Title: Receiver Operating Characteristic (ROC)-Guided Classification
and Survival Tree
Description: Receiver Operating Characteristic (ROC)-guided survival trees and ensemble algorithms are implemented, providing a unified framework for tree-structured analysis with censored survival outcomes. A time-invariant partition scheme on the survivor population was considered to incorporate time-dependent covariates. Motivated by ideas of randomized tests, generalized time-dependent ROC curves were used to evaluate the performance of survival trees and establish the optimality of the target hazard/survival function. The optimality of the target hazard function motivates us to use a weighted average of the time-dependent area under the curve (AUC) on a set of time points to evaluate the prediction performance of survival trees and to guide splitting and pruning. A detailed description of the implemented methods can be found in Sun et al. (2019) <arXiv:1809.05627>.
Author: Yifei Sun [aut],
Mei-Cheng Wang [aut],
Sy Han Chiou [aut, cre]
Maintainer: Sy Han Chiou <schiou@utdallas.edu>
Diff between rocTree versions 1.0.0 dated 2019-03-24 and 1.1.0 dated 2019-10-10
rocTree-1.0.0/rocTree/R/CV.R |only rocTree-1.0.0/rocTree/R/grow.R |only rocTree-1.0.0/rocTree/R/plot.rocForest.R |only rocTree-1.0.0/rocTree/R/predict.rocForest.R |only rocTree-1.0.0/rocTree/R/print.rocForest.R |only rocTree-1.0.0/rocTree/R/rocForest.R |only rocTree-1.0.0/rocTree/R/splitTree.R |only rocTree-1.0.0/rocTree/inst |only rocTree-1.0.0/rocTree/man/plot.rocForest.Rd |only rocTree-1.0.0/rocTree/man/plotTreeHaz.Rd |only rocTree-1.0.0/rocTree/man/predict.rocForest.Rd |only rocTree-1.0.0/rocTree/man/print.rocForest.Rd |only rocTree-1.0.0/rocTree/man/rocForest.Rd |only rocTree-1.0.0/rocTree/src/init.c |only rocTree-1.0.0/rocTree/src/tree.c |only rocTree-1.1.0/rocTree/DESCRIPTION | 15 rocTree-1.1.0/rocTree/MD5 | 63 ++-- rocTree-1.1.0/rocTree/NAMESPACE | 18 - rocTree-1.1.0/rocTree/NEWS.md | 77 ++--- rocTree-1.1.0/rocTree/R/RcppExports.R |only rocTree-1.1.0/rocTree/R/plot.predict.rocTree.R |only rocTree-1.1.0/rocTree/R/plot.rocTree.R | 183 ++++++----- rocTree-1.1.0/rocTree/R/predict.rocTree.R | 131 +++----- rocTree-1.1.0/rocTree/R/print.rocTree.R | 158 ++++------ rocTree-1.1.0/rocTree/R/rocTree.R | 367 +++++++++++------------- rocTree-1.1.0/rocTree/R/rocTree_pkg.R | 29 - rocTree-1.1.0/rocTree/R/util.R | 112 +------ rocTree-1.1.0/rocTree/man/plot.rocTree.Rd | 33 +- rocTree-1.1.0/rocTree/man/predict.rocTree.Rd | 29 + rocTree-1.1.0/rocTree/man/print.rocTree.Rd | 25 + rocTree-1.1.0/rocTree/man/rocTree-package.Rd | 20 - rocTree-1.1.0/rocTree/man/rocTree.Rd | 69 ++-- rocTree-1.1.0/rocTree/src/Data.cpp |only rocTree-1.1.0/rocTree/src/Data.h |only rocTree-1.1.0/rocTree/src/Data2.cpp |only rocTree-1.1.0/rocTree/src/Data2.h |only rocTree-1.1.0/rocTree/src/Forest.cpp |only rocTree-1.1.0/rocTree/src/Forest.h |only rocTree-1.1.0/rocTree/src/ForestPrediction.cpp |only rocTree-1.1.0/rocTree/src/ForestPrediction.h |only rocTree-1.1.0/rocTree/src/Makevars |only rocTree-1.1.0/rocTree/src/RcppExports.cpp |only rocTree-1.1.0/rocTree/src/Tree.cpp |only rocTree-1.1.0/rocTree/src/Tree.h |only rocTree-1.1.0/rocTree/src/TreeGrow.cpp |only rocTree-1.1.0/rocTree/src/TreeGrow.h |only rocTree-1.1.0/rocTree/src/TreePrediction.cpp |only rocTree-1.1.0/rocTree/src/TreePrediction.h |only rocTree-1.1.0/rocTree/src/globals.h |only rocTree-1.1.0/rocTree/src/rocTree-functions.cpp |only 50 files changed, 617 insertions(+), 712 deletions(-)
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a unified interface for model fitting, prediction, performance assessment, and presentation of results. Approaches for model fitting and prediction of numerical, categorical, or censored time-to-event outcomes include traditional regression models, regularization methods, tree-based methods, support vector machines, neural networks, ensembles, data preprocessing, filtering, and model tuning and selection. Performance metrics are provided for model assessment and can be estimated with independent test sets, split sampling, cross-validation, or bootstrap resampling. Resample estimation can be executed in parallel for faster processing and nested in cases of model tuning and selection. Modeling results can be summarized with descriptive statistics; calibration curves; variable importance; partial dependence plots; confusion matrices; and ROC, lift, and other performance curves.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 1.5.0 dated 2019-08-01 and 1.6.0 dated 2019-10-10
MachineShop-1.5.0/MachineShop/R/expand.model.R |only MachineShop-1.5.0/MachineShop/man/expand.model.Rd |only MachineShop-1.6.0/MachineShop/DESCRIPTION | 8 MachineShop-1.6.0/MachineShop/MD5 | 301 +- MachineShop-1.6.0/MachineShop/NAMESPACE | 23 MachineShop-1.6.0/MachineShop/NEWS.md | 26 MachineShop-1.6.0/MachineShop/R/AllClasses.R | 34 MachineShop-1.6.0/MachineShop/R/MLControl.R | 79 MachineShop-1.6.0/MachineShop/R/MLMetric.R | 23 MachineShop-1.6.0/MachineShop/R/MLModel.R | 60 MachineShop-1.6.0/MachineShop/R/ML_AdaBagModel.R | 14 MachineShop-1.6.0/MachineShop/R/ML_AdaBoostModel.R | 18 MachineShop-1.6.0/MachineShop/R/ML_BARTMachineModel.R | 28 MachineShop-1.6.0/MachineShop/R/ML_BARTModel.R | 34 MachineShop-1.6.0/MachineShop/R/ML_BlackBoostModel.R | 30 MachineShop-1.6.0/MachineShop/R/ML_C50Model.R | 32 MachineShop-1.6.0/MachineShop/R/ML_CForestModel.R | 24 MachineShop-1.6.0/MachineShop/R/ML_CoxModel.R | 25 MachineShop-1.6.0/MachineShop/R/ML_EarthModel.R | 18 MachineShop-1.6.0/MachineShop/R/ML_FDAModel.R | 49 MachineShop-1.6.0/MachineShop/R/ML_GAMBoostModel.R | 26 MachineShop-1.6.0/MachineShop/R/ML_GBMModel.R | 26 MachineShop-1.6.0/MachineShop/R/ML_GLMBoostModel.R | 22 MachineShop-1.6.0/MachineShop/R/ML_GLMModel.R | 31 MachineShop-1.6.0/MachineShop/R/ML_GLMNetModel.R | 28 MachineShop-1.6.0/MachineShop/R/ML_KNNModel.R | 14 MachineShop-1.6.0/MachineShop/R/ML_LARSModel.R | 20 MachineShop-1.6.0/MachineShop/R/ML_LDAModel.R | 18 MachineShop-1.6.0/MachineShop/R/ML_LMModel.R | 6 MachineShop-1.6.0/MachineShop/R/ML_MDAModel.R | 35 MachineShop-1.6.0/MachineShop/R/ML_NNetModel.R | 39 MachineShop-1.6.0/MachineShop/R/ML_NaiveBayesModel.R | 6 MachineShop-1.6.0/MachineShop/R/ML_PLSModel.R | 14 MachineShop-1.6.0/MachineShop/R/ML_POLRModel.R | 6 MachineShop-1.6.0/MachineShop/R/ML_QDAModel.R | 12 MachineShop-1.6.0/MachineShop/R/ML_RPartModel.R | 16 MachineShop-1.6.0/MachineShop/R/ML_RandomForestModel.R | 14 MachineShop-1.6.0/MachineShop/R/ML_RangerModel.R | 25 MachineShop-1.6.0/MachineShop/R/ML_SVMModel.R | 71 MachineShop-1.6.0/MachineShop/R/ML_SelectedModel.R | 39 MachineShop-1.6.0/MachineShop/R/ML_StackedModel.R | 24 MachineShop-1.6.0/MachineShop/R/ML_SuperModel.R | 30 MachineShop-1.6.0/MachineShop/R/ML_SurvRegModel.R | 27 MachineShop-1.6.0/MachineShop/R/ML_TreeModel.R | 8 MachineShop-1.6.0/MachineShop/R/ML_TunedModel.R | 48 MachineShop-1.6.0/MachineShop/R/ML_XGBModel.R | 59 MachineShop-1.6.0/MachineShop/R/MachineShop-package.R | 66 MachineShop-1.6.0/MachineShop/R/ModelFrame.R | 30 MachineShop-1.6.0/MachineShop/R/ModelList.R |only MachineShop-1.6.0/MachineShop/R/ModelRecipe.R | 13 MachineShop-1.6.0/MachineShop/R/TunedRecipe.R |only MachineShop-1.6.0/MachineShop/R/calibration.R | 111 MachineShop-1.6.0/MachineShop/R/confusion.R | 110 MachineShop-1.6.0/MachineShop/R/convert.R | 10 MachineShop-1.6.0/MachineShop/R/dependence.R | 34 MachineShop-1.6.0/MachineShop/R/deprecated.R |only MachineShop-1.6.0/MachineShop/R/diff.R | 83 MachineShop-1.6.0/MachineShop/R/expand.R |only MachineShop-1.6.0/MachineShop/R/extract.R | 34 MachineShop-1.6.0/MachineShop/R/fit.R | 70 MachineShop-1.6.0/MachineShop/R/grid.R | 8 MachineShop-1.6.0/MachineShop/R/lift.R | 38 MachineShop-1.6.0/MachineShop/R/metricinfo.R | 31 MachineShop-1.6.0/MachineShop/R/metrics.R | 39 MachineShop-1.6.0/MachineShop/R/metrics_factor.R | 81 MachineShop-1.6.0/MachineShop/R/metrics_numeric.R | 5 MachineShop-1.6.0/MachineShop/R/modelinfo.R | 47 MachineShop-1.6.0/MachineShop/R/models.R |only MachineShop-1.6.0/MachineShop/R/performance.R | 216 - MachineShop-1.6.0/MachineShop/R/performance_curve.R | 159 - MachineShop-1.6.0/MachineShop/R/plots.R | 320 +- MachineShop-1.6.0/MachineShop/R/predict.R | 43 MachineShop-1.6.0/MachineShop/R/resample.R | 229 +- MachineShop-1.6.0/MachineShop/R/response.R | 9 MachineShop-1.6.0/MachineShop/R/settings.R |only MachineShop-1.6.0/MachineShop/R/show.R | 75 MachineShop-1.6.0/MachineShop/R/summary.R | 124 - MachineShop-1.6.0/MachineShop/R/survival.R | 32 MachineShop-1.6.0/MachineShop/R/tune.R | 245 +- MachineShop-1.6.0/MachineShop/R/tune_recipe.R |only MachineShop-1.6.0/MachineShop/R/utils.R | 65 MachineShop-1.6.0/MachineShop/R/varimp.R | 12 MachineShop-1.6.0/MachineShop/inst/doc/Introduction.R | 29 MachineShop-1.6.0/MachineShop/inst/doc/Introduction.Rmd | 89 MachineShop-1.6.0/MachineShop/inst/doc/Introduction.html | 1714 +++++++-------- MachineShop-1.6.0/MachineShop/inst/doc/MLModels.Rmd | 2 MachineShop-1.6.0/MachineShop/inst/doc/MLModels.html | 34 MachineShop-1.6.0/MachineShop/man/AdaBagModel.Rd | 8 MachineShop-1.6.0/MachineShop/man/AdaBoostModel.Rd | 8 MachineShop-1.6.0/MachineShop/man/BARTMachineModel.Rd | 12 MachineShop-1.6.0/MachineShop/man/BARTModel.Rd | 4 MachineShop-1.6.0/MachineShop/man/BlackBoostModel.Rd | 14 MachineShop-1.6.0/MachineShop/man/C50Model.Rd | 12 MachineShop-1.6.0/MachineShop/man/CForestModel.Rd | 10 MachineShop-1.6.0/MachineShop/man/CoxModel.Rd | 12 MachineShop-1.6.0/MachineShop/man/EarthModel.Rd | 12 MachineShop-1.6.0/MachineShop/man/FDAModel.Rd | 25 MachineShop-1.6.0/MachineShop/man/GAMBoostModel.Rd | 14 MachineShop-1.6.0/MachineShop/man/GBMModel.Rd | 16 MachineShop-1.6.0/MachineShop/man/GLMBoostModel.Rd | 14 MachineShop-1.6.0/MachineShop/man/GLMModel.Rd | 18 MachineShop-1.6.0/MachineShop/man/GLMNetModel.Rd | 14 MachineShop-1.6.0/MachineShop/man/KNNModel.Rd | 10 MachineShop-1.6.0/MachineShop/man/LARSModel.Rd | 12 MachineShop-1.6.0/MachineShop/man/LDAModel.Rd | 14 MachineShop-1.6.0/MachineShop/man/LMModel.Rd | 4 MachineShop-1.6.0/MachineShop/man/MDAModel.Rd | 17 MachineShop-1.6.0/MachineShop/man/MLControl.Rd | 30 MachineShop-1.6.0/MachineShop/man/MLModel.Rd | 24 MachineShop-1.6.0/MachineShop/man/MachineShop-package.Rd | 66 MachineShop-1.6.0/MachineShop/man/ModelFrame-methods.Rd | 16 MachineShop-1.6.0/MachineShop/man/ModelList.Rd |only MachineShop-1.6.0/MachineShop/man/NNetModel.Rd | 10 MachineShop-1.6.0/MachineShop/man/NaiveBayesModel.Rd | 4 MachineShop-1.6.0/MachineShop/man/PLSModel.Rd | 10 MachineShop-1.6.0/MachineShop/man/POLRModel.Rd | 4 MachineShop-1.6.0/MachineShop/man/QDAModel.Rd | 8 MachineShop-1.6.0/MachineShop/man/RPartModel.Rd | 10 MachineShop-1.6.0/MachineShop/man/RandomForestModel.Rd | 10 MachineShop-1.6.0/MachineShop/man/RangerModel.Rd | 13 MachineShop-1.6.0/MachineShop/man/SVMModel.Rd | 24 MachineShop-1.6.0/MachineShop/man/SelectedModel.Rd | 34 MachineShop-1.6.0/MachineShop/man/StackedModel.Rd | 22 MachineShop-1.6.0/MachineShop/man/SuperModel.Rd | 27 MachineShop-1.6.0/MachineShop/man/SurvMatrix.Rd | 4 MachineShop-1.6.0/MachineShop/man/SurvRegModel.Rd | 14 MachineShop-1.6.0/MachineShop/man/TreeModel.Rd | 4 MachineShop-1.6.0/MachineShop/man/TunedModel.Rd | 45 MachineShop-1.6.0/MachineShop/man/TunedRecipe.Rd |only MachineShop-1.6.0/MachineShop/man/XGBModel.Rd | 28 MachineShop-1.6.0/MachineShop/man/calibration.Rd | 19 MachineShop-1.6.0/MachineShop/man/confusion.Rd | 50 MachineShop-1.6.0/MachineShop/man/dependence.Rd | 20 MachineShop-1.6.0/MachineShop/man/deprecated.Rd |only MachineShop-1.6.0/MachineShop/man/diff-methods.Rd | 28 MachineShop-1.6.0/MachineShop/man/dot-.Rd | 4 MachineShop-1.6.0/MachineShop/man/expand_model.Rd |only MachineShop-1.6.0/MachineShop/man/expand_params.Rd |only MachineShop-1.6.0/MachineShop/man/expand_steps.Rd |only MachineShop-1.6.0/MachineShop/man/extract-methods.Rd | 14 MachineShop-1.6.0/MachineShop/man/fit-methods.Rd | 37 MachineShop-1.6.0/MachineShop/man/lift.Rd | 19 MachineShop-1.6.0/MachineShop/man/metricinfo.Rd | 25 MachineShop-1.6.0/MachineShop/man/metrics.Rd | 80 MachineShop-1.6.0/MachineShop/man/modelinfo.Rd | 40 MachineShop-1.6.0/MachineShop/man/models.Rd |only MachineShop-1.6.0/MachineShop/man/performance.Rd | 60 MachineShop-1.6.0/MachineShop/man/performance_curve.Rd | 28 MachineShop-1.6.0/MachineShop/man/plot-methods.Rd | 78 MachineShop-1.6.0/MachineShop/man/predict.Rd | 25 MachineShop-1.6.0/MachineShop/man/resample-methods.Rd | 76 MachineShop-1.6.0/MachineShop/man/response-methods.Rd | 10 MachineShop-1.6.0/MachineShop/man/settings.Rd |only MachineShop-1.6.0/MachineShop/man/summary-methods.Rd | 62 MachineShop-1.6.0/MachineShop/man/t.test.Rd | 17 MachineShop-1.6.0/MachineShop/man/tune-methods.Rd | 121 - MachineShop-1.6.0/MachineShop/man/varimp.Rd | 10 MachineShop-1.6.0/MachineShop/tests/testthat/Rplots.pdf |binary MachineShop-1.6.0/MachineShop/vignettes/Introduction.Rmd | 89 MachineShop-1.6.0/MachineShop/vignettes/MLModels.Rmd | 2 160 files changed, 3920 insertions(+), 3348 deletions(-)
Title: Flux Estimation with Static Chamber Data
Description: Statistical analysis of static chamber concentration data for trace gas flux estimation.
Author: Asger R. Pedersen <asger@clin.au.dk>
Maintainer: Asger R. Pedersen <asger@clin.au.dk>
Diff between HMR versions 0.4.2 dated 2017-04-03 and 1.0.0 dated 2019-10-10
DESCRIPTION | 6 MD5 | 12 - NAMESPACE | 4 R/HMR.fit1.R | 378 ++++++++++++++++++++++-------------------- R/HMR.main.R | 211 ++++++++++++++--------- R/HMR.read.R | 32 +-- man/HMR.Rd | 529 +++++++++++++++++++++++++++++++++++------------------------ 7 files changed, 678 insertions(+), 494 deletions(-)
Title: Describe Image Patterns in Natural Structures
Description: A computational tool to describe patterns in black and white images from natural structures. 'bwimage' implemented functions for exceptionally broad subject. For instance, 'bwimage' provide examples that range from calculation of canopy openness, description of patterns in vertical vegetation structure, to patterns in bird nest structure.
Author: Carlos Biagolini-Jr.
Maintainer: Carlos Biagolini-Jr.<c.biagolini@gmail.com>
Diff between bwimage versions 1.0 dated 2019-06-28 and 1.2 dated 2019-10-10
bwimage-1.0/bwimage/R/adjusted_aggregation_with_transparence.R |only bwimage-1.0/bwimage/R/adjusted_aggregation_wo_transparence.R |only bwimage-1.0/bwimage/R/aggregation_index.R |only bwimage-1.0/bwimage/R/aggregation_matrix.R |only bwimage-1.0/bwimage/R/altitudinal_profile.R |only bwimage-1.0/bwimage/R/basic_aggregation_index.R |only bwimage-1.0/bwimage/R/denseness_column.R |only bwimage-1.0/bwimage/R/denseness_row.R |only bwimage-1.0/bwimage/R/denseness_total.R |only bwimage-1.0/bwimage/R/heigh_maximum.R |only bwimage-1.0/bwimage/R/heigh_propotion.R |only bwimage-1.0/bwimage/R/heigh_propotion_test.R |only bwimage-1.0/bwimage/R/hole_columm.R |only bwimage-1.0/bwimage/R/hole_row.R |only bwimage-1.0/bwimage/R/hole_section.R |only bwimage-1.0/bwimage/R/hole_section_data.R |only bwimage-1.0/bwimage/R/image_information.R |only bwimage-1.0/bwimage/R/light_gap.R |only bwimage-1.0/bwimage/R/max_aggregation_with_transparence.R |only bwimage-1.0/bwimage/R/max_aggregation_wo_transparence.R |only bwimage-1.0/bwimage/R/min_aggregation_with_transparence.R |only bwimage-1.0/bwimage/R/min_aggregation_wo_transparence.R |only bwimage-1.0/bwimage/R/threshold_color.R |only bwimage-1.0/bwimage/R/threshold_image_list.R |only bwimage-1.0/bwimage/R/topline.R |only bwimage-1.2/bwimage/DESCRIPTION | 8 bwimage-1.2/bwimage/MD5 | 75 +++------ bwimage-1.2/bwimage/NAMESPACE | 17 -- bwimage-1.2/bwimage/R/ImageAnalysis.R |only bwimage-1.2/bwimage/R/IntFunctions.R |only bwimage-1.2/bwimage/R/cnvIM.R |only bwimage-1.2/bwimage/build/partial.rdb |binary bwimage-1.2/bwimage/inst/extdata/Notes.txt | 1 bwimage-1.2/bwimage/inst/extdata/chesstable.png |only bwimage-1.2/bwimage/man/aggregation_index.Rd | 34 +--- bwimage-1.2/bwimage/man/altitudinal_profile.Rd | 48 ++--- bwimage-1.2/bwimage/man/bwimage-package.Rd | 11 - bwimage-1.2/bwimage/man/compress.Rd |only bwimage-1.2/bwimage/man/denseness_column.Rd | 39 +--- bwimage-1.2/bwimage/man/denseness_row.Rd | 40 +--- bwimage-1.2/bwimage/man/denseness_total.Rd | 41 ++-- bwimage-1.2/bwimage/man/heigh_maximum.Rd | 40 +--- bwimage-1.2/bwimage/man/heigh_propotion.Rd | 35 +--- bwimage-1.2/bwimage/man/heigh_propotion_test.Rd | 46 ++--- bwimage-1.2/bwimage/man/hole_columm.Rd | 47 ++--- bwimage-1.2/bwimage/man/hole_row.Rd | 45 ++--- bwimage-1.2/bwimage/man/hole_section.Rd | 39 +--- bwimage-1.2/bwimage/man/hole_section_data.Rd | 42 ++--- bwimage-1.2/bwimage/man/image_information.Rd | 30 +-- bwimage-1.2/bwimage/man/light_gap.Rd | 46 ++--- bwimage-1.2/bwimage/man/stretch.Rd |only bwimage-1.2/bwimage/man/threshold_color.Rd | 78 ++++----- bwimage-1.2/bwimage/man/threshold_image_list.Rd | 83 ++++------ bwimage-1.2/bwimage/man/topline.Rd | 47 ++--- 54 files changed, 365 insertions(+), 527 deletions(-)
Title: Bayesian Classification and Information Sharing (BaCIS) Tool for
the Design of Multi-Group Phase II Clinical Trials
Description: Provides the design of multi-group phase
II clinical trials with binary outcomes using the hierarchical Bayesian
classification and information sharing (BaCIS) model. Subgroups are classified
into two clusters on the basis of their outcomes mimicking the hypothesis
testing framework. Subsequently, information sharing takes place within
subgroups in the same cluster, rather than across all subgroups. This method can
be applied to the design and analysis of multi-group clinical trials with binary
outcomes. Reference: Nan Chen and J. Jack Lee (2019) <doi:10.1002/bimj.201700275>.
Author: Nan Chen and J. Jack Lee
Maintainer: Nan Chen <nchen2@mdanderson.org>
Diff between bacistool versions 0.9.8 dated 2018-08-24 and 0.9.9 dated 2019-10-10
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-13 1.1.3
2014-10-04 1.1.2
2014-04-07 1.1.1
2014-03-20 1.1
2014-03-12 1.0
Title: Exploratory Graphics for Pharmacometrics
Description: Supports a structured approach
for exploring PKPD data <https://opensource.nibr.com/xgx>. It also
contains helper functions for enabling the modeler to follow best R
practices (by appending the program name, figure name location, and
draft status to each plot). In addition, it enables the modeler to
follow best graphical practices (by providing a theme that
reduces chart ink, and by providing time-scale, log-scale, and
reverse-log-transform-scale functions for more readable axes).
Finally, it provides some data checking and summarizing functions for
rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
Author: Andrew Stein [aut, cre],
Alison Margolskee [aut],
Fariba Khanshan [aut],
Konstantin Krismer [aut] (<https://orcid.org/0000-0001-8994-3416>),
Matthew Fidler [ctb] (<https://orcid.org/0000-0001-8538-6691>),
Novartis Pharma AG [cph, fnd]
Maintainer: Andrew Stein <andy.stein@gmail.com>
Diff between xgxr versions 1.0.3 dated 2019-09-28 and 1.0.4 dated 2019-10-10
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- NEWS | 16 +++++++++++++++- R/xgx_geom_ci.R | 17 ++++++++++++++--- R/xgx_stat_ci.R | 11 ++++++----- README.md | 2 +- inst/doc/sad_pkpd.R | 2 +- inst/doc/sad_pkpd.Rmd | 2 +- inst/doc/sad_pkpd.html | 12 ++++++------ inst/doc/theoph.R | 8 ++++---- inst/doc/theoph.Rmd | 8 ++++---- inst/doc/theoph.html | 22 +++++++++++----------- inst/doc/xgxr_overview.html | 34 +++++++++++++++++----------------- man/xgx_geom_ci.Rd | 12 ++++++------ man/xgx_stat_ci.Rd | 12 ++++++------ vignettes/sad_pkpd.Rmd | 2 +- vignettes/theoph.Rmd | 8 ++++---- 17 files changed, 116 insertions(+), 90 deletions(-)
Title: Explorer of World Population Prospects
Description: Explore data in the 'wpp2019' (or 2017, 2015, ...) package using a 'shiny' interface.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wppExplorer versions 2.1-1 dated 2017-08-18 and 2.3-2 dated 2019-10-10
wppExplorer-2.1-1/wppExplorer/data/iso3166.R |only wppExplorer-2.1-1/wppExplorer/data/iso3166.txt |only wppExplorer-2.1-1/wppExplorer/data/iso3166ud.R |only wppExplorer-2.1-1/wppExplorer/data/iso3166ud.txt |only wppExplorer-2.3-2/wppExplorer/ChangeLog | 16 ++++ wppExplorer-2.3-2/wppExplorer/DESCRIPTION | 16 ++-- wppExplorer-2.3-2/wppExplorer/LICENSE |only wppExplorer-2.3-2/wppExplorer/MD5 | 35 +++++----- wppExplorer-2.3-2/wppExplorer/NAMESPACE | 2 wppExplorer-2.3-2/wppExplorer/R/global.R | 6 + wppExplorer-2.3-2/wppExplorer/R/wpp.R | 2 wppExplorer-2.3-2/wppExplorer/data/iso3166.rda |only wppExplorer-2.3-2/wppExplorer/data/iso3166.txt.gz |only wppExplorer-2.3-2/wppExplorer/data/iso3166ud.rda |only wppExplorer-2.3-2/wppExplorer/data/iso3166ud.txt.gz |only wppExplorer-2.3-2/wppExplorer/inst/explore/README.html | 14 ++-- wppExplorer-2.3-2/wppExplorer/inst/explore/server.R | 2 wppExplorer-2.3-2/wppExplorer/inst/explore/ui.R | 10 ++ wppExplorer-2.3-2/wppExplorer/man/wpp.explore.Rd | 4 - wppExplorer-2.3-2/wppExplorer/man/wpp.indicator.Rd | 22 +++--- wppExplorer-2.3-2/wppExplorer/man/wppExplorer-package.Rd | 12 +-- wppExplorer-2.3-2/wppExplorer/man/wpp_year.Rd | 4 - wppExplorer-2.3-2/wppExplorer/tests/testthat/test-indicators.R | 4 - 23 files changed, 87 insertions(+), 62 deletions(-)
Title: Derive Polygenic Risk Score Based on Emprical Bayes Theory
Description: EB-PRS is a novel method that leverages information for effect sizes across all the markers to improve the prediction accuracy. No parameter tuning is needed in the method, and no external information is needed. This R-package provides the calculation of polygenic risk scores from the given training summary statistics and testing data. We can use EB-PRS to extract main information, estimate Empirical Bayes parameters, derive polygenic risk scores for each individual in testing data, and evaluate the PRS according to AUC and predictive r2.
Author: Shuang Song [aut, cre], Wei Jiang [aut], Lin Hou [aut] and Hongyu Zhao [aut]
Maintainer: Shuang Song <song-s19@mails.tsinghua.edu.cn>
Diff between EBPRS versions 1.1.5 dated 2019-08-07 and 1.2.0 dated 2019-10-10
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++----- R/exdata.R |only R/extractInfo.R | 13 ++++++------- R/getEffectSize.R | 15 ++++++++++----- data |only man/extractInfo.Rd | 7 +++---- man/getEffectSize.Rd | 14 ++++++++++---- man/traindat.Rd |only 9 files changed, 41 insertions(+), 29 deletions(-)
Title: High Performance Container Data Types
Description: Provides high performance container data types such as Queue, Stack, Deque, Dict and OrderedDict. Benchmarks <https://randy3k.github.io/collections/articles/benchmark.html> have shown that these containers are asymptotically more efficient than those offered by other packages.
Author: Randy Lai [aut, cre],
Andrea Mazzoleni [cph] (tommy hash table library)
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between collections versions 0.2.0 dated 2019-10-02 and 0.2.1 dated 2019-10-10
DESCRIPTION | 8 - MD5 | 32 +++---- R/dict.R | 56 ++----------- R/ordered_dict.R | 11 +- R/stack.R | 12 +- src/collections.c | 4 src/deque.c | 41 ++++----- src/dict.c | 159 ++++++++++++++++++++++++++++++++++--- src/dict.h | 4 src/priority_queue.c | 28 +++--- src/queue.c | 16 ++- src/stack.c | 12 +- src/utils.c | 26 +++++- src/utils.h | 8 + tests/testthat/test_deque.R | 7 + tests/testthat/test_dict.R | 1 tests/testthat/test_ordered_dict.R | 11 ++ 17 files changed, 295 insertions(+), 141 deletions(-)
Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting
spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL'
bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Michael Sumner [ctb] (<https://orcid.org/0000-0002-2471-7511>),
Etienne Racine [ctb],
Adriano Fantini [ctb],
David Blodgett [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between stars versions 0.3-1 dated 2019-04-23 and 0.4-0 dated 2019-10-10
stars-0.3-1/stars/man/plot.stars.Rd |only stars-0.3-1/stars/tests/netcdf.R |only stars-0.3-1/stars/tests/netcdf.Rout.save |only stars-0.4-0/stars/DESCRIPTION | 25 stars-0.4-0/stars/MD5 | 149 + stars-0.4-0/stars/NAMESPACE | 17 stars-0.4-0/stars/NEWS.md | 46 stars-0.4-0/stars/R/aggregate.R | 7 stars-0.4-0/stars/R/dimensions.R | 36 stars-0.4-0/stars/R/geom.R | 116 + stars-0.4-0/stars/R/init.R | 8 stars-0.4-0/stars/R/mosaic.R |only stars-0.4-0/stars/R/ncdf.R | 755 ++++++++-- stars-0.4-0/stars/R/ops.R | 50 stars-0.4-0/stars/R/plot.R | 108 + stars-0.4-0/stars/R/proxy.R | 40 stars-0.4-0/stars/R/raster.R | 16 stars-0.4-0/stars/R/rasterize.R | 64 stars-0.4-0/stars/R/read.R | 14 stars-0.4-0/stars/R/sf.R | 15 stars-0.4-0/stars/R/sp.R | 12 stars-0.4-0/stars/R/spacetime.R | 10 stars-0.4-0/stars/R/stars.R | 150 + stars-0.4-0/stars/R/subset.R | 35 stars-0.4-0/stars/R/tidyverse.R | 40 stars-0.4-0/stars/R/transform.R | 7 stars-0.4-0/stars/R/warp.R | 7 stars-0.4-0/stars/R/write.R | 14 stars-0.4-0/stars/build/vignette.rds |binary stars-0.4-0/stars/inst/doc/stars1.R | 6 stars-0.4-0/stars/inst/doc/stars1.Rmd | 6 stars-0.4-0/stars/inst/doc/stars1.html | 209 +- stars-0.4-0/stars/inst/doc/stars2.R | 2 stars-0.4-0/stars/inst/doc/stars2.Rmd | 4 stars-0.4-0/stars/inst/doc/stars2.html | 153 +- stars-0.4-0/stars/inst/doc/stars3.html | 139 + stars-0.4-0/stars/inst/doc/stars4.html | 124 - stars-0.4-0/stars/inst/doc/stars5.html | 176 +- stars-0.4-0/stars/inst/nc/3B42_Daily.19991231.7.test.nc |only stars-0.4-0/stars/inst/nc/EURO-CORDEX_81_DOMAIN000_mask_int.nc.zip |only stars-0.4-0/stars/inst/nc/c201923412.out1_4.nc |only stars-0.4-0/stars/inst/nc/ncdf_tidync.R |only stars-0.4-0/stars/inst/nc/test-1.nc |only stars-0.4-0/stars/inst/nc/test_stageiv_xyt_borked.nc |only stars-0.4-0/stars/inst/nc/timeseries.cdl |only stars-0.4-0/stars/inst/nc/timeseries.nc |only stars-0.4-0/stars/man/contour.stars.Rd |only stars-0.4-0/stars/man/geom_stars.Rd | 7 stars-0.4-0/stars/man/plot.Rd |only stars-0.4-0/stars/man/read_ncdf.Rd | 17 stars-0.4-0/stars/man/read_stars.Rd | 2 stars-0.4-0/stars/man/reexports.Rd |only stars-0.4-0/stars/man/st_as_stars.Rd | 38 stars-0.4-0/stars/man/st_contour.Rd | 4 stars-0.4-0/stars/man/st_dim_to_attr.Rd |only stars-0.4-0/stars/man/st_dimensions.Rd | 4 stars-0.4-0/stars/man/st_intersects.stars.Rd |only stars-0.4-0/stars/man/st_join.stars.Rd |only stars-0.4-0/stars/man/st_mosaic.Rd |only stars-0.4-0/stars/man/st_sfc2xy.Rd |only stars-0.4-0/stars/man/st_transform.Rd | 2 stars-0.4-0/stars/man/st_xy2sfc.Rd | 4 stars-0.4-0/stars/tests/aggregate.R | 2 stars-0.4-0/stars/tests/aggregate.Rout.save | 8 stars-0.4-0/stars/tests/area.R | 2 stars-0.4-0/stars/tests/area.Rout.save | 8 stars-0.4-0/stars/tests/curvilinear.R | 2 stars-0.4-0/stars/tests/curvilinear.Rout.save | 6 stars-0.4-0/stars/tests/nc.Rout.save | 8 stars-0.4-0/stars/tests/predict.R | 1 stars-0.4-0/stars/tests/predict.Rout.save | 7 stars-0.4-0/stars/tests/proxy.Rout.save | 56 stars-0.4-0/stars/tests/raster.Rout.save | 32 stars-0.4-0/stars/tests/rasterize.Rout.save | 12 stars-0.4-0/stars/tests/sp.Rout.save | 16 stars-0.4-0/stars/tests/stars.R | 15 stars-0.4-0/stars/tests/stars.Rout.save | 53 stars-0.4-0/stars/tests/testthat.Rout.save | 6 stars-0.4-0/stars/tests/testthat/test_ncdf.R | 141 + stars-0.4-0/stars/tests/testthat/test_rectilinear.R | 5 stars-0.4-0/stars/tests/testthat/test_st_as_stars.R |only stars-0.4-0/stars/tests/transform.R | 6 stars-0.4-0/stars/tests/transform.Rout.save | 48 stars-0.4-0/stars/tests/write.Rout.save | 7 stars-0.4-0/stars/vignettes/stars1.Rmd | 6 stars-0.4-0/stars/vignettes/stars2.Rmd | 4 86 files changed, 2132 insertions(+), 957 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
Sami Samhuri [ctb, cph] (Javascript strftime library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 1.3.2 dated 2019-04-22 and 1.4.0 dated 2019-10-10
shiny-1.3.2/shiny/inst/staticdocs |only shiny-1.3.2/shiny/man/addResourcePath.Rd |only shiny-1.3.2/shiny/man/key_missing.Rd |only shiny-1.3.2/shiny/man/knitr_methods_htmltools.Rd |only shiny-1.3.2/shiny/man/mainPanel.Rd |only shiny-1.3.2/shiny/man/reactivePlot.Rd |only shiny-1.3.2/shiny/man/reactivePrint.Rd |only shiny-1.3.2/shiny/man/reactiveTable.Rd |only shiny-1.3.2/shiny/man/reactiveText.Rd |only shiny-1.3.2/shiny/man/reactiveUI.Rd |only shiny-1.3.2/shiny/man/shiny-options.Rd |only shiny-1.3.2/shiny/man/sidebarPanel.Rd |only shiny-1.3.2/shiny/tests/testthat/test-staticdocs.R |only shiny-1.4.0/shiny/DESCRIPTION | 50 shiny-1.4.0/shiny/LICENSE | 4 shiny-1.4.0/shiny/MD5 | 518 shiny-1.4.0/shiny/NAMESPACE | 17 shiny-1.4.0/shiny/NEWS.md | 70 shiny-1.4.0/shiny/R/app.R | 157 shiny-1.4.0/shiny/R/bookmark-state.R | 110 shiny-1.4.0/shiny/R/bootstrap-deprecated.R |only shiny-1.4.0/shiny/R/bootstrap-layout.R | 137 shiny-1.4.0/shiny/R/bootstrap.R | 457 shiny-1.4.0/shiny/R/cache-disk.R | 162 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shiny-1.4.0/shiny/man/flowLayout.Rd | 8 shiny-1.4.0/shiny/man/fluidPage.Rd | 21 shiny-1.4.0/shiny/man/freezeReactiveValue.Rd | 12 shiny-1.4.0/shiny/man/getQueryString.Rd | 7 shiny-1.4.0/shiny/man/headerPanel.Rd | 8 shiny-1.4.0/shiny/man/hoverOpts.Rd | 4 shiny-1.4.0/shiny/man/htmlTemplate.Rd | 1 shiny-1.4.0/shiny/man/icon.Rd | 8 shiny-1.4.0/shiny/man/include.Rd | 9 shiny-1.4.0/shiny/man/inputPanel.Rd | 2 shiny-1.4.0/shiny/man/insertTab.Rd | 14 shiny-1.4.0/shiny/man/insertUI.Rd | 18 shiny-1.4.0/shiny/man/installExprFunction.Rd | 6 shiny-1.4.0/shiny/man/invalidateLater.Rd | 2 shiny-1.4.0/shiny/man/is.reactivevalues.Rd | 2 shiny-1.4.0/shiny/man/isRunning.Rd | 2 shiny-1.4.0/shiny/man/isolate.Rd | 2 shiny-1.4.0/shiny/man/loadSupport.Rd |only shiny-1.4.0/shiny/man/maskReactiveContext.Rd | 2 shiny-1.4.0/shiny/man/memoryCache.Rd | 215 shiny-1.4.0/shiny/man/modalButton.Rd | 4 shiny-1.4.0/shiny/man/modalDialog.Rd | 2 shiny-1.4.0/shiny/man/navbarPage.Rd | 24 shiny-1.4.0/shiny/man/navlistPanel.Rd | 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shiny-1.4.0/shiny/man/removeInputHandler.Rd | 4 shiny-1.4.0/shiny/man/removeUI.Rd | 6 shiny-1.4.0/shiny/man/renderCachedPlot.Rd | 156 shiny-1.4.0/shiny/man/renderDataTable.Rd | 16 shiny-1.4.0/shiny/man/renderImage.Rd | 4 shiny-1.4.0/shiny/man/renderPlot.Rd | 44 shiny-1.4.0/shiny/man/renderPrint.Rd | 14 shiny-1.4.0/shiny/man/renderTable.Rd | 8 shiny-1.4.0/shiny/man/renderText.Rd | 15 shiny-1.4.0/shiny/man/renderUI.Rd | 8 shiny-1.4.0/shiny/man/repeatable.Rd | 4 shiny-1.4.0/shiny/man/req.Rd | 22 shiny-1.4.0/shiny/man/resourcePaths.Rd |only shiny-1.4.0/shiny/man/restoreInput.Rd | 2 shiny-1.4.0/shiny/man/runApp.Rd | 6 shiny-1.4.0/shiny/man/runGadget.Rd | 6 shiny-1.4.0/shiny/man/runUrl.Rd | 4 shiny-1.4.0/shiny/man/safeError.Rd | 2 shiny-1.4.0/shiny/man/selectInput.Rd | 67 shiny-1.4.0/shiny/man/session.Rd | 228 shiny-1.4.0/shiny/man/setBookmarkExclude.Rd | 2 shiny-1.4.0/shiny/man/shiny.appobj.Rd |only shiny-1.4.0/shiny/man/shinyApp.Rd | 45 shiny-1.4.0/shiny/man/shinyOptions.Rd | 108 shiny-1.4.0/shiny/man/shinyServer.Rd | 1 shiny-1.4.0/shiny/man/shinyUI.Rd | 1 shiny-1.4.0/shiny/man/showBookmarkUrlModal.Rd | 4 shiny-1.4.0/shiny/man/showModal.Rd | 4 shiny-1.4.0/shiny/man/showNotification.Rd | 14 shiny-1.4.0/shiny/man/showTab.Rd | 10 shiny-1.4.0/shiny/man/sidebarLayout.Rd | 30 shiny-1.4.0/shiny/man/singleton.Rd | 3 shiny-1.4.0/shiny/man/sizeGrowthRatio.Rd | 2 shiny-1.4.0/shiny/man/sliderInput.Rd | 18 shiny-1.4.0/shiny/man/splitLayout.Rd | 9 shiny-1.4.0/shiny/man/stacktrace.Rd | 68 shiny-1.4.0/shiny/man/stopApp.Rd | 4 shiny-1.4.0/shiny/man/submitButton.Rd | 15 shiny-1.4.0/shiny/man/suppressDependencies.Rd | 1 shiny-1.4.0/shiny/man/tabPanel.Rd | 9 shiny-1.4.0/shiny/man/tableOutput.Rd | 4 shiny-1.4.0/shiny/man/tabsetPanel.Rd | 12 shiny-1.4.0/shiny/man/tag.Rd | 42 shiny-1.4.0/shiny/man/textAreaInput.Rd | 36 shiny-1.4.0/shiny/man/textInput.Rd | 11 shiny-1.4.0/shiny/man/textOutput.Rd | 2 shiny-1.4.0/shiny/man/titlePanel.Rd | 4 shiny-1.4.0/shiny/man/updateActionButton.Rd | 2 shiny-1.4.0/shiny/man/updateCheckboxGroupInput.Rd | 2 shiny-1.4.0/shiny/man/updateCheckboxInput.Rd | 2 shiny-1.4.0/shiny/man/updateDateInput.Rd | 2 shiny-1.4.0/shiny/man/updateDateRangeInput.Rd | 2 shiny-1.4.0/shiny/man/updateNumericInput.Rd | 2 shiny-1.4.0/shiny/man/updateQueryString.Rd | 10 shiny-1.4.0/shiny/man/updateRadioButtons.Rd | 2 shiny-1.4.0/shiny/man/updateSelectInput.Rd | 27 shiny-1.4.0/shiny/man/updateSliderInput.Rd | 2 shiny-1.4.0/shiny/man/updateTabsetPanel.Rd | 4 shiny-1.4.0/shiny/man/updateTextAreaInput.Rd | 2 shiny-1.4.0/shiny/man/updateTextInput.Rd | 2 shiny-1.4.0/shiny/man/urlModal.Rd | 2 shiny-1.4.0/shiny/man/validate.Rd | 21 shiny-1.4.0/shiny/man/validateCssUnit.Rd | 11 shiny-1.4.0/shiny/man/varSelectInput.Rd | 60 shiny-1.4.0/shiny/man/verbatimTextOutput.Rd | 4 shiny-1.4.0/shiny/man/verticalLayout.Rd | 6 shiny-1.4.0/shiny/man/viewer.Rd | 6 shiny-1.4.0/shiny/man/withMathJax.Rd | 2 shiny-1.4.0/shiny/man/withProgress.Rd | 6 shiny-1.4.0/shiny/man/withTags.Rd | 3 shiny-1.4.0/shiny/tests/test-helpers |only shiny-1.4.0/shiny/tests/testthat/helper.R | 19 shiny-1.4.0/shiny/tests/testthat/print-reactiveValues.txt |only shiny-1.4.0/shiny/tests/testthat/test-app.R |only shiny-1.4.0/shiny/tests/testthat/test-bookmarking.R | 14 shiny-1.4.0/shiny/tests/testthat/test-bootstrap.r | 93 shiny-1.4.0/shiny/tests/testthat/test-modules.R | 8 shiny-1.4.0/shiny/tests/testthat/test-options.R | 3 shiny-1.4.0/shiny/tests/testthat/test-pkgdown.R |only shiny-1.4.0/shiny/tests/testthat/test-plot-coordmap.R | 125 shiny-1.4.0/shiny/tests/testthat/test-reactivity.r | 240 shiny-1.4.0/shiny/tests/testthat/test-stacks.R | 75 shiny-1.4.0/shiny/tests/testthat/test-text.R | 11 264 files changed, 9780 insertions(+), 8541 deletions(-)
Title: Meta-Analysis using Structural Equation Modeling
Description: A collection of functions for conducting meta-analysis using a
structural equation modeling (SEM) approach via the 'OpenMx' and
'lavaan' packages. It also implements various procedures to
perform meta-analytic structural equation modeling on the
correlation and covariance matrices.
Author: Mike Cheung [aut, cre] (<https://orcid.org/0000-0003-0113-0758>)
Maintainer: Mike Cheung <mikewlcheung@nus.edu.sg>
Diff between metaSEM versions 1.2.2 dated 2019-05-29 and 1.2.3 dated 2019-10-10
DESCRIPTION | 13 MD5 | 135 +- NAMESPACE | 1 NEWS | 15 R/as.mxMatrix.R | 3 R/create.mxModel.R | 26 R/lavaan2RAM.R | 3 R/meta2semPlot.R | 68 + R/metaX.R |only R/osmasem.R | 117 +- R/rerun.R | 92 + R/summary.R | 228 ++-- R/tssem.R | 125 +- R/uniR.R | 113 +- README.md | 4 build/vignette.rds |binary data/Aloe14.rda |binary data/BCG.rda |binary data/Becker09.rda |binary data/Becker83.rda |binary data/Becker92.rda |binary data/Becker94.rda |binary data/Berkey98.rda |binary data/Boer16.rda |binary data/Bornmann07.rda |binary data/Cheung00.rda |binary data/Cheung09.rda |binary data/Cooke16.rda |binary data/Cooper03.rda |binary data/Digman97.rda |binary data/Gleser94.rda |binary data/Gnambs18.rda |binary data/HedgesOlkin85.rda |binary data/Hox02.rda |binary data/Hunter83.rda |binary data/Jaramillo05.rda |binary data/Kalaian96.rda |only data/Mak09.rda |binary data/Nam03.rda |binary data/Nohe15A1.rda |binary data/Nohe15A2.rda |binary data/Norton13.rda |binary data/Roorda11.rda |binary data/Scalco17.rda |binary data/Stadler15.rda |binary data/Tenenbaum02.rda |only data/issp05.rda |binary data/issp89.rda |binary data/vanderPol17.rda |binary data/wvs94a.rda |binary data/wvs94b.rda |binary inst/doc/Examples.html | 1937 ++++++++++++++++++++-------------------- inst/doc/metaSEM.pdf |binary man/Becker09.Rd | 2 man/Berkey98.Rd | 1 man/Kalaian96.Rd |only man/Nohe15.Rd | 2 man/Tenenbaum02.Rd |only man/create.Tau2.Rd | 4 man/create.mxModel.Rd | 11 man/create.vechsR.Rd | 2 man/meta.Rd | 21 man/metaSEM-package.Rd | 11 man/osmasem.Rd | 7 man/plot.Rd | 12 man/rerun.Rd | 7 man/summary.Rd | 20 man/uniR2.Rd | 16 man/vcov.Rd | 15 man/wls.Rd | 86 + tests/testthat/test_utilities.R | 141 ++ 71 files changed, 1882 insertions(+), 1356 deletions(-)
Title: Utilities for Producing Maps
Description: A minimal, light-weight set of tools for producing nice looking maps in R, with support for map projections.
Author: Patrick Brown <patrick.brown@utoronto.ca>
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between mapmisc versions 1.7.2 dated 2018-04-09 and 1.7.4 dated 2019-10-10
mapmisc-1.7.2/mapmisc/inst/extdoc/mapLayers.Rmd |only mapmisc-1.7.4/mapmisc/DESCRIPTION | 14 mapmisc-1.7.4/mapmisc/MD5 | 50 mapmisc-1.7.4/mapmisc/R/000crs.R | 7257 +++++++++++++++++++++++- mapmisc-1.7.4/mapmisc/R/geonames.R | 115 mapmisc-1.7.4/mapmisc/R/legendTable.R | 6 mapmisc-1.7.4/mapmisc/R/map.new.R | 13 mapmisc-1.7.4/mapmisc/R/mapmiscCache.R | 2 mapmisc-1.7.4/mapmisc/R/moll.R | 10 mapmisc-1.7.4/mapmisc/R/openmap.R | 6 mapmisc-1.7.4/mapmisc/R/wrapPoly.R | 314 - mapmisc-1.7.4/mapmisc/build/vignette.rds |binary mapmisc-1.7.4/mapmisc/inst/doc/mapmisc.R |only mapmisc-1.7.4/mapmisc/inst/doc/mapmisc.pdf |binary mapmisc-1.7.4/mapmisc/inst/doc/north.R |only mapmisc-1.7.4/mapmisc/inst/doc/north.html | 18 mapmisc-1.7.4/mapmisc/inst/extsrc/sphere.R |only mapmisc-1.7.4/mapmisc/man/col2html.Rd | 2 mapmisc-1.7.4/mapmisc/man/colourScale.Rd | 2 mapmisc-1.7.4/mapmisc/man/crsMerc.Rd | 6 mapmisc-1.7.4/mapmisc/man/geocode.Rd | 27 mapmisc-1.7.4/mapmisc/man/gridlinesWrap.Rd | 2 mapmisc-1.7.4/mapmisc/man/modis.Rd | 6 mapmisc-1.7.4/mapmisc/man/omerc.Rd | 4 mapmisc-1.7.4/mapmisc/man/tpeqd.Rd | 7 mapmisc-1.7.4/mapmisc/man/wrapPoly.Rd | 2 mapmisc-1.7.4/mapmisc/tests/worldMap.R | 31 mapmisc-1.7.4/mapmisc/vignettes/Makefile | 2 28 files changed, 7657 insertions(+), 239 deletions(-)
Title: Fit Interpretable Models and Explain Blackbox Machine Learning
Description: Machine Learning package for training interpretable models and explaining blackbox systems. Historically, the most intelligible models were not very accurate, and the most accurate models were not intelligible. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and intelligibility. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut],
Harsha Nori [aut],
Paul Koch [aut],
Rich Caruana [aut, cre],
Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>
Diff between interpret versions 0.1.20 dated 2019-10-07 and 0.1.21 dated 2019-10-10
DESCRIPTION | 6 MD5 | 21 R/interpret_core.R | 22 src/Makevars | 1 src/core/HistogramBucket.h | 2 src/core/InteractionDetection.cpp | 8 src/core/Logging.cpp | 4 src/core/SegmentedTensor.h | 11 src/core/Training.cpp | 18 src/core/inc/ebmcore.h | 50 - src/interpret-win.def |only src/interpret_R.cpp | 1452 ++++++++++++++++++-------------------- 12 files changed, 810 insertions(+), 785 deletions(-)
Title: Highly Optimized Protocol Buffer Serializers
Description: Pure C++ implementations for reading and writing several common data
formats based on Google protocol-buffers. Currently supports 'rexp.proto' for
serialized R objects, 'geobuf.proto' for binary geojson, and 'mvt.proto' for
vector tiles. This package uses the auto-generated C++ code by protobuf-compiler,
hence the entire serialization is optimized at compile time. The 'RProtoBuf'
package on the other hand uses the protobuf runtime library to provide a general-
purpose toolkit for reading and writing arbitrary protocol-buffer data in R.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between protolite versions 1.9 dated 2019-07-02 and 2.0 dated 2019-10-10
DESCRIPTION | 29 +++++++++++++++++------------ MD5 | 31 ++++++++++++++++++++++++------- NAMESPACE | 2 ++ NEWS | 3 +++ R/RcppExports.R | 4 ++++ R/geobuf.R | 4 ++-- R/mvt.R |only configure | 13 +++++++------ inst |only man/mapbox.Rd |only src/RcppExports.cpp | 12 ++++++++++++ src/mvt.pb.cc |only src/mvt.proto |only src/unmvt.cpp |only tests/spelling.R |only tests/testdata |only tests/testthat/test-mapbox.R |only 17 files changed, 71 insertions(+), 27 deletions(-)
Title: A Minimal Wrapper Around NIH's 'iCite' API
Description: A minimal wrapper around the NIH's 'iCite' API (<https://icite.od.nih.gov/api>).
Given a vector of pubmed IDs, this package returns a dataframe of the information yielded by
the 'iCite' API. The primary metrics yielded by 'iCite' are measurements of a paper's
scientific influence and translational potential, but the API also returns other meta-data
from the paper, including author names, publication journal, publication year, paper title,
doi, and a number of other citation metrics.
Author: Travis Riddle [aut, cre]
Maintainer: Travis Riddle <travis.riddle@nih.gov>
Diff between iCiteR versions 0.1.0 dated 2019-07-04 and 0.2.0 dated 2019-10-10
iCiteR-0.1.0/iCiteR/tests/testthat/test-return-dataframe.R |only iCiteR-0.2.0/iCiteR/DESCRIPTION | 16 iCiteR-0.2.0/iCiteR/MD5 | 38 - iCiteR-0.2.0/iCiteR/NAMESPACE | 2 iCiteR-0.2.0/iCiteR/NEWS.md | 8 iCiteR-0.2.0/iCiteR/R/api_methods.R | 176 +++++-- iCiteR-0.2.0/iCiteR/R/get_metrics.R | 319 ++++++++++--- iCiteR-0.2.0/iCiteR/R/iCiteR.R |only iCiteR-0.2.0/iCiteR/README.md | 298 +++++++----- iCiteR-0.2.0/iCiteR/build/vignette.rds |binary iCiteR-0.2.0/iCiteR/inst/doc/iCiteR-usage.R | 7 iCiteR-0.2.0/iCiteR/inst/doc/iCiteR-usage.Rmd | 27 - iCiteR-0.2.0/iCiteR/inst/doc/iCiteR-usage.html | 214 +++++--- iCiteR-0.2.0/iCiteR/man/construct_query.Rd |only iCiteR-0.2.0/iCiteR/man/get_metrics.Rd | 9 iCiteR-0.2.0/iCiteR/man/iCiteR.Rd |only iCiteR-0.2.0/iCiteR/man/icite_api.Rd | 6 iCiteR-0.2.0/iCiteR/man/icite_search.Rd |only iCiteR-0.2.0/iCiteR/man/page_limited.Rd |only iCiteR-0.2.0/iCiteR/man/page_no_limit.Rd |only iCiteR-0.2.0/iCiteR/man/search_metrics.Rd |only iCiteR-0.2.0/iCiteR/man/to_dataframe.Rd | 10 iCiteR-0.2.0/iCiteR/tests/testthat/test-get-metrics.R |only iCiteR-0.2.0/iCiteR/tests/testthat/test-search-metrics.R |only iCiteR-0.2.0/iCiteR/vignettes/iCiteR-usage.Rmd | 27 - 25 files changed, 841 insertions(+), 316 deletions(-)
Title: Creates Co-Occurrence Matrices of Spatial Data
Description: Builds co-occurrence matrices based on spatial raster data.
It includes creation of weighted co-occurrence matrices (wecoma) and
integrated co-occurrence matrices
(incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>).
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Maximillian H.K. Hesselbarth [ctb] (Co-author of underlying C++ code
for get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions),
Marco Sciaini [ctb] (Co-author of underlying C++ code for
get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions),
Sebastian Hanss [ctb] (Co-author of underlying C++ code for
get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between comat versions 0.3.0 dated 2019-08-25 and 0.7.0 dated 2019-10-10
comat-0.3.0/comat/data/w.rda |only comat-0.3.0/comat/data/w_na.rda |only comat-0.3.0/comat/data/x.rda |only comat-0.3.0/comat/data/x_na.rda |only comat-0.3.0/comat/inst/tinytest/test_rcpp_get_coma.R |only comat-0.3.0/comat/man/rcpp_get_wecoma.Rd |only comat-0.3.0/comat/man/w.Rd |only comat-0.3.0/comat/man/w_na.Rd |only comat-0.3.0/comat/man/x.Rd |only comat-0.3.0/comat/man/x_na.Rd |only comat-0.3.0/comat/src/rcpp_get_cove.cpp |only comat-0.3.0/comat/src/rcpp_get_cove.h |only comat-0.3.0/comat/src/rcpp_get_wecove.cpp |only comat-0.3.0/comat/src/rcpp_get_wecove.h |only comat-0.7.0/comat/DESCRIPTION | 14 comat-0.7.0/comat/MD5 | 95 +- comat-0.7.0/comat/NAMESPACE | 5 comat-0.7.0/comat/NEWS.md | 12 comat-0.7.0/comat/R/RcppExports.R | 63 + comat-0.7.0/comat/R/comat-data.R | 32 comat-0.7.0/comat/R/get_cocoma.R |only comat-0.7.0/comat/R/get_cocove.R |only comat-0.7.0/comat/R/get_coma.R |only comat-0.7.0/comat/R/get_cove.R |only comat-0.7.0/comat/R/get_incoma.R | 41 - comat-0.7.0/comat/R/get_incove.R |only comat-0.7.0/comat/R/get_wecoma.R | 15 comat-0.7.0/comat/R/get_wecove.R | 18 comat-0.7.0/comat/README.md | 61 + comat-0.7.0/comat/data/raster_w.rda |only comat-0.7.0/comat/data/raster_w_na.rda |only comat-0.7.0/comat/data/raster_x.rda |only comat-0.7.0/comat/data/raster_x_na.rda |only comat-0.7.0/comat/inst/CITATION | 6 comat-0.7.0/comat/inst/include/comat_RcppExports.h | 261 ++++++- comat-0.7.0/comat/inst/tinytest/test_create_neighborhood.R |only comat-0.7.0/comat/inst/tinytest/test_get_cocoma.R |only comat-0.7.0/comat/inst/tinytest/test_get_coma.R |only comat-0.7.0/comat/inst/tinytest/test_get_incoma.R | 46 - comat-0.7.0/comat/inst/tinytest/test_get_normalized.R |only comat-0.7.0/comat/inst/tinytest/test_get_wecoma.R | 49 - comat-0.7.0/comat/inst/tinytest/test_rcpp_get_incoma.R |only comat-0.7.0/comat/man/comat-package.Rd | 2 comat-0.7.0/comat/man/get_cocoma.Rd |only comat-0.7.0/comat/man/get_cocove.Rd |only comat-0.7.0/comat/man/get_coma.Rd |only comat-0.7.0/comat/man/get_cove.Rd |only comat-0.7.0/comat/man/get_incoma.Rd | 11 comat-0.7.0/comat/man/get_incove.Rd |only comat-0.7.0/comat/man/get_wecoma.Rd | 13 comat-0.7.0/comat/man/get_wecove.Rd | 16 comat-0.7.0/comat/man/raster_w.Rd |only comat-0.7.0/comat/man/raster_w_na.Rd |only comat-0.7.0/comat/man/raster_x.Rd |only comat-0.7.0/comat/man/raster_x_na.Rd |only comat-0.7.0/comat/src/RcppExports.cpp | 483 ++++++++++++- comat-0.7.0/comat/src/get_normalized.cpp |only comat-0.7.0/comat/src/get_normalized.h |only comat-0.7.0/comat/src/get_unique_values.h | 2 comat-0.7.0/comat/src/rcpp_get_cocoma.cpp | 24 comat-0.7.0/comat/src/rcpp_get_cocoma.h | 8 comat-0.7.0/comat/src/rcpp_get_coma.cpp | 25 comat-0.7.0/comat/src/rcpp_get_coma.h | 7 comat-0.7.0/comat/src/rcpp_get_incoma.cpp |only comat-0.7.0/comat/src/rcpp_get_incoma.h |only comat-0.7.0/comat/src/rcpp_get_vec.cpp |only comat-0.7.0/comat/src/rcpp_get_vec.h |only comat-0.7.0/comat/src/rcpp_get_wecoma.cpp | 25 comat-0.7.0/comat/src/rcpp_get_wecoma.h | 11 comat-0.7.0/comat/src/triangular_index.cpp | 4 70 files changed, 1075 insertions(+), 274 deletions(-)
Title: Formal Psychological Models of Categorization and Learning
Description: Formal psychological models of categorization and learning, independently-replicated data sets against which to test them, and simulation archives.
Author: Andy Wills, Lenard Dome, Charlotte Edmunds, Garrett Honke, Angus Inkster, René Schlegelmilch, Stuart Spicer
Maintainer: Andy Wills <andy@willslab.co.uk>
Diff between catlearn versions 0.6.2 dated 2019-03-18 and 0.7.1 dated 2019-10-10
catlearn-0.6.2/catlearn/R/slpEXIT.R |only catlearn-0.7.1/catlearn/DESCRIPTION | 9 + catlearn-0.7.1/catlearn/MD5 | 32 ++++-- catlearn-0.7.1/catlearn/R/RcppExports.R | 20 ++-- catlearn-0.7.1/catlearn/R/convertSUSTAIN.R |only catlearn-0.7.1/catlearn/R/medin87train.R |only catlearn-0.7.1/catlearn/R/slpSUSTAIN.R | 17 +++ catlearn-0.7.1/catlearn/man/convertSUSTAIN.Rd |only catlearn-0.7.1/catlearn/man/medin87train.Rd |only catlearn-0.7.1/catlearn/man/nosof94sustain.Rd | 14 -- catlearn-0.7.1/catlearn/man/slpMack75.Rd |only catlearn-0.7.1/catlearn/man/slpSUSTAIN.Rd | 18 +++ catlearn-0.7.1/catlearn/src/RcppExports.cpp | 72 ++++++++++----- catlearn-0.7.1/catlearn/src/slpBM.cpp | 4 catlearn-0.7.1/catlearn/src/slpEXIT.cpp |only catlearn-0.7.1/catlearn/src/slpMack75.cpp |only catlearn-0.7.1/catlearn/src/slpRW.cpp | 4 catlearn-0.7.1/catlearn/src/slpcovis.cpp | 1 catlearn-0.7.1/catlearn/tests/data/test_slpMack75.RData |only catlearn-0.7.1/catlearn/tests/data/test_slpSUSTAIN.RData |binary catlearn-0.7.1/catlearn/tests/testthat/test_slpMack75.R |only catlearn-0.7.1/catlearn/tests/testthat/test_slpSUSTAIN.R | 26 +++++ 22 files changed, 152 insertions(+), 65 deletions(-)
Title: Automatic Short Form Creation
Description: Performs automatic creation of short forms of scales with an
ant colony optimization algorithm and a Tabu search. As implemented in the
package, the ant colony algorithm randomly selects items to build a model of
a specified length, then updates the probability of item selection according
to the fit of the best model within each set of searches. The algorithm
continues until the same items are selected by multiple ants a given number
of times in a row. On the other hand, the Tabu search changes one parameter at
a time to be either free, constrained, or fixed while keeping track of the
changes made and putting changes that result in worse fit in a "tabu" list
so that the algorithm does not revisit them for some number of searches.
See Leite, Huang, & Marcoulides (2008) <doi:10.1080/00273170802285743> for
an applied example of the ant colony algorithm, and Marcoulides & Falk (2018)
<doi:10.1080/10705511.2017.1409074> for an applied example of the Tabu search.
Author: Anthony Raborn [aut, cre],
Walter Leite [aut]
Maintainer: Anthony Raborn <anthony.w.raborn@gmail.com>
Diff between ShortForm versions 0.4.3 dated 2019-08-07 and 0.4.4 dated 2019-10-10
DESCRIPTION | 8 +++--- MD5 | 8 +++--- R/ACO_lavaan.R | 2 - R/Tabu_shortform.R | 49 +++++++++++++++++++++++++++++++------- R/simulated_annealing_internals.R | 2 - 5 files changed, 50 insertions(+), 19 deletions(-)
Title: Identify Moonlighting ncRNAs
Description: Identify moonlighting non-coding RNAs at the genome level based on the functional annotation and interactome data of ncRNAs and proteins. MoonFinder provides an extensive framework for the detection of protein modules and establishment of RNA-module associations.
Author: Lixin Cheng
Maintainer: Lixin Cheng <easonlcheng@gmail.com>
Diff between MoonFinder versions 1.0.1 dated 2019-02-22 and 1.0.2 dated 2019-10-10
DESCRIPTION | 19 +++++++----- MD5 | 34 ++++++++++++--------- NEWS |only R/SDI.R | 12 +++---- R/moduleCombiding.R | 45 ++++++++++++++-------------- R/moduleFunctionComparing.R | 11 +++---- R/moduleHeatmap.R | 53 +++++++++++++++++---------------- R/moduleMappingID.R | 19 ++++++------ R/moonlightingCoefficient.R | 28 ++++++++--------- R/rna2mod.R | 64 +++++++++++++++++++++-------------------- build |only inst |only man/MoonFinder-package.Rd | 3 + man/moduleCombiding.Rd | 3 + man/moduleList.Rd | 3 + man/moonlightingCoefficient.Rd | 9 +++-- man/rna2mod.Rd | 9 +++-- man/simMatBP.Rel.Rd | 3 + vignettes |only 19 files changed, 172 insertions(+), 143 deletions(-)
Title: Rstudio Addin for Version Control and Assignment Management
using Git
Description: An Rstudio addin for version control that allows users to clone
repositories, create and delete branches, and sync forks on GitHub, GitLab, etc.
Furthermore, the addin uses the GitLab API to allow instructors to create
forks and merge requests for all students/teams with one click of a button.
Author: Vincent Nijs [aut, cre],
Sanjiv Erat [aut]
Maintainer: Vincent Nijs <vnijs@ucsd.edu>
Diff between gitgadget versions 0.4.4 dated 2019-08-30 and 0.5.2 dated 2019-10-10
DESCRIPTION | 10 - MD5 | 21 +-- NAMESPACE | 1 NEWS.md | 12 ++ R/aaa.R | 4 R/gadget.R | 284 ++++++++++++++++++++++++++++++++++++++---------- R/git.R | 245 ++++++++++++++++++++++++++++++++--------- R/group_management.R |only README.md | 98 ++++++++++------ build/build_win.R | 23 ++- inst/doc/gitgadget.html | 99 ++++++++++------ man/assign_work.Rd | 7 - 12 files changed, 590 insertions(+), 214 deletions(-)