Title: Multiple-Scaled Clustering
Description: Model based clustering using
the multivariate multiple Scaled t (MST) and multivariate multiple
scaled contaminated normal (MSCN) distributions. The MST is an
extension of the multivariate Student-t distribution to include
flexible tail behaviors, Forbes, F. & Wraith, D. (2014) <doi:10.1007/s11222-013-9414-4>. The MSCN represents a heavy-tailed
generalization of the multivariate normal (MN) distribution to
model elliptical contoured scatters in the presence of mild outliers
(also referred to as "bad" points) and automatically detect bad points, Punzo, A. & Tortora, C. (2021) <doi:10.1177/1471082X19890935>.
Author: Cristina Tortora [aut, cre, cph]
,
Antonio Punzo [aut] ,
Louis Tran [aut]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between MSclust versions 1.0.3 dated 2023-05-04 and 1.0.4 dated 2024-04-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/PLRfactorization.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute. Hahsler and Dunham (2010) <doi:10.18637/jss.v035.i05>.
Author: Michael Hahsler [aut, cre, cph]
,
Margaret H. Dunham [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.2.0 dated 2022-06-25 and 1.2.1 dated 2024-04-21
rEMM-1.2.0/rEMM/src |only rEMM-1.2.1/rEMM/DESCRIPTION | 14 ++--- rEMM-1.2.1/rEMM/MD5 | 33 +++++------ rEMM-1.2.1/rEMM/NAMESPACE | 2 rEMM-1.2.1/rEMM/NEWS.md | 5 + rEMM-1.2.1/rEMM/R/SimpleMC.R | 5 - rEMM-1.2.1/rEMM/README.md | 50 +++++++++++++----- rEMM-1.2.1/rEMM/build/partial.rdb |binary rEMM-1.2.1/rEMM/build/vignette.rds |binary rEMM-1.2.1/rEMM/data/16S.rda |binary rEMM-1.2.1/rEMM/data/Derwent.rda |binary rEMM-1.2.1/rEMM/data/EMMTraffic.rda |binary rEMM-1.2.1/rEMM/data/EMMsim.rda |binary rEMM-1.2.1/rEMM/inst/CITATION | 39 +++++++------- rEMM-1.2.1/rEMM/inst/README_files/example_model-1.png |binary rEMM-1.2.1/rEMM/inst/doc/rEMM.pdf |binary rEMM-1.2.1/rEMM/man/plot.EMM.Rd | 6 +- 17 files changed, 88 insertions(+), 66 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.
Author: Michael Hahsler [aut, cre, cph]
,
Matthew Bolanos [ctb],
John Forrest [ctb],
Matthias Carnein [ctb],
Dennis Assenmacher [ctb],
Dalibor Krleza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 2.0-1 dated 2023-02-28 and 2.0-2 dated 2024-04-21
DESCRIPTION | 14 +- MD5 | 164 ++++++++++++++++----------------- NAMESPACE | 5 + NEWS.md | 14 ++ R/AAA_stream-package.R | 17 ++- R/DSC_BIRCH.R | 2 R/DSC_DBSTREAM.R | 19 +++ R/DSC_DStream.R | 9 + R/DSC_R.R | 1 R/DSC_TwoStage.R | 4 R/DSF_Convolve.R | 2 R/DSF_FeaturesSelection.R |only R/DSF_Scale.R | 3 R/DST_Runner.R | 3 R/get_assignment.R | 6 + R/recluster.R | 1 README.md | 188 ++++---------------------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/extending_stream.pdf |binary inst/doc/stream.Rnw | 2 inst/doc/stream.pdf |binary man/DSAggregate.Rd | 4 man/DSAggregate_Sample.Rd | 4 man/DSAggregate_Window.Rd | 4 man/DSC.Rd | 2 man/DSC_BIRCH.Rd | 2 man/DSC_DBSTREAM.Rd | 15 ++- man/DSC_DStream.Rd | 3 man/DSC_Macro.Rd | 2 man/DSC_Micro.Rd | 2 man/DSC_R.Rd | 2 man/DSC_SlidingWindow.Rd | 2 man/DSC_Static.Rd | 2 man/DSC_TwoStage.Rd | 2 man/DSClassifier.Rd | 2 man/DSD_BarsAndGaussians.Rd | 2 man/DSD_Benchmark.Rd | 2 man/DSD_Cubes.Rd | 2 man/DSD_Gaussians.Rd | 2 man/DSD_MG.Rd | 2 man/DSD_Memory.Rd | 2 man/DSD_Mixture.Rd | 2 man/DSD_NULL.Rd | 2 man/DSD_ReadDB.Rd | 2 man/DSD_ReadStream.Rd | 2 man/DSD_ScaleStream.Rd | 3 man/DSD_Target.Rd | 2 man/DSD_UniformNoise.Rd | 2 man/DSD_mlbenchData.Rd | 2 man/DSD_mlbenchGenerator.Rd | 2 man/DSF.Rd | 3 man/DSF_Convolve.Rd | 7 - man/DSF_Downsample.Rd | 5 - man/DSF_ExponentialMA.Rd | 5 - man/DSF_FeatureSelection.Rd |only man/DSF_Func.Rd | 5 - man/DSF_Scale.Rd | 5 - man/DSF_dplyr.Rd | 7 - man/DSOutlier.Rd | 4 man/DSRegressor.Rd | 4 man/DST.Rd | 2 man/DST_SlidingWindow.Rd | 4 man/DST_WriteStream.Rd | 4 man/animate_cluster.Rd | 6 - man/animate_data.Rd | 2 man/close_stream.Rd | 2 man/evaluate.DSC.Rd | 2 man/evaluate.Rd | 4 man/get_assignment.Rd | 2 man/get_points.Rd | 2 man/plot.DSC.Rd | 2 man/plot.DSD.Rd | 2 man/predict.Rd | 6 - man/prune_clusters.Rd | 2 man/read_saveDSC.Rd | 2 man/recluster.Rd | 2 man/reset_stream.Rd | 2 man/stream-package.Rd | 39 +++++++ man/stream_pipeline.Rd | 4 man/update.Rd | 4 tests/testthat/test-DSC_formula.R | 13 ++ tests/testthat/test-DSF.R | 20 ++++ vignettes/stream.Rnw | 2 84 files changed, 356 insertions(+), 352 deletions(-)
Title: The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and
Projection dimensionality reduction by McInnes et al. (2018)
<doi:10.48550/arXiv.1802.03426>. It also provides means to transform new data and
to carry out supervised dimensionality reduction. An implementation of
the related LargeVis method of Tang et al. (2016) <doi:10.48550/arXiv.1602.00370>
is also provided. This is a complete re-implementation in R (and C++,
via the 'Rcpp' package): no Python installation is required. See the
uwot website (<https://github.com/jlmelville/uwot>) for more
documentation and examples.
Author: James Melville [aut, cre, cph],
Aaron Lun [ctb],
Mohamed Nadhir Djekidel [ctb],
Yuhan Hao [ctb],
Dirk Eddelbuettel [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between uwot versions 0.2.1 dated 2024-04-15 and 0.2.2 dated 2024-04-21
DESCRIPTION | 10 ++++---- MD5 | 36 ++++++++++++++--------------- NEWS.md | 17 +++++++++++++- R/init.R | 40 ++++++++++++++++++++++++++++----- R/rspectra_init.R | 12 +++++++++ R/uwot.R | 2 + inst/doc/uwot.R | 1 inst/doc/uwot.Rmd | 1 inst/doc/uwot.html | 5 ++-- man/load_uwot.Rd | 2 + tests/testthat/test_errors.R | 1 tests/testthat/test_neighbors.R | 1 tests/testthat/test_normlaplacian.R | 16 ++++++++----- tests/testthat/test_output.R | 18 +++++++++----- tests/testthat/test_saveload.R | 1 tests/testthat/test_similarity_graph.R | 1 tests/testthat/test_spectral.R | 1 tests/testthat/test_transform.R | 1 vignettes/uwot.Rmd | 1 19 files changed, 123 insertions(+), 44 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 2.1.1 dated 2023-09-25 and 2.1.2 dated 2024-04-21
DESCRIPTION | 6 ++--- MD5 | 26 +++++++++++------------ NEWS | 3 ++ R/rsa.R | 11 ++++++--- build/vignette.rds |binary configure | 9 ++++++-- inst/doc/bignum.html | 32 ++++++++++++++-------------- inst/doc/crypto_hashing.R | 2 - inst/doc/crypto_hashing.html | 8 +++---- inst/doc/keys.html | 48 +++++++++++++++++++++---------------------- inst/doc/secure_rng.R | 2 - inst/doc/secure_rng.html | 18 ++++++++-------- man/rsa_encrypt.Rd | 6 +++-- src/rsa.c | 10 +++++--- 14 files changed, 98 insertions(+), 83 deletions(-)
Title: Spatial and Spatio-Temporal Models using 'INLA'
Description: Prepare objects to implement models over spatial and
spacetime domains with the 'INLA' package (<https://www.r-inla.org>).
These objects contain data to for the 'cgeneric' interface in
'INLA', enabling fast parallel computations.
We implemented the spatial barrier model, see Bakka et. al. (2019)
<doi:10.1016/j.spasta.2019.01.002>, and some of the spatio-temporal
models in Lindgren et. al. (2023) <doi:10.48550/arXiv.2006.04917>.
Details are provided in the available vignettes and from the URL bellow.
Author: Elias Teixeira Krainski [cre, aut, cph]
,
Finn Lindgren [aut] ,
Haavard Rue [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAspacetime versions 0.1.7 dated 2023-08-27 and 0.1.8 dated 2024-04-21
DESCRIPTION | 18 ++--- MD5 | 85 ++++++++++++++------------- NAMESPACE | 5 + R/INLAspacetime.R | 12 +-- R/ar2cor.R | 17 ++++- R/ar2precision.R | 5 - R/barrierModel.define.R | 13 ++-- R/ghcndUtils.R | 55 ++++++++++++++---- R/mesh.dual.R | 41 +++++++++---- R/mesh2d.R | 6 + R/mesh2fem.R | 51 +++++++++++++--- R/mesh2projector.R | 10 --- R/paramsUtils.R | 107 ++++++++++++++++++----------------- R/polyUtils.R | 46 ++++++++++++--- R/spde2precision.R | 1 R/stModel.define.R | 7 +- R/stModel.matrices.R | 95 +++++++++++-------------------- R/stats.inla.R | 12 +-- R/upperPadding.R | 2 R/worldMap.R | 119 +++++++++++++++++++++++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/website_examples.R | 4 - inst/examples/test4.R | 4 - man/Earth_poly.Rd |only man/INLAspacetime.Rd | 5 - man/Jmatrices.Rd | 4 + man/ar2cor.Rd | 2 man/ar2precision.Rd | 5 - man/barrierModel.define.Rd | 12 ++- man/downloadUtilFiles.Rd | 4 - man/ghcndSelect.Rd | 3 man/mesh.dual.Rd | 15 +++- man/mesh2d.Rd | 6 + man/paramsUtils.Rd | 56 +++++++++++++----- man/polyUtils.Rd | 22 +++++-- man/spde2precision.Rd | 1 man/stats.inla.Rd | 3 man/upperPadding.Rd | 2 man/worldMap.Rd | 28 ++++----- man/world_grid.Rd |only src/INLAspacetime_init.c |only src/ar2cor.c |only src/ar2cor.h |only vignettes/web/barrierExample.Rmd | 4 - vignettes/web/piemonte.Rmd | 18 ----- 46 files changed, 568 insertions(+), 337 deletions(-)
Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO, Artificial Neural Network (ANN), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Recursive Partitioning ('RPART') or step wise regression models are fit. Nested cross validation (or analogous for the random forest) is used to estimate and compare performances between these models with results presented in tabular or graphical means. Calibration plots can also be generated, again based upon (nested) cross validation.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied with the 'path=TRUE' options when calling glmnet() and cv.glmnet(). Within the glmnetr package the approach of path=TRUE is taken by default.
When fitting not a relaxed la [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.4-5 dated 2024-04-19 and 0.4-6 dated 2024-04-21
glmnetr-0.4-5/glmnetr/R/calplot_240409.R |only glmnetr-0.4-5/glmnetr/R/nested.glmnetr_240418.R |only glmnetr-0.4-6/glmnetr/DESCRIPTION | 8 ++++---- glmnetr-0.4-6/glmnetr/MD5 | 18 +++++++++--------- glmnetr-0.4-6/glmnetr/NAMESPACE | 1 + glmnetr-0.4-6/glmnetr/R/calplot_240420.R |only glmnetr-0.4-6/glmnetr/R/nested.glmnetr_240420.R |only glmnetr-0.4-6/glmnetr/man/calplot.Rd | 2 +- glmnetr-0.4-6/glmnetr/man/calplot0.Rd | 2 +- glmnetr-0.4-6/glmnetr/man/myaxis.Rd | 2 +- glmnetr-0.4-6/glmnetr/man/myrug.Rd | 2 +- glmnetr-0.4-6/glmnetr/man/nested.glmnetr.Rd | 2 +- 12 files changed, 19 insertions(+), 18 deletions(-)
Title: Volumetric Analysis using Graphic Double Integration
Description: Tools implementing an automated version of the graphic double integration technique (GDI) for volume implementation, and some other related utilities for paleontological image-analysis. GDI was first employed by Jerison (1973) <ISBN:9780323141086> and Hurlburt (1999) <doi:10.1080/02724634.1999.10011145> and is primarily used for volume or mass estimation of (extinct) animals. The package 'gdi' aims to make this technique as convenient and versatile as possible. The core functions of 'gdi' provide utilities for automatically measuring diameters from digital silhouettes provided as image files and calculating volume via graphic double integration with simple elliptical, superelliptical (following Motani 2001 <doi:10.1666/0094-8373(2001)027%3C0735:EBMFST%3E2.0.CO;2>) or complex cross-sectional models. Additionally, the package provides functions for estimating the center of mass position (COM), the moment of inertia (I) for 3D shapes and the second moment of area (Ix, Iy [...truncated...]
Author: Darius Nau [aut, cre]
Maintainer: Darius Nau <dariusnau@gmx.at>
Diff between gdi versions 1.5.4 dated 2023-09-07 and 1.6.0 dated 2024-04-21
DESCRIPTION | 10 ++--- MD5 | 28 ++++++++-------- NAMESPACE | 5 ++ NEWS.md | 14 ++++++++ R/gdi.r | 49 ++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/estimating_COM.R | 6 +-- inst/doc/estimating_COM.Rmd | 6 +-- inst/doc/estimating_COM.html | 74 ++++++++++++++++++++++--------------------- inst/doc/misc.R | 2 - inst/doc/misc.Rmd | 2 - inst/doc/misc.html | 29 ++++++++++++++-- man/plot_sil.Rd | 31 ++++++++++++++++-- vignettes/estimating_COM.Rmd | 6 +-- vignettes/misc.Rmd | 2 - 15 files changed, 184 insertions(+), 80 deletions(-)
Title: Fully-Latent Principal Stratification
Description: Simulation and analysis of Fully-Latent Principal Stratification (FLPS) with measurement models. Lee, Adam, Kang, & Whittaker (2023). <doi:10.1007/978-3-031-27781-8_25>. This package is supported by the Institute of Education Sciences, U.S. Department of Education, through Grant R305D210036.
Author: Sooyong Lee [aut, cre],
Adam Sales [aut],
Hyeon-Ah Kang [aut],
Tiffany Whittaker [aut]
Maintainer: Sooyong Lee <sooyongl09@gmail.com>
Diff between flps versions 1.0.0 dated 2023-11-02 and 1.1.0 dated 2024-04-21
DESCRIPTION | 24 - MD5 | 72 ++- NAMESPACE | 1 NEWS.md | 7 R/data_desc.r | 101 +++++ R/flps-package.r | 2 R/load_rstan.r | 3 R/make_FLPSdata.r | 5 R/plot_function.r | 286 +++++++++++---- R/priors.r | 1 R/run_FLPS.r | 18 R/sim_utils.r |only R/summary_function.r | 336 ++++++++++++++++-- R/z_utils.r | 153 -------- R/z_validate.r | 21 + R/zzz.r | 2 README.md | 77 ++-- build/vignette.rds |binary data/example0.rda |only data/example1.rda |only data/example2.rda |only data/example3.rda |only inst/doc/flps.html | 42 +- inst/stan/singlelevel/singlelevel_GRM.stan | 7 inst/stan/singlelevel/singlelevel_IRT.stan | 7 inst/stan/singlelevel/singlelevel_LCA.stan | 104 +++-- inst/stan/singlelevel/singlelevel_LCA_threeclass.stan | 35 + inst/stan/singlelevel/singlelevel_LPA.stan | 97 +++-- inst/stan/singlelevel/singlelevel_LPA_threeclass.stan | 31 + inst/stan/singlelevel/singlelevel_RASCH.stan | 6 inst/stan/singlelevel/singlelevel_SEM.stan | 11 man/example0.Rd |only man/example1.Rd |only man/example2.Rd |only man/example3.Rd |only man/flps-package.Rd | 3 man/flps_plot.Rd | 4 man/plot.Rd | 2 man/print.Rd | 2 man/print.summary.flps.Rd |only man/runFLPS.Rd | 14 man/summary.flps.Rd | 12 42 files changed, 1014 insertions(+), 472 deletions(-)
Title: Flexible Parametric Survival and Multi-State Models
Description: Flexible parametric models for time-to-event data,
including the Royston-Parmar spline model, generalized gamma and
generalized F distributions. Any user-defined parametric
distribution can be fitted, given at least an R function defining
the probability density or hazard. There are also tools for
fitting and predicting from fully parametric multi-state models,
based on either cause-specific hazards or mixture models.
Author: Christopher Jackson [aut, cre],
Paul Metcalfe [ctb],
Jordan Amdahl [ctb],
Matthew T. Warkentin [ctb],
Michael Sweeting [ctb],
Kevin Kunzmann [ctb]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between flexsurv versions 2.2.2 dated 2023-02-01 and 2.3 dated 2024-04-21
DESCRIPTION | 19 MD5 | 175 + NAMESPACE | 9 NEWS.md |only R/GenF.R | 12 R/GenGamma.R | 2 R/Gompertz.R | 2 R/Llogis.R | 2 R/ajfit.R | 29 R/broom-funs.R | 2 R/custom.R | 25 R/deriv.R | 155 + R/deriv2.R |only R/distributions.R | 4 R/flexsurv-package.R | 483 ++--- R/flexsurvmix.R | 29 R/flexsurvreg.R | 376 +++- R/fracpoly.R | 2 R/hr_flexsurvreg.R | 6 R/mstate.R | 3108 +++++++++++++++++----------------- R/plot.flexsurvreg.R | 11 R/predict.flexsurvreg.R | 17 R/residuals.flexsurvreg.R | 21 R/simulate_flexsurvreg.R | 4 R/spline.R | 264 ++ R/standsurv.R | 501 +++-- R/summary.flexsurvmix.R | 23 R/summary.flexsurvreg.R | 163 - R/summary.flexsurvrtrunc.R | 218 +- R/survsplinek.R | 260 +- R/utils.R | 23 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS | 9 inst/doc/distributions.Rnw | 2 inst/doc/distributions.pdf |binary inst/doc/flexsurv-examples.pdf |binary inst/doc/flexsurv.pdf |binary inst/doc/multistate.Rnw | 1724 +++++++++--------- inst/doc/multistate.pdf |binary inst/doc/standsurv.R | 4 inst/doc/standsurv.Rmd | 4 inst/doc/standsurv.html | 628 +++--- man/AIC.fmsm.Rd |only man/AICc.Rd |only man/AICc.flexsurvreg.Rd |only man/BIC.flexsurvreg.Rd |only man/GenF.Rd | 3 man/GenF.orig.Rd | 7 man/Survspline.Rd | 23 man/Survsplinek.Rd | 159 + man/ajfit_fmsm.Rd | 3 man/basis.Rd | 17 man/bootci.fmsm.Rd | 10 man/figures |only man/flexsurv-package.Rd | 6 man/flexsurvmix.Rd | 22 man/flexsurvreg.Rd | 64 man/flexsurvspline.Rd | 11 man/logLik.flexsurvreg.Rd |only man/model.frame.flexsurvmix.Rd |only man/msfit.flexsurvreg.Rd | 3 man/nobs.flexsurvreg.Rd | 11 man/pmatrix.simfs.Rd | 23 man/predict.flexsurvreg.Rd | 16 man/rmst_generic.Rd | 8 man/sim.fmsm.Rd | 2 man/standsurv.Rd | 28 man/totlos.simfs.Rd | 14 man/vcov.flexsurvreg.Rd |only tests/test_base.R | 2 tests/testthat/test-broom.R | 12 tests/testthat/test_aic.R |only tests/testthat/test_contrasts.R |only tests/testthat/test_custom.R | 350 ++- tests/testthat/test_flexsurvmix.R | 6 tests/testthat/test_flexsurvmix_opt.R |only tests/testthat/test_flexsurvreg.R | 85 tests/testthat/test_fmixmsm_outputs.R |only tests/testthat/test_fmsm.R | 122 - tests/testthat/test_genf.R | 243 +- tests/testthat/test_gompertz.R | 123 - tests/testthat/test_hess.R |only tests/testthat/test_llogis.R | 70 tests/testthat/test_mstate.R | 44 tests/testthat/test_outputs.R | 5 tests/testthat/test_residuals.R |only tests/testthat/test_rtrunc.R | 124 - tests/testthat/test_spline.R | 73 tests/testthat/test_splinedist.R | 11 tests/testthat/test_standsurv.R | 223 ++ tests/testthat/test_survsplinek.R |only tests/testthat/test_utils.R | 10 vignettes/distributions.Rnw | 2 vignettes/flexsurv.Rnw | 19 vignettes/multistate.Rnw | 1724 +++++++++--------- vignettes/standsurv.Rmd | 4 97 files changed, 6664 insertions(+), 5334 deletions(-)
Title: Interpretable Discovery and Inference of Heterogeneous Treatment
Effects
Description: Provides a new method for interpretable heterogeneous
treatment effects characterization in terms of decision rules
via an extensive exploration of heterogeneity patterns by an
ensemble-of-trees approach, enforcing high stability in the
discovery. It relies on a two-stage pseudo-outcome regression, and
it is supported by theoretical convergence guarantees. Bargagli-Stoffi,
F. J., Cadei, R., Lee, K., & Dominici, F. (2023) Causal rule ensemble:
Interpretable Discovery and Inference of Heterogeneous Treatment Effects.
arXiv preprint <doi:10.48550/arXiv.2009.09036>.
Author: Naeem Khoshnevis [aut, cre] ,
Daniela Maria Garcia [aut] ,
Riccardo Cadei [aut] ,
Kwonsang Lee [aut] ,
Falco Joannes Bargagli Stoffi [aut]
Maintainer: Naeem Khoshnevis <nkhoshnevis@g.harvard.edu>
Diff between CRE versions 0.2.5 dated 2023-12-06 and 0.2.6 dated 2024-04-21
DESCRIPTION | 10 - MD5 | 45 +++++-- NEWS.md | 8 + R/extract_rules.R | 4 R/filter_irrelevant_rules.R | 4 R/generate_rules.R | 2 R/inTrees.R |only README.md | 67 ++++------ inst/CITATION |only inst/doc/CRE.html | 158 ++++++++++++------------- inst/doc/Contribution.html | 68 +++++----- inst/doc/Testing-the-Package.html | 100 +++++++-------- tests/testthat/test-check_input_data.R |only tests/testthat/test-cre.R |only tests/testthat/test-discover_rules.R |only tests/testthat/test-estimate_cate.R |only tests/testthat/test-estimate_ite.R |only tests/testthat/test-estimate_ite_aipw.R |only tests/testthat/test-estimate_ite_bart.R |only tests/testthat/test-estimate_ite_cf.R |only tests/testthat/test-estimate_ite_poisson.R |only tests/testthat/test-estimate_ite_slearner.R |only tests/testthat/test-estimate_ite_tlearner.R |only tests/testthat/test-estimate_ite_xlearner.R |only tests/testthat/test-estimate_ps.R |only tests/testthat/test-evaluate.R |only tests/testthat/test-extract_effect_modifiers.R |only tests/testthat/test-extract_rules.R |only tests/testthat/test-filter_correlated_rules.R |only tests/testthat/test-filter_extreme_rules.R |only tests/testthat/test-filter_irrelevant_rules.R |only tests/testthat/test-generate_cre_dataset.R |only tests/testthat/test-generate_rules.R |only tests/testthat/test-generate_rules_matrix.R |only tests/testthat/test-honest_splitting.R |only tests/testthat/test-interpret_rules.R |only tests/testthat/test-predict.R |only 37 files changed, 244 insertions(+), 222 deletions(-)
Title: Structured Allometric Models for Trees
Description: Access allometric models used in forest resource analysis, such as
volume equations, taper equations, biomass models, among many others. Users
are able to efficiently find and select allometric models suitable for their
project area and use them in analysis. Additionally, 'allometric' provides a
structured framework for adding new models to an open-source models
repository.
Author: Bryce Frank [aut, cre] ,
Francisco Mauro [aut] ,
Elijah Allensworth [aut]
Maintainer: Bryce Frank <bfrank70@gmail.com>
Diff between allometric versions 2.1.0 dated 2023-11-07 and 2.3.0 dated 2024-04-21
DESCRIPTION | 6 LICENSE | 4 MD5 | 117 ++++++++-------- NAMESPACE | 3 R/install.R | 42 +++--- R/load.R | 78 +++++++++-- R/publication_processing.R | 19 ++ R/utils-pipe.R | 28 ++-- R/zzz.R | 7 - README.md | 38 ++--- inst/testdata/fixef_no_descriptors.json | 52 +++---- inst/testdata/test_parameters |only inst/testdata/test_publications |only inst/variable_defs/b.csv | 3 inst/variable_defs/e.csv | 1 inst/variable_defs/h.csv | 1 inst/variable_defs/measures.csv | 3 inst/variable_defs/n.csv | 2 inst/variable_defs/r.csv | 4 inst/variable_defs/t.csv |only inst/variable_defs/v.csv | 2 man/Publication.Rd | 100 +++++++------- man/Taxa.Rd | 60 ++++---- man/Taxon.Rd | 72 +++++----- man/add_model-Publication-FixedEffectsModel-method.Rd | 44 +++--- man/add_model-Publication-MixedEffectsModel-method.Rd | 44 +++--- man/add_model.Rd | 42 +++--- man/add_set.Rd | 46 +++--- man/aggregate_taxa.Rd | 6 man/check_args_in_predict_fn.Rd | 24 +-- man/check_descriptor_set.Rd | 28 ++-- man/check_descriptor_validity.Rd | 24 +-- man/check_models_installed.Rd | 28 ++-- man/check_parameters_in_mixed_fns.Rd | 24 +-- man/check_parameters_in_predict_fn.Rd | 24 +-- man/check_parametric_model.Rd | 24 +-- man/check_taxon_hierarchy.Rd | 24 +-- man/descriptors_to_S4.Rd | 24 +-- man/equals-Taxon-Taxon-method.Rd | 36 ++--- man/fia_trees.Rd | 58 ++++---- man/get_measure_defs.Rd | 34 ++-- man/get_params_path.Rd |only man/grapes-in-grapes-Taxa-Taxon-method.Rd | 42 +++--- man/grapes-in-grapes-Taxon-Taxa-method.Rd | 40 ++--- man/grapes-in-grapes-character-Taxa-method.Rd | 40 ++--- man/grapes-in-grapes-character-Taxon-method.Rd | 40 ++--- man/ingest_models.Rd |only man/install_models.Rd | 14 -- man/load_models.Rd | 126 +++++++++++++++--- man/load_parameter_frame.Rd | 38 ++--- man/pipe.Rd | 40 ++--- man/select_model.model_tbl.Rd | 42 +++--- man/set_params_path.Rd |only man/unnest_models.model_tbl.Rd | 42 +++--- man/unnest_taxa.Rd | 40 ++--- man/unnest_taxa.model_tbl.Rd | 40 ++--- tests/testthat.R | 22 +-- tests/testthat/test-install.R | 11 - tests/testthat/test-model-set.R | 22 +-- tests/testthat/test-model-tbl.R | 4 tests/testthat/test-publication-processing.R | 13 + tests/testthat/test-taxa.R | 17 ++ 62 files changed, 1000 insertions(+), 809 deletions(-)
Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor) or analysis of variance (for cases where more than two levels or factors exist) to calculate the fold change or relative expression. The functions also provide standard deviations and confidence limits for means and apply statistical mean comparisons. To facilitate using 'rtpcr', diffe [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 1.0.4 dated 2024-04-20 and 1.0.5 dated 2024-04-21
DESCRIPTION | 6 - MD5 | 28 ++++---- R/oneFACTORplot.r | 4 - R/qpcrANCOVA.r | 162 ++++++++++++++++++++++++++++++++++++------------- R/qpcrANOVA.r | 102 ++++++++++++++++++++++++++---- R/qpcrhlpr.r | 64 ------------------- R/threeFACTORplot.r | 6 - R/twoFACTORplot.r | 10 +-- inst/doc/vignette.R | 62 +++++++++--------- inst/doc/vignette.Rmd | 26 +++---- inst/doc/vignette.html | 83 ++++++++++++++----------- man/qpcrANCOVA.Rd | 22 ++++-- man/threeFACTORplot.Rd | 2 man/twoFACTORplot.Rd | 6 - vignettes/vignette.Rmd | 26 +++---- 15 files changed, 361 insertions(+), 248 deletions(-)
Title: Tagging and Validating Epidemiological Data
Description: Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.
Author: Hugo Gruson [aut, cre] ,
Thibaut Jombart [aut, ccp],
Tim Taylor [ctb],
Chris Hartgerink [rev]
Maintainer: Hugo Gruson <hugo@data.org>
Diff between linelist versions 1.1.2 dated 2024-04-19 and 1.1.3 dated 2024-04-21
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/linelist-package.R | 4 ++-- inst/CITATION | 2 +- inst/doc/compat-dplyr.html | 20 ++++++++++---------- inst/doc/linelist.R | 1 - inst/doc/linelist.Rmd | 1 - inst/doc/linelist.html | 45 ++++++++++++++++++++++----------------------- man/linelist-package.Rd | 4 ++-- vignettes/linelist.Rmd | 1 - 11 files changed, 57 insertions(+), 55 deletions(-)
Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of
research designs before implementation using `DeclareDesign`. Ex ante
declaration and diagnosis of designs can help researchers clarify the
strengths and limitations of their designs and to improve their
properties, and can help readers evaluate a research strategy prior
to implementation and without access to results. It can also make it
easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut, cre] ,
Jasper Cooper [aut] ,
Alexander Coppock [aut] ,
Macartan Humphreys [aut] ,
Neal Fultz [aut]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Diff between DeclareDesign versions 1.0.8 dated 2024-03-07 and 1.0.10 dated 2024-04-21
DESCRIPTION | 8 - MD5 | 80 ++++++------ NEWS.md | 5 R/compare_designs.R | 18 +- R/declare_estimator.R | 105 +++++++++-------- R/declare_measurement.R | 40 +++--- R/declare_model.R | 22 ++- R/declare_test.R | 46 ++++--- R/design_helper_functions.R | 3 R/diagnose_design.R | 16 +- R/simulate_design.R | 12 + R/utilities.R | 10 + man/compare_functions.Rd | 18 +- man/declare_estimator.Rd | 105 +++++++++-------- man/declare_measurement.Rd | 40 +++--- man/declare_model.Rd | 22 ++- man/declare_test.Rd | 46 ++++--- man/diagnose_design.Rd | 14 +- man/simulate_design.Rd | 14 +- tests/testthat/test-allow-custom-functions.R | 16 +- tests/testthat/test-alternative-df-compatibility.R | 4 tests/testthat/test-assignment.R | 36 ++--- tests/testthat/test-citation.R | 5 tests/testthat/test-compare-designs.R | 2 tests/testthat/test-declare-design.R | 44 +++++-- tests/testthat/test-demo.R | 14 +- tests/testthat/test-design-library.R | 2 tests/testthat/test-design-summary.R | 44 +++++-- tests/testthat/test-diagnosands.R | 8 - tests/testthat/test-diagnose-design.R | 30 +++- tests/testthat/test-estimators.R | 28 ++-- tests/testthat/test-factorial.R | 10 - tests/testthat/test-model.R | 11 + tests/testthat/test-modify-design.R | 19 +-- tests/testthat/test-multiple-coefficients.R | 4 tests/testthat/test-multiple-estimands-one-estimator.R | 1 tests/testthat/test-population.R | 6 tests/testthat/test-potential-outcomes.R | 39 ++++-- tests/testthat/test-reshape-diagnosis.R | 2 tests/testthat/test-sims-independent.R | 11 + tests/testthat/test-subset.R | 2 41 files changed, 579 insertions(+), 383 deletions(-)
Title: Quantifying (Animal) Sound Degradation
Description: Intended to facilitate acoustic analysis of (animal) sound transmission experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
Author: Marcelo Araya-Salas [aut, cre]
,
Michael Mahoney [rev] ,
Dena Clink [rev]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between baRulho versions 1.0.6 dated 2022-03-01 and 2.1.0 dated 2024-04-21
baRulho-1.0.6/baRulho/R/atmospheric_attenuation.R |only baRulho-1.0.6/baRulho/R/find_peaks_bRlo_int.R |only baRulho-1.0.6/baRulho/R/playback_est-data.R |only baRulho-1.0.6/baRulho/R/playback_est_unaligned-data.R |only baRulho-1.0.6/baRulho/R/prep_X_bRlo_int.R |only baRulho-1.0.6/baRulho/R/search_templates.R |only baRulho-1.0.6/baRulho/R/spcc_align.R |only baRulho-1.0.6/baRulho/R/spectral_blur_ratio.R |only baRulho-1.0.6/baRulho/R/spectral_correlation.R |only baRulho-1.0.6/baRulho/data/playback_est.rda |only baRulho-1.0.6/baRulho/data/playback_est_unaligned.rda |only baRulho-1.0.6/baRulho/inst/doc/baRulho_quantifying_sound_degradation.R |only baRulho-1.0.6/baRulho/inst/doc/baRulho_quantifying_sound_degradation.Rmd |only baRulho-1.0.6/baRulho/inst/doc/baRulho_quantifying_sound_degradation.html |only baRulho-1.0.6/baRulho/man/atmospheric_attenuation.Rd |only baRulho-1.0.6/baRulho/man/baRulho.Rd |only baRulho-1.0.6/baRulho/man/playback_est.Rd |only baRulho-1.0.6/baRulho/man/playback_est_unaligned.Rd |only baRulho-1.0.6/baRulho/man/search_templates.Rd |only baRulho-1.0.6/baRulho/man/spcc_align.Rd |only baRulho-1.0.6/baRulho/man/spectral_blur_ratio.Rd |only baRulho-1.0.6/baRulho/man/spectral_correlation.Rd |only baRulho-1.0.6/baRulho/vignettes/analysis_workflow.jpg |only baRulho-1.0.6/baRulho/vignettes/baRulho_quantifying_sound_degradation.Rmd |only baRulho-1.0.6/baRulho/vignettes/example_master.wav.jpeg |only baRulho-1.0.6/baRulho/vignettes/example_test1.wav.jpeg |only baRulho-1.0.6/baRulho/vignettes/example_test2.wav.jpeg |only baRulho-1.0.6/baRulho/vignettes/spcc_align_results.gif |only baRulho-1.0.6/baRulho/vignettes/spectral_blur_ratio_example.gif |only baRulho-1.0.6/baRulho/vignettes/spectro_synth_song.png |only baRulho-1.0.6/baRulho/vignettes/synthetic_master.wav.jpeg |only baRulho-1.0.6/baRulho/vignettes/tlalpan_playback.jpeg |only baRulho-2.1.0/baRulho/DESCRIPTION | 49 baRulho-2.1.0/baRulho/MD5 | 132 +- baRulho-2.1.0/baRulho/NAMESPACE | 49 baRulho-2.1.0/baRulho/NEWS.md | 68 + baRulho-2.1.0/baRulho/R/add_noise.R |only baRulho-2.1.0/baRulho/R/align_test_files.R | 346 +++--- baRulho-2.1.0/baRulho/R/attenuation.R |only baRulho-2.1.0/baRulho/R/auto_realign.R |only baRulho-2.1.0/baRulho/R/baRulho-package.R | 34 baRulho-2.1.0/baRulho/R/blur_ratio.R | 538 +++------- baRulho-2.1.0/baRulho/R/detection_distance.R |only baRulho-2.1.0/baRulho/R/envelope_correlation.R | 294 ++--- baRulho-2.1.0/baRulho/R/excess_attenuation.R | 392 ++----- baRulho-2.1.0/baRulho/R/find_markers.R |only baRulho-2.1.0/baRulho/R/internal_functions.R |only baRulho-2.1.0/baRulho/R/manual_realign.R |only baRulho-2.1.0/baRulho/R/master_est-data.R |only baRulho-2.1.0/baRulho/R/master_sound_file.R | 527 +++++---- baRulho-2.1.0/baRulho/R/noise_profile.R | 336 ++---- baRulho-2.1.0/baRulho/R/plot_aligned_sounds.R |only baRulho-2.1.0/baRulho/R/plot_blur_ratio.R |only baRulho-2.1.0/baRulho/R/plot_degradation.R |only baRulho-2.1.0/baRulho/R/set_reference_sounds.R |only baRulho-2.1.0/baRulho/R/signal_to_noise_ratio.R | 364 ++---- baRulho-2.1.0/baRulho/R/spcc.R | 249 ++-- baRulho-2.1.0/baRulho/R/spectrum_blur_ratio.R |only baRulho-2.1.0/baRulho/R/spectrum_correlation.R |only baRulho-2.1.0/baRulho/R/synth_sounds.R |only baRulho-2.1.0/baRulho/R/tail_to_signal_ratio.R | 340 +++--- baRulho-2.1.0/baRulho/R/template_params.R |only baRulho-2.1.0/baRulho/R/test_sounds_est-data.R |only baRulho-2.1.0/baRulho/README.md | 175 ++- baRulho-2.1.0/baRulho/build/vignette.rds |binary baRulho-2.1.0/baRulho/data/master_est.rda |only baRulho-2.1.0/baRulho/data/test_sounds_est.rda |only baRulho-2.1.0/baRulho/inst/CITATION | 11 baRulho-2.1.0/baRulho/inst/doc/align_test_sounds.R |only baRulho-2.1.0/baRulho/inst/doc/align_test_sounds.Rmd |only baRulho-2.1.0/baRulho/inst/doc/align_test_sounds.html |only baRulho-2.1.0/baRulho/inst/doc/quantify_degradation.R |only baRulho-2.1.0/baRulho/inst/doc/quantify_degradation.Rmd |only baRulho-2.1.0/baRulho/inst/doc/quantify_degradation.html |only baRulho-2.1.0/baRulho/man/add_noise.Rd |only baRulho-2.1.0/baRulho/man/align_test_files.Rd | 120 -- baRulho-2.1.0/baRulho/man/attenuation.Rd |only baRulho-2.1.0/baRulho/man/auto_realign.Rd |only baRulho-2.1.0/baRulho/man/baRulho-package.Rd |only baRulho-2.1.0/baRulho/man/blur_ratio.Rd | 111 +- baRulho-2.1.0/baRulho/man/detection_distance.Rd |only baRulho-2.1.0/baRulho/man/envelope_correlation.Rd | 78 - baRulho-2.1.0/baRulho/man/excess_attenuation.Rd | 77 - baRulho-2.1.0/baRulho/man/figures |only baRulho-2.1.0/baRulho/man/find_markers.Rd |only baRulho-2.1.0/baRulho/man/manual_realign.Rd |only baRulho-2.1.0/baRulho/man/master_est.Rd |only baRulho-2.1.0/baRulho/man/master_sound_file.Rd | 85 + baRulho-2.1.0/baRulho/man/noise_profile.Rd | 64 - baRulho-2.1.0/baRulho/man/plot_aligned_sounds.Rd |only baRulho-2.1.0/baRulho/man/plot_blur_ratio.Rd |only baRulho-2.1.0/baRulho/man/plot_degradation.Rd |only baRulho-2.1.0/baRulho/man/set_reference_sounds.Rd |only baRulho-2.1.0/baRulho/man/signal_to_noise_ratio.Rd | 94 + baRulho-2.1.0/baRulho/man/spcc.Rd | 75 - baRulho-2.1.0/baRulho/man/spectrum_blur_ratio.Rd |only baRulho-2.1.0/baRulho/man/spectrum_correlation.Rd |only baRulho-2.1.0/baRulho/man/synth_sounds.Rd |only baRulho-2.1.0/baRulho/man/tail_to_signal_ratio.Rd | 84 + baRulho-2.1.0/baRulho/man/test_sounds_est.Rd |only baRulho-2.1.0/baRulho/vignettes/align_test_sounds.Rmd |only baRulho-2.1.0/baRulho/vignettes/auto_realign_results.gif |only baRulho-2.1.0/baRulho/vignettes/baRulho_sticker.png |only baRulho-2.1.0/baRulho/vignettes/blur_ratio_example.gif |binary baRulho-2.1.0/baRulho/vignettes/manual_realign.gif |only baRulho-2.1.0/baRulho/vignettes/quantify_degradation.Rmd |only 106 files changed, 2464 insertions(+), 2228 deletions(-)
Title: Extending Lasso Model Fitting to Big Data
Description: Extend lasso and elastic-net model fitting for ultra
high-dimensional, multi-gigabyte data sets that cannot be loaded into
memory. Designed to be more memory- and computation-efficient than existing
lasso-fitting packages like 'glmnet' and 'ncvreg', thus allowing
the user to analyze big data analysis even on an ordinary laptop.
Author: Yaohui Zeng [aut],
Chuyi Wang [aut],
Tabitha Peter [aut],
Patrick Breheny [aut, cre]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between biglasso versions 1.5.2 dated 2022-10-05 and 1.6.0 dated 2024-04-21
biglasso-1.5.2/biglasso/R/cv.biglasso.R |only biglasso-1.5.2/biglasso/R/plot.biglasso.R |only biglasso-1.5.2/biglasso/R/plot.cv.biglasso.R |only biglasso-1.5.2/biglasso/R/plot.mbiglasso.R |only biglasso-1.5.2/biglasso/R/predict.cv.R |only biglasso-1.5.2/biglasso/R/summary.cv.biglasso.R |only biglasso-1.5.2/biglasso/src/Makevars.win |only biglasso-1.6.0/biglasso/DESCRIPTION | 18 biglasso-1.6.0/biglasso/MD5 | 82 +- biglasso-1.6.0/biglasso/NAMESPACE | 2 biglasso-1.6.0/biglasso/NEWS.md | 21 biglasso-1.6.0/biglasso/R/biglasso-package.R | 302 ++++----- biglasso-1.6.0/biglasso/R/biglasso.R | 117 +-- biglasso-1.6.0/biglasso/R/biglasso_fit.R |only biglasso-1.6.0/biglasso/R/biglasso_path.R |only biglasso-1.6.0/biglasso/R/cv-biglasso.R |only biglasso-1.6.0/biglasso/R/loss.R | 20 biglasso-1.6.0/biglasso/R/plot-biglasso.R |only biglasso-1.6.0/biglasso/R/plot-cv-biglasso.R |only biglasso-1.6.0/biglasso/R/plot-mbiglasso.R |only biglasso-1.6.0/biglasso/R/predict-cv.R |only biglasso-1.6.0/biglasso/R/predict.R | 56 - biglasso-1.6.0/biglasso/R/setupX.R | 48 - biglasso-1.6.0/biglasso/R/summary-cv-biglasso.R |only biglasso-1.6.0/biglasso/build/vignette.rds |binary biglasso-1.6.0/biglasso/inst/CITATION | 17 biglasso-1.6.0/biglasso/inst/doc/biglasso.R | 4 biglasso-1.6.0/biglasso/inst/doc/biglasso.Rmd | 30 biglasso-1.6.0/biglasso/inst/doc/biglasso.html | 648 +++++++++++++-------- biglasso-1.6.0/biglasso/man/biglasso-package.Rd | 306 ++++----- biglasso-1.6.0/biglasso/man/biglasso.Rd | 507 ++++++++-------- biglasso-1.6.0/biglasso/man/biglasso_fit.Rd |only biglasso-1.6.0/biglasso/man/biglasso_path.Rd |only biglasso-1.6.0/biglasso/man/colon.Rd | 82 +- biglasso-1.6.0/biglasso/man/cv.biglasso.Rd | 239 +++---- biglasso-1.6.0/biglasso/man/loss.biglasso.Rd | 76 +- biglasso-1.6.0/biglasso/man/plot.biglasso.Rd | 67 -- biglasso-1.6.0/biglasso/man/plot.cv.biglasso.Rd | 122 +-- biglasso-1.6.0/biglasso/man/plot.mbiglasso.Rd | 14 biglasso-1.6.0/biglasso/man/predict.biglasso.Rd | 207 +++--- biglasso-1.6.0/biglasso/man/predict.cv.biglasso.Rd | 168 ++--- biglasso-1.6.0/biglasso/man/setupX.Rd | 153 ++-- biglasso-1.6.0/biglasso/man/summary.cv.biglasso.Rd | 105 +-- biglasso-1.6.0/biglasso/src/Makevars | 7 biglasso-1.6.0/biglasso/src/biglasso_omp.h | 1 biglasso-1.6.0/biglasso/src/gaussian.cpp | 4 biglasso-1.6.0/biglasso/src/gaussian_simple.cpp |only biglasso-1.6.0/biglasso/src/init.c | 16 biglasso-1.6.0/biglasso/src/utilities.cpp | 208 ++++++ biglasso-1.6.0/biglasso/src/utilities.h | 35 + biglasso-1.6.0/biglasso/vignettes/biglasso.Rmd | 30 51 files changed, 2047 insertions(+), 1665 deletions(-)
Title: Explicitly Qualifying Namespaces by Automatically Adding 'pkg::'
to Functions
Description: Automatically adding 'pkg::' to a function, i.e. mutate()
becomes dplyr::mutate(). It is up to the user to determine which
packages should be used explicitly, whether to include base R packages
or use the functionality on selected text, a file, or a complete
directory. User friendly logging is provided in the 'RStudio' Markers
pane. Lives in the spirit of 'lintr' and 'styler'. Can also be used
for checking which packages are actually used in a project.
Author: Matthias Nistler
Maintainer: Matthias Nistler <m_nistler@web.de>
Diff between origin versions 1.1.1 dated 2023-09-03 and 1.1.2 dated 2024-04-21
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- NEWS.md | 8 ++++ R/fix_html_tokens.R | 74 ++++++++++++++++++++++------------------- R/run_logging.R | 2 - README.md | 4 +- build/vignette.rds |binary inst/doc/origin.R | 6 +-- tests/testthat/_snaps/print.md | 40 +++++++++++----------- tests/testthat/test-print.R | 3 + 10 files changed, 90 insertions(+), 73 deletions(-)
Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's
Biostatistics: A Foundation for Analysis in the
Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DanielBiostatistics10th versions 0.2.0 dated 2024-04-11 and 0.2.1 dated 2024-04-21
DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp7.power.R |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/autoplot.BooleanTable.Rd |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/binom2pois.Rd |only DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/DESCRIPTION | 14 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/MD5 | 38 +- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/NAMESPACE | 58 --- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/NEWS.md | 3 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/BooleanTable.R | 78 ---- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp11.R | 83 ---- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp2.R | 35 -- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp4.R | 175 ---------- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp5.6.7.R | 35 +- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp7_power.R |only DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp9.R | 83 ---- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/BooleanTable.Rd | 2 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter02.Rd | 5 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter04.Rd | 32 - DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter05to07.Rd | 37 +- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter07_power.Rd | 5 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter09.Rd | 29 - DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter11.Rd | 38 -- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter14.Rd | 12 22 files changed, 108 insertions(+), 654 deletions(-)
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Title: Handy Tools for TJU/TJUH Employees
Description: Functions for admin needs of employees of
Thomas Jefferson University and Thomas Jefferson
University Hospital, Philadelphia, PA.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between ThomasJeffersonUniv versions 0.1.0 dated 2022-05-18 and 0.1.1 dated 2024-04-21
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-03 0.0.2
2024-01-31 0.0.1