Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan'
package, which provides the R interface to the Stan C++ library for Bayesian
estimation. Users specify models via the customary R syntax with a formula and
data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut],
Imad Ali [ctb],
Sam Brilleman [ctb],
Jacqueline Buros Novik [ctb] ,
AstraZeneca [ctb] ,
Trustees of Columbia University [cph],
Simon Wood [cph] ,
R Core Deveopment Team [cph] ,
Douglas Bates [cph] ,
Martin Maechler [cph] ,
Ben Bolk [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstanarm versions 2.21.1 dated 2020-07-20 and 2.21.3 dated 2022-04-08
rstanarm-2.21.1/rstanarm/inst/include/csr_matrix_times_vector2.hpp |only rstanarm-2.21.1/rstanarm/tests/testthat/helpers |only rstanarm-2.21.1/rstanarm/tests/testthat/include/csr_matrix_times_vector2.hpp |only rstanarm-2.21.3/rstanarm/DESCRIPTION | 17 rstanarm-2.21.3/rstanarm/MD5 | 403 ++++------ rstanarm-2.21.3/rstanarm/NAMESPACE | 2 rstanarm-2.21.3/rstanarm/NEWS.md | 73 + rstanarm-2.21.3/rstanarm/R/as.matrix.stanreg.R | 3 rstanarm-2.21.3/rstanarm/R/bayes_R2.R | 8 rstanarm-2.21.3/rstanarm/R/data_block.R | 42 - rstanarm-2.21.3/rstanarm/R/doc-QR.R | 2 rstanarm-2.21.3/rstanarm/R/doc-algorithms.R | 2 rstanarm-2.21.3/rstanarm/R/doc-datasets.R | 11 rstanarm-2.21.3/rstanarm/R/doc-example_model.R | 2 rstanarm-2.21.3/rstanarm/R/doc-modeling-functions.R | 2 rstanarm-2.21.3/rstanarm/R/doc-rstanarm-package.R | 12 rstanarm-2.21.3/rstanarm/R/jm_data_block.R | 64 + rstanarm-2.21.3/rstanarm/R/jm_make_assoc_parts.R | 6 rstanarm-2.21.3/rstanarm/R/launch_shinystan.R | 3 rstanarm-2.21.3/rstanarm/R/log_lik.R | 42 - rstanarm-2.21.3/rstanarm/R/loo-kfold.R | 16 rstanarm-2.21.3/rstanarm/R/loo-prediction.R | 3 rstanarm-2.21.3/rstanarm/R/loo.R | 24 rstanarm-2.21.3/rstanarm/R/misc.R | 35 rstanarm-2.21.3/rstanarm/R/neg_binomial_2.R | 2 rstanarm-2.21.3/rstanarm/R/plots.R | 41 - rstanarm-2.21.3/rstanarm/R/posterior_interval.R | 3 rstanarm-2.21.3/rstanarm/R/posterior_linpred.R | 3 rstanarm-2.21.3/rstanarm/R/posterior_predict.R | 21 rstanarm-2.21.3/rstanarm/R/posterior_survfit.R | 11 rstanarm-2.21.3/rstanarm/R/posterior_traj.R | 22 rstanarm-2.21.3/rstanarm/R/posterior_vs_prior.R | 4 rstanarm-2.21.3/rstanarm/R/pp_check.R | 7 rstanarm-2.21.3/rstanarm/R/pp_data.R | 15 rstanarm-2.21.3/rstanarm/R/pp_validate.R | 3 rstanarm-2.21.3/rstanarm/R/predictive_error.R | 27 rstanarm-2.21.3/rstanarm/R/predictive_interval.R | 32 rstanarm-2.21.3/rstanarm/R/print-and-summary.R | 9 rstanarm-2.21.3/rstanarm/R/prior_summary.R | 3 rstanarm-2.21.3/rstanarm/R/priors.R | 13 rstanarm-2.21.3/rstanarm/R/ps_check.R | 2 rstanarm-2.21.3/rstanarm/R/stan_aov.R | 5 rstanarm-2.21.3/rstanarm/R/stan_betareg.R | 9 rstanarm-2.21.3/rstanarm/R/stan_betareg.fit.R | 7 rstanarm-2.21.3/rstanarm/R/stan_biglm.R | 21 rstanarm-2.21.3/rstanarm/R/stan_biglm.fit.R | 3 rstanarm-2.21.3/rstanarm/R/stan_clogit.R | 21 rstanarm-2.21.3/rstanarm/R/stan_gamm4.R | 11 rstanarm-2.21.3/rstanarm/R/stan_glm.R | 14 rstanarm-2.21.3/rstanarm/R/stan_glm.fit.R | 46 - rstanarm-2.21.3/rstanarm/R/stan_glmer.R | 14 rstanarm-2.21.3/rstanarm/R/stan_jm.R | 28 rstanarm-2.21.3/rstanarm/R/stan_jm.fit.R | 30 rstanarm-2.21.3/rstanarm/R/stan_lm.R | 7 rstanarm-2.21.3/rstanarm/R/stan_mvmer.R | 5 rstanarm-2.21.3/rstanarm/R/stan_nlmer.R | 6 rstanarm-2.21.3/rstanarm/R/stan_polr.R | 15 rstanarm-2.21.3/rstanarm/R/stanmvreg.R | 1 rstanarm-2.21.3/rstanarm/R/stanreg.R | 1 rstanarm-2.21.3/rstanarm/R/stanreg_list.R | 1 rstanarm-2.21.3/rstanarm/R/zzz.R | 2 rstanarm-2.21.3/rstanarm/build/partial.rdb |only rstanarm-2.21.3/rstanarm/build/vignette.rds |binary rstanarm-2.21.3/rstanarm/cleanup | 2 rstanarm-2.21.3/rstanarm/cleanup.win | 2 rstanarm-2.21.3/rstanarm/inst/CITATION | 2 rstanarm-2.21.3/rstanarm/inst/doc/ab-testing.R |only rstanarm-2.21.3/rstanarm/inst/doc/ab-testing.Rmd |only rstanarm-2.21.3/rstanarm/inst/doc/ab-testing.html |only rstanarm-2.21.3/rstanarm/inst/doc/aov.html | 88 +- rstanarm-2.21.3/rstanarm/inst/doc/betareg.html | 78 + rstanarm-2.21.3/rstanarm/inst/doc/binomial.html | 80 + rstanarm-2.21.3/rstanarm/inst/doc/continuous.html | 110 ++ rstanarm-2.21.3/rstanarm/inst/doc/count.html | 78 + rstanarm-2.21.3/rstanarm/inst/doc/glmer.Rmd | 7 rstanarm-2.21.3/rstanarm/inst/doc/glmer.html | 80 + rstanarm-2.21.3/rstanarm/inst/doc/jm.R | 2 rstanarm-2.21.3/rstanarm/inst/doc/jm.Rmd | 6 rstanarm-2.21.3/rstanarm/inst/doc/jm.html | 140 ++- rstanarm-2.21.3/rstanarm/inst/doc/lm.html | 80 + rstanarm-2.21.3/rstanarm/inst/doc/mrp.html | 224 +++-- rstanarm-2.21.3/rstanarm/inst/doc/polr.html | 76 + rstanarm-2.21.3/rstanarm/inst/doc/pooling.Rmd | 19 rstanarm-2.21.3/rstanarm/inst/doc/pooling.html | 108 ++ rstanarm-2.21.3/rstanarm/inst/doc/priors.R | 22 rstanarm-2.21.3/rstanarm/inst/doc/priors.Rmd | 32 rstanarm-2.21.3/rstanarm/inst/doc/priors.html | 186 +--- rstanarm-2.21.3/rstanarm/inst/doc/rstanarm.Rmd | 6 rstanarm-2.21.3/rstanarm/inst/doc/rstanarm.html | 94 ++ rstanarm-2.21.3/rstanarm/inst/include/CODOLS.hpp |only rstanarm-2.21.3/rstanarm/inst/include/meta_header.hpp | 2 rstanarm-2.21.3/rstanarm/inst/include/tests.cpp | 14 rstanarm-2.21.3/rstanarm/man/QR-argument.Rd | 2 rstanarm-2.21.3/rstanarm/man/as.matrix.stanreg.Rd | 3 rstanarm-2.21.3/rstanarm/man/available-algorithms.Rd | 2 rstanarm-2.21.3/rstanarm/man/available-models.Rd | 2 rstanarm-2.21.3/rstanarm/man/bayes_R2.stanreg.Rd | 8 rstanarm-2.21.3/rstanarm/man/example_model.Rd | 2 rstanarm-2.21.3/rstanarm/man/kfold.stanreg.Rd | 8 rstanarm-2.21.3/rstanarm/man/launch_shinystan.stanreg.Rd | 4 rstanarm-2.21.3/rstanarm/man/log_lik.stanreg.Rd | 3 rstanarm-2.21.3/rstanarm/man/loo.stanreg.Rd | 17 rstanarm-2.21.3/rstanarm/man/loo_predict.stanreg.Rd | 9 rstanarm-2.21.3/rstanarm/man/neg_binomial_2.Rd | 2 rstanarm-2.21.3/rstanarm/man/pairs.stanreg.Rd | 36 rstanarm-2.21.3/rstanarm/man/plot.predict.stanjm.Rd | 2 rstanarm-2.21.3/rstanarm/man/plot.stanreg.Rd | 4 rstanarm-2.21.3/rstanarm/man/plot.survfit.stanjm.Rd | 6 rstanarm-2.21.3/rstanarm/man/posterior_interval.stanreg.Rd | 3 rstanarm-2.21.3/rstanarm/man/posterior_linpred.stanreg.Rd | 3 rstanarm-2.21.3/rstanarm/man/posterior_predict.stanreg.Rd | 8 rstanarm-2.21.3/rstanarm/man/posterior_survfit.Rd | 3 rstanarm-2.21.3/rstanarm/man/posterior_traj.Rd | 5 rstanarm-2.21.3/rstanarm/man/posterior_vs_prior.Rd | 5 rstanarm-2.21.3/rstanarm/man/pp_check.stanreg.Rd | 3 rstanarm-2.21.3/rstanarm/man/pp_validate.Rd | 3 rstanarm-2.21.3/rstanarm/man/predictive_error.stanreg.Rd | 17 rstanarm-2.21.3/rstanarm/man/predictive_interval.stanreg.Rd | 22 rstanarm-2.21.3/rstanarm/man/prior_summary.stanreg.Rd | 3 rstanarm-2.21.3/rstanarm/man/priors.Rd | 13 rstanarm-2.21.3/rstanarm/man/ps_check.Rd | 2 rstanarm-2.21.3/rstanarm/man/rstanarm-datasets.Rd | 9 rstanarm-2.21.3/rstanarm/man/rstanarm-package.Rd | 18 rstanarm-2.21.3/rstanarm/man/stan_betareg.Rd | 20 rstanarm-2.21.3/rstanarm/man/stan_biglm.Rd | 14 rstanarm-2.21.3/rstanarm/man/stan_clogit.Rd | 21 rstanarm-2.21.3/rstanarm/man/stan_gamm4.Rd | 13 rstanarm-2.21.3/rstanarm/man/stan_glm.Rd | 28 rstanarm-2.21.3/rstanarm/man/stan_glmer.Rd | 13 rstanarm-2.21.3/rstanarm/man/stan_jm.Rd | 28 rstanarm-2.21.3/rstanarm/man/stan_lm.Rd | 19 rstanarm-2.21.3/rstanarm/man/stan_mvmer.Rd | 14 rstanarm-2.21.3/rstanarm/man/stan_nlmer.Rd | 19 rstanarm-2.21.3/rstanarm/man/stan_polr.Rd | 15 rstanarm-2.21.3/rstanarm/man/summary.stanreg.Rd | 3 rstanarm-2.21.3/rstanarm/src/Makevars.win | 15 rstanarm-2.21.3/rstanarm/src/init.cpp | 2 rstanarm-2.21.3/rstanarm/src/rstanarm-win.def |only rstanarm-2.21.3/rstanarm/src/stan_files/bernoulli.stan | 16 rstanarm-2.21.3/rstanarm/src/stan_files/continuous.stan | 27 rstanarm-2.21.3/rstanarm/src/stan_files/data/NKX.stan | 4 rstanarm-2.21.3/rstanarm/src/stan_files/data/data_assoc.stan | 18 rstanarm-2.21.3/rstanarm/src/stan_files/data/data_mvmer.stan | 6 rstanarm-2.21.3/rstanarm/src/stan_files/functions/common_functions.stan | 19 rstanarm-2.21.3/rstanarm/src/stan_files/functions/mvmer_functions.stan | 4 rstanarm-2.21.3/rstanarm/src/stan_files/gqs/gen_quantities_mvmer.stan | 9 rstanarm-2.21.3/rstanarm/src/stan_files/jm.stan | 4 rstanarm-2.21.3/rstanarm/src/stan_files/model/assoc_evaluate.stan | 45 - rstanarm-2.21.3/rstanarm/src/stan_files/model/eta_add_Zb.stan | 2 rstanarm-2.21.3/rstanarm/src/stan_files/model/make_eta.stan | 2 rstanarm-2.21.3/rstanarm/src/stan_files/model/make_eta_bern.stan | 31 rstanarm-2.21.3/rstanarm/src/stan_files/model/make_eta_tmp.stan | 6 rstanarm-2.21.3/rstanarm/src/stan_files/model/make_eta_tmp2.stan | 6 rstanarm-2.21.3/rstanarm/src/stan_files/model/mvmer_lp.stan | 6 rstanarm-2.21.3/rstanarm/src/stan_files/polr.stan | 13 rstanarm-2.21.3/rstanarm/tests/testthat.R | 10 rstanarm-2.21.3/rstanarm/tests/testthat/Rplots.pdf |only rstanarm-2.21.3/rstanarm/tests/testthat/helper.R |only rstanarm-2.21.3/rstanarm/tests/testthat/include/CODOLS.hpp |only rstanarm-2.21.3/rstanarm/tests/testthat/include/meta_header.hpp | 2 rstanarm-2.21.3/rstanarm/tests/testthat/include/tests.cpp | 14 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/bernoulli.stan | 16 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/continuous.stan | 27 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/data/NKX.stan | 4 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/data/data_assoc.stan | 18 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/data/data_mvmer.stan | 6 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/functions/common_functions.stan | 19 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/functions/mvmer_functions.stan | 4 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/gqs/gen_quantities_mvmer.stan | 9 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/jm.stan | 4 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/model/assoc_evaluate.stan | 45 - rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/model/eta_add_Zb.stan | 2 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/model/make_eta.stan | 2 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/model/make_eta_bern.stan | 31 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/model/make_eta_tmp.stan | 6 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/model/make_eta_tmp2.stan | 6 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/model/mvmer_lp.stan | 6 rstanarm-2.21.3/rstanarm/tests/testthat/stan_files/polr.stan | 13 rstanarm-2.21.3/rstanarm/tests/testthat/test_loo.R | 82 +- rstanarm-2.21.3/rstanarm/tests/testthat/test_methods.R | 81 +- 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rstanarm-2.21.3/rstanarm/tests/testthat/test_stan_polr.R | 27 rstanarm-2.21.3/rstanarm/tools/make_cc.R | 7 rstanarm-2.21.3/rstanarm/vignettes/ab-testing.Rmd |only rstanarm-2.21.3/rstanarm/vignettes/glmer.Rmd | 7 rstanarm-2.21.3/rstanarm/vignettes/jm.Rmd | 6 rstanarm-2.21.3/rstanarm/vignettes/pooling.Rmd | 19 rstanarm-2.21.3/rstanarm/vignettes/priors.Rmd | 32 rstanarm-2.21.3/rstanarm/vignettes/rstanarm.Rmd | 6 203 files changed, 3176 insertions(+), 1954 deletions(-)
Title: Model-Based Boosting
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Models and algorithms are described in <doi:10.1214/07-STS242>,
a hands-on tutorial is available from <doi:10.1007/s00180-012-0382-5>.
The package allows user-specified loss functions and base-learners.
Author: Torsten Hothorn [cre, aut] ,
Peter Buehlmann [aut] ,
Thomas Kneib [aut] ,
Matthias Schmid [aut] ,
Benjamin Hofner [aut] ,
Fabian Otto-Sobotka [ctb] ,
Fabian Scheipl [ctb] ,
Andreas Mayr [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mboost versions 2.9-5 dated 2021-04-13 and 2.9-6 dated 2022-04-08
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- R/varimp.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/SurvivalEnsembles.pdf |binary inst/doc/mboost.pdf |binary inst/doc/mboost_illustrations.pdf |binary inst/doc/mboost_tutorial.pdf |binary src/mboost.c | 2 +- 11 files changed, 26 insertions(+), 18 deletions(-)
Title: Field Observation Quick Analysis Toolkit
Description: Tools for quickly processing and analyzing
field observation data and air quality data. This
tools contain functions that facilitate analysis
in atmospheric chemistry (especially in ozone
pollution). Some functions of time series are also
applicable to other fields. For detail please view
homepage<https://github.com/tianshu129/foqat>.
Scientific Reference:
1. The Hydroxyl Radical (OH) Reactivity: Roger Atkinson and Janet Arey (2003) <doi:10.1021/cr0206420>.
2. Ozone Formation Potential (OFP): <https://ww2.arb.ca.gov/sites/default/files/classic/regact/2009/mir2009/mir10.pdf>, Zhang et al.(2021) <doi:10.5194/acp-21-11053-2021>.
3. Aerosol Formation Potential (AFP): Wenjing Wu et al. (2016) <doi:10.1016/j.jes.2016.03.025>.
4. TUV model: <https://www2.acom.ucar.edu/modeling/tropospheric-ultraviolet-and-visible-tuv-radiation-model>.
Author: Tianshu Chen
Maintainer: Tianshu Chen <tianshu129@163.com>
Diff between foqat versions 2.0.7 dated 2022-04-06 and 2.0.7.1 dated 2022-04-08
DESCRIPTION | 8 ++--- MD5 | 22 +++++++-------- inst/doc/Atmospheric_Radiation.R | 50 ++++++++++++++++++++---------------- inst/doc/Atmospheric_Radiation.Rmd | 8 +++++ inst/doc/Atmospheric_Radiation.html | 27 +++++-------------- inst/doc/Plot_Functions.Rmd | 6 ---- inst/doc/Plot_Functions.html | 4 -- inst/doc/Trace_Gas_Chemistry.R | 5 ++- inst/doc/Trace_Gas_Chemistry.Rmd | 3 +- vignettes/Atmospheric_Radiation.Rmd | 8 +++++ vignettes/Plot_Functions.Rmd | 6 ---- vignettes/Trace_Gas_Chemistry.Rmd | 3 +- 12 files changed, 74 insertions(+), 76 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factors (Parafac) model fit to a 3-way or 4-way data array/tensor. See Harshman (1994) <doi:10.1016/0167-9473(94)90132-5>. Uses Parafac factor weights from one mode of this model as predictors to tune parameters for one or more classification methods. Supports penalized logistic regression, support vector machine, random forest, and feed-forward neural network. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Parallel computing is implemented via the 'parallel' and 'doParallel' packages.
Author: Matthew A. Snodgress <snodg031@umn.edu>
Maintainer: Matthew A. Snodgress <snodg031@umn.edu>
Diff between cpfa versions 1.0-0 dated 2022-03-09 and 1.0-1 dated 2022-04-08
DESCRIPTION | 12 +++--- MD5 | 25 ++++++------- NAMESPACE | 6 ++- R/cpfa.R | 94 ++++++++++++++++++++++++++++++++++++++------------ R/cpm.R | 2 - R/kcv.nn.R |only R/kcv.rf.R | 2 - R/kcv.svm.R | 2 - R/predict.cpfa.R | 91 +++++++++++++++++++++++++++++++++++------------- R/print.cpfa.R | 45 +++++++++++++---------- man/cpfa-internals.Rd | 1 man/cpfa.Rd | 42 ++++++++++++++-------- man/cpm.Rd | 23 ++++++------ man/predict.cpfa.Rd | 15 ++++--- 14 files changed, 241 insertions(+), 119 deletions(-)
Title: Statistical Methods for the Analysis of Case-Control Point Data
Description: Statistical methods for analyzing case-control point data. Methods include the ratio of kernel densities, the difference in K Functions, the spatial scan statistic, and q nearest neighbors of cases.
Author: Joshua French [aut, cre]
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smacpod versions 2.4 dated 2022-01-26 and 2.4.1 dated 2022-04-08
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/logrr.R | 2 +- R/plot.logrrenv.R | 7 ++++--- build/vignette.rds |binary inst/doc/smacpod_demo.html | 21 +++++---------------- man/logrr.Rd | 2 +- man/plot.logrrenv.Rd | 2 +- 8 files changed, 22 insertions(+), 32 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of blocked and split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible. For details, see Morgan-Wall et al. (2021) <doi:10.18637/jss.v099.i01>.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 1.0.0 dated 2021-08-17 and 1.1.4 dated 2022-04-08
skpr-1.0.0/skpr/src/genOptimalDesignCoord.cpp |only skpr-1.1.4/skpr/DESCRIPTION | 12 skpr-1.1.4/skpr/MD5 | 37 - skpr-1.1.4/skpr/R/RcppExports.R | 4 skpr-1.1.4/skpr/R/effectpowermc.R | 4 skpr-1.1.4/skpr/R/eval_design.R | 7 skpr-1.1.4/skpr/R/eval_design_custom_mc.R | 112 ++++ skpr-1.1.4/skpr/R/eval_design_mc.R | 32 - skpr-1.1.4/skpr/R/eval_design_survival_mc.R | 1 skpr-1.1.4/skpr/R/gen_anticoef.R | 2 skpr-1.1.4/skpr/R/gen_design.R | 11 skpr-1.1.4/skpr/R/plot_fds.R | 2 skpr-1.1.4/skpr/R/skprGUIserver.R | 2 skpr-1.1.4/skpr/man/eval_design_custom_mc.Rd | 262 +++++------ skpr-1.1.4/skpr/man/eval_design_mc.Rd | 503 +++++++++++----------- skpr-1.1.4/skpr/src/RcppExports.cpp | 27 - skpr-1.1.4/skpr/src/exported_optimality.cpp | 2 skpr-1.1.4/skpr/src/genSplitPlotOptimalDesign.cpp | 84 +-- skpr-1.1.4/skpr/tests/testthat/Rplots.pdf |binary skpr-1.1.4/skpr/tests/testthat/testExampleCode.R | 18 20 files changed, 596 insertions(+), 526 deletions(-)
Title: Robust Land-Use Optimization
Description: Robust multi-criteria land-allocation optimization that explicitly accounts for the uncertainty of the indicators in the objective function. Solves the problem of allocating scarce land to various land-use options with regard to multiple, coequal indicators. The method aims to find the land allocation that represents the indicator composition with the best possible trade-off under uncertainty. optimLanduse includes the actual optimization procedure as described by Knoke et al. (2016) <doi:10.1038/ncomms11877> and the post-hoc calculation of the portfolio performance as presented by Gosling et al. (2020) <doi:10.1007/s10457-020-00519-0>.
Author: Kai Husmann [aut, cre] ,
Volker von Groß [aut] ,
Jasper Fuchs [aut] ,
Kai Boedeker [aut] ,
Goettingen University - Forest Economics and Sustainable Land-use
Planning [cph, fnd],
TUM School of Life Sciences - Forest Management [cph, fnd]
Maintainer: Kai Husmann <kai.husmann@uni-goettingen.de>
Diff between optimLanduse versions 0.0.4 dated 2021-02-24 and 1.0.0 dated 2022-04-08
optimLanduse-0.0.4/optimLanduse/CHANGELOG |only optimLanduse-0.0.4/optimLanduse/inst/extdata/exampleGosling_2020.xlsx |only optimLanduse-1.0.0/optimLanduse/DESCRIPTION | 36 ++- optimLanduse-1.0.0/optimLanduse/MD5 | 34 +-- optimLanduse-1.0.0/optimLanduse/NEWS.md | 1 optimLanduse-1.0.0/optimLanduse/R/calcPerformance.R | 6 optimLanduse-1.0.0/optimLanduse/R/dataPreparation.R | 14 - optimLanduse-1.0.0/optimLanduse/R/examples.R | 6 optimLanduse-1.0.0/optimLanduse/R/helper.R | 53 +++++ optimLanduse-1.0.0/optimLanduse/R/initScenario.R | 92 ++++------ optimLanduse-1.0.0/optimLanduse/R/solveScenario.R | 6 optimLanduse-1.0.0/optimLanduse/README.md | 90 +-------- optimLanduse-1.0.0/optimLanduse/build/partial.rdb |binary optimLanduse-1.0.0/optimLanduse/inst/extdata/exampleGosling.xlsx |only optimLanduse-1.0.0/optimLanduse/inst/extdata/exampleGosling_dataPrep.xlsx |only optimLanduse-1.0.0/optimLanduse/man/calcPerformance.Rd | 6 optimLanduse-1.0.0/optimLanduse/man/dataPreparation.Rd | 7 optimLanduse-1.0.0/optimLanduse/man/exampleData.Rd | 6 optimLanduse-1.0.0/optimLanduse/man/initScenario.Rd | 13 - optimLanduse-1.0.0/optimLanduse/man/solveScenario.Rd | 6 20 files changed, 179 insertions(+), 197 deletions(-)
Title: Morpheme Tokenization
Description: Tokenize text into morphemes. The morphemepiece algorithm uses a
lookup table to determine the morpheme breakdown of words, and falls back on a
modified wordpiece tokenization algorithm for words not found in the lookup
table.
Author: Jonathan Bratt [aut, cre] ,
Jon Harmon [aut] ,
Bedford Freeman & Worth Pub Grp LLC DBA Macmillan Learning [cph]
Maintainer: Jonathan Bratt <jonathan.bratt@macmillan.com>
Diff between morphemepiece versions 1.1.2 dated 2021-12-06 and 1.2.1 dated 2022-04-08
DESCRIPTION | 11 +-- MD5 | 41 ++++++----- NAMESPACE | 5 + NEWS.md | 4 + R/imports.R | 3 R/tokenize.R | 64 +++++++++++------- R/vocab.R | 111 ++++++++++++++++++++++---------- R/zzz.R |only inst/doc/algorithm_test.html | 1 inst/doc/generating_vocab.html | 1 man/dot-infer_case_from_vocab.Rd | 2 man/dot-mp_tokenize_single_string.Rd | 4 - man/dot-mp_tokenize_word.Rd | 4 - man/dot-mp_tokenize_word_bidir.Rd | 7 -- man/dot-mp_tokenize_word_lookup.Rd | 4 - man/dot-new_morphemepiece_vocabulary.Rd | 8 +- man/dot-process_mp_vocab.Rd |only man/load_or_retrieve_vocab.Rd | 10 +- man/load_vocab.Rd | 11 +-- man/morphemepiece_tokenize.Rd | 4 - man/prepare_vocab.Rd | 15 ++-- man/reexports.Rd | 5 + tests/testthat/test-vocab.R |only 23 files changed, 196 insertions(+), 119 deletions(-)
Title: Small Area Estimation using Hierarchical Bayesian Method
Description: Provides several functions for area level of small area estimation using hierarchical Bayesian (HB) method with several univariate distributions for variable of interest. The dataset that used in every function is generated accordingly in the Example. The 'rjags' package is employed to obtain parameter estimates. Model-based estimators involves the HB estimators which include the mean and the variation of mean. For the reference, see Rao and Molina (2015) <doi:10.1002/9781118735855>.
Author: Azka Ubaidillah [aut], Ika Yuni Wulansari [aut], Zaza Yuda Perwira [aut, cre]
Maintainer: Zaza Yuda Perwira <221710086@stis.ac.id>
Diff between saeHB versions 0.2.0 dated 2022-02-25 and 0.2.1 dated 2022-04-08
DESCRIPTION | 10 +++---- MD5 | 60 +++++++++++++++++++++++------------------------ R/Beta.R | 32 ++++++++++++------------- R/Binomial.R | 35 +++++++++++++-------------- R/Exponential.R | 28 ++++++++++----------- R/ExponentialDouble.R | 32 ++++++++++++------------- R/Gamma.R | 30 +++++++++++------------ R/Logistic.R | 30 +++++++++++------------ R/Lognormal.R | 30 +++++++++++------------ R/NegativeBinomial.R | 36 ++++++++++++++-------------- R/Normal.R | 32 ++++++++++++------------- R/Poisson.R | 30 +++++++++++------------ R/PoissonGamma.R | 34 +++++++++++++------------- R/Student_t.R | 30 +++++++++++------------ R/Student_tnc.R | 34 +++++++++++++------------- R/Weibull.R | 33 ++++++++++++------------- README.md | 15 ----------- man/Beta.Rd | 32 ++++++++++++------------- man/Binomial.Rd | 35 +++++++++++++-------------- man/Exponential.Rd | 28 ++++++++++----------- man/ExponentialDouble.Rd | 32 ++++++++++++------------- man/Gamma.Rd | 30 +++++++++++------------ man/Logistic.Rd | 30 +++++++++++------------ man/Lognormal.Rd | 30 +++++++++++------------ man/NegativeBinomial.Rd | 36 ++++++++++++++-------------- man/Normal.Rd | 32 ++++++++++++------------- man/Poisson.Rd | 30 +++++++++++------------ man/PoissonGamma.Rd | 34 +++++++++++++------------- man/Student_t.Rd | 30 +++++++++++------------ man/Student_tnc.Rd | 34 +++++++++++++------------- man/Weibull.Rd | 33 ++++++++++++------------- 31 files changed, 480 insertions(+), 497 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired by the end of 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] ,
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Daniel Baston [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.5-29 dated 2022-03-16 and 1.5-30 dated 2022-04-08
ChangeLog | 19 +++++++++++++++++ DESCRIPTION | 11 ++++------ MD5 | 28 +++++++++++++------------- NEWS.md | 8 ++++++- R/AAA.R | 20 +++++++++++++----- R/ogr_write.R | 2 - R/project.R | 5 ++-- configure | 18 ++++++++-------- inst/ChangeLog | 19 +++++++++++++++++ inst/SVN_VERSION | 2 - inst/doc/CRS_projections_transformations.html | 23 +++++++++++++-------- inst/doc/OGR_shape_encoding.pdf |binary inst/doc/PROJ6_GDAL3.html | 26 +++++++++++++----------- man/spTransform-methods.Rd | 2 - src/Makevars.win | 13 +++++------- 15 files changed, 130 insertions(+), 66 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative divide
in social science research. It uses a Boolean algorithm, resulting in a
minimal causal configuration that explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph] ,
Ciprian Paduraru [ctb] ,
jQuery Foundation [cph] ,
jQuery contributors [ctb, cph] ,
lp_solve [cph] ,
Vasil Dinkov [ctb, cph] ,
Dmitry Baranovskiy [ctb, cph] ,
Emmanuel Quentin [ctb, cph] ,
Jimmy Breck-McKye [ctb, cph] ,
[...truncated...]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 3.15 dated 2022-02-16 and 3.16 dated 2022-04-08
QCA-3.15/QCA/inst/staticdocs/QCA.package.html |only QCA-3.15/QCA/man/QCA-internal.Rd |only QCA-3.15/QCA/man/QCA.package.Rd |only QCA-3.16/QCA/DESCRIPTION | 8 QCA-3.16/QCA/MD5 | 120 ++++---- QCA-3.16/QCA/R/causalChain.R | 2 QCA-3.16/QCA/build/partial.rdb |binary QCA-3.16/QCA/inst/ChangeLog | 3 QCA-3.16/QCA/inst/TODO | 2 QCA-3.16/QCA/inst/gui/server.R | 4 QCA-3.16/QCA/inst/gui/www/js/maincode.js | 2 QCA-3.16/QCA/inst/staticdocs/CV.html | 4 QCA-3.16/QCA/inst/staticdocs/LegacyDatasets.html | 4 QCA-3.16/QCA/inst/staticdocs/Lipset.html | 4 QCA-3.16/QCA/inst/staticdocs/QCA_package.html |only QCA-3.16/QCA/inst/staticdocs/RS.html | 4 QCA-3.16/QCA/inst/staticdocs/SOPexpressions.html | 4 QCA-3.16/QCA/inst/staticdocs/XYplot.html | 4 QCA-3.16/QCA/inst/staticdocs/Xplot.html | 4 QCA-3.16/QCA/inst/staticdocs/calibrate.html | 4 QCA-3.16/QCA/inst/staticdocs/causalChain.html | 4 QCA-3.16/QCA/inst/staticdocs/chartFunctions.html | 4 QCA-3.16/QCA/inst/staticdocs/export.html | 4 QCA-3.16/QCA/inst/staticdocs/factorize.html | 4 QCA-3.16/QCA/inst/staticdocs/findRows.html | 4 QCA-3.16/QCA/inst/staticdocs/findTh.html | 4 QCA-3.16/QCA/inst/staticdocs/fuzzyops.html | 4 QCA-3.16/QCA/inst/staticdocs/generate.html | 4 QCA-3.16/QCA/inst/staticdocs/implicantMatrixFunctions.html | 4 QCA-3.16/QCA/inst/staticdocs/index.html | 56 ++- QCA-3.16/QCA/inst/staticdocs/intersection.html | 4 QCA-3.16/QCA/inst/staticdocs/minimize.html | 4 QCA-3.16/QCA/inst/staticdocs/modelFit.html | 4 QCA-3.16/QCA/inst/staticdocs/negate.html | 4 QCA-3.16/QCA/inst/staticdocs/pof.html | 4 QCA-3.16/QCA/inst/staticdocs/retention.html | 4 QCA-3.16/QCA/inst/staticdocs/runGUI.html | 4 QCA-3.16/QCA/inst/staticdocs/subsetsAndSupersets.html | 4 QCA-3.16/QCA/inst/staticdocs/truthTable.html | 4 QCA-3.16/QCA/man/QCA_internal.Rd |only QCA-3.16/QCA/man/QCA_package.Rd |only QCA-3.16/QCA/src/CCubes.c | 154 ++++++---- QCA-3.16/QCA/src/CCubes.h | 19 - QCA-3.16/QCA/src/QCA.c | 72 ++-- QCA-3.16/QCA/src/consistency.c | 22 - QCA-3.16/QCA/src/consistent_solution.c | 20 - QCA-3.16/QCA/src/consistent_solution.h | 6 QCA-3.16/QCA/src/find_consistent_models.c | 41 +- QCA-3.16/QCA/src/find_consistent_models.h | 6 QCA-3.16/QCA/src/find_min.c | 45 +-- QCA-3.16/QCA/src/find_min.h | 8 QCA-3.16/QCA/src/find_models.c | 114 +++---- QCA-3.16/QCA/src/find_models.h | 20 - QCA-3.16/QCA/src/row_dominance.c | 33 +- QCA-3.16/QCA/src/row_dominance.h | 2 QCA-3.16/QCA/src/sort_cols.c | 30 +- QCA-3.16/QCA/src/sort_cols.h | 2 QCA-3.16/QCA/src/sort_matrix.c | 31 +- QCA-3.16/QCA/src/sort_matrix.h | 2 QCA-3.16/QCA/src/super_rows.c | 26 + QCA-3.16/QCA/src/super_rows.h | 2 QCA-3.16/QCA/src/truthTable.c | 6 QCA-3.16/QCA/src/utils.c | 193 ++++++++++--- QCA-3.16/QCA/src/utils.h | 30 +- 64 files changed, 678 insertions(+), 507 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.5.1 dated 2022-03-01 and 0.5.2 dated 2022-04-08
DESCRIPTION | 9 MD5 | 302 ++--- NAMESPACE | 2 NEWS.md | 16 R/calc_network.R | 186 +-- R/discover_nhdplus.R | 11 R/downloading_tools.R | 35 R/geoserver_tools.R | 19 R/get_codes.R | 700 ++++++------- R/get_geometry.R | 254 ++-- R/get_hydro.R | 6 R/get_network.R | 16 R/get_nhdplus.R | 6 R/get_nhdplushr.R | 650 ++++++------ R/get_nldi.R | 572 ++++++----- R/get_oaproc.R | 26 R/get_path_lengths.R | 428 ++++---- R/get_paths.R | 1132 +++++++++++----------- R/get_vaa.R | 392 +++---- R/index_nhdplus.R | 121 +- R/map_nhdplus.R |only R/nhdplusTools.R | 918 ++++++++--------- R/plot_nhdplus.R | 106 +- R/prep_nhdplus.R | 550 +++++----- R/run_plus_attributes.R | 402 +++---- R/subset_nhdplus.R | 61 - README.md | 8 inst/CITATION | 9 inst/doc/US_data.Rmd | 710 ++++++------- inst/doc/US_data.html | 66 - inst/doc/advanced_network.Rmd | 570 +++++------ inst/doc/advanced_network.html | 8 inst/doc/indexing.R | 14 inst/doc/indexing.Rmd | 22 inst/doc/indexing.html | 32 inst/doc/nhdplusTools.Rmd | 158 +-- inst/doc/nhdplusTools.html | 2 inst/doc/nhdplushr.Rmd | 416 ++++---- inst/doc/nhdplushr.html | 12 inst/doc/plot_nhdplus.R | 3 inst/doc/plot_nhdplus.Rmd | 3 inst/doc/plot_nhdplus.html | 18 inst/extdata/get_hr_data.R | 158 +-- inst/extdata/hex.R | 20 inst/extdata/new_hope_data.R | 60 - inst/extdata/nhdplushr_data.R | 68 - inst/extdata/sample_data.R | 18 inst/extdata/sample_flines.R | 18 inst/extdata/utils.R | 88 - inst/extdata/walker_data.R | 42 man/add_plus_network_attributes.Rd | 112 +- man/align_nhdplus_names.Rd | 58 - man/calculate_arbolate_sum.Rd | 72 - man/calculate_total_drainage_area.Rd | 70 - man/disambiguate_flowline_indexes.Rd | 142 +- man/discover_nhdplus_id.Rd | 76 - man/discover_nldi_characteristics.Rd | 44 man/download_nhdplushr.Rd | 66 - man/download_nhdplusv2.Rd | 84 - man/download_rf1.Rd | 62 - man/download_vaa.Rd | 74 - man/download_wbd.Rd | 68 - man/fix_flowdir.Rd | 102 - man/get_DD.Rd | 84 - man/get_DM.Rd | 90 - man/get_UM.Rd | 88 - man/get_UT.Rd | 76 - man/get_elev_along_path.Rd | 104 +- man/get_flowline_index.Rd | 176 +-- man/get_gagesII.Rd | 82 - man/get_hr_data.Rd | 72 - man/get_huc12.Rd | 76 - man/get_huc8.Rd | 76 - man/get_hydro_location.Rd | 62 - man/get_levelpaths.Rd | 114 +- man/get_nhdarea.Rd | 76 - man/get_nhdplus.Rd | 138 +- man/get_nhdplushr.Rd | 166 +-- man/get_nldi_basin.Rd | 101 + man/get_nldi_characteristics.Rd | 58 - man/get_nldi_feature.Rd | 50 man/get_nldi_index.Rd |only man/get_node.Rd | 76 - man/get_nwis.Rd | 76 - man/get_partial_length.Rd | 108 +- man/get_path_lengths.Rd | 100 - man/get_pathlength.Rd | 54 - man/get_pfaf.Rd | 164 +-- man/get_raindrop_trace.Rd | 80 - man/get_sorted.Rd | 96 - man/get_split_catchment.Rd | 132 +- man/get_streamlevel.Rd | 96 - man/get_streamorder.Rd | 76 - man/get_terminal.Rd | 62 - man/get_tocomid.Rd | 108 +- man/get_vaa.Rd | 114 +- man/get_vaa_names.Rd | 76 - man/get_vaa_path.Rd | 74 - man/get_waterbodies.Rd | 76 - man/get_waterbody_index.Rd | 83 - man/get_wb_outlet.Rd | 68 - man/get_xs_point.Rd | 86 - man/get_xs_points.Rd | 92 - man/make_standalone.Rd | 122 +- man/map_nhdplus.Rd |only man/navigate_network.Rd | 142 +- man/navigate_nldi.Rd | 124 +- man/nhdplusTools_data_dir.Rd | 52 - man/nhdplus_path.Rd | 58 - man/plot_nhdplus.Rd | 313 +++--- man/prepare_nhdplus.Rd | 122 +- man/query_usgs_geoserver.Rd | 106 +- man/rename_geometry.Rd | 46 man/rescale_measures.Rd | 70 - man/st_compatibalize.Rd | 62 - man/stage_national_data.Rd | 102 - man/subset_nhdplus.Rd | 306 ++--- man/subset_rpu.Rd | 76 - man/subset_vpu.Rd | 76 - tests/testthat.R | 6 tests/testthat/data/coastal_net.csv | 1098 ++++++++++----------- tests/testthat/data/prep_test_data.R | 94 - tests/testthat/helper.R | 54 - tests/testthat/test_00_plot_bbox_nhdplus.R | 48 tests/testthat/test_00_plot_integration_nhdplus.R | 6 tests/testthat/test_00_plot_local_extra_nhdplus.R | 84 - tests/testthat/test_00_plot_local_nhdplus.R | 2 tests/testthat/test_00_plot_nhdplus.R | 9 tests/testthat/test_01_get_nldi.R | 18 tests/testthat/test_02_subset.R | 390 +++---- tests/testthat/test_02_subset_extras.R | 11 tests/testthat/test_03_get_functions.R | 10 tests/testthat/test_align_nhdplus_names.R | 18 tests/testthat/test_calc_network.R | 182 +-- tests/testthat/test_get_codes.R | 246 ++-- tests/testthat/test_get_geometry.R | 124 +- tests/testthat/test_get_network.R | 522 +++++----- tests/testthat/test_get_nhdplus.R | 148 +- tests/testthat/test_get_nhdplushr.R | 314 +++--- tests/testthat/test_get_path.R | 278 ++--- tests/testthat/test_get_path_lengths.R | 160 +-- tests/testthat/test_get_vaa.R | 66 - tests/testthat/test_index.R | 88 - tests/testthat/test_map_nhdplus.R |only tests/testthat/test_navigate.R | 2 tests/testthat/test_nhdplusTools.R | 400 +++---- tests/testthat/test_run_plus_attributes.R | 126 +- tests/testthat/test_wb_index.R | 6 vignettes/US_data.Rmd | 710 ++++++------- vignettes/advanced_network.Rmd | 570 +++++------ vignettes/indexing.Rmd | 22 vignettes/nhdplusTools.Rmd | 158 +-- vignettes/nhdplushr.Rmd | 416 ++++---- vignettes/plot_nhdplus.Rmd | 3 154 files changed, 11303 insertions(+), 10922 deletions(-)
Title: Clinical Trial Registry History
Description: Retrieves historical versions of clinical trial registry
entries.
Author: Benjamin Gregory Carlisle [aut, cre]
Maintainer: Benjamin Gregory Carlisle <murph@bgcarlisle.com>
Diff between cthist versions 0.1.4 dated 2022-03-14 and 1.0.0 dated 2022-04-08
DESCRIPTION | 10 MD5 | 68 ++- NEWS.md | 23 + R/clinicaltrials_gov_dates.R | 36 + R/clinicaltrials_gov_download.R | 209 +++++++-- R/clinicaltrials_gov_version.R | 88 +++- R/cthist-package.R |only R/drks_de_dates.R | 36 + R/drks_de_download.R | 210 ++++++---- R/drks_de_version.R | 103 +++- R/polite-scrape.R |only README.md | 37 + man/clinicaltrials_gov_dates.Rd | 6 man/clinicaltrials_gov_download.Rd | 42 +- man/clinicaltrials_gov_version.Rd | 16 man/cthist-package.Rd |only man/drks_de_dates.Rd | 6 man/drks_de_download.Rd | 38 + man/drks_de_version.Rd | 8 tests/testthat/test-clinicaltrials_gov_download.R | 2 tests/testthat/test-clinicaltrials_gov_version.R | 2 tests/testthat/test-clinicaltrials_gov_version_contacts.R |only tests/testthat/test-clinicaltrials_gov_version_criteria.R |only tests/testthat/test-clinicaltrials_gov_version_enrol.R |only tests/testthat/test-clinicaltrials_gov_version_gender.R |only tests/testthat/test-clinicaltrials_gov_version_max_age.R |only tests/testthat/test-clinicaltrials_gov_version_min_age.R |only tests/testthat/test-clinicaltrials_gov_version_om_data.R |only tests/testthat/test-clinicaltrials_gov_version_ostatus.R |only tests/testthat/test-clinicaltrials_gov_version_pcdate.R |only tests/testthat/test-clinicaltrials_gov_version_pcdate_precision.R |only tests/testthat/test-clinicaltrials_gov_version_pcdatetype.R |only tests/testthat/test-clinicaltrials_gov_version_sex.R |only tests/testthat/test-clinicaltrials_gov_version_sponsor_data.R |only tests/testthat/test-clinicaltrials_gov_version_startdate.R |only tests/testthat/test-clinicaltrials_gov_version_startdate_precision.R |only tests/testthat/test-clinicaltrials_gov_version_volunteers.R |only tests/testthat/test-drks_de_download.R | 2 tests/testthat/test-drks_de_version_closingdate.R |only tests/testthat/test-drks_de_version_contacts.R |only tests/testthat/test-drks_de_version_enrolno.R |only tests/testthat/test-drks_de_version_enroltype.R |only tests/testthat/test-drks_de_version_exclusion_criteria.R |only tests/testthat/test-drks_de_version_gender.R |only tests/testthat/test-drks_de_version_inclusion_criteria.R |only tests/testthat/test-drks_de_version_max_age.R |only tests/testthat/test-drks_de_version_min_age.R |only tests/testthat/test-drks_de_version_primaryoutcomes.R |only tests/testthat/test-drks_de_version_rstatus.R |only tests/testthat/test-drks_de_version_secondaryoutcomes.R |only tests/testthat/test-drks_de_version_startdate.R |only 51 files changed, 668 insertions(+), 274 deletions(-)
Title: Parse xlsx Files
Description: Uses C++ via the 'Rcpp' package to parse modern Excel files ('.xlsx').
Memory usage is kept minimal by decompressing only parts of the file at a time,
while employing multiple threads to achieve significant runtime reduction.
Uses <https://github.com/richgel999/miniz>, <https://github.com/ebiggers/libdeflate>,
and <https://github.com/lemire/fast_double_parser>.
Author: Felix Henze [aut, cre],
Rich Geldreich [ctb, cph] ,
Eric Biggers [ctb, cph] ,
Daniel Lemire [ctb, cph]
Maintainer: Felix Henze <felixhenze0@gmail.com>
Diff between SheetReader versions 1.0.1 dated 2022-03-28 and 1.0.2 dated 2022-04-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Makevars | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Models for Simulating Lion Populations
Description: Simulate the dynamic of lion populations using a specific Individual-Based Model (IBM) compiled in C.
Author: Guillaume Chapron [aut, cre],
Matthew Wijers [ctb],
Andrew Loveridge [ctb],
David Macdonald [ctb]
Maintainer: Guillaume Chapron <gchapron@carnivoreconservation.org>
Diff between pop.lion versions 1.0 dated 2022-04-01 and 1.0.1 dated 2022-04-08
DESCRIPTION | 10 - MD5 | 18 +-- NAMESPACE | 3 src/main.c | 19 +++ src/mc.c | 15 +- src/mc.h | 2 src/pop.c | 332 ++++++++++++++++++++++++++++++++++++------------------------ src/pop.h | 2 src/tools.h | 10 - tests |only 10 files changed, 248 insertions(+), 163 deletions(-)
Title: Multiple Change Point
Description: Nonparametric approach to estimate the location of block boundaries (change-points) of
non-overlapping blocks in a random symmetric matrix which consists of random variables whose
distribution changes from block to block.
BRAULT Vincent, OUADAH Sarah, SANSONNET Laure and LEVY-LEDUC Celine (2017) <doi:10.1016/j.jmva.2017.12.005>.
Author: Brault Vincent [cre, aut],
Cougoulat Glenn [ctb],
Ouadah Sarah [ctb],
Sansonnet Laure [ctb]
Maintainer: Brault Vincent <vincent.brault@univ-grenoble-alpes.fr>
Diff between MuChPoint versions 0.6.1 dated 2018-06-24 and 0.6.3 dated 2022-04-08
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++-------- R/MuChPoint.R | 6 +++--- R/MuChPoint_Class.R | 6 +++--- man/MuChPoint-proc.Rd | 2 +- man/plot-MuChPoint.Rd | 6 ++---- man/print-MuChPoint.Rd | 1 - man/summary-MuChPoint.Rd | 1 - src/RcppExports.cpp | 5 +++++ 9 files changed, 28 insertions(+), 26 deletions(-)
Title: Deep Gaussian Processes using MCMC
Description: Performs posterior inference for deep Gaussian processes following
Sauer, Gramacy, and Higdon (2020) <arXiv:2012.08015>. Models are trained through
MCMC including elliptical slice sampling of latent Gaussian layers and Metropolis-Hastings
sampling of kernel hyperparameters. Vecchia-approximation for faster computation is implemented
following Sauer, Cooper, and Gramacy (2022) <arXiv:2204.02904>. Downstream tasks include
sequential design through active learning Cohn/integrated mean squared error (ALC/IMSE; Sauer,
Gramacy, and Higdon, 2020) and optimization through expected improvement (EI;
Gramacy, Sauer, and Wycoff, 2021 <arXiv:2112.07457>). Models
extend up to three layers deep; a one layer model is equivalent to typical Gaussian
process regression. Covariance kernel options are matern (default) and squared
exponential. Applicable to both noisy and deterministic functions.
Incorporates SNOW parallelization and utilizes C and C++ under the hood.
Author: Annie Sauer <anniees@vt.edu>
Maintainer: Annie Sauer <anniees@vt.edu>
Diff between deepgp versions 0.3.1 dated 2021-12-07 and 1.0.0 dated 2022-04-08
DESCRIPTION | 37 +- MD5 | 68 ++-- NAMESPACE | 15 R/RcppExports.R | 12 R/checks.R | 132 +++++++- R/continue.R | 330 ++++++++++++++++---- R/deepgp-package.R | 159 +-------- R/fit.R | 598 ++++++++++++++++++++----------------- R/general.R | 128 +++---- R/gibbs.R | 142 +++++--- R/gibbs_vecchia.R |only R/mcmc.R | 123 ++++--- R/mcmc_vecchia.R |only R/plot.R | 59 ++- R/predict.R | 455 +++++++++++----------------- R/predict_vecchia.R |only R/seq_design.R | 785 ++++++++++++++++++++----------------------------- R/trim.R | 80 +++- R/vecchia.R |only README.md | 43 +- man/ALC.Rd | 66 +++- man/IMSE.Rd | 69 ++++ man/continue.Rd | 48 ++ man/deepgp-package.Rd | 153 +-------- man/fit_one_layer.Rd | 136 ++++---- man/fit_three_layer.Rd | 166 +++++----- man/fit_two_layer.Rd | 166 +++++----- man/plot.Rd | 25 + man/predict.Rd | 86 +++-- man/rmse.Rd | 8 man/sq_dist.Rd | 4 man/trim.Rd | 29 + src/Makevars | 1 src/RcppExports.cpp | 41 ++ src/alc.c | 60 +-- src/cov.cpp | 113 ++++--- src/imspe.c | 22 - 37 files changed, 2377 insertions(+), 1982 deletions(-)
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangómez [aut, cre, cph]
,
João Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangómez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 0.2.1 dated 2022-01-16 and 0.2.2 dated 2022-04-08
DESCRIPTION | 6 MD5 | 33 NEWS.md | 4 R/cff_create.R | 5 R/cff_validate.R | 19 README.md | 417 +++++----- build/partial.rdb |binary build/vignette.rds |binary data/cran_to_spdx.rda |binary inst/doc/bibtex_cff.html | 603 ++++++++++++-- inst/doc/cffr.html | 323 ++++++- inst/doc/crosswalk.html | 1187 +++++++++++++++++------------ inst/doc/paper.html | 291 ++++++- inst/schema |only tests/testthat/_snaps/bibtex-check-ruby.md | 346 ++++---- tests/testthat/_snaps/cff_validate.md | 20 tests/testthat/test-cff_description.R | 1 tests/testthat/test-cff_validate.R | 96 +- 18 files changed, 2270 insertions(+), 1081 deletions(-)
Title: Create Custom Taxonomies Based on the NCBI Taxonomy and GBIF
Backbone Taxonomy
Description: The NCBI taxonomy is a popular resource for taxonomic studies but it only contains
data on species with sequence data whereas the GBIF has a more extensive coverage of
extinct species. Taxonbridge is useful for the creation and analysis of custom taxonomies
based on the NCBI taxonomy and GBIF backbone taxonomy.
Author: Werner Veldsman [aut, cre]
Maintainer: Werner Veldsman <wernerpieter.veldsman@unil.ch>
Diff between taxonbridge versions 1.0.5 dated 2022-03-25 and 1.1.0 dated 2022-04-08
DESCRIPTION | 8 +- MD5 | 42 ++++++------ NEWS.md | 8 ++ R/get_methods.R | 50 ++++++++------ R/helper_methods.R | 27 +++++--- R/load_methods.R | 38 +++++++---- README.md | 23 ++++-- inst/doc/Examples.R | 48 +++++++++++++- inst/doc/Examples.Rmd | 64 ++++++++++++++++++- inst/doc/Examples.html | 117 ++++++++++++++++++++++++++--------- inst/extdata/NCBI_stub.tsv | 10 +- inst/extdata/sample.tsv.gz |binary man/annotate.Rd | 2 man/download_ncbi.Rd | 11 ++- man/fuzzy_search.Rd | 28 ++++++-- man/get_inconsistencies.Rd | 18 +++-- man/get_taxa.Rd | 4 - man/load_sample.Rd | 8 +- man/load_taxonomies.Rd | 4 - tests/testthat/test-helper_methods.R | 3 tests/testthat/test-load_methods.R | 4 - vignettes/Examples.Rmd | 64 ++++++++++++++++++- 22 files changed, 434 insertions(+), 147 deletions(-)
Title: Interface Between GRASS Geographical Information System and R
Description: Interpreted interface between 'GRASS' geographical
information system and R, based on starting R from within the 'GRASS' 'GIS'
environment, or running free-standing R in a temporary 'GRASS' location;
the package provides facilities for using all 'GRASS' commands from the
R command line. This package may not be used for 'GRASS' 6, for which
'spgrass6' should be used.
Author: Roger Bivand [cre, aut] ,
Rainer Krug [ctb] ,
Markus Neteler [ctb] ,
Sebastian Jeworutzki [ctb] ,
Floris Vanderhaeghe [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass7 versions 0.2-8 dated 2022-03-05 and 0.2-9 dated 2022-04-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 +++++- R/initGRASS.R | 29 +++++++++++++++++++---------- R/rgrass.R | 5 ++++- man/initGRASS.Rd | 4 +++- 6 files changed, 40 insertions(+), 22 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Mueller [aut, cre] ,
Antoine Fabri [ctb],
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Mueller <krlmlr+r@mailbox.org>
Diff between dm versions 0.2.7 dated 2022-02-03 and 0.2.8 dated 2022-04-08
DESCRIPTION | 12 MD5 | 118 ++++----- NEWS.md | 22 + R/check-cardinalities.R | 6 R/check_suggested.R | 2 R/db-interface.R | 65 ++++- R/dm_unnest_tbl.R | 3 R/dm_wrap.R | 39 +-- R/examine-constraints.R | 3 R/new_ticker.R | 2 R/pack_join.R | 12 R/validate.R | 11 R/zoom.R | 31 +- R/zzz.R | 2 README.md | 76 +++--- inst/doc/dm.html | 10 inst/doc/howto-dm-copy.html | 35 +- inst/doc/howto-dm-db.html | 43 ++- inst/doc/howto-dm-df.html | 4 inst/doc/howto-dm-rows.html | 89 +++---- inst/doc/howto-dm-theory.html | 23 - inst/doc/tech-dm-cdm.html | 4 inst/doc/tech-dm-class.html | 22 - inst/doc/tech-dm-draw.html | 4 inst/doc/tech-dm-filter.html | 108 +++++--- inst/doc/tech-dm-join.html | 4 inst/doc/tech-dm-low-level.html | 14 - inst/doc/tech-dm-zoom.html | 30 +- man/dm_add_tbl.Rd | 5 man/dm_bind.Rd | 5 man/dm_unpack_tbl.Rd | 7 man/dm_zoom_to.Rd | 5 tests/testthat/_snaps/add-tbl.md | 6 tests/testthat/_snaps/bind.md | 9 tests/testthat/_snaps/check_suggested.md | 10 tests/testthat/_snaps/disambiguate.md | 3 tests/testthat/_snaps/dm.md | 5 tests/testthat/_snaps/dm_pixarfilms.md | 4 tests/testthat/_snaps/dplyr.md | 16 - tests/testthat/_snaps/draw-dm/nycflight-dm.svg | 8 tests/testthat/_snaps/error-helpers.md | 313 +++++++++++++++---------- tests/testthat/_snaps/examine-cardinalities.md | 4 tests/testthat/_snaps/examine-constraints.md | 14 - tests/testthat/_snaps/filter-dm.md | 2 tests/testthat/_snaps/foreign-keys.md | 22 - tests/testthat/_snaps/key-helpers.md | 15 - tests/testthat/_snaps/pack_join.md | 20 + tests/testthat/_snaps/paste.md | 27 +- tests/testthat/_snaps/primary-keys.md | 14 - tests/testthat/_snaps/rows-db.md | 10 tests/testthat/_snaps/rows-dm.md | 8 tests/testthat/_snaps/select-tbl.md | 2 tests/testthat/_snaps/select.md | 8 tests/testthat/_snaps/tidyselect.md | 10 tests/testthat/_snaps/upgrade.md | 13 - tests/testthat/_snaps/waldo.md | 4 tests/testthat/test-pack_join.R | 10 tests/testthat/test-tidyselect.R | 2 tests/testthat/test-validate.R | 20 + tests/testthat/test-zoom.R | 16 + 60 files changed, 852 insertions(+), 559 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices, vectors,
numerical solvers and related algorithms. It supports dense and sparse
matrices on integer, floating point and complex numbers, decompositions of
such matrices, and solutions of linear systems. Its performance on many
algorithms is comparable with some of the best implementations based on
'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header
files from the 'Eigen' C++ template library (currently version 3.3.4). Thus
users do not need to install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.3.9.1 dated 2020-12-17 and 0.3.3.9.2 dated 2022-04-08
ChangeLog | 92 ++++++++++++++++++++++++++++++++++++ DESCRIPTION | 11 ++-- MD5 | 29 +++++------ R/RcppEigen.package.skeleton.R | 10 +-- R/fastLm.R | 2 README.md | 14 ++--- build/vignette.rds |binary inst/CITATION | 5 - inst/NEWS.Rd | 11 ++++ inst/doc/RcppEigen-Introduction.pdf |binary inst/include/RcppEigenWrap.h | 32 +++++++----- inst/tinytest/cpp/wrap.cpp | 20 +++++++ inst/tinytest/test_fastLm.R | 23 ++++++++- inst/tinytest/test_misc.R |only inst/tinytest/test_wrap.R | 26 +++++++++- src/fastLm.cpp | 45 ++++++++--------- 16 files changed, 246 insertions(+), 74 deletions(-)
Title: Easily Create Production-Ready Rich Text Format (RTF) Table and
Figure
Description: Create production-ready Rich Text Format (RTF) table and figure with flexible format.
Author: Yilong Zhang [aut, cre],
Siruo Wang [aut],
Simiao Ye [aut],
Fansen Kong [aut],
Nan Xiao [ctb],
Madhusudhan Ginnaram [ctb],
Ruchitbhai Patel [ctb],
Huei-Ling Chen [ctb],
Peikun Wu [ctb],
Uday Preetham Palukuru [ctb],
Daniel Woodie [ctb],
Sarad Nepal [ [...truncated...]
Maintainer: Yilong Zhang <elong0527@gmail.com>
Diff between r2rtf versions 0.3.3 dated 2022-03-07 and 0.3.4 dated 2022-04-08
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS.md | 7 ++++++- R/conversion.R | 4 +++- tests/testthat/test-independent-testing-conversion.R | 2 +- 6 files changed, 21 insertions(+), 13 deletions(-)
Title: Package Dependency Resolution and Downloads
Description: Find recursive dependencies of 'R' packages from various
sources. Solve the dependencies to obtain a consistent set of packages
to install. Download packages, and install them. It supports packages
on 'CRAN', 'Bioconductor' and other 'CRAN-like' repositories,
'GitHub', package 'URLs', and local package trees and files. It caches
metadata and package files via the 'pkgcache' package, and performs
all 'HTTP' requests, downloads, builds and installations in parallel.
'pkgdepends' is the workhorse of the 'pak' package.
Author: Gabor Csardi [aut, cre],
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pkgdepends versions 0.3.0 dated 2022-02-16 and 0.3.1 dated 2022-04-08
DESCRIPTION | 45 ++++++++++++++++------------- MD5 | 24 +++++++-------- R/pkg-plan.R | 2 - R/solve.R | 43 +++++++++++++++++++++++++++ README.md | 10 ++++++ inst/WORDLIST | 6 ++- man/lib_status.Rd | 2 - man/pkg_deps.Rd | 2 - man/pkg_download_proposal.Rd | 2 - man/pkg_downloads.Rd | 4 +- man/pkg_installation_proposal.Rd | 2 - man/pkg_resolution.Rd | 4 +- man/pkgdepends-package.Rd | 60 ++++++++++++++++++++++++--------------- 13 files changed, 140 insertions(+), 66 deletions(-)
Title: Discovery, Retrieval, and Analysis of Water Isotope Data
Description: The wiDB...() functions provide an interface to the public API
of the wiDB <https://github.com/SPATIAL-Lab/isoWater/blob/master/Protocol.md>:
build, check and submit queries, and receive and
unpack responses. Data analysis functions support Bayesian
inference of the source and source isotope composition of water
samples that may have experienced evaporation. Algorithms
adapted from Bowen et al. (2018, <doi:10.1007/s00442-018-4192-5>).
Author: Gabe Bowen [aut, cre]
Maintainer: Gabe Bowen <gabe.bowen@utah.edu>
Diff between isoWater versions 1.0.1 dated 2021-07-20 and 1.1.0 dated 2022-04-08
DESCRIPTION | 8 MD5 | 39 ++-- NAMESPACE | 3 NEWS.md | 4 R/constructors.R | 40 ++++ R/watercomp.R | 15 + R/wiDBfunctions.R | 28 +- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data |only inst/doc/isoWater.Rmd | 6 inst/doc/isoWater.html | 385 ++++++++++++++++++++++++++++++++++------ man/GMWL.Rd |only man/dex.Rd |only man/iso.Rd | 4 man/mwl.Rd | 4 man/mwlSource.Rd | 5 man/wiDB_data.Rd | 2 man/wiDB_sites.Rd | 2 tests/testthat/test-mwlSource.R | 12 + vignettes/isoWater.Rmd | 6 22 files changed, 449 insertions(+), 116 deletions(-)
Title: Class Cover Catch Digraphs
Description: Class Cover Catch Digraphs, neighborhood graphs, and
relatives.
Author: David J. Marchette <dmarchette@gmail.com>
Maintainer: David J. Marchette <dmarchette@gmail.com>
Diff between cccd versions 1.5 dated 2015-06-01 and 1.6 dated 2022-04-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 3 +++ R/cccd.R | 18 ++++++++++-------- R/ccd.R | 4 ++-- R/class.R | 2 +- R/dominate.R | 2 +- R/gg.R | 4 ++-- R/juggling.R | 4 ++-- R/nng.R | 10 +++++----- R/rng.R | 4 ++-- 11 files changed, 42 insertions(+), 37 deletions(-)
Title: Analysis of Physiologically Structured Population Models
Description: Performs demographic, bifurcation and evolutionary analysis of physiologically structured population models, which is a class of models that consistently translates continuous-time models of individual life history to the population level.
A model of individual life history has to be implemented specifying the individual-level functions that determine the life history, such as development and mortality rates and fecundity.
M.A. Kirkilionis, O. Diekmann, B. Lisser, M. Nool, B. Sommeijer & A.M. de Roos (2001) <doi:10.1142/S0218202501001264>.
O.Diekmann, M.Gyllenberg & J.A.J.Metz (2003) <doi:10.1016/S0040-5809(02)00058-8>.
A.M. de Roos (2008) <doi:10.1111/j.1461-0248.2007.01121.x>.
Author: Andre M. de Roos [aut, cre],
Ernst Hairer [ctb],
Gerhard Wanner [ctb]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>
Diff between PSPManalysis versions 0.3.7 dated 2021-12-06 and 0.3.8 dated 2022-04-08
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/csbread.R | 14 +++++++++----- build/vignette.rds |binary inst/C/PSPMdemo.c | 4 ++-- inst/C/PSPMequi.c | 4 ++-- inst/C/PSPMevodyn.c | 4 ++-- inst/C/PSPMind.c | 4 ++-- inst/C/curve.c | 16 ++++++++-------- inst/C/globals.h | 30 +++++++++++++++++++++++------- 11 files changed, 65 insertions(+), 41 deletions(-)
Title: Information-Theoretic Measures
Description: Implements various measures of information theory based on several entropy estimators.
Author: Patrick E. Meyer
Maintainer: Patrick E. Meyer <software@meyerp.com>
Diff between infotheo versions 1.2.0 dated 2014-07-26 and 1.2.0.1 dated 2022-04-08
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 9 insertions(+), 8 deletions(-)
Title: HTML Writer - Outputs R Objects in HTML Format
Description: Easy-to-use and versatile functions to output R objects in
HTML format.
Author: Gregoire Pau <gregoire.pau@gmail.com>
Maintainer: Gregoire Pau <gregoire.pau@gmail.com>
Diff between hwriter versions 1.3.2 dated 2014-09-10 and 1.3.2.1 dated 2022-04-08
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 4 ++++ build/vignette.rds |binary inst/doc/hwriter.pdf |binary man/hwriter-package.Rd | 2 +- 6 files changed, 15 insertions(+), 11 deletions(-)
Title: Flexible Cluster Algorithms
Description: The main function kcca implements a general framework for
k-centroids cluster analysis supporting arbitrary distance measures
and centroid computation. Further cluster methods include hard
competitive learning, neural gas, and QT clustering. There are
numerous visualization methods for cluster results (neighborhood
graphs, convex cluster hulls, barcharts of centroids, ...), and
bootstrap methods for the analysis of cluster stability.
Author: Friedrich Leisch [aut, cre] ,
Evgenia Dimitriadou [ctb],
Bettina Gruen [ctb]
Maintainer: Friedrich Leisch <Friedrich.Leisch@R-project.org>
Diff between flexclust versions 1.4-0 dated 2018-09-24 and 1.4-1 dated 2022-04-08
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NEWS | 16 +++++++++++++++- R/stepflexclust.R | 12 +++++++++++- man/bclust.Rd | 2 +- man/bootFlexclust.Rd | 7 ++++--- man/bundestag.Rd | 4 ++-- man/cclust.Rd | 5 +++-- src/cclust.c | 4 ++-- 9 files changed, 52 insertions(+), 26 deletions(-)
Title: Bifurcation Analysis of Ordinary Differential Equation Systems
Description: Shiny application that performs bifurcation and phaseplane analysis of systems of ordinary
differential equations. The package allows for computation of equilibrium curves as a function of
a single free parameter, detection of transcritical, saddle-node and hopf bifurcation points along
these curves, and computation of curves representing these transcritical, saddle-node and hopf
bifurcation points as a function of two free parameters. The shiny-based GUI allows visualization
of the results in both 2D- and 3D-plots. The implemented methods for solution localisation and curve
continuation are based on the book "Elements of applied bifurcation theory" (Kuznetsov, Y. A., 1995;
ISBN: 0-387-94418-4).
Author: Andre M. de Roos [aut, cre]
Maintainer: Andre M. de Roos <A.M.deRoos@uva.nl>
Diff between deBif versions 0.1.0 dated 2022-03-14 and 0.1.5 dated 2022-04-08
DESCRIPTION | 6 ++--- MD5 | 26 ++++++++++++------------- NEWS.md | 22 +++++++++++++++++++++ R/EQfuncs.R | 42 ++++++++++++++++++++++------------------ R/bif1parplot.R | 6 ++--- R/bifCheckInput.R | 16 +++++++++++---- R/bifComputeCurves.R | 53 +++++++++++++++++++++++++++++++++++++++++++-------- R/phaseCheckInput.R | 4 ++- R/phasePlot1D.R | 3 -- R/phasePlot2D.R | 38 ++++++++++++++++++------------------ R/phaseServerFuncs.R | 46 ++++++++++++++++++++++++++++++++++++++++---- R/phaseplane.R | 24 ++++++++++++++++++++--- src/curve.c | 4 +-- src/globals.h | 14 +++++++++---- 14 files changed, 218 insertions(+), 86 deletions(-)
Title: Interactive Graphics for Monitoring Clinical Trial Safety
Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the included 'Shiny' application.
Author: Jeremy Wildfire [cre, aut],
Becca Krouse [aut],
Preston Burns [aut],
Xiao Ni [aut],
James Buchanan [aut],
Susan Duke [aut]
Maintainer: Jeremy Wildfire <jwildfire@gmail.com>
Diff between safetyGraphics versions 2.0.0 dated 2021-09-22 and 2.1.0 dated 2022-04-08
safetyGraphics-2.0.0/safetyGraphics/R/meta.R |only safetyGraphics-2.0.0/safetyGraphics/data |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/chartConfiguration.Rmd |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/chartConfiguration.html |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/intro.Rmd |only safetyGraphics-2.0.0/safetyGraphics/inst/doc/intro.html |only safetyGraphics-2.0.0/safetyGraphics/man/meta.Rd |only safetyGraphics-2.0.0/safetyGraphics/vignettes/chartConfiguration.Rmd |only safetyGraphics-2.0.0/safetyGraphics/vignettes/intro.Rmd |only safetyGraphics-2.1.0/safetyGraphics/DESCRIPTION | 11 safetyGraphics-2.1.0/safetyGraphics/MD5 | 101 ++-- safetyGraphics-2.1.0/safetyGraphics/NAMESPACE | 7 safetyGraphics-2.1.0/safetyGraphics/NEWS.md | 9 safetyGraphics-2.1.0/safetyGraphics/R/app_startup.R | 16 safetyGraphics-2.1.0/safetyGraphics/R/detectStandard.R | 8 safetyGraphics-2.1.0/safetyGraphics/R/evaluateStandard.R | 49 +- safetyGraphics-2.1.0/safetyGraphics/R/makeChartConfig.R | 21 safetyGraphics-2.1.0/safetyGraphics/R/makeMapping.R | 10 safetyGraphics-2.1.0/safetyGraphics/R/makeMeta.R |only safetyGraphics-2.1.0/safetyGraphics/R/mod_safetyGraphicsServer.R | 2 safetyGraphics-2.1.0/safetyGraphics/R/mod_safetyGraphicsUI.R | 16 safetyGraphics-2.1.0/safetyGraphics/R/mod_settingsCode.R | 21 safetyGraphics-2.1.0/safetyGraphics/R/prepareChart.R | 124 +++-- safetyGraphics-2.1.0/safetyGraphics/R/safetyGraphicsApp.R | 14 safetyGraphics-2.1.0/safetyGraphics/R/safetyGraphicsInit.R | 12 safetyGraphics-2.1.0/safetyGraphics/R/util-pipe.R |only safetyGraphics-2.1.0/safetyGraphics/build/vignette.rds |binary safetyGraphics-2.1.0/safetyGraphics/inst/deploy |only safetyGraphics-2.1.0/safetyGraphics/inst/doc/ChartConfiguration.Rmd |only safetyGraphics-2.1.0/safetyGraphics/inst/doc/ChartConfiguration.html |only safetyGraphics-2.1.0/safetyGraphics/inst/doc/Cookbook.Rmd | 216 ++++++++-- safetyGraphics-2.1.0/safetyGraphics/inst/doc/Cookbook.html | 210 ++++++++- safetyGraphics-2.1.0/safetyGraphics/inst/doc/Intro.Rmd |only safetyGraphics-2.1.0/safetyGraphics/inst/doc/Intro.html |only safetyGraphics-2.1.0/safetyGraphics/inst/doc/TechnicalFAQ.Rmd | 97 ++-- safetyGraphics-2.1.0/safetyGraphics/inst/doc/TechnicalFAQ.html | 101 ++-- safetyGraphics-2.1.0/safetyGraphics/man/app_startup.Rd | 2 safetyGraphics-2.1.0/safetyGraphics/man/detectStandard.Rd | 8 safetyGraphics-2.1.0/safetyGraphics/man/evaluateStandard.Rd | 4 safetyGraphics-2.1.0/safetyGraphics/man/makeChartConfig.Rd | 2 safetyGraphics-2.1.0/safetyGraphics/man/makeMapping.Rd | 2 safetyGraphics-2.1.0/safetyGraphics/man/makeMeta.Rd |only safetyGraphics-2.1.0/safetyGraphics/man/pipe.Rd |only safetyGraphics-2.1.0/safetyGraphics/man/safetyGraphicsApp.Rd | 9 safetyGraphics-2.1.0/safetyGraphics/man/safetyGraphicsServer.Rd | 2 safetyGraphics-2.1.0/safetyGraphics/man/safetyGraphicsUI.Rd | 2 safetyGraphics-2.1.0/safetyGraphics/tests/testthat/module_examples/chartsTab/app.R | 10 safetyGraphics-2.1.0/safetyGraphics/tests/testthat/module_examples/filterTab/app.R | 8 safetyGraphics-2.1.0/safetyGraphics/tests/testthat/module_examples/mapping/app.R | 9 safetyGraphics-2.1.0/safetyGraphics/tests/testthat/module_examples/mappingColumn/app.R | 8 safetyGraphics-2.1.0/safetyGraphics/tests/testthat/module_examples/mappingDomain/app.R | 28 - safetyGraphics-2.1.0/safetyGraphics/tests/testthat/module_examples/settingsMapping/app.R | 13 safetyGraphics-2.1.0/safetyGraphics/tests/testthat/test_detectStandard.R | 46 +- safetyGraphics-2.1.0/safetyGraphics/tests/testthat/test_evaluateStandard.R | 34 - safetyGraphics-2.1.0/safetyGraphics/tests/testthat/test_makeMapping.R | 21 safetyGraphics-2.1.0/safetyGraphics/tests/testthat/test_makeMeta.R |only safetyGraphics-2.1.0/safetyGraphics/tests/testthat/test_mod_mappingColumn.R | 7 safetyGraphics-2.1.0/safetyGraphics/tests/testthat/test_mod_mappingDomain.R | 25 - safetyGraphics-2.1.0/safetyGraphics/vignettes/ChartConfiguration.Rmd |only safetyGraphics-2.1.0/safetyGraphics/vignettes/Cookbook.Rmd | 216 ++++++++-- safetyGraphics-2.1.0/safetyGraphics/vignettes/Intro.Rmd |only safetyGraphics-2.1.0/safetyGraphics/vignettes/TechnicalFAQ.Rmd | 97 ++-- 62 files changed, 1094 insertions(+), 504 deletions(-)
More information about safetyGraphics at CRAN
Permanent link
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <https://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut, cre],
Ben Goodrich [aut],
Martin Lysy [aut],
Andrew Johnson [ctb],
Hamada S. Badr [ctb],
Marco Colombo [ctb],
Stefan Siegert [ctb],
Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between rstantools versions 2.1.1 dated 2020-07-06 and 2.2.0 dated 2022-04-08
DESCRIPTION | 23 MD5 | 48 - NEWS.md | 21 R/init_cpp.R | 31 R/rstan_config.R | 218 ++++- R/rstan_create_package.R | 30 R/rstan_package_utils.R | 28 R/rstantools-package.R | 2 R/update_description.R | 5 R/use_rstan.R | 11 build/vignette.rds |binary inst/doc/developer-guidelines.Rmd | 101 +- inst/doc/developer-guidelines.html | 226 ------ inst/doc/minimal-rstan-package.R | 13 inst/doc/minimal-rstan-package.Rmd | 31 inst/doc/minimal-rstan-package.html | 452 +++--------- inst/include/sys/Makevars | 3 inst/include/sys/Makevars.win | 3 inst/include/sys/stanmodels.R | 2 man/rstan_create_package.Rd | 10 man/rstantools-package.Rd | 2 tests/testthat/RStanTest/test-rstan_package_skeleton_plus.R | 10 tests/testthat/test-rstan_config.R | 10 vignettes/developer-guidelines.Rmd | 101 +- vignettes/minimal-rstan-package.Rmd | 31 25 files changed, 562 insertions(+), 850 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-27 1.1.1
2011-01-19 1.1
2011-01-05 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-18 1.2.0
2022-02-09 1.1.0
2021-12-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-05-29 1.0-3
2007-06-11 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-02 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-18 1.1.0
Title: A 'Shiny' App for Exploration of Text Collections
Description: Facilitates dynamic exploration of text collections through an
intuitive graphical user interface and the power of regular expressions.
The package contains 1) a helper function to convert a data frame to a
'corporaexplorerobject', 2) a 'Shiny' app for fast and flexible exploration
of a 'corporaexplorerobject', and 3) a 'Shiny' app for simple
retrieval/extraction of documents from a 'corporaexplorerobject' in a
reading-friendly format. The package also includes demo apps with which
one can explore Jane Austen's novels and the State of the Union Addresses
(data from the 'janeaustenr' and 'sotu' packages respectively).
Author: Kristian Lundby Gjerde [aut, cre]
Maintainer: Kristian Lundby Gjerde <kristian.gjerde@gmail.com>
Diff between corporaexplorer versions 0.8.4 dated 2021-03-17 and 0.8.5 dated 2022-04-08
DESCRIPTION | 13 +- MD5 | 48 +++---- NEWS.md | 8 + R/explore.R | 22 +-- R/prepare_data.R | 2 README.md | 6 data/test_data.rda |binary inst/download/css/download_css.css | 9 + inst/download/server/function_corpus_info.R | 14 +- inst/download/server/server_info_on_startup.R | 4 inst/explorer/app.R | 2 inst/explorer/config/config.R | 28 ++-- inst/explorer/config/config_tests.R | 4 inst/explorer/global/function_display_document.R | 62 +++++----- inst/explorer/global/function_plot_size.R | 2 inst/explorer/global/function_visualise_document.R | 6 inst/explorer/global/functions_info.R | 8 - inst/explorer/global/functions_main_search_engine.R | 16 +- inst/explorer/js_css/explorer_css.css | 10 + inst/explorer/server/2_event_search_button/subsetting.R | 5 inst/explorer/server/3_event_corpus_map_click/preparing_day_corpus.R | 6 inst/explorer/server/functions_checking_input.R | 16 +- man/explore.Rd | 10 + man/matrix_via_r.Rd | 2 man/prepare_data.Rd | 2 25 files changed, 173 insertions(+), 132 deletions(-)
More information about corporaexplorer at CRAN
Permanent link
More information about ImportanceIndice at CRAN
Permanent link
Title: Deep Time Redox Analysis of the Geobiology Ontology Network
Description: Create, visualize, manipulate, and analyze bipartite mineral-chemistry
networks for set of focal element(s) across deep-time on Earth. The method is
described in Spielman and Moore (2020) <doi:10.3389/feart.2020.585087>.
Author: Stephanie J. Spielman [aut, cre]
Maintainer: Stephanie J. Spielman <stephanie.spielman@gmail.com>
Diff between dragon versions 1.2.0 dated 2021-07-07 and 1.2.1 dated 2022-04-08
DESCRIPTION | 14 MD5 | 37 - R/app_server.R | 2 R/app_ui.R | 12 R/fct_build-network.R | 14 README.md | 9 build/vignette.rds |binary inst/doc/dragon.html | 574 +++++++++++++++++++++++---- man/initialize_network.Rd | 4 tests/testthat/clustering.rds |only tests/testthat/edges_by_redox.csv.zip |binary tests/testthat/locality_info.csv.zip |binary tests/testthat/nodes_by_redox.csv.zip |binary tests/testthat/setup_network-style.R | 2 tests/testthat/setup_test-settings.R | 4 tests/testthat/styled_edges.csv.zip |binary tests/testthat/styled_nodes.csv.zip |binary tests/testthat/test_build-shiny-tables.R | 2 tests/testthat/test_calculate-network-info.R | 5 tests/testthat/true_mineral_nodes.csv.zip |binary 20 files changed, 561 insertions(+), 118 deletions(-)
More information about datazoom.amazonia at CRAN
Permanent link
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.2.6 dated 2022-03-31 and 1.3.0 dated 2022-04-08
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NEWS.md | 3 +++ R/RCM_est.R | 13 +++++-------- R/assess_SCA.R | 3 ++- R/assess_SSS.R | 3 ++- build/partial.rdb |binary 7 files changed, 24 insertions(+), 22 deletions(-)
Title: Feature Selection for 'mlr3'
Description: Implements methods for feature selection with
'mlr3', e.g. random search and sequential selection. Various
termination criteria can be set and combined. The class
'AutoFSelector' provides a convenient way to perform nested resampling
in combination with 'mlr3'.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 0.6.1 dated 2022-01-20 and 0.7.0 dated 2022-04-08
mlr3fselect-0.6.1/mlr3fselect/man/FSelectorDesignPoints.Rd |only mlr3fselect-0.6.1/mlr3fselect/man/FSelectorExhaustiveSearch.Rd |only mlr3fselect-0.6.1/mlr3fselect/man/FSelectorGeneticSearch.Rd |only mlr3fselect-0.6.1/mlr3fselect/man/FSelectorRFE.Rd |only mlr3fselect-0.6.1/mlr3fselect/man/FSelectorRandomSearch.Rd |only mlr3fselect-0.6.1/mlr3fselect/man/FSelectorSequential.Rd |only mlr3fselect-0.6.1/mlr3fselect/man/FSelectorShadowVariableSearch.Rd |only mlr3fselect-0.6.1/mlr3fselect/tests/testthat/helper_expectations.R |only mlr3fselect-0.6.1/mlr3fselect/tests/testthat/helper_fselector.R |only mlr3fselect-0.6.1/mlr3fselect/tests/testthat/helper_misc.R |only mlr3fselect-0.7.0/mlr3fselect/DESCRIPTION | 15 - mlr3fselect-0.7.0/mlr3fselect/MD5 | 95 +++--- mlr3fselect-0.7.0/mlr3fselect/NAMESPACE | 1 mlr3fselect-0.7.0/mlr3fselect/NEWS.md | 51 ++- mlr3fselect-0.7.0/mlr3fselect/R/FSelector.R | 138 ++++++---- mlr3fselect-0.7.0/mlr3fselect/R/FSelectorDesignPoints.R | 68 ++-- mlr3fselect-0.7.0/mlr3fselect/R/FSelectorExhaustiveSearch.R | 16 - mlr3fselect-0.7.0/mlr3fselect/R/FSelectorFromOptimizer.R | 16 - mlr3fselect-0.7.0/mlr3fselect/R/FSelectorGeneticSearch.R | 47 +-- mlr3fselect-0.7.0/mlr3fselect/R/FSelectorRFE.R | 95 +++--- mlr3fselect-0.7.0/mlr3fselect/R/FSelectorRandomSearch.R | 47 ++- mlr3fselect-0.7.0/mlr3fselect/R/FSelectorSequential.R | 54 +-- mlr3fselect-0.7.0/mlr3fselect/R/FSelectorShadowVariableSearch.R | 52 ++- mlr3fselect-0.7.0/mlr3fselect/R/assertions.R |only mlr3fselect-0.7.0/mlr3fselect/R/auto_fselector.R | 14 - mlr3fselect-0.7.0/mlr3fselect/R/fselect.R | 22 - mlr3fselect-0.7.0/mlr3fselect/R/helper.R |only mlr3fselect-0.7.0/mlr3fselect/R/mlr_fselectors.R | 42 ++- mlr3fselect-0.7.0/mlr3fselect/R/sugar.R | 2 mlr3fselect-0.7.0/mlr3fselect/R/zzz.R | 3 mlr3fselect-0.7.0/mlr3fselect/build/partial.rdb |binary mlr3fselect-0.7.0/mlr3fselect/inst/WORDLIST | 6 mlr3fselect-0.7.0/mlr3fselect/inst/testthat |only mlr3fselect-0.7.0/mlr3fselect/man/FSelector.Rd | 85 +++--- mlr3fselect-0.7.0/mlr3fselect/man/FSelectorFromOptimizer.Rd | 7 mlr3fselect-0.7.0/mlr3fselect/man/auto_fselector.Rd | 4 mlr3fselect-0.7.0/mlr3fselect/man/fselect.Rd | 4 mlr3fselect-0.7.0/mlr3fselect/man/mlr_fselectors.Rd | 35 ++ mlr3fselect-0.7.0/mlr3fselect/man/mlr_fselectors_design_points.Rd |only mlr3fselect-0.7.0/mlr3fselect/man/mlr_fselectors_exhaustive_search.Rd |only mlr3fselect-0.7.0/mlr3fselect/man/mlr_fselectors_genetic_search.Rd |only mlr3fselect-0.7.0/mlr3fselect/man/mlr_fselectors_random_search.Rd |only mlr3fselect-0.7.0/mlr3fselect/man/mlr_fselectors_rfe.Rd |only mlr3fselect-0.7.0/mlr3fselect/man/mlr_fselectors_sequential.Rd |only mlr3fselect-0.7.0/mlr3fselect/man/mlr_fselectors_shadow_variable_search.Rd |only mlr3fselect-0.7.0/mlr3fselect/tests/testthat.R | 1 mlr3fselect-0.7.0/mlr3fselect/tests/testthat/helper.R | 6 mlr3fselect-0.7.0/mlr3fselect/tests/testthat/setup.R | 5 mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_ArchiveFSelect.R | 6 mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_FSelectorDesignPoints.R | 8 mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_FSelectorExhaustiveSearch.R | 32 -- mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_FSelectorGeneticSearch.R | 4 mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_FSelectorRFE.R | 89 ++---- mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_FSelectorRandomSearch.R | 11 mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_FSelectorSequential.R | 34 +- mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_FSelectorShadowVariableSearch.R | 42 +-- mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_fselect.R | 17 - mlr3fselect-0.7.0/mlr3fselect/tests/testthat/test_mlr_fselectors.R |only 58 files changed, 667 insertions(+), 507 deletions(-)
Title: Exact Confidence Limits after a Sequential Trial
Description: The user first provides design vectors n, a and b as well as null (p0) and alternative (p1) benchmark values for the probability of success. The key function "mv.plots.SM()" calculates mean values of exact upper and lower limits based on four different rank ordering methods. These plots form the basis of selecting a rank ordering. The function "inference()" calculates exact limits from a provided realisation and ordering choice. For more information, see "Exact confidence limits after a group sequential single arm binary trial" by Lloyd, C.J. (2020), Statistics in Medicine, Volume 38, 2389-2399, <doi:10.1002/sim.8909>.
Author: Chris J. Lloyd
Maintainer: Chris J. Lloyd <c.lloyd@mbs.edu>
Diff between CLAST versions 1.0.0 dated 2022-04-05 and 1.0.1 dated 2022-04-08
DESCRIPTION | 6 - MD5 | 34 +++++----- R/ML.rank.SM.R | 29 ++++----- build/partial.rdb |binary man/CLAST-package.Rd | 2 man/CP.stats.SM.Rd | 2 man/JT.rank.SM.Rd | 5 - man/LR.stats.SM.Rd | 2 man/ML.rank.SM.Rd | 2 man/RANK.Rd | 8 +- man/cross.Rd | 5 + man/errors.SM.Rd | 7 +- man/exact.lower.limits.SM.Rd | 117 ++++++++++++++++++------------------ man/exact.upper.limits.SM.Rd | 118 ++++++++++++++++++------------------- man/mv.SM.Rd | 136 ++++++++++++++++++++++--------------------- man/mv.plots.SM.Rd | 10 +-- man/plot.sample.space.SM.Rd | 1 man/prob.SM.Rd | 3 18 files changed, 249 insertions(+), 238 deletions(-)
Title: Bayesian Additive Models for Location, Scale, and Shape (and
Beyond)
Description: Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework.
The distribution parameters may capture location, scale, shape, etc. and every parameter may depend
on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model.
The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2019)
<doi:10.1080/10618600.2017.1407325> and the R package in Umlauf, Klein, Simon, Zeileis (2021)
<doi:10.18637/jss.v100.i04>.
Author: Nikolaus Umlauf [aut, cre] ,
Nadja Klein [aut] ,
Achim Zeileis [aut] ,
Meike Koehler [ctb],
Thorsten Simon [aut] ,
Stanislaus Stadlmann [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between bamlss versions 1.1-6 dated 2021-11-24 and 1.1-7 dated 2022-04-08
DESCRIPTION | 14 +-- MD5 | 32 +++---- NAMESPACE | 1 NEWS.md | 10 ++ R/BAMLSS.R | 210 ++++++++++++++++++++++++++++++++++++++++--------- R/GAMart.R | 62 ++++++++++++++ R/families.R | 154 ++++++++++++++++++++--------------- R/optimizers.R | 86 +++++++++++++++----- R/stabsel.R | 2 R/vis.R | 7 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/bamlss.html | 48 +++++------ man/bbfit.Rd | 2 man/family.bamlss.Rd | 2 man/neighbormatrix.Rd | 4 src/bamlss_functions.c | 92 +++++++++++---------- 17 files changed, 505 insertions(+), 221 deletions(-)
Title: Analysis of the Nigeria National Data Repository (NDR)
Description: The goal is to simplify routine analysis of the Nigeria National Data Repository (NDR) <https://ndr.phis3project.org.ng> using the PEPFAR Monitoring, Evaluation, and Reporting (MER) indicators (see <https://datim.zendesk.com/hc/en-us/articles/360000084446-MER-Indicator-Reference-Guides>). It is designed to import in to R patient-level line-list downloaded as 'csv' file from the front-end of the NDR.
Author: Stephen Balogun [aut, cre] ,
Scholastica Olanrewaju [ctb],
Oluwaseun Okunuga [ctb],
Temitope Kolade [ctb],
Geraldine Abone [ctb]
Maintainer: Stephen Balogun <stephentaiyebalogun@gmail.com>
Diff between tidyndr versions 0.2.0 dated 2022-01-04 and 0.2.1 dated 2022-04-08
DESCRIPTION | 8 MD5 | 160 ++++----- NAMESPACE | 2 NEWS.md | 83 ++-- R/cot_cascade.R |only R/data-recency.R | 2 R/data.R | 2 R/disaggregate.R | 532 ++++++++++++++----------------- R/hts_recent.R | 197 +++++------ R/hts_tst_pos.R | 173 ++++------ R/read_ndr.R | 187 +++++----- R/recent_eligible.R | 201 +++++------ R/rita_recent.R | 132 +++---- R/rita_result.R | 123 +++---- R/rita_sample.R | 133 +++---- R/rtri_recent.R | 116 +++--- R/summarise_ndr.R | 89 ++--- R/summarise_recency.R | 223 ++++++------ R/summarize_ndr.R | 219 ++++++------ R/summarize_recency.R | 92 ++--- R/tx_appointment.R | 230 ++++++------- R/tx_curr.R | 192 +++++------ R/tx_ml.R | 312 +++++++++--------- R/tx_ml_outcomes.R | 91 ++--- R/tx_mmd.R | 196 +++++------ R/tx_new.R | 30 - R/tx_pvls_den.R | 121 ++++--- R/tx_pvls_num.R | 126 ++++--- R/tx_regimen.R | 259 +++++++-------- R/tx_rtt.R | 232 ++++++------- R/tx_vl_eligible.R | 169 +++++---- R/tx_vl_unsuppressed.R | 298 ++++++++++------- R/utils-fy_start.R | 41 +- R/utils-read_ndr.R | 424 ++++++++++++------------ R/utils-summarise_ndr.R | 134 +++---- R/vl_cascade.R |only README.md | 96 +++-- build/vignette.rds |binary inst/doc/Augmenting-tidyndr.html | 29 - inst/doc/tidyndr.Rmd | 2 inst/doc/tidyndr.html | 211 ++++++------ man/cot_cascade.Rd |only man/disaggregate.Rd | 1 man/hts_recent.Rd | 1 man/hts_tst_pos.Rd | 9 man/ndr_example.Rd | 2 man/recency_example.Rd | 2 man/recent_eligible.Rd | 3 man/rita_recent.Rd | 1 man/rita_sample.Rd | 1 man/rtri_recent.Rd | 1 man/summarise_recency.Rd | 1 man/summarize_recency.Rd | 1 man/tx_appointment.Rd | 5 man/tx_curr.Rd | 10 man/tx_ml.Rd | 5 man/tx_mmd.Rd | 5 man/tx_new.Rd | 11 man/tx_pvls_den.Rd | 8 man/tx_pvls_num.Rd | 10 man/tx_regimen.Rd | 5 man/tx_rtt.Rd | 5 man/tx_vl_eligible.Rd | 10 man/tx_vl_unsuppressed.Rd | 11 man/vl_cascade.Rd |only tests/testthat/test-cot_cascade.R |only tests/testthat/test-disaggregate.R | 5 tests/testthat/test-hts_recent.R | 17 tests/testthat/test-hts_tst_pos.R | 21 - tests/testthat/test-recent_eligible.R | 27 - tests/testthat/test-rita_recent.R | 21 - tests/testthat/test-rita_result.R | 19 - tests/testthat/test-rita_sample.R | 17 tests/testthat/test-rtri_recent.R | 17 tests/testthat/test-tx_curr.R | 17 tests/testthat/test-tx_mmd.R | 21 - tests/testthat/test-tx_pvls_den.R | 14 tests/testthat/test-tx_pvls_num.R | 17 tests/testthat/test-tx_regimen.R | 47 +- tests/testthat/test-tx_rtt.R | 38 +- tests/testthat/test-tx_vl_eligible.R | 9 tests/testthat/test-tx_vl_unsuppressed.R | 24 - tests/testthat/test-vl_cascade.R |only vignettes/tidyndr.Rmd | 2 84 files changed, 3225 insertions(+), 3083 deletions(-)
Title: Methods for Calculating Gradient Surface Metrics
Description: Methods for calculating gradient surface metrics for
continuous analysis of landscape features.
Author: Annie C. Smith, Phoebe Zarnetske, Kyla Dahlin, Adam Wilson, Andrew Latimer
Maintainer: Annie C. Smith <annie.smith@dnr.wa.gov>
Diff between geodiv versions 1.0.4 dated 2021-09-03 and 1.0.5 dated 2022-04-08
DESCRIPTION | 6 +++--- MD5 | 40 ++++++++++++++++++++-------------------- NAMESPACE | 1 + NEWS.md | 6 +++++- R/aacf.R | 18 +++++++++--------- R/basics.R | 39 ++++++++++++++++++++------------------- R/bearingarea.R | 34 +++++++++++++++++----------------- R/bestfit.R | 8 ++++---- R/fftshift.R | 4 ++-- R/focalmetrics.R | 2 +- R/fourier.R | 12 ++++++------ R/localsurface.R | 16 ++++++++-------- R/movingwindow.R | 8 ++++---- R/sdq.R | 4 ++-- R/sfd.R | 4 ++-- R/simpsons.R | 12 ++++++------ R/surfacearea.R | 10 +++++----- R/utilities.R | 12 ++++++------ R/zshift.R | 16 ++++++++-------- README.md | 41 ++++++++++++++++++++--------------------- inst/doc/geodiv_vignette.html | 18 +++++++++--------- 21 files changed, 158 insertions(+), 153 deletions(-)
Title: Elastic Analysis of Sparse, Dense and Irregular Curves
Description: Provides functions to align curves and to compute mean curves based on the
elastic distance defined in the square-root-velocity framework. For more details on
this framework see Srivastava and Klassen (2016, <doi:10.1007/978-1-4939-4020-2>).
For more theoretical details on our methods and algorithms see
Steyer et al. (2021, <arXiv:2104.11039>).
Author: Lisa Steyer <lisa.steyer@hu-berlin.de>
Maintainer: Lisa Steyer <lisa.steyer@hu-berlin.de>
Diff between elasdics versions 0.1.5 dated 2022-01-26 and 0.2.0 dated 2022-04-08
DESCRIPTION | 6 ++-- MD5 | 20 ++++++++-------- R/find_optimal_t_discrete.R | 3 ++ R/find_optimal_t_discrete_closed.R | 3 ++ R/fit_mean.R | 36 +++++++++++------------------ R/get_evals.R | 4 ++- tests/testthat/Rplots.pdf |binary tests/testthat/test_align_curves.R | 10 ++++++++ tests/testthat/test_compute_elastic_mean.R | 6 ++++ tests/testthat/test_plot_aligned_curves.R | 10 +++++++- tests/testthat/test_plot_elastic_mean.R | 11 ++++++++ 11 files changed, 71 insertions(+), 38 deletions(-)
Title: 'BLAS' and 'LAPACK' Routines for Native R Matrices and
'big.matrix' Objects
Description: Provides arithmetic functions for R matrix and 'big.matrix' objects as well as functions for QR factorization, Cholesky factorization, General eigenvalue, and Singular value decomposition (SVD). A method matrix multiplication and an arithmetic method -for matrix addition, matrix difference- allows for mixed type operation -a matrix class object and a big.matrix class object- and pure type operation for two big.matrix class objects.
Author: Frederic Bertrand [cre, ctb] ,
Michael J. Kane [aut],
Bryan Lewis [aut],
John W. Emerson [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between bigalgebra versions 1.0.1 dated 2021-05-12 and 1.1.0 dated 2022-04-08
DESCRIPTION | 8 ++--- MD5 | 26 ++++++++-------- NEWS.md | 8 +++++ R/bigalgebra.R | 82 +++++++++++++++++++++++++++-------------------------- R/wrappers.R | 12 +++---- README.md | 14 +++------ inst/CITATION | 4 +- man/dgeev.Rd | 24 +++++++-------- man/dgemm.Rd | 12 +++---- man/dgeqrf.Rd | 4 +- man/dgesdd.Rd | 40 ++++++++++++------------- man/dpotrf.Rd | 14 ++++----- src/Makevars | 2 - src/bigalgebra.cpp | 13 +++++--- 14 files changed, 138 insertions(+), 125 deletions(-)
Title: An Interpretable Machine Learning-Based Automatic Clinical Score
Generator
Description: A novel interpretable machine learning-based framework to automate the development of a clinical scoring model for predefined outcomes. Our novel framework consists of six modules: variable ranking with machine learning, variable transformation, score derivation, model selection, domain knowledge-based score fine-tuning, and performance evaluation.The details are described in our research paper<doi:10.2196/21798>. Users or clinicians could seamlessly generate parsimonious sparse-score risk models (i.e., risk scores), which can be easily implemented and validated in clinical practice. We hope to see its application in various medical case studies.
Author: Feng Xie [aut, cre] ,
Yilin Ning [aut] ,
Han Yuan [aut] ,
Mingxuan Liu [aut] ,
Ehsan Saffari [aut] ,
Bibhas Chakraborty [aut] ,
Nan Liu [aut]
Maintainer: Feng Xie <xief@u.duke.nus.edu>
Diff between AutoScore versions 0.2.0 dated 2021-06-16 and 0.3.0 dated 2022-04-08
DESCRIPTION | 13 MD5 | 42 - NAMESPACE | 7 R/AutoScore.R | 321 ++++++--- inst/CITATION |only inst/doc/Guide_book.R | 83 +- inst/doc/Guide_book.Rmd | 130 +++ inst/doc/Guide_book.html | 1275 ++++++++++++++++++++++-------------- man/AutoScore_parsimony.Rd | 8 man/AutoScore_rank.Rd | 6 man/AutoScore_testing.Rd | 104 +- man/AutoScore_weighting.Rd | 92 +- man/add_baseline.Rd | 38 - man/assign_score.Rd | 38 - man/change_reference.Rd | 38 - man/compute_descriptive_table.Rd | 44 - man/compute_multi_variable_table.Rd | 44 - man/conversion_table.Rd |only man/print_roc_performance.Rd | 48 - man/print_scoring_table.Rd | 44 - man/split_data.Rd | 60 - man/transform_df_fixed.Rd | 38 - vignettes/Guide_book.Rmd | 130 +++ 23 files changed, 1672 insertions(+), 931 deletions(-)