++++++------------------- 8 files changed, 40 insertions(+), 41 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Development, simulation testing, and implementation of management procedures for fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Adrian Hordyk [aut, cre],
Quang Huynh [aut],
Tom Carruthers [aut],
Chris Grandin [ctb]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 3.7.4 dated 2025-06-04 and 3.7.5 dated 2025-09-29
DESCRIPTION | 20 ++-- MD5 | 57 ++++++----- NAMESPACE | 1 NEWS.md | 14 ++ R/ASAP2OM.R | 11 +- R/Class_definitions.R | 47 +++++++-- R/Data_Functions.R | 7 - R/Data_make_update.R | 21 +++- R/Empirical_MP.R | 14 ++ R/MMSE_Object.r | 47 +-------- R/MOM_object.r | 7 + R/Misc_Exported.R | 18 ++- R/Misc_Internal.R | 4 R/OM_functions.R | 4 R/SS2Data.R | 12 +- R/SS2MOM.R | 5 - R/SS2OM.R | 25 ++++- R/SSinternal.R | 125 +++++++++++++++++++++++-- R/SampleOM.R | 41 ++++++-- R/multiMSE.R | 169 +++++++++++++++++++---------------- R/popdyn.R | 236 ++++++++++++++++++++++++++++++++++++++++--------- R/popdyn_MICE.R | 46 +++++---- R/runMSE.R | 117 +++++++++++++++++------- build/partial.rdb |binary man/ASAP2OM.Rd | 3 man/MSEextra.Rd | 4 man/print.multiHist.Rd |only man/show-MSEtool.Rd | 6 + man/tune_MP.Rd | 134 +++++++++++++-------------- src/popddynCPP.cpp | 12 +- 30 files changed, 817 insertions(+), 390 deletions(-)
Title: Access Geographic Data
Description: Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb] ,
Aniruddha Ghosh [ctb],
Alex Mandel [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between geodata versions 0.6-2 dated 2024-06-10 and 0.6-6 dated 2025-09-29
geodata-0.6-2/geodata/R/helper-functions.R |only geodata-0.6-6/geodata/DESCRIPTION | 25 +++-- geodata-0.6-6/geodata/MD5 | 37 ++++--- geodata-0.6-6/geodata/NAMESPACE | 1 geodata-0.6-6/geodata/R/countries.R | 53 +++++----- geodata-0.6-6/geodata/R/download.R |only geodata-0.6-6/geodata/R/gadm.R | 2 geodata-0.6-6/geodata/R/nasawth.R |only geodata-0.6-6/geodata/R/occurrence.R | 28 ++++- geodata-0.6-6/geodata/R/path.R |only geodata-0.6-6/geodata/R/soil_grids.R | 25 +++-- geodata-0.6-6/geodata/R/soil_isda.R | 70 +++++++++++++- geodata-0.6-6/geodata/R/worldclim.R | 128 +++++++++++++++++--------- geodata-0.6-6/geodata/build/partial.rdb |binary geodata-0.6-6/geodata/man/biooracle.Rd | 2 geodata-0.6-6/geodata/man/cmip6.Rd | 8 - geodata-0.6-6/geodata/man/geodata_path.Rd | 17 +-- geodata-0.6-6/geodata/man/soil_af_isda.Rd | 2 geodata-0.6-6/geodata/man/soil_af_isda_vsi.Rd |only geodata-0.6-6/geodata/man/soil_grids.Rd | 3 geodata-0.6-6/geodata/man/soil_grids_vsi.Rd | 2 geodata-0.6-6/geodata/man/sp_occurrence.Rd | 25 ++--- 22 files changed, 285 insertions(+), 143 deletions(-)
Title: Unified and Automatic 'Theming' of 'ggplot2', 'lattice', and
'base' R Graphics
Description: Theme 'ggplot2', 'lattice', and 'base' graphics based on a
few choices, including foreground color, background color, accent
color, and font family. Fonts that aren't available on the system, but
are available via download on 'Google Fonts', can be automatically
downloaded, cached, and registered for use with the 'showtext' and
'ragg' packages.
Author: Carson Sievert [aut, cre] ,
Barret Schloerke [aut] ,
Joe Cheng [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Carson Sievert <carson@posit.co>
Diff between thematic versions 0.1.7 dated 2025-06-19 and 0.1.8 dated 2025-09-29
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS.md | 5 +++++ R/ggplot.R | 15 ++++++++------- 4 files changed, 22 insertions(+), 16 deletions(-)
Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016).
Author: Cody L Marquart [aut, cre] ,
Zachari Swiecki [aut],
Wesley Collier [aut],
Brendan Eagan [aut],
Roman Woodward [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
This is a re-admission after prior archival of version 0.2.7 dated 2024-02-23
Diff between rENA versions 0.2.7 dated 2024-02-23 and 0.3.0 dated 2025-09-29
rENA-0.2.7/rENA/man/scale.ena.set.Rd |only rENA-0.3.0/rENA/DESCRIPTION | 20 rENA-0.3.0/rENA/MD5 | 188 +- rENA-0.3.0/rENA/NAMESPACE | 43 rENA-0.3.0/rENA/R/ENAdata.R | 14 rENA-0.3.0/rENA/R/ENAplot.R | 86 - rENA-0.3.0/rENA/R/ENAset.R | 2 rENA-0.3.0/rENA/R/RcppExports.R | 53 rENA-0.3.0/rENA/R/accumulate.data.R | 19 rENA-0.3.0/rENA/R/ena.conversations.R | 6 rENA-0.3.0/rENA/R/ena.make.set.R | 20 rENA-0.3.0/rENA/R/ena.plot.R | 24 rENA-0.3.0/rENA/R/ena.plot.group.R | 8 rENA-0.3.0/rENA/R/ena.plot.network.R | 14 rENA-0.3.0/rENA/R/ena.plot.points.R | 2 rENA-0.3.0/rENA/R/ena.plot.trajectory.R | 2 rENA-0.3.0/rENA/R/ena.rotate.by.generalized.R |only rENA-0.3.0/rENA/R/ena.rotate.by.mean.R | 2 rENA-0.3.0/rENA/R/ena.rotate.by.regression.2.R |only rENA-0.3.0/rENA/R/ena.rotate.by.regression.R | 145 +- rENA-0.3.0/rENA/R/ena.set.R | 10 rENA-0.3.0/rENA/R/ena.svd.R | 56 rENA-0.3.0/rENA/R/gmr.R |only rENA-0.3.0/rENA/R/lws.positions.sq.R | 5 rENA-0.3.0/rENA/R/move_nodes.R | 46 rENA-0.3.0/rENA/R/piped.R |only rENA-0.3.0/rENA/R/qedata_classes.R |only rENA-0.3.0/rENA/R/qedata_define.R |only rENA-0.3.0/rENA/R/rENA.R | 8 rENA-0.3.0/rENA/R/utils.R | 75 + rENA-0.3.0/rENA/R/utils.classes.R | 1 rENA-0.3.0/rENA/R/utils.matrix.R | 2 rENA-0.3.0/rENA/R/utils.plot.R | 679 ++++++---- rENA-0.3.0/rENA/R/zzz.R | 4 rENA-0.3.0/rENA/demo/fullExample.R | 6 rENA-0.3.0/rENA/inst/CITATION | 9 rENA-0.3.0/rENA/inst/examples |only rENA-0.3.0/rENA/inst/include/rENA_RcppExports.h | 44 rENA-0.3.0/rENA/inst/rmd/methods.rmd | 21 rENA-0.3.0/rENA/man/ENAplot.Rd | 62 rENA-0.3.0/rENA/man/accumulate.Rd |only rENA-0.3.0/rENA/man/add_group.Rd | 58 rENA-0.3.0/rENA/man/add_network.Rd | 47 rENA-0.3.0/rENA/man/add_nodes.Rd | 60 rENA-0.3.0/rENA/man/add_points.Rd | 66 rENA-0.3.0/rENA/man/add_trajectory.Rd | 60 rENA-0.3.0/rENA/man/as.qe.code.Rd |only rENA-0.3.0/rENA/man/as.qe.data.Rd |only rENA-0.3.0/rENA/man/as.qe.horizon.Rd |only rENA-0.3.0/rENA/man/as.qe.metadata.Rd |only rENA-0.3.0/rENA/man/as.qe.unit.Rd |only rENA-0.3.0/rENA/man/center.Rd |only rENA-0.3.0/rENA/man/check_range.Rd |only rENA-0.3.0/rENA/man/clear.Rd | 49 rENA-0.3.0/rENA/man/codes.Rd |only rENA-0.3.0/rENA/man/compute_SB.Rd |only rENA-0.3.0/rENA/man/define.Rd |only rENA-0.3.0/rENA/man/directed_node_positions.Rd |only rENA-0.3.0/rENA/man/directed_node_positions_with_ground_response_added.Rd |only rENA-0.3.0/rENA/man/ena.plot.Rd | 25 rENA-0.3.0/rENA/man/ena.plot.group.Rd | 3 rENA-0.3.0/rENA/man/ena.plot.network.Rd | 3 rENA-0.3.0/rENA/man/ena.plot.points.Rd | 2 rENA-0.3.0/rENA/man/ena.plot.trajectory.Rd | 2 rENA-0.3.0/rENA/man/ena.rotate.by.generalized.Rd |only rENA-0.3.0/rENA/man/ena.rotate.by.hena.regression.Rd | 10 rENA-0.3.0/rENA/man/ena.rotate.by.hena.regression_2.Rd |only rENA-0.3.0/rENA/man/ena.svd.Rd | 33 rENA-0.3.0/rENA/man/find_binary_cols.Rd |only rENA-0.3.0/rENA/man/fun_skip_sphere_norm.Rd | 17 rENA-0.3.0/rENA/man/fun_sphere_norm.Rd | 17 rENA-0.3.0/rENA/man/get_x1_main_effect.Rd |only rENA-0.3.0/rENA/man/gmr.Rd |only rENA-0.3.0/rENA/man/group.Rd |only rENA-0.3.0/rENA/man/horizon.Rd |only rENA-0.3.0/rENA/man/is.qe.code.Rd |only rENA-0.3.0/rENA/man/is.qe.data.Rd |only rENA-0.3.0/rENA/man/is.qe.horizon.Rd |only rENA-0.3.0/rENA/man/is.qe.metadata.Rd |only rENA-0.3.0/rENA/man/is.qe.unit.Rd |only rENA-0.3.0/rENA/man/merge_columns_c.Rd | 2 rENA-0.3.0/rENA/man/metadata.Rd |only rENA-0.3.0/rENA/man/model.Rd |only rENA-0.3.0/rENA/man/move_nodes_to_unit_circle.Rd | 6 rENA-0.3.0/rENA/man/move_nodes_to_unit_circle_with_equal_space.Rd | 4 rENA-0.3.0/rENA/man/optimize.Rd |only rENA-0.3.0/rENA/man/plot.ena.set.Rd | 61 rENA-0.3.0/rENA/man/prepare_trajectory_data.Rd | 20 rENA-0.3.0/rENA/man/project.Rd |only rENA-0.3.0/rENA/man/reclassify.Rd |only rENA-0.3.0/rENA/man/rotate.Rd |only rENA-0.3.0/rENA/man/scale.ENAplot.Rd |only rENA-0.3.0/rENA/man/show.Rd | 11 rENA-0.3.0/rENA/man/sphere_norm.Rd |only rENA-0.3.0/rENA/man/times-.ena.matrix.Rd |only rENA-0.3.0/rENA/man/units.Rd |only rENA-0.3.0/rENA/man/with.ena.matrix.Rd |only rENA-0.3.0/rENA/man/with_means.Rd | 10 rENA-0.3.0/rENA/man/with_trajectory.Rd | 21 rENA-0.3.0/rENA/src/Makevars.win | 2 rENA-0.3.0/rENA/src/RcppExports.cpp | 78 + rENA-0.3.0/rENA/src/ena.cpp | 166 ++ rENA-0.3.0/rENA/tests/testthat/test-cohens.R | 2 rENA-0.3.0/rENA/tests/testthat/test-convs.R | 10 rENA-0.3.0/rENA/tests/testthat/test-ena_group.R | 4 rENA-0.3.0/rENA/tests/testthat/test-ena_wrapper.R | 2 rENA-0.3.0/rENA/tests/testthat/test-gmr.R |only rENA-0.3.0/rENA/tests/testthat/test-piping.R |only rENA-0.3.0/rENA/tests/testthat/test-set_creator.R | 2 rENA-0.3.0/rENA/tests/testthat/test.connection.matrix.R | 8 rENA-0.3.0/rENA/tests/testthat/test.ena.accumulations.R | 12 rENA-0.3.0/rENA/tests/testthat/test.ena.make.set.R | 28 rENA-0.3.0/rENA/tests/testthat/test.ena.make.set.old.R | 2 rENA-0.3.0/rENA/tests/testthat/test.ena.plot.set.R | 381 ++--- rENA-0.3.0/rENA/tests/testthat/test.ena.use.cases.R | 42 rENA-0.3.0/rENA/tests/testthat/test.util.classes.R | 4 rENA-0.3.0/rENA/tests/testthat/test.util.matrices.R | 4 rENA-0.3.0/rENA/tests/testthat/test.utils.R | 10 118 files changed, 2089 insertions(+), 931 deletions(-)
Title: Test Investment Strategies with English-Like Code
Description: Design, backtest, and analyze portfolio strategies using simple,
English-like function chains. Includes technical indicators, flexible stock
selection, portfolio construction methods (equal weighting, signal weighting,
inverse volatility, hierarchical risk parity), and a compact backtesting
engine for portfolio returns, drawdowns, and summary metrics.
Author: Alberto Pallotta [aut, cre]
Maintainer: Alberto Pallotta <pallottaalberto@gmail.com>
Diff between PortfolioTesteR versions 0.1.1 dated 2025-09-22 and 0.1.2 dated 2025-09-29
DESCRIPTION | 6 MD5 | 87 +- NAMESPACE | 45 + NEWS.md | 65 + R/cross_sectional.R | 4 R/globals.R | 9 R/ml.R |only R/optimization.R | 782 +++++++++++++++++- R/technical_indicators.R | 166 ++- R/utils.R | 25 R/walk_forward.R | 269 ++++++ build/vignette.rds |binary inst/doc/getting-started.R | 79 + inst/doc/getting-started.Rmd | 96 ++ inst/doc/getting-started.html | 127 ++ inst/doc/optimization-walkforward.R |only inst/doc/optimization-walkforward.Rmd |only inst/doc/optimization-walkforward.html |only inst/examples/demo_cci_breakout_biweekly_rank.R |only inst/examples/demo_opt_basic.R |only inst/examples/demo_opt_heatmap.R |only inst/examples/demo_opt_surfaces.R |only inst/examples/demo_quality_momentum_inverse_vol.R |only inst/examples/demo_regime_hrp_momentum.R |only inst/examples/demo_stochrsi_acceleration_riskparity.R |only inst/examples/demo_wf_basic.R |only inst/examples/demo_wf_diagnostics.R |only inst/examples/demo_wf_full_diagnostics.R |only inst/examples/ml_sequence_quickstart.R |only inst/examples/ml_tabular_quickstart.R |only man/bucket_returns.Rd |only man/calc_market_breadth.Rd | 2 man/calc_rolling_correlation.Rd |only man/calc_sector_breadth.Rd | 2 man/calc_stochrsi.Rd |only man/cap_exposure.Rd |only man/cap_turnover.Rd |only man/carry_forward_weights.Rd |only man/combine_scores.Rd |only man/coverage_by_date.Rd |only man/cv_tune_seq.Rd |only man/demo_sector_map.Rd |only man/evaluate_scores.Rd |only man/ic_series.Rd |only man/join_panels.Rd |only man/make_labels.Rd |only man/membership_stability.Rd |only man/ml_backtest.Rd |only man/ml_backtest_seq.Rd |only man/panel_lag.Rd |only man/plot.param_grid_result.Rd |only man/plot.wf_optimization_result.Rd |only man/rebalance_calendar.Rd |only man/roll_fit_predict.Rd |only man/roll_fit_predict_seq.Rd |only man/roll_ic_stats.Rd |only man/run_param_grid.Rd | 7 man/select_top_k_scores.Rd |only man/select_top_k_scores_by_group.Rd |only man/transform_scores.Rd |only man/tune_ml_backtest.Rd |only man/turnover_by_date.Rd |only man/validate_group_map.Rd |only man/validate_no_leakage.Rd |only man/weight_from_scores.Rd |only man/wf_sweep_tabular.Rd |only tests/testthat/test-ml.R |only tests/testthat/test-optimization.R |only tests/testthat/test-walk-forward.R |only vignettes/getting-started.Rmd | 96 ++ vignettes/optimization-walkforward.Rmd |only 71 files changed, 1700 insertions(+), 167 deletions(-)
More information about PortfolioTesteR at CRAN
Permanent link
Title: Access to Open Street Map Raster Images
Description: Accesses high resolution raster maps using the OpenStreetMap
protocol. Dozens of road, satellite, and topographic map servers are directly
supported. Additionally raster maps
may be constructed using custom tile servers. Maps can be
plotted using either base graphics, or ggplot2. This package is not affiliated
with the OpenStreetMap.org mapping project.
Author: Ian Fellows [aut, cre],
Jan-Peter Stotz [aut]
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between OpenStreetMap versions 0.4.0 dated 2023-10-12 and 0.4.1 dated 2025-09-29
DESCRIPTION | 18 +++-- MD5 | 20 ++--- R/osm.R | 34 ++++------ inst/java/JMapViewer.jar |binary inst/java/RTileController.jar |binary java/RTileController.java | 2 java/org/openstreetmap/gui/jmapviewer/tilesources/BingAerialTileSource.java | 4 - man/openmap.Rd | 24 +++---- man/openproj.Rd | 4 - man/plot.OpenStreetMap.Rd | 30 ++++++++ man/raster-OpenStreetMap-method.Rd | 2 11 files changed, 86 insertions(+), 52 deletions(-)
Title: Spatial Sampling Design and Analysis
Description: A design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that [...truncated...]
Author: Michael Dumelle [aut, cre] ,
Tom Kincaid [aut],
Anthony R. Olsen [aut],
Marc Weber [aut],
Don Stevens [ctb],
Denis White [ctb],
Amanda M. Nahlik [ctb],
Sarah Lehmann [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spsurvey versions 5.5.1 dated 2024-01-09 and 5.6.0 dated 2025-09-29
spsurvey-5.5.1/spsurvey/inst/doc/EDA.R |only spsurvey-5.5.1/spsurvey/inst/doc/EDA.Rmd |only spsurvey-5.5.1/spsurvey/inst/doc/EDA.html |only spsurvey-5.5.1/spsurvey/inst/doc/analysis.R |only spsurvey-5.5.1/spsurvey/inst/doc/analysis.Rmd |only spsurvey-5.5.1/spsurvey/inst/doc/analysis.html |only spsurvey-5.5.1/spsurvey/inst/doc/sampling.R |only spsurvey-5.5.1/spsurvey/inst/doc/sampling.Rmd |only spsurvey-5.5.1/spsurvey/inst/doc/sampling.html |only spsurvey-5.5.1/spsurvey/vignettes/EDA.Rmd |only spsurvey-5.5.1/spsurvey/vignettes/analysis.Rmd |only spsurvey-5.5.1/spsurvey/vignettes/sampling.Rmd |only spsurvey-5.6.0/spsurvey/DESCRIPTION | 30 ++-- spsurvey-5.6.0/spsurvey/MD5 | 43 ++---- spsurvey-5.6.0/spsurvey/NEWS.md | 14 ++ spsurvey-5.6.0/spsurvey/R/adjwgtNR.R | 60 ++++----- spsurvey-5.6.0/spsurvey/R/dsgn_check.R | 16 ++ spsurvey-5.6.0/spsurvey/R/startup.R | 38 ++--- spsurvey-5.6.0/spsurvey/R/utils.R | 3 spsurvey-5.6.0/spsurvey/README.md | 33 ++-- spsurvey-5.6.0/spsurvey/build/vignette.rds |binary spsurvey-5.6.0/spsurvey/inst/doc/start-here.R | 4 spsurvey-5.6.0/spsurvey/inst/doc/start-here.Rmd | 42 +++--- spsurvey-5.6.0/spsurvey/inst/doc/start-here.html | 113 +++++++++-------- spsurvey-5.6.0/spsurvey/man/adjwgtNR.Rd | 24 +-- spsurvey-5.6.0/spsurvey/man/figures |only spsurvey-5.6.0/spsurvey/man/spsurvey-package.Rd | 8 - spsurvey-5.6.0/spsurvey/tests/testthat/test-adjwgtNR.R | 12 + spsurvey-5.6.0/spsurvey/vignettes/start-here.Rmd | 42 +++--- 29 files changed, 262 insertions(+), 220 deletions(-)
Title: Helper Functions for Species Delimitation Analysis
Description: Helpers functions to process, analyse, and visualize the output of
single locus species delimitation methods.
For full functionality, please install suggested software at
<https://legallab.github.io/delimtools/articles/install.html>.
Author: Pedro Bittencourt [aut, cre, cph] ,
Rupert Collins [aut, ctb, cph] ,
Tomas Hrbek [aut, ctb]
Maintainer: Pedro Bittencourt <pedro.sennabittencourt@gmail.com>
Diff between delimtools versions 0.2.0 dated 2025-03-31 and 0.2.1 dated 2025-09-29
DESCRIPTION | 20 +++--- MD5 | 83 +++++++++++++++++++++----- NEWS.md | 14 ++++ R/abgd_tbl.R | 10 ++- R/asap_tbl.R | 10 ++- R/get_delim_cols.R | 55 +++++++---------- R/hap_unite.R | 2 README.md | 43 +++++++++++-- build/vignette.rds |binary inst/doc/install.R | 16 ++--- inst/doc/install.Rmd | 20 ++---- inst/doc/install.html | 37 ++++++----- man/abgd_tbl.Rd | 4 - man/asap_tbl.Rd | 4 - man/figures/README-example-1.png |binary vignettes/geophagus.abgd.svg |only vignettes/geophagus.disthist.svg |only vignettes/geophagus.fasta |only vignettes/geophagus.fasta.Histo.svg |only vignettes/geophagus.fasta.HistoCum.svg |only vignettes/geophagus.fasta.Partition_1.csv |only vignettes/geophagus.fasta.Partition_1.txt |only vignettes/geophagus.fasta.Partition_10.csv |only vignettes/geophagus.fasta.Partition_10.txt |only vignettes/geophagus.fasta.Partition_2.csv |only vignettes/geophagus.fasta.Partition_2.txt |only vignettes/geophagus.fasta.Partition_3.csv |only vignettes/geophagus.fasta.Partition_3.txt |only vignettes/geophagus.fasta.Partition_4.csv |only vignettes/geophagus.fasta.Partition_4.txt |only vignettes/geophagus.fasta.Partition_5.csv |only vignettes/geophagus.fasta.Partition_5.txt |only vignettes/geophagus.fasta.Partition_6.csv |only vignettes/geophagus.fasta.Partition_6.txt |only vignettes/geophagus.fasta.Partition_7.csv |only vignettes/geophagus.fasta.Partition_7.txt |only vignettes/geophagus.fasta.Partition_8.csv |only vignettes/geophagus.fasta.Partition_8.txt |only vignettes/geophagus.fasta.Partition_9.csv |only vignettes/geophagus.fasta.Partition_9.txt |only vignettes/geophagus.fasta.clado.svg |only vignettes/geophagus.fasta.curve.svg |only vignettes/geophagus.fasta.groups.svg |only vignettes/geophagus.fasta.spart |only vignettes/geophagus.fasta.spart.xml |only vignettes/geophagus.fasta.svg |only vignettes/geophagus.part.1.txt |only vignettes/geophagus.part.2.txt |only vignettes/geophagus.part.3.txt |only vignettes/geophagus.part.4.txt |only vignettes/geophagus.part.5.txt |only vignettes/geophagus.part.6.txt |only vignettes/geophagus.part.7.txt |only vignettes/geophagus.part.8.txt |only vignettes/geophagus.partinit.1.txt |only vignettes/geophagus.partinit.2.txt |only vignettes/geophagus.partinit.3.txt |only vignettes/geophagus.partinit.4.txt |only vignettes/geophagus.partinit.5.txt |only vignettes/geophagus.partinit.6.txt |only vignettes/geophagus.partinit.7.txt |only vignettes/geophagus.partinit.8.txt |only vignettes/geophagus.rank.svg |only vignettes/geophagus_raxml.nwk |only vignettes/geophagus_raxml.nwk.mptp.multi.svg |only vignettes/geophagus_raxml.nwk.mptp.multi.txt |only vignettes/geophagus_raxml.nwk.mptp.single.svg |only vignettes/geophagus_raxml.nwk.mptp.single.txt |only vignettes/install.Rmd | 20 ++---- 69 files changed, 220 insertions(+), 118 deletions(-)
Title: Example BGM Files for the Atlantis Ecosystem Model
Description: A collection of box-geometry model (BGM) files for the Atlantis
ecosystem model. Atlantis is a deterministic, biogeochemical,
whole-of-ecosystem model (see <http://atlantis.cmar.csiro.au/> for more information).
Author: Michael D. Sumner [aut, cre],
Hadley Wickham [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between bgmfiles versions 0.0.6 dated 2016-08-10 and 0.1.0 dated 2025-09-29
bgmfiles-0.0.6/bgmfiles/R/bgmfiles-package.r |only bgmfiles-0.1.0/bgmfiles/DESCRIPTION | 18 bgmfiles-0.1.0/bgmfiles/MD5 | 42 bgmfiles-0.1.0/bgmfiles/NAMESPACE | 6 bgmfiles-0.1.0/bgmfiles/NEWS.md | 70 bgmfiles-0.1.0/bgmfiles/R/bgmfiles-package.R |only bgmfiles-0.1.0/bgmfiles/README.md | 179 bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/AEEC_poly_projETRS89_LAEA_snapped0p002.bgm |16134 +++++----- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/CalCurrentV3_utm.bgm | 9558 ++--- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/Final_CAM_Boxes_8.bgm | 6568 ++-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/GOM_BGM.bgm | 4974 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/Guam_utm1.bgm | 7330 ++-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/JFRE_ll.bgm | 5006 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/JFRE_xy.bgm | 5006 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/NGOM.bgm | 4472 +- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/Nordic02.bgm | 6278 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/VMPA_setas.bgm | 898 bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/ams71.bgm | 5512 +-- bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/antarctica_28.bgm | 2530 - bgmfiles-0.1.0/bgmfiles/inst/extdata/bgm/antarctica_99.bgm | 8778 ++--- bgmfiles-0.1.0/bgmfiles/man/bgmfiles.Rd | 92 bgmfiles-0.1.0/bgmfiles/tests/testthat.R | 8 bgmfiles-0.1.0/bgmfiles/tests/testthat/test-files.R | 16 23 files changed, 41758 insertions(+), 41717 deletions(-)
Title: Integer Sequence Generator
Description: Generates well-known integer sequences. 'gmp' package is adopted for computing with arbitrarily large numbers. Every function has hyperlink to its corresponding item in OEIS (The On-Line Encyclopedia of Integer Sequences) in the function help page. For interested readers, see Sloane and Plouffe (1995, ISBN:978-0125586306).
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisung.you@outlook.com>
Diff between Zseq versions 0.2.1 dated 2022-09-07 and 0.2.2 dated 2025-09-29
Zseq-0.2.1/Zseq/man/Zseq-package.Rd |only Zseq-0.2.2/Zseq/DESCRIPTION | 14 +++++++------- Zseq-0.2.2/Zseq/MD5 | 11 +++++------ Zseq-0.2.2/Zseq/R/Factorial.Double.R | 6 ++++-- Zseq-0.2.2/Zseq/R/package-Zseq.R | 3 +-- Zseq-0.2.2/Zseq/R/zzz.R | 2 +- Zseq-0.2.2/Zseq/man/A000165.Rd | 6 ++++-- 7 files changed, 22 insertions(+), 20 deletions(-)
Title: Projected Spatial Gaussian Process Methods
Description: Implements projected sparse Gaussian process Kriging ('Ingram et. al.', 2008, <doi:10.1007/s00477-007-0163-9>) as an additional method for the 'intamap' package. More details on implementation ('Barillec et. al.', 2010, <doi:10.1016/j.cageo.2010.05.008>).
Author: Ben Ingram [aut, cre] ,
Remi Barillec [aut],
Jon Olav Skoien [aut]
Maintainer: Ben Ingram <ingrambr.work@gmail.com>
Diff between psgp versions 0.3-24 dated 2025-09-26 and 0.3-25 dated 2025-09-29
DESCRIPTION | 6 +-- MD5 | 31 ++++++++++--------- src/CovarianceFunction.cpp | 1 src/GaussianProcess.cpp | 8 ++--- src/Makevars | 2 - src/Makevars.win | 6 +++ src/Matern5CF.cpp | 1 src/ModelTrainer.cpp | 8 ++--- src/PSGP.cpp | 65 +++++++++++++++++++++++++++++------------ src/RInterface.cpp | 27 +++++++++++++++-- src/SumCovarianceFunction.cpp | 3 + src/WhiteNoiseCF.cpp | 5 ++- src/psgp_common.h | 9 +++-- src/psgp_estimator.cpp | 64 ++++++++++++++++++++++++++++++---------- src/psgp_estimator.h | 1 src/sensor_metadata_parser.cpp | 7 +++- tests/error_handling.R |only 17 files changed, 171 insertions(+), 73 deletions(-)
Title: A Plotting Toolbox for 2D Oceanographic Data
Description: Plotting toolbox for 2D oceanographic data (satellite data, sea surface temperature, chlorophyll, ocean fronts & bathymetry). Recognized classes and formats include netcdf, Raster, '.nc' and '.gz' files.
Author: Robert K. Bauer [aut, cre]
Maintainer: Robert K. Bauer <marine.biologging@gmail.com>
This is a re-admission after prior archival of version 0.1.6 dated 2023-11-10
Diff between oceanmap versions 0.1.6 dated 2023-11-10 and 0.1.7 dated 2025-09-29
ChangeLog | 4 ++ DESCRIPTION | 20 ++++++---- MD5 | 30 +++++++-------- NAMESPACE | 1 R/ggplotmaply.r | 19 ++------- R/hidden.r | 23 +++++++++++ R/sysdata.rda |binary data/cmap.RData |binary data/cmap_topo.RData |binary data/parameter_definitions.RData |binary data/region_definitions.RData |binary data/region_definitions_bkp.RData |binary inst/doc/oceanmap.pdf |binary man/ggplotmaply.Rd | 75 +++++++++++++++++++------------------- man/oceanmap.Rd | 2 - man/readbin.Rd | 4 +- 16 files changed, 101 insertions(+), 77 deletions(-)
Title: Functions Based on Entropic Statistics
Description: Methods for data analysis from an entropic perspective. These methods are nonparametric and perform well on non-ordinal data. Currently includes 'HeatMap()' for visualizing distributional characteristics among multiple populations (groups).
Author: Jialin Zhang [aut, cph, cre]
Maintainer: Jialin Zhang <jzhang@math.msstate.edu>
This is a re-admission after prior archival of version 0.1.1 dated 2025-08-25
Diff between EntropicStatistics versions 0.1.1 dated 2025-08-25 and 0.1.3 dated 2025-09-29
DESCRIPTION | 18 ++--- MD5 | 9 +- NAMESPACE | 27 +++++--- R/HeatMap.R | 168 ++++++++++++++++++++++++++++++++++++++++++++---------- build |only man/HeatMap.Rd | 175 ++++++++++++++++++++++++++------------------------------- 6 files changed, 249 insertions(+), 148 deletions(-)
More information about EntropicStatistics at CRAN
Permanent link
Title: Access Colombian Data via APIs and Curated Datasets
Description: Provides a comprehensive interface to access diverse public data about
Colombia through multiple APIs and curated datasets. The package integrates
four different APIs: 'API-Colombia' for Colombian-specific data including
geography, culture, tourism, and government information; 'World Bank API'
for economic and demographic indicators; 'Nager.Date' for public holidays;
and 'REST Countries API' for general country information. The package enables
users to explore various aspects of Colombia such as geographic locations,
cultural attractions, economic indicators, demographic data, and public
holidays. Additionally, 'ColombiAPI' includes curated datasets covering
Bogota air stations, business and holiday dates, public schools, Colombian
coffee exports, cannabis licenses, Medellin rainfall, malls in Bogota, as
well as datasets on indigenous languages, student admissions and school
statistics, forest liana mortality, municipal and regional data, connectivity
and digital infrastructure, progra [...truncated...]
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ColombiAPI versions 0.2.0 dated 2025-09-17 and 0.3.0 dated 2025-09-29
DESCRIPTION | 24 MD5 | 186 ++++--- NAMESPACE | 12 NEWS.md | 39 + R/colombiapi-package.R | 4 R/data-documentation.R | 444 +++++++++++++++++- R/get_colombia_airports.R | 2 R/get_colombia_attractions.R | 2 R/get_colombia_child_mortality.R | 2 R/get_colombia_cities.R | 2 R/get_colombia_cpi.R | 2 R/get_colombia_departments.R | 2 R/get_colombia_energy_use.R | 2 R/get_colombia_gdp.R | 2 R/get_colombia_holidays.R | 2 R/get_colombia_hospital_beds.R | 2 R/get_colombia_invasive_species.R | 2 R/get_colombia_life_expectancy.R | 2 R/get_colombia_literacy_rate.R | 2 R/get_colombia_native_communities.R | 2 R/get_colombia_natural_areas.R | 2 R/get_colombia_population.R | 2 R/get_colombia_presidents.R | 2 R/get_colombia_radios.R | 2 R/get_colombia_regions.R | 2 R/get_colombia_typical_dishes.R | 2 R/get_colombia_unemployment.R | 2 R/get_country_info_co.R | 2 R/utils.R | 2 R/view_datasets_ColombiAPI.R | 2 README.md | 8 data/Bogota_airstations_df.rda |binary data/Bogota_business_Date.rda |binary data/Bogota_holidays_Date.rda |binary data/Bogota_malls_tbl_df.rda |binary data/Bucaramanga_wifi_tbl_df.rda |only data/Cannabis_Licenses_tbl_df.rda |binary data/Cartagena_wifi_tbl_df.rda |only data/Colombia_coffee_tbl_df.rda |binary data/Medellin_rain_tbl_df.rda |binary data/Tulua_Public_Schools_tbl_df.rda |binary data/admitted_students_df.rda |only data/datalist |only data/dead_lianas_df.rda |only data/digital_centers_tbl_df.rda |only data/digital_graduates_tbl_df.rda |only data/foreign_visitors_tbl_df.rda |only data/gdp_departments_tbl_df.rda |only data/indigenous_vocabulary_df.rda |only data/municipalities_tbl_df.rda |only data/school_levels_df.rda |only data/vehicle_count_tbl_df.rda |only inst/CITATION | 2 inst/doc/colombiAPI_vignette.Rmd | 9 inst/doc/colombiAPI_vignette.html | 88 ++- inst/licenses/LICENSES_DETAILS.md | 52 +- man/Bucaramanga_wifi_tbl_df.Rd |only man/Cartagena_wifi_tbl_df.Rd |only man/ColombiAPI.Rd | 2 man/admitted_students_df.Rd |only man/dead_lianas_df.Rd |only man/digital_centers_tbl_df.Rd |only man/digital_graduates_tbl_df.Rd |only man/foreign_visitors_tbl_df.Rd |only man/gdp_departments_tbl_df.Rd |only man/indigenous_vocabulary_df.Rd |only man/municipalities_tbl_df.Rd |only man/school_levels_df.Rd |only man/vehicle_count_tbl_df.Rd |only tests/testthat/test-Bogota_airstations_df.R | 2 tests/testthat/test-Bogota_business_Date.R | 2 tests/testthat/test-Bogota_holidays_Date.R | 2 tests/testthat/test-Bogota_malls_tbl_df.R | 2 tests/testthat/test-Bucaramanga_wifi_tbl_df.R |only tests/testthat/test-Cannabis_Licenses_tbl_df.R | 2 tests/testthat/test-Cartagena_wifi_tbl_df.R |only tests/testthat/test-Colombia_coffee_tbl_df.R | 2 tests/testthat/test-Medellin_rain_tbl_df.R | 2 tests/testthat/test-Tulua_Public_Schools_tbl_df.R | 2 tests/testthat/test-admitted_students_df.R |only tests/testthat/test-dead_lianas_df.R |only tests/testthat/test-digital_centers_tbl_df.R |only tests/testthat/test-digital_graduates_tbl_df.R |only tests/testthat/test-foreign_visitors_tbl_df.R |only tests/testthat/test-gdp_departments_tbl_df.R |only tests/testthat/test-get_colombia_airports.R | 2 tests/testthat/test-get_colombia_attractions.R | 2 tests/testthat/test-get_colombia_child_mortality.R | 2 tests/testthat/test-get_colombia_cities.R | 2 tests/testthat/test-get_colombia_cpi.R | 2 tests/testthat/test-get_colombia_departments.R | 2 tests/testthat/test-get_colombia_energy_use.R | 2 tests/testthat/test-get_colombia_gdp.R | 2 tests/testthat/test-get_colombia_holidays.R | 2 tests/testthat/test-get_colombia_hospital_beds.R | 2 tests/testthat/test-get_colombia_invasive_species.R | 2 tests/testthat/test-get_colombia_life_expectancy.R | 2 tests/testthat/test-get_colombia_literacy_rate.R | 2 tests/testthat/test-get_colombia_native_communities.R | 2 tests/testthat/test-get_colombia_natural_areas.R | 2 tests/testthat/test-get_colombia_population.R | 2 tests/testthat/test-get_colombia_presidents.R | 2 tests/testthat/test-get_colombia_radios.R | 2 tests/testthat/test-get_colombia_regions.R | 2 tests/testthat/test-get_colombia_typical_dishes.R | 2 tests/testthat/test-get_colombia_unemployment.R | 2 tests/testthat/test-get_country_info_co.R | 2 tests/testthat/test-indigenous_vocabulary_df.R |only tests/testthat/test-municipalities_tbl_df.R |only tests/testthat/test-school_levels_df.R |only tests/testthat/test-vehicle_count_tbl_df.R |only tests/testthat/test-view_datasets_ColombiAPI.R |only vignettes/colombiAPI_vignette.Rmd | 9 113 files changed, 796 insertions(+), 191 deletions(-)
Title: Performs Tests for Cluster Tendency of a Data Set
Description: Test for cluster tendency (clusterability) of a data set.
The methods implemented - reducing the data set to a single dimension using principal component analysis or computing
pairwise distances, and performing a multimodality test like the Dip Test or Silverman's Critical Bandwidth Test -
are described in Adolfsson, Ackerman, and Brownstein (2019) <doi:10.1016/j.patcog.2018.10.026>. Such methods can inform whether clustering algorithms
are appropriate for a data set.
Author: Zachariah Neville [aut, cre],
Naomi Brownstein [aut],
Maya Ackerman [aut],
Andreas Adolfsson [aut]
Maintainer: Zachariah Neville <zachariahneville@outlook.com>
This is a re-admission after prior archival of version 0.1.1.0 dated 2020-03-04
Diff between clusterability versions 0.1.1.0 dated 2020-03-04 and 0.2.1.0 dated 2025-09-29
DESCRIPTION | 14 MD5 | 55 +-- NAMESPACE | 8 NEWS.md | 4 R/clusterability.R | 5 R/clusterabilitytest.R | 42 ++ R/dipsilverman.R | 3 R/normals1.R | 2 R/normals2.R | 2 R/normals3.R | 2 R/normals4.R | 2 R/normals5.R | 2 R/paramchecks.R | 34 +- R/reducestandardize.R | 58 +++ README.md | 11 inst |only man/clusterability.Rd | 263 +++++++--------- man/clusterabilitytest.Rd | 266 +++++++++------- man/normals1.Rd | 56 +-- man/normals2.Rd | 52 +-- man/normals3.Rd | 54 +-- man/normals4.Rd | 54 +-- man/normals5.Rd | 56 +-- man/print.clusterability.Rd | 38 +- tests/testthat.R | 8 tests/testthat/test_printsummary.R | 146 ++++---- tests/testthat/test_reducestandardize.R | 287 ++++++++++------- tests/testthat/test_validateparams.R | 526 ++++++++++++++++---------------- 28 files changed, 1136 insertions(+), 914 deletions(-)
More information about clusterability at CRAN
Permanent link
Title: Bayesian Models for Data from Unmarked Animals using 'Stan'
Description: Fit Bayesian hierarchical models of animal abundance and occurrence
via the 'rstan' package, the R interface to the 'Stan' C++ library.
Supported models include single-season occupancy, dynamic occupancy, and
N-mixture abundance models. Covariates on model parameters are specified
using a formula-based interface similar to package 'unmarked', while also
allowing for estimation of random slope and intercept terms. References:
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>;
Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Ken Kellner [cre, aut]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between ubms versions 1.2.7 dated 2024-10-01 and 1.2.8 dated 2025-09-29
DESCRIPTION | 12 MD5 | 44 - NEWS.md | 6 R/gof.R | 2 R/inputs.R | 1 R/pcount.R | 1 R/spatial.R | 6 R/ubmsFit-methods.R | 10 build/vignette.rds |binary inst/doc/JAGS-comparison.html | 481 +++++++++--------- inst/doc/random-effects.html | 455 ++++++++++------- inst/doc/spatial-models.html | 614 ++++++++++++++--------- inst/doc/ubms.R | 14 inst/doc/ubms.Rmd | 5 inst/doc/ubms.html | 899 +++++++++++++++++++++------------- man/summary-ubmsFit-method.Rd | 4 src/exp_counts_occu.cpp | 4 src/simz.cpp | 10 tests/testthat/test_pcount.R | 7 tests/testthat/test_spatial.R | 19 tests/testthat/test_ubmsFit_methods.R | 4 vignettes/references.bib | 3 vignettes/ubms.Rmd | 5 23 files changed, 1596 insertions(+), 1010 deletions(-)
Title: Spatially Varying Change Points
Description: Implements a spatially varying change point model with
unique intercepts, slopes, variance intercepts and slopes, and
change points at each location. Inference is within the
Bayesian setting using Markov chain Monte Carlo (MCMC). The
response variable can be modeled as Gaussian (no nugget),
probit or Tobit link and the five spatially varying parameter
are modeled jointly using a multivariate conditional
autoregressive (MCAR) prior. The MCAR is a unique process that
allows for a dissimilarity metric to dictate the local spatial
dependencies. Full details of the package can be found in the accompanying vignette.
Furthermore, the details of the package can be found in the corresponding paper published in Spatial Statistics
by Berchuck et al (2019): "A spatially varying change points model for monitoring glaucoma
progression using visual field data", <doi:10.1016/j.spasta.2019.02.001>.
Author: Samuel I. Berchuck [aut, cre]
Maintainer: Samuel I. Berchuck <sib2@duke.edu>
Diff between spCP versions 1.3 dated 2022-09-05 and 1.4.0 dated 2025-09-29
DESCRIPTION | 16 +- MD5 | 21 +-- NEWS.md |only R/spCP-package.R | 3 build/vignette.rds |binary inst/doc/spCP-example.R | 26 +--- inst/doc/spCP-example.Rmd | 2 inst/doc/spCP-example.html | 288 ++++++++++++++++++++++----------------------- man/spCP.Rd | 3 src/MCMC_Samplers.cpp | 26 ++-- src/PRED_PredictFuture.cpp | 8 - vignettes/spCP-example.Rmd | 2 12 files changed, 200 insertions(+), 195 deletions(-)
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre] ,
Samuel Borms [ctb] ,
Chengua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] , ORCID:
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
Diff between sentopics versions 0.7.4 dated 2024-09-20 and 0.7.5 dated 2025-09-29
DESCRIPTION | 18 MD5 | 158 +- NAMESPACE | 200 +- NEWS.md | 84 - R/RcppExports.R | 38 R/coherence.R | 300 ++-- R/conversions.R | 1798 +++++++++++------------ R/functions.R | 940 ++++++------ R/generators.R | 440 ++--- R/merging.R | 244 +-- R/methods.R | 1726 +++++++++++------------ R/models.R | 596 +++---- R/others.R | 722 ++++----- R/sentopics.R | 301 ++-- R/timeSeries.R | 2550 +++++++++++++++++----------------- R/utils.R | 2224 ++++++++++++++--------------- R/zzz.R | 40 README.md | 308 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Basic_usage.R | 114 - inst/doc/Basic_usage.Rmd | 246 +-- inst/doc/Basic_usage.html | 1317 ++++++++--------- inst/doc/Topical_time_series.R | 140 - inst/doc/Topical_time_series.Rmd | 214 +- inst/doc/Topical_time_series.html | 1139 +++++++-------- man/ECB_press_conferences.Rd | 58 man/ECB_press_conferences_tokens.Rd | 72 man/JST.Rd | 194 +- man/LDA.Rd | 142 - man/LDAvis.Rd | 70 man/LoughranMcDonald.Rd | 72 man/PicaultRenault.Rd | 86 - man/PicaultRenault_data.Rd | 86 - man/as.LDA.Rd | 210 +- man/as.tokens.dfm.Rd | 118 - man/chainsDistances.Rd | 138 - man/chainsScores.Rd | 108 - man/coherence.Rd | 104 - man/compute_PicaultRenault_scores.Rd | 112 - man/get_ECB_press_conferences.Rd | 58 man/get_ECB_speeches.Rd | 74 man/melt.Rd | 52 man/melt.sentopicmodel.Rd | 92 - man/mergeTopics.Rd | 116 - man/plot.multiChains.Rd | 80 - man/plot.sentopicmodel.Rd | 84 - man/print.sentopicmodel.Rd | 66 man/proportion_topics.Rd | 192 +- man/rJST.Rd | 234 +-- man/reexports.Rd | 42 man/reset.Rd | 64 man/sentiment_breakdown.Rd | 208 +- man/sentiment_series.Rd | 162 +- man/sentiment_topics.Rd | 232 +-- man/sentopicmodel.Rd | 172 +- man/sentopics-conversions.Rd | 50 man/sentopics-package.Rd | 110 - man/sentopics_date.Rd | 110 - man/sentopics_labels.Rd | 134 - man/sentopics_sentiment.Rd | 230 +-- man/topWords.Rd | 212 +- tests/testthat.R | 32 tests/testthat/Rplots.pdf |binary tests/testthat/test-JST.R | 184 +- tests/testthat/test-LDA.R | 100 - tests/testthat/test-algorithm.R | 32 tests/testthat/test-basic.R | 166 +- tests/testthat/test-coherence.R | 106 - tests/testthat/test-conversions.R | 450 +++--- tests/testthat/test-generation.R | 150 +- tests/testthat/test-generics.R | 106 - tests/testthat/test-grow.R | 56 tests/testthat/test-others.R | 38 tests/testthat/test-parallel_chains.R | 350 ++-- tests/testthat/test-rJST.R | 186 +- tests/testthat/test-timeSeries.R | 390 ++--- tests/testthat/test-utils.R | 352 ++-- vignettes/Basic_usage.Rmd | 246 +-- vignettes/Topical_time_series.Rmd | 214 +- 80 files changed, 11682 insertions(+), 11677 deletions(-)
Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing
Simulator
Description: Simply and efficiently
simulates (i) variants from reference genomes and (ii) reads from both Illumina
<https://www.illumina.com/>
and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms.
It can either read reference genomes from FASTA files or simulate new ones.
Genomic variants can be simulated using summary statistics, phylogenies,
Variant Call Format (VCF) files, and coalescent simulations—the latter of which
can include selection, recombination, and demographic fluctuations.
'jackalope' can simulate single, paired-end, or mate-pair Illumina reads,
as well as PacBio reads.
These simulations include sequencing errors, mapping qualities, multiplexing,
and optical/polymerase chain reaction (PCR) duplicates.
Simulating Illumina sequencing is based on ART
by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>.
PacBio sequencing simulation is based on
SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>.
All outputs can be written t [...truncated...]
Author: Lucas A. Nell [cph, aut, cre]
Maintainer: Lucas A. Nell <lucnell@gmail.com>
Diff between jackalope versions 1.1.5 dated 2023-11-28 and 1.1.6 dated 2025-09-29
DESCRIPTION | 15 +-- MD5 | 20 ++-- NAMESPACE | 1 NEWS.md | 3 R/jackalope-package.R | 1 README.md | 11 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/jackalope-intro.R | 178 +++++++++++++++++++++--------------------- inst/doc/jackalope-intro.html | 3 src/Makevars.win | 12 -- 11 files changed, 119 insertions(+), 125 deletions(-)
Title: Add Some Van Gogh Colors and Overlay Colors on Your 'ggplot()'
Description: Works with 'ggplot2' to add a Van Gogh color palette to the user’s repertoire.
It also has a function that work alongside 'ggplot2' to create more interesting data visualizations and add contextual information to the user’s plots.
Author: Katelyn Diaz [aut, cre] ,
Silas Weden [aut],
Tess Goldmann [aut],
Aushanae Haller [edt] ,
Kathleen Hablutzel [edt]
Maintainer: Katelyn Diaz <katndiaz@gmail.com>
Diff between ggRtsy versions 0.1.0 dated 2023-09-15 and 1.2.1 dated 2025-09-29
DESCRIPTION | 14 ++++++++------ MD5 | 13 +++++++------ NEWS.md |only R/RectangleFiller.R | 17 +++++++++++++---- README.md | 3 ++- build/vignette.rds |binary inst/doc/Vignette.R | 4 ++-- inst/doc/Vignette.html | 18 +++++++++--------- 8 files changed, 41 insertions(+), 28 deletions(-)
Title: Bayesian Variable Selection using Power-Expected-Posterior Prior
Description: Performs Bayesian variable selection under normal linear
models for the data with the model parameters following as prior distributions either
the power-expected-posterior (PEP) or the intrinsic (a special case of the former)
(Fouskakis and Ntzoufras (2022) <doi: 10.1214/21-BA1288>,
Fouskakis and Ntzoufras (2020) <doi: 10.3390/econometrics8020017>).
The prior distribution on model space is the uniform over all models
or the uniform on model dimension (a special case of the beta-binomial prior).
The selection is performed by either implementing a full enumeration
and evaluation of all possible models or using the Markov Chain
Monte Carlo Model Composition (MC3) algorithm (Madigan and York (1995) <doi: 10.2307/1403615>).
Complementary functions for hypothesis testing, estimation and
predictions under Bayesian model averaging, as well as, plotting and
printing the results are also provided. The results can be compared to the
ones obtained under other well-known priors on [...truncated...]
Author: Konstantina Charmpi [aut, cre],
Dimitris Fouskakis [aut],
Ioannis Ntzoufras [aut]
Maintainer: Konstantina Charmpi <xarmpi.kon@gmail.com>
Diff between PEPBVS versions 2.1 dated 2024-11-12 and 2.2 dated 2025-09-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ build/partial.rdb |binary src/auxiliary_code.cpp | 3 ++- 5 files changed, 14 insertions(+), 9 deletions(-)
Title: Multivariate Bidirectional Mendelian Randomization Networks
Description: Addressing a central challenge encountered in Mendelian randomization (MR) studies, where MR primarily focuses on discerning the effects of individual exposures on specific outcomes and establishes causal links between them. Using a network-based methodology, the intricacy involving interdependent outcomes due to numerous factors has been tackled through this routine. Based on Ni et al. (2018) <doi:10.1214/17-BA1087>, 'MR.RGM' extends to a broader exploration of the causal landscape by leveraging on network structures and involves the construction of causal graphs that capture interactions between response variables and consequently between responses and instrument variables. The resulting Graph visually represents these causal connections, showing directed edges with effect sizes labeled. 'MR.RGM' facilitates the navigation of various data availability scenarios effectively by accommodating three input formats, i.e., individual-level data and two types of summary-level data. In [...truncated...]
Author: Bitan Sarkar [aut, cre],
Yang Ni [aut]
Maintainer: Bitan Sarkar <bitan@tamu.edu>
Diff between MR.RGM versions 0.0.4 dated 2025-03-03 and 0.0.5 dated 2025-09-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- README.md | 1 + src/Generate.cpp | 10 ++++++++++ 4 files changed, 17 insertions(+), 6 deletions(-)
Title: Optimal Experimental Designs for Dynamic/Functional Models
Description: Optimal experimental designs for functional linear and functional generalised linear models, for scalar responses and profile/dynamic factors. The designs are optimised using the coordinate exchange algorithm. The methods are discussed by Michaelides (2023) <https://eprints.soton.ac.uk/474982/1/Thesis_DamianosMichaelides_Final_pdfa_1_.pdf>.
Author: Damianos Michaelides [aut, cre],
Antony Overstall [aut],
Dave Woods [aut]
Maintainer: Damianos Michaelides <dm3g15@soton.ac.uk>
Diff between fdesigns versions 1.1 dated 2025-06-17 and 1.2 dated 2025-09-29
DESCRIPTION | 16 +++-- MD5 | 39 +++++++------ R/class_functions_all.R | 90 +++++++++---------------------- R/fdesignsR.R | 4 + R/flm_InteractionsPolynomials_mclapply.R | 18 +++--- R/flm_Interactions_mclapply.R | 13 ++-- R/flm_ME_mclapply.R | 10 +-- R/flm_general_Cstarts_mclapply.R | 61 ++++++++------------- R/hidden_functions.R | 49 ++++++++++++++++ build/partial.rdb |binary build/vignette.rds |only inst |only man/fdesigns-package.Rd | 4 - man/pflm.Rd | 33 ++++++----- man/plotfglm.Rd | 27 +++++---- man/plotflm.Rd | 26 +++++--- src/Makevars | 10 ++- src/Makevars.win | 10 ++- src/RcppExports.cpp | 12 ++-- src/fdesignscpp.cpp | 49 ++++++++++++++++ vignettes |only 21 files changed, 282 insertions(+), 189 deletions(-)
Title: Tools for Microscopy Imaging
Description: Tools for 3D imaging, mostly for biology/microscopy.
Read and write TIFF stacks. Functions for segmentation, filtering and analyzing 3D point patterns.
Author: Volker Schmid [aut, cre],
Priyanka Kukreja [ctb],
Fabian Scheipl [ctb]
Maintainer: Volker Schmid <stats@volkerschmid.de>
Diff between bioimagetools versions 1.1.8 dated 2022-05-28 and 1.1.9 dated 2025-09-29
bioimagetools-1.1.8/bioimagetools/NEWS |only bioimagetools-1.1.9/bioimagetools/DESCRIPTION | 13 +- bioimagetools-1.1.9/bioimagetools/MD5 | 10 - bioimagetools-1.1.9/bioimagetools/NEWS.md |only bioimagetools-1.1.9/bioimagetools/R/writetif.R | 104 ++++++++++--------- bioimagetools-1.1.9/bioimagetools/README.md | 6 - bioimagetools-1.1.9/bioimagetools/build/vignette.rds |binary 7 files changed, 71 insertions(+), 62 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 2.6.1 dated 2022-12-20 and 2.6.3 dated 2025-09-29
RAthena-2.6.1/RAthena/man/Query.Rd |only RAthena-2.6.1/RAthena/man/backend_dbplyr_v2.Rd |only RAthena-2.6.1/RAthena/man/dbClearResult.Rd |only RAthena-2.6.1/RAthena/man/dbColumnInfo.Rd |only RAthena-2.6.1/RAthena/man/dbDataType.Rd |only RAthena-2.6.1/RAthena/man/dbDisconnect.Rd |only RAthena-2.6.1/RAthena/man/dbExistsTable.Rd |only RAthena-2.6.1/RAthena/man/dbFetch.Rd |only RAthena-2.6.1/RAthena/man/dbGetInfo.Rd |only RAthena-2.6.1/RAthena/man/dbGetPartition.Rd |only RAthena-2.6.1/RAthena/man/dbGetQuery.Rd |only RAthena-2.6.1/RAthena/man/dbGetStatement.Rd |only RAthena-2.6.1/RAthena/man/dbGetTables.Rd |only RAthena-2.6.1/RAthena/man/dbHasCompleted.Rd |only RAthena-2.6.1/RAthena/man/dbIsValid.Rd |only RAthena-2.6.1/RAthena/man/dbListFields.Rd |only RAthena-2.6.1/RAthena/man/dbQuote.Rd |only RAthena-2.6.1/RAthena/man/dbRemoveTable.Rd |only RAthena-2.6.1/RAthena/man/dbShow.Rd |only RAthena-2.6.1/RAthena/man/dbStatistics.Rd |only RAthena-2.6.3/RAthena/DESCRIPTION | 13 RAthena-2.6.3/RAthena/MD5 | 154 - RAthena-2.6.3/RAthena/NAMESPACE | 21 RAthena-2.6.3/RAthena/NEWS.md | 15 RAthena-2.6.3/RAthena/R/Connection.R | 1039 ++++------ RAthena-2.6.3/RAthena/R/DataTypes.R | 126 - RAthena-2.6.3/RAthena/R/Driver.R | 345 +-- RAthena-2.6.3/RAthena/R/File_Parser.R | 310 +- RAthena-2.6.3/RAthena/R/Options.R | 297 +- RAthena-2.6.3/RAthena/R/RAthena.R | 3 RAthena-2.6.3/RAthena/R/Result.R | 366 +-- RAthena-2.6.3/RAthena/R/View.R | 393 ++- RAthena-2.6.3/RAthena/R/athena_low_api.R | 383 ++- RAthena-2.6.3/RAthena/R/dplyr_integration.R | 414 ++- RAthena-2.6.3/RAthena/R/fetch_utils.R | 67 RAthena-2.6.3/RAthena/R/install.R | 28 RAthena-2.6.3/RAthena/R/sql_translate_env.R | 338 +-- RAthena-2.6.3/RAthena/R/sql_translate_utils.R | 43 RAthena-2.6.3/RAthena/R/table.R | 949 ++++++--- RAthena-2.6.3/RAthena/R/utils.R | 306 ++ RAthena-2.6.3/RAthena/R/zzz.R | 37 RAthena-2.6.3/RAthena/README.md | 6 RAthena-2.6.3/RAthena/build/vignette.rds |binary RAthena-2.6.3/RAthena/inst/doc/aws_athena_query_caching.html | 123 - RAthena-2.6.3/RAthena/inst/doc/aws_athena_unload.html | 227 +- RAthena-2.6.3/RAthena/inst/doc/aws_s3_backend.R | 2 RAthena-2.6.3/RAthena/inst/doc/aws_s3_backend.Rmd | 2 RAthena-2.6.3/RAthena/inst/doc/aws_s3_backend.html | 15 RAthena-2.6.3/RAthena/inst/doc/changing_backend_file_parser.html | 53 RAthena-2.6.3/RAthena/inst/doc/convert_and_save_cost.Rmd | 2 RAthena-2.6.3/RAthena/inst/doc/convert_and_save_cost.html | 119 - RAthena-2.6.3/RAthena/inst/doc/getting_started.Rmd | 4 RAthena-2.6.3/RAthena/inst/doc/getting_started.html | 225 +- RAthena-2.6.3/RAthena/inst/doc/how_to_retry.html | 37 RAthena-2.6.3/RAthena/man/AthenaConnection.Rd | 140 + RAthena-2.6.3/RAthena/man/AthenaDriver.Rd | 14 RAthena-2.6.3/RAthena/man/AthenaListObjects.Rd |only RAthena-2.6.3/RAthena/man/AthenaPreviewObject.Rd |only RAthena-2.6.3/RAthena/man/AthenaResult.Rd |only RAthena-2.6.3/RAthena/man/AthenaWriteTables.Rd | 36 RAthena-2.6.3/RAthena/man/RAthena-package.Rd | 6 RAthena-2.6.3/RAthena/man/RAthena_options.Rd | 18 RAthena-2.6.3/RAthena/man/assume_role.Rd | 8 RAthena-2.6.3/RAthena/man/athena.Rd | 9 RAthena-2.6.3/RAthena/man/backend_dbplyr.Rd |only RAthena-2.6.3/RAthena/man/backend_dbplyr_v1.Rd | 2 RAthena-2.6.3/RAthena/man/dbConnect-AthenaDriver-method.Rd | 129 - RAthena-2.6.3/RAthena/man/dbConvertTable.Rd | 47 RAthena-2.6.3/RAthena/man/dbListTables.Rd | 8 RAthena-2.6.3/RAthena/man/db_compute.Rd | 90 RAthena-2.6.3/RAthena/man/db_copy_to.Rd | 63 RAthena-2.6.3/RAthena/man/dbplyr_edition.Rd | 2 RAthena-2.6.3/RAthena/man/install_boto.Rd | 10 RAthena-2.6.3/RAthena/man/session_token.Rd | 10 RAthena-2.6.3/RAthena/man/sqlCreateTable.Rd | 22 RAthena-2.6.3/RAthena/man/sqlData.Rd | 4 RAthena-2.6.3/RAthena/man/sql_translate_env.Rd | 12 RAthena-2.6.3/RAthena/man/work_group.Rd | 47 RAthena-2.6.3/RAthena/tests/testthat/helper.R | 138 - RAthena-2.6.3/RAthena/tests/testthat/test-append-data.R | 50 RAthena-2.6.3/RAthena/tests/testthat/test-athena-ddl.R | 90 RAthena-2.6.3/RAthena/tests/testthat/test-dbFetch-n.R | 77 RAthena-2.6.3/RAthena/tests/testthat/test-dplyr-compute.R | 34 RAthena-2.6.3/RAthena/tests/testthat/test-dplyr-copy_to.R | 30 RAthena-2.6.3/RAthena/tests/testthat/test-file-parser.R | 254 +- RAthena-2.6.3/RAthena/tests/testthat/test-metadata.R | 130 - RAthena-2.6.3/RAthena/tests/testthat/test-view.R | 223 +- RAthena-2.6.3/RAthena/vignettes/aws_s3_backend.Rmd | 2 RAthena-2.6.3/RAthena/vignettes/convert_and_save_cost.Rmd | 2 RAthena-2.6.3/RAthena/vignettes/getting_started.Rmd | 4 90 files changed, 4713 insertions(+), 3460 deletions(-)
Title: Optimal Monotone Conditional Error Functions
Description: Design and analysis of confirmatory adaptive clinical trials using the optimal conditional error framework according to Brannath and Bauer (2004) <doi:10.1111/j.0006-341X.2004.00221.x>. An extension to the optimal conditional error function using interim estimates as described in Brannath and Dreher (2024) <doi:10.48550/arXiv.2402.00814> and functions to ensure that the resulting conditional error function is non-increasing are also available.
Author: Morten Dreher [aut, cre],
Werner Brannath [aut, cph] ,
Cornelia Ursula Kunz [ctb] ,
Johanna zur Verth [aut]
Maintainer: Morten Dreher <morten.dreher@outlook.de>
Diff between optconerrf versions 1.0.0 dated 2025-09-09 and 1.0.1 dated 2025-09-29
DESCRIPTION | 6 MD5 | 120 NAMESPACE | 44 NEWS.md | 7 R/classes.R | 886 ++--- R/getDesignOptimalConditionalErrorFunction.R | 356 +- R/getExpectedSecondStageInformation.R | 116 R/getIntegral.R | 108 R/getIntegralWithConstants.R | 106 R/getLevelConstant.R | 168 - R/getLikelihoodRatio.R | 296 - R/getMonotoneFunction.R | 114 R/getMonotonisationConstants.R | 394 +- R/getNu.R | 68 R/getNuPrime.R | 54 R/getOptimalConditionalError.R | 342 +- R/getOverallPower.R | 148 R/getQ.R | 120 R/getSecondStageInformation.R | 170 - R/getSimulationResults.R | 222 - R/integrateExpectedInformation.R | 304 - R/utilities.R | 1664 +++++----- inst/doc/constraints_interim_estimates.Rmd | 602 +-- inst/doc/constraints_interim_estimates.html | 2 inst/doc/introduction.Rmd | 734 ++-- man/PowerResultsOptimalConditionalError.Rd | 20 man/SimulationResultsOptimalConditionalError.Rd | 20 man/TrialDesignOptimalConditionalError.Rd | 26 man/dot-rangeCheck.Rd | 42 man/getExpectedSecondStageInformation.Rd | 138 man/getInnerPsi.Rd | 50 man/getIntegral.Rd | 46 man/getIntegralWithConstants.Rd | 42 man/getLevelConstant.Rd | 66 man/getLikelihoodRatio.Rd | 104 man/getMonotoneFunction.Rd | 100 man/getMonotonisationConstants.Rd | 88 man/getNu.Rd | 68 man/getNuPrime.Rd | 64 man/getOptimalConditionalError.Rd | 90 man/getOverallPower.Rd | 74 man/getPsi.Rd | 58 man/getQ.Rd | 84 man/getSecondStageInformation.Rd | 100 man/getSimulationResults.Rd | 102 man/integrateExpectedInformation.Rd | 74 man/plot.TrialDesignOptimalConditionalError.Rd | 60 man/print.PowerResultsOptimalConditionalError.Rd | 38 man/print.SimulationResultsOptimalConditionalError.Rd | 38 man/print.TrialDesignOptimalConditionalError.Rd | 38 man/summary.TrialDesignOptimalConditionalError.Rd | 38 tests/testthat.R | 24 tests/testthat/test-getDesignOptimalConditionalErrorFunction.R | 104 tests/testthat/test-getExpectedSecondStageInformation.R | 184 - tests/testthat/test-getLevelConstant.R | 120 tests/testthat/test-getNuPrime.R | 16 tests/testthat/test-getOptimalConditionalError.R | 192 - tests/testthat/test-getOverallPower.R | 74 tests/testthat/test-getSecondStageInformation.R | 64 vignettes/constraints_interim_estimates.Rmd | 602 +-- vignettes/introduction.Rmd | 734 ++-- 61 files changed, 5470 insertions(+), 5463 deletions(-)
Title: 'shiny' Applications for the 'tesselle' Packages
Description: A collection of 'shiny' applications for the 'tesselle'
packages <https://www.tesselle.org/>. This package provides
applications for archaeological data analysis and visualization. These
mainly, but not exclusively, include applications for chronological
modelling (e.g. matrix seriation, aoristic analysis) and count data
analysis (e.g. diversity measures, compositional data analysis).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kinesis versions 0.3.0 dated 2025-09-05 and 0.3.1 dated 2025-09-29
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/coda_statistics.R | 9 ++++----- R/kinesis-package.R | 2 +- R/multivariate.R | 10 +++++++--- README.md | 2 +- inst/po/fr/LC_MESSAGES/R-kinesis.mo |binary man/kinesis-package.Rd | 2 +- po/R-fr.po | 28 ++++++++++++++++------------ po/R-kinesis.pot | 30 +++++++++++++++++------------- 11 files changed, 64 insertions(+), 49 deletions(-)
Title: Colour Schemes for Scientific Data Visualization
Description: Color schemes ready for each type of data (qualitative,
diverging or sequential), with colors that are distinct for all
people, including color-blind readers. This package provides an
implementation of Paul Tol (2018) and Fabio Crameri (2018)
<doi:10.5194/gmd-11-2541-2018> color schemes for use with 'graphics'
or 'ggplot2'. It provides tools to simulate color-blindness and to
test how well the colors of any palette are identifiable. Several
scientific thematic schemes (geologic timescale, land cover, FAO
soils, etc.) are also implemented.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Vincent Arel-Bundock [ctb] ,
Ulrik Stervbo [ctb] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between khroma versions 1.16.0 dated 2025-02-25 and 1.17.0 dated 2025-09-29
DESCRIPTION | 31 MD5 | 220 +++--- NAMESPACE | 30 NEWS.md | 4 R/change.R | 2 R/color.R | 4 R/info.R | 54 - R/khroma-deprecated.R | 2 R/khroma-package.R | 32 R/palettes.R | 8 R/scale_colour_crameri.R | 557 ++++++++++++++-- R/scale_colour_picker.R | 2 R/scale_colour_science.R | 4 R/scale_colour_tol.R | 34 - R/sysdata.rda |binary README.md | 150 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/crameri.R | 120 ++- inst/doc/crameri.Rmd | 180 +++-- inst/doc/crameri.html | 558 ++++++++--------- inst/doc/khroma.R |only inst/doc/khroma.Rmd |only inst/doc/khroma.html |only inst/doc/tol.Rmd | 9 inst/doc/tol.html | 335 ++++------ inst/po/fr/LC_MESSAGES/R-khroma.mo |binary inst/tinytest/_snaps/info.rds |binary inst/tinytest/_tinysnapshot/plot_colorblind_bright.svg | 10 inst/tinytest/_tinysnapshot/plot_tiles_bright.svg | 4 inst/tinytest/_tinysnapshot/scheme_muted_FALSETRUE.svg | 18 inst/tinytest/_tinysnapshot/scheme_muted_TRUEFALSE.svg | 20 inst/tinytest/_tinysnapshot/scheme_muted_TRUETRUE.svg | 38 - inst/tinytest/helpers.R |only inst/tinytest/test_ggplot2_crameri.R | 62 + inst/tinytest/test_palettes.R | 2 inst/tinytest/test_plot.R | 76 +- man/change.Rd | 2 man/colour.Rd | 4 man/crameri.Rd | 48 - man/figures/README-usage-colorblind2-1.png |binary man/figures/README-usage-colorblind2-2.png |binary man/figures/README-usage-map-1.png |binary man/figures/README-usage-plot-1.png |binary man/figures/README-usage-plot-2.png |binary man/figures/README-usage-show-1.png |binary man/khroma-deprecated.Rd | 2 man/khroma-package.Rd | 41 - man/scale_crameri_acton.Rd | 40 - man/scale_crameri_bam.Rd | 27 man/scale_crameri_bamO.Rd | 26 man/scale_crameri_bamako.Rd | 40 - man/scale_crameri_batlow.Rd | 40 - man/scale_crameri_batlowK.Rd | 40 - man/scale_crameri_batlowW.Rd | 40 - man/scale_crameri_berlin.Rd | 27 man/scale_crameri_bilbao.Rd | 40 - man/scale_crameri_broc.Rd | 27 man/scale_crameri_brocO.Rd | 26 man/scale_crameri_buda.Rd | 40 - man/scale_crameri_bukavu.Rd | 36 - man/scale_crameri_cork.Rd | 27 man/scale_crameri_corkO.Rd | 26 man/scale_crameri_davos.Rd | 40 - man/scale_crameri_devon.Rd | 40 - man/scale_crameri_fes.Rd | 36 - man/scale_crameri_glasgow.Rd |only man/scale_crameri_grayC.Rd | 40 - man/scale_crameri_hawaii.Rd | 40 - man/scale_crameri_imola.Rd | 40 - man/scale_crameri_lajolla.Rd | 40 - man/scale_crameri_lapaz.Rd | 40 - man/scale_crameri_lipari.Rd |only man/scale_crameri_lisbon.Rd | 27 man/scale_crameri_managua.Rd |only man/scale_crameri_navia.Rd |only man/scale_crameri_naviaW.Rd |only man/scale_crameri_nuuk.Rd | 40 - man/scale_crameri_oleron.Rd | 36 - man/scale_crameri_oslo.Rd | 40 - man/scale_crameri_roma.Rd | 27 man/scale_crameri_romaO.Rd | 26 man/scale_crameri_tofino.Rd | 27 man/scale_crameri_tokyo.Rd | 40 - man/scale_crameri_turku.Rd | 40 - man/scale_crameri_vanimo.Rd | 27 man/scale_crameri_vik.Rd | 27 man/scale_crameri_vikO.Rd | 26 man/scale_land.Rd | 2 man/scale_stratigraphy.Rd | 2 man/scale_tol_BuRd.Rd | 3 man/scale_tol_PRGn.Rd | 3 man/scale_tol_YlOrBr.Rd | 6 man/scale_tol_bright.Rd | 2 man/scale_tol_dark.Rd | 2 man/scale_tol_discreterainbow.Rd | 2 man/scale_tol_highcontrast.Rd | 2 man/scale_tol_incandescent.Rd | 6 man/scale_tol_iridescent.Rd | 6 man/scale_tol_light.Rd | 2 man/scale_tol_mediumcontrast.Rd | 2 man/scale_tol_muted.Rd | 2 man/scale_tol_nightfall.Rd | 3 man/scale_tol_pale.Rd | 2 man/scale_tol_smoothrainbow.Rd | 6 man/scale_tol_sunset.Rd | 3 man/scale_tol_vibrant.Rd | 2 man/science.Rd | 4 man/tol.Rd | 2 po/R-fr.po | 33 - po/R-khroma.pot | 31 tests/tinytest.R | 6 vignettes/bibliography.bib | 12 vignettes/crameri.Rmd | 180 +++-- vignettes/khroma.Rmd |only vignettes/tol.Rmd | 9 116 files changed, 2583 insertions(+), 1616 deletions(-)
Title: Access to the 'DraCor' API
Description: Provide an interface for 'Drama Corpora Project' ('DraCor') API: <https://dracor.org/documentation/api>.
Author: Ivan Pozdniakov [aut, cre]
Maintainer: Ivan Pozdniakov <bucherr@yandex.ru>
Diff between rdracor versions 1.0.5 dated 2025-08-27 and 1.0.6 dated 2025-09-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 7 ++++++- R/net.R | 6 +++--- R/text.R | 2 +- build/partial.rdb |binary 6 files changed, 19 insertions(+), 14 deletions(-)
Title: A Toolbox for Manipulating Biological Sequences
Description: Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences).
Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>.
Provides a collection of functions to perform biological conversion among classes
(transcription, translation) and basic operations on sequences
(detection, selection and replacement based on positions or patterns).
The package also provides functions to import and export sequences from and to other package formats.
Author: Francois Keck [aut, cre, cph]
Maintainer: Francois Keck <francois.keck@gmail.com>
Diff between bioseq versions 0.1.4 dated 2022-09-06 and 0.1.5 dated 2025-09-29
DESCRIPTION | 11 MD5 | 22 - NEWS.md | 4 R/seq_misc_operations.R | 5 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 24 - inst/doc/intro-bioseq.R | 8 inst/doc/intro-bioseq.html | 505 +++++++++++++++++++--------------- inst/doc/ref_database.R | 18 - inst/doc/ref_database.html | 668 +++++++++++++++++++++++++-------------------- 12 files changed, 719 insertions(+), 548 deletions(-)
Title: Manage Collections of Datasets and Objects
Description: Create, store, read and manage structured collections of
datasets and other objects using a 'workspace', then bundle it into a
compressed archive. Using open and interoperable formats makes it
possible to exchange bundled data from 'R' to other languages such as
'Python' or 'Julia'. Multiple formats are supported 'Parquet',
'JSON', 'yaml', spatial data and raster data are supported.
Author: Eli Daniels [aut, cre],
David Gohel [aut],
ArData [cph, fnd]
Maintainer: Eli Daniels <eli.daniels@ardata.fr>
Diff between workspace versions 0.1.5 dated 2025-09-11 and 0.1.6 dated 2025-09-29
DESCRIPTION | 9 ++-- MD5 | 11 ++--- NEWS.md | 56 +++++++++++++++++--------- R/readers.R | 11 ++++- R/store.R | 8 +++ man/workspace.Rd | 1 tests/testthat/test-roundtrip-comprehensive.R |only 7 files changed, 67 insertions(+), 29 deletions(-)
Title: Regularized Spatial Maximum Covariance Analysis
Description: Provide regularized maximum covariance analysis incorporating smoothness,
sparseness and orthogonality of couple patterns by using the alternating direction method
of multipliers algorithm. The method can be applied to either regularly or irregularly
spaced data, including 1D, 2D, and 3D (Wang and Huang, 2018 <doi:10.1002/env.2481>).
Author: Wen-Ting Wang [aut, cre] ,
Hsin-Cheng Huang [aut]
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatMCA versions 1.0.4 dated 2023-11-21 and 1.0.7 dated 2025-09-29
DESCRIPTION | 24 ++-- MD5 | 32 +++--- NAMESPACE | 23 ++-- NEWS.md | 18 +++ R/SpatMCA-package.R |only R/SpatMCA.R | 185 +++++++++++++++++++------------------- R/helper.R | 33 +++--- R/zzz.R | 7 + man/SpatMCA-package.Rd | 35 ++++--- man/spatmca.Rd | 182 +++++++++++++++++++------------------ src/Makevars | 8 + src/Makevars.win | 6 - src/RcppSpatMCA.cpp | 21 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/test-RcppExports.R | 5 - tests/testthat/test-SpatMCA.R | 2 tests/testthat/test-helper.R | 13 ++ tools |only 18 files changed, 328 insertions(+), 266 deletions(-)
Title: Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs, sample sizes in two-phase designs, and a stopping rule for ending data collection. A number of example data sets are included.
Author: Richard Valliant [aut, cre],
Jill A. Dever [ctb],
Frauke Kreuter [ctb],
George Zipf [aut]
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between PracTools versions 1.6.1 dated 2025-05-11 and 1.7 dated 2025-09-29
DESCRIPTION | 13 ++-- MD5 | 50 +++++++++------- NEWS.md | 4 + R/SampStop.R | 107 ++++++++++++++++-------------------- build/vignette.rds |binary data/Domainy1y2.RData |binary data/MDarea.popA.RData |binary data/TPV.RData |binary data/Test_Data_US.RData |binary data/ThirdGrade.RData |binary data/hospital.RData |binary data/labor.RData |binary data/mibrfss.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary inst/doc/Design-effects.html | 9 +-- inst/doc/Distance-and-MOS-PSUs.html | 9 +-- inst/doc/SampStop.R |only inst/doc/SampStop.Rmd |only inst/doc/SampStop.html |only inst/doc/Singlestage-samsize.html | 9 +-- inst/doc/Varcomps-multistage.html | 9 +-- man/SampStop.Rd | 71 ++++++++++++++--------- vignettes/SampStop.Rmd |only vignettes/practools.bib | 10 +++ 28 files changed, 159 insertions(+), 132 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 1.0.2 dated 2025-07-22 and 1.1.0 dated 2025-09-29
DESCRIPTION | 8 MD5 | 55 NAMESPACE | 1 R/R6Model.R | 270 ++- R/RcppExports.R | 4 R/extrafunctions.R | 29 build/partial.rdb |binary inst/include/glmmr/calculator.hpp | 2187 ++++++++++++++++--------------- inst/include/glmmr/covariance.hpp | 233 ++- inst/include/glmmr/formula.hpp | 3 inst/include/glmmr/formulaparse.h | 59 inst/include/glmmr/general.h | 1 inst/include/glmmr/hsgpcovariance.hpp | 7 inst/include/glmmr/interpreter.h | 408 +++-- inst/include/glmmr/maths.h | 109 - inst/include/glmmr/model.hpp | 4 inst/include/glmmr/modeloptim.hpp | 519 ++++--- inst/include/glmmr/optim/lbfgs.h | 15 inst/include/glmmr/optim/lbfgs/BFGSMat.h | 137 + inst/include/glmmr/optim/lbfgs/Param.h | 12 inst/include/glmmr/optim/lbfgsb.h | 2 inst/include/glmmr/optim/optim.h | 15 inst/stan/mcml.stan | 69 man/Model.Rd | 40 man/hsgp_rescale.Rd |only src/Makevars.win | 2 src/RcppExports.cpp | 13 src/model_module.cpp | 14 src/stanExports_mcml.h | 588 ++++---- 29 files changed, 2781 insertions(+), 2023 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.86 dated 2025-08-31 and 2.0.87 dated 2025-09-29
DESCRIPTION | 8 MD5 | 49 ++--- NAMESPACE | 2 NEWS | 10 + R/epi.nomogram.R | 278 +++++++++++++++++++++++++---- R/epi.ssequb.R | 18 - R/epi.ssequc.R | 14 - R/epi.ssninfb.R | 11 - R/epi.ssninfc.R | 10 - R/epi.sssupb.R | 20 +- R/epi.sssupc.R | 22 +- R/zagrestin.R |only R/zclopperpearsonn.R |only R/zexactn.r |only R/zjeffreysn.R |only R/zwilsonn.R |only inst/doc/epiR_descriptive.html | 28 +- inst/doc/epiR_measures_of_association.html | 29 ++- inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.html | 14 - man/epi.nomogram.Rd | 92 ++++++--- man/epi.prcc.Rd | 2 man/epi.ssequb.Rd | 62 +++--- man/epi.ssequc.Rd | 37 ++- man/epi.ssninfb.Rd | 25 +- man/epi.ssninfc.Rd | 21 +- man/epi.sssupb.Rd | 25 +- man/epi.sssupc.Rd | 25 +- 28 files changed, 562 insertions(+), 244 deletions(-)
Title: Generate Tile Maps
Description: Implements an algorithm for generating maps, known as tile maps,
in which each region is represented by a single tile of the same shape and
size. The algorithm was first proposed in "Generating Tile Maps" by Graham
McNeill and Scott Hale (2017) <doi:10.1111/cgf.13200>. Functions allow
users to generate, plot, and compare square or hexagon tile maps.
Author: Kaelyn Rosenberg [aut, cre]
Maintainer: Kaelyn Rosenberg <kaerosenberg@gmail.com>
Diff between tilemaps versions 0.2.0 dated 2020-07-10 and 0.2.1 dated 2025-09-29
DESCRIPTION | 15 - MD5 | 16 - NEWS.md | 4 R/create_island.R | 4 R/generate_map.R | 2 R/many_maps.R | 2 build/vignette.rds |binary inst/doc/tilemaps.R | 6 inst/doc/tilemaps.html | 466 ++++++++++++++++++++++++++++++++++++------------- 9 files changed, 370 insertions(+), 145 deletions(-)
Title: Algorithm Portfolio Selection with Machine Learning
Description: A wrapper for machine learning (ML) methods to select among a portfolio of algorithms based on the value of a key performance indicator (KPI). A number of features is used to adjust a model to predict the value of the KPI for each algorithm, then, for a new value of the features the KPI is estimated and the algorithm with the best one is chosen. To learn it can use the regression methods in 'caret' package or a custom function defined by the user. Several graphics available to analyze the results obtained. This library has been used in Ghaddar et al. (2023) <doi:10.1287/ijoc.2022.0090>).
Author: Brais Gonzalez-Rodriguez [aut, cre] ,
Ignacio Gomez-Casares [aut] ,
Beatriz Pateiro-Lopez [aut] ,
Julio Gonzalez-Diaz [aut] ,
Maria Caseiro-Arias [ctb],
Antonio Farina-Elorza [ctb],
Manuel Timiraos-Lopez [ctb]
Maintainer: Brais Gonzalez-Rodriguez <brais.gonzalez.rodriguez@uvigo.gal>
Diff between ASML versions 1.0.0 dated 2025-02-19 and 1.1.0 dated 2025-09-29
ASML-1.0.0/ASML/man/figure_comparison.as_data.Rd |only ASML-1.1.0/ASML/DESCRIPTION | 23 ASML-1.1.0/ASML/MD5 | 49 - ASML-1.1.0/ASML/NAMESPACE | 1 ASML-1.1.0/ASML/R/data.R | 39 - ASML-1.1.0/ASML/R/graphics.R | 259 +++++--- ASML-1.1.0/ASML/R/machine_learning.R | 677 ++++++++++++++--------- ASML-1.1.0/ASML/R/partition_and_normalize.R | 361 ++++++------ ASML-1.1.0/ASML/R/tables.R | 417 ++++++++------ ASML-1.1.0/ASML/data/SpMVformat.rda |only ASML-1.1.0/ASML/data/branching.rda |binary ASML-1.1.0/ASML/data/branchingsmall.rda |binary ASML-1.1.0/ASML/man/ASexplainer.Rd |only ASML-1.1.0/ASML/man/ASpredict.Rd | 18 ASML-1.1.0/ASML/man/ASpredict.as_train.Rd | 2 ASML-1.1.0/ASML/man/AStrain.Rd | 18 ASML-1.1.0/ASML/man/AStrain.as_data.Rd | 15 ASML-1.1.0/ASML/man/KPI_summary_table.Rd | 43 - ASML-1.1.0/ASML/man/KPI_summary_table.as_data.Rd |only ASML-1.1.0/ASML/man/KPI_table.Rd | 35 - ASML-1.1.0/ASML/man/KPI_table.as_data.Rd |only ASML-1.1.0/ASML/man/SpMVformat.Rd |only ASML-1.1.0/ASML/man/boxplots.Rd | 18 ASML-1.1.0/ASML/man/figure_comparison.Rd | 20 ASML-1.1.0/ASML/man/ml.Rd | 6 ASML-1.1.0/ASML/man/partition_and_normalize.Rd | 4 ASML-1.1.0/ASML/man/plot.as_data.Rd | 2 ASML-1.1.0/ASML/man/ranking.Rd | 20 ASML-1.1.0/ASML/man/topic-name.Rd |only 29 files changed, 1196 insertions(+), 831 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.13.0 dated 2025-08-19 and 0.14.0 dated 2025-09-29
tinytable-0.13.0/tinytable/R/bootstrap_build.R |only tinytable-0.13.0/tinytable/R/bootstrap_finalize.R |only tinytable-0.13.0/tinytable/R/bootstrap_group.R |only tinytable-0.13.0/tinytable/R/bootstrap_style.R |only tinytable-0.13.0/tinytable/R/strip_tt.R |only tinytable-0.13.0/tinytable/R/theme_html_bootstrap.R |only tinytable-0.13.0/tinytable/R/theme_html_raw.R |only tinytable-0.13.0/tinytable/R/theme_utils.R |only tinytable-0.13.0/tinytable/R/theme_void.R |only tinytable-0.13.0/tinytable/inst/templates/bootstrap.html |only tinytable-0.13.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-basic.pdf |only tinytable-0.13.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-complex.pdf |only tinytable-0.13.0/tinytable/inst/tinytest/_tinysnapshot/group-multilevel-empty.pdf |only tinytable-0.13.0/tinytable/inst/tinytest/_tinysnapshot/latex-theme_void.tex |only tinytable-0.13.0/tinytable/man/figures/gallery |only tinytable-0.13.0/tinytable/man/group_eval_j-tinytable_bootstrap-method.Rd |only tinytable-0.13.0/tinytable/man/strip_tt.Rd |only tinytable-0.13.0/tinytable/man/theme_void.Rd |only tinytable-0.14.0/tinytable/DESCRIPTION | 8 tinytable-0.14.0/tinytable/MD5 | 578 +++++---- tinytable-0.14.0/tinytable/NAMESPACE | 13 tinytable-0.14.0/tinytable/NEWS.md | 64 + tinytable-0.14.0/tinytable/R/aaa_class.R | 114 + tinytable-0.14.0/tinytable/R/ansi.R |only tinytable-0.14.0/tinytable/R/build_tt.R | 89 - tinytable-0.14.0/tinytable/R/colors.R | 43 tinytable-0.14.0/tinytable/R/css.R |only tinytable-0.14.0/tinytable/R/expand_style.R |only tinytable-0.14.0/tinytable/R/format_apply.R | 6 tinytable-0.14.0/tinytable/R/format_tt.R | 152 +- tinytable-0.14.0/tinytable/R/format_vector.R | 145 +- tinytable-0.14.0/tinytable/R/format_vector_misc.R |only tinytable-0.14.0/tinytable/R/format_vector_replace.R | 5 tinytable-0.14.0/tinytable/R/grid_build.R | 185 ++ tinytable-0.14.0/tinytable/R/grid_colspan.R |only 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11 tinytable-0.14.0/tinytable/inst/tinytest/test-ansi.R |only tinytable-0.14.0/tinytable/inst/tinytest/test-escape_i.R |only tinytable-0.14.0/tinytable/inst/tinytest/test-format.R | 62 tinytable-0.14.0/tinytable/inst/tinytest/test-format_vector.R |only tinytable-0.14.0/tinytable/inst/tinytest/test-group.R | 38 tinytable-0.14.0/tinytable/inst/tinytest/test-html.R | 71 - tinytable-0.14.0/tinytable/inst/tinytest/test-i_j.R | 3 tinytable-0.14.0/tinytable/inst/tinytest/test-latex.R | 8 tinytable-0.14.0/tinytable/inst/tinytest/test-markdown.R | 37 tinytable-0.14.0/tinytable/inst/tinytest/test-methods.R |only tinytable-0.14.0/tinytable/inst/tinytest/test-misc.R | 4 tinytable-0.14.0/tinytable/inst/tinytest/test-rbind2.R |only tinytable-0.14.0/tinytable/inst/tinytest/test-s3.R |only tinytable-0.14.0/tinytable/inst/tinytest/test-style.R | 38 tinytable-0.14.0/tinytable/inst/tinytest/test-style_vector.R |only tinytable-0.14.0/tinytable/inst/tinytest/test-tabulator.R | 22 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tinytable-0.14.0/tinytable/man/nrow-tinytable-method.Rd | 2 tinytable-0.14.0/tinytable/man/plot_tt.Rd | 65 - tinytable-0.14.0/tinytable/man/plot_vector.Rd |only tinytable-0.14.0/tinytable/man/print.tinytable.Rd | 7 tinytable-0.14.0/tinytable/man/save_tt.Rd | 29 tinytable-0.14.0/tinytable/man/style_eval.Rd | 2 tinytable-0.14.0/tinytable/man/style_tt.Rd | 90 + tinytable-0.14.0/tinytable/man/style_vector.Rd |only tinytable-0.14.0/tinytable/man/subset.tinytable.Rd |only tinytable-0.14.0/tinytable/man/theme_empty.Rd |only tinytable-0.14.0/tinytable/man/theme_html.Rd | 23 tinytable-0.14.0/tinytable/man/theme_latex.Rd | 8 tinytable-0.14.0/tinytable/man/theme_markdown.Rd |only tinytable-0.14.0/tinytable/man/tt.Rd | 84 - 339 files changed, 6460 insertions(+), 6403 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.19 dated 2025-08-25 and 1.20 dated 2025-09-29
DESCRIPTION | 8 - MD5 | 32 +++---- NAMESPACE | 1 NEWS.md | 15 +++ R/class-workbook-wrappers.R | 117 ++++++++++++++++++++++++-- R/class-workbook.R | 40 ++++++++ R/dates.R | 8 - R/read.R | 4 R/utils.R | 4 inst/WORDLIST | 1 man/convert_date.Rd | 21 +--- man/wbWorkbook.Rd | 9 ++ man/wb_page_setup.Rd | 80 ++++++++++++++++- tests/testthat/test-class-workbook-wrappers.R | 7 + tests/testthat/test-class-worksheet.R | 2 tests/testthat/test-read_from_created_wb.R | 22 ++++ tests/testthat/test-wb_styles.R | 43 +++++++++ 17 files changed, 358 insertions(+), 56 deletions(-)
Title: Conditional Mutual Information Estimation for Multi-Omics Data
Description: The biases introduced in association measures, particularly mutual information,
are influenced by factors such as tumor purity, mutation burden, and hypermethylation.
This package provides the estimation of conditional mutual information (CMI) and its
statistical significance with a focus on its application to multi-omics data. Utilizing
B-spline functions (inspired by Daub et al. (2004) <doi:10.1186/1471-2105-5-118>), the package offers tools to estimate the association between heterogeneous multi-
omics data, while removing the effects of confounding factors. This helps to unravel complex
biological interactions. In addition, it includes methods to evaluate the statistical significance
of these associations, providing a robust framework for multi-omics data integration and
analysis. This package is ideal for researchers in computational biology, bioinformatics,
and systems biology seeking a comprehensive tool for understanding interdependencies in
omics data.
Author: Gaojianyong Wang [aut, cre]
Maintainer: Gaojianyong Wang <gjywang@gmail.com>
Diff between conMItion versions 0.2.0 dated 2025-07-14 and 0.2.1 dated 2025-09-29
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/ComputePermutation.R | 20 ++++++++++---------- 3 files changed, 15 insertions(+), 15 deletions(-)
Title: Time-Ordered and Time-Aggregated Network Analyses
Description: Approaches for incorporating time into network analysis. Methods include: construction of time-ordered networks (temporal graphs); shortest-time and shortest-path-length analyses; resource spread calculations; data resampling and rarefaction for null model construction; reduction to time-aggregated networks with variable window sizes; application of common descriptive statistics to these networks; vector clock latencies; and plotting functionalities. The package supports <doi:10.1371/journal.pone.0020298>.
Author: Benjamin Wong Blonder [aut, cre]
Maintainer: Benjamin Wong Blonder <benjamin.blonder@berkeley.edu>
Diff between timeordered versions 1.0.1 dated 2024-09-15 and 1.0.2 dated 2025-09-29
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/transformspreadbyindividual.Rd | 4 +--- 3 files changed, 7 insertions(+), 9 deletions(-)
Title: Sound Synthesis and Acoustic Analysis
Description: Performs parametric synthesis of sounds with harmonic and noise
components such as animal vocalizations or human voice. Also offers tools
for audio manipulation and acoustic analysis, including pitch tracking,
spectral analysis, audio segmentation, pitch and formant shifting, etc.
Includes four interactive web apps for synthesizing and annotating audio,
manually correcting pitch contours, and measuring formant frequencies.
Reference: Anikin (2019) <doi:10.3758/s13428-018-1095-7>.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <andrey.anikin@cogsci.se>
Diff between soundgen versions 2.7.3 dated 2025-07-17 and 2.7.4 dated 2025-09-29
soundgen-2.7.3/soundgen/man/ERBToHz.Rd |only soundgen-2.7.3/soundgen/man/listDepth.Rd |only soundgen-2.7.3/soundgen/man/notesToHz.Rd |only soundgen-2.7.3/soundgen/man/semitonesToHz.Rd |only soundgen-2.7.4/soundgen/DESCRIPTION | 10 soundgen-2.7.4/soundgen/MD5 | 88 - soundgen-2.7.4/soundgen/NAMESPACE | 2 soundgen-2.7.4/soundgen/NEWS | 17 soundgen-2.7.4/soundgen/R/analyze.R | 35 soundgen-2.7.4/soundgen/R/audSpec.R | 42 soundgen-2.7.4/soundgen/R/formants.R | 2 soundgen-2.7.4/soundgen/R/frequency_scales.R |only soundgen-2.7.4/soundgen/R/math.R | 210 --- soundgen-2.7.4/soundgen/R/modulationSpectrum.R | 2 soundgen-2.7.4/soundgen/R/pitch_postprocessing.R | 25 soundgen-2.7.4/soundgen/R/postprocessing.R | 23 soundgen-2.7.4/soundgen/R/soundgen.R | 18 soundgen-2.7.4/soundgen/R/spectrogram.R | 174 ++- soundgen-2.7.4/soundgen/R/surprisal.R | 533 +++++++--- soundgen-2.7.4/soundgen/R/vtl.R | 30 soundgen-2.7.4/soundgen/README.md | 84 - soundgen-2.7.4/soundgen/inst/shiny/annotation_app/server.R | 12 soundgen-2.7.4/soundgen/inst/shiny/annotation_app/www/nrm66nuk.wav |only soundgen-2.7.4/soundgen/inst/shiny/pitch_app/server.R | 13 soundgen-2.7.4/soundgen/inst/shiny/pitch_app/www/temp.wav |only soundgen-2.7.4/soundgen/man/HzToERB.Rd | 38 soundgen-2.7.4/soundgen/man/HzToNotes.Rd | 20 soundgen-2.7.4/soundgen/man/HzToOther.Rd |only soundgen-2.7.4/soundgen/man/HzToSemitones.Rd | 22 soundgen-2.7.4/soundgen/man/addPitchCands.Rd | 3 soundgen-2.7.4/soundgen/man/analyze.Rd | 13 soundgen-2.7.4/soundgen/man/audSpectrogram.Rd | 25 soundgen-2.7.4/soundgen/man/dot-audSpectrogram.Rd | 23 soundgen-2.7.4/soundgen/man/dot-getSurprisal.Rd | 60 - soundgen-2.7.4/soundgen/man/dot-spectrogram.Rd | 21 soundgen-2.7.4/soundgen/man/estimateVTL.Rd | 24 soundgen-2.7.4/soundgen/man/figures/README-analysis-1.png |binary soundgen-2.7.4/soundgen/man/figures/README-synthsesis-1.png |binary soundgen-2.7.4/soundgen/man/figures/s.mp3 |binary soundgen-2.7.4/soundgen/man/getSurprisal.Rd | 203 ++- soundgen-2.7.4/soundgen/man/getSurprisal_matrix.Rd | 24 soundgen-2.7.4/soundgen/man/getSurprisal_vector.Rd | 14 soundgen-2.7.4/soundgen/man/hz2mel.Rd | 8 soundgen-2.7.4/soundgen/man/modulationSpectrum.Rd | 2 soundgen-2.7.4/soundgen/man/plotSpec.Rd | 14 soundgen-2.7.4/soundgen/man/reverb.Rd | 16 soundgen-2.7.4/soundgen/man/schwa.Rd | 8 soundgen-2.7.4/soundgen/man/soundgen.Rd | 14 soundgen-2.7.4/soundgen/man/spectrogram.Rd | 79 + 49 files changed, 1177 insertions(+), 774 deletions(-)
Title: Read Paradox Database Files into R
Description: Provides a simple and efficient way to read data from Paradox
database files (.db) directly into R as modern 'tibble' data frames.
It uses the underlying 'pxlib' C library, to handle the low-level file format
details and provides a clean, user-friendly R interface.
Author: Daniil Popov [aut, cre]
Maintainer: Daniil Popov <popov.daniil@gmail.com>
Diff between Rparadox versions 0.1.2 dated 2025-09-22 and 0.1.5 dated 2025-09-29
DESCRIPTION | 13 +- MD5 | 38 +++--- NAMESPACE | 3 NEWS.md | 31 ++++ R/pxlib_get_data.R | 29 +++- R/pxlib_metadata.R |only R/pxlib_open_file.R | 41 ++++-- R/read_paradox.R |only R/utils.R | 72 +++++++++-- README.md | 75 +++++++---- inst/doc/Rparadox.R | 33 +++-- inst/doc/Rparadox.Rmd | 54 ++++++-- inst/doc/Rparadox.html | 95 +++++++++------ man/Rparadox-package.Rd | 3 man/pxlib_metadata.Rd |only man/read_paradox.Rd |only src/init.c | 8 - src/interface.c | 232 ++++++++++++++++--------------------- src/paradox.c | 54 +------- tests/testthat/test-get-data.R | 48 +++---- tests/testthat/test-metadata.R |only tests/testthat/test-read_paradox.R |only vignettes/Rparadox.Rmd | 54 ++++++-- 23 files changed, 528 insertions(+), 355 deletions(-)
Title: Estimation of Forest Variables using the FIA Database
Description: The goal of 'rFIA' is to increase the accessibility and use of the United States Forest Services (USFS) Forest Inventory and Analysis (FIA) Database by providing a user-friendly, open source toolkit to easily query and analyze FIA Data. Designed to accommodate a wide range of potential user objectives, 'rFIA' simplifies the estimation of forest variables from the FIA Database and allows all R users (experts and newcomers alike) to unlock the flexibility inherent to the Enhanced FIA design. Specifically, 'rFIA' improves accessibility to the spatial-temporal estimation capacity of the FIA Database by producing space-time indexed summaries of forest variables within user-defined population boundaries. Direct integration with other popular R packages (e.g., 'dplyr', 'tidyr', and 'sf') facilitates efficient space-time query and data summary, and supports common data representations and API design. The package implements design-based estimation procedures outlined by Bechtold & Patterson [...truncated...]
Author: Jeffrey Doser [aut, cre],
Hunter Stanke [aut],
Andrew Finley [aut]
Maintainer: Jeffrey Doser <jwdoser@ncsu.edu>
Diff between rFIA versions 1.1.1 dated 2025-03-10 and 1.1.2 dated 2025-09-29
DESCRIPTION | 6 MD5 | 75 +++++------ NEWS.md | 6 R/areaChangeStarter.R | 14 +- R/areaStarter.R | 11 + R/biomass.R | 2 R/biomassStarter.R | 11 + R/carbonStarter.R | 13 + R/diversityStarter.R | 11 + R/dwmStarter.R | 11 + R/fsi.R | 332 +++---------------------------------------------- R/fsiStarter.R |only R/growMortStarter.R | 23 +++ R/invasiveStarter.R | 11 + R/readFIA.R | 2 R/seedlingStarter.R | 11 + R/standStructStarter.R | 10 + R/tpaStarter.R | 10 + R/util.R | 2 R/vegStructStarter.R | 11 + R/vitalRatesStarter.R | 11 + R/volumeStarter.R | 11 + data/fiaRI.rda |binary man/area.Rd | 2 man/areaChange.Rd | 2 man/biomass.Rd | 2 man/carbon.Rd | 2 man/diversity.Rd | 2 man/dwm.Rd | 2 man/fiaRI.Rd | 2 man/fsi.Rd | 2 man/growMort.Rd | 2 man/invasive.Rd | 2 man/seedling.Rd | 2 man/standStruct.Rd | 2 man/tpa.Rd | 2 man/vegStruct.Rd | 2 man/vitalRates.Rd | 2 man/volume.Rd | 2 39 files changed, 239 insertions(+), 387 deletions(-)
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data
from disparate sources. Metadata is managed throughout the process to facilitate
reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] ,
Cory Merow [aut] ,
Brian Maitner [aut] ,
Jamie M. Kass [aut] ,
Vijay Barve [aut] ,
Robert P. Guralnick [aut] ,
Damiano Oldoni [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/407>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
This is a re-admission after prior archival of version 0.6.0 dated 2025-06-16
Diff between occCite versions 0.6.0 dated 2025-06-16 and 0.6.1 dated 2025-09-29
DESCRIPTION | 19 +++++++-------- MD5 | 14 +++++------ NEWS.md | 3 ++ R/occCite_plotting.R | 7 +++++ R/studyTaxonList.R | 2 - inst/doc/a_Simple.html | 14 +++++------ inst/doc/b_Advanced.html | 54 +++++++++++++++++++++---------------------- tests/testthat/test-sumFig.R | 24 +++++++++++-------- 8 files changed, 77 insertions(+), 60 deletions(-)
Title: Draw XmR Charts for NHS 'Making Data Count' Programme
Description: Provides tools for drawing Statistical Process Control (SPC) charts. This package supports the NHS 'Making Data Count' programme, and allows users to draw XmR charts, use change points and apply rules with summary indicators for when rules are breached.
Author: Tom Smith [cre, aut],
Christopher Reading [aut],
Simon Wellesley-Miller [aut],
Zoe Turner [aut] ,
Tom Jemmett [aut] ,
Chris Mainey [aut] ,
John MacKintosh [aut],
Marcos Fabietti [aut],
Fran Barton [aut] ,
NHS-R community [cph]
Maintainer: Tom Smith <thomas.smith103@nhs.net>
Diff between NHSRplotthedots versions 0.1.0 dated 2021-11-03 and 0.2.2 dated 2025-09-29
NHSRplotthedots-0.1.0/NHSRplotthedots/inst/doc/intro.R |only NHSRplotthedots-0.1.0/NHSRplotthedots/inst/doc/intro.Rmd |only NHSRplotthedots-0.1.0/NHSRplotthedots/inst/doc/intro.html |only NHSRplotthedots-0.1.0/NHSRplotthedots/inst/logo.png |only NHSRplotthedots-0.1.0/NHSRplotthedots/man/figures/logo.png |only NHSRplotthedots-0.1.0/NHSRplotthedots/vignettes/intro.Rmd |only NHSRplotthedots-0.2.2/NHSRplotthedots/DESCRIPTION | 64 - NHSRplotthedots-0.2.2/NHSRplotthedots/MD5 | 148 +- NHSRplotthedots-0.2.2/NHSRplotthedots/NAMESPACE | 23 NHSRplotthedots-0.2.2/NHSRplotthedots/NEWS.md | 15 NHSRplotthedots-0.2.2/NHSRplotthedots/R/NHSRplotthedots-package.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/R/ZZZ.R | 12 NHSRplotthedots-0.2.2/NHSRplotthedots/R/geom_ptd_icon.R | 267 +++-- NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_add_rebase_column.R | 20 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_add_short_group_warnings.R | 27 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_add_target_column.R | 2 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_calculate_assurance_type.R | 19 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_calculate_point_type.R | 97 + NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_create_ggplot.R | 299 +++-- NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_create_plotly.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_rebase.R | 43 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_spc.R | 176 ++- NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_spc_colours.R | 23 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_spc_options.R | 36 NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_spc_standard.R | 60 - NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_target.R | 61 - NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_validate_plot_options.R | 52 - NHSRplotthedots-0.2.2/NHSRplotthedots/R/ptd_validate_spc_options.R | 12 NHSRplotthedots-0.2.2/NHSRplotthedots/R/to_datetime.R | 4 NHSRplotthedots-0.2.2/NHSRplotthedots/README.md | 251 +++- NHSRplotthedots-0.2.2/NHSRplotthedots/build/vignette.rds |binary NHSRplotthedots-0.2.2/NHSRplotthedots/inst/WORDLIST | 56 - NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/NHSRplotthedots.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/NHSRplotthedots.Rmd |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/NHSRplotthedots.html |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/deviations.R | 41 NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/deviations.Rmd | 126 +- NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/deviations.html | 514 +++++++--- NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/number-of-points-required.R | 2 NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/number-of-points-required.Rmd | 31 NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/number-of-points-required.html | 270 ++++- NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/other-spc-tools.Rmd |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/doc/other-spc-tools.html |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/hex-logo.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/icons |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/images |only NHSRplotthedots-0.2.2/NHSRplotthedots/inst/test-hex-logo.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/GeomPTDIcon.Rd |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/NHSRplotthedots-package.Rd |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example-1.png |binary NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example-ptd-create-ggplot-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example-ptd_create_ggplot-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example-with-plot-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example1-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-example2-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-limits-example-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-unnamed-chunk-2-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-unnamed-chunk-3-1.png |binary NHSRplotthedots-0.2.2/NHSRplotthedots/man/figures/README-unnamed-chunk-5-1.png |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/geom_ptd_icon.Rd |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_create_ggplot.Rd | 65 - NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_create_plotly.Rd |only NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_rebase.Rd | 37 NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_spc.Rd | 74 - NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_spc_colours.Rd | 18 NHSRplotthedots-0.2.2/NHSRplotthedots/man/ptd_target.Rd | 54 - NHSRplotthedots-0.2.2/NHSRplotthedots/tests/spelling.R | 9 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/_snaps/geom_ptd_icon.md | 20 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/_snaps/ptd_spc.md | 225 ++-- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/_snaps/ptd_spc_standard.md | 120 +- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-geom_ptd_icon.R | 174 ++- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_add_rebase_column.R | 25 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_add_short_group_warnings.R | 22 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_calculate_assurance_type.R | 56 - NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_calculate_point_type.R | 147 +- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_create_ggplot.R | 158 +-- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_create_plotly.R |only NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_spc.R | 282 +++-- NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_spc_options.R | 32 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_spc_standard.R | 31 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_validate_plot_options.R | 12 NHSRplotthedots-0.2.2/NHSRplotthedots/tests/testthat/test-ptd_validate_spc_options.R | 25 NHSRplotthedots-0.2.2/NHSRplotthedots/vignettes/NHSRplotthedots.Rmd |only NHSRplotthedots-0.2.2/NHSRplotthedots/vignettes/deviations.Rmd | 126 +- NHSRplotthedots-0.2.2/NHSRplotthedots/vignettes/number-of-points-required.Rmd | 31 NHSRplotthedots-0.2.2/NHSRplotthedots/vignettes/other-spc-tools.Rmd |only 86 files changed, 2958 insertions(+), 1536 deletions(-)
More information about NHSRplotthedots at CRAN
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Title: Causal Inference in Spatiotemporal Event Data
Description: Implementation of Matched Wake Analysis (mwa) for studying causal relationships in spatiotemporal event data, introduced by Schutte and Donnay (2014) <doi:10.1016/j.polgeo.2014.03.001>.
Author: Sebastian Schutte [aut],
Karsten Donnay [aut, cre]
Maintainer: Karsten Donnay <kdonnay@gmx.net>
Diff between mwa versions 0.4.4 dated 2022-04-26 and 0.5.0 dated 2025-09-29
DESCRIPTION | 19 ++++++++++--------- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- NEWS | 5 +++++ R/mwa.R | 35 ++++++++++++++++++++++++++++------- README.md | 4 ++-- man/matchedwake.Rd | 15 ++++++++++++--- man/plot.matchedwake.Rd | 8 +++++++- man/slideWakeMatch.Rd | 19 ++++++++++++++----- 9 files changed, 87 insertions(+), 36 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Author: Dimitris Rizopoulos [aut, cre]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.8-85 dated 2020-01-08 and 0.9-0 dated 2025-09-29
DESCRIPTION | 14 ++++++---- MD5 | 58 +++++++++++++++++++++--------------------- NAMESPACE | 2 + R/JMbayes_plot_survfitJM2.R |only R/MCMCfit.R | 2 - R/chol.transf.R | 2 - R/confint.JMbayes.R | 2 - R/dynInfo.R | 16 +++++------ R/dynPred_lme.R | 2 - R/format.perc.R | 2 - R/format.pval2.R | 2 - R/initSurvival.R | 2 - R/log.posterior.b.R | 2 - R/marglogLik.R | 6 ++-- R/methods_mvJointModelBayes.R | 5 ++- R/mvJointModelBayes.R | 25 +++++++++++++----- R/plot_survfit_mvJMbayes_hp.R |only R/predict.JMbayes.R | 8 ++--- R/predict_eventTime.R | 2 - R/print.summary.JMbayes.R | 4 +- R/survfitJM.JMbayes.R | 8 ++--- R/survfitJM.mvJMbayes.R | 11 +++++-- R/td_effect.R | 2 - R/xtable.JMbayes.R | 4 +- README.md | 8 ++--- man/JMbayes.Rd | 4 +- man/plot-survfitJM.Rd | 20 +++++++------- man/xtable.Rd | 6 ++-- src/Makevars | 5 +-- src/Makevars.win | 5 +-- src/RcppExports.cpp | 5 +++ 31 files changed, 132 insertions(+), 102 deletions(-)
Title: Intervention in Prediction Measure for Random Forests
Description: Computes intervention in prediction measure for assessing variable importance for random forests. See details at I. Epifanio (2017) <DOI:10.1186/s12859-017-1650-8>.
Author: Irene Epifanio [aut, cre],
Stefano Nembrini [aut],
Aleix Alcacer [aut],
Vicente Bolos [aut]
Maintainer: Irene Epifanio <epifanio@uji.es>
This is a re-admission after prior archival of version 1.2 dated 2017-08-09
Diff between IPMRF versions 1.2 dated 2017-08-09 and 1.3 dated 2025-09-29
IPMRF-1.2/IPMRF/R/getTreeranger.R |only IPMRF-1.2/IPMRF/R/ipmranger.R |only IPMRF-1.2/IPMRF/R/ipmrangernew.R |only IPMRF-1.2/IPMRF/man/IPMRF-internal-ranger.Rd |only IPMRF-1.2/IPMRF/man/ipmranger.Rd |only IPMRF-1.2/IPMRF/man/ipmrangernew.Rd |only IPMRF-1.3/IPMRF/DESCRIPTION | 34 ++++++++++---- IPMRF-1.3/IPMRF/MD5 | 32 +++++-------- IPMRF-1.3/IPMRF/NAMESPACE | 2 IPMRF-1.3/IPMRF/NEWS | 3 + IPMRF-1.3/IPMRF/R/prevtree.R | 2 IPMRF-1.3/IPMRF/inst/CITATION | 19 ++++--- IPMRF-1.3/IPMRF/man/IPMRF-internal-gbm.Rd | 1 IPMRF-1.3/IPMRF/man/IPMRF-internal.Rd | 1 IPMRF-1.3/IPMRF/man/IPMRF-package.Rd | 14 ++--- IPMRF-1.3/IPMRF/man/ipmgbmnew.Rd | 14 ++--- IPMRF-1.3/IPMRF/man/ipmparty.Rd | 65 +++++---------------------- IPMRF-1.3/IPMRF/man/ipmpartynew.Rd | 30 +++++------- IPMRF-1.3/IPMRF/man/ipmrf.Rd | 56 +++++++++++------------ IPMRF-1.3/IPMRF/man/ipmrfnew.Rd | 24 ++++----- 20 files changed, 139 insertions(+), 158 deletions(-)
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.2.1 dated 2025-08-25 and 0.2.2 dated 2025-09-29
DESCRIPTION | 6 +-- MD5 | 33 +++++++++-------- NEWS.md | 8 ++++ R/get_pvol.R | 1 R/get_pvol_dk.R | 6 +-- R/get_pvol_sk.R |only R/get_pvol_us.R | 4 +- R/get_weather_radars.R | 1 R/zzz.R | 2 - inst/doc/supported_sources.R | 5 +- inst/doc/supported_sources.Rmd | 5 +- inst/doc/supported_sources.html | 59 +++++++++++++++---------------- tests/testthat/teardown_remove_cache.R |only tests/testthat/test-get_pvol_dk.R | 6 ++- tests/testthat/test-get_pvol_nl.R | 34 +++++++++-------- tests/testthat/test-get_pvol_sk.R |only tests/testthat/test-get_pvol_us.R | 8 ++-- tests/testthat/test-get_weather_radars.R | 8 ---- vignettes/supported_sources.Rmd | 5 +- 19 files changed, 104 insertions(+), 87 deletions(-)
Title: Finds the Critical Sequential Point of Stability for a Pearson
Correlation
Description: Finds the critical sample size ("critical point of stability") for a
correlation to stabilize in Schoenbrodt and Perugini's definition of
sequential stability (see <doi:10.1016/j.jrp.2013.05.009>).
Author: Johannes Titz [aut, cre, cph]
Maintainer: Johannes Titz <johannes.titz@gmail.com>
Diff between fastpos versions 0.5.1 dated 2022-08-15 and 0.6.0 dated 2025-09-29
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS.md | 7 ++++++- build/partial.rdb |binary man/find_critical_pos.Rd | 2 +- src/Makevars | 13 +------------ src/Makevars.win | 15 ++------------- src/RcppExports.cpp | 4 ++-- src/rcpparma.cpp | 15 +++++++++------ 9 files changed, 35 insertions(+), 49 deletions(-)
Title: Modular Differential Evolution for Experimenting with Operators
Description: Modular implementation of the Differential Evolution algorithm for
experimenting with different types of operators.
Author: Felipe Campelo [aut, cre],
Moises Botelho [aut]
Maintainer: Felipe Campelo <f.campelo@bristol.ac.uk>
Diff between ExpDE versions 0.1.4 dated 2018-01-10 and 0.2.0 dated 2025-09-29
ExpDE-0.1.4/ExpDE/R/rastrigin.R |only ExpDE-0.1.4/ExpDE/R/sphere.R |only ExpDE-0.1.4/ExpDE/man/mutation_current_to_pbest.Rd |only ExpDE-0.2.0/ExpDE/DESCRIPTION | 21 ExpDE-0.2.0/ExpDE/MD5 | 139 +- ExpDE-0.2.0/ExpDE/NAMESPACE | 65 - ExpDE-0.2.0/ExpDE/R/ExpDE.R | 582 +++++----- ExpDE-0.2.0/ExpDE/R/ExpDE2.R |only ExpDE-0.2.0/ExpDE/R/check_stop_criteria.R | 90 - ExpDE-0.2.0/ExpDE/R/create_population.R | 56 ExpDE-0.2.0/ExpDE/R/evaluate_population.R | 126 +- ExpDE-0.2.0/ExpDE/R/function_rastrigin.R |only ExpDE-0.2.0/ExpDE/R/function_rosenbrock.R |only ExpDE-0.2.0/ExpDE/R/function_sphere.R |only ExpDE-0.2.0/ExpDE/R/gen_methods.R |only ExpDE-0.2.0/ExpDE/R/gen_problems.R |only ExpDE-0.2.0/ExpDE/R/get_exp_params_1.R |only ExpDE-0.2.0/ExpDE/R/mutation_best.R | 182 +-- ExpDE-0.2.0/ExpDE/R/mutation_current_to_pbest.R | 193 +-- ExpDE-0.2.0/ExpDE/R/mutation_mean.R | 162 +- ExpDE-0.2.0/ExpDE/R/mutation_none.R | 36 ExpDE-0.2.0/ExpDE/R/mutation_operators.R | 30 ExpDE-0.2.0/ExpDE/R/mutation_rand.R | 148 +- ExpDE-0.2.0/ExpDE/R/mutation_wgi.R | 196 +-- ExpDE-0.2.0/ExpDE/R/print_progress.R | 106 - ExpDE-0.2.0/ExpDE/R/recombination_arith.R | 68 - ExpDE-0.2.0/ExpDE/R/recombination_bin.R | 120 +- ExpDE-0.2.0/ExpDE/R/recombination_blxAlphaBeta.R | 184 +-- ExpDE-0.2.0/ExpDE/R/recombination_eigen.R | 128 +- ExpDE-0.2.0/ExpDE/R/recombination_exp.R | 142 +- ExpDE-0.2.0/ExpDE/R/recombination_geo.R | 130 +- ExpDE-0.2.0/ExpDE/R/recombination_lbga.R | 164 +- ExpDE-0.2.0/ExpDE/R/recombination_linear.R | 142 +- ExpDE-0.2.0/ExpDE/R/recombination_mmax.R | 208 +-- ExpDE-0.2.0/ExpDE/R/recombination_none.R | 48 ExpDE-0.2.0/ExpDE/R/recombination_npoint.R | 176 +-- ExpDE-0.2.0/ExpDE/R/recombination_onepoint.R | 154 +- ExpDE-0.2.0/ExpDE/R/recombination_operators.R | 50 ExpDE-0.2.0/ExpDE/R/recombination_pbest.R | 146 +- ExpDE-0.2.0/ExpDE/R/recombination_sbx.R | 112 - ExpDE-0.2.0/ExpDE/R/recombination_wright.R | 120 +- ExpDE-0.2.0/ExpDE/R/selection_standard.R | 64 - ExpDE-0.2.0/ExpDE/R/utils.R | 58 ExpDE-0.2.0/ExpDE/R/zz_get_experimental_parameters_2.R |only ExpDE-0.2.0/ExpDE/R/zz_get_experimental_parameters_vB.R |only ExpDE-0.2.0/ExpDE/R/zz_get_random_recmutpars.R |only ExpDE-0.2.0/ExpDE/man/ExpDE.Rd | 470 ++++---- ExpDE-0.2.0/ExpDE/man/ExpDE2.Rd |only ExpDE-0.2.0/ExpDE/man/check_stop_criteria.Rd | 44 ExpDE-0.2.0/ExpDE/man/create_population.Rd | 38 ExpDE-0.2.0/ExpDE/man/evaluate_population.Rd | 42 ExpDE-0.2.0/ExpDE/man/gen_methods.Rd |only ExpDE-0.2.0/ExpDE/man/gen_problems.Rd |only ExpDE-0.2.0/ExpDE/man/get_exp_params_1.Rd |only ExpDE-0.2.0/ExpDE/man/get_experimental_parameters_activity2.Rd |only ExpDE-0.2.0/ExpDE/man/get_experimental_parameters_activity_versionB.Rd |only ExpDE-0.2.0/ExpDE/man/mutation_best.Rd | 100 - ExpDE-0.2.0/ExpDE/man/mutation_mean.Rd | 84 - ExpDE-0.2.0/ExpDE/man/mutation_none.Rd | 52 ExpDE-0.2.0/ExpDE/man/mutation_operators.Rd | 28 ExpDE-0.2.0/ExpDE/man/mutation_rand.Rd | 84 - ExpDE-0.2.0/ExpDE/man/mutation_wgi.Rd | 104 - ExpDE-0.2.0/ExpDE/man/print_progress.Rd | 64 - ExpDE-0.2.0/ExpDE/man/recombination_arith.Rd | 56 ExpDE-0.2.0/ExpDE/man/recombination_bin.Rd | 88 - ExpDE-0.2.0/ExpDE/man/recombination_blxAlphaBeta.Rd | 112 - ExpDE-0.2.0/ExpDE/man/recombination_eigen.Rd | 86 - ExpDE-0.2.0/ExpDE/man/recombination_exp.Rd | 80 - ExpDE-0.2.0/ExpDE/man/recombination_geo.Rd | 82 - ExpDE-0.2.0/ExpDE/man/recombination_lbga.Rd | 76 - ExpDE-0.2.0/ExpDE/man/recombination_linear.Rd | 74 - ExpDE-0.2.0/ExpDE/man/recombination_mmax.Rd | 110 - ExpDE-0.2.0/ExpDE/man/recombination_none.Rd | 44 ExpDE-0.2.0/ExpDE/man/recombination_npoint.Rd | 88 - ExpDE-0.2.0/ExpDE/man/recombination_onepoint.Rd | 86 - ExpDE-0.2.0/ExpDE/man/recombination_operators.Rd | 30 ExpDE-0.2.0/ExpDE/man/recombination_pbest.Rd | 102 - ExpDE-0.2.0/ExpDE/man/recombination_sbx.Rd | 90 - ExpDE-0.2.0/ExpDE/man/recombination_wright.Rd | 74 - ExpDE-0.2.0/ExpDE/man/selection_standard.Rd | 48 80 files changed, 3403 insertions(+), 3379 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.8 dated 2025-06-27 and 2.2.9 dated 2025-09-29
DESCRIPTION | 27 ++-- MD5 | 97 ++++++++++------- NAMESPACE | 11 +- NEWS | 52 +++++++++ R/GHcop.R | 70 +++++++++++- R/HAIRPINcop.R |only R/JOcop.R | 52 +++++++-- R/M.R | 2 R/MOcop.R |only R/N4220cop.R |only R/NORMcop.R |only R/PSP.R | 5 R/Tcop.R |only R/W.R | 2 R/kfuncCOP_Pd.R |only R/lcomCOP.R | 63 +++++++++-- R/rmseCOP.R | 4 man/CIRCcop.Rd | 38 ++++-- man/EMPIRcop.Rd | 8 - man/FGMcop.Rd | 29 +++++ man/FRcop.Rd | 2 man/GHcop.Rd | 218 ++++++++++++++++++--------------------- man/HAIRPINcop.Rd |only man/HRcop.Rd | 6 - man/JOcopB5.Rd | 21 +++ man/LCOMDIA_GH2cop.Rd |only man/LCOMDIA_GH3cop.Rd |only man/LCOMDIA_GHcop.Rd |only man/LCOMDIA_ManyCops.Rd |only man/LzCOPpermsym.Rd | 23 ++++ man/MOcop.Rd |only man/N4220cop.Rd |only man/NORMcop.Rd |only man/ORDSUMcop.Rd | 264 +++++++++++++++++++++++++++++++++++++++++++++--- man/ORDSUWcop.Rd | 16 +- man/P.Rd | 42 ++++--- man/RAYcop.Rd | 2 man/RFcop.Rd | 2 man/Tcop.Rd |only man/W.Rd | 38 ++++++ man/breveCOP.Rd | 10 - man/composite1COP.Rd | 23 ++-- man/composite2COP.Rd | 16 ++ man/composite3COP.Rd | 4 man/copBasic-package.Rd | 148 ++++++++++++++------------ man/footCOP.Rd | 85 ++++++++++----- man/gEVcop.Rd | 39 +++---- man/glueCOP.Rd | 85 +++++++++------ man/isCOP.permsym.Rd | 6 - man/isCOP.radsym.Rd | 164 ++++++++++++++++++----------- man/kfuncCOP.Rd | 85 ++++++++------- man/kfuncCOP_Pd.Rd |only man/lcomCOP.Rd | 104 ++++++++++-------- man/rN4220cop.Rd |only man/rhoCOP.Rd | 12 +- man/spectralmeas.Rd | 100 +++++++++--------- man/tEVcop.Rd | 13 +- man/taildepCOP.Rd | 90 ++++++++-------- 58 files changed, 1378 insertions(+), 700 deletions(-)
Title: Bayesian Hierarchical Poisson Models for Multiple Grouped
Outcomes with Clustering
Description: Bayesian hierarchical methods for the detection of differences in rates of related outcomes for multiple treatments for clustered observations (Carragher et al. (2020) <doi:10.1002/sim.8563>). This software was developed for the Precision Drug Theraputics: Risk Prediction in Pharmacoepidemiology project as part of a Rutherford Fund Fellowship at Health Data Research (UK), Medical Research Council (UK) award reference MR/S003967/1 (<https://gtr.ukri.org/>). Principal Investigator: Raymond Carragher.
Author: Raymond Carragher [aut, cre]
Maintainer: Raymond Carragher <rcarragh@gmail.com>
This is a re-admission after prior archival of version 1.7 dated 2020-04-01
Diff between bhpm versions 1.7 dated 2020-04-01 and 1.8.1 dated 2025-09-29
DESCRIPTION | 24 MD5 | 181 +- NAMESPACE | 64 R/bhpm.cluster.1a.hier2.R | 76 R/bhpm.cluster.1a.hier2.lev0.R | 724 ++++----- R/bhpm.cluster.1a.hier2.lev0.convergence.R | 940 +++++------ R/bhpm.cluster.1a.hier2.lev0.summary.stats.R | 470 ++--- R/bhpm.cluster.1a.hier2.lev1.R | 664 ++++---- R/bhpm.cluster.1a.hier2.lev1.convergence.R | 960 ++++++------ R/bhpm.cluster.1a.hier2.lev1.summary.stats.R | 478 +++--- R/bhpm.cluster.1a.hier3.R | 88 - R/bhpm.cluster.1a.hier3.lev0.R | 822 +++++----- R/bhpm.cluster.1a.hier3.lev0.convergence.R | 1346 ++++++++--------- R/bhpm.cluster.1a.hier3.lev0.summary.stats.R | 700 ++++---- R/bhpm.cluster.1a.hier3.lev1.R | 800 +++++----- R/bhpm.cluster.1a.hier3.lev1.convergence.R | 1346 ++++++++--------- R/bhpm.cluster.1a.hier3.lev1.summary.stats.R | 700 ++++---- R/bhpm.cluster.1a.hier3.lev2.R | 784 ++++----- R/bhpm.cluster.1a.hier3.lev2.convergence.R | 1330 ++++++++-------- R/bhpm.cluster.1a.hier3.lev2.summary.stats.R | 686 ++++---- R/bhpm.cluster.BB.hier2.R | 92 - R/bhpm.cluster.BB.hier2.lev0.R | 764 ++++----- R/bhpm.cluster.BB.hier2.lev0.convergence.R | 758 ++++----- R/bhpm.cluster.BB.hier2.lev0.summary.stats.R | 348 ++-- R/bhpm.cluster.BB.hier2.lev1.R | 760 ++++----- R/bhpm.cluster.BB.hier2.lev1.convergence.R | 746 ++++----- R/bhpm.cluster.BB.hier2.lev1.summary.stats.R | 322 ++-- R/bhpm.cluster.BB.hier3.R | 110 - R/bhpm.cluster.BB.hier3.lev0.R | 1032 ++++++------- R/bhpm.cluster.BB.hier3.lev0.convergence.R | 1336 ++++++++-------- R/bhpm.cluster.BB.hier3.lev0.summary.stats.R | 576 +++---- R/bhpm.cluster.BB.hier3.lev1.R | 986 ++++++------ R/bhpm.cluster.BB.hier3.lev1.convergence.R | 1272 ++++++++-------- R/bhpm.cluster.BB.hier3.lev1.summary.stats.R | 546 +++--- R/bhpm.cluster.BB.hier3.lev2.R | 1004 ++++++------ R/bhpm.cluster.BB.hier3.lev2.convergence.R | 1310 ++++++++-------- R/bhpm.cluster.BB.hier3.lev2.summary.stats.R | 542 +++--- R/bhpm.cluster.ptheta.R | 174 +- R/bhpm.convergence.R | 178 +- R/bhpm.gen.initial.values.R | 878 +++++------ R/bhpm.global.sim.param.defaults.R | 72 R/bhpm.hyper.params.defaults.R | 80 - R/bhpm.monitor.defaults.R | 86 - R/bhpm.monitor.samples.R | 52 R/bhpm.npm.R | 124 - R/bhpm.params.R | 354 ++-- R/bhpm.pm.R | 146 - R/bhpm.pm.weights.R | 72 R/bhpm.ptheta.R | 50 R/bhpm.summary.stats.R | 162 +- R/global.R | 1978 ++++++++++++------------- data/bhpm.cluster.data1.txt.gz |binary data/bhpm.cluster.data2.txt.gz |binary data/bhpm.multi.treatments.random.order.txt.gz |binary data/bhpm.multi.treatments.txt.gz |binary data/demo.cluster.data.txt.gz |only man/bhpm.Package.rd | 66 man/bhpm.cluster.1a.hier2.rd | 344 ++-- man/bhpm.cluster.1a.hier3.rd | 364 ++-- man/bhpm.cluster.BB.hier2.rd | 370 ++-- man/bhpm.cluster.BB.hier3.rd | 412 ++--- man/bhpm.cluster.data1.rd | 22 man/bhpm.cluster.data2.rd | 22 man/bhpm.convergence.diag.rd | 144 - man/bhpm.gen.initial.values.rd | 122 - man/bhpm.global.sim.param.defaults.rd | 100 - man/bhpm.hyper.params.defaults.rd | 100 - man/bhpm.monitor.defaults.rd | 100 - man/bhpm.monitor.samples.rd | 98 - man/bhpm.multi.treatments.random.order.rd | 22 man/bhpm.multi.treatments.rd | 32 man/bhpm.npm.rd | 356 ++-- man/bhpm.pm.rd | 396 ++--- man/bhpm.pointmass.weights.rd | 90 - man/bhpm.print.convergence.summary.rd | 106 - man/bhpm.print.summary.stats.rd | 94 - man/bhpm.ptheta.rd | 98 - man/bhpm.sim.control.params.rd | 104 - man/bhpm.summary.stats.rd | 116 - man/demo.cluster.data.rd |only src/bhpm1a_poisson_mc_hier2_lev0.cpp | 47 src/bhpm1a_poisson_mc_hier2_lev1.cpp | 16 src/bhpm1a_poisson_mc_hier3_lev0.cpp | 19 src/bhpm1a_poisson_mc_hier3_lev1.cpp | 24 src/bhpm1a_poisson_mc_hier3_lev2.cpp | 16 src/bhpmBB_poisson_mc_hier2_lev0.cpp | 20 src/bhpmBB_poisson_mc_hier2_lev1.cpp | 16 src/bhpmBB_poisson_mc_hier3_lev0.cpp | 32 src/bhpmBB_poisson_mc_hier3_lev1.cpp | 28 src/bhpmBB_poisson_mc_hier3_lev2.cpp | 54 src/bhpm_Rdefines.h |only src/bhpm_exec.cpp | 3 src/register.cpp | 3 93 files changed, 17034 insertions(+), 17015 deletions(-)
Title: Read, Manipulate, and Write Profiler Data
Description: Defines a data structure for profiler data, and methods to read and
write from the 'Rprof' and 'pprof' file formats.
Author: Kirill Mueller [aut, cre] ,
R Consortium [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between profile versions 1.0.3 dated 2022-08-22 and 1.0.4 dated 2025-09-29
DESCRIPTION | 17 ++++++++++------- MD5 | 22 ++++++++++++---------- NEWS.md | 13 ++++++++++++- R/api.R | 14 +++++++------- man/validate_profile.Rd | 15 +++++++++------ tests/testthat.R | 8 ++++++++ tests/testthat/_snaps |only tests/testthat/test-dm.R |only tests/testthat/test-pprof-from-ds.R | 2 -- tests/testthat/test-pprof-write.R | 2 -- tests/testthat/test-rprof-from-ds.R | 2 -- tests/testthat/test-rprof-read.R | 2 -- tests/testthat/test-rprof-write.R | 2 -- 13 files changed, 58 insertions(+), 41 deletions(-)
Title: Encuesta Nacional de Hogares (Peruvian Home National Survey)
Description: Descarga, lee y analiza bases de la Encuesta Nacional de Hogares (ENAHO) y otras encuestas del Instituto Nacional de Estadística e Informática (INEI) del Perú. (Downloads, reads, and combines data from the Peruvian Home National Survey and other surveys from the National Institute for Statistics (INEI).)
Author: Andres Christiansen [aut, cre]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between enaho versions 0.2.0 dated 2025-07-23 and 0.2.5 dated 2025-09-29
DESCRIPTION | 12 - MD5 | 56 ++++- NAMESPACE | 3 NEWS.md |only R/combinar.inei.R | 19 + R/descargar.inei.R | 2 R/internal.R |only R/leer.inei.R | 162 ++++++++++++++-- R/leer.inei.web.R | 4 R/media.inei.R |only R/proporcion.inei.R |only R/variablesxperiodo.R |only README.md | 261 ++------------------------- build |only inst/doc |only inst/extdata/UBIGEOS_2022_1891_distritos.csv |only inst/extdata/codigosencuesta.rds |binary inst/extdata/enaho_2024_Modulo37_t1 |only inst/extdata/modulosdata.rds |binary inst/extdata/tildes.csv |only man/combinar.inei.Rd | 4 man/descargar.inei.Rd | 2 man/leer.inei.Rd | 12 - man/leer.inei.web.Rd | 6 man/media.inei.Rd |only man/modulos.Rd | 2 man/proporcion.inei.Rd |only man/variablesxperiodo.Rd |only vignettes |only 29 files changed, 245 insertions(+), 300 deletions(-)