Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application Wallace is a modular platform for
reproducible modeling of species niches and distributions. Wallace
guides users through a complete analysis, from the acquisition of species
occurrence and environmental data to visualizing model predictions on an
interactive map, thus bundling complex workflows into a single,
streamlined interface. An extensive vignette, which guides users through
most package functionality can be found on the package's GitHub Pages
website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.
Author: Bethany A. Johnson [aut],
Jamie M. Kass [aut],
Gonzalo E. Pinilla-Buitrago [aut],
Andrea Paz [aut],
Valentina Grisales-Betancur [aut],
Dean Attali [aut],
Matthew E. Aiello-Lammens [aut],
Cory Merow [aut],
Mary E. Blair [aut, cre],
Robert P. Anderson [...truncated...]
Maintainer: Mary E. Blair <[email protected]>
Diff between wallace versions 2.1.2 dated 2024-03-08 and 2.1.3 dated 2024-07-18
DESCRIPTION | 54 +++++----- MD5 | 94 +++++++++---------- NEWS.md | 13 ++ R/envs_worldclim.R | 41 ++++++-- R/model_bioclim.R | 8 - R/model_maxent.R | 8 - R/occs_queryDb.R | 28 ++--- R/part_partitionOccs.R | 6 - R/penvs_bgSample.R | 4 R/poccs_selectOccs.R | 4 R/run_wallace.R | 4 R/vis_bioclimPlot.R | 4 R/xfer_area.R | 5 - R/xfer_mess.R | 4 R/xfer_time.R | 2 R/xfer_userEnvs.R | 5 - README.md | 4 inst/shiny/Rmd/text_about.Rmd | 2 inst/shiny/Rmd/text_intro_tab.Rmd | 2 inst/shiny/Rmd/text_team.Rmd | 14 +- inst/shiny/Rmd/userReport_intro.Rmd | 2 inst/shiny/modules/envs_userEnvs.R | 15 ++- inst/shiny/modules/envs_userEnvs.md | 4 inst/shiny/modules/envs_worldclim.R | 8 - inst/shiny/modules/envs_worldclim.Rmd | 2 inst/shiny/modules/envs_worldclim.md | 12 +- inst/shiny/modules/envs_worldclim.yml | 4 inst/shiny/modules/model_bioclim.Rmd | 2 inst/shiny/modules/vis_bioclimPlot.R | 5 - inst/shiny/modules/vis_maxentEvalPlot.R | 4 inst/shiny/modules/vis_responsePlot.R | 7 - inst/shiny/modules/vis_responsePlot.Rmd | 15 ++- inst/shiny/modules/xfer_area.R | 10 +- inst/shiny/modules/xfer_time.R | 158 ++++++++++++++++++++------------ inst/shiny/modules/xfer_time.Rmd | 94 ++++++++++--------- inst/shiny/modules/xfer_time.md | 10 +- inst/shiny/modules/xfer_time.yml | 2 inst/shiny/modules/xfer_user.R | 4 inst/shiny/server.R | 6 - man/envs_worldclim.Rd | 4 man/model_bioclim.Rd | 2 man/model_maxent.Rd | 2 man/run_wallace.Rd | 2 man/vis_bioclimPlot.Rd | 2 man/xfer_area.Rd | 4 man/xfer_mess.Rd | 2 man/xfer_time.Rd | 2 man/xfer_userEnvs.Rd | 4 48 files changed, 407 insertions(+), 287 deletions(-)
Title: Multiomics Data Integration
Description: Provides functions to do 'O2PLS-DA' analysis for multiple omics data integration.
The algorithm came from "O2-PLS, a two-block (X±Y) latent variable regression (LVR) method with an integral OSC filter"
which published by Johan Trygg and Svante Wold at 2003 <doi:10.1002/cem.775>.
'O2PLS' is a bidirectional multivariate regression method that aims to separate the covariance between
two data sets (it was recently extended to multiple data sets) (Löfstedt and Trygg, 2011 <doi:10.1002/cem.1388>; Löfstedt et al., 2012 <doi:10.1016/j.aca.2013.06.026>)
from the systematic sources of variance being specific for each data set separately.
Author: Kai Guo [aut, cre],
Junguk Hur [aut],
Eva Feldman [aut]
Maintainer: Kai Guo <[email protected]>
Diff between o2plsda versions 0.0.22 dated 2024-07-17 and 0.0.25 dated 2024-07-18
DESCRIPTION | 6 +-- MD5 | 18 +++++----- R/o2plscv.R | 18 ++++++---- R/plot.R | 27 ++++++++++++---- README.md | 64 ++++++++++++++++++--------------------- inst/doc/o2plsda.R | 36 +++------------------ inst/doc/o2plsda.Rmd | 44 ++++---------------------- inst/doc/o2plsda.html | 82 +++++++++++++++----------------------------------- man/plot.o2plsda.Rd | 3 - vignettes/o2plsda.Rmd | 44 ++++---------------------- 10 files changed, 120 insertions(+), 222 deletions(-)
Title: Calculate MIMS Dissolved Gas Concentrations Without Getting a
Headache
Description: Calculate dissolved gas concentrations from raw MIMS
(Membrane Inlet Mass Spectrometer) signal data. Use mimsy() on
a formatted CSV file to return dissolved gas concentrations
(mg and microMole) of N2, O2, Ar based on
gas solubility at temperature, pressure, and salinity. See references
Benson and Krause (1984), Garcia and Gordon (1992), Stull (1947),
and Hamme and Emerson (2004) for more information. Easily save the
output to a nicely-formatted multi-tab 'Excel' workbook with mimsy.save().
Supports dual-temperature standard calibration for dual-bath MIMS setups.
Author: Michelle Catherine Kelly [aut, cre],
Kevin Nevorski [ctb],
Amy M. Marcarelli [ctb]
Maintainer: Michelle Catherine Kelly <[email protected]>
Diff between mimsy versions 0.6.4 dated 2024-02-22 and 0.6.5 dated 2024-07-18
DESCRIPTION | 8 ++-- MD5 | 8 ++-- NEWS.md | 6 +++ R/mimsy.R | 2 - inst/doc/mimsy.html | 100 ++++++++++++++++++++++++++-------------------------- 5 files changed, 65 insertions(+), 59 deletions(-)
Title: Fit Regularization Path for Generalized Additive Models
Description: Using overlap grouped-lasso penalties, 'gamsel' selects whether a term in a 'gam' is nonzero, linear, or a non-linear spline (up to a specified max df per variable). It fits the entire regularization path on a grid of values for the overall penalty lambda, both for gaussian and binomial families. See <doi:10.48550/arXiv.1506.03850> for more details.
Author: Alexandra Chouldechova [aut],
Trevor Hastie [aut, cre],
Balasubramanian Narasimhan [ctb],
Vitalie Spinu [ctb],
Matt Wand [ctb]
Maintainer: Trevor Hastie <[email protected]>
Diff between gamsel versions 1.8-3 dated 2024-06-25 and 1.8-4 dated 2024-07-18
gamsel-1.8-3/gamsel/inst/doc/gamselVignette.pdf |only gamsel-1.8-4/gamsel/DESCRIPTION | 12 +++++++----- gamsel-1.8-4/gamsel/MD5 | 12 ++++++++---- gamsel-1.8-4/gamsel/build |only gamsel-1.8-4/gamsel/cleanup |only gamsel-1.8-4/gamsel/inst/doc/gamsel.Rmd |only gamsel-1.8-4/gamsel/inst/doc/gamsel.html |only gamsel-1.8-4/gamsel/man/gamsel-package.Rd | 7 +++++++ gamsel-1.8-4/gamsel/src/gamsel.c | 16 ++++++++-------- gamsel-1.8-4/gamsel/vignettes |only 10 files changed, 30 insertions(+), 17 deletions(-)
Title: Client Library for SpatioTemporal Asset Catalog
Description: Provides functions to access, search and download spacetime earth
observation data via SpatioTemporal Asset Catalog (STAC). This package
supports the version 1.0.0 (and older) of the STAC specification
(<https://github.com/radiantearth/stac-spec>).
For further details see Simoes et al. (2021) <doi:10.1109/IGARSS47720.2021.9553518>.
Author: Rolf Simoes [aut],
Felipe Carvalho [aut, cre],
Brazil Data Cube Team [aut],
National Institute for Space Research [cph]
Maintainer: Felipe Carvalho <[email protected]>
Diff between rstac versions 1.0.0 dated 2024-02-14 and 1.0.1 dated 2024-07-18
DESCRIPTION | 15 +++++++------ MD5 | 36 +++++++++++++++++--------------- NAMESPACE | 4 +++ NEWS.md | 9 ++++++++ R/assets-funs.R | 25 ++++++++++++++-------- R/assets-utils.R | 37 ++++++++++++++++++++++++--------- R/check-utils.R | 8 +++++++ R/collections-funs.R |only R/collections-query.R | 9 ++++++-- R/ext_filter.R | 6 +++++ R/items-funs.R | 48 +++++++++++++++++++++++++++++-------------- R/parse-utils.R | 5 +--- R/static-funs.R | 6 +---- README.md | 2 - build/partial.rdb |binary man/assets_functions.Rd | 12 +++++++++- man/collections.Rd | 5 +++- man/collections_functions.Rd |only man/ext_filter.Rd | 9 ++++++++ man/items_functions.Rd | 28 +++++++++++++++++-------- 20 files changed, 186 insertions(+), 78 deletions(-)
Title: Tools for Conducting and Analyzing Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct
respirometry experiments. Strong emphasis is on aquatic respirometry. Tools
focus on helping the researcher setup and conduct experiments. Functions for
analysis of resulting respirometry data are also provided. This package
provides tools for intermittent, flow-through, and closed respirometry
techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <[email protected]>
Diff between respirometry versions 1.5.0 dated 2024-02-09 and 2.0.0 dated 2024-07-18
DESCRIPTION | 8 - MD5 | 50 +++++----- NAMESPACE | 5 + NEWS | 10 ++ R/Q10.R | 10 +- R/calc_MO2.R | 40 +++++--- R/calc_pcrit.R | 166 +++++++++++++++++++++++------------- R/closed.R | 2 R/conv_nh4.R | 2 R/conv_o2.R | 14 ++- R/import_pyroscience_workbench.R | 8 - R/make_bins.R | 27 +++-- R/max_MO2.R | 7 + R/scale_MO2.R | 8 + inst/extdata/pcrit_run |only man/Q10.Rd | 6 + man/calc_MO2.Rd | 17 +++ man/calc_pcrit.Rd | 27 +++-- man/closed.Rd | 2 man/conv_nh4.Rd | 2 man/conv_o2.Rd | 1 man/import_pyroscience_workbench.Rd | 2 man/make_bins.Rd | 22 ++-- man/max_MO2.Rd | 10 ++ man/plot_pcrit.Rd | 40 ++++---- man/scale_MO2.Rd | 5 - 26 files changed, 323 insertions(+), 168 deletions(-)
Title: 'osqp' Plugin for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the quadratic solver 'OSQP'. More information about
'OSQP' can be found at <https://osqp.org>.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <[email protected]>
Diff between ROI.plugin.osqp versions 1.0-1 dated 2023-07-06 and 1.0-2 dated 2024-07-18
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- R/plugin.R | 17 ++++++++--------- 3 files changed, 15 insertions(+), 15 deletions(-)
More information about ROI.plugin.osqp at CRAN
Permanent link
Title: Neutrosophic Data Sets
Description: Provides a collection of datasets related to neutrosophic sets for statistical modeling and analysis.
Author: Amin Roshani [aut, cre] ,
Mina Norouzirad [aut] ,
Danial Mazarei [aut] ,
FCT, I.P. [fnd] )
Maintainer: Amin Roshani <[email protected]>
Diff between ntsDatasets versions 0.1.0 dated 2024-07-03 and 0.2.0 dated 2024-07-18
DESCRIPTION | 6 +- MD5 | 45 +++++++++++++------- R/AGSTimes.R | 38 ++++++++--------- R/CRPK.R | 36 ++++++++-------- R/ChildMortalitySA.R |only R/ICUcovidPK.R | 60 +++++++++++++-------------- R/MRcovidNL.R | 44 +++++++++---------- R/NOx.R | 38 ++++++++--------- R/PopVillUSA.R |only R/alloy.R | 44 +++++++++---------- R/balls.R | 48 ++++++++++----------- R/batteries.R | 42 +++++++++--------- R/debt.R | 36 ++++++++-------- R/dioxins.R |only R/failure.R |only R/remission.R | 44 +++++++++---------- R/tempLahor.R |only README.md | 102 +++++++++++++++++++++++----------------------- data/ChildMortalitySA.rda |only data/PopVillUSA.rda |only data/dioxins.rda |only data/failure.rda |only data/remission.rda |binary data/tempLahor.rda |only man/ChildMortalitySA.Rd |only man/PopVillUSA.Rd |only man/balls.Rd | 48 ++++++++++----------- man/dioxins.Rd |only man/failure.Rd |only man/remission.Rd | 46 ++++++++++---------- man/tempLahor.Rd |only 31 files changed, 346 insertions(+), 331 deletions(-)
Title: Date-Time Types and Tools
Description: Provides a comprehensive library for date-time manipulations
using a new family of orthogonal date-time classes (durations, time
points, zoned-times, and calendars) that partition responsibilities so
that the complexities of time zones are only considered when they are
really needed. Capabilities include: date-time parsing, formatting,
arithmetic, extraction and updating of components, and rounding.
Author: Davis Vaughan [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <[email protected]>
Diff between clock versions 0.7.0 dated 2023-05-15 and 0.7.1 dated 2024-07-18
DESCRIPTION | 11 ++-- MD5 | 76 ++++++++++++++--------------- NAMESPACE | 18 +++++++ NEWS.md | 89 ++++++++++++++++++----------------- R/gregorian-year-day.R | 3 + R/gregorian-year-month-day.R | 3 + R/gregorian-year-month-weekday.R | 3 + R/iso-year-week-day.R | 3 + R/quarterly-year-quarter-day.R | 4 + R/week-year-week-day.R | 3 + README.md | 1 build/vignette.rds |binary inst/doc/clock.R | 14 ++--- inst/doc/faq.R | 14 ++--- inst/doc/faq.html | 6 +- inst/doc/recipes.R | 10 +-- inst/doc/recipes.html | 10 +-- man/Date-arithmetic.Rd | 2 man/clock-arithmetic.Rd | 2 man/date_build.Rd | 2 man/date_time_build.Rd | 2 man/duration-arithmetic.Rd | 2 man/iso-year-week-day-arithmetic.Rd | 2 man/iso_year_week_day.Rd | 2 man/posixt-arithmetic.Rd | 2 man/time-point-arithmetic.Rd | 2 man/weekday-arithmetic.Rd | 2 man/year-day-arithmetic.Rd | 2 man/year-month-day-arithmetic.Rd | 2 man/year-month-weekday-arithmetic.Rd | 2 man/year-quarter-day-arithmetic.Rd | 2 man/year-week-day-arithmetic.Rd | 2 man/year_day.Rd | 2 man/year_month_day.Rd | 2 man/year_month_weekday.Rd | 2 man/year_quarter_day.Rd | 2 man/year_week_day.Rd | 2 src/quarterly.h | 36 +++++++------- src/utils.h | 9 +-- 39 files changed, 197 insertions(+), 156 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Documents in registers associated with trials can also be downloaded.
Other functions identify deduplicated records,
easily find and extract variables (fields) of interest even
from complex nested data as used by the registers,
merge variables and update queries.
The package can be used for meta-analysis and trend-analysis of
the design and cond [...truncated...]
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <[email protected]>
Diff between ctrdata versions 1.19.0 dated 2024-06-30 and 1.19.1 dated 2024-07-18
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 5 +++++ R/ctrGetQueryUrl.R | 1 - R/ctrLoadQueryIntoDb.R | 3 ++- R/ctrLoadQueryIntoDbCtgov2.R | 24 +++++++++++++++++++++++- R/ctrLoadQueryIntoDbCtis.R | 4 ++-- R/ctrdata-registers.R | 4 ++-- README.md | 23 ++++++++++------------- build/vignette.rds |binary inst/doc/ctrdata_install.pdf |binary inst/doc/ctrdata_retrieve.pdf |binary inst/doc/ctrdata_summarise.pdf |binary inst/tinytest/ctrdata_ctgov2.R | 2 +- man/ctrdata-registers.Rd | 4 ++-- 15 files changed, 65 insertions(+), 41 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for acoustic structure analysis. The main features of the package are the use of loops to apply tasks through acoustic signals referenced in a selection (annotation) table and the production of spectrograms in image files that allow to organize data and verify acoustic analyzes. The package offers functions to explore, organize and manipulate multiple sound files, explore and download 'Xeno-Canto' recordings, create spectrograms of complete recordings or individual signals, run different measures of acoustic signal structure, evaluate the performance of measurement methods, catalog signals, characterize different structural levels in acoustic signals, run statistical analysis of duet coordination and consolidate databases and annotation tables, among others.
Author: Marcelo Araya-Salas [aut, cre]
,
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <[email protected]>
Diff between warbleR versions 1.1.30 dated 2024-01-23 and 1.1.31 dated 2024-07-18
warbleR-1.1.30/warbleR/R/auto_detec.R |only warbleR-1.1.30/warbleR/R/find_peaks.R |only warbleR-1.1.30/warbleR/R/lbh_selec_table2-data.R |only warbleR-1.1.30/warbleR/R/new_function_names.R |only warbleR-1.1.30/warbleR/R/selec.table-data.R |only warbleR-1.1.30/warbleR/R/try_na.R |only warbleR-1.1.30/warbleR/data/lbh_selec_table2.rda |only warbleR-1.1.30/warbleR/data/new_function_names.rda |only warbleR-1.1.30/warbleR/data/selec.table.rda |only warbleR-1.1.30/warbleR/inst/doc/Intro_to_warbleR.R |only warbleR-1.1.30/warbleR/inst/doc/Intro_to_warbleR.Rmd |only warbleR-1.1.30/warbleR/inst/doc/Intro_to_warbleR.html |only warbleR-1.1.30/warbleR/man/auto_detec.Rd |only warbleR-1.1.30/warbleR/man/autodetec.Rd |only warbleR-1.1.30/warbleR/man/check_wavs.Rd |only warbleR-1.1.30/warbleR/man/checksels.Rd |only warbleR-1.1.30/warbleR/man/color.spectro.Rd |only warbleR-1.1.30/warbleR/man/coor.graph.Rd |only warbleR-1.1.30/warbleR/man/coor.test.Rd |only warbleR-1.1.30/warbleR/man/dfDTW.Rd |only warbleR-1.1.30/warbleR/man/df_DTW.Rd |only warbleR-1.1.30/warbleR/man/duration_wavs.Rd |only warbleR-1.1.30/warbleR/man/filtersels.Rd |only warbleR-1.1.30/warbleR/man/find_peaks.Rd |only warbleR-1.1.30/warbleR/man/fixwavs.Rd |only warbleR-1.1.30/warbleR/man/frange.Rd |only warbleR-1.1.30/warbleR/man/frange.detec.Rd |only warbleR-1.1.30/warbleR/man/info_wavs.Rd |only warbleR-1.1.30/warbleR/man/lbh_selec_table2.Rd |only warbleR-1.1.30/warbleR/man/lspec.Rd |only warbleR-1.1.30/warbleR/man/lspec2pdf.Rd |only warbleR-1.1.30/warbleR/man/move_imgs.Rd |only warbleR-1.1.30/warbleR/man/mp3_2_wav.Rd |only warbleR-1.1.30/warbleR/man/new_function_names.Rd |only warbleR-1.1.30/warbleR/man/ovlp_sels.Rd |only warbleR-1.1.30/warbleR/man/print.autodetec.output.Rd |only warbleR-1.1.30/warbleR/man/print.find_peaks.output.Rd |only warbleR-1.1.30/warbleR/man/rename_waves_est.Rd |only warbleR-1.1.30/warbleR/man/resample_est_waves.Rd |only warbleR-1.1.30/warbleR/man/rm_channels.Rd |only warbleR-1.1.30/warbleR/man/rm_sil.Rd |only warbleR-1.1.30/warbleR/man/selec.table.Rd |only warbleR-1.1.30/warbleR/man/seltailor.Rd |only warbleR-1.1.30/warbleR/man/signal_2_noise.Rd |only warbleR-1.1.30/warbleR/man/sim_songs.Rd |only warbleR-1.1.30/warbleR/man/snr_specs.Rd |only warbleR-1.1.30/warbleR/man/snrspecs.Rd |only warbleR-1.1.30/warbleR/man/song_param.Rd |only warbleR-1.1.30/warbleR/man/spec_param.Rd |only warbleR-1.1.30/warbleR/man/specan.Rd |only warbleR-1.1.30/warbleR/man/specreator.Rd |only warbleR-1.1.30/warbleR/man/split_wavs.Rd |only warbleR-1.1.30/warbleR/man/trackfreqs.Rd |only warbleR-1.1.30/warbleR/man/try_na.Rd |only warbleR-1.1.30/warbleR/man/wav_dur.Rd |only warbleR-1.1.30/warbleR/man/wav_info.Rd |only warbleR-1.1.30/warbleR/man/xcmaps.Rd |only warbleR-1.1.30/warbleR/man/xcorr.Rd |only warbleR-1.1.30/warbleR/vignettes/Intro_to_warbleR.Rmd |only warbleR-1.1.31/warbleR/DESCRIPTION | 15 warbleR-1.1.31/warbleR/MD5 | 357 +--- warbleR-1.1.31/warbleR/NAMESPACE | 44 warbleR-1.1.31/warbleR/NEWS.md | 11 warbleR-1.1.31/warbleR/R/RcppExports.R | 1 warbleR-1.1.31/warbleR/R/by_element_est.R | 9 warbleR-1.1.31/warbleR/R/catalog.R | 23 warbleR-1.1.31/warbleR/R/catalog2pdf.R | 10 warbleR-1.1.31/warbleR/R/check_sels.R | 21 warbleR-1.1.31/warbleR/R/check_sound_files.R | 12 warbleR-1.1.31/warbleR/R/color_spectro.R | 18 warbleR-1.1.31/warbleR/R/compare_methods.R | 331 +-- warbleR-1.1.31/warbleR/R/consolidate.R | 11 warbleR-1.1.31/warbleR/R/cross_correlation.R | 79 warbleR-1.1.31/warbleR/R/cut_sels.R | 22 warbleR-1.1.31/warbleR/R/deprec_funs.R | 240 ++ warbleR-1.1.31/warbleR/R/duration_sound_files.R | 32 warbleR-1.1.31/warbleR/R/filter_sels.R | 14 warbleR-1.1.31/warbleR/R/find_clipping.R | 3 warbleR-1.1.31/warbleR/R/fix_wavs.R | 16 warbleR-1.1.31/warbleR/R/freq_DTW.R | 97 - warbleR-1.1.31/warbleR/R/freq_range.R | 30 warbleR-1.1.31/warbleR/R/freq_range_detec.R | 18 warbleR-1.1.31/warbleR/R/freq_ts.R | 20 warbleR-1.1.31/warbleR/R/full_spectrogram2pdf.R | 20 warbleR-1.1.31/warbleR/R/full_spectrograms.R | 190 +- warbleR-1.1.31/warbleR/R/gaps.R | 9 warbleR-1.1.31/warbleR/R/image_to_wave.R | 2 warbleR-1.1.31/warbleR/R/inflections.R | 11 warbleR-1.1.31/warbleR/R/info_sound_files.R | 21 warbleR-1.1.31/warbleR/R/internal_functions.R | 840 +++++++++- warbleR-1.1.31/warbleR/R/lbh_selec_table-data.R | 12 warbleR-1.1.31/warbleR/R/mfcc_stats.R | 15 warbleR-1.1.31/warbleR/R/move_images.R | 23 warbleR-1.1.31/warbleR/R/mp32wav.R | 21 warbleR-1.1.31/warbleR/R/multi_DTW.R | 60 warbleR-1.1.31/warbleR/R/open_wd.R | 3 warbleR-1.1.31/warbleR/R/overlapping_sels.R | 40 warbleR-1.1.31/warbleR/R/phylo_spectro.R | 3 warbleR-1.1.31/warbleR/R/plot_coordination.R | 12 warbleR-1.1.31/warbleR/R/query_xc.R | 2 warbleR-1.1.31/warbleR/R/read_sound_file.R | 10 warbleR-1.1.31/warbleR/R/read_wave.R | 9 warbleR-1.1.31/warbleR/R/remove_channels.R | 21 warbleR-1.1.31/warbleR/R/remove_silence.R | 32 warbleR-1.1.31/warbleR/R/rename_est_waves.R | 13 warbleR-1.1.31/warbleR/R/resample_est.R | 21 warbleR-1.1.31/warbleR/R/selection_table.R | 128 - 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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 <[email protected]>
Diff between tinytex versions 0.51 dated 2024-05-06 and 0.52 dated 2024-07-18
tinytex-0.51/tinytex/tests/test-travis |only tinytex-0.51/tinytex/tests/test-travis.R |only tinytex-0.52/tinytex/DESCRIPTION | 8 ++++---- tinytex-0.52/tinytex/MD5 | 10 +++++----- tinytex-0.52/tinytex/R/tlmgr.R | 2 +- tinytex-0.52/tinytex/tests/test-ci |only tinytex-0.52/tinytex/tests/test-ci.R |only 7 files changed, 10 insertions(+), 10 deletions(-)
Title: Applying Partitioning Around Medoids to Single Cell Data with
High Number of Cells
Description: PAM (Partitioning Around Medoids) algorithm application to samples of single cell sequencing techniques
with a high number of cells (as many as the computer memory allows). The package uses a binary format to
store matrices (either full, sparse or symmetric) in files written in the disk that can contain any data type
(not just double) which allows its manipulation when memory is sufficient to load them as int or float, but not
as double. The PAM implementation is done in parallel, using several/all the cores of the machine, if it has them.
This package shares a great part of its code with packages 'jmatrix' and 'parallelpam' but their functionality is
included here so there is no need to install them.
Author: Juan Domingo [aut, cre] ,
Guillermo Ayala [ctb] ,
Spanish Ministry of Science and Innovation, MCIN/AEI
<doi:10.13039/501100011033> [fnd]
Maintainer: Juan Domingo <[email protected]>
Diff between scellpam versions 1.4.6.1 dated 2024-07-03 and 1.4.6.2 dated 2024-07-18
DESCRIPTION | 8 - MD5 | 12 +- NEWS | 4 inst/doc/jmatrixsc.html | 148 ++++++++++++++++----------------- inst/doc/parallelpamsc.html | 148 +++++++++++++++++---------------- inst/doc/scellpam.html | 196 +++++++++++++++++++++----------------------- inst/include/sparsematrix.h | 4 7 files changed, 264 insertions(+), 256 deletions(-)
Title: Print Maps, Draw on Them, Scan Them Back in
Description: Enables preparation of maps to be printed and drawn on.
Modified maps can then be scanned back in, and hand-drawn marks
converted to spatial objects.
Author: Mark Padgham [aut, cre],
Michael D. Sumner [aut],
Kelly Hondula [rev] ,
Nicholas Potter [rev] ,
Stanislaw Adaszewski [cph]
Maintainer: Mark Padgham <[email protected]>
Diff between mapscanner versions 0.0.6 dated 2021-11-25 and 0.1.1 dated 2024-07-18
DESCRIPTION | 9 MD5 | 56 +- R/aggregate_polys.R | 42 +- R/file-manipulation.R | 103 ++--- R/generate-maps.R | 435 ++++++++++++----------- R/rectify-maps.R | 291 ++++++++------- R/tokens.R | 49 +- R/utils.R | 10 build/vignette.rds |binary inst/doc/mapscanner.R | 142 ++++--- inst/doc/mapscanner.Rmd | 140 ++++--- inst/doc/mapscanner.html | 643 +++++++++++++++++++++++++++------- inst/doc/mapstyles.R | 39 +- inst/doc/mapstyles.Rmd | 45 +- inst/doc/mapstyles.html | 402 ++++++++++++++++----- man/mapscanner-package.Rd | 2 man/ms_aggregate_polys.Rd | 28 - man/ms_generate_map.Rd | 5 man/ms_rectify_map.Rd | 23 + src/RcppExports.cpp | 4 src/concaveman.cpp | 5 src/concaveman.h | 188 ++++++++- tests/testthat.R | 6 tests/testthat/test-aggregate-polys.R | 26 - tests/testthat/test-file-manip.R | 32 - tests/testthat/test-generate.R | 138 ++++--- tests/testthat/test-rectify.R | 223 ++++++----- vignettes/mapscanner.Rmd | 140 ++++--- vignettes/mapstyles.Rmd | 45 +- 29 files changed, 2112 insertions(+), 1159 deletions(-)
Title: Solvers for Large-Scale Eigenvalue and SVD Problems
Description: R interface to the 'Spectra' library
<https://spectralib.org/> for large-scale eigenvalue and SVD
problems. It is typically used to compute a few
eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
which is usually more efficient than eigen() if k << n. This package
provides the 'eigs()' function that does the similar job as in 'Matlab',
'Octave', 'Python SciPy' and 'Julia'. It also provides the 'svds()' function
to calculate the largest k singular values and corresponding
singular vectors of a real matrix. The matrix to be computed on can be
dense, sparse, or in the form of an operator defined by the user.
Author: Yixuan Qiu [aut, cre],
Jiali Mei [aut] ,
Gael Guennebaud [ctb] ,
Jitse Niesen [ctb]
Maintainer: Yixuan Qiu <[email protected]>
Diff between RSpectra versions 0.16-1 dated 2022-04-24 and 0.16-2 dated 2024-07-18
DESCRIPTION | 8 MD5 | 10 - build/vignette.rds |binary inst/NEWS.Rd | 8 inst/doc/introduction.html | 204 ++++++++++++------------ inst/include/Spectra/MatOp/internal/ArnoldiOp.h | 2 6 files changed, 120 insertions(+), 112 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data and some useful functions for
tabulation and plotting, as well as a number of epidemiological data
sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <[email protected]>
Diff between Epi versions 2.52 dated 2024-07-10 and 2.53 dated 2024-07-18
Epi-2.52/Epi/build |only Epi-2.52/Epi/inst/doc/addLexis.rnw |only Epi-2.52/Epi/inst/doc/crisk.rnw |only Epi-2.52/Epi/inst/doc/flup.rnw |only Epi-2.52/Epi/inst/doc/simLexis.rnw |only Epi-2.52/Epi/inst/doc/yll.rnw |only Epi-2.53/Epi/CHANGES | 6 Epi-2.53/Epi/DESCRIPTION | 8 Epi-2.53/Epi/MD5 | 43 Epi-2.53/Epi/NAMESPACE | 1 Epi-2.53/Epi/R/ci.eta.R | 19 Epi-2.53/Epi/inst/doc/addLexis.pdf |binary Epi-2.53/Epi/inst/doc/crisk.R | 14 Epi-2.53/Epi/inst/doc/crisk.pdf |binary Epi-2.53/Epi/inst/doc/flup.R | 16 Epi-2.53/Epi/inst/doc/flup.pdf | 4595 ++++++++++++++++++------------------ Epi-2.53/Epi/inst/doc/simLexis.R | 6 Epi-2.53/Epi/inst/doc/simLexis.pdf |binary Epi-2.53/Epi/inst/doc/yll.R | 5 Epi-2.53/Epi/inst/doc/yll.pdf |binary Epi-2.53/Epi/man/ci.eta.Rd | 29 Epi-2.53/Epi/man/ci.lin.Rd | 18 Epi-2.53/Epi/man/plotCIF.Rd | 4 Epi-2.53/Epi/vignettes/addLexis.tex |only Epi-2.53/Epi/vignettes/crisk.tex |only Epi-2.53/Epi/vignettes/flup.tex |only Epi-2.53/Epi/vignettes/simLexis.tex |only Epi-2.53/Epi/vignettes/yll.tex |only 28 files changed, 2376 insertions(+), 2388 deletions(-)
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table',
giving users the speed of 'data.table' while using tidyverse-like syntax.
Author: Mark Fairbanks [aut, cre],
Abdessabour Moutik [ctb],
Matt Carlson [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb],
Robert On [ctb],
Alexander Sevostianov [ctb],
Koen ter Berg [ctb]
Maintainer: Mark Fairbanks <[email protected]>
Diff between tidytable versions 0.11.0 dated 2024-02-09 and 0.11.1 dated 2024-07-18
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 35 +++++++++++++++++++++++++++++------ NEWS.md | 13 +++++++++++++ R/dt.R | 14 ++++++++------ R/group_by.R | 2 +- R/nest_by.R | 4 ---- R/new_tidytable.R | 2 +- R/print.R | 34 ++-------------------------------- R/purrr-pmap.R | 17 +++++++++++------ R/select.R | 6 +++--- R/utils-general.R | 11 +++++------ R/utils-tidyselect.R | 12 ++++++------ man/dt.Rd | 8 ++++++-- tests/testthat/test-as_tidytable.R | 1 + tests/testthat/test-filter.R | 11 +++++++++++ tests/testthat/test-group_by.R | 10 ++++++++++ tests/testthat/test-new_tidytable.R | 1 + tests/testthat/test-purrr.R | 11 +++++++++++ 19 files changed, 142 insertions(+), 96 deletions(-)
Title: Measure Memory and CPU Usage for Parallel R Code
Description: Measures memory and CPU usage of R code by regularly taking
snapshots of calls to the system command 'ps'. The package provides an entry
point (albeit coarse) to profile usage of system resources by R code run
in parallel.
Author: Simon Couch [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <[email protected]>
Diff between syrup versions 0.1.0 dated 2024-07-09 and 0.1.1 dated 2024-07-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-syrup.R | 5 +++++ 4 files changed, 15 insertions(+), 6 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] ,
Heidi Seibold [ctb] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <[email protected]>
Diff between partykit versions 1.2-20 dated 2023-04-14 and 1.2-21 dated 2024-07-18
partykit-1.2-20/partykit/inst/doc/constparty.R.R |only partykit-1.2-21/partykit/DESCRIPTION | 8 partykit-1.2-21/partykit/MD5 | 25 +- partykit-1.2-21/partykit/build/partial.rdb |binary partykit-1.2-21/partykit/build/vignette.rds |binary partykit-1.2-21/partykit/inst/NEWS.Rd | 9 partykit-1.2-21/partykit/inst/doc/constparty.pdf |binary partykit-1.2-21/partykit/inst/doc/ctree.pdf |binary partykit-1.2-21/partykit/inst/doc/mob.pdf |binary partykit-1.2-21/partykit/inst/doc/partykit.pdf |binary partykit-1.2-21/partykit/man/cforest.Rd | 3 partykit-1.2-21/partykit/man/model.frame.rpart.Rd | 4 partykit-1.2-21/partykit/tests/regtest-party.R | 1 partykit-1.2-21/partykit/tests/regtest-party.Rout.save | 155 +++++++---------- 14 files changed, 103 insertions(+), 102 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available. The methods are described in
Hothorn et al. (2006) <doi:10.1198/106186006X133933>,
Zeileis et al. (2008) <d [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Kurt Hornik [aut] ,
Carolin Strobl [aut] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <[email protected]>
Diff between party versions 1.3-15 dated 2024-04-29 and 1.3-16 dated 2024-07-18
DESCRIPTION | 20 ++++++++++++-------- MD5 | 18 +++++++++--------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 1 + inst/NEWS | 4 ++++ inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary man/RandomForest-class.Rd | 2 +- man/mob.Rd | 2 +- 10 files changed, 28 insertions(+), 19 deletions(-)
Title: A Generic Convex-Hull-Based Model Selection Method
Description: Given a set of models for which a measure of model (mis)fit and model complexity is provided, CHull(), developed by Ceulemans and Kiers (2006) <doi:10.1348/000711005X64817>, determines the models that are located on the boundary of the convex hull and selects an optimal model by means of the scree test values.
Author: Marlies Vervloet [aut, cre, trl],
Tom Wilderjans [aut],
Jeffrey Durieux [aut],
Eva Ceulemans [aut]
Maintainer: Kristof Meers <[email protected]>
Diff between multichull versions 1.0.1 dated 2023-10-26 and 3.0.0 dated 2024-07-18
DESCRIPTION | 11 +- MD5 | 42 +++++--- NAMESPACE | 7 + NEWS.md | 12 ++ R/CHull.R | 28 +++-- R/CHull.default.R | 34 +++--- R/MultiCHull.R | 21 ++-- R/MultiCHull.default.R | 131 ++++++++++++++++---------- R/chulldata.R |only R/chulldataboot.R |only R/plot.CHull.R | 52 ++++++++-- R/plot.MultiCHull.R | 137 ++++++++++++++++++++------- R/plot.MultiCHullcom.R |only R/print.MultiCHull.R | 4 R/runShinyApp.R | 6 - R/summary.CHull.R | 4 R/summary.MultiCHull.R | 14 +- R/summary.MultiCHullcom.R |only data |only inst/ShinyApp/multichull/server.R | 169 ++++++++++++++++++++------------- inst/ShinyApp/multichull/ui.R | 190 +++++++++++++++++++++++--------------- man/CHull.Rd | 8 + man/MultiCHull.Rd | 38 +++++-- man/chulldata.Rd |only man/chulldataboot.Rd |only 25 files changed, 589 insertions(+), 319 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre] ,
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb],
Susan Scheibe [ctb]
Maintainer: Torsten Hothorn <[email protected]>
Diff between multcomp versions 1.4-25 dated 2023-06-20 and 1.4-26 dated 2024-07-18
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- build/vignette.rds |binary data/cholesterol.rda |binary data/litter.rda |binary inst/NEWS | 11 +++++++++-- inst/doc/chfls1.pdf |binary inst/doc/generalsiminf.pdf |binary inst/doc/multcomp-examples.pdf |binary man/mmm.Rd | 2 +- man/plot.cld.Rd | 2 +- 11 files changed, 27 insertions(+), 20 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014
<DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic
analysis of functional data through phase and amplitude separation.
Author: J. Derek Tucker [aut, cre] ,
Aymeric Stamm [ctb]
Maintainer: J. Derek Tucker <[email protected]>
Diff between fdasrvf versions 2.3.0 dated 2024-07-16 and 2.3.1 dated 2024-07-18
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 3 +++ README.md | 2 +- man/figures/README-1d_aligned_plot-1.png |binary man/figures/README-1d_aligned_plot-2.png |binary man/figures/README-1d_aligned_plot-3.png |binary man/figures/README-1d_aligned_plot-4.png |binary man/figures/README-1d_aligned_plot-5.png |binary man/figures/README-1d_curve_plot-1.png |binary tests/testthat/test-refactoring.R | 6 +++--- 11 files changed, 21 insertions(+), 18 deletions(-)
Title: ExifTool Functionality from R
Description: Reads, writes, and edits EXIF and other file metadata using
ExifTool <https://exiftool.org/>, returning read results as a data
frame. ExifTool supports many different metadata formats including EXIF,
GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP
and ID3, Lyrics3, as well as the maker notes of many digital cameras by
Canon, Casio, DJI, FLIR, FujiFilm, GE, GoPro, HP, JVC/Victor, Kodak, Leaf,
Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson,
Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung, Sanyo,
Sigma/Foveon and Sony.
Author: Joshua O'Brien [aut, cre]
Maintainer: Joshua O'Brien <[email protected]>
Diff between exiftoolr versions 0.2.4 dated 2024-03-28 and 0.2.5 dated 2024-07-18
DESCRIPTION | 10 ++--- MD5 | 16 ++++----- NEWS.md | 6 +++ R/exif_read.R | 76 ++++++++++++++++++++------------------------- R/install.R | 42 +++++++++++------------- R/utils.R | 27 +++++++-------- man/configure_exiftoolr.Rd | 8 +--- man/exif_read.Rd | 76 ++++++++++++++++++++------------------------- man/install_exiftool.Rd | 31 ++++++++---------- 9 files changed, 138 insertions(+), 154 deletions(-)
Title: Count Transformation Models
Description: Count transformation models featuring
parameters interpretable as discrete hazard ratios, odds ratios,
reverse-time discrete hazard ratios, or transformed expectations.
An appropriate data transformation for a count outcome and
regression coefficients are simultaneously estimated by maximising
the exact discrete log-likelihood using the computational framework
provided in package 'mlt', technical details are given in
Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>.
The package also contains an experimental implementation of
multivariate count transformation models with an application
to multi-species distribution models <DOI:10.48550/arXiv.2201.13095>.
Author: Sandra Siegfried [aut, cre] ,
Luisa Barbanti [aut] ,
Torsten Hothorn [aut]
Maintainer: Sandra Siegfried <[email protected]>
Diff between cotram versions 0.4-4 dated 2023-05-25 and 0.5-0 dated 2024-07-18
cotram-0.4-4/cotram/inst/application/ex_DVC.R |only cotram-0.4-4/cotram/inst/simulation/countDGP.R |only cotram-0.5-0/cotram/DESCRIPTION | 18 ++-- cotram-0.5-0/cotram/MD5 | 48 ++++++------ cotram-0.5-0/cotram/NAMESPACE | 9 +- cotram-0.5-0/cotram/R/mcotram.R |only cotram-0.5-0/cotram/R/methods.R | 6 - cotram-0.5-0/cotram/R/models.R | 6 + cotram-0.5-0/cotram/build/partial.rdb |binary cotram-0.5-0/cotram/build/vignette.rds |binary cotram-0.5-0/cotram/cleanup | 28 ------- cotram-0.5-0/cotram/demo |only cotram-0.5-0/cotram/inst/CITATION | 2 cotram-0.5-0/cotram/inst/NEWS.Rd | 9 ++ cotram-0.5-0/cotram/inst/README | 4 - cotram-0.5-0/cotram/inst/application/Ex_DVC.R |only cotram-0.5-0/cotram/inst/doc/cotram.Rnw | 4 - cotram-0.5-0/cotram/inst/doc/cotram.pdf |binary cotram-0.5-0/cotram/inst/simulation/SIM_countDGP.R |only cotram-0.5-0/cotram/man/confband.Rd | 2 cotram-0.5-0/cotram/man/cotram-methods.Rd | 2 cotram-0.5-0/cotram/man/cotram.Rd | 8 +- cotram-0.5-0/cotram/man/mcotram.Rd |only cotram-0.5-0/cotram/tests/Examples/cotram-Ex.Rout.save | 56 +++++++++++--- cotram-0.5-0/cotram/tests/confband-Ex.Rout.save | 10 +- cotram-0.5-0/cotram/tests/models-Ex.R | 67 ++++++++++++----- cotram-0.5-0/cotram/tests/predict-Ex.R | 15 +-- cotram-0.5-0/cotram/vignettes/cotram.Rnw | 4 - 28 files changed, 176 insertions(+), 122 deletions(-)
Title: 'Creates Color Palettes Inspired by Dune'
Description: Enables the use of color palettes inspired by the 'Dune' movies. These palettes are compatible with 'ggplot2'. See Wickham (2016) <doi:10.1007/978-3-319-24277-4> for more details on 'ggplot2'.
Author: Nicholas Vietto [aut, cre, cph]
Maintainer: Nicholas Vietto <[email protected]>
Diff between Rdune versions 1.0.2 dated 2024-07-08 and 1.1.0 dated 2024-07-18
DESCRIPTION | 6 +- MD5 | 19 ++++--- NEWS.md | 6 ++ R/Rdune-package.R |only README.md | 15 +++++ build/partial.rdb |only inst/doc/my-vignette.R | 8 --- inst/doc/my-vignette.Rmd | 14 ----- inst/doc/my-vignette.html | 97 ++++++++++++++++---------------------- man/Rdune-package.Rd |only man/figures/README-example2-1.png |binary vignettes/my-vignette.Rmd | 14 ----- 12 files changed, 77 insertions(+), 102 deletions(-)
Title: Improved Predictors
Description: Improved predictive models by indirect classification and
bagging for classification, regression and survival problems
as well as resampling based estimators of prediction error.
Author: Andrea Peters [aut],
Torsten Hothorn [aut, cre],
Brian D. Ripley [ctb],
Terry Therneau [ctb],
Beth Atkinson [ctb]
Maintainer: Torsten Hothorn <[email protected]>
Diff between ipred versions 0.9-14 dated 2023-03-09 and 0.9-15 dated 2024-07-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/NEWS | 4 ++++ inst/doc/ipred-examples.pdf |binary man/bagging.Rd | 2 +- 6 files changed, 14 insertions(+), 10 deletions(-)
Title: A Vector Spatio-Temporal Data Structure for Data Analysis
Description: A spatiotemperal data object in a relational data structure to separate the recording of time variant/ invariant variables.
Author: H. Sherry Zhang [aut, cre] ,
Dianne Cook [aut] ,
Ursula Laa [aut] ,
Nicolas Langrene [aut] ,
Patricia Menendez [aut]
Maintainer: H. Sherry Zhang <[email protected]>
Diff between cubble versions 0.3.1 dated 2024-07-02 and 0.3.2 dated 2024-07-18
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 4 ++++ R/as-cubble.R | 10 ++++++---- R/cubble-print.R | 13 +++++++++---- README.md | 2 +- inst/doc/cb1class.html | 2 +- inst/doc/cb2create.html | 38 +++++++++++++++++++------------------- inst/doc/cb3tsibblesf.html | 19 +++++++++---------- inst/doc/cb4glyph.html | 2 +- inst/doc/cb5match.html | 6 +++--- inst/doc/cb6interactive.html | 2 +- inst/doc/cb7misc.html | 2 +- man/as_cubble.Rd | 4 +++- 14 files changed, 74 insertions(+), 62 deletions(-)
Title: Single-Source Capture-Recapture Models
Description: Implementation of single-source capture-recapture methods for population size estimation using zero-truncated, zero-one truncated and zero-truncated one-inflated Poisson, Geometric and Negative Binomial regression as well as Zelterman's and Chao's regression. Package includes point and interval estimators for the population size with variances estimated using analytical or bootstrap method. Details can be found in: van der Heijden et all. (2003) <doi:10.1191/1471082X03st057oa>, Böhning and van der Heijden (2019) <doi:10.1214/18-AOAS1232>, Böhning et al. (2020) Capture-Recapture Methods for the Social and Medical Sciences or Böhning and Friedl (2021) <doi:10.1007/s10260-021-00556-8>.
Author: Piotr Chlebicki [aut, cre],
Maciej Beresewicz [aut, ctb]
Maintainer: Piotr Chlebicki <[email protected]>
Diff between singleRcapture versions 0.2.1.1 dated 2023-10-23 and 0.2.1.2 dated 2024-07-18
singleRcapture-0.2.1.1/singleRcapture/R/Methods.R |only singleRcapture-0.2.1.1/singleRcapture/R/bootstraps.R |only singleRcapture-0.2.1.2/singleRcapture/DESCRIPTION | 10 singleRcapture-0.2.1.2/singleRcapture/MD5 | 89 singleRcapture-0.2.1.2/singleRcapture/NEWS.md | 12 singleRcapture-0.2.1.2/singleRcapture/R/Chao.R | 8 singleRcapture-0.2.1.2/singleRcapture/R/Internals.R | 40 singleRcapture-0.2.1.2/singleRcapture/R/control.R | 5 singleRcapture-0.2.1.2/singleRcapture/R/documentationFiles.R | 3 singleRcapture-0.2.1.2/singleRcapture/R/estimatePopsize.R | 172 singleRcapture-0.2.1.2/singleRcapture/R/leave-one-out.R |only singleRcapture-0.2.1.2/singleRcapture/R/marginal.R | 68 singleRcapture-0.2.1.2/singleRcapture/R/miscDiagnostics.R |only singleRcapture-0.2.1.2/singleRcapture/R/miscPrints.R |only singleRcapture-0.2.1.2/singleRcapture/R/nonparametricBootstrap.R |only singleRcapture-0.2.1.2/singleRcapture/R/parametricBootstrap.R |only singleRcapture-0.2.1.2/singleRcapture/R/predict.R |only singleRcapture-0.2.1.2/singleRcapture/R/sandwichMethods.R | 2 singleRcapture-0.2.1.2/singleRcapture/R/semiparametricBootstrap.R |only singleRcapture-0.2.1.2/singleRcapture/R/simulate.R |only singleRcapture-0.2.1.2/singleRcapture/R/smallMethods.R |only singleRcapture-0.2.1.2/singleRcapture/R/strataEstimation.R |only singleRcapture-0.2.1.2/singleRcapture/R/summary.R |only singleRcapture-0.2.1.2/singleRcapture/R/updates.R |only singleRcapture-0.2.1.2/singleRcapture/R/zelterman.R | 8 singleRcapture-0.2.1.2/singleRcapture/R/zotgeom.R | 4 singleRcapture-0.2.1.2/singleRcapture/R/zotpoisson.R | 10 singleRcapture-0.2.1.2/singleRcapture/R/ztHurdlenegbin.R | 8 singleRcapture-0.2.1.2/singleRcapture/R/ztgeom.R | 4 singleRcapture-0.2.1.2/singleRcapture/R/ztnegbin.R | 2 singleRcapture-0.2.1.2/singleRcapture/R/ztoinegbin.R | 14 singleRcapture-0.2.1.2/singleRcapture/R/ztpoisson.R | 8 singleRcapture-0.2.1.2/singleRcapture/README.md | 6 singleRcapture-0.2.1.2/singleRcapture/build/singleRcapture.pdf |binary singleRcapture-0.2.1.2/singleRcapture/build/stage23.rdb |binary singleRcapture-0.2.1.2/singleRcapture/inst/tinytest/test_control_fails.R |only singleRcapture-0.2.1.2/singleRcapture/inst/tinytest/test_developer_only.R |only singleRcapture-0.2.1.2/singleRcapture/inst/tinytest/test_inflated_hurdle.R | 3932 +++++++--- singleRcapture-0.2.1.2/singleRcapture/inst/tinytest/test_methods.R | 2 singleRcapture-0.2.1.2/singleRcapture/inst/tinytest/test_simulate.R |only singleRcapture-0.2.1.2/singleRcapture/inst/tinytest/test_singleRcapture.R | 199 singleRcapture-0.2.1.2/singleRcapture/inst/tinytest/test_zerotruncated.R | 482 + singleRcapture-0.2.1.2/singleRcapture/man/confint.singleRStaticCountData.Rd | 2 singleRcapture-0.2.1.2/singleRcapture/man/controlPopVar.Rd | 5 singleRcapture-0.2.1.2/singleRcapture/man/popSizeEst.Rd | 2 singleRcapture-0.2.1.2/singleRcapture/man/predict.singleRStaticCountData.Rd | 7 singleRcapture-0.2.1.2/singleRcapture/man/redoPopEstimation.Rd | 9 singleRcapture-0.2.1.2/singleRcapture/man/regDiagSingleR.Rd | 26 singleRcapture-0.2.1.2/singleRcapture/man/simulate.Rd | 2 singleRcapture-0.2.1.2/singleRcapture/man/stratifyPopsize.Rd | 8 singleRcapture-0.2.1.2/singleRcapture/man/summary.singleRStaticCountData.Rd | 9 singleRcapture-0.2.1.2/singleRcapture/man/vcov.singleRStaticCountData.Rd | 4 singleRcapture-0.2.1.2/singleRcapture/man/vcovHC.singleRStaticCountData.Rd | 2 singleRcapture-0.2.1.2/singleRcapture/tests/tinytest.R | 3 54 files changed, 3533 insertions(+), 1634 deletions(-)
More information about singleRcapture at CRAN
Permanent link
Title: Computes Revisitation Metrics for Trajectory Data
Description: Computes revisitation metrics for trajectory data, such as the number of revisitations for each location as well as the time spent for that visit and the time since the previous visit. Also includes functions to plot data.
Author: Chloe Bracis [aut, cre]
Maintainer: Chloe Bracis <[email protected]>
Diff between recurse versions 1.3.0 dated 2024-02-18 and 1.4.0 dated 2024-07-18
DESCRIPTION | 12 LICENSE | 2 MD5 | 101 - NAMESPACE | 49 NEWS.md | 73 - R/RcppExports.R | 38 R/calculateCrossingPercentage.R | 158 +- R/calculateIntervalResidenceTime.R | 186 +- R/drawCircle.R | 88 - R/getRecursions.R | 126 +- R/getRecursions.data.frame.R | 76 - R/getRecursions.move.R | 66 - R/getRecursions.move2.R |only R/getRecursions.movestack.R | 36 R/getRecursions3D.R | 126 +- R/getRecursions3D.data.frame.R | 78 - R/getRecursions3DAtLocations.R | 134 +- R/getRecursions3DAtLocations.data.frame.R | 72 - R/getRecursionsAtLocations.R | 134 +- R/getRecursionsAtLocations.data.frame.R | 70 - R/getRecursionsAtLocations.move.R | 60 R/getRecursionsAtLocations.move2.R |only R/getRecursionsAtLocations.movestack.R | 32 R/getRecursionsInPolygon.Move.R | 66 - R/getRecursionsInPolygon.R | 127 +- R/getRecursionsInPolygon.data.frame.R | 382 +++--- R/getRecursionsInPolygon.move2.R |only R/getRecursionsInPolygon.movestack.R | 36 R/plot.recurse.R | 186 +- R/recurse.R | 139 +- README.md | 46 build/vignette.rds |binary inst/CITATION | 16 inst/doc/recurse.R | 330 ++--- inst/doc/recurse.Rmd | 650 +++++----- inst/doc/recurse.html | 1752 ++++++++++++++-------------- man/calculateIntervalResidenceTime.Rd | 98 - man/dot-calculateCrossingPercentageCmplx.Rd | 42 man/drawCircle.Rd | 98 - man/getRecursions.Rd | 239 +-- man/getRecursions3D.Rd | 184 +- man/getRecursions3DAtLocations.Rd | 202 +-- man/getRecursionsAtLocations.Rd | 264 ++-- man/getRecursionsInPolygon.Rd | 248 ++- man/martin.Rd | 48 man/plot.recurse.Rd | 88 - man/recurse.Rd | 39 man/track.Rd | 48 man/wren.Rd | 48 tests/testthat.R | 8 tests/testthat/test_crossing.R | 140 +- tests/testthat/test_recurse.R | 435 +++--- vignettes/recurse.Rmd | 650 +++++----- 53 files changed, 4208 insertions(+), 4118 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <[email protected]>
Diff between performance versions 0.12.1 dated 2024-07-15 and 0.12.2 dated 2024-07-18
DESCRIPTION | 6 - MD5 | 24 ++-- NEWS.md | 5 R/check_heterogeneity_bias.R | 5 man/check_heterogeneity_bias.Rd | 2 tests/testthat/_snaps/bootstrapped_icc_ci.md | 120 +++++++++++------------ tests/testthat/_snaps/check_collinearity.md | 74 +++++++------- tests/testthat/_snaps/mclogit.md | 44 ++++---- tests/testthat/_snaps/model_performance.rma.md | 14 +- tests/testthat/_snaps/nestedLogit.md | 24 ++-- tests/testthat/_snaps/pkg-ivreg.md | 22 ++-- tests/testthat/_snaps/windows/check_itemscale.md | 48 ++++----- tests/testthat/test-check_heterogeneity_bias.R | 1 13 files changed, 200 insertions(+), 189 deletions(-)
Title: 2D and 3D Hive Plots for R
Description: Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
Author: Bryan A. Hanson [aut, cre] ,
Vesna Memisevic [ctb],
Jonathan Chung [ctb]
Maintainer: Bryan A. Hanson <[email protected]>
Diff between HiveR versions 0.3.63 dated 2020-06-09 and 0.4.0 dated 2024-07-18
HiveR-0.3.63/HiveR/build |only HiveR-0.3.63/HiveR/inst/CITATION |only HiveR-0.3.63/HiveR/inst/doc |only HiveR-0.3.63/HiveR/vignettes |only HiveR-0.4.0/HiveR/DESCRIPTION | 16 +++--- HiveR-0.4.0/HiveR/MD5 | 39 ++++------------ HiveR-0.4.0/HiveR/NEWS.md | 4 + HiveR-0.4.0/HiveR/R/HiveR-package.R | 2 HiveR-0.4.0/HiveR/R/adj2HPD.R | 80 ++++++++++++++++----------------- HiveR-0.4.0/HiveR/R/chkHPD.R | 30 ++++++------ HiveR-0.4.0/HiveR/data/Arroyo.RData |binary HiveR-0.4.0/HiveR/data/HEC.RData |binary HiveR-0.4.0/HiveR/data/Safari.RData |binary HiveR-0.4.0/HiveR/man/HiveR-package.Rd | 8 +++ HiveR-0.4.0/HiveR/man/adj2HPD.Rd | 80 ++++++++++++++++----------------- HiveR-0.4.0/HiveR/man/plotHive.Rd | 6 +- 16 files changed, 132 insertions(+), 133 deletions(-)
Title: 'data.table' Time-Series
Description: High-frequency time-series support via 'nanotime' and 'data.table'.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <[email protected]>
Diff between dtts versions 0.1.2 dated 2024-01-31 and 0.1.3 dated 2024-07-18
ChangeLog | 21 +++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ README.md | 2 +- inst/NEWS.Rd | 10 ++++++++++ inst/tinytest/test_dtts.R | 20 ++++++++++++++++---- src/align.cpp | 4 ++-- 7 files changed, 60 insertions(+), 17 deletions(-)
Title: Plot Shipboard DAS Data
Description: A utility program oriented to create maps, plot data, and do basic data summaries of DAS data files.
These files are typically, but do not have to be
DAS <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF> data
produced by the Southwest Fisheries Science Center (SWFSC) program 'WinCruz'.
Author: Sam Woodman [aut, cre] ,
Tim Gerrodette [aut]
Maintainer: Sam Woodman <[email protected]>
Diff between CruzPlot versions 1.4.8 dated 2022-06-01 and 1.4.9 dated 2024-07-18
CruzPlot-1.4.8/CruzPlot/inst/shiny/server_files/drawInteractive.R |only CruzPlot-1.4.8/CruzPlot/inst/shiny/server_files/drawStatic.R |only CruzPlot-1.4.9/CruzPlot/DESCRIPTION | 24 ++-- CruzPlot-1.4.9/CruzPlot/MD5 | 28 ++-- CruzPlot-1.4.9/CruzPlot/NEWS.md | 15 ++ CruzPlot-1.4.9/CruzPlot/R/CruzPlot-package.R | 8 - CruzPlot-1.4.9/CruzPlot/R/cruzplot_gui.R | 2 CruzPlot-1.4.9/CruzPlot/README.md | 58 ++-------- CruzPlot-1.4.9/CruzPlot/inst/shiny/app.R | 52 +++++--- CruzPlot-1.4.9/CruzPlot/inst/shiny/rsconnect |only CruzPlot-1.4.9/CruzPlot/inst/shiny/server_1_map/cruzMapSave.R | 11 + CruzPlot-1.4.9/CruzPlot/inst/shiny/server_files/cruzDraw.R |only CruzPlot-1.4.9/CruzPlot/inst/shiny/ui_files/ui_createMap.R | 28 +++- CruzPlot-1.4.9/CruzPlot/inst/shiny/ui_files/ui_dasPlot.R | 2 CruzPlot-1.4.9/CruzPlot/man/CruzPlot-package.Rd | 5 CruzPlot-1.4.9/CruzPlot/man/cruzplot_gui.Rd | 3 16 files changed, 121 insertions(+), 115 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut]
Maintainer: Jinseob Kim <[email protected]>
Diff between jsmodule versions 1.5.5 dated 2024-06-05 and 1.5.6 dated 2024-07-18
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/utils.R | 5 ++++- build/vignette.rds |binary inst/doc/jsmodule.html | 6 +++--- 6 files changed, 23 insertions(+), 14 deletions(-)
Title: Identifying Infection with Machine Intelligence
Description: A novel machine learning method for plant viruses diagnostic using
genome sequencing data. This package includes three different machine
learning models, random forest, XGBoost, and elastic net, to train and
predict mapped genome samples. Mappability profile and unreliable regions
are introduced to the algorithm, and users can build a mappability profile
from scratch with functions included in the package. Plotting mapped sample
coverage information is provided.
Author: Haochen Ning [aut],
Ian Boyes [aut],
Ibrahim Numanagic [aut] ,
Michael Rott [aut],
Li Xing [aut] ,
Xuekui Zhang [aut, cre]
Maintainer: Xuekui Zhang <[email protected]>
Diff between iimi versions 1.0.2 dated 2024-03-07 and 1.1.0 dated 2024-07-18
DESCRIPTION | 11 MD5 | 29 +- NAMESPACE | 2 R/convert_bam_to_rle.R | 1 R/data.R | 1 R/predict_iimi.R | 25 +- R/train_iimi.R | 16 - data/example_cov.rda |binary data/example_diag.rda |binary data/trained_xgb.rda |binary inst/REFERENCES |only inst/doc/package_vignette.R | 108 ++++++-- inst/doc/package_vignette.Rmd | 334 ++++++++++++++++++--------- inst/doc/package_vignette.html | 504 ++++++++++++++++++++++++++++------------- man/trained_xgb.Rd | 2 vignettes/package_vignette.Rmd | 334 ++++++++++++++++++--------- 16 files changed, 924 insertions(+), 443 deletions(-)
Title: A Modification of Fleiss' Kappa in Case of Nominal and Ordinal
Variables
Description: The kappa statistic implemented by Fleiss is a very popular index for assessing the reliability of agreement among multiple observers. It is used both in the psychological and in the psychiatric field. Other fields of application are typically medicine, biology and engineering. Unfortunately,the kappa statistic may behave inconsistently in case of strong agreement between raters, since this index assumes lower values than it would have been expected. We propose a modification kappa implemented by Fleiss in case of nominal and ordinal variables. Monte Carlo simulations are used both to testing statistical hypotheses and to calculating percentile bootstrap confidence intervals based on proposed statistic in case of nominal and ordinal data.
Author: Daniele Giardiello [cre],
Piero Quatto [aut],
Enrico Ripamonti [aut],
Stefano Vigliani [ctb]
Maintainer: Daniele Giardiello <[email protected]>
Diff between raters versions 2.0.4 dated 2024-05-29 and 2.1.0 dated 2024-07-18
DESCRIPTION | 6 - MD5 | 10 - R/concordance.R | 289 +++++++++++++++++++++++++++----------------------- R/wlin.conc.R | 110 +++++++------------ R/wquad.conc.R | 101 ++++++----------- man/raters-package.Rd | 2 6 files changed, 248 insertions(+), 270 deletions(-)
Title: Shadow Text Grob and Layer
Description: Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for 'ggplot2'.
These functions create/draw text grob with background shadow.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <[email protected]>
Diff between shadowtext versions 0.1.3 dated 2024-01-19 and 0.1.4 dated 2024-07-18
DESCRIPTION | 8 ++--- MD5 | 14 +++++--- NEWS.md | 4 ++ R/element_shadowtext.R | 72 ++++++++++++++++++++++++++-------------------- R/shadowtext-package.R |only build/vignette.rds |binary inst/doc/shadowtext.html | 14 ++++---- man/element_shadowtext.Rd | 9 +++++ man/shadowtext-package.Rd |only 9 files changed, 74 insertions(+), 47 deletions(-)
Title: An R Interface to Open-Access Malaria Data, Hosted by the
'Malaria Atlas Project'
Description: A suite of tools to allow you to download all
publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from
the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting
the downloaded data.
Author: Mauricio van den Berg [aut, cre],
Sarah Connor [aut],
Daniel Pfeffer [aut] ,
Tim Lucas [aut] ,
Daniel May [aut] ,
Suzanne Keddie [aut] ,
Jen Rozier [aut] ,
Oliver Watson [aut] ,
Harry Gibson [aut] ,
Nick Golding [ctb],
David Smith [ctb]
Maintainer: Mauricio van den Berg <[email protected]>
Diff between malariaAtlas versions 1.5.1 dated 2023-10-27 and 1.6.1 dated 2024-07-18
DESCRIPTION | 8 +- MD5 | 49 +++++++------- NEWS.md | 7 ++ R/autoplot.MAPraster.R | 2 R/autoplot.SpatRaster.R | 2 R/autoplot.SpatRasterCollection.R | 4 - R/autoplot.pr.points.R | 2 R/autoplot.vector.points.R | 2 R/autoplotRasterHelper.R | 32 +++++++-- R/getRaster.R | 87 ++++++++++++++----------- R/getShp.R | 53 ++++++++------- R/maskedRasterHelper.R |only R/ows4r_utils.R | 11 +-- inst/doc/overview.html | 16 ++-- man/autoplot.MAPraster.Rd | 2 man/autoplot.SpatRaster.Rd | 2 man/autoplot.SpatRasterCollection.Rd | 2 man/autoplot.pr.points.Rd | 2 man/autoplot.vector.points.Rd | 2 man/download_rst.Rd |only man/get_wcs_client_from_raster_id.Rd | 2 man/get_wcs_coverage_summary_from_raster_id.Rd | 2 man/isMaskedRaster.Rd |only tests/testthat/test_autoplot.MAPraster.R | 4 - tests/testthat/test_extractRaster.R | 22 +++--- tests/testthat/test_getRaster.R | 49 ++++++++------ tests/testthat/test_getShp.R | 7 ++ 27 files changed, 216 insertions(+), 155 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-28 3.3.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-17 0.1.0
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Yihui Xie <[email protected]>
Diff between xfun versions 0.45 dated 2024-06-16 and 0.46 dated 2024-07-18
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/app.R | 2 +- R/cache.R | 2 +- R/markdown.R | 19 ++++++++++--------- R/paths.R | 4 ++-- R/session.R | 8 +++++--- inst/doc/xfun.html | 8 ++++---- man/cache_exec.Rd | 2 +- 10 files changed, 42 insertions(+), 33 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matt Higham [aut] ,
Ryan A. Hill [ctb] ,
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <[email protected]>
Diff between spmodel versions 0.6.0 dated 2024-04-16 and 0.7.0 dated 2024-07-18
DESCRIPTION | 26 MD5 | 94 - NAMESPACE | 9 NEWS.md | 18 R/AUROC.R |only R/BIC.R |only R/BIC_glm.R |only R/cov_initial_search.R | 2274 +++++++++++++++++----------------- R/cov_initial_search_glm.R | 2108 +++++++++++++++---------------- R/get_data_object.R | 1060 ++++++++------- R/get_data_object_glm.R | 1196 +++++++++-------- R/get_local_list.R | 310 ++-- R/glance.R | 118 - R/loocv_glm.R | 595 ++++---- R/predict.R | 2267 +++++++++++++++++---------------- R/predict_glm.R | 1816 +++++++++++++-------------- R/spautor.R | 542 ++++---- R/spgautor.R | 742 +++++------ R/spglm.R | 947 +++++++------- R/splm.R | 811 ++++++------ R/spmodel-package.R | 34 R/utils.R | 68 - README.md | 192 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.Rmd | 787 +++++------ inst/doc/introduction.html | 56 inst/extdata/exdata_Mpoly.rda |binary inst/extdata/exdata_Upoly.rda |binary inst/extdata/exdata_poly.rda |binary inst/references.bib | 1478 +++++++++++----------- man/AUROC.Rd |only man/BIC.spmodel.Rd |only man/figures |only man/glance.spmodel.Rd | 9 man/loocv.Rd | 23 man/predict.spmodel.Rd | 17 man/spautor.Rd | 2 man/spgautor.Rd | 2 man/spglm.Rd | 5 man/splm.Rd | 5 man/spmodel-package.Rd | 11 tests/testthat/test-extras-spgautor.R | 10 tests/testthat/test-extras-spglm.R | 20 tests/testthat/test-extras-splm.R | 6 tests/testthat/test-extras.R | 43 tests/testthat/test-spautor.R | 810 ++++++------ tests/testthat/test-spgautor.R | 845 ++++++------ tests/testthat/test-spglm.R | 917 ++++++------- tests/testthat/test-splm.R | 868 ++++++------ vignettes/introduction.Rmd | 787 +++++------ 51 files changed, 11129 insertions(+), 10799 deletions(-)
Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton [aut, cre], D.L. Parkhurst [aut], and C.A.J. Appelo [aut], with contributions
from D. Gillespie [ctb] for Chipmunk BASIC and S.D. Cohen [ctb], A.C. Hindmarsh [ctb],
R. Serban [ctb], D. Shumaker [ctb], and A.G. Taylor [ctb] for CVODE/SUN [...truncated...]
Maintainer: S.R. Charlton <[email protected]>
Diff between phreeqc versions 3.7.6 dated 2023-12-06 and 3.8.0 dated 2024-07-18
DESCRIPTION | 8 MD5 | 241 +-- R/phreeqc.R | 147 +- build/partial.rdb |binary data/databases.rda |binary data/examples.rda |binary man/Amm.dat.Rd | 3 man/ColdChem.dat.Rd | 3 man/Kinec.v2.dat.Rd |only man/PHREEQC_ThermoddemV1.10_15Dec2020.dat.Rd |only man/Tipping_Hurley.dat.Rd | 3 man/core10.dat.Rd | 3 man/ex1.Rd | 2 man/ex10.Rd | 4 man/ex11.Rd | 4 man/ex12.Rd | 4 man/ex13.Rd | 4 man/ex14.Rd | 4 man/ex15.Rd | 4 man/ex15.dat.Rd | 3 man/ex16.Rd | 4 man/ex17.Rd | 4 man/ex18.Rd | 4 man/ex19.Rd | 4 man/ex2.Rd | 2 man/ex20.Rd | 4 man/ex21.Rd | 4 man/ex22.Rd | 4 man/ex3.Rd | 4 man/ex4.Rd | 4 man/ex5.Rd | 4 man/ex6.Rd | 4 man/ex7.Rd | 4 man/ex8.Rd | 4 man/ex9.Rd | 4 man/frezchem.dat.Rd | 3 man/iso.dat.Rd | 3 man/llnl.dat.Rd | 3 man/minteq.dat.Rd | 3 man/minteq.v4.dat.Rd | 3 man/phrGetDumpFileName.Rd | 2 man/phrGetDumpFileOn.Rd | 2 man/phrGetErrorFileName.Rd | 2 man/phrGetErrorFileOn.Rd | 2 man/phrGetLogFileName.Rd | 2 man/phrGetLogFileOn.Rd | 2 man/phrGetOutputFileName.Rd | 2 man/phrGetOutputFileOn.Rd | 2 man/phrSetDumpFileName.Rd | 2 man/phrSetDumpFileOn.Rd | 2 man/phrSetDumpStringsOn.Rd | 2 man/phrSetErrorFileName.Rd | 2 man/phrSetErrorFileOn.Rd | 2 man/phrSetErrorStringsOn.Rd | 2 man/phrSetLogFileName.Rd | 2 man/phrSetLogFileOn.Rd | 2 man/phrSetLogStringsOn.Rd | 2 man/phrSetOutputFileName.Rd | 2 man/phrSetOutputFileOn.Rd | 2 man/phrSetOutputStringsOn.Rd | 2 man/phrSetSelectedOutputFileName.Rd | 2 man/phrSetSelectedOutputFileOn.Rd | 2 man/phreeqc-package.Rd | 10 man/phreeqc.dat.Rd | 3 man/phreeqc_rates.dat.Rd |only man/pitzer.dat.Rd | 3 man/sit.dat.Rd | 3 man/wateq4f.dat.Rd | 3 src/CVarhxx.h | 2 src/IPhreeqc.cpp | 45 src/IPhreeqc.h | 8 src/IPhreeqchpp.h | 2 src/R.cpp | 270 ++-- src/Var.c | 2 src/Version.h | 10 src/phreeqcpp/ChartHandler.cpp | 9 src/phreeqcpp/ChartObject.cpp | 2 src/phreeqcpp/Keywords.cpp | 20 src/phreeqcpp/Keywords.h | 4 src/phreeqcpp/NameDouble.cpp | 2 src/phreeqcpp/PBasic.cpp | 837 +++++++++++++ src/phreeqcpp/PBasic.h | 14 src/phreeqcpp/PHRQ_io.cpp | 1 src/phreeqcpp/Phreeqc.cpp | 21 src/phreeqcpp/Phreeqc.h | 100 + src/phreeqcpp/Serializer.cpp | 4 src/phreeqcpp/Solution.cpp | 23 src/phreeqcpp/Solution.h | 3 src/phreeqcpp/SolutionIsotope.cpp | 6 src/phreeqcpp/Surface.cpp | 35 src/phreeqcpp/Surface.h | 7 src/phreeqcpp/SurfaceCharge.cpp | 45 src/phreeqcpp/SurfaceCharge.h | 6 src/phreeqcpp/System.cpp | 8 src/phreeqcpp/Utils.cpp | 71 + src/phreeqcpp/Utils.h | 3 src/phreeqcpp/basicsubs.cpp | 1670 +++++++++++++++------------ src/phreeqcpp/cl1.cpp | 4 src/phreeqcpp/gases.cpp | 8 src/phreeqcpp/global_structures.h | 38 src/phreeqcpp/input.cpp | 7 src/phreeqcpp/integrate.cpp | 530 +++++--- src/phreeqcpp/inverse.cpp | 42 src/phreeqcpp/isotopes.cpp | 23 src/phreeqcpp/kinetics.cpp | 11 src/phreeqcpp/mainsubs.cpp | 24 src/phreeqcpp/model.cpp | 12 src/phreeqcpp/nvector_serial.cpp | 3 src/phreeqcpp/parse.cpp | 3 src/phreeqcpp/pitzer.cpp | 10 src/phreeqcpp/prep.cpp | 80 + src/phreeqcpp/print.cpp | 115 + src/phreeqcpp/read.cpp | 444 ++++++- src/phreeqcpp/spread.cpp | 47 src/phreeqcpp/step.cpp | 6 src/phreeqcpp/structures.cpp | 2 src/phreeqcpp/sundialsmath.cpp | 2 src/phreeqcpp/sundialsmath.h | 4 src/phreeqcpp/sundialstypes.h | 2 src/phreeqcpp/tally.cpp | 22 src/phreeqcpp/tidy.cpp | 76 - src/phreeqcpp/transport.cpp | 542 +++++--- src/phreeqcpp/utilities.cpp | 137 -- 123 files changed, 4020 insertions(+), 1980 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized
additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <[email protected]>
Diff between gam versions 1.22-3 dated 2023-11-29 and 1.22-4 dated 2024-07-18
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/predict.gam.R | 20 ++++++++++---------- 3 files changed, 16 insertions(+), 16 deletions(-)
Title: Biologically Explainable Machine Learning Framework
Description: Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <doi:10.48550/arXiv.1712.00336>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.
Author: Shunjie Zhang and Junfang Chen
Maintainer: Shunjie Zhang <[email protected]>
Diff between BioM2 versions 1.0.7 dated 2024-06-09 and 1.0.8 dated 2024-07-18
DESCRIPTION | 6 MD5 | 13 - NAMESPACE | 1 NEWS | 5 R/BioM2.R | 385 ++++++++++++++++++++++++++++++++++------ man/FindParaModule.Rd | 4 man/HyBioM2.Rd |only man/Stage1_FeartureSelection.Rd | 4 8 files changed, 353 insertions(+), 65 deletions(-)