Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Liao X, Meyer MC (2019)<doi:10.18637/jss.v089.i05> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <xiyue.liao@csulb.edu>
Diff between cgam versions 1.16 dated 2020-09-29 and 1.17 dated 2021-12-13
ChangeLog | 3 DESCRIPTION | 16 MD5 | 14 R/cgam.R | 152 +++--- R/cgamm.R | 1296 +++++++++++++++++++++++++++---------------------------- inst/CITATION | 35 - man/cgam.Rd | 422 ++++++++--------- man/plotpersp.Rd | 8 8 files changed, 989 insertions(+), 957 deletions(-)
Title: Twang Causal Mediation Modeling via Weighting
Description: Provides functions for estimating natural direct and indirect effects for mediation analysis. It uses weighting where the weights are functions of estimates of the probability of exposure or treatment assignment (Hong, G (2010). <https://cepa.stanford.edu/sites/default/files/workshops/GH_JSM%20Proceedings%202010.pdf> Huber, M. (2014). <doi:10.1002/jae.2341>). Estimation of probabilities can use generalized boosting or logistic regression. Additional functions provide diagnostics of the model fit and weights. The vignette provides details and examples.
Author: Dan McCaffrey [aut, cre],
Katherine Castellano [aut],
Donna Coffman [aut],
Brian Vegetabile [aut],
Megan Schuler [aut],
Haoyu Zhou [aut]
Maintainer: Dan McCaffrey <dmccaffrey@ets.org>
Diff between twangMediation versions 1.0 dated 2021-07-27 and 1.1 dated 2021-12-13
DESCRIPTION | 10 MD5 | 62 - R/bal.table.mediation.R | 421 +++++++----- R/data.R | 128 +-- R/desc.effects.R | 64 - R/desc.effects.mediation.R | 264 +++---- R/diag.plot.color.R | 408 ++++++------ R/dx.wts.mediation.R | 396 +++++------ R/makePlotDat.R | 276 ++++---- R/plot.mediation.R | 667 +++++++------------ R/print.bal.table.mediation.R | 115 ++- R/print.mediation.R | 178 ++--- R/summary.mediation.R | 270 +++---- R/twangMediation-package.R | 14 R/twang_functions.R | 316 ++++----- R/utils_mediation.R | 350 +++++----- R/wgtmed.R | 948 +++++++++++++++------------- build/vignette.rds |binary inst/doc/twangMediation_tutorialimport.Rnw | 12 inst/doc/twangMediation_tutorialimport.pdf |binary man/NSDUH_female.Rd | 114 +-- man/bal.table.mediation.Rd | 90 +- man/desc.effects.Rd | 86 +- man/desc.effects.mediation.Rd | 94 +- man/dx.wts.mediation.Rd | 178 ++--- man/plot.mediation.Rd | 136 +--- man/print.bal.table.mediation.Rd | 82 +- man/print.mediation.Rd | 82 +- man/summary.mediation.Rd | 92 +- man/wgtmed.Rd | 380 +++++------ vignettes/twangMediation.pdf |binary vignettes/twangMediation_tutorialimport.Rnw | 12 32 files changed, 3109 insertions(+), 3136 deletions(-)
More information about twangMediation at CRAN
Permanent link
Title: Comparing Sequences with Non-Uniform Time Intervals
Description: The SAWNUTI algorithm performs sequence comparison for finite sequences of discrete events with non-uniform time intervals. Further description of the algorithm can be found in the paper: A. Murph, A. Flynt, B. R. King (2021). Comparing finite sequences of discrete events with non-uniform time intervals, Sequential Analysis, 40(3), 291-313. <doi:10.1080/07474946.2021.1940491>.
Author: Alexander Murph [aut, cre] (<https://orcid.org/0000-0001-7170-867X>)
Maintainer: Alexander Murph <acm026@bucknell.edu>
Diff between sawnuti versions 0.1.0 dated 2021-11-08 and 0.1.1 dated 2021-12-13
DESCRIPTION | 12 +++++------ MD5 | 6 ++--- NEWS.md | 7 ++++-- README.md | 64 +++++++++++++++++++++++++++++++++++++++++++----------------- 4 files changed, 60 insertions(+), 29 deletions(-)
Title: Comparative Analysis with Annotation-Based Genomic Components
Description: A first-principle, phylogeny-aware comparative genomics tool for
investigating associations between terms used to annotate genomic
components (e.g., Pfam IDs, Gene Ontology terms,) with quantitative
or rank variables such as number of cell types, genome size, or
density of specific genomic elements. See the project website for
more information, documentation and examples.
Author: Francisco Lobo [aut],
Felipe Campelo [aut, cre],
Jorge Augusto Hongo [aut],
Giovanni Marques de Castro [aut],
Gabriel Almeida [sad, dnc]
Maintainer: Felipe Campelo <fcampelo@gmail.com>
Diff between CALANGO versions 1.0.5 dated 2021-09-02 and 1.0.8 dated 2021-12-13
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ NEWS.md | 10 +++++++++- inst/extdata/report_files/heatmap_phylo_norm.Rmd | 2 +- inst/extdata/report_files/heatmap_phylo_perc.Rmd | 2 +- inst/extdata/report_files/heatmap_phylo_raw.Rmd | 2 +- inst/extdata/report_files/table.Rmd | 17 ++++++++++------- inst/images/CALANGO_LOGO_whiteBG.png |only 8 files changed, 34 insertions(+), 22 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-25 1.1.0
2021-06-25 1.0.0
Title: Mixed Effect Excess Hazard Models
Description: Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a random effect at the cluster level (corresponding to a shared frailty). A detailed description of the package functionalities is provided in Charvat and Belot (2021) <doi: 10.18637/jss.v098.i14>.
Author: Hadrien Charvat, Aurelien Belot
Maintainer: Hadrien Charvat <chadrien@ncc.go.jp>
Diff between mexhaz versions 2.0 dated 2021-09-14 and 2.1 dated 2021-12-13
DESCRIPTION | 8 MD5 | 30 +- NAMESPACE | 2 NEWS | 64 ++-- R/marginSurvhaz.R |only R/mexhazEgh.R | 1 R/mexhazStd.R | 2 R/predict.mexhaz.R | 651 ++++++++++++++++++++++++++--------------------- R/print.mexhaz.R | 6 R/print.summary.mexhaz.R | 4 R/residuals.mexhaz.R |only R/summary.mexhaz.R | 8 R/update.mexhaz.R | 181 +++++++------ man/mexhaz-package.Rd | 2 man/predict.mexhaz.Rd | 60 ++-- man/update.mexhaz.Rd | 14 - src/GaussProcNPH.c | 2 17 files changed, 582 insertions(+), 453 deletions(-)
Title: GSL Nonlinear Least-Squares Fitting
Description: An R interface to nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquadt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.1.0 dated 2021-11-26 and 1.1.1 dated 2021-12-13
DESCRIPTION | 8 +-- MD5 | 20 +++---- NEWS.md | 5 + R/nls.R | 10 +++ R/nls_large.R | 33 ++++++++---- configure | 18 +++--- configure.ac | 2 man/gsl_nls_large.Rd | 14 ++--- src/gsl_nls.h | 38 +++++++++++++- src/nls.c | 104 ++++++++++++++++++++++++--------------- src/nls_large.c | 135 +++++++++++++++++++++++++++++---------------------- 11 files changed, 247 insertions(+), 140 deletions(-)
Title: Density, Probability, Quantile ('DPQ') Computations
Description: Computations for approximations and alternatives for the 'DPQ'
(Density (pdf), Probability (cdf) and Quantile) functions for probability
distributions in R.
Primary focus is on (central and non-central) beta, gamma and related
distributions such as the chi-squared, F, and t.
--
This is for the use of researchers in these numerical approximation
implementations, notably for my own use in order to improve standard
R pbeta(), qgamma(), ..., etc: {'"dpq"'-functions}.
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Morten Welinder [ctb] (pgamma C code, see PR#7307, Jan. 2005; further
pdhyper()),
Wolfgang Viechtbauer [ctb] (dtWV(), 2002),
Ross Ihaka [ctb] (src/qchisq_appr.c),
Marius Hofert [ctb] (lsum(), lssum()),
R-core [ctb] (src/{dpq.h, algdiv.c, pnchisq.c, bd0.c}),
R Foundation [cph] (src/qchisq-appr.c)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between DPQ versions 0.5-0 dated 2021-11-24 and 0.5-1 dated 2021-12-13
DESCRIPTION | 11 - MD5 | 38 ++--- R/beta-fns.R | 4 R/dgamma.R | 14 + build/DPQ.pdf |binary build/partial.rdb |binary inst/NEWS.Rd | 28 +++ inst/doc/Noncentral-Chisq.pdf |binary inst/doc/comp-beta.pdf |binary inst/doc/log1pmx-etc.R | 2 inst/doc/log1pmx-etc.pdf |binary man/dgamma-utils.Rd | 19 +- man/log1pmx.Rd | 2 man/numer-utils.Rd | 9 - man/p1l1.Rd | 4 man/pnchi1sq.Rd | 27 +++ src/DPQ-misc.c | 4 src/bd0.c | 73 +++++----- tests/stirlerr-tst.R | 304 ++++++++++++++++++++++++++++++++++++++---- vignettes/log1pmx-etc.Rnw | 26 +++ 20 files changed, 450 insertions(+), 115 deletions(-)
Title: Estimating Aboveground Biomass and Its Uncertainty in Tropical
Forests
Description: Contains functions to estimate aboveground biomass/carbon and its uncertainty in tropical forests.
These functions allow to (1) retrieve and to correct taxonomy, (2) estimate wood density and its uncertainty,
(3) construct height-diameter models, (4) manage tree and plot coordinates,
(5) estimate the aboveground biomass/carbon at the stand level with associated uncertainty.
To cite 'BIOMASS', please use citation("BIOMASS").
See more in the article of Réjou-Méchain et al. (2017) <doi:10.1111/2041-210X.12753>.
Author: Maxime Réjou-Méchain [aut, cre, dtc],
Arthur Pere [aut],
Guillaume Cornu [aut] (<https://orcid.org/0000-0002-7523-5176>),
Ariane Tanguy [aut],
Camille Piponiot [aut],
Jerome Chave [dtc],
Bruno Hérault [aut],
Ted Feldpausch [dtc],
Philippe Verley [ctb]
Maintainer: Maxime Réjou-Méchain <maxime.rejou@gmail.com>
Diff between BIOMASS versions 2.1.6 dated 2021-06-25 and 2.1.7 dated 2021-12-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 3 +++ R/computeFeldRegion.R | 2 +- R/predictHeight.R | 2 +- inst/doc/BIOMASS.html | 2 +- inst/doc/plot.html | 12 ++++++------ 7 files changed, 22 insertions(+), 19 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Functions introduced or changed since R v3.0.0 are re-implemented in this
package. The backports are conditionally exported in order to let R resolve
the function name to either the implemented backport, or the respective base
version, if available. Package developers can make use of new functions or
arguments by selectively importing specific backports to
support older installations.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
R Core Team [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.4.0 dated 2021-11-23 and 1.4.1 dated 2021-12-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/dotsNames.c | 29 +++++++++++++++++++---------- tests/test_dotsNames.R | 5 +++-- 5 files changed, 33 insertions(+), 19 deletions(-)
Title: Drag-and-Drop in 'shiny' Apps with 'SortableJS'
Description: Enables drag-and-drop behaviour in Shiny apps, by exposing the
functionality of the 'SortableJS' <https://sortablejs.github.io/Sortable/>
JavaScript library as an 'htmlwidget'.
You can use this in Shiny apps and widgets, 'learnr' tutorials as well as
R Markdown. In addition, provides a custom 'learnr' question type -
'question_rank()' - that allows ranking questions with drag-and-drop.
Author: Andrie de Vries [cre, aut],
Barret Schloerke [aut],
Kenton Russell [aut, ccp] (Original author),
RStudio [cph, fnd],
Lebedev Konstantin [cph] ('SortableJS',
https://sortablejs.github.io/Sortable/)
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between sortable versions 0.4.4 dated 2020-09-17 and 0.4.5 dated 2021-12-13
DESCRIPTION | 15 MD5 | 93 NEWS.md | 29 R/assertions.R | 9 R/bucket_list.R | 15 R/js.R | 2 R/sortable_options.R | 2 build/vignette.rds |binary inst/doc/built_in.Rmd | 2 inst/doc/built_in.html | 350 - inst/doc/cloning.Rmd | 2 inst/doc/cloning.html | 402 - inst/doc/novel_solutions.R | 4 inst/doc/novel_solutions.Rmd | 4 inst/doc/novel_solutions.html | 314 - inst/doc/understanding_sortable_js.R | 2 inst/doc/understanding_sortable_js.Rmd | 6 inst/doc/understanding_sortable_js.html | 4079 ---------------- inst/doc/updating_rank_list.R |only inst/doc/updating_rank_list.Rmd |only inst/doc/updating_rank_list.html |only inst/doc/using_custom_css.Rmd | 2 inst/doc/using_custom_css.html | 142 inst/examples/example_rank_list.R | 2 inst/htmlwidgets/lib/sortable/sortable.js | 3711 -------------- inst/htmlwidgets/plugins/sortable-rstudio/rank_list.css | 1 inst/htmlwidgets/sortable.yaml | 2 inst/shiny-examples/group_list |only inst/shiny-examples/shiny_tabset/app.R | 2 inst/shiny-examples/update_rank_list |only inst/tutorials/question_rank/question_rank.Rmd | 8 inst/tutorials/question_rank/question_rank.html | 23 man/bucket_list.Rd | 5 man/figures/logo.svg | 54 man/figures/sortable-logo.png |only man/rank_list.Rd | 2 man/sortable.Rd | 8 tests/testthat/test-bucket_list.R | 37 tests/testthat/test-creation.R | 6 tests/testthat/test-htmltools.R | 10 tests/testthat/test-js.R | 3 tests/testthat/test-label_ids.R | 4 tests/testthat/test-learnr-question_rank.R | 4 tests/testthat/test-rank_list.R | 4 vignettes/built_in.Rmd | 2 vignettes/cloning.Rmd | 2 vignettes/grouped_lists.R |only vignettes/grouped_lists.html |only vignettes/novel_solutions.Rmd | 4 vignettes/understanding_sortable_js.Rmd | 6 vignettes/updating_rank_list.Rmd |only vignettes/using_custom_css.Rmd | 2 52 files changed, 1058 insertions(+), 8318 deletions(-)
Title: Material Management
Description: A set of functions, classes and methods for performing ABC and ABC/XYZ analyses, identifying overperforming, underperforming and constantly performing items, and plotting, analyzing as well as predicting the temporal development of items.
Author: Leon Binder [cre, aut],
Bernhard Bauer [aut],
Michael Scholz [aut]
Maintainer: Leon Binder <leon.binder@th-deg.de>
Diff between matman versions 1.1.2 dated 2020-11-27 and 1.1.3 dated 2021-12-13
DESCRIPTION | 14 - MD5 | 36 ++--- NAMESPACE | 23 ++- NEWS.md | 7 R/ABCXYZanalysis.R | 87 +++++------- R/DataPreparation.R | 112 +++++++-------- R/Forecast.R | 2 R/Performer.R | 201 +++++++++++----------------- R/matman-package.R | 14 - man/ABCXYZComparison-class.Rd | 106 +++++++------- man/aggregateData.Rd | 114 +++++++-------- man/compare-ABCXYZData-ABCXYZData-method.Rd | 130 +++++++++--------- man/compare.Rd | 84 +++++------ man/computeABCXYZAnalysis.Rd | 146 ++++++++++---------- man/computeConstants.Rd | 120 ++++++++-------- man/matman-package.Rd | 48 +++--- man/matmanDemo.Rd | 42 ++--- man/show-ABCXYZComparison-method.Rd | 80 +++++------ man/summary-ABCXYZComparison-method.Rd | 82 +++++------ 19 files changed, 720 insertions(+), 728 deletions(-)
Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting, originating from Japan and now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'. Incorporates an interface with the OANDA
fxTrade API <https://developer.oanda.com/> for retrieving historical and
live streaming price data for major currencies, metals, commodities,
government bonds and stock indices.
Author: Charlie Gao [aut, cre] (<https://orcid.org/0000-0002-0750-061X>)
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 1.2.4 dated 2021-10-18 and 1.2.5 dated 2021-12-13
ichimoku-1.2.4/ichimoku/R/look.R |only ichimoku-1.2.4/ichimoku/src/shikokuchuo.cpp |only ichimoku-1.2.5/ichimoku/DESCRIPTION | 8 ichimoku-1.2.5/ichimoku/MD5 | 135 ++--- ichimoku-1.2.5/ichimoku/NAMESPACE | 11 ichimoku-1.2.5/ichimoku/NEWS.md | 29 + ichimoku-1.2.5/ichimoku/R/archive.R | 60 +- ichimoku-1.2.5/ichimoku/R/ichimoku-package.R | 16 ichimoku-1.2.5/ichimoku/R/ichimoku.R | 395 +-------------- ichimoku-1.2.5/ichimoku/R/iplot.R | 47 - ichimoku-1.2.5/ichimoku/R/methods.R |only ichimoku-1.2.5/ichimoku/R/mltools.R | 131 +++-- ichimoku-1.2.5/ichimoku/R/oanda.R | 436 +++++++++++------ ichimoku-1.2.5/ichimoku/R/plot.R | 49 + ichimoku-1.2.5/ichimoku/R/strat.R | 5 ichimoku-1.2.5/ichimoku/R/switch.R | 41 - ichimoku-1.2.5/ichimoku/R/sysdata.rda |binary ichimoku-1.2.5/ichimoku/R/utils.R | 134 ++++- ichimoku-1.2.5/ichimoku/README.md | 12 ichimoku-1.2.5/ichimoku/build/vignette.rds |binary ichimoku-1.2.5/ichimoku/data/sample_ohlc_data.rda |binary ichimoku-1.2.5/ichimoku/inst/doc/reference.R | 16 ichimoku-1.2.5/ichimoku/inst/doc/reference.Rmd | 47 + ichimoku-1.2.5/ichimoku/inst/doc/reference.html | 114 ++-- ichimoku-1.2.5/ichimoku/inst/doc/strategies.R | 5 ichimoku-1.2.5/ichimoku/inst/doc/strategies.Rmd | 32 - ichimoku-1.2.5/ichimoku/inst/doc/strategies.html | 100 ++- ichimoku-1.2.5/ichimoku/inst/doc/utilities.R | 14 ichimoku-1.2.5/ichimoku/inst/doc/utilities.Rmd | 27 - ichimoku-1.2.5/ichimoku/inst/doc/utilities.html | 371 ++++++-------- ichimoku-1.2.5/ichimoku/inst/doc/xoanda.R | 49 + ichimoku-1.2.5/ichimoku/inst/doc/xoanda.Rmd | 83 ++- ichimoku-1.2.5/ichimoku/inst/doc/xoanda.html | 308 ++++++------ ichimoku-1.2.5/ichimoku/man/archive.Rd | 15 ichimoku-1.2.5/ichimoku/man/as.data.frame.ichimoku.Rd | 5 ichimoku-1.2.5/ichimoku/man/as_tibble.ichimoku.Rd |only ichimoku-1.2.5/ichimoku/man/autoplot.ichimoku.Rd | 6 ichimoku-1.2.5/ichimoku/man/autostrat.Rd | 5 ichimoku-1.2.5/ichimoku/man/coredata.ichimoku.Rd | 5 ichimoku-1.2.5/ichimoku/man/df_append.Rd | 8 ichimoku-1.2.5/ichimoku/man/extraplot.Rd | 6 ichimoku-1.2.5/ichimoku/man/ichimoku-package.Rd | 4 ichimoku-1.2.5/ichimoku/man/ichimoku.Rd | 15 ichimoku-1.2.5/ichimoku/man/index.ichimoku.Rd | 14 ichimoku-1.2.5/ichimoku/man/iplot.Rd | 6 ichimoku-1.2.5/ichimoku/man/is.ichimoku.Rd | 2 ichimoku-1.2.5/ichimoku/man/look.Rd | 18 ichimoku-1.2.5/ichimoku/man/mlgrid.Rd | 33 - ichimoku-1.2.5/ichimoku/man/more.Rd |only ichimoku-1.2.5/ichimoku/man/oanda.Rd | 6 ichimoku-1.2.5/ichimoku/man/oanda_chart.Rd | 11 ichimoku-1.2.5/ichimoku/man/oanda_orders.Rd |only ichimoku-1.2.5/ichimoku/man/oanda_positions.Rd | 6 ichimoku-1.2.5/ichimoku/man/oanda_stream.Rd | 54 +- ichimoku-1.2.5/ichimoku/man/oanda_studio.Rd | 6 ichimoku-1.2.5/ichimoku/man/plot.ichimoku.Rd | 14 ichimoku-1.2.5/ichimoku/man/print.ichimoku.Rd | 12 ichimoku-1.2.5/ichimoku/man/relative.Rd | 17 ichimoku-1.2.5/ichimoku/man/str.ichimoku.Rd | 5 ichimoku-1.2.5/ichimoku/man/summary.ichimoku.Rd | 6 ichimoku-1.2.5/ichimoku/src/cpp11.cpp | 6 ichimoku-1.2.5/ichimoku/src/windowfn.cpp |only ichimoku-1.2.5/ichimoku/tests/testthat/test-archive.R | 4 ichimoku-1.2.5/ichimoku/tests/testthat/test-ichimoku.R | 21 ichimoku-1.2.5/ichimoku/tests/testthat/test-iplot.R | 4 ichimoku-1.2.5/ichimoku/tests/testthat/test-mltools.R | 18 ichimoku-1.2.5/ichimoku/tests/testthat/test-plot.R | 6 ichimoku-1.2.5/ichimoku/tests/testthat/test-utils.R | 6 ichimoku-1.2.5/ichimoku/vignettes/reference.Rmd | 47 + ichimoku-1.2.5/ichimoku/vignettes/strategies.Rmd | 32 - ichimoku-1.2.5/ichimoku/vignettes/utilities.Rmd | 27 - ichimoku-1.2.5/ichimoku/vignettes/xoanda.Rmd | 83 ++- 72 files changed, 1708 insertions(+), 1500 deletions(-)
Title: Functions for Medical Statistics Book with some Demographic Data
Description: Several utility functions for the book entitled
"Practices of Medical and Health Data Analysis using R"
(Pearson Education Japan, 2007) with Japanese demographic
data and some demographic analysis related functions.
Author: Minato Nakazawa <minatonakazawa@gmail.com>
Maintainer: Minato Nakazawa <minatonakazawa@gmail.com>
Diff between fmsb versions 0.7.1 dated 2021-05-11 and 0.7.2 dated 2021-12-13
fmsb-0.7.1/fmsb/tests |only fmsb-0.7.2/fmsb/DESCRIPTION | 15 ++++++++------- fmsb-0.7.2/fmsb/MD5 | 25 ++++++++++++------------- fmsb-0.7.2/fmsb/NAMESPACE | 2 +- fmsb-0.7.2/fmsb/NEWS | 4 ++++ fmsb-0.7.2/fmsb/R/demogjpn.R | 23 ++++++++++++++++++----- fmsb-0.7.2/fmsb/build/partial.rdb |binary fmsb-0.7.2/fmsb/man/CT.Rd | 4 ++-- fmsb-0.7.2/fmsb/man/Jfert.Rd | 2 +- fmsb-0.7.2/fmsb/man/Jpop.Rd | 17 +++++++++++------ fmsb-0.7.2/fmsb/man/Jpopl.Rd | 17 +++++++++++------ fmsb-0.7.2/fmsb/man/Jvital.Rd | 2 +- fmsb-0.7.2/fmsb/man/PEI.Rd | 2 +- fmsb-0.7.2/fmsb/man/rateratio.Rd | 2 +- 14 files changed, 71 insertions(+), 44 deletions(-)
Title: Fast Implementation of the Diffusion Decision Model
Description: Provides the probability density function (PDF) and cumulative
distribution function (CDF) of the diffusion decision model
(DDM; e.g., Ratcliff & McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>)
with across-trial variability in the drift rate. Because the PDF and CDF of
the DDM both contain an infinite sum, they needs to be approximated. 'fddm'
implements all published approximations
(Navarro & Fuss, 2009, <doi:10.1016/j.jmp.2009.02.003>;
Gondan, Blurton, & Kesselmeier, 2014, <doi:10.1016/j.jmp.2014.05.002>;
Blurton, Kesselmeier, & Gondan, 2017, <doi:10.1016/j.jmp.2016.11.003>) plus
new approximations. All approximations are implemented purely in 'C++'
providing faster speed than existing packages.
Author: Kendal B. Foster [aut],
Henrik Singmann [ctb, cre] (<https://orcid.org/0000-0002-4842-3657>)
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between fddm versions 0.4-0 dated 2021-08-06 and 0.4-1 dated 2021-12-13
DESCRIPTION | 6 - MD5 | 20 +-- NEWS.md | 10 + build/vignette.rds |binary inst/doc/benchmark.html | 40 +++---- inst/doc/example.html | 148 +++++++++++++-------------- inst/doc/math.html | 40 +++---- inst/doc/pfddm.html | 40 +++---- inst/doc/validity.html | 36 +++--- src/dfddm_helper_functions/density_funcs.h | 2 tests/testthat/test-validity_vignette_fits.R | 4 11 files changed, 177 insertions(+), 169 deletions(-)
Title: Automated Tuning and Evaluations of Ecological Niche Models
Description: Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate niche overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0.0-vignette.html>.
Author: Jamie M. Kass [aut, cre],
Robert Muscarella [aut],
Peter J. Galante [aut],
Corentin Bohl [aut],
Gonzalo E. Buitrago-Pinilla [aut],
Robert A. Boria [aut],
Mariano Soley-Guardia [aut],
Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jamie.m.kass@gmail.com>
Diff between ENMeval versions 2.0.1 dated 2021-06-11 and 2.0.2 dated 2021-12-13
ENMeval-2.0.1/ENMeval/man/boyce.cm.Rd |only ENMeval-2.0.1/ENMeval/tests/testthat/test_bioclim.R |only ENMeval-2.0.1/ENMeval/tests/testthat/test_maxent.jar.R |only ENMeval-2.0.1/ENMeval/tests/testthat/test_maxnet.R |only ENMeval-2.0.2/ENMeval/DESCRIPTION | 18 +-- ENMeval-2.0.2/ENMeval/MD5 | 44 ++++---- ENMeval-2.0.2/ENMeval/NAMESPACE | 1 ENMeval-2.0.2/ENMeval/NEWS | 10 + ENMeval-2.0.2/ENMeval/R/ENMevaluate.R | 29 ++++- ENMeval-2.0.2/ENMeval/R/ENMnulls.R | 17 ++- ENMeval-2.0.2/ENMeval/R/classes.R | 21 ++-- ENMeval-2.0.2/ENMeval/R/enm.maxent.jar.R | 2 ENMeval-2.0.2/ENMeval/R/plotting.R | 73 +++++++------ ENMeval-2.0.2/ENMeval/R/tune.enm.R | 32 ++++-- ENMeval-2.0.2/ENMeval/R/utilities.R | 89 ++--------------- ENMeval-2.0.2/ENMeval/R/zzz.R |only ENMeval-2.0.2/ENMeval/README.md | 17 ++- ENMeval-2.0.2/ENMeval/build/partial.rdb |binary ENMeval-2.0.2/ENMeval/man/ENMevaluate.Rd | 8 + ENMeval-2.0.2/ENMeval/man/enm.maxent.jar.Rd | 2 ENMeval-2.0.2/ENMeval/man/evalplot.envSim.hist.Rd | 40 ++++--- ENMeval-2.0.2/ENMeval/man/evalplot.envSim.map.Rd | 33 +++--- ENMeval-2.0.2/ENMeval/man/tune.enm.Rd | 2 ENMeval-2.0.2/ENMeval/tests/testthat.R | 2 ENMeval-2.0.2/ENMeval/tests/testthat/helper_funcs.R | 76 +++++++------- ENMeval-2.0.2/ENMeval/tests/testthat/test_mods.R |only 26 files changed, 261 insertions(+), 255 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre, cph],
Matt Dennis [ctb],
Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>),
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb],
Swechhya Bista [ctb],
Colin Fay [ctb] (<https://orcid.org/0000-0001-7343-1846>)
Maintainer: Andrew B. Collier <andrew@fathomdata.dev>
Diff between emayili versions 0.6.1 dated 2021-10-08 and 0.7.0 dated 2021-12-13
emayili-0.6.1/emayili/man/qp_decode.Rd |only emayili-0.6.1/emayili/man/qp_encode.Rd |only emayili-0.6.1/emayili/tests/testthat/setup-files.R |only emayili-0.6.1/emayili/tests/testthat/test-precedence.R |only emayili-0.7.0/emayili/DESCRIPTION | 30 - emayili-0.7.0/emayili/MD5 | 105 ++-- emayili-0.7.0/emayili/NAMESPACE | 20 emayili-0.7.0/emayili/NEWS.md | 83 ++- emayili-0.7.0/emayili/R/address.R | 27 - emayili-0.7.0/emayili/R/attachment.R | 7 emayili-0.7.0/emayili/R/body.R | 85 ++- emayili-0.7.0/emayili/R/const.R |only emayili-0.7.0/emayili/R/emayili.R | 17 emayili-0.7.0/emayili/R/encoding.R | 190 +++++--- emayili-0.7.0/emayili/R/encrypt.R |only emayili-0.7.0/emayili/R/envelope.R | 92 ++-- emayili-0.7.0/emayili/R/header-expires.R |only emayili-0.7.0/emayili/R/header-language.R |only emayili-0.7.0/emayili/R/header-mail.R | 119 ++++- emayili-0.7.0/emayili/R/header-mime.R | 44 + emayili-0.7.0/emayili/R/header-precedence.R | 3 emayili-0.7.0/emayili/R/header-receipt.R |only emayili-0.7.0/emayili/R/header-sensitivity.R |only emayili-0.7.0/emayili/R/header.R | 25 - emayili-0.7.0/emayili/R/mime.R | 229 +++++++++- emayili-0.7.0/emayili/R/render.R | 18 emayili-0.7.0/emayili/R/server.R | 173 +++++++ emayili-0.7.0/emayili/R/utils.R | 85 +++ emayili-0.7.0/emayili/README.md | 87 ++- emayili-0.7.0/emayili/man/addresses.Rd | 7 emayili-0.7.0/emayili/man/as.character.header.Rd | 4 emayili-0.7.0/emayili/man/attachment.Rd | 13 emayili-0.7.0/emayili/man/comments.Rd |only emayili-0.7.0/emayili/man/cutoff.Rd |only emayili-0.7.0/emayili/man/encrypt.Rd |only emayili-0.7.0/emayili/man/envelope.Rd | 15 emayili-0.7.0/emayili/man/html.Rd | 34 + emayili-0.7.0/emayili/man/keywords.Rd |only emayili-0.7.0/emayili/man/mime-parameters.Rd |only emayili-0.7.0/emayili/man/pipe.Rd | 10 emayili-0.7.0/emayili/man/qp.Rd |only emayili-0.7.0/emayili/man/render.Rd | 8 emayili-0.7.0/emayili/man/request_receipt_read.Rd |only emayili-0.7.0/emayili/man/response.Rd |only emayili-0.7.0/emayili/man/sensitivity.Rd |only emayili-0.7.0/emayili/man/server.Rd | 95 +++- emayili-0.7.0/emayili/man/subject.Rd | 2 emayili-0.7.0/emayili/man/text.Rd | 30 - emayili-0.7.0/emayili/tests/testthat/setup.R |only emayili-0.7.0/emayili/tests/testthat/test-address.R | 2 emayili-0.7.0/emayili/tests/testthat/test-attachment.R | 2 emayili-0.7.0/emayili/tests/testthat/test-body.R | 63 ++ emayili-0.7.0/emayili/tests/testthat/test-compatibility-microsoft365r.R |only emayili-0.7.0/emayili/tests/testthat/test-encoding.R | 29 + emayili-0.7.0/emayili/tests/testthat/test-encrypt.R |only emayili-0.7.0/emayili/tests/testthat/test-envelope.R | 19 emayili-0.7.0/emayili/tests/testthat/test-header-language.R |only emayili-0.7.0/emayili/tests/testthat/test-header-precedence.R |only emayili-0.7.0/emayili/tests/testthat/test-header-receipt.R |only emayili-0.7.0/emayili/tests/testthat/test-header-various.R |only emayili-0.7.0/emayili/tests/testthat/test-header.R | 4 emayili-0.7.0/emayili/tests/testthat/test-locale.R |only emayili-0.7.0/emayili/tests/testthat/test-message.R | 4 emayili-0.7.0/emayili/tests/testthat/test-mime.R | 21 emayili-0.7.0/emayili/tests/testthat/test-server.R | 16 emayili-0.7.0/emayili/tests/testthat/test-utils.R | 27 + emayili-0.7.0/emayili/tools |only 67 files changed, 1471 insertions(+), 373 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre, cph],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb, cph],
Simon Urbanek [ctb, cph],
Karl Forner [ctb, cph],
Alexander Ly [ctb, cph]
Maintainer: Richard D. Morey <richarddmorey@gmail.com>
Diff between BayesFactor versions 0.9.12-4.2 dated 2018-05-19 and 0.9.12-4.3 dated 2021-12-13
DESCRIPTION | 10 - MD5 | 120 ++++++++++----------- NEWS | 9 + R/BayesFactorPCL-package.R | 2 R/RcppExports.R | 8 - R/anovaBF.R | 3 R/contingency.R | 2 R/correlationBF.R | 2 R/logMean.R | 4 R/meta-ttest-utility.R | 13 +- R/methods-BFBayesFactor.R | 2 R/methods-BFodds.R | 2 R/methods-BFprobability.R | 2 R/nWayAOV-utility.R | 19 +-- R/nWayAOV.R | 2 build/vignette.rds |binary inst/doc/compare_lme4.R | 38 +++--- inst/doc/compare_lme4.html | 30 ++--- inst/doc/index.R | 2 inst/doc/manual.R | 188 ++++++++++++++++----------------- inst/doc/manual.Rmd | 30 ++--- inst/doc/manual.html | 142 +++++++++++------------- inst/doc/odds_probs.R | 20 +-- inst/doc/odds_probs.Rmd | 11 - inst/doc/odds_probs.html | 12 -- inst/doc/priors.R | 18 +-- inst/doc/priors.html | 10 - inst/include/BayesFactor_RcppExports.h | 2 man/BFBayesFactor-class.Rd | 3 man/BFBayesFactorList-class.Rd | 6 - man/BFprobability-class.Rd | 3 man/BayesFactor-package.Rd | 2 man/anovaBF.Rd | 23 ++-- man/contingencyTableBF.Rd | 16 +- man/correlationBF.Rd | 13 +- man/enumerateGeneralModels.Rd | 9 + man/extractProbabilities-methods.Rd | 3 man/generalTestBF.Rd | 23 ++-- man/lmBF.Rd | 15 ++ man/logMeanExpLogs.Rd | 4 man/meta.ttestBF.Rd | 12 +- man/model-classes.Rd | 1 man/model.matrix-methods.Rd | 1 man/nWayAOV.Rd | 19 ++- man/plot.BFBayesFactor.Rd | 16 ++ man/plot.BFBayesFactorTop.Rd | 13 +- man/posterior-methods.Rd | 33 +---- man/proportionBF.Rd | 12 +- man/puzzles.Rd | 6 - man/raceDolls.Rd | 6 - man/recompute-methods.Rd | 50 ++++++-- man/regressionBF.Rd | 12 +- man/ttest.tstat.Rd | 11 + man/ttestBF.Rd | 16 ++ src/RcppExports.cpp | 55 +++++---- src/bfcommon.h | 2 src/logSummaryStats.cpp | 2 src/logUtility.cpp | 2 vignettes/extra/socialmedia/readme.txt | 60 +++++----- vignettes/manual.Rmd | 30 ++--- vignettes/odds_probs.Rmd | 11 - 61 files changed, 655 insertions(+), 538 deletions(-)
Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams
based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between yorkr versions 0.0.28 dated 2021-11-07 and 0.0.29 dated 2021-12-13
DESCRIPTION | 10 - MD5 | 108 +++++++++++++++--- NAMESPACE | 35 +++++ R/helper.R | 37 ++---- R/helper1.R | 38 ++---- R/helper2.R | 40 ++---- R/helper3.R | 39 ++---- R/overallRunsSRDeathOversPlotT20.R |only R/overallRunsSRMiddleOversPlotT20.R |only R/overallRunsSRPPowerplayPlotT20.R |only R/overallRunsSRPlotT20.R |only R/overallWicketsERDeathOversPlotT20.R |only R/overallWicketsERMiddleOversPlotT20.R |only R/overallWicketsERPlotT20.R |only R/overallWicketsERPowerPlayPlotT20.R |only R/rankT20Batsmen.R | 118 ++++++++------------ R/rankT20Bowlers.R | 45 ++----- R/saveAllT20BattingDetails.R |only R/saveAllT20BowlingDetails.R |only R/saveAllT20MatchesAsDF.R |only R/teamERAcrossOvers.R | 4 R/teamRunSRDeathOversPlotAllOppnAllMatches.R |only R/teamRunSRDeathOversPlotMatch.R |only R/teamRunSRDeathOversPlotOppnAllMatches.R |only R/teamRunsSRMiddleOversPlotAllOppnAllMatches.R |only R/teamRunsSRMiddleOversPlotMatch.R |only R/teamRunsSRMiddleOversPlotOppnAllMatches.R |only R/teamRunsSRPlotAllOppnAllMatches.R |only R/teamRunsSRPlotMatch.R |only R/teamRunsSRPlotOppnAllMatches.R |only R/teamRunsSRPowerPlayPlotAllOppnAllMatches.R |only R/teamRunsSRPowerPlayPlotMatch.R |only R/teamRunsSRPowerPlayPlotOppnAllMatches.R |only R/teamWicketsAcrossOversAllOppnAllMatches.R | 2 R/teamWicketsERDeathOversPlotAllOppnAllMatches.R |only R/teamWicketsERDeathOversPlotMatch.R |only R/teamWicketsERDeathOversPlotOppnAllMatches.R |only R/teamWicketsERMiddleOversPlotAllOppnAllMatches.R |only R/teamWicketsERMiddleOversPlotMatch.R |only R/teamWicketsERMiddleOversPlotOppnAllMatches.R |only R/teamWicketsERPlotAllOppnAllMatches.R |only R/teamWicketsERPlotMatch.R |only R/teamWicketsERPlotOppnAllMatches.R |only R/teamWicketsERPowerPlayPlotAllOppnAllMatches.R |only R/teamWicketsERPowerPlayPlotMatch.R |only R/teamWicketsERPowerPlayPlotOppnAllMatches.R |only R/topRunsBatsmenAcrossOversOppnAllMatches.R | 2 R/topWicketsBowlerAcrossOversAllOppnAllMatches.R | 2 man/helper.Rd | 6 - man/helper1.Rd | 8 - man/helper2.Rd | 8 - man/helper3.Rd | 8 - man/overallRunsSRDeathOversPlotT20.Rd |only man/overallRunsSRMiddleOversPlotT20.Rd |only man/overallRunsSRPPowerplayPlotT20.Rd |only man/overallRunsSRPlotT20.Rd |only man/overallWicketsERDeathOversPlotT20.Rd |only man/overallWicketsERMiddleOversPlotT20.Rd |only man/overallWicketsERPlotT20.Rd |only man/overallWicketsERPowerPlayPlotT20.Rd |only man/rankT20Batsmen.Rd | 13 -- man/rankT20Bowlers.Rd | 13 -- man/saveAllT20BattingDetails.Rd |only man/saveAllT20BowlingDetails.Rd |only man/saveAllT20MatchesAsDF.Rd |only man/teamRunSRDeathOversPlotAllOppnAllMatches.Rd |only man/teamRunSRDeathOversPlotMatch.Rd |only man/teamRunSRDeathOversPlotOppnAllMatches.Rd |only man/teamRunsSRMiddleOversPlotAllOppnAllMatches.Rd |only man/teamRunsSRPMiddleOversPlotMatch.Rd |only man/teamRunsSRPMiddleOversPlotOppnAllMatches.Rd |only man/teamRunsSRPlotAllOppnAllMatches.Rd |only man/teamRunsSRPlotMatch.Rd |only man/teamRunsSRPlotOppnAllMatches.Rd |only man/teamRunsSRPowerPlayPlotAllOppnAllMatches.Rd |only man/teamRunsSRPowerPlayPlotMatch.Rd |only man/teamRunsSRPowerPlayPlotOppnAllMatches.Rd |only man/teamWicketERDeathOversPlotOppnAllMatches.Rd |only man/teamWicketERMiddleOversPlotAllOppnAllMatches.Rd |only man/teamWicketERMiddleOversPlotOppnAllMatches.Rd |only man/teamWicketERPowerPlayPlotOppnAllMatches.Rd |only man/teamWicketsAcrossOversAllOppnAllMatches.Rd | 2 man/teamWicketsERDeathOversPlotAllOppnAllMatches.Rd |only man/teamWicketsERDeathOversPlotMatch.Rd |only man/teamWicketsERMiddleOversPlotMatch.Rd |only man/teamWicketsERPlotAllOppnAllMatches.Rd |only man/teamWicketsERPlotMatch.Rd |only man/teamWicketsERPlotOppnAllMatches.Rd |only man/teamWicketsERPowerPlayPlotAllOppnAllMatches.Rd |only man/teamWicketsERPowerPlayPlotMatch.Rd |only 90 files changed, 287 insertions(+), 251 deletions(-)
Title: Rational Approximations of Fractional Stochastic Partial
Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main reference for the methods is Bolin and Kirchner (2020) <doi:10.1080/10618600.2019.1665537>, which can be generated by the citation function in R.
Author: David Bolin [cre, aut],
Alexandre Simas [aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between rSPDE versions 0.6.3 dated 2021-10-14 and 1.0.0 dated 2021-12-13
rSPDE-0.6.3/rSPDE/inst/doc/rspde.R |only rSPDE-0.6.3/rSPDE/inst/doc/rspde.Rmd |only rSPDE-0.6.3/rSPDE/inst/doc/rspde.html |only rSPDE-0.6.3/rSPDE/vignettes/rspde.Rmd |only rSPDE-1.0.0/rSPDE/DESCRIPTION | 27 rSPDE-1.0.0/rSPDE/LICENSE |only rSPDE-1.0.0/rSPDE/MD5 | 83 rSPDE-1.0.0/rSPDE/NAMESPACE | 33 rSPDE-1.0.0/rSPDE/NEWS.md | 9 rSPDE-1.0.0/rSPDE/R/fractional.computations.R | 1156 ++++++++++- rSPDE-1.0.0/rSPDE/R/fractional.operators.R | 336 ++- rSPDE-1.0.0/rSPDE/R/inla_rspde.R |only rSPDE-1.0.0/rSPDE/R/rSPDE.R | 19 rSPDE-1.0.0/rSPDE/R/sysdata.rda |binary rSPDE-1.0.0/rSPDE/R/util.R | 558 +++++ rSPDE-1.0.0/rSPDE/build/vignette.rds |binary rSPDE-1.0.0/rSPDE/inst/doc/rSPDE.html |only rSPDE-1.0.0/rSPDE/inst/doc/rSPDE.html.asis |only rSPDE-1.0.0/rSPDE/inst/doc/rspde_base.html |only rSPDE-1.0.0/rSPDE/inst/doc/rspde_base.html.asis |only rSPDE-1.0.0/rSPDE/inst/doc/rspde_cov.html |only rSPDE-1.0.0/rSPDE/inst/doc/rspde_cov.html.asis |only rSPDE-1.0.0/rSPDE/inst/doc/rspde_inla.html |only rSPDE-1.0.0/rSPDE/inst/doc/rspde_inla.html.asis |only rSPDE-1.0.0/rSPDE/man/figures |only rSPDE-1.0.0/rSPDE/man/folded.matern.covariance.Rd |only rSPDE-1.0.0/rSPDE/man/fractional.operators.Rd | 7 rSPDE-1.0.0/rSPDE/man/get.inital.values.rSPDE.Rd |only rSPDE-1.0.0/rSPDE/man/get.sparsity.graph.rspde.Rd |only rSPDE-1.0.0/rSPDE/man/matern.loglike.Rd | 98 rSPDE-1.0.0/rSPDE/man/matern.operators.Rd | 127 + rSPDE-1.0.0/rSPDE/man/plot.rspde.result.Rd |only rSPDE-1.0.0/rSPDE/man/precision.CBrSPDEobj.Rd |only rSPDE-1.0.0/rSPDE/man/predict.CBrSPDEobj.Rd |only rSPDE-1.0.0/rSPDE/man/predict.rSPDEobj.Rd | 2 rSPDE-1.0.0/rSPDE/man/rSPDE.Rd | 19 rSPDE-1.0.0/rSPDE/man/rSPDE.loglike.Rd | 9 rSPDE-1.0.0/rSPDE/man/rSPDE.matern.loglike.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.make.A.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.make.index.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.matern.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.matern.precision.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.matern.precision.integer.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.matern.precision.integer.opt.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.matern.precision.opt.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.mesh.project.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.precision.Rd |only rSPDE-1.0.0/rSPDE/man/rspde.result.Rd |only rSPDE-1.0.0/rSPDE/man/simulate.CBrSPDEobj.Rd |only rSPDE-1.0.0/rSPDE/man/simulate.rSPDEobj.Rd | 11 rSPDE-1.0.0/rSPDE/man/spde.matern.loglike.Rd | 6 rSPDE-1.0.0/rSPDE/man/spde.matern.operators.Rd | 5 rSPDE-1.0.0/rSPDE/man/summary.CBrSPDEobj.Rd |only rSPDE-1.0.0/rSPDE/man/summary.rSPDEobj.Rd | 2 rSPDE-1.0.0/rSPDE/man/summary.rspde.result.Rd |only rSPDE-1.0.0/rSPDE/man/update.CBrSPDEobj.Rd |only rSPDE-1.0.0/rSPDE/man/update.rSPDEobj.Rd |only rSPDE-1.0.0/rSPDE/tests/testthat/test.CBrSPDE.R |only rSPDE-1.0.0/rSPDE/tests/testthat/test.fractional.operators.R | 9 rSPDE-1.0.0/rSPDE/tests/testthat/test.inla_rspde.R |only rSPDE-1.0.0/rSPDE/vignettes/rSPDE.html.asis |only rSPDE-1.0.0/rSPDE/vignettes/rspde_base.html.asis |only rSPDE-1.0.0/rSPDE/vignettes/rspde_cov.html.asis |only rSPDE-1.0.0/rSPDE/vignettes/rspde_inla.html.asis |only 64 files changed, 2358 insertions(+), 158 deletions(-)
Title: Ecological Inference by Linear Programming under Homogeneity
Description: Provides a bunch of algorithms based on linear programming for estimating,
under the homogeneity hypothesis, RxC ecological contingency tables
(or vote transition matrices) using exclusively aggregate
data (from voting units). References:
Romero, Pavía, Martín and Romero (2020) <doi:10.1080/02664763.2020.1804842>.
Pavía and Romero (2021a) <doi:10.31124/advance.14716638.v1>.
Pavía and Romero (2021b) Symmetry estimating R×C vote transfer matrices from aggregate data.
Author: Jose M. Pavia [aut, cre] (<https://orcid.org/0000-0002-0129-726X>),
Rafael Romero [aut]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between lphom versions 0.3.0-7 dated 2021-09-09 and 0.3.0-11 dated 2021-12-13
DESCRIPTION | 31 MD5 | 69 - NAMESPACE | 42 R/adjust2integers.R |only R/auxiliar.R | 2650 +++++++++++++++++++++---------------------- R/confidence_intervals_pjk.R | 160 +- R/error_lphom.R | 223 +-- R/lclphom.R | 570 ++++----- R/lphom.R | 787 ++++++------ R/lphom_dual.R | 216 +-- R/lphom_joint.R | 274 ++-- R/nslphom.R | 612 +++++---- R/nslphom_dual.R | 298 ++-- R/nslphom_joint.R | 321 ++--- R/plot.R |only R/print.R |only R/summary.R |only R/tslphom.R | 440 +++---- R/tslphom_dual.R | 254 ++-- R/tslphom_joint.R | 201 +-- build/partial.rdb |binary inst/CITATION | 114 - man/France2017D.Rd | 86 - man/France2017P.Rd | 84 - man/adjust2integers.Rd |only man/error_lphom.Rd | 6 man/lclphom.Rd | 86 - man/lphom.Rd | 49 man/lphom_dual.Rd | 16 man/lphom_joint.Rd | 18 man/nslphom.Rd | 72 - man/nslphom_dual.Rd | 18 man/nslphom_joint.Rd | 24 man/plot.lphom.Rd |only man/print.lphom.Rd |only man/print.summary.lphom.Rd |only man/summary.lphom.Rd |only man/tslphom.Rd | 74 - man/tslphom_dual.Rd | 16 man/tslphom_joint.Rd | 20 40 files changed, 3997 insertions(+), 3834 deletions(-)
Title: Covariate Adjusted PCoA Plot
Description: In fields such as ecology, microbiology, and genomics, non-Euclidean distances are widely applied to describe pairwise dissimilarity between samples. Given these pairwise distances, principal coordinates analysis (PCoA) is commonly used to construct a visualization of the data. However, confounding covariates can make patterns related to the scientific question of interest difficult to observe. We provide 'aPCoA' as an easy-to-use tool to improve data visualization in this context, enabling enhanced presentation of the effects of interest. Details are described in Yushu Shi, Liangliang Zhang, Kim-Anh Do, Christine Peterson and Robert Jenq (2020) Bioinformatics, Volume 36, Issue 13, 4099-4101.
Author: Yushu Shi
Maintainer: Yushu Shi <shiyushu2006@gmail.com>
Diff between aPCoA versions 1.2 dated 2020-08-12 and 1.3 dated 2021-12-13
DESCRIPTION | 10 - MD5 | 8 - R/aPCoA.R | 354 +++++++++++++++++++++++++++--------------------------- data/Tasmania.rda |binary man/aPCoA.Rd | 92 +++++++------- 5 files changed, 237 insertions(+), 227 deletions(-)
Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Yi Xiong [aut] (<https://orcid.org/0000-0002-4370-9824>),
Longfei Zhao [aut] (<https://orcid.org/0000-0002-6277-0137>),
Kai Gu [aut] (<https://orcid.org/0000-0002-0177-0774>),
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 1.1.3 dated 2021-11-29 and 1.1.4 dated 2021-12-13
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NEWS.md | 8 +++++ R/query_value.R | 2 + R/tcga_surv.R | 6 ++-- README.md | 2 + inst/doc/api.html | 6 ++-- inst/shinyapp/modules/modules-ga-scatter-correlation.R | 3 +- inst/shinyapp/modules/modules-pcawg-survival-analysis.R | 23 +++++++++++++--- inst/shinyapp/modules/modules-survival-analysis.R | 20 +++++++++++++ 10 files changed, 71 insertions(+), 23 deletions(-)
Title: Identification of Parental Lines via Genomic Prediction
Description: Combining genomic prediction with Monte Carlo simulation, three different
strategies are implemented to select parental lines for multiple traits in plant
breeding. The selection strategies include (i) GEBV-O considers only genomic
estimated breeding values (GEBVs) of the candidate individuals; (ii) GD-O
considers only genomic diversity (GD) of the candidate individuals; and (iii)
GEBV-GD considers both GEBV and GD. The above method can be seen in Chung PY,
Liao CT (2020) <doi:10.1371/journal.pone.0243159>. Multi-trait genomic best
linear unbiased prediction (MT-GBLUP) model is used to simultaneously estimate
GEBVs of the target traits, and then a selection index is adopted to evaluate
the composite performance of an individual.
Author: Ping-Yuan Chung [cre],
Chen-Tuo Liao [aut]
Maintainer: Ping-Yuan Chung <r06621204@ntu.edu.tw>
Diff between IPLGP versions 1.3.0 dated 2021-09-08 and 2.0.0 dated 2021-12-13
DESCRIPTION | 6 MD5 | 30 +-- NAMESPACE | 1 R/GBLUP.fit.R | 131 ++++++++++++--- R/geno.d.R |only R/output.best.R | 30 ++- R/output.gain.R | 18 +- R/simu.GDO.R | 449 +++++++++++++++++++++++++++++++++++++++++++--------- R/simu.GEBVGD.R | 455 +++++++++++++++++++++++++++++++++++++++++++---------- R/simu.GEBVO.R | 418 +++++++++++++++++++++++++++++++++++++++++------- man/GBLUP.fit.Rd | 16 + man/geno.d.Rd |only man/output.best.Rd | 5 man/output.gain.Rd | 5 man/simu.GDO.Rd | 53 ++++-- man/simu.GEBVGD.Rd | 53 ++++-- man/simu.GEBVO.Rd | 49 +++-- 17 files changed, 1380 insertions(+), 339 deletions(-)
Title: GNU Privacy Guard for R
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic
methods. Includes utilities for public key encryption, creating and verifying
digital signatures, and managing your local keyring. Some functionality
depends on the version of GnuPG that is installed on the system. On Windows
this package can be used together with 'GPG4Win' which provides a GUI for
managing keys and entering passphrases.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gpg versions 1.2.5 dated 2021-12-06 and 1.2.6 dated 2021-12-13
gpg-1.2.5/gpg/tests/version.save |only gpg-1.2.6/gpg/DESCRIPTION | 27 +++--- gpg-1.2.6/gpg/MD5 | 30 +++---- gpg-1.2.6/gpg/NAMESPACE | 1 gpg-1.2.6/gpg/NEWS | 3 gpg-1.2.6/gpg/R/keys.R | 67 ++++++++++++++-- gpg-1.2.6/gpg/R/onload.R | 2 gpg-1.2.6/gpg/configure | 6 - gpg-1.2.6/gpg/inst/doc/intro.Rmd | 2 gpg-1.2.6/gpg/inst/doc/intro.html | 136 +++++++++++++++++----------------- gpg-1.2.6/gpg/man/gpg_encrypt.Rd | 6 + gpg-1.2.6/gpg/man/gpg_info.Rd | 3 gpg-1.2.6/gpg/man/gpg_keygen.Rd | 6 + gpg-1.2.6/gpg/man/gpg_keys.Rd | 21 ++++- gpg-1.2.6/gpg/man/gpg_sign.Rd | 6 + gpg-1.2.6/gpg/tests/version.Rout.save |only gpg-1.2.6/gpg/vignettes/intro.Rmd | 2 17 files changed, 191 insertions(+), 127 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-19 0.2.2