Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the maximal
peptide ratio extraction module of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a complete
pipeline for processing proteomics data in data-independent acquisition mode.
It offers additional options for protein quantification using the N most intense
fragment ions, using all
fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
Author: Thang Pham [aut, cre, cph, ctb]
(<https://orcid.org/0000-0003-0333-2492>),
Alex Henneman [ctb] (<https://orcid.org/0000-0002-3746-4410>)
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 1.0 dated 2019-11-15 and 1.1 dated 2019-11-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/iq.R | 6 ++++-- inst/doc/iq.html | 18 +++++++++--------- 4 files changed, 19 insertions(+), 17 deletions(-)
Title: Local Interpretable (Model-Agnostic) Visual Explanations
Description: Interpretability of complex machine learning models is a growing concern.
This package helps to understand key factors that drive the
decision made by complicated predictive model (so called black box model).
This is achieved through local approximations that are either based on
additive regression like model or CART like model that allows for
higher interactions. The methodology is based on Tulio Ribeiro, Singh, Guestrin (2016) <doi:10.1145/2939672.2939778>.
More details can be found in Staniak, Biecek (2018) <doi:10.32614/RJ-2018-072>.
Author: Mateusz Staniak [cre, aut],
Przemysław Biecek [aut]
Maintainer: Mateusz Staniak <mateusz.staniak@math.uni.wroc.pl>
Diff between live versions 1.5.10 dated 2019-02-28 and 1.5.11 dated 2019-11-15
DESCRIPTION | 16 MD5 | 54 +-- NAMESPACE | 57 +-- NEWS.md | 220 ++++++------- R/explain.R | 288 ++++++++--------- README.md | 14 build/vignette.rds |binary inst/CITATION | 32 - inst/doc/wine_quality.R | 64 +-- inst/doc/wine_quality.Rmd | 218 ++++++------- inst/doc/wine_quality.html | 499 ++++++++++++++++++++++-------- man/add_predictions.Rd | 108 +++--- man/euclidean_kernel.Rd | 38 +- man/fit_explanation.Rd | 100 +++--- man/gaussian_kernel.Rd | 38 +- man/identity_kernel.Rd | 42 +- man/live.Rd | 60 +-- man/live_shiny.Rd | 48 +- man/local_approximation.Rd | 98 ++--- man/local_permutation_importance.Rd | 90 ++--- man/plot.live_explainer.Rd | 72 ++-- man/plot.local_permutation_importance.Rd | 38 +- man/print.live_explainer.Rd | 32 - man/print.live_explorer.Rd | 32 - man/print.local_permutation_importance.Rd | 32 - man/sample_locally.Rd | 104 +++--- man/wine.Rd | 38 +- vignettes/wine_quality.Rmd | 218 ++++++------- 28 files changed, 1443 insertions(+), 1207 deletions(-)
Title: Hierarchical Ensemble Methods for Directed Acyclic Graphs
Description: An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).
Author: Marco Notaro [aut, cre] (<https://orcid.org/0000-0003-4309-2200>),
Alessandro Petrini [ctb] (<https://orcid.org/0000-0002-0587-1484>),
Giorgio Valentini [aut] (<https://orcid.org/0000-0002-5694-3919>)
Maintainer: Marco Notaro <marco.notaro@unimi.it>
Diff between HEMDAG versions 2.5.9 dated 2019-10-08 and 2.6.0 dated 2019-11-15
HEMDAG-2.5.9/HEMDAG/inst/HEMDAG_2.5.9.pdf |only HEMDAG-2.6.0/HEMDAG/DESCRIPTION | 10 +++++----- HEMDAG-2.6.0/HEMDAG/MD5 | 8 ++++---- HEMDAG-2.6.0/HEMDAG/NEWS.md | 11 +++++++++-- HEMDAG-2.6.0/HEMDAG/inst/HEMDAG_2.6.0.pdf |only HEMDAG-2.6.0/HEMDAG/man/HEMDAG-package.Rd | 2 +- 6 files changed, 19 insertions(+), 12 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description: Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb],
R Core Team [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 4.1-3 dated 2019-10-27 and 4.1-4 dated 2019-11-15
DESCRIPTION | 12 MD5 | 18 NEWS | 692 ++++++++--------- R/utilities.R | 1279 ++++++++++++++++----------------- inst/doc/adding-Effect-methods.R | 6 inst/doc/adding-Effect-methods.pdf |binary inst/doc/partial-residuals.R | 14 inst/doc/partial-residuals.pdf |binary inst/doc/predictor-effects-gallery.pdf |binary man/effects-package.Rd | 164 ++-- 10 files changed, 1095 insertions(+), 1090 deletions(-)
Title: Adaptive Weights Smoothing
Description: We provide a collection of R-functions implementing
adaptive smoothing procedures in 1D, 2D and 3D. This includes the
Propagation-Separation Approach to adaptive smoothing as
described in "J. Polzehl and V. Spokoiny (2006)
<DOI:10.1007/s00440-005-0464-1>",
"J. Polzehl and V. Spokoiny (2004) <DOI:10.20347/WIAS.PREPRINT.998>"
and "J. Polzehl, K. Papafitsoros, K. Tabelow (2018) <DOI:10.20347/WIAS.PREPRINT.2520>",
the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between aws versions 2.2-1.1 dated 2019-10-30 and 2.3-0 dated 2019-11-15
aws-2.2-1.1/aws/cleanup |only aws-2.2-1.1/aws/configure |only aws-2.2-1.1/aws/configure.ac |only aws-2.2-1.1/aws/src/Makevars.in |only aws-2.2-1.1/aws/src/Makevars.win |only aws-2.3-0/aws/DESCRIPTION | 13 +++++------ aws-2.3-0/aws/MD5 | 46 +++++++++++++++++---------------------- aws-2.3-0/aws/NAMESPACE | 3 +- aws-2.3-0/aws/R/ICIsmooth.r | 2 - aws-2.3-0/aws/R/aws.r | 6 ++--- aws-2.3-0/aws/R/awsgaussian.r | 6 ++--- aws-2.3-0/aws/R/awsirregular.r | 16 +++++++------ aws-2.3-0/aws/R/awspropagation.r | 10 ++++---- aws-2.3-0/aws/R/awssegment.r | 6 ++--- aws-2.3-0/aws/R/lpaws.r | 9 ++++--- aws-2.3-0/aws/R/vaws.r | 4 +-- aws-2.3-0/aws/R/vpaws.r | 4 +-- aws-2.3-0/aws/build/partial.rdb |binary aws-2.3-0/aws/src/ICIsmooth.f | 6 ++--- aws-2.3-0/aws/src/Makevars |only aws-2.3-0/aws/src/awslp.f | 32 +++++++++++++-------------- aws-2.3-0/aws/src/caws.f | 42 +++++++++++++++++------------------ aws-2.3-0/aws/src/cawsmask.f | 22 +++++++++--------- aws-2.3-0/aws/src/init.c | 42 +++++++++++++++++------------------ aws-2.3-0/aws/src/misc.f | 4 +-- aws-2.3-0/aws/src/pcaws.f | 22 +++++++++--------- aws-2.3-0/aws/src/segment.f | 12 +++++----- 27 files changed, 154 insertions(+), 153 deletions(-)
Title: Time-Based Rolling Functions
Description: Provides rolling statistical functions based
on date and time windows instead of n-lagged observations.
Author: Michael Schramm [aut, cre] (<https://orcid.org/0000-0003-1876-6592>),
Frank Harrell [ctb]
Maintainer: Michael Schramm <michael.schramm@ag.tamu.edu>
Diff between tbrf versions 0.1.2 dated 2019-02-02 and 0.1.3 dated 2019-11-15
DESCRIPTION | 8 MD5 | 30 +- NEWS.md | 6 R/tbr_binom.R | 2 R/tbr_gmean.R | 2 R/tbr_mean.R | 2 R/tbr_median.R | 2 R/tbr_misc.R | 2 R/tbr_sd.R | 2 R/tbr_sum.R | 2 README.md | 113 ++++----- build/vignette.rds |binary inst/doc/intro_to_tbrf.html | 380 +++++++++++++++++---------------- man/figures/README-tbr_hour-1.png |only man/figures/README-tbr_misc-1.png |binary man/figures/README-tbr_threehour-1.png |only tests/testthat/test-expectedValues.R | 17 - 17 files changed, 297 insertions(+), 271 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Andrew Bean [aut],
Lukas A. Widmer [aut],
Trustees of Columbia University [cph] (src/init.cpp, tools/make_cc.R,
R/stanmodels.R, src/Makevars, src/Makevars.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.4-4 dated 2019-08-29 and 0.5-3 dated 2019-11-15
OncoBayes2-0.4-4/OncoBayes2/inst/include/meta_header.hpp |only OncoBayes2-0.4-4/OncoBayes2/src/init.cpp |only OncoBayes2-0.4-4/OncoBayes2/src/stan_files |only OncoBayes2-0.5-3/OncoBayes2/DESCRIPTION | 19 OncoBayes2-0.5-3/OncoBayes2/MD5 | 162 - OncoBayes2-0.5-3/OncoBayes2/NAMESPACE | 24 OncoBayes2-0.5-3/OncoBayes2/R/OncoBayes2-package.R | 10 OncoBayes2-0.5-3/OncoBayes2/R/bind_rows_0.R |only OncoBayes2-0.5-3/OncoBayes2/R/blrm_exnex.R | 42 OncoBayes2-0.5-3/OncoBayes2/R/blrm_formula_linear.R |only OncoBayes2-0.5-3/OncoBayes2/R/blrm_trial.R |only OncoBayes2-0.5-3/OncoBayes2/R/codata_combo2.R | 12 OncoBayes2-0.5-3/OncoBayes2/R/dose_info_combo2.R |only OncoBayes2-0.5-3/OncoBayes2/R/drug_info_combo2.R |only OncoBayes2-0.5-3/OncoBayes2/R/example_combo2.R | 4 OncoBayes2-0.5-3/OncoBayes2/R/example_combo2_trial.R |only OncoBayes2-0.5-3/OncoBayes2/R/example_combo3.R | 4 OncoBayes2-0.5-3/OncoBayes2/R/example_model.R | 6 OncoBayes2-0.5-3/OncoBayes2/R/example_single_agent.R | 4 OncoBayes2-0.5-3/OncoBayes2/R/hist_SA.R | 10 OncoBayes2-0.5-3/OncoBayes2/R/hist_combo2.R | 22 OncoBayes2-0.5-3/OncoBayes2/R/hist_combo3.R | 16 OncoBayes2-0.5-3/OncoBayes2/R/nsamples.R |only OncoBayes2-0.5-3/OncoBayes2/R/posterior_interval.R | 11 OncoBayes2-0.5-3/OncoBayes2/R/posterior_linpred.R | 24 OncoBayes2-0.5-3/OncoBayes2/R/posterior_predict.R | 20 OncoBayes2-0.5-3/OncoBayes2/R/pp_data.R | 92 OncoBayes2-0.5-3/OncoBayes2/R/predictive_interval.R | 15 OncoBayes2-0.5-3/OncoBayes2/R/prior_summary.R | 37 OncoBayes2-0.5-3/OncoBayes2/R/stanmodels.R | 56 OncoBayes2-0.5-3/OncoBayes2/R/summary.R | 62 OncoBayes2-0.5-3/OncoBayes2/R/sysdata.rda |binary OncoBayes2-0.5-3/OncoBayes2/R/update.R |only OncoBayes2-0.5-3/OncoBayes2/build/vignette.rds |binary OncoBayes2-0.5-3/OncoBayes2/configure |only OncoBayes2-0.5-3/OncoBayes2/configure.win |only OncoBayes2-0.5-3/OncoBayes2/data/codata_combo2.rda |binary OncoBayes2-0.5-3/OncoBayes2/data/dose_info_combo2.rda |only OncoBayes2-0.5-3/OncoBayes2/data/drug_info_combo2.rda |only OncoBayes2-0.5-3/OncoBayes2/data/hist_SA.rda |binary OncoBayes2-0.5-3/OncoBayes2/data/hist_combo2.rda |binary OncoBayes2-0.5-3/OncoBayes2/data/hist_combo3.rda |binary OncoBayes2-0.5-3/OncoBayes2/inst/NEWS | 8 OncoBayes2-0.5-3/OncoBayes2/inst/doc/OncoBayes2.pdf |binary OncoBayes2-0.5-3/OncoBayes2/inst/doc/introduction.R | 166 - OncoBayes2-0.5-3/OncoBayes2/inst/doc/introduction.Rmd | 195 - OncoBayes2-0.5-3/OncoBayes2/inst/doc/introduction.html | 1403 +++++++--- OncoBayes2-0.5-3/OncoBayes2/inst/include/stan_meta_header.hpp |only OncoBayes2-0.5-3/OncoBayes2/inst/sbc/calibration.md5 | 6 OncoBayes2-0.5-3/OncoBayes2/inst/sbc/launch_sbc.sh | 2 OncoBayes2-0.5-3/OncoBayes2/inst/sbc/make_reference_rankhist.R | 23 OncoBayes2-0.5-3/OncoBayes2/inst/sbc/sbc_example_models.R | 2 OncoBayes2-0.5-3/OncoBayes2/inst/sbc/sbc_report.html | 278 + OncoBayes2-0.5-3/OncoBayes2/inst/sbc/sbc_tools.R | 56 OncoBayes2-0.5-3/OncoBayes2/inst/stan |only OncoBayes2-0.5-3/OncoBayes2/man/OncoBayes2.Rd | 2 OncoBayes2-0.5-3/OncoBayes2/man/bind_rows_0.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/blrm_exnex.Rd | 8 OncoBayes2-0.5-3/OncoBayes2/man/blrm_formula_linear.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/blrm_trial.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/codata_combo2.Rd | 16 OncoBayes2-0.5-3/OncoBayes2/man/dose_info_combo2.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/dot-get_strata_group_fct.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/drug_info_combo2.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/example-combo2.Rd | 8 OncoBayes2-0.5-3/OncoBayes2/man/example-combo2_trial.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/example-combo3.Rd | 16 OncoBayes2-0.5-3/OncoBayes2/man/example-single-agent.Rd | 4 OncoBayes2-0.5-3/OncoBayes2/man/hist_SA.Rd | 10 OncoBayes2-0.5-3/OncoBayes2/man/hist_combo2.Rd | 20 OncoBayes2-0.5-3/OncoBayes2/man/hist_combo3.Rd | 28 OncoBayes2-0.5-3/OncoBayes2/man/nsamples.blrmfit.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/posterior_linpred.blrmfit.Rd | 9 OncoBayes2-0.5-3/OncoBayes2/man/posterior_predict.blrmfit.Rd | 5 OncoBayes2-0.5-3/OncoBayes2/man/prior_summary.blrmfit.Rd | 13 OncoBayes2-0.5-3/OncoBayes2/man/summary.blrm_trial.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/summary.blrmfit.Rd | 3 OncoBayes2-0.5-3/OncoBayes2/man/update.blrm_trial.Rd |only OncoBayes2-0.5-3/OncoBayes2/man/update.blrmfit.Rd |only OncoBayes2-0.5-3/OncoBayes2/src/Makevars | 13 OncoBayes2-0.5-3/OncoBayes2/src/Makevars.win | 17 OncoBayes2-0.5-3/OncoBayes2/src/RcppExports.cpp |only OncoBayes2-0.5-3/OncoBayes2/src/stanExports_blrm_exnex.cc |only OncoBayes2-0.5-3/OncoBayes2/src/stanExports_blrm_exnex.h |only OncoBayes2-0.5-3/OncoBayes2/tests/testthat.R |only OncoBayes2-0.5-3/OncoBayes2/tests/testthat/helper-sampling.R | 4 OncoBayes2-0.5-3/OncoBayes2/tests/testthat/helper-trial_examples.R |only OncoBayes2-0.5-3/OncoBayes2/tests/testthat/test-blrm_exnex.R | 301 +- OncoBayes2-0.5-3/OncoBayes2/tests/testthat/test-blrm_trial.R |only OncoBayes2-0.5-3/OncoBayes2/tests/testthat/test-examples.R | 34 OncoBayes2-0.5-3/OncoBayes2/tests/testthat/test-posterior.R | 34 OncoBayes2-0.5-3/OncoBayes2/tools/build.sh | 5 OncoBayes2-0.5-3/OncoBayes2/tools/build_ref_pdf.sh | 4 OncoBayes2-0.5-3/OncoBayes2/tools/make-ds.R | 6 OncoBayes2-0.5-3/OncoBayes2/vignettes/introduction.Rmd | 195 - 95 files changed, 2405 insertions(+), 1141 deletions(-)
Title: Multivariate Nonparametric Methods
Description: A collection of multivariate nonparametric methods, selected in part to support an MS level course in nonparametric statistical methods. Methods include adjustments for multiple comparisons, implementation of multivariate Mann-Whitney-Wilcoxon testing, inversion of these tests to produce a confidence region, some permutation tests for linear models, and some algorithms for calculating exact probabilities associated with one- and two- stage testing involving Mann-Whitney-Wilcoxon statistics.
Author: John E. Kolassa [cre],
Stephane Jankowski [aut]
Maintainer: John E. Kolassa <kolassa@stat.rutgers.edu>
Diff between MultNonParam versions 1.2.8 dated 2019-09-07 and 1.3.0 dated 2019-11-15
MultNonParam-1.2.8/MultNonParam/R/zzz.r |only MultNonParam-1.3.0/MultNonParam/DESCRIPTION | 10 ++-- MultNonParam-1.3.0/MultNonParam/MD5 | 25 ++++++++--- MultNonParam-1.3.0/MultNonParam/NAMESPACE | 5 ++ MultNonParam-1.3.0/MultNonParam/R/dconcordant.R |only MultNonParam-1.3.0/MultNonParam/R/nextp.R |only MultNonParam-1.3.0/MultNonParam/R/page.test.unbalanced.R | 19 +++++++- MultNonParam-1.3.0/MultNonParam/R/pconcordant.R |only MultNonParam-1.3.0/MultNonParam/R/qconcordant.R |only MultNonParam-1.3.0/MultNonParam/R/theil.R |only MultNonParam-1.3.0/MultNonParam/inst/Makefile | 10 ++++ MultNonParam-1.3.0/MultNonParam/inst/lastinput | 32 ++------------- MultNonParam-1.3.0/MultNonParam/inst/testconcord.f90 |only MultNonParam-1.3.0/MultNonParam/man/dconcordant.Rd |only MultNonParam-1.3.0/MultNonParam/man/nextp.Rd |only MultNonParam-1.3.0/MultNonParam/man/pconcordant.Rd |only MultNonParam-1.3.0/MultNonParam/man/qconcordant.Rd |only MultNonParam-1.3.0/MultNonParam/man/theil.Rd |only MultNonParam-1.3.0/MultNonParam/src/init.c | 25 +++++++---- MultNonParam-1.3.0/MultNonParam/src/ufcn.f90 |only 20 files changed, 73 insertions(+), 53 deletions(-)
Title: Joint Quantile and Expected Shortfall Regression
Description: Simultaneous modeling of the quantile and the expected shortfall of a response variable given
a set of covariates, see Dimitriadis and Bayer (2019) <doi:10.1214/19-EJS1560>.
Author: Sebastian Bayer [aut, cre],
Timo Dimitriadis [aut]
Maintainer: Sebastian Bayer <sebastian.bayer@uni-konstanz.de>
Diff between esreg versions 0.4.0 dated 2019-01-09 and 0.5.0 dated 2019-11-15
DESCRIPTION | 12 - MD5 | 32 ++- NAMESPACE | 8 NEWS.md | 4 R/RcppExports.R | 46 +++++ R/esreg.R | 313 +++++++++++++++++++++++++++++---------- R/nuisance_quantities.R | 101 ++++++++---- man/G1_prime_prime_fun.Rd |only man/G2_prime_prime.Rd |only man/cdf_at_quantile.Rd |only man/conditional_mean_sigma.Rd |only man/density_quantile_function.Rd | 4 man/esreg.Rd | 22 +- man/estfun.esreg.Rd |only man/lambda_matrix.Rd |only man/sigma_matrix.Rd |only man/vcov.esreg.Rd | 2 man/vcovA.Rd | 37 ++-- src/RcppExports.cpp | 92 +++++++++++ src/sandwich_loops.cpp |only src/target_functions.cpp | 68 ++++++++ 21 files changed, 585 insertions(+), 156 deletions(-)
Title: Rho for Inter Rater Reliability
Description: Rho is used to test the generalization of inter rater reliability
(IRR) statistics. Calculating rho starts by generating a large number of
simulated, fully-coded data sets: a sizable collection of hypothetical
populations, all of which have a kappa value below a given threshold -- which
indicates unacceptable agreement. Then kappa is calculated on a sample from
each of those sets in the collection to see if it is equal to or higher than
the kappa in then real sample. If less than five percent of the distribution
of samples from the simulated data sets is greater than actual observed kappa,
the null hypothesis is rejected and one can conclude that if the two raters had
coded the rest of the data, we would have acceptable agreement (kappa above the
threshold).
Author: Brendan Eagan [aut],
Brad Rogers [aut],
Rebecca Pozen [aut],
Cody L Marquart [cre, aut] (<https://orcid.org/0000-0002-3387-6792>),
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rhoR versions 1.2.1.2 dated 2019-11-05 and 1.3.0.0 dated 2019-11-15
rhoR-1.2.1.2/rhoR/README.md |only rhoR-1.2.1.2/rhoR/tests/testthat/test-test-rho.R |only rhoR-1.3.0.0/rhoR/DESCRIPTION | 30 - rhoR-1.3.0.0/rhoR/MD5 | 144 ++++-- rhoR-1.3.0.0/rhoR/NAMESPACE | 20 rhoR-1.3.0.0/rhoR/NEWS.md | 3 rhoR-1.3.0.0/rhoR/R/RcppExports.R |only rhoR-1.3.0.0/rhoR/R/baserate.R | 12 rhoR-1.3.0.0/rhoR/R/baserateCT.R | 3 rhoR-1.3.0.0/rhoR/R/baserateSet.R | 7 rhoR-1.3.0.0/rhoR/R/calcKappa.R | 1 rhoR-1.3.0.0/rhoR/R/calcRho.R | 70 +-- rhoR-1.3.0.0/rhoR/R/calculations.R |only rhoR-1.3.0.0/rhoR/R/checkBRPKcombo.R | 1 rhoR-1.3.0.0/rhoR/R/codeSet.R | 1 rhoR-1.3.0.0/rhoR/R/contingencyTable.R | 1 rhoR-1.3.0.0/rhoR/R/createRandomSet.R | 13 rhoR-1.3.0.0/rhoR/R/createSimulatedCodeSet.R | 16 rhoR-1.3.0.0/rhoR/R/genPKcombo.R | 16 rhoR-1.3.0.0/rhoR/R/genPcombo.R | 1 rhoR-1.3.0.0/rhoR/R/generateKPs.R | 13 rhoR-1.3.0.0/rhoR/R/getBootPvalue.R | 5 rhoR-1.3.0.0/rhoR/R/getHandSet.R | 71 ++- rhoR-1.3.0.0/rhoR/R/getR.R | 1 rhoR-1.3.0.0/rhoR/R/getTestSet.R | 8 rhoR-1.3.0.0/rhoR/R/kappa.R | 7 rhoR-1.3.0.0/rhoR/R/kappaCT.R | 8 rhoR-1.3.0.0/rhoR/R/kappaSet.R | 3 rhoR-1.3.0.0/rhoR/R/prset.R | 18 rhoR-1.3.0.0/rhoR/R/rho.R | 81 +-- rhoR-1.3.0.0/rhoR/R/rho.file.R |only rhoR-1.3.0.0/rhoR/R/rhoCT.R | 57 +- rhoR-1.3.0.0/rhoR/R/rhoK.R | 87 ++-- rhoR-1.3.0.0/rhoR/R/rhoMin.R | 7 rhoR-1.3.0.0/rhoR/R/rhoR.R | 18 rhoR-1.3.0.0/rhoR/R/rhoSet.R | 34 - rhoR-1.3.0.0/rhoR/R/utils.R |only rhoR-1.3.0.0/rhoR/R/zzz.R |only rhoR-1.3.0.0/rhoR/demo/backup/c-benchmarks.R |only rhoR-1.3.0.0/rhoR/demo/backup/calcRho2.R |only rhoR-1.3.0.0/rhoR/demo/backup/compare.R |only rhoR-1.3.0.0/rhoR/demo/backup/coverage-report.R | 112 ++--- rhoR-1.3.0.0/rhoR/demo/backup/distTest.cpp |only rhoR-1.3.0.0/rhoR/demo/backup/mc-try-1.R |only rhoR-1.3.0.0/rhoR/demo/backup/performance-benchmarks.Rmd |only rhoR-1.3.0.0/rhoR/demo/backup/rhoCT.rmd |only rhoR-1.3.0.0/rhoR/demo/backup/rhoR-benchmarks.html |only rhoR-1.3.0.0/rhoR/demo/backup/rhoR-benchmarks.rmd |only rhoR-1.3.0.0/rhoR/demo/backup/run-mc.R |only rhoR-1.3.0.0/rhoR/demo/backup/sample.indices.R |only rhoR-1.3.0.0/rhoR/demo/backup/testRhoFile.R |only rhoR-1.3.0.0/rhoR/inst/docker/rhor-release | 4 rhoR-1.3.0.0/rhoR/inst/docker/rhor-release-test | 9 rhoR-1.3.0.0/rhoR/inst/extdata |only rhoR-1.3.0.0/rhoR/man/as.code.set.Rd |only rhoR-1.3.0.0/rhoR/man/as.contingency.table.Rd |only rhoR-1.3.0.0/rhoR/man/baserate.Rd | 3 rhoR-1.3.0.0/rhoR/man/baserateCT.Rd | 1 rhoR-1.3.0.0/rhoR/man/baserateSet.Rd | 1 rhoR-1.3.0.0/rhoR/man/cash-.rating.set.Rd |only rhoR-1.3.0.0/rhoR/man/contingency_table.Rd |only rhoR-1.3.0.0/rhoR/man/createSimulatedCodeSet.Rd | 4 rhoR-1.3.0.0/rhoR/man/generateKPs_c.Rd |only rhoR-1.3.0.0/rhoR/man/getBootPvalue_c.Rd |only rhoR-1.3.0.0/rhoR/man/getHandCT.Rd |only rhoR-1.3.0.0/rhoR/man/getHand_kappa.Rd |only rhoR-1.3.0.0/rhoR/man/getTestSet.Rd | 1 rhoR-1.3.0.0/rhoR/man/kappa.Rd | 1 rhoR-1.3.0.0/rhoR/man/kappaCT.Rd | 1 rhoR-1.3.0.0/rhoR/man/kappaSet.Rd | 1 rhoR-1.3.0.0/rhoR/man/kappa_ct.Rd |only rhoR-1.3.0.0/rhoR/man/random_contingency_table.Rd |only rhoR-1.3.0.0/rhoR/man/recall.Rd |only rhoR-1.3.0.0/rhoR/man/rho.Rd | 18 rhoR-1.3.0.0/rhoR/man/rho.file.Rd |only rhoR-1.3.0.0/rhoR/man/rhoCT.Rd | 16 rhoR-1.3.0.0/rhoR/man/rhoK.Rd | 21 rhoR-1.3.0.0/rhoR/man/rhoMin.Rd | 1 rhoR-1.3.0.0/rhoR/man/rhoR.Rd | 5 rhoR-1.3.0.0/rhoR/man/rhoSet.Rd | 13 rhoR-1.3.0.0/rhoR/man/sample_contingency_table.Rd |only rhoR-1.3.0.0/rhoR/src |only rhoR-1.3.0.0/rhoR/tests/testthat/test-genPKcombo.R | 54 ++ rhoR-1.3.0.0/rhoR/tests/testthat/test-rho-returns-pr.R |only rhoR-1.3.0.0/rhoR/tests/testthat/test-rho.R |only rhoR-1.3.0.0/rhoR/tests/testthat/test-rhoFile.R |only rhoR-1.3.0.0/rhoR/tests/testthat/test-test-createSimulatedCodeSet.R | 12 rhoR-1.3.0.0/rhoR/tests/testthat/test-util-methods.R | 216 +++++++++- rhoR-1.3.0.0/rhoR/tests/testthat/test.calckKappa.R | 7 rhoR-1.3.0.0/rhoR/tests/testthat/test.getHandSet.R | 28 + rhoR-1.3.0.0/rhoR/tests/testthat/test.getTestSet.R | 4 91 files changed, 817 insertions(+), 473 deletions(-)
Title: Estimate Global Clustering in Infectious Disease
Description: Implements various novel and standard
clustering statistics and other analyses useful for understanding the
spread of infectious disease.
Author: John Giles <giles@jhu.edu>, Henrik Salje <hsalje@jhsph.edu>, Justin Lessler <justin@jhu.edu>
Maintainer: Justin Lessler <justin@jhu.edu>
Diff between IDSpatialStats versions 0.3.5 dated 2018-06-12 and 0.3.10 dated 2019-11-15
IDSpatialStats-0.3.10/IDSpatialStats/DESCRIPTION | 14 IDSpatialStats-0.3.10/IDSpatialStats/MD5 | 191 - IDSpatialStats-0.3.10/IDSpatialStats/NAMESPACE | 6 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/est_transdist.R | 4 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/est_transdist_bootstrap_ci.R | 4 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/est_transdist_temporal.R | 11 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/est_transdist_temporal_bootstrap_ci.R | 90 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/est_transdist_theta_weights.R | 3 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/est_wt_matrix.R | 4 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/est_wt_matrix_weights.R | 4 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_cross_k.R |only IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_cross_pcf.R |only IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_pi.R | 6 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_pi_bootstrap.R | 8 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_pi_ci.R | 9 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_pi_permute.R | 9 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_pi_typed.R | 6 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_pi_typed_bootstrap.R | 6 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_pi_typed_permute.R | 6 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_tau.R | 70 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_tau_bootstrap.R | 9 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_tau_ci.R | 21 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_tau_permute.R | 8 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_tau_typed.R | 8 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_tau_typed_bootstrap.R | 28 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_tau_typed_permute.R | 21 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_theta.R | 6 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_theta_bootstrap.R | 54 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_theta_ci.R | 48 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_theta_permute.R | 51 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_theta_typed.R | 6 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_theta_typed_bootstrap.R | 6 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_theta_typed_permute.R | 9 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/get_transdist_theta.R | 4 IDSpatialStats-0.3.10/IDSpatialStats/R/examples/sim_epidemic.R | 28 IDSpatialStats-0.3.10/IDSpatialStats/R/spatialfuncs.r | 564 +++-- IDSpatialStats-0.3.10/IDSpatialStats/R/transdistfuncs.r | 1098 +++++----- IDSpatialStats-0.3.10/IDSpatialStats/R/wrapperfuncs.r |only IDSpatialStats-0.3.10/IDSpatialStats/data/DengueSimR01.rda |only IDSpatialStats-0.3.10/IDSpatialStats/data/DengueSimR02.rda |only IDSpatialStats-0.3.10/IDSpatialStats/data/DengueSimRepresentative.rda |only IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-getpi.r | 554 ++--- IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-getpibootstrap.r | 343 +-- IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-getpipermute.r | 313 +- IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-gettau.r | 548 ++-- IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-gettaubootstrap.r | 625 ++--- IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-gettaupermute.r | 360 +-- IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-gettheta.r | 328 +- IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-getthetabootstrap.r | 286 +- IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-getthetapermute.r | 126 - IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-simulateepidemic.r | 22 IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-thetaweights.r | 171 - IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-transdist.r | 25 IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-transdistbootstrapci.r | 14 IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-transdisttemporal.r | 53 IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-wallingateunis.r | 6 IDSpatialStats-0.3.10/IDSpatialStats/inst/tests/test-wrapperfuncs.r |only IDSpatialStats-0.3.10/IDSpatialStats/man/DengueSimR01.Rd | 12 IDSpatialStats-0.3.10/IDSpatialStats/man/DengueSimR02.Rd | 12 IDSpatialStats-0.3.10/IDSpatialStats/man/DengueSimRepresentative.Rd | 12 IDSpatialStats-0.3.10/IDSpatialStats/man/est.transdist.Rd | 12 IDSpatialStats-0.3.10/IDSpatialStats/man/est.transdist.bootstrap.ci.Rd | 7 IDSpatialStats-0.3.10/IDSpatialStats/man/est.transdist.temporal.Rd | 20 IDSpatialStats-0.3.10/IDSpatialStats/man/est.transdist.temporal.bootstrap.ci.Rd | 97 IDSpatialStats-0.3.10/IDSpatialStats/man/est.transdist.theta.weights.Rd | 6 IDSpatialStats-0.3.10/IDSpatialStats/man/est.wt.matrix.Rd | 7 IDSpatialStats-0.3.10/IDSpatialStats/man/est.wt.matrix.weights.Rd | 9 IDSpatialStats-0.3.10/IDSpatialStats/man/get.cross.K.Rd |only IDSpatialStats-0.3.10/IDSpatialStats/man/get.cross.PCF.Rd |only IDSpatialStats-0.3.10/IDSpatialStats/man/get.pi.Rd | 23 IDSpatialStats-0.3.10/IDSpatialStats/man/get.pi.bootstrap.Rd | 35 IDSpatialStats-0.3.10/IDSpatialStats/man/get.pi.ci.Rd | 36 IDSpatialStats-0.3.10/IDSpatialStats/man/get.pi.permute.Rd | 35 IDSpatialStats-0.3.10/IDSpatialStats/man/get.pi.typed.Rd | 11 IDSpatialStats-0.3.10/IDSpatialStats/man/get.pi.typed.bootstrap.Rd | 21 IDSpatialStats-0.3.10/IDSpatialStats/man/get.pi.typed.permute.Rd | 22 IDSpatialStats-0.3.10/IDSpatialStats/man/get.tau.Rd | 84 IDSpatialStats-0.3.10/IDSpatialStats/man/get.tau.bootstrap.Rd | 39 IDSpatialStats-0.3.10/IDSpatialStats/man/get.tau.ci.Rd | 37 IDSpatialStats-0.3.10/IDSpatialStats/man/get.tau.permute.Rd | 37 IDSpatialStats-0.3.10/IDSpatialStats/man/get.tau.typed.Rd | 17 IDSpatialStats-0.3.10/IDSpatialStats/man/get.tau.typed.bootstrap.Rd | 40 IDSpatialStats-0.3.10/IDSpatialStats/man/get.tau.typed.permute.Rd | 35 IDSpatialStats-0.3.10/IDSpatialStats/man/get.theta.Rd | 15 IDSpatialStats-0.3.10/IDSpatialStats/man/get.theta.bootstrap.Rd | 35 IDSpatialStats-0.3.10/IDSpatialStats/man/get.theta.ci.Rd | 33 IDSpatialStats-0.3.10/IDSpatialStats/man/get.theta.permute.Rd | 34 IDSpatialStats-0.3.10/IDSpatialStats/man/get.theta.typed.Rd | 13 IDSpatialStats-0.3.10/IDSpatialStats/man/get.theta.typed.bootstrap.Rd | 21 IDSpatialStats-0.3.10/IDSpatialStats/man/get.theta.typed.permute.Rd | 23 IDSpatialStats-0.3.10/IDSpatialStats/man/get.transdist.theta.Rd | 7 IDSpatialStats-0.3.10/IDSpatialStats/man/sim.epidemic.Rd | 34 IDSpatialStats-0.3.10/IDSpatialStats/man/sim.plot.Rd | 2 IDSpatialStats-0.3.10/IDSpatialStats/src/spatialfuncs.c | 10 IDSpatialStats-0.3.5/IDSpatialStats/build |only IDSpatialStats-0.3.5/IDSpatialStats/data/DengueSimRepresentative.RData |only IDSpatialStats-0.3.5/IDSpatialStats/data/DengueSimulationR01.RData |only IDSpatialStats-0.3.5/IDSpatialStats/data/DengueSimulationR02.RData |only IDSpatialStats-0.3.5/IDSpatialStats/inst/doc |only IDSpatialStats-0.3.5/IDSpatialStats/vignettes |only 100 files changed, 3908 insertions(+), 3179 deletions(-)
More information about IDSpatialStats at CRAN
Permanent link
Title: Functions for Spatial Thinning of Species Occurrence Records for
Use in Ecological Models
Description: A set of functions that can be used to spatially thin
species occurrence data. The resulting thinned data can be used in ecological
modeling, such as ecological niche modeling.
Author: Matthew E. Aiello-Lammens [aut, cre],
Robert A. Boria [aut],
Aleksandar Radosavljevic [aut],
Bruno Vilela [aut],
Robert P. Anderson [aut],
Robert Bjornson [ctb],
Steve Weston [ctb]
Maintainer: Matthew E. Aiello-Lammens <matt.lammens@gmail.com>
Diff between spThin versions 0.1.0.1 dated 2019-03-11 and 0.2.0 dated 2019-11-15
DESCRIPTION | 32 +++-- MD5 | 34 ++--- NAMESPACE | 5 R/plot_thin.R | 7 + R/thin.R | 5 R/thin.algorithm.R | 186 ++++++++++-------------------- README.md |only build/vignette.rds |binary data/Heteromys_anomalus_South_America.rda |binary inst/CITATION |only inst/doc/spThin_vignette.R | 50 +++----- inst/doc/spThin_vignette.Rmd | 51 ++++---- inst/doc/spThin_vignette.html | 148 +++++++---------------- man/Heteromys_anomalus_South_America.Rd | 10 - man/plotThin.Rd | 16 +- man/summaryThin.Rd | 6 man/thin.Rd | 37 +++-- man/thin.algorithm.Rd | 8 - vignettes/spThin_vignette.Rmd | 51 ++++---- 19 files changed, 289 insertions(+), 357 deletions(-)
Title: Calculates the Minimum Sample Size Required for Developing a
Multivariable Prediction Model
Description: Computes the minimum sample size required for the development of a new multivariable prediction model using the criteria proposed by Riley et al. (2018) <doi: 10.1002/sim.7992>. pmsampsize can be used to calculate the minimum sample size for the development of models with continuous, binary or survival (time-to-event) outcomes. Riley et al. (2018) <doi: 10.1002/sim.7992> lay out a series of criteria the sample size should meet. These aim to minimise the overfitting and to ensure precise estimation of key parameters in the prediction model.
Author: Joie Ensor [aut, cre],
Emma C. Martin [aut],
Richard D. Riley [aut]
Maintainer: Joie Ensor <j.ensor@keele.ac.uk>
Diff between pmsampsize versions 1.0.1 dated 2019-08-02 and 1.0.2 dated 2019-11-15
DESCRIPTION | 10 - MD5 | 14 - NAMESPACE | 2 NEWS.md | 8 + R/pmsampsize.R | 22 ++ R/pmsampsize_surv.R | 2 man/pmsampsize.Rd | 341 +++++++++++++++++++++++---------------------- tests/testthat/test_surv.R | 36 ++-- 8 files changed, 238 insertions(+), 197 deletions(-)
Title: Univariate Kernel Density Estimation
Description: Provides an efficient implementation of univariate local polynomial
kernel density estimators that can handle bounded and discrete data. See
Geenens (2014) <arXiv:1303.4121>,
Geenens and Wang (2018) <arXiv:1602.04862>,
Nagler (2018a) <arXiv:1704.07457>,
Nagler (2018b) <arXiv:1705.05431>.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between kde1d versions 1.0.0 dated 2019-11-15 and 1.0.1 dated 2019-11-15
DESCRIPTION | 8 ++-- MD5 | 28 ++++++++-------- NAMESPACE | 2 - NEWS.md | 23 +++++++++++-- R/jitter.R | 2 - R/kde1d-methods.R | 6 +-- inst/include/kde1d/dpik.hpp | 3 + inst/include/kde1d/interpolation.hpp | 60 ++++++++++++++++------------------- inst/include/kde1d/kde1d.hpp | 28 ++++++++-------- inst/include/kde1d/kdefft.hpp | 11 ++---- inst/include/kde1d/stats.hpp | 3 - inst/include/kde1d/tools.hpp | 43 ++++++++++++++----------- man/dkde1d.Rd | 2 - man/equi_jitter.Rd | 2 - tests/testthat/Rplots.pdf |binary 15 files changed, 122 insertions(+), 99 deletions(-)
Title: Australian Tax Policy Analysis
Description: Utilities for costing and evaluating Australian tax policy, including high-performance tax and transfer calculators, a fast method of projecting tax collections, and an interface to common indices from the Australian Bureau of Statistics. Written to support Grattan Institute's Australian Perspectives program. For access to the 'taxstats' package, please run
install.packages("taxstats", repos = "https://hughparsonage.github.io/tax-drat/", type = "source").
N.B. The 'taxstats' package is approximately 50 MB.
Author: Hugh Parsonage [aut, cre],
Tim Cameron [aut],
Brendan Coates [aut],
Matthew Katzen [aut],
William Young [aut],
Ittima Cherastidtham [dtc],
W. Karsten [ctb],
M. Enrique Garcia [ctb],
Matt Cowgill [aut]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between grattan versions 1.7.1.2 dated 2019-05-20 and 1.8.0.0 dated 2019-11-15
grattan-1.7.1.2/grattan/R/validate_fys_permitted.R |only grattan-1.7.1.2/grattan/man/validate_fys_permitted.Rd |only grattan-1.8.0.0/grattan/DESCRIPTION | 12 grattan-1.8.0.0/grattan/MD5 | 128 grattan-1.8.0.0/grattan/NAMESPACE | 1 grattan-1.8.0.0/grattan/NEWS.md | 426 - grattan-1.8.0.0/grattan/R/CG_inflator.R | 18 grattan-1.8.0.0/grattan/R/append_custom_series.R | 37 grattan-1.8.0.0/grattan/R/aus_pop_qtr_age.R | 226 grattan-1.8.0.0/grattan/R/awote.R | 8 grattan-1.8.0.0/grattan/R/carer_payment.R | 1 grattan-1.8.0.0/grattan/R/cpi_inflator.R | 7 grattan-1.8.0.0/grattan/R/cpi_inflator_quarters.R | 2 grattan-1.8.0.0/grattan/R/differentially_uprate_wage.R | 4 grattan-1.8.0.0/grattan/R/fy.year.R | 196 grattan-1.8.0.0/grattan/R/generic_inflator.R | 4 grattan-1.8.0.0/grattan/R/lf_inflator.R | 582 - grattan-1.8.0.0/grattan/R/medicare_levy.R | 9 grattan-1.8.0.0/grattan/R/model_income_tax.R | 1812 ++--- grattan-1.8.0.0/grattan/R/pension_supplement.R | 1 grattan-1.8.0.0/grattan/R/project.R | 14 grattan-1.8.0.0/grattan/R/project_to.R | 6 grattan-1.8.0.0/grattan/R/sysdata.rda |binary grattan-1.8.0.0/grattan/R/wage_inflator.R | 524 - grattan-1.8.0.0/grattan/README.md | 924 +- grattan-1.8.0.0/grattan/build/vignette.rds |binary grattan-1.8.0.0/grattan/data/residential_property_prices.rda |binary grattan-1.8.0.0/grattan/inst/doc/datatable-implementation.html | 4 grattan-1.8.0.0/grattan/inst/doc/grattan.R | 9 grattan-1.8.0.0/grattan/inst/doc/grattan.Rmd | 3119 +++++----- grattan-1.8.0.0/grattan/inst/doc/grattan.html | 17 grattan-1.8.0.0/grattan/inst/doc/model-income-tax.html | 4 grattan-1.8.0.0/grattan/inst/doc/v201515-taxstats.html | 4 grattan-1.8.0.0/grattan/man/cpi_inflator.Rd | 2 grattan-1.8.0.0/grattan/man/cpi_inflator_quarters.Rd | 2 grattan-1.8.0.0/grattan/man/differentially_uprate_wage.Rd | 2 grattan-1.8.0.0/grattan/man/figures/README_compare-30-37-42-thresholds-1.png | 280 grattan-1.8.0.0/grattan/man/figures/README_compare-30-37-42-thresholds-1.svg | 772 +- grattan-1.8.0.0/grattan/man/is.fy.Rd | 2 grattan-1.8.0.0/grattan/man/lf_inflator.Rd | 5 grattan-1.8.0.0/grattan/man/project.Rd | 4 grattan-1.8.0.0/grattan/man/wage_inflator.Rd | 2 grattan-1.8.0.0/grattan/tests/testthat/test_append_custom_series.R | 214 grattan-1.8.0.0/grattan/tests/testthat/test_aus_pop_fy_age.R | 30 grattan-1.8.0.0/grattan/tests/testthat/test_aus_pop_qtr.R | 169 grattan-1.8.0.0/grattan/tests/testthat/test_awote.R | 42 grattan-1.8.0.0/grattan/tests/testthat/test_carer_payment.R | 148 grattan-1.8.0.0/grattan/tests/testthat/test_child_care_subsidy.R | 2 grattan-1.8.0.0/grattan/tests/testthat/test_differentially_uprate_wage.R | 253 grattan-1.8.0.0/grattan/tests/testthat/test_income_tax_cpp.R | 172 grattan-1.8.0.0/grattan/tests/testthat/test_incometax_dotsATO.R | 162 grattan-1.8.0.0/grattan/tests/testthat/test_incometax_dotsATO_sfa.R | 56 grattan-1.8.0.0/grattan/tests/testthat/test_isfy.R | 196 grattan-1.8.0.0/grattan/tests/testthat/test_lf_inflator.R | 476 - grattan-1.8.0.0/grattan/tests/testthat/test_medicare_levy.R | 326 - grattan-1.8.0.0/grattan/tests/testthat/test_model_income_tax.R | 1902 +++--- grattan-1.8.0.0/grattan/tests/testthat/test_next_fy.R | 5 grattan-1.8.0.0/grattan/tests/testthat/test_project.R | 364 - grattan-1.8.0.0/grattan/tests/testthat/test_project_aus_pop.R | 68 grattan-1.8.0.0/grattan/tests/testthat/test_revenue_foregone.R | 92 grattan-1.8.0.0/grattan/tests/testthat/test_sapto.R | 444 - grattan-1.8.0.0/grattan/tests/testthat/test_utils.R | 306 grattan-1.8.0.0/grattan/tests/testthat/test_validate_fys.R | 10 grattan-1.8.0.0/grattan/tests/testthat/test_wage_inflator.R | 418 - grattan-1.8.0.0/grattan/vignettes/grattan-memory-usage.tsv | 130 grattan-1.8.0.0/grattan/vignettes/grattan.Rmd | 3119 +++++----- 66 files changed, 9119 insertions(+), 9155 deletions(-)
Title: Multi-Site Auto-Regressive Weather GENerator
Description: S3 and S4 functions are implemented for spatial multi-site
stochastic generation of daily time series of temperature and
precipitation. These tools make use of Vector AutoRegressive models (VARs).
The weather generator model is then saved as an object and is calibrated by
daily instrumental "Gaussianized" time series through the 'vars' package
tools. Once obtained this model, it can it can be used for weather
generations and be adapted to work with several climatic monthly time
series.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between RMAWGEN versions 1.3.3 dated 2017-02-10 and 1.3.6 dated 2019-11-15
DESCRIPTION | 12 - MD5 | 162 +++++++++--------- NAMESPACE | 3 R/GPCA_iteration.R | 2 R/RMAWGEN-package.R | 12 - R/adddate.R | 4 R/continuity_ratio.R | 36 ++-- R/extractdays.R | 8 R/extractmonths.R | 24 +- R/mmonths.R |only R/normalizeGaussian_prec.R | 12 - R/normalizeGaussian_sevaralstations.R | 49 +++++ R/normalizeGaussian_sevaralstations_prec.R | 4 R/plot.sample.R | 15 - R/rescaling_monthly.R | 2 R/splineInterpolateMonthlytoDaily.R | 2 data/trentino.rda |binary inst/doc/examples/test_lubridate |only man/ComprehensivePrecipitationGenerator.Rd | 30 +-- man/ComprehensiveTemperatureGenerator.Rd | 22 +- man/ElevationOf.Rd | 1 man/GPCA-class.Rd | 1 man/GPCA.Rd | 7 man/GPCA_iteration.Rd | 9 - man/GPCAiteration-class.Rd | 3 man/GPCAvarest2-class.Rd | 3 man/NewVAReventRealization.Rd | 7 man/PrecipitationEndDay.Rd | 1 man/PrecipitationStartDay.Rd | 1 man/RMAWGEN-package.Rd | 26 +- man/TemperatureEndDay.Rd | 1 man/TemperatureStartDay.Rd | 1 man/VAR_mod.Rd | 1 man/WhereIs.Rd | 1 man/acvWGEN.Rd | 4 man/adddate.Rd | 1 man/addsuffixes.Rd | 5 man/arch_test.Rd | 4 man/continuity_ratio.Rd | 13 - man/countNAs.Rd | 1 man/covariance.Rd | 13 - man/extractTnFromAnomalies.Rd | 1 man/extractTxFromAnomalies.Rd | 1 man/extractdays.Rd | 7 man/extractmonths.Rd | 21 +- man/extractyears.Rd | 5 man/findDate.Rd | 1 man/forecastEV.Rd | 1 man/forecastResidual.Rd | 7 man/generateTemperatureTimeseries.Rd | 11 - man/getDailyMean.Rd | 11 - man/getMonthlyMean.Rd | 1 man/getVARmodel.Rd | 1 man/inv_GPCA.Rd | 7 man/inv_GPCA_iteration.Rd | 5 man/is.monthly.climate.Rd | 10 - man/months_f.Rd |only man/newVARmultieventRealization.Rd | 1 man/normality_test.Rd | 1 man/normalizeGaussian.Rd | 1 man/normalizeGaussian_prec.Rd | 27 +-- man/normalizeGaussian_severalstations.Rd | 54 +++++- man/normalizeGaussian_severalstations_prec.Rd | 16 - man/plotDailyClimate.Rd | 7 man/plot_sample.Rd | 38 ++-- man/print.Rd | 7 man/qqplot.lagged.Rd | 1 man/qqplotTnTxWGEN.Rd | 5 man/qqplotTnTxWGEN_seasonal.Rd | 7 man/qqplotWGEN.Rd | 7 man/qqplot_RMAWGEN_Tx.Rd | 10 - man/qqplotprecWGEN.Rd | 5 man/qqplotprecWGEN_seasonal.Rd | 10 - man/removeNAs.Rd | 1 man/rescaling_monthly.Rd | 7 man/residuals.Rd | 3 man/serial_test.Rd | 1 man/setComprehensiveTemperatureGeneratorParameters.Rd | 7 man/splineInterpolateMonthlytoDaily.Rd | 10 - man/splineInterpolateMonthlytoDailyforSeveralYears.Rd | 10 - man/trentino.Rd | 4 man/varest-class.Rd | 3 man/varest2-class.Rd | 3 83 files changed, 459 insertions(+), 380 deletions(-)
Title: Nonparametric Methods for Cognitive Diagnosis
Description: An array of nonparametric and parametric estimation methods for cognitive diagnostic models, including nonparametric classification of examinee attribute profiles, joint maximum likelihood estimation (JMLE) of examinee attribute profiles and item parameters, and nonparametric refinement of the Q-matrix, as well as conditional maximum likelihood estimation (CMLE) of examinee attribute profiles given item parameters and CMLE of item parameters given examinee attribute profiles. Currently the nonparametric methods in the package support both conjunctive and disjunctive models, and the parametric methods in the package support the DINA model, the DINO model, the NIDA model, the G-NIDA model, and the R-RUM model.
Author: Yi Zheng [aut, cre],
Chia-Yi Chiu [aut],
Jeffrey A. Douglas [ctb]
Maintainer: Yi Zheng <yi.isabel.zheng@asu.edu>
Diff between NPCD versions 1.0-10 dated 2016-10-18 and 1.0-11 dated 2019-11-15
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 8 ++------ man/NPCD.Rd | 4 ++-- 4 files changed, 12 insertions(+), 16 deletions(-)
Title: Jump Q-Learning for Individualized Interval-Valued Dose Rule
Description: We provide tools to estimate the individualized interval-valued dose rule (I2DR) that maximizes the expected beneficial clinical outcome for each individual and returns an optimal interval-valued dose, by using the jump Q-learning (JQL) method. The jump Q-learning method directly models the conditional mean of the response given the dose level and the baseline covariates via jump penalized least squares regression under the framework of Q learning. We develop a searching algorithm by dynamic programming in order to find the optimal I2DR with the time complexity O(n2) and spatial complexity O(n). To alleviate the effects of misspecification of the Q-function, a residual jump Q-learning is further proposed to estimate the optimal I2DR. The outcome of interest includes the best partition of the entire dosage of interest, the regression coefficients of each partition, and the value function under the estimated I2DR as well as the Wald-type confidence interval of value function constructed through the Bootstrap.
Author: Hengrui Cai <hcai5@ncsu.edu>, Chengchun shi <cshi4@ncsu.edu>, Rui Song <rsong@ncsu.edu>, Wenbin Lu <wlu4@ncsu.edu>
Maintainer: Hengrui Cai <hcai5@ncsu.edu>
Diff between JQL versions 2.3.3 dated 2019-02-22 and 3.6.9 dated 2019-11-15
JQL-2.3.3/JQL/R/JQL.R |only JQL-2.3.3/JQL/man/JQL.Rd |only JQL-3.6.9/JQL/DESCRIPTION | 10 +++++----- JQL-3.6.9/JQL/MD5 | 16 ++++++++++------ JQL-3.6.9/JQL/NAMESPACE | 6 +++++- JQL-3.6.9/JQL/R/find.I2DR.R |only JQL-3.6.9/JQL/R/opt.dose.R | 16 ++++++++-------- JQL-3.6.9/JQL/R/tune.JQL.R |only JQL-3.6.9/JQL/R/tune.RJQL.R |only JQL-3.6.9/JQL/man/find.I2DR.Rd |only JQL-3.6.9/JQL/man/opt.dose.Rd | 10 +++++----- JQL-3.6.9/JQL/man/tune.JQL.Rd |only JQL-3.6.9/JQL/man/tune.RJQL.Rd |only 13 files changed, 33 insertions(+), 25 deletions(-)
Title: Assigns Colours to Values
Description: Maps one of the viridis colour palettes, or a user-specified palette to values.
Viridis colour maps are created by Stéfan van der Walt and Nathaniel Smith.
They were set as the default palette for the 'Python' 'Matplotlib' library,
introduced at SciPy 2015 conference <http://scipy2015.scipy.org/ehome/index.php?eventid=115969&>.
Other palettes available in this library have been derived from
'RColorBrewer' <https://CRAN.R-project.org/package=RColorBrewer> and
'colorspace' <https://CRAN.R-project.org/package=colorspace> packages.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between colourvalues versions 0.3.0 dated 2019-09-23 and 0.3.1 dated 2019-11-15
DESCRIPTION | 8 ++-- MD5 | 17 ++++----- R/RcppExports.R | 4 ++ inst/include/colourvalues/alpha/alpha.hpp | 35 ++++++++++--------- inst/include/colourvalues/colours/colours_hex.hpp | 10 ++--- inst/include/colourvalues/colours/colours_rgb.hpp | 10 ++--- src/RcppExports.cpp | 13 +++++++ src/alpha.cpp |only tests/testthat/test-alpha.R | 40 ++++++++++++++++++++++ tests/testthat/test-colour_values_hex.R | 1 10 files changed, 100 insertions(+), 38 deletions(-)
Title: Submit R Calculations to a 'Slurm' Cluster
Description: Functions that simplify submitting R scripts to a 'Slurm'
workload manager, in part by automating the division of embarrassingly
parallel calculations across cluster nodes.
Author: Philippe Marchand [aut],
Ian Carroll [aut],
Mike Smorul [ctb],
Rachael Blake [ctb],
Quentin Read [ctb, cre]
Maintainer: Quentin Read <qread@sesync.org>
Diff between rslurm versions 0.4.0 dated 2017-10-19 and 0.5.0 dated 2019-11-15
rslurm-0.4.0/rslurm/R/cancel_print_cleanup.R |only rslurm-0.4.0/rslurm/inst/NEWS.Rd |only rslurm-0.4.0/rslurm/man/print_job_status.Rd |only rslurm-0.5.0/rslurm/DESCRIPTION | 32 rslurm-0.5.0/rslurm/MD5 | 85 - rslurm-0.5.0/rslurm/NAMESPACE | 23 rslurm-0.5.0/rslurm/NEWS.md |only rslurm-0.5.0/rslurm/R/cancel_cleanup.R |only rslurm-0.5.0/rslurm/R/get_job_status.R |only rslurm-0.5.0/rslurm/R/get_slurm_out.R | 131 +- rslurm-0.5.0/rslurm/R/print_job_status.R |only rslurm-0.5.0/rslurm/R/rslurm-deprecated.R |only rslurm-0.5.0/rslurm/R/rslurm-package.R | 156 +- rslurm-0.5.0/rslurm/R/slurm_apply.R | 351 +++--- rslurm-0.5.0/rslurm/R/slurm_call.R | 265 ++-- rslurm-0.5.0/rslurm/R/slurm_job.R | 42 rslurm-0.5.0/rslurm/R/slurm_utils.R | 152 +- rslurm-0.5.0/rslurm/README.md | 122 +- rslurm-0.5.0/rslurm/build/vignette.rds |binary rslurm-0.5.0/rslurm/inst/doc/rslurm.Rmd | 396 +++---- rslurm-0.5.0/rslurm/inst/doc/rslurm.html | 601 +++++++---- rslurm-0.5.0/rslurm/inst/templates/slurm_run_R.txt | 43 rslurm-0.5.0/rslurm/inst/templates/slurm_run_single_R.txt | 28 rslurm-0.5.0/rslurm/inst/templates/submit_sh.txt | 25 rslurm-0.5.0/rslurm/inst/templates/submit_single_sh.txt | 24 rslurm-0.5.0/rslurm/man/cancel_slurm.Rd | 42 rslurm-0.5.0/rslurm/man/cleanup_files.Rd | 62 - rslurm-0.5.0/rslurm/man/get_job_status.Rd |only rslurm-0.5.0/rslurm/man/get_slurm_out.Rd | 85 - rslurm-0.5.0/rslurm/man/print_job_status-deprecated.Rd |only rslurm-0.5.0/rslurm/man/rslurm-deprecated.Rd |only rslurm-0.5.0/rslurm/man/rslurm-package.Rd | 172 +-- rslurm-0.5.0/rslurm/man/slurm_apply.Rd | 233 ++-- rslurm-0.5.0/rslurm/man/slurm_call.Rd | 180 +-- rslurm-0.5.0/rslurm/man/slurm_job.Rd | 56 - rslurm-0.5.0/rslurm/tests/testthat.R | 8 rslurm-0.5.0/rslurm/tests/testthat/test-local_slurm_apply.R | 170 +-- rslurm-0.5.0/rslurm/tests/testthat/test-local_slurm_call.R | 66 - rslurm-0.5.0/rslurm/tests/testthat/test-slurm_apply.R | 154 +- rslurm-0.5.0/rslurm/tests/testthat/test-slurm_call.R | 70 - rslurm-0.5.0/rslurm/vignettes/_rslurm_test_apply/f.RDS |binary rslurm-0.5.0/rslurm/vignettes/_rslurm_test_apply/params.RDS |binary rslurm-0.5.0/rslurm/vignettes/_rslurm_test_apply/slurm_run.R | 41 rslurm-0.5.0/rslurm/vignettes/_rslurm_test_apply/submit.sh | 13 rslurm-0.5.0/rslurm/vignettes/_rslurm_test_call/f.RDS |binary rslurm-0.5.0/rslurm/vignettes/_rslurm_test_call/params.RDS |binary rslurm-0.5.0/rslurm/vignettes/_rslurm_test_call/slurm_run.R | 26 rslurm-0.5.0/rslurm/vignettes/_rslurm_test_call/submit.sh | 12 rslurm-0.5.0/rslurm/vignettes/rslurm.Rmd | 396 +++---- 49 files changed, 2345 insertions(+), 1917 deletions(-)
Title: Companion to Applied Regression
Description: Functions to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Third Edition, Sage, 2019.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Ben Bolker [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Pavel Krivitsky [ctb],
Rafael Laboissiere [ctb],
Martin Maechler [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Steve Walker [ctb],
David Winsemius [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 3.0-4 dated 2019-10-27 and 3.0-5 dated 2019-11-15
DESCRIPTION | 14 MD5 | 28 NEWS | 1705 ++++++++++++++++++++++++------------------------- R/bcnPower.R | 5 R/ceresPlots.R | 5 R/crPlots.R | 4 R/infIndexPlot.R | 3 R/invResPlot.R | 93 +- R/leveragePlots.R | 3 R/marginalModelPlot.R | 649 +++++++++--------- R/recode.R | 14 R/regLine.R | 4 R/residualPlots.R | 9 R/utility-functions.R | 1080 +++++++++++++++---------------- inst/doc/embedding.pdf |binary 15 files changed, 1815 insertions(+), 1801 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the
location of the species is needed and about the environmental conditions. To test
for significance habitat associations, one of the two components is randomized.
Methods are mainly based on Plotkin et al. (2000) <doi:10.1006/jtbi.2000.2158> and
Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>)
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between shar versions 1.0.1 dated 2019-09-10 and 1.1 dated 2019-11-15
shar-1.0.1/shar/tests/testthat/Rplots.pdf |only shar-1.0.1/shar/tests/testthat/test-print.rd_mar.R |only shar-1.0.1/shar/tests/testthat/test-print.rd_pat.R |only shar-1.0.1/shar/tests/testthat/test-print.rd_ras.R |only shar-1.1/shar/DESCRIPTION | 6 shar-1.1/shar/MD5 | 97 - shar-1.1/shar/NAMESPACE | 48 shar-1.1/shar/NEWS.md | 146 - shar-1.1/shar/R/RcppExports.R | 50 shar-1.1/shar/R/plot_energy.R | 8 shar-1.1/shar/R/print.rd_mar.R | 164 +- shar-1.1/shar/R/print.rd_pat.R | 173 +- shar-1.1/shar/R/print.rd_ras.R | 13 shar-1.1/shar/R/reconstruct_pattern_cluster.R | 8 shar-1.1/shar/R/reconstruct_pattern_hetero.R | 8 shar-1.1/shar/R/reconstruct_pattern_homo.R | 11 shar-1.1/shar/R/reconstruct_pattern_marks.R | 9 shar-1.1/shar/R/results_habitat_association.R | 4 shar-1.1/shar/build/vignette.rds |binary shar-1.1/shar/inst/doc/get_started.R | 80 - shar-1.1/shar/inst/doc/get_started.html | 780 ++++------ shar-1.1/shar/man/calculate_energy.Rd | 124 - shar-1.1/shar/man/classify_habitats.Rd | 94 - shar-1.1/shar/man/create_neighbourhood.Rd | 68 shar-1.1/shar/man/estimate_pcf_fast.Rd | 84 - shar-1.1/shar/man/extract_points.Rd | 54 shar-1.1/shar/man/fit_point_process.Rd | 82 - shar-1.1/shar/man/gamma_test.Rd | 28 shar-1.1/shar/man/landscape.Rd | 36 shar-1.1/shar/man/plot_energy.Rd | 78 - shar-1.1/shar/man/plot_randomized_pattern.Rd | 96 - shar-1.1/shar/man/plot_randomized_raster.Rd | 84 - shar-1.1/shar/man/print.rd_ras.Rd | 62 shar-1.1/shar/man/random_walk.Rd | 28 shar-1.1/shar/man/randomize_raster.Rd | 100 - shar-1.1/shar/man/rcpp_sample.Rd | 54 shar-1.1/shar/man/reconstruct_pattern_cluster.Rd | 174 +- shar-1.1/shar/man/reconstruct_pattern_hetero.Rd | 178 +- shar-1.1/shar/man/reconstruct_pattern_homo.Rd | 174 +- shar-1.1/shar/man/reconstruct_pattern_marks.Rd | 154 - shar-1.1/shar/man/reconstruction.Rd | 28 shar-1.1/shar/man/results_habitat_association.Rd | 104 - shar-1.1/shar/man/shar.Rd | 62 shar-1.1/shar/man/species_a.Rd | 28 shar-1.1/shar/man/species_b.Rd | 28 shar-1.1/shar/man/torus_trans.Rd | 28 shar-1.1/shar/man/translate_raster.Rd | 96 - shar-1.1/shar/tests/testthat/test-calculate_energy.R | 9 shar-1.1/shar/tests/testthat/test-plot_energy.R | 8 shar-1.1/shar/tests/testthat/test-plot_randomized_raster.R | 36 shar-1.1/shar/tests/testthat/test-print.R |only shar-1.1/shar/tests/testthat/test-results_habitat_association.R | 16 52 files changed, 1954 insertions(+), 1846 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Author: Sacha Epskamp [aut, cre],
Giulio Costantini [aut],
Jonas Haslbeck [aut],
Adela Isvoranu [aut],
Angelique O. J. Cramer [ctb],
Lourens J. Waldorp [ctb],
Verena D. Schmittmann [ctb],
Denny Borsboom [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.6.3 dated 2019-06-19 and 1.6.4 dated 2019-11-15
DESCRIPTION | 9 +++++---- MD5 | 18 ++++++++++-------- NAMESPACE | 7 +++++++ NEWS | 6 ++++++ R/PLOT.R | 6 ++++-- R/as_ggraph.R |only R/cor_auto.R | 2 +- R/qgraph.R | 35 +++++++++++++++++++++++++++++++---- man/as.ggraph.Rd |only man/cor_auto.Rd | 2 +- man/qgraph.Rd | 1 + 11 files changed, 66 insertions(+), 20 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as getting database specific taxonomic identifiers, verifying
species names, getting taxonomic hierarchies, fetching downstream and
upstream taxonomic names, getting taxonomic synonyms, converting
scientific to common names and vice versa, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Eduard Szoecs [aut],
Zachary Foster [aut],
Zebulun Arendsee [aut],
Carl Boettiger [ctb],
Karthik Ram [ctb],
Ignasi Bartomeus [ctb],
John Baumgartner [ctb],
James O'Donnell [ctb],
Jari Oksanen [ctb],
Bastian Greshake Tzovaras [ctb],
Philippe Marchand [ctb],
Vinh Tran [ctb],
Maëlle Salmon [ctb],
Gaopeng Li [ctb],
Matthias Grenié [ctb],
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.9.9 dated 2019-10-17 and 0.9.91 dated 2019-11-15
DESCRIPTION | 11 MD5 | 227 +++-- NEWS.md | 23 R/children.R | 11 R/classification.R | 20 R/col_children.R | 7 R/col_downstream.R | 6 R/col_search.R | 103 +- R/comm2sci.R | 8 R/downstream.R | 5 R/genbank2uid.R | 6 R/get_colid.R | 7 R/get_ids.R | 31 R/get_uid.R | 11 R/id2name.R | 13 R/lowest_common.R | 1 R/ncbi_children.R | 17 R/ncbi_get_taxon_summary.R | 7 R/onload.R |only R/ping.R | 6 R/sci2comm.R | 11 R/synonyms.R | 6 R/tax_agg.R | 6 R/tax_rank.R | 7 R/taxize-package.R | 8 R/upstream.R | 2 R/zzz.R | 13 README.md | 2 man/children.Rd | 7 man/classification.Rd | 6 man/col_children.Rd | 9 man/col_downstream.Rd | 9 man/col_search.Rd | 42 - man/col_search_paginate.Rd | 5 man/comm2sci.Rd | 6 man/genbank2uid.Rd | 6 man/get_colid.Rd | 9 man/get_ids.Rd | 15 man/get_uid.Rd | 6 man/id2name.Rd | 6 man/ncbi_children.Rd | 6 man/ncbi_get_taxon_summary.Rd | 6 man/ping.Rd | 6 man/progressor.Rd | 2 man/sci2comm.Rd | 6 man/tax_agg.Rd | 4 man/tax_rank.Rd | 2 man/taxize-package.Rd | 10 tests/fixtures/children_ambiguous_ncbi.yml |only tests/fixtures/children_warn_on_db_mismatch.yml |only tests/fixtures/children_with_id.yml | 694 +++++++++++++++--- tests/fixtures/classification_warn_on_db_mismatch.yml |only tests/fixtures/col_search_older_checklist_xml.yml |only tests/fixtures/downstream_warn_on_db_mismatch.yml |only tests/fixtures/id2name_warn_on_db_mismatch.yml |only tests/fixtures/ncbi_children.yml | 189 ++-- tests/fixtures/ncbi_children_ambiguous.yml |only tests/fixtures/sci2comm_warn_on_db_mismatch.yml |only tests/fixtures/synonyms_warn_on_db_mismatch.yml |only tests/fixtures/upstream.yml |only tests/testthat/Rplots.pdf |binary tests/testthat/test-apgscraping.R | 2 tests/testthat/test-bold_search.R | 1 tests/testthat/test-children.R | 52 + tests/testthat/test-classification-pow.R | 7 tests/testthat/test-classification.R | 14 tests/testthat/test-col_children.R | 2 tests/testthat/test-col_downstream.R | 2 tests/testthat/test-col_search.R | 22 tests/testthat/test-col_search_paginate.R | 36 tests/testthat/test-comm2sci.R | 11 tests/testthat/test-downstream.R | 19 tests/testthat/test-eubon.R | 1 tests/testthat/test-fungorum.R | 5 tests/testthat/test-gbif_downstream.R | 3 tests/testthat/test-gbif_parse.R | 1 tests/testthat/test-get_boldid.R | 7 tests/testthat/test-get_colid.R | 10 tests/testthat/test-get_gbifid.R | 7 tests/testthat/test-get_ids.R | 14 tests/testthat/test-get_natservid.R | 4 tests/testthat/test-get_pow.R | 2 tests/testthat/test-get_tsn.R | 2 tests/testthat/test-get_wormsid.R | 5 tests/testthat/test-gni_details.R | 1 tests/testthat/test-gni_parse.R | 1 tests/testthat/test-gni_search.R | 1 tests/testthat/test-gnr_datasources.R | 1 tests/testthat/test-gnr_resolve.R | 4 tests/testthat/test-id2name.R | 9 tests/testthat/test-ion.R | 2 tests/testthat/test-ipni_search.R | 3 tests/testthat/test-itis_acceptname.R | 2 tests/testthat/test-itis_downstream.R | 3 tests/testthat/test-itis_getrecord.R | 1 tests/testthat/test-itis_hierarchy.R | 1 tests/testthat/test-itis_kingdomnames.R | 3 tests/testthat/test-itis_lsid.R | 1 tests/testthat/test-itis_native.R | 1 tests/testthat/test-itis_ping.R | 2 tests/testthat/test-itis_refs.R | 1 tests/testthat/test-itis_taxrank.R | 1 tests/testthat/test-itis_terms.R | 1 tests/testthat/test-iucn_id.R | 1 tests/testthat/test-iucn_summary.R | 2 tests/testthat/test-lowest_common.R | 4 tests/testthat/test-ncbi_children.R | 18 tests/testthat/test-ping.R | 36 tests/testthat/test-plantminer.R | 2 tests/testthat/test-pow_search.R | 3 tests/testthat/test-sci2comm.R | 9 tests/testthat/test-synonyms.R | 13 tests/testthat/test-tax_agg.R | 10 tests/testthat/test-tax_name.R | 1 tests/testthat/test-tax_rank.R | 1 tests/testthat/test-tnrs.R | 2 tests/testthat/test-tnrs_sources.R | 1 tests/testthat/test-upstream.R |only tests/testthat/test-utils.R |only tests/testthat/test-vascan_search.r | 1 tests/testthat/test-worms_downstream.R | 3 121 files changed, 1549 insertions(+), 452 deletions(-)
Title: Companion to "Statistics Using R: An Integrative Approach"
Description: Access to the datasets and many of the functions used in "Statistics Using R: An Integrative Approach". These datasets include a subset of the National Education Longitudinal Study, the Framingham Heart Study, as well as several simulated datasets used in the examples throughout the textbook. The functions included in the package reproduce some of the functionality of 'Stata' that is not directly available in 'R'. The package also contains a tutorial on basic data frame management, including how to handle missing data.
Author: Daphna Harel [cre, aut],
Sharon Weinberg [ctb],
Sarah Abramowitz [ctb]
Maintainer: Daphna Harel <daphna.harel@gmail.com>
Diff between sur versions 1.0.1 dated 2019-11-14 and 1.0.2 dated 2019-11-15
DESCRIPTION | 6 MD5 | 6 inst/tutorials/R_Basics/R_Basics.Rmd | 22 +-- inst/tutorials/R_Basics/R_Basics.html | 218 +++++++++++++++++----------------- 4 files changed, 126 insertions(+), 126 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. pathfindR is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
pathfindR also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in pathfindR are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for
Comprehensive Identification of Enriched Pathways in Omics Data Through
Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.
Author: Ege Ulgen [cre] (<https://orcid.org/0000-0003-2090-3621>),
Ozan Ozisik [aut] (<https://orcid.org/0000-0001-5980-8002>)
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 1.4.0 dated 2019-11-08 and 1.4.1 dated 2019-11-15
DESCRIPTION | 21 ++++-- MD5 | 80 ++++++++++++----------- NAMESPACE | 1 NEWS.md | 11 +++ R/core_functions.R | 22 +++++- R/java_ver_check.R |only R/pathfindR.R | 3 R/visualization_functions.R | 90 ++++++++++++++++---------- inst/doc/intro_vignette.R | 58 ++++++++-------- inst/doc/intro_vignette.html | 16 ++-- inst/doc/manual_execution.R | 16 ++-- inst/doc/manual_execution.Rmd | 2 inst/doc/manual_execution.html | 6 - inst/doc/non_hs_analysis.R | 26 +++---- inst/doc/non_hs_analysis.html | 4 - inst/rmd/enriched_terms.Rmd | 8 +- man/active_snw_search.Rd | 32 ++++++--- man/annotate_term_genes.Rd | 7 +- man/check_java_version.Rd |only man/cluster_enriched_terms.Rd | 11 ++- man/cluster_graph_vis.Rd | 9 ++ man/color_kegg_pathway.Rd | 9 ++ man/create_kappa_matrix.Rd | 7 +- man/enrichment.Rd | 11 ++- man/enrichment_analyses.Rd | 11 ++- man/enrichment_chart.Rd | 9 ++ man/fetch_gene_set.Rd | 10 ++ man/fetch_java_version.Rd |only man/filterActiveSnws.Rd | 8 +- man/fuzzy_term_clustering.Rd | 8 +- man/hierarchical_term_clustering.Rd | 11 ++- man/input_processing.Rd | 3 man/pathfindR.Rd | 1 man/plot_scores.Rd | 13 ++- man/run_pathfindR.Rd | 54 +++++++++++---- man/score_terms.Rd | 10 ++ man/summarize_enrichment_results.Rd | 3 man/term_gene_graph.Rd | 9 ++ man/visualize_hsa_KEGG.Rd | 17 ++++ man/visualize_terms.Rd | 9 ++ tests/testthat/test-java_ver_check.R |only tests/testthat/test-visualization_functions.R | 43 +++++++++++- vignettes/manual_execution.Rmd | 2 43 files changed, 450 insertions(+), 221 deletions(-)
Title: Tomoka Ohta D Statistics
Description: Calculate's Tomoka Ohta's partitioning of linkage disequilibrium,
deemed D-statistics, for pairs of loci. Petrowski et al. (2019) <doi:10.5334/jors.250>.
Author: Paul F. Petrowski <pfpetrowski@gmail.com> & Timothy M. Beissinger <timbeissinger@gmail.com>
Maintainer: Paul F. Petrowski <pfpetrowski@gmail.com>
Diff between ohtadstats versions 2.1.0 dated 2019-03-18 and 2.1.1 dated 2019-11-15
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- R/dparallel.R | 7 +++++-- man/dparallel.Rd | 2 +- 4 files changed, 16 insertions(+), 13 deletions(-)
Title: Covariate-Adjusted Receiver Operating Characteristic Curve
Inference
Description: Estimates the covariate-adjusted Receiver Operating Characteristic (AROC) curve and pooled (unadjusted) ROC curve by different methods. Inacio de Carvalho, V., and Rodriguez-Alvarez, M. X. (2018) <arXiv:1806.00473>.
Author: Maria Xose Rodriguez-Alvarez [aut, cre]
(<https://orcid.org/0000-0002-1329-9238>),
Vanda Inacio de Carvalho [aut]
(<https://orcid.org/0000-0001-8084-1616>)
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>
Diff between AROC versions 1.0 dated 2018-06-10 and 1.0-1 dated 2019-11-15
DESCRIPTION | 10 ++-- MD5 | 32 ++++++++------- NAMESPACE | 4 + R/AROC.f.R | 4 - R/bbase.interaction.factor.by.curve.os.R | 7 ++- R/bddp.R | 43 +++++++++++--------- R/compute.threshold.AROC.bnp.R | 37 ++++++++++------- R/compute.threshold.AROC.sp.R | 2 R/compute.threshold.pooledROC.BB.R |only R/compute.threshold.pooledROC.emp.R |only R/design.matrix.bnp.R | 65 ++++++++++++++++++++----------- R/interpret.AROCformula.R | 39 ++++++++---------- R/pooledROC.BB.R | 14 ++++-- R/pooledROC.emp.R | 1 R/predict.design.matrix.bnp.R | 37 +++++++++-------- build/partial.rdb |binary man/AROC-package.Rd | 4 - man/compute.threshold.pooledROC.BB.Rd |only man/compute.threshold.pooledROC.emp.Rd |only 19 files changed, 175 insertions(+), 124 deletions(-)
Title: A 'Shiny' App for Exploration of Text Collections
Description: Facilitates dynamic exploration of text collections through an
intuitive graphical user interface. The package contains 1) a helper function
to convert a data frame to a 'corporaexplorerobject', 2) a 'Shiny' app for
fast and flexible exploration of a 'corporaexplorerobject', and 3) a 'Shiny'
app for simple retrieval/extraction of documents from a 'corporaexplorerobject'
in a reading-friendly format.
Author: Kristian Lundby Gjerde [aut, cre]
Maintainer: Kristian Lundby Gjerde <kristian.gjerde@gmail.com>
Diff between corporaexplorer versions 0.6.3 dated 2019-10-06 and 0.7.0 dated 2019-11-15
corporaexplorer-0.6.3/corporaexplorer/inst/explorer/server/functions_checking_input_terms.R |only corporaexplorer-0.7.0/corporaexplorer/DESCRIPTION | 10 corporaexplorer-0.7.0/corporaexplorer/LICENSE |only corporaexplorer-0.7.0/corporaexplorer/MD5 | 63 ++-- corporaexplorer-0.7.0/corporaexplorer/NEWS.md | 23 + corporaexplorer-0.7.0/corporaexplorer/R/run_corpus_explorer.R | 153 +++++----- corporaexplorer-0.7.0/corporaexplorer/R/run_document_extractor.R | 3 corporaexplorer-0.7.0/corporaexplorer/README.md | 19 - corporaexplorer-0.7.0/corporaexplorer/data/test_data.rda |binary corporaexplorer-0.7.0/corporaexplorer/inst/download/global/config.R | 2 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/app.R | 21 - corporaexplorer-0.7.0/corporaexplorer/inst/explorer/config/config.R | 81 ++++- corporaexplorer-0.7.0/corporaexplorer/inst/explorer/config/config_convenience_functions.R |only corporaexplorer-0.7.0/corporaexplorer/inst/explorer/config/config_tests.R | 6 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/config/constants.R | 10 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/global/corpus_plot_functions/colours_to_plot_and_legend.R | 11 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/global/corpus_plot_functions/plotting_corpus_data_365.R | 4 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/global/corpus_plot_functions/plotting_corpus_data_dok.R | 4 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/global/corpus_plot_functions/plotting_corpus_day.R | 4 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/global/function_plot_size.R | 2 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/js_css/enter_search.js | 4 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/js_css/explorer_css.css | 89 ++--- corporaexplorer-0.7.0/corporaexplorer/inst/explorer/server/1_startup_actions.R | 3 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/server/2_event_search_button.R | 4 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/server/2_event_search_button/check_search_arguments.R | 75 ---- corporaexplorer-0.7.0/corporaexplorer/inst/explorer/server/2_event_search_button/update_session_variables.R | 10 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/server/functions_checking_input.R |only corporaexplorer-0.7.0/corporaexplorer/inst/explorer/server/functions_collect_input_terms.R | 16 - corporaexplorer-0.7.0/corporaexplorer/inst/explorer/tests/corpus_info_test.R | 4 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/tests/date_test.R | 4 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/ui/set_colours_in_search_fields.R |only corporaexplorer-0.7.0/corporaexplorer/inst/explorer/ui/ui_corpus_box.R | 10 corporaexplorer-0.7.0/corporaexplorer/inst/explorer/ui/ui_sidebar.R | 22 - corporaexplorer-0.7.0/corporaexplorer/man/prepare_data.Rd | 15 corporaexplorer-0.7.0/corporaexplorer/man/run_corpus_explorer.Rd | 99 ++++-- 35 files changed, 436 insertions(+), 335 deletions(-)
More information about corporaexplorer at CRAN
Permanent link
Title: Univariate Kernel Density Estimation
Description: Provides an efficient implementation of univariate local polynomial
kernel density estimators that can handle bounded and discrete data. See
Geenens (2014) <arXiv:1303.4121>,
Geenens and Wang (2018) <arXiv:1602.04862>,
Nagler (2018a) <arXiv:1704.07457>,
Nagler (2018b) <arXiv:1705.05431>.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between kde1d versions 0.4.0 dated 2019-04-11 and 1.0.0 dated 2019-11-15
kde1d-0.4.0/kde1d/R/kde1d_methods.R |only kde1d-0.4.0/kde1d/inst/include/dpik.hpp |only kde1d-0.4.0/kde1d/inst/include/interpolation.hpp |only kde1d-0.4.0/kde1d/inst/include/lpdens.hpp |only kde1d-0.4.0/kde1d/inst/include/stats.hpp |only kde1d-0.4.0/kde1d/inst/include/tools.hpp |only kde1d-0.4.0/kde1d/src/wrappers.cpp |only kde1d-1.0.0/kde1d/DESCRIPTION | 10 kde1d-1.0.0/kde1d/MD5 | 45 ++-- kde1d-1.0.0/kde1d/NAMESPACE | 3 kde1d-1.0.0/kde1d/NEWS.md | 25 ++ kde1d-1.0.0/kde1d/R/RcppExports.R | 40 +-- kde1d-1.0.0/kde1d/R/jitter.R |only kde1d-1.0.0/kde1d/R/kde1d-methods.R |only kde1d-1.0.0/kde1d/R/kde1d-package.R | 2 kde1d-1.0.0/kde1d/R/kde1d.R | 159 +++++++------- kde1d-1.0.0/kde1d/R/tools.R | 123 ++++++----- kde1d-1.0.0/kde1d/README.md | 3 kde1d-1.0.0/kde1d/inst/include/kde1d |only kde1d-1.0.0/kde1d/inst/include/kde1d-wrappers.hpp |only kde1d-1.0.0/kde1d/man/dkde1d.Rd | 17 - kde1d-1.0.0/kde1d/man/equi_jitter.Rd |only kde1d-1.0.0/kde1d/man/kde1d.Rd | 101 +++++---- kde1d-1.0.0/kde1d/man/plot.kde1d.Rd | 30 +- kde1d-1.0.0/kde1d/src/RcppExports.cpp | 68 +----- kde1d-1.0.0/kde1d/src/kde1d-interface.cpp |only kde1d-1.0.0/kde1d/tests/testthat/Rplots.pdf |only kde1d-1.0.0/kde1d/tests/testthat/test_kde1d.R | 244 +++++++++++----------- 28 files changed, 448 insertions(+), 422 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. Reference: Tsagris M, Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 1.9.5 dated 2019-07-12 and 1.9.6 dated 2019-11-15
Rfast-1.9.5/Rfast/R/Rnorm.R |only Rfast-1.9.5/Rfast/R/acg.mle.R |only Rfast-1.9.5/Rfast/R/allbetas.R |only Rfast-1.9.5/Rfast/R/ar1.R |only Rfast-1.9.5/Rfast/R/bc.R |only Rfast-1.9.5/Rfast/R/beta.mle.R |only Rfast-1.9.5/Rfast/R/betabinom.mle.R |only Rfast-1.9.5/Rfast/R/betageom.mle.R |only Rfast-1.9.5/Rfast/R/betaprime.mle.R |only Rfast-1.9.5/Rfast/R/bic.corfsreg.R |only Rfast-1.9.5/Rfast/R/bic.fs.reg.R |only Rfast-1.9.5/Rfast/R/binom.mle.R |only Rfast-1.9.5/Rfast/R/borel.mle.R |only Rfast-1.9.5/Rfast/R/bs.reg.R |only Rfast-1.9.5/Rfast/R/cauchy.mle.R |only Rfast-1.9.5/Rfast/R/chisq.mle.R |only Rfast-1.9.5/Rfast/R/colanovas.R |only Rfast-1.9.5/Rfast/R/colexp2.mle.R |only Rfast-1.9.5/Rfast/R/colgeom.mle.R |only Rfast-1.9.5/Rfast/R/colhameans.R |only Rfast-1.9.5/Rfast/R/colinvgauss.mle.R |only Rfast-1.9.5/Rfast/R/collaplace.mle.R |only Rfast-1.9.5/Rfast/R/collindley.mle.R |only Rfast-1.9.5/Rfast/R/colmaxboltz.mle.R |only Rfast-1.9.5/Rfast/R/colmeans.R |only Rfast-1.9.5/Rfast/R/colnormal.mle.R |only Rfast-1.9.5/Rfast/R/colnormlog.mle.R |only Rfast-1.9.5/Rfast/R/colpareto.mle.R |only Rfast-1.9.5/Rfast/R/colpoisson.mle.R |only Rfast-1.9.5/Rfast/R/colrange.R |only Rfast-1.9.5/Rfast/R/colrayleigh.mle.R |only Rfast-1.9.5/Rfast/R/colrint.regbx.R |only Rfast-1.9.5/Rfast/R/colsums.R |only Rfast-1.9.5/Rfast/R/colvarcomps.mle.R |only Rfast-1.9.5/Rfast/R/colvarcomps.mom.R |only Rfast-1.9.5/Rfast/R/colvm.mle.R |only Rfast-1.9.5/Rfast/R/colweibull.mle.R |only Rfast-1.9.5/Rfast/R/cor.fbed.R |only Rfast-1.9.5/Rfast/R/cor.fsreg.R |only Rfast-1.9.5/Rfast/R/correls.R |only Rfast-1.9.5/Rfast/R/ct.mle.R |only Rfast-1.9.5/Rfast/R/diri.nr2.R |only Rfast-1.9.5/Rfast/R/dirimultinom.mle.R |only Rfast-1.9.5/Rfast/R/exp2.mle.R |only Rfast-1.9.5/Rfast/R/expregs.R |only Rfast-1.9.5/Rfast/R/foldnorm.mle.R |only Rfast-1.9.5/Rfast/R/fs.reg.R |only Rfast-1.9.5/Rfast/R/gammanb.R |only Rfast-1.9.5/Rfast/R/gammanb.pred.R |only Rfast-1.9.5/Rfast/R/gammareg.R |only Rfast-1.9.5/Rfast/R/gammaregs.R |only Rfast-1.9.5/Rfast/R/gaussian.nb.R |only Rfast-1.9.5/Rfast/R/gaussiannb.pred.R |only Rfast-1.9.5/Rfast/R/geom.mle.R |only Rfast-1.9.5/Rfast/R/geom.nb.R |only Rfast-1.9.5/Rfast/R/geom.regs.R |only Rfast-1.9.5/Rfast/R/geomnb.pred.R |only Rfast-1.9.5/Rfast/R/glm_logistic.R |only Rfast-1.9.5/Rfast/R/glm_poisson.R |only Rfast-1.9.5/Rfast/R/group.all.R |only Rfast-1.9.5/Rfast/R/group.any.R |only Rfast-1.9.5/Rfast/R/group.mad.R |only Rfast-1.9.5/Rfast/R/group.max.R |only Rfast-1.9.5/Rfast/R/group.mean.R |only Rfast-1.9.5/Rfast/R/group.med.R |only Rfast-1.9.5/Rfast/R/group.min.R |only Rfast-1.9.5/Rfast/R/group.min_max.R |only Rfast-1.9.5/Rfast/R/group.sum.R |only Rfast-1.9.5/Rfast/R/group.var.R |only Rfast-1.9.5/Rfast/R/groupcolVars.R |only Rfast-1.9.5/Rfast/R/groupcorrels.R |only Rfast-1.9.5/Rfast/R/gumbel.mle.R |only Rfast-1.9.5/Rfast/R/halfnorm.mle.R |only Rfast-1.9.5/Rfast/R/hsecant01.mle.R |only Rfast-1.9.5/Rfast/R/iag.mle.R |only Rfast-1.9.5/Rfast/R/ibeta.mle.R |only Rfast-1.9.5/Rfast/R/invdir.mle.R |only Rfast-1.9.5/Rfast/R/invgauss.mle.R |only Rfast-1.9.5/Rfast/R/invgauss.reg.R |only Rfast-1.9.5/Rfast/R/invgauss.regs.R |only Rfast-1.9.5/Rfast/R/laplace.mle.R |only Rfast-1.9.5/Rfast/R/lindley.mle.R |only Rfast-1.9.5/Rfast/R/lmfit.R |only Rfast-1.9.5/Rfast/R/logcauchy.mle.R |only Rfast-1.9.5/Rfast/R/logistic.cat1.R |only Rfast-1.9.5/Rfast/R/logistic.mle.R |only Rfast-1.9.5/Rfast/R/logistic_only.R |only Rfast-1.9.5/Rfast/R/logitnorm.mle.R |only Rfast-1.9.5/Rfast/R/loglogistic.mle.R |only Rfast-1.9.5/Rfast/R/lognorm.mle.R |only Rfast-1.9.5/Rfast/R/logseries.mle.R |only Rfast-1.9.5/Rfast/R/lomax.mle.R |only Rfast-1.9.5/Rfast/R/maxboltz.mle.R |only Rfast-1.9.5/Rfast/R/multinom.mle.R |only Rfast-1.9.5/Rfast/R/multinom.nb.R |only Rfast-1.9.5/Rfast/R/multinom.reg.R |only Rfast-1.9.5/Rfast/R/multinom.regs.R |only Rfast-1.9.5/Rfast/R/multivmf.mle.R |only Rfast-1.9.5/Rfast/R/mvbetas.R |only Rfast-1.9.5/Rfast/R/mvlnorm.mle.R |only Rfast-1.9.5/Rfast/R/mvnorm.mle.R |only Rfast-1.9.5/Rfast/R/mvt.mle.R |only Rfast-1.9.5/Rfast/R/negbin.mle.R |only Rfast-1.9.5/Rfast/R/normal.mle.R |only Rfast-1.9.5/Rfast/R/normlog.mle.R |only Rfast-1.9.5/Rfast/R/normlog.reg.R |only Rfast-1.9.5/Rfast/R/normlog.regs.R |only Rfast-1.9.5/Rfast/R/omp.R |only Rfast-1.9.5/Rfast/R/ompr.R |only Rfast-1.9.5/Rfast/R/ordinal.mle.R |only Rfast-1.9.5/Rfast/R/pareto.mle.R |only Rfast-1.9.5/Rfast/R/poisson.cat1.R |only Rfast-1.9.5/Rfast/R/poisson.mle.R |only Rfast-1.9.5/Rfast/R/poisson_only.R |only Rfast-1.9.5/Rfast/R/prop.reg.R |only Rfast-1.9.5/Rfast/R/prop.regs.R |only Rfast-1.9.5/Rfast/R/qpois.regs.R |only Rfast-1.9.5/Rfast/R/racg.R |only Rfast-1.9.5/Rfast/R/rayleigh.mle.R |only Rfast-1.9.5/Rfast/R/rbing.R |only Rfast-1.9.5/Rfast/R/rbingham.R |only Rfast-1.9.5/Rfast/R/regression.R |only Rfast-1.9.5/Rfast/R/rint.mle.R |only Rfast-1.9.5/Rfast/R/rint.reg.R |only Rfast-1.9.5/Rfast/R/rint.regbx.R |only Rfast-1.9.5/Rfast/R/rint.regs.R |only Rfast-1.9.5/Rfast/R/rm.anova.R |only Rfast-1.9.5/Rfast/R/rm.anovas.R |only Rfast-1.9.5/Rfast/R/rm.lines.R |only Rfast-1.9.5/Rfast/R/rmvlaplace.R |only Rfast-1.9.5/Rfast/R/rmvnorm.R |only Rfast-1.9.5/Rfast/R/rmvt.R |only Rfast-1.9.5/Rfast/R/rowhameans.R |only Rfast-1.9.5/Rfast/R/rowmeans.R |only Rfast-1.9.5/Rfast/R/rowrange.R |only Rfast-1.9.5/Rfast/R/rowsums.R |only Rfast-1.9.5/Rfast/R/rvmf.R |only Rfast-1.9.5/Rfast/R/rvonmises.R |only Rfast-1.9.5/Rfast/R/score.betaregs.R |only Rfast-1.9.5/Rfast/R/score.expregs.R |only Rfast-1.9.5/Rfast/R/score.gammaregs.R |only Rfast-1.9.5/Rfast/R/score.geomregs.R |only Rfast-1.9.5/Rfast/R/score.glms.R |only Rfast-1.9.5/Rfast/R/score.invgaussregs.R |only Rfast-1.9.5/Rfast/R/score.multinomregs.R |only Rfast-1.9.5/Rfast/R/score.negbinregs.R |only Rfast-1.9.5/Rfast/R/score.weibregs.R |only Rfast-1.9.5/Rfast/R/score.ztpregs.R |only Rfast-1.9.5/Rfast/R/sort_mat.R |only Rfast-1.9.5/Rfast/R/sourceR.R |only Rfast-1.9.5/Rfast/R/sourceRd.R |only Rfast-1.9.5/Rfast/R/spatmed.reg.R |only Rfast-1.9.5/Rfast/R/spml.mle.R |only Rfast-1.9.5/Rfast/R/spml.reg.R |only Rfast-1.9.5/Rfast/R/spml.regs.R |only Rfast-1.9.5/Rfast/R/tobit.mle.R |only Rfast-1.9.5/Rfast/R/univglms.R |only Rfast-1.9.5/Rfast/R/univglms2.R |only Rfast-1.9.5/Rfast/R/varcomps.mle.R |only Rfast-1.9.5/Rfast/R/varcomps.mom.R |only Rfast-1.9.5/Rfast/R/vm.mle.R |only Rfast-1.9.5/Rfast/R/vmf.mle.R |only Rfast-1.9.5/Rfast/R/weib.reg.R |only Rfast-1.9.5/Rfast/R/weibull.mle.R |only Rfast-1.9.5/Rfast/R/wigner.mle.R |only Rfast-1.9.5/Rfast/R/wrapcauchy.mle.R |only Rfast-1.9.5/Rfast/R/zip.mle.R |only Rfast-1.9.5/Rfast/R/ztp.mle.R |only Rfast-1.9.5/Rfast/man/group.sum.Rd |only Rfast-1.9.5/Rfast/man/group.var.Rd |only Rfast-1.9.5/Rfast/src/sort_mat_p.cpp |only Rfast-1.9.5/Rfast/src/templates.h |only Rfast-1.9.6/Rfast/DESCRIPTION | 10 Rfast-1.9.6/Rfast/MD5 | 632 +++------- Rfast-1.9.6/Rfast/NAMESPACE | 37 Rfast-1.9.6/Rfast/NEWS.md | 86 + Rfast-1.9.6/Rfast/R/Sort.R | 30 Rfast-1.9.6/Rfast/R/Var.R | 32 Rfast-1.9.6/Rfast/R/col_mle.R |only Rfast-1.9.6/Rfast/R/directional_mle.R |only Rfast-1.9.6/Rfast/R/discrete_mle.R |only Rfast-1.9.6/Rfast/R/group.R | 90 - Rfast-1.9.6/Rfast/R/hamean.R |only Rfast-1.9.6/Rfast/R/knn.R | 10 Rfast-1.9.6/Rfast/R/mad2.R | 23 Rfast-1.9.6/Rfast/R/many_regression_models_correlations.R |only Rfast-1.9.6/Rfast/R/matrix.R | 9 Rfast-1.9.6/Rfast/R/mean.R |only Rfast-1.9.6/Rfast/R/median.R | 20 Rfast-1.9.6/Rfast/R/multivariate_mle.R |only Rfast-1.9.6/Rfast/R/naive_bayes.R |only Rfast-1.9.6/Rfast/R/pc.skel.R | 14 Rfast-1.9.6/Rfast/R/percentages_mle.R |only Rfast-1.9.6/Rfast/R/permcor.R | 10 Rfast-1.9.6/Rfast/R/permutation_combination.R | 6 Rfast-1.9.6/Rfast/R/positive_mle.R |only Rfast-1.9.6/Rfast/R/random_values_simulation.R |only Rfast-1.9.6/Rfast/R/ranef_mle_regressions_repeated_measures.R |only Rfast-1.9.6/Rfast/R/range.R |only Rfast-1.9.6/Rfast/R/real_mle.R |only Rfast-1.9.6/Rfast/R/regression_models.R |only Rfast-1.9.6/Rfast/R/rmdp.R | 2 Rfast-1.9.6/Rfast/R/s3operator.R | 30 Rfast-1.9.6/Rfast/R/score_tests.R |only Rfast-1.9.6/Rfast/R/source.R |only Rfast-1.9.6/Rfast/R/sum.R |only Rfast-1.9.6/Rfast/R/system_and_package.R | 14 Rfast-1.9.6/Rfast/R/variable_selection.R |only Rfast-1.9.6/Rfast/README.md |only Rfast-1.9.6/Rfast/inst |only Rfast-1.9.6/Rfast/man/AddToNamespace.Rd | 7 Rfast-1.9.6/Rfast/man/Diag.fill.Rd | 2 Rfast-1.9.6/Rfast/man/Lchoose.Rd | 4 Rfast-1.9.6/Rfast/man/Norm.Rd | 8 Rfast-1.9.6/Rfast/man/Outer.Rd | 2 Rfast-1.9.6/Rfast/man/Pmax.Rd | 8 Rfast-1.9.6/Rfast/man/Rfast-package.Rd | 40 Rfast-1.9.6/Rfast/man/Var.Rd | 9 Rfast-1.9.6/Rfast/man/XopY.sum.Rd | 4 Rfast-1.9.6/Rfast/man/acg.mle.Rd | 6 Rfast-1.9.6/Rfast/man/ancova1.Rd | 4 Rfast-1.9.6/Rfast/man/ancovas.Rd | 6 Rfast-1.9.6/Rfast/man/anova_propreg.Rd | 8 Rfast-1.9.6/Rfast/man/anova_quasipois.reg.Rd | 8 Rfast-1.9.6/Rfast/man/as.Rfast.function.Rd | 2 Rfast-1.9.6/Rfast/man/bc.Rd | 2 Rfast-1.9.6/Rfast/man/beta.mle.Rd | 12 Rfast-1.9.6/Rfast/man/bic.fs.reg.Rd | 4 Rfast-1.9.6/Rfast/man/bs.reg.Rd | 2 Rfast-1.9.6/Rfast/man/btmprobs.Rd | 2 Rfast-1.9.6/Rfast/man/checkNamespace.Rd | 2 Rfast-1.9.6/Rfast/man/check_data.Rd | 8 Rfast-1.9.6/Rfast/man/circlin.cor.Rd | 4 Rfast-1.9.6/Rfast/man/col.yule.Rd | 2 Rfast-1.9.6/Rfast/man/colAny.Rd | 2 Rfast-1.9.6/Rfast/man/colCumMaxs.Rd | 8 Rfast-1.9.6/Rfast/man/colMads.Rd | 10 Rfast-1.9.6/Rfast/man/colMedians.Rd | 4 Rfast-1.9.6/Rfast/man/colMins.Rd | 2 Rfast-1.9.6/Rfast/man/colOrder.Rd | 6 Rfast-1.9.6/Rfast/man/colPmax.Rd | 6 Rfast-1.9.6/Rfast/man/colShuffle.Rd | 2 Rfast-1.9.6/Rfast/man/colTrue.Rd | 2 Rfast-1.9.6/Rfast/man/colVars.Rd | 17 Rfast-1.9.6/Rfast/man/coldiffs.Rd | 2 Rfast-1.9.6/Rfast/man/colnth.Rd | 2 Rfast-1.9.6/Rfast/man/colprods.Rd | 4 Rfast-1.9.6/Rfast/man/colrange.Rd | 2 Rfast-1.9.6/Rfast/man/colrow.value.Rd | 4 Rfast-1.9.6/Rfast/man/columns.Rd | 2 Rfast-1.9.6/Rfast/man/colwatsons.Rd | 2 Rfast-1.9.6/Rfast/man/comb_n.Rd | 2 Rfast-1.9.6/Rfast/man/count_value.Rd | 6 Rfast-1.9.6/Rfast/man/cox.poisrat.Rd | 2 Rfast-1.9.6/Rfast/man/data.frame.to_matrix.Rd | 2 Rfast-1.9.6/Rfast/man/dcor.Rd | 4 Rfast-1.9.6/Rfast/man/dcor.ttest.Rd | 2 Rfast-1.9.6/Rfast/man/dcov.Rd | 4 Rfast-1.9.6/Rfast/man/diri.nr2.Rd | 2 Rfast-1.9.6/Rfast/man/dirknn.Rd | 5 Rfast-1.9.6/Rfast/man/dirknn.cv.Rd | 4 Rfast-1.9.6/Rfast/man/edist.Rd | 4 Rfast-1.9.6/Rfast/man/eigen.sym.Rd | 6 Rfast-1.9.6/Rfast/man/exact.ttest2.Rd | 2 Rfast-1.9.6/Rfast/man/fish.kent.Rd | 2 Rfast-1.9.6/Rfast/man/floyd.Rd | 4 Rfast-1.9.6/Rfast/man/freq.min.Rd | 2 Rfast-1.9.6/Rfast/man/fs.reg.Rd | 5 Rfast-1.9.6/Rfast/man/ftest.Rd | 10 Rfast-1.9.6/Rfast/man/g2Test.Rd | 4 Rfast-1.9.6/Rfast/man/gammamle.Rd | 2 Rfast-1.9.6/Rfast/man/gammareg.Rd | 10 Rfast-1.9.6/Rfast/man/gaussian.nb.Rd | 6 Rfast-1.9.6/Rfast/man/gaussiannb.pred.Rd | 2 Rfast-1.9.6/Rfast/man/gchi2Test.Rd | 6 Rfast-1.9.6/Rfast/man/glm_logistic.Rd | 4 Rfast-1.9.6/Rfast/man/group.Rd |only Rfast-1.9.6/Rfast/man/hash2list.Rd | 4 Rfast-1.9.6/Rfast/man/invdir.mle.Rd | 2 Rfast-1.9.6/Rfast/man/invgauss.reg.Rd | 2 Rfast-1.9.6/Rfast/man/knn.Rd | 6 Rfast-1.9.6/Rfast/man/kuiper.Rd | 8 Rfast-1.9.6/Rfast/man/logistic_only.Rd | 11 Rfast-1.9.6/Rfast/man/lower_tri.Rd | 2 Rfast-1.9.6/Rfast/man/mad2.Rd | 6 Rfast-1.9.6/Rfast/man/mat.mat.Rd | 2 Rfast-1.9.6/Rfast/man/med.Rd | 6 Rfast-1.9.6/Rfast/man/mediandir.Rd | 2 Rfast-1.9.6/Rfast/man/min_max.Rd | 2 Rfast-1.9.6/Rfast/man/multinom.mle.Rd | 4 Rfast-1.9.6/Rfast/man/multinom.reg.Rd | 4 Rfast-1.9.6/Rfast/man/mv.eeltest1.Rd | 2 Rfast-1.9.6/Rfast/man/mv.eeltest2.Rd | 4 Rfast-1.9.6/Rfast/man/mvbetas.Rd | 5 Rfast-1.9.6/Rfast/man/mvkurtosis.Rd | 2 Rfast-1.9.6/Rfast/man/mvnorm.mle.Rd | 2 Rfast-1.9.6/Rfast/man/mvt.mle.Rd | 6 Rfast-1.9.6/Rfast/man/normal.mle.Rd | 10 Rfast-1.9.6/Rfast/man/normlog.reg.Rd | 2 Rfast-1.9.6/Rfast/man/normlog.regs.Rd | 2 Rfast-1.9.6/Rfast/man/odds.ratio.Rd | 4 Rfast-1.9.6/Rfast/man/ordinal.mle.Rd | 4 Rfast-1.9.6/Rfast/man/percent.ttest.Rd | 2 Rfast-1.9.6/Rfast/man/percent.ttests.Rd | 2 Rfast-1.9.6/Rfast/man/permcor.Rd | 4 Rfast-1.9.6/Rfast/man/poisdisp.test.Rd | 12 Rfast-1.9.6/Rfast/man/poisson.anova.Rd | 8 Rfast-1.9.6/Rfast/man/poly.cor.Rd | 2 Rfast-1.9.6/Rfast/man/pooled.cov.Rd | 2 Rfast-1.9.6/Rfast/man/prop.reg.Rd | 4 Rfast-1.9.6/Rfast/man/qpois.reg.Rd | 8 Rfast-1.9.6/Rfast/man/racg.Rd | 4 Rfast-1.9.6/Rfast/man/rep_col.Rd | 2 Rfast-1.9.6/Rfast/man/rint.regbx.Rd | 2 Rfast-1.9.6/Rfast/man/rm.anova.Rd | 2 Rfast-1.9.6/Rfast/man/rm.lines.Rd | 8 Rfast-1.9.6/Rfast/man/rmvnorm.Rd | 4 Rfast-1.9.6/Rfast/man/rowMins.Rd | 2 Rfast-1.9.6/Rfast/man/rowTrue.Rd | 2 Rfast-1.9.6/Rfast/man/rvmf.Rd | 2 Rfast-1.9.6/Rfast/man/rvonmises.Rd | 2 Rfast-1.9.6/Rfast/man/score.glms.Rd | 5 Rfast-1.9.6/Rfast/man/sftests.Rd | 2 Rfast-1.9.6/Rfast/man/skew.Rd | 4 Rfast-1.9.6/Rfast/man/skew.test2.Rd | 4 Rfast-1.9.6/Rfast/man/sort_mat.Rd | 13 Rfast-1.9.6/Rfast/man/sort_unique.Rd | 2 Rfast-1.9.6/Rfast/man/spat.med.Rd | 6 Rfast-1.9.6/Rfast/man/spatmed.reg.Rd | 2 Rfast-1.9.6/Rfast/man/spdinv.Rd | 4 Rfast-1.9.6/Rfast/man/spml.reg.Rd | 3 Rfast-1.9.6/Rfast/man/squareform.Rd | 6 Rfast-1.9.6/Rfast/man/sscov.Rd | 2 Rfast-1.9.6/Rfast/man/submatrix.Rd | 2 Rfast-1.9.6/Rfast/man/topological_sort.Rd | 4 Rfast-1.9.6/Rfast/man/total.dist.Rd | 6 Rfast-1.9.6/Rfast/man/ttest.Rd | 6 Rfast-1.9.6/Rfast/man/ttest1.Rd | 4 Rfast-1.9.6/Rfast/man/twoway.anovas.Rd | 10 Rfast-1.9.6/Rfast/man/univglms.Rd | 8 Rfast-1.9.6/Rfast/man/varcomps.mom.Rd | 4 Rfast-1.9.6/Rfast/man/vm.mle.Rd | 6 Rfast-1.9.6/Rfast/man/weib.reg.Rd | 5 Rfast-1.9.6/Rfast/man/which.is.Rd | 2 Rfast-1.9.6/Rfast/man/yule.Rd | 4 Rfast-1.9.6/Rfast/man/zip.mle.Rd | 12 Rfast-1.9.6/Rfast/src/Diag.cpp | 4 Rfast-1.9.6/Rfast/src/Makevars | 2 Rfast-1.9.6/Rfast/src/Makevars.win | 2 Rfast-1.9.6/Rfast/src/Norm.cpp | 4 Rfast-1.9.6/Rfast/src/Rank.cpp | 4 Rfast-1.9.6/Rfast/src/Sort.cpp | 10 Rfast-1.9.6/Rfast/src/Table.cpp | 12 Rfast-1.9.6/Rfast/src/add_to_namespace.cpp | 63 Rfast-1.9.6/Rfast/src/apply_condition.cpp | 4 Rfast-1.9.6/Rfast/src/as_integer.cpp | 11 Rfast-1.9.6/Rfast/src/check.cpp | 45 Rfast-1.9.6/Rfast/src/cholesky.cpp | 4 Rfast-1.9.6/Rfast/src/col_row_utilities.cpp | 367 +---- Rfast-1.9.6/Rfast/src/col_row_utilities_p.cpp | 288 ---- Rfast-1.9.6/Rfast/src/col_statistical.cpp | 4 Rfast-1.9.6/Rfast/src/colrint_mle.cpp | 4 Rfast-1.9.6/Rfast/src/colweibull_mle.cpp | 2 Rfast-1.9.6/Rfast/src/cts.h | 2 Rfast-1.9.6/Rfast/src/dir_knn.cpp | 2 Rfast-1.9.6/Rfast/src/diri_nr_type2.cpp | 2 Rfast-1.9.6/Rfast/src/dista.cpp | 8 Rfast-1.9.6/Rfast/src/dists.cpp | 13 Rfast-1.9.6/Rfast/src/dists_vec.cpp | 4 Rfast-1.9.6/Rfast/src/each.cpp | 6 Rfast-1.9.6/Rfast/src/eigs_sym_c.cpp | 7 Rfast-1.9.6/Rfast/src/energy.cpp | 2 Rfast-1.9.6/Rfast/src/g2_export.cpp | 18 Rfast-1.9.6/Rfast/src/g2t.cpp | 6 Rfast-1.9.6/Rfast/src/gamma.cpp | 14 Rfast-1.9.6/Rfast/src/geom_regs.cpp | 2 Rfast-1.9.6/Rfast/src/glm.cpp | 6 Rfast-1.9.6/Rfast/src/group.cpp | 42 Rfast-1.9.6/Rfast/src/hash.cpp | 12 Rfast-1.9.6/Rfast/src/init.c | 58 Rfast-1.9.6/Rfast/src/is.cpp | 6 Rfast-1.9.6/Rfast/src/logistic_only.cpp | 28 Rfast-1.9.6/Rfast/src/lower_upper_tri.cpp | 16 Rfast-1.9.6/Rfast/src/matrices.cpp | 61 Rfast-1.9.6/Rfast/src/mn.cpp | 36 Rfast-1.9.6/Rfast/src/mn.h | 7 Rfast-1.9.6/Rfast/src/multinom_regs.cpp | 2 Rfast-1.9.6/Rfast/src/normlog_reg.cpp | 2 Rfast-1.9.6/Rfast/src/normlog_regs.cpp | 2 Rfast-1.9.6/Rfast/src/odds_helper.cpp | 2 Rfast-1.9.6/Rfast/src/partial_sort.cpp | 2 Rfast-1.9.6/Rfast/src/positive_negative.cpp | 8 Rfast-1.9.6/Rfast/src/prop.cpp | 6 Rfast-1.9.6/Rfast/src/qpois.cpp | 4 Rfast-1.9.6/Rfast/src/read.cpp | 53 Rfast-1.9.6/Rfast/src/reg_lib.cpp | 4 Rfast-1.9.6/Rfast/src/rep.cpp | 4 Rfast-1.9.6/Rfast/src/rint.cpp | 2 Rfast-1.9.6/Rfast/src/rmdp.cpp | 18 Rfast-1.9.6/Rfast/src/sort_mat.cpp | 118 - Rfast-1.9.6/Rfast/src/sort_unique.cpp | 8 Rfast-1.9.6/Rfast/src/spml.cpp | 4 Rfast-1.9.6/Rfast/src/system_files.cpp | 224 ++- Rfast-1.9.6/Rfast/src/system_files.h | 7 Rfast-1.9.6/Rfast/src/topological_sort.cpp | 2 Rfast-1.9.6/Rfast/src/total_dista.cpp | 2 Rfast-1.9.6/Rfast/src/total_dists.cpp | 2 Rfast-1.9.6/Rfast/src/utilities.cpp | 123 - Rfast-1.9.6/Rfast/src/varcomps_mle.cpp | 2 Rfast-1.9.6/Rfast/src/vecdist.cpp | 2 Rfast-1.9.6/Rfast/src/weib_reg.cpp | 2 Rfast-1.9.6/Rfast/src/weibull_mle.cpp | 12 412 files changed, 1451 insertions(+), 2048 deletions(-)
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial regression. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers listed in the URL below.
Author: Jerome Friedman [aut],
Trevor Hastie [aut, cre],
Rob Tibshirani [aut],
Balasubramanian Narasimhan [aut],
Noah Simon [aut],
Junyang Qian [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 3.0 dated 2019-11-09 and 3.0-1 dated 2019-11-15
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/Coxnet.pdf |binary inst/doc/glmnet.pdf |binary inst/doc/relax.pdf |binary 6 files changed, 14 insertions(+), 10 deletions(-)
Title: Statistics and Metrics for Seismic Data
Description: Classes and functions for metrics calculation as part of the
'IRIS DMC MUSTANG' project. The functionality in this package
builds upon the base classes of the 'IRISSeismic' package.
Metrics include basic statistics as well as higher level
'health' metrics that can help identify problematic seismometers.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Mary Templeton [aut],
Gillian Sharer [aut, cre]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>
Diff between IRISMustangMetrics versions 2.2.0 dated 2019-01-31 and 2.3.0 dated 2019-11-15
DESCRIPTION | 8 - MD5 | 14 +- NAMESPACE | 1 R/PSDMetric.R | 223 +++++++++++++++++++++----------------- R/STALTAMetric.R | 14 +- man/IRISMustangMetrics-package.Rd | 7 + man/PSDMetric.Rd | 5 man/getSingleValueMetrics.Rd | 2 8 files changed, 161 insertions(+), 113 deletions(-)
More information about IRISMustangMetrics at CRAN
Permanent link