Title: Metropolis Sampler and Supporting Functions for Estimating
Animal Movement from Archival Tags and Satellite Fixes
Description: Data handling and estimation functions for animal movement
estimation from archival or satellite tags. Helper functions are included
for making image summaries binned by time interval from Markov Chain Monte Carlo
simulations.
Author: Michael D. Sumner [aut, cre],
Simon Wotherspoon [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between tripEstimation versions 0.0-44 dated 2016-01-31 and 0.0-45 dated 2023-04-18
tripEstimation-0.0-44/tripEstimation/R/get.pimgs.R |only tripEstimation-0.0-44/tripEstimation/R/get.sst.R |only tripEstimation-0.0-44/tripEstimation/TODO |only tripEstimation-0.0-44/tripEstimation/man/get.sst.Rd |only tripEstimation-0.0-45/tripEstimation/DESCRIPTION | 14 tripEstimation-0.0-45/tripEstimation/MD5 | 120 - tripEstimation-0.0-45/tripEstimation/NAMESPACE | 175 +- tripEstimation-0.0-45/tripEstimation/NEWS | 992 ++++++------ tripEstimation-0.0-45/tripEstimation/R/as.image.pimg.R | 14 tripEstimation-0.0-45/tripEstimation/R/as.local.pimg.R | 20 tripEstimation-0.0-45/tripEstimation/R/as.matrix.pimg.R | 26 tripEstimation-0.0-45/tripEstimation/R/astro.R | 310 +-- tripEstimation-0.0-45/tripEstimation/R/behav.bin.R | 40 tripEstimation-0.0-45/tripEstimation/R/bin.pimg.R | 100 - tripEstimation-0.0-45/tripEstimation/R/bits.R | 28 tripEstimation-0.0-45/tripEstimation/R/bmvnorm.proposal.R | 80 tripEstimation-0.0-45/tripEstimation/R/chain.dim.R | 18 tripEstimation-0.0-45/tripEstimation/R/chain.read.R | 28 tripEstimation-0.0-45/tripEstimation/R/chain.write.R | 64 tripEstimation-0.0-45/tripEstimation/R/chunk.bin.R | 50 tripEstimation-0.0-45/tripEstimation/R/combine.R | 38 tripEstimation-0.0-45/tripEstimation/R/coords.pimg.R | 12 tripEstimation-0.0-45/tripEstimation/R/elevation.R | 36 tripEstimation-0.0-45/tripEstimation/R/get.mask.R | 42 tripEstimation-0.0-45/tripEstimation/R/initialize.x.R | 368 ++-- tripEstimation-0.0-45/tripEstimation/R/julday.R | 30 tripEstimation-0.0-45/tripEstimation/R/metropolis.R | 224 +- tripEstimation-0.0-45/tripEstimation/R/metropolis0.R | 250 +-- tripEstimation-0.0-45/tripEstimation/R/mkCalibration.R | 96 - tripEstimation-0.0-45/tripEstimation/R/mkLookup.R | 76 tripEstimation-0.0-45/tripEstimation/R/mkSmall.R | 22 tripEstimation-0.0-45/tripEstimation/R/mvnorm.proposal.R | 64 tripEstimation-0.0-45/tripEstimation/R/norm.proposal.R | 66 tripEstimation-0.0-45/tripEstimation/R/old.metropolis.R | 656 +++---- tripEstimation-0.0-45/tripEstimation/R/picksegs.R | 72 tripEstimation-0.0-45/tripEstimation/R/pimg.R | 24 tripEstimation-0.0-45/tripEstimation/R/pimg.list.R | 52 tripEstimation-0.0-45/tripEstimation/R/satellite.model.R | 218 +- tripEstimation-0.0-45/tripEstimation/R/solar.R | 148 - tripEstimation-0.0-45/tripEstimation/R/solar.model.R | 514 +++--- tripEstimation-0.0-45/tripEstimation/R/unzipper.R | 66 tripEstimation-0.0-45/tripEstimation/R/zzz.r | 8 tripEstimation-0.0-45/tripEstimation/README.md | 25 tripEstimation-0.0-45/tripEstimation/inst/CITATION | 60 tripEstimation-0.0-45/tripEstimation/man/as.image.pimg.Rd | 96 - tripEstimation-0.0-45/tripEstimation/man/astro.Rd | 243 +- tripEstimation-0.0-45/tripEstimation/man/behav.bin.Rd | 76 tripEstimation-0.0-45/tripEstimation/man/bits.Rd | 96 - tripEstimation-0.0-45/tripEstimation/man/chain.read.Rd | 73 tripEstimation-0.0-45/tripEstimation/man/elevation.Rd | 47 tripEstimation-0.0-45/tripEstimation/man/get.mask.Rd | 182 +- tripEstimation-0.0-45/tripEstimation/man/initialize.x.Rd | 129 - tripEstimation-0.0-45/tripEstimation/man/julday.Rd | 46 tripEstimation-0.0-45/tripEstimation/man/metropolis.Rd | 134 - tripEstimation-0.0-45/tripEstimation/man/mkCalibration.Rd | 60 tripEstimation-0.0-45/tripEstimation/man/mkLookup.Rd | 66 tripEstimation-0.0-45/tripEstimation/man/norm.proposal.Rd | 96 - tripEstimation-0.0-45/tripEstimation/man/old.metropolis.Rd | 178 +- tripEstimation-0.0-45/tripEstimation/man/pick.Rd | 110 - tripEstimation-0.0-45/tripEstimation/man/pimg.list.Rd | 68 tripEstimation-0.0-45/tripEstimation/man/satellite.model.Rd | 104 - tripEstimation-0.0-45/tripEstimation/man/solar.Rd | 56 tripEstimation-0.0-45/tripEstimation/man/solar.model.Rd | 216 +- 63 files changed, 3677 insertions(+), 3645 deletions(-)
More information about tripEstimation at CRAN
Permanent link
Title: Power Analyses for Interaction Effects in Cross-Sectional
Regressions
Description: Power analysis for regression models which test the interaction of
two independent variables on a single dependent variable. Includes options
for continuous, binary, or ordinal variables, as well as correlated
interacting variables. Also includes options to specify variable reliability.
Power analyses can be done either analytically or via simulation. Includes
tools for simulating single data sets and visualizing power analysis results.
The primary functions are power_interaction_r2() and power_interaction().
Please cite as: Baranger DAA, Finsaas MC, Goldstein BL, Vize CE, Lynam DR,
Olino TM (2022). "Tutorial: Power analyses for interaction effects in
cross-sectional regressions." <doi:10.31234/osf.io/5ptd7>.
Author: David Baranger [aut, cre] ,
Brandon Goldstein [ctb],
Megan Finsaas [ctb],
Thomas Olino [ctb],
Colin Vize [ctb],
Don Lynam [ctb]
Maintainer: David Baranger <dbaranger@gmail.com>
Diff between InteractionPoweR versions 0.2.0 dated 2022-10-20 and 0.2.1 dated 2023-04-18
DESCRIPTION | 10 +-- MD5 | 22 +++---- NEWS.md | 11 +++ R/generate_interaction.R | 40 ++++++++++++- R/plot_interaction.R | 126 +++++++++++++++++++++++++++---------------- R/power_interaction.R | 17 ++++- R/power_interaction_r2.R | 23 ++++--- R/test_interaction.R | 4 + R/transformation_functions.R | 52 ++++++++++++++++- inst/CITATION | 21 ++----- man/generate_interaction.Rd | 11 +++ man/power_interaction.Rd | 11 +++ 12 files changed, 246 insertions(+), 102 deletions(-)
More information about InteractionPoweR at CRAN
Permanent link
Title: Diagnostics for Pharmacometric Models
Description: Diagnostics for non-linear mixed-effects (population)
models from 'NONMEM' <https://www.iconplc.com/solutions/technologies/nonmem/>.
'xpose' facilitates data import, creation of numerical run summary
and provide 'ggplot2'-based graphics for data exploration and model
diagnostics.
Author: Benjamin Guiastrennec [aut, cre, cph],
Andrew C. Hooker [aut, cph],
Sebastian Ueckert [aut, cph],
Mike K. Smith [ctb],
Mats O. Karlsson [aut, cph]
Maintainer: Benjamin Guiastrennec <guiastrennec@gmail.com>
Diff between xpose versions 0.4.15 dated 2023-02-25 and 0.4.16 dated 2023-04-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 3 +++ inst/doc/access_xpdb_data.html | 36 ++++++++++++++++++------------------ inst/doc/customize_plots.html | 2 +- inst/doc/import_model_outputs.html | 2 +- inst/doc/introduction.html | 2 +- inst/doc/multiple_pages.html | 2 +- inst/doc/vpc.html | 2 +- tests/testthat/test-xpose_save.R | 4 ++-- 10 files changed, 41 insertions(+), 38 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired by the end of 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] ,
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Daniel Baston [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.6-5 dated 2023-03-02 and 1.6-6 dated 2023-04-18
DESCRIPTION | 8 MD5 | 20 - NEWS.md | 6 build/vignette.rds |binary configure | 18 - inst/SVN_VERSION | 2 inst/doc/CRS_projections_transformations.R | 4 inst/doc/CRS_projections_transformations.html | 369 ++++++++++++++++---------- inst/doc/OGR_shape_encoding.pdf |binary inst/doc/PROJ6_GDAL3.html | 116 +++++--- src/Makevars.ucrt | 3 11 files changed, 340 insertions(+), 206 deletions(-)
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Author: Karl W Broman <broman@wisc.edu> and Hao Wu, with
ideas from Gary Churchill and Saunak Sen and contributions from
Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr
Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron
Wol [...truncated...]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl versions 1.58 dated 2023-01-07 and 1.60 dated 2023-04-18
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++-------------------- NEWS.md | 13 +++++++++++++ R/addqtl.R | 6 ++++-- build/vignette.rds |binary data/badorder.RData |binary data/bristle3.RData |binary data/bristleX.RData |binary data/fake.4way.RData |binary data/fake.bc.RData |binary data/fake.f2.RData |binary data/hyper.RData |binary data/listeria.RData |binary data/locations.RData |binary data/map10.RData |binary data/mapthis.RData |binary data/multitrait.RData |binary inst/CITATION | 10 +++++----- inst/doc/bcsft.pdf |binary inst/doc/rqtltour.pdf |binary inst/doc/rqtltour2.pdf |binary 21 files changed, 46 insertions(+), 31 deletions(-)
Title: Easily Work with 'Font Awesome' Icons
Description: Easily and flexibly insert 'Font Awesome' icons into 'R Markdown'
documents and 'Shiny' apps. These icons can be inserted into HTML content
through inline 'SVG' tags or 'i' tags. There is also a utility function for
exporting 'Font Awesome' icons as 'PNG' images for those situations where
raster graphics are needed.
Author: Richard Iannone [aut, cre] ,
Christophe Dervieux [ctb] ,
Winston Chang [ctb],
Dave Gandy [ctb, cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>
Diff between fontawesome versions 0.5.0 dated 2023-01-25 and 0.5.1 dated 2023-04-18
DESCRIPTION | 14 +++---- LICENSE | 4 +- MD5 | 40 ++++++++++----------- NEWS.md | 6 ++- R/fa_brands.R | 2 - R/fa_version.R | 2 - R/sysdata.rda |binary README.md | 16 +++++--- inst/fontawesome/css/all.css | 17 ++++++-- inst/fontawesome/css/all.min.css | 9 +++- inst/fontawesome/css/v4-shims.css | 4 +- inst/fontawesome/css/v4-shims.min.css | 4 +- inst/fontawesome/webfonts/fa-brands-400.ttf |binary inst/fontawesome/webfonts/fa-brands-400.woff2 |binary inst/fontawesome/webfonts/fa-regular-400.ttf |binary inst/fontawesome/webfonts/fa-regular-400.woff2 |binary inst/fontawesome/webfonts/fa-solid-900.ttf |binary inst/fontawesome/webfonts/fa-solid-900.woff2 |binary inst/fontawesome/webfonts/fa-v4compatibility.ttf |binary inst/fontawesome/webfonts/fa-v4compatibility.woff2 |binary tests/testthat/test-fa_icon.R | 4 +- 21 files changed, 71 insertions(+), 51 deletions(-)
Title: Compound Poisson Linear Models
Description: Likelihood-based and Bayesian methods for various compound Poisson linear models based on Zhang, Yanwei (2013) <https://link.springer.com/article/10.1007/s11222-012-9343-7>.
Author: Yanwei Zhang
Maintainer: Yanwei (Wayne) Zhang <actuary_zhang@hotmail.com>
Diff between cplm versions 0.7-10 dated 2022-04-25 and 0.7-11 dated 2023-04-18
DESCRIPTION | 6 MD5 | 16 - NEWS | 476 +++++++++++++++++++++++------------------------ data/AutoClaim.RData |binary data/ClaimTriangle.RData |binary data/FineRoot.RData |binary src/bcplm.c | 21 -- src/common.h | 27 +- src/cpglmm.c | 32 +-- 9 files changed, 281 insertions(+), 297 deletions(-)
Title: Tools for Voice Analysis, Speaker Recognition and Mood Inference
Description: Tools for voice analysis, speaker recognition and mood inference.
Gathers 'R' and 'Python' tools to solve problems concerning voice and audio
in general.
Author: Zabala Filipe J. [cre, aut]
Maintainer: Zabala Filipe J. <filipezabala@gmail.com>
Diff between voice versions 0.4.17 dated 2023-03-14 and 0.4.20 dated 2023-04-18
voice-0.4.17/voice/R/conv.R |only voice-0.4.17/voice/R/conv_df.R |only voice-0.4.17/voice/R/conv_mc.R |only voice-0.4.17/voice/R/extract_features_py.R |only voice-0.4.17/voice/man/conv.Rd |only voice-0.4.17/voice/man/conv_df.Rd |only voice-0.4.17/voice/man/conv_mc.Rd |only voice-0.4.17/voice/man/extract_features_py.Rd |only voice-0.4.17/voice/tests |only voice-0.4.20/voice/DESCRIPTION | 8 voice-0.4.20/voice/MD5 | 126 ++--- voice-0.4.20/voice/NAMESPACE | 8 voice-0.4.20/voice/NEWS.md | 46 +- voice-0.4.20/voice/R/audio_time.R | 2 voice-0.4.20/voice/R/diarize.R | 61 +- voice-0.4.20/voice/R/duration.R | 3 voice-0.4.20/voice/R/enrich_rttm.R | 10 voice-0.4.20/voice/R/expand_model.R | 3 voice-0.4.20/voice/R/extract_features.R | 310 +++++++++---- voice-0.4.20/voice/R/feat_summary.R | 57 +- voice-0.4.20/voice/R/get_bit.R | 2 voice-0.4.20/voice/R/get_dur.R | 2 voice-0.4.20/voice/R/get_left.R | 2 voice-0.4.20/voice/R/get_right.R | 2 voice-0.4.20/voice/R/get_samp.rate.R | 2 voice-0.4.20/voice/R/get_tbeg.R | 2 voice-0.4.20/voice/R/get_tdur.R | 2 voice-0.4.20/voice/R/interp.R |only voice-0.4.20/voice/R/interp_df.R |only voice-0.4.20/voice/R/interp_mc.R |only voice-0.4.20/voice/R/is_mono.R | 6 voice-0.4.20/voice/R/notes.R | 14 voice-0.4.20/voice/R/notes_freq.R | 7 voice-0.4.20/voice/R/read_rttm.R | 2 voice-0.4.20/voice/R/rm0.R | 3 voice-0.4.20/voice/R/smooth_df.R | 16 voice-0.4.20/voice/R/splitw.R | 68 +-- voice-0.4.20/voice/R/tag.R | 56 +- voice-0.4.20/voice/R/write_list.R | 7 voice-0.4.20/voice/inst/doc/voicegnette_R.R | 68 ++- voice-0.4.20/voice/inst/doc/voicegnette_R.Rmd | 90 +++- voice-0.4.20/voice/inst/doc/voicegnette_R.html | 303 +++++++------ voice-0.4.20/voice/man/audio_time.Rd | 2 voice-0.4.20/voice/man/diarize.Rd | 23 - voice-0.4.20/voice/man/duration.Rd | 4 voice-0.4.20/voice/man/enrich_rttm.Rd | 8 voice-0.4.20/voice/man/expand_model.Rd | 2 voice-0.4.20/voice/man/extract_features.Rd | 83 ++- voice-0.4.20/voice/man/feat_summary.Rd | 58 +- voice-0.4.20/voice/man/get_bit.Rd | 2 voice-0.4.20/voice/man/get_dur.Rd | 2 voice-0.4.20/voice/man/get_left.Rd | 2 voice-0.4.20/voice/man/get_right.Rd | 2 voice-0.4.20/voice/man/get_samp.rate.Rd | 2 voice-0.4.20/voice/man/get_tbeg.Rd | 2 voice-0.4.20/voice/man/get_tdur.Rd | 2 voice-0.4.20/voice/man/interp.Rd |only voice-0.4.20/voice/man/interp_df.Rd |only voice-0.4.20/voice/man/interp_mc.Rd |only voice-0.4.20/voice/man/is_mono.Rd | 8 voice-0.4.20/voice/man/notes.Rd | 12 voice-0.4.20/voice/man/notes_freq.Rd | 5 voice-0.4.20/voice/man/rm0.Rd | 2 voice-0.4.20/voice/man/smooth_df.Rd | 19 voice-0.4.20/voice/man/splitw.Rd | 28 - voice-0.4.20/voice/man/tag.Rd | 56 +- voice-0.4.20/voice/man/write_list.Rd | 9 voice-0.4.20/voice/vignettes/index.html | 555 +++++++++++++++---------- voice-0.4.20/voice/vignettes/voicegnette_R.Rmd | 90 +++- 69 files changed, 1391 insertions(+), 875 deletions(-)
Title: A 'Shiny' Application for Inspecting Structural Topic Models
Description: This app enables interactive validation, interpretation and visualization of structural topic models from the 'stm' package by Roberts and others (2014) <doi:10.1111/ajps.12103>. It also includes helper functions for model diagnostics and extracting data from effect estimates.
Author: Carsten Schwemmer [aut, cre] ,
Jonne Guyt [ctb]
Maintainer: Carsten Schwemmer <c.schwem2er@gmail.com>
Diff between stminsights versions 0.4.1 dated 2021-03-29 and 0.4.2 dated 2023-04-18
DESCRIPTION | 20 +-- MD5 | 34 ++--- NAMESPACE | 4 NEWS.md | 194 +++++++++++++++--------------- R/run_app.R | 170 +++++++++++++------------- R/stm_diag.R | 192 +++++++++++++++-------------- R/stm_effects.R | 316 ++++++++++++++++++++++++------------------------- R/stm_network.R | 232 ++++++++++++++++++----------------- README.md | 32 ++-- build/vignette.rds |binary inst/doc/intro.R | 14 +- inst/doc/intro.Rmd | 270 +++++++++++++++++++++-------------------- inst/doc/intro.html | 289 +++++++++++++++++++++++++------------------- man/get_diag.Rd | 10 + man/get_effects.Rd | 8 - man/get_network.Rd | 8 - man/run_stminsights.Rd | 8 - vignettes/intro.Rmd | 270 +++++++++++++++++++++-------------------- 18 files changed, 1076 insertions(+), 995 deletions(-)
Title: Construct Nomograms for Competing Risks Regression Models
Description: Nomograms are constructed to predict the cumulative incidence
rate which is calculated after adjusting for competing causes to the event of interest.
K-fold cross-validation is implemented to validate predictive accuracy using a competing-risk version of the concordance index.
Methods are as described in: Kattan MW, Heller G,
Brennan MF (2003) <doi:10.1002/sim.1574>.
Author: Michael Kattan [aut],
Changhong Yu [aut],
Xinge Ji [aut],
Zajichek Alex [cre]
Maintainer: Zajichek Alex <zajicha2@ccf.org>
Diff between QHScrnomo versions 2.2.0 dated 2021-11-05 and 3.0.0 dated 2023-04-18
QHScrnomo-2.2.0/QHScrnomo/COPYING |only QHScrnomo-2.2.0/QHScrnomo/NEWS |only QHScrnomo-2.2.0/QHScrnomo/R/Design.levels.R |only QHScrnomo-2.2.0/QHScrnomo/R/Newlabels.cmprsk.R |only QHScrnomo-2.2.0/QHScrnomo/R/Newlevels.cmprsk.R |only QHScrnomo-2.2.0/QHScrnomo/R/QHScrnomo-package.R |only QHScrnomo-2.2.0/QHScrnomo/R/anova.cmprsk.R |only QHScrnomo-2.2.0/QHScrnomo/R/crr.fit.R |only QHScrnomo-2.2.0/QHScrnomo/R/nomo2.crr.R |only QHScrnomo-2.2.0/QHScrnomo/R/nomogram.crr.R |only QHScrnomo-2.2.0/QHScrnomo/R/nomogram.mk6.R |only QHScrnomo-2.2.0/QHScrnomo/R/oldUnclass.R |only QHScrnomo-2.2.0/QHScrnomo/R/pred.ci.R |only QHScrnomo-2.2.0/QHScrnomo/R/pred.crr.R |only QHScrnomo-2.2.0/QHScrnomo/R/pred2.crr.R |only QHScrnomo-2.2.0/QHScrnomo/R/pred3.crr.R |only QHScrnomo-2.2.0/QHScrnomo/R/predict.Design.R |only QHScrnomo-2.2.0/QHScrnomo/R/predict.cmprsk.R |only QHScrnomo-2.2.0/QHScrnomo/R/sas.cmprsk.R |only QHScrnomo-2.2.0/QHScrnomo/R/sas.crr.R |only QHScrnomo-2.2.0/QHScrnomo/R/summary.cmprsk.R |only QHScrnomo-2.2.0/QHScrnomo/R/tenf.crr.R |only QHScrnomo-2.2.0/QHScrnomo/inst/CITATION |only QHScrnomo-2.2.0/QHScrnomo/inst/doc/TODO |only QHScrnomo-2.2.0/QHScrnomo/inst/doc/introduction.R |only QHScrnomo-2.2.0/QHScrnomo/inst/doc/introduction.Rmd |only QHScrnomo-2.2.0/QHScrnomo/inst/doc/introduction.html |only QHScrnomo-2.2.0/QHScrnomo/man/addOffset4ModelFrame.Rd |only QHScrnomo-2.2.0/QHScrnomo/man/nomo2.crr.Rd |only QHScrnomo-2.2.0/QHScrnomo/man/pred2.crr.Rd |only QHScrnomo-2.2.0/QHScrnomo/man/pred3.crr.Rd |only QHScrnomo-2.2.0/QHScrnomo/man/predictDesign.Rd |only QHScrnomo-2.2.0/QHScrnomo/vignettes/introduction.Rmd |only QHScrnomo-3.0.0/QHScrnomo/DESCRIPTION | 43 - QHScrnomo-3.0.0/QHScrnomo/MD5 | 112 +-- QHScrnomo-3.0.0/QHScrnomo/NAMESPACE | 14 QHScrnomo-3.0.0/QHScrnomo/NEWS.md |only QHScrnomo-3.0.0/QHScrnomo/R/Getlim.R | 195 ++--- QHScrnomo-3.0.0/QHScrnomo/R/Newlabels.R |only QHScrnomo-3.0.0/QHScrnomo/R/Newlevels.R |only QHScrnomo-3.0.0/QHScrnomo/R/Varcov.R | 60 - QHScrnomo-3.0.0/QHScrnomo/R/anova.R |only QHScrnomo-3.0.0/QHScrnomo/R/cindex.R | 300 ++++---- QHScrnomo-3.0.0/QHScrnomo/R/crr.R |only QHScrnomo-3.0.0/QHScrnomo/R/data.R |only QHScrnomo-3.0.0/QHScrnomo/R/groupci.R | 532 ++++++++------- QHScrnomo-3.0.0/QHScrnomo/R/nomogram.R |only QHScrnomo-3.0.0/QHScrnomo/R/pred.R |only QHScrnomo-3.0.0/QHScrnomo/R/predict.R |only QHScrnomo-3.0.0/QHScrnomo/R/predictDesign.R |only QHScrnomo-3.0.0/QHScrnomo/R/sas.R |only QHScrnomo-3.0.0/QHScrnomo/R/summary.R |only QHScrnomo-3.0.0/QHScrnomo/R/tenf.R |only QHScrnomo-3.0.0/QHScrnomo/README.md |only QHScrnomo-3.0.0/QHScrnomo/build/vignette.rds |binary QHScrnomo-3.0.0/QHScrnomo/data/prostate.dat.rda |binary QHScrnomo-3.0.0/QHScrnomo/inst/doc/QHScrnomo.R |only QHScrnomo-3.0.0/QHScrnomo/inst/doc/QHScrnomo.Rmd |only QHScrnomo-3.0.0/QHScrnomo/inst/doc/QHScrnomo.html |only QHScrnomo-3.0.0/QHScrnomo/man/Newlabels.cmprsk.Rd | 109 +-- QHScrnomo-3.0.0/QHScrnomo/man/Newlevels.cmprsk.Rd | 87 +- QHScrnomo-3.0.0/QHScrnomo/man/anova.cmprsk.Rd | 77 +- QHScrnomo-3.0.0/QHScrnomo/man/cindex.Rd | 148 +--- QHScrnomo-3.0.0/QHScrnomo/man/crr.fit.Rd | 183 ++--- QHScrnomo-3.0.0/QHScrnomo/man/figures |only QHScrnomo-3.0.0/QHScrnomo/man/groupci.Rd | 260 +++---- QHScrnomo-3.0.0/QHScrnomo/man/nomogram.crr.Rd | 632 ++++++++---------- QHScrnomo-3.0.0/QHScrnomo/man/nomogram.mk6.Rd | 221 +++--- QHScrnomo-3.0.0/QHScrnomo/man/pred.ci.Rd | 82 -- QHScrnomo-3.0.0/QHScrnomo/man/predict.cmprsk.Rd | 119 +-- QHScrnomo-3.0.0/QHScrnomo/man/prostate.dat.Rd | 71 -- QHScrnomo-3.0.0/QHScrnomo/man/sas.cmprsk.Rd | 104 +- QHScrnomo-3.0.0/QHScrnomo/man/summary.cmprsk.Rd | 80 +- QHScrnomo-3.0.0/QHScrnomo/man/tenf.crr.Rd | 105 +- QHScrnomo-3.0.0/QHScrnomo/src/Cindex.c | 180 ++--- QHScrnomo-3.0.0/QHScrnomo/tests |only QHScrnomo-3.0.0/QHScrnomo/vignettes/QHScrnomo.Rmd |only 77 files changed, 1797 insertions(+), 1917 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on
'Windows', 'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gabor Csardi [aut, cre],
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between ps versions 1.7.4 dated 2023-04-02 and 1.7.5 dated 2023-04-18
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 2 ++ R/kill-tree.R | 2 ++ R/utils.R | 6 ++++++ src/api-macos.c | 14 +++++++------- src/arch/macos/process_info.c | 2 +- src/macos.c | 2 +- tests/testthat/helpers.R | 26 +++++--------------------- tests/testthat/test-cleanup-reporter.R | 25 +++++++++---------------- tests/testthat/test-connections.R | 17 +++++++++++------ 11 files changed, 58 insertions(+), 66 deletions(-)
Title: Embedding and Clustering with Alignment for Spatial Datasets
Description: An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <wei.liu@duke-nus.edu.sg>
Diff between PRECAST versions 1.5 dated 2023-03-23 and 1.6 dated 2023-04-18
DESCRIPTION | 8 - MD5 | 48 +++--- NAMESPACE | 8 - R/SetClass.R | 29 ++-- R/main.R | 14 + README.md | 9 + inst/doc/PRECAST.BreastCancer.R | 21 +- inst/doc/PRECAST.BreastCancer.Rmd | 35 +++- inst/doc/PRECAST.BreastCancer.html | 98 +++++++++---- inst/doc/PRECAST.DLPFC.R | 25 ++- inst/doc/PRECAST.DLPFC.Rmd | 47 +++++- inst/doc/PRECAST.DLPFC.html | 131 +++++++++++------- inst/doc/PRECAST.Simu.R | 35 +++- inst/doc/PRECAST.Simu.Rmd | 68 ++++++++- inst/doc/PRECAST.Simu.html | 267 +++++++++++++++++++++++++++---------- man/IntegrateSpaData.Rd | 2 man/SpaPlot.Rd | 2 man/dimPlot.Rd | 2 man/doHeatmap.Rd | 2 man/featurePlot.Rd | 2 man/idrsc.Rd | 8 - man/selectModel.Rd | 14 - vignettes/PRECAST.BreastCancer.Rmd | 35 +++- vignettes/PRECAST.DLPFC.Rmd | 47 +++++- vignettes/PRECAST.Simu.Rmd | 68 ++++++++- 25 files changed, 741 insertions(+), 284 deletions(-)
Title: Optimally Refine Strata
Description: Splits initial strata into refined strata that optimize covariate balance. For more information, please email the author for a copy of the accompanying manuscript. To solve the linear program, the 'Gurobi' commercial optimization software is recommended, but not required. The 'gurobi' R package can be installed following the instructions at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.
Author: Katherine Brumberg [aut, cre]
Maintainer: Katherine Brumberg <kbrum@wharton.upenn.edu>
Diff between optrefine versions 1.0.0 dated 2022-11-08 and 1.1.0 dated 2023-04-18
DESCRIPTION | 8 ++-- MD5 | 14 +++---- NEWS.md | 5 ++ R/refine.R | 11 +++-- R/split_stratum.R | 80 +++++++++++++++++++++++-------------------- README.md | 7 +++ man/refine.Rd | 4 +- tests/testthat/test-refine.R | 2 - 8 files changed, 77 insertions(+), 54 deletions(-)
Title: Estimation of Accuracy in Multisite Machine-Learning Models
Description: The effects of the site may severely bias the accuracy of a multisite machine-learning model, even if the analysts removed them when fitting the model in the 'training set' and applying the model in the 'test set' (Solanes et al., Neuroimage 2023, 265:119800). This simple R package estimates the accuracy of a multisite machine-learning model unbiasedly, as described in (Solanes et al., Psychiatry Research: Neuroimaging 2021, 314:111313). It currently supports the estimation of sensitivity, specificity, balanced accuracy (for binary or multinomial variables), the area under the curve, correlation, mean squarer error, and hazard ratio for binomial, multinomial, gaussian, and survival (time-to-event) outcomes.
Author: Joaquim Radua
Maintainer: Joaquim Radua <quimradua@gmail.com>
Diff between multisite.accuracy versions 1.1 dated 2022-05-05 and 1.2 dated 2023-04-18
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 8 ++++++++ R/source.R | 14 ++++++++------ man/multisite.accuracy.Rd | 3 +++ 5 files changed, 28 insertions(+), 15 deletions(-)
More information about multisite.accuracy at CRAN
Permanent link
Title: Analysis of Incubation Data
Description: Suite of functions to study animal incubation.
At the core of incR
lies an algorithm that allows for the scoring of
incubation behaviour. Additionally, several functions
extract biologically relevant metrics of incubation such as off-bout number
and off-bout duration - for a review of avian incubation studies,
see Nests, Eggs, and Incubation: New ideas about avian reproduction (2015)
edited by D. Charles Deeming and S. James Reynolds <doi:10.1093/acprof:oso/9780198718666.001.0001>.
Author: Pablo Capilla-Lasheras [aut, cre]
Maintainer: Pablo Capilla-Lasheras <pacapilla@gmail.com>
Diff between incR versions 1.1.0 dated 2018-03-21 and 2.1.0 dated 2023-04-18
DESCRIPTION | 13 MD5 | 60 ++- NAMESPACE | 2 NEWS.md | 95 +++-- R/inRt.R | 60 ++- R/incR_procdata.R | 1 R/incRatt.R | 5 R/incRenv.R | 54 --- R/incRenv_old.R |only R/incRprep.R | 16 R/incRscan.R | 377 ++++++++++------------- R/incRscan_v2.R |only R/incRscan_v3.R |only README.md |only build/vignette.rds |binary data/incR_envdata.rda |binary data/incR_procdata.rda |binary data/incR_rawdata.rda |binary inst/doc/incR_pipeline.R | 24 - inst/doc/incR_pipeline.Rmd | 19 - inst/doc/incR_pipeline.html | 705 ++++++++++++++++++++++++++++++++------------ man/incR.Rd | 1 man/incR_envdata.Rd | 6 man/incR_procdata.Rd | 7 man/incR_rawdata.Rd | 6 man/incRatt.Rd | 3 man/incRenv.Rd | 14 man/incRenv_old.Rd |only man/incRplot.Rd | 10 man/incRprep.Rd | 7 man/incRscan.Rd | 17 - man/incRscan_v2.Rd |only man/incRt.Rd | 20 - vignettes/incR_pipeline.Rmd | 19 - 34 files changed, 968 insertions(+), 573 deletions(-)
Title: Bayesian Modeling and Causal Inference for Multivariate
Longitudinal Data
Description: Easy-to-use and efficient interface for
Bayesian inference of complex panel (time series) data using dynamic
multivariate panel models by Helske and Tikka (2022)
<doi:10.31235/osf.io/mdwu5>. The package supports joint modeling of multiple
measurements per individual, time-varying and time-invariant effects, and a
wide range of discrete and continuous distributions. Estimation of these
dynamic multivariate panel models is carried out via 'Stan'.
Author: Santtu Tikka [aut, cre] ,
Jouni Helske [aut] ,
Nicholas Clark [rev],
Lucy D’Agostino McGowan [rev]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dynamite versions 1.3.1 dated 2023-03-31 and 1.3.3 dated 2023-04-18
DESCRIPTION | 6 MD5 | 28 NEWS.md | 247 ++-- R/as_data_table.R | 13 R/dynamite.R | 36 R/lfo.R | 633 +++++----- R/prepare_stan_input.R | 2457 ++++++++++++++++++++--------------------- R/priors.R | 725 ++++++------ R/stanblocks_families.R | 24 R/update.R | 216 ++- inst/doc/dynamite_priors.Rmd | 2 inst/doc/dynamite_priors.html | 8 man/lfo.Rd | 4 tests/testthat/test-extended.R | 43 vignettes/dynamite_priors.Rmd | 2 15 files changed, 2276 insertions(+), 2168 deletions(-)
Title: Create a Spatial Raster from Plain Images
Description: Create a spatial raster, as the ones provided by 'terra',
from regular pictures.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between rasterpic versions 0.2.1 dated 2022-06-10 and 0.2.2 dated 2023-04-18
rasterpic-0.2.1/rasterpic/man/figures/README-example-ggplot-1.png |only rasterpic-0.2.1/rasterpic/tests/testthat/test-plots_at.R |only rasterpic-0.2.1/rasterpic/tests/testthat/test-plots_bbox.R |only rasterpic-0.2.1/rasterpic/tests/testthat/test-plots_raster.R |only rasterpic-0.2.1/rasterpic/tests/testthat/test-plots_spatextent.R |only rasterpic-0.2.1/rasterpic/tests/testthat/test-plots_spatvector.R |only rasterpic-0.2.1/rasterpic/tests/testthat/test-plots_uk.R |only rasterpic-0.2.2/rasterpic/DESCRIPTION | 12 rasterpic-0.2.2/rasterpic/MD5 | 45 - rasterpic-0.2.2/rasterpic/NEWS.md | 12 rasterpic-0.2.2/rasterpic/R/rasterpic_img.R | 6 rasterpic-0.2.2/rasterpic/R/utils.R | 380 +++++----- rasterpic-0.2.2/rasterpic/README.md | 71 - rasterpic-0.2.2/rasterpic/build/vignette.rds |binary rasterpic-0.2.2/rasterpic/inst/WORDLIST | 5 rasterpic-0.2.2/rasterpic/inst/doc/rasterpic.R | 41 - rasterpic-0.2.2/rasterpic/inst/doc/rasterpic.Rmd | 41 - rasterpic-0.2.2/rasterpic/inst/doc/rasterpic.html | 184 ++-- rasterpic-0.2.2/rasterpic/man/figures/README-align-crop-mask-1.png |binary rasterpic-0.2.2/rasterpic/man/figures/README-example-basic-1.png |binary rasterpic-0.2.2/rasterpic/man/figures/logo.png |binary rasterpic-0.2.2/rasterpic/tests/testthat.R | 8 rasterpic-0.2.2/rasterpic/tests/testthat/test-crop_mask.R | 60 - rasterpic-0.2.2/rasterpic/tests/testthat/test-errors_messages.R | 254 +++--- rasterpic-0.2.2/rasterpic/tests/testthat/test-expand.R | 82 +- rasterpic-0.2.2/rasterpic/tests/testthat/test-fileformat.R | 348 ++++----- rasterpic-0.2.2/rasterpic/vignettes/rasterpic.Rmd | 41 - 27 files changed, 783 insertions(+), 807 deletions(-)
Title: 'Htmlwidget' for a Parallel Coordinates Plot
Description: Create a parallel coordinates plot, using 'htmlwidgets' package and 'd3.js'.
Author: Mike Bostock [aut, cph] ,
David Chazalviel [aut, cre],
Benoit Lehman [aut]
Maintainer: David Chazalviel <david.chazalviel@club-internet.fr>
Diff between parallelPlot versions 0.2.0 dated 2022-04-12 and 0.3.1 dated 2023-04-18
DESCRIPTION | 6 MD5 | 51 NAMESPACE | 2 NEWS.md | 14 R/parallelPlot.R | 247 +- README.md |only build/vignette.rds |binary inst/doc/introduction-to-parallelplot.R | 18 inst/doc/introduction-to-parallelplot.Rmd | 43 inst/doc/introduction-to-parallelplot.html | 2532 ++++++++++++++------- inst/htmlwidgets/lib/parallelPlot/parallelPlot.css | 9 inst/htmlwidgets/lib/parallelPlot/pp.js | 2343 +++++++++++++------ inst/htmlwidgets/parallelPlot.js | 12 inst/htmlwidgets/parallelPlot.yaml | 2 man/changeRow.Rd | 2 man/getPlotConfig.Rd | 101 man/getValue.Rd | 6 man/parallelPlot.Rd | 15 man/setArrangeMethod.Rd |only man/setCategoricalColorScale.Rd | 4 man/setCategoriesRep.Rd |only man/setContinuousColorScale.Rd | 4 man/setCutoffs.Rd | 6 man/setHistoVisibility.Rd | 2 man/setInvertedAxes.Rd | 92 man/setKeptColumns.Rd | 2 tests/testthat/test_parallelPlot.R | 50 vignettes/introduction-to-parallelplot.Rmd | 43 28 files changed, 3875 insertions(+), 1731 deletions(-)
Title: Exploration and Graphics for RivEr Trends
Description: Statistics and graphics for streamflow history,
water quality trends, and the statistical modeling algorithm: Weighted
Regressions on Time, Discharge, and Season (WRTDS).
Author: Robert Hirsch [aut] ,
Laura DeCicco [aut, cre] ,
Tim Cohn [ctb],
David Watkins [ctb],
Lindsay Carr [ctb],
Jennifer Murphy [aut]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between EGRET versions 3.0.8 dated 2023-03-02 and 3.0.9 dated 2023-04-18
DESCRIPTION | 6 - MD5 | 96 ++++++++++++++++--------------- NEWS | 5 + R/boxConcMonth.R | 5 + R/boxConcThree.R | 5 + R/fluxBiasEight.R | 5 + R/generalAxis.R | 5 + R/multiPlotDataOverview.R | 5 + R/plotConcHist.R | 5 + R/plotConcPred.R | 5 + R/plotConcQ.R | 5 + R/plotConcQSmooth.R | 5 + R/plotConcTime.R | 5 + R/plotConcTimeSmooth.R | 5 + R/plotContours.R | 5 + R/plotDiffContours.R | 5 + R/plotFluxTimeDaily.R | 8 +- R/plotMonthTrend.R | 22 +++++-- R/plotResidPred.R | 5 + R/printFluxUnitCheatSheet.R | 3 R/runPairs.R | 13 ++-- README.md | 81 +++++++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/EGRET.Rmd | 12 ++- inst/doc/EGRET.html | 88 +++++++++++++++++++++++++--- inst/doc/units.R |only inst/doc/units.Rmd |only inst/doc/units.html |only man/boxConcMonth.Rd | 5 + man/boxConcThree.Rd | 5 + man/figures/README-plotFours-1.png |binary man/figures/README-plotFours-2.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/fluxBiasMulti.Rd | 5 + man/generalAxis.Rd | 5 + man/multiPlotDataOverview.Rd | 5 + man/plotConcHist.Rd | 5 + man/plotConcPred.Rd | 5 + man/plotConcQ.Rd | 5 + man/plotConcQSmooth.Rd | 5 + man/plotConcTime.Rd | 5 + man/plotConcTimeSmooth.Rd | 5 + man/plotContours.Rd | 5 + man/plotDiffContours.Rd | 5 + man/plotMonthTrend.Rd | 13 +++- man/plotResidPred.Rd | 5 + man/runPairs.Rd | 9 ++ vignettes/EGRET.Rmd | 12 ++- vignettes/units.Rmd |only 51 files changed, 365 insertions(+), 145 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.44 dated 2023-02-01 and 0.45 dated 2023-04-18
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/install.R | 5 +++++ R/latex.R | 3 ++- R/tlmgr.R | 10 +++++----- man/latexmk.Rd | 2 +- man/tinytex-package.Rd | 2 +- 7 files changed, 25 insertions(+), 19 deletions(-)
Title: Prepare and Explore Data for Palaeobiological Analyses
Description: Provides functionality to support data preparation and exploration for
palaeobiological analyses, improving code reproducibility and accessibility. The
wider aim of 'palaeoverse' is to bring the palaeobiological community together
to establish agreed standards. The package currently includes functionality for
data cleaning, binning (time and space), exploration, summarisation and
visualisation. Reference datasets (i.e. Geological Time Scales <https://stratigraphy.org/chart>)
and auxiliary functions are also provided. Details can be found in:
Jones et al., (2022) <doi:10.31223/X5Z94Q>.
Author: Lewis A. Jones [aut, cre] ,
William Gearty [aut] ,
Bethany J. Allen [aut] ,
Kilian Eichenseer [aut] ,
Christopher D. Dean [aut] ,
Sofia Galvan [ctb] ,
Miranta Kouvari [ctb] ,
Pedro L. Godoy [ctb] ,
Cecily Nicholl [ctb] ,
Lucas Buffan [ctb] ,
Erin M. [...truncated...]
Maintainer: Lewis A. Jones <LewisAlan.Jones@uvigo.es>
Diff between palaeoverse versions 1.1.1 dated 2023-02-16 and 1.2.0 dated 2023-04-18
DESCRIPTION | 10 MD5 | 90 - NAMESPACE | 3 NEWS.md | 13 R/axis_geo.R | 218 +-- R/bin_space.R | 2 R/data.R | 2 R/palaeorotate.R | 191 +- R/release.R |only R/tax_range_space.R | 2 R/tax_range_time.R | 2 R/time_bins.R | 531 +++---- README.md | 4 build/vignette.rds |binary data/GTS2012.rda |binary data/GTS2020.rda |binary data/interval_key.rda |binary inst/CITATION | 26 inst/doc/phanerozoic-reefs.Rmd |only inst/doc/phanerozoic-reefs.html |only inst/doc/structure-and-standards.Rmd | 4 inst/doc/structure-and-standards.html | 2 inst/doc/tetrapod-biodiversity.Rmd |only inst/doc/tetrapod-biodiversity.html |only man/GTS2012.Rd | 1 man/GTS2020.Rd | 1 man/axis_geo.Rd | 107 - man/bin_space.Rd | 2 man/palaeorotate.Rd | 3 man/tax_range_time.Rd | 2 man/time_bins.Rd | 68 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/axis_geo/axis-geo-on-multiple-sides.svg | 708 +++++----- tests/testthat/_snaps/axis_geo/axis-geo-with-backwards-ultrametric-tree.svg | 148 +- tests/testthat/_snaps/axis_geo/axis-geo-with-downwards-fossil-tree.svg | 148 +- tests/testthat/_snaps/axis_geo/axis-geo-with-fossil-tree.svg | 148 +- tests/testthat/_snaps/axis_geo/axis-geo-with-multiple-scales.svg | 297 ++-- tests/testthat/_snaps/axis_geo/axis-geo-with-time-bins-scale.svg | 52 tests/testthat/_snaps/axis_geo/axis-geo-with-ultrametric-tree.svg | 148 +- tests/testthat/_snaps/axis_geo/axis-geo.svg | 97 - tests/testthat/test-axis_geo.R | 23 tests/testthat/test-palaeorotate.R | 37 tests/testthat/test-time_bins.R | 32 vignettes/alpha-div-plot-1-1.png |only vignettes/alpha-div-plot-2-1.png |only vignettes/alpha-div-plot-3-1.png |only vignettes/n-reef-1.png |only vignettes/phanerozoic-reefs.Rmd |only vignettes/reefs-dist-1.png |only vignettes/reefs-max-1.png |only vignettes/reefs-max-multi-1.png |only vignettes/structure-and-standards.Rmd | 4 vignettes/tetrapod-biodiversity.Rmd |only 53 files changed, 1627 insertions(+), 1499 deletions(-)
More information about DateTimeRangePicker at CRAN
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Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.3 dated 2023-03-28 and 1.9.4 dated 2023-04-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- NEWS | 8 ++++++++ inst/include/TMBad/vectorize.hpp | 4 ++++ src/solve_subset.c | 2 +- 6 files changed, 23 insertions(+), 11 deletions(-)
Title: Stability-enHanced Approaches using Resampling Procedures
Description: In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2021) <arXiv:2106.02521>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <barbara.bodinier@gmail.com>
Diff between sharp versions 1.3.0 dated 2023-01-17 and 1.4.0 dated 2023-04-18
DESCRIPTION | 25 - MD5 | 118 ++--- NAMESPACE | 10 NEWS.md | 10 R/algorithms.R | 16 R/bi_selection.R | 39 + R/calibration.R | 34 - R/check.R | 48 +- R/clustering.R | 40 + R/clustering_models.R | 14 R/decision_trees.R |only R/dimensionality_reduction.R | 13 R/explanatory_performance.R | 12 R/graphical_model.R | 43 - R/metrics.R | 24 - R/multi_block.R | 26 - R/parallelisation.R | 11 R/penalised_models.R | 880 +++++++++++++++++++++++++++++++++++++- R/s3_plot.R | 6 R/selection_performance.R | 26 - R/sharp-package.R | 13 R/stability_score.R | 138 ++--- R/structural_equation_modelling.R |only R/utils.R | 5 R/variable_selection.R | 102 ++-- README.md | 47 +- build/partial.rdb |binary inst/REFERENCES.bib | 350 ++++++++------- inst/WORDLIST | 17 man/BiSelection.Rd | 29 - man/BinomialProbabilities.Rd | 5 man/BlockLambdaGrid.Rd | 26 - man/CART.Rd |only man/CheckInputClustering.Rd | 12 man/CheckInputGraphical.Rd | 10 man/CheckParamRegression.Rd | 12 man/Clustering.Rd | 23 man/ClusteringAlgo.Rd | 4 man/CoMembership.Rd | 3 man/ConsensusScore.Rd | 83 +-- man/DBSCANClustering.Rd | 4 man/ExplanatoryPerformance.Rd | 5 man/GraphicalModel.Rd | 48 -- man/GroupPLS.Rd | 11 man/HierarchicalClustering.Rd | 4 man/Incremental.Rd | 5 man/LambdaGridGraphical.Rd | 5 man/LavaanMatrix.Rd |only man/LavaanModel.Rd |only man/LinearSystemMatrix.Rd |only man/OpenMxMatrix.Rd |only man/OpenMxModel.Rd |only man/PAMClustering.Rd | 4 man/PenalisedGraphical.Rd | 7 man/PenalisedRegression.Rd | 34 + man/PenalisedSEM.Rd |only man/SelectionAlgo.Rd | 3 man/SerialClustering.Rd | 12 man/SerialGraphical.Rd | 10 man/SerialRegression.Rd | 10 man/StabilityMetrics.Rd | 12 man/StabilityScore.Rd | 14 man/StructuralModel.Rd |only man/VariableSelection.Rd | 88 ++- man/sharp-package.Rd | 13 65 files changed, 1836 insertions(+), 727 deletions(-)
Title: Cache 'CRAN'-Like Metadata and R Packages
Description: Metadata and package cache for CRAN-like repositories. This
is a utility package to be used by package management tools that want
to take advantage of caching.
Author: Gabor Csardi [aut, cre],
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgcache versions 2.0.4 dated 2022-12-16 and 2.1.0 dated 2023-04-18
pkgcache-2.0.4/pkgcache/tests/testthat/fixtures/rspm-versions.json |only pkgcache-2.1.0/pkgcache/DESCRIPTION | 6 pkgcache-2.1.0/pkgcache/MD5 | 79 +- pkgcache-2.1.0/pkgcache/NAMESPACE | 5 pkgcache-2.1.0/pkgcache/NEWS.md | 13 pkgcache-2.1.0/pkgcache/R/bioc.R | 10 pkgcache-2.1.0/pkgcache/R/cran-app.R | 2 pkgcache-2.1.0/pkgcache/R/metadata-cache.R | 116 +++- pkgcache-2.1.0/pkgcache/R/onload.R | 274 +++++++++- pkgcache-2.1.0/pkgcache/R/package-cache.R | 88 ++- pkgcache-2.1.0/pkgcache/R/packages-gz.R | 107 ++- pkgcache-2.1.0/pkgcache/R/pkgdown.R |only pkgcache-2.1.0/pkgcache/R/platform-linux.R | 7 pkgcache-2.1.0/pkgcache/R/platform.R | 25 pkgcache-2.1.0/pkgcache/R/ppm.R |only pkgcache-2.1.0/pkgcache/R/repo-set.R | 155 +++-- pkgcache-2.1.0/pkgcache/R/utils.R | 8 pkgcache-2.1.0/pkgcache/README.md | 113 ++-- pkgcache-2.1.0/pkgcache/inst/WORDLIST | 2 pkgcache-2.1.0/pkgcache/inst/fixtures/bioc-config.yaml | 18 pkgcache-2.1.0/pkgcache/man/pkgcache-package.Rd | 95 +-- pkgcache-2.1.0/pkgcache/man/ppm_has_binaries.Rd |only pkgcache-2.1.0/pkgcache/man/ppm_platforms.Rd |only pkgcache-2.1.0/pkgcache/man/ppm_r_versions.Rd |only pkgcache-2.1.0/pkgcache/man/ppm_repo_url.Rd |only pkgcache-2.1.0/pkgcache/man/ppm_snapshots.Rd |only pkgcache-2.1.0/pkgcache/man/repo_get.Rd | 28 - pkgcache-2.1.0/pkgcache/tests/testthat/_snaps/1-metadata-cache-3.md | 5 pkgcache-2.1.0/pkgcache/tests/testthat/_snaps/6-cache-ppm.md |only pkgcache-2.1.0/pkgcache/tests/testthat/_snaps/metadata-errors.md |only pkgcache-2.1.0/pkgcache/tests/testthat/_snaps/packages-gz.md | 50 + pkgcache-2.1.0/pkgcache/tests/testthat/_snaps/platform.md | 21 pkgcache-2.1.0/pkgcache/tests/testthat/_snaps/ppm.md |only pkgcache-2.1.0/pkgcache/tests/testthat/_snaps/repo-set.md | 14 pkgcache-2.1.0/pkgcache/tests/testthat/fixtures/PACKAGES-ppm1.gz |only pkgcache-2.1.0/pkgcache/tests/testthat/fixtures/PACKAGES-ppm2.gz |only pkgcache-2.1.0/pkgcache/tests/testthat/fixtures/PACKAGES-rhub |only pkgcache-2.1.0/pkgcache/tests/testthat/fixtures/linux/debian/unstable |only pkgcache-2.1.0/pkgcache/tests/testthat/fixtures/ppm-status.json |only pkgcache-2.1.0/pkgcache/tests/testthat/fixtures/ppm-versions.json |only pkgcache-2.1.0/pkgcache/tests/testthat/helper-apps.R | 10 pkgcache-2.1.0/pkgcache/tests/testthat/setup.R | 5 pkgcache-2.1.0/pkgcache/tests/testthat/test-1-metadata-cache-1.R | 3 pkgcache-2.1.0/pkgcache/tests/testthat/test-6-cache-ppm.R |only pkgcache-2.1.0/pkgcache/tests/testthat/test-metadata-errors.R | 20 pkgcache-2.1.0/pkgcache/tests/testthat/test-metadata-utils.R | 2 pkgcache-2.1.0/pkgcache/tests/testthat/test-packages-gz.R | 42 + pkgcache-2.1.0/pkgcache/tests/testthat/test-platform.R | 12 pkgcache-2.1.0/pkgcache/tests/testthat/test-ppm.R |only pkgcache-2.1.0/pkgcache/tests/testthat/test-repo-set.R | 96 ++- 50 files changed, 1058 insertions(+), 373 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with (asymptotically) normal endpoints and known variance.
Author: Thomas Jaki <thomas.jaki@pm.me>, Dominique-Laurent Couturier <dominique.couturier@mrc-bsu.cam.ac.uk>, Dominic Magirr <d.magirr@gmail.com>, Philip Pallmann <philip.pallmann@gmx.de>
Maintainer: Thomas Jaki <thomas.jaki@pm.me>
Diff between MAMS versions 2.0.0 dated 2022-01-14 and 2.0.1 dated 2023-04-18
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- R/mams.sim.R | 2 +- build/partial.rdb |binary inst/NEWS | 10 +++++++--- src/init.c |only 6 files changed, 16 insertions(+), 11 deletions(-)
Title: Real-Time Disease Surveillance
Description: Supports modelling real-time case data to facilitate the real-time
surveillance of infectious disease. A simple grid class structure is provided to generate a computational grid over
an area of interest with methods to map covariates between geographies. An approximate log-Gaussian Cox Process
model is fit using 'rstan' or 'cmdstanr' and provides output and analysis as 'sf' objects for simple visualisation.
'cmdstanr' can be downloaded at <https://mc-stan.org/cmdstanr/>. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2020) <arXiv:2004.11408> and the
nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between rts2 versions 0.4 dated 2022-10-27 and 0.5 dated 2023-04-18
rts2-0.4/rts2/src/Makevars |only rts2-0.5/rts2/DESCRIPTION | 15 ++++++++------- rts2-0.5/rts2/MD5 | 16 +++++++++------- rts2-0.5/rts2/NAMESPACE | 3 +++ rts2-0.5/rts2/R/griddata_class.R | 1 + rts2-0.5/rts2/R/rts2-package.R | 3 +++ rts2-0.5/rts2/README.md |only rts2-0.5/rts2/configure |only rts2-0.5/rts2/configure.win |only rts2-0.5/rts2/man/grid.Rd | 4 +++- rts2-0.5/rts2/src/Makevars.win | 4 ++-- 11 files changed, 29 insertions(+), 17 deletions(-)
More information about Rdiagnosislist at CRAN
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Title: Execute and Control System Processes
Description: Tools to run system processes in the background. It can
check if a background process is running; wait on a background process
to finish; get the exit status of finished processes; kill background
processes. It can read the standard output and error of the processes,
using non-blocking connections. 'processx' can poll a process for
standard output or error, with a timeout. It can also poll several
processes at once.
Author: Gabor Csardi [aut, cre, cph] ,
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between processx versions 3.8.0 dated 2022-10-26 and 3.8.1 dated 2023-04-18
processx-3.8.0/processx/R/aaa-rstudio-detect.R |only processx-3.8.0/processx/R/errors.R |only processx-3.8.0/processx/tests/testthat/test-err.R |only processx-3.8.1/processx/DESCRIPTION | 11 +- processx-3.8.1/processx/MD5 | 21 ++-- processx-3.8.1/processx/NEWS.md | 7 + processx-3.8.1/processx/R/aaa-import-standalone-rstudio-detect.R |only processx-3.8.1/processx/R/standalone-errors.R |only processx-3.8.1/processx/src/Makevars | 4 processx-3.8.1/processx/src/client.c | 32 ++++++ processx-3.8.1/processx/tests/testthat/_snaps/standalone-errors.md |only processx-3.8.1/processx/tests/testthat/helper.R | 15 +-- processx-3.8.1/processx/tests/testthat/test-poll-curl.R | 15 --- processx-3.8.1/processx/tests/testthat/test-process.R | 46 ++++++++++ processx-3.8.1/processx/tests/testthat/test-standalone-errors.R |only 15 files changed, 117 insertions(+), 34 deletions(-)
More information about modeltime.ensemble at CRAN
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Title: Stop Detection in Timestamped Trajectory Data using
Spatiotemporal Clustering
Description: Trajectory data formed by human or animal movement is often marked
by periods of movement interspersed with periods of standing still. It is
often of interest to researchers to separate geolocation trajectories of
latitude/longitude points by clustering consecutive locations to produce a
model of this behavior. This package implements the Stay Point detection
algorithm originally described in Ye (2009) <doi:10.1109/MDM.2009.11> that
uses time and distance thresholds to characterize spatial regions as
'stops'. This package also implements the concept of merging described in
Montoliu (2013) <doi:10.1007/s11042-011-0982-z> as stay point region
estimation, which allows for clustering of temporally adjacent stops for
which distance between the midpoints is less than the provided threshold.
GPS-like data from various sources can be used, but the temporal thresholds
must be considered with respect to the sampling interval, and the spatial
thresholds must be considered with respect [...truncated...]
Author: McCool Danielle [aut, cre]
Maintainer: McCool Danielle <d.m.mccool@uu.nl>
Diff between stopdetection versions 0.1.1 dated 2022-10-14 and 0.1.2 dated 2023-04-18
DESCRIPTION | 8 + MD5 | 17 +-- NEWS.md |only R/mergingCycleFunctions.R | 8 - R/stopFinder.R | 2 README.md | 84 +++++++++-------- inst/doc/stopdetection-vignette.html | 169 ++++++++++++++++++----------------- man/mergingCycle.Rd | 8 - man/stopdetection-package.Rd | 8 + tests/testthat/test-stopFinder.R | 4 10 files changed, 165 insertions(+), 143 deletions(-)
Title: Loading Data from 'Google Ads API'
Description: Interface for loading data from 'Google Ads API',
see <https://developers.google.com/google-ads/api/docs/start>.
Package provide function for authorization and loading reports.
Author: Alexey Seleznev [aut, cre] ,
Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rgoogleads versions 0.9.1 dated 2023-03-30 and 0.9.2 dated 2023-04-18
DESCRIPTION | 8 MD5 | 14 - NAMESPACE | 103 +++---- NEWS.md | 3 R/gads_get_geo_targets.R | 89 +++--- build/vignette.rds |binary inst/doc/migrate_from_radrowds_us.html | 440 ++++++++++++++++----------------- inst/doc/migrate_from_radwords_ru.html | 434 ++++++++++++++++---------------- 8 files changed, 561 insertions(+), 530 deletions(-)
Title: Multi-Scale Geomorphometric Terrain Attributes
Description: Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Misiuk et al. (2021) <doi:10.1080/01490419.2021.1925789>; Wilson et al. (2007) <doi:10.1080/01490410701295962>; Wood (1996) <https://hdl.handle.net/2381/34503>).
Author: Alexander Ilich [aut, cre] ,
Vincent Lecours [aut],
Benjamin Misiuk [aut],
Steven Murawski [aut]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between MultiscaleDTM versions 0.7 dated 2023-04-10 and 0.7.1 dated 2023-04-18
MultiscaleDTM-0.7.1/MultiscaleDTM/DESCRIPTION | 8 - MultiscaleDTM-0.7.1/MultiscaleDTM/MD5 | 29 +++-- MultiscaleDTM-0.7.1/MultiscaleDTM/README.md | 4 MultiscaleDTM-0.7.1/MultiscaleDTM/inst/doc/README.R | 35 ++++-- MultiscaleDTM-0.7.1/MultiscaleDTM/inst/doc/README.Rmd | 3 MultiscaleDTM-0.7.1/MultiscaleDTM/inst/doc/README.html | 4 MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit01.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit02.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit03.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit04.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit05.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit06.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit07.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit08.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit09.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit10.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit11.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qfit12.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/qmetrics.jpg |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/figures/test.png |only MultiscaleDTM-0.7.1/MultiscaleDTM/man/fragments/README_Frag.Rmd | 54 ++++++---- MultiscaleDTM-0.7.1/MultiscaleDTM/vignettes/README.Rmd | 3 MultiscaleDTM-0.7/MultiscaleDTM/man/figures/README-Qfit-1.png |only 23 files changed, 89 insertions(+), 51 deletions(-)
Title: Get Executing Script's Path
Description: Determine the path of the executing script. Compatible
with a few popular GUIs: 'Rgui', 'RStudio', 'VSCode',
'Jupyter', and 'Rscript' (shell). Compatible with several
functions and packages: 'source()', 'sys.source()',
'debugSource()' in 'RStudio', 'testthat::source_file()',
'knitr::knit()',' 'compiler::loadcmp()', and 'box::use()'.
Author: Iris Simmons
Maintainer: Iris Simmons <ikwsimmo@gmail.com>
Diff between this.path versions 1.3.0 dated 2023-04-08 and 1.4.0 dated 2023-04-18
this.path-1.3.0/this.path/R/path.R |only this.path-1.4.0/this.path/DESCRIPTION | 24 this.path-1.4.0/this.path/MD5 | 129 - this.path-1.4.0/this.path/NAMESPACE | 32 this.path-1.4.0/this.path/NEWS | 94 - this.path-1.4.0/this.path/R/Args.R | 4 this.path-1.4.0/this.path/R/LINENO.R | 4 this.path-1.4.0/this.path/R/all.char.R | 2 this.path-1.4.0/this.path/R/catfile.R | 2 this.path-1.4.0/this.path/R/check.path.R | 4 this.path-1.4.0/this.path/R/from.shell.R | 4 this.path-1.4.0/this.path/R/hooks-for-namespace-events.R | 52 this.path-1.4.0/this.path/R/this.path.R | 144 -- this.path-1.4.0/this.path/R/tryCatch2.R | 2 this.path-1.4.0/this.path/R/utils.R | 29 this.path-1.4.0/this.path/R/zzz.R | 58 this.path-1.4.0/this.path/README.md | 2 this.path-1.4.0/this.path/build/partial.rdb |binary this.path-1.4.0/this.path/build/this.path.pdf |binary this.path-1.4.0/this.path/inst/NEWS.Rd | 410 +++-- this.path-1.4.0/this.path/inst/extdata/main.R | 2 this.path-1.4.0/this.path/man/Args.Rd | 59 this.path-1.4.0/this.path/man/LINENO.Rd | 42 this.path-1.4.0/this.path/man/OS.type.Rd | 9 this.path-1.4.0/this.path/man/R.from.shell.Rd | 14 this.path-1.4.0/this.path/man/Sys.putenv.Rd | 9 this.path-1.4.0/this.path/man/basename2.Rd | 34 this.path-1.4.0/this.path/man/check.path.Rd | 35 this.path-1.4.0/this.path/man/ext.Rd | 18 this.path-1.4.0/this.path/man/from.shell.Rd | 16 this.path-1.4.0/this.path/man/here.Rd | 12 this.path-1.4.0/this.path/man/macros/commonmacros.Rd | 76 - this.path-1.4.0/this.path/man/path.join.Rd | 6 this.path-1.4.0/this.path/man/path.split.Rd | 4 this.path-1.4.0/this.path/man/relpath.Rd | 15 this.path-1.4.0/this.path/man/set.this.path.jupyter.Rd | 12 this.path-1.4.0/this.path/man/shFILE.Rd | 21 this.path-1.4.0/this.path/man/this.path-defunct.Rd | 27 this.path-1.4.0/this.path/man/this.path-package.Rd | 23 this.path-1.4.0/this.path/man/this.path.Rd | 159 +- this.path-1.4.0/this.path/man/this.proj.Rd | 4 this.path-1.4.0/this.path/man/try.this.path.Rd | 26 this.path-1.4.0/this.path/man/tryCatch2.Rd | 2 this.path-1.4.0/this.path/man/wrap.source.Rd | 113 - this.path-1.4.0/this.path/src/aquarootscript.c | 2 this.path-1.4.0/this.path/src/args.c | 7 this.path-1.4.0/this.path/src/backports.c | 16 this.path-1.4.0/this.path/src/basename2.c | 17 this.path-1.4.0/this.path/src/drivewidth.c | 8 this.path-1.4.0/this.path/src/ext.c | 24 this.path-1.4.0/this.path/src/hooks-for-namespace-events.c | 30 this.path-1.4.0/this.path/src/init.c | 6 this.path-1.4.0/this.path/src/isabspath.c | 6 this.path-1.4.0/this.path/src/pathjoin.c | 10 this.path-1.4.0/this.path/src/pathsplit.c | 23 this.path-1.4.0/this.path/src/promises.c | 15 this.path-1.4.0/this.path/src/shfile.c | 12 this.path-1.4.0/this.path/src/symbols.h | 3 this.path-1.4.0/this.path/src/this.path.h | 2 this.path-1.4.0/this.path/src/thispath.c | 932 ++++++++----- this.path-1.4.0/this.path/src/thispathbackports.h | 48 this.path-1.4.0/this.path/src/thispathdefn.c | 58 this.path-1.4.0/this.path/src/thispathdefn.h | 44 this.path-1.4.0/this.path/src/utils.c | 4 this.path-1.4.0/this.path/src/wrapsource.c | 213 +- this.path-1.4.0/this.path/tools/configure.R | 125 - 66 files changed, 1905 insertions(+), 1434 deletions(-)
Title: Basic Routing for Shiny Web Applications
Description: It is a simple router for your Shiny apps.
The router allows you to create dynamic web applications with real-time
User Interface and easily share url to pages within your Shiny apps.
Author: Ryszard Szymanski [cre, aut],
Jakub Nowicki [aut],
Filip Stachura [aut],
Dominik Krzeminski [aut],
Krystian Igras [aut],
Servet Ahmet Cizmeli [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Ryszard Szymanski <opensource+ryszard@appsilon.com>
Diff between shiny.router versions 0.3.0 dated 2023-03-02 and 0.3.1 dated 2023-04-18
DESCRIPTION | 8 +++---- MD5 | 12 +++++------ R/router.R | 43 +++++++++++++++++++++++++++++++++++----- README.md | 23 ++++++++------------- inst/WORDLIST | 6 +++++ man/router_ui.Rd | 24 ++++++++++++++++++++-- tests/testthat/test-router.R | 46 +++++++++++++++++++++++++++++++++++++++++++ 7 files changed, 131 insertions(+), 31 deletions(-)
Title: The Pareto, Piecewise Pareto and Generalized Pareto Distribution
Description: Utilities for the Pareto, piecewise Pareto and generalized Pareto distribution
that are useful for reinsurance pricing. In particular, the package provides
a non-trivial algorithm that can be used to match the expected losses of a
tower of reinsurance layers with a layer-independent collective risk model.
The theoretical background of the matching algorithm and most other methods
are described in Ulrich Riegel (2018) <doi:10.1007/s13385-018-0177-3>.
Author: Ulrich Riegel [aut, cre]
Maintainer: Ulrich Riegel <ulrich.riegel@gmx.de>
Diff between Pareto versions 2.4.4 dated 2023-04-08 and 2.4.5 dated 2023-04-18
DESCRIPTION | 6 - MD5 | 18 ++--- NEWS.md | 4 + R/PGPModel.R | 2 R/PPPModel.R | 2 inst/doc/Pareto.html | 96 +++++++++++++++--------------- man/print.PGP_Model.Rd | 2 man/print.PPP_Model.Rd | 2 tests/testthat/test_functions_GenPareto.R | 3 tests/testthat/test_functions_Pareto.R | 2 10 files changed, 70 insertions(+), 67 deletions(-)
Title: Bayesian Quantile Variable Selection for G - E in Longitudinal
Studies
Description: In longitudinal studies, the same subjects are measured repeatedly over time, leading to correlations among the repeated measurements. Properly accounting for the intra-cluster correlations in the presence of data heterogeneity and long tailed distributions of the disease phenotype is challenging, especially in the context of high dimensional regressions. Here, we aim at developing novel Bayesian regularized quantile mixed effect models to tackle these challenges. We have proposed a Bayesian variable selection in the mixed effect models for longitudinal genomics studies. To dissect important gene - environment interactions, our model can simultaneously identify important main and interaction effects on the individual and group level, which have been facilitated by imposing the spike- and -slab priors through Laplacian shrinkage in the Bayesian quantile hierarchical models. The within - subject dependence among data can be accommodated by incorporating the random effects. An efficient G [...truncated...]
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between BayesQVGEL versions 0.1.0 dated 2023-04-17 and 0.1.1 dated 2023-04-18
BayesQVGEL-0.1.0/BayesQVGEL/R/LONBGLSS_1.R |only BayesQVGEL-0.1.0/BayesQVGEL/R/LONRBGLSS_1.R |only BayesQVGEL-0.1.1/BayesQVGEL/DESCRIPTION | 6 BayesQVGEL-0.1.1/BayesQVGEL/MD5 | 52 +++---- BayesQVGEL-0.1.1/BayesQVGEL/R/BayesQVGEL.R | 2 BayesQVGEL-0.1.1/BayesQVGEL/R/LONBGLSS.R | 12 - BayesQVGEL-0.1.1/BayesQVGEL/R/LONBGLSS1.R |only BayesQVGEL-0.1.1/BayesQVGEL/R/LONRBGLSS.R | 18 +- BayesQVGEL-0.1.1/BayesQVGEL/R/LONRBGLSS1.R |only BayesQVGEL-0.1.1/BayesQVGEL/R/data.R | 2 BayesQVGEL-0.1.1/BayesQVGEL/data/data.rda |binary BayesQVGEL-0.1.1/BayesQVGEL/man/BayesQVGEL.Rd | 2 BayesQVGEL-0.1.1/BayesQVGEL/man/data.Rd | 2 BayesQVGEL-0.1.1/BayesQVGEL/src/BGL.cpp | 26 +-- BayesQVGEL-0.1.1/BayesQVGEL/src/BGL1.cpp | 172 +++++++++++++------------- BayesQVGEL-0.1.1/BayesQVGEL/src/BGLSS.cpp | 38 ++--- BayesQVGEL-0.1.1/BayesQVGEL/src/BGLSS1.cpp | 172 +++++++++++++------------- BayesQVGEL-0.1.1/BayesQVGEL/src/BL.cpp | 32 ++-- BayesQVGEL-0.1.1/BayesQVGEL/src/BL1.cpp | 170 ++++++++++++------------- BayesQVGEL-0.1.1/BayesQVGEL/src/BLSS.cpp | 32 ++-- BayesQVGEL-0.1.1/BayesQVGEL/src/BLSS1.cpp | 166 ++++++++++++------------- BayesQVGEL-0.1.1/BayesQVGEL/src/RBGL.cpp | 30 ++-- BayesQVGEL-0.1.1/BayesQVGEL/src/RBGL1.cpp | 158 +++++++++++------------ BayesQVGEL-0.1.1/BayesQVGEL/src/RBGLSS.cpp | 28 +--- BayesQVGEL-0.1.1/BayesQVGEL/src/RBGLSS1.cpp | 152 +++++++++++----------- BayesQVGEL-0.1.1/BayesQVGEL/src/RBL.cpp | 54 ++++---- BayesQVGEL-0.1.1/BayesQVGEL/src/RBL1.cpp | 146 +++++++++++----------- BayesQVGEL-0.1.1/BayesQVGEL/src/RBLSS.cpp | 38 ++--- BayesQVGEL-0.1.1/BayesQVGEL/src/RBLSS1.cpp | 142 ++++++++++----------- 29 files changed, 825 insertions(+), 827 deletions(-)
Title: A Network Tool to Dissect Spatial Community Ecology
Description: Most existing approaches for network reconstruction can only infer an overall network
and, also, fail to capture a complete set of network properties. To address these issues,
a new model has been developed, which converts static data into their 'dynamic' form.
'idopNetwork' is an 'R' interface to this model, it can inferring informative, dynamic,
omnidirectional and personalized networks. For more information on functional
clustering part, see Kim et al. (2008) <doi:10.1534/genetics.108.093690>,
Wang et al. (2011) <doi:10.1093/bib/bbr032>. For more information on our model,
see Chen et al. (2019) <doi:10.1038/s41540-019-0116-1>, and Cao et al. (2022)
<doi:10.1080/19490976.2022.2106103>.
Author: Ang Dong
Maintainer: Ang Dong <fantasys05227@gmail.com>
Diff between idopNetwork versions 0.1.1 dated 2022-11-21 and 0.1.2 dated 2023-04-18
DESCRIPTION | 15 + MD5 | 11 - R/bi_functional_clustering.R | 6 R/functional_clustering.R | 6 R/power_equation_fitting.R | 2 README.md |only inst/doc/idopNetwork_vignette.html | 291 +++++++++++++++++++------------------ 7 files changed, 177 insertions(+), 154 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-12 1.0.2
2016-04-10 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-02 0.1.5
2021-10-18 0.1.4
2021-06-14 0.1.3
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.7.8 dated 2023-03-01 and 1.7.9 dated 2023-04-18
DESCRIPTION | 8 +- MD5 | 90 ++++++++++++++------------- NAMESPACE | 3 R/RcppExports.R | 8 +- R/asr_empirical_probabilities.R | 4 - R/asr_max_parsimony.R | 1 R/asr_mk_model.R | 18 +++-- R/auxiliary_routines.R | 72 ++++++++------------- R/clade_densities.R |only R/collapse_tree_at_resolution.R | 9 +- R/count_lineages_through_time.R | 7 +- R/fit_bm_model.R | 35 +++++----- R/fit_mk.R | 34 +++++----- R/fit_sbm_const.R | 2 R/fit_sbm_const_biased_sampling_unfinished.R | 2 R/fit_symmetric_mk.R | 2 R/generate_random_tree.R | 6 + R/get_independent_contrasts.R | 7 +- R/get_independent_sister_tips.R |only R/map_to_state_space.R | 62 ++++++++---------- R/mean_abs_change_scalar_OU.R |only R/root_at_midpoint.R | 2 R/root_via_outgroup.R | 27 +++++--- R/simulate_ou_model.R | 4 - R/simulate_rou_model.R | 4 - R/write_tree.R | 6 + man/asr_empirical_probabilities.Rd | 6 + man/asr_independent_contrasts.Rd | 5 + man/asr_max_parsimony.Rd | 3 man/asr_mk_model.Rd | 3 man/asr_squared_change_parsimony.Rd | 5 + man/asr_subtree_averaging.Rd | 3 man/clade_densities.Rd |only man/collapse_tree_at_resolution.Rd | 3 man/count_lineages_through_time.Rd | 5 + man/fit_bm_model.Rd | 4 - man/get_independent_contrasts.Rd | 2 man/get_independent_sister_tips.Rd |only man/get_trait_acf.Rd | 2 man/hsp_binomial.Rd | 2 man/hsp_independent_contrasts.Rd | 5 + man/hsp_squared_change_parsimony.Rd | 5 + man/hsp_subtree_averaging.Rd | 5 + man/mean_abs_change_scalar_OU.Rd |only man/root_at_midpoint.Rd | 2 man/simulate_ou_model.Rd | 15 ++-- man/simulate_rou_model.Rd | 13 ++- src/RcppExports.cpp | 18 ++--- src/phylogenetics_cpp_routines.cpp | 39 +++-------- 49 files changed, 299 insertions(+), 259 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-17 1.0.1
2021-07-01 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-13 3.2.8
2021-10-08 3.2.7
2021-04-26 3.2.6
2021-04-08 3.2.5
2019-11-02 3.2.3
2019-06-20 3.2.2
2018-09-26 3.2.1
2018-06-15 3.2.0
2018-06-14 3.1.8
2018-04-01 3.1.7
2017-11-02 3.1.6
2017-10-27 3.1.5
2016-12-28 3.1.4
2016-02-23 3.1.3
2015-08-26 3.1.2
2015-06-12 3.1.1
2015-03-13 3.1.0
2014-12-29 3.0.32
2014-09-12 3.0.30
2014-09-09 3.0.29
2014-06-30 3.0.28
2014-05-06 3.0.26
2014-04-07 3.0.24
2014-04-03 3.0.23
2013-10-01 3.0.21
2013-05-04 3.0.20
2013-04-24 3.0.18
2013-04-22 3.0.17
2013-03-15 3.0.16
2013-02-07 3.0.15
2013-01-30 3.0.13
2013-01-29 3.0.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-21 0.2.1