Title: Simultaneous Multi-Bias Adjustment
Description: Quantify the causal effect of a binary exposure on a binary
outcome with adjustment for multiple biases. The functions can
simultaneously adjust for any combination of uncontrolled confounding,
exposure/outcome misclassification, and selection bias.
The underlying method generalizes the concept of combining inverse
probability of selection weighting with predictive value weighting.
Simultaneous multi-bias analysis can be used to enhance the validity
and transparency of real-world evidence obtained from observational,
longitudinal studies. Based on the work from Paul Brendel, Aracelis Torres,
and Onyebuchi Arah (2023) <doi:10.1093/ije/dyad001>.
Author: Paul Brendel [aut, cre, cph]
Maintainer: Paul Brendel <pcbrendel@gmail.com>
Diff between multibias versions 1.5.0 dated 2024-05-05 and 1.5.1 dated 2024-06-19
DESCRIPTION | 6 MD5 | 231 ++-- NAMESPACE | 55 NEWS.md | 197 +-- R/adjust_emc.R | 380 +++--- R/adjust_emc_omc.R | 414 +++---- R/adjust_emc_sel.R | 492 ++++---- R/adjust_multinom_emc_omc.R | 702 ++++++------ R/adjust_multinom_uc_emc.R | 698 ++++++------ R/adjust_multinom_uc_emc_sel.R | 778 ++++++------- R/adjust_multinom_uc_omc.R | 698 ++++++------ R/adjust_multinom_uc_omc_sel.R | 778 ++++++------- R/adjust_omc.R | 343 +++--- R/adjust_sel.R | 362 +++--- R/adjust_uc.R | 372 +++--- R/adjust_uc_emc.R | 386 +++--- R/adjust_uc_emc_sel.R | 534 ++++----- R/adjust_uc_omc.R | 386 +++--- R/adjust_uc_omc_sel.R | 540 ++++----- R/adjust_uc_sel.R | 480 ++++---- R/adust_omc_sel.R | 482 ++++---- R/df_emc.R | 34 R/df_emc_omc.R | 36 R/df_emc_omc_source.R | 40 R/df_emc_sel.R | 40 R/df_emc_sel_source.R | 40 R/df_emc_source.R | 38 R/df_omc.R | 34 R/df_omc_sel.R | 34 R/df_omc_sel_source.R | 36 R/df_omc_source.R | 38 R/df_sel.R | 36 R/df_sel_source.R | 38 R/df_uc.R | 39 R/df_uc_emc.R | 33 R/df_uc_emc_sel.R | 40 R/df_uc_emc_sel_source.R | 42 R/df_uc_emc_source.R | 38 R/df_uc_omc.R | 33 R/df_uc_omc_sel.R | 40 R/df_uc_omc_sel_source.R | 42 R/df_uc_omc_source.R | 38 R/df_uc_sel.R | 38 R/df_uc_sel_source.R | 40 R/df_uc_source.R | 44 R/evans.R | 36 README.md | 106 - build/vignette.rds |binary data/df_uc.rda |binary data/df_uc_emc.rda |binary data/df_uc_emc_source.rda |binary data/df_uc_omc.rda |binary data/df_uc_omc_source.rda |binary data/df_uc_source.rda |binary inst/doc/multibias_examples.R | 270 ++-- inst/doc/multibias_examples.Rmd | 432 +++---- inst/doc/multibias_examples.html | 1282 +++++++++++------------ man/adjust_emc.Rd | 132 +- man/adjust_emc_omc.Rd | 154 +- man/adjust_emc_sel.Rd | 148 +- man/adjust_multinom_emc_omc.Rd | 182 +-- man/adjust_multinom_uc_emc.Rd | 182 +-- man/adjust_multinom_uc_emc_sel.Rd | 202 +-- man/adjust_multinom_uc_omc.Rd | 182 +-- man/adjust_multinom_uc_omc_sel.Rd | 202 +-- man/adjust_omc.Rd | 132 +- man/adjust_omc_sel.Rd | 150 +- man/adjust_sel.Rd | 126 +- man/adjust_uc.Rd | 132 +- man/adjust_uc_emc.Rd | 158 +- man/adjust_uc_emc_sel.Rd | 174 +-- man/adjust_uc_omc.Rd | 158 +- man/adjust_uc_omc_sel.Rd | 176 +-- man/adjust_uc_sel.Rd | 150 +- man/df_emc.Rd | 56 - man/df_emc_omc.Rd | 58 - man/df_emc_omc_source.Rd | 62 - man/df_emc_sel.Rd | 60 - man/df_emc_sel_source.Rd | 62 - man/df_emc_source.Rd | 60 - man/df_omc.Rd | 56 - man/df_omc_sel.Rd | 56 - man/df_omc_sel_source.Rd | 58 - man/df_omc_source.Rd | 60 - man/df_sel.Rd | 58 - man/df_sel_source.Rd | 60 - man/df_uc.Rd | 61 - man/df_uc_emc.Rd | 55 man/df_uc_emc_sel_source.Rd | 64 - man/df_uc_emc_source.Rd | 60 - man/df_uc_omc.Rd | 55 man/df_uc_omc_sel.Rd | 62 - man/df_uc_omc_sel_source.Rd | 64 - man/df_uc_omc_source.Rd | 60 - man/df_uc_sel.Rd | 58 - man/df_uc_sel_source.Rd | 62 - man/df_uc_source.Rd | 66 - man/evans.Rd | 62 - man/figures |only tests/testthat/test-adjust_emc.R | 443 ++++--- tests/testthat/test-adjust_emc_omc.R | 568 +++++----- tests/testthat/test-adjust_emc_sel.R | 568 +++++----- tests/testthat/test-adjust_multinom_emc_omc.R | 406 +++---- tests/testthat/test-adjust_multinom_uc_emc.R | 256 +++- tests/testthat/test-adjust_multinom_uc_emc_sel.R | 534 ++++----- tests/testthat/test-adjust_multinom_uc_omc.R | 256 +++- tests/testthat/test-adjust_multinom_uc_omc_sel.R | 534 ++++----- tests/testthat/test-adjust_omc.R | 443 ++++--- tests/testthat/test-adjust_omc_sel.R | 138 +- tests/testthat/test-adjust_sel.R | 419 +++---- tests/testthat/test-adjust_uc.R | 439 +++---- tests/testthat/test-adjust_uc_emc.R | 342 ++++-- tests/testthat/test-adjust_uc_emc_sel.R | 672 ++++++------ tests/testthat/test-adjust_uc_omc.R | 341 ++++-- tests/testthat/test-adjust_uc_omc_sel.R | 672 ++++++------ tests/testthat/test-adjust_uc_sel.R | 549 ++++----- vignettes/multibias_examples.Rmd | 432 +++---- 117 files changed, 12745 insertions(+), 11793 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] ,
George Athanasopoulos [aut] ,
Christoph Bergmeir [aut] ,
Gabriel Caceres [aut] ,
Leanne Chhay [aut],
Kirill Kuroptev [aut],
Mitchell O'Hara-Wild [aut] ,
Fotios Petropoulos [aut] ,
Slava Razbash [aut],
Earo Wang [aut] ,
F [...truncated...]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.22.0 dated 2024-03-04 and 8.23.0 dated 2024-06-19
forecast-8.22.0/forecast/tests/testthat/Rplots.pdf |only forecast-8.23.0/forecast/DESCRIPTION | 12 +-- forecast-8.23.0/forecast/MD5 | 25 +++---- forecast-8.23.0/forecast/NAMESPACE | 4 - forecast-8.23.0/forecast/NEWS.md | 4 + forecast-8.23.0/forecast/R/attach.R | 4 - forecast-8.23.0/forecast/R/ets.R | 2 forecast-8.23.0/forecast/R/ggplot.R | 12 +-- forecast-8.23.0/forecast/R/subset.R | 73 +++++++++++---------- forecast-8.23.0/forecast/build/vignette.rds |binary forecast-8.23.0/forecast/inst/doc/JSS2008.pdf |binary forecast-8.23.0/forecast/man/autolayer.Rd | 5 + forecast-8.23.0/forecast/man/autoplot.ts.Rd | 2 forecast-8.23.0/forecast/man/geom_forecast.Rd | 10 +- 14 files changed, 82 insertions(+), 71 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.11 dated 2024-04-03 and 1.9.12 dated 2024-06-19
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NAMESPACE | 3 ++- NEWS | 12 ++++++++++++ R/TMB.R | 9 +++++++++ R/abi_table.R |only inst/include/TMBad/TMBad.hpp | 3 --- inst/include/convert.hpp | 5 +++-- inst/include/tmbutils/sparse_matrix_exponential.hpp | 4 ++-- man/TMB.Version.Rd |only src/solve_subset.c | 14 +++++++------- 11 files changed, 49 insertions(+), 27 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] ,
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.6.1 dated 2024-03-06 and 1.7.0 dated 2024-06-19
RNifti-1.6.1/RNifti/tests/testthat |only RNifti-1.6.1/RNifti/tests/testthat.R |only RNifti-1.7.0/RNifti/DESCRIPTION | 12 ++--- RNifti-1.7.0/RNifti/MD5 | 37 ++++++++------- RNifti-1.7.0/RNifti/NAMESPACE | 2 RNifti-1.7.0/RNifti/NEWS | 12 +++++ RNifti-1.7.0/RNifti/R/image.R | 4 + RNifti-1.7.0/RNifti/R/rgb.R | 45 ++++++++++++++++--- RNifti-1.7.0/RNifti/README.md | 2 RNifti-1.7.0/RNifti/inst/include/RNifti.h | 4 - RNifti-1.7.0/RNifti/inst/include/RNifti/NiftiImage.h | 6 -- RNifti-1.7.0/RNifti/inst/tinytest |only RNifti-1.7.0/RNifti/man/rgbArray.Rd | 25 ++++++++-- RNifti-1.7.0/RNifti/src/main.cpp | 20 +++++++- RNifti-1.7.0/RNifti/tests/tinytest.R |only 15 files changed, 125 insertions(+), 44 deletions(-)
Title: Pretty Colour Palettes
Description: Defines aesthetically pleasing colour palettes.
Author: Nicola Rennie [aut, cre]
Maintainer: Nicola Rennie <nrennie35@gmail.com>
Diff between PrettyCols versions 1.0.1 dated 2023-01-27 and 1.1.0 dated 2024-06-19
PrettyCols-1.0.1/PrettyCols/inst/doc/using-with-python.R |only PrettyCols-1.0.1/PrettyCols/inst/doc/using-with-python.Rmd |only PrettyCols-1.0.1/PrettyCols/inst/doc/using-with-python.html |only PrettyCols-1.0.1/PrettyCols/vignettes/matplotlib-bright.png |only PrettyCols-1.0.1/PrettyCols/vignettes/using-with-python.Rmd |only PrettyCols-1.1.0/PrettyCols/DESCRIPTION | 14 PrettyCols-1.1.0/PrettyCols/MD5 | 118 +- PrettyCols-1.1.0/PrettyCols/NAMESPACE | 42 - PrettyCols-1.1.0/PrettyCols/NEWS.md | 19 PrettyCols-1.1.0/PrettyCols/R/PrettyCols-package.R |only PrettyCols-1.1.0/PrettyCols/R/PrettyColsPalettes.R | 395 ++++++---- PrettyCols-1.1.0/PrettyCols/R/colorblind_friendly.R | 34 PrettyCols-1.1.0/PrettyCols/R/colourblind_friendly.R | 34 PrettyCols-1.1.0/PrettyCols/R/prettycols.R | 122 +-- PrettyCols-1.1.0/PrettyCols/R/print_palette.R | 53 - PrettyCols-1.1.0/PrettyCols/R/scale_color_pretty_c.R | 89 +- PrettyCols-1.1.0/PrettyCols/R/scale_color_pretty_d.R | 114 +- PrettyCols-1.1.0/PrettyCols/R/scale_color_pretty_div.R |only PrettyCols-1.1.0/PrettyCols/R/scale_colour_pretty_c.R | 30 PrettyCols-1.1.0/PrettyCols/R/scale_colour_pretty_d.R | 30 PrettyCols-1.1.0/PrettyCols/R/scale_colour_pretty_div.R |only PrettyCols-1.1.0/PrettyCols/R/scale_fill_pretty_c.R | 89 +- PrettyCols-1.1.0/PrettyCols/R/scale_fill_pretty_d.R | 115 +- PrettyCols-1.1.0/PrettyCols/R/scale_fill_pretty_div.R |only PrettyCols-1.1.0/PrettyCols/R/view_all_palettes.R | 108 +- PrettyCols-1.1.0/PrettyCols/README.md | 19 PrettyCols-1.1.0/PrettyCols/build/vignette.rds |binary PrettyCols-1.1.0/PrettyCols/inst/doc/available-palettes.R | 70 - PrettyCols-1.1.0/PrettyCols/inst/doc/available-palettes.Rmd | 392 ++++----- PrettyCols-1.1.0/PrettyCols/inst/doc/available-palettes.html | 72 - PrettyCols-1.1.0/PrettyCols/inst/doc/colourblind-friendly-palettes.R | 12 PrettyCols-1.1.0/PrettyCols/inst/doc/colourblind-friendly-palettes.Rmd | 106 +- PrettyCols-1.1.0/PrettyCols/inst/doc/colourblind-friendly-palettes.html | 16 PrettyCols-1.1.0/PrettyCols/inst/doc/using-with-ggplot2.R | 81 +- PrettyCols-1.1.0/PrettyCols/inst/doc/using-with-ggplot2.Rmd | 177 ++-- PrettyCols-1.1.0/PrettyCols/inst/doc/using-with-ggplot2.html | 92 +- PrettyCols-1.1.0/PrettyCols/inst/doc/viewing-palettes.R | 16 PrettyCols-1.1.0/PrettyCols/inst/doc/viewing-palettes.Rmd | 138 +-- PrettyCols-1.1.0/PrettyCols/inst/doc/viewing-palettes.html | 42 - PrettyCols-1.1.0/PrettyCols/man/PrettyCols-package.Rd |only PrettyCols-1.1.0/PrettyCols/man/PrettyColsPalettes.Rd | 2 PrettyCols-1.1.0/PrettyCols/man/colorblind_friendly.Rd | 42 - PrettyCols-1.1.0/PrettyCols/man/colourblind_friendly.Rd | 42 - PrettyCols-1.1.0/PrettyCols/man/figures/lifecycle-archived.svg |only PrettyCols-1.1.0/PrettyCols/man/figures/lifecycle-defunct.svg |only PrettyCols-1.1.0/PrettyCols/man/figures/lifecycle-deprecated.svg |only PrettyCols-1.1.0/PrettyCols/man/figures/lifecycle-experimental.svg |only PrettyCols-1.1.0/PrettyCols/man/figures/lifecycle-maturing.svg |only PrettyCols-1.1.0/PrettyCols/man/figures/lifecycle-questioning.svg |only PrettyCols-1.1.0/PrettyCols/man/figures/lifecycle-soft-deprecated.svg |only PrettyCols-1.1.0/PrettyCols/man/figures/lifecycle-stable.svg |only PrettyCols-1.1.0/PrettyCols/man/figures/lifecycle-superseded.svg |only PrettyCols-1.1.0/PrettyCols/man/figures/logo.png |binary PrettyCols-1.1.0/PrettyCols/man/prettycols.Rd | 4 PrettyCols-1.1.0/PrettyCols/man/scale_color_pretty_c.Rd | 10 PrettyCols-1.1.0/PrettyCols/man/scale_color_pretty_d.Rd | 12 PrettyCols-1.1.0/PrettyCols/man/scale_color_pretty_div.Rd |only PrettyCols-1.1.0/PrettyCols/man/scale_colour_pretty_c.Rd | 10 PrettyCols-1.1.0/PrettyCols/man/scale_colour_pretty_d.Rd | 12 PrettyCols-1.1.0/PrettyCols/man/scale_colour_pretty_div.Rd |only PrettyCols-1.1.0/PrettyCols/man/scale_fill_pretty_c.Rd | 8 PrettyCols-1.1.0/PrettyCols/man/scale_fill_pretty_d.Rd | 12 PrettyCols-1.1.0/PrettyCols/man/scale_fill_pretty_div.Rd |only PrettyCols-1.1.0/PrettyCols/man/view_all_palettes.Rd | 54 - PrettyCols-1.1.0/PrettyCols/tests/testthat.R | 24 PrettyCols-1.1.0/PrettyCols/tests/testthat/test-display.R | 34 PrettyCols-1.1.0/PrettyCols/tests/testthat/test-scales.R | 101 +- PrettyCols-1.1.0/PrettyCols/vignettes/available-palettes.Rmd | 392 ++++----- PrettyCols-1.1.0/PrettyCols/vignettes/colourblind-friendly-palettes.Rmd | 106 +- PrettyCols-1.1.0/PrettyCols/vignettes/using-with-ggplot2.Rmd | 177 ++-- PrettyCols-1.1.0/PrettyCols/vignettes/viewing-palettes.Rmd | 138 +-- 71 files changed, 2085 insertions(+), 1734 deletions(-)
Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length
as input, the function returns the numerator and denominator coefficients
for the Padé approximant of appropriate order (Baker, 1975)
<ISBN:9780120748556>.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Pade versions 1.0.6 dated 2023-10-11 and 1.0.7 dated 2024-06-19
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ README.md | 4 +--- build/partial.rdb |binary inst/CITATION | 4 ++-- inst/NEWS.Rd | 11 +++++++++++ inst/tinytest/test_package_metadata.R |only man/Pade.Rd | 7 +++++-- 8 files changed, 30 insertions(+), 17 deletions(-)
Title: Unified Framework for Numerical Optimizers
Description: Provides a unified object-oriented framework for numerical
optimizers in R. Allows for both minimization and maximization with any
optimizer, optimization over more than one function argument, measuring of
computation time, setting a time limit for long optimization tasks.
Author: Lennart Oelschlaeger [aut, cre]
,
Marius Oetting [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between optimizeR versions 1.1.0 dated 2024-05-27 and 1.1.1 dated 2024-06-19
DESCRIPTION | 8 MD5 | 50 - NAMESPACE | 46 - NEWS.md | 206 +++--- R/debug.R | 198 +++--- R/legacy.R | 912 ++++++++++++++-------------- R/objective.R | 801 ++++++++++++------------ R/optimizeR-package.R | 64 - R/optimizer.R | 1300 ++++++++++++++++++++-------------------- R/optimizer_dictionary.R | 176 ++--- README.md | 618 +++++++++---------- man/Objective.Rd | 519 ++++++++------- man/Optimizer.Rd | 942 ++++++++++++++-------------- man/apply_optimizer.Rd | 88 +- man/define_optimizer.Rd | 308 ++++----- man/new_optimizer.Rd | 190 ++--- man/optimizeR-package.Rd | 62 - man/optimizer_dictionary.Rd | 34 - man/test_objective.Rd | 78 +- man/test_optimizer.Rd | 102 +-- man/validate_optimizer.Rd | 92 +- tests/testthat.R | 24 tests/testthat/test-debug.R | 58 - tests/testthat/test-legacy.R | 432 ++++++------- tests/testthat/test-objective.R | 186 ++--- tests/testthat/test-optimizer.R | 190 ++--- 26 files changed, 3860 insertions(+), 3824 deletions(-)
Title: A Parametric Model for Estimating the Mean Number of Events
Description: Implementation of a parametric joint model for modelling recurrent
and competing event processes using generalised survival models. The joint
model can subsequently be used to predict the mean number of events in the
presence of competing risks at different time points. Comparisons of the mean
number of event functions, e.g. the differences in mean number of events
between two exposure groups, are also available.
Author: Joshua P. Entrop [aut, cre, cph]
,
Alessandro Gasparini [ctb],
Mark Clements [ctb]
Maintainer: Joshua P. Entrop <joshuaentrop@posteo.de>
Diff between JointFPM versions 1.2.0 dated 2024-01-22 and 1.2.1 dated 2024-06-19
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++++------ NAMESPACE | 1 + NEWS.md | 5 +++++ R/JointFPM.R | 14 ++++++++++++-- R/summary.JointFPM.R |only man/JointFPM.Rd | 8 +++++++- man/summary.JointFPM.Rd |only tests/testthat/_snaps/mean_no.md | 25 +++++++++++++------------ tests/testthat/_snaps/summary.JointFPM.md |only tests/testthat/test-summary.JointFPM.R |only 11 files changed, 52 insertions(+), 25 deletions(-)
Title: Create Custom Plots for Viewing Genetic Association Results
Description: A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.
Author: Thorhildur Juliusdottir [cph, aut, cre],
Andri Stefansson [aut]
Maintainer: Thorhildur Juliusdottir <totajuliusd@gmail.com>
Diff between topr versions 2.0.1 dated 2024-03-15 and 2.0.2 dated 2024-06-19
DESCRIPTION | 6 +- MD5 | 32 ++++++------ NAMESPACE | 2 NEWS.md | 42 +++++++++------ R/dat_checks.R | 19 ++++++- R/effectplot.R | 3 - R/get_plots.R | 9 ++- R/locuszoomplot.R | 1 R/manhattan.R | 111 ++++++++++++++++++++++++++++++++++++++++-- R/plot_functions.R | 9 +-- R/regionplot.R | 10 ++- R/setters_and_getters.R | 84 ++++++++++++++++++++++++++----- R/topr.R | 5 - man/get_sign_and_sugg_loci.Rd |only man/get_snpset.Rd | 5 + man/manhattan.Rd | 10 +++ man/manhattanExtra.Rd |only man/topr.Rd | 1 18 files changed, 278 insertions(+), 71 deletions(-)
Title: My Utilities for Developing Data Science Software
Description: Some general helper functions that I and maybe others find useful
when developing data science software. Functionality includes argument
validation, density calculation, sampling, matrix printing, user
interaction, storage helpers and more. The vignettes illustrate use cases.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between oeli versions 0.5.0 dated 2024-05-22 and 0.5.2 dated 2024-06-19
DESCRIPTION | 6 ++--- MD5 | 29 ++++++++++++++++---------- NAMESPACE | 2 + NEWS.md | 10 ++++++++ R/identical_structure.R |only R/matrix_diagonal_indices.R | 2 - R/vector_occurrence.R |only README.md | 1 inst/doc/matrix_helpers.html | 8 +++---- inst/doc/storage_helpers.html | 8 +++---- inst/doc/vector_helpers.R | 8 +++++++ inst/doc/vector_helpers.Rmd | 20 +++++++++++++++++ inst/doc/vector_helpers.html | 14 ++++++++++++ man/identical_structure.Rd |only man/vector_occurrence.Rd |only tests/testthat/test-identical_structure.R |only tests/testthat/test-matrix_diagonal_indices.R |only tests/testthat/test-vector_occurrence.R |only vignettes/vector_helpers.Rmd | 20 +++++++++++++++++ 19 files changed, 105 insertions(+), 23 deletions(-)
Title: Wicked Fast, Accurate Quantiles Using t-Digests
Description: The t-Digest construction algorithm, by
Dunning et al., (2019) <doi:10.48550/arXiv.1902.04023>, uses a variant of 1-dimensional
k-means clustering to produce a very compact data structure that allows
accurate estimation of quantiles. This t-Digest data structure can be used
to estimate quantiles, compute other rank statistics or even to estimate
related measures like trimmed means. The advantage of the t-Digest over
previous digests for this purpose is that the t-Digest handles data with
full floating point resolution. The accuracy of quantile estimates produced
by t-Digests can be orders of magnitude more accurate than those produced
by previous digest algorithms. Methods are provided to create and update
t-Digests and retrieve quantiles from the accumulated distributions.
Author: Bob Rudis [aut, cre] ,
Ted Dunning [aut] ,
Andrew Werner [aut]
Maintainer: Bob Rudis <bob@rud.is>
Diff between tdigest versions 0.4.1 dated 2022-10-04 and 0.4.2 dated 2024-06-19
DESCRIPTION | 12 ++-- MD5 | 4 - src/tdigest-main.c | 144 +++++++++++++++++++++++++++-------------------------- 3 files changed, 83 insertions(+), 77 deletions(-)
Title: Flexible Multidimensional Scaling and 'smacof' Extensions
Description: Flexible multidimensional scaling (MDS) methods and extensions to the package 'smacof'. This package contains various functions, wrappers, methods and classes for fitting, plotting and displaying a large number of different flexible MDS models (some as of yet unpublished). These are: Torgerson scaling (Torgerson, 1958, ISBN:978-0471879459) with powers, Sammon mapping (Sammon, 1969, <doi:10.1109/T-C.1969.222678>) with ratio and interval optimal scaling, Multiscale MDS (Ramsay, 1977, <doi:10.1007/BF02294052>) with ratio and interval optimal scaling, S-stress MDS (ALSCAL; Takane, Young & De Leeuw, 1977, <doi:10.1007/BF02293745>) with ratio and interval optimal scaling, elastic scaling (McGee, 1966, <doi:10.1111/j.2044-8317.1966.tb00367.x>) with ratio and interval optimal scaling, r-stress MDS (De Leeuw, Groenen & Mair, 2016, <https://rpubs.com/deleeuw/142619>) with ratio, interval and non-metric optimal scaling, power-stress MDS (POST-MDS; Buja & [...truncated...]
Author: Thomas Rusch [aut, cre] ,
Jan de Leeuw [aut],
Lisha Chen [aut],
Patrick Mair [aut]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between smacofx versions 0.6-6 dated 2023-08-17 and 1.5-3 dated 2024-06-19
smacofx-0.6-6/smacofx/man/smacofx.Rd |only smacofx-1.5-3/smacofx/DESCRIPTION | 33 +---- smacofx-1.5-3/smacofx/MD5 | 104 ++++++++++-------- smacofx-1.5-3/smacofx/NAMESPACE | 2 smacofx-1.5-3/smacofx/NEWS | 70 +++++++++++- smacofx-1.5-3/smacofx/R/alscal.R | 8 - smacofx-1.5-3/smacofx/R/apStressMin.R | 13 +- smacofx-1.5-3/smacofx/R/bcmds.R | 39 +++--- smacofx-1.5-3/smacofx/R/bcsdistance.R | 4 smacofx-1.5-3/smacofx/R/biplotmds.bcmds.R |only smacofx-1.5-3/smacofx/R/biplotmds.lmds.R |only smacofx-1.5-3/smacofx/R/biplotmds.smacofP.R | 2 smacofx-1.5-3/smacofx/R/bootmds.smacofP.R | 14 +- smacofx-1.5-3/smacofx/R/conf_adjust.R | 69 ----------- smacofx-1.5-3/smacofx/R/corpsepaint-data.R |only smacofx-1.5-3/smacofx/R/elscal.R | 6 - smacofx-1.5-3/smacofx/R/icExploreGen.R | 4 smacofx-1.5-3/smacofx/R/jackmds.smacofP.R | 103 ++++++++++++++--- smacofx-1.5-3/smacofx/R/koller-data.R |only smacofx-1.5-3/smacofx/R/lmds.R | 24 ++-- smacofx-1.5-3/smacofx/R/multiscale.R | 10 - smacofx-1.5-3/smacofx/R/multistart.R | 6 - smacofx-1.5-3/smacofx/R/permtest.smacofP.R | 2 smacofx-1.5-3/smacofx/R/powerStressFast.R | 4 smacofx-1.5-3/smacofx/R/powerStressMin.R | 8 - smacofx-1.5-3/smacofx/R/procruster.R | 2 smacofx-1.5-3/smacofx/R/rStressMin.R | 4 smacofx-1.5-3/smacofx/R/rpowerStressMin.R | 4 smacofx-1.5-3/smacofx/R/sammonmap.R | 18 +-- smacofx-1.5-3/smacofx/R/smacofx-package.R | 29 ++--- smacofx-1.5-3/smacofx/R/smacofxDeleteOne.R |only smacofx-1.5-3/smacofx/R/spmdda.R | 6 - smacofx-1.5-3/smacofx/R/spmds.R | 27 ++-- smacofx-1.5-3/smacofx/data/BankingCrisesDistances.rda |binary smacofx-1.5-3/smacofx/data/corpsepaint.rda |only smacofx-1.5-3/smacofx/data/koller.rda |only smacofx-1.5-3/smacofx/man/alscal.Rd | 6 - smacofx-1.5-3/smacofx/man/apStressMin.Rd | 11 + smacofx-1.5-3/smacofx/man/bcmds.Rd | 32 ++++- smacofx-1.5-3/smacofx/man/bcsdistance.Rd | 5 smacofx-1.5-3/smacofx/man/biplotmds.bcmds.Rd |only smacofx-1.5-3/smacofx/man/biplotmds.lmds.Rd |only smacofx-1.5-3/smacofx/man/bootmds.smacofP.Rd | 5 smacofx-1.5-3/smacofx/man/corpsepaint.Rd |only smacofx-1.5-3/smacofx/man/elscal.Rd | 2 smacofx-1.5-3/smacofx/man/icExploreGen.Rd | 4 smacofx-1.5-3/smacofx/man/jackmds.smacofP.Rd | 15 +- smacofx-1.5-3/smacofx/man/koller.Rd |only smacofx-1.5-3/smacofx/man/lmds.Rd | 23 ++- smacofx-1.5-3/smacofx/man/multiscale.Rd | 4 smacofx-1.5-3/smacofx/man/multistart.Rd | 4 smacofx-1.5-3/smacofx/man/powerStressFast.Rd | 4 smacofx-1.5-3/smacofx/man/powerStressMin.Rd | 4 smacofx-1.5-3/smacofx/man/rStressMin.Rd | 4 smacofx-1.5-3/smacofx/man/rpowerStressMin.Rd | 2 smacofx-1.5-3/smacofx/man/sammonmap.Rd | 2 smacofx-1.5-3/smacofx/man/smacofx-package.Rd |only smacofx-1.5-3/smacofx/man/smacofxDeleteOne.Rd |only smacofx-1.5-3/smacofx/man/spmdda.Rd | 6 - smacofx-1.5-3/smacofx/man/spmds.Rd | 12 +- 60 files changed, 436 insertions(+), 324 deletions(-)
Title: Matching on Generalized Propensity Scores with Continuous
Exposures
Description: Provides a framework for estimating causal effects of a continuous
exposure using observational data, and implementing matching and weighting
on the generalized propensity score.
Wu, X., Mealli, F., Kioumourtzoglou, M.A., Dominici, F. and Braun, D., 2022.
Matching on generalized propensity scores with continuous exposures. Journal
of the American Statistical Association, pp.1-29.
Author: Naeem Khoshnevis [aut, cre] ,
Xiao Wu [aut] ,
Danielle Braun [aut]
Maintainer: Naeem Khoshnevis <nkhoshnevis@g.harvard.edu>
Diff between CausalGPS versions 0.4.2 dated 2024-04-13 and 0.5.0 dated 2024-06-19
CausalGPS-0.4.2/CausalGPS/R/check_arguments.R |only CausalGPS-0.4.2/CausalGPS/R/generate_wrap_sl_lib.R |only CausalGPS-0.4.2/CausalGPS/R/trim_gps.R |only CausalGPS-0.4.2/CausalGPS/man/autoplot.gpsm_erf.Rd |only CausalGPS-0.4.2/CausalGPS/man/autoplot.gpsm_pspop.Rd |only CausalGPS-0.4.2/CausalGPS/man/check_args.Rd |only CausalGPS-0.4.2/CausalGPS/man/check_args_compile_pseudo_pop.Rd |only CausalGPS-0.4.2/CausalGPS/man/check_args_estimate_gps.Rd |only CausalGPS-0.4.2/CausalGPS/man/check_args_use_cov_transformers.Rd |only CausalGPS-0.4.2/CausalGPS/man/gen_wrap_sl_lib.Rd |only CausalGPS-0.4.2/CausalGPS/man/plot.gpsm_erf.Rd |only CausalGPS-0.4.2/CausalGPS/man/plot.gpsm_pspop.Rd |only CausalGPS-0.4.2/CausalGPS/man/preprocess_data.Rd |only CausalGPS-0.4.2/CausalGPS/man/print.gpsm_erf.Rd |only CausalGPS-0.4.2/CausalGPS/man/print.gpsm_pspop.Rd |only CausalGPS-0.4.2/CausalGPS/man/summary.gpsm_erf.Rd |only CausalGPS-0.4.2/CausalGPS/man/summary.gpsm_pspop.Rd |only CausalGPS-0.4.2/CausalGPS/man/transform_it.Rd |only CausalGPS-0.4.2/CausalGPS/man/trim_gps.Rd |only CausalGPS-0.4.2/CausalGPS/tests/testthat/test-check_arguments.R |only CausalGPS-0.4.2/CausalGPS/tests/testthat/test-generate_wrap_sl_lib.R |only CausalGPS-0.4.2/CausalGPS/tests/testthat/test-trim_gps.R |only CausalGPS-0.5.0/CausalGPS/DESCRIPTION | 10 CausalGPS-0.5.0/CausalGPS/MD5 | 142 CausalGPS-0.5.0/CausalGPS/NAMESPACE | 27 CausalGPS-0.5.0/CausalGPS/NEWS.md | 13 CausalGPS-0.5.0/CausalGPS/R/absolute_corr_fun.R | 1 CausalGPS-0.5.0/CausalGPS/R/absolute_weighted_corr_fun.R | 2 CausalGPS-0.5.0/CausalGPS/R/check_covar_balance.R | 123 CausalGPS-0.5.0/CausalGPS/R/check_kolmogorov_smirnov.R | 9 CausalGPS-0.5.0/CausalGPS/R/compile_pseudo_pop.R | 73 CausalGPS-0.5.0/CausalGPS/R/compute_counter_weight.R |only CausalGPS-0.5.0/CausalGPS/R/create_matching.R | 44 CausalGPS-0.5.0/CausalGPS/R/create_weighting.R | 8 CausalGPS-0.5.0/CausalGPS/R/estimate_erf.R |only CausalGPS-0.5.0/CausalGPS/R/estimate_gps.R | 155 CausalGPS-0.5.0/CausalGPS/R/estimate_npmetric_erf.R | 31 CausalGPS-0.5.0/CausalGPS/R/estimate_pmetric_erf.R | 25 CausalGPS-0.5.0/CausalGPS/R/estimate_semipmetric_erf.R | 26 CausalGPS-0.5.0/CausalGPS/R/generate_pseudo_pop.R | 585 - CausalGPS-0.5.0/CausalGPS/R/matching_fn.R | 4 CausalGPS-0.5.0/CausalGPS/R/plot.R | 433 - CausalGPS-0.5.0/CausalGPS/R/print.R | 180 CausalGPS-0.5.0/CausalGPS/R/smooth_erf.R | 3 CausalGPS-0.5.0/CausalGPS/R/trim_it.R |only CausalGPS-0.5.0/CausalGPS/R/zzz.R | 9 CausalGPS-0.5.0/CausalGPS/README.md | 276 CausalGPS-0.5.0/CausalGPS/inst/doc/CausalGPS.Rmd | 4 CausalGPS-0.5.0/CausalGPS/man/autoplot.cgps_cw.Rd |only CausalGPS-0.5.0/CausalGPS/man/autoplot.cgps_erf.Rd |only CausalGPS-0.5.0/CausalGPS/man/autoplot.cgps_gps.Rd |only CausalGPS-0.5.0/CausalGPS/man/autoplot.cgps_pspop.Rd |only CausalGPS-0.5.0/CausalGPS/man/check_covar_balance.Rd | 104 CausalGPS-0.5.0/CausalGPS/man/check_kolmogorov_smirnov.Rd | 4 CausalGPS-0.5.0/CausalGPS/man/compile_pseudo_pop.Rd | 31 CausalGPS-0.5.0/CausalGPS/man/compute_counter_weight.Rd |only CausalGPS-0.5.0/CausalGPS/man/create_matching.Rd | 23 CausalGPS-0.5.0/CausalGPS/man/create_weighting.Rd | 6 CausalGPS-0.5.0/CausalGPS/man/estimate_erf.Rd |only CausalGPS-0.5.0/CausalGPS/man/estimate_gps.Rd | 57 CausalGPS-0.5.0/CausalGPS/man/estimate_npmetric_erf.Rd | 31 CausalGPS-0.5.0/CausalGPS/man/estimate_pmetric_erf.Rd | 25 CausalGPS-0.5.0/CausalGPS/man/estimate_semipmetric_erf.Rd | 26 CausalGPS-0.5.0/CausalGPS/man/figures/png/process_flow.png |only CausalGPS-0.5.0/CausalGPS/man/figures/png/process_flow_with_plots.png |only CausalGPS-0.5.0/CausalGPS/man/generate_pseudo_pop.Rd | 169 CausalGPS-0.5.0/CausalGPS/man/plot.cgps_cw.Rd |only CausalGPS-0.5.0/CausalGPS/man/plot.cgps_erf.Rd |only CausalGPS-0.5.0/CausalGPS/man/plot.cgps_gps.Rd |only CausalGPS-0.5.0/CausalGPS/man/plot.cgps_pspop.Rd |only CausalGPS-0.5.0/CausalGPS/man/print.cgps_cw.Rd |only CausalGPS-0.5.0/CausalGPS/man/print.cgps_erf.Rd |only CausalGPS-0.5.0/CausalGPS/man/print.cgps_gps.Rd |only CausalGPS-0.5.0/CausalGPS/man/print.cgps_pspop.Rd |only CausalGPS-0.5.0/CausalGPS/man/summary.cgps_cw.Rd |only CausalGPS-0.5.0/CausalGPS/man/summary.cgps_erf.Rd |only CausalGPS-0.5.0/CausalGPS/man/summary.cgps_gps.Rd |only CausalGPS-0.5.0/CausalGPS/man/summary.cgps_pspop.Rd |only CausalGPS-0.5.0/CausalGPS/man/trim_it.Rd |only CausalGPS-0.5.0/CausalGPS/tests/testthat/CausalGPS.log | 3168 ++++++++++ CausalGPS-0.5.0/CausalGPS/tests/testthat/test-check_covar_balance.R | 233 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-check_kolmogorov_smirnov.R | 86 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-compile_pseudo_pop.R | 71 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-compute_outer.R | 1 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-create_weighting.R | 82 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-estimate_erf.R |only CausalGPS-0.5.0/CausalGPS/tests/testthat/test-estimate_gps.R | 175 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-estimate_npmetric_erf.R | 202 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-estimate_pmetric_erf.R | 7 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-estimate_semipmetric_erf.R | 1 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-generate_pseudo_pop.R | 734 +- CausalGPS-0.5.0/CausalGPS/tests/testthat/test-generate_synthetic_data.R | 1 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-matching_fn.R | 49 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-smooth_erf.R | 1 CausalGPS-0.5.0/CausalGPS/tests/testthat/test-trim_it.R |only CausalGPS-0.5.0/CausalGPS/vignettes/CausalGPS.Rmd | 4 96 files changed, 5214 insertions(+), 2260 deletions(-)
Title: Interact with Peak Flow Data in the United Kingdom
Description: Obtain information on peak flow data from the National River Flow Archive (NRFA) in the United Kingdom, either from the Peak Flow Dataset files <https://nrfa.ceh.ac.uk/peak-flow-dataset> once these have been downloaded to the user's computer or using the NRFA's API. These files are in a format suitable for direct use in the 'WINFAP' software, hence the name of the package.
Author: Ilaria Prosdocimi [aut, cre] ,
Luke Shaw [aut]
Maintainer: Ilaria Prosdocimi <prosdocimi.ilaria@gmail.com>
Diff between winfapReader versions 0.1-5 dated 2022-09-08 and 0.1-5.1 dated 2024-06-19
DESCRIPTION | 8 MD5 | 22 +- NEWS.md | 5 R/known_Oct1.R | 3 build/vignette.rds |binary data/known_Oct1.rda |binary inst/CITATION | 24 +- inst/doc/winfapReader.R | 108 +++++----- inst/doc/winfapReader.Rmd | 463 ++++++++++++++++++++++----------------------- inst/doc/winfapReader.html | 160 +++++---------- tests/testthat/testthat.R | 332 +++++++++++++++++--------------- vignettes/winfapReader.Rmd | 463 ++++++++++++++++++++++----------------------- 12 files changed, 791 insertions(+), 797 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River
Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions:
<https://nrfa.ceh.ac.uk/costs-terms-and-conditions>). The package
contains R wrappers to the UK NRFA data temporary-API. There are
functions to retrieve stations falling in a bounding box, to generate
a map and extracting time series and general information. The package
is fully described in Vitolo et al (2016) "rnrfa: An R package to
Retrieve, Filter and Visualize Data from the UK National River Flow
Archive"
<https://journal.r-project.org/archive/2016/RJ-2016-036/RJ-2016-036.pdf>.
Author: Ilaria Prosdocimi [ctb, cre] ,
Claudia Vitolo [aut] ,
Matthew Fry [ctb] ,
Wouter Buytaert [ctb] ,
Michael Spencer [ctb] ,
Tobias Gauster [ctb]
Maintainer: Ilaria Prosdocimi <prosdocimi.ilaria@gmail.com>
Diff between rnrfa versions 2.1.0.5 dated 2024-02-14 and 2.1.0.6 dated 2024-06-19
rnrfa-2.1.0.5/rnrfa/vignettes/references.bib |only rnrfa-2.1.0.6/rnrfa/DESCRIPTION | 65 +- rnrfa-2.1.0.6/rnrfa/MD5 | 50 - rnrfa-2.1.0.6/rnrfa/NAMESPACE | 1 rnrfa-2.1.0.6/rnrfa/NEWS.md | 7 rnrfa-2.1.0.6/rnrfa/R/get_ts.R | 5 rnrfa-2.1.0.6/rnrfa/R/internals.R | 7 rnrfa-2.1.0.6/rnrfa/R/plot_trend.R | 2 rnrfa-2.1.0.6/rnrfa/R/rnrfa-package.R | 4 rnrfa-2.1.0.6/rnrfa/README.md | 6 rnrfa-2.1.0.6/rnrfa/build/vignette.rds |binary rnrfa-2.1.0.6/rnrfa/inst/doc/rnrfa-vignette.R | 10 rnrfa-2.1.0.6/rnrfa/inst/doc/rnrfa-vignette.Rmd | 23 rnrfa-2.1.0.6/rnrfa/inst/doc/rnrfa-vignette.html | 315 +++++------- rnrfa-2.1.0.6/rnrfa/man/get_ts.Rd | 1 rnrfa-2.1.0.6/rnrfa/man/plot_trend.Rd | 2 rnrfa-2.1.0.6/rnrfa/man/print.nrfa_api.Rd |only rnrfa-2.1.0.6/rnrfa/man/rnrfa-package.Rd | 3 rnrfa-2.1.0.6/rnrfa/tests/testthat.R | 19 rnrfa-2.1.0.6/rnrfa/tests/testthat/test-catalogue.R | 17 rnrfa-2.1.0.6/rnrfa/tests/testthat/test-cmr.R | 75 +- rnrfa-2.1.0.6/rnrfa/tests/testthat/test-gdf.R | 18 rnrfa-2.1.0.6/rnrfa/tests/testthat/test-get_ts.R | 19 rnrfa-2.1.0.6/rnrfa/tests/testthat/test-internals.R | 30 - rnrfa-2.1.0.6/rnrfa/tests/testthat/test-seasonal_averages.R | 50 + rnrfa-2.1.0.6/rnrfa/tests/testthat/test-station_ids.R | 25 rnrfa-2.1.0.6/rnrfa/vignettes/rnrfa-vignette.Rmd | 23 27 files changed, 453 insertions(+), 324 deletions(-)
Title: Tools to Match Corporate Lending Portfolios with Climate Data
Description: These tools implement in R a fundamental part of the software
'PACTA' (Paris Agreement Capital Transition Assessment), which is a
free tool that calculates the alignment between financial portfolios
and climate scenarios (<https://www.transitionmonitor.com/>). Financial
institutions use 'PACTA' to study how their capital allocation
decisions align with climate change mitigation goals. This package
matches data from corporate lending portfolios to asset level data
from market-intelligence databases (e.g. power plant capacities,
emission factors, etc.). This is the first step to assess if a
financial portfolio aligns with climate goals.
Author: Alex Axthelm [aut, cre] ,
Jackson Hoffart [aut, ctr] ,
Mauro Lepore [aut, ctr] ,
Klaus Hagedorn [aut],
Florence Palandri [aut],
Evgeny Petrovsky [aut],
Jacob Kastl [ctr] ,
Rocky Mountain Institute [cph, fnd]
Maintainer: Alex Axthelm <aaxthelm@rmi.org>
Diff between r2dii.match versions 0.2.0 dated 2024-03-25 and 0.2.1 dated 2024-06-19
r2dii.match-0.2.0/r2dii.match/tests/testthat/_snaps |only r2dii.match-0.2.1/r2dii.match/DESCRIPTION | 12 + r2dii.match-0.2.1/r2dii.match/MD5 | 27 +-- r2dii.match-0.2.1/r2dii.match/NEWS.md | 4 r2dii.match-0.2.1/r2dii.match/R/prioritize.R | 24 ++- r2dii.match-0.2.1/r2dii.match/README.md | 80 +++++----- r2dii.match-0.2.1/r2dii.match/inst/WORDLIST | 5 r2dii.match-0.2.1/r2dii.match/man/prioritize.Rd | 13 - r2dii.match-0.2.1/r2dii.match/man/r2dii.match-package.Rd | 1 r2dii.match-0.2.1/r2dii.match/tests/testthat/helper-expect_names_match_name.R | 8 - r2dii.match-0.2.1/r2dii.match/tests/testthat/helper-skip_if_r2dii_data_outdated.R | 2 r2dii.match-0.2.1/r2dii.match/tests/testthat/test-add_sector_and_borderline.R | 5 r2dii.match-0.2.1/r2dii.match/tests/testthat/test-helper-fake_lbk.R | 4 r2dii.match-0.2.1/r2dii.match/tests/testthat/test-match_name.R | 16 +- 14 files changed, 105 insertions(+), 96 deletions(-)
Title: Argentina's Permanent Household Survey Data and Manipulation
Utilities
Description: Tools to download and manipulate the Permanent Household Survey from Argentina
(EPH is the Spanish acronym for Permanent Household Survey).
e.g: get_microdata() for downloading the datasets, get_poverty_lines() for downloading the official poverty baskets,
calculate_poverty() for the calculation of stating if a household is in poverty or not, following the official methodology.
organize_panels() is used to concatenate observations from different periods, and organize_labels()
adds the official labels to the data. The implemented methods are based on INDEC (2016) <http://www.estadistica.ec.gba.gov.ar/dpe/images/SOCIEDAD/EPH_metodologia_22_pobreza.pdf>.
As this package works with the argentinian Permanent Household Survey and its main audience is from this country,
the documentation was written in Spanish.
Author: Carolina Pradier [aut, cre] ,
Diego Kozlowski [aut] ,
Pablo Tiscornia [aut],
Guido Weksler [aut],
Natsumi Shokida [aut],
German Rosati [aut] ,
Juan Gabriel Juara [ctb]
Maintainer: Carolina Pradier <carolinapradier@gmail.com>
Diff between eph versions 1.0.0 dated 2023-09-15 and 1.0.1 dated 2024-06-19
DESCRIPTION | 10 - MD5 | 22 ++-- NEWS.md | 3 R/organize_labels.R | 4 README.md | 40 +++++-- inst/CITATION | 2 inst/doc/eph.R | 2 inst/doc/eph.html | 202 +++++++++++++++++++-------------------- inst/doc/estimacion_pobreza.R | 28 ++--- inst/doc/estimacion_pobreza.Rmd | 2 inst/doc/estimacion_pobreza.html | 14 +- vignettes/estimacion_pobreza.Rmd | 2 12 files changed, 174 insertions(+), 157 deletions(-)
Title: Estimate Invasive and Alien Species (IAS) Introduction Rates
Description: Easily estimate the introduction rates of alien species given first records data.
It specializes in addressing the role of sampling on the pattern of discoveries,
thus providing better estimates than using Generalized Linear Models which assume perfect
immediate detection of newly introduced species.
Author: Yehezkel Buba [aut, cre, cph]
Maintainer: Yehezkel Buba <hezibuba@mail.tau.ac.il>
Diff between alien versions 1.0.1 dated 2024-04-11 and 1.0.2 dated 2024-06-19
DESCRIPTION | 6 - MD5 | 32 ++++++---- NAMESPACE | 2 NEWS.md | 10 +++ R/likelihood-space.R |only R/snc.R | 100 +++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/basic_usage.R |only inst/doc/basic_usage.Rmd |only inst/doc/basic_usage.html |only inst/doc/native_discoveries.html | 6 - inst/doc/simulations.html | 8 +- man/figures/README-plotting_data-1.png |binary man/figures/README-plotting_fit-1.png |binary man/likelihood_map.Rd |only man/likelihood_space.Rd |only man/plot_snc.Rd | 6 - man/snc.Rd | 34 +++++++---- man/summary_snc.Rd | 2 tests/testthat/test-likelihood-space.R |only vignettes/basic_usage.Rmd |only 21 files changed, 135 insertions(+), 71 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>),
Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>)
and several simulation functions. It also allows dealing with intermittent demand based on the
iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between smooth versions 4.0.1 dated 2024-04-01 and 4.0.2 dated 2024-06-19
DESCRIPTION | 8 MD5 | 62 - NEWS | 13 R/adam.R | 59 + R/adamGeneral.R | 56 + R/arimaCompact.R |only R/autoadam.R | 7 R/methods.R | 13 R/msdecompose.R | 9 R/oes.R | 4 R/oesg.R | 10 R/randomARIMA.R | 169 ++++ README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/adam.Rmd | 2 inst/doc/adam.html | 1539 ++++++++++++++++++++++----------------------- inst/doc/ces.html | 10 inst/doc/es.html | 180 ++--- inst/doc/gum.html | 8 inst/doc/oes.html | 114 +-- inst/doc/simulate.html | 72 +- inst/doc/sma.html | 24 inst/doc/smooth.html | 4 inst/doc/ssarima.html | 48 - man/adam.Rd | 4 man/figures |only man/oes.Rd | 2 man/oesg.Rd | 2 src/adamGeneral.cpp | 4 tests/testthat/test_adam.R | 2 tests/testthat/test_es.R | 2 vignettes/adam.Rmd | 2 33 files changed, 1332 insertions(+), 1099 deletions(-)
Title: Semi-Automated Marketing Mix Modeling (MMM) from Meta Marketing
Science
Description: Semi-Automated Marketing Mix Modeling (MMM) aiming to reduce human bias by means of ridge regression and evolutionary algorithms, enables actionable decision making providing a budget allocation and diminishing returns curves and allows ground-truth calibration to account for causation.
Author: Gufeng Zhou [aut],
Bernardo Lares [cre, aut],
Leonel Sentana [aut],
Igor Skokan [aut],
Meta Platforms, Inc. [cph, fnd]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between Robyn versions 3.10.3 dated 2023-05-17 and 3.11.0 dated 2024-06-19
DESCRIPTION | 12 LICENSE | 6 MD5 | 98 - NAMESPACE | 336 ++--- R/allocator.R | 2035 ++++++++++++++++--------------- R/auxiliary.R | 169 +- R/calibration.R | 270 ++-- R/checks.R | 2142 +++++++++++++++++---------------- R/clusters.R | 908 +++++++------- R/convergence.R | 440 +++--- R/data.R | 121 - R/exports.R | 435 +++--- R/imports.R | 102 - R/inputs.R | 177 +- R/json.R | 756 ++++++----- R/model.R | 2629 +++++++++++++++++++++-------------------- R/outputs.R | 641 +++++---- R/pareto.R | 1218 +++++++++--------- R/plots.R | 521 +++++--- R/refresh.R | 1157 +++++++++--------- R/response.R | 761 ++++++----- R/transformation.R | 883 ++++++------- R/zzz.R | 16 README.md | 7 data/dt_prophet_holidays.RData |binary data/dt_simulated_weekly.RData |binary man/Robyn.Rd | 62 man/adstocks.Rd | 204 +-- man/dt_prophet_holidays.Rd | 75 - man/dt_simulated_weekly.Rd | 74 - man/fit_spend_exposure.Rd | 58 man/hyper_limits.Rd | 36 man/hyper_names.Rd | 200 +-- man/mic_men.Rd | 76 - man/prophet_decomp.Rd | 85 - man/robyn_allocator.Rd | 299 ++-- man/robyn_clusters.Rd | 156 +- man/robyn_converge.Rd | 118 - man/robyn_inputs.Rd | 423 +++--- man/robyn_mmm.Rd | 194 +-- man/robyn_outputs.Rd | 283 ++-- man/robyn_refresh.Rd | 318 ++-- man/robyn_response.Rd | 287 ++-- man/robyn_run.Rd | 249 ++- man/robyn_save.Rd | 116 - man/robyn_train.Rd | 188 +- man/robyn_update.Rd | 48 man/robyn_write.Rd | 152 +- man/saturation_hill.Rd | 86 - man/set_holidays.Rd | 46 50 files changed, 10257 insertions(+), 9416 deletions(-)
Title: Manipulate Time Series of Palaeoclimate Reconstructions
Description: Methods to easily extract and manipulate palaeoclimate
reconstructions for ecological and anthropological analyses, as described
in Leonardi et al. (2023) <doi:10.1111/ecog.06481>.
Author: Michela Leonardi [aut],
Emily Y. Hallet [ctb],
Robert Beyer [ctb],
Mario Krapp [ctb],
Andrea V. Pozzi [ctb],
Andrea Manica [aut, cre]
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between pastclim versions 2.0.0 dated 2023-11-02 and 2.1.0 dated 2024-06-19
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|only pastclim-2.1.0/pastclim/R/filenames_chelsa_trace21k.R |only pastclim-2.1.0/pastclim/R/filenames_paleoclim.R |only pastclim-2.1.0/pastclim/R/filenames_worldclim_future.R |only pastclim-2.1.0/pastclim/R/filenames_worldclim_present.R |only pastclim-2.1.0/pastclim/R/get_available_datasets.R | 9 pastclim-2.1.0/pastclim/R/get_biome_classes.R | 2 pastclim-2.1.0/pastclim/R/get_data_path.R | 3 pastclim-2.1.0/pastclim/R/get_file_for_dataset.R | 7 pastclim-2.1.0/pastclim/R/get_ice_mask.R | 16 pastclim-2.1.0/pastclim/R/get_land_mask.R | 20 pastclim-2.1.0/pastclim/R/get_res.R |only pastclim-2.1.0/pastclim/R/get_time_steps.R | 21 pastclim-2.1.0/pastclim/R/get_vars_for_dataset.R | 2 pastclim-2.1.0/pastclim/R/koeppen_geiger.R |only pastclim-2.1.0/pastclim/R/list_available_datasets.R | 2 pastclim-2.1.0/pastclim/R/load_etopo.R | 16 pastclim-2.1.0/pastclim/R/location_slice.R | 2 pastclim-2.1.0/pastclim/R/location_slice_from_region_series.R | 40 pastclim-2.1.0/pastclim/R/pastclim-package.R |only pastclim-2.1.0/pastclim/R/pastclim_rast.R |only pastclim-2.1.0/pastclim/R/region_series.R | 48 pastclim-2.1.0/pastclim/R/region_slice.R | 2 pastclim-2.1.0/pastclim/R/slice_region_series.R | 2 pastclim-2.1.0/pastclim/R/sysdata.rda |binary pastclim-2.1.0/pastclim/R/time_bp.R | 2 pastclim-2.1.0/pastclim/R/time_bp_to_index.R | 23 pastclim-2.1.0/pastclim/R/url_is_valid.R |only pastclim-2.1.0/pastclim/R/validate_nc.R | 2 pastclim-2.1.0/pastclim/R/vrt_get_meta.R |only pastclim-2.1.0/pastclim/R/vrt_set_meta.R |only pastclim-2.1.0/pastclim/README.md | 42 pastclim-2.1.0/pastclim/build/partial.rdb |binary pastclim-2.1.0/pastclim/build/vignette.rds |binary pastclim-2.1.0/pastclim/data/biome4_classes.rda |only pastclim-2.1.0/pastclim/data/koeppen_classes.rda |only pastclim-2.1.0/pastclim/inst/WORDLIST | 41 pastclim-2.1.0/pastclim/inst/doc/a0_pastclim_overview.R | 17 pastclim-2.1.0/pastclim/inst/doc/a0_pastclim_overview.Rmd | 46 pastclim-2.1.0/pastclim/inst/doc/a0_pastclim_overview.html | 924 +++++----- pastclim-2.1.0/pastclim/inst/doc/a1_available_datasets.R | 3 pastclim-2.1.0/pastclim/inst/doc/a1_available_datasets.Rmd | 3 pastclim-2.1.0/pastclim/inst/doc/a1_available_datasets.html | 545 ++++- pastclim-2.1.0/pastclim/inst/doc/a2_custom_datasets.html | 47 pastclim-2.1.0/pastclim/inst/doc/a3_pastclim_present_and_future.R | 70 pastclim-2.1.0/pastclim/inst/doc/a3_pastclim_present_and_future.Rmd | 152 + pastclim-2.1.0/pastclim/inst/doc/a3_pastclim_present_and_future.html | 546 ++++- pastclim-2.1.0/pastclim/inst/extdata/delta/prec_series.nc |binary pastclim-2.1.0/pastclim/inst/extdata/delta/tavg_series.nc |binary pastclim-2.1.0/pastclim/man/Barreto2023.Rd | 2 pastclim-2.1.0/pastclim/man/Beyer2020.Rd | 2 pastclim-2.1.0/pastclim/man/CHELSA_2.1.Rd |only pastclim-2.1.0/pastclim/man/CHELSA_trace21k_1.0.Rd |only pastclim-2.1.0/pastclim/man/HYDE_3.3_baseline.Rd | 11 pastclim-2.1.0/pastclim/man/Krapp2021.Rd | 2 pastclim-2.1.0/pastclim/man/WorldClim_2.1.Rd | 15 pastclim-2.1.0/pastclim/man/bioclim_vars-methods.Rd | 2 pastclim-2.1.0/pastclim/man/biome4_classes.Rd |only pastclim-2.1.0/pastclim/man/climate_for_locations.Rd | 10 pastclim-2.1.0/pastclim/man/climate_for_time_slice.Rd | 1 pastclim-2.1.0/pastclim/man/download_chelsa.Rd | 24 pastclim-2.1.0/pastclim/man/download_chelsa_trace21k.Rd |only pastclim-2.1.0/pastclim/man/download_etopo.Rd | 11 pastclim-2.1.0/pastclim/man/download_paleoclim.Rd |only pastclim-2.1.0/pastclim/man/download_worldclim_future.Rd | 20 pastclim-2.1.0/pastclim/man/filenames_chelsa_future.Rd |only pastclim-2.1.0/pastclim/man/filenames_chelsa_present.Rd |only pastclim-2.1.0/pastclim/man/filenames_chelsa_trace21k.Rd |only pastclim-2.1.0/pastclim/man/filenames_paleoclim.Rd |only pastclim-2.1.0/pastclim/man/filenames_worldclim_future.Rd |only pastclim-2.1.0/pastclim/man/filenames_worldclim_present.Rd |only pastclim-2.1.0/pastclim/man/get_ice_mask.Rd | 3 pastclim-2.1.0/pastclim/man/get_resolution.Rd |only 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pastclim-2.1.0/pastclim/tests/testthat/test_filenames_hyde.R |only pastclim-2.1.0/pastclim/tests/testthat/test_filenames_paleoclim.R |only pastclim-2.1.0/pastclim/tests/testthat/test_filenames_worldclim_future.R |only pastclim-2.1.0/pastclim/tests/testthat/test_filenames_worldclim_present.R |only pastclim-2.1.0/pastclim/tests/testthat/test_get_file_for_dataset.R | 10 pastclim-2.1.0/pastclim/tests/testthat/test_get_time_steps.R | 13 pastclim-2.1.0/pastclim/tests/testthat/test_koeppen_geiger.R |only pastclim-2.1.0/pastclim/tests/testthat/test_location_slice.R | 2 pastclim-2.1.0/pastclim/tests/testthat/test_pastclim_rast.R |only pastclim-2.1.0/pastclim/tests/testthat/test_time_bp_to_i_series.R |only pastclim-2.1.0/pastclim/tests/testthat/test_time_bp_to_index.R |only pastclim-2.1.0/pastclim/tests/testthat/test_vrt_set_get_meta.R |only pastclim-2.1.0/pastclim/tests/testthat/test_vsi_dataset.R |only pastclim-2.1.0/pastclim/vignettes/a0_pastclim_overview.Rmd | 46 pastclim-2.1.0/pastclim/vignettes/a1_available_datasets.Rmd | 3 pastclim-2.1.0/pastclim/vignettes/a3_pastclim_present_and_future.Rmd | 152 + 125 files changed, 2583 insertions(+), 1340 deletions(-)
Title: R Interface to NLopt
Description: Solve optimization problems using an R interface to NLopt. NLopt is a
free/open-source library for nonlinear optimization, providing a common
interface for a number of different free optimization routines available
online as well as original implementations of various other algorithms.
See <https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/> for more
information on the available algorithms. Building from included sources
requires 'CMake'. On Linux and 'macOS', if a suitable system build of
NLopt (2.7.0 or later) is found, it is used; otherwise, it is built
from included sources via 'CMake'. On Windows, NLopt is obtained through
'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for
'R >= 4.2.0'.
Author: Jelmer Ypma [aut],
Steven G. Johnson [aut] ,
Aymeric Stamm [ctb, cre] ,
Hans W. Borchers [ctb],
Dirk Eddelbuettel [ctb],
Brian Ripley [ctb] ,
Kurt Hornik [ctb] ,
Julien Chiquet [ctb],
Avraham Adler [ctb] ,
Xiongtao Dai [ctb],
Jeroen Ooms [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between nloptr versions 2.0.3 dated 2022-05-26 and 2.1.0 dated 2024-06-19
nloptr-2.0.3/nloptr/R/catch-routine-registration.R |only nloptr-2.0.3/nloptr/src/test-C-API.cpp |only nloptr-2.0.3/nloptr/src/test-C-API.h |only nloptr-2.0.3/nloptr/src/test-runner.cpp |only nloptr-2.0.3/nloptr/tests/testthat |only nloptr-2.0.3/nloptr/tests/testthat.R |only nloptr-2.1.0/nloptr/DESCRIPTION | 35 nloptr-2.1.0/nloptr/MD5 | 178 ++-- nloptr-2.1.0/nloptr/NEWS.md | 258 ++++-- nloptr-2.1.0/nloptr/R/auglag.R | 253 +++--- nloptr-2.1.0/nloptr/R/ccsaq.R | 174 ++-- nloptr-2.1.0/nloptr/R/check.derivatives.R | 233 ++--- nloptr-2.1.0/nloptr/R/cobyla.R | 275 +++--- nloptr-2.1.0/nloptr/R/direct.R | 172 ++-- nloptr-2.1.0/nloptr/R/finite.diff.R | 45 - nloptr-2.1.0/nloptr/R/global.R | 415 +++++---- nloptr-2.1.0/nloptr/R/gradients.R | 107 +- nloptr-2.1.0/nloptr/R/is.nloptr.R | 391 ++++----- nloptr-2.1.0/nloptr/R/lbfgs.R | 73 - nloptr-2.1.0/nloptr/R/mlsl.R | 203 ++-- nloptr-2.1.0/nloptr/R/mma.R | 207 ++-- nloptr-2.1.0/nloptr/R/nloptions.R | 58 - nloptr-2.1.0/nloptr/R/nloptr-package.R | 159 +-- nloptr-2.1.0/nloptr/R/nloptr.R | 877 ++++++++++----------- nloptr-2.1.0/nloptr/R/nloptr.add.default.options.R | 120 +- nloptr-2.1.0/nloptr/R/nloptr.get.default.options.R | 380 ++++++--- nloptr-2.1.0/nloptr/R/nloptr.print.options.R | 87 +- nloptr-2.1.0/nloptr/R/nm.R | 109 +- nloptr-2.1.0/nloptr/R/print.nloptr.R | 114 +- nloptr-2.1.0/nloptr/R/slsqp.R | 181 ++-- nloptr-2.1.0/nloptr/R/tnewton.R | 98 +- nloptr-2.1.0/nloptr/R/varmetric.R | 78 - nloptr-2.1.0/nloptr/R/zzz.R | 8 nloptr-2.1.0/nloptr/README.md | 49 - nloptr-2.1.0/nloptr/build/vignette.rds |binary nloptr-2.1.0/nloptr/inst/CITATION | 34 nloptr-2.1.0/nloptr/inst/doc/nloptr.R | 189 ++-- nloptr-2.1.0/nloptr/inst/doc/nloptr.Rmd | 425 ++++++---- nloptr-2.1.0/nloptr/inst/doc/nloptr.html | 709 ++++++++-------- nloptr-2.1.0/nloptr/inst/tinytest |only nloptr-2.1.0/nloptr/man/auglag.Rd | 68 + nloptr-2.1.0/nloptr/man/bobyqa.Rd | 40 nloptr-2.1.0/nloptr/man/ccsaq.Rd | 76 + nloptr-2.1.0/nloptr/man/check.derivatives.Rd | 33 nloptr-2.1.0/nloptr/man/cobyla.Rd | 60 - nloptr-2.1.0/nloptr/man/crs2lm.Rd | 89 +- nloptr-2.1.0/nloptr/man/direct.Rd | 51 - nloptr-2.1.0/nloptr/man/isres.Rd | 61 - nloptr-2.1.0/nloptr/man/lbfgs.Rd | 6 nloptr-2.1.0/nloptr/man/mlsl.Rd | 111 +- nloptr-2.1.0/nloptr/man/mma.Rd | 104 +- nloptr-2.1.0/nloptr/man/neldermead.Rd | 14 nloptr-2.1.0/nloptr/man/newuoa.Rd | 30 nloptr-2.1.0/nloptr/man/nl.grad.Rd | 16 nloptr-2.1.0/nloptr/man/nloptr-package.Rd | 151 +-- nloptr-2.1.0/nloptr/man/nloptr.Rd | 244 +++-- nloptr-2.1.0/nloptr/man/nloptr.print.options.Rd | 10 nloptr-2.1.0/nloptr/man/print.nloptr.Rd | 4 nloptr-2.1.0/nloptr/man/sbplx.Rd | 16 nloptr-2.1.0/nloptr/man/slsqp.Rd | 63 - nloptr-2.1.0/nloptr/man/stogo.Rd | 40 nloptr-2.1.0/nloptr/man/tnewton.Rd | 10 nloptr-2.1.0/nloptr/man/varmetric.Rd | 6 nloptr-2.1.0/nloptr/src/Makevars.in | 1 nloptr-2.1.0/nloptr/src/Makevars.ucrt | 1 nloptr-2.1.0/nloptr/src/Makevars.win | 1 nloptr-2.1.0/nloptr/src/dummy.cpp |only nloptr-2.1.0/nloptr/src/init_nloptr.c | 2 nloptr-2.1.0/nloptr/src/nloptr.c | 26 nloptr-2.1.0/nloptr/src/nloptr.h | 1 nloptr-2.1.0/nloptr/src/scripts/cmake_config.sh | 2 nloptr-2.1.0/nloptr/tests/tinytest.R |only nloptr-2.1.0/nloptr/tools/cmake_call.sh | 2 nloptr-2.1.0/nloptr/vignettes/nloptr.Rmd | 425 ++++++---- nloptr-2.1.0/nloptr/vignettes/reflist.bib | 2 75 files changed, 4652 insertions(+), 3808 deletions(-)
Title: Data Sets Useful for Modeling Examples
Description: Data sets used for demonstrating or testing model-related
packages are contained in this package.
Author: Max Kuhn [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between modeldata versions 1.3.0 dated 2024-01-21 and 1.4.0 dated 2024-06-19
DESCRIPTION | 8 ++++---- MD5 | 35 +++++++++++++++++++---------------- NEWS.md | 6 +++++- R/ad_data.R | 2 +- R/cat_adoption.R |only R/crickets.R | 2 +- R/deliveries.R | 6 +++--- R/meats.R | 2 +- R/stackoverflow.R | 4 ++-- R/two_class_dat.R | 2 +- README.md | 2 +- build/partial.rdb |binary data/cat_adoption.rda |only man/ad_data.Rd | 2 +- man/cat_adoption.Rd |only man/crickets.Rd | 2 +- man/deliveries.Rd | 6 +++--- man/meats.Rd | 2 +- man/stackoverflow.Rd | 4 ++-- man/two_class_dat.Rd | 2 +- 20 files changed, 47 insertions(+), 40 deletions(-)
Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its
application to forecasting. The main scope of the package is in variables selection
and models specification for cases of time series data. This includes promotional
modelling, selection between different dynamic regressions with non-standard
distributions of errors, selection based on cross validation, solutions to the fat
regression model problem and more. Models developed in the package are tailored
specifically for forecasting purposes. So as a results there are several methods
that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] ,
Yves R. Sagaert [ctb]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between greybox versions 2.0.0 dated 2023-09-16 and 2.0.1 dated 2024-06-19
greybox-2.0.0/greybox/R/intermittentDemandIdentifier.R |only greybox-2.0.1/greybox/DESCRIPTION | 14 greybox-2.0.1/greybox/MD5 | 102 +- greybox-2.0.1/greybox/NAMESPACE | 15 greybox-2.0.1/greybox/NEWS | 19 greybox-2.0.1/greybox/R/AutomaticDemandIdentifier.R |only greybox-2.0.1/greybox/R/alm.R | 278 ++++-- greybox-2.0.1/greybox/R/bcnorm.R | 2 greybox-2.0.1/greybox/R/cramer.R | 8 greybox-2.0.1/greybox/R/distributions.R | 1 greybox-2.0.1/greybox/R/error-measures.R | 4 greybox-2.0.1/greybox/R/greybox-package.R | 5 greybox-2.0.1/greybox/R/lmCombine.R | 9 greybox-2.0.1/greybox/R/lmDynamic.R | 2 greybox-2.0.1/greybox/R/mcor.R | 10 greybox-2.0.1/greybox/R/methods.R | 768 +++++------------ greybox-2.0.1/greybox/R/nemenyi.R | 4 greybox-2.0.1/greybox/R/outlierdummy.R |only greybox-2.0.1/greybox/R/pointLik.R |only greybox-2.0.1/greybox/R/rmcb.R | 44 greybox-2.0.1/greybox/R/stepwise.R | 7 greybox-2.0.1/greybox/R/timeboot.R |only greybox-2.0.1/greybox/README.md | 2 greybox-2.0.1/greybox/build/partial.rdb |binary greybox-2.0.1/greybox/build/vignette.rds |binary greybox-2.0.1/greybox/inst/doc/alm.R | 5 greybox-2.0.1/greybox/inst/doc/alm.Rmd | 5 greybox-2.0.1/greybox/inst/doc/alm.html | 493 +++++----- greybox-2.0.1/greybox/inst/doc/greybox.R | 2 greybox-2.0.1/greybox/inst/doc/greybox.Rmd | 1 greybox-2.0.1/greybox/inst/doc/greybox.html | 128 +- greybox-2.0.1/greybox/inst/doc/maUsingGreybox.html | 4 greybox-2.0.1/greybox/inst/doc/ro.R | 4 greybox-2.0.1/greybox/inst/doc/ro.Rmd | 2 greybox-2.0.1/greybox/inst/doc/ro.html | 18 greybox-2.0.1/greybox/man/BCNormal.Rd | 2 greybox-2.0.1/greybox/man/Distributions.Rd | 1 greybox-2.0.1/greybox/man/adi.Rd |only greybox-2.0.1/greybox/man/alm.Rd | 27 greybox-2.0.1/greybox/man/cramer.Rd | 8 greybox-2.0.1/greybox/man/error-measures.Rd | 2 greybox-2.0.1/greybox/man/figures |only greybox-2.0.1/greybox/man/greybox.Rd | 5 greybox-2.0.1/greybox/man/lmCombine.Rd | 6 greybox-2.0.1/greybox/man/mcor.Rd | 10 greybox-2.0.1/greybox/man/measures.Rd | 2 greybox-2.0.1/greybox/man/outlierdummy.Rd | 9 greybox-2.0.1/greybox/man/plot.greybox.Rd | 6 greybox-2.0.1/greybox/man/pointIC.Rd | 2 greybox-2.0.1/greybox/man/pointLik.Rd | 6 greybox-2.0.1/greybox/man/rmcb.Rd | 26 greybox-2.0.1/greybox/man/stepwise.Rd | 6 greybox-2.0.1/greybox/man/timeboot.Rd |only greybox-2.0.1/greybox/vignettes/alm.Rmd | 5 greybox-2.0.1/greybox/vignettes/greybox.Rmd | 1 greybox-2.0.1/greybox/vignettes/ro.Rmd | 2 56 files changed, 1052 insertions(+), 1030 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII,
and a set of formatters for transforming values or sets of values into
ASCII-ready display strings.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Davide Garolini [ctb],
Emily de la Rua [ctb],
Abinaya Yogasekaram [ctb],
Joe Zhu [ctb, cre],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between formatters versions 0.5.6 dated 2024-04-15 and 0.5.8 dated 2024-06-19
DESCRIPTION | 25 - MD5 | 93 ++-- NAMESPACE | 13 NEWS.md | 21 - R/generics.R | 94 +++- R/matrix_form.R | 109 ++++- R/mpf_exporters.R | 133 ++++-- R/package.R | 4 R/page_size.R | 117 ++++- R/pagination.R | 367 ++++++++++++------ R/tostring.R | 602 +++++++++++++++++++++++++++--- inst/WORDLIST | 7 inst/doc/formatters.html | 4 man/MatrixPrintForm.Rd | 13 man/basic_pagdf.Rd | 6 man/default_horizontal_sep.Rd | 17 man/export_as_pdf.Rd | 18 man/export_as_rtf.Rd | 13 man/export_as_txt.Rd | 10 man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/font_lcpi.Rd | 10 man/font_spec.Rd |only man/formatters-package.Rd | 1 man/make_row_df.Rd | 22 - man/matrix_form.Rd | 14 man/mpf_accessors.Rd | 6 man/mpf_to_rtf.Rd | 11 man/nchar_ttype.Rd |only man/nlines.Rd | 17 man/num_rep_cols.Rd | 11 man/open_font_dev.Rd |only man/padstr.Rd | 5 man/pag_indices_inner.Rd | 9 man/pagdfrow.Rd | 8 man/page_lcpp.Rd | 6 man/paginate_indices.Rd | 17 man/propose_column_widths.Rd | 5 man/test_matrix_form.Rd | 18 man/tostring.Rd | 11 man/vert_pag_indices.Rd | 12 man/wrap_string.Rd | 7 man/wrap_string_ttype.Rd |only tests/testthat/test-exporters.R | 12 tests/testthat/test-listings.R | 8 tests/testthat/test-pagination.R | 7 tests/testthat/test-txt_wrap.R | 84 ++++ 54 files changed, 1596 insertions(+), 371 deletions(-)
Title: Dynamic Bayesian Network Learning and Inference
Description: Learning and inference over dynamic Bayesian networks of arbitrary
Markovian order. Extends some of the functionality offered by the 'bnlearn'
package to learn the networks from data and perform exact inference.
It offers three structure learning algorithms for dynamic Bayesian networks:
Trabelsi G. (2013) <doi:10.1007/978-3-642-41398-8_34>, Santos F.P. and Maciel C.D. (2014)
<doi:10.1109/BRC.2014.6880957>, Quesada D., Bielza C. and Larrañaga P. (2021)
<doi:10.1007/978-3-030-86271-8_14>. It also offers the possibility to perform
forecasts of arbitrary length. A tool for visualizing the structure of the
net is also provided via the 'visNetwork' package.
Author: David Quesada [aut, cre],
Gabriel Valverde [ctb]
Maintainer: David Quesada <dkesada@gmail.com>
Diff between dbnR versions 0.7.8 dated 2022-10-04 and 0.7.9 dated 2024-06-19
DESCRIPTION | 8 +- MD5 | 58 ++++++++++---------- NAMESPACE | 2 NEWS.md | 10 +++ R/RcppExports.R | 12 ++-- R/bnlearn_compat.R | 2 R/dbn_learn.R | 4 - R/dbn_visualization.R | 2 R/structure_learning_dmmhc.R | 10 ++- R/structure_learning_natpsoho.R | 2 R/structure_learning_psoho.R | 3 - R/utils.R | 4 - README.md | 87 ++++++++++++++++-------------- man/Velocity.Rd | 2 man/cte_times_vel_cpp.Rd | 2 man/dmmhc.Rd | 8 ++ man/fit_dbn_params.Rd | 2 man/learn_dbn_struc.Rd | 2 man/natVelocity.Rd | 2 man/nat_cte_times_vel_cpp.Rd | 2 man/nat_vel_plus_vel_cpp.Rd | 4 - man/node_levels.Rd | 2 man/randomize_vl_cpp.Rd | 2 man/rbn.dbn.fit.Rd | 4 - man/vel_plus_vel_cpp.Rd | 2 src/Makevars | 1 src/include/structure_learning_natPsoho.h | 1 src/include/structure_learning_psoho.h | 2 src/structure_learning_natPsoho.cpp | 6 +- src/structure_learning_psoho.cpp | 21 +++---- 30 files changed, 146 insertions(+), 123 deletions(-)
Title: Survival Control Charts Estimation Software
Description: Quality control charts for survival outcomes.
Allows users to construct the Continuous Time Generalized
Rapid Response CUSUM (CGR-CUSUM) <doi:10.1093/biostatistics/kxac041>,
the Biswas & Kalbfleisch (2008) <doi:10.1002/sim.3216> CUSUM,
the Bernoulli CUSUM and the risk-adjusted funnel plot for survival data
<doi:10.1002/sim.1970>.
These procedures can be used to monitor survival processes for a change
in the failure rate.
Author: Daniel Gomon [aut, cre] ,
Mirko Signorelli [ctb]
Maintainer: Daniel Gomon <dgstatsoft@gmail.com>
Diff between success versions 1.0.1 dated 2023-10-09 and 1.1.0 dated 2024-06-19
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++--------------- NEWS.md | 5 +++++ R/bernoulli_ARL.R | 34 +++++++++++----------------------- R/bk_cusum.R | 2 +- R/cgr_cusum.R | 6 +++++- R/parameter_assist.R | 24 ++++++++++++------------ README.md | 5 +++-- inst/CITATION | 11 +++++------ inst/doc/success_arxiv.pdf |binary man/bernoulli_ARL.Rd | 23 +++++++---------------- man/bernoulli_RL_cdf.Rd | 8 ++++---- man/bk_cusum.Rd | 2 +- man/cgr_cusum.Rd | 6 +++++- man/parameter_assist.Rd | 24 ++++++++++++------------ vignettes/success_arxiv_vignette.pdf |binary 16 files changed, 92 insertions(+), 100 deletions(-)
Title: Advanced Response Surface Analysis
Description: Provides tools for response surface analysis, using a comparative framework that identifies best-fitting solutions across 37 families of polynomials. Many of these tools are based upon and extend the 'RSA' package, by testing a larger scope of polynomials (+27 families), more diverse response surface probing techniques (+acceleration points), more plots (+line of congruence, +line of incongruence, both with extrema), and other useful functions for exporting results.
Author: Fernando Nunez-Regueiro [aut, cre]
,
Jacques Juhel [aut] ,
Felix Schoenbrodt [ctb] ,
Sarah Humberg [ctb]
Maintainer: Fernando Nunez-Regueiro <fernando.nr.france@gmail.com>
Diff between RSAtools versions 0.1.0 dated 2024-06-18 and 0.1.1 dated 2024-06-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/RSAmodel.R | 8 ++++---- R/RSAmodel.auxiliary.R | 4 ++-- inst/CITATION | 6 +++--- man/RSAmodel.Rd | 8 ++++---- man/RSAmodel.auxiliary.Rd | 4 ++-- 7 files changed, 24 insertions(+), 24 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 1.37.0 dated 2024-05-21 and 1.38.0 dated 2024-06-19
reticulate-1.37.0/reticulate/tests/testthat/resources/_snaps |only reticulate-1.37.0/reticulate/tests/testthat/resources/figure |only reticulate-1.37.0/reticulate/tests/testthat/resources/test-custom-root-dir.md |only reticulate-1.37.0/reticulate/tools |only reticulate-1.38.0/reticulate/DESCRIPTION | 6 reticulate-1.38.0/reticulate/MD5 | 54 +-- reticulate-1.38.0/reticulate/NAMESPACE | 2 reticulate-1.38.0/reticulate/NEWS.md | 19 - reticulate-1.38.0/reticulate/R/python-tools.R | 7 reticulate-1.38.0/reticulate/R/utils.R | 40 +- reticulate-1.38.0/reticulate/build/vignette.rds |binary reticulate-1.38.0/reticulate/inst/doc/arrays.html | 2 reticulate-1.38.0/reticulate/inst/doc/calling_python.html | 2 reticulate-1.38.0/reticulate/inst/doc/package.html | 2 reticulate-1.38.0/reticulate/inst/doc/python_dependencies.html | 2 reticulate-1.38.0/reticulate/inst/doc/python_packages.html | 2 reticulate-1.38.0/reticulate/inst/doc/python_primer.html | 36 +- reticulate-1.38.0/reticulate/inst/doc/r_markdown.html | 12 reticulate-1.38.0/reticulate/inst/doc/versions.html | 2 reticulate-1.38.0/reticulate/src/libpython.cpp | 7 reticulate-1.38.0/reticulate/src/libpython.h | 28 + reticulate-1.38.0/reticulate/src/python.cpp | 174 +++++++--- reticulate-1.38.0/reticulate/src/reticulate_types.h | 27 + reticulate-1.38.0/reticulate/tests/testthat/test-aaa.R | 16 reticulate-1.38.0/reticulate/tests/testthat/test-python-arrays.R | 17 reticulate-1.38.0/reticulate/tests/testthat/test-python-exceptions.R | 24 + reticulate-1.38.0/reticulate/tests/testthat/test-python-info.R | 14 reticulate-1.38.0/reticulate/tests/testthat/test-python-numpy.R | 44 ++ reticulate-1.38.0/reticulate/tests/testthat/test-python-pandas.R | 7 29 files changed, 383 insertions(+), 163 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Wesley Gardiner [ctb] ,
Michael T. Brannick [ctb] ,
Jack Kostal [ctb] ,
Sean Potter [ctb] ,
John Sakaluk [ctb] ,
Yuejia Teng [ctb]
Maintainer: Jeffrey A. Dahlke <jeff.dahlke.phd@gmail.com>
Diff between psychmeta versions 2.6.5 dated 2022-08-26 and 2.7.0 dated 2024-06-19
psychmeta-2.6.5/psychmeta/man/check_wt_type.Rd |only psychmeta-2.6.5/psychmeta/man/clean_warning.Rd |only psychmeta-2.6.5/psychmeta/man/convert_pq_to_p.Rd |only psychmeta-2.6.5/psychmeta/man/convert_reltype2consistency.Rd |only psychmeta-2.6.5/psychmeta/man/convert_sdd_to_sdr.Rd |only psychmeta-2.6.5/psychmeta/man/convert_sdr_to_sdd.Rd |only psychmeta-2.6.5/psychmeta/man/convert_vard_to_varr.Rd |only psychmeta-2.6.5/psychmeta/man/convert_varr_to_vard.Rd |only psychmeta-2.6.5/psychmeta/man/create_ad_array.Rd |only psychmeta-2.6.5/psychmeta/man/dot-attenuate_r_bvdrr.Rd |only psychmeta-2.6.5/psychmeta/man/dot-attenuate_r_bvirr.Rd |only psychmeta-2.6.5/psychmeta/man/dot-attenuate_r_rb.Rd |only psychmeta-2.6.5/psychmeta/man/dot-attenuate_r_uvdrr.Rd |only psychmeta-2.6.5/psychmeta/man/dot-attenuate_r_uvirr.Rd |only psychmeta-2.6.5/psychmeta/man/dot-convert_metatab.Rd |only psychmeta-2.6.5/psychmeta/man/dot-correct_r_bvdrr.Rd |only psychmeta-2.6.5/psychmeta/man/dot-correct_r_bvirr.Rd |only 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psychmeta-2.6.5/psychmeta/man/screen_u.Rd |only psychmeta-2.6.5/psychmeta/man/warning_variance.Rd |only psychmeta-2.7.0/psychmeta/DESCRIPTION | 45 psychmeta-2.7.0/psychmeta/MD5 | 247 +-- psychmeta-2.7.0/psychmeta/NAMESPACE | 2 psychmeta-2.7.0/psychmeta/NEWS.md | 8 psychmeta-2.7.0/psychmeta/R/compute_dmod.R | 16 psychmeta-2.7.0/psychmeta/R/control_psychmeta.R | 22 psychmeta-2.7.0/psychmeta/R/convert_ma.R | 183 +- psychmeta-2.7.0/psychmeta/R/correct_d.R | 4 psychmeta-2.7.0/psychmeta/R/correct_mvrr.R | 4 psychmeta-2.7.0/psychmeta/R/correct_r.R | 46 psychmeta-2.7.0/psychmeta/R/correct_r_internal.R | 11 psychmeta-2.7.0/psychmeta/R/create_ad.R | 1 psychmeta-2.7.0/psychmeta/R/create_ad_list.R | 1 psychmeta-2.7.0/psychmeta/R/create_ad_wrappers.R | 1 psychmeta-2.7.0/psychmeta/R/developer_utils.R | 1 psychmeta-2.7.0/psychmeta/R/estimate_artifacts.R | 262 ++- psychmeta-2.7.0/psychmeta/R/estimate_prods.R | 8 psychmeta-2.7.0/psychmeta/R/estimate_var_artifacts.R | 20 psychmeta-2.7.0/psychmeta/R/estimate_var_rho_int.R | 12 psychmeta-2.7.0/psychmeta/R/estimate_var_rho_tsa.R | 14 psychmeta-2.7.0/psychmeta/R/estimate_var_tsa.R | 14 psychmeta-2.7.0/psychmeta/R/filter_ma.R | 12 psychmeta-2.7.0/psychmeta/R/filters.R | 18 psychmeta-2.7.0/psychmeta/R/get_stuff.R | 40 psychmeta-2.7.0/psychmeta/R/heterogeneity.R | 21 psychmeta-2.7.0/psychmeta/R/ma_d.R | 188 +- psychmeta-2.7.0/psychmeta/R/ma_d_bb.R | 2 psychmeta-2.7.0/psychmeta/R/ma_generic.R | 2 psychmeta-2.7.0/psychmeta/R/ma_r.R | 236 +- psychmeta-2.7.0/psychmeta/R/ma_r_ad.R | 12 psychmeta-2.7.0/psychmeta/R/ma_r_ad_rb_adj.R | 16 psychmeta-2.7.0/psychmeta/R/ma_r_ad_rb_orig.R | 16 psychmeta-2.7.0/psychmeta/R/ma_r_ad_uvdrr.R | 10 psychmeta-2.7.0/psychmeta/R/ma_r_ad_uvirr.R | 25 psychmeta-2.7.0/psychmeta/R/ma_r_bb.R | 2 psychmeta-2.7.0/psychmeta/R/ma_r_ic.R | 67 psychmeta-2.7.0/psychmeta/R/ma_r_order2.R | 8 psychmeta-2.7.0/psychmeta/R/methods_anova.R | 2 psychmeta-2.7.0/psychmeta/R/methods_confint.R | 4 psychmeta-2.7.0/psychmeta/R/methods_dplyr_ma_psychmeta.R | 6 psychmeta-2.7.0/psychmeta/R/methods_dplyr_ma_table.R | 6 psychmeta-2.7.0/psychmeta/R/methods_predict.R | 4 psychmeta-2.7.0/psychmeta/R/methods_print.R | 2 psychmeta-2.7.0/psychmeta/R/output.R | 51 psychmeta-2.7.0/psychmeta/R/plotting.R | 9 psychmeta-2.7.0/psychmeta/R/psychmeta.R | 71 psychmeta-2.7.0/psychmeta/R/remove_dependency.R | 146 + psychmeta-2.7.0/psychmeta/R/sensitivity.R | 4 psychmeta-2.7.0/psychmeta/R/simulate_d.R | 4 psychmeta-2.7.0/psychmeta/R/simulate_r.R | 6 psychmeta-2.7.0/psychmeta/README.md | 2 psychmeta-2.7.0/psychmeta/build/partial.rdb |binary psychmeta-2.7.0/psychmeta/build/vignette.rds |binary psychmeta-2.7.0/psychmeta/data/data_r_roth_2015.RData |binary psychmeta-2.7.0/psychmeta/inst/CITATION | 5 psychmeta-2.7.0/psychmeta/inst/doc/ma_r.html | 881 ++++++----- psychmeta-2.7.0/psychmeta/inst/doc/overview.html | 673 ++++++-- psychmeta-2.7.0/psychmeta/man/anova.ma_psychmeta.Rd | 2 psychmeta-2.7.0/psychmeta/man/compute_dmod.Rd | 14 psychmeta-2.7.0/psychmeta/man/conf.limits.nc.chisq.Rd | 12 psychmeta-2.7.0/psychmeta/man/confint.Rd | 4 psychmeta-2.7.0/psychmeta/man/control_psychmeta.Rd | 22 psychmeta-2.7.0/psychmeta/man/convert_es.Rd | 4 psychmeta-2.7.0/psychmeta/man/correct_d.Rd | 4 psychmeta-2.7.0/psychmeta/man/correct_matrix_mvrr.Rd | 2 psychmeta-2.7.0/psychmeta/man/correct_means_mvrr.Rd | 2 psychmeta-2.7.0/psychmeta/man/correct_r.Rd | 4 psychmeta-2.7.0/psychmeta/man/correct_r_dich.Rd | 4 psychmeta-2.7.0/psychmeta/man/estimate_artifacts.Rd | 60 psychmeta-2.7.0/psychmeta/man/estimate_prod.Rd | 8 psychmeta-2.7.0/psychmeta/man/estimate_var_artifacts.Rd | 20 psychmeta-2.7.0/psychmeta/man/estimate_var_rho_int.Rd | 12 psychmeta-2.7.0/psychmeta/man/estimate_var_rho_tsa.Rd | 14 psychmeta-2.7.0/psychmeta/man/estimate_var_tsa.Rd | 14 psychmeta-2.7.0/psychmeta/man/filter_ma.Rd | 12 psychmeta-2.7.0/psychmeta/man/format_num.Rd | 20 psychmeta-2.7.0/psychmeta/man/generate_bib.Rd | 5 psychmeta-2.7.0/psychmeta/man/get_stuff.Rd | 40 psychmeta-2.7.0/psychmeta/man/heterogeneity.Rd | 2 psychmeta-2.7.0/psychmeta/man/ma_d.Rd | 200 +- psychmeta-2.7.0/psychmeta/man/ma_generic.Rd | 3 psychmeta-2.7.0/psychmeta/man/ma_r.Rd | 236 +- psychmeta-2.7.0/psychmeta/man/metabulate.Rd | 12 psychmeta-2.7.0/psychmeta/man/metabulate_rmd_helper.Rd | 16 psychmeta-2.7.0/psychmeta/man/plot_funnel.Rd | 4 psychmeta-2.7.0/psychmeta/man/predict.Rd | 4 psychmeta-2.7.0/psychmeta/man/psychmeta-package.Rd | 75 psychmeta-2.7.0/psychmeta/man/simulate_d_database.Rd | 4 psychmeta-2.7.0/psychmeta/man/simulate_r_database.Rd | 4 160 files changed, 2559 insertions(+), 1753 deletions(-)
Title: Ecological Niche Modeling using Presence-Absence Data
Description: A set of tools to perform Ecological Niche Modeling with
presence-absence data. It includes algorithms for data partitioning,
model fitting, calibration, evaluation, selection, and prediction.
Other functions help to explore signals of ecological niche using univariate
and multivariate analyses, and model features such as variable response
curves and variable importance. Unique characteristics of this package are
the ability to exclude models with concave quadratic responses, and the
option to clamp model predictions to specific variables. These tools are
implemented following principles proposed in
Cobos et al., (2022) <doi:10.17161/bi.v17i.15985>,
Cobos et al., (2019) <doi:10.7717/peerj.6281>,
and Peterson et al., (2008) <doi:10.1016/j.ecolmodel.2007.11.008>.
Author: Luis F. Arias-Giraldo [aut, cre]
,
Marlon E. Cobos [aut] ,
A. Townsend Peterson [ctb]
Maintainer: Luis F. Arias-Giraldo <lfarias.giraldo@gmail.com>
Diff between enmpa versions 0.1.5 dated 2023-12-01 and 0.1.8 dated 2024-06-19
DESCRIPTION | 14 MD5 | 75 +++-- NAMESPACE | 6 NEWS.md | 22 + R/Classes.R |only R/Methods.R |only R/calibration_glm.R | 27 + R/data_documentation.R | 18 - R/enmpa.R | 3 R/evaluation_stats.R | 22 - R/fit_glm.R | 31 +- R/model_validation.R | 14 R/predict_glm.R | 154 +++++++--- R/predict_selected.R | 50 +-- R/response_curve.R | 144 ++++++++- R/selection_helpers.R | 79 ----- R/short_helpers.R | 162 +++++++---- R/var_importance.R | 102 ++++++ README.md | 278 +++++++++++++------ data/cal_res.rda |binary data/sel_fit.rda |binary man/cal_res.Rd | 6 man/calibration_glm.Rd | 8 man/enmpa.Rd | 23 + man/enmpa_calibration.Rd |only man/enmpa_fitted_models.Rd |only man/evaluation_stats.Rd | 2 man/figures/README-figures-consensus-1.png |binary man/figures/README-figures-jackk-1.png |only man/figures/README-figures-jackk-2.png |only man/figures/README-figures-jackk-3.png |only man/figures/README-figures-jackk-4.png |only man/figures/README-figures-prediction_selected-1.png |binary man/figures/README-figures-raster_layers-1.png |binary man/figures/README-figures-rcurve_two-1.png |only man/figures/README-figures-rcurve_two-2.png |only man/figures/enmpa_logo_100dpi.png |only man/fit_glms.Rd | 5 man/predict_glm.Rd | 32 +- man/predict_selected.Rd | 29 + man/print.Rd |only man/response_curve.Rd | 20 + man/sel_fit.Rd | 12 man/summary.Rd |only man/var_importance.Rd | 17 - 45 files changed, 918 insertions(+), 437 deletions(-)
Title: Augments 'ASReml-R' in Fitting Mixed Models and Packages
Generally in Exploring Prediction Differences
Description: Assists in automating the selection of terms to include in mixed models when
'asreml' is used to fit the models. Procedures are available for choosing models that
conform to the hierarchy or marginality principle, for fitting and choosing between
two-dimensional spatial models using correlation, natural cubic smoothing spline and
P-spline models. A history of the fitting of a sequence of models is kept in a data frame.
Also used to compute functions and contrasts of, to investigate differences between and
to plot predictions obtained using any model fitting function. The content falls into
the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model
selection and description functions, (iv) Model diagnostics and simulation functions,
(v) Prediction production and presentation functions, (vi) Response transformation
functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions
(for further details see 'asremlPlus-package' in help). The [...truncated...]
Author: Chris Brien [aut, cre]
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between asremlPlus versions 4.4.32 dated 2024-04-11 and 4.4.35 dated 2024-06-19
asremlPlus-4.4.32/asremlPlus/R/alldiffs.v2.r |only asremlPlus-4.4.35/asremlPlus/DESCRIPTION | 8 asremlPlus-4.4.35/asremlPlus/MD5 | 70 +++---- asremlPlus-4.4.35/asremlPlus/NAMESPACE | 3 asremlPlus-4.4.35/asremlPlus/R/S3methodsDeprecations.r | 2 asremlPlus-4.4.35/asremlPlus/R/alldiffs.v4.r |only asremlPlus-4.4.35/asremlPlus/R/asremlPlusUtilities.r | 22 ++ asremlPlus-4.4.35/asremlPlus/R/reml4.v11.r | 12 - asremlPlus-4.4.35/asremlPlus/build/partial.rdb |binary asremlPlus-4.4.35/asremlPlus/build/vignette.rds |binary asremlPlus-4.4.35/asremlPlus/inst/NEWS.Rd | 14 + asremlPlus-4.4.35/asremlPlus/inst/doc/Ladybird.asreml.pdf |binary asremlPlus-4.4.35/asremlPlus/inst/doc/Ladybird.lm.pdf |binary asremlPlus-4.4.35/asremlPlus/inst/doc/Wheat.analysis.pdf |binary asremlPlus-4.4.35/asremlPlus/inst/doc/Wheat.infoCriteria.pdf |binary asremlPlus-4.4.35/asremlPlus/inst/doc/WheatSpatialModels.pdf |binary asremlPlus-4.4.35/asremlPlus/inst/doc/asremlPlus-manual.pdf |binary asremlPlus-4.4.35/asremlPlus/man/R2adj.asreml.Rd | 8 asremlPlus-4.4.35/asremlPlus/man/asremlPlus-package.Rd | 3 asremlPlus-4.4.35/asremlPlus/man/isCompoundSymmetric.matrix.Rd |only asremlPlus-4.4.35/asremlPlus/man/linTransform.alldiffs.Rd | 35 ++- asremlPlus-4.4.35/asremlPlus/man/plotLSDerrors.alldiffs.Rd | 4 asremlPlus-4.4.35/asremlPlus/man/plotLSDerrors.data.frame.Rd | 6 asremlPlus-4.4.35/asremlPlus/man/plotLSDs.alldiffs.Rd | 4 asremlPlus-4.4.35/asremlPlus/man/plotLSDs.data.frame.Rd | 6 asremlPlus-4.4.35/asremlPlus/man/plotPredictions.data.frame.Rd | 6 asremlPlus-4.4.35/asremlPlus/man/plotPvalues.alldiffs.Rd | 4 asremlPlus-4.4.35/asremlPlus/man/plotPvalues.data.frame.Rd | 6 asremlPlus-4.4.35/asremlPlus/man/predictPlus.asreml.Rd | 13 + asremlPlus-4.4.35/asremlPlus/man/predictPresent.asreml.Rd | 16 + asremlPlus-4.4.35/asremlPlus/tests/testthat/data/dat699.rda |only asremlPlus-4.4.35/asremlPlus/tests/testthat/test42GeneticCane.R | 2 asremlPlus-4.4.35/asremlPlus/tests/testthat/test42PredictionsPresentation.r | 11 - asremlPlus-4.4.35/asremlPlus/tests/testthat/test42Selection.r | 2 asremlPlus-4.4.35/asremlPlus/tests/testthat/test42SpatialModels.r | 27 +- asremlPlus-4.4.35/asremlPlus/tests/testthat/test42WheatSpatialVignette.r | 2 asremlPlus-4.4.35/asremlPlus/tests/testthat/test42alldiffsasr.r | 95 +++++++++- asremlPlus-4.4.35/asremlPlus/tests/testthat/test42alldiffslme.r | 2 38 files changed, 277 insertions(+), 106 deletions(-)
Title: Oncology Extension Package for ADaM in 'R' Asset Library
Description: Programming oncology specific Clinical Data Interchange Standards Consortium
(CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. ADaM datasets are a
mandatory part of any New Drug or Biologics License Application submitted to the
United States Food and Drug Administration (FDA). Analysis derivations are
implemented in accordance with the "Analysis Data Model Implementation Guide"
(CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam>).
The package is an extension package of the 'admiral' package.
Author: Stefan Bundfuss [aut, cre],
Ross Farrugia [aut],
Amit Jain [aut],
Andrew Smith [aut],
Teckla Akinyi [aut],
Samia Kabi [aut],
Stephen Gormley [aut],
Hinal Patel [aut],
Vinh Nguyen [aut],
Olga Starostecka [aut],
Uwe Bader [ctb],
Karl Kennedy [ctb],
Edo [...truncated...]
Maintainer: Stefan Bundfuss <stefan.bundfuss@roche.com>
Diff between admiralonco versions 1.0.0 dated 2023-12-20 and 1.1.0 dated 2024-06-19
DESCRIPTION | 14 MD5 | 78 - NEWS.md | 12 README.md | 6 build/vignette.rds |binary inst/WORDLIST | 10 inst/doc/admiralonco.Rmd | 2 inst/doc/admiralonco.html | 355 +++++-- inst/doc/adrs.R | 82 - inst/doc/adrs.Rmd | 40 inst/doc/adrs.html | 1968 ++++++++++++++++++++++++----------------- inst/doc/adrs_basic.R | 66 - inst/doc/adrs_basic.Rmd | 24 inst/doc/adrs_basic.html | 1422 +++++++++++++++++++---------- inst/doc/adrs_imwg.R |only inst/doc/adrs_imwg.Rmd |only inst/doc/adrs_imwg.html |only inst/doc/adtr.R | 64 - inst/doc/adtr.Rmd | 30 inst/doc/adtr.html | 1100 +++++++++++++++------- inst/doc/adtte.R | 22 inst/doc/adtte.Rmd | 6 inst/doc/adtte.html | 820 +++++++++++------ inst/doc/irecist.R | 60 - inst/doc/irecist.Rmd | 32 inst/doc/irecist.html | 1638 +++++++++++++++++++++------------- inst/doc/nactdt.R | 18 inst/doc/nactdt.Rmd | 6 inst/doc/nactdt.html | 560 ++++++++--- inst/templates/ad_adrs.R | 36 inst/templates/ad_adrs_basic.R | 22 inst/templates/ad_adtr.R | 28 inst/templates/ad_adtte.R | 6 man/admiralonco-package.Rd | 2 vignettes/admiralonco.Rmd | 2 vignettes/adrs.Rmd | 40 vignettes/adrs_basic.Rmd | 24 vignettes/adrs_imwg.Rmd |only vignettes/adtr.Rmd | 30 vignettes/adtte.Rmd | 6 vignettes/irecist.Rmd | 32 vignettes/nactdt.Rmd | 6 42 files changed, 5531 insertions(+), 3138 deletions(-)
Title: Nanosecond-Resolution Time Support for R
Description: Full 64-bit resolution date and time functionality with
nanosecond granularity is provided, with easy transition to and from
the standard 'POSIXct' type. Three additional classes offer interval,
period and duration functionality for nanosecond-resolution timestamps.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.3.7 dated 2022-10-24 and 0.3.8 dated 2024-06-19
nanotime-0.3.7/nanotime/src/Makevars.ucrt |only nanotime-0.3.8/nanotime/ChangeLog | 112 ++++++++ nanotime-0.3.8/nanotime/DESCRIPTION | 10 nanotime-0.3.8/nanotime/MD5 | 45 +-- nanotime-0.3.8/nanotime/R/nanoduration.R | 2 nanotime-0.3.8/nanotime/R/nanoperiod.R | 2 nanotime-0.3.8/nanotime/R/nanotime.R | 39 ++ nanotime-0.3.8/nanotime/README.md | 1 nanotime-0.3.8/nanotime/build/vignette.rds |binary nanotime-0.3.8/nanotime/inst/NEWS.Rd | 23 + nanotime-0.3.8/nanotime/inst/doc/nanotime-introduction.pdf |binary nanotime-0.3.8/nanotime/inst/include/nanotime/interval.hpp | 167 +++++------- nanotime-0.3.8/nanotime/inst/include/nanotime/period.hpp | 4 nanotime-0.3.8/nanotime/inst/include/nanotime/utilities.hpp | 4 nanotime-0.3.8/nanotime/inst/tinytest/test_nanoduration.R | 5 nanotime-0.3.8/nanotime/inst/tinytest/test_nanoival.R | 40 +- nanotime-0.3.8/nanotime/inst/tinytest/test_nanotime.R | 30 ++ nanotime-0.3.8/nanotime/man/nanoperiod.Rd | 2 nanotime-0.3.8/nanotime/man/nanotime.Rd | 17 - nanotime-0.3.8/nanotime/src/Makevars | 4 nanotime-0.3.8/nanotime/src/Makevars.win | 6 nanotime-0.3.8/nanotime/src/interval.cpp | 90 ++---- nanotime-0.3.8/nanotime/src/period.cpp | 17 - nanotime-0.3.8/nanotime/tests/simpleTests.R | 1 24 files changed, 399 insertions(+), 222 deletions(-)
Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for analyses of multiple social networks are delivered with this
package as described in Ostoic (2020) <DOI:10.18637/jss.v092.i11>. 'multiplex' makes
possible, among other things, to create and manipulate multiplex, multimode, and
multilevel network data with different formats. Effective ways are available to treat
multiple networks with routines that combine algebraic systems like the partially ordered
semigroup with decomposition procedures or semiring structures with the relational
bundles occurring in different types of multivariate networks. 'multiplex' provides also
an algebraic approach for affiliation networks through Galois derivations between families
of the pairs of subsets in the two domains of the network with visualization options.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>
Diff between multiplex versions 3.1.1 dated 2023-11-16 and 3.3 dated 2024-06-19
DESCRIPTION | 8 - MD5 | 84 +++++----- R/as.semigroup.R | 82 ++++++---- R/diagram.R | 210 +++++---------------------- R/hasse.R |only R/jnt.R | 12 - R/transf.R | 74 +++++---- R/trnf.R | 17 +- R/zbind.R | 324 +++++++++++++++++++++++++----------------- inst/CHANGELOG | 11 + inst/CITATION | 2 inst/doc/TwoModeNetworks.R | 4 inst/doc/TwoModeNetworks.Rnw | 14 - inst/doc/TwoModeNetworks.pdf |binary man/bundles.Rd | 6 man/comps.Rd | 2 man/decomp.Rd | 22 +- man/diagram.Rd | 88 +++++++---- man/dichot.Rd | 2 man/edgel.Rd | 2 man/expos.Rd | 2 man/fact.Rd | 59 +++---- man/fltr.Rd | 2 man/galois.Rd | 8 - man/green.rel.Rd | 18 -- man/hasse.Rd |only man/hierar.Rd | 12 + man/incubs.Rd | 24 +-- man/mlvl.Rd | 20 +- man/mnplx.Rd | 6 man/multiplex-package.Rd | 59 +++++-- man/neighb.Rd | 13 - man/pacnet.Rd | 11 - man/partial.order.Rd | 15 + man/pfvn.Rd | 2 man/read.gml.Rd | 8 - man/reduc.Rd | 11 - man/rel.sys.Rd | 19 ++ man/semigroup.Rd | 28 ++- man/semiring.Rd | 37 ++-- man/transf.Rd | 28 +-- man/write.dl.Rd | 7 man/zbind.Rd | 19 +- vignettes/TwoModeNetworks.Rnw | 14 - 44 files changed, 724 insertions(+), 662 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-18 0.1.0
Title: Two-Way Tests in Independent Groups Designs
Description: Performs two-way tests in independent groups designs. These are two-way ANOVA, two-way ANOVA under heteroscedasticity: parametric bootstrap based generalized test and generalized pivotal quantity based generalized test (Ananda et al., 2022) <doi:10.1080/03610926.2022.2059682>, two-way ANOVA for medians, trimmed means, M-estimators (Wilcox, 2011; ISBN:978-0-12-386983-8). The package performs descriptive statistics and graphical approaches. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots. All 'twowaytests' functions are designed for two-way layout.
Author: Osman Dag [aut, cre], Sam Weerahandi [aut], Malwane Ananda [aut], Muhammed Ali Yilmaz [aut], Merve Kasikci [aut]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between twowaytests versions 1.3 dated 2023-03-31 and 1.4 dated 2024-06-19
DESCRIPTION | 10 ++++----- MD5 | 22 ++++++++++---------- NAMESPACE | 7 ++++-- R/MestTwoWay.R | 57 +++++++++++++++++++++++++++++++++++++++-------------- R/aovTwoWay.R | 4 +-- R/gpTwoWay.R | 2 - R/gplotTwoWay.R | 38 ++++++++++++++++++++++++++++------- R/medTwoWay.R | 8 +++---- R/paircompTwoWay.R | 40 ++++++++++++++++++++++++++----------- R/tmeanTwoWay.R | 8 +++---- man/MestTwoWay.Rd | 8 +++---- man/gplotTwoWay.Rd | 19 ++++++++++++----- 12 files changed, 151 insertions(+), 72 deletions(-)
Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-16 dated 2024-02-23 and 1.2-17 dated 2024-06-19
ChangeLog | 12 +++ DESCRIPTION | 8 +- MD5 | 48 ++++++------ NAMESPACE | 4 + R/bfgs.r | 17 +++- R/plot.r | 118 +++++++++++++++---------------- R/predict.scam.R | 112 ++++++++++++++--------------- R/scam.fit1.r | 18 ++-- R/scam.r | 108 +++++++++++++++++++++------- R/summary.scam.R | 41 ++++------ R/uni.smooth.const-lscop.r |only R/uni.smooth.const-with-po.r | 2 build/partial.rdb |binary man/Predict.matrix.mpi.smooth.Rd | 8 +- man/anova.scam.Rd | 12 +-- man/formula.scam.Rd | 4 - man/linear.functional.terms.Rd | 2 man/logLik.scam.Rd | 6 - man/predict.scam.Rd | 4 - man/residuals.scam.Rd | 4 - man/scam.Rd | 10 +- man/scam.check.Rd | 2 man/scam.control.Rd | 13 ++- man/shape.constrained.smooth.terms.Rd | 6 + man/smooth.construct.lmpi.smooth.spec.Rd |only man/vis.scam.Rd | 6 - 26 files changed, 330 insertions(+), 235 deletions(-)
Title: Perform Pharmacokinetic Non-Compartmental Analysis
Description: Compute standard Non-Compartmental Analysis (NCA) parameters for
typical pharmacokinetic analyses and summarize them.
Author: Bill Denney [aut, cre] ,
Clare Buckeridge [aut],
Sridhar Duvvuri [ctb]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between PKNCA versions 0.10.2 dated 2023-04-29 and 0.11.0 dated 2024-06-19
PKNCA-0.10.2/PKNCA/R/interp_extrap_helpers.R |only PKNCA-0.10.2/PKNCA/man/AIC.list.Rd |only PKNCA-0.10.2/PKNCA/man/check.conc.time.Rd |only PKNCA-0.10.2/PKNCA/man/choose_interp_extrap_method.Rd |only PKNCA-0.10.2/PKNCA/man/pk.calc.vd.Rd |only PKNCA-0.10.2/PKNCA/tests/testthat/test-interp_extrap_helpers.R |only PKNCA-0.10.2/PKNCA/vignettes/2015_ACoP_PKNCA_poster.pdf |only PKNCA-0.10.2/PKNCA/vignettes/PKNCA-ISoP_New_England-2016-03-31.pptx |only PKNCA-0.10.2/PKNCA/vignettes/PKNCA-ISoP_Study_Group-2016-05-25.pptx |only PKNCA-0.11.0/PKNCA/DESCRIPTION | 10 PKNCA-0.11.0/PKNCA/MD5 | 434 +++---- PKNCA-0.11.0/PKNCA/NAMESPACE | 19 PKNCA-0.11.0/PKNCA/NEWS.md | 108 + PKNCA-0.11.0/PKNCA/R/001-add.interval.col.R | 71 - PKNCA-0.11.0/PKNCA/R/002-pk.business.rules.R | 37 PKNCA-0.11.0/PKNCA/R/AIC.list.R | 30 PKNCA-0.11.0/PKNCA/R/PKNCA.R | 6 PKNCA-0.11.0/PKNCA/R/PKNCA.options.R | 120 + PKNCA-0.11.0/PKNCA/R/as_various.R |only PKNCA-0.11.0/PKNCA/R/assertions.R |only PKNCA-0.11.0/PKNCA/R/auc.R | 195 +-- PKNCA-0.11.0/PKNCA/R/auc_integrate.R |only PKNCA-0.11.0/PKNCA/R/aucint.R | 187 +-- PKNCA-0.11.0/PKNCA/R/auciv.R | 27 PKNCA-0.11.0/PKNCA/R/check.intervals.R | 21 PKNCA-0.11.0/PKNCA/R/choose.intervals.R | 38 PKNCA-0.11.0/PKNCA/R/class-PKNCAconc.R | 98 - PKNCA-0.11.0/PKNCA/R/class-PKNCAdata.R | 76 - PKNCA-0.11.0/PKNCA/R/class-PKNCAdose.R | 78 - PKNCA-0.11.0/PKNCA/R/class-PKNCAresults.R | 394 ------ PKNCA-0.11.0/PKNCA/R/class-general.R | 47 PKNCA-0.11.0/PKNCA/R/class-summary_PKNCAresults.R |only PKNCA-0.11.0/PKNCA/R/cleaners.R | 70 - PKNCA-0.11.0/PKNCA/R/defunct.R |only PKNCA-0.11.0/PKNCA/R/exclude.R | 49 PKNCA-0.11.0/PKNCA/R/exclude_nca.R | 16 PKNCA-0.11.0/PKNCA/R/general.functions.R | 99 - PKNCA-0.11.0/PKNCA/R/half.life.R | 49 PKNCA-0.11.0/PKNCA/R/impute.R | 51 PKNCA-0.11.0/PKNCA/R/interpolate.conc.R | 199 +-- PKNCA-0.11.0/PKNCA/R/parse_formula_to_cols.R | 14 PKNCA-0.11.0/PKNCA/R/pk.calc.all.R | 163 +- PKNCA-0.11.0/PKNCA/R/pk.calc.c0.R | 55 PKNCA-0.11.0/PKNCA/R/pk.calc.simple.R | 477 ++++--- PKNCA-0.11.0/PKNCA/R/pk.calc.urine.R | 33 PKNCA-0.11.0/PKNCA/R/prepare_data.R | 42 PKNCA-0.11.0/PKNCA/R/provenance.R | 22 PKNCA-0.11.0/PKNCA/R/sparse.R | 82 - PKNCA-0.11.0/PKNCA/R/superposition.R | 189 +-- PKNCA-0.11.0/PKNCA/R/time.above.R | 17 PKNCA-0.11.0/PKNCA/R/time_calc.R | 4 PKNCA-0.11.0/PKNCA/R/tss.R | 50 PKNCA-0.11.0/PKNCA/R/tss.monoexponential.R | 93 - PKNCA-0.11.0/PKNCA/R/tss.stepwise.linear.R | 37 PKNCA-0.11.0/PKNCA/R/unit-support.R | 123 +- PKNCA-0.11.0/PKNCA/R/zzz-pk.calc.dn.R | 2 PKNCA-0.11.0/PKNCA/build/vignette.rds |binary PKNCA-0.11.0/PKNCA/inst/WORDLIST | 13 PKNCA-0.11.0/PKNCA/inst/doc/v01-introduction-and-usage.R | 6 PKNCA-0.11.0/PKNCA/inst/doc/v01-introduction-and-usage.Rmd | 32 PKNCA-0.11.0/PKNCA/inst/doc/v01-introduction-and-usage.html | 466 ++++--- PKNCA-0.11.0/PKNCA/inst/doc/v02-example-theophylline.R | 2 PKNCA-0.11.0/PKNCA/inst/doc/v02-example-theophylline.Rmd | 2 PKNCA-0.11.0/PKNCA/inst/doc/v02-example-theophylline.html | 578 ++++++--- PKNCA-0.11.0/PKNCA/inst/doc/v03-selection-of-calculation-intervals.R | 10 PKNCA-0.11.0/PKNCA/inst/doc/v03-selection-of-calculation-intervals.Rmd | 10 PKNCA-0.11.0/PKNCA/inst/doc/v03-selection-of-calculation-intervals.html | 330 +++-- PKNCA-0.11.0/PKNCA/inst/doc/v04-sparse.html | 66 - PKNCA-0.11.0/PKNCA/inst/doc/v05-auc-calculation-with-PKNCA.html | 292 ++-- PKNCA-0.11.0/PKNCA/inst/doc/v06-half-life-calculation-tobit.R |only PKNCA-0.11.0/PKNCA/inst/doc/v06-half-life-calculation-tobit.Rmd |only PKNCA-0.11.0/PKNCA/inst/doc/v06-half-life-calculation-tobit.html |only PKNCA-0.11.0/PKNCA/inst/doc/v06-half-life-calculation.html | 110 - PKNCA-0.11.0/PKNCA/inst/doc/v07-post-processing.html | 190 +-- PKNCA-0.11.0/PKNCA/inst/doc/v07-unit-conversion.R | 2 PKNCA-0.11.0/PKNCA/inst/doc/v07-unit-conversion.html | 251 ++-- PKNCA-0.11.0/PKNCA/inst/doc/v08-data-imputation.Rmd | 7 PKNCA-0.11.0/PKNCA/inst/doc/v08-data-imputation.html | 150 +- PKNCA-0.11.0/PKNCA/inst/doc/v20-superposition.html | 78 - PKNCA-0.11.0/PKNCA/inst/doc/v22-time-to-steady-state.html | 131 +- PKNCA-0.11.0/PKNCA/inst/doc/v23-auc-integration-methods.R |only PKNCA-0.11.0/PKNCA/inst/doc/v23-auc-integration-methods.Rmd |only PKNCA-0.11.0/PKNCA/inst/doc/v23-auc-integration-methods.html |only PKNCA-0.11.0/PKNCA/inst/doc/v30-training-session.R | 50 PKNCA-0.11.0/PKNCA/inst/doc/v30-training-session.Rmd | 72 - PKNCA-0.11.0/PKNCA/inst/doc/v30-training-session.html | 336 ++--- PKNCA-0.11.0/PKNCA/inst/doc/v40-options-for-controlling-PKNCA.html | 60 PKNCA-0.11.0/PKNCA/inst/doc/v60-PKNCA-validation.html | 61 PKNCA-0.11.0/PKNCA/inst/doc/v80-writing-parameter-functions.Rmd | 8 PKNCA-0.11.0/PKNCA/inst/doc/v80-writing-parameter-functions.html | 8 PKNCA-0.11.0/PKNCA/man/PKNCA.Rd | 28 PKNCA-0.11.0/PKNCA/man/PKNCA.choose.option.Rd | 11 PKNCA-0.11.0/PKNCA/man/PKNCA.options.Rd | 40 PKNCA-0.11.0/PKNCA/man/PKNCA.options.describe.Rd | 2 PKNCA-0.11.0/PKNCA/man/PKNCA.set.summary.Rd | 33 PKNCA-0.11.0/PKNCA/man/PKNCA_impute_method.Rd | 25 PKNCA-0.11.0/PKNCA/man/PKNCAconc.Rd | 56 PKNCA-0.11.0/PKNCA/man/PKNCAdata.Rd | 60 PKNCA-0.11.0/PKNCA/man/PKNCAdose.Rd | 79 - PKNCA-0.11.0/PKNCA/man/PKNCAresults.Rd | 18 PKNCA-0.11.0/PKNCA/man/add.interval.col.Rd | 64 - PKNCA-0.11.0/PKNCA/man/addProvenance.Rd | 14 PKNCA-0.11.0/PKNCA/man/add_impute_to_intervals.Rd | 2 PKNCA-0.11.0/PKNCA/man/any_sparse_dense_in_interval.Rd | 2 PKNCA-0.11.0/PKNCA/man/as.data.frame.PKNCAresults.Rd | 31 PKNCA-0.11.0/PKNCA/man/as_PKNCAconc.Rd |only PKNCA-0.11.0/PKNCA/man/as_sparse_pk.Rd | 11 PKNCA-0.11.0/PKNCA/man/assert_PKNCAdata.Rd |only PKNCA-0.11.0/PKNCA/man/assert_aucmethod.Rd |only PKNCA-0.11.0/PKNCA/man/assert_conc_time.Rd |only PKNCA-0.11.0/PKNCA/man/assert_dosetau.Rd |only PKNCA-0.11.0/PKNCA/man/assert_intervaltime_single.Rd |only PKNCA-0.11.0/PKNCA/man/assert_lambdaz.Rd |only PKNCA-0.11.0/PKNCA/man/assert_number_between.Rd |only PKNCA-0.11.0/PKNCA/man/assert_numeric_between.Rd |only PKNCA-0.11.0/PKNCA/man/auc_integrate.Rd |only PKNCA-0.11.0/PKNCA/man/business.mean.Rd | 9 PKNCA-0.11.0/PKNCA/man/check.interval.deps.Rd | 14 PKNCA-0.11.0/PKNCA/man/check.interval.specification.Rd | 8 PKNCA-0.11.0/PKNCA/man/checkProvenance.Rd | 7 PKNCA-0.11.0/PKNCA/man/choose.auc.intervals.Rd | 35 PKNCA-0.11.0/PKNCA/man/choose_interval_method.Rd |only PKNCA-0.11.0/PKNCA/man/clean.conc.blq.Rd | 59 PKNCA-0.11.0/PKNCA/man/clean.conc.na.Rd | 21 PKNCA-0.11.0/PKNCA/man/cov_holder.Rd | 20 PKNCA-0.11.0/PKNCA/man/defunct.Rd |only PKNCA-0.11.0/PKNCA/man/exclude.Rd | 34 PKNCA-0.11.0/PKNCA/man/exclude_nca.Rd | 14 PKNCA-0.11.0/PKNCA/man/filter.PKNCAresults.Rd | 9 PKNCA-0.11.0/PKNCA/man/find.tau.Rd | 31 PKNCA-0.11.0/PKNCA/man/findOperator.Rd | 12 PKNCA-0.11.0/PKNCA/man/fit_half_life.Rd | 6 PKNCA-0.11.0/PKNCA/man/geomean.Rd | 4 PKNCA-0.11.0/PKNCA/man/get.best.model.Rd | 11 PKNCA-0.11.0/PKNCA/man/get.first.model.Rd | 5 PKNCA-0.11.0/PKNCA/man/get.interval.cols.Rd | 6 PKNCA-0.11.0/PKNCA/man/get.parameter.deps.Rd | 5 PKNCA-0.11.0/PKNCA/man/getAttributeColumn.Rd | 9 PKNCA-0.11.0/PKNCA/man/getColumnValueOrNot.Rd | 16 PKNCA-0.11.0/PKNCA/man/getDataName.Rd | 4 PKNCA-0.11.0/PKNCA/man/getGroups.PKNCAconc.Rd | 17 PKNCA-0.11.0/PKNCA/man/get_impute_method.Rd |only PKNCA-0.11.0/PKNCA/man/group_vars.PKNCAconc.Rd | 6 PKNCA-0.11.0/PKNCA/man/interp.extrap.conc.Rd | 130 +- PKNCA-0.11.0/PKNCA/man/interp_extrap_conc_method.Rd | 5 PKNCA-0.11.0/PKNCA/man/model.frame.PKNCAconc.Rd | 7 PKNCA-0.11.0/PKNCA/man/mutate.PKNCAresults.Rd | 2 PKNCA-0.11.0/PKNCA/man/normalize_exclude.Rd | 4 PKNCA-0.11.0/PKNCA/man/pk.business.Rd | 12 PKNCA-0.11.0/PKNCA/man/pk.calc.ae.Rd | 8 PKNCA-0.11.0/PKNCA/man/pk.calc.aucabove.Rd | 9 PKNCA-0.11.0/PKNCA/man/pk.calc.aucint.Rd | 65 - PKNCA-0.11.0/PKNCA/man/pk.calc.auciv.Rd | 32 PKNCA-0.11.0/PKNCA/man/pk.calc.aucpext.Rd | 11 PKNCA-0.11.0/PKNCA/man/pk.calc.auxc.Rd | 40 PKNCA-0.11.0/PKNCA/man/pk.calc.c0.Rd | 26 PKNCA-0.11.0/PKNCA/man/pk.calc.cav.Rd | 10 PKNCA-0.11.0/PKNCA/man/pk.calc.ceoi.Rd | 12 PKNCA-0.11.0/PKNCA/man/pk.calc.cl.Rd | 19 PKNCA-0.11.0/PKNCA/man/pk.calc.clast.obs.Rd | 17 PKNCA-0.11.0/PKNCA/man/pk.calc.clr.Rd | 9 PKNCA-0.11.0/PKNCA/man/pk.calc.cmax.Rd | 10 PKNCA-0.11.0/PKNCA/man/pk.calc.count_conc.Rd |only PKNCA-0.11.0/PKNCA/man/pk.calc.cstart.Rd | 10 PKNCA-0.11.0/PKNCA/man/pk.calc.ctrough.Rd | 10 PKNCA-0.11.0/PKNCA/man/pk.calc.f.Rd | 8 PKNCA-0.11.0/PKNCA/man/pk.calc.fe.Rd | 8 PKNCA-0.11.0/PKNCA/man/pk.calc.half.life.Rd | 60 PKNCA-0.11.0/PKNCA/man/pk.calc.mrt.Rd | 9 PKNCA-0.11.0/PKNCA/man/pk.calc.mrt.md.Rd | 23 PKNCA-0.11.0/PKNCA/man/pk.calc.sparse_auc.Rd | 25 PKNCA-0.11.0/PKNCA/man/pk.calc.swing.Rd | 4 PKNCA-0.11.0/PKNCA/man/pk.calc.time_above.Rd | 22 PKNCA-0.11.0/PKNCA/man/pk.calc.tlag.Rd | 4 PKNCA-0.11.0/PKNCA/man/pk.calc.tlast.Rd | 6 PKNCA-0.11.0/PKNCA/man/pk.calc.tmax.Rd | 26 PKNCA-0.11.0/PKNCA/man/pk.calc.totdose.Rd |only PKNCA-0.11.0/PKNCA/man/pk.calc.vz.Rd | 3 PKNCA-0.11.0/PKNCA/man/pk.nca.Rd | 21 PKNCA-0.11.0/PKNCA/man/pk.nca.interval.Rd | 73 - PKNCA-0.11.0/PKNCA/man/pk.nca.intervals.Rd | 7 PKNCA-0.11.0/PKNCA/man/pk.tss.Rd | 14 PKNCA-0.11.0/PKNCA/man/pk.tss.data.prep.Rd | 36 PKNCA-0.11.0/PKNCA/man/pk.tss.monoexponential.Rd | 43 PKNCA-0.11.0/PKNCA/man/pk.tss.monoexponential.individual.Rd | 18 PKNCA-0.11.0/PKNCA/man/pk.tss.monoexponential.population.Rd | 22 PKNCA-0.11.0/PKNCA/man/pk.tss.stepwise.linear.Rd | 38 PKNCA-0.11.0/PKNCA/man/pk_nca_result_to_df.Rd | 2 PKNCA-0.11.0/PKNCA/man/pknca_units_table.Rd | 42 PKNCA-0.11.0/PKNCA/man/print.PKNCAconc.Rd | 2 PKNCA-0.11.0/PKNCA/man/print.PKNCAdata.Rd | 3 PKNCA-0.11.0/PKNCA/man/print.summary_PKNCAresults.Rd | 7 PKNCA-0.11.0/PKNCA/man/roundString.Rd | 6 PKNCA-0.11.0/PKNCA/man/roundingSummarize.Rd | 4 PKNCA-0.11.0/PKNCA/man/setAttributeColumn.Rd | 6 PKNCA-0.11.0/PKNCA/man/setDuration.Rd | 4 PKNCA-0.11.0/PKNCA/man/setExcludeColumn.Rd | 6 PKNCA-0.11.0/PKNCA/man/setRoute.Rd | 9 PKNCA-0.11.0/PKNCA/man/signifString.Rd | 4 PKNCA-0.11.0/PKNCA/man/sparse_auc_weight_linear.Rd | 15 PKNCA-0.11.0/PKNCA/man/sparse_mean.Rd | 16 PKNCA-0.11.0/PKNCA/man/sparse_pk_attribute.Rd | 2 PKNCA-0.11.0/PKNCA/man/sparse_to_dense_pk.Rd | 2 PKNCA-0.11.0/PKNCA/man/summary.PKNCAdata.Rd | 2 PKNCA-0.11.0/PKNCA/man/summary.PKNCAresults.Rd | 78 - PKNCA-0.11.0/PKNCA/man/superposition.Rd | 85 - PKNCA-0.11.0/PKNCA/man/time_calc.Rd | 18 PKNCA-0.11.0/PKNCA/man/tss.monoexponential.generate.formula.Rd | 8 PKNCA-0.11.0/PKNCA/man/var_sparse_auc.Rd | 2 PKNCA-0.11.0/PKNCA/tests/testthat/test-PKNCA.options.R | 69 - PKNCA-0.11.0/PKNCA/tests/testthat/test-as_various.R |only PKNCA-0.11.0/PKNCA/tests/testthat/test-assertions.R |only PKNCA-0.11.0/PKNCA/tests/testthat/test-auc.R | 30 PKNCA-0.11.0/PKNCA/tests/testthat/test-auc_integrate.R |only PKNCA-0.11.0/PKNCA/tests/testthat/test-aucint.R | 612 ++++++---- PKNCA-0.11.0/PKNCA/tests/testthat/test-check.intervals.R | 324 ++--- PKNCA-0.11.0/PKNCA/tests/testthat/test-class-PKNCAresults.R | 373 ------ PKNCA-0.11.0/PKNCA/tests/testthat/test-class-summary_PKNCAresults.R |only PKNCA-0.11.0/PKNCA/tests/testthat/test-exclude.R | 3 PKNCA-0.11.0/PKNCA/tests/testthat/test-general.functions.R | 32 PKNCA-0.11.0/PKNCA/tests/testthat/test-impute.R | 66 - PKNCA-0.11.0/PKNCA/tests/testthat/test-interpolate.conc.R | 147 +- PKNCA-0.11.0/PKNCA/tests/testthat/test-pk.business.rules.R | 16 PKNCA-0.11.0/PKNCA/tests/testthat/test-pk.calc.all.R | 102 + PKNCA-0.11.0/PKNCA/tests/testthat/test-pk.calc.c0.R | 9 PKNCA-0.11.0/PKNCA/tests/testthat/test-pk.calc.simple.R | 81 - PKNCA-0.11.0/PKNCA/tests/testthat/test-sparse.R | 12 PKNCA-0.11.0/PKNCA/tests/testthat/test-superpostion.R | 327 ++--- PKNCA-0.11.0/PKNCA/tests/testthat/test-time.above.R | 4 PKNCA-0.11.0/PKNCA/tests/testthat/test-unit-support.R | 82 + PKNCA-0.11.0/PKNCA/vignettes/v01-introduction-and-usage.Rmd | 32 PKNCA-0.11.0/PKNCA/vignettes/v02-example-theophylline.Rmd | 2 PKNCA-0.11.0/PKNCA/vignettes/v03-selection-of-calculation-intervals.Rmd | 10 PKNCA-0.11.0/PKNCA/vignettes/v06-half-life-calculation-tobit.Rmd |only PKNCA-0.11.0/PKNCA/vignettes/v06-half-life-calculation-tobit_figure_1.svg |only PKNCA-0.11.0/PKNCA/vignettes/v08-data-imputation.Rmd | 7 PKNCA-0.11.0/PKNCA/vignettes/v23-auc-integration-methods.Rmd |only PKNCA-0.11.0/PKNCA/vignettes/v30-training-session.Rmd | 72 - PKNCA-0.11.0/PKNCA/vignettes/v80-writing-parameter-functions.Rmd | 8 239 files changed, 6149 insertions(+), 5603 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 0.8.1 dated 2024-04-08 and 0.9.2 dated 2024-06-19
DESCRIPTION | 8 - MD5 | 48 ++++---- NAMESPACE | 6 - R/R6Model.R | 190 ++++++++++++++++++++++----------- R/RcppExports.R | 8 + R/lme4_functions.R |only build/partial.rdb |binary inst/include/glmmr/calculator.hpp | 148 ++++++++++++------------- inst/include/glmmr/covariance.hpp | 49 ++------ inst/include/glmmr/formula.hpp | 47 +++----- inst/include/glmmr/formulaparse.h | 189 ++++++++++++++------------------ inst/include/glmmr/hsgpcovariance.hpp | 8 - inst/include/glmmr/interpreter.h | 4 inst/include/glmmr/linearpredictor.hpp | 26 +--- inst/include/glmmr/maths.h | 15 +- inst/include/glmmr/model.hpp | 94 +++++++--------- inst/include/glmmr/modelbits.hpp | 32 ----- inst/include/glmmr/modeloptim.hpp | 18 --- inst/include/glmmr/nngpcovariance.hpp | 4 inst/include/glmmr/optim/optim.h | 2 inst/include/glmmr/randomeffects.hpp | 12 -- man/Model.Rd | 85 ++++++-------- man/lme4_to_glmmr.Rd |only man/mcml_glmer.Rd |only man/mcml_lmer.Rd |only src/RcppExports.cpp | 22 +++ src/other_functions.cpp | 33 +++++ 27 files changed, 515 insertions(+), 533 deletions(-)
Title: Create Tibbles and Lists of 'ggplot' Figures for Reporting
Description: Create tibbles and lists of 'ggplot' figures that can be modified as easily as
regular 'ggplot' figures. Typical use cases are for creating reports or web
pages where many figures are needed with different data and similar
formatting.
Author: Bill Denney [aut, cre]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between ggtibble versions 1.0.0 dated 2024-02-07 and 1.0.1 dated 2024-06-19
DESCRIPTION | 6 +-- MD5 | 25 +++++++++------- NAMESPACE | 57 +++++++++++++++++++------------------ NEWS.md |only R/gglist.R | 18 +++++++---- R/ggtibble.R | 28 +++++++++++++++++- R/labs_glue.R | 4 ++ build/vignette.rds |binary inst/doc/v01-introduction.R | 2 - inst/doc/v01-introduction.html | 61 +++++++++++++++++++--------------------- man/new_gglist.Rd |only man/new_ggtibble.Rd |only tests/testthat/test-gglist.R | 5 +++ tests/testthat/test-ggtibble.R | 57 ++++++++++++++++++++++++++++++++++++- tests/testthat/test-labs_glue.R | 7 ++++ 15 files changed, 188 insertions(+), 82 deletions(-)
Title: Estimate Incubation or Latency Time using Doubly Interval
Censored Observations
Description: Visualize contact tracing data using a 'shiny' app and estimate the incubation or latency time of an infectious disease respecting the following characteristics in the analysis; (i) doubly interval censoring with (partly) overlapping or distinct windows; (ii) an infection risk corresponding to exponential growth; (iii) right truncation allowing for individual truncation times; (iv) different choices concerning the family of the distribution. For our earlier work, we refer to Arntzen et al. (2023) <doi:10.1002/sim.9726>. A paper describing our approach in detail will follow.
Author: Vera Arntzen [aut, cre]
Maintainer: Vera Arntzen <v.h.arntzen@math.leidenuniv.nl>
Diff between doublIn versions 0.1.0 dated 2024-04-25 and 0.2.0 dated 2024-06-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/fun_Visualize_contact_tracing_data.R | 2 +- tests/testthat/app/app.R | 15 --------------- 4 files changed, 7 insertions(+), 22 deletions(-)
Title: Calibration Performance
Description: Plots calibration curves and computes statistics for assessing calibration performance. See De Cock Campo (2023) <doi:10.48550/arXiv.2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.
Author: De Cock Bavo [aut, cre],
Nieboer Daan [aut],
Van Calster Ben [aut],
Steyerberg Ewout [aut],
Vergouwe Yvonne [aut]
Maintainer: De Cock Bavo <bavo.decock@kuleuven.be>
Diff between CalibrationCurves versions 2.0.1 dated 2024-03-01 and 2.0.2 dated 2024-06-19
DESCRIPTION | 12 +++---- MD5 | 28 +++++++++-------- NAMESPACE | 5 +++ R/helperFunctions.R |only R/val.prob.ci.2.R | 55 ++++++++++++++++++++-------------- R/valProbggplot.R | 40 ++++++++++++++++-------- README.md | 2 - build/vignette.rds |binary inst/CITATION | 7 ++-- inst/doc/CalibrationCurves.R | 18 +++++------ inst/doc/CalibrationCurves.html | 29 ++++------------- man/CalibrationCurves.Rd | 4 +- man/LibraryM.Rd |only man/grapes-less-than-equals-grapes.Rd |only man/grapes-open-curly-close-grapes.Rd |only man/val.prob.ci.2.Rd | 8 ++-- man/valProbggplot.Rd | 8 ++-- 17 files changed, 117 insertions(+), 99 deletions(-)
More information about CalibrationCurves at CRAN
Permanent link
Title: Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Sets
Description: Principled methods for the imputation of zeros, left-censored and missing data in
compositional data sets (Palarea-Albaladejo and Martin-Fernandez (2015) <doi:10.1016/j.chemolab.2015.02.019>).
Author: Javier Palarea-Albaladejo [cre, aut]
,
Josep Antoni Martin-Fernandez [aut]
Maintainer: Javier Palarea-Albaladejo <javier.palarea@udg.edu>
Diff between zCompositions versions 1.5.0-3 dated 2024-03-13 and 1.5.0-4 dated 2024-06-19
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 7 +++++++ R/lrDA.R | 2 ++ R/multKM.R | 2 ++ R/multLN.R | 2 ++ R/multRepl.R | 2 ++ man/lrEM.Rd | 4 ++-- man/lrEMplus.Rd | 2 +- man/zCompositions-package.Rd | 4 ++-- 10 files changed, 33 insertions(+), 18 deletions(-)
Title: Automatic Stacked Ensemble for Regression Tasks
Description: Stacked ensemble for regression tasks based on 'mlr3' framework with a pipeline for preprocessing numeric and factor features and hyper-parameter tuning using grid or random search.
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between sense versions 1.0.0 dated 2021-09-06 and 1.1.0 dated 2024-06-19
DESCRIPTION | 10 +++---- MD5 | 6 ++-- NEWS.md | 4 +++ R/main.R | 79 +++++++++++++++++++++--------------------------------------- 4 files changed, 40 insertions(+), 59 deletions(-)
Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>.
Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 1.2.1 dated 2024-04-11 and 1.3.0 dated 2024-06-19
DESCRIPTION | 9 ++-- MD5 | 38 ++++++++++-------- NAMESPACE | 2 NEWS.md | 5 ++ R/lda.R | 19 +++++---- R/seededlda.R | 12 +++-- R/seqlda.R | 2 R/utils.R | 61 +++++++++++++++++++++++++----- inst/CITATION |only inst/WORDLIST |only man/divergence.Rd | 29 ++++++++++---- man/perplexity.Rd |only man/sizes.Rd | 3 + man/terms.Rd | 7 ++- man/textmodel_lda.Rd | 15 ++++--- man/textmodel_seededlda.Rd | 5 +- man/textmodel_seqlda.Rd | 3 + man/topics.Rd | 3 + tests/spelling.R |only tests/testthat/test-textmodel_lda.R | 4 - tests/testthat/test-textmodel_seededlda.R | 4 - tests/testthat/test-utils.R | 47 +++++++++++++++++++++++ 22 files changed, 205 insertions(+), 63 deletions(-)
Title: Interface Between 'GRASS' Geographical Information System and
'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Author: Roger Bivand [cre, aut] ,
Rainer Krug [ctb] ,
Robin Lovelace [ctb] ,
Markus Neteler [ctb] ,
Sebastian Jeworutzki [ctb] ,
Floris Vanderhaeghe [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass versions 0.4-2 dated 2024-03-17 and 0.4-3 dated 2024-06-19
DESCRIPTION | 12 MD5 | 55 - NEWS.md | 15 R/AAA.R | 114 +-- R/gdal_grass.R |only R/initGRASS.R | 856 +++++++++++++++----------- R/options.R | 83 +- R/rast_link.R | 1199 +++++++++++++++++++------------------ R/read_helpers.R |only R/rgrass.R | 411 +++++++----- R/vect_link.R | 585 +++++++++--------- R/vect_link_ng.R | 177 +++-- R/xml1.R | 1059 ++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/coerce.R | 24 inst/doc/coerce.Rmd | 24 inst/doc/coerce.html | 22 inst/doc/use.R | 15 inst/doc/use.Rmd | 78 +- inst/doc/use.html | 84 +- man/initGRASS.Rd | 2 man/readRAST.Rd | 42 - man/readVECT.Rd | 42 + tests/test_XML_xml2.R | 4 tests/test_terra_ptr.R | 4 vignettes/OSGeo4W_QGIS_Rgui.png |only vignettes/OSGeo4W_QGIS_navbar.png |only vignettes/OSGeo4W_QGIS_rstudio.png |only vignettes/OSGeo4W_Rgui.png |only vignettes/OSGeo4W_rstudio.png |only vignettes/coerce.Rmd | 24 vignettes/use.Rmd | 78 +- 32 files changed, 2847 insertions(+), 2162 deletions(-)
Title: Flexible Bayes Factor Testing of Scientific Expectations
Description: Implementation of default Bayes factors
for testing statistical hypotheses under various statistical models. The package is
intended for applied quantitative researchers in the
social and behavioral sciences, medical research,
and related fields. The Bayes factor tests can be
executed for statistical models such as
univariate and multivariate normal linear models,
correlation analysis, generalized linear models, special cases of
linear mixed models, survival models, relational
event models. Parameters that can be tested are
location parameters (e.g., group means, regression coefficients),
variances (e.g., group variances), and measures of
association (e.g,. polychoric/polyserial/biserial/tetrachoric/product
moments correlations), among others.
The statistical underpinnings are
described in
Mulder and Xin (2019) <DOI:10.1080/00273171.2021.1904809>,
Mulder and Gelissen (2019) <DOI:10.1080/02664763.2021.1992360>,
Mulder (2016) <DOI:10.1016/j.jmp.2014.09.004>,
Mulder and [...truncated...]
Author: Joris Mulder [aut, cre],
Caspar van Lissa [aut, ctb],
Donald R. Williams [aut, ctb],
Xin Gu [aut, ctb],
Anton Olsson-Collentine [aut, ctb],
Florian Boeing-Messing [aut, ctb],
Jean-Paul Fox [aut, ctb],
Janosch Menke [ctb],
Robbie van Aert [ctb],
Barry [...truncated...]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between BFpack versions 1.2.3 dated 2023-10-20 and 1.3.0 dated 2024-06-19
BFpack-1.2.3/BFpack/R/BF_cortest.R |only BFpack-1.2.3/BFpack/R/BF_methods.R |only BFpack-1.2.3/BFpack/R/BFhetcor.R |only BFpack-1.2.3/BFpack/R/BFicc.R |only BFpack-1.2.3/BFpack/R/BFmeta.R |only BFpack-1.2.3/BFpack/R/BFttest.R |only BFpack-1.2.3/BFpack/R/BFvar.R |only BFpack-1.2.3/BFpack/src/bct_continuous_final.f90 |only BFpack-1.3.0/BFpack/DESCRIPTION | 8 BFpack-1.3.0/BFpack/MD5 | 112 - BFpack-1.3.0/BFpack/NAMESPACE | 6 BFpack-1.3.0/BFpack/NEWS.md | 16 BFpack-1.3.0/BFpack/R/BF.coeftest.R | 7 BFpack-1.3.0/BFpack/R/BF.cortest.R |only BFpack-1.3.0/BFpack/R/BF.coxph.R | 8 BFpack-1.3.0/BFpack/R/BF.ergm.R | 35 BFpack-1.3.0/BFpack/R/BF.gaussian.R | 124 + BFpack-1.3.0/BFpack/R/BF.glm.R | 49 BFpack-1.3.0/BFpack/R/BF.hetcor.R |only BFpack-1.3.0/BFpack/R/BF.icc.R |only BFpack-1.3.0/BFpack/R/BF.lm.R | 753 +++++----- BFpack-1.3.0/BFpack/R/BF.meta.R |only BFpack-1.3.0/BFpack/R/BF.methods.R |only BFpack-1.3.0/BFpack/R/BF.polr.R | 6 BFpack-1.3.0/BFpack/R/BF.print.R | 30 BFpack-1.3.0/BFpack/R/BF.summary.R | 28 BFpack-1.3.0/BFpack/R/BF.survreg.R | 6 BFpack-1.3.0/BFpack/R/BF.ttest.R |only BFpack-1.3.0/BFpack/R/BF.var.R |only BFpack-1.3.0/BFpack/R/BF.zeroinfl.R | 6 BFpack-1.3.0/BFpack/R/BFpack-package.R | 2 BFpack-1.3.0/BFpack/R/cor_test.print.R | 23 BFpack-1.3.0/BFpack/R/helper_functions.R | 226 +++ BFpack-1.3.0/BFpack/R/mvt_test.R |only BFpack-1.3.0/BFpack/README.md | 21 BFpack-1.3.0/BFpack/build/vignette.rds |binary BFpack-1.3.0/BFpack/inst/doc/vignette_BFpack.Rmd | 21 BFpack-1.3.0/BFpack/inst/doc/vignette_BFpack.html | 192 +- BFpack-1.3.0/BFpack/man/BF.Rd | 151 +- BFpack-1.3.0/BFpack/man/BFpack-package.Rd | 43 BFpack-1.3.0/BFpack/man/bartlett_test.Rd | 2 BFpack-1.3.0/BFpack/man/cor_test.Rd | 23 BFpack-1.3.0/BFpack/man/mvt_test.Rd |only BFpack-1.3.0/BFpack/src/BFpack_init.c | 8 BFpack-1.3.0/BFpack/src/Makevars |only BFpack-1.3.0/BFpack/src/bct_mixedordinal.f90 |only BFpack-1.3.0/BFpack/src/bct_prior.f90 | 321 +--- BFpack-1.3.0/BFpack/tests/testthat/test_BFcortest.R | 123 - BFpack-1.3.0/BFpack/tests/testthat/test_BFcoxph.R | 11 BFpack-1.3.0/BFpack/tests/testthat/test_BFergm.R | 16 BFpack-1.3.0/BFpack/tests/testthat/test_BFglm.R | 8 BFpack-1.3.0/BFpack/tests/testthat/test_BFmeta.R | 12 BFpack-1.3.0/BFpack/tests/testthat/test_BFmlm.R | 15 BFpack-1.3.0/BFpack/tests/testthat/test_BFregression.R | 24 BFpack-1.3.0/BFpack/tests/testthat/test_BFzeroinfl.R | 2 BFpack-1.3.0/BFpack/tests/testthat/test_anova_manova.R |only BFpack-1.3.0/BFpack/tests/testthat/test_application1_BF.bain_ttest.R | 10 BFpack-1.3.0/BFpack/tests/testthat/test_application2_BF.lm.R | 24 BFpack-1.3.0/BFpack/tests/testthat/test_application3_BF.BF_bartlett.R | 7 BFpack-1.3.0/BFpack/tests/testthat/test_application4_BF.mlm_regression.R | 66 BFpack-1.3.0/BFpack/tests/testthat/test_application5_BF.glm_BF_Gaussian.R | 13 BFpack-1.3.0/BFpack/tests/testthat/test_application6_BF.mlm_correlations.R | 34 BFpack-1.3.0/BFpack/tests/testthat/test_application7_BF.lmerMod.R | 16 BFpack-1.3.0/BFpack/tests/testthat/test_bartlett.R | 24 BFpack-1.3.0/BFpack/tests/testthat/test_ttest.R | 58 BFpack-1.3.0/BFpack/tests/testthat/test_variances.R | 25 BFpack-1.3.0/BFpack/vignettes/vignette_BFpack.Rmd | 21 67 files changed, 1803 insertions(+), 933 deletions(-)
Title: Multiple Treatment Effects Regression
Description: Implements contamination bias diagnostics and alternative
estimators for regressions with multiple treatments. The implementation is
based on Goldsmith-Pinkham, Hull, and Kolesár (2024)
<doi:10.48550/arXiv.2106.05024>.
Author: Michal Kolesar [aut, cre] ,
Paul Goldsmith-Pinkham [ctb],
Peter Hull [ctb]
Maintainer: Michal Kolesar <kolesarmi@googlemail.com>
Diff between multe versions 1.0.0 dated 2024-02-14 and 1.0.1 dated 2024-06-19
DESCRIPTION | 9 +++++---- LICENSE | 2 +- MD5 | 26 +++++++++++++------------- NEWS.md | 10 +++++++++- R/multe.R | 2 +- inst/WORDLIST | 4 ++-- inst/doc/multe.R | 1 + inst/doc/multe.Rmd | 1 + inst/doc/multe.pdf |binary man/multe.Rd | 2 +- tests/testthat/test-hessian.R | 2 +- vignettes/library.bib | 4 ++-- vignettes/multe.Rmd | 1 + vignettes/vignette_head.tex | 6 ++++-- 14 files changed, 42 insertions(+), 28 deletions(-)
Title: Forecast Linear Augmented Projection
Description: The Forecast Linear Augmented Projection (flap) method reduces
forecast variance by adjusting the forecasts of multivariate time series to
be consistent with the forecasts of linear combinations (components) of the
series by projecting all forecasts onto the space where the linear
constraints are satisfied. The forecast variance can be reduced
monotonically by including more components. For a given number of
components, the flap method achieves maximum forecast variance reduction
among linear projections.
Author: Yangzhuoran Fin Yang [aut, cre]
Maintainer: Yangzhuoran Fin Yang <yangyangzhuoran@gmail.com>
Diff between flap versions 0.1.0 dated 2024-02-28 and 0.2.0 dated 2024-06-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/projection.R | 27 +++++++++------------------ 4 files changed, 20 insertions(+), 24 deletions(-)
Title: Meteorological Data Processing
Description: Set of tools aimed at processing meteorological data, converting hourly recorded data to daily, monthly and annual data.
Author: Wagner Martins dos Santos [aut, cre]
,
Edimir Xavier Leal Ferraz [aut]
,
Lady Daiane Costa de Sousa Martins [aut]
Maintainer: Wagner Martins dos Santos <wagnnerms97@gmail.com>
Diff between DataMetProcess versions 1.0.1 dated 2024-01-18 and 1.0.2 dated 2024-06-19
DESCRIPTION | 11 MD5 | 67 ++ NAMESPACE | 1 R/DMPshiny.R |only R/adjustDate.R | 69 +-- R/calculateDMY.R | 54 +- R/calculateETrefPM.R | 212 ++++----- R/list_inmet.R | 64 +- build/vignette.rds |binary inst/DataMetProcess_Shiny |only inst/doc/DataMetProcess-vignette.R | 32 - inst/doc/DataMetProcess-vignette.Rmd | 32 - inst/doc/DataMetProcess-vignette.html | 228 +++++----- inst/extdata/2019_INMET_CO_DF_A001_BRASILIA_01-01-2019_A_31-12-2019.CSV |only inst/extdata/TesteETC.csv |only man/DMPshiny.Rd |only man/calculateDMY.Rd | 10 man/calculateETrefPM.Rd | 67 +- man/list_inmet.Rd | 4 vignettes/DataMetProcess-vignette.Rmd | 32 - 20 files changed, 476 insertions(+), 407 deletions(-)
More information about DataMetProcess at CRAN
Permanent link
Title: Bayesian Estimation of Structural Vector Autoregressive Models
Description: Provides fast and efficient procedures for Bayesian analysis of Structural Vector Autoregressions. This package estimates a wide range of models, including homo-, heteroskedastic, and non-normal specifications. Structural models can be identified by adjustable exclusion restrictions, time-varying volatility, or non-normality. They all include a flexible three-level equation-specific local-global hierarchical prior distribution for the estimated level of shrinkage for autoregressive and structural parameters. Additionally, the package facilitates predictive and structural analyses such as impulse responses, forecast error variance and historical decompositions, forecasting, verification of heteroskedasticity, non-normality, and hypotheses on autoregressive parameters, as well as analyses of structural shocks, volatilities, and fitted values. Beautiful plots, informative summary functions, and extensive documentation complement all this. The implemented techniques align closely with thos [...truncated...]
Author: Tomasz Wozniak [aut, cre]
Maintainer: Tomasz Wozniak <wozniak.tom@pm.me>
Diff between bsvars versions 2.1.0 dated 2023-12-11 and 3.0 dated 2024-06-19
DESCRIPTION | 18 MD5 | 216 +++--- NAMESPACE | 56 + NEWS.md | 24 R/RcppExports.R | 6 R/bsvars-package.R | 75 +- R/compute_conditional_sd.R | 265 +++++++ R/compute_fitted_values.R | 282 +++++++- R/compute_historical_decompositions.R | 349 +++++++++- R/compute_impulse_responses.R | 200 +++++ R/compute_regime_probabilities.R | 96 ++ R/compute_structural_shocks.R | 258 +++++++ R/compute_variance_decompositions.R | 236 ++++++ R/estimate.BSVAR.R | 36 - R/estimate.BSVARMIX.R | 54 - R/estimate.BSVARMSH.R | 58 - R/estimate.BSVARSV.R | 35 - R/estimate.R | 51 - R/forecast.R | 312 ++++++++- R/normalise_posterior.R | 4 R/plot.R |only R/specify_bsvar.R | 4 R/specify_bsvar_mix.R | 8 R/specify_bsvar_msh.R | 8 R/summary.R |only R/us_fiscal_ex.R | 11 R/us_fiscal_lsuw.R | 17 R/verify.R | 28 README.md | 135 ++- build/partial.rdb |binary data/us_fiscal_ex.rda |binary data/us_fiscal_lsuw.rda |binary inst/CITATION | 27 inst/include/bsvars_RcppExports.h | 229 +++++- inst/tinytest/test_compute_variance_decomposition.R | 28 inst/tinytest/test_forecast.R | 152 ++++ man/bsvars-package.Rd | 75 +- man/compute_conditional_sd.PosteriorBSVAR.Rd |only man/compute_conditional_sd.PosteriorBSVARMIX.Rd |only man/compute_conditional_sd.PosteriorBSVARMSH.Rd |only man/compute_conditional_sd.PosteriorBSVARSV.Rd |only man/compute_conditional_sd.Rd | 26 man/compute_fitted_values.PosteriorBSVAR.Rd |only man/compute_fitted_values.PosteriorBSVARMIX.Rd |only man/compute_fitted_values.PosteriorBSVARMSH.Rd |only man/compute_fitted_values.PosteriorBSVARSV.Rd |only man/compute_fitted_values.Rd | 25 man/compute_historical_decompositions.PosteriorBSVAR.Rd |only man/compute_historical_decompositions.PosteriorBSVARMIX.Rd |only man/compute_historical_decompositions.PosteriorBSVARMSH.Rd |only man/compute_historical_decompositions.PosteriorBSVARSV.Rd |only man/compute_historical_decompositions.Rd | 37 - man/compute_impulse_responses.PosteriorBSVAR.Rd |only man/compute_impulse_responses.PosteriorBSVARMIX.Rd |only man/compute_impulse_responses.PosteriorBSVARMSH.Rd |only man/compute_impulse_responses.PosteriorBSVARSV.Rd |only man/compute_impulse_responses.Rd | 14 man/compute_regime_probabilities.PosteriorBSVARMIX.Rd |only man/compute_regime_probabilities.PosteriorBSVARMSH.Rd |only man/compute_regime_probabilities.Rd | 8 man/compute_structural_shocks.PosteriorBSVAR.Rd |only man/compute_structural_shocks.PosteriorBSVARMIX.Rd |only man/compute_structural_shocks.PosteriorBSVARMSH.Rd |only man/compute_structural_shocks.PosteriorBSVARSV.Rd |only man/compute_structural_shocks.Rd | 16 man/compute_variance_decompositions.PosteriorBSVAR.Rd |only man/compute_variance_decompositions.PosteriorBSVARMIX.Rd |only man/compute_variance_decompositions.PosteriorBSVARMSH.Rd |only man/compute_variance_decompositions.PosteriorBSVARSV.Rd |only man/compute_variance_decompositions.Rd | 18 man/estimate.BSVAR.Rd | 23 man/estimate.BSVARMIX.Rd | 48 - man/estimate.BSVARMSH.Rd | 48 - man/estimate.BSVARSV.Rd | 29 man/estimate.PosteriorBSVAR.Rd | 24 man/estimate.PosteriorBSVARMIX.Rd | 44 - man/estimate.PosteriorBSVARMSH.Rd | 48 - man/estimate.PosteriorBSVARSV.Rd | 29 man/estimate.Rd | 47 - man/figures |only man/forecast.PosteriorBSVAR.Rd | 39 + man/forecast.PosteriorBSVARMIX.Rd | 42 + man/forecast.PosteriorBSVARMSH.Rd | 42 + man/forecast.PosteriorBSVARSV.Rd | 50 + man/forecast.Rd | 22 man/normalise_posterior.Rd | 2 man/plot.Forecasts.Rd |only man/plot.PosteriorFEVD.Rd |only man/plot.PosteriorFitted.Rd |only man/plot.PosteriorHD.Rd |only man/plot.PosteriorIR.Rd |only man/plot.PosteriorRegimePr.Rd |only man/plot.PosteriorShocks.Rd |only man/plot.PosteriorSigma.Rd |only man/plot_ribbon.Rd |only man/specify_bsvar_mix.Rd | 2 man/specify_bsvar_msh.Rd | 2 man/summary.Forecasts.Rd |only man/summary.PosteriorBSVAR.Rd |only man/summary.PosteriorBSVARMIX.Rd |only man/summary.PosteriorBSVARMSH.Rd |only man/summary.PosteriorBSVARSV.Rd |only man/summary.PosteriorFEVD.Rd |only man/summary.PosteriorFitted.Rd |only man/summary.PosteriorHD.Rd |only man/summary.PosteriorIR.Rd |only man/summary.PosteriorRegimePr.Rd |only man/summary.PosteriorShocks.Rd |only man/summary.PosteriorSigma.Rd |only man/summary.SDDRautoregression.Rd |only man/summary.SDDRvolatility.Rd |only man/us_fiscal_ex.Rd | 11 man/us_fiscal_lsuw.Rd | 17 man/verify_autoregression.PosteriorBSVAR.Rd | 4 man/verify_autoregression.PosteriorBSVARMIX.Rd | 4 man/verify_autoregression.PosteriorBSVARMSH.Rd | 4 man/verify_autoregression.PosteriorBSVARSV.Rd | 4 man/verify_autoregression.Rd | 4 man/verify_volatility.PosteriorBSVAR.Rd | 8 man/verify_volatility.PosteriorBSVARMIX.Rd | 6 man/verify_volatility.PosteriorBSVARMSH.Rd | 6 man/verify_volatility.PosteriorBSVARSV.Rd | 6 man/verify_volatility.Rd | 6 src/RcppExports.cpp | 440 ++++++++++--- src/bsvar.cpp | 6 src/bsvarTOOLs.cpp | 88 ++ src/bsvarTOOLs.h | 12 src/bsvar_msh.cpp | 14 src/bsvar_sv.cpp | 8 src/forecast.cpp | 297 +++++++- src/forecast.h | 71 +- src/msh.cpp | 19 src/msh.h | 10 src/sample_ABhyper.cpp | 22 src/sample_ABhyper.h | 10 135 files changed, 4076 insertions(+), 1039 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 0.2.1 dated 2024-05-16 and 0.2.2 dated 2024-06-19
DESCRIPTION | 6 MD5 | 38 NAMESPACE | 2 R/assert.R |only R/classCdmReference.R | 8 R/classConceptSetExpression.R | 6 R/classSummarisedResult.R | 1090 ++++++++++++++-------------- R/exportSummarisedResult.R | 2 R/methodBind.R | 26 R/methodSuppress.R | 359 ++++----- R/utilities.R | 702 ++++-------------- inst/doc/a02_concept_set.html | 15 inst/doc/reexport.Rmd | 164 ++-- inst/doc/reexport.html | 5 man/getPersonIdentifier.Rd |only man/uniqueId.Rd |only tests/testthat/test-assert.R |only tests/testthat/test-classSummarisedResult.R | 574 +++++++------- tests/testthat/test-methodBind.R | 75 + tests/testthat/test-methodSuppress.R | 24 tests/testthat/test-utilities.R | 178 ++-- vignettes/reexport.Rmd | 164 ++-- 22 files changed, 1649 insertions(+), 1789 deletions(-)
Title: Micro-Macro Analysis for Social Networks
Description: Estimates micro effects on macro structures (MEMS) and average micro mediated effects (AMME).
URL: <https://github.com/sduxbury/netmediate>.
BugReports: <https://github.com/sduxbury/netmediate/issues>.
Robins, Garry, Phillipa Pattison, and Jodie Woolcock (2005) <doi:10.1086/427322>.
Snijders, Tom A. B., and Christian E. G. Steglich (2015) <doi:10.1177/0049124113494573>.
Imai, Kosuke, Luke Keele, and Dustin Tingley (2010) <doi:10.1037/a0020761>.
Duxbury, Scott (2023) <doi:10.1177/00811750231209040>.
Duxbury, Scott (2024) <doi:10.1177/00811750231220950>.
Author: Scott Duxbury [aut, cre, cph]
Maintainer: Scott Duxbury <duxbury@email.unc.edu>
Diff between netmediate versions 0.1.4 dated 2024-02-21 and 1.0.1 dated 2024-06-19
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NAMESPACE | 1 + R/MEMS_pooled_saom.R | 20 ++++++++++++++------ R/MEMS_saom.R | 15 +++++++++++---- R/compare_MEMS.R |only man/compare_MEMS.Rd |only 7 files changed, 35 insertions(+), 17 deletions(-)
Title: Enrichment Analysis using Multiple Ontologies and FDR Correction
Description: 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. 'mulea' employs an innovative empirical
false discovery rate (eFDR) correction method, specifically designed for
interconnected biological data, to accurately identify significant terms
within diverse ontologies. Beyond conventional tools, 'mulea' incorporates a
wide range of ontologies encompassing Gene Ontology, pathways, regulatory
elements, genomic locations, and protein domains. This flexibility empowers
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' provides gene s [...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 1.0.0 dated 2024-05-25 and 1.0.1 dated 2024-06-19
mulea-1.0.0/mulea/man/figures/Regulon.png |only mulea-1.0.0/mulea/man/figures/geo_main.gif |only mulea-1.0.1/mulea/DESCRIPTION | 11 - mulea-1.0.1/mulea/MD5 | 22 +- mulea-1.0.1/mulea/NEWS.md | 6 mulea-1.0.1/mulea/R/Plotting.R | 12 - mulea-1.0.1/mulea/build/vignette.rds |binary mulea-1.0.1/mulea/inst/CITATION | 1 mulea-1.0.1/mulea/inst/doc/mulea.R | 11 - mulea-1.0.1/mulea/inst/doc/mulea.Rmd | 71 ++++--- mulea-1.0.1/mulea/inst/doc/mulea.html | 265 +++++++++++++++-------------- mulea-1.0.1/mulea/vignettes/Regulon.png |only mulea-1.0.1/mulea/vignettes/geo_main.gif |only mulea-1.0.1/mulea/vignettes/mulea.Rmd | 71 ++++--- 14 files changed, 255 insertions(+), 215 deletions(-)
Title: ADaM in R Asset Library - Ophthalmology
Description: Aids the programming of Clinical Data Standards Interchange
Consortium (CDISC) compliant Ophthalmology Analysis Data Model (ADaM)
datasets in R. ADaM datasets are a mandatory part of any New Drug or
Biologics License Application submitted to the United States Food and
Drug Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>).
Author: Edoardo Mancini [aut, cre],
Ritika Aggarwal [aut],
Jane Gao [aut],
William Holmes [aut],
Josie Jackson [aut],
Sonali Jain [aut],
Yuki Matsunaga [aut],
Gordon Miller [aut],
Rachel Linacre [aut],
Lucy Palmen [aut],
Nandini R Thampi [aut],
Aldrich Salva [...truncated...]
Maintainer: Edoardo Mancini <edoardo.mancini@roche.com>
Diff between admiralophtha versions 1.0.0 dated 2023-12-18 and 1.1.0 dated 2024-06-19
DESCRIPTION | 69 +++++++++++++++++---------------- MD5 | 62 ++++++++++++++--------------- NEWS.md | 15 +++++++ R/convert_etdrs_to_logmar.R | 2 R/convert_logmar_to_etdrs.R | 2 R/derive_var_afeye.R | 14 ++---- R/derive_var_bcvacritxfl.R | 2 R/derive_var_studyeye.R | 4 - README.md | 10 ++-- inst/WORDLIST | 3 - inst/doc/adbcva.R | 18 +++++--- inst/doc/adbcva.Rmd | 12 ++++- inst/doc/adbcva.html | 62 ++++++++++++++++------------- inst/doc/admiralophtha.Rmd | 2 inst/doc/admiralophtha.html | 3 - inst/doc/adoe.R | 4 - inst/doc/adoe.Rmd | 2 inst/doc/adoe.html | 2 inst/doc/advfq.R | 36 ++++++++++------- inst/doc/advfq.Rmd | 20 ++++++--- inst/doc/advfq.html | 67 +++++++++++++++++--------------- inst/templates/ad_adbcva.R | 28 ++++++++----- inst/templates/ad_adoe.R | 18 ++++---- inst/templates/ad_advfq.R | 47 ++++++++++++++++------ man/admiralophtha-package.Rd | 2 man/convert_etdrs_to_logmar.Rd | 2 man/convert_logmar_to_etdrs.Rd | 2 tests/testthat/test-derive_var_afeye.R | 20 +-------- vignettes/adbcva.Rmd | 12 ++++- vignettes/admiralophtha.Rmd | 2 vignettes/adoe.Rmd | 2 vignettes/advfq.Rmd | 20 ++++++--- 32 files changed, 323 insertions(+), 243 deletions(-)
Title: Power and Sample Size Calculation for Non-Proportional Hazards
and Beyond
Description: Performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The package can also be used for continuous, binary, and count data. For continuous data, it can handle missing data through mixed-model for repeated measures (MMRM). In crossover designs, it can estimate direct treatment effects while accounting for carryover effects. For binary data, it can design Simon's 2-stage, modified toxicity probability-2 (mTPI-2), a [...truncated...]
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between lrstat versions 0.2.7 dated 2024-06-13 and 0.2.8 dated 2024-06-19
DESCRIPTION | 11 ++++---- MD5 | 26 +++++++++--------- NEWS.md | 4 ++ src/basket.cpp | 4 -- src/kmstat.cpp | 74 +++++++++++++++++++++++++----------------------------- src/liferegr.cpp | 55 +++++++++++++++++++--------------------- src/lrsim.cpp | 62 +++++++++++++++++++++------------------------ src/lrstat.cpp | 45 +++++++++++++++----------------- src/misc.cpp | 6 ---- src/nbstat.cpp | 3 -- src/phregr.cpp | 57 ++++++++++++++++++++--------------------- src/rmstat.cpp | 74 +++++++++++++++++++++++++----------------------------- src/utilities.cpp | 4 -- src/utilities.h | 2 - 14 files changed, 201 insertions(+), 226 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb]
,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-35.3 dated 2024-04-16 and 1.1-35.4 dated 2024-06-19
DESCRIPTION | 9 - MD5 | 36 ++--- R/AllClass.R | 2 R/lmer.R | 1 R/plot.R | 7 - R/predict.R | 17 +- inst/NEWS.Rd | 19 ++ inst/doc/PLSvGLS.pdf |binary inst/doc/Theory.pdf |binary inst/doc/lmer.R | 189 ---------------------------- inst/doc/lmer.Rnw | 2 inst/doc/lmer.pdf |binary inst/tinytest |only src/Makevars | 1 src/predModule.cpp | 11 + src/predModule.h | 2 tests/testthat/test-methods.R | 4 tests/testthat/test-predict.R | 28 ++++ tests/testthat/test-summary_testlevel_1.rda |only vignettes/lmer.Rnw | 2 20 files changed, 100 insertions(+), 230 deletions(-)
Title: Prioritize and Delete Erroneous Taxa in a Large Phylogenetic
Tree
Description: Finds, prioritizes and deletes erroneous taxa in a phylogenetic tree. This package calculates scores for taxa in a tree. Higher score means the taxon is more erroneous. If the score is zero for a taxon, the taxon is not erroneous. This package also can remove all erroneous taxa automatically by iterating score calculation and pruning taxa with the highest score.
Author: Satoshi Aoki [aut, cph, cre]
Maintainer: Satoshi Aoki <aokis1ll1@gmail.com>
Diff between Apoderoides versions 2.0.0 dated 2024-06-14 and 2.0.1 dated 2024-06-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 3 +++ inst/doc/vignette.html | 4 ++-- src/source.cpp | 9 +++------ 5 files changed, 16 insertions(+), 16 deletions(-)