Title: Stratigraphic Paleobiology Modeling Pipelines
Description: The fossil record is a joint expression of ecological, taphonomic,
evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382).
This package allowing to simulate biological processes in the time domain
(e.g., trait evolution, fossil abundance), and examine how their expression
in the rock record (stratigraphic domain) is influenced based on
age-depth models, ecological niche models, and taphonomic effects.
Functions simulating common processes used in modeling trait evolution or
event type data such as first/last occurrences are provided and can be used
standalone or as part of a pipeline. The package comes with example
data sets and tutorials in several vignettes, which can be used as a
template to set up one's own simulation.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Diff between StratPal versions 0.2.0 dated 2024-10-04 and 0.3.0 dated 2024-11-21
DESCRIPTION | 6 MD5 | 48 +- NAMESPACE | 1 NEWS.md | 64 +- R/StratPal-package.R | 12 R/apply_niche.R | 174 ++++---- R/apply_taphonomy.R | 112 ++--- R/ornstein_uhlenbeck_sl.R | 2 R/plot.pre_paleoTS.R |only R/random_walk_sl.R | 104 ++-- README.md | 206 ++++----- inst/CITATION | 16 inst/WORDLIST | 5 inst/doc/event_data.Rmd | 672 +++++++++++++++---------------- inst/doc/paleoTS_functionality.R | 4 inst/doc/paleoTS_functionality.Rmd | 6 inst/doc/paleoTS_functionality.html | 16 inst/doc/phenotypic_evolution.html | 8 man/ornstein_uhlenbeck_sl.Rd | 2 man/plot.pre_paleoTS.Rd |only man/random_walk_sl.Rd | 2 tests/testthat/test_ornstein_uhlenbeck.R | 34 - tests/testthat/test_p3.R | 42 - tests/testthat/test_p3_var_rate.R | 42 - vignettes/event_data.Rmd | 672 +++++++++++++++---------------- vignettes/paleoTS_functionality.Rmd | 6 26 files changed, 1134 insertions(+), 1122 deletions(-)
Title: Ceteris Paribus Profiles
Description: Ceteris Paribus Profiles (What-If Plots) are designed to present model
responses around selected points in a feature space.
For example around a single prediction for an interesting observation.
Plots are designed to work in a model-agnostic fashion, they are working
for any predictive Machine Learning model and allow for model comparisons.
Ceteris Paribus Plots supplement the Break Down Plots from 'breakDown' package.
Author: Przemyslaw Biecek [aut, cre]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ceterisParibus versions 0.4.2 dated 2020-03-27 and 0.6 dated 2024-11-21
ceterisParibus-0.4.2/ceterisParibus/R/plot_interactive_what_if.R |only ceterisParibus-0.4.2/ceterisParibus/README.md |only ceterisParibus-0.4.2/ceterisParibus/man/plot_interactive.Rd |only ceterisParibus-0.4.2/ceterisParibus/tests/testthat/test_plot_interactive_what_if.R |only ceterisParibus-0.6/ceterisParibus/DESCRIPTION | 11 +-- ceterisParibus-0.6/ceterisParibus/MD5 | 36 ++++------ ceterisParibus-0.6/ceterisParibus/NAMESPACE | 4 - ceterisParibus-0.6/ceterisParibus/NEWS.md | 23 +++--- ceterisParibus-0.6/ceterisParibus/R/calculate_profiles.R | 12 ++- ceterisParibus-0.6/ceterisParibus/R/calculate_profiles_lce.R | 1 ceterisParibus-0.6/ceterisParibus/R/ceteris_paribus.R | 5 - ceterisParibus-0.6/ceterisParibus/R/coral_plots.R | 4 - ceterisParibus-0.6/ceterisParibus/R/plot_ceteris_paribus.R | 2 ceterisParibus-0.6/ceterisParibus/R/plot_coral_plots.R | 2 ceterisParibus-0.6/ceterisParibus/R/select_neighbours.R | 4 - ceterisParibus-0.6/ceterisParibus/R/select_samples.R | 2 ceterisParibus-0.6/ceterisParibus/man/calculate_variable_splits.Rd | 9 ++ ceterisParibus-0.6/ceterisParibus/man/ceteris_paribus.Rd | 3 ceterisParibus-0.6/ceterisParibus/man/local_fit.Rd | 4 - ceterisParibus-0.6/ceterisParibus/man/select_neighbours.Rd | 4 - ceterisParibus-0.6/ceterisParibus/man/select_sample.Rd | 2 21 files changed, 72 insertions(+), 56 deletions(-)
More information about ceterisParibus at CRAN
Permanent link
Title: Read and Write '.gltf' and '.glb' Files
Description: The 'glTF' file format is used to describe 3D models. This package
provides read and write functions to work with it.
Author: Duncan Murdoch [aut, cre],
Morten S. Mikkelsen [cph]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl2gltf versions 1.0.5 dated 2024-09-24 and 1.0.7 dated 2024-11-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/gltfWidget.R | 19 +++++++++---------- inst/doc/shininess.html | 12 ++++++------ 5 files changed, 26 insertions(+), 23 deletions(-)
Title: Power and Sample Size Tools
Description: Power and sample size calculations for a variety of study designs and
outcomes. Methods include t tests, ANOVA (including tests for interactions,
simple effects and contrasts), proportions, categorical data (chi-square tests
and proportional odds), linear, logistic and Poisson regression, alternative
and coprimary endpoints, power for confidence intervals, correlation
coefficient tests, cluster randomized trials, individually randomized group
treatment trials, multisite trials, treatment-by-covariate interaction effects
and nonparametric tests of location. Utilities are provided for
computing various effect sizes. Companion package to the book
"Power and Sample Size in R", Crespi (2025, ISBN:9781138591622).
Author: Catherine M. Crespi [aut, cre],
Zichen Liu [aut],
Kristen M. McGreevy [ctb]
Maintainer: Catherine M. Crespi <ccrespi@ucla.edu>
Diff between powertools versions 0.1.0 dated 2024-11-14 and 0.1.2 dated 2024-11-21
DESCRIPTION | 6 +- MD5 | 20 ++++---- R/check.param.R | 2 R/chisq.gof.R | 2 man/chisq.gof.Rd | 2 man/ttest.1samp.Rd | 88 ++++++++++++++++++------------------ man/ttest.2samp.Rd | 126 ++++++++++++++++++++++++++-------------------------- man/ttest.paired.Rd | 94 +++++++++++++++++++------------------- man/ztest.1samp.Rd | 90 ++++++++++++++++++------------------- man/ztest.2samp.Rd | 114 +++++++++++++++++++++++------------------------ man/ztest.paired.Rd | 98 ++++++++++++++++++++-------------------- 11 files changed, 321 insertions(+), 321 deletions(-)
Title: Circle Packing
Description: Algorithms to find arrangements of non-overlapping circles.
Author: Michael Bedward [aut, cre],
David Eppstein [aut] ,
Peter Menzel [aut]
Maintainer: Michael Bedward <michael.bedward@gmail.com>
Diff between packcircles versions 0.3.6 dated 2023-09-08 and 0.3.7 dated 2024-11-21
DESCRIPTION | 12 +- MD5 | 44 ++++----- NEWS.md | 7 + R/circleGraphLayout.R | 5 + R/circleRemoveOverlaps.R | 19 +++- R/circleRepelLayout.R | 56 ++++++++---- R/circleVertices.R | 112 ++++++++++++++++++------- README.md | 9 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/graph_packing.R | 78 ++++++++--------- inst/doc/graph_packing.html | 10 +- inst/doc/intro.R | 6 - inst/doc/intro.html | 14 +-- inst/doc/progressive_packing.R | 2 inst/doc/progressive_packing.Rmd | 2 inst/doc/progressive_packing.html | 53 ++++++++--- man/circleLayoutVertices.Rd | 170 +++++++++++++++++++------------------- man/circlePlotData.Rd | 64 +++++++------- man/circleRemoveOverlaps.Rd | 156 +++++++++++++++++----------------- man/circleRepelLayout.Rd | 161 +++++++++++++++++------------------ man/circleVertices.Rd | 58 ++++++------ vignettes/progressive_packing.Rmd | 2 23 files changed, 582 insertions(+), 458 deletions(-)
Title: Estimating Length-Based Indicators for Fish Stock
Description: Provides tools for estimating length-based indicators from length frequency data to assess fish stock status and manage fisheries sustainably. Implements methods from Cope and Punt (2009) <doi:10.1577/C08-025.1> for data-limited stock assessment and Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> for detecting overfishing using simple indicators. Key functions include:
FrequencyTable(): Calculate the frequency table from the collected and also the extract the length frequency data from the frequency table with the upper length_range. A numeric value specifying the bin width for class intervals. If not provided, the bin width is automatically calculated using Sturges (1926) <doi:10.1080/01621459.1926.10502161> formula.
CalPar(): Calculates various lengths used in fish stock assessment as biological length indicators such as asymptotic length (Linf), maximum length (Lmax), length at sexual maturity (Lm), and optimal length (Lopt).
FishPar(): Calculates length-based [...truncated...]
Author: Ataher Ali [aut, cre],
Mohammed Shahidul Alam [aut]
Maintainer: Ataher Ali <ataher.cu.ms@gmail.com>
Diff between aLBI versions 0.1.6 dated 2024-11-13 and 0.1.7 dated 2024-11-21
DESCRIPTION | 6 - MD5 | 18 +-- NAMESPACE | 7 - R/FishPar.R | 204 +++++++++++++++++++++++++++++---------------- R/FrequencyTable.R | 73 +++++++++------- inst/doc/Introduction.R | 2 inst/doc/Introduction.Rmd | 14 +-- inst/doc/Introduction.html | 132 +++++++++++++++-------------- man/FrequencyTable.Rd | 26 ++--- vignettes/Introduction.Rmd | 14 +-- 10 files changed, 287 insertions(+), 209 deletions(-)
Title: Synthetic Microdata Generator
Description: This tool fits a non-parametric Bayesian model called a "hierarchically coupled mixture model with local dependence (HCMM-LD)" to the original microdata in order to generate synthetic microdata for privacy protection. The non-parametric feature of the adopted model is useful for capturing the joint distribution of the original input data in a highly flexible manner, leading to the generation of synthetic data whose distributional features are similar to that of the input data. The package allows the original input data to have missing values and impute them with the posterior predictive distribution, so no missing values exist in the synthetic data output. The method builds on the work of Murray and Reiter (2016) <doi:10.1080/01621459.2016.1174132>.
Author: Hang J. Kim [aut, cre],
Juhee Lee [aut],
Young-Min Kim [aut],
Jared Murray [aut]
Maintainer: Hang J. Kim <hangkim0@gmail.com>
Diff between synMicrodata versions 2.0.0 dated 2024-04-07 and 2.1.0 dated 2024-11-21
DESCRIPTION | 8 +- MD5 | 13 +-- NAMESPACE | 2 R/R_functions.R | 163 ++++++++++++++++++++++++++++++++--------- man/Rcpp_modelobject-class.Rd | 6 + man/plot.synMicro_object.Rd | 9 ++ man/readData.Rd | 9 ++ man/summary.synMicro_object.Rd |only 8 files changed, 165 insertions(+), 45 deletions(-)
Title: Analysis of Korean National Forest Inventory Database
Description: Understanding the current status of forest resources is essential for monitoring changes
in forest ecosystems and generating related statistics. In South Korea, the National Forest
Inventory (NFI) surveys over 4,500 sample plots nationwide every five years and records 70 items,
including forest stand, forest resource, and forest vegetation surveys. Many researchers use NFI
as the primary data for research, such as biomass estimation or analyzing the importance value of
each species over time and space, depending on the research purpose. However, the large volume
of accumulated forest survey data from across the country can make it challenging to manage and
utilize such a vast dataset. To address this issue, we developed an R package that efficiently
handles large-scale NFI data across time and space. The package offers a comprehensive
workflow for NFI data analysis. It starts with data processing, where read_nfi() function
reconstructs NFI data according to the researcher's needs while [...truncated...]
Author: Sinyoung Park [aut, cre] ,
Wonhee Cho [aut, ctb] ,
Inyoo Kim [aut, ctb] ,
Wontaek Lim [aut, ctb] ,
Dongwook W. Ko [aut, ths]
Maintainer: Sinyoung Park <youngsin0306@kookmin.ac.kr>
Diff between knfi versions 1.0.0 dated 2024-10-14 and 1.0.1 dated 2024-11-20
knfi-1.0.0/knfi/R/summary_NFI.R |only knfi-1.0.0/knfi/data/col_name.rda |only knfi-1.0.0/knfi/man/col_name.Rd |only knfi-1.0.1/knfi/DESCRIPTION | 8 knfi-1.0.1/knfi/MD5 | 60 +-- knfi-1.0.1/knfi/NAMESPACE | 6 knfi-1.0.1/knfi/NEWS.md | 15 knfi-1.0.1/knfi/R/biomass_nfi.R | 92 +++--- knfi-1.0.1/knfi/R/cwd_biomass_nfi.R | 35 +- knfi-1.0.1/knfi/R/diversity_nfi.R | 68 ++++ knfi-1.0.1/knfi/R/filter_nfi.R | 161 +++++----- knfi-1.0.1/knfi/R/globalvars.R | 6 knfi-1.0.1/knfi/R/info_nfi.R | 6 knfi-1.0.1/knfi/R/iv_nfi.R | 112 ++++--- knfi-1.0.1/knfi/R/read_nfi.R | 93 +++--- knfi-1.0.1/knfi/R/summary_nfi.R |only knfi-1.0.1/knfi/R/switchcol_nfi.R | 14 knfi-1.0.1/knfi/R/sysdata.rda |binary knfi-1.0.1/knfi/R/tsvis_nfi.R | 505 +++++++++++++++++++-------------- knfi-1.0.1/knfi/README.md | 1 knfi-1.0.1/knfi/data/nfi_col.rda |only knfi-1.0.1/knfi/inst/doc/knfi.R | 23 - knfi-1.0.1/knfi/inst/doc/knfi.Rmd | 23 - knfi-1.0.1/knfi/inst/doc/knfi.html | 61 ++- knfi-1.0.1/knfi/man/biomass_nfi.Rd | 7 knfi-1.0.1/knfi/man/cwd_biomass_nfi.Rd | 7 knfi-1.0.1/knfi/man/diversity_nfi.Rd | 13 knfi-1.0.1/knfi/man/iv_nfi.Rd | 11 knfi-1.0.1/knfi/man/nfi_col.Rd |only knfi-1.0.1/knfi/man/read_nfi.Rd | 17 - knfi-1.0.1/knfi/man/summary_nfi.Rd | 14 knfi-1.0.1/knfi/man/switchcol_nfi.Rd | 2 knfi-1.0.1/knfi/man/tsvis_nfi.Rd | 37 ++ knfi-1.0.1/knfi/vignettes/knfi.Rmd | 23 - 34 files changed, 875 insertions(+), 545 deletions(-)
Title: Play Minesweeper
Description: Play and record games of minesweeper using a graphics device that supports event handling.
Replay recorded games and save GIF animations of them. Based on classic minesweeper as detailed by
Crow P. (1997) <https://minesweepergame.com/math/a-mathematical-introduction-to-the-game-of-minesweeper-1997.pdf>.
Author: Harry Thompson [aut, cre, cph]
Maintainer: Harry Thompson <harry@mayesfield.uk>
Diff between minesweeper versions 1.0.0 dated 2024-08-30 and 1.0.1 dated 2024-11-20
DESCRIPTION | 8 MD5 | 93 +++++------ NEWS.md | 2 R/cell2grob.R | 24 +- R/chord.R | 22 +- R/count2str.R | 14 - R/create_viewports.R | 128 +++++++-------- R/draw_cell.R | 6 R/draw_count.R | 32 +-- R/draw_raster.R | 10 - R/flag_cell.R | 18 +- R/get_extdata.R | 6 R/hide_cells.R | 16 - R/in_smiley.R | 6 R/interpolate.R | 6 R/minesweeper-package.R | 12 - R/ndc2cell.R | 18 +- R/neighbors.R | 14 - R/new_board.R | 10 - R/new_mineplot.R | 20 +- R/new_mines.R | 12 - R/no_play.R | 6 R/on_board.R | 6 R/on_mouse_down.R | 26 +-- R/on_mouse_up.R | 32 +-- R/peek_cell.R | 8 R/peek_neighbors.R | 8 R/play_minesweeper.R | 362 +++++++++++++++++++++++--------------------- R/print.R | 10 - R/refresh_board.R | 8 R/replay.R | 98 +++++------ R/replay_minesweeper.R | 32 +-- R/reveal.R | 34 ++-- R/reveal_surrounding.R | 12 - R/save_minesweeper_gif.R | 88 +++++----- R/set_board.R | 24 +- R/update_cell.R | 12 - R/update_cells.R | 18 +- R/update_minecount.R | 10 - R/update_neighbors.R | 10 - R/update_smiley.R | 10 - R/update_timer.R | 10 - R/wind.R | 20 +- README.md | 72 ++++---- man/figures |only man/play_minesweeper.Rd | 20 ++ man/replay_minesweeper.Rd | 4 man/save_minesweeper_gif.Rd | 4 48 files changed, 730 insertions(+), 691 deletions(-)
Title: Read, Plot and Analyse Output from the DEPONS Model
Description: Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.
Author: Jacob Nabe-Nielsen [aut, cre],
Caitlin K. Frankish [aut]
Maintainer: Jacob Nabe-Nielsen <jnn@ecos.au.dk>
Diff between DEPONS2R versions 1.2.3 dated 2024-06-28 and 1.2.4 dated 2024-11-20
DESCRIPTION | 20 +++++-- MD5 | 19 +++--- NAMESPACE | 2 R/a-misc.R | 2 R/dyn-methods.R | 89 +++++++++++++++++++++++++++++++- R/track-methods.R | 25 ++++++++ build/partial.rdb |binary man/DEPONS2R.Rd | 2 man/as.data.frame-DeponsDyn-method.Rd |only man/as.data.frame-DeponsTrack-method.Rd |only man/make.DeponsDyn.Rd |only man/read.DeponsDyn.Rd | 3 - 12 files changed, 144 insertions(+), 18 deletions(-)
Title: Gaussian Location-Scale Regression
Description: The Gaussian location-scale regression model is a multi-predictor
model with explanatory variables for the mean (= location) and the standard
deviation (= scale) of a response variable. This package implements maximum
likelihood and Markov chain Monte Carlo (MCMC) inference (using algorithms
from Girolami and Calderhead (2011) <doi:10.1111/j.1467-9868.2010.00765.x>
and Nesterov (2009) <doi:10.1007/s10107-007-0149-x>), a parametric
bootstrap algorithm, and diagnostic plots for the model class.
Author: Hannes Riebl [aut, cre]
Maintainer: Hannes Riebl <hriebl@posteo.de>
Diff between lmls versions 0.1.0 dated 2022-01-18 and 0.1.1 dated 2024-11-20
DESCRIPTION | 15 ++++++++------- LICENSE | 2 +- MD5 | 24 ++++++++++++------------ NEWS.md | 6 ++++++ R/testthat-helpers.R | 2 +- README.md | 36 ++++++++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/lmls.R | 34 +++++++++++++++++----------------- inst/doc/lmls.Rmd | 18 +++++++----------- inst/doc/lmls.pdf |binary man/figures/README-abdom-plot-1.png |binary vignettes/lmls.Rmd | 18 +++++++----------- 13 files changed, 79 insertions(+), 76 deletions(-)
Title: Latent Class Capture-Recapture Models
Description: Estimation of latent class models with individual covariates for capture-recapture data. See Bartolucci, F. and Forcina, A. (2022), Estimating the size of a closed population by modeling latent and observed heterogeneity, Biometrics, 80(2), ujae017.
Author: Francesco Bartolucci [aut, cre],
Antonio Forcina [aut]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between LCCR versions 1.3 dated 2021-12-04 and 2.0 dated 2024-11-20
DESCRIPTION | 12 +- MD5 | 63 ++++++------ NAMESPACE | 4 R/aggr_data.R | 11 +- R/confint.estLCCR.R | 119 ++++++++++++++++------- R/confint.estLCCRcon.R |only R/design_matrix_logit.R | 49 +++++---- R/design_matrix_loglin.R | 30 +++-- R/estLCCR.R | 162 ++++++++++++++++++------------- R/estLCCRcon.R | 234 +++++++++++++++++++++++++++++----------------- R/freq_data.R | 10 + R/lkLCCR.R | 40 +++---- R/lkLCCRcon.R | 29 ++--- R/matrix_logit.R | 11 +- R/plot.confLCCR.R | 4 R/plot.confLCCRcon.R |only R/print.confLCCR.R | 4 R/print.confLCCRcon.R |only R/print.estLCCR.R | 6 - R/print.estLCCRcon.R | 8 - R/simLCCR.R | 35 +++--- R/sq.R | 7 - R/summary.confLCCR.R | 4 R/summary.confLCCRcon.R |only R/summary.estLCCR.R | 18 +-- R/summary.estLCCRcon.R | 20 +-- build/partial.rdb |binary man/confint.estLCCR.Rd | 17 ++- man/confint.estLCCRcon.Rd |only man/estLCCR.Rd | 18 +-- man/estLCCRcon.Rd | 20 ++- man/freq_data.Rd | 5 man/plot.Rd | 1 man/print.Rd | 1 man/simLCCR.Rd | 17 +-- 35 files changed, 582 insertions(+), 377 deletions(-)
Title: 'shiny' Application for Adverse Event Analysis of 'OnCore' Data
Description: An application for analysis of Adverse Events, as described in Chen, et al., (2023) <doi:10.3390/cancers15092521>.
The required data for the application includes demographics, follow up, adverse event, drug administration and optional tumor measurement data.
The app can produce swimmers plots of adverse events, Kaplan-Meier plots and Cox Proportional Hazards model results
for the association of adverse event biomarkers and overall survival and progression free survival.
The adverse event biomarkers include occurrence of grade 3, low grade (1-2), and treatment related adverse events.
Plots and tables of results are downloadable.
Author: Z Thompson [aut, cre],
A Obermayer [aut],
DT Chen [aut]
Maintainer: Z Thompson <zachary.thompson@moffitt.org>
Diff between AdverseEvents versions 0.0.3 dated 2024-11-04 and 0.0.4 dated 2024-11-20
DESCRIPTION | 7 +- MD5 | 11 ++-- README.md |only inst/app/server.R | 111 ++++++++++++++++++++++++++++++++++++++------ inst/doc/AdverseEvents.html | 4 - vignettes/correlations.PNG |binary vignettes/responsetests.PNG |binary 7 files changed, 110 insertions(+), 23 deletions(-)
Title: Calculate Sun Position, Sunrise, Sunset, Solar Noon and Twilight
Description: Provides a set of convenient functions for calculating sun-related information, including the sun's position (elevation and azimuth), and the times of sunrise, sunset, solar noon, and twilight for any given geographical location on Earth. These calculations are based on equations provided by the National Oceanic & Atmospheric Administration (NOAA) <https://gml.noaa.gov/grad/solcalc/calcdetails.html> as described in "Astronomical Algorithms" by Jean Meeus (1991, ISBN: 978-0-943396-35-4).
Author: Roger Bivand [aut] ,
Adriaan M. Dokter [ctb, cre] ,
Pieter Huybrechts [ctb] ,
Sebastian Luque [aut],
Greg Pelletier [ctb],
Alexander Tedeschi [ctb]
Maintainer: Adriaan M. Dokter <amd427@cornell.edu>
Diff between suntools versions 1.0.0 dated 2023-07-06 and 1.0.1 dated 2024-11-20
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 8 +++++++- R/crepuscule.R | 2 +- R/solarnoon.R | 2 +- R/sunriset.R | 2 +- man/crepuscule.Rd | 2 +- man/solarnoon.Rd | 2 +- man/sunriset.Rd | 2 +- man/suntools-package.Rd | 2 +- tests/testthat/test-sun-methods.R | 12 ++++++------ 11 files changed, 36 insertions(+), 30 deletions(-)
Title: Interface for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@data-intuitive.com>
Diff between laminr versions 0.1.0 dated 2024-11-10 and 0.2.0 dated 2024-11-20
DESCRIPTION | 21 MD5 | 58 NAMESPACE | 6 R/Artifact.R | 18 R/Instance.R | 125 + R/InstanceAPI.R | 43 R/Record.R | 116 + R/Registry.R | 204 + R/connect.R | 26 R/core_loaders.R |only R/laminr-package.R | 6 R/settings_load.R | 11 R/utils.R | 39 README.md | 20 build/vignette.rds |binary inst/doc/architecture.R | 103 inst/doc/architecture.html | 2490 ++++++++++++++++++++++- inst/doc/architecture.qmd | 105 inst/doc/development.html | 288 ++ inst/doc/development.qmd | 38 man/Instance.Rd | 74 man/Record.Rd | 21 man/Registry.Rd | 118 + man/laminr-package.Rd | 8 tests/testthat/helper-setup_lamindata_instance.R | 2 tests/testthat/test-Artifact.R |only tests/testthat/test-core_loaders.R |only vignettes/architecture.qmd | 105 vignettes/cellxgene_basic.html |only vignettes/development.qmd | 38 vignettes/example_workflow.Rmd |only vignettes/example_workflow.html |only vignettes/laminr.Rmd | 10 33 files changed, 3673 insertions(+), 420 deletions(-)
Title: Growth Models
Description: A model for the growth of self-limiting populations using three, four, or five parameter
functions, which have wide applications in a variety of fields.
The dependent variable in a dynamical modeling could be the population size at time x,
where x is the independent variable. In the analysis of quantitative polymerase chain reaction
(qPCR), the dependent variable would be the fluorescence intensity and the independent variable
the cycle number. This package then would calculate the TWW cycle threshold.
Author: Mohammad Tabatabai [aut],
Derek Wilus [aut, cre]
Maintainer: Derek Wilus <dwilus@mmc.edu>
Diff between TWW versions 0.0.1 dated 2024-09-02 and 0.1.0 dated 2024-11-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/tww.R | 23 +++++++++++++++++------ man/tww.Rd | 15 +++++++++++---- 4 files changed, 34 insertions(+), 16 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 3.0.9 dated 2023-04-18 and 3.0.10 dated 2024-11-20
EGRET-3.0.10/EGRET/DESCRIPTION | 8 EGRET-3.0.10/EGRET/MD5 | 146 - EGRET-3.0.10/EGRET/NAMESPACE | 23 EGRET-3.0.10/EGRET/NEWS | 9 EGRET-3.0.10/EGRET/R/EGRET.R | 37 EGRET-3.0.10/EGRET/R/blankTime.R | 35 EGRET-3.0.10/EGRET/R/boxConcMonth.R | 4 EGRET-3.0.10/EGRET/R/boxConcThree.R | 4 EGRET-3.0.10/EGRET/R/boxQTwice.R | 4 EGRET-3.0.10/EGRET/R/boxResidMonth.R | 6 EGRET-3.0.10/EGRET/R/calculateMonthlyResults.R | 20 EGRET-3.0.10/EGRET/R/compressData.r | 29 EGRET-3.0.10/EGRET/R/cumQdate.R | 4 EGRET-3.0.10/EGRET/R/errorStats.R | 2 EGRET-3.0.10/EGRET/R/estSurfaces.R | 2 EGRET-3.0.10/EGRET/R/genericEGRETplot.R | 6 EGRET-3.0.10/EGRET/R/kalman_functions.R | 4 EGRET-3.0.10/EGRET/R/makeAnnualSeries.R | 8 EGRET-3.0.10/EGRET/R/plot1of15.R | 2 EGRET-3.0.10/EGRET/R/plotConcQSmooth.R | 6 EGRET-3.0.10/EGRET/R/plotConcTimeSmooth.R | 6 EGRET-3.0.10/EGRET/R/plotContours.R | 24 EGRET-3.0.10/EGRET/R/plotDiffContours.R | 22 EGRET-3.0.10/EGRET/R/plotMonthTrend.R | 4 EGRET-3.0.10/EGRET/R/plotSDLogQ.R | 2 EGRET-3.0.10/EGRET/R/populateDaily.r | 2 EGRET-3.0.10/EGRET/R/populateSampleColumns.r | 7 EGRET-3.0.10/EGRET/R/printSeries.R | 2 EGRET-3.0.10/EGRET/R/processQWData.r | 9 EGRET-3.0.10/EGRET/R/readDataFromFile.r | 2 EGRET-3.0.10/EGRET/R/readMetaData.r | 4 EGRET-3.0.10/EGRET/R/readNWISSample.R |only EGRET-3.0.10/EGRET/R/readUserSample.r | 6 EGRET-3.0.10/EGRET/R/readWQPSample.R | 83 - EGRET-3.0.10/EGRET/R/runGroups.R | 2 EGRET-3.0.10/EGRET/R/runPairs.R | 4 EGRET-3.0.10/EGRET/R/runSurvReg.R | 10 EGRET-3.0.10/EGRET/R/setupYears.R | 4 EGRET-3.0.10/EGRET/R/stitch.R | 4 EGRET-3.0.10/EGRET/R/tableResults.R | 2 EGRET-3.0.10/EGRET/README.md | 143 - EGRET-3.0.10/EGRET/build/partial.rdb |binary EGRET-3.0.10/EGRET/build/vignette.rds |binary EGRET-3.0.10/EGRET/inst/CITATION | 4 EGRET-3.0.10/EGRET/inst/doc/EGRET.R | 540 +++---- EGRET-3.0.10/EGRET/inst/doc/EGRET.Rmd | 7 EGRET-3.0.10/EGRET/inst/doc/EGRET.html | 896 ++++++------ EGRET-3.0.10/EGRET/inst/doc/Overview.Rmd | 62 EGRET-3.0.10/EGRET/inst/doc/Overview.html | 247 +-- EGRET-3.0.10/EGRET/inst/doc/parallel.R | 78 - EGRET-3.0.10/EGRET/inst/doc/parallel.html | 80 - EGRET-3.0.10/EGRET/inst/doc/units.html | 130 - EGRET-3.0.10/EGRET/man/Constants.Rd | 8 EGRET-3.0.10/EGRET/man/EGRET-package.Rd | 14 EGRET-3.0.10/EGRET/man/blankTime.Rd | 10 EGRET-3.0.10/EGRET/man/boxConcMonth.Rd | 2 EGRET-3.0.10/EGRET/man/boxQTwice.Rd | 2 EGRET-3.0.10/EGRET/man/boxResidMonth.Rd | 2 EGRET-3.0.10/EGRET/man/cumQdate.Rd | 2 EGRET-3.0.10/EGRET/man/figures/README-plotFours-1.png |binary EGRET-3.0.10/EGRET/man/figures/README-plotFours-2.png |binary EGRET-3.0.10/EGRET/man/figures/README-unnamed-chunk-4-1.png |binary EGRET-3.0.10/EGRET/man/figures/README-unnamed-chunk-4-2.png |binary EGRET-3.0.10/EGRET/man/figures/README-unnamed-chunk-4-3.png |binary EGRET-3.0.10/EGRET/man/plotContours.Rd | 7 EGRET-3.0.10/EGRET/man/plotDiffContours.Rd | 6 EGRET-3.0.10/EGRET/man/processQWData.Rd | 4 EGRET-3.0.10/EGRET/man/readNWISSample.Rd | 7 EGRET-3.0.10/EGRET/man/readUserSample.Rd | 128 - EGRET-3.0.10/EGRET/tests/testthat/Rplots.pdf |binary EGRET-3.0.10/EGRET/tests/testthat/tests_imports.R | 35 EGRET-3.0.10/EGRET/tests/testthat/tests_utils.R | 6 EGRET-3.0.10/EGRET/vignettes/EGRET.Rmd | 7 EGRET-3.0.10/EGRET/vignettes/Overview.Rmd | 62 EGRET-3.0.9/EGRET/R/readNWISSample.r |only 75 files changed, 1510 insertions(+), 1537 deletions(-)
Title: Categorical Functional Data Analysis
Description: Package for the analysis of categorical functional data.
The main purpose is to compute an encoding (real functional variable) for each state <doi:10.3390/math9233074>.
It also provides functions to perform basic statistical analysis on categorical functional data.
Author: Cristian Preda [aut],
Quentin Grimonprez [aut, cre],
Vincent Vandewalle [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between cfda versions 0.11.0 dated 2023-10-07 and 0.12.0 dated 2024-11-20
DESCRIPTION | 12 MD5 | 97 ++-- NAMESPACE | 6 NEWS | 10 R/cfda-package.R | 11 R/check.R | 64 ++- R/dataPlot.R | 27 - R/datasets.R | 6 R/encoding.R | 52 +- R/estimation.R | 10 R/fmca.print.R | 8 R/generateData.R | 18 R/plotEncoding.R | 44 -- R/predict.R | 11 R/pretreatment.R | 62 +- R/reconstructData.R |only R/stat.R | 66 +-- R/zzz.R | 5 build/vignette.rds |binary inst/doc/cfda.R | 20 inst/doc/cfda.Rmd | 45 +- inst/doc/cfda.html | 506 ++++++++++++++---------- man/boxplot.timeSpent.Rd | 2 man/cfda-package.Rd | 21 man/compute_duration.Rd | 2 man/compute_number_jumps.Rd | 2 man/compute_optimal_encoding.Rd | 6 man/compute_time_spent.Rd | 2 man/convertToCfd.Rd | 20 man/estimate_Markov.Rd | 2 man/estimate_pt.Rd | 6 man/flours.Rd | 6 man/hist.duration.Rd | 2 man/hist.njump.Rd | 2 man/matrixToCfd.Rd | 13 man/plot.fmca.Rd | 2 man/plot.pt.Rd | 2 man/plotComponent.Rd | 1 man/plotEigenvalues.Rd | 1 man/plotIndicatorsReconstruction.Rd |only man/predict.fmca.Rd | 2 man/print.fmca.Rd | 2 man/reconstructIndicators.Rd |only man/summary.fmca.Rd | 2 tests/testthat/test.bootstrap.R | 3 tests/testthat/test.check.R | 74 +++ tests/testthat/test.encoding.R | 66 +-- tests/testthat/test.encoding0columnManagement.R | 2 tests/testthat/test.generate.R | 16 tests/testthat/test.stat.R | 56 +- vignettes/cfda.Rmd | 45 +- 51 files changed, 937 insertions(+), 503 deletions(-)
Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in 'movebank.org'
as well as tools to visualize and statistically analyze animal movement data,
among others functions to calculate dynamic Brownian Bridge Movement Models.
Move helps addressing movement ecology questions.
Author: Bart Kranstauber [aut, cre],
Marco Smolla [aut],
Anne K Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move versions 4.2.5 dated 2024-09-29 and 4.2.6 dated 2024-11-20
ChangeLog | 4 DESCRIPTION | 6 MD5 | 10 inst/doc/browseMovebank.html | 753 ++++++++----- inst/doc/move.html | 1418 ++++++++++++++++---------- tests/testthat/test.getDuplicatedTimestamps.R | 2 6 files changed, 1361 insertions(+), 832 deletions(-)
Title: High Dimensional Categorical Data Visualization
Description: Easy visualization for datasets with more than two categorical variables and additional continuous variables. 'diceplot' is particularly useful for exploring complex categorical data in the context of pathway analysis across multiple conditions. For a detailed documentation please visit <https://dice-and-domino-plot.readthedocs.io/en/latest/>.
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between diceplot versions 0.1.3 dated 2024-11-05 and 0.1.4 dated 2024-11-20
DESCRIPTION | 6 +-- MD5 | 10 +++--- R/diceplot.R | 63 ++++++++++++++++++++++++++------------- man/dice_plot.Rd | 11 ++++++ tests/factor_df_test.R |only tests/test_diceplots.R | 3 + tests/test_reordering_diceplot.R |only 7 files changed, 63 insertions(+), 30 deletions(-)
Title: A Toolkit for Year-Quarter, Year-Month and Year-Isoweek Dates
Description: S3 classes and methods to create and work
with year-quarter, year-month and year-isoweek vectors. Basic
arithmetic operations (such as adding and subtracting) are supported,
as well as formatting and converting to and from standard R date
types.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between dint versions 2.1.4 dated 2022-10-17 and 2.1.5 dated 2024-11-20
DESCRIPTION | 8 MD5 | 102 ++-- NAMESPACE | 13 NEWS.md | 8 R/arithmetic.R | 5 R/format.R | 1 R/increment.R | 11 R/scale_date_xx.R | 132 ++++-- R/zoo-compat.R | 6 README.md | 6 build/vignette.rds |binary inst/doc/dint.R | 4 inst/doc/dint.html | 529 ++++++++++++------------- man/Ops.date_xx.Rd | 54 +- man/Summary.date_xx.Rd | 50 +- man/as.Date.date_xx.Rd | 130 +++--- man/as_yearqtr.Rd | 126 ++--- man/c.date_xx.Rd | 52 +- man/date_xx.Rd | 98 ++-- man/date_xx_arithmetic.Rd | 76 +-- man/date_xx_arithmetic_disabled.Rd | 76 +-- man/date_xx_breaks.Rd | 64 +-- man/date_xx_sequences.Rd | 60 +- man/date_y.Rd | 86 ++-- man/date_ym.Rd | 96 ++-- man/date_yq.Rd | 96 ++-- man/date_yw.Rd | 96 ++-- man/day_of_isoweek.Rd | 102 ++-- man/day_of_isoyear.Rd | 80 +-- man/day_of_month.Rd | 110 ++--- man/day_of_quarter.Rd | 62 +- man/day_of_year.Rd | 94 ++-- man/dint-package.Rd | 49 +- man/extract_date_xx.Rd | 183 ++++---- man/first_of_yq.Rd | 88 ++-- man/format_date_xx.Rd | 212 +++++----- man/format_ym.Rd | 122 ++--- man/format_yq.Rd | 122 ++--- man/format_yw.Rd | 119 ++--- man/getters.Rd | 130 +++--- man/increment.Rd |only man/period_bounds.Rd | 98 ++-- man/print.date_xx.Rd | 36 - man/rep.date_xx.Rd | 36 - man/round_date_xx.Rd | 80 +-- man/scale_date_xx.Rd | 269 ++++++------ man/y-plus.Rd | 98 ++-- man/year.Rd | 92 ++-- man/yq.Rd | 78 +-- tests/testthat/manual_tests/ggplot_scales.html |only tests/testthat/test_date_xx.R | 6 tests/testthat/test_first_of.R | 12 tests/testthat/test_scale_date_xx.R | 5 53 files changed, 2170 insertions(+), 2098 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://euroqol.org/>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-3l/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/information-and-support/euroqol-instruments/eq-5d-5l/>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension [...truncated...]
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.15.4 dated 2024-09-04 and 0.15.5 dated 2024-11-20
DESCRIPTION | 12 +- MD5 | 34 +++---- NEWS.md | 6 + R/data.R | 194 +++++++++++++++++++++---------------------- R/sysdata.rda |binary inst/doc/eq5d.R | 2 inst/doc/eq5d.html | 59 +++++-------- man/CW.Rd | 16 +-- man/DSU3L.Rd | 4 man/DSU5L.Rd | 4 man/TTO.Rd | 63 +++++++------ man/VAS.Rd | 8 - man/VT.Rd | 85 +++++++++--------- man/Y3L.Rd | 20 ++-- man/eq5d-package.Rd | 2 tests/testthat/test-eq5d3l.R | 8 + tests/testthat/test-eq5d5l.R | 10 ++ tests/testthat/test-eq5dcw.R | 11 ++ 18 files changed, 287 insertions(+), 251 deletions(-)
Title: Comparing Two Diagnostic Tests with Dichotomous Results using
Paired Data
Description: Provides a method for comparing the results of two binary diagnostic tests using paired data.
Users can rapidly perform descriptive and inferential statistics in a single function call. Options permit users to select which parameters they are interested in comparing and methods for correction for multiple comparisons.
Confidence intervals are calculated using the methods with the best coverage. Hypothesis tests use the methods with the best asymptotic performance. A summary of the methods is available in Roldán-Nofuentes (2020) <doi:10.1186/s12874-020-00988-y>.
This package is targeted at clinical researchers who want to rapidly and effectively compare results from binary diagnostic tests.
Author: Kyle J. Wilson [cre, aut] ,
Marc Henrion [aut] ,
Jose Antonio Roldan Nofuentes [aut]
Maintainer: Kyle J. Wilson <kyle.jordan.wilson@googlemail.com>
Diff between testCompareR versions 1.1.0 dated 2024-10-02 and 1.1.1 dated 2024-11-20
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 8 ++++++++ R/compareR.R | 7 +++++++ README.md | 4 +++- inst/CITATION |only man/compareR.Rd | 4 ++++ 7 files changed, 31 insertions(+), 9 deletions(-)
Title: Fast Numerical Maximum Likelihood Estimation for Latent Markov
Models
Description: A variety of latent Markov models, including hidden Markov models, hidden semi-Markov models,
state-space models and continuous-time variants can be formulated and estimated within the same framework via directly maximising the likelihood function using the so-called forward algorithm.
Applied researchers often need custom models that standard software does not easily support.
Writing tailored 'R' code offers flexibility but suffers from slow estimation speeds.
We address these issues by providing easy-to-use functions (written in 'C++' for speed) for common tasks like the forward algorithm.
These functions can be combined into custom models in a Lego-type approach, offering up to 10-20 times faster estimation via standard numerical optimisers.
To aid in building fully custom likelihood functions, several vignettes are included that show how to simulate data from and estimate all the above model classes.
Author: Jan-Ole Koslik [aut, cre]
Maintainer: Jan-Ole Koslik <jan-ole.koslik@uni-bielefeld.de>
Diff between LaMa versions 2.0.1 dated 2024-11-13 and 2.0.2 dated 2024-11-20
LaMa-2.0.1/LaMa/vignettes/HSMMs_cache/html/model_muskox_77fd183fbf3a0b18e8b2fde0ac87056d.RData |only LaMa-2.0.1/LaMa/vignettes/HSMMs_cache/html/model_muskox_77fd183fbf3a0b18e8b2fde0ac87056d.rdb |only LaMa-2.0.1/LaMa/vignettes/HSMMs_cache/html/model_muskox_77fd183fbf3a0b18e8b2fde0ac87056d.rdx |only LaMa-2.0.1/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_278dc24685c286b1974a9aec6899b982.RData |only LaMa-2.0.1/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_278dc24685c286b1974a9aec6899b982.rdb |only LaMa-2.0.1/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_278dc24685c286b1974a9aec6899b982.rdx |only LaMa-2.0.1/LaMa/vignettes/State_space_models_cache/html/model_a83c08ae12caff79d6f80b66561349bf.RData |only LaMa-2.0.1/LaMa/vignettes/State_space_models_cache/html/model_a83c08ae12caff79d6f80b66561349bf.rdb |only LaMa-2.0.1/LaMa/vignettes/State_space_models_cache/html/model_a83c08ae12caff79d6f80b66561349bf.rdx |only LaMa-2.0.2/LaMa/DESCRIPTION | 6 - LaMa-2.0.2/LaMa/MD5 | 46 +++++----- LaMa-2.0.2/LaMa/R/decoding_functions.R | 32 ++++-- LaMa-2.0.2/LaMa/README.md | 6 - LaMa-2.0.2/LaMa/inst/doc/Continuous_time_HMMs.html | 4 LaMa-2.0.2/LaMa/inst/doc/HSMMs.html | 4 LaMa-2.0.2/LaMa/inst/doc/Inhomogeneous_HMMs.html | 4 LaMa-2.0.2/LaMa/inst/doc/Intro_to_LaMa.html | 2 LaMa-2.0.2/LaMa/inst/doc/Longitudinal_data.html | 6 - LaMa-2.0.2/LaMa/inst/doc/MMMPPs.html | 4 LaMa-2.0.2/LaMa/inst/doc/Penalised_splines.html | 6 - LaMa-2.0.2/LaMa/inst/doc/Periodic_HMMs.html | 2 LaMa-2.0.2/LaMa/inst/doc/State_space_models.Rmd | 2 LaMa-2.0.2/LaMa/inst/doc/State_space_models.html | 12 +- LaMa-2.0.2/LaMa/vignettes/HSMMs_cache/html/model_muskox_bc79f9de982e1ba8aa0670dd63a810ff.RData |only LaMa-2.0.2/LaMa/vignettes/HSMMs_cache/html/model_muskox_bc79f9de982e1ba8aa0670dd63a810ff.rdb |only LaMa-2.0.2/LaMa/vignettes/HSMMs_cache/html/model_muskox_bc79f9de982e1ba8aa0670dd63a810ff.rdx |only LaMa-2.0.2/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_69f7c62b62ac06046ca6f4be3205495c.RData |only LaMa-2.0.2/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_69f7c62b62ac06046ca6f4be3205495c.rdb |only LaMa-2.0.2/LaMa/vignettes/Longitudinal_data_cache/html/model_pool_69f7c62b62ac06046ca6f4be3205495c.rdx |only LaMa-2.0.2/LaMa/vignettes/State_space_models.Rmd | 2 LaMa-2.0.2/LaMa/vignettes/State_space_models_cache/html/model_1cac96c46f5385620f13ae0141907771.RData |only LaMa-2.0.2/LaMa/vignettes/State_space_models_cache/html/model_1cac96c46f5385620f13ae0141907771.rdb |only LaMa-2.0.2/LaMa/vignettes/State_space_models_cache/html/model_1cac96c46f5385620f13ae0141907771.rdx |only 33 files changed, 75 insertions(+), 63 deletions(-)
Title: Geographical Detectors for Assessing Spatial Factors
Description: Geographical detectors for measuring spatial stratified heterogeneity,
as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and
Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the
optimal discretization of continuous data, four primary functions of
geographical detectors, comparison of size effects of spatial unit and
the visualizations of results. To use the package and to refer the
descriptions of the package, methods and case datasets, please cite
Yongze Song (2020) <doi:10.1080/15481603.2020.1760434>. The model has
been applied in factor exploration of road performance and multi-scale
spatial segmentation for network data, as described in
Yongze Song (2018) <doi:10.3390/rs10111696> and
Yongze Song (2020) <doi:10.1109/TITS.2020.3001193>, respectively.
Author: Yongze Song [aut, cph] ,
Wenbo Lv [aut, cre]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between GD versions 10.6 dated 2024-10-30 and 10.8 dated 2024-11-20
DESCRIPTION | 8 - MD5 | 14 +-- NEWS.md | 18 ++- R/zzz.R | 2 README.md | 6 - build/vignette.rds |binary inst/doc/GD.R | 244 ++++++++++++++++++++++++++--------------------------- inst/doc/GD.html | 6 - 8 files changed, 151 insertions(+), 147 deletions(-)
Title: Calculate and Visualize 'SNOTEL' Snow Data and Seasonality
Description: Programmatic interface to the 'SNOTEL' snow data
(<https://www.nrcs.usda.gov/programs-initiatives/sswsf-snow-survey-and-water-supply-forecasting-program>). Provides easy downloads of snow
data into your R work space or a local directory. Additional post-processing
routines to extract snow season indexes are provided.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between snotelr versions 1.5.1 dated 2024-10-02 and 1.5.2 dated 2024-11-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/snotel_download.r | 9 +++++++-- R/snotel_metric.r | 3 +++ build/vignette.rds |binary inst/doc/snotelr-vignette.html | 4 ++-- man/snotel_download.Rd | 11 ++++++++++- 7 files changed, 32 insertions(+), 15 deletions(-)
Title: Permanent Random Number Sampling
Description: Survey sampling using permanent random numbers (PRN's). A solution
to the problem of unknown overlap between survey samples, which leads to a
low precision in estimates when the survey is repeated or combined with
other surveys. The PRN solution is to supply the U(0, 1) random numbers to
the sampling procedure, instead of having the sampling procedure generate
them. In Lindblom (2014) <doi:10.2478/jos-2014-0047>, and therein cited
papers, it is shown how this is carried out and how it improves the
estimates. This package supports two common fixed-size sampling procedures
(simple random sampling and probability-proportional-to-size sampling) and
includes a function for transforming the PRN's in order to control the
sample overlap.
Author: Kira Coder Gylling [aut, cre]
Maintainer: Kira Coder Gylling <kira.gylling@gmail.com>
Diff between prnsamplr versions 0.3.0 dated 2023-03-08 and 1.0.0 dated 2024-11-20
prnsamplr-0.3.0/prnsamplr/NEWS.md |only prnsamplr-0.3.0/prnsamplr/R/transf.R |only prnsamplr-0.3.0/prnsamplr/README.md |only prnsamplr-0.3.0/prnsamplr/build |only prnsamplr-0.3.0/prnsamplr/data/ExampleData.RData |only prnsamplr-1.0.0/prnsamplr/DESCRIPTION | 42 ++-- prnsamplr-1.0.0/prnsamplr/LICENSE | 2 prnsamplr-1.0.0/prnsamplr/MD5 | 38 ++-- prnsamplr-1.0.0/prnsamplr/NAMESPACE | 25 +- prnsamplr-1.0.0/prnsamplr/R/data.R |only prnsamplr-1.0.0/prnsamplr/R/pps.R | 198 +++++++++++++-------- prnsamplr-1.0.0/prnsamplr/R/prnsamplr-package.R |only prnsamplr-1.0.0/prnsamplr/R/samp.R | 58 ++++-- prnsamplr-1.0.0/prnsamplr/R/srs.R | 131 +++++++++---- prnsamplr-1.0.0/prnsamplr/R/transformprn.R |only prnsamplr-1.0.0/prnsamplr/data/ExampleData.rda |only prnsamplr-1.0.0/prnsamplr/man/ExampleData.Rd | 40 ++-- prnsamplr-1.0.0/prnsamplr/man/pps.Rd | 60 +++--- prnsamplr-1.0.0/prnsamplr/man/prnsamplr-package.Rd | 110 +++++++---- prnsamplr-1.0.0/prnsamplr/man/samp.Rd | 91 +++++---- prnsamplr-1.0.0/prnsamplr/man/srs.Rd | 52 ++--- prnsamplr-1.0.0/prnsamplr/man/transformprn.Rd | 60 +++--- prnsamplr-1.0.0/prnsamplr/tests |only 23 files changed, 563 insertions(+), 344 deletions(-)
Title: Year-Based Time Scales
Description: Provides a consistent representation of year-based time scales as a
numeric vector with an associated 'era'. There are built-in era definitions
for many year numbering systems used in contemporary and historic calendars
(e.g. Common Era, Islamic 'Hijri' years); year-based time scales used in
archaeology, astronomy, geology, and other palaeosciences (e.g.
Before Present, SI-prefixed 'annus'); and support for arbitrary user-defined
eras. Years can converted from any one era to another using a generalised
transformation function. Methods are also provided for robust casting and
coercion between years and other numeric types, type-stable arithmetic with
years, and pretty-printing in tables.
Author: Joe Roe [aut, cre]
Maintainer: Joe Roe <joe@joeroe.io>
Diff between era versions 0.4.1 dated 2022-11-17 and 0.5.0 dated 2024-11-20
DESCRIPTION | 8 MD5 | 40 ++-- NAMESPACE | 4 NEWS.md | 5 R/yr_sort_range.R |only README.md | 20 +- build/vignette.rds |binary inst/WORDLIST | 4 inst/doc/era.R | 2 inst/doc/era.html | 294 ++++++++++++++++++------------------ man/era.Rd | 4 man/era_parameters.Rd | 6 man/era_year.Rd | 4 man/era_year_parameters.Rd | 4 man/is_era.Rd | 4 man/is_era_year.Rd | 4 man/is_yr.Rd | 6 man/this_year.Rd | 6 man/yr_era.Rd | 4 man/yr_extremes.Rd |only man/yr_sort.Rd |only man/yr_transform.Rd | 4 tests/testthat/test-yr_sort_range.R |only 23 files changed, 218 insertions(+), 205 deletions(-)
Title: Vaccines Pharmacometrics
Description: Estimate vaccine efficacy (VE) using immunogenicity data.
The inclusion of immunogenicity data in regression models can increase precision in VE.
The methods are described in the publications "Elucidating vaccine efficacy using a correlate of protection, demographics, and logistic regression" and "Improving precision of vaccine efficacy evaluation using immune correlate data in time-to-event models" by Julie Dudasova, Zdenek Valenta, and Jeffrey R. Sachs (2024).
Author: Julie Dudasova [aut, cre]
Maintainer: Julie Dudasova (MSD) <julie.dudasova@merck.com>
Diff between vaxpmx versions 0.0.3 dated 2024-02-28 and 0.0.6 dated 2024-11-20
DESCRIPTION | 14 +++--- LICENSE.note | 3 - MD5 | 31 +++++++------- NAMESPACE | 1 NEWS.md | 11 +++-- R/data.R | 1 R/ve.R | 85 +++++++++++++++++++++++++++++++++++---- README.md | 17 ++++++- data/data_temp.rda |binary inst/extdata/vaxpmx_mockupData.R | 5 +- man/EfficacyCI.Rd | 2 man/coxphParametricSampling.Rd |only man/data_temp.Rd | 1 man/glmParametricSampling.Rd | 2 man/ve.Rd | 14 +++++- tests/testthat.R | 1 tests/testthat/testve.R | 24 ++++++++++- 17 files changed, 169 insertions(+), 43 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes. This package is part of the RECON
(<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.2.2 dated 2024-08-29 and 1.3.0 dated 2024-11-20
grates-1.2.2/grates/R/defunct.R |only grates-1.2.2/grates/man/grates-defunct.Rd |only grates-1.3.0/grates/DESCRIPTION | 6 grates-1.3.0/grates/MD5 | 31 ++-- grates-1.3.0/grates/NAMESPACE | 33 ++++ grates-1.3.0/grates/NEWS.md | 6 grates-1.3.0/grates/R/accessors.R | 7 grates-1.3.0/grates/R/int_period.R |only grates-1.3.0/grates/R/month.R | 4 grates-1.3.0/grates/R/scale-int_period.R |only grates-1.3.0/grates/build/vignette.rds |binary grates-1.3.0/grates/inst/doc/grates.html | 74 +++------- grates-1.3.0/grates/man/as_int_period.Rd |only grates-1.3.0/grates/man/grouped_date_accessors.Rd | 3 grates-1.3.0/grates/man/new_int_period.Rd |only grates-1.3.0/grates/man/print.grates_int_period.Rd |only grates-1.3.0/grates/man/scale_x_grates_int_period.Rd |only grates-1.3.0/grates/tests/testthat/_snaps/plots/p_breaks.png |only grates-1.3.0/grates/tests/testthat/_snaps/plots/p_breaks_centred.png |only grates-1.3.0/grates/tests/testthat/_snaps/plots/p_one.png |only grates-1.3.0/grates/tests/testthat/_snaps/plots/p_two.png |only grates-1.3.0/grates/tests/testthat/test-int_period.R |only grates-1.3.0/grates/tests/testthat/test-plots.R | 60 +++++++- 23 files changed, 152 insertions(+), 72 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with 'Rscript' to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L. Davis [aut, cre] ,
Allen Day [ctb] ,
Python Software Foundation [ctb] ,
Paul Newell [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 2.2.3 dated 2024-04-09 and 2.2.4 dated 2024-11-20
DESCRIPTION | 17 +++++++++-------- MD5 | 15 ++++++++------- NEWS.md | 5 +++++ R/argparse.R | 23 ++++++++++++----------- R/utils.R |only build/vignette.rds |binary inst/doc/argparse.html | 38 +++++++++++++++++++------------------- man/ArgumentParser.Rd | 22 +++++++++++----------- tests/testthat/test-argparse.R | 11 +++++++++++ 9 files changed, 75 insertions(+), 56 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.8.0 dated 2024-10-02 and 1.9.0 dated 2024-11-20
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targets-1.9.0/targets/R/class_qs.R | 34 targets-1.9.0/targets/R/class_rds.R | 4 targets-1.9.0/targets/R/class_record.R | 76 + targets-1.9.0/targets/R/class_reference.R |only targets-1.9.0/targets/R/class_resources_aws.R | 29 targets-1.9.0/targets/R/class_resources_clustermq.R | 7 targets-1.9.0/targets/R/class_resources_crew.R | 9 targets-1.9.0/targets/R/class_resources_custom_format.R | 10 targets-1.9.0/targets/R/class_resources_feather.R | 9 targets-1.9.0/targets/R/class_resources_fst.R | 7 targets-1.9.0/targets/R/class_resources_future.R | 9 targets-1.9.0/targets/R/class_resources_gcp.R | 15 targets-1.9.0/targets/R/class_resources_network.R | 13 targets-1.9.0/targets/R/class_resources_parquet.R | 9 targets-1.9.0/targets/R/class_resources_qs.R | 37 targets-1.9.0/targets/R/class_resources_repository_cas.R | 10 targets-1.9.0/targets/R/class_resources_url.R | 13 targets-1.9.0/targets/R/class_runtime.R | 67 + targets-1.9.0/targets/R/class_scheduler.R | 29 targets-1.9.0/targets/R/class_settings.R | 53 - targets-1.9.0/targets/R/class_stem.R | 87 +- targets-1.9.0/targets/R/class_store.R | 123 +- targets-1.9.0/targets/R/class_store_file.R | 34 targets-1.9.0/targets/R/class_store_format_custom.R | 8 targets-1.9.0/targets/R/class_store_format_custom_methods.R | 15 targets-1.9.0/targets/R/class_store_repository_cas.R | 86 +- targets-1.9.0/targets/R/class_store_repository_cas_file.R | 22 targets-1.9.0/targets/R/class_store_repository_cas_methods.R | 32 targets-1.9.0/targets/R/class_target.R | 175 +++- targets-1.9.0/targets/R/class_url.R | 17 targets-1.9.0/targets/R/class_value.R | 6 targets-1.9.0/targets/R/class_vector.R | 6 targets-1.9.0/targets/R/class_verbose.R | 2 targets-1.9.0/targets/R/class_workspace.R | 14 targets-1.9.0/targets/R/tar_config_get.R | 14 targets-1.9.0/targets/R/tar_config_set.R | 20 targets-1.9.0/targets/R/tar_definition.R | 2 targets-1.9.0/targets/R/tar_described_as.R | 8 targets-1.9.0/targets/R/tar_exist_objects.R | 3 targets-1.9.0/targets/R/tar_make.R | 29 targets-1.9.0/targets/R/tar_make_clustermq.R | 18 targets-1.9.0/targets/R/tar_make_future.R | 22 targets-1.9.0/targets/R/tar_name.R | 11 targets-1.9.0/targets/R/tar_option_set.R | 9 targets-1.9.0/targets/R/tar_outdated.R | 2 targets-1.9.0/targets/R/tar_read_raw.R | 4 targets-1.9.0/targets/R/tar_repository_cas.R | 85 +- targets-1.9.0/targets/R/tar_repository_cas_local.R | 50 - targets-1.9.0/targets/R/tar_resources.R | 5 targets-1.9.0/targets/R/tar_resources_qs.R | 21 targets-1.9.0/targets/R/tar_seed_get.R | 2 targets-1.9.0/targets/R/tar_target.R | 108 +- targets-1.9.0/targets/R/tar_target_raw.R | 5 targets-1.9.0/targets/R/tar_unblock_process.R |only targets-1.9.0/targets/R/utils_assert.R | 23 targets-1.9.0/targets/R/utils_callr.R | 24 targets-1.9.0/targets/R/utils_condition.R | 24 targets-1.9.0/targets/R/utils_data.R | 6 targets-1.9.0/targets/R/utils_hash.R | 1 targets-1.9.0/targets/R/utils_language.R | 4 targets-1.9.0/targets/R/utils_packages.R | 14 targets-1.9.0/targets/R/utils_rstudio.R | 2 targets-1.9.0/targets/R/utils_time.R | 11 targets-1.9.0/targets/inst/WORDLIST | 3 targets-1.9.0/targets/man/tar_active.Rd | 3 targets-1.9.0/targets/man/tar_backoff.Rd | 3 targets-1.9.0/targets/man/tar_call.Rd | 3 targets-1.9.0/targets/man/tar_cancel.Rd | 3 targets-1.9.0/targets/man/tar_cas_e.Rd | 9 targets-1.9.0/targets/man/tar_cas_l.Rd |only targets-1.9.0/targets/man/tar_config_set.Rd | 14 targets-1.9.0/targets/man/tar_definition.Rd | 5 targets-1.9.0/targets/man/tar_described_as.Rd | 3 targets-1.9.0/targets/man/tar_envir.Rd | 3 targets-1.9.0/targets/man/tar_format_get.Rd | 3 targets-1.9.0/targets/man/tar_group.Rd | 3 targets-1.9.0/targets/man/tar_make.Rd | 13 targets-1.9.0/targets/man/tar_make_clustermq.Rd | 11 targets-1.9.0/targets/man/tar_make_future.Rd | 11 targets-1.9.0/targets/man/tar_name.Rd | 3 targets-1.9.0/targets/man/tar_option_set.Rd | 88 +- targets-1.9.0/targets/man/tar_path.Rd | 3 targets-1.9.0/targets/man/tar_path_script.Rd | 3 targets-1.9.0/targets/man/tar_path_script_support.Rd | 3 targets-1.9.0/targets/man/tar_path_store.Rd | 3 targets-1.9.0/targets/man/tar_path_target.Rd | 3 targets-1.9.0/targets/man/tar_repository_cas.Rd | 48 - 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Title: Explore Your Data with Interactive Figures
Description: A framework for creating interactive figures for data exploration.
All plots are automatically linked and support several kinds of interactive features,
including selection, zooming, panning, and parameter manipulation. The figures
can be interacted with either manually, using a mouse and a keyboard,
or by running code from inside an active R session.
Author: Adam Bartonicek [aut, cre, cph]
Maintainer: Adam Bartonicek <bartonicek@gmail.com>
Diff between plotscaper versions 0.2.3 dated 2024-10-18 and 0.2.4 dated 2024-11-20
DESCRIPTION | 10 +- MD5 | 34 +++---- NEWS.md | 4 R/message_senders.R | 11 +- inst/doc/algebra.html | 12 +- inst/doc/available-interactions.R | 6 + inst/doc/available-interactions.Rmd | 9 + inst/doc/available-interactions.html | 124 ++++++++++++++------------- inst/doc/layout.html | 16 +-- inst/doc/performance.html | 8 - inst/doc/plotscaper.R | 3 inst/doc/plotscaper.Rmd | 3 inst/doc/plotscaper.html | 39 ++++---- inst/htmlwidgets/plotscape/main.iife.js | 4 man/figures/readme1.pngunnamed-chunk-3-1.png |binary man/set_scale.Rd | 3 vignettes/available-interactions.Rmd | 9 + vignettes/plotscaper.Rmd | 3 18 files changed, 177 insertions(+), 121 deletions(-)
Title: Natural Language Processing Infrastructure
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between NLP versions 0.3-1 dated 2024-11-13 and 0.3-2 dated 2024-11-20
DESCRIPTION | 6 +-- MD5 | 6 +-- R/language.R | 86 ++++++++++++++++++++++++++++---------------------------- man/language.Rd | 4 +- 4 files changed, 53 insertions(+), 49 deletions(-)
Title: Tide Heights
Description: Calculates tide heights based on tide station harmonics. It
includes the harmonics data for 637 US stations. The harmonics data
was converted from
<https://github.com/poissonconsulting/rtide/blob/main/data-raw/harmonics-dwf-20151227-free.tar.bz2>,
NOAA web site data processed by David Flater for 'XTide'. The code to
calculate tide heights from the harmonics is based on 'XTide'.
Author: Joe Thorley [aut] ,
Luke Miller [aut, cre],
Abram Fleishman [aut],
Poisson Consulting [cph]
Maintainer: Luke Miller <contact@lukemiller.org>
Diff between rtide versions 0.0.10 dated 2024-08-19 and 0.0.11 dated 2024-11-20
DESCRIPTION | 11 +++++------ MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/tide-height.R | 2 +- README.md | 28 +++++++++++----------------- man/rtide-package.Rd | 5 ++--- man/tide_datetimes.Rd | 2 +- tests/testthat/test-tide-height.R | 14 +++++++------- 8 files changed, 40 insertions(+), 42 deletions(-)
Title: S-Core Graph Decomposition
Description: S-Core Graph Decomposition algorithm for graphs. This is a method
for decomposition of a weighted graph, as proposed by Eidsaa and
Almaas (2013) <doi:10.1103/PhysRevE.88.062819>. The high speed and the low
memory usage make it suitable for large graphs.
Author: Christos Adam [aut, cre]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between scoredec versions 0.1.1 dated 2024-10-20 and 0.1.2 dated 2024-11-20
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NEWS.md | 6 ++++++ README.md | 7 ++++--- build/partial.rdb |binary build/vignette.rds |binary 6 files changed, 22 insertions(+), 15 deletions(-)
Title: 'Shiny' Application for Olympic Data
Description: 'Shiny' Application to visualize Olympic Data. From 1896 to
2016. Even Winter Olympics events are included. Data is from Kaggle at
<https://www.kaggle.com/heesoo37/120-years-of-olympic-history-athletes-and-results>.
Author: Amalan Mahendran [cre, aut]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between OlympicRshiny versions 1.0.1 dated 2024-02-06 and 1.0.2 dated 2024-11-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/app_server.R | 13 ++++++++----- 3 files changed, 14 insertions(+), 11 deletions(-)
Title: Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD
Description: Contains Probability Mass Functions, Cumulative Mass
Functions, Negative Log Likelihood value, parameter estimation and
modeling data using Binomial Mixture Distributions (BMD) (Manoj et al
(2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial
Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>),
also Journal article to use the package(<doi:10.21105/joss.01505>).
Author: Amalan Mahendran [aut, cre] ,
Pushpakanthie Wijekoon [aut, ctb]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between fitODBOD versions 1.5.3 dated 2024-10-10 and 1.5.4 dated 2024-11-20
DESCRIPTION | 6 MD5 | 251 ++++++++++++++++---------------- R/AddBin.R | 164 ++++++++------------ R/BMD_ABD.R | 3 R/Beta.R | 69 ++------ R/BetaCorrBin.R | 102 +++++-------- R/COMPBin.R | 34 +--- R/CorrBin.R | 48 +----- R/Data.R | 150 +++++++++---------- R/GHGbeta.R | 70 ++------ R/Gamma.R | 128 ++++------------ R/Gbeta1.R | 101 +++--------- R/Kumaraswamy.R | 83 ++-------- R/LMultiBin.R | 41 +---- R/MultiBin.R | 32 ---- R/Overdispersion.R | 6 R/SimulateBOD.R | 19 ++ R/Triangle.R | 112 ++++++-------- R/Uniform.R | 56 +------ R/ml.R | 1 build/partial.rdb |binary man/figures/Table-1.png |binary man/fitBin.Rd | 4 tests/testthat/test-AIC.R | 32 +--- tests/testthat/test-Alcohol_data.R | 25 ++- tests/testthat/test-BODextract.R | 23 +- tests/testthat/test-Chromosome_data.R | 20 +- tests/testthat/test-Course_data.R | 20 +- tests/testthat/test-Epidemic_Cold.R | 38 +--- tests/testthat/test-EstMGFBetaBin.R | 45 +---- tests/testthat/test-EstMLEAddBin.R | 38 ---- tests/testthat/test-EstMLEBetaBin.R | 30 +-- tests/testthat/test-EstMLEBetaCorrBin.R | 29 +-- tests/testthat/test-EstMLECOMPBin.R | 29 +-- tests/testthat/test-EstMLECorrBin.R | 26 +-- tests/testthat/test-EstMLEGHGBB.R | 31 +-- tests/testthat/test-EstMLEGammaBin.R | 29 +-- tests/testthat/test-EstMLEGrasiaIIBin.R | 29 +-- tests/testthat/test-EstMLELMBin.R | 29 +-- tests/testthat/test-EstMLEMcGBB.R | 29 +-- tests/testthat/test-EstMLEMultiBin.R | 29 +-- tests/testthat/test-EstMLETriBin.R | 46 ++--- tests/testthat/test-Exam_data.R | 20 +- tests/testthat/test-GenerateBOD.R |only tests/testthat/test-Male_Children.R | 12 + tests/testthat/test-NegLLAddBin.R | 71 +-------- tests/testthat/test-NegLLBetaBin.R | 55 ++----- tests/testthat/test-NegLLBetaCorrBin.R | 63 ++------ tests/testthat/test-NegLLCOMPBin.R | 54 ++---- tests/testthat/test-NegLLCorrBin.R | 74 ++------- tests/testthat/test-NegLLGHGBB.R | 61 ++----- tests/testthat/test-NegLLGammaBin.R | 55 ++----- tests/testthat/test-NegLLGrassiaIIBin.R | 53 +----- tests/testthat/test-NegLLKumBin.R | 64 ++------ tests/testthat/test-NegLLLMBin.R | 59 ++----- tests/testthat/test-NegLLMcGBB.R | 59 ++----- tests/testthat/test-NegLLMultiBin.R | 59 ++----- tests/testthat/test-NegLLTriBin.R | 55 ++----- tests/testthat/test-Overdispersion.R | 93 ----------- tests/testthat/test-Plant_DiseaseData.R | 20 +- tests/testthat/test-Terror_data_ARG.R | 20 +- tests/testthat/test-Terror_data_USA.R | 20 +- tests/testthat/test-dAddBin.R | 71 ++------- tests/testthat/test-dBETA.R | 45 +---- tests/testthat/test-dBetaBin.R | 51 ++---- tests/testthat/test-dBetaCorrBin.R | 54 ++---- tests/testthat/test-dCOMPBin.R | 53 ++---- tests/testthat/test-dCorrBin.R | 66 ++------ tests/testthat/test-dGAMMA.R | 48 ++---- tests/testthat/test-dGBeta1.R | 52 ++---- tests/testthat/test-dGHGBB.R | 58 ++----- tests/testthat/test-dGHGBeta.R | 56 ++----- tests/testthat/test-dGammaBin.R | 55 ++----- tests/testthat/test-dGrassiaIIBin.R | 55 ++----- tests/testthat/test-dKUM.R | 48 ++---- tests/testthat/test-dKumBin.R | 61 ++----- tests/testthat/test-dLMBin.R | 35 ++-- tests/testthat/test-dMcGBB.R | 58 ++----- tests/testthat/test-dMultiBin.R | 61 ++----- tests/testthat/test-dTRI.R | 46 ++--- tests/testthat/test-dTriBin.R | 54 ++---- tests/testthat/test-dUNI.R | 36 +--- tests/testthat/test-dUniBin.R | 42 ++--- tests/testthat/test-fitAddBin.R | 45 ++--- tests/testthat/test-fitBetaBin.R | 45 ++--- tests/testthat/test-fitBetaCorrBin.R | 45 ++--- tests/testthat/test-fitBin.R | 43 ++--- tests/testthat/test-fitCOMPBin.R | 45 ++--- tests/testthat/test-fitCorrBin.R | 45 ++--- tests/testthat/test-fitGHGBB.R | 43 +---- tests/testthat/test-fitGammaBin.R | 45 ++--- tests/testthat/test-fitGrassiaIIBin.R | 45 ++--- tests/testthat/test-fitKumBin.R | 45 ++--- tests/testthat/test-fitLMBin.R | 45 ++--- tests/testthat/test-fitMcGBB.R | 45 ++--- tests/testthat/test-fitMultiBin.R | 45 ++--- tests/testthat/test-fitTriBin.R | 45 ++--- tests/testthat/test-fitted.R | 24 --- tests/testthat/test-mazBETA.R | 39 +--- tests/testthat/test-mazGAMMA.R | 39 +--- tests/testthat/test-mazGBeta1.R | 42 +---- tests/testthat/test-mazGHGBeta.R | 51 ++---- tests/testthat/test-mazKUM.R | 39 +--- tests/testthat/test-mazTRI.R | 39 +--- tests/testthat/test-mazUNI.R | 27 +-- tests/testthat/test-pAddBin.R | 34 ++-- tests/testthat/test-pBETA.R | 49 ++---- tests/testthat/test-pBetaBin.R | 30 ++- tests/testthat/test-pBetaCorrBin.R | 35 +++- tests/testthat/test-pCOMPBin.R | 35 +++- tests/testthat/test-pCorrBin.R | 38 +++- tests/testthat/test-pGAMMA.R | 50 ++---- tests/testthat/test-pGBeta1.R | 52 ++---- tests/testthat/test-pGHGBB.R | 34 ++-- tests/testthat/test-pGHGBeta.R | 58 ++----- tests/testthat/test-pGammaBin.R | 35 +++- tests/testthat/test-pGrassiaIIBin.R | 34 ++-- tests/testthat/test-pKUM.R | 48 ++---- tests/testthat/test-pKumBin.R | 38 +++- tests/testthat/test-pLMBin.R | 34 ++-- tests/testthat/test-pMcGBB.R | 34 ++-- tests/testthat/test-pMultiBin.R | 38 +++- tests/testthat/test-pTRI.R | 48 ++---- tests/testthat/test-pTriBin.R | 34 ++-- tests/testthat/test-pUNI.R | 36 +--- tests/testthat/test-pUniBin.R | 30 ++- tests/testthat/test-residuals.R | 2 127 files changed, 2285 insertions(+), 3596 deletions(-)
Title: Corbae-Ouliaris Frequency Domain Filtering
Description: Corbae-Ouliaris frequency domain filtering. According to
Corbae and Ouliaris (2006) <doi:10.1017/CBO9781139164863.008>,
this is a solution for extracting cycles from time series, like
business cycles etc. when filtering. This method is valid for both
stationary and non-stationary time series.
Author: Christos Adam [aut, cre]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between corbouli versions 0.1.2 dated 2024-10-04 and 0.1.3 dated 2024-11-20
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ README.md | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.Rmd | 4 ++-- inst/doc/Introduction.html | 5 ++--- man/corbae_ouliaris.Rd | 2 +- man/figures/figure2.png |binary vignettes/Introduction.Rmd | 4 ++-- vignettes/figure2.png |binary 12 files changed, 32 insertions(+), 27 deletions(-)
Title: Sound Waves Onto Morphometric Data
Description: Implement a promising, and yet little explored protocol for bioacoustical analysis, the eigensound method by MacLeod, Krieger and Jones (2013) <doi:10.4404/hystrix-24.1-6299>. Eigensound is a multidisciplinary method focused on the direct comparison between stereotyped sounds from different species. 'SoundShape', in turn, provide the tools required for anyone to go from sound waves to Principal Components Analysis, using tools extracted from traditional bioacoustics (i.e. 'tuneR' and 'seewave' packages), geometric morphometrics (i.e. 'geomorph' package) and multivariate analysis (e.g. 'stats' package). For more information, please see Rocha and Romano (2021) and check 'SoundShape' repository on GitHub for news and updates <https://github.com/p-rocha/SoundShape>.
Author: Pedro Rocha [aut, cre]
Maintainer: Pedro Rocha <p.rocha1990@gmail.com>
Diff between SoundShape versions 1.3.1 dated 2024-10-02 and 1.3.2 dated 2024-11-20
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/eigensound.R | 4 ++-- R/hypo.surf.R | 10 +++++----- R/threeDspectro.R | 18 +++++++++--------- build/vignette.rds |binary inst/doc/Getting-started.html | 4 ++-- man/eigensound.Rd | 4 ++-- man/hypo.surf.Rd | 10 +++++----- man/threeDspectro.Rd | 18 +++++++++--------- 10 files changed, 47 insertions(+), 47 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.2-1 dated 2024-09-22 and 3.3-0 dated 2024-11-19
DESCRIPTION | 16 ++++---- MD5 | 32 ++++++++--------- NEWS | 8 ++++ build/vignette.rds |binary inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 + inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 16 ++++---- inst/doc/updates.Rnw | 82 ++++++++++++++++++++++++++++++++++++++++----- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 2 + man/spatstat-package.Rd | 6 +++ vignettes/updates.Rnw | 82 ++++++++++++++++++++++++++++++++++++++++----- 17 files changed, 199 insertions(+), 47 deletions(-)
Title: Genetic Analysis of Pooled Samples
Description: Analyzing genetic data obtained from pooled samples.
This package can read in Fragment Analysis output files, process the data,
and score peaks, as well as facilitate various analyses, including cluster
analysis, calculation of genetic distances and diversity indices,
as well as bootstrap resampling for statistical inference. Specifically
tailored to handle genetic data efficiently, researchers can explore
population structure, genetic differentiation, and genetic relatedness
among samples. We updated some functions from Covarrubias-Pazaran et al.
(2016) <doi:10.1186/s12863-016-0365-6> to allow for the use of new file formats
and referenced the following to write our genetic analysis functions:
Long et al. (2022) <doi:10.1038/s41598-022-04776-0>, Jost (2008)
<doi:10.1111/j.1365-294x.2008.03887.x>, Nei (1973)
<doi:10.1073/pnas.70.12.3321>, Foulley et al. (2006)
<doi:10.1016/j.livprodsci.2005.10.021>, Chao et al. (2008)
<doi:10.1111/j.1541-0420.2008.01010 [...truncated...]
Author: Kathleen Kuesters [aut, cre, cph]
,
Jeffrey Long [aut],
Jessica Blanton [aut],
Walter Blank [ctb],
Jeffrey Kovach [ctb],
Ronald Blanton [ctb]
Maintainer: Kathleen Kuesters <kathleen.kuesters@gmail.com>
Diff between pooledpeaks versions 1.0.6 dated 2024-09-12 and 1.0.7 dated 2024-11-19
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 2 ++ R/Pop_Gen_setup.R | 21 ++++++++++++++++++--- build/partial.rdb |binary 5 files changed, 27 insertions(+), 10 deletions(-)
Title: 'REST' API Client for Accessing Data on 'WEkEO HDA V2'
Description: Provides seamless access to the WEkEO Harmonised Data Access (HDA) API, enabling
users to query, download, and process data efficiently from the HDA platform.
With 'hdar', researchers and data scientists can integrate the extensive HDA
datasets into their R workflows, enhancing their data analysis capabilities.
Comprehensive information on the API functionality and usage is available
at <https://gateway.prod.wekeo2.eu/hda-broker/docs>.
Author: Matteo Mattiuzzi [aut, cre]
Maintainer: Matteo Mattiuzzi <matteo.mattiuzzi@eea.europa.eu>
Diff between hdar versions 1.0.2 dated 2024-09-28 and 1.0.4 dated 2024-11-19
DESCRIPTION | 6 MD5 | 18 - R/client.R | 2 R/paginator.R | 20 - R/search_results.R | 51 ++-- inst/doc/hdar.R | 598 +++++++++++++++++++++++++-------------------------- inst/doc/hdar.Rmd | 2 inst/doc/hdar.html | 2 man/SearchResults.Rd | 5 vignettes/hdar.Rmd | 2 10 files changed, 360 insertions(+), 346 deletions(-)
Title: Analyze and Visualize Data from 'Microsoft Viva Insights'
Description: Provides a versatile range of functions, including exploratory data analysis, time-series analysis, organizational network analysis, and data validation, whilst at the same time implements a set of best practices in analyzing and visualizing data specific to 'Microsoft Viva Insights'.
Author: Martin Chan [aut, cre],
Carlos Morales [aut]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between vivainsights versions 0.5.4 dated 2024-09-06 and 0.5.5 dated 2024-11-19
DESCRIPTION | 6 +- MD5 | 50 ++++++++++++---- NAMESPACE | 1 NEWS.md | 5 + R/check_query.R | 33 ----------- R/collaboration_area.R | 2 R/create_bar.R | 13 +--- R/create_dist.R | 13 +--- R/create_fizz.R | 15 ++--- R/create_line.R | 2 R/create_lorenz.R | 15 ++++- R/create_stacked.R | 8 +- R/xicor.R |only man/create_lorenz.Rd | 83 ++++++++++++++++------------ man/xicor.Rd |only tests/testthat/test_create_IV.R | 4 + tests/testthat/test_create_bar.R |only tests/testthat/test_create_bar_asis.R |only tests/testthat/test_create_boxplot.R |only tests/testthat/test_create_bubble.R |only tests/testthat/test_create_density.R |only tests/testthat/test_create_dist.R |only tests/testthat/test_create_dt.R |only tests/testthat/test_create_fizz.R |only tests/testthat/test_create_hist.R |only tests/testthat/test_create_inc.R |only tests/testthat/test_create_line.R |only tests/testthat/test_create_line_asis.R |only tests/testthat/test_create_lorenz.R |only tests/testthat/test_create_period_scatter.R |only tests/testthat/test_create_rank.R |only tests/testthat/test_create_sankey.R |only tests/testthat/test_create_scatter.R |only tests/testthat/test_create_stacked.R |only tests/testthat/test_create_tracking.R |only tests/testthat/test_create_trend.R |only tests/testthat/test_network_p2p.R | 4 + 37 files changed, 137 insertions(+), 117 deletions(-)
Title: A Robust Boosting Algorithm
Description: An implementation of robust boosting algorithms for regression in R. This includes the RRBoost method proposed in the paper "Robust Boosting for Regression Problems" (Ju X and Salibian-Barrera M. 2020) <doi:10.1016/j.csda.2020.107065>. It also implements previously proposed boosting algorithms in the simulation section of the paper: L2Boost, LADBoost, MBoost (Friedman, J. H. (2001) <doi:10.1214/aos/1013203451>) and Robloss (Lutz et al. (2008) <doi:10.1016/j.csda.2007.11.006>).
Author: Xiaomeng Ju [aut, cre],
Matias Salibian-Barrera [aut]
Maintainer: Xiaomeng Ju <xiaomeng.ju@stat.ubc.ca>
Diff between RRBoost versions 0.1 dated 2020-10-13 and 0.2 dated 2024-11-19
DESCRIPTION | 18 +++++++++------- MD5 | 16 ++++++++------- R/Boost.R | 51 ++++++++++++++++++++++++------------------------ man/Boost.Rd | 9 ++++---- man/Boost.control.Rd | 6 ++--- man/Boost.validation.Rd | 6 ++--- man/cal_imp_func.Rd | 6 ++--- man/cal_predict.Rd | 6 ++--- tests |only 9 files changed, 62 insertions(+), 56 deletions(-)
Title: Find the Pole of Inaccessibility (Visual Center) of a Polygon
Description: A wrapper around the C++ library 'polylabel' from 'Mapbox',
providing an efficient routine for finding the approximate pole of
inaccessibility of a polygon, which usually serves as an excellent candidate
for labeling of a polygon.
Author: Johan Larsson [aut, cre] ,
Kent Johnson [ctb],
Mapbox [cph]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between polylabelr versions 0.2.0 dated 2020-04-19 and 0.3.0 dated 2024-11-19
DESCRIPTION | 19 ++--- MD5 | 68 +++++++++++---------- NAMESPACE | 2 NEWS.md | 20 ++++-- R/poi.R | 15 ++-- R/poi_multi.R |only R/poi_sf.R | 22 ++---- R/utils.R |only README.md | 25 ++----- build |only inst/CITATION | 2 inst/WORDLIST | 5 - inst/include/mapbox/feature.hpp |only inst/include/mapbox/geometry.hpp | 1 inst/include/mapbox/geometry/box.hpp | 6 + inst/include/mapbox/geometry/empty.hpp |only inst/include/mapbox/geometry/envelope.hpp | 4 - inst/include/mapbox/geometry/for_each_point.hpp | 18 +++-- inst/include/mapbox/geometry/geometry.hpp | 32 ++++----- inst/include/mapbox/geometry/line_string.hpp | 6 + inst/include/mapbox/geometry/multi_line_string.hpp | 4 - inst/include/mapbox/geometry/multi_point.hpp | 4 - inst/include/mapbox/geometry/multi_polygon.hpp | 4 - inst/include/mapbox/geometry/point.hpp | 6 + inst/include/mapbox/geometry/polygon.hpp | 8 +- inst/include/mapbox/geometry_io.hpp |only inst/include/mapbox/polylabel.hpp | 16 +--- man/figures/README-unnamed-chunk-1-1.png |binary man/poi.Rd | 6 - man/poi_multi.Rd |only man/polylabelr-package.Rd | 7 -- src/Makevars | 1 src/RcppExports.cpp | 5 + src/poi.cpp | 24 ++++--- tests/testthat/helper_point_in_polygon.R | 5 - tests/testthat/test-assertions.R | 2 tests/testthat/test-poi-multi.R |only tests/testthat/test-poi-sf.R | 55 ++++++++-------- tests/testthat/test-poi.R | 2 39 files changed, 210 insertions(+), 184 deletions(-)
Title: Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 6.2 dated 2024-08-23 and 6.3 dated 2024-11-19
DESCRIPTION | 8 MD5 | 22 +- NAMESPACE | 2 NEWS | 13 + R/HelpersMG-package.R | 4 R/MHalgoGen.R | 13 + R/as.parameters.R | 3 R/plot.mcmcComposite.R | 386 ++++++++++++++++++++++++++++++---------------- inst/shiny/cutter/ui.R | 2 man/HelpersMG-package.Rd | 4 man/MHalgoGen.Rd | 7 man/plot.mcmcComposite.Rd | 53 ++++-- 12 files changed, 340 insertions(+), 177 deletions(-)
Title: Wildlife Mortality Estimator for Low Fatality Rates and
Imperfect Detection
Description: Evidence of Absence software (EoA) is a user-friendly application for estimating bird and bat fatalities at wind farms and designing search protocols. The software is particularly useful in addressing whether the number of fatalities has exceeded a given threshold and what search parameters are needed to give assurance that thresholds were not exceeded. The models are applicable even when zero carcasses have been found in searches, following Huso et al. (2015) <doi:10.1890/14-0764.1>, Dalthorp et al. (2017) <doi:10.3133/ds1055>, and Dalthorp and Huso (2015) <doi:10.3133/ofr20151227>.
Author: Daniel Dalthorp [aut, cre]
Maintainer: Daniel Dalthorp <ddalthorp@protonmail.com>
Diff between eoa3 versions 1.0.0.1 dated 2023-07-04 and 1.0.0.2 dated 2024-11-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/eoa.r | 4 ++-- man/eoa3.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: SDTM Datacut
Description: Supports the process of applying a cut to Standard Data Tabulation Model (SDTM),
as part of the analysis of specific points in time of the data, normally as part of
investigation into clinical trials. The functions support different approaches of
cutting to the different domains of SDTM normally observed.
Author: Tim Barnett [cph, aut, cre],
Nathan Rees [aut],
Alana Harris [aut],
Cara Andrews [aut]
Maintainer: Tim Barnett <timothy.barnett@roche.com>
Diff between datacutr versions 0.1.0 dated 2023-03-31 and 0.2.0 dated 2024-11-19
DESCRIPTION | 26 + MD5 | 96 +++--- NAMESPACE | 3 NEWS.md | 34 ++ R/create_dcut.R | 14 R/datcutr-package.R | 2 R/date_cut.R | 19 - R/global.R | 3 R/impute_dcutdtc.R | 9 R/process_cut.R | 157 +++++++--- R/read_out.R |only R/special_dm_cut.R | 15 - README.md | 14 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/contribution_model.html | 232 +++++++++++++++- inst/doc/datacutr.Rmd | 2 inst/doc/datacutr.html | 304 +++++++++++++++++++-- inst/doc/examplemodular.R | 7 inst/doc/examplemodular.Rmd | 5 inst/doc/examplemodular.html | 504 ++++++++++++++++++++++++----------- inst/doc/examplewrapped.R | 7 inst/doc/examplewrapped.Rmd | 5 inst/doc/examplewrapped.html | 432 ++++++++++++++++++++++-------- inst/doc/modular.R | 33 +- inst/doc/modular.Rmd | 5 inst/doc/modular.html | 479 ++++++++++++++++++++++++--------- inst/doc/variable_cut.R | 19 - inst/doc/variable_cut.Rmd | 9 inst/doc/variable_cut.html | 427 ++++++++++++++++++++++------- inst/doc/wrapper.R | 15 - inst/doc/wrapper.Rmd | 5 inst/doc/wrapper.html | 419 ++++++++++++++++++++++------- inst/read-out |only man/create_dcut.Rd | 2 man/datacutr-package.Rd | 10 man/impute_dcutdtc.Rd | 2 man/process_cut.Rd | 23 + man/read_out.Rd |only tests/testthat/test-create_dcut.R | 36 ++ tests/testthat/test-date_cut.R | 46 +++ tests/testthat/test-impute_dcutdtc.R | 26 - tests/testthat/test-process_cut.R | 53 +++ tests/testthat/test-read_out.R |only tests/testthat/test-special_dm_cut.R | 50 +++ vignettes/datacutr.Rmd | 2 vignettes/examplemodular.Rmd | 5 vignettes/examplewrapped.Rmd | 5 vignettes/modular.Rmd | 5 vignettes/variable_cut.Rmd | 9 vignettes/wrapper.Rmd | 5 51 files changed, 2720 insertions(+), 861 deletions(-)
Title: Fitting and Simulating Mixtures of Watson Distributions
Description: Tools for fitting and simulating mixtures of Watson distributions.
The random sampling scheme of the package offers two sampling
algorithms that are based of the results of Sablica, Hornik and Leydold (2022)
<https://research.wu.ac.at/en/publications/random-sampling-from-the-watson-distribution>.
What is more, the package offers a smart tool to combine these two methods,
and based on the selected parameters, it approximates the relative sampling
speed for both methods and picks the faster one. In addition, the package
offers a fitting function for the mixtures of Watson distribution, that
uses the expectation-maximization (EM) algorithm. Special features are
the possibility to use multiple variants of the E-step and M-step,
sparse matrices for the data representation and state of the art methods
for numerical evaluation of needed special functions using the results of
Sablica and Hornik (2022) <https://www.ams.org/journals/mcom/2022-91-334/S0025-5718-2021-03690-X/>.
Author: Lukas Sablica [aut, cre] ,
Kurt Hornik [aut] ,
Josef Leydold [aut] ,
Gerard Jungman [ctb, cph] ,
Brian Gough [ctb, cph]
Maintainer: Lukas Sablica <lsablica@wu.ac.at>
Diff between watson versions 0.4 dated 2023-06-01 and 0.5 dated 2024-11-19
watson-0.4/watson/R/sysdata.rda |only watson-0.5/watson/DESCRIPTION | 12 ++++--- watson-0.5/watson/MD5 | 13 ++++--- watson-0.5/watson/NAMESPACE | 5 ++ watson-0.5/watson/NEWS.md | 6 +++ watson-0.5/watson/R/watson.R | 68 ++++++++++++++++++++++++++++++++++++++++ watson-0.5/watson/man/id.Rd |only watson-0.5/watson/tests |only 8 files changed, 94 insertions(+), 10 deletions(-)
Title: Hyperbolic DEA Estimation
Description: Implements Data Envelopment Analysis (DEA) with a hyperbolic orientation using a non-linear programming solver. It enables flexible estimations with weight restrictions, non-discretionary variables, and a generalized distance function. Additionally, it allows for the calculation of slacks and super-efficiency scores. The methods are detailed in Öttl et al. (2023), <doi:10.1016/j.dajour.2023.100343>. Furthermore, the package provides a non-linear profitability estimation built upon the DEA framework.
Author: Alexander Oettl [cre, aut] ,
Daniel Gulde [aut]
Maintainer: Alexander Oettl <alexoettl34@gmail.com>
Diff between hyperbolicDEA versions 1.0.0 dated 2024-03-18 and 1.0.1 dated 2024-11-19
DESCRIPTION | 8 - MD5 | 28 ++--- NAMESPACE | 1 R/check_arguments.R | 26 ++++- R/costDEA.R | 3 R/hyperbolicDEA.R | 20 ++-- R/lprofitDEA.R | 2 R/nlprofitDEA.R | 2 R/wrDEA.R | 75 ++++++++++++++- man/costDEA.Rd | 87 +++++++++--------- man/hyperbolicDEA.Rd | 5 + man/lprofitDEA.Rd | 95 ++++++++++--------- man/nlprofitDEA.Rd | 91 +++++++++---------- man/wrDEA.Rd | 172 +++++++++++++++++++----------------- tests/testthat/test-hyperbolicDEA.R | 53 +++++++++-- 15 files changed, 410 insertions(+), 258 deletions(-)
Title: Constrained Ordinary Least Squares
Description: Constrained ordinary least squares is performed. One constraint is that all beta coefficients (including the constant) cannot be negative. They can be either 0 or strictly positive. Another constraint is that the sum of the beta coefficients equals a constant. References: Hansen, B. E. (2022). Econometrics, Princeton University Press. <ISBN:9780691235899>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between cols versions 1.2 dated 2024-10-16 and 1.3 dated 2024-11-19
cols-1.2/cols/R/mcls.R |only cols-1.3/cols/DESCRIPTION | 8 ++++---- cols-1.3/cols/MD5 | 12 +++++++----- cols-1.3/cols/NAMESPACE | 2 +- cols-1.3/cols/R/int.cls.R |only cols-1.3/cols/R/mvcls.R |only cols-1.3/cols/man/cls.Rd | 8 ++++---- cols-1.3/cols/man/cols-package.Rd | 4 ++-- cols-1.3/cols/man/int.cls.Rd |only 9 files changed, 18 insertions(+), 16 deletions(-)
Title: 'CDsampling': Constraint Sampling in Paid Research Studies
Description: In the context of paid research studies and clinical trials, budget considerations and patient sampling from available populations are subject to inherent constraints. We introduce the 'CDsampling' package, which integrates optimal design theories within the framework of constrained sampling. This package offers the possibility to find both D-optimal approximate and exact allocations for samplings with or without constraints. Additionally, it provides functions to find constrained uniform sampling as a robust sampling strategy with limited model information. Our package offers functions for the computation of the Fisher information matrix under generalized linear models (including regular linear regression model) and multinomial logistic models.To demonstrate the applications, we also provide a simulated dataset and a real dataset embedded in the package. Yifei Huang, Liping Tong, and Jie Yang (2025)<doi:10.5705/ss.202022.0414>.
Author: Yifei Huang [aut, cre],
Liping Tong [aut],
Jie Yang [aut]
Maintainer: Yifei Huang <yhuan39@uic.edu>
Diff between CDsampling versions 0.1.1 dated 2024-10-13 and 0.1.2 dated 2024-11-19
CDsampling-0.1.1/CDsampling/R/constrained_uniform.R |only CDsampling-0.1.1/CDsampling/man/constrained_uniform.Rd |only CDsampling-0.1.2/CDsampling/DESCRIPTION | 6 CDsampling-0.1.2/CDsampling/MD5 | 46 - CDsampling-0.1.2/CDsampling/NAMESPACE | 5 CDsampling-0.1.2/CDsampling/R/F_func_GLM.R | 9 CDsampling-0.1.2/CDsampling/R/F_func_MLM.R | 3 CDsampling-0.1.2/CDsampling/R/Fi_func_MLM.R | 12 CDsampling-0.1.2/CDsampling/R/W_func_GLM.R | 1 CDsampling-0.1.2/CDsampling/R/approxtoexact_constrained_func.R | 6 CDsampling-0.1.2/CDsampling/R/approxtoexact_func.R | 5 CDsampling-0.1.2/CDsampling/R/bounded_uniform.R |only CDsampling-0.1.2/CDsampling/R/liftone_GLM.R | 14 CDsampling-0.1.2/CDsampling/R/liftone_MLM.R | 16 CDsampling-0.1.2/CDsampling/R/liftone_constrained_GLM.R | 22 CDsampling-0.1.2/CDsampling/R/liftone_constrained_MLM.R | 18 CDsampling-0.1.2/CDsampling/R/print.list_output.R |only CDsampling-0.1.2/CDsampling/R/print.matrix_list.R |only CDsampling-0.1.2/CDsampling/R/print.matrix_output.R |only CDsampling-0.1.2/CDsampling/inst/doc/Intro_to_CDsampling.R | 18 CDsampling-0.1.2/CDsampling/inst/doc/Intro_to_CDsampling.Rmd | 18 CDsampling-0.1.2/CDsampling/inst/doc/Intro_to_CDsampling.html | 310 ++++++---- CDsampling-0.1.2/CDsampling/man/F_func_GLM.Rd | 6 CDsampling-0.1.2/CDsampling/man/bounded_uniform.Rd |only CDsampling-0.1.2/CDsampling/man/liftone_MLM.Rd | 2 CDsampling-0.1.2/CDsampling/man/print.list_output.Rd |only CDsampling-0.1.2/CDsampling/man/print.matrix_list.Rd |only CDsampling-0.1.2/CDsampling/man/print.matrix_output.Rd |only CDsampling-0.1.2/CDsampling/vignettes/Intro_to_CDsampling.Rmd | 18 29 files changed, 323 insertions(+), 212 deletions(-)
Title: Synthesise and Correlate Likert Scale and Related Rating-Scale
Data
Description: Synthesise Likert scale and related rating-scale data with
predefined first and second moments (mean and standard deviation),
and, optionally, correlate multiple vectors using a predefined
correlation matrix. Additionally, generate synthetic rating-scale
items with a predefined Cronbach's Alpha, or create rating-scale items
based on a predefined summated scale.
Author: Hume Winzar [cre, aut]
Maintainer: Hume Winzar <winzar@gmail.com>
Diff between LikertMakeR versions 0.3.0 dated 2024-05-19 and 0.4.0 dated 2024-11-19
LikertMakeR-0.3.0/LikertMakeR/vignettes/LikertMakeR_1.png |only LikertMakeR-0.3.0/LikertMakeR/vignettes/LikertMakeR_2.png |only LikertMakeR-0.3.0/LikertMakeR/vignettes/LikertMakeR_4.png |only LikertMakeR-0.3.0/LikertMakeR/vignettes/LikertMakeR_hex.png |only LikertMakeR-0.4.0/LikertMakeR/DESCRIPTION | 22 LikertMakeR-0.4.0/LikertMakeR/MD5 | 38 LikertMakeR-0.4.0/LikertMakeR/NAMESPACE | 2 LikertMakeR-0.4.0/LikertMakeR/NEWS.md | 10 LikertMakeR-0.4.0/LikertMakeR/R/lexact.R | 1 LikertMakeR-0.4.0/LikertMakeR/R/lfast.R | 7 LikertMakeR-0.4.0/LikertMakeR/R/makeItems.R | 3 LikertMakeR-0.4.0/LikertMakeR/R/makeItemsScale.R | 322 +- LikertMakeR-0.4.0/LikertMakeR/README.md | 225 + LikertMakeR-0.4.0/LikertMakeR/build/vignette.rds |binary LikertMakeR-0.4.0/LikertMakeR/inst/CITATION | 2 LikertMakeR-0.4.0/LikertMakeR/inst/WORDLIST |only LikertMakeR-0.4.0/LikertMakeR/inst/doc/LikertMakeR_vignette.R | 287 +- LikertMakeR-0.4.0/LikertMakeR/inst/doc/LikertMakeR_vignette.Rmd | 442 ++- LikertMakeR-0.4.0/LikertMakeR/inst/doc/LikertMakeR_vignette.html | 1263 ++++++---- LikertMakeR-0.4.0/LikertMakeR/man/figures/logo.png |binary LikertMakeR-0.4.0/LikertMakeR/man/makeItemsScale.Rd | 194 + LikertMakeR-0.4.0/LikertMakeR/vignettes/LikertMakeR_vignette.Rmd | 442 ++- LikertMakeR-0.4.0/LikertMakeR/vignettes/skew_chart.png |only 23 files changed, 2230 insertions(+), 1030 deletions(-)
Title: Gaussian Process Laboratory
Description: Gaussian process regression with an emphasis on kernels.
Quantitative and qualitative inputs are accepted. Some pre-defined
kernels are available, such as radial or tensor-sum for
quantitative inputs, and compound symmetry, low rank, group kernel
for qualitative inputs. The user can define new kernels and
composite kernels through a formula mechanism. Useful methods
include parameter estimation by maximum likelihood, simulation,
prediction and leave-one-out validation.
Author: Yves Deville [aut] ,
David Ginsbourger [aut] ,
Olivier Roustant [aut, cre],
Nicolas Durrande [ctb]
Maintainer: Olivier Roustant <roustant@insa-toulouse.fr>
Diff between kergp versions 0.5.7 dated 2024-02-05 and 0.5.8 dated 2024-11-19
DESCRIPTION | 24 ++++++++++++++++++------ MD5 | 18 +++++++++--------- build/partial.rdb |binary inst/doc/OptimMLE.pdf |binary inst/doc/beam.pdf |binary inst/doc/groupKernel.pdf |binary man/gp.Rd | 8 +++++--- man/influence.gp.Rd | 2 +- man/kergp-package.Rd | 25 ++++++++++++++----------- man/simulate.covAll.Rd | 4 ++-- 10 files changed, 49 insertions(+), 32 deletions(-)
Title: Hidden Markov Models for Reliability and Maintenance
Description: Reliability Analysis and Maintenance Optimization using Hidden Markov Models (HMM). The use of HMMs to model the state of a system which is not directly observable and instead certain indicators (signals) of the true situation are provided via a control system. A hidden model can provide key information about the system dependability, such as the reliability of the system and related measures. An estimation procedure is implemented based on the Baum-Welch algorithm. Classical structures such as K-out-of-N systems and Shock models are illustrated. Finally, the maintenance of the system is considered in the HMM context and two functions for new preventive maintenance strategies are considered. Maintenance efficiency is measured in terms of expected cost. Methods are described in Gamiz, Limnios, and Segovia-Garcia (2023) <doi:10.1016/j.ejor.2022.05.006>.
Author: M.L. Gamiz [aut, cre, cph],
N. Limnios [aut, cph],
M.C. Segovia-Garcia [aut, cph]
Maintainer: M.L. Gamiz <mgamiz@ugr.es>
Diff between HMMRel versions 0.1.0 dated 2024-11-15 and 0.1.1 dated 2024-11-19
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NEWS.md |only man/HMMRel-package.Rd | 2 +- man/cost.cspc.Rd | 4 ++-- man/cost.wspc.Rd | 9 ++++----- man/def.hmmR.Rd | 6 +++--- man/fit.hmmR.Rd | 4 ++-- 8 files changed, 23 insertions(+), 23 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Panagiotis Skintzos [aut],
Mike Bostock [cph] ,
Speros Kokenes [cph] ,
Eric Shull [cph] ,
Lee Thomason [cph] ,
Vladimir Agafonkin [cph] ,
Eric Book [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.8.10 dated 2024-05-17 and 0.8.11 dated 2024-11-19
ggiraph-0.8.10/ggiraph/inst/tinytest/test-ggiraph.R |only ggiraph-0.8.11/ggiraph/DESCRIPTION | 10 ggiraph-0.8.11/ggiraph/MD5 | 221 ++++----- ggiraph-0.8.11/ggiraph/NAMESPACE | 9 ggiraph-0.8.11/ggiraph/NEWS.md | 11 ggiraph-0.8.11/ggiraph/R/annotate_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/annotation_raster_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/element_interactive.R | 8 ggiraph-0.8.11/ggiraph/R/facet_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_abline_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_bar_interactive.R | 8 ggiraph-0.8.11/ggiraph/R/geom_bin_2d_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_boxplot_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_contour_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_count_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_crossbar_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_density_2d_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_density_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_dotplot_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_errorbarh_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_hex_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_histogram_interactive.R | 4 ggiraph-0.8.11/ggiraph/R/geom_jitter_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_map_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_path_interactive.R | 31 + ggiraph-0.8.11/ggiraph/R/geom_point_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_polygon_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_quantile_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_raster_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_rect_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_ribbon_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_segment_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_sf_interactive.R | 7 ggiraph-0.8.11/ggiraph/R/geom_smooth_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_spoke_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_text_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/geom_violin_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/ggiraph.R | 106 ---- ggiraph-0.8.11/ggiraph/R/guide_bins_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/guide_colourbar_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/guide_coloursteps_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/guide_legend_interactive.R | 2 ggiraph-0.8.11/ggiraph/R/ipar.R | 4 ggiraph-0.8.11/ggiraph/R/labeller_interactive.R | 10 ggiraph-0.8.11/ggiraph/R/scale_alpha_interactive.R | 14 ggiraph-0.8.11/ggiraph/R/scale_brewer_interactive.R | 12 ggiraph-0.8.11/ggiraph/R/scale_colour_interactive.R | 28 - ggiraph-0.8.11/ggiraph/R/scale_gradient_interactive.R | 12 ggiraph-0.8.11/ggiraph/R/scale_linetype_interactive.R | 8 ggiraph-0.8.11/ggiraph/R/scale_manual_interactive.R | 14 ggiraph-0.8.11/ggiraph/R/scale_shape_interactive.R | 10 ggiraph-0.8.11/ggiraph/R/scale_size_interactive.R | 20 ggiraph-0.8.11/ggiraph/R/scale_steps_interactive.R | 12 ggiraph-0.8.11/ggiraph/R/scale_viridis_interactive.R | 16 ggiraph-0.8.11/ggiraph/R/utils_ggplot2.R | 240 ++++++++++ ggiraph-0.8.11/ggiraph/build/vignette.rds |binary ggiraph-0.8.11/ggiraph/inst/examples/rmd/flexdashboard/flexdashboard.Rmd | 2 ggiraph-0.8.11/ggiraph/man/annotate_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/annotation_raster_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/element_interactive.Rd | 8 ggiraph-0.8.11/ggiraph/man/facet_grid_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/facet_wrap_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/geom_abline_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_bar_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_bin_2d_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_boxplot_interactive.Rd | 12 ggiraph-0.8.11/ggiraph/man/geom_contour_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_count_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_crossbar_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_density_2d_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_density_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_dotplot_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_errorbarh_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_hex_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_histogram_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_jitter_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_map_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_path_interactive.Rd | 6 ggiraph-0.8.11/ggiraph/man/geom_point_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_polygon_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_quantile_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_raster_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_rect_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_ribbon_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_segment_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_sf_interactive.Rd | 7 ggiraph-0.8.11/ggiraph/man/geom_smooth_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_spoke_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_text_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/geom_text_repel_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/geom_violin_interactive.Rd | 4 ggiraph-0.8.11/ggiraph/man/ggiraph.Rd | 62 -- ggiraph-0.8.11/ggiraph/man/ggiraphOutput.Rd | 22 ggiraph-0.8.11/ggiraph/man/guide_bins_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/guide_colourbar_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/guide_coloursteps_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/guide_legend_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/interactive_parameters.Rd | 4 ggiraph-0.8.11/ggiraph/man/label_interactive.Rd | 2 ggiraph-0.8.11/ggiraph/man/labeller_interactive.Rd | 10 ggiraph-0.8.11/ggiraph/man/renderggiraph.Rd | 18 ggiraph-0.8.11/ggiraph/man/scale_alpha_interactive.Rd | 14 ggiraph-0.8.11/ggiraph/man/scale_colour_brewer_interactive.Rd | 12 ggiraph-0.8.11/ggiraph/man/scale_colour_interactive.Rd | 28 - ggiraph-0.8.11/ggiraph/man/scale_colour_steps_interactive.Rd | 12 ggiraph-0.8.11/ggiraph/man/scale_gradient_interactive.Rd | 12 ggiraph-0.8.11/ggiraph/man/scale_linetype_interactive.Rd | 8 ggiraph-0.8.11/ggiraph/man/scale_manual_interactive.Rd | 14 ggiraph-0.8.11/ggiraph/man/scale_shape_interactive.Rd | 10 ggiraph-0.8.11/ggiraph/man/scale_size_interactive.Rd | 20 ggiraph-0.8.11/ggiraph/man/scale_viridis_interactive.Rd | 16 ggiraph-0.8.11/ggiraph/src/tinyxml2.cpp | 8 112 files changed, 719 insertions(+), 601 deletions(-)
Title: Transform Files to 'microtable' Object with 'microeco' Package
Description: Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.
Author: Chi Liu [aut, cre]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between file2meco versions 0.9.0 dated 2024-10-31 and 0.9.1 dated 2024-11-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/qiime2meco.R | 15 ++++++++++----- 3 files changed, 15 insertions(+), 10 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.1080/00031305.2023.2203177>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [aut] ,
Sandra Siegfried [aut] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.1-2 dated 2024-10-04 and 1.2-0 dated 2024-11-19
tram-1.1-2/tram/src |only tram-1.1-2/tram/vignettes/mtram-rendered.pdf |only tram-1.2-0/tram/DESCRIPTION | 18 tram-1.2-0/tram/MD5 | 62 tram-1.2-0/tram/NAMESPACE | 2 tram-1.2-0/tram/R/mtram.R | 195 +- tram-1.2-0/tram/build/partial.rdb |binary tram-1.2-0/tram/build/vignette.rds |binary tram-1.2-0/tram/demo/00Index | 13 tram-1.2-0/tram/demo/hcc.R | 2 tram-1.2-0/tram/demo/mnc.R |only tram-1.2-0/tram/demo/mtram.R | 75 tram-1.2-0/tram/demo/npb.R |only tram-1.2-0/tram/demo/stram.R | 4 tram-1.2-0/tram/demo/survtram.R | 115 - tram-1.2-0/tram/demo/tram.R |only tram-1.2-0/tram/inst/NEWS.Rd | 11 tram-1.2-0/tram/inst/doc/mtram.R |only tram-1.2-0/tram/inst/doc/mtram.Rnw | 2001 ++++++++++++++++++++++- tram-1.2-0/tram/inst/doc/mtram.pdf |binary tram-1.2-0/tram/inst/doc/tram.R | 21 tram-1.2-0/tram/inst/doc/tram.Rnw | 7 tram-1.2-0/tram/inst/doc/tram.pdf |binary tram-1.2-0/tram/inst/simulations/mtram_sim.R | 10 tram-1.2-0/tram/inst/simulations/sim2d.R | 6 tram-1.2-0/tram/inst/simulations/sim2d.Rout.save |only tram-1.2-0/tram/inst/simulations/sim2d.pdf.save |only tram-1.2-0/tram/inst/simulations/sim5d.R | 19 tram-1.2-0/tram/inst/simulations/sim5d.Rout.save |only tram-1.2-0/tram/inst/simulations/sim5d.pdf.save |only tram-1.2-0/tram/man/Coxph.Rd | 8 tram-1.2-0/tram/man/mtram.Rd | 38 tram-1.2-0/tram/tests/bugfixes.R | 6 tram-1.2-0/tram/tests/mtram-Ex.R |only tram-1.2-0/tram/tests/mtram-Ex.Rout.save |only tram-1.2-0/tram/vignettes/mtram.Rnw | 2001 ++++++++++++++++++++++- tram-1.2-0/tram/vignettes/tram.Rnw | 7 37 files changed, 4357 insertions(+), 264 deletions(-)
Title: Tools for Analyzing Factorial Experiments
Description: Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg. For details on the implemented methods, see Roland Pfister and Markus Janczyk (2016) <doi: 10.20982/tqmp.12.2.p147>.
Author: Roland Pfister [aut, cre],
Markus Janczyk [aut]
Maintainer: Roland Pfister <mail@roland-pfister.net>
Diff between schoRsch versions 1.10 dated 2022-11-01 and 1.11 dated 2024-11-19
DESCRIPTION | 18 +++++++++++++----- MD5 | 14 ++++++++------ R/bimod_coef.R |only R/cor_out.R | 25 +++++++++++++++++++------ R/t_out.R | 1 + man/bimod_coef.Rd |only man/clear_all_but.Rd | 3 ++- man/cor_out.Rd | 3 ++- man/schoRsch.Rd | 12 ++++++++---- 9 files changed, 53 insertions(+), 23 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-9 dated 2024-09-20 and 1.1-10 dated 2024-11-19
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/mlt.R | 2 +- inst/doc/mlt.Rnw | 2 +- inst/doc/mlt.pdf |binary vignettes/mlt.Rnw | 2 +- 8 files changed, 21 insertions(+), 14 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.2-2 dated 2024-09-20 and 3.2-3 dated 2024-11-19
DESCRIPTION | 16 ++++++++-------- MD5 | 13 +++++++------ NEWS | 13 +++++++++++++ R/shortestpath.R |only inst/doc/packagesizes.txt | 2 +- inst/info/packagesizes.txt | 2 +- man/pairdist.lpp.Rd | 1 + man/plot.linim.Rd | 3 ++- 8 files changed, 33 insertions(+), 17 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Create Maps of Air Pollution Data
Description: Combine the air quality data analysis methods of 'openair'
with the JavaScript 'Leaflet' (<https://leafletjs.com/>) library.
Functionality includes plotting site maps, "directional analysis"
figures such as polar plots, and air mass trajectories.
Author: Jack Davison [cre, aut] ,
David Carslaw [aut]
Maintainer: Jack Davison <jack.davison@ricardo.com>
Diff between openairmaps versions 0.9.0 dated 2024-05-19 and 0.9.1 dated 2024-11-19
DESCRIPTION | 20 +++--- MD5 | 54 ++++++++-------- NEWS.md | 24 +++++++ R/openairmaps-package.R | 96 ++++++++++++++--------------- R/polar_annulusMap.R | 6 + R/polar_diffMap.R | 18 +++-- R/polar_freqMap.R | 6 + R/polar_percentileMap.R | 6 + R/polar_polarMap.R | 56 ++++++++++++++--- R/polar_pollroseMap.R | 6 + R/polar_windroseMap.R | 6 + R/traj_trajMap.R | 107 ++++++++++++++++++++++++++------ R/utilities.R | 31 +++------ R/utils-map.R | 23 ++----- README.md | 111 ++++++++++++++++++++++------------ inst/examples-shiny/01_polarmap/app.R | 5 - inst/examples-shiny/02_trajmap/app.R | 12 +-- man/annulusMap.Rd | 15 +++- man/deprecated-static-polar-maps.Rd | 6 + man/diffMap.Rd | 17 ++++- man/freqMap.Rd | 15 +++- man/openairmaps-package.Rd | 4 - man/percentileMap.Rd | 15 +++- man/polarMap.Rd | 19 ++++- man/pollroseMap.Rd | 15 +++- man/trajMap.Rd | 25 +++++++ man/trajMapStatic.Rd | 96 ++++++++++------------------- man/windroseMap.Rd | 13 +++ 28 files changed, 535 insertions(+), 292 deletions(-)
Title: Enrichment Analysis Using Multiple Ontologies and False
Discovery Rate
Description: Background - Traditional gene set enrichment analyses are
typically limited to a few ontologies and do not account for the
interdependence of gene sets or terms, resulting in overcorrected p-values.
To address these challenges, we introduce mulea, an R package offering
comprehensive overrepresentation and functional enrichment analysis.
Results - mulea employs a progressive empirical false discovery rate
(eFDR) method, specifically designed for interconnected biological data,
to accurately identify significant terms within diverse ontologies. mulea
expands beyond traditional tools by incorporating a wide range of
ontologies, encompassing Gene Ontology, pathways, regulatory elements,
genomic locations, and protein domains. This flexibility enables
researchers to tailor enrichment analysis to their specific questions,
such as identifying enriched transcriptional regulators in gene expression
data or overrepresented protein domains in protein sets. To facilitate
seamless analysis, mulea p [...truncated...]
Author: Cezary Turek [aut] ,
Marton Olbei [aut] ,
Tamas Stirling [aut, cre] ,
Gergely Fekete [aut] ,
Ervin Tasnadi [aut] ,
Leila Gul [aut],
Balazs Bohar [aut] ,
Balazs Papp [aut] ,
Wiktor Jurkowski [aut] ,
Eszter Ari [aut, cph]
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
Diff between mulea versions 1.1.0 dated 2024-09-24 and 1.1.1 dated 2024-11-19
DESCRIPTION | 9 +- MD5 | 16 ++-- NEWS.md | 4 + build/vignette.rds |binary inst/CITATION | 19 +++-- inst/doc/mulea.R | 170 ++++++++++++++++++++++++++-------------------------- inst/doc/mulea.Rmd | 4 - inst/doc/mulea.html | 133 +++++++++++++++++++--------------------- vignettes/mulea.Rmd | 4 - 9 files changed, 182 insertions(+), 177 deletions(-)
Title: Fast and Easy Data Cleaning
Description: Data cleaning functions for classes logical,
factor, numeric, character, currency and Date to make
data cleaning fast and easy. Relying on very few dependencies, it
provides smart guessing, but with user options to override
anything if needed.
Author: Matthijs S. Berends [aut, cre]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between cleaner versions 1.5.4 dated 2022-10-29 and 1.5.5 dated 2024-11-19
DESCRIPTION | 10 ++-- MD5 | 46 +++++++++---------- NEWS.md | 6 ++ R/clean.R | 90 ++++++++++++++++++++++----------------- R/currency.R | 2 R/data.R | 2 R/format_datetime.R | 2 R/format_names.R | 2 R/format_p_value.R | 2 R/freq.R | 2 R/helpers.R | 2 R/na_replace.R | 2 R/percentage.R | 2 R/rdate.R | 11 +++- R/regex_true_false.R | 2 R/zzz.R | 2 README.md | 6 +- man/clean.Rd | 79 ++++++++++++++++++---------------- tests/testthat.R | 2 tests/testthat/test-clean.R | 2 tests/testthat/test-currency.R | 2 tests/testthat/test-freq.R | 2 tests/testthat/test-percentage.R | 2 tests/testthat/test-rdate.R | 2 24 files changed, 156 insertions(+), 126 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.3-2 dated 2024-09-19 and 3.3-3 dated 2024-11-19
DESCRIPTION | 16 ++++++++-------- MD5 | 18 +++++++++--------- NEWS | 23 +++++++++++++++++++++++ R/kppm.R | 39 +++++++++++++++++++++++++-------------- R/ppmclass.R | 15 +++++++++------ R/sysdata.rda |binary inst/doc/packagesizes.txt | 2 +- inst/info/packagesizes.txt | 2 +- man/spatstat.model-internal.Rd | 2 +- tests/testsNtoO.R | 19 ++++++++++++++----- 10 files changed, 91 insertions(+), 45 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Land Surface Temperature Retrieval for Landsat 8
Description: Calculates Land Surface Temperature from Landsat band 10 and 11.
Revision of the Single-Channel Algorithm for Land Surface Temperature Retrieval From Landsat Thermal-Infrared Data. Jimenez-Munoz JC, Cristobal J, Sobrino JA, et al (2009). <doi: 10.1109/TGRS.2008.2007125>.
Land surface temperature retrieval from LANDSAT TM 5. Sobrino JA, Jiménez-Muñoz JC, Paolini L (2004). <doi:10.1016/j.rse.2004.02.003>.
Surface temperature estimation in Singhbhum Shear Zone of India using Landsat-7 ETM+ thermal infrared data. Srivastava PK, Majumdar TJ, Bhattacharya AK (2009). <doi: 10.1016/j.asr.2009.01.023>.
Mapping land surface emissivity from NDVI: Application to European, African, and South American areas. Valor E (1996). <doi:10.1016/0034-4257(96)00039-9>.
On the relationship between thermal emissivity and the normalized difference vegetation index for natural surfaces. Van de Griend AA, Owe M (1993). <doi:10.1080/01431169308904400>.
Land Surface Temperature Retrieva [...truncated...]
Author: Bappa Das [aut, cre] ,
Debasish Roy [aut, ctb],
Debashis Chakraborty [aut, ctb],
Pooja Rathore [aut, ctb]
Maintainer: Bappa Das <bappa.iari.1989@gmail.com>
Diff between LST versions 1.1.0 dated 2021-05-17 and 2.0.0 dated 2024-11-19
LST-1.1.0/LST/R/LST.R |only LST-2.0.0/LST/DESCRIPTION | 12 +++++------- LST-2.0.0/LST/MD5 | 34 +++++++++++++++++----------------- LST-2.0.0/LST/NAMESPACE | 3 ++- LST-2.0.0/LST/R/LST_terra.R |only LST-2.0.0/LST/man/BT.Rd | 16 ++++++++-------- LST-2.0.0/LST/man/E_Skokovic.Rd | 19 +++++++++++-------- LST-2.0.0/LST/man/E_Sobrino.Rd | 19 +++++++++++-------- LST-2.0.0/LST/man/E_Valor.Rd | 13 ++++++++----- LST-2.0.0/LST/man/E_VandeGriend.Rd | 13 ++++++++----- LST-2.0.0/LST/man/E_Yu.Rd | 19 +++++++++++-------- LST-2.0.0/LST/man/MWA.Rd | 19 +++++++++++-------- LST-2.0.0/LST/man/NDVI.Rd | 16 ++++++++-------- LST-2.0.0/LST/man/Pv.Rd | 13 ++++++++----- LST-2.0.0/LST/man/RTE.Rd | 25 ++++++++++++++----------- LST-2.0.0/LST/man/SCA.Rd | 36 +++++++++++++----------------------- LST-2.0.0/LST/man/SWA.Rd | 33 ++++++++++++++++++--------------- LST-2.0.0/LST/man/Ta.Rd | 5 ++++- LST-2.0.0/LST/man/tau.Rd | 2 +- 19 files changed, 158 insertions(+), 139 deletions(-)
Title: Statically Determine Function Dependencies Between Packages
Description: Statically determine and visualize the function dependencies
within and across packages. This may be useful for managing function
dependencies across a code base of multiple R packages.
Author: Ed Peyton [aut, cre]
Maintainer: Ed Peyton <edppeyton@gmail.com>
Diff between pkgdepR versions 1.1.0 dated 2024-11-18 and 1.1.1 dated 2024-11-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/envir_deps.R | 6 +++--- R/helper_functions.R | 4 ++++ R/pkgdepR-package.R | 6 +++--- man/deps.Rd | 6 +++--- man/pkgdepR-package.Rd | 6 +++--- 7 files changed, 25 insertions(+), 21 deletions(-)
Title: Reading and Writing Open Data Format Files
Description: The Open Data Format (ODF) is a new, non-proprietary, multilingual, metadata enriched, and zip-compressed data format with metadata structured in the Data Documentation Initiative (DDI) Codebook standard. This package allows reading and writing of data files in the Open Data Format (ODF) in R, and displaying metadata in different languages. For further information on the Open Data Format, see <https://opendataformat.github.io/>.
Author: Tom Hartl [aut, cre] ,
Claudia Saalbach [ctb]
Maintainer: Tom Hartl <thartl@diw.de>
Diff between opendataformat versions 1.3.0 dated 2024-10-07 and 2.0.0 dated 2024-11-19
DESCRIPTION | 9 + MD5 | 27 ++--- NAMESPACE | 5 - R/docu_odf.R | 17 +++ R/getmetadata_odf.R | 4 R/read_odf.R | 114 ++++++++++++++--------- R/setlanguage_odf.R | 7 + R/write_odf.R | 102 +++++++++++++++----- inst/doc/opendataformat.Rmd | 6 - inst/doc/opendataformat.html | 161 ++++++++++++++++----------------- man/write_odf.Rd | 6 - tests/testthat/test-read_odf.R | 122 ++++++------------------- tests/testthat/test-write_odf.R | 4 vignettes/opendataformat-tom-D15S.html |only vignettes/opendataformat.Rmd | 6 - 15 files changed, 316 insertions(+), 274 deletions(-)
More information about opendataformat at CRAN
Permanent link
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.76 dated 2024-09-15 and 2.0.77 dated 2024-11-19
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 7 +++++++ R/epi.2by2.R | 16 ++++++++-------- inst/doc/epiR_descriptive.html | 16 ++++++++-------- inst/doc/epiR_measures_of_association.Rmd | 4 +--- inst/doc/epiR_measures_of_association.html | 28 +++++++++++----------------- inst/doc/epiR_sample_size.html | 4 ++-- inst/doc/epiR_surveillance.html | 14 +++++++------- vignettes/epiR_measures_of_association.Rmd | 4 +--- 10 files changed, 58 insertions(+), 61 deletions(-)
Title: Determining the Number of Factors in Exploratory Factor Analysis
Description: Provides a collection of standard factor retention methods in Exploratory Factor Analysis (EFA), making it easier to determine the number of factors. Traditional methods such as the scree plot by Cattell (1966) <doi:10.1207/s15327906mbr0102_10>, Kaiser-Guttman Criterion (KGC) by Guttman (1954) <doi:10.1007/BF02289162> and Kaiser (1960) <doi:10.1177/001316446002000116>, and flexible Parallel Analysis (PA) by Horn (1965) <doi:10.1007/BF02289447> based on eigenvalues form PCA or EFA are readily available. This package also implements several newer methods, such as the Empirical Kaiser Criterion (EKC) by Braeken and van Assen (2017) <doi:10.1037/met0000074>, Comparison Data (CD) by Ruscio and Roche (2012) <doi:10.1037/a0025697>, and Hull method by Lorenzo-Seva et al. (2011) <doi:10.1080/00273171.2011.564527>, as well as some AI-based methods like Comparison Data Forest (CDF) by Goretzko and Ruscio (2024) <doi:10.3758/s13428-023-02122-4> and F [...truncated...]
Author: Haijiang Qin [aut, cre, cph],
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between EFAfactors versions 1.1.0 dated 2024-09-29 and 1.1.1 dated 2024-11-19
DESCRIPTION | 9 +++--- MD5 | 22 ++++++++-------- NEWS.md | 11 +++++--- R/DNN_predictor.R | 14 +++++----- R/FF.R | 12 ++++---- R/Hull.R | 36 +++++++++++++------------- man/DNN_predictor.Rd | 14 +++++----- man/FF.Rd | 12 ++++---- man/Hull.Rd | 16 +++++++++++ tests/building.R | 4 +- tests/testthat/demo_realdata.R | 16 +++++------ tests/testthat/demo_simulate.R | 56 ++++++++++++++++++++--------------------- 12 files changed, 123 insertions(+), 99 deletions(-)
Title: Statistical Methods for Composite Material Data
Description: An implementation of the statistical methods commonly
used for advanced composite materials in aerospace applications.
This package focuses on calculating basis values (lower tolerance
bounds) for material strength properties, as well as performing the
associated diagnostic tests. This package provides functions for
calculating basis values assuming several different distributions,
as well as providing functions for non-parametric methods of computing
basis values. Functions are also provided for testing the hypothesis
that there is no difference between strength and modulus data from an
alternate sample and that from a "qualification" or "baseline" sample.
For a discussion of these statistical methods and their use, see the
Composite Materials Handbook, Volume 1 (2012, ISBN: 978-0-7680-7811-4).
Additional details about this package are available in the paper by
Kloppenborg (2020, <doi:10.21105/joss.02265>).
Author: Stefan Kloppenborg [aut, cre] ,
Billy Cheng [ctb],
Ally Fraser [ctb],
Jeffrey Borlik [ctb],
Brice Langston [ctb],
Comtek Advanced Structures, Ltd. [fnd]
Maintainer: Stefan Kloppenborg <stefan@kloppenborg.ca>
Diff between cmstatr versions 0.9.3 dated 2024-03-14 and 0.10.0 dated 2024-11-19
DESCRIPTION | 17 MD5 | 77 + NAMESPACE | 8 NEWS.md | 16 R/basis.R | 357 +++++--- R/checks.R | 107 +- R/levene.R | 16 R/mnr.R | 7 R/norm.R | 20 R/plot-failure-modes.R |only R/plot-nested.R | 2 R/summary.R |only build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/adktest.html | 3 inst/doc/cmstatr_Graphing.R | 12 inst/doc/cmstatr_Graphing.Rmd | 20 inst/doc/cmstatr_Graphing.html | 388 ++++----- inst/doc/cmstatr_Tutorial.R | 17 inst/doc/cmstatr_Tutorial.Rmd | 48 - inst/doc/cmstatr_Tutorial.html | 395 +++++---- inst/doc/cmstatr_Validation.html | 60 - inst/doc/hk_ext.html | 11 man/basis.Rd | 19 man/cmstatr-package.Rd | 1 man/condition_summary.Rd |only man/geom_jitter_failure_mode.Rd |only man/levene_test.Rd | 16 man/maximum_normed_residual.Rd | 3 man/nested_data_plot.Rd | 2 man/separate_failure_modes.Rd |only tests/testthat/Rplots.pdf |only tests/testthat/_snaps/plot-failure-modes |only tests/testthat/test-basis-factor-hk.R |only tests/testthat/test-basis-factors-nonpara1.R |only tests/testthat/test-basis-factors-nonpara2.R |only tests/testthat/test-basis-factors.R |only tests/testthat/test-basis-pooled.R |only tests/testthat/test-basis.R | 1150 +-------------------------- tests/testthat/test-checks.R | 58 + tests/testthat/test-cv.R | 5 tests/testthat/test-mnr.R | 16 tests/testthat/test-plot-failure-modes.R |only vignettes/cmstatr_Graphing.Rmd | 20 vignettes/cmstatr_Tutorial.Rmd | 48 - 45 files changed, 1196 insertions(+), 1726 deletions(-)
Title: Simple Assertions for Beautiful and Customisable Error Messages
Description: Provides simple assertions with sensible defaults and customisable error messages.
It offers convenient assertion call wrappers and a general assert function that can handle any condition.
Default error messages are user friendly and easily customized with inline code evaluation and styling powered by the 'cli' package.
Author: Sam El-Kamand [aut, cre, cph]
Maintainer: Sam El-Kamand <sam.elkamand@gmail.com>
Diff between assertions versions 0.1.0 dated 2023-06-02 and 0.2.0 dated 2024-11-19
DESCRIPTION | 19 +- MD5 | 108 +++++++----- NAMESPACE | 16 + NEWS.md |only R/assert.R | 3 R/assert_compare.R | 115 +++++++++++++ R/assert_create.R | 10 - R/assert_files.R | 16 + R/assert_length.R |only R/assert_null.R |only R/assert_set.R | 59 ++++++ R/assert_type.R | 94 ++++++++++ R/is_comparisons.R | 34 +++ R/is_functions.R | 18 +- R/set_operations.R | 47 +++++ R/utils.R | 11 + README.md | 3 build/vignette.rds |binary inst/doc/create_custom_assertions.R | 10 - inst/doc/create_custom_assertions.Rmd | 2 inst/doc/create_custom_assertions.html | 100 +++++------ man/assert.Rd | 3 man/assert_all_less_than.Rd |only man/assert_all_less_than_or_equal_to.Rd |only man/assert_character_vector.Rd | 1 man/assert_character_vector_or_glue.Rd |only man/assert_connection.Rd |only man/assert_length.Rd |only man/assert_length_greater_than.Rd |only man/assert_length_greater_than_or_equal_to.Rd |only man/assert_length_less_than.Rd |only man/assert_length_less_than_or_equal_to.Rd |only man/assert_less_than.Rd |only man/assert_less_than_or_equal_to.Rd |only man/assert_non_null.Rd |only man/assert_null.Rd |only man/assert_one_of.Rd |only man/assert_scalar.Rd |only man/assert_set_equal.Rd |only man/assert_subset.Rd | 2 man/excludes_advanced.Rd | 1 man/has_extension.Rd | 4 man/includes_advanced.Rd | 1 man/is_character_vector_or_glue.Rd |only man/is_less_than.Rd |only man/is_less_than_or_equal_to.Rd |only tests/testthat/_snaps/assert_compare.md | 230 +++++++++++++++----------- tests/testthat/_snaps/assert_create.md | 45 +++-- tests/testthat/_snaps/assert_files.md | 135 +++++++++------ tests/testthat/_snaps/assert_functions.md | 20 +- tests/testthat/_snaps/assert_includes.md | 77 ++++++-- tests/testthat/_snaps/assert_less_than.md |only tests/testthat/_snaps/assert_null.md |only tests/testthat/_snaps/assert_numerical.md | 25 +- tests/testthat/_snaps/assert_set.md | 87 +++++++++ tests/testthat/_snaps/assert_type.md | 90 ++++++---- tests/testthat/_snaps/has.md | 25 +- tests/testthat/test-assert_create.R | 53 +++++ tests/testthat/test-assert_files.R | 151 ++++++++++++++++- tests/testthat/test-assert_functions.R | 76 ++++++++ tests/testthat/test-assert_includes.R | 8 tests/testthat/test-assert_length.R |only tests/testthat/test-assert_less_than.R |only tests/testthat/test-assert_null.R |only tests/testthat/test-assert_set.R | 50 +++++ tests/testthat/test-assert_type.R | 84 +++++++++ tests/testthat/test-is_comparisons.R |only tests/testthat/test-is_functions.R |only tests/testthat/test-set_operations.R |only vignettes/create_custom_assertions.Rmd | 2 70 files changed, 1460 insertions(+), 375 deletions(-)
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.3.2 dated 2024-10-28 and 1.3.3 dated 2024-11-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ tests/testthat/test-http.R | 2 +- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Advanced Forest Plot Using 'grid' Graphics
Description: Allows the creation of forest plots with advanced features, such as
multiple confidence intervals per row, customizable fonts for individual text
elements, and flexible confidence interval drawing. It also supports mixing
text with mathematical expressions. The package extends the application of
forest plots beyond traditional meta-analyses, offering a more general version
of the original 'rmeta' package’s forestplot() function. It relies heavily on
the 'grid' package for rendering the plots.
Author: Max Gordon [aut, cre],
Thomas Lumley [aut, ctb]
Maintainer: Max Gordon <max@gforge.se>
Diff between forestplot versions 3.1.5 dated 2024-10-11 and 3.1.6 dated 2024-11-19
DESCRIPTION | 6 +- MD5 | 11 ++-- NEWS.md | 4 + R/forestplot.grouped_df.R | 118 +++++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/forestplot.html | 4 - tests/testthat/Rplots.pdf |only 7 files changed, 80 insertions(+), 63 deletions(-)
Title: Functions to Find an Acceptable Python Binary
Description: Package designed to find an acceptable python binary.
Author: Trevor L. Davis [aut, cre] ,
Paul Gilbert [aut]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between findpython versions 1.0.8 dated 2023-03-14 and 1.0.9 dated 2024-11-19
DESCRIPTION | 17 ++--- LICENSE | 2 MD5 | 18 ++--- NEWS.md | 8 ++ R/find_python_cmd.r | 59 +++++++++--------- README.md | 127 +++++++++++++++++++++++++-------------- man/can_find_python_cmd.Rd | 24 +++---- man/find_python_cmd.Rd | 20 ++---- man/is_python_sufficient.Rd | 16 +++- tests/testthat/test-findpython.r | 45 +++---------- 10 files changed, 185 insertions(+), 151 deletions(-)
Title: Biodiversity Data from the GBIF Node Network
Description: The Global Biodiversity Information Facility
('GBIF', <https://www.gbif.org>) sources data from an international network
of data providers, known as 'nodes'. Several of these nodes - the "living
atlases" (<https://living-atlases.gbif.org>) - maintain their own web
services using software originally developed by the Atlas of Living
Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community
to directly access data and resources hosted by 'GBIF' and its partner nodes.
Author: Martin Westgate [aut, cre],
Dax Kellie [aut],
Matilda Stevenson [aut],
Peggy Newman [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between galah versions 2.0.2 dated 2024-04-12 and 2.1.0 dated 2024-11-18
galah-2.0.2/galah/R/deprecated_functions.R |only galah-2.0.2/galah/man/arrange.Rd |only galah-2.0.2/galah/man/atlas_counts.Rd |only galah-2.0.2/galah/man/atlas_media.Rd |only galah-2.0.2/galah/man/atlas_occurrences.Rd |only galah-2.0.2/galah/man/atlas_species.Rd |only galah-2.0.2/galah/man/atlas_taxonomy.Rd |only galah-2.0.2/galah/man/collapse_galah.Rd |only galah-2.0.2/galah/man/collect_galah.Rd |only galah-2.0.2/galah/man/compute_galah.Rd |only galah-2.0.2/galah/man/deprecated-functions.Rd |only galah-2.0.2/galah/man/galah_apply_profile.Rd |only galah-2.0.2/galah/man/galah_filter.Rd |only galah-2.0.2/galah/man/galah_geolocate.Rd |only galah-2.0.2/galah/man/galah_group_by.Rd |only galah-2.0.2/galah/man/galah_identify.Rd |only galah-2.0.2/galah/man/galah_select.Rd |only galah-2.0.2/galah/man/slice_head.Rd |only galah-2.0.2/galah/tests/testthat/test-galah_down_to.R |only galah-2.0.2/galah/tests/testthat/test-international-Estonia.R |only galah-2.0.2/galah/tests/testthat/testdata/SECRETS.txt |only galah-2.0.2/galah/vignettes/atlases_plot.png |only galah-2.1.0/galah/DESCRIPTION | 18 galah-2.1.0/galah/MD5 | 244 - galah-2.1.0/galah/NAMESPACE | 4 galah-2.1.0/galah/NEWS.md | 19 galah-2.1.0/galah/R/arrange.R | 30 galah-2.1.0/galah/R/atlas_counts.R | 73 galah-2.1.0/galah/R/atlas_distributions.R | 3 galah-2.1.0/galah/R/atlas_media.R | 192 - galah-2.1.0/galah/R/atlas_occurrences.R | 86 galah-2.1.0/galah/R/atlas_species.R | 62 galah-2.1.0/galah/R/atlas_taxonomy.R | 53 galah-2.1.0/galah/R/build.R | 10 galah-2.1.0/galah/R/build_query_set.R | 2 galah-2.1.0/galah/R/check.R | 45 galah-2.1.0/galah/R/collapse.R | 6 galah-2.1.0/galah/R/collapse_media.R | 30 galah-2.1.0/galah/R/collapse_occurrences.R | 18 galah-2.1.0/galah/R/collapse_occurrences_count.R | 24 galah-2.1.0/galah/R/collapse_species.R | 1 galah-2.1.0/galah/R/collapse_species_count.R | 19 galah-2.1.0/galah/R/collect.R | 10 galah-2.1.0/galah/R/collect_media.R | 27 galah-2.1.0/galah/R/collect_occurrences.R | 5 galah-2.1.0/galah/R/collect_taxa.R | 18 galah-2.1.0/galah/R/compute.R | 8 galah-2.1.0/galah/R/compute_occurrences.R | 8 galah-2.1.0/galah/R/count-data_request.R |only galah-2.1.0/galah/R/galah-package.R | 67 galah-2.1.0/galah/R/galah_apply_profile.R | 42 galah-2.1.0/galah/R/galah_bbox.R | 4 galah-2.1.0/galah/R/galah_call.R | 156 - galah-2.1.0/galah/R/galah_config.R | 78 galah-2.1.0/galah/R/galah_filter.R | 204 - galah-2.1.0/galah/R/galah_geolocate.R | 87 galah-2.1.0/galah/R/galah_group_by.R | 34 galah-2.1.0/galah/R/galah_identify.R | 76 galah-2.1.0/galah/R/galah_polygon.R | 11 galah-2.1.0/galah/R/galah_radius.R | 4 galah-2.1.0/galah/R/galah_select.R | 197 - galah-2.1.0/galah/R/parse_metadata_unnest.R | 8 galah-2.1.0/galah/R/print.R | 5 galah-2.1.0/galah/R/search_all.R | 24 galah-2.1.0/galah/R/show_all.R | 3 galah-2.1.0/galah/R/show_values.R | 3 galah-2.1.0/galah/R/slice_head.R | 28 galah-2.1.0/galah/R/sysdata.rda |binary galah-2.1.0/galah/R/taxonomic-searches.R |only galah-2.1.0/galah/R/tidyverse.R | 2 galah-2.1.0/galah/R/utilities_internal.R | 155 - galah-2.1.0/galah/build/vignette.rds |binary galah-2.1.0/galah/inst/doc/choosing_an_atlas.Rmd | 10 galah-2.1.0/galah/inst/doc/choosing_an_atlas.html | 577 --- galah-2.1.0/galah/inst/doc/download_data.Rmd | 146 galah-2.1.0/galah/inst/doc/download_data.html | 124 galah-2.1.0/galah/inst/doc/look_up_information.Rmd | 92 galah-2.1.0/galah/inst/doc/look_up_information.html | 76 galah-2.1.0/galah/inst/doc/narrow_your_results.Rmd | 277 - galah-2.1.0/galah/inst/doc/narrow_your_results.html | 250 - galah-2.1.0/galah/inst/doc/object_oriented_programming.Rmd | 87 galah-2.1.0/galah/inst/doc/object_oriented_programming.html | 74 galah-2.1.0/galah/inst/doc/quick_start_guide.Rmd | 90 galah-2.1.0/galah/inst/doc/quick_start_guide.html | 70 galah-2.1.0/galah/inst/doc/spatial_filtering.Rmd | 539 +-- galah-2.1.0/galah/inst/doc/spatial_filtering.html | 623 ++-- galah-2.1.0/galah/inst/doc/taxonomic_filtering.Rmd | 1446 +++++---- galah-2.1.0/galah/inst/doc/taxonomic_filtering.html | 1511 +++++----- galah-2.1.0/galah/inst/doc/temporal_filtering.Rmd | 57 galah-2.1.0/galah/inst/doc/temporal_filtering.html | 52 galah-2.1.0/galah/man/apply_profile.Rd |only galah-2.1.0/galah/man/arrange.data_request.Rd |only galah-2.1.0/galah/man/atlas_.Rd |only galah-2.1.0/galah/man/collapse.data_request.Rd |only galah-2.1.0/galah/man/collect.data_request.Rd |only galah-2.1.0/galah/man/collect_media.Rd | 24 galah-2.1.0/galah/man/compute.data_request.Rd |only galah-2.1.0/galah/man/count.data_request.Rd |only galah-2.1.0/galah/man/figures/atlases_plot.png |binary galah-2.1.0/galah/man/filter.data_request.Rd |only galah-2.1.0/galah/man/galah.Rd | 75 galah-2.1.0/galah/man/galah_call.Rd | 103 galah-2.1.0/galah/man/geolocate.Rd |only galah-2.1.0/galah/man/group_by.data_request.Rd |only galah-2.1.0/galah/man/identify.data_request.Rd |only galah-2.1.0/galah/man/print_galah_objects.Rd | 2 galah-2.1.0/galah/man/search_all.Rd | 21 galah-2.1.0/galah/man/select.data_request.Rd |only galah-2.1.0/galah/man/show_all.Rd | 3 galah-2.1.0/galah/man/show_values.Rd | 3 galah-2.1.0/galah/man/slice_head.data_request.Rd |only galah-2.1.0/galah/man/taxonomic_searches.Rd |only galah-2.1.0/galah/man/tidyverse_functions.Rd | 2 galah-2.1.0/galah/tests/testthat/test-atlas_counts.R | 11 galah-2.1.0/galah/tests/testthat/test-atlas_media.R | 29 galah-2.1.0/galah/tests/testthat/test-atlas_occurrences.R | 5 galah-2.1.0/galah/tests/testthat/test-galah_apply_profile.R | 2 galah-2.1.0/galah/tests/testthat/test-galah_config.R | 10 galah-2.1.0/galah/tests/testthat/test-galah_filter.R | 26 galah-2.1.0/galah/tests/testthat/test-galah_select.R | 12 galah-2.1.0/galah/tests/testthat/test-international-Austria.R | 92 galah-2.1.0/galah/tests/testthat/test-international-Brazil.R | 53 galah-2.1.0/galah/tests/testthat/test-international-France.R | 37 galah-2.1.0/galah/tests/testthat/test-international-GBIF.R | 10 galah-2.1.0/galah/tests/testthat/test-international-Guatemala.R | 54 galah-2.1.0/galah/tests/testthat/test-international-Portugal.R | 4 galah-2.1.0/galah/tests/testthat/test-international-Spain.R | 80 galah-2.1.0/galah/tests/testthat/test-international-Sweden.R | 118 galah-2.1.0/galah/tests/testthat/test-international-UK.R | 37 galah-2.1.0/galah/tests/testthat/test-search_taxa.R | 11 galah-2.1.0/galah/tests/testthat/test-show_values.R | 20 galah-2.1.0/galah/vignettes/atlas_stats.csv | 21 galah-2.1.0/galah/vignettes/atlases_plot.R | 21 galah-2.1.0/galah/vignettes/choosing_an_atlas.Rmd | 10 galah-2.1.0/galah/vignettes/download_data.Rmd | 146 galah-2.1.0/galah/vignettes/look_up_information.Rmd | 92 galah-2.1.0/galah/vignettes/narrow_your_results.Rmd | 277 - galah-2.1.0/galah/vignettes/object_oriented_programming.Rmd | 87 galah-2.1.0/galah/vignettes/quick_start_guide.Rmd | 90 galah-2.1.0/galah/vignettes/spatial_filtering.Rmd | 539 +-- galah-2.1.0/galah/vignettes/taxonomic_filtering.Rmd | 1446 +++++---- galah-2.1.0/galah/vignettes/temporal_filtering.Rmd | 57 142 files changed, 6068 insertions(+), 5866 deletions(-)
Title: Spatiotemporal Clustering of Satellite Hot Spot Data
Description: An algorithm to cluster satellite hot spot data spatially and temporally.
Author: Weihao Li [aut, cre] ,
Di Cook [ctb] ,
Emily Dodwell [ctb]
Maintainer: Weihao Li <llreczx@gmail.com>
Diff between spotoroo versions 0.1.4 dated 2023-08-21 and 0.1.5 dated 2024-11-18
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/plot_fire_mov.R | 4 ++-- inst/doc/Clustering-hot-spots.R | 2 +- inst/doc/Clustering-hot-spots.html | 19 ++++++++++--------- man/figures/README-unnamed-chunk-8-1.png |binary 7 files changed, 29 insertions(+), 24 deletions(-)
Title: Wrapper Functions Around 'Sleeper' (Fantasy Sports) API
Description: For those wishing to interact with the 'Sleeper' (Fantasy Sports) API (<https://docs.sleeper.com/>) without looking too much into its documentation (found at <https://docs.sleeper.com/>), this package offers wrapper functions around the available API calls to make it easier.
Author: Nick Bultman [aut, cre, cph]
Maintainer: Nick Bultman <njbultman74@gmail.com>
Diff between sleeperapi versions 1.1.1 dated 2024-06-01 and 1.1.2 dated 2024-11-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/get_main_data.R | 35 +++++++++++++++++++++-------------- 3 files changed, 26 insertions(+), 19 deletions(-)
Title: A Tool for 'Covariate'-Sensitive Longitudinal Analysis on
'omics' Data
Description: This tool takes longitudinal dataset as input and analyzes if there is significant
change of the features over time (a proxy for treatments), while detects and controls
for 'covariates' simultaneously. 'LongDat' is able to take in several data types as input,
including count, proportion, binary, ordinal and continuous data. The output table contains
p values, effect sizes and 'covariates' of each feature, making the downstream analysis easy.
Author: Chia-Yu Chen [aut, cre] ,
Sofia Forslund [ctb]
Maintainer: Chia-Yu Chen <Chia-Yu.Chen@mdc-berlin.de>
Diff between LongDat versions 1.1.2 dated 2023-07-17 and 1.1.3 dated 2024-11-18
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 3 R/make_master_table.R | 7 README.md | 3 inst/doc/LongDat_cont_tutorial.html | 285 +++++++++++++++++----------------- inst/doc/LongDat_disc_tutorial.html | 297 +++++++++++++++++------------------- 7 files changed, 307 insertions(+), 306 deletions(-)
Title: Bayesian Change Point Detection for High-Dimensional Data
Description: Functions implementing change point detection methods using the maximum pairwise Bayes factor approach.
Additionally, the package includes tools for generating simulated datasets for comparing and evaluating change point detection techniques.
Author: JaeHoon Kim [aut, cre],
KyoungJae Lee [aut, ths]
Maintainer: JaeHoon Kim <jhkimstat@gmail.com>
Diff between hdbcp versions 0.1.0 dated 2024-11-05 and 1.0.0 dated 2024-11-18
DESCRIPTION | 6 MD5 | 24 +- R/RcppExports.R | 16 + R/aux_utils.R | 26 +++ R/combined_mxPBF.R | 32 +-- R/cov_mxPBF.R | 39 ++-- R/majority_rule.R | 88 ++++------ README.md | 23 +- man/majority_rule_mxPBF.Rd | 10 - man/mxPBF_combined.Rd | 21 +- man/mxPBF_cov.Rd | 27 +-- src/RcppExports.cpp | 65 +++++-- src/cpp_cov_mxPBF.cpp | 377 +++++++++++++++++++++++---------------------- 13 files changed, 390 insertions(+), 364 deletions(-)
Title: Transform Microplate Data into Tibbles
Description: The goal of 'tidyplate' is to help researchers convert
different types of microplates into tibbles which can be used in data
analysis. It accepts xlsx and csv files formatted in a specific way as
input. It supports all types of standard microplate formats such as
6-well, 12-well, 24-well, 48-well, 96-well, 384-well, and, 1536-well
plates.
Author: Shubham Dutta [aut, cre, cph]
Maintainer: Shubham Dutta <shubhamdutta26@gmail.com>
Diff between tidyplate versions 2.0.1 dated 2024-10-08 and 2.1.0 dated 2024-11-18
tidyplate-2.0.1/tidyplate/man/figures/tidyplate_hex_trans.png |only tidyplate-2.0.1/tidyplate/tests/testthat/test_data/12/build_plate |only tidyplate-2.0.1/tidyplate/tests/testthat/test_data/1536/build_plate |only tidyplate-2.0.1/tidyplate/tests/testthat/test_data/24/build_plate |only tidyplate-2.0.1/tidyplate/tests/testthat/test_data/384/build_plate |only tidyplate-2.0.1/tidyplate/tests/testthat/test_data/48/build_plate |only tidyplate-2.0.1/tidyplate/tests/testthat/test_data/6/build_plate |only tidyplate-2.0.1/tidyplate/tests/testthat/test_data/96/build_plate |only tidyplate-2.1.0/tidyplate/DESCRIPTION | 36 + tidyplate-2.1.0/tidyplate/MD5 | 105 ++--- tidyplate-2.1.0/tidyplate/NAMESPACE | 1 tidyplate-2.1.0/tidyplate/NEWS.md | 52 ++ tidyplate-2.1.0/tidyplate/R/build_plate.R | 103 +++-- tidyplate-2.1.0/tidyplate/R/check_plate.R | 20 - tidyplate-2.1.0/tidyplate/R/generate_plate.R |only tidyplate-2.1.0/tidyplate/R/tidy_plate.R | 40 +- tidyplate-2.1.0/tidyplate/R/tidyplate-package.R |only tidyplate-2.1.0/tidyplate/R/utils.R | 113 ++++-- tidyplate-2.1.0/tidyplate/R/view_plate_names.R | 112 +++++- tidyplate-2.1.0/tidyplate/README.md | 118 ++---- tidyplate-2.1.0/tidyplate/build/vignette.rds |binary tidyplate-2.1.0/tidyplate/inst/WORDLIST |only tidyplate-2.1.0/tidyplate/inst/doc/advanced.R |only tidyplate-2.1.0/tidyplate/inst/doc/advanced.Rmd |only tidyplate-2.1.0/tidyplate/inst/doc/advanced.html |only tidyplate-2.1.0/tidyplate/inst/doc/getting_started.R | 64 --- tidyplate-2.1.0/tidyplate/inst/doc/getting_started.Rmd | 125 +----- tidyplate-2.1.0/tidyplate/inst/doc/getting_started.html | 183 ++-------- tidyplate-2.1.0/tidyplate/inst/extdata/tidy_12_well.csv |only tidyplate-2.1.0/tidyplate/man/build_plate.Rd | 26 - tidyplate-2.1.0/tidyplate/man/check_plate.Rd | 8 tidyplate-2.1.0/tidyplate/man/figures/README_tidy_plate.png |binary tidyplate-2.1.0/tidyplate/man/figures/logo.png |binary tidyplate-2.1.0/tidyplate/man/figures/logo_file.png |only tidyplate-2.1.0/tidyplate/man/generate_plate.Rd |only tidyplate-2.1.0/tidyplate/man/tidy_plate.Rd | 7 tidyplate-2.1.0/tidyplate/man/tidyplate-package.Rd | 16 tidyplate-2.1.0/tidyplate/man/view_plate_names.Rd | 4 tidyplate-2.1.0/tidyplate/tests/spelling.R |only tidyplate-2.1.0/tidyplate/tests/testthat/test-build_plate.R | 138 ++++--- tidyplate-2.1.0/tidyplate/tests/testthat/test-check_plate.R | 100 ++--- tidyplate-2.1.0/tidyplate/tests/testthat/test-generate_plate.R |only tidyplate-2.1.0/tidyplate/tests/testthat/test-tidy_plate.R | 86 ++-- tidyplate-2.1.0/tidyplate/tests/testthat/test-utils.R | 6 tidyplate-2.1.0/tidyplate/tests/testthat/test-view_plate_names.R | 77 +++- tidyplate-2.1.0/tidyplate/tests/testthat/test_data/48/noName.csv | 2 tidyplate-2.1.0/tidyplate/tests/testthat/test_data/48/noName.xlsx |binary tidyplate-2.1.0/tidyplate/tests/testthat/test_data/6/noName.xlsx |binary tidyplate-2.1.0/tidyplate/tests/testthat/test_data/extraRow.csv |only tidyplate-2.1.0/tidyplate/tests/testthat/test_data/extraRow.xlsx |only tidyplate-2.1.0/tidyplate/tests/testthat/test_data/noNameDup.csv |only tidyplate-2.1.0/tidyplate/tests/testthat/test_data/noNameDup.xlsx |only tidyplate-2.1.0/tidyplate/tests/testthat/test_data/oneFullOnePartEmpty.csv | 26 + tidyplate-2.1.0/tidyplate/vignettes/advanced.Rmd |only tidyplate-2.1.0/tidyplate/vignettes/getting_started.Rmd | 125 +----- 55 files changed, 865 insertions(+), 828 deletions(-)
Title: Cs-137 Conversion Model
Description: A straightforward model to estimate soil migration rates across various soil contexts.
Based on the compartmental, vertically-resolved, physically-based mass balance model of Soto and Navas (2004)
<doi:10.1016/j.jaridenv.2004.02.003> and Soto and Navas (2008) <doi:10.1016/j.radmeas.2008.02.024>.
'RadEro' provides a user-friendly interface in R, utilizing input data such as 137Cs inventories and parameters directly derived
from soil samples (e.g., fine fraction density, effective volume) to accurately capture the 137Cs distribution within the soil profile.
The model simulates annual 137Cs fallout, radioactive decay, and vertical diffusion, with the diffusion coefficient calculated
from 137Cs reference inventory profiles. Additionally, it allows users to input custom parameters as calibration coefficients.
The RadEro user manual and protocol, including detailed instructions on how to format input data and configuration files, can be found at the following link: <https://gi [...truncated...]
Author: Arturo Catala [aut, cre],
Borja Latorre [aut, ctb, cph],
Leticia Gaspar [aut],
Ana Navas [aut],
Dave Gamble [ctb]
Maintainer: Arturo Catala <radero@eead.csic.es>
Diff between RadEro versions 1.0.4 dated 2024-11-11 and 1.0.5 dated 2024-11-18
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- R/RcppExports.R | 4 ---- src/RcppExports.cpp | 11 ----------- src/model.c | 9 --------- src/rcpp_hello_world.cpp | 6 +++--- 6 files changed, 16 insertions(+), 40 deletions(-)
Title: Distribution-Free Goodness-of-Fit Testing for Regression
Description: Implements distribution-free goodness-of-fit regression testing for
the mean structure of parametric models introduced in Khmaladze (2021)
<doi:10.1007/s10463-021-00786-3>.
Author: Jesse Miller [aut, cre]
Maintainer: Jesse Miller <mill9116@umn.edu>
Diff between distfreereg versions 1.0 dated 2024-11-11 and 1.0.1 dated 2024-11-18
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Title: The COR for Optimal Subset Selection in Distributed Estimation
Description: An algorithm of optimal subset selection, related to Covariance matrices,
Observation matrices and Response vectors (COR) to select the optimal subsets
in distributed estimation. The philosophy of the package is described in Guo G. (2020) <doi:10.1080/02331888.2020.1823979>.
Author: Guangbao Guo [aut, cre] ,
Haoyue Song [aut],
Lixing Zhu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between COR versions 0.0.1 dated 2021-12-06 and 0.1.0 dated 2024-11-18
DESCRIPTION | 10 ++++---- MD5 | 32 ++++++++++++++++--------- NAMESPACE | 22 +++++++++++------ R/COR.R | 32 +++++++++++++------------ R/LICbeta.R |only R/LICnew.R |only R/MSEbeta.R |only R/MSEcom.R | 41 ++++++++++++++++++--------------- R/MSEver.R | 41 +++++++++++++++++---------------- R/beta_AD.R | 18 +++++++------- R/beta_LW.R |only R/beta_cor.R | 19 +++++++-------- man/COR.Rd | 67 ++++++++++++++++++++++++++++-------------------------- man/LICbeta.Rd |only man/LICnew.Rd |only man/MSEbeta.Rd |only man/MSEcom.Rd | 69 ++++++++++++++++++++++++++++++-------------------------- man/MSEver.Rd | 68 +++++++++++++++++++++++++++++-------------------------- man/beta_AD.Rd | 66 +++++++++++++++++++++++++++-------------------------- man/beta_LW.Rd |only man/beta_cor.Rd | 65 ++++++++++++++++++++++++++-------------------------- 21 files changed, 294 insertions(+), 256 deletions(-)
Title: Visualization of Clonal Expansion for Single Cell Immune
Profiles
Description: Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.
Author: Qile Yang [cre, aut, cph]
Maintainer: Qile Yang <qile.yang@berkeley.edu>
Diff between APackOfTheClones versions 1.2.1 dated 2024-10-10 and 1.2.4 dated 2024-11-18
DESCRIPTION | 12 +++++++----- MD5 | 4 ++-- inst/CITATION | 19 ++++++++++--------- 3 files changed, 19 insertions(+), 16 deletions(-)
More information about APackOfTheClones at CRAN
Permanent link
Title: Discontinuous Regression and Image Processing
Description: A collection of functions that perform jump regression
and image analysis such as denoising, deblurring and
jump detection. The implemented methods are based on
the following research: Qiu, P. (1998) <doi:10.1214/aos/1024691468>,
Qiu, P. and Yandell, B. (1997) <doi: 10.1080/10618600.1997.10474746>,
Qiu, P. (2009) <doi: 10.1007/s10463-007-0166-9>,
Kang, Y. and Qiu, P. (2014) <doi: 10.1080/00401706.2013.844732>,
Qiu, P. and Kang, Y. (2015) <doi: 10.5705/ss.2014.054>,
Kang, Y., Mukherjee, P.S. and Qiu, P. (2018) <doi: 10.1080/00401706.2017.1415975>,
Kang, Y. (2020) <doi: 10.1080/10618600.2019.1665536>.
Author: Yicheng Kang [aut, cre],
Peihua Qiu [aut, ctb]
Maintainer: Yicheng Kang <kangyicheng0527@gmail.com>
Diff between DRIP versions 2.0 dated 2024-05-12 and 2.2 dated 2024-11-18
DRIP-2.0/DRIP/R/JPLLK_surface.r |only DRIP-2.0/DRIP/R/dKQ.r |only DRIP-2.0/DRIP/R/diffLC2K.r |only DRIP-2.0/DRIP/R/diffLCK.r |only DRIP-2.0/DRIP/R/diffLL2K.r |only DRIP-2.0/DRIP/R/diffLLK.r |only DRIP-2.0/DRIP/R/modify1.r |only DRIP-2.0/DRIP/R/modify2.r |only DRIP-2.0/DRIP/R/roofDiff.r |only DRIP-2.0/DRIP/R/roofEdge.r |only DRIP-2.0/DRIP/R/roofEdgeParSel.r |only DRIP-2.0/DRIP/R/stepEdgeLC2K.r |only DRIP-2.0/DRIP/R/stepEdgeLCK.r |only DRIP-2.0/DRIP/R/stepEdgeLL2K.r |only DRIP-2.0/DRIP/R/stepEdgeLLK.r |only DRIP-2.0/DRIP/R/stepEdgeParSelLC2K.r |only DRIP-2.0/DRIP/R/stepEdgeParSelLCK.r |only DRIP-2.0/DRIP/R/stepEdgeParSelLL2K.r |only DRIP-2.0/DRIP/R/stepEdgeParSelLLK.r |only DRIP-2.0/DRIP/R/surfaceCluster.r |only DRIP-2.0/DRIP/R/surfaceCluster_bandwidth.r |only DRIP-2.0/DRIP/R/threeStage.r |only DRIP-2.0/DRIP/R/threeStageParSel.r |only DRIP-2.0/DRIP/src/cluster_deblur.f90 |only DRIP-2.0/DRIP/src/cluster_denoise.f90 |only DRIP-2.2/DRIP/DESCRIPTION | 17 +- DRIP-2.2/DRIP/MD5 | 163 ++++++++++++++++---------- DRIP-2.2/DRIP/NAMESPACE | 17 ++ DRIP-2.2/DRIP/R/JPLLK_surface.R |only DRIP-2.2/DRIP/R/cv.jpex.R | 64 +++++++++- DRIP-2.2/DRIP/R/dKQ.R |only DRIP-2.2/DRIP/R/diffLC2K.R |only DRIP-2.2/DRIP/R/diffLCK.R |only DRIP-2.2/DRIP/R/diffLL2K.R |only DRIP-2.2/DRIP/R/diffLLK.R |only DRIP-2.2/DRIP/R/jpex.R | 12 - DRIP-2.2/DRIP/R/modify1.R |only DRIP-2.2/DRIP/R/modify2.R |only DRIP-2.2/DRIP/R/roofDiff.R |only DRIP-2.2/DRIP/R/roofEdge.R |only DRIP-2.2/DRIP/R/roofEdgeParSel.R |only DRIP-2.2/DRIP/R/stepEdgeLC2K.R |only DRIP-2.2/DRIP/R/stepEdgeLCK.R |only DRIP-2.2/DRIP/R/stepEdgeLL2K.R |only DRIP-2.2/DRIP/R/stepEdgeLLK.R |only DRIP-2.2/DRIP/R/stepEdgeParSel.R | 56 +++++++- DRIP-2.2/DRIP/R/stepEdgeParSelLC2K.R |only DRIP-2.2/DRIP/R/stepEdgeParSelLCK.R |only DRIP-2.2/DRIP/R/stepEdgeParSelLL2K.R |only DRIP-2.2/DRIP/R/stepEdgeParSelLLK.R |only DRIP-2.2/DRIP/R/surfaceCluster.R |only DRIP-2.2/DRIP/R/surfaceCluster_bandwidth.R |only DRIP-2.2/DRIP/R/threeStage.R |only DRIP-2.2/DRIP/R/threeStageParSel.R |only DRIP-2.2/DRIP/README.md |only DRIP-2.2/DRIP/build/partial.rdb |binary DRIP-2.2/DRIP/build/vignette.rds |only DRIP-2.2/DRIP/data/brain.RData |binary DRIP-2.2/DRIP/data/circles.RData |binary DRIP-2.2/DRIP/data/kid.RData |binary DRIP-2.2/DRIP/data/sar.RData |binary DRIP-2.2/DRIP/inst |only DRIP-2.2/DRIP/man/JPLLK_surface.Rd | 10 - DRIP-2.2/DRIP/man/brain.Rd | 1 DRIP-2.2/DRIP/man/circles.Rd | 1 DRIP-2.2/DRIP/man/cv.jpex.Rd | 20 +-- DRIP-2.2/DRIP/man/dKQ.Rd | 1 DRIP-2.2/DRIP/man/jpex.Rd | 2 DRIP-2.2/DRIP/man/kid.Rd | 1 DRIP-2.2/DRIP/man/lena.Rd | 1 DRIP-2.2/DRIP/man/modify1.Rd | 1 DRIP-2.2/DRIP/man/modify2.Rd | 1 DRIP-2.2/DRIP/man/peppers.Rd | 1 DRIP-2.2/DRIP/man/plot.3Stage.Rd |only DRIP-2.2/DRIP/man/plot.Cluster.Rd |only DRIP-2.2/DRIP/man/plot.JPEX.Rd |only DRIP-2.2/DRIP/man/plot.JPLLK.Rd |only DRIP-2.2/DRIP/man/print.3Stage.Rd |only DRIP-2.2/DRIP/man/print.Cluster.Rd |only DRIP-2.2/DRIP/man/print.Edge.Rd |only DRIP-2.2/DRIP/man/print.JPEX.Rd |only DRIP-2.2/DRIP/man/print.JPLLK.Rd |only DRIP-2.2/DRIP/man/roofDiff.Rd | 4 DRIP-2.2/DRIP/man/roofEdge.Rd | 2 DRIP-2.2/DRIP/man/roofEdgeParSel.Rd | 1 DRIP-2.2/DRIP/man/sar.Rd | 1 DRIP-2.2/DRIP/man/stepDiff.Rd | 4 DRIP-2.2/DRIP/man/stepEdge.Rd | 1 DRIP-2.2/DRIP/man/stepEdgeParSel.Rd | 1 DRIP-2.2/DRIP/man/stopsign.Rd | 1 DRIP-2.2/DRIP/man/summary.3Stage.Rd |only DRIP-2.2/DRIP/man/summary.Cluster.Rd |only DRIP-2.2/DRIP/man/summary.Edge.Rd |only DRIP-2.2/DRIP/man/summary.JPEX.Rd |only DRIP-2.2/DRIP/man/summary.JPLLK.Rd |only DRIP-2.2/DRIP/man/surfaceCluster.Rd | 8 - DRIP-2.2/DRIP/man/surfaceCluster_bandwidth.Rd | 5 DRIP-2.2/DRIP/man/threeStage.Rd | 1 DRIP-2.2/DRIP/man/threeStageParSel.Rd | 3 DRIP-2.2/DRIP/tests |only DRIP-2.2/DRIP/vignettes |only 101 files changed, 288 insertions(+), 113 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>),
univariate and multivariate (<doi:10.1186/s12711-022-00730-w>, <doi:10.1093/genetics/iyae179>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.11 dated 2024-10-30 and 2.2.12 dated 2024-11-18
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- R/mix.R | 2 +- man/bWGR.Rd | 7 ++++--- man/mvr.Rd | 4 +++- 5 files changed, 18 insertions(+), 14 deletions(-)
Title: Preparer of Main Scientific References for Automatic Insertion
in Academic Papers
Description: Generates a file, containing the main scientific references, prepared to be automatically inserted into an academic paper.
The articles present in the list are chosen from the main references generated, by function principal_lister(), of the package 'bibliorefer'.
The generated file contains the list of metadata of the principal references in 'BibTex' format.
Massimo Aria, Corrado Cuccurullo. (2017) <doi:10.1016/j.joi.2017.08.007>.
Caibo Zhou, Wenyan Song. (2021) <doi:10.1016/j.jclepro.2021.126943>.
Hamid Derviş. (2019) <doi:10.5530/jscires.8.3.32>.
Author: Marcio Eustaquio [cre],
Marcio Eustaquio [aut]
Maintainer: Marcio Eustaquio <marcioeustaquio@id.uff.br>
Diff between gerefer versions 0.1.0 dated 2024-10-10 and 0.1.1 dated 2024-11-18
DESCRIPTION | 6 - MD5 | 4 R/article_bib.R | 262 ++++++++++++++++++++++++++++++++++++++++++++++++++++---- 3 files changed, 252 insertions(+), 20 deletions(-)
Title: Clinical Trial Simulation
Description: Provides some basic routines for simulating a
clinical trial. The primary intent is to provide some tools to
generate trial simulations for trials with time to event outcomes.
Piecewise exponential failure rates and piecewise constant
enrollment rates are the underlying mechanism used to simulate
a broad range of scenarios such as those presented in
Lin et al. (2020) <doi:10.1080/19466315.2019.1697738>.
However, the basic generation of data is done using pipes to allow
maximum flexibility for users to meet different needs.
Author: Keaven Anderson [aut],
Yujie Zhao [ctb, cre],
John Blischak [ctb],
Nan Xiao [ctb],
Yilong Zhang [aut],
Jianxiao Yang [ctb],
Lili Ling [ctb],
Xintong Li [ctb],
Ruixue Wang [ctb],
Yi Cui [ctb],
Ping Yang [ctb],
Yalin Zhu [ctb],
Heng Zhou [ctb],
Amin Sh [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between simtrial versions 0.4.1 dated 2024-05-03 and 0.4.2 dated 2024-11-18
simtrial-0.4.1/simtrial/tests/testthat/helper-mb_weight.R |only simtrial-0.4.1/simtrial/tests/testthat/helper-sim_gs_n.R |only simtrial-0.4.1/simtrial/tests/testthat/helper-simfix.R |only simtrial-0.4.1/simtrial/vignettes/schema.png |only simtrial-0.4.1/simtrial/vignettes/workflow.png |only simtrial-0.4.2/simtrial/DESCRIPTION | 14 simtrial-0.4.2/simtrial/MD5 | 145 - simtrial-0.4.2/simtrial/NAMESPACE | 11 simtrial-0.4.2/simtrial/NEWS.md | 31 simtrial-0.4.2/simtrial/R/as_gt.R |only simtrial-0.4.2/simtrial/R/counting_process.R | 51 simtrial-0.4.2/simtrial/R/cut_data_by_date.R | 4 simtrial-0.4.2/simtrial/R/cut_data_by_event.R | 3 simtrial-0.4.2/simtrial/R/get_analysis_date.R | 2 simtrial-0.4.2/simtrial/R/get_cut_date_by_event.R | 2 simtrial-0.4.2/simtrial/R/global.R | 38 simtrial-0.4.2/simtrial/R/maxcombo.R | 8 simtrial-0.4.2/simtrial/R/mb_weight.R | 2 simtrial-0.4.2/simtrial/R/milestone.R | 13 simtrial-0.4.2/simtrial/R/randomize_by_fixed_block.R | 2 simtrial-0.4.2/simtrial/R/rmst.R | 107 - simtrial-0.4.2/simtrial/R/sim_fixed_n.R | 18 simtrial-0.4.2/simtrial/R/sim_gs_n.R | 213 +- simtrial-0.4.2/simtrial/R/sim_pw_surv.R | 6 simtrial-0.4.2/simtrial/R/simtrial-package.R | 4 simtrial-0.4.2/simtrial/R/summary.R |only simtrial-0.4.2/simtrial/R/wlr.R | 130 + simtrial-0.4.2/simtrial/R/wlr_weight.R | 2 simtrial-0.4.2/simtrial/inst/doc/arbitrary-hazard.R | 3 simtrial-0.4.2/simtrial/inst/doc/arbitrary-hazard.Rmd | 3 simtrial-0.4.2/simtrial/inst/doc/arbitrary-hazard.html | 6 simtrial-0.4.2/simtrial/inst/doc/maxcombo.R | 3 simtrial-0.4.2/simtrial/inst/doc/maxcombo.Rmd | 3 simtrial-0.4.2/simtrial/inst/doc/maxcombo.html | 43 simtrial-0.4.2/simtrial/inst/doc/modest-wlrt.R | 8 simtrial-0.4.2/simtrial/inst/doc/modest-wlrt.Rmd | 8 simtrial-0.4.2/simtrial/inst/doc/modest-wlrt.html | 10 simtrial-0.4.2/simtrial/inst/doc/parallel.R | 2 simtrial-0.4.2/simtrial/inst/doc/parallel.Rmd | 4 simtrial-0.4.2/simtrial/inst/doc/parallel.html | 13 simtrial-0.4.2/simtrial/inst/doc/rmst.R | 3 simtrial-0.4.2/simtrial/inst/doc/rmst.Rmd | 7 simtrial-0.4.2/simtrial/inst/doc/rmst.html | 20 simtrial-0.4.2/simtrial/inst/doc/routines.R | 3 simtrial-0.4.2/simtrial/inst/doc/routines.Rmd | 3 simtrial-0.4.2/simtrial/inst/doc/routines.html | 142 - simtrial-0.4.2/simtrial/inst/doc/workflow.R | 2 simtrial-0.4.2/simtrial/inst/doc/workflow.Rmd | 2 simtrial-0.4.2/simtrial/man/as_gt.Rd |only simtrial-0.4.2/simtrial/man/counting_process.Rd | 13 simtrial-0.4.2/simtrial/man/early_zero.Rd | 2 simtrial-0.4.2/simtrial/man/get_analysis_date.Rd | 2 simtrial-0.4.2/simtrial/man/get_cut_date_by_event.Rd | 2 simtrial-0.4.2/simtrial/man/maxcombo.Rd | 2 simtrial-0.4.2/simtrial/man/milestone.Rd | 2 simtrial-0.4.2/simtrial/man/randomize_by_fixed_block.Rd | 2 simtrial-0.4.2/simtrial/man/rmst.Rd | 46 simtrial-0.4.2/simtrial/man/sim_fixed_n.Rd | 2 simtrial-0.4.2/simtrial/man/sim_gs_n.Rd | 131 - simtrial-0.4.2/simtrial/man/sim_pw_surv.Rd | 2 simtrial-0.4.2/simtrial/man/summary.Rd |only simtrial-0.4.2/simtrial/man/wlr.Rd | 79 simtrial-0.4.2/simtrial/tests/testthat/test-double_programming_mb_weight.R | 25 simtrial-0.4.2/simtrial/tests/testthat/test-double_programming_sim_fixed_n.R | 77 simtrial-0.4.2/simtrial/tests/testthat/test-independent_test_early_zero_weight.R |only simtrial-0.4.2/simtrial/tests/testthat/test-independent_test_fh_weight.R | 2 simtrial-0.4.2/simtrial/tests/testthat/test-independent_test_wlr.R |only simtrial-0.4.2/simtrial/tests/testthat/test-unvalidated-data.table.R | 6 simtrial-0.4.2/simtrial/tests/testthat/test-unvalidated-rmst.R | 120 + simtrial-0.4.2/simtrial/tests/testthat/test-unvalidated-sim_gs_n.R | 904 +++++++--- simtrial-0.4.2/simtrial/tests/testthat/test-unvalidated-summary.R |only simtrial-0.4.2/simtrial/tests/testthat/test-unvalidated-wlr.R |only simtrial-0.4.2/simtrial/vignettes/arbitrary-hazard.Rmd | 3 simtrial-0.4.2/simtrial/vignettes/figures |only simtrial-0.4.2/simtrial/vignettes/maxcombo.Rmd | 3 simtrial-0.4.2/simtrial/vignettes/modest-wlrt.Rmd | 8 simtrial-0.4.2/simtrial/vignettes/parallel.Rmd | 4 simtrial-0.4.2/simtrial/vignettes/rmst.Rmd | 7 simtrial-0.4.2/simtrial/vignettes/routines.Rmd | 3 simtrial-0.4.2/simtrial/vignettes/workflow.Rmd | 2 80 files changed, 1725 insertions(+), 818 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.6-0 dated 2024-09-23 and 1.6-1 dated 2024-11-18
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- R/dpq_etc.R | 3 +++ R/methods.R | 1 - R/mlt.R | 18 ++++++++++++------ R/mmlt.R | 16 ++++++++-------- build/partial.rdb |binary inst/NEWS.Rd | 9 +++++++++ 8 files changed, 45 insertions(+), 27 deletions(-)
Title: Imputation of High-Dimensional Count Data using Side Information
Description: Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear Poisson model where main row and column effects, as well as effects of known covariates and interaction terms can be fitted. The estimation procedure is based on the convex optimization of the Poisson loss penalized by a Lasso type penalty and a nuclear norm. LORI returns estimates of main effects, covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure. The methods are described in Robin, Josse, Moulines and Sardy (2019) <doi:10.1016/j.jmva.2019.04.004>.
Author: Genevieve Robin [aut, cre]
Maintainer: Genevieve Robin <genevieve.robin@cnrs.fr>
Diff between lori versions 2.2.2 dated 2020-12-16 and 2.2.3 dated 2024-11-18
DESCRIPTION | 11 MD5 | 24 - R/lori.R | 14 R/mi.lori.R | 12 R/qut.R | 4 build/vignette.rds |binary inst/doc/aravo_data_analysis.R | 2 inst/doc/aravo_data_analysis.html | 315 +++++++++------------- inst/doc/getting_started.R | 12 inst/doc/getting_started.html | 534 +++++++++++++++++++------------------- man/lori.Rd | 3 man/mi.lori.Rd | 3 man/qut.Rd | 4 13 files changed, 466 insertions(+), 472 deletions(-)
Title: Targets for JAGS Pipelines
Description: Bayesian data analysis usually incurs long runtimes
and cumbersome custom code.
A pipeline toolkit tailored to Bayesian statisticians,
the 'jagstargets' R package is leverages
'targets' and 'R2jags' to ease this burden.
'jagstargets' makes it super easy to set up scalable
JAGS pipelines that automatically parallelize the computation
and skip expensive steps when the results are already up to date.
Minimal custom code is required, and there is no need to manually
configure branching, so usage is much easier than 'targets' alone.
For the underlying methodology, please refer
to the documentation of 'targets' <doi:10.21105/joss.02959> and 'JAGS'
(Plummer 2003) <https://www.r-project.org/conferences/DSC-2003/Proceedings/Plummer.pdf>.
Author: William Michael Landau [aut, cre]
,
David Lawrence Miller [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between jagstargets versions 1.2.1 dated 2024-09-06 and 1.2.2 dated 2024-11-18
DESCRIPTION | 20 ++--- MD5 | 51 +++++++------- NAMESPACE | 2 NEWS.md | 4 + R/tar_jags.R | 2 R/tar_jags_package.R | 2 R/tar_jags_rep.R | 2 R/tar_jags_rep_dic.R | 2 R/tar_jags_rep_draws.R | 2 R/tar_jags_rep_summary.R | 2 inst/doc/introduction.html | 52 +++++++------- inst/doc/simulation.html | 82 +++++++++++------------ man/tar_jags.Rd | 98 ++++++++++++++++------------ man/tar_jags_rep.Rd | 96 ++++++++++++++++----------- man/tar_jags_rep_data_batch.Rd | 2 man/tar_jags_rep_dic.Rd | 98 ++++++++++++++++------------ man/tar_jags_rep_draws.Rd | 98 ++++++++++++++++------------ man/tar_jags_rep_summary.Rd | 98 ++++++++++++++++------------ tests/testthat/helper-utils.R |only tests/testthat/test-tar_jags.R | 11 --- tests/testthat/test-tar_jags_df.R | 3 tests/testthat/test-tar_jags_example_file.R | 1 tests/testthat/test-tar_jags_rep_dic.R | 8 -- tests/testthat/test-tar_jags_rep_draws.R | 13 --- tests/testthat/test-tar_jags_rep_summary.R | 23 +----- tests/testthat/test-utils_data.R | 2 tests/testthat/test-utils_deprecate.R | 1 27 files changed, 423 insertions(+), 352 deletions(-)
Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'.
Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>.
Some more specific algorithms allow the user to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between graphlayouts versions 1.2.0 dated 2024-09-24 and 1.2.1 dated 2024-11-18
graphlayouts-1.2.0/graphlayouts/R/oaqc.R |only graphlayouts-1.2.0/graphlayouts/man/annotate_result.Rd |only graphlayouts-1.2.0/graphlayouts/man/as.edge_list.Rd |only graphlayouts-1.2.0/graphlayouts/man/oaqc.Rd |only graphlayouts-1.2.0/graphlayouts/src/Graph.cpp |only graphlayouts-1.2.0/graphlayouts/src/Graph.h |only graphlayouts-1.2.0/graphlayouts/src/QuadCensus.cpp |only graphlayouts-1.2.0/graphlayouts/src/QuadCensus.h |only graphlayouts-1.2.0/graphlayouts/src/init.cpp |only graphlayouts-1.2.1/graphlayouts/DESCRIPTION | 20 ++++------- graphlayouts-1.2.1/graphlayouts/MD5 | 21 +++--------- graphlayouts-1.2.1/graphlayouts/NAMESPACE | 1 graphlayouts-1.2.1/graphlayouts/NEWS.md | 4 ++ graphlayouts-1.2.1/graphlayouts/R/layout_backbone.R | 6 ++- graphlayouts-1.2.1/graphlayouts/man/graphlayouts-package.Rd | 6 --- graphlayouts-1.2.1/graphlayouts/src/RcppExports.cpp | 3 - 16 files changed, 21 insertions(+), 40 deletions(-)
Title: Balanced and Spatially Balanced Sampling
Description: Select balanced and spatially balanced probability samples in multi-dimensional spaces
with any prescribed inclusion probabilities. It contains fast (C++ via Rcpp) implementations of
the included sampling methods. The local pivotal method by Grafström, Lundström and Schelin (2012)
<doi:10.1111/j.1541-0420.2011.01699.x> and spatially correlated Poisson sampling by Grafström (2012)
<doi:10.1016/j.jspi.2011.07.003> are included. Also the cube method (for balanced sampling) and
the local cube method (for doubly balanced sampling) are included, see Grafström and Tillé (2013)
<doi:10.1002/env.2194>.
Author: Anton Grafstroem [aut, cre] ,
Wilmer Prentius [aut] ,
Jonathan Lisic [ctb]
Maintainer: Anton Grafstroem <anton.grafstrom@gmail.com>
Diff between BalancedSampling versions 2.0.6 dated 2024-03-01 and 2.1.1 dated 2024-11-18
DESCRIPTION | 23 +++++++++++++++-------- MD5 | 12 ++++++------ man/BalancedSampling.Rd | 2 +- src/CubeClass.cc | 2 +- src/IndexListClass.cc | 22 ++++++++-------------- src/IndexListClass.h | 2 +- src/hlpm2.cc | 2 +- 7 files changed, 33 insertions(+), 32 deletions(-)
More information about BalancedSampling at CRAN
Permanent link
Title: Gradient-Free Optimization Algorithm for Single and
Multi-Objective Problems
Description: An implementation of the Jaya optimization algorithm for both
single-objective and multi-objective problems. Jaya is a population-based,
gradient-free optimization algorithm capable of solving constrained and
unconstrained optimization problems without hyperparameters. This package
includes features such as multi-objective Pareto optimization, adaptive
population adjustment, and early stopping. For further details, see
R.V. Rao (2016) <doi:10.5267/j.ijiec.2015.8.004>.
Author: Neeraj Bokde [aut, cre]
Maintainer: Neeraj Bokde <neerajdhanraj@gmail.com>
Diff between Jaya versions 0.1.9 dated 2019-11-12 and 1.0.3 dated 2024-11-18
Jaya-0.1.9/Jaya/R/plotJaya.R |only Jaya-0.1.9/Jaya/R/summaryJaya.R |only Jaya-0.1.9/Jaya/inst/doc/A_guide_to_JA.R |only Jaya-0.1.9/Jaya/inst/doc/A_guide_to_JA.Rmd |only Jaya-0.1.9/Jaya/inst/doc/A_guide_to_JA.html |only Jaya-0.1.9/Jaya/vignettes/A_guide_to_JA.Rmd |only Jaya-1.0.3/Jaya/DESCRIPTION | 49 +-- Jaya-1.0.3/Jaya/LICENSE |only Jaya-1.0.3/Jaya/MD5 | 31 +- Jaya-1.0.3/Jaya/NAMESPACE | 21 - Jaya-1.0.3/Jaya/R/jaya.R | 324 ++++++++++++++---------- Jaya-1.0.3/Jaya/R/jaya_multi.R |only Jaya-1.0.3/Jaya/R/plotting.R |only Jaya-1.0.3/Jaya/R/summary.R |only Jaya-1.0.3/Jaya/build/vignette.rds |binary Jaya-1.0.3/Jaya/inst/doc/Jaya_Usage.R |only Jaya-1.0.3/Jaya/inst/doc/Jaya_Usage.Rmd |only Jaya-1.0.3/Jaya/inst/doc/Jaya_Usage.html |only Jaya-1.0.3/Jaya/man/jaya.Rd | 137 ++++++---- Jaya-1.0.3/Jaya/man/jaya_multi.Rd |only Jaya-1.0.3/Jaya/man/plot.jaya.Rd | 66 +++- Jaya-1.0.3/Jaya/man/plot_jaya_multi_pairwise.Rd |only Jaya-1.0.3/Jaya/man/summary.jaya.Rd | 77 +++-- Jaya-1.0.3/Jaya/tests |only Jaya-1.0.3/Jaya/vignettes/Jaya_Usage.Rmd |only 25 files changed, 446 insertions(+), 259 deletions(-)
Title: Padronizador de Endereços Brasileiros (Brazilian Addresses
Standardizer)
Description: Padroniza endereços brasileiros a partir de diferentes
critérios. Os métodos de padronização incluem apenas manipulações
básicas de strings, não oferecendo suporte a correspondências
probabilísticas entre strings. (Standardizes brazilian addresses using
different criteria. Standardization methods include only basic string
manipulation, not supporting probabilistic matches between strings.)
Author: Daniel Herszenhut [aut, cre] ,
Rafael H. M. Pereira [aut] ,
Lucas Mation [aut]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between enderecobr versions 0.2.0 dated 2024-10-28 and 0.2.1 dated 2024-11-18
DESCRIPTION | 13 ++++++++----- MD5 | 6 +++--- NEWS.md | 6 ++++++ man/enderecobr.Rd | 1 + 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.12.0 dated 2024-07-26 and 1.13.0 dated 2024-11-18
DESCRIPTION | 8 MD5 | 96 +- NAMESPACE | 2 R/corColumnOrder.R | 178 +++-- R/exportAsWombatP.R |only R/getUPS1acc.R | 32 R/inspectSpeciesIndic.R |only R/readAlphaPeptFile.R | 12 R/readDiaNNFile.R | 8 R/readDiaNNPeptides.R | 8 R/readFasta2.R | 28 R/readFragpipeFile.R | 8 R/readIonbotPeptides.R | 77 +- R/readMassChroQFile.R | 9 R/readMaxQuantFile.R | 101 ++ R/readMaxQuantPeptides.R | 170 +++- R/readOpenMSFile.R | 3 R/readProlineFile.R | 10 R/readProteomeDiscovererFile.R | 269 ++++++- R/readProteomeDiscovererPeptides.R | 56 + R/readSampleMetaData.R | 347 ++++++--- R/readWombatNormFile.R | 6 inst/doc/wrProteoVignette1.R | 11 inst/doc/wrProteoVignette1.Rmd | 11 inst/doc/wrProteoVignette1.html | 196 ++--- inst/doc/wrProteoVignetteUPS1.R | 53 - inst/doc/wrProteoVignetteUPS1.Rmd | 73 +- inst/doc/wrProteoVignetteUPS1.html | 1193 ++++++++++++++++++---------------- man/corColumnOrder.Rd | 17 man/dot-checkSetupGroups.Rd | 2 man/dot-commonSpecies.Rd | 2 man/dot-extrSpecPref.Rd | 15 man/dot-plotQuantDistr.Rd | 2 man/exportAsWombatP.Rd |only man/getUPS1acc.Rd | 15 man/inspectSpeciesIndic.Rd |only man/readAlphaPeptFile.Rd | 6 man/readDiaNNFile.Rd | 6 man/readDiaNNPeptides.Rd | 6 man/readFragpipeFile.Rd | 6 man/readIonbotPeptides.Rd | 28 man/readMassChroQFile.Rd | 6 man/readMaxQuantFile.Rd | 11 man/readMaxQuantPeptides.Rd | 8 man/readProlineFile.Rd | 6 man/readProteomeDiscovererFile.Rd | 8 man/readProteomeDiscovererPeptides.Rd | 6 man/readSampleMetaData.Rd | 2 man/readWombatNormFile.Rd | 6 vignettes/wrProteoVignette1.Rmd | 11 vignettes/wrProteoVignetteUPS1.Rmd | 73 +- 51 files changed, 1932 insertions(+), 1275 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax is concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.5.0 dated 2024-10-05 and 0.6.1 dated 2024-11-18
tinytable-0.5.0/tinytable/R/theme_tt.R |only tinytable-0.5.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-3level_md.txt |only tinytable-0.5.0/tinytable/inst/tinytest/_tinysnapshot/group_tt-3level_tex.txt |only tinytable-0.5.0/tinytable/man/style_grid_internal.Rd |only tinytable-0.6.1/tinytable/DESCRIPTION | 11 tinytable-0.6.1/tinytable/MD5 | 227 ++- tinytable-0.6.1/tinytable/NEWS.md | 19 tinytable-0.6.1/tinytable/R/build_tt.R | 37 tinytable-0.6.1/tinytable/R/class.R | 6 tinytable-0.6.1/tinytable/R/format_numeric.R | 1 tinytable-0.6.1/tinytable/R/format_tt.R | 73 - tinytable-0.6.1/tinytable/R/group_bootstrap.R | 32 tinytable-0.6.1/tinytable/R/group_tabularray.R | 18 tinytable-0.6.1/tinytable/R/group_tt.R | 24 tinytable-0.6.1/tinytable/R/group_typst.R | 12 tinytable-0.6.1/tinytable/R/last_style.R |only tinytable-0.6.1/tinytable/R/posit.R |only tinytable-0.6.1/tinytable/R/print.R | 11 tinytable-0.6.1/tinytable/R/sanity.R | 590 +++++----- tinytable-0.6.1/tinytable/R/save_tt.R | 4 tinytable-0.6.1/tinytable/R/style_bootstrap.R | 233 +-- tinytable-0.6.1/tinytable/R/style_grid.R | 88 - tinytable-0.6.1/tinytable/R/style_grid_dataframe.R | 2 tinytable-0.6.1/tinytable/R/style_tabularray.R | 463 ++++--- tinytable-0.6.1/tinytable/R/style_tt.R | 380 ++---- tinytable-0.6.1/tinytable/R/style_typst.R | 328 ++--- tinytable-0.6.1/tinytable/R/theme_bootstrap.R |only tinytable-0.6.1/tinytable/R/theme_default.R |only tinytable-0.6.1/tinytable/R/theme_grid.R |only tinytable-0.6.1/tinytable/R/theme_multipage.R |only tinytable-0.6.1/tinytable/R/theme_placement.R |only tinytable-0.6.1/tinytable/R/theme_resize.R |only tinytable-0.6.1/tinytable/R/theme_revealjs.R |only tinytable-0.6.1/tinytable/R/theme_rotate.R |only tinytable-0.6.1/tinytable/R/theme_spacing.R |only tinytable-0.6.1/tinytable/R/theme_striped.R |only tinytable-0.6.1/tinytable/R/theme_tabular.R |only tinytable-0.6.1/tinytable/R/theme_void.R |only tinytable-0.6.1/tinytable/R/theme_zzz.R |only tinytable-0.6.1/tinytable/R/tt.R | 11 tinytable-0.6.1/tinytable/R/tt_bootstrap.R | 15 tinytable-0.6.1/tinytable/README.md | 6 tinytable-0.6.1/tinytable/build/partial.rdb |binary tinytable-0.6.1/tinytable/inst/templates/bootstrap.html | 25 tinytable-0.6.1/tinytable/inst/templates/typst.typ | 46 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/format_tt-vignette_digits.txt | 18 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/format_tt-vignette_html_markdown.html | 36 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-3level.md |only tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-3level.tex |only tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-3level.typ | 52 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-html_tutorial_01.html | 67 - tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue165_html_centering_style.html | 86 - tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_01_html.html | 56 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_01_latex.txt | 13 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_01_typst.txt | 54 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_02_html.html | 58 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_02_latex.txt | 13 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue258_02_typst.txt | 54 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/group_tt-issue362_duplicate_colum_labels.tex |only tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-alignment.html | 61 - tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-bootstrap_css.html | 47 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-borders.html | 40 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-caption.html | 33 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-conditional_styling.html | 45 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-font_size.html | 51 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-footnote.html | 37 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-formatting.html | 40 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-heatmap.html | 105 + tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-images-portable.html | 32 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-images.html | 32 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-individual_cells.html | 43 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-issue297.txt | 32 tinytable-0.6.1/tinytable/inst/tinytest/_tinysnapshot/html-issue58.html | 98 - 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tinytable-0.6.1/tinytable/inst/tinytest/test-typst.R | 11 tinytable-0.6.1/tinytable/man/format_tt.Rd | 26 tinytable-0.6.1/tinytable/man/initialize-tinytable-method.Rd | 2 tinytable-0.6.1/tinytable/man/save_tt.Rd | 6 tinytable-0.6.1/tinytable/man/style_eval-tinytable_dataframe-method.Rd | 14 tinytable-0.6.1/tinytable/man/style_eval-tinytable_grid-method.Rd | 14 tinytable-0.6.1/tinytable/man/style_tt.Rd | 24 tinytable-0.6.1/tinytable/man/theme_tt.Rd | 2 tinytable-0.6.1/tinytable/man/tt.Rd | 36 127 files changed, 3009 insertions(+), 2409 deletions(-)
Title: Statically Determine Function Dependencies Between Packages
Description: Statically determine and visualize the function dependencies
within and across packages. This may be useful for managing function
dependencies across a code base of multiple R packages.
Author: Ed Peyton [aut, cre]
Maintainer: Ed Peyton <edppeyton@gmail.com>
Diff between pkgdepR versions 1.0.0 dated 2022-02-16 and 1.1.0 dated 2024-11-18
DESCRIPTION | 10 +++---- LICENSE | 4 +- MD5 | 38 +++++++++++++-------------- NEWS.md | 6 +++- R/S3methods.R | 38 +++++++++++++++++++++------ R/envir_deps.R | 14 ++++----- R/helper_functions.R | 26 +++++++++++------- R/pkgdepR-package.R | 2 - README.md | 31 ++++++++++++---------- inst/CITATION | 20 ++++---------- man/all_info_ns.Rd | 34 ++++++++++++------------ man/deps.Rd | 62 ++++++++++++++++++++++---------------------- man/get_functions.Rd | 34 ++++++++++++------------ man/is.pkgdepR.Rd | 34 ++++++++++++------------ man/ls_namespace_info.Rd | 38 +++++++++++++-------------- man/pipe.Rd | 16 +++++------ man/pkgdepR-package.Rd | 66 +++++++++++++++++++++++------------------------ man/plot.pkgdepR.Rd | 18 ++++++++++-- man/print.pkgdepR.Rd | 38 +++++++++++++-------------- man/summary.pkgdepR.Rd | 38 +++++++++++++-------------- 20 files changed, 303 insertions(+), 264 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
,
Christoph Burow [aut, trl, dtc]
,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 0.9.25 dated 2024-09-12 and 0.9.26 dated 2024-11-18
Luminescence-0.9.25/Luminescence/man/calc_Kars2008.Rd |only Luminescence-0.9.26/Luminescence/DESCRIPTION | 8 Luminescence-0.9.26/Luminescence/MD5 | 421 +++++----- Luminescence-0.9.26/Luminescence/NAMESPACE | 1 Luminescence-0.9.26/Luminescence/NEWS.md | 268 ++++-- Luminescence-0.9.26/Luminescence/R/CW2pHMi.R | 9 Luminescence-0.9.26/Luminescence/R/RLum.Analysis-class.R | 71 - Luminescence-0.9.26/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 5 Luminescence-0.9.26/Luminescence/R/analyse_Al2O3C_CrossTalk.R | 2 Luminescence-0.9.26/Luminescence/R/analyse_Al2O3C_ITC.R | 5 Luminescence-0.9.26/Luminescence/R/analyse_Al2O3C_Measurement.R | 6 Luminescence-0.9.26/Luminescence/R/analyse_FadingMeasurement.R | 18 Luminescence-0.9.26/Luminescence/R/analyse_IRSAR.RF.R | 8 Luminescence-0.9.26/Luminescence/R/analyse_SAR.CWOSL.R | 13 Luminescence-0.9.26/Luminescence/R/analyse_SAR.TL.R | 215 ++--- Luminescence-0.9.26/Luminescence/R/analyse_baSAR.R | 12 Luminescence-0.9.26/Luminescence/R/analyse_pIRIRSequence.R | 112 -- Luminescence-0.9.26/Luminescence/R/analyse_portableOSL.R | 14 Luminescence-0.9.26/Luminescence/R/calc_AliquotSize.R | 5 Luminescence-0.9.26/Luminescence/R/calc_AverageDose.R | 6 Luminescence-0.9.26/Luminescence/R/calc_FastRatio.R | 5 Luminescence-0.9.26/Luminescence/R/calc_Huntley2006.R | 16 Luminescence-0.9.26/Luminescence/R/calc_Kars2008.R | 93 -- Luminescence-0.9.26/Luminescence/R/calc_MinDose.R | 6 Luminescence-0.9.26/Luminescence/R/calc_OSLLxTxDecomposed.R | 4 Luminescence-0.9.26/Luminescence/R/calc_ThermalLifetime.R | 5 Luminescence-0.9.26/Luminescence/R/calc_WodaFuchs2008.R | 2 Luminescence-0.9.26/Luminescence/R/calc_gSGC.R | 4 Luminescence-0.9.26/Luminescence/R/calc_gSGC_feldspar.R | 2 Luminescence-0.9.26/Luminescence/R/combine_De_Dr.R | 6 Luminescence-0.9.26/Luminescence/R/extract_IrradiationTimes.R | 4 Luminescence-0.9.26/Luminescence/R/fit_CWCurve.R | 5 Luminescence-0.9.26/Luminescence/R/fit_EmissionSpectra.R | 13 Luminescence-0.9.26/Luminescence/R/fit_LMCurve.R | 6 Luminescence-0.9.26/Luminescence/R/fit_OSLLifeTimes.R | 7 Luminescence-0.9.26/Luminescence/R/get_Layout.R | 4 Luminescence-0.9.26/Luminescence/R/get_RLum.R | 23 Luminescence-0.9.26/Luminescence/R/internal_as.latex.table.R | 3 Luminescence-0.9.26/Luminescence/R/internals_RLum.R | 79 + Luminescence-0.9.26/Luminescence/R/merge_RLum.Data.Curve.R | 4 Luminescence-0.9.26/Luminescence/R/merge_RLum.R | 4 Luminescence-0.9.26/Luminescence/R/merge_RLum.Results.R | 5 Luminescence-0.9.26/Luminescence/R/plot_AbanicoPlot.R | 5 Luminescence-0.9.26/Luminescence/R/plot_DRCSummary.R | 5 Luminescence-0.9.26/Luminescence/R/plot_DRTResults.R | 6 Luminescence-0.9.26/Luminescence/R/plot_DetPlot.R | 3 Luminescence-0.9.26/Luminescence/R/plot_FilterCombinations.R | 8 Luminescence-0.9.26/Luminescence/R/plot_GrowthCurve.R | 4 Luminescence-0.9.26/Luminescence/R/plot_Histogram.R | 2 Luminescence-0.9.26/Luminescence/R/plot_KDE.R | 2 Luminescence-0.9.26/Luminescence/R/plot_NRt.R | 2 Luminescence-0.9.26/Luminescence/R/plot_RLum.Analysis.R | 9 Luminescence-0.9.26/Luminescence/R/plot_RLum.Data.Image.R | 4 Luminescence-0.9.26/Luminescence/R/plot_RLum.Data.Spectrum.R | 52 - Luminescence-0.9.26/Luminescence/R/plot_RLum.Results.R | 8 Luminescence-0.9.26/Luminescence/R/plot_RadialPlot.R | 5 Luminescence-0.9.26/Luminescence/R/plot_Risoe.BINfileData.R | 4 Luminescence-0.9.26/Luminescence/R/plot_ViolinPlot.R | 3 Luminescence-0.9.26/Luminescence/R/read_BIN2R.R | 6 Luminescence-0.9.26/Luminescence/R/read_Daybreak2R.R | 2 Luminescence-0.9.26/Luminescence/R/read_SPE2R.R | 4 Luminescence-0.9.26/Luminescence/R/read_XSYG2R.R | 4 Luminescence-0.9.26/Luminescence/R/report_RLum.R | 5 Luminescence-0.9.26/Luminescence/R/scale_GammaDose.R | 2 Luminescence-0.9.26/Luminescence/R/template_DRAC.R | 4 Luminescence-0.9.26/Luminescence/R/use_DRAC.R | 7 Luminescence-0.9.26/Luminescence/R/write_R2BIN.R | 51 - Luminescence-0.9.26/Luminescence/R/zzz.R | 7 Luminescence-0.9.26/Luminescence/README.md | 100 +- Luminescence-0.9.26/Luminescence/build/partial.rdb |binary Luminescence-0.9.26/Luminescence/build/vignette.rds |binary Luminescence-0.9.26/Luminescence/inst/CITATION | 2 Luminescence-0.9.26/Luminescence/man/Analyse_SAR.OSLdata.Rd | 2 Luminescence-0.9.26/Luminescence/man/CW2pHMi.Rd | 2 Luminescence-0.9.26/Luminescence/man/CW2pLM.Rd | 2 Luminescence-0.9.26/Luminescence/man/CW2pLMi.Rd | 2 Luminescence-0.9.26/Luminescence/man/CW2pPMi.Rd | 2 Luminescence-0.9.26/Luminescence/man/GitHub-API.Rd | 2 Luminescence-0.9.26/Luminescence/man/PSL2Risoe.BINfileData.Rd | 2 Luminescence-0.9.26/Luminescence/man/RLum-class.Rd | 2 Luminescence-0.9.26/Luminescence/man/RLum.Analysis-class.Rd | 4 Luminescence-0.9.26/Luminescence/man/RLum.Data.Curve-class.Rd | 2 Luminescence-0.9.26/Luminescence/man/RLum.Data.Image-class.Rd | 2 Luminescence-0.9.26/Luminescence/man/RLum.Data.Spectrum-class.Rd | 2 Luminescence-0.9.26/Luminescence/man/RLum.Results-class.Rd | 2 Luminescence-0.9.26/Luminescence/man/Risoe.BINfileData-class.Rd | 2 Luminescence-0.9.26/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 2 Luminescence-0.9.26/Luminescence/man/Second2Gray.Rd | 2 Luminescence-0.9.26/Luminescence/man/analyse_Al2O3C_CrossTalk.Rd | 2 Luminescence-0.9.26/Luminescence/man/analyse_Al2O3C_ITC.Rd | 2 Luminescence-0.9.26/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 2 Luminescence-0.9.26/Luminescence/man/analyse_FadingMeasurement.Rd | 14 Luminescence-0.9.26/Luminescence/man/analyse_IRSAR.RF.Rd | 2 Luminescence-0.9.26/Luminescence/man/analyse_SAR.CWOSL.Rd | 2 Luminescence-0.9.26/Luminescence/man/analyse_SAR.TL.Rd | 6 Luminescence-0.9.26/Luminescence/man/analyse_baSAR.Rd | 2 Luminescence-0.9.26/Luminescence/man/analyse_pIRIRSequence.Rd | 2 Luminescence-0.9.26/Luminescence/man/analyse_portableOSL.Rd | 2 Luminescence-0.9.26/Luminescence/man/apply_CosmicRayRemoval.Rd | 2 Luminescence-0.9.26/Luminescence/man/apply_EfficiencyCorrection.Rd | 2 Luminescence-0.9.26/Luminescence/man/bin_RLum.Data.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_AliquotSize.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_AverageDose.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_CentralDose.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_CobbleDoseRate.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_CommonDose.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_CosmicDoseRate.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_FadingCorr.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_FastRatio.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_FiniteMixture.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_FuchsLang2001.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_HomogeneityTest.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_Huntley2006.Rd | 4 Luminescence-0.9.26/Luminescence/man/calc_IEU.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_Lamothe2003.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_MaxDose.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_MinDose.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_OSLLxTxRatio.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_SourceDoseRate.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_Statistics.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_TLLxTxRatio.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_ThermalLifetime.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_WodaFuchs2008.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_gSGC.Rd | 2 Luminescence-0.9.26/Luminescence/man/calc_gSGC_feldspar.Rd | 2 Luminescence-0.9.26/Luminescence/man/combine_De_Dr.Rd | 2 Luminescence-0.9.26/Luminescence/man/convert_Activity2Concentration.Rd | 2 Luminescence-0.9.26/Luminescence/man/convert_BIN2CSV.Rd | 2 Luminescence-0.9.26/Luminescence/man/convert_Concentration2DoseRate.Rd | 2 Luminescence-0.9.26/Luminescence/man/convert_Daybreak2CSV.Rd | 2 Luminescence-0.9.26/Luminescence/man/convert_PSL2CSV.Rd | 2 Luminescence-0.9.26/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 2 Luminescence-0.9.26/Luminescence/man/convert_SG2MG.Rd | 2 Luminescence-0.9.26/Luminescence/man/convert_Wavelength2Energy.Rd | 2 Luminescence-0.9.26/Luminescence/man/convert_XSYG2CSV.Rd | 2 Luminescence-0.9.26/Luminescence/man/extract_IrradiationTimes.Rd | 2 Luminescence-0.9.26/Luminescence/man/extract_ROI.Rd | 2 Luminescence-0.9.26/Luminescence/man/fit_CWCurve.Rd | 2 Luminescence-0.9.26/Luminescence/man/fit_EmissionSpectra.Rd | 2 Luminescence-0.9.26/Luminescence/man/fit_LMCurve.Rd | 2 Luminescence-0.9.26/Luminescence/man/fit_OSLLifeTimes.Rd | 2 Luminescence-0.9.26/Luminescence/man/fit_SurfaceExposure.Rd | 2 Luminescence-0.9.26/Luminescence/man/fit_ThermalQuenching.Rd | 2 Luminescence-0.9.26/Luminescence/man/get_Layout.Rd | 2 Luminescence-0.9.26/Luminescence/man/get_Quote.Rd | 2 Luminescence-0.9.26/Luminescence/man/get_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/get_Risoe.BINfileData.Rd | 2 Luminescence-0.9.26/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-0.9.26/Luminescence/man/import_Data.Rd | 2 Luminescence-0.9.26/Luminescence/man/length_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/merge_RLum.Analysis.Rd | 2 Luminescence-0.9.26/Luminescence/man/merge_RLum.Data.Curve.Rd | 2 Luminescence-0.9.26/Luminescence/man/merge_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/merge_RLum.Results.Rd | 2 Luminescence-0.9.26/Luminescence/man/merge_Risoe.BINfileData.Rd | 2 Luminescence-0.9.26/Luminescence/man/names_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_AbanicoPlot.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_DRCSummary.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_DRTResults.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_DetPlot.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_FilterCombinations.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_GrowthCurve.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_Histogram.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_KDE.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_NRt.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_OSLAgeSummary.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_RLum.Analysis.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_RLum.Data.Curve.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_RLum.Data.Image.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 8 Luminescence-0.9.26/Luminescence/man/plot_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_RLum.Results.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_ROI.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_RadialPlot.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_Risoe.BINfileData.Rd | 2 Luminescence-0.9.26/Luminescence/man/plot_ViolinPlot.Rd | 2 Luminescence-0.9.26/Luminescence/man/read_BIN2R.Rd | 2 Luminescence-0.9.26/Luminescence/man/read_Daybreak2R.Rd | 2 Luminescence-0.9.26/Luminescence/man/read_HeliosOSL2R.Rd | 2 Luminescence-0.9.26/Luminescence/man/read_PSL2R.Rd | 2 Luminescence-0.9.26/Luminescence/man/read_RF2R.Rd | 2 Luminescence-0.9.26/Luminescence/man/read_SPE2R.Rd | 2 Luminescence-0.9.26/Luminescence/man/read_TIFF2R.Rd | 2 Luminescence-0.9.26/Luminescence/man/read_XSYG2R.Rd | 2 Luminescence-0.9.26/Luminescence/man/replicate_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/report_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/sTeve.Rd | 2 Luminescence-0.9.26/Luminescence/man/scale_GammaDose.Rd | 2 Luminescence-0.9.26/Luminescence/man/set_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/set_Risoe.BINfileData.Rd | 2 Luminescence-0.9.26/Luminescence/man/smooth_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/structure_RLum.Rd | 2 Luminescence-0.9.26/Luminescence/man/subset_SingleGrainData.Rd | 2 Luminescence-0.9.26/Luminescence/man/template_DRAC.Rd | 2 Luminescence-0.9.26/Luminescence/man/trim_RLum.Data.Rd | 2 Luminescence-0.9.26/Luminescence/man/tune_Data.Rd | 2 Luminescence-0.9.26/Luminescence/man/use_DRAC.Rd | 2 Luminescence-0.9.26/Luminescence/man/verify_SingleGrainData.Rd | 2 Luminescence-0.9.26/Luminescence/man/write_R2BIN.Rd | 6 Luminescence-0.9.26/Luminescence/man/write_R2TIFF.Rd | 2 Luminescence-0.9.26/Luminescence/man/write_RLum2CSV.Rd | 2 Luminescence-0.9.26/Luminescence/tests/testthat/_snaps |only Luminescence-0.9.26/Luminescence/tests/testthat/setup.R |only Luminescence-0.9.26/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 20 Luminescence-0.9.26/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 59 + Luminescence-0.9.26/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 97 ++ Luminescence-0.9.26/Luminescence/tests/testthat/test_calc_Huntley2006.R | 53 - Luminescence-0.9.26/Luminescence/tests/testthat/test_calc_MinDose.R | 9 Luminescence-0.9.26/Luminescence/tests/testthat/test_get_RLum.R | 10 Luminescence-0.9.26/Luminescence/tests/testthat/test_internals.R | 40 Luminescence-0.9.26/Luminescence/tests/testthat/test_subset_RLum.R | 3 Luminescence-0.9.26/Luminescence/tests/testthat/test_write_R2BIN.R | 8 213 files changed, 1300 insertions(+), 1104 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2024.10.5 dated 2024-10-11 and 2024.11.15 dated 2024-11-18
DESCRIPTION | 9 MD5 | 90 ++- NAMESPACE | 44 - NEWS | 324 +++++++------ R/atime.R | 548 ++++++++++++----------- R/predict.R | 236 +++++----- R/references.R | 369 +++++++-------- R/test.R | 618 +++++++++++++------------- R/versions.R | 380 ++++++++-------- build/vignette.rds |binary inst/doc/Custom_Plots.R | 144 +++--- inst/doc/Custom_Plots.Rmd | 200 ++++---- inst/doc/Custom_Plots.html | 498 ++++++++++----------- inst/doc/Custom_References.R | 134 ++--- inst/doc/Custom_References.Rmd | 284 ++++++------ inst/doc/Custom_References.html | 621 +++++++++++++------------- inst/doc/Custom_Units.R | 138 ++--- inst/doc/Custom_Units.Rmd | 320 ++++++------- inst/doc/Custom_Units.html | 643 +++++++++++++-------------- inst/doc/cum_median.R | 62 +- inst/doc/cum_median.Rmd | 104 ++-- inst/doc/cum_median.html | 408 ++++++++--------- inst/doc/regex.R | 128 ++--- inst/doc/regex.Rmd | 192 ++++---- inst/doc/regex.html | 533 +++++++++++----------- inst/doc/sparse.R |only inst/doc/sparse.Rmd |only inst/doc/sparse.html |only inst/example_tests.R | 82 +-- inst/global_edit.R | 82 +-- man/atime.Rd | 141 ++---- man/atime_grid.Rd | 184 ++++--- man/atime_pkg.Rd | 188 ++++---- man/atime_test.Rd | 128 ++--- man/atime_test_list.Rd | 164 +++--- man/atime_versions.Rd | 178 +++---- man/atime_versions_exprs.Rd | 174 +++---- man/atime_versions_remove.Rd | 26 - man/glob_find_replace.Rd | 38 - man/references_best.Rd | 131 ++--- tests/testthat.R | 2 tests/testthat/test-CRAN.R | 938 +++++++++++++++++++++------------------- vignettes/Custom_Plots.Rmd | 200 ++++---- vignettes/Custom_References.Rmd | 284 ++++++------ vignettes/Custom_Units.Rmd | 320 ++++++------- vignettes/cum_median.Rmd | 104 ++-- vignettes/regex.Rmd | 192 ++++---- vignettes/sparse.Rmd |only 48 files changed, 5336 insertions(+), 5247 deletions(-)
Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut] ,
Kurt Hornik [aut, cre] ,
Artifex Software, Inc. [ctb, cph]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tm versions 0.7-14 dated 2024-08-13 and 0.7-15 dated 2024-11-18
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary data/acq.rda |binary data/crude.rda |binary inst/NEWS.Rd | 7 +++++++ inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary man/hpc.Rd | 22 +++++++++++----------- man/matrix.Rd | 4 ++-- man/plot.Rd | 4 ++-- 12 files changed, 37 insertions(+), 30 deletions(-)
Title: Computing MSPE Estimates in Small Area Estimation
Description: Compute various common mean squared predictive error (MSPE) estimators, as well as several existing variance component predictors as a byproduct, for FH model (Fay and Herriot, 1979) and NER model (Battese et al., 1988) in small area estimation.
Author: Peiwen Xiao [aut, cre],
Xiaohui Liu [aut],
Yu Zhang [aut],
Yuzi Liu [aut],
Jiming Jiang [ths]
Maintainer: Peiwen Xiao <2569613200@qq.com>
Diff between saeMSPE versions 1.2 dated 2022-10-21 and 1.3 dated 2024-11-18
DESCRIPTION | 20 - MD5 | 56 +-- NAMESPACE | 15 R/RcppExports.R | 40 +- R/mspeFHlin.R | 154 +++++++- R/mspeNERlin.R | 100 ++++- man/mspeFHdb.Rd | 38 +- man/mspeFHjack.Rd | 38 +- man/mspeFHlin.Rd | 42 +- man/mspeFHpb.Rd | 36 + man/mspeFHsumca.Rd | 38 +- man/mspeNERdb.Rd | 111 +++--- man/mspeNERjack.Rd | 107 +++-- man/mspeNERlin.Rd | 117 +++--- man/mspeNERpb.Rd | 105 +++-- man/mspeNERsumca.Rd | 109 +++--- man/saeMSPE-package.Rd | 2 man/varfh.Rd | 45 +- man/varner.Rd | 100 +++-- src/Makevars | 11 src/Makevars.win | 11 src/RcppExports.cpp | 140 ++++--- src/saeMSPE-function.cpp | 853 +++++++++++++++++++++++++++++++++-------------- tests |only 24 files changed, 1544 insertions(+), 744 deletions(-)
Title: 'OpenStreetMap' API
Description: Interface to 'OpenStreetMap API' for fetching and saving data
from/to the 'OpenStreetMap' database
(<https://wiki.openstreetmap.org/wiki/API_v0.6>).
Author: Joan Maspons [aut, cre, cph] ,
Jon Harmon [rev] ,
Carlos Camara [rev]
Maintainer: Joan Maspons <joanmaspons@gmail.com>
Diff between osmapiR versions 0.2.1 dated 2024-09-05 and 0.2.2 dated 2024-11-18
osmapiR-0.2.1/osmapiR/tests/testthat/mock_query_changesets/osm.org/api/0.6/changesets-190728.xml |only osmapiR-0.2.2/osmapiR/DESCRIPTION | 10 osmapiR-0.2.2/osmapiR/MD5 | 79 +- osmapiR-0.2.2/osmapiR/NEWS.md | 9 osmapiR-0.2.2/osmapiR/R/osm_get_changesets.R | 88 +- osmapiR-0.2.2/osmapiR/R/osm_get_gpx_metadata.R | 16 osmapiR-0.2.2/osmapiR/R/osm_get_notes.R | 42 - osmapiR-0.2.2/osmapiR/R/osm_get_points_gps.R | 26 osmapiR-0.2.2/osmapiR/R/osm_get_user_details.R | 46 - osmapiR-0.2.2/osmapiR/R/osm_query_changesets.R | 98 +-- osmapiR-0.2.2/osmapiR/R/osmapiR_connection.R | 8 osmapiR-0.2.2/osmapiR/R/osmapi_changesets.R | 301 +++++----- osmapiR-0.2.2/osmapiR/R/osmapi_elements.R | 83 +- osmapiR-0.2.2/osmapiR/R/osmapi_gps_traces.R | 112 +-- osmapiR-0.2.2/osmapiR/R/osmapi_map_notes.R | 84 +- osmapiR-0.2.2/osmapiR/R/osmapi_miscellaneous.R | 58 - osmapiR-0.2.2/osmapiR/R/osmapi_user_data.R | 250 ++++---- osmapiR-0.2.2/osmapiR/inst/CITATION | 7 osmapiR-0.2.2/osmapiR/inst/WORDLIST | 6 osmapiR-0.2.2/osmapiR/inst/doc/how_to_edit_gps_traces.html | 4 osmapiR-0.2.2/osmapiR/inst/doc/how_to_edit_osm.html | 4 osmapiR-0.2.2/osmapiR/inst/doc/osmapiR.html | 196 +++--- osmapiR-0.2.2/osmapiR/man/osm_details_logged_user.Rd | 44 - osmapiR-0.2.2/osmapiR/man/osm_get_changesets.Rd | 88 +- osmapiR-0.2.2/osmapiR/man/osm_get_gpx_metadata.Rd | 16 osmapiR-0.2.2/osmapiR/man/osm_get_notes.Rd | 42 - osmapiR-0.2.2/osmapiR/man/osm_get_points_gps.Rd | 26 osmapiR-0.2.2/osmapiR/man/osm_get_user_details.Rd | 46 - osmapiR-0.2.2/osmapiR/man/osm_history_object.Rd | 2 osmapiR-0.2.2/osmapiR/man/osm_list_gpxs.Rd | 20 osmapiR-0.2.2/osmapiR/man/osm_permissions.Rd | 1 osmapiR-0.2.2/osmapiR/man/osm_preferences_user.Rd | 8 osmapiR-0.2.2/osmapiR/man/osm_query_changesets.Rd | 88 +- osmapiR-0.2.2/osmapiR/man/osm_read_bbox_notes.Rd | 42 - osmapiR-0.2.2/osmapiR/man/osm_redaction_object.Rd | 5 osmapiR-0.2.2/osmapiR/man/osm_update_object.Rd | 2 osmapiR-0.2.2/osmapiR/tests/testthat/_snaps/changesets.md | 18 osmapiR-0.2.2/osmapiR/tests/testthat/mock_query_changesets/osm.org/api/0.6/changesets-b87e70.xml |only osmapiR-0.2.2/osmapiR/tests/testthat/mock_query_changesets/osm.org/api/0.6/changesets-fce339.xml |only osmapiR-0.2.2/osmapiR/tests/testthat/test-changesets.R | 10 osmapiR-0.2.2/osmapiR/tests/testthat/test-tags_list-wide.R | 8 osmapiR-0.2.2/osmapiR/tests/testthat/test-user_data.R | 2 42 files changed, 1083 insertions(+), 912 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oehlschlaegel [ctb, cph],
Suman Rakshit [ctb], [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.3-3 dated 2024-09-18 and 3.3-4 dated 2024-11-18
DESCRIPTION | 18 ++--- MD5 | 33 +++++----- NAMESPACE | 3 NEWS | 33 ++++++++++ R/options.R | 36 +++++++++-- R/persp.ppp.R | 92 +++++++++++++++++++++++++---- R/quadscheme.R | 7 -- R/tess.R | 129 +++++++++++++++++++++++++++++++----------- R/window.R | 16 +++-- inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/default.image.colours.Rd |only man/marks.tess.Rd | 8 +- man/persp.ppp.Rd | 53 +++++++++++++++-- man/pixelquad.Rd | 6 + man/plot.im.Rd | 7 +- man/spatstat.geom-internal.Rd | 2 man/tess.Rd | 3 18 files changed, 352 insertions(+), 96 deletions(-)
Title: Interface R to MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for
arbitrary precision floating point numbers, including transcendental
("special") functions. To this end, the package interfaces to
the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library
which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Author: Martin Maechler [aut, cre] ,
Richard M. Heiberger [ctb] , *Bin, *Dec),
John C. Nash [ctb] , origin of unirootR),
Hans W. Borchers [ctb] ; origin of
hjkMpfr),
Mikael Jagan [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between Rmpfr versions 0.9-5 dated 2024-01-21 and 1.0-0 dated 2024-11-18
Rmpfr-0.9-5/Rmpfr/tests/bit-repr.Rout.save |only Rmpfr-1.0-0/Rmpfr/DESCRIPTION | 21 + Rmpfr-1.0-0/Rmpfr/MD5 | 61 ++--- Rmpfr-1.0-0/Rmpfr/NAMESPACE | 1 Rmpfr-1.0-0/Rmpfr/R/AllClasses.R | 7 Rmpfr-1.0-0/Rmpfr/R/as.R | 5 Rmpfr-1.0-0/Rmpfr/R/formatHex.R | 2 Rmpfr-1.0-0/Rmpfr/R/gmp-convert.R | 78 ++++++ Rmpfr-1.0-0/Rmpfr/R/special-fun.R | 13 - Rmpfr-1.0-0/Rmpfr/TODO | 3 Rmpfr-1.0-0/Rmpfr/build/partial.rdb |binary Rmpfr-1.0-0/Rmpfr/build/vignette.rds |binary Rmpfr-1.0-0/Rmpfr/inst/NEWS.Rd | 40 +++ Rmpfr-1.0-0/Rmpfr/inst/doc/Maechler_useR_2011-abstr.pdf |binary Rmpfr-1.0-0/Rmpfr/inst/doc/Rmpfr-pkg.pdf |binary Rmpfr-1.0-0/Rmpfr/inst/doc/log1mexp-note.pdf |binary Rmpfr-1.0-0/Rmpfr/man/asNumeric-methods.Rd | 2 Rmpfr-1.0-0/Rmpfr/man/gmp-conversions.Rd | 16 - Rmpfr-1.0-0/Rmpfr/man/mpfr-class.Rd | 2 Rmpfr-1.0-0/Rmpfr/man/mpfr-utils.Rd | 2 Rmpfr-1.0-0/Rmpfr/man/mpfr.Rd | 3 Rmpfr-1.0-0/Rmpfr/man/mpfrArray.Rd | 4 Rmpfr-1.0-0/Rmpfr/man/mpfrMatrix-utils.Rd | 4 Rmpfr-1.0-0/Rmpfr/man/num2bigq.Rd |only Rmpfr-1.0-0/Rmpfr/man/pbetaI.Rd | 27 +- Rmpfr-1.0-0/Rmpfr/man/utils.Rd | 2 Rmpfr-1.0-0/Rmpfr/src/Ops.c | 28 +- Rmpfr-1.0-0/Rmpfr/src/Rmpfr_utils.h | 11 Rmpfr-1.0-0/Rmpfr/src/convert.c | 180 +++++++++------- Rmpfr-1.0-0/Rmpfr/src/utils.c | 14 - Rmpfr-1.0-0/Rmpfr/tests/lowlevel.R | 3 Rmpfr-1.0-0/Rmpfr/tests/special-fun-dgamma.R |only Rmpfr-1.0-0/Rmpfr/tests/special-fun-ex.R | 43 --- 33 files changed, 350 insertions(+), 222 deletions(-)
Title: Database Interface and MariaDB Driver
Description: Implements a DBI-compliant interface to MariaDB
(<https://mariadb.org/>) and MySQL (<https://www.mysql.com/>)
databases.
Author: Kirill Mueller [aut, cre] ,
Jeroen Ooms [aut] ,
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RMariaDB versions 1.3.2 dated 2024-05-27 and 1.3.3 dated 2024-11-18
DESCRIPTION | 8 ++--- MD5 | 17 +++++------ NEWS.md | 11 +++++++ R/dbQuoteIdentifier_MariaDBConnection_Id.R | 7 +++- man/Client-flags.Rd | 2 - man/dbConnect-MariaDBDriver-method.Rd | 2 - man/mariadb-tables.Rd | 2 - man/query.Rd | 10 +++--- src/DbConnection.cpp | 13 +++++++- tests/testthat/test-dbQuoteIdentifier_MariaDBConnection_Id.R |only 10 files changed, 50 insertions(+), 22 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 14.0.2-1 dated 2024-09-12 and 14.2.0-1 dated 2024-11-18
ChangeLog | 31 DESCRIPTION | 10 MD5 | 152 +-- build/partial.rdb |binary build/vignette.rds |binary configure | 18 configure.ac | 2 inst/NEWS.Rd | 17 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/RcppArmadillo/interface/RcppArmadilloAs.h | 26 inst/include/armadillo_bits/Base_bones.hpp | 8 inst/include/armadillo_bits/CubeToMatOp_bones.hpp | 3 inst/include/armadillo_bits/Cube_bones.hpp | 9 inst/include/armadillo_bits/Gen_bones.hpp | 3 inst/include/armadillo_bits/Glue_bones.hpp | 3 inst/include/armadillo_bits/Glue_meat.hpp | 13 inst/include/armadillo_bits/Mat_bones.hpp | 11 inst/include/armadillo_bits/Mat_meat.hpp | 13 inst/include/armadillo_bits/Op_bones.hpp | 3 inst/include/armadillo_bits/Op_meat.hpp | 13 inst/include/armadillo_bits/Proxy.hpp | 16 inst/include/armadillo_bits/SpBase_bones.hpp | 8 inst/include/armadillo_bits/SpToDGlue_bones.hpp | 3 inst/include/armadillo_bits/SpToDOp_bones.hpp | 3 inst/include/armadillo_bits/arma_forward.hpp | 2 inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/auxlib_bones.hpp | 36 inst/include/armadillo_bits/auxlib_meat.hpp | 777 ++++++++++++++-- inst/include/armadillo_bits/compiler_check.hpp | 6 inst/include/armadillo_bits/compiler_setup.hpp | 8 inst/include/armadillo_bits/config.hpp | 25 inst/include/armadillo_bits/def_lapack.hpp | 112 ++ inst/include/armadillo_bits/diagview_bones.hpp | 3 inst/include/armadillo_bits/diagview_meat.hpp | 53 - inst/include/armadillo_bits/eGlue_bones.hpp | 3 inst/include/armadillo_bits/eGlue_meat.hpp | 11 inst/include/armadillo_bits/eOp_bones.hpp | 3 inst/include/armadillo_bits/eOp_meat.hpp | 13 inst/include/armadillo_bits/fn_misc.hpp | 90 + inst/include/armadillo_bits/fn_powext.hpp | 16 inst/include/armadillo_bits/glue_solve_bones.hpp | 3 inst/include/armadillo_bits/glue_solve_meat.hpp | 93 + inst/include/armadillo_bits/glue_times_meat.hpp | 14 inst/include/armadillo_bits/gmm_diag_meat.hpp | 4 inst/include/armadillo_bits/gmm_full_meat.hpp | 4 inst/include/armadillo_bits/mtGlue_bones.hpp | 3 inst/include/armadillo_bits/mtGlue_meat.hpp | 13 inst/include/armadillo_bits/mtOp_bones.hpp | 5 inst/include/armadillo_bits/mtOp_meat.hpp | 13 inst/include/armadillo_bits/op_cond_meat.hpp | 11 inst/include/armadillo_bits/op_expmat_meat.hpp | 18 inst/include/armadillo_bits/op_inv_gen_meat.hpp | 48 inst/include/armadillo_bits/op_inv_spd_meat.hpp | 8 inst/include/armadillo_bits/op_log_det_meat.hpp | 2 inst/include/armadillo_bits/op_logmat_meat.hpp | 6 inst/include/armadillo_bits/op_pinv_meat.hpp | 12 inst/include/armadillo_bits/op_powmat_meat.hpp | 43 inst/include/armadillo_bits/op_rank_meat.hpp | 12 inst/include/armadillo_bits/op_rcond_meat.hpp | 25 inst/include/armadillo_bits/op_sqrtmat_meat.hpp | 6 inst/include/armadillo_bits/operator_minus.hpp | 102 -- inst/include/armadillo_bits/operator_plus.hpp | 103 -- inst/include/armadillo_bits/subview_bones.hpp | 7 inst/include/armadillo_bits/subview_cube_each_bones.hpp | 3 inst/include/armadillo_bits/subview_each_bones.hpp | 3 inst/include/armadillo_bits/subview_elem1_bones.hpp | 3 inst/include/armadillo_bits/subview_elem1_meat.hpp | 82 - inst/include/armadillo_bits/subview_elem2_bones.hpp | 3 inst/include/armadillo_bits/subview_elem2_meat.hpp | 13 inst/include/armadillo_bits/subview_meat.hpp | 13 inst/include/armadillo_bits/sym_helper.hpp | 148 +-- inst/include/armadillo_bits/traits.hpp | 24 inst/include/armadillo_bits/translate_lapack.hpp | 144 ++ inst/include/armadillo_bits/typedef_elem.hpp | 5 inst/include/armadillo_bits/unwrap.hpp | 12 inst/tinytest/test_rng.R | 3 77 files changed, 1764 insertions(+), 776 deletions(-)
Title: Students' Performance Dataset in Physics Education Research
(SPHERE)
Description: A multidimensional dataset of students' performance assessment in high school physics. The SPHERE dataset was collected from 497 students in four public high schools specifically measuring their conceptual understanding, scientific ability, and attitude toward physics [see Santoso et al. (2024) <doi:10.17632/88d7m2fv7p.1>]. The data collection was conducted using some research based assessments established by the physics education research community. They include the Force Concept Inventory, the Force and Motion Conceptual Evaluation, the Rotational and Rolling Motion Conceptual Survey, the Fluid Mechanics Concept Inventory, the Mechanical Waves Conceptual Survey, the Thermal Concept Evaluation, the Survey of Thermodynamic Processes and First and Second Laws, the Scientific Abilities Assessment Rubrics, and the Colorado Learning Attitudes about Science Survey. Students' attributes related to gender, age, socioeconomic status, domicile, literacy, physics identity, and test results [...truncated...]
Author: Purwoko Haryadi Santoso [aut, cre]
,
Edi Istiyono [ctb],
Haryanto Haryanto [ctb]
Maintainer: Purwoko Haryadi Santoso <purwokoharyadisantoso@unsulbar.ac.id>
Diff between spheredata versions 0.1.1 dated 2024-10-12 and 0.1.2 dated 2024-11-18
DESCRIPTION | 6 +- MD5 | 72 ++++++++++++++++++--------- NAMESPACE | 3 + R/aikenV.R |only R/binary.R | 9 +-- R/lawsheCVR.R |only data/CLASScontentvalidity.rda |only data/FCIcontentvalidity.rda |only data/FMCEcontentvalidity.rda |only data/FMCIcontentvalidity.rda |only data/MWCScontentvalidity.rda |only data/RRMCScontentvalidity.rda |only data/SAAR.rda |binary data/SAARcontentvalidity.rda |only data/STPFASLcontentvalidity.rda |only data/TCEcontentvalidity.rda |only man/CLASS.Rd | 83 ++++++++++++++++---------------- man/CLASScontentvalidity.Rd |only man/FCI.Rd | 69 +++++++++++++------------- man/FCIcontentvalidity.Rd |only man/FCIkey.Rd | 15 ++--- man/FMCE.Rd | 103 ++++++++++++++++++++-------------------- man/FMCEcontentvalidity.Rd |only man/FMCEkey.Rd | 15 ++--- man/FMCI.Rd | 71 ++++++++++++++------------- man/FMCIcontentvalidity.Rd |only man/FMCIkey.Rd | 13 +---- man/MWCS.Rd | 53 ++++++++++---------- man/MWCScontentvalidity.Rd |only man/MWCSkey.Rd | 13 +---- man/RRMCS.Rd | 69 +++++++++++++------------- man/RRMCScontentvalidity.Rd |only man/RRMCSkey.Rd | 15 ++--- man/SAAR.Rd | 41 ++++++++------- man/SAARcontentvalidity.Rd |only man/STPFASL.Rd | 75 +++++++++++++++-------------- man/STPFASLcontentvalidity.Rd |only man/STPFASLkey.Rd | 15 ++--- man/TCE.Rd | 67 ++++++++++++-------------- man/TCEcontentvalidity.Rd |only man/TCEkey.Rd | 15 ++--- man/aikenV.Rd |only man/binary.Rd | 5 + man/demographic.Rd | 11 ++-- man/lawsheCVR.Rd |only man/literacy.Rd | 7 +- man/physicsidentity.Rd | 7 +- man/teachersjudgment.Rd | 7 +- 48 files changed, 448 insertions(+), 411 deletions(-)
Title: Small Area Estimation with Cluster Information for Estimation of
Non-Sampled Areas
Description: Implementation of small area estimation (Fay-Herriot model) with EBLUP (Empirical Best Linear Unbiased Prediction) Approach for non-sampled area estimation by adding cluster information and assuming that there are similarities among particular areas. See also Rao & Molina (2015, ISBN:978-1-118-73578-7) and Anisa et al. (2013) <doi:10.9790/5728-10121519>.
Author: Ridson Al Farizal P [aut, cre, cph]
,
Azka Ubaidillah [aut]
Maintainer: Ridson Al Farizal P <alfrzlp@gmail.com>
Diff between saens versions 0.1.1 dated 2024-10-24 and 0.1.2 dated 2024-11-17
saens-0.1.1/saens/data/milk.rda |only saens-0.1.1/saens/man/milk.Rd |only saens-0.1.2/saens/DESCRIPTION | 6 - saens-0.1.2/saens/MD5 | 23 ++-- saens-0.1.2/saens/NAMESPACE | 43 ++++---- saens-0.1.2/saens/NEWS.md |only saens-0.1.2/saens/R/data.R | 24 ---- saens-0.1.2/saens/R/eblupfh.R | 10 +- saens-0.1.2/saens/R/eblupfh_cluster.R | 153 +++++++++++++++++-------------- saens-0.1.2/saens/R/eblupfh_ns.R |only saens-0.1.2/saens/README.md | 38 ++++++- saens-0.1.2/saens/data/mys.rda |binary saens-0.1.2/saens/man/eblupfh_cluster.Rd | 3 saens-0.1.2/saens/man/eblupfh_ns.Rd |only saens-0.1.2/saens/man/mys.Rd | 2 15 files changed, 167 insertions(+), 135 deletions(-)
Title: Basic Pipe and Open Channel Hydraulics
Description: Functions for basic hydraulic calculations related to
water flow in circular pipes both flowing full (under pressure), and
partially full (gravity flow), and trapezoidal open channels. For
pressure flow this includes friction loss calculations by solving
the Darcy-Weisbach equation for head loss, flow or diameter,
plotting a Moody diagram, matching a pump characteristic curve to a system
curve, and solving for flows in a pipe network using the Hardy-Cross method.
The Darcy-Weisbach friction factor is calculated using the Colebrook
(or Colebrook-White equation), the basis of the Moody diagram, the original
citation being Colebrook (1939) <doi:10.1680/ijoti.1939.13150>. For gravity
flow, the Manning equation is used, again solving for missing parameters.
The derivation of and solutions using the Darcy-Weisbach equation and the
Manning equation are outlined in many fluid mechanics texts such as
Finnemore and Maurer (2024, ISBN:978-1-264-78729-6). Some gradually- and
rapidly-varied f [...truncated...]
Author: Ed Maurer [aut, cre],
Irucka Embry [aut, ctb]
Maintainer: Ed Maurer <emaurer@scu.edu>
Diff between hydraulics versions 0.7.0 dated 2024-03-06 and 0.7.1 dated 2024-11-17
DESCRIPTION | 17 + MD5 | 14 - NEWS.md | 5 R/pumpcurve.R | 2 inst/doc/hydraulics_vignette.R | 33 ++- inst/doc/hydraulics_vignette.Rmd | 33 ++- inst/doc/hydraulics_vignette.html | 387 +++++++++++++++++++------------------- vignettes/hydraulics_vignette.Rmd | 33 ++- 8 files changed, 291 insertions(+), 233 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>, is used to estimate the generalized, variable, and complete persistence models, Mariano et al. (2010) <doi:10.3102/1076998609346967>. These are multiple-membership linear mixed models with teachers modeled as "G-side" effects and students modeled with either "G-side" or "R-side" effects.
Author: Andrew Karl [cre, aut] ,
Yan Yang [aut],
Sharon Lohr [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.1-1 dated 2024-10-15 and 3.1-2 dated 2024-11-17
DESCRIPTION | 12 ++-- MD5 | 10 +-- NAMESPACE | 1 NEWS | 4 + R/bias.test.custom.R | 144 +++++++++++++++++++++++------------------------- man/bias.test.custom.Rd | 48 ++++++++++++---- 6 files changed, 123 insertions(+), 96 deletions(-)
Title: Crew Launcher Plugins for Traditional High-Performance Computing
Clusters
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'crew.cluster' package extends the 'mirai'-powered
'crew' package with worker launcher plugins for traditional
high-performance computing systems.
Inspiration also comes from packages 'mirai' by Gao (2023)
<https://github.com/shikokuchuo/mirai>,
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischl, and Surmann (2017).
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Michael Gilbert Levin [aut] ,
Brendan Furneaux [aut] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew.cluster versions 0.3.2 dated 2024-07-10 and 0.3.3 dated 2024-11-17
DESCRIPTION | 16 - LICENSE.note |only MD5 | 127 +++++---- NAMESPACE | 12 NEWS.md | 10 R/crew_controller_lsf.R | 36 +- R/crew_controller_pbs.R | 38 +- R/crew_controller_sge.R | 38 +- R/crew_controller_slurm.R | 38 +- R/crew_launcher_cluster.R | 221 +++++++--------- R/crew_launcher_lsf.R | 304 ++++++---------------- R/crew_launcher_pbs.R | 336 ++++++------------------- R/crew_launcher_sge.R | 372 ++++++---------------------- R/crew_launcher_slurm.R | 318 +++++++---------------- R/crew_options_cluster.R |only R/crew_options_lsf.R |only R/crew_options_pbs.R |only R/crew_options_sge.R |only R/crew_options_slurm.R |only R/crew_package.R | 2 R/utils_assert.R |only R/utils_options.R |only inst/WORDLIST | 1 man/crew_class_launcher_cluster.Rd | 39 -- man/crew_class_launcher_lsf.Rd | 128 +-------- man/crew_class_launcher_pbs.Rd | 135 +--------- man/crew_class_launcher_sge.Rd | 143 +--------- man/crew_class_launcher_slurm.Rd | 128 +-------- man/crew_class_monitor_cluster.Rd | 3 man/crew_class_monitor_sge.Rd | 3 man/crew_class_monitor_slurm.Rd | 3 man/crew_controller_lsf.Rd | 152 ++++------- man/crew_controller_pbs.Rd | 160 ++++-------- man/crew_controller_sge.Rd | 174 +++++-------- man/crew_controller_slurm.Rd | 153 ++++------- man/crew_launcher_cluster.Rd | 84 +++--- man/crew_launcher_lsf.Rd | 146 ++++------ man/crew_launcher_pbs.Rd | 154 ++++------- man/crew_launcher_sge.Rd | 168 ++++-------- man/crew_launcher_slurm.Rd | 147 ++++------- man/crew_monitor_cluster.Rd | 15 - man/crew_monitor_sge.Rd | 15 - man/crew_monitor_slurm.Rd | 15 - man/crew_options_cluster.Rd |only man/crew_options_lsf.Rd |only man/crew_options_pbs.Rd |only man/crew_options_sge.Rd |only man/crew_options_slurm.Rd |only tests/lsf/minimal.R | 6 tests/lsf/persistent.R | 4 tests/pbs/minimal.R | 6 tests/pbs/persistent.R | 4 tests/sge/minimal.R | 6 tests/sge/monitor.R | 12 tests/sge/persistent.R | 4 tests/sge/retries.R |only tests/slurm/minimal.R | 6 tests/slurm/monitor.R | 12 tests/slurm/persistent.R | 4 tests/testthat/test-crew_controller_lsf.R | 67 +++-- tests/testthat/test-crew_controller_pbs.R | 64 +++- tests/testthat/test-crew_controller_sge.R | 74 ++++- tests/testthat/test-crew_controller_slurm.R | 63 +++- tests/testthat/test-crew_launcher_cluster.R | 124 ++++++--- tests/testthat/test-crew_launcher_lsf.R | 50 ++- tests/testthat/test-crew_launcher_pbs.R | 64 ++-- tests/testthat/test-crew_launcher_sge.R | 76 ++--- tests/testthat/test-crew_launcher_slurm.R | 48 ++- tests/testthat/test-crew_options_cluster.R |only tests/testthat/test-crew_options_lsf.R |only tests/testthat/test-crew_options_pbs.R |only tests/testthat/test-crew_options_sge.R |only tests/testthat/test-crew_options_slurm.R |only tests/testthat/test-utils_assert.R |only tests/testthat/test-utils_options.R |only 75 files changed, 1735 insertions(+), 2793 deletions(-)
Title: A Crew Launcher Plugin for AWS Batch
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'crew.aws.batch' package extends the 'mirai'-powered
'crew' package with a worker launcher plugin for AWS Batch.
Inspiration also comes from packages 'mirai' by Gao (2023)
<https://github.com/shikokuchuo/mirai>,
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischl, and Surmann (2017).
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew.aws.batch versions 0.0.6 dated 2024-07-10 and 0.0.7 dated 2024-11-17
crew.aws.batch-0.0.6/crew.aws.batch/R/utils_aws_batch.R |only crew.aws.batch-0.0.7/crew.aws.batch/DESCRIPTION | 14 crew.aws.batch-0.0.7/crew.aws.batch/MD5 | 47 - crew.aws.batch-0.0.7/crew.aws.batch/NAMESPACE | 2 crew.aws.batch-0.0.7/crew.aws.batch/NEWS.md | 13 crew.aws.batch-0.0.7/crew.aws.batch/R/crew_controller_aws_batch.R | 20 crew.aws.batch-0.0.7/crew.aws.batch/R/crew_definition_aws_batch.R | 12 crew.aws.batch-0.0.7/crew.aws.batch/R/crew_launcher_aws_batch.R | 458 +++------- crew.aws.batch-0.0.7/crew.aws.batch/R/crew_monitor_aws_batch.R | 21 crew.aws.batch-0.0.7/crew.aws.batch/R/crew_options_aws_batch.R |only crew.aws.batch-0.0.7/crew.aws.batch/R/utils_assert.R |only crew.aws.batch-0.0.7/crew.aws.batch/R/utils_logic.R | 4 crew.aws.batch-0.0.7/crew.aws.batch/R/utils_options.R |only crew.aws.batch-0.0.7/crew.aws.batch/inst/WORDLIST | 2 crew.aws.batch-0.0.7/crew.aws.batch/man/crew_aws_batch_job_name.Rd |only crew.aws.batch-0.0.7/crew.aws.batch/man/crew_class_definition_aws_batch.Rd | 16 crew.aws.batch-0.0.7/crew.aws.batch/man/crew_class_launcher_aws_batch.Rd | 88 - crew.aws.batch-0.0.7/crew.aws.batch/man/crew_class_monitor_aws_batch.Rd | 11 crew.aws.batch-0.0.7/crew.aws.batch/man/crew_controller_aws_batch.Rd | 175 +-- crew.aws.batch-0.0.7/crew.aws.batch/man/crew_launcher_aws_batch.Rd | 175 +-- crew.aws.batch-0.0.7/crew.aws.batch/man/crew_options_aws_batch.Rd |only crew.aws.batch-0.0.7/crew.aws.batch/tests/definition/test-definition.R | 2 crew.aws.batch-0.0.7/crew.aws.batch/tests/monitor/test-monitor.R | 2 crew.aws.batch-0.0.7/crew.aws.batch/tests/testthat/test-crew_controller_aws_batch.R | 108 ++ crew.aws.batch-0.0.7/crew.aws.batch/tests/testthat/test-crew_launcher_aws_batch.R | 66 + crew.aws.batch-0.0.7/crew.aws.batch/tests/testthat/test-crew_options_aws_batch.R |only crew.aws.batch-0.0.7/crew.aws.batch/tests/testthat/test-utils_assert.R |only crew.aws.batch-0.0.7/crew.aws.batch/tests/testthat/test-utils_logic.R | 8 crew.aws.batch-0.0.7/crew.aws.batch/tests/testthat/test-utils_options.R |only 29 files changed, 587 insertions(+), 657 deletions(-)
More information about crew.aws.batch at CRAN
Permanent link
Title: Auto Visual Inference with Computer Vision Models
Description: Provides automated visual inference of residual plots using computer vision models, facilitating diagnostic checks for classical normal linear regression models.
Author: Weihao Li [aut, cre, cph]
Maintainer: Weihao Li <llreczx@gmail.com>
Diff between autovi versions 0.4.0 dated 2024-06-25 and 0.4.1 dated 2024-11-17
autovi-0.4.0/autovi/man/AUTO_VI-cash-select_feature.Rd |only autovi-0.4.1/autovi/DESCRIPTION | 6 autovi-0.4.1/autovi/MD5 | 35 +- autovi-0.4.1/autovi/NAMESPACE | 1 autovi-0.4.1/autovi/NEWS.md |only autovi-0.4.1/autovi/R/auto_visual_inference.R | 249 +++++++++++---- autovi-0.4.1/autovi/R/get_keras_model.R | 123 +++++++ autovi-0.4.1/autovi/R/utils.R | 21 - autovi-0.4.1/autovi/R/zzz_auto_visual_inference.R | 278 +++++++++++++---- autovi-0.4.1/autovi/README.md | 6 autovi-0.4.1/autovi/man/AUTO_VI-cash-boot_method.Rd |only autovi-0.4.1/autovi/man/AUTO_VI-cash-boot_vss.Rd | 5 autovi-0.4.1/autovi/man/AUTO_VI-cash-check.Rd | 4 autovi-0.4.1/autovi/man/AUTO_VI-cash-feature_pca.Rd | 16 autovi-0.4.1/autovi/man/AUTO_VI-cash-p_value.Rd | 21 - autovi-0.4.1/autovi/man/AUTO_VI-cash-plot_lineup.Rd |only autovi-0.4.1/autovi/man/AUTO_VI-cash-plot_pair.Rd |only autovi-0.4.1/autovi/man/AUTO_VI-cash-save_plot.Rd |only autovi-0.4.1/autovi/man/AUTO_VI-cash-summary.Rd |only autovi-0.4.1/autovi/man/AUTO_VI.Rd | 22 + autovi-0.4.1/autovi/man/get_keras_model.Rd | 18 - autovi-0.4.1/autovi/man/save_plot.Rd | 8 22 files changed, 625 insertions(+), 188 deletions(-)
Title: R Functions to Download and Clean Brazilian Electoral Data
Description: Offers a set of functions to easily download and clean
Brazilian electoral data from the Superior Electoral Court and 'CepespData' websites.
Among other features, the package retrieves data on local and
federal elections for all positions (city councilor, mayor, state deputy,
federal deputy, governor, and president) aggregated by
state, city, and electoral zones.
Author: Denisson Silva [aut, cre],
Fernando Meireles [aut],
Beatriz Costa [ctb]
Maintainer: Denisson Silva <denissoncsol@gmail.com>
Diff between electionsBR versions 0.4.0 dated 2024-02-05 and 0.5.0 dated 2024-11-17
DESCRIPTION | 14 MD5 | 156 ++--- NAMESPACE | 52 - NEWS.md | 146 ++-- R/candidate.R | 162 ++--- R/candidate_add_infor.R |only R/candidate_fed.R | 104 +-- R/candidate_local.R | 96 +-- R/details_mun_zone.R | 154 ++--- R/details_mun_zone_fed.R | 104 +-- R/details_mun_zone_local.R | 98 +-- R/electionsBR.R | 24 R/elections_cepesp.R | 164 ++--- R/elections_tse.R | 364 ++++++------ R/electionsbr_rda.R | 74 +- R/legend_fed.R | 104 +-- R/legend_local.R | 96 +-- R/legends.R | 158 ++--- R/party_mun_zone.R | 156 ++--- R/party_mun_zone_fed.R | 106 +-- R/party_mun_zone_local.R | 96 +-- R/personal_finances.R | 146 ++-- R/personal_finances_fed.R | 98 +-- R/personal_finances_local.R | 88 +-- R/pipe.R | 16 R/seats.R | 152 ++--- R/seats_fed.R | 106 +-- R/seats_local.R | 96 +-- R/social_media.R | 131 ++-- R/utils.R | 604 ++++++++++---------- R/vote_mun_zone.R | 152 ++--- R/vote_mun_zone_fed.R | 112 +-- R/vote_mun_zone_local.R | 162 ++--- R/vote_section.R | 140 ++-- R/vote_section_fed.R | 92 +-- R/vote_section_local.R | 94 +-- R/voter_profile.R | 156 ++--- R/voter_profile_by_section.R | 167 ++--- README.md | 220 +++---- build/vignette.rds |binary inst/CITATION | 24 inst/doc/introduction.R | 108 +-- inst/doc/introduction.Rmd | 357 ++++++------ inst/doc/introduction.html | 1169 +++++++++++++++++++--------------------- man/candidate.Rd | 104 +-- man/candidate_add_infor.Rd |only man/candidate_fed.Rd | 98 +-- man/candidate_local.Rd | 78 +- man/details_mun_zone.Rd | 104 +-- man/details_mun_zone_fed.Rd | 98 +-- man/details_mun_zone_local.Rd | 78 +- man/electionsBR-package.Rd | 56 - man/elections_cepesp.Rd | 62 +- man/elections_rda.Rd | 56 - man/elections_tse.Rd | 157 ++--- man/legend_fed.Rd | 98 +-- man/legend_local.Rd | 72 +- man/legends.Rd | 104 +-- man/parties_br.Rd | 40 - man/party_mun_zone.Rd | 104 +-- man/party_mun_zone_fed.Rd | 98 +-- man/party_mun_zone_local.Rd | 78 +- man/personal_finances.Rd | 98 +-- man/personal_finances_fed.Rd | 92 +-- man/personal_finances_local.Rd | 74 +- man/pipe.Rd | 24 man/seats.Rd | 104 +-- man/seats_fed.Rd | 98 +-- man/seats_local.Rd | 78 +- man/social_media.Rd | 68 +- man/uf_br.Rd | 22 man/vote_mun_zone.Rd | 104 +-- man/vote_mun_zone_fed.Rd | 104 +-- man/vote_mun_zone_local.Rd | 168 ++--- man/vote_section.Rd | 94 +-- man/vote_section_fed.Rd | 78 +- man/vote_section_local.Rd | 78 +- man/voter_profile.Rd | 72 +- man/voter_profile_by_section.Rd | 85 +- vignettes/introduction.Rmd | 357 ++++++------ 80 files changed, 5065 insertions(+), 5036 deletions(-)
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 [aut, cre, cph]
Maintainer: Stilianos Louca <louca.research@gmail.com>
Diff between castor versions 1.8.2 dated 2024-06-29 and 1.8.3 dated 2024-11-17
DESCRIPTION | 13 +++++++------ MD5 | 8 +++++--- NAMESPACE | 1 + R/auxiliary_routines.R | 22 ---------------------- R/read_fasta.R |only man/read_fasta.Rd |only 6 files changed, 13 insertions(+), 31 deletions(-)
Title: Truncated Positive Normal Model and Extensions
Description: Provide data generation and estimation tools for the truncated positive normal (tpn)
model discussed in Gomez, Olmos, Varela and Bolfarine (2018)
<doi:10.1007/s11766-018-3354-x>, the slash tpn distribution discussed in Gomez,
Gallardo and Santoro (2021) <doi:10.3390/sym13112164>, the bimodal tpn distribution
discussed in Gomez et al. (2022) <doi:10.3390/sym14040665> and the flexible tpn model.
Author: Diego Gallardo [aut, cre],
Hector J. Gomez [aut],
Yolanda M. Gomez [aut]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>
Diff between tpn versions 1.8 dated 2023-12-10 and 1.9 dated 2024-11-17
DESCRIPTION | 8 ++++---- INDEX | 2 ++ MD5 | 20 +++++++++++++------- NAMESPACE | 4 ++-- NEWS.md | 10 ++++++++++ R/dtpt.R |only R/est.tpt.R |only R/est.utpn.R | 29 ++++++----------------------- R/ptpt.R |only R/rtpn.R | 2 ++ R/rtpt.R |only man/est.tpt.Rd |only man/tpn.Rd | 2 +- man/tpt.Rd |only 14 files changed, 40 insertions(+), 37 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine and for various extensions in a recent version is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 2.3.7 dated 2024-05-27 and 2.3.8 dated 2024-11-17
DESCRIPTION | 14 MD5 | 40 NAMESPACE | 1 NEWS.md | 22 R/import-standalone-check_suggested.R | 10 R/initExtension.R | 13 inst/doc/RSQLite.html | 46 man/SQLite.Rd | 2 man/SQLiteConnection-class.Rd | 2 man/SQLiteDriver-class.Rd | 6 man/SQLiteResult-class.Rd | 4 man/initExtension.Rd | 13 man/keywords-dep.Rd | 2 man/query-dep.Rd | 4 src/SqliteResultImpl.cpp | 2 src/ext-uuid.c |only src/vendor/extensions/series.c | 256 - src/vendor/extensions/uuid.c |only src/vendor/sqlite3/sqlite3.c | 8415 ++++++++++++++++++++++------------ src/vendor/sqlite3/sqlite3.h | 193 tests/testthat/setup.R |only tests/testthat/test-dbSendQuery.R | 16 tests/testthat/test-uuid.R |only 23 files changed, 6116 insertions(+), 2945 deletions(-)
Title: An Automatic Suite for Estimation of Various Effect Size
Measures
Description: Automatically estimate 11 effect size measures from a well-formatted dataset. Various other functions can help, for example, removing dependency between several effect sizes, or identifying differences between two datasets.
This package is mainly designed to assist in conducting a systematic review with a meta-analysis but can be useful to any researcher interested in estimating an effect size.
Author: Corentin J. Gosling [aut, cre],
Samuele Cortese [aut],
Marco Solmi [aut],
Belen Haza [aut],
Eduard Vieta [aut],
Richard Delorme [aut],
Paolo Fusar-Poli [aut],
Joaquim Radua [aut]
Maintainer: Corentin J. Gosling <corentin.gosling@parisnanterre.fr>
Diff between metaConvert versions 1.0.1 dated 2024-10-26 and 1.0.2 dated 2024-11-17
DESCRIPTION | 8 MD5 | 26 +- NAMESPACE | 2 NEWS.md | 9 R/data_extraction.R | 4 R/es_from_stand_COR.R | 2 R/metaConvert.R | 2 R/zzz.R | 78 ++++++ README.md | 20 + inst/doc/Tutorial.R | 9 inst/doc/Tutorial.Rmd | 13 - inst/doc/Tutorial.html | 550 +++++++++++++++++++++++++++++++++++++++++++++++-- man/see_input_data.Rd | 2 vignettes/Tutorial.Rmd | 13 - 14 files changed, 675 insertions(+), 63 deletions(-)
Title: Sensitivity Analysis for Irregular Assessment Times
Description: Sensitivity analysis for trials with irregular and informative
assessment times, based on a new influence function-based, augmented
inverse intensity-weighted estimator.
Author: Andrew Redd [aut, cre] ,
Yujing Gao [aut],
Shu Yang [aut],
Bonnie Smith [aut],
Agatha Mallett [ctb, ctr],
Daniel Scharfstein [pdr, aut] ,
University of Utah [cph]
Maintainer: Andrew Redd <andrew.redd@hsc.utah.edu>
Diff between SensIAT versions 0.1.0 dated 2024-11-01 and 0.1.1 dated 2024-11-17
DESCRIPTION | 6 - MD5 | 10 +- NEWS.md | 14 ++- R/jackknife.R | 156 +++++++++++++++++++------------------- src/common.h | 2 tests/testthat/test-splinebasis.R | 34 ++++---- 6 files changed, 113 insertions(+), 109 deletions(-)
Title: An API Wrapper for 'DAWA' - 'The Danish Address Web API'
Description: Functions for interacting with all sections of
the official 'Danish Address Web API' (also known as 'DAWA')
<https://api.dataforsyningen.dk>. The development of this package is
completely independent from the government agency, Klimadatastyrelsen,
who maintains the API.
Author: Aleksander Bang-Larsen [aut, cre, cph]
Maintainer: Aleksander Bang-Larsen <contact@aleksanderbl.dk>
Diff between dawaR versions 0.2.3 dated 2024-10-31 and 0.2.4 dated 2024-11-17
DESCRIPTION | 6 - MD5 | 18 ++--- NEWS.md | 5 + R/utils.R | 6 + README.md | 9 ++ build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/dawaR.html | 5 + inst/doc/renv-issues.R | 38 +++++----- tests/testthat/_snaps/get_data.md | 134 +++++++++++++++++++------------------- 10 files changed, 123 insertions(+), 101 deletions(-)
Title: Collection of Utility Functions
Description: A handy collection of utility functions designed to aid in
package development, plotting and scientific research. Package
development functionalities includes among others tools such as
cross-referencing package imports with the description file, analysis
of redundant package imports, editing of the description file and the
creation of package badges for GitHub. Some of the other
functionalities include automatic package installation and loading,
plotting points without overlap, creating nice breaks for plots,
overview tables and many more handy utility functions.
Author: H.G. van den Boorn [aut, cre]
Maintainer: H.G. van den Boorn <hvdboorn@gmail.com>
Diff between hgutils versions 0.2.11 dated 2022-03-31 and 0.2.13 dated 2024-11-17
DESCRIPTION | 12 ++++++------ MD5 | 37 +++++++++++++++++++------------------ NAMESPACE | 2 +- NEWS | 1 + R/description-utils.R | 4 ++-- R/flowchart-utils.R | 2 +- R/loading-animations.R | 21 +++++++++++++-------- R/misc-utils.R | 27 ++++++++++++++++++++++++++- R/plot-utils.R | 8 -------- R/table-utils.R | 1 + README.md | 6 +++--- man/add_badges.Rd | 2 +- man/create_text_table.Rd | 3 ++- man/default.Rd |only man/get_breaks.Rd | 9 --------- man/startup.Rd | 5 ++++- man/wrap_text_table.Rd | 6 +++--- tests/testthat/DESCRIPTION | 2 +- tests/testthat/test-plot-utils.R | 6 +++--- tools/build_package.R | 18 ++++++++++-------- 20 files changed, 97 insertions(+), 75 deletions(-)
Title: Knock Errors Off Nice Guesses
Description: Miscellaneous functions and data used in Qingyao's psychological research and teaching. Keng currently has a built-in dataset depress, and could (1) scale a vector, (2) test the significance and compute the cut-off values of Pearson's r without raw data, (3) compare lm()'s fitted outputs using R-squared and PRE (Proportional Reduction in Error, also called partial R-squared or partial Eta-squared).
Author: Qingyao Zhang [aut, cre]
Maintainer: Qingyao Zhang <qingyaozhang@outlook.com>
Diff between Keng versions 2024.11.02 dated 2024-11-04 and 2024.11.17 dated 2024-11-17
DESCRIPTION | 13 +++++++----- MD5 | 28 ++++++++++++++++++++------ NAMESPACE | 1 NEWS.md |only R/Scale.R |only R/compare_lm.R | 41 +++++++++++++++++++-------------------- R/data.R |only README.md | 19 ++++++++++++++---- build |only data |only inst |only man/Scale.Rd |only man/compare_lm.Rd | 6 ++--- man/depress.Rd |only tests/testthat/test-Scale.R |only tests/testthat/test-compare_lm.R | 8 +++---- vignettes |only 17 files changed, 73 insertions(+), 43 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 13. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood est [...truncated...]
Author: Anthony Hammond [aut, cre]
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.3.7 dated 2024-09-20 and 0.3.8 dated 2024-11-17
UKFE-0.3.7/UKFE/R/RainAPI.R |only UKFE-0.3.7/UKFE/man/AMextract.Rd |only UKFE-0.3.7/UKFE/man/GetFlowStage_EA.Rd |only UKFE-0.3.7/UKFE/man/GetMetOffice.Rd |only UKFE-0.3.7/UKFE/man/GetNRFA.Rd |only UKFE-0.3.7/UKFE/man/GetRainEA.Rd |only UKFE-0.3.7/UKFE/man/GetRainSEPA.Rd |only UKFE-0.3.7/UKFE/man/GridRefConvert.Rd |only UKFE-0.3.7/UKFE/man/Lmoms.Rd |only UKFE-0.3.7/UKFE/man/UncSS.Rd |only UKFE-0.3.8/UKFE/DESCRIPTION | 6 UKFE-0.3.8/UKFE/MD5 | 56 - UKFE-0.3.8/UKFE/R/All.R | 912 +++++++++++++------------------ UKFE-0.3.8/UKFE/R/FlowAnalysis.R |only UKFE-0.3.8/UKFE/R/GISfuncs.R | 56 + UKFE-0.3.8/UKFE/R/GetData.R |only UKFE-0.3.8/UKFE/man/AMplot.Rd | 4 UKFE-0.3.8/UKFE/man/AnnualStat.Rd |only UKFE-0.3.8/UKFE/man/Bootstrap.Rd |only UKFE-0.3.8/UKFE/man/ConvertGridRef.Rd |only UKFE-0.3.8/UKFE/man/DesHydro.Rd | 47 - UKFE-0.3.8/UKFE/man/ERPlot.Rd | 6 UKFE-0.3.8/UKFE/man/EVPlotAdd.Rd | 4 UKFE-0.3.8/UKFE/man/FlowDurationCurve.Rd |only UKFE-0.3.8/UKFE/man/GEVPars.Rd | 4 UKFE-0.3.8/UKFE/man/GenLogPars.Rd | 4 UKFE-0.3.8/UKFE/man/GenParetoPars.Rd | 4 UKFE-0.3.8/UKFE/man/GetCDs.Rd | 2 UKFE-0.3.8/UKFE/man/GetDataEA_QH.Rd |only UKFE-0.3.8/UKFE/man/GetDataEA_Rain.Rd |only UKFE-0.3.8/UKFE/man/GetDataMetOffice.Rd |only UKFE-0.3.8/UKFE/man/GetDataNRFA.Rd |only UKFE-0.3.8/UKFE/man/GetDataSEPA_Rain.Rd |only UKFE-0.3.8/UKFE/man/GumbelPars.Rd | 2 UKFE-0.3.8/UKFE/man/HydroPlot.Rd | 7 UKFE-0.3.8/UKFE/man/Kappa3Pars.Rd | 2 UKFE-0.3.8/UKFE/man/LMoments.Rd |only UKFE-0.3.8/UKFE/man/LRatioChange.Rd | 2 UKFE-0.3.8/UKFE/man/MonthlyStats.Rd | 21 UKFE-0.3.8/UKFE/man/Uncertainty.Rd | 55 + 40 files changed, 563 insertions(+), 631 deletions(-)
Title: Standard and User-Defined RGB Color Spaces, with Conversion
Between RGB and CIE XYZ and Lab
Description: Standard RGB spaces included are sRGB, 'Adobe' RGB, 'ProPhoto' RGB, BT.709, and others. User-defined RGB spaces are also possible. There is partial support for ACES Color workflows.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesRGB versions 1.5-0 dated 2024-01-23 and 1.6-1 dated 2024-11-17
DESCRIPTION | 15 MD5 | 32 - NAMESPACE | 4 NEWS.md | 8 R/OETFs.R | 41 +- R/conversion.R | 80 ++++ build/vignette.rds |binary inst/doc/spacesRGB-guide.R | 2 inst/doc/spacesRGB-guide.Rmd | 2 inst/doc/spacesRGB-guide.html | 763 ++++++++++++++++++++++++++++++------------ man/OOTF.Rd | 2 man/PODT.Rd | 2 man/RGBfromXYZ.Rd | 41 +- man/XYZfromRGB.Rd | 58 ++- tests/test-conversions.R | 43 ++ vignettes/bibliography.bib | 2 vignettes/spacesRGB-guide.Rmd | 2 17 files changed, 815 insertions(+), 282 deletions(-)
Title: Fit Sparse Linear Regression Models via Nonconvex Optimization
Description: Efficient procedure for fitting regularization paths between L1 and L0, using the MC+ penalty of Zhang, C.H. (2010)<doi:10.1214/09-AOS729>. Implements the methodology described in Mazumder, Friedman and Hastie (2011) <DOI: 10.1198/jasa.2011.tm09738>. Sparsenet computes the regularization surface over both the family parameter and the tuning parameter by coordinate descent.
Author: Trevor Hastie [aut, cre],
Rahul Mazumder [aut],
Jerome Friedman [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between sparsenet versions 1.6 dated 2024-02-05 and 1.7 dated 2024-11-16
DESCRIPTION | 27 +++++++++++++++++++-------- MD5 | 8 ++++---- NAMESPACE | 2 +- R/sparsenet.R | 20 ++++++++++++++------ man/sparsenet.Rd | 4 +++- 5 files changed, 41 insertions(+), 20 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 <b@bxc.dk>
Diff between Epi versions 2.56 dated 2024-10-01 and 2.57 dated 2024-11-16
CHANGES | 7 DESCRIPTION | 8 MD5 | 53 +- NAMESPACE | 3 R/lexis.R | 32 - R/mod.Lexis.R | 75 +-- build/vignette.rds |binary inst/doc/addLexis.pdf |binary inst/doc/addLexis.rnw | 2 inst/doc/crisk.R | 114 +++-- inst/doc/crisk.pdf |binary inst/doc/crisk.rnw | 42 +- inst/doc/flup.R | 329 +++++++-------- inst/doc/flup.pdf |binary inst/doc/flup.rnw | 912 +++++++++++++++++++++++--------------------- inst/doc/simLexis.pdf |binary inst/doc/simLexis.rnw | 2 inst/doc/yll.pdf |binary inst/doc/yll.rnw | 2 man/Lexis.Rd | 2 man/mod.Lexis.Rd | 40 + vignettes/Wilhelm_Lexis.jpg |only vignettes/addLexis.rnw | 2 vignettes/crisk.rnw | 42 +- vignettes/flup.rnw | 912 +++++++++++++++++++++++--------------------- vignettes/simLexis.rnw | 2 vignettes/topreport.tex | 24 + vignettes/yll.rnw | 2 28 files changed, 1415 insertions(+), 1192 deletions(-)
Title: Linear Discriminant Function and Canonical Correlation Analysis
Description: Produces SPSS- and SAS-like output for linear discriminant
function analysis and canonical correlation analysis. The methods are described in
Manly & Alberto (2017, ISBN:9781498728966),
Rencher (2002, ISBN:0-471-41889-7), and
Tabachnik & Fidell (2019, ISBN:9780134790541).
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between DFA.CANCOR versions 0.2.8 dated 2023-06-29 and 0.3.6 dated 2024-11-16
DFA.CANCOR-0.2.8/DFA.CANCOR/R/boc.R |only DFA.CANCOR-0.2.8/DFA.CANCOR/R/steiger.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/DESCRIPTION | 17 +- DFA.CANCOR-0.3.6/DFA.CANCOR/MD5 | 21 ++- DFA.CANCOR-0.3.6/DFA.CANCOR/NAMESPACE | 25 ++-- DFA.CANCOR-0.3.6/DFA.CANCOR/R/DFA.R | 9 - DFA.CANCOR-0.3.6/DFA.CANCOR/R/GROUP.PROFILES.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/R/NORMALITY.R | 132 ++++++++++++---------- DFA.CANCOR-0.3.6/DFA.CANCOR/R/OUTLIERS.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/R/onAttach.R | 1 DFA.CANCOR-0.3.6/DFA.CANCOR/R/umvn.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/R/utilities_boc.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/R/utilities_steiger.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/man/GROUP.PROFILES.Rd |only DFA.CANCOR-0.3.6/DFA.CANCOR/man/NORMALITY.Rd | 35 +++-- DFA.CANCOR-0.3.6/DFA.CANCOR/man/OUTLIERS.Rd |only 16 files changed, 145 insertions(+), 95 deletions(-)
Title: Bayesian Spatial Analysis
Description: For spatial data analysis; provides exploratory spatial analysis tools, spatial regression, spatial econometric, and disease mapping models, model diagnostics, and special methods for inference with small area survey data (e.g., the America Community Survey (ACS)) and censored population health monitoring data. Models are pre-specified using the Stan programming language, a platform for Bayesian inference using Markov chain Monte Carlo (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022) <doi:10.21105/joss.04716>; Donegan, Chun and Hughes (2020) <doi:10.1016/j.spasta.2020.100450>; Donegan, Chun and Griffith (2021) <doi:10.3390/ijerph18136856>; Morris et al. (2019) <doi:10.1016/j.sste.2019.100301>.
Author: Connor Donegan [aut, cre] ,
Mitzi Morris [ctb],
Amy Tims [ctb]
Maintainer: Connor Donegan <connor.donegan@gmail.com>
Diff between geostan versions 0.7.0 dated 2024-09-18 and 0.8.0 dated 2024-11-16
geostan-0.7.0/geostan/inst/stan/parts/trans_params_expression_car.stan |only geostan-0.7.0/geostan/tests/testthat/test-information-criteria.R |only geostan-0.8.0/geostan/DESCRIPTION | 16 geostan-0.8.0/geostan/MD5 | 135 geostan-0.8.0/geostan/NAMESPACE | 7 geostan-0.8.0/geostan/NEWS.md | 18 geostan-0.8.0/geostan/R/convenience-functions.R | 215 geostan-0.8.0/geostan/R/geostan_fit-methods.R | 256 geostan-0.8.0/geostan/R/impacts.R |only geostan-0.8.0/geostan/R/information-criteria.R | 4 geostan-0.8.0/geostan/R/internal-functions.R | 80 geostan-0.8.0/geostan/R/moran.R | 15 geostan-0.8.0/geostan/R/posterior_predict.R | 181 geostan-0.8.0/geostan/R/stan_car.R | 180 geostan-0.8.0/geostan/R/stan_esf.R | 29 geostan-0.8.0/geostan/R/stan_glm.R | 124 geostan-0.8.0/geostan/R/stan_icar.R | 19 geostan-0.8.0/geostan/R/stan_sar.R | 305 geostan-0.8.0/geostan/README.md | 236 geostan-0.8.0/geostan/build/vignette.rds |binary geostan-0.8.0/geostan/inst/doc/custom-spatial-models.R | 78 geostan-0.8.0/geostan/inst/doc/custom-spatial-models.Rmd | 236 geostan-0.8.0/geostan/inst/doc/custom-spatial-models.html | 311 geostan-0.8.0/geostan/inst/doc/measuring-sa.Rmd | 22 geostan-0.8.0/geostan/inst/doc/measuring-sa.html | 66 geostan-0.8.0/geostan/inst/doc/raster-regression.R | 48 geostan-0.8.0/geostan/inst/doc/raster-regression.Rmd | 81 geostan-0.8.0/geostan/inst/doc/raster-regression.html | 189 geostan-0.8.0/geostan/inst/doc/spatial-analysis.R |only geostan-0.8.0/geostan/inst/doc/spatial-analysis.Rmd |only geostan-0.8.0/geostan/inst/doc/spatial-analysis.html |only geostan-0.8.0/geostan/inst/doc/spatial-me-models.R | 2 geostan-0.8.0/geostan/inst/doc/spatial-me-models.Rmd | 68 geostan-0.8.0/geostan/inst/doc/spatial-me-models.html | 317 geostan-0.8.0/geostan/inst/doc/spatial-weights-matrix.html | 77 geostan-0.8.0/geostan/inst/stan/foundation.stan | 44 geostan-0.8.0/geostan/inst/stan/parts/data.stan | 5 geostan-0.8.0/geostan/inst/stan/parts/model.stan | 151 geostan-0.8.0/geostan/inst/stan/parts/params.stan | 9 geostan-0.8.0/geostan/inst/stan/parts/priors.stan | 92 geostan-0.8.0/geostan/inst/stan/parts/trans_data.stan | 26 geostan-0.8.0/geostan/inst/stan/parts/trans_params_declaration.stan | 6 geostan-0.8.0/geostan/inst/stan/parts/trans_params_expression_auto-model.stan | 69 geostan-0.8.0/geostan/man/figures/README-unnamed-chunk-3-1.png |binary geostan-0.8.0/geostan/man/figures/README-unnamed-chunk-5-1.png |binary geostan-0.8.0/geostan/man/figures/README-unnamed-chunk-8-1.png |only geostan-0.8.0/geostan/man/figures/README-unnamed-chunk-9-1.png |only geostan-0.8.0/geostan/man/impacts.Rd |only geostan-0.8.0/geostan/man/posterior_predict.Rd | 52 geostan-0.8.0/geostan/man/predict.geostan_fit.Rd | 89 geostan-0.8.0/geostan/man/row_standardize.Rd | 7 geostan-0.8.0/geostan/man/shape2mat.Rd | 2 geostan-0.8.0/geostan/man/sim_sar.Rd | 78 geostan-0.8.0/geostan/man/sp_diag.Rd | 2 geostan-0.8.0/geostan/man/stan_car.Rd | 110 geostan-0.8.0/geostan/man/stan_esf.Rd | 6 geostan-0.8.0/geostan/man/stan_glm.Rd | 106 geostan-0.8.0/geostan/man/stan_icar.Rd | 4 geostan-0.8.0/geostan/man/stan_sar.Rd | 203 geostan-0.8.0/geostan/src/stanExports_foundation.h | 3791 +++++----- geostan-0.8.0/geostan/tests/check-ME-estimates-monte-carlo-output.csv |only geostan-0.8.0/geostan/tests/check-ME-estimates-monte-carlo.R |only geostan-0.8.0/geostan/tests/check-SEM-CAR-GLM-estimates-monte-carlo-output.csv |only geostan-0.8.0/geostan/tests/check-SEM-CAR-GLM-estimates-monte-carlo.R |only geostan-0.8.0/geostan/tests/check-SLM-estimates-monte-carlo-output.csv |only geostan-0.8.0/geostan/tests/check-SLM-estimates-monte-carlo.R |only geostan-0.8.0/geostan/tests/missing-y.R |only geostan-0.8.0/geostan/tests/model-comparison.R |only geostan-0.8.0/geostan/tests/testthat/test-stan-glm.R | 2 geostan-0.8.0/geostan/tests/testthat/test-stan-sar.R | 40 geostan-0.8.0/geostan/vignettes/autonormal.stan |only geostan-0.8.0/geostan/vignettes/car_poisson.stan |only geostan-0.8.0/geostan/vignettes/custom-spatial-models.Rmd | 236 geostan-0.8.0/geostan/vignettes/measuring-sa.Rmd | 22 geostan-0.8.0/geostan/vignettes/raster-regression.Rmd | 81 geostan-0.8.0/geostan/vignettes/spatial-analysis.Rmd |only geostan-0.8.0/geostan/vignettes/spatial-analysis.bib |only geostan-0.8.0/geostan/vignettes/spatial-me-models.Rmd | 68 geostan-0.8.0/geostan/vignettes/wcar-lpdf.stan | 30 79 files changed, 5433 insertions(+), 3213 deletions(-)
Title: Cox Model for Case-Cohort Data with Stratified
Subcohort-Selection
Description: Contains a function, also called 'cchs', that calculates Estimator III of Borgan et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
Author: E. Jones [aut, cre]
Maintainer: E. Jones <edmundjones79@gmail.com>
Diff between cchs versions 0.4.4 dated 2024-01-31 and 0.4.5 dated 2024-11-16
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- build/partial.rdb |binary man/cchs.Rd | 18 +++++++++--------- man/cchsData.Rd | 6 +++--- 5 files changed, 22 insertions(+), 21 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 1.3.12 dated 2024-10-28 and 1.3.14 dated 2024-11-16
DESCRIPTION | 6 ++-- MD5 | 45 ++++++++++++++++----------------- NAMESPACE | 3 +- NEWS.md | 19 ++++++++++++++ R/convertScene.R | 61 ++++++++++++++++++++++++++++++++++++++++++++- R/r3d.rgl.R | 15 +++++++++-- R/scene.R | 5 ++- inst/doc/WebGL.R | 8 ++--- inst/doc/WebGL.html | 34 ++++++++++++------------- inst/doc/demos.html | 60 ++++++++++++++++++++++---------------------- inst/doc/deprecation.html | 2 - inst/doc/pkgdown.R | 2 - inst/doc/pkgdown.html | 6 ++-- inst/doc/rgl.R | 30 +++++++++++----------- inst/doc/rgl.html | 38 ++++++++++++++-------------- inst/doc/transparency.html | 18 ++++++------- man/axes3d.Rd | 26 +++++++++++-------- man/persp3d.function.Rd | 4 +- man/rgl.incrementID.Rd |only man/setAxisCallbacks.Rd | 2 - src/api.cpp | 7 +++++ src/api.h | 2 + src/init.cpp | 2 + src/subscene.cpp | 8 +---- 24 files changed, 254 insertions(+), 149 deletions(-)
Title: Identify and Correct Invalid HGNC Human Gene Symbols and MGI
Mouse Gene Symbols
Description: Contains functions for
identifying and correcting HGNC human gene symbols and MGI mouse gene symbols
which have been converted to date format by Excel, withdrawn, or aliased.
Also contains functions for reversibly converting between HGNC
symbols and valid R names.
Author: Sehyun Oh [aut],
Ayush Aggarwal [aut],
Markus Riester [aut],
Levi Waldron [aut, cre]
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Diff between HGNChelper versions 0.8.14 dated 2024-05-18 and 0.8.15 dated 2024-11-16
DESCRIPTION | 10 +-- MD5 | 22 +++---- NEWS | 7 +- R/data.R | 2 R/getCurrentMaps.R | 7 +- build/vignette.rds |binary data/hgnc.table.rda |binary data/mouse.table.rda |binary inst/doc/index.html | 110 +++++++++++++++++------------------ inst/extdata/date_of_last_update.txt | 2 man/hgnc.table.Rd | 4 - man/mouse.table.Rd | 2 12 files changed, 86 insertions(+), 80 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 0.5.2 dated 2023-08-19 and 0.5.3 dated 2024-11-16
DESCRIPTION | 12 +-- MD5 | 38 +++++----- NEWS.md | 10 ++ R/fa_brands.R | 2 R/fa_i.R | 2 R/fa_version.R | 2 R/sysdata.rda |binary inst/fontawesome/css/all.css | 74 +++++++++++++++++++-- inst/fontawesome/css/all.min.css | 10 +- 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 | 11 +++ 20 files changed, 125 insertions(+), 44 deletions(-)
Title: Estimation and Projection of Age-Specific Mortality Rates
Description: Age-specific mortality rates are estimated and projected using
the Kannisto, Lee-Carter and related methods as described in
Sevcikova et al. (2016) <doi:10.1007/978-3-319-26603-9_15>.
Author: Hana Sevcikova [cre, aut],
Nan Li [aut],
Patrick Gerland [aut]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between MortCast versions 2.7-0 dated 2022-03-31 and 2.8-0 dated 2024-11-16
ChangeLog | 8 ++++++++ DESCRIPTION | 30 +++++++++++++++++++++++------- MD5 | 22 +++++++++++----------- R/LC.R | 3 ++- R/MortCast-data.R | 2 +- R/other_methods.R | 29 ++++++++++++++++++++++++----- build/partial.rdb |binary man/MortCast-package.Rd | 4 +--- man/PMDrho.Rd | 2 +- man/mortcast.blend.Rd | 4 ++-- man/pmdgroup.Rd | 8 +++++--- src/functions.c | 37 ++++++++++++++++++++++++++++++++----- 12 files changed, 110 insertions(+), 39 deletions(-)
Title: Pollution-Associated Risk Geospatial Analysis Site
Description: Offers tools to estimate and visualize levels of major pollutants
(CO, NO2, SO2, Ozone, PM2.5 and PM10) across the conterminous
United States for user-defined time ranges. Provides functions to
retrieve pollutant data from the U.S. Environmental Protection
Agency’s 'Air Quality System' (AQS) API service
<https://aqs.epa.gov/aqsweb/documents/data_api.html> for
interactive visualization through a 'shiny' application, allowing
users to explore pollutant levels for a given location over time
relative to the National Ambient Air Quality Standards (NAAQS).
Author: Jaehyun Joo [aut, cre],
Rebecca Greenblatt [aut],
Avantika Diwadkar [aut],
Nisha Narayanan [aut],
Blanca Himes [aut]
Maintainer: Jaehyun Joo <jaehyunjoo@outlook.com>
Diff between pargasite versions 2.1.0 dated 2024-04-23 and 2.1.1 dated 2024-11-16
DESCRIPTION | 8 ++-- MD5 | 14 +++---- R/draw_map.R | 32 +++++++++------- R/server.R | 106 ++++++++++++++++++++++++++++++++++------------------- R/subset_data.R | 4 +- R/summarize_by.R | 4 +- R/ui_functions.R | 5 +- build/vignette.rds |binary 8 files changed, 106 insertions(+), 67 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial stratified heterogeneity, while also taking into account local spatial dependencies, spatial interpretability, complex spatial interactions, and robust spatial stratification. Additionally, it supports the spatial stratified heterogeneity family established in academic literature.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.2 dated 2024-11-07 and 1.3 dated 2024-11-16
gdverse-1.2/gdverse/R/isp.R |only gdverse-1.2/gdverse/R/utils_helper.R |only gdverse-1.2/gdverse/inst/python/__pycache__ |only gdverse-1.2/gdverse/man/figures/gdm.png |only gdverse-1.2/gdverse/man/generate_subsets.Rd |only gdverse-1.2/gdverse/man/inverse_distance_weight.Rd |only gdverse-1.2/gdverse/man/isp.Rd |only gdverse-1.2/gdverse/man/plot.isp_result.Rd |only gdverse-1.2/gdverse/man/print.isp_result.Rd |only gdverse-1.3/gdverse/DESCRIPTION | 35 gdverse-1.3/gdverse/MD5 | 186 +- gdverse-1.3/gdverse/NAMESPACE | 5 gdverse-1.3/gdverse/NEWS.md | 138 - gdverse-1.3/gdverse/R/gd.R | 181 +- gdverse-1.3/gdverse/R/gd_bestunidisc.R | 188 +- gdverse-1.3/gdverse/R/geodetector.R | 1144 ++++++------- gdverse-1.3/gdverse/R/globals.R | 30 gdverse-1.3/gdverse/R/gozh.R | 467 ++--- gdverse-1.3/gdverse/R/idsa.R | 399 ++-- gdverse-1.3/gdverse/R/lesh.R | 383 ++-- gdverse-1.3/gdverse/R/opgd.R | 268 +-- gdverse-1.3/gdverse/R/pid_idsa.R | 44 gdverse-1.3/gdverse/R/psd_pseudop.R | 51 gdverse-1.3/gdverse/R/psd_spade.R | 38 gdverse-1.3/gdverse/R/r_interact_py.R | 92 - gdverse-1.3/gdverse/R/rgd.R | 269 +-- gdverse-1.3/gdverse/R/rid.R | 196 +- gdverse-1.3/gdverse/R/sesu_gozh.R | 384 ++-- gdverse-1.3/gdverse/R/sesu_opgd.R | 374 ++-- gdverse-1.3/gdverse/R/spade.R | 326 +-- gdverse-1.3/gdverse/R/spd_lesh.R | 68 gdverse-1.3/gdverse/R/srs_geodetecor.R | 752 ++++---- gdverse-1.3/gdverse/R/srsgd.R | 196 +- gdverse-1.3/gdverse/R/utils.R |only gdverse-1.3/gdverse/README.md | 30 gdverse-1.3/gdverse/inst/doc/gd.Rmd | 20 gdverse-1.3/gdverse/inst/doc/gd.html | 30 gdverse-1.3/gdverse/inst/doc/idsa.Rmd | 200 +- gdverse-1.3/gdverse/inst/doc/idsa.html | 4 gdverse-1.3/gdverse/inst/doc/opgd.Rmd | 428 ++--- gdverse-1.3/gdverse/inst/doc/opgd.html | 14 gdverse-1.3/gdverse/inst/doc/rgdrid.Rmd | 222 +- gdverse-1.3/gdverse/inst/doc/rgdrid.html | 46 gdverse-1.3/gdverse/inst/doc/sesu.Rmd | 1270 +++++++-------- gdverse-1.3/gdverse/inst/doc/sesu.html | 36 gdverse-1.3/gdverse/inst/doc/shegd.Rmd | 392 ++-- gdverse-1.3/gdverse/inst/doc/shegd.html | 108 - gdverse-1.3/gdverse/inst/doc/spade.Rmd | 442 ++--- gdverse-1.3/gdverse/inst/doc/spade.html | 63 gdverse-1.3/gdverse/inst/python/cpd_disc.py | 114 - gdverse-1.3/gdverse/man/all2int.Rd | 2 gdverse-1.3/gdverse/man/cpsd_disc.Rd | 6 gdverse-1.3/gdverse/man/cpsd_spade.Rd | 2 gdverse-1.3/gdverse/man/figures/gd/ed-1.png |binary gdverse-1.3/gdverse/man/figures/gd/fd-1.png |binary gdverse-1.3/gdverse/man/figures/gd/gd_all-1.png |binary gdverse-1.3/gdverse/man/figures/gd/id-1.png |binary gdverse-1.3/gdverse/man/figures/gd/rd-1.png |binary gdverse-1.3/gdverse/man/figures/idsa/idsa_modeling-1.png |binary gdverse-1.3/gdverse/man/figures/opgd/opgd_plot-1.png |binary gdverse-1.3/gdverse/man/figures/rgdrid/rgd_id-1.png |binary gdverse-1.3/gdverse/man/figures/rgdrid/rid_plot-1.png |binary gdverse-1.3/gdverse/man/figures/sesu/gozh1-1.png |binary gdverse-1.3/gdverse/man/figures/sesu/gozh2-1.png |binary gdverse-1.3/gdverse/man/figures/sesu/opgd-1.png |binary gdverse-1.3/gdverse/man/figures/shegd/gozh_bi-1.png |binary gdverse-1.3/gdverse/man/figures/shegd/gozh_uni-1.png |binary gdverse-1.3/gdverse/man/figures/shegd/lesh-1.png |binary gdverse-1.3/gdverse/man/figures/shegd/lesh_only-1.png |binary gdverse-1.3/gdverse/man/figures/spade/spade-1.png |binary gdverse-1.3/gdverse/man/gozh.Rd | 6 gdverse-1.3/gdverse/man/lesh.Rd | 6 gdverse-1.3/gdverse/man/pid_idsa.Rd | 2 gdverse-1.3/gdverse/man/pipe.Rd | 2 gdverse-1.3/gdverse/man/plot.rid_result.Rd | 48 gdverse-1.3/gdverse/man/psd_iev.Rd | 2 gdverse-1.3/gdverse/man/psd_pseudop.Rd | 3 gdverse-1.3/gdverse/man/psd_spade.Rd | 3 gdverse-1.3/gdverse/man/psmd_pseudop.Rd | 6 gdverse-1.3/gdverse/man/psmd_spade.Rd | 10 gdverse-1.3/gdverse/man/rgd.Rd | 25 gdverse-1.3/gdverse/man/rid.Rd | 25 gdverse-1.3/gdverse/man/shuffle_vector.Rd | 2 gdverse-1.3/gdverse/man/weight_assign.Rd | 2 gdverse-1.3/gdverse/tests/testthat/test-data_type.R | 16 gdverse-1.3/gdverse/tests/testthat/test-multicores.R | 18 gdverse-1.3/gdverse/tests/testthat/test-psd_spade.R | 2 gdverse-1.3/gdverse/vignettes/gd.Rmd | 20 gdverse-1.3/gdverse/vignettes/idsa.Rmd | 200 +- gdverse-1.3/gdverse/vignettes/idsa.Rmd.orig | 110 - gdverse-1.3/gdverse/vignettes/opgd.Rmd | 428 ++--- gdverse-1.3/gdverse/vignettes/opgd.Rmd.orig | 166 - gdverse-1.3/gdverse/vignettes/rgdrid.Rmd | 222 +- gdverse-1.3/gdverse/vignettes/rgdrid.Rmd.orig | 158 - gdverse-1.3/gdverse/vignettes/sesu.Rmd | 1270 +++++++-------- gdverse-1.3/gdverse/vignettes/shegd.Rmd | 392 ++-- gdverse-1.3/gdverse/vignettes/shegd.Rmd.orig | 194 +- gdverse-1.3/gdverse/vignettes/spade.Rmd | 442 ++--- gdverse-1.3/gdverse/vignettes/spade.Rmd.orig | 16 99 files changed, 6690 insertions(+), 6749 deletions(-)
Title: Diagnostic Analysis Using Forward Search Procedure for Various
Models
Description: Identifies potential data outliers and their impact on estimates and
analyses. Tool for evaluation of study credibility. Uses the forward
search approach of Atkinson and Riani, "Robust Diagnostic Regression
Analysis", 2000,<ISBN: o-387-95017-6> to prepare descriptive statistics
of a dataset that is to be analyzed by functions lm {stats}, glm {stats},
nls {stats}, lme {nlme}, or coxph {survival}, or their equivalent in
another language. Includes graphics functions to display the
descriptive statistics.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>
Diff between forsearch versions 6.2.0 dated 2024-07-13 and 6.3.0 dated 2024-11-16
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Title: Hierarchical and Geographically Weighted Regression
Description: This model divides coefficients into three types,
i.e., local fixed effects, global fixed effects, and random effects (Hu et al., 2022)<doi:10.1177/23998083211063885>.
If data have spatial hierarchical structures (especially are overlapping on some locations),
it is worth trying this model to reach better fitness.
Author: Yigong Hu [aut, cre],
Richard Harris [aut],
Richard Timmerman [aut]
Maintainer: Yigong Hu <yigong.hu@bristol.ac.uk>
Diff between hgwrr versions 0.6-0 dated 2024-11-07 and 0.6-1 dated 2024-11-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/hetero.R | 2 +- build/partial.rdb |binary 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Reliability Growth Analysis
Description: Modeling and plotting functions for Reliability Growth Analysis (RGA). Models include the Duane (1962) <doi:10.1109/TA.1964.4319640>, Non-Homogeneous Poisson Process (NHPP) by Crow (1975) <https://apps.dtic.mil/sti/citations/ADA020296>, Piecewise Weibull NHPP by Guo et al. (2010) <doi:10.1109/RAMS.2010.5448029>, and Piecewise Weibull NHPP with Change Point Detection based on the 'segmented' package by Muggeo (2024) <https://cran.r-project.org/package=segmented>.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between ReliaGrowR versions 0.1.1 dated 2024-11-01 and 0.1.3 dated 2024-11-15
DESCRIPTION | 6 +- MD5 | 18 +++--- NAMESPACE | 2 NEWS.md | 12 ++++ R/duane_plot.R | 25 +++++---- R/rga.R | 123 +++++++++++++++++++++------------------------- inst/WORDLIST | 9 ++- man/duane_plot.Rd | 3 + tests/testthat/Rplots.pdf |binary tests/testthat/test-rga.R | 22 ++++---- 10 files changed, 120 insertions(+), 100 deletions(-)
Title: Wrapper for 'Visa Chart Components'
Description: Provides a set of wrapper functions for 'Visa Chart Components'.
'Visa Chart Components' <https://github.com/visa/visa-chart-components> is an accessibility focused,
framework agnostic set of data experience design systems components for the web.
Author: Christopher DeMartini [aut, cre],
Stephanie Modica [aut],
David Kutas [aut],
Jaime Tanner [aut],
Frank Elavsky [aut],
Wojtek Kostelecki [ctb],
Visa Data Experience Team [aut, fnd],
Visa, Inc. [cph]
Maintainer: Christopher DeMartini <chris.demartini.npm@gmail.com>
Diff between visachartR versions 3.3.0 dated 2024-03-16 and 4.0.1 dated 2024-11-15
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Title: Likelihood Based Inference
Description: Maximum likelihood estimation and likelihood ratio test are essential for modern statistics. This package supports in calculating likelihood based inference.
Reference: Pawitan Y. (2001, ISBN:0-19-850765-8).
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between LBI versions 0.2.0 dated 2024-10-16 and 0.2.1 dated 2024-11-15
DESCRIPTION | 6 +++--- MD5 | 37 ++++++++++++++++++++----------------- R/LBCIvar.R | 31 ++++++++++++++----------------- R/LIbin.R | 4 ++-- R/LInorm.R | 16 +++++++++++----- R/LInormVar.R | 22 ++++++++++++---------- R/LIpois.R | 35 ++++++++++++++++++++++++++--------- R/LIvRatio.R |only R/LIvar.R | 35 ++++++++++++++++------------------- R/LIvtest.R | 29 ++++++++++------------------- inst/NEWS.Rd | 10 ++++++++++ inst/doc |only man/LBCIvar.Rd | 2 +- man/LBI-package.Rd | 2 +- man/LIbin.Rd | 2 +- man/LInorm.Rd | 4 ++-- man/LInormVar.Rd | 2 +- man/LIpois.Rd | 21 ++++++++++++++------- man/LIvRatio.Rd |only man/LIvar.Rd | 29 ++++++++++++----------------- man/LIvtest.Rd | 14 ++++++-------- 21 files changed, 162 insertions(+), 139 deletions(-)
Title: Group Sequential Design with Non-Constant Effect
Description: The goal of 'gsDesign2' is to enable fixed or group sequential
design under non-proportional hazards. To enable highly flexible enrollment,
time-to-event and time-to-dropout assumptions, 'gsDesign2' offers piecewise
constant enrollment, failure rates, and dropout rates for a stratified
population. This package includes three methods for designs:
average hazard ratio, weighted logrank tests in Yung and Liu (2019)
<doi:10.1111/biom.13196>, and MaxCombo tests.
Substantial flexibility on top of what is in the 'gsDesign' package
is intended for selecting boundaries.
Author: Keaven Anderson [aut],
Yilong Zhang [aut],
Yujie Zhao [aut, cre],
Jianxiao Yang [aut],
Nan Xiao [aut],
Amin Shirazi [ctb],
Ruixue Wang [ctb],
Yi Cui [ctb],
Ping Yang [ctb],
Xin Tong Li [ctb],
Chenxiang Li [ctb],
Hiroaki Fukuda [ctb],
Hongtao Zhang [c [...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between gsDesign2 versions 1.1.2 dated 2024-04-09 and 1.1.3 dated 2024-11-15
gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-ahr.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-expected_accrual.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-expected_event.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-expected_time.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-fixed_design.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-gs_design_combo.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-gs_design_npe.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-gs_info_ahr.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-gs_info_combo.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-gs_power_ahr.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-gs_power_combo.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-ppwe.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-AHR.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-eAccrual.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-eEvents.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-eEvents_df.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-gridpts_h1_hupdate.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-gs_design_ahr.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-gs_design_npe.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-gs_info_ahr.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-gs_power_ahr.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-gs_power_npe.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-reference-tEvents.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/helper-utility_combo.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/test-double_programming_ppwe.R |only gsDesign2-1.1.2/gsDesign2/tests/testthat/test-fastlag.R |only gsDesign2-1.1.3/gsDesign2/DESCRIPTION | 11 gsDesign2-1.1.3/gsDesign2/MD5 | 242 +- gsDesign2-1.1.3/gsDesign2/NAMESPACE | 7 gsDesign2-1.1.3/gsDesign2/NEWS.md | 51 gsDesign2-1.1.3/gsDesign2/R/ahr.R | 31 gsDesign2-1.1.3/gsDesign2/R/ahr_blinded.R | 37 gsDesign2-1.1.3/gsDesign2/R/as_gt.R | 554 +---- gsDesign2-1.1.3/gsDesign2/R/as_rtf.R | 563 ----- gsDesign2-1.1.3/gsDesign2/R/check_arg.R | 2 gsDesign2-1.1.3/gsDesign2/R/define.R | 4 gsDesign2-1.1.3/gsDesign2/R/expected_accural.R | 4 gsDesign2-1.1.3/gsDesign2/R/expected_time.R | 6 gsDesign2-1.1.3/gsDesign2/R/fixed_design_ahr.R | 6 gsDesign2-1.1.3/gsDesign2/R/fixed_design_fh.R | 6 gsDesign2-1.1.3/gsDesign2/R/fixed_design_lf.R | 4 gsDesign2-1.1.3/gsDesign2/R/fixed_design_maxcombo.R | 14 gsDesign2-1.1.3/gsDesign2/R/fixed_design_mb.R | 21 gsDesign2-1.1.3/gsDesign2/R/fixed_design_milestone.R | 2 gsDesign2-1.1.3/gsDesign2/R/fixed_design_rd.R | 12 gsDesign2-1.1.3/gsDesign2/R/fixed_design_rmst.R | 2 gsDesign2-1.1.3/gsDesign2/R/globals.R | 4 gsDesign2-1.1.3/gsDesign2/R/gsDesign2-package.R | 16 gsDesign2-1.1.3/gsDesign2/R/gs_b.R | 13 gsDesign2-1.1.3/gsDesign2/R/gs_design_ahr.R | 24 gsDesign2-1.1.3/gsDesign2/R/gs_design_combo.R | 8 gsDesign2-1.1.3/gsDesign2/R/gs_design_npe.R | 5 gsDesign2-1.1.3/gsDesign2/R/gs_design_rd.R | 35 gsDesign2-1.1.3/gsDesign2/R/gs_design_wlr.R | 246 +- gsDesign2-1.1.3/gsDesign2/R/gs_info_ahr.R | 107 - gsDesign2-1.1.3/gsDesign2/R/gs_info_rd.R | 16 gsDesign2-1.1.3/gsDesign2/R/gs_info_wlr.R | 2 gsDesign2-1.1.3/gsDesign2/R/gs_power_ahr.R | 84 gsDesign2-1.1.3/gsDesign2/R/gs_power_combo.R | 10 gsDesign2-1.1.3/gsDesign2/R/gs_power_npe.R | 4 gsDesign2-1.1.3/gsDesign2/R/gs_power_rd.R | 10 gsDesign2-1.1.3/gsDesign2/R/gs_power_wlr.R | 43 gsDesign2-1.1.3/gsDesign2/R/gs_spending_bound.R | 3 gsDesign2-1.1.3/gsDesign2/R/gs_spending_combo.R | 76 gsDesign2-1.1.3/gsDesign2/R/gs_update_ahr.R | 453 ++-- gsDesign2-1.1.3/gsDesign2/R/pw_info.R | 149 - gsDesign2-1.1.3/gsDesign2/R/pwe.R | 7 gsDesign2-1.1.3/gsDesign2/R/rmst.R | 8 gsDesign2-1.1.3/gsDesign2/R/summary.R | 986 +-------- gsDesign2-1.1.3/gsDesign2/R/to_integer.R | 457 +++- gsDesign2-1.1.3/gsDesign2/R/utility_combo.R | 18 gsDesign2-1.1.3/gsDesign2/R/utility_tidy_tbl.R | 50 gsDesign2-1.1.3/gsDesign2/R/utility_wlr.R | 112 - gsDesign2-1.1.3/gsDesign2/R/utils.R |only gsDesign2-1.1.3/gsDesign2/R/wlr_weight.R | 8 gsDesign2-1.1.3/gsDesign2/inst/WORDLIST | 21 gsDesign2-1.1.3/gsDesign2/inst/doc/gsDesign2.html | 1047 +++++----- gsDesign2-1.1.3/gsDesign2/man/ahr.Rd | 12 gsDesign2-1.1.3/gsDesign2/man/ahr_blinded.Rd | 15 gsDesign2-1.1.3/gsDesign2/man/as_gt.Rd | 6 gsDesign2-1.1.3/gsDesign2/man/as_rtf.Rd | 20 gsDesign2-1.1.3/gsDesign2/man/fixed_design.Rd | 17 gsDesign2-1.1.3/gsDesign2/man/gs_b.Rd | 13 gsDesign2-1.1.3/gsDesign2/man/gs_create_arm.Rd | 8 gsDesign2-1.1.3/gsDesign2/man/gs_design_ahr.Rd | 9 gsDesign2-1.1.3/gsDesign2/man/gs_design_rd.Rd | 19 gsDesign2-1.1.3/gsDesign2/man/gs_design_wlr.Rd | 58 gsDesign2-1.1.3/gsDesign2/man/gs_info_ahr.Rd | 16 gsDesign2-1.1.3/gsDesign2/man/gs_power_ahr.Rd | 34 gsDesign2-1.1.3/gsDesign2/man/gs_power_combo.Rd | 2 gsDesign2-1.1.3/gsDesign2/man/gs_power_wlr.Rd | 16 gsDesign2-1.1.3/gsDesign2/man/gs_spending_combo.Rd | 75 gsDesign2-1.1.3/gsDesign2/man/gs_update_ahr.Rd | 122 - gsDesign2-1.1.3/gsDesign2/man/pw_info.Rd | 51 gsDesign2-1.1.3/gsDesign2/man/summary.Rd | 166 - gsDesign2-1.1.3/gsDesign2/man/to_integer.Rd | 126 + gsDesign2-1.1.3/gsDesign2/man/wlr_weight.Rd | 6 gsDesign2-1.1.3/gsDesign2/tests/testthat/_snaps/independent_as_gt.md | 306 +- gsDesign2-1.1.3/gsDesign2/tests/testthat/_snaps/independent_as_rtf |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-developer-summary.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-double-programming-expected_accrual.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-double-programming-expected_event.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-double-programming-expected_time.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-double-programming-gs_design_combo.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-double-programming-gs_info_ahr.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-double-programming-ppwe.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-AHR_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-eAccrual_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-eEvents_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-gridpts_h1_hupdate.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-gs_design_ahr_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-gs_design_npe_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-gs_info_ahr_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-gs_power_ahr_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-gs_power_npe_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old-version-tEvents_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-old_version-eEvents_df_.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper-support-as_rtf.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/helper.R | 10 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-developer-ahr.R | 69 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-developer-expected_time.R | 11 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-developer-fastlag.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/test-developer-gs_design_ahr.R | 18 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-developer-gs_design_wlr.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/test-developer-gs_power_ahr.R | 25 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-developer-pw_info.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/test-developer-summary.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/test-developer-to_integer.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-ahr.R | 30 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-ahr_blinded.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-fixed_design.R | 56 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-gs_design_combo.R | 8 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-gs_design_npe.R | 12 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-gs_info_ahr.R | 6 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-gs_info_combo.R | 35 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-gs_power_ahr.R | 51 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-gs_power_combo.R | 81 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-gs_update_ahr.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-utility_combo.R | 551 ++++- gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent-utility_tbl.R | 6 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent_as_gt.R | 24 gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent_as_rtf.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent_ppwe.R |only gsDesign2-1.1.3/gsDesign2/tests/testthat/test-independent_test_gs_design_wlr.R | 4 144 files changed, 3848 insertions(+), 3847 deletions(-)
Title: Geometric Morphometric Analyses of 2D and 3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.0.8 dated 2024-06-24 and 4.0.9 dated 2024-11-15
DESCRIPTION | 8 +- MD5 | 44 +++++++----- NAMESPACE | 6 + NEWS.md | 17 ++++ R/extended.pgls.r |only R/geomorph.support.code.r | 18 +++++ R/geomorph.utils.r | 118 ++++++++++++++++++++++++++++++++ R/gm.measurement.error.R | 5 - R/gm.prcomp.R | 19 +++++ R/morphol.disparity.r | 3 R/physignal.eigen.R |only R/readland.fcsv.r | 15 +++- R/shared.support.code.R | 5 + data/pupfish.ws.rda |only inst/CITATION | 4 - inst/doc/geomorph.digitize3D.R | 10 +- inst/doc/geomorph.digitize3D.html | 14 +-- man/extended.pgls.Rd |only man/gm.measurement.error.Rd | 5 + man/gm.prcomp.Rd | 3 man/physignal.eigen.Rd |only man/plot.physignal.eigen.Rd |only man/print.physignal.eigen.Rd |only man/pupfish.ws.Rd |only man/readland.fcsv.Rd | 10 ++ man/summary.physignal.eigen.Rd |only tests/testthat/test-geomorph.R | 136 ++++++++++++++++++++++---------------- vignettes/cran-comments.md |only 28 files changed, 340 insertions(+), 100 deletions(-)
Title: Tools and Metrics for 3D Surfaces and Objects
Description: A collection of functions for sampling and simulating 3D surfaces and objects
and estimating metrics like rugosity, fractal dimension, convexity, sphericity, circularity,
second moments of area and volume, and more.
Author: Joshua Madin [aut] ,
Nina Schiettekatte [aut, cre]
Maintainer: Nina Schiettekatte <nina.schiettekatte@gmail.com>
Diff between habtools versions 1.0.5 dated 2024-03-01 and 1.0.7 dated 2024-11-15
DESCRIPTION | 8 - MD5 | 50 ++++++----- NAMESPACE | 1 NEWS.md |only R/dem_sample.R | 8 - R/fd_area.R | 2 R/fd_hvar.R | 4 R/fd_sd.R | 4 R/rg.R | 2 R/z.R |only README.md | 17 ++- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/DEM_intro.R | 4 inst/doc/DEM_intro.html | 148 +++++++++++++++++---------------- inst/doc/fractal_intro.R | 2 inst/doc/fractal_intro.html | 157 ++++++++++++++++++----------------- inst/doc/mesh_intro.R | 6 - inst/doc/mesh_intro.html | 158 +++++++++++++++++++----------------- man/dem_sample.Rd | 4 man/figures/README-example1-1.png |binary man/figures/README-example1-2.png |binary man/figures/README-example1-3.png |binary man/figures/README-example2-1.png |binary man/figures/README-example2-2.png |binary man/figures/README-setup2-1-rgl.png |binary man/z.Rd |only 28 files changed, 306 insertions(+), 269 deletions(-)
Title: Regression Data Analysis System
Description: Perform a supervised data analysis on a database through a 'shiny' graphical interface. It includes methods such as linear regression, penalized regression, k-nearest neighbors, decision trees, ada boosting, extreme gradient boosting, random forest, neural networks, deep learning and support vector machines.
Author: Oldemar Rodriguez [aut, cre],
Andres Navarro D. [ctb, prg],
Diego Jimenez A. [ctb, prg],
Ariel Arroyo S. [ctb, prg],
Joseline Quiros M. [ctb, prg]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between regressoR versions 3.0.2 dated 2023-06-29 and 4.0.3 dated 2024-11-15
regressoR-3.0.2/regressoR/R/mod_boosting.R |only regressoR-3.0.2/regressoR/R/mod_boosting_fct.R |only regressoR-3.0.2/regressoR/R/mod_boosting_utils.R |only regressoR-3.0.2/regressoR/R/mod_comparacion.R |only regressoR-3.0.2/regressoR/R/mod_cross_validation.R |only regressoR-3.0.2/regressoR/R/mod_cv_boosting.R |only regressoR-3.0.2/regressoR/R/mod_cv_dt.R |only regressoR-3.0.2/regressoR/R/mod_cv_knn.R |only regressoR-3.0.2/regressoR/R/mod_cv_rd.R |only regressoR-3.0.2/regressoR/R/mod_cv_rf.R |only regressoR-3.0.2/regressoR/R/mod_cv_rl.R |only regressoR-3.0.2/regressoR/R/mod_cv_rlr.R |only regressoR-3.0.2/regressoR/R/mod_cv_svm.R |only regressoR-3.0.2/regressoR/R/mod_dimension_reduction.R |only regressoR-3.0.2/regressoR/R/mod_dimension_reduction_utils.R |only regressoR-3.0.2/regressoR/R/mod_knn.R |only regressoR-3.0.2/regressoR/R/mod_knn_utils.R |only regressoR-3.0.2/regressoR/R/mod_l_regression.R |only regressoR-3.0.2/regressoR/R/mod_l_regression_utils.R |only regressoR-3.0.2/regressoR/R/mod_neural_net.R |only regressoR-3.0.2/regressoR/R/mod_neural_net_utils.R |only regressoR-3.0.2/regressoR/R/mod_penalized_l_r.R |only regressoR-3.0.2/regressoR/R/mod_penalized_l_r_utils.R |only regressoR-3.0.2/regressoR/R/mod_r_forest.R |only regressoR-3.0.2/regressoR/R/mod_r_forest_fct.R |only regressoR-3.0.2/regressoR/R/mod_r_forest_utils.R |only regressoR-3.0.2/regressoR/R/mod_regression_trees.R |only regressoR-3.0.2/regressoR/R/mod_regression_trees_utils.R |only regressoR-3.0.2/regressoR/R/mod_svm.R |only regressoR-3.0.2/regressoR/man/app_server.Rd |only regressoR-3.0.2/regressoR/man/boosting_importance_plot.Rd |only regressoR-3.0.2/regressoR/man/calibrate_boosting.Rd |only regressoR-3.0.2/regressoR/man/coef_lambda.Rd |only regressoR-3.0.2/regressoR/man/datos.disyuntivos.Rd |only regressoR-3.0.2/regressoR/man/disp_models.Rd |only regressoR-3.0.2/regressoR/man/dt_plot.Rd |only regressoR-3.0.2/regressoR/man/e_coeff_landa.Rd |only regressoR-3.0.2/regressoR/man/general_indices.Rd |only regressoR-3.0.2/regressoR/man/importance_plot_rf.Rd |only regressoR-3.0.2/regressoR/man/nn_plot.Rd |only regressoR-3.0.2/regressoR/man/pairs_power.Rd |only regressoR-3.0.2/regressoR/man/plot_RMSE.Rd |only regressoR-3.0.2/regressoR/man/plot_pred_rd.Rd |only regressoR-3.0.2/regressoR/man/plot_var_pred_rd.Rd |only regressoR-3.0.2/regressoR/man/rd_model.Rd |only regressoR-3.0.2/regressoR/man/rd_prediction.Rd |only regressoR-3.0.2/regressoR/man/rd_type.Rd |only regressoR-3.0.2/regressoR/man/rl_coeff.Rd |only regressoR-3.0.2/regressoR/man/rlr_model.Rd |only regressoR-3.0.2/regressoR/man/rlr_prediction.Rd |only regressoR-3.0.2/regressoR/man/rlr_type.Rd |only regressoR-4.0.3/regressoR/DESCRIPTION | 33 regressoR-4.0.3/regressoR/MD5 | 117 -- regressoR-4.0.3/regressoR/NAMESPACE | 50 regressoR-4.0.3/regressoR/R/app_server.R | 203 +-- regressoR-4.0.3/regressoR/R/app_ui.R | 157 +- regressoR-4.0.3/regressoR/R/general_plots.R | 72 - 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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 (2024)
<doi:10.1016/j.alcr.2024.100617>. 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'. For an in-depth tutorial of the package, see
(Tikka and Helske, 2024) <doi:10.48550/arXiv.2302.01607>.
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 1.5.2 dated 2024-05-28 and 1.5.5 dated 2024-11-15
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dynamite-1.5.5/dynamite/tests/testthat/test-recovery.R | 1198 +- dynamite-1.5.5/dynamite/tests/testthat/test-warnings.R | 36 dynamite-1.5.5/dynamite/vignettes/custommodelplot-1.png |only dynamite-1.5.5/dynamite/vignettes/dag.png |only dynamite-1.5.5/dynamite/vignettes/dynamite.bib |only dynamite-1.5.5/dynamite/vignettes/dynamite.qmd |only dynamite-1.5.5/dynamite/vignettes/dynamite_custom.qmd |only dynamite-1.5.5/dynamite/vignettes/dynamite_priors.qmd |only dynamite-1.5.5/dynamite/vignettes/dynamite_simulation.qmd |only dynamite-1.5.5/dynamite/vignettes/gaussianplot-1.png |only dynamite-1.5.5/dynamite/vignettes/nuplot-1.png |only dynamite-1.5.5/dynamite/vignettes/vbplot-1.png |only 132 files changed, 18286 insertions(+), 18364 deletions(-)
Title: Fast Alternatives to 'tidyverse' Functions
Description: A full set of fast data manipulation tools with a tidy
front-end and a fast back-end using 'collapse' and 'cheapr'.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between fastplyr versions 0.3.0 dated 2024-10-20 and 0.4.0 dated 2024-11-15
DESCRIPTION | 6 MD5 | 67 +- NAMESPACE | 2 NEWS.md | 103 ++-- R/GRP_utils.R | 9 R/abc.R | 1 R/add_id.R | 17 R/cpp11.R | 28 - R/df_utils.R | 654 ++++++++++++++------------ R/f_bind.R | 337 +++++++------ R/f_count.R | 4 R/f_distinct.R | 4 R/f_duplicates.R | 4 R/f_expand.R | 6 R/f_fill.R |only R/f_group_by.R | 2 R/f_join.R | 16 R/f_nest_by.R | 9 R/f_rowwise.R | 2 R/f_select.R | 235 ++++----- R/f_slice.R | 856 +++++++++++++++++------------------ R/f_summarise.R | 58 +- R/f_tibble.R | 2 R/group_collapse.R | 57 ++ R/group_id.R | 649 +++++++++++++------------- R/tidy_quantiles.R | 586 ++++++++++++----------- R/tidy_utils.R | 632 ++++++++++++------------- README.md | 96 +-- man/f_fill.Rd |only man/f_select.Rd | 67 +- man/f_slice.Rd | 8 man/group_id.Rd | 3 src/cpp11.cpp | 80 +-- src/fastplyr.cpp | 393 ++++++++++++---- tests/testthat/test-f_summarise.R |only tests/testthat/test-tidy_quantiles.R | 62 ++ 36 files changed, 2783 insertions(+), 2272 deletions(-)
Title: Checks for Various Computing Environments
Description: A collection of lightweight functions that can be used to
determine the computing environment in which your code is running.
This includes operating systems, continuous integration (CI)
environments, containers, and more.
Author: Brian Connelly [aut, cre, cph]
,
Mark Padgham [ctb] ,
Lluis Revilla Sancho [ctb]
Maintainer: Brian Connelly <bdc@bconnelly.net>
Diff between ami versions 0.2.0 dated 2024-10-25 and 0.2.1 dated 2024-11-15
DESCRIPTION | 6 +++--- MD5 | 14 ++++++++++---- NAMESPACE | 4 ++++ NEWS.md | 6 ++++++ R/positron.R |only R/python_venv.R |only README.md | 6 ------ man/positron.Rd |only man/python_venv.Rd |only tests/testthat/test-positron.R |only tests/testthat/test-python_venv.R |only 11 files changed, 23 insertions(+), 13 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.5.1.2 dated 2024-08-26 and 1.5.4 dated 2024-11-15
DESCRIPTION | 8 MD5 | 94 R/GPModel.R | 98 R/gpb.cv.R | 152 R/gpboost.R | 16 README.md | 5 configure.ac | 2 demo/GPBoost_algorithm.R | 157 demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 28 man/GPModel.Rd | 26 man/GPModel_shared_params.Rd | 17 man/fit.GPModel.Rd | 13 man/fit.Rd | 11 man/fitGPModel.Rd | 43 man/gpb.cv.Rd | 56 man/gpb.grid.search.tune.parameters.Rd | 125 man/gpb_shared_params.Rd | 21 man/predict.GPModel.Rd | 2 man/set_optim_params.GPModel.Rd | 11 man/set_optim_params.Rd | 11 man/summary.GPModel.Rd | 2 src/CG_utils.cpp | 7 src/Vecchia_utils.cpp | 1013 + src/c_api.cpp | 2 src/gpboost_R.cpp | 4 src/gpboost_R.h | 2 src/include/GPBoost/CG_utils.h | 4 src/include/GPBoost/Vecchia_utils.h | 968 - src/include/GPBoost/cov_fcts.h | 2936 +--- src/include/GPBoost/likelihoods.h | 959 + src/include/GPBoost/optim_utils.h | 54 src/include/GPBoost/re_comp.h | 183 src/include/GPBoost/re_model.h | 2 src/include/GPBoost/re_model_template.h | 2908 ++-- src/include/GPBoost/sparse_matrix_utils.h | 44 src/include/GPBoost/utils.h | 8 src/include/LBFGS.h | 116 src/include/LBFGSpp/LineSearchBacktracking.h | 2 src/include/LBFGSpp/LineSearchNocedalWright.h | 4 src/include/LightGBM/c_api.h | 2 src/include/unconstrained/bfgs.hpp | 28 src/include/unconstrained/nm.hpp | 31 src/re_model.cpp | 62 tests/testthat/test_GPModel_gaussian_process.R | 248 tests/testthat/test_GPModel_grouped_random_effects.R | 5 tests/testthat/test_GPModel_non_Gaussian_data.R | 6206 ++++------ tests/testthat/test_basic.R | 16 tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 70 48 files changed, 8577 insertions(+), 8205 deletions(-)
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested fra [...truncated...]
Author: Virginie Rondeau [aut, cre] ,
Juan R. Gonzalez [aut],
Yassin Mazroui [aut],
Audrey Mauguen [aut],
Amadou Diakite [aut],
Alexandre Laurent [aut],
Myriam Lopez [aut],
Agnieszka Krol [aut],
Casimir L. Sofeu [aut],
Julien Dumerc [aut],
Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>
Diff between frailtypack versions 3.6.3 dated 2024-10-19 and 3.6.4 dated 2024-11-15
DESCRIPTION | 8 +- MD5 | 12 +-- NEWS | 3 R/longiPenal.R | 63 ++++++++-------- R/plot.longiPenal.R | 187 ++++++++++++++++++++++++------------------------- R/print.longiPenal.R | 30 +++---- R/summary.longiPenal.R | 16 ++-- 7 files changed, 161 insertions(+), 158 deletions(-)
Title: Interface with the United Nations Comtrade API
Description: Interface with and extract data from the United Nations 'Comtrade'
API <https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping
data for a variety of commodities, these functions allow for easy API query
and data returned as a tidy data frame.
Author: Paul Bochtler [aut, cre, cph] ,
Harriet Goers [aut],
Chris Muir [aut],
Alicia Schep [rev] ,
Rafael Hellwig [rev] ,
Ernest Guevarra [rev] ,
Nicholas Potter [rev] ,
Juergen Amann [ctb]
Maintainer: Paul Bochtler <paulbochtler.gh@gmail.com>
Diff between comtradr versions 1.0.2 dated 2024-09-20 and 1.0.3 dated 2024-11-15
DESCRIPTION | 8 MD5 | 36 +-- NEWS.md | 5 R/ct_get_bulk.R | 7 R/ct_get_data.R | 1 R/ct_process_response.R | 4 R/utils.R | 26 -- README.md | 14 - build/vignette.rds |binary inst/doc/bulk_files.html | 2 inst/doc/caching.html | 2 inst/doc/comtradr.html | 8 inst/doc/large_data.html | 4 inst/doc/transition.html | 4 tests/testthat/data/comtradeapi.un.org/data/v1/get/C/A/HS-60a6ad.json | 2 tests/testthat/goods/comtradeapi.un.org/data/v1/get/C/A/HS-5e2730.R | 58 ----- tests/testthat/services/comtradeapi.un.org/data/v1/get/S/A/EB-b31ccb.R | 28 -- tests/testthat/test-ct_get_bulk.R | 115 ++++++---- tests/testthat/test-ct_get_data.R | 84 ++++--- 19 files changed, 185 insertions(+), 223 deletions(-)
Title: Archetypes for Targets
Description: Function-oriented Make-like declarative pipelines for
Statistics and data science are supported in the 'targets' R package.
As an extension to 'targets', the 'tarchetypes' package provides
convenient user-side functions to make 'targets' easier to use.
By establishing reusable archetypes for common kinds of
targets and pipelines, these functions help express complicated
reproducible pipelines concisely and compactly.
The methods in this package were influenced by the 'targets' R package.
by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre]
,
Rudolf Siegel [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between tarchetypes versions 0.10.0 dated 2024-09-26 and 0.11.0 dated 2024-11-15
DESCRIPTION | 19 ++- MD5 | 107 +++++++++--------- NAMESPACE | 1 NEWS.md | 8 + R/tar_force.R | 2 R/tar_map.R | 4 R/tar_map2_raw.R | 6 - R/tar_map_rep.R | 2 R/tar_map_rep_raw.R | 18 ++- R/tar_package.R | 2 R/tar_quarto.R | 2 R/tar_quarto_files.R | 87 +++++++++++--- R/tar_quarto_raw.R | 14 ++ R/tar_quarto_rep_raw.R | 11 + R/tar_render_rep_raw.R | 6 - R/tar_rep2_raw.R | 6 - R/tar_rep_raw.R | 3 R/utils_targets.R | 9 + man/tar_age.Rd | 78 ++++++------- man/tar_change.Rd | 80 +++++++------ man/tar_combine.Rd | 80 +++++++------ man/tar_download.Rd | 78 ++++++------- man/tar_file_read.Rd | 80 +++++++------ man/tar_files.Rd | 80 +++++++------ man/tar_files_input.Rd | 34 ++++- man/tar_force.Rd | 80 +++++++------ man/tar_formats.Rd | 80 +++++++------ man/tar_formats_superseded.Rd | 80 +++++++------ man/tar_group_by.Rd | 80 +++++++------ man/tar_group_count.Rd | 80 +++++++------ man/tar_group_select.Rd | 80 +++++++------ man/tar_group_size.Rd | 80 +++++++------ man/tar_knit.Rd | 48 +++++--- man/tar_map2.Rd | 80 +++++++------ man/tar_map2_count.Rd | 80 +++++++------ man/tar_map2_size.Rd | 80 +++++++------ man/tar_map_rep.Rd | 88 ++++++++------ man/tar_quarto.Rd | 55 ++++++--- man/tar_quarto_files.Rd | 10 + man/tar_quarto_files_get_source_files.Rd |only man/tar_quarto_rep.Rd | 48 +++++--- man/tar_render.Rd | 48 +++++--- man/tar_render_rep.Rd | 48 +++++--- man/tar_rep.Rd | 80 +++++++------ man/tar_rep2.Rd | 80 +++++++------ man/tar_rep_map.Rd | 80 +++++++------ man/tar_rep_map_raw.Rd | 80 +++++++------ man/tar_skip.Rd | 80 +++++++------ tests/testthat/helper-utils.R | 9 + tests/testthat/test-tar_hook_before.R | 30 +++-- tests/testthat/test-tar_hook_inner.R | 24 ++-- tests/testthat/test-tar_hook_outer.R | 24 ++-- tests/testthat/test-tar_map_rep.R | 183 +++++++++++++++---------------- tests/testthat/test-tar_quarto.R | 157 ++++++++++++++++++++++++++ tests/testthat/test-tar_quarto_files.R | 102 +++++++++++++++++ 55 files changed, 1755 insertions(+), 1136 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Lennart Schneider [cre, aut] ,
Jakob Richter [aut] ,
Marc Becker [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Lennart Schneider <lennart.sch@web.de>
Diff between mlr3mbo versions 0.2.6 dated 2024-10-16 and 0.2.7 dated 2024-11-15
DESCRIPTION | 30 ++--- MD5 | 138 +++++++++++++---------- NAMESPACE | 7 + NEWS.md | 8 + R/AcqFunction.R | 8 + R/AcqFunctionMulti.R | 2 R/AcqFunctionSmsEgo.R | 18 ++- R/AcqFunctionStochasticCB.R |only R/AcqFunctionStochasticEI.R |only R/AcqOptimizer.R | 28 ++-- R/OptimizerADBO.R |only R/OptimizerAsyncMbo.R |only R/OptimizerMbo.R | 98 +++++++++------- R/ResultAssigner.R | 2 R/ResultAssignerArchive.R | 17 +- R/ResultAssignerSurrogate.R | 23 ++- R/Surrogate.R | 56 +++++++-- R/SurrogateLearner.R | 40 ++++++ R/SurrogateLearnerCollection.R | 72 +++++++++++- R/TunerADBO.R |only R/TunerAsyncMbo.R |only R/TunerMbo.R | 7 - R/bayesopt_ego.R | 4 R/bayesopt_emo.R | 4 R/bayesopt_mpcl.R | 4 R/bayesopt_parego.R | 6 - R/bayesopt_smsego.R | 4 R/bibentries.R | 11 + R/mbo_defaults.R | 31 +++-- R/sugar.R | 4 R/zzz.R | 2 README.md | 8 - build/partial.rdb |binary man/AcqFunction.Rd | 17 ++ man/AcqOptimizer.Rd | 23 +++ man/ResultAssigner.Rd | 2 man/Surrogate.Rd | 20 +++ man/SurrogateLearner.Rd | 6 + man/SurrogateLearnerCollection.Rd | 8 + man/acqo.Rd | 4 man/default_acqfunction.Rd | 8 - man/default_surrogate.Rd | 19 ++- man/mlr_acqfunctions.Rd | 4 man/mlr_acqfunctions_aei.Rd | 5 man/mlr_acqfunctions_cb.Rd | 5 man/mlr_acqfunctions_ehvi.Rd | 5 man/mlr_acqfunctions_ehvigh.Rd | 5 man/mlr_acqfunctions_ei.Rd | 5 man/mlr_acqfunctions_eips.Rd | 5 man/mlr_acqfunctions_mean.Rd | 5 man/mlr_acqfunctions_multi.Rd | 7 - man/mlr_acqfunctions_pi.Rd | 5 man/mlr_acqfunctions_sd.Rd | 5 man/mlr_acqfunctions_smsego.Rd | 27 ++++ man/mlr_acqfunctions_stochastic_cb.Rd |only man/mlr_acqfunctions_stochastic_ei.Rd |only man/mlr_loop_functions_ego.Rd | 4 man/mlr_loop_functions_emo.Rd | 4 man/mlr_loop_functions_mpcl.Rd | 4 man/mlr_loop_functions_parego.Rd | 6 - man/mlr_loop_functions_smsego.Rd | 4 man/mlr_optimizers_adbo.Rd |only man/mlr_optimizers_async_mbo.Rd |only man/mlr_optimizers_mbo.Rd | 44 +++++-- man/mlr_result_assigners_archive.Rd | 2 man/mlr_result_assigners_surrogate.Rd | 4 man/mlr_tuners_adbo.Rd |only man/mlr_tuners_async_mbo.Rd |only man/mlr_tuners_mbo.Rd | 4 tests/testthat/helper.R | 35 ++++- tests/testthat/test_AcqFunctionSmsEgo.R | 5 tests/testthat/test_AcqFunctionStochasticCB.R |only tests/testthat/test_AcqFunctionStochasticEI.R |only tests/testthat/test_OptimizerADBO.R |only tests/testthat/test_OptimizerAsyncMbo.R |only tests/testthat/test_SurrogateLearner.R | 3 tests/testthat/test_SurrogateLearnerCollection.R | 3 tests/testthat/test_TunerADBO.R |only tests/testthat/test_TunerAsyncMbo.R |only 79 files changed, 674 insertions(+), 270 deletions(-)
Title: Profile R Code and Visualize with 'Pprof'
Description: Like similar profiling tools,
the 'proffer' package automatically detects
sources of slowness in R code.
The distinguishing feature of 'proffer' is its utilization of
'pprof', which supplies interactive visualizations
that are efficient and easy to interpret.
Behind the scenes, the 'profile' package converts
native Rprof() data to a protocol buffer
that 'pprof' understands.
For the documentation of 'proffer',
visit <https://r-prof.github.io/proffer/>.
To learn about the implementations and methodologies of
'pprof', 'profile', and protocol buffers,
visit <https://github.com/google/pprof>.
<https://protobuf.dev>,
and <https://github.com/r-prof/profile>, respectively.
Author: William Michael Landau [aut, cre]
,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between proffer versions 0.2.1 dated 2024-10-30 and 0.2.2 dated 2024-11-15
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/package.R | 1 + R/pprof.R | 8 +++++++- R/record.R | 30 +++++++++++++++++++++++------- man/pprof.Rd | 6 ++++++ man/record_pprof.Rd | 10 +++++++--- man/record_rprof.Rd | 7 ++++++- tests/local/test-interactive.R | 8 ++++++++ 11 files changed, 78 insertions(+), 27 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, trl],
Tom Wilderjans [aut],
Jeffrey Durieux [aut],
Eva Ceulemans [aut],
Kristof Meers [cre]
Maintainer: Kristof Meers <kristof.meers+cran@kuleuven.be>
Diff between multichull versions 3.0.0 dated 2024-07-18 and 3.0.1 dated 2024-11-15
DESCRIPTION | 27 ++++++++++++++++++++++----- MD5 | 6 +++--- NEWS.md | 3 +++ R/plot.MultiCHullcom.R | 2 +- 4 files changed, 29 insertions(+), 9 deletions(-)
Title: Regression and Clustering in Multivariate Response Scenarios
Description: Fitting multivariate response models with random effects on one or two levels; whereby the (one-dimensional) random effect represents a latent variable approximating the multivariate space of outcomes, after possible adjustment for covariates. The method is particularly useful for multivariate, highly correlated outcome variables with unobserved heterogeneities. Applications include regression with multivariate responses, as well as multivariate clustering or ranking problems. See Zhang and Einbeck (2024) <doi:10.1007/s42519-023-00357-0>.
Author: Yingjuan Zhang [aut, cre],
Jochen Einbeck [aut, ctb]
Maintainer: Yingjuan Zhang <yingjuan.zhang@durham.ac.uk>
Diff between mult.latent.reg versions 0.2.0 dated 2024-10-24 and 0.2.1 dated 2024-11-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/trading_data.R | 6 +++--- man/trading_data.Rd | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
More information about mult.latent.reg at CRAN
Permanent link
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007) (temporarily unavailable)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via by modsem it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8 [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.3 dated 2024-09-23 and 1.0.4 dated 2024-11-15
DESCRIPTION | 26 ++- MD5 | 222 +++++++++++++++++--------------- NAMESPACE | 2 R/calc_se_da.R | 164 +++++++++++++---------- R/check_model_da.R |only R/constraints_pi_ca.R | 149 ++++++++++++--------- R/construct_matrices_da.R | 164 ++++++++++++----------- R/cov_model.R | 34 ++-- R/create_labels_pi_ca.R | 8 - R/datasets.R | 159 ++++++++++++++++------ R/equations_qml.R | 86 ++++++++---- R/est_lms.R | 55 ++++--- R/est_qml.R | 24 +-- R/fit_modsem_da.R | 36 ++--- R/generics.R | 166 +++++++++++++---------- R/generics_modsem_da.R | 107 +++++++-------- R/generics_modsem_mplus.R | 34 ++-- R/generics_modsem_pi.R | 38 ++++- R/inspect_da.R | 16 +- R/labelled_params_da.R | 31 ++-- R/lavaan_labels.R | 6 R/lexer.R | 2 R/method_settings_da.R | 52 +++---- R/method_settings_pi.R | 2 R/model_da.R | 129 +++++++++--------- R/model_parameters_da.R | 48 +++--- R/model_pi.R | 59 ++++---- R/modsem.R | 56 ++++---- R/modsem_da.R | 69 +++++---- R/modsem_mplus.R | 48 +++--- R/modsem_pi.R | 176 +++++++++++++------------ R/optimize_da.R | 84 ++++++------ R/parser.R | 12 - R/plot_interaction.R | 44 +++--- R/print_partable.R | 106 +++++++-------- R/quadrature.R | 6 R/residual_cov_pi.R | 6 R/run_multiple_models.R | 6 R/set_threads.R | 4 R/simulate_partable.R | 67 ++++----- R/tokenizer.R | 8 - R/trace_paths_wright.R | 74 +++++----- R/utils.R | 121 +++++++++++++---- R/utils_da.R | 128 +++++------------- R/utils_pi.R | 125 +++++++++++++++--- R/zzz.R |only README.md | 29 +++- build/vignette.rds |binary data/TPB_1SO.rda |only data/TPB_2SO.rda |only inst/CITATION |only inst/doc/customizing.R | 78 +++++------ inst/doc/customizing.Rmd | 29 +--- inst/doc/customizing.html | 96 ++++--------- inst/doc/higher_order_interactions.R |only inst/doc/higher_order_interactions.Rmd |only inst/doc/higher_order_interactions.html |only inst/doc/interaction_two_etas.R | 66 ++++----- inst/doc/interaction_two_etas.Rmd | 52 ++----- inst/doc/interaction_two_etas.html | 82 ++++++----- inst/doc/lavaan.R | 32 ++-- inst/doc/lms_qml.R | 84 ++++++------ inst/doc/lms_qml.Rmd | 51 ++----- inst/doc/lms_qml.html | 79 ++++++----- inst/doc/methods.R | 41 +++-- inst/doc/methods.Rmd | 39 +++-- inst/doc/methods.html | 56 ++++---- inst/doc/modsem.R | 173 ++++++++++++------------ inst/doc/modsem.Rmd | 70 ++++------ inst/doc/modsem.html | 166 ++++++++++++----------- inst/doc/observed_lms_qml.R | 89 ++++++------ inst/doc/observed_lms_qml.Rmd | 58 ++------ inst/doc/observed_lms_qml.html | 91 ++++++------- inst/doc/plot_interactions.R | 8 - inst/doc/plot_interactions.Rmd | 31 ++-- inst/doc/plot_interactions.html | 32 ++-- inst/doc/quadratic.R | 48 +++--- inst/doc/quadratic.Rmd | 10 - inst/doc/quadratic.html | 27 ++- man/TPB.Rd | 6 man/TPB_1SO.Rd |only man/TPB_2SO.Rd |only man/TPB_UK.Rd | 12 - man/coef_modsem_da.Rd | 2 man/compare_fit.Rd | 6 man/extract_lavaan.Rd | 6 man/fit_modsem_da.Rd | 8 - man/get_pi_data.Rd | 6 man/get_pi_syntax.Rd | 6 man/jordan.Rd | 22 +-- man/modsem-package.Rd | 8 + man/modsem.Rd | 30 ++-- man/modsem_da.Rd | 29 ++-- man/modsem_inspect.Rd | 4 man/modsem_mplus.Rd | 8 - man/modsem_pi.Rd | 31 ++-- man/plot_interaction.Rd | 4 man/standardized_estimates.Rd | 16 +- man/summary.Rd | 4 man/trace_path.Rd | 6 man/var_interactions.Rd | 2 man/vcov_modsem_da.Rd | 2 tests/testthat/test_higher_order.R |only tests/testthat/test_intchecks.R |only tests/testthat/test_labels_lav.R |only tests/testthat/test_lav_models.R | 22 ++- tests/testthat/test_linear_da.R |only tests/testthat/test_lms.R | 63 ++++----- tests/testthat/test_ovchecks_da.R |only tests/testthat/test_tpb.R | 4 vignettes/customizing.Rmd | 29 +--- vignettes/higher_order_interactions.Rmd |only vignettes/interaction_two_etas.Rmd | 52 ++----- vignettes/lms_qml.Rmd | 51 ++----- vignettes/methods.Rmd | 39 +++-- vignettes/modsem.Rmd | 70 ++++------ vignettes/observed_lms_qml.Rmd | 58 ++------ vignettes/plot_interactions.Rmd | 31 ++-- vignettes/quadratic.Rmd | 10 - vignettes/set_eval_false.bash |only vignettes/set_eval_true.bash |only 121 files changed, 2764 insertions(+), 2459 deletions(-)
Title: A Distributed Worker Launcher Framework
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'NNG'-powered 'mirai' R package by Gao (2023)
<doi:10.5281/zenodo.7912722> is a sleek
and sophisticated scheduler that
efficiently processes these intense workloads.
The 'crew' package extends 'mirai' with a unifying
interface for third-party worker launchers.
Inspiration also comes from packages.
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischel, and Surmann (2017)
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Daniel Woodie [ctb],
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew versions 0.10.1 dated 2024-11-03 and 0.10.2 dated 2024-11-15
crew-0.10.1/crew/tests/local/test-launch_max.R |only crew-0.10.2/crew/DESCRIPTION | 17 crew-0.10.2/crew/MD5 | 58 - crew-0.10.2/crew/NAMESPACE | 2 crew-0.10.2/crew/NEWS.md | 11 crew-0.10.2/crew/R/crew_controller_local.R | 15 crew-0.10.2/crew/R/crew_eval.R | 6 crew-0.10.2/crew/R/crew_launcher.R | 130 +- crew-0.10.2/crew/R/crew_launcher_local.R | 19 crew-0.10.2/crew/R/crew_options_metrics.R | 15 crew-0.10.2/crew/R/crew_package.R | 1 crew-0.10.2/crew/R/crew_worker.R | 6 crew-0.10.2/crew/R/utils_packages.R | 11 crew-0.10.2/crew/inst/WORDLIST | 1 crew-0.10.2/crew/inst/doc/plugins.Rmd | 24 crew-0.10.2/crew/inst/doc/plugins.html | 541 +++++------ crew-0.10.2/crew/man/crew_class_launcher.Rd | 39 crew-0.10.2/crew/man/crew_class_launcher_local.Rd | 5 crew-0.10.2/crew/man/crew_controller_local.Rd | 30 crew-0.10.2/crew/man/crew_launcher.Rd | 30 crew-0.10.2/crew/man/crew_launcher_local.Rd | 28 crew-0.10.2/crew/man/crew_options_metrics.Rd | 15 crew-0.10.2/crew/man/crew_worker.Rd | 5 crew-0.10.2/crew/tests/local/test-backlog_seconds_idle.R | 3 crew-0.10.2/crew/tests/local/test-crashes_error.R |only crew-0.10.2/crew/tests/local/test-launcher-system2.R | 4 crew-0.10.2/crew/tests/testthat/test-crew_controller_local.R | 2 crew-0.10.2/crew/tests/testthat/test-crew_launcher.R | 36 crew-0.10.2/crew/tests/testthat/test-crew_worker.R | 3 crew-0.10.2/crew/tests/testthat/test-plugins.R | 12 crew-0.10.2/crew/vignettes/plugins.Rmd | 24 31 files changed, 640 insertions(+), 453 deletions(-)
Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following
the method described in Kang et al. (2010), <doi:10.1038/ng.548>.
One of a series of statistical genetic packages for streamlining the
analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre]
,
Willem Kruijer [aut] ,
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb] ,
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zh [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGWAS versions 1.0.9 dated 2022-10-13 and 1.0.10 dated 2024-11-15
statgenGWAS-1.0.10/statgenGWAS/DESCRIPTION | 14 statgenGWAS-1.0.10/statgenGWAS/MD5 | 51 statgenGWAS-1.0.10/statgenGWAS/NAMESPACE | 2 statgenGWAS-1.0.10/statgenGWAS/NEWS.md | 10 statgenGWAS-1.0.10/statgenGWAS/R/EMMA.R | 151 - statgenGWAS-1.0.10/statgenGWAS/R/GWASHelp.R | 5 statgenGWAS-1.0.10/statgenGWAS/R/createGData.R | 17 statgenGWAS-1.0.10/statgenGWAS/R/geneticMapPlot.R | 15 statgenGWAS-1.0.10/statgenGWAS/R/manhattanPlot.R | 2 statgenGWAS-1.0.10/statgenGWAS/R/qqPlot.R | 3 statgenGWAS-1.0.10/statgenGWAS/R/qtlPlot.R | 39 statgenGWAS-1.0.10/statgenGWAS/R/runSingleTraitGwas.R | 4 statgenGWAS-1.0.10/statgenGWAS/R/statgenGWAS.R | 1 statgenGWAS-1.0.10/statgenGWAS/build/partial.rdb |binary statgenGWAS-1.0.10/statgenGWAS/build/vignette.rds |binary statgenGWAS-1.0.10/statgenGWAS/configure | 1637 +++++++++------ statgenGWAS-1.0.10/statgenGWAS/configure.ac | 3 statgenGWAS-1.0.10/statgenGWAS/inst/doc/GWAS.R | 10 statgenGWAS-1.0.10/statgenGWAS/inst/doc/GWAS.Rmd | 21 statgenGWAS-1.0.10/statgenGWAS/inst/doc/GWAS.html | 598 ++--- statgenGWAS-1.0.10/statgenGWAS/man/plot.GWAS.Rd | 444 ++-- statgenGWAS-1.0.10/statgenGWAS/man/plot.gData.Rd | 120 - statgenGWAS-1.0.10/statgenGWAS/man/runSingleTraitGwas.Rd | 2 statgenGWAS-1.0.10/statgenGWAS/src/Makevars.in | 1 statgenGWAS-1.0.10/statgenGWAS/src/Makevars.win | 2 statgenGWAS-1.0.10/statgenGWAS/vignettes/GWAS.Rmd | 21 statgenGWAS-1.0.9/statgenGWAS/R/writeFlapJack.R |only 27 files changed, 1804 insertions(+), 1369 deletions(-)
Title: Sequence Symmetry Analysis Using the Observational Medical
Outcomes Partnership Common Data Model
Description: Calculating crude sequence ratio, adjusted sequence ratio and
confidence intervals using data mapped to the Observational Medical
Outcomes Partnership Common Data Model.
Author: Xihang Chen [aut, cre] ,
Tyman Stanford [aut] ,
Berta Raventos [aut] ,
Nicole Pratt [aut] ,
Ed Burn [aut] ,
Marti Catala [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez [aut] ,
Marta Alcalde-He [...truncated...]
Maintainer: Xihang Chen <xihang.chen@ndorms.ox.ac.uk>
Diff between CohortSymmetry versions 0.1.3 dated 2024-09-23 and 0.1.4 dated 2024-11-15
CohortSymmetry-0.1.3/CohortSymmetry/R/adjustedSequenceRatio.R |only CohortSymmetry-0.1.3/CohortSymmetry/R/utils-pipe.R |only CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort_set.R |only CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort_set.Rmd |only CohortSymmetry-0.1.3/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort_set.html |only CohortSymmetry-0.1.3/CohortSymmetry/man/pipe.Rd |only CohortSymmetry-0.1.3/CohortSymmetry/vignettes/a02_Generate_a_sequence_cohort_set.Rmd |only CohortSymmetry-0.1.4/CohortSymmetry/DESCRIPTION | 23 CohortSymmetry-0.1.4/CohortSymmetry/MD5 | 92 CohortSymmetry-0.1.4/CohortSymmetry/NAMESPACE | 3 CohortSymmetry-0.1.4/CohortSymmetry/R/CohortSymmetry-package.R | 21 CohortSymmetry-0.1.4/CohortSymmetry/R/crudeSequenceRatio.R | 30 CohortSymmetry-0.1.4/CohortSymmetry/R/displayTables.R | 496 +- CohortSymmetry-0.1.4/CohortSymmetry/R/generateSequenceCohortSet.R | 692 +-- CohortSymmetry-0.1.4/CohortSymmetry/R/getConfidenceInterval.R | 89 CohortSymmetry-0.1.4/CohortSymmetry/R/getSummarisedResult.R | 134 CohortSymmetry-0.1.4/CohortSymmetry/R/helpers.R |only CohortSymmetry-0.1.4/CohortSymmetry/R/inputValidation.R | 17 CohortSymmetry-0.1.4/CohortSymmetry/R/mockCohortSymmetry.R | 182 CohortSymmetry-0.1.4/CohortSymmetry/R/nullSequenceRatio.R | 243 - CohortSymmetry-0.1.4/CohortSymmetry/R/plotSequenceRatios.R | 226 - CohortSymmetry-0.1.4/CohortSymmetry/R/plotTemporalSymmetry.R | 164 CohortSymmetry-0.1.4/CohortSymmetry/R/summariseSequenceRatios.R | 399 -- CohortSymmetry-0.1.4/CohortSymmetry/README.md | 8 CohortSymmetry-0.1.4/CohortSymmetry/build/vignette.rds |binary CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a01_Introduction.Rmd | 268 - CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a01_Introduction.html | 154 CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort.R |only CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort.Rmd |only CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort.html |only CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.R | 6 CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.Rmd | 247 - CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.html | 70 CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.Rmd | 372 - CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.html | 450 +- CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.Rmd | 244 - CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.html | 24 CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.Rmd | 262 - CohortSymmetry-0.1.4/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.html | 12 CohortSymmetry-0.1.4/CohortSymmetry/man/CohortSymmetry-package.Rd | 4 CohortSymmetry-0.1.4/CohortSymmetry/man/generateSequenceCohortSet.Rd | 15 CohortSymmetry-0.1.4/CohortSymmetry/man/summariseSequenceRatios.Rd | 5 CohortSymmetry-0.1.4/CohortSymmetry/tests/testthat/test-attrition.R | 28 CohortSymmetry-0.1.4/CohortSymmetry/tests/testthat/test-eunomia.R | 138 CohortSymmetry-0.1.4/CohortSymmetry/tests/testthat/test-generateSequenceCohortSet.R | 1991 ++++------ CohortSymmetry-0.1.4/CohortSymmetry/tests/testthat/test-plotTemporalSymmetry.R | 278 - CohortSymmetry-0.1.4/CohortSymmetry/tests/testthat/test-summariseSequenceRatios.R | 1931 ++++----- CohortSymmetry-0.1.4/CohortSymmetry/vignettes/a01_Introduction.Rmd | 268 - CohortSymmetry-0.1.4/CohortSymmetry/vignettes/a02_Generate_a_sequence_cohort.Rmd |only CohortSymmetry-0.1.4/CohortSymmetry/vignettes/a03_Summarise_sequence_ratios.Rmd | 247 - CohortSymmetry-0.1.4/CohortSymmetry/vignettes/a04_Visualise_sequence_ratios.Rmd | 372 - CohortSymmetry-0.1.4/CohortSymmetry/vignettes/a05_Summarise_temporal_symmetry.Rmd | 244 - CohortSymmetry-0.1.4/CohortSymmetry/vignettes/a06_Visualise_temporal_symmetry.Rmd | 262 - 53 files changed, 5301 insertions(+), 5410 deletions(-)
More information about CohortSymmetry at CRAN
Permanent link
Title: Extract Tables from PDF Documents
Description: Bindings for the 'Tabula' <https://tabula.technology/> 'Java'
library, which can extract tables from PDF files. This tool can reduce time
and effort in data extraction processes in fields like investigative
journalism. It allows for automatic and manual table extraction, the latter
facilitated through a 'Shiny' interface, enabling manual areas selection\
with a computer mouse for data retrieval.
Author: Thomas J. Leeper [aut] ,
Mauricio Vargas Sepulveda [aut, cre]
,
Tom Paskhalis [aut] ,
Manuel Aristaran [ctb],
David Gohel [ctb] ,
Lincoln Mullen [ctb] ,
Munk School of Global Affairs and Public Policy [fnd]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Diff between tabulapdf versions 1.0.5-3 dated 2024-05-21 and 1.0.5-5 dated 2024-11-15
DESCRIPTION | 15 +++++++++------ MD5 | 29 ++++++++++++++++------------- NEWS.md | 12 ++++++++++++ R/extract_text.R | 5 ----- R/get_page_dims.R | 1 - R/locate_area.R | 23 +++++++++++++++++------ R/make_thumbnails.R | 4 ++-- build/vignette.rds |binary inst/doc/tabulapdf.R | 4 ++-- inst/doc/tabulapdf.Rmd | 4 ++-- inst/doc/tabulapdf.html | 4 ++-- inst/examples/argentina.pdf |only inst/examples/quebec.pdf |only inst/examples/xbar.pdf |only man/extract_areas.Rd | 3 +++ tests/testthat/test_non-latin.R | 6 ++++-- vignettes/tabulapdf.Rmd | 4 ++-- 17 files changed, 71 insertions(+), 43 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre],
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 2.6.1 dated 2024-08-06 and 2.6.2 dated 2024-11-15
Rdpack-2.6.1/Rdpack/inst/auto |only Rdpack-2.6.1/Rdpack/inst/examples/RdpackTester/inst/auto |only Rdpack-2.6.1/Rdpack/vignettes/auto |only Rdpack-2.6.2/Rdpack/DESCRIPTION | 6 Rdpack-2.6.2/Rdpack/MD5 | 25 Rdpack-2.6.2/Rdpack/NEWS.md | 15 Rdpack-2.6.2/Rdpack/R/RStudio.R | 84 +-- Rdpack-2.6.2/Rdpack/R/bib.R | 275 ++++------ Rdpack-2.6.2/Rdpack/build/partial.rdb |binary Rdpack-2.6.2/Rdpack/inst/REFERENCES.bib | 3 Rdpack-2.6.2/Rdpack/inst/doc/Inserting_bibtex_references.pdf |binary Rdpack-2.6.2/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary Rdpack-2.6.2/Rdpack/man/RStudio_reprompt.Rd | 2 Rdpack-2.6.2/Rdpack/man/macros/refmacros.Rd | 50 - Rdpack-2.6.2/Rdpack/tests/testthat/test-bib.R | 2 15 files changed, 237 insertions(+), 225 deletions(-)
Title: 3D Prioritization Algorithm
Description: Three-dimensional systematic conservation planning, conducting
nested prioritization analyses across multiple depth levels and
ensuring efficient resource allocation throughout the water column.
It provides a structured workflow designed to address biodiversity
conservation and management challenges in the 3 dimensions, while
facilitating users’ choices and parameterization (Doxa et al. 2024
<doi:10.1016/j.ecolmodel.2024.110919>).
Author: Aggeliki Doxa [aut] ,
Christos Adam [aut, cre],
Nikolaos Nagkoulis [aut] ,
Antonios D. Mazaris [aut] ,
Stelios Katsanevakis [aut]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between prior3D versions 0.1.2 dated 2024-11-06 and 0.1.3 dated 2024-11-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ README.md | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 +- 7 files changed, 19 insertions(+), 13 deletions(-)
Title: Draw Flows (Migration, Goods, Money, Information) on 'ggplot2'
Plots
Description: Adds flow maps to 'ggplot2' plots. The flow maps consist of 'ggplot2' layers which visualize the nodes as circles and the bilateral flows between the nodes as bidirectional half-arrows.
Author: Johannes Mast [aut, cre]
Maintainer: Johannes Mast <johannes.mast@dlr.de>
Diff between flowmapper versions 0.1.2 dated 2024-09-06 and 0.1.3 dated 2024-11-15
DESCRIPTION | 8 - MD5 | 11 +- NAMESPACE | 1 NEWS.md | 4 R/add_flowmap.R | 235 ++++++++++++++++++++++++++++++++++++++--------------- inst |only man/add_flowmap.Rd | 7 + 7 files changed, 188 insertions(+), 78 deletions(-)
Title: CFO-Type Designs in Phase I/II Clinical Trials
Description: In phase I clinical trials, the primary objective is to ascertain the maximum tolerated dose (MTD) corresponding to a specified target toxicity rate. The subsequent phase II trials are designed to examine the potential efficacy of the drug based on the MTD obtained from the phase I trials, with the aim of identifying the optimal biological dose (OBD). The 'CFO' package facilitates the implementation of dose-finding trials by utilizing calibration-free odds type (CFO-type) designs. Specifically, it encompasses the calibration-free odds (CFO) (Jin and Yin (2022) <doi:10.1177/09622802221079353>), randomized CFO (rCFO), precision CFO (pCFO), two-dimensional CFO (2dCFO) (Wang et al. (2023) <doi:10.3389/fonc.2023.1294258>), time-to-event CFO (TITE-CFO) (Jin and Yin (2023) <doi:10.1002/pst.2304>), fractional CFO (fCFO), accumulative CFO (aCFO), TITE-aCFO, and f-aCFO (Fang and Yin (2024) <doi: 10.1002/sim.10127>). It supports phase I/II trials for the CFO design and onl [...truncated...]
Author: Jialu Fang [aut, cre],
Ninghao Zhang [aut],
Wenliang Wang [aut],
Guosheng Yin [aut]
Maintainer: Jialu Fang <u3008682@connect.hku.hk>
Diff between CFO versions 2.1.0 dated 2024-10-15 and 2.2.0 dated 2024-11-15
DESCRIPTION | 8 MD5 | 24 - NAMESPACE | 1 R/CFO.oc.R | 486 +++++++++++++++++------------------ R/CFO.simu.R | 461 ++++++++++++++++----------------- R/lateonset.next.R | 690 ++++++++++++++++++++++++-------------------------- R/lateonset.simu.R | 525 +++++++++++++++++++------------------- R/pCFO.next.R |only R/plot.cfo.R | 1 man/CFO.oc.Rd | 20 - man/CFO.simu.Rd | 12 man/lateonset.next.Rd | 13 man/lateonset.simu.Rd | 4 man/pCFO.next.Rd |only 14 files changed, 1124 insertions(+), 1121 deletions(-)
Title: Datasets for 'spatstat' Family
Description: Contains all the datasets for the 'spatstat' family of packages.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut] ,
W Aherne [ctb],
Freda Alexander [ctb],
Qi Wei Ang [ctb],
Sourav Banerjee [ctb],
Mark Berman [ctb],
R Bernhardt [ctb],
Thomas Berndtsen [ctb],
Andrew Bevan [ctb],
Jeffrey Betts [ctb],
[...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 3.1-2 dated 2024-06-21 and 3.1-4 dated 2024-11-15
DESCRIPTION | 8 +- MD5 | 128 ++++++++++++++++++++++----------------------- NEWS | 20 +++++++ data/Kovesi.rda |binary data/amacrine.rda |binary data/anemones.rda |binary data/ants.rda |binary data/austates.rda |binary data/bdspots.rda |binary data/bei.rda |binary data/betacells.rda |binary data/bramblecanes.rda |binary data/bronzefilter.rda |binary data/btb.rda |binary data/cells.rda |binary data/cetaceans.rda |binary data/chicago.rda |binary data/chorley.rda |binary data/clmfires.rda |binary data/concrete.rda |binary data/copper.rda |binary data/demohyper.rda |binary data/demopat.rda |binary data/dendrite.rda |binary data/finpines.rda |binary data/flu.rda |binary data/ganglia.rda |binary data/gordon.rda |binary data/gorillas.rda |binary data/hamster.rda |binary data/heather.rda |binary data/humberside.rda |binary data/hyytiala.rda |binary data/japanesepines.rda |binary data/lansing.rda |binary data/letterR.rda |binary data/longleaf.rda |binary data/mucosa.rda |binary data/murchison.rda |binary data/nbfires.rda |binary data/nztrees.rda |binary data/osteo.rda |binary data/paracou.rda |binary data/ponderosa.rda |binary data/pyramidal.rda |binary data/redwood.rda |binary data/redwood3.rda |binary data/redwoodfull.rda |binary data/residualspaper.rda |binary data/shapley.rda |binary data/shelling.rda |only data/simba.rda |binary data/simdat.rda |binary data/simplenet.rda |binary data/spiders.rda |binary data/sporophores.rda |binary data/spruces.rda |binary data/stonetools.rda |binary data/swedishpines.rda |binary data/urkiola.rda |binary data/vesicles.rda |binary data/waka.rda |binary data/waterstriders.rda |binary inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 1 man/shelling.Rd |only 66 files changed, 92 insertions(+), 67 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Designed for simplicity, a 'mirai' evaluates an R expression
asynchronously in a parallel process, locally or distributed over the
network, with the result automatically available upon completion. Modern
networking and concurrency built on 'nanonext' and 'NNG' (Nanomsg Next Gen)
ensure reliable and efficient scheduling, over fast inter-process
communications or TCP/IP secured by TLS. Advantages include being inherently
queued thus handling many more tasks than available processes, no storage on
the file system, support for otherwise non-exportable reference objects, an
event-driven promises implementation, and built-in asynchronous parallel
map.
Author: Charlie Gao [aut, cre] ,
Joe Cheng [ctb],
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 1.3.0 dated 2024-10-09 and 1.3.1 dated 2024-11-15
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Title: Classifications and Codelists for Statistics Norway
Description: Functions to search, retrieve, apply and update classifications
and codelists using Statistics Norway's API <https://www.ssb.no/klass>
from the system 'KLASS'. Retrieves classifications by date with options
to choose language, hierarchical level and formatting.
Author: Susie Jentoft [aut, cre],
Diana-Cristina Iancu [aut],
Lisa Li [aut],
Oeyvind I. Berntsen [aut],
Statistics Norway [cph]
Maintainer: Susie Jentoft <susie.jentoft@ssb.no>
Diff between klassR versions 0.2.4 dated 2024-08-16 and 1.0.0 dated 2024-11-15
klassR-0.2.4/klassR/man/ApplyKlass.Rd |only klassR-0.2.4/klassR/man/CorrespondList.Rd |only klassR-0.2.4/klassR/man/GetFamily.Rd |only klassR-0.2.4/klassR/man/GetKlass.Rd |only klassR-0.2.4/klassR/man/GetName.Rd |only klassR-0.2.4/klassR/man/GetVersion.Rd |only klassR-0.2.4/klassR/man/ListFamily.Rd |only klassR-0.2.4/klassR/man/ListKlass.Rd |only klassR-0.2.4/klassR/man/SearchKlass.Rd |only klassR-1.0.0/klassR/DESCRIPTION | 23 klassR-1.0.0/klassR/MD5 | 79 +- klassR-1.0.0/klassR/NAMESPACE | 13 klassR-1.0.0/klassR/NEWS.md | 5 klassR-1.0.0/klassR/R/Convert_table.R | 26 klassR-1.0.0/klassR/R/Hent_data.R | 351 +++++----- klassR-1.0.0/klassR/R/KLASS.R | 244 ++++-- klassR-1.0.0/klassR/R/Klass_list.R | 242 ++++-- klassR-1.0.0/klassR/R/Levels.R | 10 klassR-1.0.0/klassR/R/UpdateKlass-graph-build.R |only klassR-1.0.0/klassR/R/UpdateKlass-graph-navigate.R |only klassR-1.0.0/klassR/R/UpdateKlass.R |only klassR-1.0.0/klassR/R/checkLevel.R | 17 klassR-1.0.0/klassR/R/data.R | 21 klassR-1.0.0/klassR/R/format.R | 51 - klassR-1.0.0/klassR/data/klass_131_1964_graph.RData |only klassR-1.0.0/klassR/data/klass_131_2020_graph.RData |only klassR-1.0.0/klassR/data/klass_131_graph.RData |only klassR-1.0.0/klassR/data/klassdata.RData |binary klassR-1.0.0/klassR/man/MakeUrl.Rd | 4 klassR-1.0.0/klassR/man/apply_klass.Rd |only klassR-1.0.0/klassR/man/correspond_list.Rd |only klassR-1.0.0/klassR/man/count_neighbors.Rd |only klassR-1.0.0/klassR/man/find_dates.Rd |only klassR-1.0.0/klassR/man/find_name.Rd |only klassR-1.0.0/klassR/man/find_variant_from.Rd |only klassR-1.0.0/klassR/man/find_variant_to.Rd |only klassR-1.0.0/klassR/man/formattering.Rd | 4 klassR-1.0.0/klassR/man/get_family.Rd |only klassR-1.0.0/klassR/man/get_klass.Rd |only klassR-1.0.0/klassR/man/get_klass_changes.Rd |only klassR-1.0.0/klassR/man/get_name.Rd |only klassR-1.0.0/klassR/man/get_version.Rd |only klassR-1.0.0/klassR/man/is_combined.Rd |only klassR-1.0.0/klassR/man/is_split.Rd |only klassR-1.0.0/klassR/man/klass_131_1964_graph.Rd |only klassR-1.0.0/klassR/man/klass_131_2020_graph.Rd |only klassR-1.0.0/klassR/man/klass_131_graph.Rd |only klassR-1.0.0/klassR/man/klass_graph.Rd |only klassR-1.0.0/klassR/man/klass_node.Rd |only klassR-1.0.0/klassR/man/levelCheck.Rd | 2 klassR-1.0.0/klassR/man/list_family.Rd |only klassR-1.0.0/klassR/man/list_klass.Rd |only klassR-1.0.0/klassR/man/search_klass.Rd |only klassR-1.0.0/klassR/man/update_code.Rd |only klassR-1.0.0/klassR/man/update_klass.Rd |only klassR-1.0.0/klassR/man/update_klass_node.Rd |only klassR-1.0.0/klassR/tests/testthat/test-UpdateKlass-graph-navigate.R |only klassR-1.0.0/klassR/tests/testthat/test-UpdateKlass.R |only klassR-1.0.0/klassR/tests/testthat/test_ApplyKlass.R | 219 +++--- klassR-1.0.0/klassR/tests/testthat/test_GetKlass.R | 158 ++-- klassR-1.0.0/klassR/tests/testthat/test_ListKlass.R | 26 klassR-1.0.0/klassR/tests/testthat/test_formattering.R |only 62 files changed, 869 insertions(+), 626 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.5 dated 2024-10-20 and 1.3.6 dated 2024-11-15
DESCRIPTION | 16 MD5 | 43 - NAMESPACE | 11 NEWS.md | 6 R/CreateTableOneJS.R | 104 ++- R/cox2.R | 36 - R/forestcox.R | 1053 ++++++++++++++++++++------------ R/forestglm.R | 40 + R/svyCreateTableOneJS.R | 87 ++ build/vignette.rds |binary inst/doc/jstable.html | 42 - man/CreateTableOne2.Rd | 5 man/CreateTableOneJS.Rd | 8 man/TableSubgroupCox.Rd | 11 man/TableSubgroupGLM.Rd | 5 man/TableSubgroupMultiCox.Rd | 11 man/TableSubgroupMultiGLM.Rd | 5 man/count_event_by.Rd |only man/svyCreateTableOne2.Rd | 5 man/svyCreateTableOneJS.Rd | 5 tests/testthat/test-CreateTableOneJS.R | 2 tests/testthat/test-forestcox.R | 26 tests/testthat/test-svyCreateTableOne.R | 6 23 files changed, 1054 insertions(+), 473 deletions(-)
Title: Generalized Random Forests
Description: Forest-based statistical estimation and inference.
GRF provides non-parametric methods for heterogeneous treatment effects estimation
(optionally using right-censored outcomes, multiple treatment arms or outcomes, or instrumental variables),
as well as least-squares regression, quantile regression, and survival regression,
all with support for missing covariates.
Author: Julie Tibshirani [aut],
Susan Athey [aut],
Rina Friedberg [ctb],
Vitor Hadad [ctb],
David Hirshberg [ctb],
Luke Miner [ctb],
Erik Sverdrup [aut, cre],
Stefan Wager [aut],
Marvin Wright [ctb]
Maintainer: Erik Sverdrup <erik.sverdrup@monash.edu>
Diff between grf versions 2.3.2 dated 2024-02-25 and 2.4.0 dated 2024-11-15
grf-2.3.2/grf/R/deprecated.R |only grf-2.3.2/grf/man/average_late.Rd |only grf-2.3.2/grf/man/average_partial_effect.Rd |only grf-2.3.2/grf/man/custom_forest.Rd |only grf-2.3.2/grf/man/get_sample_weights.Rd |only grf-2.3.2/grf/man/tune_causal_forest.Rd |only grf-2.3.2/grf/man/tune_instrumental_forest.Rd |only grf-2.3.2/grf/man/tune_regression_forest.Rd |only grf-2.4.0/grf/DESCRIPTION | 8 grf-2.4.0/grf/MD5 | 324 ++++------ grf-2.4.0/grf/NAMESPACE | 8 grf-2.4.0/grf/R/RcppExports.R | 40 - grf-2.4.0/grf/R/average_treatment_effect.R | 4 grf-2.4.0/grf/R/causal_forest.R | 6 grf-2.4.0/grf/R/causal_survival_forest.R | 6 grf-2.4.0/grf/R/get_scores.R | 9 grf-2.4.0/grf/R/grf_options.R |only grf-2.4.0/grf/R/input_utilities.R | 12 grf-2.4.0/grf/R/instrumental_forest.R | 6 grf-2.4.0/grf/R/ll_regression_forest.R | 6 grf-2.4.0/grf/R/lm_forest.R | 5 grf-2.4.0/grf/R/multi_arm_causal_forest.R | 8 grf-2.4.0/grf/R/multi_regression_forest.R | 6 grf-2.4.0/grf/R/probability_forest.R | 6 grf-2.4.0/grf/R/quantile_forest.R | 6 grf-2.4.0/grf/R/rank_average_treatment.R | 4 grf-2.4.0/grf/R/regression_forest.R | 6 grf-2.4.0/grf/R/survival_forest.R | 6 grf-2.4.0/grf/R/tune_forest.R | 1 grf-2.4.0/grf/man/average_treatment_effect.Rd | 4 grf-2.4.0/grf/man/grf_options.Rd |only grf-2.4.0/grf/man/multi_arm_causal_forest.Rd | 2 grf-2.4.0/grf/man/predict.causal_forest.Rd | 2 grf-2.4.0/grf/man/predict.causal_survival_forest.Rd | 2 grf-2.4.0/grf/man/predict.instrumental_forest.Rd | 2 grf-2.4.0/grf/man/predict.ll_regression_forest.Rd | 2 grf-2.4.0/grf/man/predict.lm_forest.Rd | 2 grf-2.4.0/grf/man/predict.multi_arm_causal_forest.Rd | 2 grf-2.4.0/grf/man/predict.multi_regression_forest.Rd | 2 grf-2.4.0/grf/man/predict.probability_forest.Rd | 2 grf-2.4.0/grf/man/predict.quantile_forest.Rd | 2 grf-2.4.0/grf/man/predict.regression_forest.Rd | 2 grf-2.4.0/grf/man/predict.survival_forest.Rd | 2 grf-2.4.0/grf/man/rank_average_treatment_effect.Rd | 2 grf-2.4.0/grf/src/AnalysisToolsBindings.cpp | 4 grf-2.4.0/grf/src/CausalForestBindings.cpp | 7 grf-2.4.0/grf/src/CausalSurvivalForestBindings.cpp | 7 grf-2.4.0/grf/src/InstrumentalForestBindings.cpp | 7 grf-2.4.0/grf/src/MultiCausalForestBindings.cpp | 7 grf-2.4.0/grf/src/MultiRegressionForestBindings.cpp | 7 grf-2.4.0/grf/src/ProbabilityForestBindings.cpp | 7 grf-2.4.0/grf/src/QuantileForestBindings.cpp | 9 grf-2.4.0/grf/src/RcppExports.cpp | 90 +- grf-2.4.0/grf/src/RcppUtilities.cpp | 2 grf-2.4.0/grf/src/RcppUtilities.h | 2 grf-2.4.0/grf/src/RegressionForestBindings.cpp | 12 grf-2.4.0/grf/src/SurvivalForestBindings.cpp | 7 grf-2.4.0/grf/src/optional/optional.hpp | 118 ++- grf-2.4.0/grf/src/src/analysis/SplitFrequencyComputer.cpp | 4 grf-2.4.0/grf/src/src/analysis/SplitFrequencyComputer.h | 4 grf-2.4.0/grf/src/src/commons/Data.cpp | 4 grf-2.4.0/grf/src/src/commons/Data.h | 2 grf-2.4.0/grf/src/src/commons/utility.cpp | 2 grf-2.4.0/grf/src/src/commons/utility.h | 2 grf-2.4.0/grf/src/src/forest/Forest.cpp | 2 grf-2.4.0/grf/src/src/forest/Forest.h | 2 grf-2.4.0/grf/src/src/forest/ForestOptions.cpp | 12 grf-2.4.0/grf/src/src/forest/ForestOptions.h | 6 grf-2.4.0/grf/src/src/forest/ForestPredictor.cpp | 2 grf-2.4.0/grf/src/src/forest/ForestPredictor.h | 2 grf-2.4.0/grf/src/src/forest/ForestPredictors.cpp | 2 grf-2.4.0/grf/src/src/forest/ForestPredictors.h | 2 grf-2.4.0/grf/src/src/forest/ForestTrainer.cpp | 9 grf-2.4.0/grf/src/src/forest/ForestTrainer.h | 2 grf-2.4.0/grf/src/src/forest/ForestTrainers.cpp | 2 grf-2.4.0/grf/src/src/forest/ForestTrainers.h | 2 grf-2.4.0/grf/src/src/prediction/CausalSurvivalPredictionStrategy.cpp | 2 grf-2.4.0/grf/src/src/prediction/CausalSurvivalPredictionStrategy.h | 2 grf-2.4.0/grf/src/src/prediction/DefaultPredictionStrategy.h | 2 grf-2.4.0/grf/src/src/prediction/InstrumentalPredictionStrategy.cpp | 2 grf-2.4.0/grf/src/src/prediction/InstrumentalPredictionStrategy.h | 2 grf-2.4.0/grf/src/src/prediction/LLCausalPredictionStrategy.cpp | 2 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grf-2.4.0/grf/src/src/prediction/ProbabilityPredictionStrategy.h | 2 grf-2.4.0/grf/src/src/prediction/QuantilePredictionStrategy.cpp | 2 grf-2.4.0/grf/src/src/prediction/QuantilePredictionStrategy.h | 2 grf-2.4.0/grf/src/src/prediction/RegressionPredictionStrategy.cpp | 2 grf-2.4.0/grf/src/src/prediction/RegressionPredictionStrategy.h | 2 grf-2.4.0/grf/src/src/prediction/SurvivalPredictionStrategy.cpp | 2 grf-2.4.0/grf/src/src/prediction/SurvivalPredictionStrategy.h | 4 grf-2.4.0/grf/src/src/prediction/collector/DefaultPredictionCollector.cpp | 2 grf-2.4.0/grf/src/src/prediction/collector/DefaultPredictionCollector.h | 2 grf-2.4.0/grf/src/src/prediction/collector/OptimizedPredictionCollector.cpp | 2 grf-2.4.0/grf/src/src/prediction/collector/OptimizedPredictionCollector.h | 2 grf-2.4.0/grf/src/src/prediction/collector/PredictionCollector.h | 2 grf-2.4.0/grf/src/src/prediction/collector/SampleWeightComputer.cpp | 4 grf-2.4.0/grf/src/src/prediction/collector/SampleWeightComputer.h | 4 grf-2.4.0/grf/src/src/prediction/collector/TreeTraverser.cpp | 4 grf-2.4.0/grf/src/src/prediction/collector/TreeTraverser.h | 4 grf-2.4.0/grf/src/src/relabeling/CausalSurvivalRelabelingStrategy.cpp | 2 grf-2.4.0/grf/src/src/relabeling/CausalSurvivalRelabelingStrategy.h | 2 grf-2.4.0/grf/src/src/relabeling/InstrumentalRelabelingStrategy.cpp | 2 grf-2.4.0/grf/src/src/relabeling/InstrumentalRelabelingStrategy.h | 2 grf-2.4.0/grf/src/src/relabeling/LLRegressionRelabelingStrategy.cpp | 2 grf-2.4.0/grf/src/src/relabeling/LLRegressionRelabelingStrategy.h | 2 grf-2.4.0/grf/src/src/relabeling/MultiCausalRelabelingStrategy.cpp | 2 grf-2.4.0/grf/src/src/relabeling/MultiCausalRelabelingStrategy.h | 2 grf-2.4.0/grf/src/src/relabeling/MultiNoopRelabelingStrategy.cpp | 2 grf-2.4.0/grf/src/src/relabeling/MultiNoopRelabelingStrategy.h | 2 grf-2.4.0/grf/src/src/relabeling/NoopRelabelingStrategy.cpp | 2 grf-2.4.0/grf/src/src/relabeling/NoopRelabelingStrategy.h | 2 grf-2.4.0/grf/src/src/relabeling/QuantileRelabelingStrategy.cpp | 2 grf-2.4.0/grf/src/src/relabeling/QuantileRelabelingStrategy.h | 2 grf-2.4.0/grf/src/src/relabeling/RelabelingStrategy.h | 2 grf-2.4.0/grf/src/src/sampling/RandomSampler.cpp | 2 grf-2.4.0/grf/src/src/sampling/RandomSampler.h | 2 grf-2.4.0/grf/src/src/sampling/SamplingOptions.cpp | 2 grf-2.4.0/grf/src/src/sampling/SamplingOptions.h | 2 grf-2.4.0/grf/src/src/splitting/CausalSurvivalSplittingRule.cpp | 2 grf-2.4.0/grf/src/src/splitting/CausalSurvivalSplittingRule.h | 4 grf-2.4.0/grf/src/src/splitting/InstrumentalSplittingRule.cpp | 2 grf-2.4.0/grf/src/src/splitting/InstrumentalSplittingRule.h | 4 grf-2.4.0/grf/src/src/splitting/MultiCausalSplittingRule.cpp | 2 grf-2.4.0/grf/src/src/splitting/MultiCausalSplittingRule.h | 2 grf-2.4.0/grf/src/src/splitting/MultiRegressionSplittingRule.cpp | 2 grf-2.4.0/grf/src/src/splitting/MultiRegressionSplittingRule.h | 2 grf-2.4.0/grf/src/src/splitting/ProbabilitySplittingRule.cpp | 2 grf-2.4.0/grf/src/src/splitting/ProbabilitySplittingRule.h | 2 grf-2.4.0/grf/src/src/splitting/RegressionSplittingRule.cpp | 2 grf-2.4.0/grf/src/src/splitting/RegressionSplittingRule.h | 2 grf-2.4.0/grf/src/src/splitting/SplittingRule.h | 2 grf-2.4.0/grf/src/src/splitting/SurvivalSplittingRule.cpp | 2 grf-2.4.0/grf/src/src/splitting/SurvivalSplittingRule.h | 2 grf-2.4.0/grf/src/src/splitting/factory/CausalSurvivalSplittingRuleFactory.cpp | 2 grf-2.4.0/grf/src/src/splitting/factory/CausalSurvivalSplittingRuleFactory.h | 2 grf-2.4.0/grf/src/src/splitting/factory/InstrumentalSplittingRuleFactory.cpp | 2 grf-2.4.0/grf/src/src/splitting/factory/InstrumentalSplittingRuleFactory.h | 2 grf-2.4.0/grf/src/src/splitting/factory/MultiCausalSplittingRuleFactory.cpp | 2 grf-2.4.0/grf/src/src/splitting/factory/MultiCausalSplittingRuleFactory.h | 2 grf-2.4.0/grf/src/src/splitting/factory/MultiRegressionSplittingRuleFactory.cpp | 2 grf-2.4.0/grf/src/src/splitting/factory/MultiRegressionSplittingRuleFactory.h | 4 grf-2.4.0/grf/src/src/splitting/factory/ProbabilitySplittingRuleFactory.cpp | 2 grf-2.4.0/grf/src/src/splitting/factory/ProbabilitySplittingRuleFactory.h | 2 grf-2.4.0/grf/src/src/splitting/factory/RegressionSplittingRuleFactory.cpp | 2 grf-2.4.0/grf/src/src/splitting/factory/RegressionSplittingRuleFactory.h | 2 grf-2.4.0/grf/src/src/splitting/factory/SplittingRuleFactory.h | 2 grf-2.4.0/grf/src/src/splitting/factory/SurvivalSplittingRuleFactory.cpp | 2 grf-2.4.0/grf/src/src/splitting/factory/SurvivalSplittingRuleFactory.h | 2 grf-2.4.0/grf/src/src/tree/Tree.cpp | 2 grf-2.4.0/grf/src/src/tree/Tree.h | 2 grf-2.4.0/grf/src/src/tree/TreeOptions.cpp | 2 grf-2.4.0/grf/src/src/tree/TreeOptions.h | 2 grf-2.4.0/grf/src/src/tree/TreeTrainer.cpp | 2 grf-2.4.0/grf/src/src/tree/TreeTrainer.h | 2 168 files changed, 700 insertions(+), 356 deletions(-)
Title: Extending 'dendrogram' Functionality in R
Description: Offers a set of functions for extending
'dendrogram' objects in R, letting you visualize and compare trees of
'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different 'dendrograms' to one another.
Author: Tal Galili [aut, cre, cph] ,
Yoav Benjamini [ths],
Gavin Simpson [ctb],
Gregory Jefferis [aut, ctb] ,
Marco Gallotta [ctb] ,
Johan Renaudie [ctb] ,
The R Core Team [ctb] ,
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvat [...truncated...]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between dendextend versions 1.18.1 dated 2024-10-12 and 1.19.0 dated 2024-11-15
DESCRIPTION | 8 MD5 | 91 ++++--- NAMESPACE | 4 NEWS.md | 12 R/all.equal.R | 15 + R/dendlist.R | 1 R/pvclust.R | 3 R/untangle.R | 8 inst/doc/Cluster_Analysis.html | 4 inst/doc/FAQ.html | 4 inst/doc/Quick_Introduction.html | 4 inst/doc/dendextend.html | 8 man/all.equal.dendrogram.Rd | 20 - tests/testthat/Rplots.pdf |only tests/testthat/test-Hmisc.R |only tests/testthat/test-all.equal.R |only tests/testthat/test-attr_access.R | 209 ++++++++++++++++ tests/testthat/test-bk_method.R | 113 ++++++++ tests/testthat/test-branches_attr_by.R | 108 ++++++++ tests/testthat/test-circlize.R |only tests/testthat/test-color_branches.R |only tests/testthat/test-colored_bars.R |only tests/testthat/test-colored_dots.R |only tests/testthat/test-common_subtrees.R | 50 +++ tests/testthat/test-cor.dendlist.R |only tests/testthat/test-cor_bakers_gamma.R | 45 +++ tests/testthat/test-cut_lower_fun.R | 9 tests/testthat/test-cutree.dendrogram.R | 93 +++++++ tests/testthat/test-dendlist.R | 76 +++++ tests/testthat/test-depth.R |only tests/testthat/test-dist_long.R |only tests/testthat/test-distinct_edges.R | 63 ++++ tests/testthat/test-entanglement.R | 44 +++ tests/testthat/test-find_dend.R |only tests/testthat/test-find_k.R |only tests/testthat/test-get_nodes_xy.R | 74 +++++ tests/testthat/test-ggdend.R | 30 ++ tests/testthat/test-ggdendro.R |only tests/testthat/test-has_edgePar.R |only tests/testthat/test-highlight_branches.R | 6 tests/testthat/test-is.functions.R |only tests/testthat/test-labels-assign.R | 72 +++++ tests/testthat/test-labels_colors.R | 48 +++ tests/testthat/test-nleaves.R | 50 +++ tests/testthat/test-noded_with_condition.R |only tests/testthat/test-prune.R |only tests/testthat/test-pvclust_extract.R | 139 ++++++++++ tests/testthat/test-rainbow_fun.R |only tests/testthat/test-rect.dendrogram.R | 116 +++++++- tests/testthat/test-rotate.R | 128 +++++++++ tests/testthat/test-sample.dendrogram.R |only tests/testthat/test-seriate_dendrogram.R |only tests/testthat/test-set.dendrogram.R | 52 ++++ tests/testthat/test-stats_imports.R |only tests/testthat/test-tanglegram.R |only tests/testthat/test-unbranch.R | 43 +++ tests/testthat/test-untangle.R | 374 +++++++++++++++++++++++++---- tests/testthat/test-zzz.R |only 58 files changed, 1984 insertions(+), 140 deletions(-)
Title: Spatial Data Science Complementary Features
Description: Wrapping and supplementing commonly used functions in the R ecosystem related to spatial data science,
while serving as a basis for other packages maintained by Wenbo Lv.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between sdsfun versions 0.4.2 dated 2024-11-11 and 0.4.3 dated 2024-11-15
DESCRIPTION | 8 ++-- MD5 | 19 ++++++---- NAMESPACE | 2 + NEWS.md | 4 ++ R/ssh_test.R | 17 +++++++++ R/utils.R | 83 ---------------------------------------------- R/vector_toolkits.R |only man/discretize_vector.Rd | 2 - man/generate_subsets.Rd |only man/geodetector_q.Rd |only man/normalize_vector.Rd | 2 - man/standardize_vector.Rd | 2 - 12 files changed, 41 insertions(+), 98 deletions(-)
Title: Background Resource Logging
Description: Intense parallel workloads can be difficult to monitor.
Packages 'crew.cluster', 'clustermq', and 'future.batchtools'
distribute hundreds of worker processes over multiple computers.
If a worker process exhausts its available memory,
it may terminate silently, leaving the underlying problem difficult
to detect or troubleshoot.
Using the 'autometric' package, a worker can proactively monitor
itself in a detached background thread.
The worker process itself runs normally,
and the thread writes to a log every few seconds.
If the worker terminates unexpectedly, 'autometric' can read and
visualize the log file to reveal potential resource-related
reasons for the crash. The 'autometric' package borrows heavily from
the methods of packages 'ps' <doi:10.32614/CRAN.package.ps> and 'psutil'.
Author: William Michael Landau [aut, cre]
,
Eli Lilly and Company [cph, fnd],
Posit Software, PBC [cph] ,
Jay Loden [cph] ,
Dave Daeschler [cph] ,
Giampaolo Rodola [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between autometric versions 0.1.1 dated 2024-11-14 and 0.1.2 dated 2024-11-15
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/log_phase_set.R | 4 ---- R/log_plot.R | 2 +- inst/WORDLIST | 1 + src/thread.c | 2 +- src/version.h | 2 +- 8 files changed, 20 insertions(+), 17 deletions(-)
Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation models, and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R.
Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Author: Timothy C. Bates [aut, cre] ,
Nathan Gillespie [wit],
Hermine Maes [ctb],
Michael C. Neale [ctb],
Joshua N. Pritikin [ctb],
Luis De Araujo [ctb],
Brenton Wiernik [ctb],
Michael Zakharin [wit]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
Diff between umx versions 4.20.0 dated 2024-04-10 and 4.21.0 dated 2024-11-14
DESCRIPTION | 26 - MD5 | 629 +++++++++++++------------- NAMESPACE | 3 NEWS.md | 21 R/build_run_modify.R | 107 ++-- R/deprecated.R | 4 R/fit_and_reporting.R | 173 +++---- R/misc_and_utility.R | 202 ++++---- R/tmx.R | 4 R/umxCLPM.R | 660 +++++++++++++++++++++------- R/umxDoC.R | 4 R/umxMRDoC.R | 2 R/umxMatrixFree.R | 2 R/umx_build_high_level_models.R | 38 - R/umx_build_polychoricMatrix3.R | 6 R/umx_build_umxACEv.R | 9 R/umx_build_umxGxEbiv.R | 4 R/umx_build_umxSexLim.R | 6 R/umx_build_umxSimplex.R | 6 R/umx_fit_stash_CIs.R | 4 R/umx_fit_umxFitIndices.R | 6 R/xmu.R | 46 - R/xmu_make_top_twin_models.R | 2 build/partial.rdb |binary inst/WORDLIST | 1 man/FishersMethod.Rd | 4 man/RMSEA.MxModel.Rd | 10 man/RMSEA.Rd | 6 man/RMSEA.summary.mxmodel.Rd | 10 man/SE_from_p.Rd | 4 man/dl_from_dropbox.Rd | 4 man/extractAIC.MxModel.Rd | 15 man/figures/CP.pdf |binary man/figures/CP.svg | 267 ++++------- man/figures/umx_help_figures.graffle |binary man/fin_interest.Rd | 12 man/geometric_mean.Rd | 14 man/ggAddR.Rd | 12 man/harmonic_mean.Rd | 8 man/install.OpenMx.Rd | 4 man/libs.Rd | 4 man/loadings.MxModel.Rd | 6 man/loadings.Rd | 6 man/noNAs.Rd | 4 man/oddsratio.Rd | 4 man/plot.MxLISRELModel.Rd | 16 man/plot.MxModel.Rd | 17 man/plot.MxModelTwinMaker.Rd | 10 man/power.ACE.test.Rd | 14 man/prolific_anonymize.Rd | 4 man/prolific_check_ID.Rd | 4 man/prolific_read_demog.Rd | 4 man/qm.Rd | 4 man/reliability.Rd | 4 man/residuals.MxModel.Rd | 10 man/tmx_is.identified.Rd | 4 man/tmx_show.MxMatrix.Rd | 6 man/tmx_show.Rd | 6 man/umx-deprecated.Rd | 4 man/umx.Rd | 24 - man/umxACE.Rd | 16 man/umxACEcov.Rd | 16 man/umxACEv.Rd | 18 man/umxAPA.Rd | 6 man/umxAlgebra.Rd | 4 man/umxBrownie.Rd | 9 man/umxCI.Rd | 10 man/umxCI_boot.Rd | 14 man/umxCLPM.Rd | 65 +- man/umxCP.Rd | 16 man/umxCompare.Rd | 12 man/umxConfint.Rd | 14 man/umxCov2cor.Rd | 4 man/umxDiagnose.Rd | 12 man/umxDiffMZ.Rd | 14 man/umxDiscTwin.Rd | 14 man/umxDoC.Rd | 14 man/umxDoCp.Rd | 12 man/umxEFA.Rd | 10 man/umxEquate.Rd | 8 man/umxExpCov.Rd | 18 man/umxExpMeans.Rd | 20 man/umxFactor.Rd | 20 man/umxFactorScores.Rd | 6 man/umxFitIndices.Rd | 14 man/umxFixAll.Rd | 6 man/umxGetLatents.Rd | 4 man/umxGetManifests.Rd | 4 man/umxGetModel.Rd | 4 man/umxGetParameters.Rd | 10 man/umxGxE.Rd | 14 man/umxGxE_window.Rd | 16 man/umxGxEbiv.Rd | 16 man/umxHetCor.Rd | 8 man/umxIP.Rd | 16 man/umxJiggle.Rd | 6 man/umxLav2RAM.Rd | 4 man/umxMI.Rd | 10 man/umxMRDoC.Rd | 16 man/umxMatrix.Rd | 8 man/umxMatrixFree.Rd | 2 man/umxModel.Rd | 5 man/umxModelNames.Rd | 8 man/umxModify.Rd | 12 man/umxParameters.Rd | 6 man/umxParan.Rd | 4 man/umxPath.Rd | 8 man/umxPlot.Rd | 10 man/umxPlotACE.Rd | 12 man/umxPlotACEcov.Rd | 14 man/umxPlotACEv.Rd | 12 man/umxPlotCP.Rd | 14 man/umxPlotDoC.Rd | 12 man/umxPlotFun.Rd | 12 man/umxPlotGxE.Rd | 10 man/umxPlotGxEbiv.Rd | 10 man/umxPlotIP.Rd | 12 man/umxPlotSexLim.Rd | 14 man/umxPlotSimplex.Rd | 12 man/umxRAM.Rd | 8 man/umxRAM2Lav.Rd | 4 man/umxReduce.Rd | 24 - man/umxReduceACE.Rd | 19 man/umxReduceGxE.Rd | 17 man/umxRenameMatrix.Rd | 3 man/umxRotate.MxModelCP.Rd | 16 man/umxRotate.Rd | 8 man/umxRun.Rd | 10 man/umxSetParameters.Rd | 16 man/umxSexLim.Rd | 16 man/umxSimplex.Rd | 16 man/umxSummarizeTwinData.Rd | 14 man/umxSummary.MxModel.Rd | 4 man/umxSummary.Rd | 6 man/umxSummaryACE.Rd | 16 man/umxSummaryACEcov.Rd | 2 man/umxSummaryACEv.Rd | 16 man/umxSummaryCP.Rd | 2 man/umxSummaryDoC.Rd | 16 man/umxSummaryGxE.Rd | 2 man/umxSummaryGxEbiv.Rd | 16 man/umxSummaryIP.Rd | 2 man/umxSummarySexLim.Rd | 16 man/umxSummarySimplex.Rd | 18 man/umxSuperModel.Rd | 10 man/umxThresholdMatrix.Rd | 2 man/umxTwinMaker.Rd | 14 man/umxTwoStage.Rd | 21 man/umxUnexplainedCausalNexus.Rd | 4 man/umxVersion.Rd | 6 man/umxWeightedAIC.Rd | 4 man/umx_APA_pval.Rd | 3 man/umx_aggregate.Rd | 4 man/umx_apply.Rd | 4 man/umx_array_shift.Rd | 4 man/umx_as_numeric.Rd | 4 man/umx_check_OS.Rd | 2 man/umx_check_model.Rd | 2 man/umx_check_names.Rd | 6 man/umx_check_parallel.Rd | 9 man/umx_cont_2_quantiles.Rd | 8 man/umx_cor.Rd | 4 man/umx_explode.Rd | 4 man/umx_explode_twin_names.Rd | 4 man/umx_file_load_pseudo.Rd | 4 man/umx_find_object.Rd | 4 man/umx_fun_mean_sd.Rd | 3 man/umx_get_bracket_addresses.Rd | 3 man/umx_get_checkpoint.Rd | 4 man/umx_get_options.Rd | 4 man/umx_grep.Rd | 6 man/umx_has_CIs.Rd | 6 man/umx_has_been_run.Rd | 4 man/umx_has_means.Rd | 6 man/umx_has_square_brackets.Rd | 2 man/umx_is_MxData.Rd | 2 man/umx_is_MxMatrix.Rd | 4 man/umx_is_MxModel.Rd | 4 man/umx_is_RAM.Rd | 4 man/umx_is_class.Rd | 4 man/umx_is_cov.Rd | 2 man/umx_is_endogenous.Rd | 6 man/umx_is_exogenous.Rd | 6 man/umx_is_numeric.Rd | 4 man/umx_is_ordered.Rd | 6 man/umx_long2wide.Rd | 4 man/umx_lower.tri.Rd | 4 man/umx_lower2full.Rd | 10 man/umx_make.Rd | 3 man/umx_make_MR_data.Rd | 4 man/umx_make_TwinData.Rd | 8 man/umx_make_fake_data.Rd | 4 man/umx_make_raw_from_cov.Rd | 4 man/umx_make_sql_from_excel.Rd | 4 man/umx_make_twin_data_nice.Rd | 4 man/umx_means.Rd | 4 man/umx_merge_randomized_columns.Rd | 4 man/umx_move_file.Rd | 4 man/umx_msg.Rd | 4 man/umx_names.Rd | 6 man/umx_open.Rd | 4 man/umx_open_CRAN_page.Rd | 4 man/umx_pad.Rd | 4 man/umx_paste_names.Rd | 6 man/umx_polychoric.Rd | 6 man/umx_polypairwise.Rd | 8 man/umx_polytriowise.Rd | 4 man/umx_print.Rd | 4 man/umx_r_test.Rd | 4 man/umx_read_lower.Rd | 4 man/umx_rename.Rd | 4 man/umx_rename_file.Rd | 4 man/umx_reorder.Rd | 4 man/umx_residualize.Rd | 14 man/umx_rot.Rd | 8 man/umx_round.Rd | 6 man/umx_scale.Rd | 10 man/umx_scale_wide_twin_data.Rd | 4 man/umx_score_scale.Rd | 6 man/umx_select_valid.Rd | 4 man/umx_set_auto_plot.Rd | 4 man/umx_set_auto_run.Rd | 4 man/umx_set_checkpoint.Rd | 4 man/umx_set_condensed_slots.Rd | 4 man/umx_set_cores.Rd | 4 man/umx_set_data_variance_check.Rd | 4 man/umx_set_dollar_symbol.Rd | 4 man/umx_set_optimization_options.Rd | 4 man/umx_set_optimizer.Rd | 4 man/umx_set_plot_file_suffix.Rd | 4 man/umx_set_plot_format.Rd | 6 man/umx_set_plot_use_hrbrthemes.Rd | 4 man/umx_set_separator.Rd | 4 man/umx_set_silent.Rd | 4 man/umx_set_table_format.Rd | 4 man/umx_stack.Rd | 4 man/umx_standardize.Rd | 5 man/umx_str_chars.Rd | 6 man/umx_str_from_object.Rd | 6 man/umx_string_to_algebra.Rd | 5 man/umx_strings2numeric.Rd | 4 man/umx_time.Rd | 6 man/umx_trim.Rd | 6 man/umx_var.Rd | 6 man/umx_wide2long.Rd | 4 man/umx_write_to_clipboard.Rd | 4 man/xmuHasSquareBrackets.Rd | 3 man/xmuLabel.Rd | 10 man/xmuLabel_MATRIX_Model.Rd | 7 man/xmuLabel_Matrix.Rd | 7 man/xmuLabel_RAM_Model.Rd | 7 man/xmuMI.Rd | 5 man/xmuMakeDeviationThresholdsMatrices.Rd | 3 man/xmuMakeOneHeadedPathsFromPathList.Rd | 3 man/xmuMakeTwoHeadedPathsFromPathList.Rd | 3 man/xmuMaxLevels.Rd | 3 man/xmuMinLevels.Rd | 3 man/xmuPropagateLabels.Rd | 5 man/xmuRAM2Ordinal.Rd | 5 man/xmuTwinSuper_Continuous.Rd | 3 man/xmuTwinSuper_NoBinary.Rd | 3 man/xmuTwinUpgradeMeansToCovariateModel.Rd | 3 man/xmuValues.Rd | 8 man/xmu_CI_merge.Rd | 5 man/xmu_CI_stash.Rd | 7 man/xmu_DF_to_mxData_TypeCov.Rd | 7 man/xmu_PadAndPruneForDefVars.Rd | 3 man/xmu_bracket_address2rclabel.Rd | 3 man/xmu_cell_is_on.Rd | 5 man/xmu_check_levels_identical.Rd | 3 man/xmu_check_needs_means.Rd | 5 man/xmu_check_variance.Rd | 3 man/xmu_clean_label.Rd | 3 man/xmu_data_missing.Rd | 3 man/xmu_data_swap_a_block.Rd | 3 man/xmu_describe_data_WLS.Rd | 9 man/xmu_dot_make_paths.Rd | 3 man/xmu_dot_make_residuals.Rd | 3 man/xmu_dot_maker.Rd | 5 man/xmu_dot_move_ranks.Rd | 3 man/xmu_dot_rank_str.Rd | 3 man/xmu_equate_threshold_values.Rd |only man/xmu_extract_column.Rd | 5 man/xmu_get_CI.Rd | 5 man/xmu_lavaan_process_group.Rd | 3 man/xmu_make_TwinSuperModel.Rd | 5 man/xmu_make_bin_cont_pair_data.Rd | 3 man/xmu_make_mxData.Rd | 7 man/xmu_match.arg.Rd | 3 man/xmu_name_from_lavaan_str.Rd | 3 man/xmu_path2twin.Rd | 3 man/xmu_path_regex.Rd | 3 man/xmu_print_algebras.Rd | 3 man/xmu_rclabel_2_bracket_address.Rd | 3 man/xmu_relevel_factors.Rd |only man/xmu_safe_run_summary.Rd | 7 man/xmu_scale_wide_data.Rd |only man/xmu_set_sep_from_suffix.Rd | 3 man/xmu_show_fit_or_comparison.Rd | 5 man/xmu_simplex_corner.Rd | 3 man/xmu_standardize_ACE.Rd | 1 man/xmu_standardize_ACEcov.Rd | 3 man/xmu_standardize_ACEv.Rd | 3 man/xmu_standardize_CP.Rd | 3 man/xmu_standardize_IP.Rd | 3 man/xmu_standardize_RAM.Rd | 5 man/xmu_standardize_SexLim.Rd | 3 man/xmu_standardize_Simplex.Rd | 3 man/xmu_start_value_list.Rd | 3 man/xmu_starts.Rd | 3 man/xmu_summary_RAM_group_parameters.Rd | 3 man/xmu_twin_add_WeightMatrices.Rd | 3 man/xmu_twin_check.Rd | 3 man/xmu_twin_get_var_names.Rd | 3 man/xmu_twin_make_def_means_mats_and_alg.Rd | 3 man/xmu_twin_upgrade_selDvs2SelVars.Rd | 3 tests/testthat/test_umx_CLPM.r | 70 ++ 317 files changed, 2409 insertions(+), 1912 deletions(-)
Title: Recording Tree-Ring Shapes of Tree Disks with Manual Digitizing
and Interpolating Model
Description: Record all tree-ring Shapefile of tree disk with GIS soft 'Qgis' and interpolating model from high resolution tree disk image.
Author: Megumi ISHIDA [aut, cre, cph]
Maintainer: Megumi ISHIDA <ishidam@sanchikanri.com>
Diff between TreeRingShape versions 3.0.3 dated 2024-04-22 and 3.0.5 dated 2024-11-14
DESCRIPTION | 21 ++++++++------- MD5 | 25 +++++++++--------- NEWS.md | 16 +++++++++--- R/ShapeFile.R | 9 ++++++ R/TreeRingsInterpolation.R | 58 ++++++++++++++++++++++++++++++++++++++++++-- R/calculation.R | 2 - README.md | 28 ++------------------- build/vignette.rds |binary inst/doc/TreeRingShape.Rmd | 2 - inst/doc/TreeRingShape.html | 6 ++-- man/DiskInfo.Rd |only man/TreeRingShape.Rd | 5 ++- tests/testthat.R | 3 -- vignettes/TreeRingShape.Rmd | 2 - 14 files changed, 114 insertions(+), 63 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Tomasz Kalinowski [ctb, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between reticulate versions 1.39.0 dated 2024-09-05 and 1.40.0 dated 2024-11-14
reticulate-1.39.0/reticulate/tests/testthat/resources/figure |only reticulate-1.39.0/reticulate/tests/testthat/resources/test-custom-root-dir.md |only reticulate-1.40.0/reticulate/DESCRIPTION | 6 reticulate-1.40.0/reticulate/MD5 | 79 +- reticulate-1.40.0/reticulate/NEWS.md | 39 + reticulate-1.40.0/reticulate/R/RcppExports.R | 8 reticulate-1.40.0/reticulate/R/ark-variables-methods.R |only reticulate-1.40.0/reticulate/R/array.R | 7 reticulate-1.40.0/reticulate/R/conda.R | 44 + reticulate-1.40.0/reticulate/R/config.R | 41 + reticulate-1.40.0/reticulate/R/miniconda.R | 5 reticulate-1.40.0/reticulate/R/package.R | 7 reticulate-1.40.0/reticulate/R/python-tools.R | 52 - reticulate-1.40.0/reticulate/R/python.R | 7 reticulate-1.40.0/reticulate/R/thread.R | 32 reticulate-1.40.0/reticulate/R/virtualenv.R | 13 reticulate-1.40.0/reticulate/R/zzz.R | 97 ++ reticulate-1.40.0/reticulate/build/vignette.rds |binary reticulate-1.40.0/reticulate/inst/doc/arrays.html | 2 reticulate-1.40.0/reticulate/inst/doc/calling_python.html | 2 reticulate-1.40.0/reticulate/inst/doc/package.html | 2 reticulate-1.40.0/reticulate/inst/doc/python_dependencies.html | 2 reticulate-1.40.0/reticulate/inst/doc/python_packages.Rmd | 2 reticulate-1.40.0/reticulate/inst/doc/python_packages.html | 4 reticulate-1.40.0/reticulate/inst/doc/python_primer.html | 2 reticulate-1.40.0/reticulate/inst/doc/r_markdown.html | 12 reticulate-1.40.0/reticulate/inst/doc/versions.html | 2 reticulate-1.40.0/reticulate/inst/python/rpytools/ark_variables.py |only reticulate-1.40.0/reticulate/inst/python/rpytools/run.py | 22 reticulate-1.40.0/reticulate/src/RcppExports.cpp | 23 reticulate-1.40.0/reticulate/src/libpython.cpp | 36 - reticulate-1.40.0/reticulate/src/libpython.h | 12 reticulate-1.40.0/reticulate/src/python.cpp | 330 +++++++--- reticulate-1.40.0/reticulate/src/readline.cpp | 27 reticulate-1.40.0/reticulate/src/reticulate_types.h | 6 reticulate-1.40.0/reticulate/tests/testthat/resources/test-chunking.md | 2 reticulate-1.40.0/reticulate/tests/testthat/test-delay-load.R | 26 reticulate-1.40.0/reticulate/tests/testthat/test-python-class.R | 87 +- reticulate-1.40.0/reticulate/tests/testthat/test-python-numpy.R | 12 reticulate-1.40.0/reticulate/tests/testthat/test-python-objects.R | 37 + reticulate-1.40.0/reticulate/tests/testthat/test-python-threads.R | 21 reticulate-1.40.0/reticulate/vignettes/python_packages.Rmd | 2 42 files changed, 781 insertions(+), 329 deletions(-)
Title: Retrieve, Harmonise and Map Open Data Regarding the Italian
School System
Description: Compiles and displays the available data sets regarding the Italian school system, with a focus on the infrastructural aspects.
Input datasets are downloaded from the web, with the aim of updating everything to real time.
The functions are divided in four main modules, namely
'Get', to scrape raw data from the web
'Util', various utilities needed to process raw data
'Group', to aggregate data at the municipality or province level
'Map', to visualize the output datasets.
Author: Leonardo Cefalo [aut, cre] ,
Alessio Pollice [ctb, ths] ,
Paolo Maranzano [ctb]
Maintainer: Leonardo Cefalo <leonardo.cefalo@uniba.it>
Diff between SchoolDataIT versions 0.2.1 dated 2024-10-01 and 0.2.2 dated 2024-11-14
DESCRIPTION | 8 ++-- MD5 | 52 +++++++++++++-------------- NEWS.md | 11 +++++ R/Get_BroadBand.R | 11 ++++- R/Get_DB_MIUR.R | 9 ++++ R/Get_InnerAreas.R | 19 +++++++++- R/Get_Invalsi_IS.R | 33 ++++++++--------- R/Get_Registry.R | 15 ++++++-- R/Get_School2mun.R | 31 +++++++++++++--- R/Get_Shapefile.R | 2 - R/Get_nstud.R | 10 ++++- R/Get_nteachers_prov.R | 12 ++++-- R/Group_DB_MIUR.R | 2 - R/Map_DB.R | 28 ++++++++------- R/Map_Invalsi.R | 28 ++++++++++----- R/Map_School_Buildings.R | 33 +++++++++-------- R/Set_DB.R | 82 ++++++++++++++++++++++++++++++++------------ R/Util_DB_MIUR_num.R | 2 - README.md | 2 - man/Get_BroadBand.Rd | 2 - man/Get_Invalsi_IS.Rd | 4 +- man/Get_Shapefile.Rd | 2 - man/Map_DB.Rd | 7 ++- man/Map_Invalsi.Rd | 7 ++- man/Map_School_Buildings.Rd | 7 ++- man/Set_DB.Rd | 2 - man/Util_DB_MIUR_num.Rd | 2 - 27 files changed, 280 insertions(+), 143 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.14.0 dated 2024-09-06 and 0.15.0 dated 2024-11-14
adbcdrivermanager-0.14.0/adbcdrivermanager/src/c/driver/framework/catalog.cc |only adbcdrivermanager-0.14.0/adbcdrivermanager/src/c/driver/framework/catalog.h |only adbcdrivermanager-0.14.0/adbcdrivermanager/src/c/vendor/sqlite3 |only adbcdrivermanager-0.15.0/adbcdrivermanager/DESCRIPTION | 10 adbcdrivermanager-0.15.0/adbcdrivermanager/MD5 | 90 adbcdrivermanager-0.15.0/adbcdrivermanager/configure | 3 adbcdrivermanager-0.15.0/adbcdrivermanager/man/adbcdrivermanager-package.Rd | 2 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/common/utils.c | 66 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/common/utils.h | 6 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/framework/base_driver.h | 11 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/framework/connection.h | 6 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/framework/objects.cc | 175 + adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/framework/objects.h | 120 + adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/framework/statement.h | 3 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/framework/status.h | 38 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/framework/utility.cc |only adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/framework/utility.h |only adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/bind_stream.h | 552 +---- adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/connection.cc | 1086 ++++------ adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/connection.h | 8 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/copy/reader.h | 5 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/copy/writer.h | 10 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/database.cc | 269 +- adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/database.h | 23 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/error.cc | 73 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/error.h | 73 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/postgres_type.h | 96 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/postgresql.cc | 32 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/result_helper.cc | 89 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/result_helper.h | 86 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/result_reader.cc | 108 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/result_reader.h | 29 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/statement.cc | 296 +- adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/postgresql/statement.h | 24 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/sqlite/sqlite.cc | 62 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/sqlite/statement_reader.c | 19 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver/sqlite/statement_reader.h | 5 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/driver_manager/adbc_driver_manager.cc | 63 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/include/arrow-adbc/adbc.h | 2 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/include/arrow-adbc/adbc_driver_manager.h | 5 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/validation/adbc_validation.h | 54 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/validation/adbc_validation_connection.cc | 35 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/validation/adbc_validation_statement.cc | 147 + adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/validation/adbc_validation_util.cc | 60 adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/validation/adbc_validation_util.h | 127 - adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/vendor/nanoarrow/nanoarrow.c | 701 +++++- adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/vendor/nanoarrow/nanoarrow.h | 602 ++++- adbcdrivermanager-0.15.0/adbcdrivermanager/src/c/vendor/nanoarrow/nanoarrow.hpp | 13 48 files changed, 3285 insertions(+), 1999 deletions(-)
More information about adbcdrivermanager at CRAN
Permanent link
Title: 'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcsqlite versions 0.14.0 dated 2024-09-06 and 0.15.0 dated 2024-11-14
adbcsqlite-0.14.0/adbcsqlite/src/c/driver/framework/catalog.cc |only adbcsqlite-0.14.0/adbcsqlite/src/c/driver/framework/catalog.h |only adbcsqlite-0.15.0/adbcsqlite/DESCRIPTION | 12 adbcsqlite-0.15.0/adbcsqlite/MD5 | 90 adbcsqlite-0.15.0/adbcsqlite/configure | 3 adbcsqlite-0.15.0/adbcsqlite/man/adbcsqlite-package.Rd | 3 adbcsqlite-0.15.0/adbcsqlite/src/Makevars.in | 4 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/common/utils.c | 66 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/common/utils.h | 6 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/framework/base_driver.h | 11 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/framework/connection.h | 6 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/framework/objects.cc | 175 + adbcsqlite-0.15.0/adbcsqlite/src/c/driver/framework/objects.h | 120 + adbcsqlite-0.15.0/adbcsqlite/src/c/driver/framework/statement.h | 3 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/framework/status.h | 38 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/framework/utility.cc |only adbcsqlite-0.15.0/adbcsqlite/src/c/driver/framework/utility.h |only adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/bind_stream.h | 552 +---- adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/connection.cc | 1086 ++++------ adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/connection.h | 8 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/copy/reader.h | 5 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/copy/writer.h | 10 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/database.cc | 269 +- adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/database.h | 23 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/error.cc | 73 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/error.h | 73 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/postgres_type.h | 96 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/postgresql.cc | 32 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/result_helper.cc | 89 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/result_helper.h | 86 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/result_reader.cc | 108 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/result_reader.h | 29 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/statement.cc | 296 +- adbcsqlite-0.15.0/adbcsqlite/src/c/driver/postgresql/statement.h | 24 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/sqlite/sqlite.cc | 62 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/sqlite/statement_reader.c | 19 adbcsqlite-0.15.0/adbcsqlite/src/c/driver/sqlite/statement_reader.h | 5 adbcsqlite-0.15.0/adbcsqlite/src/c/driver_manager/adbc_driver_manager.cc | 63 adbcsqlite-0.15.0/adbcsqlite/src/c/include/arrow-adbc/adbc.h | 2 adbcsqlite-0.15.0/adbcsqlite/src/c/include/arrow-adbc/adbc_driver_manager.h | 5 adbcsqlite-0.15.0/adbcsqlite/src/c/validation/adbc_validation.h | 54 adbcsqlite-0.15.0/adbcsqlite/src/c/validation/adbc_validation_connection.cc | 35 adbcsqlite-0.15.0/adbcsqlite/src/c/validation/adbc_validation_statement.cc | 147 + adbcsqlite-0.15.0/adbcsqlite/src/c/validation/adbc_validation_util.cc | 60 adbcsqlite-0.15.0/adbcsqlite/src/c/validation/adbc_validation_util.h | 127 - adbcsqlite-0.15.0/adbcsqlite/src/c/vendor/nanoarrow/nanoarrow.c | 701 +++++- adbcsqlite-0.15.0/adbcsqlite/src/c/vendor/nanoarrow/nanoarrow.h | 602 ++++- adbcsqlite-0.15.0/adbcsqlite/src/c/vendor/nanoarrow/nanoarrow.hpp | 13 48 files changed, 3289 insertions(+), 2002 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Description: Provides a developer-facing interface to the 'Arrow' Database
Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level
database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is
an API standard for database access libraries that uses 'Arrow' for result
sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcpostgresql versions 0.14.0 dated 2024-09-06 and 0.15.0 dated 2024-11-14
adbcpostgresql-0.14.0/adbcpostgresql/src/c/driver/framework/catalog.cc |only adbcpostgresql-0.14.0/adbcpostgresql/src/c/driver/framework/catalog.h |only adbcpostgresql-0.14.0/adbcpostgresql/src/c/vendor/sqlite3 |only adbcpostgresql-0.15.0/adbcpostgresql/DESCRIPTION | 12 adbcpostgresql-0.15.0/adbcpostgresql/MD5 | 96 adbcpostgresql-0.15.0/adbcpostgresql/configure | 5 adbcpostgresql-0.15.0/adbcpostgresql/man/adbcpostgresql-package.Rd | 3 adbcpostgresql-0.15.0/adbcpostgresql/src/Makevars.in | 5 adbcpostgresql-0.15.0/adbcpostgresql/src/Makevars.ucrt | 5 adbcpostgresql-0.15.0/adbcpostgresql/src/Makevars.win | 5 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/common/utils.c | 66 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/common/utils.h | 6 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/framework/base_driver.h | 11 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/framework/connection.h | 6 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/framework/objects.cc | 175 + adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/framework/objects.h | 120 + adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/framework/statement.h | 3 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/framework/status.h | 38 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/framework/utility.cc |only adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/framework/utility.h |only adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/bind_stream.h | 552 +---- adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/connection.cc | 1086 ++++------ adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/connection.h | 8 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/copy/reader.h | 5 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/copy/writer.h | 10 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/database.cc | 269 +- adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/database.h | 23 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/error.cc | 73 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/error.h | 73 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/postgres_type.h | 96 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/postgresql.cc | 32 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/result_helper.cc | 89 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/result_helper.h | 86 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/result_reader.cc | 108 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/result_reader.h | 29 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/statement.cc | 296 +- adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/postgresql/statement.h | 24 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/sqlite/sqlite.cc | 62 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/sqlite/statement_reader.c | 19 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver/sqlite/statement_reader.h | 5 adbcpostgresql-0.15.0/adbcpostgresql/src/c/driver_manager/adbc_driver_manager.cc | 63 adbcpostgresql-0.15.0/adbcpostgresql/src/c/include/arrow-adbc/adbc.h | 2 adbcpostgresql-0.15.0/adbcpostgresql/src/c/include/arrow-adbc/adbc_driver_manager.h | 5 adbcpostgresql-0.15.0/adbcpostgresql/src/c/validation/adbc_validation.h | 54 adbcpostgresql-0.15.0/adbcpostgresql/src/c/validation/adbc_validation_connection.cc | 35 adbcpostgresql-0.15.0/adbcpostgresql/src/c/validation/adbc_validation_statement.cc | 147 + adbcpostgresql-0.15.0/adbcpostgresql/src/c/validation/adbc_validation_util.cc | 60 adbcpostgresql-0.15.0/adbcpostgresql/src/c/validation/adbc_validation_util.h | 127 - adbcpostgresql-0.15.0/adbcpostgresql/src/c/vendor/nanoarrow/nanoarrow.c | 701 +++++- adbcpostgresql-0.15.0/adbcpostgresql/src/c/vendor/nanoarrow/nanoarrow.h | 602 ++++- adbcpostgresql-0.15.0/adbcpostgresql/src/c/vendor/nanoarrow/nanoarrow.hpp | 13 51 files changed, 3299 insertions(+), 2011 deletions(-)
More information about adbcpostgresql at CRAN
Permanent link
Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse
set of pipelining operators ('PipeOps') that can be composed into graphs.
Operations exist for data preprocessing, model fitting, and ensemble
learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can
therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre],
Florian Pfisterer [aut] ,
Lennart Schneider [aut] ,
Bernd Bischl [aut] ,
Michel Lang [aut] ,
Sebastian Fischer [aut] ,
Susanne Dandl [aut],
Keno Mersmann [ctb],
Maximilian Muecke [ctb] ,
Lona Koers [ctb]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr3pipelines versions 0.7.0 dated 2024-09-24 and 0.7.1 dated 2024-11-14
DESCRIPTION | 31 +- MD5 | 274 +++++++++++++------------- NAMESPACE | 8 NEWS.md | 16 + R/Graph.R | 5 R/GraphLearner.R | 89 ++++++-- R/PipeOpADAS.R | 4 R/PipeOpBLSmote.R | 4 R/PipeOpBoxCox.R | 5 R/PipeOpClassifAvg.R | 4 R/PipeOpEncodeLmer.R | 6 R/PipeOpFilter.R | 6 R/PipeOpICA.R | 4 R/PipeOpImputeLearner.R | 4 R/PipeOpKernelPCA.R | 4 R/PipeOpLearner.R | 4 R/PipeOpLearnerCV.R | 4 R/PipeOpLearnerPICVPlus.R |only R/PipeOpLearnerQuantiles.R |only R/PipeOpNMF.R | 8 R/PipeOpNearmiss.R |only R/PipeOpOVR.R | 8 R/PipeOpProxy.R | 4 R/PipeOpRandomResponse.R | 4 R/PipeOpRegrAvg.R | 4 R/PipeOpSmote.R | 4 R/PipeOpSmoteNC.R | 4 R/PipeOpTextVectorizer.R | 6 R/PipeOpThreshold.R | 4 R/PipeOpTomek.R |only R/PipeOpTrafo.R | 12 - R/PipeOpTuneThreshold.R | 8 R/PipeOpVtreat.R | 4 R/PipeOpYeoJohnson.R | 4 R/TaskRegr_boston_housing.R |only R/bibentries.R | 39 +++ R/mlr_graphs.R | 4 R/mlr_pipeops.R | 4 R/pipeline_bagging.R | 4 R/pipeline_ovr.R | 4 R/pipeline_robustify.R | 4 R/pipeline_stacking.R | 6 R/pipeline_targettrafo.R | 4 R/po.R | 4 R/ppl.R | 4 R/utils.R | 31 -- R/zzz.R | 1 man/Graph.Rd | 5 man/PipeOp.Rd | 4 man/PipeOpEnsemble.Rd | 4 man/PipeOpImpute.Rd | 4 man/PipeOpTargetTrafo.Rd | 4 man/PipeOpTaskPreproc.Rd | 4 man/PipeOpTaskPreprocSimple.Rd | 4 man/mlr3pipelines-package.Rd | 1 man/mlr_graphs.Rd | 4 man/mlr_graphs_bagging.Rd | 4 man/mlr_graphs_ovr.Rd | 4 man/mlr_graphs_robustify.Rd | 4 man/mlr_graphs_stacking.Rd | 6 man/mlr_graphs_targettrafo.Rd | 4 man/mlr_learners_graph.Rd | 40 ++- man/mlr_pipeops.Rd | 8 man/mlr_pipeops_adas.Rd | 8 man/mlr_pipeops_blsmote.Rd | 8 man/mlr_pipeops_boxcox.Rd | 8 man/mlr_pipeops_branch.Rd | 4 man/mlr_pipeops_chunk.Rd | 4 man/mlr_pipeops_classbalancing.Rd | 4 man/mlr_pipeops_classifavg.Rd | 8 man/mlr_pipeops_classweights.Rd | 4 man/mlr_pipeops_colapply.Rd | 4 man/mlr_pipeops_collapsefactors.Rd | 4 man/mlr_pipeops_colroles.Rd | 4 man/mlr_pipeops_copy.Rd | 4 man/mlr_pipeops_datefeatures.Rd | 4 man/mlr_pipeops_encode.Rd | 4 man/mlr_pipeops_encodeimpact.Rd | 4 man/mlr_pipeops_encodelmer.Rd | 10 man/mlr_pipeops_featureunion.Rd | 4 man/mlr_pipeops_filter.Rd | 10 man/mlr_pipeops_fixfactors.Rd | 4 man/mlr_pipeops_histbin.Rd | 4 man/mlr_pipeops_ica.Rd | 8 man/mlr_pipeops_imputeconstant.Rd | 4 man/mlr_pipeops_imputehist.Rd | 4 man/mlr_pipeops_imputelearner.Rd | 9 man/mlr_pipeops_imputemean.Rd | 4 man/mlr_pipeops_imputemedian.Rd | 4 man/mlr_pipeops_imputemode.Rd | 4 man/mlr_pipeops_imputeoor.Rd | 4 man/mlr_pipeops_imputesample.Rd | 4 man/mlr_pipeops_kernelpca.Rd | 8 man/mlr_pipeops_learner.Rd | 12 - man/mlr_pipeops_learner_cv.Rd | 8 man/mlr_pipeops_learner_pi_cvplus.Rd |only man/mlr_pipeops_learner_quantiles.Rd |only man/mlr_pipeops_missind.Rd | 4 man/mlr_pipeops_modelmatrix.Rd | 4 man/mlr_pipeops_multiplicityexply.Rd | 4 man/mlr_pipeops_multiplicityimply.Rd | 4 man/mlr_pipeops_mutate.Rd | 4 man/mlr_pipeops_nearmiss.Rd |only man/mlr_pipeops_nmf.Rd | 12 - man/mlr_pipeops_nop.Rd | 4 man/mlr_pipeops_ovrsplit.Rd | 8 man/mlr_pipeops_ovrunite.Rd | 8 man/mlr_pipeops_pca.Rd | 4 man/mlr_pipeops_proxy.Rd | 8 man/mlr_pipeops_quantilebin.Rd | 4 man/mlr_pipeops_randomprojection.Rd | 4 man/mlr_pipeops_randomresponse.Rd | 8 man/mlr_pipeops_regravg.Rd | 8 man/mlr_pipeops_removeconstants.Rd | 4 man/mlr_pipeops_renamecolumns.Rd | 4 man/mlr_pipeops_replicate.Rd | 4 man/mlr_pipeops_rowapply.Rd | 4 man/mlr_pipeops_scale.Rd | 4 man/mlr_pipeops_scalemaxabs.Rd | 4 man/mlr_pipeops_scalerange.Rd | 4 man/mlr_pipeops_select.Rd | 4 man/mlr_pipeops_smote.Rd | 8 man/mlr_pipeops_smotenc.Rd | 8 man/mlr_pipeops_spatialsign.Rd | 4 man/mlr_pipeops_subsample.Rd | 4 man/mlr_pipeops_targetinvert.Rd | 4 man/mlr_pipeops_targetmutate.Rd | 8 man/mlr_pipeops_targettrafoscalerange.Rd | 8 man/mlr_pipeops_textvectorizer.Rd | 10 man/mlr_pipeops_threshold.Rd | 8 man/mlr_pipeops_tomek.Rd |only man/mlr_pipeops_tunethreshold.Rd | 12 - man/mlr_pipeops_unbranch.Rd | 4 man/mlr_pipeops_updatetarget.Rd | 8 man/mlr_pipeops_vtreat.Rd | 8 man/mlr_pipeops_yeojohnson.Rd | 8 man/mlr_tasks_boston_housing.Rd |only man/po.Rd | 4 man/ppl.Rd | 4 tests/testthat/test_GraphLearner.R | 36 ++- tests/testthat/test_dictionary.R | 6 tests/testthat/test_pipeop_learnerpicvplus.R |only tests/testthat/test_pipeop_learnerquantiles.R |only tests/testthat/test_pipeop_nearmiss.R |only tests/testthat/test_pipeop_tomek.R |only 145 files changed, 782 insertions(+), 430 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.6.4 dated 2024-07-26 and 3.6.5 dated 2024-11-14
DESCRIPTION | 16 MD5 | 48 - NEWS.md | 21 R/toInteger.R | 83 +- build/vignette.rds |binary inst/doc/ConditionalErrorSpending.html | 825 ++++++++++++------------ inst/doc/ConditionalPowerPlot.html | 183 ++--- inst/doc/GentleIntroductionToGSD.html | 162 ++-- inst/doc/PoissonMixtureModel.html | 287 ++++---- inst/doc/SpendingFunctionOverview.html | 3 inst/doc/SurvivalOverview.R | 2 inst/doc/SurvivalOverview.html | 328 ++++----- inst/doc/VaccineEfficacy.html | 717 ++++++++++---------- inst/doc/binomialSPRTExample.html | 321 ++++----- inst/doc/gsDesignPackageOverview.html | 51 - inst/doc/gsSurvBasicExamples.R | 26 inst/doc/gsSurvBasicExamples.html | 857 ++++++++++++------------- inst/doc/nNormal.html | 109 +-- inst/doc/toInteger.R | 73 -- inst/doc/toInteger.Rmd | 108 +-- inst/doc/toInteger.html | 259 +++---- man/gsDesign-package.Rd | 5 man/toInteger.Rd | 54 + tests/testthat/test-developer-test-toInteger.R |only tests/testthat/test-independent-test-as_rtf.R |only vignettes/toInteger.Rmd | 108 +-- 26 files changed, 2305 insertions(+), 2341 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.10 dated 2024-10-17 and 1.11 dated 2024-11-14
DESCRIPTION | 6 MD5 | 56 ++++----- NEWS.md | 14 ++ R/RcppExports.R | 12 - R/class-workbook-wrappers.R | 55 ++++++++ R/class-workbook.R | 42 ++++-- R/converters.R | 2 R/helper-functions.R | 10 + R/read.R | 2 R/utils.R | 1 R/wb_functions.R | 4 R/wb_styles.R | 7 - R/write.R | 15 +- build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/Update-from-openxlsx.R | 50 ++++---- inst/doc/conditional-formatting.R | 32 ++--- inst/doc/openxlsx2.R | 32 ++--- man/wb_add_numfmt.Rd | 72 +++++++++++ man/wb_add_slicer.Rd | 1 src/RcppExports.cpp | 40 ++---- src/helper_functions.cpp | 217 +++++++---------------------------- src/load_workbook.cpp | 10 - src/openxlsx2.h | 116 ++++++++++++++++++ src/pugi.cpp | 6 src/strings_xml.cpp | 8 - tests/testthat/test-class-workbook.R | 20 +++ tests/testthat/test-pugi_cpp.R | 2 tests/testthat/test-write.R | 55 +++++++- 29 files changed, 546 insertions(+), 342 deletions(-)
Title: Define and Enforce Contracts for Dataframes as Function
Parameters
Description: A dataframe validation framework for package builders who use
dataframes as function parameters. It performs checks on column names, coerces
data-types, and checks grouping to make sure user inputs conform to a
specification provided by the package author. It provides a mechanism for
package authors to automatically document supported dataframe inputs and
selectively dispatch to functions depending on the format of a dataframe much
like S3 does for classes. It also contains some developer tools to make
working with and documenting dataframe specifications easier. It helps package
developers to improve their documentation and simplifies parameter validation
where dataframes are used as function parameters.
Author: Robert Challen [aut, cre, cph]
Maintainer: Robert Challen <rob.challen@bristol.ac.uk>
Diff between interfacer versions 0.2.3 dated 2024-08-01 and 0.3.2 dated 2024-11-14
DESCRIPTION | 8 +-- MD5 | 76 +++++++++++++++++++----------- NAMESPACE | 10 ++++ NEWS.md | 24 +++++++++ R/devtools.R | 9 +-- R/idispatch.R | 12 ++-- R/iface-class.R | 20 ++++---- R/igroup-process.R | 12 ++++ R/imapper.R | 6 +- R/interfacer.R | 26 ++++++++-- R/params_check_consistent.R |only R/params_check_framework.R |only R/params_check_types.R |only R/params_recycle.R |only R/params_resolve_missing.R |only R/type-coerce.R | 96 +++++++++++++++++++++++++++++++-------- README.md | 12 ++++ build/vignette.rds |binary inst/WORDLIST | 3 - inst/doc/consistency.R |only inst/doc/consistency.Rmd |only inst/doc/consistency.html |only inst/doc/dispatch.Rmd | 2 inst/doc/dispatch.html | 2 inst/doc/interfacer.html | 21 ++++---- inst/doc/nesting.html | 2 man/check_character.Rd |only man/check_consistent.Rd |only man/check_date.Rd |only man/check_integer.Rd |only man/check_logical.Rd |only man/check_numeric.Rd |only man/check_single.Rd |only man/figures |only man/iconvert.Rd | 4 - man/idispatch.Rd | 13 ++--- man/iface.Rd | 8 +-- man/imapper.Rd | 6 +- man/recycle.Rd |only man/resolve_missing.Rd |only man/type.double.Rd | 5 +- man/type.group_unique.Rd | 4 - man/type.numeric.Rd | 5 +- man/type.unique_id.Rd |only tests/testthat/helper-data.R | 4 + tests/testthat/test-interfacer.R | 47 ++++++++++--------- tests/testthat/test-roxygen.R |only vignettes/consistency.Rmd |only vignettes/dispatch.Rmd | 2 49 files changed, 297 insertions(+), 142 deletions(-)
Title: Inference for Spatiotemporal Partially Observed Markov Processes
Description: Inference on panel data using spatiotemporal partially-observed Markov process (SpatPOMP) models. The 'spatPomp' package extends 'pomp' to include algorithms taking advantage of the spatial structure in order to assist with handling high dimensional processes. See Asfaw et al. (2024) <doi:10.48550/arXiv.2101.01157> for further description of the package.
Author: Kidus Asfaw [aut],
Edward Ionides [cre, aut],
Aaron A. King [aut],
Allister Ho [ctb],
Joonha Park [ctb],
Jesse Wheeler [ctb],
Jifan Li [ctb],
Ning Ning [ctb],
Haogao Gu [ctb]
Maintainer: Edward Ionides <ionides@umich.edu>
Diff between spatPomp versions 0.36.1 dated 2024-08-20 and 1.0.0 dated 2024-11-14
DESCRIPTION | 24 ++++----- MD5 | 104 ++++++++++++++++++++-------------------- R/abf.R | 4 - R/abfir.R | 2 R/bpfilter.R | 4 - R/conc.R | 2 R/enkf.R | 2 R/eunit_measure.R | 2 R/girf.R | 2 R/ibpf.R | 6 +- R/ienkf.R | 2 R/igirf.R | 4 - R/init.R |only R/iubf.R | 2 R/listie.R | 5 + R/loglik.R | 4 - R/lorenz.R | 2 R/munit_measure.R | 2 R/plot.R | 79 +++++++++++++++--------------- R/runit_measure.R | 2 R/spatPomp.R | 2 R/vec_dmeasure.R | 2 R/vec_rmeasure.R | 2 R/vunit_measure.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/ibpf.pdf |binary inst/doc/tutorial.pdf |binary man/abf.Rd | 12 +++- man/abfir.Rd | 2 man/bpfilter.Rd | 4 - man/conc.Rd | 2 man/enkf.Rd | 2 man/eunit_measure.Rd | 2 man/girf.Rd | 2 man/ibpf.Rd | 6 +- man/ienkf.Rd | 2 man/igirf.Rd | 4 - man/iubf.Rd | 2 man/listie.Rd | 5 + man/loglik.Rd | 4 - man/lorenz.Rd | 2 man/munit_measure.Rd | 2 man/plot.Rd | 39 ++++++--------- man/runit_measure.Rd | 2 man/spatPomp.Rd | 2 man/vec_dmeasure.Rd | 2 man/vec_rmeasure.Rd | 2 man/vunit_measure.Rd | 2 tests/bm.R | 3 - tests/bm.Rout.save | 3 - vignettes/README |only vignettes/ibpf-original.pdf |binary vignettes/tutorial-original.pdf |binary 54 files changed, 189 insertions(+), 181 deletions(-)
Title: Continuous and Dichotomized Index Predictors Based on
Distribution Quantiles
Description: Select optimal functional regression or dichotomized
quantile predictors for survival/logistic/numeric outcome
and perform optimistic bias correction for any optimally
dichotomized numeric predictor(s), as in Yi, et. al.
(2023) <doi:10.1016/j.labinv.2023.100158>.
Author: Tingting Zhan [aut, cre, cph] ,
Misung Yi [aut, cph] ,
Inna Chervoneva [aut, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between Qindex versions 0.1.6 dated 2024-10-07 and 0.1.7 dated 2024-11-14
Qindex-0.1.6/Qindex/R/lim_trans.R |only Qindex-0.1.6/Qindex/inst |only Qindex-0.1.7/Qindex/DESCRIPTION | 27 +++---- Qindex-0.1.7/Qindex/MD5 | 44 +++++------- Qindex-0.1.7/Qindex/NAMESPACE | 5 + Qindex-0.1.7/Qindex/R/BBC_dichotom.R | 30 +++++++- Qindex-0.1.7/Qindex/R/Qindex.R | 8 -- Qindex-0.1.7/Qindex/R/bootid.R | 13 +-- Qindex-0.1.7/Qindex/R/clusterQp.R | 99 ++++++++++++++++------------ Qindex-0.1.7/Qindex/R/defunct.R |only Qindex-0.1.7/Qindex/R/integrandSurface.R | 42 ++++++----- Qindex-0.1.7/Qindex/R/predict.Qindex.R | 2 Qindex-0.1.7/Qindex/R/std_.R | 6 - Qindex-0.1.7/Qindex/build/partial.rdb |binary Qindex-0.1.7/Qindex/man/BBC_cutoff.Rd |only Qindex-0.1.7/Qindex/man/BBC_dichotom.Rd | 4 - Qindex-0.1.7/Qindex/man/Qindex-package.Rd | 19 +++-- Qindex-0.1.7/Qindex/man/bootid.Rd | 11 +-- Qindex-0.1.7/Qindex/man/clusterQp.Rd | 38 ++++------ Qindex-0.1.7/Qindex/man/defunct.Rd |only Qindex-0.1.7/Qindex/man/integrandSurface.Rd | 26 +++---- Qindex-0.1.7/Qindex/man/predict.Qindex.Rd | 2 Qindex-0.1.7/Qindex/man/std_.Rd | 6 - 23 files changed, 212 insertions(+), 170 deletions(-)
Title: Flexible and General Mediation Analysis Using Riesz Representers
Description: Implements a modern, unified estimation strategy for common
mediation estimands (natural effects, organic effects, interventional effects,
and recanting twins) in combination with modified treatment policies as
described in Liu, Williams, Rudolph, and Díaz (2024)
<doi:10.48550/arXiv.2408.14620>. Estimation makes use of recent advancements
in Riesz-learning to estimate a set of required nuisance parameters with
deep learning. The result is the capability to estimate mediation effects with
binary, categorical, continuous, or multivariate exposures with
high-dimensional mediators and mediator-outcome confounders using machine
learning.
Author: Nicholas Williams [aut, cre, cph]
,
Richard Liu [ctb],
Ivan Diaz [aut, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between crumble versions 0.1.0 dated 2024-09-18 and 0.1.1 dated 2024-11-14
DESCRIPTION | 9 ++-- MD5 | 32 +++++++------- NAMESPACE | 10 ++++ NEWS.md | 6 ++ R/assertions.R | 8 ++- R/calc_estimates.R | 62 +++++++++------------------- R/crumble.R | 67 ++++++++++++++---------------- R/crumble_data.R | 49 ++++++++++++---------- R/crumble_vars.R | 1 R/eif.R | 37 +++++++++-------- R/helpers.R | 16 ------- R/phi.R | 7 ++- R/print.R | 104 ++++++++++------------------------------------- R/tidy.R | 113 +--------------------------------------------------- README.md | 28 ++++++++---- inst/references.bib | 6 ++ man/crumble.Rd | 2 17 files changed, 200 insertions(+), 357 deletions(-)
Title: Excess Mortality
Description: Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".
Author: Rafael A. Irizarry [aut, cre],
Rolando Acosta [aut],
Monica Robles-Fontan [aut],
Ferenci Tamas [ctb]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between excessmort versions 0.7.0 dated 2024-03-13 and 0.8.0 dated 2024-11-14
DESCRIPTION | 10 ++++---- MD5 | 16 ++++++------- R/puerto_rico_counts.R | 5 +++- build/vignette.rds |binary data/puerto_rico_counts.rda |binary data/puerto_rico_icd.rda |binary inst/doc/excessmort.html | 54 +++++++++++++++++++++----------------------- man/puerto_rico_counts.Rd | 7 ++++- man/puerto_rico_icd.Rd | 2 - 9 files changed, 50 insertions(+), 44 deletions(-)
Title: Versatile Curation of Table Metadata
Description: A YAML-based
mechanism for working with table metadata. Supports
compact syntax for creating, modifying, viewing, exporting,
importing, displaying, and plotting metadata coded as column
attributes. The 'yamlet' dialect is valid 'YAML' with
defaults and conventions chosen to improve readability.
See ?yamlet, ?decorate, ?modify, ?io_csv, and ?ggplot.decorated.
Author: Tim Bergsma [aut, cre]
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 1.1.4 dated 2024-10-21 and 1.1.5 dated 2024-11-14
DESCRIPTION | 6 +- MD5 | 26 +++++----- R/mimic.R | 6 +- inst/doc/scripted-html.html | 4 - inst/doc/scripted-pdf.pdf |binary inst/doc/yamlet-introduction.html | 4 - man/mimic.classified.Rd | 1 tests/testthat/086.rds |binary tests/testthat/090.rds |binary tests/testthat/091.rds |binary tests/testthat/094.rds |binary tests/testthat/096.rds |binary vignettes/scripted-pdf_files/figure-latex/unnamed-chunk-4-1.pdf |binary vignettes/scripted-pdf_files/figure-latex/unnamed-chunk-5-1.pdf |binary 14 files changed, 26 insertions(+), 21 deletions(-)
Title: Removal of Unwanted Technical Variation from UK Biobank NMR
Metabolomics Biomarker Data
Description: A suite of utilities for working with the UK Biobank
<https://www.ukbiobank.ac.uk/> Nuclear Magnetic Resonance spectroscopy (NMR)
metabolomics data <https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220>.
Includes functions for extracting biomarkers from decoded UK Biobank field
data, removing unwanted technical variation from biomarker concentrations,
computing an extended set of lipid, fatty acid, and cholesterol fractions,
and for re-deriving composite biomarkers and ratios after adjusting data
for unwanted biological variation. For further details on methods see
Ritchie SC et al. Sci Data (2023) <doi:10.1038/s41597-023-01949-y>.
Author: Scott C Ritchie [aut, cre]
Maintainer: Scott C Ritchie <sritchie73@gmail.com>
Diff between ukbnmr versions 2.2 dated 2023-08-23 and 3.2.0 dated 2024-11-14
ukbnmr-2.2/ukbnmr/man/compute_nightingale_ratio_qc_flags.Rd |only ukbnmr-2.2/ukbnmr/man/compute_nightingale_ratios.Rd |only ukbnmr-3.2.0/ukbnmr/DESCRIPTION | 10 ukbnmr-3.2.0/ukbnmr/MD5 | 57 - ukbnmr-3.2.0/ukbnmr/NAMESPACE | 4 ukbnmr-3.2.0/ukbnmr/NEWS.md | 42 + ukbnmr-3.2.0/ukbnmr/R/biomarker_qc.R | 191 +++- ukbnmr-3.2.0/ukbnmr/R/compute_biomarkers_user.R | 63 - ukbnmr-3.2.0/ukbnmr/R/compute_qc_flags_user.R | 44 - ukbnmr-3.2.0/ukbnmr/R/data.R | 4 ukbnmr-3.2.0/ukbnmr/R/detect_format.R | 3 ukbnmr-3.2.0/ukbnmr/R/extractor_functions.R | 158 ++- ukbnmr-3.2.0/ukbnmr/R/process_data.R | 42 - ukbnmr-3.2.0/ukbnmr/R/ukbnmr.R | 50 - ukbnmr-3.2.0/ukbnmr/R/utils.R | 16 ukbnmr-3.2.0/ukbnmr/build/vignette.rds |binary ukbnmr-3.2.0/ukbnmr/data/test_data.rda |binary ukbnmr-3.2.0/ukbnmr/inst/doc/ukbnmr.R | 111 ++ ukbnmr-3.2.0/ukbnmr/inst/doc/ukbnmr.Rmd | 254 ++++-- ukbnmr-3.2.0/ukbnmr/inst/doc/ukbnmr.html | 483 ++++++++---- ukbnmr-3.2.0/ukbnmr/inst/extdata/test_data.csv | 2 ukbnmr-3.2.0/ukbnmr/man/extract_biomarker_qc_flags.Rd | 51 - ukbnmr-3.2.0/ukbnmr/man/extract_biomarkers.Rd | 48 - ukbnmr-3.2.0/ukbnmr/man/extract_sample_qc_flags.Rd | 55 - ukbnmr-3.2.0/ukbnmr/man/recompute_derived_biomarkers.Rd | 6 ukbnmr-3.2.0/ukbnmr/man/remove_technical_variation.Rd | 117 +- ukbnmr-3.2.0/ukbnmr/man/test_data.Rd | 4 ukbnmr-3.2.0/ukbnmr/man/ukbnmr.Rd | 52 - ukbnmr-3.2.0/ukbnmr/vignettes/img/gwas_improvement_v3.png |only ukbnmr-3.2.0/ukbnmr/vignettes/img/r2_explained_v3.png |only ukbnmr-3.2.0/ukbnmr/vignettes/img/repeatability_v3.png |only ukbnmr-3.2.0/ukbnmr/vignettes/ukbnmr.Rmd | 254 ++++-- 32 files changed, 1340 insertions(+), 781 deletions(-)
Title: Tabulate Descriptive Statistics in Multiple Formats
Description: Creates a table of descriptive statistics
for factor and numeric columns in a data frame. Displays
these by groups, if any. Highly customizable, with support
for 'html' and 'pdf' provided by 'kableExtra'. Respects
original column order, column labels, and factor level order.
See ?tablet.data.frame and vignettes.
Author: Tim Bergsma [aut, cre]
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between tablet versions 0.6.11 dated 2024-10-25 and 0.6.12 dated 2024-11-14
DESCRIPTION | 6 - MD5 | 16 +- R/tablet.R | 188 +++++++++++++++++++++++++-------- inst/doc/tablet-introduction-html.html | 4 inst/doc/tablet-introduction-pdf.pdf |binary man/tablet.data.frame.Rd | 4 man/tablette.groupwise.Rd | 4 man/widgets.devalued.Rd | 2 tests/testthat/test-tablet.R | 16 ++ 9 files changed, 177 insertions(+), 63 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.1.4 dated 2024-11-01 and 0.1.5 dated 2024-11-14
DESCRIPTION | 8 +-- MD5 | 50 +++++++++++-------- NAMESPACE | 5 + NEWS.md | 37 ++++++++++++++ R/NMexec.R | 23 ++++++-- R/NMreadSim.R | 63 ++++++++++++++++-------- R/NMreadSimModTab.R | 7 -- R/NMrunWin.R | 57 +++++++++++----------- R/NMsim.R | 54 +++++++++++---------- R/addEVID2.R | 10 +-- R/dcastSe.R |only R/expandCovs.R | 21 ++++++-- R/reportFailedRun.R |only R/summarizeCovs.R |only README.md | 64 +++++++++++++++---------- man/NMreadSim.Rd | 26 ++++++---- man/NMreadSimModTab.Rd | 20 +++---- man/NMreadSimModTabOne.Rd | 14 ++--- man/addEVID2.Rd | 10 +-- man/expandCovs.Rd | 8 ++- man/figures/ACOP_logo_transp.png |only man/figures/intro-tab.png |only man/summarizeCovs.Rd |only tests/testthat/testReference/expandCovs_01.rds |binary tests/testthat/testReference/expandCovs_02.rds |binary tests/testthat/testReference/expandCovs_03.rds |binary tests/testthat/testReference/expandCovs_04.rds |only tests/testthat/testReference/fnAppend_02.rds |only tests/testthat/testReference/fnAppend_03.rds |only tests/testthat/testReference/fnAppend_1.rds |only tests/testthat/test_expandCovs.R | 23 ++++++++ 31 files changed, 325 insertions(+), 175 deletions(-)
Title: Fetch Data from Yahoo Finance API
Description: Obtain historical and near real time data related to stocks, index
and currencies from the Yahoo Finance API. This package is community maintained
and is not officially supported by 'Yahoo'. The accuracy of data is only as
correct as provided on <https://finance.yahoo.com/>.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between yahoofinancer versions 0.3.0 dated 2024-02-03 and 0.4.0 dated 2024-11-14
DESCRIPTION | 8 MD5 | 22 +- NEWS.md | 10 + R/ticker.R | 314 +++++++++++------------------------ README.md | 35 ++- man/Ticker-class.Rd | 32 ++- man/yahoofinancer.Rd | 1 tests/testthat/test-currency.R | 2 tests/testthat/test-index.R | 2 tests/testthat/test-market-summary.R | 2 tests/testthat/test-ticker.R | 2 tests/testthat/test-trending.R | 2 12 files changed, 177 insertions(+), 255 deletions(-)
Title: NNG (Nanomsg Next Gen) Lightweight Messaging Library
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is
a socket library implementing 'Scalability Protocols', a reliable,
high-performance standard for common communications patterns including
publish/subscribe, request/reply and service discovery, over in-process,
IPC, TCP, WebSocket and secure TLS transports. As its own threaded
concurrency framework, provides a toolkit for asynchronous programming and
distributed computing, with intuitive 'aio' objects which resolve
automatically upon completion of asynchronous operations, and
synchronisation primitives allowing R to wait upon events signalled by
concurrent threads.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph],
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between nanonext versions 1.3.1 dated 2024-11-13 and 1.3.2 dated 2024-11-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/tests.R | 7 ++++--- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Copula-Based Regression Models for Multivariate Censored Data
Description: Copula-based regression models for multivariate censored data, including
bivariate right-censored data, bivariate interval-censored data, and right/interval-censored
semi-competing risks data. Currently supports Clayton, Gumbel, Frank, Joe, AMH and
Copula2 copula models. For marginal models, it supports parametric (Weibull, Loglogistic,
Gompertz) and semiparametric (Cox and transformation) models. Includes methods for
convenient prediction and plotting. Also provides a bivariate time-to-event simulation
function and an information ratio-based goodness-of-fit test for copula. Method details
can be found in Sun et.al (2019) Lifetime Data Analysis, Sun et.al (2021) Biostatistics,
Sun et.al (2022) Statistical Methods in Medical Research, Sun et.al (2022) Biometrics, and
Sun et al. (2023+) JRSSC.
Author: Tao Sun [aut, cre] ,
Ying Ding [aut]
Maintainer: Tao Sun <sun.tao@ruc.edu.cn>
Diff between CopulaCenR versions 1.2.3 dated 2023-09-23 and 1.2.4 dated 2024-11-14
DESCRIPTION | 22 ++++++++++++++++------ MD5 | 11 ++++++++--- NAMESPACE | 1 + R/fun_rc_scmprisk_Cox.R |only R/rc_scmprisk_Cox.R |only data/data_scmprisk.RData |binary data/data_scmprisk_rc.RData |only man/data_scmprisk_rc.Rd |only man/rc_scmprisk_Cox.Rd |only 9 files changed, 25 insertions(+), 9 deletions(-)
Title: Miscellaneous Functions for 'SciViews::R'
Description: Functions required for the 'SciViews::R' dialect or for general
use: manage a temporary environment attached to the search path, define
synonyms for R functions using aka(), test if 'Aqua', 'Mac', 'Win' ... Show
progress bar, etc.
Author: Philippe Grosjean [aut, cre] ,
Romain Francois [ctb],
Kamil Barton [ctb]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between svMisc versions 1.2.3 dated 2021-10-11 and 1.4.3 dated 2024-11-14
svMisc-1.2.3/svMisc/R/Install.R |only svMisc-1.2.3/svMisc/R/pkgman.R |only svMisc-1.4.3/svMisc/DESCRIPTION | 39 svMisc-1.4.3/svMisc/MD5 | 74 - svMisc-1.4.3/svMisc/NAMESPACE | 20 svMisc-1.4.3/svMisc/NEWS.md | 215 ++- svMisc-1.4.3/svMisc/R/about.R | 51 svMisc-1.4.3/svMisc/R/aka.R |only svMisc-1.4.3/svMisc/R/capture_all.R | 2 svMisc-1.4.3/svMisc/R/cut_quantile.R |only svMisc-1.4.3/svMisc/R/file_edit.R | 90 - svMisc-1.4.3/svMisc/R/install.R |only svMisc-1.4.3/svMisc/R/pkgMan.R |only svMisc-1.4.3/svMisc/R/rbenchmark.R |only svMisc-1.4.3/svMisc/R/section.R |only svMisc-1.4.3/svMisc/R/svMisc-package.R | 20 svMisc-1.4.3/svMisc/build/vignette.rds |binary svMisc-1.4.3/svMisc/inst/CITATION | 35 svMisc-1.4.3/svMisc/inst/WORDLIST | 17 svMisc-1.4.3/svMisc/inst/doc/svMisc.R | 8 svMisc-1.4.3/svMisc/inst/doc/svMisc.Rmd | 18 svMisc-1.4.3/svMisc/inst/doc/svMisc.html | 991 ++++++++++------ svMisc-1.4.3/svMisc/inst/doc/temporary_environment.R | 8 svMisc-1.4.3/svMisc/inst/doc/temporary_environment.Rmd | 14 svMisc-1.4.3/svMisc/inst/doc/temporary_environment.html | 240 +++ svMisc-1.4.3/svMisc/inst/figures |only svMisc-1.4.3/svMisc/man/Install.Rd | 2 svMisc-1.4.3/svMisc/man/about.Rd | 8 svMisc-1.4.3/svMisc/man/aka.Rd |only svMisc-1.4.3/svMisc/man/capture_all.Rd | 2 svMisc-1.4.3/svMisc/man/cut_quantile.Rd |only svMisc-1.4.3/svMisc/man/figures |only svMisc-1.4.3/svMisc/man/file_edit.Rd | 12 svMisc-1.4.3/svMisc/man/pkgman_describe.Rd | 2 svMisc-1.4.3/svMisc/man/rbenchmark.Rd |only svMisc-1.4.3/svMisc/man/section.Rd |only svMisc-1.4.3/svMisc/man/svMisc-package.Rd | 11 svMisc-1.4.3/svMisc/po/R-fr.po | 2 svMisc-1.4.3/svMisc/tests/spelling.R | 2 svMisc-1.4.3/svMisc/tests/testthat.R | 8 svMisc-1.4.3/svMisc/tests/testthat/test-capture_all.R | 57 svMisc-1.4.3/svMisc/tests/testthat/test-parse_text.R | 66 - svMisc-1.4.3/svMisc/tests/testthat/test-temp_env.R | 56 svMisc-1.4.3/svMisc/vignettes/svMisc.Rmd | 18 svMisc-1.4.3/svMisc/vignettes/temporary_environment.Rmd | 14 45 files changed, 1353 insertions(+), 749 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018)
<DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 2.23.0 dated 2024-08-27 and 2.24.0 dated 2024-11-14
DESCRIPTION | 14 +-- MD5 | 26 +++--- NEWS.md | 5 + R/abfit.R | 129 +++++++++++++++++++++++---------- R/interactive_plotting.R | 12 ++- R/utils.R | 24 ++++-- inst/doc/spant-intro.html | 132 +++++++++++++++++----------------- inst/doc/spant-preprocessing.html | 4 - man/abfit_opts.Rd | 8 ++ man/ortho3.Rd | 5 + tests/testthat/abfit_res_coarse.rds |binary tests/testthat/abfit_res_default.rds |binary tests/testthat/abfit_res_fine.rds |binary tests/testthat/abfit_res_no_optim.rds |binary 14 files changed, 222 insertions(+), 137 deletions(-)
Title: Statistical Methodology for Graphical Extreme Value Models
Description: Statistical methodology for sparse multivariate extreme value models. Methods are
provided for exact simulation and statistical inference for multivariate Pareto distributions
on graphical structures as described in the paper 'Graphical Models for Extremes' by
Engelke and Hitz (2020) <doi:10.1111/rssb.12355>.
Author: Sebastian Engelke [aut, cre],
Adrien S. Hitz [aut],
Nicola Gnecco [aut],
Manuel Hentschel [aut]
Maintainer: Sebastian Engelke <sebastian.engelke@unige.ch>
Diff between graphicalExtremes versions 0.3.2 dated 2024-04-18 and 0.3.3 dated 2024-11-14
DESCRIPTION | 12 ++++---- MD5 | 50 ++++++++++++++++++------------------ R/data.R | 4 +- R/matrix_completions_main.R | 8 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/applicationDanube.html | 45 ++++++++++++++++++++------------ inst/doc/applicationFlights.html | 19 ++++++++----- man/complete_Gamma.Rd | 9 ++++-- man/complete_Gamma_decomposable.Rd | 6 ++-- man/complete_Gamma_general.Rd | 4 +- man/complete_Gamma_general_demo.Rd | 4 +- man/complete_Gamma_general_split.Rd | 4 +- man/data2mpareto.Rd | 2 - man/emp_vario.Rd | 2 - man/emtp2.Rd | 2 - man/flights.Rd | 4 +- man/fmpareto_HR_MLE.Rd | 2 - man/fmpareto_graph_HR.Rd | 2 - man/graphicalExtremes.Rd | 1 man/loglik_HR.Rd | 2 - man/plotFlights.Rd | 2 - man/rmpareto.Rd | 4 +- man/rmpareto_tree.Rd | 4 +- man/rmstable.Rd | 2 - man/rmstable_tree.Rd | 2 - 26 files changed, 110 insertions(+), 86 deletions(-)
More information about graphicalExtremes at CRAN
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