Title: Scaled Logistic Regression
Description: Maximum likelihood estimation of the scaled logit model parameters
proposed in Dunning (2006) <doi:10.1002/sim.2282>.
Author: Arseniy Khvorov [aut, cre]
Maintainer: Arseniy Khvorov <khvorov45@gmail.com>
Diff between sclr versions 0.1.0 dated 2019-09-04 and 0.2.0 dated 2019-10-24
sclr-0.1.0/sclr/R/fitting.R |only sclr-0.1.0/sclr/data/sclr_one_titre_data.rda |only sclr-0.1.0/sclr/data/sclr_two_titre_data.rda |only sclr-0.1.0/sclr/man/sclr_one_titre_data.Rd |only sclr-0.1.0/sclr/man/sclr_two_titre_data.Rd |only sclr-0.1.0/sclr/tests/testthat/test_predict.R |only sclr-0.1.0/sclr/tests/testthat/test_sclr_return.R |only sclr-0.1.0/sclr/tests/testthat/test_sclr_usage.R |only sclr-0.2.0/sclr/DESCRIPTION | 8 - sclr-0.2.0/sclr/MD5 | 66 +++++----- sclr-0.2.0/sclr/NAMESPACE | 26 ++++ sclr-0.2.0/sclr/NEWS.md | 24 +++ sclr-0.2.0/sclr/R/data.R | 84 +++++++------ sclr-0.2.0/sclr/R/jacobian.R | 115 +++++++++++------- sclr-0.2.0/sclr/R/likelihood.R | 47 ++++--- sclr-0.2.0/sclr/R/mathfuns.R | 30 +++- sclr-0.2.0/sclr/R/methods.R | 74 +++++++---- sclr-0.2.0/sclr/R/protection.R | 29 ++-- sclr-0.2.0/sclr/R/sclr.R |only sclr-0.2.0/sclr/R/sclr_fit.R |only sclr-0.2.0/sclr/R/sclr_ideal_data.R |only sclr-0.2.0/sclr/R/scores.R | 65 +++++++--- sclr-0.2.0/sclr/R/utilities.R | 81 ++++++++---- sclr-0.2.0/sclr/README.md | 24 ++- sclr-0.2.0/sclr/data/one_titre_data.rda |only sclr-0.2.0/sclr/data/two_titre_data.rda |only sclr-0.2.0/sclr/inst/doc/Usage.R | 4 sclr-0.2.0/sclr/inst/doc/Usage.Rmd | 4 sclr-0.2.0/sclr/inst/doc/Usage.html | 104 ++++++++-------- sclr-0.2.0/sclr/man/coef.sclr.Rd | 20 ++- sclr-0.2.0/sclr/man/new_sclr.Rd |only sclr-0.2.0/sclr/man/one_titre_data.Rd |only sclr-0.2.0/sclr/man/print.sclr.Rd | 6 sclr-0.2.0/sclr/man/sclr.Rd | 66 ++++++---- sclr-0.2.0/sclr/man/sclr_fit.Rd | 37 +++-- sclr-0.2.0/sclr/man/sclr_ideal_data.Rd |only sclr-0.2.0/sclr/man/sclr_log_likelihood.Rd | 20 ++- sclr-0.2.0/sclr/man/two_titre_data.Rd |only sclr-0.2.0/sclr/tests/testthat/test-likelihood.R |only sclr-0.2.0/sclr/tests/testthat/test-methods.R |only sclr-0.2.0/sclr/tests/testthat/test-protection.R |only sclr-0.2.0/sclr/tests/testthat/test-sclr.R |only sclr-0.2.0/sclr/tests/testthat/test-sclr_fit.R |only sclr-0.2.0/sclr/tests/testthat/test-sclr_ideal_data.R |only sclr-0.2.0/sclr/tests/testthat/test-utilities.R |only sclr-0.2.0/sclr/vignettes/Usage.Rmd | 4 46 files changed, 598 insertions(+), 340 deletions(-)
Title: A Visual Tool for Behavior Analysis over Time
Description: A graphical R package designed to visualize behavioral observations over time. Based on raw time data extracted from video recorded sessions of experimental observations, ViSiElse grants a global overview of a process by combining the visualization of multiple actions timestamps for all participants in a single graph. Individuals and/or group behavior can easily be assessed. Supplementary features allow users to further inspect their data by adding summary statistics (mean, standard deviation, quantile or statistical test) and/or time constraints to assess the accuracy of the realized actions.
Author: Nastasia Fouret [aut, cph],
Mederic Descoins [aut, cph],
Elodie Garnier [aut, cre, cph],
CEPOI - EA 7388 [cph]
Maintainer: Elodie Garnier <e.garnier30@gmail.com>
Diff between ViSiElse versions 1.2.1 dated 2018-10-31 and 1.2.2 dated 2019-10-24
DESCRIPTION | 23 +- MD5 | 64 ++++-- NEWS.md | 11 + R/ConvertoViSibook.r | 4 R/ViSibook.r | 31 +-- R/ViSigrid.r | 6 R/buildL.r | 4 R/coffee.R |only R/initialize.ViSibook.r | 14 - R/intubation.R |only R/plot.ViSibook.R | 4 R/plotL.r | 6 R/plotpunctual.r | 2 R/shoppingBehavior.R |only R/summary.ViSigrid.r | 2 R/typDay.R |only R/visielse.r | 41 ++-- build/vignette.rds |binary data |only inst/doc/ViSiElSe_Paper_Walkthrough.R |only inst/doc/ViSiElSe_Paper_Walkthrough.Rmd |only inst/doc/ViSiElSe_Paper_Walkthrough.html |only inst/doc/ViSiElSe_Step_by_Step.R | 110 ++++++----- inst/doc/ViSiElSe_Step_by_Step.Rmd | 263 ++++++++++++++++----------- inst/doc/ViSiElSe_Step_by_Step.html | 296 ++++++++++++++++++------------- man/ConvertoViSibook.Rd | 4 man/ViSiElse.Rd | 41 ++-- man/ViSibook-class.Rd | 10 - man/ViSigrid-class.Rd | 6 man/coffee.Rd |only man/initialize-ViSibook-methods.Rd | 14 - man/intubation.Rd |only man/plot-ViSibook-methods.Rd | 4 man/shoppingBehavior.Rd |only man/summary-ViSigrid-methods.Rd | 2 man/typDay.Rd |only vignettes/ViSiElSe_Paper_Walkthrough.Rmd |only vignettes/ViSiElSe_Step_by_Step.Rmd | 263 ++++++++++++++++----------- 38 files changed, 701 insertions(+), 524 deletions(-)
Title: R Client for the eBird Database of Bird Observations
Description: A programmatic client for the eBird database, including functions
for searching for bird observations by geographic location (latitude,
longitude), eBird hotspots, location identifiers, by notable sightings, by
region, and by taxonomic name.
Author: Rafael Maia [aut],
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Andy Teucher [aut],
Guy Babineau [ctb],
Sebastian Pardo [aut, cre] (<https://orcid.org/0000-0002-4147-5796>)
Maintainer: Sebastian Pardo <sebpardo@gmail.com>
Diff between rebird versions 1.0.0 dated 2018-09-27 and 1.1.0 dated 2019-10-24
DESCRIPTION | 10 MD5 | 51 +-- NAMESPACE | 5 NEWS.md | 10 R/ebirdhistorical.R |only R/ebirdhotspot.R | 2 R/ebirdloc.R | 2 R/ebirdregioninfo.R | 64 +++- R/sysdata.rda |binary R/zzz.R | 16 - README.md | 319 ++++++++++++--------- build/vignette.rds |binary inst/doc/rebird_vignette.Rmd | 498 +++++++++++++++++++-------------- inst/doc/rebird_vignette.html | 487 ++++++++++++++++++-------------- inst/vign/rebird_vignette.Rmd | 29 + inst/vign/rebird_vignette.md | 498 +++++++++++++++++++-------------- man/ebirdhistorical.Rd |only man/ebirdregioninfo.Rd | 37 +- man/rebird-package.Rd | 5 tests/testthat/test-ebirdfreq.R | 4 tests/testthat/test-ebirdhistorical.R |only tests/testthat/test-ebirdhotspot.R | 4 tests/testthat/test-ebirdloc.R | 26 - tests/testthat/test-ebirdregion.R | 2 tests/testthat/test-ebirdregioncheck.R | 34 +- tests/testthat/test-ebirdregioninfo.R | 15 tests/testthat/test-nearestobs.R | 9 vignettes/rebird_vignette.Rmd | 498 +++++++++++++++++++-------------- 28 files changed, 1557 insertions(+), 1068 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-29 dated 2019-09-20 and 1.8-30 dated 2019-10-24
ChangeLog | 31 +++++++++++++++++++++ DESCRIPTION | 6 ++-- MD5 | 22 +++++++-------- R/bam.r | 77 ++++++++++++++++++++++++++++++++++++----------------- R/gam.fit4.r | 2 - R/gamlss.r | 15 ++++++---- R/mgcv.r | 22 ++++++++++----- R/plots.r | 9 ++++++ R/soap.r | 7 ++++ man/anova.gam.Rd | 6 ++-- man/in.out.Rd | 4 +- man/predict.gam.Rd | 2 - 12 files changed, 146 insertions(+), 57 deletions(-)
Title: Bayesian Effect Fusion for Categorical Predictors
Description: Variable selection and Bayesian effect fusion for categorical predictors in linear and
logistic regression models. Effect fusion aims at the question which categories have a similar
effect on the response and therefore can be fused to obtain a sparser representation of the model.
Effect fusion and variable selection can be obtained either with a prior that has an interpretation
as spike and slab prior on the level effect differences or with a sparse finite mixture prior on
the level effects. The regression coefficients are estimated with a flat uninformative prior after
model selection or by taking model averages. Posterior inference is accomplished by an MCMC
sampling scheme which makes use of a data augmentation strategy (Polson, Scott & Windle
(2013)) based on latent Polya-Gamma random variables in the case of logistic regression.
The code for data augmentation is taken from Polson et al. (2013), who own the copyright.
Author: Daniela Pauger [aut],
Magdalena Leitner [aut, cre],
Helga Wagner [aut] (<https://orcid.org/0000-0002-7003-9512>),
Gertraud Malsiner-Walli [aut] (<https://orcid.org/0000-0002-1213-4749>),
Nicholas G. Polson [ctb],
James G. Scott [ctb],
Jesse Windle [ctb],
Bettina Grün [ctb] (<https://orcid.org/0000-0001-7265-4773>)
Maintainer: Magdalena Leitner <effectfusion.jku@gmail.com>
Diff between effectFusion versions 1.1.1 dated 2019-01-19 and 1.1.2 dated 2019-10-24
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++------------- R/dic.R | 2 +- R/effect_fusion.R | 2 +- R/model.R | 2 +- R/plot.R | 2 +- R/print.R | 2 +- R/summary.R | 2 +- man/dic.Rd | 2 +- man/effectFusion.Rd | 2 +- man/model.Rd | 2 +- man/plot.fusion.Rd | 2 +- man/print.fusion.Rd | 2 +- man/summary.fusion.Rd | 2 +- 14 files changed, 31 insertions(+), 31 deletions(-)
Title: Descriptive mAchine Learning EXplanations
Description: Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance, but such black-box models usually lack of interpretability.
DALEX package contains various explainers that help to understand the link between input variables and model output.
The single_variable() explainer extracts conditional response of a model as a function of a single selected variable.
It is a wrapper over packages 'pdp' (Greenwell 2017) <doi:10.32614/RJ-2017-016>,
'ALEPlot' (Apley 2018) <arXiv:1612.08468> and 'factorMerger' (Sitko and Biecek 2017) <arXiv:1709.04412>.
The single_prediction() explainer attributes parts of a model prediction to particular variables used in the model.
It is a wrapper over 'breakDown' package (Staniak and Biecek 2018) <doi:10.32614/RJ-2018-072>.
The variable_dropout() explainer calculates variable importance scores based on variable shuffling
(Fisher at al. 2018) <arXiv:1801.01489>.
All these explainers can be plotted with generic plot() function and compared across different models.
'DALEX' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Szymon Maksymiuk [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 0.4.7 dated 2019-08-25 and 0.4.9 dated 2019-10-24
DESCRIPTION | 6 MD5 | 74 ++-- NAMESPACE | 140 ++++--- NEWS.md | 264 +++++++------- R/explain.R | 515 ++++++++++++++++------------- R/model_info.R |only R/titanic.R | 103 ++--- R/update.R |only R/yhat.R | 14 data/titanic_imputed.rda |binary man/HR.Rd | 66 +-- man/apartments.Rd | 58 +-- man/colors_drwhy.Rd | 58 +-- man/dragons.Rd | 64 +-- man/explain.Rd | 203 ++++++----- man/feature_response.Rd | 156 ++++---- man/figures/logo.png |binary man/install_dependencies.Rd | 32 - man/loss_functions.Rd | 84 ++-- man/model_info.Rd |only man/model_performance.Rd | 86 ++-- man/plot.feature_response_explainer.Rd | 88 ++-- man/plot.model_performance_explainer.Rd | 120 +++--- man/plot.prediction_breakdown_explainer.Rd | 170 ++++----- man/plot.variable_importance_explainer.Rd | 158 ++++---- man/plot.variable_response_explainer.Rd | 102 ++--- man/predict.Rd | 66 +-- man/prediction_breakdown.Rd | 154 ++++---- man/print.description.Rd | 32 - man/print.explainer.Rd | 62 +-- man/print.model_info.Rd |only man/print.model_performance_explainer.Rd | 56 +-- man/theme_drwhy.Rd | 44 +- man/titanic.Rd | 117 +++--- man/update_data.Rd |only man/update_label.Rd |only man/variable_importance.Rd | 124 +++--- man/variable_response.Rd | 144 ++++---- man/yhat.Rd | 140 ++++--- tests/testthat/helper-objects.R | 3 tests/testthat/test_explain.R | 60 ++- 41 files changed, 1868 insertions(+), 1695 deletions(-)
Title: Stochastic Gradient Markov Chain Monte Carlo
Description: Provides functions that performs popular stochastic gradient Markov chain Monte Carlo (SGMCMC) methods on user specified models. The required gradients are automatically calculated using 'TensorFlow' <https://www.tensorflow.org/>, an efficient library for numerical computation. This means only the log likelihood and log prior functions need to be specified. The methods implemented include stochastic gradient Langevin dynamics (SGLD), stochastic gradient Hamiltonian Monte Carlo (SGHMC), stochastic gradient Nose-Hoover thermostat (SGNHT) and their respective control variate versions for increased efficiency. References: M. Welling, Y. W. Teh (2011) <http://www.icml-2011.org/papers/398_icmlpaper.pdf>; T. Chen, E. B. Fox, C. E. Guestrin (2014) <arXiv:1402.4102>; N. Ding, Y. Fang, R. Babbush, C. Chen, R. D. Skeel, H. Neven (2014) <https://papers.nips.cc/paper/5592-bayesian-sampling-using-stochastic-gradient-thermostats>; J. Baker, P. Fearnhead, E. B. Fox, C. Nemeth (2017) <arXiv:1706.05439>. For more details see <doi:10.18637/jss.v091.i03>.
Author: Jack Baker [aut, cre, cph],
Christopher Nemeth [aut, cph],
Paul Fearnhead [aut, cph],
Emily B. Fox [aut, cph],
STOR-i [cph]
Maintainer: Jack Baker <jackbaker92@mail.com>
Diff between sgmcmc versions 0.2.4 dated 2019-05-01 and 0.2.5 dated 2019-10-24
DESCRIPTION | 12 MD5 | 17 - README.md | 22 + build/vignette.rds |binary inst/CITATION |only inst/doc/gaussMixture.html | 412 ++++++++++++++++++++++---------- inst/doc/logisticRegression.html | 405 ++++++++++++++++++++++--------- inst/doc/mvGauss.html | 362 ++++++++++++++++++++-------- inst/doc/nn.html | 497 ++++++++++++++++++++++++++------------- inst/doc/sgmcmc.html | 371 ++++++++++++++++++++--------- 10 files changed, 1456 insertions(+), 642 deletions(-)
Title: ROBustness in Network
Description: Many community detection algorithms have been developed in network
analysis. However, their applications leave unaddressed the statistical
validation of the results, for this reason we developed ROBIN (ROBustness
In Network), a useful method for the validation of community detection.
It has a double aim, it studies the robustness of a single community
detection algorithm and compares two community detection algorithms to
understand which provides the best partition. Reference in Annamaria Carissimo,
Luisa Cutillo, Italia De Feis (2018) <doi:10.1016/j.csda.2017.10.006>.
Author: Valeria Policastro [aut, cre],
Dario Righelli [aut],
Luisa Cutillo [aut],
Italia De Feis [aut],
Annamaria Carissimo [aut]
Maintainer: Valeria Policastro <valeria.policastro@gmail.com>
Diff between robin versions 0.99.0 dated 2019-10-20 and 0.99.1 dated 2019-10-24
DESCRIPTION | 8 MD5 | 21 - R/ROBIN.R | 627 ------------------------------------------- README.md | 87 +++++ inst/NEWS |only inst/doc/robin.R | 8 inst/doc/robin.Rmd | 133 ++++----- inst/doc/robin.html | 336 +++++++++++++---------- man/createITPSplineResult.Rd | 572 --------------------------------------- man/rewireCompl.Rd | 4 man/rewireOnl.Rd | 4 vignettes/robin.Rmd | 133 ++++----- 12 files changed, 424 insertions(+), 1509 deletions(-)
Title: Identify and Correct Invalid HGNC Human Gene Symbols and MGI
Mouse Gene Symbols
Description: Contains functions for
identifying and correcting HGNC human gene symbols and MGI mouse gene symbols
which have been converted to date format by Excel, withdrawn, or aliased.
Also contains functions for reversibly converting between HGNC
symbols and valid R names.
Author: Levi Waldron and Markus Riester
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Diff between HGNChelper versions 0.7.1 dated 2019-03-05 and 0.8.1 dated 2019-10-24
HGNChelper-0.7.1/HGNChelper/README.md |only HGNChelper-0.8.1/HGNChelper/DESCRIPTION | 9 HGNChelper-0.8.1/HGNChelper/MD5 | 34 HGNChelper-0.8.1/HGNChelper/NEWS | 9 HGNChelper-0.8.1/HGNChelper/R/checkGeneSymbols.R | 5 HGNChelper-0.8.1/HGNChelper/R/getCurrentMaps.R | 51 HGNChelper-0.8.1/HGNChelper/build/HGNChelper.pdf |binary HGNChelper-0.8.1/HGNChelper/data/hgnc.table.rda |binary HGNChelper-0.8.1/HGNChelper/data/mouse.table.rda |binary HGNChelper-0.8.1/HGNChelper/inst/doc/index.Rmd | 4 HGNChelper-0.8.1/HGNChelper/inst/doc/index.html | 49 HGNChelper-0.8.1/HGNChelper/inst/extdata/date_of_last_update.txt |only HGNChelper-0.8.1/HGNChelper/inst/extdata/mog_map.csv | 533 ++++------ HGNChelper-0.8.1/HGNChelper/man/HGNChelper-package.Rd | 58 - HGNChelper-0.8.1/HGNChelper/man/hgnc.table.Rd | 2 HGNChelper-0.8.1/HGNChelper/man/mouse.table.Rd | 2 HGNChelper-0.8.1/HGNChelper/tests/testthat/test_checkGeneSymbols.R | 13 HGNChelper-0.8.1/HGNChelper/tests/testthat/test_miscfunctions.R | 8 HGNChelper-0.8.1/HGNChelper/vignettes/index.Rmd | 4 19 files changed, 385 insertions(+), 396 deletions(-)
Title: Create Full Text Browsers from Annotated Token Lists
Description: Create browsers for reading full texts from a token list format.
Information obtained from text analyses (e.g., topic modeling, word scaling)
can be used to annotate the texts.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between tokenbrowser versions 0.1.0 dated 2019-05-17 and 0.1.1 dated 2019-10-24
tokenbrowser-0.1.0/tokenbrowser/R/tokenbrowser.r |only tokenbrowser-0.1.1/tokenbrowser/DESCRIPTION | 6 +++--- tokenbrowser-0.1.1/tokenbrowser/MD5 | 9 ++++----- tokenbrowser-0.1.1/tokenbrowser/R/token_nav.r | 10 ++++++++-- tokenbrowser-0.1.1/tokenbrowser/R/tokenvis.r | 2 ++ tokenbrowser-0.1.1/tokenbrowser/tests/testthat/test_tokenvis.r | 2 ++ 6 files changed, 19 insertions(+), 10 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph],
Henrik Singmann [ctb],
Jonathon Love [ctb],
Paul Buerkner [ctb],
Maxime Herve [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.4.1 dated 2019-09-12 and 1.4.2 dated 2019-10-24
DESCRIPTION | 8 - MD5 | 90 ++++++++--------- NAMESPACE | 1 NEWS.md | 25 ++++ R/MCMC-support.R | 12 ++ R/contrast.R | 100 +++++++++++++----- R/eff-size.R |only R/emm-contr.R | 85 +++++++++------- R/emmGrid-methods.R | 8 + R/emtrends.R | 195 ++++++++++++++++++++++--------------- R/helpers.R | 32 +++--- R/ref-grid.R | 154 +++++++++++++++++++++-------- R/xtable-method.R | 2 R/zzz.R | 8 + inst/doc/FAQs.Rmd | 24 ++-- inst/doc/FAQs.html | 17 +-- inst/doc/basics.R | 7 - inst/doc/basics.Rmd | 38 ++++--- inst/doc/basics.html | 31 +++-- inst/doc/comparisons.R | 9 + inst/doc/comparisons.Rmd | 28 +++++ inst/doc/comparisons.html | 39 ++++++- inst/doc/confidence-intervals.Rmd | 14 +- inst/doc/confidence-intervals.html | 14 +- inst/doc/interactions.html | 42 +++---- inst/doc/messy-data.html | 4 inst/doc/models.Rmd | 4 inst/doc/models.html | 8 - inst/doc/predictions.html | 4 inst/doc/sophisticated.html | 4 inst/doc/transformations.html | 4 inst/doc/utilities.html | 4 inst/doc/vignette-topics.Rmd | 6 + inst/doc/vignette-topics.html | 10 + inst/doc/xtending.html | 8 - man/contrast.Rd | 57 ++++++---- man/eff_size.Rd |only man/emm_options.Rd | 4 man/emmc-functions.Rd | 55 +++++----- man/emtrends.Rd | 92 +++++++++++++---- man/ref_grid.Rd | 93 +++++++++++------ vignettes/FAQs.Rmd | 24 ++-- vignettes/basics.Rmd | 38 ++++--- vignettes/comparisons.Rmd | 28 +++++ vignettes/confidence-intervals.Rmd | 14 +- vignettes/models.Rmd | 4 vignettes/vignette-topics.Rmd | 6 + 47 files changed, 971 insertions(+), 483 deletions(-)
Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population
management. Some functions assist survey sampling tasks (calculate sample
size for simple and complex designs, select sampling units and estimate
population parameters) while others assist the modelling of population
dynamics. For demographic characterizations and population management
evaluations see: "Baquero, et al." (2018),
<doi:10.1016/j.prevetmed.2018.07.006>. For modelling of
population dynamics see: "Baquero et al." (2016),
<doi:10.1016/j.prevetmed.2015.11.009>. For sampling methods
see: "Levy PS & Lemeshow S" (2013), "ISBN-10: 0470040076";
"Lumley" (2010), "ISBN: 978-0-470-28430-8".
Author: Oswaldo Santos Baquero [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>
Diff between capm versions 0.13.10 dated 2019-04-19 and 0.14.0 dated 2019-10-24
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS | 17 ++++++++++++----- R/DesignSurvey.R | 25 +++++++++++-------------- R/SummarySurvey.R | 8 ++++---- R/capm-package.R | 4 ++-- README.md | 10 +++++----- man/SummarySurvey.Rd | 6 +++--- man/capm-package.Rd | 4 ++-- 9 files changed, 52 insertions(+), 48 deletions(-)
Title: Maximum Likelihood Estimation for Probability Functions from
Data Sets
Description: A routine for parameter estimation for any probability density or
mass function implemented in R via maximum likelihood (ML) given a data set. This
routine is a wrapper function specifically developed for ML estimation. There are
included optimization procedures such as 'nlminb' and 'optim' from base package,
and 'DEoptim' Mullen (2011) <doi: 10.18637/jss.v040.i06>. Standard errors are
estimated with 'numDeriv' Gilbert (2011) <http://CRAN.R-project.org/package=numDeriv>
or the option 'Hessian = TRUE' of 'optim' function.
Author: Jaime Mosquera [aut, cre] (<https://orcid.org/0000-0002-1684-4756>),
Freddy Hernandez [aut] (<https://orcid.org/0000-0001-7459-3329>)
Maintainer: Jaime Mosquera <jmosquerag@unal.edu.co>
Diff between EstimationTools versions 1.2.0 dated 2019-06-11 and 1.2.1 dated 2019-10-24
DESCRIPTION | 17 +- MD5 | 51 ++++++-- R/LinkFunc.R | 4 R/is_maxlogL.R |only R/maxlogL.R | 167 +++++++++++++++----------- R/summary.R | 306 ++++++++++++++++++++++++++++++++----------------- R/zzz.R |only README.md | 30 +++- build/partial.rdb |binary build/vignette.rds |only inst/doc |only inst/refs.bib |only man/NegInv_link.Rd | 2 man/logit_link.Rd | 2 man/maxlogL.Rd | 56 ++++++-- man/summary.maxlogL.Rd | 57 ++++++++- vignettes |only 17 files changed, 469 insertions(+), 223 deletions(-)
More information about EstimationTools at CRAN
Permanent link
Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom' (<https://www.dexcom.com>), 'iPro 2' (<http://professional.medtronicdiabetes.com/ipro2-professional-cgm>), Diasend (<https://diasend.com//us>), Libre (<https://www.freestylelibre.us/>) or Carelink (<https://www.medtronicdiabetes.com/products/carelink-personal-diabetes-software>) data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload ("--1" is added to each subject ID automatically for double data entry). cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <tim.b.vigers@gmail.com>
Diff between cgmanalysis versions 2.4 dated 2019-05-22 and 2.5 dated 2019-10-24
DESCRIPTION | 8 MD5 | 14 R/cgmvariables.R | 66 - R/cleandata.R | 65 - inst/extdata/Cleaned/Dexcom.csv | 2240 +++++++++++++++++------------------ inst/extdata/Cleaned/Libre.csv | 2498 ++++++++++++++++++++-------------------- man/cgmvariables.Rd | 9 man/cleandata.Rd | 10 8 files changed, 2503 insertions(+), 2407 deletions(-)
Title: Stationary Linear Models
Description: Provides statistical procedures for linear regression in the general context where the errors are assumed to be correlated. Different ways to estimate the asymptotic covariance matrix of the least squares estimators are available. Starting from this estimation of the covariance matrix, the confidence intervals and the usual tests on the parameters are modified. The functions of this package are very similar to those of 'lm': it contains methods such as summary(), plot(), confint() and predict(). The 'slm' package is described in the paper by E. Caron, J. Dedecker and B. Michel (2019), "Linear regression with stationary errors: the R package slm", arXiv preprint <arXiv:1906.06583>.
Author: Emmanuel Caron, Jérôme Dedecker, Bertrand Michel
Maintainer: Emmanuel Caron <emmanuelcaron3@gmail.com>
Diff between slm versions 1.0.0 dated 2019-07-23 and 1.1.0 dated 2019-10-24
DESCRIPTION | 8 +-- MD5 | 35 ++++++++-------- NAMESPACE | 2 R/auxiliary-fun.R | 41 ++++++++++++------- R/generative.R | 6 +- R/slm-main.R | 91 ++++++++++++++++++++++++++------------------ R/slm-method.R | 43 +++++++++++++++++++- R/slm.R | 9 +++- man/Rboot.Rd | 2 man/cov_efromovich.Rd | 4 - man/cov_kernel.Rd | 2 man/cov_matrix_estimator.Rd | 20 +++++++-- man/cov_spectralproj.Rd | 2 man/generative_model.Rd | 3 - man/generative_process.Rd | 2 man/slm-package.Rd | 11 +++-- man/slm.Rd | 12 ++--- man/summary.slm.Rd | 2 man/vcov.slm.Rd |only 19 files changed, 191 insertions(+), 104 deletions(-)
Title: Read and write JPEG images
Description: This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between jpeg versions 0.1-8 dated 2014-01-23 and 0.1-8.1 dated 2019-10-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/Makevars.win | 16 ++++++++-------- src/rjcommon.h | 2 +- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Interface to the 'iPTMnet' API
Description: Provides an R interface to the 'iPTMnet' database REST API, which can be used to retrieve
Post Translational Modification (PTM) data in systems biology context. This package handles all the aspects
of communicating with the API, which involve sending the request, checking the error codes and parsing the
response in a format that is ready to integrate into existing workflows.
Author: Sachin Gavali
Maintainer: Sachin Gavali <saching@udel.edu>
Diff between iptmnetr versions 0.1.5 dated 2018-09-27 and 0.1.6 dated 2019-10-24
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 27 ++++++++++++++------------- NAMESPACE | 1 + R/api.R | 40 +++++++++++++++++++++++++++++++--------- man/get_host_url.Rd | 2 +- man/get_info.Rd | 2 +- man/get_ppi_for_proteoforms.Rd | 2 +- man/get_proteoforms.Rd | 2 +- man/get_ptm_dependent_ppi.Rd | 2 +- man/get_substrates.Rd | 2 +- man/get_variants.Rd |only man/search_iptmnet.Rd | 2 -- man/set_host_url.Rd | 2 +- tests/testthat/test_api.R | 14 ++++++-------- 15 files changed, 64 insertions(+), 44 deletions(-)
Title: Detect Runs of Homozygosity and Runs of Heterozygosity in
Diploid Genomes
Description: Detection of runs of homozygosity and of heterozygosity
in diploid genomes using two methods: sliding windows (Purcell et al (2007)
<doi:10.1086/519795>) and consecutive runs (Marras et al (2015)
<doi:10.1111/age.12259>).
Author: Filippo Biscarini [aut, cre],
Paolo Cozzi [aut],
Giustino Gaspa [aut],
Gabriele Marras [aut]
Maintainer: Filippo Biscarini <filippo.biscarini@gmail.com>
Diff between detectRUNS versions 0.9.5 dated 2018-02-06 and 0.9.6 dated 2019-10-24
DESCRIPTION | 11 MD5 | 21 - R/RcppExports.R | 2 build/vignette.rds |binary inst/doc/detectRUNS.vignette.html | 715 +++++++++++++++----------------------- man/consecutiveRUNS.run.Rd | 5 man/consecutiveRunsCpp.Rd | 6 man/plot_DistributionRuns.Rd | 3 man/plot_InbreedingChr.Rd | 6 man/slidingRUNS.run.Rd | 8 src/functions.cpp | 2 vignettes/rog.png |only 12 files changed, 331 insertions(+), 448 deletions(-)
Title: Markov-Switching GARCH Models
Description: Fit (by Maximum Likelihood or MCMC/Bayesian), simulate, and forecast various Markov-Switching GARCH models as described in Ardia et al. (2019) <doi:10.18637/jss.v091.i04>.
Author: David Ardia [aut],
Keven Bluteau [aut, cre],
Kris Boudt [ctb],
Leopoldo Catania [aut],
Alexios Ghalanos [ctb],
Brian Peterson [ctb],
Denis-Alexandre Trottier [aut]
Maintainer: Keven Bluteau <Keven.Bluteau@unine.ch>
Diff between MSGARCH versions 2.3 dated 2018-05-16 and 2.31 dated 2019-10-24
DESCRIPTION | 12 +++--- MD5 | 64 ++++++++++++++++---------------- NAMESPACE | 98 ++++++++++++++++++++++++------------------------- NEWS | 2 + R/CreateSpec.R | 25 ++++++++++-- R/DIC.R | 3 + R/FitMCMC.R | 18 +++++++-- R/FitML.R | 8 +++- R/Inference.R | 3 + R/Kernel.R | 1 R/Likelihood.R | 3 + R/MSGARCH.R | 46 +++++++++++++++++------ R/Plot.R | 3 + R/Print.R | 2 + R/RcppExports.R | 8 ++-- R/Samplers.R | 1 R/predict.R | 1 R/simulate.R | 7 ++- R/zzz.R | 21 +++++++--- inst/CITATION | 59 +++++++++++------------------ man/CreateSpec.Rd | 20 +++++++--- man/DIC.Rd | 1 man/FitMCMC.Rd | 11 +++-- man/FitML.Rd | 8 +++- man/MSGARCH-package.Rd | 24 +++++++++--- man/PIT.Rd | 12 +++--- man/PredPdf.Rd | 6 +-- man/Risk.Rd | 6 +-- man/SMI.Rd | 6 +-- man/dem2gbp.Rd | 2 + man/simulate.Rd | 6 +-- src/Makevars.win | 2 - src/RcppExports.cpp | 44 +++++++++++----------- 33 files changed, 314 insertions(+), 219 deletions(-)
Title: Multiple Pairwise Comparison Tests
Description: Multiple pairwise comparison tests for one-way
analysis of variance for both between-subjects and within-subjects
designs. Currently, it supports only the most common types of
statistical analyses and tests: parametric (Welch's and Student's
t-test), nonparametric (Durbin-Conover test and
Dwass-Steel-Crichtlow-Fligner test), robust (Yuen’s trimmed means test).
Author: Indrajeet Patil [cre, aut, ctb]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between pairwiseComparisons versions 0.1.1 dated 2019-09-17 and 0.1.2 dated 2019-10-24
DESCRIPTION | 10 +++--- MD5 | 18 +++++------ NEWS.md | 7 ++++ README.md | 46 +++++++++++------------------ inst/doc/tests_and_coverage.html | 2 - man/figures/README-ggisignif-1.png |binary man/pairwise_comparisons.Rd | 32 ++++++++++++++++---- man/pairwise_comparisons_caption.Rd | 20 ++++++++++-- man/reexports.Rd | 8 ++--- tests/testthat/test-pairwise_comparisons.R | 12 +++---- 10 files changed, 93 insertions(+), 62 deletions(-)
More information about pairwiseComparisons at CRAN
Permanent link
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.4.0 dated 2019-06-25 and 0.4.1 dated 2019-10-24
rlang-0.4.0/rlang/tests/testthat/test-on-error-message-options.txt |only rlang-0.4.1/rlang/DESCRIPTION | 10 rlang-0.4.1/rlang/MD5 | 213 +- rlang-0.4.1/rlang/NAMESPACE | 9 rlang-0.4.1/rlang/NEWS.md | 68 rlang-0.4.1/rlang/R/attr.R | 1 rlang-0.4.1/rlang/R/call.R | 10 rlang-0.4.1/rlang/R/cnd-abort.R |only rlang-0.4.1/rlang/R/cnd-entrace.R |only rlang-0.4.1/rlang/R/cnd-error.R |only rlang-0.4.1/rlang/R/cnd-handlers.R | 113 + rlang-0.4.1/rlang/R/cnd-message.R |only rlang-0.4.1/rlang/R/cnd-restarts.R | 3 rlang-0.4.1/rlang/R/cnd-signal.R |only rlang-0.4.1/rlang/R/cnd.R | 908 ---------- rlang-0.4.1/rlang/R/compat-friendly-type.R |only rlang-0.4.1/rlang/R/compat-lifecycle.R | 1 rlang-0.4.1/rlang/R/deparse.R | 5 rlang-0.4.1/rlang/R/dots.R | 39 rlang-0.4.1/rlang/R/env-binding.R | 31 rlang-0.4.1/rlang/R/env.R | 1 rlang-0.4.1/rlang/R/eval.R | 1 rlang-0.4.1/rlang/R/fn.R | 36 rlang-0.4.1/rlang/R/lifecycle-retired.R | 3 rlang-0.4.1/rlang/R/lifecycle.R | 1 rlang-0.4.1/rlang/R/operators.R | 10 rlang-0.4.1/rlang/R/quasiquotation.R | 2 rlang-0.4.1/rlang/R/rlang.R | 52 rlang-0.4.1/rlang/R/sexp.R | 16 rlang-0.4.1/rlang/R/stack.R | 2 rlang-0.4.1/rlang/R/trace.R | 101 - rlang-0.4.1/rlang/R/types.R | 59 rlang-0.4.1/rlang/R/utils-encoding.R | 2 rlang-0.4.1/rlang/R/utils.R | 10 rlang-0.4.1/rlang/R/vec-na.R | 3 rlang-0.4.1/rlang/R/vec-new.R | 3 rlang-0.4.1/rlang/build/rlang.pdf |binary rlang-0.4.1/rlang/man/abort.Rd | 18 rlang-0.4.1/rlang/man/are_na.Rd | 1 rlang-0.4.1/rlang/man/as_function.Rd | 20 rlang-0.4.1/rlang/man/as_utf8_character.Rd | 1 rlang-0.4.1/rlang/man/caller_fn.Rd | 1 rlang-0.4.1/rlang/man/catch_cnd.Rd | 2 rlang-0.4.1/rlang/man/cnd.Rd | 11 rlang-0.4.1/rlang/man/cnd_message.Rd |only rlang-0.4.1/rlang/man/cnd_muffle.Rd | 3 rlang-0.4.1/rlang/man/cnd_signal.Rd | 2 rlang-0.4.1/rlang/man/cnd_type.Rd | 1 rlang-0.4.1/rlang/man/dots_n.Rd | 1 rlang-0.4.1/rlang/man/dots_values.Rd | 1 rlang-0.4.1/rlang/man/entrace.Rd | 13 rlang-0.4.1/rlang/man/env_bury.Rd | 1 rlang-0.4.1/rlang/man/env_lock.Rd | 1 rlang-0.4.1/rlang/man/has_length.Rd | 1 rlang-0.4.1/rlang/man/is_callable.Rd | 1 rlang-0.4.1/rlang/man/is_condition.Rd | 1 rlang-0.4.1/rlang/man/is_copyable.Rd | 1 rlang-0.4.1/rlang/man/is_function.Rd | 16 rlang-0.4.1/rlang/man/is_reference.Rd | 1 rlang-0.4.1/rlang/man/is_stack.Rd | 1 rlang-0.4.1/rlang/man/lang_head.Rd | 1 rlang-0.4.1/rlang/man/last_error.Rd | 2 rlang-0.4.1/rlang/man/lifecycle.Rd | 1 rlang-0.4.1/rlang/man/missing.Rd | 1 rlang-0.4.1/rlang/man/new-vector-along-retired.Rd | 1 rlang-0.4.1/rlang/man/new-vector.Rd | 1 rlang-0.4.1/rlang/man/op-get-attr.Rd | 4 rlang-0.4.1/rlang/man/op-na-default.Rd | 5 rlang-0.4.1/rlang/man/prim_name.Rd | 1 rlang-0.4.1/rlang/man/quasiquotation.Rd | 2 rlang-0.4.1/rlang/man/restarting.Rd | 1 rlang-0.4.1/rlang/man/return_from.Rd | 1 rlang-0.4.1/rlang/man/rlang_backtrace_on_error.Rd | 8 rlang-0.4.1/rlang/man/rst_abort.Rd | 1 rlang-0.4.1/rlang/man/rst_list.Rd | 1 rlang-0.4.1/rlang/man/string.Rd | 1 rlang-0.4.1/rlang/man/tidy-dots.Rd | 33 rlang-0.4.1/rlang/man/trace_back.Rd | 8 rlang-0.4.1/rlang/man/with_abort.Rd | 31 rlang-0.4.1/rlang/man/with_env.Rd | 1 rlang-0.4.1/rlang/man/with_restarts.Rd | 1 rlang-0.4.1/rlang/src/export/exported.c | 29 rlang-0.4.1/rlang/src/export/init.c | 4 rlang-0.4.1/rlang/src/internal/eval-tidy.c | 6 rlang-0.4.1/rlang/src/lib/env.c | 72 rlang-0.4.1/rlang/src/lib/replace-na.c | 71 rlang-0.4.1/rlang/tests/testthat/fixtures/error-backtrace-conditionMessage.R |only rlang-0.4.1/rlang/tests/testthat/fixtures/error-backtrace-parent.R |only rlang-0.4.1/rlang/tests/testthat/fixtures/error-backtrace.R |only rlang-0.4.1/rlang/tests/testthat/helper-rlang.R | 17 rlang-0.4.1/rlang/tests/testthat/output-cnd-abort-parent-trace.txt |only rlang-0.4.1/rlang/tests/testthat/output-cnd-abort-trace-reminder.txt |only rlang-0.4.1/rlang/tests/testthat/test-attr.R | 5 rlang-0.4.1/rlang/tests/testthat/test-call.R | 8 rlang-0.4.1/rlang/tests/testthat/test-cnd-abort.R |only rlang-0.4.1/rlang/tests/testthat/test-cnd-bullets-lazy.txt |only rlang-0.4.1/rlang/tests/testthat/test-cnd-entrace.R |only rlang-0.4.1/rlang/tests/testthat/test-cnd-error-conditionMessage.txt |only rlang-0.4.1/rlang/tests/testthat/test-cnd-error-parent-default.txt | 22 rlang-0.4.1/rlang/tests/testthat/test-cnd-error-parent-full.txt |only rlang-0.4.1/rlang/tests/testthat/test-cnd-error-parent-trace.txt |only rlang-0.4.1/rlang/tests/testthat/test-cnd-error-parent.txt | 71 rlang-0.4.1/rlang/tests/testthat/test-cnd-error-print-base-parent.txt | 6 rlang-0.4.1/rlang/tests/testthat/test-cnd-error-print-no-message.txt | 3 rlang-0.4.1/rlang/tests/testthat/test-cnd-error-str.txt | 16 rlang-0.4.1/rlang/tests/testthat/test-cnd-error.R |only rlang-0.4.1/rlang/tests/testthat/test-cnd-error.txt | 59 rlang-0.4.1/rlang/tests/testthat/test-cnd-handlers.R |only rlang-0.4.1/rlang/tests/testthat/test-cnd-message.R |only rlang-0.4.1/rlang/tests/testthat/test-cnd-signal-trace.txt |only rlang-0.4.1/rlang/tests/testthat/test-cnd-signal.R |only rlang-0.4.1/rlang/tests/testthat/test-cnd.R | 496 ----- rlang-0.4.1/rlang/tests/testthat/test-deparse.R | 4 rlang-0.4.1/rlang/tests/testthat/test-env.R | 13 rlang-0.4.1/rlang/tests/testthat/test-error-print-conditionMessage.txt |only rlang-0.4.1/rlang/tests/testthat/test-eval-tidy.R | 12 rlang-0.4.1/rlang/tests/testthat/test-expr.R | 3 rlang-0.4.1/rlang/tests/testthat/test-operators.R | 22 rlang-0.4.1/rlang/tests/testthat/test-trace.R | 18 rlang-0.4.1/rlang/tests/testthat/test-with-abort.txt | 32 120 files changed, 971 insertions(+), 1936 deletions(-)
Title: Calculates Disproportionate Impact When Binary Success Data are
Disaggregated by Subgroups
Description: Implements methods for calculating disproportionate impact: the percentage point gap, proportionality index, and the 80% index.
California Community Colleges Chancellor's Office (2017). Percentage Point Gap Method. <https://www.cccco.edu/-/media/CCCCO-Website/About-Us/Divisions/Digital-Innovation-and-Infrastructure/Research/Files/PercentagePointGapMethod2017.ashx>.
California Community Colleges Chancellor's Office (2014). Guidelines for Measuring Disproportionate Impact in Equity Plans. <https://www.cccco.edu/-/media/CCCCO-Website/About-Us/Divisions/Digital-Innovation-and-Infrastructure/Network-Operations/Accountability/Files/GUIDELINES-FOR-MEASURING-DISPROPORTIONATE-IMPACT-IN-EQUITY-PLANS.ashx>.
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>
Diff between DisImpact versions 0.0.4 dated 2019-04-24 and 0.0.5 dated 2019-10-24
DESCRIPTION | 12 ++--- MD5 | 39 +++++++++--------- NAMESPACE | 6 ++ NEWS | 3 + R/80_percent_index.R | 7 +-- R/data_student_equity.R | 5 +- R/percentage_point_gap.R | 78 +++++++++++++++++++++++++++++++++--- R/proportionality_index.R | 7 +-- README.md | 6 +- build/vignette.rds |binary data/student_equity.rda |binary inst/doc/Tutorial.R | 10 ++++ inst/doc/Tutorial.Rmd | 19 +++++++- inst/doc/Tutorial.html | 98 +++++++++++++++++++++++++++++++++++++--------- man/di_80_index.Rd | 4 - man/di_ppg.Rd | 8 +-- man/di_ppg_iterate.Rd |only man/di_prop_index.Rd | 4 - man/ppg_moe.Rd | 5 -- man/student_equity.Rd | 2 vignettes/Tutorial.Rmd | 19 +++++++- 21 files changed, 252 insertions(+), 80 deletions(-)
Title: Statistical Methods for Graphs
Description: Contains statistical methods to analyze graphs, such as
graph parameter estimation, model selection based on the GIC
(Graph Information Criterion), statistical tests to
discriminate two or more populations of graphs (ANOGVA -
Analysis of Graph Variability), correlation between graphs, and
clustering of graphs. References: Takahashi et al. (2012)
<doi:10.1371/journal.pone.0049949>, Futija et al. (2017)
<doi:10.3389/fnins.2017.00066>, Fujita et al. (2017)
<doi:10.1016/j.csda.2016.11.016>, Tang et al. (2017)
<doi:10.3150/15-BEJ789>, Tang et al. (2017)
<doi:10.1080/10618600.2016.1193505>, Ghoshdastidar et al.
(2017) <arXiv:1705.06168>, Ghoshdastidar et al. (2017)
<arXiv:1707.00833>, Cerqueira et al. (2017)
<doi:10.1109/TNSE.2017.2674026>, Fraiman and Fraiman (2018)
<doi:10.1038/s41598-018-23152-5>, Fujita et al. (2019)
<doi:10.1093/comnet/cnz028>.
Author: Suzana S. Santos [aut],
Eduardo S. Lira [aut],
Andre Fujita [aut, cre]
Maintainer: Andre Fujita <fujita@ime.usp.br>
Diff between statGraph versions 0.2.0 dated 2019-01-10 and 0.3.0 dated 2019-10-24
DESCRIPTION | 35 ++- MD5 | 16 + NAMESPACE | 2 R/statGraph-package.R |only R/statGraph.R | 440 ++++++++++++++++++++++++++++++++++++++++++----- build |only inst |only man/cerqueira.Rd |only man/fraiman.Rd |only man/sp.anogva.Rd | 38 ++-- man/statGraph-package.Rd |only man/tang.Rd | 27 +- 12 files changed, 482 insertions(+), 76 deletions(-)
Title: Heteroskedastic Gaussian Process Modeling and Design under
Replication
Description: Performs Gaussian process regression with heteroskedastic noise following Binois, M., Gramacy, R., Ludkovski, M. (2016) <arXiv:1611.05902>. The input dependent noise is modeled as another Gaussian process. Replicated observations are encouraged as they yield computational savings. Sequential design procedures based on the integrated mean square prediction error and lookahead heuristics are provided, and notably fast update functions when adding new observations.
Author: Mickael Binois, Robert B. Gramacy
Maintainer: Mickael Binois <mickael.binois@inria.fr>
Diff between hetGP versions 1.1.1 dated 2019-01-10 and 1.1.2 dated 2019-10-24
DESCRIPTION | 14 MD5 | 54 - NAMESPACE | 9 NEWS | 13 R/IMSE.R | 74 + R/TestFunctions.R | 58 + R/contour.R | 79 + R/hetGP.R | 134 ++ R/hetTP.R | 40 R/optim.R | 79 + build/vignette.rds |binary inst/doc/hetGP_vignette.R | 400 +++----- inst/doc/hetGP_vignette.Rnw | 1940 ++++++++++++++++++++----------------------- inst/doc/hetGP_vignette.pdf |binary man/IMSPE_optim.Rd | 14 man/ato.Rd | 18 man/crit_MCU.Rd | 23 man/crit_MEE.Rd |only man/crit_optim.Rd | 16 man/f1d.Rd | 4 man/f1d2.Rd |only man/f1d2_n.Rd |only man/f1d_n.Rd |only man/logLikH.Rd |only man/mleHetGP.Rd | 9 man/mleHetTP.Rd | 9 man/mleHomGP.Rd | 5 man/mleHomTP.Rd | 6 man/scores.Rd |only vignettes/hetGP_vignette.Rnw | 1940 ++++++++++++++++++++----------------------- vignettes/refs.bib | 149 ++- 31 files changed, 2626 insertions(+), 2461 deletions(-)
Title: Bayesian Seemingly Unrelated Regression
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Banterle et al. (2018) <doi:10.1101/467019>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Alex Lewin [aut],
Manuela Zucknick [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 1.0-0 dated 2019-10-14 and 1.0-1 dated 2019-10-24
DESCRIPTION | 18 MD5 | 60 - NAMESPACE | 1 R/BayesSUR.R | 13 R/RcppExports.R | 4 R/example_GDSC.R | 9 R/example_GDSC_targets.R | 10 R/example_eQTL.R | 10 R/plot.BayesSUR.R | 3 R/plotEstimator.R | 71 - R/plotMCMCdiag.R | 2 configure.ac | 1 inst/doc/BayesSUR.pdf |binary man/BayesSUR.Rd | 12 man/example_GDSC.Rd | 10 man/example_GDSC_targets.Rd | 12 man/example_eQTL.Rd | 10 man/plot.BayesSUR.Rd | 3 man/plotEstimator.Rd | 11 man/plotMCMCdiag.Rd | 2 src/BayesSUR.cpp | 4 src/ESS_Sampler.h | 296 ++--- src/HRR_Chain.cpp | 922 ++++++++--------- src/HRR_Chain.h | 2 src/RcppExports.cpp | 9 src/SUR_Chain.cpp | 2319 ++++++++++++++++++++++---------------------- src/SUR_Chain.h | 2 src/distr.cpp | 16 src/drive.cpp | 2103 ++++++++++++++++++++------------------- src/drive.h | 3 src/utils.h | 2 31 files changed, 3058 insertions(+), 2882 deletions(-)
Title: Automated Test Assembly
Description: Automated test assembly of linear and adaptive tests using the
mixed-integer programming. The full documentation and tutorials are at
<https://github.com/xluo11/Rata>.
Author: Xiao Luo [aut, cre]
Maintainer: Xiao Luo <xluo1986@gmail.com>
Diff between Rata versions 0.0.1 dated 2019-08-27 and 0.0.2 dated 2019-10-24
DESCRIPTION | 14 ++-- MD5 | 18 ++--- NAMESPACE | 2 R/ata.R | 33 ++++----- R/glpk.R | 194 ++++++++++++++++++++++++++++----------------------------- R/helpers.R | 106 +++++++------------------------ R/lpsolve.R | 140 ++++++++++++++++++++--------------------- R/methods.R | 45 ++----------- man/ata.Rd | 15 ++-- man/helpers.Rd | 4 - 10 files changed, 244 insertions(+), 327 deletions(-)
Title: Unified Handling of Graphics Devices
Description: Functions for creating plots and image files in a unified way
regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default
device options as well as scales and aspect ratios are controlled in a uniform
way across all device types. Switching output format requires minimal changes
in code. This package is ideal for large-scale batch processing, because it
will never leave open graphics devices or incomplete image files behind, even on
errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.devices versions 2.16.0 dated 2018-07-21 and 2.16.1 dated 2019-10-24
DESCRIPTION | 8 MD5 | 20 +- NEWS | 336 +++++++++++++++++++++------------------- R/devOptions.R | 2 R/recordedplot-methods.R | 18 +- R/toNNN.R | 225 ++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/R.devices-overview.R | 2 inst/doc/R.devices-overview.pdf |binary man/R.devices-package.Rd | 4 man/capturePlot.Rd | 2 11 files changed, 429 insertions(+), 188 deletions(-)
Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows
for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rqdatatable versions 1.2.2 dated 2019-09-13 and 1.2.3 dated 2019-10-24
rqdatatable-1.2.2/rqdatatable/R/ex_relop_list.R |only rqdatatable-1.2.2/rqdatatable/R/rq_ufn.R |only rqdatatable-1.2.2/rqdatatable/R/ufn_rq.R |only rqdatatable-1.2.2/rqdatatable/inst/unit_tests/test_ex_relop_list.R |only rqdatatable-1.2.2/rqdatatable/man/ApplyTo.Rd |only rqdatatable-1.2.2/rqdatatable/man/ex_data_table.relop_list.Rd |only rqdatatable-1.2.2/rqdatatable/man/format.rq_u_fn_w.Rd |only rqdatatable-1.2.2/rqdatatable/man/rq_fn_wrapper.Rd |only rqdatatable-1.2.2/rqdatatable/man/rq_u_fn_w-class.Rd |only rqdatatable-1.2.2/rqdatatable/man/rq_ufn.Rd |only rqdatatable-1.2.2/rqdatatable/man/show-rq_u_fn_w-method.Rd |only rqdatatable-1.2.3/rqdatatable/DESCRIPTION | 12 - rqdatatable-1.2.3/rqdatatable/MD5 | 35 +-- rqdatatable-1.2.3/rqdatatable/NAMESPACE | 20 -- rqdatatable-1.2.3/rqdatatable/NEWS.md | 6 rqdatatable-1.2.3/rqdatatable/R/relop_extend.R | 3 rqdatatable-1.2.3/rqdatatable/R/relop_natural_join.R | 4 rqdatatable-1.2.3/rqdatatable/R/relop_project.R | 6 rqdatatable-1.2.3/rqdatatable/README.md | 28 +- rqdatatable-1.2.3/rqdatatable/build/vignette.rds |binary rqdatatable-1.2.3/rqdatatable/inst/doc/GroupedSampling.html | 45 ++-- rqdatatable-1.2.3/rqdatatable/inst/doc/R_mapping.html | 19 + rqdatatable-1.2.3/rqdatatable/inst/doc/logisticexample.html | 100 +++++----- rqdatatable-1.2.3/rqdatatable/inst/unit_tests/test_dtmsg.R |only rqdatatable-1.2.3/rqdatatable/inst/unit_tests/test_project_example.R |only 25 files changed, 141 insertions(+), 137 deletions(-)
Title: Index Construction for Time Series Data
Description: Derivation of indexes for benchmarking purposes. A methodology with flexible number of constituents is implemented. Also functions for market capitalization and volume weighted indexes with fixed number of constituents are available. The main function of the package, indexComp(), provides the derived index, suitable for analysis purposes. The functions indexUpdate(), indexMemberSelection() and indexMembersUpdate() are components of indexComp() and enable one to construct and continuously update an index, e.g. for display on a website. The methodology behind the functions provided gets introduced in Trimborn and Haerdle (2018) <doi:10.1016/j.jempfin.2018.08.004>.
Author: Simon Trimborn <simon.trimborn@nus.edu.sg>
Maintainer: Simon Trimborn <simon.trimborn@nus.edu.sg>
Diff between IndexConstruction versions 0.1-1 dated 2019-03-29 and 0.1-2 dated 2019-10-24
IndexConstruction-0.1-1/IndexConstruction/R/CRIXwrappers.R |only IndexConstruction-0.1-1/IndexConstruction/man/CRIX.Rd |only IndexConstruction-0.1-1/IndexConstruction/man/ECRIX.Rd |only IndexConstruction-0.1-1/IndexConstruction/man/EFCRIX.Rd |only IndexConstruction-0.1-1/IndexConstruction/man/LCRIX.Rd |only IndexConstruction-0.1-1/IndexConstruction/man/LECRIX.Rd |only IndexConstruction-0.1-1/IndexConstruction/man/LEFCRIX.Rd |only IndexConstruction-0.1-2/IndexConstruction/DESCRIPTION | 10 IndexConstruction-0.1-2/IndexConstruction/MD5 | 42 IndexConstruction-0.1-2/IndexConstruction/NAMESPACE | 15 IndexConstruction-0.1-2/IndexConstruction/R/IndexComp.R | 448 +++++----- IndexConstruction-0.1-2/IndexConstruction/R/IndexEval.R | 100 +- IndexConstruction-0.1-2/IndexConstruction/R/IndexLoop.R | 388 ++++---- IndexConstruction-0.1-2/IndexConstruction/R/IndexMemberSelection.R | 294 +++--- IndexConstruction-0.1-2/IndexConstruction/R/IndexMembersUpdate.R | 186 ++-- IndexConstruction-0.1-2/IndexConstruction/R/IndexUpdate.R | 6 IndexConstruction-0.1-2/IndexConstruction/R/RelativeWeights.R | 6 IndexConstruction-0.1-2/IndexConstruction/R/SwitchDates.R | 48 - IndexConstruction-0.1-2/IndexConstruction/R/class_CRIX.R |only IndexConstruction-0.1-2/IndexConstruction/data/CryptoData.RData |binary IndexConstruction-0.1-2/IndexConstruction/man/IndexComp.Rd | 59 - IndexConstruction-0.1-2/IndexConstruction/man/IndexMemberSelection.Rd | 28 IndexConstruction-0.1-2/IndexConstruction/man/IndexMembersUpdate.Rd | 14 IndexConstruction-0.1-2/IndexConstruction/man/IndexUpdate.Rd | 14 IndexConstruction-0.1-2/IndexConstruction/man/RelativeWeights.Rd | 64 - IndexConstruction-0.1-2/IndexConstruction/man/SwitchDates.Rd | 12 26 files changed, 886 insertions(+), 848 deletions(-)
More information about IndexConstruction at CRAN
Permanent link
Title: A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer
Maintainer: James Dalgleish <james.dalgleish@nih.gov>
Diff between CNVScope versions 2.7.7 dated 2019-10-14 and 2.8.1 dated 2019-10-24
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 18 ++++++++++++++++++ 3 files changed, 26 insertions(+), 8 deletions(-)