Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics. These can be used to run survival models under a frequentist (based on maximum likelihood) or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian Monte Carlo). The user can specify a set of parametric models using a common notation and select the preferred mode of inference. The results can also be post-processed to produce probabilistic sensitivity analysis and can be used to export the output to an Excel file (e.g. for a Markov model, as often done by modellers and practitioners).
Author: Gianluca Baio [aut, cre]
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between survHE versions 1.0.65 dated 2018-11-09 and 1.1 dated 2020-08-06
survHE-1.0.65/survHE/README.md |only survHE-1.0.65/survHE/inst/doc |only survHE-1.1/survHE/DESCRIPTION | 10 survHE-1.1/survHE/MD5 | 22 survHE-1.1/survHE/R/make.surv.R | 2 survHE-1.1/survHE/R/plot.survHE.R | 10 survHE-1.1/survHE/R/print.survHE.R | 2 survHE-1.1/survHE/R/survHE.R | 625 ++++++++++++++----------- survHE-1.1/survHE/R/test.linear.assumptions.R | 2 survHE-1.1/survHE/man/digitise.Rd | 8 survHE-1.1/survHE/man/plot.survHE.Rd | 3 survHE-1.1/survHE/man/survHE-package.Rd | 8 survHE-1.1/survHE/src/stan_files/Gompertz.stan | 30 - 13 files changed, 422 insertions(+), 300 deletions(-)
Title: Supervised Data Transformation by Means of Neural Network Hidden
Layer
Description: A supervised transformation of datasets is performed.
The aim is similar to that of Principal Component Analysis (PCA), that is, to carry out data transformation and dimensionality reduction, but in a supervised way.
This is achieved by first training a 3-layer Multi-Layer Perceptron and then using the activations of the hidden layer as a transformation of the input features.
In fact, it takes advantage of the change of representation provided by the hidden layer of a neural network.
This can be useful as data pre-processing for Machine Learning methods in general, specially for those that do not work well with many irrelevant or redundant features.
It uses the nnet package under the hood.
Rumelhart, D.E., Hinton, G.E. and Williams, R.J. (1986) "Learning representations by back-propagating errors" <doi:10.1038/323533a0>.
Author: Ricardo Aler [aut, cre],
Jose Valls [aut],
Ines Galvan [aut],
David Camacho [aut]
Maintainer: Ricardo Aler <ricardo.aler@uc3m.es>
Diff between nntrf versions 0.1.2 dated 2020-07-27 and 0.1.3 dated 2020-08-06
nntrf-0.1.2/nntrf/inst/extdata/error_knn_nntrf_xavier_orthog_tune.rda |only nntrf-0.1.2/nntrf/inst/extdata/error_knn_nntrf_xavier_tune.rda |only nntrf-0.1.3/nntrf/DESCRIPTION | 9 nntrf-0.1.3/nntrf/MD5 | 51 + nntrf-0.1.3/nntrf/NEWS.md | 4 nntrf-0.1.3/nntrf/R/nntrf.R | 269 +++++++--- nntrf-0.1.3/nntrf/README.md | 33 - nntrf-0.1.3/nntrf/build/vignette.rds |binary nntrf-0.1.3/nntrf/data/doughnut.rda |binary nntrf-0.1.3/nntrf/data/doughnutRand.rda |binary nntrf-0.1.3/nntrf/data/doughnutRandRotated.rda |binary nntrf-0.1.3/nntrf/inst/doc/nntrf.R | 2 nntrf-0.1.3/nntrf/inst/doc/nntrf.Rmd | 11 nntrf-0.1.3/nntrf/inst/doc/nntrf.html | 17 nntrf-0.1.3/nntrf/inst/doc/nntrf_regresion.R |only nntrf-0.1.3/nntrf/inst/doc/nntrf_regresion.Rmd |only nntrf-0.1.3/nntrf/inst/doc/nntrf_regresion.html |only nntrf-0.1.3/nntrf/inst/doc/nntrf_tuning.R | 95 --- nntrf-0.1.3/nntrf/inst/doc/nntrf_tuning.Rmd | 123 ---- nntrf-0.1.3/nntrf/inst/doc/nntrf_tuning.html | 214 +------ nntrf-0.1.3/nntrf/inst/extdata/error_knn_nntrf.rda |binary nntrf-0.1.3/nntrf/inst/extdata/error_knn_nntrf_regression.rda |only nntrf-0.1.3/nntrf/inst/extdata/error_knn_nntrf_tune.rda |binary nntrf-0.1.3/nntrf/inst/extdata/error_knn_pca_tune.rda |binary nntrf-0.1.3/nntrf/inst/extdata/error_knn_pca_tune_regression.rda |only nntrf-0.1.3/nntrf/inst/extdata/error_knn_tune.rda |binary nntrf-0.1.3/nntrf/inst/extdata/error_knn_tune_regression.rda |only nntrf-0.1.3/nntrf/man/nntrf.Rd | 34 - nntrf-0.1.3/nntrf/vignettes/nntrf.Rmd | 11 nntrf-0.1.3/nntrf/vignettes/nntrf_regresion.Rmd |only nntrf-0.1.3/nntrf/vignettes/nntrf_tuning.Rmd | 123 ---- 31 files changed, 363 insertions(+), 633 deletions(-)
Title: Nanosecond-Resolution Time for R
Description: Full 64-bit resolution date and time support with resolution up
to nanosecond granularity is provided, with easy transition to and from the
standard 'POSIXct' type.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.2.4 dated 2019-05-25 and 0.3.0 dated 2020-08-06
nanotime-0.2.4/nanotime/inst/unitTests |only nanotime-0.2.4/nanotime/tests/runTests.R |only nanotime-0.3.0/nanotime/ChangeLog | 294 ++++ nanotime-0.3.0/nanotime/DESCRIPTION | 20 nanotime-0.3.0/nanotime/MD5 | 74 - nanotime-0.3.0/nanotime/NAMESPACE | 81 + nanotime-0.3.0/nanotime/R/RcppExports.R |only nanotime-0.3.0/nanotime/R/nanoduration.R |only nanotime-0.3.0/nanotime/R/nanoival.R |only nanotime-0.3.0/nanotime/R/nanoperiod.R |only nanotime-0.3.0/nanotime/R/nanotime.R | 799 ++++++++++--- nanotime-0.3.0/nanotime/README.md | 191 ++- nanotime-0.3.0/nanotime/build |only nanotime-0.3.0/nanotime/cleanup |only nanotime-0.3.0/nanotime/inst/NEWS.Rd | 21 nanotime-0.3.0/nanotime/inst/doc |only nanotime-0.3.0/nanotime/inst/include |only nanotime-0.3.0/nanotime/inst/tinytest |only nanotime-0.3.0/nanotime/man/all.equal.nanoduration.Rd |only nanotime-0.3.0/nanotime/man/all.equal.nanoival.Rd |only nanotime-0.3.0/nanotime/man/all.equal.nanoperiod.Rd |only nanotime-0.3.0/nanotime/man/all.equal.nanotime.Rd |only nanotime-0.3.0/nanotime/man/is.unsorted-nanoival-method.Rd |only nanotime-0.3.0/nanotime/man/nano_year.Rd |only nanotime-0.3.0/nanotime/man/nanoduration.Rd |only nanotime-0.3.0/nanotime/man/nanoival.Rd |only nanotime-0.3.0/nanotime/man/nanoperiod.Rd |only nanotime-0.3.0/nanotime/man/nanoperiod.month.Rd |only nanotime-0.3.0/nanotime/man/nanotime.Rd | 175 +- nanotime-0.3.0/nanotime/man/rep-nanoduration-method.Rd |only nanotime-0.3.0/nanotime/man/rep-nanoival-method.Rd |only nanotime-0.3.0/nanotime/man/rep-nanoperiod-method.Rd |only nanotime-0.3.0/nanotime/man/rep-nanotime-method.Rd |only nanotime-0.3.0/nanotime/man/rounding.Rd |only nanotime-0.3.0/nanotime/man/seq-nanoival-method.Rd |only nanotime-0.3.0/nanotime/man/seq.nanoduration.Rd |only nanotime-0.3.0/nanotime/man/seq.nanotime.Rd |only nanotime-0.3.0/nanotime/man/set_operations.Rd |only nanotime-0.3.0/nanotime/man/sort-nanoival-method.Rd |only nanotime-0.3.0/nanotime/src |only nanotime-0.3.0/nanotime/tests/tinytest.R |only nanotime-0.3.0/nanotime/vignettes |only 42 files changed, 1355 insertions(+), 300 deletions(-)
Title: Journal Abbreviations for BibTeX Documents
Description: Since the reference management software (such as 'Zotero', 'Mendeley') exports Bib file journal abbreviation is not detailed enough, the 'journalabbr' package only abbreviates the journal field of Bib file, and then outputs a new Bib file for generating reference format with journal abbreviation on other software (such as 'texstudio'). The abbreviation table is from 'JabRef'. At the same time, 'Shiny' application is provided to generate 'thebibliography', a reference format that can be directly used for latex paper writing based on 'Rmd' files.
Author: ShuCai Zou [aut, cre],
Yu Chen [aut]
Maintainer: ShuCai Zou <zscmoyujian@163.com>
Diff between journalabbr versions 0.2.1 dated 2020-07-27 and 0.2.2 dated 2020-08-06
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++++--- NAMESPACE | 5 +++++ R/rbind_bib.R |only R/unique_bib.R |only R/write_tib2bib.R | 4 ++-- inst/extdata/testfile_2.bib |only inst/extdata/testfile_3.bib |only inst/extdata/testfile_4.bib |only man/rbind_bib.Rd |only man/unique_bib.Rd |only 11 files changed, 21 insertions(+), 9 deletions(-)
Title: Clustering Algorithm for Data Integration and Disease Subtyping
Description: Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et.al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et.al. (2017)<DOI: 10.1101/gr.215129.116>).
Author: Hung Nguyen, Bang Tran, Duc Tran and Tin Nguyen
Maintainer: Hung Nguyen <hungnp@nevada.unr.edu>
Diff between PINSPlus versions 2.0.4 dated 2020-05-30 and 2.0.5 dated 2020-08-06
DESCRIPTION | 10 - MD5 | 16 +- R/perturbation-clustering.R | 231 +++++++++++++++++++++------------------ R/subtyping-omics-data-helpers.R | 49 +++++--- R/subtyping-omics-data.R | 215 ++++++++++++++++++++++++++++++++---- man/KIRC.Rd | 2 man/PerturbationClustering.Rd | 7 - man/SubtypingOmicsData.Rd | 7 - vignettes/PINSPlus.html | 18 +-- 9 files changed, 382 insertions(+), 173 deletions(-)
Title: Quality Assessment for Seasonal Adjustment
Description: Add-in to the 'RJDemetra' package on seasonal adjustments.
It allows to produce quality assessments outputs (dashboards, quality report matrix, etc.).
Author: Alain Quartier-la-Tente [aut, cre]
(<https://orcid.org/0000-0001-7890-3857>)
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between rjdqa versions 0.1.0 dated 2019-06-17 and 0.1.1 dated 2020-08-06
rjdqa-0.1.0/rjdqa/R/QR_export.R |only rjdqa-0.1.0/rjdqa/R/QR_extract_functions.R |only rjdqa-0.1.0/rjdqa/R/QR_functions.R |only rjdqa-0.1.0/rjdqa/R/QR_matrix_classes.R |only rjdqa-0.1.0/rjdqa/R/quality_matrix.R |only rjdqa-0.1.1/rjdqa/DESCRIPTION | 16 - rjdqa-0.1.1/rjdqa/MD5 | 24 - rjdqa-0.1.1/rjdqa/NEWS.md |only rjdqa-0.1.1/rjdqa/R/sa_dashboard_moving_holiday.R | 147 ++++++---- rjdqa-0.1.1/rjdqa/R/sa_dashboard_net_effects.R | 44 ++- rjdqa-0.1.1/rjdqa/R/sa_dashboard_trading_day.R | 160 +++++++---- rjdqa-0.1.1/rjdqa/R/seasonal_dashboard.R | 6 rjdqa-0.1.1/rjdqa/README.md | 16 - rjdqa-0.1.1/rjdqa/man/figures/README-dashboard_exemple-1.png |binary rjdqa-0.1.1/rjdqa/man/plot.sa_dashboard.Rd | 15 - rjdqa-0.1.1/rjdqa/man/sa_dashboard.Rd | 3 16 files changed, 289 insertions(+), 142 deletions(-)
Title: Plane Geometry
Description: An extensive set of plane geometry routines. Provides R6 classes representing triangles, circles, circular arcs, ellipses, elliptical arcs and lines, and their plot methods. Also provides R6 classes representing transformations: rotations, reflections, homotheties, scalings, general affine transformations, inversions, Möbius transformations.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between PlaneGeometry versions 1.1.0 dated 2020-02-24 and 1.2.0 dated 2020-08-06
DESCRIPTION | 8 MD5 | 20 NEWS.md | 8 R/Ellipse.R | 115 ++++ R/Mobius.R | 10 build/vignette.rds |binary inst/doc/examples.R | 49 ++ inst/doc/examples.Rmd | 62 ++ inst/doc/examples.html | 1168 ++++++++++++++++++++++++++++++------------------- man/Ellipse.Rd | 153 ++++++ vignettes/examples.Rmd | 62 ++ 11 files changed, 1181 insertions(+), 474 deletions(-)
Title: A Collection of Fluorescence Fluctuation Spectroscopy Methods
Description: A set of tools for fluorescence fluctuation spectroscopy data analysis performance is provided in this package.
It includes techniques such as single-point fluorescence correlation spectroscopy, autocorrelation and pair correlation functions, number & brightness (raster line scan) and a novel, recently developed method by Hinde and co-workers, pair correlation of molecular brightness (doi:10.1038/ncomms11047).
A set of simulations and real experimental data is used for the examples of each function provided in this package.
For an in-depth description of the basics behind each function here included and a detailed step-by-step guide on how to use them on your own data, please refer to the Supplementary Material file provided at (<https://github.com/RPintoC/FCSlib>).
Author: Raul Pinto Camara, Adan Guerrero.
Maintainer: Raul Pinto Camara <vasto.lorde.rp@gmail.com>
Diff between FCSlib versions 1.1.0 dated 2020-02-12 and 1.1.1 dated 2020-08-06
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++++-------- NAMESPACE | 5 ++++- R/fitFCS.R | 23 ++++++++++++++++------- R/readFileFcs.R |only R/readFileModel.R |only R/simplifyFCS.R | 25 ++++++++++++++++++------- man/Cy5_100nM.Rd | 4 +++- man/V2.Rd | 4 +++- man/fitFCS.Rd | 8 ++++++-- man/readFileFCS.Rd |only man/readFileModel.Rd |only man/simplifyFCS.Rd | 15 +++++++++++---- 13 files changed, 80 insertions(+), 38 deletions(-)
Title: R Interface to Access CalPASS API
Description: Implements methods for querying data from CalPASS using its API.
CalPASS Plus. MMAP API V1. <https://mmap.calpassplus.org/docs/index.html>.
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>
Diff between calpassapi versions 0.0.2 dated 2018-08-27 and 0.0.3 dated 2020-08-06
DESCRIPTION | 8 MD5 | 20 +- NEWS | 6 R/calpassapi.R | 53 +++++- build/vignette.rds |binary inst/doc/Tutorial.R | 12 + inst/doc/Tutorial.Rmd | 14 + inst/doc/Tutorial.html | 414 +++++++++++++++++++++++++++++++---------------- man/calpass_get_token.Rd | 13 - man/calpass_query.Rd | 40 +++- vignettes/Tutorial.Rmd | 14 + 11 files changed, 414 insertions(+), 180 deletions(-)
Title: Methods for Fitting and Simulating Non-Stationary ARFIMA Models
Description: Routines for fitting and simulating data under autoregressive fractionally integrated moving average (ARFIMA) models, without the constraint of covariance stationarity. Two fitting methods are implemented, a pseudo-maximum likelihood method and a minimum distance estimator. Mayoral, L. (2007) <doi:10.1111/j.1368-423X.2007.00202.x>. Beran, J. (1995) <doi:10.1111/j.2517-6161.1995.tb02054.x>.
Author: Benjamin Groebe [aut, cre]
Maintainer: Benjamin Groebe <ben.groebe@gmail.com>
Diff between nsarfima versions 0.1.0.0 dated 2019-09-20 and 0.2.0.0 dated 2020-08-06
DESCRIPTION | 10 MD5 | 12 NAMESPACE | 13 R/nsarfima.R | 1828 ++++++++++++++++++++++++------------------------------ man/arfima.sim.Rd | 54 - man/mde.arfima.Rd | 47 - man/mle.arfima.Rd | 46 - 7 files changed, 937 insertions(+), 1073 deletions(-)
Title: Copy Number Profile Curve-Based Association Test
Description: Implements a kernel-based association test for copy number
variation (CNV) aggregate analysis
in a certain genomic region (e.g., gene set, chromosome, or genome) that is
robust to the within-locus and across-locus etiological heterogeneity, and
bypass the need to define a "locus" unit for CNVs.
Brucker, A., et al. (2020) <doi:10.1101/666875>.
Author: Amanda Brucker, Shannon T. Holloway, Jung-Ying Tzeng
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between CONCUR versions 1.2 dated 2020-03-25 and 1.3 dated 2020-08-06
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/cnvData.R | 2 +- R/concur.R | 29 +++++++++++++++++++---------- R/pv_func.R | 2 ++ man/cnvData.Rd | 8 +++++--- man/concur.Rd | 40 ++++++++++++++++++++++++++++------------ man/covData.Rd | 6 ++++-- man/phenoData.Rd | 6 ++++-- 9 files changed, 76 insertions(+), 43 deletions(-)
Title: Model-Based Boosting
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut] (<https://orcid.org/0000-0001-8301-0471>),
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut, cre] (<https://orcid.org/0000-0003-2810-3186>),
Fabian Sobotka [ctb],
Fabian Scheipl [ctb],
Andreas Mayr [ctb]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between mboost versions 2.9-2.1 dated 2020-08-02 and 2.9-3 dated 2020-08-06
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/bmono.R | 1 - R/helpers.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++++ inst/doc/SurvivalEnsembles.pdf |binary inst/doc/mboost.pdf |binary inst/doc/mboost_illustrations.pdf |binary inst/doc/mboost_tutorial.R | 1 + inst/doc/mboost_tutorial.pdf |binary man/mboost_package.Rd | 4 ++-- 13 files changed, 29 insertions(+), 20 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 1.9.1 dated 2020-07-02 and 1.10.0 dated 2020-08-06
DESCRIPTION | 8 - MD5 | 22 +-- NEWS.md | 15 ++ R/Connection.R | 6 - R/Driver.R | 12 +- R/util.R | 19 +++ build/vignette.rds |binary inst/doc/getting_started.Rmd | 27 ++++ inst/doc/getting_started.html | 198 +++++++++++++++++++---------------- man/dbConnect-AthenaDriver-method.Rd | 3 tests/testthat/test-metadata.R | 2 vignettes/getting_started.Rmd | 27 ++++ 12 files changed, 227 insertions(+), 112 deletions(-)
Title: Nonlinear Time Series Analysis
Description: Simulation, estimation, prediction procedure, and model identification methods for nonlinear time series analysis, including threshold autoregressive models, Markov-switching models, convolutional functional autoregressive models, nonlinearity tests, Kalman filters and various sequential Monte Carlo methods. More examples and details about this package can be found in the book "Nonlinear Time Series Analysis" by Ruey S. Tsay and Rong Chen, John Wiley & Sons, 2018 (ISBN: 978-1-119-26407-1).
Author: Ruey Tsay [aut],
Rong Chen [aut],
Xialu Liu [aut, cre]
Maintainer: Xialu Liu <xialu.liu@sdsu.edu>
Diff between NTS versions 1.1.1 dated 2020-08-05 and 1.1.2 dated 2020-08-06
DESCRIPTION | 6 MD5 | 46 NAMESPACE | 22 R/SMC.r | 2436 ++++++++++++++++++------------------------- man/F_test_cfar.Rd | 10 man/F_test_cfarh.Rd | 18 man/MKF.Full.RB.Rd |only man/MKFstep.fading.Rd |only man/MSM.fit.Rd |only man/NNsetting.Rd |only man/SISstep.fading.Rd |only man/SMC.Full.RB.Rd |only man/SMC.Full.Rd |only man/SMC.Rd |only man/SMC.Smooth.Rd |only man/Sstep.Clutter.Full.RB.Rd |only man/Sstep.Clutter.Full.Rd |only man/Sstep.Clutter.Rd |only man/Sstep.Smooth.Sonar.Rd |only man/Sstep.Sonar.Rd |only man/clutterKF.Rd |only man/cvlm.Rd |only man/est_cfar.Rd | 14 man/est_cfarh.Rd | 22 man/g_cfar.Rd | 19 man/g_cfar1.Rd | 24 man/g_cfar2.Rd | 27 man/g_cfar2h.Rd | 29 man/p_cfar.Rd | 20 man/p_cfar_part.Rd | 10 man/simPassiveSonar.Rd |only man/simuTargetClutter.Rd |only man/simu_fading.Rd |only man/wrap.SMC.Rd |only 34 files changed, 1103 insertions(+), 1600 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Simulation tools for management strategy evaluation are provided for the 'DLMtool' operating model to inform data-rich fisheries.
'MSEtool' provides complementary assessment models of varying complexity with standardized reporting, diagnostic tools for evaluating
assessment models within closed-loop simulation, and helper functions for building more complex operating models and model-based management procedures.
Author: Quang Huynh [aut],
Tom Carruthers [aut, cre],
Adrian Hordyk [aut],
Chris Grandin [ctb] (iSCAM functions)
Maintainer: Tom Carruthers <t.carruthers@oceans.ubc.ca>
Diff between MSEtool versions 1.7.0 dated 2020-06-24 and 2.0.0 dated 2020-08-06
DESCRIPTION | 8 MD5 | 73 ++--- NAMESPACE | 2 NEWS.md | 14 + R/Misc_fun.R | 4 R/SRA_scope.R | 461 +++++++++--------------------------- R/SRA_scope_data.R | 305 ++++++++++++++++++++--- R/SS2Data.R | 497 ++++++++++++++++++++------------------- R/SS2OM.R | 51 +++- R/define_S4_class_SRA.R | 76 +++-- R/define_S4_generic_SRA_scope.R |only R/report_SCA.R | 6 R/report_SCA_Pope.R | 6 R/report_VPA.R | 4 R/report_auxiliary.R | 10 R/rmd_report.R | 3 inst/doc/Delay_difference.html | 4 inst/doc/MSEtool.html | 4 inst/doc/SCA.html | 4 inst/doc/SRA_scope.html | 4 inst/doc/SRA_scope_eq.Rmd | 27 +- inst/doc/SRA_scope_eq.html | 71 +++-- inst/doc/SRA_scope_sel.R | 18 + inst/doc/SRA_scope_sel.Rmd | 78 +++--- inst/doc/SRA_scope_sel.html | 142 +++++------ inst/doc/Surplus_production.html | 4 inst/doc/VPA.html | 4 inst/doc/multiMSE.html | 18 - inst/include/SRA_scope.hpp | 75 ++--- inst/include/functions.hpp | 11 inst/include/ns/ns_SCA.hpp | 5 inst/include/ns/ns_SRA_scope.hpp | 86 ++---- man/SRA-class.Rd | 3 man/SRA_scope.Rd | 134 ++++++---- man/SS2Data.Rd | 149 +++++------ man/SS2OM.Rd | 192 +++++++-------- vignettes/SRA_scope_eq.Rmd | 27 +- vignettes/SRA_scope_sel.Rmd | 78 +++--- 38 files changed, 1422 insertions(+), 1236 deletions(-)
Title: Tidy IP Addresses
Description: Classes and functions for working with IP (Internet
Protocol) addresses and networks, inspired by the Python 'ipaddress'
module. Offers full support for both IPv4 and IPv6 (Internet Protocol
versions 4 and 6) address spaces. It is specifically designed to work
well with the 'tidyverse'.
Author: David Hall [aut, cre] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between ipaddress versions 0.3.0 dated 2020-05-12 and 0.4.0 dated 2020-08-06
ipaddress-0.3.0/ipaddress/inst/doc/ipaddress.R |only ipaddress-0.3.0/ipaddress/inst/doc/ipaddress.Rmd |only ipaddress-0.3.0/ipaddress/inst/doc/ipaddress.html |only ipaddress-0.3.0/ipaddress/tests/testthat/test-network_masks.R |only ipaddress-0.3.0/ipaddress/vignettes/ipaddress.Rmd |only ipaddress-0.4.0/ipaddress/DESCRIPTION | 12 ipaddress-0.4.0/ipaddress/MD5 | 104 ++-- ipaddress-0.4.0/ipaddress/NAMESPACE | 8 ipaddress-0.4.0/ipaddress/NEWS.md | 24 + ipaddress-0.4.0/ipaddress/R/RcppExports.R | 16 ipaddress-0.4.0/ipaddress/R/common_network.R |only ipaddress-0.4.0/ipaddress/R/ip_address.R | 2 ipaddress-0.4.0/ipaddress/R/ip_interface.R | 2 ipaddress-0.4.0/ipaddress/R/ip_network.R | 18 ipaddress-0.4.0/ipaddress/R/ip_version.R | 8 ipaddress-0.4.0/ipaddress/R/network_mask.R | 57 ++ ipaddress-0.4.0/ipaddress/R/other_repr.R | 3 ipaddress-0.4.0/ipaddress/R/pillar.R | 19 ipaddress-0.4.0/ipaddress/R/sample.R | 2 ipaddress-0.4.0/ipaddress/R/sequence.R | 6 ipaddress-0.4.0/ipaddress/R/summarize_address_range.R |only ipaddress-0.4.0/ipaddress/R/traverse_hierarchy.R |only ipaddress-0.4.0/ipaddress/R/vctrs-arithmetic.R | 19 ipaddress-0.4.0/ipaddress/R/within_network.R | 23 - ipaddress-0.4.0/ipaddress/README.md | 42 + ipaddress-0.4.0/ipaddress/build/vignette.rds |binary ipaddress-0.4.0/ipaddress/inst/doc/ipaddress-classes.R |only ipaddress-0.4.0/ipaddress/inst/doc/ipaddress-classes.Rmd |only ipaddress-0.4.0/ipaddress/inst/doc/ipaddress-classes.html |only ipaddress-0.4.0/ipaddress/inst/doc/ipaddress-examples.R |only ipaddress-0.4.0/ipaddress/inst/doc/ipaddress-examples.Rmd |only ipaddress-0.4.0/ipaddress/inst/doc/ipaddress-examples.html |only ipaddress-0.4.0/ipaddress/man/common_network.Rd |only ipaddress-0.4.0/ipaddress/man/ip_address.Rd | 3 ipaddress-0.4.0/ipaddress/man/ip_interface.Rd | 3 ipaddress-0.4.0/ipaddress/man/ip_network.Rd | 14 ipaddress-0.4.0/ipaddress/man/netmask.Rd | 36 + ipaddress-0.4.0/ipaddress/man/network_in_network.Rd | 23 - ipaddress-0.4.0/ipaddress/man/sequence.Rd | 2 ipaddress-0.4.0/ipaddress/man/summarize_address_range.Rd |only ipaddress-0.4.0/ipaddress/man/traverse_hierarchy.Rd |only ipaddress-0.4.0/ipaddress/src/IpAddressVector.cpp | 219 +++++++--- ipaddress-0.4.0/ipaddress/src/IpAddressVector.h | 9 ipaddress-0.4.0/ipaddress/src/IpNetworkVector.cpp | 215 +++++++-- ipaddress-0.4.0/ipaddress/src/IpNetworkVector.h | 17 ipaddress-0.4.0/ipaddress/src/RcppExports.cpp | 51 ++ ipaddress-0.4.0/ipaddress/src/iterative.h |only ipaddress-0.4.0/ipaddress/src/masking.h | 84 +++ ipaddress-0.4.0/ipaddress/src/utils.h | 17 ipaddress-0.4.0/ipaddress/src/wrapper.cpp | 26 + ipaddress-0.4.0/ipaddress/tests/testthat/test-arithmetic.R | 10 ipaddress-0.4.0/ipaddress/tests/testthat/test-common_network.R |only ipaddress-0.4.0/ipaddress/tests/testthat/test-ip_address_v4.R | 12 ipaddress-0.4.0/ipaddress/tests/testthat/test-ip_address_v6.R | 10 ipaddress-0.4.0/ipaddress/tests/testthat/test-ip_interface.R | 15 ipaddress-0.4.0/ipaddress/tests/testthat/test-ip_network_v4.R | 27 - ipaddress-0.4.0/ipaddress/tests/testthat/test-ip_network_v6.R | 25 - ipaddress-0.4.0/ipaddress/tests/testthat/test-network_mask.R |only ipaddress-0.4.0/ipaddress/tests/testthat/test-other_repr.R | 2 ipaddress-0.4.0/ipaddress/tests/testthat/test-sample.R | 9 ipaddress-0.4.0/ipaddress/tests/testthat/test-summarize_address_range.R |only ipaddress-0.4.0/ipaddress/tests/testthat/test-traverse_hierarchy.R |only ipaddress-0.4.0/ipaddress/tests/testthat/test-within_network.R | 4 ipaddress-0.4.0/ipaddress/vignettes/ipaddress-classes.Rmd |only ipaddress-0.4.0/ipaddress/vignettes/ipaddress-examples.Rmd |only 65 files changed, 886 insertions(+), 312 deletions(-)
Title: Hierarchical and Grouped Time Series
Description: Provides methods for analysing and forecasting hierarchical and
grouped time series. The available forecast methods include bottom-up,
top-down, optimal combination reconciliation (Hyndman et al. 2011)
<doi:10.1016/j.csda.2011.03.006>, and trace minimization reconciliation
(Wickramasuriya et al. 2018) <doi:10.1080/01621459.2018.1448825>.
Author: Rob Hyndman [aut] (Package creator),
Alan Lee [aut] (Fast computation using recursive methods),
Earo Wang [aut, cre],
Shanika Wickramasuriya [aut] (Reconciliation via trace minimization)
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between hts versions 6.0.0 dated 2020-04-03 and 6.0.1 dated 2020-08-06
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/forecast-gts.R | 2 +- R/hts.R | 2 +- build/vignette.rds |binary inst/doc/hts.pdf |binary tests/testthat/test-combinef.R | 2 +- tests/testthat/test-forecast.R | 2 +- 9 files changed, 20 insertions(+), 16 deletions(-)
Title: Calculation of Covariance Between Markers for Half-Sib Families
Description: The theoretical covariance between pairs of markers is calculated
from either paternal haplotypes and maternal linkage disequilibrium (LD) or
vise versa. A genetic map is required. Grouping of markers is based on the
correlation matrix and a representative marker is suggested for each group.
Employing the correlation matrix, optimal sample size can be derived for
association studies based on a SNP-BLUP approach.
The implementation relies on paternal half-sib families and biallelic
markers. If maternal half-sib families are used, the roles of sire/dam are
swapped. Multiple families can be considered.
Wittenburg, Bonk, Doschoris, Reyer (2019) "Design of Experiments for
Fine-Mapping Quantitative Trait Loci in Livestock Populations"
<doi:10.1101/2019.12.17.879106>.
Carlson, Eberle, Rieder, Yi, Kruglyak, Nickerson (2004) "Selecting a
maximally informative set of single-nucleotide polymorphisms for association
analyses using linkage disequilibrium" <doi:10.1086/381000>.
Author: Dörte Wittenburg [aut, cre],
Michael Doschoris [aut],
Jan Klosa [ctb]
Maintainer: Dörte Wittenburg <wittenburg@fbn-dummerstorf.de>
Diff between hscovar versions 0.2.1 dated 2020-04-15 and 0.4.0 dated 2020-08-06
DESCRIPTION | 7 ++++--- MD5 | 20 ++++++++++---------- NAMESPACE | 1 - NEWS.md | 9 +++++++++ R/covmat.R | 23 +++++++++++++---------- R/functions.R | 2 +- R/powercalc.R | 8 -------- R/tagSNP.R | 7 ++++--- man/CovMat.Rd | 16 ++++++++++------ man/LDsire.Rd | 2 +- man/coeff.beta.k.Rd | 8 -------- 11 files changed, 52 insertions(+), 51 deletions(-)
Title: Social Mixing Matrices for Infectious Disease Modelling
Description: Provides methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.
Author: Sebastian Funk [aut, cre],
Maria Bekker-Nielsen Dunbar [ctb],
Carl A. B. Pearson [ctb],
Sam Clifford [ctb],
Christopher Jarvis [ctb],
Alexis Robert [ctb]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between socialmixr versions 0.1.6 dated 2020-01-10 and 0.1.7 dated 2020-08-06
DESCRIPTION | 27 - MD5 | 26 - NEWS.md | 7 R/clean.r | 14 R/contact_matrix.r | 268 ++++++++----- R/limits_to_agegroups.r | 9 build/vignette.rds |binary inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 805 ++++++++++++++++++---------------------- man/contact_matrix.Rd | 5 man/polymod.Rd | 6 tests/testthat/test-agegroups.r | 10 tests/testthat/test-matrix.r | 55 ++ vignettes/introduction.Rmd | 4 14 files changed, 668 insertions(+), 572 deletions(-)
Title: Graphical User Interface ('Shiny' App) for Package 'brms'
Description: A graphical user interface (GUI) for fitting Bayesian
regression models using the package 'brms' which in turn relies on
'Stan' (<https://mc-stan.org/>). The 'shinybrms' GUI is a 'Shiny'
(<https://shiny.rstudio.com/>) app.
Author: Frank Weber [aut, cre] (<https://orcid.org/0000-0002-4842-7922>)
Maintainer: Frank Weber <fweber144@protonmail.com>
Diff between shinybrms versions 1.2.1 dated 2020-06-25 and 1.3.0 dated 2020-08-06
DESCRIPTION | 24 MD5 | 12 NEWS.md | 69 +- R/launch_shinybrms.R | 22 README.md | 93 +-- inst/shinybrms_app/app.R | 1426 +++++++++++++++++++++++++++++++---------------- man/launch_shinybrms.Rd | 20 7 files changed, 1114 insertions(+), 552 deletions(-)
Title: Cartography for Statistical Analysis
Description: Creating maps for statistical analysis such as proportional circles, chroropleth, typology and flows. Some functions use 'shiny' or 'leaflet' technologies for dynamism and interactivity.
The great features are :
- Create maps in a web environment where the parameters are modifiable on the fly ('shiny' and 'leaflet' technology).
- Create interactive maps through zoom and pop-up ('leaflet' technology).
- Create frozen maps with the possibility to add labels.
Author: Sébastien CALVET - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [cre, aut],
Sophie AUDRIC - PSAR-AT - DR Provence-Alpes-Cote d'Azur - INSEE [aut],
SED - DR Hauts-de-France - INSEE [ctb],
PSAR-SL - DR Auvergne-Rhone-Alpes - INSEE [ctb],
PSAR-EEP - DR Occitanie - INSEE [ctb],
SED - DR Pays-de-la-Loire - INSEE [ctb]
Maintainer: Sébastien CALVET <sebastien.calvet@insee.fr>
Diff between oceanis versions 1.7.4 dated 2020-07-03 and 1.7.5 dated 2020-08-06
DESCRIPTION | 8 - MD5 | 100 +++++++++--------- NEWS | 16 ++- R/add_typo_symboles.R | 2 R/construction_lignes_legende.R | 18 +-- R/construction_ronds_legende.R | 34 +++--- R/extract_fond_leaflet_classes.R | 32 +++--- R/extract_fond_leaflet_classes_ronds.R | 64 ++++++------ R/extract_fond_leaflet_joignantes.R | 56 +++++----- R/extract_fond_leaflet_oursins.R | 38 +++---- R/extract_fond_leaflet_ronds.R | 62 +++++------ R/extract_fond_leaflet_ronds_classes.R | 72 ++++++------- R/extract_fond_leaflet_saphirs.R | 56 +++++----- R/extract_fond_leaflet_typo.R | 30 ++--- R/flux_legende_joignantes.R | 12 +- R/flux_legende_joignantes_pl.R | 18 +-- R/flux_legende_saphirs.R | 12 +- R/flux_legende_saphirs_pl.R | 18 +-- R/k_oursins.R | 55 +++++----- R/k_typo.R | 39 ++++--- R/leaflet_classes.R | 24 ++-- R/leaflet_classes_ronds.R | 28 ++--- R/leaflet_fonds_simples.R | 4 R/leaflet_joignantes.R | 24 ++-- R/leaflet_oursins.R | 24 ++-- R/leaflet_ronds.R | 30 ++--- R/leaflet_ronds_classes.R | 28 ++--- R/leaflet_saphirs.R | 24 ++-- R/leaflet_typo.R | 28 ++--- R/plot_classes.R | 10 - R/plot_classes_ronds.R | 14 +- R/plot_joignantes.R | 14 +- R/plot_oursins.R | 8 - R/plot_ronds.R | 14 +- R/plot_ronds_classes.R | 16 +-- R/plot_saphirs.R | 12 +- R/plot_typo.R | 6 - R/plot_typo_symboles.R | 8 - R/set_fonds_simples.R | 2 R/set_pop_up.R | 29 ++--- R/shiny_classes.R | 50 ++++----- R/shiny_classes_ronds.R | 68 ++++++------ R/shiny_joignantes.R | 52 ++++----- R/shiny_oursins.R | 52 ++++----- R/shiny_ronds.R | 80 +++++++-------- R/shiny_ronds_classes.R | 68 ++++++------ R/shiny_saphirs.R | 58 +++++----- R/shiny_typo.R | 48 ++++----- inst/doc/integration_shiny.html | 4 inst/doc/oceanis.html | 176 ++++++++++++++++----------------- man/set_pop_up.Rd | 15 +- 51 files changed, 893 insertions(+), 867 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-31 1.4.2
2020-07-22 1.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-21 0.0.2.0
2019-10-13 0.0.1.4
Title: Method Functions for Confidence Intervals and to Distill
Information from an Object
Description: Some very simple method functions for confidence interval calculation, bootstrap resampling aimed at atmospheric science applications, and to distill pertinent information from a potentially complex object; primarily used in common with packages extRemes and SpatialVx.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between distillery versions 1.0-7 dated 2020-04-17 and 1.1 dated 2020-08-06
DESCRIPTION | 10 +++++----- MD5 | 4 +++- R/MatrixSqrt.R |only man/MatrixSqrt.Rd |only 4 files changed, 8 insertions(+), 6 deletions(-)