Title: Estimation for Scale-Shape Mixtures of Skew-Normal Distributions
Description: Provide data generation and estimation tools for the multivariate scale mixtures of normal
presented in Lange and Sinsheimer (1993) <doi:10.2307/1390698>, the multivariate scale
mixtures of skew-normal presented in Zeller, Lachos and Vilca (2011)
<doi:10.1080/02664760903406504>, the multivariate skew scale mixtures of normal
presented in Louredo, Zeller and Ferreira (2021) <doi:10.1007/s13571-021-00257-y>
and the multivariate scale mixtures of skew-normal-Cauchy presented in Kahrari et al. (2020)
<doi:10.1080/03610918.2020.1804582>.
Author: Clecio Ferreira [aut],
Diego Gallardo [aut, cre],
Camila Zeller [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>
Diff between skewMLRM versions 1.1 dated 2021-09-03 and 1.2 dated 2021-09-17
DESCRIPTION | 10 ++--- INDEX | 1 MD5 | 96 +++++++++++++++++++++++++------------------------ NAMESPACE | 3 + NEWS.md | 4 ++ R/FI.MCN.R | 2 - R/FI.MN.R | 4 +- R/FI.MSCEC.R | 4 +- R/FI.MSCN.R | 2 - R/FI.MSCN2.R | 2 - R/FI.MSL.R | 2 - R/FI.MSN.R | 2 - R/FI.MSNC.R | 4 +- R/FI.MSSL.R | 2 - R/FI.MSSL2.R | 2 - R/FI.MSSLEC.R | 4 +- R/FI.MSTEC.R | 4 +- R/FI.MSTN.R | 2 - R/FI.MSTT.R | 2 - R/FI.MT.R | 2 - R/choose.MSMN.R | 2 - R/choose.MSMSN.R | 2 - R/choose.MSMSNC.R | 2 - R/choose.MSSMN.R | 2 - R/choose.models.R | 2 - R/choose2.R | 2 - R/distMahal.R | 2 - R/estimate.MCN.R | 16 ++++---- R/estimate.MN.R | 12 +++--- R/estimate.MSCEC.R | 26 ++++++------- R/estimate.MSCN.R | 20 +++++----- R/estimate.MSCN2.R | 94 +++++++++++++++++++++++------------------------ R/estimate.MSL.R | 20 +++++----- R/estimate.MSN.R | 20 +++++----- R/estimate.MSNC.R | 14 +++---- R/estimate.MSSL.R | 22 +++++------ R/estimate.MSSL2.R | 54 +++++++++++++-------------- R/estimate.MSSLEC.R | 14 +++---- R/estimate.MSTEC.R | 14 +++---- R/estimate.MSTN.R | 22 +++++------ R/estimate.MSTT.R | 54 +++++++++++++-------------- R/estimate.MT.R | 18 ++++----- R/mbackcrit.R | 2 - R/mbacksign.R | 2 - R/solve2.R |only R/summary.skewMLRM.R | 2 - man/chooseM.Rd | 2 - man/plotskewMLRM.Rd | 2 + man/solve2.Rd |only man/summaryskewMLRM.Rd | 2 + 50 files changed, 306 insertions(+), 294 deletions(-)
Title: Autograph R for 'Tensorflow'
Description: Translate R control flow expressions into 'Tensorflow' graphs.
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <kalinowskit@gmail.com>
Diff between tfautograph versions 0.3.1 dated 2021-08-19 and 0.3.2 dated 2021-09-17
DESCRIPTION | 15 ++---- MD5 | 18 +++---- NEWS.md | 4 + R/utils.R | 5 +- R/view.R | 5 +- R/zzz-autograph.R | 105 ++++++++++++++++++++++++++++++++++++------ README.md | 19 ++----- tests/testthat.R | 16 ++---- tests/testthat/helper-utils.R | 11 ---- tests/testthat/test-break.R | 4 - 10 files changed, 131 insertions(+), 71 deletions(-)
Title: Odds Ratios, Contingency Table, and Model Significance from a
Generalized Linear Model Object
Description: Computes odds ratios and 95% confidence intervals from a generalized linear model object. It also computes model significance with the chi-squared statistic and p-value and it computes model fit using a contingency table to determine the percent of observations for which the model correctly predicts the value of the outcome. Calculates model sensitivity and specificity.
Author: Jenine Harris [aut, cre]
Maintainer: Jenine Harris <harrisj@wustl.edu>
Diff between odds.n.ends versions 0.1.3 dated 2021-01-10 and 0.1.4 dated 2021-09-17
DESCRIPTION | 7 MD5 | 16 - R/or_function.R | 10 - build/vignette.rds |binary inst/doc/oddsnends-vignette.R | 30 --- inst/doc/oddsnends-vignette.Rmd | 37 +--- inst/doc/oddsnends-vignette.html | 319 +++------------------------------------ man/odds.n.ends.Rd | 92 +++++------ vignettes/oddsnends-vignette.Rmd | 37 +--- 9 files changed, 122 insertions(+), 426 deletions(-)
Title: Uganda Time Series Database API
Description: An R API providing easy access to a relational database with macroeconomic,
financial and development related time series data for Uganda.
Overall more than 5000 series at varying frequency (daily, monthly,
quarterly, annual in fiscal or calendar years) can be accessed through
the API. The data is provided by the Bank of Uganda,
the Ugandan Ministry of Finance, Planning and Economic Development,
the IMF and the World Bank. The database is being updated once a month.
Author: Sebastian Krantz [aut, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between ugatsdb versions 0.2.0 dated 2021-08-18 and 0.2.1 dated 2021-09-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/accessdb.R | 26 ++++++++++++++++---------- man/ugatsdb_reconnect.Rd | 4 +++- 5 files changed, 31 insertions(+), 19 deletions(-)
Title: Geostatistics for Compositional Analysis
Description: Support for geostatistical analysis of multivariate data,
in particular data with restrictions, e.g. positive amounts data,
compositional data, distributional data, microstructural data, etc.
It includes descriptive analysis and modelling for such data, both
from a two-point Gaussian perspective and multipoint perspective.
The methods mainly follow Tolosana-Delgado, Mueller and van den
Boogaart (2018) <doi:10.1007/s11004-018-9769-3>.
Author: Raimon Tolosana-Delgado [aut] (<https://orcid.org/0000-0001-9847-0462>),
Ute Mueller [aut],
K. Gerald van den Boogaart [ctb, cre],
Hassan Talebi [ctb, cph],
Helmholtz-Zentrum Dresden-Rossendorf [cph],
Edith Cowan University [cph]
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between gmGeostats versions 0.10-8 dated 2021-07-15 and 0.10-9 dated 2021-09-17
DESCRIPTION | 8 ++-- MD5 | 36 +++++++++--------- NEWS.md | 17 ++++++++ R/abstractClasses.R | 5 ++ R/gmAnisotropy.R | 7 +++ R/gmSimulation.R | 16 ++++---- R/gstatCompatibility.R | 34 ++++++++++++++++- R/uncorrelationTest.R | 8 ++-- R/variograms.R | 10 ++++- inst/doc/register_new_layer_datatype.Rmd | 28 ++++++++++++-- inst/doc/register_new_layer_datatype.html | 20 +++++++--- man/EmpiricalStructuralFunctionSpecification-class.Rd | 5 ++ man/ModelStructuralFunctionSpecification-class.Rd | 5 ++ man/as.gmCgram.Rd | 5 ++ man/gmTrainingImage-class.Rd | 4 +- man/gsi.DS.Rd | 16 ++++---- man/noSpatCorr.test.Rd | 8 ++-- src/gmGeostats.c | 2 - vignettes/register_new_layer_datatype.Rmd | 28 ++++++++++++-- 19 files changed, 198 insertions(+), 64 deletions(-)
Title: Generic Functions for Cross Validation
Description: Contains generic functions for performing
cross validation and for computing diagnostic errors.
Author: Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between crossval versions 1.0.3 dated 2015-07-08 and 1.0.4 dated 2021-09-17
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 5 +++++ man/confusionMatrix.Rd | 2 +- man/crossval.Rd | 24 +++++++----------------- man/crossval.package.Rd | 4 ++-- man/diagnosticErrors.Rd | 2 +- 7 files changed, 27 insertions(+), 32 deletions(-)
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.6.1 dated 2019-12-14 and 0.7.0 dated 2021-09-17
robustHD-0.6.1/robustHD/R/fortify.R |only robustHD-0.6.1/robustHD/man/fortify.seqModel.Rd |only robustHD-0.7.0/robustHD/DESCRIPTION | 12 robustHD-0.7.0/robustHD/MD5 | 131 robustHD-0.7.0/robustHD/NAMESPACE | 242 - robustHD-0.7.0/robustHD/NEWS | 20 robustHD-0.7.0/robustHD/R/coef.R | 10 robustHD-0.7.0/robustHD/R/fitted.R | 10 robustHD-0.7.0/robustHD/R/grplars.R | 7 robustHD-0.7.0/robustHD/R/plot.R | 1935 ++++------ robustHD-0.7.0/robustHD/R/residuals.R | 10 robustHD-0.7.0/robustHD/R/rlars.R | 2 robustHD-0.7.0/robustHD/R/robustHD-deprecated.R | 797 +++- robustHD-0.7.0/robustHD/R/setupCoefPlot.R |only robustHD-0.7.0/robustHD/R/setupCritPlot.R |only robustHD-0.7.0/robustHD/R/setupDiagnosticPlot.R |only robustHD-0.7.0/robustHD/R/sparseLTS.R | 4 robustHD-0.7.0/robustHD/R/tslars.R | 7 robustHD-0.7.0/robustHD/R/tslarsP.R | 7 robustHD-0.7.0/robustHD/R/utils.R | 59 robustHD-0.7.0/robustHD/build/partial.rdb |binary robustHD-0.7.0/robustHD/data/TopGear.RData |binary robustHD-0.7.0/robustHD/data/datalist |only robustHD-0.7.0/robustHD/data/nci60.RData |only robustHD-0.7.0/robustHD/inst/doc/examples/example-AIC.R | 64 robustHD-0.7.0/robustHD/inst/doc/examples/example-coef.R | 70 robustHD-0.7.0/robustHD/inst/doc/examples/example-coefPlot.R | 64 robustHD-0.7.0/robustHD/inst/doc/examples/example-critPlot.R | 64 robustHD-0.7.0/robustHD/inst/doc/examples/example-diagnosticPlot.R | 62 robustHD-0.7.0/robustHD/inst/doc/examples/example-fitted.R | 70 robustHD-0.7.0/robustHD/inst/doc/examples/example-fortify.R | 62 robustHD-0.7.0/robustHD/inst/doc/examples/example-lambda0.R | 40 robustHD-0.7.0/robustHD/inst/doc/examples/example-perry.R | 52 robustHD-0.7.0/robustHD/inst/doc/examples/example-plot.R | 70 robustHD-0.7.0/robustHD/inst/doc/examples/example-predict.R | 70 robustHD-0.7.0/robustHD/inst/doc/examples/example-residuals.R | 70 robustHD-0.7.0/robustHD/inst/doc/examples/example-rgrplars.R | 24 robustHD-0.7.0/robustHD/inst/doc/examples/example-rlars.R | 38 robustHD-0.7.0/robustHD/inst/doc/examples/example-setupCoefPlot.R |only robustHD-0.7.0/robustHD/inst/doc/examples/example-setupCritPlot.R |only robustHD-0.7.0/robustHD/inst/doc/examples/example-setupDiagnosticPlot.R |only robustHD-0.7.0/robustHD/inst/doc/examples/example-sparseLTS.R | 46 robustHD-0.7.0/robustHD/inst/doc/examples/example-weights.R | 52 robustHD-0.7.0/robustHD/inst/tests/test-fastLasso-highdim.R | 18 robustHD-0.7.0/robustHD/inst/tests/test-fastLasso-multiple.R | 24 robustHD-0.7.0/robustHD/inst/tests/test-fastLasso-simple.R | 20 robustHD-0.7.0/robustHD/man/AIC.seqModel.Rd | 3 robustHD-0.7.0/robustHD/man/TopGear.Rd | 42 robustHD-0.7.0/robustHD/man/coef.seqModel.Rd | 16 robustHD-0.7.0/robustHD/man/coefPlot.Rd | 246 - robustHD-0.7.0/robustHD/man/corHuber.Rd | 15 robustHD-0.7.0/robustHD/man/critPlot.Rd | 228 - robustHD-0.7.0/robustHD/man/diagnosticPlot.Rd | 362 - robustHD-0.7.0/robustHD/man/fitted.seqModel.Rd | 12 robustHD-0.7.0/robustHD/man/getScale.Rd | 3 robustHD-0.7.0/robustHD/man/grplars.Rd | 64 robustHD-0.7.0/robustHD/man/lambda0.Rd | 14 robustHD-0.7.0/robustHD/man/nci60.Rd |only robustHD-0.7.0/robustHD/man/partialOrder.Rd |only robustHD-0.7.0/robustHD/man/perry.seqModel.Rd | 24 robustHD-0.7.0/robustHD/man/plot.seqModel.Rd | 9 robustHD-0.7.0/robustHD/man/predict.seqModel.Rd | 3 robustHD-0.7.0/robustHD/man/residuals.seqModel.Rd | 16 robustHD-0.7.0/robustHD/man/rlars.Rd | 35 robustHD-0.7.0/robustHD/man/robustHD-deprecated.Rd | 203 - robustHD-0.7.0/robustHD/man/setupCoefPlot.Rd |only robustHD-0.7.0/robustHD/man/setupCritPlot.Rd |only robustHD-0.7.0/robustHD/man/setupDiagnosticPlot.Rd |only robustHD-0.7.0/robustHD/man/sparseLTS.Rd | 39 robustHD-0.7.0/robustHD/man/standardize.Rd | 10 robustHD-0.7.0/robustHD/man/tslars.Rd | 53 robustHD-0.7.0/robustHD/man/tslarsP.Rd | 53 robustHD-0.7.0/robustHD/man/weights.sparseLTS.Rd | 10 robustHD-0.7.0/robustHD/man/winsorize.Rd | 26 74 files changed, 3261 insertions(+), 2458 deletions(-)
Title: Create Interactive Linked Charts with Minimal Code
Description: An easy-to-use tool to employ interactivity in every-day exploratory analysis. It contains
a collection of most commonly used types of charts (such as scatter plots, line plots, heatmaps, bar charts),
which can be linked to each other or to other interactive elements with just few lines of code.
Author: Svetlana Ovchinnikova [aut, cre],
Simon Anders [aut]
Maintainer: Svetlana Ovchinnikova <s.ovchinnikova@zmbh.uni-heidelberg.de>
Diff between rlc versions 0.3.0 dated 2020-09-30 and 0.4.0 dated 2021-09-17
DESCRIPTION | 15 +- MD5 | 36 +++--- NEWS.md | 25 ++++ R/lc.R | 202 +++++++++++++++++++++++------------- inst/http_root/linked-charts.css | 19 +-- inst/http_root/linked-charts.min.js | 2 inst/http_root/rlc.js | 6 + man/LCApp.Rd | 30 ++--- man/dat.Rd | 4 man/lc_bars.Rd | 17 ++- man/lc_colourSlider.Rd | 2 man/lc_heatmap.Rd | 24 +++- man/lc_hist.Rd | 2 man/lc_html.Rd | 2 man/lc_image.Rd | 4 man/lc_input.Rd | 2 man/lc_line.Rd | 24 +++- man/lc_scatter.Rd | 24 +++- man/updateCharts.Rd | 2 19 files changed, 294 insertions(+), 148 deletions(-)
Title: Spatial Designs for Ecological and Environmental Surveys
Description: Provides spatially survey balanced designs using the quasi-random number method described Robinson et al. (2013) <doi:10.1111/biom.12059>. These designs can accommodate, without substantial detrimental effects on spatial balance, legacy sites (Foster et al., 2017 <doi:10.1111/2041-210X.12782>), and for both point samples and transect samples (Foster et al. 2020, <doi:10.1111/2041-210X.13321>). Additional information about the package use itself is given in Foster (2021) <doi:10.1111/2041-210X.13535>.
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@data61.csiro.au>
Diff between MBHdesign versions 2.1.8 dated 2020-08-25 and 2.1.9 dated 2021-09-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary inst/CITATION | 34 ++++++++++++++++++++++++++++------ inst/doc/MBHdesign.R | 48 ++++++++++++++++++++++++------------------------ inst/doc/MBHdesign.pdf |binary man/transectSamp.Rd | 2 +- 7 files changed, 63 insertions(+), 41 deletions(-)
Title: Resampling-Based Analysis of Multivariate Data and Repeated
Measures Designs
Description: Implemented are various tests for semi-parametric repeated measures
and general MANOVA designs that do neither assume multivariate normality nor
covariance homogeneity, i.e., the procedures are applicable for a wide range
of general multivariate factorial designs. In addition to asymptotic inference
methods, novel bootstrap and permutation approaches are implemented as well. These provide more
accurate results in case of small to moderate sample sizes. Furthermore, post-hoc
comparisons are provided for the multivariate analyses.
Friedrich, S., Konietschke, F. and Pauly, M. (2019) <doi:10.32614/RJ-2019-051>.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@math.uni-augsburg.de>
Diff between MANOVA.RM versions 0.5.1 dated 2021-05-21 and 0.5.2 dated 2021-09-17
DESCRIPTION | 10 MD5 | 7 inst/doc/Introduction_to_MANOVA.RM.R | 36 - inst/doc/Introduction_to_MANOVA.RM.html | 795 ++++++++++++-------------------- vignettes/Introduction_to_MANOVA.RM.md |only 5 files changed, 336 insertions(+), 512 deletions(-)
Title: Generalised Joint Regression Modelling
Description: Routines for fitting various joint (and univariate) regression models, with several types of covariate effects, in the presence of equations' errors association, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <rosalba.radice@city.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between GJRM versions 0.2-4 dated 2021-04-12 and 0.2-5 dated 2021-09-17
ChangeLog | 3 DESCRIPTION | 6 MD5 | 162 ++++++++-------- NAMESPACE | 12 - R/CopulaCLM.r | 20 + R/LM.bpm.r | 8 R/S.m.r | 35 +++ R/SemiParBIV.fit.R | 8 R/SemiParBIV.r | 26 +- R/SemiParROY.fit.post.r |only R/SemiParROY.r |only R/SemiParTRIV.r | 33 ++- R/ass.ms.r | 2 R/bcontSurvG_extended.R |only R/bcorrecDiscr.R | 2 R/bdiscrcont.R | 4 R/bdiscrcont12.R | 4 R/bdiscrcont13.R | 2 R/bdiscrcont23.R | 2 R/bprobgHsBinROY.r |only R/bprobgHsCont2ROY.r |only R/bprobgHsCont3ROY.r |only R/bprobgHsCont3binTWSS.R |only R/bprobgHsContUniv.r | 2 R/bprobgHsDiscr1.r | 2 R/bprobgHsDiscr1ROY.r |only R/bprobgHsDiscr1SS.r | 2 R/bprobgHsDiscr2.r | 2 R/bprobgHsDiscr2ROY.r |only R/bprobgHsDiscr2SS.r | 2 R/conv.check.r | 2 R/copulaSampleSel.r | 148 +++++++++++--- R/distrHs.r | 78 +++++-- R/distrHsATDiscr.r | 32 +++ R/distrHsATDiscr2.r | 25 ++ R/distrHsDiscr.r | 80 +++++++ R/edf.loop.r | 16 - R/eta.tr.R | 8 R/form.check.r | 18 + R/form.eq12.r | 26 +- R/form.gaml.r | 85 ++++++++ R/func.OPT.r | 41 +++- R/gamls.upsv.r | 144 ++++++++++++++ R/gamlss.R | 151 +++++++++++---- R/ggmtrust.R | 2 R/gjrm.r | 326 +++++++++++++++++++++++--------- R/imputeCounter.r | 8 R/imputeSS.r | 8 R/int.postcheck.R | 14 - R/jc.probs.r | 1 R/lmc.R | 2 R/overall.svG.R | 422 ++++++++++++++++++++++++++++++++++++++++-- R/pen.r | 79 +++++++ R/plot.SemiParBIV.r | 2 R/post.check.R | 8 R/postVb.r | 2 R/pp.r | 8 R/pream.wm.r | 117 ++++++++++- R/pred.gp.r | 57 +++-- R/pred.mvt.r | 2 R/pred.var.r | 98 +++++++++ R/predict.SemiParBIV.r | 5 R/print.gamlss.r | 6 R/print.summary.SemiParTRIV.r | 8 R/pscr.r | 4 R/pscr0.r | 10 R/r.resp.R | 21 +- R/rIC.R | 2 R/resp.check.R | 14 - R/rob.const.R | 2 R/sim.resp.R | 18 + R/startsn.r | 2 R/susu.r | 20 + R/susutsn.r | 2 R/vis.gam2.r | 2 R/vis.gjrm.r | 8 man/GJRM-package.Rd | 21 ++ man/SemiParBIV.fit.post.Rd | 1 man/SemiParROY.Rd |only man/bprobgHs.Rd | 1 man/bprobgHsCont.Rd | 4 man/bprobgHsContSS.Rd | 1 man/bprobgHsContUniv.Rd | 1 man/bprobgHsDiscr1.Rd | 4 man/eta.tr.Rd | 4 man/gamlss.Rd | 13 - man/gjrm.Rd | 43 ++-- 87 files changed, 2077 insertions(+), 489 deletions(-)
Title: Miscellaneous Functions for 'ggplot2'
Description: Useful functions to edit 'ggplot' object (e.g., setting fonts for theme and layers, adding rounded rectangle as background for each of the legends).
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>),
Shuangbin Xu [aut] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.0.3 dated 2021-08-17 and 0.0.4 dated 2021-09-17
DESCRIPTION | 8 MD5 | 46 ++-- NAMESPACE | 58 +++--- NEWS.md |only R/add-facet.R |only R/facet_set.R |only R/ggelement.R | 122 ++++++------ R/gglegend.R | 96 +++++----- R/keybox.R | 72 +++---- R/method-ggplot-add.R |only R/reexport.R | 6 R/set_font.R | 84 ++++---- R/utilities.R | 115 ++++++++++- build/vignette.rds |binary inst/doc/ggfun.R | 90 +++++---- inst/doc/ggfun.Rmd | 201 ++++++++++++-------- inst/doc/ggfun.html | 451 +++++++++++++++++++++++++---------------------- man/element_roundrect.Rd | 104 +++++----- man/facet_set.Rd |only man/get_aes_var.Rd | 44 ++-- man/ggbreak2ggplot.Rd |only man/gglegend.Rd | 74 +++---- man/is-ggbreak.Rd |only man/is.ggtree.Rd |only man/keybox.Rd | 58 +++--- man/reexports.Rd | 32 +-- man/set_font.Rd | 70 +++---- vignettes/ggfun.Rmd | 201 ++++++++++++-------- 28 files changed, 1081 insertions(+), 851 deletions(-)
Title: Tests for General Factorial Designs
Description: Implemented are the Wald-type statistic,
a permuted version thereof as well as the ANOVA-type statistic
for general factorial designs, even with non-normal error terms
and/or heteroscedastic variances, for crossed designs with an
arbitrary number of factors and nested designs with up to three factors.
Friedrich et al. (2017) <doi:10.18637/jss.v079.c01>.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly, Marc Ditzhaus, Philipp Steinhauer
Maintainer: Sarah Friedrich <sarah.friedrich@math.uni-augsburg.de>
Diff between GFD versions 0.2.9 dated 2020-12-10 and 0.3.2 dated 2021-09-17
DESCRIPTION | 20 - MD5 | 16 - NAMESPACE | 19 + R/qanova.R |only R/qanova_statistics.R |only R/shinyGFD.R |only R/utility_functions.R | 147 +++++++----- inst/doc/IntroductionToGFD.R | 12 - inst/doc/IntroductionToGFD.html | 466 ++++++++++++++++------------------------ man/GFD_GUI.Rd |only man/QANOVA.Rd |only vignettes/IntroductionToGFD.md |only 12 files changed, 330 insertions(+), 350 deletions(-)
Title: Extracts the Backbone from Weighted Graphs
Description: Provides methods for extracting from a weighted graph
a binary or signed backbone that retains only the significant edges.
The user may input a weighted graph, or a bipartite graph
from which a weighted graph is first constructed via projection.
Backbone extraction methods include the stochastic degree sequence model (SDSM; Neal, Z. P. (2014). <doi:10.1016/j.socnet.2014.06.001>),
the fixed degree sequence model (FDSM; Zweig, K. A., and Kaufmann, M. (2011). <doi:10.1007/s13278-011-0021-0>),
the fixed row model (FRM; Neal, Z. P. (2013). <doi:10.1007/s13278-013-0107-y>),
the fixed column model (FCM; Neal, Domagalski, and Sagan (2021). <arXiv:2105.13396>),
the fixed fill model (FFM; Neal, Domagalski, and Sagan (2021). <arXiv:2105.13396>),
and a universal threshold method.
Author: Zachary Neal [aut, cre],
Rachel Domagalski [aut],
Bruce Sagan [aut]
Maintainer: Zachary Neal <zpneal@msu.edu>
Diff between backbone versions 1.5.0 dated 2021-06-04 and 1.5.1 dated 2021-09-17
backbone-1.5.0/backbone/tests |only backbone-1.5.1/backbone/DESCRIPTION | 6 ++--- backbone-1.5.1/backbone/MD5 | 14 ++++------- backbone-1.5.1/backbone/NEWS.md | 4 +++ backbone-1.5.1/backbone/README.md | 19 +++++++++++++++ backbone-1.5.1/backbone/build/partial.rdb |binary backbone-1.5.1/backbone/inst/doc/backbone.html | 30 ++++++++++++------------- 7 files changed, 45 insertions(+), 28 deletions(-)
Title: Using Cytogenetics Data in R
Description: Defines classes and methods to process text-based
cytogenetics using the CytoGPS web site, then import the results
into R for further analysis and graphing.
Author: Kevin R. Coombes, Dwayne Tally
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between RCytoGPS versions 1.1.1 dated 2021-02-10 and 1.2.1 dated 2021-09-17
DESCRIPTION | 10 +- MD5 | 45 +++++------ NAMESPACE | 2 NEWS | 19 ++++ R/01-chromosome.R | 4 - R/02-genome.R | 11 ++ R/03-plotOne.R | 9 +- R/04-simpleIdio.R | 10 +- R/06-Objects.R | 5 - R/sysdata.rda |binary build/vignette.rds |binary data/cytoData.rda |binary data/cytobandLocations.rda |binary inst/doc/Gallery.R | 10 +- inst/doc/Gallery.Rmd | 10 +- inst/doc/Gallery.html | 169 +++++++++++--------------------------------- inst/doc/IntroRCytoGPS.R | 10 ++ inst/doc/IntroRCytoGPS.Rmd | 14 ++- inst/doc/IntroRCytoGPS.html | 165 +++++++++++------------------------------- man/01-cytobandLocations.Rd | 3 man/04-Image.Rd | 6 + tests/testclip.R |only vignettes/Gallery.Rmd | 10 +- vignettes/IntroRCytoGPS.Rmd | 14 ++- 24 files changed, 214 insertions(+), 312 deletions(-)
Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data
Analysis Tools
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Author: Jan-Philipp Quast [aut, cre],
Dina Schuster [aut],
ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Diff between protti versions 0.1.1 dated 2021-05-10 and 0.2.0 dated 2021-09-17
protti-0.1.1/protti/R/diff_abundance.R |only protti-0.1.1/protti/R/go_enrichment.R |only protti-0.1.1/protti/R/kegg_enrichment.R |only protti-0.1.1/protti/R/median_normalisation.R |only protti-0.1.1/protti/R/network_analysis.R |only protti-0.1.1/protti/R/peptide_type.R |only protti-0.1.1/protti/R/plot_drc_4p.R |only protti-0.1.1/protti/R/plot_peptide_profiles.R |only protti-0.1.1/protti/R/plot_pval_distribution.R |only protti-0.1.1/protti/R/sequence_coverage.R |only protti-0.1.1/protti/R/treatment_enrichment.R |only protti-0.1.1/protti/R/volcano_protti.R |only protti-0.2.0/protti/DESCRIPTION | 10 protti-0.2.0/protti/MD5 | 319 +++--- protti-0.2.0/protti/NAMESPACE | 29 protti-0.2.0/protti/NEWS.md | 45 protti-0.2.0/protti/R/analyse_functional_network.R |only protti-0.2.0/protti/R/anova_protti.R | 34 protti-0.2.0/protti/R/assign_missingness.R | 172 ++- protti-0.2.0/protti/R/assign_peptide_type.R |only protti-0.2.0/protti/R/barcode_plot.R | 12 protti-0.2.0/protti/R/calculate_aa_scores.R |only protti-0.2.0/protti/R/calculate_diff_abundance.R |only protti-0.2.0/protti/R/calculate_go_enrichment.R |only protti-0.2.0/protti/R/calculate_imputation.R | 52 - protti-0.2.0/protti/R/calculate_kegg_enrichment.R |only protti-0.2.0/protti/R/calculate_protein_abundance.R | 169 ++- protti-0.2.0/protti/R/calculate_sequence_coverage.R |only protti-0.2.0/protti/R/calculate_treatment_enrichment.R |only protti-0.2.0/protti/R/create_queue.R | 114 +- protti-0.2.0/protti/R/create_structure_contact_map.R |only protti-0.2.0/protti/R/create_synthetic_data.R | 275 ++++- protti-0.2.0/protti/R/data.R | 47 protti-0.2.0/protti/R/drc_4p.R | 22 protti-0.2.0/protti/R/drc_4p_plot.R |only protti-0.2.0/protti/R/extract_metal_binders.R | 130 ++ protti-0.2.0/protti/R/fetch_alphafold_prediction.R |only protti-0.2.0/protti/R/fetch_chebi.R | 100 +- protti-0.2.0/protti/R/fetch_go.R | 29 protti-0.2.0/protti/R/fetch_kegg.R | 23 protti-0.2.0/protti/R/fetch_metal_pdb.R |only protti-0.2.0/protti/R/fetch_mobidb.R | 51 - protti-0.2.0/protti/R/fetch_pdb.R |only protti-0.2.0/protti/R/fetch_pdb_structure.R |only protti-0.2.0/protti/R/fetch_uniprot.R | 55 - protti-0.2.0/protti/R/fetch_uniprot_proteome.R | 21 protti-0.2.0/protti/R/filter_cv.R | 85 + protti-0.2.0/protti/R/find_all_subs.R | 37 protti-0.2.0/protti/R/find_chebis.R | 28 protti-0.2.0/protti/R/find_peptide.R | 48 protti-0.2.0/protti/R/find_peptide_in_structure.R |only protti-0.2.0/protti/R/fit_drc_4p.R | 374 +++++-- protti-0.2.0/protti/R/impute.R | 167 ++- protti-0.2.0/protti/R/map_peptides_on_structure.R |only protti-0.2.0/protti/R/normalise.R |only protti-0.2.0/protti/R/parallel_fit_drc_4p.R | 258 +++-- protti-0.2.0/protti/R/peptide_profile_plot.R |only protti-0.2.0/protti/R/pval_distribution_plot.R |only protti-0.2.0/protti/R/qc_charge_states.R | 91 + protti-0.2.0/protti/R/qc_contaminants.R | 49 - 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protti-0.2.0/protti/inst/doc/data_analysis_dose_response_workflow.html | 103 +- protti-0.2.0/protti/inst/doc/data_analysis_single_dose_treatment_workflow.R | 86 - protti-0.2.0/protti/inst/doc/data_analysis_single_dose_treatment_workflow.Rmd | 136 +- protti-0.2.0/protti/inst/doc/data_analysis_single_dose_treatment_workflow.html | 258 ++--- protti-0.2.0/protti/inst/doc/input_preparation_workflow.R | 25 protti-0.2.0/protti/inst/doc/input_preparation_workflow.Rmd | 27 protti-0.2.0/protti/inst/doc/input_preparation_workflow.html | 257 ++--- protti-0.2.0/protti/inst/doc/quality_control_workflow.R | 8 protti-0.2.0/protti/inst/doc/quality_control_workflow.Rmd | 18 protti-0.2.0/protti/inst/doc/quality_control_workflow.html | 72 - protti-0.2.0/protti/man/analyse_functional_network.Rd |only protti-0.2.0/protti/man/anova_protti.Rd | 34 protti-0.2.0/protti/man/assign_missingness.Rd | 99 +- protti-0.2.0/protti/man/assign_peptide_type.Rd |only protti-0.2.0/protti/man/calculate_aa_scores.Rd |only protti-0.2.0/protti/man/calculate_diff_abundance.Rd |only protti-0.2.0/protti/man/calculate_go_enrichment.Rd |only protti-0.2.0/protti/man/calculate_imputation.Rd | 38 protti-0.2.0/protti/man/calculate_kegg_enrichment.Rd |only protti-0.2.0/protti/man/calculate_protein_abundance.Rd | 120 +- protti-0.2.0/protti/man/calculate_sequence_coverage.Rd |only protti-0.2.0/protti/man/calculate_treatment_enrichment.Rd |only protti-0.2.0/protti/man/create_queue.Rd | 106 +- protti-0.2.0/protti/man/create_structure_contact_map.Rd |only protti-0.2.0/protti/man/create_synthetic_data.Rd | 91 + protti-0.2.0/protti/man/diff_abundance.Rd | 105 -- protti-0.2.0/protti/man/drc_4p.Rd | 22 protti-0.2.0/protti/man/drc_4p_plot.Rd |only protti-0.2.0/protti/man/extract_metal_binders.Rd | 73 + protti-0.2.0/protti/man/fetch_alphafold_prediction.Rd |only protti-0.2.0/protti/man/fetch_chebi.Rd | 12 protti-0.2.0/protti/man/fetch_go.Rd | 13 protti-0.2.0/protti/man/fetch_kegg.Rd | 12 protti-0.2.0/protti/man/fetch_metal_pdb.Rd |only protti-0.2.0/protti/man/fetch_mobidb.Rd | 16 protti-0.2.0/protti/man/fetch_pdb.Rd |only protti-0.2.0/protti/man/fetch_pdb_structure.Rd |only protti-0.2.0/protti/man/fetch_uniprot.Rd | 17 protti-0.2.0/protti/man/fetch_uniprot_proteome.Rd | 14 protti-0.2.0/protti/man/figures/README-volcano-1.png |binary protti-0.2.0/protti/man/figures/lifecycle-archived.svg |only protti-0.2.0/protti/man/figures/lifecycle-defunct.svg |only protti-0.2.0/protti/man/figures/lifecycle-deprecated.svg |only protti-0.2.0/protti/man/figures/lifecycle-experimental.svg |only protti-0.2.0/protti/man/figures/lifecycle-maturing.svg |only protti-0.2.0/protti/man/figures/lifecycle-questioning.svg |only protti-0.2.0/protti/man/figures/lifecycle-stable.svg |only protti-0.2.0/protti/man/figures/lifecycle-superseded.svg |only protti-0.2.0/protti/man/filter_cv.Rd | 58 - 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Title: Portmanteau Local Feature Discrimination for Matrix-Variate Data
Description: The portmanteau local feature discriminant approach first identifies
the local discriminant features and their differential structures,
then constructs the discriminant rule by pooling the identified local
features together. This method is applicable to high-dimensional
matrix-variate data.
Author: Zengchao Xu [aut, cre],
Shan Luo [aut],
Zehua Chen [aut]
Maintainer: Zengchao Xu <zengc.xu@aliyun.com>
Diff between PLFD versions 0.1.0 dated 2021-08-09 and 0.1.1 dated 2021-09-17
PLFD-0.1.0/PLFD/man/print.plfd.Rd |only PLFD-0.1.1/PLFD/DESCRIPTION | 8 PLFD-0.1.1/PLFD/MD5 | 33 +- PLFD-0.1.1/PLFD/NAMESPACE | 1 PLFD-0.1.1/PLFD/NEWS.md | 10 PLFD-0.1.1/PLFD/R/plfd.R | 21 - PLFD-0.1.1/PLFD/R/predict-plfd.R | 14 - PLFD-0.1.1/PLFD/R/print-plfd.R | 5 PLFD-0.1.1/PLFD/README.md | 13 PLFD-0.1.1/PLFD/build/PLFD.pdf |binary PLFD-0.1.1/PLFD/build/partial.rdb |binary PLFD-0.1.1/PLFD/inst/doc/PLFD.R | 1 PLFD-0.1.1/PLFD/inst/doc/PLFD.Rmd | 3 PLFD-0.1.1/PLFD/inst/doc/PLFD.html | 494 ++++++++++++++++++++---------------- PLFD-0.1.1/PLFD/man/plfd.Rd | 21 - PLFD-0.1.1/PLFD/man/predict.plfd.Rd | 12 PLFD-0.1.1/PLFD/src/cxxFuns.cpp | 2 PLFD-0.1.1/PLFD/vignettes/PLFD.Rmd | 3 18 files changed, 356 insertions(+), 285 deletions(-)
Title: Instrumental Variables: Extrapolation by Marginal Treatment
Effects
Description: The marginal treatment effect was introduced by Heckman and
Vytlacil (2005) <doi:10.1111/j.1468-0262.2005.00594.x> to provide a
choice-theoretic interpretation to instrumental variables models that
maintain the monotonicity condition of Imbens and Angrist (1994)
<doi:10.2307/2951620>. This interpretation can be used to extrapolate from
the compliers to estimate treatment effects for other subpopulations. This
package provides a flexible set of methods for conducting this
extrapolation. It allows for parametric or nonparametric sieve estimation,
and allows the user to maintain shape restrictions such as monotonicity. The
package operates in the general framework developed by Mogstad, Santos and
Torgovitsky (2018) <doi:10.3982/ECTA15463>, and accommodates either point
identification or partial identification (bounds). In the partially
identified case, bounds are computed using either linear programming
or quadratically constrained quadratic programming. Support for
four solvers is provided. Gurobi and the Gurobi R API
can be obtained from <http://www.gurobi.com/index>. CPLEX can be obtained
from <https://www.ibm.com/analytics/cplex-optimizer>. CPLEX R APIs 'Rcplex'
and 'cplexAPI' are available from CRAN. MOSEK and the MOSEK R API can be
obtained from <https://www.mosek.com/>. The lp_solve library is freely
available from <http://lpsolve.sourceforge.net/5.5/>, and is included when
installing its API 'lpSolveAPI', which is available from CRAN.
Author: Alexander Torgovitsky [aut],
Joshua Shea [aut, cre]
Maintainer: Joshua Shea <jkcshea@uchicago.edu>
Diff between ivmte versions 1.2.0 dated 2020-04-18 and 1.4.0 dated 2021-09-17
DESCRIPTION | 26 MD5 | 161 NAMESPACE | 5 R/audit.R | 1087 ++- R/data.R | 7 R/lp.R | 1198 +++- R/monobound.R | 183 R/mst.R | 2891 +++++++--- R/mtr.R | 14 R/propensity.R | 2 R/sweights.R | 13 README.md |only build/partial.rdb |only build/vignette.rds |binary data/AE.rda |binary inst/doc/ivmte.R | 134 inst/doc/ivmte.Rmd | 86 inst/doc/ivmte.html | 1713 +++-- inst/extdata/AE.R | 6 man/AE.Rd | 13 man/audit.Rd | 206 man/bound.Rd | 57 man/combinemonobound.Rd | 2 man/criterionMin.Rd | 42 man/genGamma.Rd | 11 man/genGammaSplines.Rd | 13 man/genGammaSplinesTT.Rd | 3 man/genSSet.Rd | 29 man/genTarget.Rd | 55 man/genboundA.Rd | 45 man/gendist1e.Rd | 3 man/gendist3e.Rd | 3 man/gendist5e.Rd | 3 man/gendistSplines.Rd | 4 man/genmonoA.Rd | 48 man/genmonoboundA.Rd | 63 man/gmmEstimate.Rd | 19 man/ivEstimate.Rd | 11 man/ivmte.Rd | 269 man/ivmteEstimate.Rd | 244 man/ivmteSimData.Rd | 6 man/lpSetup.Rd | 84 man/lpSetupBound.Rd | 25 man/lpSetupCriterion.Rd | 2 man/lpSetupCriterionBoot.Rd | 12 man/lpSetupEqualCoef.Rd |only man/lpSetupInfeasible.Rd | 2 man/lpSetupSolver.Rd | 6 man/matrixTriplets.Rd |only man/negationCheck.Rd | 10 man/olsj.Rd | 4 man/optionsCplexAPI.Rd | 2 man/optionsCplexAPISingle.Rd | 2 man/optionsGurobi.Rd | 5 man/optionsLpSolveAPI.Rd | 2 man/optionsRmosek.Rd |only man/piv.Rd | 11 man/polyparse.Rd | 9 man/propensity.Rd | 3 man/qpSetup.Rd |only man/qpSetupBound.Rd |only man/qpSetupCriterion.Rd |only man/qpSetupInfeasible.Rd |only man/rescaleX.Rd |only man/runCplexAPI.Rd | 11 man/runGurobi.Rd | 17 man/runLpSolveAPI.Rd | 10 man/runMosek.Rd |only man/selectViolations.Rd | 24 man/splinesBasis.Rd | 3 man/statusString.Rd |only man/uSplineBasis.Rd | 4 man/uSplineInt.Rd | 4 tests/testthat/test_covariates.R | 5 tests/testthat/test_direct.R |only tests/testthat/test_single.R | 5 tests/testthat/test_splines.R | 17 vignettes/ivmte.Rmd | 86 vignettes/ivmte_files/figure-gfm/bootstrap.plot-1.png |binary vignettes/ivmte_files/figure-gfm/draw.plots-1.png |binary vignettes/ivmte_files/figure-gfm/weights.plot.combine-1.png |binary vignettes/ivmte_files/figure-html/bootstrap.plot-1.png |binary vignettes/ivmte_files/figure-html/draw.plots-1.png |binary vignettes/ivmte_files/figure-html/weights.plot.combine-1.png |binary vignettes/refs.bib | 8 vignettes/vignettes/ivmte_files/figure-gfm/bootstrap.plot-1.png |binary vignettes/vignettes/ivmte_files/figure-gfm/draw.plots-1.png |binary vignettes/vignettes/ivmte_files/figure-gfm/weights.plot.combine-1.png |binary 88 files changed, 6266 insertions(+), 2782 deletions(-)
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive (GMVAR) model, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2020) <arXiv:2007.04713>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 1.4.2 dated 2021-05-12 and 1.5.0 dated 2021-09-17
gmvarkit-1.4.2/gmvarkit/data/eurusd.rda |only gmvarkit-1.4.2/gmvarkit/data/usamone.rda |only gmvarkit-1.4.2/gmvarkit/data/usamone_prec.rda |only gmvarkit-1.4.2/gmvarkit/man/eurusd.Rd |only gmvarkit-1.4.2/gmvarkit/man/usamone.Rd |only gmvarkit-1.4.2/gmvarkit/man/usamone_prec.Rd |only gmvarkit-1.5.0/gmvarkit/DESCRIPTION | 6 gmvarkit-1.5.0/gmvarkit/MD5 | 280 ++--- gmvarkit-1.5.0/gmvarkit/NAMESPACE | 2 gmvarkit-1.5.0/gmvarkit/NEWS.md | 15 gmvarkit-1.5.0/gmvarkit/R/GIRFandGFEVD.R | 228 ++-- gmvarkit-1.5.0/gmvarkit/R/GMVARconstruction.R | 253 ++--- gmvarkit-1.5.0/gmvarkit/R/MAINest.R | 50 - gmvarkit-1.5.0/gmvarkit/R/WaldAndLR.R | 84 + gmvarkit-1.5.0/gmvarkit/R/argumentChecks.R | 49 - gmvarkit-1.5.0/gmvarkit/R/data.R | 83 - gmvarkit-1.5.0/gmvarkit/R/diagnosticPlot.R | 59 - gmvarkit-1.5.0/gmvarkit/R/generateParams.R | 7 gmvarkit-1.5.0/gmvarkit/R/gmvarkit.R | 24 gmvarkit-1.5.0/gmvarkit/R/loglikelihood.R | 42 gmvarkit-1.5.0/gmvarkit/R/matcal.R | 6 gmvarkit-1.5.0/gmvarkit/R/morePlots.R | 22 gmvarkit-1.5.0/gmvarkit/R/numericalDifferentiation.R | 19 gmvarkit-1.5.0/gmvarkit/R/parameterReforms.R | 11 gmvarkit-1.5.0/gmvarkit/R/pickParams.R | 36 gmvarkit-1.5.0/gmvarkit/R/plotMethods.R | 76 + gmvarkit-1.5.0/gmvarkit/R/predictMethod.R | 35 gmvarkit-1.5.0/gmvarkit/R/printMethods.R | 81 - gmvarkit-1.5.0/gmvarkit/R/quantileResidualTests.R | 33 gmvarkit-1.5.0/gmvarkit/R/quantileResiduals.R | 60 - gmvarkit-1.5.0/gmvarkit/R/simulateGMVAR.R | 68 - gmvarkit-1.5.0/gmvarkit/R/standardErrors.R | 31 gmvarkit-1.5.0/gmvarkit/R/uncondMoments.R | 109 -- gmvarkit-1.5.0/gmvarkit/README.md | 60 - gmvarkit-1.5.0/gmvarkit/data/gdpdef.rda |only gmvarkit-1.5.0/gmvarkit/inst/doc/intro-to-gmvarkit.html | 4 gmvarkit-1.5.0/gmvarkit/man/GFEVD.Rd | 58 - gmvarkit-1.5.0/gmvarkit/man/GIRF.Rd | 206 ++-- gmvarkit-1.5.0/gmvarkit/man/GMVAR.Rd | 76 - gmvarkit-1.5.0/gmvarkit/man/LR_test.Rd | 40 gmvarkit-1.5.0/gmvarkit/man/VAR_pcovmat.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/Wald_test.Rd | 45 gmvarkit-1.5.0/gmvarkit/man/Wvec.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/add_data.Rd | 47 gmvarkit-1.5.0/gmvarkit/man/all_pos_ints.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/alt_gmvar.Rd | 9 gmvarkit-1.5.0/gmvarkit/man/calc_gradient.Rd | 19 gmvarkit-1.5.0/gmvarkit/man/change_parametrization.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/change_regime.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/check_constraints.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/check_data.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/check_gmvar.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/check_null_data.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/check_pMd.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/check_parameters.Rd | 19 gmvarkit-1.5.0/gmvarkit/man/check_same_means.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/cond_moment_plot.Rd | 22 gmvarkit-1.5.0/gmvarkit/man/cond_moments.Rd | 18 gmvarkit-1.5.0/gmvarkit/man/diagnostic_plot.Rd | 43 gmvarkit-1.5.0/gmvarkit/man/dlogmultinorm.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/fitGMVAR.Rd | 42 gmvarkit-1.5.0/gmvarkit/man/form_boldA.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/format_valuef.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/gdpdef.Rd |only gmvarkit-1.5.0/gmvarkit/man/get_IC.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/get_Sigmas.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/get_alpha_mt.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/get_boldA_eigens.Rd | 13 gmvarkit-1.5.0/gmvarkit/man/get_minval.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/get_omega_eigens.Rd | 13 gmvarkit-1.5.0/gmvarkit/man/get_regime_autocovs.Rd | 32 gmvarkit-1.5.0/gmvarkit/man/get_regime_autocovs_int.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/get_regime_means.Rd | 41 gmvarkit-1.5.0/gmvarkit/man/get_regime_means_int.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/get_test_Omega.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/get_unconstrained_structural_pars.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/gmvar_to_sgmvar.Rd | 13 gmvarkit-1.5.0/gmvarkit/man/gmvarkit.Rd | 6 gmvarkit-1.5.0/gmvarkit/man/in_paramspace.Rd | 21 gmvarkit-1.5.0/gmvarkit/man/in_paramspace_int.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/is_stationary.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/iterate_more.Rd | 7 gmvarkit-1.5.0/gmvarkit/man/loglikelihood.Rd | 21 gmvarkit-1.5.0/gmvarkit/man/loglikelihood_int.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/n_params.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_Am.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_Ami.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_Omegas.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_W.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_allA.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_all_phi0_A.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_alphas.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_lambdas.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_phi0.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/pick_regime.Rd | 2 gmvarkit-1.5.0/gmvarkit/man/plot.gmvarpred.Rd | 1 gmvarkit-1.5.0/gmvarkit/man/predict.gmvar.Rd | 36 gmvarkit-1.5.0/gmvarkit/man/print.gmvarpred.Rd | 22 gmvarkit-1.5.0/gmvarkit/man/print.gmvarsum.Rd | 20 gmvarkit-1.5.0/gmvarkit/man/print_std_errors.Rd | 14 gmvarkit-1.5.0/gmvarkit/man/profile_logliks.Rd | 16 gmvarkit-1.5.0/gmvarkit/man/quantile_residual_tests.Rd | 32 gmvarkit-1.5.0/gmvarkit/man/quantile_residuals.Rd | 58 - 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gmvarkit-1.5.0/gmvarkit/tests/testthat/test_MAINest.R | 29 gmvarkit-1.5.0/gmvarkit/tests/testthat/test_S3methods.R | 99 +- gmvarkit-1.5.0/gmvarkit/tests/testthat/test_argumentChecks.R | 20 gmvarkit-1.5.0/gmvarkit/tests/testthat/test_generateParams.R | 2 gmvarkit-1.5.0/gmvarkit/tests/testthat/test_gmvarConstruction.R | 49 - gmvarkit-1.5.0/gmvarkit/tests/testthat/test_loglikelihood.R | 477 ++++------ gmvarkit-1.5.0/gmvarkit/tests/testthat/test_parameterReforms.R | 12 gmvarkit-1.5.0/gmvarkit/tests/testthat/test_quantileResidualTests.R | 151 +-- gmvarkit-1.5.0/gmvarkit/tests/testthat/test_quantileResiduals.R | 117 +- gmvarkit-1.5.0/gmvarkit/tests/testthat/test_simulateGMVAR.R | 91 + gmvarkit-1.5.0/gmvarkit/tests/testthat/test_standardErrors.R | 134 -- gmvarkit-1.5.0/gmvarkit/tests/testthat/test_waldAndLR.R | 33 145 files changed, 2061 insertions(+), 2354 deletions(-)
Title: Tools for Nonlinear Regression Analysis
Description: Several tools for assessing the quality of fit of a gaussian nonlinear model are provided.
Author: Florent Baty [aut],
Marie-Laure Delignette-Muller [aut],
Sandrine Charles [ctb],
Jean-Pierre Flandrois [ctb],
Christian Ritz [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between nlstools versions 1.0-2 dated 2015-07-31 and 2.0-0 dated 2021-09-17
DESCRIPTION | 42 +++++++++++++--------- MD5 | 46 +++++++++++++++--------- NAMESPACE | 11 ++++- R/nlsBoot.R | 3 + R/nlsBootpredict.R |only README.md |only build |only inst/CITATION | 49 +++++++++++++------------ inst/NEWS | 10 ++++- inst/doc |only man/L.minor.Rd | 56 +++++++++++------------------ man/O2K.Rd | 20 +++------- man/confint2.Rd | 91 ++++++++++++++++++------------------------------ man/michaelisdata.Rd | 62 ++++++++++++++------------------ man/michaelismodels.Rd | 39 ++++++-------------- man/nlsBoot.Rd | 63 +++++++++++++-------------------- man/nlsBootpredict.Rd |only man/nlsConfRegions.Rd | 54 +++++++++++----------------- man/nlsContourRSS.Rd | 58 ++++++++++++------------------ man/nlsJack.Rd | 51 +++++++++++--------------- man/nlsResiduals.Rd | 61 +++++++++++--------------------- man/nlstools-defunct.Rd | 36 ------------------ man/nlstools.Rd | 67 +++++++++++++++-------------------- tests |only vignettes |only 25 files changed, 346 insertions(+), 473 deletions(-)
Title: Nonlinear Regression in Predictive Microbiology
Description: Data sets and nonlinear regression models dedicated to predictive microbiology.
Author: Florent Baty [aut],
Marie-Laure Delignette-Muller [aut],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between nlsMicrobio versions 0.0-1 dated 2014-06-25 and 0.0-3 dated 2021-09-17
nlsMicrobio-0.0-1/nlsMicrobio/ChangeLog |only nlsMicrobio-0.0-1/nlsMicrobio/inst/doc/nlstools_vignette.pdf |only nlsMicrobio-0.0-3/nlsMicrobio/DESCRIPTION | 28 - nlsMicrobio-0.0-3/nlsMicrobio/MD5 | 26 - nlsMicrobio-0.0-3/nlsMicrobio/README.md |only nlsMicrobio-0.0-3/nlsMicrobio/build |only nlsMicrobio-0.0-3/nlsMicrobio/inst/doc/nlsMicrobio_vignette.R |only nlsMicrobio-0.0-3/nlsMicrobio/inst/doc/nlsMicrobio_vignette.Rnw |only nlsMicrobio-0.0-3/nlsMicrobio/inst/doc/nlsMicrobio_vignette.pdf |only nlsMicrobio-0.0-3/nlsMicrobio/man/competitioncurve.Rd | 81 +-- nlsMicrobio-0.0-3/nlsMicrobio/man/competitionmodels.Rd | 244 ++++------ nlsMicrobio-0.0-3/nlsMicrobio/man/growthcurve.Rd | 26 - nlsMicrobio-0.0-3/nlsMicrobio/man/growthmodels.Rd | 105 +--- nlsMicrobio-0.0-3/nlsMicrobio/man/ross.Rd | 31 - nlsMicrobio-0.0-3/nlsMicrobio/man/secondary.Rd | 152 ++---- nlsMicrobio-0.0-3/nlsMicrobio/man/survivalcurve.Rd | 25 - nlsMicrobio-0.0-3/nlsMicrobio/man/survivalmodels.Rd | 134 ++--- nlsMicrobio-0.0-3/nlsMicrobio/vignettes |only 18 files changed, 386 insertions(+), 466 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph],
Constantin Ahlmann-Eltze [ctb],
Hector Corrada Bravo [ctb],
Robert Gentleman [ctb],
Jan Gleixner [ctb],
Peter Hickey [ctb],
Ola Hossjer [ctb],
Harris Jaffee [ctb],
Dongcan Jiang [ctb],
Peter Langfelder [ctb],
Brian Montgomery [ctb],
Angelina Panagopoulou [ctb],
Hugh Parsonage [ctb],
Jakob Peder Pettersen [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.60.1 dated 2021-08-23 and 0.61.0 dated 2021-09-17
DESCRIPTION | 11 +- MD5 | 76 +++++++++--------- NEWS | 20 ++++ R/rowQuantiles.R | 4 R/validateIndices.R | 8 + R/zzz.R | 7 + inst/doc/matrixStats-methods.html | 2 man/validateIndices.Rd | 2 src/colOrderStats.c | 2 src/rowOrderStats.c | 2 tests/allocArray.R | 6 - tests/allocMatrix.R | 10 +- tests/allocVector.R | 8 + tests/anyMissing.R | 12 +- tests/anyMissing_subset.R | 2 tests/benchmark.R | 2 tests/binCounts.R | 8 - tests/binMeans,binCounts.R | 28 +++--- tests/count.R | 6 - tests/mean2.R | 24 ++--- tests/psortKM.R | 8 - tests/rowAllAnys.R | 158 ++++++++++++++++---------------------- tests/rowCounts.R | 27 +++--- tests/rowCumMinMaxs.R | 10 +- tests/rowCumprods.R | 12 +- tests/rowCumsums.R | 12 +- tests/rowDiffs.R | 12 +- tests/rowLogSumExps.R | 10 +- tests/rowMads.R | 10 +- tests/rowOrderStats.R | 29 ++++-- tests/rowOrderStats_subset.R | 4 tests/rowRanges.R | 18 ++-- tests/rowRanks.R | 2 tests/rowSds.R | 10 +- tests/rowTabulates.R | 1 tests/rowVarDiffs.R | 10 +- tests/rowVars.R | 12 +- tests/signTabulate.R | 2 tests/validateIndices.R | 5 - 39 files changed, 313 insertions(+), 279 deletions(-)
Title: Vector Logistic Smooth Transition Models / Realized Covariances
Construction
Description: Allows the user to estimate a vector logistic smooth transition autoregressive model via maximum log-likelihood or nonlinear least squares. It further permits to test for linearity in the multivariate framework against a vector logistic smooth transition autoregressive model with a single transition variable. The estimation method is discussed in Terasvirta and Yang (2014, <doi:10.1108/S0731-9053(2013)0000031008>). Also, realized covariances can be constructed from stock market prices or returns, as explained in Andersen et al. (2001, <doi:10.1016/S0304-405X(01)00055-1>).
Author: Andrea Bucci [aut, cre, cph],
Giulio Palomba [aut],
Eduardo Rossi [aut],
Andrea Faragalli [ctb]
Maintainer: Andrea Bucci <andrea.bucci@unich.it>
Diff between starvars versions 1.1.5 dated 2021-09-13 and 1.1.7 dated 2021-09-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/VLSTAR.R | 2 +- man/VLSTAR.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: VAR Modelling
Description: Estimation, lag selection, diagnostic testing, forecasting, causality analysis, forecast error variance decomposition and impulse response functions of VAR models and estimation of SVAR and SVEC models.
Author: Bernhard Pfaff [aut, cre],
Matthieu Stigler [ctb]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between vars versions 1.5-3 dated 2018-08-06 and 1.5-6 dated 2021-09-17
vars-1.5-3/vars/build |only vars-1.5-3/vars/inst/doc |only vars-1.5-3/vars/vignettes |only vars-1.5-6/vars/DESCRIPTION | 15 ++++--- vars-1.5-6/vars/MD5 | 25 +++--------- vars-1.5-6/vars/R/causality.R | 76 +++++++++++++++++++++++++++++--------- vars-1.5-6/vars/data/Canada.RData |binary vars-1.5-6/vars/inst/CITATION | 6 +-- vars-1.5-6/vars/man/Canada.Rd | 7 ++- vars-1.5-6/vars/man/plot.Rd | 2 - vars-1.5-6/vars/man/stability.Rd | 2 - 11 files changed, 83 insertions(+), 50 deletions(-)
Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications.
Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
David Granjon [aut],
Ian Fellows [ctb] (Methods for mutating vertical tabs &
updateMultiInput),
Wil Davis [ctb] (numericRangeInput function),
Spencer Matthews [ctb] (autoNumeric methods),
JavaScript and CSS libraries authors [ctb, cph] (All authors are listed
in LICENSE.md)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.6.1 dated 2021-09-06 and 0.6.2 dated 2021-09-17
DESCRIPTION | 8 MD5 | 840 +- NAMESPACE | 352 - NEWS.md | 8 R/actionBttn.R | 360 - R/addSpinner.R | 504 - R/bootstrap-utils.R | 200 R/chooseSliderSkin.R | 490 - R/color-pickr.R | 324 R/demos.R | 136 R/dependencies.R | 890 +- R/drop-menu.R | 482 - R/execute_safely.R | 112 R/input-actiongroupbuttons.R | 192 R/input-airDatepicker.R | 794 +- R/input-autonumeric.R | 1224 +-- R/input-awesomecheckbox.R | 708 +- R/input-awesomeradio.R | 512 - R/input-checkboxgroupbuttons.R | 690 - R/input-circlebutton.R | 152 R/input-colorselector.R | 356 - R/input-dropdown.R | 486 - R/input-icon.R | 592 - R/input-knob.R | 430 - R/input-materialswitch.R | 182 R/input-multi.R | 438 - R/input-noUiSlider.R | 556 - R/input-numericRange.R | 244 R/input-pretty.R | 1472 ++-- R/input-radiogroupbuttons.R | 622 - R/input-search.R | 336 R/input-selectpicker.R | 648 - R/input-sliderText.R | 504 - R/input-spectrum.R | 340 R/input-switch.R | 680 - R/input-textaddon.R | 100 R/module-pickerGroup.R | 602 - R/module-selectizeGroup.R | 524 - R/module-utils.R | 108 R/onLoad.R | 106 R/pickerOptions.R | 236 R/progressBars.R | 390 - R/set-background.R | 422 - R/setShadow.R | 226 R/setSliderColor.R | 170 R/shinyWidgets.R | 24 R/shinyWidgetsGallery.R | 44 R/stati-card.R | 168 R/sw-dropdown.R | 484 - R/sweetalert.R | 1194 +-- R/useArgonDash.R | 336 R/useBs4Dash.R | 266 R/useShinydashboard.R | 220 R/useShinydashboardPlus.R | 344 R/useTablerDash.R | 50 R/utils.R | 350 - R/vertical-tab.R | 670 - README.md | 1 inst/assets/air-datepicker/datepicker-bindings.js | 480 - inst/assets/air-datepicker/datepicker.min.css | 2 inst/assets/air-datepicker/i18n/datepicker.it.js | 24 inst/assets/air-datepicker/i18n/datepicker.ja.js | 22 inst/assets/air-datepicker/i18n/datepicker.ru.js | 24 inst/assets/air-datepicker/i18n/datepicker.tr.js | 24 inst/assets/air-datepicker2/LICENSE.md | 42 inst/assets/air-datepicker2/airdatepicker-custom.css | 54 inst/assets/air-datepicker2/datepicker-bindings.js | 630 - 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Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the user's formatting
intent.
Author: Kirill Müller [aut],
Lorenz Walthert [cre, aut]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between styler versions 1.5.1 dated 2021-07-13 and 1.6.1 dated 2021-09-17
DESCRIPTION | 14 MD5 | 103 NEWS.md | 44 R/roxygen-examples-add-remove.R | 20 R/roxygen-examples-parse.R | 2 R/roxygen-examples.R | 19 R/rules-line-breaks.R | 28 R/set-assert-args.R | 4 R/testing.R | 45 R/transform-code.R | 14 R/ui-caching.R | 3 R/ui-styling.R | 23 R/utils-files.R | 2 R/zzz.R | 47 README.md | 5 inst/doc/customizing_styler.html | 12 inst/doc/introducing_styler.html | 2 inst/doc/styler.html | 2 inst/doc/third-party-integrations.Rmd | 14 inst/doc/third-party-integrations.html | 3 man/add_roxygen_mask.Rd | 8 man/local_test_setup.Rd |only man/prettify_any.Rd | 2 man/prettify_pkg.Rd | 2 man/remind_removing_old_cache.Rd |only man/set_line_break_before_curly_opening.Rd | 14 man/style_dir.Rd | 4 man/style_file.Rd | 2 man/style_pkg.Rd | 4 tests/testthat/line_breaks_and_other/base-pipe-line-breaks-in.R | 5 tests/testthat/line_breaks_and_other/base-pipe-line-breaks-in_tree | 53 tests/testthat/line_breaks_and_other/base-pipe-line-breaks-out.R | 5 tests/testthat/line_breaks_and_other/pipe-line-breaks-in.R | 71 tests/testthat/line_breaks_and_other/pipe-line-breaks-in_tree | 1152 ++++++---- tests/testthat/line_breaks_and_other/pipe-line-breaks-out.R | 71 tests/testthat/public-api/xyz-r-and-rmd-dir/random-rmd-script.Rmarkdown |only tests/testthat/public-api/xyzfile_rmd/random.Rmarkdown |only tests/testthat/public-api/xyzfile_rmd/random2.Rmarkdown |only tests/testthat/public-api/xyzpackage-rmd/vignettes/random.Rmarkdown |only tests/testthat/rmd/no-tidy-in.Rmd | 46 tests/testthat/rmd/no-tidy-out.Rmd | 46 tests/testthat/roxygen-examples-complete/25-ordinary-comment-in-example-in.R |only tests/testthat/roxygen-examples-complete/25-ordinary-comment-in-example-in_tree |only tests/testthat/roxygen-examples-complete/25-ordinary-comment-in-example-out.R |only tests/testthat/test-cache-high-level-api.R | 62 tests/testthat/test-cache-interaction-base-indention.R | 19 tests/testthat/test-cache-interaction-more-specs.R | 5 tests/testthat/test-cache-interaction-roxygen-code-examples.R | 8 tests/testthat/test-cache-low-level-api.R | 8 tests/testthat/test-cache-with-r-cache.R | 27 tests/testthat/test-interaction-caching-comments.R | 6 tests/testthat/test-interaction-caching-stylerignore.R | 23 tests/testthat/test-parsing.R | 2 tests/testthat/test-public_api.R | 45 tests/testthat/test-roxygen-examples-complete.R | 9 tests/testthat/test-testing.R |only tests/testthat/test-zzz.R |only vignettes/third-party-integrations.Rmd | 14 58 files changed, 1480 insertions(+), 639 deletions(-)
Title: Searching Shared HLA Amino Acid Residue Prevalence
Description: Processes amino acid alignments produced by the 'IPD-IMGT/HLA (Immuno Polymorphism-ImMunoGeneTics/Human Leukocyte Antigen) Database' to identify user-defined amino acid residue motifs shared across HLA alleles, and calculates the frequencies of those motifs based on HLA allele frequency data. 'SSHAARP' (Searching Shared HLA Amino Acid Residue Prevalence) uses 'Generic Mapping Tools (GMT)' software and the 'GMT' R package to generate global frequency heat maps that illustrate the distribution of each user-defined map around the globe. 'SSHAARP' analyzes the allele frequency data described by Solberg et al. (2008) <doi:10.1016/j.humimm.2008.05.001>, a global set of 497 population samples from 185 published datasets, representing 66,800 individuals total.
Author: Livia Tran [aut, cre],
Steven Mack [aut],
Josh Bredeweg [ctb],
Dale Steinhardt [ctb]
Maintainer: Livia Tran <livia.tran@ucsf.edu>
Diff between SSHAARP versions 1.0.1 dated 2020-10-09 and 1.1.0 dated 2021-09-17
DESCRIPTION | 9 ++++----- MD5 | 14 +++++++------- NEWS | 5 +++++ R/BLAASD.R | 11 +++++++---- build/vignette.rds |binary inst/doc/vignette.Rmd | 4 ++-- inst/doc/vignette.html | 15 +++------------ vignettes/vignette.Rmd | 4 ++-- 8 files changed, 30 insertions(+), 32 deletions(-)
Title: Morpheme Tokenization
Description: Tokenize text into morphemes. The morphemepiece algorithm uses a
lookup table to determine the morpheme breakdown of words, and falls back on a
modified wordpiece tokenization algorithm for words not found in the lookup
table.
Author: Jonathan Bratt [aut, cre] (<https://orcid.org/0000-0003-2859-0076>),
Jon Harmon [aut] (<https://orcid.org/0000-0003-4781-4346>),
Bedford Freeman & Worth Pub Grp LLC DBA Macmillan Learning [cph]
Maintainer: Jonathan Bratt <jonathan.bratt@macmillan.com>
Diff between morphemepiece versions 1.0.0 dated 2021-09-09 and 1.0.1 dated 2021-09-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/vocab.R | 8 ++++---- README.md | 19 +++++-------------- tests/testthat/test-morphemepiece.R | 4 ++-- 6 files changed, 24 insertions(+), 28 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package. The main references for excursions are Bolin and Lindgren (2015) <doi:10.1111/rssb.12055>, Bolin and Lindgren (2017) <doi:10.1080/10618600.2016.1228537>, and Bolin and Lindgren (2018) <doi:10.18637/jss.v086.i05>. These can be generated by the citation function in R.
Author: David Bolin [cre, aut],
Finn Lindgren [aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between excursions versions 2.5.1 dated 2021-01-21 and 2.5.2 dated 2021-09-17
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 7 +++++++ R/contourmap.inla.R | 8 +++++--- R/excursions.inla.R | 18 ++++++++++++------ R/simconf.inla.R | 11 +++++++---- man/contourmap.inla.Rd | 6 ++++-- man/excursions.inla.Rd | 7 ++++--- man/simconf.inla.Rd | 7 ++++--- src/integration.cpp | 12 ++++++------ tests/testthat/helper-data.R | 12 ++++++++---- 11 files changed, 71 insertions(+), 45 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre],
Matt Dennis [ctb],
Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>),
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb]
Maintainer: Andrew B. Collier <andrew@fathomdata.dev>
Diff between emayili versions 0.4.18 dated 2021-09-06 and 0.5.0 dated 2021-09-17
emayili-0.4.18/emayili/man/format.mime.Rd |only emayili-0.4.18/emayili/man/mime.Rd |only emayili-0.4.18/emayili/man/parameter_value_encode.Rd |only emayili-0.4.18/emayili/man/vec_ptype_abbr.vctrs_address.Rd |only emayili-0.4.18/emayili/man/vec_ptype_full.vctrs_address.Rd |only emayili-0.5.0/emayili/DESCRIPTION | 16 emayili-0.5.0/emayili/MD5 | 78 +- emayili-0.5.0/emayili/NAMESPACE | 15 emayili-0.5.0/emayili/NEWS.md | 15 emayili-0.5.0/emayili/R/address.R | 51 + emayili-0.5.0/emayili/R/attachment.R | 48 - emayili-0.5.0/emayili/R/body.R | 49 - emayili-0.5.0/emayili/R/emayili.R | 28 emayili-0.5.0/emayili/R/encoding.R | 8 emayili-0.5.0/emayili/R/envelope.R | 56 + emayili-0.5.0/emayili/R/message.R | 49 - emayili-0.5.0/emayili/R/mime.R | 356 +++++++--- emayili-0.5.0/emayili/R/render.R |only emayili-0.5.0/emayili/R/server.R | 41 - emayili-0.5.0/emayili/R/subject.R | 15 emayili-0.5.0/emayili/R/utils.R | 50 + emayili-0.5.0/emayili/README.md | 124 ++- emayili-0.5.0/emayili/man/append.Rd |only emayili-0.5.0/emayili/man/append.envelope.Rd |only emayili-0.5.0/emayili/man/as.address.Rd | 2 emayili-0.5.0/emayili/man/as.character.MIME.Rd |only emayili-0.5.0/emayili/man/as.character.envelope.Rd | 23 emayili-0.5.0/emayili/man/attachment.Rd | 11 emayili-0.5.0/emayili/man/compliant.Rd | 4 emayili-0.5.0/emayili/man/figures/screenshot-email-rendered.png |only emayili-0.5.0/emayili/man/html.Rd | 16 emayili-0.5.0/emayili/man/pipe.Rd | 2 emayili-0.5.0/emayili/man/render.Rd |only emayili-0.5.0/emayili/man/subject.Rd | 17 emayili-0.5.0/emayili/man/text.Rd | 8 emayili-0.5.0/emayili/tests/testthat/setup-files.R | 60 + emayili-0.5.0/emayili/tests/testthat/teardown-files.R | 2 emayili-0.5.0/emayili/tests/testthat/test-address.R | 46 + emayili-0.5.0/emayili/tests/testthat/test-attachment.R | 6 emayili-0.5.0/emayili/tests/testthat/test-body.R | 36 + emayili-0.5.0/emayili/tests/testthat/test-compliant.R | 4 emayili-0.5.0/emayili/tests/testthat/test-envelope.R | 6 emayili-0.5.0/emayili/tests/testthat/test-mime.R | 30 emayili-0.5.0/emayili/tests/testthat/test-parties.R |only emayili-0.5.0/emayili/tests/testthat/test-server.R | 31 emayili-0.5.0/emayili/tests/testthat/test-subject.R | 7 46 files changed, 920 insertions(+), 390 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-14 0.3.1
2020-05-02 0.1.0
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Kevin Ushey [aut, cre],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/)
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between reticulate versions 1.21 dated 2021-09-14 and 1.22 dated 2021-09-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/conda.R | 26 -------------------------- R/pip.R | 11 ----------- build/vignette.rds |binary 6 files changed, 13 insertions(+), 45 deletions(-)
Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-011-0040-5>. Subnational probabilistic projections are also supported.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Peiran Liu (prliu@uw.edu), Adrian Raftery (raftery@uw.edu), Bailey Fosdick (bfosdick@uw.edu), Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesTFR versions 7.0-4 dated 2021-04-03 and 7.0-5 dated 2021-09-17
ChangeLog | 10 ++++++++ DESCRIPTION | 10 ++++---- MD5 | 10 ++++---- R/diagnostics.R | 54 +++++++++++++++++++++++++++--------------------- R/plot_functions.R | 10 +++++--- man/tfr.raftery.diag.Rd | 12 +++++----- 6 files changed, 63 insertions(+), 43 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: CRAN Team [ctb, cre] (de facto maintainer since 2013),
Duncan Temple Lang [aut] (<https://orcid.org/0000-0003-0159-1546>),
Tomas Kalibera [ctb]
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between XML versions 3.99-0.7 dated 2021-08-17 and 3.99-0.8 dated 2021-09-17
DESCRIPTION | 6 MD5 | 8 configure | 3207 +++++++++++++++++++++++++++++---------------------- configure.ac | 122 - man/readHTMLTable.Rd | 2 5 files changed, 1887 insertions(+), 1458 deletions(-)
Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <https://curl.se/libcurl/>
Provides functions to allow one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: CRAN Team [ctb, cre] (de facto maintainer since 2013),
Duncan Temple Lang [aut] (<https://orcid.org/0000-0003-0159-1546>)
Maintainer: CRAN Team <CRAN@r-project.org>
Diff between RCurl versions 1.98-1.4 dated 2021-08-17 and 1.98-1.5 dated 2021-09-17
DESCRIPTION | 6 MD5 | 6 configure | 2639 ++++++++++++++++++++++++++++++++++++----------------------- configure.ac | 32 4 files changed, 1661 insertions(+), 1022 deletions(-)
Title: Automated Method for Verbal Autopsy
Description: Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. The methods implemented include 'InterVA4' by Byass et al (2012) <doi:10.3402/gha.v5i0.19281>, 'InterVA5' by Byass at al (2019) <doi:10.1186/s12916-019-1333-6>, 'InSilicoVA' by McCormick et al (2016) <doi:10.1080/01621459.2016.1152191>, 'NBC' by Miasnikof et al (2015) <doi:10.1186/s12916-015-0521-2>, and a replication of 'Tariff' method by James et al (2011) <doi:10.1186/1478-7954-9-31> and Serina, et al. (2015) <doi:10.1186/s12916-015-0527-9>. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics. The 'NBC' method is implemented by the 'nbc4va' package that can be installed from <https://github.com/rrwen/nbc4va>. Note that this package was not developed by authors affiliated with the Institute for Health Metrics and Evaluation and thus unintentional discrepancies may exist in the implementation of the 'Tariff' method.
Author: Zehang Richard Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Richard Li <lizehang@gmail.com>
Diff between openVA versions 1.0.12 dated 2021-02-03 and 1.0.13 dated 2021-09-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/CSMF.r | 1 + R/ConvertData.r | 7 ------- R/VAmain.r | 40 +--------------------------------------- R/attach.R | 4 ++-- 7 files changed, 18 insertions(+), 58 deletions(-)
Title: Tidy C++ Header-Only Definitions for Parts of the C API of R
Description: Core parts of the C API of R are wrapped in a C++ namespace via a set
of inline functions giving a tidier representation of the underlying data structures
and functionality using a header-only implementation without additional dependencies.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tidyCpp versions 0.0.4 dated 2021-09-05 and 0.0.5 dated 2021-09-17
ChangeLog | 15 +++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary inst/include/tidy/numvec.h | 7 +++---- inst/include/tidy/protect.h | 18 ++++++++---------- 6 files changed, 35 insertions(+), 23 deletions(-)
Title: Leadership-Inference Framework for Multivariate Time Series
Description: A leadership-inference framework for multivariate time series. The framework for multiple-faction-leadership inference from coordinated activities or 'mFLICA' uses a notion of a leader as an individual who initiates collective patterns that everyone in a group follows. Given a set of time series of individual activities, our goal is to identify periods of coordinated activity, find factions of coordination if more than one exist, as well as identify leaders of each faction. For each time step, the framework infers following relations between individual time series, then identifying a leader of each faction whom many individuals follow but it follows no one. A faction is defined as a group of individuals that everyone follows the same leader. 'mFLICA' reports following relations, leaders of factions, and members of each faction for each time step. Please see Chainarong Amornbunchornvej and Tanya Berger-Wolf (2018) <doi:10.1137/1.9781611975321.62> for methodology and Chainarong Amornbunchornvej (2021) <doi:10.1016/j.softx.2021.100781> for software when referring to this package in publications.
Author: Chainarong Amornbunchornvej [aut, cre]
(<https://orcid.org/0000-0003-3131-0370>)
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>
Diff between mFLICA versions 0.1.1 dated 2020-04-03 and 0.1.3 dated 2021-09-17
mFLICA-0.1.1/mFLICA/R/getReachibleNodes.R |only mFLICA-0.1.1/mFLICA/man/getReachibleNodes.Rd |only mFLICA-0.1.3/mFLICA/DESCRIPTION | 14 ++--- mFLICA-0.1.3/mFLICA/MD5 | 42 +++++++++------ mFLICA-0.1.3/mFLICA/NAMESPACE | 4 - mFLICA-0.1.3/mFLICA/NEWS.md | 7 ++ mFLICA-0.1.3/mFLICA/R/followingNetwork.R | 12 ++-- mFLICA-0.1.3/mFLICA/R/followingRelation.R | 9 ++- mFLICA-0.1.3/mFLICA/R/getDynamicFollNet.R | 20 +++---- mFLICA-0.1.3/mFLICA/R/getFactions.R | 14 ++--- mFLICA-0.1.3/mFLICA/R/getReachableNodes.R |only mFLICA-0.1.3/mFLICA/R/mFLICA.R | 10 ++- mFLICA-0.1.3/mFLICA/R/supportFuncs.R | 6 +- mFLICA-0.1.3/mFLICA/README.md | 15 +++-- mFLICA-0.1.3/mFLICA/build/vignette.rds |binary mFLICA-0.1.3/mFLICA/inst/doc/mFLICA-SoftwareArticle.ltx |only mFLICA-0.1.3/mFLICA/inst/doc/mFLICA-SoftwareArticle.pdf |only mFLICA-0.1.3/mFLICA/inst/doc/mFLICA_demo.html | 8 +- mFLICA-0.1.3/mFLICA/man/TS.Rd | 6 +- mFLICA-0.1.3/mFLICA/man/getReachableNodes.Rd |only mFLICA-0.1.3/mFLICA/vignettes/ChaiRef.bib |only mFLICA-0.1.3/mFLICA/vignettes/FIG |only mFLICA-0.1.3/mFLICA/vignettes/mFLICA-SoftwareArticle.ltx |only 23 files changed, 104 insertions(+), 63 deletions(-)
Title: Tools for 'iNZight'
Description: Provides a collection of wrapper functions for common variable and dataset manipulation workflows primarily used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Additionally, many of the functions return the 'tidyverse' code used to obtain the result in an effort to bridge the gap between GUI and coding.
Author: Tom Elliott [aut, cre] (<https://orcid.org/0000-0002-7815-6318>),
Christoph Knopf [ctb],
Akshay Gupta [ctb],
Owen Jin [aut] (Tidyverse variable/data manipulation functions),
Lushi Cai [ctb],
Yiwen He [aut] (Dates/times and dataset manipulation),
Daniel Barnett [aut] (Data validation)
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>
Diff between iNZightTools versions 1.11.2 dated 2021-07-13 and 1.12.0 dated 2021-09-17
iNZightTools-1.11.2/iNZightTools/tests/testthat/test-read_text.R |only iNZightTools-1.11.2/iNZightTools/tests/testthat/test-test_tidy_code.R |only iNZightTools-1.11.2/iNZightTools/tests/testthat/test_filterLevels.R |only iNZightTools-1.11.2/iNZightTools/tests/testthat/test_filterNumeric.R |only iNZightTools-1.12.0/iNZightTools/DESCRIPTION | 10 iNZightTools-1.12.0/iNZightTools/MD5 | 111 +-- iNZightTools-1.12.0/iNZightTools/NAMESPACE | 3 iNZightTools-1.12.0/iNZightTools/R/aggregate_data.R | 2 iNZightTools-1.12.0/iNZightTools/R/class_intervals.R | 6 iNZightTools-1.12.0/iNZightTools/R/extfromdt.R | 4 iNZightTools-1.12.0/iNZightTools/R/import_data.R | 8 iNZightTools-1.12.0/iNZightTools/R/import_survey.R | 44 + iNZightTools-1.12.0/iNZightTools/R/metadata_object.R | 17 iNZightTools-1.12.0/iNZightTools/R/metadata_read.R | 188 ++++- iNZightTools-1.12.0/iNZightTools/R/read_text.R | 9 iNZightTools-1.12.0/iNZightTools/R/rename_levels.R | 3 iNZightTools-1.12.0/iNZightTools/R/tidycode.R | 343 ---------- iNZightTools-1.12.0/iNZightTools/R/unite_cols.R | 15 iNZightTools-1.12.0/iNZightTools/inst |only iNZightTools-1.12.0/iNZightTools/man/as_survey.inzsvyspec.Rd |only iNZightTools-1.12.0/iNZightTools/man/tidy_all_code.Rd | 2 iNZightTools-1.12.0/iNZightTools/tests/testthat/messy_census.txt | 10 iNZightTools-1.12.0/iNZightTools/tests/testthat/messy_gapminder.txt | 4 iNZightTools-1.12.0/iNZightTools/tests/testthat/meta_chars.csv |only iNZightTools-1.12.0/iNZightTools/tests/testthat/meta_multi.csv |only iNZightTools-1.12.0/iNZightTools/tests/testthat/meta_nacodes.csv |only iNZightTools-1.12.0/iNZightTools/tests/testthat/test_Extfromdt.R | 20 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_add_suffix.R | 2 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_aggregateData.R | 52 - iNZightTools-1.12.0/iNZightTools/tests/testthat/test_appendrows.R | 4 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_catvars.R | 6 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_classintervals.R | 31 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_collapseLevels.R | 16 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_contodt.R | 2 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_createvar.R | 10 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_filter_levels.R |only iNZightTools-1.12.0/iNZightTools/tests/testthat/test_filter_numeric.R |only iNZightTools-1.12.0/iNZightTools/tests/testthat/test_filter_random.R | 9 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_filter_rows.R | 11 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_helpers.R | 2 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_joins.R | 30 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_load_save.R | 4 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_metadata_file.R |only iNZightTools-1.12.0/iNZightTools/tests/testthat/test_missing.R | 19 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_model_fitting.R | 8 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_rankvars.R | 14 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_read_metadata.R | 34 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_read_text.R |only iNZightTools-1.12.0/iNZightTools/tests/testthat/test_rename_levels.R | 29 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_renamevars.R | 14 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_reorderlevels.R | 10 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_reshape.R | 4 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_select_vars.R | 9 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_separate.R | 9 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_smart_read.R | 67 - iNZightTools-1.12.0/iNZightTools/tests/testthat/test_sort.R | 14 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_stackvars.R | 9 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_standardize_vars.R | 14 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_survey_design.R | 79 +- iNZightTools-1.12.0/iNZightTools/tests/testthat/test_tidy_code.R | 103 +-- iNZightTools-1.12.0/iNZightTools/tests/testthat/test_transform_var.R | 16 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_unite.R | 18 iNZightTools-1.12.0/iNZightTools/tests/testthat/test_validation.R | 8 63 files changed, 702 insertions(+), 754 deletions(-)