Title: Penalized Cox Proportional Hazard Model for Time-Dependent
Covariates
Description: Fits penalized models for both time-independent and time-dependent survival data. It fully implements elastic net and uses proximal gradient descent to solve the optimization problem. The package is an implementation of Steve Cygu and Benjamin M. Bolker. (2021) <arXiv:2102.02297>.
Author: Bicko Cygu [aut, cre] ,
Ben Bolker [aut] ,
Trevor Hastie [cph]
Maintainer: Bicko Cygu <cygubicko@gmail.com>
Diff between pcoxtime versions 1.0.3 dated 2021-11-13 and 1.0.4 dated 2022-05-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/pcoxtime.R | 32 ++++++++++++++++++++++++++------ build/partial.rdb |binary man/pcoxtime.Rd | 2 +- 5 files changed, 34 insertions(+), 14 deletions(-)
Title: Tidy Model Stacking
Description: Model stacking is an ensemble technique
that involves training a model to combine the outputs of many
diverse statistical models, and has been shown to improve
predictive performance in a variety of settings. 'stacks'
implements a grammar for 'tidymodels'-aligned model stacking.
Author: Simon Couch [aut, cre],
Max Kuhn [aut],
RStudio [cph, fnd]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>
Diff between stacks versions 0.2.2 dated 2022-01-05 and 0.2.3 dated 2022-05-12
stacks-0.2.2/stacks/tests/testthat/out |only stacks-0.2.3/stacks/DESCRIPTION | 22 stacks-0.2.3/stacks/MD5 | 118 +- stacks-0.2.3/stacks/NAMESPACE | 2 stacks-0.2.3/stacks/NEWS.md | 26 stacks-0.2.3/stacks/R/add_candidates.R | 45 - stacks-0.2.3/stacks/R/blend_predictions.R | 40 stacks-0.2.3/stacks/R/butcher.R | 5 stacks-0.2.3/stacks/R/collect_parameters.R | 4 stacks-0.2.3/stacks/R/fit_members.R | 69 + stacks-0.2.3/stacks/R/predict.R | 4 stacks-0.2.3/stacks/R/stacks.R | 2 stacks-0.2.3/stacks/R/utils.R | 30 stacks-0.2.3/stacks/README.md | 6 stacks-0.2.3/stacks/build/partial.rdb |binary stacks-0.2.3/stacks/build/vignette.rds |binary stacks-0.2.3/stacks/data/class_folds.rda |binary stacks-0.2.3/stacks/data/class_res_nn.rda |binary stacks-0.2.3/stacks/data/class_res_rf.rda |binary stacks-0.2.3/stacks/data/log_res_nn.rda |binary stacks-0.2.3/stacks/data/log_res_rf.rda |binary stacks-0.2.3/stacks/data/reg_folds.rda |binary stacks-0.2.3/stacks/data/reg_res_lr.rda |binary stacks-0.2.3/stacks/data/reg_res_sp.rda |binary stacks-0.2.3/stacks/data/reg_res_svm.rda |binary stacks-0.2.3/stacks/data/tree_frogs_class_test.rda |binary stacks-0.2.3/stacks/data/tree_frogs_reg_test.rda |binary stacks-0.2.3/stacks/inst/doc/basics.R | 13 stacks-0.2.3/stacks/inst/doc/basics.Rmd | 14 stacks-0.2.3/stacks/inst/doc/basics.html | 452 +++++++++-- stacks-0.2.3/stacks/inst/doc/classification.R | 13 stacks-0.2.3/stacks/inst/doc/classification.Rmd | 15 stacks-0.2.3/stacks/inst/doc/classification.html | 404 +++++++-- stacks-0.2.3/stacks/man/add_candidates.Rd | 3 stacks-0.2.3/stacks/man/axe_model_stack.Rd | 5 stacks-0.2.3/stacks/man/blend_predictions.Rd | 13 stacks-0.2.3/stacks/man/collect_parameters.Rd | 2 stacks-0.2.3/stacks/man/fit_members.Rd | 6 stacks-0.2.3/stacks/man/predict.model_stack.Rd | 5 stacks-0.2.3/stacks/man/stacks_description.Rd | 2 stacks-0.2.3/stacks/tests/testthat/_snaps |only stacks-0.2.3/stacks/tests/testthat/test_add_candidates.R | 55 + stacks-0.2.3/stacks/tests/testthat/test_blend_predictions.R | 36 stacks-0.2.3/stacks/tests/testthat/test_butcher.R | 31 stacks-0.2.3/stacks/tests/testthat/test_collect_parameters.R | 16 stacks-0.2.3/stacks/tests/testthat/test_cran.R | 14 stacks-0.2.3/stacks/tests/testthat/test_expressions.R | 14 stacks-0.2.3/stacks/tests/testthat/test_fit_members.R | 46 + stacks-0.2.3/stacks/tests/testthat/test_plots.R | 14 stacks-0.2.3/stacks/tests/testthat/test_predict.R | 14 stacks-0.2.3/stacks/tests/testthat/test_print.R | 73 - stacks-0.2.3/stacks/tests/testthat/test_utils.R | 25 stacks-0.2.3/stacks/vignettes/basics.Rmd | 14 stacks-0.2.3/stacks/vignettes/classification.Rmd | 15 54 files changed, 1324 insertions(+), 363 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, surface slope, and orientation patch count for teeth using scans of
enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph],
Edward Fuselier [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 4.5 dated 2020-03-03 and 5.0 dated 2022-05-12
molaR-4.5/molaR/R/face_areas.R |only molaR-4.5/molaR/R/plyClip.R |only molaR-4.5/molaR/R/read.AVIZO.ply.R |only molaR-4.5/molaR/man/DNE_Legend.Rd |only molaR-4.5/molaR/man/Directional_Bins.Rd |only molaR-4.5/molaR/man/Equal_Vertex_Normals.Rd |only molaR-4.5/molaR/man/Face_Normals.Rd |only molaR-4.5/molaR/man/OPC_Legend.Rd |only molaR-4.5/molaR/man/RFI_Legend.Rd |only molaR-4.5/molaR/man/Slope_Legend.Rd |only molaR-4.5/molaR/man/cSize.Rd |only molaR-4.5/molaR/man/clustered_patches.Rd |only molaR-4.5/molaR/man/compute_energy_per_face.Rd |only molaR-4.5/molaR/man/cross.Rd |only molaR-4.5/molaR/man/edge_vertices.Rd |only molaR-4.5/molaR/man/face_areas.Rd |only molaR-4.5/molaR/man/index_paired_directed_faces.Rd |only molaR-4.5/molaR/man/molaR_bgplot.Rd |only molaR-4.5/molaR/man/patch_details.Rd |only molaR-4.5/molaR/man/patches_for_each_direction.Rd |only molaR-4.5/molaR/man/patches_per.Rd |only molaR-4.5/molaR/man/plyClip.Rd |only molaR-4.5/molaR/man/read.AVIZO.ply.Rd |only molaR-4.5/molaR/man/remove_boundary_faces.Rd |only molaR-4.5/molaR/man/remove_outliers.Rd |only molaR-4.5/molaR/man/repmat.Rd |only molaR-4.5/molaR/man/tr.Rd |only molaR-4.5/molaR/man/vertex_to_face_list.Rd |only molaR-5.0/molaR/DESCRIPTION | 12 molaR-5.0/molaR/MD5 | 161 molaR-5.0/molaR/NAMESPACE | 12 molaR-5.0/molaR/R/CurveOrientation.R |only molaR-5.0/molaR/R/DNE.R | 284 - molaR-5.0/molaR/R/DNE3d.R | 324 - molaR-5.0/molaR/R/DNE3dDiscard.R |only molaR-5.0/molaR/R/DNEDensities.R |only molaR-5.0/molaR/R/DNE_Discard_Legend.R |only molaR-5.0/molaR/R/DNE_Legend.R | 167 molaR-5.0/molaR/R/DNEbar.R |only molaR-5.0/molaR/R/DNEpie.R |only molaR-5.0/molaR/R/Directional_Bins.R | 3 molaR-5.0/molaR/R/Equal_Vertex_Normals.R | 81 molaR-5.0/molaR/R/Face_Normals.R | 2 molaR-5.0/molaR/R/Hills.R |only molaR-5.0/molaR/R/OPC.R | 111 molaR-5.0/molaR/R/OPC3d.R | 153 molaR-5.0/molaR/R/OPC_Legend.R | 122 molaR-5.0/molaR/R/OPCbinareas.R |only molaR-5.0/molaR/R/OPCr.R | 125 molaR-5.0/molaR/R/RFI.R | 87 molaR-5.0/molaR/R/RFI3d.R | 246 molaR-5.0/molaR/R/RFI_Legend.R | 72 molaR-5.0/molaR/R/Slope.R | 177 molaR-5.0/molaR/R/Slope3d.R | 77 molaR-5.0/molaR/R/Slope_Legend.R | 102 molaR-5.0/molaR/R/Tooth.R |only molaR-5.0/molaR/R/cSize.R | 2 molaR-5.0/molaR/R/ccolor.gradient.R |only molaR-5.0/molaR/R/clipDisplay.R |only molaR-5.0/molaR/R/clustered_patches.R | 3 molaR-5.0/molaR/R/compute_energy_per_face.R | 1 molaR-5.0/molaR/R/cross.R | 3 molaR-5.0/molaR/R/edge_vertices.R | 2 molaR-5.0/molaR/R/findA.R |only molaR-5.0/molaR/R/index_paired_directed_faces.R | 2 molaR-5.0/molaR/R/interpolate_faces_to_vertices.R |only molaR-5.0/molaR/R/meshClip.R |only molaR-5.0/molaR/R/molaR_Batch.R | 497 - molaR-5.0/molaR/R/molaR_Clean.R | 165 molaR-5.0/molaR/R/molaR_bgplot.R | 2 molaR-5.0/molaR/R/patch_details.R | 3 molaR-5.0/molaR/R/patches_for_each_direction.R | 3 molaR-5.0/molaR/R/patches_per.R | 3 molaR-5.0/molaR/R/plyPlaneCut.R |only molaR-5.0/molaR/R/remove_boundary_faces.R | 3 molaR-5.0/molaR/R/remove_outliers.R | 1 molaR-5.0/molaR/R/repmat.R | 75 molaR-5.0/molaR/R/signedcolor.gradient.R |only molaR-5.0/molaR/R/tr.R | 3 molaR-5.0/molaR/R/triCondition.R |only molaR-5.0/molaR/R/vertex_to_face_list.R | 56 molaR-5.0/molaR/build/vignette.rds |binary molaR-5.0/molaR/inst/doc/molaR_vignette.R | 196 molaR-5.0/molaR/inst/doc/molaR_vignette.Rmd | 391 + molaR-5.0/molaR/inst/doc/molaR_vignette.html | 5825 ++------------------- molaR-5.0/molaR/man/DNE.Rd | 52 molaR-5.0/molaR/man/DNE3d.Rd | 138 molaR-5.0/molaR/man/DNE3dDiscard.Rd |only molaR-5.0/molaR/man/DNEDensities.Rd |only molaR-5.0/molaR/man/DNEbar.Rd |only molaR-5.0/molaR/man/DNEpie.Rd |only molaR-5.0/molaR/man/Hills.Rd | 20 molaR-5.0/molaR/man/OPC.Rd | 17 molaR-5.0/molaR/man/OPC3d.Rd | 77 molaR-5.0/molaR/man/OPCbinareas.Rd |only molaR-5.0/molaR/man/OPCr.Rd | 25 molaR-5.0/molaR/man/OPCr_Example1.Rd | 4 molaR-5.0/molaR/man/OPCr_Example2.Rd | 4 molaR-5.0/molaR/man/RFI.Rd | 50 molaR-5.0/molaR/man/RFI3d.Rd | 89 molaR-5.0/molaR/man/Slope.Rd | 31 molaR-5.0/molaR/man/Slope3d.Rd | 53 molaR-5.0/molaR/man/Tooth.Rd | 20 molaR-5.0/molaR/man/molaR_Batch.Rd | 141 molaR-5.0/molaR/man/molaR_Clean.Rd | 10 molaR-5.0/molaR/man/plyPlaneCut.Rd |only molaR-5.0/molaR/vignettes/molaR_vignette.Rmd | 391 + 107 files changed, 3493 insertions(+), 7183 deletions(-)
Title: Utility Functions for Forest Inventory Estimation and Analysis
Description: A set of tools for data wrangling, spatial data analysis,
statistical modeling (including direct, model-assisted, photo-based, and
small area tools), and USDA Forest Service data base tools. These tools are
aimed to help Foresters, Analysts, and Scientists extract and perform
analyses on USDA Forest Service data.
Author: Tracey Frescino [aut],
Chris Toney [aut],
Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTAutils versions 1.1.0 dated 2022-04-28 and 1.1.1 dated 2022-05-12
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/DBinternal.R | 8 ++++---- R/DBtestSQLite.R | 2 +- R/MAest.pbar.R | 2 +- R/aaa.R | 2 +- R/checks.R | 4 ++-- R/cool_functions.R | 4 ++-- R/pcheck.functions.R | 34 +++++++++++++++++----------------- R/raster_functions.R | 2 +- R/spatial_functions.R | 10 +++++----- man/internal_desc.Rd | 14 +++++++------- 14 files changed, 64 insertions(+), 58 deletions(-)
Title: Functions to Declare Missing Values
Description: A set of functions to declare labels and missing values, coupled with
associated functions to create (weighted) tables of frequencies and various
other summary measures.
Various base functions are rewritten to make use of the specific information
about the missing values, most importantly to distinguish between empty and
declared missing values.
Many functions have a similar functionality with the corresponding functions
from packages "haven" and "labelled". A lot of effort was spent to ensure as
much compatibility as possible with these packages, with the intention to
offer a complementary alternative for the objects of class "declared".
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between declared versions 0.15 dated 2022-04-13 and 0.16 dated 2022-05-12
DESCRIPTION | 8 +++--- MD5 | 25 +++++++++++---------- NAMESPACE | 2 - R/declared.R | 18 ++++++--------- R/haven.R | 11 ++------- R/onLoad.R | 58 +++++++++++++------------------------------------- R/pillar.R | 2 - R/print.R | 3 +- R/vroom.R |only R/w_table.R | 13 ++++++++--- build/vignette.rds |binary inst/ChangeLog | 11 ++++++--- inst/doc/declared.pdf |binary man/declared.Rd | 17 ++++++++------ 14 files changed, 75 insertions(+), 93 deletions(-)
Title: Calling Haplotype-Based and Variant-Based Pedigree
Disequilibrium Test for Rare Variants in Pedigrees
Description: To detecting rare variants for binary traits using general pedigrees, the pedigree disequilibrium tests are proposed by collapsing rare haplotypes/variants with/without weights. To run the test, MERLIN is needed in Linux for haplotyping.
Author: Wei Guo <wei.guo3@nih.gov>
Maintainer: Wei Guo <wei.guo3@nih.gov>
Diff between rvHPDT versions 3.0 dated 2014-05-14 and 4.0 dated 2022-05-12
DESCRIPTION | 13 +++++++------ MD5 | 4 ++-- NAMESPACE | 28 +++++++++++++++------------- 3 files changed, 24 insertions(+), 21 deletions(-)
Title: Auxiliary Functions for Phenological Data Analysis
Description: Provides some easy-to-use functions for time series
analyses of (plant-) phenological data sets. These functions
mainly deal with the estimation of combined phenological time
series and are usually wrappers for functions that are already
implemented in other R packages adapted to the special
structure of phenological data and the needs of phenologists.
Some date conversion functions to handle Julian dates are also
provided.
Author: Joerg Schaber
Maintainer: Maximilian Lange <maximilian.lange@ufz.de>
Diff between pheno versions 1.6 dated 2012-10-23 and 1.7-0 dated 2022-05-12
DESCRIPTION | 15 +++++++------ MD5 | 29 +++++++++++++------------ NAMESPACE | 53 ++++++++++++++++++++++++---------------------- R/connectedSets.R | 2 - R/date2jul1.R | 2 - R/date2jul2.R | 2 - R/daylength.R | 2 - R/daysbetween.R | 2 - R/jul2date1.R | 2 - R/jul2date2.R | 2 - R/leapyear.R | 2 - R/maxdaylength.R | 2 - man/pheno.mlm.fit.Rd | 10 ++++---- man/seqMK.Rd | 2 - man/tau.Rd | 58 +++++++++++++++++++++++++-------------------------- src/pheno_init.c |only 16 files changed, 95 insertions(+), 90 deletions(-)
Title: Interpretable Machine Learning
Description: Interpretability methods to analyze the behavior and
predictions of any machine learning model. Implemented methods are:
Feature importance described by Fisher et al. (2018)
<arXiv:1801.01489>, accumulated local effects plots described by Apley
(2018) <arXiv:1612.08468>, partial dependence plots described by
Friedman (2001) <www.jstor.org/stable/2699986>, individual conditional
expectation ('ice') plots described by Goldstein et al. (2013)
<doi:10.1080/10618600.2014.907095>, local models (variant of 'lime')
described by Ribeiro et. al (2016) <arXiv:1602.04938>, the Shapley
Value described by Strumbelj et. al (2014)
<doi:10.1007/s10115-013-0679-x>, feature interactions described by
Friedman et. al <doi:10.1214/07-AOAS148> and tree surrogate models.
Author: Christoph Molnar [aut, cre],
Patrick Schratz [aut]
Maintainer: Christoph Molnar <christoph.molnar@gmail.com>
Diff between iml versions 0.10.1 dated 2020-09-24 and 0.11.0 dated 2022-05-12
iml-0.10.1/iml/tests/testthat/Rplots.pdf |only iml-0.10.1/iml/tests/testthat/check-mlr3.R |only iml-0.11.0/iml/DESCRIPTION | 50 iml-0.11.0/iml/MD5 | 70 - iml-0.11.0/iml/NEWS.md | 21 iml-0.11.0/iml/R/Data.R | 4 iml-0.11.0/iml/R/FeatureEffect-ale.R | 49 iml-0.11.0/iml/R/FeatureEffect.R | 83 + iml-0.11.0/iml/R/FeatureImp.R | 66 + iml-0.11.0/iml/R/LocalModel.R | 21 iml-0.11.0/iml/R/utils.R | 3 iml-0.11.0/iml/build/vignette.rds |binary iml-0.11.0/iml/inst/doc/intro.html | 843 ++++++++-------- iml-0.11.0/iml/inst/doc/parallel.html | 657 +++++++----- iml-0.11.0/iml/man/FeatureEffect.Rd | 15 iml-0.11.0/iml/man/FeatureEffects.Rd | 2 iml-0.11.0/iml/man/FeatureImp.Rd | 32 iml-0.11.0/iml/man/Interaction.Rd | 2 iml-0.11.0/iml/man/LocalModel.Rd | 12 iml-0.11.0/iml/man/calculate.ale.num.Rd | 4 iml-0.11.0/iml/man/calculate.ale.num.cat.Rd | 4 iml-0.11.0/iml/man/calculate.ale.num.num.Rd | 6 iml-0.11.0/iml/tests/testthat/helper.R | 2 iml-0.11.0/iml/tests/testthat/setup.R | 6 iml-0.11.0/iml/tests/testthat/test-Data.R | 8 iml-0.11.0/iml/tests/testthat/test-FeatureEffect.R | 151 ++ iml-0.11.0/iml/tests/testthat/test-FeatureEffects.R | 8 iml-0.11.0/iml/tests/testthat/test-FeatureImp.R | 48 iml-0.11.0/iml/tests/testthat/test-Interaction.R | 2 iml-0.11.0/iml/tests/testthat/test-LocalModel.R | 52 iml-0.11.0/iml/tests/testthat/test-MarginalGenerator.R | 2 iml-0.11.0/iml/tests/testthat/test-Predictor.R | 28 iml-0.11.0/iml/tests/testthat/test-Shapley.R | 4 iml-0.11.0/iml/tests/testthat/test-TreeSurrogate.R | 2 iml-0.11.0/iml/tests/testthat/test-create_predict_fun.R | 15 iml-0.11.0/iml/tests/testthat/test-inferTask.R | 2 iml-0.11.0/iml/tests/testthat/test-utils.R | 3 37 files changed, 1425 insertions(+), 852 deletions(-)
Title: Spatio-Temporal Radial Basis Functions with Distance-Based
Methods (Optimization, Prediction and Cross Validation)
Description: Spatio-temporal radial basis functions (optimization, prediction and cross-validation), summary statistics from cross-validation, Adjusting distance-based linear regression model and generation of the principal coordinates of a new individual from Gower's distance.
Author: Carlos Melo [aut, cre] ,
Oscar Melo [aut] ,
Sandra Melo [aut]
Maintainer: Carlos Melo <cmelo@udistrital.edu.co>
Diff between geosptdb versions 1.0-0 dated 2022-05-12 and 1.0-1 dated 2022-05-12
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- inst/CITATION | 6 +++--- man/geosptdb-package.Rd | 4 ++-- man/graph.rbfST.Rd | 18 +++++++++--------- 5 files changed, 24 insertions(+), 24 deletions(-)
Title: Coarsened Mixtures of Hierarchical Skew Kernels
Description: Bayesian fit of a Dirichlet Process Mixture with hierarchical multivariate skew normal kernels and coarsened posteriors. For more information, see Gorsky, Chan and Ma (2020) <arXiv:2001.06451>.
Author: S. Gorsky [aut, cre],
C. Chan [ctb],
L. Ma [ctb]
Maintainer: S. Gorsky <sgorsky@umass.edu>
Diff between COMIX versions 0.1.4 dated 2022-05-10 and 0.1.6 dated 2022-05-12
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/RcppExports.R | 4 ++-- R/comix.R | 5 +++-- man/comix.Rd | 4 +++- src/Makevars | 3 ++- src/RcppExports.cpp | 9 +++++---- src/main.cpp | 4 ++-- src/perturbedSN_pmc.cpp | 18 +++++++++++++----- src/perturbedSN_pmc.h | 12 ++++++++---- 10 files changed, 50 insertions(+), 33 deletions(-)
Title: R Interface to the 'Deutsche Nationalbibliothek (German National
Library) API'
Description: A wrapper for the 'Deutsche Nationalbibliothek (German National
Library) API', available at <https://www.dnb.de/EN/Home/home_node.html>.
The German National Library is the German central archival library,
collecting, archiving, bibliographically classifying all German and
German-language publications, foreign publications about Germany,
translations of German works, and the works of German-speaking emigrants
published abroad between 1933 and 1945.
Author: Christian Graul [aut, cre]
Maintainer: Christian Graul <christian.graul@gmail.com>
Diff between rdnb versions 0.1-4 dated 2021-04-18 and 0.1-5 dated 2022-05-12
DESCRIPTION | 21 +++++++++++---------- MD5 | 22 +++++++++++----------- R/gets.R | 1 + R/rdnb.R | 2 +- R/utils.R | 4 ++-- build/vignette.rds |binary inst/CITATION | 6 +++--- inst/NEWS | 4 ++++ inst/doc/rdnb_vignette.Rmd | 12 ++++++------ inst/doc/rdnb_vignette.html | 12 ++++++------ man/rdnb.Rd | 2 +- vignettes/rdnb_vignette.Rmd | 12 ++++++------ 12 files changed, 52 insertions(+), 46 deletions(-)
Title: 'R Markdown' Format for Scientific and Technical Writing
Description: Scientific and technical article format for the web.
'Distill' articles feature attractive, reader-friendly typography,
flexible layout options for visualizations, and full support for
footnotes and citations.
Author: Christophe Dervieux [aut, cre]
,
JJ Allaire [aut] ,
Rich Iannone [aut],
Alison Presmanes Hill [aut] ,
Yihui Xie [aut] ,
RStudio, PBC [cph, fnd],
Google LLC [ctb, cph] ,
Nick Williams [ctb, cph] ,
Denis Demchenko [ctb, cph] ,
The Polymer Authors [ctb, [...truncated...]
Maintainer: Christophe Dervieux <cderv@rstudio.com>
Diff between distill versions 1.3 dated 2021-10-13 and 1.4 dated 2022-05-12
distill-1.3/distill/tests/testthat/setup.R |only distill-1.3/distill/tests/testthat/test-article.R |only distill-1.3/distill/tests/testthat/test-blog.R |only distill-1.3/distill/tests/testthat/test-website.R |only distill-1.4/distill/DESCRIPTION | 70 +++++----- distill-1.4/distill/MD5 | 42 +++--- distill-1.4/distill/NEWS.md | 36 +++-- distill-1.4/distill/R/collections.R | 11 + distill-1.4/distill/R/create.R | 6 distill-1.4/distill/R/distill-package.R |only distill-1.4/distill/R/distill_article.R | 2 distill-1.4/distill/R/distill_website.R | 5 distill-1.4/distill/R/metadata.R | 2 distill-1.4/distill/R/navigation.R | 2 distill-1.4/distill/R/rstudio.R | 33 ++++ distill-1.4/distill/R/sitemap.R | 10 + distill-1.4/distill/inst/rmarkdown/templates/distill_article/resources/arrow.theme | 13 + distill-1.4/distill/inst/rmarkdown/templates/distill_article/resources/default.html | 2 distill-1.4/distill/inst/rmarkdown/templates/distill_article/resources/distill.html | 39 ++++- distill-1.4/distill/man/create_theme.Rd | 4 distill-1.4/distill/man/create_website.Rd | 2 distill-1.4/distill/man/distill-package.Rd |only distill-1.4/distill/man/distill_article.Rd | 2 distill-1.4/distill/tests/testthat/helpers.R |only distill-1.4/distill/tests/testthat/test-collections.R |only distill-1.4/distill/tests/testthat/test-create.R |only distill-1.4/distill/tests/testthat/test-distill_article.R |only 27 files changed, 192 insertions(+), 89 deletions(-)
Title: Bayesian Composition Estimator: Estimating Sample (Taxonomic)
Composition from Biomarker Data
Description: Function to estimate taxonomic compositions from biomarker data, using a Bayesian approach.
Author: Karel Van den Meersche <karel.van_den_meersche@cirad.fr>, Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karel Van den Meersche <karel.van_den_meersche@cirad.fr>
Diff between BCE versions 2.1 dated 2014-05-22 and 2.2.0 dated 2022-05-12
BCE-2.1/BCE/data/datalist |only BCE-2.1/BCE/inst |only BCE-2.2.0/BCE/DESCRIPTION | 20 - BCE-2.2.0/BCE/MD5 | 19 - BCE-2.2.0/BCE/NAMESPACE | 2 BCE-2.2.0/BCE/NEWS |only BCE-2.2.0/BCE/R/summary.bce.R | 2 BCE-2.2.0/BCE/data/bceInput.rda |binary BCE-2.2.0/BCE/data/bceOutput.rda |binary BCE-2.2.0/BCE/man/BCE-1_5.Rd | 592 +++++++++++++++++++-------------------- BCE-2.2.0/BCE/man/bce1.Rd | 540 +++++++++++++++++------------------ BCE-2.2.0/BCE/man/tlsce.Rd | 256 ++++++++-------- 12 files changed, 716 insertions(+), 715 deletions(-)
Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between StereoMorph versions 1.6.4 dated 2021-05-25 and 1.6.5 dated 2022-05-12
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- R/findCheckerboardCorners.R | 6 +++--- R/list2XML4R.R | 14 +++++++------- R/readShapes.R | 6 +++--- R/reflectMissingLandmarks.R | 2 +- R/reflectMissingShapes.R | 3 ++- README.md |only inst/CITATION | 6 +++--- man/StereoMorph-package.Rd | 6 +++--- 10 files changed, 36 insertions(+), 34 deletions(-)
Title: Methods to Analyse Seasonal Radial Tree Growth Data
Description: Methods for comparing different regression algorithms for
describing the temporal dynamics of secondary tree growth (xylem and
phloem). Users can compare the accuracy of the most common fitting methods
usually used to analyse xylem and phloem data, i.e., Gompertz function and
General Additive Models (GAMs); and an algorithm newly introduced to the
field, i.e., Bayesian Regularised Neural Networks (brnn). The core function
of the package is XPSgrowth(), while the results can be interpreted using
implemented generic S3 methods, such as plot() and summary().
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between rTG versions 1.0.0 dated 2022-02-19 and 1.0.1 dated 2022-05-12
DESCRIPTION | 8 - MD5 | 23 ++-- NAMESPACE | 3 NEWS.md | 6 + R/XPSgrowth.R | 252 ++++++++++++++++++++++++--------------------- R/data_dendrometers.R |only R/data_trees.R | 7 - R/generics.R | 8 - R/generics2.R | 10 - data/data_dendrometers.rda |only data/data_trees.rda |binary man/XPSgrowth.Rd | 30 +++-- man/data_dendrometers.Rd |only man/data_trees.Rd | 7 - 14 files changed, 198 insertions(+), 156 deletions(-)
Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit
Data
Description: Implements a class of univariate and multivariate spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, or Poisson, but for some models only the binomial and Poisson data likelihoods are available. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) style prior distributions. A number of different random effects structures are available, including models similar to Rushworth et al. (2014) <doi:10.1016/j.sste.2014.05.001>. Full details are given in the vignette accompanying this package. The creation and development of this package was supported by the Engineering and Physical Sciences Research Council (EPSRC) grants EP/J017442/1 and EP/T004878/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee, Alastair Rushworth, Gary Napier and William Pettersson
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesST versions 3.2.3 dated 2022-04-26 and 3.3 dated 2022-05-12
CARBayesST-3.2.3/CARBayesST/vignettes/SMRmap.pdf |only CARBayesST-3.2.3/CARBayesST/vignettes/figsim1.png |only CARBayesST-3.2.3/CARBayesST/vignettes/salesmap.pdf |only CARBayesST-3.2.3/CARBayesST/vignettes/salesmapest.png |only CARBayesST-3.3/CARBayesST/DESCRIPTION | 12 - CARBayesST-3.3/CARBayesST/MD5 | 116 +++++----- CARBayesST-3.3/CARBayesST/NAMESPACE | 28 +- CARBayesST-3.3/CARBayesST/R/MVST.CARar.R | 2 CARBayesST-3.3/CARBayesST/R/ST.CARadaptive.R | 2 CARBayesST-3.3/CARBayesST/R/ST.CARanova.R | 2 CARBayesST-3.3/CARBayesST/R/ST.CARar.R | 2 CARBayesST-3.3/CARBayesST/R/ST.CARlinear.R | 2 CARBayesST-3.3/CARBayesST/R/ST.CARlocalised.R | 2 CARBayesST-3.3/CARBayesST/R/ST.CARsepspatial.R | 2 CARBayesST-3.3/CARBayesST/R/binomial.CARadaptive.R | 14 - CARBayesST-3.3/CARBayesST/R/binomial.CARanova.R | 24 +- CARBayesST-3.3/CARBayesST/R/binomial.CARar1.R | 12 - CARBayesST-3.3/CARBayesST/R/binomial.CARar2.R | 14 - CARBayesST-3.3/CARBayesST/R/binomial.CARclustrends.R | 4 CARBayesST-3.3/CARBayesST/R/binomial.CARlinear.R | 16 - CARBayesST-3.3/CARBayesST/R/binomial.CARlocalised.R | 19 - CARBayesST-3.3/CARBayesST/R/binomial.CARsepspatial.R | 14 - CARBayesST-3.3/CARBayesST/R/binomial.MVCARar1.R | 43 ++- CARBayesST-3.3/CARBayesST/R/binomial.MVCARar2.R | 43 ++- CARBayesST-3.3/CARBayesST/R/coef.CARBayesST.R | 2 CARBayesST-3.3/CARBayesST/R/gaussian.CARadaptive.R | 14 - CARBayesST-3.3/CARBayesST/R/gaussian.CARanova.R | 14 - CARBayesST-3.3/CARBayesST/R/gaussian.CARar1.R | 12 - CARBayesST-3.3/CARBayesST/R/gaussian.CARar2.R | 14 - CARBayesST-3.3/CARBayesST/R/gaussian.CARlinear.R | 16 - CARBayesST-3.3/CARBayesST/R/gaussian.MVCARar1.R | 44 ++-- CARBayesST-3.3/CARBayesST/R/gaussian.MVCARar2.R | 63 +++-- CARBayesST-3.3/CARBayesST/R/poisson.CARadaptive.R | 14 - CARBayesST-3.3/CARBayesST/R/poisson.CARanova.R | 24 +- CARBayesST-3.3/CARBayesST/R/poisson.CARar1.R | 12 - CARBayesST-3.3/CARBayesST/R/poisson.CARar2.R | 14 - CARBayesST-3.3/CARBayesST/R/poisson.CARclustrends.R | 4 CARBayesST-3.3/CARBayesST/R/poisson.CARlinear.R | 16 - CARBayesST-3.3/CARBayesST/R/poisson.CARlocalised.R | 17 - CARBayesST-3.3/CARBayesST/R/poisson.CARsepspatial.R | 14 - CARBayesST-3.3/CARBayesST/R/poisson.MVCARar1.R | 45 ++-- CARBayesST-3.3/CARBayesST/R/poisson.MVCARar2.R | 46 ++-- CARBayesST-3.3/CARBayesST/build/vignette.rds |binary CARBayesST-3.3/CARBayesST/inst/doc/CARBayesST.R | 88 ++++---- CARBayesST-3.3/CARBayesST/inst/doc/CARBayesST.Rnw | 197 +++++++++--------- CARBayesST-3.3/CARBayesST/inst/doc/CARBayesST.pdf |binary CARBayesST-3.3/CARBayesST/man/CARBayesST-package.Rd | 8 CARBayesST-3.3/CARBayesST/man/MVST.CARar.Rd | 47 +++- CARBayesST-3.3/CARBayesST/man/ST.CARadaptive.Rd | 6 CARBayesST-3.3/CARBayesST/man/ST.CARanova.Rd | 6 CARBayesST-3.3/CARBayesST/man/ST.CARar.Rd | 6 CARBayesST-3.3/CARBayesST/man/ST.CARclustrends.Rd | 4 CARBayesST-3.3/CARBayesST/man/ST.CARlinear.Rd | 8 CARBayesST-3.3/CARBayesST/man/ST.CARlocalised.Rd | 6 CARBayesST-3.3/CARBayesST/man/ST.CARsepspatial.Rd | 6 CARBayesST-3.3/CARBayesST/man/coef.CARBayesST.Rd | 2 CARBayesST-3.3/CARBayesST/man/print.CARBayesST.Rd | 2 CARBayesST-3.3/CARBayesST/vignettes/CARBayesST.Rnw | 197 +++++++++--------- CARBayesST-3.3/CARBayesST/vignettes/JSS2728.bib | 31 ++ CARBayesST-3.3/CARBayesST/vignettes/SMRmap.png |only CARBayesST-3.3/CARBayesST/vignettes/salesmap.png |only CARBayesST-3.3/CARBayesST/vignettes/salestrend.png |binary 62 files changed, 771 insertions(+), 601 deletions(-)
Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, multinomial, Poisson or zero-inflated Poisson (ZIP), and spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution. A number of different models are available for univariate spatial data, including models with no random effects as well as random effects modelled by different types of CAR prior, including the BYM model (Besag et al., 1991, <doi:10.1007/BF00116466>) and Leroux model (Leroux et al., 2000, <doi:10.1007/978-1-4612-1284-3_4>). Additionally, a multivariate CAR (MCAR) model for multivariate spatial data is available, as is a two-level hierarchical model for modelling data relating to individuals within areas. Full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development has been supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1, ESRC grant ES/K006460/1, Innovate UK / Natural Environment Research Council (NERC) grant NE/N007352/1 and the TB Alliance.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayes versions 5.2.5 dated 2021-09-30 and 5.3 dated 2022-05-12
CARBayes-5.2.5/CARBayes/R/combine.data.shapefile.R |only CARBayes-5.2.5/CARBayes/R/summarise.lincomb.R |only CARBayes-5.2.5/CARBayes/R/summarise.samples.R |only CARBayes-5.2.5/CARBayes/man/combine.data.shapefile.Rd |only CARBayes-5.2.5/CARBayes/man/summarise.lincomb.Rd |only CARBayes-5.2.5/CARBayes/man/summarise.samples.Rd |only CARBayes-5.3/CARBayes/DESCRIPTION | 18 CARBayes-5.3/CARBayes/MD5 | 121 CARBayes-5.3/CARBayes/NAMESPACE | 8 CARBayes-5.3/CARBayes/R/MVS.CARleroux.R | 4 CARBayes-5.3/CARBayes/R/RcppExports.R | 80 CARBayes-5.3/CARBayes/R/S.CARbym.R | 2 CARBayes-5.3/CARBayes/R/S.CARdissimilarity.R | 2 CARBayes-5.3/CARBayes/R/S.CARleroux.R | 2 CARBayes-5.3/CARBayes/R/S.CARlocalised.R | 2 CARBayes-5.3/CARBayes/R/S.CARmultilevel.R | 8 CARBayes-5.3/CARBayes/R/S.glm.R | 2 CARBayes-5.3/CARBayes/R/binomial.MVlerouxCAR.R | 1013 +++---- CARBayes-5.3/CARBayes/R/binomial.bymCAR.R | 26 CARBayes-5.3/CARBayes/R/binomial.dissimilarityCAR.R | 20 CARBayes-5.3/CARBayes/R/binomial.glm.R | 6 CARBayes-5.3/CARBayes/R/binomial.lerouxCAR.R | 18 CARBayes-5.3/CARBayes/R/binomial.localisedCAR.R | 24 CARBayes-5.3/CARBayes/R/binomial.multilevelCAR.R | 141 - CARBayes-5.3/CARBayes/R/coef.CARBayes.R | 6 CARBayes-5.3/CARBayes/R/gaussian.MVlerouxCAR.R | 961 +++---- CARBayes-5.3/CARBayes/R/gaussian.dissimilarityCAR.R | 12 CARBayes-5.3/CARBayes/R/gaussian.glm.R | 6 CARBayes-5.3/CARBayes/R/gaussian.lerouxCAR.R | 10 CARBayes-5.3/CARBayes/R/gaussian.multilevelCAR.R | 137 - CARBayes-5.3/CARBayes/R/highlight.borders.R | 66 CARBayes-5.3/CARBayes/R/multinomial.MVlerouxCAR.R | 1025 +++---- CARBayes-5.3/CARBayes/R/multinomial.glm.R | 4 CARBayes-5.3/CARBayes/R/poisson.MVlerouxCAR.R | 956 +++---- CARBayes-5.3/CARBayes/R/poisson.bymCAR.R | 26 CARBayes-5.3/CARBayes/R/poisson.dissimilarityCAR.R | 20 CARBayes-5.3/CARBayes/R/poisson.glm.R | 7 CARBayes-5.3/CARBayes/R/poisson.lerouxCAR.R | 18 CARBayes-5.3/CARBayes/R/poisson.localisedCAR.R | 22 CARBayes-5.3/CARBayes/R/poisson.multilevelCAR.R | 141 - CARBayes-5.3/CARBayes/R/print.CARBayes.R | 6 CARBayes-5.3/CARBayes/R/residuals.CARBayes.R | 2 CARBayes-5.3/CARBayes/R/zip.bymCAR.R | 30 CARBayes-5.3/CARBayes/R/zip.glm.R | 10 CARBayes-5.3/CARBayes/R/zip.lerouxCAR.R | 22 CARBayes-5.3/CARBayes/build/vignette.rds |binary CARBayes-5.3/CARBayes/inst/doc/CARBayes.R | 102 CARBayes-5.3/CARBayes/inst/doc/CARBayes.Rnw | 267 + CARBayes-5.3/CARBayes/inst/doc/CARBayes.pdf |binary CARBayes-5.3/CARBayes/man/CARBayes-package.Rd | 9 CARBayes-5.3/CARBayes/man/MVS.CARleroux.Rd | 35 CARBayes-5.3/CARBayes/man/S.CARbym.Rd | 14 CARBayes-5.3/CARBayes/man/S.CARdissimilarity.Rd | 10 CARBayes-5.3/CARBayes/man/S.CARleroux.Rd | 14 CARBayes-5.3/CARBayes/man/S.CARlocalised.Rd | 10 CARBayes-5.3/CARBayes/man/S.CARmultilevel.Rd | 59 CARBayes-5.3/CARBayes/man/S.glm.Rd | 12 CARBayes-5.3/CARBayes/man/coef.CARBayes.Rd | 2 CARBayes-5.3/CARBayes/man/highlight.borders.Rd | 26 CARBayes-5.3/CARBayes/man/print.CARBayes.Rd | 2 CARBayes-5.3/CARBayes/src/CARBayes.cpp | 1339 +--------- CARBayes-5.3/CARBayes/src/RcppExports.cpp | 354 -- CARBayes-5.3/CARBayes/vignettes/CARBayes.Rnw | 267 + CARBayes-5.3/CARBayes/vignettes/Rplots-2021-782b46ba4442-winl.pdf |only CARBayes-5.3/CARBayes/vignettes/jss996.bib | 1084 ++++---- 65 files changed, 3589 insertions(+), 5001 deletions(-)
Title: A Collection of Physical and Chemical Adsorption Isotherm Models
Description: The PUPAIM R package can generally fit any adsorption experimental data to any of the 51 available adsorption isotherm models - 28 nonlinear models and 23 linear models. This package provides parameter estimation, model accuracy analysis, model error analysis, and adsorption plot created using the package 'ggplot2'. This package will help the users for a much easier way of adsorption model data fitting.
Author: Keith T. Ostan [aut] ,
Paul Angelo C. Manlapaz [aut] ,
Jemnimah Christine L. Mesias [aut]
,
Chester C. Deocaris [aut, ths, cre]
Maintainer: Chester C. Deocaris <ccdeocaris@pup.edu.ph>
Diff between PUPAIM versions 0.2.0 dated 2020-03-23 and 0.3.0 dated 2022-05-12
PUPAIM-0.2.0/PUPAIM/R/1storderkinetics.R |only PUPAIM-0.2.0/PUPAIM/R/2ndorderkinetics.R |only PUPAIM-0.2.0/PUPAIM/R/5paramplot.R |only PUPAIM-0.2.0/PUPAIM/R/BETplot.R |only PUPAIM-0.2.0/PUPAIM/R/Banana.R |only PUPAIM-0.2.0/PUPAIM/R/Moringa.r |only PUPAIM-0.2.0/PUPAIM/R/PUPAIM-deprecated.r |only PUPAIM-0.2.0/PUPAIM/R/WVVanalysis.R |only PUPAIM-0.2.0/PUPAIM/R/WVVplot.R |only PUPAIM-0.2.0/PUPAIM/R/bauduplot.R |only PUPAIM-0.2.0/PUPAIM/R/deltaG.R |only PUPAIM-0.2.0/PUPAIM/R/dubininradushkevichplot.R |only PUPAIM-0.2.0/PUPAIM/R/dubininradushkevishnlanalysis.R |only PUPAIM-0.2.0/PUPAIM/R/elovichanalysis.R |only PUPAIM-0.2.0/PUPAIM/R/elovichkinetics.R |only PUPAIM-0.2.0/PUPAIM/R/elovichplot.R |only PUPAIM-0.2.0/PUPAIM/R/fiveparamanalysis.R |only PUPAIM-0.2.0/PUPAIM/R/floryhugginsplot.R |only PUPAIM-0.2.0/PUPAIM/R/fowlerguggenheimanalysis.r |only PUPAIM-0.2.0/PUPAIM/R/fowlerguggenheimplot.R |only PUPAIM-0.2.0/PUPAIM/R/fractionalpower.R |only PUPAIM-0.2.0/PUPAIM/R/freundlich.r |only PUPAIM-0.2.0/PUPAIM/R/freundlichLManalysis.R |only PUPAIM-0.2.0/PUPAIM/R/freundlichplot.R |only PUPAIM-0.2.0/PUPAIM/R/fritzschlunderplot.r |only PUPAIM-0.2.0/PUPAIM/R/fritzsclunderanalysis.R |only PUPAIM-0.2.0/PUPAIM/R/halseyplot.R |only PUPAIM-0.2.0/PUPAIM/R/harkinsjuraplot.R |only PUPAIM-0.2.0/PUPAIM/R/henryanalysis.R |only PUPAIM-0.2.0/PUPAIM/R/henryplot.R |only PUPAIM-0.2.0/PUPAIM/R/hillanalysis.r |only PUPAIM-0.2.0/PUPAIM/R/hilldeboeranalysis.r |only PUPAIM-0.2.0/PUPAIM/R/hilldeboerplot.R |only PUPAIM-0.2.0/PUPAIM/R/hillplot.R |only PUPAIM-0.2.0/PUPAIM/R/jossensanalysis.R |only PUPAIM-0.2.0/PUPAIM/R/jossensplot.R |only PUPAIM-0.2.0/PUPAIM/R/jovanovicanalysis.r |only PUPAIM-0.2.0/PUPAIM/R/jovanovicplot.R |only PUPAIM-0.2.0/PUPAIM/R/kahnplot.R |only PUPAIM-0.2.0/PUPAIM/R/kiselevlanalysis.R |only PUPAIM-0.2.0/PUPAIM/R/kiselevplot.R |only PUPAIM-0.2.0/PUPAIM/R/koblecarriganplot.R |only PUPAIM-0.2.0/PUPAIM/R/langmuirFanalysis.R |only PUPAIM-0.2.0/PUPAIM/R/langmuirFplot.R |only 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PUPAIM-0.2.0/PUPAIM/man/dubininradanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/elovichkinetics.Rd |only PUPAIM-0.2.0/PUPAIM/man/elovichplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/fgplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/fhanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/fhplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/firstorder.Rd |only PUPAIM-0.2.0/PUPAIM/man/fivePplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/fiveparamanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/fowlerganalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/fractionalpower.Rd |only PUPAIM-0.2.0/PUPAIM/man/freundlichplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/fritzanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/fsplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/halseyplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/hdplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/henryanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/henryanalysisplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/hillplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/hjplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/jossensplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/jovanovicplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/kahnplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/kcarriganplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/kiselevplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/langmuir.LM1.Rd |only PUPAIM-0.2.0/PUPAIM/man/langmuirFanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/langmuirFplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/langmuiranalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/langmuirplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/marcJplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/mjanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/moringa.Rd |only PUPAIM-0.2.0/PUPAIM/man/raudkePplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/raudkepanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/redlichpanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/rpplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/secondorder.Rd |only PUPAIM-0.2.0/PUPAIM/man/sipsplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/summaryanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/summaryplots-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/temkinplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/tothanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/man/tothplot-deprecated.Rd |only PUPAIM-0.2.0/PUPAIM/man/webervvanalysis.Rd |only PUPAIM-0.2.0/PUPAIM/tests |only PUPAIM-0.3.0/PUPAIM/DESCRIPTION | 25 - PUPAIM-0.3.0/PUPAIM/MD5 | 258 +++++++--------- PUPAIM-0.3.0/PUPAIM/NAMESPACE | 106 ++---- PUPAIM-0.3.0/PUPAIM/R/BETLM.r |only PUPAIM-0.3.0/PUPAIM/R/BETanalysis.R | 130 +++++--- PUPAIM-0.3.0/PUPAIM/R/FS3analysis.R |only PUPAIM-0.3.0/PUPAIM/R/FS4analysis.R |only PUPAIM-0.3.0/PUPAIM/R/PUPAIM.R |only PUPAIM-0.3.0/PUPAIM/R/SSLangmuir1.R |only PUPAIM-0.3.0/PUPAIM/R/SSLangmuir1analysis.R |only PUPAIM-0.3.0/PUPAIM/R/SSLangmuir2.R |only PUPAIM-0.3.0/PUPAIM/R/SSLangmuir2analysis.R |only PUPAIM-0.3.0/PUPAIM/R/SSLangmuir3.R |only PUPAIM-0.3.0/PUPAIM/R/SSLangmuir3analysis.R |only PUPAIM-0.3.0/PUPAIM/R/SSLangmuir4.R |only PUPAIM-0.3.0/PUPAIM/R/SSLangmuir4analysis.R |only PUPAIM-0.3.0/PUPAIM/R/aranovichanalysis.R |only PUPAIM-0.3.0/PUPAIM/R/bauduanalysis.R | 135 +++++--- PUPAIM-0.3.0/PUPAIM/R/dubininradushkevichLM.R |only PUPAIM-0.3.0/PUPAIM/R/dubininradushkevichanalysis.R |only PUPAIM-0.3.0/PUPAIM/R/elovichLM.r |only PUPAIM-0.3.0/PUPAIM/R/elovichanalysis.r |only PUPAIM-0.3.0/PUPAIM/R/floryhugginsLM.R |only PUPAIM-0.3.0/PUPAIM/R/floryhugginsanalysis.R | 131 +++++--- PUPAIM-0.3.0/PUPAIM/R/fowlerguggenheimLM.R |only PUPAIM-0.3.0/PUPAIM/R/fowlerguggenheimanalysis.R |only PUPAIM-0.3.0/PUPAIM/R/freundlichLM.R |only PUPAIM-0.3.0/PUPAIM/R/freundlichanalysis.R |only PUPAIM-0.3.0/PUPAIM/R/halseyLM.R |only PUPAIM-0.3.0/PUPAIM/R/halseyanalysis.R | 125 ++++--- PUPAIM-0.3.0/PUPAIM/R/harkinsjuraLM.R |only PUPAIM-0.3.0/PUPAIM/R/harkinsjuraanalysis.R | 128 +++++-- PUPAIM-0.3.0/PUPAIM/R/henryLM.r |only PUPAIM-0.3.0/PUPAIM/R/hillLM.R |only PUPAIM-0.3.0/PUPAIM/R/hillanalysis.R |only PUPAIM-0.3.0/PUPAIM/R/hilldeboerLM.R |only PUPAIM-0.3.0/PUPAIM/R/hilldeboeranalysis.R |only PUPAIM-0.3.0/PUPAIM/R/jossensLM.r |only PUPAIM-0.3.0/PUPAIM/R/jossensanalysis.r |only PUPAIM-0.3.0/PUPAIM/R/jovanovicLM.R |only PUPAIM-0.3.0/PUPAIM/R/jovanovicanalysis.R |only PUPAIM-0.3.0/PUPAIM/R/kahnanalysis.R | 134 +++++--- PUPAIM-0.3.0/PUPAIM/R/kiselevLM.R |only PUPAIM-0.3.0/PUPAIM/R/kiselevanalysis.R |only PUPAIM-0.3.0/PUPAIM/R/koblecarrigananalysis.R | 129 +++++--- PUPAIM-0.3.0/PUPAIM/R/koblecorriganLM.R |only PUPAIM-0.3.0/PUPAIM/R/langmuiranalysis.R | 138 +++++--- PUPAIM-0.3.0/PUPAIM/R/marckzewskijaroniecanalysis.r |only PUPAIM-0.3.0/PUPAIM/R/radkeprausnitzanalysis.R |only PUPAIM-0.3.0/PUPAIM/R/radkepraustnitzLM.R |only PUPAIM-0.3.0/PUPAIM/R/redlichpetersonLM.R |only PUPAIM-0.3.0/PUPAIM/R/redlichpetersonanalysis.R | 142 +++++--- PUPAIM-0.3.0/PUPAIM/R/sipsLM.R |only PUPAIM-0.3.0/PUPAIM/R/sipsanalysis.R | 135 +++++--- PUPAIM-0.3.0/PUPAIM/R/temkinLM.R |only PUPAIM-0.3.0/PUPAIM/R/temkinanalysis.r |only PUPAIM-0.3.0/PUPAIM/R/tothanalysis.R | 131 +++++--- PUPAIM-0.3.0/PUPAIM/R/volmeranalysis.R |only PUPAIM-0.3.0/PUPAIM/R/webervanvlietanalysis.r |only PUPAIM-0.3.0/PUPAIM/build |only PUPAIM-0.3.0/PUPAIM/inst |only PUPAIM-0.3.0/PUPAIM/man/BET.LM.Rd |only PUPAIM-0.3.0/PUPAIM/man/BETanalysis.Rd | 21 - PUPAIM-0.3.0/PUPAIM/man/FS3analysis.Rd |only PUPAIM-0.3.0/PUPAIM/man/FS4analysis.Rd |only PUPAIM-0.3.0/PUPAIM/man/PUPAIM.Rd |only PUPAIM-0.3.0/PUPAIM/man/SSLangmuir1.Rd |only PUPAIM-0.3.0/PUPAIM/man/SSLangmuir1analysis.Rd |only PUPAIM-0.3.0/PUPAIM/man/SSLangmuir2.Rd |only PUPAIM-0.3.0/PUPAIM/man/SSLangmuir2analysis.Rd |only PUPAIM-0.3.0/PUPAIM/man/SSLangmuir3.Rd |only PUPAIM-0.3.0/PUPAIM/man/SSLangmuir3analysis.Rd |only PUPAIM-0.3.0/PUPAIM/man/SSLangmuir4.Rd |only PUPAIM-0.3.0/PUPAIM/man/SSLangmuir4analysis.Rd |only PUPAIM-0.3.0/PUPAIM/man/aranovichanalysis.Rd |only PUPAIM-0.3.0/PUPAIM/man/bauduanalysis.Rd | 30 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files changed, 1414 insertions(+), 906 deletions(-)
Title: Generic Machine Learning Inference
Description: Generic Machine Learning Inference on heterogeneous treatment effects in randomized experiments as proposed in Chernozhukov, Demirer, Duflo and Fernández-Val (2020) <arXiv:1712.04802>. This package's workhorse is the 'mlr3' framework of Lang et al. (2019) <doi:10.21105/joss.01903>, which enables the specification of a wide variety of machine learners. The main functionality, GenericML(), runs Algorithm 1 in Chernozhukov, Demirer, Duflo and Fernández-Val (2020) <arXiv:1712.04802> for a suite of user-specified machine learners. All steps in the algorithm are customizable via setup functions. Methods for printing and plotting are available for objects returned by GenericML(). Parallel computing is supported.
Author: Max Welz [aut, cre] ,
Andreas Alfons [aut] ,
Mert Demirer [aut],
Victor Chernozhukov [aut]
Maintainer: Max Welz <welz@ese.eur.nl>
Diff between GenericML versions 0.2.0 dated 2022-05-06 and 0.2.1 dated 2022-05-12
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 5 +++++ R/GenericML.R | 4 ++-- R/accessors.R | 13 ++++++++++--- R/input-checks.R | 6 +++--- R/misc.R | 4 ++-- R/plot.R | 2 +- R/print.R | 2 +- R/sample-split.R | 2 +- build/partial.rdb |binary inst/CITATION | 8 ++++---- man/GenericML.Rd | 4 ++-- man/setup_stratify.Rd | 2 +- 14 files changed, 48 insertions(+), 36 deletions(-)
Title: Data Used in the Vignettes Accompanying the CARBayes and
CARBayesST Packages
Description: Spatio-temporal data from Scotland used in the vignettes accompanying the CARBayes (spatial modelling) and CARBayesST (spatio-temporal modelling) packages. Most of the data relate to the set of 271 Intermediate Zones (IZ) that make up the 2001 definition of the Greater Glasgow and Clyde health board.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesdata versions 2.2 dated 2020-08-26 and 3.0 dated 2022-05-12
CARBayesdata-2.2/CARBayesdata/data/GGHB.IG.rda |only CARBayesdata-2.2/CARBayesdata/data/lipdbf.rda |only CARBayesdata-2.2/CARBayesdata/data/lipshp.rda |only CARBayesdata-2.2/CARBayesdata/man/GGHB.IG.Rd |only CARBayesdata-2.2/CARBayesdata/man/lipdbf.Rd |only CARBayesdata-2.2/CARBayesdata/man/lipshp.Rd |only CARBayesdata-3.0/CARBayesdata/DESCRIPTION | 14 ++--- CARBayesdata-3.0/CARBayesdata/MD5 | 36 +++++-------- CARBayesdata-3.0/CARBayesdata/NAMESPACE | 3 - CARBayesdata-3.0/CARBayesdata/data/GGHB.IZ.rda |only CARBayesdata-3.0/CARBayesdata/data/datalist | 6 -- CARBayesdata-3.0/CARBayesdata/data/lipdata.rda |binary CARBayesdata-3.0/CARBayesdata/data/pollutionhealthdata.rda |binary CARBayesdata-3.0/CARBayesdata/data/pricedata.rda |binary CARBayesdata-3.0/CARBayesdata/data/respiratorydata.rda |binary CARBayesdata-3.0/CARBayesdata/data/salesdata.rda |binary CARBayesdata-3.0/CARBayesdata/man/CARBayesdata-package.Rd | 19 ++---- CARBayesdata-3.0/CARBayesdata/man/GGHB.IZ.Rd |only CARBayesdata-3.0/CARBayesdata/man/lipdata.Rd | 6 +- CARBayesdata-3.0/CARBayesdata/man/pollutionhealthdata.Rd | 4 - CARBayesdata-3.0/CARBayesdata/man/pricedata.Rd | 6 +- CARBayesdata-3.0/CARBayesdata/man/respiratorydata.Rd | 5 + CARBayesdata-3.0/CARBayesdata/man/salesdata.Rd | 4 - 23 files changed, 45 insertions(+), 58 deletions(-)
Title: K-Means with Simultaneous Outlier Detection
Description: An implementation of the 'k-means--' algorithm proposed
by Chawla and Gionis, 2013 in their paper,
"k-means-- : A unified approach to clustering and outlier detection.
SIAM International Conference on Data Mining (SDM13)",
<doi:10.1137/1.9781611972832.21>
and using 'ordering' described by Howe, 2013 in the thesis,
Clustering and anomaly detection in tropical cyclones".
Useful for creating (potentially) tighter clusters than
standard k-means and simultaneously finding outliers inexpensively
in multidimensional space.
Author: David Charles Howe [aut, cre]
Maintainer: David Charles Howe <kmodR@edgecondition.com>
Diff between kmodR versions 0.1.0 dated 2015-03-26 and 0.2.0 dated 2022-05-12
DESCRIPTION | 30 +++++++++++++++++++++--------- MD5 | 14 ++++++++------ NAMESPACE | 6 +++++- NEWS.md |only R/kmod.R | 35 ++++++++++++++++++++++++----------- README.md | 38 ++++++++++++++++++++------------------ build |only man/kmod.Rd | 31 ++++++++++++++++++++++++------- tests/testthat.R | 1 + 9 files changed, 103 insertions(+), 52 deletions(-)
Title: Spatio-Temporal Radial Basis Functions with Distance-Based
Methods (Optimization, Prediction and Cross Validation)
Description: Spatio-temporal radial basis functions (optimization, prediction and cross-validation), summary statistics from cross-validation, Adjusting distance-based linear regression model and generation of the principal coordinates of a new individual from Gower's distance.
Author: Carlos Melo [aut, cre] ,
Oscar Melo [aut],
Sandra Melo [aut]
Maintainer: Carlos Melo <cmelo@udistrital.edu.co>
Diff between geosptdb versions 0.5-0 dated 2015-06-23 and 1.0-0 dated 2022-05-12
geosptdb-0.5-0/geosptdb/R/criterioST.cv.R |only geosptdb-0.5-0/geosptdb/man/criterioST.cv.Rd |only geosptdb-1.0-0/geosptdb/DESCRIPTION | 30 ++++++++++++++-------- geosptdb-1.0-0/geosptdb/MD5 | 18 +++++++------ geosptdb-1.0-0/geosptdb/NAMESPACE | 10 ++++++- geosptdb-1.0-0/geosptdb/R/criteriaST.cv.R |only geosptdb-1.0-0/geosptdb/data/croatia2008.rda |only geosptdb-1.0-0/geosptdb/inst/CITATION | 14 ++++------ geosptdb-1.0-0/geosptdb/man/criteriaST.cv.Rd |only geosptdb-1.0-0/geosptdb/man/croatia2008.Rd |only geosptdb-1.0-0/geosptdb/man/geosptdb-package.Rd | 18 ++++++------- geosptdb-1.0-0/geosptdb/man/idwST.Rd | 32 ++++++++++++------------ geosptdb-1.0-0/geosptdb/man/idwST.tcv.Rd | 6 ++-- 13 files changed, 71 insertions(+), 57 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-30 2015.4-1
2013-09-29 2013.8-2
2012-10-01 2012.8-1
2012-05-05 2012.4-1
2011-11-02 2011.11-1
2011-08-14 2011.8-3
2011-08-12 2011.8-2
2011-08-05 2011.8-1
2011-07-25 2011.7-1
2011-03-23 2011.3-1
2011-01-05 2011.1-1
2010-05-31 2010.5-1
2010-04-11 2009.12-1
2009-10-27 2009.10-1
2009-03-22 2009.3-1
2008-11-03 2008.11-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-10 0.2.0
Title: sas7bdat Reverse Engineering Documentation
Description: Documentation and prototypes for the earliest (circa 2010) open-source effort to reverse engineer the sas7bdat file format. The package includes a prototype reader for sas7bdat files. However, newer packages (notably the haven package) contain more robust readers for sas7bdat files.
Author: Matt Shotwell [aut, cre],
Clint Cummins [ctb]
Maintainer: Matt Shotwell <matt.shotwell@vanderbilt.edu>
Diff between sas7bdat versions 0.5 dated 2014-06-04 and 0.6 dated 2022-05-12
DESCRIPTION | 20 - MD5 | 20 - NAMESPACE | 1 R/sas7bdat.R | 23 - build/vignette.rds |binary inst/doc/reverse-engineering.pdf |binary inst/doc/sas7bdat.Rnw | 704 +++++++++++++++++++++------------------ inst/doc/sas7bdat.pdf |binary man/read.sas7bdat.Rd | 5 vignettes/sas7bdat.Rnw | 704 +++++++++++++++++++++------------------ vignettes/sas7bdat.rst | 40 ++ 11 files changed, 844 insertions(+), 673 deletions(-)
Title: A Collection of Functions Related to Item Response Theory (IRT)
Description: A collection of functions useful in learning and practicing IRT,
which can be combined into larger programs. Provides basic CTT analysis,
a simple common interface to the estimation of item
parameters in IRT models for binary responses with three different programs
(ICL, BILOG-MG, and ltm), ability estimation (MLE, BME, EAP, WLE, plausible
values), item and person fit statistics, scaling methods (MM, MS, Stocking-Lord,
and the complete Hebaera method), and a rich array of parametric and
non-parametric (kernel) plots. Estimates and plots Haberman's interaction model
when all items are dichotomously scored.
Author: Ivailo Partchev [aut, cre],
Gunter Maris [aut],
Tamaki Hattori [ctb]
Maintainer: Ivailo Partchev <partchev@gmail.com>
Diff between irtoys versions 0.2.1 dated 2017-12-15 and 0.2.2 dated 2022-05-12
DESCRIPTION | 12 - MD5 | 58 +++--- NEWS | 4 R/estimate.R | 15 - R/irtoys-package.R | 16 - build/vignette.rds |binary inst/doc/irtoys-vignette.R | 26 +-- inst/doc/irtoys-vignette.Rmd | 2 inst/doc/irtoys-vignette.html | 354 ++++++++++++++++++++++++++---------------- man/Scored.Rd | 4 man/Scored2pl.Rd | 4 man/Unscored.Rd | 6 man/b1.Rd | 4 man/b2.Rd | 4 man/b3.Rd | 4 man/est.Rd | 38 ++-- man/irfPlot.Rd | 10 - man/irtoys-package.Rd | 18 -- man/itf.Rd | 21 ++ man/normal.qu.Rd | 3 man/npp.Rd | 15 + man/plot.iif.Rd | 10 - man/plot.imp.Rd | 12 + man/plot.irf.Rd | 10 - man/plot.tif.Rd | 3 man/plot.trf.Rd | 3 man/sca.Rd | 12 + man/tgf.Rd | 10 - vignettes/irtoys-vignette.Rmd | 2 vignettes/irtoys.bib | 17 +- 30 files changed, 427 insertions(+), 270 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees
Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Author: Luke Harmon, Matthew Pennell, Chad Brock, Joseph Brown, Wendell Challenger,
Jon Eastman, Rich FitzJohn, Rich Glor, Gene Hunt, Liam Revell, Graham Slater,
Josef Uyeda, Jason Weir and CRAN team
Maintainer: Luke Harmon <lukeh@uidaho.edu>
Diff between geiger versions 2.0.7.1 dated 2022-05-09 and 2.0.9 dated 2022-05-12
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- README.md | 14 ++++++-------- man/aov.phylo.Rd | 3 ++- man/congruify.phylo.Rd | 2 ++ man/dtt.Rd | 4 ++-- man/fitContinuous.Rd | 4 ++-- man/fitDiscrete.Rd | 3 ++- man/nodelabel.phylo.Rd | 2 ++ man/sim.char.Rd | 3 ++- man/subset.phylo.Rd | 3 ++- 11 files changed, 38 insertions(+), 31 deletions(-)
More information about IPEDSuploadables at CRAN
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Title: Estimation of CCI and CLFS Functions
Description: The currentSurvival package contains functions for
the estimation of the current cumulative incidence (CCI) and
the current leukaemia-free survival (CLFS). The CCI is the
probability that a patient is alive and in any disease
remission (e.g. complete cytogenetic remission in chronic
myeloid leukaemia) after initiating his or her therapy (e.g.
tyrosine kinase therapy for chronic myeloid leukaemia). The
CLFS is the probability that a patient is alive and in any
disease remission after achieving the first disease remission.
Author: Eva Koritakova , Tomas Pavlik, Jiri Mayer, Ladislav Dusek
Maintainer: Eva Koritakova <koritakova@iba.muni.cz>
Diff between currentSurvival versions 1.0 dated 2013-01-19 and 1.1 dated 2022-05-12
DESCRIPTION | 33 +++++++++++++++++---------------- MD5 | 6 +++--- NAMESPACE | 2 ++ man/cml.Rd | 2 +- 4 files changed, 23 insertions(+), 20 deletions(-)
More information about currentSurvival at CRAN
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-05 1.1.9
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as suggested by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.1.0 dated 2022-03-30 and 0.2.0 dated 2022-05-12
DESCRIPTION | 19 ++- MD5 | 29 ++++- NAMESPACE | 8 + NEWS.md | 32 ++++++ R/calibrate_to_estimate.R |only R/calibrate_to_sample.R |only R/example_data.R |only R/svrep-package.R | 24 +++- README.md | 138 +++++++++++++++++++++++++++- build |only data |only inst |only man/calibrate_to_estimate.Rd |only man/calibrate_to_sample.Rd |only man/lou_pums_microdata.Rd |only man/lou_vax_survey.Rd |only man/lou_vax_survey_control_totals.Rd |only tests/testthat/test-calibrate_to_estimate.R |only tests/testthat/test-calibrate_to_sample.R |only vignettes |only 20 files changed, 229 insertions(+), 21 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-25 3.7-16
2021-04-22 3.6-45
2020-05-06 3.5-19
2020-03-10 3.4-26
2019-08-23 3.3-10
2019-07-04 3.2-24
2019-03-18 3.1-45
2018-12-10 3.0-21
2018-09-30 2.13-15
2018-05-25 2.12-18
2018-05-02 2.11-93
2018-03-29 2.10-24
2018-02-26 2.9-35
2017-11-16 2.8-21
2017-10-19 2.7-56
2017-08-13 2.6-2
2017-08-08 2.5-14
2017-06-30 2.4-9
2017-06-25 2.3-18
2017-06-17 2.2-49
2017-05-11 2.1-43
2017-04-12 2.0-37
2017-03-02 1.99999-31
2017-02-06 1.99993-0
2017-01-23 1.99992-0
2016-05-31 1.995-0
2016-04-15 1.99-6
2016-03-11 1.17-0
2016-02-01 1.16-0
2015-12-16 1.15-0
2015-10-15 1.14-0
2015-08-29 1.13-0
2015-08-27 1.12-0
2015-08-11 1.11-0
2015-07-25 1.10-0
2015-06-30 1.9-0
2015-06-26 1.8-0
2015-06-05 1.7-1
2015-04-03 1.6-0
2015-02-24 1.5-2
2015-01-16 1.4-1
2015-01-06 1.3
2014-11-22 1.2
2014-10-19 1.1
2014-09-08 1.0-3.18-1
2014-06-27 1.0-3
2014-05-02 1.0-2.1
2014-04-02 1.0-2
2014-02-02 1.0-1
2014-01-01 1.0-0
2013-11-02 0.99-7
2013-10-13 0.9-9
2013-10-03 0.8-19
2013-09-15 0.7-35
2013-08-28 0.6-26
2013-07-28 0.5-21
2013-07-01 0.04-43
Previous versions (as known to CRANberries) which should be available via the Archive link are:
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2021-11-23 1.0.0
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2021-12-10 0.1.1
2020-05-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-09 0.5-15
2019-05-06 0.4-17
2018-06-07 0.3-48
2018-03-20 0.2-9
2017-11-24 0.1-22
2017-05-11 0.0-17
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-05 0.1-53
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-21 1.5-8
2020-05-12 1.4-12
2019-04-16 1.3-18
2019-01-11 1.2-4
2019-01-07 1.1-51
2018-11-06 1.0-18
2018-10-16 0.11-7
2018-09-12 0.10-13
2018-08-08 0.9-43
2018-07-09 0.8-47
2018-04-24 0.7-19
2018-02-16 0.6-17
2018-01-22 0.5-27
2017-08-20 0.4-15
2017-07-12 0.3-11
2017-02-07 0.2-0
2017-01-26 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-09 3.11-21
2021-09-23 3.10-118
2020-02-17 3.9-4
2020-02-15 3.8-11
2019-11-04 3.7-40
2019-08-01 3.6-21
2019-06-20 3.5-53
2019-05-03 3.4-64
2019-03-18 3.3-26
2019-02-08 3.2-39
2019-01-04 3.1-80
2018-11-22 3.0-32
2018-07-10 2.7-50
2018-03-22 2.6-9
2018-03-13 2.5-45
2018-01-29 2.4-20
2017-11-23 2.3-57
2017-09-20 2.2-14
2017-08-09 2.1-24
2017-05-11 2.0-25
2017-03-02 1.15-41
2017-01-11 1.14-0
2016-11-17 1.13-1
2016-07-19 1.12-2
2016-05-30 1.11-0
2016-01-29 1.10-0
2015-11-04 1.9-0
2015-06-28 1.8-9
2015-06-05 1.7-0
2015-05-20 1.6-0
2015-03-03 1.5-0
2015-01-06 1.3
2014-12-12 1.2
2014-11-23 1.1
2014-10-27 1.0-3
2014-08-30 0.47-36
2014-08-05 0.46-15
2014-05-30 0.45-23
2014-04-27 0.44-47
2014-04-27 0.44-48
2014-03-12 0.43-70
2014-01-31 0.42-25
2014-01-07 0.41-21
2013-12-09 0.40-9
2013-11-17 0.39-30
2013-10-23 0.38-25
2013-10-03 0.37-24
2013-09-08 0.36-30
2013-08-13 0.34-36
2013-07-09 0.33-16
2013-05-29 0.31-20
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-13 1.2-19
2018-12-10 1.1-35
2018-04-24 1.0-138
2017-04-27 0.8-5
2017-01-18 0.7-0
2016-10-28 0.6-0
2016-05-31 0.5-0
2016-03-07 0.4-0
2016-01-22 0.3-0
2015-11-04 0.2-0
2015-09-14 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-12 3.1
2019-03-03 3.0
2016-12-02 2.0
2016-08-17 1.3
2015-11-21 1.2
2015-08-19 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-04 1.2-35
2018-12-13 1.1-6
2018-12-12 1.0-6
2018-11-12 0.5-28
2018-06-08 0.4-24
2018-03-21 0.3-24
2017-11-24 0.2-10
2017-08-27 0.1-51
2017-05-12 0.0-9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-02 8.0-5
2022-04-11 7.6-11
2020-03-10 7.5-15
2019-09-05 7.4-19
2019-03-18 7.3-17
2019-02-08 7.2-30
2018-12-13 7.1-20
2018-11-06 7.0-12
2018-09-30 6.6-5
2018-08-16 6.5-12
2018-07-06 6.4-23
2018-05-28 6.3-45
2018-05-02 6.2-91
2018-02-26 6.1-10
2017-11-21 6.0-101
2017-10-06 5.9-27
2017-08-07 5.8-9
2017-06-25 5.7-16
2017-06-17 5.6-16
2017-04-11 5.5-21
2017-02-08 5.4-0
2017-01-11 5.3-0
2016-10-14 5.2-1
2016-08-29 5.1-0
2016-07-11 5.0-0
2016-05-31 4.991-1
2016-03-10 4.8-0
2016-01-30 4.7-0
2015-11-04 4.6-0
2015-08-29 4.5-0
2015-07-01 4.4-1
2015-06-05 4.3-0
2015-02-23 4.2-12
2014-12-17 4.1
2014-11-21 4.0
2014-08-31 3.4-21
2014-05-25 3.3-24
2014-04-23 3.2-6
2014-03-21 3.1-14
2014-02-26 3.0-29
2014-01-30 2.7-7
2014-01-19 2.6-13
2014-01-16 2.5-48
2013-10-24 2.4-9
2013-09-06 2.3-15
2013-08-21 2.2-20
2013-07-27 2.01-11
2013-07-09 1.5-12
2013-07-01 1.4-16
2013-05-15 1.3-17
2012-07-29 1.1-0
2011-10-27 1.0-0
Title: Poly-Pharmacology Toolkit for Traditional Chinese Medicine
Research
Description: Toolkit for Poly-pharmacology Research of Traditional Chinese Medicine. Based on the
biological descriptors and drug-disease interaction networks, it can
analyze the potential poly-pharmacological mechanisms of Traditional Chinese Medicine and be
used for drug-repositioning in Traditional Chinese Medicine.
Author: Yuanlong Hu [aut, cre]
Maintainer: Yuanlong Hu <huyuanlong1996@163.com>
Diff between immcp versions 0.9.2 dated 2020-11-14 and 1.0.3 dated 2022-05-12
immcp-0.9.2/immcp/R/AllClasses.R |only immcp-0.9.2/immcp/R/AllGenerics.R |only immcp-0.9.2/immcp/R/extrFP.R |only immcp-0.9.2/immcp/R/get_result.R |only immcp-0.9.2/immcp/R/immcp-package.R |only immcp-0.9.2/immcp/R/plot_density.R |only immcp-0.9.2/immcp/R/plot_network.R |only immcp-0.9.2/immcp/R/res_rank.R |only immcp-0.9.2/immcp/R/score_fp.R |only immcp-0.9.2/immcp/R/simFP.R |only immcp-0.9.2/immcp/R/sysdata.rda |only immcp-0.9.2/immcp/R/use_DOSE.R |only immcp-0.9.2/immcp/data/drugResult.rda |only immcp-0.9.2/immcp/data/drugSample.rda |only immcp-0.9.2/immcp/man/ScoreFP-class.Rd |only immcp-0.9.2/immcp/man/ScoreResult-class.Rd |only immcp-0.9.2/immcp/man/as.data.frame.Rd |only immcp-0.9.2/immcp/man/drugResult.Rd |only immcp-0.9.2/immcp/man/drugSample.Rd |only immcp-0.9.2/immcp/man/extrFP.Rd |only immcp-0.9.2/immcp/man/getDEG.Rd |only immcp-0.9.2/immcp/man/getF.Rd |only immcp-0.9.2/immcp/man/get_result.Rd |only immcp-0.9.2/immcp/man/head.Rd |only immcp-0.9.2/immcp/man/imm_centr.Rd |only immcp-0.9.2/immcp/man/immcp-package.Rd |only immcp-0.9.2/immcp/man/overlap_pathway.Rd |only immcp-0.9.2/immcp/man/plot_density.Rd |only immcp-0.9.2/immcp/man/plot_network.Rd |only immcp-0.9.2/immcp/man/res_rank.Rd |only immcp-0.9.2/immcp/man/score_fp.Rd |only immcp-0.9.2/immcp/man/simFP.Rd |only immcp-0.9.2/immcp/man/tail.Rd |only immcp-0.9.2/immcp/man/viewpathway.Rd |only immcp-1.0.3/immcp/DESCRIPTION | 45 ++-- immcp-1.0.3/immcp/MD5 | 105 +++++----- immcp-1.0.3/immcp/NAMESPACE | 169 +++++++++------- immcp-1.0.3/immcp/NEWS.md | 5 immcp-1.0.3/immcp/R/AllClass.R |only immcp-1.0.3/immcp/R/AllGeneric.R |only immcp-1.0.3/immcp/R/CreateBasicData.R | 237 +++++------------------ immcp-1.0.3/immcp/R/CreateDisDrugNet.R |only immcp-1.0.3/immcp/R/PrepareData.R |only immcp-1.0.3/immcp/R/data.R |only immcp-1.0.3/immcp/R/do_geneset.R | 62 ++++-- immcp-1.0.3/immcp/R/get_biodescr.R |only immcp-1.0.3/immcp/R/network_char.R |only immcp-1.0.3/immcp/R/network_node_ks.R |only immcp-1.0.3/immcp/R/plot_BioDescr.R |only immcp-1.0.3/immcp/R/plot_graph.R |only immcp-1.0.3/immcp/R/score_network.R | 261 ++++++++------------------ immcp-1.0.3/immcp/R/score_rule.R |only immcp-1.0.3/immcp/R/score_sim.R |only immcp-1.0.3/immcp/R/subset_network.R |only immcp-1.0.3/immcp/README.md | 10 immcp-1.0.3/immcp/build/vignette.rds |binary immcp-1.0.3/immcp/data/drugdemo.rda |only immcp-1.0.3/immcp/inst/doc/immcp.R | 51 +---- immcp-1.0.3/immcp/inst/doc/immcp.Rmd | 87 ++------ immcp-1.0.3/immcp/inst/doc/immcp.html | 146 ++++++-------- immcp-1.0.3/immcp/man/BasicData-class.Rd | 14 - immcp-1.0.3/immcp/man/BioDescr-class.Rd |only immcp-1.0.3/immcp/man/CreateBasicData.Rd | 25 +- immcp-1.0.3/immcp/man/CreateDisDrugNet.Rd |only immcp-1.0.3/immcp/man/HerbResult-class.Rd |only immcp-1.0.3/immcp/man/PrepareData.Rd | 25 +- immcp-1.0.3/immcp/man/diff_network_char.Rd |only immcp-1.0.3/immcp/man/drugdemo.Rd |only immcp-1.0.3/immcp/man/enrich_f.Rd |only immcp-1.0.3/immcp/man/exportCytoscape.Rd |only immcp-1.0.3/immcp/man/extr_biodescr-method.Rd |only immcp-1.0.3/immcp/man/extr_biodescr.Rd |only immcp-1.0.3/immcp/man/natural_connectivity.Rd |only immcp-1.0.3/immcp/man/network_char.Rd |only immcp-1.0.3/immcp/man/network_node_ks.Rd |only immcp-1.0.3/immcp/man/plot_BioDescr.Rd |only immcp-1.0.3/immcp/man/plot_graph-method.Rd |only immcp-1.0.3/immcp/man/read_gmt.Rd | 6 immcp-1.0.3/immcp/man/score_network.Rd | 30 +- immcp-1.0.3/immcp/man/score_rule.Rd |only immcp-1.0.3/immcp/man/score_sim.Rd |only immcp-1.0.3/immcp/man/to_biodescr.Rd |only immcp-1.0.3/immcp/man/to_df.Rd | 9 immcp-1.0.3/immcp/man/to_list.Rd | 5 immcp-1.0.3/immcp/man/write_gmt.Rd | 2 immcp-1.0.3/immcp/vignettes/immcp.Rmd | 87 ++------ 86 files changed, 569 insertions(+), 812 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-01 0.4-0
2015-05-30 0.3-3
2015-04-09 0.3-2
2014-10-23 0.3-1
2014-09-12 0.3-0
2014-07-09 0.2-1
2014-04-28 0.2-0
2014-03-13 0.1-2
2014-01-28 0.1-1
2014-01-20 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-31 1.2
2015-10-07 1.1
2015-09-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-25 0.3.6.1
2021-12-10 0.3.5
2021-11-05 0.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-15 0.2.28
2018-09-26 0.2.22
2018-02-12 0.2.20
2017-07-20 0.2.18
2017-03-08 0.2.15
2016-11-20 0.2.9
2016-05-19 0.2.6
2016-05-17 0.2.4
2016-04-14 0.2.2
2016-04-03 0.2.0
2014-05-07 0.1.0