Title: Efficient Plotting of Large-Sized Data
Description: A tool to plot data with a large sample size using 'shiny' and 'plotly'.
Relatively small samples are obtained from the original data using a specific algorithm.
The samples are updated according to a user-defined x range.
Jonas Van Der Donckt, Jeroen Van Der Donckt, Emiel Deprost (2022) <https://github.com/predict-idlab/plotly-resampler>.
Author: Junta Tagusari [aut, cre, cph],
Jonas Van Der Donckt [cph],
Jeroen Van Der Donckt [cph],
Emiel Deprost [cph]
Maintainer: Junta Tagusari <j.tagusari@eng.hokudai.ac.jp>
Diff between shinyHugePlot versions 0.2.1 dated 2022-11-16 and 0.2.2 dated 2022-11-30
shinyHugePlot-0.2.1/shinyHugePlot/tests/dash |only shinyHugePlot-0.2.2/shinyHugePlot/DESCRIPTION | 11 shinyHugePlot-0.2.2/shinyHugePlot/MD5 | 64 ++-- shinyHugePlot-0.2.2/shinyHugePlot/NAMESPACE | 1 shinyHugePlot-0.2.2/shinyHugePlot/NEWS.md | 5 shinyHugePlot-0.2.2/shinyHugePlot/R/LTTB_aggregator.R | 2 shinyHugePlot-0.2.2/shinyHugePlot/R/aggregator.R | 2 shinyHugePlot-0.2.2/shinyHugePlot/R/downsampler.R | 78 +++-- shinyHugePlot-0.2.2/shinyHugePlot/R/min_max_aggregator.R | 2 shinyHugePlot-0.2.2/shinyHugePlot/R/noise_fluct.R | 14 - shinyHugePlot-0.2.2/shinyHugePlot/R/plotly_build_light.R | 2 shinyHugePlot-0.2.2/shinyHugePlot/R/plotly_datahandler.R | 134 +++++----- shinyHugePlot-0.2.2/shinyHugePlot/R/rng_aggregator.R | 14 - shinyHugePlot-0.2.2/shinyHugePlot/R/shinyHugePlot.R | 5 shinyHugePlot-0.2.2/shinyHugePlot/R/shiny_hugeplot.R | 113 +++++--- shinyHugePlot-0.2.2/shinyHugePlot/R/updatePlotlyH.R | 46 --- shinyHugePlot-0.2.2/shinyHugePlot/README.md | 41 +-- shinyHugePlot-0.2.2/shinyHugePlot/man/aggregator.Rd | 2 shinyHugePlot-0.2.2/shinyHugePlot/man/downsampler.Rd | 77 +++-- shinyHugePlot-0.2.2/shinyHugePlot/man/min_max_aggregator.Rd | 2 shinyHugePlot-0.2.2/shinyHugePlot/man/noise_fluct.Rd | 10 shinyHugePlot-0.2.2/shinyHugePlot/man/plotly_build_light.Rd | 2 shinyHugePlot-0.2.2/shinyHugePlot/man/plotly_datahandler.Rd | 45 +-- shinyHugePlot-0.2.2/shinyHugePlot/man/rng_aggregator.Rd | 14 - shinyHugePlot-0.2.2/shinyHugePlot/man/shinyHugePlot.Rd | 5 shinyHugePlot-0.2.2/shinyHugePlot/man/shiny_hugeplot.Rd | 100 ++++--- shinyHugePlot-0.2.2/shinyHugePlot/man/updatePlotlyH.Rd | 48 --- shinyHugePlot-0.2.2/shinyHugePlot/tests/manual/test-addtrace.R | 14 - shinyHugePlot-0.2.2/shinyHugePlot/tests/manual/test-shiny.R | 112 +++----- shinyHugePlot-0.2.2/shinyHugePlot/tests/testthat/test-downsampler.R | 95 +++---- 30 files changed, 575 insertions(+), 485 deletions(-)
Title: Random Forests, Linear Trees, and Gradient Boosting for
Inference and Interpretability
Description: Provides fast implementations of Honest Random Forests,
Gradient Boosting, and Linear Random Forests, with an emphasis on inference
and interpretability. Additionally contains methods for variable
importance, out-of-bag prediction, regression monotonicity, and
several methods for missing data imputation. Soren R. Kunzel,
Theo F. Saarinen, Edward W. Liu, Jasjeet S. Sekhon (2019) <arXiv:1906.06463>.
Author: Soeren Kuenzel [aut],
Theo Saarinen [aut, cre],
Simon Walter [aut],
Edward Liu [aut],
Allen Tang [aut],
Jasjeet Sekhon [aut]
Maintainer: Theo Saarinen <theo_s@berkeley.edu>
Diff between Rforestry versions 0.9.0.116 dated 2022-07-21 and 0.9.0.144 dated 2022-11-30
DESCRIPTION | 8 MD5 | 56 ++-- R/RcppExports.R | 12 R/compute_rf_lp.R | 63 ++++- R/forestry.R | 395 +++++++++++--------------------- R/plottree.R | 68 ++--- man/compute_lp-forestry.Rd | 26 ++ man/correctedPredict-forestry.Rd | 33 -- man/forestry.Rd | 30 +- man/multilayer-forestry.Rd | 22 - src/RFNode.cpp | 269 ++++++++++++++++----- src/RFNode.h | 30 ++ src/RcppExports.cpp | 27 +- src/forestry.cpp | 278 ++++++---------------- src/forestry.h | 23 + src/forestryTree.cpp | 182 +++++++------- src/forestryTree.h | 13 - src/multilayerForestry.cpp | 1 src/rcpp_cppBuildInterface.cpp | 139 ++++------- src/sampling.cpp |only src/sampling.h |only src/utils.cpp | 38 --- src/utils.h | 22 - tests/testthat/test-compute_rf_lp.R | 15 - tests/testthat/test-correctedPredict.R | 15 - tests/testthat/test-groupSampling.R | 95 ++++++- tests/testthat/test-impute_features.R | 8 tests/testthat/test-nodesizeStrictAvg.R | 2 tests/testthat/test-plottree.R | 21 + tests/testthat/test-saveMultilayer.R | 1 30 files changed, 952 insertions(+), 940 deletions(-)
Title: Word Embedding Research Framework for Psychological Science
Description: An integrated toolbox of word embedding research that provides:
(1) a collection of 'pre-trained' static word vectors in the '.RData'
compressed format <https://psychbruce.github.io/WordVector_RData.pdf>;
(2) a series of functions to process, analyze, and visualize word vectors;
(3) a range of tests to examine conceptual associations, including
the Word Embedding Association Test <doi:10.1126/science.aal4230>
and the Relative Norm Distance <doi:10.1073/pnas.1720347115>,
with permutation test of significance;
(4) a set of training methods to locally train (static) word vectors
from text corpora, including 'Word2Vec' <arXiv:1301.3781>,
'GloVe' <doi:10.3115/v1/D14-1162>, and 'FastText' <arXiv:1607.04606>;
(5) a group of functions to download 'pre-trained' language models
(e.g., 'GPT', 'BERT'), extract contextualized (dynamic) word vectors
(based on the R package 'text'), and perform language analysis tasks
(e.g., fill in the blank masks).
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between PsychWordVec versions 0.1.2 dated 2022-11-03 and 0.2.0 dated 2022-11-30
PsychWordVec-0.1.2/PsychWordVec/R/PsychWordVec.R |only PsychWordVec-0.1.2/PsychWordVec/man/data_wordvec_reshape.Rd |only PsychWordVec-0.2.0/PsychWordVec/DESCRIPTION | 30 ++- PsychWordVec-0.2.0/PsychWordVec/MD5 | 62 ++++--- PsychWordVec-0.2.0/PsychWordVec/NAMESPACE | 29 +++ PsychWordVec-0.2.0/PsychWordVec/NEWS.md | 45 +++++ PsychWordVec-0.2.0/PsychWordVec/R/PWV1_static.R |only PsychWordVec-0.2.0/PsychWordVec/R/PWV2_dynamic.R |only PsychWordVec-0.2.0/PsychWordVec/R/utils.R | 85 +++++++++- PsychWordVec-0.2.0/PsychWordVec/README.md | 49 +++-- PsychWordVec-0.2.0/PsychWordVec/man/as_wordvec.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/cosine_similarity.Rd | 22 +- PsychWordVec-0.2.0/PsychWordVec/man/data_transform.Rd | 24 ++ PsychWordVec-0.2.0/PsychWordVec/man/data_wordvec_load.Rd | 28 ++- PsychWordVec-0.2.0/PsychWordVec/man/data_wordvec_normalize.Rd | 16 + PsychWordVec-0.2.0/PsychWordVec/man/data_wordvec_subset.Rd | 64 ++++--- PsychWordVec-0.2.0/PsychWordVec/man/demodata.Rd | 9 - PsychWordVec-0.2.0/PsychWordVec/man/dict_expand.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/dict_reliability.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/figures |only PsychWordVec-0.2.0/PsychWordVec/man/get_wordvec.Rd | 11 - PsychWordVec-0.2.0/PsychWordVec/man/get_wordvecs.Rd | 13 - PsychWordVec-0.2.0/PsychWordVec/man/most_similar.Rd | 43 +++-- PsychWordVec-0.2.0/PsychWordVec/man/orth_procrustes.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/pair_similarity.Rd | 9 - PsychWordVec-0.2.0/PsychWordVec/man/plot_similarity.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/plot_wordvec.Rd | 22 +- PsychWordVec-0.2.0/PsychWordVec/man/plot_wordvec_tSNE.Rd | 16 + PsychWordVec-0.2.0/PsychWordVec/man/reexports.Rd | 2 PsychWordVec-0.2.0/PsychWordVec/man/sum_wordvec.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/tab_similarity.Rd | 41 +++- PsychWordVec-0.2.0/PsychWordVec/man/test_RND.Rd | 36 ++-- PsychWordVec-0.2.0/PsychWordVec/man/test_WEAT.Rd | 34 ++-- PsychWordVec-0.2.0/PsychWordVec/man/text_init.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/text_model_download.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/text_model_remove.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/text_to_vec.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/text_unmask.Rd |only PsychWordVec-0.2.0/PsychWordVec/man/tokenize.Rd | 13 - PsychWordVec-0.2.0/PsychWordVec/man/train_wordvec.Rd | 39 ++-- 40 files changed, 520 insertions(+), 222 deletions(-)
Title: Superior Identification Index and Its Extensions
Description: Calculate superior identification index and its extensions.
Measure the performance of journals based on how well they could
identify the top papers by any index (e.g. citation indices) according to Huang & Yang.
(2022) <doi:10.1007/s11192-022-04372-z>. These methods could be extended to
evaluate other entities such as institutes, countries, etc.
Author: Tian-Yuan Huang [aut, cre]
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between siie versions 0.2.0 dated 2022-11-24 and 0.3.0 dated 2022-11-30
DESCRIPTION | 6 - MD5 | 10 +-- inst/doc/Introduction.R | 10 ++- inst/doc/Introduction.Rmd | 35 ++++++++--- inst/doc/Introduction.html | 138 ++++++++++++++++++++++++--------------------- vignettes/Introduction.Rmd | 35 ++++++++--- 6 files changed, 142 insertions(+), 92 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Helps with trivial but tedious tasks and tries to identify errors to save time on debugging. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.0.14 dated 2022-11-16 and 0.0.15 dated 2022-11-30
DESCRIPTION | 8 +- MD5 | 80 ++++++++++---------- NEWS.md | 7 + R/NMscanInput.R | 6 + R/NMtransInp.R | 3 R/addTAPD.R | 1 R/summary_NMdata.R | 6 - tests/testthat/testOutput/NMwriteData10.rds |binary tests/testthat/testOutput/NMwriteData11.rds |binary tests/testthat/testReference/NMcheckColnames_1.rds |binary tests/testthat/testReference/NMcheckColnames_2.rds |binary tests/testthat/testReference/NMcheckDataFile_01.rds |binary tests/testthat/testReference/NMscanData1.rds |binary tests/testthat/testReference/NMscanData11.rds |binary tests/testthat/testReference/NMscanData13.rds |binary tests/testthat/testReference/NMscanData14.rds |binary tests/testthat/testReference/NMscanData15b.rds |binary tests/testthat/testReference/NMscanData16.rds |binary tests/testthat/testReference/NMscanData17.rds |binary tests/testthat/testReference/NMscanData18.rds |binary tests/testthat/testReference/NMscanData2.rds |binary tests/testthat/testReference/NMscanData20.rds |binary tests/testthat/testReference/NMscanData22.rds |binary tests/testthat/testReference/NMscanData23.rds |binary tests/testthat/testReference/NMscanData24.rds |binary tests/testthat/testReference/NMscanData25.rds |binary tests/testthat/testReference/NMscanData27.rds |binary tests/testthat/testReference/NMscanData28.rds |binary tests/testthat/testReference/NMscanData28b.rds |binary tests/testthat/testReference/NMscanData3.rds |binary tests/testthat/testReference/NMscanData4.rds |binary tests/testthat/testReference/NMscanData_31.rds |binary tests/testthat/testReference/NMscanInput4.rds |binary tests/testthat/testReference/NMscanInput6.rds |binary tests/testthat/testReference/NMscanInput_08.rds |binary tests/testthat/testReference/NMscanInput_1.rds |binary tests/testthat/testReference/NMscanInput_2.rds |binary tests/testthat/testReference/NMscanInput_7.rds |binary tests/testthat/test_NMcheckColnames.R | 3 tests/testthat/test_NMwriteData.R | 4 - tests/testthat/test_addTAPD.R | 3 41 files changed, 62 insertions(+), 59 deletions(-)
Title: Explainable Machine Learning in Survival Analysis
Description: Survival analysis models are commonly used in medicine and other areas. Many of them
are too complex to be interpreted by human. Exploration and explanation is needed, but
standard methods do not give a broad enough picture. 'survex' provides easy-to-apply
methods for explaining survival models, both complex black-boxes and simpler statistical models.
They include methods specific to survival analysis such as SurvSHAP(t) described in Krzyzinski et al., (2022)
<arXiv:2208.11080>, SurvLIME introduced in Kovalev et al., (2020) <doi:10.1016/j.knosys.2020.106164> as well as
extensions of existing ones described in Biecek et al., (2021) <doi:10.1201/9780429027192>.
Author: Mikolaj Spytek [aut, cre],
Mateusz Krzyzinski [aut],
Hubert Baniecki [aut] ,
Przemyslaw Biecek [aut]
Maintainer: Mikolaj Spytek <mikolajspytek@gmail.com>
Diff between survex versions 0.1.1 dated 2022-09-05 and 0.2.2 dated 2022-11-30
DESCRIPTION | 13 MD5 | 170 +++--- NAMESPACE | 5 NEWS.md | 16 R/explain.R | 200 +++---- R/metrics.R | 233 ++++++-- R/model_info.R | 264 ++++----- R/model_parts.R | 212 +++---- R/model_performance.R | 147 ++--- R/model_profile.R | 32 - R/plot_feature_importance.R |only R/plot_model_parts_survival.R | 5 R/plot_model_performance_survival.R | 12 R/plot_model_profile_survival.R | 35 - R/plot_predict_parts_survival.R | 101 +-- R/plot_predict_profile_survival.R | 107 +-- R/plot_surv_ceteris_paribus.R | 492 ++++++++--------- R/plot_surv_feature_importance.R | 177 +++--- R/plot_surv_lime.R | 40 - R/plot_surv_model_performance.R | 277 +++++---- R/plot_surv_model_performance_rocs.R | 27 R/plot_surv_shap.R | 133 ++-- R/predict_parts.R | 179 +++--- R/predict_profile.R | 49 - R/predict_surv_explainer.R | 8 R/surv_aggregate_profiles.R | 3 R/surv_ceteris_paribus.R | 2 R/surv_feature_importance.R | 88 +-- R/surv_integrated_feature_importance.R | 23 R/surv_lime.R | 5 R/surv_model_performance.R | 39 - R/surv_shap.R | 6 README.md | 53 + inst/doc/custom-explainers.Rmd | 228 ++++---- inst/doc/custom-explainers.html | 19 inst/doc/survex-usage.R | 37 + inst/doc/survex-usage.Rmd | 391 +++++++------ inst/doc/survex-usage.html | 56 - man/brier_score.Rd | 10 man/c_index.Rd | 12 man/cd_auc.Rd | 16 man/cumulative_hazard_to_survival.Rd | 56 - man/explain_survival.Rd | 151 +---- man/integrated_brier_score.Rd | 26 man/integrated_cd_auc.Rd | 22 man/loss_adapt_mlr3proba.Rd |only man/loss_integrate.Rd |only man/loss_one_minus_c_index.Rd | 7 man/loss_one_minus_cd_auc.Rd | 6 man/loss_one_minus_integrated_cd_auc.Rd | 16 man/model_parts.surv_explainer.Rd | 7 man/model_performance.surv_explainer.Rd | 38 + man/model_profile.surv_explainer.Rd | 5 man/plot.feature_importance_explainer.Rd |only man/plot.model_parts_survival.Rd | 5 man/plot.model_performance_survival.Rd | 12 man/plot.model_profile_survival.Rd | 14 man/plot.predict_parts_survival.Rd | 9 man/plot.predict_profile_survival.Rd | 7 man/plot.surv_ceteris_paribus.Rd | 10 man/plot.surv_feature_importance.Rd | 11 man/plot.surv_lime.Rd | 12 man/plot.surv_model_performance.Rd | 9 man/plot.surv_model_performance_rocs.Rd | 12 man/plot.surv_shap.Rd | 12 man/predict.surv_explainer.Rd | 6 man/predict_parts.surv_explainer.Rd | 13 man/predict_profile.surv_explainer.Rd | 3 man/risk_from_chf.Rd | 72 +- man/surv_aggregate_profiles.Rd | 76 +- man/surv_ceteris_paribus.Rd | 2 man/surv_feature_importance.Rd | 8 man/surv_integrated_feature_importance.Rd | 96 +-- man/surv_lime.Rd | 9 man/surv_model_info.Rd | 140 ++-- man/surv_model_performance.Rd | 12 man/surv_shap.Rd | 11 man/survival_to_cumulative_hazard.Rd | 60 +- man/transform_to_stepfunction.Rd | 96 +-- tests/testthat/Rplots.pdf |binary tests/testthat/test-explain.R | 842 +++++++++++++++--------------- tests/testthat/test-model_parts.R | 14 tests/testthat/test-model_performance.R | 32 - tests/testthat/test-model_profile.R | 146 ++--- tests/testthat/test-predict_parts.R | 190 +++--- tests/testthat/test-utils.R | 178 +++--- vignettes/custom-explainers.Rmd | 228 ++++---- vignettes/survex-usage.Rmd | 391 +++++++------ 88 files changed, 3656 insertions(+), 3338 deletions(-)
Title: Graph-Constrained Robust Covariance Estimation
Description: Contains a function by the same name,
which provides two types of robust t-M-estimators of scatter
subject to zero-constraints in the inverse. The methodology
is described in Vogel & Tyler (2014) <doi:10.1093/biomet/asu041>.
See the robFitConGraph function documentation for further details.
A tutorial including background information is given by
Vogel, Watt & Wiedemann (2022) <arXiv:2204.04291>.
Author: Stuart Watt, Daniel Vogel
Maintainer: Daniel Vogel <daniel.vogel@tu-dortmund.de>
Diff between robFitConGraph versions 0.1.0 dated 2019-02-08 and 0.4.1 dated 2022-11-30
robFitConGraph-0.1.0/robFitConGraph/R/auxFunc.R |only robFitConGraph-0.1.0/robFitConGraph/src/auxFuncC.cpp |only robFitConGraph-0.4.1/robFitConGraph/DESCRIPTION | 26 robFitConGraph-0.4.1/robFitConGraph/MD5 | 36 robFitConGraph-0.4.1/robFitConGraph/NAMESPACE | 2 robFitConGraph-0.4.1/robFitConGraph/R/MLEfunc.R | 469 +++++++--- robFitConGraph-0.4.1/robFitConGraph/R/PackageDescription.R | 16 robFitConGraph-0.4.1/robFitConGraph/R/RcppExports.R | 16 robFitConGraph-0.4.1/robFitConGraph/R/SigmaFunctions.R |only robFitConGraph-0.4.1/robFitConGraph/R/cov_trob_fast.R |only robFitConGraph-0.4.1/robFitConGraph/R/data.R |only robFitConGraph-0.4.1/robFitConGraph/data |only robFitConGraph-0.4.1/robFitConGraph/man/anxieties.Rd |only robFitConGraph-0.4.1/robFitConGraph/man/find_eta.Rd |only robFitConGraph-0.4.1/robFitConGraph/man/find_sigma1.Rd |only robFitConGraph-0.4.1/robFitConGraph/man/robFitConGraph-package.Rd | 36 robFitConGraph-0.4.1/robFitConGraph/man/robFitConGraph.Rd | 466 +++++---- robFitConGraph-0.4.1/robFitConGraph/src/CapplyC.cpp |only robFitConGraph-0.4.1/robFitConGraph/src/CapplyC.h |only robFitConGraph-0.4.1/robFitConGraph/src/Makevars |only robFitConGraph-0.4.1/robFitConGraph/src/Makevars.win |only robFitConGraph-0.4.1/robFitConGraph/src/RcppExports.cpp | 69 + robFitConGraph-0.4.1/robFitConGraph/src/covTrobC.cpp |only robFitConGraph-0.4.1/robFitConGraph/src/mahalanobis_fast_aux.cpp |only robFitConGraph-0.4.1/robFitConGraph/src/mahalanobis_fast_aux.h |only robFitConGraph-0.4.1/robFitConGraph/src/myFitConGraphC.cpp |only robFitConGraph-0.4.1/robFitConGraph/src/myFitConGraphC_alt.cpp |only robFitConGraph-0.4.1/robFitConGraph/src/myFitConGraphC_alt.h |only robFitConGraph-0.4.1/robFitConGraph/src/regMLEdirect_loop.cpp |only 29 files changed, 754 insertions(+), 382 deletions(-)
More information about robFitConGraph at CRAN
Permanent link
Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and
their confidence intervals using methods approved for use in the production
of Public Health England indicators such as those presented via Fingertips
(<http://fingertips.phe.org.uk/>). It provides functions for the generation
of proportions, crude rates, means, directly standardised rates, indirectly
standardised rates, standardised mortality ratios, slope and relative index
of inequality and life expectancy.
Statistical methods are referenced in the following publications.
Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>.
Dobson et al (1991) <doi:10.1002/sim.4780100317>.
Armitage P, Berry G (2002) <doi:10.1002/9780470773666>.
Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>.
Altman DG et al (2000, ISBN: 978-0-727-91375-3).
Chiang CL. (1968, ISBN: 978-0-882-75200-6).
Newell C. (1994, ISBN: 978-0-898-62451-9).
Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>.
Si [...truncated...]
Author: Anderson Georgina [aut, cre],
Fox Sebastian [ctb],
Francis Matthew [ctb],
Fryers Paul [ctb],
Clegg Emma [ctb]
Maintainer: Anderson Georgina <georgina.anderson@dhsc.gov.uk>
Diff between PHEindicatormethods versions 1.4.1 dated 2022-08-08 and 1.4.2 dated 2022-11-30
DESCRIPTION | 10 MD5 | 44 - NAMESPACE | 4 NEWS.md | 3 R/DSR.R | 86 +- R/Funnels.R | 2 R/ISR_deprecated.R | 61 - R/ISRate.R | 61 - R/ISRatio.R | 63 - R/LifeExpectancy.R | 147 ++-- R/Means.R | 37 - R/PHEindicatormethods.R | 72 -- R/Proportions.R | 16 R/Quantiles.R | 23 R/Rates.R | 17 R/SII_function.R | 95 +- R/SMR_deprecated.R | 61 - R/utils.R | 1 README.md | 2 build/vignette.rds |binary inst/doc/DSR-vignette.html | 170 ++--- inst/doc/Introduction_to_PHEindicatormethods.html | 739 +++++++++++----------- inst/doc/WorkedExamples_phe_sii.html | 209 +++--- 23 files changed, 959 insertions(+), 964 deletions(-)
More information about PHEindicatormethods at CRAN
Permanent link
Title: Match Cases to Controls Based on Genotype Principal Components
Description: Matches cases to controls based on genotype principal components (PC).
In order to produce better results, matches are based on the weighted
distance of PCs where the weights are equal to the % variance explained
by that PC. A weighted Mahalanobis distance metric (Kidd et al. (1987)
<DOI:10.1016/0031-3203(87)90066-5>) is used to determine matches.
Author: Derek W. Brown [aut, cre] ,
Mitchel J. Machiela [aut] ,
Timothy A. Myers [ctb] ,
NCI [cph, fnd]
Maintainer: Derek W. Brown <derek9@gwmail.gwu.edu>
Diff between PCAmatchR versions 0.3.2 dated 2022-03-01 and 0.3.3 dated 2022-11-30
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 6 ++++++ 3 files changed, 14 insertions(+), 8 deletions(-)
Title: Implements Generalized Meta-Analysis Using Iterated Reweighted
Least Squares Algorithm
Description: Generalized meta-analysis is a technique for estimating parameters associated with a multiple regression model through meta-analysis of studies which may have information only on partial sets of the regressors. It estimates the effects of each variable while fully adjusting for all other variables that are measured in at least one of the studies. Using algebraic relationships between regression parameters in different dimensions, a set of moment equations is specified for estimating the parameters of a maximal model through information available on sets of parameter estimates from a series of reduced models available from the different studies. The specification of the equations requires a reference dataset to estimate the joint distribution of the covariates. These equations are solved using the generalized method of moments approach, with the optimal weighting of the equations taking into account uncertainty associated with estimates of the parameters of the reduced models. The propo [...truncated...]
Author: Prosenjit Kundu [aut, cre],
Runlong Tang [aut],
Nilanjan Chatterjee [aut]
Maintainer: Prosenjit Kundu <28pkundu1992@gmail.com>
Diff between GENMETA versions 0.1 dated 2018-12-03 and 0.2.0 dated 2022-11-30
DESCRIPTION | 17 +++----- MD5 | 10 ++-- NAMESPACE | 7 +++ R/GENMETA.R | 59 ++++++++++++++++------------ R/myoptim.R | 116 +++++++++++++++++++++++++++++++++++++++++++++++++-------- man/GENMETA.Rd | 13 ++++-- 6 files changed, 164 insertions(+), 58 deletions(-)
Title: Early Detection of Public Health Threats from 'Twitter' Data
Description: It allows you to automatically monitor trends of tweets by time, place and topic aiming at detecting public health threats early through the detection of signals (e.g. an unusual increase in the number of tweets). It was designed to focus on infectious diseases, and it can be extended to all hazards or other fields of study by modifying the topics and keywords. More information is available in the 'epitweetr' peer-review publication (<https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2022.27.39.2200177>).
Author: Laura Espinosa [aut, fnd, cre]
,
Francisco Orchard [aut, ctr] ,
Ariana Wijermans [ctb] ,
Thomas Mollet [ctb, fnd] ,
Adrian Prodan [ctb],
Thomas Czernichow [ctb],
Maria Prieto Gonzalez [ctb],
Esther Kissling [ctb],
Michael Hoehle [ctb]
Maintainer: Laura Espinosa <laura.espinosa@ecdc.europa.eu>
Diff between epitweetr versions 2.0.3 dated 2022-01-05 and 2.2.13 dated 2022-11-30
DESCRIPTION | 24 - MD5 | 92 +++--- NAMESPACE | 10 R/aggregate.R | 70 ++--- R/alert.R | 220 ++++++++++++++-- R/check.R | 300 ++++++++++++++++++++-- R/config.R | 26 + R/dataviz.R | 33 +- R/fs.R | 14 - R/geo-tagging.R | 25 + R/migration.R | 9 R/paths.R | 59 +++- R/scheduler.R | 361 +++++++++++++++++++++++--- R/search.R | 10 R/shiny-app.R | 215 ++++++++++++--- R/spark-bridge.R | 26 - R/twitter-api.R | 65 +++- build/vignette.rds |binary inst/doc/epitweetr-vignette.Rmd | 293 ++++++++++++--------- inst/doc/epitweetr-vignette.html | 368 ++++++++++++++------------- inst/extdata/sbt-deps.txt | 2 inst/extdata/topics.xlsx |binary inst/extdata/users.xlsx |binary inst/java/ecdc-twitter-bundle_2.12-1.0.jar |binary java/ecdc-twitter-bundle_2.12-1.0-source.zip |binary man/create_snapshot.Rd |only man/create_topchart.Rd | 2 man/create_topwords.Rd | 2 man/detect_loop.Rd | 2 man/download_dependencies.Rd | 4 man/fs_loop.Rd | 2 man/generate_alerts.Rd | 2 man/geolocate_text.Rd | 6 man/get_alerts.Rd | 3 man/get_todays_sample_tweets.Rd | 6 man/health_check.Rd | 4 man/is_detect_running.Rd |only man/is_fs_running.Rd |only man/is_search_running.Rd |only man/json2lucene.Rd | 3 man/register_detect_runner_task.Rd |only man/register_fs_monitor.Rd | 6 man/register_fs_runner_task.Rd |only man/register_search_runner_task.Rd |only man/search_tweets.Rd | 2 man/set_twitter_app_auth.Rd | 16 - man/stop_detect_runner_task.Rd |only man/stop_fs_runner_task.Rd |only man/stop_search_runner_task.Rd |only man/update_geonames.Rd | 2 man/update_languages.Rd | 2 vignettes/epitweetr-vignette.Rmd | 293 ++++++++++++--------- 52 files changed, 1820 insertions(+), 759 deletions(-)
Title: Sample Size and Power Calculations using the APPLE, SEPPLE,
APPLE+ and SEPPLE+ Methods
Description: Provides sample size and power calculations when the treatment time-lag effect is present and the lag duration is either homogeneous across the individual subject, or varies heterogeneously from individual to individual within a certain domain and following a specific pattern. The methods used are described in Xu, Z., Zhen, B., Park, Y., & Zhu, B. (2017) <doi:10.1002/sim.7157>.
Author: Zhenzhen Xu <Zhenzhen.Xu@fda.hhs.gov> , Boguang Zhen<Boguang.Zhen@fda.hhs.gov>, Yongsoek Park <yongpark@pitt.edu> and Bin Zhu <bin.zhu@nih.gov>
Maintainer: Bill Wheeler <wheelerb@imsweb.com>
Diff between DelayedEffect.Design versions 0.0.4 dated 2017-09-01 and 1.1.2 dated 2022-11-30
DESCRIPTION | 20 +-- MD5 | 29 ++++- NAMESPACE | 8 - R/source.R | 207 +++++++---------------------------------- R/source_check.R |only R/source_plus.R |only data |only man/GPW.logrank.Rd |only man/HR.APPLE.plus.Rd |only man/N.APPLE.Rd | 2 man/N.APPLE.plus.Rd |only man/data.Rd |only man/package.Rd | 49 +++++---- man/pow.APPLE.Rd | 2 man/pow.APPLE.plus.Rd |only man/pow.SEPPLE.Rd | 2 man/pow.SEPPLE.plus.Rd |only man/pow.SEPPLE.random.DE.Rd |only man/pow.logRank.Rd | 2 man/pow.sim.logrk.random.DE.Rd |only src |only 21 files changed, 107 insertions(+), 214 deletions(-)
More information about DelayedEffect.Design at CRAN
Permanent link
Title: Development Tools for the Admiral Package Family
Description: Utility functions to check data, variables and conditions for functions used in
'admiral' and 'admiral' extension packages. Additional utility helper functions to assist developers
with maintaining documentation, testing and general upkeep of 'admiral' and 'admiral' extension packages.
Author: Ben Straub [aut, cre],
Stefan Bundfuss [aut],
Thomas Neitmann [aut],
Samia Kabi [aut],
Pooja Kumari [aut],
Syed Mubasheer [aut],
Ross Farrugia [aut],
Sadchla Mascary [aut],
Zelos Zhu [aut],
Jeffrey Dickinson [aut],
Ania Golab [aut],
Ondrej Slama [ctb [...truncated...]
Maintainer: Ben Straub <ben.x.straub@gsk.com>
Diff between admiraldev versions 0.1.0 dated 2022-08-26 and 0.2.0 dated 2022-11-30
admiraldev-0.1.0/admiraldev/R/reexports.R |only admiraldev-0.1.0/admiraldev/man/is_date.Rd |only admiraldev-0.1.0/admiraldev/man/is_timeunit.Rd |only admiraldev-0.1.0/admiraldev/man/is_valid_date_entry.Rd |only admiraldev-0.1.0/admiraldev/man/is_valid_day.Rd |only admiraldev-0.1.0/admiraldev/man/is_valid_hour.Rd |only admiraldev-0.1.0/admiraldev/man/is_valid_month.Rd |only admiraldev-0.1.0/admiraldev/man/is_valid_sec_min.Rd |only admiraldev-0.1.0/admiraldev/man/is_valid_time_entry.Rd |only admiraldev-0.1.0/admiraldev/man/negate_vars.Rd |only admiraldev-0.1.0/admiraldev/man/reexports.Rd |only admiraldev-0.1.0/admiraldev/man/set_dataset.Rd |only admiraldev-0.2.0/admiraldev/DESCRIPTION | 26 admiraldev-0.2.0/admiraldev/MD5 | 173 - admiraldev-0.2.0/admiraldev/NAMESPACE | 23 admiraldev-0.2.0/admiraldev/NEWS.md | 35 admiraldev-0.2.0/admiraldev/R/addin_format_testthat.R | 22 admiraldev-0.2.0/admiraldev/R/admiraldev-package.R | 9 admiraldev-0.2.0/admiraldev/R/admiraldev_environment.R |only admiraldev-0.2.0/admiraldev/R/assertions.R | 230 ++ admiraldev-0.2.0/admiraldev/R/datasets.R | 33 admiraldev-0.2.0/admiraldev/R/dev_utilities.R | 73 admiraldev-0.2.0/admiraldev/R/expect_dfs_equal.R | 35 admiraldev-0.2.0/admiraldev/R/get.R | 8 admiraldev-0.2.0/admiraldev/R/global.R | 1 admiraldev-0.2.0/admiraldev/R/is.R | 250 -- admiraldev-0.2.0/admiraldev/R/quo.R | 134 + admiraldev-0.2.0/admiraldev/R/tmp_vars.R | 2 admiraldev-0.2.0/admiraldev/R/warnings.R | 2 admiraldev-0.2.0/admiraldev/README.md | 24 admiraldev-0.2.0/admiraldev/build/vignette.rds |binary admiraldev-0.2.0/admiraldev/inst/WORDLIST | 2 admiraldev-0.2.0/admiraldev/inst/doc/admiraldev.Rmd | 10 admiraldev-0.2.0/admiraldev/inst/doc/admiraldev.html | 23 admiraldev-0.2.0/admiraldev/man/add_suffix_to_vars.Rd |only admiraldev-0.2.0/admiraldev/man/admiraldev-package.Rd | 7 admiraldev-0.2.0/admiraldev/man/arg_name.Rd | 3 admiraldev-0.2.0/admiraldev/man/as_name.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_atomic_vector.Rd |only admiraldev-0.2.0/admiraldev/man/assert_character_scalar.Rd | 6 admiraldev-0.2.0/admiraldev/man/assert_character_vector.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_data_frame.Rd | 6 admiraldev-0.2.0/admiraldev/man/assert_date_vector.Rd |only admiraldev-0.2.0/admiraldev/man/assert_expr.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_filter_cond.Rd | 9 admiraldev-0.2.0/admiraldev/man/assert_function.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_function_param.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_has_variables.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_integer_scalar.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_list_element.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_list_of.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_logical_scalar.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_named_exprs.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_numeric_vector.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_one_to_one.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_order_vars.Rd | 7 admiraldev-0.2.0/admiraldev/man/assert_param_does_not_exist.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_s3_class.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_same_type.Rd |only admiraldev-0.2.0/admiraldev/man/assert_symbol.Rd | 9 admiraldev-0.2.0/admiraldev/man/assert_unit.Rd | 3 admiraldev-0.2.0/admiraldev/man/assert_vars.Rd | 21 admiraldev-0.2.0/admiraldev/man/assert_varval_list.Rd | 5 admiraldev-0.2.0/admiraldev/man/contains_vars.Rd |only admiraldev-0.2.0/admiraldev/man/convert_dtm_to_dtc.Rd | 3 admiraldev-0.2.0/admiraldev/man/expect_dfs_equal.Rd | 36 admiraldev-0.2.0/admiraldev/man/extract_vars.Rd | 3 admiraldev-0.2.0/admiraldev/man/filter_if.Rd | 3 admiraldev-0.2.0/admiraldev/man/get_dataset.Rd | 8 admiraldev-0.2.0/admiraldev/man/grapes-notin-grapes.Rd | 3 admiraldev-0.2.0/admiraldev/man/grapes-or-grapes.Rd | 3 admiraldev-0.2.0/admiraldev/man/is_auto.Rd | 10 admiraldev-0.2.0/admiraldev/man/is_named.Rd | 10 admiraldev-0.2.0/admiraldev/man/is_order_vars.Rd | 16 admiraldev-0.2.0/admiraldev/man/is_valid_dtc.Rd | 10 admiraldev-0.2.0/admiraldev/man/quo_c.Rd | 5 admiraldev-0.2.0/admiraldev/man/quo_not_missing.Rd | 5 admiraldev-0.2.0/admiraldev/man/remove_tmp_vars.Rd | 2 admiraldev-0.2.0/admiraldev/man/replace_symbol_in_quo.Rd |only admiraldev-0.2.0/admiraldev/man/replace_values_by_names.Rd | 22 admiraldev-0.2.0/admiraldev/man/valid_time_units.Rd | 5 admiraldev-0.2.0/admiraldev/man/vars2chr.Rd | 5 admiraldev-0.2.0/admiraldev/man/warn_if_inconsistent_list.Rd | 2 admiraldev-0.2.0/admiraldev/tests/testthat/test-addin_format_testthat.R | 12 admiraldev-0.2.0/admiraldev/tests/testthat/test-assertions.R | 972 +++++++++- admiraldev-0.2.0/admiraldev/tests/testthat/test-compat_friendly_type.R | 66 admiraldev-0.2.0/admiraldev/tests/testthat/test-dataset_vignette.R | 53 admiraldev-0.2.0/admiraldev/tests/testthat/test-dev_utilities.R | 56 admiraldev-0.2.0/admiraldev/tests/testthat/test-get.R | 33 admiraldev-0.2.0/admiraldev/tests/testthat/test-is.R | 37 admiraldev-0.2.0/admiraldev/tests/testthat/test-quo.R | 129 + admiraldev-0.2.0/admiraldev/tests/testthat/test-quote.R | 12 admiraldev-0.2.0/admiraldev/tests/testthat/test-test_helpers.R | 4 admiraldev-0.2.0/admiraldev/tests/testthat/test-tmp_vars.R | 13 admiraldev-0.2.0/admiraldev/tests/testthat/test-warnings.R | 28 admiraldev-0.2.0/admiraldev/tests/testthat/test-what.R | 16 admiraldev-0.2.0/admiraldev/vignettes/admiraldev.Rmd | 10 97 files changed, 2110 insertions(+), 718 deletions(-)
Title: Algorithms for Helping Build Dynamic TOPMODEL Implementations
from Spatial Data
Description: A set of algorithms based on Quinn et al. (1991) <doi:10.1002/hyp.3360050106> for processing river network and digital elevation data to build implementations of Dynamic TOPMODEL, a semi-distributed hydrological model proposed in Beven and Freer (2001) <doi:10.1002/hyp.252>. The 'dynatop' package implements simulation code for Dynamic TOPMODEL based on the output of 'dynatopGIS'.
Author: Paul Smith [aut, cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between dynatopGIS versions 0.2.3 dated 2022-10-10 and 0.2.4 dated 2022-11-30
DESCRIPTION | 12 - MD5 | 24 +- NAMESPACE | 2 NEWS.md | 6 R/dygis.R | 470 ++++++++++++++++++++++++++--------------------- R/dynatopGIS-package.R | 2 build/vignette.rds |binary inst/doc/Banding.html | 14 - inst/doc/dynatopGIS.R | 16 - inst/doc/dynatopGIS.Rmd | 16 - inst/doc/dynatopGIS.html | 200 ++++++++++---------- man/dynatopGIS.Rd | 12 - vignettes/dynatopGIS.Rmd | 16 - 13 files changed, 433 insertions(+), 357 deletions(-)
Title: Chart Generation for 'Microsoft Word' and 'Microsoft PowerPoint'
Documents
Description: Create native charts for 'Microsoft PowerPoint' and 'Microsoft Word' documents.
These can then be edited and annotated. Functions are provided to let users create charts, modify
and format their content. The chart's underlying data is automatically saved within the
'Word' document or 'PowerPoint' presentation. It extends package 'officer' that does
not contain any feature for 'Microsoft' native charts production.
Author: David Gohel [aut, cre],
ArData [cph],
YouGov [fnd],
Jan Marvin Garbuszus [ctb] ,
Marlon Molina [ctb] ,
Rokas Klydzia [ctb] ,
David Camposeco [ctb] ,
Dan Joplin [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between mschart versions 0.3.1 dated 2021-09-02 and 0.4.0 dated 2022-11-30
mschart-0.3.1/mschart/inst/tinytest/utils |only mschart-0.4.0/mschart/DESCRIPTION | 14 mschart-0.4.0/mschart/MD5 | 88 +- mschart-0.4.0/mschart/NAMESPACE | 3 mschart-0.4.0/mschart/NEWS.md | 13 mschart-0.4.0/mschart/R/as_series.R | 101 ++- mschart-0.4.0/mschart/R/axis_codes.R | 76 +- mschart-0.4.0/mschart/R/axis_setting.R | 43 - mschart-0.4.0/mschart/R/chart_data_styles.R | 22 mschart-0.4.0/mschart/R/chart_labels.R | 35 - mschart-0.4.0/mschart/R/chart_settings.R | 99 +-- mschart-0.4.0/mschart/R/excel_series.R | 70 +- mschart-0.4.0/mschart/R/ms_chart.R | 394 ++++++------ mschart-0.4.0/mschart/R/table_codes.R |only mschart-0.4.0/mschart/R/table_setting.R |only mschart-0.4.0/mschart/R/theme.R | 4 mschart-0.4.0/mschart/R/to_pml.R | 19 mschart-0.4.0/mschart/R/utils.R | 6 mschart-0.4.0/mschart/inst/tinytest/test-custom-labels.R | 12 mschart-0.4.0/mschart/inst/tinytest/test-utf8.R | 11 mschart-0.4.0/mschart/inst/tinytest/test_areachart.R | 11 mschart-0.4.0/mschart/inst/tinytest/test_linechart.R | 14 mschart-0.4.0/mschart/man/chart_ax_x.Rd | 20 mschart-0.4.0/mschart/man/chart_ax_y.Rd | 28 mschart-0.4.0/mschart/man/chart_labels.Rd | 12 mschart-0.4.0/mschart/man/chart_settings.Rd | 43 - mschart-0.4.0/mschart/man/chart_table.Rd |only mschart-0.4.0/mschart/man/figures/fig_chart_ax_x_1.png |binary mschart-0.4.0/mschart/man/figures/fig_chart_ax_y_1.png |binary mschart-0.4.0/mschart/man/figures/fig_chart_settings_1.png |binary mschart-0.4.0/mschart/man/figures/fig_chart_settings_2.png |binary mschart-0.4.0/mschart/man/figures/fig_chart_settings_3.png |binary mschart-0.4.0/mschart/man/figures/fig_ms_barchart_1.png |binary mschart-0.4.0/mschart/man/figures/fig_ms_barchart_2.png |binary mschart-0.4.0/mschart/man/figures/fig_ms_barchart_3.png |binary mschart-0.4.0/mschart/man/figures/fig_ms_barchart_4.png |only mschart-0.4.0/mschart/man/figures/fig_ms_barchart_5.png |only mschart-0.4.0/mschart/man/figures/fig_ms_barchart_6.png |only mschart-0.4.0/mschart/man/figures/fig_ms_linechart_1.png |binary mschart-0.4.0/mschart/man/figures/fig_ms_linechart_2.png |binary mschart-0.4.0/mschart/man/figures/fig_ms_linechart_3.png |only mschart-0.4.0/mschart/man/figures/fig_ms_scatterchart_1.png |binary mschart-0.4.0/mschart/man/figures/fig_ms_scatterchart_2.png |binary mschart-0.4.0/mschart/man/ms_areachart.Rd | 20 mschart-0.4.0/mschart/man/ms_barchart.Rd | 111 ++- mschart-0.4.0/mschart/man/ms_linechart.Rd | 36 - mschart-0.4.0/mschart/man/ms_scatterchart.Rd | 25 mschart-0.4.0/mschart/man/mschart.Rd | 2 mschart-0.4.0/mschart/man/set_theme.Rd | 3 49 files changed, 777 insertions(+), 558 deletions(-)
Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional
disaggregated indicators. So far, estimation methods comprise direct estimation,
the model-based unit-level approach Empirical Best Prediction (see "Small area
estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>),
the area-level model (see "Estimates of income for small places: An
application of James-Stein procedures to Census Data" by Fay and Herriot (1979)
<doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance
estimation methods, log and arcsin transformation, spatial, robust and measurement
error models), as well as their precision estimates. The assessment of the used model
is supported by a summary and diagnostic plots. For a suitable presentation of
estimates, map plots can be easily created. Furthermore, results can easily be
exported to excel. For a detailed description of the package and the methods used
see "The R Package emdi for Estima [...truncated...]
Author: Sylvia Harmening [aut],
Ann-Kristin Kreutzmann [aut],
Soeren Pannier [aut, cre],
Felix Skarke [aut],
Natalia Rojas-Perilla [aut],
Nicola Salvati [aut],
Timo Schmid [aut],
Matthias Templ [aut],
Nikos Tzavidis [aut],
Nora Wuerz [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>
Diff between emdi versions 2.1.2 dated 2022-08-20 and 2.1.3 dated 2022-11-30
DESCRIPTION | 10 +++++----- MD5 | 38 +++++++++++++++++++------------------- NEWS.md | 6 ++++++ R/FH.R | 12 ++++++------ R/back_transformation.R | 2 +- R/compare_plot.R | 6 +++--- R/compare_plot.ebp.R | 6 +++--- R/compare_plot.fh.R | 4 ++-- R/estim_sigmau2.R | 8 ++++---- R/framework_fh.R | 5 ++--- R/mse.R | 10 +++++----- R/optimal_parameter.R | 6 +++--- R/plot.ebp.R | 2 +- R/print.emdi.R | 4 ++-- R/summary.ebp.R | 6 +++--- R/summary.fh.R | 6 +++--- R/variable_selection.R | 32 ++++++++++++++++---------------- R/write.excel.emdi.R | 4 ++-- R/write.ods.emdi.R | 4 ++-- inst/doc/vignette_fh.pdf |binary 20 files changed, 88 insertions(+), 83 deletions(-)
Title: Adaptive Lasso Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects solves longitudinal data, considering the individual intercepts as fixed effects. The parametric set of this type of problem used to be huge. Thus penalized methods such as Lasso are currently applied. Adaptive Lasso presents oracle proprieties, which include Gaussianity and correct model selection. Bayesian information criteria (BIC) estimates the optimal tuning parameter lambda. Plot tools are also available.
Author: Ian Meneghel Danilevicz [aut, cre]
,
Pascal Bondon [aut],
Valderio A. Reisen [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>
Diff between alqrfe versions 1.0 dated 2022-09-19 and 1.1 dated 2022-11-30
DESCRIPTION | 14 ++++++++------ MD5 | 8 ++++---- build/partial.rdb |binary man/alqrfe-package.Rd | 42 ++++++++++-------------------------------- src/RcppExports.cpp | 5 +++++ 5 files changed, 27 insertions(+), 42 deletions(-)
Title: Probabilistic Forecast Combination Using CRPS Learning
Description: Combine probabilistic forecasts using CRPS learning algorithms proposed in Berrisch, Ziel (2021) <arXiv:2102.00968> <doi:10.1016/j.jeconom.2021.11.008>. The package implements multiple online learning algorithms like Bernstein online aggregation; see Wintenberger (2014) <arXiv:1404.1356>. Quantile regression is also implemented for comparison purposes. Model parameters can be tuned automatically with respect to the loss of the forecast combination. Methods like predict(), update(), plot() and print() are available for convenience. This package utilizes the optim C++ library for numeric optimization <https://github.com/kthohr/optim>.
Author: Jonathan Berrisch [cre] ,
Florian Ziel [aut]
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>
Diff between profoc versions 0.9.3 dated 2022-04-21 and 0.9.4 dated 2022-11-30
DESCRIPTION | 10 +- MD5 | 22 ++-- NEWS.md | 10 ++ R/misc.R | 44 ++++++++ R/online.R | 143 +++++++++++++++++++++-------- R/splines.R | 60 +++++++----- build/partial.rdb |binary man/online.Rd | 27 +++-- src/conline.cpp | 7 - tests/testthat/test-combination_sampling.R | 2 tests/testthat/test-grids.R | 2 tests/testthat/test-user_supplied_grid.R | 95 ++++++++++++++----- 12 files changed, 306 insertions(+), 116 deletions(-)
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics. Supported by grant NSF DMS 1712839. See Kolassa and Seifu (2013) <doi:10.1016/j.acra.2013.03.006>.
Author: John E. Kolassa [cre],
Stephane Jankowski [aut]
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.3.7 dated 2022-10-21 and 1.3.8 dated 2022-11-30
DESCRIPTION | 14 +++++++------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 3 ++- R/kweffectsize.R | 7 +++++-- R/kwpower.R | 7 +++++-- R/kwsamplesize.R | 13 ++++++++----- R/pairwiseprobabilities.R | 10 ++++++---- R/shiftcr.R | 21 +++++++++++---------- R/theil.R | 4 +++- man/kweffectsize.Rd | 7 +++++-- man/kwpower.Rd | 7 +++++-- man/kwsamplesize.Rd | 13 ++++++++----- man/pairwiseprobabilities.Rd | 4 ++-- man/probabilityderiv.Rd | 2 +- man/shiftcr.Rd | 7 ++++--- 15 files changed, 86 insertions(+), 61 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.9.0 dated 2022-09-23 and 1.10.0 dated 2022-11-30
DESCRIPTION | 15 MD5 | 153 - NAMESPACE | 8 NEWS.md | 20 R/assert_package.R | 55 R/broom.helpers-package.R | 2 R/helpers.R | 1 R/model_compute_terms_contributions.R | 5 R/model_get_coefficients_type.R | 17 R/model_get_contrasts.R | 2 R/model_get_model_matrix.R | 9 R/model_get_n.R | 12 R/model_get_response.R | 3 R/model_get_weights.R | 3 R/model_get_xlevels.R | 1 R/model_identify_variables.R | 25 R/model_list_contrasts.R | 8 R/model_list_terms_levels.R | 2 R/model_list_variables.R | 39 R/reexport.R | 1 R/select_helpers.R | 4 R/select_utilities.R | 38 R/tidiers.R | 85 R/tidy_add_coefficients_type.R | 2 R/tidy_add_contrasts.R | 3 R/tidy_add_estimate_to_reference_rows.R | 45 R/tidy_add_header_rows.R | 28 R/tidy_add_n.R | 2 R/tidy_add_reference_rows.R | 26 R/tidy_add_term_labels.R | 6 R/tidy_and_attach.R | 6 R/tidy_disambiguate_terms.R | 16 R/tidy_plus_plus.R | 7 R/tidy_select_variables.R | 24 README.md | 153 - build/vignette.rds |binary data/supported_models.rda |binary inst/WORDLIST | 6 inst/doc/tidy.R | 57 inst/doc/tidy.Rmd | 59 inst/doc/tidy.html | 2709 +++++++++---------- man/assert_package.Rd | 11 man/figures/broom.helpers.svg | 396 +- man/model_get_coefficients_type.Rd | 3 man/model_get_model_matrix.Rd | 3 man/model_get_n.Rd | 3 man/model_identify_variables.Rd | 3 man/model_list_variables.Rd | 7 man/supported_models.Rd | 3 man/tidy_add_contrasts.Rd | 3 man/tidy_add_estimate_to_reference_rows.Rd | 4 man/tidy_add_header_rows.Rd | 4 man/tidy_add_n.Rd | 2 man/tidy_add_reference_rows.Rd | 4 man/tidy_disambiguate_terms.Rd | 8 man/tidy_multgee.Rd |only man/tidy_parameters.Rd | 5 man/tidy_plus_plus.Rd | 5 man/tidy_select_variables.Rd | 4 man/tidy_with_broom_or_parameters.Rd | 1 tests/spelling.R | 2 tests/testthat.R | 8 tests/testthat/test-add_coefficients_type.R | 23 tests/testthat/test-add_contrasts.R | 1 tests/testthat/test-add_estimate_to_reference_rows.R | 44 tests/testthat/test-add_header_rows.R | 5 tests/testthat/test-add_n.R | 1 tests/testthat/test-add_reference_rows.R | 14 tests/testthat/test-add_term_labels.R | 2 tests/testthat/test-add_variable_labels.R | 18 tests/testthat/test-assert_package.R | 16 tests/testthat/test-disambiguate_terms.R | 13 tests/testthat/test-identify_variables.R | 24 tests/testthat/test-model_get_n.R | 5 tests/testthat/test-select_helpers.R | 3 tests/testthat/test-select_variables.R | 28 tests/testthat/test-tidy_plus_plus.R | 115 vignettes/tidy.Rmd | 59 78 files changed, 2468 insertions(+), 2039 deletions(-)
Title: Collecting and Analyzing Mastodon Data
Description: An implementation of calls designed to collect and organize Mastodon data via its Application Program Interfaces (API), which can be found at the following URL: <https://docs.joinmastodon.org/>.
Author: David Schoch [aut, cre] ,
Chung-hong Chan [aut] ,
Johannes Gruber [ctb]
Maintainer: David Schoch <david@schochastics.net>
Diff between rtoot versions 0.1.0 dated 2022-11-11 and 0.2.0 dated 2022-11-30
DESCRIPTION | 11 - MD5 | 149 ++++++++++------ NAMESPACE | 9 - NEWS.md | 11 + R/accounts.R | 206 ++++++++++------------- R/auth.R | 167 ++++++++++++------ R/datastructure.R | 36 +--- R/instances.R | 42 +++- R/post.R | 13 - R/rtoot-package.R |only R/stream_statuses.R |only R/sysdata.rda |only R/timelines_statuses.R | 117 ++++--------- R/utils.R | 140 +++++++++++++-- README.md | 38 +++- build/vignette.rds |binary inst/doc/auth.R | 7 inst/doc/auth.Rmd | 19 ++ inst/doc/auth.html | 125 +++++++------ inst/doc/rtoot.Rmd | 8 inst/doc/rtoot.html | 124 +++++++------ inst/doc/stream.R |only inst/doc/stream.Rmd |only inst/doc/stream.html |only man/auth_setup.Rd | 23 ++ man/convert_token_to_envvar.Rd |only man/get_account_blocks.Rd | 18 +- man/get_account_bookmarks.Rd | 14 + man/get_account_favourites.Rd | 18 +- man/get_account_followers.Rd | 12 + man/get_account_following.Rd | 14 + man/get_account_mutes.Rd | 18 +- man/get_account_statuses.Rd | 26 ++ man/get_fedi_instances.Rd | 2 man/get_instance.Rd | 10 + man/get_timeline_hashtag.Rd | 8 man/get_timeline_home.Rd | 12 + man/get_timeline_public.Rd | 8 man/parse_stream.Rd |only man/post_toot.Rd | 7 man/post_user.Rd | 4 man/rtoot-package.Rd |only man/search_accounts.Rd | 3 man/stream_timeline.Rd |only man/verify_credentials.Rd | 16 + tests/fixtures/auth_setup_1.yml |only tests/fixtures/auth_setup_verbose.yml |only tests/fixtures/envvar.yml |only tests/fixtures/envvar_silent.yml |only tests/fixtures/get_account_statuses_default.yml | 2 tests/fixtures/get_account_statuses_limit.yml |only tests/fixtures/get_account_statuses_noparse.yml | 2 tests/fixtures/get_instance_blocks_default.yml |only tests/fixtures/get_instance_rules_default.yml |only tests/fixtures/handle_params_max_id.yml |only tests/fixtures/post_toot_silent.yml |only tests/fixtures/post_toot_verbose.yml |only tests/fixtures/post_user_pin_silent.yml |only tests/fixtures/process_created_token.yml |only tests/fixtures/process_request_bigger.yml |only tests/fixtures/process_request_equal1.yml |only tests/fixtures/process_request_smaller.yml |only tests/testdata/fake_headers.RDS |only tests/testdata/mastodonsocial.json |only tests/testdata/timeline |only tests/testthat/setup-rtoot.R | 2 tests/testthat/test-auth_check_token_rtoot.R |only tests/testthat/test-auth_create_token.R |only tests/testthat/test-auth_envvar.R |only tests/testthat/test-auth_process_created_token.R |only tests/testthat/test-auth_setup.R |only tests/testthat/test-auth_verify.R |only tests/testthat/test-get_account.R | 3 tests/testthat/test-get_account_auth.R | 3 tests/testthat/test-get_account_statuses.R | 13 + tests/testthat/test-get_context.R | 3 tests/testthat/test-get_favourited_by.R | 3 tests/testthat/test-get_poll.R | 3 tests/testthat/test-get_reblogged_by.R | 3 tests/testthat/test-get_status.R | 3 tests/testthat/test-get_timeline_hashtag.R | 3 tests/testthat/test-get_timeline_home.R | 3 tests/testthat/test-get_timeline_list.R | 3 tests/testthat/test-get_timeline_public.R | 3 tests/testthat/test-handle_params.R |only tests/testthat/test-instances.R | 22 ++ tests/testthat/test-pagination.R |only tests/testthat/test-parse_status.R | 20 ++ tests/testthat/test-post.R | 37 +++- tests/testthat/test-rate_limit.R |only tests/testthat/test-search_accounts.R | 23 +- tests/testthat/test-stream.R |only vignettes/auth.Rmd | 19 ++ vignettes/rtoot.Rmd | 8 vignettes/stream.Rmd |only 95 files changed, 1024 insertions(+), 592 deletions(-)
Title: Spatial Capture-Recapture (SCR) Methods Using 'nimble'
Description: Provides utility functions, distributions, and fitting methods for Bayesian Spatial Capture-Recapture (SCR) and Open Population Spatial Capture-Recapture (OPSCR) modelling using the nimble package (de Valpine et al. 2017 <doi:10.1080/10618600.2016.1172487 >). Development of the package was motivated primarily by the need for flexible and efficient analysis of large-scale SCR data (Bischof et al. 2020 <doi:10.1073/pnas.2011383117 >). Computational methods and techniques implemented in nimbleSCR include those discussed in Turek et al. 2021 <doi:10.1002/ecs2.3385>; among others. For a recent application of nimbleSCR, see Milleret et al. (2021) <doi:10.1098/rsbl.2021.0128>.
Author: Richard Bischof [aut],
Daniel Turek [aut, cre],
Cyril Milleret [aut],
Torbjoern Ergon [aut],
Pierre Dupont [aut],
Soumen Dey [aut],
Wei Zhang [aut],
Perry de Valpine [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between nimbleSCR versions 0.2.0 dated 2022-09-02 and 0.2.1 dated 2022-11-30
DESCRIPTION | 12 - MD5 | 28 +- NAMESPACE | 8 R/calculateDensity.R |only R/dcatState1Alive1Dead.R |only R/dcatState1Alive2Dead.R |only R/dcatState2Alive2Dead.R |only R/sampler_categorical_general.R |only R/zzz.R | 113 +++++++++- inst/NEWS | 11 inst/doc/Fit_with_dbinomLocal_normalPlateau_and_HomeRangeAreaComputation.html | 4 inst/doc/Point_Process.html | 4 inst/doc/Simulate_and_fit_SCR_models_with_dbinomLocal_normal.html | 4 inst/doc/WolverinePointProcess.html | 4 inst/doc/wolverine_example.html | 4 man/calculateDensity.Rd |only man/dcatState1Alive1Dead.Rd |only man/dcatState1Alive2Dead.Rd |only man/dcatState2Alive2Dead.Rd |only man/sampler_categorical_general.Rd |only 20 files changed, 166 insertions(+), 26 deletions(-)
Title: Geostatistics for Compositional Analysis
Description: Support for geostatistical analysis of multivariate data,
in particular data with restrictions, e.g. positive amounts data,
compositional data, distributional data, microstructural data, etc.
It includes descriptive analysis and modelling for such data, both
from a two-point Gaussian perspective and multipoint perspective.
The methods mainly follow Tolosana-Delgado, Mueller and van den
Boogaart (2018) <doi:10.1007/s11004-018-9769-3>.
Author: Raimon Tolosana-Delgado [aut] ,
Ute Mueller [aut],
K. Gerald van den Boogaart [ctb, cre],
Hassan Talebi [ctb, cph],
Helmholtz-Zentrum Dresden-Rossendorf [cph],
Edith Cowan University [cph]
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between gmGeostats versions 0.11.1 dated 2022-05-03 and 0.11.2 dated 2022-11-30
DESCRIPTION | 10 MD5 | 43 - NEWS.md | 11 R/accuracy.R | 53 - R/compositionsCompatibility.R | 2 R/exploratools.R | 1186 +++++++++++++++--------------- R/genDiag.R | 12 R/gmValidationStrategy.R | 4 R/gstatCompatibility.R | 6 R/mask.R | 2 R/variograms.R | 2 build/partial.rdb |only inst/doc/gmGeostats.html | 372 ++++++--- inst/doc/register_new_layer_datatype.Rmd | 8 inst/doc/register_new_layer_datatype.html | 884 ++++++++++++---------- man/Maf.data.frame.Rd | 2 man/accuracy.Rd | 41 - man/coloredBiplot.genDiag.Rd | 6 man/unmask.data.frame.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 src/gmGeostats.c | 10 vignettes/register_new_layer_datatype.Rmd | 8 23 files changed, 1474 insertions(+), 1194 deletions(-)
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture
hidden Markov models for social sequence data and other categorical time series.
Also some more restricted versions of these type of models are available: Markov
models, mixture Markov models, and latent class models. The package supports
models for one or multiple subjects with one or multiple parallel sequences
(channels). External covariates can be added to explain cluster membership in
mixture models. The package provides functions for evaluating and comparing
models, as well as functions for visualizing of multichannel sequence data and
hidden Markov models. Models are estimated using maximum likelihood via the EM
algorithm and/or direct numerical maximization with analytical gradients. All
main algorithms are written in C++ with support for parallel computation.
Documentation is available via several vignettes in this page, and the
paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] ,
Satu Helske [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 1.2.1-1 dated 2022-05-25 and 1.2.2 dated 2022-11-30
DESCRIPTION | 10 MD5 | 32 NEWS.md | 6 R/HMMplot.R | 4 R/SSPlotter.R | 4 R/mc_to_sc.R | 63 R/mc_to_sc_data.R | 31 R/mssplot.R | 27 R/plot.hmm.R | 1302 +-- build/vignette.rds |binary inst/doc/seqHMM.pdf | 6300 +++++++++----- inst/doc/seqHMM_algorithms.pdf |binary inst/doc/seqHMM_estimation.pdf |binary inst/doc/seqHMM_visualization.pdf |16267 +++++++++++++++++++------------------- man/mc_to_sc.Rd | 6 man/mc_to_sc_data.Rd | 6 man/seqHMM-deprecated.Rd | 9 17 files changed, 13106 insertions(+), 10961 deletions(-)
Title: Use Browser Cookies with 'shiny'
Description: Browser cookies are name-value pairs that are saved in a user's
browser by a website. Cookies allow websites to persist information about
the user and their use of the website. Here we provide tools for working
with cookies in 'shiny' apps, in part by wrapping the 'js-cookie' JavaScript
library <https://github.com/js-cookie/js-cookie>.
Author: Jon Harmon [aut, cre, cph] ,
Klaus Hartl [cph] ,
Fagner Brack [cph]
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Diff between cookies versions 0.1.0 dated 2022-11-01 and 0.2.0 dated 2022-11-30
DESCRIPTION | 8 +- MD5 | 31 ++++---- NAMESPACE | 4 + NEWS.md | 26 ++++-- R/data_prep.R | 13 +-- R/onload.R | 8 +- R/requests.R | 6 + R/server.R | 24 ++++++ R/ui_wrapper.R | 74 ++++++++++--------- README.md | 151 ++++++++++++++++------------------------ man/extract_cookie.Rd | 5 + man/get_cookie.Rd |only man/set_cookie_response.Rd | 6 + tests/testthat/_snaps/server.md | 2 tests/testthat/test-onload.R | 4 - tests/testthat/test-requests.R | 16 +++- tests/testthat/test-server.R | 16 +++- 17 files changed, 225 insertions(+), 169 deletions(-)
Title: Bayesian Network Structure Learning from Data with Missing
Values
Description: Bayesian Network Structure Learning from Data with Missing Values.
The package implements the Silander-Myllymaki complete search,
the Max-Min Parents-and-Children, the Hill-Climbing, the
Max-Min Hill-climbing heuristic searches, and the Structural
Expectation-Maximization algorithm. Available scoring functions are
BDeu, AIC, BIC. The package also implements methods for generating and using
bootstrap samples, imputed data, inference.
Author: Francesco Sambo [aut],
Alberto Franzin [aut, cre]
Maintainer: Alberto Franzin <afranzin@ulb.ac.be>
Diff between bnstruct versions 1.0.13 dated 2022-11-30 and 1.0.14 dated 2022-11-30
bnstruct-1.0.13/bnstruct/inst/doc/bnstruct.R |only bnstruct-1.0.14/bnstruct/DESCRIPTION | 8 bnstruct-1.0.14/bnstruct/MD5 | 12 bnstruct-1.0.14/bnstruct/build/vignette.rds |binary bnstruct-1.0.14/bnstruct/inst/doc/bnstruct.Rnw | 1000 ----------------- bnstruct-1.0.14/bnstruct/inst/doc/bnstruct.pdf |binary bnstruct-1.0.14/bnstruct/vignettes/bnstruct-static.pdf |only bnstruct-1.0.14/bnstruct/vignettes/bnstruct.Rnw | 1000 ----------------- 8 files changed, 14 insertions(+), 2006 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Provides a common framework for optimization of black-box
functions for other packages, e.g. 'mlr3tuning' or 'mlr3fselect'. It
offers various optimization methods e.g. grid search, random search,
generalized simulated annealing and iterated racing.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 0.7.0 dated 2022-11-04 and 0.7.1 dated 2022-11-30
DESCRIPTION | 8 - MD5 | 16 +-- NEWS.md | 4 R/Archive.R | 5 + README.md | 59 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/bbotk.html | 238 ++++++++++++++++++++++++++-------------------------- man/Archive.Rd | 4 9 files changed, 173 insertions(+), 161 deletions(-)
Title: Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Description: Import, manipulate and explore results generated by 'Antares', a
powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems
(more information about 'Antares' here : <https://antares-simulator.org/>).
Author: Veronique Bachelier [aut, cre],
Jalal-Edine ZAWAM [aut],
Frederic Breant [ctb],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Victor Perrier [ctb],
Etienne Sanchez [ctb],
RTE [cph]
Maintainer: Veronique Bachelier <veronique.bachelier@rte-france.com>
Diff between antaresRead versions 2.3.0 dated 2022-10-10 and 2.3.1 dated 2022-11-30
DESCRIPTION | 8 LICENSE | 2 MD5 | 248 +- NEWS.md | 10 R/API-methods.R | 8 R/aggregateResult.R | 2356 ++++++++++++------------- R/asAntaresDataList.R | 140 - R/asAntaresDataTable.R | 102 - R/changeTimeStep.R | 410 ++-- R/copyToClipboard.R | 172 - R/extractDataList.R | 206 +- R/getAreas.R | 186 - R/getLinks.R | 204 +- R/getNtcOutput.R | 48 R/giveSize.R | 414 ++-- R/groupByDistrict.R | 170 - R/h5_antaresReadH5.R | 1960 ++++++++++---------- R/h5_readInputs.R | 108 - R/h5_setSimulationPathH5.R | 154 - R/h5_timeManagement.R | 266 +- R/h5_transformData.R | 72 R/h5_writeData.R | 314 +-- R/h5_writeH5ByYear.R | 984 +++++----- R/h5utils.R | 52 R/hvdcModification.R | 220 +- R/importInput.R | 760 ++++---- R/importOutput.R | 1502 +++++++-------- R/ponderateMcAggregation.R | 78 R/readAntares.R | 1769 +++++++++--------- R/readBindingConstraints.R | 336 +-- R/readClusterDesc.R | 274 +- R/readIniFile.R | 216 +- R/readInputTS.R | 336 +-- R/readLayout.R | 374 +-- R/removeVirtualAreas.R | 1284 ++++++------- R/reorderCols.R | 100 - R/setHvdcAreas.R | 108 - R/setSimulationPath.R | 1206 ++++++------ R/showAliases.R | 196 +- R/simOptions.R | 118 - R/subset.R | 264 +- R/utils_api.R | 35 R/viewAntares.R | 108 - R/zzz.R | 570 +++--- build/vignette.rds |binary inst/API/demo_api.R | 414 ++-- inst/API/demo_api_enr.R | 388 ++-- inst/ENR_cluster/test_clusters_enr.R | 184 - inst/doc/antaresH5.Rmd | 288 +-- inst/doc/antaresH5.html | 248 -- inst/doc/antaresRead.Rmd | 316 +-- inst/doc/antaresRead.html | 320 --- inst/format_output/h5Struct.csv | 522 ++--- inst/format_output/tableOutput.csv | 502 ++--- inst/format_output/tableOutput_aggreg.csv | 594 +++--- man/API-methods.Rd | 90 man/aggregatate_mc_all.Rd | 124 - man/as.antaresDataList.Rd | 98 - man/as.antaresDataTable.Rd | 70 man/changeTimeStep.Rd | 104 - man/copyToClipboard.Rd | 88 man/dot-writeIni.Rd | 58 man/extractDataList.Rd | 56 man/getAreas.Rd | 128 - man/getLinks.Rd | 170 - man/hvdcModification.Rd | 56 man/ponderateMcAggregation.Rd | 54 man/read-ini.Rd | 122 - man/readAntares.Rd | 450 ++-- man/readAntaresAreas.Rd | 118 - man/readBindingConstraints.Rd | 96 - man/readClusterDesc.Rd | 130 - man/readInputTS.Rd | 216 +- man/readLayout.Rd | 100 - man/readOptimCriteria.Rd | 62 man/removeVirtualAreas.Rd | 338 +-- man/setAlias.Rd | 122 - man/setHvdcAreas.Rd | 62 man/setSimulationPath.Rd | 396 ++-- man/setTimeoutAPI.Rd | 46 man/simOptions.Rd | 102 - man/subset.antaresDataList.Rd | 100 - man/viewAntares.Rd | 66 man/writeAntaresH5.Rd | 260 +- tests/testthat.R | 34 tests/testthat/helper_init.R | 340 +-- tests/testthat/test-.timeIdToDate.R | 118 - tests/testthat/test-API.R | 46 tests/testthat/test-RemoveInputColumn.R | 88 tests/testthat/test-aliases.R | 86 tests/testthat/test-asAntaresData.R | 140 - tests/testthat/test-bindingConstraints.R | 74 tests/testthat/test-changeTimeStep.R | 102 - tests/testthat/test-extractDataList.R | 78 tests/testthat/test-getAreas.R | 106 - tests/testthat/test-getLinks.R | 50 tests/testthat/test-getStartDate.R | 274 +- tests/testthat/test-groupByDistrict.R | 50 tests/testthat/test-h5ReadAntares.R | 350 +-- tests/testthat/test-h5_nodata.R | 28 tests/testthat/test-h5_readInputs.R | 84 tests/testthat/test-h5_setSimulationPathH5.R | 38 tests/testthat/test-h5_write.R | 122 - tests/testthat/test-hvdcModification.R | 62 tests/testthat/test-mcaggreg.R | 110 - tests/testthat/test-opts-api.R | 80 tests/testthat/test-ponderate.R | 106 - tests/testthat/test-ponderateMcAggregation.R | 26 tests/testthat/test-print.R | 86 tests/testthat/test-readAntares.R | 310 +-- tests/testthat/test-readAntares_districts.R | 74 tests/testthat/test-readAntares_inputs.R | 128 - tests/testthat/test-readAntares_mustRun.R | 154 - tests/testthat/test-readAntares_time_columns.R | 64 tests/testthat/test-readInputAPI.R | 38 tests/testthat/test-readInputTS.R | 248 +- tests/testthat/test-readLayout.R | 90 tests/testthat/test-read_optim_criteria.R | 40 tests/testthat/test-removeVirtualAreas.R | 976 +++++----- tests/testthat/test-setHvdcAreas.R | 48 tests/testthat/test-setup.R | 358 +-- tests/testthat/test-subset_antaresDataList.R | 158 - tests/testthat/test-viewAntares.R | 90 vignettes/antaresH5.Rmd | 288 +-- vignettes/antaresRead.Rmd | 316 +-- 125 files changed, 15852 insertions(+), 16312 deletions(-)
Title: Africa Macroeconomic Monitor Database API
Description: An R API providing access to a relational database with macroeconomic data for Africa.
The database contains >700 macroeconomic time series from mostly international sources,
grouped into 50 macroeconomic and development-related topics. Series are carefully selected
on the basis of data coverage for Africa, frequency, and relevance to the macro-development context.
The project is part of the 'Kiel Institute Africa Initiative'
<https://www.ifw-kiel.de/institute/initiatives/kielinstituteafricainitiative/>,
which, amongst other things, aims to develop a parsimonious database with highly relevant indicators
to monitor macroeconomic developments in Africa, accessible through a fast API and a web-based platform
at <https://africamonitor.ifw-kiel.de/>.
The database is maintained at the Kiel Institute for the World Economy <https://www.ifw-kiel.de/>.
Author: Sebastian Krantz [aut, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between africamonitor versions 0.2.1 dated 2022-10-16 and 0.2.2 dated 2022-11-30
DESCRIPTION | 7 ++-- MD5 | 23 +++++++------- NAMESPACE | 2 - NEWS.md | 10 ++++++ R/accessdb.R | 65 ++++++++++++++++++++++++++--------------- R/africamonitor.R | 3 + data/am_countries_wld.rda |only man/africamonitor-package.Rd | 1 man/am_as_date.Rd | 2 - man/am_countries.Rd | 17 +++++++--- man/am_data.Rd | 4 +- man/am_expand_date.Rd | 11 ++++-- tests/testthat/test-accessdb.R | 2 - 13 files changed, 95 insertions(+), 52 deletions(-)
Title: Ordinal Forests: Prediction and Variable Ranking with Ordinal
Target Variables
Description: The ordinal forest (OF) method allows ordinal regression with high-dimensional
and low-dimensional data. After having constructed an OF prediction rule using a training dataset,
it can be used to predict the values of the ordinal target variable for new observations.
Moreover, by means of the (permutation-based) variable importance measure of OF, it is also
possible to rank the covariates with respect to their importance in the prediction of the
values of the ordinal target variable.
OF is presented in Hornung (2020).
NOTE: Starting with package version 2.4, it is also possible to obtain class probability
predictions in addition to the class point predictions. Moreover, the variable importance values
can also be based on the class probability predictions. Preliminary results indicate that
this might lead to a better discrimination between influential and non-influential covariates.
The main functions of the package are: ordfor() (construction of OF) and predict.ordfor()
(prediction of [...truncated...]
Author: Roman Hornung
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between ordinalForest versions 2.4-2 dated 2021-06-25 and 2.4-3 dated 2022-11-30
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/predict.R | 2 +- R/rangerordfor.R | 4 ++-- build/partial.rdb |binary src/Forest.cpp | 2 +- src/RcppExports.cpp | 5 +++++ 7 files changed, 20 insertions(+), 15 deletions(-)
Title: Tools for Multimodal Network Analysis
Description: A set of tools for analysing multimodal networks.
All functions operate with matrices, edge lists,
and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
It includes functions for measuring
centrality, centralization, cohesion, closure, and constraint,
as well as for network block-modelling, regression, and diffusion models.
The package is released as a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book in addition to other network data.
Author: James Hollway [cre, aut, ctb] ,
Jael Tan [ctb] ,
Bernhard Bieri [ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 0.12.1 dated 2022-10-04 and 0.13.0 dated 2022-11-30
migraph-0.12.1/migraph/inst/doc/p2visualisation.R |only migraph-0.12.1/migraph/inst/doc/p2visualisation.Rmd |only migraph-0.12.1/migraph/inst/doc/p2visualisation.html |only migraph-0.12.1/migraph/inst/doc/p3centrality.R |only migraph-0.12.1/migraph/inst/doc/p3centrality.Rmd |only migraph-0.12.1/migraph/inst/doc/p3centrality.html |only migraph-0.12.1/migraph/inst/doc/p5equivalence.R |only migraph-0.12.1/migraph/inst/doc/p5equivalence.Rmd |only migraph-0.12.1/migraph/inst/doc/p5equivalence.html |only migraph-0.12.1/migraph/inst/doc/p7linearmodel.R |only migraph-0.12.1/migraph/inst/doc/p7linearmodel.Rmd |only migraph-0.12.1/migraph/inst/doc/p7linearmodel.html |only migraph-0.12.1/migraph/man/autographr.Rd |only migraph-0.12.1/migraph/tests/testthat/test-manip_is.R |only migraph-0.12.1/migraph/vignettes/p2visualisation.Rmd |only migraph-0.12.1/migraph/vignettes/p2visualisation.Rmd.orig |only migraph-0.12.1/migraph/vignettes/p3centrality.Rmd |only migraph-0.12.1/migraph/vignettes/p3centrality.Rmd.orig |only migraph-0.12.1/migraph/vignettes/p5equivalence.Rmd |only migraph-0.12.1/migraph/vignettes/p5equivalence.Rmd.orig |only migraph-0.12.1/migraph/vignettes/p7linearmodel.Rmd |only migraph-0.12.1/migraph/vignettes/p7linearmodel.Rmd.orig |only migraph-0.12.1/migraph/vignettes/teaching |only migraph-0.13.0/migraph/DESCRIPTION | 16 migraph-0.13.0/migraph/MD5 | 180 +++------ migraph-0.13.0/migraph/NAMESPACE | 51 ++ migraph-0.13.0/migraph/NEWS.md | 183 +++++++++- migraph-0.13.0/migraph/R/class_models.R |only migraph-0.13.0/migraph/R/class_motifs.R | 3 migraph-0.13.0/migraph/R/data_ison.R | 12 migraph-0.13.0/migraph/R/data_mpn.R | 6 migraph-0.13.0/migraph/R/make_create.R | 43 +- migraph-0.13.0/migraph/R/make_generate.R | 4 migraph-0.13.0/migraph/R/make_play.R |only migraph-0.13.0/migraph/R/manip_add.R | 6 migraph-0.13.0/migraph/R/manip_to.R | 167 ++++++++- migraph-0.13.0/migraph/R/mark_is.R | 37 ++ migraph-0.13.0/migraph/R/mark_nodes.R | 56 ++- migraph-0.13.0/migraph/R/measure_closure.R | 22 + migraph-0.13.0/migraph/R/measure_diversity.R | 52 ++ migraph-0.13.0/migraph/R/measure_features.R | 122 +++++- migraph-0.13.0/migraph/R/member_community.R | 60 +++ migraph-0.13.0/migraph/R/model_regression.R | 180 --------- migraph-0.13.0/migraph/R/motif_census.R | 86 ++++ migraph-0.13.0/migraph/R/viz_autographr.R | 74 ++-- migraph-0.13.0/migraph/README.md | 176 +++++---- migraph-0.13.0/migraph/build/partial.rdb |binary migraph-0.13.0/migraph/build/vignette.rds |binary migraph-0.13.0/migraph/data/ison_lotr.rda |only migraph-0.13.0/migraph/inst/doc/p1data.html | 111 +++--- migraph-0.13.0/migraph/inst/tutorials |only migraph-0.13.0/migraph/man/add.Rd | 1 migraph-0.13.0/migraph/man/as.Rd | 1 migraph-0.13.0/migraph/man/auto_graph.Rd |only migraph-0.13.0/migraph/man/brokerage_census.Rd |only migraph-0.13.0/migraph/man/closure.Rd | 14 migraph-0.13.0/migraph/man/community.Rd | 56 +++ migraph-0.13.0/migraph/man/create.Rd | 3 migraph-0.13.0/migraph/man/diversity.Rd | 32 + migraph-0.13.0/migraph/man/features.Rd | 72 +++ migraph-0.13.0/migraph/man/grab.Rd | 1 migraph-0.13.0/migraph/man/grid_layouts.Rd | 2 migraph-0.13.0/migraph/man/is.Rd | 21 + migraph-0.13.0/migraph/man/ison_lotr.Rd |only migraph-0.13.0/migraph/man/mark_nodes.Rd | 19 - migraph-0.13.0/migraph/man/mpn_cow.Rd | 6 migraph-0.13.0/migraph/man/network_census.Rd | 16 migraph-0.13.0/migraph/man/node_census.Rd | 24 + migraph-0.13.0/migraph/man/partition_layouts.Rd | 2 migraph-0.13.0/migraph/man/play.Rd |only migraph-0.13.0/migraph/man/reexports.Rd | 2 migraph-0.13.0/migraph/man/reformat.Rd | 1 migraph-0.13.0/migraph/man/regression.Rd | 3 migraph-0.13.0/migraph/man/split.Rd |only migraph-0.13.0/migraph/man/tests.Rd | 1 migraph-0.13.0/migraph/man/transform.Rd | 3 migraph-0.13.0/migraph/tests/testthat/test-make_create.R | 8 migraph-0.13.0/migraph/tests/testthat/test-mark_is.R |only migraph-0.13.0/migraph/tests/testthat/test-measure_closure.R | 4 migraph-0.13.0/migraph/tests/testthat/test-measure_diversity.R | 6 migraph-0.13.0/migraph/tests/testthat/test-measure_features.R | 2 migraph-0.13.0/migraph/tests/testthat/test-member_community.R | 18 migraph-0.13.0/migraph/tests/testthat/test-viz_autographr.R | 26 + 83 files changed, 1464 insertions(+), 527 deletions(-)
Title: Easy Study of Patient DICOM Data in Oncology
Description: Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.
Author: Cathy Fontbonne [aut, cre] ,
Jean-Marc Fontbonne [aut] ,
Nathan Azemar [ctb]
Maintainer: Cathy Fontbonne <contact.espadon@lpccaen.in2p3.fr>
Diff between espadon versions 1.1.1 dated 2022-10-26 and 1.2.0 dated 2022-11-30
DESCRIPTION | 6 MD5 | 78 NAMESPACE | 3 NEWS.md | 37 R/RcppExports.R | 4 R/add_margin.R | 3 R/dicom_browser.R | 5 R/display_3D_contour.R | 3 R/display_kplane.R | 17 R/display_obj_links.R | 295 R/espadon_hidden.R | 145 R/get_obj_connection.R | 12 R/get_rigid_M.R | 4 R/load_patient_from_Rdcm.R | 40 R/load_patient_from_dicom.R | 9 R/nesting_bin.R | 52 R/nesting_cube.R | 3 R/nesting_roi.R | 2 R/rt_chi_index.R | 56 R/rt_gamma_index.R | 214 R/rt_indices_from_roi.R | 119 R/vol_create.R | 8 R/vol_median.R | 1 R/vol_oversampling.R |only R/vol_regrid.R | 12 R/vol_subsampling.R |only build/espadon.pdf |16231 +++++++++++++++++++++-------------------- build/partial.rdb |binary inst/doc/espadon_overview.html | 4 man/add.margin.Rd | 3 man/nesting.bin.Rd | 11 man/nesting.cube.Rd | 3 man/nesting.roi.Rd | 4 man/rt.chi.index.Rd | 9 man/rt.gamma.index.Rd | 14 man/rt.indices.from.roi.Rd | 6 man/vol.create.Rd | 4 man/vol.oversampling.Rd |only man/vol.subsampling.Rd |only src/RcppExports.cpp | 9 src/gammaindex.cpp | 210 src/medianfilterC.cpp | 14 42 files changed, 9263 insertions(+), 8387 deletions(-)
Title: Web Interface to 'R' Functions
Description: Web front end for your 'R' functions producing plots or tables.
If you have a function or set of related functions, you can make them
available over the internet through a web browser. This is the same
motivation as the 'shiny' package, but note that the development of
'shinylight' is not in any way linked to that of 'shiny' (beyond the use of
the 'httpuv' package). You might prefer 'shinylight' to 'shiny' if you want
a lighter weight deployment with easier horizontal scaling, or if you want
to develop your front end yourself in JavaScript and HTML just using
a lightweight remote procedure call interface to your R code on the
server.
Author: Pieter Vermeesch [aut],
Tim Band [aut, cre]
Maintainer: Tim Band <t.band@ucl.ac.uk>
Diff between shinylight versions 1.1.1 dated 2022-11-21 and 1.1.2 dated 2022-11-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/shinylight.R | 11 +++++++++-- 3 files changed, 15 insertions(+), 8 deletions(-)
Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Kamil Zyla [aut, cre],
Jakub Nowicki [aut],
Leszek Sieminski [aut],
Marek Rogala [aut],
Recle Vibal [aut],
Tymoteusz Makowski [aut],
Appsilon Sp. z o.o. [cph]
Maintainer: Kamil Zyla <opensource+kamil@appsilon.com>
Diff between rhino versions 1.2.0 dated 2022-11-27 and 1.2.1 dated 2022-11-30
DESCRIPTION | 6 MD5 | 114 NAMESPACE | 28 NEWS.md | 76 R/addins.R | 16 R/app.R | 280 R/config.R | 164 R/data.R | 24 R/init.R | 320 R/log.R | 88 R/node.R | 68 R/rhino.R | 198 R/tools.R | 680 inst/WORDLIST | 96 inst/as_top_level.R | 24 inst/rstudio/addins.dcf | 8 inst/rstudio/addins/module.R | 32 inst/rstudio/templates/project/init.dcf | 16 inst/templates/app_structure/app.R | 4 inst/templates/app_structure/app/logic/__init__.R | 4 inst/templates/app_structure/app/main.R | 40 inst/templates/app_structure/app/view/__init__.R | 4 inst/templates/app_structure/config.yml | 6 inst/templates/app_structure/dot.lintr | 10 inst/templates/app_structure/dot.rscignore | 14 inst/templates/app_structure/rhino.yml | 2 inst/templates/e2e_tests/tests/cypress.json | 10 inst/templates/e2e_tests/tests/cypress/dot.gitignore | 4 inst/templates/e2e_tests/tests/cypress/integration/app.spec.js | 14 inst/templates/github_ci/dot.github/workflows/rhino-test.yml | 168 inst/templates/node/babel.config.json | 10 inst/templates/node/dot.eslintrc.json | 32 inst/templates/node/dot.gitignore | 2 inst/templates/node/dot.stylelintrc.json | 18 inst/templates/node/package-lock.json |26720 +++++----- inst/templates/node/package.json | 64 inst/templates/node/webpack.config.js | 42 inst/templates/renv/dot.Rprofile | 18 inst/templates/renv/dot.renvignore | 6 inst/templates/rproj/Rproj.template | 34 inst/templates/unit_tests/tests/testthat/test-main.R | 26 man/app.Rd | 114 man/build_js.Rd | 100 man/build_sass.Rd | 76 man/diagnostics.Rd | 40 man/format_r.Rd | 60 man/init.Rd | 92 man/lint_js.Rd | 82 man/lint_r.Rd | 52 man/lint_sass.Rd | 48 man/log.Rd | 104 man/rhinos.Rd | 48 man/test_e2e.Rd | 50 man/test_r.Rd | 40 tests/testthat.R | 8 tests/testthat/test-app.R | 34 tests/testthat/test-config.R | 86 tests/testthat/test-rhino.R | 24 58 files changed, 15275 insertions(+), 15273 deletions(-)
Title: Space-Time Point Pattern Simulation, Visualisation and Analysis
Description: Many of the models encountered in applications of point process methods to the study of spatio-temporal phenomena are covered in 'stpp'. This package provides statistical tools for analyzing the global and local second-order properties of spatio-temporal point processes, including estimators of the space-time inhomogeneous K-function and pair correlation function. It also includes tools to get static and dynamic display of spatio-temporal point patterns. See Gabriel et al (2013) <doi:10.18637/jss.v053.i02>.
Author: Edith Gabriel [aut, cre],
Peter J Diggle [aut],
Barry Rowlingson [aut],
Francisco J Rodriguez-Cortes [aut]
Maintainer: Edith Gabriel <edith.gabriel@inrae.fr>
Diff between stpp versions 2.0-6 dated 2022-03-11 and 2.0-7 dated 2022-11-30
stpp-2.0-6/stpp/data/fmd.R |only stpp-2.0-6/stpp/data/northcumbria.R |only stpp-2.0-7/stpp/CHANGES | 34 - stpp-2.0-7/stpp/DESCRIPTION | 10 stpp-2.0-7/stpp/MD5 | 52 - stpp-2.0-7/stpp/NAMESPACE | 88 +- stpp-2.0-7/stpp/R/KLISTAhat.R | 334 +++++----- stpp-2.0-7/stpp/R/PCFhat.R | 366 +++++------ stpp-2.0-7/stpp/R/gsp.R | 360 +++++------ stpp-2.0-7/stpp/R/gte.R | 446 +++++++------- stpp-2.0-7/stpp/R/kmmr.R | 324 +++++----- stpp-2.0-7/stpp/R/kmmt.R | 426 ++++++------- stpp-2.0-7/stpp/R/kmr.R | 326 +++++----- stpp-2.0-7/stpp/R/kmt.R | 288 ++++----- stpp-2.0-7/stpp/R/rpp.R | 1038 +++++++++++++++++----------------- stpp-2.0-7/stpp/R/sthpcpp.R | 58 - stpp-2.0-7/stpp/README.md | 90 +- stpp-2.0-7/stpp/build/vignette.rds |binary stpp-2.0-7/stpp/data/fmd.rda |only stpp-2.0-7/stpp/data/northcumbria.rda |only stpp-2.0-7/stpp/inst/doc/docs.html | 415 ++++++++++--- stpp-2.0-7/stpp/man/KLISTAhat.Rd | 110 +-- stpp-2.0-7/stpp/man/gsp.Rd | 164 ++--- stpp-2.0-7/stpp/man/gte.Rd | 168 ++--- stpp-2.0-7/stpp/man/kmmr.Rd | 170 ++--- stpp-2.0-7/stpp/man/kmmt.Rd | 170 ++--- stpp-2.0-7/stpp/man/kmr.Rd | 168 ++--- stpp-2.0-7/stpp/man/kmt.Rd | 166 ++--- stpp-2.0-7/stpp/man/stpp-package.Rd | 200 +++--- 29 files changed, 3108 insertions(+), 2863 deletions(-)
Title: Specification of Generalised Linear Mixed Models
Description: Specification of generalised linear mixed models using the 'R6' object-orientated class system. The package provides classes 'Covariance', 'MeanFunction' and 'Model', which allow for flexible specification of generalised linear mixed models, as well as functionality to produce relevant matrices, values, and analyses.
See <https://github.com/samuel-watson/glmmrBase/blob/master/README.md> for a detailed manual.
Author: Sam Watson [aut, cre],
Yi Pan [aut]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 0.1.3 dated 2022-11-03 and 0.2.1 dated 2022-11-30
glmmrBase-0.1.3/glmmrBase/man/blockMat.Rd |only glmmrBase-0.1.3/glmmrBase/man/loglikD.Rd |only glmmrBase-0.2.1/glmmrBase/DESCRIPTION | 8 glmmrBase-0.2.1/glmmrBase/MD5 | 43 - glmmrBase-0.2.1/glmmrBase/R/R6Model.R | 272 ++++++--- glmmrBase-0.2.1/glmmrBase/R/R6covariance.R | 227 ++++---- glmmrBase-0.2.1/glmmrBase/R/R6meanfunction.R | 128 ++-- glmmrBase-0.2.1/glmmrBase/R/RcppExports.R | 66 +- glmmrBase-0.2.1/glmmrBase/R/parallel_crt.R | 2 glmmrBase-0.2.1/glmmrBase/R/staircase_crt.R | 2 glmmrBase-0.2.1/glmmrBase/R/steppedwedge.R | 2 glmmrBase-0.2.1/glmmrBase/build/partial.rdb |binary glmmrBase-0.2.1/glmmrBase/inst/include/glmmr |only glmmrBase-0.2.1/glmmrBase/inst/include/glmmr.h | 697 ------------------------- glmmrBase-0.2.1/glmmrBase/man/Covariance.Rd | 39 + glmmrBase-0.2.1/glmmrBase/man/MeanFunction.Rd | 81 +- glmmrBase-0.2.1/glmmrBase/man/Model.Rd | 305 +++++++--- glmmrBase-0.2.1/glmmrBase/man/genCholD.Rd | 19 glmmrBase-0.2.1/glmmrBase/man/genD.Rd | 15 glmmrBase-0.2.1/glmmrBase/man/gen_dhdmu.Rd | 4 glmmrBase-0.2.1/glmmrBase/man/sample_re.Rd |only glmmrBase-0.2.1/glmmrBase/src/RcppExports.cpp | 63 +- glmmrBase-0.2.1/glmmrBase/src/gen_d.cpp | 112 +--- 23 files changed, 830 insertions(+), 1255 deletions(-)
Title: Distance Based Cell Lineage Reconstruction
Description: R codes for distance based cell lineage reconstruction. Our methods won both sub-challenges 2 and 3 of the Allen Institute Cell Lineage Reconstruction DREAM Challenge in 2020.
References: Gong et al. (2021) <doi:10.1016/j.cels.2021.05.008>, Gong et al. (2022) <doi:10.1186/s12859-022-04633-x>.
Author: Il-Youp Kwak [aut, cre],
Wuming Gong [aut]
Maintainer: Il-Youp Kwak <ikwak2@cau.ac.kr>
Diff between DCLEAR versions 1.0.8 dated 2021-09-03 and 1.0.11 dated 2022-11-30
DESCRIPTION | 15 - MD5 | 52 ++- NAMESPACE | 3 R/AllClass.r | 5 R/DCLEAR.r | 3 R/as_igraph.r | 29 ++ R/as_lineage_tree.r | 1 R/dist_replacement.r | 107 +++----- R/globals.r |only R/process_sequence.r | 57 ++-- R/prune.r | 1 R/simulate.r | 292 ++++++++++++++++------ R/substr_kmer.r | 30 +- R/summarize_kmer.r | 9 README.md | 2 build/vignette.rds |binary inst/doc/PrepC3.html | 4 inst/doc/WHhowto.Rmd | 2 inst/doc/WHhowto.html | 18 - man/add_deletion.Rd |only man/add_dropout.Rd |only man/as_igraph-data.frame-method.Rd |only man/get_sequence.Rd |only man/process_sequence-phyDat-method.Rd | 16 + man/sample_mutation_outcome.Rd |only man/sample_mutation_site.Rd |only man/score_simulation.Rd |only man/simulate-lineage_tree_config-phyDat-method.Rd | 6 man/simulate_core.Rd | 11 src/DCLEAR.cpp | 12 vignettes/WHhowto.Rmd | 2 31 files changed, 443 insertions(+), 234 deletions(-)
Title: Modern Text Mining Framework for R
Description: Fast and memory-friendly tools for text vectorization, topic
modeling (LDA, LSA), word embeddings (GloVe), similarities. This package
provides a source-agnostic streaming API, which allows researchers to perform
analysis of collections of documents which are larger than available RAM. All
core functions are parallelized to benefit from multicore machines.
Author: Dmitriy Selivanov [aut, cre, cph],
Manuel Bickel [aut, cph] ,
Qing Wang [aut, cph]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between text2vec versions 0.6.2 dated 2022-09-11 and 0.6.3 dated 2022-11-30
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/distance.R | 2 +- R/mc_queue.R | 6 ------ R/model_Collocations.R | 3 +-- R/model_bns.R | 2 +- R/model_tfidf.R | 2 +- R/tcm.R | 6 +++--- R/utils_matrix.R | 4 ++-- inst/doc/files-multicore.html | 6 +++--- inst/doc/glove.html | 4 ++-- inst/doc/text-vectorization.html | 22 +++++++++++----------- man/Collocations.Rd | 3 +-- 13 files changed, 42 insertions(+), 50 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Florian Stijven, Fenny Ong, Paul Meyvisch, Alvaro Florez Poveda, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 2.4 dated 2022-08-13 and 2.5 dated 2022-11-30
DESCRIPTION | 14 ++-- MD5 | 13 +++ NAMESPACE | 131 ++++++++++++++++++++++---------------- R/fit_model_SurvSurv.R |only R/goodness_of_fit_SurvSurv.R |only R/log_likelihoods.R |only R/sensitivity_analysis_SurvSurv.R |only R/utils.R |only man/fit_model_SurvSurv.Rd |only man/ica_SurvSurv_sens.Rd |only man/marginal_gof_scr.Rd |only man/model_fit_measures.Rd |only 12 files changed, 96 insertions(+), 62 deletions(-)
Title: A General Algorithm to Enhance the Performance of Variable
Selection Methods in Correlated Datasets
Description: An implementation of the selectboost algorithm (Bertrand et al. 2020, 'Bioinformatics', <doi:10.1093/bioinformatics/btaa855>), which is a general algorithm that improves the precision of any existing variable selection method. This algorithm is based on highly intensive simulations and takes into account the correlation structure of the data. It can either produce a confidence index for variable selection or it can be used in an experimental design planning perspective.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Ismail Aouadi [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between SelectBoost versions 2.2.1 dated 2022-11-29 and 2.2.2 dated 2022-11-30
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NEWS.md | 6 +++++- inst/doc/benchmarking-selectboost-networks.Rmd | 2 +- inst/doc/benchmarking-selectboost-networks.html | 2 +- inst/doc/confidence-indices-Cascade-networks.Rmd | 2 +- inst/doc/confidence-indices-Cascade-networks.html | 2 +- inst/doc/sim-with-sb.Rmd | 2 +- inst/doc/sim-with-sb.html | 2 +- vignettes/benchmarking-selectboost-networks.Rmd | 2 +- vignettes/confidence-indices-Cascade-networks.Rmd | 2 +- vignettes/sim-with-sb.Rmd | 2 +- 12 files changed, 31 insertions(+), 27 deletions(-)
Title: A simple interface to the PROJ.4 cartographic projections
library
Description: A simple interface to lat/long projection and datum
transformation of the PROJ.4 cartographic projections library. It
allows transformation of geographic coordinates from one projection
and/or datum to another.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between proj4 versions 1.0-11 dated 2022-01-31 and 1.0-12 dated 2022-11-30
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.ucrt | 4 ++-- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Local Polynomial Density Estimation and Inference
Description: Without imposing stringent distributional assumptions or shape restrictions, nonparametric estimation has been popular in economics and other social sciences for counterfactual analysis, program evaluation, and policy recommendations. This package implements a novel density (and derivatives) estimator based on local polynomial regressions, documented in Cattaneo, Jansson and Ma (2022) <doi:10.18637/jss.v101.i02>: lpdensity() to construct local polynomial based density (and derivatives) estimator, and lpbwdensity() to perform data-driven bandwidth selection.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between lpdensity versions 2.3.1 dated 2022-05-03 and 2.3.2 dated 2022-11-30
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 + R/lpdensity-package.R | 3 ++- R/lpdensity.R | 2 +- R/lpdensity_methods.R | 5 +++-- build/partial.rdb |binary man/lpdensity-package.Rd | 2 +- man/lpdensity.Rd | 2 +- 9 files changed, 21 insertions(+), 18 deletions(-)
Title: Java Graphics Device
Description: Graphics device routing all graphics commands to a Java
program. The actual functionality of the JavaGD depends
on the Java-side implementation. Simple AWT and Swing
implementations are included.
Author: Simon Urbanek <Simon.Urbanek@R-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@R-project.org>
Diff between JavaGD versions 0.6-4 dated 2020-11-02 and 0.6-5 dated 2022-11-30
DESCRIPTION | 9 MD5 | 23 NEWS | 17 configure | 2869 +++++++++++++++++++++++++++------------------------ configure.ac | 9 inst/java/javaGD.jar |binary src/config.h.in | 16 src/dummy.c |only src/jGDtalk.c | 42 src/javaGD.c | 6 src/javaGD.h | 2 tools/config.guess |only tools/config.sub |only tools/getsp.class |binary 14 files changed, 1612 insertions(+), 1381 deletions(-)
Title: The Hilbert-Huang Transform: Tools and Methods
Description: Builds on the EMD package to provide additional tools for empirical mode decomposition (EMD) and Hilbert spectral analysis. It also implements the ensemble empirical decomposition (EEMD) and the complete ensemble empirical mode decomposition (CEEMD) methods to avoid mode mixing and intermittency problems found in EMD analysis. The package comes with several plotting methods that can be used to view intrinsic mode functions, the HHT spectrum, and the Fourier spectrum.
Author: Daniel C. Bowman [aut, cre],
Jonathan M. Lees [ctb]
Maintainer: Daniel C. Bowman <danny.c.bowman@gmail.com>
Diff between hht versions 2.1.4 dated 2021-03-28 and 2.1.5 dated 2022-11-30
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 3 ++- NEWS | 56 ++++++++++++++++++++++++++++++++++++++------------------ 4 files changed, 48 insertions(+), 27 deletions(-)
Title: Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis.
Risk regression models for survival endpoints also in the presence of competing
risks are fitted using binomial regression based on a time sequence of binary
event status variables. A formula interface for the Fine-Gray regression model
and an interface for the combination of cause-specific Cox regression models.
A toolbox for assessing and comparing performance of risk predictions (risk
markers and risk prediction models). Prediction performance is measured by the
Brier score and the area under the ROC curve for binary possibly time-dependent
outcome. Inverse probability of censoring weighting and pseudo values are used
to deal with right censored data. Lists of risk markers and lists of risk models
are assessed simultaneously. Cross-validation repeatedly splits the data, trains
the risk prediction models on one part of each split and then summarizes and
compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre],
Johan Sebastian Ohlendorff [aut],
Paul Blanche [ctb],
Rikke Mortensen [ctb],
Marvin Wright [ctb],
Nikolaj Tollenaar [ctb],
John Muschelli [ctb],
Ulla Brasch Mogensen [ctb],
Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 2022.11.21 dated 2022-11-22 and 2022.11.28 dated 2022-11-30
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- src/Makevars | 13 +++++++++++-- src/RcppExports.cpp | 12 ++++++------ src/baseHaz.cpp | 5 ++--- src/calcSeCSC.cpp | 9 ++++----- src/calcSeCox.cpp | 3 +-- src/confBand.cpp | 21 ++++++++++----------- src/iidCox.cpp | 7 +++---- src/predictCIF.cpp | 3 +-- src/sweepCenterScale.cpp | 1 - src/weightedAverageIFCumhazard.cpp | 1 - 12 files changed, 52 insertions(+), 51 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: Fuzzy Measure Tools
Description: Various tools for handling fuzzy measures, calculating Shapley value and interaction index, Choquet and Sugeno integrals, as well as fitting fuzzy measures to empirical data are provided. Construction of fuzzy measures from empirical data is done by solving a linear programming problem by using 'lpsolve' package, whose source in C adapted to the R environment
is included. The description of the basic theory of fuzzy measures is in the manual in the Doc folder in this package. Please refer to the following:
[1] <https://personal-sites.deakin.edu.au/~gleb/fmtools.html>
[2] G. Beliakov, H. Bustince, T. Calvo, 'A Practical Guide to Averaging', Springer, (2016, ISBN: 978-3-319-24753-3).
[3] G. Beliakov, S. James, J-Z. Wu, 'Discrete Fuzzy Measures', Springer, (2020, ISBN: 978-3-030-15305-2).
Author: Gleb Beliakov [aut, cre],
Quan Vu [ctb],
Andrei Kelarev [ctb],
Michel Berkelaar [ctb],
Kjell Eikland [ctb],
Samuel E. Buttrey [ctb],
Stefan I. Larimore [ctb],
Timothy A. Davis [ctb],
John Gilbert [ctb],
Esmond Ng [ctb],
Peter Notebaert [ctb],
Richard [...truncated...]
Maintainer: Gleb Beliakov <gleb@deakin.edu.au>
Diff between Rfmtool versions 4.1.8 dated 2022-03-27 and 4.1.9 dated 2022-11-30
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/Rfmtool_manual.pdf |binary src/fmrandom.h | 2 +- src/lp_matrix.c | 2 +- src/yacc_read.c | 4 ++-- 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Manipulation Testing Based on Density Discontinuity
Description: Density discontinuity testing (a.k.a. manipulation testing) is commonly employed in regression discontinuity designs and other program evaluation settings to detect perfect self-selection (manipulation) around a cutoff where treatment/policy assignment changes. This package implements manipulation testing procedures using the local polynomial density estimators: rddensity() to construct test statistics and p-values given a prespecified cutoff, rdbwdensity() to perform data-driven bandwidth selection, and rdplotdensity() to construct density plots.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between rddensity versions 2.2 dated 2021-03-03 and 2.3 dated 2022-11-30
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/rdbwdensity.R | 7 +++---- R/rddensity-package.R | 18 +++++++++--------- R/rddensity.R | 14 +++++++------- R/rddensity_fun.R | 14 ++++---------- R/rddensity_senate.R | 2 +- R/rdplotdensity.R | 22 ++++++++++++---------- build/partial.rdb |binary man/rdbwdensity.Rd | 4 ++-- man/rddensity-package.Rd | 18 +++++++++--------- man/rddensity.Rd | 14 +++++++------- man/rddensity_senate.Rd | 2 +- man/rdplotdensity.Rd | 21 ++++++++++++--------- 14 files changed, 84 insertions(+), 86 deletions(-)
Title: Degrees of Freedom and Statistical Inference for Partial Least
Squares Regression
Description: The plsdof package provides Degrees of Freedom estimates
for Partial Least Squares (PLS) Regression. Model selection for
PLS is based on various information criteria (aic, bic, gmdl)
or on cross-validation. Estimates for the mean and covariance
of the PLS regression coefficients are available. They allow
the construction of approximate confidence intervals and the
application of test procedures (Kramer and Sugiyama
2012 <doi:10.1198/jasa.2011.tm10107>).
Further, cross-validation procedures for Ridge Regression and
Principal Components Regression are available.
Author: Nicole Kraemer, Mikio L. Braun
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between plsdof versions 0.3-0 dated 2021-03-14 and 0.3-2 dated 2022-11-30
DESCRIPTION | 12 MD5 | 14 NEWS.md | 10 R/pls.ic.R | 4 R/plsdof-package.R | 2 README.md | 978 ++++++++++++------------------------ man/figures/README-pls1pnaive-1.png |binary man/plsdof-package.Rd | 2 8 files changed, 370 insertions(+), 652 deletions(-)
Title: Phylogenetic Comparative Methods with Uncertainty Estimates
Description: A framework for analytically computing the asymptotic confidence intervals and maximum-likelihood estimates of a class of continuous-time Gaussian branching processes defined by Mitov V, Bartoszek K, Asimomitis G, Stadler T (2019) <doi:10.1016/j.tpb.2019.11.005>. The class of model includes the widely used Ornstein-Uhlenbeck and Brownian motion branching processes. The framework is designed to be flexible enough so that the users can easily specify their own sub-models, or re-parameterizations, and obtain the maximum-likelihood estimates and confidence intervals of their own custom models.
Author: Hao Chi Kiang [cre, aut]
Maintainer: Hao Chi Kiang <hello@hckiang.com>
Diff between glinvci versions 1.1.20 dated 2022-11-16 and 1.1.21 dated 2022-11-30
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- configure.ac | 2 +- inst/doc/Getting_Started.pdf |binary src/oumods.f90 | 1 - src/phytr.c | 27 ++++++++++++++------------- 6 files changed, 24 insertions(+), 24 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associ [...truncated...]
Author: Moreno Bevilacqua [aut, cre] ,
Victor Morales-Onate [aut] ,
Christian Caamano-Carrillo [aut]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 1.0.3 dated 2022-10-23 and 1.0.4 dated 2022-11-30
DESCRIPTION | 8 - MD5 | 48 +++--- R/GeoCompositeLik2.R | 142 ++++++++++++++------ R/GeoCorrFct.r | 5 R/GeoCorrFct_Cop.R | 4 R/GeoCovmatrix.r | 3 R/GeoFit.r | 6 R/GeoFit2.R | 2 R/GeoKrig.r | 2 R/GeoPit.R | 18 +- R/GeoQQ.R | 42 +----- R/GeoResiduals.r | 37 ++--- R/GeoSim.r | 1 R/GeoSimCopula.R | 2 man/Anomalies.Rd | 1 man/GeoAniso.Rd | 2 man/GeoCorrFct_Cop.Rd | 2 man/GeoCovariogram.Rd | 8 - src/CompositeLikelihood2.c | 213 ++++++++++++++++++++---------- src/CompositeLikelihood2_ani.c | 157 +++++----------------- src/CompositeLikelihoodCond2.c | 251 ------------------------------------ src/CompositeLikelihoodCond2_ani.c | 255 ------------------------------------- src/Distributions.c | 156 +++++++++++++++++++--- src/GeoModels_init.c | 175 ++++++++++--------------- src/header.h | 2 25 files changed, 563 insertions(+), 979 deletions(-)
Title: Covariate-Adaptive Randomization for Clinical Trials
Description: Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria.
Author: Fuyi Tu [aut],
Xiaoqing Ye [aut, cre],
Wei Ma [aut, ths],
Feifang Hu [aut, ths]
Maintainer: Xiaoqing Ye <ye_xiaoq@163.com>
Diff between carat versions 2.0.2 dated 2021-10-16 and 2.1.0 dated 2022-11-30
DESCRIPTION | 8 +-- MD5 | 20 ++++---- R/test_Rfunction.R | 2 data/pats.rda |binary inst/NEWS.Rd | 6 ++ man/CompPower.Rd | 2 man/corr.test.Rd | 2 man/evalPower.Rd | 8 +-- man/getData.Rd | 4 - man/rand.test.Rd | 2 src/InnerFun.cpp | 124 +++++++++++++++++++++++++++++++++++++++++++++-------- 11 files changed, 137 insertions(+), 41 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-29 0.3.0
2022-09-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-25 0.1.4
2022-11-16 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-28 0.2-9
2020-11-18 0.2-8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-20 1.0.13
2022-01-09 1.0.12
2021-05-19 1.0.11
2021-05-06 1.0.10
2021-03-09 1.0.9
2020-05-22 1.0.8
2020-05-09 1.0.7
2019-07-09 1.0.6
2019-07-02 1.0.5
2018-08-31 1.0.4
2016-12-13 1.0.2
2016-11-10 1.0.1
2015-07-30 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-21 1.1.0
2022-04-19 1.0.1