Title: Online Principal Component Analysis
Description: Online PCA for multivariate and functional data using perturbation methods, low-rank incremental methods, and stochastic optimization methods.
Author: David Degras [aut, cre], Herve Cardot [ctb]
Maintainer: David Degras <ddegrasv@gmail.com>
Diff between onlinePCA versions 1.3.1 dated 2016-09-21 and 1.3.2 dated 2023-11-14
onlinePCA-1.3.1/onlinePCA/R/onlinePCA-internal.R |only onlinePCA-1.3.2/onlinePCA/DESCRIPTION | 8 +- onlinePCA-1.3.2/onlinePCA/MD5 | 17 ++--- onlinePCA-1.3.2/onlinePCA/R/RcppExports.R | 10 +-- onlinePCA-1.3.2/onlinePCA/man/batchpca.Rd | 2 onlinePCA-1.3.2/onlinePCA/man/incRpca.Rd | 2 onlinePCA-1.3.2/onlinePCA/man/onlinePCA-package.Rd | 12 ---- onlinePCA-1.3.2/onlinePCA/man/perturbationRpca.Rd | 2 onlinePCA-1.3.2/onlinePCA/man/secularRpca.Rd | 2 onlinePCA-1.3.2/onlinePCA/src/RcppExports.cpp | 60 +++++++++++++-------- 10 files changed, 62 insertions(+), 53 deletions(-)
Title: Time Series Exploration, Modelling and Forecasting
Description: Includes: (i) tests and visualisations that can help the modeller explore time series components and perform decomposition; (ii) modelling shortcuts, such as functions to construct lagmatrices and seasonal dummy variables of various forms; (iii) an implementation of the Theta method; (iv) tools to facilitate the design of the forecasting process, such as ABC-XYZ analyses; and (v) "quality of life" functions, such as treating time series for trailing and leading values.
Author: Nikolaos Kourentzes [aut, cre],
Ivan Svetunkov [ctb],
Oliver Schaer [ctb]
Maintainer: Nikolaos Kourentzes <nikolaos@kourentzes.com>
Diff between tsutils versions 0.9.3 dated 2022-07-05 and 0.9.4 dated 2023-11-14
DESCRIPTION | 8 +- MD5 | 69 ++++++++++++------------- NEWS.md | 5 + R/abc.R | 8 +- R/abcxyz.R | 4 - R/coxstuart.R | 12 ++-- R/decomp.R | 16 ++--- R/getOptK.R | 12 ++-- R/lambdaseq.R | 8 +- R/mseastest.R | 12 ++-- R/nemenyi.R | 37 +++++++------ R/residout.R | 6 +- R/seasdummy.R | 4 - R/seasplot.R | 35 ++++++------ R/theta.R | 46 ++++++++-------- R/trendtest.R | 4 - R/tsutils-package.R | 51 +++++++++--------- R/xyz.R | 16 ++--- README.md | 3 - man/abc.Rd | 12 ++-- man/abcxyz.Rd | 4 - man/coxstuart.Rd | 12 ++-- man/decomp.Rd | 16 ++--- man/getOptK.Rd | 12 ++-- man/lambdaseq.Rd | 8 +- man/mseastest.Rd | 12 ++-- man/nemenyi.Rd | 37 +++++++------ man/residout.Rd | 6 +- man/seasdummy.Rd | 4 - man/seasplot.Rd | 26 ++++----- man/theta.Rd | 50 +++++++++--------- man/trendtest.Rd | 4 - man/tsutils-package.Rd |only man/tsutils.Rd | 133 ++++++++++++++++++++++++------------------------- man/wins.Rd | 6 +- man/xyz.Rd | 16 ++--- 36 files changed, 363 insertions(+), 351 deletions(-)
Title: Time Series Forecasting with Neural Networks
Description: Automatic time series modelling with neural networks.
Allows fully automatic, semi-manual or fully manual specification of networks. For details of the
specification methodology see: (i) Crone and Kourentzes (2010) <doi:10.1016/j.neucom.2010.01.017>;
and (ii) Kourentzes et al. (2014) <doi:10.1016/j.eswa.2013.12.011>.
Author: Nikolaos Kourentzes [aut, cre]
Maintainer: Nikolaos Kourentzes <nikolaos@kourentzes.com>
Diff between nnfor versions 0.9.8 dated 2022-07-09 and 0.9.9 dated 2023-11-14
DESCRIPTION | 8 +++---- MD5 | 42 ++++++++++++++++++++------------------ NEWS.md | 4 +++ R/elm.R | 52 ++++++++++++++++++++++++------------------------ R/elm.fast.R | 42 +++++++++++++++++++------------------- R/forecast.net.R | 2 - R/linscale.R | 4 +-- R/mlp.R | 38 +++++++++++++++++------------------ R/net.thief.R | 16 +++++++------- R/nnfor-package.R | 12 +++++++---- README.md | 2 + build |only man/elm.Rd | 50 +++++++++++++++++++++++----------------------- man/elm.fast.Rd | 32 ++++++++++++++--------------- man/elm.thief.Rd | 16 +++++++------- man/forecast.elm.Rd | 12 +++++------ man/forecast.mlp.Rd | 12 +++++------ man/linscale.Rd | 4 +-- man/mlp.Rd | 38 +++++++++++++++++------------------ man/mlp.thief.Rd | 16 +++++++------- man/nnfor-package.Rd |only man/nnfor.Rd | 8 ++----- man/predict.elm.fast.Rd | 4 +-- 23 files changed, 212 insertions(+), 202 deletions(-)
Title: Applying Landscape Genomic Methods on 'SNP' and 'Silicodart'
Data
Description: Provides landscape genomic functions to analyse 'SNP' (single nuclear
polymorphism) data, such as least cost path analysis and isolation by distance.
Therefore each sample needs to have coordinate data attached (lat/lon) to be
able to run most of the functions. 'dartR.spatial' is a package that belongs
to the 'dartRverse' suit of packages and depends on 'dartR.base' and 'dartR.data'.
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.spatial versions 0.76 dated 2023-08-17 and 0.78 dated 2023-11-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/gl.grm2.r | 1 + R/gl.spatial.autoCorr.r | 4 ++-- R/zzz.r | 4 ++-- man/gl.grm2.Rd | 1 + man/zzz.Rd | 4 ++-- 7 files changed, 18 insertions(+), 16 deletions(-)
Title: Simple, Consistent Wrappers for Common String Operations
Description: A consistent, simple and easy to use set of wrappers around
the fantastic 'stringi' package. All function and argument names (and
positions) are consistent, all functions deal with "NA"'s and zero
length vectors in the same way, and the output from one function is
easy to feed into the input of another.
Author: Hadley Wickham [aut, cre, cph],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between stringr versions 1.5.0 dated 2022-12-02 and 1.5.1 dated 2023-11-14
DESCRIPTION | 31 LICENSE | 2 MD5 | 62 - NEWS.md | 7 R/detect.R | 2 R/replace.R | 5 R/split.R | 23 R/subset.R | 2 R/trunc.R | 7 R/view.R | 6 README.md | 4 build/vignette.rds |binary inst/doc/from-base.R | 43 + inst/doc/from-base.Rmd | 85 +- inst/doc/from-base.html | 1375 ++++++++++++++++++++++++-------------- inst/doc/regular-expressions.R | 2 inst/doc/regular-expressions.html | 296 ++++---- inst/doc/stringr.R | 2 inst/doc/stringr.html | 396 +++++----- man/figures/logo.png |binary man/str_detect.Rd | 2 man/str_replace.Rd | 5 man/str_split.Rd | 24 man/str_starts.Rd | 2 man/str_subset.Rd | 2 man/str_view.Rd | 4 man/str_which.Rd | 4 man/stringr-package.Rd | 4 tests/testthat/_snaps/view.md | 66 + tests/testthat/test-trunc.R | 41 - tests/testthat/test-view.R | 44 - vignettes/from-base.Rmd | 85 +- 32 files changed, 1586 insertions(+), 1047 deletions(-)
Title: Threshold Indicator Taxa Analysis
Description: Uses indicator species scores across binary partitions of
a sample set to detect congruence in taxon-specific changes of abundance
and occurrence frequency along an environmental gradient as evidence of
an ecological community threshold. Relevant references include Baker and King
(2010) <doi:10.1111/j.2041-210X.2009.00007.x>, King and Baker (2010)
<doi:10.1899/09-144.1>, and Baker and King (2013) <doi:10.1899/12-142.1>.
Author: Matthew E. Baker [aut, cph] ,
Ryan S. King [aut, cph] ,
David Kahle [aut, cph, cre]
Maintainer: David Kahle <david@kahle.io>
Diff between TITAN2 versions 2.4.2 dated 2023-05-31 and 2.4.3 dated 2023-11-14
DESCRIPTION | 19 MD5 | 58 +- NAMESPACE | 16 NEWS.md | 49 + R/TITAN2.R | 19 R/boot.functions.R | 24 R/control.functions.R | 70 +- R/core.functions.R | 10 R/plot_cps.R | 12 R/plot_sumz_density.R | 2 R/plot_taxa.R | 263 +++------ R/plot_taxa_ridges.R | 221 ++++--- R/titan.R | 16 build/vignette.rds |binary inst/doc/titan2-intro.R | 107 ++- inst/doc/titan2-intro.Rmd | 591 +++++++++++--------- inst/doc/titan2-intro.pdf |binary man/TITAN2.Rd | 12 man/boot.titan.Rd | 2 man/env.part.Rd | 2 man/getivz.Rd | 2 man/obs.summ.Rd | 2 man/plot-taxa.Rd | 12 man/plot_taxa_ridges.Rd | 17 man/smallBigBoot.Rd | 2 man/sumz.tab.Rd | 2 man/tboot.Rd | 2 man/titan.Rd | 4 vignettes/titan2-intro.Rmd | 591 +++++++++++--------- vignettes/titan2-intro.html | 1240 +++++++++++++++++++++++--------------------- 30 files changed, 1797 insertions(+), 1570 deletions(-)
Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for descriptive statistics (e.g., frequency table, cross tabulation, multilevel descriptive statistics, multilevel R-squared measures, within-group and between-group correlation matrix, various effect size measures), data management (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and group scores, reading and writing SPSS and Excel files), missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), item analysis (e.g., coefficient alpha and omega, multilevel confirmatory factor analysis, between-group and longitudinal measurement equivalence evaluation, cross-level measurement equivalence evaluation, and multilevel composite reliability), and statistical analysis (e.g., confidence intervals, collinearity and residual diagnostics, dominance analysis, between- and within-subject analysis of variance, latent class anal [...truncated...]
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.5.3 dated 2023-09-17 and 0.5.4 dated 2023-11-14
DESCRIPTION | 8 +++--- MD5 | 58 +++++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS.md | 10 ++++++- R/center.R | 6 ++-- R/ci.mean.R | 2 - R/ci.mean.diff.R | 2 - R/ci.median.R | 2 - R/ci.prop.R | 2 - R/ci.prop.diff.R | 2 - R/ci.sd.R | 2 - R/ci.var.R | 2 - R/cohens.d.R | 2 - R/dominance.manual.R | 2 - R/item.omega.R | 4 --- R/libraries.R | 2 - R/multilevel.descript.R | 2 - R/multilevel.indirect.R | 4 +-- R/multilevel.invar.R | 46 ++++++++++++++++++++++++++++++----- R/run.mplus.R | 2 - R/shift.R |only R/test.welch.R | 2 - R/write.sav.R | 2 - man/center.Rd | 4 +-- man/ci.mean.diff.Rd | 2 - man/cohens.d.Rd | 2 - man/item.cfa.Rd | 34 ++++++++++++++++++++++++++ man/multilevel.indirect.Rd | 4 +-- man/shift.Rd |only man/test.welch.Rd | 2 - man/write.sav.Rd | 4 +-- 31 files changed, 146 insertions(+), 71 deletions(-)
Title: An Interface to IMF (International Monetary Fund) Data JSON API
Description: A straightforward interface for accessing the IMF
(International Monetary Fund) data JSON API,
available at <https://data.imf.org/>. This package offers direct access to
the primary API endpoints: Dataflow, DataStructure, and CompactData.
And, it provides an intuitive interface for exploring available
dimensions and attributes, as well as querying individual time-series datasets.
Additionally, the package implements a rate limit on API calls to reduce the
chances of exceeding service limits (limited to 10 calls every 5 seconds)
and encountering response errors.
Author: Pedro Baltazar [aut, cre]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between imf.data versions 0.1.0 dated 2023-11-07 and 0.1.1 dated 2023-11-14
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ NEWS.md | 6 +++++ R/database.R | 51 ++++++++++++++++++++++++++++++++---------------- R/methods.R | 19 ++++++++++++++++- R/request.R | 11 ++++++++-- man/imf.data-package.Rd | 2 - 7 files changed, 77 insertions(+), 30 deletions(-)
Title: Behavioral Economic Easy Discounting
Description: Facilitates some of the analyses performed in studies of
behavioral economic discounting. The package supports scoring of the 27-Item Monetary Choice
Questionnaire (see Kaplan et al., 2016; <doi:10.1007/s40614-016-0070-9>) and scoring of the
minute discounting task (see Koffarnus & Bickel, 2014; <doi:10.1037/a0035973>) using the
Qualtrics 5-trial discounting template (see the Qualtrics Minute Discounting User Guide;
<doi:10.13140/RG.2.2.26495.79527>), which is also available as a .qsf file in this package.
Author: Brent Kaplan [aut, cre, cph]
Maintainer: Brent Kaplan <bkaplan.ku@gmail.com>
Diff between beezdiscounting versions 0.2.0 dated 2023-11-02 and 0.3.0 dated 2023-11-14
beezdiscounting-0.2.0/beezdiscounting/R/five.fivetrial.R |only beezdiscounting-0.2.0/beezdiscounting/data/five.fivetrial.rda |only beezdiscounting-0.2.0/beezdiscounting/man/five.fivetrial.Rd |only beezdiscounting-0.3.0/beezdiscounting/DESCRIPTION | 8 beezdiscounting-0.3.0/beezdiscounting/MD5 | 33 +- beezdiscounting-0.3.0/beezdiscounting/NAMESPACE | 4 beezdiscounting-0.3.0/beezdiscounting/NEWS.md | 17 + beezdiscounting-0.3.0/beezdiscounting/R/beezdiscounting-package.R | 3 beezdiscounting-0.3.0/beezdiscounting/R/five.fivetrial_dd.R |only beezdiscounting-0.3.0/beezdiscounting/R/five.fivetrial_pd.R |only beezdiscounting-0.3.0/beezdiscounting/R/fivetrial.R | 137 +++++++++- beezdiscounting-0.3.0/beezdiscounting/README.md | 84 +++++- beezdiscounting-0.3.0/beezdiscounting/data/five.fivetrial_dd.rda |only beezdiscounting-0.3.0/beezdiscounting/data/five.fivetrial_pd.rda |only beezdiscounting-0.3.0/beezdiscounting/man/ans_dd.Rd | 2 beezdiscounting-0.3.0/beezdiscounting/man/ans_pd.Rd |only beezdiscounting-0.3.0/beezdiscounting/man/calc_dd.Rd | 2 beezdiscounting-0.3.0/beezdiscounting/man/calc_pd.Rd |only beezdiscounting-0.3.0/beezdiscounting/man/five.fivetrial_dd.Rd |only beezdiscounting-0.3.0/beezdiscounting/man/five.fivetrial_pd.Rd |only beezdiscounting-0.3.0/beezdiscounting/man/score_dd.Rd | 2 beezdiscounting-0.3.0/beezdiscounting/man/score_pd.Rd |only beezdiscounting-0.3.0/beezdiscounting/man/timing_dd.Rd | 2 beezdiscounting-0.3.0/beezdiscounting/man/timing_pd.Rd |only 24 files changed, 264 insertions(+), 30 deletions(-)
More information about beezdiscounting at CRAN
Permanent link
Title: Robust Linear Mixed Effects Models
Description: Implements the Robust Scoring Equations estimator to fit linear
mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <kollerma@proton.me>
Diff between robustlmm versions 3.2-3 dated 2023-10-05 and 3.2-5 dated 2023-11-14
DESCRIPTION | 10 ++++----- MD5 | 32 +++++++++++++++--------------- NAMESPACE | 1 R/emmeans.R | 7 ++++++ R/generateAnovaDatasets.R | 2 - R/generateMixedEffectDatasets.R | 4 +-- R/manageDatasets.R | 6 ++--- R/processFit.R | 30 +++++++++++++--------------- inst/doc/ggplot.theme.R | 2 - inst/doc/rlmer.pdf |binary inst/doc/simulationStudies.pdf |binary inst/simulationStudy/robustnessDiagonal.R | 2 - man/generateAnovaDatasets.Rd | 2 - man/prepareMixedEffectDataset.Rd | 4 +-- man/processFit.Rd | 30 +++++++++++++--------------- man/splitDatasets.Rd | 6 ++--- src/rlmerMatrixUtils.cpp | 4 +-- 17 files changed, 71 insertions(+), 71 deletions(-)
Title: INsulin Secretion ANalysEr
Description: A user-friendly interface, using Shiny, to analyse glucose-stimulated insulin secretion (GSIS)
assays in pancreatic beta cells or islets.
The package allows the user to import several sets of experiments from different spreadsheets
and to perform subsequent steps: summarise in a tidy format, visualise data quality
and compare experimental conditions without omitting to account for technical confounders
such as the date of the experiment or the technician.
Together, insane is a comprehensive method that optimises pre-processing and analyses of
GSIS experiments in a friendly-user interface.
The Shiny App was initially designed for EndoC-betaH1 cell line following method described
in Ndiaye et al., 2017 (<doi:10.1016/j.molmet.2017.03.011>).
Author: Mickael Canouil [aut, cre]
Maintainer: Mickael Canouil <pro@mickael.canouil.dev>
Diff between insane versions 1.0.2 dated 2023-04-01 and 1.0.3 dated 2023-11-14
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NAMESPACE | 1 - NEWS.md | 17 ++++++++++++----- R/go_insane.R | 1 - build/partial.rdb |binary build/vignette.rds |binary inst/app/app.R | 4 +--- inst/doc/insane.R | 20 ++++++++++---------- inst/doc/insane.html | 6 +++--- inst/doc/protocol.html | 3 ++- 11 files changed, 44 insertions(+), 40 deletions(-)
Title: Retrieve Global River Gauge Data
Description: Provides access to global river gauge data from a variety of national-level river agencies. The package interfaces with the national-level agency websites to provide access to river gauge locations, river discharge, and river stage. Currently, the package is available for the following countries: Australia, Brazil, Canada, Chile, France, Japan, South Africa, the United Kingdom, and the United States.
Author: Ryan Riggs [aut, cre] ,
Simon Moulds [aut] ,
Michel Wortmann [aut] ,
Louise Slater [aut] ,
George Allen [aut]
Maintainer: Ryan Riggs <rriggs@tamu.edu>
Diff between RivRetrieve versions 0.1.2 dated 2023-11-03 and 0.1.3 dated 2023-11-14
DESCRIPTION | 12 ++++++------ MD5 | 28 ++++++++++++++-------------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/RivRetrieve-package.R | 1 + R/australia.R | 5 +++-- R/brazil.R | 3 ++- R/chile.R | 3 ++- R/france.R | 1 + R/japan.R | 3 ++- R/southAfrica.R | 5 +++-- R/uk.R | 5 +++-- R/usa.R | 5 +++-- README.md | 2 ++ inst/doc/my-vignette.html | 4 ++-- 15 files changed, 49 insertions(+), 33 deletions(-)
Title: CAnopy IMage ANalysis
Description: Classify hemispherical
photographs of the plant canopy with algorithms specially developed for
such a task and well documented in
Díaz and Lencinas (2015) <doi:10.1109/lgrs.2015.2425931> and
Díaz and Lencinas (2018) <doi:10.1139/cjfr-2018-0006>. It supports
non-circular hemispherical photography, such as those acquired with
15mm lenses or with auxiliary fish-eye lenses attached to mobile devices.
For smartphone-based hemispherical photography see
Díaz (2023) <doi:10.1111/2041-210x.14059>. Most of the functions also
support restricted view photography.
Author: Gaston Mauro Diaz [aut, cre]
Maintainer: Gaston Mauro Diaz <gastonmaurodiaz@gmail.com>
Diff between rcaiman versions 1.1.2 dated 2023-05-19 and 1.2.2 dated 2023-11-14
rcaiman-1.1.2/rcaiman/R/calc_zenith_raster_coord.R |only rcaiman-1.1.2/rcaiman/R/rcaiman.R |only rcaiman-1.1.2/rcaiman/R/thr_image.R |only rcaiman-1.1.2/rcaiman/inst/external/DSCN6342.pgm |only rcaiman-1.1.2/rcaiman/inst/external/b4_2_5724.jpg |only rcaiman-1.1.2/rcaiman/man/calc_zenith_raster_coord.Rd |only rcaiman-1.1.2/rcaiman/man/rcaiman.Rd |only rcaiman-1.1.2/rcaiman/man/thr_image.Rd |only rcaiman-1.2.2/rcaiman/DESCRIPTION | 13 rcaiman-1.2.2/rcaiman/MD5 | 283 ++-- rcaiman-1.2.2/rcaiman/NAMESPACE | 17 rcaiman-1.2.2/rcaiman/NEWS.md | 80 + rcaiman-1.2.2/rcaiman/R/apply_thr.R | 23 rcaiman-1.2.2/rcaiman/R/azimuth_image.R | 36 rcaiman-1.2.2/rcaiman/R/calc_co.R | 68 + rcaiman-1.2.2/rcaiman/R/calc_diameter.R | 61 - rcaiman-1.2.2/rcaiman/R/calc_relative_radius.R |only rcaiman-1.2.2/rcaiman/R/calc_zenith_colrow.R |only rcaiman-1.2.2/rcaiman/R/calibrate_lens.R | 248 ++-- rcaiman-1.2.2/rcaiman/R/chessboard.R | 12 rcaiman-1.2.2/rcaiman/R/cie_sky_model_raster.R | 14 rcaiman-1.2.2/rcaiman/R/colorfulness.R | 60 - rcaiman-1.2.2/rcaiman/R/correct_vignetting.R |only rcaiman-1.2.2/rcaiman/R/crop_caim.R |only rcaiman-1.2.2/rcaiman/R/crosscalibrate_lens.R | 76 - rcaiman-1.2.2/rcaiman/R/defuzzify.R | 26 rcaiman-1.2.2/rcaiman/R/enhance_caim.R | 183 +-- rcaiman-1.2.2/rcaiman/R/expand_noncircular.R | 42 rcaiman-1.2.2/rcaiman/R/extract_dn.R | 60 - rcaiman-1.2.2/rcaiman/R/extract_feature.R | 38 rcaiman-1.2.2/rcaiman/R/extract_radiometry.R |only rcaiman-1.2.2/rcaiman/R/extract_rl.R | 78 - rcaiman-1.2.2/rcaiman/R/extract_sky_points.R | 74 - rcaiman-1.2.2/rcaiman/R/extract_sky_points_simple.R |only rcaiman-1.2.2/rcaiman/R/extract_sun_coord.R | 37 rcaiman-1.2.2/rcaiman/R/find_sky_pixels.R | 33 rcaiman-1.2.2/rcaiman/R/find_sky_pixels_nonnull.R | 90 - rcaiman-1.2.2/rcaiman/R/fisheye_to_equidistant.R | 133 +- rcaiman-1.2.2/rcaiman/R/fisheye_to_pano.R | 4 rcaiman-1.2.2/rcaiman/R/fit_cie_sky_model.R | 266 ++-- rcaiman-1.2.2/rcaiman/R/fit_coneshaped_model.R | 57 rcaiman-1.2.2/rcaiman/R/fit_trend_surface.R | 71 - rcaiman-1.2.2/rcaiman/R/fix_reconstructed_sky.R | 58 - rcaiman-1.2.2/rcaiman/R/gbc.R | 23 rcaiman-1.2.2/rcaiman/R/interpolate_sky_points.R | 120 -- rcaiman-1.2.2/rcaiman/R/label_cfa.R |only rcaiman-1.2.2/rcaiman/R/lens.R | 67 - rcaiman-1.2.2/rcaiman/R/local_fuzzy_thresholding.R | 71 - rcaiman-1.2.2/rcaiman/R/mask_hs.R | 12 rcaiman-1.2.2/rcaiman/R/mask_sunlit_canopy.R | 20 rcaiman-1.2.2/rcaiman/R/masking.R | 19 rcaiman-1.2.2/rcaiman/R/membership_to_color.R | 47 rcaiman-1.2.2/rcaiman/R/normalize.R | 30 rcaiman-1.2.2/rcaiman/R/obia.R | 56 rcaiman-1.2.2/rcaiman/R/ootb_mblt.R | 162 +- rcaiman-1.2.2/rcaiman/R/ootb_obia.R | 136 +- rcaiman-1.2.2/rcaiman/R/ootb_sky_reconstruction.R | 579 ++++++++-- rcaiman-1.2.2/rcaiman/R/optim_normalize.R |only rcaiman-1.2.2/rcaiman/R/percentage_of_clipped_highlights.R |only rcaiman-1.2.2/rcaiman/R/polar_qtree.R | 22 rcaiman-1.2.2/rcaiman/R/qtree.R | 30 rcaiman-1.2.2/rcaiman/R/rcaiman-package.R |only rcaiman-1.2.2/rcaiman/R/read_bin.R | 4 rcaiman-1.2.2/rcaiman/R/read_caim.R | 102 - rcaiman-1.2.2/rcaiman/R/read_caim_raw.R |only rcaiman-1.2.2/rcaiman/R/read_manual_input.R | 8 rcaiman-1.2.2/rcaiman/R/read_opt_sky_coef.R | 4 rcaiman-1.2.2/rcaiman/R/regional_thresholding.R | 59 - rcaiman-1.2.2/rcaiman/R/rings_segmentation.R | 10 rcaiman-1.2.2/rcaiman/R/row_col_from_zenith_azimuth.R | 49 rcaiman-1.2.2/rcaiman/R/sectors_segmentation.R | 8 rcaiman-1.2.2/rcaiman/R/sky_grid_segmentation.R | 20 rcaiman-1.2.2/rcaiman/R/test_lens_coef.R | 18 rcaiman-1.2.2/rcaiman/R/thr_isodata.R | 10 rcaiman-1.2.2/rcaiman/R/thr_mblt.R |only rcaiman-1.2.2/rcaiman/R/utils.R | 24 rcaiman-1.2.2/rcaiman/R/utils_for_ckecking.R | 9 rcaiman-1.2.2/rcaiman/R/write_bin.R | 4 rcaiman-1.2.2/rcaiman/R/write_caim.R | 11 rcaiman-1.2.2/rcaiman/R/write_sky_points.R | 19 rcaiman-1.2.2/rcaiman/R/write_sun_coord.R | 12 rcaiman-1.2.2/rcaiman/R/zenith_azimuth_from_row_col.R | 65 - rcaiman-1.2.2/rcaiman/R/zenith_image.R | 57 rcaiman-1.2.2/rcaiman/build/partial.rdb |binary rcaiman-1.2.2/rcaiman/inst/REFERENCES.bib | 74 + rcaiman-1.2.2/rcaiman/inst/REFERENCES.bib.sav | 86 + rcaiman-1.2.2/rcaiman/inst/external/example.tif |only rcaiman-1.2.2/rcaiman/inst/external/points_over_perimeter.csv | 38 rcaiman-1.2.2/rcaiman/inst/external/sky_points.csv |only rcaiman-1.2.2/rcaiman/man/apply_thr.Rd | 101 - rcaiman-1.2.2/rcaiman/man/azimuth_image.Rd | 43 rcaiman-1.2.2/rcaiman/man/calc_co.Rd |only rcaiman-1.2.2/rcaiman/man/calc_diameter.Rd | 167 +- rcaiman-1.2.2/rcaiman/man/calc_relative_radius.Rd |only rcaiman-1.2.2/rcaiman/man/calc_zenith_colrow.Rd |only rcaiman-1.2.2/rcaiman/man/calibrate_lens.Rd | 273 ++-- rcaiman-1.2.2/rcaiman/man/chessboard.Rd | 14 rcaiman-1.2.2/rcaiman/man/cie_sky_model_raster.Rd | 84 - rcaiman-1.2.2/rcaiman/man/colorfulness.Rd | 141 +- rcaiman-1.2.2/rcaiman/man/correct_vignetting.Rd |only rcaiman-1.2.2/rcaiman/man/crop_caim.Rd |only rcaiman-1.2.2/rcaiman/man/crosscalibrate_lens.Rd |only rcaiman-1.2.2/rcaiman/man/defuzzify.Rd | 142 +- rcaiman-1.2.2/rcaiman/man/enhance_caim.Rd | 327 ++--- rcaiman-1.2.2/rcaiman/man/expand_noncircular.Rd | 48 rcaiman-1.2.2/rcaiman/man/extract_dn.Rd | 71 - rcaiman-1.2.2/rcaiman/man/extract_feature.Rd | 36 rcaiman-1.2.2/rcaiman/man/extract_radiometry.Rd |only rcaiman-1.2.2/rcaiman/man/extract_rl.Rd | 87 - rcaiman-1.2.2/rcaiman/man/extract_sky_points.Rd | 85 - rcaiman-1.2.2/rcaiman/man/extract_sky_points_simple.Rd |only rcaiman-1.2.2/rcaiman/man/extract_sun_coord.Rd | 69 - rcaiman-1.2.2/rcaiman/man/figures |only rcaiman-1.2.2/rcaiman/man/find_sky_pixels.Rd | 57 rcaiman-1.2.2/rcaiman/man/find_sky_pixels_nonnull.Rd | 108 + rcaiman-1.2.2/rcaiman/man/fisheye_to_equidistant.Rd | 71 - rcaiman-1.2.2/rcaiman/man/fisheye_to_pano.Rd | 18 rcaiman-1.2.2/rcaiman/man/fit_cie_sky_model.Rd | 208 +-- rcaiman-1.2.2/rcaiman/man/fit_coneshaped_model.Rd | 53 rcaiman-1.2.2/rcaiman/man/fit_trend_surface.Rd | 84 - rcaiman-1.2.2/rcaiman/man/fix_reconstructed_sky.Rd | 45 rcaiman-1.2.2/rcaiman/man/gbc.Rd | 23 rcaiman-1.2.2/rcaiman/man/interpolate_sky_points.Rd | 86 - rcaiman-1.2.2/rcaiman/man/lens.Rd | 63 - rcaiman-1.2.2/rcaiman/man/local_fuzzy_thresholding.Rd | 65 - rcaiman-1.2.2/rcaiman/man/mask_hs.Rd | 10 rcaiman-1.2.2/rcaiman/man/mask_sunlit_canopy.Rd | 32 rcaiman-1.2.2/rcaiman/man/masking.Rd | 23 rcaiman-1.2.2/rcaiman/man/membership_to_color.Rd | 37 rcaiman-1.2.2/rcaiman/man/normalize.Rd | 12 rcaiman-1.2.2/rcaiman/man/obia.Rd | 68 - rcaiman-1.2.2/rcaiman/man/ootb_mblt.Rd | 119 +- rcaiman-1.2.2/rcaiman/man/ootb_obia.Rd | 149 +- rcaiman-1.2.2/rcaiman/man/ootb_sky_reconstruction.Rd | 217 ++- rcaiman-1.2.2/rcaiman/man/optim_normalize.Rd |only rcaiman-1.2.2/rcaiman/man/percentage_of_clipped_highlights.Rd |only rcaiman-1.2.2/rcaiman/man/polar_qtree.Rd | 14 rcaiman-1.2.2/rcaiman/man/qtree.Rd | 26 rcaiman-1.2.2/rcaiman/man/rcaiman-package.Rd |only rcaiman-1.2.2/rcaiman/man/read_bin.Rd | 10 rcaiman-1.2.2/rcaiman/man/read_caim.Rd | 93 - rcaiman-1.2.2/rcaiman/man/read_caim_raw.Rd |only rcaiman-1.2.2/rcaiman/man/read_manual_input.Rd | 6 rcaiman-1.2.2/rcaiman/man/read_opt_sky_coef.Rd | 4 rcaiman-1.2.2/rcaiman/man/regional_thresholding.Rd | 64 - rcaiman-1.2.2/rcaiman/man/rings_segmentation.Rd | 10 rcaiman-1.2.2/rcaiman/man/row_col_from_zenith_azimuth.Rd | 18 rcaiman-1.2.2/rcaiman/man/sectors_segmentation.Rd | 10 rcaiman-1.2.2/rcaiman/man/sky_grid_segmentation.Rd | 19 rcaiman-1.2.2/rcaiman/man/test_lens_coef.Rd | 21 rcaiman-1.2.2/rcaiman/man/thr_isodata.Rd | 11 rcaiman-1.2.2/rcaiman/man/thr_mblt.Rd |only rcaiman-1.2.2/rcaiman/man/write_bin.Rd | 10 rcaiman-1.2.2/rcaiman/man/write_caim.Rd | 17 rcaiman-1.2.2/rcaiman/man/write_sky_points.Rd | 11 rcaiman-1.2.2/rcaiman/man/write_sun_coord.Rd | 8 rcaiman-1.2.2/rcaiman/man/zenith_azimuth_from_row_col.Rd | 24 rcaiman-1.2.2/rcaiman/man/zenith_image.Rd | 27 rcaiman-1.2.2/rcaiman/tests/testthat/test-normalize.R | 5 159 files changed, 4507 insertions(+), 3463 deletions(-)
Title: Evapotranspiration Based on FAO Penman-Monteith Equation
Description: Calculation of Evapotranspiration by FAO Penman-Monteith equation based on Allen, R. G., Pereira, L. S., Raes, D., Smith, M. (1998, ISBN:92-5-104219-5) "Crop evapotranspiration - Guidelines for computing crop water requirements - FAO Irrigation and drainage paper 56".
Author: Ali Ahani [aut, cre] <a_ahani@sbu.ac.ir> ,
S. Saeid Mousavi Nadoushani [aut] <sa_mousavi@sbu.ac.ir>
Maintainer: Ali Ahani <ali.ahani66@gmail.com>
Diff between FAO56 versions 0.1.0 dated 2021-11-17 and 1.0 dated 2023-11-14
DESCRIPTION | 14 +++++++------- MD5 | 19 +++++++++++-------- NEWS.md |only R/Acknowledgement.R |only R/FAO56.R | 2 +- R/FAOPMETo.R | 8 ++++---- R/Radiation.R | 10 +++------- README.md |only man/ETo_FPM.Rd | 8 ++++---- man/FAO56-package.Rd | 2 +- tests/testthat/test-ETo_FPM.R | 2 +- tests/testthat/test-Rad.R | 6 +++--- 12 files changed, 35 insertions(+), 36 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Description: Creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Provides diverse quality criteria. Provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <ulrike.groemping@bht-berlin.de>
Diff between DoE.base versions 1.2-3 dated 2023-10-17 and 1.2-4 dated 2023-11-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/halfnormal.R | 3 +-- build/partial.rdb |binary inst/NEWS | 4 ++++ 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Power Analyses for SEM
Description: Provides a-priori, post-hoc, and compromise power-analyses
for structural equation models (SEM).
Author: Morten Moshagen [aut, cre] ,
Martina Bader [aut]
Maintainer: Morten Moshagen <morten.moshagen@uni-ulm.de>
Diff between semPower versions 2.0.1 dated 2023-05-16 and 2.1.0 dated 2023-11-14
DESCRIPTION | 6 MD5 | 49 ++++--- NEWS | 6 R/aPriori.R | 13 +- R/compromise.R | 3 R/convenienceFunctions.R | 111 ++++++++++++----- R/effectSizes.R | 88 +++++++++++-- R/onAttach.R | 4 R/postHoc.R | 13 +- R/semPower-package.R | 2 R/simulate.R | 2 R/validator.R | 61 ++++++++- R/zUnitTests.R | 146 ++++++++++++++++++++++- README.md | 26 ++-- man/getCFI.Sigma.Rd | 4 man/getCFI.Sigma.mgroups.Rd | 11 + man/getDiscrepancyFunctionFromFittingFunction.Rd |only man/getF.Rd | 5 man/getF.Sigma.Rd | 12 + man/getFittingFunctionFromEstimator.Rd |only man/getWLSv.Rd |only man/powerPrepare.Rd | 3 man/semPower.aPriori.Rd | 3 man/semPower.compromise.Rd | 3 man/semPower.postHoc.Rd | 3 man/semPower.powerLav.Rd | 3 man/validateInput.Rd | 3 27 files changed, 468 insertions(+), 112 deletions(-)
Title: A Toolkit for Sports Injury Data Analysis
Description: Sports Injury Data analysis aims to identify and describe the
magnitude of the injury problem, and to gain more insights (e.g. determine
potential risk factors) by statistical modelling approaches. The 'injurytools'
package provides standardized routines and utilities that simplify such
analyses. It offers functions for data preparation, informative visualizations
and descriptive and model-based analyses.
Author: Lore Zumeta Olaskoaga [aut, cre]
,
Dae-Jin Lee [ctb]
Maintainer: Lore Zumeta Olaskoaga <lzumeta@bcamath.org>
Diff between injurytools versions 1.0.2 dated 2023-09-27 and 1.0.3 dated 2023-11-14
DESCRIPTION | 10 +- MD5 | 64 +++++++++---------- NEWS.md | 6 + R/data.R | 2 R/gg_injprev_polar.R | 2 R/gg_injriskmatrix.R | 30 ++++++-- README.md | 26 +++---- build/vignette.rds |binary inst/doc/estimate-epi-measures.R | 8 +- inst/doc/estimate-epi-measures.Rmd | 18 ++--- inst/doc/estimate-epi-measures.html | 36 +++++----- inst/doc/model-injury-data-i.R | 27 +++----- inst/doc/model-injury-data-i.Rmd | 31 +++------ inst/doc/model-injury-data-i.html | 45 ++++++------- inst/doc/model-injury-data-ii.R | 16 ++-- inst/doc/model-injury-data-ii.Rmd | 28 ++++---- inst/doc/model-injury-data-ii.html | 114 +++++++++++++++++----------------- inst/doc/prepare-injury-data.Rmd | 12 +-- inst/doc/prepare-injury-data.html | 24 +++---- inst/doc/visualize-injury-data.R | 44 ++++++++++--- inst/doc/visualize-injury-data.Rmd | 46 ++++++++++--- inst/doc/visualize-injury-data.html | 69 ++++++++++++-------- man/gg_injprev_polar.Rd | 2 man/gg_injriskmatrix.Rd | 18 ++++- man/injd.Rd | 2 man/injurytools.Rd | 4 - tests/testthat/_snaps/prepare_data.md | 3 tests/testthat/test-prepare_data.R | 4 - vignettes/estimate-epi-measures.Rmd | 18 ++--- vignettes/model-injury-data-i.Rmd | 31 +++------ vignettes/model-injury-data-ii.Rmd | 28 ++++---- vignettes/prepare-injury-data.Rmd | 12 +-- vignettes/visualize-injury-data.Rmd | 46 ++++++++++--- 33 files changed, 474 insertions(+), 352 deletions(-)
Title: Estimate Gaussian and Student's t Mixture Vector Autoregressive
Models
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t
mixture vector autoregressive models, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2022) <arXiv:2007.04713>,
Savi Virolainen (2022) <arXiv:2109.13648>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 2.0.10 dated 2023-08-19 and 2.1.0 dated 2023-11-14
DESCRIPTION | 6 MD5 | 225 ++++++----- NAMESPACE | 4 NEWS.md | 20 + R/GIRFandGFEVD.R | 121 ++++-- R/GSMVARconstruction.R | 135 ++++--- R/MAINest.R | 236 +++++++++--- R/WaldAndLR.R | 14 R/argumentChecks.R | 76 +++- R/data.R | 31 + R/diagnosticPlot.R | 21 - R/generateParams.R | 61 +-- R/geneticAlgorithm.R | 82 +++- R/linearIRF.R |only R/loglikelihood.R | 186 +++++++-- R/matcal.R | 66 +++ R/morePlots.R | 18 R/numericalDifferentiation.R | 10 R/parameterReforms.R | 137 +++++-- R/pickParams.R | 6 R/plotMethods.R | 107 +++++ R/predictMethod.R | 20 - R/printMethods.R | 73 +++ R/quantileResidualTests.R | 13 R/quantileResiduals.R | 13 R/simulate.R | 93 +++- R/standardErrors.R | 52 ++ R/uncondMoments.R | 27 - data/usamon.rda |only inst/doc/gmvarkit-vignette.Rnw | 77 +++- inst/doc/gmvarkit-vignette.pdf |binary man/GAfit.Rd | 32 + man/GFEVD.Rd | 42 +- man/GIRF.Rd | 33 + man/GMVAR.Rd | 39 +- man/GSMVAR.Rd | 44 +- man/Pearson_residuals.Rd |only man/change_parametrization.Rd | 44 +- man/change_regime.Rd | 41 +- man/check_constraints.Rd | 19 - man/check_pMd.Rd | 5 man/check_parameters.Rd | 44 +- man/cond_moment_plot.Rd | 5 man/cond_moments.Rd | 44 +- man/create_J_matrix.Rd |only man/estimate_sgsmvar.Rd | 2 man/fitGMVAR.Rd | 23 + man/fitGSMVAR.Rd | 42 ++ man/form_boldA.Rd | 5 man/gdpdef.Rd | 6 man/get_Sigmas.Rd | 5 man/get_alpha_mt.Rd | 5 man/get_regime_autocovs_int.Rd | 44 +- man/get_regime_means_int.Rd | 44 +- man/get_symmetric_sqrt.Rd |only man/get_test_Omega.Rd | 44 +- man/get_unconstrained_structural_pars.Rd | 9 man/get_varying_h.Rd | 30 + man/gmvar_to_sgmvar.Rd | 3 man/gsmvar_to_sgsmvar.Rd | 6 man/in_paramspace.Rd | 44 +- man/in_paramspace_int.Rd | 30 + man/is_stationary.Rd | 24 - man/iterate_more.Rd | 2 man/linear_IRF.Rd |only man/loglikelihood.Rd | 44 +- man/loglikelihood_int.Rd | 44 +- man/mat_power.Rd |only man/n_params.Rd | 19 - man/pick_Am.Rd | 39 +- man/pick_Ami.Rd | 39 +- man/pick_Omegas.Rd | 24 - man/pick_W.Rd | 24 - man/pick_allA.Rd | 24 - man/pick_all_phi0_A.Rd | 24 - man/pick_alphas.Rd | 15 man/pick_df.Rd | 15 man/pick_lambdas.Rd | 24 - man/pick_phi0.Rd | 24 - man/pick_regime.Rd | 45 +- man/quantile_residuals_int.Rd | 44 +- man/random_covmat.Rd | 19 - man/random_df.Rd | 13 man/random_ind.Rd | 19 - man/random_ind2.Rd | 19 - man/redecompose_Omegas.Rd | 5 man/reform_constrained_pars.Rd | 44 +- man/reform_structural_pars.Rd | 39 +- man/simulate.gsmvar.Rd | 18 man/simulateGMVAR.Rd | 18 man/smart_covmat.Rd | 19 - man/smart_df.Rd | 13 man/smart_ind.Rd | 29 + man/sort_W_and_lambdas.Rd | 15 man/sort_and_standardize_alphas.Rd | 21 - man/sort_components.Rd | 24 - man/standard_errors.Rd | 44 +- man/stmvarpars_to_gstmvar.Rd | 54 ++ man/unWvec.Rd | 9 man/uncond_moments_int.Rd | 44 +- man/usamon.Rd |only man/usamone.Rd | 2 man/warn_df.Rd | 30 + tests/testthat/test_GIRFandGFEVD.R | 112 ++++- tests/testthat/test_S3methods.R | 76 ++-- tests/testthat/test_argumentChecks.R | 269 +++++++++++++- tests/testthat/test_gsmvarConstruction.R | 92 ++++ tests/testthat/test_linearIRF.R |only tests/testthat/test_loglikelihood.R | 470 ++++++++++++++++++------- tests/testthat/test_matcal.R | 113 ++++++ tests/testthat/test_parameterReforms.R | 526 ++++++++++++++++++++++++---- tests/testthat/test_pickParams.R | 44 ++ tests/testthat/test_quantileResidualTests.R | 51 +- tests/testthat/test_quantileResiduals.R | 32 + tests/testthat/test_simulate.R | 16 tests/testthat/test_uncondMoments.R | 67 +++ vignettes/gmvarkit-vignette.Rnw | 77 +++- vignettes/refs.bib | 13 118 files changed, 4260 insertions(+), 1334 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-15 0.1.0
Title: R Bindings for the 'prql-compiler' Rust Library
Description: Provides a function to convert 'PRQL' strings to 'SQL' strings.
Combined with other R functions that take 'SQL' as an argument,
'PRQL' can be used on R.
Author: Tatsuya Shima [aut, cre],
Authors of the dependency Rust crates [aut]
Maintainer: Tatsuya Shima <ts1s1andn@gmail.com>
Diff between prqlr versions 0.5.4 dated 2023-10-07 and 0.6.0 dated 2023-11-14
DESCRIPTION | 13 ++--- LICENSE.note | 40 +++++++-------- MD5 | 33 ++++++------ NEWS.md | 6 ++ README.md | 13 +---- cleanup.win |only configure | 25 ++++++++- configure.win | 64 ------------------------- inst/AUTHORS | 4 - inst/doc/knitr.html | 20 +++---- inst/doc/prqlr.html | 4 - src/rust/Cargo.lock | 87 +++++++++++++++++----------------- src/rust/Cargo.toml | 4 - src/rust/vendor.tar.xz |binary tests/testthat/_snaps/compile.md | 35 ++++++++++++- tests/testthat/_snaps/knitr-engine.md | 4 - tests/testthat/test-compile.R | 3 - tools/lib-sums.tsv | 10 +-- 18 files changed, 179 insertions(+), 186 deletions(-)
Title: Draw Ordered Oxford Grids and Chord Diagrams
Description: Use standard genomics file format (BED) and a table of orthologs to
illustrate synteny conservation at the genome-wide scale.
Significantly conserved linkage groups are identified as described in Simakov et al. (2020) <doi:10.1038/s41559-020-1156-z>
and displayed on an Oxford Grid (Edwards (1991) <doi:10.1111/j.1469-1809.1991.tb00394.x>) or a chord diagram as in Simakov et al. (2022) <doi:10.1126/sciadv.abi5884>.
The package provides a function that uses a network-based greedy algorithm to find communities (Clauset et al. (2004) <doi:10.1103/PhysRevE.70.066111>)
and so automatically order the chromosomes on the plot to improve interpretability.
Author: Sami El Hilali [aut, cre] ,
Richard Copley [aut]
Maintainer: Sami El Hilali <elhilali.sami@gmail.com>
Diff between macrosyntR versions 0.2.19 dated 2023-03-29 and 0.3.3 dated 2023-11-14
macrosyntR-0.2.19/macrosyntR/inst/extdata/Bflo.protein_products.bed |only macrosyntR-0.2.19/macrosyntR/inst/extdata/Pech.protein_products.bed |only macrosyntR-0.3.3/macrosyntR/DESCRIPTION | 16 macrosyntR-0.3.3/macrosyntR/MD5 | 61 macrosyntR-0.3.3/macrosyntR/NAMESPACE | 9 macrosyntR-0.3.3/macrosyntR/NEWS.md | 29 macrosyntR-0.3.3/macrosyntR/R/compute_linkage_groups.R |only macrosyntR-0.3.3/macrosyntR/R/compute_macrosynteny.R | 7 macrosyntR-0.3.3/macrosyntR/R/get_ideograms_coordinates.R |only macrosyntR-0.3.3/macrosyntR/R/get_syntenic_genes.R | 8 macrosyntR-0.3.3/macrosyntR/R/load_orthologs.R | 137 macrosyntR-0.3.3/macrosyntR/R/plot_chord_diagram.R |only macrosyntR-0.3.3/macrosyntR/R/plot_macrosynteny.R | 4 macrosyntR-0.3.3/macrosyntR/R/plot_oxford_grid.R | 11 macrosyntR-0.3.3/macrosyntR/R/reorder_macrosynteny.R | 11 macrosyntR-0.3.3/macrosyntR/R/reorder_multiple_macrosyntenies.R |only macrosyntR-0.3.3/macrosyntR/R/reverse_species_order.R | 9 macrosyntR-0.3.3/macrosyntR/R/subset_linkage_orthologs.R |only macrosyntR-0.3.3/macrosyntR/README.md | 71 macrosyntR-0.3.3/macrosyntR/inst/doc/macrosyntR.R | 50 macrosyntR-0.3.3/macrosyntR/inst/doc/macrosyntR.Rmd | 169 macrosyntR-0.3.3/macrosyntR/inst/doc/macrosyntR.html | 494 macrosyntR-0.3.3/macrosyntR/inst/extdata/Bflo.bed |only macrosyntR-0.3.3/macrosyntR/inst/extdata/Bflo_vs_Pech.tab | 5988 +++++----- macrosyntR-0.3.3/macrosyntR/inst/extdata/Bflo_vs_Pyes.tab |only macrosyntR-0.3.3/macrosyntR/inst/extdata/Pech.bed |only macrosyntR-0.3.3/macrosyntR/inst/extdata/Pyes.bed |only macrosyntR-0.3.3/macrosyntR/inst/extdata/Single_copy_orthologs.tsv |only macrosyntR-0.3.3/macrosyntR/inst/extdata/my_orthologs.tab | 5706 +++++---- macrosyntR-0.3.3/macrosyntR/inst/img/Chord_diagram_3species.png |only macrosyntR-0.3.3/macrosyntR/man/compute_linkage_groups.Rd |only macrosyntR-0.3.3/macrosyntR/man/get_syntenic_genes.Rd | 8 macrosyntR-0.3.3/macrosyntR/man/load_orthologs.Rd | 38 macrosyntR-0.3.3/macrosyntR/man/plot_chord_diagram.Rd |only macrosyntR-0.3.3/macrosyntR/man/plot_macrosynteny.Rd | 4 macrosyntR-0.3.3/macrosyntR/man/plot_oxford_grid.Rd | 8 macrosyntR-0.3.3/macrosyntR/man/reorder_multiple_macrosyntenies.Rd |only macrosyntR-0.3.3/macrosyntR/man/reverse_species_order.Rd | 9 macrosyntR-0.3.3/macrosyntR/man/subset_linkage_orthologs.Rd |only macrosyntR-0.3.3/macrosyntR/vignettes/macrosyntR.Rmd | 169 40 files changed, 7773 insertions(+), 5243 deletions(-)
Title: Useful Tools for Cognitive Diagnosis Modeling
Description: Provides useful tools for cognitive diagnosis modeling (CDM). The package includes functions for empirical Q-matrix estimation and validation, such as the Hull method (Nájera, Sorrel, de la Torre, & Abad, 2021, <doi:10.1111/bmsp.12228>) and the discrete factor loading method (Wang, Song, & Ding, 2018, <doi:10.1007/978-3-319-77249-3_29>). It also contains dimensionality assessment procedures for CDM, including parallel analysis and automated fit comparison as explored in Nájera, Abad, and Sorrel (2021, <doi:10.3389/fpsyg.2021.614470>). Other relevant methods and features for CDM applications, such as the restricted DINA model (Nájera et al., 2023; <doi:10.3102/10769986231158829>), the general nonparametric classification method (Chiu et al., 2018; <doi:10.1007/s11336-017-9595-4>), and corrected estimation of the classification accuracy via multiple imputation (Kreitchmann et al., 2022; <doi:10.3758/s13428-022-01967-5>) are also available. Last [...truncated...]
Author: Pablo Najera [aut, cre, cph],
Miguel A. Sorrel [aut, cph],
Francisco J. Abad [aut, cph],
Rodrigo S. Kreitchmann [ctb]
Maintainer: Pablo Najera <pablo.najera@uam.es>
Diff between cdmTools versions 1.0.3 dated 2023-03-30 and 1.0.4 dated 2023-11-14
DESCRIPTION | 12 +-- MD5 | 34 +++++----- NAMESPACE | 2 NEWS.md | 4 + R/CA.MI.R | 2 R/RDINA.R | 4 - R/estQ.R | 8 +- R/genQ.R | 29 ++++----- R/is.Qid.R | 164 +++++++++++++++++++++++++++++++++++++++++------------ R/missQ.R | 24 +++---- R/personFit.R |only R/print.cdmTools.R | 17 +++++ README.md | 3 man/CA.MI.Rd | 2 man/estQ.Rd | 2 man/genQ.Rd | 4 - man/is.Qid.Rd | 25 ++------ man/missQ.Rd | 4 - man/personFit.Rd |only 19 files changed, 225 insertions(+), 115 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Jeff Goldsmith [aut],
Fabian Scheipl [aut],
Lei Huang [aut],
Julia Wrobel [aut, cre],
Chongzhi Di [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip T. [...truncated...]
Maintainer: Julia Wrobel <julia.wrobel@emory.edu>
Diff between refund versions 0.1-32 dated 2023-07-23 and 0.1-33 dated 2023-11-14
DESCRIPTION | 8 MD5 | 30 R/XtSiginvX.R | 19 R/af_old.R | 52 - R/fosr.perm.R | 6 R/fpca.face.R | 55 + R/fpca.sc.R | 8 R/pffr-methods.R | 1022 ++++++++++++++++----------------- R/pi_basis.R | 48 - man/Xt_siginv_X.Rd | 3 man/af_old.Rd | 6 man/fosr.perm.Rd | 6 man/fpca.face.Rd | 20 man/fpca.sc.Rd | 2 man/qq.pffr.Rd | 2 man/smooth.construct.pi.smooth.spec.Rd | 6 16 files changed, 654 insertions(+), 639 deletions(-)
Title: Manipulate Date, POSIXct and hms Vectors
Description: Manipulates date ('Date'), date time ('POSIXct') and time
('hms') vectors. Date/times are considered discrete and are floored
whenever encountered. Times are wrapped and time zones are maintained
unless explicitly altered by the user.
Author: Joe Thorley [aut] ,
Ayla Pearson [aut, cre] ,
Poisson Consulting [cph, fnd]
Maintainer: Ayla Pearson <ayla@poissonconsulting.ca>
Diff between dttr2 versions 0.4.2 dated 2022-09-26 and 0.5.0 dated 2023-11-14
dttr2-0.4.2/dttr2/tests/testthat/test-POSIXct.R |only dttr2-0.5.0/dttr2/DESCRIPTION | 12 dttr2-0.5.0/dttr2/MD5 | 187 ++++++------ dttr2-0.5.0/dttr2/NAMESPACE | 4 dttr2-0.5.0/dttr2/NEWS.md | 19 + dttr2-0.5.0/dttr2/R/add.R | 2 dttr2-0.5.0/dttr2/R/check.R | 5 dttr2-0.5.0/dttr2/R/complete.R | 5 dttr2-0.5.0/dttr2/R/completed.R | 8 dttr2-0.5.0/dttr2/R/date-add-time.R | 6 dttr2-0.5.0/dttr2/R/date-from-ints.R |only dttr2-0.5.0/dttr2/R/date-time-from-ints.R |only dttr2-0.5.0/dttr2/R/date-time.R | 6 dttr2-0.5.0/dttr2/R/day-decimal.R | 6 dttr2-0.5.0/dttr2/R/dayte-time.R | 7 dttr2-0.5.0/dttr2/R/deprecated.R | 3 dttr2-0.5.0/dttr2/R/diff.R | 6 dttr2-0.5.0/dttr2/R/dtt.R | 3 dttr2-0.5.0/dttr2/R/excel_to_date.R | 16 - dttr2-0.5.0/dttr2/R/excel_to_date_time.R |only dttr2-0.5.0/dttr2/R/hour-decimal.R | 9 dttr2-0.5.0/dttr2/R/minute-decimal.R | 9 dttr2-0.5.0/dttr2/R/minute.R | 3 dttr2-0.5.0/dttr2/R/month-decimal.R | 6 dttr2-0.5.0/dttr2/R/na.R | 8 dttr2-0.5.0/dttr2/R/namespace.R | 1 dttr2-0.5.0/dttr2/R/season.R | 13 dttr2-0.5.0/dttr2/R/second.R | 3 dttr2-0.5.0/dttr2/R/seq.R | 12 dttr2-0.5.0/dttr2/R/study-year.R | 17 - dttr2-0.5.0/dttr2/R/template.R | 19 - dttr2-0.5.0/dttr2/R/time-from-ints.R |only dttr2-0.5.0/dttr2/R/units.R | 4 dttr2-0.5.0/dttr2/R/year-decimal.R | 6 dttr2-0.5.0/dttr2/README.md | 10 dttr2-0.5.0/dttr2/inst/WORDLIST | 2 dttr2-0.5.0/dttr2/man/dtt.Rd | 3 dttr2-0.5.0/dttr2/man/dtt_date_add_time.Rd | 6 dttr2-0.5.0/dttr2/man/dtt_date_from_ints.Rd |only dttr2-0.5.0/dttr2/man/dtt_date_time_from_ints.Rd |only dttr2-0.5.0/dttr2/man/dtt_day_decimal.Rd | 6 dttr2-0.5.0/dttr2/man/dtt_dayte.Rd | 3 dttr2-0.5.0/dttr2/man/dtt_dayte_time.Rd | 10 dttr2-0.5.0/dttr2/man/dtt_daytt.Rd | 3 dttr2-0.5.0/dttr2/man/dtt_diff.Rd | 6 dttr2-0.5.0/dttr2/man/dtt_excel_to_date.Rd | 11 dttr2-0.5.0/dttr2/man/dtt_excel_to_date_time.Rd |only dttr2-0.5.0/dttr2/man/dtt_hour_decimal.Rd | 9 dttr2-0.5.0/dttr2/man/dtt_minute.Rd | 3 dttr2-0.5.0/dttr2/man/dtt_minute_decimal.Rd | 9 dttr2-0.5.0/dttr2/man/dtt_month_decimal.Rd | 6 dttr2-0.5.0/dttr2/man/dtt_season.Rd | 17 - dttr2-0.5.0/dttr2/man/dtt_second.Rd | 3 dttr2-0.5.0/dttr2/man/dtt_seq.Rd | 3 dttr2-0.5.0/dttr2/man/dtt_study_year.Rd | 17 - dttr2-0.5.0/dttr2/man/dtt_time_from_ints.Rd |only dttr2-0.5.0/dttr2/man/dtt_units.Rd | 4 dttr2-0.5.0/dttr2/man/dtt_year_decimal.Rd | 6 dttr2-0.5.0/dttr2/man/params.Rd | 13 dttr2-0.5.0/dttr2/tests/spelling.R |only dttr2-0.5.0/dttr2/tests/testthat/test-add.R | 30 + dttr2-0.5.0/dttr2/tests/testthat/test-aggregate.R | 34 +- dttr2-0.5.0/dttr2/tests/testthat/test-check.R | 5 dttr2-0.5.0/dttr2/tests/testthat/test-complete.R | 141 ++++++--- dttr2-0.5.0/dttr2/tests/testthat/test-completed.R | 97 +++++- dttr2-0.5.0/dttr2/tests/testthat/test-date-add-time.R | 42 ++ dttr2-0.5.0/dttr2/tests/testthat/test-date-from-ints.R |only dttr2-0.5.0/dttr2/tests/testthat/test-date-time-from-ints.R |only dttr2-0.5.0/dttr2/tests/testthat/test-date-time.R | 89 ++++- dttr2-0.5.0/dttr2/tests/testthat/test-date.R | 89 +++-- dttr2-0.5.0/dttr2/tests/testthat/test-day-decimal.R | 24 + dttr2-0.5.0/dttr2/tests/testthat/test-day.R | 9 dttr2-0.5.0/dttr2/tests/testthat/test-days-in-month.R | 14 dttr2-0.5.0/dttr2/tests/testthat/test-days-in-year.R | 14 dttr2-0.5.0/dttr2/tests/testthat/test-dayte-time.R | 46 ++ dttr2-0.5.0/dttr2/tests/testthat/test-dayte.R | 37 +- dttr2-0.5.0/dttr2/tests/testthat/test-decade.R | 10 dttr2-0.5.0/dttr2/tests/testthat/test-diff.R | 39 ++ dttr2-0.5.0/dttr2/tests/testthat/test-doy-decimal.R | 6 dttr2-0.5.0/dttr2/tests/testthat/test-doy.R | 30 + dttr2-0.5.0/dttr2/tests/testthat/test-excel_to_date.R |only dttr2-0.5.0/dttr2/tests/testthat/test-excel_to_date_time.R |only dttr2-0.5.0/dttr2/tests/testthat/test-floor.R | 55 +++ dttr2-0.5.0/dttr2/tests/testthat/test-floored.R | 4 dttr2-0.5.0/dttr2/tests/testthat/test-hour-decimal.R | 29 + dttr2-0.5.0/dttr2/tests/testthat/test-hour.R | 9 dttr2-0.5.0/dttr2/tests/testthat/test-leap-year.R | 15 dttr2-0.5.0/dttr2/tests/testthat/test-minute-decimal.R | 32 +- dttr2-0.5.0/dttr2/tests/testthat/test-minute.R | 21 + dttr2-0.5.0/dttr2/tests/testthat/test-month-decimal.R | 24 + dttr2-0.5.0/dttr2/tests/testthat/test-month.R | 12 dttr2-0.5.0/dttr2/tests/testthat/test-season.R | 59 +++ dttr2-0.5.0/dttr2/tests/testthat/test-second.R | 28 + dttr2-0.5.0/dttr2/tests/testthat/test-seq.R | 140 +++++++- dttr2-0.5.0/dttr2/tests/testthat/test-study-year.R | 60 +++ dttr2-0.5.0/dttr2/tests/testthat/test-subtract.R | 100 +++++- dttr2-0.5.0/dttr2/tests/testthat/test-time-from-ints.R |only dttr2-0.5.0/dttr2/tests/testthat/test-time.R | 45 ++ dttr2-0.5.0/dttr2/tests/testthat/test-tz.R | 30 + dttr2-0.5.0/dttr2/tests/testthat/test-utils.R | 12 dttr2-0.5.0/dttr2/tests/testthat/test-year-decimal.R | 26 + dttr2-0.5.0/dttr2/tests/testthat/test-year.R | 19 - 102 files changed, 1524 insertions(+), 507 deletions(-)
Title: Truncated Exponential Family
Description: Handles truncated members from the exponential family of
probability distributions. Contains functions such as rtruncnorm() and
dtruncpois(), which are truncated versions of rnorm() and dpois() from the
stats package that also offer richer output containing, for example, the
distribution parameters. It also provides functions to retrieve the original
distribution parameters from a truncated sample by maximum-likelihood
estimation.
Author: Rene Holst [aut],
Waldir Leoncio [cre, aut]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between TruncExpFam versions 1.0.1 dated 2023-08-22 and 1.1.0 dated 2023-11-14
TruncExpFam-1.0.1/TruncExpFam/R/a_dtrunc.R |only TruncExpFam-1.0.1/TruncExpFam/R/logGammaFunction.R |only TruncExpFam-1.0.1/TruncExpFam/man/init.parms.Rd |only TruncExpFam-1.1.0/TruncExpFam/DESCRIPTION | 13 - TruncExpFam-1.1.0/TruncExpFam/MD5 | 104 +++++---- TruncExpFam-1.1.0/TruncExpFam/NAMESPACE | 103 +++++---- TruncExpFam-1.1.0/TruncExpFam/NEWS.md |only TruncExpFam-1.1.0/TruncExpFam/R/TruncExpFam-package.R | 23 +- TruncExpFam-1.1.0/TruncExpFam/R/a_rtrunc.R | 94 ++------ TruncExpFam-1.1.0/TruncExpFam/R/averageT.R |only TruncExpFam-1.1.0/TruncExpFam/R/beta.R | 65 ++--- TruncExpFam-1.1.0/TruncExpFam/R/binomial.R | 59 ++--- TruncExpFam-1.1.0/TruncExpFam/R/chisq.R | 45 +-- TruncExpFam-1.1.0/TruncExpFam/R/contbernoulli.R | 104 +++++---- TruncExpFam-1.1.0/TruncExpFam/R/exponential.R | 42 +-- TruncExpFam-1.1.0/TruncExpFam/R/gamma.R | 62 +++-- TruncExpFam-1.1.0/TruncExpFam/R/genericFunctions.R | 50 +++- TruncExpFam-1.1.0/TruncExpFam/R/inverse-gamma.R | 54 ++-- TruncExpFam-1.1.0/TruncExpFam/R/inverse-gaussian.R | 83 +++---- TruncExpFam-1.1.0/TruncExpFam/R/log-normal.R | 49 +--- TruncExpFam-1.1.0/TruncExpFam/R/misc.R | 22 + TruncExpFam-1.1.0/TruncExpFam/R/mlEstimationTruncDist.R | 92 ++++++-- TruncExpFam-1.1.0/TruncExpFam/R/negative-binomial.R | 60 ++--- TruncExpFam-1.1.0/TruncExpFam/R/normal.R | 48 +--- TruncExpFam-1.1.0/TruncExpFam/R/numericVector.R |only TruncExpFam-1.1.0/TruncExpFam/R/poisson.R | 42 +-- TruncExpFam-1.1.0/TruncExpFam/R/prepEta.R |only TruncExpFam-1.1.0/TruncExpFam/R/print.R | 2 TruncExpFam-1.1.0/TruncExpFam/R/probdist-class.R |only TruncExpFam-1.1.0/TruncExpFam/R/rescaledDensities.R |only TruncExpFam-1.1.0/TruncExpFam/R/rtrunc_direct.R |only TruncExpFam-1.1.0/TruncExpFam/R/sampleFromUntruncated.R | 15 - TruncExpFam-1.1.0/TruncExpFam/R/validateDomain.R | 47 ++-- TruncExpFam-1.1.0/TruncExpFam/R/validateFamily.R |only TruncExpFam-1.1.0/TruncExpFam/R/validateNaturalParms.R |only TruncExpFam-1.1.0/TruncExpFam/R/validateSupport.R | 114 +++++----- TruncExpFam-1.1.0/TruncExpFam/build |only TruncExpFam-1.1.0/TruncExpFam/inst |only TruncExpFam-1.1.0/TruncExpFam/man/TruncExpFam.Rd | 17 + TruncExpFam-1.1.0/TruncExpFam/man/averageT.Rd |only TruncExpFam-1.1.0/TruncExpFam/man/dot-onAttach.Rd | 3 TruncExpFam-1.1.0/TruncExpFam/man/dtrunc.Rd | 86 +++++-- TruncExpFam-1.1.0/TruncExpFam/man/empiricalParameters.Rd |only TruncExpFam-1.1.0/TruncExpFam/man/empiricalParameters.numeric.Rd |only TruncExpFam-1.1.0/TruncExpFam/man/mlEstimationTruncDist.Rd | 41 ++- TruncExpFam-1.1.0/TruncExpFam/man/natural2parameters.Rd | 11 TruncExpFam-1.1.0/TruncExpFam/man/parameters2natural.Rd | 9 TruncExpFam-1.1.0/TruncExpFam/man/probdist-class.Rd |only TruncExpFam-1.1.0/TruncExpFam/man/rtrunc.Rd | 35 ++- TruncExpFam-1.1.0/TruncExpFam/man/validateFamilyParms.Rd | 6 TruncExpFam-1.1.0/TruncExpFam/tests/testthat.R | 5 TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-aliases.R | 26 +- TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-direct-sampling.R |only TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-dtrunc.R |only TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-empirical-parameters.R |only TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-estimating-from-classless.R |only TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-exceptions.R | 72 +++++- TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-internals.R |only TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-parameters2natural.R |only TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-printing.R | 6 TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-probdist.R |only TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-sampling-and-estimation.R | 71 +++++- TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-support.R | 15 + TruncExpFam-1.1.0/TruncExpFam/tests/testthat/test-truncation.R | 40 ++- TruncExpFam-1.1.0/TruncExpFam/vignettes |only 65 files changed, 1078 insertions(+), 757 deletions(-)
Title: Normal aka Gaussian 1-d Mixture Models
Description: Onedimensional Normal (i.e. Gaussian) Mixture Models (S3) Classes,
for, e.g., density estimation or clustering algorithms research and teaching;
providing the widely used Marron-Wand densities. Efficient random
number generation and graphics. Fitting to data by efficient ML (Maximum
Likelihood) or traditional EM estimation.
Author: Martin Maechler [aut, cre] ,
Friedrich Leisch [ctb] ,
<https://orcid.org/0000-0001-7278-1983>),
Erik Joergensen [ctb] , qnorMix)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between nor1mix versions 1.3-0 dated 2019-06-13 and 1.3-2 dated 2023-11-14
ChangeLog | 19 +++++++++++++++-- DESCRIPTION | 20 ++++++++++------- MD5 | 23 ++++++++++---------- R/norMix.R | 59 ++++++++++++++++++++++++++++------------------------- R/norMixEM.R | 18 +++++++++------- TODO | 2 - build/partial.rdb |binary man/MarronWand.Rd | 10 ++++---- man/dnorMix.Rd | 2 - man/llnorMix.Rd | 2 - man/norMixFit.Rd | 8 ++++++- man/pnorMix.Rd | 2 - tests/MW.Rout.save |only 13 files changed, 100 insertions(+), 65 deletions(-)
Title: Modeling for Single-Cell Open Chromatin Analysis
Description: A statistical framework and analysis tool for open chromatin
analysis designed specifically for single cell ATAC-seq (Assay for
Transposase-Accessible Chromatin) data, after cell type/cluster
identification. These novel modules remove unwanted technical variation,
identify open chromatin, robustly models repeated measures in single cell
data, implement advanced statistical frameworks to model zero-inflation for
differential and co-accessibility analyses, and integrate with existing
databases and modules for downstream analyses to reveal biological insights.
MOCHA provides a statistical foundation for complex downstream analysis to
help advance the potential of single cell ATAC-seq for applied studies.
Methods for zero-inflated statistics are as described in:
Ghazanfar, S., Lin, Y., Su, X. et al. (2020) <doi:10.1038/s41592-020-0885-x>.
Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated
Data" (2009) <https://scholarworks.wmich.edu/dissertations/721/>.
Author: Samir Rachid Zaim [aut, ctb],
Mark-Phillip Pebworth [aut, ctb],
Imran McGrath [aut, cre],
Lauren Okada [aut, ctb],
Xiaojun Li [aut, ctb]
Maintainer: Imran McGrath <aifi.compbio.support@alleninstitute.org>
Diff between MOCHA versions 1.0.0 dated 2023-06-12 and 1.0.1 dated 2023-11-14
MOCHA-1.0.0/MOCHA/man/simplifiedSampleTile.Rd |only MOCHA-1.0.0/MOCHA/tests/testthat/_snaps/1sample/testCoAccessibilityChromVar.md |only MOCHA-1.0.0/MOCHA/tests/testthat/_snaps/3sample/testCoAccessibilityChromVar.md |only MOCHA-1.0.0/MOCHA/tests/testthat/test_testCoAccessibilityChromVar.R |only MOCHA-1.0.0/MOCHA/tests/testthat/test_testCoAccessibilityRandom.R |only MOCHA-1.0.1/MOCHA/DESCRIPTION | 15 MOCHA-1.0.1/MOCHA/MD5 | 43 MOCHA-1.0.1/MOCHA/NAMESPACE | 1 MOCHA-1.0.1/MOCHA/NEWS.md | 5 MOCHA-1.0.1/MOCHA/R/callOpenTiles.R | 75 - MOCHA-1.0.1/MOCHA/R/singlePopulationSampleTileMatrix.R | 6 MOCHA-1.0.1/MOCHA/R/testCoAccessibility.R | 146 +- MOCHA-1.0.1/MOCHA/README.md | 16 MOCHA-1.0.1/MOCHA/inst/doc/COVID-walkthrough.html | 320 ++-- MOCHA-1.0.1/MOCHA/inst/doc/ImportingFromOtherSources.html | 718 +++++----- MOCHA-1.0.1/MOCHA/man/pilotZIGLMM.Rd | 17 MOCHA-1.0.1/MOCHA/man/runZIGLMM.Rd | 36 MOCHA-1.0.1/MOCHA/man/testCoAccessibility.Rd |only MOCHA-1.0.1/MOCHA/man/testCoAccessibilityChromVar.Rd | 6 MOCHA-1.0.1/MOCHA/man/testCoAccessibilityRandom.Rd | 7 MOCHA-1.0.1/MOCHA/tests/testthat/_snaps/3sample/testCoAccessibilityRandom.md | 10 MOCHA-1.0.1/MOCHA/tests/testthat/_snaps/getSampleTileMatrix.md | 2 MOCHA-1.0.1/MOCHA/tests/testthat/test_callOpenTiles.R | 2 MOCHA-1.0.1/MOCHA/tests/testthat/test_combineSampleTileMatrix.R | 5 MOCHA-1.0.1/MOCHA/tests/testthat/test_dimensionalityReduction.R | 2 MOCHA-1.0.1/MOCHA/tests/testthat/test_testCoAccessibility.R |only 26 files changed, 797 insertions(+), 635 deletions(-)
Title: The Scalable Highly Adaptive Lasso
Description: A scalable implementation of the highly adaptive lasso algorithm,
including routines for constructing sparse matrices of basis functions of the
observed data, as well as a custom implementation of Lasso regression tailored
to enhance efficiency when the matrix of predictors is composed exclusively of
indicator functions. For ease of use and increased flexibility, the Lasso
fitting routines invoke code from the 'glmnet' package by default. The highly
adaptive lasso was first formulated and described by MJ van der Laan (2017)
<doi:10.1515/ijb-2015-0097>, with practical demonstrations of its performance
given by Benkeser and van der Laan (2016) <doi:10.1109/DSAA.2016.93>. This
implementation of the highly adaptive lasso algorithm was described by Hejazi,
Coyle, and van der Laan (2020) <doi:10.21105/joss.02526>.
Author: Jeremy Coyle [aut, cre] ,
Nima Hejazi [aut] ,
Rachael Phillips [aut] ,
Lars van der Laan [aut],
David Benkeser [ctb] ,
Oleg Sofrygin [ctb],
Weixin Cai [ctb] ,
Mark van der Laan [aut, cph, ths]
Maintainer: Jeremy Coyle <jeremyrcoyle@gmail.com>
Diff between hal9001 versions 0.4.3 dated 2022-02-09 and 0.4.6 dated 2023-11-14
hal9001-0.4.3/hal9001/R/cv_lasso.R |only hal9001-0.4.3/hal9001/R/cv_lasso_early_stopping.R |only hal9001-0.4.3/hal9001/R/lassi.R |only hal9001-0.4.3/hal9001/man/cv_lasso.Rd |only hal9001-0.4.3/hal9001/man/cv_lasso_early_stopping.Rd |only hal9001-0.4.3/hal9001/man/formula_helpers.Rd |only hal9001-0.4.3/hal9001/man/lassi.Rd |only hal9001-0.4.3/hal9001/man/lassi_fit_module.Rd |only hal9001-0.4.3/hal9001/man/lassi_origami.Rd |only hal9001-0.4.3/hal9001/man/lassi_predict.Rd |only hal9001-0.4.3/hal9001/man/predict.lassi.Rd |only hal9001-0.4.3/hal9001/src/lassi_fit.cpp |only hal9001-0.4.6/hal9001/DESCRIPTION | 8 hal9001-0.4.6/hal9001/MD5 | 72 hal9001-0.4.6/hal9001/NAMESPACE | 8 hal9001-0.4.6/hal9001/NEWS.md | 21 hal9001-0.4.6/hal9001/R/RcppExports.R | 10 hal9001-0.4.6/hal9001/R/formula_hal9001.R | 52 hal9001-0.4.6/hal9001/R/hal.R | 169 - hal9001-0.4.6/hal9001/R/make_basis.R | 5 hal9001-0.4.6/hal9001/R/predict.R | 100 hal9001-0.4.6/hal9001/R/sl_hal9001.R | 38 hal9001-0.4.6/hal9001/R/summary.R | 522 ++-- hal9001-0.4.6/hal9001/README.md | 96 hal9001-0.4.6/hal9001/build/vignette.rds |binary hal9001-0.4.6/hal9001/inst/doc/intro_hal9001.R | 114 hal9001-0.4.6/hal9001/inst/doc/intro_hal9001.Rmd | 114 hal9001-0.4.6/hal9001/inst/doc/intro_hal9001.html | 1267 ++++++---- hal9001-0.4.6/hal9001/man/SL.hal9001.Rd | 28 hal9001-0.4.6/hal9001/man/fit_hal.Rd | 68 hal9001-0.4.6/hal9001/man/generate_all_rules.Rd |only hal9001-0.4.6/hal9001/man/num_knots_generator.Rd | 4 hal9001-0.4.6/hal9001/man/predict.hal9001.Rd | 6 hal9001-0.4.6/hal9001/src/RcppExports.cpp | 17 hal9001-0.4.6/hal9001/tests/testthat/test-cv_lasso.R | 107 hal9001-0.4.6/hal9001/tests/testthat/test-formula.R | 9 hal9001-0.4.6/hal9001/tests/testthat/test-general_families.R | 24 hal9001-0.4.6/hal9001/tests/testthat/test-hal_binomial.R | 24 hal9001-0.4.6/hal9001/tests/testthat/test-hal_hazards.R | 2 hal9001-0.4.6/hal9001/tests/testthat/test-hal_multivariate.R |only hal9001-0.4.6/hal9001/tests/testthat/test-lasso.R | 99 hal9001-0.4.6/hal9001/tests/testthat/test-reduce_basis_filter.R | 10 hal9001-0.4.6/hal9001/tests/testthat/test-sl_ecpolley.R | 12 hal9001-0.4.6/hal9001/vignettes/intro_hal9001.Rmd | 114 44 files changed, 1709 insertions(+), 1411 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-03 0.2
Title: R Commander Plugin for Teaching Statistical Methods
Description: R Commander plugin for teaching statistical methods.
It adds a new menu for making easier the teaching of the main concepts about the main statistical methods.
Author: Tomas R. Cotos Yanez [aut] ,
Manuel A. Mosquera Rodriguez [aut, cre]
,
Ana Perez Gonzalez [aut] ,
Benigno Reguengo Lareo [aut]
Maintainer: Manuel A. Mosquera Rodriguez <mamrguez@uvigo.es>
Diff between RcmdrPlugin.TeachStat versions 1.1.2 dated 2023-10-16 and 1.1.3 dated 2023-11-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 9 +++++++++ R/contrastHipotesisProporcion.R | 16 ++++++++-------- R/resumenNumericoVDiscreta.R | 2 +- man/RcmdrPlugin.TeachStat-package.Rd | 2 +- man/plotRegions.Rd | 2 +- 7 files changed, 29 insertions(+), 20 deletions(-)
More information about RcmdrPlugin.TeachStat at CRAN
Permanent link
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between httr2 versions 0.2.3 dated 2023-05-08 and 1.0.0 dated 2023-11-14
httr2-0.2.3/httr2/R/compat-friendly-type.R |only httr2-0.2.3/httr2/R/compat-purrr.R |only httr2-0.2.3/httr2/man/oauth_flow_auth_code.Rd |only httr2-0.2.3/httr2/man/oauth_flow_bearer_jwt.Rd |only httr2-0.2.3/httr2/man/oauth_flow_client_credentials.Rd |only httr2-0.2.3/httr2/man/oauth_flow_device.Rd |only httr2-0.2.3/httr2/man/oauth_flow_password.Rd |only httr2-0.2.3/httr2/man/oauth_flow_refresh.Rd |only httr2-0.2.3/httr2/man/req_stream.Rd |only httr2-0.2.3/httr2/man/with_mock.Rd |only httr2-1.0.0/httr2/DESCRIPTION | 22 httr2-1.0.0/httr2/MD5 | 358 +++++--- httr2-1.0.0/httr2/NAMESPACE | 31 httr2-1.0.0/httr2/NEWS.md | 167 ++++ httr2-1.0.0/httr2/R/content-type.R |only httr2-1.0.0/httr2/R/curl.R | 146 ++- httr2-1.0.0/httr2/R/headers.R | 24 httr2-1.0.0/httr2/R/httr2-package.R | 4 httr2-1.0.0/httr2/R/import-standalone-obj-type.R |only httr2-1.0.0/httr2/R/import-standalone-purrr.R |only httr2-1.0.0/httr2/R/import-standalone-types-check.R |only httr2-1.0.0/httr2/R/iterate-helpers.R |only httr2-1.0.0/httr2/R/iterate-responses.R |only httr2-1.0.0/httr2/R/iterate.R |only httr2-1.0.0/httr2/R/jwt.R | 16 httr2-1.0.0/httr2/R/multi-req.R | 197 +++- httr2-1.0.0/httr2/R/oauth-client.R | 69 - httr2-1.0.0/httr2/R/oauth-flow-auth-code.R | 409 +++++++--- httr2-1.0.0/httr2/R/oauth-flow-client-credentials.R | 48 - httr2-1.0.0/httr2/R/oauth-flow-device.R | 78 - httr2-1.0.0/httr2/R/oauth-flow-jwt.R | 88 +- httr2-1.0.0/httr2/R/oauth-flow-password.R | 64 - httr2-1.0.0/httr2/R/oauth-flow-refresh.R | 59 - httr2-1.0.0/httr2/R/oauth-flow.R | 73 + httr2-1.0.0/httr2/R/oauth-token.R | 12 httr2-1.0.0/httr2/R/oauth.R | 117 ++ httr2-1.0.0/httr2/R/progress-bars.R |only httr2-1.0.0/httr2/R/progress.R |only httr2-1.0.0/httr2/R/req-auth.R | 20 httr2-1.0.0/httr2/R/req-body.R | 141 ++- httr2-1.0.0/httr2/R/req-cache.R | 108 ++ httr2-1.0.0/httr2/R/req-cookies.R |only httr2-1.0.0/httr2/R/req-error.R | 58 + httr2-1.0.0/httr2/R/req-headers.R | 53 - httr2-1.0.0/httr2/R/req-method.R | 8 httr2-1.0.0/httr2/R/req-mock.R | 75 + httr2-1.0.0/httr2/R/req-options.R | 55 - httr2-1.0.0/httr2/R/req-perform-stream.R |only httr2-1.0.0/httr2/R/req-perform.R | 137 +-- httr2-1.0.0/httr2/R/req-policy.R | 13 httr2-1.0.0/httr2/R/req-retries.R | 12 httr2-1.0.0/httr2/R/req-template.R | 37 httr2-1.0.0/httr2/R/req-throttle.R | 8 httr2-1.0.0/httr2/R/req-url.R | 53 - httr2-1.0.0/httr2/R/req.R | 37 httr2-1.0.0/httr2/R/resp-body.R | 109 +- httr2-1.0.0/httr2/R/resp-headers.R | 40 httr2-1.0.0/httr2/R/resp-status.R | 17 httr2-1.0.0/httr2/R/resp-url.R |only httr2-1.0.0/httr2/R/resp.R | 85 +- httr2-1.0.0/httr2/R/roxygen2.R |only httr2-1.0.0/httr2/R/secret.R | 141 ++- httr2-1.0.0/httr2/R/sequential.R |only httr2-1.0.0/httr2/R/test.R | 52 + httr2-1.0.0/httr2/R/url.R | 53 - httr2-1.0.0/httr2/R/utils-multi.R |only httr2-1.0.0/httr2/R/utils.R | 146 ++- httr2-1.0.0/httr2/README.md | 22 httr2-1.0.0/httr2/build/vignette.rds |binary httr2-1.0.0/httr2/cleanup |only httr2-1.0.0/httr2/configure |only httr2-1.0.0/httr2/configure.win |only httr2-1.0.0/httr2/inst/doc/httr2.R | 56 - httr2-1.0.0/httr2/inst/doc/httr2.Rmd | 62 - httr2-1.0.0/httr2/inst/doc/httr2.html | 320 +++---- httr2-1.0.0/httr2/man/curl_translate.Rd | 10 httr2-1.0.0/httr2/man/example_url.Rd | 15 httr2-1.0.0/httr2/man/figures/lifecycle-archived.svg | 22 httr2-1.0.0/httr2/man/figures/lifecycle-defunct.svg | 22 httr2-1.0.0/httr2/man/figures/lifecycle-deprecated.svg | 22 httr2-1.0.0/httr2/man/figures/lifecycle-experimental.svg | 22 httr2-1.0.0/httr2/man/figures/lifecycle-maturing.svg | 22 httr2-1.0.0/httr2/man/figures/lifecycle-questioning.svg | 22 httr2-1.0.0/httr2/man/figures/lifecycle-soft-deprecated.svg |only httr2-1.0.0/httr2/man/figures/lifecycle-stable.svg | 30 httr2-1.0.0/httr2/man/figures/lifecycle-superseded.svg | 22 httr2-1.0.0/httr2/man/figures/logo.png |only httr2-1.0.0/httr2/man/httr2-package.Rd | 3 httr2-1.0.0/httr2/man/iterate_with_offset.Rd |only httr2-1.0.0/httr2/man/jwt_claim.Rd | 2 httr2-1.0.0/httr2/man/last_response.Rd | 2 httr2-1.0.0/httr2/man/multi_req_perform.Rd | 57 - httr2-1.0.0/httr2/man/oauth_cache_path.Rd |only httr2-1.0.0/httr2/man/oauth_client.Rd | 8 httr2-1.0.0/httr2/man/oauth_client_req_auth.Rd | 16 httr2-1.0.0/httr2/man/oauth_flow_auth_code_url.Rd |only httr2-1.0.0/httr2/man/oauth_redirect_uri.Rd |only httr2-1.0.0/httr2/man/oauth_token.Rd | 6 httr2-1.0.0/httr2/man/oauth_token_cached.Rd |only httr2-1.0.0/httr2/man/obfuscate.Rd | 19 httr2-1.0.0/httr2/man/progress_bars.Rd |only httr2-1.0.0/httr2/man/req_auth_basic.Rd | 6 httr2-1.0.0/httr2/man/req_auth_bearer_token.Rd | 6 httr2-1.0.0/httr2/man/req_body.Rd | 76 + httr2-1.0.0/httr2/man/req_cache.Rd | 34 httr2-1.0.0/httr2/man/req_cookie_preserve.Rd |only httr2-1.0.0/httr2/man/req_dry_run.Rd | 8 httr2-1.0.0/httr2/man/req_error.Rd | 52 + httr2-1.0.0/httr2/man/req_headers.Rd | 43 - httr2-1.0.0/httr2/man/req_method.Rd | 6 httr2-1.0.0/httr2/man/req_oauth.Rd | 5 httr2-1.0.0/httr2/man/req_oauth_auth_code.Rd | 129 ++- httr2-1.0.0/httr2/man/req_oauth_bearer_jwt.Rd | 45 - httr2-1.0.0/httr2/man/req_oauth_client_credentials.Rd | 35 httr2-1.0.0/httr2/man/req_oauth_device.Rd | 64 + httr2-1.0.0/httr2/man/req_oauth_password.Rd | 59 + httr2-1.0.0/httr2/man/req_oauth_refresh.Rd | 44 - httr2-1.0.0/httr2/man/req_options.Rd | 6 httr2-1.0.0/httr2/man/req_perform.Rd | 29 httr2-1.0.0/httr2/man/req_perform_iterative.Rd |only httr2-1.0.0/httr2/man/req_perform_parallel.Rd |only httr2-1.0.0/httr2/man/req_perform_sequential.Rd |only httr2-1.0.0/httr2/man/req_perform_stream.Rd |only httr2-1.0.0/httr2/man/req_progress.Rd |only httr2-1.0.0/httr2/man/req_proxy.Rd | 4 httr2-1.0.0/httr2/man/req_retry.Rd | 12 httr2-1.0.0/httr2/man/req_template.Rd | 8 httr2-1.0.0/httr2/man/req_throttle.Rd | 4 httr2-1.0.0/httr2/man/req_timeout.Rd | 2 httr2-1.0.0/httr2/man/req_url.Rd | 39 httr2-1.0.0/httr2/man/req_user_agent.Rd | 8 httr2-1.0.0/httr2/man/req_verbose.Rd | 14 httr2-1.0.0/httr2/man/resp_body_raw.Rd | 16 httr2-1.0.0/httr2/man/resp_check_content_type.Rd |only httr2-1.0.0/httr2/man/resp_content_type.Rd | 10 httr2-1.0.0/httr2/man/resp_date.Rd | 4 httr2-1.0.0/httr2/man/resp_headers.Rd | 18 httr2-1.0.0/httr2/man/resp_link_url.Rd | 3 httr2-1.0.0/httr2/man/resp_raw.Rd | 6 httr2-1.0.0/httr2/man/resp_retry_after.Rd | 4 httr2-1.0.0/httr2/man/resp_status.Rd | 10 httr2-1.0.0/httr2/man/resp_url.Rd |only httr2-1.0.0/httr2/man/response.Rd | 16 httr2-1.0.0/httr2/man/resps_successes.Rd |only httr2-1.0.0/httr2/man/secrets.Rd | 24 httr2-1.0.0/httr2/man/signal_total_pages.Rd |only httr2-1.0.0/httr2/man/url_parse.Rd | 5 httr2-1.0.0/httr2/man/with_mocked_responses.Rd |only httr2-1.0.0/httr2/man/with_verbosity.Rd | 2 httr2-1.0.0/httr2/tests/testthat/_snaps/content-type.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/curl.md | 105 ++ httr2-1.0.0/httr2/tests/testthat/_snaps/headers.md | 12 httr2-1.0.0/httr2/tests/testthat/_snaps/iterate-helpers.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/iterate.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/multi-req.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/oauth-client.md | 36 httr2-1.0.0/httr2/tests/testthat/_snaps/oauth-flow-auth-code.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/oauth-flow-jwt.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/oauth-flow-refresh.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/oauth-flow.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/oauth.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/req-body.md | 18 httr2-1.0.0/httr2/tests/testthat/_snaps/req-cache.md | 23 httr2-1.0.0/httr2/tests/testthat/_snaps/req-cookies.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/req-error.md | 12 httr2-1.0.0/httr2/tests/testthat/_snaps/req-headers.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/req-mock.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/req-options.md | 15 httr2-1.0.0/httr2/tests/testthat/_snaps/req-perform-stream.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/req-perform.md | 33 httr2-1.0.0/httr2/tests/testthat/_snaps/req-policy.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/req-template.md | 18 httr2-1.0.0/httr2/tests/testthat/_snaps/req-url.md | 37 httr2-1.0.0/httr2/tests/testthat/_snaps/req.md | 4 httr2-1.0.0/httr2/tests/testthat/_snaps/resp-body.md | 41 - httr2-1.0.0/httr2/tests/testthat/_snaps/resp.md | 21 httr2-1.0.0/httr2/tests/testthat/_snaps/secret.md | 10 httr2-1.0.0/httr2/tests/testthat/_snaps/sequential.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/url.md | 35 httr2-1.0.0/httr2/tests/testthat/_snaps/utils-multi.md |only httr2-1.0.0/httr2/tests/testthat/_snaps/utils.md | 23 httr2-1.0.0/httr2/tests/testthat/test-content-type.R |only httr2-1.0.0/httr2/tests/testthat/test-curl.R | 72 + httr2-1.0.0/httr2/tests/testthat/test-headers.R | 1 httr2-1.0.0/httr2/tests/testthat/test-iterate-helpers.R |only httr2-1.0.0/httr2/tests/testthat/test-iterate-responses.R |only httr2-1.0.0/httr2/tests/testthat/test-iterate.R |only httr2-1.0.0/httr2/tests/testthat/test-multi-req.R | 53 - httr2-1.0.0/httr2/tests/testthat/test-oauth-client.R | 14 httr2-1.0.0/httr2/tests/testthat/test-oauth-flow-auth-code.R |only httr2-1.0.0/httr2/tests/testthat/test-oauth-flow-jwt.R | 8 httr2-1.0.0/httr2/tests/testthat/test-oauth-flow-refresh.R | 9 httr2-1.0.0/httr2/tests/testthat/test-oauth-flow.R |only httr2-1.0.0/httr2/tests/testthat/test-oauth.R | 78 + httr2-1.0.0/httr2/tests/testthat/test-req-auth.R | 2 httr2-1.0.0/httr2/tests/testthat/test-req-body.R | 78 + httr2-1.0.0/httr2/tests/testthat/test-req-cache.R | 87 ++ httr2-1.0.0/httr2/tests/testthat/test-req-cookies.R |only httr2-1.0.0/httr2/tests/testthat/test-req-headers.R | 21 httr2-1.0.0/httr2/tests/testthat/test-req-mock.R | 37 httr2-1.0.0/httr2/tests/testthat/test-req-options.R | 7 httr2-1.0.0/httr2/tests/testthat/test-req-perform-stream.R |only httr2-1.0.0/httr2/tests/testthat/test-req-perform.R | 39 httr2-1.0.0/httr2/tests/testthat/test-req-policy.R |only httr2-1.0.0/httr2/tests/testthat/test-req-throttle.R | 4 httr2-1.0.0/httr2/tests/testthat/test-req-url.R | 44 - 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Title: Tools for Fast Computing and Visualizing Euclidean Minimum
Spanning Trees
Description: Fast and easily computes an Euclidean Minimum Spanning Tree (EMST) from data,
relying on the R API for 'mlpack' - the C++ Machine Learning Library (Curtin et. al., 2013).
'emstreeR' uses the Dual-Tree Boruvka (March, Ram, Gray, 2010, <doi:10.1145/1835804.1835882>),
which is theoretically and empirically the fastest algorithm for computing an EMST. This package also provides
functions and an S3 method for readily visualizing Minimum Spanning Trees (MST) using either the
style of the 'base', 'scatterplot3d', or 'ggplot2' libraries; and functions to export the MST output to shapefiles.
Author: Allan Quadros [aut, cre],
Duncan Garmonsway [ctb]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between emstreeR versions 3.0.0 dated 2022-03-21 and 3.1.2 dated 2023-11-14
emstreeR-3.0.0/emstreeR/man/emstreeR-package.Rd |only emstreeR-3.1.2/emstreeR/DESCRIPTION | 20 +- emstreeR-3.1.2/emstreeR/MD5 | 23 +- emstreeR-3.1.2/emstreeR/NAMESPACE | 3 emstreeR-3.1.2/emstreeR/R/ComputeMST.R | 3 emstreeR-3.1.2/emstreeR/R/export-edges-to-shapefile.R |only emstreeR-3.1.2/emstreeR/R/export-vertices-to-shapefile.R |only emstreeR-3.1.2/emstreeR/R/plot.MST.R | 10 - emstreeR-3.1.2/emstreeR/README.md | 108 +++++++++--- emstreeR-3.1.2/emstreeR/man/README-figures/qgis1.png |only emstreeR-3.1.2/emstreeR/man/README-figures/qgis2.png |only emstreeR-3.1.2/emstreeR/man/README-figures/qgis3.png |only emstreeR-3.1.2/emstreeR/man/README-figures/qgis4.png |only emstreeR-3.1.2/emstreeR/man/README-figures/qgis5.png |only emstreeR-3.1.2/emstreeR/man/README-figures/qgis6.png |only emstreeR-3.1.2/emstreeR/man/export_edges_to_shapefile.Rd |only emstreeR-3.1.2/emstreeR/man/export_vertices_to_shapefile.Rd |only emstreeR-3.1.2/emstreeR/man/plot.MST.Rd | 10 - 18 files changed, 123 insertions(+), 54 deletions(-)
Title: Reference Interval Estimation using Real-World Data
Description: Indirect method for the estimation of reference intervals using
Real-World Data ('RWD'). It takes routine measurements of diagnostic
tests, containing pathological and non-pathological samples as input
and uses sophisticated statistical methods to derive a model describing
the distribution of the non-pathological samples. This distribution can
then be used to derive reference intervals. Furthermore, the package
offers functions for printing and plotting the results of the algorithm.
See ?refineR for a more comprehensive description of the features.
Version 1.0 of the algorithm is described in detail in 'Ammer et al. (2021)'
<doi:10.1038/s41598-021-95301-2>. Additional guidance on the usage of
the algorithm is given in 'Ammer et al. (2023)' <doi:10.1093/jalm/jfac101>.
Author: Tatjana Ammer [aut, cre],
Christopher M Rank [aut],
Andre Schuetzenmeister [aut]
Maintainer: Tatjana Ammer <tatjana.ammer@roche.com>
Diff between refineR versions 1.6.0 dated 2023-03-08 and 1.6.1 dated 2023-11-14
refineR-1.6.0/refineR/data/datalist |only refineR-1.6.0/refineR/vignettes/figures |only refineR-1.6.1/refineR/DESCRIPTION | 25 +++-- refineR-1.6.1/refineR/MD5 | 24 ++-- refineR-1.6.1/refineR/NAMESPACE | 9 - refineR-1.6.1/refineR/NEWS.md | 11 ++ refineR-1.6.1/refineR/R/algoInvHist.R | 58 ++++++----- refineR-1.6.1/refineR/build/vignette.rds |binary refineR-1.6.1/refineR/inst/doc/refineR_package.R | 16 +++ refineR-1.6.1/refineR/inst/doc/refineR_package.Rmd | 34 ++++++ refineR-1.6.1/refineR/inst/doc/refineR_package.html | 100 +++++++++++--------- refineR-1.6.1/refineR/man/refineR-Package.Rd | 4 refineR-1.6.1/refineR/vignettes/refineR_package.Rmd | 34 ++++++ 13 files changed, 206 insertions(+), 109 deletions(-)
Title: Computational Tools for the IG and IGL Copula Families
Description: Compute distributional quantities for an
Integrated Gamma (IG) or Integrated Gamma Limit (IGL) copula, such
as a cdf and density. Compute corresponding conditional quantities
such as the cdf and quantiles. Generate
data from an IG or IGL copula. See the vignette for formulas,
or for a derivation, see Coia, V (2017) "Forecasting of Nonlinear
Extreme Quantiles Using Copula Models." PhD Dissertation,
The University of British Columbia.
Author: Vincenzo Coia [aut, cre],
Harry Joe [aut]
Maintainer: Vincenzo Coia <vincenzo.coia@gmail.com>
Diff between igcop versions 1.0.1 dated 2021-10-13 and 1.0.2 dated 2023-11-14
DESCRIPTION | 13 - MD5 | 20 +- NEWS.md | 6 R/igcop-package.R | 2 README.md | 24 +- build/vignette.rds |binary inst/doc/Formulas.R | 2 inst/doc/Formulas.Rmd | 2 inst/doc/Formulas.html | 438 ++++++++++++++++++++++++++++++++++++++++--------- man/igcop.Rd | 10 + vignettes/Formulas.Rmd | 2 11 files changed, 413 insertions(+), 106 deletions(-)
Title: Bayesian Solutions for the Factor Zoo: We Just Ran Two
Quadrillion Models
Description: Contains the functions to use the econometric methods in the paper Bryzgalova, Huang, and Julliard (2023) <doi:10.1111/jofi.13197>. In this package, we provide a novel Bayesian framework for analyzing linear asset pricing models: simple, robust, and applicable to high-dimensional problems. For a stand-alone model, we provide functions including BayesianFM() and BayesianSDF() to deliver reliable price of risk estimates for both tradable and nontradable factors. For competing factors and possibly nonnested models, we provide functions including continuous_ss_sdf(), continuous_ss_sdf_v2(), and dirac_ss_sdf_pvalue() to analyze high-dimensional models. If you use this package, please cite the paper. We are thankful to Yunan Ding and Jingtong Zhang for their research assistance. Any errors or omissions are the responsibility of the authors.
Author: Svetlana Bryzgalova [aut],
Jiantao Huang [cre],
Christian Julliard [aut]
Maintainer: Jiantao Huang <huangjt@hku.hk>
Diff between BayesianFactorZoo versions 0.0.0.1 dated 2023-11-02 and 0.0.0.2 dated 2023-11-14
BayesianFactorZoo-0.0.0.1/BayesianFactorZoo/R/convergence_test.R |only BayesianFactorZoo-0.0.0.1/BayesianFactorZoo/man/convergence_test.Rd |only BayesianFactorZoo-0.0.0.2/BayesianFactorZoo/DESCRIPTION | 8 ++++---- BayesianFactorZoo-0.0.0.2/BayesianFactorZoo/MD5 | 8 +++----- BayesianFactorZoo-0.0.0.2/BayesianFactorZoo/NAMESPACE | 3 --- BayesianFactorZoo-0.0.0.2/BayesianFactorZoo/build/partial.rdb |binary 6 files changed, 7 insertions(+), 12 deletions(-)
More information about BayesianFactorZoo at CRAN
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Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of sparse and dense matrix classes,
including general, symmetric, triangular, and diagonal matrices
with numeric, logical, or pattern entries. Efficient methods for
operating on such matrices, often wrapping the 'BLAS', 'LAPACK',
and 'SuiteSparse' libraries.
Author: Douglas Bates [aut] ,
Martin Maechler [aut, cre] ,
Mikael Jagan [aut] ,
Timothy A. Davis [ctb] )),
Jens Oehlschlaegel [ctb] ),
Jason Riedy [ctb] and onenormest, Copyright: Regents of the
University of California),
R Core Team [ctb]
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.6-2 dated 2023-11-07 and 1.6-3 dated 2023-11-14
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- build/Matrix.pdf |binary build/stage23.rdb |binary inst/NEWS.Rd | 15 ++++++++++++++- inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/include/Matrix/version.h | 4 ++-- inst/test-tools-Matrix.R | 9 ++++++--- src/version.h | 4 ++-- tests/group-methods.R | 10 ++++++---- 14 files changed, 47 insertions(+), 29 deletions(-)
Title: Plot Positive and Negative Predictive Values for Medical Tests
Description: Functions to plot and help understand positive and negative
predictive values (PPV and NPV), and their relationship with
sensitivity, specificity, and prevalence. See Akobeng, A.K. (2007)
<doi:10.1111/j.1651-2227.2006.00180.x> for a theoretical overview of
the technical concepts and Navarrete et al. (2015) for a practical
explanation about the importance of their understanding
<doi:10.3389/fpsyg.2015.01327>.
Author: Gorka Navarrete [aut, cre]
Maintainer: Gorka Navarrete <gorkang@gmail.com>
Diff between BayesianReasoning versions 0.4.1 dated 2022-01-07 and 0.4.2 dated 2023-11-14
BayesianReasoning-0.4.1/BayesianReasoning/R/BayesianReasoning.R |only BayesianReasoning-0.4.1/BayesianReasoning/man/BayesianReasoning.Rd |only BayesianReasoning-0.4.2/BayesianReasoning/DESCRIPTION | 18 BayesianReasoning-0.4.2/BayesianReasoning/MD5 | 66 BayesianReasoning-0.4.2/BayesianReasoning/NAMESPACE | 16 BayesianReasoning-0.4.2/BayesianReasoning/NEWS.md | 16 BayesianReasoning-0.4.2/BayesianReasoning/R/BayesianReasoning-package.R |only BayesianReasoning-0.4.2/BayesianReasoning/R/PPV_diagnostic_vs_screening.R | 112 BayesianReasoning-0.4.2/BayesianReasoning/R/PPV_heatmap.R | 338 +- BayesianReasoning-0.4.2/BayesianReasoning/R/globals.R | 3 BayesianReasoning-0.4.2/BayesianReasoning/R/helper_functions.R | 1299 ++++------ BayesianReasoning-0.4.2/BayesianReasoning/R/min_possible_prevalence.R | 45 BayesianReasoning-0.4.2/BayesianReasoning/R/plot_cutoff.R |only BayesianReasoning-0.4.2/BayesianReasoning/README.md | 47 BayesianReasoning-0.4.2/BayesianReasoning/build/partial.rdb |only BayesianReasoning-0.4.2/BayesianReasoning/build/vignette.rds |binary BayesianReasoning-0.4.2/BayesianReasoning/inst/doc/PPV_NPV.R | 4 BayesianReasoning-0.4.2/BayesianReasoning/inst/doc/PPV_NPV.html | 448 ++- BayesianReasoning-0.4.2/BayesianReasoning/inst/doc/introduction.R | 30 BayesianReasoning-0.4.2/BayesianReasoning/inst/doc/introduction.Rmd | 39 BayesianReasoning-0.4.2/BayesianReasoning/inst/doc/introduction.html | 566 +++- BayesianReasoning-0.4.2/BayesianReasoning/man/BayesianReasoning-package.Rd |only BayesianReasoning-0.4.2/BayesianReasoning/man/PPV_diagnostic_vs_screening.Rd | 18 BayesianReasoning-0.4.2/BayesianReasoning/man/PPV_heatmap.Rd | 12 BayesianReasoning-0.4.2/BayesianReasoning/man/figures/README_files/figure-markdown_strict/cutoff-1.png |only BayesianReasoning-0.4.2/BayesianReasoning/man/figures/README_files/figure-markdown_strict/line-1.png |binary BayesianReasoning-0.4.2/BayesianReasoning/man/figures/README_files/figure-markdown_strict/line-2-1.png |binary BayesianReasoning-0.4.2/BayesianReasoning/man/figures/README_files/figure-markdown_strict/remove-cutoff-1.png |only BayesianReasoning-0.4.2/BayesianReasoning/man/figures/README_files/figure-markdown_strict/remove-cutoff-2.png |only BayesianReasoning-0.4.2/BayesianReasoning/man/figures/README_files/figure-markdown_strict/remove-cutoff-3.png |only BayesianReasoning-0.4.2/BayesianReasoning/man/figures/README_files/figure-markdown_strict/remove-cutoff-4.png |only BayesianReasoning-0.4.2/BayesianReasoning/man/min_possible_prevalence.Rd | 4 BayesianReasoning-0.4.2/BayesianReasoning/man/plot_cutoff.Rd |only BayesianReasoning-0.4.2/BayesianReasoning/man/remove_layers_cutoff_plot.Rd |only BayesianReasoning-0.4.2/BayesianReasoning/tests/testthat/_snaps |only BayesianReasoning-0.4.2/BayesianReasoning/tests/testthat/test-PPV_diagnostic_vs_screening.R | 16 BayesianReasoning-0.4.2/BayesianReasoning/tests/testthat/test-PPV_heatmap.R | 1017 +++++-- BayesianReasoning-0.4.2/BayesianReasoning/tests/testthat/test-min_possible_prevalence.R | 8 BayesianReasoning-0.4.2/BayesianReasoning/tests/testthat/test-snapshots.R |only BayesianReasoning-0.4.2/BayesianReasoning/vignettes/introduction.Rmd | 39 40 files changed, 2638 insertions(+), 1523 deletions(-)
More information about BayesianReasoning at CRAN
Permanent link
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play data are also available for the Spanish league. Methods for analysis include a population pyramid,
2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps,
team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls and offensive rebounds.
Please see Vinue (2020) <doi:10.1089/big.2018.0124>.
Author: Guillermo Vinue
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between BAwiR versions 1.3 dated 2023-09-26 and 1.3.1 dated 2023-11-14
DESCRIPTION | 14 +++++++------- MD5 | 14 +++++++------- NAMESPACE | 1 - NEWS | 4 ++++ R/get_pop_pyramid.R | 5 ++--- inst/doc/BAwiR.html | 4 ++-- inst/doc/BAwiR_pbp.html | 4 ++-- man/BAwiR-package.Rd | 4 ++-- 8 files changed, 26 insertions(+), 24 deletions(-)
Title: Obtaining Star Databases from Flat Tables
Description: Data in multidimensional systems is obtained from operational
systems and is transformed to adapt it to the new structure.
Frequently, the operations to be performed aim to transform a flat
table into a ROLAP (Relational On-Line Analytical Processing) star
database. The main objective of the package is to allow the definition
of these transformations easily. The implementation of the
multidimensional database obtained can be exported to work with
multidimensional analysis tools on spreadsheets or relational
databases.
Author: Jose Samos [aut, cre, cph]
Maintainer: Jose Samos <jsamos@ugr.es>
Diff between rolap versions 2.3.0 dated 2023-10-16 and 2.4.0 dated 2023-11-14
rolap-2.3.0/rolap/R/dimension_schema.R |only rolap-2.3.0/rolap/R/dimension_table.R |only rolap-2.3.0/rolap/R/fact_schema.R |only rolap-2.3.0/rolap/R/fact_table.R |only rolap-2.3.0/rolap/R/star_operation.R |only rolap-2.3.0/rolap/R/star_schema.R |only rolap-2.3.0/rolap/data/transactions_db.rda |only rolap-2.3.0/rolap/inst/doc/v20-rdbms-dm.R |only rolap-2.3.0/rolap/inst/doc/v20-rdbms-dm.Rmd |only rolap-2.3.0/rolap/inst/doc/v20-rdbms-dm.html |only rolap-2.3.0/rolap/inst/doc/v30-dim-instances.R |only rolap-2.3.0/rolap/inst/doc/v30-dim-instances.Rmd |only rolap-2.3.0/rolap/inst/doc/v30-dim-instances.html |only rolap-2.3.0/rolap/man/get_dimension_name.dimension_schema.Rd |only rolap-2.3.0/rolap/man/transactions_db.Rd |only rolap-2.3.0/rolap/vignettes/v20-rdbms-dm.Rmd |only rolap-2.3.0/rolap/vignettes/v30-dim-instances.Rmd |only rolap-2.4.0/rolap/DESCRIPTION | 12 rolap-2.4.0/rolap/MD5 | 256 rolap-2.4.0/rolap/NAMESPACE | 29 rolap-2.4.0/rolap/NEWS.md | 12 rolap-2.4.0/rolap/R/common.R | 341 - rolap-2.4.0/rolap/R/constellation.R | 16 rolap-2.4.0/rolap/R/data.R | 775 +- rolap-2.4.0/rolap/R/deploy.R |only rolap-2.4.0/rolap/R/flat_table.R | 21 rolap-2.4.0/rolap/R/flat_table_join.R | 600 - rolap-2.4.0/rolap/R/flat_table_transform.R | 2091 +++--- rolap-2.4.0/rolap/R/generic.R | 79 rolap-2.4.0/rolap/R/operations.R |only rolap-2.4.0/rolap/R/refresh.R | 1142 +-- rolap-2.4.0/rolap/R/role_playing.R | 26 rolap-2.4.0/rolap/R/schemas.R |only rolap-2.4.0/rolap/R/star_database.R | 154 rolap-2.4.0/rolap/R/star_database_export.R | 643 + rolap-2.4.0/rolap/R/star_query.R |only rolap-2.4.0/rolap/R/tables_fact_dimension.R |only rolap-2.4.0/rolap/R/update_according_to.R | 2149 +++--- rolap-2.4.0/rolap/R/utils.R |only rolap-2.4.0/rolap/README.md | 288 rolap-2.4.0/rolap/build/vignette.rds |binary rolap-2.4.0/rolap/data/mrs_db.rda |binary rolap-2.4.0/rolap/data/us_census_state.rda |only rolap-2.4.0/rolap/inst/doc/rolap.Rmd | 4 rolap-2.4.0/rolap/inst/doc/rolap.html | 10 rolap-2.4.0/rolap/inst/doc/v05-flat-table-op.html | 12 rolap-2.4.0/rolap/inst/doc/v10-rpd.html | 12 rolap-2.4.0/rolap/inst/doc/v40-refresh.html | 111 rolap-2.4.0/rolap/inst/doc/v50-deploy.R |only rolap-2.4.0/rolap/inst/doc/v50-deploy.Rmd |only rolap-2.4.0/rolap/inst/doc/v50-deploy.html |only rolap-2.4.0/rolap/inst/doc/v60-export.R |only rolap-2.4.0/rolap/inst/doc/v60-export.Rmd |only rolap-2.4.0/rolap/inst/doc/v60-export.html |only rolap-2.4.0/rolap/inst/doc/v70-star_query.R |only rolap-2.4.0/rolap/inst/doc/v70-star_query.Rmd |only rolap-2.4.0/rolap/inst/doc/v70-star_query.html |only rolap-2.4.0/rolap/inst/figures/pivottabler.png |only rolap-2.4.0/rolap/man/add_operation.star_operation.Rd | 2 rolap-2.4.0/rolap/man/add_surrogate_key.dimension_table.Rd | 40 rolap-2.4.0/rolap/man/apply_filter_dimension.Rd |only rolap-2.4.0/rolap/man/apply_select_dimension.Rd |only rolap-2.4.0/rolap/man/apply_select_fact.Rd |only rolap-2.4.0/rolap/man/as_csv_files.Rd |only rolap-2.4.0/rolap/man/as_dm_class.Rd | 13 rolap-2.4.0/rolap/man/as_multistar.Rd |only rolap-2.4.0/rolap/man/as_rdb.Rd |only rolap-2.4.0/rolap/man/as_single_tibble_list.Rd | 9 rolap-2.4.0/rolap/man/as_star_database.Rd | 2 rolap-2.4.0/rolap/man/as_tibble_list.Rd | 7 rolap-2.4.0/rolap/man/as_xlsx_file.Rd |only rolap-2.4.0/rolap/man/cancel_deployment.Rd |only rolap-2.4.0/rolap/man/conform_dimensions.Rd | 36 rolap-2.4.0/rolap/man/constellation.Rd | 10 rolap-2.4.0/rolap/man/db_finest.Rd | 12 rolap-2.4.0/rolap/man/db_summary.Rd | 12 rolap-2.4.0/rolap/man/default_disconnect.Rd |only rolap-2.4.0/rolap/man/define_dimension.Rd | 122 rolap-2.4.0/rolap/man/define_facts.Rd | 166 rolap-2.4.0/rolap/man/deploy.Rd |only rolap-2.4.0/rolap/man/dimension_schema.Rd | 92 rolap-2.4.0/rolap/man/dimension_table.Rd | 46 rolap-2.4.0/rolap/man/draw_tables.Rd |only rolap-2.4.0/rolap/man/fact_schema.Rd | 152 rolap-2.4.0/rolap/man/fact_table.Rd | 2 rolap-2.4.0/rolap/man/filter_dimension.Rd |only rolap-2.4.0/rolap/man/filter_rpd_dimensions.Rd |only rolap-2.4.0/rolap/man/flat_table.Rd | 3 rolap-2.4.0/rolap/man/generate_refresh_sql.Rd |only rolap-2.4.0/rolap/man/generate_table_sql_delete.Rd |only rolap-2.4.0/rolap/man/generate_table_sql_insert.Rd |only rolap-2.4.0/rolap/man/generate_table_sql_update.Rd |only rolap-2.4.0/rolap/man/get_agg_functions.fact_schema.Rd | 36 rolap-2.4.0/rolap/man/get_attribute_names_schema.dimension_schema.Rd | 2 rolap-2.4.0/rolap/man/get_attribute_names_schema.star_schema.Rd | 2 rolap-2.4.0/rolap/man/get_deployment_names.Rd |only rolap-2.4.0/rolap/man/get_dimension_names.Rd | 9 rolap-2.4.0/rolap/man/get_existing_fact_instances.Rd | 2 rolap-2.4.0/rolap/man/get_fact_name.fact_schema.Rd | 36 rolap-2.4.0/rolap/man/get_fact_names.Rd | 3 rolap-2.4.0/rolap/man/get_lookup_tables.Rd | 2 rolap-2.4.0/rolap/man/get_measure_names_schema.fact_schema.Rd | 2 rolap-2.4.0/rolap/man/get_measure_names_schema.star_schema.Rd | 2 rolap-2.4.0/rolap/man/get_new_dimension_instances.Rd | 2 rolap-2.4.0/rolap/man/get_next_operation.star_operation.Rd | 2 rolap-2.4.0/rolap/man/get_nrow_agg.fact_schema.Rd | 36 rolap-2.4.0/rolap/man/get_role_playing_dimension_names.Rd | 13 rolap-2.4.0/rolap/man/get_star_database.Rd | 36 rolap-2.4.0/rolap/man/get_star_query_schema.Rd |only rolap-2.4.0/rolap/man/get_star_schema.Rd | 2 rolap-2.4.0/rolap/man/get_surrogate_key.dimension_table.Rd | 36 rolap-2.4.0/rolap/man/get_table.Rd | 2 rolap-2.4.0/rolap/man/get_table_names.Rd | 3 rolap-2.4.0/rolap/man/get_transformation_code.Rd | 2 rolap-2.4.0/rolap/man/get_transformation_file.Rd | 2 rolap-2.4.0/rolap/man/get_unknown_value_defined.Rd | 2 rolap-2.4.0/rolap/man/get_unknown_values.Rd | 2 rolap-2.4.0/rolap/man/group_dimension_instances.Rd | 3 rolap-2.4.0/rolap/man/group_facts.Rd |only rolap-2.4.0/rolap/man/incremental_refresh.Rd | 15 rolap-2.4.0/rolap/man/interpret_operation_transform_attribute_format.Rd | 2 rolap-2.4.0/rolap/man/is_new_operation.star_operation.Rd | 2 rolap-2.4.0/rolap/man/load_star_database.Rd |only rolap-2.4.0/rolap/man/lookup_table.Rd | 3 rolap-2.4.0/rolap/man/mrs_ft.Rd | 15 rolap-2.4.0/rolap/man/mrs_ft_new.Rd | 15 rolap-2.4.0/rolap/man/multiple_value_key.Rd |only rolap-2.4.0/rolap/man/new_multistar.Rd |only rolap-2.4.0/rolap/man/purge_dimension.Rd |only rolap-2.4.0/rolap/man/purge_dimension_instances.Rd |only rolap-2.4.0/rolap/man/purge_dimension_instances_star_database.Rd |only rolap-2.4.0/rolap/man/refresh_deployments.Rd |only rolap-2.4.0/rolap/man/remove_duplicate_dimension_rows.Rd |only rolap-2.4.0/rolap/man/role_playing_dimension.Rd | 3 rolap-2.4.0/rolap/man/run_query.Rd |only rolap-2.4.0/rolap/man/select_dimension.Rd |only rolap-2.4.0/rolap/man/select_fact.Rd |only rolap-2.4.0/rolap/man/set_attribute_names.Rd | 26 rolap-2.4.0/rolap/man/set_measure_names.Rd | 12 rolap-2.4.0/rolap/man/snake_case_table.dimension_table.Rd | 36 rolap-2.4.0/rolap/man/snake_case_table.fact_table.Rd | 36 rolap-2.4.0/rolap/man/star_database.Rd | 3 rolap-2.4.0/rolap/man/star_operation.Rd | 2 rolap-2.4.0/rolap/man/star_query.Rd |only rolap-2.4.0/rolap/man/star_schema.Rd | 70 rolap-2.4.0/rolap/man/string_to_vector.Rd | 2 rolap-2.4.0/rolap/man/transform_attribute_format.Rd | 8 rolap-2.4.0/rolap/man/update_according_to.Rd | 2 rolap-2.4.0/rolap/man/us_census_state.Rd |only rolap-2.4.0/rolap/man/validate_facts.Rd |only rolap-2.4.0/rolap/man/validate_names.Rd |only rolap-2.4.0/rolap/man/vector_to_string.Rd | 2 rolap-2.4.0/rolap/tests/testthat/test-constellation.R | 6 rolap-2.4.0/rolap/tests/testthat/test-flat_table.R | 28 rolap-2.4.0/rolap/tests/testthat/test-flat_table_update_according_to_file.R | 3313 +++++----- rolap-2.4.0/rolap/tests/testthat/test-refresh.R | 332 - rolap-2.4.0/rolap/tests/testthat/test-star_database.R | 92 rolap-2.4.0/rolap/tests/testthat/test-utils.R |only rolap-2.4.0/rolap/tests/testthat/test-vignette_05.R |only rolap-2.4.0/rolap/tests/testthat/test-vignette_10.R |only rolap-2.4.0/rolap/tests/testthat/test-vignette_30.R |only rolap-2.4.0/rolap/tests/testthat/test-vignette_40.R |only rolap-2.4.0/rolap/tests/testthat/test-vignette_50.R |only rolap-2.4.0/rolap/tests/testthat/test-vignette_60.R |only rolap-2.4.0/rolap/tests/testthat/test-vignette_70.R |only rolap-2.4.0/rolap/vignettes/rolap.Rmd | 4 rolap-2.4.0/rolap/vignettes/v50-deploy.Rmd |only rolap-2.4.0/rolap/vignettes/v60-export.Rmd |only rolap-2.4.0/rolap/vignettes/v70-star_query.Rmd |only 169 files changed, 7348 insertions(+), 6429 deletions(-)
Title: Rank Intraclass Correlation for Clustered Data
Description: Estimates the rank intraclass correlation coefficient (ICC) for clustered continuous and ordinal data. See Tu et al. (2023) <DOI:10.1002/sim.9864> for details.
Author: Shengxin Tu [aut, cre],
Chun Li [aut],
Donglin Zeng [aut],
Bryan Shepherd [aut]
Maintainer: Shengxin Tu <shengxin.tu@vanderbilt.edu>
Diff between rankICC versions 1.0.1 dated 2023-01-24 and 1.0.2 dated 2023-11-14
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/rankICC.R | 2 +- R/rankICC3levels.R | 2 +- man/rankICC.Rd | 2 +- man/rankICC3levels.Rd | 2 +- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: Phase I Shewhart X-Bar Chart
Description: The purpose of 'PH1XBAR' is to build a Phase I Shewhart control chart for the basic Shewhart, the variance components and the ARMA models in R for subgrouped and individual data. More details can be found: Yao and Chakraborti (2020) <doi: 10.1002/qre.2793>, and Yao and Chakraborti (2021) <doi: 10.1080/08982112.2021.1878220>.
Author: Yuhui Yao [aut, cre],
Subha Chakraborti [ctb],
Tyler Thomas [ctb],
Jason Parton [ctb],
Xin Yang [ctb]
Maintainer: Yuhui Yao <yyao17@ua.edu>
Diff between PH1XBAR versions 0.10.1 dated 2021-09-23 and 0.11.1 dated 2023-11-14
PH1XBAR-0.10.1/PH1XBAR/man/00_PH1XBAR-package.Rd |only PH1XBAR-0.11.1/PH1XBAR/ChangeLog | 28 PH1XBAR-0.11.1/PH1XBAR/DESCRIPTION | 10 PH1XBAR-0.11.1/PH1XBAR/MD5 | 40 PH1XBAR-0.11.1/PH1XBAR/NAMESPACE | 32 PH1XBAR-0.11.1/PH1XBAR/R/PH1ARMA.R | 189 ++- PH1XBAR-0.11.1/PH1XBAR/R/PH1XBAR.R | 175 +-- PH1XBAR-0.11.1/PH1XBAR/R/data.R | 64 - PH1XBAR-0.11.1/PH1XBAR/R/getCC.ARMA.R | 1206 ++++++++++------------- PH1XBAR-0.11.1/PH1XBAR/R/getCC.BA.R | 6 PH1XBAR-0.11.1/PH1XBAR/R/getCC.XBAR.R | 112 -- PH1XBAR-0.11.1/PH1XBAR/R/getCC.exact.R | 97 - PH1XBAR-0.11.1/PH1XBAR/R/others.R | 120 +- PH1XBAR-0.11.1/PH1XBAR/README.md | 183 +-- PH1XBAR-0.11.1/PH1XBAR/data/snowfall_data.rda |only PH1XBAR-0.11.1/PH1XBAR/man/PH1ARMA.Rd | 148 +- PH1XBAR-0.11.1/PH1XBAR/man/PH1XBAR-package.Rd |only PH1XBAR-0.11.1/PH1XBAR/man/PH1XBAR.Rd | 10 PH1XBAR-0.11.1/PH1XBAR/man/bore_diameter_data.Rd | 46 PH1XBAR-0.11.1/PH1XBAR/man/getCC.ARMA.Rd | 102 - PH1XBAR-0.11.1/PH1XBAR/man/getCC.XBAR.Rd | 120 +- PH1XBAR-0.11.1/PH1XBAR/man/preston_data.Rd | 18 PH1XBAR-0.11.1/PH1XBAR/man/snowfall_data.Rd |only 23 files changed, 1306 insertions(+), 1400 deletions(-)
Title: Isoscape Computation and Inference of Spatial Origins using
Mixed Models
Description: Building isoscapes using mixed models and inferring the geographic
origin of samples based on their isotopic ratios. This package is essentially a
simplified interface to several other packages which implements a new
statistical framework based on mixed models. It uses 'spaMM' for fitting and
predicting isoscapes, and assigning an organism's origin depending on its
isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for
plotting the maps produced with 'terra' using 'lattice'.
Author: Alexandre Courtiol [aut, cre] ,
Francois Rousset [aut] ,
Marie-Sophie Rohwaeder [aut],
Stephanie Kramer-Schadt [aut]
Maintainer: Alexandre Courtiol <alexandre.courtiol@gmail.com>
Diff between IsoriX versions 0.9.1 dated 2023-09-25 and 0.9.2 dated 2023-11-14
IsoriX-0.9.1/IsoriX/R/interim_avoid_sp.R |only IsoriX-0.9.1/IsoriX/data/PrecipBrickDE.rda |only IsoriX-0.9.1/IsoriX/inst/NEWS.Rd |only IsoriX-0.9.2/IsoriX/DESCRIPTION | 19 IsoriX-0.9.2/IsoriX/MD5 | 109 +- IsoriX-0.9.2/IsoriX/NAMESPACE | 13 IsoriX-0.9.2/IsoriX/NEWS.md |only IsoriX-0.9.2/IsoriX/R/IsoriX-datasets.R | 387 ++++----- IsoriX-0.9.2/IsoriX/R/IsoriX-package.R | 14 IsoriX-0.9.2/IsoriX/R/S4classes.R |only IsoriX-0.9.2/IsoriX/R/calibfit.R | 593 +++++++------- IsoriX-0.9.2/IsoriX/R/create_aliens.R | 140 +-- IsoriX-0.9.2/IsoriX/R/defunct.R | 4 IsoriX-0.9.2/IsoriX/R/getelev.R | 160 +-- IsoriX-0.9.2/IsoriX/R/isofind.R | 353 ++++---- IsoriX-0.9.2/IsoriX/R/isofit.R | 212 ++--- IsoriX-0.9.2/IsoriX/R/isoscape.R | 659 ++++++++------- IsoriX-0.9.2/IsoriX/R/options.R | 36 IsoriX-0.9.2/IsoriX/R/plots.R | 761 +++++++++--------- IsoriX-0.9.2/IsoriX/R/prepcipitate.R | 73 - IsoriX-0.9.2/IsoriX/R/prepraster.R | 220 ++--- IsoriX-0.9.2/IsoriX/R/prepsources.R | 163 ++- IsoriX-0.9.2/IsoriX/R/reexport.R | 13 IsoriX-0.9.2/IsoriX/R/serialize.R |only IsoriX-0.9.2/IsoriX/R/zzz.R | 262 ++++-- IsoriX-0.9.2/IsoriX/inst/WORDLIST |only IsoriX-0.9.2/IsoriX/inst/extdata/PrecipBrickDE.rds |only IsoriX-0.9.2/IsoriX/man/AssignDataAlien.Rd | 54 - IsoriX-0.9.2/IsoriX/man/AssignDataBat.Rd | 2 IsoriX-0.9.2/IsoriX/man/CALIBFIT-class.Rd |only IsoriX-0.9.2/IsoriX/man/CalibDataAlien.Rd | 57 - IsoriX-0.9.2/IsoriX/man/CalibDataBat.Rd | 2 IsoriX-0.9.2/IsoriX/man/CalibDataBat2.Rd | 4 IsoriX-0.9.2/IsoriX/man/CountryBorders.Rd | 2 IsoriX-0.9.2/IsoriX/man/ElevRasterDE.Rd | 5 IsoriX-0.9.2/IsoriX/man/GNIPDataDE.Rd | 2 IsoriX-0.9.2/IsoriX/man/GNIPDataEUagg.Rd | 2 IsoriX-0.9.2/IsoriX/man/ISOFIND-class.Rd |only IsoriX-0.9.2/IsoriX/man/ISOSCAPE-class.Rd |only IsoriX-0.9.2/IsoriX/man/OceanMask.Rd | 3 IsoriX-0.9.2/IsoriX/man/PrecipBrickDE.Rd | 6 IsoriX-0.9.2/IsoriX/man/calibfit.Rd | 244 +++-- IsoriX-0.9.2/IsoriX/man/create_aliens.Rd | 80 - IsoriX-0.9.2/IsoriX/man/getprecip.Rd | 2 IsoriX-0.9.2/IsoriX/man/isofind.Rd | 144 +-- IsoriX-0.9.2/IsoriX/man/isofit.Rd | 26 IsoriX-0.9.2/IsoriX/man/isomultifit.Rd | 23 IsoriX-0.9.2/IsoriX/man/isomultiscape.Rd | 74 - IsoriX-0.9.2/IsoriX/man/isopalette2.Rd | 56 - IsoriX-0.9.2/IsoriX/man/isoscape.Rd | 88 +- IsoriX-0.9.2/IsoriX/man/options.Rd | 1 IsoriX-0.9.2/IsoriX/man/prepcipitate.Rd | 18 IsoriX-0.9.2/IsoriX/man/prepraster.Rd | 90 +- IsoriX-0.9.2/IsoriX/man/prepsources.Rd | 46 - IsoriX-0.9.2/IsoriX/man/serialize.Rd |only IsoriX-0.9.2/IsoriX/tests/local_tests.R |only IsoriX-0.9.2/IsoriX/tests/spelling.R | 7 IsoriX-0.9.2/IsoriX/tests/testthat/setup.R |only IsoriX-0.9.2/IsoriX/tests/testthat/test_RDS.R |only IsoriX-0.9.2/IsoriX/tests/testthat/test_internals.R | 13 IsoriX-0.9.2/IsoriX/tests/testthat/test_na_handling.R | 46 - IsoriX-0.9.2/IsoriX/tests/testthat/test_options.R | 6 IsoriX-0.9.2/IsoriX/tests/testthat/test_tibbles.R | 33 63 files changed, 2872 insertions(+), 2455 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associ [...truncated...]
Author: Moreno Bevilacqua [aut, cre] ,
Victor Morales-Onate [aut] ,
Christian Caamano-Carrillo [aut]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 1.1.4 dated 2023-10-21 and 1.1.5 dated 2023-11-14
DESCRIPTION | 8 +-- MD5 | 30 ++++++------ R/GeoAniso.R | 3 - R/GeoCV.R | 14 ++++-- R/GeoCompositeLik2.R | 9 ++- R/GeoCorrFct.r | 54 +++++++++++++++-------- R/GeoCovariogram.r | 18 ++++--- R/GeoFit.r | 33 ++++++-------- R/GeoFit2.R | 14 +++--- R/GeoLik.r | 105 ++++++++++++++++++++++++++++++++++----------- R/GeoResiduals.r | 17 ++++++- R/GeoTest.r | 37 ++++++++++----- man/GeoCorrFct.Rd | 49 ++++++++++++++++++++- man/GeoTests.Rd | 83 +++++++++++++++++++++++++++++++---- src/CompositeLikelihood2.c | 2 src/Godambe.c | 3 + 16 files changed, 351 insertions(+), 128 deletions(-)
Title: eBird Data Extraction and Processing in R
Description: Extract and process bird sightings records from
eBird (<http://ebird.org>), an online tool for recording bird
observations. Public access to the full eBird database is via the
eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download>
for access), a downloadable text file. This package is an interface to
AWK for extracting data from the EBD based on taxonomic, spatial, or
temporal filters, to produce a manageable file size that can be
imported into R.
Author: Matthew Strimas-Mackey [aut, cre]
,
Eliot Miller [aut],
Wesley Hochachka [aut],
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between auk versions 0.6.0 dated 2022-10-29 and 0.7.0 dated 2023-11-14
auk-0.6.0/auk/R/auk-set-awk-path.R |only auk-0.6.0/auk/R/auk-set-ebd-path.R |only auk-0.6.0/auk/man/auk.Rd |only auk-0.7.0/auk/DESCRIPTION | 10 auk-0.7.0/auk/MD5 | 120 - auk-0.7.0/auk/NAMESPACE | 2 auk-0.7.0/auk/NEWS.md | 9 auk-0.7.0/auk/R/auk-bcr.R | 4 auk-0.7.0/auk/R/auk-ebd.R | 21 auk-0.7.0/auk/R/auk-exotic.R |only auk-0.7.0/auk/R/auk-filter.R | 16 auk-0.7.0/auk/R/auk-package.R | 10 auk-0.7.0/auk/R/auk-rollup.R | 29 auk-0.7.0/auk/R/auk-set-awk-path.r |only auk-0.7.0/auk/R/auk-set-ebd-path.r |only auk-0.7.0/auk/R/auk-unique.R | 4 auk-0.7.0/auk/R/auk-version.R | 6 auk-0.7.0/auk/R/auk-zerofill.R | 8 auk-0.7.0/auk/R/filter-repeat-visits.R | 4 auk-0.7.0/auk/R/format-unmarked-occu.R | 18 auk-0.7.0/auk/R/get-ebird-taxonomy.R | 2 auk-0.7.0/auk/R/read.R | 1 auk-0.7.0/auk/R/utils.R | 1 auk-0.7.0/auk/build/vignette.rds |binary auk-0.7.0/auk/data/ebird_states.rda |binary auk-0.7.0/auk/data/ebird_taxonomy.rda |binary auk-0.7.0/auk/inst/CITATION | 14 auk-0.7.0/auk/inst/doc/auk.Rmd | 4 auk-0.7.0/auk/inst/doc/auk.html | 902 ++++++------- auk-0.7.0/auk/inst/doc/development.html | 176 +- auk-0.7.0/auk/inst/extdata/ebd-rollup-ex.txt | 44 auk-0.7.0/auk/inst/extdata/ebd-sample.txt | 902 +++++-------- auk-0.7.0/auk/inst/extdata/zerofill-ex_ebd.txt | 490 +++---- auk-0.7.0/auk/inst/extdata/zerofill-ex_sampling.txt | 1372 ++++++++++---------- auk-0.7.0/auk/man/auk-package.Rd |only auk-0.7.0/auk/man/auk_bbox.Rd | 1 auk-0.7.0/auk/man/auk_bcr.Rd | 5 auk-0.7.0/auk/man/auk_breeding.Rd | 1 auk-0.7.0/auk/man/auk_complete.Rd | 1 auk-0.7.0/auk/man/auk_country.Rd | 1 auk-0.7.0/auk/man/auk_county.Rd | 1 auk-0.7.0/auk/man/auk_date.Rd | 1 auk-0.7.0/auk/man/auk_distance.Rd | 1 auk-0.7.0/auk/man/auk_duration.Rd | 1 auk-0.7.0/auk/man/auk_exotic.Rd |only auk-0.7.0/auk/man/auk_extent.Rd | 1 auk-0.7.0/auk/man/auk_filter.Rd | 1 auk-0.7.0/auk/man/auk_last_edited.Rd | 1 auk-0.7.0/auk/man/auk_observer.Rd | 1 auk-0.7.0/auk/man/auk_project.Rd | 1 auk-0.7.0/auk/man/auk_protocol.Rd | 1 auk-0.7.0/auk/man/auk_set_awk_path.Rd | 9 auk-0.7.0/auk/man/auk_set_ebd_path.Rd | 10 auk-0.7.0/auk/man/auk_species.Rd | 1 auk-0.7.0/auk/man/auk_state.Rd | 1 auk-0.7.0/auk/man/auk_time.Rd | 1 auk-0.7.0/auk/man/auk_year.Rd | 1 auk-0.7.0/auk/tests/testthat/setup.R |only auk-0.7.0/auk/tests/testthat/test_auk-filter.r | 2 auk-0.7.0/auk/tests/testthat/test_auk-keep-drop.r | 4 auk-0.7.0/auk/tests/testthat/test_auk-rollup.r | 2 auk-0.7.0/auk/tests/testthat/test_auk-split.r | 2 auk-0.7.0/auk/tests/testthat/test_auk-zerofill.r | 4 auk-0.7.0/auk/tests/testthat/test_filters.r | 15 auk-0.7.0/auk/tests/testthat/test_set-env.R |only auk-0.7.0/auk/vignettes/auk.Rmd | 4 66 files changed, 2140 insertions(+), 2104 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-01 0.6.1
2021-11-28 0.4.0
2021-06-23 0.3.0
2021-01-14 0.1.0
Title: Enterprise Streamlined 'shiny' Application Framework Using
'bs4Dash'
Description: A framework for building enterprise, scalable and UI-standardized 'shiny' applications.
It brings enhanced features such as 'bootstrap' v4 <https://getbootstrap.com/docs/4.0/getting-started/introduction/>,
additional and enhanced 'shiny' modules, customizable UI features, as well as an enhanced application file
organization paradigm. This update allows developers to harness the ability to build powerful applications and
enriches the 'shiny' developers' experience when building and maintaining applications.
Author: Mohammed Ali [aut, cre],
Constance Brett [ctb],
Aggregate Genius Inc [spn]
Maintainer: Mohammed Ali <mohammed@aggregate-genius.com>
Diff between periscope2 versions 0.1.3 dated 2023-08-24 and 0.1.4 dated 2023-11-14
periscope2-0.1.3/periscope2/tests/testthat/_snaps/app_reset.md |only periscope2-0.1.4/periscope2/DESCRIPTION | 11 periscope2-0.1.4/periscope2/MD5 | 256 ++++----- periscope2-0.1.4/periscope2/NAMESPACE | 1 periscope2-0.1.4/periscope2/NEWS.md | 43 + periscope2-0.1.4/periscope2/R/announcementConfigurationsAddin.R |only periscope2-0.1.4/periscope2/R/downloadableTable.R | 1 periscope2-0.1.4/periscope2/R/fw_helpers_external.R | 24 periscope2-0.1.4/periscope2/R/generate_template.R | 6 periscope2-0.1.4/periscope2/R/periscope2.R | 2 periscope2-0.1.4/periscope2/R/ui_helpers.R | 44 - periscope2-0.1.4/periscope2/README.md | 46 - periscope2-0.1.4/periscope2/build/vignette.rds |binary periscope2-0.1.4/periscope2/inst/WORDLIST | 9 periscope2-0.1.4/periscope2/inst/doc/announcement-module.R | 6 periscope2-0.1.4/periscope2/inst/doc/announcement-module.Rmd | 3 periscope2-0.1.4/periscope2/inst/doc/announcement-module.html | 8 periscope2-0.1.4/periscope2/inst/doc/announcement_addin.Rmd |only periscope2-0.1.4/periscope2/inst/doc/announcement_addin.html |only periscope2-0.1.4/periscope2/inst/doc/applicationReset-module.R | 6 periscope2-0.1.4/periscope2/inst/doc/applicationReset-module.Rmd | 1 periscope2-0.1.4/periscope2/inst/doc/applicationReset-module.html | 6 periscope2-0.1.4/periscope2/inst/doc/downloadFile-module.R | 6 periscope2-0.1.4/periscope2/inst/doc/downloadFile-module.Rmd | 1 periscope2-0.1.4/periscope2/inst/doc/downloadFile-module.html | 6 periscope2-0.1.4/periscope2/inst/doc/downloadablePlot-module.R | 4 periscope2-0.1.4/periscope2/inst/doc/downloadablePlot-module.Rmd | 1 periscope2-0.1.4/periscope2/inst/doc/downloadablePlot-module.html | 6 periscope2-0.1.4/periscope2/inst/doc/downloadableTable-module.R | 6 periscope2-0.1.4/periscope2/inst/doc/downloadableTable-module.Rmd | 2 periscope2-0.1.4/periscope2/inst/doc/downloadableTable-module.html | 6 periscope2-0.1.4/periscope2/inst/doc/logViewer-module.R | 4 periscope2-0.1.4/periscope2/inst/doc/logViewer-module.Rmd | 1 periscope2-0.1.4/periscope2/inst/doc/logViewer-module.html | 6 periscope2-0.1.4/periscope2/inst/doc/new-application.R | 68 -- periscope2-0.1.4/periscope2/inst/doc/new-application.Rmd | 41 - periscope2-0.1.4/periscope2/inst/doc/new-application.html | 76 +- periscope2-0.1.4/periscope2/inst/fw_templ/global.R | 2 periscope2-0.1.4/periscope2/inst/fw_templ/p_blank/global.R | 4 periscope2-0.1.4/periscope2/inst/fw_templ/p_blank/server_global.R | 2 periscope2-0.1.4/periscope2/inst/fw_templ/p_blank/server_local.R | 2 periscope2-0.1.4/periscope2/inst/fw_templ/p_blank/ui_body.R | 2 periscope2-0.1.4/periscope2/inst/fw_templ/p_blank/ui_footer.R | 8 periscope2-0.1.4/periscope2/inst/fw_templ/p_blank/ui_header.R | 20 periscope2-0.1.4/periscope2/inst/fw_templ/p_blank/ui_left_sidebar.R | 34 - periscope2-0.1.4/periscope2/inst/fw_templ/p_blank/ui_right_sidebar.R | 12 periscope2-0.1.4/periscope2/inst/fw_templ/p_example/custom.css | 58 +- periscope2-0.1.4/periscope2/inst/fw_templ/p_example/global.R | 6 periscope2-0.1.4/periscope2/inst/fw_templ/p_example/periscope_style.yaml | 4 periscope2-0.1.4/periscope2/inst/fw_templ/p_example/plots.R | 47 - periscope2-0.1.4/periscope2/inst/fw_templ/p_example/server_global.R | 12 periscope2-0.1.4/periscope2/inst/fw_templ/p_example/server_local.R | 34 - periscope2-0.1.4/periscope2/inst/fw_templ/p_example/ui_body.R | 38 - periscope2-0.1.4/periscope2/inst/fw_templ/p_example/ui_body_no_left_sidebar.R | 36 - periscope2-0.1.4/periscope2/inst/fw_templ/p_example/ui_footer.R | 6 periscope2-0.1.4/periscope2/inst/fw_templ/p_example/ui_header.R | 20 periscope2-0.1.4/periscope2/inst/fw_templ/p_example/ui_left_sidebar.R | 24 periscope2-0.1.4/periscope2/inst/fw_templ/p_example/ui_right_sidebar.R | 12 periscope2-0.1.4/periscope2/inst/fw_templ/server.R | 8 periscope2-0.1.4/periscope2/inst/fw_templ/ui.R | 2 periscope2-0.1.4/periscope2/inst/fw_templ/www/custom.css | 56 + periscope2-0.1.4/periscope2/inst/fw_templ/www/periscope_style.yaml | 4 periscope2-0.1.4/periscope2/inst/fw_templ/www/widgets |only periscope2-0.1.4/periscope2/inst/rstudio |only periscope2-0.1.4/periscope2/man/announcementConfigurationsAddin.Rd |only periscope2-0.1.4/periscope2/man/get_url_parameters.Rd | 4 periscope2-0.1.4/periscope2/man/set_app_parameters.Rd | 6 periscope2-0.1.4/periscope2/tests/testthat/_snaps/ui_functions.md | 281 +++++++++- periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/global.R | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/program/fxn/plots.R | 40 - periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/program/global.R | 5 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/program/server_global.R | 12 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/program/server_local.R | 12 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/program/ui_body.R | 28 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/program/ui_footer.R | 6 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/program/ui_header.R | 20 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/program/ui_left_sidebar.R | 22 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/program/ui_right_sidebar.R | 12 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/server.R | 8 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/ui.R | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_both_sidebars/www/css/custom.css | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/global.R | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/program/fxn/plots.R | 41 - periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/program/global.R | 5 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/program/server_global.R | 12 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/program/server_local.R | 12 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/program/ui_body.R | 28 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/program/ui_footer.R | 6 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/program/ui_header.R | 20 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/program/ui_left_sidebar.R | 22 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/server.R | 8 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/ui.R | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_left_sidebar/www/css/custom.css | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/global.R | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/program/fxn/plots.R | 39 - periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/program/global.R | 5 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/program/server_global.R | 12 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/program/server_local.R | 8 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/program/ui_body.R | 28 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/program/ui_footer.R | 4 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/program/ui_header.R | 18 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/server.R | 8 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/ui.R | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_no_both_sidebars/www/css/custom.css | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/global.R | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/program/fxn/plots.R | 41 - periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/program/global.R | 5 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/program/server_global.R | 12 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/program/server_local.R | 12 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/program/ui_body.R | 28 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/program/ui_footer.R | 4 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/program/ui_header.R | 20 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/program/ui_right_sidebar.R | 10 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/server.R | 8 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/ui.R | 2 periscope2-0.1.4/periscope2/tests/testthat/sample_app_right_sidebar/www/css/custom.css | 2 periscope2-0.1.4/periscope2/tests/testthat/test_addins.R |only periscope2-0.1.4/periscope2/tests/testthat/test_app_reset.R | 6 periscope2-0.1.4/periscope2/tests/testthat/test_create_application.R | 4 periscope2-0.1.4/periscope2/tests/testthat/test_ui_functions.R | 126 ++++ periscope2-0.1.4/periscope2/vignettes/announcement-module.Rmd | 3 periscope2-0.1.4/periscope2/vignettes/announcement_addin.Rmd |only periscope2-0.1.4/periscope2/vignettes/applicationReset-module.Rmd | 1 periscope2-0.1.4/periscope2/vignettes/downloadFile-module.Rmd | 1 periscope2-0.1.4/periscope2/vignettes/downloadablePlot-module.Rmd | 1 periscope2-0.1.4/periscope2/vignettes/downloadableTable-module.Rmd | 2 periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_1.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_10.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_11.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_12.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_2.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_4.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_5.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_6.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_7.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_8.png |only periscope2-0.1.4/periscope2/vignettes/figures/add_ins_announce_9.png |only periscope2-0.1.4/periscope2/vignettes/logViewer-module.Rmd | 1 periscope2-0.1.4/periscope2/vignettes/new-application.Rmd | 41 - 139 files changed, 1393 insertions(+), 849 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-08 1.2.0
2019-03-18 1.1.0
2018-05-08 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-24 4.16.0
2022-09-20 4.15.1
2021-12-16 4.10.50
2021-11-29 4.10.10
2021-07-04 4.9.0
2021-05-31 4.8.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-05 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-30 0.0.0.3
2021-07-22 0.0.0.2
2021-07-01 0.0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-06 0.1.4
2023-01-11 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-05 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-21 2.0.1
2023-09-13 2.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-30 0.2.1
2023-08-25 0.2.0
2023-05-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-09 0.8.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-28 0.2.6
2022-02-13 0.2.4
2019-12-12 0.2.3
2019-05-02 0.2.2
2018-12-18 0.2.0
2018-11-18 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-06-23 1.0.4
2022-09-15 1.0.3
2022-08-23 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-28 0.5.0
2023-08-13 0.4.0
2023-04-12 0.3.0
2023-01-12 0.2.1
2023-01-06 0.2.0
2022-11-23 0.1.1
2022-10-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-27 1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-20 0.1.8.2
2022-03-09 0.1.6.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-23 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-04 1.0.1
2019-05-28 1.0.0
2019-05-23 0.4.0
2016-12-12 0.3.0
2016-07-03 0.2.0
2015-03-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-18 3.1
2016-08-18 3.0
2016-07-14 2.0
2016-02-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-07 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-04 0.2.2
2022-02-07 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-05 1.0.0
Title: Automatically Search Errors or Warnings
Description: Provides environment hooks that obtain errors and warnings which
occur during the execution of code to automatically search for solutions.
Author: James Balamuta [aut, cre, cph]
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between errorist versions 0.1.1 dated 2023-03-05 and 0.1.2 dated 2023-11-14
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++-------- NEWS.md | 32 +++++++++++++++++++++++--------- R/handlers.R | 13 +++++++++---- README.md | 7 +++---- build/vignette.rds |binary inst/doc/working-with-errorist.R | 4 ++-- inst/doc/working-with-errorist.html | 28 ++++++++++++++-------------- man/errorist-package.Rd | 5 +++-- 9 files changed, 68 insertions(+), 48 deletions(-)
Title: Compare Data Frames
Description: A toolbox for comparing two data frames. This package is defunct. I recommend you use the "versus" package instead.
Author: Ryan Dickerson [aut, cre]
Maintainer: Ryan Dickerson <fresh.tent5866@fastmail.com>
Diff between tablecompare versions 0.1.0 dated 2022-06-21 and 0.1.1 dated 2023-11-14
tablecompare-0.1.0/tablecompare/tests |only tablecompare-0.1.1/tablecompare/DESCRIPTION | 13 - tablecompare-0.1.1/tablecompare/MD5 | 20 +-- tablecompare-0.1.1/tablecompare/NAMESPACE | 9 + tablecompare-0.1.1/tablecompare/R/compare.R | 5 tablecompare-0.1.1/tablecompare/R/draft_funs.R |only tablecompare-0.1.1/tablecompare/R/internal-helpers.R | 11 + tablecompare-0.1.1/tablecompare/R/tablecompare.R | 7 - tablecompare-0.1.1/tablecompare/README.md | 125 ------------------- tablecompare-0.1.1/tablecompare/man/tblcompare.Rd | 6 10 files changed, 51 insertions(+), 145 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430>.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb]
Maintainer: Samuel Marsh <samuel.marsh@childrens.harvard.edu>
Diff between scCustomize versions 1.1.3 dated 2023-07-19 and 2.0.0 dated 2023-11-14
DESCRIPTION | 18 MD5 | 149 ++--- NAMESPACE | 16 NEWS.md | 62 ++ R/Color_Palettes.R | 24 R/Data.R | 53 + R/Internal_Utilities.R | 975 ++++++++++++++++++++++++++++++---- R/LIGER_Plotting.R | 28 R/LIGER_Utilities.R | 93 +-- R/Nebulosa_Plotting.R | 18 R/Object_Utilities.R | 425 ++++++++++++++ R/Plotting_Utilities.R | 253 ++++++++ R/QC_Plotting_Seq_10X.R | 437 +++++++++++---- R/QC_Plotting_Seurat.R | 257 +++++++- R/Read_&_Write_Data.R | 244 ++++---- R/Seurat_Iterative_Plotting.R | 265 +++++---- R/Seurat_Plotting.R | 558 ++++++++++++++++--- R/Statistics.R | 283 +++++++-- R/Statistics_Plotting.R | 37 - R/Utilities.R | 183 +----- R/sysdata.rda |binary R/zzz.R | 6 build/partial.rdb |binary data/ieg_gene_list.rda |only data/msigdb_qc_gene_list.rda |only man/Add_Cell_QC_Metrics.Rd |only man/Add_Mito_Ribo_LIGER.Rd | 4 man/Add_Mito_Ribo_Seurat.Rd | 9 man/Add_Top_Gene_Pct_Seurat.Rd |only man/Barcode_Plot.Rd |only man/Case_Check.Rd | 5 man/CellBender_Diff_Plot.Rd | 4 man/CellBender_Feature_Diff.Rd | 12 man/Cell_Highlight_Plot.Rd | 4 man/Cluster_Highlight_Plot.Rd | 4 man/DotPlot_scCustom.Rd | 4 man/Extract_Sample_Meta.Rd | 6 man/FeaturePlot_DualAssay.Rd | 7 man/FeaturePlot_scCustom.Rd | 11 man/FeatureScatter_scCustom.Rd |only man/Iterate_Barcode_Rank_Plot.Rd |only man/Iterate_DimPlot_bySample.Rd | 3 man/Iterate_FeaturePlot_scCustom.Rd | 7 man/Iterate_VlnPlot_scCustom.Rd | 7 man/Liger_to_Seurat.Rd | 2 man/MAD_Stats.Rd |only man/Median_Stats.Rd | 3 man/Merge_Seurat_List.Rd | 2 man/Meta_Highlight_Plot.Rd | 4 man/Percent_Expressing.Rd | 7 man/QC_Histogram.Rd |only man/QC_Plot_UMIvsGene.Rd | 4 man/QC_Plots_Combined_Vln.Rd | 3 man/QC_Plots_Complexity.Rd | 3 man/QC_Plots_Feature.Rd | 3 man/QC_Plots_Genes.Rd | 3 man/QC_Plots_Mito.Rd | 3 man/QC_Plots_UMIs.Rd | 3 man/Read_Metrics_10X.Rd | 3 man/Seq_QC_Plot_Alignment_Combined.Rd | 3 man/Seq_QC_Plot_Antisense.Rd | 3 man/Seq_QC_Plot_Basic_Combined.Rd | 3 man/Seq_QC_Plot_Exonic.Rd | 3 man/Seq_QC_Plot_Genes.Rd | 3 man/Seq_QC_Plot_Genome.Rd | 3 man/Seq_QC_Plot_Intergenic.Rd | 3 man/Seq_QC_Plot_Intronic.Rd | 3 man/Seq_QC_Plot_Number_Cells.Rd | 3 man/Seq_QC_Plot_Reads_in_Cells.Rd | 3 man/Seq_QC_Plot_Reads_per_Cell.Rd | 3 man/Seq_QC_Plot_Saturation.Rd | 3 man/Seq_QC_Plot_Total_Genes.Rd | 3 man/Seq_QC_Plot_Transcriptome.Rd | 3 man/Seq_QC_Plot_UMIs.Rd | 3 man/Split_FeatureScatter.Rd | 9 man/VariableFeaturePlot_scCustom.Rd | 4 man/VlnPlot_scCustom.Rd | 9 man/ieg_gene_list.Rd |only man/msigdb_qc_gene_list.Rd |only man/scCustomize-package.Rd | 3 man/scCustomize_Palette.Rd | 9 81 files changed, 3648 insertions(+), 945 deletions(-)
Title: Automatic Linear and Logistic Regression and Survival Analysis
Description: Make summary tables for descriptive statistics and select explanatory variables
automatically in various regression models. Support linear models, generalized linear
models and cox-proportional hazard models. Generate publication-ready tables summarizing
result of regression analysis and plots. The tables and plots can be exported in "HTML",
"pdf('LaTex')", "docx('MS Word')" and "pptx('MS Powerpoint')" documents.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between autoReg versions 0.3.2 dated 2023-04-11 and 0.3.3 dated 2023-11-14
DESCRIPTION | 6 MD5 | 33 +- NEWS | 7 R/expectedPlot.R | 19 - R/loglogplot.R | 9 build/vignette.rds |binary inst/doc/Automatic_Regression_Modeling.R | 4 inst/doc/Automatic_Regression_Modeling.html | 162 +++++----- inst/doc/Bootstrap_Prediction.R | 2 inst/doc/Bootstrap_Prediction.html | 120 +++---- inst/doc/Getting_started.R | 4 inst/doc/Getting_started.html | 260 +++++++--------- inst/doc/Statiastical_test_in_gaze.R | 2 inst/doc/Statiastical_test_in_gaze.html | 452 ++++++++++++++-------------- inst/doc/Survival.R | 6 inst/doc/Survival.html | 328 ++++++++++---------- man/label_parse.Rd |only man/loglogplot.Rd | 1 18 files changed, 716 insertions(+), 699 deletions(-)